Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000722.1 Hibiscus syriacus cultivar Beakdansim tig00001401_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: 56580
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:260 original size:31 final size:29
Alignment explanation
Indices: 222--288 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
212 TTTTTAAATT
222 TTTCAAAAA-TAACATATTTTTTAAAAACAAA
1 TTTCAAAAATTAAC--ATTTTTTAAAAA-AAA
*
253 TTTCAAAAATTGACATTTTTTAAAAAAAA
1 TTTCAAAAATTAACATTTTTTAAAAAAAA
*
282 TCTCAAA
1 TTTCAAA
289 TTTTATAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 9 0.27
30 12 0.36
31 9 0.27
32 3 0.09
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.36
Consensus pattern (29 bp):
TTTCAAAAATTAACATTTTTTAAAAAAAA
Found at i:429 original size:16 final size:16
Alignment explanation
Indices: 408--457 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 16
398 GAATGAAATT
408 TTTTAATTAAAATTTA
1 TTTTAATTAAAATTTA
*
424 TTTTAATTAAAAGTTATT
1 TTTTAATTAAAA-TT-TA
442 TTTTAATTAAATATTT
1 TTTTAATTAAA-ATTT
458 TTCATTTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.40
17 3 0.10
18 14 0.47
19 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTAATTAAAATTTA
Found at i:445 original size:18 final size:17
Alignment explanation
Indices: 405--452 Score: 71
Period size: 16 Copynumber: 2.8 Consensus size: 17
395 TATGAATGAA
405 ATTTTTTAATTAAAATT
1 ATTTTTTAATTAAAATT
*
422 -TATTTTAATTAAAAGTT
1 ATTTTTTAATTAAAA-TT
439 ATTTTTTAATTAAA
1 ATTTTTTAATTAAA
453 TATTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
ATTTTTTAATTAAAATT
Found at i:459 original size:16 final size:15
Alignment explanation
Indices: 406--459 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 15
396 ATGAATGAAA
406 TTTTTTAATTAAAAT
1 TTTTTTAATTAAAAT
421 TTATTTTAATTAAAAGTT
1 TT-TTTTAATTAAAA--T
439 ATTTTTTAATTAAATAT
1 -TTTTTTAATTAAA-AT
456 TTTT
1 TTTT
460 CATTTTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.06
16 16 0.47
17 1 0.03
18 12 0.35
19 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTTTTAATTAAAAT
Found at i:1953 original size:14 final size:15
Alignment explanation
Indices: 1934--1966 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1924 GAGGAACACT
1934 AAGAAAAATGG-AAG
1 AAGAAAAATGGTAAG
1948 AAGAAAAATGGTAAG
1 AAGAAAAATGGTAAG
1963 AAGA
1 AAGA
1967 TGATAATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (15 bp):
AAGAAAAATGGTAAG
Found at i:7248 original size:23 final size:23
Alignment explanation
Indices: 7222--7268 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
7212 AATACCCAAG
*
7222 ATAAA-TATAAATCTACCATTAAA
1 ATAAAGTATAAA-CAACCATTAAA
*
7245 ATAAAGTTTAAACAACCATTAAA
1 ATAAAGTATAAACAACCATTAAA
7268 A
1 A
7269 CAACCCCATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (23 bp):
ATAAAGTATAAACAACCATTAAA
Found at i:20809 original size:24 final size:25
Alignment explanation
Indices: 20769--20817 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
20759 GTTCTAGTAA
*
20769 TTTTAAAAAAAATTCTTTAAATTTT
1 TTTTAAAAAAAATTCTTAAAATTTT
