Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005349.1 Hibiscus syriacus cultivar Beakdansim tig00012136_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: 1796274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 8 of 8
Found at i:1670247 original size:839 final size:839
Alignment explanation
Indices: 1668629--1670310 Score: 3310
Period size: 839 Copynumber: 2.0 Consensus size: 839
1668619 GAAAAAAACA
1668629 TGTTTAAACAAGATGTTGAAAGTAGAAAATACTACAGTGGTAGATAACAACTTTCATTTGTTTAT
1 TGTTTAAACAAGATGTTGAAAGTAGAAAATACTACAGTGGTAGATAACAACTTTCATTTGTTTAT
1668694 TTATCATGCCTCATCAATCCTTGAATGTTGAGTGTGTACTTGGGCCAGGATTTTCATCTTTATTT
66 TTATCATGCCTCATCAATCCTTGAATGTTGAGTGTGTACTTGGGCCAGGATTTTCATCTTTATTT
1668759 GCCCCATTTCTTGATCATTTCTTGTGTCAAGACTCCTTTGTCAACAAGCATCTCTATTTCTTTTA
131 GCCCCATTTCTTGATCATTTCTTGTGTCAAGACTCCTTTGTCAACAAGCATCTCTATTTCTTTTA
1668824 ACAATAGCCTACAATTGCCCGTGGAATGCCCTAATACCCCTAAGTGGAAATCACAAACACTACCT
196 ACAATAGCCTACAATTGCCCGTGGAATGCCCTAATACCCCTAAGTGGAAATCACAAACACTACCT
1668889 TGATCATAACTATGAGCAGAAGGGTTTGGTGGCATTTTCATTAGTCTTGGTGTGATGTATTGACC
261 TGATCATAACTATGAGCAGAAGGGTTTGGTGGCATTTTCATTAGTCTTGGTGTGATGTATTGACC
1668954 TTTAATCAAATGAGGGTACAAGTCTGAAATAGAAGTTTGGAACATCTCCAAAGTATTTCTTGATC
326 TTTAATCAAATGAGGGTACAAGTCTGAAATAGAAGTTTGGAACATCTCCAAAGTATTTCTTGATC
*
1669019 GTGTGACTTTCTTTGGTCGATCCGAACAAATACTTGCTCTTTTTCTTTTGCAGTTGCAAGGACTC
391 GTGTGACTTTCTTTGGTCGATCCAAACAAATACTTGCTCTTTTTCTTTTGCAGTTGCAAGGACTC
1669084 TGGATGCAACATTCATTCACATCATCAGCTTTCACTTTCTGATCCGTCGGGCCCTTGCATGTGAC
456 TGGATGCAACATTCATTCACATCATCAGCTTTCACTTTCTGATCCGTCGGGCCCTTGCATGTGAC
1669149 TTTTGAGTTTCCTTTGTTGATCACATTTTCAATTAATTCTCCATTTGTCATAAGATTTTCAAATT
521 TTTTGAGTTTCCTTTGTTGATCACATTTTCAATTAATTCTCCATTTGTCATAAGATTTTCAAATT
1669214 TCTTCGTCGGATTTGCTAGCATTAACTCGAAGAAAGGAGCAGGAAGGGAATCACGAAACATATGT
586 TCTTCGTCGGATTTGCTAGCATTAACTCGAAGAAAGGAGCAGGAAGGGAATCACGAAACATATGT
1669279 GATATCTCTTCTTCTAACATGGGAGGTTAAACTTGTGCTGCAACTCCTCTCCATCTTAAGGCATA
651 GATATCTCTTCTTCTAACATGGGAGGTTAAACTTGTGCTGCAACTCCTCTCCATCTTAAGGCATA
1669344 CTTCTGAAACCCTTCATTGGCTTTCATCTTGACTCCTTGAAGATCCATACGTGTTGGAGCTAAGC
716 CTTCTGAAACCCTTCATTGGCTTTCATCTTGACTCCTTGAAGATCCATACGTGTTGGAGCTAAGC
1669409 CTTTAACATACCGATATTGTCCTAAAAATGCATCAGCTAGATCAACCCATCTCTTGATC
781 CTTTAACATACCGATATTGTCCTAAAAATGCATCAGCTAGATCAACCCATCTCTTGATC
*
1669468 TGTTTAAACAAGATGTTGAAAGTAGAAAATACTACAGTGGTAGATAACAACTTTCTTTTGTTTAT
1 TGTTTAAACAAGATGTTGAAAGTAGAAAATACTACAGTGGTAGATAACAACTTTCATTTGTTTAT
*
1669533 TTATCATGCCTCATCATTCCTTGAATGTTGAGTGTGTACTTGGGCCAGGATTTTCATCTTTATTT
66 TTATCATGCCTCATCAATCCTTGAATGTTGAGTGTGTACTTGGGCCAGGATTTTCATCTTTATTT
1669598 GCCCCATTTCTTGATCATTTCTTGTGTCAAGACTCCTTTGTCAACAAGCATCTCTATTTCTTTTA
131 GCCCCATTTCTTGATCATTTCTTGTGTCAAGACTCCTTTGTCAACAAGCATCTCTATTTCTTTTA
1669663 ACAATAGCCTACAATTGCCCGTGGAATGCCCTAATACCCCTAAGTGGAAATCACAAACACTACCT
