Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007475.1 Kokia drynarioides strain JFW-HI SEQ_122097, 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: 120306
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:4059 original size:50 final size:49
Alignment explanation
Indices: 3972--4341 Score: 296
Period size: 50 Copynumber: 7.5 Consensus size: 49
3962 GAAACATGAT
* * *
3972 GGGAAAGATCTAAGACCACAATGACGGATCCAGTACCGCAAAGACATAAAA
1 GGGAAAGATCTAAG-CCGCAATGGCGGATCCAGTACCACAAAGACAT-AAA
* * * * *
4023 GGGAAAGATCTAAGCTGCAACGGCGGATCCAGTACCGCAAAGATACAAGA
1 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACAAAGACATAA-A
* * * * * *
4073 GGGAAAGATTTAAGCCGCAATGGAGAATCTAGTACCACAACGAAATAAA
1 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACAAAGACATAAA
* * * * * * *
4122 GGGAAAAATTTAAGTCGCAATGGC-GAACTCAGTACCTCAGAGACATGAA
1 GGGAAAGATCTAAGCCGCAATGGCGGATC-CAGTACCACAAAGACATAAA
* * * *
4171 GGGAAAGATCTAAGCCGTAACGGCGGATCCAGTACCACGAAGACA-CAA
1 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACAAAGACATAAA
* * * * * * *
4219 GGGAAAGATTTAAGTCGTAATGGCGAACCCAGTACCTCAGAAGACATGAA
1 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACA-AAGACATAAA
* * * * * *
4269 GGGAAAGATCTAAGCCGCAACGGCAGATCCAATAACACGAAGAC-GAAA
1 GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACAAAGACATAAA
* * * *
4317 GAGAAAGGTTTAAGTCGCAATGGCG
1 GGGAAAGATCTAAGCCGCAATGGCG
4342 AACCTTATAC
Statistics
Matches: 250, Mismatches: 64, Indels: 13
0.76 0.20 0.04
Matches are distributed among these distances:
48 57 0.23
49 81 0.32
50 98 0.39
51 14 0.06
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (49 bp):
GGGAAAGATCTAAGCCGCAATGGCGGATCCAGTACCACAAAGACATAAA
Found at i:4186 original size:98 final size:98
Alignment explanation
Indices: 3965--4358 Score: 345
Period size: 98 Copynumber: 4.0 Consensus size: 98
3955 GCACCATGAA
* * * * * *
3965 ACATGATGGGAAAGATCTAAGACCACAA-TGACGGATCCAGTACCGCAAAGACATAAAAGGGAAA
1 ACATGAAGGGAAAGATCTAAG-CCGCAACGGA-GAATCCAGTACCACGAAGA-A-AAAAGGGAAA
* * * * * *
4029 GATCTAAG-CTGCAACGGCGGATCCAGTACCGCA-AAG
62 AATTTAAGTC-GCAATGGCGAACCCAGTACCTCAGAAG
* * * *
4065 ATACAAG-AGGGAAAGATTTAAGCCGCAATGGAGAATCTAGTACCAC-AACGAAATAAAGGGAAA
1 --ACATGAAGGGAAAGATCTAAGCCGCAACGGAGAATCCAGTACCACGAA-GAAA-AAAGGGAAA
*
4128 AATTTAAGTCGCAATGGCGAACTCAGTACCTCAG-AG
62 AATTTAAGTCGCAATGGCGAACCCAGTACCTCAGAAG
* * * * * *
4164 ACATGAAGGGAAAGATCTAAGCCGTAACGGCGGATCCAGTACCACGAAGACACAAGGGAAAGATT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGGAGAATCCAGTACCACGAAGAAAAAAGGGAAAAATT
*
4229 TAAGTCGTAATGGCGAACCCAGTACCTCAGAAG
66 TAAGTCGCAATGGCGAACCCAGTACCTCAGAAG
* * ** * **
4262 ACATGAAGGGAAAGATCTAAGCCGCAACGGCAG-ATCCAATAACACGAAGACGAAAGAGAAAGGT
1 ACATGAAGGGAAAGATCTAAGCCGCAACGG-AGAATCCAGTACCACGAAGAAAAAAGGGAAAAAT
*
4326 TTAAGTCGCAATGGCGAACCTTA-TACCTCAGAA
65 TTAAGTCGCAATGGCGAACC-CAGTACCTCAGAA
4359 TCAGAAAAGG
Statistics
Matches: 245, Mismatches: 37, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
97 43 0.18
98 122 0.50
99 42 0.17
100 19 0.08
101 15 0.06
102 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (98 bp):
ACATGAAGGGAAAGATCTAAGCCGCAACGGAGAATCCAGTACCACGAAGAAAAAAGGGAAAAATT
TAAGTCGCAATGGCGAACCCAGTACCTCAGAAG
Found at i:4243 original size:97 final size:97
Alignment explanation
Indices: 4119--4357 Score: 347
Period size: 98 Copynumber: 2.5 Consensus size: 97
