Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005127.1 Kokia drynarioides strain JFW-HI SEQ_118962, 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: 46013
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:3074 original size:16 final size:16
Alignment explanation
Indices: 3050--3092 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
3040 GACGTGCTTA
* *
3050 ATAATTTTATATATTT
1 ATAAATTTATATATAT
*
3066 ATAAATTTACATATAT
1 ATAAATTTATATATAT
3082 A-AAATTTATAT
1 ATAAATTTATAT
3093 GCTATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
ATAAATTTATATATAT
Found at i:4841 original size:17 final size:18
Alignment explanation
Indices: 4812--4846 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
4802 ATTATATAAT
4812 ATTTAAATATATAATTTA
1 ATTTAAATATATAATTTA
*
4830 ATTTAAAT-TATATTTTA
1 ATTTAAATATATAATTTA
4847 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTAAATATATAATTTA
Found at i:4973 original size:90 final size:90
Alignment explanation
Indices: 4710--4998 Score: 230
Period size: 90 Copynumber: 3.1 Consensus size: 90
4700 TGTGTTAGCC
* * *
4710 TTATTTATTATTTATTTTTTTAAAATTTAAATTTAGTTTTTTGGTGGA-ACTATTTTAAAT-GAC
1 TTATTTATTATTTATTTTATAAAAATTTAAATTTATTTTTTTGGTGGAGAC-ATTTTAAATAG-C
* ** *
4773 GTCACCCAATTGATTTGTTTTATTTAT
64 GTCACCCAATTAATTAATTTTAATTAT
* * * * *
4800 TTATTATATAATATTTAAATATATAATTTAATTTAAATTATATTTTATTTTTGGTGGTGCCATTT
1 TTATT-TAT--TATTT-ATTTTATAA--AAATTTAAATT-TA--TT-TTTTTGGTGGAGACATTT
* *
4865 TAAATAGTGTCACTCAATTAATTAATTATTAATTA-
56 TAAATAGCGTCACCCAATTAATTAATT-TTAATTAT
* *
4900 TTATTTATTATTTATTTTCTAAAAATTTAAATTTATTTTTTTGGTGGAGTCATTTTAAATAGCG-
1 TTATTTATTATTTATTTTATAAAAATTTAAATTTATTTTTTTGGTGGAGACATTTTAAATAGCGT
* ** *
4964 CTACCCAATTGATT--TTTTTGTTTT
66 C-ACCCAATTAATTAATTTTAATTAT
4988 TTATTTATTAT
1 TTATTTATTAT
4999 ATAATATTTA
Statistics
Matches: 158, Mismatches: 26, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
87 4 0.03
88 13 0.08
89 1 0.01
90 39 0.25
91 5 0.03
93 7 0.04
94 15 0.09
96 16 0.10
97 7 0.04
99 4 0.03
100 39 0.25
101 8 0.05
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (90 bp):
TTATTTATTATTTATTTTATAAAAATTTAAATTTATTTTTTTGGTGGAGACATTTTAAATAGCGT
CACCCAATTAATTAATTTTAATTAT
Found at i:5023 original size:17 final size:17
Alignment explanation
Indices: 4987--5041 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
4977 TTTTTTGTTT
*
4987 TTTATTT-ATTATATAA
1 TTTATTTAAATATATAA
5003 --TATTTAAATATATAA
1 TTTATTTAAATATATAA
*
5018 TTTATTTTAAAT-TATAT
1 TTTA-TTTAAATATATAA
5035 TTTATTT
1 TTTATTT
5042 TTGGTGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 3 0.09
17 10 0.30
18 7 0.21
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATTTAAATATATAA
Found at i:5043 original size:18 final size:18
Alignment explanation
Indices: 5005--5042 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
4995 TTATATAATA
5005 TTTAAATATATAATTTAT
1 TTTAAATATATAATTTAT
*
5023 TTTAAAT-TATATTTTAT
1 TTTAAATATATAATTTAT
5040 TTT
1 TTT
