Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013189.1 Kokia drynarioides strain JFW-HI SEQ_128208, 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: 51242
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 121 characters in sequence are not A, C, G, or T
Found at i:3898 original size:10 final size:9
Alignment explanation
Indices: 3885--3953 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
3875 ATATATATTG
3885 TTTTCTTTT
1 TTTTCTTTT
*
3894 CTTT-TTTT
1 TTTTCTTTT
*
3902 TTTCCTTTT
1 TTTTCTTTT
3911 TGTTCTCTTTT
1 T-TT-TCTTTT
3922 TTTT-TGTCTT
1 TTTTCT-T-TT
*
3932 TTTTCCTTT
1 TTTTCTTTT
*
3941 TTTTGTTTT
1 TTTTCTTTT
3950 TTTT
1 TTTT
3954 TTGTGTATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
8 7 0.15
9 23 0.49
10 11 0.23
11 6 0.13
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:3909 original size:12 final size:11
Alignment explanation
Indices: 3885--3935 Score: 57
Period size: 12 Copynumber: 4.5 Consensus size: 11
3875 ATATATATTG
*
3885 TTTTCTTTTCT
1 TTTTTTTTTCT
3896 TTTTTTTTTCCT
1 TTTTTTTTT-CT
* *
3908 TTTTGTTCTCT
1 TTTTTTTTTCT
3919 TTTTTTTTGTCT
1 TTTTTTTT-TCT
3931 TTTTT
1 TTTTT
3936 CCTTTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTCT
Found at i:3916 original size:21 final size:21
Alignment explanation
Indices: 3890--3944 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
3880 TATTGTTTTC
3890 TTTTCTTTTTTTTTT-CCTTT
1 TTTTCTTTTTTTTTTGCCTTT
*
3910 TTGTTCTCTTTTTTTTTGTCTTT
1 TT-TTCT-TTTTTTTTTGCCTTT
*
3933 TTTCCTTTTTTT
1 TTTTCTTTTTTT
3945 GTTTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 2 0.07
21 10 0.33
22 12 0.40
23 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTCTTTTTTTTTTGCCTTT
Found at i:3937 original size:31 final size:29
Alignment explanation
Indices: 3899--3957 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 29
3889 CTTTTCTTTT
3899 TTTTTTCCTTTTTGTTCTCTTTTTTTTTGTC
1 TTTTTTCCTTTTT-TTCT-TTTTTTTTTGTC
*
3930 TTTTTTCCTTTTTTTGTTTTTTTTTTGT
1 TTTTTTCCTTTTTTTCTTTTTTTTTTGT
3958 GTATGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 3 0.11
31 13 0.48
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (29 bp):
TTTTTTCCTTTTTTTCTTTTTTTTTTGTC
Found at i:5320 original size:72 final size:74
Alignment explanation
Indices: 5168--5327 Score: 218
Period size: 75 Copynumber: 2.2 Consensus size: 74
5158 TTATGAGCAC
* * * *
5168 GCCTTATT-TTAGAGTTTCTTCTGTGAACAAAAATGTTGTACTTCTTGATGTTCTGCAATAATAA
1 GCCTTATTCTT-GAATTTCTTCTGTGAAAAAAAATATTGTACTTCTTGATGTTC-GCAACAATAA
5232 GGCGTGGGCAT
64 GGCGTGGGCAT
* *
5243 GCCTTATTCTTGAATTTCTTTTGTGAAAAAAAATATTGTACTTCTTGATGTTC-C-ACACTAAGG
1 GCCTTATTCTTGAATTTCTTCTGTGAAAAAAAATATTGTACTTCTTGATGTTCGCAACAATAAGG
5306 CGTGGGCAT
66 CGTGGGCAT
*
5315 GCCTTACTCTTGA
1 GCCTTATTCTTGA
5328 TTCACCCAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 5
0.87 0.08 0.06
Matches are distributed among these distances:
72 28 0.36
73 1 0.01
75 46 0.60
76 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (74 bp):
GCCTTATTCTTGAATTTCTTCTGTGAAAAAAAATATTGTACTTCTTGATGTTCGCAACAATAAGG
CGTGGGCAT
Found at i:8996 original size:17 final size:17
Alignment explanation
Indices: 8974--9008 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
8964 ACAATCCATG
8974 AAGGGAAAAAGAATAGA
1 AAGGGAAAAAGAATAGA
8991 AAGGGAAAAAGAATAGA
1 AAGGGAAAAAGAATAGA
9008 A
1 A
9009 GAATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.06
Consensus pattern (17 bp):
AAGGGAAAAAGAATAGA
Found at i:13912 original size:30 final size:30
Alignment explanation
Indices: 13869--14147 Score: 227
Period size: 30 Copynumber: 9.4 Consensus size: 30
13859 AAAGGGGCCA
* *
13869 AAAATA-AAGTTTTGGAGAATTTTAAGGGTT
1 AAAATATAA-TTTTGGAAAAGTTTAAGGGTT
* *
13899 AAAACATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* *
13929 AAAATGTAATTTTGGAAAAGTTT--GTGGTC
1 AAAATATAATTTTGGAAAAGTTTAAG-GGTT
*
13958 AAAATGTAATTTTGGAAAAGTTTAA-GGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* * * *
13987 AAAACATGATTTTGGAAAACTTTAGGGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* * *
14017 AAAA-GTAATTTTAGAAAAGTTTAATGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
** *
14046 AAAATATAATTTTCAAAAAGTTT-ATGGTT
1 AAAATATAATTTTGGAAAAGTTTAAGGGTT
* *
14075 CAAAATGTAATTTT-CAAGAAGTTT-A-GGTT
1 -AAAATATAATTTTGGAA-AAGTTTAAGGGTT
**
14104 CAAAATATAATTTTTGGTGAAGTTTAAGGG-T
1 -AAAATATAA-TTTTGGAAAAGTTTAAGGGTT
* *
14135 CAAATGTAATTTT
1 AAAATATAATTTT
14148 AAAAAGGTTT
Statistics
Matches: 207, Mismatches: 30, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
28 1 0.00
29 97 0.47
30 103 0.50
31 4 0.02
32 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AAAATATAATTTTGGAAAAGTTTAAGGGTT
