Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004070.1 Kokia drynarioides strain JFW-HI SEQ_117230, 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: 42337
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3983 original size:17 final size:18
Alignment explanation
Indices: 3961--3994 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3951 TATAATTAAT
3961 TTTATTA-GTTTAATATC
1 TTTATTACGTTTAATATC
*
3978 TTTATTACTTTTAATAT
1 TTTATTACGTTTAATAT
3995 GATTAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTATTACGTTTAATATC
Found at i:4629 original size:97 final size:97
Alignment explanation
Indices: 4463--4656 Score: 273
Period size: 97 Copynumber: 2.0 Consensus size: 97
4453 AACCTTGGAA
* * *
4463 AAGGGTATTCGATTATCCCGATTTGAAGAAAAGTCACGCCTAGTAAGTTAAGGCACAAATTTCCG
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAATTAAGGCACAAATTTCCA
* *
4528 AAA-CCAGAGATAAAGAAATATTGCCTCGATTT
66 AAACCCA-AAATAAAGAAATATTACCTCGATTT
** * *
4560 AAGGGTATTCGATTATCTTGATTTGAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAATTAAGGCACAAATTTCCA
* *
4625 AAACCCAAAATAAAGGAATATTATCTCGATTT
66 AAACCCAAAATAAAGAAATATTACCTCGATTT
4657 TAGATATTTT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
97 82 0.96
98 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAATTAAGGCACAAATTTCCA
AAACCCAAAATAAAGAAATATTACCTCGATTT
Found at i:4921 original size:28 final size:30
Alignment explanation
Indices: 4865--4935 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 30
4855 AGGAAAAATC
4865 GGGGTTGAAAATGAAGTTTTGAAGAG-TTT-
1 GGGGTT-AAAATGAAGTTTTGAAGAGTTTTA
4894 GGGGTTAAAATGCAA-TTTTGAA-ATGTTTTA
1 GGGGTTAAAATG-AAGTTTTGAAGA-GTTTTA
*
4924 GGGGTAAAAATG
1 GGGGTTAAAATG
4936 TCATTTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
27 1 0.03
28 14 0.38
29 11 0.30
30 11 0.30
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.34
Consensus pattern (30 bp):
GGGGTTAAAATGAAGTTTTGAAGAGTTTTA
Found at i:4985 original size:29 final size:30
Alignment explanation
Indices: 4923--5107 Score: 170
Period size: 30 Copynumber: 6.3 Consensus size: 30
4913 GAAATGTTTT
* * * *
4923 AGGGGTAAAAATGTCATTTTAGGAAAATTC-
1 AGGGGAAAAAATGTGATTTTTGG-AAGTTCG
* *
4953 -GGGGTAAAAA-GTGATTTTTGGATGTTCG
1 AGGGGAAAAAATGTGATTTTTGGAAGTTCG
* * *
4981 AGGGGGTAAAAATGTGATTTTTGAAAGTTTG
1 A-GGGGAAAAAATGTGATTTTTGGAAGTTCG
*
5012 -GGGGAAAAAATGTGATTTTTGGATGTTCG
1 AGGGGAAAAAATGTGATTTTTGGAAGTTCG
*
5041 AGGGGAAAAAATGTGATTTTTAGAAGTTCG
1 AGGGGAAAAAATGTGATTTTTGGAAGTTCG
*
5071 A--GG-AAAAATG-GAATTTTTGAAAGTTCG
1 AGGGGAAAAAATGTG-ATTTTTGGAAGTTCG
*
5098 AGGGTAAAAA
1 AGGGGAAAAA
5108 TGAAAGTTTT
Statistics
Matches: 130, Mismatches: 16, Indels: 18
0.79 0.10 0.11
Matches are distributed among these distances:
26 1 0.01
27 25 0.19
28 11 0.08
29 36 0.28
30 42 0.32
31 15 0.12
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.31
Consensus pattern (30 bp):
AGGGGAAAAAATGTGATTTTTGGAAGTTCG
Found at i:4991 original size:59 final size:59
