Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 50 of 51
Found at i:12334325 original size:20 final size:20
Alignment explanation
Indices: 12334300--12334372 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
12334290 TTGTCGACTA
12334300 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
12334320 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
12334340 TCGCATTGCGATTTTACATAT
1 TCGCATTGCGA-TTTACATAT
12334361 TCGCATTGCGAT
1 TCGCATTGCGAT
12334373 AGTCAAGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 32 0.62
21 20 0.38
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:12334384 original size:41 final size:41
Alignment explanation
Indices: 12334300--12334426 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 41
12334290 TTGTCGACTA
*
12334300 TCGCATTGCGA-TTTACATATTCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATTTTACATATTCGCATTGCGATAGT-CA-AGT
12334340 TCGCATTGCGATTTTACATATTCGCATTGCGATAGTCAAGT
1 TCGCATTGCGATTTTACATATTCGCATTGCGATAGTCAAGT
** * *
12334381 TCGCATTGCGATAGTCCA-AGTTCGCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATTTTACATA-TTCGCATTGCGATAGTC-AAGT
12334423 TCGC
1 TCGC
12334427 GTTGTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 8
0.86 0.06 0.09
Matches are distributed among these distances:
40 13 0.17
41 55 0.71
42 9 0.12
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (41 bp):
TCGCATTGCGATTTTACATATTCGCATTGCGATAGTCAAGT
Found at i:12334385 original size:20 final size:21
Alignment explanation
Indices: 12334258--12334426 Score: 129
Period size: 21 Copynumber: 8.2 Consensus size: 21
12334248 TTAATGTAAA
* *
12334258 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGT
* * * *
12334279 TCGCATTACGATTGT-CGACT
1 TCGCATTGCGATAGTACAAGT
*
12334299 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTACA-AGT
*
12334320 TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTACA-AGT
**
12334340 TCGCATTGCGATTTTACATA-T
1 TCGCATTGCGATAGTACA-AGT
12334361 TCGCATTGCGATAGT-CAAGT
1 TCGCATTGCGATAGTACAAGT
*
12334381 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGT
*
12334402 TCGCGTTGCGATAGT-CGAAGT
1 TCGCATTGCGATAGTAC-AAGT
12334423 TCGC
1 TCGC
12334427 GTTGTGAATC
Statistics
Matches: 130, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.01
20 55 0.42
21 73 0.56
22 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATAGTACAAGT
Found at i:12337869 original size:11 final size:11
Alignment explanation
Indices: 12337824--12337868 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
12337814 GCATGCATGT
12337824 CAGCAATAATG
1 CAGCAATAATG
* *
12337835 CTGCAAGTATTG
1 CAGCAA-TAATG
12337847 CAGCAATAATG
1 CAGCAATAATG
*
12337858 GAGCAATAATG
1 CAGCAATAATG
12337869 GTGGGAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (11 bp):
CAGCAATAATG
Found at i:12338019 original size:17 final size:17
Alignment explanation
Indices: 12337971--12338037 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 17
12337961 CCTGGAGTGA
*
12337971 AAGAAAGAAGAGGAGAAG
1 AAGAAAGAAGA-AAGAAG
* *
12337989 AAAAAAG-AGAAAAGAGG
1 AAGAAAGAAG-AAAGAAG
12338006 AAGAAAGAAGAAAGAAG
1 AAGAAAGAAGAAAGAAG
12338023 -AGAAAAGAA-AAAGAA
1 AAG-AAAGAAGAAAGAA
12338038 ATAAGATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 8 0.20
17 24 0.59
18 9 0.22
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAGAAAGAAGAAAGAAG
Found at i:12338036 original size:20 final size:20
Alignment explanation
Indices: 12337970--12338043 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
12337960 ACCTGGAGTG
12337970 AAAGAAAGAAGAGGAGAAGAAA
1 AAAGAAAGAAGA-GAGAAG-AA
12337992 AAAGAGAA-AAGAG-GAAGAA
1 AAAGA-AAGAAGAGAGAAGAA
*
12338011 AGAAGAAAGAAGAGAAAAGAA
1 A-AAGAAAGAAGAGAGAAGAA
*
12338032 AAAGAAATAAGA
1 AAAGAAAGAAGA
12338044 TGATAATCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 5 0.11
20 23 0.50
21 7 0.15
22 9 0.20
23 2 0.04
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (20 bp):
AAAGAAAGAAGAGAGAAGAA
Found at i:12338036 original size:27 final size:27
Alignment explanation
Indices: 12337970--12338043 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
12337960 ACCTGGAGTG
*
12337970 AAAGAAAGAAGAGGAGAAGAAAAAAGAGA
1 AAAGAAA-AAGA-AAGAAGAAAAAAGAGA
** *
12337999 AAAGAGGAAGAAAGAAGAAAGAAGAGA
1 AAAGAAAAAGAAAGAAGAAAAAAGAGA
*
12338026 AAAGAAAAAGAAATAAGA
1 AAAGAAAAAGAAAGAAGA
12338044 TGATAATCGG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
27 29 0.76
28 4 0.11
29 5 0.13
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.01
Consensus pattern (27 bp):
AAAGAAAAAGAAAGAAGAAAAAAGAGA
Found at i:12338718 original size:20 final size:21
Alignment explanation
Indices: 12338671--12338725 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
12338661 GAGAGCGATG
*
12338671 ATGTTATTATTATTTAATAAA
1 ATGTTATAATTATTTAATAAA
* * *
12338692 ATATTATAATT-TTTTATTAA
1 ATGTTATAATTATTTAATAAA
*
12338712 ATGTTATAAATATT
1 ATGTTATAATTATT
12338726 AATGTTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
ATGTTATAATTATTTAATAAA
Found at i:12339752 original size:18 final size:18
Alignment explanation
Indices: 12339731--12339774 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12339721 ATTATAGTTT
* *
12339731 TTAATTTAATTTAATTAA
1 TTAATTTAAATCAATTAA
12339749 TTAATTTAAATCAATTAA
1 TTAATTTAAATCAATTAA
12339767 TTATATTT
1 TTA-ATTT
12339775 TTTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAATTTAAATCAATTAA
Found at i:12340909 original size:29 final size:30
Alignment explanation
Indices: 12340878--12340992 Score: 101
Period size: 34 Copynumber: 3.8 Consensus size: 30
12340868 GTTTTGCATT
*
12340878 AATTATTATAAAATCAAGTTAATTTA-GTT
1 AATTATTATAAAATCAAGTTAATTTACGTA
* * *
12340907 AATTATTATAGAATCAA-TT-ATATACATA
1 AATTATTATAAAATCAAGTTAATTTACGTA
* * * *
12340935 AATTACTAAAAAATAAAGTTAATTATTATGCATA
1 AATTATTATAAAATCAAGTTAA-T-TTA--CGTA
12340969 AATTATTATAAAATCAAGTTAATT
1 AATTATTATAAAATCAAGTTAATT
12340993 ATTATAAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
27 4 0.06
28 16 0.24
29 18 0.27
30 1 0.01
31 1 0.01
32 3 0.04
33 1 0.01
34 23 0.34
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (30 bp):
AATTATTATAAAATCAAGTTAATTTACGTA
Found at i:12340970 original size:34 final size:34
Alignment explanation
Indices: 12340922--12340998 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
12340912 TTATAGAATC
12340922 AATTA-TATACATAAATTACTAAAAAATAAAGTT
1 AATTATTATACATAAATTACTAAAAAATAAAGTT
* * * *
12340955 AATTATTATGCATAAATTATTATAAAATCAAGTT
1 AATTATTATACATAAATTACTAAAAAATAAAGTT
12340989 AATTATTATA
1 AATTATTATA
12340999 AAAATTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
33 5 0.13
34 33 0.87
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (34 bp):
AATTATTATACATAAATTACTAAAAAATAAAGTT
Found at i:12360564 original size:23 final size:22
Alignment explanation
Indices: 12360538--12360582 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
12360528 TTTCAAGCTA
12360538 AATTACCATAA-TACCCTTATAAT
1 AATT-CCATAATTACCCTT-TAAT
*
12360561 AATTTCATAATTACCCTTTAAT
1 AATTCCATAATTACCCTTTAAT
12360583 CCAACACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTCCATAATTACCCTTTAAT
Found at i:12361179 original size:21 final size:21
Alignment explanation
Indices: 12361153--12361192 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
12361143 TTAGTGAATA
12361153 AGTTAAGGATGCAAGTTGGCG
1 AGTTAAGGATGCAAGTTGGCG
12361174 AGTTAAGGATGCAAGTTGG
1 AGTTAAGGATGCAAGTTGG
12361193 TGAAAGTTCC
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:0.30, C:0.07, G:0.38, T:0.25
Consensus pattern (21 bp):
AGTTAAGGATGCAAGTTGGCG
Found at i:12364393 original size:19 final size:19
Alignment explanation
Indices: 12364355--12364415 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
12364345 TAATCTGAGA
* *
12364355 AGAGGTCAGAATAGAAATC
1 AGAGATCAGAACAGAAATC
*
12364374 AGAGATCAGAACAGATATC
1 AGAGATCAGAACAGAAATC
* * *
12364393 A-AGTTTCAGAGCAGAAATT
1 AGAG-ATCAGAACAGAAATC
12364412 AGAG
1 AGAG
12364416 GTCAAATTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 2 0.06
19 29 0.88
20 2 0.06
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.18
Consensus pattern (19 bp):
AGAGATCAGAACAGAAATC
Found at i:12365860 original size:22 final size:22
Alignment explanation
Indices: 12365812--12365862 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
12365802 TAATTTTTTT
* *
12365812 GGTCAAAGTCAACGGTTAGACC
1 GGTCAAAGTCAACGGTCAAACC
* *
12365834 AGTCAAAGTTAACGGTCAAACC
1 GGTCAAAGTCAACGGTCAAACC
12365856 GGTCAAA
1 GGTCAAA
12365863 TATCAACGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.18
Consensus pattern (22 bp):
GGTCAAAGTCAACGGTCAAACC
Found at i:12368619 original size:240 final size:240
Alignment explanation
Indices: 12368195--12368675 Score: 809
Period size: 240 Copynumber: 2.0 Consensus size: 240
12368185 TCAACTTAGG
* * *
12368195 TCCATAAGAAATTACCAGTCAGTGTTGAACCTATACAAGGAATTACCAATAGCGACTGAACCTGC
1 TCCATAAGAAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAATAGCAACTGAACCTAC
*
12368260 CAGTGTCTTCAGCTATACCAGAGTCCCAGAGTACCCCGCATGAAAATAATTTCAGTCAGTAAATA
66 CAGTGTCTTCAACTATACCAGAGTCCCAGAGTACCCCGCATGAAAATAATTTCAGTCAGTAAATA
* * * *
12368325 GAGATATCATTAATTTGAGAAGAGATCATAACAGAAATAAAAGATCATAATAAATATCAAGTTTT
131 GAGACATCATTAATCTGAGAAGAGATCATAACAAAAATAAAAGATCAGAATAAATATCAAGTTTT
*
12368390 AGAGAAGAAATCAGAGGTCAGATTGTTTTTCAAATAACATGTACA
196 AGAGAAGAAATCAGAGGTCAGATTATTTTTCAAATAACATGTACA
* * *
12368435 TCCATAAGAAATTATCAGTCGGTGCTGAACCTATAGAAGGAATTACCAATAGCAACTGAACCTAC
1 TCCATAAGAAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAATAGCAACTGAACCTAC
* * *
12368500 CAGTGTCTTCAATTATACCAGAGTCCCAGAGTATCCCGTATGAAAATAATTTCAGTCAGTAAATA
66 CAGTGTCTTCAACTATACCAGAGTCCCAGAGTACCCCGCATGAAAATAATTTCAGTCAGTAAATA
12368565 GAGACATCATTAATCTGAGAAGAGATCATAACAAAAATAAAAGATCAGAATAAATATCAAGTTTT
131 GAGACATCATTAATCTGAGAAGAGATCATAACAAAAATAAAAGATCAGAATAAATATCAAGTTTT
* *
12368630 AGAGTAGAAATCAGAGGTCATATTATTTTTCAAATAACATGTACA
196 AGAGAAGAAATCAGAGGTCAGATTATTTTTCAAATAACATGTACA
12368675 T
1 T
12368676 ACTTTTAAAA
Statistics
Matches: 224, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
240 224 1.00
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (240 bp):
TCCATAAGAAATTACCAGTCAGTGCTGAACCTATACAAGGAATTACCAATAGCAACTGAACCTAC
CAGTGTCTTCAACTATACCAGAGTCCCAGAGTACCCCGCATGAAAATAATTTCAGTCAGTAAATA
GAGACATCATTAATCTGAGAAGAGATCATAACAAAAATAAAAGATCAGAATAAATATCAAGTTTT
AGAGAAGAAATCAGAGGTCAGATTATTTTTCAAATAACATGTACA
Found at i:12372862 original size:21 final size:19
Alignment explanation
Indices: 12372821--12372864 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
12372811 ATTTGGGGAA
12372821 ATAC-GATGAAGAGTATCG
1 ATACTGATGAAGAGTATCG
*
12372839 ATACTGATGCAAGTAGTTTCG
1 ATACTGATG-AAG-AGTATCG
12372860 ATACT
1 ATACT
12372865 ATTGTGGGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 3 0.14
21 11 0.50
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (19 bp):
ATACTGATGAAGAGTATCG
Found at i:12373275 original size:54 final size:54
Alignment explanation
Indices: 12373193--12373313 Score: 197
Period size: 54 Copynumber: 2.2 Consensus size: 54
12373183 ACCGAACGAA
*
12373193 ACTGTGTGTGCAACTTAAGAAATCCATAATAAGTTTATGAATTTCCATATTGGC
1 ACTGTGTGTGCAACATAAGAAATCCATAATAAGTTTATGAATTTCCATATTGGC
* *
12373247 ACTGTGTGTGCAACATAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
1 ACTGTGTGTGCAACATAAGAAATCCATAATAAGTTTATGAATTTCCATATTGGC
* *
12373301 ATTGTGTATGCAA
1 ACTGTGTGTGCAA
12373314 ACCATAGAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (54 bp):
ACTGTGTGTGCAACATAAGAAATCCATAATAAGTTTATGAATTTCCATATTGGC
Found at i:12377937 original size:35 final size:36
Alignment explanation
Indices: 12377892--12377969 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 36
12377882 TGAGCAAGAA
* * *
12377892 AAAAATTGTTTCAAGAGAAAC-A-CTTCATGTGAGAT