Found at i:13971 original size:29 final size:30
Alignment explanation
Indices: 13878--14176 Score: 220
Period size: 29 Copynumber: 10.1 Consensus size: 30
13868 AAAAATAAAG
* * * * **
13878 TTTTGGAGAATTTTAAGGGTTAAAACATAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
*
13908 TTTTGGAAAAGTTTAGGGGTTAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
*
13938 TTTTGGAAAAGTTT-GTGGTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
* * *
13967 TTTTGGAAAAGTTTAAGGTTAAAACATG--A
1 TTTTGGAAAAGTTTAGGGGTCAAA-ATGTAA
* *
13996 TTTTGGAAAACTTTAGGGGTTAAAA-GTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
* ** * *
14025 TTTTAGAAAAGTTTAATGGTTAAAATATAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
** * *
14055 TTTTCAAAAAGTTTATGGTTCAAAATGTAA
1 TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
* * *
14085 TTTT-CAAGAAGTTTA-GGTTCAAAATATAA
1 TTTTGGAA-AAGTTTAGGGGTCAAAATGTAA
** *
14114 TTTTTGGTGAAGTTTAAGGGTC-AAATGTAA
1 -TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
* * *
14144 TTTT-AAAAAGGTTT-GGGGTCAAATTTTAA
1 TTTTGGAAAA-GTTTAGGGGTCAAAATGTAA
14173 TTTT
1 TTTT
14177 TTGTGATGTT
Statistics
Matches: 218, Mismatches: 40, Indels: 23
0.78 0.14 0.08
Matches are distributed among these distances:
27 1 0.00
28 8 0.04
29 103 0.47
30 99 0.45
31 7 0.03
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (30 bp):
TTTTGGAAAAGTTTAGGGGTCAAAATGTAA
Found at i:13975 original size:59 final size:58
Alignment explanation
Indices: 13905--14147 Score: 246
Period size: 59 Copynumber: 4.1 Consensus size: 58
13895 GGTTAAAACA
*
13905 TAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTT-GTGGTCAAAATG
1 TAATTTTGGAAAAGTTTA--GGTTAAAATATAATTTTGGAAAAGTTTAGTGGTCAAAATG
* * * * *
13964 TAATTTTGGAAAAGTTTAAGGTTAAAACATGATTTTGGAAAACTTTAGGGGTTAAAA-G
1 TAATTTTGGAAAAGTTT-AGGTTAAAATATAATTTTGGAAAAGTTTAGTGGTCAAAATG
* **
14022 TAATTTTAGAAAAGTTTAATGGTTAAAATATAATTTTCAAAAAGTTTA-TGGTTCAAAATG
1 TAATTTTGGAAAAGTTT-A-GGTTAAAATATAATTTTGGAAAAGTTTAGTGG-TCAAAATG
* **
14082 TAATTTT-CAAGAAGTTTAGGTTCAAAATATAATTTTTGGTGAAGTTTAAG-GGTC-AAATG
1 TAATTTTGGAA-AAGTTTAGGTT-AAAATATAA-TTTTGGAAAAGTTT-AGTGGTCAAAATG
14141 TAATTTT
1 TAATTTT
14148 AAAAAGGTTT
Statistics
Matches: 155, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
58 48 0.31
59 77 0.50
60 27 0.17
61 3 0.02
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (58 bp):
TAATTTTGGAAAAGTTTAGGTTAAAATATAATTTTGGAAAAGTTTAGTGGTCAAAATG
Found at i:14019 original size:88 final size:88
Alignment explanation
Indices: 13869--14088 Score: 273
Period size: 88 Copynumber: 2.5 Consensus size: 88
13859 AAAGGGGCCA
* * *
13869 AAAATA-AAGTTTTGGAGAATTTTAAGGGTTAAAACATAATTTTGGAAAAGTTTAGGGGTTAAAA
1 AAAATATAA-TTTTGGAAAAGTTTAA-GGTTAAAACATAATTTTGGAAAACTTTAGGGGTTAAAA
* *
13933 TGTAATTTTGGAAAAGTTT-GTGGTC
64 -GTAATTTTAGAAAAGTTTAATGGTC
* *
13958 AAAATGTAATTTTGGAAAAGTTTAAGGTTAAAACATGATTTTGGAAAACTTTAGGGGTTAAAAGT
1 AAAATATAATTTTGGAAAAGTTTAAGGTTAAAACATAATTTTGGAAAACTTTAGGGGTTAAAAGT
*
14023 AATTTTAGAAAAGTTTAATGGTT
66 AATTTTAGAAAAGTTTAATGGTC
** * **
14046 AAAATATAATTTTCAAAAAGTTTATGGTTCAAAATGTAATTTT
1 AAAATATAATTTTGGAAAAGTTTAAGGTT-AAAACATAATTTT
14089 CAAGAAGTTT
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
87 17 0.15
88 65 0.58
89 29 0.26
90 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (88 bp):
AAAATATAATTTTGGAAAAGTTTAAGGTTAAAACATAATTTTGGAAAACTTTAGGGGTTAAAAGT
AATTTTAGAAAAGTTTAATGGTC
Found at i:14166 original size:59 final size:60
Alignment explanation
Indices: 13869--14207 Score: 185
Period size: 59 Copynumber: 5.7 Consensus size: 60
13859 AAAGGGGCCA
* * * * ** ** *
13869 AAAATA-AAGTTTTGGAGAATTTTAAGGGTTAAAACATAATTTTGGAAAAGTTTAGGGGTT
1 AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTTCAAAAAGTTTA-GGGTC
* ** ** * *
13929 AAAATGTAA-TTTTGGAAAAGTTT--GTGGTCAAAATGTAATTTTGGAAAAGTTTAAGGTT
1 AAAATATAATTTTTGGTGAAGTTTAAG-GGTCAAAATGTAATTTTCAAAAAGTTTAGGGTC
* * ** * * * * *
13987 AAAACATGA-TTTTGGAAAACTTTAGGGGTTAAAA-GTAATTTT-AGAAAAGTTTAATGGTT
1 AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTTCA-AAAAGTTT-AGGGTC
**** * * * *
14046 AAAATATAA-TTTTCAAAAAGTTTATGGTTCAAAATGTAATTTTCAAGAAGTTTAGGTTC
1 AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTTCAAAAAGTTTAGGGTC
*
14105 AAAATATAATTTTTGGTGAAGTTTAAGGGTC-AAATGTAATTTT-AAAAAGGTTTGGGGTC
1 AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTTCAAAAA-GTTTAGGGTC
* * * * * * * *
14164 AAATTTTAATTTTTTGTGATGTTTACGAGTTAAAATGTGATTTT
1 AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTT
14208 TAGATAAAAA
Statistics
Matches: 225, Mismatches: 43, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
58 44 0.20
59 119 0.53
60 59 0.26
61 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.39