Alignment explanation
Indices: 4923--5109 Score: 199
Period size: 59 Copynumber: 3.2 Consensus size: 59
4913 GAAATGTTTT
* *
4923 AGGGGTAAAAATGTCATTTTAGGAAA-ATTCGGGGTAAAAA-GTGATTTTTGGATGTTCG
1 AGGGGTAAAAATGTGATTTT-GGAAAGATTCGGGGAAAAAATGTGATTTTTGGATGTTCG
* * *
4981 AGGGGGTAAAAATGTGATTTTTGAAAGTTTGGGGGAAAAAATGTGATTTTTGGATGTTCG
1 A-GGGGTAAAAATGTGATTTTGGAAAGATTCGGGGAAAAAATGTGATTTTTGGATGTTCG
* * * * *
5041 AGGGGAAAAAATGTGATTTT-TAGAAG-TTCGAGG-AAAAATG-GAATTTTTGAAAGTTCG
1 AGGGGTAAAAATGTGATTTTGGA-AAGATTCGGGGAAAAAATGTG-ATTTTTGGATGTTCG
5098 A-GGGTAAAAATG
1 AGGGGTAAAAATG
5110 AAAGTTTTGG
Statistics
Matches: 112, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
56 11 0.10
57 21 0.19
58 11 0.10
59 50 0.45
60 19 0.17
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (59 bp):
AGGGGTAAAAATGTGATTTTGGAAAGATTCGGGGAAAAAATGTGATTTTTGGATGTTCG
Found at i:5086 original size:27 final size:29
Alignment explanation
Indices: 4925--5109 Score: 175
Period size: 29 Copynumber: 6.4 Consensus size: 29
4915 AATGTTTTAG
* * *
4925 GGGTAAAAATGTCATTTTAGGAAAATTCG-
1 GGGTAAAAATGTGATTTT-TGAAAGTTCGA
* *
4954 GGGTAAAAA-GTGATTTTTGGATGTTCGA
1 GGGTAAAAATGTGATTTTTGAAAGTTCGA
* *
4982 GGGGGTAAAAATGTGATTTTTGAAAGTTTGG
1 --GGGTAAAAATGTGATTTTTGAAAGTTCGA
* * *
5013 GGGAAAAAATGTGATTTTTGGATGTTCGA
1 GGGTAAAAATGTGATTTTTGAAAGTTCGA
*
5042 GGGGAAAAAATGTGATTTTT-AGAAGTTCGA
1 -GGGTAAAAATGTGATTTTTGA-AAGTTCGA
5072 -GG-AAAAATG-GAATTTTTGAAAGTTCGA
1 GGGTAAAAATGTG-ATTTTTGAAAGTTCGA
5099 GGGTAAAAATG
1 GGGTAAAAATG
5110 AAAGTTTTGG
Statistics
Matches: 130, Mismatches: 16, Indels: 20
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.01
27 27 0.21
28 12 0.09
29 40 0.31
30 35 0.27
31 15 0.12
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
GGGTAAAAATGTGATTTTTGAAAGTTCGA
Found at i:5117 original size:29 final size:29
Alignment explanation
Indices: 4872--5118 Score: 150
Period size: 29 Copynumber: 8.5 Consensus size: 29
4862 ATCGGGGTTG
* * *
4872 AAAATG-AAGTTTTGAAGAGTTTG-GGGTT
1 AAAATGTAATTTTTGAA-AGTTCGAGGGTA
* **
4900 AAAATGCAA-TTTTGAAATGTTTTAGGGGTA
1 AAAATGTAATTTTTGAAA-GTTCGA-GGGTA
* * *
4930 AAAATGTCATTTTAGGAAAATTCG-GGGTA
1 AAAATGTAATTTT-TGAAAGTTCGAGGGTA
* * *
4959 AAAA-GTGATTTTTGGATGTTCGAGGGGGTA
1 AAAATGTAATTTTTGAAAGTTCGA--GGGTA
* * * *
4989 AAAATGTGATTTTTGAAAGTTTGGGGGAA
1 AAAATGTAATTTTTGAAAGTTCGAGGGTA
* * * *
5018 AAAATGTGATTTTTGGATGTTCGAGGGGAA
1 AAAATGTAATTTTTGAAAGTTCGA-GGGTA
*
5048 AAAATGTGATTTTT-AGAAGTTCGA-GG-A
1 AAAATGTAATTTTTGA-AAGTTCGAGGGTA
*
5075 AAAATGGAATTTTTGAAAGTTCGAGGGTA
1 AAAATGTAATTTTTGAAAGTTCGAGGGTA
* *
5104 AAAATGAAAGTTTTG
1 AAAATGTAATTTTTG
5119 GGGTGAAAAT
Statistics
Matches: 176, Mismatches: 28, Indels: 29
0.76 0.12 0.12
Matches are distributed among these distances:
27 28 0.16
28 29 0.16
29 49 0.28
30 46 0.26
31 20 0.11
32 4 0.02
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTCGAGGGTA
Found at i:5169 original size:30 final size:29
