Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009487.1 Kokia drynarioides strain JFW-HI SEQ_124196, 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: 117535
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:1500 original size:13 final size:13
Alignment explanation
Indices: 1484--1508 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1474 CAATTTGGGC
1484 TTGTAATTGGACT
1 TTGTAATTGGACT
1497 TTGTAATTGGAC
1 TTGTAATTGGAC
1509 ATTATTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
TTGTAATTGGACT
Found at i:2229 original size:205 final size:205
Alignment explanation
Indices: 1934--2542 Score: 893
Period size: 205 Copynumber: 3.0 Consensus size: 205
1924 GGAAGATGGT
* * * * * *
1934 TTTGGTTCACTTCCCCGTATTTCGTCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAG
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTCGACCTGCTTCTCAG
* *
1999 TATCTCATCAAGAAGATGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTAGTCTTC
65 TATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTC
*
2064 TTCTCGGTATCTCATCAGGAAGATGACCGCGTCCTTCGCTTCAATCCGCTTCTCTGCACCTCATC
130 TTCTCGGTATCTCATCAGGAAGATGACCGCGTCCTTCGCTTCAATCCGCTTCTCTGTACCTCATC
2129 AGGAAGACGAA
195 AGGAAGACGAA
* *
2140 TTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGACCTACTTCTCAGT
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* *
2205 ATCTCATCAAGAAGCTGTGATTCGAAGATTTACTCACATTGAGCGTGGGTTTGATTTGGTCTTCT
66 ATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
* * *
2270 TCTTGGTATCTCATCAGGAAGATGACCGCGTCATTCACTTCAATCCGCTTCTCTGTACCTCATCA
131 TCTCGGTATCTCATCAGGAAGATGACCGCGTCCTTCGCTTCAATCCGCTTCTCTGTACCTCATCA
2335 GGAAGACGAA
196 GGAAGACGAA
* *
2345 TTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGCTTCAACCTGCTTCTCAGT
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
* * * * * *
2410 ATCTCGTCAGGAAGCTGGGGTTCGAGGATTTGCTCACATC-A-CGTGGATTTGATTTGGTCTTCT
66 ATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
* * * * * *
2473 TCTCAGTATCTCAAT-AGGAAGATGACTGCATCGCTT-GTTTCAATCCGCTTCTCTATATCTCAT
131 TCTCGGTATCTC-ATCAGGAAGATGACCGCGTC-CTTCGCTTCAATCCGCTTCTCTGTACCTCAT
2536 CAGGAAG
194 CAGGAAG
2543 TTGGGATTCG
Statistics
Matches: 364, Mismatches: 37, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
203 76 0.21
204 5 0.01
205 251 0.69
206 32 0.09
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.34
Consensus pattern (205 bp):
TTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGT
ATCTCATCAAGAAGCTGGGATTCGAAGATTTACTCACATCGAGCGTGGGTTTGATTTGGTCTTCT
TCTCGGTATCTCATCAGGAAGATGACCGCGTCCTTCGCTTCAATCCGCTTCTCTGTACCTCATCA
GGAAGACGAA
Found at i:3571 original size:45 final size:46
Alignment explanation
Indices: 3507--3594 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
3497 TTGGTTCCAG
*
3507 GACGCCCTTTGCGGGTTTTCATCTTGAA-CCCCTTTT-TTTTTCCGA
1 GACGCCCTTTACGGGTTTTCATCTT-AATCCCCTTTTGTTTTTCCGA
*
3552 GACGCCTTTTACGGGTTTTCATCTTAATTCCCCTTTTGTTTTT
1 GACGCCCTTTACGGGTTTTCATCTTAA-TCCCCTTTTGTTTTT
3595 AGGCGAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 2 0.05
45 23 0.61
46 8 0.21
47 5 0.13
ACGTcount: A:0.11, C:0.26, G:0.16, T:0.47
Consensus pattern (46 bp):
GACGCCCTTTACGGGTTTTCATCTTAATCCCCTTTTGTTTTTCCGA
Found at i:14708 original size:30 final size:29
Alignment explanation
Indices: 14518--14808 Score: 231
Period size: 29 Copynumber: 9.9 Consensus size: 29
14508 CCTAGGGGGC
* ** *
14518 AAAATGGTAATTTTGGGAAAATTCAGGGTTA
1 AAAATGG-AATTTTTGGAAGTTTGAGGG-TA
* * *
14549 AAAAGGGAATTTTTAGACA-TTTGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTA
*
14577 AAAATGGTAA-TTTT-GAGAGTTTTGA-GGTCG
1 AAAATGG-AATTTTTGGA-AG-TTTGAGGGT-A
* *
14607 AAAATGGAGTTTTTGGACA-TTCGAGGGTA
1 AAAATGGAATTTTTGGA-AGTTTGAGGGTA
* *
14636 AAATTGGATTTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGAGGGT-A
* * * *
14666 AAAATGTCATTTTTTTGAAGTTTTAGGGTCA
1 AAAATG-GAATTTTTGGAAGTTTGAGGGT-A
*
14697 AAAATGGATTTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
*
14726 AAAATGGAATTTTTGGAAGTTTGATGGT-
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* *
14754 AAAATGGAATTTTTGGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
14783 AAAATGGAATTTTTGGAAGTTT-AGGG
1 AAAATGGAATTTTTGGAAGTTTGAGGG
14809 ACCTTCAGGG
Statistics
Matches: 215, Mismatches: 30, Indels: 33
0.77 0.11 0.12
Matches are distributed among these distances:
27 3 0.01
28 42 0.20
29 79 0.37
30 58 0.27
31 33 0.15
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTA
Found at i:16411 original size:13 final size:13
Alignment explanation
Indices: 16395--16419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16385 CAATTTGGGC
16395 TTGTAATTGGACT
1 TTGTAATTGGACT
16408 TTGTAATTGGAC
1 TTGTAATTGGAC
16420 ATTATTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (13 bp):
TTGTAATTGGACT
Found at i:16458 original size:17 final size:16
Alignment explanation
Indices: 16436--16503 Score: 91
Period size: 17 Copynumber: 4.1 Consensus size: 16
16426 TAGATAAATT
16436 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
16453 TAAATTTAAATTTCAAA
1 TAAATTTAAATTT-AAA
16470 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
* *
16487 TAAACTTAATTTTAAA
1 TAAATTTAAATTTAAA
16503 T
1 T
16504 TCTGTTGGGC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.09
17 42 0.89
