Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001736.1 Hibiscus syriacus cultivar Beakdansim tig00003507_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: 1778036
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1716568 original size:20 final size:19
Alignment explanation
Indices: 1716554--1716600 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1716544 CGATATAACA
1716554 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1716574 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1716594 GGTAAAA
1 GGTAAAA
1716601 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1716602 original size:17 final size:19
Alignment explanation
Indices: 1716563--1716605 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1716553 AGGTAAAAAT
1716563 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
1716583 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
1716600 ATGATA
1 ATGATA
1716606 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:1718272 original size:15 final size:15
Alignment explanation
Indices: 1718254--1718291 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1718244 AAGGCTTGAA
1718254 GGGTGAATTCAATTG
1 GGGTGAATTCAATTG
1718269 GGGTGAATTCAATTG
1 GGGTGAATTCAATTG
*
1718284 GGCTGAAT
1 GGGTGAAT
1718292 ATATCCATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.34, T:0.32
Consensus pattern (15 bp):
GGGTGAATTCAATTG
Found at i:1718861 original size:21 final size:21
Alignment explanation
Indices: 1718837--1718880 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1718827 AAGACAATCA
1718837 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
1718858 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1718879 AG
1 AG
1718881 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1718975 original size:32 final size:33
Alignment explanation
Indices: 1718914--1718978 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1718904 AAATAGATGG
*
1718914 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1718947 AGTGGTGAAAGAAGTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1718979 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1720793 original size:19 final size:19
Alignment explanation
Indices: 1720769--1720817 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1720759 AATGTAGGGT
1720769 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1720788 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
1720807 TATTTTTGTAT
1 TAATTTTGTAT
1720818 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1721277 original size:199 final size:198
Alignment explanation
Indices: 1720936--1722103 Score: 2138
Period size: 198 Copynumber: 5.9 Consensus size: 198
1720926 CAATATGGCC
*
1720936 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AAC
1721001 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
1721066 GAATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
1721131 TGGAA
194 TGGAA
*
1721136 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCTAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1721201 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
1721266 AATATGTCTAAATAATGTGTCGACACTATTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACT-TTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAAT
1721331 GGAA
195 GGAA
*
1721335 AACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
* * *
1721400 CAAAAGTATAATGTAATATATAAGTTTTCAATCTAACCGGTACAAATATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
1721465 AATATGTCTAAATAATGTGTCGACACGTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
1721530 GAA
196 GAA
*
1721533 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACGTCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1721598 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATGCCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
* *
1721663 AATATGTCTAAATAATGTGTTGACACTTTTTAGTTTGTGTCGATAGTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
1721728 GAA
196 GAA
1721731 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
*
1721796 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTGTGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
1721861 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTGGTGTCGATATTTTTGGTCCAGAATGAATG
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
1721926 GAA
196 GAA
* *
1721929 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATTGAACC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
1721994 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
*
1722059 AATATGTCTAAATAATGTGTCGACACGTTTTAGTTTGTGTCGATA
131 AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATA
1722104 CTAATTTAAA
Statistics
Matches: 939, Mismatches: 29, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
198 591 0.63
199 288 0.31
200 60 0.06
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (198 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATG
GAA
Found at i:1723589 original size:12 final size:12
