Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014648.1 Kokia drynarioides strain JFW-HI SEQ_129687, 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: 363951
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:318 original size:13 final size:13
Alignment explanation
Indices: 286--319 Score: 59
Period size: 14 Copynumber: 2.5 Consensus size: 13
276 GTTTGTTTGA
286 TTGAAAATAATTT
1 TTGAAAATAATTT
299 TTAGAAAATAATTT
1 TT-GAAAATAATTT
313 TTGAAAA
1 TTGAAAA
320 ATGAATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 7 0.35
14 13 0.65
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (13 bp):
TTGAAAATAATTT
Found at i:402 original size:32 final size:32
Alignment explanation
Indices: 344--415 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 32
334 CGTAAAAGTT
*
344 AATATTTTTTGGTGTTTGGATGAATTTGTAT-AA
1 AATATTTTTTAGTGTTTGGA-GAATTT-TATGAA
* *
377 AATATTTTTTATTGTTTGGCA-AATTTTCTGAA
1 AATATTTTTTAGTGTTTGG-AGAATTTTATGAA
409 AATATTT
1 AATATTT
416 CAGGAAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 2 0.06
32 14 0.41
33 17 0.50
34 1 0.03
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (32 bp):
AATATTTTTTAGTGTTTGGAGAATTTTATGAA
Found at i:2136 original size:43 final size:43
Alignment explanation
Indices: 2088--2171 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
2078 TGAACATATC
2088 CTTAACATCATAATCAAACAAGACACTAATTCATTCATCAACA
1 CTTAACATCATAATCAAACAAGACACTAATTCATTCATCAACA
* * *
2131 CTTAACATCATAATCAAACAGGATACTGATTCATTCATCAA
1 CTTAACATCATAATCAAACAAGACACTAATTCATTCATCAA
2172 TGCTTACACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.44, C:0.24, G:0.05, T:0.27
Consensus pattern (43 bp):
CTTAACATCATAATCAAACAAGACACTAATTCATTCATCAACA
Found at i:9044 original size:22 final size:22
Alignment explanation
Indices: 9003--9045 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
8993 AGTCCCTAAG
*
9003 TTTTTATTTTATGGAATTTAAT
1 TTTTTATTTTATAGAATTTAAT
* *
9025 TTTTTATTTTTTAGATTTTAA
1 TTTTTATTTTATAGAATTTAA
9046 AATTCAAGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
TTTTTATTTTATAGAATTTAAT
Found at i:10019 original size:27 final size:27
Alignment explanation
Indices: 9984--10037 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
9974 ATTAAAAAAA
9984 AATCAATTGAAGTAATTTGAAAATTGT
1 AATCAATTGAAGTAATTTGAAAATTGT
* *
10011 AATCAATTGAATTATTTTGAAAATTGT
1 AATCAATTGAAGTAATTTGAAAATTGT
10038 TGGATAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (27 bp):
AATCAATTGAAGTAATTTGAAAATTGT
Found at i:10837 original size:16 final size:15
Alignment explanation
Indices: 10815--10868 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
10805 TATGAAATTT
10815 AAATATTTTATTTAA
1 AAATATTTTATTTAA
*
10830 ATAATATTTTACTTATA
1 A-AATATTTTATTTA-A
10847 AAATCATTTTTATTTAA
1 AAAT-A-TTTTATTTAA
10864 TAAAT
1 -AAAT
10869 TATAACTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 15 0.47
17 4 0.12
18 12 0.38
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATATTTTATTTAA
Found at i:13156 original size:13 final size:13
Alignment explanation
Indices: 13138--13191 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
13128 TTAAATAAAA
13138 TAAAATAAAAATC
1 TAAAATAAAAATC
* *
13151 TAAAATTAAAATT
1 TAAAATAAAAATC
** *
13164 TAATTTAAAACTC
1 TAAAATAAAAATC
*
13177 TCAAATAAAAATC
1 TAAAATAAAAATC
13190 TA
1 TA
13192 TAAAAACCAT
Statistics
Matches: 29, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAATAAAAATC
Found at i:23154 original size:27 final size:27
Alignment explanation
Indices: 23110--23240 Score: 154
Period size: 27 Copynumber: 4.8 Consensus size: 27
23100 TTGAGGAGTA
* * *
23110 TCTGATTTTGGCTCGAAAGAGCGTTAT
1 TCTGATTCTAGCTCGAAAGAGCATTAT
*
23137 TCTGATTCTAGCTTGAAAGAGCATTAT
1 TCTGATTCTAGCTCGAAAGAGCATTAT
* * *
23164 TCTAATTCTAGCTCGAAAGAGCGTTAC
1 TCTGATTCTAGCTCGAAAGAGCATTAT
* *
23191 TCTGATTCTGGCTTGAAAGAGCATTAT
1 TCTGATTCTAGCTCGAAAGAGCATTAT
* *
23218 TCTGATTCTGGGCTCGTAAGAGC
1 TCTGATTCT-AGCTCGAAAGAGC
23241 TAACCATTCT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 77 0.88
28 11 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (27 bp):
TCTGATTCTAGCTCGAAAGAGCATTAT
Found at i:23183 original size:54 final size:55
Alignment explanation
Indices: 23120--23240 Score: 190
Period size: 54 Copynumber: 2.2 Consensus size: 55
23110 TCTGATTTTG
*
23120 GCTCGAAAGAGCGTTATTCTGATTCTAGCTTGAAAGAGCATTATTCTAATTCT-A
1 GCTCGAAAGAGCGTTACTCTGATTCTAGCTTGAAAGAGCATTATTCTAATTCTGA
* * *
23174 GCTCGAAAGAGCGTTACTCTGATTCTGGCTTGAAAGAGCATTATTCTGATTCTGG
1 GCTCGAAAGAGCGTTACTCTGATTCTAGCTTGAAAGAGCATTATTCTAATTCTGA
*
23229 GCTCGTAAGAGC
1 GCTCGAAAGAGC
23241 TAACCATTCT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
54 50 0.82
55 11 0.18
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (55 bp):
GCTCGAAAGAGCGTTACTCTGATTCTAGCTTGAAAGAGCATTATTCTAATTCTGA
Found at i:23291 original size:24 final size:24
Alignment explanation
Indices: 23222--23282 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
23212 CATTATTCTG
23222 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
23246 ATTCTGAGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
23270 ATTCTGGGCTCGT
1 ATTCTGGGCTCGT
23283 GTGGGCTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:25054 original size:11 final size:12
Alignment explanation
Indices: 25039--25071 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
25029 TTAGATTTTT
25039 TATTTTTAAATA
1 TATTTTTAAATA
*
25051 -ATTTTAAAATA
1 TATTTTTAAATA
25062 TATTTTTAAA
1 TATTTTTAAA
25072 CTGATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTTTAAATA
Found at i:25223 original size:18 final size:18
Alignment explanation
Indices: 25200--25237 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25190 TTTTATTATT
25200 TTTTAACTATTTTTAATG
1 TTTTAACTATTTTTAATG
* *
25218 TTTTAAGTATTTTTAGTG
1 TTTTAACTATTTTTAATG
25236 TT
1 TT
25238 ATAAAGTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.11, T:0.63
Consensus pattern (18 bp):
TTTTAACTATTTTTAATG
Found at i:25244 original size:19 final size:18
Alignment explanation
Indices: 25207--25252 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
25197 ATTTTTTAAC
*
25207 TATTTTTAATGTTTTAAG
1 TATTTTTAATGTTTAAAG
*
25225 TATTTTTAGTGTTATAAAG
1 TATTTTTAATGTT-TAAAG
*
25244 TAGTTTTAA
1 TATTTTTAA
25253 AACATTGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (18 bp):
TATTTTTAATGTTTAAAG
Found at i:26653 original size:2 final size:2
Alignment explanation
Indices: 26646--26701 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
26636 GTGACCAACC
26646 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26688 AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT A
26702 AAGCAGCAAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31139 original size:50 final size:50
Alignment explanation
Indices: 31033--31143 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 50
31023 CACACGAGCT
* *
31033 GACACACGGGCGTGTGTCTAGACCGTGTAACTCACTGTTTGTGCATTAGG
1 GACACACGGGCGTGTGTCTAGACCGTGTAACTCAATGTTTGTGAATTAGG
* * *
31083 GCCACACGGGTGTGTGTCTA-AGCCGTGTAACTCAATGTTT-TGAATATATG
1 GACACACGGGCGTGTGTCTAGA-CCGTGTAACTCAATGTTTGTGAAT-TAGG
31133 GACACACGGGC
1 GACACACGGGC
31144 ACTCACACGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 5 0.10
50 47 0.90
ACGTcount: A:0.23, C:0.22, G:0.29, T:0.27
Consensus pattern (50 bp):
GACACACGGGCGTGTGTCTAGACCGTGTAACTCAATGTTTGTGAATTAGG
Found at i:33980 original size:34 final size:35
Alignment explanation
Indices: 33910--33990 Score: 128
Period size: 34 Copynumber: 2.3 Consensus size: 35
33900 ATGTTTCTTG
*
33910 GATTATTATGTAATAGTAACAACATTACTCATAGT
1 GATTATTATGTAATAGTAACAACATTACTCACAGT
*
33945 GATTATTTTGTAATAGTAACAA-ATTACTCACAGT
1 GATTATTATGTAATAGTAACAACATTACTCACAGT
*
33979 GATTACTATGTA
1 GATTATTATGTA
33991 TACGATCCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 21 0.50
35 21 0.50
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (35 bp):
GATTATTATGTAATAGTAACAACATTACTCACAGT
Found at i:44025 original size:21 final size:20
Alignment explanation
Indices: 43990--44041 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
43980 TAGAAATAAG
*
43990 ACTTGTATCTGTAGAAGAGTC
1 ACTTGTATC-GTAGAACAGTC
*
44011 ACTTGTATCGATAGAACTGTC
1 ACTTGTATCG-TAGAACAGTC
*
44032 ACATGTATCG
1 ACTTGTATCG
44042 GTAAAAGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (20 bp):
ACTTGTATCGTAGAACAGTC
Found at i:45657 original size:24 final size:24
Alignment explanation
Indices: 45629--45681 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
45619 TTAATAAGAG
*
45629 TTTAACTGAAACAAATAAACAGAA
1 TTTAACTGAAACAAATAAACAAAA
* *
45653 TTTAATTGAAATAAATAAACAAAA
1 TTTAACTGAAACAAATAAACAAAA
45677 TTTAA
1 TTTAA
45682 TTAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (24 bp):
TTTAACTGAAACAAATAAACAAAA
Found at i:52609 original size:20 final size:20
Alignment explanation
Indices: 52580--52627 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
