Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:239027 original size:32 final size:32
Alignment explanation
Indices: 238984--239085 Score: 161
Period size: 32 Copynumber: 3.2 Consensus size: 32
238974 TTAACTCAAC
* * *
238984 ATAATTGAAATACTTAAATACTTCCAAGTTTG
1 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
239016 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
1 ATAATTCAAATACTTAAAAACTTCCAAGTTCG
239048 ATAAATTCAAATACTTAAAAACTT-CAAGTTCG
1 AT-AATTCAAATACTTAAAAACTTCCAAGTTCG
239080 ATAATT
1 ATAATT
239086 GAAACAAGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
31 4 0.06
32 41 0.62
33 21 0.32
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (32 bp):
ATAATTCAAATACTTAAAAACTTCCAAGTTCG
Found at i:241416 original size:12 final size:12
Alignment explanation
Indices: 241399--241430 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
241389 TTCGGATAAA
241399 AACCGGTTTTTT
1 AACCGGTTTTTT
241411 AACCGGTTTTTT
1 AACCGGTTTTTT
*
241423 ATCCGGTT
1 AACCGGTT
241431 AAAAAACCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.19, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:245954 original size:14 final size:14
Alignment explanation
Indices: 245935--245964 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
245925 TCCATCATAC
245935 ATTTTAATTTTTAA
1 ATTTTAATTTTTAA
245949 ATTTTAATTTTTAA
1 ATTTTAATTTTTAA
245963 AT
1 AT
245965 AAACTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTTAATTTTTAA
Found at i:252886 original size:31 final size:31
Alignment explanation
Indices: 252851--252959 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
252841 TAAGTCCCGA
* * *
252851 AGAACCTAGGTAAACTGTCCATATATTCCTT
1 AGAACATAGGTAAACTGTCCATATGTTCCAT
* * *
252882 AGAACATAGGTATACTGTCCATATGTCTCGAA
1 AGAACATAGGTAAACTGTCCATATGT-TCCAT
*
252914 AG-ACATAGGTAATTCTGTCCATATGTTCCAT
1 AGAACATAGGTAA-ACTGTCCATATGTTCCAT
252945 AGAACATAGGTAAAC
1 AGAACATAGGTAAAC
252960 CCTCGACTCT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 38 0.59
32 26 0.41
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (31 bp):
AGAACATAGGTAAACTGTCCATATGTTCCAT
Found at i:256667 original size:2 final size:2
Alignment explanation
Indices: 256662--256737 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
256652 ATATCCATTC
256662 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256738 CATTGCATTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:257079 original size:30 final size:31
Alignment explanation
Indices: 257040--257106 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
257030 GAATGACCTA
* * * *
257040 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* *
257070 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
257101 TCCATA
1 TCCATA
257107 TGTTCCTTAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:257103 original size:31 final size:31
Alignment explanation
Indices: 257065--257192 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
257055 GAACCTCGGC
* *
257065 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
257096 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * * *
257127 TATTGTCCATATATCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
* * *
257158 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTCCCGAAGAACATAGGTA
257190 AAC
1 AAC
257193 CCTCGACTCT
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
30 1 0.01
31 49 0.66
32 23 0.31
33 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:259480 original size:20 final size:22
Alignment explanation
Indices: 259441--259482 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
259431 GTCCCAACAA
*
259441 AACAGTTAAGAATTATAAATCT
1 AACAGTTAAGAATCATAAATCT
259463 AACAGTT-AG-ATCATAAATCT
1 AACAGTTAAGAATCATAAATCT
259483 CTGAAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.31
Consensus pattern (22 bp):
AACAGTTAAGAATCATAAATCT
Found at i:265406 original size:20 final size:20
Alignment explanation
Indices: 265368--265406 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
265358 CTATGACAAA
*
265368 TATAAAATAAATTTTAAAAT
1 TATAAAATAAATTTGAAAAT
265388 TATAAAA-AAATGTTGAAAA
1 TATAAAATAAAT-TTGAAAA
265407 AATCAGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TATAAAATAAATTTGAAAAT
Found at i:270958 original size:3 final size:3
Alignment explanation
Indices: 270924--270984 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
270914 TCTACAAAAA
270924 TAT T-T TAT TA- TAT TA- TAT ATATT TATT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT -TA-T TA-T TAT TAT TAT TAT TAT TAT
*
270968 TAT TTT TAT T-T TAT TAT
1 TAT TAT TAT TAT TAT TAT
270985 ATTTGCAGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
2 10 0.20
3 30 0.61
4 8 0.16
5 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:270969 original size:25 final size:24
Alignment explanation
Indices: 270928--270984 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
270918 CAAAAATATT
270928 TTATTA-TATTATATATATTTATTTA
1 TTATTATTATTATATATA-TT-TTTA
270953 TTATTATTATTAT-TATATTTTTA
1 TTATTATTATTATATATATTTTTA
270976 TT-TTATTAT
1 TTATTATTAT
270985 ATTTGCAGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.23
23 6 0.19
24 2 0.06
25 10 0.32
26 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TTATTATTATTATATATATTTTTA
Found at i:271503 original size:2 final size:2
Alignment explanation
Indices: 271496--271538 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
271486 TTTTATTTAT
271496 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
271538 T
1 T
271539 TTTTACTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:271594 original size:21 final size:21
Alignment explanation
Indices: 271532--271600 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
271522 TATATATATA
*
271532 TATATATTTTTACTTTTTATTAT
1 TATATATTTTTTCTTTTTA-T-T
* *
271555 TATTTTATTTATTT-GTTTTATT
1 TA-TATATTT-TTTCTTTTTATT
*
271577 TATATATTTTTTCTTTTTCTT
1 TATATATTTTTTCTTTTTATT
271598 TAT
1 TAT
271601 TTTTTATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
20 3 0.08
21 15 0.41
22 3 0.08
23 3 0.08
24 11 0.30
25 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (21 bp):
TATATATTTTTTCTTTTTATT
Found at i:271632 original size:27 final size:28
Alignment explanation
Indices: 271575--271634 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
271565 ATTTGTTTTA
* * *
271575 TTTATATATTTTTTCTTTTTCTTTATTT
1 TTTATATATTTTTTATTTTACTTTATAT
271603 TTTATATA-TTTTTATTTTAC-TTACTAT
1 TTTATATATTTTTTATTTTACTTTA-TAT
271630 TTTAT
1 TTTAT
271635 CTTTGTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.11
27 17 0.61
28 8 0.29
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (28 bp):
TTTATATATTTTTTATTTTACTTTATAT
Found at i:271632 original size:28 final size:28
Alignment explanation
Indices: 271540--271624 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
271530 TATATATATT
*
271540 TTTACTTTTTAT-TATTATTTTA-TTTA-
1 TTTATTTTTTATATATT-TTTTATTTTAC
* * *
271566 TTTGTTTTATTTATATATTTTTTCTTTTTC
1 TTT-ATTT-TTTATATATTTTTTATTTTAC
271596 TTTATTTTTTATATA-TTTTTATTTTAC
1 TTTATTTTTTATATATTTTTTATTTTAC
271623 TT
1 TT
271625 ACTATTTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
26 3 0.06
27 14 0.30
28 17 0.36
29 10 0.21
30 3 0.06
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (28 bp):
TTTATTTTTTATATATTTTTTATTTTAC
Found at i:272323 original size:110 final size:110
Alignment explanation
Indices: 272031--272313 Score: 503
Period size: 110 Copynumber: 2.6 Consensus size: 110
272021 TTCGGGCCCA
*
272031 AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTTGAGA
1 AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA
* *
272096 CAACACAAATTCAACTTCACAGCGAAGGGGCGACTGATTGTCAAC
66 CAACACAAATTCAACTTCACAACGAAGGGGCGACTGACTGTCAAC
*
272141 AAACAACTTTTCAATTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA
1 AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA
* *
272206 CAACACAAGTTCAACTTCACAACGAATGGGCGACTGACTGTCAAC
66 CAACACAAATTCAACTTCACAACGAAGGGGCGACTGACTGTCAAC
*
272251 AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGA
1 AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA
272314 AGCGACACAA
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 165 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (110 bp):
AAACAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGA
CAACACAAATTCAACTTCACAACGAAGGGGCGACTGACTGTCAAC
Found at i:275748 original size:34 final size:34
Alignment explanation
Indices: 275710--275796 Score: 115
Period size: 33 Copynumber: 2.6 Consensus size: 34
275700 AGTTCTACTT
**
275710 GGACTCAAAATGTTTTGGTTTTAGTGTTTCAATA
1 GGACTCAAAATACTTTGGTTTTAGTGTTTCAATA
*
275744 GGACTC-AAATACTTTGGTTTTAGTGTTTTAATA
1 GGACTCAAAATACTTTGGTTTTAGTGTTTCAATA
* *
275777 TGACTC-AAATACGTTGGTTT
1 GGACTCAAAATACTTTGGTTT
275797 ATTTTCTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 42 0.88
34 6 0.12
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (34 bp):
GGACTCAAAATACTTTGGTTTTAGTGTTTCAATA
Found at i:275765 original size:33 final size:33
Alignment explanation
Indices: 275723--275796 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
275713 CTCAAAATGT
275723 TTTGGTTTTAGTGTTTCAATAGGACTCAAATAC
1 TTTGGTTTTAGTGTTTCAATAGGACTCAAATAC
* *
275756 TTTGGTTTTAGTGTTTTAATATGACTCAAATAC
1 TTTGGTTTTAGTGTTTCAATAGGACTCAAATAC
*
275789 GTTGGTTT
1 TTTGGTTT
275797 ATTTTCTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.47
Consensus pattern (33 bp):
TTTGGTTTTAGTGTTTCAATAGGACTCAAATAC
Found at i:275875 original size:3 final size:3
Alignment explanation
Indices: 275846--275927 Score: 57
Period size: 3 Copynumber: 27.3 Consensus size: 3
275836 GGCCTACAAA
* *
275846 AAT AAT AA- AAT AAA AAT -AT ATT AAT AAT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
275890 AAAT AAAT AAAT AAA AAT -AT ATAT AAT -AT AAT -AT AAT A
1 -AAT -AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
275928 TTTTTATAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
2 10 0.15
3 38 0.58
4 18 0.27
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:275894 original size:31 final size:31
Alignment explanation
Indices: 275843--275928 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
275833 CGGGGCCTAC
*
275843 AAAAATAATAA-AAT-AA-AAATATATTAAT
1 AAAAATAATAATAATAAATAAATATATAAAT
* *
275871 AATAATAATAATAATAAATAAATAAATAAAT
1 AAAAATAATAATAATAAATAAATATATAAAT
275902 AAAAAT-ATATATAATATAATATAATAT
1 AAAAATAATA-ATAATA-AATA-AATAT
275929 TTTTATAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 10 0.21
29 3 0.06
30 5 0.11
31 21 0.45
32 4 0.09
33 4 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAAATAATAATAATAAATAAATATATAAAT
Found at i:276998 original size:18 final size:18
Alignment explanation
Indices: 276975--277011 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
276965 TTATTTTTAT
276975 TTTATTATTTGGATTCTC
1 TTTATTATTTGGATTCTC
*
276993 TTTATTATTTTGATTCTC
1 TTTATTATTTGGATTCTC
277011 T
1 T
277012 AAATAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.65
Consensus pattern (18 bp):
TTTATTATTTGGATTCTC
Found at i:277042 original size:24 final size:24
Alignment explanation
Indices: 277021--277065 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
277011 TAAATAATTT
*
277021 TAATATA-ATTTTATTATTTAATA
1 TAATATATATATTATTATTTAATA
*
277044 TAATTTATATATTATTATTTAA
1 TAATATATATATTATTATTTAA
277066 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
TAATATATATATTATTATTTAATA
Found at i:277170 original size:16 final size:17
Alignment explanation
Indices: 277141--277173 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
277131 CTCTAAATAA
277141 TTTTAATATAATTTTAT
1 TTTTAATATAATTTTAT
*
277158 TTTTACTAT-ATTTTAT
1 TTTTAATATAATTTTAT
277174 ATATTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATATAATTTTAT
Found at i:277233 original size:120 final size:121
Alignment explanation
Indices: 277001--277239 Score: 376
Period size: 120 Copynumber: 2.0 Consensus size: 121
276991 TCTTTATTAT
277001 TTTGATTCTCTAAATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTAA
1 TTTGATTCTCTAAATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTT-A
*
277066 AAAAGAATTTTAGAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTTGA
65 AAAAGAATTATAGAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTTGA
* *
277123 TTTGAATTCTCTAAATAATTTTAATATAATTTTATT-TTTACTATATTTTATATATTATTATTT-
1 TTTG-ATTCTCTAAATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTA
* * *
277186 TAAAGTAATTATA-AAAATAATTTAAATAAAAATATTAAACTCGTTTTTATTTTT
65 AAAAG-AATTATAGAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTT
277240 AAGTTTTACA
Statistics
Matches: 109, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
120 43 0.39
121 6 0.06
122 29 0.27
123 31 0.28
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (121 bp):
TTTGATTCTCTAAATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTAA
AAAGAATTATAGAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTTGA
Found at i:277270 original size:120 final size:121
Alignment explanation
Indices: 277013--277268 Score: 335
Period size: 120 Copynumber: 2.1 Consensus size: 121
277003 TGATTCTCTA
*
277013 AATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTAAAAAAGAATTTTA
1 AATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTT-AAAAAGAATTATA
* **
277078 GAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTTGATTTGAATTCTCT
65 GAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTAGATTTGAATTAACT
* * *
277135 AAATAATTTTAATATAATTTTATT-TTTACTATATTTTATATATTATTATTT-TAAAGTAATTAT
1 -AATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTAAAAAG-AATTAT
* * *
277198 A-AAAATAATTTAAATAAAAATATTAAACTCGTTTTTATTTTTA-AGTTTTACATTAACT
64 AGAAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTAGA-TTTGA-ATTAACT
277256 -ATAA-TTTAATATA
1 AATAATTTTAATATA
277269 TATATATATA
Statistics
Matches: 120, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
118 9 0.08
119 5 0.04
120 47 0.39
121 11 0.09
122 25 0.21
123 23 0.19
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (121 bp):
AATAATTTTAATATAATTTTATTATTTAATATAATTTATATATTATTATTTAAAAAGAATTATAG
AAAAGAATTTAAATAAAAATATTAAACTCATTTTTATTTTTAGATTTGAATTAACT
Found at i:277271 original size:2 final size:2
Alignment explanation
Indices: 277264--277292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
277254 CTATAATTTA
277264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
277293 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:280150 original size:18 final size:19
Alignment explanation
Indices: 280127--280163 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
280117 CATATTTGTC
*
280127 ATTTTAA-TAAAAATATTA
1 ATTTTAATTAAAAAAATTA
280145 ATTTTAATTAAAAAAATTA
1 ATTTTAATTAAAAAAATTA
280164 TGGTTTGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTTAATTAAAAAAATTA
Found at i:282478 original size:20 final size:21
Alignment explanation
Indices: 282453--282516 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 21
282443 ATATTTTTCT
282453 TTTTATT-TACTATAT-TATAA
1 TTTTATTATA-TATATATATAA
282473 TTTTATTATATATATATATATTA
1 TTTTATTATATATATATATA--A
* *
282496 TCGTTATTTTATATATATATA
1 T-TTTATTATATATATATATA
282517 TATAGGTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 12 0.32
21 6 0.16
23 2 0.05
24 17 0.46
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATATATATATAA
Found at i:282492 original size:26 final size:26
Alignment explanation
Indices: 282463--282519 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
282453 TTTTATTTAC
282463 TATATTATAATT-TTATTATATATATA
1 TATATTATAATTATT-TTATATATATA
**
282489 TATATTATCGTTATTTTATATATATA
1 TATATTATAATTATTTTATATATATA
282515 TATAT
1 TATAT
282520 AGGTATAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
TATATTATAATTATTTTATATATATA
Found at i:282757 original size:3 final size:3
Alignment explanation
Indices: 282727--282770 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
282717 TCATTTGTTC
* *
282727 ATT ATAT ATAT ATT ACT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
282771 TTCTGATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 29 0.81
4 7 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:293285 original size:10 final size:9
Alignment explanation
Indices: 293270--293294 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
293260 ATCCTAATTC
293270 AAAAAAAAG
1 AAAAAAAAG
293279 AAAAAAAAG
1 AAAAAAAAG
293288 AAAAAAA
1 AAAAAAA
293295 CGTTTAGGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:293359 original size:16 final size:16
