Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001451.1 Hibiscus syriacus cultivar Beakdansim tig00002803_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: 99032
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:250 original size:30 final size:30
Alignment explanation
Indices: 216--273 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
206 GGTAAATTAC
*
216 ACATTTAGTACCTAAACTATCAGTTTTGAT
1 ACATTTAGTACCTAAACTATCAATTTTGAT
*
246 ACATTTTGTACCTAAACTATCAATTTTG
1 ACATTTAGTACCTAAACTATCAATTTTG
274 TCCCGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (30 bp):
ACATTTAGTACCTAAACTATCAATTTTGAT
Found at i:294 original size:32 final size:31
Alignment explanation
Indices: 219--303 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 31
209 AAATTACACA
*
219 TTTAGTACCTAAACTATCAGTTTTGATACAT
1 TTTAGTACCTAAACTATCAATTTTGATACAT
* *
250 TTT-GTACCTAAACTATCAATTTTG-TCCCGTT
1 TTTAGTACCTAAACTATCAATTTTGAT-AC-AT
*
281 TTTAGTACCTAAACT-TCCATTTT
1 TTTAGTACCTAAACTATCAATTTT
304 TTTCAAAAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.02
30 21 0.45
31 14 0.30
32 11 0.23
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAATTTTGATACAT
Found at i:1824 original size:331 final size:333
Alignment explanation
Indices: 1070--2717 Score: 2654
Period size: 331 Copynumber: 5.0 Consensus size: 333
1060 ACAAATAAAT
1070 ATCTAAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATG-ATAACTTGCGCTTTCA
1 ATCT-AATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
*
1134 ATGAAAATAAT-ATTTTTTTATAGAATTGAAATCTGAGATTAGTATATTAA-TTATTTAATCACT
65 ATGAAAA-AATAATTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACT
*
1197 TGTAAGAGATG-------AAAA-TT-AA--AA----AATT-AAATCTGAGATTATAATATGGGTT
129 TGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGTT
* *
1246 GATG-AATATTATAAGCAGGTATAGACGTAGGATTTATGTTAAGGGAGGTAAACCTGAACTTATA
194 GATGAAATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTATA
*
1310 AAATTTTAGGGGGAG-ATTTAAACTTAT-AAATTCCAGAGGTCAAAACAGATATTTGATAGAAAA
259 AAATTTTAGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAAAA
1373 TCATTAAAAAA
324 TCATT-AAAAA
*
1384 ATCTAAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGTGCTTTCA
1 ATCT-AATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
*
1449 ATGAAAAAATAATATTTTTTATAGAATTG-AATCTGAGATTAGTCTATTAATTTATTTAACCACT
65 ATGAAAAAATAAT-TTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACT
*
1513 TGTAAGAGATGAAATTTAAAAACTTAAATTAATTTC-ATTGAAATCTGAGATTATAATACGGGTT
129 TGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGTT
* *
1577 GATGAAAGATATTATAAGCAGGTAAAAACGTAGGATTT-TGTTAAGGGAGGTAAACTTGAACTTA
194 GATG-AA-ATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTA
*
1641 TAAAATTTTAGGGGGAG-ATTTAAACTTATAAAATTCCATGGGTCAAAACAGATATTTGATAGAA
257 TAAAATTTTAGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAA
1705 AATCATTAAAAA
322 AATCATTAAAAA
1717 ATCTAA-TGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCAA
1 ATCTAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCAA
1781 TGAAAAAATAATTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACTTG
66 TGAAAAAATAATTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACTTG
*
1846 TAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATATGGGTTGA
131 TAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGTTGA
*
1911 TGAAATATTATAAGTAGGTACAGACGTAGGATTTATG-TAAGGGAGGTAAACTTGAACTTATAAA
196 TGAAATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTATAAA
1975 ATTTT-GGGGAGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAAAAT
261 ATTTTAGGGG-GAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAAAAT
2039 CATT--AAA
325 CATTAAAAA
*
2046 ATCTAAATTGTTTTCATTAACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
1 ATCT-AATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
*
2111 ATG-AAAAATAATATTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTT-ATCACTT
65 ATGAAAAAATAATTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACTT
* *
2174 GTAAAATATGAAATTTAAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGG-T
130 GTAAGAGATGAAATTT-AAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGTT
2238 GATGAAAGATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTA
194 GATG-AA-ATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTA
*
2303 TAAAATTTTAGGGGGAGAATTTAAACTTATAAAATTCAAGGGGTCAAAACAGATA-TTGATAGAA
257 TAAAATTTTAGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAA
*
2367 AATGATT-AAAA
322 AATCATTAAAAA
2378 ATCTATATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
1 ATCTA-ATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCA
* *
2443 ATGAATAAATAATTTTTTTTATTGAATTGAAATCTGAGATT-GTCTATTAATTTATTTAATCACT
65 ATGAAAAAATAA-TTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACT
*
2507 TGTAAGAGATGAAATTTAAAAAATTTAAATTAATTTCAATTGAAATCTAAGATTATAATACGGGT
129 TGTAAGAGATGAAATTT-AAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGT
*
2572 TGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTAT
193 TGATGAAATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTAT
* *
2637 AAAATTTTA-GGGGAGAATTTAAACTTATAAAATTTCAGGGGTC-AAACAAATATTTGATAGAAA
258 AAAATTTTAGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAAA
2700 ATCATTAAAAAA