Consensus pattern (60 bp):
AAAATATAATTTTTGGTGAAGTTTAAGGGTCAAAATGTAATTTTCAAAAAGTTTAGGGTC
Found at i:14591 original size:27 final size:28
Alignment explanation
Indices: 14546--14601 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
14536 TTTAAAACTC
*
14546 AAAAAAATCACTTTACCCCTTTTATTTT
1 AAAAAAATCACTTTACCCCTCTTATTTT
*
14574 AAAAAAATCTAC-TT-CCCCTCTTCTTTT
1 AAAAAAATC-ACTTTACCCCTCTTATTTT
14601 A
1 A
14602 TTTCAAAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.48
28 11 0.44
29 2 0.08
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAAAAATCACTTTACCCCTCTTATTTT
Found at i:16030 original size:48 final size:48
Alignment explanation
Indices: 15958--16050 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
15948 ATTGAGTTTC
* * *
15958 GCTTCATTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACT
1 GCTTCATTGATTTGATCCACTTCTCCGTATCTCATCAGGAAGATGACT
* *
16006 GCTTCATTGTTTTGATCCATTTCTCCGTATCTCATCAGGAAGATG
1 GCTTCATTGATTTGATCCACTTCTCCGTATCTCATCAGGAAGATG
16051 GAGTTTGAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (48 bp):
GCTTCATTGATTTGATCCACTTCTCCGTATCTCATCAGGAAGATGACT
Found at i:16123 original size:123 final size:123
Alignment explanation
Indices: 15902--16179 Score: 382
Period size: 123 Copynumber: 2.3 Consensus size: 123
15892 TTTTAGTCCT
* * ** * *
15902 CTTCTCTGTATCTCGTCAGGAAGATGTG-GTTGGAAGTTTCACTCGTATTGAGTTTCGCTTCATT
1 CTTCTCTGTATCTCATCAGGAAGATG-GAGTTTGAAGTTTCACTCACATTGAGCTTCGCTCCATT
* *
15966 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGA-CTGCTTCATTGTTTTGATCCA
65 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATC-GCTTCATTATTTTGATCCA
* *
16025 TTTCTCCGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTCCATTG
1 CTTCTCTGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTCCATTG
* * *
16090 ATTTGGTTTATTTCTCTGTATCTCATCAAGAAGATTATCGCTTCATTATTTTGATCCA
66 ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTATTTTGATCCA
* *
16148 CTTCTTTGTATCTCATCAAGAAGATGGA-TTTG
1 CTTCTCTGTATCTCATCAGGAAGATGGAGTTTG
16180 GTCCACTTCA
Statistics
Matches: 136, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
122 5 0.04
123 130 0.96
124 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (123 bp):
CTTCTCTGTATCTCATCAGGAAGATGGAGTTTGAAGTTTCACTCACATTGAGCTTCGCTCCATTG
ATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGATCGCTTCATTATTTTGATCCA
Found at i:28082 original size:28 final size:29
Alignment explanation
Indices: 28051--28122 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 29
28041 TAATAAAATA
28051 CAAAATACGAAGAAAAAAAAACG-TGAA-T
1 CAAAATACGAAGAAAAAAAAA-GATGAATT
* *
28079 CAAAAT-C-AACGAAAAAACAAGATTAATT
1 CAAAATACGAA-GAAAAAAAAAGATGAATT
*
28107 TAAAATACGAAGAAAA
1 CAAAATACGAAGAAAA
28123 TAATTTAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
26 3 0.08
27 13 0.36
28 12 0.33
29 6 0.17
30 2 0.06
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (29 bp):
CAAAATACGAAGAAAAAAAAAGATGAATT
Found at i:28238 original size:29 final size:29
Alignment explanation
Indices: 28200--28429 Score: 209
Period size: 29 Copynumber: 7.8 Consensus size: 29
28190 TATGGAGAAT
28200 TTTAGAGGTCAAAATGTAATTTTGGAAAG
1 TTTAGAGGTCAAAATGTAATTTTGGAAAG
* * *
28229 TTTAGGGGTCAAAAATGTAATTTTAGAAAAA
1 TTTAGAGGTC-AAAATGTAATTTT-GGAAAG
*
28260 TTT-G-GGTCAAAATATAATTTTGGAAAAG
1 TTTAGAGGTCAAAATGTAATTTTGG-AAAG
* *
28288 TTTA-AGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGAGGTCAAAATGTAATTTT-GGAAAG
**
28317 TTTA-AGGGTCAAAATGTAATTTTCAAGAAG
1 TTTAGA-GGTCAAAATGTAATTTTGGA-AAG
* *
28347 CTTA-AGGTCAAAATATAATTTTGGAAAAG
1 TTTAGAGGTCAAAATGTAATTTTGG-AAAG
* * *
28376 TTTAGAGGTCAAATTTTAATTTTTGGTGAAG
1 TTTAGAGGTCAAAATGTAA-TTTTGG-AAAG
* *
28407 TTTAGGGGTCAAAATGTATTTTT
1 TTTAGAGGTCAAAATGTAATTTT
28430 AGACAAAATA
Statistics
Matches: 166, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
27 1 0.01
28 18 0.11
29 61 0.37
30 55 0.33
31 31 0.19
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (29 bp):
TTTAGAGGTCAAAATGTAATTTTGGAAAG
Found at i:28337 original size:59 final size:59
Alignment explanation
Indices: 28200--28432 Score: 251
Period size: 59 Copynumber: 3.9 Consensus size: 59
28190 TATGGAGAAT
* *
28200 TTTAGAGGTCAAAATGTAATTTTGG-AAAGTTTAGGGGTCAAAAATGTAATTTTAGAAAAA
1 TTTAG-GGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTC-AAAATGTAATTTTAGAAAAG
* *
28260 TTT-GGGTCAAAATATAATTTTGGAAAAGTTTA-AGGTTAAAATGTAATTTTAGAAAAG
1 TTTAGGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTCAAAATGTAATTTTAGAAAAG
* * * *
28317 TTTAAGGGTCAAAATGTAATTTT-CAAGAAGCTTA-AGGTCAAAATATAATTTTGGAAAAG
1 TTT-AGGGTCAAAATGTAATTTTGGAA-AAGTTTAGAGGTCAAAATGTAATTTTAGAAAAG
* * ** * *
28376 TTTAGAGGTCAAATTTTAATTTTTGGTGAAGTTTAGGGGTCAAAATGTATTTTTAGA
