Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012687.1 Kokia drynarioides strain JFW-HI SEQ_127698, 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: 28474
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 81 characters in sequence are not A, C, G, or T
Found at i:2744 original size:23 final size:23
Alignment explanation
Indices: 2682--2784 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
2672 CACGCTAAAT
* * *
2682 AGAGAGTACACAAAGTACTAATT
1 AGAGAGCACACAAAGTGCTAATC
2705 AGAGAGCACACAAAGTGCTAATC
1 AGAGAGCACACAAAGTGCTAATC
* *
2728 AGAGAGCACACATAGTGCAAATAAC
1 AGAGAGCACACAAAGTGCTAAT--C
* *
2753 AGAGAGCACGAC-GAGTGCTAAAC
1 AGAGAGCAC-ACAAAGTGCTAATC
2776 AGAGAGCAC
1 AGAGAGCAC
2785 GAGATGTGCT
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
23 50 0.72
25 17 0.25
26 2 0.03
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (23 bp):
AGAGAGCACACAAAGTGCTAATC
Found at i:2785 original size:23 final size:23
Alignment explanation
Indices: 2675--2804 Score: 102
Period size: 23 Copynumber: 5.6 Consensus size: 23
2665 GAGAGCACAC
* * *
2675 GCTAAATAGAGAGTACACAAAGT
1 GCTAAACAGAGAGCACACAGAGT
* ** *
2698 ACTAATTAGAGAGCACACAAAGT
1 GCTAAACAGAGAGCACACAGAGT
* *
2721 GCTAATCAGAGAGCACACATAGT
1 GCTAAACAGAGAGCACACAGAGT
*
2744 GCAAATAACAGAGAGCACGAC-GAGT
1 GC-TA-AACAGAGAGCAC-ACAGAGT
*
2769 GCTAAACAGAGAGCAC-GAGATGT
1 GCTAAACAGAGAGCACACAGA-GT
*
2792 GCTAAATAGAGAG
1 GCTAAACAGAGAG
2805 TACGCTAGTG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
22 2 0.02
23 68 0.76
24 2 0.02
25 16 0.18
26 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (23 bp):
GCTAAACAGAGAGCACACAGAGT
Found at i:6066 original size:30 final size:28
Alignment explanation
Indices: 5976--6174 Score: 143
Period size: 29 Copynumber: 6.8 Consensus size: 28
5966 TCTGAAGTTG
* * *
5976 AAAATGTGATTTTTGGAAA-TTTGGAGGT
1 AAAATGT-AATTTTGGAAAGTTTAGAGGC
* *
6004 AAAATGGTAATTTTTGG-ATGTTTAGGGGC
1 AAAAT-GTAA-TTTTGGAAAGTTTAGAGGC
*
6033 AAAATGGTAATTTTGGAGAAGTTTCGAGGC
1 AAAAT-GTAATTTTGGA-AAGTTTAGAGGC
** * **
6063 AAAATGTAATTTTGGAAAAATTCGACGTT
1 AAAATGTAATTTTGGAAAGTTTAGA-GGC
* *
6092 AAAATGTAATTTTGGAATAGTTTAGGGGTT
1 AAAATGTAATTTTGGAA-AGTTTAGAGG-C
*
6122 AAAATGTAATTTTAGAAATGTTTAG-GGTC
1 AAAATGTAATTTTGGAAA-GTTTAGAGG-C
*
6151 AAAATGTAATTTTAGAGAAGTTTA
1 AAAATGTAATTTTGGA-AAGTTTA
6175 AGGGTTAAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 19
0.79 0.11 0.11
Matches are distributed among these distances:
28 20 0.14
29 79 0.56
30 43 0.30
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.37
Consensus pattern (28 bp):
AAAATGTAATTTTGGAAAGTTTAGAGGC
Found at i:6133 original size:59 final size:59
Alignment explanation
Indices: 6032--6222 Score: 192
Period size: 59 Copynumber: 3.2 Consensus size: 59
6022 TGTTTAGGGG
* * * *
6032 CAAAATGGTAATTTTGGAGAAGTTTCGAGG-CAAAATGTAATTTTGGAAAAATTCGA-CGT
