Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014195.1 Kokia drynarioides strain JFW-HI SEQ_129228, 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: 94677
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Warning! 31 characters in sequence are not A, C, G, or T
Found at i:3469 original size:2 final size:2
Alignment explanation
Indices: 3464--3510 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
3454 AGAAGAAAAC
*
3464 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GG
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3506 GA GA G
1 GA GA G
3511 GGAATCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20805 original size:27 final size:27
Alignment explanation
Indices: 20766--20828 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
20756 TCATGTGGCA
20766 ATTAAAATAAAAACAATAA-ATTTAAAT
1 ATTAAAATAAAAACAATAATA-TTAAAT
* *
20793 -TTAGAATAGAAAACTATAATATTAAAT
1 ATTAAAATA-AAAACAATAATATTAAAT
20820 ATTAAAATA
1 ATTAAAATA
20829 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 7 0.23
27 15 0.50
28 8 0.27
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
ATTAAAATAAAAACAATAATATTAAAT
Found at i:20969 original size:83 final size:83
Alignment explanation
Indices: 20804--20971 Score: 282
Period size: 83 Copynumber: 2.0 Consensus size: 83
20794 TAGAATAGAA
* *
20804 AACTATAATATTAAATATTAAAATATTAAAAAATACCTTTTTAAAAAATGAAAACAAAGTACGGA
1 AACTATAATATTAAATATTAAAATATTAAAAAATACCTTTTTAAAAAACGAAAACAAAGTACAGA
*
20869 GGCAAATTAGACGTTTAG
66 GGCAAATTAGACATTTAG
* * *
20887 AACTATAATATTAAATATTAAAATATTAAAAAATGCCTTTTTAGAAAACGAAAATAAAGTACAGA
1 AACTATAATATTAAATATTAAAATATTAAAAAATACCTTTTTAAAAAACGAAAACAAAGTACAGA
20952 GGCAAATTAGACATTTAG
66 GGCAAATTAGACATTTAG
20970 AA
1 AA
20972 ATTTTAGGTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (83 bp):
AACTATAATATTAAATATTAAAATATTAAAAAATACCTTTTTAAAAAACGAAAACAAAGTACAGA
GGCAAATTAGACATTTAG
Found at i:22168 original size:7 final size:7
Alignment explanation
Indices: 22156--22243 Score: 61
Period size: 7 Copynumber: 12.7 Consensus size: 7
22146 AATTTGACGA
22156 GTTTAGG
1 GTTTAGG
22163 GTTTAGG
1 GTTTAGG
*
22170 TTTTA-G
1 GTTTAGG
* *
22176 TTTTATG
1 GTTTAGG
*
22183 GTTTAAG
1 GTTTAGG
*
22190 GTTTATG
1 GTTTAGG
* **
22197 TTTTATA
1 GTTTAGG
22204 GTTTAGG
1 GTTTAGG
22211 GTTTAGG
1 GTTTAGG
**
22218 GTTTATT
1 GTTTAGG
*
22225 GTTTATG
1 GTTTAGG
*
22232 ATTTAGG
1 GTTTAGG
22239 GTTTA
1 GTTTA
22244 TGATTTCAAT
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
6 6 0.09
7 59 0.91
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (7 bp):
GTTTAGG
Found at i:22193 original size:21 final size:22
Alignment explanation
Indices: 22157--22214 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 22
22147 ATTTGACGAG
*
22157 TTTAGGGTTT-AGGTTTTA-GT
1 TTTATGGTTTAAGGTTTTATGT
22177 TTTATGGTTTAAGG-TTTATGT
1 TTTATGGTTTAAGGTTTTATGT
* *
22198 TTTATAGTTTAGGGTTT
1 TTTATGGTTTAAGGTTT
22215 AGGGTTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
21 17 0.53
22 2 0.06
ACGTcount: A:0.17, C:0.00, G:0.26, T:0.57
Consensus pattern (22 bp):
TTTATGGTTTAAGGTTTTATGT
Found at i:22222 original size:21 final size:21
Alignment explanation
Indices: 22163--22244 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 21
22153 CGAGTTTAGG
* * *
22163 GTTTAGGTTTTA-GTTTTATG
1 GTTTAGGGTTTAGGGTTTATA
* * *
22183 GTTTAAGGTTTATGTTTTATA
1 GTTTAGGGTTTAGGGTTTATA
*
22204 GTTTAGGGTTTAGGGTTTATT
1 GTTTAGGGTTTAGGGTTTATA
* *
22225 GTTTATGATTTAGGGTTTAT
1 GTTTAGGGTTTAGGGTTTAT
22245 GATTTCAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
20 10 0.19
21 42 0.81
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.56
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTTTATA
Found at i:22244 original size:14 final size:14
Alignment explanation
Indices: 22205--22316 Score: 57
Period size: 14 Copynumber: 7.7 Consensus size: 14
22195 TGTTTTATAG
* *
22205 TTTAGGGTTTAGGG
1 TTTAGGGTTTATGA
**
22219 TTTATTGTTTATGA
1 TTTAGGGTTTATGA
22233 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
* * * *
22247 TTTCAATTTAGGATTCTAA
1 TTT--A---GGGTTTATGA
* *
22266 TTTAGGGTTTAAGG
1 TTTAGGGTTTATGA
*
22280 TTTATGGTTTCA--A