*
20794 TTTTAAATAAAA-TCTTAAAATTTT
1 TTTTAAAAAAAATTCTTAAAATTTT
20818 CAAATCTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
TTTTAAAAAAAATTCTTAAAATTTT
Found at i:22866 original size:33 final size:33
Alignment explanation
Indices: 22818--22881 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
22808 TAAATCAACA
* *
22818 TATTTGAGTCCTATTGAAACACTAAAACTAATG
1 TATTTAAGTCATATTGAAACACTAAAACTAATG
22851 TATTTAAGTCATATTGAAACACTAAAACTAA
1 TATTTAAGTCATATTGAAACACTAAAACTAA
22882 AGCATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (33 bp):
TATTTAAGTCATATTGAAACACTAAAACTAATG
Found at i:27043 original size:854 final size:854
Alignment explanation
Indices: 25396--27109 Score: 3428
Period size: 854 Copynumber: 2.0 Consensus size: 854
25386 CATTCTGTTT
25396 GAATTTGTTTTTCATTTTTTTCTCAAGTTTTTGTAAGGACTTTTAAATAAATTTATGTTACTTTA
1 GAATTTGTTTTTCATTTTTTTCTCAAGTTTTTGTAAGGACTTTTAAATAAATTTATGTTACTTTA
25461 AAGACGTTAAGCAATGAATCACATTTGCAAACTTGTAATTCTTTGAATATCATCTGAATTAAGAA
66 AAGACGTTAAGCAATGAATCACATTTGCAAACTTGTAATTCTTTGAATATCATCTGAATTAAGAA
25526 ACTCTATAAATGGTTTAAAGTTACAGATCTTTGACGAAGTAATATGATTTAAAACAAGGAATTTG
131 ACTCTATAAATGGTTTAAAGTTACAGATCTTTGACGAAGTAATATGATTTAAAACAAGGAATTTG
25591 ACTTTACCCAGAATATGCACTCAAACATCGTACCCTGCTCTTGCAATAAACCAATATAACCTTTT
196 ACTTTACCCAGAATATGCACTCAAACATCGTACCCTGCTCTTGCAATAAACCAATATAACCTTTT
25656 CATTTCATAAGGTGCGGACAACATGGGGCATCCTTTTGCATATGACATTAGTATACTTTTTATTT
261 CATTTCATAAGGTGCGGACAACATGGGGCATCCTTTTGCATATGACATTAGTATACTTTTTATTT
25721 AAAATGTTCAATGATGATCATTATCTTTACAGATGGAACAGTCGAGTAGGTAAATCTAGTTTAGG
326 AAAATGTTCAATGATGATCATTATCTTTACAGATGGAACAGTCGAGTAGGTAAATCTAGTTTAGG
25786 TCAGTTGCTTGGAAATTGAACTATAAAAATGAGATTCATTGACTTTCAACAACACCTAACTATAA
391 TCAGTTGCTTGGAAATTGAACTATAAAAATGAGATTCATTGACTTTCAACAACACCTAACTATAA
25851 CAGGTTCTTCTTGACAAACTTAATAAATTAAATCCGTAAGGCTGAGCTATTCCACTAAGGCAATT
456 CAGGTTCTTCTTGACAAACTTAATAAATTAAATCCGTAAGGCTGAGCTATTCCACTAAGGCAATT
25916 GGTTATTGAAGAAACTTGAAAGCCCTGACCTTATGAGTAGATTACGTTTAAACCATGACATTGCT
521 GGTTATTGAAGAAACTTGAAAGCCCTGACCTTATGAGTAGATTACGTTTAAACCATGACATTGCT
25981 CGAACACTTGGCAATTCGGTGTTTGCTCCACTGTTATTGTCCGGCCGAAGACTTTGTGATGAGAT
586 CGAACACTTGGCAATTCGGTGTTTGCTCCACTGTTATTGTCCGGCCGAAGACTTTGTGATGAGAT
26046 GAACCCTTCAGTTAACTTGATAAAACTGATTATAATGTTAAGTTGTCACTCTAAAGCAATTGGTT
651 GAACCCTTCAGTTAACTTGATAAAACTGATTATAATGTTAAGTTGTCACTCTAAAGCAATTGGTT
26111 AAACGCCTAGGCTTTACGGATTCAACTAGCAAGATAACGACAAATTAAATCAAATTTATCTAAGC
716 AAACGCCTAGGCTTTACGGATTCAACTAGCAAGATAACGACAAATTAAATCAAATTTATCTAAGC
26176 AAGAAATTTTCGGTAATGATGAACTAAGGGAGTTAAGGAACACCTGTTATAGTCAACTTCACATG
781 AAGAAATTTTCGGTAATGATGAACTAAGGGAGTTAAGGAACACCTGTTATAGTCAACTTCACATG
26241 AGCACTCAA
846 AGCACTCAA
26250 GAATTTGTTTTTCATTTTTTTCTCAAGTTTTTGTAAGGACTTTTAAATAAATTTATGTTACTTTA
1 GAATTTGTTTTTCATTTTTTTCTCAAGTTTTTGTAAGGACTTTTAAATAAATTTATGTTACTTTA
26315 AAGACGTTAAGCAATGAATCACATTTGCAAACTTGTAATTCTTTGAATATCATCTGAATTAAGAA
66 AAGACGTTAAGCAATGAATCACATTTGCAAACTTGTAATTCTTTGAATATCATCTGAATTAAGAA
26380 ACTCTATAAATGGTTTAAAGTTACAGATCTTTGACGAAGTAATATGATTTAAAACAAGGAATTTG
