Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014936.1 Kokia drynarioides strain JFW-HI SEQ_129979, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 436333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 808 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:948 original size:21 final size:20
Alignment explanation
Indices: 924--962 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
914 TTCAGAATTT
*
924 GGACTTTGAAATTTGTAAAAG
1 GGACATTGAAATTT-TAAAAG
*
945 GGACATTGATATTTTAAA
1 GGACATTGAAATTTTAAA
963 TTTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (20 bp):
GGACATTGAAATTTTAAAAG
Found at i:3592 original size:2 final size:2
Alignment explanation
Indices: 3585--3615 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3575 TTTATATTCT
3585 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3616 TTTAACTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:28780 original size:6 final size:6
Alignment explanation
Indices: 28754--28829 Score: 120
Period size: 6 Copynumber: 13.0 Consensus size: 6
28744 TTTGCTTTAT
* *
28754 CAAAAG -AAAAG -AAAAG AAAAAG TAAAAG CAAAAG CAAAAG CAAAAG
1 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG
28800 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG
1 CAAAAG CAAAAG CAAAAG CAAAAG CAAAAG
28830 ATACGGCGTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
5 10 0.15
6 57 0.85
ACGTcount: A:0.70, C:0.12, G:0.17, T:0.01
Consensus pattern (6 bp):
CAAAAG
Found at i:40122 original size:15 final size:15
Alignment explanation
Indices: 40102--40131 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40092 TATTTATTTT
*
40102 ATTTTATTTTTTATA
1 ATTTTATTATTTATA
40117 ATTTTATTATTTATA
1 ATTTTATTATTTATA
40132 TAAATAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTATTTATA
Found at i:42168 original size:16 final size:17
Alignment explanation
Indices: 42131--42170 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
42121 TTCATAATTT
*
42131 TATATTTAAAAATATTA
1 TATATTCAAAAATATTA
*
42148 CATATTCAAAAATATATA
1 TATATTCAAAAATAT-TA
42166 TATAT
1 TATAT
42171 ATTTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TATATTCAAAAATATTA
Found at i:46188 original size:21 final size:20
Alignment explanation
Indices: 46145--46260 Score: 94
Period size: 20 Copynumber: 5.6 Consensus size: 20
46135 TTAAATATAT
* *
46145 AAAAATTATAAAAAAATTGTA
1 AAAAATTAT-TAAATATTGTA
* *
46166 AATAATTATTAAATGTTGTTA
1 AAAAATTATTAAATATTG-TA
*
46187 AAAACATTTTTAAA-ATTGTA
1 AAAA-ATTATTAAATATTGTA
*
46207 AAAAAGTTATTAAATATTATAA
1 AAAAA-TTATTAAATATTGT-A
46229 AAAAATTATTTAAA-ATTTGT-
1 AAAAATTA-TTAAATA-TTGTA
46249 AAAAATTATTAA
1 AAAAATTATTAA
46261 TAATTGGGAA
Statistics
Matches: 78, Mismatches: 10, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
19 5 0.06
20 27 0.35
21 24 0.31
22 22 0.28
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAAATTATTAAATATTGTA
Found at i:46189 original size:41 final size:41
Alignment explanation
Indices: 46144--46298 Score: 131
Period size: 41 Copynumber: 3.8 Consensus size: 41
46134 TTTAAATATA
* *
46144 TAAAAATTATAAAAAAATTGTAAATAATTATTAAATGTTGT
1 TAAAAATTATTAAAAAATTGTAAATAATTATTAAATATTGT
* * *
46185 TAAAAACATT-TT-TAAAATTGTAAAAAAGTTATTAAATATTAT
1 T-AAAA-ATTATTAAAAAATTGTAAATAA-TTATTAAATATTGT
* * *
46227 AAAAAAATTATTTAAAATTTGTAAA-AATTATT-AATAATTG-
1 -TAAAAATTATTAAAAAATTGTAAATAATTATTAAAT-ATTGT
** *
46267 GGAAAATTATTAAAAAATTGCAAATAATTATT
1 TAAAAATTATTAAAAAATTGTAAATAATTATT
46299 TAAAATTTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
39 19 0.21
40 10 0.11
41 25 0.27
42 25 0.27
43 13 0.14
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (41 bp):
TAAAAATTATTAAAAAATTGTAAATAATTATTAAATATTGT
Found at i:46265 original size:20 final size:18
Alignment explanation
Indices: 46229--46305 Score: 64
Period size: 20 Copynumber: 3.9 Consensus size: 18
46219 AATATTATAA
*
46229 AAAAATTATTTAAAATTTGT
1 AAAAATTA-TTAAAA-TTGC
*
46249 AAAAATTATTAATAATTGG
1 AAAAATTATTAA-AATTGC
*
46268 GAAAATTATTAAAAAATTGC
1 AAAAATTATT--AAAATTGC
46288 AAATAATTATTTAAAATT
1 AAA-AATTA-TTAAAATT
46306 TTTTAACTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
19 16 0.33
20 23 0.48
21 7 0.15
22 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.06, T:0.39
Consensus pattern (18 bp):
AAAAATTATTAAAATTGC
Found at i:46282 original size:10 final size:10
Alignment explanation
Indices: 46144--46265 Score: 52
Period size: 10 Copynumber: 11.8 Consensus size: 10
46134 TTTAAATATA
46144 TAAAAATTAT
1 TAAAAATTAT
* *
46154 AAAAAAATT-G
1 -TAAAAATTAT
46164 TAAATAATTAT
1 TAAA-AATTAT
** *
46175 TAAATGTTGT
1 TAAAAATTAT
46185 TAAAAACATT-T
1 T-AAAA-ATTAT
* *
46196 TTAAAATTGT
1 TAAAAATTAT
*
46206 AAAAAAGTTAT
1 TAAAAA-TTAT
*
46217 TAAATATTAT
1 TAAAAATTAT
*
46227 AAAAAAATTAT
1 -TAAAAATTAT
*
46238 TTAAAATT-T
1 TAAAAATTAT
46247 GTAAAAATTAT
1 -TAAAAATTAT
*
46258 TAATAATT
1 TAAAAATT
46266 GGGAAAATTA
Statistics
Matches: 81, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
9 7 0.09
10 40 0.49
11 32 0.40
12 2 0.02
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:46560 original size:9 final size:10
Alignment explanation
Indices: 46546--46638 Score: 50
Period size: 10 Copynumber: 9.4 Consensus size: 10
46536 ATTATTTATG
46546 ATTTTTAATA
1 ATTTTTAATA
*
46556 ATTTTTAAAA
1 ATTTTTAATA
* *
46566 AATTTAAATA
1 ATTTTTAATA
*
46576 ATGTTTTATTA
1 AT-TTTTAATA
46587 A--TTTAATA
1 ATTTTTAATA
* *
46595 ACTTTTTTACA
1 A-TTTTTAATA
*
46606 A-TTTTAAAA
1 ATTTTTAATA
*
46615 TATTTTTAACA
1 -ATTTTTAATA
*
46626 ATATTTAA-A
1 ATTTTTAATA
46635 ATTT
1 ATTT
46639 ATATAAAATA
Statistics
Matches: 62, Mismatches: 15, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.11
9 10 0.16
10 25 0.40
11 20 0.32
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:46571 original size:19 final size:19
Alignment explanation
Indices: 46549--46652 Score: 59
Period size: 20 Copynumber: 5.2 Consensus size: 19
46539 ATTTATGATT
46549 TTTAATAATTTTTAAAAAA
1 TTTAATAATTTTTAAAAAA
**
46568 TTTAAATAATGTTTT-ATTAA
1 TTT-AATAAT-TTTTAAAAAA
* * *
46588 TTTAATAACTTTTTTACAAT
1 TTTAATAA-TTTTTAAAAAA
* *
46608 TTTAAAATATTTTTAACAATA
1 TTTAATA-ATTTTTAA-AAAA
*
46629 TTTAA-AATTTATATAAAATA
1 TTTAATAATTT-T-TAAAAAA
46649 TTTA
1 TTTA
46653 TTTTCAAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
19 16 0.24
20 37 0.55
21 14 0.21
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (19 bp):
TTTAATAATTTTTAAAAAA
Found at i:46611 original size:20 final size:21
Alignment explanation
Indices: 46597--46652 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
46587 ATTTAATAAC
*
46597 TTTTTTACAAT-TTTAAAATA
1 TTTTTAACAATATTTAAAATA
46617 TTTTTAACAATATTTAAAAT-
1 TTTTTAACAATATTTAAAATA
*
46637 TTATATAA-AATATTTA
1 TT-TTTAACAATATTTA
46653 TTTTCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTTAACAATATTTAAAATA
Found at i:48482 original size:11 final size:10
Alignment explanation
Indices: 48461--48485 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48451 TATATTCACC
48461 AAAAGAAAAA
1 AAAAGAAAAA
48471 AAAAGAAAAA
1 AAAAGAAAAA
48481 AAAAG
1 AAAAG
48486 GATGGTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:57735 original size:60 final size:60
Alignment explanation
Indices: 57642--57763 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
57632 GCAAGGAGTA
57642 ATAAGAGAAGAATATCAACCTTTTTGTTATAAGTACTACAAGATTTTAAATTGAAAATTT
1 ATAAGAGAAGAATATCAACCTTTTTGTTATAAGTACTACAAGATTTTAAATTGAAAATTT
57702 ATAAGAGAAGAATATCAACCTTTTTGTTATAAGTACTACAAGATTTTAAATTGAAAATTT
1 ATAAGAGAAGAATATCAACCTTTTTGTTATAAGTACTACAAGATTTTAAATTGAAAATTT
57762 AT
1 AT
57764 TCTCTTTAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.37
Consensus pattern (60 bp):
ATAAGAGAAGAATATCAACCTTTTTGTTATAAGTACTACAAGATTTTAAATTGAAAATTT
Found at i:58761 original size:23 final size:22
Alignment explanation
Indices: 58733--58811 Score: 86
Period size: 23 Copynumber: 3.5 Consensus size: 22
58723 ACATTAGTGC
58733 GCTTACTGTTCAGCACTGTGTGT
1 GCTTACTGTTC-GCACTGTGTGT
* *
58756 GCTTACTGATTCGCACTATATGT
1 GCTTACTG-TTCGCACTGTGTGT
* *
58779 GCTTACTAATTTGCACTGTGTGT
1 GCTTACT-GTTCGCACTGTGTGT
*
58802 GTTTACTGTT
1 GCTTACTGTT
58812 TCCCTAGCAC
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
22 2 0.04
23 41 0.89
24 3 0.07
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (22 bp):
GCTTACTGTTCGCACTGTGTGT
Found at i:60927 original size:36 final size:36
Alignment explanation
Indices: 60887--60965 Score: 158
Period size: 36 Copynumber: 2.2 Consensus size: 36
60877 GACTCGAATC
60887 CAGGCCACACTTGAGGTAGTGAACACTTTTGACCAT
1 CAGGCCACACTTGAGGTAGTGAACACTTTTGACCAT
60923 CAGGCCACACTTGAGGTAGTGAACACTTTTGACCAT
1 CAGGCCACACTTGAGGTAGTGAACACTTTTGACCAT
60959 CAGGCCA
1 CAGGCCA
60966 ATACACGGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (36 bp):
CAGGCCACACTTGAGGTAGTGAACACTTTTGACCAT
Found at i:81519 original size:105 final size:104
Alignment explanation
Indices: 81338--81528 Score: 301
Period size: 105 Copynumber: 1.8 Consensus size: 104
81328 GTTACTAAAT
* * * *
81338 AATGGTCGCATGATTTTTTGATGGAATTGACGTATCTTCCATAGAATTTGTCCCTATTACTAAAG
1 AATGGTCGCATGATTTTTTGATGAAATTAACGTATCTTCAATAGAATTTGCCCCTATTACTAAAG
81403 ATTTCTTACAAATCAAGCAATGAACTTATTATTAAATCA
66 ATTTCTTACAAATCAAGCAATGAACTTATTATTAAATCA
* * *
81442 AATGGTGGTATGATTTTTTTGATGAAATTAACGTATCTTCAATAGATTTTGCCCCTATTACTAAA
1 AATGGTCGCATGA-TTTTTTGATGAAATTAACGTATCTTCAATAGAATTTGCCCCTATTACTAAA
*
81507 GGTTTCTTACAAATCAAGCAAT
65 GATTTCTTACAAATCAAGCAAT
81529 TACTGAATCG
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
104 11 0.14
105 67 0.86
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (104 bp):
AATGGTCGCATGATTTTTTGATGAAATTAACGTATCTTCAATAGAATTTGCCCCTATTACTAAAG
ATTTCTTACAAATCAAGCAATGAACTTATTATTAAATCA
Found at i:89403 original size:18 final size:17
Alignment explanation
Indices: 89369--89403 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
89359 ATACTTTGGC