4109 ACAACGAAAT
*
4119 AAAGGGAAAAATTTAAGTCGCAATGGCGAACTCAGTACCTCAGAGACATGAAGGGAAAGATCTAA
1 AAAGGGAAAGATTTAAGTCGCAATGGCGAACTCAGTACCTCAGAGACATGAAGGGAAAGATCTAA
* * * *
4184 GCCGTAACGGCGGATCCAGTACCACGAAGAC-
66 GCCGCAACGGCAGATCCAATAACACGAAGACG
* *
4215 ACAAGGGAAAGATTTAAGTCGTAATGGCGAACCCAGTACCTCAGAAGACATGAAGGGAAAGATCT
1 A-AAGGGAAAGATTTAAGTCGCAATGGCGAACTCAGTACCTCAG-AGACATGAAGGGAAAGATCT
4280 AAGCCGCAACGGCAGATCCAATAACACGAAGACG
64 AAGCCGCAACGGCAGATCCAATAACACGAAGACG
* * *
4314 AAAGAGAAAGGTTTAAGTCGCAATGGCGAACCTTA-TACCTCAGA
1 AAAGGGAAAGATTTAAGTCGCAATGGCGAA-CTCAGTACCTCAGA
4358 ATCAGAAAAG
Statistics
Matches: 127, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
96 1 0.01
97 40 0.31
98 83 0.65
99 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (97 bp):
AAAGGGAAAGATTTAAGTCGCAATGGCGAACTCAGTACCTCAGAGACATGAAGGGAAAGATCTAA
GCCGCAACGGCAGATCCAATAACACGAAGACG
Found at i:4819 original size:17 final size:17
Alignment explanation
Indices: 4791--4894 Score: 113
Period size: 17 Copynumber: 6.1 Consensus size: 17
4781 CTCAACTCAT
4791 TTTAAA-TTATTTTAAGA
1 TTTAAATTTATTTTAA-A
4808 -TTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4824 TTTAAATTTAGTCTAAA
1 TTTAAATTTATTTTAAA
* *
4841 TTTTAAATTTAATTTAAG
1 -TTTAAATTTATTTTAAA
4859 TTTAAATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
* *
4877 TTTAAAATTATTGTAAA
1 TTTAAATTTATTTTAAA
4894 T
1 T
4895 AATAAAATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
16 6 0.08
17 39 0.53
18 29 0.39
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4827 original size:6 final size:6
Alignment explanation
Indices: 4808--4882 Score: 75
Period size: 6 Copynumber: 12.8 Consensus size: 6
4798 TATTTTAAGA
* * *
4808 TTAAAT TT-ATT TTAAAT TTAAAT TT-AGT CTAAATT TTAAAT TT-AAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT
* *
4854 TTAAGT TTAAAT TTATAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
4883 ATTATTGTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
5 12 0.22
6 38 0.69
7 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:4850 original size:35 final size:35
Alignment explanation
Indices: 4808--4894 Score: 104
Period size: 35 Copynumber: 2.5 Consensus size: 35
4798 TATTTTAAGA
*
4808 TTAAATTTATTTTAAATTTAAATTTA-GTCTAAATT
1 TTAAATTTATTTTAAATTTAAATTTATATCTAAA-T
* * *
4843 TTAAATTTAATTTAAGTTTAAATTTATATTTAAAT
1 TTAAATTTATTTTAAATTTAAATTTATATCTAAAT
* *
4878 TTAAAATTATTGTAAAT
1 TTAAATTTATTTTAAAT
4895 AATAAAATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 38 0.88
36 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTAAATTTATTTTAAATTTAAATTTATATCTAAAT
Found at i:4881 original size:24 final size:25
Alignment explanation
Indices: 4816--4881 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 25
4806 GATTAAATTT
4816 ATTTTAAATTTAAATTT-AGTCTAA
1 ATTTTAAATTTAAATTTAAGTCTAA
*
4840 ATTTTAAATTT-AATTTAAGTTTAA
1 ATTTTAAATTTAAATTTAAGTCTAA
*
4864 A-TTTATATTTAAATTTAA
1 ATTTTAAATTTAAATTTAA
4882 AATTATTGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 13 0.34
24 25 0.66
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
ATTTTAAATTTAAATTTAAGTCTAA
Found at i:5623 original size:12 final size:12
Alignment explanation
Indices: 5542--5646 Score: 63
Period size: 12 Copynumber: 8.5 Consensus size: 12
5532 CTGATAATAA
5542 TAATAATATTAT
1 TAATAATATTAT
* ** *
5554 TACTAATAACAC
