Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011802.1 Kokia drynarioides strain JFW-HI SEQ_126797, 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: 48973
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:2222 original size:2 final size:2
Alignment explanation
Indices: 2215--2239 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2205 CTTTGATCAT
2215 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2240 TATATATCAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5242 original size:17 final size:18
Alignment explanation
Indices: 5220--5255 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5210 TAAATGAGTT
5220 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
5237 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
5255 A
1 A
5256 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:9070 original size:30 final size:30
Alignment explanation
Indices: 9036--9110 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
9026 CATTTAACAC
*
9036 AACAGTCACTCAACTT-T-GAAAATGTGACAA
1 AACAGTCACT-AACTTATCGAAAA-ATGACAA
*
9066 AACAGTCACTAATGTTATCGAAAAATGACAA
1 AACAGTCACTAA-CTTATCGAAAAATGACAA
9097 AACAGTCACTAACT
1 AACAGTCACTAACT
9111 CAACCCCCTC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
29 2 0.05
30 13 0.33
31 19 0.49
32 5 0.13
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.23
Consensus pattern (30 bp):
AACAGTCACTAACTTATCGAAAAATGACAA
Found at i:10059 original size:3 final size:3
Alignment explanation
Indices: 10045--10084 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
10035 AGACCCGAAC
*
10045 CTT CTC CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT -TT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
10085 ATTTACTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:11517 original size:24 final size:26
Alignment explanation
Indices: 11489--11537 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
11479 CAAGTCCATG
*
11489 TTAACAATTAA-T-TAATTTTTAAAA
1 TTAACAAATAATTATAATTTTTAAAA
11513 TTAACAAATAATTATAATTTTTAAA
1 TTAACAAATAATTATAATTTTTAAA
11538 TAATCTGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
26 11 0.50
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAACAAATAATTATAATTTTTAAAA
Found at i:17584 original size:16 final size:17
Alignment explanation
Indices: 17555--17587 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
17545 TTTTATGGAC
17555 AATTATTATTCTTATTA
1 AATTATTATTCTTATTA
17572 AATTATT-TTCTTATTA
1 AATTATTATTCTTATTA
17588 CCATTGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTATTATTCTTATTA
Found at i:17902 original size:31 final size:30
Alignment explanation
Indices: 17864--17931 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 30
17854 TACAATTTGA
17864 TCATTGAATTATTCGAAA-GTTTTCATTTAAG
1 TCATTGAATTATT-GAAAGGTTTT-ATTTAAG
*
17895 TCATTGAATTATTTAAATGGTTTTATTTAAG
1 TCATTGAATTATTGAAA-GGTTTTATTTAAG
17926 TCATTG
1 TCATTG
17932 GATTGTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.09
31 26 0.76
32 5 0.15
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.49
Consensus pattern (30 bp):
TCATTGAATTATTGAAAGGTTTTATTTAAG
Found at i:17910 original size:169 final size:170
Alignment explanation
Indices: 17628--18077 Score: 577
