Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007027.1 Kokia drynarioides strain JFW-HI SEQ_121634, 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: 111443
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:3177 original size:6 final size:6
Alignment explanation
Indices: 3166--3208 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
3156 TCTCTAATCA
*
3166 TCTTTT TCTTTT TCTTTT TCTTTCT TTTCTTT TC-TTT TCTTTT
1 TCTTTT TCTTTT TCTTTT TCTTT-T TCT-TTT TCTTTT TCTTTT
3209 ATAGCTAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 5 0.16
6 20 0.62
7 5 0.16
8 2 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TCTTTT
Found at i:3191 original size:4 final size:5
Alignment explanation
Indices: 3169--3208 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
3159 CTAATCATCT
3169 TTTTC TTTTTC TTTT- TCTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC -TTTTC TTTTC T-TTTC TTTTC TTTTC TTTTC TTTT
3209 ATAGCTAAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.03
5 25 0.78
6 6 0.19
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:11958 original size:23 final size:24
Alignment explanation
Indices: 11932--11976 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
11922 TAGTATTTAA
* *
11932 AACACAAATA-TATATTTAAAAAT
1 AACACAAACATTAGATTTAAAAAT
*
11955 AACATAAACATTAGATTTAAAA
1 AACACAAACATTAGATTTAAAA
11977 CTAATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.29
Consensus pattern (24 bp):
AACACAAACATTAGATTTAAAAAT
Found at i:12347 original size:3 final size:3
Alignment explanation
Indices: 12339--12364 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
12329 TTTATACACA
12339 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
12365 CAGCACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:16152 original size:51 final size:51
Alignment explanation
Indices: 15797--16133 Score: 523
Period size: 51 Copynumber: 6.6 Consensus size: 51
15787 GTTATAAACG
*
15797 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTTTACGGATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
* * ** *
15849 AAAGGTCCGATGACTAAGTGTCATTGTAAGTGTACGAATCGTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
*
15900 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
* * *
15951 AAAGGTCCGATTACTATGAGTCATCGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
16002 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTA-GAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACG-GATT
* * *
16053 AAAGGTTCGATAACTAAGAGTCATCGTGAGTAAACGAATCCTCTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
*
16104 AAAGGTCCGATGACTCAGTGTCATCGTGAG
1 AAAGGTCCGATGACTAAGTGTCATCGTGAG
16134 ATATGAATTT
Statistics
Matches: 257, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
50 1 0.00
51 250 0.97
52 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTCTACGGATT
Found at i:25145 original size:14 final size:14
Alignment explanation
Indices: 25126--25156 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
25116 TCTAATTATC
25126 TTTTAGAATTTAGA
1 TTTTAGAATTTAGA
25140 TTTTAGAATTTAGA
1 TTTTAGAATTTAGA
25154 TTT
1 TTT
25157 GATTCAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (14 bp):
TTTTAGAATTTAGA
Found at i:31522 original size:21 final size:22
Alignment explanation
Indices: 31497--31551 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
31487 AGGCAACCCA
*
31497 ATTATTTTTATTTTATTT-TTT
1 ATTATTTTTATCTTATTTATTT
31518 ATTATTTTTCTATCTTATTTATTT
1 ATTA-TTTT-TATCTTATTTATTT
31542 ATTTATTTTT
1 A-TTATTTTT