Alignment explanation
Indices: 1723572--1723630 Score: 82
Period size: 12 Copynumber: 4.9 Consensus size: 12
1723562 GGTCGCAGAA
*
1723572 GATGAAGCTGAC
1 GATGAAGATGAC
1723584 GATGAAGATGAC
1 GATGAAGATGAC
*
1723596 GATGATGATGAC
1 GATGAAGATGAC
*
1723608 GATGAAGCTGAC
1 GATGAAGATGAC
*
1723620 GTTGAAGATGA
1 GATGAAGATGA
1723631 TGACGATGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.36, C:0.10, G:0.34, T:0.20
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1723593 original size:6 final size:6
Alignment explanation
Indices: 1723569--1723660 Score: 58
Period size: 6 Copynumber: 15.3 Consensus size: 6
1723559 AGCGGTCGCA
* * * * * *
1723569 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* * * * * * * *
1723617 GACGTT GAAGAT GATGAC GATGAT GATGAT TATGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1723661 TGATCCAAAC
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.37, C:0.08, G:0.33, T:0.23
Consensus pattern (6 bp):
GAAGAT
Found at i:1723604 original size:3 final size:3
Alignment explanation
Indices: 1723584--1723664 Score: 63
Period size: 3 Copynumber: 27.0 Consensus size: 3
1723574 TGAAGCTGAC
* * * * * * * *
1723584 GAT GAA GAT GAC GAT GAT GAT GAC GAT GAA GCT GAC GTT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * *
1723632 GAC GAT GAT GAT GAT TAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1723665 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 22, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.32, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:1723619 original size:36 final size:36
Alignment explanation
Indices: 1723572--1723642 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
1723562 GGTCGCAGAA
*
1723572 GATGAAGCTGACGATGAAGATGACGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGAC
* *
1723608 GATGAAGCTGACGTTGAAGATGATGACGATGATGA
1 GATGAAGCTGACGATGAAGATGACGACGATGATGA
1723643 TGATTATGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.34, T:0.21
Consensus pattern (36 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGAC
Found at i:1723641 original size:12 final size:12
Alignment explanation
Indices: 1723580--1723664 Score: 80
Period size: 12 Copynumber: 7.1 Consensus size: 12
1723570 AAGATGAAGC
*
1723580 TGACGATGAAGA
1 TGACGATGATGA
1723592 TGACGATGATGA
1 TGACGATGATGA
* *
1723604 TGACGATGAAGC
1 TGACGATGATGA
* *
1723616 TGACGTTGAAGA
1 TGACGATGATGA
* *
1723628 TGATGACGATGA
1 TGACGATGATGA
* *
1723640 TGATGATTATGA
1 TGACGATGATGA
*
1723652 TGAAGATGATGA
1 TGACGATGATGA
1723664 T
1 T
1723665 CCAAACAAGT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 60 1.00
ACGTcount: A:0.35, C:0.07, G:0.32, T:0.26
Consensus pattern (12 bp):
TGACGATGATGA
Found at i:1727972 original size:25 final size:25
Alignment explanation
Indices: 1727944--1728008 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
1727934 TTATCATTAA
1727944 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
1727969 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
1727994 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
1728009 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:1728383 original size:23 final size:23
Alignment explanation
Indices: 1728352--1728424 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1728342 ATAGGTAAAA
*
1728352 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1728375 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1728398 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1728421 ATAT
1 ATAT
1728425 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1728449 original size:46 final size:45
Alignment explanation
Indices: 1728352--1728449 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
1728342 ATAGGTAAAA
* * *
1728352 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTT
* *
1728398 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTT
*
1728444 TTATAA
1 ATATAA
1728450 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTT
Found at i:1728870 original size:23 final size:23
Alignment explanation
Indices: 1728839--1728911 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1728829 ATAGGTAAAA
*
1728839 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1728862 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1728885 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1728908 ATAT
1 ATAT
1728912 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1728936 original size:46 final size:45
Alignment explanation
Indices: 1728839--1728936 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
1728829 ATAGGTAAAA
* * *
1728839 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATAT-ATGTAATAGCTATCCTTT
* *
1728885 ATATAATGTAATAGGTAGTGCTTATAT-TGTAAAGTATCTATCCTTT
1 ATATAATGTAATAGGTAGCGCTTATATATGT-AA-TAGCTATCCTTT
*
1728931 TTATAA
1 ATATAA
1728937 AAGTGTCCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 3 0.07
45 2 0.05
46 39 0.89
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (45 bp):
