Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005427.1 Kokia drynarioides strain JFW-HI SEQ_119456, 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: 92573
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Found at i:520 original size:19 final size:19
Alignment explanation
Indices: 484--521 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
474 ACAAATATCG
*
484 AATCATTTTATAATTTTCT
1 AATCATTTTATAAATTTCT
503 AATCA-TTTATGAAATTTCT
1 AATCATTTTAT-AAATTTCT
522 TCCTCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.34, C:0.11, G:0.03, T:0.53
Consensus pattern (19 bp):
AATCATTTTATAAATTTCT
Found at i:1206 original size:13 final size:13
Alignment explanation
Indices: 1174--1203 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1164 AATAATTATA
1174 TATTTATTATTTG
1 TATTTATTATTTG
1187 TATTTATTATTTG
1 TATTTATTATTTG
1200 -ATTT
1 TATTT
1204 TATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TATTTATTATTTG
Found at i:1638 original size:15 final size:15
Alignment explanation
Indices: 1595--1642 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1585 GTTAAATGCG
*
1595 AATTTTAGAACCCAA
1 AATTTCAGAACCCAA
* *
1610 AA-TGCTGAAGCCCAA
1 AATTTCAGAA-CCCAA
1625 AATTTCAGAACCCAA
1 AATTTCAGAACCCAA
1640 AAT
1 AAT
1643 GACAGTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 5 0.19
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (15 bp):
AATTTCAGAACCCAA
Found at i:9554 original size:24 final size:24
Alignment explanation
Indices: 9503--9554 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
9493 TTCGTAGGTC
* *
9503 AAATAAATTATGCTAATAAATGCA
1 AAATAAATTATACTAATAAATACA
* *
9527 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACA
9551 AAAT
1 AAAT
9555 CTTATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACA
Found at i:13520 original size:20 final size:21
Alignment explanation
Indices: 13495--13533 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
13485 TCCTCATTGT
13495 GCTTCTTCTTTTT-TCCTTGC
1 GCTTCTTCTTTTTATCCTTGC
13515 GCTTCTTCTTTTTATCCTT
1 GCTTCTTCTTTTTATCCTT
13534 CAAACCAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.03, C:0.28, G:0.08, T:0.62
Consensus pattern (21 bp):
GCTTCTTCTTTTTATCCTTGC
Found at i:32737 original size:21 final size:21
Alignment explanation
Indices: 32713--32754 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32703 GTTGTTGAGA
*
32713 AGGAAGT-TGATGTTGGAGAGG
1 AGGAAGTCTG-TGTTGAAGAGG
32734 AGGAAGTCTGTGTTGAAGAGG
1 AGGAAGTCTGTGTTGAAGAGG
32755 TGAAAGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (21 bp):
AGGAAGTCTGTGTTGAAGAGG
Found at i:38921 original size:25 final size:23
Alignment explanation
Indices: 38883--38930 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
38873 AAAATATGAA
* *
38883 GTATATGAATATGAACTTGAAATT
1 GTATATGAAAATGAAATT-AAATT
38907 GTATAATGAAAATGAAATTAAATT
1 GTAT-ATGAAAATGAAATTAAATT
38931 TAGGGTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (23 bp):
GTATATGAAAATGAAATTAAATT
Found at i:39407 original size:24 final size:24
Alignment explanation
Indices: 39257--39398 Score: 169
