Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001743.1 Kokia drynarioides strain JFW-HI SEQ_113454, 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: 27382
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 33 characters in sequence are not A, C, G, or T
Found at i:969 original size:38 final size:37
Alignment explanation
Indices: 880--974 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 37
870 ATGGTCAATA
880 CAAAAAAATTT-AA-TTTTTTACCAAATGGCCGACAC
1 CAAAAAAATTTAAATTTTTTTACCAAATGGCCGACAC
*
915 CAAAAAAATTTGAAATTTTTTTATCTGAAATGGCCGACAC
1 CAAAAAAATTT-AAATTTTTTTA-C-CAAATGGCCGACAC
*
955 C-CAAAAATTTAAATTTTTTT
1 CAAAAAAATTTAAATTTTTTT
975 TCTCAAAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
35 11 0.21
37 2 0.04
38 17 0.32
39 9 0.17
40 14 0.26
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (37 bp):
CAAAAAAATTTAAATTTTTTTACCAAATGGCCGACAC
Found at i:1013 original size:58 final size:58
Alignment explanation
Indices: 943--1101 Score: 196
Period size: 59 Copynumber: 2.7 Consensus size: 58
933 TTTTATCTGA
* * *
943 AATGGCCGACACCCAAAAATTTAAATTTTTTTTCTCAAAAAGAGGGTGTCGGCCATTG-
1 AATGGCCAACACCAAAAAATTTAAATTTTTTTTCTCAAAAAGAGGGTGTCGACCA-TGC
* *
1001 TATGGCCAACACCAAAAAATTTTGAAATTTTTTTTCTC-AAAAGGGGGTGTCGACCATGC
1 AATGGCCAACACCAAAAAA-TTT-AAATTTTTTTTCTCAAAAAGAGGGTGTCGACCATGC
* ** *
1060 AATAGCCAACACCAAAAAATGCAATTTTTTTTTCTCAAAAAG
1 AATGGCCAACACCAAAAAATTTAAATTTTTTTTCTCAAAAAG
1102 GCATGGCCAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
57 13 0.15
58 24 0.28
59 36 0.41
60 14 0.16
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (58 bp):
AATGGCCAACACCAAAAAATTTAAATTTTTTTTCTCAAAAAGAGGGTGTCGACCATGC
Found at i:2297 original size:25 final size:24
Alignment explanation
Indices: 2264--2325 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
2254 TCATAGAGTT
* *
2264 AAAT-ATTTTATTATTATTGTATTA
1 AAATAATTTTATTAGT-TTGTATAA
*
2288 AAATAATTTTTATAAGTTTGTATAA
1 AAATAA-TTTTATTAGTTTGTATAA
2313 AAATAA-TTTATTA
1 AAATAATTTTATTA
2326 AACTTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 6 0.19
24 4 0.12
25 14 0.44
26 8 0.25
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (24 bp):
AAATAATTTTATTAGTTTGTATAA
Found at i:4149 original size:19 final size:20
Alignment explanation
Indices: 4125--4162 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4115 AGAATATATT
*
4125 AATTTTAT-TTTATAATTTA
1 AATTTTATGTTAATAATTTA
4144 AATTTTATGTTAATAATTT
1 AATTTTATGTTAATAATTT
4163 TATCTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (20 bp):
AATTTTATGTTAATAATTTA
Found at i:6374 original size:16 final size:17
Alignment explanation
Indices: 6345--6377 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6335 TAAATTTTAA
6345 AAAATATTAATTTAATAT
1 AAAATATT-ATTTAATAT
6363 AAAATATT-TTTAATA
1 AAAATATTATTTAATA
6378 CTATAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAAATATTATTTAATAT
Found at i:7130 original size:22 final size:21
Alignment explanation
