Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold110
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: 1159294
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
File 4 of 6
Found at i:481490 original size:19 final size:18
Alignment explanation
Indices: 481420--481490 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
481410 TACAAGCCAA
481420 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
481440 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
481453 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
481472 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
481491 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:484035 original size:13 final size:13
Alignment explanation
Indices: 484017--484041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484007 ATAATCACCC
484017 TGTATCGATACAT
1 TGTATCGATACAT
484030 TGTATCGATACA
1 TGTATCGATACA
484042 AAGAAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:487972 original size:21 final size:21
Alignment explanation
Indices: 487943--487987 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
487933 AAGTTTTTAT
*
487943 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
487963 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
487985 TTT
1 TTT
487988 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:490225 original size:13 final size:13
Alignment explanation
Indices: 490207--490232 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490197 CAATTTTTGG
490207 TGTATCGATACAT
1 TGTATCGATACAT
490220 TGTATCGATACAT
1 TGTATCGATACAT
490233 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:490244 original size:32 final size:33
Alignment explanation
Indices: 490187--490250 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
490177 TACAAGCCAA
**
490187 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
490220 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
490251 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:490257 original size:19 final size:18
Alignment explanation
Indices: 490187--490257 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
490177 TACAAGCCAA
490187 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
490207 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
490220 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
490239 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
490258 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:492567 original size:21 final size:20
Alignment explanation
Indices: 492529--492568 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
492519 CAAAAATAGT
*
492529 AAAATTTCAAGAAAAAAAAG
1 AAAAATTCAAGAAAAAAAAG
* *
492549 AAAAATTCATGAAATAAAAG
1 AAAAATTCAAGAAAAAAAAG
492569 GAATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.10, T:0.17
Consensus pattern (20 bp):
AAAAATTCAAGAAAAAAAAG
Found at i:492750 original size:166 final size:162
Alignment explanation
Indices: 492274--492799 Score: 569
Period size: 166 Copynumber: 3.2 Consensus size: 162
492264 TCTAATGACA
* * * * * * * **
492274 ATATTAGATGAATTTTAAAAATTTTAAACTCAGAAAAATCCTCCCAAAAACATTTATGGAATGCA
1 ATATTTGATGAATTTTAAAAATTATAAA-TAAGAAAAATCCT-TCGAAAACATTTACGGAGTAAA
* * * * *
492339 AAACTCAATTTTTCAAAAATAGGAGAATTTCAAAG-AAAAAATAAAAAACTTATAACAAT-AAAT
64 AAACTCAATATTTCAAAAATA-GA-AATTTCAAAGAAAAAAATGAAAAACTCATGA-AATAAAAA
*
492402 GAATTTTTTCAAAACTAATTTACTATG-AATTAAATGATG
126 GAA-TTTTTCAAAACTGATTTA--ATGTAATTAAATGATG
* * *
492441 ATATTTGATGAATATTAAAAATTATAAATCTAGAAAAATGCCTTCGAAAACATTTACGGAGTAGA
1 ATATTTGATGAATTTTAAAAATTATAAAT-AAGAAAAAT-CCTTCGAAAACATTTACGGAGTAAA
* * * *
492506 AAACTCTATATTTCAAAAATAGTAAAATTTC-AAGAAAAAAAAGAAAAATTCATGAAATAAAAGG
64 AAACTCAATATTTCAAAAATAG--AAATTTCAAAGAAAAAAATGAAAAACTCATGAAATAAAAAG
*
492570 AATTTTTTAAAACTGATTTAATGTAAATTAAATGATG
127 AATTTTTCAAAACTGATTTAATGT-AATTAAATGATG
*
492607 ATATTTGATGAATTTTAAAAATTATAAATGAAGAAAAATCCCTTTGAAAACATTTACGGAGTAAA
1 ATATTTGATGAATTTTAAAAATTATAAAT-AAGAAAAAT-CCTTCGAAAACATTTACGGAGTAAA
* *
492672 AAACTCCATATTTCAAAAAGAGAAATTTCAAAGAAAAAAATGAAAAACTCATGAAATAAAAAGAA
64 AAACTCAATATTTCAAAAATAGAAATTTCAAAGAAAAAAATGAAAAACTCATGAAATAAAAAGAA
* * * *
492737 TTTTTCAAAAACTGA-TTAATTGGTGATTAAGTAATA
129 TTTTTC-AAAACTGATTTAA-T-GTAATTAAATGATG
*
492773 ATATTTTATGAATTTTAAAAATT-TAAA
1 ATATTTGATGAATTTTAAAAATTATAAA
492800 CCAATGAAAA
Statistics
Matches: 310, Mismatches: 37, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
164 10 0.03
165 45 0.15
166 154 0.50
167 97 0.31
168 4 0.01
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.31
Consensus pattern (162 bp):
ATATTTGATGAATTTTAAAAATTATAAATAAGAAAAATCCTTCGAAAACATTTACGGAGTAAAAA
ACTCAATATTTCAAAAATAGAAATTTCAAAGAAAAAAATGAAAAACTCATGAAATAAAAAGAATT
TTTCAAAACTGATTTAATGTAATTAAATGATG
Found at i:493277 original size:24 final size:20
Alignment explanation
Indices: 493216--493269 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
493206 TTTTCACAAT
* * *
493216 TTGTATCAATACGTTGTTCA
1 TTGTATCGATACATGGTTCA
493236 TTGTATCGATACATGGTTCA
1 TTGTATCGATACATGGTTCA
493256 TTGTATCGATACAT
1 TTGTATCGATACAT
493270 TCTGGGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATGGTTCA
Found at i:495685 original size:51 final size:51
Alignment explanation
Indices: 495622--495792 Score: 225
Period size: 51 Copynumber: 3.3 Consensus size: 51
495612 TTATTTTCGA
* * * * *
495622 GGGGATACTCCAACCTCGGCTTTATTTCTAAAATATTGATTTTTCACAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACAATC
* **
495673 GGGGCTACTCCAACCCCAGTTTTATTTCTAAAACACCAATCTTTTCACAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGAT-TTTTCACAATC
* * *
495725 AGGGATACTCCAACCCCAGTTTTATTTCCAGAACACTGATTTTTCACAATC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACAATC
*
495776 GAGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
495793 GTTATTTTCA
Statistics
Matches: 103, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 58 0.56
52 45 0.44
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACACTGATTTTTCACAATC
Found at i:508248 original size:20 final size:21
Alignment explanation
Indices: 508223--508265 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
508213 TTCTTTTAAG
*
508223 AAAAACAAAA-AAATAAAAAA
1 AAAAACAAAACAAAGAAAAAA
508243 AAAAACAAAACAAAGAAAAAA
1 AAAAACAAAACAAAGAAAAAA
508264 AA
1 AA
508266 GAGAGAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.88, C:0.07, G:0.02, T:0.02
Consensus pattern (21 bp):
AAAAACAAAACAAAGAAAAAA
Found at i:508266 original size:9 final size:9
Alignment explanation
Indices: 508220--508279 Score: 52
Period size: 9 Copynumber: 6.8 Consensus size: 9
508210 ACATTCTTTT
508220 AAGAAAAACA
1 AAGAAAAA-A
*
508230 AA-AAAATA
1 AAGAAAAAA
508238 AA-AAAAAA
1 AAGAAAAAA
* *
508246 AACAAAACA
1 AAGAAAAAA
508255 AAGAAAAAA
1 AAGAAAAAA
* *
508264 AAGAGAGAA
1 AAGAAAAAA
508273 AAGAAAA
1 AAGAAAA
508280 GAACCTACTT
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
8 10 0.25
9 28 0.70
10 2 0.05
ACGTcount: A:0.83, C:0.05, G:0.10, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:509399 original size:62 final size:63
Alignment explanation
Indices: 509249--509703 Score: 609
Period size: 62 Copynumber: 7.3 Consensus size: 63
509239 TCTTTTCACC
* * *
509249 TTTAGTCCTCAAAAAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTT
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * *
509310 TTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCTACACGAGCTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
509372 TTTAGTCCTTAAAGAGTAGGACGCC-TTTTCCTTTCAAAGTCCACACAAGTTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
509434 TCTAGTCCTCAAAAAGTTGGACACCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACC-T
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * * *
509496 CTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTAGTGGCACC-C
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
509558 TTTAATCCTCAAAGAGTAGGACGCCTTTTTCTTTTCGAAGCCTACACAAGTTGGTGGCACCTT
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
* *
509621 TCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACC-T
1 TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
*
509683 CTTAGTCCTCAAAGAGTAGGA
1 TTTAGTCCTCAAAGAGTAGGA
509704 TGCTTTTTTT
Statistics
Matches: 340, Mismatches: 50, Indels: 7
0.86 0.13 0.02
Matches are distributed among these distances:
61 59 0.17
62 194 0.57
63 87 0.26
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (63 bp):
TTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTT
Found at i:509556 original size:125 final size:124
Alignment explanation
Indices: 509245--509703 Score: 629
Period size: 125 Copynumber: 3.7 Consensus size: 124
509235 TTTCTCTTTT
* * * *
509245 CACC-TTTAGTCCTCAAAAAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCAC
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * * *
509308 TTTTTAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCTACACGAGCTGGTGG
66 CTTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGG
* * * * *
509366 CACCTTTTTAGTCCTTAAAGAGTAGGACGCC-TTTTCCTTTCAAAGTCCACACAAGTTGGTGGCA
1 CACC-TTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
509430 CCTTTCTAGTCCTCAAAAAGTTGGACACCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGG
65 CCTTT-TAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGG
* * *
509491 CACCTCTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTAGTGGCAC
1 CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
509556 CCTTTAATCCTCAAAGAGTAGGACGCCTTTTTCTTTTCGAAGCCTACACAAGTTGGTGG
66 CTTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGG
509615 CACCTTTCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CACCTTT-TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
509680 CCTCTTAGTCCTCAAAGAGTAGGA
65 CCTTTTAGTCCTCAAAGAGTAGGA
509704 TGCTTTTTTT
Statistics
Matches: 295, Mismatches: 36, Indels: 10
0.87 0.11 0.03
Matches are distributed among these distances:
121 4 0.01
122 7 0.02
123 49 0.17
124 105 0.36
125 130 0.44
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (124 bp):
CACCTTTTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
CTTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCTACACAAGTTGGTGG
Found at i:509665 original size:187 final size:186
Alignment explanation
Indices: 509251--509703 Score: 696
Period size: 187 Copynumber: 2.4 Consensus size: 186
509241 TTTTCACCTT
* * * *
509251 TAGTCCTCAAAAAGTAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTTAG
1 TAGTCCTCAAAAAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAG
* * * * *
509315 TCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCTACACGAGCTGGTGGCACCTTTTTAGTCC