18 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:16473 original size:11 final size:10
Alignment explanation
Indices: 16423--16480 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
16413 ATTGGACATT
*
16423 ATTTAGATAA
1 ATTTAAATAA
16433 ATTTAAATTTAA
1 ATTTAAA--TAA
16445 ATTTATAATAA
1 ATTTA-AATAA
16456 ATTTAAAT--
1 ATTTAAATAA
*
16464 -TTCAAATAA
1 ATTTAAATAA
16473 ATTTAAAT
1 ATTTAAAT
16481 TTAAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
7 6 0.15
10 15 0.38
11 8 0.21
12 8 0.21
13 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:16479 original size:23 final size:23
Alignment explanation
Indices: 16429--16485 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
16419 CATTATTTAG
**
16429 ATAAATTTAAATTTAAATTTATA
1 ATAAATTTAAATTTAAATAAATA
16452 ATAAATTTAAATTTCAAATAAAT-
1 ATAAATTTAAATTT-AAATAAATA
*
16475 TTAAATTTAAA
1 ATAAATTTAAA
16486 ATAAACTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 24 0.80
24 6 0.20
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATAAATTTAAATTTAAATAAATA
Found at i:16487 original size:7 final size:6
Alignment explanation
Indices: 16430--16504 Score: 70
Period size: 6 Copynumber: 13.0 Consensus size: 6
16420 ATTATTTAGA
16430 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT TCAAA-- TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT
* * *
16476 TAAATT TAAA-A TAAACT TAATTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT
16505 CTGTTGGGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 14
0.75 0.07 0.18
Matches are distributed among these distances:
4 5 0.09
5 7 0.12
6 40 0.70
7 5 0.09
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:21166 original size:29 final size:28
Alignment explanation
Indices: 21121--21399 Score: 154
Period size: 29 Copynumber: 9.5 Consensus size: 28
21111 GTAAAAGGGT
21121 AATTTTT-GAGAGTTTCGAGGTCAAAAATGG
1 AATTTTTGGA-AG-TTCGAGGTC-AAAATGG
*
21151 AATTTTTGGAAGTTCGAGGGT-AAAATGAT
1 AATTTTTGGAAGTTCGA-GGTCAAAATG-G
* * *
21180 AACTTTTT-AAAGTTTTGAGGTC-AAATCG
1 AA-TTTTTGGAAG-TTCGAGGTCAAAATGG
*
21208 AGATTTTTGGAAGTTCGGGGGT-AAAATGG
1 A-ATTTTTGGAAGTTC-GAGGTCAAAATGG
*** *
21237 TAATTTTCAAAAGTTTCGAGGTCAAATTGG
1 -AATTTTTGGAAG-TTCGAGGTCAAAATGG
* *
21267 GATTTTTGGAAGTTTCGAGGTAAAAATGG
1 AATTTTTGGAAG-TTCGAGGTCAAAATGG
* * * *
21296 AATTTTTAGAAGTTCGGGGGTAAAAATGT
1 AATTTTTGGAAGTTC-GAGGTCAAAATGG
* **
21325 AATTTTTGGTTAGTTTTAGGGTCAAAATGG
1 AATTTTTGG-AAGTTCGA-GGTCAAAATGG
* * * **
21355 AATTTTGGAGAAGGTTGGGGGTCAAAATAT
1 AATTTTTG-GAA-GTTCGAGGTCAAAATGG
21385 AATTTTTGGATAGTT
1 AATTTTTGGA-AGTT
21400 TAGGGACCTT
Statistics
Matches: 191, Mismatches: 39, Indels: 39
0.71 0.14 0.14
Matches are distributed among these distances:
28 17 0.09
29 99 0.52
30 69 0.36
31 6 0.03
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (28 bp):
AATTTTTGGAAGTTCGAGGTCAAAATGG
Found at i:21232 original size:58 final size:57
Alignment explanation
Indices: 21108--21309 Score: 221
Period size: 58 Copynumber: 3.5 Consensus size: 57
21098 TGGACATCTT
* * *
21108 GGGGTAAAAGGGTAATTTTTGAGAGTTTCGAGGTCAAAAATGGA-ATTTTTGGAAGTTCG
1 GGGGTAAAATGGTAATTTTT-AAAGTTTCGAGGTC--AAATCGAGATTTTTGGAAGTTCG
* * *
21167 AGGGTAAAATGATAACTTTTTAAAGTTTTGAGGTCAAATCGAGATTTTTGGAAGTTCG
1 GGGGTAAAATGGTAA-TTTTTAAAGTTTCGAGGTCAAATCGAGATTTTTGGAAGTTCG
* * *
21225 GGGGTAAAATGGTAATTTTCAAAAGTTTCGAGGTCAAATTGGGATTTTTGGAAGTTTC-
1 GGGGTAAAATGGTAATTTT-TAAAGTTTCGAGGTCAAATCGAGATTTTTGGAAG-TTCG
*
21283 GAGGTAAAAATGG-AATTTTTAGAAGTT
1 GGGGT-AAAATGGTAATTTTTA-AAGTT
21310 CGGGGGTAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
57 11 0.09
58 73 0.59
59 34 0.28
60 5 0.04
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTTAAAGTTTCGAGGTCAAATCGAGATTTTTGGAAGTTCG
Found at i:21388 original size:60 final size:58
Alignment explanation
Indices: 21268--21404 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 58
21258 TCAAATTGGG
* * * *
21268 ATTTTTGGA-AGTTTCGAGGTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATGTA
1 ATTTTTGGATAGTTTAG-GGTCAAAATGGAATTTTGAGAAGTTCGGGGGTAAAAATATA
* *
21326 ATTTTTGGTTAGTTTTAGGGTCAAAATGGAATTTTGGAGAAGGTT-GGGGGTCAAAATATA
1 ATTTTTGGATAG-TTTAGGGTCAAAATGGAATTTT-GAGAA-GTTCGGGGGTAAAAATATA
21386 ATTTTTGGATAGTTTAGGG
1 ATTTTTGGATAGTTTAGGG
21405 ACCTTCAAGA
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
58 8 0.12
59 25 0.37
60 32 0.47
61 3 0.04
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (58 bp):
ATTTTTGGATAGTTTAGGGTCAAAATGGAATTTTGAGAAGTTCGGGGGTAAAAATATA
Found at i:22603 original size:207 final size:201
Alignment explanation
Indices: 22082--22604 Score: 683
Period size: 199 Copynumber: 2.6 Consensus size: 201
22072 TTTGGTGTCG
* * * *
22082 TTGATTTGGTCTACTTCTTATTATCTTATCAGGAAGATGACTGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTTA-TATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* * * * * *
22147 CTCTGTACCTCATCAGGAAGACAAATTTGGTCTACTTCTCAGGATTTGATCAAGAAGCTAACCAT
65 CTCTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACAAT
* *
22212 TTTATTGCTTCGACCTGTTTCTTAGTATTTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACAT
22277 CGAGCCC
195 CGAGCCC
* * * * ** *
22284 -TGAGTTGGTATAT-TTC-TATGTCTCATCAGGAAGATAACCGCCCCGTTTGTTTTAATCCGCTT
1 TTGATTTGGTCT-TCTTCTTATATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTT
* *