52570 CCAACTAAAA
*
52580 AATTATTTAAAA-AAAATATT
1 AATTAATTAAAACAAAAT-TT
52600 AATTAATTAAAACAAAATTT
1 AATTAATTAAAACAAAATTT
52620 AATTAATT
1 AATTAATT
52628 TTTTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATTAATTAAAACAAAATTT
Found at i:53117 original size:23 final size:23
Alignment explanation
Indices: 53090--53143 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
53080 AAATCTATAT
* *
53090 ATTTTTATAGAA-ATTATAATTTC
1 ATTTTTATAGAATATAATAA-TTA
* *
53113 ATTTTAATATAATATAATAATTA
1 ATTTTTATAGAATATAATAATTA
53136 ATTTTTAT
1 ATTTTTAT
53144 CAAAAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTTTTATAGAATATAATAATTA
Found at i:57389 original size:6 final size:6
Alignment explanation
Indices: 57380--57465 Score: 91
Period size: 6 Copynumber: 14.3 Consensus size: 6
57370 CGCGCGCGCG
* * * *
57380 CACACA CACACA CACACA CACACA CACGCA CACGCA CACGCA CACGCA
1 CACACA CACACA CACACA CACACA CACACA CACACA CACACA CACACA
* * * * *
57428 CACGCG CACACG CACACT CACACA CGCACA CACACA CA
1 CACACA CACACA CACACA CACACA CACACA CACACA CA
57466 AATCAAAGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 73 1.00
ACGTcount: A:0.40, C:0.50, G:0.09, T:0.01
Consensus pattern (6 bp):
CACACA
Found at i:57399 original size:14 final size:14
Alignment explanation
Indices: 57380--57465 Score: 91
Period size: 14 Copynumber: 6.1 Consensus size: 14
57370 CGCGCGCGCG
57380 CACACACACACACA
1 CACACACACACACA
*
57394 CACACACACACACG
1 CACACACACACACA
* *
57408 CACACGCACACGCA
1 CACACACACACACA
* * *
57422 CACGCACACGCGCA
1 CACACACACACACA
* *
57436 CACGCACACTCACA
1 CACACACACACACA
*
57450 CACGCACACACACA
1 CACACACACACACA
57464 CA
1 CA
57466 AATCAAAGAT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 62 1.00
ACGTcount: A:0.40, C:0.50, G:0.09, T:0.01
Consensus pattern (14 bp):
CACACACACACACA
Found at i:59139 original size:42 final size:42
Alignment explanation
Indices: 59080--59167 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
59070 CATTTACTTA
* *
59080 TCAAAGGTTAGTTTAGTCGGTCATATTGGCATAGGTATATTT
1 TCAAAGGTTAGTTTAGTCAGTCATATTGGCATAGGTATATGT
* *
59122 TCAAAGGTTAGTTTAGTCAGTCGTATTGGCATAGGTGTATGT
1 TCAAAGGTTAGTTTAGTCAGTCATATTGGCATAGGTATATGT
59164 TCAA
1 TCAA
59168 GAGATAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (42 bp):
TCAAAGGTTAGTTTAGTCAGTCATATTGGCATAGGTATATGT
Found at i:63337 original size:7 final size:7
Alignment explanation
Indices: 63325--63437 Score: 90
Period size: 7 Copynumber: 16.7 Consensus size: 7
63315 ATCGTTTACT
63325 GTTGACC
1 GTTGACC
63332 GTTGACC
1 GTTGACC
** *
63339 GTCAACT
1 GTTGACC
63346 GTTGA-C
1 GTTGACC
*
63352 -TTGACT
1 GTTGACC
*
63358 GTTGATC
1 GTTGACC
63365 GTTGACC
1 GTTGACC
*
63372 GTTGACT
1 GTTGACC
63379 GTTGACC
1 GTTGACC
*
63386 GTTGATC
1 GTTGACC
63393 GTTGACC
1 GTTGACC
**
63400 GTCAACC
1 GTTGACC
63407 GTTGA-C
1 GTTGACC
*
63413 -TTGACT
1 GTTGACC
*
63419 GTTGATC
1 GTTGACC
*
63426 GTTGATC
1 GTTGACC
63433 GTTGA
1 GTTGA
63438 TTATTGACTT
Statistics
Matches: 81, Mismatches: 21, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
5 8 0.10
6 1 0.01
7 72 0.89
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (7 bp):
GTTGACC
Found at i:63444 original size:21 final size:21
Alignment explanation
Indices: 63352--63437 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
63342 AACTGTTGAC
* *
63352 TTGACTGTTGATCGTTGACCG
1 TTGACTGTTGACCGTTGATCG
63373 TTGACTGTTGACCGTTGATCG
1 TTGACTGTTGACCGTTGATCG
* **
63394 TTGACCGTCAACCGTTGA-C-
1 TTGACTGTTGACCGTTGATCG
*
63413 TTGACTGTTGATCGTTGATCG
1 TTGACTGTTGACCGTTGATCG
63434 TTGA
1 TTGA
63438 TTATTGACTT
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 14 0.26
20 2 0.04
21 38 0.70
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (21 bp):
TTGACTGTTGACCGTTGATCG
Found at i:63445 original size:61 final size:61
Alignment explanation
Indices: 63325--63445 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
63315 ATCGTTTACT
* *
63325 GTTGACCGTTGACCGTCAACTGTTGACTTGACTGTTGATCGTTGACCGTTGACTGTTGACC
1 GTTGACCGTTGACCGTCAACCGTTGACTTGACTGTTGATCGTTGACCGTTGACTATTGACC
* * *
63386 GTTGATCGTTGACCGTCAACCGTTGACTTGACTGTTGATCGTTGATCGTTGATTATTGAC
1 GTTGACCGTTGACCGTCAACCGTTGACTTGACTGTTGATCGTTGACCGTTGACTATTGAC
63446 TTTTTTGTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (61 bp):
GTTGACCGTTGACCGTCAACCGTTGACTTGACTGTTGATCGTTGACCGTTGACTATTGACC
Found at i:63457 original size:19 final size:20
Alignment explanation
Indices: 63433--63471 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
63423 ATCGTTGATC
63433 GTTGATTA-TTGACTTTTTT
1 GTTGATTAGTTGACTTTTTT
63452 GTTGATTAGTTGACTTTTTT
1 GTTGATTAGTTGACTTTTTT
63472 CTAGAAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.15, C:0.05, G:0.18, T:0.62
Consensus pattern (20 bp):
GTTGATTAGTTGACTTTTTT
Found at i:71849 original size:2 final size:2
Alignment explanation
Indices: 71842--71872 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
71832 TTTACATACG
*
71842 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
71873 TCTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:76391 original size:33 final size:33
Alignment explanation
Indices: 76315--76391 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 33
76305 CCTATTTACT
* * * ** *
76315 TAAAATAAATAATTTTAGTCAAAATGAAATTAG
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
*
76348 CAAAAT-AACAAATTTAATCAAAACAAAATTAA
1 TAAAATAAACAAATTTAATCAAAACAAAATTAA
76380 TAAAATAAACAA
1 TAAAATAAACAA
76392 TTTTGACTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 25 0.71
33 10 0.29
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (33 bp):
TAAAATAAACAAATTTAATCAAAACAAAATTAA
Found at i:82185 original size:19 final size:19
Alignment explanation
Indices: 82137--82193 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
82127 AACCGAACCA
* *
82137 TTGACCATTGATCGTTGAC
1 TTGATCATTGACCGTTGAC
*
82156 TTGAAT-GTTGACCGTTGAC
1 TTG-ATCATTGACCGTTGAC
82175 TTGATCATTGACCGTTGAC
1 TTGATCATTGACCGTTGAC
82194 CGTTGACTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.06
19 29 0.91
20 1 0.03
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (19 bp):
TTGATCATTGACCGTTGAC
Found at i:82185 original size:26 final size:26
Alignment explanation
Indices: 82156--82211 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
82146 GATCGTTGAC
*
82156 TTGAATGTTGACCGTTGACTTGATCA
1 TTGAACGTTGACCGTTGACTTGATCA
* *
82182 TTGACCGTTGACCGTTGACTTGATCG
1 TTGAACGTTGACCGTTGACTTGATCA
82208 TTGA
1 TTGA
82212 CCAATTGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (26 bp):
TTGAACGTTGACCGTTGACTTGATCA
Found at i:82204 original size:19 final size:20
Alignment explanation
Indices: 82137--82213 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 20
82127 AACCGAACCA
* *
82137 TTGACCATTGATCGTTGA-C
1 TTGATCATTGACCGTTGACC
*
82156 TTGAAT-GTTGACCGTTGA-C
1 TTG-ATCATTGACCGTTGACC
82175 TTGATCATTGACCGTTGACC
1 TTGATCATTGACCGTTGACC
*
82195 GTTGA-C-TTGATCGTTGACC
1 -TTGATCATTGACCGTTGACC
82214 AATTGACTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 2 0.04
19 40 0.82
20 3 0.06
21 4 0.08
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGATCATTGACCGTTGACC
Found at i:82212 original size:26 final size:26
Alignment explanation
Indices: 82162--82213 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
82152 TGACTTGAAT
82162 GTTGACCGTTGACTTGATCATTGACC
1 GTTGACCGTTGACTTGATCATTGACC
*
82188 GTTGACCGTTGACTTGATCGTTGACC
1 GTTGACCGTTGACTTGATCATTGACC
82214 AATTGACTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (26 bp):
GTTGACCGTTGACTTGATCATTGACC
Found at i:86385 original size:28 final size:30
Alignment explanation
Indices: 86338--86396 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
86328 GATTTTTTTG
* *
86338 TAAAAGTTGGTTGTTAA-TTTTGTGAATAT
1 TAAAAGTTAGTTGTTAATTTTTGTAAATAT
*
86367 TAAAA-TTAGTTGTTCATTTTTGTAAATAT
1 TAAAAGTTAGTTGTTAATTTTTGTAAATAT
86396 T
1 T
86397 TTTAAAACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 9 0.35
29 17 0.65
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (30 bp):
TAAAAGTTAGTTGTTAATTTTTGTAAATAT
Found at i:87938 original size:18 final size:17
Alignment explanation
Indices: 87912--88050 Score: 100
Period size: 18 Copynumber: 8.4 Consensus size: 17
87902 ACAAGCTAAA
*
87912 AAGAAGAAGAAGACCCT
1 AAGAAGAAGAAGATCCT
*
87929 GAAGATGAAGAAGATCC-
1 -AAGAAGAAGAAGATCCT
87946 -AGAAG-AG--GATCCT
1 AAGAAGAAGAAGATCCT
*
87959 AAGGAAGAAGAAGACCCT
1 AA-GAAGAAGAAGATCCT
*
87977 GAAGATGAAGAAGATCC-
1 -AAGAAGAAGAAGATCCT
87994 -AGAAG-AG--GATCCT
1 AAGAAGAAGAAGATCCT
*
88007 AAGGAAGAAGAAGACCCT
1 AA-GAAGAAGAAGATCCT
*
88025 AAAGATGAAGAAGATCCT
1 -AAGAAGAAGAAGATCCT
88043 GAAGAAGA
1 -AAGAAGA
88051 TCCTGTGGAG
Statistics
Matches: 95, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
12 10 0.11
14 6 0.06
15 16 0.17
16 4 0.04
18 55 0.58
19 4 0.04
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.10
Consensus pattern (17 bp):