323 ATCATT-AAAAA
2712 ATCTAA
1 ATCTAA
2718 AATATAAGGT
Statistics
Matches: 1252, Mismatches: 37, Indels: 71
0.92 0.03 0.05
Matches are distributed among these distances:
314 51 0.04
315 44 0.04
316 38 0.03
323 4 0.00
324 2 0.00
325 2 0.00
327 2 0.00
329 37 0.03
330 181 0.14
331 337 0.27
332 220 0.18
333 158 0.13
334 171 0.14
335 5 0.00
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (333 bp):
ATCTAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCTTTCAA
TGAAAAAATAATTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATCACTTG
TAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATACGGGTTGA
TGAAATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTTATAAA
ATTTTAGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAAAATC
ATTAAAAA
Found at i:2490 original size:663 final size:662
Alignment explanation
Indices: 1065--2709 Score: 2706
Period size: 663 Copynumber: 2.5 Consensus size: 662
1055 AATTGACAAA
*
1065 TAAATATCTAAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATG-ATAACTTGCGC
1 TAAAAATCT-AATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGC
*
1129 TTTCAATG-AAAATAATATTTTTTTATAGAATTGAAATCTGAGATTAGTATATTAA-TTATTTAA
65 TTTCAATGAAAAATAAT-TTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAA
1192 TCACTTGTAAGAGATG-------AAAA-TT-AA--AA----AATT-AAATCTGAGATTATAATAT
129 TCACTTGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATAT
* * *
1241 GGGTTGATG-AATATTATAAGCAGGTATAGACGTAGGATTTATGTTAAGGGAGGTAAACCTGAAC
194 GGGTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAAC
*
1305 TTATAAAATTTTAGGGGGAG-ATTTAAACTTAT-AAATTCCAGAGGTCAAAACAGATATTTGATA
259 TTATAAAATTTT-GGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATA
*
1368 GAAAATCATTAAAAAAATCTAAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGA
323 GAAAATCATT---AAAATCTAAATTGTTTTCATTAACGAATACTAACAATCTTTCTATATCATGA
*
1433 ATAACTTGTGCTTTCAATGAAAAAATAATATTTTTTATAGAATTGAATCTGAGATTAGTCTATTA
385 ATAACTTGCGCTTTCAATGAAAAAATAATATTTTTTATAGAATTGAATCTGAGATTAGTCTATTA
*
1498 ATTTATTTAACCACTTGTAAGAGATGAAATTTAAAAACTTAAATTAATTTCATTGAAATCTGAGA
450 ATTTATTTAACCACTTGTAAAAGATGAAATTTAAAAACTTAAATTAATTTCATTGAAATCTGAGA
1563 TTATAATACGGGTTGATGAAAGATATTATAAGCAGGTAAAAACGTAGGATTTTGTTAAGGGAGGT
515 TTATAATACGGGTTGATGAAAGATATTATAAGCAGGTAAAAACGTAGGATTTTGTTAAGGGAGGT
* *
1628 AAACTTGAACTTATAAAATTTTAGGGGGAGATTTAAACTTATAAAATTCCATGGGTCAAAACAGA
580 AAACTTGAACTTATAAAATTTTAGGGGGAGATTTAAACTTATAAAATTCAAGGGGTCAAAACAGA
1693 TATTTGATAGAAAATCAT
645 TATTTGATAGAAAATCAT
1711 TAAAAAATCTAA-TGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGC
1 T-AAAAATCTAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGC
1775 TTTCAATGAAAAAATAA-TTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAA
65 TTTCAATG-AAAAATAATTTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAA
1839 TCACTTGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATAT
129 TCACTTGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATAT
1904 GGGTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATG-TAAGGGAGGTAAACTTGAAC
194 GGGTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAAC
1968 TTATAAAATTTTGGGGAGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATA
259 TTATAAAATTTTGGGG-GAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATA
2033 GAAAATCATTAAAATCTAAATTGTTTTCATTAACGAATACTAACAATCTTTCTATATCATGAATA
323 GAAAATCATTAAAATCTAAATTGTTTTCATTAACGAATACTAACAATCTTTCTATATCATGAATA
2098 ACTTGCGCTTTCAATG-AAAAATAATA-TTTTTATAGAATTGAAATCTGAGATTAGTCTATTAAT
388 ACTTGCGCTTTCAATGAAAAAATAATATTTTTTATAGAATTG-AATCTGAGATTAGTCTATTAAT
* * *
2161 TTATTT-ATCACTTGTAAAATATGAAATTTAAAAAATTTAAATTAATTTCAATTGAAATCTGAGA
452 TTATTTAACCACTTGTAAAAGATGAAATTT-AAAAACTTAAATTAATTTC-ATTGAAATCTGAGA
* *
2225 TTATAATACGGG-TGATGAAAGATATTATAAGCAGGTACAGACGTAGGATTTATGTTAAGGGAGG
515 TTATAATACGGGTTGATGAAAGATATTATAAGCAGGTAAAAACGTAGGATTT-TGTTAAGGGAGG
2289 TAAACTTGAACTTATAAAATTTTAGGGGGAGAATTTAAACTTATAAAATTCAAGGGGTCAAAACA
579 TAAACTTGAACTTATAAAATTTTAGGGGGAG-ATTTAAACTTATAAAATTCAAGGGGTCAAAACA
*
2354 GATA-TTGATAGAAAATGAT
643 GATATTTGATAGAAAATCAT
2373 TAAAAATCTATATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGC
1 TAAAAATCTA-ATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGC
*
2438 TTTCAATGAATAAATAATTTTTTTTATTGAATTGAAATCTGAGATT-GTCTATTAATTTATTTAA
65 TTTCAATGAA-AAATAATTTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAA
*
2502 TCACTTGTAAGAGATGAAATTTAAAAAATTTAAATTAATTTCAATTGAAATCTAAGATTATAATA
129 TCACTTGTAAGAGATGAAATTT-AAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATA
*
2567 CGGGTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAA
193 TGGGTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAA
* * *
2632 CTTATAAAATTTTAGGGGAGAATTTAAACTTATAAAATTTCAGGGGTC-AAACAAATATTTGATA
258 CTTATAAAATTTTGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATA
2696 GAAAATCATTAAAA
323 GAAAATCATTAAAA
2710 AAATCTAAAA
Statistics
Matches: 940, Mismatches: 23, Indels: 55
0.92 0.02 0.05
Matches are distributed among these distances:
645 40 0.04
646 59 0.06
647 31 0.03
648 7 0.01
654 4 0.00
655 2 0.00
656 2 0.00
658 2 0.00
660 34 0.04
661 102 0.11
662 164 0.17
663 232 0.25
664 186 0.20
665 75 0.08
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (662 bp):