Period size: 169 Copynumber: 2.6 Consensus size: 170
17618 AATAAATTAT
* * * * * *
17628 ACCATTTATCACTAAATTTTAGGTAAGTTTTTGTTTTGATCATTTAATTAAAAAATTTACAATTT
1 ACCATTTGTCACTAAATTATAGGTAAGTTTTCGTTTTGGTCATTTAACTAAAAAAATTACAATTT
* * * *
17693 GATCATTAAAATATTCTAAGGTTTTCATTTAAGTCACTGAACTATTTAAATGATTTTATTTAAGT
66 GATCATT-AATTATTCGAAAGTTTTCATTTAAGTCATTGAACTATTTAAATGATTTTATTTAAGT
17758 CACTAGG-CTGTTAA-GTTTTTTAAAAAAAAG-GTAAACTAC
130 CA-TAGGACTGTTAATGTTTTTTAAAAAAAAGAGTAAACTAC
* * * *
17797 ACCATTTGTTACTAAATTATAGGTAAATTTTCATTTTGGTCACTTAACTAAAAAAATTACAATTT
1 ACCATTTGTCACTAAATTATAGGTAAGTTTTCGTTTTGGTCATTTAACTAAAAAAATTACAATTT
* *
17862 GATCATTGAATTATTCGAAAGTTTTCATTTAAGTCATTGAATTATTTAAATGGTTTTATTTAAGT
66 GATCATT-AATTATTCGAAAGTTTTCATTTAAGTCATTGAACTATTTAAATGATTTTATTTAAGT
* * * ** *
17927 CATTGGATTGTTAATTTTTTTTTTAAATAAGAGTAAACTAC
130 CATAGGACTGTTAATGTTTTTTAAAAAAAAGAGTAAACTAC
* * *
17968 ACAATTTGTCACTAAATTATGGGTAAGTTTTCGTTTTGGTCATTTAACTATAAAAAGTTACAATT
1 ACCATTTGTCACTAAATTATAGGTAAGTTTTCGTTTTGGTCATTTAACTA-AAAAAATTACAATT
* *
18033 TGGTCATT--TCTATTCGAAAGTTTTCATTTAAGTTATTGAACTATT
65 TGATCATTAAT-TATTCGAAAGTTTTCATTTAAGTCATTGAACTATT
18078 CAAAGGTTTT
Statistics
Matches: 243, Mismatches: 33, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
168 3 0.01
169 122 0.50
170 45 0.19
171 53 0.22
172 20 0.08
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (170 bp):
ACCATTTGTCACTAAATTATAGGTAAGTTTTCGTTTTGGTCATTTAACTAAAAAAATTACAATTT
GATCATTAATTATTCGAAAGTTTTCATTTAAGTCATTGAACTATTTAAATGATTTTATTTAAGTC
ATAGGACTGTTAATGTTTTTTAAAAAAAAGAGTAAACTAC
Found at i:23807 original size:459 final size:450
Alignment explanation
Indices: 22929--23821 Score: 1222
Period size: 459 Copynumber: 1.9 Consensus size: 450
22919 CCTATAGTAT
* * *
22929 CATGTCTTTTCATATAAATATCATAGTTAGGATTTTATATTTGTCTACCTAGTATATTGTATAAT
1 CATGTCTTTTCATATAAATATCATAGTTAGGACTTTATATCTGTCTACCTAGTATATTATATAAT
* * * * * *
22994 AGATTATAATATGTTATACGTTTTTGTATTTTTTTATACATTTGAAATTTAATCTTTTTATATTT
66 AGATTATAATATGCTACAAGTCTTTGTACTTTTTTATACATTTAAAATTTAATCTTTTTATATTT
*
23059 CGATTTTAAAAATTCAAGTACAATTGTTAAAATTATTCTATTCAATATGTTGGTGTCAAGGGTGG
131 CGATTTTAAAAATTCAAGTACAATTGTTAAAATTATTCTATTCAATATGTTGGTGTCAAAGGTGG
* * *
23124 AAAGAGAGAGAGAAGGGGGGGGGGGGCAGGCAGTGGCCTTAACCACTCCTAAAACATGAAATTGT
196 -AAGAGAGAGAGAA--------GGGCCAGGCAGTGGCCTTAACCACTCCCAAAACATGAAATTCT
*
23189 TTATATAATCCCTAGAAAATCACAAGTTAGTATAATGGTAAATTTGCACTTTAACTCCCCAAAAT
252 TTATATAATCCCTAAAAAATCACAAGTTAGTATAATGGTAAATTTGCACTTTAACTCCCCAAAAT
** * * * *
23254 TTTTATTTTTATTTTGGCCCCTAAATCAATTTTCTAACTTCGATCCTAGTTAGTGTGAGATTTTG
317 TTTTATTCATATTTTGGCCCCTAAATCAATTTCCTAACTTCGATCCTAGTTAATGTAACATTTTG
23319 AAATGATAAAAATATTCATCTGATAATCATGTAATAATAAAAATGACATTATAATGGACTTCAAC
382 AAATGATAAAAATATTCATCTGATAATCATGTAATAATAAAAATGACATTATAATGGACTTCAAC
23384 TTAA
447 TTAA
*
23388 CATGTCTTTTCATATAAATATCATAGTTAGGACTTTATATCTGTCTACCTAGTATATTATATATT
1 CATGTCTTTTCATATAAATATCATAGTTAGGACTTTATATCTGTCTACCTAGTATATTATATAAT
* *
23453 AGATTATAATATGCTACAAGTCTTTGTACTTTTTTATATATTTAAAATTTAAT-TTTTTATTTTT
66 AGATTATAATATGCTACAAGTCTTTGTACTTTTTTATACATTTAAAATTTAATCTTTTTATATTT
*
23517 CGATTTTAAAAATTCAAGTATAATTGTTAAAATCCTTAAAATTATTCTATTC-ATATGTTGGTGT
131 CGATTTTAAAAATTCAAGTACAATTG---------TTAAAATTATTCTATTCAATATGTTGGTGT