Alignment explanation
Indices: 5108--5253 Score: 161
Period size: 30 Copynumber: 4.9 Consensus size: 29
5098 AGGGTAAAAA
* *
5108 TGAAAGTTTTG-GGGTGAAAATGCAATTTT
1 TGAAAG-TTTGAGGGTAAAAATGTAATTTT
*
5137 AGAAAGTTTGAGGGTAAAAATGTAATTTT
1 TGAAAGTTTGAGGGTAAAAATGTAATTTT
5166 TAGAAAGTTT-ATGGGTAAAAATGTAATTTT
1 T-GAAAGTTTGA-GGGTAAAAATGTAATTTT
* *
5196 TGAGAAGTTTGAGGGTCAAAATATAATTTT
1 TGA-AAGTTTGAGGGTAAAAATGTAATTTT
* * *
5226 TGTAAAGTTCGAGGGTTAAAATATAATT
1 TG-AAAGTTTGAGGGTAAAAATGTAATT
5254 GTTGGGAAGT
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
28 4 0.04
29 24 0.23
30 73 0.71
31 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (29 bp):
TGAAAGTTTGAGGGTAAAAATGTAATTTT
Found at i:5682 original size:23 final size:23
Alignment explanation
Indices: 5638--5684 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5628 GATCATCGCT
* *
5638 CATCGTCGATCGCTGCCAACTGC
1 CATCGTCCATCGCTACCAACTGC
5661 CATCGTCCATCGCTACGC-ACTGC
1 CATCGTCCATCGCTAC-CAACTGC
5684 C
1 C
5685 GTCCATGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 20 0.95
24 1 0.05
ACGTcount: A:0.17, C:0.43, G:0.19, T:0.21
Consensus pattern (23 bp):
CATCGTCCATCGCTACCAACTGC
Found at i:5859 original size:13 final size:13
Alignment explanation
Indices: 5841--5870 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5831 GATCTGTTTG
5841 TTTTCCCTTTTTA
1 TTTTCCCTTTTTA
*
5854 TTTTCCTTTTTTA
1 TTTTCCCTTTTTA
5867 TTTT
1 TTTT
5871 TGCTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCCCTTTTTA
Found at i:10305 original size:22 final size:22
Alignment explanation
Indices: 10261--10305 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10251 TTTCATAATT
* *
10261 AACTTAATTAATCATCTTTTTA
1 AACTTAATTAATCATATTATTA
*
10283 AACTTAATTAATCCTATTATTA
1 AACTTAATTAATCATATTATTA
10305 A
1 A
10306 TCAATATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (22 bp):
AACTTAATTAATCATATTATTA
Found at i:15614 original size:21 final size:21
Alignment explanation
Indices: 15588--15661 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
15578 AGACTTTTAT
15588 CGATACAAGTATTCTAACTAC
1 CGATACAAGTATTCTAACTAC
* *
15609 CGATACAAATATGCTTAGTACTAC
1 CGATACAAGTATTC-TA--ACTAC
* ** * *
15633 CGAAACTTGAATTCCAACTAC
1 CGATACAAGTATTCTAACTAC
15654 CGATACAA
1 CGATACAA
15662 CTCAAGTTAG
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 22 0.58
22 2 0.05
23 1 0.03
24 13 0.34
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (21 bp):
CGATACAAGTATTCTAACTAC
Found at i:16278 original size:41 final size:41
Alignment explanation
Indices: 16209--16381 Score: 235
Period size: 41 Copynumber: 4.2 Consensus size: 41
16199 TCTAGCCATA
*
16209 AGTCTTCCTTTAA-CTATATTCTCATTCTCATTTCGAGACATG
1 AGTCTTCC-TTAATC-ATAATCTCATTCTCATTTCGAGACATG
16251 AGTCTTCCTTAATCATAATCTCATTCTCA-TTCTGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATTTC-GAGACATG
* * *
16292 AGTTTTCCTTATTCATAATCTCATTCTCATTCCGAGACATG
1 AGTCTTCCTTAATCATAATCTCATTCTCATTTCGAGACATG
