Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005661.1 Kokia drynarioides strain JFW-HI SEQ_119832, 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: 149614
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:30313 original size:24 final size:24
Alignment explanation
Indices: 30284--30334 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
30274 GCCTAGACAA
*
30284 TTAGCTCTCACAAGCCCAGGATGG
1 TTAGCTCTCACAAGCCCAGAATGG
* *
30308 TTAGCTCTTACGAGCCCAGAATGG
1 TTAGCTCTCACAAGCCCAGAATGG
30332 TTA
1 TTA
30335 ACCAGTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (24 bp):
TTAGCTCTCACAAGCCCAGAATGG
Found at i:35167 original size:18 final size:18
Alignment explanation
Indices: 35138--35181 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
35128 AAATGTACTA
*
35138 ACAAAT-AAAATGCAGTG
1 ACAAATAAAAATGCAATG
35155 ACAAATAAAAATGCAATG
1 ACAAATAAAAATGCAATG
*
35173 ACAACTAAA
1 ACAAATAAA
35182 TGAGATGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 6 0.25
18 18 0.75
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (18 bp):
ACAAATAAAAATGCAATG
Found at i:59260 original size:29 final size:30
Alignment explanation
Indices: 59228--59294 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 30
59218 TACTAACCCC
* *
59228 TTTAAT-TTTT-TTAATTTTAATTTAATTTA
1 TTTAATATTTTATTAATATTAATTTAA-TAA
59257 TTTAATAATTTTAATTAATATTAATTTAATAA
1 TTTAAT-ATTTT-ATTAATATTAATTTAATAA
59289 TTTAAT
1 TTTAAT
59295 CAAAGGAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
31 4 0.12
32 8 0.25
33 14 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TTTAATATTTTATTAATATTAATTTAATAA
Found at i:59281 original size:33 final size:31
Alignment explanation
Indices: 59230--59294 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
59220 CTAACCCCTT
* * *
59230 TAATTTTTTTAATTTTAATTTAATTTATTTAA
1 TAATTTTATTAATATTAATTTAA-TAATTTAA
59262 TAATTTTAATTAATATTAATTTAATAATTTAA
1 TAATTTT-ATTAATATTAATTTAATAATTTAA
59294 T
1 T
59295 CAAAGGAGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (31 bp):
TAATTTTATTAATATTAATTTAATAATTTAA
Found at i:59288 original size:24 final size:23
Alignment explanation
Indices: 59228--59291 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 23
59218 TACTAACCCC
59228 TTTAATTT-TTT--TAATTTTAA
1 TTTAATTTATTTAATAATTTTAA
59248 TTTAATTTATTTAATAATTTTAA
1 TTTAATTTATTTAATAATTTTAA
59271 -TTAATATTAATTTAATAATTT
1 TTTAAT-TT-ATTTAATAATTT
59292 AATCAAAGGA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.21
21 3 0.08
22 5 0.13
23 11 0.28
24 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTAATTTATTTAATAATTTTAA
Found at i:59293 original size:13 final size:13
Alignment explanation
Indices: 59250--59294 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
59240 AATTTTAATT
59250 TAATTT-ATTTAA
1 TAATTTAATTTAA
59262 TAATTTTAA-TTAA
1 TAA-TTTAATTTAA
59275 T-A-TTAATTTAA
1 TAATTTAATTTAA
59286 TAATTTAAT
1 TAATTTAAT
59295 CAAAGGAGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
10 4 0.14
11 5 0.18
12 5 0.18
13 13 0.46
14 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TAATTTAATTTAA
Found at i:65177 original size:194 final size:194
Alignment explanation
Indices: 64842--65278 Score: 499
