Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold160
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: 5021213
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 92036 characters in sequence are not A, C, G, or T
File 4 of 30
Found at i:437359 original size:32 final size:30
Alignment explanation
Indices: 437316--437376 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
437306 ATATAAACGA
* *
437316 ATTAATTTTTTTATTTAAACTTGTTTTTAAAG
1 ATTAATATTTTTATTCAAA-TT-TTTTTAAAG
437348 ATTAATATTTTTATTCAAATTTTTTTAAA
1 ATTAATATTTTTATTCAAATTTTTTTAAA
437377 TATCAAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 8 0.30
31 2 0.07
32 17 0.63
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
ATTAATATTTTTATTCAAATTTTTTTAAAG
Found at i:437677 original size:60 final size:60
Alignment explanation
Indices: 437609--437728 Score: 213
Period size: 60 Copynumber: 2.0 Consensus size: 60
437599 GAAAATTCAA
437609 AATCCTAAATATTTCTTATTAGGATAAATTTATAAACTTGTATAAGTATTATAAATATTT
1 AATCCTAAATATTTCTTATTAGGATAAATTTATAAACTTGTATAAGTATTATAAATATTT
* * *
437669 AATCCTAAATATTTCTTATTATGATAAATTTATAAACTTGTATAAGTGTTATGAATATTT
1 AATCCTAAATATTTCTTATTAGGATAAATTTATAAACTTGTATAAGTATTATAAATATTT
437729 TATTAAGAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (60 bp):
AATCCTAAATATTTCTTATTAGGATAAATTTATAAACTTGTATAAGTATTATAAATATTT
Found at i:438093 original size:25 final size:26
Alignment explanation
Indices: 438070--438122 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
438060 ATTATATCTC
*
438070 TATTTAGTGGTGAATTTGAAATCTTA
1 TATTTAGTGGTAAATTTGAAATCTTA
* *
438096 TATTTATTTGTAAATTTGAAAT-TTA
1 TATTTAGTGGTAAATTTGAAATCTTA
438121 TA
1 TA
438123 GTTTTATGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (26 bp):
TATTTAGTGGTAAATTTGAAATCTTA
Found at i:441513 original size:127 final size:127
Alignment explanation
Indices: 441287--441542 Score: 476
Period size: 127 Copynumber: 2.0 Consensus size: 127
441277 GACGCCCGAT
*
441287 GAAAAAGTACTTTTAGATAATCGAAGCTTTTTGTCAAGCATAGATCCATTTCCCATCATCTCAAG
1 GAAAAAGTACTTTTAGATAATCGAAGCTTTTTGTCAAGCACAGATCCATTTCCCATCATCTCAAG
441352 TTGAGATAAGGTGTCCAAGAGGCAAAAAGTATGAAAAAGTCATATTTTTTCTTATATGTATC
66 TTGAGATAAGGTGTCCAAGAGGCAAAAAGTATGAAAAAGTCATATTTTTTCTTATATGTATC
*
441414 GAAAAATTACTTTTAGATAATCGAAGCTTTTTGTCAAGCACAGATCCATTTCCCATCATCTCAAG
1 GAAAAAGTACTTTTAGATAATCGAAGCTTTTTGTCAAGCACAGATCCATTTCCCATCATCTCAAG
* *
441479 TTGAGATAAGGTGTTCGAGAGGCAAAAAGTATGAAAAAGTCATATTTTTTCTTATATGTATC
66 TTGAGATAAGGTGTCCAAGAGGCAAAAAGTATGAAAAAGTCATATTTTTTCTTATATGTATC
441541 GA
1 GA
441543 TGCATGCCTT
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 125 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (127 bp):
GAAAAAGTACTTTTAGATAATCGAAGCTTTTTGTCAAGCACAGATCCATTTCCCATCATCTCAAG
TTGAGATAAGGTGTCCAAGAGGCAAAAAGTATGAAAAAGTCATATTTTTTCTTATATGTATC
Found at i:441558 original size:21 final size:21
Alignment explanation
Indices: 441533--441588 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
441523 TTTTTTCTTA
* *
441533 TATGTATCGATGCATGCCTTT
1 TATGTATCGATACATGCCTTC
441554 TATGTATCGATACATGCCTTC
1 TATGTATCGATACATGCCTTC
* *
441575 AATGTATCAATACA
1 TATGTATCGATACA
441589 AGGTCCCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.38
Consensus pattern (21 bp):
TATGTATCGATACATGCCTTC
Found at i:441667 original size:20 final size:20
Alignment explanation
Indices: 441629--441698 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
441619 CTATGATTTA
* *
441629 TATCAATACAATAAGTGAATG
1 TATCGATAC-ATAACTGAATG
441650 TATCGATACATAACTGAATG
1 TATCGATACATAACTGAATG
* *
441670 TATTGATACAT-GCTGGAAATG
1 TATCGATACATAACT-G-AATG
441691 TATCGATA
1 TATCGATA
441699 TAGGACAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 21 0.50
21 19 0.45
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
TATCGATACATAACTGAATG
Found at i:441773 original size:24 final size:24
Alignment explanation
Indices: 441746--441798 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
441736 AAATATATCG
* *
441746 ATACATT-TTTCATTGTATTGATAC
1 ATACATTCTTT-AATGTATCGATAC
441770 ATACATTCTTTAATGTATCGATAC
1 ATACATTCTTTAATGTATCGATAC
441794 ATACA
1 ATACA
441799 GGTAAATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (24 bp):
ATACATTCTTTAATGTATCGATAC
Found at i:443200 original size:19 final size:20
Alignment explanation
Indices: 443176--443214 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
443166 CACATTTTTG
443176 TCAAG-ATGTATCGATACAT
1 TCAAGAATGTATCGATACAT
443195 TCAAGAAATGTATCGATACA
1 TCAAG-AATGTATCGATACA
443215 AGGTCTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
TCAAGAATGTATCGATACAT
Found at i:443376 original size:20 final size:20
Alignment explanation
Indices: 443305--443372 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
443295 TACCCAGATT
*
443305 TATCGATACGTTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
443325 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
*
443345 TATCGATATATTTTTCAATG
1 TATCGATACATTTTTCAATG
443365 TATCGATA
1 TATCGATA
443373 TATTCTGTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:449989 original size:13 final size:13
Alignment explanation
Indices: 449971--449997 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
449961 ACATTATGCT
449971 TTGTATCGATACA
1 TTGTATCGATACA
449984 TTGTATCGATACA
1 TTGTATCGATACA
449997 T
1 T
449998 GCATAATTGT
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:451670 original size:3 final size:3
Alignment explanation
Indices: 451655--451685 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
451645 AACCATCAAA
*
451655 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
451686 TTGACTCGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:452888 original size:34 final size:34
Alignment explanation
Indices: 452844--452921 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
452834 CTATAACAAA
* *
452844 AAGGGAGAGAAATGATTGAAAATAATTTTTTATC
1 AAGGGGGAGAAATGATTGAAAATAAATTTTTATC
* ***
452878 AAGGGGGAG-AATGTTTTTTAATAAATTTTTATC
1 AAGGGGGAGAAATGATTGAAAATAAATTTTTATC
452911 AAGGGGGAGAA
1 AAGGGGGAGAA
452922 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
33 28 0.76
34 9 0.24
ACGTcount: A:0.40, C:0.03, G:0.26, T:0.32
Consensus pattern (34 bp):
AAGGGGGAGAAATGATTGAAAATAAATTTTTATC
Found at i:452907 original size:33 final size:32
Alignment explanation
Indices: 452864--452930 Score: 116
Period size: 33 Copynumber: 2.1 Consensus size: 32
452854 AATGATTGAA
*
452864 AATAATTTTTTATCAAGGGGGAGAATGTTTTTT
1 AATAAATTTTTATCAAGGGGGAGAAT-TTTTTT
452897 AATAAATTTTTATCAAGGGGGAGAATTTTTTT
1 AATAAATTTTTATCAAGGGGGAGAATTTTTTT
452929 AA
1 AA
452931 AACAAAAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.24
33 25 0.76
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (32 bp):
AATAAATTTTTATCAAGGGGGAGAATTTTTTT
Found at i:453673 original size:20 final size:20
Alignment explanation
Indices: 453631--453684 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
453621 CTACCACTGT
* * *
453631 TTGTATCAATACATGGCACA
1 TTGTATCGATACATGACAAA
*
453651 TTGTATCGATACATGATAAA
1 TTGTATCGATACATGACAAA
*
453671 TTGTATTGATACAT
1 TTGTATCGATACAT
453685 TACTTCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGACAAA
Found at i:462211 original size:1 final size:1
Alignment explanation
Indices: 462205--462306 Score: 69
Period size: 1 Copynumber: 102.0 Consensus size: 1
462195 CATTATTCTT
* * * ** * * * * *
462205 AAAAAAACAAACAAACAAAAAAATTAAAAAAACAAACAAACAAAAAACAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** *
462270 AAAACAAAAACAAAAACCAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
462307 GGAAGGGTCT
Statistics
Matches: 75, Mismatches: 26, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:462222 original size:8 final size:7
Alignment explanation
Indices: 462206--462306 Score: 107
Period size: 7 Copynumber: 13.9 Consensus size: 7
462196 ATTATTCTTA
462206 AAAAAAC
1 AAAAAAC
462213 AAACAAAC
1 AAA-AAAC
*
462221 AAAAAAATTA
1 -AAAAAA--C
462231 AAAAAAC
1 AAAAAAC
462238 AAACAAAC
1 AAA-AAAC
462246 AAAAAAC
1 AAAAAAC
462253 AAAAAAAC
1 -AAAAAAC
*
462261 AAAAAAA
1 AAAAAAC
462268 AAAAAAC
1 AAAAAAC
462275 -AAAAAC
1 AAAAAAC
*
462281 AAAAACC
1 AAAAAAC
462288 AAAAAA-
1 AAAAAAC
462294 AAAAAAC
1 AAAAAAC
462301 AAAAAA
1 AAAAAA
462307 GGAAGGGTCT
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
6 12 0.15
7 38 0.47
8 21 0.26
9 9 0.11
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (7 bp):
AAAAAAC
Found at i:462231 original size:25 final size:24
Alignment explanation
Indices: 462205--462306 Score: 122
Period size: 25 Copynumber: 4.2 Consensus size: 24
462195 CATTATTCTT
*
462205 AAAAAAACAAACAAACAAAAAAATT
1 AAAAAAACAAACAAACAAAAAAA-C
462230 AAAAAAACAAACAAAC-AAAAAAC
1 AAAAAAACAAACAAACAAAAAAAC
462253 AAAAAAACAAA-AAA-AAAAAAAC
1 AAAAAAACAAACAAACAAAAAAAC
*
462275 AAAAACAA-AAACCAAAAAAAAAAAAC
1 AAAAA-AACAAA-C-AAACAAAAAAAC
462301 AAAAAA
1 AAAAAA
462307 GGAAGGGTCT
Statistics
Matches: 70, Mismatches: 1, Indels: 12
0.84 0.01 0.14
Matches are distributed among these distances:
22 18 0.26
23 13 0.19
24 6 0.09
25 20 0.29
26 13 0.19
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (24 bp):
AAAAAAACAAACAAACAAAAAAAC
Found at i:462300 original size:40 final size:42
Alignment explanation
Indices: 462205--462306 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 42
462195 CATTATTCTT
* *
462205 AAAAAAACAAACAAACAAAAAAATTAAAAAAACAAACAAACAA
1 AAAAAAAAAAACAAA-AAAAAAATAAAAAAAACAAACAAACAA
*
462248 AAAACAAAAAAACAAAAAAAAAA-AAACAAAAAC-AA-AAACCA
1 AAAA-AAAAAAACAAAAAAAAAATAAA-AAAAACAAACAAACAA
462289 AAAAAAAAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
462307 GGAAGGGTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
40 14 0.26
41 9 0.17
42 4 0.07
43 17 0.31
44 10 0.19
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.02
Consensus pattern (42 bp):
AAAAAAAAAAACAAAAAAAAAATAAAAAAAACAAACAAACAA
Found at i:463973 original size:13 final size:13
Alignment explanation
Indices: 463955--463980 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
463945 ACAATTCTTC
463955 ATGTATCGATACA
1 ATGTATCGATACA
463968 ATGTATCGATACA
1 ATGTATCGATACA
463981 TTGTCCTATG
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:464055 original size:19 final size:19
Alignment explanation
Indices: 464029--464100 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
464019 CTGCCAGTTT
*
464029 CATGTATCGATACAATTAG
1 CATGTATCGATACAATGAG
**
464048 GTTGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
* *
464067 CATGTATCGATACAAGGCAT
1 CATGTATCGATACAATG-AG
*
464087 AATGTATCGATACA
1 CATGTATCGATACA
464101 TCTGGGTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 30 0.68
20 14 0.32
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:466539 original size:48 final size:48
Alignment explanation
Indices: 466486--466582 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 48
466476 TTTGAGTTTG
466486 AAAGCTTAAGGTTGAGAGGATTTGAGTGAGTGTA-TCATTAGAAAATGA
1 AAAGCTTAAGGTTGAGAGGATTTGAGTGAGTGTATTCA-TAGAAAATGA
** *
466534 AAAGCTTGGGGTTGAGAGGATTTGAGTGAGTGTATTGATAGAAAATGA
1 AAAGCTTAAGGTTGAGAGGATTTGAGTGAGTGTATTCATAGAAAATGA
