Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007909.1 Hibiscus syriacus cultivar Beakdansim tig00110303_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: 3382237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 17
Found at i:152863 original size:19 final size:19
Alignment explanation
Indices: 152830--152868 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
152820 ATTGCGATAA
**
152830 TAGAGATCGTGTTGCAATT
1 TAGAGATCGCATTGCAATT
*
152849 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCAATT
152868 T
1 T
152869 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (19 bp):
TAGAGATCGCATTGCAATT
Found at i:156804 original size:21 final size:22
Alignment explanation
Indices: 156764--156810 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
156754 ATTTTCCATC
156764 TTTTAAATTTGAGTTATT-AAT
1 TTTTAAATTTGAGTTATTAAAT
* * *
156785 TTTTAAATTTTATTTTTTAAAT
1 TTTTAAATTTGAGTTATTAAAT
156807 TTTT
1 TTTT
156811 TTCAGCGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (22 bp):
TTTTAAATTTGAGTTATTAAAT
Found at i:159459 original size:14 final size:14
Alignment explanation
Indices: 159440--159468 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
159430 GGGTGTGAAA
159440 GATCAATTTATGGT
1 GATCAATTTATGGT
159454 GATCAATTTATGGT
1 GATCAATTTATGGT
159468 G
1 G
159469 CTGATGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (14 bp):
GATCAATTTATGGT
Found at i:160762 original size:2 final size:2
Alignment explanation
Indices: 160755--160782 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
160745 AGATATAACA
160755 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
160783 TCAAGTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:166311 original size:22 final size:22
Alignment explanation
Indices: 166268--166308 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
166258 AAAAATTATT
166268 TTTTTATTAAATATTTTTAATA
1 TTTTTATTAAATATTTTTAATA
*
166290 TTTTTATTTAAT-TTTTTAA
1 TTTTTATTAAATATTTTTAA
166309 ATAATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTATTAAATATTTTTAATA
Found at i:166776 original size:14 final size:14
Alignment explanation
Indices: 166736--166781 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
166726 GCGTTTAATA
166736 ATTTGTTTGTTTAT
1 ATTTGTTTGTTTAT
* * **
166750 GTTCGTTCATTTAT
1 ATTTGTTTGTTTAT
166764 ATTTGTTTGTTTAT
1 ATTTGTTTGTTTAT
166778 ATTT
1 ATTT
166782 AGTCCAATCT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.15, C:0.04, G:0.13, T:0.67
Consensus pattern (14 bp):
ATTTGTTTGTTTAT
Found at i:171020 original size:20 final size:21
Alignment explanation
Indices: 170991--171185 Score: 89
Period size: 20 Copynumber: 9.6 Consensus size: 21
170981 AAATGATCAA
170991 CAAATTCGCAACGCGAA-CTC
1 CAAATTCGCAACGCGAATCTC
* * *
171011 CAATTTCGCAAC-CCAATTTC
1 CAAATTCGCAACGCGAATCTC
* *
171031 CAAATTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAATCTC
* ** * *
171052 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGAATCTC
* * *
171072 CAAATTCGCAACGTGAATATG
1 CAAATTCGCAACGCGAATCTC
* ** * *
171093 TAAA-TCGCATTGCGATTTTC
1 CAAATTCGCAACGCGAATCTC
* ** *
171113 TAAATTCGCAACGCGAAAATG
1 CAAATTCGCAACGCGAATCTC
* *
171134 TAAA-TCGTAACGCGAATCTC
1 CAAATTCGCAACGCGAATCTC
* * *
171154 TAAA-TCGCAACACTGAAT-TT
1 CAAATTCGCAACGC-GAATCTC
171174 CAAATTCGCAAC
1 CAAATTCGCAAC
171186 TCGATTTTCG
Statistics
Matches: 128, Mismatches: 41, Indels: 11
0.71 0.23 0.06
Matches are distributed among these distances:
19 3 0.02
20 79 0.62
21 46 0.36
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (21 bp):
CAAATTCGCAACGCGAATCTC
Found at i:171084 original size:41 final size:41
Alignment explanation
Indices: 171027--171140 Score: 201
Period size: 41 Copynumber: 2.8 Consensus size: 41
171017 CGCAACCCAA
171027 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTGCGAT
*
171068 TTTCCAAATTCGCAACGTGAATATGTAAATCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTGCGAT
* *
171109 TTTCTAAATTCGCAACGCGAAAATGTAAATCG
1 TTTCCAAATTCGCAACGCGAATATGTAAATCG
171141 TAACGCGAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
TTTCCAAATTCGCAACGCGAATATGTAAATCGCATTGCGAT
Found at i:171194 original size:20 final size:20
Alignment explanation
Indices: 171171--171225 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
171161 CAACACTGAA
*
171171 TTTCAAATTCGCAACTCGAT
1 TTTCGAATTCGCAACTCGAT
*
171191 TTTCGATTTCGCAACTCGAT
1 TTTCGAATTCGCAACTCGAT
171211 TTTCGAATTCGCAAC
1 TTTCGAATTCGCAAC
171226 ATGAATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTCGAATTCGCAACTCGAT
Found at i:171241 original size:20 final size:19
Alignment explanation
Indices: 171158--171264 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 19
171148 AATCTCTAAA
* *
171158 TCGCAACACTGAATTTCAAAT
1 TCGCAACA-TG-ATTTTAATT
*
171179 TCGCAAC-TCGATTTTCGATT
1 TCGCAACAT-GATTTT-AATT
171199 TCGCAAC-TCGATTTTCGAA-T
1 TCGCAACAT-GATTTT--AATT
171219 TCGCAACATGAATTTTAATT
1 TCGCAACATG-ATTTTAATT
* *
171239 TCGCAACA-GGTTTTATTT
1 TCGCAACATGATTTTAATT
171257 TCGCAACA
1 TCGCAACA
171265 CAAATGTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
18 15 0.21
19 8 0.11
20 36 0.49
21 14 0.19
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (19 bp):
TCGCAACATGATTTTAATT
Found at i:172243 original size:24 final size:24
Alignment explanation
Indices: 172186--172245 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
172176 TAGTCAGTAT
172186 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
172210 -CCAGACTTTGATCTTGGTCAATAC
1 TCGA-AATTTGATCTTGGTCAATAC
*
172234 TCGAATTTTGAT
1 TCGAAATTTGAT
172246 GATGTTTCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 26 0.87
25 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:175002 original size:25 final size:25
Alignment explanation
Indices: 174974--175023 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
174964 AAATCAATTA
*
174974 AACATTGTTGTGGGTAAATTATTTG
1 AACATTGTTATGGGTAAATTATTTG
*
174999 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTAAATTATTTG
175024 GAAAATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTAAATTATTTG
Found at i:175430 original size:18 final size:18
Alignment explanation
Indices: 175409--175445 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
175399 GTAATTGGAG
175409 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
175427 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
175445 T
1 T
175446 ATAAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:175452 original size:24 final size:24
Alignment explanation
Indices: 175401--175453 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
175391 TTTAATATGT
* * *
175401 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
175425 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
175449 AATTT
1 AATTT
175454 TGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:176534 original size:31 final size:31
Alignment explanation
Indices: 176496--176558 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
176486 CCCGAAGGAC
*
176496 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* *
176527 CAGTCCATATGTTCCGAAGAACATATGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
176558 C
1 C
176559 CCTCGACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:177323 original size:64 final size:63
Alignment explanation
Indices: 177215--177371 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 63
177205 TAATGAAGGT
* * * * * **
177215 ATGCATCGATGCACTACTAATGCATTGGTGCATAAAATGTATTCGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTATTCATT-TTAA-AAG
* * *
177279 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATTTTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTATTCATTTTAAAAG
* * *
177342 AGCGCATCGATGCACTTCTTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
177372 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 2 0.03
64 71 0.91
65 5 0.06
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTATTCATTTTAAAAG
Found at i:181384 original size:64 final size:64
