Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012042.1 Kokia drynarioides strain JFW-HI SEQ_127040, 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: 63690
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:21029 original size:43 final size:43
Alignment explanation
Indices: 20968--21219 Score: 333
Period size: 43 Copynumber: 5.8 Consensus size: 43
20958 GTGAATTCTT
20968 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
21011 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* * * * *
21054 AATGGAAGATTTATGTCTCGGCTAGAGCATAATATTTTTTTTGTA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGA--TTGTTTATA
* *
21099 AATGGAAGAACTTATGTCTCGATTAGAGCATAAGATTGTTTTTA
1 AATGGAAG-ACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* * * * *
21143 AATGGAAGACTTATATCTTGGCTAGAGCATAAGATTATTTGTA
1 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
* * *
21186 AATGGAAGAACTTATGACTTGGATAGAGCATAAG
1 AATGGAAG-ACTTATGTCTCGGTTAGAGCATAAG
21220 GTTAATTCAA
Statistics
Matches: 185, Mismatches: 20, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
43 111 0.60
44 37 0.20
45 15 0.08
46 22 0.12
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (43 bp):
AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATA
Found at i:21138 original size:89 final size:87
Alignment explanation
Indices: 20968--21219 Score: 355
Period size: 89 Copynumber: 2.9 Consensus size: 87
20958 GTGAATTCTT
* * * *
20968 AATGGAAGACTTATGTCTCGGTTAGAGCATAAGATTGTTTATAAATGGAAG-ACTTATGTCTCGG
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGTAAATGGAAGAACTTATGTCTCGA
21032 TTAGAGCATAAGATTGTTTATA
66 TTAGAGCATAAGATTGTTTATA
* * *
21054 AATGGAAGATTTATGTCTCGGCTAGAGCATAATATTTTTTTTGTAAATGGAAGAACTTATGTCTC
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGA--TTATTTGTAAATGGAAGAACTTATGTCTC
*
21119 GATTAGAGCATAAGATTGTTTTTA
64 GATTAGAGCATAAGATTGTTTATA
* * * *
21143 AATGGAAGACTTATATCTTGGCTAGAGCATAAGATTATTTGTAAATGGAAGAACTTATGACTTGG
1 AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGTAAATGGAAGAACTTATGTC-TCG
21208 A-TAGAGCATAAG
65 ATTAGAGCATAAG
21220 GTTAATTCAA
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
86 31 0.21
87 36 0.24
88 18 0.12
89 63 0.43
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (87 bp):
AATGGAAGACTTATGTCTCGGCTAGAGCATAAGATTATTTGTAAATGGAAGAACTTATGTCTCGA
TTAGAGCATAAGATTGTTTATA
Found at i:21589 original size:2 final size:2
Alignment explanation
Indices: 21582--21610 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21572 TCAAGTATGC
21582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21611 AGGTATTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26193 original size:22 final size:22
Alignment explanation
Indices: 26165--26208 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
26155 ATAATAGAGA
26165 AAGACTACTCGATCGAAGCATT
1 AAGACTACTCGATCGAAGCATT
26187 AAGACTACTCGATCGAAGCATT
1 AAGACTACTCGATCGAAGCATT
26209 CATACTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (22 bp):
AAGACTACTCGATCGAAGCATT
Found at i:26847 original size:36 final size:36
Alignment explanation
Indices: 26800--26868 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
26790 TGCCAGGCCG
26800 TGTGGGGCACACGACCT-TGTGTGATTTTGTAGCATT
1 TGTGGGGCACAC-ACCTATGTGTGATTTTGTAGCATT
* **
26836 TGTGGTGCACACAGTTATGTGTGATTTTGTAGC
1 TGTGGGGCACACACCTATGTGTGATTTTGTAGC