TAAAAATCTAATTGTTTTCATTGACGAATACTAACAATCTTTCTATATCATGAATAACTTGCGCT
TTCAATGAAAAATAATTTTTTTTATAGAATTGAAATCTGAGATTAGTCTATTAATTTATTTAATC
ACTTGTAAGAGATGAAATTTAAAAATTTAAATTAATTTCAATTGAAATCTGAGATTATAATATGG
GTTGATGAAATATTATAAGTAGGTACAGACGTAGGATTTATGTTAAGGGAGGTAAACTTGAACTT
ATAAAATTTTGGGGGAGAATTTAAACTTATAAAATTCCAGGGGTCAAAACAGATATTTGATAGAA
AATCATTAAAATCTAAATTGTTTTCATTAACGAATACTAACAATCTTTCTATATCATGAATAACT
TGCGCTTTCAATGAAAAAATAATATTTTTTATAGAATTGAATCTGAGATTAGTCTATTAATTTAT
TTAACCACTTGTAAAAGATGAAATTTAAAAACTTAAATTAATTTCATTGAAATCTGAGATTATAA
TACGGGTTGATGAAAGATATTATAAGCAGGTAAAAACGTAGGATTTTGTTAAGGGAGGTAAACTT
GAACTTATAAAATTTTAGGGGGAGATTTAAACTTATAAAATTCAAGGGGTCAAAACAGATATTTG
ATAGAAAATCAT
Found at i:6166 original size:22 final size:20
Alignment explanation
Indices: 6141--6194 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6131 TGTTGAGACT
* *
6141 GGTATCAATACCTTGAGGGATG
1 GGTATCGATACCTT-AAGGA-G
*
6163 GGTATCGGTACCTTAAGGAG
1 GGTATCGATACCTTAAGGAG
6183 GGTATCGATACC
1 GGTATCGATACC
6195 CCTAAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (20 bp):
GGTATCGATACCTTAAGGAG
Found at i:6719 original size:21 final size:21
Alignment explanation
Indices: 6676--6725 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
6666 GCGTTATGAA
* *
6676 AATATGAACTTTGAACATGTG
1 AATATGAACTTCGAACATATG
6697 AATATGAACTTCGAATCA-ATG
1 AATATGAACTTCGAA-CATATG
*
6718 AATGTGAA
1 AATATGAA
6726 TATACTCTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (21 bp):
AATATGAACTTCGAACATATG
Found at i:6934 original size:23 final size:22
Alignment explanation
Indices: 6879--6952 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 22
6869 TCAGGACAAT
* *
6879 TATGTGGTCCTCCGG-GACAAA-
1 TATGTGGTACTTCGGTG-CAAAC
* *
6900 TATGTGGCACTTCGGTGCAACC
1 TATGTGGTACTTCGGTGCAAAC
* *
6922 TTATGTGGTACTTTGGTGTAAAC
1 -TATGTGGTACTTCGGTGCAAAC
6945 TATGTGGT
1 TATGTGGT
6953 CCTTTGGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 15 0.36
22 9 0.21
23 18 0.43
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (22 bp):
TATGTGGTACTTCGGTGCAAAC
Found at i:6951 original size:22 final size:23
Alignment explanation
Indices: 6900--6959 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
6890 CCGGGACAAA
* * *
6900 TATGTGGCACTTCGGTGCAACCT
1 TATGTGGTACTTTGGTGCAAACT
*
6923 TATGTGGTACTTTGGTGTAAAC-
1 TATGTGGTACTTTGGTGCAAACT
*
6945 TATGTGGTCCTTTGG
1 TATGTGGTACTTTGG
6960 GACAATTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (23 bp):
TATGTGGTACTTTGGTGCAAACT
Found at i:6971 original size:21 final size:21
Alignment explanation
Indices: 6858--6972 Score: 92
Period size: 21 Copynumber: 5.3 Consensus size: 21
6848 GTTGAGGGTA
*
6858 TATGTGGTCCTTCAGGACAAT
1 TATGTGGTCCTTCGGGACAAT
* *
6879 TATGTGGTCCTCCGGGACAAA
1 TATGTGGTCCTTCGGGACAAT
6900 TATGTGG-CACTTCGGTG-CAACCT
1 TATGTGGTC-CTTCGG-GACAA--T
* * *
6923 TATGTGGTACTTTGGTGTA-AAC
1 TATGTGGTCCTTCGG-G-ACAAT
*
6945 TATGTGGTCCTTTGGGACAAT
1 TATGTGGTCCTTCGGGACAAT
6966 TATGTGG
1 TATGTGG
6973 CAATTCGATG
Statistics
Matches: 76, Mismatches: 10, Indels: 16
0.75 0.10 0.16
Matches are distributed among these distances:
20 2 0.03
21 43 0.57
22 15 0.20
23 14 0.18
24 2 0.03
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAT
Found at i:13207 original size:54 final size:54
Alignment explanation
Indices: 13138--13252 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 54
13128 GGGATGAGTG
*
13138 TCGGTACCTTAAGGAGGGTATCAATACCC-TAAAACATCGAATGCCA-TTTGTGTA
1 TCGGTACCTTAAGGA-GGTATCAATACCCTTAAAACATCGAATGCAATTTTG-GTA
* * **
13192 TCGGTACCTTGAGGAGGTATCGATACCCTTGCAACATCGAATGCAATTTTGGTA
1 TCGGTACCTTAAGGAGGTATCAATACCCTTAAAACATCGAATGCAATTTTGGTA
13246 TCGGTAC
1 TCGGTAC
13253 ATGCGTAGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
53 12 0.22
54 38 0.70
55 4 0.07
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (54 bp):
TCGGTACCTTAAGGAGGTATCAATACCCTTAAAACATCGAATGCAATTTTGGTA
Found at i:13263 original size:53 final size:54
Alignment explanation
Indices: 13138--13272 Score: 141
Period size: 54 Copynumber: 2.5 Consensus size: 54
13128 GGGATGAGTG
* * * ** *
13138 TCGGTACCTTAAGGAGGGTATCAATACCC-TAAAACATCGAATGCCATTTGTGTA
1 TCGGTACCATGAGGA-GGTATCGATACCCTTGCAACATCGAATGCAATTTGTGTA
*
13192 TCGGTACCTTGAGGAGGTATCGATACCCTTGCAACATCGAATGCAATTT-TGGTA
1 TCGGTACCATGAGGAGGTATCGATACCCTTGCAACATCGAATGCAATTTGT-GTA
* * *
13246 TCGGTA-CATGCGTAGGTATTGATACCC
1 TCGGTACCATGAGGAGGTATCGATACCC
13273 CTGAAGGGTG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
53 30 0.43
54 40 0.57
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (54 bp):
TCGGTACCATGAGGAGGTATCGATACCCTTGCAACATCGAATGCAATTTGTGTA
Found at i:13685 original size:21 final size:21
Alignment explanation
Indices: 13661--13710 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
13651 GTGTTATGAA
*
13661 AATATGAACTTTGAA-CATGTG
1 AATATGAACTTCGAATCA-GTG
13682 AATATGAACTTCGAATCAGTG
1 AATATGAACTTCGAATCAGTG
*
13703 AATGTGAA
1 AATATGAA
13711 TATTCTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (21 bp):
AATATGAACTTCGAATCAGTG
Found at i:13881 original size:21 final size:21
Alignment explanation
Indices: 13844--13892 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
13834 GTCGAGGGTC
** * *
13844 TATGTGGTCCTTTGGGATAAT
1 TATGTGGTCCTCCGGGACAAA
13865 TATGTGGTCCTCCGGGACAAA