1 CAAAAT-GTAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAATT-GAGCGT
* ** * *
6091 TAAAATGTAATTTTGGA-ATAGTTTAGGGGTTAAAATGTAATTTTAGAAATGTTTAGGGT
1 CAAAATGTAATTTTGGAGA-AGTTTAGGGGTTAAAATGTAATTTTAGAAAAATTGAGCGT
* * * *
6150 CAAAATGTAATTTTAGAGAAGTTTAAGGGTTAAAATGTGATTTTAGAAAAATTTG-GGGT
1 CAAAATGTAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAA-TTGAGCGT
*
6209 CAAAATATAATTTT
1 CAAAATGTAATTTT
6223 AAAATAAAAC
Statistics
Matches: 110, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
57 1 0.01
58 20 0.18
59 86 0.78
60 3 0.03
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (59 bp):
CAAAATGTAATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTAGAAAAATTGAGCGT
Found at i:6185 original size:30 final size:28
Alignment explanation
Indices: 6003--6223 Score: 156
Period size: 29 Copynumber: 7.5 Consensus size: 28
5993 AATTTGGAGG
* * * *
6003 TAAAATGGTAATTTTTGGATGTTTAGGGG
1 TAAAAT-GTAATTTTAGAAAGTTTAGGGT
* * *
6032 CAAAATGGTAATTTTGGAGAAGTTTCGAGG-
1 TAAAAT-GTAATTTTAGA-AAGTTTAG-GGT
* * ** * *
6062 CAAAATGTAATTTTGGAAAAATTCGACGT
1 TAAAATGTAATTTTAGAAAGTTTAG-GGT
*
6091 TAAAATGTAATTTTGGAATAGTTTAGGGGT
1 TAAAATGTAATTTTAGAA-AGTTTA-GGGT
6121 TAAAATGTAATTTTAGAAATGTTTAGGGT
1 TAAAATGTAATTTTAGAAA-GTTTAGGGT
*
6150 CAAAATGTAATTTTAGAGAAGTTTAAGGGT
1 TAAAATGTAATTTTAGA-AAGTTT-AGGGT
* * *
6180 TAAAATGTGATTTTAGAAAAATTTGGGGT
1 TAAAATGTAATTTTAG-AAAGTTTAGGGT
* *
6209 CAAAATATAATTTTA
1 TAAAATGTAATTTTA
6224 AAATAAAACA
Statistics
Matches: 161, Mismatches: 22, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.05
29 84 0.52
30 65 0.40
31 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (28 bp):
TAAAATGTAATTTTAGAAAGTTTAGGGT
Found at i:6223 original size:59 final size:59
Alignment explanation
Indices: 6063--6228 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 59
6053 GTTTCGAGGC
* * ** * * *
6063 AAAATGTAATTTTGGAAAAATTCGACGTTAAAATGTAATTTTGGAATAGTTTAGGGGTT
1 AAAATGTAATTTTAGAAAAATTTGGGGTCAAAATGTAATTTTAGAATAGTTTAAGGGTT
** *
6122 AAAATGTAATTTTAGAAATGTTTAGGGTCAAAATGTAATTTTAGAGA-AGTTTAAGGGTT
1 AAAATGTAATTTTAGAAAAATTTGGGGTCAAAATGTAATTTTAGA-ATAGTTTAAGGGTT
* * *
6181 AAAATGTGATTTTAGAAAAATTTGGGGTCAAAATATAATTTTAAAATA
1 AAAATGTAATTTTAGAAAAATTTGGGGTCAAAATGTAATTTTAGAATA
6229 AAACAGGGAC
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
58 1 0.01
59 87 0.98
60 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTAGAAAAATTTGGGGTCAAAATGTAATTTTAGAATAGTTTAAGGGTT
Found at i:8462 original size:20 final size:20
Alignment explanation
Indices: 8406--8462 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
8396 GATGCAAAAC
8406 AGGGGCACCA-AAGTGCATAT
1 AGGGGCA-CAGAAGTGCATAT
* *
8426 AAGGGCACTGAAGTGCATAT
1 AGGGGCACAGAAGTGCATAT
*
8446 AGGGGCACAGAAATGCA
1 AGGGGCACAGAAGTGCA
8463 AACAAGGGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.37, C:0.18, G:0.32, T:0.14