Alignment explanation
Indices: 181251--181407 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
181241 TAATGAAGGT
* * * * * *
181251 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTCATTATTAAAGAG
* * *
181315 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGT-TTCATTATTAAAGAG
* * * *
181378 AGTGCATTGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
181408 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 2 0.03
64 71 0.91
65 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAAATGCATTCGATGTTTCATTATTAAAGAG
Found at i:185423 original size:64 final size:64
Alignment explanation
Indices: 185288--185430 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 64
185278 TAATGAAGGT
* * * * * *
185288 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTAATGATGCATCGATGCACAAAATGTATTCGATATTTCATTATTAAAGAG
* * * * *
185352 ATACATCGATGCACTAATTATGCATCGATGCACGAATTGTATTCGATATATTTATT-TTAAA-AG
1 ATGCATCGATGCACTAATGATGCATCGATGCACAAAATGTATTCGATAT-TTCATTATTAAAGAG
185415 AGTGCATCGATGCACT
1 A-TGCATCGATGCACT
185431 TCCTGTGCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 2 0.03
64 58 0.89
65 5 0.08
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTAATGATGCATCGATGCACAAAATGTATTCGATATTTCATTATTAAAGAG
Found at i:186779 original size:18 final size:18
Alignment explanation
Indices: 186756--186793 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
186746 AGAAAAAGGA
*
186756 AATCAAAATCGCAATCAC
1 AATCAAAATCCCAATCAC
186774 AATCAAAATCCCAATCAC
1 AATCAAAATCCCAATCAC
186792 AA
1 AA
186794 CCGGCTTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.29, G:0.03, T:0.16
Consensus pattern (18 bp):
AATCAAAATCCCAATCAC
Found at i:187317 original size:14 final size:14
Alignment explanation
Indices: 187295--187331 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
187285 CATAAATTAA
187295 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
187309 ACAATTCAACTTTT
1 ACAAATCAACTTTT
187323 ACAAATCAA
1 ACAAATCAA
187332 TTAAACAAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:187371 original size:78 final size:78
Alignment explanation
Indices: 187231--187423 Score: 277
Period size: 78 Copynumber: 2.5 Consensus size: 78
187221 ATTTAAAACA
187231 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATAAATTAAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATAAATTAAA
*
187296 CAAATCAACTTTT
66 CAAATCAAATTTT
* * * * *
187309 ACAATTCAACTTTTACAAATCAATTAAACAAGCAAAACATAATTCTT-TATTCCTCATCAATTAA
1 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTAT-TTACACATAAATTAA
187373 ACAAATCAAATTTT
65 ACAAATCAAATTTT
*
187387 ACAAATCAA--TGTA-AAATTCAATTAAACAAGCAAAAAA
1 ACAAATCAACTTTTACAAA-TCAATTAAACAAGCAAAAAA
187424 AGTGTACCCC
Statistics
Matches: 104, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
75 3 0.03
76 22 0.21
77 1 0.01
78 78 0.75
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATAAATTAAA
CAAATCAAATTTT
Found at i:190953 original size:20 final size:20
Alignment explanation
Indices: 190914--190953 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
190904 TGCGATTTTG
* * *
190914 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
190934 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
190954 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:191319 original size:22 final size:22
Alignment explanation
Indices: 191289--191333 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
191279 GATGGAGATA
*
191289 GACGGATTTCG-CTGGAGATGGG
1 GACGAATTTCGTC-GGAGATGGG
191311 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
191333 G
1 G
191334 GCAGATGTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.20, C:0.13, G:0.44, T:0.22
Consensus pattern (22 bp):
GACGAATTTCGTCGGAGATGGG
Found at i:191523 original size:20 final size:20
Alignment explanation
Indices: 191498--191536 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
191488 AGCTCTTTGC
191498 GAATTTGACTTATGTGTTGT
1 GAATTTGACTTATGTGTTGT
*
191518 GAATTTGACTTCTGTGTTG
1 GAATTTGACTTATGTGTTG
191537 CGATTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.08, G:0.26, T:0.49
Consensus pattern (20 bp):
GAATTTGACTTATGTGTTGT
Found at i:192573 original size:21 final size:20
Alignment explanation
Indices: 192548--192586 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
192538 TTTAGTTATA
192548 ATTTAAATAATATTATCTAAG
1 ATTTAAAT-ATATTATCTAAG
* *
192569 ATTTACATATATTTTCTA
1 ATTTAAATATATTATCTA
192587 TTTTTTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTAAATATATTATCTAAG
Found at i:196661 original size:3 final size:3
Alignment explanation
Indices: 196653--196714 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
196643 TTTATATAAA
*
196653 TAT TAT TAT AAT TAT T-T TAT TAT TA- TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
196697 TAT TA- AAT TAT T-T TAT TA
1 TAT TAT TAT TAT TAT TAT TA
196715 CGTTTCAGAC
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 7 0.14
3 41 0.82
4 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:196707 original size:32 final size:32
Alignment explanation
Indices: 196653--196713 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
196643 TTTATATAAA
**
196653 TATTATTATAATTATTTTATTATTATATTTAT
1 TATTATTATAATTATTAAATTATTATATTTAT
* *
196685 TATTATTATTATTATTAAATTATTTTATT
1 TATTATTATAATTATTAAATTATTATATT
196714 ACGTTTCAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
TATTATTATAATTATTAAATTATTATATTTAT
Found at i:197757 original size:14 final size:13
Alignment explanation
Indices: 197732--197771 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
197722 CACTATTTAG
197732 TTATATTTTAATT
1 TTATATTTTAATT
197745 TTATATATTTAATT
1 TTATAT-TTTAATT
**
197759 CAATATTTTAATT
1 TTATATTTTAATT
197772 ATCATTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:197766 original size:37 final size:38
Alignment explanation
Indices: 197694--197766 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
197684 TATTTTAGTA
* *
197694 TTATAGTTTCAATTTTATTTATTTTAATCACTATTTAG
1 TTATAGTTTCAATTTTATATATTTTAATCAATATTTAG
*
197732 TTATA-TTTTAATTTTATATA-TTTAATTCAATATTT
1 TTATAGTTTCAATTTTATATATTTTAA-TCAATATTT
197767 TAATTATCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 5 0.16
37 21 0.68
38 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (38 bp):
TTATAGTTTCAATTTTATATATTTTAATCAATATTTAG
Found at i:199218 original size:75 final size:76
Alignment explanation
Indices: 199095--199246 Score: 263
Period size: 75 Copynumber: 2.0 Consensus size: 76
199085 CCTTGCCATC
*
199095 TCTCTAGTCAGACATCATTATTCTTGACGTTGATTGGCCATCGAGATTACGTGGTGTCGTAATTT
1 TCTCTAGTCAGACATCATCATTCTTGACGTTGATTGGCCATCGAGATTACGTGGTGTCGTAATTT
199160 GCAA-TTTTTT
66 GCAACTTTTTT
199170 TCTCTAGTCAGACATCATCATTCTTGACGTT-ATTTGGCCATCGAGATTACGTGGTGTCGTAATT
1 TCTCTAGTCAGACATCATCATTCTTGACGTTGA-TTGGCCATCGAGATTACGTGGTGTCGTAATT
*
199234 TGTAACTTTTTT
65 TGCAACTTTTTT
199246 T
1 T
199247 TTGCGTTGAG
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
74 1 0.01
75 65 0.89
76 7 0.10
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (76 bp):
TCTCTAGTCAGACATCATCATTCTTGACGTTGATTGGCCATCGAGATTACGTGGTGTCGTAATTT
GCAACTTTTTT
Found at i:207838 original size:35 final size:35
Alignment explanation
Indices: 207798--207868 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
207788 AAAATGATTT
207798 AAAAAATGGAAAAAAGTAACATACTCATGCGCACG
1 AAAAAATGGAAAAAAGTAACATACTCATGCGCACG
207833 AAAAAATGGAAAAAAGTAACATACTCATGCGCACG
1 AAAAAATGGAAAAAAGTAACATACTCATGCGCACG
207868 A
1 A
207869 CTAACTGACG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.52, C:0.17, G:0.17, T:0.14
Consensus pattern (35 bp):
AAAAAATGGAAAAAAGTAACATACTCATGCGCACG
Found at i:208832 original size:139 final size:139
Alignment explanation
Indices: 208539--208864 Score: 532
Period size: 139 Copynumber: 2.4 Consensus size: 139
208529 GGCATGACAA
*
208539 TGCGCCTTCCCTTTTTTT-TCCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCG
1 TGCGCCTTCCCTTTTTTTGT-CAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCA
208603 GCGTGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAAGTGGTGAAAGCGCG
65 GCGTGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAAGTGGTGAAAGCGCG
208668 TTTTAGGGGG
130 TTTTAGGGGG
** *
208678 CACGCCTTCCCTTTTTTTGTTAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCAG
1 TGCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCAG
* * * *
208743 TGTGGCACTATTCATGTTAGTACCTATCATGTTTGA-GGGATGCAATAATGTGGTGAAAGCGCGT
66 CGTGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAAGTGGTGAAAGCGCGT
208807 TTTAGGGGG
131 TTTAGGGGG
* *
208816 TGCGCCTTCCC-TTTTTTGTCAGATAATAGGTTATAATTGCCCTATTATG
1 TGCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATG
208865 CTTGAAATTT
Statistics
Matches: 173, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
137 35 0.20
138 44 0.25
139 93 0.54
140 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (139 bp):
TGCGCCTTCCCTTTTTTTGTCAGAGAATATGTTATAATTGCCCTATTATGTGTGATGTCCCCCAG
CGTGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAAGTGGTGAAAGCGCGT
TTTAGGGGG
Found at i:208912 original size:20 final size:20
Alignment explanation
Indices: 208866--208912 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
208856 CCTATTATGC
**
208866 TTGAAATTTATGTTAGAGTG
1 TTGAAATTTATGTTAGAAAG
208886 TTG-AATTTGATGTTAGAAAG
1 TTGAAATTT-ATGTTAGAAAG
208906 -TGAAATT
1 TTGAAATT
208913 GGGTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGAAATTTATGTTAGAAAG
Found at i:209900 original size:21 final size:21
Alignment explanation
Indices: 209876--209948 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
209866 GGTGTCATAA
*
209876 AACCTTGCGGGCTGGGCATGT
1 AACCTTGCGGGCTGGGAATGT
*
209897 AACCTTGCGGGCTGGGTAT-T
1 AACCTTGCGGGCTGGGAATGT
* * *
209917 TACCTCTGTGGGCTAGGAATGT
1 AACCT-TGCGGGCTGGGAATGT
*
209939 AACCCTGCGG
1 AACCTTGCGG
209949 AGATGGCATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 5 0.12
21 33 0.79
22 4 0.10
ACGTcount: A:0.16, C:0.23, G:0.34, T:0.26
Consensus pattern (21 bp):
AACCTTGCGGGCTGGGAATGT
Found at i:210020 original size:42 final size:42
Alignment explanation
Indices: 209924--210029 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
209914 ATTTACCTCT
* **
209924 GTGGGCTAGGAATGTAACCC-TGCGGAGATGGCATATGAACTG
1 GTGGGCTAGGCATGT-ACCCTTGCGGAGATGAAATATGAACTG
* * *
209966 GTGGGCTTGGCATATACCCTTGCGGAGATGAAATCTGAACTG
1 GTGGGCTAGGCATGTACCCTTGCGGAGATGAAATATGAACTG
*
210008 GTGGGCTAGGCATGCACCCTTG
1 GTGGGCTAGGCATGTACCCTTG
210030 TGGCATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.07
42 50 0.93
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (42 bp):
GTGGGCTAGGCATGTACCCTTGCGGAGATGAAATATGAACTG
Found at i:210784 original size:20 final size:20
Alignment explanation
Indices: 210759--210797 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
210749 TTTTCAAGGA
210759 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
210779 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
210798 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:213084 original size:16 final size:16
Alignment explanation
Indices: 213063--213095 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
213053 ATTGATGATC
213063 TTAAAACTTCTTTTAA
1 TTAAAACTTCTTTTAA
213079 TTAAAACTTCTTTTAA
1 TTAAAACTTCTTTTAA
213095 T
1 T
213096 AAGGTTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAACTTCTTTTAA
Found at i:218499 original size:20 final size:20
Alignment explanation
Indices: 218474--218527 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
218464 AGTGCATTTG
218474 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
218494 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
218514 ATGCATCGATGCAC
1 ATGCATCGATGCAC
218528 TCGGGCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:219393 original size:17 final size:17
Alignment explanation
Indices: 219371--219405 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
219361 AAACTGAAAC
219371 ATAAATAT-ATACTTCTA
1 ATAAATATAATA-TTCTA
219388 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
219405 A
1 A
219406 CTATATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:223849 original size:29 final size:29
Alignment explanation
Indices: 223784--223855 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
223774 CGGGGTGATA
* *
223784 TTTACGGGTTGAAATGATTGTTGTGTTAT
1 TTTACGGGTTGAGATGATTGTTGTGTAAT
*
223813 TTTTCGGGTTGAGATGATTGTTGTG-AAT
1 TTTACGGGTTGAGATGATTGTTGTGTAAT
223841 GTTTACGGGTTGAGA
1 -TTTACGGGTTGAGA
223856 ACGTATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.19, C:0.04, G:0.32, T:0.44
Consensus pattern (29 bp):
TTTACGGGTTGAGATGATTGTTGTGTAAT
Found at i:224642 original size:21 final size:21
Alignment explanation
Indices: 224618--224658 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
224608 AATGAGATTG
224618 ATTTTTTATATATTAATATTA
1 ATTTTTTATATATTAATATTA
224639 ATTTTTTATATATTAATATT
1 ATTTTTTATATATTAATATT
224659 TTTCTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTTTATATATTAATATTA
Found at i:224670 original size:21 final size:20
Alignment explanation
Indices: 224618--224671 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
224608 AATGAGATTG
*
224618 ATTTTTTATATATTAATATT
1 ATTTTTAATATATTAATATT
*
224638 AATTTTTTATATATTAATATT
1 -ATTTTTAATATATTAATATT
224659 -TTTCTTAA-ATATT
1 ATTT-TTAATATATT
224672 TGTTGACTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 8 0.26
20 3 0.10
21 20 0.65
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
ATTTTTAATATATTAATATT
Found at i:226148 original size:24 final size:24
Alignment explanation
Indices: 226116--226176 Score: 122
Period size: 24 Copynumber: 2.5 Consensus size: 24
226106 ACAAAAGCAT
226116 TTTAAATGAATAATCAAAACATAA
1 TTTAAATGAATAATCAAAACATAA
226140 TTTAAATGAATAATCAAAACATAA
1 TTTAAATGAATAATCAAAACATAA
226164 TTTAAATGAATAA
1 TTTAAATGAATAA
226177 AAGAAGTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.31
Consensus pattern (24 bp):
TTTAAATGAATAATCAAAACATAA
Found at i:228195 original size:32 final size:31
Alignment explanation
Indices: 228129--228224 Score: 86
Period size: 32 Copynumber: 3.0 Consensus size: 31
228119 GGTCAATATC
**
228129 GGGTCAGGTCAATA-TTAGATCAGTTGATTTTTT
1 GGGTCAGGTCAATACCGA-ATCAGTTGA--TTTT
* * *
228162 GGGTCGGGTTAATACCGAATCGGTTAGATTTT
1 GGGTCAGGTCAATACCGAATCAGTT-GATTTT
* *
228194 GGGTCAGGTCAATATCGGATCAGTTGATTTT
1 GGGTCAGGTCAATACCGAATCAGTTGATTTT
228225 CGGTTTAGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
31 6 0.12
32 24 0.47
33 18 0.35
34 3 0.06
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.38
Consensus pattern (31 bp):
GGGTCAGGTCAATACCGAATCAGTTGATTTT
Found at i:228487 original size:30 final size:30
Alignment explanation
Indices: 228453--228516 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
228443 TGATCCTATA
*
228453 ATATGTGTTATAATTTGTTATCAAAATTTT
1 ATATGTGTTAGAATTTGTTATCAAAATTTT
* *
228483 ATATGTGTTAGATTTTGTTATCAAATTTTT
1 ATATGTGTTAGAATTTGTTATCAAAATTTT
228513 ATAT
1 ATAT
228517 TAAGCTCGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.55
Consensus pattern (30 bp):
ATATGTGTTAGAATTTGTTATCAAAATTTT
Found at i:231390 original size:33 final size:33
Alignment explanation
Indices: 231279--231393 Score: 124
Period size: 33 Copynumber: 3.5 Consensus size: 33
231269 ATTTCTGTTT
* * * *
231279 AGGTTGCTTTCGGGTCGGATTAAAA-TTGGTTC
1 AGGTTTCTTTCAGTTCGGGTTAAAATTTGGTTC
* * * *
231311 AAGTTGCTTTCAGATCGGTTTAAAATTTGGTTC
1 AGGTTTCTTTCAGTTCGGGTTAAAATTTGGTTC
* * *
231344 GGGTTTCTTTCAGTTTGGGTTAAAATTTAGTTC
1 AGGTTTCTTTCAGTTCGGGTTAAAATTTGGTTC
231377 AGGTTTCTTTCAGTTCG
1 AGGTTTCTTTCAGTTCG
231394 AGTTGCTTTC
Statistics
Matches: 69, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
32 21 0.30
33 48 0.70
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.43
Consensus pattern (33 bp):
AGGTTTCTTTCAGTTCGGGTTAAAATTTGGTTC
Found at i:241045 original size:23 final size:23
Alignment explanation
Indices: 241019--241067 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