1 TAATAATATTAT
*
5566 TAATAATAAATAT
1 TAATAAT-ATTAT
5579 TAATAATAATTAGCAT
1 TAATAAT-ATT---AT
* *
5595 TAATGAATATCAA
1 TAAT-AATATTAT
5608 TAATAATATTAT
1 TAATAATATTAT
5620 TAATAATATTA-
1 TAATAATATTAT
*
5631 -AATAATACT-T
1 TAATAATATTAT
5641 TAATAA
1 TAATAA
5647 AAAAGGAAAC
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
10 8 0.11
11 5 0.07
12 31 0.42
13 18 0.25
16 8 0.11
17 3 0.04
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (12 bp):
TAATAATATTAT
Found at i:8171 original size:18 final size:18
Alignment explanation
Indices: 8144--8186 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
8134 CAGATGTGAA
8144 GGAAAAGAAGAAAGAGAT
1 GGAAAAGAAGAAAGAGAT
* **
8162 GGAAAGGAAGCGAGAGAT
1 GGAAAAGAAGAAAGAGAT
8180 GAGAAAA
1 G-GAAAA
8187 TCACGATTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.37, T:0.05
Consensus pattern (18 bp):
GGAAAAGAAGAAAGAGAT
Found at i:10699 original size:30 final size:28
Alignment explanation
Indices: 10665--10829 Score: 118
Period size: 30 Copynumber: 5.6 Consensus size: 28
10655 AAACTTTTCC
*
10665 AAAATTTCATTTTTAGCCTCGAATTTTTTG
1 AAAATTACATTTTTA-CCTCGAA-TTTTTG
*
10695 AAAATTACATTTTTACCCTCGAACTTTCT-
1 AAAATTACATTTTTA-CCTCGAA-TTTTTG
10724 AAAATT-CAATTTTTTTACCTCGAATTTTTG
1 AAAATTAC-A--TTTTTACCTCGAATTTTTG
* * * **
10754 AAAATTACATTTTTTACCCCAAACTTTCC
1 AAAATTACA-TTTTTACCTCGAATTTTTG
* ** * *
10783 AAAATTCCATTTTTAACCTTAAACTTTCTA
1 AAAATTACATTTTT-ACCTCGAA-TTTTTG
10813 AAAATTACATTTTTACC
1 AAAATTACATTTTTACC
10830 CTTAAAGTTT
Statistics
Matches: 110, Mismatches: 18, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
28 6 0.05
29 43 0.39
30 54 0.49
31 7 0.06
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (28 bp):
AAAATTACATTTTTACCTCGAATTTTTG
Found at i:10728 original size:29 final size:29
Alignment explanation
Indices: 10651--10913 Score: 182
Period size: 29 Copynumber: 9.0 Consensus size: 29
10641 ATATTTTGAC
* *
10651 CCCT-AAACTTTTCCAAAATTTCATTTTTA
1 CCCTCAAAC-TTTCTAAAATTACATTTTTA
* * * *
10680 GCCTCGAATTTTTTGAAAATTACATTTTTA
1 CCCTCAAACTTTCT-AAAATTACATTTTTA
*
10710 CCCTCGAACTTTCTAAAATT-CAATTTTTTTA
1 CCCTCAAACTTTCTAAAATTAC-A--TTTTTA
* *
10741 -CCTCGAA-TTTTTGAAAATTACATTTTTTA
1 CCCTCAAACTTTCT-AAAATTACA-TTTTTA
* *
10770 CCC-CAAACTTTCCAAAATTCCATTTTTA
1 CCCTCAAACTTTCTAAAATTACATTTTTA
* *
10798 ACCTTAAACTTTCTAAAAATTACATTTTTA
1 CCCTCAAACTTTCT-AAAATTACATTTTTA
* * *
10828 CCCTTAAAGTTTCTAAAATTCCATTTTTGA
1 CCCTCAAACTTTCTAAAATTACATTTTT-A
** *
10858 CCCT-AATTTTTCCAAAATTACCA-TTTTA
1 CCCTCAAACTTTCTAAAATTA-CATTTTTA
* *
10886 CCC-CTAAACTTTCCAAAATTTCATTTTT
1 CCCTC-AAACTTTCTAAAATTACATTTTT
10914 TTAACCCCGA
Statistics
Matches: 190, Mismatches: 28, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
28 15 0.08
29 89 0.47
30 79 0.42
31 7 0.04
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (29 bp):
CCCTCAAACTTTCTAAAATTACATTTTTA
Found at i:10947 original size:31 final size:30
Alignment explanation
Indices: 10842--11011 Score: 87
Period size: 31 Copynumber: 5.6 Consensus size: 30
10832 TAAAGTTTCT
* * *
10842 AAAATTCCATTTTTGACCCTAATTTTTCC-A
1 AAAATACCA-TTTTAACCCCAATTTTTCCAA
* **
10872 AAATTACCATTTT-ACCCCTAAACTTTCCAA
1 AAAATACCATTTTAACCCC-AATTTTTCCAA
** *** *
10902 AATTTCATTTTTTTAACCCCGATTTTTCCAA
1 AAAAT-ACCATTTTAACCCCAATTTTTCCAA
* **
10933 AAAATGACCATTTTACCCCCAAACTTT-C-A
1 AAAAT-ACCATTTTAACCCCAATTTTTCCAA
* * *
