Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:2086225 original size:7 final size:7
Alignment explanation
Indices: 2086178--2086242 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
2086168 CAAAAAGGGC
2086178 AAAAAG-
1 AAAAAGA
2086184 AAAAAGA
1 AAAAAGA
*
2086191 AAAGAAGC
1 AAA-AAGA
2086199 AAAAAGAA
1 AAAAAG-A
*
2086207 AAAGAAGC
1 AAA-AAGA
2086215 AAAAAG-
1 AAAAAGA
2086221 AAAAA-A
1 AAAAAGA
*
2086227 CAAAAGA
1 AAAAAGA
2086234 AAAAAGA
1 AAAAAGA
2086241 AA
1 AA
2086243 GAACAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
6 15 0.31
7 18 0.38
8 12 0.25
9 3 0.06
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:2086257 original size:19 final size:19
Alignment explanation
Indices: 2086216--2086277 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
2086206 AAAAGAAGCA
* *
2086216 AAAAGAAAAAACAAAAGA-A
1 AAAAGAAAGAACAAAA-ATC
2086235 AAAAGAAAGAACAAAAATC
1 AAAAGAAAGAACAAAAATC
2086254 AAAAGGAAAAAGGAACAAAAATC
1 AAAA-G--AAA-GAACAAAAATC
2086277 A
1 A
2086278 CATGAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 19 0.53
20 1 0.03
22 3 0.08
23 12 0.33
ACGTcount: A:0.76, C:0.08, G:0.13, T:0.03
Consensus pattern (19 bp):
AAAAGAAAGAACAAAAATC
Found at i:2087352 original size:18 final size:18
Alignment explanation
Indices: 2087318--2087353 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2087308 TCAACATCAA
* *
2087318 ATATTGGGGTATTTTTGG
1 ATATTGGGGCATCTTTGG
2087336 ATATTGGGGCATCTTTGG
1 ATATTGGGGCATCTTTGG
2087354 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.33, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCTTTGG
Found at i:2088719 original size:106 final size:106
Alignment explanation
Indices: 2088566--2088777 Score: 311
Period size: 106 Copynumber: 2.0 Consensus size: 106
2088556 ACGCCATTCA
*
2088566 AGACAACACAAGTTCAACATCACAACGAAGGGACGACTGGTTATCAACAAACAATCTT-CTAATT
1 AGACAACACAAGTTCAACATCACAACGAAGGGACGACTGGTTATCAACAAACAAT-TTCCCAATT
* *
2088630 TCAGAGCCAATTTCAACTTCAACG-CGAAAGATATTGGACTCG
65 CCAGAACCAATTTCAACTTC-ACGACGAAAGATATTGGACTCG
* * * *
2088672 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAGTTC
1 AGACAACACAAGTTCAACATCACAACGAAGGGACGACTGGTTATCAACAAACAATTTCCCAATTC
* *
2088737 CAGAACCAATTTCAACTTCACGACGGAGGATATTGGACTCG
66 CAGAACCAATTTCAACTTCACGACGAAAGATATTGGACTCG
2088778 GAACAATACT
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 5 0.05
106 90 0.95
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (106 bp):
AGACAACACAAGTTCAACATCACAACGAAGGGACGACTGGTTATCAACAAACAATTTCCCAATTC
CAGAACCAATTTCAACTTCACGACGAAAGATATTGGACTCG
Found at i:2090839 original size:4 final size:4
Alignment explanation
Indices: 2090830--2090862 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
2090820 TTTAATTATC
2090830 ATTT ATTT ATTT ATTT A-TT ATTT ATATT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT A
2090863 ATAAGTTAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 3 0.11
4 20 0.74
5 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:2090845 original size:12 final size:12
Alignment explanation
Indices: 2090830--2090862 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
2090820 TTTAATTATC
2090830 ATTTATTTATTT
1 ATTTATTTATTT
2090842 ATTTA-TTATTT
1 ATTTATTTATTT
2090853 ATATTATTTA
1 AT-TTATTTA
2090863 ATAAGTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTATTTATTT
Found at i:2090847 original size:19 final size:20
Alignment explanation
Indices: 2090820--2090864 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
2090810 AAATTTATGT
2090820 TTTAATTATCATTTAT-TTA
1 TTTAATTATCATTTATATTA
* *
2090839 TTTATTTATTATTTATATTA
1 TTTAATTATCATTTATATTA
2090859 TTTAAT
1 TTTAAT
2090865 AAGTTAACGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTAATTATCATTTATATTA
Found at i:2091754 original size:2 final size:2
Alignment explanation
Indices: 2091747--2091772 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2091737 ACCCTTAATA
2091747 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
2091773 CCACACACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2094455 original size:46 final size:46
Alignment explanation
Indices: 2094198--2094455 Score: 336
Period size: 46 Copynumber: 5.6 Consensus size: 46
2094188 AATTTAATGA
* ** *
2094198 ATAAATGAAAATGAATAACAATGCATTATTGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * *
2094244 ACAAATGAAAATGCATAACGTTGCATTATCGGCATGAAAGGATGCT
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* ** *
2094290 ATAAATGAAAATGCAAAACGGTGCATTATCGGTATGAAAGGATGTC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
*
2094336 ATAAATGAAAATGCATAACAGTGCATTATCGACATGAAAGGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * * *
2094382 ATAAATGAAAATGCATAACAGTGCATTATTGTCATGAAATGATGCC
1 ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
* * *
2094428 ACAAATGAAAATGCATAATGGTACATTA
1 ATAAATGAAAATGCATAACGGTGCATTA
2094456 ATGGCATAAA
Statistics
Matches: 187, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 187 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.24
Consensus pattern (46 bp):
ATAAATGAAAATGCATAACGGTGCATTATCGACATGAAAGGATGCC
Found at i:2094455 original size:138 final size:138
Alignment explanation
Indices: 2094198--2094455 Score: 392
Period size: 138 Copynumber: 1.9 Consensus size: 138
2094188 AATTTAATGA
*
2094198 ATAAATGAAAATGAATAACAATGCATTATTGACATGAAAGGATGCCACAAATGAAAATGCATAAC
1 ATAAATGAAAATGAATAACAATGCATTATCGACATGAAAGGATGCCACAAATGAAAATGCATAAC
* * *
2094263 GTTGCATTATCGGCATGAAAGGATGCTATAAATGAAAATGCAAAACGGTGCATTATCGGTATGAA
66 GTTGCATTATCGGCATGAAAGGATGCCACAAATGAAAATGCAAAACGGTACATTATCGGTATGAA
2094328 AGGATGTC
131 AGGATGTC
* * *
2094336 ATAAATGAAAATGCATAACAGTGCATTATCGACATGAAAGGATGCCATAAATGAAAATGCATAAC
1 ATAAATGAAAATGAATAACAATGCATTATCGACATGAAAGGATGCCACAAATGAAAATGCATAAC
* * * * *
2094401 AG-TGCATTATTGTCATGAAATGATGCCACAAATGAAAATGCATAATGGTACATTA
66 -GTTGCATTATCGGCATGAAAGGATGCCACAAATGAAAATGCAAAACGGTACATTA
2094456 ATGGCATAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
138 106 0.99
139 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.24
Consensus pattern (138 bp):
ATAAATGAAAATGAATAACAATGCATTATCGACATGAAAGGATGCCACAAATGAAAATGCATAAC
GTTGCATTATCGGCATGAAAGGATGCCACAAATGAAAATGCAAAACGGTACATTATCGGTATGAA
AGGATGTC
Found at i:2096030 original size:7 final size:7
Alignment explanation
Indices: 2096018--2096091 Score: 60
Period size: 8 Copynumber: 9.7 Consensus size: 7
2096008 CTTTTATTCA
2096018 TTTTCTTT
1 TTTTC-TT
2096026 TTTCTCTT
1 TTT-TCTT
*
2096034 TTTTCTCA
1 TTTTCT-T
2096042 TTTTC-T
1 TTTTCTT
2096048 TTTTCTT
1 TTTTCTT
*
2096055 TGTTCTT
1 TTTTCTT
2096062 CTTTTCTTT
1 -TTTTC-TT
2096071 TTCTTCATT
1 TT-TTC-TT
2096080 TTTTCTT
1 TTTTCTT
2096087 TTTTC
1 TTTTC
2096092 CATTATTTAG
Statistics
Matches: 55, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 5 0.09
7 17 0.31
8 22 0.40
9 11 0.20
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (7 bp):
TTTTCTT
Found at i:2096060 original size:21 final size:22
Alignment explanation
Indices: 2096014--2096075 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 22
2096004 CCTCCTTTTA
*
2096014 TTCATTTTCTTTTTTCTCTT-TTT
1 TTCATTTTC-TTTTTCT-TTGTTC
2096037 TCTCATTTTCTTTTTCTTTGTTC
1 T-TCATTTTCTTTTTCTTTGTTC
2096060 TTC-TTTTCTTTTTCTT
1 TTCATTTTCTTTTTCTT
2096076 CATTTTTTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 13 0.36
22 4 0.11
23 11 0.31
24 8 0.22
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (22 bp):
TTCATTTTCTTTTTCTTTGTTC
Found at i:2102773 original size:40 final size:40
Alignment explanation
Indices: 2102718--2102874 Score: 145
Period size: 40 Copynumber: 3.9 Consensus size: 40
2102708 AAGTGGGATT
* *
2102718 AAAAATTATGCTAATACAACTCTTTATGTGATGGACGAAC
1 AAAAATGATGCTAATACAACTCCTTATGTGATGGACGAAC
* *
2102758 AAAAATGATGCTAATACAACTCCTTATATGATGGACGAGC
1 AAAAATGATGCTAATACAACTCCTTATGTGATGGACGAAC
** * * * *
2102798 AAAAGCGATGTTGAT-CTAACTCCTTATGTGATGGACCAGC
1 AAAAATGATGCTAATAC-AACTCCTTATGTGATGGACGAAC
** * * *
2102838 GATATGATGATGTTGATCCAACTCCTTATGTGATGGA
1 -A-AAAATGATGCTAATACAACTCCTTATGTGATGGA
2102875 TAAGCCAAGG
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 1 0.01
40 68 0.69
41 1 0.01
42 28 0.28
43 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (40 bp):
AAAAATGATGCTAATACAACTCCTTATGTGATGGACGAAC
Found at i:2102863 original size:42 final size:40
Alignment explanation
Indices: 2102734--2102915 Score: 148
Period size: 40 Copynumber: 4.5 Consensus size: 40
2102724 TATGCTAATA
* * * ** * * *
2102734 CAACTCTTTATGTGATGGACGAACAAAAATGATGCTAATA
1 CAACTCCTTATGTGATGGACCAGCAAAAGCGATGTTGATC
* *
2102774 CAACTCCTTATATGATGGACGAGCAAAAGCGATGTTGATC
1 CAACTCCTTATGTGATGGACCAGCAAAAGCGATGTTGATC
* * * *
2102814 TAACTCCTTATGTGATGGACCAGCGATATGATGATGTTGATC
1 CAACTCCTTATGTGATGGACCAGC-AAAAG-CGATGTTGATC
** * * * *
2102856 CAACTCCTTATGTGATGGATAAGCCAAGGTCGATGCTGTTC
1 CAACTCCTTATGTGATGGACCAGCAAAAG-CGATGTTGATC
*
2102897 CAACTCATTATGTGATGGA
1 CAACTCCTTATGTGATGGA
2102916 ATCGAGCTAA
Statistics
Matches: 115, Mismatches: 25, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
40 53 0.46
41 31 0.27
42 31 0.27
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (40 bp):
CAACTCCTTATGTGATGGACCAGCAAAAGCGATGTTGATC
Found at i:2103118 original size:117 final size:117
Alignment explanation
Indices: 2102907--2103126 Score: 316