Alignment explanation
Indices: 293337--293373 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
293327 AATTGAGAAA
293337 AAAAAAAGAA-AAAAG
1 AAAAAAAGAACAAAAG
293352 AGAAAAAAGAACAAAAG
1 A-AAAAAAGAACAAAAG
293369 AAAAA
1 AAAAA
293374 TAAGTTTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 13 0.65
17 6 0.30
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAACAAAAG
Found at i:296723 original size:2 final size:2
Alignment explanation
Indices: 296716--296780 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
296706 TTTAAACGTT
296716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
296758 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
296781 CTCTATCTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:296819 original size:15 final size:15
Alignment explanation
Indices: 296796--296842 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
296786 TCTTTTCAAT
296796 TTTACTTTTTTTTTTA
1 TTTA-TTTTTTTTTTA
*
296812 TATT-TTTTCTTTTTA
1 T-TTATTTTTTTTTTA
*
296827 TTTATTTATTTTTTA
1 TTTATTTTTTTTTTA
296842 T
1 T
296843 CCCCTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 2 0.08
15 21 0.81
16 1 0.04
17 2 0.08
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTATTTTTTTTTTA
Found at i:299167 original size:40 final size:40
Alignment explanation
Indices: 299123--299202 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
299113 TAATGCCTAT
299123 ATAATATGAATATGCTTTCAATGTTAACACTGAAAAGGGG
1 ATAATATGAATATGCTTTCAATGTTAACACTGAAAAGGGG
299163 ATAATATGAATATGCTTTCAATGTTAACACTGAAAAGGGG
1 ATAATATGAATATGCTTTCAATGTTAACACTGAAAAGGGG
299203 CCAAAGGGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (40 bp):
ATAATATGAATATGCTTTCAATGTTAACACTGAAAAGGGG
Found at i:299454 original size:20 final size:20
Alignment explanation
Indices: 299418--299463 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
299408 ATCCTTCGAC
299418 TTTATTAACTTTATTTAAATT
1 TTTATTAACTTTATTT-AATT
* *
299439 TTTATT-ACTTTTTTTATTT
1 TTTATTAACTTTATTTAATT
299458 TTTATT
1 TTTATT
299464 TTTAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 9 0.39
20 8 0.35
21 6 0.26
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTAACTTTATTTAATT
Found at i:304005 original size:15 final size:15
Alignment explanation
Indices: 303985--304016 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
303975 TTACTTGGAC
*
303985 GAATAATATTTGTAG
1 GAATAATATTTATAG
304000 GAATAATATTTATAG
1 GAATAATATTTATAG
304015 GA
1 GA
304017 GGAGATTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (15 bp):
GAATAATATTTATAG
Found at i:305936 original size:93 final size:93
Alignment explanation
Indices: 305823--306030 Score: 335
Period size: 93 Copynumber: 2.2 Consensus size: 93
305813 CTCACTAGTA
* * *
305823 TCTAGCCTCACATAGCCATCATACACTAGTTAACTGAGGGAACCCAATGTCACATAGCATCAGTA
1 TCTAGTCTCACATAGCCATCAGACACTAGTTAACTGAGGGAACCCAATGCCACATAGCATCAGTA
* * *
305888 AAATTTCAACTAAGTTGTTGAATGATCT
66 AAATTCCAACTAAGTTGCTGAACGATCT
*
305916 TCTAGTCTCACATAGCCATCAGACACTAGTTAACTGAGGGAACCCAATGCCATATAGCATCAGTA
1 TCTAGTCTCACATAGCCATCAGACACTAGTTAACTGAGGGAACCCAATGCCACATAGCATCAGTA
*
305981 AAATTCCAACTAATTTGCTGAACGATCT
66 AAATTCCAACTAAGTTGCTGAACGATCT
*
306009 TCTGGTCTCACATAGCCATCAG
1 TCTAGTCTCACATAGCCATCAG
306031 GTTGATGATG
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 106 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (93 bp):
TCTAGTCTCACATAGCCATCAGACACTAGTTAACTGAGGGAACCCAATGCCACATAGCATCAGTA
AAATTCCAACTAAGTTGCTGAACGATCT
Found at i:320428 original size:13 final size:13
Alignment explanation
Indices: 320410--320435 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320400 AAAATTTGAA
320410 ATTTACTTTTTAT
1 ATTTACTTTTTAT
320423 ATTTACTTTTTAT
1 ATTTACTTTTTAT
320436 GATATTATTA
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTACTTTTTAT
Found at i:325626 original size:23 final size:24
Alignment explanation
Indices: 325571--325626 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
325561 CATTTATATG
* *
325571 ATAAACGAACACAAATGAATGAAC
1 ATAAACGAACACAAATAAACGAAC
*
325595 ATAAGCGAACAC-AATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
325618 GTAAACGAA
1 ATAAACGAA
325627 TATAAATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:325822 original size:14 final size:14
Alignment explanation
Indices: 325803--325842 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
325793 ATTGAGTTAA
325803 ACATAAATGAACGC
1 ACATAAATGAACGC
*
325817 ACATAAACGAACGC
1 ACATAAATGAACGC
325831 ACATAAATGAAC
1 ACATAAATGAAC
325843 ATAAATGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.53, C:0.23, G:0.12, T:0.12
Consensus pattern (14 bp):
ACATAAATGAACGC
Found at i:325853 original size:28 final size:28
Alignment explanation
Indices: 325803--325856 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
325793 ATTGAGTTAA
* *
325803 ACATAAATGAACGCACATAAACGAACGC
1 ACATAAATGAACACAAATAAACGAACGC
* *
325831 ACATAAATGAACATAAATGAACGAAC
1 ACATAAATGAACACAAATAAACGAAC
325857 ATATTACCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.54, C:0.20, G:0.13, T:0.13
Consensus pattern (28 bp):
ACATAAATGAACACAAATAAACGAACGC
Found at i:325856 original size:14 final size:14
Alignment explanation
Indices: 325802--325859 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
325792 GATTGAGTTA
325802 AACATAAATGAACG
1 AACATAAATGAACG
* *
325816 CACATAAACGAACG
1 AACATAAATGAACG
*
325830 CACATAAAT----G
1 AACATAAATGAACG
325840 AACATAAATGAACG
1 AACATAAATGAACG
325854 AACATA
1 AACATA
325860 TTACCGAAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 9 0.25
14 27 0.75
ACGTcount: A:0.55, C:0.19, G:0.12, T:0.14
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:328548 original size:20 final size:20
Alignment explanation
Indices: 328513--328550 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
328503 TTCAATTAAA
328513 TTAATATTTTAGTATTTTAT
1 TTAATATTTTAGTATTTTAT
328533 TTAATTATTTTA-TATTTT
1 TTAA-TATTTTAGTATTTT
328551 TTTTGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
TTAATATTTTAGTATTTTAT
Found at i:328700 original size:27 final size:28
Alignment explanation
Indices: 328670--328723 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
328660 TTAGTAATAA
*
328670 TTTATTTATTTAATTTTT-T-ATTATTAG
1 TTTATATA-TTAATTTTTGTAATTATTAG
328697 TTTATATATTAATTTTTGTAATTATTA
1 TTTATATATTAATTTTTGTAATTATTA
328724 ATAATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 8 0.33
28 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (28 bp):
TTTATATATTAATTTTTGTAATTATTAG
Found at i:332575 original size:23 final size:23
Alignment explanation
Indices: 332529--332575 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
332519 GTATTTCTAC
*
332529 GTGAAACTTCGGTGCAATTCTAT
1 GTGAAACTTCGGTGCAATTATAT
*
332552 GTGACACTTCGGTG-AATATATAT
1 GTGAAACTTCGGTGCAAT-TATAT
332575 G
1 G
332576 AGATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (23 bp):
GTGAAACTTCGGTGCAATTATAT
Found at i:333008 original size:2 final size:2
Alignment explanation
Indices: 333001--333027 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
332991 AAATGGTATG
333001 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
333028 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:337490 original size:34 final size:34
Alignment explanation
Indices: 337447--337523 Score: 120
Period size: 34 Copynumber: 2.3 Consensus size: 34
337437 ATTACAGGAG
*
337447 AAATGATATTGA-TTATATGAGTATATGTATATGT
1 AAATGATATT-ATTTATATAAGTATATGTATATGT
337481 AAATGATATTATTTATATAAGTATATGTATATGT
1 AAATGATATTATTTATATAAGTATATGTATATGT
*
337515 GAATGATAT
1 AAATGATAT
337524 GAAAATGAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
33 1 0.03
34 39 0.98
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (34 bp):
AAATGATATTATTTATATAAGTATATGTATATGT
Found at i:337881 original size:23 final size:23
Alignment explanation
Indices: 337855--337899 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
337845 TTCAGTGTAT
337855 TTCTACGCGACACTTCGGTGCAA
1 TTCTACGCGACACTTCGGTGCAA
* *
337878 TTCTACGTGGCACTTCGGTGCA
1 TTCTACGCGACACTTCGGTGCA
337900 TATATACGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.29, G:0.24, T:0.29
Consensus pattern (23 bp):