66 TCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTCTTTAATCC
*
509380 TTAAAGAGTAGGACGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTC
131 TCAAAGAGTAGGACGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTC
* *
509436 TAGTCCTCAAAAAGTTGGACACCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTCTTAG
1 TAGTCCTCAAAAAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAG
*
509501 TCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGCTAGTGGCACC-CTTTAATC
66 TCCTCAAAGAGCAGGACACCTTTTCCTTTT-AAAGCCCACACAAGCTAGTGGCACCTCTTTAATC
* *
509565 CTCAAAGAGTAGGACGCCTTTTTCTTTTCGAAG-CCTACACAAGTTGGTGGCACCTTTC
130 CTCAAAGAGTAGGACGCC-TTTTCCTTTCAAAGTCC-ACACAAGTTGGTGGCACCTTTC
* *
509623 TAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAG
1 TAGTCCTCAAAAAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAG
*
509688 TCCTCAAAGAGTAGGA
66 TCCTCAAAGAGCAGGA
509704 TGCTTTTTTT
Statistics
Matches: 244, Mismatches: 20, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
185 30 0.12
186 82 0.34
187 132 0.54
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (186 bp):
TAGTCCTCAAAAAGTAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACCTCTTAG
TCCTCAAAGAGCAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTAGTGGCACCTCTTTAATCC
TCAAAGAGTAGGACGCCTTTTCCTTTCAAAGTCCACACAAGTTGGTGGCACCTTTC
Found at i:509843 original size:88 final size:83
Alignment explanation
Indices: 509684--509889 Score: 197
Period size: 88 Copynumber: 2.5 Consensus size: 83
509674 GTGGCACCTC
* * * * * * * **
509684 TTAGTCCTCAAAGAGTAGGATG--CTTTTTTTCTTTTTTCTTTTGTCTTCAAAGAGTAGGATGCA
1 TTAGTTCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAAAGTAGGACACA
*
509747 CTTCATTTCTATCTTTTCCCT
66 CTTAATTTC---CTTTTCCCT
509768 TCTAGTTCTCAAAGAGCAGGATGCACTTTATTCTCCTTTTTCCTTTGTCCTCAAAAAGTAGGACA
1 T-TAGTTCTCAAAGAGCAGGATGCACTTTATT-TCCTTTTTCCTTTGTCCTCAAAAAGTAGGACA
* *
509833 CATTTAATTTCCTTTTTCCT
64 CACTTAATTTCCTTTTCCCT
* *
509853 TT-G-TCTTCAAAG-GCATGATGCATTTTATTTCCTTTTT
1 TTAGTTC-TCAAAGAGCAGGATGCACTTTATTTCCTTTTT
509890 TTTCCCTTTT
Statistics
Matches: 103, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
81 8 0.08
82 17 0.17
83 7 0.07
84 2 0.02
85 28 0.27
87 6 0.06
88 35 0.34
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (83 bp):
TTAGTTCTCAAAGAGCAGGATGCACTTTATTTCCTTTTTCCTTTGTCCTCAAAAAGTAGGACACA
CTTAATTTCCTTTTCCCT
Found at i:509890 original size:41 final size:42
Alignment explanation
Indices: 509691--509890 Score: 164
Period size: 41 Copynumber: 4.8 Consensus size: 42
509681 CTCTTAGTCC
* *
509691 TCAAAGAGTAGGATGC-TTTT-TTT-CTTTTTTCTTTTGTCT
1 TCAAAGAGCAGGATGCATTTTATTTCCTTTTTTCCTTTGTCT
* * *
509730 TCAAAGAGTAGGATGCACTTCATTT-CTATCTTTTCCCTTCTAGT-T
1 TCAAAGAGCAGGATGCATTTTATTTCCT-T-TTTT-CCTT-T-GTCT
* *
509775 CTCAAAGAGCAGGATGCACTTTATTCTCC-TTTTTCCTTTGTCC
1 -TCAAAGAGCAGGATGCATTTTATT-TCCTTTTTTCCTTTGTCT
* * ** *
509818 TCAAAAAGTAGGACACATTTAATTTCC-TTTTTCCTTTGTCT
1 TCAAAGAGCAGGATGCATTTTATTTCCTTTTTTCCTTTGTCT
*
509859 TCAAAG-GCATGATGCATTTTATTTCCTTTTTT
1 TCAAAGAGCAGGATGCATTTTATTTCCTTTTTT
509891 TTCCCTTTTT
Statistics
Matches: 130, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
39 16 0.12
40 17 0.13
41 31 0.24
42 21 0.16
43 5 0.04
44 7 0.05
45 6 0.05
46 25 0.19
47 1 0.01
48 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.13, T:0.46
Consensus pattern (42 bp):
TCAAAGAGCAGGATGCATTTTATTTCCTTTTTTCCTTTGTCT
Found at i:510012 original size:62 final size:62
Alignment explanation
Indices: 509940--510094 Score: 240
Period size: 61 Copynumber: 2.5 Consensus size: 62
509930 CTTTCCCTTT
* *
509940 GTCCTTAAAGAGCAAGACACCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTA
1 GTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTA
* *
510002 GTCCTCAAAGAGCATGACGCC-TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACTTTTTA
1 GTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTA
** *
510063 GTCCTCAAAGAGCGGGACGCCTTTTCCTTTTC
1 GTCCTCAAAGAGCAAGACGCCTTTTTCTTTTC
510095 TCCTTTGCCC
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
61 58 0.68
62 27 0.32
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (62 bp):
GTCCTCAAAGAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTTTA
Found at i:510118 original size:38 final size:38
Alignment explanation
Indices: 510065--510156 Score: 148
Period size: 38 Copynumber: 2.4 Consensus size: 38
510055 ACTTTTTAGT
*
510065 CCTCAAAGAGCGGGACGCCTTTTCCTTTTCTCCTTTGC
1 CCTCAAAGAGCGGGACGCCTTTTCCTTTTCTCCTCTGC
*
510103 CCTCAAAGAGTGGGACGCCTTTTCCTTTTCTCCTCTGC
1 CCTCAAAGAGCGGGACGCCTTTTCCTTTTCTCCTCTGC
* *
510141 CCTCAAAAAGCAGGAC
1 CCTCAAAGAGCGGGAC
510157 ACATTTCATT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.18, C:0.34, G:0.18, T:0.29
Consensus pattern (38 bp):
CCTCAAAGAGCGGGACGCCTTTTCCTTTTCTCCTCTGC
Found at i:510329 original size:42 final size:41
Alignment explanation
Indices: 510063--510437 Score: 184
Period size: 42 Copynumber: 9.0 Consensus size: 41
510053 GCACTTTTTA
* *
510063 GTCCTCAAAGAGCGGGACGC--CT-TT-TCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTATTCTCCTTTT-TCCTTT
* ** * *
510101 GCCCTCAAAGAGTGGGACGC--CT-TT-TCCTTTTCTCCTCT
1 GTCCTCAAAGAGCAGGACGCATTTATTCTCCTTTT-TCCTTT
* * *
510139 GCCCTCAAAAAGCAGGACACATTTCATT-TCCTTTTTTTCCATTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATTCTCC--TTTTTCC--TTT
* * * * * * * *
510184 GTCTTCAAAGAGCAGAATG-TTTTTTTTTCTTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACGCATTTATTCTCCTTTTTCCTTT
* * * *
510224 GTCCTCAAAGAGCAAGACGCACTTCACTTCCTTCTTTTCCCTTCT
1 GTCCTCAAAGAGCAGGACGCA-TTTA-TT-CTCCTTTTTCCTT-T
* *
510269 AGTTCTCAAAGAGTAGGACGCACTTTATTCTCCTTTTTCCTTT
1 -GTCCTCAAAGAGCAGGACGCA-TTTATTCTCCTTTTTCCTTT
* * *
510312 ATCCTCAAAAAGCAGGACACATTTAATT-TCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATTCTCCTTTTTCCTTT
* * * *
510353 GTCTTCAAAGGGTAGGATGCATTTTATT-TCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCA-TTTATTCTCC-TTTTTCCTTT
* * *
510395 GTCCT-TAAGAAGCAGGACCCATTTCATTCT-CTTTTTCTTTT
1 GTCCTCAAAG-AGCAGGACGCATTT-ATTCTCCTTTTTCCTTT
510436 GT
1 GT
510438 TTTTAAAGAG
Statistics
Matches: 260, Mismatches: 56, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
38 51 0.20
40 19 0.07
41 53 0.20
42 60 0.23
43 9 0.03
44 28 0.11
45 18 0.07
46 22 0.08
ACGTcount: A:0.19, C:0.25, G:0.13, T:0.42
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACGCATTTATTCTCCTTTTTCCTTT
Found at i:510389 original size:83 final size:84
Alignment explanation
Indices: 510123--510455 Score: 311
Period size: 83 Copynumber: 3.9 Consensus size: 84
510113 TGGGACGCCT
* * *
510123 TTTCCTTTTCTCCTCTGCCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTTCCATTTTGTCT
1 TTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCC-TTTTTTCC--TTTGTCT
* * *
510188 TCAAAGAGCAGAATG--TTTTT
63 TCAAAGAGTAGGATGCATTTTA
* * * * * * *
510208 TTTTCTTTTTTCTTTTGTCCTCAAAGAGCAAGACGCACTTCACTTCCTTCTTTTCCCTTCTAGT-
1 TTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTT-TTTT-CCTT-T-GTC
* *
510272 TCTCAAAGAGTAGGACGCACTTTA
62 T-TCAAAGAGTAGGATGCATTTTA
* *
510296 TTCTCC-TTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAATTTCC-TTTTTCCTTTGTCTTC
1 TT-TCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTCCTTTGTCTTC
*
510359 AAAGGGTAGGATGCATTTTA
65 AAAGAGTAGGATGCATTTTA
* * * * * *
510379 TTTCCTTTTTTCCTTTGTCCTTAAGAAGCAGGACCCATTTCA-TT-CTCTTTTTCTTTTGTTTTT
1 TTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCT-TTTTTCCTTTGTCTTC
510442 AAAGAGTAGGATGC
65 AAAGAGTAGGATGC
510456 CCCATTCCTT
Statistics
Matches: 200, Mismatches: 36, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
81 1 0.00
82 5 0.03
83 80 0.40
84 6 0.03
85 47 0.23
86 20 0.10
87 1 0.00
88 38 0.19
89 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (84 bp):
TTTCCTTTTTTCCTTTGTCCTCAAAAAGCAGGACACATTTCATTTCCTTTTTTCCTTTGTCTTCA
AAGAGTAGGATGCATTTTA
Found at i:511116 original size:20 final size:20
Alignment explanation
Indices: 511091--511144 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
511081 TTTACCTATA
511091 TTTATCGATACATTATTCAT
1 TTTATCGATACATTATTCAT
* **
511111 TTTATCAATACATGGTTCAT
1 TTTATCGATACATTATTCAT
*
511131 TGTATCGATACATT
1 TTTATCGATACATT
511145 TTGGGCTTAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (20 bp):
TTTATCGATACATTATTCAT
Found at i:513773 original size:78 final size:78
Alignment explanation
Indices: 513606--513834 Score: 316
Period size: 78 Copynumber: 2.9 Consensus size: 78
513596 TCTCATGATT
* *
513606 GGGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATCTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAA-CCCAGTTTTATTTCTAGAACACCAAT-TTTTCACAATCGGGGATACTCCAA
**
513671 CCCCGTTATTTTTGA
64 CCCCGTTATTTTCAA
*
513686 -GGGATACTCCAACCCAGTTTTATTTCCAGAACACCAATTTTTCACAATCGGGGATACTCCAACC
1 GGGGATACTCCAACCCAGTTTTATTTCTAGAACACCAATTTTTCACAATCGGGGATACTCCAACC
513750 CCGTTATTTTCAA
66 CCGTTATTTTCAA
* * * * * *
513763 GGGGATACTCCAACCCTGATTTTATTTCTAGAACACCCATTTTCCATAGTCAGGGGATACTCCAG
1 GGGGATACTCCAACCCAG-TTTTATTTCTAGAACACCAATTTTTCACAATC-GGGGATACTCCAA
513828 CCCCGTT
64 CCCCGTT
513835 GTCATCTCTA
Statistics
Matches: 134, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
77 37 0.28
78 39 0.29
79 39 0.29
80 19 0.14
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (78 bp):
GGGGATACTCCAACCCAGTTTTATTTCTAGAACACCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCAA
Found at i:515778 original size:20 final size:20
Alignment explanation
Indices: 515750--515801 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 20
515740 GTAACTAAAA
* * *
515750 GTATTGATACATTTAGGGAT
1 GTATCGATACATTTAAGAAT
*
515770 GTATCGATACA--AAAGAAT
1 GTATCGATACATTTAAGAAT
515788 GTATCGATACATTT
1 GTATCGATACATTT
515802 TCATGTATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 15 0.60
20 10 0.40
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (20 bp):
GTATCGATACATTTAAGAAT
Found at i:519666 original size:10 final size:10
Alignment explanation
Indices: 519647--519677 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
519637 GTATCGATAC
519647 ATGAACAGTG
1 ATGAACAGTG
*
519657 ATGAATAGTG
1 ATGAACAGTG
519667 ATGAACAGTG
1 ATGAACAGTG
519677 A
1 A
519678 AAAAAATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:523023 original size:21 final size:21
Alignment explanation
Indices: 522998--523052 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
522988 CACTTGCAAC
*
522998 TCATTTCTTTTCTCCTCTAAT
1 TCATTTATTTTCTCCTCTAAT
**
523019 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCCTCTAAT
* *
523040 TCACTTAATTTCT
1 TCATTTATTTTCT
523053 TTTCAAGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCCTCTAAT
Found at i:523053 original size:21 final size:21
Alignment explanation