22346 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCAAGAAACTAACAAT
65 CTCTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACAAT
* * *
22411 TTTATTGCTTTGACCTGCTTCTCAGTATTTCATCAGGAAGCTGGGATTCGAAGGTTTGCTCACAT
130 TTTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACAT
22476 CGAGCCC
195 CGAGCCC
*
22483 TGGGTTTGATTTGGTCTTCTTCTTAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATC
1 -----TTGATTTGGTCTTCTTCTTA-TATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATC
* * * * *
22548 TGCATCTCAGTATCTCATCAGGAAGACAAATTTGGTCCATTTCTCAGTATCTCATCA
60 CGCTTCTCTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCA
22605 GGAAGCTAGG
Statistics
Matches: 273, Mismatches: 38, Indels: 15
0.84 0.12 0.05
Matches are distributed among these distances:
199 160 0.59
200 2 0.01
201 12 0.04
204 1 0.00
205 12 0.04
206 2 0.01
207 84 0.31
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (201 bp):
TTGATTTGGTCTTCTTCTTATATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCGCTTC
TCTGTACCTCATCAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAACTAACAATT
TTATTGCTTCGACCTGCTTCTCAGTATTTCATCAGGAAGCTGAGATTCGAAGATTTGCTCACATC
GAGCCC
Found at i:22834 original size:39 final size:39
Alignment explanation
Indices: 22726--22907 Score: 150
Period size: 39 Copynumber: 4.7 Consensus size: 39
22716 TGCCCCGTGA
* * * *
22726 TCGGGGTAGGAGATTAGTTGACGGTGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
* ** * * * ***
22765 TCGAGGTAAGAGATTGAATGGCTATAATCTACCCTTGGC
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
*
22804 TTGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
* * ** * * * *
22843 TCGGGGTAAAAGATCGAATGAC-TTCAATCTGCCCTAAGC
1 TCGGGGTAAGAGATTGGTTGACGAT-GATCTACCCCAAGC
22882 TCGGGGTAAGAGATTGGTTGACGATG
1 TCGGGGTAAGAGATTGGTTGACGATG
22908 TAACTTCACT
Statistics
Matches: 103, Mismatches: 38, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
38 1 0.01
39 101 0.98
40 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGC
Found at i:22840 original size:78 final size:78
Alignment explanation
Indices: 22726--22907 Score: 240
Period size: 78 Copynumber: 2.3 Consensus size: 78
22716 TGCCCCGTGA
* * * * * * *
22726 TCGGGGTAGGAGATTAGTTGACGGTGATCTGCCCCAAGCTCGAGGTAAGAGATTGAATGGCTAT-
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGCTCGAGGTAAAAGATCGAATGACT-TC
**
22790 AATCTACCCTTGGC
65 AATCTACCCTAAGC
* *
22804 TTGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGCTCGGGGTAAAAGATCGAATGACTTCA
1 TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGCTCGAGGTAAAAGATCGAATGACTTCA
*
22869 ATCTGCCCTAAGC
66 ATCTACCCTAAGC
22882 TCGGGGTAAGAGATTGGTTGACGATG
1 TCGGGGTAAGAGATTGGTTGACGATG
22908 TAACTTCACT
Statistics
Matches: 90, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 89 0.99
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (78 bp):
TCGGGGTAAGAGATTGGTTGACGATGATCTACCCCAAGCTCGAGGTAAAAGATCGAATGACTTCA
ATCTACCCTAAGC
Found at i:23163 original size:101 final size:101
Alignment explanation
Indices: 22962--23156 Score: 291
Period size: 101 Copynumber: 1.9 Consensus size: 101
22952 GCTGCTGTAG
* ** * * * *
22962 TTTTATTCCAACTTTTTTGCAACTTCAGGAAGATAAGATTTGATGTTGAAGCTTCATCTTTCTCT
1 TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAAGAATTGATGTTAAAGCTTCATCTTGCTCT
23027 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
* * *
23063 TTTTAATCCAACTTTACTGTAACTTCAAGAGGATATGAATTGATGTTAAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAAGAATTGATGTTAAAGCTTCATCTTGCTCT
*
23128 TACTGCAACTTCAGAGAGATAAAGACTTG
66 TACTACAACTTCAGAGAGATAAAGACTTG
23157 TCATTGTAGT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
101 83 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.37
Consensus pattern (101 bp):
TTTTAATCCAACTTTACTGCAACTTCAAGAAGATAAGAATTGATGTTAAAGCTTCATCTTGCTCT
TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
Found at i:23318 original size:50 final size:50
Alignment explanation
Indices: 23264--23739 Score: 252
Period size: 50 Copynumber: 9.5 Consensus size: 50
23254 GCCATTACAA
* * *
23264 CTTAAACCTTTCCCTTTCAAATCTTTGTGGAACTGGATTCGCCGTTGCGG
1 CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTCGCCGTTGCGG
* * * * * * *
23314 CTTAAATCTTT-CCTTTCTTTTCTTCTGAGGTACACGG-TCCGCCGTTGTGA
1 CTTAAATCTTTCCCTTTCATATCTT-TGTGGTAC-TGGATTCGCCGTTGCGG
* ** * *
23364 CTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCATTGCGG
1 CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTCGCCGTTGCGG
* * * ** **
23414 TCTTAGATC-TTCCCCTTCATGTCTTCATGGTACTGGATTCGTTGTTGCGG
1 -CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTCGCCGTTGCGG
* * * ** * * **
23464 CTTAAATCTTTCCC-TTCTTGTCTTCTGAGGTACAAGATCCGTCGTTGCAA
1 CTTAAATCTTTCCCTTTCATATCTT-TGTGGTACTGGATTCGCCGTTGCGG
* * **
23514 CTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGA-TCTGCCGTTGCGG
1 CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTC-GCCGTTGCGG
** * ** * * *
23564 TCTTGGATCTTTCCC-TTCATGTCTTCATGGTACTAGATTCACCGTTGCAG
1 -CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTCGCCGTTGCGG
* * * ** * *
23614 CTTAAATCTTTCCC-TTCGTGTCTTCTGAGGTAC-ACAGTCCTGCCGTTGCGA
1 CTTAAATCTTTCCCTTTCATATCTT-TGTGGTACTGGA-TTC-GCCGTTGCGG
* * ** * **
23665 CTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTAGA-TCTGCCGTTGCAAT