10962 AAAATTCCATTTTTGACCCCAATTCTTCCAA
1 AAAATACCA-TTTTAACCCCAATTTTTCCAA
* *
10993 AAAGTACCATTTTACCCCC
1 AAAATACCATTTTAACCCC
11012 CGAATGTCTA
Statistics
Matches: 101, Mismatches: 32, Indels: 14
0.69 0.22 0.10
Matches are distributed among these distances:
28 7 0.07
29 29 0.29
30 22 0.22
31 38 0.38
32 5 0.05
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATACCATTTTAACCCCAATTTTTCCAA
Found at i:11025 original size:59 final size:59
Alignment explanation
Indices: 10643--11064 Score: 317
Period size: 59 Copynumber: 7.1 Consensus size: 59
10633 CAGAAATCAT
* * * * **
10643 ATTTTGACCCCTAAACTTTTCCAAAATTTCATTTTT-AGCCTCGAATTTTT-TGAAAATTA-C
1 ATTTT-ACCCCCAAAC-TTTCTAAAATTCCATTTTTGA-CC-CCAATTTTTCCAAAAATTACC
* * * * * *
10703 ATTTTTACCCTCGAACTTTCTAAAATTCAATTTTTTTACCTCGAATTTTT--GAAAATTA-C
1 A-TTTTACCCCCAAACTTTCTAAAATTCCA-TTTTTGACC-CCAATTTTTCCAAAAATTACC
* * ** ** *
10762 ATTTTTTA-CCCCAAACTTTCCAAAATTCCATTTTTAACCTTAAACTTTCTAAAAATTA-C
1 A--TTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACC
** * *
10821 ATTTTTACCCTTAAAGTTTCTAAAATTCCATTTTTGACCCTAATTTTTCC-AAAATTACC
1 A-TTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACC
* * * * * *
10880 ATTTTACCCCTAAACTTTCCAAAATTTCATTTTTTTAACCCCGATTTTTCCAAAAAATGACC
1 ATTTTACCCCCAAACTTTCTAAAATTCCA--TTTTTGACCCCAATTTTTCC-AAAAATTACC
* * *
10942 ATTTTACCCCCAAACTTTCAAAAATTCCATTTTTGACCCCAATTCTTCCAAAAAGTACC
1 ATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACC
* * *
11001 ATTTTACCCCCCGAA-TGTCTAAAATTCCATTTTTGACCCCCAA-TTTTCCTAAAATTACC
1 ATTTTA-CCCCCAAACTTTCTAAAATTCCATTTTTGA-CCCCAATTTTTCCAAAAATTACC
11060 ATTTT
1 ATTTT
11065 GCCCTCGGAT
Statistics
Matches: 301, Mismatches: 47, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
57 5 0.02
58 45 0.15
59 134 0.45
60 78 0.26
61 5 0.02
62 34 0.11
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.41
Consensus pattern (59 bp):
ATTTTACCCCCAAACTTTCTAAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACC
Found at i:11053 original size:30 final size:28
Alignment explanation
Indices: 10643--11064 Score: 181
Period size: 29 Copynumber: 14.2 Consensus size: 28
10633 CAGAAATCAT
* * *
10643 ATTTTGACCCCTAAACTTTTCCAAAATTTC
1 ATTTTTACCCC-AAA-TTTTCTAAAATTCC
* * * *
10673 ATTTTTAGCCTCGAATTTTTTGAAAATTAC
1 ATTTTTA-CCCCAAATTTTCT-AAAATTCC
* * *
10703 ATTTTTACCCTCGAACTTTCTAAAATTCA
1 ATTTTTACCC-CAAATTTTCTAAAATTCC
* * *
10732 ATTTTTTTACCTCGAATTTT-TGAAAATTAC
1 A--TTTTTACCCCAAATTTTCT-AAAATTCC
* *
10762 ATTTTTTACCCCAAACTTTCCAAAATTCC
1 A-TTTTTACCCCAAATTTTCTAAAATTCC
** * *
10791 ATTTTTAACCTTAAACTTTCTAAAAATTAC
1 ATTTTT-ACCCCAAATTTTCT-AAAATTCC
* *
10821 ATTTTTACCCTTAAAGTTTCTAAAATTCC
1 ATTTTTACCC-CAAATTTTCTAAAATTCC
* * *
10850 ATTTTTGACCCTAATTTTTCCAAAATTACC
1 ATTTTT-ACCCCAAATTTTCTAAAATT-CC
* * *
10880 A-TTTTACCCCTAAACTTTCCAAAATTTC
1 ATTTTTACCCC-AAATTTTCTAAAATTCC
* * * *
10908 ATTTTTTTAACCCCGATTTTTCCAAAAAATGACC
1 A--TTTTT-ACCCCAAATTTT-C-TAAAAT-TCC
* *
10942 A-TTTTACCCCCAAACTTTCAAAAATTCC
1 ATTTTTA-CCCCAAATTTTCTAAAATTCC
* *
10970 ATTTTTGACCCC-AATTCTTCCAAAAAGTACC
1 ATTTTT-ACCCCAAATT-TT-CTAAAA-TTCC
* *
11001 A-TTTTACCCCCCGAA-TGTCTAAAATTCC
1 ATTTTTA--CCCCAAATTTTCTAAAATTCC
*
11029 ATTTTTGACCCCCAATTTTCCTAAAATTACC
1 ATTTTT-ACCCCAAATTTT-CTAAAATT-CC
11060 ATTTT
1 ATTTT
11065 GCCCTCGGAT
Statistics
Matches: 307, Mismatches: 51, Indels: 67
0.72 0.12 0.16
