Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006211.1 Hibiscus syriacus cultivar Beakdansim tig00014792_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: 45547
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:623 original size:43 final size:43
Alignment explanation
Indices: 575--715 Score: 194
Period size: 43 Copynumber: 3.3 Consensus size: 43
565 CCTAATTTTC
* **
575 AGGGGTTTCTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
* * * *
618 AGGGGTTTCTTGAGGACAAGTTTGAGGGACCATCATGATATGT
1 AGGGGTTCCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
*
661 AGGGGTTCCTTGATGACACA-CTTGAGGGACCAACGTGATATGT
1 AGGGGTTCCTTGATGACA-AGCTTGAGGGACCATCGTGATATGT
704 AGGGGTTCCTTG
1 AGGGGTTCCTTG
716 GTTACAACTA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 86 0.99
44 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (43 bp):
AGGGGTTCCTTGATGACAAGCTTGAGGGACCATCGTGATATGT
Found at i:973 original size:86 final size:88
Alignment explanation
Indices: 803--994 Score: 271
Period size: 86 Copynumber: 2.2 Consensus size: 88
793 AAGCATGATG
*
803 TGTAAGTCCTCCAGGCCATCCATAAGACCTTCAGTACAGGATGTTTTCAAACGAGATTTTAGAAA
1 TGTAAGTCCT-CAGGGCATCCATAAGACCTTCAGTACAGGATGTTTTCAAAC-AGATTTTAGAAA
*
868 CTAAGTCTTCGGGGCTTTCTTGAGT
64 CTAAGCCTTCGGGGCTTTCTTGAGT
* * * *
893 TGTAAGTCCTCTGGGCATCCAT-AGACCTTCAGTGCAGGATGTTTTCAAA-TGATTTTATAAACT
1 TGTAAGTCCTCAGGGCATCCATAAGACCTTCAGTACAGGATGTTTTCAAACAGATTTTAGAAACT
* *
956 AAGCCTTCGGGGGTTTCTTGATT
66 AAGCCTTCGGGGCTTTCTTGAGT
*
979 TGTAAGTCCTCCGGGC
1 TGTAAGTCCTCAGGGC
995 CATCAGTAAG
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
86 47 0.51
88 26 0.28
89 10 0.11
90 10 0.11
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (88 bp):
TGTAAGTCCTCAGGGCATCCATAAGACCTTCAGTACAGGATGTTTTCAAACAGATTTTAGAAACT
AAGCCTTCGGGGCTTTCTTGAGT
Found at i:1540 original size:132 final size:132
Alignment explanation
Indices: 894--2024 Score: 1698
Period size: 132 Copynumber: 8.7 Consensus size: 132
884 TTCTTGAGTT
*
894 GTAAGTCC-TCTGGG-CATCCAT-AGACCTTCAGTGCAGGATGTTTTCAAAT--GATTTTATAAA
1 GTAAGTCCTTC-GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
*
954 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGTATGA
65 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGA
1019 TGC
130 TGC
* *
1022 GTAAGTCC-TCGGGACATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
*
1086 TAAGCCTTC-GGGGTTTACTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCAAGCATGA
66 TAAGCCTTCGGGGGTTT-CTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGA
1150 TGC
130 TGC
* *
1153 TTAAG----TC-GGCCATCCATAAGACTTTCAGTGCA-GATGTTTTC-AATGAGA-TTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* * *
1210 TAAACCTTCGGGGGTTTCTTGATTTTTAAGTCC-CCAGGCCATCAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1274 GC
131 GC
* *
1276 GTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATG-TTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* ** *
1340 TAAGCCTTCGGGGGTTTCTTGATTGGTAAGTCCTTTGAG---TCAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
*
1402 AC
131 GC
* * *
1404 GTAAGTCCTTCGGGCCATACATAAGACTTTCAATGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1469 TAATCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTTCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1534 GC
131 GC
* * *