241009 ATAAAGAACC
* *
241019 AAAATAAA-TTTAAATATACCATT
1 AAAATAAAGTCTAAACAT-CCATT
241042 AAAATAAAGTCTAAACATCCATT
1 AAAATAAAGTCTAAACATCCATT
241065 AAA
1 AAA
241068 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGTCTAAACATCCATT
Found at i:249116 original size:23 final size:23
Alignment explanation
Indices: 249090--249138 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
249080 ATAAAGAACC
*
249090 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
249113 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
249136 AAA
1 AAA
249139 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:250894 original size:76 final size:75
Alignment explanation
Indices: 250803--250967 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
250793 TTAAACTCAA
*
250803 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
250867 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
250879 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
250944 TTTAATTAGG
66 TTTAATTAAG
*
250954 ATTTAGAATATTAT
1 ATTTAGGATATTAT
250968 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:250953 original size:19 final size:19
Alignment explanation
Indices: 250925--250987 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
250915 TGTATTTTAG
*
250925 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
250944 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
250963 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
250984 TTTA
1 TTTA
250988 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:257310 original size:15 final size:15
Alignment explanation
Indices: 257290--257321 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
257280 AGGCAACACA
257290 TTTCGTTATATTTTT
1 TTTCGTTATATTTTT
*
257305 TTTCGTTTTATTTTT
1 TTTCGTTATATTTTT
257320 TT
1 TT
257322 AGCGAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.09, C:0.06, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTCGTTATATTTTT
Found at i:259266 original size:76 final size:75
Alignment explanation
Indices: 259175--259339 Score: 226
Period size: 76 Copynumber: 2.2 Consensus size: 75
259165 TTAAACTCAA
*
259175 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAAT-GTGTTTTTAG
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAG-G-TTTTAG
259238 TATTTTAATTAAG
63 TATTTTAATTAAG
* * * *
259251 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
259316 TTTAATTAGG
66 TTTAATTAAG
*
259326 ATTTAGAATATTAT
1 ATTTAGGATATTAT
259340 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
75 37 0.47
76 41 0.52
77 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:259988 original size:21 final size:20
Alignment explanation
Indices: 259963--260010 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
259953 CTTTAATTTG
*
259963 TTTATTTAATTATTTTTTTCT
1 TTTATTTAATTATTATTTT-T
*
259984 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
260004 TTTATTT
1 TTTATTT
260011 TAACCACAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTAATTATTATTTTT
Found at i:260067 original size:9 final size:9
Alignment explanation
Indices: 260040--260083 Score: 54
Period size: 9 Copynumber: 5.0 Consensus size: 9
260030 AATCCCCCTT
*
260040 TTATATTTA
1 TTATTTTTA
*
260049 TTA-TTATA
1 TTATTTTTA
260057 TTATTTTTA
1 TTATTTTTA
260066 TTATTTTTA
1 TTATTTTTA
*
260075 TTTTTTTTA
1 TTATTTTTA
260084 ATATATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 6 0.20
9 24 0.80
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTATTTTTA
Found at i:262445 original size:30 final size:31
Alignment explanation
Indices: 262394--262467 Score: 107
Period size: 30 Copynumber: 2.4 Consensus size: 31
262384 TTAAATAATA
*
262394 AATCTGAATTTTTATTATTTTATAT-AAATG
1 AATCTGATTTTTTATTATTTTATATCAAATG
*
262424 AATCTG-TTTTTTATTTTTTTTATATCAAATG
1 AATCTGATTTTTTA-TTATTTTATATCAAATG
262455 AATCTGATTTTTT
1 AATCTGATTTTTT
262468 TTCTTGCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 6 0.15
30 16 0.41
31 11 0.28
32 6 0.15
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.58
Consensus pattern (31 bp):
AATCTGATTTTTTATTATTTTATATCAAATG
Found at i:262712 original size:22 final size:22
Alignment explanation
Indices: 262686--262727 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
262676 AGCAAATCAC
262686 ATTAGTAGATGCAAAAAGTAAT
1 ATTAGTAGATGCAAAAAGTAAT
*
262708 ATTAGTAGGTGCAAAAAGTA
1 ATTAGTAGATGCAAAAAGTA
262728 TCCCCAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.05, G:0.21, T:0.26
Consensus pattern (22 bp):
ATTAGTAGATGCAAAAAGTAAT
Found at i:263382 original size:12 final size:12
Alignment explanation
Indices: 263365--263389 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
263355 GATGTGCGTC
263365 TCATATTTTGAA
1 TCATATTTTGAA
263377 TCATATTTTGAA
1 TCATATTTTGAA
263389 T
1 T
263390 TTGATTGTAC
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TCATATTTTGAA
Found at i:264865 original size:22 final size:21
Alignment explanation
Indices: 264821--264873 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
264811 ATAATCATTT
264821 AAAAAATTAAATAAAAATACA
1 AAAAAATTAAATAAAAATACA
*
264842 AAAAATATTTAATAAAAA-ATCA
1 AAAAA-ATTAAATAAAAATA-CA
264864 AACAAAATTA
1 AA-AAAATTA
264874 GGTTGAACCG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.22
22 18 0.67
23 3 0.11
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:275058 original size:5 final size:5
Alignment explanation
Indices: 275048--275072 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
275038 GTACCTTTTT
275048 CTTTC CTTTC CTTTC CTTTC CTTTC
1 CTTTC CTTTC CTTTC CTTTC CTTTC
275073 ATTGTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
CTTTC
Found at i:277150 original size:51 final size:51
Alignment explanation
Indices: 277074--277176 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
277064 CTAGATTCGA
277074 GCAGCATTGTTTTGTTTGTACGGTGTAAGAGTTTATCCAAATAAAGAACAT
1 GCAGCATTGTTTTGTTTGTACGGTGTAAGAGTTTATCCAAATAAAGAACAT
277125 GCAGCATTGTTTTGTTTGTACGGTGTAAGAGTTTATCCAAATAAAGAACAT
1 GCAGCATTGTTTTGTTTGTACGGTGTAAGAGTTTATCCAAATAAAGAACAT
277176 G
1 G
277177 ATAGATACTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (51 bp):
GCAGCATTGTTTTGTTTGTACGGTGTAAGAGTTTATCCAAATAAAGAACAT
Found at i:279952 original size:32 final size:31
Alignment explanation
Indices: 279877--279953 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
279867 TTATCCTTAT
*
279877 TATATATTTATTTTTTTAACAAATTAGAAAA
1 TATATATTTATTTTTTTAAAAAATTAGAAAA
* * * *
279908 TATTTATATATTTTCTTTAAAAAATT-TAAAT
1 TATATATTTATTTT-TTTAAAAAATTAGAAAA
279939 TCATATATTTATTTT
1 T-ATATATTTATTTT
279954 ATAAAATTGA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
31 16 0.43
32 21 0.57
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (31 bp):
TATATATTTATTTTTTTAAAAAATTAGAAAA
Found at i:285200 original size:2 final size:2
Alignment explanation
Indices: 285193--285223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
285183 TCAATGTCTA
285193 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
285224 AACAACATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:285308 original size:33 final size:35
Alignment explanation
Indices: 285271--285339 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
285261 TACTTTAAAC
* *
285271 ATTTTAAGA-G-AACGATCTCATATAATTTTAGTA
1 ATTTTAAGAGGTAACGATCTCATAAAATTTAAGTA
285304 ATTTTAAGAGGTAACGATCTCATAAAATTTAAGTA
1 ATTTTAAGAGGTAACGATCTCATAAAATTTAAGTA
285339 A
1 A
285340 ATCAAAACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 9 0.28
34 1 0.03
35 22 0.69
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (35 bp):
ATTTTAAGAGGTAACGATCTCATAAAATTTAAGTA
Found at i:285471 original size:20 final size:20
Alignment explanation
Indices: 285446--285488 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
285436 ATCCATCCAT
*
285446 GGACTCACGTAAAAGATAAA
1 GGACTCACATAAAAGATAAA
*
285466 GGACTCGCATAAAAGATAAA
1 GGACTCACATAAAAGATAAA
285486 GGA
1 GGA
285489 TGAGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.23, T:0.14
