Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004781.1 Hibiscus syriacus cultivar Beakdansim tig00010782_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: 48334
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:6704 original size:21 final size:22
Alignment explanation
Indices: 6662--6726 Score: 114
Period size: 21 Copynumber: 3.0 Consensus size: 22
6652 CTCGTATAAA
*
6662 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
6684 TGCACCGTAGTGCCC-TAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
6705 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
6727 GATGTCCATA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 21 0.51
22 20 0.49
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:8368 original size:21 final size:21
Alignment explanation
Indices: 8344--8388 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
8334 TCTTGTTCGT
* *
8344 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
8365 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
8386 TTG
1 TTG
8389 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:11479 original size:22 final size:22
Alignment explanation
Indices: 11462--11527 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
11452 CTCGTATAAA
*
11462 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
11484 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
11506 TGCACCGTAGTGCCCGTAGAAT
1 TGCACCGTAGTGCCCGTAGAAT
11528 GATGTCCATA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.21
Consensus pattern (22 bp):
TGCACCGTAGTGCCCGTAGAAT
Found at i:11493 original size:13 final size:13
Alignment explanation
Indices: 11475--11515 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
11465 ACCGAAGTGC
11475 CCGTAGAATTGCA
1 CCGTAGAATTGCA
11488 CCGTAG---TGC-
1 CCGTAGAATTGCA
11497 CCGTAGAATTGCA
1 CCGTAGAATTGCA
11510 CCGTAG
1 CCGTAG
11516 TGCCCGTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 6 0.25
10 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:13191 original size:21 final size:21
Alignment explanation
Indices: 13167--13211 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13157 TCTTGTTCGT
* *
13167 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
13188 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
13209 TTG
1 TTG
13212 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:14421 original size:28 final size:29
Alignment explanation
Indices: 14350--14424 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
14340 AATTTGTAGA
* * *
14350 TTAAAACACATAGGTGCTCAATCATTTTT
1 TTAAAGCACATAGGTGTTCAATCATTTTC
*
14379 TTAAAGCACAGAGGTGTTCAATCA-TTTC
1 TTAAAGCACATAGGTGTTCAATCATTTTC
*
14407 TTAAAGTACATAGGTGTT
1 TTAAAGCACATAGGTGTT
14425 AATTTGTGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 19 0.47
29 21 0.52
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (29 bp):
TTAAAGCACATAGGTGTTCAATCATTTTC
Found at i:18357 original size:17 final size:17
Alignment explanation
Indices: 18314--18357 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
18304 GTACTTTACT
*
18314 ATTAACTATATTAAAAA
1 ATTAAATATATTAAAAA
*
18331 ATT--ATGTATTAAAAA
1 ATTAAATATATTAAAAA
18346 ATTAAATATATT
1 ATTAAATATATT
18358 CACATCCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
ATTAAATATATTAAAAA
Found at i:20013 original size:60 final size:60
Alignment explanation
Indices: 19894--20016 Score: 144