1 CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTC-GCCGTTGC-GG
* *
23716 CTTAGATCTTTCCC-TTCATGTCTT
1 CTTAAATCTTTCCCTTTCATATCTT
23740 CATGGTGCTG
Statistics
Matches: 321, Mismatches: 88, Indels: 34
0.72 0.20 0.08
Matches are distributed among these distances:
49 52 0.16
50 181 0.56
51 78 0.24
52 10 0.03
ACGTcount: A:0.15, C:0.26, G:0.19, T:0.40
Consensus pattern (50 bp):
CTTAAATCTTTCCCTTTCATATCTTTGTGGTACTGGATTCGCCGTTGCGG
Found at i:23517 original size:150 final size:149
Alignment explanation
Indices: 23295--23745 Score: 686
Period size: 150 Copynumber: 3.0 Consensus size: 149
23285 TCTTTGTGGA
* * *
23295 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCTTTCTTTTCTTCTGAGGTACACGGTCCGCCGTT
1 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACA-AGTCCGCCGTT
* * * *
23360 GTGACTTAAACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCGCCATTGCGGTCTTAGATCTT
65 GCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTT
*
23425 CCCCTTCATGTCTTCATGGT
130 TCCCTTCATGTCTTCATGGT
** *
23445 ACTGGATTCGTTGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACAAGATCCGTCGTT
1 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACAAG-TCCGCCGTT
* *
23510 GCAACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTGGATCTT
65 GCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTT
23575 TCCCTTCATGTCTTCATGGT
130 TCCCTTCATGTCTTCATGGT
* * * *
23595 ACTAGATTCACCGTTGCAGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTCCTGCCGT
1 ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACA-AGTCC-GCCGT
* **
23660 TGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCAATCTTAGATCT
64 TGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCT
23725 TTCCCTTCATGTCTTCATGGT
129 TTCCCTTCATGTCTTCATGGT
23746 GCTGAGACCT
Statistics
Matches: 273, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
149 1 0.00
150 185 0.68
151 87 0.32
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (149 bp):
ACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACAAGTCCGCCGTTG
CGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTT
CCCTTCATGTCTTCATGGT
Found at i:23663 original size:101 final size:101
Alignment explanation
Indices: 23552--23740 Score: 231
Period size: 101 Copynumber: 1.9 Consensus size: 101
23542 GGTACTGGAT
* * *
23552 CTGCCGTTGCGGTCTTGGATCTTTCCCTTCATG-TCTTCATGGTACTAGAT-TCACCGTTGC-AG
1 CTGCCGTTGC-GACTTAGACCTTTCCCTT-ATGATCTTCATGGTACTAGATCT-ACCGTTGCAAG
*
23614 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACAGTC
63 CTTAAATCTTTCCCTTCATGTCTTCTGAGGTACACAGTC
* ** * *
23653 CTGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCTGCCGTTGCAATCT
1 CTGCCGTTGCGACTTAGACCTTTCCCTTATG-ATCTTCATGGTACTAGATCTACCGTTGCAAGCT
*
23718 TAGATCTTTCCCTTCATGTCTTC
65 TAAATCTTTCCCTTCATGTCTTC
23741 ATGGTGCTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
99 2 0.03
100 15 0.20
101 32 0.43
102 25 0.34
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.40
Consensus pattern (101 bp):
CTGCCGTTGCGACTTAGACCTTTCCCTTATGATCTTCATGGTACTAGATCTACCGTTGCAAGCTT
AAATCTTTCCCTTCATGTCTTCTGAGGTACACAGTC
Found at i:24807 original size:3 final size:3
Alignment explanation
Indices: 24794--24829 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
24784 CTTTCCCTTT
*
24794 TTC TTC TTTC TTC TTT TTC TTC TTC TTC TTC TTC TT
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
24830 TTTTTCTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:24812 original size:9 final size:9
Alignment explanation
Indices: 24790--24836 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
24780 TTTGCTTTCC
24790 CTTTTTCTT
1 CTTTTTCTT
24799 CTTTCTTCTT
1 CTTT-TTCTT
24809 -TTTCTTCTT
1 CTTT-TTCTT
*
24818 CTTCTTCTT
1 CTTTTTCTT
24827 CTTTTT-TT
1 CTTTTTCTT
24835 CT
1 CT
24837 GTATCTGAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 4 0.12
9 23 0.68
10 7 0.21
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (9 bp):
CTTTTTCTT
Found at i:30565 original size:29 final size:30
Alignment explanation
Indices: 30532--30964 Score: 112
Period size: 29 Copynumber: 14.8 Consensus size: 30
30522 CTCTTGGGGG
30532 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
* * * ****
30562 AAAAACGG-AATTTTTAG-ACCCCCGAGGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGA-GGT
* * ** **
30591 -AAAAGGGTAATTTTTAGAAAAATCGAAAT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
* * * * *
30620 CGAAAA-CGAAATTTTTGGACA-TCTTGGGGT
1 C-AAAATGGTAATTTTTGGAAAGT-TCGAGGT
* * *
30650 -AAAAGGGTAATTTTT-GAGAGTTTCGGGGT
1 CAAAATGGTAATTTTTGGAAAG-TTCGAGGT
*
30679 CAAAATGG-AATTTTT-GAAAGTTCGGGGGT
1 CAAAATGGTAATTTTTGGAAAGTTC-GAGGT
* * *
30708 -AAAATGATAATTTTT-GAAAGTTTTGGGGT
1 CAAAATGGTAATTTTTGGAAAG-TTCGAGGT
* * *
30737 C-AAATTG-AGATTTTTAG-AAGTTCAAGGGT
1 CAAAATGGTA-ATTTTTGGAAAGTTCGA-GGT
* *
30766 -AAAATGATAATTTTTGG-AAGTTTTGAGGT
1 CAAAATGGTAATTTTTGGAAAG-TTCGAGGT
* *
30795 C-AAATCAG-AATTTTT-GAAAGTTCGGGGGT
1 CAAAAT-GGTAATTTTTGGAAAGTTC-GAGGT
* * ** *
30824 AAAAAT-GTAA-TTTTAGAACTTTTGAGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGAGGT
*
30852 CAAAAATGG-AATTTTTGG-AAGTTCGGGGGT
1 C-AAAATGGTAATTTTTGGAAAGTTC-GAGGT
* * **
30882 AAAAAT-GTGATTTTT-GAAAGTTTTAGGGT
1 CAAAATGGTAATTTTTGGAAAGTTCGA-GGT
* *
30911 CAAAATGG-AA-TTTTGGAGAAGTTTAGGGGT
1 CAAAATGGTAATTTTTGGA-AAG-TTCGAGGT
* *
30941 CAAAAT-ATAATTTTTGGACAGTTC