Period size: 24 Copynumber: 6.0 Consensus size: 24
39247 TTTTTATCTG
* * * *
39257 AGTGGTTGATGAGCAAAAACATAT
1 AGTGGCTGACGAGCATAAACGTAT
*
39281 AGTGGCTGACGAGAATAAACGTAT
1 AGTGGCTGACGAGCATAAACGTAT
* *
39305 AGTGGCTGGCGAGCATAAAAGTAT
1 AGTGGCTGACGAGCATAAACGTAT
* * *
39329 AGTGGCCGACAAGCAAAAACGTAT
1 AGTGGCTGACGAGCATAAACGTAT
*
39353 AGTGGCTGACGAGCATAAA-GTAC
1 AGTGGCTGACGAGCATAAACGTAT
*
39376 AGTAGCTGACGAGCATAAACGTA
1 AGTGGCTGACGAGCATAAACGTA
39399 CATTAGCTGG
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
23 21 0.21
24 78 0.79
ACGTcount: A:0.38, C:0.15, G:0.28, T:0.19
Consensus pattern (24 bp):
AGTGGCTGACGAGCATAAACGTAT
Found at i:46779 original size:12 final size:12
Alignment explanation
Indices: 46762--46802 Score: 73
Period size: 12 Copynumber: 3.3 Consensus size: 12
46752 TGAACTTATA
46762 TATATGTGAAAT
1 TATATGTGAAAT
46774 TATATGTGAAAT
1 TATATGTGAAAT
46786 TATATGTGAAAT
1 TATATGTGAAAT
46798 GTATA
1 -TATA
46803 CTGAATTATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 24 0.86
13 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (12 bp):
TATATGTGAAAT
Found at i:46807 original size:24 final size:23
Alignment explanation
Indices: 46762--46811 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
46752 TGAACTTATA
*
46762 TATATGTGAAATTATATGTGAAAT
1 TATATGTGAAATTATATCTG-AAT
46786 TATATGTGAAATGTATA-CTGAAT
1 TATATGTGAAAT-TATATCTGAAT
46809 TAT
1 TAT
46812 GAAATATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 14 0.58
25 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.42
Consensus pattern (23 bp):
TATATGTGAAATTATATCTGAAT
Found at i:48065 original size:29 final size:29
Alignment explanation
Indices: 48023--48081 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
48013 GAAAATTAAG
48023 ATGTTAGGGATATTTTGTAATTTTACATT
1 ATGTTAGGGATATTTTGTAATTTTACATT
48052 ATGTTAGGGATATTTTGTAATTTTACATT
1 ATGTTAGGGATATTTTGTAATTTTACATT
48081 A
1 A
48082 AGATGGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (29 bp):
ATGTTAGGGATATTTTGTAATTTTACATT
Found at i:48785 original size:24 final size:24
Alignment explanation
Indices: 48757--48825 Score: 93
Period size: 24 Copynumber: 2.9 Consensus size: 24
48747 TTTTTATCTA
*
48757 AGTGGTTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
48781 AGTGGCTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
* * * *
48805 ATTAGCTGGCGAGCGTAAACG
1 AGTGGCTGACGAGCATAAACG
48826 CACTAAACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.19
Consensus pattern (24 bp):
AGTGGCTGACGAGCATAAACGTAC
Found at i:54881 original size:17 final size:17
Alignment explanation
Indices: 54830--54884 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
54820 ATATGAAAAA
54830 TTAAGGAAGATGGAAGG
1 TTAAGGAAGATGGAAGG
*
54847 TTAAATGTCAAG--GG-AGG
1 TT-AA-G-GAAGATGGAAGG
54864 TTAAGGAAGATGGAAGG
1 TTAAGGAAGATGGAAGG
54881 TTAA
1 TTAA
54885 AAGTCAAGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
14 3 0.10
15 1 0.03
16 4 0.13
17 14 0.47
18 4 0.13
19 1 0.03
20 3 0.10
ACGTcount: A:0.40, C:0.02, G:0.36, T:0.22
Consensus pattern (17 bp):
