Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011796.1 Kokia drynarioides strain JFW-HI SEQ_126791, 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: 228864
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:2812 original size:40 final size:39
Alignment explanation
Indices: 2719--2854 Score: 125
Period size: 41 Copynumber: 3.4 Consensus size: 39
2709 CAAGTGTCAT
* *
2719 TAATGCTCTGACCTTTAGCGAT-ATTT-TTGAGGAAGCGCAAC
1 TAATGCTC-GACCTTTAGCG-TCATTTATT-AGAAAGCGC-GC
2760 TAATGCTCGACCTTTAGC-TCATTTATTAGAAAGCGTCGC
1 TAATGCTCGACCTTTAGCGTCATTTATTAGAAAGCG-CGC
* * * * *
2799 TAATGCTCTGACCTATAGCGACGTTTATTTGAAAGTGACGC
1 TAATGCTC-GACCTTTAGCGTCATTTATTAGAAAGCG-CGC
2840 TAATGCTCGACCTTT
1 TAATGCTCGACCTTT
2855 GCTGCGTTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
38 1 0.01
39 20 0.25
40 28 0.35
41 32 0.40
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (39 bp):
TAATGCTCGACCTTTAGCGTCATTTATTAGAAAGCGCGC
Found at i:13739 original size:18 final size:18
Alignment explanation
Indices: 13718--13758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
13708 TGAGCGTGAT
13718 CGTGACCATGATAGAGAA
1 CGTGACCATGATAGAGAA
* * *
13736 CGTGATCGTGATAGAGAC
1 CGTGACCATGATAGAGAA
13754 CGTGA
1 CGTGA
13759 GCGTTATAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.17, G:0.32, T:0.20
Consensus pattern (18 bp):
CGTGACCATGATAGAGAA
Found at i:13767 original size:18 final size:18
Alignment explanation
Indices: 13726--13767 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
13716 ATCGTGACCA
*
13726 TGATAGAGAACGTGATCG
1 TGATAGAGAACGTGAGCG
*
13744 TGATAGAGACCGTGAGCG
1 TGATAGAGAACGTGAGCG
*
13762 TTATAG
1 TGATAG
13768 GGAGAGGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.33, T:0.24
Consensus pattern (18 bp):
TGATAGAGAACGTGAGCG
Found at i:17816 original size:29 final size:31
Alignment explanation
Indices: 17783--17844 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
17773 AGTATCAATG
*
17783 TATAAAGATTAAATTTATAA-TTTT-AAAAA
1 TATAAAAATTAAATTTATAATTTTTGAAAAA
*
17812 TATAAAAATTAAATTTTTAATTTTTGAAAAA
1 TATAAAAATTAAATTTATAATTTTTGAAAAA
17843 TA
1 TA
17845 CAGGGACTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.62
30 4 0.14
31 7 0.24
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (31 bp):
TATAAAAATTAAATTTATAATTTTTGAAAAA
Found at i:30873 original size:15 final size:15
Alignment explanation
Indices: 30849--30888 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
30839 TAGTAGGATA
30849 TATTTTTT-AATTTT
1 TATTTTTTAAATTTT
30863 TATTTTATTAAATTTT
1 TATTTT-TTAAATTTT
30879 TATTTATTTA
1 TATTT-TTTA
30889 TTAGCAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 2 0.09
16 14 0.61
17 1 0.04
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTTTAAATTTT
Found at i:37670 original size:70 final size:70
Alignment explanation
Indices: 37583--37718 Score: 247
Period size: 70 Copynumber: 1.9 Consensus size: 70
37573 AACCAGAGTT
*
37583 GAGAAATTGGTGCATATCCTTAAATTATATTTTTAAA-AATAATAATATATATGATGCAATCTAG
1 GAGAAATTGGTGCATATCCTTAAATTATA-TTTTAAAGAATAATAATATATATGATACAATCTAG
37647 ATTTTA
65 ATTTTA
37653 GAGAAATTGGTGCATATCCTTAAATTATATTTTAAAGAATAATAATATATATGATACAATCTAGA
1 GAGAAATTGGTGCATATCCTTAAATTATATTTTAAAGAATAATAATATATATGATACAATCTAGA
37718 T
66 T
37719 CTTACTTATC
Statistics
Matches: 64, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
69 7 0.11
70 57 0.89
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (70 bp):
GAGAAATTGGTGCATATCCTTAAATTATATTTTAAAGAATAATAATATATATGATACAATCTAGA
TTTTA
Found at i:40845 original size:8 final size:8
Alignment explanation
Indices: 40832--40857 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40822 CACTTCAATT
40832 TTTTATTA
1 TTTTATTA
40840 TTTTATTA
1 TTTTATTA
40848 TTTTATTA
1 TTTTATTA
40856 TT
1 TT
40858 AATCGATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTATTA
Found at i:42151 original size:19 final size:19
Alignment explanation
Indices: 42106--42153 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
42096 TTGATATCTA
42106 TAAAATTA--TTAAATAAT
1 TAAAATTATTTTAAATAAT
*
42123 TATAATTATTTTAAATAA-
1 TAAAATTATTTTAAATAAT
42141 TAAAATATATTTT
1 TAAAAT-TATTTT
42154 TAATGTGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAATTATTTTAAATAAT
Found at i:43290 original size:15 final size:16
Alignment explanation
Indices: 43270--43299 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43260 CTTTTTCAAA
43270 TTTTAATT-TATTTAC
1 TTTTAATTATATTTAC
43285 TTTTAATTATATTTA
1 TTTTAATTATATTTA
43300 TTTGTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAATTATATTTAC
Found at i:44585 original size:31 final size:31
Alignment explanation
Indices: 44550--44611 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
44540 TTACAAAATG
* *
44550 GTCACTGAACTATTCGAAAGTTTTTTTTTAA
1 GTCACTAAACTATTCGAAAGTTTTTATTTAA
*
44581 GTCACTAAACTATTTGAAAGTTTTTATTTAA
1 GTCACTAAACTATTCGAAAGTTTTTATTTAA
44612 CTCATTCGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (31 bp):
GTCACTAAACTATTCGAAAGTTTTTATTTAA
Found at i:57673 original size:33 final size:35
Alignment explanation
Indices: 57606--57673 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 35
57596 TTAAGTCCGA
*
57606 ATCCAATTTTTATTTTAAACGAACTTAATTTTTTT
1 ATCCAATTTTTATTTTAAACGAACTTAATATTTTT
** *
57641 ATCCAA-TTTTATTTT-TTCGAATTTAATATTTTT
1 ATCCAATTTTTATTTTAAACGAACTTAATATTTTT
57674 TAAACCCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 14 0.48
34 9 0.31
35 6 0.21
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.57
Consensus pattern (35 bp):
ATCCAATTTTTATTTTAAACGAACTTAATATTTTT
Found at i:62639 original size:5 final size:5
Alignment explanation
Indices: 62629--62702 Score: 89
Period size: 5 Copynumber: 15.0 Consensus size: 5
62619 TCGGTGTCGG
* * *
62629 TGAGT TGAGT TGAGT TGAGT TGAGG TGTCGG TGAGT TGAGT TGAGT TGAGT
1 TGAGT TGAGT TGAGT TGAGT TGAGT TG-AGT TGAGT TGAGT TGAGT TGAGT
*
62680 TGAGT TGAG- T-AGT TGAGT AGAGT
1 TGAGT TGAGT TGAGT TGAGT TGAGT
62703 AATAAATGCT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 53 0.87
6 4 0.07
ACGTcount: A:0.20, C:0.01, G:0.42, T:0.36
Consensus pattern (5 bp):
TGAGT
Found at i:62659 original size:31 final size:31
Alignment explanation
Indices: 62621--62683 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
62611 ACTCAATGTC
62621 GGTGTCGGTGAGTTGAGTTGAGTTGAGTTGA
1 GGTGTCGGTGAGTTGAGTTGAGTTGAGTTGA
62652 GGTGTCGGTGAGTTGAGTTGAGTTGAGTTGA
1 GGTGTCGGTGAGTTGAGTTGAGTTGAGTTGA
62683 G
1 G
62684 TTGAGTAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.16, C:0.03, G:0.46, T:0.35
Consensus pattern (31 bp):
GGTGTCGGTGAGTTGAGTTGAGTTGAGTTGA
Found at i:63761 original size:29 final size:31
Alignment explanation
Indices: 63715--63781 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 31
63705 ATATCCCTGC
63715 AAAA-TTTAATAAAATTT-GAGAGACTAATT
1 AAAATTTTAATAAAATTTGGAGAGACTAATT
* * *
63744 AAAATTTTAA-AAATTTTGGAGGGCCTAATT
1 AAAATTTTAATAAAATTTGGAGAGACTAATT
63774 AAAATTTT
1 AAAATTTT
63782 CTAAAACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.37
Consensus pattern (31 bp):
AAAATTTTAATAAAATTTGGAGAGACTAATT
Found at i:76250 original size:23 final size:22
Alignment explanation
Indices: 76221--76344 Score: 81
Period size: 23 Copynumber: 5.5 Consensus size: 22
76211 ACAATAAACG
76221 CACACAGTGCAATCCAGTAGGCA
1 CACACAGTGCAAT-CAGTAGGCA
* *
76244 CACACAGTGCAATCAATAGGCG
1 CACACAGTGCAATCAGTAGGCA
* **
76266 CACATAACGCAAATCAGTAGGCA
1 CACACAGTGC-AATCAGTAGGCA
* * *
76289 CACGA-GGTGCGAAACAGTAAGCA
1 CAC-ACAGTGC-AATCAGTAGGCA
* * *
76312 CATGA-AGTGCGAAACAGTAAGCA
1 CA-CACAGTGC-AATCAGTAGGCA
76335 CACACAGTGC
1 CACACAGTGC
76345 TGAACAGTAA
Statistics
Matches: 81, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
22 15 0.19
23 65 0.80
24 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.12
Consensus pattern (22 bp):
CACACAGTGCAATCAGTAGGCA
Found at i:76350 original size:23 final size:23
Alignment explanation
Indices: 76295--76358 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
76285 GGCACACGAG
*
76295 GTGCGAAACAGTAAGCACATGAA
1 GTGCGAAACAGTAAGCACATCAA
76318 GTGCGAAACAGTAAGCACA-CACA
1 GTGCGAAACAGTAAGCACATCA-A
76341 GTGCTG-AACAGTAAGCAC
1 GTGC-GAAACAGTAAGCAC
76359 GCTAGCGTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
GTGCGAAACAGTAAGCACATCAA
Found at i:78218 original size:24 final size:24
Alignment explanation
Indices: 78186--78382 Score: 277
Period size: 24 Copynumber: 8.2 Consensus size: 24
78176 AAGTTTAGTG