Period size: 117 Copynumber: 1.9 Consensus size: 117
2102897 CAACTCATTA
* * * * * * * **
2102907 TGTGATGGAATCGAGCTAAGGTTGAACAAGTATTTCTTATTATGTATTTCTTCTCCCTCATCGGA
1 TGTGATGGAATCAAACCAAGGTTGAAAAAGTATTTCTCATTATGAACTTCTTCTCCCTCATCAAA
2102972 TGAGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATTCACGTCCTTC
66 TGAGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATTCACGTCCTTC
*
2103024 TGTGATGGAATCAAACCAAGGTTGAAAAAGT-TCTTCTCATTATGAACTTCTTCTCCTTCATCAA
1 TGTGATGGAATCAAACCAAGGTTGAAAAAGTAT-TTCTCATTATGAACTTCTTCTCCCTCATCAA
* *
2103088 ATGAGTTCTTCTCATTATGAACTCTTCACTAGAAATGTT
65 ATGAGTTCTTCTCATTATGAACTATCCACTAGAAATGTT
2103127 GATCCTCCTC
Statistics
Matches: 90, Mismatches: 12, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
116 1 0.01
117 89 0.99
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (117 bp):
TGTGATGGAATCAAACCAAGGTTGAAAAAGTATTTCTCATTATGAACTTCTTCTCCCTCATCAAA
TGAGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATTCACGTCCTTC
Found at i:2103147 original size:117 final size:117
Alignment explanation
Indices: 2102909--2103152 Score: 310
Period size: 117 Copynumber: 2.1 Consensus size: 117
2102899 ACTCATTATG
* * * * * * * **
2102909 TGATGGAATCGAGCTAAGGTTGAACAAGTATTTCTTATTATGTATTTCTTCTCCCTCATCGGATG
1 TGATGGAATCAAACCAAGGTTGAAAAAGTATTTCTCATTATGAACTTCTTCTCCCTCATCAAATG
* * * *
2102974 AGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATTCACGTCCTTCTG
66 AGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATCCACCTCCTCCTA
*
2103026 TGATGGAATCAAACCAAGGTTGAAAAAGT-TCTTCTCATTATGAACTTCTTCTCCTTCATCAAAT
1 TGATGGAATCAAACCAAGGTTGAAAAAGTAT-TTCTCATTATGAACTTCTTCTCCCTCATCAAAT
* * * *
2103090 GAGTTCTTCTCATTATGAACTCTTCACTAGAAATGTTGATCCTCCTCCTCCTA
65 GAGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATCCACCTCCTCCTA
2103143 TGATGGAATC
1 TGATGGAATC
2103153 GAACAAACTG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
116 1 0.01
117 107 0.99
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (117 bp):
TGATGGAATCAAACCAAGGTTGAAAAAGTATTTCTCATTATGAACTTCTTCTCCCTCATCAAATG
AGTTCTTCTCATTATGAACTATCCACTAGAAATGTTAATCCACCTCCTCCTA
Found at i:2103418 original size:22 final size:20
Alignment explanation
Indices: 2103375--2103420 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
2103365 GTTGATCAAG
2103375 TTCTTCTCATTATGAAGTTC
1 TTCTTCTCATTATGAAGTTC
2103395 TTCTTCCTCATTA-GATGAGTTC
1 TTCTT-CTCATTATGA--AGTTC
2103417 TTCT
1 TTCT
2103421 CATTATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 7 0.30
22 9 0.39
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (20 bp):
TTCTTCTCATTATGAAGTTC
Found at i:2104088 original size:25 final size:25
Alignment explanation
Indices: 2104059--2104106 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
2104049 ACAATAAAGT
2104059 TTTCAAAATCAGTTCAATATTAAGG
1 TTTCAAAATCAGTTCAATATTAAGG
2104084 TTTCAAAATCAGTTCAATATTAA
1 TTTCAAAATCAGTTCAATATTAA
2104107 AATCATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (25 bp):
TTTCAAAATCAGTTCAATATTAAGG
Found at i:2107007 original size:12 final size:12
Alignment explanation
Indices: 2106981--2107042 Score: 81
Period size: 12 Copynumber: 5.1 Consensus size: 12
2106971 AAATTTAATT
2106981 ATAATATATTAATA
1 ATAATATA-T-ATA
2106995 ATAATATATATA
1 ATAATATATATA
2107007 ATAATATATATA
1 ATAATATATATA
*
2107019 ATAATAT-TATT
1 ATAATATATATA
*
2107030 ATAATATTTATA
1 ATAATATATATA
2107042 A
1 A
2107043 CGAATCGGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.22
12 26 0.58
13 1 0.02
14 8 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATAATATATATA
Found at i:2107261 original size:35 final size:36
Alignment explanation
Indices: 2107215--2107352 Score: 221
Period size: 35 Copynumber: 3.9 Consensus size: 36
2107205 TCAATCCGTA
2107215 CTTCACTACTCTTTTGTGAAGGC-TGAATTGCATTG
1 CTTCACTACTCTTTTGTGAAGGCTTGAATTGCATTG
2107250 CTTCACTACTCTTTTGTGAAGGCTTG-ATTGCATTG
1 CTTCACTACTCTTTTGTGAAGGCTTGAATTGCATTG
* *
2107285 CTTCAGTACTC-TTTGTGAAGG-TTGATTTGCATTG
1 CTTCACTACTCTTTTGTGAAGGCTTGAATTGCATTG
*
2107319 CTTCACTACTCTTTTGTGAAGGCTTGATTTGCAT
1 CTTCACTACTCTTTTGTGAAGGCTTGAATTGCAT
2107353 AGAAAGAATT
Statistics
Matches: 96, Mismatches: 3, Indels: 7
0.91 0.03 0.07
Matches are distributed among these distances:
33 3 0.03
34 28 0.29
35 52 0.54
36 13 0.14
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTCACTACTCTTTTGTGAAGGCTTGAATTGCATTG
Found at i:2107315 original size:69 final size:71
Alignment explanation
Indices: 2107215--2107352 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 71
2107205 TCAATCCGTA
2107215 CTTCACTACTCTTTTGTGAAGGCTGAATTGCATTGCTTCACTACTCTTTTGTGAAGGCTTGA-TT
1 CTTCACTACTCTTTTGTGAAGGCTGAATTGCATTGCTTCACTACTCTTTTGTGAAGGCTTGATTT
2107279 GCATTG
66 GCATTG
* * *
2107285 CTTCAGTACTC-TTTGTGAAGGTTGATTTGCATTGCTTCACTACTCTTTTGTGAAGGCTTGATTT
1 CTTCACTACTCTTTTGTGAAGGCTGAATTGCATTGCTTCACTACTCTTTTGTGAAGGCTTGATTT
2107349 GCAT
66 GCAT
2107353 AGAAAGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
69 48 0.75
70 16 0.25
ACGTcount: A:0.18, C:0.19, G:0.20, T:0.43
Consensus pattern (71 bp):
CTTCACTACTCTTTTGTGAAGGCTGAATTGCATTGCTTCACTACTCTTTTGTGAAGGCTTGATTT
GCATTG
Found at i:2122346 original size:13 final size:11
Alignment explanation
Indices: 2122321--2122352 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2122311 GGCAGTAGGA
2122321 AAAAATTCAAG
1 AAAAATTCAAG
2122332 AAAAATTCAAG
1 AAAAATTCAAG
*
2122343 AGAAATTCAA
1 AAAAATTCAA
2122353 TTTTAGTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (11 bp):
AAAAATTCAAG
Found at i:2131029 original size:138 final size:137
Alignment explanation
Indices: 2130788--2131040 Score: 325
Period size: 138 Copynumber: 1.8 Consensus size: 137
2130778 CCGTTGATCG
* * * *
2130788 TTGACTTTTACCAAAAAAGTCAAAATTTTCGAAAAGTCATATTTTATGTTTGTCGACGTCCTGAG
1 TTGACTTTAACCAAAAAAGTCAAAATTTTCAAAAAATCATATTTTATGTTTGTCGACGTCCTGAA
*
2130853 TCCGGATACTGAAATCTGTTTTTCCAAATTTAAACCCGAAAGCCTCCAAATTGTCAATCAAACCC
66 TCCGGATACTGAAATCTGTTTTGCCAAATTTAAACCCGAAAGCC-CCAAATTGTCAATCAAACCC
2130918 ATTGACTT
130 ATTGACTT
* *
2130926 TTGACTTTAACC-AAAAAGTCAAAATTTTCAAAAAAAATCATATTTTATGTTTTTCGATGTCCTG
1 TTGACTTTAACCAAAAAAGTCAAAATTTTC--AAAAAATCATATTTTATGTTTGTCGACGTCCTG
* * * * *
2130990 AAT-CTGATTA-TGAAGTTTGTTTTGCTAAATTCT-GACCCGAAAGCCCCAAAT
64 AATCCGGA-TACTGAAATCTGTTTTGCCAAATT-TAAACCCGAAAGCCCCAAAT
2131041 CGAGCTCGTT
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
137 23 0.23
138 42 0.42
139 34 0.34
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.35
Consensus pattern (137 bp):
TTGACTTTAACCAAAAAAGTCAAAATTTTCAAAAAATCATATTTTATGTTTGTCGACGTCCTGAA
TCCGGATACTGAAATCTGTTTTGCCAAATTTAAACCCGAAAGCCCCAAATTGTCAATCAAACCCA
TTGACTT
Found at i:2131492 original size:31 final size:29
Alignment explanation
Indices: 2131451--2131512 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2131441 TTGGTGATAA
2131451 TTCTAAATATTGTTACGACATGATACCTGAT
1 TTCTAAATATTGTT--GACATGATACCTGAT
* * *
2131482 TTCTGAATATTGTTTACATGATATCTGAT
1 TTCTAAATATTGTTGACATGATACCTGAT
2131511 TT
1 TT
2131513 ACCGTACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
31 13 0.46
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (29 bp):
TTCTAAATATTGTTGACATGATACCTGAT
Found at i:2134650 original size:40 final size:40
Alignment explanation
Indices: 2134533--2134643 Score: 159
Period size: 40 Copynumber: 2.8 Consensus size: 40
2134523 ATCGTAGTGC
* * * * *
2134533 TACACATAAGGTCTTGGCCACAATATACACCGAAGAGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
2134573 TACACATAAGGTCGTGCACACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
2134613 TACACATAAGGTCGTGCCCACCATATTACAC
1 TACACATAAGGTCGTGCCCACCATA-TACAC
2134644 TTAGTGTCTT
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 58 0.92
41 5 0.08
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:2141276 original size:24 final size:24
Alignment explanation
Indices: 2141249--2141296 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2141239 AGTCTTCATG
2141249 ATGATCTATAAAACATCTATGTAC
1 ATGATCTATAAAACATCTATGTAC
* *
2141273 ATGATGTGTAAAACATCTATGTAC
1 ATGATCTATAAAACATCTATGTAC
2141297 CACGTCATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (24 bp):
ATGATCTATAAAACATCTATGTAC
Found at i:2154424 original size:15 final size:15
Alignment explanation
Indices: 2154384--2154425 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
2154374 GTCGGGCAGT
*
2154384 CGGTTCGGGTAAGAC
1 CGGTTCGGGTCAGAC
*
2154399 CAGG-TCAGGTCAGAC
1 C-GGTTCGGGTCAGAC
2154414 CGGTTCGGGTCA
1 CGGTTCGGGTCA
2154426 ACTGGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.19, C:0.24, G:0.38, T:0.19
Consensus pattern (15 bp):
CGGTTCGGGTCAGAC
Found at i:2158782 original size:30 final size:30
Alignment explanation
Indices: 2158714--2158786 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
2158704 AATGGATTTA
*
2158714 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAATTTGGTAAAG
* *
2158744 TTTGGTGACTAAAGTATAAACTTT-G-AAACG
1 TTTAGTGACCAAAGTATAAA-TTTGGTAAA-G
2158774 TTTAGTGACCAAA
1 TTTAGTGACCAAA
2158787 ATGTAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 3 0.08
30 30 0.83
31 3 0.08
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGGTAAAG
Found at i:2166055 original size:27 final size:28
Alignment explanation
Indices: 2166006--2166063 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
