Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013872.1 Kokia drynarioides strain JFW-HI SEQ_128900, 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: 245807
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:13168 original size:3 final size:3
Alignment explanation
Indices: 13160--13188 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13150 AAAAAGTCAA
13160 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
13189 ATTACAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20412 original size:20 final size:20
Alignment explanation
Indices: 20361--20413 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
20351 TATAAAAGTC
* *
20361 TACAAGAAAATATGGATAAA
1 TACAAGAATATATGGAAAAA
* *
20381 TA-AAGCATATATTGAAAAA
1 TACAAGAATATATGGAAAAA
20400 TACAAGAATATATG
1 TACAAGAATATATG
20414 AATTTTCTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.57, C:0.06, G:0.13, T:0.25
Consensus pattern (20 bp):
TACAAGAATATATGGAAAAA
Found at i:30840 original size:24 final size:25
Alignment explanation
Indices: 30816--30863 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
30806 AAACAACTTC
30816 TAAAAAAAAACTC-AAGAGCAATTCT
1 TAAAAAAAAACTCAAAGAG-AATTCT
* *
30841 TGAAGAAAAACTCAAAGAGAATT
1 TAAAAAAAAACTCAAAGAGAATT
30864 ATTATTTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (25 bp):
TAAAAAAAAACTCAAAGAGAATTCT
Found at i:47508 original size:13 final size:11
Alignment explanation
Indices: 47473--47520 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
47463 CTTATATTAC
47473 TTTTATAATAT
1 TTTTATAATAT
*
47484 TTTTAAAATAT
1 TTTTATAATAT
47495 TATTTATTAATAT
1 T-TTTA-TAATAT
47508 TTTT-TATATAT
1 TTTTATA-ATAT
47519 TT
1 TT
47521 ATGATTGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 2 0.06
11 17 0.53
12 7 0.22
13 6 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTTATAATAT
Found at i:47518 original size:24 final size:25
Alignment explanation
Indices: 47465--47519 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
47455 CTCGAAACCT
47465 TATATTACTTTTATAATATTTTTAA
1 TATATTACTTTTATAATATTTTTAA
* *
47490 AATATTA--TTTATTAATATTTTTTA
1 TATATTACTTTTA-TAATATTTTTAA
47514 TATATT
1 TATATT
47520 TATGATTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 16 0.62
25 6 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATATTACTTTTATAATATTTTTAA
Found at i:50389 original size:21 final size:22
Alignment explanation
Indices: 50350--50390 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
50340 AATTTTCCTA
*
50350 TTTTCTTATGTATTTAAACCAT
1 TTTTCTTATGTATTGAAACCAT
*
50372 TTTTCTTTTGT-TTGAAACC
1 TTTTCTTATGTATTGAAACC
50391 CTTTCTCTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (22 bp):
TTTTCTTATGTATTGAAACCAT
Found at i:62935 original size:20 final size:20
Alignment explanation
Indices: 62907--62945 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62897 CTGAAACTCT
62907 TTCTCTTTCTTCTCCTTCTA
1 TTCTCTTTCTTCTCCTTCTA
* *
62927 TTCTGTTTCTTCTTCTTCT
1 TTCTCTTTCTTCTCCTTCT
62946 TCTTTCTCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.64
Consensus pattern (20 bp):
TTCTCTTTCTTCTCCTTCTA
Found at i:63678 original size:21 final size:21
Alignment explanation
Indices: 63652--63723 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
63642 TGATTCAGTT
* *
63652 TTCTACCAATACAAGTGTCAG
1 TTCTACCAATACAAGTCTCAC
63673 TTCTACCGAA-ACAAGTCTCAC
1 TTCTACC-AATACAAGTCTCAC
* *
63694 TTCTACCGATACAAGTCTAAC
1 TTCTACCAATACAAGTCTCAC
*
63715 TTTTACCAA
1 TTCTACCAA
63724 CACCAAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.93
22 2 0.05
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.29
Consensus pattern (21 bp):
TTCTACCAATACAAGTCTCAC
Found at i:64492 original size:36 final size:36
Alignment explanation
Indices: 64391--64492 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
64381 TTTGTTATTT
* *
64391 GTTTTACTCCTTATTGACCCAAAGGTCATAATGCTA
1 GTTTTACTCCCTATTGACCCAAAGGTCATGATGCTA
* *
64427 GTTTTACTCCCTATT-AGCCCAGAGGTCATGATGCTC
1 GTTTTACTCCCTATTGA-CCCAAAGGTCATGATGCTA
* *
64463 GTTTTACTCCCTATTGACCTAAAAGTCATG
1 GTTTTACTCCCTATTGACCCAAAGGTCATG
64493 CCTGTTACAG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
35 1 0.02
36 55 0.96
37 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (36 bp):
GTTTTACTCCCTATTGACCCAAAGGTCATGATGCTA
Found at i:70837 original size:19 final size:20
Alignment explanation
Indices: 70813--70854 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
70803 CATTACGTCA
70813 GAAATAA-CCTACTTCTATC
1 GAAATAAGCCTACTTCTATC
*
70832 GAAATAAGTCTTACTTCTATC
1 GAAATAAG-CCTACTTCTATC
70853 GA
1 GA
70855 TACAAGTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
GAAATAAGCCTACTTCTATC
Found at i:70848 original size:21 final size:21
Alignment explanation
Indices: 70822--70871 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