Consensus pattern (20 bp):
GGACTCACATAAAAGATAAA
Found at i:288516 original size:14 final size:14
Alignment explanation
Indices: 288461--288508 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
288451 CCAACCCAAA
*
288461 TATATTAATAT-TT
1 TATAATAATATATT
*
288474 TAAAATAATATAATT
1 TATAATAATAT-ATT
288489 TATAATAATATATT
1 TATAATAATATATT
288503 TATAAT
1 TATAAT
288509 TATTTATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
13 9 0.30
14 9 0.30
15 12 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATAATAATATATT
Found at i:288561 original size:19 final size:19
Alignment explanation
Indices: 288494--288565 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 19
288484 TAATTTATAA
*
288494 TAATATATTTATAATTATTT
1 TAATAT-TTTATAATAATTT
*
288514 ATTATATTTTA-AATAATTAAAT
1 -TAATATTTTATAATAATT---T
288536 TAAAATATTTTATAATAATTT
1 T--AATATTTTATAATAATTT
288557 TAATATTTT
1 TAATATTTT
288566 CAATAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
19 14 0.33
20 4 0.10
21 8 0.19
22 1 0.02
23 8 0.19
24 7 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TAATATTTTATAATAATTT
Found at i:297558 original size:16 final size:16
Alignment explanation
Indices: 297537--297593 Score: 89
Period size: 16 Copynumber: 3.6 Consensus size: 16
297527 ACAGAGCCTC
297537 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
297553 TGAATCATTCAACATT
1 TGAATCATTCAGCATT
*
297569 TGAATCATTCAGCACT
1 TGAATCATTCAGCATT
297585 T-AATCATTC
1 TGAATCATTC
297594 TGAAGTAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
15 8 0.21
16 30 0.79
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:298954 original size:38 final size:39
Alignment explanation
Indices: 298894--298968 Score: 89
Period size: 38 Copynumber: 1.9 Consensus size: 39
298884 CATTTTTACC
* * **
298894 TCCATCCAGCAGCCCCTCCACG-TGCATTTCCAGCAGTT
1 TCCATCCAACAACCCCTCCACGTTGCAGCTCCAGCAGTT
* *
298932 TCCATCCAACAACCCTTTCACGTTGCAGCTCCAGCAG
1 TCCATCCAACAACCCCTCCACGTTGCAGCTCCAGCAG
298969 CTCCTAGCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
38 18 0.60
39 12 0.40
ACGTcount: A:0.21, C:0.41, G:0.15, T:0.23
Consensus pattern (39 bp):
TCCATCCAACAACCCCTCCACGTTGCAGCTCCAGCAGTT
Found at i:299644 original size:5 final size:5
Alignment explanation
Indices: 299634--299659 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
299624 TGGTCTCGTA
299634 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
299660 GTCCTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:299977 original size:11 final size:11
Alignment explanation
Indices: 299949--299982 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
299939 ATATGTTTAA
*
299949 ATTATTACTTTC
1 ATTATTA-TTTT
299961 ATTATTATTTT
1 ATTATTATTTT
299972 ATTATTATTTT
1 ATTATTATTTT
299983 CATCTTAGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:300268 original size:132 final size:129
Alignment explanation
Indices: 300026--300268 Score: 326
Period size: 132 Copynumber: 1.9 Consensus size: 129
300016 TAAATAATAT
* * *
300026 TATTTTTTTATTTTTAATATTAAGAAATGTGTTATCTTAAAGCAACTAGAAGTCATTTTCTGATA
1 TATTTATTTATTTTTAATATTAAGAAATGGGTTATCTTAAAGCAACTAGAAGTCATTTTCTAATA
* * **
300091 TTTTTAGATAAATAAATATTTTACTTTTATAAATTATAATTTTATTATTATTAGGAAAATTTTTC
66 TTTTTAAATAAATAAATACTTTAC-TTTATAAATTATAAAATTATTATTATTAGGAAAATTTTTC
* * *
300156 TATTTATTTATTTATTAATATTAAAGAAATGGGTTGTCTTATAGCAACTAGAAGTCCTTTTTCTA
1 TATTTATTTATTT-TTAATATT-AAGAAATGGGTTATCTTAAAGCAACTAGAAGT-CATTTTCTA
* *
300221 ATATTTTTAAATAAATAAATACTTTA-TTTATCATTTATAAAAATTATT
63 ATATTTTTAAATAAATAAATACTTTACTTTATAAATTAT-AAAATTATT
300269 TTAATATTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
130 12 0.12
131 18 0.19
132 36 0.37
133 31 0.32
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (129 bp):
TATTTATTTATTTTTAATATTAAGAAATGGGTTATCTTAAAGCAACTAGAAGTCATTTTCTAATA
TTTTTAAATAAATAAATACTTTACTTTATAAATTATAAAATTATTATTATTAGGAAAATTTTTC
Found at i:302060 original size:19 final size:19
Alignment explanation
Indices: 302036--302081 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
302026 AGGAGTTGTA
302036 CGAGAAGCTACTTGAAGCG
1 CGAGAAGCTACTTGAAGCG
302055 CGAGAAGCTACTTGAAGCG
1 CGAGAAGCTACTTGAAGCG
302074 CGAGAAGC
1 CGAGAAGC
302082 AGCTCCGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.13
Consensus pattern (19 bp):
CGAGAAGCTACTTGAAGCG
Found at i:303171 original size:26 final size:26
Alignment explanation
Indices: 303132--303208 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 26
303122 ACCTTTGTTG
* *
303132 CATTTGCATTTTGCATTCGTAATTTTTT
1 CATTTACA-TTTGCATT-GTAATATTTT
* *
303160 CA-TTACATTTGCATTTTTATATTTT
1 CATTTACATTTGCATTGTAATATTTT
* *
303185 CATTTACATTTTCATT-TTATATTT
1 CATTTACATTTGCATTGTAATATTT
303209 GCATCTTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
25 17 0.40
26 20 0.47
27 4 0.09
28 2 0.05
ACGTcount: A:0.22, C:0.13, G:0.05, T:0.60
Consensus pattern (26 bp):
CATTTACATTTGCATTGTAATATTTT
Found at i:303202 original size:25 final size:25
Alignment explanation
Indices: 303156--303208 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
303146 ATTCGTAATT
303156 TTTTCATTACATTTGCATTTTTATA
1 TTTTCATTACATTTGCATTTTTATA
*
303181 TTTTCATTTACATTTTCA-TTTTATA
1 TTTTCA-TTACATTTGCATTTTTATA
303206 TTT
1 TTT
303209 GCATCTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (25 bp):
TTTTCATTACATTTGCATTTTTATA
Found at i:305404 original size:72 final size:72
Alignment explanation
Indices: 305313--305456 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
305303 ATACAATAAA
* *
305313 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAAT
1 GCTTGAGTTATCACCCTAAAACAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAAT
305378 ATGTTAT
66 ATGTTAT
*
305385 GCTTGAGTTATCACCCTAAAACAATTGGTTAATAGCCCCGACTTTATGGATAATATTCAGCTAAT
1 GCTTGAGTTATCACCCTAAAACAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAAT
*
305450 TTGTTAT
66 ATGTTAT
305457 ACTATTATAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCACCCTAAAACAATTGGTTAATAGCCCCAACTTTATGGATAATATTCAGCTAAT
ATGTTAT
Found at i:307707 original size:75 final size:75
Alignment explanation
Indices: 307614--307767 Score: 202
Period size: 75 Copynumber: 2.1 Consensus size: 75
307604 TGGGACATCT
* * *
307614 TGAAAGCCCATTTCAATCAAAAATTA-GAATATTAACGCATTTTGAATGTTTGTATCAGTAAATA
1 TGAAAGCCCATTTCAATC-AAAATCAGGAATATTAACGCATTTTGAACGTTTGTATCAGCAAATA
*
307678 CGGGGGCATAC
65 CAGGGGCATAC
* * ** *
307689 TGAAAGCCCATTTCAATCAGAATCAGGAATGTTGGCGCATTTTGAACGTTTGTATCTGCAAATAC
1 TGAAAGCCCATTTCAATCAAAATCAGGAATATTAACGCATTTTGAACGTTTGTATCAGCAAATAC
*
307754 AGGGGCATGC
66 AGGGGCATAC
307764 TGAA
1 TGAA
307768 GGCTCATATC
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 5 0.07
75 63 0.93
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (75 bp):
TGAAAGCCCATTTCAATCAAAATCAGGAATATTAACGCATTTTGAACGTTTGTATCAGCAAATAC
AGGGGCATAC
Found at i:309138 original size:22 final size:22
Alignment explanation
Indices: 309110--309169 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
309100 ATATCTACAT
309110 TCTTCAAAGATGAAAGATTCTC
1 TCTTCAAAGATGAAAGATTCTC
* * *
309132 TCTTCAAAGATGATATATTCTT
1 TCTTCAAAGATGAAAGATTCTC
*
309154 TTTTCAAAGATGAAAG
1 TCTTCAAAGATGAAAG
309170 CTTTATTGGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGAAAGATTCTC
Found at i:309949 original size:76 final size:76
Alignment explanation
Indices: 309823--310009 Score: 293
Period size: 76 Copynumber: 2.5 Consensus size: 76
309813 CTATTTCCCA
* *
309823 CATCTGTAAGCCCTTCAGTGTATAATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATGTTTTCAA
*
309888 AGCCTTCGGGT
66 AACCTTCGGGT
* * *
309899 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCTTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATGTTTTCAA
309964 AACCTTCGGGT
66 AACCTTCGGGT
* **
309975 CATCTGCAAGCCCTAAAGTGCATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
310010 GCCTTCGGGT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 102 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:310016 original size:45 final size:45