Indices: 7102--7194 Score: 109
Period size: 22 Copynumber: 4.3 Consensus size: 21
7092 TATATTGTTA
7102 TTTTGGTGCTGTTTTTTTACTG
1 TTTTGGTGCT-TTTTTTTACTG
*
7124 TTTTGGTTGCTATTTTTTACTG
1 TTTTGG-TGCTTTTTTTTACTG
7146 TTTTGGTG-TTGTGTTTTTACTG
1 TTTTGGTGCTT-T-TTTTTACTG
*
7168 TTTTGATGC-TTTTTTTACTG
1 TTTTGGTGCTTTTTTTTACTG
*
7188 CTTTGGT
1 TTTTGGT
7195 TACTATTTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
20 15 0.24
21 4 0.06
22 39 0.63
23 4 0.06
ACGTcount: A:0.06, C:0.09, G:0.22, T:0.63
Consensus pattern (21 bp):
TTTTGGTGCTTTTTTTTACTG
Found at i:7165 original size:44 final size:42
Alignment explanation
Indices: 7102--7194 Score: 132
Period size: 44 Copynumber: 2.2 Consensus size: 42
7092 TATATTGTTA
* *
7102 TTTTGGTGCTGTTTTTTTACTGTTTTGGTTGCTATTTTTTACTG
1 TTTTGGTGCTGTGTTTTTACTGTTTT-GATGCT-TTTTTTACTG
*
7146 TTTTGGTGTTGTGTTTTTACTGTTTTGATGCTTTTTTTACTG
1 TTTTGGTGCTGTGTTTTTACTGTTTTGATGCTTTTTTTACTG
*
7188 CTTTGGT
1 TTTTGGT
7195 TACTATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 16 0.36
43 5 0.11
44 24 0.53
ACGTcount: A:0.06, C:0.09, G:0.22, T:0.63
Consensus pattern (42 bp):
TTTTGGTGCTGTGTTTTTACTGTTTTGATGCTTTTTTTACTG
Found at i:7270 original size:22 final size:22
Alignment explanation
Indices: 7200--7281 Score: 71
Period size: 22 Copynumber: 3.7 Consensus size: 22
7190 TTGGTTACTA
* *
7200 TTTTGATGCTATTTTTTACTAT
1 TTTTGTTGCTATTTTTTAGTAT
7222 TTTGGTGTTG-T-TTTTATT-GTTAT
1 TTT--TGTTGCTATTTT-TTAG-TAT
7245 TTTTGTTGCTATTTTTTAGTAT
1 TTTTGTTGCTATTTTTTAGTAT
* *
7267 TTTTATTGCTGTTTT
1 TTTTGTTGCTATTTT
7282 GGTTGTTATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
21 5 0.10
22 26 0.53
23 14 0.29
24 4 0.08
ACGTcount: A:0.12, C:0.05, G:0.15, T:0.68
Consensus pattern (22 bp):
TTTTGTTGCTATTTTTTAGTAT
Found at i:7288 original size:46 final size:45
Alignment explanation
Indices: 7200--7298 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
7190 TTGGTTACTA
* * * *
7200 TTTTGATGCTATTTTTTACTATTTTGGTGTTGTTTTTATTGTTAT
1 TTTTGTTGCTATTTTTTACTATTTTAGTGCTGTTTTGATTGTTAT
* * *
7245 TTTTGTTGCTATTTTTTAGTATTTTTATTGCTGTTTTGGTTGTTAT
1 TTTTGTTGCTATTTTTTACTA-TTTTAGTGCTGTTTTGATTGTTAT
*
7291 TTTGGTTG
1 TTTTGTTG
7299 TTTGGATGTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 19 0.42
46 26 0.58
ACGTcount: A:0.11, C:0.04, G:0.18, T:0.67
Consensus pattern (45 bp):
TTTTGTTGCTATTTTTTACTATTTTAGTGCTGTTTTGATTGTTAT
Found at i:7294 original size:45 final size:44
Alignment explanation
Indices: 7189--7294 Score: 113
Period size: 45 Copynumber: 2.4 Consensus size: 44
7179 TTTTTACTGC
** * *
7189 TTTGGTTACTATTTTGATGCTATTTTTTACTATTTTGGTGTTGT
1 TTTGGTTGTTATTTTGATGCTATTTTTTACTATTTTAGTGCTGT
** * * *
7233 TTTTATTGTTATTTTTGTTGCTATTTTTTAGTATTTTTATTGCTGT
1 TTTGGTTGTTA-TTTTGATGCTATTTTTTACTA-TTTTAGTGCTGT
7279 TTTGGTTGTTATTTTG
1 TTTGGTTGTTATTTTG
7295 GTTGTTTGGA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
44 7 0.14
45 24 0.49
46 18 0.37
ACGTcount: A:0.12, C:0.05, G:0.17, T:0.66
Consensus pattern (44 bp):