70812 AGAAATAACC
*
70822 TACTTCTATCGAAATAAGTCT
1 TACTTCTATCGAAACAAGTCT
*
70843 TACTTCTATCGATACAAGTCT
1 TACTTCTATCGAAACAAGTCT
70864 TACTTCTA
1 TACTTCTA
70872 CCGACACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (21 bp):
TACTTCTATCGAAACAAGTCT
Found at i:92745 original size:32 final size:32
Alignment explanation
Indices: 92703--92769 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
92693 TTTTTCGAGT
* *
92703 TTTAGATTTTAAAATTTTTGGGAATTTAGGGA
1 TTTAGATTTTAAAAATTTAGGGAATTTAGGGA
* * *
92735 TTTAGGTTTTAAAAATTTAGGGATTTTTGGGA
1 TTTAGATTTTAAAAATTTAGGGAATTTAGGGA
92767 TTT
1 TTT
92770 TTAGTGTTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.49
Consensus pattern (32 bp):
TTTAGATTTTAAAAATTTAGGGAATTTAGGGA
Found at i:92865 original size:44 final size:45
Alignment explanation
Indices: 92781--92868 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
92771 TAGTGTTGTT
* * *
92781 GGGTTTGGGGAATTTGGTTTAGGTTTAAGAAATTTGGGGATTTTG
1 GGGTTTGGAGAATTTGGTTTAAGTTTAAGAAATTTAGGGATTTTG
*
92826 GGGTTTGGAGATTTTGGTTTAAGTTTAA-AAATTTAGGGATTTT
1 GGGTTTGGAGAATTTGGTTTAAGTTTAAGAAATTTAGGGATTTT
92869 CGGGACTTAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (45 bp):
GGGTTTGGAGAATTTGGTTTAAGTTTAAGAAATTTAGGGATTTTG
Found at i:93366 original size:22 final size:22
Alignment explanation
Indices: 93341--93385 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
93331 TGTTTAATAA
93341 TGTTTAATCGATGTTGCTATTT
1 TGTTTAATCGATGTTGCTATTT
93363 TGTTTAATCGATGTTGCTATTT
1 TGTTTAATCGATGTTGCTATTT
93385 T
1 T
93386 ATCGACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.56
Consensus pattern (22 bp):
TGTTTAATCGATGTTGCTATTT
Found at i:94856 original size:109 final size:109
Alignment explanation
Indices: 94727--94944 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 109
94717 CCTAAAATGC
*
94727 CATCCTTTTTTGGCTTCTAGTTTTCATACTCGTACCCAACTGAGAACAACAATCAGAACCCAAAT
1 CATCCTTTTTTGGCTTCTAGTTCTCATACTCGTACCCAACTGAGAACAACAATCAGAACCCAAAT
94792 TAAATTTAAATAATTTGGAATTGACAATGAGAAAGTGTTTACAA
66 TAAATTTAAATAATTTGGAATTGACAATGAGAAAGTGTTTACAA
94836 CATCCTTTTTTGGCTTCTAGTTCTCATACTCGTACCCAACTGAGAACAACAATCAGAACCCAAAT
1 CATCCTTTTTTGGCTTCTAGTTCTCATACTCGTACCCAACTGAGAACAACAATCAGAACCCAAAT
*
94901 TAAATTTAAATAATTTGGAATTGACAATGAGAAATTGTTTACAA
66 TAAATTTAAATAATTTGGAATTGACAATGAGAAAGTGTTTACAA
94945 TATACCTGTG
Statistics
Matches: 107, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 107 1.00
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (109 bp):
CATCCTTTTTTGGCTTCTAGTTCTCATACTCGTACCCAACTGAGAACAACAATCAGAACCCAAAT
TAAATTTAAATAATTTGGAATTGACAATGAGAAAGTGTTTACAA
Found at i:96131 original size:36 final size:32
Alignment explanation
Indices: 96056--96135 Score: 106
Period size: 32 Copynumber: 2.4 Consensus size: 32
96046 GACTCTATAA
* *
96056 TTTAAATTAAAAAACATAAGTATGCTGCCAAT
1 TTTAAATTAAAAAACATAAGTACGCTACCAAT
96088 TTTAAATTAAAAAACATAAGTACGTCTACTATCAAT
1 TTTAAATTAAAAAACATAAGTACG-CTAC---CAAT
96124 TTTAAATTAAAA
1 TTTAAATTAAAA
96136 CAAAACACTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 23 0.55
33 3 0.07
36 16 0.38
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (32 bp):
TTTAAATTAAAAAACATAAGTACGCTACCAAT
Found at i:98108 original size:36 final size:36
Alignment explanation
Indices: 98031--98116 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
98021 TCACCCTCAA
* *
98031 CACCTTCAACACCTTCACTAACAGCACCCCTTCCCT
1 CACCCTCAACACCTTCACTAACAGCACCCCTTCACT
98067 CACCCTCAACACCTTCACTAACAGCA-CCCTT-ACT
1 CACCCTCAACACCTTCACTAACAGCACCCCTTCACT
*
98101 CGAACCCTCACCACCT
1 C--ACCCTCAACACCT
98117 CTCAAACCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
34 3 0.07
35 5 0.11
36 37 0.82
ACGTcount: A:0.27, C:0.50, G:0.03, T:0.20
Consensus pattern (36 bp):
CACCCTCAACACCTTCACTAACAGCACCCCTTCACT
Found at i:99694 original size:44 final size:45
Alignment explanation
Indices: 99645--99732 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
99635 GTAAGTCCCG
*
99645 AAAATCCCCAAATTT-TTAAACATAAACCAAAATCTCCAAACCCC
1 AAAATCCCCAAATTTCTTAAACATAAACCAAAATCCCCAAACCCC
* * *
99689 AAAATCCCTAAATTTCTTAAACCTAAACCAAATTCCCCAAACCC
1 AAAATCCCCAAATTTCTTAAACATAAACCAAAATCCCCAAACCC
99733 AACAACCCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (45 bp):
AAAATCCCCAAATTTCTTAAACATAAACCAAAATCCCCAAACCCC
Found at i:99734 original size:44 final size:44
Alignment explanation
Indices: 99645--99744 Score: 132
Period size: 44 Copynumber: 2.3 Consensus size: 44
99635 GTAAGTCCCG
* *
99645 AAAATCCCCAAATTTTTAAACATAAACCAAAATCTCCAAACCCC
1 AAAATCCCTAAATTTTTAAACATAAACCAAAATCCCCAAACCCC
* *
99689 AAAATCCCTAAATTTCTTAAACCTAAACCAAATTCCCCAAA-CCC
1 AAAATCCCTAAATTT-TTAAACATAAACCAAAATCCCCAAACCCC
99733 AACAA-CCCTAAA
1 AA-AATCCCTAAA
99745 AATCTCAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
44 26 0.52
45 24 0.48
