Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002442.1 Hibiscus syriacus cultivar Beakdansim tig00004998_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: 75641
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3718 original size:65 final size:64
Alignment explanation
Indices: 3585--3741 Score: 230
Period size: 65 Copynumber: 2.4 Consensus size: 64
3575 TGCACTAAGG
* * *
3585 GTGCATCGATGCATAAAATGCATTTGATGTTTAAAAATAGCCTGAGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATATTTAAAAATAGCCCGAGTGCATCGATGCATGGCTT
3649 GTGCATCGATGCATAAAATGCATTCGATAATTTCATAAAA-A-CCCGAGTGCATCGATGCATGG-
1 GTGCATCGATGCATAAAATGCATTCGAT-ATTT-A-AAAATAGCCCGAGTGCATCGATGCATGGC
3711 TAT
63 T-T
3714 GTGCATCGATGCATAAAATGCATTCGAT
1 GTGCATCGATGCATAAAATGCATTCGAT
3742 GTTCAATTTA
Statistics
Matches: 86, Mismatches: 3, Indels: 7
0.90 0.03 0.07
Matches are distributed among these distances:
64 28 0.33
65 52 0.60
66 2 0.02
67 4 0.05
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATATTTAAAAATAGCCCGAGTGCATCGATGCATGGCTT
Found at i:3783 original size:65 final size:64
Alignment explanation
Indices: 3585--3786 Score: 202
Period size: 65 Copynumber: 3.1 Consensus size: 64
3575 TGCACTAAGG
* ** * *
3585 GTGCATCGATGCATAAAATGCATTTGATGTTTAA-AAATAGC-CTGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTAATTTATAACAATGAGTGCATCGATGCATGG-T
3648 T
64 T
* *
3649 GTGCATCGATGCATAAAATGCATTCGA---TAATTTCATAAAAACCCGAGTGCATCGATGCATGG
1 GTGCATCGATGCATAAAATGCATTCGATGTTAATTT-ATAACAA--TGAGTGCATCGATGCATGG
3711 TAT
63 T-T
*
3714 GTGCATCGATGCATAAAATGCATTCGATGTTCAATTTAT-TCAATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTT-AATTTATAACAATGAGTGCATCGATGCATGG-T
3777 T
64 T
3778 GGTGCATCG
1 -GTGCATCG
3787 GTACACTCTT
Statistics
Matches: 116, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
60 3 0.03
62 3 0.03
64 44 0.38
65 56 0.48
67 2 0.02
68 3 0.03
69 5 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTAATTTATAACAATGAGTGCATCGATGCATGGTT
Found at i:10743 original size:27 final size:26
Alignment explanation
Indices: 10713--10777 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 26
10703 TTCCTTAATC
10713 TTTAACTGATGATATCATGACATATAA
1 TTTAA-TGATGATATCATGACATATAA
*
10740 TTT-A-GATGATATCATGTCATATAA
1 TTTAATGATGATATCATGACATATAA
*
10764 TATAGATGATGATA
1 TTTA-ATGATGATA
10778 ATCAATGCAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 21 0.64
26 2 0.06
27 10 0.30
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (26 bp):
TTTAATGATGATATCATGACATATAA
Found at i:10752 original size:24 final size:24
Alignment explanation
Indices: 10720--10773 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
10710 ATCTTTAACT
*
10720 GATGATATCATGACATATAATTTA
1 GATGATATCATGACATATAATATA
*
10744 GATGATATCATGTCATATAATATA
1 GATGATATCATGACATATAATATA
10768 GATGAT
1 GATGAT
10774 GATAATCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (24 bp):
GATGATATCATGACATATAATATA
Found at i:13203 original size:42 final size:42
Alignment explanation
Indices: 13154--13282 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 42
13144 GCATGAGACA
*
13154 GAGGTTGAGAAGT-TGAAAATTGAGACTGAGGGTGCTCAGGGT
1 GAGGTTGAGAAGTCT-AAAACTGAGACTGAGGGTGCTCAGGGT
** * *
13196 GAGGTTGAGAAGTCTAAAACTGAGGGTGAGGGTGCTGATGGT
1 GAGGTTGAGAAGTCTAAAACTGAGACTGAGGGTGCTCAGGGT
* ** * *
13238 GAGGTTGAAAAGTC-AACAA-TGAGGGTGAGGGTTCTAAGGGT
1 GAGGTTGAGAAGTCTAA-AACTGAGACTGAGGGTGCTCAGGGT
13279 GAGG
1 GAGG
13283 CTGATAGTGA
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 25 0.33
42 50 0.66
43 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.42, T:0.22
Consensus pattern (42 bp):
GAGGTTGAGAAGTCTAAAACTGAGACTGAGGGTGCTCAGGGT
Found at i:13942 original size:40 final size:41
Alignment explanation
Indices: 13886--13977 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 41
13876 ATTGTTCAAT
* * * *
13886 AACTTTATGTGTTTTGTCAAATCTTGAATGGAAA-TATGGTC
1 AACTTTATATATTTTGT-AAATATTGAATGAAAATTATGGTC