1 TTTAGGGTTT-ATGA
22293 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
22307 TTTAGGGTTT
1 TTTAGGGTTT
22317 TAATTTATTT
Statistics
Matches: 71, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
12 1 0.01
13 9 0.13
14 49 0.69
15 1 0.01
16 1 0.01
17 1 0.01
19 9 0.13
ACGTcount: A:0.21, C:0.03, G:0.25, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:22257 original size:20 final size:20
Alignment explanation
Indices: 22232--22309 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
22222 ATTGTTTATG
22232 ATTTAGGGTTTATGATTTCA
1 ATTTAGGGTTTATGATTTCA
*
22252 ATTTAGGATTCTA--ATTT-A
1 ATTTAGGGTT-TATGATTTCA
* * *
22270 GGGTTTAAGGTTTATGGTTTCA
1 --ATTTAGGGTTTATGATTTCA
22292 ATTTAGGGTTTATGATTT
1 ATTTAGGGTTTATGATTT
22310 AGGGTTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
18 1 0.02
19 6 0.14
20 31 0.70
21 5 0.11
22 1 0.02
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (20 bp):
ATTTAGGGTTTATGATTTCA
Found at i:22283 original size:27 final size:27
Alignment explanation
Indices: 22252--22323 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
22242 TATGATTTCA
22252 ATTTAGGATTCTAATTTAGGGTTTAAG
1 ATTTAGGATTCTAATTTAGGGTTTAAG
* * *
22279 GTTTATGGTTTC-AATTTAGGGTTTATG
1 ATTTA-GGATTCTAATTTAGGGTTTAAG
* *
22306 ATTTAGGGTTTTAATTTA
1 ATTTAGGATTCTAATTTA
22324 TTTTTATGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
26 4 0.11
27 28 0.76
28 5 0.14
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (27 bp):
ATTTAGGATTCTAATTTAGGGTTTAAG
Found at i:22283 original size:40 final size:40
Alignment explanation
Indices: 22233--22316 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
22223 TTGTTTATGA
*
22233 TTTAGGGTTTATGATTTCAATTTAGGATTCTA-ATTTAGGG
1 TTTAAGGTTTATGATTTCAATTTAGGATT-TAGATTTAGGG
* *
22273 TTTAAGGTTTATGGTTTCAATTTAGGGTTTATGATTTAGGG
1 TTTAAGGTTTATGATTTCAATTTAGGATTTA-GATTTAGGG
22314 TTT
1 TTT
22317 TAATTTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
39 2 0.05
40 26 0.67
41 11 0.28
ACGTcount: A:0.23, C:0.04, G:0.24, T:0.50
Consensus pattern (40 bp):
TTTAAGGTTTATGATTTCAATTTAGGATTTAGATTTAGGG
Found at i:22301 original size:13 final size:13
Alignment explanation
Indices: 22247--22323 Score: 61
Period size: 14 Copynumber: 5.8 Consensus size: 13
22237 GGGTTTATGA
22247 TTTCAATTTA-GG
1 TTTCAATTTAGGG
*
22259 ATTCTAATTTAGGG
1 TTTC-AATTTAGGG
*
22273 TTT-AAGGTTTATGG
1 TTTCAA--TTTAGGG
22287 TTTCAATTTAGGG
1 TTTCAATTTAGGG
22300 TTT-ATGATTTAGGG
1 TTTCA--ATTTAGGG
*
22314 TTTTAATTTA
1 TTTCAATTTA
22324 TTTTTATGGT
Statistics
Matches: 53, Mismatches: 4, Indels: 15
0.74 0.06 0.21
Matches are distributed among these distances:
12 6 0.11
13 20 0.38
14 24 0.45
15 3 0.06
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.51
Consensus pattern (13 bp):
TTTCAATTTAGGG
Found at i:22323 original size:20 final size:20
Alignment explanation
Indices: 22300--22414 Score: 99
Period size: 20 Copynumber: 5.8 Consensus size: 20
22290 CAATTTAGGG
* *
22300 TTTATGATTTAGGGTTTTAA
1 TTTAGGATTTAGGGTTCTAA
** *
22320 TTTA-TTTTTATGGTTCTAA
1 TTTAGGATTTAGGGTTCTAA
* **
22339 TTTAGGGTTTAATGTTCTAA
1 TTTAGGATTTAGGGTTCTAA
* *
22359 TTTAGGGTTTAGTGTTCTAA
1 TTTAGGATTTAGGGTTCTAA
*
22379 TTTAGGATTTCA-AGTTCTAA
1 TTTAGGATTT-AGGGTTCTAA
*
22399 TTTAAGATTTAGGGTT
1 TTTAGGATTTAGGGTT
22415 TTGGATTTTA
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.20
20 62 0.78
21 1 0.01
ACGTcount: A:0.24, C:0.04, G:0.19, T:0.52
Consensus pattern (20 bp):
TTTAGGATTTAGGGTTCTAA
Found at i:22342 original size:13 final size:12
Alignment explanation
Indices: 22251--22323 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 12
22241 TTATGATTTC
*
22251 AATTTAGGATTCT
1 AATTTAGGGTT-T
22264 AATTTAGGGTTT
1 AATTTAGGGTTT
*
22276 AAGGTTTATGGTTT
1 AA--TTTAGGGTTT
22290 CAATTTAGGGTTT
1 -AATTTAGGGTTT
22303 ATGATTTAGGGTTTT
1 A--ATTTAGGG-TTT
22318 AATTTA
1 AATTTA
22324 TTTTTATGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.08
13 24 0.47
14 17 0.33
15 6 0.12
ACGTcount: A:0.26, C:0.03, G:0.22, T:0.49
Consensus pattern (12 bp):
AATTTAGGGTTT
Found at i:22410 original size:40 final size:40
Alignment explanation