Matches are distributed among these distances:
28 27 0.09
29 122 0.40
30 96 0.31
31 47 0.15
32 8 0.03
33 5 0.02
34 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.04, T:0.41
Consensus pattern (28 bp):
ATTTTTACCCCAAATTTTCTAAAATTCC
Found at i:11091 original size:59 final size:59
Alignment explanation
Indices: 10842--11092 Score: 188
Period size: 60 Copynumber: 4.2 Consensus size: 59
10832 TAAAGTTTCT
* * * ** **
10842 AAAATTCCATTTTTGACCCTAATTTTTCC-AAAATTACCATTTTA-CCCCTAAACTTTCC
1 AAAATTCCATTTTTGACCCCAATTCTTCCAAAAAGTACCATTTTACCCCCCGAA-TACCC
* * * * * * ** *
10900 AAAATTTCATTTTTTTAACCCCGATTTTTCCAAAAAATGACCATTTTA-CCCCCAAACTTTCA
1 AAAATTCCA--TTTTTGACCCCAATTCTTCCAAAAAGT-ACCATTTTACCCCCCGAA-TACCC
** *
10962 AAAATTCCATTTTTGACCCCAATTCTTCCAAAAAGTACCATTTTACCCCCCGAATGTCT
1 AAAATTCCATTTTTGACCCCAATTCTTCCAAAAAGTACCATTTTACCCCCCGAATACCC
* * * * *
11021 AAAATTCCATTTTTGACCCCCAATT-TTCCTAAAATTACCATTTT-GCCCTCGGATACCC
1 AAAATTCCATTTTTGA-CCCCAATTCTTCCAAAAAGTACCATTTTACCCCCCGAATACCC
11079 AAAATTCTCATTTT
1 AAAATTC-CATTTT
11093 CAACTCTGAT
Statistics
Matches: 163, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
58 23 0.14
59 51 0.31
60 55 0.34
61 5 0.03
62 29 0.18
ACGTcount: A:0.31, C:0.28, G:0.04, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCCCAATTCTTCCAAAAAGTACCATTTTACCCCCCGAATACCC
Found at i:11470 original size:97 final size:97
Alignment explanation
Indices: 11299--11482 Score: 221
Period size: 97 Copynumber: 1.9 Consensus size: 97
11289 AAAAACTTTA
* * * * * *
11299 AAATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCATGAT
1 AAATCGAGGCAATATTCTTTTATCTCGAGTTCTAAAAATTTGTACCTAAACTTACTAGGCACGAT
*
11364 TTTTCTTCAAATCGAAATAATCAAATATGCTT
66 TTTTCTTCAAAACGAAATAATCAAATATGCTT
* **
11396 AAATCGAGGCAATGTTTCTTTATATCT-GA-TTCTAAAAATTTGTACCTAAACTTACTAGGTGCG
1 AAATCGAGGCAAT-ATTCTTT-TATCTCGAGTTCTAAAAATTTGTACCTAAACTTACTAGGCACG
*
11459 ACTTTTT-TTCAAAACGAGATAATC
64 A-TTTTTCTTCAAAACGAAATAATC
11483 GAACATCCTT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
97 56 0.77
98 13 0.18
99 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.39
Consensus pattern (97 bp):
AAATCGAGGCAATATTCTTTTATCTCGAGTTCTAAAAATTTGTACCTAAACTTACTAGGCACGAT
TTTTCTTCAAAACGAAATAATCAAATATGCTT
Found at i:12316 original size:17 final size:17
Alignment explanation
Indices: 12294--12327 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
12284 ATTAAATTGG
12294 GTTCATAATATGGGTGA
1 GTTCATAATATGGGTGA
12311 GTTCATAATATGGGTGA
1 GTTCATAATATGGGTGA
12328 AAACCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (17 bp):
GTTCATAATATGGGTGA
Found at i:17436 original size:18 final size:18
Alignment explanation
Indices: 17397--17452 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 18
17387 ATCATCATCT
*
17397 ATATTTTTGTAAA-ATTAT
1 ATATTTTT-TAAATATTAA
*
17415 ATATTTTTTAAATTTTAA
1 ATATTTTTTAAATATTAA
*
17433 ATATAATTTTAAATAATTAA
1 ATAT-TTTTTAAAT-ATTAA
17453 GTGATGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.13
18 15 0.48
19 8 0.26
20 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATATTTTTTAAATATTAA
Found at i:32906 original size:14 final size:15
Alignment explanation
Indices: 32877--32909 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
32867 ATTTTTTTTA
*
32877 TTTATATTTGTATTT
1 TTTATATTTATATTT
32892 TTTAT-TTTATATTT
1 TTTATATTTATATTT
32906 TTTA
1 TTTA