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (44 bp):
AAAATCCCTAAATTTTTAAACATAAACCAAAATCCCCAAACCCC
Found at i:112010 original size:20 final size:20
Alignment explanation
Indices: 111973--112032 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
111963 CATTCTTACA
111973 TTTATGTTTATTTC-TTTTTT
1 TTTA-GTTTATTTCTTTTTTT
111993 TTTAGTTTATTTCTTTTTTT
1 TTTAGTTTATTTCTTTTTTT
112013 TTTAGTTTATTTCTTCTTTT
1 TTTAGTTTATTTCTT-TTTT
112033 ATCTGTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 9 0.24
20 25 0.66
21 4 0.11
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTAGTTTATTTCTTTTTTT
Found at i:113522 original size:11 final size:11
Alignment explanation
Indices: 113506--113557 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
113496 CACTTAGAAA
*
113506 AAAAAGAAAAT
1 AAAAAGAAAAG
113517 AAAAAG-AAAG
1 AAAAAGAAAAG
*
113527 AAGAAGAAAAG
1 AAAAAGAAAAG
113538 AAAAA-AAGAAG
1 AAAAAGAA-AAG
113549 AAAAA-AAAA
1 AAAAAGAAAA
113558 TATTGCTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
10 12 0.33
11 24 0.67
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:113546 original size:16 final size:15
Alignment explanation
Indices: 113503--113557 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 15
113493 AGTCACTTAG
*
113503 AAAAAAAAGAAAATAA
1 AAAAAAAAGAAGA-AA
113519 AAAGAAAGAAGAAGAAA
1 AAA-AAA-AAGAAGAAA
113536 AGAAAAAAAGAAGAAA
1 A-AAAAAAAGAAGAAA
113552 AAAAAA
1 AAAAAA
113558 TATTGCTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
15 5 0.14
16 13 0.37
17 9 0.26
18 8 0.23
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (15 bp):
AAAAAAAAGAAGAAA
Found at i:124615 original size:379 final size:378
Alignment explanation
Indices: 123892--124643 Score: 1274
Period size: 379 Copynumber: 2.0 Consensus size: 378
123882 AAAATTCTTG
* * * *
123892 ATATCATTTCCTTTCTCCAAATGTTGTTTATACAGGAGCTTAGGCACATAATACATGTTGTCAGA
1 ATATCATTTCCTTCCTCCAAATGTTGTTTATACAGGAGCTTAGGCACACAATACACGTTGCCAGA
*
123957 TCCGTTTTTCTAGGGGTTCTAGAGCCCTCCTAGAGTCTTTTAATGCAGACCATAAATATATCTGG
66 TCCGTTTTTCTAGGGGTTCTAGAGCCCTCCTAGAGTCTTTTAAAGCAGACCATAAATATATCTGG
* * *
124022 CTTGTTTCAACAGCTTGTGTGCCTGGTACTACTAGAGCGTTTAACAGCTACAAAGTTTGGCTACT
131 CTTGTTTCAACAGCTTGCGTGCCTGGTACTACTAGAGCATTTAACAGCTACAAAGTTTGGCTACG
* *
124087 TTCGCTCCCCAACAGAGCATTGTTATTNGGCCTGGTACTCTCATCTTCCTCCACCTTCTCCTACA
196 TTCGCTCCCCAACAGAGCATTGTTATTAGGCCTCGTACTCTCATCTTCCTCCACCTTCTCCTACA
* *
124152 TCTAGAAACATGTACCAACAAGCATAGTTTGCTACAACATAAAGGGTAAAATGTATATATTCTAC
261 TCCAAAAACATGTACCAACAAGCATAGTTTGCTACAACATAAAGGGTAAAATGTATATATTCTAC
*
124217 CAGTTTAGGCACAACACAACTCCAAGGACAAAAACATATAAAAACACTTTGTC
326 CAGTTTAGGCACAACACAACTCCAAGGACAAAAACATAAAAAAACACTTTGTC
* * *
124270 ATATCATTTCCTTCCTCTAAATGTTGTTTATATAGGAGCTTGGGCACACAATACACGTTGCCAGA
1 ATATCATTTCCTTCCTCCAAATGTTGTTTATACAGGAGCTTAGGCACACAATACACGTTGCCAGA
124335 TCCGTTTTTCTAGGGGTTCTAGAGCCCTCCTAGAGTCTTTTAAAGCAGACCATAAATATATCTGG
66 TCCGTTTTTCTAGGGGTTCTAGAGCCCTCCTAGAGTCTTTTAAAGCAGACCATAAATATATCTGG
* * *
124400 CTTGTTTCAGCAGAATCTTGCGTGCCTGGTAGTACTAGAGCATTT-ACAGCTACAAAGTTTTGCT
131 CTTGTTTCAACAG---CTTGCGTGCCTGGTACTACTAGAGCATTTAACAGCTACAAAGTTTGGCT
*
124464 ACGTTCGCTCCCCAACAGTGCATTGTTATT-GGCCTCGTACTCTCATCTTCCTCCACCTTCTCCT
193 ACGTTCGCTCCCCAACAGAGCATTGTTATTAGGCCTCGTACTCTCATCTTCCTCCACCTTCTCCT
124528 ACATCCAAAAACATGTACCAACAAGCATAGTTTGCTACAACATAAAGGGTAAAATGTATATATTC
258 ACATCCAAAAACATGTACCAACAAGCATAGTTTGCTACAACATAAAGGGTAAAATGTATATATTC
*
124593 TGCCAGTTTAGGCACAACACAACTCCAAGGACAAAAACATAAAAAAACACT
323 TACCAGTTTAGGCACAACACAACTCCAAGGACAAAAACATAAAAAAACACT
124644 AAAAATGTTA
Statistics
Matches: 351, Mismatches: 20, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
378 134 0.38
379 145 0.41
380 46 0.13
381 26 0.07
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (378 bp):
ATATCATTTCCTTCCTCCAAATGTTGTTTATACAGGAGCTTAGGCACACAATACACGTTGCCAGA
TCCGTTTTTCTAGGGGTTCTAGAGCCCTCCTAGAGTCTTTTAAAGCAGACCATAAATATATCTGG
CTTGTTTCAACAGCTTGCGTGCCTGGTACTACTAGAGCATTTAACAGCTACAAAGTTTGGCTACG
TTCGCTCCCCAACAGAGCATTGTTATTAGGCCTCGTACTCTCATCTTCCTCCACCTTCTCCTACA
TCCAAAAACATGTACCAACAAGCATAGTTTGCTACAACATAAAGGGTAAAATGTATATATTCTAC
CAGTTTAGGCACAACACAACTCCAAGGACAAAAACATAAAAAAACACTTTGTC
Found at i:126011 original size:35 final size:36
Alignment explanation
Indices: 125941--126060 Score: 89
Period size: 36 Copynumber: 3.5 Consensus size: 36
125931 AAATAAAATG
** * *
125941 TTTAAAATAAAAAATAGGATAAATGGATTGCAATTT
1 TTTAAAATAAAAAATAAAATAAAAGGATTGAAATTT
125977 TTTAAAAT-AAAAATAAAAATAAAAGGATT-AAA---
1 TTTAAAATAAAAAAT-AAAATAAAAGGATTGAAATTT
*
126009 TTTAAAA-AAAAAA-AGAATAAAAGG---GAAATTT
1 TTTAAAATAAAAAATAAAATAAAAGGATTGAAATTT
126040 TTTACAAGAATAAAAAATAAA
1 TTT--AA-AATAAAAAATAAA
126061 TGGTTTTAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
28 3 0.04
30 10 0.15
31 3 0.04
32 12 0.18
33 2 0.03
34 2 0.03
35 14 0.21