1 AAAATTTGTTTCAAGAAAAACAATCTT-AAGTGAGAT
*
12377927 AAAATTTGTTTTAAGAAAAACAATCTTAAGTGAGAT
1 AAAATTTGTTTCAAGAAAAACAATCTTAAGTGAGAT
12377963 AAAATTT
1 AAAATTT
12377970 TCAGTGAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 18 0.49
36 16 0.43
37 3 0.08
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (36 bp):
AAAATTTGTTTCAAGAAAAACAATCTTAAGTGAGAT
Found at i:12378270 original size:73 final size:73
Alignment explanation
Indices: 12378099--12378277 Score: 227
Period size: 73 Copynumber: 2.5 Consensus size: 73
12378089 AGAGAATTTT
* * *
12378099 TTTTAAGAAAAACAATCTCAAGTGAAACAAAATTTGTTTCAAGAAAAAACAATCCCAAATGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAATATGTTTCAAGAAAAAACAATCCCAAATGAGAA
*
12378164 AAACTATC
66 AAACTATA
* * * * **
12378172 TTTTAA-AGAAAACTATCTCAAGTGAGATGAAATATGTTTTAAGAAAAAACAATCTCATGTGAGA
1 TTTTAAGA-AAAACAATCTCAAGTGAGATAAAATATGTTTCAAGAAAAAACAATCCCAAATGAGA
*
12378236 TTAAA-TATA
65 -AAAACTATA
12378245 TTTTAAGAAAAACAATCTCAAGTGAGATAAAAT
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAAAT
12378278 CTCAAGTGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
72 1 0.01
73 85 0.94
74 4 0.04
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (73 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAAATATGTTTCAAGAAAAAACAATCCCAAATGAGAA
AAACTATA
Found at i:12378272 original size:36 final size:36
Alignment explanation
Indices: 12378054--12378277 Score: 220
Period size: 36 Copynumber: 6.2 Consensus size: 36
12378044 CAATCTTAAG
* *
12378054 TAAAATTTGTTTTTAGAAAAACAATCTCGAAG-GAGA
1 TAAAATATGTTTTAAGAAAAACAATCTC-AAGTGAGA
* * * * *
12378090 GAGAATTTTTTTTAAGAAAAACAATCTCAAGTGAAA
1 TAAAATATGTTTTAAGAAAAACAATCTCAAGTGAGA
* * * * *
12378126 CAAAATTTGTTTCAAGAAAAAACAATCCCAAATGAGA
1 TAAAATATGTTTTAAG-AAAAACAATCTCAAGTGAGA
* *
12378163 -AAAACTATCTTTTAA-AGAAAACTATCTCAAGTGAGA
1 TAAAA-TATGTTTTAAGA-AAAACAATCTCAAGTGAGA
* *
12378199 TGAAATATGTTTTAAGAAAAAACAATCTCATGTGAGA
1 TAAAATATGTTTTAAG-AAAAACAATCTCAAGTGAGA
* *
12378236 TTAAATATATTTTAAGAAAAACAATCTCAAGTGAGA
1 TAAAATATGTTTTAAGAAAAACAATCTCAAGTGAGA
12378272 TAAAAT
1 TAAAAT
12378278 CTCAAGTGAA
Statistics
Matches: 155, Mismatches: 26, Indels: 14
0.79 0.13 0.07
Matches are distributed among these distances:
35 4 0.03
36 92 0.59
37 58 0.37
38 1 0.01
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (36 bp):
TAAAATATGTTTTAAGAAAAACAATCTCAAGTGAGA
Found at i:12378280 original size:17 final size:17
Alignment explanation
Indices: 12378258--12378291 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12378248 TAAGAAAAAC
*
12378258 AATCTCAAGTGAGATAA
1 AATCTCAAGTGAAATAA
12378275 AATCTCAAGTGAAATAA
1 AATCTCAAGTGAAATAA
12378292 TTCTGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.24
Consensus pattern (17 bp):
AATCTCAAGTGAAATAA
Found at i:12378392 original size:44 final size:44
Alignment explanation
Indices: 12378328--12378483 Score: 150
Period size: 44 Copynumber: 3.7 Consensus size: 44
12378318 AAGCGAGAAT
* * * *
12378328 ATGATGATCCAATTCTTTATGTGATGGAATCAAACGAAATGGTG
1 ATGATGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGGTG
* * * * *
12378372 ATGTTGATCTAACTCCTTATGTGATTGG-ATCGAGTGAATTGTTG
1 ATGATGATCCAACTCCTTATGTGA-TGGAATCGAGCGAAATGGTG
*
12378416 ATGATGATCCAACTCTTTATGTGATGGAATCGAGCG-AA-----
1 ATGATGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGGTG
12378454 AT-AT-ATCCAACTCCTTATGTGATGGAATCG
1 ATGATGATCCAACTCCTTATGTGATGGAATCG
12378484 GCTAAGGTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
36 25 0.26
37 2 0.02
38 2 0.02
43 4 0.04
44 59 0.62
45 3 0.03
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.34
Consensus pattern (44 bp):
ATGATGATCCAACTCCTTATGTGATGGAATCGAGCGAAATGGTG
Found at i:12378922 original size:22 final size:21
Alignment explanation
Indices: 12378897--12378965 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
12378887 GGTCCGAAGA
12378897 ACTTAATCACCATGCTCAAAAG
1 ACTTAATCA-CATGCTCAAAAG
*
12378919 ACTTACT-A-ATGACTCAAAAG
1 ACTTAATCACATG-CTCAAAAG
* *
12378939 ATTTAATCATCATGCTCGAAAG
1 ACTTAATCA-CATGCTCAAAAG
12378961 ACTTA
1 ACTTA
12378966 CTGATGACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 3 0.08
20 13 0.34
21 2 0.05
22 17 0.45
23 3 0.08
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.28
Consensus pattern (21 bp):
ACTTAATCACATGCTCAAAAG
Found at i:12378936 original size:20 final size:20
Alignment explanation
Indices: 12378911--12378980 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
12378901 AATCACCATG
12378911 CTCAAAAGACTTACTAATGA
1 CTCAAAAGACTTACTAATGA
* *
12378931 CTCAAAAGATTTAATCATCATG-
1 CTCAAAAGACTT-A-C-TAATGA
* *
12378953 CTCGAAAGACTTACTGATGA
1 CTCAAAAGACTTACTAATGA
*
12378973 CCCAAAAG
1 CTCAAAAG
12378981 GTTTAATCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.10
20 18 0.46
21 2 0.05
22 11 0.28
23 4 0.10
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.24
Consensus pattern (20 bp):
CTCAAAAGACTTACTAATGA
Found at i:12378945 original size:42 final size:42
Alignment explanation
Indices: 12378899--12378989 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
12378889 TCCGAAGAAC
*
12378899 TTAATCACCATGCTCAAAAGACTTACTAATGACTCAAAAGAT
1 TTAATCACCATGCTCAAAAGACTTACTAATGACCCAAAAGAT
* * * *
12378941 TTAATCATCATGCTCGAAAGACTTACTGATGACCCAAAAGGT
1 TTAATCACCATGCTCAAAAGACTTACTAATGACCCAAAAGAT
12378983 TTAATCA
1 TTAATCA
12378990 AGCAATAAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.27
Consensus pattern (42 bp):
TTAATCACCATGCTCAAAAGACTTACTAATGACCCAAAAGAT
Found at i:12379080 original size:73 final size:74
Alignment explanation
Indices: 12378996--12379171 Score: 214
Period size: 74 Copynumber: 2.4 Consensus size: 74
12378986 ATCAAGCAAT
* * * *
12378996 AAACCTTTGAAAGTCAAACTTAGT-TTCTTTAAAAATTC-ATTTGAAACTATCATATCGTTGA-G
1 AAACCTTTGAAAATCAAACTT-GTCTTCTTTAAAAATTCAATTGGAAAC-ATCATATCGGTCAGG
12379058 TAATCATCAAG
64 TAATCATCAAG
* ** * *
12379069 AAACCTCTGAAAATTGAACTTTTCTTCTTTATAAATTCAATTGGAAACATCATATCGGTCAGGTA
1 AAACCTTTGAAAATCAAACTTGTCTTCTTTAAAAATTCAATTGGAAACATCATATCGGTCAGGTA
12379134 ATCATCAAG
66 ATCATCAAG
* *
12379143 AAACCTTTGAAAATCAAACTGGACTTCTT
1 AAACCTTTGAAAATCAAACTTGTCTTCTT
12379172 AAAGATTTAT
Statistics
Matches: 85, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
72 1 0.01
73 41 0.48
74 43 0.51
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (74 bp):
AAACCTTTGAAAATCAAACTTGTCTTCTTTAAAAATTCAATTGGAAACATCATATCGGTCAGGTA
ATCATCAAG
Found at i:12379195 original size:74 final size:73
Alignment explanation
Indices: 12379020--12379198 Score: 173
Period size: 74 Copynumber: 2.4 Consensus size: 73
12379010 CAAACTTAGT
* * * * * * **
12379020 TTCTTTAAAAATTCATTTGAAACTATCATATCGTTGAGTAATCATCAAGAAACCTCTGAAAATTG
1 TTCTTTATAAATTCAATTAAAAATATCATATCGGTCAGTAATCATCAAGAAACCTCTGAAAATCA
***
12379085 AACTTTTC
66 AACTGGAC
** * *
12379093 TTCTTTATAAATTCAATTGGAAACATCATATCGGTCAGGTAATCATCAAGAAACCTTTGAAAATC
1 TTCTTTATAAATTCAATTAAAAATATCATATCGGTCA-GTAATCATCAAGAAACCTCTGAAAATC
12379158 AAACTGGAC
65 AAACTGGAC
*
12379167 TTC-TTA-AAGATTTATATTAAAAATATCATATC
1 TTCTTTATAA-ATTCA-ATTAAAAATATCATATC
12379199 AGTTGAGTAA
Statistics
Matches: 86, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
72 2 0.02
73 37 0.43
74 47 0.55
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (73 bp):
TTCTTTATAAATTCAATTAAAAATATCATATCGGTCAGTAATCATCAAGAAACCTCTGAAAATCA
AACTGGAC
Found at i:12383800 original size:18 final size:18
Alignment explanation
Indices: 12383777--12383846 Score: 122
Period size: 18 Copynumber: 3.9 Consensus size: 18
12383767 TCAAAAGGAC
12383777 TGAAGTAAATGATAAGTT
1 TGAAGTAAATGATAAGTT
12383795 TGAAGTAAATGATAAGTT
1 TGAAGTAAATGATAAGTT
12383813 TGAAGTAAATGATAAGTT
1 TGAAGTAAATGATAAGTT
* *
12383831 TGAATTAAATAATAAG
1 TGAAGTAAATGATAAG
12383847 ACCGGACGGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (18 bp):
TGAAGTAAATGATAAGTT
Found at i:12392068 original size:21 final size:20
Alignment explanation
Indices: 12392042--12392177 Score: 100
Period size: 21 Copynumber: 6.6 Consensus size: 20
12392032 GTTTCCATAT
12392042 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
*
12392063 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
* *
12392084 TCACAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
* *
12392104 TCGCAATGCGATAGTCGGCTA
1 TCGCAATGCGA-ATTCGACTA
*
12392125 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
* *
12392145 TCACAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
12392166 TCGCAATGCGAA
1 TCGCAATGCGAA
12392178 CCAAAATCGC
Statistics
Matches: 91, Mismatches: 14, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
20 30 0.33
21 61 0.67
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATTCGACTA
Found at i:12392107 original size:41 final size:41
Alignment explanation
Indices: 12392062--12392177 Score: 155
Period size: 41 Copynumber: 2.8 Consensus size: 41
12392052 AACTTCGACT
*
12392062 ATCGCAATGCGA-ACTTGGACTATCACAATGCGAATATGTAA
1 ATCGCAATGCGATA-TTGGACTATCGCAATGCGAATATGTAA
*
12392103 ATCGCAATGCGATAGTCGG-CTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-TTGGACTATCGCAATGCGAATATGTAA
* * *
12392144 ATCACAATGCGATAGTCGACTATCGCAATGCGAA
1 ATCGCAATGCGATATTGGACTATCGCAATGCGAA
12392178 CCAAAATCGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.02
41 61 0.92
42 4 0.06
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGATATTGGACTATCGCAATGCGAATATGTAA
Found at i:12392112 original size:20 final size:20
Alignment explanation
Indices: 12392087--12392155 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
12392077 TGGACTATCA
12392087 CAATGCGAATATGTAAATCG
1 CAATGCGAATATGTAAATCG
***
12392107 CAATGCG-ATAGTCGGCTATCG
1 CAATGCGAATA-T-GTAAATCG
*
12392128 CAATGCGAATATGTAAATCA
1 CAATGCGAATATGTAAATCG
12392148 CAATGCGA
1 CAATGCGA
12392156 TAGTCGACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 3 0.08
20 20 0.51
21 13 0.33
22 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
CAATGCGAATATGTAAATCG
Found at i:12392310 original size:5 final size:5
Alignment explanation
Indices: 12392302--12392332 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
12392292 ACACCCGACC
12392302 CGAGA CGAGA CGAGA CGAGA CGAGA CG-GA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
12392333 GCAGCGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.35, C:0.23, G:0.42, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:12392967 original size:23 final size:23
Alignment explanation
Indices: 12392925--12393073 Score: 188
Period size: 23 Copynumber: 6.8 Consensus size: 23
12392915 ATTTTGGACT
*
12392925 ATCGCAA--CGAACTTGAAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
12392946 ATCGCAACGCGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
12392969 ATCGCAACGCGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
12392992 ATCGCAA--CGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
* *
12393013 ATCGCAACGCGAACTTTGACT--
1 ATCGCAACGCGAACTTGGAATAA
12393034 ATCGCAA--CGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAA
*
12393055 ATCACAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
12393074 CTATCGCAAT
Statistics
Matches: 110, Mismatches: 10, Indels: 14
0.82 0.07 0.10
Matches are distributed among these distances:
19 10 0.09
21 40 0.36
23 60 0.55
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (23 bp):
ATCGCAACGCGAACTTGGAATAA
Found at i:12393003 original size:44 final size:44
Alignment explanation
Indices: 12392925--12393073 Score: 207
Period size: 44 Copynumber: 3.4 Consensus size: 44
12392915 ATTTTGGACT
*
12392925 ATCGCAA--CGAACTTGAAATAAATCGCAACGCGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAAATCGCAA--CGAATTTGGAATAA
12392969 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAA
* * *
12393013 ATCGCAACGCGAACTTTGACT--ATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAA
*