2165996 AGGGGTGCAC
2166006 AAAAAATCCGAATATCCGATTTTGCGAA
1 AAAAAATCCGAATATCCGATTTTGCGAA
* *
2166034 AAAAATATCCGAA-A-CCGGTTTTGGGAA
1 AAAAA-ATCCGAATATCCGATTTTGCGAA
2166061 AAA
1 AAA
2166064 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 14 0.52
28 6 0.22
29 7 0.26
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (28 bp):
AAAAAATCCGAATATCCGATTTTGCGAA
Found at i:2168439 original size:21 final size:21
Alignment explanation
Indices: 2168415--2168454 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2168405 TTTATTTTAT
2168415 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
2168436 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
2168455 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:2168502 original size:33 final size:33
Alignment explanation
Indices: 2168449--2168547 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2168439 TTTGTTTCAA
2168449 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2168481 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
2168514 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
2168547 T
1 T
2168548 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:2168576 original size:13 final size:13
Alignment explanation
Indices: 2168533--2168587 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2168523 TTGGAAGTAT
2168533 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
2168546 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
2168560 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
2168573 TTAAGTATTTGAA
1 TTAAGTATTTCAA
2168586 TT
1 TT
2168588 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:2169006 original size:15 final size:15
Alignment explanation
Indices: 2168981--2169036 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
2168971 ATCTGGAATA
*
2168981 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
2168996 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
2169011 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
2169028 TTAAAACCG
1 TTAAAACCG
2169037 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:2169045 original size:21 final size:18
Alignment explanation
Indices: 2169000--2169033 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2168990 GTTTTTTTAT
2169000 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
2169017 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
2169034 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:2169153 original size:15 final size:17
Alignment explanation
Indices: 2169127--2169158 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2169117 TTCTATGGGA
2169127 AAAAATCGGAT-CGGAT
1 AAAAATCGGATCCGGAT
2169143 AAAAATC-GATCCGGAT
1 AAAAATCGGATCCGGAT
2169159 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (17 bp):
AAAAATCGGATCCGGAT
Found at i:2170635 original size:20 final size:20
Alignment explanation
Indices: 2170612--2170652 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2170602 GGATCAAAGC
*
2170612 GAGTCAACCTAAATCGGTCT
1 GAGTCAACCTAAATAGGTCT
*
2170632 GAGTTAACCTAAATAGGTCT
1 GAGTCAACCTAAATAGGTCT
2170652 G
1 G
2170653 TCCCTTTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (20 bp):
GAGTCAACCTAAATAGGTCT
Found at i:2171316 original size:17 final size:17
Alignment explanation
Indices: 2171290--2171322 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2171280 AGATGTAAAA
2171290 TGACATGGA-TTGACCC
1 TGACATGGATTTGACCC
2171306 TGACAATGGATTTGACC
1 TGAC-ATGGATTTGACC
2171323 TGAGCATTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (17 bp):
TGACATGGATTTGACCC
Found at i:2172698 original size:39 final size:39
Alignment explanation
Indices: 2172652--2172770 Score: 139
Period size: 39 Copynumber: 3.1 Consensus size: 39
2172642 CTACAGCTAT
* * *
2172652 GGTAAGTCCTTACCGTAGGCTCATTTTCTTTGTTCATAG
1 GGTAAGTCCTTACCGTAAGCTCATTTACTTTGTGCATAG
* * * * *
2172691 GGTAAGTCCTTACCGCAAACTCCTTTGCTTTGTGCACAG
1 GGTAAGTCCTTACCGTAAGCTCATTTACTTTGTGCATAG
* * *
2172730 GGTAAGTTCTTACTGTATGCTCATTTACTTTGTGCATAG
1 GGTAAGTCCTTACCGTAAGCTCATTTACTTTGTGCATAG
2172769 GG
1 GG
2172771 GAAAACTTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 65 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (39 bp):
GGTAAGTCCTTACCGTAAGCTCATTTACTTTGTGCATAG
Found at i:2180024 original size:20 final size:20
Alignment explanation
Indices: 2179999--2180048 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
2179989 TAAAACCACC
2179999 AAATGCAACTTCATAGACTT
1 AAATGCAACTTCATAGACTT
2180019 AAATGCAACTTCATAGACTT
1 AAATGCAACTTCATAGACTT
2180039 AAATGCAACT
1 AAATGCAACT
2180049 ATATGTAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (20 bp):
AAATGCAACTTCATAGACTT
Found at i:2181419 original size:74 final size:73
Alignment explanation
Indices: 2181299--2181444 Score: 256
Period size: 74 Copynumber: 2.0 Consensus size: 73
2181289 TGAACCCTAG
*
2181299 TGTTAAATGTAAGATACGAGTAGTATCGGATACGAGTACGTTCCAACCAAGTACATTCTCTGGAA
1 TGTTAAATGTAAGATACGAGTAGTATCGGATACGAGTACGTGCCAACCAAGTACATTCTCTGGAA
2181364 AGGGTCTA
66 AGGGTCTA
* *
2181372 TGTTAAATGTAAGATACGAGTACGTATCGGATATGAGTACGTGCCAACCAAGTACATTTTCTGGA
1 TGTTAAATGTAAGATACGAGTA-GTATCGGATACGAGTACGTGCCAACCAAGTACATTCTCTGGA
2181437 AAGGGTCT
65 AAGGGTCT
2181445 CTTTGGCCAT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 22 0.32
74 47 0.68
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (73 bp):
TGTTAAATGTAAGATACGAGTAGTATCGGATACGAGTACGTGCCAACCAAGTACATTCTCTGGAA
AGGGTCTA
Found at i:2191359 original size:3 final size:3
Alignment explanation
Indices: 2191353--2191402 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2191343 ATACTTTACC
2191353 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2191401 AT
1 AT
2191403 ACAATAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2192598 original size:31 final size:31
Alignment explanation
Indices: 2192523--2192601 Score: 81
Period size: 31 Copynumber: 2.5 Consensus size: 31
2192513 ATGATTGTGG
* * *
2192523 AGTGATCAGTTTGTTACAAATTAATAACGTT
1 AGTGAACAATTTGTTACAAAGTAATAACGTT
* *
2192554 AGTG-ACTATTTTGTTAC-AAGTAGATAATGTT
1 AGTGAAC-AATTTGTTACAAAGTA-ATAACGTT
2192585 AGTGAACAATTTGTTAC
1 AGTGAACAATTTGTTAC
2192602 TCTAGAAACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.12
31 33 0.82
32 2 0.05
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (31 bp):
AGTGAACAATTTGTTACAAAGTAATAACGTT
Found at i:2193722 original size:50 final size:49
Alignment explanation
Indices: 2193616--2193724 Score: 146
Period size: 49 Copynumber: 2.2 Consensus size: 49
2193606 TGAAAAAAAA
* * *
2193616 ACTAAAAAAGAGTTTGTTATAACAATAACCACATGAAAAAAACATGAAG
1 ACTAAAAAAGAGTTTGTTACAACAATAAACACATGAAAAAAACATAAAG
* * * *
2193665 GCAAAAAAAGAGTTTGTTGCAACAATAAACACATGACAAATAACATAAAG
1 ACTAAAAAAGAGTTTGTTACAACAATAAACACATGA-AAAAAACATAAAG
2193715 ACTAAAAAAG
1 ACTAAAAAAG
2193725 TTAGCTCCAA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 31 0.62
50 19 0.38
ACGTcount: A:0.56, C:0.13, G:0.13, T:0.18
Consensus pattern (49 bp):
ACTAAAAAAGAGTTTGTTACAACAATAAACACATGAAAAAAACATAAAG
Found at i:2197032 original size:331 final size:330
Alignment explanation
Indices: 2196424--2197082 Score: 1165
Period size: 331 Copynumber: 2.0 Consensus size: 330
2196414 GTAATTTCTA
* **
2196424 TTCATATGGATCCGAGGAAATATTGGAAGATGATTTCATTATTGAGGGTGTTCGAATGGAATTTA
1 TTCATATGGATCCGAGGAAAAATTGGAAGATGATTTCAAGATTGAGGGTGTTCGAATGGAATTTA
2196489 ATGGTTGATCAATATTGCACAGAAATCAAGGTAATACTTTACTACCTCTTTATGCTTTATAGAAT
66 ATGGTTGATCAATATTGCACAGAAATCAAGGTAATACTTTACTACCTCTTTATGCTTTATAGAAT
*
2196554 ATGTTGATAATGAAAATGCATGAATAAGATAATGTTGGTCACTGTTGTGGAGTTGAATAATTTAT
131 ATGTTGATAATGAAAATGCATGAATAAGATAATGTTGGTCACTGCTGTGGAGTTGAATAATTTAT
*
2196619 ACACTTGATATAAATGTAGTAGAAATTCTATAGCTGAATACGGATCGAATGAGTAATATAAGAGA
196 ACACTTGATATAAATGTAGTAGAAATTCTATAACTGAATACGGATCGAATGAGTAATATAAGAGA
2196684 TTGAGGAATTATTAGAATTAAATTACAAGTTTGTGATTAGTGATAAAGAAATCAACTATGGATTT
261 TTGAGGAATTATTAGAATTAAATTACAAGTTTGTGATTAGTGATAAAGAAATCAACTATGGATTT
2196749 GTATG
326 GTATG
2196754 TTCATATGGATCCGAGGAAAAATTGGAAGATGATTTCAAGATTGAGGGTGTTCGAATGGAATTTA
1 TTCATATGGATCCGAGGAAAAATTGGAAGATGATTTCAAGATTGAGGGTGTTCGAATGGAATTTA
* ** * *
2196819 ATGGTTGATCAGTATTGCAGGGAAATCGAGGTAATACTTTACTACCTCTTTATGCTTTATGGAAT
66 ATGGTTGATCAATATTGCACAGAAATCAAGGTAATACTTTACTACCTCTTTATGCTTTATAGAAT
* *
2196884 ATGTTGATATTGGTAAATGCATGAATAAGATAATGTTGGTCACTGCTGTGGAGTTGAATAATTTA
131 ATGTTGATAAT-GAAAATGCATGAATAAGATAATGTTGGTCACTGCTGTGGAGTTGAATAATTTA
*
2196949 TACACTTGATATGAATGTAGTAGAAATTCTATAACTGAATACGGATCGAATGAGTAATATAAGAG
195 TACACTTGATATAAATGTAGTAGAAATTCTATAACTGAATACGGATCGAATGAGTAATATAAGAG
* * *
2197014 ATTGAGGAATTGTTAGAATTAAATTACAAGTTTGTGATTAGTGATTAAGAAATCAACTCTGGATT
260 ATTGAGGAATTATTAGAATTAAATTACAAGTTTGTGATTAGTGATAAAGAAATCAACTATGGATT
2197079 TGTA
325 TGTA
2197083 ACTTATATTT
Statistics
Matches: 312, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
330 132 0.42
331 180 0.58
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (330 bp):
TTCATATGGATCCGAGGAAAAATTGGAAGATGATTTCAAGATTGAGGGTGTTCGAATGGAATTTA
ATGGTTGATCAATATTGCACAGAAATCAAGGTAATACTTTACTACCTCTTTATGCTTTATAGAAT
ATGTTGATAATGAAAATGCATGAATAAGATAATGTTGGTCACTGCTGTGGAGTTGAATAATTTAT
ACACTTGATATAAATGTAGTAGAAATTCTATAACTGAATACGGATCGAATGAGTAATATAAGAGA
TTGAGGAATTATTAGAATTAAATTACAAGTTTGTGATTAGTGATAAAGAAATCAACTATGGATTT