36 21 0.31
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.27
Consensus pattern (36 bp):
TTTAAAATAAAAAATAAAATAAAAGGATTGAAATTT
Found at i:126029 original size:21 final size:21
Alignment explanation
Indices: 125990--126029 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
125980 AAAATAAAAA
* * *
125990 TAAAAATAAAAGGATTAAATT
1 TAAAAAAAAAAAGAATAAATT
126011 TAAAAAAAAAAAGAATAAA
1 TAAAAAAAAAAAGAATAAA
126030 AGGGAAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAAAAAAAAAGAATAAATT
Found at i:126864 original size:3 final size:3
Alignment explanation
Indices: 126856--126893 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
126846 AAGGGCCCAA
126856 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
126894 TAGGGTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:127769 original size:51 final size:50
Alignment explanation
Indices: 127536--127977 Score: 169
Period size: 51 Copynumber: 8.8 Consensus size: 50
127526 TAAAAAAGAG
*** *
127536 AAAGTTTAAATTTTT-A-AAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
1 AAAGTTTAAATTTTTAACAAAATATTGAT-T-TTTTTTAATTATTTTAAA-AA
* * * * * * *
127587 AAAATTTAAAATTTTAACAAAGTTTTGA-TTTTTTTAACTATTTCGAAATA
1 AAAGTTTAAATTTTTAACAAAATATTGATTTTTTTTAATTATTT-TAAAAA
** * **
127637 AAAGTTTGGATTTTTAAGCAAAATAGTGA--TTTTTTAA--A--AAAAAAGA
1 AAAGTTTAAATTTTTAA-CAAAATATTGATTTTTTTTAATTATTTTAAAA-A
* *** *
127683 GAAAGTTTAGATTTTT-A-AAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
1 -AAAGTTTAAATTTTTAACAAAATATTGAT-T-TTTTTTAATTATTTTAAA-AA
* * * * * *
127735 AAAGTTTAAAATTTTAACAAAGTTTTGATTTTTTTTAACTATTTCGAAATA
1 AAAGTTTAAATTTTTAACAAAATATTGATTTTTTTTAATTATTT-TAAAAA
** * * * ***
127786 AAAGTTTGGATTTTTAAGTAAAATAGTGA-TTTTCTTAA--A-AAAAAAAA
1 AAAGTTTAAATTTTTAA-CAAAATATTGATTTTTTTTAATTATTTTAAAAA
* *** *
127833 GAAAGTTTAGATTTTTAA-AAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
1 -AAAGTTTAAATTTTTAACAAAATATTGAT-T-TTTTTTAATTATTTTAAA-AA
* * *
127886 AAAGTTTAAATTTTTAACAAAGTTTTGATTTTTTTTAATTATTTTGAAATA
1 AAAGTTTAAATTTTTAACAAAATATTGATTTTTTTTAATTATTTT-AAAAA
** * * *
127937 AAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTTGTTTAAT
1 AAAGTTTAAATTTTTAA-CAAAATATTGATTTTT-TTTAAT
127978 CAAATGAAAA
Statistics
Matches: 287, Mismatches: 73, Indels: 60
0.68 0.17 0.14
Matches are distributed among these distances:
44 7 0.02
45 3 0.01
46 9 0.03
47 18 0.06
48 25 0.09
49 7 0.02
50 35 0.12
51 104 0.36
52 53 0.18
53 26 0.09
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (50 bp):
AAAGTTTAAATTTTTAACAAAATATTGATTTTTTTTAATTATTTTAAAAA
Found at i:128011 original size:151 final size:150
Alignment explanation
Indices: 127310--127969 Score: 1048
Period size: 148 Copynumber: 4.4 Consensus size: 150
127300 TTTGAGAAAT
* * *
127310 GTTTTGATTTTTTTCAAACAATTTCGAAATAAAAGCTTT-GATTTTTTTAAGCAAAATAATGATT
1 GTTTTGATTTTTTT-TAACTATTTCGAAATAAAAG-TTTGGA--TTTTTAAGCAAAATAGTGATT
*
127374 TTCTT--TAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTA-TTTTTAGTTATTTTAAA
62 TTCTTAAAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAA
*
127436 GAAAAAATTTAAATTTTTAACAAA
127 GAAAAAATTTAAAATTTTAACAAA
* * *
127460 GTTTTGATTTTTTTAAACTATTTCGAAATAAAAATTTGAATTTTTAAGCAAAATAGTGATTTTCT
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCT
* *
127525 T--TAAAAAAGAGAAAGTTTAAATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
66 TAAAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
127588 AAATTTAAAATTTTAACAAA
131 AAATTTAAAATTTTAACAAA
127608 GTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTT-T
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCT
127671 TAAAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
66 TAAAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
*
127736 AAGTTTAAAATTTTAACAAA
131 AAATTTAAAATTTTAACAAA
*
127756 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCT
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCT
*
127821 TAAAAAAAAAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
66 TAAAAAAAAAGAGAAAGTTTAGATTTTT-AAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAA
* *
127886 AAAGTTTAAATTTTTAACAAA
130 AAAATTTAAAATTTTAACAAA
* * * *
127907 GTTTTGATTTTTTTTAATTATTTTGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTT
1 GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTT
127970 TGTTTAATCA
Statistics
Matches: 485, Mismatches: 18, Indels: 13
0.94 0.03 0.03
Matches are distributed among these distances:
146 2 0.00
147 116 0.24
148 136 0.28
149 73 0.15
150 42 0.09
151 116 0.24
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.44
Consensus pattern (150 bp):
GTTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGCAAAATAGTGATTTTCT
TAAAAAAAAAGAGAAAGTTTAGATTTTTAAAAATAAAAATCTATTTTTTAGTTATTTTAAAGAAA
AAATTTAAAATTTTAACAAA
Found at i:129429 original size:238 final size:237