12393055 ATCACAACGCGAACTTGGA
1 ATCGCAACGCGAACTTGGA
12393074 CTATCGCAAT
Statistics
Matches: 97, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
42 37 0.38
44 40 0.41
46 20 0.21
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (44 bp):
ATCGCAACGCGAACTTGGAATAAATCGCAACGAATTTGGAATAA
Found at i:12393051 original size:42 final size:42
Alignment explanation
Indices: 12392946--12393082 Score: 202
Period size: 42 Copynumber: 3.2 Consensus size: 42
12392936 CTTGAAATAA
*
12392946 ATCGCAACGCGAATTTGGAATAAATCGCAACGCGAACTTGGAAT
1 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTGGACT
*
12392990 AAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTTGACT
1 --ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
* *
12393034 ATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
12393076 ATCGCAA
1 ATCGCAA
12393083 TGCGAATATG
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
42 46 0.53
44 33 0.38
46 7 0.08
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:12394901 original size:168 final size:166
Alignment explanation
Indices: 12394679--12395005 Score: 395
Period size: 168 Copynumber: 2.0 Consensus size: 166
12394669 TAAAAGGATC
* * * * * ** * *
12394679 AAATAAGGAAAAGATTAAAAATCCACCAAAAACTCGAACAAAAGATATATACAAATGAATCTGAT
1 AAATAAGGAAAAAATTAAAAACCCACAAAAAACTCGAACAAAAAATAGATACAAACAAACCTGAC
** * * * *
12394744 TGCATTGGTAAAATAAACAACAAGAATG-GATCAAACTACTGAAGACCATCGACAACCGCAAATT
66 TGCATCAGTAAAATAAACAACAACAA-GAGATCAAACTACCGAAGACCACCGACAACCGCAAACT
* * *
12394808 AGAATTAAAGCTTCGTGAGTAAACTATCTATGAAAGT
130 AGAATCAAAGCATCGTGAGGAAACTATCTATGAAAGT
*
12394845 AAATAAGGGAAAAAATTAAAAACCCACAAAAAAACTCGAACAAAAAATAGATACAAACAAACCTT
1 AAATAA-GGAAAAAATTAAAAACCCAC-AAAAAACTCGAACAAAAAATAGATACAAACAAACCTG
* * * *
12394910 ACTGCATCAGTAAAGTGAACCACAACAAGAGATCAAACTACCGAAGACCACCGACAACCGTAAAC
64 ACTGCATCAGTAAAATAAACAACAACAAGAGATCAAACTACCGAAGACCACCGACAACCGCAAAC
* *
12394975 TAGAGTCAAAGCATCGTGAGGAATCTATCTA
129 TAGAATCAAAGCATCGTGAGGAAACTATCTA
12395006 CAAATACAAA
Statistics
Matches: 133, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
166 6 0.05
167 19 0.14
168 108 0.81
ACGTcount: A:0.50, C:0.19, G:0.14, T:0.18
Consensus pattern (166 bp):
AAATAAGGAAAAAATTAAAAACCCACAAAAAACTCGAACAAAAAATAGATACAAACAAACCTGAC
TGCATCAGTAAAATAAACAACAACAAGAGATCAAACTACCGAAGACCACCGACAACCGCAAACTA
GAATCAAAGCATCGTGAGGAAACTATCTATGAAAGT
Found at i:12395984 original size:18 final size:18
Alignment explanation
Indices: 12395961--12395996 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
12395951 TAGTTTAGTG
12395961 TAACATTTATTTCGTTTC
1 TAACATTTATTTCGTTTC
12395979 TAACATTTATTTCGTTTC
1 TAACATTTATTTCGTTTC
12395997 AGATTGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (18 bp):
TAACATTTATTTCGTTTC
Found at i:12397798 original size:12 final size:12
Alignment explanation
Indices: 12397776--12397834 Score: 54
Period size: 12 Copynumber: 5.0 Consensus size: 12
12397766 ACTAATCTCC
12397776 CAAAA-AAATAA
1 CAAAATAAATAA
12397787 CAAAATAAATAA
1 CAAAATAAATAA
12397799 CATAAAATAAAGT--
1 C--AAAATAAA-TAA
*
12397812 -AAAATAAAAAA
1 CAAAATAAATAA
12397823 CAAAATAAATAA
1 CAAAATAAATAA
12397835 ATAAAACAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
10 8 0.21
11 5 0.13
12 17 0.44
14 8 0.21
15 1 0.03
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (12 bp):
CAAAATAAATAA
Found at i:12397802 original size:39 final size:37
Alignment explanation
Indices: 12397753--12397855 Score: 106
Period size: 35 Copynumber: 2.8 Consensus size: 37
12397743 AAGAAATATC
* *
12397753 TAAATAACATAAAACTAATCTCCCAAAA-AAATAACAAAA
1 TAAATAACATAAAACTAAACT---AAAATAAAAAACAAAA
*
12397792 TAAATAACATAAAA-TAAAGTAAAATAAAAAACAAAA
1 TAAATAACATAAAACTAAACTAAAATAAAAAACAAAA
**
12397828 TAAATAA-ATAAAAC-AAGGTAAAATAAAA
1 TAAATAACATAAAACTAAACTAAAATAAAA
12397856 TAGAAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
35 23 0.40
36 17 0.29
38 4 0.07
39 14 0.24
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (37 bp):
TAAATAACATAAAACTAAACTAAAATAAAAAACAAAA
Found at i:12397820 original size:15 final size:14
Alignment explanation
Indices: 12397788--12397944 Score: 67
Period size: 14 Copynumber: 10.9 Consensus size: 14
12397778 AAAAAATAAC
*
12397788 AAAATAAATAACAT
1 AAAATAAATAAAAT
12397802 AAAATAAAGTAAAAT
1 AAAATAAA-TAAAAT
*
12397817 -AAA-AAACAAAAT
1 AAAATAAATAAAAT
*
12397829 -AAATAAATAAAAC
1 AAAATAAATAAAAT
**
12397842 AAGGTAAAATAAAAT
1 AAAAT-AAATAAAAT
*
12397857 AGAAA-AAA-AAGAT
1 A-AAATAAATAAAAT
* *
12397870 TAAATCAAATAAAAAA
1 AAAAT-AAAT-AAAAT
* * *
12397886 AGAAACAAACAAACAA
1 A-AAATAAATAAA-AT
12397902 ACAAATAAAT-AAAT
1 A-AAATAAATAAAAT
12397916 AAAACTACAATAAAA-
1 AAAA-TA-AATAAAAT
12397931 AGAAATAAATAAAA
1 A-AAATAAATAAAA
12397945 AGGAATATAT
Statistics
Matches: 108, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
12 11 0.10
13 17 0.16
14 30 0.28
15 25 0.23
16 22 0.20
17 3 0.03
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:12397832 original size:36 final size:36
Alignment explanation
Indices: 12397780--12397857 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 36
12397770 ATCTCCCAAA
*
12397780 AAAATAACAAAATAAATAACATAAAATAAAGTAAAAT
1 AAAATAACAAAATAAATAA-ATAAAACAAAGTAAAAT
*
12397817 AAAA-AACAAAATAAATAAATAAAACAAGGTAAAAT
1 AAAATAACAAAATAAATAAATAAAACAAAGTAAAAT
12397852 AAAATA
1 AAAATA
12397858 GAAAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
35 19 0.50
36 15 0.39
37 4 0.11
ACGTcount: A:0.74, C:0.05, G:0.04, T:0.17
Consensus pattern (36 bp):
AAAATAACAAAATAAATAAATAAAACAAAGTAAAAT
Found at i:12397863 original size:23 final size:22
Alignment explanation
Indices: 12397800--12397886 Score: 77
Period size: 23 Copynumber: 3.8 Consensus size: 22
12397790 AATAAATAAC
*
12397800 ATAAAATAAAGTAAAATAAAAA-
1 ATAAAATAAA-TAAAAAAAAAAG
* *
12397822 ACAAAATAAATAAATAAAACAAG
1 ATAAAATAAATAAA-AAAAAAAG
* *
12397845 GTAAAATAAAATAGAAAAAAAAG
1 ATAAAAT-AAATAAAAAAAAAAG
*
12397868 ATTAAATCAAATAAAAAAA
1 ATAAAAT-AAATAAAAAAA
12397887 GAAACAAACA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
21 4 0.08
22 14 0.27
23 27 0.53
24 6 0.12
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (22 bp):
ATAAAATAAATAAAAAAAAAAG
Found at i:12397864 original size:24 final size:21
Alignment explanation
Indices: 12397800--12397886 Score: 77
Period size: 22 Copynumber: 3.9 Consensus size: 21
12397790 AATAAATAAC
12397800 ATAAAATAAAGTAAAATAAAAA-
1 ATAAAATAAA-TAAAA-AAAAAG
*
12397822 ACAAAATAAATAAATAAAACAAG
1 ATAAAATAAATAAA-AAAA-AAG
*
12397845 GTAAAATAAAATAGAAAAAAAAG
1 ATAAAAT-AAATA-AAAAAAAAG
*
12397868 ATTAAATCAAATAAAAAAA
1 ATAAAAT-AAATAAAAAAA
12397887 GAAACAAACA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.13
22 18 0.33
23 18 0.33
24 9 0.17
25 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (21 bp):
ATAAAATAAATAAAAAAAAAG
Found at i:12397943 original size:14 final size:14
Alignment explanation
Indices: 12397904--12397951 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
12397894 ACAAACAAAC
12397904 AAATAAATAAATAA-
1 AAATAAATAAA-AAG
*
12397918 AACTACAATAAAAAG
1 AAATA-AATAAAAAG
12397933 AAATAAATAAAAAG
1 AAATAAATAAAAAG
*
12397947 GAATA
1 AAATA
12397952 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 19 0.66
15 10 0.34
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (14 bp):
AAATAAATAAAAAG
Found at i:12399228 original size:20 final size:19
Alignment explanation
Indices: 12399203--12399247 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
12399193 TCCACTGTGG
12399203 GCCACTGTTATAATGGGTCA
1 GCCACT-TTATAATGGGTCA
*
12399223 GCCAC-TTGTAATGGGTCA
1 GCCACTTTATAATGGGTCA
12399241 GCCACTT
1 GCCACTT
12399248 GTAATGGGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 17 0.74
19 1 0.04
20 5 0.22
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (19 bp):
GCCACTTTATAATGGGTCA
Found at i:12399236 original size:18 final size:18
Alignment explanation
Indices: 12399213--12399255 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
12399203 GCCACTGTTA
12399213 TAATGGGTCAGCCACTTG
1 TAATGGGTCAGCCACTTG
12399231 TAATGGGTCAGCCACTTG
1 TAATGGGTCAGCCACTTG
12399249 TAATGGG
1 TAATGGG
12399256 CTTCAAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (18 bp):
TAATGGGTCAGCCACTTG
Found at i:12401058 original size:25 final size:26
Alignment explanation
Indices: 12401016--12401074 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
12401006 ACCTTATTTT
* *
12401016 TTTTTCTTTTTCTTTTTTTTTTCAAC
1 TTTTTCTTCTTCTCTTTTTTTTCAAC
* *
12401042 TTTTTCTTCTTC-CTTTTTTTTTAAT
1 TTTTTCTTCTTCTCTTTTTTTTCAAC
12401067 TTTTTCTT
1 TTTTTCTT
12401075 TTTTTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 18 0.62
26 11 0.38
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTTCTTCTTCTCTTTTTTTTCAAC
Found at i:12411561 original size:5 final size:5
Alignment explanation
Indices: 12411553--12411718 Score: 83
Period size: 5 Copynumber: 33.4 Consensus size: 5
12411543 AAAAGAAAAT
** * * *
12411553 AATAA AAT-A AATAA CGTAA AA-AA AAAAA AATAT AAT-A AATAA AACAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
** * * * * *
12411600 GGTAA AATAA AATAGA AATAA AATAT GA-AA AAGAA AATTA AATCA AATAA
1 AATAA AATAA AATA-A AATAA AATAA AATAA AATAA AATAA AATAA AATAA
* * * *
12411650 AAAAGA AACAA ACAAACA AACAA AA-ATA AATAA AATAA AATAA AATAA
1 AATA-A AATAA A-ATA-A AATAA AATA-A AATAA AATAA AATAA AATAA
* *
12411698 TAGAA AATAA AA-AA AATAA AA
1 AATAA AATAA AATAA AATAA AA
12411719 CTACTATAAA
Statistics
Matches: 121, Mismatches: 29, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
4 18 0.15
5 87 0.72
6 14 0.12
7 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:12411605 original size:33 final size:32
Alignment explanation
Indices: 12411540--12411620 Score: 83
Period size: 33 Copynumber: 2.5 Consensus size: 32
12411530 ACTAATCTCC
* *
12411540 AAAAAAAGAAAATAATAAAATAAATAACGTAA
1 AAAAAAAAAAAATAATAAAATAAACAACGTAA
*
12411572 AAAAAAAAAAATATAAT-AAATAAAACAAGGTAA
1 AAAAAAAAAAA-ATAATAAAAT-AAACAACGTAA
* *
12411605 AATAAAATAGAAATAA
1 AA-AAAAAAAAAATAA
12411621 AATATGAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
32 14 0.34
33 20 0.49
34 7 0.17
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.16
Consensus pattern (32 bp):
AAAAAAAAAAAATAATAAAATAAACAACGTAA
Found at i:12411696 original size:19 final size:19
Alignment explanation
Indices: 12411553--12411717 Score: 88
Period size: 19 Copynumber: 8.6 Consensus size: 19
12411543 AAAAGAAAAT
**
12411553 AATAAAATAAATAACGTAA
1 AATAAAATAAATAAAATAA
* * *
12411572 AAAAAAAAAAATATAAT-A
1 AATAAAATAAATAAAATAA
* *
12411590 AATAAAACAAGGTAAAATAA
1 AATAAAATAA-ATAAAATAA
**
12411610 AATAGAAATAAAATATGA-AA
1 AATA-AAAT-AAATAAAATAA
* *
12411630 AAGAAAATTAAATCAAATAA
1 AATAAAA-TAAATAAAATAA
* * *
12411650 AAAAGAAACAAACAAACA-AA
1 AATA-AAATAAATAAA-ATAA
*
12411670 CA-AAAATAAATAAAATAA
1 AATAAAATAAATAAAATAA
*
12411688 AATAAAATAATAGAAAATAA
1 AATAAAATAA-ATAAAATAA
12411708 AA-AAAATAAA
1 AATAAAATAAA
12411718 ACTACTATAA
Statistics
Matches: 109, Mismatches: 26, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
17 1 0.01
18 22 0.20
19 40 0.37
20 34 0.31
21 10 0.09
22 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (19 bp):
AATAAAATAAATAAAATAA
Found at i:12411809 original size:17 final size:16
Alignment explanation
Indices: 12411790--12411849 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
12411780 TTATGTGAAG
12411790 AAAAATAAAAGAAAAA
1 AAAAATAAAAGAAAAA
** *
12411806 GAAAAAGGAAGGAAGAAA
1 -AAAAATAAAAGAA-AAA
12411824 AAAAATAAAA-AAAATA
1 AAAAATAAAAGAAAA-A
12411840 AAAAATAAAA
1 AAAAATAAAA
12411850 AATATATTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 13 0.37
17 17 0.49
18 3 0.09
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAATAAAAGAAAAA
Found at i:12411888 original size:27 final size:28
Alignment explanation