Period size: 60 Copynumber: 2.0 Consensus size: 60
19884 TATTTAGGGT
* * *
19894 AAAATATACAAATGATCTCTGGATTATAAGGTATTATTTTGCTGAGTTCATCGATTATTA
1 AAAATATACAAATGATCTCTGGATTATAAGATATTATTTTGCTGAGTCCATCGACTATTA
* * *
19954 AAAAT-TACAAAATGATC-CTTTGATTATAAGATGTTATTTTGTTGAGTCC-TACGACTATTA
1 AAAATATAC-AAATGATCTC-TGGATTATAAGATATTATTTTGCTGAGTCCAT-CGACTATTA
20014 AAA
1 AAA
20017 TGATCGTTCG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
59 5 0.09
60 49 0.91
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (60 bp):
AAAATATACAAATGATCTCTGGATTATAAGATATTATTTTGCTGAGTCCATCGACTATTA
Found at i:20347 original size:59 final size:58
Alignment explanation
Indices: 20230--20358 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 58
20220 ATATGAATAG
* * *
20230 TCAGATAATCATTTTATAACTTTTAATAGTCGATGATTTAATAAAATAACACTATATAA
1 TCAGATAATTATTTTATAACTTTTAATAGTCGAAGATTTAACAAAATAACAC-ATATAA
* * * *
20289 TTAGATAATTATTTTATAATTTTTAATAGTTGAAAGATTTAACAAACAGTATC-C-TATAA
1 TCAGATAATTATTTTATAACTTTTAATAGTCG-AAGATTTAACAAA-A-TAACACATATAA
20348 TCAGAT-ATTAT
1 TCAGATAATTAT
20359 ATGTGTACTT
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
58 5 0.08
59 38 0.64
60 11 0.19
61 2 0.03
62 3 0.05
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.41
Consensus pattern (58 bp):
TCAGATAATTATTTTATAACTTTTAATAGTCGAAGATTTAACAAAATAACACATATAA
Found at i:23629 original size:37 final size:38
Alignment explanation
Indices: 23579--23659 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 38
23569 TTTATTTTGT
*
23579 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
* *
23616 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTTGGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
23654 TCGGGT
1 TCGGGT
23660 TCAGGTTTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
37 10 0.25
38 30 0.75
ACGTcount: A:0.12, C:0.10, G:0.38, T:0.40
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCGAG
Found at i:23906 original size:226 final size:218
Alignment explanation
Indices: 23615--24152 Score: 730
Period size: 226 Copynumber: 2.4 Consensus size: 218
23605 TTCGGGTCGA
* * * *
23615 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTTGGGTCGGGTTCAGGTTTAGGGTGAAAAAA
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAA
* *
23680 CCAGACCGACCCAAAAATATATATAATTCGGGTCGGGTCGGGTCGGATTAAGTCACTGTTTTTAT
65 CCGGACCGACCCAAAAATATATATAATT----TCGGGTCGGGTCAGATTAAGTCACTGTTTTTAT
*
23745 TAAATAAAAATAAAATTTTTATTATTTC-GT-GTCGGATCGTATTTCTAATTCATATATTTGGGT
126 TAAATAAAAAT-AAATTTTTATTATTTCGGTGGTCGGATCGGATTTCTAATTCATATA--T---T
* * *
23808 CGGGTCGGGTCGGATGAAACTTTATTTTGTTCGG
185 CGAGTCGGGTAGGATGAAACTTTATTTTGTTCAG
* *
23842 GTCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGGGTCGAGTTCGGGTTTAGGGTAAAAAAAC
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAAC
23907 CGGACCGACCCAAAAATATATATAA-TTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAAT
66 CGGACCGACCCAAAAATATATATAATTTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAAT
** *
23971 AAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGAGTCGG
131 AAAAATAAATTTTTATTATTTC-GGT--GGTCGGATCGGATTTCTAATTCATATATTCGAGTCGG
24036 GTAGGATGAAACTTTATTTTGTTCAG
193 GTAGGATGAAACTTTATTTTGTTCAG
* *
24062 GTCGGGTC--G--TGTTAAGTGTGATATTCGGGTCAGGTCGGGTTCGGGTTTAGGGTGAAAAAAA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGT-AAAAAAA
24123 CCGGACCGACCCGAAAAATATATATAATTT
65 CCGGACCGACCC-AAAAATATATATAATTT