32910 AGTTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATATTTATATTT
Found at i:38204 original size:27 final size:28
Alignment explanation
Indices: 38173--38227 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
38163 CAACAAATAG
38173 TTGGAAGAAGTTTGAATATT-AAATCAT
1 TTGGAAGAAGTTTGAATATTGAAATCAT
* *
38200 TTGGATGAAGTTTGAATCTTGAAATCAT
1 TTGGAAGAAGTTTGAATATTGAAATCAT
38228 AATTGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (28 bp):
TTGGAAGAAGTTTGAATATTGAAATCAT
Found at i:39232 original size:8 final size:8
Alignment explanation
Indices: 39196--39232 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
39186 TTGGATGTAA
*
39196 TAATATAT
1 TAATATTT
39204 TAATA--T
1 TAATATTT
39210 TAATATTT
1 TAATATTT
39218 TAATATTT
1 TAATATTT
39226 TAATATT
1 TAATATT
39233 AACATCTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
8 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TAATATTT
Found at i:46468 original size:6 final size:6
Alignment explanation
Indices: 46450--46487 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
46440 TGCAAATGAA
46450 TCATTT CTCATTT TCATTT TCATTT TCATTT TCATTT T
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT T
46488 GAGAAAACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (6 bp):
TCATTT
Found at i:48313 original size:15 final size:16
Alignment explanation
Indices: 48286--48315 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48276 AATATGTTAT
48286 TTAAAAAATATAATAA
1 TTAAAAAATATAATAA
48302 TTAAAAAA-ATAATA
1 TTAAAAAATATAATA
48316 TCATAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAAATATAATAA
Found at i:55247 original size:43 final size:43
Alignment explanation
Indices: 55168--55250 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
55158 GTTTTTTATA
* *
55168 ATTTAATATTATATATATCGACTTAATAAATCAATCTTATACG
1 ATTTAATACTATATATATCGACTTAACAAATCAATCTTATACG
* * * *
55211 ATTTAATACTATATTTATTGATTTAACAAATTAATCTTAT
1 ATTTAATACTATATATATCGACTTAACAAATCAATCTTAT
55251 TTAATGCAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.46
Consensus pattern (43 bp):
ATTTAATACTATATATATCGACTTAACAAATCAATCTTATACG
Found at i:60041 original size:283 final size:282
Alignment explanation
Indices: 59535--60099 Score: 1085
Period size: 283 Copynumber: 2.0 Consensus size: 282
59525 AGTTATATTA
59535 AACTCTACTCGAAATTCGATTCGGAAATTTTTTTTATACACATTTCTAACTGAAGACCTTCTTAA
1 AACTCTACTCGAAATTCGATTCGGAAATTTTTTTTATACACATTTCTAACTGAAGACCTTCTTAA
* *
59600 GGGGTCTGTTGAGGAAACGATCTTGATTTTTATTTTTCTTTCTTTTTGATAGGATTTTCTTCTTC
66 GGGGTCTGTTGAGGAAACGATCTTGATTTTTATTTTTCTTTCTTTTTGAGAGGATTTTCTTCCTC
59665 TCTAATCTAACCATCTATGTTAGAAAAGAAGATGAATCGATTAACGCGACGACCAACTAAATCTT
131 TCTAATCTAACCATCTATGTTAGAAAAGAAGATGAATCGATTAACGCGACGACCAACTAAATCTT
59730 GTATCAACAATAAATATGTTTTGTTCTCCAATCCAAATCCATTTGTTATCTATATTAAATTTGAT
196 GTATCAACAATAAATATGTTTTGTTCTCCAATCCAAATCCATTTGTTATCTATATTAAATTTGAT
59795 CACACTATTTGAATGAATTAAT
261 CACACTATTTGAATGAATTAAT
59817 AACTCTACTCGAAATTCGATTCGGAAATTTTTTTTTATACACATTTCTAACTGAAGACCTTCTTA
1 AACTCTACTCGAAATTCGATTCGGAAA-TTTTTTTTATACACATTTCTAACTGAAGACCTTCTTA
59882 AGGGGTCTGTTGAGGAAACGATCTTGATTTTTATTTTTCTTTCTTTTTGAGAGGATTTTCTTCCT
65 AGGGGTCTGTTGAGGAAACGATCTTGATTTTTATTTTTCTTTCTTTTTGAGAGGATTTTCTTCCT
*
59947 CTCTAATCTAACCATCTATGTTAGAAAAGAAGATGAATCGATTAACGCGGCGACCAACTAAATCT
130 CTCTAATCTAACCATCTATGTTAGAAAAGAAGATGAATCGATTAACGCGACGACCAACTAAATCT