1 CAAAATGGTAATTTTTGGAAAGTTC
30965 AAGAACCTCC
Statistics
Matches: 294, Mismatches: 69, Indels: 81
0.66 0.16 0.18
Matches are distributed among these distances:
28 47 0.16
29 165 0.56
30 69 0.23
31 13 0.04
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.33
Consensus pattern (30 bp):
CAAAATGGTAATTTTTGGAAAGTTCGAGGT
Found at i:30719 original size:58 final size:59
Alignment explanation
Indices: 30657--30956 Score: 330
Period size: 58 Copynumber: 5.2 Consensus size: 59
30647 GGTAAAAGGG
* *
30657 TAATTTTTGAGAGTTTCGGGGTCAAAATGGAATTTTTGAAAGTTCGGGGGT-AAAATGA
1 TAATTTTTGAAAGTTTTGGGGTCAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGA
* **
30715 TAATTTTTGAAAGTTTTGGGGTC-AAATTGAGATTTTT-AGAAGTTCAAGGGT-AAAATGA
1 TAATTTTTGAAAGTTTTGGGGTCAAAATGGA-ATTTTTGA-AAGTTCGGGGGTAAAAATGA
* * *
30773 TAATTTTTGGAAGTTTTGAGGTC-AAATCAGAATTTTTGAAAGTTCGGGGGTAAAAATG-
1 TAATTTTTGAAAGTTTTGGGGTCAAAAT-GGAATTTTTGAAAGTTCGGGGGTAAAAATGA
* * * *
30831 TAATTTTAG-AACTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATG-
1 TAATTTTTGAAAGTTTTGGGGTC-AAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGA
* * * ** *
30889 TGATTTTTGAAAGTTTTAGGGTCAAAATGGAATTTTGGAGAAGTTTAGGGGTCAAAAT-A
1 TAATTTTTGAAAGTTTTGGGGTCAAAATGGAATTTTTGA-AAGTTCGGGGGTAAAAATGA
30948 TAATTTTTG
1 TAATTTTTG
30957 GACAGTTCAA
Statistics
Matches: 207, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
57 19 0.09
58 142 0.69
59 46 0.22
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (59 bp):
TAATTTTTGAAAGTTTTGGGGTCAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGA
Found at i:30750 original size:87 final size:88
Alignment explanation
Indices: 30659--30964 Score: 288
Period size: 87 Copynumber: 3.5 Consensus size: 88
30649 TAAAAGGGTA
*
30659 ATTTTTGAG-AGTTTCGGGGTCAAAATGGAATTTTTGAAAGTTCGGGGGTAAAATGATAATTTTT
1 ATTTTTGAGAAGTTTCGGGGTCAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTT
*
30723 GAAAGTTTTGGGGTCAAATTGAG
66 GAAAGTTTTGGGGTCAAAATGAG
* * ** * * * *
30746 ATTTTT-AGAAG-TTCAAGGGT-AAAATGATAATTTTTGGAAGTTTTGAGGTCAAATCAGAATTT
1 ATTTTTGAGAAGTTTC-GGGGTCAAAATG-GAATTTTTGGAAGTTCGGGGGTAAAATGATAATTT
** *
30808 TTGAAAGTTCGGGGGTAAAAATGTA-
64 TTGAAAGTTTTGGGGTCAAAATG-AG
* * * *
30833 A-TTTT-AGAACTTTTGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATG-TGATTT
1 ATTTTTGAGAAGTTTCGGGGTC-AAAATGGAATTTTTGGAAGTTCGGGGGT-AAAATGATAATTT
*
30895 TTGAAAGTTTTAGGGTCAAAATG-G
64 TTGAAAGTTTTGGGGTCAAAATGAG
* * **
30919 AATTTTGGAGAAGTTTAGGGGTCAAAATATAATTTTTGGACAGTTC
1 -ATTTTTGAGAAGTTTCGGGGTCAAAATGGAATTTTTGGA-AGTTC
30965 AAGAACCTCC
Statistics
Matches: 171, Mismatches: 35, Indels: 24
0.74 0.15 0.10
Matches are distributed among these distances:
86 22 0.13
87 103 0.60
88 29 0.17
89 17 0.10
ACGTcount: A:0.33, C:0.05, G:0.26, T:0.36
Consensus pattern (88 bp):
ATTTTTGAGAAGTTTCGGGGTCAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGATAATTTTT
GAAAGTTTTGGGGTCAAAATGAG
Found at i:32813 original size:17 final size:16
Alignment explanation
Indices: 32791--32857 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
32781 ATTTAATTTT
32791 AATTTAAAATAAACTTA
1 AATTTAAAATAAA-TTA
*
32808 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATT-A
* * *
32825 AACTCAAAATAAATTTTG
1 AATTTAAAATAAA--TTA
32843 AATTTAAAATAAATT
1 AATTTAAAATAAATT
32858 CAAACTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.10
17 23 0.57
18 11 0.28
19 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (16 bp):
AATTTAAAATAAATTA
Found at i:32882 original size:35 final size:35
Alignment explanation
Indices: 32796--32863 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
32786 ATTTTAATTT
* *
32796 AAAATAAACTT-AAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAAATTTAAAATAAATTCAAACTC
**
32830 AAAATAAATTTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAAATTTAAAATAAATTCAAACT
32864 TATTTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (35 bp):
AAAATAAATTTAAAATTTAAAATAAATTCAAACTC
Found at i:35207 original size:17 final size:17
Alignment explanation
Indices: 35187--35249 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
35177 TTATTTTAAT
35187 TTAAAATAAATTTAAAA
1 TTAAAATAAATTTAAAA
* *
35204 TTAAAGTAAA-TTCAAA
1 TTAAAATAAATTTAAAA
* * * *
35220 TTCAAAGTGAATTTGAAT
1 TT-AAAATAAATTTAAAA
35238 TTAAAATAAATT
1 TTAAAATAAATT
35250 CAAACTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.19
17 24 0.65
18 6 0.16
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
TTAAAATAAATTTAAAA
Found at i:36199 original size:31 final size:28
Alignment explanation
Indices: 36142--36199 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
36132 AAATTTATTA
* *
36142 GAAATTAAAATAGAGAAATATTACAAAC
1 GAAATTAAAATAGAGAAAAATAACAAAC
36170 GAAATTAAAATGTAGCAGAAAAATAACAAA
1 GAAATTAAAA--TAG-AGAAAAATAACAAA
36200 ACAAAGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
30 3 0.12
31 12 0.48
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (28 bp):
GAAATTAAAATAGAGAAAAATAACAAAC
Found at i:36552 original size:18 final size:18
Alignment explanation
Indices: 36529--36563 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
36519 TAGACGAAAA
*
36529 CGTGCCATAAGGCAGAAG
1 CGTGCCACAAGGCAGAAG
36547 CGTGCCACAAGGCAGAA
1 CGTGCCACAAGGCAGAA
36564 AAAAAGCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.26, G:0.31, T:0.09