GTATG
Found at i:2213157 original size:45 final size:45
Alignment explanation
Indices: 2213023--2213236 Score: 333
Period size: 45 Copynumber: 4.8 Consensus size: 45
2213013 GGTAAGTATG
* * *
2213023 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTAGGTTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
* *
2213067 AAAATAAGCTTATGAGCTTATGGAAT-AATGGAAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
2213111 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
2213156 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
* * *
2213201 AAAATAAGCTTACAAGCTTATGAGATTAAATTGTAA
1 AAAATAAGCTTACGAGCTTATG-GAATAAATGGTAA
2213237 ATATTTTGAT
Statistics
Matches: 159, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
44 65 0.41
45 83 0.52
46 11 0.07
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
Found at i:2226990 original size:12 final size:12
Alignment explanation
Indices: 2226973--2226997 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2226963 AGTGTGCACT
2226973 ATAATTCTGGGA
1 ATAATTCTGGGA
2226985 ATAATTCTGGGA
1 ATAATTCTGGGA
2226997 A
1 A
2226998 AACCAGTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (12 bp):
ATAATTCTGGGA
Found at i:2232591 original size:3 final size:3
Alignment explanation
Indices: 2232571--2232705 Score: 234
Period size: 3 Copynumber: 45.0 Consensus size: 3
2232561 TGCCTATAAA
* *
2232571 ATT ATT AGT ATT AGT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2232619 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2232667 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2232706 TTAAATACAT
Statistics
Matches: 124, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 124 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2232906 original size:30 final size:30
Alignment explanation
Indices: 2232870--2232934 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
2232860 AAATTCAGAG
2232870 GACCCAAGGTCAAAGGTTCGACCCGATCCA
1 GACCCAAGGTCAAAGGTTCGACCCGATCCA
2232900 GACCCAAGGTCAAAGGTTCGACCCGATCCA
1 GACCCAAGGTCAAAGGTTCGACCCGATCCA
*
2232930 AACCC
1 GACCC
2232935 GCTGGAGCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.31, C:0.35, G:0.22, T:0.12
Consensus pattern (30 bp):
GACCCAAGGTCAAAGGTTCGACCCGATCCA
Found at i:2234107 original size:14 final size:14
Alignment explanation
Indices: 2234088--2234125 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
2234078 CCTTTTAAGC
2234088 ACTTACATTTCATT
1 ACTTACATTTCATT
2234102 ACTTACATTTCATT
1 ACTTACATTTCATT
2234116 ACTTACATTT
1 ACTTACATTT
2234126 AAGTCACTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
ACTTACATTTCATT
Found at i:2238225 original size:28 final size:26
Alignment explanation
Indices: 2238190--2238251 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 26
2238180 AGATCAAATC
*
2238190 AAAACAAAGAGAAAAGAAGCAAAAAGAA
1 AAAACAAAGAAAAAAGAAGC--AAAGAA
2238218 AAAACAAAGAAAAAAGAAGCAAAGAA
1 AAAACAAAGAAAAAAGAAGCAAAGAA
2238244 AAAACAAA
1 AAAACAAA
2238252 TAGCATATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 14 0.42
28 19 0.58
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAACAAAGAAAAAAGAAGCAAAGAA
Found at i:2238242 original size:15 final size:15
Alignment explanation
Indices: 2238194--2238247 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
2238184 CAAATCAAAA
*
2238194 CAAAGAGAAAAGAAG
1 CAAAGAAAAAAGAAG
2238209 CAAA-AAGAAAA-AA-
1 CAAAGAA-AAAAGAAG
2238222 CAAAGAAAAAAGAAG
1 CAAAGAAAAAAGAAG
2238237 CAAAGAAAAAA
1 CAAAGAAAAAA
2238248 CAAATAGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 8 0.24
14 7 0.21
15 19 0.56
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (15 bp):
CAAAGAAAAAAGAAG
Found at i:2239830 original size:67 final size:66
Alignment explanation
Indices: 2239673--2239866 Score: 234
Period size: 66 Copynumber: 2.9 Consensus size: 66
2239663 TTAAAAAAAA
* * *
2239673 TTGTCTCTCTTGAGACAGTTTCTCGTGAAACACCAAACTTTGAGATTGTTTCCCTTGAAACAAGT
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGATTGTTTCCCTTGAAACAAGT
2239738 T
66 T
*
2239739 TTGTC-CTCCTTGAGATAGTTTCTCTTGAAACACCCATCTTTGAGATTGTTTTCCCTTGAAACGA
1 TTGTCTCT-CTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGATTG-TTTCCCTTGAAAC-A
2239803 A-TT
63 AGTT
*** * * *
2239806 TTGTCTCTCTTGAGACAACATCTCTTGAAGCA-TCATCTTTGAG-TCTCTTTCCCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGAT-TGTTTCCCTTGAAACA
2239867 TTATCCTTAA
Statistics
Matches: 112, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
64 1 0.01
65 16 0.14
66 52 0.46
67 39 0.35
68 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (66 bp):
TTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCCATCTTTGAGATTGTTTCCCTTGAAACAAGT
T
Found at i:2240108 original size:131 final size:131
Alignment explanation
Indices: 2239900--2240170 Score: 373
Period size: 131 Copynumber: 2.1 Consensus size: 131
2239890 TTTTTATCGT
* *
2239900 GTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCATGTCAACCTTAGATA
1 GTAGGAACCGTGTCATCCACCGACCAGACCACCTCATCACGTAGGAGCCATGTCAAACTTAGATA
*
2239965 ACCAGTCATCCTCAACACGTAGGAACCGTGTTATAATCCCTAAAGATAGCATGCTGTCCTCAACA
66 ACCAGTCATCCTCAACACGTAGGAACCATGTTATAATCCCTAAAGATAGCATGCTGTCCTCAACA
2240030 C
131 C
* * * * *
2240031 GTAGGAATCGTGTCATCCACTGACCGGACCACCTCATCATGTAGGAGCCGTGTCAAACTTAGATA
1 GTAGGAACCGTGTCATCCACCGACCAGACCACCTCATCACGTAGGAGCCATGTCAAACTTAGATA
* * * * * * ** *
2240096 ACCA-TCCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTACCATCCTCATC
66 ACCAGT-CATCCTCAACACGTAGGAACCATGTTATAATCCCTAAAGATAGCATGCTGTCCTCAAC
2240160 AC
130 AC
2240162 GTAGGAACC
1 GTAGGAACC
2240171 ATGTTATCAT
Statistics
Matches: 121, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
130 1 0.01
131 120 0.99
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (131 bp):
GTAGGAACCGTGTCATCCACCGACCAGACCACCTCATCACGTAGGAGCCATGTCAAACTTAGATA
ACCAGTCATCCTCAACACGTAGGAACCATGTTATAATCCCTAAAGATAGCATGCTGTCCTCAACA
C
Found at i:2240156 original size:48 final size:48
Alignment explanation
Indices: 2240101--2240218 Score: 236
Period size: 48 Copynumber: 2.5 Consensus size: 48
2240091 AGATAACCAT
2240101 CCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTA
1 CCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTA
2240149 CCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTA
1 CCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTA
2240197 CCATCCTCATCACGTAGGAACC
1 CCATCCTCATCACGTAGGAACC
2240219 TTATCATCCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.25
Consensus pattern (48 bp):
CCATCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCCTA
Found at i:2240545 original size:3 final size:3
Alignment explanation
Indices: 2240537--2240564 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2240527 TCTACAAAAA
2240537 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2240565 GTTGTTGTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2240569 original size:3 final size:3
Alignment explanation
Indices: 2240563--2240600 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2240553 ATTATTATTA
*
2240563 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
2240601 TTTATTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:2249527 original size:21 final size:21
Alignment explanation
Indices: 2249501--2249552 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
2249491 GCGAGTACAT
2249501 GAGGCGGCGATTCAATCGTCG
1 GAGGCGGCGATTCAATCGTCG
2249522 GAGGCGGCGATTCAATCGTCG
1 GAGGCGGCGATTCAATCGTCG
2249543 GAGGCGGCGA
1 GAGGCGGCGA
2249553 GAGGCGACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.15
Consensus pattern (21 bp):
GAGGCGGCGATTCAATCGTCG
Found at i:2252892 original size:44 final size:44
Alignment explanation
Indices: 2252829--2252917 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
2252819 TCAGCATCAA
2252829 GATCACCAGAGTTATCGACATTCCCAAACATAAAACCCAGAAGC
1 GATCACCAGAGTTATCGACATTCCCAAACATAAAACCCAGAAGC
2252873 GATCACCAGAGTTATCGACATTCCCAAACATAAAACCCAGAAGC
1 GATCACCAGAGTTATCGACATTCCCAAACATAAAACCCAGAAGC
2252917 G
1 G
2252918 GATTACTCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (44 bp):
GATCACCAGAGTTATCGACATTCCCAAACATAAAACCCAGAAGC
Found at i:2255073 original size:13 final size:13
Alignment explanation
Indices: 2255057--2255081 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2255047 TTTATACTAA
2255057 AAATATCTACTTC
1 AAATATCTACTTC
2255070 AAATATCTACTT
1 AAATATCTACTT
2255082 ATTTCTCAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATCTACTTC
Found at i:2264880 original size:25 final size:25
Alignment explanation
Indices: 2264830--2264881 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2264820 TTGTTTTTTA
*
2264830 TTTTTTATTTGTTTTTCTTTGCTCT
1 TTTTTTATTTGTTTTTCTTTGATCT
*
2264855 TTTTTTCTTTGTTTTTAC-TTGATCT
1 TTTTTTATTTGTTTTT-CTTTGATCT
2264880 TT
1 TT
2264882 GCACTCTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.06, C:0.12, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTTTTATTTGTTTTTCTTTGATCT
Found at i:2268011 original size:44 final size:45
Alignment explanation
Indices: 2267916--2268013 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
2267906 AACTCAACGG
** * *
2267916 TAACGATA-CATCTCAAGGAGTATCGATACTACTATGTGTAGTAG
1 TAACGATACCATCTCAAGGAGTATCGATACTACTATGTAAAATAA
*
2267960 TAACGATACCATC-CAAGGAGTATTGATACTACTATGTAAAATAA
1 TAACGATACCATCTCAAGGAGTATCGATACTACTATGTAAAATAA