466582 A
1 A
466583 GAGAGGGGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.32, T:0.29
Consensus pattern (48 bp):
AAAGCTTAAGGTTGAGAGGATTTGAGTGAGTGTATTCATAGAAAATGA
Found at i:466593 original size:48 final size:48
Alignment explanation
Indices: 466495--466594 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
466485 GAAAGCTTAA
***
466495 GGTTGAGAGGATTTGAGTGAGTGTATCATTAGAAAATGAAAAGCTTGG
1 GGTTGAGAGGATTTGAGTGAGTGTATCATTAGAAAATGAAAAGAGGGG
* *
466543 GGTTGAGAGGATTTGAGTGAGTGTATTGA-TAGAAAATGAAGAGAGGGG
1 GGTTGAGAGGATTTGAGTGAGTGTA-TCATTAGAAAATGAAAAGAGGGG
466591 GGTT
1 GGTT
466595 CGAACTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 44 0.96
49 2 0.04
ACGTcount: A:0.32, C:0.02, G:0.38, T:0.28
Consensus pattern (48 bp):
GGTTGAGAGGATTTGAGTGAGTGTATCATTAGAAAATGAAAAGAGGGG
Found at i:472893 original size:19 final size:19
Alignment explanation
Indices: 472867--472919 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
472857 CTATCAGTTT
472867 CATGTATCGATACAATTG-G
1 CATGTATCGATACAA-TGAG
**
472886 GTTGTATCGATACAATGAG
1 CATGTATCGATACAATGAG
472905 CATGTATCGATACAA
1 CATGTATCGATACAA
472920 GGCATAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 2 0.07
19 27 0.93
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:472931 original size:20 final size:19
Alignment explanation
Indices: 472888--472935 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
472878 ACAATTGGGT
* *
472888 TGTATCGATACAATGAGCA
1 TGTATCGATACAAGGAGAA
*
472907 TGTATCGATACAAGGCATAA
1 TGTATCGATACAAGG-AGAA
472927 TGTATCGAT
1 TGTATCGAT
472936 GCATTTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (19 bp):
TGTATCGATACAAGGAGAA
Found at i:473227 original size:28 final size:27
Alignment explanation
Indices: 473128--473343 Score: 166
Period size: 28 Copynumber: 7.4 Consensus size: 27
473118 GCAACGTCTC
*
473128 TCAAAGCCCACAAGTCAGTGGCACCCCT
1 TCAAAGCCCACAAGTCAGTGGCA-CCTT
473156 T-AAAGCCCACACAAGTC-GATGGCAACCTCT
1 TCAAAG-CC-CACAAGTCAG-TGGC-ACCT-T
*
473186 CTCAAACCCCACAAGTCAGTGGCACCGTT
1 -TCAAAGCCCACAAGTCAGTGGCACC-TT
* *
473215 TCAAAGCCCACAAGTTAATGGCACCGTT
1 TCAAAGCCCACAAGTCAGTGGCACC-TT
* * *
473243 TCGAAGCCCACAAATCAATGGCATCCTT
1 TCAAAGCCCACAAGTCAGTGGCA-CCTT
*
473271 TTAAAGCCCACAAGTCAGTGGCAACCCTT
1 TCAAAGCCCACAAGTCAGTGGC-A-CCTT
* **
473300 CCAAAGCCTACACAAGTTGGTGGCAACCTTT
1 TCAAAGCC--CACAAGTCAGTGGC-ACC-TT
473331 TCTAAAGCCCACA
1 TC-AAAGCCCACA
473344 CAAGTTGGTG
Statistics
Matches: 155, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.03
28 69 0.45
29 31 0.20
30 21 0.14
31 21 0.14
32 9 0.06
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (27 bp):
TCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:473314 original size:115 final size:117
Alignment explanation
Indices: 473131--473343 Score: 260
Period size: 115 Copynumber: 1.8 Consensus size: 117
473121 ACGTCTCTCA
* * *
473131 AAGCCCACAAGTCAGTGGCACCCCTTAAAGCCCACACAAGTCGATGGCAACCTCTCTCAAACCCC
1 AAGCCCACAAATCAATGGCACCCCTTAAAGCCCACACAAGTCGATGGCAACCTCTCTCAAACCAC
473196 ACAAGTCAGTGGC-ACCGTTTC-AAAGCCCACAAGTTAATGGCACCGTTTCG
66 ACAAGTCAGTGGCAACCGTTTCTAAAGCCCACAAGTTAATGGCACCGTTTCG
**
473246 AAGCCCACAAATCAATGGCATCCTTTTAAAG-CC-CACAAGTC-AGTGGCAACC-CT-TCCAAAG
1 AAGCCCACAAATCAATGGCA-CCCCTTAAAGCCCACACAAGTCGA-TGGCAACCTCTCT-CAAA-
** *
473306 CCTACACAAGTTGGTGGCAACCTTTTCTAAAGCCCACA
62 CC-ACACAAGTCAGTGGCAACCGTTTCTAAAGCCCACA
473344 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
112 1 0.01
113 7 0.08
114 18 0.22
115 32 0.39
116 15 0.18
117 10 0.12
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (117 bp):
AAGCCCACAAATCAATGGCACCCCTTAAAGCCCACACAAGTCGATGGCAACCTCTCTCAAACCAC
ACAAGTCAGTGGCAACCGTTTCTAAAGCCCACAAGTTAATGGCACCGTTTCG
Found at i:480267 original size:20 final size:21
Alignment explanation
Indices: 480242--480288 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
480232 AGCATGTATT
*
480242 GATACATTCACTTA-TATATC
1 GATACATTAACTTATTATATC
480262 GATACATTAACTTATTATATC
1 GATACATTAACTTATTATATC
*
480283 AATACA
1 GATACA
480289 AATTGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.38
Consensus pattern (21 bp):
GATACATTAACTTATTATATC
Found at i:485181 original size:13 final size:13
Alignment explanation
Indices: 485163--485188 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
485153 TACACAAAGT
485163 ATGTATCGATACA
1 ATGTATCGATACA
485176 ATGTATCGATACA
1 ATGTATCGATACA
485189 CCAAAAAATT
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:485186 original size:32 final size:34
Alignment explanation
Indices: 485145--485209 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
485135 TAGCCAAACT
**
485145 TGTATCGATACA-CAAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAAATTGTATCGATACAA
485177 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAAATTGTATCGATACA
485210 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.41
33 5 0.17
34 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAATTGTATCGATACAA
Found at i:491440 original size:20 final size:19
Alignment explanation
Indices: 491399--491441 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
491389 ATCTTTTGCA
491399 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
491419 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
491439 AAA
1 AAA
491442 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:493849 original size:13 final size:13
Alignment explanation
Indices: 493831--493856 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493821 TACACAAAGT
493831 ATGTATCGATACA
1 ATGTATCGATACA
493844 ATGTATCGATACA
1 ATGTATCGATACA
493857 CCAAAAAATT
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:497483 original size:148 final size:148
Alignment explanation
Indices: 497216--497615 Score: 511
Period size: 148 Copynumber: 2.7 Consensus size: 148
497206 GTGATCTTAG
* * * ** * *
497216 AGGACTTAAAAAGGAAAAGGAAATCTATGCCTAATATGTACCC-TCGGCATAGAAGCAACTCGGT
1 AGGACTTAAAAAGGAAAAGTAAACCTATGCCTAATATGTACCCATCGACATAGAAGTGACCCAGT
* *
497280 GACAAATTAGGACTCGATTCTA-AAACTTACGAAAATAG-CCCTATAGGTATACCTTCGACATTA
66 GACAAATTAGGACTCGATTCTAGAAA-TTATGAAAAT-GCCCCTATAGGTATACCTTCGACATGA
497343 AAGTAT-CTCGATAACCCTAA
129 AAGTATCCT-GATAACCCTAA
* * * *
497363 AGGACTTAAAAAAGAAAAGTAAACCTATGCCTAATATGTACCCATTGACATAAAAGTGACCCATT
1 AGGACTTAAAAAGGAAAAGTAAACCTATGCCTAATATGTACCCATCGACATAGAAGTGACCCAGT
* *
497428 GACAAATTAGGACTCAATTTTAGAAATTATGAAAATGCCCCTATAGGTATACCTTCGACATGAAA
66 GACAAATTAGGACTCGATTCTAGAAATTATGAAAATGCCCCTATAGGTATACCTTCGACATGAAA
*
497493 GTATCCTGGTAACCCTAA
131 GTATCCTGATAACCCTAA
* * * * ** *
497511 AAGACTTAAAAAGGAAAAGTGAACCTATGCCTAATCTATACATAATCGACATAGAAGTGATCCAG
1 AGGACTTAAAAAGGAAAAGTAAACCTATGCCTAATATGTAC-CCATCGACATAGAAGTGACCCAG
* *
497576 TGACAAATTAGGACTCGATTCTAGGAATTATGCAAATGCC
65 TGACAAATTAGGACTCGATTCTAGAAATTATGAAAATGCC
497616 ATTAGGAGGT
Statistics
Matches: 217, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
147 41 0.19
148 118 0.54
149 58 0.27
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (148 bp):
AGGACTTAAAAAGGAAAAGTAAACCTATGCCTAATATGTACCCATCGACATAGAAGTGACCCAGT
GACAAATTAGGACTCGATTCTAGAAATTATGAAAATGCCCCTATAGGTATACCTTCGACATGAAA
GTATCCTGATAACCCTAA
Found at i:497642 original size:148 final size:148
Alignment explanation
Indices: 497218--497672 Score: 454
Period size: 148 Copynumber: 3.1 Consensus size: 148
497208 GATCTTAGAG
* * * * * * ** * *
497218 GACTTAAAAAGGAAAAGGAAATCTATGCCTAATATGTACC-CTCGGCATAGAAGCAACTCGGTGA
1 GACTTAAAAAGGAAAAGTAAACCTATGCCTAATATATACCAATCGACATAAAAGTGACCCAGTGA
* * * *
497282 CAAATTAGGACTCGATTCTA-AAACTTACGAAAATAGCC-CTATAGGTATACCTTCGACATTAAA
66 CAAATTAGGACTCAATTCTAGAAA-TTATGAAAAT-GCCACTAGAGGTATACCTTCGACATAAAA
* *
497345 GTATCTC-GATAACCCTAAAG
129 GTATCCCAG-TAACCCTAAAA
* * * * *
497365 GACTTAAAAAAGAAAAGTAAACCTATGCCTAATATGTACCCATTGACATAAAAGTGACCCATTGA
1 GACTTAAAAAGGAAAAGTAAACCTATGCCTAATATATACCAATCGACATAAAAGTGACCCAGTGA
* * * *
497430 CAAATTAGGACTCAATTTTAGAAATTATGAAAATGCCCCTATAGGTATACCTTCGACATGAAAGT
66 CAAATTAGGACTCAATTCTAGAAATTATGAAAATGCCACTAGAGGTATACCTTCGACATAAAAGT
**
497495 ATCCTGGTAACCCTAAAA
131 ATCCCAGTAACCCTAAAA
* * * * *
497513 GACTTAAAAAGGAAAAGTGAACCTATGCCTAATCTATACATAATCGACATAGAAGTGATCCAGTG
1 GACTTAAAAAGGAAAAGTAAACCTATGCCTAATATATAC-CAATCGACATAAAAGTGACCCAGTG
* * * * * *
497578 ACAAATTAGGACTCGATTCTAGGAATTATGCAAATGCCATTAGGAGGTA-A-CTTTGACGTAAAA
65 ACAAATTAGGACTCAATTCTAGAAATTATGAAAATGCCACTA-GAGGTATACCTTCGACATAAAA
* *
497641 GTATCCCAGCAACCTTAAAA
129 GTATCCCAGTAACCCTAAAA
*
497661 GACTTGAAAAGG
1 GACTTAAAAAGG
497673 GTGGAAAAGA
Statistics
Matches: 258, Mismatches: 44, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
147 40 0.16
148 153 0.59
149 60 0.23
150 5 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (148 bp):
GACTTAAAAAGGAAAAGTAAACCTATGCCTAATATATACCAATCGACATAAAAGTGACCCAGTGA
CAAATTAGGACTCAATTCTAGAAATTATGAAAATGCCACTAGAGGTATACCTTCGACATAAAAGT
ATCCCAGTAACCCTAAAA
Found at i:498182 original size:13 final size:13
Alignment explanation
Indices: 498164--498188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
498154 ACACAAAGTA
498164 TGTATCGATACAT
1 TGTATCGATACAT
498177 TGTATCGATACA
1 TGTATCGATACA
498189 CCAAAAAATG
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:498185 original size:32 final size:33
Alignment explanation
Indices: 498144--498211 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
498134 GTAGCCAAAC
**
498144 TTGTATCGATACA-CAAAGTATGTATCGATACA
1 TTGTATCGATACACCAAAAAATGTATCGATACA
*
498176 TTGTATCGATACACCAAAAAATGTTTCGATACA
1 TTGTATCGATACACCAAAAAATGTATCGATACA
498209 TTG
1 TTG
498212 GCTTGTAACG
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:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCAAAAAATGTATCGATACA
Found at i:501086 original size:51 final size:51
Alignment explanation
Indices: 501031--501127 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
501021 CTAATCCCGG
501031 TTTTATTACTAAAACACCAATTTTCCACAATC-GAGGATACTCCAACTCTGA
1 TTTTATTACTAAAACACCAATTTTCCACAATCAG-GGATACTCCAACTCTGA
* * * *
501082 TTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAAC
1 TTTTATTACTAAAACACCAATTTTCCACAATCAGGGATACTCCAAC
501128 CCCGTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (51 bp):
TTTTATTACTAAAACACCAATTTTCCACAATCAGGGATACTCCAACTCTGA
Found at i:501148 original size:79 final size:79
Alignment explanation
Indices: 501065--501447 Score: 327
Period size: 79 Copynumber: 4.9 Consensus size: 79
501055 CCACAATCGA
*
501065 GGATACTCCAACTCTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACCC
1 GGATACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACCC
501130 CGTTATTTTCGAGG
66 CGTTATTTTCGAGG
* * * ** ** *
501144 GGATACTCCAA-CCTCAGCTTTATTTCTAAAATATTGATACCTT-ACAATC-GGGATACTCCAAC
1 GGATACTCCAACCCTGA-TTTTATTTCTAAAACATCAAT-TTTTCATAATCAGGGATACTCCAAC
501206 CCCGTTATTTTC-ATGG
64 CCCGTTATTTTCGA-GG
* * * * *
501222 GGATACTCCAACCCCAGCCTTTT-TTTCTAAAGCATCAATTTTTCACAATCGGGGATACTCCAAC
1 GGATACTCCAA-CCCTG-ATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAAC
* * **
501286 CTCATTATTTTTAAGG
64 CCCGTTATTTTCGAGG
* * * *
501302 GTATACTCCAACCCCGATTTTATTTTCT-AAACACCGA-TTTTCTATAATCAGGGATACTCCAAC