1536 GTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* * *
1601 TAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGCAAGTCTTTCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1666 GC
131 GC
* * *
1668 GTAAGTCCTACGGGCCTTCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1733 TAAGCCTTCTGGGGTTTCTTGATTTGTAAGTTCTCCGGG--A-CAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1795 GC
131 GC
* * * *
1797 GTAAGT-CTTCGGTCCATCTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAGAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1861 TAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCTGGGCCATCAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
*
1926 AC
131 GC
* *
1928 GTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1993 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
2025 ATTCGGAACA
Statistics
Matches: 911, Mismatches: 69, Indels: 42
0.89 0.07 0.04
Matches are distributed among these distances:
123 35 0.04
124 32 0.04
125 14 0.02
126 9 0.01
127 26 0.03
128 194 0.21
129 122 0.13
130 48 0.05
131 102 0.11
132 329 0.36
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (132 bp):
GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
GC
Found at i:1557 original size:260 final size:262
Alignment explanation
Indices: 894--2024 Score: 1660
Period size: 260 Copynumber: 4.4 Consensus size: 262
884 TTCTTGAGTT
*
894 GTAAGTCC-TCTGGG-CATCCAT-AGACCTTCAGTGCAGGATGTTTTCAAAT--GATTTTATAAA
1 GTAAGTCCTTC-GGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAA
*
954 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGTATGA
65 CTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGA
* * *
1019 TGCGTAAGTCCT-CGGGACATTCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGA
130 TGCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGA
*
1083 AACTAAGCCTTC-GGGGTTTACTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCAAGCA
195 AACTAAGCCTTCAGGGGTTT-CTTGATTTGTAAGTCCTCCGGG-C-TCAGTAAGTCTTCCGAGCA
*
1147 TGATGC
257 TGATAC
* *
1153 TTAAG----TC-GGCCATCCATAAGACTTTCAGTGCA-GATGTTTTC-AATGAGA-TTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* * *
1210 TAAACCTTCGGGGGTTTCTTGATTTTTAAGTCC-CCAGGCCATCAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1274 GCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATG-TTTCAAATGAGATTTTAGAA
131 GCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAA
* * ** *
1338 ACTAAGCCTTCGGGGGTTTCTTGATTGGTAAGTCCTTTGAG-TCAGTAAGTCTTCCGAGCATGAT
196 ACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGGCTCAGTAAGTCTTCCGAGCATGAT
1402 AC
261 AC
* * *
1404 GTAAGTCCTTCGGGCCATACATAAGACTTTCAATGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1469 TAATCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTTCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
*
1534 GCGTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCA-AGATGTTTTCAAATGAGATTTTAGA
131 GCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGA-ATGTTTTCAAATGAGATTTTAGA
* *
1598 AACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGCAAGTCTTTCGAGCAT
195 AACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGG-C-TCAGTAAGTCTTCCGAGCAT
*
1663 GATGC
258 GATAC
* * *
1668 GTAAGTCCTACGGGCCTTCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1733 TAAGCCTTCTGGGGTTTCTTGATTTGTAAGTTCTCCGGG--A-CAGTAAGTCTTCCGAGCATGAT