Period size: 194 Copynumber: 2.2 Consensus size: 194
64832 CAATAAATGT
* * * * *
64842 GGTATCGCATATGTTTCAAGTCCTCGACAGTTCGTGTGAGTAGCATCATGAGTCCGAAAATGAGT
1 GGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCCGAAAATGAGT
* * ** *
64907 AAAGAATCCAAGAATGGATTACAGGCCTTACGACAGCTGAGATTTATGCATAAGTGCATATTCTC
66 AAAGAATCCAAGAATGAATTACAGGCCTTACGACAGCTGAGACTTATGCATAAGTGCATACACCC
* ** * *
64972 GACAGCTCATGTGAGCAGCATCGTTA-GAGAACAGTTATATGCATAGATACC-ACATCAATGGCT
131 GACAACTCATGTGAGCAGCATCGTTAGGAG-ACAGTTATATAAACAGACACCGAC-T-AATGGCT
65035 GA
193 GA
* * *
65037 GGTATCGCATATGTTGCGAGTCCTCGACAGCTCATGTAAGCAGCATCGTGAGTCTGAAAAAT-AG
1 GGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCCG-AAAATGAG
* * ** *
65101 -ATATGAATCC-AGAATGAATTACAGGCCTTGCGATGGCT-AGGACTTATGCATAAGTGCATGCA
65 TA-AAGAATCCAAGAATGAATTACAGGCCTTACGACAGCTGA-GACTTATGCATAAGTGCATACA
* *
65163 CCCGACAACTCATGTGAGTAGCATCGTTAGGAGACAGTTATATAAACAGACACCGTACTGATGGC
128 CCCGACAACTCATGTGAGCAGCATCGTTAGGAGACAGTTATATAAACAGACACCG-ACTAATGGC
*
65228 TGG
192 TGA
* * * *
65231 GGTACCGCATATGTTGTGAGTCCTCGACATCTCGTGTGACCAGCATCG
1 GGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
65279 AGTACTAGTA
Statistics
Matches: 204, Mismatches: 32, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
193 1 0.00
194 135 0.66
195 61 0.30
196 7 0.03
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.25
Consensus pattern (194 bp):
GGTATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCCGAAAATGAGT
AAAGAATCCAAGAATGAATTACAGGCCTTACGACAGCTGAGACTTATGCATAAGTGCATACACCC
GACAACTCATGTGAGCAGCATCGTTAGGAGACAGTTATATAAACAGACACCGACTAATGGCTGA
Found at i:69095 original size:39 final size:41
Alignment explanation
Indices: 69052--69136 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 41
69042 TTAAAATGCG
*
69052 ATAAT-TTGTA-ATAATAGTTGTAGGAGTAATAACTTGAAA
1 ATAATATTGTAGATAATAGTTGTAGGAGCAATAACTTGAAA
* *
69091 ATAATATTTTATGATAATAGTTGTCGGAGCAATAACTTGAAA
1 ATAATATTGTA-GATAATAGTTGTAGGAGCAATAACTTGAAA
69133 ATAA
1 ATAA
69137 AAACGAACTG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 5 0.12
40 4 0.10
42 31 0.77
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (41 bp):
ATAATATTGTAGATAATAGTTGTAGGAGCAATAACTTGAAA
Found at i:70468 original size:15 final size:14
Alignment explanation
Indices: 70445--70483 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
70435 TATACATATA
70445 TTTTTTCTTTTCCC
1 TTTTTTCTTTTCCC
*
70459 TTTTTCTCTTTTCTC
1 TTTTT-TCTTTTCCC
70474 TTTTTT-TTTT
1 TTTTTTCTTTT
70484 ATATGTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 13 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTTTTCCC
Found at i:71062 original size:17 final size:17
Alignment explanation
Indices: 71012--71072 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
71002 CTCTAAATTA
*
71012 CAATGACAAATTGAAATG
1 CAATGAC-AATTAAAATG
* * **
71030 CAATAATAATGCAAATG
1 CAATGACAATTAAAATG
71047 CAATGACAATTAAAATG
1 CAATGACAATTAAAATG
*
71064 TAATGACAA
1 CAATGACAA
71073 CGAGAATGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
17 29 0.85
18 5 0.15
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.23
Consensus pattern (17 bp):
CAATGACAATTAAAATG