AAGAAGAAGAAGATCCT
Found at i:88045 original size:12 final size:12
Alignment explanation
Indices: 88030--88055 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
88020 ACCCTAAAGA
88030 TGAAGAAGATCC
1 TGAAGAAGATCC
88042 TGAAGAAGATCC
1 TGAAGAAGATCC
88054 TG
1 TG
88056 TGGAGATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (12 bp):
TGAAGAAGATCC
Found at i:88068 original size:48 final size:48
Alignment explanation
Indices: 87914--88054 Score: 255
Period size: 48 Copynumber: 2.9 Consensus size: 48
87904 AAGCTAAAAA
87914 GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCTAAG
1 GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCTAAG
87962 GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCTAAG
1 GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCTAAG
* * *
88010 GAAGAAGAAGACCCTAAAGATGAAGAAGATCCTGAAGAAGATCCT
1 GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCT
88055 GTGGAGATTG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 90 1.00
ACGTcount: A:0.46, C:0.15, G:0.28, T:0.11
Consensus pattern (48 bp):
GAAGAAGAAGACCCTGAAGATGAAGAAGATCCAGAAGAGGATCCTAAG
Found at i:89365 original size:6 final size:6
Alignment explanation
Indices: 89354--89404 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
89344 AATGATGCTC
* *
89354 AGAAAA AGAAAA A-AAAA AGAAAA GGAAAA A-AAAA AGAAAA AGGAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
89400 AGAAA
1 AGAAA
89405 GCATATGTAC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:89385 original size:18 final size:18
Alignment explanation
Indices: 89354--89400 Score: 80
Period size: 17 Copynumber: 2.7 Consensus size: 18
89344 AATGATGCTC
89354 AGAAAAA-GAAAAAAAAA
1 AGAAAAAGGAAAAAAAAA
89371 AG-AAAAGGAAAAAAAAA
1 AGAAAAAGGAAAAAAAAA
89388 AGAAAAAGGAAAA
1 AGAAAAAGGAAAA
89401 GAAAGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.14
17 14 0.50
18 10 0.36
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AGAAAAAGGAAAAAAAAA
Found at i:96333 original size:2 final size:2
Alignment explanation
Indices: 96328--96364 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
96318 TAAAAAATTA
96328 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96365 GTAAGTCTAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:96442 original size:31 final size:32
Alignment explanation
Indices: 96400--96487 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
96390 ATATATATTT
*
96400 TAATTTT-AATTTTAGGAATAAAGTTATAT-A
1 TAATTTTAAATTTTAGAAATAAAGTTATATAA
* * *
96430 TCATTTTAAATTTTAGAAATATA-TATATCTAA
1 TAATTTTAAATTTTAGAAATAAAGT-TATATAA
*
96462 TAATTTTAAAATTTAGAAATAAAGTT
1 TAATTTTAAATTTTAGAAATAAAGTT
96488 TCATATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 7 0.15
31 17 0.36
32 22 0.47
33 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (32 bp):
TAATTTTAAATTTTAGAAATAAAGTTATATAA
Found at i:96934 original size:22 final size:20
Alignment explanation
Indices: 96909--96948 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
96899 TTATGGTAAT
96909 TAAATAATATTTATATTTATGA
1 TAAATAAT-TTTAT-TTTATGA
96931 TAAATAATTTTATTTTAT
1 TAAATAATTTTATTTTAT
96949 TATTGCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TAAATAATTTTATTTTATGA
Found at i:97521 original size:18 final size:17
Alignment explanation
Indices: 97500--97559 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 17
97490 ATGTTAATGT
*
97500 TAAATTTTATTATTGAAA
1 TAAATTTTAATATT-AAA
*
97518 TAAAATTATAATATTAAA
1 T-AAATTTTAATATTAAA
* *
97536 TAATTTTTAA-AAT-AA
1 TAAATTTTAATATTAAA
97551 TAAATTTTA
1 TAAATTTTA
97560 TTAATAATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 10 0.29
16 2 0.06
17 7 0.20
18 5 0.14
19 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATTTTAATATTAAA
Found at i:100009 original size:19 final size:19
Alignment explanation
Indices: 99971--100009 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
99961 TAAAATTTTC
* * *
99971 TAGTCAATTTTATTTCTTT
1 TAGTCAATGTTATGTATTT
99990 TAGTCAATGTTATGTATTT
1 TAGTCAATGTTATGTATTT
100009 T
1 T
100010 TTTTGGTGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.10, T:0.59
Consensus pattern (19 bp):
TAGTCAATGTTATGTATTT
Found at i:102199 original size:158 final size:158
Alignment explanation
Indices: 101911--102227 Score: 553
Period size: 158 Copynumber: 2.0 Consensus size: 158
101901 GCTCAAACCA
* * ** *
101911 ATTCACAATCTCAGCATTCAATACTGTCACATAATTCAATTTAAGGCAAGTAATAGTCTTACCTT
1 ATTCACAACCTCAGCATTCAATACCGTCACATAATTCAATTTAAAACAAGTAATAGTCTTACCTG
*
101976 AATAGTTAATATGCAACAAACATGAATATGCATGTTTATAAATGGAATGATCTTGAATCATAAAA
66 AATAGTTAATATACAACAAACATGAATATGCATGTTTATAAATGGAATGATCTTGAATCATAAAA
*
102041 GTACAAATGAAGCTTTCATCAGTTGTTT
131 GTACAAATGAAGCTTTCATCAATTGTTT
102069 ATTCACAACCTCAGCATTCAATACCGTCACATAATTCAATTTAAAACAAGTAATAGTCTTACCTG
1 ATTCACAACCTCAGCATTCAATACCGTCACATAATTCAATTTAAAACAAGTAATAGTCTTACCTG
*
102134 AATAGTTAATATACAACAAACATGTATATGCATGTTTATAAATGGAATGATCTTGAATCATAAAA
66 AATAGTTAATATACAACAAACATGAATATGCATGTTTATAAATGGAATGATCTTGAATCATAAAA
*
102199 GTACAAATGAAGCTTTCGTCAATTGTTT
131 GTACAAATGAAGCTTTCATCAATTGTTT
102227 A
1 A
102228 CGACTTTTGT
Statistics
Matches: 150, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
158 150 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (158 bp):
ATTCACAACCTCAGCATTCAATACCGTCACATAATTCAATTTAAAACAAGTAATAGTCTTACCTG
AATAGTTAATATACAACAAACATGAATATGCATGTTTATAAATGGAATGATCTTGAATCATAAAA
GTACAAATGAAGCTTTCATCAATTGTTT
Found at i:103568 original size:21 final size:21
Alignment explanation
Indices: 103530--103570 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
103520 GTTTCAAGTC
*
103530 TATCCATCCTTATCCCTTACA
1 TATCCATCCATATCCCTTACA
103551 TATCCATCCAT-TCACCTTAC
1 TATCCATCCATATC-CCTTAC
103571 TAAAGCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.24, C:0.39, G:0.00, T:0.37
Consensus pattern (21 bp):
TATCCATCCATATCCCTTACA
Found at i:111557 original size:15 final size:14
Alignment explanation
Indices: 111516--111564 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
111506 TTGTTTTTCG
111516 TTTC-TTTCTTTAT
1 TTTCATTTCTTTAT
111529 TTTCATTTCTTTAT
1 TTTCATTTCTTTAT
111543 TTTC-TTTGCCTTTAT
1 TTTCATTT--CTTTAT
111558 TTTCATT
1 TTTCATT
111565 GTAACTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.22
14 13 0.41
15 10 0.31
16 2 0.06
ACGTcount: A:0.10, C:0.16, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTCATTTCTTTAT
Found at i:123620 original size:24 final size:23
Alignment explanation
Indices: 123589--123663 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 23
123579 ACAAACAACA
* * *
123589 TTAGCTCTCACGAGCCCAATATGT
1 TTAGCTCTTATGAGCCCAA-ATGG
*
123613 TTAGCTCTTATGAACCCAGAATGG
1 TTAGCTCTTATGAGCCCA-AATGG
123637 TTAGCTCTTATGAGCCCAAAATGG
1 TTAGCTCTTATGAGCCC-AAATGG
123661 TTA
1 TTA
123664 ACCAGTATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
24 42 0.95
25 2 0.05
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (23 bp):
TTAGCTCTTATGAGCCCAAATGG
Found at i:135670 original size:3 final size:3
Alignment explanation
Indices: 135657--135701 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
135647 AAAATTAAGG
135657 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
135702 GTTTATGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:135707 original size:6 final size:6
Alignment explanation
Indices: 135698--135723 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
135688 ATTATTATTA
135698 TTATGT TTATGT TTATGT TTATGT TT
1 TTATGT TTATGT TTATGT TTATGT TT
135724 TTCCCTTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTATGT
Found at i:135713 original size:18 final size:18
Alignment explanation
Indices: 135668--135707 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
135658 TATTTTATTA
135668 TTATTATTATTATTAT-T
1 TTATTATTATTATTATGT
135685 ATTATTATTATTATTATGT
1 -TTATTATTATTATTATGT
135704 TTAT
1 TTAT
135708 GTTTATGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTATTATTATTATTATGT
Found at i:141104 original size:21 final size:21
Alignment explanation
Indices: 141057--141105 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
141047 TTTAGTATTG
* *
141057 GTAGAAGCATAAATAGTTTCG
1 GTAGATGCATAAATAGTTTCA
141078 GTAGATGCATAAATAGTTTCA
1 GTAGATGCATAAATAGTTTCA
141099 GTAGATG
1 GTAGATG
141106 TTTCACTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (21 bp):
GTAGATGCATAAATAGTTTCA
Found at i:146118 original size:48 final size:48
Alignment explanation
Indices: 146047--146142 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
146037 TCACAAATCA
146047 AATCAACAAATATGTCCTTTTGGGGCCTAACTTTTCCTCTTTTTTCAT
1 AATCAACAAATATGTCCTTTTGGGGCCTAACTTTTCCTCTTTTTTCAT
146095 AATCAACAAATATGTCCTTTTGGGGCCTAACTTTTCCTCTTTTTTCAT
1 AATCAACAAATATGTCCTTTTGGGGCCTAACTTTTCCTCTTTTTTCAT
146143 TTTTGATCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.44
Consensus pattern (48 bp):
AATCAACAAATATGTCCTTTTGGGGCCTAACTTTTCCTCTTTTTTCAT