Indices: 523013--523056 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
523003 TCTTTTCTCC
* *
523013 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
523034 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
523055 TC
1 TC
523057 AAGAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:525198 original size:52 final size:52
Alignment explanation
Indices: 525115--525219 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
525105 GTTGGACTCA
* *
525115 ATATATCGATACTATTCACAATGTATTGATACATGAACAGTGATGAACAGTG
1 ATATATCGATACTATTCAAAATGTATCGATACATGAACAGTGATGAACAGTG
525167 ATATATCGATACTATTCAAAATGTATCGATACATGAACAGTGATGAACAGTG
1 ATATATCGATACTATTCAAAATGTATCGATACATGAACAGTGATGAACAGTG
525219 A
1 A
525220 AAAATCTTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (52 bp):
ATATATCGATACTATTCAAAATGTATCGATACATGAACAGTGATGAACAGTG
Found at i:525308 original size:20 final size:20
Alignment explanation
Indices: 525283--525337 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
525273 TTTTACCTAG
*
525283 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
525303 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
525323 ATGTATCGATACATT
1 ATGTATCGATACATT
525338 CTGTCTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:525360 original size:26 final size:26
Alignment explanation
Indices: 525324--525374 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
525314 CATGTATGAA
525324 TGTATCGATACATTCTGTCTTTTTAT
1 TGTATCGATACATTCTGTCTTTTTAT
*
525350 TGTATTGATACATTCTGTCTTTTTA
1 TGTATCGATACATTCTGTCTTTTTA
525375 CCCAGATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.55
Consensus pattern (26 bp):
TGTATCGATACATTCTGTCTTTTTAT
Found at i:528538 original size:27 final size:27
Alignment explanation
Indices: 528497--528557 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
528487 TTATGAGGTG
*
528497 AATGTCGGATCGTCTCATCAGGCAATA
1 AATGTCAGATCGTCTCATCAGGCAATA
*
528524 AATGTCAGATTGTCTCATCAGGCAATA
1 AATGTCAGATCGTCTCATCAGGCAATA
528551 AATGTCA
1 AATGTCA
528558 TTTCAATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (27 bp):
AATGTCAGATCGTCTCATCAGGCAATA
Found at i:536853 original size:15 final size:16
Alignment explanation
Indices: 536833--536862 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
536823 TCTATCAAAC
536833 CTGCCAGTG-TTGGTA
1 CTGCCAGTGCTTGGTA
536848 CTGCCAGTGCTTGGT
1 CTGCCAGTGCTTGGT
536863 CATCCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.23, G:0.33, T:0.33
Consensus pattern (16 bp):
CTGCCAGTGCTTGGTA
Found at i:539097 original size:1 final size:1
Alignment explanation
Indices: 539091--539175 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
539081 CTTTCGTACC
* * * ** * * ** *
539091 AAAAAAAACAAAACAAAAACAAAAAAAACCAAGAAAAAAAAATAAAAAAAAAACTAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
539156 AAAAAACAAACAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAA
539176 GGGGTCCAGA
Statistics
Matches: 61, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.85, C:0.12, G:0.01, T:0.02
Consensus pattern (1 bp):
A
Found at i:539110 original size:11 final size:10
Alignment explanation
Indices: 539091--539175 Score: 77
Period size: 10 Copynumber: 8.4 Consensus size: 10
539081 CTTTCGTACC
539091 AAAAAAAACA
1 AAAAAAAACA
539101 AAACAAAAACA
1 AAA-AAAAACA
*
539112 AAAAAAACCA
1 AAAAAAAACA
539122 AGAAAAAAA-A
1 A-AAAAAAACA
539132 ATAAAAAAA-A
1 A-AAAAAAACA
*
539142 AACTAAAAACA
1 AA-AAAAAACA
539153 AAAAAAAA-A
1 AAAAAAAACA
* *
539162 CAAACAAACA
1 AAAAAAAACA
539172 AAAA
1 AAAA
539176 GGGGTCCAGA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
9 8 0.13
10 35 0.56
11 19 0.31
ACGTcount: A:0.85, C:0.12, G:0.01, T:0.02
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:540613 original size:89 final size:87
Alignment explanation
Indices: 540403--541011 Score: 540
Period size: 89 Copynumber: 6.9 Consensus size: 87
540393 CTAGAACGTT
* ** *
540403 CATCTCTTCAAAACCCACACAAGT-TGATGGCAACTCTTTTTTCAAAGCGTACAAGTCAGTGGCA
1 CATCTCTTCAAAACCC-CACAAGTCAG-TGGC-ACTC--TTTTCAAAGCCCACAAGTCAGTGGAA
* *
540467 -TCTCTTCAAAAGCCCACAAGTCGATGG
61 CTCTTTTC-AAAGCCCACAAGTCAATGG
* * * *
540494 CA-CCCTTTCAAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTCGGTGGAAAC
1 CATCTC-TTCAAAACCC-CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGG-AAC
540558 TCTTTTCAAAGCCCACAAGTCAATGG
62 TCTTTTCAAAGCCCACAAGTCAATGG
** **
540584 CATCTCTTCAAAATACCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACACAAGTTGGTGGCAACT
1 CATCTCTTCAAAACCCCACAAGTCAGTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGG-AACT
*
540648 CTTTTCAAAGCCCACAAGTCAGTGG
63 CTTTTCAAAGCCCACAAGTCAATGG
* * * * *
540673 CATCTCTTCAAAAGCCCATAAGTCGGTGGCAC-CCTTTCAAAGCCCACACAAGTCGGTGGCAACT
1 CATCTCTTCAAAACCCCACAAGTCAGTGGCACTCTTTTCAAAG-CC-CACAAGTCAGTGG-AACT
*
540737 CTTTTCAAAGCTCACAAGTCAATGG
63 CTTTTCAAAGCCCACAAGTCAATGG
** * * * * * * * *
540762 CATCTCTTCAAAAGACCACAAGTTAATGGCA-TCCTTTCAAAGCCCATAGGTTAGTGGCAC-CCT
1 CATCTCTTCAAAACCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGAACTCTT
*
540825 TTCAAAGCTCACAAGTCAATGG
66 TTCAAAGCCCACAAGTCAATGG
* * * *
540847 CA-CTCTTTCAAAGCCCACACAAGTTAGTGGCAACTCTTTTCAAAGCCCACAAGTAAGTGGTA-T
1 CATCTC-TTCAAAACCC-CACAAGTCAGTGGC-ACTCTTTTCAAAGCCCACAAGTCAGTGGAACT
* * * *
540910 CTCTTCAAAGCCCAAAAGTGAGTGG
63 CTTTTCAAAGCCCACAAGTCAATGG
* * * *
540935 CATC-CTTTCACAA-CCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCATCGC
1 CATCTC-TTCAAAACCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGG-AACTC
*
540997 CTTTCAAAGCCCACA
64 TTTTCAAAGCCCACA
541012 CAAGTCGGTG
Statistics
Matches: 440, Mismatches: 62, Indels: 37
0.82 0.12 0.07
Matches are distributed among these distances:
84 26 0.06
85 35 0.08
86 41 0.09
87 22 0.05
88 57 0.13
89 192 0.44
90 30 0.07
91 36 0.08
92 1 0.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (87 bp):
CATCTCTTCAAAACCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGAACTCTT
TTCAAAGCCCACAAGTCAATGG
Found at i:540819 original size:28 final size:28
Alignment explanation
Indices: 540442--541011 Score: 447
Period size: 30 Copynumber: 19.5 Consensus size: 28
540432 GCAACTCTTT
**
540442 TTTCAAAGCGTACAAGTCAGTGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
540469 TCTTCAAAAGCCCACAAGTC-GATGGCACCC
1 T-TTC-AAAGCCCACAAGTCAG-TGGCATCC
* *
540499 TTTCAAAGCCCACACAAGTCGGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
* * *
540531 TTTCAAAGCCCACAAGTCGGTGGAAACTCT
1 TTTCAAAGCCCACAAGTCAGTGG-CA-TCC
*
540561 TTTCAAAGCCCACAAGTCAATGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
**
540588 TCTTCAAAATACCACAAGTCAGTGGCA-CC
1 T-TTC-AAAGCCCACAAGTCAGTGGCATCC
** *
540617 TTTTCAAAGCCCACACAAGTTGGTGGCAACTCT
1 -TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
540650 TTTCAAAGCCCACAAGTCAGTGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
540677 TCTTCAAAAGCCCATAAGTCGGTGGCACCC
1 T-TTC-AAAGCCCACAAGTCAGTGGCATCC
* *
540707 TTTCAAAGCCCACACAAGTCGGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
* *
540739 TTTCAAAGCTCACAAGTCAATGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
540766 TCTTCAAAAGACCACAAGTTAATGGCATCC
1 T-TTC-AAAGCCCACAAGTCAGTGGCATCC
* * * *
540796 TTTCAAAGCCCATAGGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
540824 TTTCAAAGCTCACAAGTCAATGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* *
540852 TTTCAAAGCCCACACAAGTTAGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
* *
540884 TTTCAAAGCCCACAAGTAAGTGGTAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
540911 TCTTCAAAGCCCAAAAGTGAGTGGCATCC
1 T-TTCAAAGCCCACAAGTCAGTGGCATCC
*
540940 TTTCACAA-CCCACAAGTCAGTGGCACCC
1 TTTCA-AAGCCCACAAGTCAGTGGCATCC
540968 TTTCAAAGCCCACAAGTCAGTGGCATCGCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT--CC
540998 TTTCAAAGCCCACA
1 TTTCAAAGCCCACA
541012 CAAGTCGGTG
Statistics
Matches: 444, Mismatches: 58, Indels: 79
0.76 0.10 0.14
Matches are distributed among these distances:
27 8 0.02
28 141 0.32
29 100 0.23
30 147 0.33
31 12 0.03
32 34 0.08
33 2 0.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:541054 original size:84 final size:80
Alignment explanation
Indices: 540777--541054 Score: 199
Period size: 88 Copynumber: 3.3 Consensus size: 80
540767 CTTCAAAAGA
* * * * * *
540777 CCAC-AAGTTAATGGCATCCTTTCAAAGCCCATAGGTTAGTGGCA-CCCTTTCAAAGCTCACAAG
1 CCACAAAGTTAGTGGCA-CCTTTCAAAGCCCACAAGTAAGTGGCATCCC-TTCAAAGCCCAAAAG
* *
540840 TCAATGGCACTCTTTCAAAGC
64 TGAGTGG--C-CTTTC-AAGC
* *
540861 CCACACAAGTTAGTGGCAACTCTTTTCAAAGCCCACAAGTAAGTGGTATCTCTTCAAAGCCCAAA
1 CCACA-AAGTTAGTGGC-AC-C-TTTCAAAGCCCACAAGTAAGTGGCATCCCTTCAAAGCCCAAA
*
540926 AGTGAGTGGCATCCTTTCACAAC
62 AGTGAGTGG---CCTTTCA-AGC
* *
540949 CCAC-AAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCATCGCCTTTCAAAGCCCACAC
1 CCACAAAGTTAGTGGCA-CCTTTCAAAGCCCACAAGTAAGTGGCATC-CC-TTCAAAGCCCA-A-
541013 AAGTCG-GTGG-C-TTCGAAGC
61 AAGT-GAGTGGCCTTTC-AAGC
541032 CCACATAAGTTAGTGGCACCTTT
1 CCACA-AAGTTAGTGGCACCTTT
541055 TTTTAAAAGC
Statistics
Matches: 158, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
83 9 0.06
84 36 0.23
85 14 0.09
86 33 0.21
87 4 0.03
88 58 0.37
89 4 0.03
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.23
Consensus pattern (80 bp):
CCACAAAGTTAGTGGCACCTTTCAAAGCCCACAAGTAAGTGGCATCCCTTCAAAGCCCAAAAGTG
AGTGGCCTTTCAAGC
Found at i:541068 original size:116 final size:116
Alignment explanation
Indices: 540455--541054 Score: 430
Period size: 119 Copynumber: 5.2 Consensus size: 116
540445 CAAAGCGTAC
* *
540455 AAGTCAGTGGCAT-CTCTTCAAAAGCCCACAAGTCGATGGCACCCTTTCAAAGCCCACACAAGTC
1 AAGTGAGTGGCATCCT-TTCAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTC
* * * * ** *
540519 GGTGGCAACTCTTTTCAAAGCCCACAAGTC-GGTGGAAACTCTTTTCAAAGCCCAC
65 AGTGGCAACGCCTTTCAAAGCCCACAAG-CAAGTGG--A-TCGCTTCAAAGCCCAA
* * ** * * *
540574 AAGTCAATGGCAT-CTCTTCAAAATACCACAAGTCAGTGGCACCTTTTCAAAGCCCACACAAGTT
1 AAGTGAGTGGCATCCT-TTCAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTC
* * * * *
540638 GGTGGCAACTCTTTTCAAAGCCCACAAGTC-AGTGGCATCTCTTCAAAAGCCCAT
65 AGTGGCAACGCCTTTCAAAGCCCACAAG-CAAGTGG-ATCGCTTC-AAAGCCCAA
* ** * *
540692 AAGTCG-GTGGCACCCTTTC-AAAGCCCACACAAGTCGGTGGCAACTCTTTTCAAAG--CTCACA
1 AAGT-GAGTGGCATCCTTTCAAAAG-CC-CACAAGTCAATGGC-AC-CCTTTCAAAGCCCACACA
* * * * * *
540753 AGTCAATGGCATC-TC-TTCAAAAGACCACAAGTTAA-TGGCATC-CTTTCAAAGCCCAT
61 AGTCAGTGGCAACGCCTTTC-AAAGCCCACAAG-CAAGTGG-ATCGC-TTCAAAGCCCAA
* * * * * *
540809 AGGTTAGTGGCACCCTTTC-AAAGCTCACAAGTCAATGGCACTCTTTCAAAGCCCACACAAGTTA
1 AAGTGAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTCA
* * * *
540873 GTGGCAACTCTTTTCAAAGCCCACAAGTAAGTGGTATCTCTTCAAAGCCCAA
66 GTGGCAACGCCTTTCAAAGCCCACAAGCAAGTGG-ATCGCTTCAAAGCCCAA