5043 TGGTGGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATATATAATTTAT
Found at i:5044 original size:102 final size:106
Alignment explanation
Indices: 4937--5167 Score: 326
Period size: 105 Copynumber: 2.2 Consensus size: 106
4927 TAAATTTATT
* * *
4937 TTTTTGGTGGAGTCATTTTAAATAGCGCTACCCAATTGA-TTTTT-TTGTTTT-TTATTTATTAT
1 TTTTTGGTGGAGTCATTTTAAATAGCACCACCCAATTAATTTTTTGTTGTTTTATTATTTATTAT
*
4999 ATAATATTTAAATATATAATTTATTTTAAAT-TATATTTTA
66 ATAATATTTAAATATATAATTTAATTTAAATGTATATTTTA
* * * *
5039 TTTTTGGTGGAATCATTTTAAATGGCACCATCCAATTAATTTTTTGTTTTTTTATTATTTATTAT
1 TTTTTGGTGGAGTCATTTTAAATAGCACCACCCAATTAATTTTTTGTTGTTTTATTATTTATTAT
* *
5104 TTAATATTTAAATATATAGTTTAATTTAAATGTATATTTTA
66 ATAATATTTAAATATATAATTTAATTTAAATGTATATTTTA
* *
5145 TTTTTGGTGGAGCCATTCTAAAT
1 TTTTTGGTGGAGTCATTTTAAAT
5168 GGTGCCACCA
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
102 33 0.29
103 5 0.04
104 6 0.05
105 39 0.35
106 29 0.26
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (106 bp):
TTTTTGGTGGAGTCATTTTAAATAGCACCACCCAATTAATTTTTTGTTGTTTTATTATTTATTAT
ATAATATTTAAATATATAATTTAATTTAAATGTATATTTTA
Found at i:5058 original size:192 final size:190
Alignment explanation
Indices: 4710--5061 Score: 548
Period size: 192 Copynumber: 1.8 Consensus size: 190
4700 TGTGTTAGCC
* *
4710 TTATTTATTATTTATTTTTTTAAAATTTAAATTTAGTTTTTTGGTGGAACTATTTTAAATGACGT
1 TTATTTATTATTTATTTTCTAAAAATTTAAATTTAGTTTTTTGGTGGAACTATTTTAAATGACGT
4775 CACCCAATTGATTTGTTTTATTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATTA
66 CACCCAATTGATTTGTTTTATTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATTA
**
4840 TATTTTATTTTTGGTGGTGCCATTTTAAATAGTGTCACTCAATTAATTAATTATTAATTA
131 TATTTTATTTTTGGTGGAACCATTTTAAATAGTGTCACTCAATTAATTAATTATTAATTA
* *
4900 TTATTTATTATTTATTTTCTAAAAATTTAAATTTATTTTTTTGGTGG-AGTCATTTTAAAT-AGC
1 TTATTTATTATTTATTTTCTAAAAATTTAAATTTAGTTTTTTGGTGGAACT-ATTTTAAATGA-C
* * *
4963 G-CTACCCAATTGATTTTTTTGTTTTTTATTTATTATATAATATTTAAATATATAATTTATTTTA
64 GTC-ACCCAATTGA-TTTGTT-TTATTTATTTATTATATAATATTTAAATATATAATTTAATTTA
*
5027 AATTATATTTTATTTTTGGTGGAATCATTTTAAAT
126 AATTATATTTTATTTTTGGTGGAACCATTTTAAAT
5062 GGCACCATCC
Statistics
Matches: 147, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
189 4 0.03
190 65 0.44
191 5 0.03
192 73 0.50
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (190 bp):
TTATTTATTATTTATTTTCTAAAAATTTAAATTTAGTTTTTTGGTGGAACTATTTTAAATGACGT
CACCCAATTGATTTGTTTTATTTATTTATTATATAATATTTAAATATATAATTTAATTTAAATTA
TATTTTATTTTTGGTGGAACCATTTTAAATAGTGTCACTCAATTAATTAATTATTAATTA
Found at i:5132 original size:18 final size:18
Alignment explanation
Indices: 5109--5144 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5099 ATTATTTAAT
5109 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
5127 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
5145 TTTTTGGTGG
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:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:5179 original size:105 final size:102
Alignment explanation
Indices: 4747--5180 Score: 282