1 TATGTGGTCCTCCGGGACAAA
13886 TATGTGG
1 TATGTGG
13893 CACTTCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.31, T:0.35
Consensus pattern (21 bp):
TATGTGGTCCTCCGGGACAAA
Found at i:13917 original size:23 final size:23
Alignment explanation
Indices: 13890--13951 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
13880 GACAAATATG
13890 TGGCACTTCGGTGCAACCTTATA
1 TGGCACTTCGGTGCAACCTTATA
*
13913 TGGCACTTCGGTGCAACCTTATG
1 TGGCACTTCGGTGCAACCTTATA
13936 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
13952 ACTATATAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTTCGGTGCAACCTTATA
Found at i:13992 original size:43 final size:44
Alignment explanation
Indices: 13877--13995 Score: 136
Period size: 46 Copynumber: 2.7 Consensus size: 44
13867 TGTGGTCCTC
* * *
13877 CGGGACAAATATGTGGCACTTCGGTGCAACCTTATATGGCACTT
1 CGGGACAATTATGTGGCACTTCGGTGCAAACTTATATAGCACTT
*
13921 CGGTG-CAACCTTATGTGGCACTTCGGTGCAAAC-TATATAGTACTAT
1 CGG-GACAA--TTATGTGGCACTTCGGTGCAAACTTATATAGCACT-T
*
13967 -GGGACAATTATGTGGTACTTCGGTGCAAA
1 CGGGACAATTATGTGGCACTTCGGTGCAAA
13996 TTACGAGATG
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
43 21 0.32
44 7 0.11
45 15 0.23
46 22 0.34
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (44 bp):
CGGGACAATTATGTGGCACTTCGGTGCAAACTTATATAGCACTT
Found at i:18338 original size:23 final size:23
Alignment explanation
Indices: 18290--18335 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
18280 TTTTAATTAT
18290 ATTTTAAAAATTAAATAAATAAA
1 ATTTTAAAAATTAAATAAATAAA
*
18313 ATTTTGAAAA-TAAATAAATAAA
1 ATTTTAAAAATTAAATAAATAAA
18335 A
1 A
18336 ATTAAGGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
ATTTTAAAAATTAAATAAATAAA
Found at i:19620 original size:20 final size:20
Alignment explanation
Indices: 19595--19728 Score: 133
Period size: 20 Copynumber: 6.6 Consensus size: 20
19585 TAATTGAAAA
*
19595 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
19615 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
19635 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
19656 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
19676 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
19697 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
19717 TCGCATTGCGAT
1 TCGCGTTGCGAT
19729 AGTCTACAGT
Statistics
Matches: 88, Mismatches: 24, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
20 59 0.67
21 29 0.33
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:19639 original size:61 final size:61
Alignment explanation
Indices: 19570--19687 Score: 227
Period size: 61 Copynumber: 1.9 Consensus size: 61
19560 ATTCTCGTTG
19570 CATTTCGCGTTGCGATAATTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAATTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATTTTC
*
19631 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGATAATTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGAT
19688 AGTTGAAAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (61 bp):
CATTTCGCGTTGCGATAATTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATTTTC
Found at i:19660 original size:41 final size:41
Alignment explanation
Indices: 19615--19731 Score: 216
Period size: 41 Copynumber: 2.9 Consensus size: 41
19605 CTTTTCCATT
19615 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
19656 TCGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
*
19697 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
19732 CTACAGTTGT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAA
Found at i:19726 original size:61 final size:61
Alignment explanation
Indices: 19574--19708 Score: 189
Period size: 61 Copynumber: 2.2 Consensus size: 61
19564 TCGTTGCATT
* * * * **
19574 TCGCGTTGCGATAATTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATGTTCAAAA
* *
19635 TCGCGTTGCGATAGTTGAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGAT-GTTCAAAA
19697 TCGCGTTGCGAT
1 TCGCGTTGCGAT
19709 TTTCCATTTC
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
61 52 0.78
62 15 0.22
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (61 bp):
TCGCGTTGCGATAGTTCAAAATCGCGTTGCGCTTTTCCATTTCGCGTTGCGATGTTCAAAA
Found at i:19750 original size:22 final size:22
Alignment explanation
Indices: 19722--19772 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
19712 CCATTTCGCA
19722 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
19744 TTGCGATAGTCTACAGTTGTCG
1 TTGCGATAGTCTACAGTTGTCG
19766 TTGCGAT
1 TTGCGAT
19773 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (22 bp):
TTGCGATAGTCTACAGTTGTCG
Found at i:19896 original size:6 final size:6
Alignment explanation
Indices: 19885--19929 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
19875 GACACGTATT
19885 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
19930 CGAGACGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:20374 original size:21 final size:22
Alignment explanation
Indices: 20330--20374 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
20320 TATTGGAAAC
** *
20330 ACTATTCGCAACGCGATTTTCA
1 ACTATTCGCAACGCGAAATGCA
20352 ACTA-TCGCAACGCGAAATGCA
1 ACTATTCGCAACGCGAAATGCA
20373 AC
1 AC
20375 GCGAATTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (22 bp):
ACTATTCGCAACGCGAAATGCA