131 ACTCTATAAATGGTTTAAAGTTACAGATCTTTGACGAAGTAATATGATTTAAAACAAGGAATTTG
26445 ACTTTACCCAGAATATGCACTCAAACATCGTACCCTGCTCTTGCAATAAACCAATATAACCTTTT
196 ACTTTACCCAGAATATGCACTCAAACATCGTACCCTGCTCTTGCAATAAACCAATATAACCTTTT
26510 CATTTCATAAGGTGCGGACAACATGGGGCATCCTTTTGCATATGACATTAGTATACTTTTTATTT
261 CATTTCATAAGGTGCGGACAACATGGGGCATCCTTTTGCATATGACATTAGTATACTTTTTATTT
26575 AAAATGTTCAATGATGATCATTATCTTTACAGATGGAACAGTCGAGTAGGTAAATCTAGTTTAGG
326 AAAATGTTCAATGATGATCATTATCTTTACAGATGGAACAGTCGAGTAGGTAAATCTAGTTTAGG
26640 TCAGTTGCTTGGAAATTGAACTATAAAAATGAGATTCATTGACTTTCAACAACACCTAACTATAA
391 TCAGTTGCTTGGAAATTGAACTATAAAAATGAGATTCATTGACTTTCAACAACACCTAACTATAA
26705 CAGGTTCTTCTTGACAAACTTAATAAATTAAATCCGTAAGGCTGAGCTATTCCACTAAGGCAATT
456 CAGGTTCTTCTTGACAAACTTAATAAATTAAATCCGTAAGGCTGAGCTATTCCACTAAGGCAATT
26770 GGTTATTGAAGAAACTTGAAAGCCCTGACCTTATGAGTAGATTACGTTTAAACCATGACATTGCT
521 GGTTATTGAAGAAACTTGAAAGCCCTGACCTTATGAGTAGATTACGTTTAAACCATGACATTGCT
26835 CGAACACTTGGCAATTCGGTGTTTGCTCCACTGTTATTGTCCGGCCGAAGACTTTGTGATGAGAT
586 CGAACACTTGGCAATTCGGTGTTTGCTCCACTGTTATTGTCCGGCCGAAGACTTTGTGATGAGAT
26900 GAACCCTTCAGTTAACTTGATAAAACTGATTATAATGTTAAGTTGTCACTCTAAAGCAATTGGTT
651 GAACCCTTCAGTTAACTTGATAAAACTGATTATAATGTTAAGTTGTCACTCTAAAGCAATTGGTT
26965 AAACGCCTAGGCTTTACGGATTCAACTAGCAAGATAACGACAAATTAAATCAAATTTATCTAAGC
716 AAACGCCTAGGCTTTACGGATTCAACTAGCAAGATAACGACAAATTAAATCAAATTTATCTAAGC
27030 AAGAAATTTTCGGTAATGATGAACTAAGGGAGTTAAGGAACACCTGTTATAGTCAACTTCACATG
781 AAGAAATTTTCGGTAATGATGAACTAAGGGAGTTAAGGAACACCTGTTATAGTCAACTTCACATG
27095 AGCACTCAA
846 AGCACTCAA
27104 GAATTT
1 GAATTT
27110 CATTTTTAGA
Statistics
Matches: 860, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
854 860 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (854 bp):
GAATTTGTTTTTCATTTTTTTCTCAAGTTTTTGTAAGGACTTTTAAATAAATTTATGTTACTTTA
AAGACGTTAAGCAATGAATCACATTTGCAAACTTGTAATTCTTTGAATATCATCTGAATTAAGAA
ACTCTATAAATGGTTTAAAGTTACAGATCTTTGACGAAGTAATATGATTTAAAACAAGGAATTTG
ACTTTACCCAGAATATGCACTCAAACATCGTACCCTGCTCTTGCAATAAACCAATATAACCTTTT
CATTTCATAAGGTGCGGACAACATGGGGCATCCTTTTGCATATGACATTAGTATACTTTTTATTT
AAAATGTTCAATGATGATCATTATCTTTACAGATGGAACAGTCGAGTAGGTAAATCTAGTTTAGG
TCAGTTGCTTGGAAATTGAACTATAAAAATGAGATTCATTGACTTTCAACAACACCTAACTATAA
CAGGTTCTTCTTGACAAACTTAATAAATTAAATCCGTAAGGCTGAGCTATTCCACTAAGGCAATT
GGTTATTGAAGAAACTTGAAAGCCCTGACCTTATGAGTAGATTACGTTTAAACCATGACATTGCT
CGAACACTTGGCAATTCGGTGTTTGCTCCACTGTTATTGTCCGGCCGAAGACTTTGTGATGAGAT
GAACCCTTCAGTTAACTTGATAAAACTGATTATAATGTTAAGTTGTCACTCTAAAGCAATTGGTT
AAACGCCTAGGCTTTACGGATTCAACTAGCAAGATAACGACAAATTAAATCAAATTTATCTAAGC
AAGAAATTTTCGGTAATGATGAACTAAGGGAGTTAAGGAACACCTGTTATAGTCAACTTCACATG
AGCACTCAA
Found at i:27943 original size:110 final size:110
Alignment explanation
Indices: 27702--28016 Score: 508
Period size: 110 Copynumber: 2.9 Consensus size: 110
27692 GATGGTGGTT
* *
27702 GCTCAACTTCACAGCGAAGGGGCGACTGACGGTCAACAAACAACTTTTCAGTTTCATTCAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTC
* *
27767 AA-TTCAACTTCACAACGAATGATATTAGACTCGAGACAACACAA
