Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003961.1 Hibiscus syriacus cultivar Beakdansim tig00008576_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: 94276
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:309 original size:6 final size:6
Alignment explanation
Indices: 269--321 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
259 CCAAGAGGTC
* * * * *
269 ATGAAG ATGAAG ATGACG ATGAAG ATGATG ATGATG ATGATG ATTATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
317 ATGAT
1 ATGAT
322 CCAAACAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (6 bp):
ATGATG
Found at i:1265 original size:11 final size:11
Alignment explanation
Indices: 1247--1306 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
1237 TGTTGTGGGT
1247 ACATTATTTGA
1 ACATTATTTGA
*
1258 ATATTATTTGA
1 ACATTATTTGA
* *
1269 ACATTGTTAGTA
1 ACATTATTTG-A
1281 A-ATTATTTGA
1 ACATTATTTGA
1291 ACATTATTTGA
1 ACATTATTTGA
1302 ACATT
1 ACATT
1307 GTTTTGTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 2 0.05
11 37 0.90
12 2 0.05
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (11 bp):
ACATTATTTGA
Found at i:1590 original size:15 final size:15
Alignment explanation
Indices: 1570--1606 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1560 TCTCCACAAC
*
1570 AAAGTTTTCATACAT
1 AAAGTTTTCAAACAT
*
1585 AAAGTTTTCAAACTT
1 AAAGTTTTCAAACAT
1600 AAAGTTT
1 AAAGTTT
1607 CCCATAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.41
Consensus pattern (15 bp):
AAAGTTTTCAAACAT
Found at i:2071 original size:198 final size:195
Alignment explanation
Indices: 1607--2738 Score: 597
Period size: 198 Copynumber: 5.8 Consensus size: 195
1597 CTTAAAGTTT
* * * *
1607 CCCAT-AAGTGTTGATAC-AGTTTAAAAAGTATCGATCCTAGAAACATCGAAAACAATAAATAAA
1 CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCCA-AAACATCGAAAACCATAAAT-AA
* ** * * *
1670 TGTAATAGGTAATTTTGTAATATAACCGGTAAAAATATATCGGTTTTATGTGAGAATAGGTCTAC
64 TGTAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAGAATAGATATAC
* * * * * * * *
1735 ATAATGTGTCGACACTTGTTAATGTGTGTCGATACTTTTTGCCATAATGAATGCCCAAACGGGTG
129 ATAATATATCGACACTTGTGAATGTGTGTCGATACTTTTGGCCACAAGGAATGCCAAAAAGGGTG
1800 AA
194 AA
* * *
1802 CGCATAAAGTGTCGATACAATTATAAAAAGTATCGATCCCAAAAATATC-AAAACCGATAATTAT
1 CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCC-AAAACATCGAAAACC-ATAA--AT
* * *
1866 AATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAATCGGTTTT-TTTGAGAAAATAGAT
62 AATGTAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAG--AATAGAT
*
1930 ATACATAATATATCGACACTTGTAGAATTTGTGTCGATACTTTTGGTCCACAAGGAAAAT-CCAA
125 ATACATAATATATCGACACTTGT-GAATGTGTGTCGATACTTTTGG-CCACAAGG--AATGCCAA
*
1994 AAAGGGTGCA
186 AAAGGGTGAA
* * * *
2004 CCCATAAAGTGTCGATGCATTTTTAAATAGTATCGATCCCAAAACATCGAAATCCATAAAT-ATG
1 CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCCAAAACATCGAAAACCATAAATAATG
* * * *
2068 TAATAGGT-AA-TT----T-T-----GT---AATATA-CGGTTTTATGTTAGAATAGTTCTACAT
66 TAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAGAATAGATATACAT
* * * * *
2117 AATGTGTCGACAC-------------T---T--TTTT-GCCAGAATGAATGCCCAAAAGGGTGAA
131 AATATATCGACACTTGTGAATGTGTGTCGATACTTTTGGCCACAAGGAATGCCAAAAAGGGTGAA
* ** * *
2163 CGCATAAAGTGTTTATAC-ATTTAAAAAAGTATCGATCCCAAAAATATCG-AAACCGATAATTTA
1 CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCC-AAAACATCGAAAACC-ATAA---A
* * ** * ** * * * *
2226 TAATGTAATAGGTAAATTTACAATGTAACC-GTATAAATGTACCAATTTTTTGAGAAAATAGGTG
61 TAATGTAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAGAATAGAT-
* * *
2290 A-ACATAATGTATCGACACGTT-TTAGATTTGTGTCGATACTTTTGGTCCACAAGGAAAAT-CCA
125 ATACATAATATATCGACAC-TTGTGA-ATGTGTGTCGATACTTTTGG-CCACAAGG--AATGCCA
* *
2352 AAAAGGTTGCA
185 AAAAGGGTGAA
* * *
2363 CCCATAAAGTGTCGATACATTTTTAAACAGTATCGATCCCTAAAACATCGAAACCCCTAATTATA
1 CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCC-AAAACATCGAAA-ACC--A-TA-A
* * * ** * * * * * *
2428 TTTTAATAGTTAATTTTGTAGTTAATTTGTAATATAACCAGTATAAATATACCGATTTTATGTCA
60 --ATAAT-G-TAA--TAG--GTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGA
* * * * * * * * * *
2493 GAATAGGTCTACATAATTTGTTGACACTTTTAAATGATGTGTCGATACTTTTTGCCAGAATGAAT
117 GAATAGATATACATAATATATCGACACTTGTGAATG-TGTGTCGATACTTTTGGCCACAAGGAAT
*
2558 GCCCAAAAGGGTGAA
181 GCCAAAAAGGGTGAA
* * * *
2573 CGCAGAAAGTTTCGATAC-ATTTATAAAAAGTATCGATCCCAAAAACATCG-AAACCGTAATTAT
1 CCCATAAAGTGTCGATACAATTT-TAAAAAGTATCGATCCC-AAAACATCGAAAACCATAA--AT
* * ** * * * *
2636 AATGTAATAGGTAAATTTACAATGTAA-CGGTATAAATGTA-CCGTTTTATGAGAAAATAGGTGA
62 AATGTAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAGAATAGAT-A
* *
2699 -ACATAATATATCGACACGTT-TTAGATTTGTGTCGATACTT