Found at i:21585 original size:25 final size:28
Alignment explanation
Indices: 21548--21606 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 28
21538 TTAGTTGAGT
* *
21548 CGAAAATTATACGAA-GAT-TGT-CAAC
1 CGAAAATGATACGAACAATGTGTGCAAC
*
21573 CGAAAATGGTACGAACAATGTGTGCAAC
1 CGAAAATGATACGAACAATGTGTGCAAC
21601 CGAAAA
1 CGAAAA
21607 ATGTTAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 13 0.46
26 2 0.07
27 3 0.11
28 10 0.36
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (28 bp):
CGAAAATGATACGAACAATGTGTGCAAC
Found at i:24185 original size:23 final size:24
Alignment explanation
Indices: 24146--24193 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
24136 AAAAAAGAAA
*
24146 AAAATAATTTATATATTTATAAAT
1 AAAATAATTTATATATTTAAAAAT
*
24170 AAAAT-ATTTATTTATTTAAAAAT
1 AAAATAATTTATATATTTAAAAAT
24193 A
1 A
24194 TCAGAAAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAATAATTTATATATTTAAAAAT
Found at i:25791 original size:3 final size:3
Alignment explanation
Indices: 25783--25856 Score: 69
Period size: 3 Copynumber: 24.0 Consensus size: 3
25773 AATTATTTTT
*
25783 TAA TAA TAA TAA TAA T-A TATA TATA TATA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TA-A TA-A TAA TAA TAA TAA TAA TAA
* * * *
25830 TTA TAA TAA TAA TTA TTA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
25857 AAAATTAGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.03
3 48 0.79
4 11 0.18
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:25854 original size:12 final size:12
Alignment explanation
Indices: 25783--25845 Score: 83
Period size: 12 Copynumber: 5.1 Consensus size: 12
25773 AATTATTTTT
*
25783 TAATAATAATAA
1 TAATAATAATTA
25795 TAAT-ATATATATA
1 TAATAATA-AT-TA
25808 TATATAATAATTA
1 TA-ATAATAATTA
25821 TAATAATAATTA
1 TAATAATAATTA
25833 TAATAATAATTA
1 TAATAATAATTA
25845 T
1 T
25846 TATAGTAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
11 3 0.07
12 29 0.63
13 7 0.15
14 4 0.09
15 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:33328 original size:22 final size:23
Alignment explanation
Indices: 33302--33347 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
33292 ACGGTCAATG
* *
33302 GTCAGACCGGTCAA-AGTTAACA
1 GTCAGACCGATCAACAGTCAACA
33324 GTCAGACCGATCAACAGTCAACA
1 GTCAGACCGATCAACAGTCAACA
33347 G
1 G
33348 ATCAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (23 bp):
GTCAGACCGATCAACAGTCAACA
Found at i:33352 original size:15 final size:16
Alignment explanation
Indices: 33320--33352 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
33310 GGTCAAAGTT
*
33320 AACAGTCAGACCGATC
1 AACAGTCAGACAGATC
33336 AACAGTCA-ACAGATC
1 AACAGTCAGACAGATC
33351 AA
1 AA
33353 GTCAAAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.27, G:0.15, T:0.12
Consensus pattern (16 bp):
AACAGTCAGACAGATC
Found at i:35030 original size:31 final size:31
Alignment explanation
Indices: 34992--35053 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
34982 TCAGACAGAC
34992 ATTCTCATAATCGTTCGTTTGTCGTCACGTT
1 ATTCTCATAATCGTTCGTTTGTCGTCACGTT
*
35023 ATTCTCATAATCGTTTGTTTGTCGTCACGTT
1 ATTCTCATAATCGTTCGTTTGTCGTCACGTT
35054 GTAAGGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (31 bp):
ATTCTCATAATCGTTCGTTTGTCGTCACGTT
Found at i:38359 original size:30 final size:31
Alignment explanation
Indices: 38325--38398 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 31
38315 AAATTACGTG
38325 TTTAGTATTTAAATTATCAATTTTGATCT-T
1 TTTAGTATTTAAATTATCAATTTTGATCTGT
* *
38355 TTTAGTACTTAAATTATTAATTTTGATCTGT
1 TTTAGTATTTAAATTATCAATTTTGATCTGT
*
38386 TTTAGTATCTAAA
1 TTTAGTATTTAAA
38399 CTTTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 27 0.69
31 12 0.31
ACGTcount: A:0.31, C:0.07, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTAGTATTTAAATTATCAATTTTGATCTGT
Found at i:40774 original size:6 final size:6
Alignment explanation
Indices: 40753--40789 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
40743 GTCCGTCTCG
40753 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
40790 ATTGGTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:40968 original size:25 final size:22
Alignment explanation
Indices: 40913--40971 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
40903 AATTTAGAAA
*
40913 ATCGCAACGACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
40935 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
40957 ATCGCAACAACAACT
1 ATCGCAACAACAACT
40972 ATAGCAACGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.41, C:0.29, G:0.14, T:0.17
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:41002 original size:20 final size:20
Alignment explanation
Indices: 40975--41085 Score: 78
Period size: 20 Copynumber: 5.5 Consensus size: 20
40965 AACAACTATA
40975 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
* *** ** * *
40995 GTAACGCGGTTTTCAACTATA
1 GCAACGCGAAATGGAA-AATC
41016 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
* ** ** *
41036 GTAACGCGATTTTCAACTATC
1 GCAACGCGAAATGGAA-AATC
41057 GCAACGCGAAATGGAAAATC
1 GCAACGCGAAATGGAAAATC
41077 GCAACGCGA
1 GCAACGCGA
41086 TTTTCAACTA
Statistics
Matches: 61, Mismatches: 28, Indels: 4
0.66 0.30 0.04
Matches are distributed among these distances:
20 35 0.57
21 26 0.43
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.18