66 AATTTTAACTTCACAACGAATGATATTGGACTCGAGACAACACAA
* * * *
27811 ACTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAATAACTTTTCAGTTTCATTTAGAGAC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTC
* *
27876 AATTTTAATTTCACAATGAATGATATTGGACTCGAGACAACACAA
66 AATTTTAACTTCACAACGAATGATATTGGACTCGAGACAACACAA
*
27921 GCTCAACTTCACAGCGAAGGGGCGAATGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTC
1 GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTC
27986 AATTTTAACTTCACAACGAA-GTATATTGGAC
66 AATTTTAACTTCACAACGAATG-ATATTGGAC
28017 CCCAAGTTCA
Statistics
Matches: 187, Mismatches: 17, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
109 62 0.33
110 125 0.67
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (110 bp):
GCTCAACTTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTC
AATTTTAACTTCACAACGAATGATATTGGACTCGAGACAACACAA
Found at i:28091 original size:95 final size:95
Alignment explanation
Indices: 27928--28111 Score: 296
Period size: 95 Copynumber: 1.9 Consensus size: 95
27918 CAAGCTCAAC
* * *
27928 TTCACAGCGAAGGGGCGAATGACTGTCAACAAACAACTTTTCAGTTTCATTTAGAGTCAATTTTA
1 TTCACAACGAAGGGGCGAATGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCA
*
27993 ACTTCACAACGAAGTATATTGGACCCCAAG
66 ACTTCACAACGAAGGATATTGGACCCCAAG
* * *
28023 TTCACAACGAATGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTTATTCAGAGTCAATTTCA
1 TTCACAACGAAGGGGCGAATGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCA
*
28088 ACTTCACAGCGAAGGATATTGGAC
66 ACTTCACAACGAAGGATATTGGAC
28112 TCGAGACAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 81 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (95 bp):
TTCACAACGAAGGGGCGAATGACTGTCAACAAACAACTTTTCAGTTTCATTCAGAGTCAATTTCA
ACTTCACAACGAAGGATATTGGACCCCAAG
Found at i:28466 original size:81 final size:84
Alignment explanation
Indices: 28317--28530 Score: 258
Period size: 81 Copynumber: 2.6 Consensus size: 84
28307 CAAAATGCCT
* *
28317 TCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGAGC
1 TCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGAGC
28381 TATC-TG-CC-AAAGACCC
66 TATCGTGACCAAAAGACCC
* * * * * * * * * *
28397 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTATAAGGGT
1 TCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGAGC
*
28462 TATCTGTGACCAAAAGACCT
66 TATC-GTGACCAAAAGACCC
*
28482 TCGAGTTCGACTACGCTCAG-TTCCAAGGCATATCATTTGCAGCATAACT
1 TCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACT
28531 GTAACGTCCT
Statistics
Matches: 109, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
80 19 0.17
81 37 0.34
83 2 0.02
84 26 0.24
85 25 0.23
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (84 bp):
TCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAACTCAAGGCAAGAAGAGC
TATCGTGACCAAAAGACCC
Found at i:29296 original size:21 final size:21
Alignment explanation
Indices: 29254--29296 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
29244 TTTATGGGCT
* * *
29254 AGGGGAATTGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
29275 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