*
2268004 TATCGATACC
1 TAACGATACC
2268014 GATAATGATA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 43 0.91
45 4 0.09
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (45 bp):
TAACGATACCATCTCAAGGAGTATCGATACTACTATGTAAAATAA
Found at i:2268386 original size:19 final size:19
Alignment explanation
Indices: 2268362--2268398 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2268352 TCGAATAATT
*
2268362 AAATCGAATATAATATTTG
1 AAATCGAATATAAAATTTG
2268381 AAATCGAATATAAAATTT
1 AAATCGAATATAAAATTT
2268399 TAGAATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
AAATCGAATATAAAATTTG
Found at i:2268834 original size:17 final size:17
Alignment explanation
Indices: 2268793--2268834 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2268783 ATCATTCATA
*
2268793 ATCAATCATCCAAAAAT
1 ATCAAACATCCAAAAAT
2268810 AT-AAACATCCAAAACAT
1 ATCAAACATCCAAAA-AT
2268827 -TCAAACAT
1 ATCAAACAT
2268835 AAATAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.55, C:0.24, G:0.00, T:0.21
Consensus pattern (17 bp):
ATCAAACATCCAAAAAT
Found at i:2270301 original size:18 final size:18
Alignment explanation
Indices: 2270278--2270312 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2270268 AAAACAATAT
2270278 AATTAAATCAAAAACAAC
1 AATTAAATCAAAAACAAC
*
2270296 AATTAAGTCAAAAACAA
1 AATTAAATCAAAAACAA
2270313 TTTTTTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.03, T:0.17
Consensus pattern (18 bp):
AATTAAATCAAAAACAAC
Found at i:2270730 original size:22 final size:20
Alignment explanation
Indices: 2270702--2270752 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2270692 GCATGAACAA
2270702 TATCGATACTTGATGATAGCAG
1 TATCGATAC-T-ATGATAGCAG
* *
2270724 TATCGATACTATGCTAGTAG
1 TATCGATACTATGATAGCAG
2270744 TATCGATAC
1 TATCGATAC
2270753 CTAGCAAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 17 0.63
21 1 0.04
22 9 0.33
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
TATCGATACTATGATAGCAG
Found at i:2270770 original size:22 final size:21
Alignment explanation
Indices: 2270742--2270795 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
2270732 CTATGCTAGT
*
2270742 AGTATCGATACCTAGCAAGAGC
1 AGTATCGATACCT-GCAAGACC
* * *
2270764 AGTATCGGTA-CTGGATGACC
1 AGTATCGATACCTGCAAGACC
2270784 AGTATCGATACC
1 AGTATCGATACC
2270796 AAGTGCACAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.54
21 3 0.12
22 9 0.35
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (21 bp):
AGTATCGATACCTGCAAGACC
Found at i:2275416 original size:11 final size:11
Alignment explanation
Indices: 2275384--2275409 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2275374 GATGATGTTC
2275384 TCTCGTATTCA
1 TCTCGTATTCA
2275395 TCTCGTATTCA
1 TCTCGTATTCA
2275406 TCTC
1 TCTC
2275410 TTCTTCACTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (11 bp):
TCTCGTATTCA
Found at i:2276444 original size:44 final size:45
Alignment explanation
Indices: 2276371--2276469 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 45
2276361 AACTCAATGA
* * * * **
2276371 TATCTATACC-TCTCAAGGAGTATCGATACTACTATGTGTAGTAG
1 TATCAATACCGTCTCAAGGAGTACCAATACTACTATATAAAGTAG
2276415 TATCAATACCGTC-CAAGGAGTACCAATACTACTATATAAAGTAG
1 TATCAATACCGTCTCAAGGAGTACCAATACTACTATATAAAGTAG
*
2276459 TATCGATACCG
1 TATCAATACCG
2276470 GTAATGGTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (45 bp):
TATCAATACCGTCTCAAGGAGTACCAATACTACTATATAAAGTAG
Found at i:2276858 original size:19 final size:19
Alignment explanation
Indices: 2276817--2276858 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2276807 TTGAATAATT
*
2276817 AAATCAAATATAATATTTG
1 AAATCAAATATAATATTTA
*
2276836 AAATCGAATATAA-ATCTTA
1 AAATCAAATATAATAT-TTA
2276855 AAAT
1 AAAT
2276859 TCATTAACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
AAATCAAATATAATATTTA
Found at i:2282610 original size:19 final size:19
Alignment explanation
Indices: 2282586--2282643 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
2282576 GGCTGCTGGA
2282586 AACCGGTTTAACCGGT-TCG
1 AACCGGTTTAACCGGTCT-G
*
2282605 AACCGGTTTGACCGGTCTG
1 AACCGGTTTAACCGGTCTG
* *
2282624 AACCGGTCTGACCGGTCTG
1 AACCGGTTTAACCGGTCTG
2282643 A
1 A
2282644 CCCAACCCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 35 0.97
20 1 0.03
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (19 bp):
AACCGGTTTAACCGGTCTG
Found at i:2282631 original size:10 final size:10
Alignment explanation
Indices: 2282586--2282643 Score: 61
Period size: 9 Copynumber: 6.1 Consensus size: 10
2282576 GGCTGCTGGA
*
2282586 AACCGGT-TT
1 AACCGGTCTG
2282595 AACCGGT-TCG
1 AACCGGTCT-G
*
2282605 AACCGGTTTG
1 AACCGGTCTG
2282615 -ACCGGTCTG
1 AACCGGTCTG
2282624 AACCGGTCTG
1 AACCGGTCTG
2282634 -ACCGGTCTG
1 AACCGGTCTG
2282643 A
1 A
2282644 CCCAACCCGA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 25 0.58
10 17 0.40
11 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (10 bp):
AACCGGTCTG
Found at i:2282640 original size:9 final size:9
Alignment explanation
Indices: 2282606--2282645 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
2282596 ACCGGTTCGA
*
2282606 ACCGGTTTG
1 ACCGGTCTG
2282615 ACCGGTCTG
1 ACCGGTCTG
2282624 AACCGGTCTG
1 -ACCGGTCTG
2282634 ACCGGTCTG
1 ACCGGTCTG
2282643 ACC
1 ACC
2282646 CAACCCGACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.15, C:0.33, G:0.30, T:0.23
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:2282667 original size:5 final size:5
Alignment explanation
Indices: 2282659--2282720 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
2282649 CCCGACCGTT
* *
2282659 GACCC GACCC GACCC GACCGTT GACCC GACCC GA-CC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
2282707 GACCC GACCC GACC
1 GACCC GACCC GACC
2282721 GTTGACCGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
4 4 0.08
5 36 0.75
7 8 0.17
ACGTcount: A:0.19, C:0.52, G:0.23, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:2282668 original size:22 final size:22
Alignment explanation
Indices: 2282642--2282727 Score: 156
Period size: 22 Copynumber: 4.0 Consensus size: 22
2282632 TGACCGGTCT
*
2282642 GACCCAACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2282664 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2282686 GACCCGA-CCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2282707 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2282728 GTTGACCGTT
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
21 21 0.34
22 41 0.66
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2282727 original size:17 final size:17
Alignment explanation
Indices: 2282664--2282715 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 17
2282654 CCGTTGACCC
2282664 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
2282681 GACCCGACCCGACCGACCGTT
1 GACCCGA--C--CCGACCGTT
2282702 GACCCGACCCGACC
1 GACCCGACCCGACC
2282716 CGACCGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 13 0.42
19 2 0.06
21 16 0.52
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:2282729 original size:7 final size:7
Alignment explanation
Indices: 2282717--2282747 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2282707 GACCCGACCC
2282717 GACCGTT
1 GACCGTT
2282724 GACCGTT
1 GACCGTT
2282731 GACCGTT
1 GACCGTT
2282738 GACCGTT
1 GACCGTT
2282745 GAC
1 GAC
2282748 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2289909 original size:9 final size:9
Alignment explanation
Indices: 2289895--2289948 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
2289885 GGCTGCTGGA
2289895 AACCGGTTT
1 AACCGGTTT
*
2289904 AACCGGTTCG
1 AACCGGTT-T
2289914 AACCGGTTT
1 AACCGGTTT
* *
2289923 GACCGGTCTG
1 AACCGGT-TT
2289933 AACCGGTTT
1 AACCGGTTT
*
2289942 GACCGGT
1 AACCGGT
2289949 CTGACCCAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
9 21 0.58
10 15 0.42
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (9 bp):
AACCGGTTT
Found at i:2289919 original size:19 final size:20
Alignment explanation
Indices: 2289895--2289952 Score: 86
Period size: 19 Copynumber: 3.0 Consensus size: 20
2289885 GGCTGCTGGA
*
2289895 AACCGGTTTAACCGGTTC-G
1 AACCGGTTTGACCGGTTCTG
2289914 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
2289933 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
2289952 A
1 A
2289953 CCCAACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
18 2 0.05
19 35 0.95
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:2289953 original size:9 final size:9
Alignment explanation
Indices: 2289915--2289954 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2289905 ACCGGTTCGA
*
2289915 ACCGGTTTG
1 ACCGGTCTG
2289924 ACCGGTCTG
1 ACCGGTCTG
*
2289933 AACCGGTTTG
1 -ACCGGTCTG
2289943 ACCGGTCTG
1 ACCGGTCTG
2289952 ACC
1 ACC
2289955 CAACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:2289976 original size:5 final size:5
Alignment explanation
Indices: 2289968--2290030 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
2289958 CCCGACCGTT
* *
2289968 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
2290017 GACCC GACCC GACC
1 GACCC GACCC GACC
2290031 GTTGACCGTT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.06
Consensus pattern (5 bp):
GACCC
Found at i:2289977 original size:22 final size:22
Alignment explanation
Indices: 2289951--2290037 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