Alignment explanation
Indices: 129012--129481 Score: 814
Period size: 238 Copynumber: 2.0 Consensus size: 237
129002 AAAATCATAA
* *
129012 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTAATATTTCTCTTAATTCATTAGTAACTTT
1 TAATGATAAAAGATCGAACAAGTTGTAAATGAATTTAATATTTCTCTTAATTCATTAGTAACTTT
* *
129077 TAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAATATATTTTACTAGAGTTA
66 TAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATTA
*
129142 TTTAGGTATCCTTTAGGGTTTTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
131 TTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
* *
129207 GTTTGGTGAACACGTTTTAATCAAGTTACAAGTAAATCGGAG
196 GTTTGGTGAACACGTCTTAATCAAATTACAAGTAAATCGGAG
* *
129249 TAATGATAAAAGATTGAACAAGTTGTAAATGAATTTTAATATTTTTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAACAAGTTGTAAATGAA-TTTAATATTTCTCTTAATTCATTAGTAACTT
* *
129314 TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGGAGGTATTTTACTAGAATT
65 TTAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATT
*
129379 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTTGATA
130 ATTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
*
129444 AGTTTGGTGAACACGTCTTAGTCAAATTACAAGTAAAT
195 AGTTTGGTGAACACGTCTTAATCAAATTACAAGTAAAT
129482 TAGAGGCATT
Statistics
Matches: 219, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
237 30 0.14
238 189 0.86
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (237 bp):
TAATGATAAAAGATCGAACAAGTTGTAAATGAATTTAATATTTCTCTTAATTCATTAGTAACTTT
TAGGCTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAGATATTTTACTAGAATTA
TTTAGGTATCCTTTAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATAA
GTTTGGTGAACACGTCTTAATCAAATTACAAGTAAATCGGAG
Found at i:130329 original size:15 final size:16
Alignment explanation
Indices: 130298--130330 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
130288 TCTTTTTCAT
130298 TTGTTTTTGCTCCTTG
1 TTGTTTTTGCTCCTTG
*
130314 TTGTTTTT-CTCTTTG
1 TTGTTTTTGCTCCTTG
130329 TT
1 TT
130331 TCATTTCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.00, C:0.15, G:0.15, T:0.70
Consensus pattern (16 bp):
TTGTTTTTGCTCCTTG
Found at i:131174 original size:46 final size:45
Alignment explanation
Indices: 131059--131616 Score: 542
Period size: 45 Copynumber: 12.9 Consensus size: 45
131049 AGTTTTGTGT
* * *
131059 GTGGCTTCAATCTGTCCCTCTGGATTTAAGGGTATAAGATTGGAT-
1 GTGGCTTCAATCTGCCCCTCTGGA-TTAGGGGTAAAAGATTGGATG
*
131104 GTGGCTTCAATCTGTCCCTCTGGATTTAGGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGA-TTAGGGGTAAAAGATTGGATG
* * *
131150 GTGGCTTCAATCTACCCCTTTGGATTAGGGGTAAATGATTGGA--
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
* * *
131193 -TGACTTCAATCTGCTCCTCTGAATTTAGGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGA-TTAGGGGTAAAAGATTGGATG
* * * *
131238 GTGACTTCAATCTACTCATCTGGATTTAGGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGA-TTAGGGGTAAAAGATTGGATG
*** * *
131284 GTGGCTTCAATCTTTTCCTCTAGATTAGGGGTAAAATATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
* * * * **
131329 ATGACTTCAATCTGCCTCTTTAAATTAGGGGTAAAAGATTGGA--
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
* * * *
131372 -TGGCTTCAATATGCCCCTTTTGATTAGCGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
131416 GTGGC-TCTAATCTGCCCCTCTGGA-T-GGGGTAAAAGATTGGATG
1 GTGGCTTC-AATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
*
131459 GT--CTTCAATCT-TCCCTCTGG-TTA-GGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
* * * *
131499 GTGTCTTCAATCT-ACCCTCT-GTTTA-GGGTAAAAGATTGAATG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
* * *
131541 AT--CTTTAATCTG-CCCTTTGG-TT-GGGGTAAAAGATTGGATG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
131581 GT--CTTCAATCTG-CCCTCTGG-TTA-GGGTAAAAGATTG
1 GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTG
131617 AATAGTCTAA
Statistics
Matches: 444, Mismatches: 50, Indels: 43
0.83 0.09 0.08
Matches are distributed among these distances:
40 91 0.20
41 8 0.02
42 91 0.20
43 37 0.08
44 3 0.01
45 132 0.30
46 82 0.18
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (45 bp):
GTGGCTTCAATCTGCCCCTCTGGATTAGGGGTAAAAGATTGGATG
Found at i:131363 original size:179 final size:170
Alignment explanation
Indices: 131062--131616 Score: 616
Period size: 179 Copynumber: 3.2 Consensus size: 170
131052 TTTGTGTGTG
* * *
131062 GCTTCAATCTGTCCCTCTGGATTTAAGGGTATAAGATTGGAT-GTGGCTTCAATCTGTCCCTCTG
1 GCTTCAATCTG-CCCTCTGGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTTTCCCTCT-
* * *
131126 GATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTACCCCTTTGGATTAGGGGTAAATGATTG
63 GA-TTAGGGGTAAAAGATTGGATGGTGACTTCAATCTACCTCTTT--ATTAGGGGTAAAAGATTG
*
131191 GATGACTTCAATCTGCTCCTCTGAATTTAGGGGTAAAAGATTGGATGGT
125 GATGACTTCAATCTGC-CCTTTG-A-TTAGGGGTAAAAGATTGGATGGT
* * *