* * *
78186 CGTTTATGCTCGCCAGCTAATGTA
1 CGTTTATGCTCGTCAGCCACTGTA
*
78210 CGTTTATGCTCGTCAGCCATTGTA
1 CGTTTATGCTCGTCAGCCACTGTA
* * *
78234 CGTTTATACTCGTCAACCACTATA
1 CGTTTATGCTCGTCAGCCACTGTA
78258 CGTTTATGCTCGTCAGCCACTGTA
1 CGTTTATGCTCGTCAGCCACTGTA
**
78282 CGTTTATGCAAGTCAGCCACTGTA
1 CGTTTATGCTCGTCAGCCACTGTA
*
78306 CGTTTATGCTCGTTAGCCACTGTA
1 CGTTTATGCTCGTCAGCCACTGTA
* * *
78330 CGTTTATGCTCATCAACCACTATA
1 CGTTTATGCTCGTCAGCCACTGTA
78354 CGTTTATGCTCGTCAGCCACTGTA
1 CGTTTATGCTCGTCAGCCACTGTA
78378 CGTTT
1 CGTTT
78383 GATTCTTTTA
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 151 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.35
Consensus pattern (24 bp):
CGTTTATGCTCGTCAGCCACTGTA
Found at i:83271 original size:24 final size:23
Alignment explanation
Indices: 83235--83281 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
83225 TACTATTAAT
*
83235 TTTATCTTAATTTGCTTTGACAA
1 TTTATCTTAATTTGCGTTGACAA
*
83258 TTTATTTTATATTTGCGTTGACAA
1 TTTATCTTA-ATTTGCGTTGACAA
83282 ACTAACTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (23 bp):
TTTATCTTAATTTGCGTTGACAA
Found at i:91017 original size:18 final size:19
Alignment explanation
Indices: 90991--91048 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
90981 AAGGAAATCC
*
90991 CTGAGGAAGAGAA-AGGAA
1 CTGAAGAAGAGAAGAGGAA
91009 CTGAAGAAGAGAAGGAGGAA
1 CTGAAGAAGAGAA-GAGGAA
*
91029 GTGAAGAAGAATGAAGAGGA
1 CTGAAGAAG-A-GAAGAGGA
91049 TAAAGATGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.35
20 13 0.38
21 6 0.18
22 3 0.09
ACGTcount: A:0.50, C:0.03, G:0.40, T:0.07
Consensus pattern (19 bp):
CTGAAGAAGAGAAGAGGAA
Found at i:91470 original size:17 final size:17
Alignment explanation
Indices: 91445--91487 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
91435 ATGCATCTCA
91445 TTTAATTGTCATTGCAT
1 TTTAATTGTCATTGCAT
*
91462 TTTAGTTGTCATTGCAT
1 TTTAATTGTCATTGCAT
*
91479 TTTACTTGT
1 TTTAATTGT
91488 TAGTTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (17 bp):
TTTAATTGTCATTGCAT
Found at i:93658 original size:24 final size:23
Alignment explanation
Indices: 93621--93667 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
93611 AACTATTCAC
93621 TTTATCTTAATTTGC-TCTGACAA
1 TTTATCTTAATTTGCAT-TGACAA
*
93644 TTTATTTTATATTTGCATTGACAA
1 TTTATCTTA-ATTTGCATTGACAA
93668 ACTAACTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.51
Consensus pattern (23 bp):
TTTATCTTAATTTGCATTGACAA
Found at i:94055 original size:22 final size:23
Alignment explanation
Indices: 94025--94069 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
94015 GCTTACGTAA
*
94025 AAAACTATAGCAAGG-TTCGTATG
1 AAAACTATAACAAGGCTT-GTATG
94048 AAAA-TATAACAAGGCTTGTATG
1 AAAACTATAACAAGGCTTGTATG
94070 TTACTATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.42, C:0.11, G:0.20, T:0.27
Consensus pattern (23 bp):
AAAACTATAACAAGGCTTGTATG
Found at i:94943 original size:26 final size:26
Alignment explanation
Indices: 94839--94937 Score: 198
Period size: 26 Copynumber: 3.8 Consensus size: 26
94829 TTCACATGCT
94839 TACCTAGCTTTCCTTAGCACGAAAAC
1 TACCTAGCTTTCCTTAGCACGAAAAC
94865 TACCTAGCTTTCCTTAGCACGAAAAC
1 TACCTAGCTTTCCTTAGCACGAAAAC
94891 TACCTAGCTTTCCTTAGCACGAAAAC
1 TACCTAGCTTTCCTTAGCACGAAAAC
94917 TACCTAGCTTTCCTTAGCACG
1 TACCTAGCTTTCCTTAGCACG
94938 CGAACTCATG
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.28, C:0.31, G:0.12, T:0.28
Consensus pattern (26 bp):
TACCTAGCTTTCCTTAGCACGAAAAC
Found at i:101983 original size:159 final size:159
Alignment explanation
Indices: 101690--102003 Score: 538
Period size: 159 Copynumber: 2.0 Consensus size: 159
101680 GAAATGCACT
* *
101690 CCATTAGGGCGGATGTAAAACAAGTACAGTCTGATTGCACTAATACTGCCAGATCTATCATAAAG
1 CCATTAGGGCAGATGTAAAACAAGTACAGTCTGATTGAACTAATACTGCCAGATCTATCATAAAG
* * * * *
101755 CTAGAGTAGAGGATGGACAAATTAATTAGTATGGAAAGTGATCTTTCAAGACAAATTGGTTCAGG
66 CTAGAGCAGAAGATGGAAAAATTAATTAGTATGAAAAGTGATCTTTCAAGACAAATTGGTTCAGA
101820 GATCCCTAGCAACACTGAGAATAATACTA
131 GATCCCTAGCAACACTGAGAATAATACTA
* *
101849 CCATTAGGGCAGATGTAAAACAAGTGCAGTCTGATTGAATTAATACTGCCAGATCTATCATAAAG
1 CCATTAGGGCAGATGTAAAACAAGTACAGTCTGATTGAACTAATACTGCCAGATCTATCATAAAG
101914 CTAGAGCAGAAGATGGAAAAATTAATTAGTATGAAAAGTGATCTTTCAAGACAAATTGGTTCAGA