1 TTTAG-GGTCAAAATGTAA-TTTTGGAAAAGTTTAGAGGTCAAAATGTAATTTTAGA
28433 CAAAATAGGG
Statistics
Matches: 145, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
57 22 0.15
58 25 0.17
59 68 0.47
60 13 0.09
61 17 0.12
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (59 bp):
TTTAGGGTCAAAATGTAATTTTGGAAAAGTTTAGAGGTCAAAATGTAATTTTAGAAAAG
Found at i:30918 original size:13 final size:13
Alignment explanation
Indices: 30900--30925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30890 ATGTTTGTTT
30900 AAGCTAAATAAAC
1 AAGCTAAATAAAC
30913 AAGCTAAATAAAC
1 AAGCTAAATAAAC
30926 GAGTATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AAGCTAAATAAAC
Found at i:31181 original size:23 final size:24
Alignment explanation
Indices: 31129--31182 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
31119 ATTTTTCGTA
31129 AACATGTTCAATTATATGTTCATG
1 AACATGTTCAATTATATGTTCATG
* **
31153 AA-ATGTTCATTTA-ATGTTTGTG
1 AACATGTTCAATTATATGTTCATG
31175 AACATGTT
1 AACATGTT
31183 TGATTAAGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 9 0.35
23 15 0.58
24 2 0.08
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.44
Consensus pattern (24 bp):
AACATGTTCAATTATATGTTCATG
Found at i:32620 original size:74 final size:74
Alignment explanation
Indices: 32499--32706 Score: 398
Period size: 74 Copynumber: 2.8 Consensus size: 74
32489 TTCCATACAT
32499 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAAACATATTTCT
1 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAAACATATTTCT
32564 GTATATCCG
66 GTATATCCG
32573 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAAACATATTTCT
1 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAAACATATTTCT
32638 GTATATCCG
66 GTATATCCG
*
32647 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAGCAAACACAT
1 GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAA-ACAT
32707 GAAATCAAGT
Statistics
Matches: 132, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
74 128 0.97
75 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (74 bp):
GAAATAAAAGCAAACAGCTTTGCTTGTCATCTATTTCTATGATTTATCTAACAAAACATATTTCT
GTATATCCG
Found at i:38197 original size:30 final size:31
Alignment explanation
Indices: 38161--38221 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
38151 AAAGGTTAAT
38161 AATTATTTAAAATTTTAAAA-TTTTATAAAA
1 AATTATTTAAAATTTTAAAATTTTTATAAAA
38191 AATTATTTAAAATTTTAAAATTTTTATAAAA
1 AATTATTTAAAATTTTAAAATTTTTATAAAA
38222 GAAATTGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
AATTATTTAAAATTTTAAAATTTTTATAAAA
Found at i:40546 original size:29 final size:29
Alignment explanation
Indices: 40512--40696 Score: 119
Period size: 29 Copynumber: 6.4 Consensus size: 29
40502 AAAATGTCCC
* *
40512 AAAATTTCATTTTAACCTCGAACTTTTCA
1 AAAATTACATTTTAACCTCAAACTTTTCA
* * *
40541 AAAATTACATTTTTACTCTCGAAC-TTCCA
1 AAAATTACATTTTAAC-CTCAAACTTTTCA
* ** ** * *
40570 AAAATCATGTTTTTGCCCTTAAACTTCT-A
1 AAAATTA-CATTTTAACCTCAAACTTTTCA
* * *
40599 AAAATTGCATTTTAACCTCGAACTTCTCA
1 AAAATTACATTTTAACCTCAAACTTTTCA
* * *
40628 AAAATAACATTTTTACCCCCAAAC-TTTCA
1 AAAATTACA-TTTTAACCTCAAACTTTTCA
* *
40657 AAAATCACATTTTACCCTCAAAC--TTCAA
1 AAAATTACATTTTAACCTCAAACTTTTC-A
40685 AAAATTACATTT
1 AAAATTACATTT
40697 CTGCTCCCGA
Statistics
Matches: 121, Mismatches: 29, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
27 3 0.02
28 39 0.32
29 55 0.45
30 24 0.20
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACATTTTAACCTCAAACTTTTCA
Found at i:40604 original size:58 final size:57
Alignment explanation
Indices: 40536--40787 Score: 177
Period size: 58 Copynumber: 4.3 Consensus size: 57
40526 ACCTCGAACT
* ** * **
40536 TTTCAAAAATTACATTTTTACTCTCGAACTTCCAAAAATCATGTTTTTGCCCTTAAAC
1 TTTCAAAAATTACATTTTTAC-CTCGAACTTCCAAAAATAACATTTTTACCCCCAAAC
* *
40594 -TTCTAAAAATTGCATTTTAACCTCGAACTTCTCAAAAATAACATTTTTACCCCCAAAC
1 TTTC-AAAAATTACATTTTTACCTCGAACTTC-CAAAAATAACATTTTTACCCCCAAAC
* * * * * * * *
40652 TTTCAAAAATCACA-TTTTACCCTCAAACTTCAAAAAATTACATTTCTGCTCCCGAAC
1 TTTCAAAAATTACATTTTTA-CCTCGAACTTCCAAAAATAACATTTTTACCCCCAAAC
* * ** * * * *
40709 TTCCAATAATTACCA-TTTTACCTATTAACTTCCAAAAATTACTTTTTTTTAACCCCGAAC
1 TTTCAAAAATTA-CATTTTTACCT-CGAACTTCCAAAAATAAC--ATTTTTACCCCCAAAC
*
40769 TTTTCAAAAATCACATTTT
1 -TTTCAAAAATTACATTTT
40788 GCCCCCAAAC
Statistics
Matches: 152, Mismatches: 32, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
57 49 0.32
58 75 0.49
59 3 0.02
60 13 0.09
61 12 0.08
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (57 bp):
TTTCAAAAATTACATTTTTACCTCGAACTTCCAAAAATAACATTTTTACCCCCAAAC
Found at i:40629 original size:87 final size:86
Alignment explanation
Indices: 40472--40696 Score: 270