Found at i:147800 original size:13 final size:13
Alignment explanation
Indices: 147782--147806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
147772 AAATTTTGGG
147782 AGTAAAGTTGAAA
1 AGTAAAGTTGAAA
147795 AGTAAAGTTGAA
1 AGTAAAGTTGAA
147807 CACAATGTGA
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:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
AGTAAAGTTGAAA
Found at i:158482 original size:208 final size:208
Alignment explanation
Indices: 158110--158498 Score: 511
Period size: 208 Copynumber: 1.9 Consensus size: 208
158100 TTTCTAGAAC
* * * *
158110 GAAATAAAGGGTTTAAAAAGCTAAAAAGTGTTGGAAGTTTACCACCTTTCCACCATTAGAATGAG
1 GAAATAAAGGGTTTAAAAAGCTAAAAAGTGATGAAAGTTTACCACCTTTCCACCATTAAAATGAC
* * * *
158175 CAAAAGGTTGAAAATTGAGCTCTTGAGGGTATCAAAGTACAGAGTTTTGGGATTTTGGGAAATGG
66 CAAAAGGTTGAAAATTGAGCTCTTGAAGGTATCAAAGTACAGAGTCTTGGGATTCTGAGAAATGG
* * *
158240 GTATTGAGAATCTTGAACTCAGTGTTCCCTGATTAATGAAATTTTCAGAAACTGCGAGTCGTAAC
131 GTATTGAGAATCTTGAACTCAGTGGTCCCTGATTAACGAAAATTTCAGAAACTGCGAGTCGTAAC
158305 TCTCTATTTAAAA
196 TCTCTATTTAAAA
158318 GAAATAAAGGGTTTAAAAAGCTCAAAAA-TGATGAAAGTTTACCACCTTTTCCACCATTAAAATG
1 GAAATAAAGGGTTTAAAAAGCT-AAAAAGTGATGAAAGTTTACCACC-TTTCCACCATTAAAATG
** *
158382 ACCAAAAGGTTGAGGATTGAGCTTTTGAAGGTATCAAAGTACTA-AGTCTT-GGATTCTGAGAAA
64 ACCAAAAGGTTGAAAATTGAGCTCTTGAAGGTATCAAAGTAC-AGAGTCTTGGGATTCTGAGAAA
* * ** *
158445 TGGTTATTGA-AGT-TTTCA-TCAGGTTTGGTCTCTGATTAACGAAAATTTCAGAAA
128 TGGGTATTGAGAATCTTGAACTCA-G--TGGTCCCTGATTAACGAAAATTTCAGAAA
158499 ACTTTGAGTT
Statistics
Matches: 156, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
205 3 0.02
206 4 0.03
207 2 0.01
208 83 0.53
209 63 0.40
210 1 0.01
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (208 bp):
GAAATAAAGGGTTTAAAAAGCTAAAAAGTGATGAAAGTTTACCACCTTTCCACCATTAAAATGAC
CAAAAGGTTGAAAATTGAGCTCTTGAAGGTATCAAAGTACAGAGTCTTGGGATTCTGAGAAATGG
GTATTGAGAATCTTGAACTCAGTGGTCCCTGATTAACGAAAATTTCAGAAACTGCGAGTCGTAAC
TCTCTATTTAAAA
Found at i:166636 original size:12 final size:12
Alignment explanation
Indices: 166619--166676 Score: 64
Period size: 12 Copynumber: 4.8 Consensus size: 12
166609 GCTCAAGCAT
166619 GAGCTTGATCTC
1 GAGCTTGATCTC
*
166631 GAGCTTGAGCAT-
1 GAGCTTGATC-TC
166643 GAGCTTGATCTC
1 GAGCTTGATCTC
* *
166655 GAGCTCGAGCTC
1 GAGCTTGATCTC
*
166667 GAGCATGATC
1 GAGCTTGATC
166677 CGGAGCCCGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 1 0.03
12 35 0.95
13 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (12 bp):
GAGCTTGATCTC
Found at i:166646 original size:24 final size:24
Alignment explanation
Indices: 166609--166695 Score: 106
Period size: 24 Copynumber: 3.6 Consensus size: 24
166599 ATCCGCCTGT
*
166609 GCTCAAGCATGAGCTTGATCTCGA
1 GCTCGAGCATGAGCTTGATCTCGA
*
166633 GCTTGAGCATGAGCTTGATCTCGA
1 GCTCGAGCATGAGCTTGATCTCGA
*
166657 GCTCGAGC-TCGAGCATGATC-CGGA
1 GCTCGAGCAT-GAGCTTGATCTC-GA
*
166681 GCCCGAGCATGAGCT
1 GCTCGAGCATGAGCT
166696 AAACTCCGAG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.04
24 51 0.94
25 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.30, T:0.22
Consensus pattern (24 bp):
GCTCGAGCATGAGCTTGATCTCGA
Found at i:168385 original size:88 final size:89
Alignment explanation
Indices: 168212--168399 Score: 261
Period size: 88 Copynumber: 2.1 Consensus size: 89
168202 GACCCATTCT
*
168212 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTATTGATAGCTAAGA
1 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATAGCTAAGA
* ** *
168277 TCTGGTATATGTTACGGATTCTCC
66 TCCGACATATGTTACAGATTCTCC
* * * *
168301 ACAGCTCGTGTGAGCATTACATGTTATAT-GGTGTTGGTCTTAGATGTCTTACTGATGGCTGAGA
1 ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATAGCTAAGA
*
168365 TCCGACATATGTTCCAGATTCTCC
66 TCCGACATATGTTACAGATTCTCC
* *
168389 GCAGGTCGTGT
1 ACAGCTCGTGT
168400 AAGTAGCATC
Statistics
Matches: 87, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
88 58 0.67
89 29 0.33
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (89 bp):
ACAGCTCGTGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGTCCTACTGATAGCTAAGA
TCCGACATATGTTACAGATTCTCC
Found at i:170256 original size:36 final size:36
Alignment explanation
Indices: 170210--170299 Score: 126
Period size: 37 Copynumber: 2.5 Consensus size: 36
170200 GAAATATTCC
*
170210 TGCAGCGACAGTTTTGGTGCAATCTGGAAGTGCTCA
1 TGCAACGACAGTTTTGGTGCAATCTGGAAGTGCTCA
** * *
170246 TGTGATGACAGTTTTTGGTGTAATCTGGAAGTGCTCA
1 TGCAACGACAG-TTTTGGTGCAATCTGGAAGTGCTCA
170283 TGCAACGACAGTTTTGG
1 TGCAACGACAGTTTTGG
170300 GAGTAAATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
36 13 0.29
37 32 0.71
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (36 bp):
TGCAACGACAGTTTTGGTGCAATCTGGAAGTGCTCA
Found at i:171358 original size:27 final size:27
Alignment explanation
Indices: 171328--171384 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
171318 CCGGATGGTC
* *
171328 AGGCGATAGATATCATACGAGTTGATT
1 AGGCCATAGATATAATACGAGTTGATT
* * *
171355 AGGCCATGGATATAATACGGGTTGGTT
1 AGGCCATAGATATAATACGAGTTGATT
171382 AGG
1 AGG
171385 TCAGGAGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.28
Consensus pattern (27 bp):
AGGCCATAGATATAATACGAGTTGATT
Found at i:171850 original size:14 final size:13
Alignment explanation
Indices: 171833--171885 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
171823 TTAATTTACA
171833 GTTTAGTGTTTAGG
1 GTTTAG-GTTTAGG
*
171847 GTTTAAGGTTTTGG
1 GTTT-AGGTTTAGG
*
171861 CTTTTAGGTTTAGG
1 -GTTTAGGTTTAGG
171875 GTTTAAGGTTT
1 GTTT-AGGTTT
171886 GTTCCAACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.09
14 24 0.75
15 5 0.16
ACGTcount: A:0.15, C:0.02, G:0.32, T:0.51
Consensus pattern (13 bp):
GTTTAGGTTTAGG
Found at i:171974 original size:16 final size:15
Alignment explanation
Indices: 171947--171985 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
171937 ATATTATATC
*
171947 CCTAAAACCCTAAAA
1 CCTAAAAACCTAAAA
*
171962 CCTTAAAAACCTAAAT
1 CC-TAAAAACCTAAAA
171978 CCTAAAAA
1 CCTAAAAA
171986 GAGTTTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.54, C:0.28, G:0.00, T:0.18
Consensus pattern (15 bp):
CCTAAAAACCTAAAA
Found at i:172665 original size:21 final size:21
Alignment explanation
Indices: 172641--172699 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
172631 AACCCTAAAT
*
172641 AAACATTATACCTTAAACCCA
1 AAACATTATACCTTAAACACA
* * *
172662 AAACCTTAAACCTTAAACACT
1 AAACATTATACCTTAAACACA
172683 AAACATT-TAACCTTAAA
1 AAACATTAT-ACCTTAAA
172700 AATAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACATTATACCTTAAACACA
Found at i:172672 original size:7 final size:7
Alignment explanation
Indices: 172640--172699 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
172630 AAACCCTAAA
*
172640 TAAACAT
1 TAAACCT
*
172647 TATACCT
1 TAAACCT
*
172654 TAAACCC
1 TAAACCT
*
172661 AAAACCT
1 TAAACCT
172668 TAAACCT
1 TAAACCT
172675 TAAACAC-
1 TAAAC-CT
*
172682 TAAACAT
1 TAAACCT
*
172689 TTAACCT
1 TAAACCT
172696 TAAA
1 TAAA
172700 AATAAAAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
7 39 0.98
8 1 0.03
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:172731 original size:15 final size:15
Alignment explanation
Indices: 172713--172782 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
172703 AAAAAAAACC
172713 TAAACCCTAAAATCA
1 TAAACCCTAAAATCA
* *
172728 TAAACCTTAAACTCA
1 TAAACCCTAAAATCA
* * *
172743 -AAACTC-AAAAACC
1 TAAACCCTAAAATCA
* *
172756 TTAACCCTAAAATCT
1 TAAACCCTAAAATCA
172771 TAAAACCCTAAA
1 T-AAACCCTAAA
172783 CCCTAAATAC
Statistics
Matches: 40, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
13 4 0.10
14 8 0.20
15 19 0.47
16 9 0.22
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAACCCTAAAATCA
Found at i:172754 original size:22 final size:22
Alignment explanation
Indices: 172706--172789 Score: 93
Period size: 22 Copynumber: 3.9 Consensus size: 22
172696 TAAAAATAAA
172706 AAAAACC-TAAACCCTAAAATC
1 AAAAACCTTAAACCCTAAAATC
* *
172727 ATAAACCTTAAACTC-AAAACTC
1 AAAAACCTTAAACCCTAAAA-TC
172749 AAAAACCTT-AACCCTAAAATC
1 AAAAACCTTAAACCCTAAAATC
* *
172770 TTAAAACCCTAAACCCTAAA
1 -AAAAACCTTAAACCCTAAA
172790 TACAAACATC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 16 0.31
22 27 0.52
23 9 0.17
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAAACCTTAAACCCTAAAATC
Found at i:172790 original size:22 final size:23
Alignment explanation
Indices: 172706--172789 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
172696 TAAAAATAAA
172706 AAAAACCTAAACCCTAAAATC--
1 AAAAACCTAAACCCTAAAATCTT
* * *
172727 ATAAACCTTAAACTC-AAAA-CTC
1 AAAAACC-TAAACCCTAAAATCTT
*
172749 AAAAACCTTAACCCTAAAATCTT
1 AAAAACCTAAACCCTAAAATCTT
*
172772 AAAACCCTAAACCCTAAA
1 AAAAACCTAAACCCTAAA
172790 TACAAACATC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.02
21 15 0.30
22 16 0.32
23 18 0.36
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (23 bp):
AAAAACCTAAACCCTAAAATCTT
Found at i:172822 original size:26 final size:26