Found at i:84789 original size:9 final size:9
Alignment explanation
Indices: 84775--84799 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
84765 AAAAACAGAC
84775 AAAGCAATT
1 AAAGCAATT
84784 AAAGCAATT
1 AAAGCAATT
84793 AAAGCAA
1 AAAGCAA
84800 AGTACATGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (9 bp):
AAAGCAATT
Found at i:88606 original size:63 final size:66
Alignment explanation
Indices: 88460--88635 Score: 279
Period size: 67 Copynumber: 2.7 Consensus size: 66
88450 CATTTTCTTA
88460 TTATT-TTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTT
1 TTATTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTT
88524 GTT
65 G-T
* *
88527 TTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTG
1 TTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
88592 -
66 T
*
88592 TT-TTA-TTATTTATTTATTATTTTATGAATATAGATAAATAAATA
1 TTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATA
88636 AATAACAAAC
Statistics
Matches: 103, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
63 36 0.35
64 3 0.03
65 2 0.02
67 47 0.46
68 15 0.15
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (66 bp):
TTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTG
T
Found at i:91139 original size:31 final size:31
Alignment explanation
Indices: 91103--91174 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
91093 TGCATAAGCA
* *
91103 TTCATGCATTCATAAAATTTTGCATTGTATT
1 TTCATGCATTCATAAAATTTTGCATCGCATT
* *
91134 TTCATGTATTCATAAAGTTTTGCATCGCATT
1 TTCATGCATTCATAAAATTTTGCATCGCATT
91165 TTCATGCATT
1 TTCATGCATT
91175 AAAAGTTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.26, C:0.15, G:0.11, T:0.47
Consensus pattern (31 bp):
TTCATGCATTCATAAAATTTTGCATCGCATT
Found at i:95648 original size:50 final size:50
Alignment explanation
Indices: 95542--95675 Score: 148
Period size: 50 Copynumber: 2.7 Consensus size: 50
95532 ATCCTATACC
** ** *
95542 CTTAAAGTTGTAGAGGAACAGATTGAAGGCACG--ATGGTGAATCTCATATA
1 CTTAAAGTTGTAGAGGGGCAGATTGAA-GC-CGTAATGGCAAATATCATATA
*
95592 CCTAAAGTTGTAGAGGGGCAGATTGAAGCCGTAATGGCAAATATCAT-TCA
1 CTTAAAGTTGTAGAGGGGCAGATTGAAGCCGTAATGGCAAATATCATAT-A
* *
95642 CTTAAAGTTGTAGAGGGGTAGATTGAAGTCGTAA
1 CTTAAAGTTGTAGAGGGGCAGATTGAAGCCGTAA
95676 GGATGAATCT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
48 2 0.03
49 3 0.04
50 67 0.93
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (50 bp):
CTTAAAGTTGTAGAGGGGCAGATTGAAGCCGTAATGGCAAATATCATATA
Found at i:95764 original size:40 final size:40
Alignment explanation
Indices: 95709--96113 Score: 414
Period size: 40 Copynumber: 10.2 Consensus size: 40
95699 CTGAAATGGA
95709 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
* * *
95749 CAGATTGAAAACCATCCGATCTCTTACTCCGACCATG-GGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCA-GAGGG
* * * * * *
95789 CAAATTGAAGACCATTCGATCTTTTACCTCGACCAGAAGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
* * *
95829 CAGATTGAAGACCATCTGATCTCTTACCCCGATCATG-GGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCA-GAGGG
* * * *
95869 CAAATTG-A-ACCAATCCGATCTTTTACCCTAACTAGAGGG
1 CAGATTGAAGACC-ATCCGATCTCTTACCCCAACCAGAGGG
*
95908 CAGATTGAAGGCCATCCGATCTCTTACCCCAACCATG-GGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCA-GAGGG