131240 GACTTCAATCTACTCATCTGGATTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTTTTCCTCT
1 G-CTTCAATCTGC-CCTCTGGA-TTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTTTCCCTCT
* * *
131305 AGATTAGGGGTAAAATATTGGATGATGACTTCAATCTGCCTCTTTAAATTAGGGGTAAAAGATTG
63 -GATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTACCTCTTT--ATTAGGGGTAAAAGATTG
* * *
131370 GATGGCTTCAATATGCCCCTTTTGATTAGCGGTAAAAGATTGGATGGT
125 GATGACTTCAATCTG-CCC-TTTGATTAGGGGTAAAAGATTGGATGGT
131418 GGC-TCTAATCTGCCCCTCTGGA-T-GGGGTAAAAGATTGGATGGT--CTTCAATC-TTCCCTCT
1 -GCTTC-AATCTG-CCCTCTGGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTTTCCCTCT
* * * *
131477 GGTTA-GGGTAAAAGATTGGATGGTGTCTTCAATCTACCCTCTGT-TTA-GGGTAAAAGATTGAA
63 GATTAGGGGTAAAAGATTGGATGGTGACTTCAATCTA-CCTCTTTATTAGGGGTAAAAGATTGGA
* *
131539 TGATCTTTAATCTGCCCTTTGGTT-GGGGTAAAAGATTGGATGGT
127 TGA-CTTCAATCTGCCCTTTGATTAGGGGTAAAAGATTGGATGGT
131583 -CTTCAATCTGCCCTCTGG-TTA-GGGTAAAAGATTG
1 GCTTCAATCTGCCCTCTGGATTAGGGGTAAAAGATTG
131617 AATAGTCTAA
Statistics
Matches: 330, Mismatches: 34, Indels: 42
0.81 0.08 0.10
Matches are distributed among these distances:
162 22 0.07
163 7 0.02
164 2 0.01
165 19 0.06
166 6 0.02
167 19 0.06
168 11 0.03
170 27 0.08
171 10 0.03
172 7 0.02
173 8 0.02
175 20 0.06
176 1 0.00
177 2 0.01
178 37 0.11
179 107 0.32
180 25 0.08
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (170 bp):
GCTTCAATCTGCCCTCTGGATTAGGGGTAAAAGATTGGATGGTGGCTTCAATCTTTCCCTCTGAT
TAGGGGTAAAAGATTGGATGGTGACTTCAATCTACCTCTTTATTAGGGGTAAAAGATTGGATGAC
TTCAATCTGCCCTTTGATTAGGGGTAAAAGATTGGATGGT
Found at i:132764 original size:21 final size:21
Alignment explanation
Indices: 132740--132787 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
132730 ATGATCAGTT
132740 GAAGGAACATGAAGA-AGAAGA
1 GAAGGAACATG-AGACAGAAGA
* * *
132761 GAAGAAAGATGAGACTGAAGA
1 GAAGGAACATGAGACAGAAGA
132782 GAAGGA
1 GAAGGA
132788 CCTTGCCGAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.54, C:0.04, G:0.35, T:0.06
Consensus pattern (21 bp):
GAAGGAACATGAGACAGAAGA
Found at i:136939 original size:18 final size:18
Alignment explanation
Indices: 136916--136952 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
136906 TCATCTTGAC
136916 TTTTTTTCTATTCTCTTT
1 TTTTTTTCTATTCTCTTT
* *
136934 TTTTTTTCTTTTTTCTTT
1 TTTTTTTCTATTCTCTTT
136952 T
1 T
136953 CTTTCCTTGG
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:0.03, C:0.14, G:0.00, T:0.84
Consensus pattern (18 bp):
TTTTTTTCTATTCTCTTT
Found at i:136945 original size:11 final size:12
Alignment explanation
Indices: 136917--136956 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
136907 CATCTTGACT
136917 TTTTTTCTATTCTC
1 TTTTTTCT-TT-TC
136931 TTTTTT-TTTTC
1 TTTTTTCTTTTC
136942 TTTTTTCTTTTC
1 TTTTTTCTTTTC
136954 TTT
1 TTT
136957 CCTTGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.32
12 10 0.40
13 1 0.04
14 6 0.24
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTCTTTTC
Found at i:137326 original size:14 final size:13
Alignment explanation
Indices: 137303--137332 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
137293 GTCAATGTAA
137303 TCAGAGTTAAATG
1 TCAGAGTTAAATG
137316 TCAGAAGTTAAATG
1 TCAG-AGTTAAATG
137330 TCA
1 TCA
137333 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (13 bp):
TCAGAGTTAAATG
Found at i:137952 original size:11 final size:11
Alignment explanation
Indices: 137936--137962 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
137926 TCGTCAGAAG
137936 TTGCTGCAGTC
1 TTGCTGCAGTC
137947 TTGCTGCAGTC
1 TTGCTGCAGTC
137958 TTGCT
1 TTGCT
137963 TCATTAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.26, G:0.26, T:0.41
Consensus pattern (11 bp):
TTGCTGCAGTC
Found at i:139177 original size:23 final size:23
Alignment explanation
Indices: 139150--139199 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
139140 GGACATCTTT
139150 TTGTTGACGCATTAAAGCACAGA
1 TTGTTGACGCATTAAAGCACAGA
* *
139173 TTGTTGATGCATTAAAGCATAGA
1 TTGTTGACGCATTAAAGCACAGA
139196 TTGT
1 TTGT
139200 CGATACATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.22, T:0.34
Consensus pattern (23 bp):
TTGTTGACGCATTAAAGCACAGA
Found at i:142042 original size:14 final size:14
Alignment explanation
Indices: 142032--142058 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
142022 TGAAAAAGAA
142032 AGAAAAGAAAAAAG
1 AGAAAAGAAAAAAG
142046 AGAAAAGAAAAAA
1 AGAAAAGAAAAAA
142059 AATTTATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAAAAG
Found at i:162761 original size:8 final size:8
Alignment explanation
Indices: 162747--162791 Score: 63
Period size: 8 Copynumber: 5.5 Consensus size: 8
162737 AATTTAAAAT
162747 AAATTAAA
1 AAATTAAA
*
162755 AAGTTAAA
1 AAATTAAA
162763 AAATTAAA
1 AAATTAAA
162771 TAAATTAAA
1 -AAATTAAA
*
162780 AAATTAGA
1 AAATTAAA
162788 AAAT
1 AAAT
162792 AAATTTCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