26869 CCGTGTGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.38
Consensus pattern (36 bp):
TGTGGGGCACACACCTATGTGTGATTTTGTAGCATT
Found at i:26953 original size:85 final size:85
Alignment explanation
Indices: 26798--26954 Score: 203
Period size: 85 Copynumber: 1.8 Consensus size: 85
26788 TGTGCCAGGC
* *** * *
26798 CGTGTGGGGCACACGACCTTGTGTGATTTTGTAGCATTTGTGGTGCACACAGTTATGTGTGATTT
1 CGTGTAGGGCACACGACCTTGTGTGATTTTGTAGCATTTGTGGTGCACACAACCATGTATAATTT
*
26863 TGTAGCCCGTGTGAGTAGGT
66 CGTAGCCCGTGTGAGTAGGT
26883 CGTGTAGGGCACACGA-CTGTGTGTGATTTTGTAGC-TTGTGTGG-GACACACAACCATGTATAA
1 CGTGTAGGGCACACGACCT-TGTGTGATTTTGTAGCATT-TGTGGTG-CACACAACCATGTATAA
26945 TTTCGTAGCC
63 TTTCGTAGCC
26955 TATGTGGGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 5 0.08
85 57 0.92
ACGTcount: A:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (85 bp):
CGTGTAGGGCACACGACCTTGTGTGATTTTGTAGCATTTGTGGTGCACACAACCATGTATAATTT
CGTAGCCCGTGTGAGTAGGT
Found at i:34074 original size:60 final size:58
Alignment explanation
Indices: 34000--34204 Score: 212
Period size: 60 Copynumber: 3.4 Consensus size: 58
33990 GAATTTAGGA
* * *
34000 TCAAAATGTAATTTTAGAAAAATTTAGGGGTTAAAATATAATTTTAGTAAATGTTTGGGG
1 TCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTT-GTAAA-GTTTGGGG
* * * * *
34060 TCAAAATGTGATTTTAGAAAGGTTTAGGAGTCAAAATGTGATTTTGGGAAAGTTTGGGGG
1 TCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTT-GTAAAGTTT-GGGG
* * * * *
34120 TTAAAATGTGCTTTTGGGAAAGTTTAGGGGTTAAAATGTAATTTTGTAAAAGTTTGAAGG
1 TCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGT-AAAGTTTG-GGG
* * *
34180 TCAAAATGTAATTGTGGAAAAGTTT
1 TCAAAATGTGATTTTAGAAAAGTTT
34205 GAAGCCAAAA
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
59 6 0.05
60 112 0.95
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (58 bp):
TCAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTGTAAAGTTTGGGG
Found at i:34156 original size:90 final size:90
Alignment explanation
Indices: 33993--34205 Score: 236
Period size: 90 Copynumber: 2.4 Consensus size: 90
33983 TATCGAAGAA
* * * *
33993 TTTAGGA-TCAAAATGTAATTTTAGAAAAATTTAGGGGTTAAAATATAATTTTAGTAAATGTTTG
1 TTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTGGGGGTTAAAATATAATTTTAGGAAATGTTTG
* *
34057 GGGTCAAAATGTGATTTTAG-AAAGG
66 GGGTCAAAATGTAATTTT-GTAAAAG
* * * ** *
34082 TTTAGGAGTCAAAATGTGATTTTGGGAAAGTTTGGGGGTTAAAATGTGCTTTTGGGAAA-GTTTA
1 TTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTGGGGGTTAAAATATAATTTTAGGAAATGTTT-
*
34146 GGGGTTAAAATGTAATTTTGTAAAAG
65 GGGGTCAAAATGTAATTTTGTAAAAG
* *
34172 TTT-GAAGGTCAAAATGTAATTGTGGAAAAGTTTG
1 TTTAGGA-GTCAAAATGTAATTTTGGAAAAGTTTG
34206 AAGCCAAAAT
Statistics
Matches: 103, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
89 14 0.14
90 89 0.86
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (90 bp):
TTTAGGAGTCAAAATGTAATTTTGGAAAAGTTTGGGGGTTAAAATATAATTTTAGGAAATGTTTG
GGGTCAAAATGTAATTTTGTAAAAG
Found at i:34205 original size:30 final size:30
Alignment explanation
Indices: 34000--34242 Score: 192
Period size: 30 Copynumber: 8.1 Consensus size: 30
33990 GAATTTAGGA
* *
34000 TCAAAATGTAATTTTAGAAAAATTT-AGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGA-GGG
* * * *
34030 TTAAAATATAATTTTAGTAAATGTTTG-GGG
1 TCAAAATGTAATTTT-GGAAAAGTTTGAGGG
* * *
34060 TCAAAATGTGATTTTAGAAAGGTTT-AGGAG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGG-G