Period size: 105 Copynumber: 4.4 Consensus size: 102
4737 TAAATTTAGT
* * * * * *
4747 TTTTTGGTGGA-ACTATTTTAAATGACGTCACCCAATTGA-TTTGTT-TTATTTATTTATTATAT
1 TTTTTGGTGGAGTC-ATTTTAAATGGCGCCACCCAATTAATTTTTTTGTTTTTTATTTATTATAT
4809 AATATTTAAATATATAATTTAATTTAAATTATATTTTA
65 AATATTTAAATATATAATTTAATTTAAATTATATTTTA
* * * * * * * ** *
4847 TTTTTGGTGGTGCCATTTTAAATAGTGTCACTCAATTAATTAATTATTAATTATTATTTATTAT-
1 TTTTTGGTGGAGTCATTTTAAATGGCGCCACCCAATTAATT--TTTTTGTTTTTTATTTATTATA
*
4911 T--TATTT---TCTA-AA---AATTTAAATT-TATTTT-
64 TAATATTTAAATATATAATTTAATTTAAATTATATTTTA
* * * * ** * * * *
4939 TTTGGTGGAGTCA-T--TTTAAATA-GCGCTAC-CCAATTGATTTTTTT-GTTTTTTATTTATTA
1 TTT-TTGGTG-GAGTCATTTTAA-ATG-GCGCCACCCAATTAATTTTTTTGTTTTTTATTTATTA
*
4998 TATAATATTTAAATATATAATTTATTTTAAATTATATTTTA
62 TATAATATTTAAATATATAATTTAATTTAAATTATATTTTA
* * * *
5039 TTTTTGGTGGAATCATTTTAAATGGCACCATCCAATTAATTTTTTGTTTTTTTATTATTTATTAT
1 TTTTTGGTGGAGTCATTTTAAATGGCGCCACCCAATTAA-TTTTT-TTGTTTT-TTATTTATTAT
* *
5104 TTAATATTTAAATATATAGTTTAATTTAAATGTATATTTTA
63 ATAATATTTAAATATATAATTTAATTTAAAT-TATATTTTA
* * *
5145 TTTTTGGTGGAGCCATTCTAAATGGTGCCA-CCAATT
1 TTTTTGGTGGAGTCATTTTAAATGGCGCCACCCAATT
5181 CTTGATGATA
Statistics
Matches: 250, Mismatches: 53, Indels: 57
0.69 0.15 0.16
Matches are distributed among these distances:
88 13 0.05
89 4 0.02
91 16 0.06
92 6 0.02
93 10 0.04
94 13 0.05
95 2 0.01
97 2 0.01
98 13 0.05
99 11 0.04
100 37 0.15
101 17 0.07
102 5 0.02
103 6 0.02
104 16 0.06
105 45 0.18
106 34 0.14
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.52
Consensus pattern (102 bp):
TTTTTGGTGGAGTCATTTTAAATGGCGCCACCCAATTAATTTTTTTGTTTTTTATTTATTATATA
ATATTTAAATATATAATTTAATTTAAATTATATTTTA
Found at i:5195 original size:105 final size:103
Alignment explanation
Indices: 5010--5198 Score: 229
Period size: 106 Copynumber: 1.8 Consensus size: 103
5000 TAATATTTAA
* * *
5010 ATATATAATTTATTTTAAATTATATTTTATTTTTGGTGGAATCATTTTAAATGGCACCATCCAAT
1 ATATATAATTTAATTTAAATTATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAAT
* **
5075 TAATTTTTTGTTTTTTTATTATTTATTATTTAATATTTAA
66 T-ACTTGATGTTTTTTT-TTATTTATTATTTAATATTTAA
* * **
5115 ATATATAGTTTAATTTAAATGTATATTTTATTTTTGGTGGAGCCATTCTAAATGGTGCCA-CCAA
1 ATATATAATTTAATTTAAAT-TATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAA
5179 TT-CTTGATGATATTTTTTTT
65 TTACTTGATG-T-TTTTTTTT
5199 TGTTTGTTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
103 4 0.06
104 3 0.04
105 30 0.42
106 34 0.48
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (103 bp):
ATATATAATTTAATTTAAATTATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAAT
TACTTGATGTTTTTTTTTATTTATTATTTAATATTTAA
Found at i:5209 original size:105 final size:104
Alignment explanation
Indices: 5010--5210 Score: 235
Period size: 105 Copynumber: 1.9 Consensus size: 104
5000 TAATATTTAA
* * *
5010 ATATATAATTTATTTTAAATTATATTTTATTTTTGGTGGAATCATTTTAAATGGCACCATCCAAT
1 ATATATAATTTAATTTAAATTATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAAT
* ** *
5075 TAATTTTTTGTTTTTTTATTATTTATTATTTAATATTTAA
66 T-ACTTGATGTTTTTTTTTTATTTATTATTTAATATTTAA
* * **
5115 ATATATAGTTTAATTTAAATGTATATTTTATTTTTGGTGGAGCCATTCTAAATGGTGCCA-CCAA
1 ATATATAATTTAATTTAAAT-TATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAA
* *
5179 TT-CTTGATGATATTTTTTTTTGTTTGTTATTT
65 TTACTTGATG-T-TTTTTTTTTATTTATTATTT
5211 TTTTTTTAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
103 4 0.05
104 1 0.01
105 41 0.51
106 34 0.43
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.54
Consensus pattern (104 bp):
ATATATAATTTAATTTAAATTATATTTTATTTTTGGTGGAACCATTCTAAATGGCACCATCCAAT
TACTTGATGTTTTTTTTTTATTTATTATTTAATATTTAA
Found at i:10829 original size:19 final size:19
Alignment explanation
Indices: 10805--10844 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
10795 ATTAAATAGA
10805 AATGAAATA-TAAATAAAAC
1 AATGAAA-AGTAAATAAAAC
*
10824 AATGAAAAGTAAATAATAC
1 AATGAAAAGTAAATAAAAC
10843 AA
1 AA
10845 ATGTAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 1 0.05
19 18 0.95
ACGTcount: A:0.68, C:0.05, G:0.07, T:0.20
Consensus pattern (19 bp):
AATGAAAAGTAAATAAAAC
Found at i:16949 original size:20 final size:21
Alignment explanation
Indices: 16911--16950 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
16901 TAAACCTAGC
*
16911 ATTACTGAGTTAGAAAATGCG
1 ATTACTAAGTTAGAAAATGCG
16932 ATTACTAAGTTA-AAAATGC
1 ATTACTAAGTTAGAAAATGC
16951 TAAAAATGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.30
Consensus pattern (21 bp):
ATTACTAAGTTAGAAAATGCG
Found at i:19419 original size:50 final size:50
Alignment explanation
Indices: 19340--19440 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 50
19330 AAATATTAGT
*
19340 TATTTAATATTGTGATATCATCAATATCGTATTAAGTTTTGGTTATGAAA
1 TATTTAATATTGTGATATCATCAACATCGTATTAAGTTTTGGTTATGAAA
*
19390 TATTTAATATTGTGATGTCATCAACATCGTATTAAGTTTTGGTTATGAAA
1 TATTTAATATTGTGATATCATCAACATCGTATTAAGTTTTGGTTATGAAA
19440 T
1 T
19441 TTTGACGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (50 bp):
TATTTAATATTGTGATATCATCAACATCGTATTAAGTTTTGGTTATGAAA
Found at i:25191 original size:21 final size:21
Alignment explanation
Indices: 25167--25215 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25157 ACTTGTTTTG
25167 GTAGAAGAGACACTTGTATCA
1 GTAGAAGAGACACTTGTATCA
** * *
25188 GTAGAACTGCCACTTGTATCG
1 GTAGAAGAGACACTTGTATCA
25209 GTAGAAG
1 GTAGAAG
25216 TCTGCAATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (21 bp):
GTAGAAGAGACACTTGTATCA
Found at i:25564 original size:30 final size:29
Alignment explanation
Indices: 25523--25622 Score: 110
Period size: 30 Copynumber: 3.3 Consensus size: 29
25513 AGTACGTGTG
*
25523 TTCAAAGGTTGATCCTCCAGGTCGAGCTC
1 TTCATAGGTTGATCCTCCAGGTCGAGCTC
* * *
25552 TACCATAGGTTGATCCTCCATGTCGAACTCC
1 T-TCATAGGTTGATCCTCCAGGTCGAGCT-C
* * *
25583 TTTATAGGTTGATCCTCAAGGTCAAGCTC
1 TTCATAGGTTGATCCTCCAGGTCGAGCTC
25612 TGTCATAGGTT
1 T-TCATAGGTT
25623 AATTTTCACG
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
29 3 0.05
30 52 0.91
31 2 0.04