29296 A
1 A
29297 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:29759 original size:30 final size:31
Alignment explanation
Indices: 29705--29775 Score: 108
Period size: 30 Copynumber: 2.3 Consensus size: 31
29695 GTTATATGAA
29705 TTATGTGATAAAGGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
*
29736 TTATGTGATAAAGGTAT-GAAAATGATATGT
1 TTATGTGATAAAGGTATGGAAAATGAAATGT
* *
29766 CTATGCGATA
1 TTATGTGATA
29776 TAAATTATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 20 0.54
31 17 0.46
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (31 bp):
TTATGTGATAAAGGTATGGAAAATGAAATGT
Found at i:29991 original size:24 final size:24
Alignment explanation
Indices: 29968--30046 Score: 97
Period size: 26 Copynumber: 3.2 Consensus size: 24
29958 ATATATGGTC
29968 CTTCGGGACAAATTCTACGCGGT-
1 CTTCGGGACAAATTCTACGCGGTA
29991 CATTCGGGACAAATTTCTACGCGGTA
1 C-TTCGGGACAAA-TTCTACGCGGTA
* *
30017 CTTCGGTGTAAAAACTCTACGCGGTA
1 CTTCGG-G-ACAAATTCTACGCGGTA
30043 CTTC
1 CTTC
30047 AGTGCAATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 7
0.84 0.03 0.12
Matches are distributed among these distances:
23 1 0.02
24 11 0.22
25 16 0.33
26 17 0.35
27 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (24 bp):
CTTCGGGACAAATTCTACGCGGTA
Found at i:30014 original size:25 final size:24
Alignment explanation
Indices: 29964--30041 Score: 86
Period size: 24 Copynumber: 3.1 Consensus size: 24
29954 ATTTATATAT
*
29964 GGTCCTTCGGGACAAATTCTACGC
1 GGTCATTCGGGACAAATTCTACGC
29988 GGTCATTCGGGACAAATTTCTACGC
1 GGTCATTCGGGACAAA-TTCTACGC
* *
30013 GGT-ACTTCGGTGTAAAAACTCTACGC
1 GGTCA-TTCGG-G-ACAAATTCTACGC
30039 GGT
1 GGT
30042 ACTTCAGTGC
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
24 16 0.34
25 16 0.34
26 11 0.23
27 4 0.09
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (24 bp):
GGTCATTCGGGACAAATTCTACGC
Found at i:36107 original size:21 final size:21
Alignment explanation
Indices: 36065--36107 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
36055 TTTCTGGGCT
* *
36065 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
36086 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
36107 A
1 A
36108 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:36552 original size:31 final size:30
Alignment explanation
Indices: 36516--36586 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
36506 GTTATATGAA
*
36516 TTATGTGATAAATGTATGGAAAATGAAATGT
1 TTATGTGATAAAGGTATGG-AAATGAAATGT
*
36547 TTATGTGATAAAGGTATGGAAATGATATGT
1 TTATGTGATAAAGGTATGGAAATGAAATGT
* *
36577 CTATGCGATA
1 TTATGTGATA
36587 TAAATTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 18 0.50
31 18 0.50
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.35
Consensus pattern (30 bp):
TTATGTGATAAAGGTATGGAAATGAAATGT
Found at i:36837 original size:25 final size:24
Alignment explanation
Indices: 36786--36839 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
36776 TATGTGGTCA
* *
36786 TTCGGGACAAATTCTACGCTGTCC
1 TTCGGAACAAATTCTACGCTGGCC
36810 TTCGGAACAAATTTCTACGC-GGCAC