31552 GTCCAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 10 0.34
24 8 0.28
25 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTATTTTTATCTTATTTATTT
Found at i:33922 original size:22 final size:22
Alignment explanation
Indices: 33896--33955 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
33886 TCGACTTCTT
33896 TATTTTCTATTT-CTTTTAATTA
1 TATTTTCT-TTTACTTTTAATTA
* *
33918 TATTTTCTTTTATTTTTAATTC
1 TATTTTCTTTTACTTTTAATTA
* *
33940 T-GTTTCTTTTATTTTT
1 TATTTTCTTTTACTTTT
33956 CCTCATATCG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTTCTTTTACTTTTAATTA
Found at i:33940 original size:15 final size:15
Alignment explanation
Indices: 33894--33953 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 15
33884 CTTCGACTTC
33894 TTTATTTTCTATTTCT
1 TTTATTTT-TATTTCT
* *
33910 TTTAATTATATTTTCT
1 TTTATTTTTA-TTTCT
*
33926 TTTATTTTTAATTCT
1 TTTATTTTTATTTCT
*
33941 GTTT-CTTTTATTT
1 -TTTATTTTTATTT
33954 TTCCTCATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
15 13 0.37
16 22 0.63
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATTTCT
Found at i:44020 original size:167 final size:167
Alignment explanation
Indices: 43744--44081 Score: 640
Period size: 167 Copynumber: 2.0 Consensus size: 167
43734 TTGAAAGTAA
*
43744 AGAGATGGAGTTCAAGGTAACTAGAATTTCTTATCATTCTGTAGAGATATCGATTTGATTAGTGG
1 AGAGATGGAGTTCAAGGTAACTAGAATTCCTTATCATTCTGTAGAGATATCGATTTGATTAGTGG
43809 AAATACACAAGTAGGGAAAAGAGTGATAATATGGAAATTTATAGGGAACATCAGAAATAGACAAA
66 AAATACACAAGTAGGGAAAAGAGTGATAATATGGAAATTTATAGGGAACATCAGAAATAGACAAA
* *
43874 AGAAATTAGAGTGAAGCAAGGAAACTGGTATAGAAAG
131 AGAAATTAGAGTGAAGCAAGGAAACAGATATAGAAAG
*
43911 AGAGATGGAGTTCAAGGTAACTAGAATTCCTTATCATTCTGTAGAGATATTGATTTGATTAGTGG
1 AGAGATGGAGTTCAAGGTAACTAGAATTCCTTATCATTCTGTAGAGATATCGATTTGATTAGTGG
43976 AAATACACAAGTAGGGAAAAGAGTGATAATATGGAAATTTATAGGGAACATCAGAAATAGACAAA
66 AAATACACAAGTAGGGAAAAGAGTGATAATATGGAAATTTATAGGGAACATCAGAAATAGACAAA
44041 AGAAATTAGAGTGAAGCAAGGAAACAGATATAGAAAG
131 AGAAATTAGAGTGAAGCAAGGAAACAGATATAGAAAG
44078 AGAG
1 AGAG
44082 GATTTAAGGG
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.44, C:0.08, G:0.25, T:0.24
Consensus pattern (167 bp):
AGAGATGGAGTTCAAGGTAACTAGAATTCCTTATCATTCTGTAGAGATATCGATTTGATTAGTGG
AAATACACAAGTAGGGAAAAGAGTGATAATATGGAAATTTATAGGGAACATCAGAAATAGACAAA
AGAAATTAGAGTGAAGCAAGGAAACAGATATAGAAAG
Found at i:50880 original size:184 final size:180
Alignment explanation
Indices: 50543--50882 Score: 396
Period size: 184 Copynumber: 1.8 Consensus size: 180
50533 GTAACAAGTT
* ** * * *
50543 TTGGTTGTCCAGTAAAAAAAACTGAGAACAAATGGAAAGGATGTAGAGCTATTTTATGACAACCC
1 TTGGTTGTCCAGGAAAAAAAACTGAGAACAAACAGAAAGGATGTACAGCTATTGTAGGACAACCC
50608 TTGAAACTAACATCCAGTGTACCATTTAAAGGACAGAATAGTTATATTAACACTTCCATGAAGGC
66 TTGAAACTAACATCCAGTGTACCATTTAAAGGACAGAATAGTTATATTAACACTTCCATGAAGGC
*
50673 ATCATTTTCCTCAAAATAAAAAAAAGGGAAAAAGAGGAAATGATAGTCTGACTC
131 ATCATTTTACTC---A-AAAAAAAAGGGAAAAAGAGGAAATGATAGTCTGACTC
* * * *
50727 TTGGTTGTCCGGGAAAAAGAACTGAGAACAAACAGAAAGGGA-GTACAGCTATTGTAGGGCTACC
1 TTGGTTGTCCAGGAAAAAAAACTGAGAACAAACAGAAA-GGATGTACAGCTATTGTAGGACAACC
** * ** *
50791 CTTGAAACTAACATCTTGTGTACCATTTAAAGGGCAGAACAGAATGGTTAATATTATTACTTTCA
65 CTTGAAACTAACATCCAGTGTACCATTTAAA--G--G-ACAGAATAGTT-ATATTAACACTTCCA
**
50856 TGAAGGC-TTTTTTTACTCAAAAAAAAA
124 TGAAGGCATCATTTTACTCAAAAAAAAA
50883 AAAAAAAAGA
Statistics
Matches: 130, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
184 79 0.61
185 11 0.08
186 2 0.02
188 1 0.01
189 18 0.14
190 19 0.15
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (180 bp):