Consensus pattern (20 bp):
GCAACGCGAAATGGAAAATC
Found at i:41013 original size:41 final size:41
Alignment explanation
Indices: 40967--41110 Score: 252
Period size: 41 Copynumber: 3.5 Consensus size: 41
40957 ATCGCAACAA
*
40967 CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGGTTTT
1 CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGATTTT
41008 CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGATTTT
1 CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGATTTT
* *
41049 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTT
1 CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGATTTT
*
41090 CAACTATCGCAACGCGAAATG
1 CAACTATAGCAACGCGAAATG
41111 CAACGCGAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (41 bp):
CAACTATAGCAACGCGAAATGGAAAATCGTAACGCGATTTT
Found at i:41114 original size:21 final size:21
Alignment explanation
Indices: 40967--41114 Score: 95
Period size: 21 Copynumber: 7.2 Consensus size: 21
40957 ATCGCAACAA
*
40967 CAACTATAGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * *** *
40988 GAA-AATCGTAACGCGGTTTT
1 CAACTATCGCAACGCGAAATG
*
41008 CAACTATAGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
41029 GAA-AATCGTAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
41049 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
41070 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
41090 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
41111 CAAC
1 CAAC
41115 GCGAATTTGC
Statistics
Matches: 85, Mismatches: 39, Indels: 6
0.65 0.30 0.05
Matches are distributed among these distances:
20 40 0.47
21 45 0.53
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:52950 original size:33 final size:33
Alignment explanation
Indices: 52912--52979 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
52902 AATACTTTAA
52912 AAAATGATATATTTTTATCATATTATTAAAATC
1 AAAATGATATATTTTTATCATATTATTAAAATC
52945 AAAATGATATATTTTTATCATATTATTAAAATC
1 AAAATGATATATTTTTATCATATTATTAAAATC
52978 AA
1 AA
52980 TAATTGCACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (33 bp):
AAAATGATATATTTTTATCATATTATTAAAATC
Found at i:54371 original size:16 final size:16
Alignment explanation
Indices: 54345--54398 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
54335 CCAGTTTCGG
54345 TTTGAAAAAAAAATCGA
1 TTTG-AAAAAAAATCGA
*
54362 TTTGAAAAAAAATCAGT
1 TTTGAAAAAAAATC-GA
** *
54379 TTTTTAAAAAAATCGG
1 TTTGAAAAAAAATCGA
54395 TTTG
1 TTTG
54399 TAGCCATGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (16 bp):
TTTGAAAAAAAATCGA
Found at i:55563 original size:29 final size:29
Alignment explanation
Indices: 55529--55710 Score: 140
Period size: 29 Copynumber: 6.4 Consensus size: 29
55519 CCGTTGACCG
*
55529 GGTGGTATTTTGGTAATTATTTTGAAATT
1 GGTGGTATTTTGGTAATTATTTTGAAAAT
*
55558 GGTGGTATTCTGGTAATTATTTTGAAAAT
1 GGTGGTATTTTGGTAATTATTTTGAAAAT
* * *
55587 GGTGTTATTTTTGT-ATT-TTTT-AAAAA
1 GGTGGTATTTTGGTAATTATTTTGAAAAT
** * **
55613 AATGCTATTTTCCTAA-T-TTTTGAAAAAAT
1 GGTGGTATTTTGGTAATTATTTTG--AAAAT
* * * * *
55642 AGTGATATTTTAGTAAATATTTTTAAAAT
1 GGTGGTATTTTGGTAATTATTTTGAAAAT
* * *
55671 GGTGCTATTTTGCTAATTATTTTTAAAAT
1 GGTGGTATTTTGGTAATTATTTTGAAAAT
*
55700 GGTGCTATTTT
1 GGTGGTATTTT
55711 TATAAATTTT
Statistics
Matches: 125, Mismatches: 22, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
26 18 0.14
27 5 0.04
28 3 0.02
29 94 0.75
30 1 0.01
31 4 0.03
ACGTcount: A:0.30, C:0.04, G:0.16, T:0.50
Consensus pattern (29 bp):
GGTGGTATTTTGGTAATTATTTTGAAAAT
Found at i:55687 original size:58 final size:58
Alignment explanation
Indices: 55615--55727 Score: 140
Period size: 58 Copynumber: 1.9 Consensus size: 58
55605 TTTAAAAAAA
55615 TGCTATTTTCCTAATT-TTTGAAAAAATAGTGATA-TTTTAGTAAATATTTTTAAAATGG
1 TGCTATTTTCCTAATTATTT-AAAAAATAGTGATATTTTTA-TAAATATTTTTAAAATGG
* ** * * *
55673 TGCTATTTTGCTAATTATTTTTAAAATGGTGCTATTTTTATAAATTTTTTTAAAA
1 TGCTATTTTCCTAATTATTTAAAAAATAGTGATATTTTTATAAATATTTTTAAAA
55728 AAGTGATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 39 0.83
59 8 0.17
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (58 bp):
TGCTATTTTCCTAATTATTTAAAAAATAGTGATATTTTTATAAATATTTTTAAAATGG
Found at i:55722 original size:29 final size:29
Alignment explanation
Indices: 55649--55727 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
55639 AATAGTGATA
*
55649 TTTTAGTAAATATTTTTAAAATGGTGCTAT
1 TTTTA-TAAATTTTTTTAAAATGGTGCTAT
**
55679 TTTGCT-AATTATTTTTAAAATGGTGCTAT
1 TTTTATAAATT-TTTTTAAAATGGTGCTAT
55708 TTTTATAAATTTTTTTAAAA
1 TTTTATAAATTTTTTTAAAA
55728 AAGTGATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 3 0.07
29 32 0.76
30 7 0.17
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (29 bp):
TTTTATAAATTTTTTTAAAATGGTGCTAT
Found at i:61258 original size:21 final size:21
Alignment explanation
Indices: 61232--61277 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
61222 CTCTAAATTG
*
61232 TTGGCCTTTTGATGGGAAGCT
1 TTGGCCTCTTGATGGGAAGCT
61253 TTGGCCTCTTGATGGGAAGCT
1 TTGGCCTCTTGATGGGAAGCT
61274 TTGG
1 TTGG
61278 ATCAATGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.15, G:0.35, T:0.37
Consensus pattern (21 bp):
TTGGCCTCTTGATGGGAAGCT
Found at i:62945 original size:29 final size:30
Alignment explanation