66 CTAGAGCAGAAGATGGAAAAATTAATTAGTATGAAAAGTGATCTTTCAAGACAAATTGGTTCAGA
*
101979 GATCCCTAGCAACTCTGAGAATAAT
131 GATCCCTAGCAACACTGAGAATAAT
102004 CCCCGACGGG
Statistics
Matches: 145, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
159 145 1.00
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (159 bp):
CCATTAGGGCAGATGTAAAACAAGTACAGTCTGATTGAACTAATACTGCCAGATCTATCATAAAG
CTAGAGCAGAAGATGGAAAAATTAATTAGTATGAAAAGTGATCTTTCAAGACAAATTGGTTCAGA
GATCCCTAGCAACACTGAGAATAATACTA
Found at i:113990 original size:17 final size:17
Alignment explanation
Indices: 113965--113998 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
113955 TGTTAGTAAG
*
113965 CATTGTCATTGCATTTT
1 CATTATCATTGCATTTT
113982 CATTATCATTGCATTTT
1 CATTATCATTGCATTTT
113999 AGTGTTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (17 bp):
CATTATCATTGCATTTT
Found at i:116355 original size:17 final size:17
Alignment explanation
Indices: 116333--116365 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
116323 TTTGAAAGCA
116333 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
116350 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
116366 GGCAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:122341 original size:17 final size:17
Alignment explanation
Indices: 122319--122351 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
122309 TTTGAAAGCA
122319 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
122336 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
122352 GGCAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:140111 original size:33 final size:33
Alignment explanation
Indices: 140069--140142 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 33
140059 ATATTTTCAT
*
140069 AATTAA-ATAA-AATAAAT-A-ATATTTAAATA
1 AATTAATATAATAATAAATGACATATTTAAAAA
*
140098 ATTTAATATAATAATAAATGACATATTTAAAAA
1 AATTAATATAATAATAAATGACATATTTAAAAA
140131 AATTAATATAAT
1 AATTAATATAAT
140143 TTTATATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 5 0.13
30 4 0.11
31 7 0.18
32 1 0.03
33 21 0.55
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (33 bp):
AATTAATATAATAATAAATGACATATTTAAAAA
Found at i:140159 original size:26 final size:25
Alignment explanation
Indices: 140126--140176 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
140116 TGACATATTT
140126 AAAAAAATTAATATAATTTTATATA
1 AAAAAAATTAATATAATTTTATATA
* *
140151 AAAATAAATTAATCTAATTTTGTATA
1 AAAA-AAATTAATATAATTTTATATA
140177 CCTTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAAAAATTAATATAATTTTATATA
Found at i:140163 original size:21 final size:21
Alignment explanation
Indices: 140092--140163 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
140082 AAATAATATT
* *
140092 TAAA-TAATTTAATATAATAA
1 TAAATTAATTTTATATAAAAA
*
140112 TAAATGACATATTTA-A-AAAAA
1 TAAATTA-AT-TTTATATAAAAA
*
140133 TTAATATAATTTTATATAAAAA
1 TAAAT-TAATTTTATATAAAAA
140155 TAAATTAAT
1 TAAATTAAT
140164 CTAATTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
20 8 0.20
21 16 0.40
22 13 0.32
23 3 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
TAAATTAATTTTATATAAAAA
Found at i:142889 original size:69 final size:68
Alignment explanation
Indices: 142778--143027 Score: 193
Period size: 69 Copynumber: 3.6 Consensus size: 68
142768 GCAGCATCTG
** * * **
142778 TGTCATTTTAAGGTTCACAAGTAAAGAGTCGTAACCTCCAACATCGTTAGCGAAAGCAAAGCTAT
1 TGTCATTTTAAGGTTTGCAAGCAAAGAGCCACAACCTCCAACATCGTTAGCGAAAGCAAAGCT-T
*
142843 TAAT
65 TAGT
* * * * *
142847 TGTCATTTTAAGGTTTGCAAGCGAAGAGCCACAACATCCAACA-CAATTAACAAAAAGCAAAGCT
1 TGTCATTTTAAGGTTTGCAAGCAAAGAGCCACAACCTCCAACATC-GTTAGC-GAAAGCAAAGCT
*
142911 TCTAGC
64 T-TAGT
* * * * ** * * *
142917 TGCCATTTTAAGGTTAGTAGGCAAAGAGCTGCAACCTCCATCATAGTTAGCGAGAGCAAAGCTCT
1 TGTCATTTTAAGGTTTGCAAGCAAAGAGCCACAACCTCCAACATCGTTAGCGAAAGCAAAGCT-T
142982 TAGT
65 TAGT
* *
142986 TG-CATTTTAAGG-TT-CATAGGCGAAGAGCCACAACCTTCAACA
1 TGTCATTTTAAGGTTTGCA-A-GCAAAGAGCCACAACCTCCAACA
143028 CAATTTTTGA
Statistics
Matches: 138, Mismatches: 36, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
66 1 0.01
67 1 0.01
68 29 0.21
69 55 0.40
70 52 0.38
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (68 bp):
TGTCATTTTAAGGTTTGCAAGCAAAGAGCCACAACCTCCAACATCGTTAGCGAAAGCAAAGCTTT