* *
540925 AAGTGAGTGGCATCCTTTCACAA-CCCACAAGTCAGTGGCACCCTTTCAAAG-CC-CACAAGTCA
1 AAGTGAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTCA
* * *
540987 GTGGCATCGCCTTTCAAAGCCCAC-A-CAAGTCGG-TGGCTTCGAAGCCCACA
66 GTGGCAACGCCTTTCAAAGCCCACAAGCAAGT-GGATCGCTTCAAAGCCCA-A
*
541037 TAAGTTAGTGGCA-CCTTT
1 -AAGTGAGTGGCATCCTTT
541055 TTTTAAAAGC
Statistics
Matches: 402, Mismatches: 58, Indels: 49
0.79 0.11 0.10
Matches are distributed among these distances:
111 12 0.03
112 10 0.02
113 22 0.05
114 31 0.08
115 32 0.08
116 70 0.17
117 48 0.12
118 44 0.11
119 121 0.30
120 2 0.00
121 10 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (116 bp):
AAGTGAGTGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCCCACACAAGTCA
GTGGCAACGCCTTTCAAAGCCCACAAGCAAGTGGATCGCTTCAAAGCCCAA
Found at i:541189 original size:45 final size:46
Alignment explanation
Indices: 541125--541291 Score: 178
Period size: 48 Copynumber: 3.6 Consensus size: 46
541115 AAGTCGGATA
* *
541125 TCGCTGGCATTGAATCAGCATATTGG-CACCTTTT-TTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCCA-CTTTTCTTAGCTCAATG
* *
541170 TCGCTGGCCTTGTATCAGCACATTGTCCACTTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGGCCACTTTT--CTTAGCTCAATG
** *
541218 TCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCCTTAG-TCGATG
1 TCGCTGGCCTTGAATCAGCACATTGGCCACTTTT--CTTAGCTCAATG
* **
541265 TCGTTGGCCTTGAATTGGCACATTGGC
1 TCGCTGGCCTTGAATCAGCACATTGGC
541292 ACTCCTCTCA
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
45 27 0.25
46 2 0.02
47 27 0.25
48 50 0.47
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.35
Consensus pattern (46 bp):
TCGCTGGCCTTGAATCAGCACATTGGCCACTTTTCTTAGCTCAATG
Found at i:541286 original size:47 final size:48
Alignment explanation
Indices: 541159--541288 Score: 199
Period size: 48 Copynumber: 2.7 Consensus size: 48
541149 GGCACCTTTT
* *
541159 TTAGCTCAATGTCGCTGGCCTTGTATCAGCACATTGTCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
541207 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
* * **
541255 TTAG-TCGATGTCGTTGGCCTTGAATTGGCACATT
1 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATT
541289 GGCACTCCTC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
47 26 0.34
48 50 0.66
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.35
Consensus pattern (48 bp):
TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTATCCACTTTTCCC
Found at i:542050 original size:20 final size:20
Alignment explanation
Indices: 542025--542076 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
542015 TACCTAGATG
*
542025 TATCGATACATTTTTCAATA
1 TATCGATACATTTATCAATA
* * *
542045 TATCGATACATGTATGAATG
1 TATCGATACATTTATCAATA
542065 TATCGATACATT
1 TATCGATACATT
542077 CTGTTTTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTTATCAATA
Found at i:542118 original size:20 final size:20
Alignment explanation
Indices: 542093--542148 Score: 94
Period size: 21 Copynumber: 2.8 Consensus size: 20
542083 TTTTGCCCAG
*
542093 ATGTATTGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
542113 ATGTATCGATACATTTTTTCA
1 ATGTATCGATACA-TTTTTCA
542134 ATGTATCGATACATT
1 ATGTATCGATACATT
542149 CTGTCTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.46
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:542169 original size:72 final size:72
Alignment explanation
Indices: 542011--542199 Score: 290
Period size: 72 Copynumber: 2.6 Consensus size: 72
542001 GAAAGTCACA
* *
542011 TTTTTACCTAGATGTATCGATACATTTTTCAATATATCGATACA-TGTATGAATGTATCGATACA
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTGTATCAATGTATCGATACA
*
542075 TTCTGTT
66 TTCTGTC
* * * * *
542082 TTTTTGCCCAGATGTATTGATACATTTTTCAATGTATCGATACATTTTTTCAATGTATCGATACA
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTGTATCAATGTATCGATACA
542147 TTCTGTC
66 TTCTGTC
*
542154 TTTTTACCTAGATGTATCGATACATTCTTCAATGTATCGATACATT
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATT
542200 CTATTTTTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
71 40 0.38
72 65 0.62
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (72 bp):
TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTGTATCAATGTATCGATACA
TTCTGTC
Found at i:542195 original size:51 final size:51
Alignment explanation
Indices: 542113--542250 Score: 206
Period size: 51 Copynumber: 2.7 Consensus size: 51
542103 ACATTTTTCA
*
542113 ATGTATCGATACATTTTTTCAATGTATCGATACATTCTGTCTTT-TTACCTAG
1 ATGTATCGATACA-TTTTTCAATGTATCGATACATTCTATCTTTCTTACC-AG
* * *
542165 ATGTATCGATACATTCTTCAATGTATCGATACATTCTATTTTTCTTTCCAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTCTTACCAG
*
542216 GTGTATCGATACATTTTTCAATGTATCGATACATT
1 ATGTATCGATACATTTTTCAATGTATCGATACATT
542251 TAGTTAAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
51 62 0.78
52 17 0.22
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (51 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTCTTACCAG
Found at i:544168 original size:11 final size:11
Alignment explanation
Indices: 544152--544176 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
544142 TAGAACCTTC
544152 AAATAAATTCG
1 AAATAAATTCG
544163 AAATAAATTCG
1 AAATAAATTCG
544174 AAA
1 AAA
544177 AGAAGCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (11 bp):
AAATAAATTCG
Found at i:546102 original size:33 final size:32
Alignment explanation
Indices: 546060--546127 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
546050 CGTTACAAGC
*
546060 CAATGTATCGATACATTTTGGGATGTATCAATA
1 CAATGTATCGATACATATTGGG-TGTATCAATA
* *
546093 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCAATA
546125 CAA
1 CAA
546128 ATAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCAATA
Found at i:546215 original size:20 final size:21
Alignment explanation
Indices: 546168--546220 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
546158 ACCAATCACC
*
546168 TGTATCGATACATTCTTTGCA
1 TGTATCGATACATTCTGTGCA
*
546189 AGTATCGATACATT-TG-GTCA
1 TGTATCGATACATTCTGTG-CA
546209 TGTATCGATACA
1 TGTATCGATACA
546221 ATGTATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 14 0.50
21 13 0.46
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTGCA
Found at i:546265 original size:20 final size:19
Alignment explanation
Indices: 546242--546280 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
546232 CTTTGCATTA
*
546242 TGTATCGATACATTTGAAGG
1 TGTATCAATACATTT-AAGG
546262 TGTATCAATACATTTAAGG
1 TGTATCAATACATTTAAGG
546281 GTTTTGACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (19 bp):
TGTATCAATACATTTAAGG
Found at i:548737 original size:33 final size:33
Alignment explanation
Indices: 548695--548759 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
548685 ATAAACCCTT
548695 TGTATCGATACAGAGAATGCTGCATCGATACAA
1 TGTATCGATACAGAGAATGCTGCATCGATACAA
* *
548728 TGTATCGATATAGAGAATGCTGTATCGATACA
1 TGTATCGATACAGAGAATGCTGCATCGATACA
548760 TCTAAGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (33 bp):
TGTATCGATACAGAGAATGCTGCATCGATACAA
Found at i:554913 original size:13 final size:13
Alignment explanation
Indices: 554895--554920 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
554885 ACATTTTGGG
554895 ATGTATCGATACA
1 ATGTATCGATACA
554908 ATGTATCGATACA
1 ATGTATCGATACA
554921 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:554937 original size:32 final size:33
Alignment explanation
Indices: 554873--554940 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
554863 CGTTACAAGC
* *
554873 CAATGTATTGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
*
554906 CAATGTATCGATACATATTGTG-TGTATCGATA
1 CAATGTATCGATACATATTGGGATGTATCGATA
554938 CAA
1 CAA
554941 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (33 bp):
CAATGTATCGATACATATTGGGATGTATCGATA
Found at i:556666 original size:17 final size:17
Alignment explanation
Indices: 556644--556706 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
556634 TGGTGGTTGT
556644 TGTCTTCTTCTTGCTGC
1 TGTCTTCTTCTTGCTGC
* **
556661 TGTCTTTTTCTTGCAAC
1 TGTCTTCTTCTTGCTGC
*
556678 -GATCTTCTTCTTACTGC
1 TG-TCTTCTTCTTGCTGC
* *
556695 TATCTTTTTCTT
1 TGTCTTCTTCTT
556707 CCAGTTGGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
16 1 0.03
17 34 0.97
ACGTcount: A:0.08, C:0.25, G:0.11, T:0.56
Consensus pattern (17 bp):
TGTCTTCTTCTTGCTGC
Found at i:557264 original size:13 final size:13
Alignment explanation
Indices: 557246--557303 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
557236 ATTTTTTTTA
557246 TATTATAATATTT
1 TATTATAATATTT
557259 TATTAT-ATATTT
1 TATTATAATATTT
*
557271 TATTATTATTATTAT
1 TATTA-TAATATT-T
557286 T-TTATATATATTT
1 TATTATA-ATATTT
557299 T-TTAT
1 TATTAT
557304 TTTATTAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 11 0.28
13 15 0.38
14 11 0.28
15 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTATAATATTT
Found at i:557264 original size:18 final size:18
Alignment explanation
Indices: 557238--557308 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 18
557228 TGGGATTTAT
*
557238 TTTTTTTATATTATAATA
1 TTTTATTATATTATAATA
* *
557256 TTTTATTATATATTTTATTA
1 TTTTA-T-TATATTATAATA
*
557276 TTATTATTATTTTATATATA
1 TT-TTATTATATTATA-ATA
*
557296 TTTT-TTATTTTAT
1 TTTTATTATATTAT
557309 TAGTTTATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 13 0.30
19 10 0.23
20 17 0.40
21 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATATTATAATA
Found at i:557270 original size:12 final size:12
Alignment explanation
Indices: 557246--557310 Score: 62
Period size: 12 Copynumber: 5.4 Consensus size: 12
557236 ATTTTTTTTA
557246 TATTATAATATTT
1 TATTAT-ATATTT
557259 TATTATATATTT
1 TATTATATATTT
557271 TATTAT-TATTAT
1 TATTATATATT-T
* *
557283 TATTTTATA-TA
1 TATTATATATTT
* *
557294 TATTTTTTATTT
1 TATTATATATTT
557306 TATTA
1 TATTA
557311 GTTTATATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 12 0.27
12 24 0.55
13 8 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTATATATTT
Found at i:557279 original size:28 final size:28
Alignment explanation
Indices: 557241--557318 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
557231 GATTTATTTT
557241 TTTTA-TATTA-TAATATTTTATTATATA
1 TTTTATTATTATTAATATTTTA-TATATA
*
557268 TTTTATTATTATTATTATTTTATATATA
1 TTTTATTATTATTAATATTTTATATATA
* *
557296 TTTT-TTATT-TTATTAGTTTATAT
1 TTTTATTATTATTAATATTTTATAT
557319 TAAATAAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
26 13 0.28
27 10 0.21
28 15 0.32
29 9 0.19
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (28 bp):
TTTTATTATTATTAATATTTTATATATA
Found at i:557290 original size:26 final size:26
Alignment explanation
Indices: 557261--557318 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
557251 TAATATTTTA
*