* * * *
95948 CAGATTGAAG-CAATCCAATCTTTTACCCTAACCAGAGGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
* * *
95987 CAAATTGAAGACCATCCGATCTCTTACCCCGACCATA-GG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
* * * * * *
96026 CAGATTGAAG-CAATCCAATATTTTACCCTAACCAGATGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
* *
96065 CAGATTGAAGACCATTCGATCTCTTACCCCGACCATG-GGG
1 CAGATTGAAGACCATCCGATCTCTTACCCCAACCA-GAGGG
96105 CAGATTGAA
1 CAGATTGAA
96114 ATAATCTAAT
Statistics
Matches: 296, Mismatches: 56, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
38 24 0.08
39 82 0.28
40 184 0.62
41 6 0.02
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (40 bp):
CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGG
Found at i:95929 original size:79 final size:79
Alignment explanation
Indices: 95709--96136 Score: 531
Period size: 79 Copynumber: 5.4 Consensus size: 79
95699 CTGAAATGGA
* * * *
95709 CAGATTGAAGACC-ATCCGATCTCTTACCCCAACCAGAGGGCAGATTGAAAACCATCCGATCTCT
1 CAGATTG-A-ACCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCT
*
95773 TACTCCGACCATGGGG
64 TACCCCGACCATGGGG
* * * * * *
95789 CAAATTGAAGACC-ATTCGATCTTTTA-CCTCGACCAGAAGGCAGATTGAAGACCATCTGATCTC
1 CAGATTG-A-ACCAATCCAATCTTTTACCCT-AACCAGAGGGCAGATTGAAGACCATCCGATCTC
*
95852 TTACCCCGATCATGGGG
63 TTACCCCGACCATGGGG
* * * *
95869 CAAATTGAACCAATCCGATCTTTTACCCTAACTAGAGGGCAGATTGAAGGCCATCCGATCTCTTA
1 CAGATTGAACCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
*
95934 CCCCAACCATGGGG
66 CCCCGACCATGGGG
* *
95948 CAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGACCATCCGATCTCTTA
1 CAGATTGAACCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
*
96013 CCCCGACCAT-AGG
66 CCCCGACCATGGGG
* * * *
96026 CAGATTGAAGCAATCCAATATTTTACCCTAACCAGATGGCAGATTGAAGACCATTCGATCTCTTA
1 CAGATTGAACCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
96091 CCCCGACCATGGGG
66 CCCCGACCATGGGG
** *
96105 CAGATTGAAATAATCTAATCTTTTACCTCTAA
1 CAGATTGAACCAATCCAATCTTTTACC-CTAA
96137 AATTATAAAA
Statistics
Matches: 308, Mismatches: 35, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
78 76 0.25
79 151 0.49
80 81 0.26
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (79 bp):
CAGATTGAACCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
CCCCGACCATGGGG
Found at i:96088 original size:157 final size:158
Alignment explanation
Indices: 95709--96136 Score: 563
Period size: 157 Copynumber: 2.7 Consensus size: 158
95699 CTGAAATGGA
* * * *
95709 CAGATTGAAGACCATCCGATCTCTTACCCCAACCAGAGGGCAGATTGAAAACCATCCGATCTCTT
1 CAGATTGAAG-CAATCCGATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTT
* * * * * * *
95774 ACTCCGACCATGGGGCAAATTGAAGACCATTCGATCTTTTA-CCTCGACCAGAAGGCAGATTGAA
65 ACCCCGACCATGGGGCAGATTGAAG-CAATCCAATCTTTTACCCT-AACCAGAAGGCAAATTGAA
* * *
95838 GACCATCTGATCTCTTACCCCGATCATGGGG
128 GACCATCCGATCTCTTACCCCGACCATGAGG
* * * *
95869 CAAATTGAACCAATCCGATCTTTTACCCTAACTAGAGGGCAGATTGAAGGCCATCCGATCTCTTA
1 CAGATTGAAGCAATCCGATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
* *
95934 CCCCAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAAATTGAAGAC
66 CCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAAGGCAAATTGAAGAC
95999 CATCCGATCTCTTACCCCGACCAT-AGG
131 CATCCGATCTCTTACCCCGACCATGAGG
* * * *
96026 CAGATTGAAGCAATCCAATATTTTACCCTAACCAGATGGCAGATTGAAGACCATTCGATCTCTTA
1 CAGATTGAAGCAATCCGATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
** *
96091 CCCCGACCATGGGGCAGATTGAAATAATCTAATCTTTTACCTCTAA
66 CCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACC-CTAA
96137 AATTATAAAA
Statistics
Matches: 234, Mismatches: 32, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
157 96 0.41
158 57 0.24
159 73 0.31
160 8 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (158 bp):
CAGATTGAAGCAATCCGATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTA
CCCCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAAGGCAAATTGAAGAC
CATCCGATCTCTTACCCCGACCATGAGG
Found at i:96757 original size:63 final size:63
Alignment explanation
Indices: 96651--96815 Score: 267
Period size: 63 Copynumber: 2.6 Consensus size: 63
96641 ACCCAATTTC
*
96651 ATTTTTCTTATTATTTTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTGTTTTATT
1 ATTTTT-TTATTA-TTTTATGAATATAAATAAATAAATATAAAATAATATTAACTTTGTTTTATT
* *
96716 ATTTTTTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAACTTTGTTTTATT
1 ATTTTTTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAACTTTGTTTTATT
* *
96779 ATTTATTTATTATTTTATGAATATAGATAAATAAATA
1 ATTTTTTTATTATTTTATGAATATAAATAAATAAATA
96816 AATAAATATC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
63 81 0.87
64 6 0.06
65 6 0.06
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (63 bp):
ATTTTTTTATTATTTTATGAATATAAATAAATAAATATAAAATAATATTAACTTTGTTTTATT
Found at i:99807 original size:14 final size:14
Alignment explanation
Indices: 99783--99816 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
99773 TCTCTTGACA
*
99783 ATTTTTTTTTTATG
1 ATTTTTGTTTTATG
*
99797 GTTTTTGTTTTATG
1 ATTTTTGTTTTATG
99811 ATTTTT
1 ATTTTT
99817 TATTATTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (14 bp):
ATTTTTGTTTTATG
Found at i:102951 original size:37 final size:37
Alignment explanation
Indices: 102900--102970 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
102890 TTCCGGCTTA
*
102900 TAGACATCTTTTCTATGAATATATAAAGCATTCAAAT
1 TAGACATCTGTTCTATGAATATATAAAGCATTCAAAT
*
102937 TAGACATCTGTTCTATGAATATATGAAGCATTCA
1 TAGACATCTGTTCTATGAATATATAAAGCATTCA
102971 TATTTCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (37 bp):
TAGACATCTGTTCTATGAATATATAAAGCATTCAAAT
Found at i:104684 original size:13 final size:15
Alignment explanation
Indices: 104650--104687 Score: 55
Period size: 13 Copynumber: 2.7 Consensus size: 15
104640 ATTTTTTAAA
104650 TAATA-TTAATGTGT
1 TAATATTTAATGTGT
104664 TAATATTTAATG-GT
1 TAATATTTAATGTGT
104678 T-ATATTTAAT
1 TAATATTTAAT
104688 ATTTAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.39
14 8 0.35
15 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.53
Consensus pattern (15 bp):
TAATATTTAATGTGT
Found at i:105667 original size:136 final size:133
Alignment explanation
Indices: 105372--105755 Score: 471
Period size: 136 Copynumber: 2.8 Consensus size: 133
105362 GTTTGTTCAC
* * * * *
105372 AATCAGCAGTAAGAAAGAAAAATATTAAATACCCACAAAGGGATTATGGGTAAACAAGCCGATAC