1 GGATACTCCAACCCTGATTTTA-TTTCTAAAACATCAATTTTTC-ATAATCAGGGATACTCCAAC
*** *
501365 CTTATTATTTCCGAGG
64 CCCGTTATTTTCGAGG
* * *** * *
501381 GGATACTCTAACCTCT-ATTTTATTTCCAGTGC--CAATTTTCCATAATCAGGGATACTCCAGCC
1 GGATACTCCAACC-CTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACC
501443 CCGTT
65 CCGTT
501448 GTTATCCCCA
Statistics
Matches: 242, Mismatches: 47, Indels: 32
0.75 0.15 0.10
Matches are distributed among these distances:
77 25 0.10
78 60 0.25
79 109 0.45
80 47 0.19
81 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (79 bp):
GGATACTCCAACCCTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAACCC
CGTTATTTTCGAGG
Found at i:501191 original size:130 final size:128
Alignment explanation
Indices: 500934--501205 Score: 289
Period size: 130 Copynumber: 2.1 Consensus size: 128
500924 TTTCATTTCA
* * * *
500934 GGGACACTCCAAC-CTCAATTTTATTCCCAAAACATCAATTTTTCACAATCGGGGATACTCTAAC
1 GGGATACTCCAACTCT-GATTTTATTCCCAAAACATCAATTTTTCACAATCAGGGATACTCCAAC
* * * * * * **
500998 TCTGTTATTTTTGAGGAGATACTCTAATCCCGGTTTTATTACTAAAACACCAATTTTCCACAATC
65 CCCGTTATTTTCGAGGAGATACTCCAATCCCAGCTTTATTACTAAAACACCAACCTT-CACAATC
* * *
501063 GAGGATACTCCAACTCTGATTTTATTTCTAAAACATCAATTTTTCATAATCAGGGATACTCCAAC
1 G-GGATACTCCAACTCTGATTTTATTCCCAAAACATCAATTTTTCACAATCAGGGATACTCCAAC
* * * **
501128 CCCGTTATTTTCGAGGGGATACTCCAA-CCTCAGCTTTATTTCTAAAATATTGATACCTT-ACAA
65 CCCGTTATTTTCGAGGAGATACTCCAATCC-CAGCTTTATTACTAAAACA-CCA-ACCTTCACAA
501191 TC
127 TC
501193 GGGATACTCCAAC
1 GGGATACTCCAAC
501206 CCCGTTATTT
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
129 15 0.13
130 97 0.82
131 3 0.03
132 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (128 bp):
GGGATACTCCAACTCTGATTTTATTCCCAAAACATCAATTTTTCACAATCAGGGATACTCCAACC
CCGTTATTTTCGAGGAGATACTCCAATCCCAGCTTTATTACTAAAACACCAACCTTCACAATC
Found at i:503322 original size:52 final size:52
Alignment explanation
Indices: 503266--503519 Score: 228
Period size: 52 Copynumber: 4.9 Consensus size: 52
503256 TTAGGAATAT
* * * * * *
503266 TAAAGATGCTAATATGCTGATTCAAGGCTAGCGATATCAGACTTAAAGATAA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGATAA
* *
503318 TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAAATGAA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGAT-AA
* * * * * * *
503371 -AAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAATTAAAGA-AGA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGATA-A
**
503422 TAAAGGCACCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGA-AA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGATAA
* * * * * *
503473 GCAAAAAGTGCCAA-AGTGTTGATTCAAGGCCAACGACATTGGACTTA
1 --TAAAGGTGCCAATA-TGCTAATTCAAGGCCAACGATATTAGACTTA
503520 GAAAGAGATG
Statistics
Matches: 164, Mismatches: 32, Indels: 11
0.79 0.15 0.05
Matches are distributed among these distances:
50 1 0.01
51 2 0.01
52 124 0.76
53 37 0.23
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (52 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGATAA
Found at i:503380 original size:156 final size:156
Alignment explanation
Indices: 503220--503519 Score: 354
Period size: 156 Copynumber: 1.9 Consensus size: 156
503210 ATGAGAAGAA
* * ** * * ** *
503220 TGCCAATATGCTGATTCAAAGTTAGTGACATTGGGCTT-AGGAATATTAAAGATGCTAATATGCT
1 TGCCAATATGCTGATTCAAAGCTAGCGACATTGGAATTAAAGAAGA-TAAAGACACCAATATGCT
* * * * *
503284 GATTCAAGGCTAGCGATATCAGACTTAAAGATAA-TAAAGGTGCCAATA-TGCTAATTCAAGGCC
65 AATTCAAGGCCAACGATATCAGACTTAAAGA-AACAAAAAGTGCCAA-AGTGCTAATTCAAGGCC
*
503347 AACGATATTGGACTTAAAAATGAAAAAGG
128 AACGACATTGGACTTAAAAATGAAAAAGG
* * *
503376 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAATTAAAGAAGATAAAGGCACCAATATGCTA
1 TGCCAATATGCTGATTCAAAGCTAGCGACATTGGAATTAAAGAAGATAAAGACACCAATATGCTA
* * *
503441 ATTCAAGGCCAACGATATTAGACTTAAAGAAAGCAAAAAGTGCCAAAGTGTTGATTCAAGGCCAA
66 ATTCAAGGCCAACGATATCAGACTTAAAGAAA-CAAAAAGTGCCAAAGTGCTAATTCAAGGCCAA
503506 CGACATTGGACTTA
130 CGACATTGGACTTA
503520 GAAAGAGATG
Statistics
Matches: 119, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
155 2 0.02
156 74 0.62
157 43 0.36
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (156 bp):
TGCCAATATGCTGATTCAAAGCTAGCGACATTGGAATTAAAGAAGATAAAGACACCAATATGCTA
ATTCAAGGCCAACGATATCAGACTTAAAGAAACAAAAAGTGCCAAAGTGCTAATTCAAGGCCAAC
GACATTGGACTTAAAAATGAAAAAGG
Found at i:503416 original size:104 final size:104
Alignment explanation
Indices: 503109--503519 Score: 352
Period size: 104 Copynumber: 3.9 Consensus size: 104
503099 GACAAAAATG
* * * * *
503109 ATAAAGGTGCCAATATGCTAATTCAAGGCCAATGATATTGGGCTTAAATATGTGAAGAA-TGCCA
1 ATAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGA-ATGAAAAAGTGCCA
* * ** *
503173 ATATGCTGAATCACA-GCCAGTGACATTAGACTCGAAGATG
65 ATATGCTGATTCA-AGGCCAGCGACATTAGACTTAAAGATA
* * * * ** ** * * * *
503213 A-GAAGAATGCCAATATGCTGATTCAAAGTTAGTGACATTGGGCTT-AGGAAT-ATTAAAGATGC
1 ATAAAG-GTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGAATGA-AAAAG-TGC
* * * *
503275 TAATATGCTGATTCAAGGCTAGCGATATCAGACTTAAAGATA
63 CAATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATA
503317 ATAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAA-AATGAAAAAGGTGCCA
1 ATAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGAATGAAAAA-GTGCCA
* * * *
503381 ATGTGCTGATTCAAGGCTAGCGACATTGGAATTAAAGA-A
65 ATATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATA
** * *
503420 GATAAAGGCACCAATATGCTAATTCAAGGCCAACGATATTAGACTTAAAGAAAGCAAAAAGTGCC
1 -ATAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGAATG-AAAAAGTGCC
* * *
503485 AA-AGTGTTGATTCAAGGCCAACGACATTGGACTTA
64 AATA-TGCTGATTCAAGGCCAGCGACATTAGACTTA
503520 GAAAGAGATG
Statistics
Matches: 245, Mismatches: 49, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
101 1 0.00
102 3 0.01
103 7 0.03
104 186 0.76
105 43 0.18
106 5 0.02
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (104 bp):
ATAAAGGTGCCAATATGCTAATTCAAGGCCAACGATATTGGACTTAAAGAATGAAAAAGTGCCAA
TATGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATA
Found at i:503692 original size:28 final size:28
Alignment explanation
Indices: 503659--503813 Score: 125
Period size: 28 Copynumber: 5.4 Consensus size: 28
503649 TGGTAACTTG
* *
503659 TGGGCTTTGATAGGGTGCCACTAGCTTG
1 TGGGCTTTGAAAGGGTGCCACTAGCTTA
** * *
503687 TGGGCTTCAAAAAGGTGCCA-TCGACTTA
1 TGGGCTTTGAAAGGGTGCCACTAG-CTTA
* *
503715 TGGGCTTTGAAAGGATGCCACTAACTTA
1 TGGGCTTTGAAAGGGTGCCACTAGCTTA
*
503743 TGGGCTTTGAAAGGATGCCACT-GACTTA
1 TGGGCTTTGAAAGGGTGCCACTAG-CTTA
* * * *
503771 TGAGCTTTGAAGGAGGTTGCTACTAGCTTGTG
1 TGGGCTTTGAA--AGGGTGCCACTAGC-T-TA
503803 TGGGCTTTGAA
1 TGGGCTTTGAA
503814 GAAGGGTTGC
Statistics
Matches: 101, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.02
28 75 0.74
29 1 0.01
30 10 0.10
31 2 0.02
32 11 0.11
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
TGGGCTTTGAAAGGGTGCCACTAGCTTA
Found at i:503734 original size:56 final size:56
Alignment explanation
Indices: 503654--503867 Score: 171
Period size: 56 Copynumber: 3.6 Consensus size: 56
503644 GCTGCTGGTA
* * *
503654 ACTTGTGGGCTTTGATAGGGTGCCACTAGCTTGTGGGCTTCAAAAAGG-TGCCATCG
1 ACTTATGGGCTTTGAAAGGTTGCCACTAGCTTGTGGGCTT-AAAAAGGATGCCATCG
* * * **
503710 ACTTATGGGCTTTGAAAGGATGCCACTAACTTATGGGCTTTGAAAGGATGCCA-CTG
1 ACTTATGGGCTTTGAAAGGTTGCCACTAGCTTGTGGGCTTAAAAAGGATGCCATC-G
* * * *
503766 ACTTATGAGCTTTGAAGGAGGTTGCTACTAGCTTGTGTGGGCTTTGAAGAAGGGTTGCCATCG
1 ACTTATGGGCTTTGAA--AGGTTGCCACTAGC-T-TGTGGGC-TT-AA-AAAGGATGCCATCG
* *
503829 ACTTGTGTGGGCTTTGAAGAAGGTTGCCACCAGCTTGTG
1 AC-T-TATGGGCTTTG-A-AAGGTTGCCACTAGCTTGTG
503868 TGGGCTTTGA
Statistics
Matches: 124, Mismatches: 20, Indels: 21
0.75 0.12 0.13
Matches are distributed among these distances:
55 6 0.05
56 56 0.45
58 11 0.09
59 1 0.01
60 6 0.05
61 2 0.02
63 16 0.13
64 3 0.02
65 21 0.17
66 1 0.01
67 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.30
Consensus pattern (56 bp):
ACTTATGGGCTTTGAAAGGTTGCCACTAGCTTGTGGGCTTAAAAAGGATGCCATCG
Found at i:503866 original size:32 final size:32
Alignment explanation
Indices: 503774--503883 Score: 159
Period size: 32 Copynumber: 3.4 Consensus size: 32
503764 TGACTTATGA
* * *
503774 GCTTTGAAGGAGGTTGCTACTAGCTTGTGTGG
1 GCTTTGAAGAAGGTTGCCACCAGCTTGTGTGG
*
503806 GCTTTGAAGAAGGGTTGCCATC-GACTTGTGTGG
1 GCTTTGAAGAA-GGTTGCCACCAG-CTTGTGTGG
503839 GCTTTGAAGAAGGTTGCCACCAGCTTGTGTGG
1 GCTTTGAAGAAGGTTGCCACCAGCTTGTGTGG
503871 GCTTTGAAGAAGG
1 GCTTTGAAGAAGG
503884 AAAAAAGATT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
32 42 0.60
33 28 0.40
ACGTcount: A:0.19, C:0.15, G:0.36, T:0.30
Consensus pattern (32 bp):
GCTTTGAAGAAGGTTGCCACCAGCTTGTGTGG
Found at i:510663 original size:36 final size:36
Alignment explanation
Indices: 510619--510691 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
510609 GGAAAAATGT
510619 TTAGAAAATTTGTAAAAATCGTCTATTGGGCCTGAA
1 TTAGAAAATTTGTAAAAATCGTCTATTGGGCCTGAA
* *
510655 TTAGAAAATTTGTACAAATCGTTTATTGGGCCTGAA
1 TTAGAAAATTTGTAAAAATCGTCTATTGGGCCTGAA
510691 T
1 T
510692 GACCTAACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (36 bp):
TTAGAAAATTTGTAAAAATCGTCTATTGGGCCTGAA
Found at i:515139 original size:20 final size:20
Alignment explanation
Indices: 515114--515151 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
515104 TTGGGGCCAA
*
515114 ATGTATTGATACATTTCACC
1 ATGTATTGATACAATTCACC
515134 ATGTATTGATACAATTCA
1 ATGTATTGATACAATTCA
515152 ATTATGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATTGATACAATTCACC
Found at i:522876 original size:28 final size:28
Alignment explanation
Indices: 522836--522895 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 28
522826 CTTCAATGGA
522836 ATACAAGGTCCATTCATGATT-TTTTGCC
1 ATACAAGGTCCATTCATGATTATTTT-CC
522864 ATACAAGGTCCATTCATGATTATTTTCC
1 ATACAAGGTCCATTCATGATTATTTTCC
522892 ATAC
1 ATAC
522896 TTCATAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (28 bp):
ATACAAGGTCCATTCATGATTATTTTCC
Found at i:523627 original size:20 final size:20
Alignment explanation
Indices: 523602--523639 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
523592 TTGGGGCCAA
*
523602 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
523622 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
523640 ATTATGAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:523755 original size:33 final size:32
Alignment explanation
Indices: 523695--523756 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
523685 CATTTTATGG
* *
523695 TGTATCGATACAATGAACATGTATCGATATCA
1 TGTATCAATACAAAGAACATGTATCGATATCA
*
523727 TGTATCAATACAAAGCAATATGTATCGATA
1 TGTATCAATACAAAG-AACATGTATCGATA
523757 CATCTAGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 13 0.50
33 13 0.50
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (32 bp):
TGTATCAATACAAAGAACATGTATCGATATCA
Found at i:523882 original size:21 final size:22
Alignment explanation
Indices: 523856--523899 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
523846 ATACTTTAAA
*
523856 TAATTT-TTACTTTAAAAACAT
1 TAATTTATTACTTGAAAAACAT
*
523877 TAATTTATTGCTTGAAAAACAT
1 TAATTTATTACTTGAAAAACAT
523899 T
1 T
523900 TATACTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
TAATTTATTACTTGAAAAACAT