126 TACATAATATATCGACAC-TTGTGA-ATGTGTGTCGATACTT
2739 GTAATAACAC
Statistics
Matches: 727, Mismatches: 129, Indels: 161
0.71 0.13 0.16
Matches are distributed among these distances:
158 25 0.03
159 38 0.05
160 6 0.01
161 1 0.00
162 6 0.01
163 11 0.02
164 3 0.00
165 2 0.00
167 1 0.00
169 1 0.00
170 1 0.00
174 2 0.00
177 5 0.01
178 30 0.04
181 22 0.03
182 7 0.01
183 9 0.01
186 2 0.00
191 1 0.00
192 2 0.00
195 5 0.01
196 63 0.09
197 54 0.07
198 69 0.09
199 36 0.05
200 47 0.06
201 46 0.06
202 56 0.08
203 6 0.01
204 8 0.01
205 10 0.01
206 2 0.00
207 3 0.00
208 2 0.00
209 10 0.01
210 51 0.07
211 25 0.03
212 59 0.08
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (195 bp):
CCCATAAAGTGTCGATACAATTTTAAAAAGTATCGATCCCAAAACATCGAAAACCATAAATAATG
TAATAGGTAAATTTACAATATAACCGGTAAAAATAAATCGGTTTTATGTGAGAATAGATATACAT
AATATATCGACACTTGTGAATGTGTGTCGATACTTTTGGCCACAAGGAATGCCAAAAAGGGTGAA
Found at i:2627 original size:210 final size:202
Alignment explanation
Indices: 2118--2738 Score: 620
Period size: 210 Copynumber: 3.1 Consensus size: 202
2108 GTTCTACATA
* *
2118 ATGTGTCGACACTTTTTTGCCAGAATGAATGCCCAAAAGGGTGAACGCATAAAGTGTT-TATACA
1 ATGTGTCGATAC-TTTTTGCCAGAATGAATGCCCAAAAGGGTGAACGCATAAAGT-TTCGATACA
* *
2182 TTTA-AAAAAGTATCGATCCCAAAAATATCGAAACCGATAATT-TA-TAAT-GTAATAGGTAAAT
64 TTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATATTAATAGTAATAGGTAAAT
* * * * *
2243 TTACAATGTAACCGTATAAATGTACCAATTTTTTGAGAAAATAGGTGAACATAATGTATCGACAC
129 TTACAATATAACCGTATAAATATACCAATTTTATGACAAAATAGGTCAACATAATGTATCGACAC
*
2308 GTTTTAGAT
194 GTTTTAAAT
* * * * * * * * *
2317 TTGTGTCGATACTTTTGGTCCACAAGGAAAAT-CCAAAAAGGTTGCACCCATAAAGTGTCGATAC
1 ATGTGTCGATACTTTTTG-CCAGAATG--AATGCCCAAAAGGGTGAACGCATAAAGTTTCGATAC
* * * * *
2381 ATTTTTAAACAGTATCGATCCCTAAAACATCGAAACCCCTAATTATATTTTAATAGTTAATTTTG
63 ATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATA--TTAATAG-TAA--TAG
* ** * * * * *
2446 TAGTTAATTTGTAATATAACCAGTATAAATATACCGATTTTATGTCAGAATAGGTCTACATAATT
123 --GTAAATTTACAATATAACC-GTATAAATATACCAATTTTATGACAAAATAGGTCAACATAATG
* *
2511 TGTTGACAC-TTTTAAAT
185 TATCGACACGTTTTAAAT
*
2528 GATGTGTCGATACTTTTTGCCAGAATGAATGCCCAAAAGGGTGAACGCAGAAAGTTTCGATACAT
1 -ATGTGTCGATACTTTTTGCCAGAATGAATGCCCAAAAGGGTGAACGCATAAAGTTTCGATACAT
*
2593 TTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCGTAA-T-TA-TAAT-GTAATAGGTAAATT
65 TTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATATTAATAGTAATAGGTAAATT
* * * * * * *
2653 TACAATGTAACGGTATAAATGTACC-GTTTTATGAGAAAATAGGTGAACATAATATATCGACACG
130 TACAATATAACCGTATAAATATACCAATTTTATGACAAAATAGGTCAACATAATGTATCGACACG
*
2717 TTTTAGAT
195 TTTTAAAT
*
2725 TTGTGTCGATACTT
1 ATGTGTCGATACTT
2739 GTAATAACAC
Statistics
Matches: 337, Mismatches: 66, Indels: 41
0.76 0.15 0.09
Matches are distributed among these distances:
196 42 0.12
197 19 0.06
198 19 0.06
199 17 0.05
200 30 0.09
201 36 0.11
202 5 0.01
203 1 0.00
204 4 0.01
205 4 0.01
206 1 0.00
207 5 0.01
208 1 0.00
209 10 0.03
210 58 0.17
211 28 0.08
212 57 0.17
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (202 bp):
ATGTGTCGATACTTTTTGCCAGAATGAATGCCCAAAAGGGTGAACGCATAAAGTTTCGATACATT
TATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATATTAATAGTAATAGGTAAATTT
ACAATATAACCGTATAAATATACCAATTTTATGACAAAATAGGTCAACATAATGTATCGACACGT
TTTAAAT
Found at i:6484 original size:195 final size:198
Alignment explanation
Indices: 6004--6668 Score: 590
Period size: 196 Copynumber: 3.4 Consensus size: 198
5994 CACATTTTCT
* * ** *
6004 AAAAGTATC-AACCC-AAAA-ATCGAAACCAATAATTATAATGTAATAGGTAAATTAACAATGTA
1 AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATATA
* * * * * * * *
6066 ACTGTTATAAATATATCGG-TTAATTAGAAAACAGGTCA-ACATAATGTATCGACAC-TTCTGTA
66 ACCGGTAT-AATATACCGGTTTTATGAGAAAATAGGT-ATACATAAAGTATCGACACAAT-T-TA
** * ** *
6128 AT-TTGTGTCGATAC-TTT-TCC---AT-AATGCCCAAACGGGGTGCACGCATAAA-----GATA
127 ATGAAGTGCCGATACTTTTGTCCAGAATGAATGCCCAAA-TAGGTGAACGCATAAAGTGTCGATA
* *
6181 CAATTATT
191 CATTTATA
* * * * *
6189 AAAAGTATCGAT-CCAATAAA-ATTGAAACCGATAATTATAATATAATATGTAAATTTACAATGT
1 AAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATAT
6252 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAT-CATAAAGTATCGACACAAATTTA
65 AACCGGTAT-AATATACCGGTTTTATGAGAAAATAGGT-ATACATAAAGTATCGACAC-AATTTA
* * * * * *
6316 AT-AAGTGTCGATACATTTTGTCCATAATGAATG-CCAGA-CGGTGCACTCATAAAGTGTCGATA
127 ATGAAGTGCCGATAC-TTTTGTCCAGAATGAATGCCCAAATAGGTGAACGCATAAAGTGTCGATA
*
6378 CATTTTTA
191 CATTTATA
* *
6386 AAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTGTAATATA
1 AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATATA
* * * * * * * ** *
6450 ACTGGTAT-TTATACCGGTTTTATGTGAGAATAGGTGTACATAATGTGTCGACACTTTTTAATGT