TTAAGGAAGATGGAAGG
Found at i:55079 original size:2 final size:2
Alignment explanation
Indices: 55074--55113 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55064 TATATATATA
55074 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
55114 AATTTACTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:59172 original size:17 final size:17
Alignment explanation
Indices: 59140--59182 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
59130 AATAAAAAAT
*
59140 AGTTATAAGAATATGAAA
1 AGTTA-AAGAAGATGAAA
59158 AGTTAAAGAAGATGAAA
1 AGTTAAAGAAGATGAAA
59175 AGTTAAAG
1 AGTTAAAG
59183 GTCAAGGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (17 bp):
AGTTAAAGAAGATGAAA
Found at i:60179 original size:20 final size:20
Alignment explanation
Indices: 60140--60205 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
60130 TTTATATTGT
* *
60140 TGTTTTGGTGCTGTTTTTTAC
1 TGTTTTAGTGTTG-TTTTTAC
*
60161 TGTTTTTGTGTTGTTTTTAC
1 TGTTTTAGTGTTGTTTTTAC
* *
60181 TGTTTTAATGTT-TTTTTAT
1 TGTTTTAGTGTTGTTTTTAC
60200 TGTTTT
1 TGTTTT
60206 GTTTTGGTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.30
20 17 0.43
21 11 0.28
ACGTcount: A:0.08, C:0.05, G:0.18, T:0.70
Consensus pattern (20 bp):
TGTTTTAGTGTTGTTTTTAC
Found at i:60231 original size:12 final size:12
Alignment explanation
Indices: 60216--60305 Score: 68
Period size: 12 Copynumber: 8.1 Consensus size: 12
60206 GTTTTGGTAC
60216 TATTTTTGTTGT
1 TATTTTTGTTGT
*
60228 TATTTTTGTTGC
1 TATTTTTGTTGT
60240 TA--TTT-TTGT
1 TATTTTTGTTGT
60249 TA-TTTT-TT-T
1 TATTTTTGTTGT
*
60258 TA-TTTTATTGT
1 TATTTTTGTTGT
* *
60269 TATTTTTGCTGC
1 TATTTTTGTTGT
* * *
60281 TGTTTTGGTTAT
1 TATTTTTGTTGT
60293 TATTTTTGTTGT
1 TATTTTTGTTGT
60305 T
1 T
60306 TAGATGTTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
9 12 0.20
10 10 0.16
11 3 0.05
12 36 0.59
ACGTcount: A:0.10, C:0.03, G:0.14, T:0.72
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:60234 original size:24 final size:24
Alignment explanation
Indices: 60193--60258 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
60183 TTTTAATGTT
*
60193 TTTTTATTGTTTTGTTTTGGTACTA
1 TTTTTGTTGTTTT-TTTTGGTACTA
* * *
60218 TTTTTGTTGTTATTTTTGTTGCTA
1 TTTTTGTTGTTTTTTTTGGTACTA
*
60242 TTTTTGTTATTTTTTTT
1 TTTTTGTTGTTTTTTTT
60259 ATTTTATTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
24 24 0.69
25 11 0.31
ACGTcount: A:0.09, C:0.03, G:0.14, T:0.74
Consensus pattern (24 bp):
TTTTTGTTGTTTTTTTTGGTACTA
Found at i:60238 original size:65 final size:64
Alignment explanation
Indices: 60139--60306 Score: 157
Period size: 65 Copynumber: 2.6 Consensus size: 64
60129 ATTTATATTG
*
60139 TTGTTTTGGTGCTGTTTTT-TACTGTT-TTTGTGTTGTTTTTACTGTT-TTAATGTTT-TTTTAT
1 TTGTTTTGGTGCTGTTTTTGT--TGTTATTTTTGTTGTTTTT--TGTTATT-ATGTTTATTTTAT
60200 TGTT
61 TGTT
* * * *
60204 TTGTTTTGGTACTATTTTTGTTGTTATTTTTGTTGCTATTTTTGTTATTTTTTTTATTTTATTGT
1 TTGTTTTGGTGCTGTTTTTGTTGTTATTTTTGTTG-T-TTTTTGTTATTATGTTTATTTTATTGT
60269 T
64 T
* * * *
60270 AT-TTTTGCTGCTGTTTTGGTTATTATTTTTGTTGTTT
1 TTGTTTTGGTGCTGTTTTTGTTGTTATTTTTGTTGTTT
60307 AGATGTTATT