Consensus pattern (20 bp):
AGGGGCACAGAAGTGCATAT
Found at i:10817 original size:24 final size:23
Alignment explanation
Indices: 10789--10850 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
10779 AACAAATTAA
*
10789 AAAAACTCAAATAAAAACTTAGTAG
1 AAAAACTC-AAT-AAAACTTAATAG
*
10814 AAAAATTCAATAAAACTTAATAG
1 AAAAACTCAATAAAACTTAATAG
*
10837 AAAAATTCAATAAA
1 AAAAACTCAATAAA
10851 TTCAAAGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 25 0.71
24 3 0.09
25 7 0.20
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.23
Consensus pattern (23 bp):
AAAAACTCAATAAAACTTAATAG
Found at i:10832 original size:23 final size:23
Alignment explanation
Indices: 10802--10850 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
10792 AACTCAAATA
*
10802 AAAACTTAGTAGAAAAATTCAAT
1 AAAACTTAATAGAAAAATTCAAT
10825 AAAACTTAATAGAAAAATTCAAT
1 AAAACTTAATAGAAAAATTCAAT
10848 AAA
1 AAA
10851 TTCAAAGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.24
Consensus pattern (23 bp):
AAAACTTAATAGAAAAATTCAAT
Found at i:11137 original size:25 final size:24
Alignment explanation
Indices: 11109--11170 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
11099 AACAAATTAA
* *
11109 AAAAACTCAAATAAAAACTTAGTAG
1 AAAAATTC-AATAAAAACTTAATAG
*
11134 AAAAATTCAAT-TAAACTTAATAG
1 AAAAATTCAATAAAAACTTAATAG
11157 AAAAATTCAATAAA
1 AAAAATTCAATAAA
11171 TTCAAAGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 21 0.66
24 4 0.12
25 7 0.22
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (24 bp):
AAAAATTCAATAAAAACTTAATAG
Found at i:13125 original size:269 final size:268
Alignment explanation
Indices: 12640--13451 Score: 1437
Period size: 268 Copynumber: 3.0 Consensus size: 268
12630 ATAACTCAGA
* * *
12640 AGATAAAATAGACCAGAGAACTGGACATGTATAAACTAATTTTGAGACAGAATATGGATCAAACC
1 AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
12705 ATAACTAAAAAATCTCATTCCTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
66 ATAACTAAAAAATCTCATT-CTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
12770 AAGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAA
130 AAGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAA
12835 AACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTACTTTTAAGGATCAGACCTTTTA
195 AACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTACTTTTAAGGATCAGACCTTTTA
*
12900 TCTTATATG
260 TCCTATATG
12909 AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
1 AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
*
12974 ATAACTAAAATATCTCATTCGTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
66 ATAACTAAAAAATCTCATTC-TCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
13039 AAGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAA
130 AAGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAA
13104 AACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTAC-TTTAAGGATCAGACCTTTTA
195 AACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTACTTTTAAGGATCAGACCTTTTA
13168 TCCTATATG
260 TCCTATATG
13177 AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
1 AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
13242 ATAACTAAAAAATCTCATTACTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
66 ATAACTAAAAAATCTCATT-CTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGA
* * * *
13307 AAGAAAAGCGCATCATATTTATGACAACTTGGAAAATTTTCAATCACTATAGAACCACGACTGAA
130 AAGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAA
* **
13372 AACCCAATCAATGTGAAGGAAACCTTTGTTATCTGTATGATTACTATAAATATCCGGATCAGACC
195 AACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTACT-T---T-TAAGGATCAGACC
13437 TTTTATCCTATATG
255 TTTTATCCTATATG
13451 A
1 A
13452 TTAAAAAAAC
Statistics
Matches: 522, Mismatches: 13, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
268 260 0.50
269 234 0.45
270 1 0.00
273 1 0.00
274 26 0.05
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (268 bp):
AGATAGAATAGACCAGAGAACTAGACATGTATAAACTAATTTTGAGACAGAATATGGACCAAACC
ATAACTAAAAAATCTCATTCTCAATGCTCAAGTAGAAACTTAAAATTTAAGACCAAAAATAAGAA
AGAAAAGTGCATCATATTAATGACAACTAGGAAAATTTTCAATCACTATAGAACCAAGACTGAAA
ACCCAATCAATGTGAAGGAAACCTTTATTATCTGTATGATTACTTTTAAGGATCAGACCTTTTAT
CCTATATG
Found at i:18898 original size:40 final size:41
Alignment explanation
Indices: 18838--18950 Score: 133
Period size: 40 Copynumber: 2.8 Consensus size: 41
18828 ATCACCGGCT
*
18838 AAAGCCTACTAAGCCCTAGCTTGAAA-GACATCATCGACTC
1 AAAGCCTACTAAGCCGTAGCTTGAAATGACATCATCGACTC
* * * * *
18878 GAAGCCTGCTAAACCGTAGCTT-AAATTACATCATCGGCTC
1 AAAGCCTACTAAGCCGTAGCTTGAAATGACATCATCGACTC
* *
18918 AAAGCCTACTAAGTCGTAGCTTG-AATTACATCA
1 AAAGCCTACTAAGCCGTAGCTTGAAATGACATCA
18951 CTGACCCATA
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
39 3 0.05
40 58 0.95
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (41 bp):
AAAGCCTACTAAGCCGTAGCTTGAAATGACATCATCGACTC
Found at i:18964 original size:40 final size:39
Alignment explanation
Indices: 18839--18964 Score: 119
Period size: 40 Copynumber: 3.2 Consensus size: 39
18829 TCACCGGCTA
* ** *
18839 AAGCCTACTAAGCCCTAGCTTGAAAGACATCATCGACTCG
1 AAGCCTACTAAGCCGTAGCTTGAATTACATCATCGAC-CC
* * * * *
18879 AAGCCTGCTAAACCGTAGCTTAAATTACATCATCGGCTCA
1 AAGCCTACTAAGCCGTAGCTTGAATTACATCATCGAC-CC
*
18919 AAGCCTACTAAGTCGTAGCTTGAATTACATCA-CTGACCC
1 AAGCCTACTAAGCCGTAGCTTGAATTACATCATC-GACCC
18958 ATAGCCT
1 A-AGCCT
18965 GCTAGGCTCA
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
39 3 0.04
40 67 0.96
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.24
Consensus pattern (39 bp):
AAGCCTACTAAGCCGTAGCTTGAATTACATCATCGACCC
Found at i:21813 original size:29 final size:29
Alignment explanation
Indices: 21780--21983 Score: 187