66 ACCGGTATAATATACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAATTTAATGA
* * *
6514 TGTGCCGATACTTTTTTCCAGAATGAATGCCCAAATAGGTGAACGCATATAGTGTCGATACATTT
131 AGTGCCGATACTTTTGTCCAGAATGAATGCCCAAATAGGTGAACGCATAAAGTGTCGATACATTT
6579 ATA
196 ATA
* * *
6582 AAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATGTT
1 AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATATA
6647 ACCGGTATAAATATACCGGTTT
66 ACCGGTAT-AATATACCGGTTT
6669 ACTTATAAAA
Statistics
Matches: 396, Mismatches: 56, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
185 11 0.03
186 2 0.01
187 58 0.15
188 45 0.11
189 1 0.00
190 4 0.01
191 3 0.01
192 13 0.03
194 29 0.07
195 55 0.14
196 76 0.19
197 58 0.15
198 30 0.08
199 11 0.03
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTGCAATATA
ACCGGTATAATATACCGGTTTTATGAGAAAATAGGTATACATAAAGTATCGACACAATTTAATGA
AGTGCCGATACTTTTGTCCAGAATGAATGCCCAAATAGGTGAACGCATAAAGTGTCGATACATTT
ATA
Found at i:6781 original size:87 final size:87
Alignment explanation
Indices: 6686--6848 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
6676 AAATAGGTCA
* *
6686 ATATAAGCGCTACCTATTACATTATATAAGCTTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTAGTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
6751 CCGGTTAAATACCTATTTCATT
66 CCGGTTAAATACCTATTTCATT
6773 ATATAAGCGCTACCTAGTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTAGTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
6838 CTGGTTAAATA
66 CCGGTTAAATA
6849 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (87 bp):
ATATAAGCGCTACCTAGTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTCATT
Found at i:6795 original size:23 final size:23
Alignment explanation
Indices: 6760--6811 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
6750 TCCGGTTAAA
* *
6760 TACCTATTTCATTATATAAGCGC
1 TACCTAGTACATTATATAAGCGC
*
6783 TACCTAGTACATTATATAAGCGT
1 TACCTAGTACATTATATAAGCGC
6806 TACCTA
1 TACCTA
6812 ATATGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (23 bp):
TACCTAGTACATTATATAAGCGC
Found at i:10262 original size:12 final size:12
Alignment explanation
Indices: 10222--10253 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
10212 CTAAAAATCA
10222 AAAAAAGAAAAG
1 AAAAAAGAAAAG
10234 AAAAAAGAAAAG
1 AAAAAAGAAAAG
10246 AAAAAAGA
1 AAAAAAGA
10254 GAATAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:26337 original size:16 final size:16
Alignment explanation
Indices: 26316--26375 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 16
26306 TAACTCTGTC
26316 AAAAATTTAAAAAATA
1 AAAAATTTAAAAAATA
*
26332 AAAAA-TTATAAAATGA
1 AAAAATTTAAAAAAT-A
*
26348 ATAAATTATAAAAAAATTA
1 AAAAATT-T-AAAAAA-TA
26367 AAAAATTTA
1 AAAAATTTA
26376 GCATTTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 8 0.23
16 10 0.29
17 2 0.06
18 2 0.06
19 12 0.34
20 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAAATTTAAAAAATA
Found at i:29295 original size:17 final size:17
Alignment explanation
Indices: 29273--29323 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
29263 TCTACTCGAA
*
29273 TGAACTCGATTTGAGTT
1 TGAACTCGATTCGAGTT
29290 TGAACTCGATTCGAGTT
1 TGAACTCGATTCGAGTT
*
29307 TGAACTCGACTCGAGTT
1 TGAACTCGATTCGAGTT
29324 CTTAATGAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (17 bp):
TGAACTCGATTCGAGTT
Found at i:29515 original size:36 final size:36
Alignment explanation
Indices: 29436--29520 Score: 84
Period size: 36 Copynumber: 2.3 Consensus size: 36
29426 AATTATTAAT
** *
29436 AATATTAACATTTAAGTGTTGATTGTTTTTAAAATGT
1 AATA-TAACATTTAAGTGTTGATTGTTTAAAAAATGC
*
29473 AGTATAACATTTATA-TGTTGATT-TTTAAAAAAATGC
1 AATATAACATTTA-AGTGTTGATTGTTT-AAAAAATGC
*
29509 AATATAAGATTT
1 AATATAACATTT
29521 TTTTTATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
35 3 0.08
36 33 0.82
37 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.45
Consensus pattern (36 bp):
AATATAACATTTAAGTGTTGATTGTTTAAAAAATGC
Found at i:29539 original size:16 final size:17
Alignment explanation
Indices: 29518--29549 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29508 CAATATAAGA
29518 TTTTTTTTA-TTTCAAG
1 TTTTTTTTAGTTTCAAG
29534 TTTTTTTTAGTTTCAA
1 TTTTTTTTAGTTTCAA
29550 TTCATGGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.19, C:0.06, G:0.06, T:0.69
Consensus pattern (17 bp):
TTTTTTTTAGTTTCAAG
Found at i:32359 original size:42 final size:43
Alignment explanation
Indices: 32304--32502 Score: 231
Period size: 43 Copynumber: 4.7 Consensus size: 43
32294 GTAGAGATCA
* * **
32304 ATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAATGTCAAACCT
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATAT
* * * ** *
32346 ATAGCGGCATTTTTGGA-ACAAGCACAACAAAAGGTTAGATAT