1 AATCAACAGTAAGAAAGAAAAAT-TTGAATACCCACAAAGGGATTGTGGGTAAAAAAGCCGATTC
*
105437 AAATCAGAAAAAATCGGATTGAGAAACTAATTATTCAAGAACCTGGAATACAACAAAGGTAAATC
65 AGAT-A-AAAAAATCGGATTGAGAAAC-AATTATTCAAGAACCTGGAATACAACAAAGGTAAATC
**
105502 GGCACAA
127 AACACAA
* * **
105509 AATCAGCAGTAAGAAAGAAAAATTTGGAATACCCACAAAGTGATTGTGGGTAAAAAAGCTAATTC
1 AATCAACAGTAAGAAAGAAAAATTT-GAATACCCACAAAGGGATTGTGGGTAAAAAAGCCGATTC
* * * * *
105574 AGATAAAAAAATTGGATTAAGAAATCAATTATTCAAGAACTTGGAGTACCCACAAAGGTAAATCA
65 AGATAAAAAAATCGGATTGAGAAA-CAATTATTCAAGAACCTGGAATA-CAACAAAGGTAAATCA
105639 ACACAA
128 ACACAA
* * ***
105645 AATCAATAGTAAGAAAGAAAAATCTAGAATACCCACAAAGGGATTGTGAACAAAAAAGCCGATTC
1 AATCAACAGTAAGAAAGAAAAAT-TTGAATACCCACAAAGGGATTGTGGGTAAAAAAGCCGATTC
* *
105710 AGATAAAAAAATCGAATTGAGAAACCAATTATTCAAGAACCAGGAA
65 AGATAAAAAAATCGGATTGAGAAA-CAATTATTCAAGAACCTGGAA
105756 AGAACAGGAA
Statistics
Matches: 212, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
135 37 0.17
136 116 0.55
137 59 0.28
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (133 bp):
AATCAACAGTAAGAAAGAAAAATTTGAATACCCACAAAGGGATTGTGGGTAAAAAAGCCGATTCA
GATAAAAAAATCGGATTGAGAAACAATTATTCAAGAACCTGGAATACAACAAAGGTAAATCAACA
CAA
Found at i:105978 original size:14 final size:14
Alignment explanation
Indices: 105959--105986 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
105949 GTTTAAAATT
105959 TTTATTTAATTAAA
1 TTTATTTAATTAAA
105973 TTTATTTAATTAAA
1 TTTATTTAATTAAA
105987 AATCTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTTAATTAAA
Found at i:106350 original size:13 final size:13
Alignment explanation
Indices: 106334--106358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106324 ACTTTTCAAA
106334 AACACTTTTTTAC
1 AACACTTTTTTAC
106347 AACACTTTTTTA
1 AACACTTTTTTA
106359 AATCAAAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (13 bp):
AACACTTTTTTAC
Found at i:113882 original size:19 final size:20
Alignment explanation
Indices: 113844--113884 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
113834 TTTCTAAACC
113844 CTCATTCTCAATTATTTCTCT
1 CTCATTCTC-ATTATTTCTCT
*
113865 CTCATTCTC-TTTTTTCTCT
1 CTCATTCTCATTATTTCTCT
113884 C
1 C
113885 CCAAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (20 bp):
CTCATTCTCATTATTTCTCT
Found at i:125243 original size:21 final size:21
Alignment explanation
Indices: 125199--125246 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
125189 CTTGTGATTG
* **
125199 TTCTACCGATACAAGTGTTAC
1 TTCTACCGAAACAAGTCATAC
*
125220 TTCTACCGAAACAAGTCATGC
1 TTCTACCGAAACAAGTCATAC
125241 TTCTAC
1 TTCTAC
125247 TTATATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (21 bp):
TTCTACCGAAACAAGTCATAC
Found at i:127504 original size:20 final size:21
Alignment explanation
Indices: 127479--127517 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
127469 TAGACTTTCA
127479 TCATTAA-CTTAATTAATCTC
1 TCATTAACCTTAATTAATCTC
127499 TCATTAACCTTAATTAATC
1 TCATTAACCTTAATTAATC
127518 CTATTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.44
Consensus pattern (21 bp):
TCATTAACCTTAATTAATCTC
Found at i:133028 original size:21 final size:21
Alignment explanation
Indices: 133004--133069 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