89369 TTAAATTTTTGAATTAA
1 TTAAATTTTTGAATTAA
*
89386 TTAAATTTATTTAATTAA
1 TTAAATTT-TTGAATTAA
89404 AAATATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAATTTTTGAATTAA
Found at i:89445 original size:21 final size:19
Alignment explanation
Indices: 89420--89469 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
89410 ATTCTCATCT
89420 CATTTGAAAACTCGTGTTGA
1 CATTT-AAAACTCGTGTTGA
*
89440 CGATTTTCAAACTCGTGTTGA
1 C-A-TTTAAAACTCGTGTTGA
89461 CATTTAAAA
1 CATTTAAAA
89470 TCTAATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 15 0.58
22 3 0.12
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
CATTTAAAACTCGTGTTGA
Found at i:101313 original size:24 final size:23
Alignment explanation
Indices: 101279--101326 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
101269 ATCCACTATA
101279 TTTATTAAAAAATTAAAATATATT
1 TTTATT-AAAAATTAAAATATATT
* * *
101303 TTTATTTAAAATTTAAGTATATT
1 TTTATTAAAAATTAAAATATATT
101326 T
1 T
101327 CTTTACATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTATTAAAAATTAAAATATATT
Found at i:120755 original size:44 final size:44
Alignment explanation
Indices: 120618--120755 Score: 140
Period size: 44 Copynumber: 3.1 Consensus size: 44
120608 GCATGCAATT
120618 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTG
1 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTG
* * * * * * *
120662 TTTGC-TTTTGTTT-ATTGCAGTGAT-AATGTTCTTGATA-ATGTTCTG
1 TTTGCACTGTATTTCATTGGAG-G-TCAA--TTC-TCACAGCTGTTCTG
120707 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTG
1 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTG
120751 TTTGC
1 TTTGC
120756 TTTTGTTTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
42 6 0.08
43 11 0.15
44 21 0.30
45 16 0.23
46 11 0.15
47 6 0.08
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (44 bp):
TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTG
Found at i:120769 original size:89 final size:89
Alignment explanation
Indices: 120618--120786 Score: 338
Period size: 89 Copynumber: 1.9 Consensus size: 89
120608 GCATGCAATT
120618 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTGTTTGCTTTTGTTTATTGCAGT
1 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTGTTTGCTTTTGTTTATTGCAGT
120683 GATAATGTTCTTGATAATGTTCTG
66 GATAATGTTCTTGATAATGTTCTG
120707 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTGTTTGCTTTTGTTTATTGCAGT
1 TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTGTTTGCTTTTGTTTATTGCAGT
120772 GATAATGTTCTTGAT
66 GATAATGTTCTTGAT
120787 TTCATGGTTA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 80 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (89 bp):
TTTGCACTGTATTTCATTGGAGGTCAATTCTCACAGCTGTTCTGTTTGCTTTTGTTTATTGCAGT
GATAATGTTCTTGATAATGTTCTG
Found at i:153334 original size:68 final size:67
Alignment explanation
Indices: 153220--153359 Score: 199
Period size: 68 Copynumber: 2.1 Consensus size: 67
153210 TGGCATTGCT
* * * * *
153220 AAAGACCTATACTAGCATTGATCGTAACAGCCATTATAGTATAAACAACGAATCGTTTTTCTCAC
1 AAAGCCCTATACTAGCATTGATCATAACAGCAATAATAGTATAAACAACGAATC-ATTTTCTCAC
153285 TTC
65 TTC
* * *
153288 AAAGCCCTATCCTAGCATTGATCATAACAGCAATAATAGTATAAACAGCGAATCATTTTCTCATT
1 AAAGCCCTATACTAGCATTGATCATAACAGCAATAATAGTATAAACAACGAATCATTTTCTCACT
153353 TC
66 TC
153355 AAAGC
1 AAAGC
153360 GATTTTCATA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 16 0.25
68 48 0.75
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (67 bp):
AAAGCCCTATACTAGCATTGATCATAACAGCAATAATAGTATAAACAACGAATCATTTTCTCACT
TC
Found at i:157310 original size:30 final size:31
Alignment explanation
Indices: 157243--157311 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
157233 ACAGTTAATC
* *
157243 AGTGACTGTTTTGTTATTTTTCGATAACGTT
1 AGTGACTGTTTTGTCAATTTTCGATAACGTT
157274 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTTTGTCA-ATTTTCGATAACGTT
157303 GAGTGACTG
1 -AGTGACTG
157312 AAATGTAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.09
30 10 0.29
31 16 0.47
32 5 0.15
ACGTcount: A:0.22, C:0.12, G:0.22, T:0.45
Consensus pattern (31 bp):
AGTGACTGTTTTGTCAATTTTCGATAACGTT
Found at i:158507 original size:19 final size:18
Alignment explanation
Indices: 158465--158508 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
158455 TATTTATATT
* *
158465 ATTGAATTTTTTAATAAT
1 ATTGAATTTTATAATAAA
*
158483 ATTGAATTCTTATATTAAA
1 ATTGAATT-TTATAATAAA
158502 ATTGAAT
1 ATTGAAT
158509 AATTAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (18 bp):
ATTGAATTTTATAATAAA
Found at i:158738 original size:133 final size:133
Alignment explanation
Indices: 158594--158854 Score: 513
Period size: 133 Copynumber: 2.0 Consensus size: 133
158584 TTTTATTAAA
158594 AAAAATCACTTTTTTACATTTAATCTATTTTTTAATTTCAAAATACATAGTAATAATAATTAAAA
1 AAAAATCACTTTTTTACATTTAATCTATTTTTTAATTTCAAAATACATAGTAATAATAATTAAAA
158659 GATAATTAAAGCAACAAAGTACGCAAAGAAGCTAACCCTATATCAAATATTAATAAATAAATTTT
66 GATAATTAAAGCAACAAAGTACGCAAAGAAGCTAACCCTATATCAAATATTAATAAATAAATTTT
158724 TTT
131 TTT
*
158727 AAAAATTACTTTTTTACATTTAATCTATTTTTTAATTTCAAAATACATAGTAATAATAATTAAAA
1 AAAAATCACTTTTTTACATTTAATCTATTTTTTAATTTCAAAATACATAGTAATAATAATTAAAA
158792 GATAATTAAAGCAACAAAGTACGCAAAGAAGCTAACCCTATATCAAATATTAATAAATAAATT
66 GATAATTAAAGCAACAAAGTACGCAAAGAAGCTAACCCTATATCAAATATTAATAAATAAATT
158855 ATAAAGTGAT
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 127 1.00
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.35
Consensus pattern (133 bp):
AAAAATCACTTTTTTACATTTAATCTATTTTTTAATTTCAAAATACATAGTAATAATAATTAAAA
GATAATTAAAGCAACAAAGTACGCAAAGAAGCTAACCCTATATCAAATATTAATAAATAAATTTT
TTT
Found at i:163838 original size:24 final size:23
Alignment explanation
Indices: 163811--163868 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
163801 ACATATGATT
163811 TGAAAATTAATTAATAATAATACA
1 TGAAAATTAATTAATAATAATA-A
* **
163835 TGAAATATGAA-TAATGTTAATAA
1 TGAAA-ATTAATTAATAATAATAA
163858 TGAAAA-TAATT
1 TGAAAATTAATT
163869 GTGTATTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 6 0.21
24 14 0.50
25 4 0.14
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (23 bp):
TGAAAATTAATTAATAATAATAA
Found at i:167686 original size:6 final size:6
Alignment explanation
Indices: 167645--167685 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
167635 TTCTGCTTCT
* *
167645 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGA GAAAGA GAAAG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG GAAAG
167686 AAATTTCTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:170898 original size:3 final size:3
Alignment explanation
Indices: 170890--170915 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
170880 GCCTTTAATG
170890 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
170916 GTCAGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:175284 original size:4 final size:4
Alignment explanation
Indices: 175275--175313 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
175265 CTGGTGTTTG
*
175275 ATGT ATGT ATGT ATGT ATGT ATGT ATGC ATG- ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
175314 CTGTTGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.26, C:0.03, G:0.26, T:0.46
Consensus pattern (4 bp):
ATGT
Found at i:182298 original size:32 final size:30
Alignment explanation
Indices: 182237--182311 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 30
182227 CTTGAACTAG
*
182237 GAGTAAGATTATACTTTAGTCACTTTATTAAAAA
1 GAGTAA-ATTA-ACTTTAGTCACGTTATT--AAA
*
182271 TGAGTAAATTAACTTTTGT-ACGTTATTAAA
1 -GAGTAAATTAACTTTAGTCACGTTATTAAA
182301 GAGTAAATTAA
1 GAGTAAATTAA
182312 TCATTTTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
29 11 0.29
30 3 0.08
32 7 0.18
33 7 0.18
34 4 0.11
35 6 0.16
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (30 bp):
GAGTAAATTAACTTTAGTCACGTTATTAAA
Found at i:184687 original size:17 final size:16
Alignment explanation
Indices: 184664--184710 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
184654 AGATTTAAAA
184664 TATAATTTTATTATTT
1 TATAATTTTATTATTT
184680 TAATAA-TTTATATATTT
1 T-ATAATTTTAT-TATTT
184697 T-TAATTTTATTATT
1 TATAATTTTATTATT
184711 ATTTGACTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.25
16 11 0.39
17 10 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TATAATTTTATTATTT
Found at i:197567 original size:15 final size:15
Alignment explanation
Indices: 197530--197568 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
197520 TTATGTGTAC
*
197530 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
197545 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
197559 TTAATTCTTG
1 TTAATTCTTG
197569 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:200010 original size:6 final size:6
Alignment explanation
Indices: 199999--200043 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
199989 TGATCAAAAT
* * *
199999 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
200044 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:203276 original size:12 final size:12
Alignment explanation
Indices: 203254--203283 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
203244 CCCTATTCCC
203254 TTGTAGTCTTTTT
1 TTGT-GTCTTTTT
203267 TTGTGTCTTTTT
1 TTGTGTCTTTTT
203279 TTGTG
1 TTGTG
203284 CTTGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.03, C:0.07, G:0.20, T:0.70
Consensus pattern (12 bp):
TTGTGTCTTTTT
Found at i:207599 original size:23 final size:22
Alignment explanation
Indices: 207563--207606 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
207553 TAAATATTTC
*
207563 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
207586 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
207607 TTATTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:221599 original size:3 final size:3
Alignment explanation
Indices: 221591--221619 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
221581 AGGAAGACTT
221591 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