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATAT
* * *
32388 ATAGCGGCGTTTTTAGATACAAAAGCCGCAAAAGGTCAGATCT
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATAT
* * *
32431 ATAACGGCGTTTTTGGACACAAACGCCGCAAAATGTCAGATAT
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATAT
*
32474 ATAGCGGTGTTTTTGGATACAAACGCCGC
1 ATAGCGGCGTTTTTGGATACAAACGCCGC
32503 TAATTACCAT
Statistics
Matches: 128, Mismatches: 28, Indels: 1
0.82 0.18 0.01
Matches are distributed among these distances:
42 47 0.37
43 81 0.63
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (43 bp):
ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGATAT
Found at i:32439 original size:43 final size:42
Alignment explanation
Indices: 32279--32502 Score: 209
Period size: 43 Copynumber: 5.2 Consensus size: 42
32269 TTGTGAAATA
* * *
32279 AAAATGCCGCAAAAAGTAGAGATCAATAGCGGCGTTTTTGGAAC
1 AAAA-GCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
32323 AAACGCCGCAAAATGTCAAACCTATAGCGGCATTTTTGGAAC
1 AAAAGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
* * * *
32365 --AAGCACAACAAAAGGTTAGATATATAGCGGCGTTTTTAGATAC
1 AAAAGC-C-GCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
*
32408 AAAAGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGACAC
1 AAAAGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
* * * *
32451 AAACGCCGCAAAATGTCAGATATATAGCGGTGTTTTTGGATAC
1 AAAAGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-AC
*
32494 AAACGCCGC
1 AAAAGCCGC
32503 TAATTACCAT
Statistics
Matches: 147, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
40 3 0.02
41 1 0.01
42 46 0.31
43 89 0.61
44 4 0.03
45 4 0.03
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (42 bp):
AAAAGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAC
Found at i:32493 original size:86 final size:85
Alignment explanation
Indices: 32304--32502 Score: 256
Period size: 86 Copynumber: 2.3 Consensus size: 85
32294 GTAGAGATCA
* * *
32304 ATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAATGTCAAACCTATAGCGGCATTTTTGGAACAAG
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAACCTATAACGGCATTTTTGGAACAAA
*
32368 CACAACAAAAGGTTAGATAT
66 CACAACAAAAGGTCAGATAT
* * * * *
32388 ATAGCGGCGTTTTTAGATACAAAAGCCGCAAAAGGTCAGATCTATAACGGCGTTTTTGGACACAA
1 ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAACCTATAACGGCATTTTTGGA-ACAA
* ** *
32453 ACGCCGCAAAATGTCAGATAT
65 ACACAACAAAAGGTCAGATAT
*
32474 ATAGCGGTGTTTTTGGATACAAACGCCGC
1 ATAGCGGCGTTTTTGGATACAAACGCCGC
32503 TAATTACCAT
Statistics
Matches: 97, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 16 0.16
85 36 0.37
86 45 0.46
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (85 bp):
ATAGCGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAAACCTATAACGGCATTTTTGGAACAAA
CACAACAAAAGGTCAGATAT
Found at i:35186 original size:42 final size:42
Alignment explanation
Indices: 35100--35186 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
35090 TACTACTCTT
* *
35100 TTGCGGTGTTTGTTGAAAAAATGCCACTATAGTCAAAACCTA
1 TTGCGGTGTTTGTTGAAAAAACGCCACTATAGTCAAAACATA
* * * **
35142 TTGCGTTGTTTTTTGAAAAAACGCTACTATAGTTGAAACATA
1 TTGCGGTGTTTGTTGAAAAAACGCCACTATAGTCAAAACATA
35184 TTG
1 TTG
35187 TGGTATTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (42 bp):
TTGCGGTGTTTGTTGAAAAAACGCCACTATAGTCAAAACATA
Found at i:35196 original size:42 final size:42
Alignment explanation
Indices: 35100--35196 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 42
35090 TACTACTCTT
* * * *
35100 TTGCGGTGTTTGTTGAAAAAATGCCACTATAGTCAAAACCTA
1 TTGCGGTATTTTTTGAAAAAACGCCACTATAGTCAAAACATA
* * * **
35142 TTGCGTTGTTTTTTGAAAAAACGCTACTATAGTTGAAACATA
1 TTGCGGTATTTTTTGAAAAAACGCCACTATAGTCAAAACATA
*
35184 TTGTGGTATTTTT
1 TTGCGGTATTTTT
35197 ATACAAACGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (42 bp):
TTGCGGTATTTTTTGAAAAAACGCCACTATAGTCAAAACATA
Found at i:35996 original size:21 final size:21
Alignment explanation
Indices: 35944--35990 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
35934 ACTGAGCTGG
35944 TAATGGTTTGTTAGAAGAATC
1 TAATGGTTTGTTAGAAGAATC
35965 TAATGGTTTGTTAGAAGAATC
1 TAATGGTTTGTTAGAAGAATC
35986 TAATG
1 TAATG
35991 CGTTGTCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.38
Consensus pattern (21 bp):
TAATGGTTTGTTAGAAGAATC
Found at i:44926 original size:30 final size:30
Alignment explanation
Indices: 44887--44954 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
44877 ACGCCAAATC
*
44887 TCAAGCTCCAGATTTTTCAATAAAAATCCT
1 TCAAACTCCAGATTTTTCAATAAAAATCCT
44917 TCAAACTCCAGATTTTTCAATAAAAATCCT
1 TCAAACTCCAGATTTTTCAATAAAAATCCT
44947 TCAAACTC
1 TCAAACTC
44955 TGATAACAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.32