196 ACAATAGCCTACAATTGCCCGTGGAATGCCCTAATACCCCTAAGTGGAAATCACAAACACTACCT
*
1669728 TGATCATAACTATGAGCAGAAGTGTTTGGTGGCATTTTCATTAGTCTTGGTGTGATGTATTGACC
261 TGATCATAACTATGAGCAGAAGGGTTTGGTGGCATTTTCATTAGTCTTGGTGTGATGTATTGACC
1669793 TTTAATCAAATGAGGGTACAAGTCTGAAATAGAAGTTTGGAACATCTCCAAAGTATTTCTTGATC
326 TTTAATCAAATGAGGGTACAAGTCTGAAATAGAAGTTTGGAACATCTCCAAAGTATTTCTTGATC
*
1669858 GTGTGACTTTCTTTGGTCGATCCAAACAAATACTTGCTCTTTTTCTTTTGCAGTTGCGAGGACTC
391 GTGTGACTTTCTTTGGTCGATCCAAACAAATACTTGCTCTTTTTCTTTTGCAGTTGCAAGGACTC
1669923 TGGATGCAACATTCATTCACATCATCAGCTTTCACTTTCTGATCCGTCGGGCCCTTGCATGTGAC
456 TGGATGCAACATTCATTCACATCATCAGCTTTCACTTTCTGATCCGTCGGGCCCTTGCATGTGAC
1669988 TTTTGAGTTTCCTTTGTTGATCACATTTTCAATTAATTCTCCATTTGTCATAAGATTTTCAAATT
521 TTTTGAGTTTCCTTTGTTGATCACATTTTCAATTAATTCTCCATTTGTCATAAGATTTTCAAATT
1670053 TCTTCGTCGGATTTGCTAGCATTAACTCGAAGAAAGGAGCAGGAAGGGAATCACGAAACATATGT
586 TCTTCGTCGGATTTGCTAGCATTAACTCGAAGAAAGGAGCAGGAAGGGAATCACGAAACATATGT
1670118 GATATCTCTTCTTCTAACATGGGAGGTTAAACTTGTGCTGCAACTCCTCTCCATCTTAAGGCATA
651 GATATCTCTTCTTCTAACATGGGAGGTTAAACTTGTGCTGCAACTCCTCTCCATCTTAAGGCATA
*
1670183 CTTTTGAAACCCTTCATTGGCTTTCATCTTGACTCCTTGAAGATCCATACGTGTTGGAGCTAAGC
716 CTTCTGAAACCCTTCATTGGCTTTCATCTTGACTCCTTGAAGATCCATACGTGTTGGAGCTAAGC
1670248 CTTTAACATACCGATATTGTCCTAAAAATGCATCAGCTAGATCAACCCATCTCTTGATC
781 CTTTAACATACCGATATTGTCCTAAAAATGCATCAGCTAGATCAACCCATCTCTTGATC
1670307 TGTT
1 TGTT
1670311 CTTGGGTTCA
Statistics
Matches: 837, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
839 837 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (839 bp):
TGTTTAAACAAGATGTTGAAAGTAGAAAATACTACAGTGGTAGATAACAACTTTCATTTGTTTAT
TTATCATGCCTCATCAATCCTTGAATGTTGAGTGTGTACTTGGGCCAGGATTTTCATCTTTATTT
GCCCCATTTCTTGATCATTTCTTGTGTCAAGACTCCTTTGTCAACAAGCATCTCTATTTCTTTTA
ACAATAGCCTACAATTGCCCGTGGAATGCCCTAATACCCCTAAGTGGAAATCACAAACACTACCT
TGATCATAACTATGAGCAGAAGGGTTTGGTGGCATTTTCATTAGTCTTGGTGTGATGTATTGACC
TTTAATCAAATGAGGGTACAAGTCTGAAATAGAAGTTTGGAACATCTCCAAAGTATTTCTTGATC
GTGTGACTTTCTTTGGTCGATCCAAACAAATACTTGCTCTTTTTCTTTTGCAGTTGCAAGGACTC
TGGATGCAACATTCATTCACATCATCAGCTTTCACTTTCTGATCCGTCGGGCCCTTGCATGTGAC
TTTTGAGTTTCCTTTGTTGATCACATTTTCAATTAATTCTCCATTTGTCATAAGATTTTCAAATT
TCTTCGTCGGATTTGCTAGCATTAACTCGAAGAAAGGAGCAGGAAGGGAATCACGAAACATATGT
GATATCTCTTCTTCTAACATGGGAGGTTAAACTTGTGCTGCAACTCCTCTCCATCTTAAGGCATA
CTTCTGAAACCCTTCATTGGCTTTCATCTTGACTCCTTGAAGATCCATACGTGTTGGAGCTAAGC
CTTTAACATACCGATATTGTCCTAAAAATGCATCAGCTAGATCAACCCATCTCTTGATC
Found at i:1675512 original size:3 final size:3
Alignment explanation
Indices: 1675504--1675596 Score: 118
Period size: 3 Copynumber: 31.0 Consensus size: 3
1675494 ATTTTTTATT
* * *
1675504 TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TGTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