221620 TTGGACACGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:222675 original size:13 final size:14
Alignment explanation
Indices: 222652--222682 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
222642 AAGTTTAGTA
222652 AAATATTATAAAAG
1 AAATATTATAAAAG
222666 AAAT-TTATAAAAG
1 AAATATTATAAAAG
222679 AAAT
1 AAAT
222683 GAGAGACATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
AAATATTATAAAAG
Found at i:223042 original size:19 final size:18
Alignment explanation
Indices: 223009--223048 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
222999 TCGCTGTAGT
223009 ATACTACCAATTTATTAA
1 ATACTACCAATTTATTAA
* *
223027 ATACTAACCCATTTATTTA
1 ATACT-ACCAATTTATTAA
223046 ATA
1 ATA
223049 GTGTAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.40
Consensus pattern (18 bp):
ATACTACCAATTTATTAA
Found at i:229010 original size:33 final size:33
Alignment explanation
Indices: 228973--229038 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
228963 TTTATTGATA
228973 AATTTACAATAATATTTAAAATTAATAATAAAG
1 AATTTACAATAATATTTAAAATTAATAATAAAG
229006 AATTTACAATAATATTTAAAATTAATAATAAAG
1 AATTTACAATAATATTTAAAATTAATAATAAAG
229039 TATCACTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (33 bp):
AATTTACAATAATATTTAAAATTAATAATAAAG
Found at i:229672 original size:97 final size:97
Alignment explanation
Indices: 229506--229686 Score: 344
Period size: 97 Copynumber: 1.9 Consensus size: 97
229496 NNNNNNNNNN
229506 TAAAAACTAAAATTAGTATATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTAAATTTG
1 TAAAAACTAAAATTAGTATATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTAAATTTG
229571 AATTATTATTTAATTACACCAATCAATTTCAA
66 AATTATTATTTAATTACACCAATCAATTTCAA
* *
229603 TAAAAACTAATATTAGTATATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTATATTTG
1 TAAAAACTAAAATTAGTATATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTAAATTTG
229668 AATTATTATTTAATTACAC
66 AATTATTATTTAATTACAC
229687 TAATTTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (97 bp):
TAAAAACTAAAATTAGTATATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTAAATTTG
AATTATTATTTAATTACACCAATCAATTTCAA
Found at i:229673 original size:47 final size:47
Alignment explanation
Indices: 229525--229677 Score: 118
Period size: 47 Copynumber: 3.2 Consensus size: 47
229515 AAATTAGTAT
*
229525 ATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTAAATTTGA
1 ATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTATATTTGA
* ** *** * *
229572 ATTATTATT--T-AA-TTACACCAATCAATTTC-AATAAAAACTAATATTAGTA
1 ATTATTATTCATAAAGTTA-A--AA--AA-ATCAAATGTATTTTTATATTTG-A
229621 TATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTATATTTGA
1 -ATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTATATTTGA
229669 ATTATTATT
1 ATTATTATT
229678 TAATTACACT
Statistics
Matches: 76, Mismatches: 17, Indels: 26
0.64 0.14 0.22
Matches are distributed among these distances:
43 3 0.04
44 3 0.04
45 1 0.01
46 2 0.03
47 18 0.24
48 15 0.20
49 16 0.21
50 9 0.12
51 2 0.03
52 1 0.01
53 3 0.04
54 3 0.04
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (47 bp):
ATTATTATTCATAAAGTTAAAAAAATCAAATGTATTTTTATATTTGA
Found at i:230972 original size:13 final size:13
Alignment explanation
Indices: 230954--230980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
230944 CTCGAGAGTC
230954 GGTTACGTGTGAG
1 GGTTACGTGTGAG
230967 GGTTACGTGTGAG
1 GGTTACGTGTGAG
230980 G
1 G
230981 AATGATTAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.48, T:0.30
Consensus pattern (13 bp):
GGTTACGTGTGAG
Found at i:233724 original size:114 final size:113
Alignment explanation
Indices: 233512--233823 Score: 417
Period size: 114 Copynumber: 2.7 Consensus size: 113
233502 GCTATTTGTT
* *
233512 TTAACCCACTTCTTTGTACCTCACCAGGAAGATGGGATTTAAAGTCTCACTCCACTCCACTGTAT
1 TTAACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAT
* * *
233577 CCTCATGGACGTTGAGCTCTACTTCGTCGTTTTGATTCAACACACTGTA
66 CCTCAGGGACGTTGAGCT-TACTTCATCATTTTGATTCAACACACTGTA
* * *
233626 TTAACCCACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAGTCTCACTTCACTCCAGTGTAT
1 TTAACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAT
* * * * *
233691 CCTCAGGGACATTGAGCTTGTCTTCATTATTTTGATTCAACATACTGTT
66 CCTCAGGGACGTTGAGCTT-ACTTCATCATTTTGATTCAACACACTGTA
* * * * *
233740 TTGACCTACTTCTCTGTACTTCACCAGGAAGATGGGATTTGAAGTCTTACTCCACTCTACTGTAT
1 TTAACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAT
** *
233805 TATCAGGGACGTTAAGCTT
66 CCTCAGGGACGTTGAGCTT
233824 TCACTATTTT
Statistics
Matches: 172, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
113 1 0.01
114 171 0.99
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (113 bp):
TTAACCCACTTCTCTGTACCTCACCAGGAAGATGGGATTTGAAGTCTCACTCCACTCCACTGTAT
CCTCAGGGACGTTGAGCTTACTTCATCATTTTGATTCAACACACTGTA
Found at i:233903 original size:92 final size:94
Alignment explanation
Indices: 233738--233983 Score: 336
Period size: 92 Copynumber: 2.6 Consensus size: 94
233728 CAACATACTG
* * * *
233738 TTTTGACCTACTTCTCTGTACTTCACCAGGAAGATGGGATTTGAAGTCTTACTCCACTCTACTGT
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTTACTCCACTCTACTAT
*
233803 ATTATCAGGGACGTTAAGC-T-TTCACTA
66 ATCATCAGGGACGTTAAGCTTCTTCACTA
* *
233830 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTCACTCTACT-TCACTA
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTTACTCCACTCT-ACTA
* * *
233894 TATCCTCAGGGACGTTGAGCTTTGCTTCATTA
65 TATCATCAGGGACGTTAAGC-TT-CTTCACTA
* *
233926 TTTTGACCCACTTCTTTGTACCTCACCAAGAAGATGAGATTTGAAGTCTTACTCCACT
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTTACTCCACT
233984 GTATCCTTAG
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
91 1 0.01
92 73 0.54
94 1 0.01
96 60 0.44
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (94 bp):
TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTTACTCCACTCTACTAT
ATCATCAGGGACGTTAAGCTTCTTCACTA
Found at i:234033 original size:96 final size:94
Alignment explanation
Indices: 233738--234024 Score: 282
Period size: 92 Copynumber: 3.1 Consensus size: 94
233728 CAACATACTG
* * * * * * *
233738 TTTTGACCTACTTCTCTGTACTTCACCAGGAAGATGGGATTTGAAGTCTTACTCCACTCTACTGT
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTGAAG-C-TACTCTACTCCACTAT
** * * *
233803 ATTATCAGGGACGTTAAG--CT--TTCACTA
64 ATCCTCAGAGACGTTGAGCTCTACTTCATTA
* *
233830 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGGGATTTGAAGTCTCACTCTACTTCACTAT
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTGAAG-CT-ACTCTACTCCACTAT
* * *
233895 ATCCTCAGGGACGTTGAGCTTTGCTTCATTA
64 ATCCTCAGAGACGTTGAGCTCTACTTCATTA
* *
233926 TTTTGACCCACTTCTTTGTACCTCACCAAGAAGATGAGATTTGAAG-T-CT-TACTCCACTGTAT
1 TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTGAAGCTACTCTACTCCACTATAT
* * * *
233988 CCTTAGAGATGTTGAGCTCTACTTCGTTG
66 CCTCAGAGACGTTGAGCTCTACTTCATTA
234017 TTTTGACC
1 TTTTGACC
234025 TGACCCACTA
Statistics
Matches: 167, Mismatches: 23, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
91 42 0.25
92 73 0.44
94 2 0.01
96 50 0.30
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (94 bp):
TTTTGACCCACTTCTCTGTACCTCACCAAGAAGATGAGATTTGAAGCTACTCTACTCCACTATAT
CCTCAGAGACGTTGAGCTCTACTTCATTA
Found at i:234666 original size:97 final size:97
Alignment explanation
Indices: 234364--234802 Score: 351
Period size: 97 Copynumber: 4.5 Consensus size: 97
234354 CCTGTCATGT
* * ** *
234364 TTCTAAGGTACTA-GGTTCGCCATTGCAACCTCAACATTTCCCTTTATATTTTTATGGTACTAGA
1 TTCTAAGGTAC-AGGGTTCGCCGTTGCAACCTCAACCTTTCCC-TT-TATTTCCATGATACTAGA
** * * * * * * *
234428 TCCACTTTTAGGGCATCGAGCCTTCCCGTCACATC
63 TCCACCGTTACGACCTCAATCTTTCCCATCACATC
* **** *** * ** *
234463 TTCTAATGG-ACAAGGTTCATTATTGTGGCCTCAACCTTTCTCTTTATATTTTTATGGTACTAGA
1 TTCTAA-GGTACAGGGTTCGCCGTTGCAACCTCAACCTTTC-CCTT-TATTTCCATGATACTAGA
* ** * *
234527 TTCGTCGTTGCGGCCTCAATCTTTCCCATCACATC
63 TCCACCGTTACGACCTCAATCTTTCCCATCACATC
* *
234562 TTCTAAGGTACAGGGTTCGCCGTTACAACCTCAACCTTTCCCTTTATTTCCATGATATTAGATCC
1 TTCTAAGGTACAGGGTTCGCCGTTGCAACCTCAACCTTTCCCTTTATTTCCATGATACTAGATCC
* * * **
234627 ACCGTTATGACCTCGATCTTTCTCATCATGTC
66 ACCGTTACGACCTCAATCTTTCCCATCACATC
* * * * *
234659 TTCTAAGGTAAAGGATTCGTCGTTGCAACCTCAACCTTTCCCTTTATTTCCATGGTACTAGATTC
1 TTCTAAGGTACAGGGTTCGCCGTTGCAACCTCAACCTTTCCCTTTATTTCCATGATACTAGATCC
* * * *
234724 ACCGTTGCGGCCTTAATCCTTCCCATCACATC
66 ACCGTTACGACCTCAATCTTTCCCATCACATC
* * **
234756 TTCTAAAGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTAT
1 TTCTAAGGTACAGGGTTCGCCGTTGCAACCTCAACCTTTCCCTTTAT
234803 ATCTTCATGT
Statistics
Matches: 269, Mismatches: 67, Indels: 10
0.78 0.19 0.03
Matches are distributed among these distances:
97 160 0.59
98 6 0.02
99 100 0.37
100 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (97 bp):
TTCTAAGGTACAGGGTTCGCCGTTGCAACCTCAACCTTTCCCTTTATTTCCATGATACTAGATCC
ACCGTTACGACCTCAATCTTTCCCATCACATC
Found at i:234731 original size:47 final size:46
Alignment explanation
Indices: 234581--234729 Score: 109
Period size: 47 Copynumber: 3.1 Consensus size: 46
234571 ACAGGGTTCG
* *
234581 CCGTTACAACCTCAACCTTTCCCTTTATTTCCATGATATTAGATCCA
1 CCGTTACAACCTCAACCTTTCCCTTTATTTCCATGGTA-TAGATTCA
** * * * * * * * * *
234628 CCGTTATGACCTCGATCTTTCTCATCATGTCTTCTAAGGTAAAGGATTCG
1 CCGTTACAACCTCAACCTTTC-CCT-TTAT-TTCCATGGTATA-GATTCA
* *
234678 TCGTTGCAACCTCAACCTTTCCCTTTATTTCCATGGTACTAGATTCA
1 CCGTTACAACCTCAACCTTTCCCTTTATTTCCATGGTA-TAGATTCA
234725 CCGTT
1 CCGTT
234730 GCGGCCTTAA
Statistics
Matches: 70, Mismatches: 27, Indels: 10
0.65 0.25 0.09
Matches are distributed among these distances:
47 34 0.49
48 5 0.07
49 5 0.07
50 26 0.37
ACGTcount: A:0.22, C:0.29, G:0.12, T:0.37
Consensus pattern (46 bp):
CCGTTACAACCTCAACCTTTCCCTTTATTTCCATGGTATAGATTCA
Found at i:234807 original size:50 final size:50
Alignment explanation
Indices: 234489--234808 Score: 181
Period size: 50 Copynumber: 6.5 Consensus size: 50
234479 TCATTATTGT
* * * * * *