Indices: 22332--22410 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
22322 TATTTTTATG
* * *
22332 GTTCTAATTTAGGGTTTAATGTTCTAATTTAGGGTTTAGT
1 GTTCTAATTTAGGATTTAATGTTCTAATTTAAGATTTAGT
22372 GTTCTAATTTAGGATTTCAA-GTTCTAATTTAAGATTTAG
1 GTTCTAATTTAGGATTT-AATGTTCTAATTTAAGATTTAG
22411 GGTTTTGGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (40 bp):
GTTCTAATTTAGGATTTAATGTTCTAATTTAAGATTTAGT
Found at i:24440 original size:3 final size:3
Alignment explanation
Indices: 24432--24463 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24422 CGACATCATT
24432 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
24464 TGTTGATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28906 original size:9 final size:9
Alignment explanation
Indices: 28892--28916 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28882 AAGTAGGAGG
28892 AAAGGAAGA
1 AAAGGAAGA
28901 AAAGGAAGA
1 AAAGGAAGA
28910 AAAGGAA
1 AAAGGAA
28917 AAGAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (9 bp):
AAAGGAAGA
Found at i:29615 original size:77 final size:75
Alignment explanation
Indices: 29465--29618 Score: 211
Period size: 77 Copynumber: 2.0 Consensus size: 75
29455 AATAAAAATC
* * * *
29465 TTTTAAAAATTTTAAAATTTTAAATTATTAAAGATAAAATTATATTTTCATCCTTCATAAAAATT
1 TTTTAAAAATTATAAAAATATAAATTATTAAAGATAAAATTATATTTTCATCCTTAATAAAAATT
29530 TAATTTAATT
66 TAATTTAATT
* * *
29540 TTTTAAAAATTATAAAAATATAAATTATTTAAATGATAAAATTATATTTTTA-CTTTAATACAAA
1 TTTTAAAAATTATAAAAATATAAATTA-TTAAA-GATAAAATTATATTTTCATCCTTAATAAAAA
29604 TTATAATTTAATT
64 TT-TAATTTAATT
29617 TT
1 TT
29619 GACCAATAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 24 0.35
76 16 0.23
77 29 0.42
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (75 bp):
TTTTAAAAATTATAAAAATATAAATTATTAAAGATAAAATTATATTTTCATCCTTAATAAAAATT
TAATTTAATT
Found at i:34551 original size:25 final size:24
Alignment explanation
Indices: 34497--34551 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
34487 ATCCCATTCC
*
34497 CAAAACAGTAAAAAAAAAAAAACA
1 CAAAACAATAAAAAAAAAAAAACA
* * *
34521 CTAAAACAATATAAAAATAACAACAA
1 C-AAAACAATAAAAAAAAAAAAAC-A
34547 CAAAA
1 CAAAA
34552 AAAACAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.88
26 2 0.08
ACGTcount: A:0.75, C:0.15, G:0.02, T:0.09
Consensus pattern (24 bp):
CAAAACAATAAAAAAAAAAAAACA
Found at i:35576 original size:23 final size:22
Alignment explanation
Indices: 35529--35577 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
35519 ATTAATCTAG
35529 AAAAAGTTTGATTCATATTTGA
1 AAAAAGTTTGATTCATATTTGA
*
35551 AAAAAGTTTGGTTCATATTTGA
1 AAAAAGTTTGATTCATATTTGA
35573 AAAAA
1 AAAAA
35578 AAAATATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.45, C:0.04, G:0.14, T:0.37
Consensus pattern (22 bp):
AAAAAGTTTGATTCATATTTGA
Found at i:38240 original size:9 final size:9
Alignment explanation
Indices: 38226--38250 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
38216 GAACAGTTGG
38226 TTTGTTTGA
1 TTTGTTTGA
38235 TTTGTTTGA
1 TTTGTTTGA
38244 TTTGTTT
1 TTTGTTT
38251 AGCATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.20, T:0.72
Consensus pattern (9 bp):
TTTGTTTGA
Found at i:43873 original size:13 final size:13
Alignment explanation
Indices: 43855--43886 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43845 AATTATATTG
43855 GGTGGTAATTCTC
1 GGTGGTAATTCTC
43868 GGTGGTAATTCTC
1 GGTGGTAATTCTC
*
43881 CGTGGT
1 GGTGGT
43887 CTTTATGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.34, T:0.38
Consensus pattern (13 bp):
GGTGGTAATTCTC
Found at i:46765 original size:12 final size:12
Alignment explanation
Indices: 46748--46778 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
46738 TCATGTTATA
46748 TATGTGTGTGTG
1 TATGTGTGTGTG
46760 TATGTGTGTGTG
1 TATGTGTGTGTG
*
46772 TCTGTGT
1 TATGTGT
46779 TCTTTAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.03, G:0.39, T:0.52
Consensus pattern (12 bp):
TATGTGTGTGTG
Found at i:59257 original size:5 final size:5
Alignment explanation
Indices: 59247--59273 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59237 CGGCAATCAG
59247 CTATA CTATA CTATA CTATA CTATA CT
1 CTATA CTATA CTATA CTATA CTATA CT