Alignment explanation
Indices: 309952--310200 Score: 336
Period size: 45 Copynumber: 5.5 Consensus size: 45
309942 GGGAGCTTTT
* * *
309952 TGATGTTTTCAAAACCTTCGGGTCATCTGCAAGCCCTAAAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
* * *
309997 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGATCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
* *
310042 GGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
* * *
310087 TGATGTTTTTAAAACCTTCAGGTCATCTGTAAGACCTACAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
* * **
310132 GGATGTTTTCAAAACCTTCGGGTCAACCATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
*
310177 AGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
310201 AGCTTTTTGA
Statistics
Matches: 180, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
45 168 0.93
46 4 0.02
47 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:310288 original size:45 final size:45
Alignment explanation
Indices: 310224--310353 Score: 206
Period size: 45 Copynumber: 2.9 Consensus size: 45
310214 TTAAAGCCTC
* * *
310224 CGGGTCATCTGTAAGACCTATAGTGCATGATGTTTTCAAAACATT
1 CGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAACATT
* *
310269 CGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAACCTT
1 CGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAACATT
*
310314 CGGGTCATTCGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 CGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAA
310354 GAATATTTTA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (45 bp):
CGGGTCATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAACATT
Found at i:311685 original size:2 final size:2
Alignment explanation
Indices: 311672--311707 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
311662 TCATTTAGTC
*
311672 AT AT AA 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
311708 TTGTTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:312021 original size:21 final size:22
Alignment explanation
Indices: 311995--312045 Score: 95
Period size: 21 Copynumber: 2.4 Consensus size: 22
311985 CTTATTATCC
311995 AATTAAATATGAAAAGATCAT-
1 AATTAAATATGAAAAGATCATA
312016 AATTAAATATGAAAAGATCATA
1 AATTAAATATGAAAAGATCATA
312038 AATTAAAT
1 AATTAAAT
312046 TCATATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (22 bp):
AATTAAATATGAAAAGATCATA
Found at i:319166 original size:29 final size:29
Alignment explanation
Indices: 319129--319186 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
319119 CAAAACAATG
* *
319129 AAATTTTACTT-GTTAGGCATCCTTTCTCT
1 AAATATTACTTAGTTA-GCATCATTTCTCT
*
319158 AAATATTACTTATTTAGCATCATTTCTCT
1 AAATATTACTTAGTTAGCATCATTTCTCT
319187 CACATGAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.88
30 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (29 bp):
AAATATTACTTAGTTAGCATCATTTCTCT
Found at i:319445 original size:15 final size:15
Alignment explanation
Indices: 319427--319493 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
319417 AAAAATATTA
319427 AAAAACAAAATAAAT
1 AAAAACAAAATAAAT
319442 AAAAATTCAATAATTAAAT
1 AAAAA--CAA-AA-TAAAT
* *
319461 AATAAA-AACATTAAT
1 AA-AAACAAAATAAAT
319476 --AAACAAAATAAAT
1 AAAAACAAAATAAAT
319489 AAAAA
1 AAAAA
319494 GTCCATATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 16
0.67 0.07 0.27
Matches are distributed among these distances:
12 3 0.08
13 7 0.17
15 12 0.30
16 1 0.03
17 5 0.12
18 2 0.05
19 7 0.17
20 3 0.08
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAACAAAATAAAT
Found at i:319445 original size:24 final size:23
Alignment explanation
Indices: 319410--319493 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 23
319400 GCCAATAATT
319410 AAATAATAAAAATATTAAAAAACA
1 AAATAATAAAAA-ATTAAAAAACA
* * **
319434 AAATAA-ATAAAAATTCAATAATT
1 AAATAATA-AAAAATTAAAAAACA
*
319457 AAATAATAAAAACATTAATAAACA
1 AAATAATAAAAA-ATTAAAAAACA
319481 AAATAAATAAAAA
1 AAAT-AATAAAAA
319494 GTCCATATTA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
23 18 0.38
24 21 0.45
25 8 0.17
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (23 bp):
AAATAATAAAAAATTAAAAAACA
Found at i:319456 original size:47 final size:47
Alignment explanation
Indices: 319402--319621 Score: 234
Period size: 47 Copynumber: 5.0 Consensus size: 47
319392 TTATCTGAGC
* * *
319402 CAATAATTAAATAATAAAAATATTAAAAAACAAAATAAATAAAAATT
1 CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGT
*
319449 CAATAATTAAATAATAAAAACATTAATAAACAAAATAAATAAAAAGT
1 CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGT
*
319496 CCAT-ATTAAATAATAAAAACATTAAGAAACAAAA-AAAT-----GT
1 CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGT
** * * *
319536 CCGTAATT--A-AATAAAAATAGTAAGAAACAAAATAAATAAAAAATT
1 CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAAT-AAAAAGT
*
319581 C-ATAATT--A-AATAAAAACACTAAGAAACAAAATAAATAAAAA
1 CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAA
319622 CAAGTCTATC
Statistics
Matches: 153, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
38 21 0.14
39 5 0.03
40 5 0.03
41 3 0.02
43 5 0.03
44 32 0.21
45 6 0.04
46 29 0.19
47 47 0.31
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.22
Consensus pattern (47 bp):
CAATAATTAAATAATAAAAACATTAAGAAACAAAATAAATAAAAAGT
Found at i:319477 original size:12 final size:12
Alignment explanation
Indices: 319413--319493 Score: 51
Period size: 12 Copynumber: 6.8 Consensus size: 12
319403 AATAATTAAA
*
319413 TAATAAAAATAT
1 TAATAAAAAAAT
*
319425 TAA-AAAACAAAA
1 TAATAAAA-AAAT
*
319437 TAA-ATAAAAAT
1 TAATAAAAAAAT
**
319448 TCAATAATTAAA-
1 T-AATAAAAAAAT
*
319460 TAATAAAAACAT
1 TAATAAAAAAAT
319472 TAATAAACAAAAT
1 TAATAAA-AAAAT
*
319485 AAATAAAAA
1 TAATAAAAA
319494 GTCCATATTA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
11 15 0.29
12 23 0.44
13 14 0.27
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (12 bp):
TAATAAAAAAAT
Found at i:319530 original size:84 final size:81
Alignment explanation
Indices: 319442--319611 Score: 191
Period size: 84 Copynumber: 2.0 Consensus size: 81
319432 CAAAATAAAT
* * *
319442 AAAAAT-TCAATAATTAAATAATAAAAACATTAATAAACAAAATAAATAAAAAGTCCAT-ATTAA
1 AAAAATGTCAATAATT--A-AATAAAAACAGTAAGAAACAAAATAAATAAAAAATCCATAATT--
*
319505 ATAATAAAAACATTAAGAAACAA
61 A-AATAAAAACACTAAGAAAC-A
** * *
319528 AAAAATGTCCGTAATTAAATAAAAATAGTAAGAAACAAAATAAATAAAAAATTCATAATTAAATA
1 AAAAATGTCAATAATTAAATAAAAACAGTAAGAAACAAAATAAATAAAAAATCCATAATTAAATA
319593 AAAACACTAAGAAACA
66 AAAACACTAAGAAACA
319609 AAA
1 AAA
319612 TAAATAAAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
81 4 0.05
82 18 0.24
83 1 0.01
84 34 0.46
85 4 0.05
86 6 0.08
87 7 0.09
ACGTcount: A:0.66, C:0.08, G:0.04, T:0.22
Consensus pattern (81 bp):
AAAAATGTCAATAATTAAATAAAAACAGTAAGAAACAAAATAAATAAAAAATCCATAATTAAATA
AAAACACTAAGAAACA
Found at i:322285 original size:31 final size:31
Alignment explanation
Indices: 322250--322324 Score: 75
Period size: 31 Copynumber: 2.4 Consensus size: 31
322240 GAAAATTATT
322250 AAATAATTATTAAATTTATATAATAAT-TA-AA
1 AAATAATTATTAAATTTAT-TAA-AATATATAA
* *
322281 AAAT-ATACAATAAATTTATTAAAATGATATAA
1 AAATAAT-TATTAAATTTATTAAAAT-ATATAA
322313 AAATAATTATTA
1 AAATAATTATTA
322325 GAACATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
29 3 0.09
30 5 0.14
31 16 0.46
32 9 0.26
33 2 0.06
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (31 bp):
AAATAATTATTAAATTTATTAAAATATATAA
Found at i:323134 original size:28 final size:28
Alignment explanation
Indices: 323075--323135 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
323065 CTAGAATATG
* *
323075 TTCAACATCCTCCCTGCTGCTTCAATTC
1 TTCAACATCCTCCCTGCTGCTCCAACTC
*
323103 TTCAACATCCTTCCTGCTGCTCCAAGCT-
1 TTCAACATCCTCCCTGCTGCTCCAA-CTC
323131 TTCAA
1 TTCAA
323136 ACGGTAACAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.20, C:0.38, G:0.08, T:0.34
Consensus pattern (28 bp):
TTCAACATCCTCCCTGCTGCTCCAACTC
Found at i:337731 original size:22 final size:22
Alignment explanation
Indices: 337700--337755 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