24153 TACCTTTTAT
Statistics
Matches: 284, Mismatches: 19, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
216 40 0.14
217 19 0.07
218 15 0.05
219 2 0.01
220 54 0.19
221 43 0.15
222 2 0.01
223 1 0.00
225 25 0.09
226 72 0.25
227 11 0.04
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.35
Consensus pattern (218 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAAC
CGGACCGACCCAAAAATATATATAATTTCGGGTCGGGTCAGATTAAGTCACTGTTTTTATTAAAT
AAAAATAAATTTTTATTATTTCGGTGGTCGGATCGGATTTCTAATTCATATATTCGAGTCGGGTA
GGATGAAACTTTATTTTGTTCAG
Found at i:24641 original size:33 final size:33
Alignment explanation
Indices: 24596--24681 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
24586 TCTGACATGT
* *
24596 CTGCGAACCAAACAGAATATCCAATTTCATTTC
1 CTGCCAACCAAACAGAATATCCAATTCCATTTC
* *
24629 TTGCCAACCAAACATAATATCCAATTCCATTTC
1 CTGCCAACCAAACAGAATATCCAATTCCATTTC
*
24662 CTGTCAACCAAACAGAATAT
1 CTGCCAACCAAACAGAATAT
24682 TAAATTGGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (33 bp):
CTGCCAACCAAACAGAATATCCAATTCCATTTC
Found at i:24725 original size:18 final size:17
Alignment explanation
Indices: 24690--24734 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
24680 ATTAAATTGG
24690 ATTCCAATT-CTTACAT
1 ATTCCAATTCCTTACAT
24706 ATTCCAATTCCTTCACAT
1 ATTCCAATTCCTT-ACAT
*
24724 ATTTCAATTCC
1 ATTCCAATTCC
24735 CTCATAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 9 0.35
17 3 0.12
18 14 0.54
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTCCAATTCCTTACAT
Found at i:33842 original size:21 final size:19
Alignment explanation
Indices: 33792--33843 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 19
33782 TTGTCTTCGA
33792 TTTTTTTCTTATTATTTTT
1 TTTTTTTCTTATTATTTTT
*
33811 TATTCTATTCTTATATATTTTAT
1 T-TT-TTTTCTTAT-TATTTT-T
33834 TTTTTTTCTT
1 TTTTTTTCTT
33844 TCTTTGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 2 0.07
21 14 0.52
22 8 0.30
23 2 0.07
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTATTATTTTT
Found at i:33966 original size:12 final size:12
Alignment explanation
Indices: 33946--34012 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
33936 TTTATTTTGA
33946 TTTATTTTATTAT
1 TTTA-TTTATTAT
*
33959 TTTATTTATTTT
1 TTTATTTATTAT
*
33971 TTTCTTTGATTTAT
1 TTTATTT-A-TTAT
33985 TTAATATTTATTAT
1 TT--TATTTATTAT
33999 TATTA-TTATTAT
1 T-TTATTTATTAT
34011 TT
1 TT
34013 CTAACATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
11 1 0.02
12 21 0.47
13 7 0.16
14 10 0.22
15 2 0.04
16 4 0.09
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.73
Consensus pattern (12 bp):
TTTATTTATTAT
Found at i:33967 original size:17 final size:17
Alignment explanation
Indices: 33937--34008 Score: 69
Period size: 17 Copynumber: 4.3 Consensus size: 17
33927 TTTTCATTCT
33937 TTATTTTGATTTATTTTA
1 TTATTTT-ATTTATTTTA
*
33955 TTATTTTATTTATTTTT
1 TTATTTTATTTATTTTA
* *
33972 TTCTTTGATTTA-TTTA
1 TTATTTTATTTATTTTA
*
33988 ATA-TTTA-TTATTATTA
1 TTATTTTATTTATT-TTA
34004 TTATT
1 TTATT
34009 ATTTCTAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
14 3 0.07
15 4 0.09
16 9 0.21
17 20 0.47
18 7 0.16
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (17 bp):
TTATTTTATTTATTTTA
Found at i:33969 original size:9 final size:9
Alignment explanation
Indices: 33936--34012 Score: 70
Period size: 9 Copynumber: 8.3 Consensus size: 9
33926 TTTTTCATTC
33936 TTTATTTTGA
1 TTTATTTT-A