Indices: 12411845--12411897 Score: 65
Period size: 27 Copynumber: 1.9 Consensus size: 28
12411835 AAATAAAAAA
* *
12411845 TAAAAAATATATTTAAATAA-AAATATT
1 TAAAAAATATATGTAAAAAAGAAATATT
12411872 TAAAAAATA-ATGGTAAAAAAGAAATA
1 TAAAAAATATAT-GTAAAAAAGAAATA
12411898 AACCAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 2 0.09
27 15 0.68
28 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (28 bp):
TAAAAAATATATGTAAAAAAGAAATATT
Found at i:12413967 original size:2 final size:2
Alignment explanation
Indices: 12413960--12414003 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
12413950 TTTAAAAATA
12413960 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
12414002 AT
1 AT
12414004 TAAAATGTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12419388 original size:3 final size:3
Alignment explanation
Indices: 12419380--12419413 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
12419370 AATAATTATT
12419380 TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12419414 ATAGGACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:12419390 original size:17 final size:17
Alignment explanation
Indices: 12419370--12419416 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
12419360 GGCTTGTAAA
* *
12419370 AATAATTATTTAATAAT
1 AATAATAATATAATAAT
12419387 AATAATAATATAATAAT
1 AATAATAATATAATAAT
12419404 AATAA-AATA-AATA
1 AATAATAATATAATA
12419417 GGACAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 20 0.71
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAATATAATAAT
Found at i:12419399 original size:11 final size:11
Alignment explanation
Indices: 12419380--12419413 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12419370 AATAATTATT
12419380 TAATAATAATAA
1 TAAT-ATAATAA
12419392 TAATATAATAA
1 TAATATAATAA
*
12419403 TAATAAAATAA
1 TAATATAATAA
12419414 ATAGGACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATATAATAA
Found at i:12419399 original size:14 final size:14
Alignment explanation
Indices: 12419381--12419413 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12419371 ATAATTATTT
12419381 AATAATAATAATAA
1 AATAATAATAATAA
*
12419395 TATAATAATAATAA
1 AATAATAATAATAA
12419409 AATAA
1 AATAA
12419414 ATAGGACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAATAA
Found at i:12419657 original size:47 final size:47
Alignment explanation
Indices: 12419579--12420688 Score: 416
Period size: 47 Copynumber: 21.9 Consensus size: 47
12419569 AGAGATATTT
* *
12419579 GGAAAACGAATATGCT-CATCTCTTCTATCAGGGAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCA-CTCTTCTTTCAGGGAGATAAGATCCAAG
* * * *
12419626 GGAAGACGAATCTGCTCCATTCTTTTTTCAGGGAGATAAGACTCGAAAAATCTTTG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA-----G
** * * *
12419682 TAAAAACGGATTTGCTCCACTATTCTTTCAGGGAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * *
12419729 GGAAGACGAATCTACTCCACTCTTCCTTCAGGGAGATAAGACTCAAGAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCCA-AG
* * * *
12419778 ATCTTTGGAAAACGGATATGCTCCACTCTTCTTTCATGGATATAAGATCCAAG
1 ------GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
12419831 GGAAGATGAATCTGTTCCATTCTTCTTTCAGGGAGATAAGAATCGAGAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAG-ATCCA-AG
* * * *
12419880 ATCTTTGTAAAACGGATCTGCTCCGCTCTTCTTTCAGGGAGATAGGATCCAAG
1 ------GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * *
12419933 GGAAGACGAATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTT
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA----G
* * * *
12419988 AGAAAAC-ATATTTGCT-CATCTCTTTTTTTAGGGAGATAAGATCCAAG
1 GGAAAACGA-ATCTGCTCCA-CTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
12420035 GGAAGAA-TAATCTGCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTA
1 GGAA-AACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA----G
** * * * ** *
12420090 AAAAAACGAATCTACTCCTCTATTCTTTCAGGGAGATAAGACTTTAGAAATCTTT
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA---T-CCAA----G
* * * * *
12420145 GTAAAACGGATATGCTCCACTATTCTTTCAGGGAGATAAAATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * * *
12420192 GGAAGATGAATCTGCTTCACTCTTCTTTCAAGGAGATAAGACTCGAGAAATCTTC
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA----G
* * * * * *
12420247 GTAAAATGGATATGCTCCACTCTACTTTCGGGGAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
12420294 CGAAGATGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATATTT
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC----CA-A--G
* * * * * * *
12420349 GTAAAATGGATCT-CTTTCACTCTTCTTTAAGAGAGATATGATCCAAG
1 GGAAAACGAATCTGC-TCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * *
12420396 GGAAAACGAATATGTTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTT
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TC---CAA----G
* * * * *
12420451 GGAAAATGGATATACTCCACTATTCTTTCAGGGAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * * * ***
12420498 GGAAGAA-GAAATATGCTCTACTCTTTTTTCAAGAGGATAAGACTTGATAAAT-CTTT
1 GGAA-AACG-AATCTGCTCCACTCTTCTTTC-AG-GG---AGA--T-A-AGATCCAAG
** * *
12420554 GGAAAATAAATATGCTCCACTCTTCTTTCAAGGAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* *
12420601 GGAAGACGAATCTGCTCCACTCTTCTTTCAGGTAGATAAGATCCAAG
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
* * *
12420648 GGAAGACGAATCTGCTCCACTATTCTTTTAGGGAGATAAGA
1 GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGA
12420689 CTCAAAATTA
Statistics
Matches: 792, Mismatches: 181, Indels: 180
0.69 0.16 0.16
Matches are distributed among these distances:
46 3 0.00
47 342 0.43
48 45 0.06
49 7 0.01
50 6 0.01
51 18 0.02
52 4 0.01
53 10 0.01
54 22 0.03
55 291 0.37
56 40 0.05
57 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (47 bp):
GGAAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAG
Found at i:12419823 original size:55 final size:54
Alignment explanation
Indices: 12419729--12420493 Score: 297
Period size: 55 Copynumber: 14.8 Consensus size: 54
12419719 AAGATCCAAG
* * * *
12419729 GGAAGACGAATCTACTCCACTCTTCCTTCAGGGAGATAAGACTCAAGAGATCTTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* * * *
12419784 GGAAAACGGATATGCTCCACTCTTCTTTCATGGATATAAGATCCA-AG------
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
* * * * * *
12419831 GGAAGATGAATCTGTTCCATTCTTCTTTCAGGGAGATAAGAATCGAGAGATCTTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAG-ATCAAGAGATCTTT
* * * *
12419886 GTAAAACGGATCTGCTCCGCTCTTCTTTCAGGGAGATAGGATCCA-AG------
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
* * * * * ** *
12419933 GGAAGACGAATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* ** * * * *
12419988 AGAAAACATATTTGCT-CATCTCTTTTTTTAGGGAGATAAGATCCA-AG------
1 GGAAAACGGATCTGCTCCA-CTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
** * * * * *
12420035 GGAAGAA-TAATCTGCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTA
1 GGAA-AACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
** * * * * ** *
12420090 AAAAAACGAATCTACTCCTCTATTCTTTCAGGGAGATAAGACTTTAGAAATCTTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* * * * *
12420145 GTAAAACGGATATGCTCCACTATTCTTTCAGGGAGATAAAATCCA-AG------
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
* * * * * * * *
12420192 GGAAGATGAATCTGCTTCACTCTTCTTTCAAGGAGATAAGACTCGAGAAATCTTC
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* * * * * *
12420247 GTAAAATGGATATGCTCCACTCTACTTTCGGGGAGATAAGATCCA-AG--C---
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
* * * * * *
12420295 -GAAGATGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATATTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* * * * * * *
12420349 GTAAAATGGATCT-CTTTCACTCTTCTTTAAGAGAGATATGATCCA-AG------
1 GGAAAACGGATCTGC-TCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
* * * * * *
12420396 GGAAAACGAATATGTTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTT
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGA-TCAAGAGATCTTT
* * * *
12420451 GGAAAATGGATATACTCCACTATTCTTTCAGGGAGATAAGATC
1 GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATC
12420494 CAAGGGAAGA
Statistics
Matches: 522, Mismatches: 134, Indels: 109
0.68 0.18 0.14
Matches are distributed among these distances:
47 189 0.36
48 22 0.04
49 7 0.01
51 1 0.00
53 8 0.02
54 24 0.05
55 271 0.52
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (54 bp):
GGAAAACGGATCTGCTCCACTCTTCTTTCAGGGAGATAAGATCAAGAGATCTTT
Found at i:12419855 original size:102 final size:102
Alignment explanation
Indices: 12419532--12420130 Score: 716
Period size: 102 Copynumber: 5.9 Consensus size: 102
12419522 CTTAATGGGA
* * * * *
12419532 AATCTGCTCCACTCTTCTTTTAGGGAGATAAGATTCGAGAGATATTTGGAAAACGAATATGCT-C
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
*
12419596 ATCTCTTCTATCAGGGAGATAAGATCCAAGGGAAGACG
66 A-CTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
* * * * *
12419634 AATCTGCTCCATTCTTTTTTCAGGGAGATAAGACTCGAAAAATCTTTGTAAAAACGGATTTGCTC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTG-GAAAACGGATATGCTC
*
12419699 CACTATTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
65 CACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
* * * *
12419737 AATCTACTCCACTCTTCCTTCAGGGAGATAAGACTCAAGAGATCTTTGGAAAACGGATATGCTCC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
* * *
12419802 ACTCTTCTTTCATGGATATAAGATCCAAGGGAAGATG
66 ACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
* * * * * *
12419839 AATCTGTTCCATTCTTCTTTCAGGGAGATAAGAATCGAGAGATCTTTGTAAAACGGATCTGCTCC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
* *
12419904 GCTCTTCTTTCAGGGAGATAGGATCCAAGGGAAGACG
66 ACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
* * * * * ** *
12419941 AATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTTAGAAAACATATTTGCT-C
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
* * **
12420005 ATCTCTTTTTTTAGGGAGATAAGATCCAAGGGAAGAAT
66 A-CTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
* * *** * * *
12420043 AATCTGCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAAACGAATCTACTCC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
* *
12420108 TCTATTCTTTCAGGGAGATAAGA
66 ACTCTTCTTTCAGGGAGATAAGA
12420131 CTTTAGAAAT
Statistics
Matches: 424, Mismatches: 69, Indels: 8
0.85 0.14 0.02
Matches are distributed among these distances:
101 1 0.00
102 333 0.79
103 88 0.21
104 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (102 bp):
AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGGAAAACGGATATGCTCC
ACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGACG
Found at i:12419890 original size:205 final size:205
Alignment explanation
Indices: 12419532--12420130 Score: 803
Period size: 204 Copynumber: 2.9 Consensus size: 205
12419522 CTTAATGGGA
* * *
12419532 AATCTGCTCCACTCTTCTTTTAGGGAGATAAGATTCGAGAGATATTTGGAAAACGAATATGCTCA
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAGATCTTTGGAAAACGAATATGCTCA
* * *
12419597 TCTCTTCTATCAGGGAGATAAGATCCAAGGGAAGACGAATCTGCTCCATTCTTTTTTCAGGGAGA
66 TCTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTCCATTCTTCTTTCAGGGAGA
* *
12419662 TAAGACTCGAAAAATCTTTGTAAAAACGGATTTGCTCCACTATTCTTTCAGGGAGATAAGATCCA
131 TAAGACTCGAGAAATCTTTGTAAAAACGGATCTGCTCCACTATTCTTTCAGGGAGATAAGATCCA
12419727 AGGGAAGACG
196 AGGGAAGACG
* * * *
12419737 AATCTACTCCACTCTTCCTTCAGGGAGATAAGACTCAAGAGATCTTTGGAAAACGGATATGCTCC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAGATCTTTGGAAAACGAATATGCT-C
* * *
12419802 A-CTCTTCTTTCATGGATATAAGATCCAAGGGAAGATGAATCTGTTCCATTCTTCTTTCAGGGAG
65 ATCTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTCCATTCTTCTTTCAGGGAG
* * * * *
12419866 ATAAGAATCGAGAGATCTTTGT-AAAACGGATCTGCTCCGCTCTTCTTTCAGGGAGATAGGATCC
130 ATAAGACTCGAGAAATCTTTGTAAAAACGGATCTGCTCCACTATTCTTTCAGGGAGATAAGATCC
12419930 AAGGGAAGACG
195 AAGGGAAGACG
* * * * * * *