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
* * * * * *
1795 GCGTAAGT-CTTCGGTCCATCTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAG
131 GCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAA
*
1859 ACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCTGGGCCATCAGTAAGTCTTCCGAGCATG
196 ACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGG-C-TCAGTAAGTCTTCCGAGCATG
1924 ATAC
259 ATAC
* *
1928 GTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
1993 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
66 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
2025 ATTCGGAACA
Statistics
Matches: 796, Mismatches: 55, Indels: 41
0.89 0.06 0.05
Matches are distributed among these distances:
251 27 0.03
254 94 0.12
255 93 0.12
256 40 0.05
257 9 0.01
258 7 0.01
259 45 0.06
260 278 0.35
261 85 0.11
262 1 0.00
264 117 0.15
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (262 bp):
GTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
GCGTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATGTTTTCAAATGAGATTTTAGAA
ACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGGCTCAGTAAGTCTTCCGAGCATGAT
AC
Found at i:1850 original size:392 final size:388
Alignment explanation
Indices: 894--2024 Score: 1734
Period size: 392 Copynumber: 2.9 Consensus size: 388
884 TTCTTGAGTT
*
894 GTAAGTCCTCTGGG-CATCCAT-AGACCTTCAGTGCAGGATGTTTTCAAAT--GATTTTATAAAC
1 GTAAGTCCTC-GGGCCATCCATAAGACCTTCAGTGCA-GATGTTTTCAAATGAGATTTTAGAAAC
*
955 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGTATGAT
64 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGG--A-CAGTAAGTCTTCCGAGCATGAT
* * *
1020 GCGTAAGTCCTCGGGACAT-TCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAA
126 GCGTAAGTCTTCGGGCCATCT-ATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAA
*
1084 ACTAAGCCTTCGGGGTTTACTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCAAGCATG
190 ACTAAGCCTTCGGGGTTT-CTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATG
*
1149 ATGCTTAAG---T-C-GGCCATCCATAAGACTTTCAGTGC-AGATGTTTTC-AATGAGA-TTTAG
254 ATGCGTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAG
* * *
1206 AAACTAAACCTTCGGGGGTTTCTTGATTTTTAAGTCCCCAGGCCATCAGTAAGTCTTCCGAGCAT
319 AAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCCCAGGCCATCAGCAAGTCTTCCGAGCAT
1271 GATGC
384 GATGC
1276 GTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCAGAATG-TTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCT-CGGGCCATCCATAAGACCTTCAGTGCAG-ATGTTTTCAAATGAGATTTTAGAAAC
* ** * * *
1340 TAAGCCTTCGGGGGTTTCTTGATTGGTAAGTCCTTTGAGTCAGTAAGTCTTCCGAGCATGATACG
64 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGACAGTAAGTCTTCCGAGCATGATGCG
*
1405 TAAGTCCTTCGGGCCATAC-ATAAGACTTTCAATGCAGGATGTTTTCAAATGAGATTTTAGAAAC
129 TAAGT-CTTCGGGCCAT-CTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAAC
* *
1469 TAATCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTTCGAGCATGAT
192 TAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGAT
1534 GCGTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAA
256 GCGTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAA
* * *
1599 ACTAAGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGCAAGTCTTTCGAGCATG
321 ACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCC-CCAGGCCATCAGCAAGTCTTCCGAGCATG