1 TTCGGAACAAA-TTCTACGCTGGC-C
36835 TTCGG
1 TTCGG
36840 TGCAATTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (24 bp):
TTCGGAACAAATTCTACGCTGGCC
Found at i:37620 original size:81 final size:82
Alignment explanation
Indices: 37443--37741 Score: 277
Period size: 84 Copynumber: 3.6 Consensus size: 82
37433 ACTTAAGTCG
* * *
37443 AGAAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCA-AGGCACATCAT
1 AGAAGGGCTATCTGCC-AC-AAAGACCTTCGAGTTCGACTACACTCAGCTCGAGA-GCACATCAT
* * *
37507 TTGCAGCATAGCTTAAGTCG
63 TTGCAGCATAGCTCAAGGCA
* *
37527 AGAAGGGCTATCTG-C-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATCATTT
1 AGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGACTACACTCAGC-TCGAGAGCACATCATTT
* * * *
37590 ACGGCATAACTCAAGGCT
65 GCAGCATAGCTCAAGGCA
* * * * * * *
37608 ATAAGGGTTATCTGTCAACAAAGACCTTTGAGTTCAACTCCACTCAGCTC-AAAGACACCATCAT
1 AGAAGGGCTATCTG-CCACAAAGACCTTCGAGTTCGACTACACTCAGCTCGAGAG-CA-CATCAT
*
37672 TTGCAGTATAGCTCAAGGCA
63 TTGCAGCATAGCTCAAGGCA
* * * *
37692 AGAAGGGCTATCTG-C-CAAAGACCTTCGAGTTTGATTCCATTCAGCTCGAG
1 AGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGACTACACTCAGCTCGAG
37742 GGCGTATCAA
Statistics
Matches: 173, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
80 26 0.15
81 66 0.38
82 5 0.03
83 5 0.03
84 71 0.41
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (82 bp):
AGAAGGGCTATCTGCCACAAAGACCTTCGAGTTCGACTACACTCAGCTCGAGAGCACATCATTTG
CAGCATAGCTCAAGGCA
Found at i:37670 original size:84 final size:79
Alignment explanation
Indices: 37463--37722 Score: 286
Period size: 84 Copynumber: 3.2 Consensus size: 79
37453 TCTGCCAACT
* * * * *
37463 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACACTCAGCT-CAAGACACATCATTTGCAGCATAGCTCAAGGCAA
37528 GAAGGGCTATCTGCC
65 GAAGGGCTATCTGCC
* * * * * * *
37543 AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGAGCACATCATTTACGGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGACTACACTCAGC-TCAAGA-CACATCATTTGCAGCATAGCTCAAGGCA
* *
37608 ATAAGGGTTATCTGTCAAC
64 AGAAGGGCTATCTG-C--C
* * * *
37627 AAAGACCTTTGAGTTCAACTCCACTCAGCTCAAAGACACCATCATTTGCAGTATAGCTCAAGGCA
1 AAAGACCTTCGAGTTCGACTACACTCAGCTC-AAGACA-CATCATTTGCAGCATAGCTCAAGGCA
37692 AGAAGGGCTATCTGCC
64 AGAAGGGCTATCTGCC
37708 AAAGACCTTCGAGTT
1 AAAGACCTTCGAGTT
37723 TGATTCCATT
Statistics
Matches: 146, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
80 29 0.20
81 50 0.34
82 1 0.01
83 5 0.03
84 61 0.42
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.23
Consensus pattern (79 bp):
AAAGACCTTCGAGTTCGACTACACTCAGCTCAAGACACATCATTTGCAGCATAGCTCAAGGCAAG
AAGGGCTATCTGCC
Found at i:37722 original size:165 final size:164
Alignment explanation
Indices: 37445--37741 Score: 434
Period size: 165 Copynumber: 1.8 Consensus size: 164
37435 TTAAGTCGAG
* * * *
37445 AAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCAACTACACTCAGCTCAAAGACACATCATTTG
* * *
37510 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
66 CAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGC-TC
37575 GAGAGCACATCATTTACGGCATAACTCAAGGCTAT