132994 TTTAATGTGA
*
133004 TATTTGAACTATCAATATATG
1 TATTTGAACTATTAATATATG
* * *
133025 TATTTAGAAAATATTTAATGTA-A
1 TATTT-G-AACTA-TTAATATATG
133048 TATTTGAACTATTAATATATG
1 TATTTGAACTATTAATATATG
133069 T
1 T
133070 TTTATCATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 2 0.06
23 9 0.26
24 6 0.18
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (21 bp):
TATTTGAACTATTAATATATG
Found at i:133038 original size:44 final size:43
Alignment explanation
Indices: 132988--133073 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 43
132978 ATACTTTCAC
*
132988 AAAATATTTAATGTGATATTTGAACTATCAATATATGTATTTAG
1 AAAATATTTAATGTAATATTTGAACTATCAATATATGT-TTTAG
*
133032 AAAATATTTAATGTAATATTTGAACTATTAATATATGTTTTA
1 AAAATATTTAATGTAATATTTGAACTATCAATATATGTTTTA
133074 TCATGGTTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 4 0.10
44 36 0.90
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (43 bp):
AAAATATTTAATGTAATATTTGAACTATCAATATATGTTTTAG
Found at i:133062 original size:20 final size:20
Alignment explanation
Indices: 132995--133063 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
132985 CACAAAATAT
*
132995 TTAATGTGATATTTGAACTA
1 TTAATGTAATATTTGAACTA
* * * *
133015 TCAATATATGTATTTAGAAAATA
1 TTAATGTA-ATATTT-G-AACTA
133038 TTTAATGTAATATTTGAACTA
1 -TTAATGTAATATTTGAACTA
133059 TTAAT
1 TTAAT
133064 ATATGTTTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 8
0.68 0.17 0.15
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 2 0.06
23 9 0.25
24 6 0.17
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (20 bp):
TTAATGTAATATTTGAACTA
Found at i:133181 original size:8 final size:8
Alignment explanation
Indices: 133168--133197 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
133158 AATACAAATA
133168 AATAAAGT
1 AATAAAGT
133176 AATAAAGT
1 AATAAAGT
133184 AATAAAGT
1 AATAAAGT
133192 AATAAA
1 AATAAA
133198 ATTAAAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (8 bp):
AATAAAGT
Found at i:140702 original size:15 final size:15
Alignment explanation
Indices: 140666--140702 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
140656 GAAGAGGACT
* *
140666 GGGAAGATATCTCTA
1 GGGAAGGTATCTCCA
140681 GGGAAGGTATCTCCA
1 GGGAAGGTATCTCCA
140696 GGGAAGG
1 GGGAAGG
140703 ATCACTGCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.38, T:0.19
Consensus pattern (15 bp):
GGGAAGGTATCTCCA
Found at i:145029 original size:28 final size:29
Alignment explanation
Indices: 144989--145046 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
144979 GAAATTTTTT
*
144989 TTTCTTCGAGCCAACTTGATA-AAAAAAA
1 TTTCTTCAAGCCAACTTGATAGAAAAAAA
145017 TTTCTTCAAGCCAACTTGATAGAAAAAAA
1 TTTCTTCAAGCCAACTTGATAGAAAAAAA
145046 T
1 T
145047 CCATACGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.29
Consensus pattern (29 bp):
TTTCTTCAAGCCAACTTGATAGAAAAAAA
Found at i:146459 original size:3 final size:3
Alignment explanation
Indices: 146439--146478 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
146429 ATTTTTGTTT
*
146439 TTA TT- TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
146479 GTATAAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:146498 original size:4 final size:4