2289941 TGACCGGTCT
*
2289951 GACCCAACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2289973 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2289995 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
2290017 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
2290038 GTTGACCGTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:2290039 original size:7 final size:7
Alignment explanation
Indices: 2290027--2290057 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2290017 GACCCGACCC
2290027 GACCGTT
1 GACCGTT
2290034 GACCGTT
1 GACCGTT
2290041 GACCGTT
1 GACCGTT
2290048 GACCGTT
1 GACCGTT
2290055 GAC
1 GAC
2290058 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:2294275 original size:3 final size:3
Alignment explanation
Indices: 2294257--2294328 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
2294247 TGTAATATTA
* * * * * *
2294257 AAT AAT ATAT ATT AAT AAT AAT AAT TAT TAT TAT TAT AAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2294303 AAT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2294329 CATTAAAATG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2294590 original size:17 final size:17
Alignment explanation
Indices: 2294568--2294627 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2294558 TTGAATAAGC
2294568 TCTTCTTATTATGAACT
1 TCTTCTTATTATGAACT
* *
2294585 TCTTCTTCTCCTGATG-AGT
1 TCTTCTTAT--T-ATGAACT
* *
2294604 TCTTCTCATTATGAGCT
1 TCTTCTTATTATGAACT
2294621 TCTTCTT
1 TCTTCTT
2294628 CCTTCTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 8
0.68 0.15 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.50
19 10 0.31
20 3 0.09
ACGTcount: A:0.15, C:0.23, G:0.10, T:0.52
Consensus pattern (17 bp):
TCTTCTTATTATGAACT
Found at i:2294608 original size:16 final size:17
Alignment explanation
Indices: 2294586--2294626 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2294576 TTATGAACTT
*
2294586 CTTCTTCTCCTGATGAG
1 CTTCTTCTCATGATGAG
*
2294603 -TTCTTCTCATTATGAG
1 CTTCTTCTCATGATGAG
2294619 CTTCTTCT
1 CTTCTTCT
2294627 TCCTTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.12, C:0.27, G:0.12, T:0.49
Consensus pattern (17 bp):
CTTCTTCTCATGATGAG
Found at i:2294615 original size:36 final size:39
Alignment explanation
Indices: 2294568--2294660 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 39
2294558 TTGAATAAGC
* *
2294568 TCTTCTTATTATGAACTTCTTCTT-C-TC-CTGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGT
*
2294604 TCTTCTCATTATGAGCTTCTTCTTCCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCCTTC-TCAGATGAGT
2294644 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
2294661 CGAACTGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 22 0.45
37 1 0.02
38 2 0.04
40 24 0.49
ACGTcount: A:0.17, C:0.24, G:0.11, T:0.48
Consensus pattern (39 bp):
TCTTCTCATTATGAACTTCTTCTTCCTTCTCAGATGAGT
Found at i:2294754 original size:113 final size:113
Alignment explanation
Indices: 2294603--2295712 Score: 2046
Period size: 113 Copynumber: 9.8 Consensus size: 113
2294593 TCCTGATGAG
*
2294603 TTCTTCTCATTATGAGCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
*
2294668 GAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
* *
2294716 TTCCTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
*
2294781 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTAAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
2294829 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
2294894 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
2294942 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
2295007 GAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
* *
2295055 TTCCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
2295120 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
*
2295168 TTCTTCTCATTAT-AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
2295232 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
2295280 TTCTTCTCATTATGAACTTCTTCATT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
1 TTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
2295344 GGAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
2295393 TTCTTCTCATTATGAACTTCTTCATT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
1 TTCTTCTCATTATGAACTTCTTC-TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACT
2295457 GGAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
2295506 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
2295571 GAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
*
2295619 TTCCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
2295684 GAAAAGCTAATCTATCAAGTGATGGATTT
66 GAAAAGCTAATCCATCAAGTGATAGATTT
2295713 AAATCTTTGC
Statistics
Matches: 971, Mismatches: 23, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
112 112 0.12
113 857 0.88
114 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
Found at i:2295689 original size:564 final size:565
Alignment explanation
Indices: 2294603--2295712 Score: 2116
Period size: 564 Copynumber: 2.0 Consensus size: 565
2294593 TCCTGATGAG
*
2294603 TTCTTCTCATTATGAGCTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
*
2294668 GAAAAGCTAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCCTCTCATTATGAAC
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCCTCTCATTATGAAC
*
2294733 TTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCA
131 TTCTTCATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCA
2294798 AGTGATAGATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
196 AGTGATAGATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
2294863 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATAGATTTGAGCA
261 GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATAGATTTGAGCA
2294928 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
326 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2294993 ATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC
391 ATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC
2295058 CTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACAGGAA
456 CTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACAGGAA
2295123 AAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
521 AAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
*
2295168 TTCTTCTCATTAT-AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
*
2295232 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCCTCTCATTATGAAC
2295297 TTCTTCATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCA
131 TTCTTCATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCA
*
2295362 AGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATT-CTTCTTC
196 AGTGATAGATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTC-TTCCTTCTTC
2295426 AGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATAGATTTGAGC
260 AGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATAGATTTGAGC
2295491 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
325 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
2295556 TATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
390 TATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATT
*
2295621 CCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGA
455 CCTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACAGGA
* *
2295686 AAAGCTAATCTATCAAGTGATGGATTT
520 AAAGCTAATCCATCAAGTGATAGATTT
2295713 AAATCTTTGC
Statistics
Matches: 535, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
564 520 0.97
565 15 0.03
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (565 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GAAAAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCCTCTCATTATGAAC
TTCTTCATTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCA
AGTGATAGATTTGAGCAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGCTAATCCATCAAGTGATAGATTTGAGCA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTC
CTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACAGGAA
AAGCTAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
Found at i:2296592 original size:83 final size:83
Alignment explanation
Indices: 2296407--2296797 Score: 683
Period size: 83 Copynumber: 4.7 Consensus size: 83
2296397 AAACCAAATT
* * *
2296407 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTCATCTTTCCAAATTC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATCTTT-CAAATTC
*
2296472 AATAACTCATTTTACCAAACC
63 AATAACTCGTTTTACCAAACC
2296493 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
2296558 AACTCGTTTTACCAAACC
66 AACTCGTTTTACCAAACC
*
2296576 AGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
*
2296641 AACTGGTTTTACCAAACC
66 AACTCGTTTTACCAAACC
*
2296659 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCATT
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
*
2296724 AACTGGTTTTACCAAACC
66 AACTCGTTTTACCAAACC
2296742 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
2296798 CAGCTAATGT
Statistics
Matches: 297, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
83 245 0.82
84 11 0.04
85 3 0.01
86 38 0.13
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.27
Consensus pattern (83 bp):
AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAAT
AACTCGTTTTACCAAACC
Found at i:2297949 original size:1 final size:1
Alignment explanation
Indices: 2297945--2298013 Score: 57