AGT
Found at i:143020 original size:68 final size:68
Alignment explanation
Indices: 142810--143027 Score: 210
Period size: 70 Copynumber: 3.2 Consensus size: 68
142800 AAAGAGTCGT
* * *
142810 AACCTCCAACATCGTTAGCGAAAGCAAAGCTATTAATTGTCATTTTAAGGTTTGCA-A-GCGAAG
1 AACCTCCAACATAGTTAGCGAAAGCAAAGCT-TTAGTTGCCATTTTAAGG-TT-CATAGGCGAAG
142873 AGCCAC
63 AGCCAC
* * * * * * *
142879 AACATCCAACACAATTAACAAAAAGCAAAGCTTCTAGCTGCCATTTTAAGGTT-AGTAGGCAAAG
1 AACCTCCAACATAGTTAGC-GAAAGCAAAGCTT-TAGTTGCCATTTTAAGGTTCA-TAGGCGAAG
**
142943 AGCTGC
63 AGCCAC
* *
142949 AACCTCCATCATAGTTAGCGAGAGCAAAGCTCTTAGTTG-CATTTTAAGGTTCATAGGCGAAGAG
1 AACCTCCAACATAGTTAGCGAAAGCAAAGCT-TTAGTTGCCATTTTAAGGTTCATAGGCGAAGAG
143013 CCAC
65 CCAC
*
143017 AACCTTCAACA
1 AACCTCCAACA
143028 CAATTTTTGA
Statistics
Matches: 117, Mismatches: 25, Indels: 15
0.75 0.16 0.10
Matches are distributed among these distances:
67 1 0.01
68 33 0.28
69 34 0.29
70 49 0.42
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.23
Consensus pattern (68 bp):
AACCTCCAACATAGTTAGCGAAAGCAAAGCTTTAGTTGCCATTTTAAGGTTCATAGGCGAAGAGC
CAC
Found at i:143148 original size:58 final size:58
Alignment explanation
Indices: 143070--143346 Score: 376
Period size: 58 Copynumber: 4.8 Consensus size: 58
143060 TTTAAGTATG
* * * *
143070 AGATAGCTCGCGGATTCACATCCCAGCTTATTATTGTTAAGAAAATTTTCTAAGTCTG
1 AGATAGCTAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTCTA
** * * * *
143128 AGGCAACTAGCGAATTCACATCCCAACTTATTATTTTTAAGAAAAATTTCTAAGTTTA
1 AGATAGCTAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTCTA
* * *
143186 AAATAGCTTAG-GGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTTTG
1 AGATAGC-TAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTCTA
* * * *
143244 AGATAGCTAGTGGATTCACATCCCATCTTATAATTTTTCAGAAAATTTTCTAAGTCTA
1 AGATAGCTAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTCTA
*
143302 AGATAGCTCGCGGATTCACATCCCAACTTATTATTTTTAAGAAAA
1 AGATAGCTAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAA
143347 AATTTTAATT
Statistics
Matches: 189, Mismatches: 28, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
57 3 0.02
58 183 0.97
59 3 0.02
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (58 bp):
AGATAGCTAGCGGATTCACATCCCAACTTATTATTTTTAAGAAAATTTTCTAAGTCTA
Found at i:146429 original size:28 final size:28
Alignment explanation
Indices: 146375--146429 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
146365 ATTTGTTAAT
* * *
146375 AAAACTTTGATTATTGTTGAAGAAAAAA
1 AAAACTTTGATTATTCTTAAACAAAAAA
*
146403 AAAACTTTGATTA-TCTTAAACATAAAA
1 AAAACTTTGATTATTCTTAAACAAAAAA
146430 CAGGGTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (28 bp):
AAAACTTTGATTATTCTTAAACAAAAAA
Found at i:150009 original size:40 final size:40
Alignment explanation
Indices: 149965--150046 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
149955 AGTATTAATA
* * *
149965 TTGTTACCTATACAGAAGGATATGAATAAATGCATTTATC
1 TTGTTACCTATACAGAAAGACATGAATAAATACATTTATC
* *
150005 TTGTTATCTATACAGAAAGACATGAGTAAATACATTTATC
1 TTGTTACCTATACAGAAAGACATGAATAAATACATTTATC
150045 TT
1 TT
150047 TCTATTTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (40 bp):
TTGTTACCTATACAGAAAGACATGAATAAATACATTTATC
Found at i:159809 original size:12 final size:12
Alignment explanation
Indices: 159794--159818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
159784 TGTTGCCAGA
159794 TTTTCCTTTCTC
1 TTTTCCTTTCTC
159806 TTTTCCTTTCTC
1 TTTTCCTTTCTC
159818 T
1 T
159819 CTCTCCTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTCCTTTCTC
Found at i:166994 original size:19 final size:19
Alignment explanation
Indices: 166970--167013 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
166960 TTTGAGAAAG
166970 ATGAGAAAGAAATGAACGA
1 ATGAGAAAGAAATGAACGA
* **
166989 ATGAGATATCAATGAACGA
1 ATGAGAAAGAAATGAACGA
167008 ATGAGA
1 ATGAGA
167014 TATCAGACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.25, T:0.16
Consensus pattern (19 bp):
ATGAGAAAGAAATGAACGA
Found at i:167014 original size:19 final size:19
Alignment explanation
Indices: 166980--167018 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
166970 ATGAGAAAGA
166980 AATGAACGAATGAGATATC
1 AATGAACGAATGAGATATC