* *
13927 -ACTTTATATATTTTGTTAATATTGAATGAAAATTTTGGTC
1 AACTTTATATATTTTGTAAATATTGAATGAAAATTATGGTC
*
13967 AAGTTTATATA
1 AACTTTATATA
13978 ACCGTAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
39 13 0.31
40 20 0.48
41 9 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.46
Consensus pattern (41 bp):
AACTTTATATATTTTGTAAATATTGAATGAAAATTATGGTC
Found at i:14890 original size:38 final size:38
Alignment explanation
Indices: 14812--14909 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
14802 TAAAATCGAA
* *
14812 AAGAACTCTAAAAACAAATT-GTGAAAATACACAAACG
1 AAGAACCCTAGAAACAAATTCGTGAAAATACACAAACG
* * * *
14849 AAGAATCCT-GCAAACAAATTCGTTAAAGTACCCAAACG
1 AAGAACCCTAG-AAACAAATTCGTGAAAATACACAAACG
14887 AAGAACCCTAGAAACAAATTCGT
1 AAGAACCCTAGAAACAAATTCGT
14910 CAAATTGCCC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 16 0.31
38 34 0.67
39 1 0.02
ACGTcount: A:0.50, C:0.20, G:0.12, T:0.17
Consensus pattern (38 bp):
AAGAACCCTAGAAACAAATTCGTGAAAATACACAAACG
Found at i:14921 original size:38 final size:38
Alignment explanation
Indices: 14812--14922 Score: 118
Period size: 38 Copynumber: 2.9 Consensus size: 38
14802 TAAAATCGAA
* * * *
14812 AAGAACTCTAAAAACAAATT-GTGAAAATACACAAACG
1 AAGAACCCTAGAAACAAATTCGTCAAAATACCCAAACG
* * *
14849 AAGAATCCT-GCAAACAAATTCGTTAAAGTACCCAAACG
1 AAGAACCCTAG-AAACAAATTCGTCAAAATACCCAAACG
* *
14887 AAGAACCCTAGAAACAAATTCGTCAAATTGCCCAAA
1 AAGAACCCTAGAAACAAATTCGTCAAAATACCCAAA
14923 AGAAATCGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
37 16 0.26
38 44 0.72
39 1 0.02
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.17
Consensus pattern (38 bp):
AAGAACCCTAGAAACAAATTCGTCAAAATACCCAAACG
Found at i:15277 original size:29 final size:29
Alignment explanation
Indices: 15232--15298 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
15222 TAACGGCAGA
*
15232 AAACATTATGTAGTTAATCGATAATTTTT
1 AAACATTATGTAATTAATCGATAATTTTT
15261 AAACATTATGTAATTAATCGATAATTTTT
1 AAACATTATGTAATTAATCGATAATTTTT
*
15290 AAACTTTAT
1 AAACATTAT
15299 ATATGAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (29 bp):
AAACATTATGTAATTAATCGATAATTTTT
Found at i:25019 original size:22 final size:22
Alignment explanation
Indices: 24990--25059 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
24980 TGGTGTATCA
* *
24990 TATC-ACATGGTAATGATAAGT
1 TATCTACATTGTAATGATAAGC
** *
25011 TATCTACATTGTAATGACGAGG
1 TATCTACATTGTAATGATAAGC
*
25033 TATCTAAATTTGTAATGATAAGC
1 TATCTACA-TTGTAATGATAAGC
25056 TATC
1 TATC
25060 GCATATCAAG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 4 0.10
22 20 0.51
23 15 0.38
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (22 bp):
TATCTACATTGTAATGATAAGC
Found at i:30445 original size:15 final size:15
Alignment explanation
Indices: 30427--30503 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
30417 TTGGTCATTT
*
30427 TTTATATTTTTATCA
1 TTTATATTTTTATTA
*
30442 TTTATATGTTTAAATTA
1 TTTATAT-TTT-TATTA
* *
30459 -GTATTTTATTTATTTA
1 TTTATATT-TTTA-TTA
* *
30475 TTCATATATTTATTA
1 TTTATATTTTTATTA
30490 TTTATATTTTTATT
1 TTTATATTTTTATT
30504 CACTAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
15 24 0.52
16 16 0.35
17 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTATATTTTTATTA
Found at i:30497 original size:29 final size:28
Alignment explanation
Indices: 30460--30516 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
30450 TTTAAATTAG
30460 TATTTTATTTATTTATTCA-T-ATATTTAT
1 TATTTTA-TT-TTTATTCACTAATATTTAT
30488 TATTTATATTTTTATTCACTAATATTTAT
1 TATTT-TATTTTTATTCACTAATATTTAT
30517 ATGAAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 10 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTTATTTTTATTCACTAATATTTAT
Found at i:30501 original size:27 final size:29
Alignment explanation
Indices: 30463--30516 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
30453 AAATTAGTAT
30463 TTTATTTATTTATTCA-T-ATATTTATTA