* * *
34090 TCAAAATGTGATTTTGGGAAAGTTTGGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* ** *
34120 TTAAAATGTGCTTTTGGGAAAGTTT-AGGGG
1 TCAAAATGTAATTTTGGAAAAGTTTGA-GGG
* * *
34150 TTAAAATGTAATTTTGTAAAAGTTTGAAGG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* *
34180 TCAAAATGTAATTGTGGAAAAGTTTGA-AG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGGG
* *
34209 CCAAAATGTAATTTTGGAAAATTTTG-GGTG
1 TCAAAATGTAATTTTGGAAAAGTTTGAGG-G
34239 TCAA
1 TCAA
34243 TATGCAGTTT
Statistics
Matches: 171, Mismatches: 33, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
29 33 0.19
30 129 0.75
31 9 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTGAGGG
Found at i:34226 original size:29 final size:30
Alignment explanation
Indices: 34152--34234 Score: 123
Period size: 29 Copynumber: 2.8 Consensus size: 30
34142 TTTAGGGGTT
* *
34152 AAAATGTAATTTTGTAAAAGTTTGAAGGTC
1 AAAATGTAATTTTGGAAAAGTTTGAAGGCC
*
34182 AAAATGTAATTGTGGAAAAGTTTGAA-GCC
1 AAAATGTAATTTTGGAAAAGTTTGAAGGCC
*
34211 AAAATGTAATTTTGGAAAATTTTG
1 AAAATGTAATTTTGGAAAAGTTTG
34235 GGTGTCAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 24 0.50
30 24 0.50
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (30 bp):
AAAATGTAATTTTGGAAAAGTTTGAAGGCC
Found at i:35945 original size:39 final size:37
Alignment explanation
Indices: 35901--36023 Score: 111
Period size: 39 Copynumber: 3.2 Consensus size: 37
35891 CCTCTAATTA
35901 GGGTAAGAGATTGCATGCTTCAATCTGCTCTCATGATCG
1 GGGTAAGAGATTGCATGCTTCAATCTGC-C-CATGATCG
** * * * * *
35940 GGGTAAGAGATTGGTGTGTCTTCAATCTACCCTTTAACTA
1 GGGTAAGAGATT-GCATG-CTTCAATCTGCCCATGATC-G
* *
35980 GGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATCG
1 GGGTAAGAGATTGCATGCTTCAATCTG-CCCATGATCG
36018 GGGTAA
1 GGGTAA
36024 AATATTGGTG
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
38 15 0.23
39 25 0.38
40 15 0.23
41 10 0.15
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (37 bp):
GGGTAAGAGATTGCATGCTTCAATCTGCCCATGATCG
Found at i:35991 original size:40 final size:40
Alignment explanation
Indices: 35940--36071 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 40
35930 CTCATGATCG
* * *
35940 GGGTAAGAGATTGGTGTGTCTTCAATCTACCCTTTAACTA
1 GGGTAAAAGATTGGTGTGTCTTCAATCTACCCTATGACTA
* * * *
35980 GGGTAAAAGATTGG-ATG-CTTCAATCTGCCCCATGA-TCG
1 GGGTAAAAGATTGGTGTGTCTTCAATCTACCCTATGACT-A
* *
36018 GGGTAAAATATTGGTGTGTCTTCAATCTACCCTCTGACTA
1 GGGTAAAAGATTGGTGTGTCTTCAATCTACCCTATGACTA
36058 GGGTAAAAGATTGG
1 GGGTAAAAGATTGG
36072 ATACCTCAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
37 1 0.01
38 27 0.36
39 4 0.05
40 41 0.55
41 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (40 bp):
GGGTAAAAGATTGGTGTGTCTTCAATCTACCCTATGACTA
Found at i:36022 original size:38 final size:39
Alignment explanation
Indices: 35899--36083 Score: 137
Period size: 40 Copynumber: 4.7 Consensus size: 39
35889 ACCCTCTAAT
* * *
35899 TAGGGTAAGAGATTGCATGCTTCAATCTGCTCTCATGATC
1 TAGGGTAAAAGATTGGATGCTTCAATCTGC-CCCATGATC
* * * * * * *
35939 -GGGGTAAGAGATTGGTGTGTCTTCAATCT-ACCCTTTAAC
1 TAGGGTAAAAGATTGG-ATG-CTTCAATCTGCCCCATGATC
35978 TAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
1 TAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
* * * *
36017 -GGGGTAAAATATTGGTGTGTCTTCAATCTACCCTC-TGA-C
1 TAGGGTAAAAGATTGG-ATG-CTTCAATCTGCCC-CATGATC
* *