TTCTACGCGACACTTCGGTGCAA
Found at i:340764 original size:14 final size:14
Alignment explanation
Indices: 340745--340772 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
340735 TGTGGAGATC
340745 ATTAGTTTTATTAA
1 ATTAGTTTTATTAA
340759 ATTAGTTTTATTAA
1 ATTAGTTTTATTAA
340773 TCATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
ATTAGTTTTATTAA
Found at i:341581 original size:16 final size:17
Alignment explanation
Indices: 341549--341581 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
341539 GCAATTTATA
341549 ATGCACTAACATAAAAC
1 ATGCACTAACATAAAAC
341566 ATGCACTAAC-TAAAAC
1 ATGCACTAACATAAAAC
341582 CCTAACAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18
Consensus pattern (17 bp):
ATGCACTAACATAAAAC
Found at i:342149 original size:33 final size:33
Alignment explanation
Indices: 342084--342175 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
342074 GTTGGGTGAT
* **
342084 TATCAGATCAGTT-ATTTTTCGATTCGGATCAA
1 TATCAGATCAGTTGATTTTTTGGGTCGGATCAA
*
342116 TATCAGATCAGTTGATTTTTTGGGTCGGGTCAA
1 TATCAGATCAGTTGATTTTTTGGGTCGGATCAA
*
342149 TATCAGATCGGTTGA-TTTTTGGGTCGG
1 TATCAGATCAGTTGATTTTTTGGGTCGG
342176 TTATATTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.46
33 29 0.54
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (33 bp):
TATCAGATCAGTTGATTTTTTGGGTCGGATCAA
Found at i:342173 original size:32 final size:32
Alignment explanation
Indices: 342084--342175 Score: 123
Period size: 32 Copynumber: 2.8 Consensus size: 32
342074 GTTGGGTGAT
**
342084 TATCAGATCAGTT-ATTTTTCGATTCGGATCAA
1 TATCAGATCAGTTGATTTTT-GGGTCGGATCAA
*
342116 TATCAGATCAGTTGATTTTTTGGGTCGGGTCAA
1 TATCAGATCAGTTGA-TTTTTGGGTCGGATCAA
*
342149 TATCAGATCGGTTGATTTTTGGGTCGG
1 TATCAGATCAGTTGATTTTTGGGTCGG
342176 TTATATTTCG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
32 25 0.46
33 24 0.44
34 5 0.09
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (32 bp):
TATCAGATCAGTTGATTTTTGGGTCGGATCAA
Found at i:343160 original size:2 final size:2
Alignment explanation
Indices: 343135--343189 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
343125 TTAGTTTTAA
* *
343135 AT AT -T AT AT AA AT AA AT A- AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
343174 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
343190 TAAGTATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 43 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:346357 original size:271 final size:275
Alignment explanation
Indices: 345680--346444 Score: 810
Period size: 271 Copynumber: 2.7 Consensus size: 275
345670 GTGAATCGAA
* * * *
345680 AAAGCGTGGGAAAATGTTATC-TTTGAATCTTTTTATATATCTAATGTTCTTTCAAAGTTTAAAG
1 AAAGCGCGGGAAAATGTTATCGTTTGAATTTTTTTATATATCTAACGTGCTTTCAAAGTTTAAAG
** * * * * * **
345744 TGCAAGAGTTTTGACGTCTTCGATTTCGCCGATGAGGACGAGAGAGTTGAGAAGGTGTCCGCAGT
66 CACAAGGGTTTTGATGTTTTCGATCTCGCCGATGAGGACGAGAGAGTTGAG-AGG-ATCCGTGGT
* * * *
345809 GTTTCCTGCGAGGTTCAAGAACCCTTATCATGAGTCATCACTGCAAGACATATTCTCCTCCCAAG
129 GTTTCTTGCGAGGTTCAAGAACCC-TA--AT-CGT--T-GCTGCAAGAC--ATTCTCCTCTCAAG
* * * * *
345874 AAATACGACTTCCTTAAATGTTGTAACTTTTATCTCATTTTCTCTGTTCTTTCTTGTCTGTTAAC
185 AAATACGACTTTCTTAAATGTTGTAACTTTCATCTCACTTTCTCTGTTCTTTCTTATCTATT---
* *
345939 CCCCTGGCGATTACTCTGGTCGGTGAACCGAG
247 --CCTGGCGAATACTCT-GTCGGTGAACCAAG
* * * *
345971 AAAGTGTGGGGGAAATGTTATCGTTTGAA-TTTATTATATATCTAACGTGCTTTCAAAGTTTAAA
1 AAAGCG-CGGGAAAATGTTATCGTTTGAATTTTTTTATATATCTAACGTGCTTTCAAAGTTTAAA
*
346035 GCACAAGGGTTTTGATGTCTTT-GATCTCGCCGATGAGGACGAGATAGTTGAGAGCGATCCGTGG
65 GCACAAGGGTTTTGATGT-TTTCGATCTCGCCGATGAGGACGAGAGAGTTGAGAG-GATCCGTGG
*
346099 TGTTTCTTGCGAGGTTCGAGAACCCTAATCGTTGCTGCAAGACA-TCTCCTCTCAAGAAATACGA
128 TGTTTCTTGCGAGGTTCAAGAACCCTAATCGTTGCTGCAAGACATTCTCCTCTCAAGAAATACGA
* * ***
346163 CTTTCTTAAATGTTGTAACTTTCATCTCGCTTTCTCTGTTCTTTCTTATCTATT-GTTTTGAAT-
193 CTTTCTTAAATGTTGTAACTTTCATCTCACTTTCTCTGTTCTTTCTTATCTATTCCTGGCGAATA
346226 CTCT-T-GGTGAACCAAG
258 CTCTGTCGGTGAACCAAG
* *
346242 AAAGCGCGAGAAAATGTTATCGTTTGAATTTTTTTATATATCTAACGTGATTTCAAAGTTTAAAG
1 AAAGCGCGGGAAAATGTTATCGTTTGAATTTTTTTATATATCTAACGTGCTTTCAAAGTTTAAAG
* * * * **
346307 CACAAGGGTTTCGATGTTTTCGATGTCGCCGATGAGGACGAAAGAGTTGAGAGAGAGTCCTTGAC
66 CACAAGGGTTTTGATGTTTTCGATCTCGCCGATGAGGACGAGAGAGTTGAGAG-GA-TCCGTGGT
* * * * *
346372 GATTCTTGCGAGGTTTAAAAACCCTAATCGTGGCTGCAAGGCATTTTCTCCTCTCAAGAAATAC-
129 GTTTCTTGCGAGGTTCAAGAACCCTAATCGTTGCTGCAAGACA--TTCTCCTCTCAAGAAATACG
346436 ATCTTTCTT
192 A-CTTTCTT
346445 CAATACTTAC
Statistics
Matches: 409, Mismatches: 54, Indels: 38
0.82 0.11 0.08
Matches are distributed among these distances:
270 22 0.05
271 96 0.23
272 43 0.11
274 5 0.01
275 29 0.07
281 67 0.16
282 1 0.00
284 9 0.02
285 1 0.00
287 2 0.00
288 2 0.00
290 2 0.00
291 35 0.09
292 87 0.21
293 8 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (275 bp):
AAAGCGCGGGAAAATGTTATCGTTTGAATTTTTTTATATATCTAACGTGCTTTCAAAGTTTAAAG
CACAAGGGTTTTGATGTTTTCGATCTCGCCGATGAGGACGAGAGAGTTGAGAGGATCCGTGGTGT
TTCTTGCGAGGTTCAAGAACCCTAATCGTTGCTGCAAGACATTCTCCTCTCAAGAAATACGACTT
TCTTAAATGTTGTAACTTTCATCTCACTTTCTCTGTTCTTTCTTATCTATTCCTGGCGAATACTC
TGTCGGTGAACCAAG
Found at i:352876 original size:21 final size:22
Alignment explanation
Indices: 352847--352888 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
352837 TGATACAAGT
352847 TATGCGACA-TAAACTACGTGA
1 TATGCGACAGTAAACTACGTGA
* *
352868 TATGTGACAGTGAACTACGTG
1 TATGCGACAGTAAACTACGTG
352889 TTTATATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (22 bp):
TATGCGACAGTAAACTACGTGA
Found at i:353009 original size:18 final size:18
Alignment explanation
Indices: 352986--353130 Score: 137
Period size: 18 Copynumber: 7.4 Consensus size: 18
352976 AGGGATTATC
*
352986 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
353004 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
353022 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
353040 AGTGGTCCTTTGGGACATAT
1 AGTGGTCCTTCGGGAC--AT
*
353060 ACAGTGGTCATTCGGGACATAT
1 --AGTGGTCCTTCGGGAC--AT
*
353082 AAAGTGGTCATTCGGGACATAT
1 --AGTGGTCCTTCGGGAC--AT
*
353104 ACAGTGATCCTTCGGGACAT
1 --AGTGGTCCTTCGGGACAT
353124 AGTGGTC
1 AGTGGTC
353131 TTACGGGATG
Statistics
Matches: 114, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
18 56 0.49
20 4 0.04
22 54 0.47
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:353068 original size:22 final size:22
Alignment explanation
Indices: 353040--353124 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
353030 TTCGGGACAT
* *
353040 AGTGGTCCTTTGGGACATATAC
1 AGTGGTCATTCGGGACATATAC
*
353062 AGTGGTCATTCGGGACATATAA
1 AGTGGTCATTCGGGACATATAC
353084 AGTGGTCATTCGGGACATATAC
1 AGTGGTCATTCGGGACATATAC
* *
353106 AGTGATCCTTCGGGACATA
1 AGTGGTCATTCGGGACATA
353125 GTGGTCTTAC
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (22 bp):
AGTGGTCATTCGGGACATATAC
Found at i:355057 original size:20 final size:20
Alignment explanation
Indices: 355020--355057 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
355010 CTTAAACTTC
*
355020 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
355040 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
355058 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:355240 original size:23 final size:23
Alignment explanation
Indices: 355214--355282 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
355204 CATCACAACT
*
355214 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * **
355237 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGAAGTGCCA
355260 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
355283 TATAATATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:355638 original size:2 final size:2
Alignment explanation
Indices: 355631--355676 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
355621 ACCAAATCAA
355631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
355673 AT AT
1 AT AT
355677 TATGCAATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:359993 original size:18 final size:18
Alignment explanation
Indices: 359970--360104 Score: 81
Period size: 18 Copynumber: 6.8 Consensus size: 18
359960 GGATTATCAA
359970 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
359988 TGGTCCTTCGGGATATAG
1 TGGTCCTTCGGGACATAG
* *
360006 TTGTCCTTCAGGACATATACAG