Alignment explanation
Indices: 172786--172944 Score: 201
Period size: 26 Copynumber: 6.0 Consensus size: 26
172776 CCCTAAACCC
*
172786 TAAATACAAACATCAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
*
172812 TAAATACAAACATCAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
*
172838 TAAATACAAACATAAATATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
* *
172864 TAAATACAAACATAAAAATTATTAAT
1 TAAATACAAACATAAACATAATTAAT
**
172890 TAAATACAAATTTAAACATAATTAAT
1 TAAATACAAACATAAACATAATTAAT
* ** *
172916 TCCAAATTCATTCATAAACTTAATTAAT
1 T--AAATACAAACATAAACATAATTAAT
172944 T
1 T
172945 CCAAATGAAA
Statistics
Matches: 117, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
26 97 0.83
28 20 0.17
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAATACAAACATAAACATAATTAAT
Found at i:180774 original size:42 final size:42
Alignment explanation
Indices: 180658--180853 Score: 218
Period size: 42 Copynumber: 4.6 Consensus size: 42
180648 TAAAGACTTG
* *
180658 ATGTATAAATGGAAGACTTATCTCTCGGGATGAGCATGAGATT
1 ATGTTTAAA-GGAAGACTTATGTCTCGGGATGAGCATGAGATT
* * * * *
180701 ATGTATAAACAGAAGACTCATGACTCAGGATGAGCATGAGATT
1 ATGTTTAAA-GGAAGACTTATGTCTCGGGATGAGCATGAGATT
* *
180744 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCGGGATGAGCATGAGATT
* * *
180786 AAGTTTAAAGGAAGACTTATGTCTCGGTA-G-GCATAAGATT
1 ATGTTTAAAGGAAGACTTATGTCTCGGGATGAGCATGAGATT
*
180826 -TGTTTAGAAAGGAAGACTTATGACTCGG
1 ATGTTT--AAAGGAAGACTTATGTCTCGG
180854 TTAGAGCATA
Statistics
Matches: 133, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
39 4 0.03
40 8 0.06
41 21 0.16
42 55 0.41
43 45 0.34
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTTATGTCTCGGGATGAGCATGAGATT
Found at i:182672 original size:46 final size:44
Alignment explanation
Indices: 182589--182676 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 44
182579 GCATCGTTTC
182589 ATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCT
1 ATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCT
*
182633 ATTCAACCAAACA-ACTGAAATACTGATTACAAC-CATATTCCATT
1 ATTCAACCAAACACA-AG-AATACT-ATTACAACTC-TATTCCATT
182677 ATAGTTCTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
43 1 0.03
44 14 0.36
45 7 0.18
46 17 0.44
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.28
Consensus pattern (44 bp):
ATTCAACCAAACACAAGAATACTATTACAACTCTATTCCATTCT
Found at i:191031 original size:36 final size:36
Alignment explanation
Indices: 190955--191031 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
190945 ACATAATAAG
* **
190955 TCACATGGCATGAAGAACATACCCACATATTTTTTA
1 TCACATGGCATGAAGAACATACCCAAATATTACTTA
*
190991 TCACATGGCATGAATAACATACCCAAATATTCACTT-
1 TCACATGGCATGAAGAACATACCCAAATATT-ACTTA
191027 TCACA
1 TCACA
191032 ATAGTCATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
36 34 0.94
37 2 0.06
ACGTcount: A:0.38, C:0.25, G:0.09, T:0.29
Consensus pattern (36 bp):
TCACATGGCATGAAGAACATACCCAAATATTACTTA
Found at i:193980 original size:18 final size:17
Alignment explanation
Indices: 193953--193986 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
193943 CAAGGACTTC
193953 GCTAGAGGATACTATTT
1 GCTAGAGGATACTATTT
*
193970 GCTATGAGGATTCTATT
1 GCTA-GAGGATACTATT
193987 GTTCAGTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (17 bp):
GCTAGAGGATACTATTT
Found at i:196973 original size:35 final size:35
Alignment explanation
Indices: 196898--196985 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
196888 CGTAGGACCT
* * *
196898 ATATATACTGTTTACACGGTGTCGTCCTGAAGAAC
1 ATATATACAGTTTACACAGTGTCGCCCTGAAGAAC
* * * **
196933 CTATATACAATTTACACAGTTTCGCCCTGAAGGGC
1 ATATATACAGTTTACACAGTGTCGCCCTGAAGAAC
*
196968 ATATATACCGTTTACACA
1 ATATATACAGTTTACACA
196986 ATTCACTCAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.31
Consensus pattern (35 bp):
ATATATACAGTTTACACAGTGTCGCCCTGAAGAAC
Found at i:198027 original size:18 final size:20
Alignment explanation
Indices: 198004--198043 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
197994 TTCATTATAA
*
198004 TAATTTT-TT-TATACATTT
1 TAATTTTATTGTACACATTT
198022 TAATTTTATTGTACACATTT
1 TAATTTTATTGTACACATTT
198042 TA
1 TA
198044 TTACCTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
TAATTTTATTGTACACATTT
Found at i:198232 original size:23 final size:22
Alignment explanation
Indices: 198205--198255 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
198195 ATCCAAACAG
*
198205 AATTTAAATTTAAATTTATTGTA
1 AATTTAAATTTAAAATTATT-TA
*
198228 AATTTAAGTTTAAAATTATTTA
1 AATTTAAATTTAAAATTATTTA
198250 AATTTA
1 AATTTA
198256 CTAATATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTTAAATTTAAAATTATTTA
Found at i:198958 original size:15 final size:15
Alignment explanation
Indices: 198919--198960 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
198909 ATAAATAAAC
198919 ATTA-AATAATAATA
1 ATTATAATAATAATA
* **
198933 ATTTTGTTAATAATA
1 ATTATAATAATAATA
198948 ATTATAATAATAA
1 ATTATAATAATAA
198961 GAACCGAAAG
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTATAATAATAATA
Found at i:200045 original size:30 final size:29
Alignment explanation
Indices: 199980--200197 Score: 187
Period size: 29 Copynumber: 7.5 Consensus size: 29
199970 CTGAACTCTC
**
199980 CAAAAATTACA-TTGACCCCTAAACTTCT
1 CAAAAATTACATTTTTCCCCTAAACTTCT
200008 C-AAAATTACATTTTTGCCCCTAAACTTCT
1 CAAAAATTACATTTTT-CCCCTAAACTTCT
*
200037 CAAAAATTACATTTTTACCCTCAAACTTCT
1 CAAAAATTACATTTTTCCCCT-AAACTTCT
* * * *
200067 CATAAGTTACATTTTTCCTC-GAACTT-T
1 CAAAAATTACATTTTTCCCCTAAACTTCT
* *
200094 CCAAAAATTATAATTTTTCCCCTGAACTTC-
1 -CAAAAATTA-CATTTTTCCCCTAAACTTCT
* * * * *
200124 CAAAAATCATATTTTTACCCTTAAATTTTT
1 CAAAAATTACATTTTT-CCCCTAAACTTCT
* *
200154 CAAAAATTACATTTTGCCCCCAAACTTC-
1 CAAAAATTACATTTTTCCCCTAAACTTCT
*
200182 CAAAAATCACCATTTT
1 CAAAAATTA-CATTTT
200198 ACCCTCAAGC
Statistics
Matches: 153, Mismatches: 26, Indels: 21
0.76 0.13 0.10
Matches are distributed among these distances:
27 10 0.07
28 29 0.19
29 57 0.37
30 57 0.37
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
CAAAAATTACATTTTTCCCCTAAACTTCT
Found at i:200197 original size:87 final size:88
Alignment explanation
Indices: 199980--200197 Score: 223
Period size: 87 Copynumber: 2.5 Consensus size: 88
199970 CTGAACTCTC
*
199980 CAAAAATTACA--TTGACCCCTAAACTTCTC-AAAATTACATTTTTGCCCCTAAACTTCTCAAAA
1 CAAAAATTACATTTTG-CCCCCAAACTTC-CAAAAATTACATTTTTGCCCCTAAACTTCTCAAAA
*
200042 ATTACATTTTTACCCTCAAACTTCT
64 ATCACATTTTTACCCTCAAACTTCT
* * * * * * *
200067 CATAAGTTACATTTT-TCCTCGAACTTTCCAAAAATTATAATTTTT-CCCCTGAACTTC-CAAAA
1 CAAAAATTACATTTTGCCCCCAAAC-TTCCAAAAATTA-CATTTTTGCCCCTAAACTTCTCAAAA
* * * *
200129 ATCATATTTTTACCCTTAAATTTTT
64 ATCACATTTTTACCCTCAAACTTCT
*
200154 CAAAAATTACATTTTGCCCCCAAACTTCCAAAAATCACCATTTT
1 CAAAAATTACATTTTGCCCCCAAACTTCCAAAAATTA-CATTTT
200198 ACCCTCAAGC
Statistics
Matches: 104, Mismatches: 21, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
87 69 0.66
88 27 0.26
89 8 0.08
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (88 bp):
CAAAAATTACATTTTGCCCCCAAACTTCCAAAAATTACATTTTTGCCCCTAAACTTCTCAAAAAT
CACATTTTTACCCTCAAACTTCT
Found at i:200244 original size:29 final size:29
Alignment explanation
Indices: 200032--200244 Score: 116
Period size: 29 Copynumber: 7.3 Consensus size: 29
200022 TGCCCCTAAA
*
200032 CTTCTCAAAAATTA-CATTTTTACCCTCAAA
1 CTTC-CAAAAATTACCA-TTTTACCCTCAAT
* * *
200062 CTTCTCATAAGTTA-CATTTT-TCCTCGAA-
1 CTTC-CAAAAATTACCATTTTACCCTC-AAT
** * *
200090 CTTTCCAAAAATTATAATTTTTCCCCTGAA-
1 C-TTCCAAAAATTACCA-TTTTACCCTCAAT
* * *
200120 CTTCCAAAAATCA-TATTTTTACCCTTAAAT
1 CTTCCAAAAATTACCA-TTTTACCC-TCAAT
* * * * *
200150 TTTTCAAAAATTA-CATTTTGCCCCCAAA
1 CTTCCAAAAATTACCATTTTACCCTCAAT
* *
200178 CTTCCAAAAATCACCATTTTACCCTCAAG
1 CTTCCAAAAATTACCATTTTACCCTCAAT
*
200207 CATCCAAAAATTACCATTTTACCCTCAAT
1 CTTCCAAAAATTACCATTTTACCCTCAAT
* *
200236 TTTCTAAAA
1 CTTCCAAAA
200245 GTTCGACTTC
Statistics
Matches: 143, Mismatches: 32, Indels: 17
0.74 0.17 0.09
Matches are distributed among these distances:
28 33 0.23
29 75 0.52
30 32 0.22
31 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
CTTCCAAAAATTACCATTTTACCCTCAAT
Found at i:205247 original size:22 final size:22
Alignment explanation
Indices: 205214--205275 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
205204 ACGTTAACAA
*
205214 ATGATTTTAAAATTATTT-ATT
1 ATGATATTAAAATTATTTAATT
205235 ATGATATATAAAATTATTTAAATT
1 ATGATAT-TAAAATTATTT-AATT
*
205259 ATTATATTAAAA-TATTT
1 ATGATATTAAAATTATTT
205276 TTTTAACGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 6 0.17
22 16 0.44
23 5 0.14
24 9 0.25
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
ATGATATTAAAATTATTTAATT
Found at i:214085 original size:36 final size:36
Alignment explanation
Indices: 214038--214110 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
214028 AAAAAAACTT
214038 GTGTTTTGATCCCCCTTTTTAAGCTAATTAACCTTA
1 GTGTTTTGATCCCCCTTTTTAAGCTAATTAACCTTA