Consensus pattern (18 bp):
CGTGCCACAAGGCAGAAG
Found at i:36588 original size:21 final size:23
Alignment explanation
Indices: 36544--36594 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
36534 CATAAGGCAG
36544 AAGCGTGCCACAAGGCAGAAAAA
1 AAGCGTGCCACAAGGCAGAAAAA
* *
36567 AAGCGTG-C-CAAGGTAGAGAAA
1 AAGCGTGCCACAAGGCAGAAAAA
36588 AAGCGTG
1 AAGCGTG
36595 TCATGAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 18 0.69
22 1 0.04
23 7 0.27
ACGTcount: A:0.43, C:0.18, G:0.31, T:0.08
Consensus pattern (23 bp):
AAGCGTGCCACAAGGCAGAAAAA
Found at i:38818 original size:26 final size:28
Alignment explanation
Indices: 38784--38846 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
38774 GAGAGTGTTC
*
38784 TTTAGTAAA-TGT-GGGATTAAAATTAA
1 TTTATTAAACTGTAGGGATTAAAATTAA
*
38810 TTTATTAAACTTTTAAGGGATTAAAATTAA
1 TTTATTAAAC-TGT-AGGGATTAAAATTAA
38840 TTT-TTAA
1 TTTATTAA
38847 TAAAACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.26
28 2 0.06
29 4 0.13
30 17 0.55
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (28 bp):
TTTATTAAACTGTAGGGATTAAAATTAA
Found at i:40968 original size:17 final size:16
Alignment explanation
Indices: 40946--41012 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 16
40936 ATTTAATTTT
40946 AATTTAAAATAAACTTA
1 AATTTAAAATAAA-TTA
*
40963 AATTTAAAGTAAATTCA
1 AATTTAAAATAAATT-A
* * *
40980 AACTCAAAATAAATTTTG
1 AATTTAAAATAAA--TTA
40998 AATTTAAAATAAATT
1 AATTTAAAATAAATT
41013 CAAACTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
16 4 0.10
17 23 0.57
18 11 0.28
19 2 0.05
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (16 bp):
AATTTAAAATAAATTA
Found at i:41037 original size:35 final size:35
Alignment explanation
Indices: 40951--41018 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
40941 ATTTTAATTT
* *
40951 AAAATAAACTT-AAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAAATTTAAAATAAATTCAAACTC
**
40985 AAAATAAATTTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAAATTTAAAATAAATTCAAACT
41019 TATTTAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (35 bp):
AAAATAAATTTAAAATTTAAAATAAATTCAAACTC
Found at i:43362 original size:17 final size:17
Alignment explanation
Indices: 43342--43404 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
43332 TTATTTTAAT
43342 TTAAAATAAATTTAAAA
1 TTAAAATAAATTTAAAA
* *
43359 TTAAAGTAAA-TTCAAA
1 TTAAAATAAATTTAAAA
* * * *
43375 TTCAAAGTGAATTTGAAT
1 TT-AAAATAAATTTAAAA
43393 TTAAAATAAATT
1 TTAAAATAAATT
43405 CAAACTTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 7 0.19
17 24 0.65
18 6 0.16
ACGTcount: A:0.54, C:0.03, G:0.06, T:0.37
Consensus pattern (17 bp):
TTAAAATAAATTTAAAA
Found at i:44354 original size:31 final size:28
Alignment explanation
Indices: 44297--44354 Score: 71
Period size: 31 Copynumber: 2.0 Consensus size: 28
44287 AAATTTATTA
* *
44297 GAAATTAAAATAGAGAAATATTACAAAC
1 GAAATTAAAATAGAGAAAAATAACAAAC
44325 GAAATTAAAATGTAGCAGAAAAATAACAAA
1 GAAATTAAAA--TAG-AGAAAAATAACAAA
44355 ACAAAGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.40
30 3 0.12
31 12 0.48
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.19
Consensus pattern (28 bp):
GAAATTAAAATAGAGAAAAATAACAAAC
Found at i:44707 original size:18 final size:18
Alignment explanation
Indices: 44684--44718 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44674 TAGACGAAAA
*
44684 CGTGCCATAAGGCAGAAG
1 CGTGCCACAAGGCAGAAG
44702 CGTGCCACAAGGCAGAA
1 CGTGCCACAAGGCAGAA
44719 AAAAAGCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.26, G:0.31, T:0.09
Consensus pattern (18 bp):
CGTGCCACAAGGCAGAAG
Found at i:44743 original size:21 final size:23
Alignment explanation
Indices: 44699--44749 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
44689 CATAAGGCAG
44699 AAGCGTGCCACAAGGCAGAAAAA
1 AAGCGTGCCACAAGGCAGAAAAA
* *
44722 AAGCGTG-C-CAAGGTAGAGAAA
1 AAGCGTGCCACAAGGCAGAAAAA
44743 AAGCGTG
1 AAGCGTG
44750 TCATGAAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 18 0.69
22 1 0.04
23 7 0.27
ACGTcount: A:0.43, C:0.18, G:0.31, T:0.08
Consensus pattern (23 bp):
AAGCGTGCCACAAGGCAGAAAAA
Found at i:46973 original size:26 final size:28
Alignment explanation
Indices: 46939--47001 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 28
46929 GAGAGTGTTC
*
46939 TTTAGTAAA-TGT-GGGATTAAAATTAA
1 TTTATTAAACTGTAGGGATTAAAATTAA
*
46965 TTTATTAAACTTTTAAGGGATTAAAATTAA
1 TTTATTAAAC-TGT-AGGGATTAAAATTAA
46995 TTT-TTAA
1 TTTATTAA
47002 TAAAACTAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 8 0.26
28 2 0.06
29 4 0.13
30 17 0.55
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.44
Consensus pattern (28 bp):
TTTATTAAACTGTAGGGATTAAAATTAA
Found at i:48609 original size:24 final size:23
Alignment explanation
Indices: 48582--48649 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
48572 ATTAACATTG
48582 TTCATGAACATGTTCAATTATATA
1 TTCATGAACATGTTCAATTA-ATA
* ** *
48606 TTCATGAACATATTCGTTTAATG
1 TTCATGAACATGTTCAATTAATA
*
48629 TTCGTGAACATGTTCAATTAA
1 TTCATGAACATGTTCAATTAA
48650 GGTAAACGAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 19 0.53
24 17 0.47
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.41
Consensus pattern (23 bp):
TTCATGAACATGTTCAATTAATA
Found at i:55917 original size:5 final size:5