Consensus pattern (30 bp):
TCAAACTCCAGATTTTTCAATAAAAATCCT
Found at i:47942 original size:16 final size:17
Alignment explanation
Indices: 47923--47960 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
47913 TTCATAATAA
47923 TAATTATAAT-TATTAT
1 TAATTATAATATATTAT
47939 TAA-TATAATATATTAT
1 TAATTATAATATATTAT
47955 T-ATTAT
1 TAATTAT
47961 TATTTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TAATTATAATATATTAT
Found at i:47942 original size:19 final size:19
Alignment explanation
Indices: 47917--47959 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 19
47907 TTTTTTTTCA
47917 TAATAATAATTATAATTATTAT
1 TAAT-ATAA-TAT-ATTATTAT
47939 TAATATAATATATTATTAT
1 TAATATAATATATTATTAT
47958 TA
1 TA
47960 TTATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 4 0.19
22 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAATATATTATTAT
Found at i:47956 original size:22 final size:22
Alignment explanation
Indices: 47917--47962 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
47907 TTTTTTTTCA
47917 TAATAATAATTATAATTATTAT
1 TAATAATAATTATAATTATTAT
*
47939 TAAT-ATAATATATTATTATTAT
1 TAATAATAAT-TATAATTATTAT
47961 TA
1 TA
47963 TTTATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATAATAATTATAATTATTAT
Found at i:47968 original size:16 final size:16
Alignment explanation
Indices: 47927--47969 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
47917 TAATAATAAT
47927 TATAA-TTATTATTAA
1 TATAATTTATTATTAA
* *
47942 TATAATATATTATTAT
1 TATAATTTATTATTAA
*
47958 TATTATTTATTA
1 TATAATTTATTA
47970 AATTTATATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATAATTTATTATTAA
Found at i:48825 original size:28 final size:26
Alignment explanation
Indices: 48767--48824 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
48757 AGAGAGAAGC
*
48767 GAGAGAAATGATATTTCTCTTCTCTA
1 GAGAGAAATAATATTTCTCTTCTCTA
48793 GAGAGAAATAATATTTCTCTTCTCTA
1 GAGAGAAATAATATTTCTCTTCTCTA
48819 GAGAGA
1 GAGAGA
48825 GAAGAGAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (26 bp):
GAGAGAAATAATATTTCTCTTCTCTA
Found at i:59808 original size:22 final size:22
Alignment explanation
Indices: 59782--59833 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
59772 TACACTCTTC
59782 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
59804 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
59826 AAAGATGA
1 AAAGATGA
59834 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:60659 original size:165 final size:165
Alignment explanation
Indices: 60346--60672 Score: 530
Period size: 165 Copynumber: 2.0 Consensus size: 165
60336 CACAAGAATG
**
60346 AGCATTATCTTGAGATTGGGTTATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA
1 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA
**
60411 CGATTTCCATAGTTTCTCATTTTATCTTTTCGAAAATGAAATTGTTGAAAAGTAAGAAAACGATT
66 CGATTTCCATAGTTTCTCATTCAATCTTTTCGAAAATGAAATTGTTGAAAAGTAAGAAAACGATT
* * * *
60476 TTCTTAGTTTTTTTACTTAGTAAACTATTTCCAAC
131 TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC
* *
60511 AGCATTATCTTGAGATTGGGGCATGTTACCCAATTAACATGTTATTTTGAAAAATAATGAGAAAA
1 AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA
* *
60576 CGATTTTCATAGTTTCTCATTCAATCTTTTTTGAAAATGAAATTGTTGAAAAGTAAGAAAACGAT
66 CGATTTCCATAGTTTCTCATTCAATC-TTTTCGAAAATGAAATTGTTGAAAAGTAAGAAAACGAT
60641 TTCCATA-TTATCTTACTTAGTAAACTATTTCC
130 TTCCATAGTTATCTTACTTAGTAAACTATTTCC
60673 CACATCCATA
Statistics
Matches: 149, Mismatches: 12, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
165 107 0.72
166 42 0.28
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (165 bp):
AGCATTATCTTGAGATTGGGGCATGTTACCCAATCAACATGATATTTTGAAAAATAATGAGAAAA
CGATTTCCATAGTTTCTCATTCAATCTTTTCGAAAATGAAATTGTTGAAAAGTAAGAAAACGATT
TCCATAGTTATCTTACTTAGTAAACTATTTCCAAC
Found at i:60910 original size:74 final size:73
Alignment explanation
Indices: 60714--61061 Score: 615
Period size: 73 Copynumber: 4.7 Consensus size: 73
60704 TTCAAATAGC
60714 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
60779 GAAACAGA
66 GAAACAGA
* *
60787 ACTTTATCTCACTTGAGATTGTTTTTGTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
60852 GAAACAGAA
66 GAAACAG-A
60861 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
60926 GAAATAGA
66 GAAACAGA
* * *
60934 ACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCACTT
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
60999 GAAACAAA
66 GAAACAGA
61007 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGA
61062 GAATTATTTC
Statistics
Matches: 261, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
73 175 0.67
74 86 0.33
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (73 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