*
60012 TGTATCAACAATAAATATGTTTTGTTCTCCAATCTAAATCCATTTGTTATCTATATTAAATTTGA
195 TGTATCAACAATAAATATGTTTTGTTCTCCAATCCAAATCCATTTGTTATCTATATTAAATTTGA
60077 TCACACTATTTGAATGAATTAAT
260 TCACACTATTTGAATGAATTAAT
60100 GAATTTATTT
Statistics
Matches: 278, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
282 27 0.10
283 251 0.90
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.40
Consensus pattern (282 bp):
AACTCTACTCGAAATTCGATTCGGAAATTTTTTTTATACACATTTCTAACTGAAGACCTTCTTAA
GGGGTCTGTTGAGGAAACGATCTTGATTTTTATTTTTCTTTCTTTTTGAGAGGATTTTCTTCCTC
TCTAATCTAACCATCTATGTTAGAAAAGAAGATGAATCGATTAACGCGACGACCAACTAAATCTT
GTATCAACAATAAATATGTTTTGTTCTCCAATCCAAATCCATTTGTTATCTATATTAAATTTGAT
CACACTATTTGAATGAATTAAT
Found at i:64741 original size:25 final size:25
Alignment explanation
Indices: 64712--64761 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
64702 TTTATTTTTA
*
64712 AAAAAT-AAAAATCTAAAAAATATAT
1 AAAAATGAAAAAT-TAAAAAAAATAT
*
64737 AAAAATGATAAATTAAAAAAAATAT
1 AAAAATGAAAAATTAAAAAAAATAT
64762 TTCTTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAATGAAAAATTAAAAAAAATAT
Found at i:66046 original size:20 final size:21
Alignment explanation
Indices: 66010--66060 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
66000 CCAAATTGAT
* *
66010 AAAA-AAAATTTAGATAT-AC
1 AAAAGAAATTTTAAATATAAC
*
66029 AAAAGAAATTTTAAATATCAAT
1 AAAAGAAATTTTAAATAT-AAC
66051 AAAAGAAATT
1 AAAAGAAATT
66061 GACAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 11 0.42
22 11 0.42
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (21 bp):
AAAAGAAATTTTAAATATAAC
Found at i:68349 original size:191 final size:191
Alignment explanation
Indices: 68019--68399 Score: 663
Period size: 191 Copynumber: 2.0 Consensus size: 191
68009 ACCACATTTC
* * *
68019 GAAGCTTTCAATGTCTCAAAGTAAATAGTTCGCGAGCTGTCTATGATGCTTGTGTCTGGCAACAT
1 GAAGCCTTCAATGTCTCAAAGTAAATAGTTCGCGAGCTGTCCATAATGCTTGTGTCTGGCAACAT
* *
68084 TCTCTCAAATGGTATCAATATCATATCCCATCAATCACAATAGTTACCCAAACATGCTATCATTG
66 TCTCTCAAATGGTATCAATATCATACCCCATCAATCACAATAATTACCCAAACATGCTATCATTG
* *
68149 TATAATTACAAGTAATAACACTCAAATCCAGTTACTAGTTGACTTTCCAAATATTATCTTT
131 TATAATTACAAGTAATAACACTCAAATCCAATTACTAGGTGACTTTCCAAATATTATCTTT
*
68210 GAAGCCTTCAATGTCTCAAAGTAAATAGTTCGCGAGCTGTCCATAATGCTTGTGTTTGGCAACAT
1 GAAGCCTTCAATGTCTCAAAGTAAATAGTTCGCGAGCTGTCCATAATGCTTGTGTCTGGCAACAT
68275 TCTCTCAAATGGTATCAATATCATACCCCATCAATCACAATAATTACCCAAACATGCTATCATTG
66 TCTCTCAAATGGTATCAATATCATACCCCATCAATCACAATAATTACCCAAACATGCTATCATTG
* * *
68340 TGTAATTACATGTAATTACACTCAAATCCAATTACTAGGTGACTTTCCAAATATTATCTT
131 TATAATTACAAGTAATAACACTCAAATCCAATTACTAGGTGACTTTCCAAATATTATCTT
68400 AGTGTTTTTG
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
191 179 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (191 bp):
GAAGCCTTCAATGTCTCAAAGTAAATAGTTCGCGAGCTGTCCATAATGCTTGTGTCTGGCAACAT
TCTCTCAAATGGTATCAATATCATACCCCATCAATCACAATAATTACCCAAACATGCTATCATTG
TATAATTACAAGTAATAACACTCAAATCCAATTACTAGGTGACTTTCCAAATATTATCTTT
Found at i:74455 original size:25 final size:25
Alignment explanation
Indices: 74427--74488 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
74417 ATTGATCTTT
74427 CTGTTAAAAATTTCATTTATTTTTA
1 CTGTTAAAAATTTCATTTATTTTTA
74452 CTGTTAAAAATTTCATTTATTTTTA
1 CTGTTAAAAATTTCATTTATTTTTA
* *
74477 ATATTAAAAATT
1 CTGTTAAAAATT