Alignment explanation
Indices: 55907--55946 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
55897 AATAGTGCAT
55907 AATAA AATAA AATAAAA AATAA AATAA AATAA AACTAA AA
1 AATAA AATAA AAT--AA AATAA AATAA AATAA AA-TAA AA
55947 ACTAAAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 22 0.69
6 5 0.16
7 5 0.16
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AATAA
Found at i:55930 original size:6 final size:6
Alignment explanation
Indices: 55910--56002 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
55900 AGTGCATAAT
* *
55910 AAAAT- AAAATA AAAA-A TAAAAT- AAAATA AAACTA AAAACTA AAACTAA
1 AAAATA AAAATA AAAATA -AAAATA AAAATA AAAATA AAAA-TA AAAAT-A
* * * * *
55958 AAAACTA AAATTG GAAATG AAAATG AAAATA AAAATA AAAATA AA
1 AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
56003 TTTACTAATT
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
5 11 0.15
6 46 0.65
7 13 0.18
8 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:58897 original size:3 final size:3
Alignment explanation
Indices: 58891--58925 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
58881 CAAATAATAA
*
58891 AAC AAC AAC AAC GAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
58926 TAATAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:60969 original size:23 final size:22
Alignment explanation
Indices: 60943--60988 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
60933 CATACATAAC
60943 ATTACTCAATTCAT-TCAAAGCAT
1 ATTAC-CAATTCATGTCAAA-CAT
*
60966 ATTACCTATTCATGTCAAACAT
1 ATTACCAATTCATGTCAAACAT
60988 A
1 A
60989 AATATTTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (22 bp):
ATTACCAATTCATGTCAAACAT
Found at i:69484 original size:8 final size:7
Alignment explanation
Indices: 69470--69511 Score: 50
Period size: 7 Copynumber: 5.7 Consensus size: 7
69460 AATTTAAAAT
69470 AAATTAA
1 AAATTAA
69477 AAAGTTAA
1 AAA-TTAA
69485 TAAATTAA
1 -AAATTAA
69493 AAATTATA
1 AAATTA-A
69501 AAA-TAA
1 AAATTAA
69507 AAATT
1 AAATT
69512 TATTACCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 4 0.13
7 12 0.39
8 12 0.39
9 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
AAATTAA
Found at i:69507 original size:14 final size:15
Alignment explanation
Indices: 69467--69511 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
69457 AACAATTTAA
69467 AATAAATTAAAAAGTT
1 AATAAATTAAAAA-TT
69483 AATAAATTAAAAATT
1 AATAAATTAAAAATT
*
69498 -ATAAAATAAAAATT
1 AATAAATTAAAAATT
69512 TATTACCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 13 0.46
15 2 0.07
16 13 0.46
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
AATAAATTAAAAATT
Found at i:78683 original size:23 final size:23
Alignment explanation
Indices: 78657--78761 Score: 111
Period size: 23 Copynumber: 4.6 Consensus size: 23
78647 GTGTTTTTAT
* *
78657 ATTTGTGCTTAAATATTAATATA
1 ATTTATGCTTAAATATTAATATG
* ** * *
78680 ATTTTTTATCAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
*
78703 ATTTATGCTTAAATATTAGTATG
1 ATTTATGCTTAAATATTAATATG
*
78726 ATTTATGCTTAAATATTAATGTG
1 ATTTATGCTTAAATATTAATATG
* *
78749 ATATGTGCTTAAA
1 ATTTATGCTTAAA
78762 GAATTAAGAT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (23 bp):
ATTTATGCTTAAATATTAATATG
Found at i:78740 original size:46 final size:46
Alignment explanation
Indices: 78657--78761 Score: 138
Period size: 46 Copynumber: 2.3 Consensus size: 46
78647 GTGTTTTTAT
* *
78657 ATTTGTGCTTAAATATTAATATAATTTTTTATCAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATATAATTTATGATCAAATATTAATGTG
* * * * *
78703 ATTTATGCTTAAATATTAGTATGATTTATGCTTAAATATTAATGTG
1 ATTTGTGCTTAAATATTAATATAATTTATGATCAAATATTAATGTG
*
78749 ATATGTGCTTAAA
1 ATTTGTGCTTAAA
78762 GAATTAAGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (46 bp):
ATTTGTGCTTAAATATTAATATAATTTATGATCAAATATTAATGTG
Found at i:83896 original size:38 final size:40
Alignment explanation
Indices: 83829--83904 Score: 111
Period size: 38 Copynumber: 1.9 Consensus size: 40
83819 ATAAGAGCTC
* *
83829 AGTCAATAATTCGCTCTTAAGAGCTAATATTGCTCTTATG
1 AGTCAATAATTCGCTCTTAAGAGCCAATATCGCTCTTATG
*
83869 AGTCAAT-ATT-GCTCTTACGAGCCAATATCGCTCTTA
1 AGTCAATAATTCGCTCTTAAGAGCCAATATCGCTCTTA
83905 CGAGCCAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 23 0.70
39 3 0.09
40 7 0.21
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (40 bp):
AGTCAATAATTCGCTCTTAAGAGCCAATATCGCTCTTATG
Found at i:83910 original size:19 final size:19
Alignment explanation
Indices: 83839--83911 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
83829 AGTCAATAAT
* *
83839 TCGCTCTTAAGAGCTAATA
1 TCGCTCTTACGAGCCAATA
* * *
83858 TTGCTCTTATGAGTCAATA
1 TCGCTCTTACGAGCCAATA
*
83877 TTGCTCTTACGAGCCAATA
1 TCGCTCTTACGAGCCAATA
83896 TCGCTCTTACGAGCCA
1 TCGCTCTTACGAGCCA
83912 GTGCAGTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (19 bp):
TCGCTCTTACGAGCCAATA
Found at i:94157 original size:51 final size:51
Alignment explanation
Indices: 94102--94215 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
94092 AGAGGAACAA
*
94102 ATTGAAGCCATGATGGTGAATCTCATATACCTAAAGCTATAGAGAGGGCAG
1 ATTGAAGCCATGATGGCGAATCTCATATACCTAAAGCTATAGAGAGGGCAG
* *
94153 ATTGAAGCCACGATGGCGAATCTCATATACCTAAAGCTGTAGAGAGGGCAG
1 ATTGAAGCCATGATGGCGAATCTCATATACCTAAAGCTATAGAGAGGGCAG
94204 ATTGAAGACCAT
1 ATTGAAG-CCAT