12419941 AATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTTAGAAAAC-ATATTTGCTC
1 AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAGATCTTTGGAAAACGA-ATATGCTC
* * * * *
12420005 ATCTCTTTTTTTAGGGAGATAAGATCCAAGGGAAGAAT-AATCTGCTCCACTATTCTTTCAGAGA
65 ATCTCTTCTTTCAGGGAGATAAGATCCAAGGGAAG-ATGAATCTGCTCCATTCTTCTTTCAGGGA
** * * *
12420069 GATAAGACTCGAGAAATC-TTAAAAAAACGAATCTACTCCTCTATTCTTTCAGGGAGATAAGA
129 GATAAGACTCGAGAAATCTTTGTAAAAACGGATCTGCTCCACTATTCTTTCAGGGAGATAAGA
12420131 CTTTAGAAAT
Statistics
Matches: 341, Mismatches: 48, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
203 4 0.01
204 201 0.59
205 134 0.39
206 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (205 bp):
AATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAGATCTTTGGAAAACGAATATGCTCA
TCTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTCCATTCTTCTTTCAGGGAGA
TAAGACTCGAGAAATCTTTGTAAAAACGGATCTGCTCCACTATTCTTTCAGGGAGATAAGATCCA
AGGGAAGACG
Found at i:12420152 original size:259 final size:258
Alignment explanation
Indices: 12419853--12420344 Score: 684
Period size: 259 Copynumber: 1.9 Consensus size: 258
12419843 TGTTCCATTC
* * * *
12419853 TTCTTTCAGGGAGATAAGAATCGAGAGATCTTTGTAAAACGGATCTGCTCCGCTCTTCTTTCAGG
1 TTCTTTCAGGGAGATAAGAATCGAGAAATCTTTGTAAAACGGATATGCTCCACTATTCTTTCAGG
** * * *
12419918 GAGATAGGATCCAAGGGAAGACGAATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAA
66 GAGATAAAATCCAAGGGAAGACGAATATGCTCCACTATTCTTTCAAGGAGATAAGACTCGAGAAA
* ** * *
12419983 TCTTTAGAAAACAT-ATTTGCT-CATCTCTTTTTTTAGGGAGATAAGATCCAAGGGAAGAAT-AA
131 TC-TTAGAAAA-ATGATATGCTCCA-CTCTACTTTCAGGGAGATAAGATCCAAGCGAAG-ATGAA
12420045 TCTGCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAAACGAATCTACTCCTC
192 TCTGCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAAACGAATCTACTCCTC
12420110 TA
257 TA
* **
12420112 TTCTTTCAGGGAGATAAGACTTTAGAAATCTTTGTAAAACGGATATGCTCCACTATTCTTTCAGG
1 TTCTTTCAGGGAGATAAGAATCGAGAAATCTTTGTAAAACGGATATGCTCCACTATTCTTTCAGG
* * * *
12420177 GAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAAGGAGATAAGACTCGAGAAA
66 GAGATAAAATCCAAGGGAAGACGAATATGCTCCACTATTCTTTCAAGGAGATAAGACTCGAGAAA
* * *
12420242 TCTTCGTAAAATGGATATGCTCCACTCTACTTTCGGGGAGATAAGATCCAAGCGAAGATGAATCT
131 TCTTAGAAAAAT-GATATGCTCCACTCTACTTTCAGGGAGATAAGATCCAAGCGAAGATGAATCT
* *
12420307 GCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAAT
195 GCTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAAT
12420345 ATTTGTAAAA
Statistics
Matches: 203, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
257 2 0.01
258 8 0.04
259 191 0.94
260 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (258 bp):
TTCTTTCAGGGAGATAAGAATCGAGAAATCTTTGTAAAACGGATATGCTCCACTATTCTTTCAGG
GAGATAAAATCCAAGGGAAGACGAATATGCTCCACTATTCTTTCAAGGAGATAAGACTCGAGAAA
TCTTAGAAAAATGATATGCTCCACTCTACTTTCAGGGAGATAAGATCCAAGCGAAGATGAATCTG
CTCCACTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAAACGAATCTACTCCTCTA
Found at i:12420198 original size:361 final size:360
Alignment explanation
Indices: 12419734--12420491 Score: 995
Period size: 361 Copynumber: 2.1 Consensus size: 360
12419724 CCAAGGGAAG
* * *
12419734 ACGAATCTACTCCACTCTTCCTTCAGGGAGATAAGACTCAAGAGATCTTTGGAAAACGGATATGC
1 ACGAATCTACTCCACTATTCTTTCAGGGAGATAAGACTCAAGAAATCTTTGGAAAACGGATATGC
* * * * * *
12419799 TCCACTCTTCTTTCATGGATATAAGATCCAAGGGAAGATGAATCTG-TTCCATTCTTCTTTCAGG
66 TCCACTATTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAATCTGCTT-CACTCTTCTTTCAAG
* * * * * *
12419863 GAGATAAGAATCGAGAGATCTTTGTAAAACGGATCTGCTCCGCTCTTCTTTCAGGGAGATAGGAT
130 GAGATAAGAATCGAGAAATCTTCGTAAAACGGATATGCTCCACTCTACTTTCAGGGAGATAAGAT
* * * *
12419928 CCAAGGGAAGACGAATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTTAGAAA
195 CCAAGCGAAGACGAATATGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATATTT-GAAA
* * * * *
12419993 ACAT-AT-T-TGCTCATCTCTTTTTTTAGGGAGATAAGATCCAAGGGAAGAA-TAATCTGCTCCA
259 A-ATGATCTCT-CTCA-CTCTTCTTTAAGAGAGATAAGATCCAAGGGAA-AACGAATATGCTCCA
12420054 CTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAA
320 CTATTCTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAA
* ** *
12420095 ACGAATCTACTCCTCTATTCTTTCAGGGAGATAAGACTTTAGAAATCTTTGTAAAACGGATATGC
1 ACGAATCTACTCCACTATTCTTTCAGGGAGATAAGACTCAAGAAATCTTTGGAAAACGGATATGC
12420160 TCCACTATTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAAGG
66 TCCACTATTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAAGG
* * *
12420225 AGATAAGACTCGAGAAATCTTCGTAAAATGGATATGCTCCACTCTACTTTCGGGGAGATAAGATC
131 AGATAAGAATCGAGAAATCTTCGTAAAACGGATATGCTCCACTCTACTTTCAGGGAGATAAGATC
* * * *
12420290 CAAGCGAAGATGAATCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATATTTGTAAAA
196 CAAGCGAAGACGAATATGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATATTTGAAAAA
* * * *
12420355 TGGATCTCTTTCACTCTTCTTTAAGAGAGATATGATCCAAGGGAAAACGAATATGTTCCACTCTT
261 T-GATCTCTCTCACTCTTCTTTAAGAGAGATAAGATCCAAGGGAAAACGAATATGCTCCACTATT
* * ***
12420420 CTTTTAGGGAGATAAGACTCGAGAAATCTTTGGAAA
325 CTTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAA
* * *
12420456 ATGGATATACTCCACTATTCTTTCAGGGAGATAAGA
1 ACGAATCTACTCCACTATTCTTTCAGGGAGATAAGA
12420492 TCCAAGGGAA
Statistics
Matches: 343, Mismatches: 48, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
359 2 0.01
360 6 0.02
361 328 0.96
362 6 0.02
363 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (360 bp):
ACGAATCTACTCCACTATTCTTTCAGGGAGATAAGACTCAAGAAATCTTTGGAAAACGGATATGC
TCCACTATTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAAGG
AGATAAGAATCGAGAAATCTTCGTAAAACGGATATGCTCCACTCTACTTTCAGGGAGATAAGATC
CAAGCGAAGACGAATATGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATATTTGAAAAA
TGATCTCTCTCACTCTTCTTTAAGAGAGATAAGATCCAAGGGAAAACGAATATGCTCCACTATTC
TTTCAGAGAGATAAGACTCGAGAAATCTTAAAAAA
Found at i:12420227 original size:102 final size:102
Alignment explanation
Indices: 12420112--12420641 Score: 638
Period size: 102 Copynumber: 5.2 Consensus size: 102
12420102 TACTCCTCTA
* ** * *
12420112 TTCTTTCAGGGAGATAAGACTTTAGAAATCTTTGTAAAACGGATATGCTCCACTATTCTTTCAGG
1 TTCTTTCAAGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCACTCTTCTTTCAGG
* *
12420177 GAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTC
66 GAGATAAGATCCAAGGGAAGACGAATCTGCTTCACTC
* * *
12420214 TTCTTTCAAGGAGATAAGACTCGAGAAATCTTCGTAAAATGGATATGCTCCACTCTACTTTCGGG
1 TTCTTTCAAGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCACTCTTCTTTCAGG
* * *
12420279 GAGATAAGATCCAAGCGAAGATGAATCTGCTCCACTC
66 GAGATAAGATCCAAGGGAAGACGAATCTGCTTCACTC
* * * * *
12420316 TTCTTTCAGGGAGATAAGACTCGAGAAATATTTGTAAAATGGATCT-CTTTCACTCTTCTTTAAG
1 TTCTTTCAAGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGC-TCCACTCTTCTTTCAG
* * * *
12420380 AGAGATATGATCCAAGGGAAAACGAATATG-TTCCACTC
65 GGAGATAAGATCCAAGGGAAGACGAATCTGCTT-CACTC
* * * * *
12420418 TTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGGAAAATGGATATACTCCACTATTCTTTCAGG
1 TTCTTTCAAGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCACTCTTCTTTCAGG
* *
12420483 GAGATAAGATCCAAGGGAAGAAGAAATATGC-TCTACTC
66 GAGATAAGATCCAAGGGAAGACG-AATCTGCTTC-ACTC
* * * * ** *
12420521 TTTTTTCAA-GAGGATAAGACTTGATAAATCTTTGGAAAATAAATATGCTCCACTCTTCTTTCAA
1 TTCTTTCAAGGA-GATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCACTCTTCTTTCAG
*
12420585 GGAGATAAGATCCAAGGGAAGACGAATCTGCTCCACTC
65 GGAGATAAGATCCAAGGGAAGACGAATCTGCTTCACTC
12420623 TTCTTTC-AGGTAGATAAGA
1 TTCTTTCAAGG-AGATAAGA
12420642 TCCAAGGGAA
Statistics
Matches: 367, Mismatches: 51, Indels: 20
0.84 0.12 0.05
Matches are distributed among these distances:
101 3 0.01
102 276 0.75
103 88 0.24
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (102 bp):
TTCTTTCAAGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCACTCTTCTTTCAGG
GAGATAAGATCCAAGGGAAGACGAATCTGCTTCACTC
Found at i:12420275 original size:157 final size:154
Alignment explanation
Indices: 12419933--12420691 Score: 508
Period size: 157 Copynumber: 4.9 Consensus size: 154
12419923 AGGATCCAAG
* * * *
12419933 GGAAGACGAATATGCTCCATTATTCTTTCAGGGAGATAAGACTCGGGAAATCTTTAGAAAAC-AT
1 GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACT--TGAAATCTTT-GAAAACGA-
* * * * *
12419997 ATTTGCT-CATCTCTTTTTTTAGGGAGATAAGATCCAAGGGAAGAAT-AATCTGCTCCACTATTC
62 ATATGCTCCA-CTCTTCTTTCAGGGAGATAAGATCCAAGGGAAG-ATGAATCTGCTTCACTCTTC
12420060 TTTC-AGAGAGATAAGACTCGAGAAATCTTA
125 TTTCAAG-GAGATAAGACTCGAGAAATCTTA
** * * * * *
12420090 AAAAAACGAATCTACTCCTCTATTCTTTCAGGGAGATAAGACTTTAGAAATCTTTGTAAAACGGA
1 GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGAC-TT-GAAATCTTTG-AAAACGAA
* *
12420155 TATGCTCCACTATTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTT
63 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTT
*
12420220 CAAGGAGATAAGACTCGAGAAATCTTC
128 CAAGGAGATAAGACTCGAGAAATCTTA
* * * * * ** * * * *
12420247 GTAAAATGGATATGCTCCACTCTACTTTCGGGGAGATAAGA--TCCAAGC---GAAGATGAATCT
1 GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACTTGAAATCTTTGAAAACGAATAT
* * * * *
12420307 GCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATATTTGTAAAATGGATCT-CTTTCACTC
66 GCTCCACTCTTCTTTCAGGGAGATAAGA-TC----CA-A--GGGAAGATGAATCTGC-TTCACTC
* * *
12420371 TTCTTT-AAGAGAGATATGA-TC---CAA----G
122 TTCTTTCAAG-GAGATAAGACTCGAGAAATCTTA
* * * * *
12420396 GGAAAACGAATATGTTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGGAAAATGGA
1 GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACT--TGAAATCTTT-GAAAACGAA
* * * * *
12420461 TATACTCCACTATTCTTTCAGGGAGATAAGATCCAAGGGAAGAAGAAATATGC-TCTACTCTTTT
63 TATGCTCCACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATG-AATCTGCTTC-ACTCTTCT
* * *
12420525 TTCAA-GAGGATAAGACTTGATAAATCTTT
126 TTCAAGGA-GATAAGACTCGAGAAATCTTA
** * ** ** * *
12420554 GGAAAATAAATATGCTCCACTCTTCTTTCAAGGAGATAAGA--TCCAA---GGGAAGACGAATCT
1 GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACTTGAAATCTTTGAAAACGAATAT
* * * * * *
12420614 GCTCCACTCTTCTTTCAGGTAGATAAGATCCAAGGGAAGACGAATCTGCTCCACTATTCTTTTAG
66 GCTCCACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAA
12420679 GGAGATAAGACTC
131 GGAGATAAGACTC
12420692 AAAATTAATT
Statistics
Matches: 465, Mismatches: 97, Indels: 88
0.72 0.15 0.14
Matches are distributed among these distances:
149 100 0.22
150 70 0.15
151 5 0.01
152 1 0.00
153 8 0.02
154 6 0.01
155 1 0.00
156 11 0.02
157 222 0.48
158 41 0.09
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (154 bp):
GGAAAACGAATATGCTCCACTCTTCTTTCAGGGAGATAAGACTTGAAATCTTTGAAAACGAATAT
GCTCCACTCTTCTTTCAGGGAGATAAGATCCAAGGGAAGATGAATCTGCTTCACTCTTCTTTCAA
GGAGATAAGACTCGAGAAATCTTA
Found at i:12421099 original size:62 final size:62
Alignment explanation
Indices: 12420808--12421101 Score: 347
Period size: 62 Copynumber: 4.7 Consensus size: 62
12420798 GGAGTTGAGA
* * * * *
12420808 ATAACAAAATGTTGACTTCTCTTCACAAGGAAGTCAATTATTAACTCTATTGGGGATTCAGGG
1 ATAACAAAA-GTTTACTTCTCTTCACAAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGG
* * * * *
12420871 ATACCAAAAATTTATTTCTCTTCACAAGGAAGTCAAGTATTGACTCTACTAGGGAGTTAGGG
1 ATAACAAAAGTTTACTTCTCTTCACAAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGG
* * * *
12420933 ATAACAAAGGTTTACTTTTCTTCACAAGGAA-TGCAAGTATTAACTCTACTGGGGAGTCAGGT
1 ATAACAAAAGTTTACTTCTCTTCACAAGGAAGT-CAAGTATTGACTCTACTGGGGAGTCAGGG
* * * * *
12420995 ATAACAAAGGTTTACTTCTCTTTACGAGGAAGTCAAGTATTGACTCCACTGGGGAGTCATGG
1 ATAACAAAAGTTTACTTCTCTTCACAAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGG
* * * * *
12421057 ATAACAAAAGTTGAATTCTCATCACGAGGAAGTCAAGGATTGACT
1 ATAACAAAAGTTTACTTCTCTTCACAAGGAAGTCAAGTATTGACT
12421102 TCTCTTTATA
Statistics
Matches: 197, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
61 1 0.01
62 187 0.95
63 9 0.05
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (62 bp):
ATAACAAAAGTTTACTTCTCTTCACAAGGAAGTCAAGTATTGACTCTACTGGGGAGTCAGGG
Found at i:12421167 original size:91 final size:91
Alignment explanation