* *
16333 AGTCTTCCTTATTCATAATCTCATTCTCATCTCGAGACACT-
1 AGTCTTCCTTAATCATAATCTCATTCTCATTTCGAGACA-TG
16374 AGTCTTCC
1 AGTCTTCC
16382 ATTTATACAA
Statistics
Matches: 120, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
40 3 0.03
41 105 0.88
42 12 0.10
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.40
Consensus pattern (41 bp):
AGTCTTCCTTAATCATAATCTCATTCTCATTTCGAGACATG
Found at i:16421 original size:43 final size:41
Alignment explanation
Indices: 16242--16426 Score: 151
Period size: 41 Copynumber: 4.5 Consensus size: 41
16232 ATTCTCATTT
* * **
16242 CGAGACATGAGTCTTCCTTA-ATCATAATCTCATTCTCATTC
1 CGAGACATGAGTCTTCCTTATA-CATAATATCATGCTCAACC
* * * * * **
16283 TGAGACATGAGTTTTCCTTATTCATAATCTCATTCTCATTC
1 CGAGACATGAGTCTTCCTTATACATAATATCATGCTCAACC
* * * * *
16324 CGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTATACATAATATCATGCTCAACC
*
16365 CGAGACACT-AGTCTTCCATTTATACA-ATTTATCATGCTCAACC
1 CGAGACA-TGAGTCTTCC--TTATACATA-ATATCATGCTCAACC
16408 CGAGACATGAGTCTTCCTT
1 CGAGACATGAGTCTTCCTT
16427 TTTCTAAACC
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
41 91 0.73
42 3 0.02
43 31 0.25
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTATACATAATATCATGCTCAACC
Found at i:17095 original size:3 final size:3
Alignment explanation
Indices: 17087--17114 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17077 TGTCGTGTAG
17087 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
17115 AGAAAATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17241 original size:22 final size:21
Alignment explanation
Indices: 17194--17241 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
17184 GACTTTCATA
*
17194 ATTAACTAAATTAATCATCTT
1 ATTAACTAAATTAATCATATT
* * *
17215 TTTAACCTTAATTAATCTTATT
1 ATTAA-CTAAATTAATCATATT
17237 ATTAA
1 ATTAA
17242 TCAATATTTG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTAACTAAATTAATCATATT
Found at i:17977 original size:20 final size:20
Alignment explanation
Indices: 17952--17990 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
17942 ATGTGGTGAC
17952 ATTAGTAGCAAAAGTAGGAT
1 ATTAGTAGCAAAAGTAGGAT
17972 ATTAGTAGCAAAAGTAGGA
1 ATTAGTAGCAAAAGTAGGA
17991 CAAAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.05, G:0.26, T:0.23
Consensus pattern (20 bp):
ATTAGTAGCAAAAGTAGGAT
Found at i:18398 original size:3 final size:3
Alignment explanation
Indices: 18392--18452 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
18382 TATATAAACA
18392 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
18440 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
18453 TCAACTGAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19045 original size:17 final size:17
Alignment explanation
Indices: 19025--19067 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
19015 AAATACAACT
19025 ACAATGCAAATGCG-TCG
1 ACAATGCAAATGCGAT-G
**
19042 ACAATTAAAATGCGATG
1 ACAATGCAAATGCGATG
19059 ACAATGCAA