* *
23581 CAAAGGTGG-AGAGAGAGAGAA-GGCCAGGCAGTGGCCTTGACCACTCCCAAAACATGAATTTCT
187 CAAAGGTGGAAGAGAGAGAGAAGGGCCAGGCAGTGGCCTTAACCACTCCCAAAACATGAAATTCT
* *
23644 TTATATAATCTCTAAAAAATCACAAGTTAGTATAATGGTAAATTTGCACTTTAACTCCTC-AAAT
252 TTATATAATCCCTAAAAAATCACAAGTTAGTATAATGGTAAATTTGCACTTTAACTCCCCAAAAT
* * *
23708 TTTTATTCATATTTTGGCCCCTAAATTAATTTCCTAGCTTCGTTTCGTTCCTAGTTAATGTAACA
317 TTTTATTCATATTTTGGCCCCTAAATCAATTTCCTA---AC--TTCGATCCTAGTTAATGTAACA
* * *
23773 TTTTGAAATGATGAAAATGTTCA-CTTAGTAATCATGTAATAATAAAAAT
377 TTTTGAAATGATAAAAATATTCATCTGA-TAATCATGTAATAATAAAAAT
23822 AATGTTGTAA
Statistics
Matches: 385, Mismatches: 34, Indels: 30
0.86 0.08 0.07
Matches are distributed among these distances:
454 36 0.09
455 94 0.24
457 1 0.00
458 38 0.10
459 167 0.43
464 12 0.03
466 20 0.05
467 17 0.04
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40
Consensus pattern (450 bp):
CATGTCTTTTCATATAAATATCATAGTTAGGACTTTATATCTGTCTACCTAGTATATTATATAAT
AGATTATAATATGCTACAAGTCTTTGTACTTTTTTATACATTTAAAATTTAATCTTTTTATATTT
CGATTTTAAAAATTCAAGTACAATTGTTAAAATTATTCTATTCAATATGTTGGTGTCAAAGGTGG
AAGAGAGAGAGAAGGGCCAGGCAGTGGCCTTAACCACTCCCAAAACATGAAATTCTTTATATAAT
CCCTAAAAAATCACAAGTTAGTATAATGGTAAATTTGCACTTTAACTCCCCAAAATTTTTATTCA
TATTTTGGCCCCTAAATCAATTTCCTAACTTCGATCCTAGTTAATGTAACATTTTGAAATGATAA
AAATATTCATCTGATAATCATGTAATAATAAAAATGACATTATAATGGACTTCAACTTAA
Found at i:24673 original size:29 final size:32
Alignment explanation
Indices: 24635--24695 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 32
24625 TATGAACAAT
* *
24635 TGGACCTAAATTTTTAA-AT-CTAAAAGTAAA
1 TGGACCTAAATTTTGAATATACGAAAAGTAAA
24665 TGGA-CTAAATTTTGAATATACGAAAAGTAAA
1 TGGACCTAAATTTTGAATATACGAAAAGTAAA
24696 AAGAGTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 11 0.41
30 6 0.22
31 10 0.37
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (32 bp):
TGGACCTAAATTTTGAATATACGAAAAGTAAA
Found at i:26860 original size:18 final size:19
Alignment explanation
Indices: 26839--26875 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26829 TTTTAAAAAA
26839 TATAAAT-TTTAGAATTTT
1 TATAAATATTTAGAATTTT
*
26857 TATAAATATTTTGAATTTT
1 TATAAATATTTAGAATTTT
26876 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTAGAATTTT
Found at i:26902 original size:20 final size:19
Alignment explanation
Indices: 26844--26915 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
26834 AAAAATATAA
*
26844 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAAAAATT
26864 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
26883 ATTTTGGATTTCTGAAAATT
1 ATTTTGAATTT-TAAAAATT
26903 ATTTTGTAATTTT
1 ATTTTG-AATTTT
26916 TTTAGAGAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.18
19 14 0.31
20 19 0.42
21 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:28000 original size:11 final size:12
Alignment explanation
Indices: 27979--28071 Score: 67
Period size: 11 Copynumber: 8.3 Consensus size: 12
27969 GATTTATTTC
*
27979 TAAAATTAAATT
1 TAAATTTAAATT
*
27991 T-ACTTTAAATT
1 TAAATTTAAATT
28002 TAAATTTAAA-T
1 TAAATTTAAATT
*
28013 T-AATTT--TTT
1 TAAATTTAAATT
28022 TAAATTTAAATT
1 TAAATTTAAATT
*
28034 T-AGTTTAAATT
1 TAAATTTAAATT
*
28045 TGAAA--TAATTT
1 T-AAATTTAAATT
*
28056 TAAACTTAAATT
1 TAAATTTAAATT
28068 TAAA
1 TAAA
28072 ATCAATTACA