94216 CCAATCTCTT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 55 0.95
52 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (51 bp):
ATTGAAGCCATGATGGCGAATCTCATATACCTAAAGCTATAGAGAGGGCAG
Found at i:94327 original size:79 final size:79
Alignment explanation
Indices: 94195--94583 Score: 581
Period size: 79 Copynumber: 4.9 Consensus size: 79
94185 AAAGCTGTAG
* *
94195 AGAGGGCAGATTGAAGACCATCCA-ATCTCTTACCCCA-ACCATGGGGCAAATTGAAACAATCCA
1 AGAGGGCAGATTGAAGACCAT-CAGATCTCTTA-CCCAGACCATGGGGCAGATTGAAGCAATCCA
*
94258 ATCTTTTACCCTAACT
64 ATCTTTTACCCTAACC
*
94274 AGAGGGCAGATTAAAGACCATCAGATCTCTTACCCAGACCATGGGGCAGATTGAAGCAATCCAAT
1 AGAGGGCAGATTGAAGACCATCAGATCTCTTACCCAGACCATGGGGCAGATTGAAGCAATCCAAT
94339 CTTTTACCCTAACC
66 CTTTTACCCTAACC
* * * *
94353 AGATGGCAGATTGAAGACCAT-ACGATCTCTTACCCCGACCATGGGGCAAATTGAAGCAATTCAA
1 AGAGGGCAGATTGAAGACCATCA-GATCTCTTACCCAGACCATGGGGCAGATTGAAGCAATCCAA
94417 TCTTTTACCCTAACC
65 TCTTTTACCCTAACC
* * *
94432 AGAGGGCAGATTGAAGACCATCTGATCTCTTACCCCGACCATTGGGCAGATTGAAGCAATCCAAT
1 AGAGGGCAGATTGAAGACCATCAGATCTCTTACCCAGACCATGGGGCAGATTGAAGCAATCCAAT
94497 CTTTTACCCTAACC
66 CTTTTACCCTAACC
* *
94511 AGAAGGCAGATTGAAGACCATTC-GATCTCTTACCTC-GACCATGGGGCAGATTGAAGCAATCTA
1 AGAGGGCAGATTGAAGACCA-TCAGATCTCTTACC-CAGACCATGGGGCAGATTGAAGCAATCCA
94574 ATCTTTTACC
64 ATCTTTTACC
94584 TTTAAAACTA
Statistics
Matches: 287, Mismatches: 17, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
78 7 0.02
79 277 0.97
80 3 0.01
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (79 bp):
AGAGGGCAGATTGAAGACCATCAGATCTCTTACCCAGACCATGGGGCAGATTGAAGCAATCCAAT
CTTTTACCCTAACC
Found at i:95235 original size:63 final size:63
Alignment explanation
Indices: 95112--95292 Score: 274
Period size: 63 Copynumber: 2.8 Consensus size: 63
95102 TTCTTATTAT
*
95112 TTTTATTTATTTATTTATTATTTTTATGAATATAAATAAATAAATATAAAATAGTATTAATTTTG
1 TTTTATTTATTTATTTATTA-TTTTATGAATATAAA-AAATAAATATAAAATAATATTAATTTTG
* *
95177 TTTTATTTATTTATTTATTATTATATGAATATAAAAAATAAATGTAAAATAATATTAATTTTG
1 TTTTATTTATTTATTTATTATTTTATGAATATAAAAAATAAATATAAAATAATATTAATTTTG
* *
95240 TTTTA-TTATTTATTTATTATTTTATGAATATAGATAAATAAATAAATAAATAA
1 TTTTATTTATTTATTTATTATTTTATGAATATA-AAAAATAAATATA-AAATAA
95293 CAAACCCAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
62 26 0.24
63 41 0.38
64 20 0.19
65 20 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (63 bp):
TTTTATTTATTTATTTATTATTTTATGAATATAAAAAATAAATATAAAATAATATTAATTTTG
Found at i:100946 original size:18 final size:17
Alignment explanation
Indices: 100903--100946 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
100893 TAATTAGTCT
*
100903 AAAATAA-TAAAAATTT
1 AAAATAATTAAAAATTG
100919 AAAATAAATTAAAAATTAG
1 AAAAT-AATTAAAAATT-G
100938 AAAATAATT
1 AAAATAATT
100947 TCTTACCATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 5 0.21
17 2 0.08
18 12 0.50
19 5 0.21
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATAATTAAAAATTG
Found at i:101636 original size:21 final size:20
Alignment explanation
Indices: 101598--101647 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
101588 ACAAATTATA
*
101598 AAAATGAAT-TTATAATTTT
1 AAAATAAATATTATAATTTT
* *
101617 ATATTAAATATTATCAATTTT
1 AAAATAAATATTAT-AATTTT
101638 AAAATAAATA
1 AAAATAAATA
101648 ACATAAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 6 0.25
20 4 0.17
21 14 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAATAAATATTATAATTTT
Found at i:101731 original size:28 final size:30
Alignment explanation
Indices: 101685--101741 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
101675 TGTTTTAAAA
101685 TATTTACAGAAAAAGACAA-CAAATTTTAG
1 TATTTACAGAAAAAGACAACCAAATTTTAG
101714 TATTTAC--AAAAAGAACAACCAAATTTTA
1 TATTTACAGAAAAAG-ACAACCAAATTTTA
101742 CAAAAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.23
28 4 0.15
29 16 0.62
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (30 bp):
TATTTACAGAAAAAGACAACCAAATTTTAG
Found at i:105005 original size:18 final size:18
Alignment explanation
Indices: 104982--105033 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
104972 TAAAATAAAA
104982 AAAATTTTAAATTATTTT
1 AAAATTTTAAATTATTTT
**
105000 AAAATTTATTTATT-TTTT
1 AAAATTT-TAAATTATTTT
* *
105018 AAAATATAAAATTATT
1 AAAATTTTAAATTATT
105034 AAAATTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATTTTAAATTATTTT
Found at i:105021 original size:45 final size:45
Alignment explanation
Indices: 104964--105050 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 45
104954 ATTATTAAAA
104964 TTATTTTCTAAAATAAAAAAAATT-TT-AAATTATTTTAAAATTTAT
1 TTATTTTCTAAAAT--AAAAAATTATTAAAATTATTTTAAAATTTAT
* *
105009 TTATTTTTTAAAATATAAAATTATTAAAATTATTTTAAAATT
1 TTATTTTCTAAAATAAAAAATTATTAAAATTATTTTAAAATT
105051 ATAATCATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 7 0.18
44 2 0.05
45 29 0.76
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (45 bp):
TTATTTTCTAAAATAAAAAATTATTAAAATTATTTTAAAATTTAT
Found at i:116494 original size:16 final size:17
Alignment explanation
Indices: 116473--116509 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
116463 AACTTTCATT
116473 TCTTTAATTTTTGTAA-
1 TCTTTAATTTTTGTAAC
116489 TCTTTAATTTTTGTAAC
1 TCTTTAATTTTTGTAAC
116506 TCTT
1 TCTT
116510 CAACCATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (17 bp):
TCTTTAATTTTTGTAAC
Done.