Period size: 1 Copynumber: 69.0 Consensus size: 1
2297935 CCTTTTCTTC
* * * * * * * * *
2297945 TTTTTTCTTTTTTTTTTATTTTTTCTCTTTTTTTTCTTTTTTTCTTTTCTTTCTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2298010 TTTT
1 TTTT
2298014 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.01, C:0.12, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2297956 original size:8 final size:8
Alignment explanation
Indices: 2297936--2298012 Score: 82
Period size: 8 Copynumber: 9.0 Consensus size: 8
2297926 ACCCCCCCCC
*
2297936 CTTTTCTT
1 CTTTTTTT
2297944 CTTTTTTCTT
1 C-TTTTT-TT
*
2297954 TTTTTTTT
1 CTTTTTTT
*
2297962 ATTTTTTCT
1 CTTTTTT-T
2297971 CTTTTTTTT
1 C-TTTTTTT
2297980 CTTTTTTT
1 CTTTTTTT
2297988 CTTTTCTTT
1 CTTTT-TTT
2297997 CTTTTTTT
1 CTTTTTTT
2298005 CTTTTTTT
1 CTTTTTTT
2298013 TCTTCAAGCA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
8 32 0.53
9 20 0.33
10 8 0.13
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.84
Consensus pattern (8 bp):
CTTTTTTT
Found at i:2297957 original size:9 final size:9
Alignment explanation
Indices: 2297937--2298016 Score: 101
Period size: 9 Copynumber: 8.8 Consensus size: 9
2297927 CCCCCCCCCC
2297937 TTTTCTTCTT
1 TTTTCTT-TT
2297947 TTTTCTTTT
1 TTTTCTTTT
*
2297956 TTTTTTATTT
1 TTTTCT-TTT
2297966 TTTCTCTTTT
1 TTT-TCTTTT
2297976 TTTTC-TTT
1 TTTTCTTTT
2297984 TTTTCTTTT
1 TTTTCTTTT
*
2297993 CTTTC-TTT
1 TTTTCTTTT
2298001 TTTTCTTTT
1 TTTTCTTTT
2298010 TTTTCTT
1 TTTTCTT
2298017 CAAGCATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
8 15 0.24
9 26 0.42
10 19 0.31
11 2 0.03
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:2297966 original size:17 final size:16
Alignment explanation
Indices: 2297946--2298016 Score: 79
Period size: 17 Copynumber: 4.1 Consensus size: 16
2297936 CTTTTCTTCT
*
2297946 TTTTTCTTTTTTTTTTA
1 TTTTT-TTTTTTTTTTC
2297963 TTTTTTCTCTTTTTTTTC
1 TTTTTT-T-TTTTTTTTC
*
2297981 TTTTTTTCTTTTCTTTC
1 TTTTTTT-TTTTTTTTC
2297998 TTTTTTTCTTTTTTTTC
1 TTTTTTT-TTTTTTTTC
2298015 TT
1 TT
2298017 CAAGCATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
16 1 0.02
17 34 0.69
18 14 0.29
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.86
Consensus pattern (16 bp):
TTTTTTTTTTTTTTTC
Found at i:2310503 original size:14 final size:15
Alignment explanation
Indices: 2310484--2310540 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2310474 TGGGCTTGTA
2310484 ATATTAA-ATAATAT
1 ATATTAATATAATAT
2310498 ATATTAATATAATA-
1 ATATTAATATAATAT
* *
2310512 ATAATTATTATTATA-
1 AT-ATTAATATAATAT
2310527 AT-TATAATATAATA
1 ATAT-TAATATAATA
2310541 ATTATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 1 0.03
14 17 0.47
15 18 0.50
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATTAATATAATAT
Found at i:2310512 original size:3 final size:3
Alignment explanation
Indices: 2310490--2310559 Score: 63
Period size: 3 Copynumber: 23.7 Consensus size: 3
2310480 TGTAATATTA
* * * * *
2310490 AAT AAT ATAT ATT AAT -AT AAT AAT AAT TAT TAT TAT AAT TAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2310535 -AT AAT AAT TAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2310560 CATTAAAATG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
AAT
Found at i:2310556 original size:29 final size:29
Alignment explanation
Indices: 2310502--2310557 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2310492 TAATATATAT
* * *
2310502 TAATATAATAATAATTATTATTATAATTA
1 TAATATAATAATAATAATAATAATAATTA
*
2310531 TAATATAATAATTATAATAATAATAAT
1 TAATATAATAATAATAATAATAATAAT
2310558 AACATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAATATAATAATAATAATAATAATAATTA
Found at i:2310558 original size:18 final size:19
Alignment explanation
Indices: 2310482--2310559 Score: 76
Period size: 18 Copynumber: 4.3 Consensus size: 19
2310472 TTTGGGCTTG
2310482 TAAT-ATTA-AATAATATA
1 TAATAATTATAATAATATA
*
2310499 TATTAA-TATAATAATA-A
1 TAATAATTATAATAATATA
* * *
2310516 TTATTATTATAATTATAATA
1 TAATAATTATAATAAT-ATA
2310536 TAATAATTATAATAATA-A
1 TAATAATTATAATAATATA
2310554 TAATAA
1 TAATAA
2310560 CATTAAAATG
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
17 9 0.19
18 23 0.48
19 2 0.04
20 14 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAATTATAATAATATA
Found at i:2312441 original size:40 final size:40
Alignment explanation
Indices: 2312397--2312474 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
2312387 GAGAAGTTCT
* ** * *
2312397 TGAACAAGGTTTTATGTTTGTTTAATTAAATGAATGAATA
1 TGAACAAAGTTTTATACTCGTTTAATTAAAAGAATGAATA
*
2312437 TGAACAAAGTTTTCTACTCGTTTAATTAAAAGAATGAA
1 TGAACAAAGTTTTATACTCGTTTAATTAAAAGAATGAA
2312475 CACAAACAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (40 bp):
TGAACAAAGTTTTATACTCGTTTAATTAAAAGAATGAATA
Found at i:2313213 original size:9 final size:10
Alignment explanation
Indices: 2313198--2313248 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 10
2313188 AAATCAGAAA
2313198 ATAATAATAT
1 ATAATAATAT
2313208 -TAATAATAT
1 ATAATAATAT
2313217 ATAATATATAT
1 ATAATA-ATAT
2313228 ATATATATATAT
1 ATA-ATA-ATAT
2313240 ATATATAAT
1 ATA-ATAAT
2313249 GAACAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.24
10 5 0.13
11 9 0.24
12 15 0.39
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATAATAATAT
Found at i:2313225 original size:2 final size:2
Alignment explanation
Indices: 2313213--2313246 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2313203 AATATTAATA
2313213 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2313247 ATGAACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2313353 original size:29 final size:31
Alignment explanation
Indices: 2313301--2313365 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 31
2313291 TGAAGGGGGT
2313301 AATAAATAAATAAATAAATGTAAAA-AGTAAA
1 AATAAATAAATAAATAAATGTAAAATAG-AAA
2313332 AATATAATAAA-AAAT-AA-GTAAAATAGAAA
1 AATA-AATAAATAAATAAATGTAAAATAGAAA
2313361 AATAA
1 AATAA
2313366 GATAGAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
28 1 0.03
29 13 0.41
30 4 0.12
31 8 0.25
32 6 0.19
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (31 bp):
AATAAATAAATAAATAAATGTAAAATAGAAA
Found at i:2313513 original size:15 final size:16
Alignment explanation
Indices: 2313495--2313531 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
2313485 ATAACGATAT
2313495 AAAATATACAT-AATA
1 AAAATATACATAAATA
*
2313510 AAAATATATATAAATA
1 AAAATATACATAAATA
2313526 AAAATA
1 AAAATA
2313532 GAGGAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATATACATAAATA
Found at i:2314293 original size:20 final size:20
Alignment explanation
Indices: 2314268--2314305 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2314258 TTACAAAATA
2314268 TGCTTCGGAAACTTTGTGTT
1 TGCTTCGGAAACTTTGTGTT
* *
2314288 TGCTTCGTAATCTTTGTG
1 TGCTTCGGAAACTTTGTG
2314306 CGTATTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (20 bp):
TGCTTCGGAAACTTTGTGTT
Found at i:2316686 original size:19 final size:19
Alignment explanation
Indices: 2316660--2316710 Score: 86
Period size: 18 Copynumber: 2.7 Consensus size: 19
2316650 TTCTCTTTTC
2316660 TCTTTTTTCAATTTTTCTT
1 TCTTTTTTCAATTTTTCTT
*
2316679 T-TTTTTTTAATTTTTCTT
1 TCTTTTTTCAATTTTTCTT
2316697 TCTTTTTTCAATTT
1 TCTTTTTTCAATTT
2316711 AGGGCGCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.59
19 12 0.41
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (19 bp):
TCTTTTTTCAATTTTTCTT
Found at i:2321904 original size:13 final size:13
Alignment explanation
Indices: 2321869--2321909 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2321859 TAATAATTTG
2321869 TAAACAAA-AATAA
1 TAAACAAATAA-AA
*
2321882 -AAAGAAATAAAA
1 TAAACAAATAAAA
2321894 TAAACAAATAAAA
1 TAAACAAATAAAA
2321907 TAA
1 TAA
2321910 TATGAAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (13 bp):
TAAACAAATAAAA
Found at i:2335777 original size:3 final size:3
Alignment explanation
Indices: 2335771--2335834 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
2335761 ATAAGAAGAA
* * * *
2335771 AAT AAT AAT AAT AAT AAT AAT AAT AGT AGT -AT AA- AAA AAT AAA AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
2335818 AAT ATAT ATAT AAT AAT
1 AAT A-AT A-AT AAT AAT
2335835 TTGTAAACAA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 3 0.06
3 40 0.77
4 9 0.17
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2335873 original size:13 final size:13
Alignment explanation
Indices: 2335838--2335878 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
2335828 TAATAATTTG
2335838 TAAACAAA-AATAA
1 TAAACAAATAA-AA
*
2335851 -AAAGAAATAAAA
1 TAAACAAATAAAA
2335863 TAAACAAATAAAA
1 TAAACAAATAAAA
2335876 TAA
1 TAA
2335879 TATGAAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.15
Consensus pattern (13 bp):
TAAACAAATAAAA
Found at i:2341029 original size:55 final size:55
Alignment explanation
Indices: 2340968--2341132 Score: 285
Period size: 55 Copynumber: 3.0 Consensus size: 55
2340958 GGATGACAAA
2340968 CAAGCAACAAACATGTTGATTCATGTGATAAATAGTTTGATATTATTTAAGTAGG
1 CAAGCAACAAACATGTTGATTCATGTGATAAATAGTTTGATATTATTTAAGTAGG
*
2341023 CAAGCAACAAACATGTTGATTCATGTGATAAATAATTTGATATTATTTAAGTAGG
1 CAAGCAACAAACATGTTGATTCATGTGATAAATAGTTTGATATTATTTAAGTAGG
** * *
2341078 CAAGCAACAAACGGGTTGATTCATGTAATAAACAGTTTGATATTATTTAAGTAGG
1 CAAGCAACAAACATGTTGATTCATGTGATAAATAGTTTGATATTATTTAAGTAGG