1 TTTATTTATTTATTCACTAATATTTATTA
30490 TTTATATT-TTTATTCACTAATATTTAT
1 TTTAT-TTATTTATTCACTAATATTTAT
30517 ATGAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 8 0.33
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATTTATTTATTCACTAATATTTATTA
Found at i:32991 original size:14 final size:14
Alignment explanation
Indices: 32953--33006 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
32943 ATTTTAAATA
*
32953 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
32967 TTTTACATTTGCAT
1 ATTTACATTTGCAT
32981 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
32996 CTTTGCATTTG
1 ATTTACATTTG
33007 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:40290 original size:22 final size:22
Alignment explanation
Indices: 40259--40313 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
40249 ATCTACACTC
**
40259 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
40281 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
40303 TTCAAAGATGA
1 TTCAAAGATGA
40314 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:41053 original size:112 final size:112
Alignment explanation
Indices: 40715--41259 Score: 698
Period size: 112 Copynumber: 4.9 Consensus size: 112
40705 AGCAAAGTTC
* * * * *
40715 AAATCCATCATTCAATGGATCAACA-TTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
40779 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * *
40827 AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
40892 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * * *
40940 AAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
41005 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
** * * * *
41052 AAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
41117 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCT
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
* * * *** * * *
41164 GAATTCATCACTT-GATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA
1 AAATTCATCA-TTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAA
*
41228 GAGGAAGAAGAAGTTCATAATGAGAAGAACTT
65 GAAGAAGAAGAAGTTCATAATGAGAAGAACTT
41260 ATCTGAAGAG
Statistics
Matches: 382, Mismatches: 49, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
112 244 0.64
113 138 0.36
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTT
Found at i:41236 original size:19 final size:19
Alignment explanation
Indices: 41212--41275 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
41202 TTCATAATGA
41212 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
41231 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
41251 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
41270 GAAGAA
1 GAAGAA
41276 GAAGTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:41238 original size:22 final size:22
Alignment explanation
Indices: 41211--41278 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
41201 GTTCATAATG
41211 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
41233 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
41250 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
41272 AGAAGAA
1 AGAAGAA
41279 GTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:41253 original size:39 final size:39
Alignment explanation
Indices: 41199--41298 Score: 200
Period size: 39 Copynumber: 2.6 Consensus size: 39
41189 TTTCCAGAGA
41199 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
41238 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
41277 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
41299 GTTTAACCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 61 1.00
ACGTcount: A:0.46, C:0.08, G:0.24, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:41257 original size:151 final size:151
Alignment explanation
Indices: 41088--41407 Score: 534
Period size: 151 Copynumber: 2.1 Consensus size: 151
41078 TGCCAGTTAG
*
41088 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