ATATAATGTAATAGGTAGCGCTTATATATGTAATAGCTATCCTTT
Found at i:1729359 original size:23 final size:23
Alignment explanation
Indices: 1729328--1729400 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
1729318 ATAGGTAAAA
* *
1729328 ATATGATGTAATTGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1729351 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1729374 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1729397 ATAT
1 ATAT
1729401 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1729391 original size:489 final size:489
Alignment explanation
Indices: 1728008--1729566 Score: 3018
Period size: 487 Copynumber: 3.2 Consensus size: 489
1727998 AGGTATATAC
1728008 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1728073 GTTACGGTATATATTATTATTAAATT-AAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
1728137 TTTGGTTAATGTTGTTAAATTTAAATTCTAAATATTA-TTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATGTTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
1728201 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
*
1728266 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACA
261 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
1728331 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
326 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
1728396 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
391 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
1728461 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
1728495 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1728560 GTTACGGTATATATTATTATTAAATTAAAAACAATAAAC--ATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
1728623 TTTGGTTAATGTTGTTAAATTTAAATTCAAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATGTTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
1728688 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
1728753 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
261 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
1728818 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
326 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
1728883 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
391 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
1728948 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
*
1728982 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTATAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1729047 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
1729112 TTTGGTTAATGTTGTTAAATTGAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATGTTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
1729177 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTTGAAAACATGAAACACTGTTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
1729242 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
261 AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
*
1729307 CTTTCAATATAATAGGTAAAAATATGATGTAATTGGTAGCGCTTATATAATGTAATAGGTATCGT
326 CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
*
1729372 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTCTCCATA
391 TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
1729437 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
1729471 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
1729536 GTTACGATATATATTATTATTAAATTAAAAA
66 GTTACGGTATATATTATTATTAAATTAAAAA
1729567 TTCTAAATAT
Statistics
Matches: 1058, Mismatches: 10, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
486 60 0.06
487 514 0.49
488 12 0.01
489 472 0.45
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (489 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
TTTGGTTAATGTTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTTAAAA
AATTGAAACATAAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACA
CTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGT
TTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATA
CTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:1729790 original size:23 final size:23
Alignment explanation
Indices: 1729759--1729831 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
1729749 ATAGGTAAAA
*
1729759 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1729782 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
1729805 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1729828 ATAT
1 ATAT
1729832 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1729936 original size:431 final size:431
Alignment explanation
Indices: 1729126--1730182 Score: 1976
Period size: 431 Copynumber: 2.5 Consensus size: 431
1729116 GTTAATGTTG
* *
1729126 TTAAATT-GAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
* *
1729190 ATGAAATTATTAAATTAATATTGTAGGTTGAAAACATGAAACACTGTT--AAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
* *
1729253 AAATTACATAACTTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTCAATATA
131 AAATTACATAAC-TTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATA
* *
1729318 ATAGGTAAAAATATGATGTAATTGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGT
195 ATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGT
1729383 AATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTCTCCATACTTTTTTCACT
260 AATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTCTCCATACTTTTTTCACT
1729448 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
325 GTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAG
1729513 GCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
390 GCGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
1729555 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
* *
1729620 ATGAAATTATTAAATTAATATTGTCGGTGGAAAACATAAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
1729685 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
1729750 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTA
196 TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTA
*
1729815 ATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTG
261 ATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTCTCCATACTTTTTTCACTG
1729880 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
326 TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
1729945 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
391 CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
1729986 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1 TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
1730051 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
66 ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
*
1730116 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTTAATATAA
131 AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
1730181 TA
196 TA
1730183 TAATGTAATA
Statistics
Matches: 611, Mismatches: 14, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
429 7 0.01
430 99 0.16
431 478 0.78
432 27 0.04
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (431 bp):
TTAAATTAAAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAA
ATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT
AAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAA
TAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTA
ATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTCTCCATACTTTTTTCACTG
TGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGG
CGTCTAATGATTTATTTTTTACGTTACGATATATATTATTA
Found at i:1735082 original size:23 final size:23
Alignment explanation
Indices: 1735056--1735099 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1735046 AATGCATTGA
*
1735056 CAAACGTTAAACGAACATGTTCG
1 CAAACGTTAAACAAACATGTTCG
* *
1735079 CAAATGTTAAGCAAACATGTT
1 CAAACGTTAAACAAACATGTT
1735100 TGCGAATGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (23 bp):
CAAACGTTAAACAAACATGTTCG
Found at i:1735107 original size:23 final size:23
Alignment explanation
Indices: 1735063--1735116 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1735053 TGACAAACGT
* *
1735063 TAAACGAACATGTTCGCAAATGT
1 TAAACAAACATGTTCGCAAATGC
* * *
1735086 TAAGCAAACATGTTTGCGAATGC
1 TAAACAAACATGTTCGCAAATGC
1735109 TAAACAAA
1 TAAACAAA
1735117 TCAAACACGA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (23 bp):
TAAACAAACATGTTCGCAAATGC
Found at i:1735553 original size:3 final size:3
Alignment explanation
Indices: 1735545--1735635 Score: 182
Period size: 3 Copynumber: 30.3 Consensus size: 3
1735535 TATACTAATT
1735545 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1735593 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1735636 ATATCAAATA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1736077 original size:153 final size:150
Alignment explanation
Indices: 1735898--1736179 Score: 415
Period size: 153 Copynumber: 1.9 Consensus size: 150
1735888 GTGGTTTAAA
* *
1735898 TTTGGTAAAAAAAACGAACTTAAAATAAATGACAAATTGAATG-AATAAGGAGATTATGAAAAAA
1 TTTGGTAAAAAAAACGAACTTAAAATAAACGACAAATTG-AGGAAATAAGGAGATTATGAAAAAA
* * * *
1735962 TGAATGACTAAATTGAAAAATGAAAAAAGTTT-TTATCAAAAAGAGGAATTGAAAGTACACATGT
65 TGAAGGACTAAATTAAAAAAT--AAAAA-TTTGTTACCAAAAAGAGGAATTGAAAGTAAACATGT
1736026 ATTCCACTATGTTTTTTACTCAAG
127 ATTCCACTATGTTTTTTACTCAAG
* * * *
1736050 TTTGGTAAAAAAAATTGAACTTGAAATAAACGACGAATTGAGGAAATAAGGAGATTATGAAAAAT
1 TTTGGTAAAAAAAA-CGAACTTAAAATAAACGACAAATTGAGGAAATAAGGAGATTATGAAAAAA
1736115 TGAAGGACTAAATTAAAAAATAAAAATTTGTTACCAAAAAGAGGAATTGAAAGTAAACATGTATT
65 TGAAGGACTAAATTAAAAAATAAAAATTTGTTACCAAAAAGAGGAATTGAAAGTAAACATGTATT
1736180 ATACTATGAT
Statistics
Matches: 117, Mismatches: 10, Indels: 7
0.87 0.07 0.05
Matches are distributed among these distances:
150 3 0.03
151 38 0.32
152 16 0.14
153 60 0.51
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (150 bp):
TTTGGTAAAAAAAACGAACTTAAAATAAACGACAAATTGAGGAAATAAGGAGATTATGAAAAAAT
GAAGGACTAAATTAAAAAATAAAAATTTGTTACCAAAAAGAGGAATTGAAAGTAAACATGTATTC
CACTATGTTTTTTACTCAAG
Found at i:1741301 original size:3 final size:3
Alignment explanation