214074 GTGTTTTGATCCCCCTTTTTAAGCTAATTAACCTTA
1 GTGTTTTGATCCCCCTTTTTAAGCTAATTAACCTTA
214110 G
1 G
214111 CACGTTGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (36 bp):
GTGTTTTGATCCCCCTTTTTAAGCTAATTAACCTTA
Found at i:218228 original size:30 final size:30
Alignment explanation
Indices: 218158--218228 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 30
218148 TAAAATATGC
* *
218158 TTTAAAATCCTTAATACTTTTTTTTTTGTATT
1 TTTAAAAT--TTAATACTTTTATTTTTGCATT
* *
218190 TTTTAAATTTAATCCTTTTATTTTT-CATGT
1 TTTAAAATTTAATACTTTTATTTTTGCAT-T
218220 TTTAAAATT
1 TTTAAAATT
218229 CTGGTACAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 2 0.06
30 24 0.73
32 7 0.21
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTAAAATTTAATACTTTTATTTTTGCATT
Found at i:221692 original size:69 final size:69
Alignment explanation
Indices: 221529--221693 Score: 206
Period size: 69 Copynumber: 2.4 Consensus size: 69
221519 CGACTTTTTG
*** * * *
221529 CCTGCGAACCTTAGAATTGTAGTTGAGAGCTTTGCTCTCGCTAATTGTGTTAAAAGTTGAGGCTA
1 CCTGCGAACCTTAGAATAACAGTTGGGAGCTTTACTCTCGCTAACTGTGTTAAAAGTTGAGGCTA
221594 TTCA
66 TTCA
* * ** *
221598 CTTGCGAACCTTAGAATAACAGTTGGGAGCTTTACTCTCGCTAGCTGTGTT-GGAGCTTGTGGCT
1 CCTGCGAACCTTAGAATAACAGTTGGGAGCTTTACTCTCGCTAACTGTGTTAAAAG-TTGAGGCT
*
221662 CTTCA
65 ATTCA
221667 CCTGCGAACCTTAGAATAACAGTTGGG
1 CCTGCGAACCTTAGAATAACAGTTGGG
221694 CCCTACACCC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
68 2 0.02
69 80 0.98
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (69 bp):
CCTGCGAACCTTAGAATAACAGTTGGGAGCTTTACTCTCGCTAACTGTGTTAAAAGTTGAGGCTA
TTCA
Found at i:222529 original size:18 final size:18
Alignment explanation
Indices: 222508--222543 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
222498 TATTTTCTTC
*
222508 TTTTAATTTAAATTTATT
1 TTTTAATTTAAATATATT
222526 TTTTAATTTAAATATATT
1 TTTTAATTTAAATATATT
222544 ACTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTAATTTAAATATATT
Found at i:222664 original size:66 final size:65
Alignment explanation
Indices: 222508--222967 Score: 467
Period size: 66 Copynumber: 6.8 Consensus size: 65
222498 TATTTTCTTC
* * * ** * *
222508 TTTTAATTTAAA-TTTATTTTTTAATTTAAATATATTACTTTAAATTAAAATA-GCTAATTATTT
1 TTTTAA-TTAAATTTTATTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCT--TTAATT
*
222571 CTT
63 ATT
* * *
222574 CTTTCAATTAAATTTTACTTTTTAAATTGAAATATATTGCTTTAAATTGATTTATTATTTAATTA
1 -TTTTAATTAAATTTTA-TTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAATTA
222639 TT
64 TT
* *
222641 TTTTAATTAAATTTTACTTTTTAAATTTAAATATATTGATTTAAATTGATTTATTCTCTAATTAT
1 TTTTAATTAAATTTTA-TTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAATTAT
222706 T
65 T
* *
222707 TTTTAATTAAATTCTATTTTTTAAATTTAAATATATTGCTTTAAATTCATTTATTCTTTAATTAT
1 TTTTAATTAAATTTTA-TTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAATTA-
222772 TTCT
64 -T-T
* * *
222776 TCTTTAAATTGAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTTATTTATTCTTTAATTA
1 T-TTT-AATTAAATTTTATTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTT-A--A
222841 TTTATT
61 -TTATT
* *
222847 CTTTTAATTAAATTCTATTTTTAAATTTAAATATATTACTTTAAATTGATTTATTCTTTAATTAT
1 -TTTTAATTAAATTTTATTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAATTA-
222912 TTCTT
64 ---TT
** * *
222917 CTTTTAATTAAGCTTTATTTTCTTTAATTT-AATTTATTGCTTTAAATTGAT
1 -TTTTAATTAAATTTTA-TTT-TTAAATTTAAATATATTGCTTTAAATTGAT
222968 ATGGGGAAAC
Statistics
Matches: 338, Mismatches: 36, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
66 128 0.38
67 17 0.05
68 31 0.09
69 4 0.01
70 108 0.32
71 37 0.11
72 9 0.03
73 1 0.00
74 3 0.01
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (65 bp):
TTTTAATTAAATTTTATTTTTAAATTTAAATATATTGCTTTAAATTGATTTATTCTTTAATTATT
Found at i:222733 original size:19 final size:18
Alignment explanation
Indices: 222702--222964 Score: 160
Period size: 19 Copynumber: 14.8 Consensus size: 18
222692 TATTCTCTAA
*
222702 TTATT-TTTTAATTAAAT
1 TTATTCTTTAAATTAAAT
*
222719 TCTATTTTTTAAATTTAAAT
1 T-TATTCTTTAAA-TTAAAT
* *
222739 ATATTGCTTTAAATT-CAT
1 TTATT-CTTTAAATTAAAT
222757 TTATTCTTT-AATT--AT
1 TTATTCTTTAAATTAAAT
* *
222772 TTCTTCTTTAAATTGAATT
1 TTATTCTTTAAATT-AAAT
* *
222791 TTATTTTTTAATTTAAAT
1 TTATTCTTTAAATTAAAT
* *
222809 ATATTGCTTTAAATT-TAT
1 TTATT-CTTTAAATTAAAT
222827 TTATTCTTT-AATT--AT
1 TTATTCTTTAAATTAAAT
*
222842 TTATTCTTTTAATTAAAT
1 TTATTCTTTAAATTAAAT
222860 TCTATT-TTTAAATTTAAAT
1 T-TATTCTTTAAA-TTAAAT
* *
222879 ATATTACTTTAAATT-GAT
1 TTATT-CTTTAAATTAAAT
222897 TTATTCTTT-AATT--AT
1 TTATTCTTTAAATTAAAT
* * *
222912 TTCTTCTTTTAATTAAGCT
1 TTATTCTTTAAATTAA-AT
*
222931 TTATTTTCTTT-AATTTAAT
1 TTA--TTCTTTAAATTAAAT
222950 TTATTGCTTTAAATT
1 TTATT-CTTTAAATT
222965 GATATGGGGA
Statistics
Matches: 197, Mismatches: 25, Indels: 46
0.74 0.09 0.17
Matches are distributed among these distances:
15 31 0.16
16 24 0.12
17 15 0.08
18 45 0.23
19 53 0.27
20 23 0.12
21 6 0.03
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (18 bp):
TTATTCTTTAAATTAAAT
Found at i:222736 original size:20 final size:18
Alignment explanation
Indices: 222703--222878 Score: 68
Period size: 18 Copynumber: 9.9 Consensus size: 18
222693 ATTCTCTAAT
222703 TATTTTTTAATTAAATTC
1 TATTTTTTAATTAAATTC
*
222721 TATTTTTTAAATTTAAA-TA
1 TATTTTTT-AA-TTAAATTC
* *
222740 TATTGCTTTAAATT-CATT-
1 TATT--TTTTAATTAAATTC
* *
222758 TATTCTTTAATT-ATTTC
1 TATTTTTTAATTAAATTC
* * * *
222775 T-TCTTTAAATTGAATTT
1 TATTTTTTAATTAAATTC
*
222792 TATTTTTTAATTTAAA-TA
1 TATTTTTTAA-TTAAATTC
* *
222810 TATTGCTTTAAATT-TATT-
1 TATT--TTTTAATTAAATTC
*
222828 TATTCTTTAATT--ATT-
1 TATTTTTTAATTAAATTC
222843 TATTCTTTTAATTAAATTC
1 TATT-TTTTAATTAAATTC
*
222862 TATTTTTAAATTTAAAT
1 TATTTTTTAA-TTAAAT
222879 ATATTACTTT
Statistics
Matches: 119, Mismatches: 22, Indels: 33
0.68 0.13 0.19
Matches are distributed among these distances:
15 7 0.06
16 28 0.24
17 5 0.04
18 37 0.31
19 27 0.23
20 12 0.10
21 3 0.03
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (18 bp):
TATTTTTTAATTAAATTC
Found at i:222778 original size:15 final size:16
Alignment explanation
Indices: 222740--222925 Score: 83
Period size: 18 Copynumber: 10.8 Consensus size: 16
222730 AATTTAAATA
222740 TATTGCTTTAAATTCATT
1 TATT-CTTT-AATTCATT
222758 TATTCTTTAATT-ATT
1 TATTCTTTAATTCATT
* *
222773 TCTTCTTTAAATTGAATTT
1 TATTCTTT-AATT-CA-TT
* * *
222792 TATTTTTTAATTTAAATA
1 TATTCTTTAA-TT-CATT
*
222810 TATTGCTTTAAATTTATT
1 TATT-CTTT-AATTCATT
222828 TATTCTTTAATT-ATT
1 TATTCTTTAATTCATT
*
222843 TATTCTTTTAATTAAATT
1 TATTC-TTTAATT-CATT
* *
222861 CTATT-TTTAAATTTAAATA
1 -TATTCTTT-AA-TT-CATT
*
222880 TATTACTTTAAATTGATT
1 TATT-CTTT-AATTCATT
222898 TATTCTTTAATT-ATT
1 TATTCTTTAATTCATT
*
222913 TCTTCTTTTAATT
1 TATTC-TTTAATT
222926 AAGCTTTATT
Statistics
Matches: 140, Mismatches: 12, Indels: 34
0.75 0.06 0.18
Matches are distributed among these distances:
15 25 0.18
16 30 0.21
17 15 0.11
18 33 0.24
19 29 0.21
20 8 0.06
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (16 bp):
TATTCTTTAATTCATT
Found at i:222819 original size:70 final size:70
Alignment explanation
Indices: 222501--222967 Score: 559
Period size: 70 Copynumber: 6.8 Consensus size: 70
222491 TGTTCTTTAT
* * ** *
222501 TTTCTTCTTTTAATTTAAA-TTTATTTTTTAATTTAAATATATTACTTTAAATTAAAATA-GC--
1 TTTCTTCTTTTAA-TTAAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTT
222562 TAATTA
65 TAATTA
* * * *
222568 TTTCTTCTTTCAATTAAATTTTACTTTTTAAATTGAAATATATTGCTTTAAATTGATTTATTATT
1 TTTCTTCTTTTAATTAAATTTTA-TTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTT
222633 TAATTA
65 TAATTA
* * *
222639 ----TT-TTTTAATTAAATTTTACTTTTTAAATTTAAATATATTGATTTAAATTGATTTATTCTC
1 TTTCTTCTTTTAATTAAATTTTA-TTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTT
222699 TAATTA
65 TAATTA
* *
222705 ----TT-TTTTAATTAAATTCTATTTTTTAAATTTAAATATATTGCTTTAAATTCATTTATTCTT
1 TTTCTTCTTTTAATTAAATTTTATTTTTT-AATTTAAATATATTGCTTTAAATTGATTTATTCTT
222765 TAATTA
65 TAATTA
* * *
222771 TTTCTTCTTTAAATTGAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTTATTTATTCTTT
1 TTTCTTCTTTTAATTAAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTTT
222836 AATTA
66 AATTA
* * * *
222841 TTTATTCTTTTAATTAAATTCTATTTTTAAATTTAAATATATTACTTTAAATTGATTTATTCTTT
1 TTTCTTCTTTTAATTAAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTTT
222906 AATTA
66 AATTA
** *
222911 TTTCTTCTTTTAATTAAGCTTTATTTTCTTTAATTT-AATTTATTGCTTTAAATTGAT
1 TTTCTTCTTTTAATTAAATTTTA-TTT-TTTAATTTAAATATATTGCTTTAAATTGAT
222968 ATGGGGAAAC
Statistics
Matches: 350, Mismatches: 37, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
65 5 0.01
66 119 0.34
67 18 0.05
68 30 0.09
70 124 0.35
71 47 0.13
72 7 0.02
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (70 bp):
TTTCTTCTTTTAATTAAATTTTATTTTTTAATTTAAATATATTGCTTTAAATTGATTTATTCTTT
AATTA
Found at i:222834 original size:55 final size:52
Alignment explanation
Indices: 222768--222909 Score: 148
