Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011745.1 Kokia drynarioides strain JFW-HI SEQ_126739, 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: 18858
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Found at i:1048 original size:17 final size:17
Alignment explanation
Indices: 1026--1069 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
1016 ATTGTTTAAT
*
1026 TTTAAATTTATAATAAA
1 TTTAAATTTACAATAAA
* *
1043 TTTAAAATTCCAATAAA
1 TTTAAATTTACAATAAA
1060 TTTAAATTTA
1 TTTAAATTTA
1070 AATTTTGTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTAAATTTACAATAAA
Found at i:1919 original size:58 final size:57
Alignment explanation
Indices: 1801--1957 Score: 162
Period size: 58 Copynumber: 2.8 Consensus size: 57
1791 TAGTTTGGAG
* * *
1801 CTTAAACTTGATAATTCTTTTACATT-GAGGTTTGAA--TTTTTTTTTCAAGTTAAAT
1 CTTAAACTTGACAATTATTTTACATTGGA-GTTTGAATTTTTTTTTTTCAAGTTAAAC
* *
1856 TTTAAACTTGACAATTGTTCTTACATTGGAGTTTGAATTTTTTTTTTTCAAAGTT-AAC
1 CTTAAACTTGACAATTATT-TTACATTGGAGTTTGAATTTTTTTTTTTC-AAGTTAAAC
* * *
1914 CTTAAATTTGACAAATATTTTCACATTTGGA-CTTGAATTTTTTT
1 CTTAAACTTGACAATTATTTT-ACA-TTGGAGTTTGAATTTTTTT
1958 CATTCATGTT
Statistics
Matches: 86, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
55 16 0.19
56 14 0.16
57 4 0.05
58 42 0.49
59 10 0.12
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (57 bp):
CTTAAACTTGACAATTATTTTACATTGGAGTTTGAATTTTTTTTTTTCAAGTTAAAC
Found at i:2776 original size:15 final size:14
Alignment explanation
Indices: 2742--2768 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2732 AGGAATAGTA
2742 AAATATTAAAAAAG
1 AAATATTAAAAAAG
2756 AAATATTAAAAAA
1 AAATATTAAAAAA
2769 ATACATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATATTAAAAAAG
Found at i:3654 original size:6 final size:6
Alignment explanation
Indices: 3643--3702 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
3633 CAAATGTATT
**
3643 TTTAAA TTTAAA TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
3689 TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TT
3703 GATTTAAAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
5 7 0.15
6 39 0.85
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:3677 original size:17 final size:17
Alignment explanation
Indices: 3643--3702 Score: 84
Period size: 17 Copynumber: 3.5 Consensus size: 17
3633 CAAATGTATT
3643 TTTAAATTTAAATTTAAA
1 TTTAAATTT-AATTTAAA
**
3661 TTTAAATTTGCTTTAAA
1 TTTAAATTTAATTTAAA
*
3678 TTTAAATTTAATTAAAA
1 TTTAAATTTAATTTAAA
3695 TTTAAATT
1 TTTAAATT
3703 GATTTAAAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 28 0.76
18 9 0.24
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTAAATTTAATTTAAA
Found at i:3698 original size:23 final size:23
Alignment explanation
Indices: 3644--3702 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
3634 AAATGTATTT
3644 TTAAATTTAAATTTAAATTTAAA
1 TTAAATTTAAATTTAAATTTAAA
***
3667 TTTGCTTTAAATTTAAATTT-AA
1 TTAAATTTAAATTTAAATTTAAA
3689 TTAAAATTTAAATT
1 TT-AAATTTAAATT