166999 AATGAACGAATGAGATATC
1 AATGAACGAATGAGATATC
167018 A
1 A
167019 GACTTTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.10, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGAACGAATGAGATATC
Found at i:167469 original size:14 final size:14
Alignment explanation
Indices: 167447--167482 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
167437 ACTTACTAAG
*
167447 CTATAAAAGCTTAC
1 CTATGAAAGCTTAC
167461 CTATGAAAGCTTAC
1 CTATGAAAGCTTAC
*
167475 TTATGAAA
1 CTATGAAA
167483 TTTTTGTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (14 bp):
CTATGAAAGCTTAC
Found at i:173905 original size:17 final size:18
Alignment explanation
Indices: 173885--173918 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
173875 GTTTCTTGTT
*
173885 TAGTTTAGTT-AGAGTTC
1 TAGTTTAATTAAGAGTTC
173902 TAGTTTAATTAAGAGTT
1 TAGTTTAATTAAGAGTT
173919 TTATTTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (18 bp):
TAGTTTAATTAAGAGTTC
Found at i:175788 original size:14 final size:14
Alignment explanation
Indices: 175769--175796 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
175759 GAGACTAAAG
175769 GAGACCCTTTTTTT
1 GAGACCCTTTTTTT
175783 GAGACCCTTTTTTT
1 GAGACCCTTTTTTT
175797 TTTTCCTTGT
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:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GAGACCCTTTTTTT
Found at i:176047 original size:55 final size:55
Alignment explanation
Indices: 175926--176085 Score: 158
Period size: 55 Copynumber: 2.9 Consensus size: 55
175916 TTATCCGGAT
* * * * * * * *
175926 AACTATCAAATACGGAGACAATTTTGGGTGCAATTTTGGATCTACTCATGTAACG
1 AACTATCAGATGCGAAGACAATTTTGGGCGCAATTCTGGATATGCTCATGCAACG
* * *
175981 AACTGTTAGATGCGAAGATAATTTTGGGCGCAATTCTGGATATGCTCATGCAACG
1 AACTATCAGATGCGAAGACAATTTTGGGCGCAATTCTGGATATGCTCATGCAACG
* ** * * * *
176036 AGCTATCAGATGCGGTGACAATTCTGGACTCAATTCTGTATATGCTCATG
1 AACTATCAGATGCGAAGACAATTTTGGGCGCAATTCTGGATATGCTCATG
176086 TATCGACATT
Statistics
Matches: 84, Mismatches: 21, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 84 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (55 bp):
AACTATCAGATGCGAAGACAATTTTGGGCGCAATTCTGGATATGCTCATGCAACG
Found at i:181302 original size:16 final size:16
Alignment explanation
Indices: 181277--181307 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
181267 ATAATGTGAA
181277 AATAAAAATGAAATGC
1 AATAAAAATGAAATGC
*
181293 AATAATAATGAAATG
1 AATAAAAATGAAATG
181308 GGGTCCCCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.13, T:0.23
Consensus pattern (16 bp):
AATAAAAATGAAATGC
Found at i:182135 original size:55 final size:55
Alignment explanation
Indices: 182074--182178 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
182064 ATTCGGACAA
* *
182074 CTGTCAGATGCGAAGACTATTCTGGGCGCAATTCTAGACATGTTCATGCAGCGAG
1 CTGTCAGATGCGAAGACAATTCTGGGCGCAATTCTAGACATGCTCATGCAGCGAG
* * * *
182129 CTGTCAGATGCGATGACAATTCTTGGCGCAATTCTGGATATGCTCATGCA
1 CTGTCAGATGCGAAGACAATTCTGGGCGCAATTCTAGACATGCTCATGCA
182179 ACAACATTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (55 bp):
CTGTCAGATGCGAAGACAATTCTGGGCGCAATTCTAGACATGCTCATGCAGCGAG
Found at i:184834 original size:21 final size:21
Alignment explanation
Indices: 184810--184853 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
184800 GAGAAAAATA
* *
184810 AAAAAGAAACGAAAAATGAGT
1 AAAAACAAAAGAAAAATGAGT
**
184831 AAAAACAAAAGAATCATGAGT
1 AAAAACAAAAGAAAAATGAGT
184852 AA
1 AA
184854 GAAAACATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.07, G:0.16, T:0.11
Consensus pattern (21 bp):
AAAAACAAAAGAAAAATGAGT
Found at i:192519 original size:146 final size:146
Alignment explanation
Indices: 192254--192547 Score: 498
Period size: 146 Copynumber: 2.0 Consensus size: 146
192244 AATGTATTGG
* * *
192254 TGGCCAGGCATGAAACGAGAAATCTCTCAGTTTGTGATTCAATGTCTAGTGTGTCAACAAGTAAA
1 TGGCCAGGCATGAAACGAGAAATCTCTAAGTTTGTGACTAAATGTCTAGTGTGTCAACAAGTAAA
* *
192319 AGCTGAGCATCAGGTACCATCTAGATTACTACATCCTATTACCATTCCGGAGTGGAAATAGGAAC
66 AGCTGAGCATCAGCTACCATCTAGATTACTACATCCTATTACCATTCCGAAGTGGAAATAGGAAC
192384 GAGTTACTATGGATTT
131 GAGTTACTATGGATTT
* * *
192400 TGGCCAGGCATGAAACGGGAAATCTCTAAGTTTGTGACTAAATGTCTAGTGTTTTAACAAGTAAA
1 TGGCCAGGCATGAAACGAGAAATCTCTAAGTTTGTGACTAAATGTCTAGTGTGTCAACAAGTAAA