74489 GATTTTTGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.53
Consensus pattern (25 bp):
CTGTTAAAAATTTCATTTATTTTTA
Found at i:75174 original size:30 final size:31
Alignment explanation
Indices: 75133--75190 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
75123 AAATTATTAT
75133 TAAACTATTTAAA-ATTCTTATTTAAGTCAC
1 TAAACTATTTAAATATTCTTATTTAAGTCAC
* * *
75163 TAAATTATTTAAATGTTTTTATTTAAGT
1 TAAACTATTTAAATATTCTTATTTAAGT
75191 TTTAGATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (31 bp):
TAAACTATTTAAATATTCTTATTTAAGTCAC
Found at i:79496 original size:10 final size:10
Alignment explanation
Indices: 79476--79504 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
79466 ATTCACACAC
79476 AAAAAAG-AA
1 AAAAAAGAAA
79485 AAAAAAGAAA
1 AAAAAAGAAA
79495 AAAAAAGAAA
1 AAAAAAGAAA
79505 TCAAGTTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:95040 original size:22 final size:20
Alignment explanation
Indices: 95001--95042 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
94991 AGAACGTGTC
*
95001 CAATTAAAAAGTTTAAATTA
1 CAATTAAAAAATTTAAATTA
95021 CAATTAAAAAATATTGAAATTA
1 CAATTAAAAAAT-TT-AAATTA
95043 AATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 2 0.11
22 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
CAATTAAAAAATTTAAATTA
Found at i:107005 original size:52 final size:52
Alignment explanation
Indices: 106948--107050 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
106938 ATAATATGAT
*
106948 ACGTGGTGACTTGCATGCGAGCCACTCATATAATCATTGTAAGGATTTTTAA
1 ACGTGGTGACTTGCATGCGAGCCACGCATATAATCATTGTAAGGATTTTTAA
*
107000 ACGTGGTGACTTGCATGCGAGCCACGCATATTATCATTGTAAGGATTTTTA
1 ACGTGGTGACTTGCATGCGAGCCACGCATATAATCATTGTAAGGATTTTTA
107051 GTGTATATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (52 bp):
ACGTGGTGACTTGCATGCGAGCCACGCATATAATCATTGTAAGGATTTTTAA
Found at i:109278 original size:14 final size:14
Alignment explanation
Indices: 109259--109292 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
109249 AGTGGAAGTT
109259 GGAGAGAGAGAGAG
1 GGAGAGAGAGAGAG
109273 GGAGAGAGAGAGAG
1 GGAGAGAGAGAGAG
109287 GGAGAG
1 GGAGAG
109293 GGATGAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (14 bp):
GGAGAGAGAGAGAG
Found at i:116006 original size:19 final size:19
Alignment explanation
Indices: 115971--116007 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
115961 ATAATTACAA
*
115971 ATATTGTAATTTAAAATAT
1 ATATTGTAAATTAAAATAT
*
115990 ATATTGTAAATTGAAATA
1 ATATTGTAAATTAAAATA
116008 AACCCAAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (19 bp):
ATATTGTAAATTAAAATAT
Found at i:118031 original size:15 final size:15
Alignment explanation
Indices: 118007--118038 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
117997 TAATATTTAA
*
118007 TTTTTGAATTTAATT
1 TTTTTCAATTTAATT
118022 TTTTTCAATTTAATT
1 TTTTTCAATTTAATT
118037 TT
1 TT
118039 GAAATTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTTCAATTTAATT
Found at i:118077 original size:25 final size:25
Alignment explanation
Indices: 118031--118087 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
118021 TTTTTTCAAT
***
118031 TTAATTTTGAAATTTCTTATTTATA
1 TTAATTTTGAAATTTAACATTTATA
* *
118056 TTAATTTTGAAATTTAACATTTTTT
1 TTAATTTTGAAATTTAACATTTATA
118081 TTAATTT
1 TTAATTT
118088 GATCCTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (25 bp):
TTAATTTTGAAATTTAACATTTATA
Done.