Indices: 62900--62959 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
62890 ATTAATATTA
*
62900 TGCATCGATACGCTACAGT-ACTACTACAG
1 TGCATAGATACGCTACAGTAACTACTACAG
* *
62929 TGCATAGATACGTTACAGTAACTGCTACAG
1 TGCATAGATACGCTACAGTAACTACTACAG
62959 T
1 T
62960 AATTTCAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (30 bp):
TGCATAGATACGCTACAGTAACTACTACAG
Found at i:63398 original size:44 final size:44
Alignment explanation
Indices: 63347--63477 Score: 244
Period size: 44 Copynumber: 3.0 Consensus size: 44
63337 TCATTTAATT
63347 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
*
63391 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCCTTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
*
63435 CATAAGCTCGTAAGCATATTTTACCAATATACTTACCATTATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATT
63478 TACAGCACTG
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
Found at i:63680 original size:59 final size:60
Alignment explanation
Indices: 63615--63742 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 60
63605 ATATACTTAA
* * *
63615 TATGATTTCCTCCT-CA-TTTTAGCACACGAAGTGCCCTATGCGAGAATCCATACCATTAG
1 TATGATTTCCT-CTACATTTTTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
* * * *
63674 TATGA-TTCCTTTACCATTTTTAGCACATAAAGTGCCCTATATGAAAATCCATACTATTAG
1 TATGATTTCCTCTA-CATTTTTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
63734 TATGATTTC
1 TATGATTTC
63743 TTTATCCTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
57 1 0.02
58 5 0.09
59 7 0.12
60 42 0.72
61 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (60 bp):
TATGATTTCCTCTACATTTTTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
Found at i:63816 original size:59 final size:59
Alignment explanation
Indices: 63555--64055 Score: 421
Period size: 59 Copynumber: 8.5 Consensus size: 59
63545 TGTACAATTC
* * * * ** * * * *
63555 GTATAATTTCCTTATAATATTAACAGTCTCAGTGCTCTATCTGGAATAT-CATATACTTA
1 GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAA-ATCCATACACTCA
* ** ** *
63614 ATATGATTTCCTCCTCATTTTAGCACACGAAGTGC-CC-TATGCGAGAATCCATAC-CATTA
1 GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATG-GA-AATCCATACAC-TCA
* * * *
63673 GTATGA-TTCCTTTACCATTTTTAGCACA-TAAAGTGC-CCTATATGAAAATCCATACTA-TTA
1 GTATGATTTCC-TTATCA-TTTTAGCACACT-CAGTGCTCC-ATATGGAAATCCATAC-ACTCA
* * * * * *** *
63733 GTATGATTTCTTTATCCTTGTAGCACCCTTAGTGCTTTTTCTGGAAATCCATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* * * * * *
63792 GTATGATTCCCTTACCATTTTAGCACA-TATAATGC-CCTATATGGAAATCCATATATTCA
1 GTATGATTTCCTTATCATTTTAGCACACT-CAGTGCTCC-ATATGGAAATCCATACACTCA
* * * *
63851 ATTTGATTTCCTTATTATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTC-
1 GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* *
63909 GATATGATTTCCTTATCTTTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTCA
1 G-TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
* *
63969 GTATGATTTCCTTATCTTTTTAGCACACTCGGTGCTCCATATGGAAATCCATACACTCA
1 GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
*
64028 ATATGATTTCCTTATCATTTTAGCACAC
1 GTATGATTTCCTTATCATTTTAGCACAC
64056 ATATAGTGCC
Statistics
Matches: 358, Mismatches: 63, Indels: 42
0.77 0.14 0.09
Matches are distributed among these distances:
57 3 0.01
58 12 0.03
59 290 0.81
60 45 0.13
61 4 0.01
62 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (59 bp):
GTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCA
Found at i:65852 original size:30 final size:30
Alignment explanation
Indices: 65818--65889 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
65808 ATCAAACGTG
*
65818 GGCACTAAATTGGACCCGAGACAAATATTA
1 GGCACTAAATTGGACCCGAGACAAAGATTA
* *
65848 GGCACTAAACTGGACCCGAGACAAAGGTTA
1 GGCACTAAATTGGACCCGAGACAAAGATTA
*
65878 GACACTAAATTG
1 GGCACTAAATTG
65890 AAAAACAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18
Consensus pattern (30 bp):
GGCACTAAATTGGACCCGAGACAAAGATTA
Found at i:67341 original size:57 final size:57
Alignment explanation
Indices: 67247--67418 Score: 299
Period size: 57 Copynumber: 3.0 Consensus size: 57
67237 AATTTGAATA
*
67247 ACCTAAAAATATCAATATAGTTAATAGCTAATAAACAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
* *
67304 ACCTAAAAATATCAATATAGTTAATAGTTAATTAACAAAATAATTTAATCAACATGT
1 ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
* *
67361 ACCTAAAAATATCAATATAATTAACAGTTAATAAACAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
67418 A
1 A
67419 ACAAAATAAC
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 108 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.30
Consensus pattern (57 bp):
ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
Found at i:67386 original size:29 final size:29
Alignment explanation
Indices: 67247--67387 Score: 87
Period size: 29 Copynumber: 4.9 Consensus size: 29
67237 AATTTGAATA
* *
67247 ACCTAAAAATATCAATATAGTTAATAGCT
1 ACCTAAAAATATCAATATAATTAACAGCT
* * * *
67276 A-ATAAACAAAAT-AATTTAATCAACATGC-
1 ACCTAAA-AATATCAATATAATTAACA-GCT
* * *
67304 ACCTAAAAATATCAATATAGTTAATAGTT
1 ACCTAAAAATATCAATATAATTAACAGCT
** * *
67333 AATTAACAAA-AT-AATTTAATCAACATG-T
1 ACCTAA-AAATATCAATATAATTAACA-GCT
67361 ACCTAAAAATATCAATATAATTAACAG
1 ACCTAAAAATATCAATATAATTAACAG
67388 TTAATAAACA
Statistics
Matches: 80, Mismatches: 23, Indels: 19