1664 ATGC
385 ATGC
*
1668 GTAAGTCCTACGGGCCTTCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
1 GTAAGTCCT-CGGGCCATCCATAAGACCTTCAGTGCA-GATGTTTTCAAATGAGATTTTAGAAAC
* *
1733 TAAGCCTTCTGGGGTTTCTTGATTTGTAAGTTCTCCGGGACAGTAAGTCTTCCGAGCATGATGCG
64 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGACAGTAAGTCTTCCGAGCATGATGCG
* *
1798 TAAGTCTTCGGTCCATCTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAGACTA
129 TAAGTCTTCGGGCCATCTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTA
* *
1863 AGCCTTCAGGGGTTTCTTGATTTGTAAGTCCTCTGGGCCATCAGTAAGTCTTCCGAGCATGATAC
194 AGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATGC
* *
1928 GTAAGTCCTCCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATGAGATTTTAGAAAC
258 GTAAGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAAC
1993 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
323 TAAGCCTTCGGGGGTTTCTTGATTTGTAAGTC
2025 ATTCGGAACA
Statistics
Matches: 684, Mismatches: 43, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
382 40 0.06
383 129 0.19
384 24 0.04
385 46 0.07
386 1 0.00
387 1 0.00
388 24 0.04
389 10 0.01
390 7 0.01
391 40 0.06
392 277 0.40
393 85 0.12
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (388 bp):
GTAAGTCCTCGGGCCATCCATAAGACCTTCAGTGCAGATGTTTTCAAATGAGATTTTAGAAACTA
AGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTCCGGGACAGTAAGTCTTCCGAGCATGATGCGTA
AGTCTTCGGGCCATCTATAAGACTTTCAGTGCAGGATGTTTTCAAATGAGATTTTAGAAACTAAG
CCTTCGGGGTTTCTTGATTTGTAAGTCCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATGCGTA
AGTCCTCCGGGCCATCCATAAGACTTTCAGTGCAAGATGTTTTCAAATGAGATTTTAGAAACTAA
GCCTTCGGGGGTTTCTTGATTTGTAAGTCCCCAGGCCATCAGCAAGTCTTCCGAGCATGATGC
Found at i:6534 original size:18 final size:18
Alignment explanation
Indices: 6511--6550 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6501 TTGTAATCAT
6511 GGTTTTCAGAACCGGACC
1 GGTTTTCAGAACCGGACC
* *
6529 GGTTTTTAGAATCGGACC
1 GGTTTTCAGAACCGGACC
6547 GGTT
1 GGTT
6551 AGCGAACCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (18 bp):
GGTTTTCAGAACCGGACC
Found at i:10341 original size:12 final size:12
Alignment explanation
Indices: 10324--10349 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10314 TCAAAGGTCA
10324 TTTAATGGCCGC
1 TTTAATGGCCGC
10336 TTTAATGGCCGC
1 TTTAATGGCCGC
10348 TT
1 TT
10350 AAAGCCGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (12 bp):
TTTAATGGCCGC
Found at i:10507 original size:29 final size:29
Alignment explanation
Indices: 10400--10618 Score: 221
Period size: 29 Copynumber: 7.6 Consensus size: 29
10390 AAATTCGAAA
* *
10400 ATTT-CCAAAATATCACTTTTTTTCAAAAT
1 ATTTCCCAAAATGTCAC-CTTTTTCAAAAT
* ** *
10429 AATTCATAGAATGTCACC-TTTTCAAAAT
1 ATTTCCCAAAATGTCACCTTTTTCAAAAT
* * * *
10457 AATTCTCATAATATCACCTTTTTCAAAAT
1 ATTTCCCAAAATGTCACCTTTTTCAAAAT
*
10486 ATTT-CCAAAATGTCACTTTTTTCAAAAT
1 ATTTCCCAAAATGTCACCTTTTTCAAAAT
* *
10514 ATTTCCCAGAATGTC-CCATTTTTTAAAAT
1 ATTTCCCAAAATGTCACC-TTTTTCAAAAT
* *
10543 ATTTCCCAAAATGTCACCTATTTCGAAAT
1 ATTTCCCAAAATGTCACCTTTTTCAAAAT
* * *
10572 ATTTCCCAGAATGTAACCTATTTCAAAAT
1 ATTTCCCAAAATGTCACCTTTTTCAAAAT
*
10601 ATTTCCCAGAATGTCACC
1 ATTTCCCAAAATGTCACC
10619 AGGTCGGGTC
Statistics
Matches: 159, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
28 49 0.31
29 100 0.63
30 10 0.06
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (29 bp):