33946 TTTATTTTA
1 TTTATTTTA
33955 -TTATTTTA
1 TTTATTTTA
33963 TTTATTTT-
1 TTTATTTTA
* *
33971 TTTCTTTGA
1 TTTATTTTA
33980 TTTATTTAATA
1 TTTATTT--TA
33991 TTTATTATTA
1 TTTATT-TTA
34001 -TTATTATTA
1 TTTATT-TTA
34010 TTT
1 TTT
34013 CTAACATTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
8 14 0.25
9 23 0.40
10 12 0.21
11 7 0.12
12 1 0.02
ACGTcount: A:0.23, C:0.01, G:0.03, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:37956 original size:95 final size:94
Alignment explanation
Indices: 37840--38032 Score: 264
Period size: 95 Copynumber: 2.0 Consensus size: 94
37830 TTATAAATTA
* * *
37840 TATATATACAATAAAGCTTGAGTTGTCCCTC-TAGAGCAATTGGTTAAACGCCTCGGA-TTTATG
1 TATATATACAATAAAGCTTGAGCTGTCCCTCAAAG-GCAATTGGTTAAACG-CTCCGACTTTATG
* *
37903 GATAATATTCAGCTAGCCTGATAAAGGTAAT
64 GATAAGATTCAGCTAACCTGATAAAGGTAAT
*
37934 TATACTATACAATAAAGTTTGAGCTGTCCCTCAAAGGCAATTGGTTAAACGCTCCGACTTTATGG
1 TATA-TATACAATAAAGCTTGAGCTGTCCCTCAAAGGCAATTGGTTAAACGCTCCGACTTTATGG
* * *
37999 ATAAGATTTAGCTAACCTGATAAATGTATT
65 ATAAGATTCAGCTAACCTGATAAAGGTAAT
38029 TATA
1 TATA
38033 AATTAAGTTG
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 9 0.10
95 76 0.87
96 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (94 bp):
TATATATACAATAAAGCTTGAGCTGTCCCTCAAAGGCAATTGGTTAAACGCTCCGACTTTATGGA
TAAGATTCAGCTAACCTGATAAAGGTAAT
Found at i:39370 original size:84 final size:84
Alignment explanation
Indices: 39216--40249 Score: 1037
Period size: 84 Copynumber: 12.4 Consensus size: 84
39206 TAAAGAAACT
* * * * * * *
39216 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAAGACTTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
* *
39281 GTCAGCTCAAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * * **
39300 ATTTACAACATAACTTAAATCGAGAAGAGCTATCTTCCAACAAAAGACCTTTGAGTTCGACTATG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
*
39365 CTCAGCTCCAAGGCATATC
66 CTCAGCTCCAAGGCACATC
* * *
39384 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
39449 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
39468 ATTTGCAGCATAACTTAAATCGAGAAGGGCTATC-TGC--C-AAAGACCCTCGAGTTCGATTATA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
* *
39529 CTCAGCTTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * * * * * *
39549 ATTTACAGTATAACTCAAGTCTAGAAGGGTTATCTGT-GACCTAAAGACTTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTAC
* * *
39613 GCTCAGCTCCAAGGCATATT
65 ACTCAGCTCCAAGGCACATC
* *
39633 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
39698 CTCAGCTCCAAGGCACATC
66 CTCAGCTCCAAGGCACATC
* * * * * *
39717 ATTTGCAGCATAGCTTAAATCGAGAAGGGCTATC-TGC--C-AAAGA-CTCTCGAGTTCAATTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCT-TCGAGTTCGACTAC
* * *
39777 ACTCAGCTTCGAGGGCACATA
65 ACTCAGC-TCCAAGGCACATC
* * *
39798 ATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGT-CAA-AAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTAC
*
39861 ACTCAGCTCCAAGGCATATC
65 ACTCAGCTCCAAGGCACATC
*
39881 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGT-CAACCAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTAC
*
39945 GCTCAGCTCCAAGGCACATC
65 ACTCAGCTCCAAGGCACATC
* * * * * *
39965 ATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATC-TGC--C-AAAG-CCCTCGAGTTCGATTAAA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
* *
40025 CTCAGCGTCGAGGGCACATC
66 CTCAGC-TCCAAGGCACATC
* * * * * *