1675550 TAT TAA TAA -AGA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1675594 TAA
1 TAA
1675597 AAGCAAAATG
Statistics
Matches: 80, Mismatches: 6, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
2 3 0.04
3 74 0.93
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1697264 original size:17 final size:18
Alignment explanation
Indices: 1697242--1697275 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1697232 TATACCTCAA
1697242 ATTTATT-TTTTAATTAG
1 ATTTATTATTTTAATTAG
*
1697259 ATTTATTATTTTTATTA
1 ATTTATTATTTTAATTA
1697276 AAATGACAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
ATTTATTATTTTAATTAG
Found at i:1699378 original size:77 final size:78
Alignment explanation
Indices: 1699242--1699393 Score: 175
Period size: 77 Copynumber: 2.0 Consensus size: 78
1699232 TTTCAAACTA
** *
1699242 AAAATCTTATTTAATTAATTCAAATTAAATATACATTAAAGACTTATAATTTGATTTACAATC-T
1 AAAATCTTATTTAATTAATTCAAATTAAATATACATTAAAGACTTATAATTAAAATTACAATCTT
*
1699306 TTAATGTTTATTT
66 TTAAGGTTTATTT
* ** * * *
1699319 AAAATCTTATTTAATT-ATTCTGAATTAAATAT-CAATTAATTAGTTGTAATTAAAATTACATTC
1 AAAATCTTATTTAATTAATTC-AAATTAAATATAC-ATTAAAGACTTATAATTAAAATTACAATC
1699382 TTTTAAGGTTTA
64 TTTTAAGGTTTA
1699394 CTTACGATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
76 5 0.08
77 47 0.76
78 10 0.16
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (78 bp):
AAAATCTTATTTAATTAATTCAAATTAAATATACATTAAAGACTTATAATTAAAATTACAATCTT
TTAAGGTTTATTT
Found at i:1705001 original size:27 final size:26
Alignment explanation
Indices: 1704964--1705016 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 26
1704954 AAAAACCCTA
1704964 AGCCTAGACTACTCTCTAGGTATCTT
1 AGCCTAGACTACTCTCTAGGTATCTT
1704990 AGCCTAAGACTACTCTCTAGGTATCTT
1 AGCCT-AGACTACTCTCTAGGTATCTT
1705017 CTCACCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (26 bp):
AGCCTAGACTACTCTCTAGGTATCTT
Found at i:1705223 original size:2 final size:2
Alignment explanation
Indices: 1705211--1705242 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1705201 AAAAACAAAC
1705211 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1705243 CACACGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1709745 original size:2 final size:2
Alignment explanation
Indices: 1709734--1709775 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
1709724 TAAAGACGAT
1709734 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1709775 T
1 T
1709776 TGTATGCATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1711013 original size:22 final size:23
Alignment explanation
Indices: 1710977--1711021 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1710967 TCACCTACCC
*
1710977 ATTTCACCCCATCCACCCACTCT
1 ATTTCAACCCATCCACCCACTCT
*
1711000 ATTTCAACCC-TCCACTCACTCT
1 ATTTCAACCCATCCACCCACTCT
1711022 CTCTTATTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.22, C:0.49, G:0.00, T:0.29