234489 GGCCTCAACCTTTCTCTTTATAT-TTTTATGGTACTAGATTCGTCGTTGC
1 GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
* * * * * *
234538 GGCCTCAATCTTTCCCATCACATCTTCTAAGGTACAGGGTTCGCCGTTAC
1 GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
** * * * ** * * **
234588 AACCTCAACCTTTCCC-TT-TAT-TTCCATGATATTAGATCCACCGTTAT
1 GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
* * * * * * *
234635 GACCTCGATCTTTCTCATCATGTCTTCTAAGGTA-AAGGATTCGTCGTTGC
1 GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAA-GATTCGCCGTTGC
** * * * *
234685 AACCTCAACCTTTCCC-TT-TAT-TTCCATGGTACTAGATTCACCGTTGC
1 GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
* * * * *
234732 GGCCTTAATCC-TTCCCATCACATCTTCTAAAGTACAAGGTTCGCCGTTGC
1 GGCCTCAA-CCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
*
234782 GGCCTCAACCTTTCCCTTTATATCTTC
1 GGCCTCAACCTTTCCCATTATATCTTC
234809 ATGTTTCCTC
Statistics
Matches: 192, Mismatches: 68, Indels: 21
0.68 0.24 0.07
Matches are distributed among these distances:
47 57 0.30
48 9 0.05
49 27 0.14
50 99 0.52
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.36
Consensus pattern (50 bp):
GGCCTCAACCTTTCCCATTATATCTTCTAAGGTACAAGATTCGCCGTTGC
Found at i:235426 original size:105 final size:107
Alignment explanation
Indices: 235240--235442 Score: 252
Period size: 105 Copynumber: 1.9 Consensus size: 107
235230 TCATTAGACT
*** *
235240 AATAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTTTTAAGGTGAATGAAATTGACTTT
1 AATAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCGCAAGGTGAATGAAATTGAATTT
*
235305 GATTGAAGGCAGAGCTCGA-ATAAATGAAAAGATCATTGGTTC
66 GATTGAAGGCAAAGCTC-ACATAAATGAAAAGATCATTGGTTC
** * *
235347 AATAACCGTTATTT-TGATGCAGAAATGCTTGAA-CATGGTCGCAAGGTGAAT-AACATTGAATT
1 AATAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCGCAAGGTGAATGAA-ATTGAATT
* * *
235409 TTATTGGAGGCAAAGCTCACATGAATGAAAAGAT
65 TGATTGAAGGCAAAGCTCACATAAATGAAAAGAT
235443 TAAAAATGAC
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 3 0.04
105 49 0.60
106 16 0.20
107 14 0.17
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (107 bp):
AATAACCGTTATTTCAAATGCAAAAATGCTTGAATCAAGGTCGCAAGGTGAATGAAATTGAATTT
GATTGAAGGCAAAGCTCACATAAATGAAAAGATCATTGGTTC
Found at i:240625 original size:13 final size:13
Alignment explanation
Indices: 240599--240635 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
240589 AAAAAAAAAC
*
240599 TTCTCCTCTCTTTT
1 TTCT-CTCTTTTTT
240613 TTCTCTCTTTTTT
1 TTCTCTCTTTTTT
240626 TTCTCTCTTT
1 TTCTCTCTTT
240636 CTTCCGTCCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTCTCTTTTTT
Found at i:246766 original size:22 final size:22
Alignment explanation
Indices: 246741--246813 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 22
246731 TTTGCAATTG
246741 ATTTTTTAATTCAATTCAATCA
1 ATTTTTTAATTCAATTCAATCA
* * * **
246763 A-TTTTGAGTACAATTTTGCAATTG
1 ATTTTTTAATTCAA--TT-CAATCA
*
246787 ATTTTTTAACTCAATTCAATCA
1 ATTTTTTAATTCAATTCAATCA
246809 ATTTT
1 ATTTT
246814 GAGTAGTTCG
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
21 9 0.25
22 10 0.28
23 4 0.11
24 5 0.14
25 8 0.22
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.49
Consensus pattern (22 bp):
ATTTTTTAATTCAATTCAATCA
Found at i:246791 original size:46 final size:46
Alignment explanation
Indices: 246724--246818 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
246714 CTTTTAACAC
*
246724 GTACAATTTTGCAATTGATTTTTTAATTCAATTCAATCAATTTTGA
1 GTACAATTTTGCAATTGATTTTTTAACTCAATTCAATCAATTTTGA
246770 GTACAATTTTGCAATTGATTTTTTAACTCAATTCAATCAATTTTGA
1 GTACAATTTTGCAATTGATTTTTTAACTCAATTCAATCAATTTTGA
246816 GTA
1 GTA
246819 GTTCGTATGC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.46
Consensus pattern (46 bp):
GTACAATTTTGCAATTGATTTTTTAACTCAATTCAATCAATTTTGA
Found at i:247104 original size:16 final size:16
Alignment explanation
Indices: 247083--247121 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
247073 ATGATTCGAG
* *
247083 TCAATTTTATATTTAA
1 TCAATTTTAAATTGAA
247099 TCAATTTTAAATTGAA
1 TCAATTTTAAATTGAA
247115 TCGAATT
1 TC-AATT
247122 CCGAGTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (16 bp):
TCAATTTTAAATTGAA
Found at i:251483 original size:2 final size:2
Alignment explanation
Indices: 251476--251508 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
251466 ATGTACATGC
251476 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
251509 GGAAGTGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:251877 original size:31 final size:31
Alignment explanation
Indices: 251808--251886 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
251798 GAAATTTTTA
* * **
251808 AATTTAAAAATTAAAAAAACTAAAATTGATC
1 AATTTAAAAAATAAAAAAAATAAAATAAATC
*
251839 AATTTAAAAAATAAAAAAAATAAAATAAACTG
1 AATTTAAAAAATAAAAAAAATAAAATAAA-TC
*
251871 AA-TTAAAATATAAAAA
1 AATTTAAAAAATAAAAA
251887 TTAAATCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 38 0.93
32 3 0.07
ACGTcount: A:0.68, C:0.04, G:0.03, T:0.25
Consensus pattern (31 bp):
AATTTAAAAAATAAAAAAAATAAAATAAATC
Found at i:253374 original size:25 final size:28
Alignment explanation
Indices: 253342--253396 Score: 89
Period size: 25 Copynumber: 2.1 Consensus size: 28
253332 GTCACACAAT
253342 TTTTTAACAGTA-AAAAT-AGATGA-AA
1 TTTTTAACAGTAGAAAATGAGATGATAA
253367 TTTTTAACAGTAGAAAATGAGATGATAA
1 TTTTTAACAGTAGAAAATGAGATGATAA
253395 TT
1 TT
253397 GCTAAGTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 12 0.44
26 5 0.19
27 6 0.22
28 4 0.15
ACGTcount: A:0.47, C:0.04, G:0.15, T:0.35
Consensus pattern (28 bp):
TTTTTAACAGTAGAAAATGAGATGATAA
Found at i:255030 original size:29 final size:28
Alignment explanation
Indices: 255011--255067 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
255001 ATAGATGAAT
255011 TAAATTCATAAAAATAAAAATAAAAAAAC
1 TAAATTC-TAAAAATAAAAATAAAAAAAC
* *
255040 TAAATTCTAAATATAAAAAATACAAAAA
1 TAAATTCTAAAAAT-AAAAATAAAAAAA
255068 TTTGAAGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 6 0.24
29 19 0.76
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (28 bp):
TAAATTCTAAAAATAAAAATAAAAAAAC
Found at i:256543 original size:15 final size:15
Alignment explanation
Indices: 256503--256534 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
256493 TTATTTTTTA
256503 TTTTAATTAAT--CT
1 TTTTAATTAATAACT
256516 TTTTAATTAATAACT
1 TTTTAATTAATAACT
256531 TTTT
1 TTTT
256535 TATTCATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.65
15 6 0.35
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAATTAATAACT
Found at i:260067 original size:81 final size:81
Alignment explanation
Indices: 259982--260136 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
259972 TACGATAGTA
* * * * *
259982 AAAATATAATTTTATCATT-TTAATATTTATATTTTTATAATTTTTAAATAGT-TAAATCAAATT
1 AAAATATAATTTTATCATTATT-A-ATTTAAAATTTTATAAATTATAAAAAGTGTAAATCAAATT
260045 TTTATCATTTTTAGGGTT
64 TTTATCATTTTTAGGGTT
*
260063 AAAATATAATTTTATCATTATTAATTTAAAATTTTATAAATTATAAAAAGTGTAAATTAAATTTT
1 AAAATATAATTTTATCATTATTAATTTAAAATTTTATAAATTATAAAAAGTGTAAATCAAATTTT
260128 TATCATTTT
66 TATCATTTT
260137 AAGAGATCAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 23 0.35
81 41 0.62
82 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (81 bp):
AAAATATAATTTTATCATTATTAATTTAAAATTTTATAAATTATAAAAAGTGTAAATCAAATTTT
TATCATTTTTAGGGTT
Found at i:267106 original size:18 final size:18
Alignment explanation
Indices: 267085--267171 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 18
267075 CTCATTTTGG
267085 GTTTAAATTTAATTTAAA
1 GTTTAAATTTAATTTAAA
* **
267103 GTTTGAACTTTTTTTTTAAA
1 GTTT-AA-ATTTAATTTAAA
*
267123 GTTTAAATTTAAATT-AA
1 GTTTAAATTTAATTTAAA
* *
267140 GTTTAAAATTAATTTGAA
1 GTTTAAATTTAATTTAAA
267158 -TTTAAAATTTAATT
1 GTTT-AAATTTAATT
267172 AATATAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
17 18 0.33
18 20 0.36
19 4 0.07
20 13 0.24
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (18 bp):
GTTTAAATTTAATTTAAA
Found at i:267143 original size:17 final size:17
Alignment explanation
Indices: 267121--267173 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
267111 TTTTTTTTTA
267121 AAGTTTAAATTTAAATT
1 AAGTTTAAATTTAAATT
* *
267138 AAGTTTAAAATTAATTT
1 AAGTTTAAATTTAAATT
267155 GAA-TTTAAAATTT-AATT
1 -AAGTTT-AAATTTAAATT
267172 AA
1 AA
267174 TATAAAAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.07
17 21 0.70
18 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
AAGTTTAAATTTAAATT
Found at i:268946 original size:29 final size:28
Alignment explanation
Indices: 268908--269232 Score: 262
Period size: 29 Copynumber: 11.1 Consensus size: 28
268898 GAGGTCCCTA
268908 AACTGTCCAAAAATTCCATTTTTACCCTCG
1 AACT-TCCAAAAATTCCATTTTTACCC-CG
* * * *
268938 AACTTCCAATAATCCCATTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTACCCC-G
* *
268967 AACTTCCAAAAATCCCATTTTTTGACCCCAA
1 AACTTCCAAAAATTCCA-TTTTT-ACCCC-G
*** **
268998 AACTTCCAAAAATTTTGTTTTTACCCTTA
1 AACTTCCAAAAATTCCATTTTTACCC-CG
* * *
269027 AATTTCCAAAAATCCCATTTTTAACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCC-G
269057 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCC-CG
*
269086 AACTTCCAAAAA-TCTCATTTTGACCCCG
1 AACTTCCAAAAATTC-CATTTTTACCCCG
* * *
269114 AAACTTCTAAAAATTCCATATTTACCCCTA
1 -AACTTCCAAAAATTCCATTTTTACCCC-G
* *
269144 AACTTCCAAAAATCCCATTTTTGACCTCG
1 AACTTCCAAAAATTCCATTTTT-ACCCCG
269173 AAACTTCCAAAAATTACCA-TTTTACCCCCG
1 -AACTTCCAAAAATT-CCATTTTTA-CCCCG
*
269203 AA-TGT-CAAAAATTCTATTTTTAACCCCG
1 AACT-TCCAAAAATTCCATTTTT-ACCCCG
269231 AA
1 AA
269233 TTTTCCTAAA
Statistics
Matches: 244, Mismatches: 33, Indels: 38
0.77 0.10 0.12
Matches are distributed among these distances:
27 2 0.01
28 25 0.10
29 128 0.52
30 66 0.27
31 23 0.09
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
AACTTCCAAAAATTCCATTTTTACCCCG
Found at i:269200 original size:59 final size:58
Alignment explanation
Indices: 268903--269200 Score: 343
Period size: 59 Copynumber: 5.1 Consensus size: 58