TTGGTTGTCCAGGAAAAAAAACTGAGAACAAACAGAAAGGATGTACAGCTATTGTAGGACAACCC
TTGAAACTAACATCCAGTGTACCATTTAAAGGACAGAATAGTTATATTAACACTTCCATGAAGGC
ATCATTTTACTCAAAAAAAAAGGGAAAAAGAGGAAATGATAGTCTGACTC
Found at i:51427 original size:22 final size:22
Alignment explanation
Indices: 51401--51449 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
51391 TTATTTGCTT
*
51401 GACTTAGTCAATTGTTGTTTCA
1 GACTTAGTCAATTATTGTTTCA
51423 GACTTAGTCAATTATTGTTTCA
1 GACTTAGTCAATTATTGTTTCA
*
51445 TACTT
1 GACTT
51450 CTATAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.47
Consensus pattern (22 bp):
GACTTAGTCAATTATTGTTTCA
Found at i:54604 original size:189 final size:189
Alignment explanation
Indices: 54284--54663 Score: 724
Period size: 189 Copynumber: 2.0 Consensus size: 189
54274 TCACCTGTAA
*
54284 GTTGATTGTTCAAACATCAGGCTGTGGGGTGGAGTAGTGGAGTCAACTTTTAAGATCTATGTTTT
1 GTTGATTGTTCAAACATCAGGCTGTGGGGTGGAGTAGTAGAGTCAACTTTTAAGATCTATGTTTT
* *
54349 TGAGTTTGTTATATACAAATAAATGTTCTTTTATGTGCATTTTTTTGCACCTTGCTTTTGTTGCA
66 TGAGTGTGCTATATACAAATAAATGTTCTTTTATGTGCATTTTTTTGCACCTTGCTTTTGTTGCA
*
54414 TGAGTATATTTTTGGCAATTTACCTCTGGATTAGTACAGGGGTTTCTAGTCTGTTGATG
131 TGAGTACATTTTTGGCAATTTACCTCTGGATTAGTACAGGGGTTTCTAGTCTGTTGATG
54473 GTTGATTGTTCAAACATCAGGCTGTGGGGTGGAGTAGTAGAGTCAACTTTTAAGATCTATGTTTT
1 GTTGATTGTTCAAACATCAGGCTGTGGGGTGGAGTAGTAGAGTCAACTTTTAAGATCTATGTTTT
54538 TGAGTGTGCTATATACAAATAAATGTTCTTTTATGTGCATTTTTTTGCACCTTGCTTTTGTTGCA
66 TGAGTGTGCTATATACAAATAAATGTTCTTTTATGTGCATTTTTTTGCACCTTGCTTTTGTTGCA
54603 TGAGTACATTTTTGGCAATTTACCTCTGGATTAGTACAGGGGTTTCTAGTCTGTTGATG
131 TGAGTACATTTTTGGCAATTTACCTCTGGATTAGTACAGGGGTTTCTAGTCTGTTGATG
54662 GT
1 GT
54664 GCTTTTCAAC
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
189 187 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (189 bp):
GTTGATTGTTCAAACATCAGGCTGTGGGGTGGAGTAGTAGAGTCAACTTTTAAGATCTATGTTTT
TGAGTGTGCTATATACAAATAAATGTTCTTTTATGTGCATTTTTTTGCACCTTGCTTTTGTTGCA
TGAGTACATTTTTGGCAATTTACCTCTGGATTAGTACAGGGGTTTCTAGTCTGTTGATG
Found at i:56494 original size:18 final size:18
Alignment explanation
Indices: 56461--56496 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56451 ATTACTAACC
*
56461 CATTAAATAAGGCCAGAA
1 CATTAAATAAAGCCAGAA
*
56479 CATTAAATAAATCCAGAA
1 CATTAAATAAAGCCAGAA
56497 ACACTATCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (18 bp):
CATTAAATAAAGCCAGAA
Found at i:62696 original size:15 final size:16
Alignment explanation
Indices: 62676--62708 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
62666 TAATGTATGT
62676 TTATGTCATAT-TATA
1 TTATGTCATATATATA
*
62691 TTATGTTATATATATA
1 TTATGTCATATATATA
62707 TT
1 TT
62709 GTGGGACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
TTATGTCATATATATA
Found at i:68673 original size:2 final size:2
Alignment explanation
Indices: 68666--68694 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
68656 TCCTTTTATG
68666 TA TA 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 TA TA T
68695 TAGATTTTTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73213 original size:21 final size:20
Alignment explanation
Indices: 73189--73229 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
73179 ATATATATTT
73189 TTATAATTTTTA-AATATTAAA
1 TTAT-ATTTTTATAAT-TTAAA
73210 TTATATTTTTATAATTTAAA
1 TTATATTTTTATAATTTAAA
73230 AAAACCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATTTTTATAATTTAAA
Found at i:73746 original size:22 final size:19
Alignment explanation
Indices: 73718--73759 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
73708 CAATTAAGCC
73718 TTTATTTTGTATTATTTTCAAA