40045 ATTTTCAACATAACTCAAGGCTAAAAGGGTTATCTGT-CAACAAAAGACCTTCGAGTTCGACTAC
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT-TCCAACAAAAGACCTTCGAGTTCGACTAC
* * *
40109 GCTTAGCTCCAAGGTACATC
65 ACTCAGCTCCAAGGCACATC
* * * * * * *
40129 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCGACCAAATACCTTCGAGTTCGATTACA
1 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
* *
40194 CTTAGCT-CAGAGGCAAATC
66 CTCAGCTCCA-AGGCACATC
* * * * *
40213 AGATTTACAACATAACTCAAGGCAAGAAGGGTTATCT
1 --ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
40250 GTCAATAAAT
Statistics
Matches: 784, Mismatches: 138, Indels: 54
0.80 0.14 0.06
Matches are distributed among these distances:
79 22 0.03
80 91 0.12
81 81 0.10
82 3 0.00
83 54 0.07
84 460 0.59
85 45 0.06
86 28 0.04
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (84 bp):
ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTTCCAACAAAAGACCTTCGAGTTCGACTACA
CTCAGCTCCAAGGCACATC
Found at i:39845 original size:333 final size:328
Alignment explanation
Indices: 39216--40251 Score: 1091
Period size: 333 Copynumber: 3.1 Consensus size: 328
39206 TAAAGAAACT
* * * *
39216 ATTTGCAGCATAACTCAAGGCTATAAGGGTTATCTGCCAACAAAAGACTTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTG-TAACCAAAGACTTTCGAGTTCGACTACG
* * * * * * * *
39281 GTCAGCTCAAAGGCACATCATTTACAACATAACTTAAATCGAGAAGAGCTATCTTCCAACAAAAG
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* ** * *
39346 ACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAG
130 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAG
* * * *
39411 GGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
195 GGCTATCTG---ACCAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATAATTTGCAG
* * * * * * *
39476 CATAACTTAAATCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTATACTCAGCTTCGAG
257 CATAACTCAAAGCGAGAAGGGCTATCTGCAAAAGACCCTCGAGTTCGACTACACTCAGC-TCCAA
39541 GGCACATC
321 GGCACATC
* * *
39549 ATTTACAGTATAACTCAAGTCTAGAAGGGTTATCTGTGACCTAAAGACTTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTAACC-AAAGACTTTCGAGTTCGACTACG
* * *
39614 CTCAGCTCCAAGGCATATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
*
39679 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAATCGAGAAG
130 ACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAG
* * *
39744 GGCTATCTG-CCAAAGA-CTCTCGAGTTCAATTACACTCAGCTTCGAGGGCACATAATTTGCAGC
195 GGCTATCTGACCAAAGACCT-TCGAGTTCAACTACACTCAGC-TCCAAGGCACATAATTTGCAGC
* * * *
39807 ATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAGACCTTCGAGTTCGACTACACTCAGCTCCA
258 ATAACTCAAAGCGAGAAGGGCTATCTG-C--AAAAGACCCTCGAGTTCGACTACACTCAGCTCCA
*
39872 AGGCATATC
320 AGGCACATC
* * *
39881 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCAACCAAAGACCTTCGAGTTCGACTACG
1 ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGT-AACCAAAGACTTTCGAGTTCGACTACG
* *
39946 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGTTATCTG-C--C-AAAG
65 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAG
* * * * * * * * ** * *
40007 -CCCTCGAGTTCGATTAAACTCAGCGTCGAGGGCACATCATTTTCAACATAACTCAAGGCTAAAA
130 ACCTTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAA
* * * * * * *
40071 GGGTTATCTGTCAACAAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGGTACATCATTTGCA
194 GGGCTATCTG---ACCAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATAATTTGCA
* * * * * *
40136 GCATAGCT-TAAGTCGAGAAGGGCTATCTGCCGACCAAATACCTTCGAGTTCGATTACACTTAGC