Found at i:524861 original size:157 final size:156
Alignment explanation
Indices: 524674--524977 Score: 371
Period size: 157 Copynumber: 1.9 Consensus size: 156
524664 AAAATTTATC
* * * * *
524674 AAATATTATTATTTAATTCATATTATATTAGTTTTCAAAAATACATTCATTTTCATGGATTTTAT
1 AAATATTATTATTTAATTCACATTAAATTAGTTTTAAAAAATACAATCATTTTCATGCATTTT-T
* * * *
524739 AATTTTTTCCTCAAAATTCCCTTATTTTCAAAAAAAAT-GAGTTTTTTACTCTATAAATTTTTTC
65 AATTTTTTCCTCAAAA-TCCC-TATTTTCAAAAAAAATCGAGTTTTCTAATCCATAAATATTTTC
524803 GGGAGGATTTT-TCTTGGTTTTTAATTTCA
128 GGGAGGATTTTCT-TTGGTTTTTAATTTCA
* * * * *
524832 AAAT-TTATTATTTAGTTCGCATTAAATTAGTTTTAAAAAATTCAATCATTTTCATTCATTTTTT
1 AAATATTATTATTTAATTCACATTAAATTAGTTTTAAAAAATACAATCATTTTCATGCATTTTTA
* * * **
524896 ATTTTTTCTTTAAAATCTCTATTTTCCTAAAAAATCGAGTTTTCTAATCCATAAATATTTTCGGG
66 ATTTTTTCCTCAAAATCCCTATTTTCAAAAAAAATCGAGTTTTCTAATCCATAAATATTTTCGGG
*
524961 GGGATTTTCTTTGGTTT
131 AGGATTTTCTTTGGTTT
524978 AAAATTTTTA
Statistics
Matches: 124, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
154 14 0.11
155 42 0.34
156 15 0.12
157 49 0.40
158 4 0.03
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (156 bp):
AAATATTATTATTTAATTCACATTAAATTAGTTTTAAAAAATACAATCATTTTCATGCATTTTTA
ATTTTTTCCTCAAAATCCCTATTTTCAAAAAAAATCGAGTTTTCTAATCCATAAATATTTTCGGG
AGGATTTTCTTTGGTTTTTAATTTCA
Found at i:525565 original size:9 final size:9
Alignment explanation
Indices: 525546--525593 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
525536 GCAGCAAGTG
525546 AAAAGAAAA
1 AAAAGAAAA
525555 AGAAA-AAAA
1 A-AAAGAAAA
525564 AGAAAGAAAA
1 A-AAAGAAAA
*
525574 AAGAGAAAA
1 AAAAGAAAA
525583 AATAAGAAAA
1 AA-AAGAAAA
525593 A
1 A
525594 TAGCAAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:525574 original size:20 final size:19
Alignment explanation
Indices: 525546--525593 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
525536 GCAGCAAGTG
525546 AAAAG-AAAAAGAAAAAAA
1 AAAAGAAAAAAGAAAAAAA
*
525564 AGAAAGAAAAAAGAGAAAAA
1 A-AAAGAAAAAAGAAAAAAA
*
525584 ATAAGAAAAA
1 AAAAGAAAAA
525594 TAGCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 1 0.04
19 12 0.46
20 13 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (19 bp):
AAAAGAAAAAAGAAAAAAA
Found at i:526426 original size:13 final size:12
Alignment explanation
Indices: 526403--526435 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
526393 ATTTTCAAAG
526403 ATAAA-AAAATA
1 ATAAATAAAATA
526414 ATAATATAAAATA
1 ATAA-ATAAAATA
526427 ATAAATAAA
1 ATAAATAAA
526436 TATTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 4 0.20
12 6 0.30
13 10 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAATAAAATA
Found at i:527224 original size:155 final size:155
Alignment explanation
Indices: 526934--527233 Score: 372
Period size: 155 Copynumber: 1.9 Consensus size: 155
526924 CGAAGGTAAG
*
526934 TATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTTAGGAGTATTAGGTACTTTT
1 TATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTTAGCAGTATTAGGTACTTTT
* * * * * * *
526999 ACGTCGAAGGTATCTCATAGAGGCATTTTTGTAATTTTCCAGAACCAACCCTTAGGTAGTCACTG
66 ACGACAAAGGTATCTCATAGAGGCAATTTTGTAATTTTCCAAAACCAACCCTTAAGTAATCACCG
*
527064 GGTTCGCTTTTATGCTGAAGGTGGA
131 AGTTCGCTTTTATGCTGAAGGTGGA
* *
527089 TATTTAGGATAGGTTCATCC-CTCTTAAAATCCTTTTTAAGTCCTTTAGCAGTATTGGGTACTTT
1 TATTTAGGATAGGTTCATCCGATC-TAAAATCCTTTTTAAGTCCTTTAGCAGTATTAGGTACTTT
* * * ** * **
527153 TACGACAAAGGTATC-CTTTAGGGGTAATTTTGTAATTTTTTAAAACTTAGTCC-TAAGTAATCA
65 TACGACAAAGGTATCTC-ATAGAGGCAATTTTGTAATTTTCCAAAAC-CAACCCTTAAGTAATCA
*
527216 CCGAGTTCGTTTTTATGC
128 CCGAGTTCGCTTTTATGC
527234 CGAGAGTAGG
Statistics
Matches: 122, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
154 3 0.02
155 116 0.95
156 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (155 bp):
TATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTTAGCAGTATTAGGTACTTTT
ACGACAAAGGTATCTCATAGAGGCAATTTTGTAATTTTCCAAAACCAACCCTTAAGTAATCACCG
AGTTCGCTTTTATGCTGAAGGTGGA
Found at i:527256 original size:155 final size:154
Alignment explanation
Indices: 526915--527261 Score: 369
Period size: 155 Copynumber: 2.2 Consensus size: 154
526905 ACCAGGTTTA
** *
526915 CTTTTATATCGAAGGTAAGTATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTT
1 CTTTTATGCCGAAGGT-GGTATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTT
* * * * *
526980 AGGAGTATTAGGTACTTTTACGTCGAAGGTATCTCATAGAGGCATTTTTGTAATTTTCCAGAACC
65 AGCAGTATTAGGTACTTTTACGACAAAGGTATCTCATAGAGGCAATTTTGTAATTTTCCAAAACC
* * * *
527045 AACCCTTAGGTAGTCACTGGGTTCG
130 AACCCTTAAGTAATCACCGAGTTCG
* *
527070 CTTTTATGCTGAAGGTGGATATTTAGGATAGGTTCATCC-CTCTTAAAATCCTTTTTAAGTCCTT
1 CTTTTATGCCGAAGGTGG-TATTTAGGATAGGTTCATCCGATC-TAAAATCCTTTTTAAGTCCTT
* * * * **
527134 TAGCAGTATTGGGTACTTTTACGACAAAGGTATC-CTTTAGGGGTAATTTTGTAATTTTTTAAAA
64 TAGCAGTATTAGGTACTTTTACGACAAAGGTATCTC-ATAGAGGCAATTTTGTAATTTTCCAAAA
* **
527198 CTTAGTCC-TAAGTAATCACCGAGTTCG
128 C-CAACCCTTAAGTAATCACCGAGTTCG
* * *
527225 TTTTTATGCCG-AGAGTAGGTATTAAGAATAGGTTCAT
1 CTTTTATGCCGAAG-GT-GGTATTTAGGATAGGTTCAT
527262 ATTTTTTTGT
Statistics
Matches: 159, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
154 6 0.04
155 148 0.93
156 5 0.03
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.38
Consensus pattern (154 bp):
CTTTTATGCCGAAGGTGGTATTTAGGATAGGTTCATCCGATCTAAAATCCTTTTTAAGTCCTTTA
GCAGTATTAGGTACTTTTACGACAAAGGTATCTCATAGAGGCAATTTTGTAATTTTCCAAAACCA
ACCCTTAAGTAATCACCGAGTTCG
Found at i:528347 original size:34 final size:34
Alignment explanation
Indices: 528309--528376 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
528299 GAAAAATGAG
528309 ATGAATAAA-GAAAACAAAAAAAG-CAAAAGAAAAA
1 ATGAA-AAATGAAAA-AAAAAAAGACAAAAGAAAAA
* *
528343 ATGAAAAATTAAAAAAAAAAAGACAAAGGAAAAA
1 ATGAAAAATGAAAAAAAAAAAGACAAAAGAAAAA
528377 TGGCATATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 11 0.37
34 19 0.63
ACGTcount: A:0.76, C:0.04, G:0.12, T:0.07
Consensus pattern (34 bp):
ATGAAAAATGAAAAAAAAAAAGACAAAAGAAAAA
Found at i:535096 original size:60 final size:60
Alignment explanation
Indices: 534955--535712 Score: 409
Period size: 60 Copynumber: 12.6 Consensus size: 60
534945 GGTTGCTAGG
* * * *
534955 CTGTATTCAGTTAAGTCTTTTCTTATTTGACTATACTTGA-TCAAATTAT-ACCCT-TTTTGA
1 CTGTATTCAGTCAAGTC-TTTCTCATTTGACTATA-TTCAGTCAAATT-TCACCCTCTCTTGA
** ** * * * * *
535015 CTGTATTTGGTCAAAACCTTTCTCATTTGATTGTATTCGGTCAAATTTCACCTTTTCTTGA
1 CTGTATTCAGTC-AAGTCTTTCTCATTTGACTATATTCAGTCAAATTTCACCCTCTCTTGA
* * * *
535076 CTGTATTTAGTCAAGTCTTTC-CTTATTGACTGTATTCAGTCAAATCTT-A-CCACTCTTGA
1 CTGTATTCAGTCAAGTCTTTCTCAT-TTGACTATATTCAGTCAAAT-TTCACCCTCTCTTGA
* ** * * *
535135 CTGTATTAAACCAAGACTTTCTCATTTGACTATATTCAGTCAAACTTCACCCTCACTTGA
1 CTGTATTCAGTCAAGTCTTTCTCATTTGACTATATTCAGTCAAATTTCACCCTCTCTTGA
* * *
535195 TTGTATTCAGTCAAGTGTTTCCTCATTTGACTATACTT-AGTCAAATCTT-ACCC-CTTTTGA
1 CTGTATTCAGTCAAGTCTTT-CTCATTTGACTATA-TTCAGTCAAAT-TTCACCCTCTCTTGA
* * * * * *
535255 CTATATGC-GATCAAGACCTTCCTCATTTGACTGTATT-GGTCAAATTTCACCCTCTCTTGA
1 CTGTATTCAG-TCAAG-TCTTTCTCATTTGACTATATTCAGTCAAATTTCACCCTCTCTTGA
* * ** * * *
535315 TTGTATTTAGTCAAGTCTTTCCTCATTTGACGGTAATCAATCAAA-TCCTACCC-CTCTTGA
1 CTGTATTCAGTCAAGTCTTT-CTCATTTGACTATATTCAGTCAAATTTC-ACCCTCTCTTGA
* * * * *
535375 TTGTATTCGGTCAAGACCTTCCTCATTTGACTATATTCAGTTAAATTTCACCCT-TGCTTGA
1 CTGTATTCAGTCAAG-TCTTTCTCATTTGACTATATTCAGTCAAATTTCACCCTCT-CTTGA
* * * * *
535436 CTGTATTCAGTCAAGACTATCCTCATTTGATTATACTCGGTCAAATCTT-ACCC-CTCTTGA
1 CTGTATTCAGTCAAGTCT-TTCTCATTTGACTATATTCAGTCAAAT-TTCACCCTCTCTTGA
* * * * * ** * * *
535496 CTATATT-TGATCAAGACTATCCTTATTTGACTGCACTT-AGTCCAATCTT-ACCCTGT-TCGA
1 CTGTATTCAG-TCAAGTCT-TTCTCATTTGACTATA-TTCAGTCAAAT-TTCACCCTCTCTTGA
* * * * * * *
535556 CTGTATTTAATCAAGTGTTTCTTCATTTGACTGTACTC-GATCAAATCTT-ACCCTGT-TCGA
1 CTGTATTCAGTCAAGTCTTTC-TCATTTGACTATATTCAG-TCAAAT-TTCACCCTCTCTTGA
* * * * *
535616 CTGTATTC-GATCAAGTTTTTCTTCATTTAACTATACTCAATCAAATCTT-A-ACT-TGCTTGA
1 CTGTATTCAG-TCAAGTCTTTC-TCATTTGACTATATTCAGTCAAAT-TTCACCCTCT-CTTGA
* *
535676 CTATATTCAGTCAAGTTTTTCATCATTTGACTATATT
1 CTGTATTCAGTCAAGTCTTTC-TCATTTGACTATATT
535713 TGATCAAATC
Statistics
Matches: 550, Mismatches: 109, Indels: 78
0.75 0.15 0.11
Matches are distributed among these distances:
58 5 0.01
59 72 0.13
60 355 0.65
61 112 0.20
62 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (60 bp):
CTGTATTCAGTCAAGTCTTTCTCATTTGACTATATTCAGTCAAATTTCACCCTCTCTTGA
Found at i:535111 original size:29 final size:30
Alignment explanation
Indices: 535072--535256 Score: 89
Period size: 30 Copynumber: 6.2 Consensus size: 30
535062 TCACCTTTTC
* * * *
535072 TTGACTGTATTTAGTCAAGTCTTTCC-TTA
1 TTGACTGTATTCAGTCAAATCTTACCACTA
*
535101 TTGACTGTATTCAGTCAAATCTTACCACTC
1 TTGACTGTATTCAGTCAAATCTTACCACTA
* ** *
535131 TTGACTGTATTAAACCAAGA-CTTTCTCA-T-
1 TTGACTGTATTCAGTCAA-ATCTTAC-CACTA
*
535160 TTGACTATATTCAGTCAAA-CTTCACC-CTCA
1 TTGACTGTATTCAGTCAAATCTT-ACCACT-A
* * * * *
535190 CTTGATTGTATTCAGTCAAGTGTTTCCTC-A
1 -TTGACTGTATTCAGTCAAATCTTACCACTA
* * *
535220 TTTGACTATACTT-AGTCAAATCTTACCCCTT
1 -TTGACTGTA-TTCAGTCAAATCTTACCACTA
535251 TTGACT
1 TTGACT
535257 ATATGCGATC
Statistics
Matches: 117, Mismatches: 27, Indels: 23
0.70 0.16 0.14
Matches are distributed among these distances:
28 6 0.05
29 38 0.32
30 47 0.40
31 23 0.20
32 3 0.03
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (30 bp):
TTGACTGTATTCAGTCAAATCTTACCACTA
Found at i:535297 original size:120 final size:121
Alignment explanation
Indices: 534955--535750 Score: 672
Period size: 120 Copynumber: 6.6 Consensus size: 121
534945 GGTTGCTAGG
* * * * *
534955 CTGTATTCAGTTAAGTCTTTTCTTATTTGACTATACTT-GATCAAAT-TATACCCTTTTTGACTG
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAG-TCAAATCT-TACCCCTCTTGACTG
* * * * * * * *
535018 TATTTGGTCAAAACCTTTCTCATTTGATTGTATTCGGTCAAATTTCACCTTTTCTTGA
64 TATTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCTCTCTTGA
* * * *
535076 CTGTATTTAGTCAAGTCTTTCCTTA-TTGACTGTA-TTCAGTCAAATCTTACCACTCTTGACTGT
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTT-AGTCAAATCTTACCCCTCTTGACTGT
** * * * * *
535139 ATTAAACCAAGA-CTTTCTCATTTGACTATATTCAGTCAAACTTCACCCTCACTTGA
65 ATTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCTCTCTTGA
* * * *
535195 TTGTATTCAGTCAAGTGTTTCCTCATTTGACTATACTTAGTCAAATCTTACCCCTTTTGACTATA
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTGTA
* *
535260 TGCGATCAAGACCTTCCTCATTTGACTGTATT-GGTCAAATTTCACCCTCTCTTGA
66 TTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCTCTCTTGA
* * ** * * * * *
535315 TTGTATTTAGTCAAGTCTTTCCTCATTTGACGGTAATCAATCAAATCCTACCCCTCTTGATTGTA
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTGTA
* * *
535380 TTCGGTCAAGACCTTCCTCATTTGACTATATTCAGTTAAATTTCACCCT-TGCTTGA
66 TTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCTCT-CTTGA
* * * ** *
535436 CTGTATTCAGTCAAGACTATCCTCATTTGATTATACTCGGTCAAATCTTACCCCTCTTGACTATA
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTGTA
* * * * * *
535501 TTTGATCAAGA-CTATCCTTATTTGACTGCACTT-AGTCCAATCTT-ACCCTGT-TCGA
66 TTCGATCAAGACCT-TCCTCATTTGACTGTA-TTCAGTCAAAT-TTCACCCTCTCTTGA
* * * * * * *
535556 CTGTATTTAATCAAGTGTTTCTTCATTTGACTGTAC-TCGATCAAATCTTA-CCCTGTTCGACTG