Period size: 87 Copynumber: 2.6 Consensus size: 86
40462 AAAGGTCCCT
* ** *
40472 AAACTATCCAAAAATCATATTTTGACCCTTAAAATGTCCCAAAATTTCATTTTAACCTCGAACTT
1 AAACT-TCCAAAAATCATATTTTG-CCCTTAAACT-TCAAAAAATTACATTTTAACCTCGAACTT
* * * *
40537 TTCAAAAATTACATTTTTACTCTC
63 CTCAAAAATAACATTTTTACCCCC
* * * *
40561 GAACTTCCAAAAATCATGTTTTTGCCCTTAAACTTCTAAAAATTGCATTTTAACCTCGAACTTCT
1 AAACTTCCAAAAATCAT-ATTTTGCCCTTAAACTTCAAAAAATTACATTTTAACCTCGAACTTCT
40626 CAAAAATAACATTTTTACCCCC
65 CAAAAATAACATTTTTACCCCC
* * * *
40648 AAACTTTCAAAAATCACATTTTACCCTCAAACTTCAAAAAATTACATTT
1 AAACTTCCAAAAATCATATTTTGCCCTTAAACTTCAAAAAATTACATTT
40697 CTGCTCCCGA
Statistics
Matches: 117, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
86 27 0.23
87 60 0.51
88 21 0.18
89 9 0.08
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.35
Consensus pattern (86 bp):
AAACTTCCAAAAATCATATTTTGCCCTTAAACTTCAAAAAATTACATTTTAACCTCGAACTTCTC
AAAAATAACATTTTTACCCCC
Found at i:40806 original size:28 final size:28
Alignment explanation
Indices: 40590--40957 Score: 183
Period size: 28 Copynumber: 12.8 Consensus size: 28
40580 TTTTGCCCTT
* * *
40590 AAACTTCTAAAAATTGCATTTTAACCTC
1 AAACTTCTAAAAATTACATTTTACCCCC
* *
40618 GAACTTCTCAAAAATAACATTTTTACCCCC
1 AAACTTCT-AAAAATTACA-TTTTACCCCC
* *
40648 AAACTT-TCAAAAATCACATTTTACCCTC
1 AAACTTCT-AAAAATTACATTTTACCCCC
* * *
40676 AAACTTCAAAAAATTACATTTCTGCTCCC
1 AAACTTCTAAAAATTACATTT-TACCCCC
* * * ***
40705 GAACTTCCAATAATTACCATTTTACCTAT
1 AAACTTCTAAAAATTA-CATTTTACCCCC
* * * *
40734 TAACTTCCAAAAATTACTTTTTTTTAACCCC
1 AAACTTCTAAAAATTAC---ATTTTACCCCC
* * * *
40765 GAACTTTTCAAAAATCACATTTTGCCCCC
1 AAACTTCT-AAAAATTACATTTTACCCCC
*
40794 AAACTTCTAAAAATTACCATTTTACCCTC
1 AAACTTCTAAAAATTA-CATTTTACCCCC
* * * ***
40823 -GA-TGTCGAAAAAATACATTTTTGACCTTG
1 AAACT-TCTAAAAATTACA-TTTT-ACCCCC
** **
40852 AAA-TTCCCAAAATTACCATTTTACCATC
1 AAACTTCTAAAAATTA-CATTTTACCCCC
* *
40880 AAACATCCAAAAATTACCA-TTTACCCCC
1 AAACTTCTAAAAATTA-CATTTTACCCCC
* *
40908 AAACATCTAAAAA-TACCATTTTACCCTC
1 AAACTTCTAAAAATTA-CATTTTACCCCC
40936 AAA-TGTCTAAAAATTACATTTT
1 AAACT-TCTAAAAATTACATTTT
40958 TGACCCTGAA
Statistics
Matches: 263, Mismatches: 58, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
27 8 0.03
28 107 0.41
29 107 0.41
30 22 0.08
31 11 0.04
32 8 0.03
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (28 bp):
AAACTTCTAAAAATTACATTTTACCCCC
Found at i:40889 original size:146 final size:147
Alignment explanation
Indices: 40608--40896 Score: 351
Period size: 146 Copynumber: 2.0 Consensus size: 147
40598 AAAAATTGCA
*
40608 TTTTAACCTCGAACTTCTCAAAAATAACATTTTTACCCCCAAACTTTCAAAAATCACATTTTACC
1 TTTTAACCCCGAACTTCTCAAAAATAACATTTTTACCCCCAAACTTTCAAAAATCACATTTTACC
* *
40673 CTCAAACTTCAAAAAATTACATTTCTGCTCCCGAACTTCCAATAATTACCATTTTACCTATTAAC
66 CTCAAACTTCAAAAAATTACATTTCTGCTCCCGAAATTCCAATAATTACCATTTTACCTATAAAC
*
40738 TTCCAAAAATTACTTTT
131 ATCCAAAAATTACTTTT
* * * *
40755 TTTTAACCCCGAACTTTTCAAAAATCACA-TTTTGCCCCCAAAC-TTCTAAAAATTACCATTTTA
1 TTTTAACCCCGAACTTCTCAAAAATAACATTTTTACCCCCAAACTTTC-AAAAATCA-CATTTTA
* * **
40818 CCCTC-GA-TGTCGAAAAAA-TACATTTTTGAC-CTTGAAATTCCCAA-AATTACCATTTTACC-
64 CCCTCAAACT-TC-AAAAAATTACATTTCTG-CTCCCGAAATT-CCAATAATTACCATTTTACCT
40877 ATCAAACATCCAAAAATTAC
125 AT-AAACATCCAAAAATTAC
40897 CATTTACCCC
Statistics
Matches: 123, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
145 6 0.05
146 68 0.55
147 49 0.40
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (147 bp):
TTTTAACCCCGAACTTCTCAAAAATAACATTTTTACCCCCAAACTTTCAAAAATCACATTTTACC
CTCAAACTTCAAAAAATTACATTTCTGCTCCCGAAATTCCAATAATTACCATTTTACCTATAAAC
ATCCAAAAATTACTTTT
Found at i:41003 original size:114 final size:113
Alignment explanation
Indices: 40789--41101 Score: 288
Period size: 114 Copynumber: 2.7 Consensus size: 113
40779 TCACATTTTG
* * * * *
40789 CCCCCAAACTTCTAAAAATTACCATTTTACCCTCGATGTCGAAAAAATACATTTTTGACCTTGAA
1 CCCCCAAACATCTAAAAA-TACCATTTTACCCTCAATGTCTAAAAATTACATTTTTGACCCTGAA
* * * *
40854 ATTCCCAAAATTACCATTTTACCATCAAACATCCAAAAATTA-CCATTTA
65 CTTTCAAAAATTACCA-TATACCATCAAACATCCAAAAATTATCCATTTA
40903 CCCCCAAACATCTAAAAATACCATTTTACCCTCAAATGTCTAAAAATTACATTTTTGACCCTGAA
1 CCCCCAAACATCTAAAAATACCATTTTACCCTC-AATGTCTAAAAATTACATTTTTGACCCTGAA
* * ** *** **
40968 CTTTTCAAAAATTACCATATAGCGTTTAGTGTCCAAAAATTATCGTTTTA
65 C-TTTCAAAAATTACCATATACCATCAAACATCCAAAAATTATCCATTTA
* * * * * * * *
41018 CCCCCAATCGTCCCAAAATTACCATTTTACCCACTTAGGCATCTAAAAATTACTTTTTTG-CCCT
1 CCCCCAAACAT-CTAAAAATACCATTTTACCCTC-AATG--TCTAAAAATTACATTTTTGACCCT
* *
41082 AAACTTTCAAAAGTTACCAT
62 GAACTTTCAAAAATTACCAT
41102 TTTGCCCCCG
Statistics
Matches: 164, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
113 15 0.09
114 61 0.37
115 27 0.16
116 36 0.22