256 GCATAACTCAAAG-CGAGAAGGGCTATCTG-C-A--AAAGACCCTCGAGTTCGACTACACTCAGC
*
40200 T-CAGAGGCAAATC
316 TCCA-AGGCACATC
* * * *
40213 AGATTTACAACATAACTCAAGGCAAGAAGGGTTATCTGT
1 --ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGT
40252 CAATAAATTT
Statistics
Matches: 592, Mismatches: 92, Indels: 37
0.82 0.13 0.05
Matches are distributed among these distances:
327 21 0.04
328 44 0.07
329 26 0.04
330 44 0.07
331 42 0.07
332 176 0.30
333 207 0.35
334 32 0.05
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (328 bp):
ATTTGCAGCATAACTCAAGTCTAGAAGGGTTATCTGTAACCAAAGACTTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACAAAAGA
CCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAATCGAGAAGG
GCTATCTGACCAAAGACCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATAATTTGCAGCATA
ACTCAAAGCGAGAAGGGCTATCTGCAAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCAC
ATC
Found at i:39967 original size:248 final size:248
Alignment explanation
Indices: 39292--40188 Score: 1384
Period size: 249 Copynumber: 3.6 Consensus size: 248
39282 TCAGCTCAAA
* * ** * * * *
39292 GGCACATCATTTACAACATAACTTAAATCGAGAAGAGCTATCT-TCCAACAAAAGACCTTTGAGT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGT-CAA-AAAAGACCTTCGAGT
*
39356 TCGACTATGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
64 TCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
*
39421 CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAA
129 CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAA
*
39486 ATCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTATACTCAGCTTCGAG
194 ATCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAAACTCAGCTTCGAG
* * * ** *
39541 GGCACATCATTTACAGTATAACTCAAGTCTAGAAGGGTTATCTGTGACCTAAAGACTTTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA-AAAAAGACCTTCGAGTT
*
39606 CGACTACGCTCAGCTCCAAGGCATATTATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC
65 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC
*
39671 AACCAAAGACCTTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAA
130 AACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAA
* * *
39736 TCGAGAAGGGCTATCTGCCAAAGACTCTCGAGTTCAATTACACTCAGCTTCGAG
195 TCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAAACTCAGCTTCGAG
* *
39790 GGCACATAATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAGACCTTCGAGTTC
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAGACCTTCGAGTTC
* *
39855 GACTACACTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGTCA
66 GACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
*
39920 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGT
131 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAAT
* * *
39985 CAAGAAGGGTTATCTGCCAAAG-CCCTCGAGTTCGATTAAACTCAGCGTCGAG
196 CGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAAACTCAGCTTCGAG
* * *
40037 GGCACATCATTTTCAACATAACTCAAGGCTAAAAGGGTTATCTGTCAACAAAAGACCTTCGAGTT
1 GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAA-AAAAGACCTTCGAGTT
* * * * *
40102 CGACTACGCTTAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC
65 CGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC
* *
40167 GACCAAATACCTTCGAGTTCGA
130 AACCAAAGACCTTCGAGTTCGA
40189 TTACACTTAG
Statistics
Matches: 594, Mismatches: 51, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
247 70 0.12
248 254 0.43
249 269 0.45