Consensus pattern (23 bp):
ATTTCAACCCATCCACCCACTCT
Found at i:1715484 original size:48 final size:49
Alignment explanation
Indices: 1715412--1715509 Score: 189
Period size: 48 Copynumber: 2.0 Consensus size: 49
1715402 AATTTTGGGT
1715412 CTAGTGCCTTCCTTAGAGGTTACTAACCGTTTATCAATAATCTTTCGTA
1 CTAGTGCCTTCCTTAGAGGTTACTAACCGTTTATCAATAATCTTTCGTA
1715461 CTAGTGCCTT-CTTAGAGGTTACTAACCGTTTATCAATAATCTTTCGTA
1 CTAGTGCCTTCCTTAGAGGTTACTAACCGTTTATCAATAATCTTTCGTA
1715509 C
1 C
1715510 AAAATAGGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 39 0.80
49 10 0.20
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.39
Consensus pattern (49 bp):
CTAGTGCCTTCCTTAGAGGTTACTAACCGTTTATCAATAATCTTTCGTA
Found at i:1718846 original size:14 final size:14
Alignment explanation
Indices: 1718827--1718856 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1718817 CTTAAGCATA
1718827 TCATAACAAATCAT
1 TCATAACAAATCAT
1718841 TCATAACAAATCAT
1 TCATAACAAATCAT
1718855 TC
1 TC
1718857 TAGACTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (14 bp):
TCATAACAAATCAT
Found at i:1743600 original size:31 final size:32
Alignment explanation
Indices: 1743511--1743646 Score: 123
Period size: 32 Copynumber: 4.3 Consensus size: 32
1743501 TTAGGCATAG
* * * * * *
1743511 GAGCCAACCTAAGGGATTATCTTGGGTCGTGA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* ** *
1743543 GAGCCTACCCAAGAGTGTACCTTGGGG-CTAA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* *
1743574 GAGCCTACCCAAGGGAATATCATGGGGCCTTA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
* *
1743606 GATCCTACCCAAGGAAATATCTTGGGGCCTCAA
1 GAGCCTACCCAAGGGAATATCTTGGGGCCT-AA
1743639 -AGCCTACC
1 GAGCCTACC
1743647 TAAGTGTCAC
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
31 24 0.29
32 57 0.70
33 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (32 bp):
GAGCCTACCCAAGGGAATATCTTGGGGCCTAA
Found at i:1745692 original size:33 final size:33
Alignment explanation
Indices: 1745655--1745717 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
1745645 ATGGCTAGTC
*
1745655 AACGCTCGGTCAATGCCCGATCAATACCCAGTT
1 AACGCCCGGTCAATGCCCGATCAATACCCAGTT
**
1745688 AACGCCCGGTCAATTTCCGATCAATACCCA
1 AACGCCCGGTCAATGCCCGATCAATACCCA
1745718 ATCAACACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.21
Consensus pattern (33 bp):
AACGCCCGGTCAATGCCCGATCAATACCCAGTT
Found at i:1746613 original size:7 final size:8
Alignment explanation
Indices: 1746597--1746621 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1746587 ATTTAAATAA
1746597 TTTTATTT
1 TTTTATTT
1746605 TTTTATTT
1 TTTTATTT
1746613 TTTTATTT
1 TTTTATTT
1746621 T
1 T
1746622 AAAATGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:1749263 original size:77 final size:78
Alignment explanation
Indices: 1749127--1749278 Score: 184