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAG-TCAAATCTTACCCCTCTT-GACTG
*** * * * * * *
535619 TATTCGATCAAGTTTTTCTTCATTTAACTATACTCAATCAAATCTT-A-ACT-TGCTTGA
64 TATTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAAT-TTCACCCTCT-CTTGA
* * * * * * *
535676 CTATATTCAGTCAAGTTTTTCATCATTTGACTATA-TTTGATCAAATCTTACCTCGCTTGATTGT
1 CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAG-TCAAATCTTACCCCTCTTGACTGT
535740 ATTCGATCAAG
65 ATTCGATCAAG
535751 CTTTTCCTTA
Statistics
Matches: 546, Mismatches: 109, Indels: 41
0.78 0.16 0.06
Matches are distributed among these distances:
118 1 0.00
119 70 0.13
120 317 0.58
121 153 0.28
122 5 0.01
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (121 bp):
CTGTATTCAGTCAAGTCTTTCCTCATTTGACTATACTTAGTCAAATCTTACCCCTCTTGACTGTA
TTCGATCAAGACCTTCCTCATTTGACTGTATTCAGTCAAATTTCACCCTCTCTTGA
Found at i:535599 original size:30 final size:30
Alignment explanation
Indices: 535565--535664 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 30
535555 ACTGTATTTA
*
535565 ATCAAGTGTTTCTTCATTTGACTGTACTCG
1 ATCAAGTCTTTCTTCATTTGACTGTACTCG
* * * *
535595 ATCAAATCTTAC--CCTGTTCGACTGTATTCG
1 ATCAAGTCTTTCTTCAT-TT-GACTGTACTCG
* * * *
535625 ATCAAGTTTTTCTTCATTTAACTATACTCA
1 ATCAAGTCTTTCTTCATTTGACTGTACTCG
*
535655 ATCAAATCTT
1 ATCAAGTCTT
535665 AACTTGCTTG
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 43 0.84
31 2 0.04
32 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (30 bp):
ATCAAGTCTTTCTTCATTTGACTGTACTCG
Found at i:535719 original size:60 final size:60
Alignment explanation
Indices: 535426--535756 Score: 244
Period size: 60 Copynumber: 5.5 Consensus size: 60
535416 TAAATTTCAC
* ** * * * *
535426 CCTTGCTTGACTGTATTC-AGTCAAGACTATCCTCATTTGATTATACTCGGTCAAATCTTA
1 CCTTGCTTGACTATATTCGA-TCAAGTTTTTCTTCATTTGACTATACTCGATCAAATCTTA
* * * * * ** * *
535486 CCCCT-CTTGACTATATTTGATCAAGACTATCCTT-ATTTGACTGCACT-TAGTCCAATCTTA
1 -CCTTGCTTGACTATATTCGATCAAG-TTTTTCTTCATTTGACTATACTCGA-TCAAATCTTA
* * ** * *
535546 CCCTG-TTCGACTGTATTTAATCAAGTGTTTCTTCATTTGACTGTACTCGATCAAATCTTA
1 CCTTGCTT-GACTATATTCGATCAAGTTTTTCTTCATTTGACTATACTCGATCAAATCTTA
* * * *
535606 CCCTG-TTCGACTGTATTCGATCAAGTTTTTCTTCATTTAACTATACTCAATCAAATCTTA
1 CCTTGCTT-GACTATATTCGATCAAGTTTTTCTTCATTTGACTATACTCGATCAAATCTTA
* * * *
535666 ACTTGCTTGACTATATTC-AGTCAAGTTTTTCATCATTTGACTATATTTGATCAAATCTTA
1 CCTTGCTTGACTATATTCGA-TCAAGTTTTTCTTCATTTGACTATACTCGATCAAATCTTA
* * * *
535726 CCTCGCTTGATTGTATTCGATCAAGCTTTTC
1 CCTTGCTTGACTATATTCGATCAAGTTTTTC
535757 CTTATCTGCC
Statistics
Matches: 217, Mismatches: 43, Indels: 21
0.77 0.15 0.07
Matches are distributed among these distances:
59 11 0.05
60 196 0.90
61 10 0.05
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (60 bp):
CCTTGCTTGACTATATTCGATCAAGTTTTTCTTCATTTGACTATACTCGATCAAATCTTA
Found at i:537752 original size:9 final size:9
Alignment explanation
Indices: 537733--537780 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
537723 GCAGCAAGTG
537733 AAAAGAAAA
1 AAAAGAAAA
537742 AGAAA-AAAA
1 A-AAAGAAAA
537751 AGAAAGAAAA
1 A-AAAGAAAA
*
537761 AAGAGAAAAA
1 AAAAG-AAAA
537771 AAAAGAAAA
1 AAAAGAAAA
537780 A
1 A
537781 TAGCAAAACT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 18 0.53
10 16 0.47
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:537756 original size:13 final size:13
Alignment explanation
Indices: 537740--537774 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
537730 GTGAAAAGAA
537740 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
*
537753 AAAGAAAAAAGAG
1 AAAGAAAAAAAAG
537766 AAA-AAAAAA
1 AAAGAAAAAA
537775 GAAAAATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:537758 original size:19 final size:18
Alignment explanation
Indices: 537733--537780 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 18
537723 GCAGCAAGTG
537733 AAAAGAAAAAGAAAAAAA
1 AAAAGAAAAAGAAAAAAA
*
537751 AGAAAGAAAAAAGAGAAAAA
1 A-AAAG-AAAAAGAAAAAAA
537771 AAAAGAAAAA
1 AAAAGAAAAA
537781 TAGCAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 6 0.22
19 8 0.30
20 13 0.48
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAGAAAAAAA
Found at i:537788 original size:19 final size:18
Alignment explanation
Indices: 537733--537780 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
537723 GCAGCAAGTG
537733 AAAAG-AAAAAGAAAAAAA
1 AAAAGAAAAAAG-AAAAAA
537751 AGAAAGAAAAAAGAGAAAAA
1 A-AAAGAAAAAAGA-AAAAA
537771 AAAAGAAAAA
1 AAAAGAAAAA
537781 TAGCAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAA
Found at i:540287 original size:19 final size:18
Alignment explanation
Indices: 540262--540319 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
540252 TTGTATCGAT
*
540262 ACATTGTATCAATACATG
1 ACATTGTATCGATACATG
540280 ATCATTGTATCGATACATGG
1 A-CATTGTATCGATACAT-G
540300 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
540319 A
1 A
540320 AACTGGCAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.50
20 17 0.47
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:540308 original size:20 final size:20
Alignment explanation
Indices: 540263--540318 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
540253 TGTATCGATA
*
540263 CATTGTATCAATACAT-GAT
1 CATTGTATCGATACATGGAT
540282 CATTGTATCGATACATGGA-
1 CATTGTATCGATACATGGAT
540301 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
540319 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CATTGTATCGATACATGGAT
Found at i:542027 original size:9 final size:9
Alignment explanation
Indices: 541996--542029 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
541986 GTCAACCATC
541996 AATGATGAT
1 AATGATGAT
*
542005 AAAGATGAT
1 AATGATGAT
542014 AATGATGAT
1 AATGATGAT
*
542023 GATGATG
1 AATGATG
542030 GTGACTCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:546747 original size:21 final size:22
Alignment explanation
Indices: 546735--546776 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
546725 CAAATTTCTT
546735 ATTTTTCACTTCAAAATACTTC
1 ATTTTTCACTTCAAAATACTTC
546757 ATTTTTCA--TCAAAAT-CTTC
1 ATTTTTCACTTCAAAATACTTC
546776 A
1 A
546777 ACAAAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
22 8 0.40
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (22 bp):
ATTTTTCACTTCAAAATACTTC
Found at i:546770 original size:20 final size:20
Alignment explanation
Indices: 546731--546776 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
546721 TTTTCAAATT
546731 TCTT-ATTTTTCACTTCAAAA
1 TCTTCATTTTTCAC-TCAAAA
546751 TACTTCATTTTTCA-TCAAAA
1 T-CTTCATTTTTCACTCAAAA
546771 TCTTCA
1 TCTTCA
546777 ACAAAAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 8 0.33
21 3 0.12
22 8 0.33
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (20 bp):
TCTTCATTTTTCACTCAAAA
Found at i:549017 original size:20 final size:20
Alignment explanation
Indices: 548992--549038 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
548982 ATACTTCAAA
548992 GTATCGATACAGAGGTATTT
1 GTATCGATACAGAGGTATTT
549012 GTATCGATACAGAGGTATTT
1 GTATCGATACAGAGGTATTT
549032 GTATCGA
1 GTATCGA
549039 CACATTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.34
Consensus pattern (20 bp):
GTATCGATACAGAGGTATTT
Found at i:549247 original size:33 final size:32
Alignment explanation
Indices: 549186--549247 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
549176 CCACTATTTA
549186 TATCGATACATGGATATTGTATCAATACAATG
1 TATCGATACATGGATATTGTATCAATACAATG
*
549218 TATCGATACAT-GATGAATTGTATCGATACA
1 TATCGATACATGGAT--ATTGTATCAATACA
549248 TTGCTTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 3 0.11
32 11 0.41
33 13 0.48
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (32 bp):
TATCGATACATGGATATTGTATCAATACAATG
Found at i:552496 original size:155 final size:155
Alignment explanation
Indices: 552320--553273 Score: 765
Period size: 155 Copynumber: 6.2 Consensus size: 155
552310 AAAAAGGCTC
* *
552320 GATA-CCCTAAAGGACTTAAAAAGGATTATAGAAT-GGATGAACCTATCCTAAATATCTACCTTC
1 GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCACCTT-
* * * *
552383 GACAT-AAAGGCAGACCCGGTGACAACCTAAGACTCGATTTTAAAAAATTACAAAACTACCCCAA
65 GGCATGAAA-GCAGACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACAAAAATACCCCAA
*
552447 GGAGATACCTTCGACATAAAAGTACCA
129 GGAGATACCTTCGACGTAAAAGTACCA
* *
552474 GATACCCCTAAAGGACTTAAAAA-GATTAGA-AATGGGATGAACCTATCCTAAATACCCACATTT
1 GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCAC-CTT
* * * * * ** * * * *
552537 GGCATAAAAACCGGATCCAGTGATGACTTAGGAGTTGGTTCTAAAAAATTACAAAAATACCCCTA
65 GGCAT-GAAAGCAGACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACAAAAATACCCC-A
* * *
552602 TGGATATACCTTCGACGTGAAAGTATCCCA
128 AGGAGATACCTTCGACGTAAAAGTA--CCA
** * * * *
552632 -ATAATCCTAAAGGACTTAAAAAGGA-TATAG-ATGGGGTGAACTTATCCTAAATACTCACTTTT
1 GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCAC-CTT
* * *
552694 GGCATGAAAGCAGACCCGATGACAACCTAGGACTCGATTCTAAAAAAATA-ATGAAAATACCCCT
65 GGCATGAAAGCAGACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACA--AAAATACCCCA
* ** * *
552758 AGGGGATATTTTCGACGTATAAGTGCCTA
128 AGGAGATACCTTCGACGTAAAAGTACC-A
* * *
552787 -ATA-TCCTAAAGGACTTAAAAAGGATTATAAAATGAGATGAACCTATCCTAAATACCCACCATT
1 GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCACC-TT
* * * * * * * **
552850 GGCATTAAAGC-GAACTCGGTGACAACTTAGGACTTCG-TTCTAGACAGTTACAAAAATGCCTTA
65 GGCATGAAAGCAG-ACCCGGTGACAACCTAGGAC-TCGATTCTAAAAAATTACAAAAATACCCCA
* * * **
552913 AGG-GATGCCTTTGACATAAAAGTACTT
128 AGGAGATACCTTCGACGTAAAAGTACCA
* * *
552940 GATACCTCCTAAAGAACCTAAAAAGGATT-TA-AGATGGGGGTG-A---A--CTAAATACCCACC
1 GATACC-CCTAAAGGACTTAAAAAGGATTATAGA-AT-GGGATGAACCTATCCTAAATACCCACC
* * * * *
552997 TTTAGCATGAAAGCAGACCCAGTGACAACCTAGGACTCGATTCTAAAAAATTACGAAAATGCCTC
63 -TTGGCATGAAAGCAGACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACAAAAATACCCC
* * *
553062 TAGGGGATACCTTCGATGTAAAAGTACCTA
127 AAGGAGATACCTTCGACGTAAAAGTACC-A
* * * * * * * *
553092 -CTACCCCTAAAAGACTTAAAGAGGATAATAG-ACGAGATGAACCTATCCTAAATATCTACCTTC
1 GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCACCTT-
* * * ** * * *
553155 GGCAT-AAA-AATGAACCCGGTGACAACCTAGGACTCGGTCCTAAAAAATTATGAAAATGCCTCT
65 GGCATGAAAGCA-G-ACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACAAAAATACCCCA
*
553218 AGGAGATACCTTCGATGTAAAAGTACTC-
128 AGGAGATACCTTCGACGTAAAAGTAC-CA
*
553246 GGTACCCCTAAAGGACTTAAAAAGGATT
1 GATACCCCTAAAGGACTTAAAAAGGATT
553274 GGTAATGATG
Statistics
Matches: 636, Mismatches: 123, Indels: 81
0.76 0.15 0.10
Matches are distributed among these distances:
149 7 0.01
150 83 0.13
151 25 0.04
152 1 0.00
153 5 0.01
154 85 0.13
155 194 0.31
156 161 0.25
157 70 0.11
158 5 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.23
Consensus pattern (155 bp):
GATACCCCTAAAGGACTTAAAAAGGATTATAGAATGGGATGAACCTATCCTAAATACCCACCTTG
GCATGAAAGCAGACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTACAAAAATACCCCAAGG
AGATACCTTCGACGTAAAAGTACCA
Found at i:554850 original size:12 final size:11
Alignment explanation
Indices: 554810--554849 Score: 52
Period size: 10 Copynumber: 4.0 Consensus size: 11
554800 TTATTTCATC
554810 ATTTTTT-TCT
1 ATTTTTTCTCT
554820 -TTTTTTCT-T
1 ATTTTTTCTCT
554829 ATTTTTTCTCT
1 ATTTTTTCTCT