36056 TAGGGTAAAAGATTGGATACCTCAATCT
1 TAGGGTAAAAGATTGGATGCTTCAATCT
36084 TTCTCGTCAT
Statistics
Matches: 113, Mismatches: 24, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
38 30 0.27
39 30 0.27
40 43 0.38
41 10 0.09
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (39 bp):
TAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATC
Found at i:36046 original size:78 final size:79
Alignment explanation
Indices: 35861--36083 Score: 304
Period size: 78 Copynumber: 2.8 Consensus size: 79
35851 TCTTTAGGGC
* * * * *
35861 TAAAAGATTTGGATGATGTTTTCAATATACCCTCTAATTAGGGTAAGAGATTGCATGCTTCAATC
1 TAAAAGA-TTGG-TG-TGTCTTCAATCTACCCTCTAACTAGGGTAAAAGATTGGATGCTTCAATC
*
35926 TGCTCTCATGATCGGGG
63 TGCTCCCATGATCGGGG
* *
35943 TAAGAGATTGGTGTGTCTTCAATCTACCCTTTAACTAGGGTAAAAGATTGGATGCTTCAATCTGC
1 TAAAAGATTGGTGTGTCTTCAATCTACCCTCTAACTAGGGTAAAAGATTGGATGCTTCAATCTGC
36008 -CCCATGATCGGGG
66 TCCCATGATCGGGG
* * * *
36021 TAAAATATTGGTGTGTCTTCAATCTACCCTCTGACTAGGGTAAAAGATTGGATACCTCAATCT
1 TAAAAGATTGGTGTGTCTTCAATCTACCCTCTAACTAGGGTAAAAGATTGGATGCTTCAATCT
36084 TTCTCGTCAT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
78 69 0.54
79 46 0.36
80 2 0.02
81 4 0.03
82 6 0.05
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.33
Consensus pattern (79 bp):
TAAAAGATTGGTGTGTCTTCAATCTACCCTCTAACTAGGGTAAAAGATTGGATGCTTCAATCTGC
TCCCATGATCGGGG
Found at i:36287 original size:99 final size:99
Alignment explanation
Indices: 36101--36695 Score: 520
Period size: 99 Copynumber: 6.0 Consensus size: 99
36091 CATGTTTTCT
** * * * * *
36101 TAAGGTA-CTGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTAATGGTGCCA-GATT
1 TAAGGTATC-GGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATATCTTCACGGT-ACAGGGTT
* * * *
36164 CGCCGTTGCGGCCTCAATCATTCCCATCACATCTTC
64 CGTCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
* *** * * * *
36200 TAAAGTATCGGGTTTACCATTACGACCTCAACCTTTCCTTTCATATCTTTACGGTATC-GGGTTC
1 TAAGGTATCGGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATATCTTCACGGTA-CAGGGTTC
** * *
36264 GTCGTTGTTGCCTTAACCTTTCCCATCACATCTTT
65 GTCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
** ** * * * *
36299 TAAGGTATCAAGTTCACCATTGCAACCTCAACCTTTCCCTTCATATCTTCATGGTACAGGGTTTG
1 TAAGGTATCGGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATATCTTCACGGTACAGGGTTCG
* *
36364 TTGTTGCAGCCTCAACCTTTCCCATCACATCTTT
66 TCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
* * * * *
36398 TAAGGTA-CTAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCNTC-CTCGTACTGGGTT
1 TAAGGTATC-GGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATATCTTCAC-GGTACAGGGTT
* * *
36461 CGTTGTTGCGGCCTCAACCTTTCTCATCACATCTTC
64 CGTCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
* * * * *
36497 TAAGGTATCGAGTTTGTCGTTGC-AGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTT
1 TAAGGTATCGGGTTCGTCGTTGCGA-CCTCAACCTTTCCCTTCATATCTTCACGGTACAGGGTTC
* * *
36561 GTCGTTACGGCTTCAACCTTTCCCATCACATCTTC
65 GTCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
* * * * * *
36596 TAAGGTATCGGGTTCGTCGTTACGGCCTCAACCTTT-CCTATCACATCTTCTAAGGTACCGGATT
1 TAAGGTATCGGGTTCGTCGTTGCGACCTCAACCTTTCCCT-TCATATCTTC-ACGGTACAGGGTT
** * * * *
36660 CACCGTTACAGCCTCAACATTTCCCTTCATATCTTC
64 CGTCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
36696 ATGGTACCAG
Statistics
Matches: 411, Mismatches: 73, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