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
63 2 0.02
64 5 0.06
65 60 0.70
66 15 0.17
67 4 0.05
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (64 bp):
TTGTTTTGGTGCTGTTTTTGTTGTTATTTTTGTTGTTTTTTGTTATTATGTTTATTTTATTGTT
Found at i:60252 original size:9 final size:9
Alignment explanation
Indices: 60224--60276 Score: 52
Period size: 9 Copynumber: 5.3 Consensus size: 9
60214 ACTATTTTTG
60224 TTGTTATTT
1 TTGTTATTT
60233 TTGTTGCTATTT
1 TTG-T--TATTT
60245 TTGTTATTT
1 TTGTTATTT
*
60254 TTTTTATTTT
1 TTGTTA-TTT
60264 ATTGTTATTT
1 -TTGTTATTT
60274 TTG
1 TTG
60277 CTGCTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 16 0.43
10 7 0.19
11 6 0.16
12 8 0.22
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.75
Consensus pattern (9 bp):
TTGTTATTT
Found at i:60269 original size:41 final size:41
Alignment explanation
Indices: 60219--60299 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 41
60209 TTGGTACTAT
* * * *
60219 TTTTGTTGTTATTTTTGTTGCTATTTTTGTTATTTTTTTTA
1 TTTTATTGTTATTTTTGCTGCTATTTTGGTTATTATTTTTA
*
60260 TTTTATTGTTATTTTTGCTGCTGTTTTGGTTATTATTTTT
1 TTTTATTGTTATTTTTGCTGCTATTTTGGTTATTATTTTT
60300 GTTGTTTAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.10, C:0.04, G:0.14, T:0.73
Consensus pattern (41 bp):
TTTTATTGTTATTTTTGCTGCTATTTTGGTTATTATTTTTA
Found at i:60305 original size:21 final size:20
Alignment explanation
Indices: 60267--60328 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 20
60257 TTATTTTATT
*
60267 GTTATTTTTGCTGCTGTTTTG-
1 GTTATTTTT-TTG-TGTTTTGA
*
60288 GTTATTATTTTTGTTGTTTAGA
1 GTTATT-TTTTTG-TGTTTTGA
60310 TGTTATTTTTTTGTGTTTT
1 -GTTATTTTTTTGTGTTTT
60329 TACTATTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 19 0.56
22 9 0.26
23 6 0.18
ACGTcount: A:0.10, C:0.03, G:0.19, T:0.68
Consensus pattern (20 bp):
GTTATTTTTTTGTGTTTTGA
Found at i:60314 original size:44 final size:41
Alignment explanation
Indices: 60225--60319 Score: 111
Period size: 41 Copynumber: 2.2 Consensus size: 41
60215 CTATTTTTGT
* * *
60225 TGTTATTTTTGTTGCTATTTTTGTTATTTTTTTTATTTTAT
1 TGTTATTTTTGCTGCTATTTTGGTTATTTTTTTTATTTTAA
*
60266 TGTTATTTTTGCTGCTGTTTTGGTTATTATTTTTGT-TGTTTAGA
1 TGTTATTTTTGCTGCTATTTTGGTTATT-TTTTT-TAT-TTTA-A
60310 TGTTATTTTT
1 TGTTATTTTT
60320 TTGTGTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
41 25 0.54
42 6 0.13
43 5 0.11
44 10 0.22
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.71
Consensus pattern (41 bp):
TGTTATTTTTGCTGCTATTTTGGTTATTTTTTTTATTTTAA
Found at i:67466 original size:14 final size:14
Alignment explanation
Indices: 67429--67470 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
67419 CTATATTTTA
67429 AATATTTAAATA-T
1 AATATTTAAATATT
67442 AATCA-TTAAATATT
1 AAT-ATTTAAATATT
*
67456 TATATTTAAATATT
1 AATATTTAAATATT
67470 A
1 A
67471 GCACAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
AATATTTAAATATT
Found at i:72287 original size:12 final size:13
Alignment explanation
Indices: 72254--72292 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
72244 TCAAGCGAGA
72254 ATATTATTTTGGT
1 ATATTATTTTGGT
* *
72267 ATTTTATTTT-TT