117 7 0.04
118 18 0.11
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.32
Consensus pattern (113 bp):
CCCCCAAACATCTAAAAATACCATTTTACCCTCAATGTCTAAAAATTACATTTTTGACCCTGAAC
TTTCAAAAATTACCATATACCATCAAACATCCAAAAATTATCCATTTA
Found at i:46463 original size:14 final size:14
Alignment explanation
Indices: 46442--46482 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
46432 AAAAAATGGG
*
46442 AAGAAAAAAAGAAA
1 AAGAAAAGAAGAAA
*
46456 AAGGAAAAGGAGAAA
1 AA-GAAAAGAAGAAA
46471 AAGAAAAGAAGA
1 AAGAAAAGAAGA
46483 GGTCGAGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAAAGAAGAAA
Found at i:47544 original size:50 final size:49
Alignment explanation
Indices: 47402--47698 Score: 246
Period size: 49 Copynumber: 6.0 Consensus size: 49
47392 AGAAAAACAT
* * *
47402 GAAGATTTGAACGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTAA
1 GAAGA-TTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTAA
* * *
47452 GAAGATT-AAGGGAAAAGATTGAGGCCGCGACGGCGAATCTGGTACCTAA
1 GAAGATTGAAGGG-AAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTAA
* * * *
47501 GAAGATGTGATGGGAAAGGTTAAGGCTGCAACGGCGAACCTGGTACC-AT
1 GAAGAT-TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTAA
* * * *
47550 GAAGATATGAAGGGAAAGGTTGAGGCCACAACAGCAAAAACCCGGTACCATGAA
1 GAAGAT-TGAAGGGAAAGGTTGAGGCCGCAACGGC--GAACCTGGTACC-T-AA
* * * * * *
47604 -AAGA-TGAAGGGAAAGATTGAAGCCACGACGACGAA-TTCGGTACCTTAA
1 GAAGATTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GGTACC-TAA
* * *
47652 -AAGATGTGACGGGAAAGGTTGAGGCCGCAACGACAAACCTGGTACCT
1 GAAGAT-TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCT
47699 TAAAAAACAA
Statistics
Matches: 197, Mismatches: 38, Indels: 25
0.76 0.15 0.10
Matches are distributed among these distances:
48 10 0.05
49 79 0.40
50 65 0.33
51 38 0.19
53 4 0.02
54 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.15
Consensus pattern (49 bp):
GAAGATTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGGTACCTAA
Found at i:47668 original size:150 final size:148
Alignment explanation
Indices: 47399--47697 Score: 381
Period size: 150 Copynumber: 2.0 Consensus size: 148
47389 CTGAGAAAAA
* * * * *
47399 CATGAAGATTTGAACGGAAAGGTTGAGGCCGCAACGGCGAACCCGATACCTAAGAAGATTAAGGG
1 CATGAAGATATGAACGGAAAGGTTGAGGCCACAACAGCAAACCCGATACCTAAGAAGATGAAGGG
* * * * *
47464 AAAAGATTGAGGCCGCGACGGCGAATCTGGTACCTAAGAAGATGTGATGGGAAAGGTTAAGGCTG
66 AAAAGATTGAAGCCACGACGACGAATCTGGTACCTAAGAAGATGTGACGGGAAAGGTTAAGGCCG
* *
47529 CAACGGCGAACCTGGTAC
131 CAACGACAAACCTGGTAC
* *
47547 CATGAAGATATGAAGGGAAAGGTTGAGGCCACAACAGCAAAAACCCGGTACCATGAA-AAGATGA
1 CATGAAGATATGAACGGAAAGGTTGAGGCCACAACAGC--AAACCCGATACC-T-AAGAAGATGA
*
47611 AGGG-AAAGATTGAAGCCACGACGACGAAT-TCGGTACCTTAA-AAGATGTGACGGGAAAGGTTG
62 AGGGAAAAGATTGAAGCCACGACGACGAATCT-GGTACC-TAAGAAGATGTGACGGGAAAGGTTA
47673 AGGCCGCAACGACAAACCTGGTAC
125 AGGCCGCAACGACAAACCTGGTAC
47697 C
1 C
47698 TTAAAAAACA
Statistics
Matches: 130, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
148 34 0.26
149 1 0.01
150 79 0.61
151 14 0.11
152 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (148 bp):
CATGAAGATATGAACGGAAAGGTTGAGGCCACAACAGCAAACCCGATACCTAAGAAGATGAAGGG
AAAAGATTGAAGCCACGACGACGAATCTGGTACCTAAGAAGATGTGACGGGAAAGGTTAAGGCCG
CAACGACAAACCTGGTAC
Found at i:47950 original size:41 final size:42
Alignment explanation
Indices: 47867--47951 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 42
47857 ATTTAATATT
* * * *
47867 TTACCCTTTAGTCAAGAAGGGTAGATTGAAGATTTCAGTCTC
1 TTACCCTTTAATCAAGAAGGGCAGAGTGAAGATTCCAGTCTC
*
47909 TTACCC-TTAATCAAGAGGGGCAGAGTGAAGATTCC-GATCTC
1 TTACCCTTTAATCAAGAAGGGCAGAGTGAAGATTCCAG-TCTC
47950 TT
1 TT
47952 GCCCCGAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.03
41 30 0.81
42 6 0.16
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (42 bp):
TTACCCTTTAATCAAGAAGGGCAGAGTGAAGATTCCAGTCTC
Found at i:48070 original size:38 final size:39
Alignment explanation
Indices: 47980--48078 Score: 110
Period size: 38 Copynumber: 2.5 Consensus size: 39
47970 TCACCATCAG
* * *
47980 CCAATCTCTTACCCCGAGCTTGGGGCAGATTACAAGCCAT
1 CCAATCTCTTA-CCCGACCATGGGGCAGATCACAAGCCAT
* * * *
48020 TCGATCTTTTACCCGACCATGGGGTAGATCAC-AGCCAT
1 CCAATCTCTTACCCGACCATGGGGCAGATCACAAGCCAT
*
48058 CCAATCTCTTACCCGATCATG
1 CCAATCTCTTACCCGACCATG
48079 AGGCTGATTG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 23 0.48
39 17 0.35
40 8 0.17
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.25
Consensus pattern (39 bp):
CCAATCTCTTACCCGACCATGGGGCAGATCACAAGCCAT
Found at i:48707 original size:207 final size:210
Alignment explanation
Indices: 48099--48974 Score: 1109
Period size: 207 Copynumber: 4.2 Consensus size: 210
48089 CAGTTATCCA