* *
192465 AGCTGAGCATCAGCTACCATCTGGATTACTACATCCTATTACCATTCCGAAGTGGAAATGGGAAC
66 AGCTGAGCATCAGCTACCATCTAGATTACTACATCCTATTACCATTCCGAAGTGGAAATAGGAAC
192530 GAGTTACTATGGATTT
131 GAGTTACTATGGATTT
192546 TG
1 TG
192548 TCATAGGACT
Statistics
Matches: 138, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
146 138 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (146 bp):
TGGCCAGGCATGAAACGAGAAATCTCTAAGTTTGTGACTAAATGTCTAGTGTGTCAACAAGTAAA
AGCTGAGCATCAGCTACCATCTAGATTACTACATCCTATTACCATTCCGAAGTGGAAATAGGAAC
GAGTTACTATGGATTT
Found at i:195860 original size:2 final size:2
Alignment explanation
Indices: 195855--195884 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
195845 GTGATATATA
195855 TG TG 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 TG TG
195885 AAGTGATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:201843 original size:24 final size:22
Alignment explanation
Indices: 201807--201853 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 22
201797 GTGAAAATTT
201807 CACATCTAGACTTCGATGTCGCGA
1 CACATCTAGACTT-G-TGTCGCGA
201831 CACA-CTAGAACTTGTGTCGCGA
1 CACATCTAG-ACTTGTGTCGCGA
201853 C
1 C
201854 GAAGCCATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.41
23 5 0.23
24 8 0.36
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (22 bp):
CACATCTAGACTTGTGTCGCGA
Found at i:208466 original size:12 final size:12
Alignment explanation
Indices: 208430--208468 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
208420 AAAGAATAGT
*
208430 GAAAAATCAAAA
1 GAAAAATGAAAA
208442 GAAAAA-GAAAA
1 GAAAAATGAAAA
*
208453 GAAAAATGAGAA
1 GAAAAATGAAAA
208465 GAAA
1 GAAA
208469 CTCATGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (12 bp):
GAAAAATGAAAA
Found at i:212008 original size:5 final size:5
Alignment explanation
Indices: 211998--212028 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
211988 GTCAAAAAAA
211998 TTTAT TTTAT TTTAT TTTAT TTTA- TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
212029 AATGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:221312 original size:47 final size:47
Alignment explanation
Indices: 221261--221416 Score: 213
Period size: 47 Copynumber: 3.3 Consensus size: 47
221251 TCACACTAAT
* * *
221261 GCAAATAAACTGCAAATAATCAAAATTATGGACAAGCCACTAAAATC
1 GCAAATAAACTGCAAATAATCAATATCATGGACAAGCCACCAAAATC
* *
221308 GCAAATACACTGCCAATAATCAATATCATGGACAAGCCACCAAAATC
1 GCAAATAAACTGCAAATAATCAATATCATGGACAAGCCACCAAAATC
* * *
221355 ACAAATATACTGCAAATAATCAATATCATGGACAAGGCACCAAAATC
1 GCAAATAAACTGCAAATAATCAATATCATGGACAAGCCACCAAAATC
* * *
221402 GTAAAAAAATTGCAA
1 GCAAATAAACTGCAA
221417 TAACTTCCAC
Statistics
Matches: 95, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 95 1.00
ACGTcount: A:0.49, C:0.21, G:0.11, T:0.19
Consensus pattern (47 bp):
GCAAATAAACTGCAAATAATCAATATCATGGACAAGCCACCAAAATC
Found at i:226188 original size:30 final size:28
Alignment explanation
Indices: 226154--226517 Score: 224
Period size: 29 Copynumber: 12.5 Consensus size: 28
226144 CTAAAATCAT
* *
226154 ATTTTGACCCTTGAACTCTTCAAAAATTAC
1 ATTTT-ACCCTCGAACT-TCCAAAAATTAC
* ** *
226184 ATTTTACACTTAAACTTTCTAAAAATTAC
1 ATTTTACCCTCGAAC-TTCCAAAAATTAC
*
226213 ATTTTTACCC-CTAAACTTCACAAAAATTAC
1 A-TTTTACCCTC-GAACTTC-CAAAAATTAC
* *
226243 ATTAATT-CCCTCGAACTTCCTAAAAACTAT
1 ATT--TTACCCTCGAACTTCC-AAAAATTAC
* *
226273 ATTTTTACCCCCAAACTTCCAAAAATTACC
1 A-TTTTACCCTCGAACTTCCAAAAATTA-C
*
226303 ATTTTACCCTCGAACTTCCAAAAAATAC
1 ATTTTACCCTCGAACTTCCAAAAATTAC
*
226331 ATTTTTACCCTCGAACTTTCAAAAA-TACC
1 A-TTTTACCCTCGAACTTCCAAAAATTA-C
*
226360 ATTTTAACCCT-AAACTTCCAAAAA-TATC
1 ATTTT-ACCCTCGAACTTCCAAAAATTA-C
* **
226388 ATATCTACCCTCG-GGTGTCCAAAAATTACC
1 AT-TTTACCCTCGAACT-TCCAAAAATTA-C
* *
226418 ATTTTAACCTTGAACTTCCAAAAA-TATC
1 ATTTTACCCTCGAACTTCCAAAAATTA-C
* * *
226446 ATTTTTGCCCCCTAA-TATCCAAAAATTATC
1 A-TTTTACCCTCGAACT-TCCAAAAATTA-C
* * *
226476 GTTTTACCC-CTAAATCTCCAAAAATTACC
1 ATTTTACCCTCGAACT-TCCAAAAATTA-C
226505 ATTTTACCCTCGA
1 ATTTTACCCTCGA
226518 GTATCCAAAA
Statistics
Matches: 267, Mismatches: 43, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
28 39 0.15
29 155 0.58
30 68 0.25
31 5 0.02
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.34