1 ATATTATTTTGGT
72279 ATATTATTTTGGT
1 ATATTATTTTGGT
72292 A
1 A
72293 AAAAATCCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (13 bp):
ATATTATTTTGGT
Found at i:73799 original size:16 final size:17
Alignment explanation
Indices: 73773--73804 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
73763 ATTGTGATTT
73773 TAGTCTAGAAATTGTTA
1 TAGTCTAGAAATTGTTA
73790 TAGT-TAGAAATTGTT
1 TAGTCTAGAAATTGTT
73805 GTAAGTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (17 bp):
TAGTCTAGAAATTGTTA
Found at i:74065 original size:25 final size:26
Alignment explanation
Indices: 74015--74069 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
74005 GCGCGCTATT
*
74015 CGTTATTTAGTACGTATTGTGCTCTC
1 CGTTATTTAGCACGTATTGTGCTCTC
* *
74041 CGTTATTTAGCATGT-TTGTTCTCTC
1 CGTTATTTAGCACGTATTGTGCTCTC
74066 CGTT
1 CGTT
74070 TAGCACCCTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (26 bp):
CGTTATTTAGCACGTATTGTGCTCTC
Found at i:74518 original size:47 final size:47
Alignment explanation
Indices: 74449--74543 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
74439 TGACCTCTCA
*
74449 TCACATCACATTTTGAAGGGTAACAATATTGACATTTTATTTTGTAT
1 TCACATCACATTTTGAAGGGTAAAAATATTGACATTTTATTTTGTAT
74496 TCACATCACATTTTGAAGGGTAAAAATATTGACATTTTATTTTGTAT
1 TCACATCACATTTTGAAGGGTAAAAATATTGACATTTTATTTTGTAT
74543 T
1 T
74544 AAAATGGCAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (47 bp):
TCACATCACATTTTGAAGGGTAAAAATATTGACATTTTATTTTGTAT
Found at i:87062 original size:15 final size:14
Alignment explanation
Indices: 87036--87080 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 14
87026 TGTGGGTGTT
87036 GAAGAGGAAGAAAAG
1 GAAGA-GAAGAAAAG
87051 GAAAGAGAAGAAGAAG
1 G-AAGAGAAGAA-AAG
87067 GAAGAGAAGAAAAG
1 GAAGAGAAGAAAAG
87081 AAAAAAGACA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.11
15 17 0.61
16 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (14 bp):
GAAGAGAAGAAAAG
Found at i:89936 original size:35 final size:36
Alignment explanation
Indices: 89854--89940 Score: 124
Period size: 36 Copynumber: 2.4 Consensus size: 36
89844 CATATTTGTG
* *
89854 TTGTCAGTTTATCCGACTAGTGCTGGGCACAAATCT
1 TTGTCGGTTTATCCGACTAGTGCTAGGCACAAATCT
*
89890 TTGTCGGTTTATCCGACTAGTGC-AGG-ACACATCT
1 TTGTCGGTTTATCCGACTAGTGCTAGGCACAAATCT
89924 ATTGTCGGTTTATCCGA
1 -TTGTCGGTTTATCCGA
89941 TTAGCGCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
34 7 0.15
35 18 0.38
36 22 0.47
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (36 bp):
TTGTCGGTTTATCCGACTAGTGCTAGGCACAAATCT
Found at i:90910 original size:42 final size:42
Alignment explanation
Indices: 90846--90937 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
90836 TGGGCAGACG
* * * *
90846 CACGGCCTGGGACACGGTCGTGTGGCCCAAGTCAGTGAGTTA
1 CACGGCCTAGGACACGGGCGTGTGGCCCAAGTAAGTAAGTTA
* *
90888 CACGGCCTATGACACGGGCGTGTGGCTCAAGTAAGTAAGTTA
1 CACGGCCTAGGACACGGGCGTGTGGCCCAAGTAAGTAAGTTA
*
90930 CATGGCCT
1 CACGGCCT
90938 GTGGCATGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.21
Consensus pattern (42 bp):
CACGGCCTAGGACACGGGCGTGTGGCCCAAGTAAGTAAGTTA
Done.