59274 TTCCACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATA
Found at i:64075 original size:6 final size:6
Alignment explanation
Indices: 64036--64073 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
64026 ATTATTCCCA
*
64036 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAATTG GA
1 GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GAGTTG GA
64074 ATATGGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (6 bp):
GAGTTG
Found at i:67445 original size:11 final size:11
Alignment explanation
Indices: 67429--67503 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
67419 TCCAATAAAC
67429 TTAAATTTATT
1 TTAAATTTATT
*
67440 TTAAATTTAAAT
1 TTAAATTT-ATT
* * *
67452 TT-AGTTGAAAT
1 TTAAATT-TATT
67463 TTAAATTTATT
1 TTAAATTTATT
*
67474 ATAAATTTAAATT
1 TTAAATTT--ATT
*
67487 TAAAATTTATT
1 TTAAATTTATT
67498 TTAAAT
1 TTAAAT
67504 ATCCAAAGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
11 33 0.67
12 7 0.14
13 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:67448 original size:6 final size:6
Alignment explanation
Indices: 67424--67495 Score: 62
Period size: 6 Copynumber: 12.3 Consensus size: 6
67414 CTGGATCCAA
* * * *
67424 TAAACT TAAATT T-ATTT TAAATT TAAATT T-AGTT GAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
67470 T--ATT ATAAATT TAAATT TAAAATT TA
1 TAAATT -TAAATT TAAATT T-AAATT TA
67496 TTTTAAATAT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
4 3 0.06
5 8 0.15
6 33 0.62
7 9 0.17
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:67449 original size:17 final size:17
Alignment explanation
Indices: 67424--67488 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
67414 CTGGATCCAA
*
67424 TAAACTTAAATTTATTT
1 TAAATTTAAATTTATTT
*
67441 TAAATTTAAATTTAGTT
1 TAAATTTAAATTTATTT
* *
67458 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
67475 TAAATTTAAATTTA
1 TAAATTTAAATTTA
67489 AAATTTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:67497 original size:24 final size:23
Alignment explanation
Indices: 67459--67503 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
67449 AATTTAGTTG
67459 AAATTTAAATTTATTATAAATTT
1 AAATTTAAATTTATTATAAATTT
*
67482 AAATTTAAAATTTATTTTAAAT
1 AAATTT-AAATTTATTATAAAT
67504 ATCCAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATTTATTATAAATTT
Found at i:67952 original size:13 final size:13
Alignment explanation
Indices: 67934--67964 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
67924 AAAAACAGAG
67934 CATTCAATATTAT
1 CATTCAATATTAT
67947 CATTCAATATTAT
1 CATTCAATATTAT
67960 CATTC
1 CATTC
67965 GAAGAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (13 bp):
CATTCAATATTAT
Found at i:68284 original size:16 final size:15
Alignment explanation
Indices: 68263--68307 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
68253 AATAAATATA
68263 TATTAAATAATAAGAG
1 TATTAAATAATAA-AG
68279 TATTAAATAATATAAG
1 TATTAAATAATA-AAG
*
68295 TATTAAATGATAA
1 TATTAAATAATAA
68308 TAAAAGAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (15 bp):
TATTAAATAATAAAG
Found at i:68634 original size:24 final size:25
Alignment explanation
Indices: 68593--68641 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
68583 ATAGATTTGA
* *
68593 GAATAAAAAGACATTTTTTTTGAAG
1 GAATAAAAAGACAGTTTTTTCGAAG
*
68618 GAATAAAAA-AGAGTTTTTTCGAAG
1 GAATAAAAAGACAGTTTTTTCGAAG
68642 ATCTGAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.45, C:0.04, G:0.18, T:0.33
Consensus pattern (25 bp):
GAATAAAAAGACAGTTTTTTCGAAG
Found at i:69406 original size:30 final size:29
Alignment explanation
Indices: 69320--69726 Score: 293
Period size: 29 Copynumber: 13.9 Consensus size: 29
69310 TGGAGGTCTT
* *
69320 AAACTGTCCGAAAATTACCATTTTACCTTC-
1 AAACT-TCCAAAAATTACCATTTTACC-CCA
* *
69350 GAACTTCCAATAAA-TCCCATTTTTAACCCCA
1 AAACTTCCAA-AAATTACCA-TTTT-ACCCCA
*
69381 AAACTTCCAAAAATTATCATTTTAACCCC-
1 AAACTTCCAAAAATTACCATTTT-ACCCCA
* * * *
69410 GAACTTCAAAAAATTATCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCA
* * *
69439 GAACTTCTAAAAA-TCCCATTTTTTGACCCCA
1 AAACTTCCAAAAATTACCA--TTTT-ACCCCA
*
69470 AAACTTCCAAAAA-TATCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCA
*
69500 AAACTTCC--AAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCA
* *
69527 AAACTTCCAAAAA-TCCCATTTTTGACCCCG
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCA
*
69557 AAACTAT-C-AAAATTACCATTTTACCCCC
1 AAACT-TCCAAAAATTACCATTTTACCCCA
* *
69585 AAACTT-CAAAAAGTCCCATTTTTTACCCC-
1 AAACTTCCAAAAATTACCA--TTTTACCCCA
* *
69614 GAACTTCCAAAAATTACCATTTTACCCTA
1 AAACTTCCAAAAATTACCATTTTACCCCA
* *
69643 AAACTTCCTAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCA
* * *
69672 GAACTTCCAAAAATCTTA--TTTTTGACCCCG
1 AAACTTCCAAAAA--TTACCATTTT-ACCCCA
* *
69702 ACACTTCCAAAAATTACCAATTTAC
1 AAACTTCCAAAAATTACCATTTTAC
69727 TCCCGGATGT
Statistics
Matches: 310, Mismatches: 41, Indels: 53
0.77 0.10 0.13
Matches are distributed among these distances:
27 15 0.05
28 48 0.15
29 107 0.35
30 102 0.33
31 38 0.12
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCA
Found at i:79387 original size:56 final size:57
Alignment explanation
Indices: 79327--79559 Score: 197
Period size: 57 Copynumber: 4.1 Consensus size: 57
79317 TTCAGTTCTC
* *
79327 TAAAAAT-TTTTTTTAGGTGTTTGACACTCAATAACCTACACCACTTTTCCCAAATT
1 TAAAAATATTTTTTTAGGTGTTTGTCACCCAATAACCTACACCACTTTTCCCAAATT
* * * * * * * *
79383 TAAAAATATTTTTTT-GAGTGTTTGCCTCCCAATAGCTTATATCACCTTTCCAAAATT
1 TAAAAATATTTTTTTAG-GTGTTTGTCACCCAATAACCTACACCACTTTTCCCAAATT
* *** ** **
79440 TAAAAATA-TTTTTTGGGTGTTTGTCACCCAATGGTCTACACCA-TATTTTTCTGATT
1 TAAAAATATTTTTTTAGGTGTTTGTCACCCAATAACCTACACCACT-TTTCCCAAATT
* * * *
79496 TAAAAATATTTTTTTAGGTCTTTGTCATCCAATGACCTACATCACCTTTT-CCAAATTT
1 TAAAAATATTTTTTTAGGTGTTTGTCACCCAATAACCTACACCA-CTTTTCCCAAA-TT
79554 TAAAAA
1 TAAAAA
79560 ACAATTAAAT
Statistics
Matches: 138, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
56 48 0.35
57 78 0.57
58 11 0.08
59 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (57 bp):
TAAAAATATTTTTTTAGGTGTTTGTCACCCAATAACCTACACCACTTTTCCCAAATT
Found at i:81234 original size:83 final size:83
Alignment explanation
Indices: 81095--81266 Score: 344
Period size: 83 Copynumber: 2.1 Consensus size: 83
81085 ATAAGCAGTT
81095 AATAATGAATATTAAATAACACGAAGTAAGATAATTAAGAAGATAAATGGTAAGCAAAAATAAAA
1 AATAATGAATATTAAATAACACGAAGTAAGATAATTAAGAAGATAAATGGTAAGCAAAAATAAAA
81160 AAATACAAAATACGAGTG
66 AAATACAAAATACGAGTG
81178 AATAATGAATATTAAATAACACGAAGTAAGATAATTAAGAAGATAAATGGTAAGCAAAAATAAAA
1 AATAATGAATATTAAATAACACGAAGTAAGATAATTAAGAAGATAAATGGTAAGCAAAAATAAAA
81243 AAATACAAAATACGAGTG
66 AAATACAAAATACGAGTG
81261 AATAAT
1 AATAAT
81267 AGTTAAAATT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 89 1.00
ACGTcount: A:0.59, C:0.06, G:0.14, T:0.21
Consensus pattern (83 bp):
AATAATGAATATTAAATAACACGAAGTAAGATAATTAAGAAGATAAATGGTAAGCAAAAATAAAA
AAATACAAAATACGAGTG
Found at i:81512 original size:59 final size:59
Alignment explanation
Indices: 81409--81568 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 59
81399 GTTCGAGGTT
* * * * * * *
81409 AAAAATGGAATTTTTAGACACCCGAGGGTAAAACGATAACTTTTAAAAAAATCGATATC
1 AAAAATAGAATTTTTAGACATCCGGGGGTAAAATGGTAATTTTTAAAAAAATCGAGATC
** *
81468 AAAAA-AGAAATTTTTAGACATCCGGGGGTAAAATGGTAATTTTTAGGAAAATCGGGATC
1 AAAAATAG-AATTTTTAGACATCCGGGGGTAAAATGGTAATTTTTAAAAAAATCGAGATC
* **
81527 AAAAATAGAATTTTTGGACATTTGGGGGTAAAAAT-GTAATTT
1 AAAAATAGAATTTTTAGACATCCGGGGGT-AAAATGGTAATTT
81569 GGGGGTAAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 1 0.01
59 77 0.91
60 7 0.08
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (59 bp):
AAAAATAGAATTTTTAGACATCCGGGGGTAAAATGGTAATTTTTAAAAAAATCGAGATC
Found at i:81579 original size:20 final size:19
Alignment explanation
Indices: 81546--81587 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
81536 ATTTTTGGAC
81546 ATTTGGGGGTAAAAATGTA
1 ATTTGGGGGTAAAAATGTA
81565 ATTTGGGGGTAAAAATGTA
1 ATTTGGGGGTAAAAATGTA
81584 ATTT
1 ATTT
81588 TTGGAAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (19 bp):
ATTTGGGGGTAAAAATGTA
Found at i:81585 original size:78 final size:78
Alignment explanation
Indices: 81491--81646 Score: 210
Period size: 78 Copynumber: 2.0 Consensus size: 78
81481 TTAGACATCC
81491 GGGGGTAAAATGGTAATTTTTAGGAA-AATCG-GGATCAAAAATAGAATTTTTGGACATTTGGGG