554840 A-TTTTTCTCT
1 ATTTTTTCTCT
554850 CCAAGTTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 7 0.26
10 18 0.67
11 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTTTCTCT
Found at i:554978 original size:21 final size:21
Alignment explanation
Indices: 554939--554979 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
554929 TGACTGAAAG
*
554939 TCATCTTTTTCTTTCTTTTTA
1 TCATCTTTTTCATTCTTTTTA
554960 TCATACTTTTTCATT-TTTTT
1 TCAT-CTTTTTCATTCTTTTT
554980 CTTTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (21 bp):
TCATCTTTTTCATTCTTTTTA
Found at i:556408 original size:83 final size:83
Alignment explanation
Indices: 556286--556447 Score: 261
Period size: 83 Copynumber: 2.0 Consensus size: 83
556276 CTTTTCATAA
* * *
556286 TGTATTGATACATGCATTTAAAATTTATAGCCGTTAGGCACAATGTATCAATACTTTTTACCATA
1 TGTATCGATACATGCATTTAAAATTTATAACCGTTAGGCACAATGTATCAATACATTTTACCATA
556351 TATCGATACAATGTCCTG
66 TATCGATACAATGTCCTG
* * *
556369 TGTATCGATACATGCATTTGAAATTTATAACCGTTAGGCACAATGTGTCAATACATTTTACCATG
1 TGTATCGATACATGCATTTAAAATTTATAACCGTTAGGCACAATGTATCAATACATTTTACCATA
*
556434 TATCGATATAATGT
66 TATCGATACAATGT
556448 ATCGATACAA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (83 bp):
TGTATCGATACATGCATTTAAAATTTATAACCGTTAGGCACAATGTATCAATACATTTTACCATA
TATCGATACAATGTCCTG
Found at i:556449 original size:13 final size:13
Alignment explanation
Indices: 556431--556460 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
556421 ACATTTTACC
*
556431 ATGTATCGATATA
1 ATGTATCGATACA
556444 ATGTATCGATACA
1 ATGTATCGATACA
556457 ATGT
1 ATGT
556461 CCTATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:556531 original size:20 final size:19
Alignment explanation
Indices: 556505--556577 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
556495 CTGCTAGTTT
556505 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
* *
556525 TATGTATCGATATAATGAG
1 CATGTATCGATACAATGAG
* * *
556544 CATGTATCAATACAAAGCAT
1 CATGTATCGATACAATG-AG
*
556564 AATGTATCGATACA
1 CATGTATCGATACA
556578 TCTGGATTTG
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
19 17 0.40
20 26 0.60
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:556548 original size:19 final size:20
Alignment explanation
Indices: 556505--556558 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
556495 CTGCTAGTTT
556505 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
556525 TATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTGAG
*
556544 CATGTATCAATACAA
1 CATGTATCGATACAA
556559 AGCATAATGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:559187 original size:12 final size:12
Alignment explanation
Indices: 559170--559194 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
559160 TCGATACTAA
559170 GCAAAATGTATC
1 GCAAAATGTATC
559182 GCAAAATGTATC
1 GCAAAATGTATC
559194 G
1 G
559195 ATACATCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GCAAAATGTATC
Found at i:559299 original size:21 final size:21
Alignment explanation
Indices: 559259--559299 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
559249 GTCAACCTTG
*
559259 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
559280 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
559300 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:566751 original size:19 final size:19
Alignment explanation
Indices: 566709--566761 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
566699 TCAGTTTCAG
*
566709 GTATCGATACAATTGAATAT
1 GTATCGATACAA-TGAACAT
*
566729 GTATCGATACAATGAGCAT
1 GTATCGATACAATGAACAT
566748 GTATCGATACAATG
1 GTATCGATACAATG
566762 TATCGATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
GTATCGATACAATGAACAT
Found at i:566764 original size:13 final size:13
Alignment explanation
Indices: 566746--566772 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
566736 TACAATGAGC
566746 ATGTATCGATACA
1 ATGTATCGATACA
566759 ATGTATCGATACA
1 ATGTATCGATACA
566772 A
1 A
566773 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:568680 original size:19 final size:19
Alignment explanation
Indices: 568656--568694 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
568646 CATCCCAAAT
568656 GGTGATCATTTTATTATAA
1 GGTGATCATTTTATTATAA
568675 GGTGATCATTTTATTATAA
1 GGTGATCATTTTATTATAA
568694 G
1 G
568695 AAAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (19 bp):
GGTGATCATTTTATTATAA
Found at i:572317 original size:20 final size:21
Alignment explanation
Indices: 572294--572346 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
572284 ACAATTCAAA
***
572294 GTATCGATACATGTTGAA-AT
1 GTATCGATACATGAAAAAGAT
572314 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
572335 GTATCGATACAT
1 GTATCGATACAT
572347 CTCTTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:572403 original size:13 final size:13
Alignment explanation
Indices: 572385--572410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
572375 TACAACAAGT
572385 ATGTATCGATACA
1 ATGTATCGATACA
572398 ATGTATCGATACA
1 ATGTATCGATACA
572411 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:574658 original size:21 final size:21
Alignment explanation
Indices: 574625--574669 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
574615 TTGCAAGTTG
*
574625 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
574647 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
574667 AAA
1 AAA
574670 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:578060 original size:13 final size:13
Alignment explanation
Indices: 578042--578080 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
578032 ACATTTTTCT
578042 TTGTATCGATACA
1 TTGTATCGATACA
578055 TTGTATCGATACA
1 TTGTATCGATACA
*
578068 CTGTATCGATACA
1 TTGTATCGATACA
578081 GGAGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:578244 original size:20 final size:19
Alignment explanation
Indices: 578203--578245 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
578193 ATCTTTTACA
578203 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
578223 AAATCACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
578243 AAA
1 AAA
578246 ACCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:580559 original size:20 final size:21
Alignment explanation
Indices: 580536--580588 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
580526 ACAATTCAAA
***
580536 GTATCGATACATGTTGAA-AT
1 GTATCGATACATGAAAAAGAT
580556 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGAAAAAGAT
580577 GTATCGATACAT
1 GTATCGATACAT
580589 CTCTTGGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (21 bp):
GTATCGATACATGAAAAAGAT
Found at i:580645 original size:13 final size:13
Alignment explanation
Indices: 580627--580652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
580617 TACAACAAGT
580627 ATGTATCGATACA
1 ATGTATCGATACA
580640 ATGTATCGATACA
1 ATGTATCGATACA
580653 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:581911 original size:21 final size:22
Alignment explanation
Indices: 581887--581944 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
581877 GAACTAGAGG
*
581887 AGAAAATGAATGAGTTGGAAA-
1 AGAAAATGAATGAGTTGCAAAT
581908 AGAAAA-GAAATGAGTTGCAAAT
1 AGAAAATG-AATGAGTTGCAAAT
*
581930 TGAAAATG-ATGAGTT
1 AGAAAATGAATGAGTT
581945 AACTAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 25 0.78
22 5 0.16
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.22
Consensus pattern (22 bp):
AGAAAATGAATGAGTTGCAAAT
Found at i:584149 original size:21 final size:21
Alignment explanation
Indices: 584118--584162 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
584108 CTTAATCTCG
*
584118 TTTATTTTATTTTTTATTTTTT
1 TTTATTTTATTTTTT-TTTTAT
584140 TTTA-TTTATTTTTTTTTTAT
1 TTTATTTTATTTTTTTTTTAT
584160 TTT
1 TTT
584163 CATGAATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 10 0.45
22 4 0.18
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (21 bp):
TTTATTTTATTTTTTTTTTAT
Found at i:584152 original size:15 final size:14
Alignment explanation
Indices: 584118--584161 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
584108 CTTAATCTCG
*
584118 TTTA-TTTTATTT-
1 TTTATTTTTTTTTA
584130 TTTATTTTTTTTTA
1 TTTATTTTTTTTTA
584144 TTTATTTTTTTTTTA
1 TTTA-TTTTTTTTTA
584159 TTT
1 TTT
584162 TCATGAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 4 0.14
13 7 0.25
14 4 0.14
15 13 0.46
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTATTTTTTTTTA
Found at i:585144 original size:20 final size:19
Alignment explanation
Indices: 585094--585150 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
585084 TTGTATCGAT
*
585094 ACATTATATCGATACATGT
1 ACATTATATCGATACATGG
*
585113 TCATTATATCGATACATGG
1 ACATTATATCGATACATGG
*
585132 ACAATTGTATCGATACATG
1 AC-ATTATATCGATACATG
585151 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
ACATTATATCGATACATGG
Found at i:587973 original size:32 final size:33
Alignment explanation
Indices: 587930--587993 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
587920 TAGCCAAACT
* **
587930 TGTATCGATACA-CAAAGTATGTATCGATACAA
1 TGTATCAATACACCAAAAAATGTATCGATACAA
*
587962 TGTATCAATACACCAAAAAATGTATTGATACA
1 TGTATCAATACACCAAAAAATGTATCGATACA
587994 TTGGCTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACCAAAAAATGTATCGATACAA
Found at i:592629 original size:13 final size:13
Alignment explanation
Indices: 592608--592643 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
592598 ATATTCTTTG
*
592608 TATCAATACATTA
1 TATCGATACATTA
*
592621 TATCGATACATTG
1 TATCGATACATTA
592634 TATCGATACA
1 TATCGATACA
592644 AGGGTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (13 bp):
TATCGATACATTA
Found at i:594349 original size:32 final size:31
Alignment explanation
Indices: 594284--594371 Score: 151
Period size: 31 Copynumber: 2.8 Consensus size: 31
594274 AAATAAATTT
594284 TTATCAAGGGGGAGAAAATCTTTTTAACCGA
1 TTATCAAGGGGGAGAAAATCTTTTTAACCGA
594315 TTATCAAGGGGGAGAAAATCTTTTGTAACCGA
1 TTATCAAGGGGGAGAAAATCTTTT-TAACCGA
*
594347 TTATCAAGGGGGAG-AAATTTTTTTA
1 TTATCAAGGGGGAGAAAATCTTTTTA
594372 TCAAAGGGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 2 0.04
31 32 0.58
32 21 0.38
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (31 bp):
TTATCAAGGGGGAGAAAATCTTTTTAACCGA
Found at i:594973 original size:19 final size:20
Alignment explanation
Indices: 594949--595002 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
594939 ACATTATGCT
* **
594949 TTGTATCGAGACATGTTC-A
1 TTGTATCGATACATGGACAA
594968 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
594988 TTGTATCGATACATG
1 TTGTATCGATACATG
595003 AAACTGGCAG
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:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:601771 original size:61 final size:60
Alignment explanation
Indices: 601678--602135 Score: 402
Period size: 61 Copynumber: 7.6 Consensus size: 60
601668 CTGGACTCGA
* * * *
601678 TCAAATCTT-ACCCCTCTTGACTGTATTCAGTCACGACCTTCCTTATTTGATTGTATTCGA
1 TCAAAT-TTCACCCTTCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * * * * *
601738 TCGAATTTCACCTTTACTTGACTGTATTTAGTCAAGTCCTTCCTCATTTGAGTGTACTCGG
1 TCAAATTTCACCCTT-CTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * * ** ***