8 25 0.76
9 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (8 bp):
AAATTAAA
Found at i:162761 original size:26 final size:25
Alignment explanation
Indices: 162743--162795 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
162733 TAACAATTTA
162743 AAATAAATTAAAAAGTTAAAAAATT
1 AAATAAATTAAAAAGTTAAAAAATT
* *
162768 AAATAAATTAAAAAATTAGAAAA-T
1 AAATAAATTAAAAAGTTAAAAAATT
162792 AAAT
1 AAAT
162796 TTCTTACTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (25 bp):
AAATAAATTAAAAAGTTAAAAAATT
Found at i:162780 original size:17 final size:16
Alignment explanation
Indices: 162747--162791 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
162737 AATTTAAAAT
*
162747 AAATTAAAAAGTTAAA
1 AAATTAAAAAATTAAA
162763 AAATTAAATAAATTAAA
1 AAATTAAA-AAATTAAA
*
162780 AAATTAGAAAAT
1 AAATTAAAAAAT
162792 AAATTTCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (16 bp):
AAATTAAAAAATTAAA
Found at i:168454 original size:18 final size:18
Alignment explanation
Indices: 168421--168478 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
168411 GATATTGGGC
168421 ATAATTTTAGTA-AATTTT
1 ATAATTTTA-TATAATTTT
168439 ATAATTTTATATAATTTAGT
1 ATAATTTTATATAATTT--T
* *
168459 ATTATTTTTACATAATTTT
1 A-TAATTTTATATAATTTT
168478 A
1 A
168479 CTATTTTAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 2 0.06
18 14 0.41
19 2 0.06
20 2 0.06
21 14 0.41
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (18 bp):
ATAATTTTATATAATTTT
Found at i:177108 original size:11 final size:12
Alignment explanation
Indices: 177092--177120 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
177082 ATATACACTT
177092 TTTTTTCTTG-A
1 TTTTTTCTTGTA
177103 TTTTTTCTTGTA
1 TTTTTTCTTGTA
177115 TTTTTT
1 TTTTTT
177121 ATTTCCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTCTTGTA
Found at i:193314 original size:22 final size:22
Alignment explanation
Indices: 193286--193330 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
193276 TTTGCCAAAT
*
193286 TTACAACATTGGACTATTGAAG
1 TTACAACATTGAACTATTGAAG
193308 TTACAACATTGAACTATTGAAG
1 TTACAACATTGAACTATTGAAG
193330 T
1 T
193331 CGCGACATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (22 bp):
TTACAACATTGAACTATTGAAG
Found at i:193636 original size:3 final size:3
Alignment explanation
Indices: 193628--193666 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
193618 ATGGGGTGTT
*
193628 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
193667 TTGGTGAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:200882 original size:9 final size:9
Alignment explanation
Indices: 200868--200906 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
200858 AAAAATTAGG
200868 AATAAAAAT
1 AATAAAAAT
200877 AAT-AAAAT
1 AATAAAAAT
*
200885 AATAAAACT
1 AATAAAAAT
*
200894 AATAAATAT
1 AATAAAAAT
200903 AATA
1 AATA
200907 TTGGGCTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
8 8 0.31
9 18 0.69
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAAAAAT
Found at i:200885 original size:8 final size:8
Alignment explanation
Indices: 200872--200906 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
200862 ATTAGGAATA
200872 AAAATAAT
1 AAAATAAT
200880 AAAATAAT
1 AAAATAAT
200888 AAAACTAAT
1 AAAA-TAAT
200897 AAATATAAT
1 AAA-ATAAT
200906 A
1 A
200907 TTGGGCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 12 0.48
9 12 0.48
10 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (8 bp):
AAAATAAT
Found at i:200890 original size:17 final size:18
Alignment explanation
Indices: 200868--200906 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
200858 AAAAATTAGG
200868 AATAAAAATAATAAA-AT
1 AATAAAAATAATAAATAT
*
200885 AATAAAACTAATAAATAT
1 AATAAAAATAATAAATAT
200903 AATA
1 AATA
200907 TTGGGCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AATAAAAATAATAAATAT
Found at i:201533 original size:13 final size:13
Alignment explanation
Indices: 201506--201557 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
201496 TAGTTCTCAA
*
201506 AATAAA-TATTTT
1 AATAAATTAATTT
201518 AATAAATTAATTT
1 AATAAATTAATTT
* *
201531 AATTAATTAAATT
1 AATAAATTAATTT
201544 AACTAAATTAATTT
1 AA-TAAATTAATTT
201558 TTTTAATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
12 6 0.18
13 18 0.55
14 9 0.27
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AATAAATTAATTT
Found at i:201536 original size:9 final size:9
Alignment explanation
Indices: 201516--201556 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
201506 AATAAATATT
201516 TTAA-TAAA
1 TTAATTAAA
*
201524 TTAATTTAA
1 TTAATTAAA
201533 TTAATTAAA
1 TTAATTAAA
*
201542 TTAACTAAA
1 TTAATTAAA
201551 TTAATT
1 TTAATT
201557 TTTTTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
8 4 0.14
9 24 0.86
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAATTAAA
Found at i:217676 original size:24 final size:24