GAAACAGA
Found at i:60981 original size:147 final size:146
Alignment explanation
Indices: 60714--61061 Score: 642
Period size: 147 Copynumber: 2.4 Consensus size: 146
60704 TTCAAATAGC
60714 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
*
60779 GAAACAGAACTTTATCTCACTTGAGATTGTTTTTGTTAAAACAAAATTTGTCTCGCTTGAGACAG
66 GAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAG
60844 TTTCACTCGAAACAGAA
131 TTTCACTCGAAACA-AA
60861 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
* *
60926 GAAATAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAG
66 GAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAG
*
60991 TTTCACTTGAAACAAA
131 TTTCACTCGAAACAAA
61007 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGA
61062 GAATTATTTC
Statistics
Matches: 196, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
146 39 0.20
147 157 0.80
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.39
Consensus pattern (146 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTTCACTC
GAAACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAG
TTTCACTCGAAACAAA
Found at i:61461 original size:3 final size:3
Alignment explanation
Indices: 61449--61500 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
61439 CATAATAATA
* * *
61449 ATT ATA ATT ATT ATT AAT A-T AAT 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
61496 ATT AT
1 ATT AT
61501 ATATATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:61461 original size:9 final size:9
Alignment explanation
Indices: 61443--61501 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
61433 TTTTTTCATA
*
61443 ATAATAATT
1 ATAATTATT
61452 ATAATTATT
1 ATAATTATT
*
61461 ATTAATATAAT
1 A-TAAT-TATT
*
61472 ATTATTATT
1 ATAATTATT
*
61481 ATTATTATT
1 ATAATTATT
*
61490 ATTATTATT
1 ATAATTATT
61499 ATA
1 ATA
61502 TATATATATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 32 0.74
10 7 0.16
11 4 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
ATAATTATT
Found at i:61505 original size:2 final size:2
Alignment explanation
Indices: 61498--61534 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61488 TTATTATTAT
61498 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61535 TACAAATTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66002 original size:12 final size:12
Alignment explanation
Indices: 65985--66016 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
65975 GGGAGAAATA
65985 AACAATAATAAT
1 AACAATAATAAT
*
65997 AACAATAGTAAT
1 AACAATAATAAT
66009 AACAATAA
1 AACAATAA
66017 GTCCTAGTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.66, C:0.09, G:0.03, T:0.22
Consensus pattern (12 bp):
AACAATAATAAT
Found at i:69584 original size:23 final size:24
Alignment explanation
Indices: 69545--69591 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
69535 ATCAAAACTG
* *
69545 TATACTAGTTTTATTTATGAAAAT
1 TATACTAGTATTATTTATAAAAAT
69569 TATACTA-TATTATTTATAAAAAT
1 TATACTAGTATTATTTATAAAAAT
69592 CACATAAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (24 bp):
TATACTAGTATTATTTATAAAAAT
Found at i:74322 original size:27 final size:28
Alignment explanation
Indices: 74282--74335 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
74272 TGTGGCACAA
74282 AAACAAACGACGC-AAAAAGCGACACTG
1 AAACAAACGACGCAAAAAAGCGACACTG
74309 AAACAAAC-ACCGCAAAAAAGCGACACT
1 AAACAAACGA-CGCAAAAAAGCGACACT
74336 TGTCATTGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 1 0.04
27 11 0.44
28 13 0.52
ACGTcount: A:0.54, C:0.28, G:0.15, T:0.04
Consensus pattern (28 bp):
AAACAAACGACGCAAAAAAGCGACACTG
Found at i:74934 original size:19 final size:19
Alignment explanation
Indices: 74912--74967 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
74902 ATTTAGTTGC
*
74912 CTAAATTATAACCTAATTA
1 CTAAATTATAGCCTAATTA
74931 CTAAATTATAGCCTAATTA
1 CTAAATTATAGCCTAATTA
74950 CTAAATTATAGCCTAATT
1 CTAAATTATAGCCTAATT
74968 GTTAGGATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.38
Consensus pattern (19 bp):
CTAAATTATAGCCTAATTA
Found at i:79412 original size:19 final size:19
Alignment explanation
Indices: 79390--79426 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
79380 ATTTAGTTGC
79390 CTAAATTATAGCCTAATTA
1 CTAAATTATAGCCTAATTA
79409 CTAAATTATAGCCTAATT
1 CTAAATTATAGCCTAATT
79427 GTTAGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
CTAAATTATAGCCTAATTA
Found at i:82551 original size:41 final size:41
Alignment explanation
Indices: 82506--82620 Score: 115
Period size: 40 Copynumber: 2.8 Consensus size: 41
82496 AATACGAGTC
* *
82506 GTATAAAAATGTCACTAAAGTATGAGTGTTTAGCCACGTTT
1 GTATAAAAATGCCACTAAAGTATGAGTATTTAGCCACGTTT