1 TTTATTTT-TA-TATTTT-AAA
73740 TTTATTTTTATATTTTAAA
1 TTTATTTTTATATTTTAAA
73759 T
1 T
73760 ACATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 6 0.30
21 2 0.10
22 8 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTTTTATATTTTAAA
Found at i:75378 original size:18 final size:18
Alignment explanation
Indices: 75355--75398 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
75345 AAATTATTTT
* *
75355 TATAAATTTTATATAAAA
1 TATAAATTATAAATAAAA
*
75373 TATAAAATATAAATAAAA
1 TATAAATTATAAATAAAA
*
75391 AATAAATT
1 TATAAATT
75399 CTCCTAATTG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAAATTATAAATAAAA
Found at i:85260 original size:6 final size:6
Alignment explanation
Indices: 85251--85294 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
85241 TGATCTTGAG
85251 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GG
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GG
85295 ATTAAGTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (6 bp):
GGTTTT
Found at i:85303 original size:18 final size:18
Alignment explanation
Indices: 85264--85305 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
85254 TTTGGTTTTG
* **
85264 GTTTTGGTTTTGGTTTTG
1 GTTTTGGTTTTGGATTAA
85282 GTTTTGGTTTTGGATTAA
1 GTTTTGGTTTTGGATTAA
85300 GTTTTG
1 GTTTTG
85306 CCCTCATTTA
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:0.07, C:0.00, G:0.31, T:0.62
Consensus pattern (18 bp):
GTTTTGGTTTTGGATTAA
Found at i:85865 original size:13 final size:13
Alignment explanation
Indices: 85847--85880 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
85837 CCAATTTTGA
*
85847 ATTGGTTTGATCC
1 ATTGGTTCGATCC
85860 ATTGGTTCGATCC
1 ATTGGTTCGATCC
85873 ATTGGTTC
1 ATTGGTTC
85881 TCAGAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.18, G:0.24, T:0.44
Consensus pattern (13 bp):
ATTGGTTCGATCC
Found at i:94973 original size:16 final size:18
Alignment explanation
Indices: 94941--94980 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
94931 TGGTGAGATG
94941 CTGTTTTGGACTTGTGTA
1 CTGTTTTGGACTTGTGTA
*
94959 -TGTTTT-GATTTGTGTA
1 CTGTTTTGGACTTGTGTA
94975 CTGTTT
1 CTGTTT
94981 GCTGTAGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.10, C:0.07, G:0.25, T:0.57
Consensus pattern (18 bp):
CTGTTTTGGACTTGTGTA
Found at i:99159 original size:25 final size:24
Alignment explanation
Indices: 99102--99160 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
99092 AAAAGTAGGT
* *
99102 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
99125 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
99149 TATTTTAATAAT
1 TATATT-ATAAT
99161 AATTATGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:99171 original size:15 final size:14
Alignment explanation
Indices: 99152--99239 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 14
99142 TAATTCATAT
99152 TTTAATAATAATTA
1 TTTAATAATAATTA
*
99166 TGTTAAAAAT-ATTA
1 T-TTAATAATAATTA
* *
99180 TTAAATTATATATTA
1 TTTAATAATA-ATTA
* *
99195 TTTTATTAA-ATTGTA
1 -TTTAATAATAAT-TA
99210 TTTAATAATAATTA
1 TTTAATAATAATTA
*
99224 TCTTAAGATATAATTA
1 T-TTAATA-ATAATTA
99240 AATTGATTAT
Statistics
Matches: 55, Mismatches: 11, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 5 0.09
14 17 0.31
15 21 0.38
16 12 0.22
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (14 bp):
TTTAATAATAATTA
Found at i:99182 original size:58 final size:58
Alignment explanation
Indices: 99136--99279 Score: 159
Period size: 58 Copynumber: 2.5 Consensus size: 58
99126 ATATTATAAT
*
99136 TTTTACT-AATTCATATTTTAATAATAATTATGTTAAAAATATTATTAAATTATATATTA
