Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002534.1 Kokia drynarioides strain JFW-HI SEQ_114713, 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: 30483
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:617 original size:59 final size:59
Alignment explanation
Indices: 523--1097 Score: 781
Period size: 59 Copynumber: 9.8 Consensus size: 59
513 GCACGGGGGC
* * * *
523 AAAATGGTAGTTTTGGGGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTT-TGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
583 AAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGGACTTTTT-GAAGTTC-AGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGA-TTTTTGGAAGTTCGA-GGGT
* * * *
642 -AAATGGTAA-TTTTGGAAGGTTCGAGGTCAAAAATGGGACTTTTGGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGA-TTTTTGGAAGTTCGAGGGT
*
700 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * **
759 AAAAT-GTAATTTTTGGAAGGTTCGGGGTTTAAAATGGGATATTTGGAATTTTAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
817 AAAATGTTAATTTTTTGGAAGTTTAGGGATTAAAAATGGGATTTTTGGAAGTTCG-GGGT
1 AAAATGGTAA-TTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
876 AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGACTTTTTGGAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGA-TTTTTGGAAGTTCGA-GGGT
*
936 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAAGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
*
995 AAAATGGTAA-TTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTTTG-GGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAG-TTCGAGGGT
* *
1053 AAAATGGCAATTTTTGGAAGGTTCGGGGTTAAAAATGGTATTTTT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTT
1098 TTTTAAGTTT
Statistics
Matches: 460, Mismatches: 41, Indels: 29
0.87 0.08 0.05
Matches are distributed among these distances:
57 32 0.07
58 149 0.32
59 155 0.34
60 124 0.27
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:2954 original size:35 final size:35
Alignment explanation
Indices: 2915--3025 Score: 122
Period size: 35 Copynumber: 3.2 Consensus size: 35
2905 TTTTAGCTTC
* *
2915 ATTTAAATC-TATAATAATTTTAAATTTGAAAATAA
1 ATTTAAATCTTA-AATAAATTTAAATTTCAAAATAA
2950 ATTTAAA-CTTAAATTAAATTTAAA-TTCAAAATAA
1 ATTTAAATCTTAAA-TAAATTTAAATTTCAAAATAA
* * *
2984 ATTTAAATTTTTAAACAAATTT-AATTTTAAAATAA
1 ATTTAAA-TCTTAAATAAATTTAAATTTCAAAATAA
3019 ATTTAAA
1 ATTTAAA
3026 GGGAATTTGG
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
34 21 0.32
35 40 0.61
36 5 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (35 bp):
ATTTAAATCTTAAATAAATTTAAATTTCAAAATAA
Found at i:2969 original size:17 final size:17
Alignment explanation
Indices: 2927--3025 Score: 92
Period size: 17 Copynumber: 5.7 Consensus size: 17
2917 TTAAATCTAT
* *
2927 AATAATTTTAAATTTGAA
1 AATAAATTTAAA-TTCAA
2945 AATAAATTTAAACTT-AA
1 AATAAATTTAAA-TTCAA
*
2962 ATTAAATTTAAATTCAA
1 AATAAATTTAAATTCAA
**
2979 AATAAATTTAAATTTTTA
1 AATAAATTTAAA-TTCAA
* * *
2997 AACAAATTTAATTTTAA
1 AATAAATTTAAATTCAA
3014 AATAAATTTAAA
1 AATAAATTTAAA
3026 GGGAATTTGG
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