Period size: 55 Copynumber: 2.7 Consensus size: 52
222758 TATTCTTTAA
*
222768 TTATTTCTTCTTTAAATTGAATTTTATTTTTTAATTTAAA-TATATTGCTTTAAAT
1 TTATTTATTCTTTAAATTG-A-TTTATTTTTTAATTTAAATTATATT--TTTAAAT
*
222823 TTATTTATTCTTT-AATT-ATTTATTCTTTTAA-TTAAATTCTATTTTTAAAT
1 TTATTTATTCTTTAAATTGATTTATT-TTTTAATTTAAATTATATTTTTAAAT
* *
222873 TTAAATATATTACTTTAAATTGATTTATTCTTTAATT
1 TT--ATTTATT-CTTTAAATTGATTTATTTTTTAATT
222910 ATTTCTTCTT
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
50 9 0.12
51 11 0.15
52 18 0.24
53 4 0.05
54 13 0.17
55 20 0.27
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.61
Consensus pattern (52 bp):
TTATTTATTCTTTAAATTGATTTATTTTTTAATTTAAATTATATTTTTAAAT
Found at i:222853 original size:33 final size:32
Alignment explanation
Indices: 222740--222964 Score: 164
Period size: 32 Copynumber: 6.4 Consensus size: 32
222730 AATTTAAATA
*
222740 TATTGCTTTAAATTCATTTATTCTTTAATTATT
1 TATT-CTTTAAATTAATTTATTCTTTAATTATT
* * *
222773 TCTTCTTTAAATTGAATTTTATTTTTTAATTTAAATA
1 TATTCTTTAAATT-AA-TTTATTCTTTAA-TT--ATT
*
222810 TATTGCTTTAAATTTATTTATTCTTTAATTATT
1 TATT-CTTTAAATTAATTTATTCTTTAATTATT
* *
222843 TATTCTTTTAATTAAATTCTATT-TTTAAATTTAAATA
1 TATTCTTTAAATT-AATT-TATTCTTT-AA-TT--ATT
*
222880 TATTACTTTAAATTGATTTATTCTTTAATTATT
1 TATT-CTTTAAATTAATTTATTCTTTAATTATT
* *
222913 TCTTCTTTTAATTAAGCTTTATTTTCTTTAATTTAATT
1 TATTCTTTAAATTAA--TTTA--TTCTTTAA-TT-ATT
222951 TATTGCTTTAAATT
1 TATT-CTTTAAATT
222965 GATATGGGGA
Statistics
Matches: 152, Mismatches: 19, Indels: 36
0.73 0.09 0.17
Matches are distributed among these distances:
32 26 0.17
33 21 0.14
34 21 0.14
35 8 0.05
36 25 0.16
37 20 0.13
38 23 0.15
39 8 0.05
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (32 bp):
TATTCTTTAAATTAATTTATTCTTTAATTATT
Found at i:222907 original size:37 final size:36
Alignment explanation
Indices: 222721--222907 Score: 160
Period size: 37 Copynumber: 5.3 Consensus size: 36
222711 AATTAAATTC
* *
222721 TATTTTTTAAATTTAAATATATTGCTTTAAATTCATT
1 TATTCTTTAAATTTAAATATATT-CTTTAAATTGATT
* *
222758 TATTCTTT-AA-TT--ATTTCTTCTTTAAATTGAATTT
1 TATTCTTTAAATTTAAATATATTCTTTAAATTG-A-TT
* *
222792 TATT-TTTTAATTTAAATATATTGCTTTAAATTTATT
1 TATTCTTTAAATTTAAATATATT-CTTTAAATTGATT
* * *
222828 TATTCTTT-AA-TT--ATTTATTCTTTTAATTAAATT
1 TATTCTTTAAATTTAAATATATTCTTTAAATT-GATT
222861 CTATT-TTTAAATTTAAATATATTACTTTAAATTGATT
1 -TATTCTTTAAATTTAAATATATT-CTTTAAATTGATT
222898 TATTCTTTAA
1 TATTCTTTAA
222908 TTATTTCTTC
Statistics
Matches: 121, Mismatches: 13, Indels: 32
0.73 0.08 0.19
Matches are distributed among these distances:
32 17 0.14
33 21 0.17
34 14 0.12
35 8 0.07
36 14 0.12
37 30 0.25
38 17 0.14
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (36 bp):
TATTCTTTAAATTTAAATATATTCTTTAAATTGATT
Found at i:224034 original size:18 final size:17
Alignment explanation
Indices: 224000--224032 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
223990 ATTGATTTTA
224000 ATTTTTTTAAAATAAAT
1 ATTTTTTTAAAATAAAT
*
224017 ATTTTTTTATAATAAA
1 ATTTTTTTAAAATAAA
224033 ATGTCTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTTAAAATAAAT
Found at i:227064 original size:82 final size:83
Alignment explanation
Indices: 226952--227117 Score: 262
Period size: 82 Copynumber: 2.0 Consensus size: 83
226942 ATCTAAACCA
* *
226952 CCCTAATAACTTCACACTATCAATTCAACAAACACCAATGATTCAATGATGAATATAATGAATAA
1 CCCTAATAACTTCACACAAACAATTCAACAAACACCAATGATTCAATGATGAATATAATGAATAA
*
227017 AAGACGAGAATTATCCCT
66 AAGACAAGAATTATCCCT
* * * *
227035 CCCT-ATATCTTCACACAAACAATTCAACAAACATCAATGATTCAATGATGAATGTAATGAATCA
1 CCCTAATAACTTCACACAAACAATTCAACAAACACCAATGATTCAATGATGAATATAATGAATAA
227099 AAGACAAGAATTATCCCT
66 AAGACAAGAATTATCCCT
227117 C
1 C
227118 TAATCTAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
82 72 0.95
83 4 0.05
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25
Consensus pattern (83 bp):
CCCTAATAACTTCACACAAACAATTCAACAAACACCAATGATTCAATGATGAATATAATGAATAA
AAGACAAGAATTATCCCT
Found at i:228079 original size:26 final size:26
Alignment explanation
Indices: 228036--228090 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
228026 AACAAAATAT
* *
228036 ATAAACGTTAAAGACTAATTTTGTTA
1 ATAAACATTAAAGACTAATTCTGTTA
* *
228062 ATAAACATTGAAGGCTAATTCTGTTA
1 ATAAACATTAAAGACTAATTCTGTTA
228088 ATA
1 ATA
228091 TACTAATCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (26 bp):
ATAAACATTAAAGACTAATTCTGTTA
Found at i:241272 original size:18 final size:18
Alignment explanation
Indices: 241246--241286 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
241236 CGATAAGTAG
*
241246 TAAATGTATTTGTATCAA
1 TAAACGTATTTGTATCAA
* *
241264 TAAACGTATTTGTTTCAG
1 TAAACGTATTTGTATCAA
241282 TAAAC
1 TAAAC
241287 TTTTGGTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (18 bp):
TAAACGTATTTGTATCAA
Found at i:249326 original size:24 final size:24
Alignment explanation
Indices: 249175--249325 Score: 146
Period size: 24 Copynumber: 6.4 Consensus size: 24
249165 GTTCGTGCTC
* *
249175 GTTCGTTTAT-CGTTCACAAACAT
1 GTTCGTTTATACGTTCGCGAACAT
***
249198 GTTCGTTTA-ACGTTCATAAACAT
1 GTTCGTTTATACGTTCGCGAACAT
* * *
249221 GTTCATTTA-ACGTTTGTGAACAT
1 GTTCGTTTATACGTTCGCGAACAT
* * *
249244 GTTCATTTATATGTTCGTGAACAT
1 GTTCGTTTATACGTTCGCGAACAT
* * *
249268 GTTCGTTTATGCATTCGCGAGCAT
1 GTTCGTTTATACGTTCGCGAACAT
*
249292 GTTCGTTTATGCGTTCGCGAACAT
1 GTTCGTTTATACGTTCGCGAACAT
249316 GTTCGTTTAT
1 GTTCGTTTAT
249326 GTTAACTAAC
Statistics
Matches: 111, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
23 49 0.44
24 62 0.56
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.42
Consensus pattern (24 bp):
GTTCGTTTATACGTTCGCGAACAT
Found at i:249374 original size:19 final size:18
Alignment explanation
Indices: 249337--249377 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
249327 TTAACTAACC
*
249337 AAAACAAAAAAATTAAAT
1 AAAACAAAAAAACTAAAT
*
249355 AAAACAAAACCAACTAAAT
1 AAAACAAAA-AAACTAAAT
249374 AAAA
1 AAAA
249378 AACTTAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (18 bp):
AAAACAAAAAAACTAAAT
Found at i:253273 original size:12 final size:12
Alignment explanation
Indices: 253250--253327 Score: 81
Period size: 12 Copynumber: 6.7 Consensus size: 12
253240 GATGAGTCTA
253250 ATAAACGAGCTT
1 ATAAACGAGCTT
* *
253262 ATAAATGGGCTT
1 ATAAACGAGCTT
253274 -TAAACGAGCTT
1 ATAAACGAGCTT
253285 ATAAACGAGCTT
1 ATAAACGAGCTT
*
253297 -TATACGAGC-T
1 ATAAACGAGCTT
* *
253307 ATTAAATGAGCTA
1 A-TAAACGAGCTT
253320 ATAAACGA
1 ATAAACGA
253328 AGCATAAACA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
10 1 0.02
11 17 0.32
12 34 0.64
13 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:253281 original size:23 final size:23
Alignment explanation
Indices: 253251--253327 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
253241 ATGAGTCTAA
*
253251 TAAACGAGCTTATAAATGGGCTT
1 TAAACGAGCTTATAAATGAGCTT
*
253274 TAAACGAGCTTATAAACGAGCTT
1 TAAACGAGCTTATAAATGAGCTT
* *
253297 TATACGAGC-TATTAAATGAGCTAA
1 TAAACGAGCTTA-TAAATGAGCT-T
253321 TAAACGA
1 TAAACGA
253328 AGCATAAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 2 0.04
23 38 0.83
24 6 0.13
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.27
Consensus pattern (23 bp):
TAAACGAGCTTATAAATGAGCTT
Found at i:253296 original size:35 final size:35
Alignment explanation
Indices: 253247--253327 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
253237 TCTGATGAGT
* *
253247 CTAATAAACGAGCTTATAAATGGGCT-TTAAACGAG
1 CTAATAAACGAGCTT-TAAACGAGCTATTAAACGAG
* * *
253282 CTTATAAACGAGCTTTATACGAGCTATTAAATGAG
1 CTAATAAACGAGCTTTAAACGAGCTATTAAACGAG
253317 CTAATAAACGA
1 CTAATAAACGA
253328 AGCATAAACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 7 0.18
35 32 0.82
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (35 bp):
CTAATAAACGAGCTTTAAACGAGCTATTAAACGAG
Found at i:254626 original size:19 final size:18
Alignment explanation
Indices: 254602--254646 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
254592 AAATGTCAGC
*
254602 TTTTTTTAAATTTATTATA
1 TTTTTTTAAATTTA-AATA
*
254621 TTTTTTAAAAATTTAAATA
1 TTTTTT-TAAATTTAAATA
254640 TTTTTTT
1 TTTTTTT
254647 GGTAGTGCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTAAATTTAAATA
Found at i:254659 original size:93 final size:93
Alignment explanation
Indices: 254492--254764 Score: 291
Period size: 93 Copynumber: 2.8 Consensus size: 93
254482 TTGGTGGCAC
** *
254492 CAAATGTCATCTTTTTTTAATGATTTATTATTTATTATTTTTTAAATTAAAATTTTTTTTTTGGT
1 CAAATGTCA-CTTTTTTTAA--ATTTATTA--TATT-TTTTAAAAATTTAAATTTTTTTTTTGGT
254557 GGTGCCATATTAAATGGCGCCAACACTTCAC-CAA
60 GGTGCCATATTAAATGGCGCCAACACTTC-CTCAA
* *
254591 CAAATGTCAGCTTTTTTTAAATTTATTATATTTTTTAAAAATTTAAA-TATTTTTTTGGTAGTGC
1 CAAATGTCA-CTTTTTTTAAATTTATTATATTTTTTAAAAATTTAAATTTTTTTTTTGGTGGTGC
* * *
254655 CATATTAAATAGCGCCACCACTTCCTTAA
65 CATATTAAATGGCGCCAACACTTCCTCAA
* * * * * *
254684 AAAATGTTACTTATTTATT-TATTTATTATTTATTTTTAAAAGTTTAAATTTTTTTTTTGGTGGA