* * * * ***
82547 GTATAAAAACGCCACTAAAATAT-AATCTTTAGCGGTGTTT
1 GTATAAAAATGCCACTAAAGTATGAGTATTTAGCCACGTTT
* * *
82587 ATATAAAAATACCACTAAAGTACGAGTATTTAGC
1 GTATAAAAATGCCACTAAAGTATGAGTATTTAGC
82621 GGCGTTCTTT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
40 30 0.52
41 28 0.48
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (41 bp):
GTATAAAAATGCCACTAAAGTATGAGTATTTAGCCACGTTT
Found at i:88295 original size:11 final size:12
Alignment explanation
Indices: 88259--88293 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
88249 ATTGTTCTAC
88259 AGCGGCGTTTTT
1 AGCGGCGTTTTT
88271 AGCGGCGTTTTT
1 AGCGGCGTTTTT
88283 AGCGGCGTTTT
1 AGCGGCGTTTT
88294 AGGAGTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.09, C:0.17, G:0.34, T:0.40
Consensus pattern (12 bp):
AGCGGCGTTTTT
Found at i:88615 original size:166 final size:166
Alignment explanation
Indices: 88402--88926 Score: 779
Period size: 166 Copynumber: 3.2 Consensus size: 166
88392 AGGTTCATCG
* * * * *
88402 ATAGTGGCGTTT-T-TTCAACAAACGCCGCAAAAGAGT-AGTACTTTAGTGGTGTTTTTATACAA
1 ATAGTGGCGTTTGTGTT-TACAAACGCCGCTAAAGACTCA-TAATTTAGTGGCGTTTTTATACAA
* * * *
88464 ACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACACCGCTATAGAATTGTACTTTA
64 ACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAAAGACTCGTACTTTA
* *
88529 TTGGCGTTTTTATACAAACGCCATTATACA-TATGTACT
129 GTGGCGTTTTTATTCAAACGCCATTATACACT-TGTACT
88567 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAAC
1 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAAC
* * * *
88632 GCCGCTAAAGACTCATACTTTAGTGGCATTTTTATACAAACTCTGCTAAAGACGCGTACTTTAGT
66 GCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAAAGACTCGTACTTTAGT
*
88697 GGCATTTTTATTCAAACGCCATTATACACTTGTACT
131 GGCGTTTTTATTCAAACGCCATTATACACTTGTACT
* * *
88733 ATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAAC
1 ATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAAC
* * **
88798 GCCGCTAAAGACTCGTACTTTATTGACATTTTTATACAAACGTCGCTAAAGACTCGTACTTTAGT
66 GCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAAAGACTCGTACTTTAGT
88863 GGCGTTTTTATTCAAACGCCATTATACACTTGTACT
131 GGCGTTTTTATTCAAACGCCATTATACACTTGTACT
*
88899 ATAGTGGCATTTGTGTTTACAAACGCCG
1 ATAGTGGCGTTTGTGTTTACAAACGCCG
88927 TAAGTTTACA
Statistics
Matches: 327, Mismatches: 29, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
165 12 0.04
166 311 0.95
167 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (166 bp):
ATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAAC
GCCGCTAAAGACTCGTACTTTAGTGGCATTTTTATACAAACACCGCTAAAGACTCGTACTTTAGT
GGCGTTTTTATTCAAACGCCATTATACACTTGTACT
Found at i:88691 original size:125 final size:123
Alignment explanation
Indices: 88419--88926 Score: 489
Period size: 125 Copynumber: 4.1 Consensus size: 123
88409 CGTTTTTTCA
* * ** *
88419 ACAAACGCCGCAAAAGAGTA-GTACTTTAGTGGTGTTTTTATACAAACGCCGCTAAAGACTCGTA
1 ACAAACGCCGCTAAAGA-CACGTACTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGACTCGTA
* * * * * * *
88483 ATTTAGTGGCATTTTTATACAAACACCGCTATAGAATTGTACTTTATTGGCGTTTTTAT
65 ATTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
** * * * * * * *
88542 ACAAACGCCATTATACATATGTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCAT
1 ACAAACGCCGCTAAAGACACGTACTTTAGTGGCATTT-T-TTTACAAACGCCGCTAAAGACTCGT
*
88607 AATTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCATTTTTAT
64 AATTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
* * * ** * * *
88667 ACAAACTCTGCTAAAGACGCGTACTTTAGTGGCATTTTTATT-CAAACGCCATTATACACTTGTA
1 ACAAACGCCGCTAAAGACACGTACTTTAGTGGCATTTTT-TTACAAACGCCGCTAAAGACTCGTA
* * * * *
88731 CTATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTAT
65 ATTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
* * * * * *
88792 ACAAACGCCGCTAAAGACTCGTACTTTATTGACATTTTTATACAAACGTCGCTAAAGACTCGTAC
1 ACAAACGCCGCTAAAGACACGTACTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGACTCGTAA
* ** * * * * *
88857 TTTAGTGGCGTTTTTATTCAAACGCCATTATACACTTGTACTATAGTGGCATTTGTGTTT
66 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTT-T-TAT
88917 ACAAACGCCG
1 ACAAACGCCG
88927 TAAGTTTACA
Statistics
Matches: 312, Mismatches: 64, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
122 2 0.01
123 86 0.28
124 8 0.03
125 216 0.69
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (123 bp):
ACAAACGCCGCTAAAGACACGTACTTTAGTGGCATTTTTTTACAAACGCCGCTAAAGACTCGTAA
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCATTTTTAT
Found at i:88906 original size:41 final size:41
Alignment explanation
Indices: 88403--88882 Score: 507
Period size: 41 Copynumber: 11.6 Consensus size: 41
88393 GGTTCATCGA
* * *
88403 TAGTGGCGTTTTT-TCAACAAACGCCGCAAAAGAGTAGTACTT