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (29 bp):
TTCATAGGTTGATCCTCCAGGTCGAGCTC
Found at i:27268 original size:27 final size:27
Alignment explanation
Indices: 27226--27278 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27216 TTTCACATAA
*
27226 AATTTCATCATTATATTTACTATTTCC
1 AATTTCATCATCATATTTACTATTTCC
* *
27253 AATTTCATCCTCATATTTTCTATTTC
1 AATTTCATCATCATATTTACTATTTC
27279 ACATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (27 bp):
AATTTCATCATCATATTTACTATTTCC
Found at i:27683 original size:24 final size:23
Alignment explanation
Indices: 27632--27698 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
27622 AAAATATTTA
* * *
27632 AAATTAAAATTAAAATTAGAAGG
1 AAATTAAAATAAAAAATAAAAGG
27655 AAATTAAAATAAAAAATAAAAGG
1 AAATTAAAATAAAAAATAAAAGG
*
27678 AGAATTATAAA-AATAAATAAA
1 A-AATTA-AAATAAAAAATAAA
27699 TAATGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 21 0.55
24 14 0.37
25 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (23 bp):
AAATTAAAATAAAAAATAAAAGG
Found at i:36177 original size:36 final size:36
Alignment explanation
Indices: 36076--36177 Score: 150
Period size: 36 Copynumber: 2.8 Consensus size: 36
36066 TTCGTTATTT
* * *
36076 GTTTTACTTCCTGTTGACCCAAAGGTCATAATGCTC
1 GTTTTACTCCCTATTGACCCAAAGGTCATGATGCTC
* * *
36112 GTTTTACTCCCAATTGACCTAGAGGTCATGATGCTC
1 GTTTTACTCCCTATTGACCCAAAGGTCATGATGCTC
36148 GTTTTACTCCCTATTGACCCAAAGGTCATG
1 GTTTTACTCCCTATTGACCCAAAGGTCATG
36178 CCTGTTACCA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (36 bp):
GTTTTACTCCCTATTGACCCAAAGGTCATGATGCTC
Found at i:43580 original size:18 final size:18
Alignment explanation
Indices: 43557--43606 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
43547 AAAATGCAGG
43557 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
*
43575 AAATGATGTTCAA-ATTTC
1 AAATGATGTT-AACACTTC
43593 AAATGATGTTAACA
1 AAATGATGTTAACA
43607 TTGATGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 2 0.07
18 25 0.86
19 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:44182 original size:72 final size:72
Alignment explanation
Indices: 44029--44355 Score: 559
Period size: 72 Copynumber: 4.6 Consensus size: 72
44019 CAATACAAAA
44029 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTT-TGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
44093 GTGCAAT
66 GTGCAAT
* * *
44100 CTAGTTTTATCAGTAATTGTTTATGTTTGATTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
44165 GTGTAAT
66 GTGCAAT
*
44172 CTAGTTTTATCTATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
44237 GTGCAAT
66 GTGCAAT
44244 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
44309 GTGTAAT
66 GTGCAAT
* * *
44316 TTAGTTTTATCAATAGTTGTTTATATTT-GATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATAT
44356 AAAATTTGTT
Statistics
Matches: 241, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
71 56 0.23
72 185 0.77
ACGTcount: A:0.22, C:0.06, G:0.16, T:0.56
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGCAAT
Done.