16 2 0.03
17 40 0.59
18 26 0.38
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (17 bp):
AATAAATTTAAATTCAA
Found at i:2971 original size:52 final size:52
Alignment explanation
Indices: 2927--3025 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 52
2917 TTAAATCTAT
* * *
2927 AATAATTTTAAATTTGAAAATAAATTTAAACTTAAATTAAATTTAAATTCAA
1 AATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAATTCAA
** **
2979 AATAAATTTAAATTTTTAAACAAATTTAATTTTAAAATAAATTTAAA
1 AATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAA
3026 GGGAATTTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 40 1.00
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (52 bp):
AATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAATTTAAATTCAA
Found at i:2972 original size:11 final size:11
Alignment explanation
Indices: 2934--2992 Score: 57
Period size: 11 Copynumber: 5.2 Consensus size: 11
2924 TATAATAATT
2934 TTAAATTTGAAA
1 TTAAATTT-AAA
*
2946 ATAAATTTAAA
1 TTAAATTTAAA
2957 CTTAAA-TTAAA
1 -TTAAATTTAAA
*
2968 TTTAAATTCAAA
1 -TTAAATTTAAA
*
2980 ATAAATTTAAA
1 TTAAATTTAAA
2991 TT
1 TT
2993 TTTAAACAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 23 0.61
12 15 0.39
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3025 original size:6 final size:6
Alignment explanation
Indices: 2933--2993 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
2923 CTATAATAAT
* * *
2933 TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA -TTAAA TTTAAA TTCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
2980 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
2994 TTAAACAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
5 11 0.25
6 30 0.68
7 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:3118 original size:29 final size:29
Alignment explanation
Indices: 3077--3208 Score: 137
Period size: 29 Copynumber: 4.6 Consensus size: 29
3067 CCAAACTTCT
*
3077 CAAAAATCA-CATTTTGACCCTAAACATC
1 CAAAAATTACCATTTTGACCCTAAACATC
*
3105 CAAAAATTACCATTTT-ACCCCTAAATATC
1 CAAAAATTACCATTTTGA-CCCTAAACATC
* *
3134 CAAAAATTATCATTTTGCCCCCT-AACATC
1 CAAAAATTACCATTTTG-ACCCTAAACATC
** * *
3163 CAAAAATTACCATTTT-TTCCTCGAGCATC
1 CAAAAATTACCATTTTGACCCT-AAACATC
3192 CAAAAATTACCATTTTG
1 CAAAAATTACCATTTTG
3209 TCCTCAGATT
Statistics
Matches: 88, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
27 3 0.03
28 9 0.10
29 72 0.82
30 4 0.05
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (29 bp):
CAAAAATTACCATTTTGACCCTAAACATC
Found at i:3208 original size:58 final size:57
Alignment explanation
Indices: 3063--3178 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 57
3053 GGTTCAACAA
* * *
3063 ACCCCCAAACTTCTCAAAAATCACATTTTGACCCTAAACATCCAAAAATTACCATTTT
1 ACCCCTAAACATC-CAAAAATTACATTTTGACCCTAAACATCCAAAAATTACCATTTT
* *
3121 ACCCCTAAATATCCAAAAATTATCATTTTGCCCCCT-AACATCCAAAAATTACCATTTT
1 ACCCCTAAACATCCAAAAATTA-CATTTTG-ACCCTAAACATCCAAAAATTACCATTTT
3179 TTCCTCGAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 8 0.16
58 39 0.76
59 4 0.08
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.29