337690 CCTTTACGTA
337700 ACACCGCAACACACTATAAATT
1 ACACCGCAACACACTATAAATT
* *
337722 GCGCCGCAACACACTATAAATT
1 ACACCGCAACACACTATAAATT
337744 ACACCGCAACAC
1 ACACCGCAACAC
337756 CGCAACAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.41, C:0.36, G:0.09, T:0.14
Consensus pattern (22 bp):
ACACCGCAACACACTATAAATT
Found at i:340639 original size:16 final size:16
Alignment explanation
Indices: 340602--340642 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
340592 GTTTACTTCA
340602 GAATGATT-AAACGCT
1 GAATGATTCAAACGCT
*
340617 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
*
340633 GATTGATTCA
1 GAATGATTCA
340643 GAAGTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:352705 original size:2 final size:2
Alignment explanation
Indices: 352698--352726 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
352688 CTCCTTTTAT
352698 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
352727 CAAAAGACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:353205 original size:2 final size:2
Alignment explanation
Indices: 353174--353233 Score: 60
Period size: 2 Copynumber: 32.5 Consensus size: 2
353164 TGATTATTTC
353174 AT AT AT -T AT A- AT AT A- AT -T AT -T AT CAT 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
*
353212 AT AT AT AT AT AT -T AT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
353234 GTTATTATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
1 6 0.12
2 41 0.84
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355476 original size:35 final size:36
Alignment explanation
Indices: 355431--355506 Score: 109
Period size: 35 Copynumber: 2.1 Consensus size: 36
355421 AAAATACTTT
355431 AATTTAGGGTTTAAAATGTAATTAAAGTA-TTTTGG
1 AATTTAGGGTTTAAAATGTAATTAAAGTATTTTTGG
* ** *
355466 AATTTGGGGTTTAGGATGTAATTGAAGTATTTTTGG
1 AATTTAGGGTTTAAAATGTAATTAAAGTATTTTTGG
355502 AATTT
1 AATTT
355507 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 25 0.69
36 11 0.31
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (36 bp):
AATTTAGGGTTTAAAATGTAATTAAAGTATTTTTGG
Found at i:356664 original size:30 final size:31
Alignment explanation
Indices: 356629--356689 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
356619 TTTGATTAAG
356629 AAGAAAAAAAACT-GATGGTTTTGG-TCAAAA
1 AAGAAAAAAAA-TAGATGGTTTTGGTTCAAAA
356659 AAGAAAAAAAATAGATGGTTTTGGTTCAAAA
1 AAGAAAAAAAATAGATGGTTTTGGTTCAAAA
356690 CTAACACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 1 0.03
30 22 0.76
31 6 0.21
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.25
Consensus pattern (31 bp):
AAGAAAAAAAATAGATGGTTTTGGTTCAAAA
Found at i:359063 original size:3 final size:3
Alignment explanation
Indices: 359055--359137 Score: 91
Period size: 3 Copynumber: 28.0 Consensus size: 3
359045 CCATTTGTTT
*
359055 TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
359102 GTA TTA TT- TTA TT- TATA CTA TTA TTTA TTA GTA TTA
1 TTA TTA TTA TTA TTA T-TA TTA TTA -TTA TTA TTA TTA
359138 ATAATAAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.07
3 59 0.88
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:359391 original size:15 final size:15
Alignment explanation
Indices: 359371--359408 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
359361 GGGCCACGCG
359371 GCCGCCGCCTCTGTT
1 GCCGCCGCCTCTGTT
359386 GCCGCCGCCTCTGTT
1 GCCGCCGCCTCTGTT
359401 GCCGCCGC
1 GCCGCCGC
359409 TCCACTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.00, C:0.50, G:0.29, T:0.21
Consensus pattern (15 bp):
GCCGCCGCCTCTGTT
Found at i:360560 original size:29 final size:28
Alignment explanation
Indices: 360520--360581 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
360510 TTATTTGCAA
360520 TATTATTTCATTACTATTTT-TGATATAT
1 TATTATTTCATTACTATTTTATGAT-TAT
* *
360548 TATTATGTTCATTATTATTTTATTATTAT
1 TATTAT-TTCATTACTATTTTATGATTAT
360577 TATTA
1 TATTA
360582 CTTAGTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 21 0.70
30 3 0.10
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (28 bp):
TATTATTTCATTACTATTTTATGATTAT
Found at i:360602 original size:2 final size:2
Alignment explanation
Indices: 360589--360627 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
360579 TTACTTAGTC
*
360589 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
360628 ATAAATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:361489 original size:28 final size:26
Alignment explanation
Indices: 361458--361528 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 26
361448 TAATTCTTTC
*
361458 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAATATTTTTATATATA-TTATT
* *
361485 ATTTTCGTAATATTTATATGTATATTATT
1 -TTTTC--AATATTTTTATATATATTATT
361514 TTTT-AATATTTTTAT
1 TTTTCAATATTTTTAT
361529 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
25 10 0.27
28 9 0.24
29 5 0.14
30 13 0.35
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (26 bp):
TTTTCAATATTTTTATATATATTATT
Found at i:362925 original size:43 final size:44
Alignment explanation
Indices: 362864--362950 Score: 124
Period size: 43 Copynumber: 2.0 Consensus size: 44
362854 TGGCTTCAGA
*
362864 GAAGTTAGGAGGGAAAGTTATCCCCTAT-ATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCT-TCATGTAAAAGTTTTGTT
* *
362907 GAAGTTAGGACTGAAAGTTGTCCCCTTCATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTTCATGTAAAAGTTTTGTT
362951 TGATGCACGA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 1 0.03
43 27 0.69
44 11 0.28
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTTCATGTAAAAGTTTTGTT
Found at i:363058 original size:27 final size:26
Alignment explanation
Indices: 363027--363077 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
363017 TTCATATTTA
* *
363027 CGTTTGCATTTGCAATTTGCATTTTTG
1 CGTTTGCATTTAC-ATTTACATTTTTG
*
363054 CGTTTGTATTTACATTTACATTTT
1 CGTTTGCATTTACATTTACATTTT
363078 CATTTTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 10 0.48
27 11 0.52
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (26 bp):
CGTTTGCATTTACATTTACATTTTTG
Found at i:370236 original size:22 final size:22
Alignment explanation
Indices: 370205--370291 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
370195 ACATCTACAT
*
370205 TCTTCCAAGATGAGAGATTCT-
1 TCTTCAAAGATGAGAGATTCTC
*
370226 TGCTTCAAAGATGATAGATTCTC
1 T-CTTCAAAGATGAGAGATTCTC
* * * *
370249 TTTTCAAAGATGATATATTATC
1 TCTTCAAAGATGAGAGATTCTC
* *
370271 TCTTTAAAGATGATAGATTCT
1 TCTTCAAAGATGAGAGATTCT
370292 ATTTTCGAAG
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
21 1 0.02
22 53 0.96
23 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGAGAGATTCTC
Found at i:371094 original size:120 final size:122
Alignment explanation
Indices: 370793--371105 Score: 490
Period size: 120 Copynumber: 2.6 Consensus size: 122
370783 GCCAGGTAGA
*
370793 GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 GTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
*
370858 ACCTTTTGCTCGACGCTATCACAGAAAGAGATAGATCAGCATCAACTTTTCCAGAAAAAT
65 ACC-TTTGCTCGACGCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAG-AAAAT
* * *
370918 -TTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAGGAACTTGTTCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* *
370982 CCTTTGCAT-GACTCTATCACA-AAAGAGATAGATCAGCATCAACATTTCCAG-AAGT
66 CCTTTGC-TCGACGCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAGAAAAT
*
371037 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGATCAA
1 GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
371102 CCTT
66 CCTT
371106 ACCTTAATTC
Statistics
Matches: 175, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
119 3 0.02
120 64 0.37
121 29 0.17
122 16 0.09
123 36 0.21
124 27 0.15
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (122 bp):
GTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
CCTTTGCTCGACGCTATCACAGAAAGAGATAGATCAGCATCAACATTTCCAGAAAAT
Found at i:371481 original size:3 final size:3
Alignment explanation
Indices: 371473--371540 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