268893 CCCCGGAGGT
* * *
268903 CCCTAAACTGTCCAAAAATTCCATTTTT-ACCCTCG-AACTTCCAATAATCCCATTTTGAC
1 CCCTAAACT-TCCAAAAATCCCATTTTTGACCC-CGAAACTTCCAAAAATTCCATTTT-AC
* * ***
268962 CCCAAAACTTCCAAAAATCCCATTTTTTGACCCCAAAACTTCCAAAAATTTTGTTTTTAC
1 CCCTAAACTTCCAAAAATCCCA-TTTTTGACCCCGAAACTTCCAAAAA-TTCCATTTTAC
* * * *
269022 CCTTAAATTTCCAAAAATCCCATTTTTAACCCCAAAACTTCCAAAAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCA-TTTTAC
* * *
269080 CCCTCGAACTTCCAAAAATCTCA-TTTTGACCCCGAAACTTCTAAAAATTCCATATTTAC
1 CCCT-AAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCAT-TTTAC
*
269139 CCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTACCATTTTAC
1 CCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATT-CCATTTTAC
269198 CCC
1 CCC
269201 CGAATGTCAA
Statistics
Matches: 203, Mismatches: 26, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
57 1 0.00
58 63 0.31
59 94 0.46
60 40 0.20
61 5 0.02
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTAC
Found at i:270289 original size:28 final size:27
Alignment explanation
Indices: 270235--270292 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
270225 CATTTGGGTG
* * *
270235 TTTGGTCACTTTGGCTCTTAAGATTTT
1 TTTGGTCACTTTGGCCCCTAACATTTT
*
270262 TTTGGCTCACTTTGGCCCCTAACCTTTT
1 TTTGG-TCACTTTGGCCCCTAACATTTT
270290 TTT
1 TTT
270293 TTGGGTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.12, C:0.22, G:0.16, T:0.50
Consensus pattern (27 bp):
TTTGGTCACTTTGGCCCCTAACATTTT
Found at i:270398 original size:12 final size:12
Alignment explanation
Indices: 270381--270440 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 12
270371 TTTCCACATG
270381 AATATATTTTAA
1 AATATATTTTAA
*
270393 AATATAATTTAAAAAA
1 AATAT-ATTT---TAA
270409 AATATATTTTAA
1 AATATATTTTAA
*
270421 AAT-TAATTTAA
1 AATATATTTTAA
270432 AAT-TATTTT
1 AATATATTTT
270441 TTAAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 15 0.38
12 10 0.25
13 4 0.10
15 4 0.10
16 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATATATTTTAA
Found at i:270412 original size:16 final size:16
Alignment explanation
Indices: 270391--270422 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
270381 AATATATTTT
270391 AAAATATAATTTAAAA
1 AAAATATAATTTAAAA
*
270407 AAAATATATTTTAAAA
1 AAAATATAATTTAAAA
270423 TTAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATATAATTTAAAA
Found at i:270421 original size:28 final size:27
Alignment explanation
Indices: 270381--270433 Score: 97
Period size: 28 Copynumber: 1.9 Consensus size: 27
270371 TTTCCACATG
270381 AATATATTTTAAAATATAATTTAAAAAA
1 AATATATTTTAAAAT-TAATTTAAAAAA
270409 AATATATTTTAAAATTAATTTAAAA
1 AATATATTTTAAAATTAATTTAAAA
270434 TTATTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATATATTTTAAAATTAATTTAAAAAA
Found at i:270762 original size:28 final size:29
Alignment explanation
Indices: 270730--270788 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
270720 AAACCCATTT
270730 CAAAA-GAAATAAAAACTTTGTTGAAAAA
1 CAAAACGAAATAAAAACTTTGTTGAAAAA
* *
270758 CAAAACGAATTAAAAACTTTGTTGAAGAA
1 CAAAACGAAATAAAAACTTTGTTGAAAAA
270787 CA
1 CA
270789 TGGATAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (29 bp):
CAAAACGAAATAAAAACTTTGTTGAAAAA
Found at i:271331 original size:21 final size:22
Alignment explanation
Indices: 271290--271331 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
271280 AAAATTATTT
*
271290 AATAATTTTATTATTTCAAAAA
1 AATAATTTTATTATTTAAAAAA
271312 AATAATTTTA-TATTTAAAAA
1 AATAATTTTATTATTTAAAAA
271332 TATTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAATTTTATTATTTAAAAAA
Found at i:271347 original size:47 final size:49
Alignment explanation
Indices: 271278--271370 Score: 129
Period size: 47 Copynumber: 1.9 Consensus size: 49
271268 AAAATTGAAA
*
271278 TTAAAATTATTTAATAATTTTATTA-TTTCAAAAAAATAAT-TTTATAT
1 TTAAAAATATTTAATAATTTTATTATTTTCAAAAAAATAATATTTATAT
**
271325 TTAAAAATATTTAA-ATATTTTATTATTTTTTAAAAAATAATATTTA
1 TTAAAAATATTTAATA-ATTTTATTATTTTCAAAAAAATAATATTTA
271371 AAATTTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
46 1 0.03
47 22 0.55
48 13 0.32
49 4 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (49 bp):
TTAAAAATATTTAATAATTTTATTATTTTCAAAAAAATAATATTTATAT
Found at i:273688 original size:31 final size:31
Alignment explanation
Indices: 273625--273689 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
273615 ATAATCTATA
*
273625 TTTTCATAATTTTTAAAAAACTAAATTAAAT
1 TTTTCATAATTTTTAAAAAACAAAATTAAAT
*
273656 TTTTTATAA-TTTTAAAAAATCAAAA-TATAAT
1 TTTTCATAATTTTTAAAAAA-CAAAATTA-AAT
273687 TTT
1 TTT
273690 ACCATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 12 0.40
31 18 0.60
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (31 bp):
TTTTCATAATTTTTAAAAAACAAAATTAAAT
Found at i:282701 original size:22 final size:22
Alignment explanation
Indices: 282671--282721 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
282661 TCAAAACTAG
* *
282671 GTCTCGAGACACAAGTTGTAGT
1 GTCTTGAGACACAAGTTGCAGT
*
282693 GTCTTGAGACATAAGTTGCAGT
1 GTCTTGAGACACAAGTTGCAGT
282715 GTCTTGA
1 GTCTTGA
282722 AACGTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (22 bp):
GTCTTGAGACACAAGTTGCAGT
Found at i:285540 original size:12 final size:13
Alignment explanation
Indices: 285521--285551 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
285511 TAGGGAAATA
285521 ACAAAACTTAACG
1 ACAAAACTTAACG
285534 A-AAAACTTAACG
1 ACAAAACTTAACG
285546 ACAAAA
1 ACAAAA
285552 TGACTATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.61, C:0.19, G:0.06, T:0.13
Consensus pattern (13 bp):
ACAAAACTTAACG
Found at i:287068 original size:33 final size:33
Alignment explanation
Indices: 287029--287141 Score: 122
Period size: 33 Copynumber: 3.4 Consensus size: 33
287019 AGCCACCTCT
* *
287029 GAGATCTTTTCATCAACCTCTGAAGTCTCTTCT
1 GAGATCTTTTCATCAACCTCTGAAGCCTCTTCA
* **
287062 GAGATCTTTTCATCAGCCTCCAAAGCCATC-TCA
1 GAGATCTTTTCATCAACCTCTGAAGCC-TCTTCA
* *
287095 GAGATATTTTCATCAACCTTTGAA-CCTACTTCA
1 GAGATCTTTTCATCAACCTCTGAAGCCT-CTTCA
*
287128 GAAATCTTTTCATC
1 GAGATCTTTTCATC
287142 TGCCCCATCC
Statistics
Matches: 65, Mismatches: 12, Indels: 6
0.78 0.14 0.07
Matches are distributed among these distances:
31 1 0.02
32 3 0.05
33 59 0.91
34 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (33 bp):
GAGATCTTTTCATCAACCTCTGAAGCCTCTTCA
Found at i:287105 original size:66 final size:66
Alignment explanation
Indices: 287017--287141 Score: 171
Period size: 66 Copynumber: 1.9 Consensus size: 66
287007 ATCCGCTTCT
* * * * *
287017 AAAGCCACCTCTGAGATCTTTTCATCAACCTCTGAAGTCT-CTTCTGAGATCTTTTCATCAGCCT
1 AAAGCCACCTCAGAGATATTTTCATCAACCTCTGAA-CCTACTTCAGAAATCTTTTCATCAGCCT
287081 CC
65 CC
* *
287083 AAAGCCATCTCAGAGATATTTTCATCAACCTTTGAACCTACTTCAGAAATCTTTTCATC
1 AAAGCCACCTCAGAGATATTTTCATCAACCTCTGAACCTACTTCAGAAATCTTTTCATC
287142 TGCCCCATCC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 2 0.04
66 49 0.96
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (66 bp):
AAAGCCACCTCAGAGATATTTTCATCAACCTCTGAACCTACTTCAGAAATCTTTTCATCAGCCTC
C
Found at i:290279 original size:85 final size:85
Alignment explanation
Indices: 290136--290305 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
290126 TAACATGACA
290136 AAACCAGCACTTTTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACATTGAGATGTCTC
1 AAACCAGCACTTTTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACATTGAGATGTCTC
290201 AAATGCATCATATCAGTCTT
66 AAATGCATCATATCAGTCTT
290221 AAACCAGCACTTTTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACATTGAGATGTCTC
1 AAACCAGCACTTTTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACATTGAGATGTCTC
290286 AAATGCATCATATCAGTCTT
66 AAATGCATCATATCAGTCTT
290306 CCTCTTTGCT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (85 bp):
AAACCAGCACTTTTAAATCACATAATTGATATACAAGTAAAATCTAGAAGACATTGAGATGTCTC
AAATGCATCATATCAGTCTT
Found at i:296505 original size:16 final size:16
Alignment explanation
Indices: 296484--296541 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
296474 AATATCTATG
296484 TCAATCGAGTTAAAAC
1 TCAATCGAGTTAAAAC
*
296500 TCAATCGATAATTATAATA-
1 TCAATCG--AGTTA-AA-AC
*
296519 TCAATCGAGCTAAAAC
1 TCAATCGAGTTAAAAC
296535 TCAATCG
1 TCAATCG
296542 GCAATTATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 1 0.03
16 16 0.47
17 3 0.09
18 4 0.12
19 9 0.26
20 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (16 bp):
TCAATCGAGTTAAAAC
Found at i:296533 original size:35 final size:35
Alignment explanation
Indices: 296484--296550 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
296474 AATATCTATG
* *
296484 TCAATCGAGTTAAAACTCAATCGATAATTATAATA
1 TCAATCGAGCTAAAACTCAATCGACAATTATAATA
*
296519 TCAATCGAGCTAAAACTCAATCGGCAATTATA
1 TCAATCGAGCTAAAACTCAATCGACAATTATA
296551 TGATGTGATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.28
Consensus pattern (35 bp):
TCAATCGAGCTAAAACTCAATCGACAATTATAATA
Found at i:304163 original size:2 final size:2
Alignment explanation
Indices: 304127--304152 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
304117 TTTGGCACAA
304127 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
304153 TGCACATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:308084 original size:31 final size:28
Alignment explanation
Indices: 308014--308090 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
308004 CGGTTACATT
*
308014 TAACACAACAGTCACTCAACTTTGAAAA
1 TAACAAAACAGTCACTCAACTTTGAAAA
308042 TATGACAAAACAGTCACT-AACGTTATCGAAAA
1 TA--ACAAAACAGTCACTCAAC-TT-T-GAAAA
*
308074 GTAACAAAACAATCACT
1 -TAACAAAACAGTCACT
308091 GATTAACAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
28 2 0.05
29 3 0.07
30 15 0.37
31 14 0.34
32 5 0.12
33 2 0.05
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.21
Consensus pattern (28 bp):
TAACAAAACAGTCACTCAACTTTGAAAA
Found at i:308474 original size:61 final size:62
Alignment explanation
Indices: 308365--308481 Score: 146