Consensus pattern (57 bp):
ACCCCTAAACATCCAAAAATTACATTTTGACCCTAAACATCCAAAAATTACCATTTT
Found at i:3222 original size:29 final size:30
Alignment explanation
Indices: 3077--3225 Score: 121
Period size: 29 Copynumber: 5.2 Consensus size: 30
3067 CCAAACTTCT
* * * *
3077 CAAAAATCA-CATTTTG-ACCCTAAACATC
1 CAAAAATTACCATTTTGTCCCCTAGATATC
* *
3105 CAAAAATTACCATTTT-ACCCCTAAATATC
1 CAAAAATTACCATTTTGTCCCCTAGATATC
* * *
3134 CAAAAATTATCATTTTGCCCCCTA-ACATC
1 CAAAAATTACCATTTTGTCCCCTAGATATC
* * * *
3163 CAAAAATTACCATTTTTTCCTCGAG-CATC
1 CAAAAATTACCATTTTGTCCCCTAGATATC
* *
3192 CAAAAATTACCATTTTGTCCTC-AGATTTC
1 CAAAAATTACCATTTTGTCCCCTAGATATC
3221 CAAAA
1 CAAAA
3226 GCCACATTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
28 10 0.10
29 86 0.84
30 6 0.06
ACGTcount: A:0.38, C:0.28, G:0.04, T:0.31
Consensus pattern (30 bp):
CAAAAATTACCATTTTGTCCCCTAGATATC
Found at i:13069 original size:99 final size:98
Alignment explanation
Indices: 12820--13149 Score: 459
Period size: 99 Copynumber: 3.4 Consensus size: 98
12810 AGATATAAAG
*
12820 GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCATGAAGAGATGAAGGGAAGGATTGAGGCCG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCCG
* **
12885 CGACGACGAATCTGGTACC--CGAAGATACGA-A
66 CGACGACGAATC-GGTACCTTAGAAGATGTGATA
* * * * *
12916 GGGAAAGGTTGAGGCCACAATGACGAACCCAGTACCAGGAAGAGATGAAGGGAAGGATTGAGGTC
1 -GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCC
*
12981 GCGACGACGAATACGGTACCTTAGAAGATGTGATT
65 GCGACGACGAAT-CGGTACCTTAGAAGATGTGATA
* * * *
13016 GGAAAGGTTGAGGCTGCAACGGCGAACTCGGTACCAAGAAAAGATGAAGGGAAGGATTGAGGCCG
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCCG
* *
13081 CGGCGATGAATCCGGTACCTTAGAAGATGTGATA
66 CGACGACGAAT-CGGTACCTTAGAAGATGTGATA
13115 GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACC
1 GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACC
13150 TTAGAAAATA
Statistics
Matches: 204, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
97 77 0.38
98 1 0.00
99 126 0.62
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.14
Consensus pattern (98 bp):
GGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAAGAAGAGATGAAGGGAAGGATTGAGGCCG
CGACGACGAATCGGTACCTTAGAAGATGTGATA
Found at i:13168 original size:50 final size:49
Alignment explanation
Indices: 12810--13185 Score: 224
Period size: 49 Copynumber: 7.6 Consensus size: 49
12800 AATACCCTGG
* *
12810 AGATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCAT-GA
1 AGATATAAA-GGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* * * * * ** *
12859 AGAGATGAAGGGAAGGATTGAGGCCGCGACGACGAATCTGGTACC--CGA
1 AGATATAAAGGAAAGG-TTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* * * *
12907 AGATACGAAGGGAAAGGTTGAGGCCACAATGACGAACCCAGTACC--AGGA
1 AGATA-TAAAGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTA-GA
* * * * * ** *
12956 AGAGATGAAGGGAAGGATTGAGGTCGCGACGACGAATACGGTACCTTAGA
1 AGATATAAAGGAAAGG-TTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* ** * * * * *
13006 AGATGTGATTGGAAAGGTTGAGGCTGCAACGGCGAACTCGGTACC-AAGA