371463 CATTTGTTTT
* *
371473 TTA TTA TTA TTA ATA TTA TTA -TA TTA TTA GTA TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
371519 CTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TTA
371541 ATAAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:371499 original size:17 final size:17
Alignment explanation
Indices: 371477--371550 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
371467 TGTTTTTTAT
371477 TATTATTAATATTATTA
1 TATTATTAATATTATTA
* *
371494 TATTATTAGTATTATTT
1 TATTATTAATATTATTA
*
371511 TATT-TATACTATTATT-
1 TATTAT-TAATATTATTA
* *
371527 TATTATTATTATTAATA
1 TATTATTAATATTATTA
*
371544 AATTATT
1 TATTATT
371551 TTATTACATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
16 13 0.27
17 35 0.73
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (17 bp):
TATTATTAATATTATTA
Found at i:371732 original size:21 final size:21
Alignment explanation
Indices: 371708--371748 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
371698 GGATCTGGCA
371708 AGATCCAACGGCCTTGATGCC
1 AGATCCAACGGCCTTGATGCC
371729 AGATCCAACGGCCTTGATGC
1 AGATCCAACGGCCTTGATGC
371749 TTCCAGACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.20
Consensus pattern (21 bp):
AGATCCAACGGCCTTGATGCC
Found at i:372973 original size:15 final size:14
Alignment explanation
Indices: 372928--372987 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
372918 TTATTTGCAA
*
372928 TATTATTTCATTAC
1 TATTATTTCATTAT
*
372942 TATT-TTTGATATAT
1 TATTATTTCAT-TAT
372956 TATTATGTTCATTAT
1 TATTAT-TTCATTAT
372971 TATTATTT--TTAT
1 TATTATTTCATTAT
372983 TATTA
1 TATTA
372988 CTTAGTCATA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 9 0.22
13 5 0.12
14 12 0.30
15 10 0.25
16 4 0.10
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.63
Consensus pattern (14 bp):
TATTATTTCATTAT
Found at i:373374 original size:2 final size:2
Alignment explanation
Indices: 373363--373402 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
373353 ATAAATATCT
373363 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
373402 T
1 T
373403 TTTCTTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:374798 original size:31 final size:31
Alignment explanation
Indices: 374733--374800 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
374723 TAACAAATTA
* * *
374733 GTCACTAACATTATCGGTTTGTTATGAATAG
1 GTCACTAACATTATCGGTTTATAATAAATAG
374764 GTCACTAACATTAT-GGATTTATAATAAA-ATG
1 GTCACTAACATTATCGG-TTTATAATAAATA-G
374795 GTCACT
1 GTCACT
374801 CCACTATCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
GTCACTAACATTATCGGTTTATAATAAATAG
Found at i:376994 original size:42 final size:42
Alignment explanation
Indices: 376937--377019 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
376927 ACGCGGTAGT
* *
376937 CGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCAATAGG
1 CGAAGTCCGCATTGCGATTCATTCCAAATTCGTTGCAATAGG
* *
376979 CGAAGTCCGCGTTGCGATTCATTCCAAATTCGTTGCGATAG
1 CGAAGTCCGCATTGCGATTCATTCCAAATTCGTTGCAATAG
377020 TCCAAATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (42 bp):
CGAAGTCCGCATTGCGATTCATTCCAAATTCGTTGCAATAGG
Found at i:377917 original size:19 final size:19
Alignment explanation
Indices: 377893--377960 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
377883 CAAATGCAAT
377893 ATTTGGACTATCGCAACGA
1 ATTTGGACTATCGCAACGA
*
377912 ATTTGGAATGAATCGCAACGCGA
1 ATTTGGACT--ATCGCAA--CGA
* * *
377935 ACTTCGCCTATCGCAACGA
1 ATTTGGACTATCGCAACGA
377954 ATTTGGA
1 ATTTGGA
377961 ATGAATCGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 15 0.41
21 14 0.38
23 8 0.22
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (19 bp):
ATTTGGACTATCGCAACGA
Found at i:377928 original size:21 final size:21
Alignment explanation
Indices: 377902--377973 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
377892 TATTTGGACT
377902 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAATTTGGAATGA
* * **
377923 ATCGCAACGCGAACTTCGCCT--
1 ATCGCAA--CGAATTTGGAATGA
377944 ATCGCAACGAATTTGGAATGA
1 ATCGCAACGAATTTGGAATGA
377965 ATCGCAACG
1 ATCGCAACG
377974 CGAACTTCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.59
23 8 0.21
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATGA
Found at i:377947 original size:42 final size:42
Alignment explanation
Indices: 377898--377987 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
377888 GCAATATTTG
377898 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
*
377940 GCCTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
377982 GACTAT
1 GACTAT
377988 AGCGTTGCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTC
Found at i:379776 original size:112 final size:112
Alignment explanation
Indices: 379652--379856 Score: 306
Period size: 112 Copynumber: 1.8 Consensus size: 112
379642 TCGTTTTTTG
* *
379652 TGTTCAAATCCTTTTGCTCTTCTCATTCCTTTTTGTTTTTTTTCTTCTT-TTTTTTTCAAACTCT
1 TGTTCAAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTT-TTCTTTTTTT-AAACTCT
*
379716 CTTTGATTCTCTCTCTATC-TTTTTTCATCCTACCCCATATTTTTCCCT
64 CTTTGATTCTCACTCTATCTTTTTTTCATCCTACCCCATATTTTTCCCT
* * * * *
379764 TGTTCGAATCCTTTTGCTTTTCTCCTCCCTTTTTGGTTTTTTTCTTTTCTTTTTTTGAACTCTTT
1 TGTTCAAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTTTTCTTTTTTTAAACTCTCT
379829 TTGATTCTCACTCTATCTTTTTTTCATC
66 TTGATTCTCACTCTATCTTTTTTTCATC
379857 TGCCCCTGGA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
111 25 0.30
112 58 0.70
ACGTcount: A:0.10, C:0.25, G:0.05, T:0.60
Consensus pattern (112 bp):
TGTTCAAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTTTTCTTTTTTTAAACTCTCT
TTGATTCTCACTCTATCTTTTTTTCATCCTACCCCATATTTTTCCCT
Found at i:379879 original size:112 final size:112
Alignment explanation
Indices: 379652--379887 Score: 291
Period size: 112 Copynumber: 2.1 Consensus size: 112
379642 TCGTTTTTTG
* * *
379652 TGTTCAAATCCTTTTGCTCTTCTCATTCCTTTTTGTTTTTTTTCTTCTTTTTTTTTCAAACTCTC
1 TGTTCGAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTTCTTTTTTTTTCAAACTCTC
* * *
379717 TTTGATTCTCTCTCTATCTTTTTTCATCCTACCCCATATTTTTCCCT
66 TTTGATTCTCACTCTATCTTTTTTCATCCTACCCCATATCTCTCCCT
* * *
379764 TGTTCGAATCCTTTTGCTTTTCTCCTCCCTTTTTGGTTTTTTTCTT-TTCTTTTTTT-GAACTCT
1 TGTTCGAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTTCTT-TTTTTTTCAAACTCT
* * *
379827 TTTTGATTCTCACTCTATCTTTTTTTCAT-CTGCCCC-TGGATCTCTCCTT
65 CTTTGATTCTCACTCTATC-TTTTTTCATCCTACCCCAT--ATCTCTCCCT
*
379876 TGTTAGAATCCT
1 TGTTCGAATCCT
379888 CCCCTTTTCT
Statistics
Matches: 107, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
110 1 0.01
111 31 0.29
112 75 0.70
ACGTcount: A:0.11, C:0.26, G:0.07, T:0.57
Consensus pattern (112 bp):
TGTTCGAATCCTTTTGCTCTTCTCATCCCTTTTTGGTTTTTTTCTTCTTTTTTTTTCAAACTCTC
TTTGATTCTCACTCTATCTTTTTTCATCCTACCCCATATCTCTCCCT
Found at i:380208 original size:3 final size:3
Alignment explanation
Indices: 380202--380253 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
380192 TGTATTATTA
* *
380202 AAT AAT AAT AA- AAC AA- ATAT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT -AAT AAT AAT AAT
380247 AAT AAT A
1 AAT AAT A
380254 TAAAAACTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 3 0.07
3 36 0.84
4 4 0.09
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:380664 original size:5 final size:5
Alignment explanation
Indices: 380654--380679 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
380644 TGACTTAAAA
380654 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
380680 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:381074 original size:23 final size:22
Alignment explanation
Indices: 381033--381094 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
381023 ATAAAGATTT
* *
381033 AATTTAAATTAATCATTAATTAA
1 AATTTAATTTAATTATTAA-TAA
* *
381056 AATTTAATTTAATTTTTAATAG
1 AATTTAATTTAATTATTAATAA
*
381078 AATTATATTTTAATTAT
1 AATT-TAATTTAATTAT
381095 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 6 0.19
23 26 0.81
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTTAATTTAATTATTAATAA
Done.