557261 TTATATAT-TTTATTATTATTATTATT
1 TTATATATATTTATTATT-TTATTAGT
*
557287 TTATATATATTTTTTATTTTATTAGT
1 TTATATATATTTATTATTTTATTAGT
557313 TTATAT
1 TTATAT
557319 TAAATAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATATATATTTATTATTTTATTAGT
Found at i:557320 original size:42 final size:42
Alignment explanation
Indices: 557234--557320 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
557224 TCAGTGGGAT
*
557234 TTATTTTTTTTATATTATAATATTTTATTATATATTTTATTA
1 TTATTTTTTTTATATTATAATATTTTATTATATAGTTTATTA
* *
557276 TTATTATTATTTTATA-TAT-ATTTTTTATTTTATTAGTTTA-TA
1 TTATT-TT-TTTTATATTATAATATTTTATTATA-TAGTTTATTA
557318 TTA
1 TTA
557321 AATAAATCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
42 21 0.54
43 11 0.28
44 7 0.18
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (42 bp):
TTATTTTTTTTATATTATAATATTTTATTATATAGTTTATTA
Found at i:558084 original size:97 final size:97
Alignment explanation
Indices: 557879--558104 Score: 265
Period size: 97 Copynumber: 2.3 Consensus size: 97
557869 TCATGATGAT
* * *
557879 ACTCC-AACCCATTCTTTCGAGGGGATACTCCAACCTCATTTTTAAACTCGTTAAGATTGAAACC
1 ACTCCAAACCCATTCTTTCGAAGGGATACTCCAACCCCATTTTTAAACTCGTCAAGATTGAAACC
* ** *
557943 TTATTTTTGCTTAAATTATCATCATTGGGGAT
66 TTATTTTTGCCTAAATTATCATCATAAGGGAC
* * * * * **
557975 ACTCCAAACCCATTCTTTCGAAGGAATACTCCAACCCCTTTTTTAAATTTGTCAAGATTTAAATT
1 ACTCCAAACCCATTCTTTCGAAGGGATACTCCAACCCCATTTTTAAACTCGTCAAGATTGAAACC
* *
558040 TTATTTTTGCCTAAATTGTCATCATAAGTGAC
66 TTATTTTTGCCTAAATTATCATCATAAGGGAC
* ** *
558072 ACTCTAGCCCCATTCTTCCGAAGGGATACTCCA
1 ACTCCAAACCCATTCTTTCGAAGGGATACTCCA
558105 TCCCTGTTTT
Statistics
Matches: 108, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
96 5 0.05
97 103 0.95
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (97 bp):
ACTCCAAACCCATTCTTTCGAAGGGATACTCCAACCCCATTTTTAAACTCGTCAAGATTGAAACC
TTATTTTTGCCTAAATTATCATCATAAGGGAC
Found at i:559219 original size:164 final size:164
Alignment explanation
Indices: 559024--559341 Score: 512
Period size: 164 Copynumber: 1.9 Consensus size: 164
559014 ATCGCAACCA
* ** *
559024 CATAGATTATCATTGTTAGGTGTGAACACCAGCAGATGGGGTTAATGGTATTGGCTGTTGTT-GA
1 CATAGATTATCATTGTTAGGTGTGAACACCAGCAGATGGGGCTAACAGTATTGGCTGCTGTTAGA
559088 CGTAAAGCCTAACAATGAGGCCTGCCTTACATGAGGTGTCACTGGGATGCAAACCTTGATAGCAG
66 CGTAAAGCCTAACAATGAGGCCTGCCTTACATGAGGTGTCACT-GGATGCAAACCTTGATAGCAG
559153 CCACCTGTACAAGCACTGAATGCCAGTCACAACAG
130 CCACCTGTACAAGCACTGAATGCCAGTCACAACAG
559188 CATAGATTATCATTGTTAGGTGTGAACACCAGCAGATGGGGCTAACAGTATTGGCTGCTGTTAGA
1 CATAGATTATCATTGTTAGGTGTGAACACCAGCAGATGGGGCTAACAGTATTGGCTGCTGTTAGA
* * * ** *
559253 CGTAAAGCCTAATAATGAGGTCTGTCTTACATGAGGTGTCACTGGATGTGAACCTTGATAGCAGT
66 CGTAAAGCCTAACAATGAGGCCTGCCTTACATGAGGTGTCACTGGATGCAAACCTTGATAGCAGC
**
559318 CACCTGTACAAGTGCTGAATGCCA
131 CACCTGTACAAGCACTGAATGCCA
559342 ACAAGCATCT
Statistics
Matches: 141, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
164 99 0.70
165 42 0.30
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (164 bp):
CATAGATTATCATTGTTAGGTGTGAACACCAGCAGATGGGGCTAACAGTATTGGCTGCTGTTAGA
CGTAAAGCCTAACAATGAGGCCTGCCTTACATGAGGTGTCACTGGATGCAAACCTTGATAGCAGC
CACCTGTACAAGCACTGAATGCCAGTCACAACAG
Found at i:560345 original size:15 final size:15
Alignment explanation
Indices: 560327--560357 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
560317 GTCTTAACTA
560327 AGGAGGATTTAAGGT
1 AGGAGGATTTAAGGT
560342 AGGAGGATTTAAGGT
1 AGGAGGATTTAAGGT
560357 A
1 A
560358 ACATATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (15 bp):
AGGAGGATTTAAGGT
Found at i:566458 original size:38 final size:37
Alignment explanation
Indices: 566415--566488 Score: 103
Period size: 38 Copynumber: 2.0 Consensus size: 37
566405 ATACCGCTAG
566415 CTTGTGCAGGCTTTGACTCAAACTTAGGTTGCCACCAA
1 CTTGTGCAGGCTTTGACTCAAAC-TAGGTTGCCACCAA
** **
566453 CTTGTGTGGGCTTTGACTCGGACTAGGTTGCCACCA
1 CTTGTGCAGGCTTTGACTCAAACTAGGTTGCCACCA
566489 GCTCCTATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 13 0.41
38 19 0.59
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (37 bp):
CTTGTGCAGGCTTTGACTCAAACTAGGTTGCCACCAA
Found at i:567009 original size:13 final size:13
Alignment explanation
Indices: 566991--567056 Score: 91
Period size: 13 Copynumber: 5.2 Consensus size: 13
566981 AATGAAAGGG
566991 TCTTGACAAAAGT
1 TCTTGACAAAAGT
567004 TCTTGACAAAA-T
1 TCTTGACAAAAGT
567016 TCTTGAC-AAAGT
1 TCTTGACAAAAGT
* *
567028 TTTTGACAAATGT
1 TCTTGACAAAAGT
*
567041 TCTCGACAAAAGT
1 TCTTGACAAAAGT
567054 TCT
1 TCT
567057 AAATTATATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
11 3 0.07
12 15 0.33
13 28 0.61
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (13 bp):
TCTTGACAAAAGT
Found at i:567022 original size:25 final size:26
Alignment explanation
Indices: 566991--567056 Score: 91
Period size: 24 Copynumber: 2.6 Consensus size: 26
566981 AATGAAAGGG
566991 TCTTGACAAAAGTTCTTGACAAA-AT
1 TCTTGACAAAAGTTCTTGACAAATAT
* *
567016 TCTTGAC-AAAGTTTTTGACAAATGT
1 TCTTGACAAAAGTTCTTGACAAATAT
*
567041 TCTCGACAAAAGTTCT
1 TCTTGACAAAAGTTCT
567057 AAATTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.40
25 14 0.40
26 7 0.20
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (26 bp):
TCTTGACAAAAGTTCTTGACAAATAT
Found at i:567399 original size:28 final size:27
Alignment explanation
Indices: 567368--567457 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 27
567358 GACTTTAATG
* * *
567368 GGGATTGCTATTCGTCTTGTTTCCACTA
1 GGGATTGCAATT-GTCCTGATTCCACTA
* *
567396 GGGATTGGAATTTTCCTGATTCCACTA
1 GGGATTGCAATTGTCCTGATTCCACTA
* * * **
567423 GGGATTGTAGGTTGTCCAGGCTCCACTA
1 GGGATTGCA-ATTGTCCTGATTCCACTA
567451 GGGATTG
1 GGGATTG
567458 TAGGTTATCC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
27 20 0.40
28 30 0.60
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.36
Consensus pattern (27 bp):
GGGATTGCAATTGTCCTGATTCCACTA
Found at i:567458 original size:28 final size:28
Alignment explanation
Indices: 567389--567511 Score: 140
Period size: 28 Copynumber: 4.4 Consensus size: 28
567379 TCGTCTTGTT
* * * * *
567389 TCCACTAGGGATTGGA-ATTTTCCTGAT
1 TCCACTAGGGATTGTAGGTTGTCCAGAC
*
567416 TCCACTAGGGATTGTAGGTTGTCCAGGC
1 TCCACTAGGGATTGTAGGTTGTCCAGAC
* *
567444 TCCACTAGGGATTGTAGGTTATCCAAAC
1 TCCACTAGGGATTGTAGGTTGTCCAGAC
*
567472 TCCACTAGGGATTGTAAGTTGTCCAGAC
1 TCCACTAGGGATTGTAGGTTGTCCAGAC
* *
567500 TTCACTAAGGAT
1 TCCACTAGGGAT
567512 ACGACATAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 15 0.19
28 66 0.81
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (28 bp):
TCCACTAGGGATTGTAGGTTGTCCAGAC
Found at i:571769 original size:21 final size:21
Alignment explanation
Indices: 571745--571803 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
571735 AAAGACTTTA
*
571745 AAAAAATAAAATAAAAAAGTC
1 AAAAAATAAAATAAAAAAATC
*
571766 AAAAAAT-ATATGAAAAAAATC
1 AAAAAATAAAAT-AAAAAAATC
571787 AAGAAAATAAAATAAAA
1 AA-AAAATAAAATAAAA
571804 CAAGGGTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 3 0.09
21 17 0.53
22 9 0.28
23 3 0.09
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.15
Consensus pattern (21 bp):
AAAAAATAAAATAAAAAAATC
Found at i:572718 original size:28 final size:28
Alignment explanation
Indices: 572651--572739 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 28
572641 TTTATGTCAT
* * *
572651 ATCCTTAATGGAGTCTGGACAACTTGCT
1 ATCCCTAATGGAGTCTAGACAACTTGCA
* * *
572679 ATACTTAGTGGAGTCTAGACAACTTGCA
1 ATCCCTAATGGAGTCTAGACAACTTGCA
* * *
572707 ATCCCTAATGGAGCCTAGACAACCTACA
1 ATCCCTAATGGAGTCTAGACAACTTGCA
572735 ATCCC
1 ATCCC
572740 CAGTGGAATC
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 51 1.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (28 bp):
ATCCCTAATGGAGTCTAGACAACTTGCA
Found at i:572746 original size:28 final size:28
Alignment explanation
Indices: 572685--572746 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
572675 TGCTATACTT
* * * *
572685 AGTGGAGTCTAGACAACTTGCAATCCCT
1 AGTGGAGCCTAGACAACCTACAATCCCC
*
572713 AATGGAGCCTAGACAACCTACAATCCCC
1 AGTGGAGCCTAGACAACCTACAATCCCC
572741 AGTGGA
1 AGTGGA
572747 ATCAGGAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.19
Consensus pattern (28 bp):
AGTGGAGCCTAGACAACCTACAATCCCC
Found at i:573132 original size:12 final size:12
Alignment explanation
Indices: 573115--573161 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
573105 GTTGAGAATG
573115 TTTGTCAAAAAC
1 TTTGTCAAAAAC
573127 TTTGTC-AAAAC
1 TTTGTCAAAAAC
*
573138 TTTCGTCAAGAAC
1 TTT-GTCAAAAAC
573151 TTGTGTCAAAA
1 TT-TGTCAAAA
573162 CCCTTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
11 8 0.27
12 9 0.30
13 12 0.40
14 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (12 bp):
TTTGTCAAAAAC
Found at i:573158 original size:13 final size:11
Alignment explanation
Indices: 573115--573162 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 11
573105 GTTGAGAATG
573115 TTTGTCAAAAAC
1 TTTGTC-AAAAC
573127 TTTGTCAAAAC
1 TTTGTCAAAAC
573138 TTTCGTCAAGAAC
1 TTT-GTCAA-AAC
573151 TTGTGTCAAAAC
1 TT-TGTCAAAAC
573163 CCTTTCATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.24
12 14 0.42
13 10 0.30
14 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (11 bp):
TTTGTCAAAAC
Found at i:573175 original size:27 final size:24
Alignment explanation
Indices: 573119--573176 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 24
573109 AGAATGTTTG
* *
573119 TCAAAAACTTTGTCAAAACTTTCG
1 TCAAGAACTTTGTCAAAACTTTCA
573143 TCAAGAACTTGTGTCAAAACCCTTTCA
1 TCAAGAACTT-TGTCAAAA--CTTTCA
*
573170 TTAAGAA
1 TCAAGAA
573177 ATTTTTGTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.32
25 8 0.29
27 11 0.39
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (24 bp):
TCAAGAACTTTGTCAAAACTTTCA
Found at i:573599 original size:28 final size:27
Alignment explanation
Indices: 573559--573613 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
573549 GTCGAATCCT
573559 TTCAAAGCCCATAAGTCAA-TGGCACCTC
1 TTCAAAGCCCATAA-T-AAGTGGCACCTC
*
573587 TTCAAAGTCCATAATAAGTGGCACCTC
1 TTCAAAGCCCATAATAAGTGGCACCTC
573614 CCGTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 2 0.08
27 10 0.40
28 13 0.52
ACGTcount: A:0.33, C:0.29, G:0.15, T:0.24
Consensus pattern (27 bp):
TTCAAAGCCCATAATAAGTGGCACCTC
Found at i:576335 original size:19 final size:18
Alignment explanation
Indices: 576311--576374 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 18
576301 TAGCCAAACT
576311 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
576330 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
576343 TGTATCGATACACAAAAAA
1 TGTATCGATACAC-AAAAA
576362 TTGTATCGATACA
1 -TGTATCGATACA
576375 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 11 0.29