TTTGGTTGTTATTTTGATGCTATTTTTTACTATTTTAGTGCTGT
Found at i:8029 original size:19 final size:20
Alignment explanation
Indices: 7979--8054 Score: 84
Period size: 19 Copynumber: 3.8 Consensus size: 20
7969 GTTGGGTGCA
* *
7979 GTTTTTTTACTGTTTTGGTT
1 GTTTTTTTACTGTTTTTGAT
7999 GTTATTTTTTACTGTTTTTG-T
1 G-T-TTTTTTACTGTTTTTGAT
* *
8020 GTTTTGTTACTG-CTTTGAT
1 GTTTTTTTACTGTTTTTGAT
8039 GTTTTTTTACTGTTTT
1 GTTTTTTTACTGTTTT
8055 GGTTGTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
18 4 0.09
19 21 0.45
20 4 0.09
21 3 0.06
22 15 0.32
ACGTcount: A:0.08, C:0.07, G:0.17, T:0.68
Consensus pattern (20 bp):
GTTTTTTTACTGTTTTTGAT
Found at i:8114 original size:23 final size:22
Alignment explanation
Indices: 8033--8131 Score: 76
Period size: 23 Copynumber: 4.4 Consensus size: 22
8023 TTGTTACTGC
* *
8033 TTTGATGTT-TTTT-TACTGTT
1 TTTGTTGTTGTTTTATATTGTT
* *
8053 TTGGTTGTTGTTTTGATGTTGTT
1 TTTGTTGTTGTTTT-ATATTGTT
* * *
8076 TTTGCTGTTACTTTTATTTTTGTT
1 TTTGTTGTT-GTTTTA-TATTGTT
*
8100 TTTGTTGTTGTTTTACTATTATT
1 TTTGTTGTTGTTTTA-TATTGTT
8123 TTTGTTGTT
1 TTTGTTGTT
8132 TTGATGCTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 7 0.11
21 4 0.07
23 32 0.52
24 18 0.30
ACGTcount: A:0.08, C:0.04, G:0.18, T:0.70
Consensus pattern (22 bp):
TTTGTTGTTGTTTTATATTGTT
Found at i:8141 original size:23 final size:20
Alignment explanation
Indices: 8098--8151 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 20
8088 TTTATTTTTG
8098 TTTTTGTTGTTGTTTTACTA
1 TTTTTGTTGTTGTTTTACTA
8118 TTATTT-TTGTTGTTTTGATGCTA
1 TT-TTTGTTGTTGTTTT-A--CTA
8141 TTTTTGTTGTT
1 TTTTTGTTGTT
8152 TGGATGTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 12 0.41
21 4 0.14
22 3 0.10
23 10 0.34
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (20 bp):
TTTTTGTTGTTGTTTTACTA
Found at i:8157 original size:20 final size:19
Alignment explanation
Indices: 8119--8164 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
8109 GTTTTACTAT
*
8119 TATTTTTGTTGTTTTGATG
1 TATTTTTGTTGTTTGGATG
8138 CTATTTTTGTTGTTTGGATG
1 -TATTTTTGTTGTTTGGATG
8158 TATTTTT
1 TATTTTT
8165 ATGCGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.11, C:0.02, G:0.20, T:0.67
Consensus pattern (19 bp):
TATTTTTGTTGTTTGGATG
Found at i:8598 original size:24 final size:23
Alignment explanation
Indices: 8557--8602 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
8547 CTCGGCCTGG
8557 ATTTATAATAATAATTTTATTTTT
1 ATTTATAATAATAATTTT-TTTTT
* * *
8581 ATTTTTAATACTACTTTTTTTT
1 ATTTATAATAATAATTTTTTTT
8603 GCTTGTAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTATAATAATAATTTTTTTTT
Found at i:9049 original size:206 final size:206
Alignment explanation
Indices: 8695--9142 Score: 842
Period size: 206 Copynumber: 2.2 Consensus size: 206
8685 ACATGCAAAC
* *
8695 AAATTTGAAAAAGGCAAAACAAATCCCCCAAATCTCGATTTGCTCCCTTAGCCTCCTAATAGTAC
1 AAATTTGACAAAGGCAAAACAAATCCCCCAAATCTCGATATGCTCCCTTAGCCTCCTAATAGTAC
*
8760 TCTTCACTGACTAATCCTATGTTTAAGGGTTCATCTCTCCCCTTCCACTTGATCATCCAAATCTC