1 AGATAT-AAAGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* * * * ** * * *
13055 AAAGATGAAGGGAAGGATTGAGGCCGCGGCGATGAATCCGGTACCTTAGA
1 AGATATAAAGGAAAGG-TTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* * *
13105 AGATGTGATAGGAAAGGTTGAGGCCGCAACGGCGAACCCAGTACCTTAGA
1 AGATAT-AAAGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAGA
* * *
13155 AAATATAAAAGGAAAGGTTGACGCCGTAACG
1 AGATAT-AAAGGAAAGGTTGAGGCCGCAACG
13186 GCAAACTTAG
Statistics
Matches: 238, Mismatches: 78, Indels: 21
0.71 0.23 0.06
Matches are distributed among these distances:
48 47 0.20
49 91 0.38
50 86 0.36
51 14 0.06
ACGTcount: A:0.35, C:0.18, G:0.33, T:0.15
Consensus pattern (49 bp):
AGATATAAAGGAAAGGTTGAGGCCGCAACGACGAACCCAGTACCTTAGA
Found at i:13186 original size:50 final size:50
Alignment explanation
Indices: 13095--13206 Score: 134
Period size: 50 Copynumber: 2.2 Consensus size: 50
13085 GATGAATCCG
* * * * * *
13095 GTACCTTAGAAGATGTGATAGGAAAGGTTGAGGCCGCAACGGCGAACCCA
1 GTACCTTAGAAAATATAAAAGGAAAGGTTGACGCCGCAACGGCAAACCCA
* **
13145 GTACCTTAGAAAATATAAAAGGAAAGGTTGACGCCGTAACGGCAAACTTA
1 GTACCTTAGAAAATATAAAAGGAAAGGTTGACGCCGCAACGGCAAACCCA
*
13195 GCACCTTAGAAA
1 GTACCTTAGAAA
13207 CGTGACATGA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.18
Consensus pattern (50 bp):
GTACCTTAGAAAATATAAAAGGAAAGGTTGACGCCGCAACGGCAAACCCA
Found at i:13626 original size:17 final size:17
Alignment explanation
Indices: 13606--13640 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13596 TAATAAAAAA
*
13606 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
13623 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
13640 A
1 A
13641 AAATGTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:15568 original size:30 final size:29
Alignment explanation
Indices: 15532--15792 Score: 239
Period size: 30 Copynumber: 8.9 Consensus size: 29
15522 CCCAGAAGGT
*
15532 CCCTAAACTTTCTAAAAATCATATTTTAAC
1 CCCTAAACTTTCT-AAAATCACATTTTAAC
*
15562 CCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAAC-TTTCTAAAATCACATTTTAAC
*
15592 CCCTAAACTTCTCT-AAATTACATTTTAA-
1 CCCTAAACTT-TCTAAAATCACATTTTAAC
*
15620 CCCTAAACTTCTCCAAAATCACATTTTAAC
1 CCCTAAACTT-TCTAAAATCACATTTTAAC
* *
15650 CCCTAAACTTTTCCAAAATCACATTTTCA-
1 CCCTAAAC-TTTCTAAAATCACATTTTAAC
* * *
15679 CTCTAAACTTTTCCAAAATTACATTTT--C
1 CCCTAAAC-TTTCTAAAATCACATTTTAAC
* *
15707 CCCTCCAAACCTTTCTAAAAGCACATTTTCAC
1 CCCT--AAA-CTTTCTAAAATCACATTTTAAC
* * * *
15739 TCC-AAAGTTTGT-AAATTACATTTTAAC
1 CCCTAAACTTTCTAAAATCACATTTTAAC
*
15766 CCCTAAACTTCTCAAAAATCACATTTT
1 CCCTAAACTT-TCTAAAATCACATTTT
15793 GACTCCAAAT
Statistics
Matches: 195, Mismatches: 22, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
27 14 0.07
28 25 0.13
29 58 0.30
30 87 0.45
31 8 0.04
32 3 0.02
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTTTCTAAAATCACATTTTAAC
Found at i:15622 original size:59 final size:58
Alignment explanation
Indices: 15532--15822 Score: 242
Period size: 59 Copynumber: 5.0 Consensus size: 58
15522 CCCAGAAGGT
* *
15532 CCCTAAACTTTCTAAAAATCATATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAAC
1 CCCTAAACTTTCT--AAATCACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
15592 CCCTAAACTTCTCTAAATTACATTTTAA-CCCTAAACTTCTCCAAAATCACATTTTAAC
1 CCCTAAACTT-TCTAAATCACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAAC
* * *
15650 CCCTAAACTTTTCCAAAATCACATTTTCA-CTCTAAACTTTTCCAAAATTACATTTT--C
1 CCCTAAAC-TTT-CTAAATCACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAAC
* * * *
15707 CCCTCCAAACCTTTCTAAAAGCACATTTTCACTCC-AAAGTTTGT---AAATTACATTTTAAC
1 CCCT--AAA-CTTTCT-AAATCACATTTTAACCCCTAAACTTT-TCCAAAATTACATTTTAAC
* * * * *
15766 CCCTAAACTTCTCAAAAATCACATTTTGACTCC-AAA-TATTCAAAAATTACCATTTTA
1 CCCTAAACTT-TC-TAAATCACATTTTAACCCCTAAACTTTTCCAAAATTA-CATTTTA
15823 CCCTTGAACA
Statistics
Matches: 194, Mismatches: 20, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
55 1 0.01
56 5 0.03
57 41 0.21
58 43 0.22
59 88 0.45
60 13 0.07
61 3 0.02
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.36
Consensus pattern (58 bp):
CCCTAAACTTTCTAAATCACATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:15698 original size:88 final size:88
Alignment explanation
Indices: 15532--15792 Score: 268
Period size: 88 Copynumber: 3.0 Consensus size: 88
15522 CCCAGAAGGT
* * *
15532 CCCTAAACTTTCTAAAAATCATATTTTAACCCCTAAACTTTTCTAAAATTACATTTTAACCCCTA
1 CCCTAAACTTTCTAAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCCCTA
*
15597 AACTTCTCTAAATTACATTTTAA
66 AACTTCTCAAAATTACATTTTAA
* * *
15620 CCCTAAAC-TTCTCCAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTCA-CTCT
1 CCCTAAACTTTCT-AAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCCCT
* *
15683 AAACTTTTCCAAAATTACATTTT-C
65 AAACTTCT-CAAAATTACATTTTAA
* * * * *
15707 CCCTCCAAACCTTTCT-AAAAGCACATTTTCACTCC-AAAGTTTGT---AAATTACATTTTAACC
1 CCCT--AAA-CTTTCTAAAAATCACATTTTAACCCCTAAACTTT-TCCAAAATCACATTTTAACC
*
15767 CCTAAACTTCTCAAAAATCACATTTT
62 CCTAAACTTCTC-AAAATTACATTTT
15793 GACTCCAAAT
Statistics
Matches: 146, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
86 13 0.09
87 40 0.27
88 68 0.47
89 20 0.14
90 1 0.01
91 4 0.03
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (88 bp):
CCCTAAACTTTCTAAAAATCACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTAACCCCTA
AACTTCTCAAAATTACATTTTAA
Found at i:15819 original size:29 final size:28
Alignment explanation
Indices: 15751--15913 Score: 145
Period size: 29 Copynumber: 5.6 Consensus size: 28
15741 CAAAGTTTGT
*
15751 AAATTA-CATTTTAACCCCTAAACTTCTCAA
1 AAATTACCATTTT-A-CCCTAAACAT-TCAA
* *
15781 AAATCA-CATTTTGACTCC-AAATATTCAA
1 AAATTACCATTTT-AC-CCTAAACATTCAA
* *
15809 AAATTACCATTTTACCCTTGAACATCCAA
1 AAATTACCATTTTACCC-TAAACATTCAA
*
15838 AAATTACCATTTTACCCTTTAACATTCAA
1 AAATTACCATTTTACCC-TAAACATTCAA
* *
15867 AAATTACCATTTT-CCCATTAAGCATCCAA
1 AAATTACCATTTTACCC--TAAACATTCAA
15896 AAATTACCATTTTACCCT
1 AAATTACCATTTTACCCT
15914 CAAATTTCCA
Statistics
Matches: 114, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
27 2 0.02
28 15 0.13
29 80 0.70
30 17 0.15
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.34