3703 GATTTAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTTAAA
Found at i:3711 original size:17 final size:16
Alignment explanation
Indices: 3654--3710 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
3644 TTAAATTTAA
3654 ATTTAAATTTAAATTTG
1 ATTTAAATTTAAA-TTG
* *
3671 CTTTAAATTTAAATTTA
1 ATTTAAATTTAAA-TTG
*
3688 ATTAAAATTTAAATTG
1 ATTTAAATTTAAATTG
3704 ATTTAAA
1 ATTTAAA
3711 ACTTAATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
16 8 0.24
17 26 0.76
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (16 bp):
ATTTAAATTTAAATTG
Found at i:4410 original size:3 final size:3
Alignment explanation
Indices: 4402--4486 Score: 125
Period size: 3 Copynumber: 28.0 Consensus size: 3
4392 ATGTTAGCAT
4402 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * *
4450 TAA TAA TAA TAAA TGC TAT TAA TAA TAA CAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
4487 CTTTTTTTTA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
3 71 0.96
4 3 0.04
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5557 original size:30 final size:29
Alignment explanation
Indices: 5521--5788 Score: 165
Period size: 29 Copynumber: 9.1 Consensus size: 29
5511 AGAGGTCCCG
*
5521 AAACTTCTAAAAATTCTATTTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTT-ACCCCA
* *
5551 AAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCTAAAAATTCCATTTTTACCC-CA
* * * * *
5580 GAACTTTTGAAAATTCCATTTTTTACCTCG
1 AAACTTCTAAAAATTCCA-TTTTTACCCCA
* *
5610 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCTAAAAATTCCATTTTTACCCCA
* * **
5639 AAACCTCGAAATTTTCCATTTTTGACCCCA
1 AAACTTCTAAAAATTCCATTTTT-ACCCCA
*
5669 AAACTT-TCAAAAATTACCA-GTTTACCCTC-
1 AAACTTCT-AAAAATT-CCATTTTTACCC-CA
* * * *
5698 AAA-TGTCCAAAAACTCCATTTTTGACCTCG
1 AAACT-TCTAAAAATTCCATTTTT-ACCCCA
* *
5728 AAAC-TCTCAAAATTACCA-TTTTACCCCC
1 AAACTTCTAAAAATT-CCATTTTTACCCCA
*
5756 GAA-TATCTAAAAATTCCATTTTTTAACCCCA
1 AAACT-TCTAAAAATTCCA-TTTTT-ACCCCA
5787 AA
1 AA
5789 CTATGCCAAA
Statistics
Matches: 181, Mismatches: 38, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
28 13 0.07
29 84 0.46
30 75 0.41
31 9 0.05
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTCCATTTTTACCCCA
Found at i:5577 original size:29 final size:29
Alignment explanation
Indices: 5521--5683 Score: 125
Period size: 30 Copynumber: 5.5 Consensus size: 29
5511 AGAGGTCCCG
*
5521 AAACTTCTAAAAA-TTCTATTTTTGACCCCA
1 AAACTTCCAAAAATTTC-ATTTTT-ACCCCA
5551 AAACTTCCAAAAATTTCATTTTTACCCTC-
1 AAACTTCCAAAAATTTCATTTTTACCC-CA
* *** * * *
5580 GAACTTTTGAAAATTCCATTTTTTACCTCG
1 AAACTTCCAAAAATTTCA-TTTTTACCCCA
* *
5610 AAACTTCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTTCATTTTTACCCCA
* * *
5639 AAACCT-CGAAATTTTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTT-CATTTTT-ACCCCA
*
5669 AAACTTTCAAAAATT
1 AAACTTCCAAAAATT
5684 ACCAGTTTAC
Statistics
Matches: 105, Mismatches: 21, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
28 6 0.06
29 39 0.37
30 51 0.49
31 9 0.09
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