Period size: 61 Copynumber: 1.9 Consensus size: 62
308355 GTATAATAAT
* * * * *
308365 AAATTTAACCTTCAATATTTAACCATTTTGTTAATTTAATCCCGATTTT-AAAATTTTCAAC
1 AAATTTAACCCTCAATATTTAAACATTCTGTCAATTTAATCCCAATTTTGAAAATTTTCAAC
* * **
308426 AAATTTAACCCTCCATATTTAAATATTCTGTCAATTTAATCTTAATTTTGAAAATT
1 AAATTTAACCCTCAATATTTAAACATTCTGTCAATTTAATCCCAATTTTGAAAATT
308482 AAAAATTGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
61 40 0.87
62 6 0.13
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.44
Consensus pattern (62 bp):
AAATTTAACCCTCAATATTTAAACATTCTGTCAATTTAATCCCAATTTTGAAAATTTTCAAC
Found at i:308695 original size:6 final size:6
Alignment explanation
Indices: 308684--308736 Score: 88
Period size: 6 Copynumber: 8.7 Consensus size: 6
308674 GGTTTATTTG
*
308684 ATTTTC ATTTTC ATTTTC ATTTTT ATTTTC ATTTTC ATTTTC ATTTTC
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC
308732 GATTT
1 -ATTT
308737 AAGGTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
6 40 0.91
7 4 0.09
ACGTcount: A:0.17, C:0.13, G:0.02, T:0.68
Consensus pattern (6 bp):
ATTTTC
Found at i:309356 original size:24 final size:24
Alignment explanation
Indices: 309323--309373 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
309313 AGAAATAATC
* *
309323 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
309347 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
309371 TTT
1 TTT
309374 GAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:315889 original size:17 final size:18
Alignment explanation
Indices: 315853--315890 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
315843 ATATAAAATA
* *
315853 TTTATTAATATTTTAGAT
1 TTTATAAATATTCTAGAT
315871 TTTATAAATATTCTA-AT
1 TTTATAAATATTCTAGAT
315888 TTT
1 TTT
315891 TCATATAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTATAAATATTCTAGAT
Found at i:316022 original size:27 final size:28
Alignment explanation
Indices: 315990--316057 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
315980 AATACTTTTA
315990 ATTTTAAATTTTCAAAATT-TTATT-AAT
1 ATTTTAAATTTTCAAAATTATT-TTGAAT
* *
316017 ATTTTAAATTTTAAAAATTATTTTGATT
1 ATTTTAAATTTTCAAAATTATTTTGAAT
*
316045 TTTTTAAATTTTC
1 ATTTTAAATTTTC
316058 GTTGAATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.57
28 15 0.43
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTTAAATTTTCAAAATTATTTTGAAT
Found at i:321210 original size:13 final size:13
Alignment explanation
Indices: 321192--321222 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
321182 ATTTACTTGA
321192 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
321205 TTCTTTTTCTTTT
1 TTCTTTTTCTTTT
*
321218 ATCTT
1 TTCTT
321223 CTTTTGTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTTTCTTTT
Found at i:328018 original size:58 final size:59
Alignment explanation
Indices: 327921--328060 Score: 149
Period size: 58 Copynumber: 2.4 Consensus size: 59
327911 GATACTCGGG
** **
327921 GGGTAAAATGGTAATTTTGGGAAAAATTAGGGTTTAAAATGGA-ATTTTAGACACTCGA
1 GGGTAAAATGGTAATTTTTAGAAAAATTAGGGTAAAAAATGGAGATTTTAGACACTCGA
* * * * ** *
327979 GGGTAAAACGGTAATTTTTAGAAAAA-TCGGGATAAAAAATGGAGTTTTTGGACTTTCGG
1 GGGTAAAATGGTAATTTTTAGAAAAATTAGGG-TAAAAAATGGAGATTTTAGACACTCGA
*
328038 GGGTAAAATGGTATTTTTTAGAA
1 GGGTAAAATGGTAATTTTTAGAA
328061 GTTTCAAGGT
Statistics
Matches: 67, Mismatches: 13, Indels: 3
0.81 0.16 0.04
Matches are distributed among these distances:
57 4 0.06
58 32 0.48
59 31 0.46
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.32
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTAGAAAAATTAGGGTAAAAAATGGAGATTTTAGACACTCGA
Found at i:328076 original size:59 final size:58
Alignment explanation
Indices: 328013--328175 Score: 179
Period size: 59 Copynumber: 2.8 Consensus size: 58
328003 AATCGGGATA
* * *
328013 AAAAATGGAGTTTTTGGACTTTCGGGGGTAAAATGGT-ATTTTTTAGAAGTTTCAAGGTT
1 AAAAATGGAATTTTTGGACTTT-GAGGGTAAAATGGTAATTTTTGAG-AGTTTCAAGGTT
* * **
328072 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAATGGTAATTTTTGAGAGTTTTGAGGTT
1 AAAAATGGAATTTTTGG-ACTTTGAGGGTAAAATGGTAATTTTTGAGAGTTTCAAGGTT
*
328131 AAAAATGGAATTTTTGGAAGTTTTGA-GGTCAAAATGG-AATTTTTG
1 AAAAATGGAATTTTTGG-A-CTTTGAGGGT-AAAATGGTAATTTTTG
328176 TATAGTTTAG
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
59 67 0.74
60 24 0.26
ACGTcount: A:0.32, C:0.02, G:0.26, T:0.39
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACTTTGAGGGTAAAATGGTAATTTTTGAGAGTTTCAAGGTT
Found at i:328086 original size:30 final size:30
Alignment explanation
Indices: 328042--328175 Score: 145
Period size: 30 Copynumber: 4.5 Consensus size: 30
328032 TTTCGGGGGT
* * *
328042 AAAATGGTATTTTTTAGAAGTTTCAAGGTTA
1 AAAATGGTAATTTTTGGAAGTTT-GAGGTTA
*
328073 AAAAT-GTAATTTTTGGAAGTTTGAGGGT-
1 AAAATGGTAATTTTTGGAAGTTTGAGGTTA
328101 AAAATGGTAATTTTT-GAGAGTTTTGAGGTTA
1 AAAATGGTAATTTTTGGA-AG-TTTGAGGTTA
*
328132 AAAATGG-AATTTTTGGAAGTTTTGAGG-TC
1 AAAATGGTAATTTTTGGAAG-TTTGAGGTTA
328161 AAAATGG-AATTTTTG
1 AAAATGGTAATTTTTG
328176 TATAGTTTAG
Statistics
Matches: 92, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
28 7 0.08
29 31 0.34
30 40 0.43
31 14 0.15
ACGTcount: A:0.34, C:0.01, G:0.25, T:0.40
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAGTTTGAGGTTA
Found at i:329447 original size:17 final size:18
Alignment explanation
Indices: 329425--329469 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
329415 AAAATGAATT
*
329425 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
329442 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
329460 TAAATCTAAA
1 TAAATTTAAA
329470 ACCCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:330512 original size:206 final size:206
Alignment explanation
Indices: 329923--330589 Score: 968
Period size: 206 Copynumber: 3.3 Consensus size: 206
329913 AATTTGGTCC
*
329923 ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGTATTGAGCGTGGGTTTGAT
1 ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGAT
329988 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCACATCGCTTGTTTCAATCCGCTTCTCTG
66 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCACATCGCTTGTTTCAATCCGCTTCTCTG
*
330053 TATCTTATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
131 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
* *
330118 TGCTTTGACCT
196 TGCTTCGCCCT
* * * * * * *
330129 GCTTCTCAGTATCTCATCAGGAAGCTGAGGTTTGAAGATTTGCTCGCTTTTAGCCTCGAG-TTGG
1 ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCGT-GGGTTTGA
* * * * **
330193 TAT--TCTTCTT-T--GTATCTCATCAGGAAGATAACCACCTTACTTGTTTCAATCCGCTTCTCT
65 TTTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCACATCGCTTGTTTCAATCCGCTTCTCT
* * *
330253 GTATCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTA
130 GTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTA
330318 TTGCTTCGCCCT
195 TTGCTTCGCCCT
* *
330330 ACTTCTCAGTATCTCATCAGGAAGCTGGGGGTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGAT
1 ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGAT
* * * * *
330395 TTGGTCTTCTTCTCAGTATCTTATTAGGAAGGTGACCGCATCGCTTATTTCAATCCGCTTCTTTG
66 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCACATCGCTTGTTTCAATCCGCTTCTCTG
* *
330460 TATCTCATCAGGAAGATGAATTTGGTTCACTTTTCAGTATCTCATCAGGAAGCTAACCATTTTAT
131 TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
*
330525 TGCTTCGCTCT
196 TGCTTCGCCCT
* * * * *
330536 GCTTCTCAGTATCTAATCAGGAAGCTGAGATTCGAAGATTTGCTCACATCGAGC
1 ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGC
330590 CCTGAGTTGG
Statistics
Matches: 401, Mismatches: 53, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
200 2 0.00
201 169 0.42
203 8 0.02
204 8 0.02
206 212 0.53
207 2 0.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (206 bp):
ACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCGCATTGAGCGTGGGTTTGAT
TTGGTCTTCTTCTCAGTATCTCATCAGGAAGGTGACCACATCGCTTGTTTCAATCCGCTTCTCTG
TATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTAT
TGCTTCGCCCT
Found at i:337054 original size:22 final size:21
Alignment explanation
Indices: 337028--337070 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
337018 AATTCCCTGC
337028 ATCGCATCG-ATTTTCTCCTCTA
1 ATCGCAT-GTATTTT-TCCTCTA
*
337050 ATCGCCTGTATTTTTCCTCTA
1 ATCGCATGTATTTTTCCTCTA
337071 TTTGTCTAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.16, C:0.30, G:0.09, T:0.44
Consensus pattern (21 bp):
ATCGCATGTATTTTTCCTCTA
Found at i:341481 original size:29 final size:28
Alignment explanation
Indices: 341439--341641 Score: 208
Period size: 29 Copynumber: 6.9 Consensus size: 28
341429 AAAATGGTGT
*
341439 TAAAAATAGAATTTTTGGAAGTTTGAGGG
1 TAAAAATGGAATTTTTGGAAGTTTG-GGG
* *
341468 TAAAAATGGTATTTTTTGAGAGTTTTGGGG
1 TAAAAATGGAATTTTTGGA-AG-TTTGGGG
*
341498 TTAAAAATGGAATTTTTGAAAGTTTGAGGG
1 -TAAAAATGGAATTTTTGGAAGTTTG-GGG
* *
341528 TAAAAAATGGAATTTTTGGAAATTCGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTGGGG
** *
341557 ATAAAAATATAATTTTTGGAAGTTTGAGGA
1 -TAAAAATGGAATTTTTGGAAGTTTG-GGG
*
341587 TAAAAATGTAATTTTTGGAAGTTTTGGGG
1 TAAAAATGGAATTTTTGGAAG-TTTGGGG
*
341616 TCAAAAAAGGAATTTTTGGACAGTTT
1 T-AAAAATGGAATTTTTGGA-AGTTT
341642 AGAGACCTCC
Statistics
Matches: 146, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
29 67 0.46
30 57 0.39
31 22 0.15
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTTGGGG
Found at i:341622 original size:59 final size:58
Alignment explanation
Indices: 341439--341641 Score: 241
Period size: 59 Copynumber: 3.4 Consensus size: 58
341429 AAAATGGTGT
*
341439 TAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAATGGT-ATTTTTTGAGAGTTTTGGGG
1 TAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAAT-GTAATTTTTGGA-AGTTTTGGGG
* * * * *
341498 TTAAAAATGGAATTTTTGAAAGTTTGAGGGTAAAAAATGGAATTTTTGGAA-ATTCGGGG
1 -TAAAAATAGAATTTTTGGAAGTTTGAGGGT-AAAAATGTAATTTTTGGAAGTTTTGGGG
* *
341557 ATAAAAATATAATTTTTGGAAGTTTGAGGATAAAAATGTAATTTTTGGAAGTTTTGGGG
1 -TAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGG
341616 TCAAAAA-AGGAATTTTTGGACAGTTT
1 T-AAAAATA-GAATTTTTGGA-AGTTT
341642 AGAGACCTCC
Statistics
Matches: 122, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
58 20 0.16
59 53 0.43
60 35 0.29
61 14 0.11
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (58 bp):
TAAAAATAGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGGGG
Found at i:342936 original size:17 final size:18
Alignment explanation
Indices: 342914--342958 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
342904 AAAATGAATT
*
342914 TAAATTTAAATTTA-AAG
1 TAAATTTAAATTTAGAAA
*
342931 TAAATTTAATTTTAGAAA
1 TAAATTTAAATTTAGAAA
*
342949 TAAATCTAAA
1 TAAATTTAAA
342959 ACTCATCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
TAAATTTAAATTTAGAAA
Found at i:344526 original size:5 final size:5
Alignment explanation
Indices: 344518--344546 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
344508 TGGGGTGGGG
344518 TTGGC TTGGC TTGGC TTGGC TTGGC TTGG
1 TTGGC TTGGC TTGGC TTGGC TTGGC TTGG
344547 TGGGTGAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.41, T:0.41
Consensus pattern (5 bp):
TTGGC
Found at i:347412 original size:9 final size:9
Alignment explanation
Indices: 347398--347430 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
347388 ATAGACAATA
347398 TTTAATAAC
1 TTTAATAAC
*
347407 TTTAATCAC
1 TTTAATAAC
347416 TTTAATAA-
1 TTTAATAAC
347424 TTTAATA
1 TTTAATA
347431 CAATTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAATAAC
Found at i:348955 original size:22 final size:22
Alignment explanation
Indices: 348930--349005 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
348920 AGAGCAGTGT
348930 AGTGCTAAACAGAGAGCACTAA
1 AGTGCTAAACAGAGAGCACTAA
**
348952 AGTGCTAAGTAGAGAGCACTAA
1 AGTGCTAAACAGAGAGCACTAA
* * * *
348974 AGTGCTGAACAAAGAGCGCAAA
1 AGTGCTAAACAGAGAGCACTAA
*
348996 AGCGCTAAAC
1 AGTGCTAAAC
349006 CCGTACAAGC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.13
Consensus pattern (22 bp):
AGTGCTAAACAGAGAGCACTAA
Found at i:353804 original size:20 final size:20
Alignment explanation
Indices: 353781--353821 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
353771 ACATATTATT
353781 ATTGTTTACGACATGATCTC
1 ATTGTTTACGACATGATCTC
* *
353801 ATTGTTTATGACTTGATCTC
1 ATTGTTTACGACATGATCTC
353821 A
1 A
353822 CTATTCTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTGTTTACGACATGATCTC
Found at i:365121 original size:16 final size:18
Alignment explanation
Indices: 365098--365142 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
365088 AATTGAGATC
*
365098 TAAT-AAAATTATT-AAA
1 TAATAAAAAATATTAAAA
365114 T-ATAAAAAATATTAAAA
1 TAATAAAAAATATTAAAA
365131 TAATAAAAAATA
1 TAATAAAAAATA
365143 ATCTAACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 4 0.16
18 10 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATAAAAAATATTAAAA
Found at i:370721 original size:99 final size:99
Alignment explanation
Indices: 370516--370817 Score: 588
Period size: 99 Copynumber: 3.1 Consensus size: 99
370506 TATGACATTA
370516 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCT-AACCATAGTGAT
1 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
370580 TTATTAGTAACATGAATTTATTATTTATTATGAT
66 TTATTAGTAACATGAATTTATTATTTATTATGAT
370614 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
1 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
*
370679 TTATTAGTAACATAAATTTATTATTTATTATGAT
66 TTATTAGTAACATGAATTTATTATTTATTATGAT
370713 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
1 TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
370778 TTATTAGTAACATGAATTTATTATTTATTATGAT
66 TTATTAGTAACATGAATTTATTATTTATTATGAT
370812 TAATAT
1 TAATAT
370818 ATGTTTTATT
Statistics
Matches: 201, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
98 52 0.26
99 149 0.74
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.49
Consensus pattern (99 bp):
TAATATTTTACATTTTGTTGTGTTATGATATATATAAAAATATATATTATCTAAACCATAGTGAT
TTATTAGTAACATGAATTTATTATTTATTATGAT
Found at i:373582 original size:30 final size:29
Alignment explanation
Indices: 373360--373569 Score: 242
Period size: 29 Copynumber: 7.2 Consensus size: 29
373350 TTTGAAAGTA
*
373360 AAAAATAGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * *
373389 AAAAATGGTATTTTTAGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * *
373418 AAAAATGGAATTTTTGGATGTTTCGAGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
*
373447 CAAAAATGGGA-TTTTGGAAGTTTAGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * *
373476 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTGGAAGTTT-GGGGGT
* * *
373506 AAAAATGGGATTTTTGGAAATTTTGAGGTT
1 AAAAATGGGATTTTTGG-AAGTTTGGGGGT
373536 AAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
373565 AAAAA
1 AAAAA
373570 ATAGAATTTT
Statistics
Matches: 152, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.06
29 87 0.57
30 51 0.34
31 5 0.03
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTTGGGGGT
Found at i:373608 original size:51 final size:50
Alignment explanation
Indices: 373526--373632 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 50
373516 TTTTTGGAAA
* * * * *
373526 TTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAAATAGAAT
1 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGT-AAAAATAGAAT
* *
373577 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAGTGGAAT
1 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAATAGAAT
373627 TTTTGG
1 TTTTGG
373633 ACAGTTTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 15 0.31
51 34 0.69
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.36
Consensus pattern (50 bp):
TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAATAGAAT
Found at i:374191 original size:13 final size:13
Alignment explanation
Indices: 374175--374201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
374165 AAAAAAAAAA
374175 CAAAAAAACCTCT
1 CAAAAAAACCTCT
374188 CAAAAAAACCTCT
1 CAAAAAAACCTCT
374201 C
1 C
374202 GTCCCTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAAAACCTCT
Found at i:375480 original size:17 final size:17
Alignment explanation
Indices: 375436--375502 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
375426 TAAAATAAAT
* *
375436 AATAAATTTAAATTTCA
1 AATAAACTTAAATTTAA
** * *
375453 ACCAAATTTAAATTTAG
1 AATAAACTTAAATTTAA
*
375470 AATAAACTTAATTTTAA
1 AATAAACTTAAATTTAA
* *
375487 AATAAATTTAAGTTTA
1 AATAAACTTAAATTTA
375503 TTGGGCCCAG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAAACTTAAATTTAA
Found at i:376261 original size:206 final size:206
Alignment explanation
Indices: 375871--376440 Score: 815
Period size: 206 Copynumber: 2.8 Consensus size: 206
375861 TGTTTTGATC
* * * * * * *
375871 CACTTCTCTGTGTTTCATCAGGAAGC-GATCGTTTTATTACTTCGACCTGCTCCTCAGTATATGA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * *
375935 TCAGAAAGCTGTGGTTCGAAGATTTGCTCACATCAAGTGTGGGTTTGATTTGGTCTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
*
376000 TATTTCATCGGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
131 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
376065 CGAATTTGGTT
196 CGAATTTGGTT
* * *
376076 CACTTCTCAGTGTCTCATCCGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * *
376141 TCAGGAATCTGTGGTTCGAAGATTTGCTCACATCGAGCGTTGGTCTGATTTGGTCTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
** *
376206 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCT-ATCCGCTTCTCTGTATTTCATTAGGAAG
131 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTT-TAATCCGCTTCTCAATATTTCATCAGGAAG
376270 ACGAATTTGGTT
195 ACGAATTTGGTT
* * * * *
376282 GACTTCTCAGTATCTCATTAGGAAGCTAACCG-TTTATTGCTTCGACCTGTTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * * *
376346 TCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTTGGTTTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
* *
376411 TATGTT-ATTAGGAAGATGACCGCGTCGTTT
131 TAT-TTCATCAGGAAGATGACTGCGTCGTTT
376441 ATGGGTAATC
Statistics
Matches: 325, Mismatches: 37, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
205 134 0.41
206 190 0.58
207 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (206 bp):
CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
CGAATTTGGTT
Found at i:376956 original size:27 final size:28
Alignment explanation
Indices: 376926--376986 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
376916 TCAAGAATTC
*
376926 TATTAAAAAG-AGGATCAAAGGAAGCAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
*
376953 TATTAAAAAGAAGGATCAAATGAAACAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
376981 TCATTA
1 T-ATTA
376987 GTTGGAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.33
28 16 0.53
29 4 0.13
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (28 bp):
TATTAAAAAGAAGGATCAAAGGAAACAA
Found at i:385230 original size:30 final size:29
Alignment explanation
Indices: 385008--385217 Score: 242
Period size: 29 Copynumber: 7.2 Consensus size: 29
384998 TTTGAAAGTA
*
385008 AAAAATAGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * *
385037 AAAAATGGTATTTTTAGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * * *
385066 AAAAATGGAATTTTTGGATGTTTCGAGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
*
385095 CAAAAATGGGA-TTTTGGAAGTTTAGGGGT
1 -AAAAATGGGATTTTTGGAAGTTTGGGGGT
* * *
385124 AAAAATGGAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGGATTTTTGGAAGTTT-GGGGGT
* * *
385154 AAAAATGGGATTTTTGGAAATTTTGAGGTT
1 AAAAATGGGATTTTTGG-AAGTTTGGGGGT
385184 AAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTTGGGGGT
385213 AAAAA
1 AAAAA
385218 ATAGAATTTT
Statistics
Matches: 152, Mismatches: 25, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.06
29 87 0.57
30 51 0.34
31 5 0.03
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTTGGGGGT
Found at i:385256 original size:51 final size:50
Alignment explanation
Indices: 385174--385280 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 50