Indices: 12421008--12421185 Score: 257
Period size: 91 Copynumber: 2.0 Consensus size: 91
12420998 ACAAAGGTTT
* * *
12421008 ACTTCTCTTTACGAGGAAGTCAAGTATTGACTCCACTGGGGAGTCATGGATAACAAAAGTTGAAT
1 ACTTCTCTTTACAAGGAAGTCAAGTATTGACTCCACTAGGGAGTCAGGGATAACAAAAGTTGAAT
*
12421073 TCTCATCACGAGGAAGTCAAGGATTG
66 TCTCATCACGAGAAAGTCAAGGATTG
* ** * * *
12421099 ACTTCTCTTTATAAGGAAGTCAAGTATTGACTCTTCTAGGGAGTCAGGGATAACAAAGGTTTACT
1 ACTTCTCTTTACAAGGAAGTCAAGTATTGACTCCACTAGGGAGTCAGGGATAACAAAAGTTGAAT
*
12421164 TCTCTTCACGAGAAAGTCAAGG
66 TCTCATCACGAGAAAGTCAAGG
12421186 GTTAACTCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 76 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.28
Consensus pattern (91 bp):
ACTTCTCTTTACAAGGAAGTCAAGTATTGACTCCACTAGGGAGTCAGGGATAACAAAAGTTGAAT
TCTCATCACGAGAAAGTCAAGGATTG
Found at i:12421182 original size:62 final size:61
Alignment explanation
Indices: 12421115--12421318 Score: 248
Period size: 62 Copynumber: 3.3 Consensus size: 61
12421105 CTTTATAAGG
** * ** *
12421115 AAGTCAAGTATTGACTCTTCTAGGGAGTCAGGGATAACAAAGGTTTACTTCTCTTCACGAGA
1 AAGTCAAGGGTTGACTCTACT-GGGAGTCAGAAATAACAAAGGTTAACTTCTCTTCACGAGA
* * * *
12421177 AAGTCAAGGGTTAACTCTACTGGGGAGTCAGAAATAACAAAGGTTGACTTTTCTTCACGAGT
1 AAGTCAAGGGTTGACTCTACT-GGGAGTCAGAAATAACAAAGGTTAACTTCTCTTCACGAGA
* * *
12421239 AAGTCAAGGGTTGACTATACTGGGAGTCAGAAATAACAAAAGTTAACTTCT-TCTCACGAGG
1 AAGTCAAGGGTTGACTCTACTGGGAGTCAGAAATAACAAAGGTTAACTTCTCT-TCACGAGA
*
12421300 AATTCAAGGGTTGACTCTA
1 AAGTCAAGGGTTGACTCTA
12421319 GGAAACAAGA
Statistics
Matches: 123, Mismatches: 18, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
60 1 0.01
61 51 0.41
62 71 0.58
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (61 bp):
AAGTCAAGGGTTGACTCTACTGGGAGTCAGAAATAACAAAGGTTAACTTCTCTTCACGAGA
Found at i:12421236 original size:153 final size:153
Alignment explanation
Indices: 12420958--12421254 Score: 409
Period size: 153 Copynumber: 1.9 Consensus size: 153
12420948 TTTTCTTCAC
* * *
12420958 AAGGAATGCAAGTATTAACTCTACTGGGGAGTCAGGTATAACAAAGGTTTACTTCTCTTTACGAG
1 AAGGAATGCAAGTATTAACTCTACTAGGGAGTCAGGGATAACAAAGGTTTACTTCTCTTCACGAG
* * * *
12421023 GAAGTCAAGTATTGACTCCACTGGGGAGTCATGGATAACAAAAGTTGAATTCTCATCACGAGGAA
66 AAAGTCAAGGATTAACTCCACTGGGGAGTCATGAATAACAAAAGTTGAATTCTCATCACGAGGAA
12421088 GTCAAGGATTGACTTCTCTTTAT
131 GTCAAGGATTGACTTCTCTTTAT
* *
12421111 AAGGAA-GTCAAGTATTGACTCTTCTAGGGAGTCAGGGATAACAAAGGTTTACTTCTCTTCACGA
1 AAGGAATG-CAAGTATTAACTCTACTAGGGAGTCAGGGATAACAAAGGTTTACTTCTCTTCACGA
* * * * * * *
12421175 GAAAGTCAAGGGTTAACTCTACTGGGGAGTCA-GAAATAACAAAGGTTGACTTTTCTTCACGAGT
65 GAAAGTCAAGGATTAACTCCACTGGGGAGTCATG-AATAACAAAAGTTGAATTCTCATCACGAGG
*
12421239 AAGTCAAGGGTTGACT
129 AAGTCAAGGATTGACT
12421255 ATACTGGGAG
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
152 2 0.02
153 123 0.98
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (153 bp):
AAGGAATGCAAGTATTAACTCTACTAGGGAGTCAGGGATAACAAAGGTTTACTTCTCTTCACGAG
AAAGTCAAGGATTAACTCCACTGGGGAGTCATGAATAACAAAAGTTGAATTCTCATCACGAGGAA
GTCAAGGATTGACTTCTCTTTAT
Found at i:12423354 original size:2 final size:2
Alignment explanation
Indices: 12423347--12423408 Score: 92
Period size: 2 Copynumber: 32.0 Consensus size: 2
12423337 TCAACTTTAT
12423347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
* *
12423388 TA TA TG TA TG TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
12423409 ATCACCTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
1 2 0.04
2 52 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12423572 original size:99 final size:98
Alignment explanation
Indices: 12423398--12423601 Score: 264
Period size: 99 Copynumber: 2.1 Consensus size: 98
12423388 TATATGTATG
** * *
12423398 TATATATTATAATCACCTTTATAGGCTAGTTGAATCTTATCCATAAAGACAGGGCGTTTAACCAA
1 TATATATTATAATCACCTTTATAGGCTAGCAGAATATTATCCATAAAGACAGGGCATTTAACCAA
* *
12423463 TTGCTCTAGAGGGACAACTCAAGCTTTATTGTA
66 TTACTCTAGAGGAACAACTCAAGCTTTATTGTA
* * * * *
12423496 TATATATTATTATTACCTTTATAAGTCTAGCAGAATATTATCCTTAAAGACGGGGCATTTAACCA
1 TATATATTATAATCACCTTTAT-AGGCTAGCAGAATATTATCCATAAAGACAGGGCATTTAACCA
* **
12423561 ATTACTTTAGAGGAACAGTTCAAGCTTTATTGTA
65 ATTACTCTAGAGGAACAACTCAAGCTTTATTGTA
*
12423595 TACATAT
1 TATATAT
12423602 AATATTATAT
Statistics
Matches: 90, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
98 20 0.22
99 70 0.78
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.36
Consensus pattern (98 bp):
TATATATTATAATCACCTTTATAGGCTAGCAGAATATTATCCATAAAGACAGGGCATTTAACCAA
TTACTCTAGAGGAACAACTCAAGCTTTATTGTA
Found at i:12424910 original size:17 final size:17
Alignment explanation
Indices: 12424888--12424929 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
12424878 CATTTGCTTT
12424888 AATCCTTATTCCTTAAA
1 AATCCTTATTCCTTAAA
12424905 AATCCTTATTCCTTAAA
1 AATCCTTATTCCTTAAA
*
12424922 GATCCTTA
1 AATCCTTA
12424930 CACTTTGGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.40
Consensus pattern (17 bp):
AATCCTTATTCCTTAAA
Found at i:12451205 original size:3 final size:3
Alignment explanation
Indices: 12451199--12451272 Score: 60
Period size: 3 Copynumber: 25.0 Consensus size: 3
12451189 CAACAACAAC
* * * * * * *
12451199 AAT AAT AAT AGT AAT AGT AGT AGT AGT AAT AAT AAT AAT AAT TAT TAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
12451247 TAT TAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
12451273 GGTTGAAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:12454377 original size:28 final size:28
Alignment explanation
Indices: 12454344--12454417 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
12454334 CCAGGGCTTG
* *
12454344 GGGTATTTTAGGTCATTTCACACTTCAT
1 GGGTATTTTAGGTCATTTCACACTTAAA
* * *
12454372 GGGTATTTT-GGTCATTTTATAGTTAAA
1 GGGTATTTTAGGTCATTTCACACTTAAA
12454399 GGGTATTTTA-GTCATTTCA
1 GGGTATTTTAGGTCATTTCA
12454418 TTCCGTCCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 30 0.77
28 9 0.23
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.46
Consensus pattern (28 bp):
GGGTATTTTAGGTCATTTCACACTTAAA
Found at i:12467384 original size:36 final size:35
Alignment explanation
Indices: 12467335--12467437 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 35
12467325 TTGAGCCTAT
12467335 ACAAGGAATTACCAGCAGTGACTGAACCTACCAGAG
1 ACAAGGAATTACCAGCAGTGACTGAACCT-CCAGAG
* * *
12467371 ATAAGGAATTACCAGTCGGTG-CTGAACCT----AT
1 ACAAGGAATTACCAG-CAGTGACTGAACCTCCAGAG
*
12467402 ACAAGGAATTACCAGCAGAGACTGAACCTGCCAGAG
1 ACAAGGAATTACCAGCAGTGACTGAACCT-CCAGAG
12467438 TCTTCAGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
30 3 0.06
31 23 0.43
36 23 0.43
37 4 0.08
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (35 bp):
ACAAGGAATTACCAGCAGTGACTGAACCTCCAGAG
Found at i:12467411 original size:31 final size:31
Alignment explanation
Indices: 12467306--12467416 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 31
12467296 TTAGGCCCAT
* * * *
12467306 AAGGAAATACCAGTTGGTGTTGAGCCTATAC
1 AAGGAATTACCAGTCGGTGCTGAACCTATAC
* * *
12467337 AAGGAATTACCAG-CAGTGACTGAACCTACCAGAGAT
1 AAGGAATTACCAGTCGGTG-CTGAACCT-----ATAC
12467373 AAGGAATTACCAGTCGGTGCTGAACCTATAC
1 AAGGAATTACCAGTCGGTGCTGAACCTATAC
12467404 AAGGAATTACCAG
1 AAGGAATTACCAG
12467417 CAGAGACTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 14
0.72 0.11 0.16
Matches are distributed among these distances:
30 3 0.05
31 33 0.52
36 23 0.37
37 4 0.06
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (31 bp):
AAGGAATTACCAGTCGGTGCTGAACCTATAC
Found at i:12467412 original size:67 final size:67
Alignment explanation
Indices: 12467304--12467437 Score: 214
Period size: 67 Copynumber: 2.0 Consensus size: 67
12467294 CCTTAGGCCC
* * * *
12467304 ATAAGGAAATACCAGTTGGTGTTGAGCCTATACAAGGAATTACCAGCAGTGACTGAACCTACCAG
1 ATAAGGAAATACCAGTCGGTGCTGAACCTATACAAGGAATTACCAGCAGAGACTGAACCTACCAG
12467369 AG
66 AG
* *
12467371 ATAAGGAATTACCAGTCGGTGCTGAACCTATACAAGGAATTACCAGCAGAGACTGAACCTGCCAG
1 ATAAGGAAATACCAGTCGGTGCTGAACCTATACAAGGAATTACCAGCAGAGACTGAACCTACCAG
12467436 AG
66 AG
12467438 TCTTCAGTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (67 bp):
ATAAGGAAATACCAGTCGGTGCTGAACCTATACAAGGAATTACCAGCAGAGACTGAACCTACCAG
AG
Found at i:12471680 original size:66 final size:67
Alignment explanation
Indices: 12471559--12471691 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 67
12471549 CTTTAGGTCT
* * *
12471559 ATAAGGAATTTCCAATCGGTGTTGAACCTATACAAGGAATTACCAGCAGCGACTGAACCTGCCAG
1 ATAAGGAATTACCAATCGGTGTTGAACCTATACAAGGAATTACAAGCAGCAACTGAACCTGCCAG
12471624 AG
66 AG
* *
12471626 ATAATGAATTACCAGTCGGTGTTGAACCTA-ACAAGGAATTACAAGCAGCAACTGAACCTGCCAG
1 ATAAGGAATTACCAATCGGTGTTGAACCTATACAAGGAATTACAAGCAGCAACTGAACCTGCCAG
12471690 AG
66 AG
12471692 TCTTCTGTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
66 34 0.56
67 27 0.44
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (67 bp):
ATAAGGAATTACCAATCGGTGTTGAACCTATACAAGGAATTACAAGCAGCAACTGAACCTGCCAG
AG
Found at i:12473364 original size:7 final size:7
Alignment explanation
Indices: 12473352--12473393 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
12473342 TTCAACCAAA
12473352 GTCAACG
1 GTCAACG
12473359 GTCAACG
1 GTCAACG
12473366 GTCAGACCG
1 GTCA-A-CG
*
12473375 GTCAA-A
1 GTCAACG
12473381 GTCAACG
1 GTCAACG
12473388 GTCAAC
1 GTCAAC
12473394 AGATTGACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
6 5 0.17
7 17 0.57
8 2 0.07
9 6 0.20
ACGTcount: A:0.31, C:0.29, G:0.26, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:12473412 original size:30 final size:29
Alignment explanation
Indices: 12473348--12473415 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
12473338 CTTATTCAAC
* *
12473348 CAAAGTCAACGGTCAACGGTCAGACCGGT
1 CAAAGTCAACGGTCAACGATCAGACCGAT
*
12473377 CAAAGTCAACGGTCAACAGAT-TGACTCGAT
1 CAAAGTCAACGGTCAAC-GATCAGAC-CGAT
12473407 CAAAGTCAA
1 CAAAGTCAA
12473416 TAGTTGACCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 20 0.59
30 14 0.41
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.16
Consensus pattern (29 bp):
CAAAGTCAACGGTCAACGATCAGACCGAT
Found at i:12474853 original size:40 final size:40
Alignment explanation
Indices: 12474799--12474931 Score: 160
Period size: 40 Copynumber: 3.3 Consensus size: 40
12474789 AACTCTTTGA
*
12474799 CTGAGTA-CTGATACTTCTGAACTAGGGTATCGATATTATC
1 CTGAGTATC-GATACTTCTGAACTAGGGTATCGATACTATC
* * * *
12474839 CTGATTATCGATACTACTGAACTAGGGTATCCATACCATC
1 CTGAGTATCGATACTTCTGAACTAGGGTATCGATACTATC
* * * *
12474879 CTAAGTATTGATAATTCTGAACTAGGGTATCGATACTATG
1 CTGAGTATCGATACTTCTGAACTAGGGTATCGATACTATC
*
12474919 TTGAGTATCGATA
1 CTGAGTATCGATA
12474932 TAAAAAAATG
Statistics
Matches: 76, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 75 0.99
41 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (40 bp):
CTGAGTATCGATACTTCTGAACTAGGGTATCGATACTATC
Found at i:12480958 original size:15 final size:16
Alignment explanation
Indices: 12480928--12480958 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12480918 TTTTATGTTA
12480928 TTCTAGTTGTTATTGT
1 TTCTAGTTGTTATTGT
12480944 TTCTAGTTG-TATTGT
1 TTCTAGTTGTTATTGT
12480959 ATTTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.13, C:0.06, G:0.19, T:0.61
Consensus pattern (16 bp):
TTCTAGTTGTTATTGT
Found at i:12481197 original size:21 final size:21
Alignment explanation
Indices: 12481170--12481225 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
12481160 GAAGGAATGG
*
12481170 TAGTATCGATACTCTTAGACTA
1 TAGTATCGATACTCTGA-ACTA
*
12481192 -AGTATCGAAACTTCTGAACTA
1 TAGTATCGATAC-TCTGAACTA
12481213 TAGTATCGATACT
1 TAGTATCGATACT
12481226 ATCATGAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
TAGTATCGATACTCTGAACTA
Found at i:12502106 original size:3 final size:3
Alignment explanation
Indices: 12502100--12502127 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12502090 GAAGCCGGCA
12502100 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