***
41153 ACCTTTTCC-CTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
41217 ACTTATCTGAAGAGGAAGAAGA
130 ACTTATCTGAAGAGGAAGAAGA
* * *
41239 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* *
41304 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
41369 CTTATCTGAAGAGGAAGAAGA
131 CTTATCTGAAGAGGAAGAAGA
*
41390 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
41408 TTTGTTTAAC
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
151 157 0.99
152 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGA
Found at i:41277 original size:263 final size:264
Alignment explanation
Indices: 40976--41519 Score: 856
Period size: 263 Copynumber: 2.1 Consensus size: 264
40966 TACCAGTTAG
*
40976 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** *
41041 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
41106 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
** * *
41171 TCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAG
196 TCACTTGATGAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
41235 AAGA
261 AAGA
* * *
41239 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* ** * * *
41304 ACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
* * *
41369 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
*
41434 TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
196 TCACTTGATGAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
41499 AAGA
261 AAGA
41503 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
41520 GCTTGTTCAA
Statistics
Matches: 255, Mismatches: 25, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
263 228 0.89
264 27 0.11
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATTCATCACCCGATGGATCAACAGTGCCAGAGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
TCACTTGATGAATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
AAGA
Found at i:41435 original size:112 final size:112
Alignment explanation
Indices: 41238--41534 Score: 506
Period size: 112 Copynumber: 2.6 Consensus size: 112
41228 GAGGAAGAAG
41238 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
41303 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
66 AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
* *
41350 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
*
41415 AACCTTTTGC-CTGAATTCATCACTTGATGGATTAACTTTTCCAGAGA
66 AACCTTTTGCTC-GAATTCATCACTTGATGGATTAACATTTCCAGAGA
* * *
41462 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
41527 CAACCTTT
65 TAACCTTT
41535 GTTTGATGCT
Statistics
Matches: 174, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
111 1 0.01
112 135 0.78
113 38 0.22
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTTGCTCGAATTCATCACTTGATGGATTAACATTTCCAGAGA
Found at i:42984 original size:15 final size:15
Alignment explanation
Indices: 42966--43042 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
42956 TTGGTCATTT
*
42966 TTTATATTTTTATCA
1 TTTATATTTTTATTA
*
42981 TTTATATGTTTAAATTA
1 TTTATAT-TTT-TATTA
* *
42998 -GTATTTTATTTATTTA
1 TTTATATT-TTTA-TTA
* *
43014 TTCATATATTTATTA
1 TTTATATTTTTATTA
43029 TTTATATTTTTATT
1 TTTATATTTTTATT
43043 CACTAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
15 24 0.52
16 16 0.35
17 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTATATTTTTATTA
Found at i:43036 original size:29 final size:28
Alignment explanation
Indices: 42999--43055 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
42989 TTTAAATTAG
42999 TATTTTATTTATTTATTCA-T-ATATTTAT
1 TATTTTA-TT-TTTATTCACTAATATTTAT
43027 TATTTATATTTTTATTCACTAATATTTAT
1 TATTT-TATTTTTATTCACTAATATTTAT
43056 ATGAAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 10 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTTATTTTTATTCACTAATATTTAT
Found at i:43040 original size:27 final size:29
Alignment explanation
Indices: 43002--43055 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
42992 AAATTAGTAT
43002 TTTATTTATTTATTCA-T-ATATTTATTA