601799 TCAAATCTT-ACCCCTCTTGATTGTATTCGGTCAAGATATTCCTCATTTGACTAAAATT-GG
1 TCAAAT-TTCACCCTTCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGA-TTGTATTCGG
* * * * * * * * * *
601859 TCAAATTTCACCCTCGCTTTATTGTATTTAGTCAAGTCTTTCCTCATTTGACTATACTCGA
1 TCAAATTTCACCCT-TCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * * * * *
601920 TCAAATTTTACCCATCTTGACTGTATTCAATCAAGACCTTCCTCATTTGACTATATTTGG
1 TCAAATTTCACCCTTCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * * * *
601980 TCAAATTTCACCCTTGCTTAACTGTATTTAGTCAAGTCTTTCCTCATTTGATTGTACTCGG
1 TCAAATTTCACCCTT-CTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * * *
602041 TCAAATCTT-ACCCCTCTTGATTGTATTCAGTCAAGACCTTCCTTATTTGATTGTATTCAG
1 TCAAAT-TTCACCCTTCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
* * *
602101 TCAAATTTCACACTTGCTTAACTGTATTTAGTCAA
1 TCAAATTTCACCCTT-CTTGACTGTATTCAGTCAA
602136 ATTTCACCCT
Statistics
Matches: 313, Mismatches: 74, Indels: 21
0.77 0.18 0.05
Matches are distributed among these distances:
59 6 0.02
60 149 0.48
61 154 0.49
62 4 0.01
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (60 bp):
TCAAATTTCACCCTTCTTGACTGTATTCAGTCAAGACCTTCCTCATTTGATTGTATTCGG
Found at i:601866 original size:121 final size:121
Alignment explanation
Indices: 601650--602135 Score: 598
Period size: 121 Copynumber: 4.0 Consensus size: 121
601640 GAATTCGATT
* * * * *
601650 AAGTTTTTCCTTATTTGTCTGGACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCACGAC
1 AAGTCTTTCCTCATTTGACTGTACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCAAGAC
* * * * * * * *
601715 CTTCCTTATTTGATTGTATTCGATCGAATTTCACCTTTACTTGACTGTATTTAGTC
66 CTTCCTCATTTGATAGAATTCGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
* * * * * *
601771 AAGTCCTTCCTCATTTGAGTGTACTCGGTCAAATCTTACCCCTCTTGATTGTATTCGGTCAAGAT
1 AAGTCTTTCCTCATTTGACTGTACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCAAGAC
* * * * *
601836 ATTCCTCATTTGACTAAAATT-GGTCAAATTTCACCCTCGCTTTATTGTATTTAGTC
66 CTTCCTCATTTGA-TAGAATTCGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
* * * *
601892 AAGTCTTTCCTCATTTGACTATACTCGATCAAATTTTACCCATCTTGACTGTATTCAATCAAGAC
1 AAGTCTTTCCTCATTTGACTGTACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCAAGAC
* *
601957 CTTCCTCATTTGACTA-TATTTGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
66 CTTCCTCATTTGA-TAGAATTCGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
* * *
602013 AAGTCTTTCCTCATTTGATTGTACTCGGTCAAATCTTACCCCTCTTGATTGTATTCAGTCAAGAC
1 AAGTCTTTCCTCATTTGACTGTACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCAAGAC
* * * * *
602078 CTTCCTTATTTGATTGTATTCAGTCAAATTTCACACTTGCTTAACTGTATTTAGTC
66 CTTCCTCATTTGATAGAATTCGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
602134 AA
1 AA
602136 ATTTCACCCT
Statistics
Matches: 312, Mismatches: 50, Indels: 6
0.85 0.14 0.02
Matches are distributed among these distances:
120 4 0.01
121 304 0.97
122 4 0.01
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (121 bp):
AAGTCTTTCCTCATTTGACTGTACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCAAGAC
CTTCCTCATTTGATAGAATTCGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTC
Found at i:602044 original size:30 final size:30
Alignment explanation
Indices: 602002--602104 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 30
601992 CTTGCTTAAC
*
602002 TGTATTTAGTCAAGTCTTTCCTCATTTGAT
1 TGTATTCAGTCAAGTCTTTCCTCATTTGAT
* * * * *
602032 TGTACTCGGTCAAATCTTACC-CCTCTTGAT
1 TGTATTCAGTCAAGTCTTTCCTCAT-TTGAT
* * *
602062 TGTATTCAGTCAAGACCTTCCTTATTTGAT
1 TGTATTCAGTCAAGTCTTTCCTCATTTGAT
602092 TGTATTCAGTCAA
1 TGTATTCAGTCAA
602105 ATTTCACACT
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 2 0.04
30 54 0.95
31 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.14, T:0.43
Consensus pattern (30 bp):
TGTATTCAGTCAAGTCTTTCCTCATTTGAT
Found at i:602106 original size:242 final size:242
Alignment explanation
Indices: 601672--602135 Score: 669
Period size: 242 Copynumber: 1.9 Consensus size: 242
601662 ATTTGTCTGG
* * * * * *
601672 ACTCGATCAAATCTTACCCCTCTTGACTGTATTCAGTCACGACCTTCCTTATTTGATTGTATTCG
1 ACTCGATCAAATCTTACCCATCTTGACTGTATTCAATCAAGACCTTCCTCATTTGACTATATTCG
* * *
601737 ATCGAATTTCACCTTTACTTGACTGTATTTAGTCAAGTCCTTCCTCATTTGAGTGTACTCGGTCA
66 ATCAAATTTCACCCTTACTTAACTGTATTTAGTCAAGTCCTTCCTCATTTGAGTGTACTCGGTCA
* * *
601802 AATCTTACCCCTCTTGATTGTATTCGGTCAAGATATTCCTCATTTGACTAAAATTGGTCAAATTT
131 AATCTTACCCCTCTTGATTGTATTCAGTCAAGACATTCCTCATTTGACTAAAATTAGTCAAATTT
* * *
601867 CACCCTCGCTTTATTGTATTTAGTCAAGTCTTTCCTCATTTGACTAT
196 CACACTCGCTTAACTGTATTTAGTCAAGTCTTTCCTCATTTGACTAT
* *
601914 ACTCGATCAAATTTTACCCATCTTGACTGTATTCAATCAAGACCTTCCTCATTTGACTATATTTG
1 ACTCGATCAAATCTTACCCATCTTGACTGTATTCAATCAAGACCTTCCTCATTTGACTATATTCG
* * * *
601979 GTCAAATTTCACCCTTGCTTAACTGTATTTAGTCAAGTCTTTCCTCATTTGATTGTACTCGGTCA
66 ATCAAATTTCACCCTTACTTAACTGTATTTAGTCAAGTCCTTCCTCATTTGAGTGTACTCGGTCA
* * ***
602044 AATCTTACCCCTCTTGATTGTATTCAGTCAAGACCTTCCTTATTTGA-TTGTATTCAGTCAAATT
131 AATCTTACCCCTCTTGATTGTATTCAGTCAAGACATTCCTCATTTGACTAAAATT-AGTCAAATT
*
602108 TCACACTTGCTTAACTGTATTTAGTCAA
195 TCACACTCGCTTAACTGTATTTAGTCAA
602136 ATTTCACCCT
Statistics
Matches: 194, Mismatches: 27, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
241 4 0.02
242 190 0.98
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (242 bp):
ACTCGATCAAATCTTACCCATCTTGACTGTATTCAATCAAGACCTTCCTCATTTGACTATATTCG
ATCAAATTTCACCCTTACTTAACTGTATTTAGTCAAGTCCTTCCTCATTTGAGTGTACTCGGTCA
AATCTTACCCCTCTTGATTGTATTCAGTCAAGACATTCCTCATTTGACTAAAATTAGTCAAATTT
CACACTCGCTTAACTGTATTTAGTCAAGTCTTTCCTCATTTGACTAT
Found at i:602134 original size:31 final size:31
Alignment explanation
Indices: 602092--602166 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
602082 CTTATTTGAT
602092 TGTATTCAGTCAAATTTCACACTTGCTTAAC
1 TGTATTCAGTCAAATTTCACACTTGCTTAAC
* * * *
602123 TGTATTTAGTCAAATTTCACCCTTGCTTGAT
1 TGTATTCAGTCAAATTTCACACTTGCTTAAC
*
602154 TATATTCAGTCAA
1 TGTATTCAGTCAA
602167 GACTATCCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (31 bp):
TGTATTCAGTCAAATTTCACACTTGCTTAAC
Found at i:602219 original size:60 final size:60
Alignment explanation
Indices: 602148--602262 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
602138 TTCACCCTTG
*
602148 CTTGATTATATTCAG-TCAAGACTATCCTTATTTGATTGTACCCGATCAAATCTTACCTCT
1 CTTGACTATATTC-GCTCAAGACTATCCTTATTTGATTGTACCCGATCAAATCTTACCTCT
** *
602208 CTTGACTATATTCGCTCAAGACTATCCTTATTTGATTGTACTGGGTCAAATCTTA
1 CTTGACTATATTCGCTCAAGACTATCCTTATTTGATTGTACCCGATCAAATCTTA
602263 TCTTGTTCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 49 0.98
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (60 bp):
CTTGACTATATTCGCTCAAGACTATCCTTATTTGATTGTACCCGATCAAATCTTACCTCT
Found at i:602256 original size:152 final size:152
Alignment explanation
Indices: 601973--602258 Score: 396
Period size: 152 Copynumber: 1.9 Consensus size: 152
601963 CATTTGACTA
* * * * * *
601973 TATTTGGTCAAATTTCACCCTTGCTTAACTGTATTTAGTCAAGTCTTTCCTCATTTGATTGTACT
1 TATTTAGTCAAATTTCACCCTTGCTTAACTATATTCAGTCAAGACTATCCTCATTTGATTGTACC
* * * *
602038 CGGTCAAATCTTACCCCTCTTGATTGTATTCAGTCAAGACCTTCCTTATTTGATTGTATTCAGTC
66 CGATCAAATCTTACCCCTCTTGACTATATTCAGTCAAGACCTTCCTTATTTGATTGTACTCAGTC
602103 AAATTTCACACTTGCTTAACTG
131 AAATTTCACACTTGCTTAACTG
* * *
602125 TATTTAGTCAAATTTCACCCTTGCTTGATTATATTCAGTCAAGACTATCCTTATTTGATTGTACC
1 TATTTAGTCAAATTTCACCCTTGCTTAACTATATTCAGTCAAGACTATCCTCATTTGATTGTACC
* **
602190 CGATCAAATCTTACCTCTCTTGACTATATTC-GCTCAAGA-CTATCCTTATTTGATTGTACTGGG
66 CGATCAAATCTTACCCCTCTTGACTATATTCAG-TCAAGACCT-TCCTTATTTGATTGTACTCAG
602253 TCAAAT
129 TCAAAT
602259 CTTATCTTGT
Statistics
Matches: 116, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
151 3 0.03
152 113 0.97
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (152 bp):
TATTTAGTCAAATTTCACCCTTGCTTAACTATATTCAGTCAAGACTATCCTCATTTGATTGTACC
CGATCAAATCTTACCCCTCTTGACTATATTCAGTCAAGACCTTCCTTATTTGATTGTACTCAGTC
AAATTTCACACTTGCTTAACTG
Found at i:602302 original size:60 final size:60
Alignment explanation
Indices: 602253--602445 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
602243 TTGTACTGGG
* * * *
602253 TCAAATCTTATCTTGTTCGACTGTATTTAGTCAATTCTTTCTTCGTTTGACTATACTCGA
1 TCAAATCTTACCTTGTTCGATTGTATTTAGTCAAGTCTTTCTTCATTTGACTATACTCGA
* * * * *
602313 TCAAATCTCACCTTGCTCGATTGTATTTGGTTAAGTCTTTCTTCATTTAACTATACTCGA
1 TCAAATCTTACCTTGTTCGATTGTATTTAGTCAAGTCTTTCTTCATTTGACTATACTCGA
* * * *
602373 TCAAATCTTACCTTGTTTGATTGTA-TTCGATCAAGTCTTTCTTCATTTGACTATATTTGA
1 TCAAATCTTACCTTGTTCGATTGTATTTAG-TCAAGTCTTTCTTCATTTGACTATACTCGA
* *
602433 ACAAATTTTACCT
1 TCAAATCTTACCT
602446 CACTTCATTA
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
59 3 0.03
60 110 0.97
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (60 bp):
TCAAATCTTACCTTGTTCGATTGTATTTAGTCAAGTCTTTCTTCATTTGACTATACTCGA
Found at i:602405 original size:30 final size:30
Alignment explanation
Indices: 602026--602411 Score: 84
Period size: 30 Copynumber: 12.8 Consensus size: 30
602016 TCTTTCCTCA
* * *
602026 TTTGATTGTACTCGGTCAAATCTTACCCCT-
1 TTTGATTGTATTCGATCAAATCTTA-CCTTG
* * *
602056 CTTGATTGTATTC-AGTCAAGACCTT-CCTTA
1 TTTGATTGTATTCGA-TCAA-ATCTTACCTTG
602086 TTTGATTGTATTC-AGTCAAAT-TTCACACTTG
1 TTTGATTGTATTCGA-TCAAATCTT-AC-CTTG
* * * *
602117 CTTAACTGTATT-TAGTCAAAT-TTCACCCTTG
1 TTTGATTGTATTCGA-TCAAATCTT-A-CCTTG
* * *
602148 CTTGATTATATTC-AGTCAAGA-C-TATCCTTA
1 TTTGATTGTATTCGA-TCAA-ATCTTA-CCTTG
**
602178 TTTGATTGTACCCGATCAAATCTTACCTCT-
1 TTTGATTGTATTCGATCAAATCTTACCT-TG
* * * * *
602208 CTTGACTATATTCGCTCAAGA-C-TATCCTTA
1 TTTGATTGTATTCGATCAA-ATCTTA-CCTTG
* * * *
602238 TTTGATTGTACTGGGTCAAATCTTATCTTG
1 TTTGATTGTATTCGATCAAATCTTACCTTG
* * * * *
602268 TTCGACTGTATT-TAGTCAATTCTT-TCTTCG
1 TTTGATTGTATTCGA-TCAAATCTTACCTT-G
* * * *
602298 TTTGACTATACTCGATCAAATCTCACCTTG
1 TTTGATTGTATTCGATCAAATCTTACCTTG
* * * * * * * *
602328 CTCGATTGTATTTGGTTAAGTCTT-TCTTCA
1 TTTGATTGTATTCGATCAAATCTTACCTT-G
* * * *
602358 TTTAACTATACTCGATCAAATCTTACCTTG
1 TTTGATTGTATTCGATCAAATCTTACCTTG
*
602388 TTTGATTGTATTCGATCAAGTCTT
1 TTTGATTGTATTCGATCAAATCTT
602412 TCTTCATTTG
Statistics
Matches: 254, Mismatches: 76, Indels: 52
0.66 0.20 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.06
30 172 0.68
31 62 0.24
32 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (30 bp):
TTTGATTGTATTCGATCAAATCTTACCTTG
Found at i:602422 original size:30 final size:30
Alignment explanation
Indices: 602331--602422 Score: 78
Period size: 30 Copynumber: 3.1 Consensus size: 30
602321 CACCTTGCTC
* * *
602331 GATTGTATTTGGTTAAGTCTTTCTTCATTT
1 GATTGTATTCGATCAAGTCTTTCTTCATTT
* * * * * * *
602361 AACTATACTCGATCAAATCTTACCTT-GTTT
1 GATTGTATTCGATCAAGTCTT-TCTTCATTT
602391 GATTGTATTCGATCAAGTCTTTCTTCATTT
1 GATTGTATTCGATCAAGTCTTTCTTCATTT
602421 GA
1 GA
602423 CTATATTTGA
Statistics
Matches: 43, Mismatches: 17, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
29 3 0.07
30 37 0.86
31 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.48
Consensus pattern (30 bp):
GATTGTATTCGATCAAGTCTTTCTTCATTT
Found at i:602460 original size:60 final size:60
Alignment explanation