Indices: 1741293--1741342 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
1741283 GGCCCGTTTG
1741293 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
1741338 TAA TA
1 TAA TA
1741343 GTAAATGGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1741880 original size:115 final size:110
Alignment explanation
Indices: 1741694--1742140 Score: 535
Period size: 115 Copynumber: 4.0 Consensus size: 110
1741684 ATAGAATTAT
** * *
1741694 GCAAAAGGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTTCTTCTTCAGATGAGTTCTTCTAA
1 GCAAAA-GGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
* *
1741757 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTA
65 TTATGAACTTTATCTGGAAAAGTTGATCCATCAATTGATGGATTTA
1741803 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACAAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTC-TTCTTCTTCAGATG---AGTTCTT
* * * *
1741868 CTCATTATGAACTTTATCTGGCAATGTTGATCCATCAAATGATGAATTTA
61 CTCATTATGAACTTTATCTGGAAAAGTTGATCCATCAATTGATGGATTTA
*
1741918 GCAAAAGGTTGAACAAATTCTTCTCATTAT-AAAT-TTCTTCTTCTTCAGATGACGAGTTCTTCT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGAT---GAGTTCTTCT
* * * * *
1741981 CATTATGAACTCTACCTGTCAATA-CTGATCCATCAATTGATGGATTTGA
63 CATTATGAACTTTATCTG-GAAAAGTTGATCCATCAATTGATGGATTT-A
* *
1742030 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTT-CTTCTTCAGATGAGTTCTTCTC
** * * *
1742095 ATTATGAACTCGAACTGGTAATGTTGATCCATCAATTGATGGATTT
64 ATTATGAACTTTATCTGGAAAAGTTGATCCATCAATTGATGGATTT
1742141 GAATCTTTGC
Statistics
Matches: 292, Mismatches: 29, Indels: 30
0.83 0.08 0.09
Matches are distributed among these distances:
108 24 0.08
109 6 0.02
111 62 0.21
112 50 0.17
113 50 0.17
114 4 0.01
115 85 0.29
116 11 0.04
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (110 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTATCTGGAAAAGTTGATCCATCAATTGATGGATTTA
Found at i:1743109 original size:93 final size:93
Alignment explanation
Indices: 1742928--1743215 Score: 488
Period size: 94 Copynumber: 3.1 Consensus size: 93
1742918 CTTAATTCTA
* * *
1742928 CTATGAGTACATTCATCTTTCAAATCCAATGATTGGTTCTTTGAGGTTCATATCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTT-TTTGAGGTTCATATCAAACCAGATCA
1742993 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
* *
1743022 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTT-AGGGTTTATATTAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGA-GGTTCATATCAAACCAGATCA
1743086 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
1743115 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGAGGTTCATATCAAACCAGATCA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGG-TTTTTGAGGTTCATATCAAACCAGATCA
*
1743180 GATAACTCAAAGAACACTTCTAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
1743209 CTATGAG
1 CTATGAG
1743216 TCTACGGCAC
Statistics
Matches: 183, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
92 1 0.01
93 87 0.48
94 94 0.51
95 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (93 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGAGGTTCATATCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:1748407 original size:3 final size:3
Alignment explanation
Indices: 1748399--1748448 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
1748389 GGCCCGTTTG
1748399 TAA TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1748444 TAA TA
1 TAA TA
1748449 GTAAATGGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1748981 original size:115 final size:111
Alignment explanation
Indices: 1748797--1749131 Score: 424
Period size: 115 Copynumber: 3.0 Consensus size: 111
1748787 ACAGAATTAT
** * *
1748797 GCAAAAGGGTTGAACAAGCTCTTCTCATTGTGAA--CTTC-TTCTTCTTCAGATGAGTTCTTCTA
1 GCAAAA-GGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
* * * *
1748859 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTA
65 ATTATGAACTTTATCTGGAAATGTTGATCCATCAAATGATGGATTTA
*
1748906 GCAAAAGGTTGAACAAATTATTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACAAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATG---AGTTCTT
* *
1748971 CTCATTATGAACTTTATCTGGCAATGTTGATCCATCAAATGATGAATTTA
62 CTCATTATGAACTTTATCTGGAAATGTTGATCCATCAAATGATGGATTTA
* * *
1749021 GCAAAAGGTTGAACAAATTCTTCTCACTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
** * * *
1749086 ATTATGAACTCGAACTGGTAATGTTGATCCATCAATTGATGGATTT
65 ATTATGAACTTTATCTGGAAATGTTGATCCATCAAATGATGGATTT
1749132 GAATCTTTGC
Statistics
Matches: 197, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
108 23 0.12
109 6 0.03
111 4 0.02
112 64 0.32
115 100 0.51
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (111 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTATCTGGAAATGTTGATCCATCAAATGATGGATTTA
Found at i:1750078 original size:93 final size:93
Alignment explanation
Indices: 1749909--1750195 Score: 497
Period size: 94 Copynumber: 3.1 Consensus size: 93
1749899 TTATTTCTAA
* *
1749909 TATGAGTACATTCATCTTTCAAA-TCAAATGATTGGTTCTTTGAGGTTCATATCAAACCAGATCA