1 ACAATGCAA
19068 TTACAACTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 20 0.95
18 1 0.05
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.19
Consensus pattern (17 bp):
ACAATGCAAATGCGATG
Found at i:26075 original size:41 final size:43
Alignment explanation
Indices: 26022--26109 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 43
26012 TACAGTTAAA
*
26022 AATATTAAAACAAATATTAAAATAACAAACAAATT-AAAA-AC
1 AATATTAAAACAAATAGTAAAATAACAAACAAATTGAAAATAC
* * *
26063 AATATTAAAACAATTCGTAAAATAACTAACAAATTGAAAATAC
1 AATATTAAAACAAATAGTAAAATAACAAACAAATTGAAAATAC
26106 AATA
1 AATA
26110 AGAACCCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 31 0.76
42 4 0.10
43 6 0.15
ACGTcount: A:0.64, C:0.10, G:0.02, T:0.24
Consensus pattern (43 bp):
AATATTAAAACAAATAGTAAAATAACAAACAAATTGAAAATAC
Found at i:32299 original size:15 final size:16
Alignment explanation
Indices: 32279--32316 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
32269 GTACTGCCTC
32279 TTTTTTCCTACTCT-T
1 TTTTTTCCTACTCTCT
*
32294 TTTTTTCCTGCTCTCT
1 TTTTTTCCTACTCTCT
32310 TTTTTTC
1 TTTTTTC
32317 AACAATGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTTTCCTACTCTCT
Found at i:32733 original size:31 final size:31
Alignment explanation
Indices: 32697--32771 Score: 141
Period size: 31 Copynumber: 2.4 Consensus size: 31
32687 TATGATAGAG
32697 AAGAATGGGGTTTTTTGTGTGATATCATGGA
1 AAGAATGGGGTTTTTTGTGTGATATCATGGA
*
32728 TAGAATGGGGTTTTTTGTGTGATATCATGGA
1 AAGAATGGGGTTTTTTGTGTGATATCATGGA
32759 AAGAATGGGGTTT
1 AAGAATGGGGTTT
32772 GACACAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.39
Consensus pattern (31 bp):
AAGAATGGGGTTTTTTGTGTGATATCATGGA
Found at i:33014 original size:16 final size:16
Alignment explanation
Indices: 32993--33023 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
32983 ATAATGTGAA
32993 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
33009 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
33024 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:33848 original size:26 final size:26
Alignment explanation
Indices: 33805--33858 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
33795 ATTTTGGGCG
33805 CAATTCTGGACACATTCATGCAGCGA
1 CAATTCTGGACACATTCATGCAGCGA
* **
33831 CAATTCTGTACATGTTCATGCAGCGA
1 CAATTCTGGACACATTCATGCAGCGA
33857 CA
1 CA
33859 TTCCTGGCTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACACATTCATGCAGCGA
Found at i:39574 original size:27 final size:28
Alignment explanation
Indices: 39526--39579 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
39516 AATCAGTACA
* *
39526 TCAGTCTGATATTTCAGTCAAT-TCATT
1 TCAGTCTGATAATTCACTCAATATCATT
39553 TCAGTCT-ATAATTCACTACAATATCAT
1 TCAGTCTGATAATTCACT-CAATATCAT
39580 ATAACTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 8 0.35
27 11 0.48
28 4 0.17
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.41
Consensus pattern (28 bp):
TCAGTCTGATAATTCACTCAATATCATT
Done.