1 TGGTCCTTCGGGAC--AT--AG
* *
360028 TGGTCCTTCAGGATATATATAG
1 TGGTCCTTC-GG---GACATAG
*
360050 TGGTCCTTTGGGACATATACAG
1 TGGTCCTTCGGGAC--AT--AG
**
360072 TGGTCCTTCAAGACATAG
1 TGGTCCTTCGGGACATAG
*
360090 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
360105 AATTCTACGC
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
18 43 0.49
20 6 0.07
21 2 0.02
22 33 0.38
23 1 0.01
24 2 0.02
26 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:360034 original size:22 final size:22
Alignment explanation
Indices: 360008--360088 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
359998 GGATATAGTT
360008 GTCCTTCAGGACATATACAGTG
1 GTCCTTCAGGACATATACAGTG
* *
360030 GTCCTTCAGGATATATATAGTG
1 GTCCTTCAGGACATATACAGTG
**
360052 GTCCTTTGGGACATATACAGTG
1 GTCCTTCAGGACATATACAGTG
*
360074 GTCCTTCAAGACATA
1 GTCCTTCAGGACATA
360089 GTGGTCCTAC
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (22 bp):
GTCCTTCAGGACATATACAGTG
Found at i:360103 original size:40 final size:40
Alignment explanation
Indices: 359970--360104 Score: 134
Period size: 44 Copynumber: 3.4 Consensus size: 40
359960 GGATTATCAA
**
359970 TGGTCCTTCGGGAC--AT--AGTGGTCCTTCGGGATATAG
1 TGGTCCTTCGGGACATATACAGTGGTCCTTCAAGATATAG
* * *
360006 TTGTCCTTCAGGACATATACAGTGGTCCTTCAGGATATATATAG
1 TGGTCCTTCGGGACATATACAGTGGTCCTTC---A-AGATATAG
* *
360050 TGGTCCTTTGGGACATATACAGTGGTCCTTCAAGACATAG
1 TGGTCCTTCGGGACATATACAGTGGTCCTTCAAGATATAG
*
360090 TGGTCCTACGGGACA
1 TGGTCCTTCGGGACA
360105 AATTCTACGC
Statistics
Matches: 79, Mismatches: 12, Indels: 12
0.77 0.12 0.12
Matches are distributed among these distances:
36 12 0.15
38 2 0.03
40 30 0.38
41 1 0.01
44 34 0.43
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
TGGTCCTTCGGGACATATACAGTGGTCCTTCAAGATATAG
Found at i:361488 original size:24 final size:24
Alignment explanation
Indices: 361460--361511 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
361450 ACTTTATGCA
361460 ATATCAATTGTTGTATTTAAGAGC
1 ATATCAATTGTTGTATTTAAGAGC
361484 ATATCAATTGTTGTATTTAAGAGC
1 ATATCAATTGTTGTATTTAAGAGC
361508 ATAT
1 ATAT
361512 GCATAAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (24 bp):
ATATCAATTGTTGTATTTAAGAGC
Found at i:361516 original size:30 final size:26
Alignment explanation
Indices: 361454--361511 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 26
361444 TAATATACTT
361454 TATGCAATATCAATTGTTGTATTTAAG
1 TATGC-ATATCAATTGTTGTATTTAAG
361481 -A-GCATATCAATTGTTGTATTTAAG
1 TATGCATATCAATTGTTGTATTTAAG
361505 -A-GCATAT
1 TATGCATAT
361512 GCATAAAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 28 0.90
25 2 0.06
26 1 0.03
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (26 bp):
TATGCATATCAATTGTTGTATTTAAG
Found at i:365757 original size:31 final size:31
Alignment explanation
Indices: 365716--365782 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
365706 AATTCACTAT
*
365716 TTGCATCAACAGTTTAGCAACAATCTTGATC
1 TTGCACCAACAGTTTAGCAACAATCTTGATC
365747 TTGCACCAACAGTTTAGCAACAATCTTGATC
1 TTGCACCAACAGTTTAGCAACAATCTTGATC
365778 TTGCA
1 TTGCA
365783 TGAACTGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (31 bp):
TTGCACCAACAGTTTAGCAACAATCTTGATC
Found at i:366693 original size:8 final size:8
Alignment explanation
Indices: 366680--366718 Score: 60
Period size: 8 Copynumber: 4.6 Consensus size: 8
366670 TTAGAGAGTC
366680 AAAAAATA
1 AAAAAATA
366688 AAAAAATA
1 AAAAAATA
366696 AAAAAATAA
1 AAAAAAT-A
366705 AATAAAATA
1 AA-AAAATA
366714 AAAAA
1 AAAAA
366719 TAATGTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 18 0.62
9 6 0.21
10 5 0.17
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:366721 original size:17 final size:17
Alignment explanation
Indices: 366680--366718 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
366670 TTAGAGAGTC
366680 AAAAAAT-AAAAAAATA
1 AAAAAATAAAAAAAATA
366696 AAAAAATAAAATAAAATA
1 AAAAAATAAAA-AAAATA
366714 AAAAA
1 AAAAA
366719 TAATGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 11 0.52
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (17 bp):
AAAAAATAAAAAAAATA
Found at i:367363 original size:2 final size:2
Alignment explanation
Indices: 367356--367388 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
367346 GACCATAGAT
367356 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
367389 GTTAGATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:372312 original size:2 final size:2
Alignment explanation
Indices: 372307--372342 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
372297 TCACACAAAC
372307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
372343 TAAAGTATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:373388 original size:24 final size:23
Alignment explanation
Indices: 373336--373388 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
373326 CGACTACTCC
* *
373336 CCTCCCCTCTTCCCATAAATACC
1 CCTCCCCTCTTCCCATAAACACA
*
373359 CTCTCCCCTCTTCCCCTAAACACAA
1 C-CTCCCCTCTTCCCATAAACAC-A
373384 CCTCC
1 CCTCC
373389 AAACTACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 1 0.04
24 23 0.92
25 1 0.04
ACGTcount: A:0.21, C:0.55, G:0.00, T:0.25
Consensus pattern (23 bp):
CCTCCCCTCTTCCCATAAACACA
Found at i:375749 original size:18 final size:17
Alignment explanation
Indices: 375719--375752 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
375709 GTTCAAATTG
375719 TTTTTATTATTTAGTTC
1 TTTTTATTATTTAGTTC
*
375736 TTTTTACTTTTTTAGTT
1 TTTTTA-TTATTTAGTT
375753 GTATCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTTATTATTTAGTTC
Found at i:377098 original size:29 final size:29
Alignment explanation
Indices: 377042--377117 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
377032 CACGTGAATG
* * *
377042 GATAGGTCGTCAGGGCATCCCAGCGACAT
1 GATAGGACGCCAGGGCATCCCAACGACAT
* * *
377071 TATAGGACGCCATGGCATCCCAATGACAT
1 GATAGGACGCCAGGGCATCCCAACGACAT
* *
377100 GGTAGGTCGCCAGGGCAT
1 GATAGGACGCCAGGGCAT
377118 GATGCCAGGG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.26, G:0.30, T:0.18
Consensus pattern (29 bp):
GATAGGACGCCAGGGCATCCCAACGACAT
Found at i:377294 original size:23 final size:22
Alignment explanation
Indices: 377266--377341 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 22
377256 ATTCAGCTGC
377266 ATTATTGCAGCACTTATTGTTGT
1 ATTATTGCAGC-CTTATTGTTGT
*
377289 ATTATTACAGTCCTTATTGTTGT
1 ATTATTGCAG-CCTTATTGTTGT
377312 ATTATTGCAGCCTTTATTGTTGT
1 ATTATTGCAGCC-TTATTGTTGT
377335 ATTATTG
1 ATTATTG
377342 TAGTCATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.04
23 46 0.94
24 1 0.02
ACGTcount: A:0.21, C:0.12, G:0.16, T:0.51
Consensus pattern (22 bp):
ATTATTGCAGCCTTATTGTTGT
Found at i:377629 original size:43 final size:45
Alignment explanation
Indices: 377561--377666 Score: 162
Period size: 43 Copynumber: 2.4 Consensus size: 45
377551 ATTTTAAATT
377561 ATTAGTTTGTTAGTTTATGGTTTAAGGTAAAACAAAAGTTTAGTTA
1 ATTAGTTTGTTAGTTTA-GGTTTAAGGTAAAACAAAAGTTTAGTTA
* * *
377607 ATTAGTTAGTTA-TTTA-GTTTAAGGTAAAATAAAATTTTAGTTA
1 ATTAGTTTGTTAGTTTAGGTTTAAGGTAAAACAAAAGTTTAGTTA
377650 ATTAGTTTGTTAGTTTA
1 ATTAGTTTGTTAGTTTA
377667 AGTTATATTA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
43 36 0.65
44 4 0.07
45 4 0.07
46 11 0.20
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.47
Consensus pattern (45 bp):
ATTAGTTTGTTAGTTTAGGTTTAAGGTAAAACAAAAGTTTAGTTA
Found at i:377680 original size:21 final size:21
Alignment explanation
Indices: 377656--377695 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
377646 GTTAATTAGT
*
377656 TTGTTAGTTTAAGTTATATTA
1 TTGTTACTTTAAGTTATATTA
377677 TTGTTACTTTAAGTTATAT
1 TTGTTACTTTAAGTTATAT
377696 GATACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.12, T:0.57
Consensus pattern (21 bp):
TTGTTACTTTAAGTTATATTA
Found at i:377782 original size:28 final size:27
Alignment explanation
Indices: 377751--377803 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
377741 ATATTAAAAA
377751 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
377779 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
377804 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:377809 original size:27 final size:29
Alignment explanation
Indices: 377750--377814 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
377740 TATATTAAAA