385164 TTTTTGGAAA
* * * * *
385174 TTTTGAGGTTAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAAATAGAAT
1 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGT-AAAAATAGAAT
* *
385225 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAGTGGAAT
1 TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAATAGAAT
385275 TTTTGG
1 TTTTGG
385281 ACAGTTTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 15 0.31
51 34 0.69
ACGTcount: A:0.33, C:0.01, G:0.31, T:0.36
Consensus pattern (50 bp):
TTTTGGGGTCAAAAATGGGATTATTGAAAGTTTGAGGGTAAAAATAGAAT
Found at i:385839 original size:13 final size:13
Alignment explanation
Indices: 385823--385849 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
385813 AAAAAAAAAA
385823 CAAAAAAACCTCT
1 CAAAAAAACCTCT
385836 CAAAAAAACCTCT
1 CAAAAAAACCTCT
385849 C
1 C
385850 GTCCCTCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (13 bp):
CAAAAAAACCTCT
Found at i:387128 original size:17 final size:17
Alignment explanation
Indices: 387084--387150 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
387074 TAAAATAAAT
* *
387084 AATAAATTTAAATTTCA
1 AATAAACTTAAATTTAA
** * *
387101 ACCAAATTTAAATTTAG
1 AATAAACTTAAATTTAA
*
387118 AATAAACTTAATTTTAA
1 AATAAACTTAAATTTAA
* *
387135 AATAAATTTAAGTTTA
1 AATAAACTTAAATTTA
387151 TTGGGCCCAG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (17 bp):
AATAAACTTAAATTTAA
Found at i:387909 original size:206 final size:206
Alignment explanation
Indices: 387519--388088 Score: 815
Period size: 206 Copynumber: 2.8 Consensus size: 206
387509 TGTTTTGATC
* * * * * * *
387519 CACTTCTCTGTGTTTCATCAGGAAGC-GATCGTTTTATTACTTCGACCTGCTCCTCAGTATATGA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * *
387583 TCAGAAAGCTGTGGTTCGAAGATTTGCTCACATCAAGTGTGGGTTTGATTTGGTCTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
*
387648 TATTTCATCGGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
131 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
387713 CGAATTTGGTT
196 CGAATTTGGTT
* * *
387724 CACTTCTCAGTGTCTCATCCGGAAGCTAACCGTTTTATTACTTTGACTTGCTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * *
387789 TCAGGAATCTGTGGTTCGAAGATTTGCTCACATCGAGCGTTGGTCTGATTTGGTCTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
** *
387854 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTCT-ATCCGCTTCTCTGTATTTCATTAGGAAG
131 TATTTCATCAGGAAGATGACTGCGTCGTTTGTTT-TAATCCGCTTCTCAATATTTCATCAGGAAG
387918 ACGAATTTGGTT
195 ACGAATTTGGTT
* * * * *
387930 GACTTCTCAGTATCTCATTAGGAAGCTAACCG-TTTATTGCTTCGACCTGTTTCTCAGTATCTCA
1 CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
* * * *
387994 TCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGACTTGGTTTTCTTCTCAG
66 TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
* *
388059 TATGTT-ATTAGGAAGATGACCGCGTCGTTT
131 TAT-TTCATCAGGAAGATGACTGCGTCGTTT
388089 ATGGGTAATC
Statistics
Matches: 325, Mismatches: 37, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
205 134 0.41
206 190 0.58
207 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (206 bp):
CACTTCTCAGTGTCTCATCAGGAAGCTAACCGTTTTATTACTTCGACCTGCTTCTCAGTATCTCA
TCAGGAAGCTGTGGTTCGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAG
TATTTCATCAGGAAGATGACTGCGTCGTTTGTTTTAATCCGCTTCTCAATATTTCATCAGGAAGA
CGAATTTGGTT
Found at i:388604 original size:27 final size:28
Alignment explanation
Indices: 388574--388634 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
388564 TCAAGAATTC
*
388574 TATTAAAAAG-AGGATCAAAGGAAGCAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
*
388601 TATTAAAAAGAAGGATCAAATGAAACAA
1 TATTAAAAAGAAGGATCAAAGGAAACAA
388629 TCATTA
1 T-ATTA
388635 GTTGGAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 10 0.33
28 16 0.53
29 4 0.13
ACGTcount: A:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (28 bp):
TATTAAAAAGAAGGATCAAAGGAAACAA
Found at i:399851 original size:23 final size:22
Alignment explanation
Indices: 399823--399866 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
399813 ACACGGGGGT
399823 AAAATGGTAATTTTTAGAAGTTA
1 AAAATGG-AATTTTTAGAAGTTA
*
399846 AAAATGGGATTTTTAGAAGTT
1 AAAATGGAATTTTTAGAAGTT
399867 CGAGGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (22 bp):
AAAATGGAATTTTTAGAAGTTA
Found at i:399943 original size:59 final size:59
Alignment explanation
Indices: 399844--400194 Score: 255
Period size: 59 Copynumber: 6.1 Consensus size: 59
399834 TTTTAGAAGT
* * ** * *
399844 TAAAAATGGGATTTTTAG-AAGTTCGAGGGAAAAAAATGGGATTTTTGAAAGTTCGGGGG
1 TAAAAATGGAATTTTTAGAAATTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
* * *
399903 TAAAATTGGATTTTTTAGAAATTTCGAGGTCAAAATTGGGATTTTTGGAAGTTTGGGGG
1 TAAAAATGGAATTTTTAGAAATTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
* * * * * *
399962 TAAAAATGGAATTTTTGGAAGTTTCGGGGTTAAAAAAGGGATTTTTGGAAGTTTGAGGG
1 TAAAAATGGAATTTTTAGAAATTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
* * *
400021 TAAAAATGAAATTTTT-G-------G-GGTCAAAAATGAGATTTTTTGAAGTTTGGGGG
1 TAAAAATGGAATTTTTAGAAATTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
* ** * * * * * *
400071 TAAAATTGGTTTTTTTTGGAAGTTT-TAGGGTCAAAAATGGGATATTTGGAAGTTTCGAGG
1 TAAAAATGG-AATTTTTAGAAATTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
* * * * *
400131 TCAAAAAT-GAGA-TTTT-GGAAGTTCGGGGGT-AAAAATGGAATTTTTGGAAGTTTTGGGG
1 T-AAAAATGGA-ATTTTTAGAAATTTC-GAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
400189 TAAAAA
1 TAAAAA
400195 ATGAGATTAT
Statistics
Matches: 231, Mismatches: 46, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
50 34 0.15
51 6 0.03
52 1 0.00
57 5 0.02
58 30 0.13
59 114 0.49
60 36 0.16
61 5 0.02
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
TAAAAATGGAATTTTTAGAAATTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
Found at i:400034 original size:29 final size:29
Alignment explanation
Indices: 399844--400247 Score: 255
Period size: 30 Copynumber: 14.0 Consensus size: 29
399834 TTTTAGAAGT
* *
399844 TAAAAATGGGATTTTTAGAAGTTCGAGGG
1 TAAAAATGGGATTTTTGGAAGTTTGAGGG
* * * *
399873 AAAAAAATGGGATTTTTGAAAGTTCGGGGG
1 -TAAAAATGGGATTTTTGGAAGTTTGAGGG
* * *
399903 T-AAAATTGGATTTTTTAGAAATTTCGA-GG
1 TAAAAATGGGA-TTTTTGGAAGTTT-GAGGG
* *
399932 TCAAAATTGGGATTTTTGGAAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGAGGG
*
399962 TAAAAATGGAATTTTTGGAAGTTTCG-GGG
1 TAAAAATGGGATTTTTGGAAGTTT-GAGGG
*
399991 TTAAAAAAGGGATTTTTGGAAGTTTGAGGG
1 -TAAAAATGGGATTTTTGGAAGTTTGAGGG
**
400021 TAAAAAT--GA-AATT-----TTTG-GGG
1 TAAAAATGGGATTTTTGGAAGTTTGAGGG
* * *
400041 TCAAAAATGAGATTTTTTGAAGTTTGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGAGGG
* ** *
400071 TAAAATTGGTTTTTTTTGGAAGTTTTAGGG
1 TAAAAATGG-GATTTTTGGAAGTTTGAGGG
*
400101 TCAAAAATGGGATATTTGGAAGTTTCGA-GG
1 T-AAAAATGGGATTTTTGGAAGTTT-GAGGG
* * *
400131 TCAAAAATGAGA-TTTTGGAAGTTCGGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGAGGG
*
400160 TAAAAATGGAATTTTTGGAAGTTTTG-GGG
1 TAAAAATGGGATTTTTGGAAG-TTTGAGGG
* * ** *
400189 TAAAAAATGAGATTATTGGAAGTTCAAGGA
1 T-AAAAATGGGATTTTTGGAAGTTTGAGGG
* **
400219 TAAAAGTGAAATTTTTGGATAGTTT-AGGG
1 TAAAAATGGGATTTTTGGA-AGTTTGAGGG
400248 ACCTCCGAGG
Statistics
Matches: 292, Mismatches: 55, Indels: 55
0.73 0.14 0.14
Matches are distributed among these distances:
20 4 0.01
21 10 0.03
23 2 0.01
24 2 0.01
26 2 0.01
27 2 0.01
28 17 0.06
29 100 0.34
30 138 0.47
31 15 0.05
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTGAGGG
Found at i:400037 original size:21 final size:21
Alignment explanation
Indices: 400013--400057 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
400003 TTTTTGGAAG
400013 TTTGAGGGT-AAAAATGAAATT
1 TTTG-GGGTCAAAAATGAAATT
*
400034 TTTGGGGTCAAAAATGAGATT
1 TTTGGGGTCAAAAATGAAATT
400055 TTT
1 TTT
400058 TGAAGTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (21 bp):
TTTGGGGTCAAAAATGAAATT
Found at i:400148 original size:110 final size:109
Alignment explanation
Indices: 399930--400146 Score: 292
Period size: 110 Copynumber: 2.0 Consensus size: 109
399920 GAAATTTCGA
* * * *
399930 GGTCAAAATTGGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCGGGGTTAA
1 GGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCAA
*
399995 AAAAGGGATTTTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGG
66 AAAAGGGATATTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGG
* * ** *
400039 GGTCAAAAATGAGATTTTTTGAAGTTTGGGGGTAAAATTGGTTTTTTTTGGAAGTTTTAGGGTCA
1 GGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGG-AATTTTTGGAAGTTTCAGGGTCA
* *
400104 AAAATGGGATATTTGGAAGTTTCGA-GGTCAAAAATGAGATTTT
65 AAAAAGGGATATTTGGAAGTTT-GAGGGT-AAAAATGAAATTTT
400147 GGAAGTTCGG
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
109 37 0.40
110 41 0.44
111 15 0.16
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (109 bp):
GGTCAAAAATGAGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCAGGGTCAA
AAAAGGGATATTTGGAAGTTTGAGGGTAAAAATGAAATTTTTGG
Found at i:400235 original size:88 final size:90
Alignment explanation
Indices: 400039--400242 Score: 247
Period size: 88 Copynumber: 2.3 Consensus size: 90
400029 AAATTTTTGG
* * * ** *
400039 GGTCAAAAATGAGATTTTTTGAAGTTTGGGGGTAAAATTGGTTTTTTTTGGAAGTTTTAGGGTCA
1 GGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTAGGGTAA
* *
400104 AAAATGGGATATTTGGAAGTTTCGA
66 AAAATGAGATATTTGGAAGTTTCAA
*
400129 GGTCAAAAATGAGA-TTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTAA
1 GGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTAGGGTAA
400192 AAAATGAGAT-TATTGGAAG-TTCAA
66 AAAATGAGATAT-TTGGAAGTTTCAA
* *
400216 GGAT-AAAAGTGAAATTTTTGGATAGTT
1 GG-TCAAAAATGAGATTTTTGGA-AGTT
400243 TAGGGACCTC
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
87 15 0.15
88 43 0.43
89 27 0.27
90 14 0.14
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (90 bp):
GGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTAGGGTAA
AAAATGAGATATTTGGAAGTTTCAA
Done.