1 TTTATTTATTTATTCACTAATATTTATTA
43029 TTTATATT-TTTATTCACTAATATTTAT
1 TTTAT-TTATTTATTCACTAATATTTAT
43056 ATGAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 8 0.33
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATTTATTTATTCACTAATATTTATTA
Found at i:46276 original size:17 final size:18
Alignment explanation
Indices: 46239--46278 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
46229 TTGTTCAATG
46239 AGTATTGATACTATTGCAT
1 AGTATTGATACTA-TGCAT
46258 AGTATTGATACTA-GCAT
1 AGTATTGATACTATGCAT
46275 AGTA
1 AGTA
46279 ATTTAGATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
19 13 0.62
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (18 bp):
AGTATTGATACTATGCAT
Found at i:46468 original size:21 final size:21
Alignment explanation
Indices: 46425--46477 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
46415 CTCGGGGAAA
46425 TATCGATACCTCAATAAAGGAG
1 TATCGATA-CTCAATAAAGGAG
*
46447 TATCGATACTCAAGTTAA-GAG
1 TATCGATACTCAA-TAAAGGAG
46468 TATCGATACT
1 TATCGATACT
46478 ACCTAGTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
TATCGATACTCAATAAAGGAG
Found at i:58113 original size:17 final size:17
Alignment explanation
Indices: 58072--58111 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
58062 TTAAATTTAA
*
58072 ATTTTTTAAAAAATAAT
1 ATTTTTTAATAAATAAT
58089 ATTTTTTAATAAA-AAT
1 ATTTTTTAATAAATAAT
58105 ATTTTTT
1 ATTTTTT
58112 TATATAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTAATAAATAAT
Found at i:58118 original size:18 final size:19
Alignment explanation
Indices: 58072--58119 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
58062 TTAAATTTAA
58072 ATTTTTT-A-AAAAATAAT
1 ATTTTTTAATAAAAATAAT
58089 ATTTTTTAATAAAAAT-AT
1 ATTTTTTAATAAAAATAAT
58107 -TTTTTTATATAAA
1 ATTTTTTA-ATAAA
58120 TCTAATATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.50
18 8 0.29
19 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTTTTAATAAAAATAAT
Found at i:58394 original size:21 final size:21
Alignment explanation
Indices: 58370--58411 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
58360 TGATAAAAAA
58370 TTATCGAAAATATTATTATTT
1 TTATCGAAAATATTATTATTT
***
58391 TTATCGATTTTATTATTATTT
1 TTATCGAAAATATTATTATTT
58412 GATACTTTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TTATCGAAAATATTATTATTT
Found at i:58458 original size:21 final size:21
Alignment explanation
Indices: 58434--58477 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
58424 TAAATATTAA
*
58434 AAAAATATTAATATTTTAAGT
1 AAAAATAATAATATTTTAAGT
*
58455 AAAAATAATAATATTTTACGT
1 AAAAATAATAATATTTTAAGT
58476 AA
1 AA
58478 TTTTTACCGA
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:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:58955 original size:13 final size:13
Alignment explanation
Indices: 58937--58961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58927 CGAAAAAATC
58937 ATTTTTTTACCGG
1 ATTTTTTTACCGG
58950 ATTTTTTTACCG
1 ATTTTTTTACCG
58962 CGTTTACCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTTTTTTACCGG
Found at i:66230 original size:29 final size:29
Alignment explanation
Indices: 66175--66251 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
66165 TGCATTCCTA
* *
66175 ATTCTGCATGGGATTATATCCCCGTCTTG
1 ATTCTGCATGGGATTATATACACGTCTTG
* *
66204 ATTCTGCATGGGATTATATATATGTCTTG
1 ATTCTGCATGGGATTATATACACGTCTTG
* * * *
66233 TTTTTACATGGGATCATAT
1 ATTCTGCATGGGATTATAT
66252 TCCTGTCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (29 bp):
ATTCTGCATGGGATTATATACACGTCTTG
Found at i:68137 original size:24 final size:26
Alignment explanation
Indices: 68099--68146 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
68089 AAGTGAGTAA
68099 CTATAGACTCTTTC-AGT-AGATTAC
1 CTATAGACTCTTTCAAGTAAGATTAC
68123 CTATA-ACTCTGTTCAAGTAAGATT
1 CTATAGACTCT-TTCAAGTAAGATT
68147 TAGTATGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 8 0.38
25 3 0.14
26 5 0.24
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (26 bp):