Consensus pattern (28 bp):
ATTTTACCCTCGAACTTCCAAAAATTAC
Found at i:226237 original size:59 final size:58
Alignment explanation
Indices: 226174--226370 Score: 211
Period size: 60 Copynumber: 3.3 Consensus size: 58
226164 TTGAACTCTT
* ** * *
226174 CAAAAATTACATTTTACACTTAAACTTTCTAAAAATTACATTTTTACCCCTAAACTTC
1 CAAAAATTACATTTTACCCTCGAACTTTCTAAAAAATACATTTTTACCCCCAAACTTC
* * *
226232 ACAAAAATTACATTAATT-CCCTCGAACTTCCTAAAAACTATATTTTTACCCCCAAACTTC
1 -CAAAAATTACATT--TTACCCTCGAACTTTCTAAAAAATACATTTTTACCCCCAAACTTC
* * * *
226292 CAAAAATTACCATTTTACCCTCGAAC-TTCCAAAAAATACATTTTTACCCTCGAACTTT
1 CAAAAATTA-CATTTTACCCTCGAACTTTCTAAAAAATACATTTTTACCCCCAAACTTC
226350 CAAAAA-TACCATTTTAACCCT
1 CAAAAATTA-CATTTT-ACCCT
226371 AAACTTCCAA
Statistics
Matches: 119, Mismatches: 14, Indels: 11
0.83 0.10 0.08
Matches are distributed among these distances:
57 9 0.08
58 38 0.32
59 31 0.26
60 39 0.33
61 2 0.02
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.34
Consensus pattern (58 bp):
CAAAAATTACATTTTACCCTCGAACTTTCTAAAAAATACATTTTTACCCCCAAACTTC
Found at i:226354 original size:58 final size:60
Alignment explanation
Indices: 226149--226529 Score: 260
Period size: 58 Copynumber: 6.5 Consensus size: 60
226139 ACTTTCTAAA
* * * * ** * *
226149 ATCATATTTTGACCCTTGAACTCTTCAAAAATTA-CATTTTACACTTAAACTTTCTAAAAAT
1 ATCAT-TTTT-ACCCTCGAACTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAT
* *
226210 -TACATTTTTACCC-CTAAACT-TCACAAAAATTA-CATTAATT-CCCTCGAACTTCCTAAAAAC
1 AT-CATTTTTACCCTC-GAACTATC-CAAAAATTACCATT--TTACCCTCGAACTTCC-AAAAAA
226270 T
60 T
* *
226271 AT-ATTTTTACCCCCAAACT-TCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAT
1 ATCATTTTTACCCTCGAACTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAT
* *
226329 A-CATTTTTACCCTCGAACT-TTCAAAAA-TACCATTTTAACCCT-AAACTTCC-AAAAAT
1 ATCATTTTTACCCTCGAACTATCCAAAAATTACCATTTT-ACCCTCGAACTTCCAAAAAAT
* * ** * * *
226385 ATCATATCTACCCTCG-GGTGTCCAAAAATTACCATTTTAACCTTGAACTTCC-AAAAAT
1 ATCATTTTTACCCTCGAACTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAT
* * * * * * * *
226443 ATCATTTTTGCCCCCTAA-TATCCAAAAATTATCGTTTTACCC-CTAAATCTCCAAAAATT
1 ATCATTTTTACCCTCGAACTATCCAAAAATTACCATTTTACCCTCGAACT-TCCAAAAAAT
* *
226502 ACCA-TTTTACCCTCG-AGTATCCAAAAAT
1 ATCATTTTTACCCTCGAACTATCCAAAAAT
226530 CACTTTTTTA
Statistics
Matches: 261, Mismatches: 39, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
56 8 0.03
57 43 0.16
58 112 0.43
59 51 0.20
60 35 0.13
61 11 0.04
62 1 0.00
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (60 bp):
ATCATTTTTACCCTCGAACTATCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAAAT
Found at i:226397 original size:86 final size:85
Alignment explanation
Indices: 226226--226544 Score: 231
Period size: 86 Copynumber: 3.7 Consensus size: 85
226216 TTTACCCCTA
* * *
226226 AACTTCACAAAAATTACATTAATT-CCCTCGAACTTCCTAAAAACTATATTTTTACCCCCAAACT
1 AACTTC-CAAAAATTACATT-TTTACCCTCGAACTTCC-AAAAA-TACA-TTTTAACCCCAAACT
*
226290 TCCAAAAATTACCATTTTACCCTCG
61 TCCAAAAATTACCATTCTACCCTCG
* * *
226315 AACTTCCAAAAAATACATTTTTACCCTCGAACTTTCAAAAATACCATTTTAACCCTAAACTTCCA
1 AACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATA-CATTTTAACCCCAAACTTCCA
*
226380 AAAA-TATCATATCTACCCTCG
65 AAAATTACCAT-TCTACCCTCG
** * * ** *
226401 -GGTGTCCAAAAATTACCA-TTTTAACCTTGAACTTCCAAAAATATCATTTTTGCCCCCTAA-TA
1 AACT-TCCAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATA-CA-TTTTAACCCCAAACT-
* * * *
226463 TCCAAAAATTATCGTTTTACCC-CT
61 TCCAAAAATTACCATTCTACCCTCG
* * * *
226487 AAATCTCCAAAAATTACCA-TTTTACCCTCG-AGTATCCAAAAATCACTTTTTTACCCCA
1 AACT-TCCAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAAT-ACATTTTAACCCCA
226545 TTTGTTTTGC
Statistics
Matches: 187, Mismatches: 32, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
85 6 0.03
86 78 0.42
87 67 0.36
88 30 0.16
89 6 0.03
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (85 bp):
AACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATACATTTTAACCCCAAACTTCCAA
AAATTACCATTCTACCCTCG
Found at i:228830 original size:2 final size:2
Alignment explanation
Indices: 228823--228864 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
228813 TTCATTTTTA
228823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.