AAACTTCCAAAAATTTCATTTTTACCCCA
Found at i:5656 original size:59 final size:59
Alignment explanation
Indices: 5530--5809 Score: 204
Period size: 59 Copynumber: 4.7 Consensus size: 59
5520 GAAACTTCTA
* * * * *
5530 AAAATTCTATTTTTGACCCCAAAACTTCCAAAAATTTCATTTTTACCCTCGAACTTTTG
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTCTCG
* * *
5589 AAAATTCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTACCC-CTAAAC-CTCG
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTC-AAACTCTCG
* * * * *
5647 AAATTTTCCATTTTTGACCCCAAAACTTTCAAAAATTACCA-GTTTACCCTCAAA-TGTCCA
1 AAA-ATTCCATTTTTGACCCCAAAACTTCCAAAAATT-CCATTTTTACCCTCAAACTCT-CG
* * * * *
5707 AAAACTCCATTTTTGACCTCGAAAC-TCTC-AAAATTACCA-TTTTACCCCCGAATA-TCT-A
1 AAAATTCCATTTTTGACCCCAAAACTTC-CAAAAATT-CCATTTTTACCCTC-AA-ACTCTCG
*
5765 AAAATTCCATTTTTTAACCCC-AAACTATGCC-AAAATTACCATTTT
1 AAAATTCCA-TTTTTGACCCCAAAACT-T-CCAAAAATT-CCATTTT
5810 GCCCCGAGAT
Statistics
Matches: 180, Mismatches: 27, Indels: 26
0.77 0.12 0.11
Matches are distributed among these distances:
58 38 0.21
59 115 0.64
60 23 0.13
61 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCCTCAAACTCTCG
Found at i:5768 original size:58 final size:57
Alignment explanation
Indices: 5653--5814 Score: 162
Period size: 58 Copynumber: 2.7 Consensus size: 57
5643 CTCGAAATTT
* * * *
5653 TCCATTTTTGACCCCAAAACTTTCAAAAATTACCAGTTTACCCTCAAATGTCCAAAAAC
1 TCCATTTTTGA-CCCAAAACTATC-AAAATTACCATTTTACCCCCAAATATCCAAAAAC
* * * * *
5712 TCCATTTTTGACCTCGAAACTCTCAAAATTACCATTTTACCCCCGAATATCTAAAAAT
1 TCCATTTTTGACC-CAAAACTATCAAAATTACCATTTTACCCCCAAATATCCAAAAAC
* * *
5770 TCCATTTTTTAACCCCAAACTATGCCAAAATTACCATTTTGCCCC
1 TCCA-TTTTTGACCCAAAACTAT--CAAAATTACCATTTTACCCC
5815 GAGATCCAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
58 41 0.47
59 27 0.31
60 19 0.22
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (57 bp):
TCCATTTTTGACCCAAAACTATCAAAATTACCATTTTACCCCCAAATATCCAAAAAC
Found at i:5779 original size:118 final size:119
Alignment explanation
Indices: 5521--5835 Score: 292
Period size: 118 Copynumber: 2.7 Consensus size: 119
5511 AGAGGTCCCG
* * * * *
5521 AAACTTCTAAAAATTCTATTTTTGACCCCAAAACTTCCAAAAATT-TCATTTTTACCCTCGAACT
1 AAACATCTAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATGTTTACCCTCGAAAT
*** * * *
5585 TTTGAAAATTCCATTTTTTACCTCGAAACTTCCAAAAATTCCATTTTTACCCCT
66 TCCAAAAACTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCC
* * ** *
5639 AAACCTCGAAATTTTCCATTTTTGACCCCAAAACTTTCAAAAATTACCA-GTTTACCCTC-AAAT
1 AAACATCTAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATGTTTACCCTCGAAAT
5702 GTCCAAAAACTCCATTTTTGACCTCGAAAC-TCTC-AAAATTACCA-TTTTACCCCC
66 -TCCAAAAACTCCATTTTTGACCTCGAAACTTC-CAAAAATT-CCATTTTTACCCCC
* * * *
5756 GAATATCTAAAAATTCCATTTTTTAACCCC-AAACTATGCC-AAAATTACCAT-TTTGCCC-CGA
1 AAACATCTAAAAATTCCA-TTTTTGACCCCAAAACT-T-CCAAAAATTACCATGTTTACCCTCGA
* * *
5817 GA-TCCAAAATCACCATTTT
63 AATTCCAAAAACTCCATTTT
5836 ATCTTCGGGT
Statistics
Matches: 161, Mismatches: 27, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