12502128 ATGTTCACGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:12507350 original size:17 final size:17
Alignment explanation
Indices: 12507328--12507361 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12507318 AAGTAAATTG
* *
12507328 TTTTTACTATATAATAT
1 TTTTTAATATAAAATAT
12507345 TTTTTAATATAAAATAT
1 TTTTTAATATAAAATAT
12507362 AATCTTTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAATATAAAATAT
Found at i:12517455 original size:54 final size:54
Alignment explanation
Indices: 12517306--12517730 Score: 602
Period size: 54 Copynumber: 7.9 Consensus size: 54
12517296 CTCTATGTAC
* * * * *
12517306 TATCGGCACTAAGTGTGCAACCCACGGAATGCATCATATGTTAATGAATGATCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12517360 TATTGGCACTAATTGTGCAACCCAC--AATTCATCATATGTTGATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * *
12517412 TATCAGTACTAAGTGTACAACCCATGAAATTCATCATATGTTGATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12517466 TATCGGCACTAAGTGTACAACCCACAAAATTCATCATATGTTGATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* *
12517520 TATCGGCACTAAGTGTGCAACCCACGTAATTCATCATATGTTGATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12517574 TATCGGCACTAAGTGTGTAACCCACGGAATTTATCATATGTTGATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* *
12517628 TATCGGCACTAAGTGTGCAACCCACGAAATTCATTATATGTTGATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12517682 TATCGGCAATAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAAC
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAAC
12517731 AACAGTATTG
Statistics
Matches: 335, Mismatches: 34, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
52 41 0.12
54 294 0.88
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:12519666 original size:21 final size:21
Alignment explanation
Indices: 12519637--12519677 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12519627 GCATTCCATC
*
12519637 TTTTTGTTGAGCCT-GTATTT
1 TTTTTGTTGACCCTGGTATTT
12519657 TTTTTAGTTGACCCTGGTATT
1 TTTTT-GTTGACCCTGGTATT
12519678 ACACACTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.12, C:0.12, G:0.20, T:0.56
Consensus pattern (21 bp):
TTTTTGTTGACCCTGGTATTT
Found at i:12523779 original size:20 final size:17
Alignment explanation
Indices: 12523734--12523766 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12523724 GATGCAAATA
12523734 GTATCGATA-TATGAGG
1 GTATCGATACTATGAGG
12523750 GTATCGATACTATGAGG
1 GTATCGATACTATGAGG
12523767 AAGGTATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.30
Consensus pattern (17 bp):
GTATCGATACTATGAGG
Found at i:12524637 original size:26 final size:26
Alignment explanation
Indices: 12524605--12524698 Score: 80
Period size: 25 Copynumber: 3.8 Consensus size: 26
12524595 AGAAAAAACA
12524605 AAATAAAGTAAAAATATAATATATAT
1 AAATAAAGTAAAAATATAATATATAT
*
12524631 AAATAAA-TAAAAACA-AA-A-ATAT
1 AAATAAAGTAAAAATATAATATATAT
*
12524653 AATATTAAG--AAAATAT-ATATATAT
1 AA-ATAAAGTAAAAATATAATATATAT
12524677 --ATAAACGTATAAAATATAATAT
1 AAATAAA-GTA-AAAATATAATAT
12524699 TAAGAAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
21 4 0.07
22 13 0.24
23 6 0.11
24 6 0.11
25 14 0.26
26 11 0.20
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (26 bp):
AAATAAAGTAAAAATATAATATATAT
Found at i:12524670 original size:18 final size:17
Alignment explanation
Indices: 12524645--12524712 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 17
12524635 AAATAAAAAC
12524645 AAAAATATAATATTAAG
1 AAAAATATAATATTAAG
12524662 AAAATATATATATATATAAACG
1 AAAA-ATATA-ATAT-T-AA-G
12524684 TATAAAATATAATATTAAG
1 -A-AAAATATAATATTAAG
12524703 AAAAAATATA
1 -AAAAATATA
12524713 TATACATAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
17 4 0.09
18 13 0.30
19 6 0.14
20 3 0.07
21 3 0.07
22 5 0.12
23 6 0.14
24 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (17 bp):
AAAAATATAATATTAAG
Found at i:12524758 original size:2 final size:2
Alignment explanation
Indices: 12524746--12524798 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
12524736 TTAATACATC
* *
12524746 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA CA TA -A TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
12524788 -A GA TA TA TA TA
1 TA TA TA TA TA TA
12524799 ATAAAAATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 2 0.05
2 39 0.91
3 2 0.05
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (2 bp):
TA
Found at i:12524811 original size:25 final size:27
Alignment explanation
Indices: 12524763--12524813 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
12524753 ATATATATAT
* *
12524763 ATATATATATATACATAATGATATAAG
1 ATATATATATATACAAAATAATATAAG
12524790 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATACAAAATAATATAA
12524814 TATAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (27 bp):
ATATATATATATACAAAATAATATAAG
Found at i:12524852 original size:20 final size:20
Alignment explanation
Indices: 12524816--12524854 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12524806 TAATATAATA
*
12524816 TAAATAAAAAAGGAATATAG
1 TAAATAAAAAAGAAATATAG
12524836 TAAATAAATAAA-AAATATA
1 TAAATAAA-AAAGAAATATA
12524855 ATTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (20 bp):
TAAATAAAAAAGAAATATAG
Found at i:12526446 original size:110 final size:107
Alignment explanation
Indices: 12526189--12526447 Score: 312
Period size: 110 Copynumber: 2.4 Consensus size: 107
12526179 TGTATTGTTC
*
12526189 CGAGTCCAATATCCTC-CGTCGTGAAGTTGAAATTGGCTCTG--GAACTGAGAAATTGTTTATTG
1 CGAGTCCAATATCCTCGC-T-GTGAAGTTGAAATTGGCTCTGAAGAACTGAGAAATTATTTATTG
* *
12526251 ACAGCCAGCAGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCT
64 ACAACCAGCAGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
* * ** *
12526295 CGAGTTCAATATCCTTTGCTGTGAAGTTGAAATTGAATCTGAATGAAACTGA-AAAGTTATTTGT
1 CGAGTCCAATATCC-TCGCTGTGAAGTTGAAATTGGCTCTGAA-G-AACTGAGAAA-TTATTTAT
* *
12526359 TGACAATCAGTC-GCCCCTTCGTTATGAAGTTGAGCTTGTGTTGTCT
62 TGACAACCAG-CAGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
*
12526405 TGAGTCCAATATCACTCGCTGTGAAGTTGAAATTGGCTCTGAA
1 CGAGTCCAATATC-CTCGCTGTGAAGTTGAAATTGGCTCTGAA
12526448 ACTGGGAAGC
Statistics
Matches: 129, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
106 32 0.25
107 2 0.02
108 1 0.01
109 4 0.03
110 88 0.68
111 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (107 bp):
CGAGTCCAATATCCTCGCTGTGAAGTTGAAATTGGCTCTGAAGAACTGAGAAATTATTTATTGAC
AACCAGCAGCCCCTTCGCTATGAAGTTGAGCTTGTGTTGTCT
Found at i:12527295 original size:67 final size:66
Alignment explanation
Indices: 12527163--12527312 Score: 187
Period size: 68 Copynumber: 2.3 Consensus size: 66
12527153 AAGATATCTG
* * * * **
12527163 TTGTTTCATGAAAAACGGTCTCAAGGGAAATAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGA-
12527228 TT
65 TT
*
12527230 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTT-AGGAGAAATAAATTCAAAG
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGG-GAAATAAATTCAAAG
12527293 ATT
64 ATT
*
12527296 TTGTTTCAAGGGAAACT
1 TTGTTTCAAGAGAAACT
12527313 TGGAAATTGT
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
65 15 0.21
66 6 0.08
67 23 0.32
68 29 0.40
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:12527657 original size:106 final size:106
Alignment explanation
Indices: 12527462--12527707 Score: 269
Period size: 106 Copynumber: 2.3 Consensus size: 106
12527452 TATTGTTCCA
* * *
12527462 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGTTCTGGAACTAAGAAATTATTTGTTGACAGC
1 AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTATTTGTTGACAAC
* * *
12527527 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCG
66 CAGCCACCACTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
* * * ** *
12527568 AGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTCCGTC-GTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTATTTGTTGACAA
* * * * *
12527632 CCAGCCATCATTTCGTTGTGGAGTTGAACTTGTGTTGTCTCG
65 CCAGCCACCACTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
* * *
12527674 AGTGGCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT--C-CAATATCCTCCGTCGTGAAGTTAAAAT
12527708 CGCAGGTGGC
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
105 1 0.01
106 90 0.78
108 1 0.01
109 22 0.19
110 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTCCGTCGTGAAGTTAAAATTGGCTCTGAAACTAAGAAATTATTTGTTGACAAC
CAGCCACCACTTCGCTGTGAAGTTGAACTTGTGCTGTCTCG
Found at i:12528310 original size:32 final size:32
Alignment explanation
Indices: 12528274--12528365 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 32
12528264 CCCAAAGATG
* *
12528274 CCCCAATATTCGATGTTGAATCTCAAAAAATA
1 CCCCAACATTTGATGTTGAATCTCAAAAAATA
* * *
12528306 CCCCAACATTTGATGTTAAATCTAAAAAAATT
1 CCCCAACATTTGATGTTGAATCTCAAAAAATA
12528338 CCCCAACATTTGATGTTGAATCTTCAAA
1 CCCCAACATTTGATGTTGAATC-TCAAA
12528366 GATATTGTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 48 0.92
33 4 0.08
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (32 bp):
CCCCAACATTTGATGTTGAATCTCAAAAAATA
Found at i:12529366 original size:69 final size:69
Alignment explanation
Indices: 12529251--12529388 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 69
12529241 TGTCTCTCTC
* * * *
12529251 TTGATGGTCTATGATCTTCGAGTGGAGGGATTCAGTGATTTAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTAGGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
12529316 TCAT
66 TCAT
*
12529320 TTGATGCTCTAGGATCTTCGAGTGAAGTGG-TTCAGTGATTCGGAAATGATTGTGCTTGATCAAT
1 TTGATGCTCTAGGATCTTCGAGTGAAG-GGATTCAGTGATTCAGAAATGATTGTGCTTGATCAAT
12529384 CTCAT
65 CTCAT
12529389 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 61 0.97
70 2 0.03
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTAGGATCTTCGAGTGAAGGGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:12529494 original size:14 final size:13
Alignment explanation
Indices: 12529462--12529513 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
12529452 TTTTCTTCAA
*
12529462 TTTTC-CTTTGTT
1 TTTTCTCTTTTTT
*
12529474 TTTTCT-TTTTTA
1 TTTTCTCTTTTTT
12529486 TTTTCTCTTTGTTT
1 TTTTCTCTTT-TTT
12529500 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
12529513 T
1 T
12529514 CTCTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 15 0.44
13 7 0.21
14 12 0.35
ACGTcount: A:0.02, C:0.13, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:12529500 original size:24 final size:26
Alignment explanation
Indices: 12529461--12529519 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 26
12529451 CTTTTCTTCA
12529461 ATTTTC-CTTTGTTTTTTCTT-T-TTT
1 ATTTTCTCTTTGTTTTTT-TTCTCTTT
12529485 ATTTTCTCTTTG-TTTTTTTCTCTTT
1 ATTTTCTCTTTGTTTTTTTTCTCTTT
12529510 -TTTTCTCTTT
1 ATTTTCTCTTT
12529520 TTGTTCTGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
23 2 0.06
24 22 0.69
25 8 0.25
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.78
Consensus pattern (26 bp):
ATTTTCTCTTTGTTTTTTTTCTCTTT
Found at i:12529512 original size:10 final size:10
Alignment explanation
Indices: 12529497--12529526 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
12529487 TTTCTCTTTG
12529497 TTTTTTTCTC
1 TTTTTTTCTC
12529507 TTTTTTTCTC
1 TTTTTTTCTC
12529517 TTTTTGTTCT
1 TTTTT-TTCT
12529527 GATTGAATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:12529522 original size:26 final size:26
Alignment explanation
Indices: 12529441--12529524 Score: 75
Period size: 26 Copynumber: 3.2 Consensus size: 26
12529431 TATATGCATC
* *
12529441 TTGTTTTCTTCTTTTCTTCAATTTTC-CT
1 TTGTTTTTTTCTTTT-TT--ATTCTCTCT
*
12529469 TTG-TTTTTTCTTTTTTATTTTCTCT
1 TTGTTTTTTTCTTTTTTATTCTCTCT
*
12529494 TTGTTTTTTTCTCTTTTT-TTCTCTTT
1 TTGTTTTTTTCT-TTTTTATTCTCTCT
12529520 TTGTT
1 TTGTT
12529525 CTGATTGAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
24 6 0.12
25 5 0.10
26 21 0.42
27 15 0.30
28 3 0.06
ACGTcount: A:0.04, C:0.15, G:0.05, T:0.76