Statistics
Matches: 63, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.03
10 13 0.21
11 27 0.43
12 20 0.32
13 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:28003 original size:6 final size:6
Alignment explanation
Indices: 27979--28071 Score: 67
Period size: 6 Copynumber: 16.7 Consensus size: 6
27969 GATTTATTTC
* * *
27979 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAA-T T-AATT T--TTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
28022 TAAATT TAAATT T-AGTT TAAATT TGAAA-- TAATTT TAAACT TAAATT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT
28068 TAAA
1 TAAA
28072 ATCAATTACA
Statistics
Matches: 68, Mismatches: 11, Indels: 16
0.72 0.12 0.17
Matches are distributed among these distances:
4 7 0.10
5 13 0.19
6 45 0.66
7 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:28004 original size:17 final size:17
Alignment explanation
Indices: 27965--28069 Score: 75
Period size: 17 Copynumber: 6.6 Consensus size: 17
27955 TTAGATGGGT
*
27965 TTTAGATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
* *
27983 ATTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
28000 TTT-AA---A-TTTAAA
1 TTTAAATTTATTTTAAA
28012 -TT-AATTT-TTTTAAA
1 TTTAAATTTATTTTAAA
*
28026 TTTAAATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
28043 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
28060 CTTAAATTTA
1 TTTAAATTTA
28070 AAATCAATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
11 4 0.06
12 6 0.09
13 1 0.01
14 6 0.09
15 2 0.03
16 10 0.14
17 27 0.39
18 13 0.19
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28025 original size:37 final size:37
Alignment explanation
Indices: 27984--28056 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
27974 ATTTCTAAAA
*
27984 TTAAATTT-ACTTTAAATTTAAATTT-AAATTAATTTTT
1 TTAAATTTAAATTT-AATTTAAATTTGAAA-TAATTTTT
*
28021 TTAAATTTAAATTTAGTTTAAATTTGAAATAATTTT
1 TTAAATTTAAATTTAATTTAAATTTGAAATAATTTT
28057 AAACTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (37 bp):
TTAAATTTAAATTTAATTTAAATTTGAAATAATTTTT
Found at i:29606 original size:30 final size:29
Alignment explanation
Indices: 29475--29730 Score: 222
Period size: 29 Copynumber: 8.8 Consensus size: 29
29465 AAAAGTCCCT
* * *
29475 AAACTGTCCAAAAATTCTATTTTCACCCCCG
1 AAACT-TCCAAAAATCCCATTTTTA-CCCCG
* *
29506 -AACTTCCAAAAATCCCATTTTGACCCTG
1 AAACTTCCAAAAATCCCATTTTTACCCCG
* * *
29534 AAACTTCAAAAAATTCCATTTTTATCCTC-
1 AAACTTCCAAAAATCCCATTTTTA-CCCCG
* ** *
29563 AAAATTCTGAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCG
*
29593 AAACTTCCAAAAATTCCATTTTTACCCCTCG
1 AAACTTCCAAAAATCCCATTTTTA-CCC-CG
*
29624 -AACTTCTAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATCCCA-TTTTTACCCCG
* *
29653 -AACTTCCAAAAATTCCA-TTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCCG
* *
29680 AAAATTCCAAAAATCCCA--TTGACCCCG
1 AAACTTCCAAAAATCCCATTTTTACCCCG
29707 AAACTTCCAAAAATTCCC-TTTTTA
1 AAACTTCCAAAAA-TCCCATTTTTA
29731 AACCCGAATT
Statistics
Matches: 185, Mismatches: 29, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
27 28 0.15
28 23 0.12
29 80 0.43
30 46 0.25
31 8 0.04
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATCCCATTTTTACCCCG
Found at i:29610 original size:59 final size:57
Alignment explanation