1 TAGTGGCGTTTTTAT--ACAAACGCCGCTAAAGACTCGTACTT
* *
88445 TAGTGGTGTTTTTATACAAACGCCGCTAAAGACTCGTAATT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * * *
88486 TAGTGGCATTTTTATACAAACACCGCTATAGAATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* ** * *
88527 TATTGGCGTTTTTATACAAACGCCATTATACATA-T-GTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTA-A-AGACTCGTACTT
* * *
88568 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
*
88611 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
88652 TAGTGGCATTTTTATACAAACTCTGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * ** * * * *
88693 TAGTGGCATTTTTATTCAAACGCCATTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * *
88734 TAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
*
88777 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
88818 TATTGACATTTTTATACAAACGTCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
*
88859 TAGTGGCGTTTTTATTCAAACGCC
1 TAGTGGCGTTTTTATACAAACGCC
88883 ATTATACACT
Statistics
Matches: 361, Mismatches: 68, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
41 283 0.78
42 19 0.05
43 59 0.16
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:92854 original size:42 final size:43
Alignment explanation
Indices: 92705--93226 Score: 578
Period size: 43 Copynumber: 12.2 Consensus size: 43
92695 ATGGAAATTA
* * *
92705 GCGGCGTTTGTATAAAAAAACGCCGCTATAAATATGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
*
92748 GCGGCGTTTGTAT-CAAAAAACGCCGTTATAGATCTGACCTTTT
1 GCGGCGTTTGTATAC-AAAAACGCCGCTATAGATCTGACCTTTT
* *
92791 GCGGCGTTTGTATACAAAAACGCCACTATAGATCTGACTTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
* *
92834 GCAGCGTTTGTATAC-AAAACGCCACTATAGATCTGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
* * * *
92876 GTGACGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
* * ** * *
92919 GTGGCGTTTGT-TGCAAAAATACTGCTATAGATCTTGACTTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATC-TGACCTTTT
* *
92962 GCGGCATTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
** * *
93004 GCGGCGTTTGT-TGTAAAAATGTCGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
* * *
93046 ACGGCGTTTGT-TGCAAAAATGCCGCTATAGATCTTGA-CTTCTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATC-TGACCTT-TT
* * *
93089 GCGACGTTTGT-TCCAAAAACACCGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCT-GACCTTTT
* * **
93132 GCGGCGTTTGTATCCAAAAATGATGCTATAGATCTCGACCTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATCT-GACCTTTT
* * *
93176 GCAGCGTTTAT-TTCAAAAACGCCGCTATAGATCTTGA-CTTTT
1 GCGGCGTTTGTATACAAAAACGCCGCTATAGATC-TGACCTTTT
93218 GCGGCGTTT
1 GCGGCGTTT
93227 TTATTTTACA
Statistics
Matches: 417, Mismatches: 52, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
42 148 0.35
43 227 0.54
44 42 0.10
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (43 bp):
GCGGCGTTTGTATACAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:92886 original size:85 final size:85
Alignment explanation
Indices: 92705--93226 Score: 597
Period size: 85 Copynumber: 6.1 Consensus size: 85
92695 ATGGAAATTA
** * *
92705 GCGGCGTTTGTATAAAAAAACGCCGCTATAAATATGACCTTTTGCGGCGTTTG-TATCAAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTA-C-AAAAAC
*
92769 GCCGTTATAGATCTGACCTTTT
64 GCCGCTATAGATCTGACCTTTT
* * * *
92791 GCGGCGTTTGTATACAAAAACGCCACTATAGATCTGACTTTTTGCAGCGTTTGTATAC-AAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TACAAAAACG
*
92855 CCACTATAGATCTGACCTTTT
65 CCGCTATAGATCTGACCTTTT
* * * * * **
92876 GTGACGTTTGTATCCAAAAATGCCGCTATAGATCTGACCTTTTGTGGCGTTTGTTGCAAAAATAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTACAAAAACGC
* *
92941 TGCTATAGATCTTGACTTTTT
66 CGCTATAGATC-TGACCTTTT
* ** * *
92962 GCGGCATTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTGTAAAAATGT
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTACAAAAACGC
93026 CGCTATAGATCTGACCTTTT
66 CGCTATAGATCTGACCTTTT
* * * * *
93046 ACGGCGTTTGT-TGCAAAAATGCCGCTATAGATCTTGA-CTTCTTGCGACGTTTGTTCCAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTT-TTGCGGCGTTTGTTACAAAAAC
*
93109 ACCGCTATAGATCTCGACCTTTT
64 GCCGCTATAGATCT-GACCTTTT
* ** * * *
93132 GCGGCGTTTGTATCCAAAAATGATGCTATAGATCTCGACCTTTTGCAGCGTTTATTTCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGGCGTTTGTTACAAAAACG
93197 CCGCTATAGATCTTGA-CTTTT
65 CCGCTATAGATC-TGACCTTTT
93218 GCGGCGTTT
1 GCGGCGTTT
93227 TTATTTTACA
Statistics
Matches: 374, Mismatches: 51, Indels: 22
0.84 0.11 0.05
Matches are distributed among these distances:
84 42 0.11
85 176 0.47
86 96 0.26
87 54 0.14
88 6 0.02
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTACAAAAACGC
CGCTATAGATCTGACCTTTT
Done.