0.66 0.19 0.16
Matches are distributed among these distances:
27 3 0.04
28 36 0.45
29 38 0.47
30 3 0.04
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (29 bp):
ACCTAAAAATATCAATATAATTAACAGCT
Found at i:67492 original size:28 final size:29
Alignment explanation
Indices: 67448--67504 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
67438 ATATTTTAAC
*
67448 AGTTAAGAAACACCACCAAA-ACACCAAA
1 AGTTAAGAAACAACACCAAATACACCAAA
* *
67476 AGTTAATAAACAACACCAAATGCACCAAA
1 AGTTAAGAAACAACACCAAATACACCAAA
67505 TAACCAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.56, C:0.26, G:0.07, T:0.11
Consensus pattern (29 bp):
AGTTAAGAAACAACACCAAATACACCAAA
Found at i:74143 original size:21 final size:21
Alignment explanation
Indices: 74098--74143 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
74088 TACCACCTCG
*
74098 ATTGCCATGTCAGCACCATGG
1 ATTGCCATGTCAGCACCATGA
* *
74119 ATTGCTATGTCAGCACCGTGA
1 ATTGCCATGTCAGCACCATGA
74140 ATTG
1 ATTG
74144 TCACATTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (21 bp):
ATTGCCATGTCAGCACCATGA
Found at i:81067 original size:2 final size:2
Alignment explanation
Indices: 81060--81101 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
81050 TGTCAGAACC
81060 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81102 CGATCACTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82809 original size:60 final size:60
Alignment explanation
Indices: 82698--82810 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
82688 TATAAGATAC
* * * ** *
82698 TACTTTTTAGAATCCCTTGACTGTTAAAAGTTACAAAATTATCTTTTGACTATAGGAAAT
1 TACTTTTTAGAATCCCGTGACTATTAAAAGTTACAAAATGATCACTCGACTATAGGAAAT
* *
82758 TACTTTTTTGAGA-CCCGTGACTATTAAAAGTTACAAAATGGTCACTCGACTAT
1 TACTTTTTAGA-ATCCCGTGACTATTAAAAGTTACAAAATGATCACTCGACTAT
82811 TCATTATGTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (60 bp):
TACTTTTTAGAATCCCGTGACTATTAAAAGTTACAAAATGATCACTCGACTATAGGAAAT
Found at i:84801 original size:21 final size:21
Alignment explanation
Indices: 84751--84801 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
84741 AAAATCAAAA
* *
84751 AATAAAAGAAAATAAAAATAT
1 AATAAAAAAAAATAAAAAGAT
* * *
84772 GATATAAAAAAATAAAACGAT
1 AATAAAAAAAAATAAAAAGAT
84793 AATAAAAAA
1 AATAAAAAA
84802 TACCGACGAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (21 bp):
AATAAAAAAAAATAAAAAGAT
Found at i:87573 original size:22 final size:22
Alignment explanation
Indices: 87543--87626 Score: 60
Period size: 22 Copynumber: 3.5 Consensus size: 22
87533 ATTGTGTTAT
87543 TTTAATTATTTTGAATGTTTTG
1 TTTAATTATTTTGAATGTTTTG
* * **
87565 TTTATTTATTTATTAGTATTATATTATAT
1 TTTAATTA-TT-TT-G-A--ATGTT-TTG
87594 TTTAATTATTTTGAATGTTTTG
1 TTTAATTATTTTGAATGTTTTG
*
87616 TTTATTTATTT
1 TTTAATTATTT
87627 ATTTAGTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 14
0.67 0.13 0.20
Matches are distributed among these distances:
22 18 0.39
23 6 0.13
24 2 0.04
25 2 0.04
26 2 0.04
27 2 0.04
28 6 0.13
29 8 0.17
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (22 bp):
TTTAATTATTTTGAATGTTTTG
Found at i:87616 original size:51 final size:51
Alignment explanation
Indices: 87540--87651 Score: 208
Period size: 51 Copynumber: 2.2 Consensus size: 51
87530 TAAATTGTGT
87540 TATTTTAATTATTTTGAATGTTTTGTTTATTTATTTA-TTAGTATTATATTA
1 TATTTTAATTATTTTGAATGTTTTGTTTATTTATTTATTTAGTATTAT-TTA
87591 TATTTTAATTATTTTGAATGTTTTGTTTATTTATTTATTTAGTATTATTTA
1 TATTTTAATTATTTTGAATGTTTTGTTTATTTATTTATTTAGTATTATTTA
87642 TATTTTAATT
1 TATTTTAATT
87652 TGTATACTAT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 50 0.83
52 10 0.17
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (51 bp):
TATTTTAATTATTTTGAATGTTTTGTTTATTTATTTATTTAGTATTATTTA
Found at i:92480 original size:18 final size:18
Alignment explanation
Indices: 92440--92480 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
92430 TCCATTTATT
*
92440 ATTGTTTTTATCTAATAA
1 ATTGATTTTATCTAATAA
92458 A-TGATTTTATCTGAA-AA
1 ATTGATTTTATCT-AATAA
92475 ATTGAT
1 ATTGAT
92481 GGTCTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (18 bp):
ATTGATTTTATCTAATAA
Found at i:93775 original size:16 final size:17
Alignment explanation
Indices: 93740--93780 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
93730 TATTCATATA
*
93740 ATTTATTAGATAAATTT
1 ATTTATTTGATAAATTT
93757 A-TTATTTGAT-AATTAT
1 ATTTATTTGATAAATT-T
93773 ATTTATTT
1 ATTTATTT
93781 ATCTCGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTATTTGATAAATTT
Found at i:96770 original size:15 final size:15
Alignment explanation
Indices: 96750--96785 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
96740 TCTATTATTC
*
96750 CCCTTCAATTATTGT
1 CCCTTCAACTATTGT
*
96765 CCCTTCCACTATTGT
1 CCCTTCAACTATTGT
96780 CCCTTC
1 CCCTTC
96786 CACGATGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.39, G:0.06, T:0.42
Consensus pattern (15 bp):
CCCTTCAACTATTGT
Found at i:96786 original size:15 final size:15
Alignment explanation
Indices: 96759--96788 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96749 CCCCTTCAAT
96759 TATTGTCCCTTCCAC
1 TATTGTCCCTTCCAC
96774 TATTGTCCCTTCCAC
1 TATTGTCCCTTCCAC
96789 GATGTTGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.40, G:0.07, T:0.40
Consensus pattern (15 bp):
TATTGTCCCTTCCAC
Done.