Indices: 29475--29730 Score: 259
Period size: 59 Copynumber: 4.4 Consensus size: 57
29465 AAAAGTCCCT
* * * * * * *
29475 AAACTGTCCAAAAATTCTATTTTCACCCCCGAACTTCCAAAAATCCCATTTTGACCCTG
1 AAACT-TCCAAAAATTCCATTTTTA-CCTCAAAATTCTAAAAATCCCATTTTGACCCCG
* * * *
29534 AAACTTCAAAAAATTCCATTTTTATCCTCAAAATTCTGAAAATCCCATTTTTTACCTCG
1 AAACTTCCAAAAATTCCATTTTTA-CCTCAAAATTCTAAAAATCCCA-TTTTGACCCCG
* * *
29593 AAACTTCCAAAAATTCCATTTTTACCCCTCGAACTTCTAAAAATCCCATTTTTTACCCCG
1 AAACTTCCAAAAATTCCATTTTTA--CCTCAAAATTCTAAAAATCCCA-TTTTGACCCCG
* *
29653 -AACTTCCAAAAATTCCA-TTTTACCCCTAAAATTCCAAAAATCCCA--TTGACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCTC-AAAATTCTAAAAATCCCATTTTGACCCCG
*
29707 AAACTTCCAAAAATTCCCTTTTTA
1 AAACTTCCAAAAATTCCATTTTTA
29731 AACCCGAATT
Statistics
Matches: 168, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
54 8 0.05
55 16 0.10
56 8 0.05
57 15 0.09
58 38 0.23
59 53 0.32
60 30 0.18
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTACCTCAAAATTCTAAAAATCCCATTTTGACCCCG
Found at i:30166 original size:96 final size:96
Alignment explanation
Indices: 29996--30180 Score: 241
Period size: 96 Copynumber: 1.9 Consensus size: 96
29986 AAAACTTAAA
* **
29996 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGGAAACTTGCGCCTTAACTTACTAGGTGCAATT
1 AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAACTTGCGCCTTAACTTACTAGGTGCAACC
* *
30061 TTTCTTCAAATCGAAATAATCGAATACCCTT
66 TTGCATCAAATCGAAATAATCGAATACCCTT
* *
30092 AATCGAGGCAATGTT-TCTTTATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAATATTCT-TTTAT-TTCGAGTTTC-GAAAACTTGCGCCTTAACTTACTAGGTGCA
**
30154 ACCTTGCATCAAATCGGGATAATCGAA
63 ACCTTGCATCAAATCGAAATAATCGAA
30181 CATCCTTTTC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
95 4 0.05
96 68 0.88
97 5 0.06
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTTCGAAAACTTGCGCCTTAACTTACTAGGTGCAACC
TTGCATCAAATCGAAATAATCGAATACCCTT
Found at i:34829 original size:19 final size:19
Alignment explanation
Indices: 34807--34844 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
34797 ATTTTTTTAC
34807 AAAATTAT-TAAGATTTCTT
1 AAAATTATCTAA-ATTTCTT
*
34826 AAAATTTTCTAAATTTCTT
1 AAAATTATCTAAATTTCTT
34845 TGAAAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.50
Consensus pattern (19 bp):
AAAATTATCTAAATTTCTT
Found at i:37540 original size:51 final size:51
Alignment explanation
Indices: 37459--37561 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
37449 AAACATAGAC
*
37459 TAAGTCATCAAGTTGATCTAAAAGTACATACAATGAGAAAAAAGTATCATT
1 TAAGCCATCAAGTTGATCTAAAAGTACATACAATGAGAAAAAAGTATCATT
*
37510 TAAGCCATCAAGTTGATCTAAAAGTACATACAATGAGAACAAAGTATCATT
1 TAAGCCATCAAGTTGATCTAAAAGTACATACAATGAGAAAAAAGTATCATT
37561 T
1 T
37562 CTTATAATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (51 bp):
TAAGCCATCAAGTTGATCTAAAAGTACATACAATGAGAAAAAAGTATCATT
Found at i:41489 original size:29 final size:30
Alignment explanation
Indices: 41457--41515 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
41447 TATGGTTTAA
*
41457 TGTGCAATTGTATATATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
41486 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
41516 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:41725 original size:30 final size:31