250 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (248 bp):
GGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAAAAAAGACCTTCGAGTTC
GACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAAT
CGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTAAACTCAGCTTCGAG
Found at i:41803 original size:10 final size:10
Alignment explanation
Indices: 41788--41833 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
41778 TGTCTTTGAT
41788 TTTTTTCTTA
1 TTTTTTCTTA
41798 TTTTTTCTTA
1 TTTTTTCTTA
*
41808 TTATATTCTTA
1 TT-TTTTCTTA
*
41819 TTTATT-TTA
1 TTTTTTCTTA
41828 TTTTTT
1 TTTTTT
41834 TCTTTCTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
9 8 0.24
10 16 0.48
11 9 0.27
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCTTA
Found at i:41860 original size:61 final size:58
Alignment explanation
Indices: 41770--41895 Score: 132
Period size: 61 Copynumber: 2.1 Consensus size: 58
41760 TATTTTTTCC
* * *
41770 TTTTTTGTTGTCTTTGATTTTTTTCTTA-T-TTTTTCTTATTATATTCTTATTTATTTTAT
1 TTTTTTCTTGTCTTTGATTTTTTTCTTATTATTTTTCTTATT-T-TTC-AATTTATTTAAT
*
41829 TTTTTTCTT-TCTTTGATTAATTGTTTTTTATTTATTTTTCTTATTTTTCAATTTATTTAAT
1 TTTTTTCTTGTCTTTGATT--TT-TTTCTTA-TTATTTTTCTTATTTTTCAATTTATTTAAT
41890 TTTTTT
1 TTTTTT
41896 GTTTAATCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
58 9 0.16
59 8 0.14
60 2 0.04
61 22 0.39
62 3 0.05
63 2 0.04
64 11 0.19
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (58 bp):
TTTTTTCTTGTCTTTGATTTTTTTCTTATTATTTTTCTTATTTTTCAATTTATTTAAT
Found at i:41975 original size:16 final size:16
Alignment explanation
Indices: 41932--41981 Score: 73
Period size: 16 Copynumber: 3.0 Consensus size: 16
41922 TTTTTCGTTC
41932 TTTCTTTTGATTTATTT
1 TTTC-TTTGATTTATTT
*
41949 TATTATTTGATTTATTT
1 T-TTCTTTGATTTATTT
41966 TTTCTTTGATTTATTT
1 TTTCTTTGATTTATTT
41982 AATATTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 14 0.47
17 14 0.47
18 2 0.07
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTCTTTGATTTATTT
Found at i:44401 original size:60 final size:60
Alignment explanation
Indices: 44321--44491 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 60
44311 TATAACTCCA
* * * * * *
44321 ATTT-TAAATTGGTCCTTAAACTTTTAAATATTTTAATTTCATCCTCAAATTATG-TCTCT
1 ATTTCTAAATTAGTCTTTAAACTTTGAAATATTCTAATTTCATCCCCAAATTATGAAC-CT
* *
44380 CA-TTCTAAATTAGTCTTTAAACTTTGAAACATTCTAATTTCATCCCCAAACTATGAACCT
1 -ATTTCTAAATTAGTCTTTAAACTTTGAAATATTCTAATTTCATCCCCAAATTATGAACCT
*
44440 ATTTCTAAATTAGT-TCTCAAACATTTGAAAT-TTCTAATTTCATCCCCAAATT
1 ATTTCTAAATTAGTCT-TTAAAC-TTTGAAATATTCTAATTTCATCCCCAAATT
44492 CATCCAAATA
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
59 4 0.04
60 83 0.87
61 8 0.08
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (60 bp):
ATTTCTAAATTAGTCTTTAAACTTTGAAATATTCTAATTTCATCCCCAAATTATGAACCT
Found at i:44430 original size:29 final size:29
Alignment explanation
Indices: 44398--44489 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
44388 ATTAGTCTTT
44398 AAACTTTGAAACATTCTAATTTCATCCCC
1 AAACTTTGAAACATTCTAATTTCATCCCC
* * * * *
44427 AAACTATGAACCTATTTCTAAATT-AGTTCTC
1 AAACTTTGAAAC-A-TTCTAATTTCA-TCCCC
*
44458 AAACATTTGAAA-TTTCTAATTTCATCCCC
1 AAAC-TTTGAAACATTCTAATTTCATCCCC
44487 AAA
1 AAA
44490 TTCATCCAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
29 24 0.51
30 3 0.06
31 15 0.32
32 5 0.11
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (29 bp):
AAACTTTGAAACATTCTAATTTCATCCCC
Done.