1 TATGAGCACATTCATCTTCCAAATTC-AATGATTGGTT-TTTGAGGTTCATATCAAACCAGATCA
1749973 GATAACTCAAAGAACACTTCCAGAAGATGC
64 GATAACTCAAAGAACACTTCCAGAAGATGC
*
1750003 TATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTT-AGGGTTCATATTAAACCAGATCAG
1 TATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGA-GGTTCATATCAAACCAGATCAG
1750067 ATAACTCAAAGAACACTTCCAGAAGATGC
65 ATAACTCAAAGAACACTTCCAGAAGATGC
1750096 TATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTTGAGGTTCATATCAAACCAGATCAG
1 TATGAGCACATTCATCTTCCAAATTCAATGATTGG-TTTTTGAGGTTCATATCAAACCAGATCAG
1750161 ATAACTCAAAGAACACTTCCAGAAGATGC
65 ATAACTCAAAGAACACTTCCAGAAGATGC
1750190 TATGAG
1 TATGAG
1750196 TCTACGGAAC
Statistics
Matches: 185, Mismatches: 4, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
92 1 0.01
93 88 0.48
94 93 0.50
95 3 0.02
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (93 bp):
TATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTTGAGGTTCATATCAAACCAGATCAGA
TAACTCAAAGAACACTTCCAGAAGATGC
Found at i:1751160 original size:7 final size:7
Alignment explanation
Indices: 1751148--1751180 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1751138 CCTTGACCCC
1751148 CTTTTTT
1 CTTTTTT
1751155 CTTTTTT
1 CTTTTTT
1751162 CTTTTTT
1 CTTTTTT
1751169 -TCTTTTT
1 CT-TTTTT
1751176 CTTTT
1 CTTTT
1751181 CTTTCTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.04
7 22 0.92
8 1 0.04
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
CTTTTTT
Found at i:1751169 original size:15 final size:15
Alignment explanation
Indices: 1751149--1751187 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
1751139 CTTGACCCCC
1751149 TTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
1751164 TTTTTTC-TTTTTCT
1 TTTTTTCTTTTTTCT
1751178 TTTCTTTCTT
1 TTT-TTTCTT
1751188 CAAGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 11 0.50
16 1 0.05
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTCTTTTTTCT
Found at i:1762333 original size:23 final size:24
Alignment explanation
Indices: 1762282--1762334 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1762272 AAGTATGAGA
*
1762282 AGAAA-AAAAATTTATATATATTT
1 AGAAATAAAAATTTATATATAGTT
*
1762305 ATAAATAAAATATTTAT-T-TAGTT
1 AGAAATAAAA-ATTTATATATAGTT
1762328 AGAAATA
1 AGAAATA
1762335 TCAGAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 14 0.56
24 5 0.20
25 6 0.24
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
AGAAATAAAAATTTATATATAGTT
Found at i:1764031 original size:3 final size:3
Alignment explanation
Indices: 1764018--1764093 Score: 82
Period size: 3 Copynumber: 25.3 Consensus size: 3
1764008 ATTTGTATCT
* * * * *
1764018 ATA ATA A-A ATA ATA ATA ATA ATA TTA TTA TTA TTA ATA CTA ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
1764066 ATA ATA ATA ATC ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1764094 AAAAAAACTA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 60 0.92
4 3 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:1764357 original size:2 final size:2
Alignment explanation
Indices: 1764350--1764396 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1764340 GTGATTGATG
*
1764350 AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT CT 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
1764391 AT AT AT
1 AT AT AT
1764397 TTGATAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1764872 original size:19 final size:19
Alignment explanation
Indices: 1764848--1764885 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1764838 TAAGGCGGGT
1764848 AAAATTAAATTTGAATTAA
1 AAAATTAAATTTGAATTAA
*
1764867 AAAATTTAATTTGAATTAA
1 AAAATTAAATTTGAATTAA
1764886 TTTCGAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATTAAATTTGAATTAA
Found at i:1769681 original size:16 final size:17
Alignment explanation
Indices: 1769593--1769687 Score: 65
Period size: 16 Copynumber: 5.6 Consensus size: 17
1769583 ATGAAAAAAT
* *
1769593 ATATTATAATA-AATAA
1 ATATAATAATATATTAA
*
1769609 ATAAAATAATATTCATTAA
1 ATATAATAATA-T-ATTAA
*
1769628 CA-ATATTAAT-TATTAA
1 -ATATAATAATATATTAA
1769644 ATATAATAA-ATAATTAAA
1 ATATAATAATAT-ATT-AA
1769662 ATATAATAATATA-TAA
1 ATATAATAATATATTAA
*
1769678 ATATAGTAAT
1 ATATAATAAT
1769688 TAAAATAGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
15 1 0.02
16 32 0.51
17 5 0.08
18 12 0.19
19 12 0.19
20 1 0.02
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (17 bp):
ATATAATAATATATTAA
Found at i:1772559 original size:45 final size:45
Alignment explanation
Indices: 1772466--1772589 Score: 205
Period size: 45 Copynumber: 2.8 Consensus size: 45
1772456 GTAAGTATTC
*
1772466 AAATAAGCTTACGAGCTTATGGGAT-AATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
* * *
1772510 AAATAAGCTTTCGAGCTTATAGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
1772555 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1772590 AGATTTTATA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
44 22 0.31
45 50 0.69
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTA
Done.