1 GGGGGTAAAATGGTAATTTTT-GGAAGAATCGAGG-TCAAAAATAGAATTTTTGGACATTTGGGG
*
81554 GTAAAAATGTAATTT
64 GTAAAAATATAATTT
** * * *
81569 GGGGGTAAAAAT-GTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGATATTTGGGGG
1 GGGGGT-AAAATGGTAATTTTTGGAAGAATCGAGGTCAAAAATAGAATTTTTGGACATTTGGGGG
81633 TAAAAATATAATTT
65 TAAAAATATAATTT
81647 TTGGAAGTTT
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
77 4 0.06
78 58 0.84
79 7 0.10
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (78 bp):
GGGGGTAAAATGGTAATTTTTGGAAGAATCGAGGTCAAAAATAGAATTTTTGGACATTTGGGGGT
AAAAATATAATTT
Found at i:81636 original size:29 final size:28
Alignment explanation
Indices: 81564--81652 Score: 115
Period size: 30 Copynumber: 3.1 Consensus size: 28
81554 GTAAAAATGT
81564 AATTTGGGGGTAAAAATGTAATTTTTGG
1 AATTTGGGGGTAAAAATGTAATTTTTGG
* * *
81592 AAGTTTCGAGGTTAAAAATGGAATTTTTGG
1 AA-TTT-GGGGGTAAAAATGTAATTTTTGG
*
81622 ATATTTGGGGGTAAAAATATAATTTTTGG
1 A-ATTTGGGGGTAAAAATGTAATTTTTGG
81651 AA
1 AA
81653 GTTTCGAGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
28 3 0.06
29 23 0.45
30 24 0.47
31 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.26, T:0.38
Consensus pattern (28 bp):
AATTTGGGGGTAAAAATGTAATTTTTGG
Found at i:81637 original size:59 final size:59
Alignment explanation
Indices: 81565--81739 Score: 226
Period size: 59 Copynumber: 3.0 Consensus size: 59
81555 TAAAAATGTA
* *
81565 ATTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGAT
1 ATTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAT
* * *
81624 ATTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTCAAAATTGG-ATTTTTTGAT
1 ATTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAT
* * * *** * *
81682 GTTCGAGGGTAAAAATATAATTTTCAAAAATTTCGAGGTAAAAAATGGACTTTTTGGA
1 ATTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGA
81740 CAATTTAGGG
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
58 48 0.48
59 52 0.52
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (59 bp):
ATTTGGGGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGAATTTTTGGAT
Found at i:81667 original size:29 final size:29
Alignment explanation
Indices: 81572--81725 Score: 134
Period size: 29 Copynumber: 5.3 Consensus size: 29
81562 GTAATTTGGG
*
81572 GGTAAAAATGTAATTTTTGGAAGTTTCGA
1 GGTAAAAATATAATTTTTGGAAGTTTCGA
** * *
81601 GGTTAAAAATGGAATTTTTGGATA-TTTGGG
1 GG-TAAAAATATAATTTTTGGA-AGTTTCGA
81631 GGTAAAAATATAATTTTTGGAAGTTTCGA
1 GGTAAAAATATAATTTTTGGAAGTTTCGA
* * * *
81660 GGTCAAAAT-TGGATTTTTTGATG-TTCGA
1 GGTAAAAATAT-AATTTTTGGAAGTTTCGA
*** *
81688 GGGTAAAAATATAATTTTCAAAAATTTCGA
1 -GGTAAAAATATAATTTTTGGAAGTTTCGA
81718 GGTAAAAA
1 GGTAAAAA
81726 ATGGACTTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
28 7 0.07
29 62 0.62
30 30 0.30
31 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (29 bp):
GGTAAAAATATAATTTTTGGAAGTTTCGA
Found at i:81696 original size:58 final size:58
Alignment explanation
Indices: 81571--81737 Score: 208
Period size: 58 Copynumber: 2.9 Consensus size: 58
81561 TGTAATTTGG
* * * * *
81571 GGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTTAAAAATGGAATTTTTGGATATTTGG
1 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGG-ATTTTTTGATATTCGA
* * *
81630 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTCAAAATTGGATTTTTTGATGTTCGA
1 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGATTTTTTGATATTCGA
*** * *
81688 GGGTAAAAATATAATTTTCAAAAATTTCGAGGTAAAAAATGGACTTTTTG
1 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGATTTTTTG
81738 GACAATTTAG
Statistics
Matches: 94, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
58 55 0.59
59 39 0.41
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (58 bp):
GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTAAAAAATGGATTTTTTGATATTCGA
Found at i:82612 original size:20 final size:20
Alignment explanation
Indices: 82568--82612 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
82558 AATTATTAAT
*
82568 ATTA-TTATTATTAATTACT
1 ATTAGTTATTATTAATTACC
*
82587 AATAGTTATTATTAATTACC
1 ATTAGTTATTATTAATTACC
82607 ATTAGT
1 ATTAGT
82613 AATGCTTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (20 bp):
ATTAGTTATTATTAATTACC