Alignment explanation
Indices: 41655--41727 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
41645 ATGATTAAAT
* *
41655 CAAAATTAAAATTTCAAGTATACATTTGAAC
1 CAAAATTAAAGTTTCAAGTATACAATTGAAC
* * * *
41686 CATAATTAAAGTTTCATGTATATAATTGCA-
1 CAAAATTAAAGTTTCAAGTATACAATTGAAC
41716 CAAAATTAAAGT
1 CAAAATTAAAGT
41728 ACGTGTAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.34
Consensus pattern (31 bp):
CAAAATTAAAGTTTCAAGTATACAATTGAAC
Found at i:44350 original size:3 final size:3
Alignment explanation
Indices: 44342--44409 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
44332 TATCAAAGAA
44342 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44390 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
44410 AGGGGTCAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:44578 original size:30 final size:30
Alignment explanation
Indices: 44441--44619 Score: 136
Period size: 30 Copynumber: 6.1 Consensus size: 30
44431 GAAGAATTTG
* **
44441 GGGTTAAAATATAATTTTGAGAGAA-TTCGA
1 GGGTTAAAATATAATTTTGA-AAAAGTTTAA
* * * *
44471 GGGTTAAAATGTGATTTT-AGGAAAGTTT-G
1 GGGTTAAAATATAATTTTGA-AAAAGTTTAA
* * *
44500 GGGTCAAAATATAATTTTGGAAAAG-TGAA
1 GGGTTAAAATATAATTTTGAAAAAGTTTAA
*
44529 -GGTTAAAATGTAATTTTGAAAAAGTTTAA
1 GGGTTAAAATATAATTTTGAAAAAGTTTAA
* *
44558 GGGTTAAAATGTAATTTTGAAAAAGTATAA
1 GGGTTAAAATATAATTTTGAAAAAGTTTAA
* * * *
44588 TGGTCAAAATATGATTTTTG-AAAAGTTCAA
1 GGGTTAAAATAT-AATTTTGAAAAAGTTTAA
44618 GG
1 GG
44620 ACCTCTTTAT
Statistics
Matches: 118, Mismatches: 25, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
28 22 0.19
29 26 0.22
30 64 0.54
31 6 0.05
ACGTcount: A:0.41, C:0.02, G:0.23, T:0.34
Consensus pattern (30 bp):
GGGTTAAAATATAATTTTGAAAAAGTTTAA
Found at i:44583 original size:87 final size:88
Alignment explanation
Indices: 44442--44613 Score: 206
Period size: 87 Copynumber: 2.0 Consensus size: 88
44432 AAGAATTTGG
* * * * **
44442 GGTTAAAATATAATTTTGAGAGAATTCGAGGGTTAAAATGTGATTTTAGGAAAGT-TTGGGGTCA
1 GGTTAAAATATAATTTTGAGAAAATTCAAGGGTTAAAATGTAATTTTAGAAAAGTATAAGGGTCA
44506 AAATATAATTTTGGAAAAGTGAA
66 AAATATAATTTTGGAAAAGTGAA
* * *
44529 GGTTAAAATGTAATTTTGA-AAAAGTTTAAGGGTTAAAATGTAATTTT-GAAAAAGTATAATGGT
1 GGTTAAAATATAATTTTGAGAAAA-TTCAAGGGTTAAAATGTAATTTTAG-AAAAGTATAAGGGT
* *
44592 CAAAATATGATTTTTGAAAAGT
64 CAAAATATAATTTTGGAAAAGT
44614 TCAAGGACCT
Statistics
Matches: 71, Mismatches: 11, Indels: 5
0.82 0.13 0.06
Matches are distributed among these distances:
86 4 0.06
87 43 0.61
88 24 0.34
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.35
Consensus pattern (88 bp):
GGTTAAAATATAATTTTGAGAAAATTCAAGGGTTAAAATGTAATTTTAGAAAAGTATAAGGGTCA
AAATATAATTTTGGAAAAGTGAA
Found at i:46801 original size:201 final size:202
Alignment explanation
Indices: 46389--47050 Score: 790
Period size: 201 Copynumber: 3.2 Consensus size: 202
46379 TCATCTTTCA
** * ** * *
46389 GTTCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTATTTTTATCCACTTCTCTGTATC
1 GTTCACTTCTCTACATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATC
* * *
46454 TCATCTGGAAGATGGGTGTTTTGAAGTTTCATTCGTATTGAGTTTCACTTCATTTATTTGGTCTA
66 TCATCAGGAAGATGGG-G-TTTGAAGTCTCATTCGTATT-AG---C-C-TCATTGATTTGGTCTA
* * * *
46519 CTTCTTTGTATCTCATCAGGAAGAT-AACTG-CTTCATTGTTTTAATCTACTTCTTTGTGTCTCA