130 GAGAGCACATCATTTACGGCATAACTCAAGGCTAT
* * *
37610 AAGGGTTATCTGTCAAC-AAAGACCTTTGAGTTCAACTCCACTCAGCTCAAAGACACCATCATTT
1 AAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCAACTACACTCAGCTCAAAGACA-CATCATTT
* * * * *
37674 GCAGTATAGCTCAAGGCAAGAAGGGCTATCTGCCAAAGACCTTCGAGTTTGATTCCATTCAGCTC
65 GCAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTC
37739 GAG
130 GAG
37742 GGCGTATCAA
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
164 37 0.32
165 79 0.68
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (164 bp):
AAGGGTTATCTGCCAACTAAAGACCTTCGAGTTCAACTACACTCAGCTCAAAGACACATCATTTG
CAGCATAGCTCAAGGCAAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCG
AGAGCACATCATTTACGGCATAACTCAAGGCTAT
Found at i:38106 original size:3 final size:3
Alignment explanation
Indices: 38070--38142 Score: 64
Period size: 3 Copynumber: 23.7 Consensus size: 3
38060 CAAAAACATT
38070 TTA TTA -TA TTA TATA TTTA TTTA TTTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA -TTA -TTA -TTA -TTA TTA TTA TTA TTA TTA
38116 TTA TTA TTA -TA TT- TGTA TT- TTA TTA TT
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT
38143 TTTACAGGCC
Statistics
Matches: 63, Mismatches: 0, Indels: 14
0.82 0.00 0.18
Matches are distributed among these distances:
2 7 0.11
3 38 0.60
4 17 0.27
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38144 original size:8 final size:8
Alignment explanation
Indices: 38067--38144 Score: 56
Period size: 8 Copynumber: 9.6 Consensus size: 8
38057 CTACAAAAAC
38067 ATTTTATT
1 ATTTTATT
*
38075 ATATTA-T
1 ATTTTATT
38082 ATATTTATT
1 AT-TTTATT
38091 -TATTTATT
1 AT-TTTATT
*
38099 -TATTATT
1 ATTTTATT
38106 ATTATTATT
1 ATT-TTATT
38115 ATTATTATT
1 ATT-TTATT
*
38124 ATATTT-GT
1 AT-TTTATT
38132 ATTTTATT
1 ATTTTATT
38140 ATTTT
1 ATTTT
38145 TACAGGCCCC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
7 11 0.19
8 27 0.47
9 19 0.33
10 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (8 bp):
ATTTTATT
Found at i:38234 original size:33 final size:33
Alignment explanation
Indices: 38192--38278 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
38182 TTCAGAAAAT
38192 AAACCAACGTATTTGAGTCCTATTGAAACACTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
* *
38225 AAACCAACGTATTTGAATCCTATTGAAACATTA
1 AAACCAACGTATTTGAGTCCTATTGAAACACTA
* *
38258 AAACCAAAGCATTTTGAGTCC
1 AAACCAACGTA-TTTGAGTCC
38279 AAGTAGGACT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 40 0.83
34 8 0.17
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (33 bp):
AAACCAACGTATTTGAGTCCTATTGAAACACTA
Found at i:43764 original size:17 final size:18
Alignment explanation
Indices: 43734--43774 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
43724 CAATGTAAAT
43734 AAATATATAAAAAATTAA
1 AAATATATAAAAAATTAA
* *
43752 AAAT-TATATAAAATTAT
1 AAATATATAAAAAATTAA
43769 AAATAT
1 AAATAT
43775 TTTATACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATATATAAAAAATTAA
Found at i:44164 original size:18 final size:18
Alignment explanation