Alignment explanation
Indices: 146489--146533 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
146479 GTATAAATAC
*
146489 AAAT AAAT AAAT AAAT -AAT AAAT TAAT -AA- AAAT AAA- AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
146533 A
1 A
146534 CCAATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
3 10 0.28
4 26 0.72
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:146502 original size:8 final size:8
Alignment explanation
Indices: 146489--146533 Score: 53
Period size: 7 Copynumber: 6.1 Consensus size: 8
146479 GTATAAATAC
146489 AAATAAAT
1 AAATAAAT
146497 AAATAAAT
1 AAATAAAT
146505 -AATAAAT
1 AAATAAAT
*
146512 TAAT-AA-
1 AAATAAAT
146518 AAATAAA-
1 AAATAAAT
146525 AAATAAAT
1 AAATAAAT
146533 A
1 A
146534 CCAATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
6 3 0.09
7 18 0.55
8 12 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATAAAT
Found at i:146510 original size:11 final size:11
Alignment explanation
Indices: 146489--146533 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
146479 GTATAAATAC
146489 AAATAAATAAAT
1 AAAT-AATAAAT
146501 AAATAATAAAT
1 AAATAATAAAT
*
146512 TAATAA-AAAT
1 AAATAATAAAT
*
146522 AAAAAATAAAT
1 AAATAATAAAT
146533 A
1 A
146534 CCAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 8 0.28
11 17 0.59
12 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:146523 original size:17 final size:17
Alignment explanation
Indices: 146489--146533 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
146479 GTATAAATAC
*
146489 AAATAAATAAATAAATAAT
1 AAATAAAT-AA-AAATAAA
*
146508 AAATTAATAAAAATAAA
1 AAATAAATAAAAATAAA
146525 AAATAAATA
1 AAATAAATA
146534 CCAATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 14 0.61
18 2 0.09
19 7 0.30
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAATAAAAATAAA
Found at i:147610 original size:30 final size:30
Alignment explanation
Indices: 147488--147606 Score: 168
Period size: 30 Copynumber: 4.0 Consensus size: 30
147478 AAAATTATGT
* * *
147488 TTTGACCCCTAAACTTTCCAAAAAATTGAA
1 TTTGACCCTTGAACTTTCCAAAAAATTCAA
*
147518 TTTGACCCTCGAACTTTCCAAAAAATTCAA
1 TTTGACCCTTGAACTTTCCAAAAAATTCAA
* *
147548 TTTGACCCTTGGACTTTCCAAAAATTTCAA
1 TTTGACCCTTGAACTTTCCAAAAAATTCAA
*
147578 TTTGACCCTTGAAC-TTCCCAAAAATTCAA
1 TTTGACCCTTGAACTTTCCAAAAAATTCAA
147607 ATTTTATCCT
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
29 13 0.16
30 66 0.84
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (30 bp):
TTTGACCCTTGAACTTTCCAAAAAATTCAA
Found at i:147631 original size:10 final size:10
Alignment explanation
Indices: 147616--147640 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
147606 AATTTTATCC
147616 TATGTGTGTG
1 TATGTGTGTG
147626 TATGTGTGTG
1 TATGTGTGTG
147636 TATGT
1 TATGT
147641 ATGTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.00, G:0.36, T:0.52
Consensus pattern (10 bp):
TATGTGTGTG
Found at i:147649 original size:2 final size:2
Alignment explanation
Indices: 147644--147668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
147634 TGTATGTATG
147644 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
147669 TACATGCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.