Period size: 29 Copynumber: 7.0 Consensus size: 29
21770 TTTGCCCATT
*
21780 AGCCCTCAACTTTAGTAAAATTGCAATAA
1 AGCCCTCAACTTTAGTAAAATTACAATAA
* * *
21809 AGCCCTTAACTTTAGTAAAATTGCATTAA
1 AGCCCTCAACTTTAGTAAAATTACAATAA
* *
21838 TGCTCTCAACTTTAGTAAAATTACAATAA
1 AGCCCTCAACTTTAGTAAAATTACAATAA
* * * * *
21867 CGCCCTCAACTTTAATAAAATTATAGTGA
1 AGCCCTCAACTTTAGTAAAATTACAATAA
* *
21896 CG-CCTCAACTTTAGTAAAATTAAAATAA
1 AGCCCTCAACTTTAGTAAAATTACAATAA
**
21924 TA-CCCTCAAACTTTAGTAAAATTGTAATAA
1 -AGCCCTC-AACTTTAGTAAAATTACAATAA
* * * * *
21954 AGCTCTAAAACTTTGGAAAAACTACAATAA
1 AGCCCT-CAACTTTAGTAAAATTACAATAA
21984 TACCCCCAAA
Statistics
Matches: 143, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.15
29 81 0.57
30 40 0.28
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (29 bp):
AGCCCTCAACTTTAGTAAAATTACAATAA
Found at i:21878 original size:58 final size:58
Alignment explanation
Indices: 21784--21983 Score: 215
Period size: 58 Copynumber: 3.4 Consensus size: 58
21774 CCCATTAGCC
* * * * *
21784 CTCAACTTTAGTAAAATTGCAATAAAGCCCTTAACTTTAGTAAAATTGCATTAATGCT
1 CTCAACTTTAGTAAAATTACAATAAAGCCCTCAACTTTAGTAAAATTGTAATAAAGCT
* * * * * *
21842 CTCAACTTTAGTAAAATTACAATAACGCCCTCAACTTTAATAAAATTATAGTGACGC-
1 CTCAACTTTAGTAAAATTACAATAAAGCCCTCAACTTTAGTAAAATTGTAATAAAGCT
*
21899 CTCAACTTTAGTAAAATTAAAATAATA-CCCTCAAACTTTAGTAAAATTGTAATAAAGCT
1 CTCAACTTTAGTAAAATTACAATAA-AGCCCTC-AACTTTAGTAAAATTGTAATAAAGCT
* * * *
21958 CTAAAACTTTGGAAAAACTACAATAA
1 CT-CAACTTTAGTAAAATTACAATAA
21984 TACCCCCAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
57 29 0.25
58 68 0.58
59 2 0.02
60 18 0.15
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (58 bp):
CTCAACTTTAGTAAAATTACAATAAAGCCCTCAACTTTAGTAAAATTGTAATAAAGCT
Found at i:21913 original size:28 final size:29
Alignment explanation
Indices: 21781--21946 Score: 190
Period size: 29 Copynumber: 5.7 Consensus size: 29
21771 TTGCCCATTA
* *
21781 GCCCTCAACTTTAGTAAAATTGCAATAAA
1 GCCCTCAACTTTAGTAAAATTACAATAAC
* * * *
21810 GCCCTTAACTTTAGTAAAATTGCATTAAT
1 GCCCTCAACTTTAGTAAAATTACAATAAC
*
21839 GCTCTCAACTTTAGTAAAATTACAATAAC
1 GCCCTCAACTTTAGTAAAATTACAATAAC
* * * *
21868 GCCCTCAACTTTAATAAAATTATAGTGAC
1 GCCCTCAACTTTAGTAAAATTACAATAAC
* *
21897 G-CCTCAACTTTAGTAAAATTAAAATAAT
1 GCCCTCAACTTTAGTAAAATTACAATAAC
*
21925 ACCCTCAAACTTTAGTAAAATT
1 GCCCTC-AACTTTAGTAAAATT
21947 GTAATAAAGC
Statistics
Matches: 116, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
28 22 0.19
29 79 0.68
30 15 0.13
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (29 bp):
GCCCTCAACTTTAGTAAAATTACAATAAC
Found at i:25602 original size:47 final size:46
Alignment explanation
Indices: 25546--25708 Score: 173
Period size: 47 Copynumber: 3.5 Consensus size: 46
25536 TACTATACTA
* * * *
25546 TATCAGGCCTTGTGCTTAACAGGCTTTAATGCCGGTGTATTGTACCG
1 TATCGGGCCTTGTGCCTAGCAGG-TTTAATGTCGGTGTATTGTACCG