Alignment explanation
Indices: 217638--217708 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 24
217628 ATTCATCGGT
*
217638 TCGAAGCTT-ACTAAAATCACTGGC
1 TCGAAGCTTGA-TAAAATCACCGGC
217662 TCGAAGCTTGATAAATAATCACCGGC
1 TCGAAGCTTGAT-AA-AATCACCGGC
* * *
217688 TCAAACCCTGATAAAATCACC
1 TCGAAGCTTGATAAAATCACC
217709 TTCTAATACC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 17 0.43
25 5 0.12
26 18 0.45
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (24 bp):
TCGAAGCTTGATAAAATCACCGGC
Found at i:220228 original size:19 final size:19
Alignment explanation
Indices: 220201--220244 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
220191 TTCCATTAAT
*
220201 CTTTACTTACCTGTTGAAC
1 CTTTTCTTACCTGTTGAAC
220220 CTTTTCTTACCTGTTGAAC
1 CTTTTCTTACCTGTTGAAC
220239 CTTTTC
1 CTTTTC
220245 AAATAACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48
Consensus pattern (19 bp):
CTTTTCTTACCTGTTGAAC
Found at i:235608 original size:9 final size:9
Alignment explanation
Indices: 235594--235628 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
235584 CAAGATTTGG
235594 TTTCTTGAT
1 TTTCTTGAT
235603 TTTCTTGAT
1 TTTCTTGAT
235612 TTTCTTGAT
1 TTTCTTGAT
*
235621 TGTCTTGA
1 TTTCTTGA
235629 AAACAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.11, C:0.11, G:0.14, T:0.63
Consensus pattern (9 bp):
TTTCTTGAT
Found at i:237588 original size:17 final size:17
Alignment explanation
Indices: 237568--237600 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
237558 TTAAGAAAAT
237568 AAAAATAAATAAAATAC
1 AAAAATAAATAAAATAC
*
237585 AAAATTAAATAAAATA
1 AAAAATAAATAAAATA
237601 GACAAGAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAAATAAAATAC
Found at i:239883 original size:195 final size:195
Alignment explanation
Indices: 239448--239872 Score: 578
Period size: 195 Copynumber: 2.2 Consensus size: 195
239438 GAAACCGATG
* *
239448 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTCAATAGCTCATGTGAGCAGCATCGTGAGTCG
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTTAATAGCTCGTGTGAGCAGCATCGTGAGTCG
**
239513 AAAAATAAAAAATGAATCCTAGAATGGATTACAGACCCTGTGATGGCTGGGATTTATGCATAAGT
66 AAAAATAAAAAATGAATCCTAGAATGGATTACAGACCCTACGATGGCTGGGATTTATGCATAAGT
* * * *
239578 GCATATTCTCGACAGCTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACGCAAATATAGTAT
131 GCATATTCTAGACAACTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACGCAAACATAGTAC
* * * *
239643 CGATGGCTGAGGTATCGTATATATTGCGAGTCCTTAATAGCTCGTGTGAGTAGCATCGTGAGTC-
1 CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTTAATAGCTCGTGTGAGCAGCATCGTGAGTCG
* *
239707 AAAAA-AAGAGATATGAATCCTAGAATGGATTACAGGCCCTACGAT-GCTTGGGATTTATGCATA
66 AAAAATAA-A-AAATGAATCCTAGAATGGATTACAGACCCTACGATGGC-TGGGATTTATGCATA
*
239770 AGTGCATATTCTAGACAACTCGTGTGAGTAGCATCATTA-GGAGACAGTTATATA-G-ATAGACA
128 AGTGCATATTCTAGACAACTCGTGTGAGCAGCATCATTAGGGA-ACAGTTATATACGCA-A-ACA
239832 CT-GTAC
190 -TAGTAC
*
239838 CGATGGCT-AGGGTACCACATATGTTGCGAGTCCTT
1 CGATGGCTGA-GGTACCGCATATGTTGCGAGTCCTT
239873 GACGGCTCGT
Statistics
Matches: 203, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
193 3 0.01
194 14 0.07
195 185 0.91
196 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (195 bp):
CGATGGCTGAGGTACCGCATATGTTGCGAGTCCTTAATAGCTCGTGTGAGCAGCATCGTGAGTCG
AAAAATAAAAAATGAATCCTAGAATGGATTACAGACCCTACGATGGCTGGGATTTATGCATAAGT
GCATATTCTAGACAACTCGTGTGAGCAGCATCATTAGGGAACAGTTATATACGCAAACATAGTAC
Found at i:244717 original size:192 final size:192
Alignment explanation
Indices: 244390--244764 Score: 714
Period size: 192 Copynumber: 2.0 Consensus size: 192
244380 ATCCTCTTAA
*
244390 TTATCAATATGGTTGGGACCTACATTTAGGTTTGTCATATTGCTGTGAGAAACTTTTAGATAGTA
1 TTATCAATATGGTTGGGACCTACATTTAGGTTTGTCATATTGCGGTGAGAAACTTTTAGATAGTA
244455 GTGTGATATATTTTTTCTAGGTGAAATTTCTTTTATTTCTTAAGATGTTTTCTCCAATACTTGGC
66 GTGTGATATATTTTTTCTAGGTGAAATTTCTTTTATTTCTTAAGATGTTTTCTCCAATACTTGGC
*
244520 AATTTTCATTGTTCTCAGTTTTCTTTAAGTAACAAGGAGAAATTTACTGTCTTATGGGTATG
131 AATTTTCATTGTTCTCAATTTTCTTTAAGTAACAAGGAGAAATTTACTGTCTTATGGGTATG
*
244582 TTATCAATATGGTTGGGACCTACATTTGGGTTTGTCATATTGCGGTGAGAAACTTTTAGATAGTA
1 TTATCAATATGGTTGGGACCTACATTTAGGTTTGTCATATTGCGGTGAGAAACTTTTAGATAGTA
*
244647 GTGTGATATATTTTTTCTAGGTGAAATTTCTTTTATTTCTTAAGATGTTTTCTCCAATATTTGGC
66 GTGTGATATATTTTTTCTAGGTGAAATTTCTTTTATTTCTTAAGATGTTTTCTCCAATACTTGGC
244712 AATTTTCATTGTTCTCAATTTTCTTTAAGTAACAAGGAGAAATTTACTGTCTT
131 AATTTTCATTGTTCTCAATTTTCTTTAAGTAACAAGGAGAAATTTACTGTCTT
244765 TGTCTTCAAT
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
192 179 1.00
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (192 bp):
TTATCAATATGGTTGGGACCTACATTTAGGTTTGTCATATTGCGGTGAGAAACTTTTAGATAGTA
GTGTGATATATTTTTTCTAGGTGAAATTTCTTTTATTTCTTAAGATGTTTTCTCCAATACTTGGC
AATTTTCATTGTTCTCAATTTTCTTTAAGTAACAAGGAGAAATTTACTGTCTTATGGGTATG
Done.