66 TCTTCACTGACTAATCCTATGTTTAAGGGTTCATCTCTCCCCTCCCACTTGATCATCCAAATCTC
8825 ATCAATTGCTTGTCAAATTCATCCAAAAAAAAAAGACTAGCTGCTTCTCCCTCAACTTCTCTGTG
131 ATCAATTGCTTGTCAAATTCATCCAAAAAAAAAAGACTAGCTGCTTCTCCCTCAACTTCTCTGTG
8890 CATGAATATAT
196 CATGAATATAT
*
8901 AAATTTGACAAAGGCAAAACAAATCCCCCAAATCTCGATATGCTCCCTTTGCCTCCTAATAGTAC
1 AAATTTGACAAAGGCAAAACAAATCCCCCAAATCTCGATATGCTCCCTTAGCCTCCTAATAGTAC
8966 TCTTCACTGACTAATCCTATGTTTAAGGGTTCATCTCTCCCCTCCCACTTGATCATCCAAATCTC
66 TCTTCACTGACTAATCCTATGTTTAAGGGTTCATCTCTCCCCTCCCACTTGATCATCCAAATCTC
9031 ATCAATTGCTTGTCAAATTCATCCAAAAAAAAAAGACTAGCTGCTTCTCCCTCAACTTCTCTGTG
131 ATCAATTGCTTGTCAAATTCATCCAAAAAAAAAAGACTAGCTGCTTCTCCCTCAACTTCTCTGTG
*
9096 CATGAATATTT
196 CATGAATATAT
*
9107 AAATTTGACAAAGGCAAAACAAATCCCCTAAATCTC
1 AAATTTGACAAAGGCAAAACAAATCCCCCAAATCTC
9143 ATCAAATGCT
Statistics
Matches: 236, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
206 236 1.00
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (206 bp):
AAATTTGACAAAGGCAAAACAAATCCCCCAAATCTCGATATGCTCCCTTAGCCTCCTAATAGTAC
TCTTCACTGACTAATCCTATGTTTAAGGGTTCATCTCTCCCCTCCCACTTGATCATCCAAATCTC
ATCAATTGCTTGTCAAATTCATCCAAAAAAAAAAGACTAGCTGCTTCTCCCTCAACTTCTCTGTG
CATGAATATAT
Found at i:9513 original size:41 final size:41
Alignment explanation
Indices: 9463--9542 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 41
9453 GATTATTGTA
* *
9463 TTTTCAATTTGTTTGTTGTTTTACGAATTGTTTTAATATCG
1 TTTTCAATTTGTTTGTTGGTTTAAGAATTGTTTTAATATCG
* * *
9504 TTTTTAATTTGTTTGTTGGTTTAATATTTGTTTTAATAT
1 TTTTCAATTTGTTTGTTGGTTTAAGAATTGTTTTAATAT
9543 TTTTAAGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.20, C:0.04, G:0.14, T:0.62
Consensus pattern (41 bp):
TTTTCAATTTGTTTGTTGGTTTAAGAATTGTTTTAATATCG
Found at i:14295 original size:23 final size:23
Alignment explanation
Indices: 14259--14349 Score: 103
Period size: 23 Copynumber: 3.9 Consensus size: 23
14249 GTTCATTTAT
*
14259 TTAATCAAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* *
14282 TTAATCGAATATGTTCACAAACA
1 TTAATCGAACATGTTCACGAACA
*
14305 TTACA-CGAACATGTTCATGAACA
1 TTA-ATCGAACATGTTCACGAACA
* *
14328 TATAATTGAACACGTTCACGAA
1 T-TAATCGAACATGTTCACGAA
14350 TAATAAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
23 40 0.71
24 16 0.29
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:15010 original size:18 final size:19
Alignment explanation
Indices: 14987--15022 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
14977 AATCGAGTTG
*
14987 TTCGAGTTAAC-CGAATTA
1 TTCGAGTCAACTCGAATTA
15005 TTCGAGTCAACTCGAATT
1 TTCGAGTCAACTCGAATT
15023 TTTTTCGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (19 bp):
TTCGAGTCAACTCGAATTA
Found at i:15189 original size:28 final size:30
Alignment explanation
Indices: 15158--15214 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
15148 ATTTTTATTT
15158 TTCC-CCCAAAACTTTTACTCCT-TCTCAC
1 TTCCTCCCAAAACTTTTACTCCTCTCTCAC
* *
15186 TTCCTCCCAAAATTTTTATTCCTCTCTCA
1 TTCCTCCCAAAACTTTTACTCCTCTCTCA
15215 TCCCNNNNNN