20 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:576347 original size:13 final size:13
Alignment explanation
Indices: 576329--576354 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
576319 TACACAAAAT
576329 ATGTATCGATACA
1 ATGTATCGATACA
576342 ATGTATCGATACA
1 ATGTATCGATACA
576355 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:576352 original size:32 final size:33
Alignment explanation
Indices: 576311--576374 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
576301 TAGCCAAACT
*
576311 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
576343 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
576375 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:580433 original size:15 final size:15
Alignment explanation
Indices: 580413--580443 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
580403 TAAAAATGTC
*
580413 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
580428 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
580443 C
1 C
580444 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:582536 original size:13 final size:13
Alignment explanation
Indices: 582518--582555 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
582508 CATTTTTCTT
582518 TGTATCGATACAA
1 TGTATCGATACAA
*
582531 TGTATCGATACAC
1 TGTATCGATACAA
582544 TGTATCGATACA
1 TGTATCGATACA
582556 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:582710 original size:20 final size:20
Alignment explanation
Indices: 582667--582712 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
582657 AAATCTTTTG
582667 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
582688 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
582708 CAAAA
1 CAAAA
582713 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:584980 original size:20 final size:20
Alignment explanation
Indices: 584957--585050 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
584947 ACCCTTAAAA
* *
584957 GTATCGATACACAGTTCCAA-
1 GTATCGATACA-TGTTGCAAT
584977 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
584997 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
585017 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
585037 GTATCGATACATGT
1 GTATCGATACATGT
585051 CATTGGGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
19 6 0.08
20 65 0.92
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:585104 original size:19 final size:18
Alignment explanation
Indices: 585080--585143 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 18
585070 TAGCCAAACT
585080 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAA-A
585099 TGTATCGAT--AC---AA
1 TGTATCGATACACAAAAA
585112 TGTATCGATACACAAAAAA
1 TGTATCGATACAC-AAAAA
585131 TTGTATCGATACA
1 -TGTATCGATACA
585144 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 11 0.29
20 12 0.32
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (18 bp):
TGTATCGATACACAAAAA
Found at i:585116 original size:13 final size:13
Alignment explanation
Indices: 585098--585123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
585088 TACACAAAAT
585098 ATGTATCGATACA
1 ATGTATCGATACA
585111 ATGTATCGATACA
1 ATGTATCGATACA
585124 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:585121 original size:32 final size:33
Alignment explanation
Indices: 585080--585143 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
585070 TAGCCAAACT
*
585080 TGTATCGATACACAAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
585112 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
585144 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:591027 original size:79 final size:79
Alignment explanation
Indices: 590922--591345 Score: 645
Period size: 79 Copynumber: 5.4 Consensus size: 79
590912 CGATGATTAG
590922 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
1 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
590987 AAATTAATATTTTA
66 AAATTAATATTTTA
* * * * *
591001 GAAATAAAACCGGGGTTGGAGCATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAA
1 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
*
591066 AAATTGATGA-TTTA
66 AAATTAAT-ATTTTA
* *
591080 GAAATAAAATCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCAATTATGAG
1 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
591145 AAATTAATATTTTA
66 AAATTAATATTTTA
* *
591159 GAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
1 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
591224 AAATTAATATTTTA
66 AAATTAATATTTTA
* * * *
591238 GAAATAAAACCGGGATTGGAGTATCCCCTCAGAAATAACGAGGTTGGAGTATCCCCGATTGTGAA
1 GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
** * *
591303 AAATTGGTGTTTTTG
66 AAATTAAT-ATTTTA
591318 GAAATAAAATC-GGAGTTGGAGTATCCCC
1 GAAATAAAATCGGGA-TTGGAGTATCCCC
591346 GATTATAGAA
Statistics
Matches: 314, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
78 1 0.00
79 285 0.91
80 28 0.09
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
GAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAG
AAATTAATATTTTA
Found at i:591106 original size:158 final size:158
Alignment explanation
Indices: 590827--591345 Score: 721
Period size: 158 Copynumber: 3.3 Consensus size: 158
590817 ATATGTCCCC
* * *
590827 ATGAGAAATTTAATATTTTGGAGATAATAAT-GGGGTTGGAGTATCCCCT-TGAAAATAACGGGG
1 ATGAGAAA-TTAATATTTTAGAAATAA-AATCGGGGTTGGAGTATCCCCTCAG-AAATAACGGGG
* * *
590890 TTAGAGTA----CGGTTGTGAAAAATCGATGA-TTAGGAAATAAAATCGGGATTGGAGTATCCCC
63 TTGGAGTATCCCCGATTGTGAAAAATTGATGATTTA-GAAATAAAATCGGGATTGGAGTATCCCC
590950 TCAGAAATAACGGGGTTGGAGTATCCCCGATT
127 TCAGAAATAACGGGGTTGGAGTATCCCCGATT
* *
590982 ATGAGAAATTAATATTTTAGAAATAAAACCGGGGTTGGAGCATCCCCTCAGAAATAACGGGGTTG
1 ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTG
*
591047 GAGTATCCCCGATTGTGAAAAATTGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCGG
66 GAGTATCCCCGATTGTGAAAAATTGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCAG
*
591112 AAATAACGGGGTTGGAGTATCCCCAATT
131 AAATAACGGGGTTGGAGTATCCCCGATT
*
591140 ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTG
1 ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTG
* * * *
591205 GAGTATCCCCGATTATGAGAAATTAAT-ATTTTAGAAATAAAACCGGGATTGGAGTATCCCCTCA
66 GAGTATCCCCGATTGTGAAAAATTGATGA-TTTAGAAATAAAATCGGGATTGGAGTATCCCCTCA
*
591269 GAAATAACGAGGTTGGAGTATCCCCGATT
130 GAAATAACGGGGTTGGAGTATCCCCGATT
* * ** * * *
591298 GTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 ATGAGAAATTAAT-ATTTTAGAAATAAAATCGGGGTTGGAGTATCCCC
591346 GATTATAGAA
Statistics
Matches: 328, Mismatches: 27, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
153 2 0.01
154 51 0.16
155 9 0.03
157 1 0.00
158 231 0.70
159 34 0.10
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.27
Consensus pattern (158 bp):
ATGAGAAATTAATATTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTG
GAGTATCCCCGATTGTGAAAAATTGATGATTTAGAAATAAAATCGGGATTGGAGTATCCCCTCAG
AAATAACGGGGTTGGAGTATCCCCGATT
Found at i:591338 original size:52 final size:51
Alignment explanation
Indices: 591280--591514 Score: 303
Period size: 51 Copynumber: 4.6 Consensus size: 51
591270 AAATAACGAG
* *
591280 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGAAAATAAAACCGGA
* *
591332 GTTGGAGTATCCCCGATTAT-AGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAACCGGA
** * * *
591383 GTTGGAGTATCCCTAATTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
* *
591434 GTTAGAGTATCCCCGATTGTGAAAAATTAGGTGTTTT-AGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATT-GGTGTTTTGA-AAATAAAACCGGA
* *
591486 GTTGGAGTACCCCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
591515 AGAAACTTAA
Statistics
Matches: 158, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
51 86 0.54
52 72 0.46
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
Found at i:591467 original size:103 final size:103
Alignment explanation
Indices: 591279--591514 Score: 334
Period size: 103 Copynumber: 2.3 Consensus size: 103
591269 GAAATAACGA
* * * *
591279 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCC
1 GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTAGAGTATCC
591344 CCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCGG
66 CCGATTATAGAAAATTGGTGTTTTAG-AAATAAAACCGG
* *
591382 GGTTGGAGTATCCCTAATTGTGGAAAATTGGTG-TTTCGAAAATAAAATCGGAGTTAGAGTATCC
1 GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTAGAGTATCC
*
591446 CCGATTGT-GAAAAATTAGGTGTTTTAGAAATAAAACCGG
66 CCGATTATAG-AAAATT-GGTGTTTTAGAAATAAAACCGG
* * *
591485 GGTTGGAGTACCCCCGATTATGAAAAATTG
1 GGTTGGAGTATCCCCAATTGTGAAAAATTG
591515 AGAAACTTAA
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 41 0.35
103 75 0.64
104 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (103 bp):
GGTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGGAGTTAGAGTATCC
CCGATTATAGAAAATTGGTGTTTTAGAAATAAAACCGG
Found at i:593173 original size:13 final size:13
Alignment explanation
Indices: 593155--593180 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
593145 ACAAAGATCC
593155 ATGTATCGATACA
1 ATGTATCGATACA
593168 ATGTATCGATACA
1 ATGTATCGATACA
593181 TGGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:594451 original size:61 final size:60
Alignment explanation
Indices: 594078--594710 Score: 662
Period size: 55 Copynumber: 10.9 Consensus size: 60
594068 AAAATAAGGT
* * * *
594078 GCATCCTGCTCTTTGAGGACT-AAAAAGTGCCACCAACTCGTGTGGGATTT----G-AAAG
1 GCATCCTGCTCTTTGAGGACTGGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
*
594133 GCATCCTGCTCTTTGAGGACT-GAAAGATGCCACCAACTTGTGTGGGCTTT--AAG---AG
1 GCATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
** *
594188 GTGTCCTGCTCTTTGAGGACTGGAAAATGCCAACAACTTGTGTGGGCTTTAAAAG-----
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* *
594243 GCATCCTGCTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAG-----
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* *
594298 GCATCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT--AAG---AG
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* * * *
594353 GCGTCCTGCTCTTTGAGGACTGGGAAGTGCTACCAACTTGTGTGGGCTTTAAAAAGAAAAA
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAA
* * *
594414 GCATCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAG
1 GCATCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAGAAAAA
* * ** * * *
594475 GCGTCCTGCTTTTTGAGGACT-GAAGGTGCCACCAATTTGTGTAGGCTTTAAAAGAAAAT
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* *
594534 GCGTCCTGCTCTTTGAGGACTGGAAAATGCCACCAATTTGTGTGGGCTTTAAAAGAAAAA
1 GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* *
594594 GGCATCCTGCTCTTTGAGGAATGGAAAATGCCACCGACTTGTGTGGGCTTTAAAAGAAAAA
1 -GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
* * * *