Consensus pattern (28 bp):
AAATTACCATTTTACCCTAAACATTCAA
Found at i:15865 original size:58 final size:58
Alignment explanation
Indices: 15803--15913 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
15793 GACTCCAAAT
15803 ATTCAAAAATTACCATTTTACCC-TTGAA-CATCCAAAAATTACCATTTTACCCTTTAAC
1 ATTCAAAAATTACCATTTT-CCCATT-AAGCATCCAAAAATTACCATTTTACCCTTTAAC
15861 ATTCAAAAATTACCATTTTCCCATTAAGCATCCAAAAATTACCATTTTACCCT
1 ATTCAAAAATTACCATTTTCCCATTAAGCATCCAAAAATTACCATTTTACCCT
15914 CAAATTTCCA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
57 5 0.10
58 46 0.90
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (58 bp):
ATTCAAAAATTACCATTTTCCCATTAAGCATCCAAAAATTACCATTTTACCCTTTAAC
Found at i:15926 original size:58 final size:58
Alignment explanation
Indices: 15798--15926 Score: 176
Period size: 58 Copynumber: 2.2 Consensus size: 58
15788 ATTTTGACTC
15798 CAAATATTCAAAAATTACCATTTTACCCTTGAACATCCAAAAATTACCATTTTACCCTT
1 CAAAT-TTCAAAAATTACCATTTTACCCTTGAACATCCAAAAATTACCATTTTACCCTT
*
15857 TAACA-TTCAAAAATTACCATTTT-CCCATT-AAGCATCCAAAAATTACCATTTTACCC-T
1 CAA-ATTTCAAAAATTACCATTTTACCC-TTGAA-CATCCAAAAATTACCATTTTACCCTT
*
15914 CAAATTTCCAAAA
1 CAAATTTCAAAAA
15927 GTCACATTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
56 1 0.02
57 15 0.24
58 44 0.70
59 2 0.03
60 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.02, T:0.33
Consensus pattern (58 bp):
CAAATTTCAAAAATTACCATTTTACCCTTGAACATCCAAAAATTACCATTTTACCCTT
Found at i:16940 original size:39 final size:39
Alignment explanation
Indices: 16849--17018 Score: 142
Period size: 39 Copynumber: 4.4 Consensus size: 39
16839 TGTTGCGGTG
* * * *
16849 TTTACAGTGTCACCGCTAGTTCAGTATAGCATTATAGTG
1 TTTACAGTGTCACTGCCAGTTCAGTATAGCATTACAGTA
* * **
16888 TTTACAGTATCACTGCCAGTTCAGTGTATTATTACAGTA
1 TTTACAGTGTCACTGCCAGTTCAGTATAGCATTACAGTA
* * * * ** **
16927 TTTACAGTGTCACTTCCAGTCCAATATAACGCTGTAGTA
1 TTTACAGTGTCACTGCCAGTTCAGTATAGCATTACAGTA
* * * * *
16966 TTTACAATGTCACTGTCGGTTCAGTATAACATTGCAGTA
1 TTTACAGTGTCACTGCCAGTTCAGTATAGCATTACAGTA
*
17005 TTCACAGTGTCACT
1 TTTACAGTGTCACT
17019 ATTGGTTCAG
Statistics
Matches: 101, Mismatches: 30, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
39 101 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (39 bp):
TTTACAGTGTCACTGCCAGTTCAGTATAGCATTACAGTA
Found at i:20690 original size:26 final size:26
Alignment explanation
Indices: 20659--20714 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
20649 TGGAGTATAT
20659 CAAAATGTTGTCTATAAAGACTATCA
1 CAAAATGTTGTCTATAAAGACTATCA
20685 CAAAATGTTGTCTATAAAGACTATCA
1 CAAAATGTTGTCTATAAAGACTATCA
20711 CAAA
1 CAAA
20715 CCTATCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (26 bp):
CAAAATGTTGTCTATAAAGACTATCA
Found at i:23789 original size:39 final size:39
Alignment explanation
Indices: 23746--23919 Score: 195
Period size: 39 Copynumber: 4.5 Consensus size: 39
23736 CTACTACTTT
* * *
23746 AGTATAACGTTGCGGTGTTTACAGTATCACCGCCAGTTC
1 AGTATAACATTGCAGTGTTTACAGTATCACTGCCAGTTC
* * * *
23785 AGTATAGCATTGTAGTGTTTATAGTATCACTGTCAGTTC
1 AGTATAACATTGCAGTGTTTACAGTATCACTGCCAGTTC