**
48099 AAGCAATAAAGCGGTTA-CTTTCTTGATGAGATACA-AAGAAGTGAACCAGATCCGTCTTCCTGA
1 AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAA-AAGTGAACCAGATCCGTCTTCCTGA
* * *
48162 TGAGACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGGGATATTGAGAAGT
65 TGAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGT
* * * * *
48227 AGACCAAATCGATGAAGCAAAGCTTAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTAATTTGAG
130 AGACCAAATCAATGAAACAAGGCTCAAAGAGAGCAAATCTTCGAACCCCAGCTTCCTAA--TGAG
* * *
48292 ATATTGAGAAGCAGGTCG
193 ATACTAAGAAACAGGTCG
* *
48310 AAGCAATAAAATGGTTAGC-TTCTTGATAAGATACAGATAAGTGAACCAGATCCGTCTTCCTGAT
1 AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAAAAGTGAACCAGATCCGTCTTCCTGAT
*
48374 GAGACACAGAGAAGTGGAT-AAAACACA---ATGCAGTCATCTTCCTGATGAGATACTGAAAAGT
66 GAGACACAGAGAAGTGGATCAAAACA-AGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGT
* * * * * * *
48435 AGACCAAGTCAATGAAACTAGGCTTAGAGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGAT
130 AGACCAAATCAATGAAACAAGGCTCAAAGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGAT
* **
48500 ACTAAGAAGCAAATCG
195 ACTAAGAAACAGGTCG
* * *
48516 AAGCAATAAAATGGTCAGCTTTC-TGATGAGATACAGAAAAGTGAACTAGATCCGTCTTCCTAAT
1 AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAAAAGTGAACCAGATCCGTCTTCCTGAT
* * * *
48580 GATACACAGAGAAGTGGATCAAAAC-A-TGAGGCAGTCATCTTCTTGATGAGATATTGAGAAGTA
66 GAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTA
* *
48643 GACCAAATCAATGAAATC-AGGCTCAAAGAGAGCAAATCTTCAAACCCCAGCTTCCTGATGAGAT
131 GACCAAATCAATGAAA-CAAGGCTCAAAGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGAT
48707 ACTAAGAAACAGGTCG
195 ACTAAGAAACAGGTCG
* * * * * * *
48723 AAGCAATAAAACGTTTA-CCTTCCTAATGAGATACAGAGAAGTGAACCAGATCCGTCTTCTTGAT
1 AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAAAAGTGAACCAGATCCGTCTTCCTGAT
* * *
48787 GAGACACAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTTCTGATGAGATACTGAGAAGTA
66 GAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTA
* *
48852 GACCAATTCAATGAAACAAGGCTCAATATGAGAG-AAA-CTTCGAACCCCAGCTTCCTAATGAGG
131 GACCAAATCAATGAAACAAGGCTCAA-A-GAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGA
*
48915 TACTGAGAAACAGGTCG
194 TACTAAGAAACAGGTCG
* * *
48932 AAGCAATAAAATGATCAAC-TTCTTGATGAGATACA-AAGAAGTG
1 AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAA-AAGTG
48975 GATCAAAATA
Statistics
Matches: 583, Mismatches: 66, Indels: 34
0.85 0.10 0.05
Matches are distributed among these distances:
205 1 0.00
206 95 0.16
207 182 0.31
208 85 0.15
209 126 0.22
210 11 0.02
211 81 0.14
212 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (210 bp):
AAGCAATAAAATGGTTAGCTTTCTTGATGAGATACAGAAAAGTGAACCAGATCCGTCTTCCTGAT
GAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATACTGAGAAGTA
GACCAAATCAATGAAACAAGGCTCAAAGAGAGCAAATCTTCGAACCCCAGCTTCCTAATGAGATA
CTAAGAAACAGGTCG
Found at i:49066 original size:171 final size:172
Alignment explanation
Indices: 48778--49145 Score: 476
Period size: 171 Copynumber: 2.1 Consensus size: 172
48768 CCAGATCCGT
* * *
48778 CTTCTTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATACGGTCATCTTTCTGATGAGATAC
1 CTTCTTGATGAGACACAAAGAAGTGGATCAAAACAAGTGAGACGGTCATCTTCCTGATGAGATAC
* *
48843 TGAGAAGTAGACCAATTCAATGAAACAAGGCTCAATATGAGAGAAACTTCGAACCCCAGCTTCCT
66 TAAGAAGTAGACCAAATCAATGAAACAAGGCTCAATATGAGAGAAACTTCGAACCCCAGCTTCCT
* *
48908 AATGAGGTACTGAGAAACAGGTCGAAGCAATAAAATGATCAA
131 AATAAGATACTGAGAAACAGGTCGAAGCAATAAAATGATCAA
* * **
48950 CTTCTTGATGAGATACAAAGAAGTGGATCAAAATAA-TGAGGTGGTCATCTTCCTGATGAGATAC
1 CTTCTTGATGAGACACAAAGAAGTGGATCAAAACAAGTGAGACGGTCATCTTCCTGATGAGATAC
*
49014 TAAGAAGTAGACCAAATCAATGAAACCAA-GTTCAA-A-GTA-AGCAAATCTTCGAACCCCAGCT
66 TAAGAAGTAGACCAAATCAATGAAA-CAAGGCTCAATATG-AGAG-AAA-CTTCGAACCCCAGCT
* * ** * *
49075 TCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCAC
127 TCCTAATAAGATACTGAGAAACAGGTCGAAGCAATAAAATGATCAA
* * *
49121 CTTCCTGTTGAGACACAGAGAAGTG
1 CTTCTTGATGAGACACAAAGAAGTG
49146 AACTAGATCC
Statistics
Matches: 170, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
169 3 0.02
170 5 0.03
171 126 0.74
172 36 0.21
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (172 bp):
CTTCTTGATGAGACACAAAGAAGTGGATCAAAACAAGTGAGACGGTCATCTTCCTGATGAGATAC
TAAGAAGTAGACCAAATCAATGAAACAAGGCTCAATATGAGAGAAACTTCGAACCCCAGCTTCCT
AATAAGATACTGAGAAACAGGTCGAAGCAATAAAATGATCAA
Found at i:49315 original size:208 final size:206
Alignment explanation
Indices: 48957--49588 Score: 838
Period size: 208 Copynumber: 3.0 Consensus size: 206
48947 CAACTTCTTG
* * * *
48957 ATGAGATACAAAGAAGTGGATCAAAATAATGAGGTGGTCATCTTCCTGATGAGATACTAAGAAGT
1 ATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGT
* * * * *