594655 GACGTCCTACTCTTTGAGGACT--AAAAGGTGCCACCAACTTGTGTGGGGTTTGAAAG
1 G-CATCCTGCTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTGGGCTTTAAAAG
594711 GCGTCCTGCT
Statistics
Matches: 510, Mismatches: 48, Indels: 34
0.86 0.08 0.06
Matches are distributed among these distances:
53 3 0.01
55 231 0.45
56 5 0.01
57 4 0.01
58 3 0.01
59 32 0.06
60 60 0.12
61 172 0.34
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (60 bp):
GCATCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGAAAAA
Found at i:595712 original size:1 final size:1
Alignment explanation
Indices: 595706--595755 Score: 55
Period size: 1 Copynumber: 50.0 Consensus size: 1
595696 AAGCAGGTTC
* * * * *
595706 TTTTTTTTTTCTTTTTTCTTTTTTCTTTTTTTTTGTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
595756 AAAAAGAATG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.06, G:0.04, T:0.90
Consensus pattern (1 bp):
T
Found at i:595726 original size:18 final size:17
Alignment explanation
Indices: 595703--595755 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
595693 CTTAAGCAGG
595703 TTCTTTTTTTTTTCTTTT
1 TTCTTTTTTTTTT-TTTT
*
595721 TTCTTTTTTCTTTTTTT
1 TTCTTTTTTTTTTTTTT
*
595738 TTGTTTTTTTGTTTTTTT
1 TTCTTTTTTT-TTTTTTT
595756 AAAAAGAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.89
Consensus pattern (17 bp):
TTCTTTTTTTTTTTTTT
Found at i:595729 original size:14 final size:13
Alignment explanation
Indices: 595706--595755 Score: 66
Period size: 14 Copynumber: 3.7 Consensus size: 13
595696 AAGCAGGTTC
595706 TTTTTTTTTTCTT
1 TTTTTTTTTTCTT
595719 TTTTCTTTTTTCTT
1 TTTT-TTTTTTCTT
595733 TTTTTTTGTTT-TT
1 TTTTTTT-TTTCTT
595746 TTGTTTTTTT
1 TT-TTTTTTT
595756 AAAAAGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.00, C:0.06, G:0.04, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTCTT
Found at i:595731 original size:25 final size:25
Alignment explanation
Indices: 595703--595754 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
595693 CTTAAGCAGG
595703 TTCTTTTTTTTT-TCTTTTTTCTTTT
1 TTCTTTTTTTTTGT-TTTTTTCTTTT
*
595728 TTCTTTTTTTTTGTTTTTTTGTTTT
1 TTCTTTTTTTTTGTTTTTTTCTTTT
595753 TT
1 TT
595755 TAAAAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.00, C:0.08, G:0.04, T:0.88
Consensus pattern (25 bp):
TTCTTTTTTTTTGTTTTTTTCTTTT
Found at i:599191 original size:19 final size:20
Alignment explanation
Indices: 599167--599217 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
599157 TAGCTAAACT
**
599167 TGTATCGATACA-CATAGTA
1 TGTATCGATACACCATAAAA
599186 TGTATCGATACACCATAAAA
1 TGTATCGATACACCATAAAA
599206 TGTATCGATACA
1 TGTATCGATACA
599218 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (20 bp):
TGTATCGATACACCATAAAA
Found at i:607172 original size:4 final size:4
Alignment explanation
Indices: 607163--607197 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
607153 CGATAAAACA
607163 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
607198 CACCTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:609368 original size:79 final size:78
Alignment explanation
Indices: 609263--609706 Score: 577
Period size: 79 Copynumber: 5.6 Consensus size: 78
609253 GAGATAATAA
* * * **
609263 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT-A
609328 -TTAGGAAATAAAAT
65 TTTA-GAAATAAAAT
* *
609342 CGGGATTGGAGTATCCCCTC-AGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA
1 CGGGGTTGGAGTATCCCCTCGA-AAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA
*
609406 TTTTAGAAATAAAAC
65 -TTTAGAAATAAAAT
** * **
609421 CAAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAAT-A
609486 TTTAGAAATAAAAT
65 TTTAGAAATAAAAT
* * * ** *
609500 CGGGATTAGAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA-
609565 TTTAGAAATAAAAT
65 TTTAGAAATAAAAT
* * * *
609579 CGGGGTTTGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCTCCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATA-
*
609644 TTTAGAAATAAAAC
65 TTTAGAAATAAAAT
* *
609658 CGGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
609707 GATTAACGGG
Statistics
Matches: 319, Mismatches: 40, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
78 3 0.01
79 311 0.97
80 5 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTAATAT
TTAGAAATAAAAT
Found at i:609445 original size:158 final size:157
Alignment explanation
Indices: 609266--609706 Score: 643
Period size: 158 Copynumber: 2.8 Consensus size: 157
609256 ATAATAACGG
* *
609266 GGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGA-TT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
609330 AGGAAATAAAATCGGGATTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATG
66 A-GAAATAAAATCGGGATTGGAGTATCCCCTC-GAAATAATGGGGTTGGAGTATCCCCGATTATG
609395 AAAAATTAATATTTTAGAAATAAAACCAA
129 AAAAATTAATATTTTAGAAATAAAACCAA
609424 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
* ** **
609489 AGAAATAAAATCGGGATTAGAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGA
66 AGAAATAAAATCGGGATTGGAGTATCCCCTCG-AAATAATGGGGTTGGAGTATCCCCGATTATGA
* * **
609554 GAAATTAATATTTTAGAAATAAAATCGG
130 AAAATTAATATTTTAGAAATAAAACCAA
* * * * * **
609582 GGTTTGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCTCCGATTATGAGAAATTAAT-ATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA-TT
* *
609646 TAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATCCCCGAT
65 TAGAAATAAAATCGGGATTGGAGTATCCCCTC-GAAATAATGGGGTTGGAGTATCCCCGAT
609707 GATTAACGGG
Statistics
Matches: 254, Mismatches: 25, Indels: 8
0.89 0.09 0.03
Matches are distributed among these distances:
157 2 0.01
158 248 0.98
159 4 0.02
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (157 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
AGAAATAAAATCGGGATTGGAGTATCCCCTCGAAATAATGGGGTTGGAGTATCCCCGATTATGAA
AAATTAATATTTTAGAAATAAAACCAA
Found at i:609693 original size:237 final size:237
Alignment explanation
Indices: 609271--609706 Score: 669
Period size: 237 Copynumber: 1.8 Consensus size: 237
609261 AACGGGGTTG
* * ** * * *
609271 GAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCCCCGGTTGTGAAAAATCGATGATTAGGAAA
1 GAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGAAAAATCAATGATTAGGAAA
* *
609336 TAAAATCGGGATTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAAT
66 TAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAAT
609401 TAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
131 TAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
609466 CGATTGTGAAAAATCGATGATTTAGAAATAAAATCGGGATTA
196 CGATTGTGAAAAATCGATGATTTAGAAATAAAATCGGGATTA
* *
609508 GAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGAGAAATTAAT-ATTTTA-GA
1 GAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGAAAAATCAATGA--TTAGGA
* * * *
609571 AATAAAATCGGGGTTTGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCTCCGATTATGAGAA
64 AATAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAA
** * *
609636 ATTAATATTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGGAAATAATGGGGTTGGAGTATC
129 ATTAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATC
609701 CCCGAT
194 CCCGAT
609707 GATTAACGGG
Statistics
Matches: 178, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
236 1 0.01
237 174 0.98
238 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.27
Consensus pattern (237 bp):
GAGTATCCCCTCGAAAATAACAGGGTCAGAGTATCCCCGATTATGAAAAATCAATGATTAGGAAA
TAAAATCGGGATTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAAT
TAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
CGATTGTGAAAAATCGATGATTTAGAAATAAAATCGGGATTA
Found at i:609778 original size:51 final size:51
Alignment explanation
Indices: 609717--609949 Score: 308
Period size: 51 Copynumber: 4.6 Consensus size: 51
609707 GATTAACGGG
* * *
609717 GTTGGGGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
* *
609768 GTTGGAGTATCCCCGATTAT-AGAAAATTGGTGTTTTGAAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAACCGGA
* * * *
609819 GTTGGAGTATCCCCAATTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
* * *
609870 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTT-AGAAATAAAACCGGG
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAACCGGA
* *
609921 GTTGGAGTACCCCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTGTGAAAAATTG
609950 AGAAACTTAA
Statistics
Matches: 157, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.01
51 155 0.99
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAACCGGA
Found at i:609845 original size:102 final size:102
Alignment explanation
Indices: 609713--609949 Score: 352
Period size: 102 Copynumber: 2.3 Consensus size: 102
609703 CGATGATTAA
* * *
609713 CGGGGTTGGGGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGAGTTGGAGTAT
*
609778 CCCCGATTAT-AGAAAATTGGTGTTTT-GAAAATAAAAC
66 CCCCGATTATGA-AAAATTAGTGTTTTAG-AAATAAAAC
* *
609815 CGGGGTTGGAGTATCCCCAATTGTGGAAAATTGGTGTTTCGAAAATAAAATCGGAGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGAGTTGGAGTAT
* *
609880 CCTCGATTGTGAAAAATTAGTGTTTTAGAAATAAAAC
66 CCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAAC
* *
609917 CGGGGTTGGAGTACCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTG
609950 AGAAACTTAA
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
102 119 0.98
103 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (102 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGAGTTGGAGTAT
CCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAAC
Found at i:612319 original size:12 final size:12
Alignment explanation
Indices: 612302--612338 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
612292 TCGATACAAA
612302 GATCCATGTATC
1 GATCCATGTATC
612314 GATCCATGTATC
1 GATCCATGTATC
*
612326 GATACAATGTATC
1 GAT-CCATGTATC
612339 AATACATAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 15 0.65
13 8 0.35
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (12 bp):
GATCCATGTATC
Found at i:612337 original size:13 final size:13
Alignment explanation
Indices: 612307--612344 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
612297 ACAAAGATCC
*
612307 ATGTATCGAT-CC
1 ATGTATCGATACA
612319 ATGTATCGATACA
1 ATGTATCGATACA
*
612332 ATGTATCAATACA
1 ATGTATCGATACA
612345 TAGAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:612426 original size:32 final size:32
Alignment explanation
Indices: 612383--612554 Score: 326
Period size: 32 Copynumber: 5.4 Consensus size: 32
612373 GCAGTAGCTT
612383 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
612415 TGTATCTATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
612447 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
612479 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