Indices: 44141--44179 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
44131 TTTAACAAAG
* *
44141 AACACAAATTGATACCAA
1 AACACAAATTAAAACCAA
*
44159 AACACAACTTAAAACCAA
1 AACACAAATTAAAACCAA
44177 AAC
1 AAC
44180 CACTTTAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.26, G:0.03, T:0.13
Consensus pattern (18 bp):
AACACAAATTAAAACCAA
Found at i:44167 original size:45 final size:45
Alignment explanation
Indices: 44064--44170 Score: 180
Period size: 45 Copynumber: 2.4 Consensus size: 45
44054 AATAGTTAAC
* *
44064 ACCAAAACACAACCTAATTTCATTTAACAAACGGCACAAATTGAT
1 ACCAAAACACAACTTAATTTCATTTAACAAACGACACAAATTGAT
44109 ACCAAAACACAACTTAATTTCATTTAACAAA-GAACACAAATTGAT
1 ACCAAAACACAACTTAATTTCATTTAACAAACG-ACACAAATTGAT
44154 ACCAAAACACAACTTAA
1 ACCAAAACACAACTTAA
44171 AACCAAAACC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
44 1 0.02
45 58 0.98
ACGTcount: A:0.50, C:0.23, G:0.05, T:0.21
Consensus pattern (45 bp):
ACCAAAACACAACTTAATTTCATTTAACAAACGACACAAATTGAT
Found at i:46895 original size:2 final size:2
Alignment explanation
Indices: 46888--46913 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
46878 TCATATACAA
46888 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
46914 TTGTATTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47383 original size:17 final size:18
Alignment explanation
Indices: 47361--47401 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
47351 TCCTTTCAAA
47361 ATTTTAAAT-TTTTATAT
1 ATTTTAAATATTTTATAT
*
47378 ATTTTAAATAATTTTTTAT
1 ATTTTAAAT-ATTTTATAT
47397 ATTTT
1 ATTTT
47402 TATTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
19 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTAAATATTTTATAT
Found at i:47397 original size:19 final size:19
Alignment explanation
Indices: 47367--47424 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
47357 CAAAATTTTA
47367 AATTTTTATATATTTTAAAT
1 AATTTTT-TATATTTTAAAT
* *
47387 AATTTTTTATATTTTTATT
1 AATTTTTTATATTTTAAAT
* *
47406 AAATATTTATATTTATAAA
1 AATTTTTTATATTT-TAAA
47425 CACAATATAC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTTATATTTTAAAT
Found at i:47901 original size:4 final size:4
Alignment explanation
Indices: 47844--47886 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
47834 GGCGGAGAGT
*
47844 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
47887 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:49517 original size:21 final size:21
Alignment explanation
Indices: 49484--49533 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
49474 TCATTAAAAT
49484 TAATAAATATTTATACATTAA
1 TAATAAATATTTATACATTAA
* *
49505 TAATATAAT-TTTATATATTAT
1 TAATA-AATATTTATACATTAA
*
49526 TGATAAAT
1 TAATAAAT
49534 TAAATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATAAATATTTATACATTAA
Found at i:53403 original size:2 final size:2
Alignment explanation
Indices: 53398--53424 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53388 TTTTTTCTTA
53398 AT 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 A
53425 ATGGACTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.