Found at i:83337 original size:34 final size:34
Alignment explanation
Indices: 83299--83424 Score: 94
Period size: 34 Copynumber: 3.6 Consensus size: 34
83289 CATTATTTAT
* * *
83299 TTTAAATTTATAA-TAATTTCAATTTTAAAATAAA
1 TTTAAACTTA-AATTAAATTCAAATTTAAAATAAA
*
83333 TTTAAACTTAAATTAAATTCAAATTTAAAATTAAT
1 TTTAAACTTAAATTAAATTCAAATTTAAAA-TAAA
* * *
83368 TTTAAGAAAATTAATTTTAAA-TCTAAATTTAAAACAAA
1 TTT---AAACTTAA-ATTAAATTC-AAATTTAAAATAAA
* *
83406 TTTAATCTTAAAATAAATT
1 TTTAAACTTAAATTAAATT
83425 TAAAAAGGGC
Statistics
Matches: 72, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
33 2 0.03
34 28 0.39
35 13 0.18
38 14 0.19
39 15 0.21
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.43
Consensus pattern (34 bp):
TTTAAACTTAAATTAAATTCAAATTTAAAATAAA
Found at i:83343 original size:17 final size:17
Alignment explanation
Indices: 83323--83428 Score: 68
Period size: 17 Copynumber: 5.9 Consensus size: 17
83313 AATTTCAATT
83323 TTAAAATAAATTTAAAC
1 TTAAAATAAATTTAAAC
* * *
83340 TTAAATTAAATTCAAAT
1 TTAAAATAAATTTAAAC
* *
83357 TTAAAATTAATTTTAAGAAAA
1 TTAAAA-TAAATTT---AAAC
** * *
83378 TTAATTTTAAATCTAAAT
1 TTAA-AATAAATTTAAAC
* *
83396 TTAAAACAAATTTAATC
1 TTAAAATAAATTTAAAC
83413 TTAAAATAAATTTAAA
1 TTAAAATAAATTTAAA
83429 AAGGGCCCGG
Statistics
Matches: 64, Mismatches: 20, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
17 40 0.62
18 12 0.19
21 12 0.19
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TTAAAATAAATTTAAAC
Found at i:83344 original size:12 final size:11
Alignment explanation
Indices: 83322--83410 Score: 54
Period size: 11 Copynumber: 7.5 Consensus size: 11
83312 TAATTTCAAT
*
83322 TTTAAAATAAA
1 TTTAAATTAAA
83333 TTTAAACTTAAA
1 TTTAAA-TTAAA
83345 -TTAAATTCAAA
1 TTTAAATT-AAA
*
83356 TTTAAAATTAAT
1 TTT-AAATTAAA
*
83368 TTTAAGAAAATTAAT
1 TTT----AAATTAAA
83383 TTTAAATCTAAA
1 TTTAAAT-TAAA
**
83395 TTTAAAACAAA
1 TTTAAATTAAA
83406 TTTAA
1 TTTAA
83411 TCTTAAAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
10 2 0.03
11 26 0.40
12 20 0.31
13 5 0.08
15 12 0.18
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:83379 original size:15 final size:15
Alignment explanation
Indices: 83359--83387 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
83349 ATTCAAATTT
83359 AAAATTAATTTTAAG
1 AAAATTAATTTTAAG
83374 AAAATTAATTTTAA
1 AAAATTAATTTTAA
83388 ATCTAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAAATTAATTTTAAG
Found at i:83406 original size:28 final size:27
Alignment explanation
Indices: 83354--83430 Score: 84
Period size: 28 Copynumber: 2.8 Consensus size: 27
83344 ATTAAATTCA
* * *
83354 AATTTAAAATTAATTTTAAGAAAA-TT
1 AATTTTAAATTAAATTTAAAAAAATTT
83380 AATTTTAAATCTAAATTTAAAACAAATTT
1 AATTTTAAAT-TAAATTTAAAA-AAATTT
* *
83409 AATCTTAAAATAAATTTAAAAA
1 AATTTTAAATTAAATTTAAAAA
83431 GGGCCCGGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
26 9 0.21
27 10 0.23
28 14 0.33
29 10 0.23
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTTTAAATTAAATTTAAAAAAATTT
Found at i:84248 original size:201 final size:201
Alignment explanation
Indices: 83856--84373 Score: 748
Period size: 201 Copynumber: 2.6 Consensus size: 201
83846 TTCTCCGTAT
*
83856 CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTC
1 CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * * * * * * *
83921 ACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGGCCGCATCATT
66 ACATCGAGC-----CTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCACATCACT
* *
83986 TGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCAT
126 TGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCAT
*
84051 TAGGAAACTAA
191 CAGGAAACTAA
* *
84062 CCATTTTATTGCTTCGACCTGCTTCTCAATATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTC
1 CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* *
84127 ACATCGAGCCTCGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCACCTCACTTGTTT
66 ACATCGAGCCTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTT
* * *
84192 CTATCCGCTTCTCTATATCTCATCAGGAAGACAAATTTGGTCCGCTTCTTAGTATCTCATCAGGA
131 CAATCCGCTTCTCTATATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGA
*
84257 AGCTAA
196 AACTAA