49022 AGACCAAATCAATGAAACCAAGTTCAAAGTAAGCAAATCTTCGAACCCCAGCTTCCTGATAAGAT
66 ACACCAAATCAATGAAA-CAAGCTCAAA-TGAGTAAATCTTCGAACCCCAGCTTCCTGATGAGAT
* * * * * *
49087 ACTGAGAAGCAGGTCGAAGCAATAAAGCGGTCACCTTCCTGTTGAGACACAGAGAAGTGAACTAG
129 ACTGAGAAGCAGGTCGAAGCAATAAAGTGGTCACCTTCCTGATGAGATACAAAGAAGTGAACCAA
*
49152 ATCCGTCTTCCTA
194 ATTCGTCTTCCTA
*
49165 ATGAGATACAGAGAAGTGGATCAAAACAAAGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGT
1 ATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGT
*
49230 ACACCAAATCAATGAAACAAGGCTCAATATGAGTAAATCTTCTAACCCCAGCTTCCTGATGAGAT
66 ACACCAAATCAATGAAACAA-GCTCAA-ATGAGTAAATCTTCGAACCCCAGCTTCCTGATGAGAT
* * * * ** **
49295 ACTGAGAAGCAGGTCGAAGCAAAAAAGTGTTCATCTCCCTGACAAGATGGAAAGAAGTGAACCAA
129 ACTGAGAAGCAGGTCGAAGCAATAAAGTGGTCACCTTCCTGATGAGATACAAAGAAGTGAACCAA
* *
49360 ATTCATCTTCCTG
194 ATTCGTCTTCCTA
* * *
49373 ATGAGATACAGAGAAGTGGATCAAAACAAGTGAGGCGATCATCTTCTTGATAAGATA-TAGAGAA
1 ATGAGATACAGAGAAGTGGATCAAAACAA-TGAGGCGGTCATCTTCCTGATGAGATACT-GAGAA
* * *
49437 GTATACCAACTCAATGAAACAAAGCTC-AATGAGTGAAA-CTTCGAACCCCAGCTTCTTGATGAG
64 GTACACCAAATCAATGAAAC-AAGCTCAAATGAGT-AAATCTTCGAACCCCAGCTTCCTGATGAG
* * *
49500 ATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAAAGAAGTGGACC
127 ATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTCACCTTCCTGATGAGATACAAAGAAGTGAACC
49565 AAATTCGTCTTCCTA
192 AAATTCGTCTTCCTA
49580 ATGAGATAC
1 ATGAGATAC
49589 CGGTTATCTT
Statistics
Matches: 370, Mismatches: 48, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
207 109 0.29
208 208 0.56
209 51 0.14
210 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (206 bp):
ATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCCTGATGAGATACTGAGAAGT
ACACCAAATCAATGAAACAAGCTCAAATGAGTAAATCTTCGAACCCCAGCTTCCTGATGAGATAC
TGAGAAGCAGGTCGAAGCAATAAAGTGGTCACCTTCCTGATGAGATACAAAGAAGTGAACCAAAT
TCGTCTTCCTA
Found at i:49742 original size:183 final size:181
Alignment explanation
Indices: 49413--49771 Score: 603
Period size: 183 Copynumber: 2.0 Consensus size: 181
49403 TGAGGCGATC
* *
49413 ATCTTCTTGATAAGATATAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGAGTGAAACTT
1 ATCTTCCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGAGTGAAACTT
49478 CGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTG
66 CGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTG
*
49543 ATGAGATACAAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACCGGTT
131 ATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTAATGAGATACCGGTT
* *
49594 ATCTTCCTGATGAGATACAGAGAAGTATATCAACTCAATGAAACAAAGCTCAATGCGAGTGAAAC
1 ATCTTCCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAAT--GAGTGAAAC
*
49659 TTCGAACCCCAGTTTCCTT-ATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTC
64 TTCGAACCCCAGCTT-CTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTC
* * *
49723 CTGATGAGATACTAAGAAGTGGACCAAATTCATTTTCCTGATGAGATAC
128 CTGATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTAATGAGATAC
49772 AGAGAAGTGG
Statistics
Matches: 166, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
181 50 0.30
183 113 0.68
184 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (181 bp):
ATCTTCCTGATAAGATACAGAGAAGTATACCAACTCAATGAAACAAAGCTCAATGAGTGAAACTT
CGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTG
ATGAGATACAAAGAAGTGGACCAAATTCATCTTCCTAATGAGATACCGGTT
Found at i:49862 original size:160 final size:160
Alignment explanation
Indices: 49597--49911 Score: 402
Period size: 160 Copynumber: 2.0 Consensus size: 160
49587 ACCGGTTATC
* * * * *
49597 TTCCTGATGAGATACAGAGAAGTATATCAACTCAATGAAACAAAGCTCAATGCGAGTGAAACTTC
1 TTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATACGAATGAAACTTC
* * ** * * *
49662 GAACCCCAGTTTCCTTATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCCTGA
66 AAACCCCAGTTTCCTGATGAGATACAAAGAAACAGGTCGAAGCAATAAAACGGTCAGCTTCCTAA
*
49727 TGAGATACTA-AGAAGTGGACCAAATTCATT
131 TGAGATAC-AGAGAAGTAGACCAAATTCATT
* * * *
49757 TTCCTGATGAGATACAGAGAAGTGGACCAAATCCAA-GAAGCGAAGCTCAATACGAATGAGACTT
1 TTCCTGATGAGATACAGAGAAGTAGACCAAAT-CAATGAAACAAAGCTCAATACGAATGAAACTT
** *
49821 CAAACCCCA-TCTTCCTGATGAGATACAAAGAAATGGGTCGAAGCAATAAAACGGTCATCTTCCT
65 CAAACCCCAGT-TTCCTGATGAGATACAAAGAAACAGGTCGAAGCAATAAAACGGTCAGCTTCCT
49885 AATGAGATACAGAGAAGTAGACCAAAT
129 AATGAGATACAGAGAAGTAGACCAAAT
49912 CGAATGAAGA
Statistics
Matches: 132, Mismatches: 20, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
159 2 0.02
160 127 0.96
161 3 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (160 bp):
TTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATACGAATGAAACTTC
AAACCCCAGTTTCCTGATGAGATACAAAGAAACAGGTCGAAGCAATAAAACGGTCAGCTTCCTAA
TGAGATACAGAGAAGTAGACCAAATTCATT
Done.