ATTTCCCAAAATGTCACCTTTTTCAAAAT
Found at i:10670 original size:22 final size:22
Alignment explanation
Indices: 10622--10672 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
10612 TGTCACCAGG
*
10622 TCGGGTCGGTCAACGGGTCAGA
1 TCGGGTCGATCAACGGGTCAGA
* * *
10644 CCGGGTCGATCAACGGGTCGGT
1 TCGGGTCGATCAACGGGTCAGA
10666 TCGGGTC
1 TCGGGTC
10673 CGACCGCTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.14, C:0.25, G:0.41, T:0.20
Consensus pattern (22 bp):
TCGGGTCGATCAACGGGTCAGA
Found at i:17938 original size:29 final size:29
Alignment explanation
Indices: 17880--18039 Score: 218
Period size: 29 Copynumber: 5.6 Consensus size: 29
17870 AAATTTGAAA
* *
17880 ATTT-CCAAAATGTCA-TTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* *
17907 AATTCCTAGAATGTCACCTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* *
17936 AATTCCCATAATGTCA-CTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
* *
17964 ATTTCCCATAATGTTACCTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
*
17993 ATTTCCTAGAATGTCACCTTTTTCAAAAT
1 ATTTCCCAGAATGTCACCTTTTTCAAAAT
18022 ATTTCCCAGAATGTCACC
1 ATTTCCCAGAATGTCACC
18040 GGGTCGGGTC
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
27 3 0.03
28 35 0.30
29 80 0.68
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (29 bp):
ATTTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:17958 original size:57 final size:57
Alignment explanation
Indices: 17879--18039 Score: 223
Period size: 57 Copynumber: 2.8 Consensus size: 57
17869 TAAATTTGAA
* * * *
17879 AATTTCCAAAATGTCATTTTTTCAAAATAATTCCTAGAATGTCACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACTTTTTCAAAATATTTCCCAGAATGTCACCTTTTTCAAAAT
* * *
17936 AATTCCCATAATGTCACTTTTTCAAAATATTTCCCATAATGTTACCTTTTTCAAAAT
1 AATTCCCAAAATGTCACTTTTTCAAAATATTTCCCAGAATGTCACCTTTTTCAAAAT
* * *
17993 ATTTCCTAGAATGTCACCTTTTTCAAAATATTTCCCAGAATGTCACC
1 AATTCCCAAAATGTCA-CTTTTTCAAAATATTTCCCAGAATGTCACC
18040 GGGTCGGGTC
Statistics
Matches: 91, Mismatches: 12, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
57 63 0.69
58 28 0.31
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.40
Consensus pattern (57 bp):
AATTCCCAAAATGTCACTTTTTCAAAATATTTCCCAGAATGTCACCTTTTTCAAAAT
Found at i:18078 original size:19 final size:19
Alignment explanation
Indices: 18056--18100 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
18046 GGTCGGGTCC
18056 GACCGGTCAACCCGGTTCA
1 GACCGGTCAACCCGGTTCA
*
18075 GACCGGTCAATCCGGTTCA
1 GACCGGTCAACCCGGTTCA
*
18094 GATCGGT
1 GACCGGT
18101 TTGGACTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.31, G:0.29, T:0.20
Consensus pattern (19 bp):
GACCGGTCAACCCGGTTCA
Found at i:29397 original size:15 final size:15
Alignment explanation
Indices: 29377--29407 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29367 ATAATAAATT
*
29377 AGAAAATTAAGAGAA
1 AGAAAATTAAAAGAA
29392 AGAAAATTAAAAGAA
1 AGAAAATTAAAAGAA
29407 A
1 A
29408 CCGTGTGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.13
Consensus pattern (15 bp):
AGAAAATTAAAAGAA
Found at i:30371 original size:40 final size:39
Alignment explanation
Indices: 30276--30379 Score: 138
Period size: 39 Copynumber: 2.6 Consensus size: 39
30266 TTGAACAAAA
* *
30276 ATACTAAAATTAAACAAAAACTAAAGTCTTTAACGACGG
1 ATACTAAAATAAAACAAAAACTAAAGTCTTTAACGACAG
* *