377750 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
377779 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
377805 AAATAGTTAA
1 AAATAATTAA
377815 GTTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:378045 original size:21 final size:21
Alignment explanation
Indices: 378020--378059 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
378010 GTTAATTAGT
378020 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
378041 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
378060 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:380650 original size:14 final size:13
Alignment explanation
Indices: 380616--380651 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
380606 ATTAGTATCA
380616 AATAATTAAATATT
1 AATAA-TAAATATT
380630 AATAATAAATTATT
1 AATAATAAA-TATT
380644 AATAATAA
1 AATAATAA
380652 TAATTACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATAATAAATATT
Found at i:380682 original size:14 final size:14
Alignment explanation
Indices: 380665--380745 Score: 80
Period size: 14 Copynumber: 6.1 Consensus size: 14
380655 TTACTAAATC
*
380665 ATTATTAAATTATT
1 ATTATTAAATCATT
*
380679 ATTATCAAATCATT
1 ATTATTAAATCATT
*
380693 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
380705 ATTACTAAATCATT
1 ATTATTAAATCATT
*
380719 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
380731 ATTATCAAATCATT
1 ATTATTAAATCATT
380745 A
1 A
380746 CTAAATTACC
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
12 20 0.36
13 2 0.04
14 33 0.60
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.47
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:380714 original size:26 final size:26
Alignment explanation
Indices: 380638--380745 Score: 141
Period size: 26 Copynumber: 4.2 Consensus size: 26
380628 TTAATAATAA
* *
380638 ATTATTAATAATAATAATTA-CTAAATC
1 ATTATT-ATAATGATTATTATC-AAATC
*
380665 ATTATTA-AATTATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
380690 ATTATTATAATGATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
380716 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
380742 ATTA
1 ATTA
380746 CTAAATTACC
Statistics
Matches: 74, Mismatches: 3, Indels: 9
0.86 0.03 0.10
Matches are distributed among these distances:
25 22 0.30
26 45 0.61
27 7 0.09
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:380788 original size:11 final size:11
Alignment explanation
Indices: 380654--380814 Score: 67
Period size: 11 Copynumber: 13.2 Consensus size: 11
380644 AATAATAATA
*
380654 ATTACTAAATC
1 ATTATTAAATC
*
380665 ATTATTAAATT
1 ATTATTAAATC
380676 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
380690 ATTATTATAATG
1 ATTATTA-AATC
380702 ATTATTACTAAATC
1 ATTA-T--TAAATC
*
380716 ATTATTATAATG
1 ATTATTA-AATC
380728 ATTATTATCAAATC
1 ATTA-T-T-AAATC
*
380742 ATTACTAAATTACC
1 ATTATTAAA-T--C
*
380756 AGTACATTAAAT-
1 A-T-TATTAAATC
380768 ATTA--AAATC
1 ATTATTAAATC
380777 ATTATTAAATC
1 ATTATTAAATC
380788 ATTATTATCATATC
1 ATTATTA--A-ATC
*
380802 ATTACTAAATC
1 ATTATTAAATC
380813 AT
1 AT
380815 ATAATTATTA
Statistics
Matches: 116, Mismatches: 12, Indels: 44
0.67 0.07 0.26
Matches are distributed among these distances:
8 4 0.03
9 4 0.03
10 1 0.01
11 37 0.32
12 20 0.17
13 6 0.05
14 34 0.29
15 5 0.04
16 5 0.04
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.43
Consensus pattern (11 bp):
ATTATTAAATC
Found at i:381304 original size:21 final size:20
Alignment explanation
Indices: 381278--381346 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
381268 TAACTTCATG
381278 ATTACTAATAATTACTAAATT
1 ATTACTAATAATTA-TAAATT
*
381299 ATTACT-ATCAAATCATTAAA-T
1 ATTACTAAT--AATTA-TAAATT
*
381320 ATTAATAATAATT-T-AATT
1 ATTACTAATAATTATAAATT
381338 ATTACTAAT
1 ATTACTAAT
381347 CATTGCTATC
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
17 2 0.05
18 10 0.26
20 5 0.13
21 12 0.31
22 10 0.26
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.43
Consensus pattern (20 bp):
ATTACTAATAATTATAAATT
Found at i:381359 original size:49 final size:49
Alignment explanation
Indices: 381283--381452 Score: 277
Period size: 49 Copynumber: 3.4 Consensus size: 49
381273 TCATGATTAC
* *
381283 TAATAATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATT
1 TAATTATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAATT
*
381333 TAATTATTACTAATCATTGCTATCAAATCATTAAATATTAATAATAATT
1 TAATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATT
*
381382 TAATTATTACTAATCATTACTATCAAATCATTACATATTAATAATAATT
1 TAATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATT
* *
381431 TTATTATTACCAATCATTACTA
1 TAATTATTACTAATCATTACTA
381453 AATCATTACT
Statistics
Matches: 113, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 103 0.91
50 10 0.09
ACGTcount: A:0.45, C:0.11, G:0.01, T:0.43
Consensus pattern (49 bp):
TAATTATTACTAATCATTACTATCAAATCATTAAATATTAATAATAATT
Found at i:381393 original size:109 final size:109
Alignment explanation
Indices: 381278--381767 Score: 468
Period size: 120 Copynumber: 4.3 Consensus size: 109
381268 TAACTTCATG
* *
381278 ATTACTAATAATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTAC
1 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTAC
* *
381343 TAATCATTGCTATCAAATCATTAAATATTAATAATAATTTAATT
66 TAATCATTACTATCAAATAATTAAATATTAATAATAATTTAATT
* * * * * ** *
381387 ATTACTAATCATTACTATCAAATCATTACATAT-TAAT-AAT-AAT-TTTATTATTA-CCAATCA
1 ATTACTAATCATTAC--T-AAATCATTAC-TATCAAATCATTAAATATTAATAATAATTTAATTA
*
381447 TTACTAAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATT
62 TTACT-AATCATTACTATCAAATAATTAAATATTAATAATAATTTAATT
* *
381496 ATTACTAATCATTACTAAATCATTATTATCAAATCATTAAATATTAATAATAATTTTATTATTAC
1 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTAC
* * *
381561 TAATCATTACTAAATCATTACTATTAAATCATTAAATATAAATAATAATTTCATT
66 TAATCATTACT--ATCA--A--A-T-AAT--TAA-ATATTAATAATAATTTAATT
* *
381616 ATTACTAGTCATTAATAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAA--T--TTA--A-
* *
381681 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
59 T--T-ATTACT-AATCATTACTATCAAATAATTAAATATTAATAATAATTTAATT
*
381736 ATTACTAATCATTATTATCAAATCATTACTAT
1 ATTACTAATCATTA--CT-AAATCATTACTAT
381768 TAAGTGTTCC
Statistics
Matches: 313, Mismatches: 33, Indels: 56
0.78 0.08 0.14
Matches are distributed among these distances:
105 3 0.01
106 12 0.04
107 3 0.01
108 12 0.04
109 93 0.30
110 11 0.04
111 7 0.02
112 12 0.04
113 4 0.01
115 1 0.00
116 1 0.00
117 3 0.01
119 2 0.01
120 101 0.32
121 2 0.01
122 3 0.01
123 15 0.05
124 3 0.01
125 1 0.00
126 1 0.00
127 2 0.01
129 5 0.02
130 6 0.02
131 10 0.03
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (109 bp):
ATTACTAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTAC
TAATCATTACTATCAAATAATTAAATATTAATAATAATTTAATT
Found at i:381462 original size:60 final size:60
Alignment explanation
Indices: 381382--381767 Score: 630
Period size: 60 Copynumber: 6.4 Consensus size: 60
381372 AATAATAATT
* * *
381382 TAATTATTACT-AATCATTACTATCAAATCATTACATATTAATAATAATTTTATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
* *
381441 CAATCATTACTAAATCATTACTATCAAATAATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
* *
381501 TAATCATTACTAAATCATTATTATCAAATCATTAAATATTAATAATAATTTTATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
* *
381561 TAATCATTACTAAATCATTACTATTAAATCATTAAATATAAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
* *
381621 TAGTCATTAATAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
381681 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
1 TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
*
381741 TAATCATTATTATCAAATCATTACTAT
1 TAATCATTA--CT-AAATCATTACTAT
381768 TAAGTGTTCC
Statistics
Matches: 303, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
59 9 0.03
60 280 0.92
62 1 0.00
63 13 0.04
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (60 bp):
TAATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTAC
Found at i:381483 original size:98 final size:98
Alignment explanation
Indices: 381283--381486 Score: 263
Period size: 98 Copynumber: 2.1 Consensus size: 98
381273 TCATGATTAC
* *
381283 TAATAATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACTAATC
1 TAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACCAATC
* *
381348 ATTGCTATCAAATCATTAAATATTAATAATAATT
66 ATTAC-ATCAAATCATTAAATATAAATAATAATT
* * *
381382 TAATTATTACT-AATCATTACTATCAAATCATTACATATTAATAATAATTTTATTATTACCAATC
1 TAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACCAATC
*
381446 ATTAC-T-AAATCATT-ACTATCAAATAATTAAATAT
66 ATTACATCAAATCATTAAATAT-AAATAA-T-AAT-T
381480 TAATAAT
1 TAATAAT
381487 AATTTCATTA
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
94 4 0.04
95 13 0.14
96 2 0.02
97 3 0.03
98 60 0.65
99 10 0.11
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (98 bp):
TAATAATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTAATTATTACCAATC
ATTACATCAAATCATTAAATATAAATAATAATT
Found at i:381679 original size:25 final size:25
Alignment explanation
Indices: 381651--381739 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
381641 CTATCAAATC
381651 ATTAAATATTAATAATAATTTCATT
1 ATTAAATATTAATAATAATTTCATT
* * *
381676 ATTACTAATCATTACTAAATCATTACTATCAAATC
1 ATTA--AAT-ATTAAT-AAT-A--A-TTTC--ATT
381711 ATTAAATATTAATAATAATTTCATT
1 ATTAAATATTAATAATAATTTCATT
381736 ATTA
1 ATTA
381740 CTAATCATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 20
0.65 0.08 0.27
Matches are distributed among these distances:
25 10 0.21
27 6 0.12
28 6 0.12
29 3 0.06
30 2 0.04
31 3 0.06
32 6 0.12
33 6 0.12
35 6 0.12
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTAAATATTAATAATAATTTCATT
Found at i:381749 original size:13 final size:14
Alignment explanation
Indices: 381731--381763 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
381721 AATAATAATT
*
381731 TCATTATTA-CTAA
1 TCATTATTATCAAA
381744 TCATTATTATCAAA
1 TCATTATTATCAAA
381758 TCATTA
1 TCATTA
381764 CTATTAAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.45
Consensus pattern (14 bp):
TCATTATTATCAAA
Found at i:384796 original size:21 final size:22
Alignment explanation
Indices: 384780--384822 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
384770 TATAAATTAA
384780 ACAAAATATTTTTTAAAACAAC
1 ACAAAATATTTTTTAAAACAAC
*
384802 ACTAAATA-TTTTTAAACACAA
1 ACAAAATATTTTTTAAA-ACAA
384823 TCTTTTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.33
Consensus pattern (22 bp):
ACAAAATATTTTTTAAAACAAC
Found at i:385092 original size:5 final size:5
Alignment explanation
Indices: 385082--385112 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
385072 AATTAATTTG
*
385082 ATATA ATATA ATATA ATATA TTATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA A
385113 CTTAAACTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:385322 original size:21 final size:21
Alignment explanation
Indices: 385296--385350 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
385286 CGAATATGTA
385296 AATCGCAACGCGATAAT-ACAT
1 AATCGCAACGCGATAATGAC-T
* *
385317 AATCGCAACTCGATTATGACT
1 AATCGCAACGCGATAATGACT
385338 -ATCGCAACGCGAT
1 AATCGCAACGCGAT
385351 TCTGACTGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.40
21 16 0.53
22 2 0.07
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATAATGACT
Found at i:385343 original size:20 final size:20
Alignment explanation
Indices: 385297--385365 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
385287 GAATATGTAA
*
385297 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTATGAC-T
*
385317 AATCGCAACTCGATTATGACT
1 -ATCGCAACGCGATTATGACT
*
385338 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
*
385358 GTCGCAAC
1 ATCGCAAC
385366 ACTGAATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.60
21 15 0.36
22 2 0.05
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:386239 original size:24 final size:24
Alignment explanation
Indices: 386181--386227 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
386171 AGTCGGTATT
*
386181 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
386205 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
386228 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:387214 original size:21 final size:21
Alignment explanation
Indices: 387186--387262 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
387176 ACGATGACAT
387186 GGGCCTCTTGAACGGTGGGAG
1 GGGCCTCTTGAACGGTGGGAG
* * **
387207 GGGACTCTTG-AGGGATGATAG
1 GGGCCTCTTGAACGG-TGGGAG
* *
387228 GGGCCTCTTGAACGATAGGAG
1 GGGCCTCTTGAACGGTGGGAG
*
387249 AGGCCTCTTGAACG
1 GGGCCTCTTGAACG
387263 ATGACAGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.07
21 38 0.88
22 2 0.05
ACGTcount: A:0.21, C:0.18, G:0.40, T:0.21
Consensus pattern (21 bp):
GGGCCTCTTGAACGGTGGGAG
Found at i:387266 original size:42 final size:42
Alignment explanation
Indices: 387168--387270 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 42
387158 TGTTGAAGGA
* * * * *
387168 CCTCTTCAACGATGACATGGGCCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGG
* ** *
387210 ACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGAGAGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGG
387252 CCTCTTGAACGATGACAGG
1 CCTCTTGAACGATGACAGG
387271 TGAGTAGGGC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAACGATAGGAGAGG
Found at i:387798 original size:20 final size:20
Alignment explanation
Indices: 387773--387821 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
387763 AGAAACTTAA
387773 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
387793 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
*
387813 ATCGTAACG
1 ATCGCAACG
387822 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:387858 original size:19 final size:20
Alignment explanation
Indices: 387826--387864 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
387816 GTAACGGGAT
387826 AATCGCAATGCGAAA-TAAA
1 AATCGCAATGCGAAACTAAA
387845 AATCGCAACT-CGAAACTAAA
1 AATCGCAA-TGCGAAACTAAA
387865 TTTGCGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.51, C:0.21, G:0.13, T:0.15
Consensus pattern (20 bp):
AATCGCAATGCGAAACTAAA
Found at i:387961 original size:20 final size:20
Alignment explanation
Indices: 387936--388004 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
387926 GCAATTATCC
*
387936 CGTTGCGATAGTCAACTTCG
1 CGTTGCGATAGTCAATTTCG
387956 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
387976 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
387996 CGTTGCGAT
1 CGTTGCGAT
388005 TTAAGTTTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:389934 original size:20 final size:20
Alignment explanation
Indices: 389911--390027 Score: 77
Period size: 20 Copynumber: 6.2 Consensus size: 20
389901 GAAACTTAAA
389911 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
389931 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
* *
389951 ATCG-TA-ACG-AGAT-A--
1 ATCGCAACACGAAAATGACT
* * **
389965 ATCACAACGCG-AAATGAAA
1 ATCGCAACACGAAAATGACT
389984 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
390004 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
390024 ATCG
1 ATCG
390028 TTGCAATTTT
Statistics
Matches: 73, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 6 0.08
17 3 0.04
18 2 0.03
19 10 0.14
20 48 0.66
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:390641 original size:21 final size:21
Alignment explanation
Indices: 390568--390641 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
390558 CTAATGGCGC
*
390568 TTTG-AAAATCGCATTGCGAT
1 TTTGTAAAATCGCGTTGCGAT
**
390588 TTTGTATTATCGCGTTGCGA-
1 TTTGTAAAATCGCGTTGCGAT
* *
390608 -TAGTCAGAATCGCGTTGCGAT
1 TTTGT-AAAATCGCGTTGCGAT
390629 TTTGTAAAATCGC
1 TTTGTAAAATCGC
390642 AACGCGAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.07
20 17 0.40
21 19 0.45
22 3 0.07
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTGTAAAATCGCGTTGCGAT
Found at i:390648 original size:21 final size:21
Alignment explanation
Indices: 390624--390690 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
390614 GAATCGCGTT
* *
390624 GCGATTTTGTAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
390645 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
*
390666 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTGGAAAATCGCAAC
390687 GCGA
1 GCGA
390691 TAGTCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:391063 original size:28 final size:28
Alignment explanation
Indices: 391025--391078 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