Consensus pattern (26 bp):
TTGTTTTTTTCTTTTTTATTCTCTCT
Found at i:12534249 original size:17 final size:17
Alignment explanation
Indices: 12534229--12534286 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
12534219 CAAAAATAGA
12534229 ATATTAACAAAAAATAT
1 ATATTAACAAAAAATAT
* *
12534246 ATATAAACGTATAAAATAT
1 ATATTAAC--AAAAAATAT
*
12534265 AATATTAAGAAAAAATAT
1 -ATATTAACAAAAAATAT
12534283 ATAT
1 ATAT
12534287 ACATAGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
17 11 0.33
18 8 0.24
19 8 0.24
20 6 0.18
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
ATATTAACAAAAAATAT
Found at i:12534282 original size:18 final size:18
Alignment explanation
Indices: 12534220--12534283 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
12534210 AAATAAAAAC
* *
12534220 AAAAATAGAATATTAACA
1 AAAAATATAATATTAAGA
*
12534238 AAAAATAT-ATATAAACGTA
1 AAAAATATAATATTAA-G-A
*
12534257 TAAAATATAATATTAAGA
1 AAAAATATAATATTAAGA
12534275 AAAAATATA
1 AAAAATATA
12534284 TATACATAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
17 6 0.16
18 16 0.43
19 9 0.24
20 6 0.16
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (18 bp):
AAAAATATAATATTAAGA
Found at i:12534374 original size:25 final size:25
Alignment explanation
Indices: 12534326--12534398 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 25
12534316 CTATACATAT
* *
12534326 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATA-AAAATAATATAAG
12534353 ATATATATAATAAAAATAATAT-AG
1 ATATATATAATAAAAATAATATAAG
*
12534377 -TAAATA-AATAAATAA-AATATAA
1 ATATATATAATAAA-AATAATATAA
12534399 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 11 0.27
23 8 0.20
24 2 0.05
25 8 0.20
26 3 0.07
27 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:12535265 original size:54 final size:54
Alignment explanation
Indices: 12535180--12535629 Score: 604
Period size: 54 Copynumber: 8.4 Consensus size: 54
12535170 CTCTGTGTAC
* * *
12535180 TATCGACATTAAGTGTGCAACCCAC-ATAATTCATCATATGTTCATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * *
12535234 TATCGACACTAAGTGTGCAACCCACGAAATTCATCATATGTGGATGAACAACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12535288 TACCAGCACTAAGTGTGCAACCCACAAAATTCATCATATGTTGAT-AAGCGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAA-CGACCG
12535342 TATCGGCACTAAGTGTGCAACCCAC-AGAATTCATCATATGTTGATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
** *
12535396 TATCAACACTAAGTGTGCAACCCACG-AATTCATCATATGTTGATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * **
12535449 TATAGGCACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAGCGACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
12535503 TATTGGCACTAACTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * * *
12535557 TATAGGCACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAATGACCG
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
*
12535611 TATCGGCACTACGTGTGCA
1 TATCGGCACTAAGTGTGCA
12535630 TCTCAAAGAA
Statistics
Matches: 355, Mismatches: 33, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
53 52 0.15
54 299 0.84
55 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:12535578 original size:215 final size:216
Alignment explanation
Indices: 12535180--12535629 Score: 636
Period size: 215 Copynumber: 2.1 Consensus size: 216
12535170 CTCTGTGTAC
* * *
12535180 TATCGACATTAAGTGTGCAACCCACATAATTCATCATATGTTCATGAACGACCGTATCGACACTA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATCATATGTTCATGAACGACCGTATAGACACTA
* *
12535245 AGTGTGCAACCCACGAAATTCATCATATGTGGATGAACAACCGTACCAGCACTAAGTGTGCAACC
66 AGTGTGCAACCCACGAAATTCATCATATGTGGATGAACAACCATACCAGCACTAACTGTGCAACC
*
12535310 CACAAAATTCATCATATGTTGATAAGCGACCGTATCGGCACTAAGTGTGCAACCCAC-AGAATTC
131 CACAAAATTCATCATATGTTGATAAGCGACCGTATAGGCACTAAGTGTGCAACCCACGA-AATTC
*
12535374 ATCATATGTTGATGAACGACCG
195 ATAATATGTTGATGAACGACCG
* * * *
12535396 TATCAACACTAAGTGTGCAACCCAC-GAATTCATCATATGTTGATGAACGACTGTATAGGCACTA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATCATATGTTCATGAACGACCGTATAGACACTA
* * * * * ***
12535460 AGTGTGCAACCCACGGAATTCATCATATGTTGATGAGCGACTATATTGGCACTAACTGTGCAACC
66 AGTGTGCAACCCACGAAATTCATCATATGTGGATGAACAACCATACCAGCACTAACTGTGCAACC
* *
12535525 CACATAATTCATCATATGTTGATGAA-CGACTGTATAGGCACTAAGTGTGCAACCCACGAAATTC
131 CACAAAATTCATCATATGTTGAT-AAGCGACCGTATAGGCACTAAGTGTGCAACCCACGAAATTC
* *
12535589 ATAATATGTTTATGAATGACCG
195 ATAATATGTTGATGAACGACCG
* *
12535611 TATCGGCACTACGTGTGCA
1 TATCGACACTAAGTGTGCA
12535630 TCTCAAAGAA
Statistics
Matches: 206, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
215 180 0.87
216 26 0.13
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (216 bp):
TATCGACACTAAGTGTGCAACCCACAGAATTCATCATATGTTCATGAACGACCGTATAGACACTA
AGTGTGCAACCCACGAAATTCATCATATGTGGATGAACAACCATACCAGCACTAACTGTGCAACC
CACAAAATTCATCATATGTTGATAAGCGACCGTATAGGCACTAAGTGTGCAACCCACGAAATTCA
TAATATGTTGATGAACGACCG
Found at i:12540697 original size:27 final size:30
Alignment explanation
Indices: 12540666--12540723 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
12540656 CTCAAAGCAT
*
12540666 TATTATTTCA-TAT-A-TTTAATATTAATA
1 TATTATTTCAGTATCATTTTAATAATAATA
*
12540693 TATTATTTTAGTATCATTTTAATAATAATA
1 TATTATTTCAGTATCATTTTAATAATAATA
12540723 T
1 T
12540724 TAATCATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 9 0.35
28 3 0.12
29 1 0.04
30 13 0.50
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (30 bp):
TATTATTTCAGTATCATTTTAATAATAATA
Found at i:12540797 original size:29 final size:29
Alignment explanation
Indices: 12540731--12540797 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
12540721 TATTAATCAT
* *
12540731 TAAATTATATTTATTGATAATTATTATAA
1 TAAATTATTTTTATTGATAATAATTATAA
*
12540760 TATAA-TATTTTTATT-TTAATAATATATAA
1 TA-AATTATTTTTATTGATAATAAT-TATAA
12540789 TAAATTATT
1 TAAATTATT
12540798 AATAAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 8 0.25
29 22 0.69
30 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (29 bp):
TAAATTATTTTTATTGATAATAATTATAA
Found at i:12540831 original size:22 final size:24
Alignment explanation
Indices: 12540799--12540843 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
12540789 TAAATTATTA
*
12540799 ATAAAACTAAT-TTATT-AATTTC
1 ATAAAAATAATATTATTGAATTTC
12540821 ATAAAAATAATATTATTGAATTT
1 ATAAAAATAATATTATTGAATTT
12540844 TTAAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAAAATAATATTATTGAATTTC
Found at i:12540976 original size:43 final size:43
Alignment explanation
Indices: 12540925--12541010 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
12540915 ATAATATTAA
* * *
12540925 TTATTTTAATAATTAATTAATATACTTAATAATA-TATTATTTT
1 TTATTTTAAAAAATAATTAATATAATT-ATAATATTATTATTTT
* *
12540968 TTATTTTAAAAAATATTTAATATAATTATAATATTGTTATTTT
1 TTATTTTAAAAAATAATTAATATAATTATAATATTATTATTTT
12541011 AATAAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
42 6 0.16
43 31 0.84
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (43 bp):
TTATTTTAAAAAATAATTAATATAATTATAATATTATTATTTT
Found at i:12540983 original size:36 final size:36
Alignment explanation
Indices: 12540943--12541038 Score: 101
Period size: 36 Copynumber: 2.6 Consensus size: 36
12540933 ATAATTAATT
12540943 AATATACTTAATAATATATTATTTT-TTATTTTAA-AA
1 AATATA-TTAATAATA-ATTATTTTGTTATTTTAATAA
12540979 AATAT-TTAAT-ATAATTATAATATTGTTATTTTAATAA
1 AATATATTAATAATAATTAT--T-TTGTTATTTTAATAA
* *
12541016 AATATAATAATAATAATAATTTT
1 AATATATTAATAATAATTATTTT
12541039 ATTTAAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
32 5 0.10
33 3 0.06
34 6 0.12
35 2 0.04
36 16 0.31
37 8 0.16
38 4 0.08
39 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (36 bp):
AATATATTAATAATAATTATTTTGTTATTTTAATAA
Found at i:12541065 original size:14 final size:14
Alignment explanation
Indices: 12541005--12541076 Score: 62
Period size: 14 Copynumber: 5.3 Consensus size: 14
12540995 ATAATATTGT
12541005 TATTTTAATAA-AA
1 TATTTTAATAATAA
**
12541018 TATAATAATAATAA
1 TATTTTAATAATAA
*
12541032 TAATTTT-AT-TTAA
1 T-ATTTTAATAATAA
*
12541045 AATTTTAGAT-ATAA
1 TATTTTA-ATAATAA
12541059 TATTTTAATAATAA
1 TATTTTAATAATAA
12541073 TATT
1 TATT
12541077 GACATAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
12 5 0.11
13 14 0.30
14 24 0.52
15 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:12542391 original size:14 final size:14
Alignment explanation
Indices: 12542372--12542408 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12542362 TAACTTTTAA
*
12542372 GTTTAATTTTAAAT
1 GTTTAATTATAAAT
12542386 GTTTAATTATAAAT
1 GTTTAATTATAAAT
12542400 GTTTAATTA
1 GTTTAATTA
12542409 GTGTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (14 bp):
GTTTAATTATAAAT
Found at i:12548640 original size:21 final size:21
Alignment explanation
Indices: 12548616--12548732 Score: 123
Period size: 21 Copynumber: 5.6 Consensus size: 21
12548606 TCGTACCAAG
*
12548616 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
12548637 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
12548658 GACGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
* * *
12548679 GATGAGAAGACCCTTCATAAA
1 GACGAGAAGACCATTCATCAA
* *
12548700 GACGAGAAGACC-TTCGTAAA
1 GACGAGAAGACCATTCATCAA
*
12548720 TACGAGAAGACCA
1 GACGAGAAGACCA
12548733 CATCGCGTGG
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
20 19 0.22
21 65 0.76
22 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:12551277 original size:11 final size:10
Alignment explanation
Indices: 12551263--12551352 Score: 61
Period size: 9 Copynumber: 9.6 Consensus size: 10
12551253 AAATGAGAGA
12551263 AAAAAAGATAG
1 AAAAAAGA-AG
12551274 AAAAAAGAAG
1 AAAAAAGAAG
12551284 AAAAAAG-A-
1 AAAAAAGAAG
*
12551292 AAAAATG-AG
1 AAAAAAGAAG
*
12551301 AAAAAATAA-
1 AAAAAAGAAG
*
12551310 AAGAAAG-AG
1 AAAAAAGAAG
*
12551319 -AAAAGGAA-
1 AAAAAAGAAG
12551327 AAGAAAAGAAG
1 AA-AAAAGAAG
*
12551338 AAAGAA-AAG
1 AAAAAAGAAG
12551347 AAAAAA
1 AAAAAA
12551353 TTGAAAATGA
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
8 12 0.19
9 21 0.34
10 19 0.31
11 10 0.16
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:12551293 original size:29 final size:28
Alignment explanation
Indices: 12551260--12551352 Score: 84
Period size: 27 Copynumber: 3.3 Consensus size: 28
12551250 AAAAAATGAG
12551260 AGAAAAAAAGATAGAAAAAAGAAGAAAAA
1 AGAAAAAAAGA-AGAAAAAAGAAGAAAAA
* * *
12551289 AGAAAAAATG-AGAAAAAATAA-AAGAA
1 AGAAAAAAAGAAGAAAAAAGAAGAAAAA
* *
12551315 AGAGAAAAGGAA-AAGAAAAGAAGAAAGAAA
1 AGAAAAAAAGAAGAA-AAAAGAAG-AA-AAA
12551345 AGAAAAAA
1 AGAAAAAA
12551353 TTGAAAATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
26 14 0.27
27 17 0.33
29 11 0.22
30 9 0.18
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (28 bp):
AGAAAAAAAGAAGAAAAAAGAAGAAAAA
Found at i:12551328 original size:41 final size:40
Alignment explanation
Indices: 12551250--12551328 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 40
12551240 ATATATAAGT
* *
12551250 AAAAAATGAGAGAAAAAAAGATAGAAAAAAGAAGAAAAAAG
1 AAAAAATGAGAAAAAAAAAGAAAGAAAAAAG-AGAAAAAAG
*
12551291 AAAAAATGAGAAAAAATAAAAGAAAGAGAAAAG-GAAAA
1 AAAAAATGAG-AAAAA-AAAAGAAAGAAAAAAGAGAAAA
12551329 GAAAAGAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 15 0.45
42 4 0.12
43 14 0.42
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.05
Consensus pattern (40 bp):
AAAAAATGAGAAAAAAAAAGAAAGAAAAAAGAGAAAAAAG
Found at i:12551334 original size:5 final size:5
Alignment explanation
Indices: 12551303--12551350 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
12551293 AAAATGAGAA
*
12551303 AAAAT AAAAG AAAGAG AAAAGG AAAAG AAAAG AAGAAAG AAAAG AAAA
1 AAAAG AAAAG AAA-AG AAAA-G AAAAG AAAAG -A-AAAG AAAAG AAAA
12551351 AATTGAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 22 0.58
6 12 0.32
7 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (5 bp):
AAAAG
Done.