116 15 0.09
117 38 0.24
118 105 0.65
119 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (119 bp):
AAACATCTAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATGTTTACCCTCGAAAT
TCCAAAAACTCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:10117 original size:22 final size:21
Alignment explanation
Indices: 10076--10118 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
10066 CCTAGACAAA
*
10076 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
10097 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
10119 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:17201 original size:116 final size:115
Alignment explanation
Indices: 16975--17299 Score: 393
Period size: 116 Copynumber: 2.8 Consensus size: 115
16965 GAGGCTCAAA
* * * * * * *
16975 GCGAGCAAATCTTTGAACCACAGCTTCCTAATGAGATACTGAGAAGCAGGTCGAAATAATAAAAT
1 GCGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTTGAAACAATAAAAC
* * *
17040 AGTTAGCTTCCTGATGAGATACAAAGAAGTATACCAACTCAGGGCTCGAT
66 GGTCAGCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGAT
* * * ** *
17090 GTGATCAAATCTTCGAATCTTAGCTTCCTGATGAGATAC-AGAGAAGC-GGATTGAAACAAGTAA
1 GCGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTA-AGAAGCAGG-TTGAAACAA-TAA
* * * *
17153 GACGGTCATCTTCCTGATGAGATACAGAGAAGAATACCTACTCAGGGCTCGAT
63 AACGGTCAGCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGAT
* *
17206 GCGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTTGAAGCAATAAAAT
1 GCGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTTGAAACAATAAAAC
* *
17271 GGTTAGCTTCCTGATGAGATACTAAGAAG
66 GGTCAGCTTCCTGATGAGATACAAAGAAG
17300 TGAACCAAAT
Statistics
Matches: 174, Mismatches: 31, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
114 2 0.01
115 74 0.43
116 95 0.55
117 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (115 bp):
GCGAACAAATCTTCGAACCCCAGCTTCCTAATGAGATACTAAGAAGCAGGTTGAAACAATAAAAC
GGTCAGCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGAT
Found at i:17521 original size:197 final size:196
Alignment explanation
Indices: 17113--17790 Score: 636
Period size: 197 Copynumber: 3.4 Consensus size: 196
17103 CGAATCTTAG
*
17113 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGT-AAGACGGTCATCTTCCTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATG-CGGTCATCTTCCTGATGAGATA
** * * *
17177 C--AG-AGA-AG--AATACCTACTCAGGGCTCGATGCGAACAAATCTTCGAACCCCAGCTTCCTA
65 CTAAGAAGAGAGCAAAT-CAAACCCA-CGCTCGATGCGAACAAATCTTCGAACCCCAGCTTCCTG
* * * *
17236 ATGAGATACTAAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGT
128 ATGAGATACTAAGAAGTA-G--G--GC----GAATGATTAGCTTCCTGATGAGATACCAAGAAGT
17301 GAACCAAATTCGT
184 GAACCAAATTCGT
*
17314 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCACCTT-CTCGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCT-GATGAGATA
* * *
17378 CTAAGAAGAGGAGCAAATCAAACCCACGCTCAAGGCGAACAAATCTTCGAACCCCAACTTCCTGA
65 CTAAGAAGA-GAGCAAATCAAACCCACGCTCGATGCGAACAAATCTTCGAACCCCAGCTTCCTGA
* * * *