** * * *
23824 AGTATATTATTGCAGTGTTTACAGTGTCACTGCCAATCC
1 AGTATAACATTGCAGTGTTTACAGTATCACTGCCAGTTC
* * * * *
23863 AATATAACGTTGCAGTGTTTACAGTGTCACTACCGGTTC
1 AGTATAACATTGCAGTGTTTACAGTATCACTGCCAGTTC
23902 AGTATAACATTGCAGTGT
1 AGTATAACATTGCAGTGT
23920 CACTATCGGT
Statistics
Matches: 110, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 110 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (39 bp):
AGTATAACATTGCAGTGTTTACAGTATCACTGCCAGTTC
Found at i:23847 original size:78 final size:78
Alignment explanation
Indices: 23720--23919 Score: 202
Period size: 78 Copynumber: 2.6 Consensus size: 78
23710 TTAGTCTAGT
* * * * * * * * *
23720 AGTGTTTATAGTGTCACTACTACTTTAGTATAACGTTGCGGTGTTTACAGTATCACCGCCAGTTC
1 AGTGTTTACAGTATCACTACCAGTTCAGTATAACATTGCAGTGTTTACAGTATCACCGCCAATCC
* * *
23785 AGTATAGCATTGT
66 AATATAACATTGC
* ** ** * *
23798 AGTGTTTATAGTATCACTGTCAGTTCAGTATATTATTGCAGTGTTTACAGTGTCACTGCCAATCC
1 AGTGTTTACAGTATCACTACCAGTTCAGTATAACATTGCAGTGTTTACAGTATCACCGCCAATCC
*
23863 AATATAACGTTGC
66 AATATAACATTGC
* *
23876 AGTGTTTACAGTGTCACTACCGGTTCAGTATAACATTGCAGTGT
1 AGTGTTTACAGTATCACTACCAGTTCAGTATAACATTGCAGTGT
23920 CACTATCGGT
Statistics
Matches: 97, Mismatches: 25, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
78 97 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (78 bp):
AGTGTTTACAGTATCACTACCAGTTCAGTATAACATTGCAGTGTTTACAGTATCACCGCCAATCC
AATATAACATTGC
Found at i:26854 original size:33 final size:32
Alignment explanation
Indices: 26804--26872 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
26794 GTATTAATTT
*
26804 AAAATATTTAATGATTTTTAAGTAATTTTTCTA
1 AAAAAATTTAATGATTTTT-AGTAATTTTTCTA
** *
26837 AAAAAATTATAAT-ATTTTTCTTCATTTTTCTA
1 AAAAAATT-TAATGATTTTTAGTAATTTTTCTA
26869 AAAA
1 AAAA
26873 CTTTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 14 0.45
33 13 0.42
34 4 0.13
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.49
Consensus pattern (32 bp):
AAAAAATTTAATGATTTTTAGTAATTTTTCTA
Found at i:26908 original size:11 final size:11
Alignment explanation
Indices: 26892--26917 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26882 TATTTTAAAA
26892 TTTTCTATAAT
1 TTTTCTATAAT
26903 TTTTCTATAAT
1 TTTTCTATAAT
26914 TTTT
1 TTTT
26918 AAATATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTCTATAAT
Found at i:29676 original size:17 final size:17
Alignment explanation
Indices: 29652--29708 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 17
29642 TTGGAAATTG
29652 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
29669 AGTTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
29686 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
29703 AATTTA
1 AATTTA
29709 AGAAAGTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:30406 original size:3 final size:3
Alignment explanation
Indices: 30400--30429 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
30390 AAAAAAAAAC
30400 AAT AAT AAT AAT AAT AAT AATT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA
30430 AAAAGGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.