98 5 0.01
99 365 0.89
100 41 0.10
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (99 bp):
TAAGGTATCGGGTTCGTCGTTGCGACCTCAACCTTTCCCTTCATATCTTCACGGTACAGGGTTCG
TCGTTGCAGCCTCAACCTTTCCCATCACATCTTC
Found at i:36336 original size:50 final size:50
Alignment explanation
Indices: 36175--36859 Score: 174
Period size: 50 Copynumber: 13.8 Consensus size: 50
36165 GCCGTTGCGG
* * * * * * * *
36175 CCTCAATCATTCCCATCACATCTTCTAAAGTATCGGGTTTACCATTACGA
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
** * * * ** * ***
36225 CCTCAACCTTTCCTTTCATATC-TTTACGGTATCGGGTTCGTCGTTGTTG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
* *
36274 CCTTAACCTTTCCCATCACATCTTTTAAGGTATCAAGTTCACCATTGCAA
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
* * * * ***** *
36324 CCTCAACCTTTCCCTTCATATC-TTCATGGTA-CAGGGTTTGTTGTTGCAG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCA-GGTTCACCATTGCAA
** * **
36373 CCTCAACCTTTCCCATCACATCTTTTAAGGTA-CTAGGTTCGTCGTTGCGG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATC-AGGTTCACCATTGCAA
* * ** * * **** **
36423 CCTCAACCTTTCCCTTCATATCNTCCT--CGTA-CTGGGTTCGTTGTTGCGG
1 CCTCAACCTTTCCCATCACATC-TTTTAAGGTATC-AGGTTCACCATTGCAA
* * *** * *
36472 CCTCAACCTTTCTCATCACATCTTCTAAGGTATC-GAGTTTGTCGTTGCAG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAG-GTTCACCATTGCAA
* * * * * * *** * * **
36522 CCTCAACCTTTCCCTTCATATC-TTCATGGTACCGGGTTTGTCGTTACGG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
* * * ** * * **
36571 CTTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGTCGTTACGG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
* * * * * *
36621 CCTCAACCTTTCCTATCACATCTTCTAAGGTA-CCGGATTCACCGTTACAG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGG-TTCACCATTGCAA
* * * * * * ** ** * *
36671 CCTCAACATTTCCCTTCATATC-TTCATGGTACCAGGTTTGCTGTT-TAGG
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCA-A
* * * * **
36720 CCTCAACCTTTTCCATCACGTCTTCTAAGGATATCGGGTTCACCATTGCGG
1 CCTCAACCTTTCCCATCACATCTTTTAAGG-TATCAGGTTCACCATTGCAA
* * * * * * * ** *
36771 TCTCAACCTTTCCCTTCATATC-TTCATGGTACCGGGTTTGCCGTTG-AA
1 CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
* *
36819 GCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTC
1 -CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTC
36860 GCCGTTGTAG
Statistics
Matches: 480, Mismatches: 136, Indels: 38
0.73 0.21 0.06
Matches are distributed among these distances:
48 6 0.01
49 211 0.44
50 231 0.48
51 32 0.07
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (50 bp):
CCTCAACCTTTCCCATCACATCTTTTAAGGTATCAGGTTCACCATTGCAA
Found at i:36435 original size:149 final size:149
Alignment explanation
Indices: 36100--36866 Score: 627
Period size: 149 Copynumber: 5.2 Consensus size: 149
36090 TCATGTTTTC
** ** * * ** * *
36100 TTAAGGTACTGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATC-T-TAATGGTGCCAGAT
1 TTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAA-GGTATCGGGT
* * * * * * * * * *
36163 TCGCCGTTGCGGCCTCAATCATTCCCATCACATCTTCTAAAGTATCGGGTTTACCATTAC-GACC
65 TCACCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAG-CC
*
36227 TCAACCTTTCCTTTCATATCT
129 TCAACCTTTCCCTTCATATCT
* * * ** * * **
36248 TTACGGTATCGGGTTCGTCGTTGTTGCCTTAACCTTTCCCATCACATCTTTTAAGGTATCAAGTT
1 TTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTT
** * * * **
36313 CACCATTGCAACCTCAACCTTTCCCTTCATATCTTC-ATGGTACAGGGTTTGTTGTTGCAGCCTC
66 CACCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAGCCTC
* *
36377 AACCTTTCCCATCACATCTT
131 AACCTTTCCCTTCATATC-T
* * * * *
36397 TTAAGGTACTAGGTTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCNTCCT--CGTA-CTGGG
1 TTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATC-TTCTAAGGTATC-GGG
**** * * * * *
36459 TTCGTTGTTGCGGCCTCAACCTTTCTCATCACATCTTCTAAGGTATCGAGTTTGTCGTTGCAGCC
64 TTCACCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAGCC
36524 TCAACCTTTCCCTTCATATCT
129 TCAACCTTTCCCTTCATATCT
* * * * * *
36545 TCATGGTACCGGGTTTGTCGTTACGGCTTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTT
1 TTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTT
** * * * ** *
36610 CGTCGTTACGGCCTCAACCTTT-CCTATCACATCTTCTAAGGTACCGGATTCACCGTTACAGCCT
66 CACCATTGCGGCCTCAACCTTTCCCT-TCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAGCCT
*
36674 CAACATTTCCCTTCATATCT
130 CAACCTTTCCCTTCATATCT
* * * ** * *
36694 TCATGGTACCAGGTTTG-CTGTTTAGGCCTCAACCTTTTCCATCACGTCTTCTAAGGATATCGGG
1 TTAAGGTACCAGGTTCGTC-GTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGG-TATCGGG
* * * *
36758 TTCACCATTGCGGTCTCAACCTTTCCCTTCATATCTTC-ATGGTACCGGGTTTGCCGTTGAAGCC
64 TTCACCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAGCC
* *
36822 TCAACCTTTCCCATCACATCT
129 TCAACCTTTCCCTTCATATCT
* * *
36843 TCTAAGGTATCGGGTTCGCCGTTG
1 T-TAAGGTACCAGGTTCGTCGTTG
36867 TAGCCTTAAC
Statistics
Matches: 489, Mismatches: 114, Indels: 30
0.77 0.18 0.05
Matches are distributed among these distances:
147 4 0.01
148 145 0.30
149 281 0.57
150 55 0.11
151 4 0.01
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (149 bp):
TTAAGGTACCAGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTT
CACCATTGCGGCCTCAACCTTTCCCTTCACATCTTCTAAGGTACCGGGTTTGCCGTTGCAGCCTC
AACCTTTCCCTTCATATCT
Found at i:36725 original size:198 final size:198
Alignment explanation
Indices: 36119--36903 Score: 663
Period size: 198 Copynumber: 4.0 Consensus size: 198
36109 TGGGTTCACC
* * * * * * *
36119 GTTGCGGCCTCAACCTTTCCCTTCATATCTTAATGGTGCCAGATTCGCCGTTGCGGCCTCAATCA
1 GTTGCAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCT
* ** * * * *
36184 TTCCCATCACATCTTCTAAAGTATCGGGTTTACCATTACGACCTCAACCTTTCCTTTCATATCTT
66 TTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTACGGCCTCAACCTTTCCTATCACATCTT
* * * ** * * *
36249 -TACGGTATCGGGTTCGTCGTTGTTGCCTTAACCTTTCCCATCACATCTTTTAAGGTATCAAGTT
131 CTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCACATC-TTCAAGGTATCAGGTT
** *
36313 CACC
195 TGCT
* * * * ** *
36317 ATTGCAACCTCAACCTTTCCCTTCATATCTTCATGGTACAGGGTTTGTTGTTGCAGCCTCAACCT
1 GTTGCAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCT
* * * * *
36382 TTCCCATCACATCTTTTAAGGTA-CTAGGTTCGTCGTTGCGGCCTCAACCTTTCCCT-TCATATC
66 TTCCCATCACATCTTCTAAGGTATC-GGGTTCGCCGTTACGGCCTCAACCTTT-CCTATCACATC
* * * ** * *
36445 NTCCT--CGTACTGGGTTCGTTGTTGCGGCCTCAACCTTTCTCATCACATCTTCTAAGGTATC-G
129 -TTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTC-AAGGTATCAG
36507 AGTTTG-T
192 -GTTTGCT
* * * *
36514 CGTTGCAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTTGTCGTTACGGCTTCAACC
1 -GTTGCAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACC
*
36579 TTTCCCATCACATCTTCTAAGGTATCGGGTTCGTCGTTACGGCCTCAACCTTTCCTATCACATCT