30315 ATACTAAACA-AAAACAAAAACTAAATTCTTTAATGACAG
1 ATACTAAA-ATAAAACAAAAACTAAAGTCTTTAACGACAG
*
30354 AGTACTAAAATGAAACAAAAACTAAA
1 A-TACTAAAATAAAACAAAAACTAAA
30380 ATTTAGGTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
39 35 0.61
40 22 0.39
ACGTcount: A:0.57, C:0.14, G:0.08, T:0.21
Consensus pattern (39 bp):
ATACTAAAATAAAACAAAAACTAAAGTCTTTAACGACAG
Found at i:33944 original size:20 final size:20
Alignment explanation
Indices: 33921--33992 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
33911 TTGGTACAAG
33921 TATTGTTCTTCCAGTACCGA
1 TATTGTTCTTCCAGTACCGA
* *
33941 TATTGTTCATCCTTAGTATCGA
1 TATTGTTCTTCC--AGTACCGA
*
33963 TATTGTTCTTCAAGTACCGA
1 TATTGTTCTTCCAGTACCGA
*
33983 TATTATTCTT
1 TATTGTTCTT
33993 ATAGCATCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 27 0.61
22 17 0.39
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.46
Consensus pattern (20 bp):
TATTGTTCTTCCAGTACCGA
Found at i:35606 original size:15 final size:15
Alignment explanation
Indices: 35557--35609 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
35547 TTAATATATA
35557 CTATGTGAATGTGTT
1 CTATGTGAATGTGTT
* * *
35572 TTACGTGGAAAGTGTT
1 CTATGT-GAATGTGTT
*
35588 CTATGTGAATGTGTG
1 CTATGTGAATGTGTT
35603 CTATGTG
1 CTATGTG
35610 GATAAAAGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.21, C:0.08, G:0.30, T:0.42
Consensus pattern (15 bp):
CTATGTGAATGTGTT
Found at i:38052 original size:29 final size:29
Alignment explanation
Indices: 38010--38125 Score: 153
Period size: 29 Copynumber: 4.0 Consensus size: 29
38000 CGACCCGACC
38010 CGGTGATATTTTGGTAATTATTTTTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
38039 CGGTGATATTTTGGTAATTATTTTTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
* * **
38068 CGATTATATTTTTATAATTATTTTTAAAGA
1 CGGTGATATTTTGGTAATTATTTTTAAA-A
* * *
38098 -GGTGATATTGTCGTAAATATTTTTAAAA
1 CGGTGATATTTTGGTAATTATTTTTAAAA
38126 ATAGTGCTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
28 1 0.01
29 74 0.97
30 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (29 bp):
CGGTGATATTTTGGTAATTATTTTTAAAA
Found at i:38145 original size:29 final size:29
Alignment explanation
Indices: 38012--38144 Score: 124
Period size: 29 Copynumber: 4.6 Consensus size: 29
38002 ACCCGACCCG
* **
38012 GTGATATTTTGGTAATTATTTTTAAAACG
1 GTGATATTTTCGTAATTATTTTTAAAAAA
* *
38041 GTGATATTTTGGTAATTATTTTT-AAAAC
1 GTGATATTTTCGTAATTATTTTTAAAAAA
* ** * *
38069 GATTATATTTTTATAATTATTTTTAAAGAG
1 G-TGATATTTTCGTAATTATTTTTAAAAAA
* *
38099 GTGATATTGTCGTAAATATTTTTAAAAATA
1 GTGATATTTTCGTAATTATTTTTAAAAA-A
*
38129 GTGCTATTTTCGTAAT
1 GTGATATTTTCGTAAT
38145 AATTACTGTG
Statistics
Matches: 84, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
28 4 0.05
29 63 0.75
30 17 0.20
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (29 bp):
GTGATATTTTCGTAATTATTTTTAAAAAA
Found at i:40087 original size:42 final size:42
Alignment explanation
Indices: 40038--40121 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
40028 TAGATTTACA
*
40038 GACAGTTGATCCTGATCCTACGACCCCGAGAAATTTACCTCC
1 GACAGTTGATCCTGATCCTACGACCCCAAGAAATTTACCTCC
40080 GACAGTTGATCCTGATCCTACGACCCCAAGAAATTTACCTCC
1 GACAGTTGATCCTGATCCTACGACCCCAAGAAATTTACCTCC
40122 TGCCGCTGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (42 bp):
GACAGTTGATCCTGATCCTACGACCCCAAGAAATTTACCTCC
Done.