CTATAGACTCTTTCAAGTAAGATTAC
Found at i:72999 original size:2 final size:2
Alignment explanation
Indices: 72994--73029 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
72984 ACACACACAC
72994 AT AT AT AT AT 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 AT AT AT AT AT
73030 TTGAAGCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75070 original size:23 final size:22
Alignment explanation
Indices: 75044--75090 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
75034 TTTAAACAAA
75044 TTAAGATAAGAACAAAATATATT
1 TTAAGATAAGAA-AAAATATATT
* * *
75067 TTAAGGTACGAAAAAATATTTT
1 TTAAGATAAGAAAAAATATATT
75089 TT
1 TT
75091 TAACTTAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.49, C:0.04, G:0.11, T:0.36
Consensus pattern (22 bp):
TTAAGATAAGAAAAAATATATT
Found at i:75124 original size:25 final size:22
Alignment explanation
Indices: 75095--75144 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 22
75085 TTTTTTTAAC
75095 TTAAGATAATTATAAAAAATATTAT
1 TTAAGATAA--ATAAAAAATA-TAT
* *
75120 TTAAGTTAAATAAAATATATAT
1 TTAAGATAAATAAAAAATATAT
75142 TTA
1 TTA
75145 TTTTTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 6 0.26
23 9 0.39
25 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
TTAAGATAAATAAAAAATATAT
Found at i:75249 original size:5 final size:5
Alignment explanation
Indices: 75239--75419 Score: 288
Period size: 5 Copynumber: 37.4 Consensus size: 5
75229 GAGTTTAAAT
75239 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATAATA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A-A TATAA
75290 TATAA TATAA TAT-A TATAA TATAA TAT-A TATAA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
75337 TATAA TAT-A TATAA TATAA TATAA TATAA TAT-A TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
75385 TAT-A TATAA TATAA TA-AA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TA
75420 ACGTTGTCAA
Statistics
Matches: 166, Mismatches: 0, Indels: 20
0.89 0.00 0.11
Matches are distributed among these distances:
4 32 0.19
5 129 0.78
6 1 0.01
7 4 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:75412 original size:33 final size:34
Alignment explanation
Indices: 75239--75419 Score: 278
Period size: 33 Copynumber: 5.2 Consensus size: 34
75229 GAGTTTAAAT
75239 TATAATATAATATAATATAATATAATATAATATAA
1 TATAATAT-ATATAATATAATATAATATAATATAA
75274 TATATATAATATATAATATAATATAATAT-ATATAA
1 TATA-AT-ATATATAATATAATATAATATAATATAA
75309 TATAATATATATAATATAATATAATATATATAATATA
1 TATAATATATATAATATAATATAATATA-AT-ATA-A
75346 TATAATATAATATAATATAATAT-ATATAATATAA
1 TATAATAT-ATATAATATAATATAATATAATATAA
75380 TATAATATATATAATATAATA-AATATAATATAA
1 TATAATATATATAATATAATATAATATAATATAA
75413 TATAATA
1 TATAATA
75420 ACGTTGTCAA
Statistics
Matches: 138, Mismatches: 0, Indels: 18
0.88 0.00 0.12
Matches are distributed among these distances:
33 52 0.38
34 11 0.08
35 19 0.14
36 26 0.19
37 16 0.12
38 14 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
TATAATATATATAATATAATATAATATAATATAA
Found at i:75420 original size:19 final size:20
Alignment explanation
Indices: 75239--75419 Score: 288
Period size: 19 Copynumber: 9.3 Consensus size: 20
75229 GAGTTTAAAT
75239 TATAATATAATATAATATAA
1 TATAATATAATATAATATAA
75259 TATAATATAATATAATAT-A
1 TATAATATAATATAATATAA
75278 TATAATATATAATATAATATAA
1 TAT-A-ATATAATATAATATAA
75300 TAT-ATATAATATAATAT-A
1 TATAATATAATATAATATAA
75318 TATAATATAATATAATAT-A
1 TATAATATAATATAATATAA
75337 TATAATAT-ATATAATATAA
1 TATAATATAATATAATATAA
75356 TATAATATAATAT-ATATAA
1 TATAATATAATATAATATAA
75375 TATAATATAATAT-ATATAA
1 TATAATATAATATAATATAA
75394 TATAATA-AATATAATATAA
1 TATAATATAATATAATATAA
75413 TATAATA
1 TATAATA
75420 ACGTTGTCAA
Statistics
Matches: 154, Mismatches: 0, Indels: 15
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.12
19 95 0.62
20 23 0.15
21 14 0.09
22 4 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATAATATAATATAATATAA
Done.