65 TTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTACGGCCTCAACCTTTCCTATCACATCT
* * * * * * * *
36644 TCTAAGGTACCGGATTCACCGTTACAGCCTCAACATTTCCCTTCATATCTTCATGGTACCAGGTT
130 TCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCAAGGTATCAGGTT
36709 TGCT
195 TGCT
* * * ** * * * * *
36713 GTT-TAGGCCTCAACCTTTTCCATCACGTCTTCTAAGGATATCGGGTTCACCATTGCGGTCTCAA
1 GTTGCA-GCCTCAACCTTTCCCTTCATATCTTC-ATGG-TACCGGGTTCGCCGTTGCGGCCTCAA
* * * * * * *
36777 CCTTTCCCTTCATATCTTC-ATGGTACCGGGTTTGCCGTTGA-AGCCTCAACCTTTCCCATCACA
63 CCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTT-ACGGCCTCAACCTTTCCTATCACA
* * * * * * * *
36840 TCTTCTAAGGTATCGGGTTCGCCGTTGTAGCCTTAACTTTTCCCTTCATAACTTCAGGGTATCA
127 TCTTCTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCAAGGTATCA
36904 AATTTCGCTG
Statistics
Matches: 475, Mismatches: 95, Indels: 33
0.79 0.16 0.05
Matches are distributed among these distances:
197 10 0.02
198 293 0.62
199 135 0.28
200 37 0.08
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (198 bp):
GTTGCAGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCGCCGTTGCGGCCTCAACCT
TTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTACGGCCTCAACCTTTCCTATCACATCTT
CTAAGGTACCGGGTTCGCCGTTGCAGCCTCAACCTTTCCCATCACATCTTCAAGGTATCAGGTTT
GCT
Found at i:36733 original size:100 final size:98
Alignment explanation
Indices: 36619--36900 Score: 366
Period size: 100 Copynumber: 2.8 Consensus size: 98
36609 TCGTCGTTAC
* * *
36619 GGCCTCAACCTTTCCTATCACATCTTCTAAGGTACCGGATTCACCGTTACAGCCTCAACATTTCC
1 GGCCTCAACCTTTCC-ATCACATCTTCTAAGGTATCGGGTTCACCGTTGCAGCCTCAACATTTCC
* *
36684 CTTCATATCTTCATGGTACCAGGTTTGCTGTTTA
65 CTTCATATCTTCATGGTACCAGGTTTGCCGTTGA
* * * * *
36718 GGCCTCAACCTTTTCCATCACGTCTTCTAAGGATATCGGGTTCACCATTGCGGTCTCAACCTTTC
1 GGCCTCAACC-TTTCCATCACATCTTCTAAGG-TATCGGGTTCACCGTTGCAGCCTCAACATTTC
*
36783 CCTTCATATCTTCATGGTACCGGGTTTGCCGTTGA
64 CCTTCATATCTTCATGGTACCAGGTTTGCCGTTGA
* * * * *
36818 AGCCTCAACCTTTCCCATCACATCTTCTAAGGTATCGGGTTCGCCGTTGTAGCCTTAACTTTTCC
1 GGCCTCAACCTTT-CCATCACATCTTCTAAGGTATCGGGTTCACCGTTGCAGCCTCAACATTTCC
* *
36883 CTTCATAACTTCAGGGTA
65 CTTCATATCTTCATGGTA
36901 TCAAATTTCG
Statistics
Matches: 158, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
99 70 0.44
100 88 0.56
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (98 bp):
GGCCTCAACCTTTCCATCACATCTTCTAAGGTATCGGGTTCACCGTTGCAGCCTCAACATTTCCC
TTCATATCTTCATGGTACCAGGTTTGCCGTTGA
Found at i:42446 original size:6 final size:6
Alignment explanation
Indices: 42425--42464 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
42415 TTTAGACATT
*
42425 TTTAAA CTTAAA --TAAA TTTAAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
42465 ATTTGTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:44447 original size:27 final size:27
Alignment explanation
Indices: 44407--44472 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
44397 TAAAACACCA
* * *
44407 AAAAAGAAACGCCTTTGTGGCAACCACT
1 AAAAGGAAA-GCCTTCGTGGCAAACACT
* * *
44435 TAAAGGAAAGCCTTCGTTGCAAACTCT
1 AAAAGGAAAGCCTTCGTGGCAAACACT
44462 AAAAGGAAAGC
1 AAAAGGAAAGC
44473 GCTTGCGGCG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (27 bp):
AAAAGGAAAGCCTTCGTGGCAAACACT
Found at i:44605 original size:27 final size:28
Alignment explanation
Indices: 44502--44685 Score: 108
Period size: 27 Copynumber: 6.5 Consensus size: 28
44492 AGAACAATAC