* * *** *
84263 CCATTTTATTACTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTGATATTCAAAGATTTGCTC
1 CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
*
84328 ACATCGAGCCTTGAGTTGGTATACTTCTCTGTATCTAATCAGGAAG
66 ACATCGAGCCTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAG
84374 CTAACCATTT
Statistics
Matches: 282, Mismatches: 30, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
201 211 0.75
206 71 0.25
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (201 bp):
CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
ACATCGAGCCTTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCACATCACTTGTTT
CAATCCGCTTCTCTATATCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGA
AACTAA
Found at i:84436 original size:115 final size:115
Alignment explanation
Indices: 84243--84453 Score: 332
Period size: 115 Copynumber: 1.8 Consensus size: 115
84233 CCGCTTCTTA
* * * *
84243 GTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATTTCATCAGGAAGC
1 GTATCTAATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAGTATCTCATCAGAAAGC
*
84308 TGATATTCAAAGATTTGCTCACATCGAGCCTTGAGTTGGTATACTTCTCT
66 TGAGATTCAAAGATTTGCTCACATCGAGCCTTGAGTTGGTATACTTCTCT
84358 GTATCTAATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAGTATCTCATCAGAAAGC
1 GTATCTAATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAGTATCTCATCAGAAAGC
* * * * *
84423 TGGGGTTCGAAGATTTGCTCACTTTGAGCCT
66 TGAGATTCAAAGATTTGCTCACATCGAGCCT
84454 CGTTTCATTG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 86 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (115 bp):
GTATCTAATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAGTATCTCATCAGAAAGC
TGAGATTCAAAGATTTGCTCACATCGAGCCTTGAGTTGGTATACTTCTCT
Found at i:84615 original size:324 final size:316
Alignment explanation
Indices: 84034--84703 Score: 923
Period size: 324 Copynumber: 2.1 Consensus size: 316
84024 AATTTGGTCC
* * * * *
84034 ACTTCTCAGTATCTCATTAGGAAACTAACCATTTTATTGCTTCGACCTGCTTCTCAATATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAATATCTCAT
* * * *
84099 TAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGAGTTGGTATACTTCTCTGTATCTC
66 CAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGAGTTAGTATACTTCTCAGTATCTC
*
84164 ATCAGGAAGATGACCACCTCACTTGTTTCTATCCGCTTCTCTATATCTCATCAGGAAGACAAATT
131 ATCAGGAAGATGACCACCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACAAATT
* * *
84229 TGGTCCGCTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTA
196 TGGTCCACTTCTGAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTA
* *
84294 TTTCATCAGGAAGCTGATATTCAAAGATTTGCTCACATCGAGC-CTTGAGTTGGTAT
261 TCTCATCAGGAAGCTGAGATTCAAAGATTTGCTCACATCGAGCGC-TGAGTTGGTAT
* *
84350 ACTTCTCTGTATCTAATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAATATCTCAT
* * *
84415 CAGAAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTCGTTTCATTGATTTAGTCTACTTCTC
66 CAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTCG----A--G--TTAGTATACTTCTC
* * * *
84480 AGTATCTCATCAGGAAGATGACCGCGC-CATTTGTTTCAATCCGCTTCTCTGTATCTTATCAGGA
123 AGTATCTCATCAGGAAGATGACCAC-CTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAGGA
* **
84544 AGACGAATTTGGTCCACTTCTCGA-TATCTCATCAGGAAGCTAACCATTTTATTGTTTCAACCTG
187 AGACAAATTTGGTCCACTTCT-GAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTG
* * * *
84608 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCATATCGAGCGCTGAGTTGGTA
251 CTTCTCAGTATCTCATCAGGAAGCTGAGATTCAAAGATTTGCTCACATCGAGCGCTGAGTTGGTA
84673 T
316 T
* *
84674 ACTTCTCTGTATATCATCAGGAAGATAACC
1 ACTTCTCTGTATCTCATCAGGAAGCTAACC
84704 GCCTCACTCG
Statistics
Matches: 309, Mismatches: 34, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
316 95 0.31
320 1 0.00
322 1 0.00
324 209 0.68
325 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (316 bp):
ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCACAATATCTCAT
CAGAAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTCGAGTTAGTATACTTCTCAGTATCTC
ATCAGGAAGATGACCACCTCACTTGTTTCAATCCGCTTCTCTATATCTCATCAGGAAGACAAATT
TGGTCCACTTCTGAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTA
TCTCATCAGGAAGCTGAGATTCAAAGATTTGCTCACATCGAGCGCTGAGTTGGTAT
Done.