123 CTTCTTTGTATCTCATCAGGAAGATGAAC-GCCTT-ATTGTTTCAATCCACTTCTCTGTATCTCA
46582 TCAAGAAGACGGATTTG
186 TCAAGAAGACGGATTTG
* * *
46599 GTTCACTTCTCTACATCTCGTCAAGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTGTC
1 GTTCACTTCTCTACATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATC
*
46664 TCATCAGAAAGATGGGGTTTGAAGTCTCATTCGTATT-GCCTCATTGATTTGGTCTACTTCTTTG
66 TCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTAGCCTCATTGATTTGGTCTACTTCTTTG
* * * *
46728 TATCTCATCGGGAAGATGATCGCCTTATTGTTTCAATCCACTTCTCTGTATCTCATTAGGAAGAC
131 TATCTCATCAGGAAGATGAACGCCTTATTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGAC
*
46793 GAATTTG
196 GGATTTG
* * *
46800 GTTCACTTCTCTACATCTCGTCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTTTGAATC
1 GTTCACTTCTCTACATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATC
* * *
46865 TCATTAGGAAGAAGGGGTTTGAAGTCTCATTCATATTGAGCTTCGCCTCATTGATTTGGTCTACT
66 TCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATT-A-----GCCTCATTGATTTGGTCTACT
* * * * * * *
46930 TCTCTGTATCTCATCAAGAAGATGACCACCTCATTGTTTCAACCCACTTCTCTATATCTCATCAA
125 TCTTTGTATCTCATCAGGAAGATGAACGCCTTATTGTTTCAATCCACTTCTCTGTATCTCATCAA
46995 GAAGACGGATTTG
190 GAAGACGGATTTG
* ** * *
47008 GTCCACTTCTCTGTATCTCATTAGGAAGATGACCGCTTTATTG
1 GTTCACTTCTCTACATCTCATCAGGAAGATGACCACTTTATTG
47051 GTTCGGACGA
Statistics
Matches: 395, Mismatches: 48, Indels: 20
0.85 0.10 0.04
Matches are distributed among these distances:
201 173 0.44
202 6 0.02
203 1 0.00
206 1 0.00
208 144 0.36
209 1 0.00
210 69 0.17
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.39
Consensus pattern (202 bp):
GTTCACTTCTCTACATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATC
TCATCAGGAAGATGGGGTTTGAAGTCTCATTCGTATTAGCCTCATTGATTTGGTCTACTTCTTTG
TATCTCATCAGGAAGATGAACGCCTTATTGTTTCAATCCACTTCTCTGTATCTCATCAAGAAGAC
GGATTTG
Found at i:47118 original size:39 final size:39
Alignment explanation
Indices: 47059--47181 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
47049 TGGTTCGGAC
*
47059 GATTGCAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
1 GATTGCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* * * ***
47098 GATTGCAATCTACCCTATGATCAGGGTAAAAGATCAAAT
1 GATTGCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
* *
47137 GATGGCTGCAATTTGCCCTATGATCGAGGTAAGAGATTGGAT
1 GAT---TGCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
47179 GAT
1 GAT
47182 GATGGCTACA
Statistics
Matches: 66, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
39 35 0.53
42 31 0.47
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (39 bp):
GATTGCAATCTGCCCTATGATCGGGGTAAGAGATTGGAT
Found at i:47205 original size:45 final size:46
Alignment explanation
Indices: 47135--47222 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 46
47125 AAAAGATCAA
*
47135 ATGATGGCTGCAATTTGCCCTATGATCGA-GG-TAAGAGATTGGATG
1 ATGATGGCTACAATTTGCCCTATGAT-GAGGGATAAGAGATTGGATG
*
47180 ATGATGGCTACAATTTGTCCC-ATGATTAGGGATAAGAGATTGG
1 ATGATGGCTACAATTTG-CCCTATGATGAGGGATAAGAGATTGG
47223 TGTGTCCTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
44 1 0.03
45 23 0.61
46 14 0.37
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (46 bp):
ATGATGGCTACAATTTGCCCTATGATGAGGGATAAGAGATTGGATG
Found at i:47327 original size:41 final size:40