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 16 0.64
30 5 0.20
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.40
Consensus pattern (30 bp):
TTCCTCCCAAAACTTTTACTCCTCTCTCAC
Found at i:15936 original size:19 final size:19
Alignment explanation
Indices: 15912--15948 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
15902 TGAAAGTAAT
*
15912 AACAAATTTGATTACGGTG
1 AACAAATTTAATTACGGTG
15931 AACAAATTTAATTACGGT
1 AACAAATTTAATTACGGT
15949 AGATGACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
AACAAATTTAATTACGGTG
Found at i:20107 original size:31 final size:29
Alignment explanation
Indices: 20034--20109 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
20024 TGGATCAAAC
*
20034 CAAAATTTCATGTATAAAATTATACAAAAT
1 CAAAA-TTCATGTATAAAATTACACAAAAT
* *
20064 CAAAATTTATGTATACAATTACACATTAAAT
1 CAAAATTCATGTATAAAATTACACA--AAAT
*
20095 CATAATTCATGTATA
1 CAAAATTCATGTATA
20110 GTTTTAAGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 17 0.44
30 5 0.13
31 17 0.44
ACGTcount: A:0.49, C:0.12, G:0.04, T:0.36
Consensus pattern (29 bp):
CAAAATTCATGTATAAAATTACACAAAAT
Found at i:26869 original size:24 final size:25
Alignment explanation
Indices: 26836--26914 Score: 74
Period size: 25 Copynumber: 3.1 Consensus size: 25
26826 GGAACCAACG
*
26836 AAAAGTGAAAGAAA-AAAAAAAGAA
1 AAAAGAGAAAGAAAGAAAAAAAGAA
*
26860 AAAAGAGAAAGAAAGAAAGAAAGAA
1 AAAAGAGAAAGAAAGAAAAAAAGAA
*
26885 GAAGAAG-G-AAGAATGAGAAAGAAAGAA
1 -AA-AAGAGAAAGAA--AGAAAAAAAGAA
26912 AAA
1 AAA
26915 GTAATGTGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
24 13 0.27
25 15 0.31
26 5 0.10
27 15 0.31
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (25 bp):
AAAAGAGAAAGAAAGAAAAAAAGAA
Found at i:26872 original size:4 final size:4
Alignment explanation
Indices: 26842--26912 Score: 60
Period size: 4 Copynumber: 18.0 Consensus size: 4
26832 AACGAAAAGT
* *
26842 GAAA GAAA -AAA AAAA GAAA AAAGA GAAA GAAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA
*
26888 G-AA GGAA GAATGA GAAA GAAA GAAA
1 GAAA GAAA GAA--A GAAA GAAA GAAA
26913 AAGTAATGTG
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
3 12 0.21
4 39 0.67
5 3 0.05
6 4 0.07
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:26880 original size:21 final size:20
Alignment explanation
Indices: 26845--26886 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
26835 GAAAAGTGAA
26845 AGAAAAAAAAAAGAAAAAAG
1 AGAAAAAAAAAAGAAAAAAG
* *
26865 AGAAAGAAAGAAAGAAAGAAG
1 AGAAA-AAAAAAAGAAAAAAG
26886 A
1 A
26887 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AGAAAAAAAAAAGAAAAAAG
Found at i:27292 original size:20 final size:21
Alignment explanation
Indices: 27251--27292 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27241 TAATTTACTT
27251 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
* *
27272 TAATTTTATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
27292 T
1 T
27293 TGTAGTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Done.