Indices: 602283--602481 Score: 175
Period size: 60 Copynumber: 3.3 Consensus size: 60
602273 CTGTATTTAG
* * * * ** * * *
602283 TCAATTCTTTCTTCGTTTGACTATACTCGATCAAATCTCACCTTGC-TCGATTGTATTTGG
1 TCAAGTCTTTCTTCATTTGACTATACTCGAACAAATCTTACCTCACTTC-ATTATATTCGA
* * * *** * *
602343 TTAAGTCTTTCTTCATTTAACTATACTCGATCAAATCTTACCTTGTTTGATTGTATTCGA
1 TCAAGTCTTTCTTCATTTGACTATACTCGAACAAATCTTACCTCACTTCATTATATTCGA
* * * *
602403 TCAAGTCTTTCTTCATTTGACTATATTTGAACAAATTTTACCTCACTTCATTATATTCGG
1 TCAAGTCTTTCTTCATTTGACTATACTCGAACAAATCTTACCTCACTTCATTATATTCGA
* *
602463 TCAAGCCTTTCCTCATTTG
1 TCAAGTCTTTCTTCATTTG
602482 CCTACATTCA
Statistics
Matches: 115, Mismatches: 23, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
60 114 0.99
61 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (60 bp):
TCAAGTCTTTCTTCATTTGACTATACTCGAACAAATCTTACCTCACTTCATTATATTCGA
Found at i:602473 original size:120 final size:120
Alignment explanation
Indices: 602194--602480 Score: 263
Period size: 120 Copynumber: 2.4 Consensus size: 120
602184 TGTACCCGAT
* * * * * * * * * * * * *
602194 CAAATCTTACCTCTCTTGACTATATTCGCTCAAGACTATCCTTATTTGATTGTACTGGGTCAAAT
1 CAAATCTCACCTCACTCGATTATATTCGGTCAAGCCTTTCCTCATTTAACTATACTCGATCAAAT
* * * * *
602259 CTTATCTTGTTCGACTGTATTTAGTCAATTCTTTCTTCGTTTGACTATACTCGAT
66 CTTACCTTGTTCGACTGTATTGAGTCAAGTCTTTCTTCATTTGACTATACTCGAA
** * * * * *
602314 CAAATCTCACCTTGCTCGATTGTATTTGGTTAAGTCTTTCTTCATTTAACTATACTCGATCAAAT
1 CAAATCTCACCTCACTCGATTATATTCGGTCAAGCCTTTCCTCATTTAACTATACTCGATCAAAT
* * * *
602379 CTTACCTTGTTTGATTGTATTCGA-TCAAGTCTTTCTTCATTTGACTATATTTGAA
66 CTTACCTTGTTCGACTGTATT-GAGTCAAGTCTTTCTTCATTTGACTATACTCGAA
* *
602434 CAAATTTTACCTCACTTC-ATTATATTCGGTCAAGCCTTTCCTCATTT
1 CAAATCTCACCTCAC-TCGATTATATTCGGTCAAGCCTTTCCTCATTT
602481 GCCTACATTC
Statistics
Matches: 129, Mismatches: 36, Indels: 4
0.76 0.21 0.02
Matches are distributed among these distances:
120 126 0.98
121 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (120 bp):
CAAATCTCACCTCACTCGATTATATTCGGTCAAGCCTTTCCTCATTTAACTATACTCGATCAAAT
CTTACCTTGTTCGACTGTATTGAGTCAAGTCTTTCTTCATTTGACTATACTCGAA
Found at i:603769 original size:165 final size:163
Alignment explanation
Indices: 603553--604008 Score: 456
Period size: 166 Copynumber: 2.8 Consensus size: 163
603543 AAATTATGGG
* * * **
603553 GTTTTCTTCTCCGTAAATTGTTTTGGGGGATTTTCACGGATTTAAAATTTTTAAAATTCATCAAA
1 GTTTTCTACTCAGTAAATTTTTTTGGGGGATTTTCTTGG-TTTAAAATTTTTAAAATTCATCAAA
* **
603618 TATTATTTTTTAATTAATATTAAATCAGTTTTTAAAAATTTGTTAATTTT-ATTG-GTTTTTGAA
65 TATTATTATTTAATT-ATATTAAATCAGTTTTTAAAAATTCATTAATTTTCA-TGAGTTTTTG-A
* * *
603681 TTTTTTTCCTTGAAATTACC-TTGTTTTC-AAAAAATAGA
127 -TTTTTTCCTTAAAATCACCATT-TTCTCGAAAAAAT-GA
* * ** *
603719 GTTTTCTACTCTGTAAATTTTTTTGGGGGAGTTTCTTGGTTTTTAATTTTTAAAATTTATCAAAT
1 GTTTTCTACTCAGTAAATTTTTTTGGGGGATTTTCTTGGTTTAAAATTTTTAAAATTCATCAAAT
* * * *
603784 ATTATTATTTAATTCACATTAAATTAGTTTTGAAAAATTCATTCATTTTCATGAGTTTTTGATTT
66 ATTATTATTTAATT-ATATTAAATCAGTTTTTAAAAATTCATTAATTTTCATGAGTTTTTGATTT
* * * *
603849 TTTCTTTAAAATCCCCATTTTCTCGGAAAACTGA
130 TTTCCTTAAAATCACCATTTTCTCGAAAAAATGA
* * * * *
603883 GTTTTCTAATAAGTAAATATTTTTAGGGGGATTTTCTTTGGTTTAAAATTTTTAGAATTCATCTA
1 GTTTTCTACTCAGTAAAT-TTTTTTGGGGGATTTTC-TTGGTTTAAAATTTTTAAAATTCATCAA
* * * *
603948 ATATTATCATTTAATTTTCATTAAATCAATTTTTGAAAAA-TCAATTTATTTT-ATGAGTTTT
64 ATATTATTATTTAATTAT-ATTAAATCAGTTTTT-AAAAATTC-ATTAATTTTCATGAGTTTT
604009 GAATTTGTTT
Statistics
Matches: 240, Mismatches: 41, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
164 36 0.15
165 89 0.37
166 102 0.43
167 13 0.05
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (163 bp):
GTTTTCTACTCAGTAAATTTTTTTGGGGGATTTTCTTGGTTTAAAATTTTTAAAATTCATCAAAT
ATTATTATTTAATTATATTAAATCAGTTTTTAAAAATTCATTAATTTTCATGAGTTTTTGATTTT
TTCCTTAAAATCACCATTTTCTCGAAAAAATGA
Found at i:605578 original size:13 final size:13
Alignment explanation
Indices: 605554--605587 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
605544 ATTTTTGAAG
605554 ATAAAA-AAAATA
1 ATAAAATAAAATA
605566 ATAAAATAAAATA
1 ATAAAATAAAATA
605579 AT-AAATAAA
1 ATAAAATAAA
605588 TATTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:605584 original size:12 final size:12
Alignment explanation
Indices: 605554--605587 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
605544 ATTTTTGAAG
*
605554 ATAAAAAAAATA
1 ATAAATAAAATA
605566 ATAAAATAAAATA
1 AT-AAATAAAATA
605579 ATAAATAAA
1 ATAAATAAA
605588 TATTTTTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAAATAAAATA
Found at i:609593 original size:52 final size:51
Alignment explanation
Indices: 609530--609658 Score: 156
Period size: 52 Copynumber: 2.5 Consensus size: 51
609520 AGATGCATCA
* **
609530 ATACATTGAAGAATGTATCGATACATTTGGG-TCAAAAACTTAAAATGTATCG
1 ATACAATGAAGAATGTATCGATACATTTGGGATC--AAACCCAAAATGTATCG
* *
609582 ATACAATGAAGAATGTATCAATACA-TTGGGATCAAACCCAGAATGTATCG
1 ATACAATGAAGAATGTATCGATACATTTGGGATCAAACCCAAAATGTATCG
* *
609632 ATACAAT-AAAAATATATCGATACATTT
1 ATACAATGAAGAATGTATCGATACATTT
609659 TCTTTCCAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
49 14 0.21
50 23 0.34
51 5 0.07
52 25 0.37
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (51 bp):
ATACAATGAAGAATGTATCGATACATTTGGGATCAAACCCAAAATGTATCG
Found at i:609725 original size:20 final size:21
Alignment explanation
Indices: 609696--609747 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
609686 ACAAGGTCTA
*
609696 GTATCGATACATTCACTT-AT
1 GTATCAATACATTCACTTGAT
*
609716 GTATCAATACATTCACTTGTT
1 GTATCAATACATTCACTTGAT
609737 GTATCAATACA
1 GTATCAATACA
609748 AATTGTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (21 bp):
GTATCAATACATTCACTTGAT
Found at i:610429 original size:52 final size:52
Alignment explanation
Indices: 610264--610771 Score: 468
Period size: 52 Copynumber: 9.7 Consensus size: 52
610254 GTCCGCAATG
* * * * * ** *
610264 TGCCAATATGCAGATTTAAGGCCTA-CAACACTGGACTTAATGATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCC-AGCGATATTGGACTTAAAAATGATAAAGA
* * * * *
610316 TGCTAATGTGCTGATTCAAGGCCAGCGATATTTGGACTTAAAGATAAGAATAG-
1 TGCCAATATGCTGATTCAAGGCCAGCGATA-TTGGACTTAAAAATGATAA-AGA
* * * * *
610369 TGCTAATATGCTAATTTAAGGCCAGGGAGATTGGACTTAAAAATGATAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* *
610421 TGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAAATGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* * * *
610473 TGCCAATATACTGATTCAAAGCCAGCAATATTGGACTTAAAGATGAT-AAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* * * * *
610524 GTGCCAATGTGCTAATTCAAGGCTAGCGATATTAGACTTAAAAATGATAAAAA
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* * * * * * *
610577 GTACCAATATGCTAATTGAAAGCCAACGATATTGGACTTAAAAAGGA-GAAGA
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* ** ** *
610629 GTGCCAATGTGCTGATTCAAGGCCAGTAATATTGGACTTAATGATGAGAAAGA
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
* * * * *
610682 TGGCAATATGCTCATTTAAGGCCAGTGGA-ATTGGACTTAAAAATGATAAAAGG
1 TGCCAATATGCTGATTCAAGGCCAG-CGATATTGGACTTAAAAATGAT-AAAGA
* *
610735 TGCCAATATGTTGATTCAAGGCCAGCAATATTGGACT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
610772 CCAAGATAAC
Statistics
Matches: 368, Mismatches: 78, Indels: 19
0.79 0.17 0.04
Matches are distributed among these distances:
51 6 0.02
52 240 0.65
53 120 0.33
54 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGA
Found at i:610450 original size:105 final size:103
Alignment explanation
Indices: 610295--610807 Score: 485
Period size: 105 Copynumber: 4.9 Consensus size: 103
610285 CCTACAACAC
** * *
610295 TGGACTTAATGATGATAAAGGTGCTAATGTGCTGATTCAAGGCCAGCGATATTTGGACTTAAAGA
1 TGGACTTAAAAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAGCGATA-TTGGACTTAAAGA
* * * *
610360 TAAGAATAGTGCTAATATGCTAATTTAAGGCCAGGGAGAT
65 TAAGAA-AGTGCCAATATGCTAATTCAAGGCCAGCGATAT
* * *
610400 TGGACTTAAAAATGATAAAGATGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAAAT
1 TGGACTTAAAAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
* * * * * *
610465 GATAAAGGTGCCAATATACTGATTCAAAGCCAGCAATAT
66 AAGAAA-GTGCCAATATGCTAATTCAAGGCCAGCGATAT
* * * *
610504 TGGACTTAAAGATGAT-AAGAGTGCCAATGTGCTAATTCAAGGCTAGCGATATTAGACTTAAAAA
1 TGGACTTAAAAATGATAAAGA-TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT--AAA
* * * *
610568 TGATAA-AAAGTACCAATATGCTAATTGAAAGCCAACGATAT
63 -GATAAGAAAGTGCCAATATGCTAATTCAAGGCCAGCGATAT
* * ** *
610609 TGGACTTAAAAAGGA-GAAGAGTGCCAATGTGCTGATTCAAGGCCAGTAATATTGGACTTAATGA
1 TGGACTTAAAAATGATAAAGA-TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * * * *
610673 TGAGAAAGATGGCAATATGCTCATTTAAGGCCAGTGGA-AT
65 TAAGAAAG-TGCCAATATGCTAATTCAAGGCCAG-CGATAT
* * * * **
610713 TGGACTTAAAAATGATAAAAGGTGCCAATATGTTGATTCAAGGCCAGCAATATTGGACTCCAAGA
1 TGGACTTAAAAATGAT-AAAGATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
* * * *
610778 TAACAAGAGTGCTAATGTACTAATTCAAGG
65 TAAGAA-AGTGCCAATATGCTAATTCAAGG
610808 TCAACAATAT
Statistics
Matches: 334, Mismatches: 62, Indels: 24
0.80 0.15 0.06
Matches are distributed among these distances:
102 4 0.01
103 11 0.03
104 125 0.37
105 180 0.54
106 11 0.03
107 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (103 bp):
TGGACTTAAAAATGATAAAGATGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT
AAGAAAGTGCCAATATGCTAATTCAAGGCCAGCGATAT
Found at i:610584 original size:157 final size:155
Alignment explanation
Indices: 610263--610771 Score: 592
Period size: 157 Copynumber: 3.2 Consensus size: 155
610253 CGTCCGCAAT
* * * * * ** *
610263 GTGCCAATATGCAGATTTAAGGCCTA-CAACACTGGACTTAATGATGATAAAGGTGCTAATGTGC
1 GTGCCAATATGCTGATTCAAGGCC-AGCGATATTGGACTTAAAAATGATAAAGGTGCCAATGTGC
* * *
610327 TGATTCAAGGCCAGCGATATTTGGACTTAAAGATAAGAATAGTGCTAATATGCTAATTTAAGGCC
65 TGATTCAAGGCCAGCAATA-TTGGACTTAAAGATGAGAA-AGTGCCAATATGCTAATTTAAGGCC
*
610392 AGGGAGATTGGACTTAAAAATGATAAAGA
128 AGGGA-ATTGGACTTAAAAATGATAAAAA
* * *
610421 -TGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAAATGATAAAGGTGCCAATATACT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGGTGCCAATGTGCT
* * * * *
610485 GATTCAAAGCCAGCAATATTGGACTTAAAGATGATAAGAGTGCCAATGTGCTAATTCAAGGCTAG
66 GATTCAAGGCCAGCAATATTGGACTTAAAGATGAGAA-AGTGCCAATATGCTAATTTAAGGCCAG
* *
610550 CGATATTAGACTTAAAAATGATAAAAA
130 GGA-ATTGGACTTAAAAATGATAAAAA
* * * * * * *
610577 GTACCAATATGCTAATTGAAAGCCAACGATATTGGACTTAAAAAGGA-GAAGAGTGCCAATGTGC
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAG-GTGCCAATGTGC
* * * *
610641 TGATTCAAGGCCAGTAATATTGGACTTAATGATGAGAAAGATGGCAATATGCTCATTTAAGGCCA
65 TGATTCAAGGCCAGCAATATTGGACTTAAAGATGAGAAAG-TGCCAATATGCTAATTTAAGGCCA
*
610706 GTGGAATTGGACTTAAAAATGATAAAAG
129 G-GGAATTGGACTTAAAAATGATAAAAA
* *
610734 GTGCCAATATGTTGATTCAAGGCCAGCAATATTGGACT
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
610772 CCAAGATAAC
Statistics
Matches: 293, Mismatches: 53, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
156 69 0.24
157 222 0.76
158 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (155 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATAAAGGTGCCAATGTGCT
GATTCAAGGCCAGCAATATTGGACTTAAAGATGAGAAAGTGCCAATATGCTAATTTAAGGCCAGG
GAATTGGACTTAAAAATGATAAAAA
Done.