2341133 TTTCAAATTC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 104 1.00
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (55 bp):
CAAGCAACAAACATGTTGATTCATGTGATAAATAGTTTGATATTATTTAAGTAGG
Found at i:2344390 original size:21 final size:20
Alignment explanation
Indices: 2344363--2344427 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 20
2344353 ATTCATTTTT
2344363 TAAAAAATCAATAAAAATGCAA
1 TAAAAAAT-AATAAAAATG-AA
*
2344385 TAAAAAATAATTAAAAGTGAA
1 TAAAAAATAA-TAAAAATGAA
** *
2344406 TAAAATTTAATAAAAAAGAA
1 TAAAAAATAATAAAAATGAA
2344426 TA
1 TA
2344428 TAAAGCTAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 10 0.27
21 12 0.32
22 15 0.41
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.23
Consensus pattern (20 bp):
TAAAAAATAATAAAAATGAA
Found at i:2349451 original size:20 final size:20
Alignment explanation
Indices: 2349405--2349451 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2349395 AGTTAGAAAA
* *
2349405 AATTGTTAAATTTGAATATT
1 AATTTTTAAATTTGAATATC
*
2349425 AAATTTTAAATTT-AAGTATC
1 AATTTTTAAATTTGAA-TATC
2349445 AATTTTT
1 AATTTTT
2349452 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (20 bp):
AATTTTTAAATTTGAATATC
Found at i:2354786 original size:19 final size:20
Alignment explanation
Indices: 2354762--2354853 Score: 152
Period size: 20 Copynumber: 4.7 Consensus size: 20
2354752 AATGCATTTT
*
2354762 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
*
2354781 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
2354800 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
2354820 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
2354840 ATGCATCGATGCAC
1 ATGCATCGATGCAC
2354854 TCAGACTTTT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
19 33 0.46
20 38 0.54
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.18
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:2360762 original size:23 final size:22
Alignment explanation
Indices: 2360691--2360772 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
2360681 ACACTTAACA
2360691 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCA-CCC-TTGAAT
* * *
2360715 GTGCATCGATACA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
2360736 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
2360759 GTGCATCGATGCAC
1 GTGCATCGATGCAC
2360773 AAGGCCATGC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 15 0.31
22 2 0.04
23 19 0.40
24 12 0.25
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:2363521 original size:45 final size:46
Alignment explanation
Indices: 2363472--2363563 Score: 141
Period size: 45 Copynumber: 2.0 Consensus size: 46
2363462 TCAAACTTCG
* * *
2363472 AATGCATTTTATGCATCGATCCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATCCACAAGACCATGCATCAATGCACTC
*
2363517 AATGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTC
1 AATGCATTTGATGCATCGATCCACAAGACCATGCATCAATGCACTC
2363563 A
1 A
2363564 GGCTTTTTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.52
46 20 0.48
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATCCACAAGACCATGCATCAATGCACTC
Found at i:2367909 original size:134 final size:131
Alignment explanation
Indices: 2367638--2367964 Score: 379
Period size: 134 Copynumber: 2.5 Consensus size: 131
2367628 GTCGTGTGAC
* * * * *
2367638 CCGTGTCATCCCCCGACCAGACCTCCTCATCACATAGAAGCCATATCACCCCT-GATAACCAGCC
1 CCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCC
* * *
2367702 GTCTTCATCACATGGGAACCGTGTTATCATCCCTAAAGATGGCATGCTCTCCTCATCACATAGGA
66 GTCCTCATCACATAGGAACCGTGTTATCATCCCTAAAGATGGCATACTCTCCTCATCACATAGGA
2367767 A
131 A
* ** *
2367768 CCATGTCATCCACTAACCAGACCTCCTCATCATGTAGGAGCCGTGTCACCCCTAGATAACCAGCC
1 CCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCC
** * * ***
2367833 GTCCTCATTGCGTAGGAACCGTGTTATCAACCTCCCTAAAGATGGCCTAC-CGTCCTCATCGTGT
66 GTCCTCATCACATAGGAACCGTGTTATC-A--TCCCTAAAGATGGCATACTC-TCCTCATCACAT
2367897 AGGAA
127 AGGAA
* * * * * *
2367902 CCGTGTCATCCTCCGACCAGATCTTCTCATAACGTAGGAGCCGTGTCACCCATAGATGACCAG
1 CCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAG
2367965 AAGTCTTCAT
Statistics
Matches: 163, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
130 44 0.27
131 34 0.21
132 1 0.01
133 1 0.01
134 83 0.51
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (131 bp):
CCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGCC
GTCCTCATCACATAGGAACCGTGTTATCATCCCTAAAGATGGCATACTCTCCTCATCACATAGGA
A
Found at i:2368165 original size:3 final size:3
Alignment explanation
Indices: 2368141--2368179 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2368131 CGGGTCTTTT
* * *
2368141 TTA TTT TTA ATA TTA TTG TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2368180 ATAATACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2369915 original size:22 final size:22
Alignment explanation
Indices: 2369890--2369948 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 22
2369880 TTTTATTTTA
2369890 ATGGCAATGTTTGTTTCTTAAG
1 ATGGCAATGTTTGTTTCTTAAG
2369912 ATGGC-ATGTTAGGTTGTTTCTTAAG
1 ATGGCAATG-T---TTGTTTCTTAAG
2369937 ATGGCAATGTTT
1 ATGGCAATGTTT
2369949 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
21 3 0.09
22 8 0.25
25 18 0.56
26 3 0.09
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.44
Consensus pattern (22 bp):
ATGGCAATGTTTGTTTCTTAAG
Found at i:2372209 original size:13 final size:13
Alignment explanation
Indices: 2372187--2372229 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
2372177 GTCATAACCC
2372187 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2372200 GACCCAACCCGTT
1 GACCCGACCCGTT
2372213 GACCCGACCCGTT
1 GACCCGACCCGTT
2372226 GACC
1 GACC
2372230 GTTGACCGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.19, C:0.47, G:0.21, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2375079 original size:39 final size:38
Alignment explanation
Indices: 2374961--2375080 Score: 106
Period size: 37 Copynumber: 3.2 Consensus size: 38
2374951 TGTCATCTTG
* * *
2374961 CTTGAGACAAGTTTT-CTTAAAAA-TAATTTTTGTCTCG
1 CTTGAGACAATTTTTAC-TAAAAACAAATTTTTGTCTCA
*
2374998 CTAGAGAC--TGTTTTATCTAAAAACAAA-TTTTGTCTCA
1 CTTGAGACAAT-TTTTA-CTAAAAACAAATTTTTGTCTCA
* * *
2375035 ATTGAGACAATTTTTACTCAAAACAAAGTTTTTGTCTCT
1 CTTGAGACAATTTTTACTAAAAACAAA-TTTTTGTCTCA
2375074 CTTGAGA
1 CTTGAGA
2375081 TAGTTTCTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
36 4 0.06
37 38 0.58
38 8 0.12
39 16 0.24
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (38 bp):
CTTGAGACAATTTTTACTAAAAACAAATTTTTGTCTCA
Found at i:2375136 original size:66 final size:66
Alignment explanation
Indices: 2375054--2375226 Score: 188
Period size: 66 Copynumber: 2.6 Consensus size: 66
2375044 ATTTTTACTC
*
2375054 AAAACAAAGTTTTTGTCTCTCTTGAGATAGTTTCTTTTGAAACATA-AATCTTTGAG-TCTATTT
1 AAAAC-AAG-TTTTGTCTCTCTTGAGATAGTTTCTATTGAAACA-ACAATCTTTGAGAT-TATTT
*
2375117 CTCTT
62 CCCTT
* * * * * *
2375122 AAAACAAGTTTTGTCTCTATTGAGACAATTTCCATTGAAACAACTATCTTTGAGATTGTTTCCCT
1 AAAACAAGTTTTGTCTCTCTTGAGATAGTTTCTATTGAAACAACAATCTTTGAGATTATTTCCCT
2375187 T
66 T
* * * *
2375188 GAAACAAATTTTGTCTCTCTTGAGATAGCTTCTCTTGAA
1 AAAACAAGTTTTGTCTCTCTTGAGATAGTTTCTATTGAA
2375227 GCATCAATTT
Statistics
Matches: 87, Mismatches: 16, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
65 1 0.01
66 77 0.89
67 4 0.05
68 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (66 bp):
AAAACAAGTTTTGTCTCTCTTGAGATAGTTTCTATTGAAACAACAATCTTTGAGATTATTTCCCT
T
Found at i:2375766 original size:134 final size:132
Alignment explanation
Indices: 2375263--2375748 Score: 558
Period size: 131 Copynumber: 3.7 Consensus size: 132
2375253 GAAACAAATA
* * * * * * *
2375263 CCTAAAGAAT-GCATGCCGTCCTCATCATGTAGGAAACATGTCATCCACAGATCAGACCTCCTCA
1 CCTAAAG-ATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
* * * **
2375327 TCAT-GTAGGAGTCATGTCACCCCTA-ATTACCAGTCATCCTCATCACAT-AGGAACCGTGTTAT
65 TCATCGTAGGAGCCGTGTCACCCCTAGATAACCAACCATCCTCATCACATGA-GAACCGTGTTAT
*
2375389 AATC
129 CATC
** * *
2375393 CCTAAAGATGGGTTTACCATCCTTATCACGTAGGAACCGTGTCATCCCCCGACCAGACCTCCTCA
1 CCTAAAGAT-GGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
*
2375458 TCA-CGTAGGAGCCATGTCACCCCT-GATAACCAACCATCCTCATCACATGAGAACCGTGTTATC
65 TCATCGTAGGAGCCGTGTCACCCCTAGATAACCAACCATCCTCATCACATGAGAACCGTGTTATC
2375521 ATC
130 ATC
* * * *
2375524 CCTAAAGGTGGCATGCTATCCTCATCACGTAGGAACCATGTCATCCACCGACCAGACCTCCTCAT
1 CCTAAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCAT
* * * * *
2375589 CAT-GTAGGAGCCGTGTCACCCCTAGTTAACCAACCGTCCTCATCGCGTGGGAACCGTGTTATCA
66 CATCGTAGGAGCCGTGTCACCCCTAGATAACCAACCATCCTCATCACATGAGAACCGTGTTATCA
2375653 CCCTC
131 ---TC
* * *
2375658 CCTAAAGATGGCCA-ACCGTCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGATCTTCTCA
1 CCTAAAGATGG-CATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCA
* *
2375722 T-ATCGTAGGAGCCGTGTCTCCCATAGA
65 TCATCGTAGGAGCCGTGTCACCCCTAGA
2375749 CGACCAAAAC
Statistics
Matches: 304, Mismatches: 40, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
129 2 0.01
130 77 0.25
131 143 0.47
132 1 0.00
133 2 0.01
134 77 0.25
135 2 0.01
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.23
Consensus pattern (132 bp):
CCTAAAGATGGCATACCATCCTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTCAT
CATCGTAGGAGCCGTGTCACCCCTAGATAACCAACCATCCTCATCACATGAGAACCGTGTTATCA
TC
Done.