1 TTTTACTAAATT-ATA-TTTAATAATAATTATCTTAAAAATATTATTAAATTATATATTA
* * * * *
99195 TTTTATTAAATTGTATTTAATAATAATTATCTT-AAGATATAATTAAATTGAT-TATTTT
1 TTTTACTAAATTATATTTAATAATAATTATCTTAAAAATATTATTAAATT-ATATA-TTA
* *
99253 TTTTATTAAATTATATTTAATGATAAT
1 TTTTACTAAATTATATTTAATAATAAT
99280 CTTATTAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
57 16 0.22
58 46 0.62
59 8 0.11
60 4 0.05
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (58 bp):
TTTTACTAAATTATATTTAATAATAATTATCTTAAAAATATTATTAAATTATATATTA
Found at i:99472 original size:16 final size:16
Alignment explanation
Indices: 99451--99505 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
99441 TGAATTATTG
99451 ATTACAGTCCTATTCC
1 ATTACAGTCCTATTCC
*
99467 ATTACAG-CTTTATTCC
1 ATTACAGTC-CTATTCC
* *
99483 ATTACACTTCTATTCC
1 ATTACAGTCCTATTCC
99499 ATTACAG
1 ATTACAG
99506 CGAACCAAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.27, C:0.27, G:0.05, T:0.40
Consensus pattern (16 bp):
ATTACAGTCCTATTCC
Found at i:107538 original size:21 final size:23
Alignment explanation
Indices: 107498--107539 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
107488 AAAAAAAGTC
107498 AAATTTGATTATTATCTTTAAAA
1 AAATTTGATTATTATCTTTAAAA
*
107521 AAATTTG-TTGTT-TCTTTAA
1 AAATTTGATTATTATCTTTAA
107540 TATTAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (23 bp):
AAATTTGATTATTATCTTTAAAA
Found at i:107635 original size:5 final size:6
Alignment explanation
Indices: 107617--107651 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
107607 AAGCTAAATT
107617 TTTTTAA TTTTTA -TTTTA TTTTTA TTTTTA TTTTT
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
107652 TAAAATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:107643 original size:17 final size:18
Alignment explanation
Indices: 107617--107650 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
107607 AAGCTAAATT
107617 TTTTTAATTTTTATTTTA
1 TTTTTAATTTTTATTTTA
107635 TTTTT-ATTTTTATTTT
1 TTTTTAATTTTTATTTT
107651 TTAAAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTAATTTTTATTTTA
Found at i:107660 original size:18 final size:19
Alignment explanation
Indices: 107639--107680 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
107629 ATTTTATTTT
*
107639 TATTTT-TATTTTTTAAAA
1 TATTTTATAATTTTTAAAA
*
107657 TATTTTATAATTTTTAAAT
1 TATTTTATAATTTTTAAAA
107676 TATTT
1 TATTT
107681 GTTGATCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTATAATTTTTAAAA
Found at i:109129 original size:22 final size:22
Alignment explanation
Indices: 109087--109129 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
109077 ATGATAAAAA
*
109087 AAATAATTTTAAATATATTAAT
1 AAATAATTTAAAATATATTAAT
109109 AAATAATATTAAAATAT-TTAA
1 AAATAAT-TTAAAATATATTAA
109130 ATCAAAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
AAATAATTTAAAATATATTAAT
Found at i:109462 original size:16 final size:18
Alignment explanation
Indices: 109423--109456 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
109413 TAAGTTTATA
109423 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
109440 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
109457 AATTTAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:109610 original size:15 final size:16
Alignment explanation
Indices: 109590--109629 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
109580 ATAAATATAA
109590 AAATATAAAAAT-ATT
1 AAATATAAAAATAATT
*
109605 AAATATTAAAATAATT
1 AAATATAAAAATAATT
*
109621 TAATATAAA
1 AAATATAAA
109630 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATAAAAATAATT
Done.