391015 ATAATCTAAT
*
391025 ATATAATTTAAACTAACAAACTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
391053 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
391079 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:391085 original size:28 final size:28
Alignment explanation
Indices: 391021--391085 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
391011 TTATATAATC
*
391021 TAATATATAATTTAAACTAACAAACTAA
1 TAATATATAACTTAAACTAACAAACTAA
391049 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
391077 TAATTTATA
1 TAATATATA
391086 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:391088 original size:21 final size:21
Alignment explanation
Indices: 391055--391103 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
391045 CTAATATAAT
391055 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
391076 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
391097 ATTAACT
1 A-TAACT
391104 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:391687 original size:29 final size:29
Alignment explanation
Indices: 391652--391780 Score: 168
Period size: 29 Copynumber: 4.4 Consensus size: 29
391642 GGGAGTGCAT
* *
391652 GCATGGCGACCTACAAGGTCGCACAGAAG
1 GCATGGCGACCTACAAGGTCGCCCAGAGG
* *
391681 GCATGGCGACCTACAAGGTCTCCCGGAGG
1 GCATGGCGACCTACAAGGTCGCCCAGAGG
* * *
391710 GCATGACGACCTACAAGGTCTCCCGGAGG
1 GCATGGCGACCTACAAGGTCGCCCAGAGG
*
391739 GCATGACGACCTACAAGGTCGCCCAGAGG
1 GCATGGCGACCTACAAGGTCGCCCAGAGG
* *
391768 GAATGGTGACCTA
1 GCATGGCGACCTA
391781 TGGTTGGGGA
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.26, C:0.29, G:0.32, T:0.13
Consensus pattern (29 bp):
GCATGGCGACCTACAAGGTCGCCCAGAGG
Found at i:394481 original size:30 final size:29
Alignment explanation
Indices: 394426--394482 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
394416 ATATTTTATA
394426 TATCTTAACTTTAAAATATAATTTATTTT
1 TATCTTAACTTTAAAATATAATTTATTTT
* *
394455 TATCTTAACTTATTAAATATATTTTATT
1 TATCTTAACTT-TAAAATATAATTTATT
394483 ATCAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (29 bp):
TATCTTAACTTTAAAATATAATTTATTTT
Found at i:394575 original size:30 final size:30
Alignment explanation
Indices: 394539--394611 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
394529 CTTATCTAAC
*
394539 TTAAAAATATATTT-TACCTCATCTTAACTT
1 TTAAAAATATATTTATA-ATCATCTTAACTT
*
394569 TTAAAAATACT-TTTATAATCATTTTAACTT
1 TTAAAAATA-TATTTATAATCATCTTAACTT
*
394599 TTAAAAATGTATT
1 TTAAAAATATATT
394612 GTATTCTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.03
30 33 0.89
31 3 0.08
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.48
Consensus pattern (30 bp):
TTAAAAATATATTTATAATCATCTTAACTT
Found at i:394727 original size:28 final size:27
Alignment explanation
Indices: 394674--394840 Score: 118
Period size: 30 Copynumber: 5.7 Consensus size: 27
394664 ATATTTTTTT
* *
394674 TAAAATAAAATACATTTTGAGTTTAAAA
1 TAAAATAAAATATATTTTAAG-TTAAAA
394702 TAAAATTAAAATATATTTTAAGTTAAAA
1 TAAAA-TAAAATATATTTTAAGTTAAAA
*
394730 TAAAATTAAAATAAATATTTTAAATTAAAAA
1 TAAAA-TAAAAT--ATATTTTAAGTT-AAAA
* * *
394761 TAATAAATAAAATATTTTTCTAAAATTAAAT
1 T-A-AAATAAAATATATTT-T-AAGTTAAAA
* * *
394792 TGAGAATAAAATGTATTCAATAAGTTAAAA
1 T-AAAATAAAATATATT--TTAAGTTAAAA
*
394822 TAAAAGTAAAATATGTTTT
1 TAAAA-TAAAATATATTTT
394841 TTAAAGTTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
28 24 0.21
29 17 0.15
30 44 0.39
31 12 0.11
32 12 0.11
33 3 0.03
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (27 bp):
TAAAATAAAATATATTTTAAGTTAAAA
Found at i:394773 original size:19 final size:19
Alignment explanation
Indices: 394727--394773 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
394717 TTTTAAGTTA
394727 AAATAAAATTAAAATAAAT
1 AAATAAAATTAAAATAAAT
** *
394746 ATTTTAAATTAAAA-ATAAT
1 AAATAAAATTAAAATA-AAT
394765 AAATAAAAT
1 AAATAAAAT
394774 ATTTTTCTAA
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATAAAATTAAAATAAAT
Found at i:395101 original size:20 final size:19
Alignment explanation
Indices: 395062--395102 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
395052 TGATTAATGG
*
395062 AAAATAAATATATTAATTT
1 AAAATAAATATATCAATTT
*
395081 AAAATAAATTTAATCAATTT
1 AAAATAAATAT-ATCAATTT
395101 AA
1 AA
395103 TCCTTTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAAATATATCAATTT
Found at i:395312 original size:22 final size:22
Alignment explanation
Indices: 395269--395310 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
395259 ATCTGTTAAC
* *
395269 AATTGATTGATAATAATTAAAT
1 AATTAATTGATAAAAATTAAAT
395291 AATTAATTGA-AAAAATTAAA
1 AATTAATTGATAAAAATTAAA
395311 ATTTGATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AATTAATTGATAAAAATTAAAT
Found at i:395934 original size:18 final size:18
Alignment explanation
Indices: 395911--395965 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 18
395901 ATATGGTAAC
395911 AATTTTATATTATATTTT
1 AATTTTATATTATATTTT
*
395929 AATTTTA-ATTA-GTTTT
1 AATTTTATATTATATTTT
395945 AATATTT-TATT-TA-TTT
1 AAT-TTTATATTATATTTT
395961 AATTT
1 AATTT
395966 GTTTAGTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
15 2 0.06
16 13 0.41
17 10 0.31
18 7 0.22
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTTTATATTATATTTT
Found at i:402111 original size:15 final size:15
Alignment explanation
Indices: 402093--402133 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
402083 AAATTTTGGC
402093 TTTTTGGCTTTTTTGT
1 TTTTTGG-TTTTTTGT
*
402109 TTTTTTGTTTTTTGT
1 TTTTTGGTTTTTTGT
402124 TTTTT-GTTTT
1 TTTTTGGTTTT
402134 AAAAATAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (15 bp):
TTTTTGGTTTTTTGT
Found at i:402119 original size:6 final size:7
Alignment explanation
Indices: 402101--402133 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
402091 GCTTTTTGGC
402101 TTTTTTG
1 TTTTTTG
402108 TTTTTTTG
1 -TTTTTTG
402116 TTTTTTG
1 TTTTTTG
402123 TTTTTTG
1 TTTTTTG
402130 TTTT
1 TTTT
402134 AAAAATAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTTG
Found at i:405924 original size:60 final size:60
Alignment explanation
Indices: 405831--405947 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
405821 CACGCTGTCG
* * * * * *
405831 ACATTTAGGTTGAACAAGCTGGTAGTTGCATGCCT-TCCCATTGAA-CTTGAAGGCATCTCA
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCTCCC--TGAAGCTTAAAGGCATCTCA
*
405891 ACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCTCTCCCTGAAGCTTAAAGGCATC
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCTCCCTGAAGCTTAAAGGCATC
405948 GTGTCAAATG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 4 0.08
60 40 0.83
61 4 0.08
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (60 bp):
ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCTCCCTGAAGCTTAAAGGCATCTCA
Found at i:407631 original size:24 final size:24
Alignment explanation
Indices: 407570--407659 Score: 85
Period size: 23 Copynumber: 3.8 Consensus size: 24
407560 TGCCACATAG
*
407570 TTGTCCCGAATGACCACATAAGTT
1 TTGTCCCGAAGGACCACATAAGTT
* * *
407594 TT-TCCTGAAGGACCATATAGGTT
1 TTGTCCCGAAGGACCACATAAGTT
* *
407617 TTGTCCCAAAGGACCACA-AAATT
1 TTGTCCCGAAGGACCACATAAGTT
** *
407640 TTGTTACGAATGACCACATA
1 TTGTCCCGAAGGACCACATA
407660 GAACCCTCGA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
23 36 0.71
24 15 0.29
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (24 bp):
TTGTCCCGAAGGACCACATAAGTT
Found at i:412194 original size:60 final size:58
Alignment explanation
Indices: 412024--412204 Score: 173
Period size: 60 Copynumber: 3.0 Consensus size: 58
412014 TATTTCCCGG
* * * *
412024 ACTATAATCTTTATTCTAAATTAGTCCTTAGACTTTAAAATATTCTAATTTCATGCTCAA
1 ACTATAA-CATTATTCTAAATTAGTCC-TAAACTTTTAAATATTCTAATTTCATCCTCAA
* * * * * *
412084 ACTATGATATTCATTCTAAATTAGTCTTTAAACTTTTGAACATTCCAATTTCATCCTCAA
1 ACTATAACATT-ATTCTAAATTAGTC-CTAAACTTTTAAATATTCTAATTTCATCCTCAA
* * * * *
412144 ACTATAACCCTTATTCCAAATTAGTCACTAAACTTTTAAATTTTTTAATTTCATTCTCAA
1 ACTATAA-CATTATTCTAAATTAGTC-CTAAACTTTTAAATATTCTAATTTCATCCTCAA
412204 A
1 A
412205 TTCATCCAAA
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
59 2 0.02
60 92 0.96
61 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.43
Consensus pattern (58 bp):
ACTATAACATTATTCTAAATTAGTCCTAAACTTTTAAATATTCTAATTTCATCCTCAA
Done.