**
44502 GCCTTTGTGGCAAACCTCTTAAAGGAAA
1 GCCTTTGTGGCAATTCTCTTAAAGGAAA
* ** * *
44530 ACCTTTGTGGCAAAACTCTAAAAATGGTAA
1 GCCTTTGTGGCAATTCTCT-TAAA-GGAAA
* * * ** *
44560 GTCTTTATGGTAAACCTCTTAAATG-AA
1 GCCTTTGTGGCAATTCTCTTAAAGGAAA
44587 GCCTTTGTGGCAATTCTCTTAAAGGAAAA
1 GCCTTTGTGGCAATTCTCTTAAAGG-AAA
* * *
44616 GGCC-TTGTGGCGATCTCTGTTAAAAG-AA
1 -GCCTTTGTGGCAAT-TCTCTTAAAGGAAA
* *
44644 GCTTTTGTGGCAATT-TCTATAAA-GTAA
1 GCCTTTGTGGCAATTCTCT-TAAAGGAAA
*
44671 GCCCTTGTGGCAATT
1 GCCTTTGTGGCAATT
44686 GTTTGGAAAG
Statistics
Matches: 122, Mismatches: 25, Indels: 19
0.73 0.15 0.11
Matches are distributed among these distances:
26 3 0.02
27 43 0.35
28 29 0.24
29 17 0.14
30 30 0.25
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (28 bp):
GCCTTTGTGGCAATTCTCTTAAAGGAAA
Found at i:50161 original size:6 final size:6
Alignment explanation
Indices: 50150--50192 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
50140 CCCTATATCC
* * * *
50150 ACCTCT ACCTCT ACCTGT TCCTCT TCCTCT ACCTCT TCCTCT A
1 ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT ACCTCT A
50193 GCACCGAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.12, C:0.47, G:0.02, T:0.40
Consensus pattern (6 bp):
ACCTCT
Found at i:50172 original size:18 final size:18
Alignment explanation
Indices: 50151--50192 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
50141 CCTATATCCA
*
50151 CCTCTACCTCTACCTGTT
1 CCTCTACCTCTACCTCTT
*
50169 CCTCTTCCTCTACCTCTT
1 CCTCTACCTCTACCTCTT
50187 CCTCTA
1 CCTCTA
50193 GCACCGAAGC
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:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CCTCTACCTCTACCTCTT
Found at i:50184 original size:12 final size:12
Alignment explanation
Indices: 50151--50192 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
50141 CCTATATCCA
*
50151 CCTCTACCTCTA
1 CCTCTACCTCTT
* *
50163 CCTGTTCCTCTT
1 CCTCTACCTCTT
50175 CCTCTACCTCTT
1 CCTCTACCTCTT
50187 CCTCTA
1 CCTCTA
50193 GCACCGAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (12 bp):
CCTCTACCTCTT
Found at i:61248 original size:16 final size:17
Alignment explanation
Indices: 61227--61267 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
61217 TTAAAATATG
61227 TAACAATTATTTT-TTA
1 TAACAATTATTTTATTA
61243 TAACAA-TATTTTATTA
1 TAACAATTATTTTATTA
61259 TAACAATTA
1 TAACAATTA
61268 ATTGTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.26
16 15 0.65
17 2 0.09
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (17 bp):
TAACAATTATTTTATTA
Found at i:61547 original size:23 final size:23
Alignment explanation
Indices: 61525--61568 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61515 TAAATGAAAT
61525 TACATT-TATAAATTTTATTAAA
1 TACATTATATAAATTTTATTAAA
* *
61547 TATATTATTTAAATTTTATTAA
1 TACATTATATAAATTTTATTAA
61569 TTAATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
TACATTATATAAATTTTATTAAA
Found at i:62385 original size:22 final size:23
Alignment explanation
Indices: 62341--62387 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
62331 ATTACAATTG
*
62341 AAAAACTGACAATTAATTATTAT
1 AAAAACTGACAATTAAATATTAT
62364 AAAAA-TGACAATTAAA-ATTTAT
1 AAAAACTGACAATTAAATA-TTAT
62386 AA
1 AA
62388 GAAAGTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 16 0.73
23 5 0.23
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (23 bp):
AAAAACTGACAATTAAATATTAT
Done.