* * * *
25593 TATTGGGCCTTGTGCCTAGTAGGATTTAATGTCGGTGTACTGTACTG
1 TATCGGGCCTTGTGCCTAGCAGG-TTTAATGTCGGTGTATTGTACCG
* * **
25640 TATCGTGCCTTATGCCTAGCAGGTTTAATGTCGAAGTATTGTACCG
1 TATCGGGCCTTGTGCCTAGCAGGTTTAATGTCGGTGTATTGTACCG
* * *
25686 TGTCGGGTCTTATGCCTAGCAGG
1 TATCGGGCCTTGTGCCTAGCAGG
25709 CTTCATGCTA
Statistics
Matches: 96, Mismatches: 20, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
46 39 0.41
47 57 0.59
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (46 bp):
TATCGGGCCTTGTGCCTAGCAGGTTTAATGTCGGTGTATTGTACCG
Found at i:25763 original size:40 final size:39
Alignment explanation
Indices: 25688--25803 Score: 108
Period size: 40 Copynumber: 2.9 Consensus size: 39
25678 TTGTACCGTG
* **
25688 TCGGGTCTT-ATGCCTAGCAGGCTTCATGCTAGTGTATCTA
1 TCGGG-CTTAATGCCTAGCAGGCTTCGTGCCGGTGTAT-TA
* *
25728 TCGGGCTTAATGCCTAGTAAGCTTCGTGCCGGTGTAATTA
1 TCGGGCTTAATGCCTAGCAGGCTTCGTGCCGGTGT-ATTA
* * * * *
25768 ACGAGCTTAAAGACTAGCAGGCTTCGAGCCGGTGTA
1 TCGGGCTTAATGCCTAGCAGGCTTCGTGCCGGTGTA
25804 ACAGAATTTA
Statistics
Matches: 62, Mismatches: 12, Indels: 5
0.78 0.15 0.06
Matches are distributed among these distances:
39 4 0.06
40 56 0.90
41 2 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (39 bp):
TCGGGCTTAATGCCTAGCAGGCTTCGTGCCGGTGTATTA
Found at i:27016 original size:17 final size:17
Alignment explanation
Indices: 26984--27038 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 17
26974 GCCCCTTTTT
26984 AATTTATTTT-AATTTA
1 AATTTATTTTAAATTTA
*
27000 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
27017 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
27034 AATTT
1 AATTT
27039 GTTGAAGCCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:27167 original size:17 final size:17
Alignment explanation
Indices: 27145--27195 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
27135 AACTTTTCTT
27145 TTAAGTTTAAATTTAAA
1 TTAAGTTTAAATTTAAA
* *
27162 TTAAGTTTAAAATTAAT
1 TTAAGTTTAAATTTAAA
27179 TTGAA-TTTAAAATTTAA
1 TT-AAGTTT-AAATTTAA
27196 CTAATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 20 0.69
18 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TTAAGTTTAAATTTAAA
Found at i:27286 original size:16 final size:16
Alignment explanation
Indices: 27265--27303 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
27255 CTAACCTAAT
*
27265 CCCAAATTCTAAAGGA
1 CCCAAATCCTAAAGGA
*
27281 CCCAAA-CCTAAAGGG
1 CCCAAATCCTAAAGGA
27296 CCCAAATC
1 CCCAAATC
27304 GGCCCGAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (16 bp):
CCCAAATCCTAAAGGA
Found at i:27968 original size:3 final size:3
Alignment explanation
Indices: 27921--27952 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
27911 ATAAATTCAT
27921 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27953 ATGAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Done.