612511 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
612543 TGTATTGATACA
1 TGTATCGATACA
612555 AATCGCTGAA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 137 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:614313 original size:15 final size:15
Alignment explanation
Indices: 614293--614327 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
614283 AACCATCAAA
614293 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
614308 GATGATGATGATAAT
1 GATGATGAAGATAAT
614323 GATGA
1 GATGA
614328 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:618680 original size:13 final size:13
Alignment explanation
Indices: 618662--618701 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
618652 ACAATATTCT
618662 TTGTATCGATACA
1 TTGTATCGATACA
*
618675 TTGTATCGATATA
1 TTGTATCGATACA
* *
618688 ATATATCGATACA
1 TTGTATCGATACA
618701 T
1 T
618702 GGGTTACTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:620574 original size:19 final size:20
Alignment explanation
Indices: 620550--620603 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
620540 ACATTATGCT
* **
620550 TTATATCGATACATGTTC-A
1 TTATATTGATACATGCACAA
620569 TTATATTGATACATGCACAA
1 TTATATTGATACATGCACAA
620589 TTATATTGATACATG
1 TTATATTGATACATG
620604 AAACTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (20 bp):
TTATATTGATACATGCACAA
Found at i:620694 original size:20 final size:20
Alignment explanation
Indices: 620632--620705 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 20
620622 CTACCACTGT
* *
620632 TTGTATCAATTCATGGCACA
1 TTGTATCGATACATGGCACA
620652 TTGTATCGATACATGGCACA
1 TTGTATCGATACATGGCACA
620672 TTGTATCGATACATGAAG-A-A
1 TTGTATCGATACATG--GCACA
620692 TTGTATCGATACAT
1 TTGTATCGATACAT
620706 TGTCCTAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 48 0.96
21 1 0.02
22 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (20 bp):
TTGTATCGATACATGGCACA
Found at i:625576 original size:35 final size:35
Alignment explanation
Indices: 625510--625578 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
625500 CAACTGTTCA
* * * *
625510 CATACTATTCGTGTTTCATGTTCCTCATACTGTTG
1 CATACTATTCATGATACATGTTCATCATACTGTTG
625545 CATACTATTCATGATAC-TGTTCATCATTACTGTT
1 CATACTATTCATGATACATGTTCATCA-TACTGTT
625579 TATTTTTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 8 0.28
35 21 0.72
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.45
Consensus pattern (35 bp):
CATACTATTCATGATACATGTTCATCATACTGTTG
Found at i:628467 original size:10 final size:10
Alignment explanation
Indices: 628452--628486 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
628442 TTTGAAAATA
628452 TAGCTGTTAC
1 TAGCTGTTAC
628462 TAGCTGTTAC
1 TAGCTGTTAC
*
628472 TAGCCGTTAC
1 TAGCTGTTAC
*
628482 AAGCT
1 TAGCT
628487 AATGTATCGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (10 bp):
TAGCTGTTAC
Found at i:628527 original size:13 final size:13
Alignment explanation
Indices: 628509--628534 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
628499 CATTTTTTGG
628509 TGTATCGATACAT
1 TGTATCGATACAT
628522 TGTATCGATACAT
1 TGTATCGATACAT
628535 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:628549 original size:32 final size:33
Alignment explanation
Indices: 628489--628552 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
628479 TACAAGCTAA
**
628489 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
628522 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
628553 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:630891 original size:21 final size:19
Alignment explanation
Indices: 630840--630891 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
630830 TTGTTTTTGA
630840 AAGTGATTTTGATGAAAAAC
1 AAGT-ATTTTGATGAAAAAC
*
630860 AATGTAATTTGTAGTGAAAAAC
1 AA-GTATTTTG-A-TGAAAAAC
630882 AAGTATTTTG
1 AAGTATTTTG
630892 CAAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 7 0.26
21 10 0.37
22 10 0.37
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (19 bp):
AAGTATTTTGATGAAAAAC
Found at i:637253 original size:32 final size:33
Alignment explanation
Indices: 637193--637256 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
637183 TACAAGCTAA
* **
637193 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCAATACATACTTTGGTGTATCGATACAT
637226 TGTATCAATACATACTTT-GTGTATCGATACA
1 TGTATCAATACATACTTTGGTGTATCGATACA
637257 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.46
33 15 0.54
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCAATACATACTTTGGTGTATCGATACAT
Found at i:642637 original size:18 final size:18
Alignment explanation
Indices: 642614--642649 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
642604 TGGGTGATTA
*
642614 GGAATTCCTCCTTTAGGG
1 GGAATTACTCCTTTAGGG
*
642632 GGAATTACTGCTTTAGGG
1 GGAATTACTCCTTTAGGG
642650 ACAAAATCAA
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:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (18 bp):
GGAATTACTCCTTTAGGG
Found at i:649297 original size:20 final size:19
Alignment explanation
Indices: 649272--649320 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
649262 AAAAATTATT
649272 TAAATATTTTGAATAAATAA
1 TAAATATTTT-AATAAATAA
* * *
649292 TAAATATATTATTTAATAA
1 TAAATATTTTAATAAATAA
649311 TATAATATTT
1 TA-AATATTT
649321 CATATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAAATATTTTAATAAATAA
Found at i:651241 original size:69 final size:68
Alignment explanation
Indices: 651130--651262 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 68
651120 GTGTGCTAGT
* * *
651130 TATTGCTTAATCCCTAAAGCTTTTAATTTTCTTTTATGTTTTAGTTGACTTTTAAATTCCTTAGC
1 TATTGCTTAATCCCCAAAGCTTTTAATTTTCTTTTATATTTTAGTTAACTTTT-AATTCCTTAGC
651195 CACC
65 CACC
* *
651199 TATTGCTTAATCCCCAAAGCTTTTAGTTTT-TATTTATATTTTAGTTAACTTTTAATTTCTTAGC
1 TATTGCTTAATCCCCAAAGCTTTTAATTTTCT-TTTATATTTTAGTTAACTTTTAATTCCTTAGC
651263 TTCATGTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
68 11 0.19
69 47 0.81
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (68 bp):
TATTGCTTAATCCCCAAAGCTTTTAATTTTCTTTTATATTTTAGTTAACTTTTAATTCCTTAGCC
ACC
Found at i:652093 original size:23 final size:22
Alignment explanation
Indices: 652056--652115 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 22
652046 CAATTGGACA
** *
652056 TTTAGTTTAGGTTTAGATGGGCT
1 TTTAGTTTAAATTTAAATGGG-T
652079 TTTAGTTTAAATTTAAATGGGT
1 TTTAGTTTAAATTTAAATGGGT
* *
652101 TTAAGTTCAAATTTA
1 TTTAGTTTAAATTTA
652116 TATGTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.48
Consensus pattern (22 bp):
TTTAGTTTAAATTTAAATGGGT
Found at i:652112 original size:22 final size:23
Alignment explanation
Indices: 652067--652115 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
652057 TTAGTTTAGG
* * *
652067 TTTAGATGGGCTTTTAGTTTAAA
1 TTTAAATGGGCTTTAAGTTCAAA
652090 TTTAAATGGG-TTTAAGTTCAAA
1 TTTAAATGGGCTTTAAGTTCAAA
652112 TTTA
1 TTTA
652116 TATGTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.18, T:0.47
Consensus pattern (23 bp):
TTTAAATGGGCTTTAAGTTCAAA
Found at i:655652 original size:158 final size:156
Alignment explanation
Indices: 655480--656116 Score: 475
Period size: 158 Copynumber: 4.1 Consensus size: 156
655470 GGCTATCACA
** * * ** *
655480 AGAATCCAGGTTTGTTTTATTTGAGGGATGAACTTTGATCTTAAGGAACGTGGTAGAAAGAAAAG
1 AGAATCCAAATTTGTCTCATTTGAGGGATGAACTTTGAT-TTAAGGAAAATAGTAGAAAGAAAAG
* * * * *
655545 CTTTTTCGAAAAACCAAGGCATCAATATTAAGTATCCCAATGAAGAGAACGTGTTTATGTTGCCC
65 CTTTTT-GAAAAACCAAAGCATCAATATCATGTATCCCAATGAAGAGAACGTGTTTATGATACCC
**
655610 AATCATGAAATGAATGGAGAATATTATG
129 AATCATGAAAAAAATGGAGAATATTATG
* * * * * *
655638 AGAATCCACATTTGTCTCATTTGAGTGATGAAATTTGGTTTTAGGGAAAACAGTAGAAAGAAAAG
1 AGAATCCAAATTTGTCTCATTTGAGGGATGAACTTT-GATTTAAGGAAAATAGTAGAAAGAAAAG
** * * * * * * *
655703 CTTTCTTGTGAAATCAAAGCATTAATATCATGTAT-CCATAAGAGGAGAGCATTTTTAT-ATACC
65 CTTT-TTGAAAAACCAAAGCATCAATATCATGTATCCCA-ATGAAGAGAACGTGTTTATGATACC
* *
655766 CAATCAAGAAAAAAATGGAGATTATTATG
128 CAATCATGAAAAAAATGGAGAATATTATG
** * * *
655795 AGAATCCAAATTTCACTCATTCGAGGGACT-AACTTTGATTTAAGGAAAATAATAAAAAGAAAAG
1 AGAATCCAAATTTGTCTCATTTGAGGGA-TGAACTTTGATTTAAGGAAAATAGTAGAAAGAAAAG
* * * * * *
655859 CTTTTCTTGAAAAACCAAAGTATCCATATCATGTATCCCAATGAAAAGAATAG-GTTGATGGTAC
65 C-TTT-TTGAAAAACCAAAGCATCAATATCATGTATCCCAATGAAGAGAA-CGTGTTTATGATAC
* **
655923 CCAATAATGAAGCAAATGGAGAATATTATG
127 CCAATCATGAAAAAAATGGAGAATATTATG
* ** * * *
655953 AGAATGCTTATTTGTCACATTTAAGGGATGAA-TATTGATTCTAAGGAAAAT-GCTGGGAAA-AA
1 AGAATCCAAATTTGTCTCATTTGAGGGATGAACT-TTGATT-TAAGGAAAATAG-T-AGAAAGAA
* * ** * * ** *
656015 AGGCATTTTTGGAAAA-TGAAGCATCAATATCATGTAT-CTAATGAGGAGAATTTGTTT-TCATT
62 AAGC-TTTTTGAAAAACCAAAGCATCAATATCATGTATCCCAATGAAGAGAACGTGTTTATGA-T
* ** * **
656077 GCCCAATCACAAAAAAAATGGAGATTGCTATG
125 ACCCAATCATGAAAAAAATGGAGAATATTATG
656109 AGAATCCA
1 AGAATCCA
656117 TGTTTATCTC
Statistics
Matches: 366, Mismatches: 98, Indels: 32
0.74 0.20 0.06
Matches are distributed among these distances:
155 1 0.00
156 67 0.18
157 116 0.32
158 156 0.43
159 23 0.06
160 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (156 bp):
AGAATCCAAATTTGTCTCATTTGAGGGATGAACTTTGATTTAAGGAAAATAGTAGAAAGAAAAGC
TTTTTGAAAAACCAAAGCATCAATATCATGTATCCCAATGAAGAGAACGTGTTTATGATACCCAA
TCATGAAAAAAATGGAGAATATTATG
Found at i:655865 original size:157 final size:157
Alignment explanation
Indices: 655536--655896 Score: 370
Period size: 157 Copynumber: 2.3 Consensus size: 157
655526 AACGTGGTAG
* * * * * * * *
655536 AAAGAAAAGCTTT-TTCGAAAAACCAAGGCATCAATATTAAGTATCCCA-ATGAAGAGAACGTGT
1 AAAGAAAAGCTTTCTT-GAAAAACCAAAGCATCAATATCATGTAT-CCATAAGAGGAGAGCATTT
* * * ** * ** * *
655599 TTATGTTGCCCAATCATGAAATGAATGGAGAATATTATGAGAATCCACATTTGTCTCATTTGAGT
64 TTAT-ATACCCAATCAAGAAAAAAATGGAGAATATTATGAGAATCCAAATTTCACTCATTCGAGG
* * * *
655664 GATGAAATTTGGTTTTAGGGAAAACAGTAG
128 GATGAAATTTGGATTTAAGGAAAACAATAA
** * *
655694 AAAGAAAAGCTTTCTTGTGAAATCAAAGCATTAATATCATGTATCCATAAGAGGAGAGCATTTTT
1 AAAGAAAAGCTTTCTTGAAAAACCAAAGCATCAATATCATGTATCCATAAGAGGAGAGCATTTTT
*
655759 ATATACCCAATCAAGAAAAAAATGGAGATTATTATGAGAATCCAAATTTCACTCATTCGAGGGAC
66 ATATACCCAATCAAGAAAAAAATGGAGAATATTATGAGAATCCAAATTTCACTCATTCGAGGGA-
* *
655824 T-AACTTT-GATTTAAGGAAAATAATAA
130 TGAAATTTGGATTTAAGGAAAACAATAA
* *
655850 AAAGAAAAGCTTTTCTTGAAAAACCAAAGTATCCATATCATGTATCC
1 AAAGAAAAGC-TTTCTTGAAAAACCAAAGCATCAATATCATGTATCC
655897 CAATGAAAAG
Statistics
Matches: 164, Mismatches: 35, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
156 24 0.15
157 89 0.54
158 49 0.30
159 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (157 bp):
AAAGAAAAGCTTTCTTGAAAAACCAAAGCATCAATATCATGTATCCATAAGAGGAGAGCATTTTT
ATATACCCAATCAAGAAAAAAATGGAGAATATTATGAGAATCCAAATTTCACTCATTCGAGGGAT
GAAATTTGGATTTAAGGAAAACAATAA
Done.