1 CAAATGTCACTT-TTT-TTAAATTTATTATAT-TTTTTAAAAATTTAAATTTTTTTTTTGGTGGT
*
254748 GCCATTTTAAATGGCGC
63 GCCATATTAAATGGCGC
254765 AACCCAATTG
Statistics
Matches: 150, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
92 4 0.03
93 59 0.39
94 29 0.19
95 31 0.21
97 8 0.05
99 19 0.13
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.48
Consensus pattern (93 bp):
CAAATGTCACTTTTTTTAAATTTATTATATTTTTTAAAAATTTAAATTTTTTTTTTGGTGGTGCC
ATATTAAATGGCGCCAACACTTCCTCAA
Found at i:254819 original size:18 final size:18
Alignment explanation
Indices: 254796--254831 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
254786 ACTATTTAAT
254796 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
254814 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
254832 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:254866 original size:2 final size:2
Alignment explanation
Indices: 254859--254887 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
254849 TATCCTATTT
254859 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
254888 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:255059 original size:7 final size:7
Alignment explanation
Indices: 255047--255072 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
255037 AACCCAATTG
255047 ATTTATT
1 ATTTATT
255054 ATTTATT
1 ATTTATT
255061 ATTTATT
1 ATTTATT
255068 ATTTA
1 ATTTA
255073 AATATATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
ATTTATT
Found at i:255091 original size:18 final size:18
Alignment explanation
Indices: 255068--255103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
255058 ATTATTTATT
255068 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
255086 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
255104 TTTTTGGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:255730 original size:27 final size:25
Alignment explanation
Indices: 255671--255743 Score: 128
Period size: 25 Copynumber: 2.9 Consensus size: 25
255661 ACCAAAGTAC
255671 TAACAGAGAGCACATAAGTGCTGGG
1 TAACAGAGAGCACATAAGTGCTGGG
255696 TAACAGAGAGCACATAAGTGCTGGG
1 TAACAGAGAGCACATAAGTGCTGGG
*
255721 TAACAGAGAGCACACACAGTGCT
1 TAACAGAGAGCACATA-AGTGCT
255744 AAACAGAGAG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 40 0.87
26 6 0.13
ACGTcount: A:0.37, C:0.19, G:0.29, T:0.15
Consensus pattern (25 bp):
TAACAGAGAGCACATAAGTGCTGGG
Found at i:255748 original size:23 final size:23
Alignment explanation
Indices: 255650--255871 Score: 148
Period size: 23 Copynumber: 9.5 Consensus size: 23
255640 TATACGGAAC
* *
255650 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
*
255672 -AACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
255693 GGGTAACAGAGAGCACA-TAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
255718 GGGTAACAGAGAGCACACACAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
255744 AAACAGAGAGTACACAAAGTTCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
255767 AATCAGAGAGCAAACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
** *
255790 AATTAGAGAGCACACAAAGTGAT
1 AAACAGAGAGCACACAAAGTGCT
* * *
255813 AATCAGAGAGCACACACAGTTCT
1 AAACAGAGAGCACACAAAGTGCT
* *
255836 AAAAACAGAGAGCACGA-GACGTGCT
1 --AAACAGAGAGCAC-ACAAAGTGCT
255861 AAACAGAGAGC
1 AAACAGAGAGC
255872 GCGCTAATGT
Statistics
Matches: 165, Mismatches: 26, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
21 17 0.10
23 87 0.53
25 54 0.33
26 7 0.04
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:258124 original size:38 final size:38
Alignment explanation
Indices: 258073--258145 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
258063 AAAATTATGG
* **
258073 TGGGAGTTTGTATAACAACCCTGCCTTGGGTCCCCGTT
1 TGGGAGTTCGTATAACAACCCTGCCTCAGGTCCCCGTT
*
258111 TGGGAGTTCGTATAACAACCTTGCCTCAGGTCCCC
1 TGGGAGTTCGTATAACAACCCTGCCTCAGGTCCCC
258146 ATTTACAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.29
Consensus pattern (38 bp):
TGGGAGTTCGTATAACAACCCTGCCTCAGGTCCCCGTT
Found at i:260679 original size:6 final size:6
Alignment explanation
Indices: 260668--260700 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
260658 AAAAGAATCC
*
260668 TCCCCT TCCCCT TCCCCT TCCCCT TCCCTT TCC
1 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCC
260701 ATTTCCCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCCT
Found at i:260706 original size:18 final size:18
Alignment explanation
Indices: 260668--260708 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
260658 AAAAGAATCC
*
260668 TCCCCTTCCCCTTCCCCT
1 TCCCCTTCCCCTTCCACT
* *
260686 TCCCCTTCCCTTTCCATT
1 TCCCCTTCCCCTTCCACT
260704 TCCCC
1 TCCCC
260709 CATCATTGCC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.02, C:0.61, G:0.00, T:0.37
Consensus pattern (18 bp):
TCCCCTTCCCCTTCCACT
Found at i:262643 original size:43 final size:43
Alignment explanation
Indices: 262571--262655 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
262561 TGTGTAAGCA
**
262571 TTGATGAATGAATCAGTATCCTGTTTGATTATGATGTTAAGGG
1 TTGATGAATGAATCAGTATCCTGAATGATTATGATGTTAAGGG
* *
262614 TTGATGAATGAATCAGTGTCTTGAATGATTATGATGTTAAGG
1 TTGATGAATGAATCAGTATCCTGAATGATTATGATGTTAAGG
262656 ATATGTTCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (43 bp):
TTGATGAATGAATCAGTATCCTGAATGATTATGATGTTAAGGG
Found at i:264433 original size:14 final size:14
Alignment explanation
Indices: 264414--264449 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
264404 GAAAAATAAT
* *
264414 TCATTTTTCAGAAA
1 TCATTTTCCAAAAA
264428 TCATTTTCCAAAAA
1 TCATTTTCCAAAAA
264442 TCATTTTC
1 TCATTTTC
264450 AATCAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.03, T:0.44
Consensus pattern (14 bp):
TCATTTTCCAAAAA
Found at i:270708 original size:22 final size:21
Alignment explanation
Indices: 270658--270709 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
270648 TTCCTAAATT
270658 TATTTTAAATATATAATATTA
1 TATTTTAAATATATAATATTA
* * *
270679 TATATTTAAATCTTTATTAGTTA
1 TAT-TTTAAATATATAATA-TTA
270702 TATTTTAA
1 TATTTTAA
270710 TATTTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 3 0.12
22 17 0.65
23 6 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TATTTTAAATATATAATATTA
Found at i:270747 original size:20 final size:21
Alignment explanation
Indices: 270703--270749 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
270693 TATTAGTTAT
270703 ATTTTA-ATATTTAAAATATA
1 ATTTTATATATTTAAAATATA
* *
270723 A-TTTATATATTTGAATTA-A
1 ATTTTATATATTTAAAATATA
270742 ATTTTATA
1 ATTTTATA
270750 AATAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTATATATTTAAAATATA
Found at i:270974 original size:60 final size:59
Alignment explanation
Indices: 270881--271018 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 59
270871 TTAATATAAC
* * * * *
270881 ATTTGGTACTTGAACTTAATACTTTTGCTTAATTTCGTACCTAAACTTTTTTTTTACCTA
1 ATTTGGTACCTGAACTTAACACTTTTGCCTAATTTCGTAACTAAAC-TTTTTTTTACCCA
* * * * *
270941 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTTGTAATTAAACTTTTTTTTACCCA
1 ATTTGGTACCTGAACTTAACACTTTTGCCTAATTTCGTAACTAAACTTTTTTTTACCCA
*
271000 ATTTGATACCTGAACTTAA
1 ATTTGGTACCTGAACTTAA
271019 TATTTTCCCC
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 28 0.43
60 37 0.57
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTAACACTTTTGCCTAATTTCGTAACTAAACTTTTTTTTACCCA
Found at i:271031 original size:59 final size:59
Alignment explanation
Indices: 270881--271054 Score: 181
Period size: 59 Copynumber: 2.9 Consensus size: 59
270871 TTAATATAAC
* * * * ** *
270881 ATTTGGTACTTGAACTTAATACTTTTGCTTAATTTCGTACCTAAACTTTTTTTTTACCTA
1 ATTTGGTACCTGAACTTAATACTTTTCCCTAATTTTGTAATTAAAC-TTTTTTTTACCCA
* * * *
270941 ATTTGGTACCTAAACTTGACACTTTTTCCTAATTTTGTAATTAAACTTTTTTTTACCCA
1 ATTTGGTACCTGAACTTAATACTTTTCCCTAATTTTGTAATTAAACTTTTTTTTACCCA
* * *
271000 ATTTGATACCTGAACTTAATA-TTTTCCCCTAA-TTTGATATTTAAGCTTTTTTTTA
1 ATTTGGTACCTGAACTTAATACTTTT-CCCTAATTTTG-TAATTAAACTTTTTTTTA
271055 TATTCAATTT
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
58 8 0.08
59 50 0.53
60 37 0.39
ACGTcount: A:0.26, C:0.17, G:0.07, T:0.49
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTAATACTTTTCCCTAATTTTGTAATTAAACTTTTTTTTACCCA
Found at i:271272 original size:25 final size:25
Alignment explanation
Indices: 271242--271292 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
271232 AAAAAATGTC
* *
271242 AAATTTGAGTACCAAATTAAAAAAA
1 AAATTTAAATACCAAATTAAAAAAA
271267 AAATTTAAATACCAAATTAAAAAAA
1 AAATTTAAATACCAAATTAAAAAAA
271292 A
1 A
271293 GTGTCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATTTAAATACCAAATTAAAAAAA
Found at i:273410 original size:25 final size:25
Alignment explanation
Indices: 273359--273410 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
273349 GAAAATTAAA
* * *
273359 TTATAATTTTTAATAGTCTATATTT
1 TTATAATTTTTAAAAATCTAAATTT
273384 TTATAATTTTTAAAAAT-TAAATATT
1 TTATAATTTTTAAAAATCTAAAT-TT
273409 TT
1 TT
273411 TTTATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TTATAATTTTTAAAAATCTAAATTT
Done.