17443 TGAGGTACTGAGAAGTAGGGCGAATGATTAGCTTCCTGATGAGATACCGAGAAGTGGACCAAATT
129 TGAGATACTAAGAAGTAGGGCGAATGATTAGCTTCCTGATGAGATACCAAGAAGTGAACCAAATT
*
17508 CTT
194 CGT
* * *
17511 CTTCCTGATGAGATACAGAGAAGCGGATTG-AACTAAGCGATACGGTCATCTTCCTGATGAAATA
1 CTTCCTGATGAGATACAGAGAAGCGGATTGAAAC-AAGTGATGCGGTCATCTTCCTGATGAGATA
* * ** *
17575 TTAAGAAGAAGACCAAAAGAAACCCACGCTCGATGTGAACAAATCTTCGAACCCCAGCTTCCTGA
65 CTAAGAAG-AGAGCAAATCAAACCCACGCTCGATGCGAACAAATCTTCGAACCCCAGCTTCCTGA
* * * * * * **
17640 TGAGATACTTAGAAGTAGGTCGAAGCAATAAATGGTTAGCTTCTTGTTGAAATACTGAGAAGTGA
129 TGAGATACTAAGAAGTA-G--G--GC---GAATGATTAGCTTCCTGATGAGATACCAAGAAGTGA
*
17705 ACCAAATCCGT
186 ACCAAATTCGT
* * * * * * ** * *
17716 CTTCCTGGTGAAACACAGAGAAGTGGTTTAAAAAACAAGTGATATGGTCGTCTTCTTGATGAGAT
1 CTTCCTGATGAGATACAGAGAAGCGGATT--GAAACAAGTGATGCGGTCATCTTCCTGATGAGAT
*
17781 ACTGAGAAGA
64 ACTAAGAAGA
17791 AGGTCAAGTT
Statistics
Matches: 399, Mismatches: 55, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
196 3 0.01
197 164 0.41
198 4 0.01
200 3 0.01
201 59 0.15
202 4 0.01
203 3 0.01
204 3 0.01
205 63 0.16
206 51 0.13
207 36 0.09
208 6 0.02
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (196 bp):
CTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
TAAGAAGAGAGCAAATCAAACCCACGCTCGATGCGAACAAATCTTCGAACCCCAGCTTCCTGATG
AGATACTAAGAAGTAGGGCGAATGATTAGCTTCCTGATGAGATACCAAGAAGTGAACCAAATTCG
T
Found at i:18189 original size:6 final size:6
Alignment explanation
Indices: 18180--18246 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
18170 CAAATTTATT
** **
18180 TTTAAA TTTAAA TTTATCT TTTAAA TTTAAA TTT-GC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
18228 TTT-AA TTAAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TT
18247 GATTTAAAAC
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
5 7 0.15
6 37 0.77
7 4 0.08
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:18221 original size:17 final size:17
Alignment explanation
Indices: 18180--18246 Score: 89
Period size: 17 Copynumber: 3.8 Consensus size: 17
18170 CAAATTTATT
18180 TTTAAATTTAAATTTATC
1 TTTAAATTTAAATTTA-C
*
18198 TTTTAAATTTAAATTTGC
1 -TTTAAATTTAAATTTAC
*
18216 TTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAC
*
18233 TTAAAATTTAAATT
1 TTTAAATTTAAATT
18247 GATTTAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
17 28 0.64
18 1 0.02
19 15 0.34
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTAAATTTAC
Found at i:18253 original size:17 final size:17
Alignment explanation
Indices: 18183--18260 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
18173 ATTTATTTTT
* *
18183 AAATTTAAATTTATCTTTT
1 AAATTTAAATTGA--TTTA
*
18202 AAATTTAAATTTGCTTT-
1 AAATTTAAA-TTGATTTA
* *
18219 AAATTTAAATTTAATTA
1 AAATTTAAATTGATTTA
18236 AAATTTAAATTGATTTA
1 AAATTTAAATTGATTTA
*
18253 AAACTTAA
1 AAATTTAA
18261 TTAAACATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
16 4 0.08
17 31 0.63
18 3 0.06
19 9 0.18
20 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTGATTTA
Done.