Period size: 77 Copynumber: 2.0 Consensus size: 78
1749117 TTTCAAACTA
** *
1749127 AAAATCTTATTTAATTAATTGAAATTAAATATACATTAAAGACTTATAATTTGATTTACAATC-T
1 AAAATCTTATTTAATTAATTGAAATTAAATATACATTAAAGACTTATAATTAAAATTACAATCTT
*
1749191 TTAATGTTTATTT
66 TTAAGGTTTATTT
* ** * *
1749204 AAAATCTTATTTAATTATTCTG-AATTAAATAT-CAATTAATTACTTGTAATTAAAATTACATTC
1 AAAATCTTATTTAATTAAT-TGAAATTAAATATAC-ATTAAAGACTTATAATTAAAATTACAATC
1749267 TTTTAAGGTTTA
64 TTTTAAGGTTTA
1749279 CTTACGATAT
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.02
77 50 0.79
78 12 0.19
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (78 bp):
AAAATCTTATTTAATTAATTGAAATTAAATATACATTAAAGACTTATAATTAAAATTACAATCTT
TTAAGGTTTATTT
Found at i:1759854 original size:14 final size:14
Alignment explanation
Indices: 1759836--1759885 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 14
1759826 TTACTTTTCC
*
1759836 TTTTATTATCTTTC
1 TTTTATTATCTTTA
*
1759850 TTTTATT-CCTTTA
1 TTTTATTATCTTTA
*
1759863 TTTTTTTAT-TTTA
1 TTTTATTATCTTTA
1759876 TTTT-TTATCT
1 TTTTATTATCT
1759886 CCTTCTATCC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 4 0.13
13 19 0.63
14 7 0.23
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTATCTTTA
Found at i:1790888 original size:32 final size:32
Alignment explanation
Indices: 1790850--1790916 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1790840 CTATTTATCA
1790850 AAAGTAGGACAACCAAAAATCCATAAGTGATC
1 AAAGTAGGACAACCAAAAATCCATAAGTGATC
1790882 AAAGTAGGACAACCAAAAATCCATAAGTGATC
1 AAAGTAGGACAACCAAAAATCCATAAGTGATC
1790914 AAA
1 AAA
1790917 AGTAACATCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (32 bp):
AAAGTAGGACAACCAAAAATCCATAAGTGATC
Found at i:1793132 original size:30 final size:29
Alignment explanation
Indices: 1793054--1793133 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
1793044 AAGAGTGTAC
*
1793054 CTTGGGG-CTAAGAGCCTACCCAAGGGAAT
1 CTTGGGGCCTAA-AGCCTACCCAAGGAAAT
* * *
1793083 CATGGGGCCTTAGATCCTACCCAAGGAAAT
1 CTTGGGGCC-TAAAGCCTACCCAAGGAAAT
1793113 CTTGGGGCCTCAAAGCCTACC
1 CTTGGGGCCT-AAAGCCTACC
1793134 TAAGTGTCAC
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
29 7 0.17
30 32 0.78
31 2 0.05
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (29 bp):
CTTGGGGCCTAAAGCCTACCCAAGGAAAT
Found at i:1795137 original size:32 final size:32
Alignment explanation
Indices: 1795101--1795170 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
1795091 TCAATGGCTA
1795101 GTCAACGCTC-GGTCAATGCCCGATCAATACCC
1 GTCAACGC-CAGGTCAATGCCCGATCAATACCC
**
1795133 GTCAACGCCAGGTCAATTTCCGATCAATACCC
1 GTCAACGCCAGGTCAATGCCCGATCAATACCC
*
1795165 ATCAAC
1 GTCAAC
1795171 ACCTGGCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 1 0.03
32 33 0.97
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.20
Consensus pattern (32 bp):
GTCAACGCCAGGTCAATGCCCGATCAATACCC
Done.