Alignment explanation
Indices: 47230--47610 Score: 357
Period size: 41 Copynumber: 9.3 Consensus size: 40
47220 TGGTGTGTCC
*
47230 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATAAGGGAATCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGAT---GGAATCT
* *
47273 TAAATTTGCCCCTCTTGATTAGGGGTAAAAGACTGGAATCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGA-TGGAATCT
* *
47314 TCAATCTGTCCCTCTTGATT----TTAAAAGATTGGAATCGCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGA-TGGAAT--CT
* *
47353 TCAATCTGTCCTTCTTGATTAGGGGTAAAAGATTGGAATCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGA-TGGAATCT
* * * **
47394 TCAATCTGTCTCTTTTGATTAAAGGTAAAAGATCGGAATCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGAT-GGAATCT
* * **
47435 TCAATCTG--CCTACATGATTAAGGGTAAAAGATCGG-ATGA
1 TCAATCTGCCCCT-CTTGATTAGGGGTAAAAGAT-GGAATCT
* *
47474 TCAATCTTCCCCTCTTGATTAGGGGTAAAAAACTGGAATCGCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGA-TGGAAT--CT
* *
47517 TCAATCTGCCCCCCTTGATTAGGGGTAAAAGATTGAAATCT
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGA-TGGAATCT
*
47558 TCAATCTACCCCTCTTGATTAGGGGTAAAAGATCGG-AT-T
1 TCAATCTGCCCCTCTTGATTAGGGGTAAAAGAT-GGAATCT
47597 ATCAATCTGCCCCT
1 -TCAATCTGCCCCT
47611 GTGACACCTT
Statistics
Matches: 285, Mismatches: 36, Indels: 37
0.80 0.10 0.10
Matches are distributed among these distances:
37 13 0.05
39 33 0.12
40 54 0.19
41 107 0.38
43 77 0.27
44 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (40 bp):
TCAATCTGCCCCTCTTGATTAGGGGTAAAAGATGGAATCT
Found at i:47374 original size:80 final size:80
Alignment explanation
Indices: 47285--47579 Score: 312
Period size: 80 Copynumber: 3.6 Consensus size: 80
47275 AATTTGCCCC
* *
47285 TCTTGATTAGGGGTAAAAGACTGGAATCTTCAATCTGTCCCTCTTGATT-TTAAAAGATTGGAAT
1 TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGTCCCTCTTGATTAGTAAAAGATTGGAAT
47349 CGCTTCAATCTGTCCT
66 CGCTTCAATCTG-CCT
* * *
47365 TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGTCTCTTTTGATTAAAGGTAAAAGATCGG
1 TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGTCCCTCTTGATT--A-GTAAAAGATTGG
47430 AAT--CTTCAATCTGCCT
63 AATCGCTTCAATCTGCCT
* * * * ** * *
47446 ACATGATTAAGGGTAAAAGATCGG-ATGATCAATCT-TCCCCTCTTGATTAGGGGTAAAAAACTG
1 TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGT-CCCTCTTGATTA---GTAAAAGATTG
*
47509 GAATCGCTTCAATCTGCCCC
62 GAATCGCTTCAATCTG-CCT
* * **
47529 CCTTGATTAGGGGTAAAAGATTGAAATCTTCAATCTACCCCTCTTGATTAG
1 TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGTCCCTCTTGATTAG
47580 GGGTAAAAGA
Statistics
Matches: 178, Mismatches: 25, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
78 1 0.01
79 1 0.01
80 77 0.43
81 24 0.13
82 20 0.11
83 21 0.12
84 34 0.19
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (80 bp):
TCTTGATTAGGGGTAAAAGATTGGAATCTTCAATCTGTCCCTCTTGATTAGTAAAAGATTGGAAT
CGCTTCAATCTGCCT
Found at i:48629 original size:18 final size:18
Alignment explanation
Indices: 48606--48644 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
48596 AAAAATCAAA
*
48606 TTTCACTTCAATTCT-ATT
1 TTTCACATC-ATTCTCATT
48624 TTTCACATCATTCTCATT
1 TTTCACATCATTCTCATT
48642 TTT
1 TTT
48645 TGTCTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTCACATCATTCTCATT
Done.