Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000146.1 Hibiscus syriacus cultivar Beakdansim tig00000261_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: 68311
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:3926 original size:26 final size:26
Alignment explanation
Indices: 3879--3928 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3869 AGCATTTTTA
*
3879 TTTTACTTGTTCATTTTTTTGTATAG
1 TTTTACTTGTTCATTTTCTTGTATAG
3905 TTTTACTTGTT-ATTTTCCTTGTAT
1 TTTTACTTGTTCATTTT-CTTGTAT
3929 TTTTCAGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (26 bp):
TTTTACTTGTTCATTTTCTTGTATAG
Found at i:3931 original size:11 final size:12
Alignment explanation
Indices: 3876--3931 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
3866 CAAAGCATTT
3876 TTATTTTACTTG
1 TTATTTTACTTG
*
3888 TTCATTTT-TTTG
1 TT-ATTTTACTTG
3900 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
3914 TTATTTTCCTTG
1 TTATTTTACTTG
3926 -TATTTT
1 TTATTTT
3932 TCAGGTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.16
12 15 0.41
13 12 0.32
14 4 0.11
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:9315 original size:20 final size:22
Alignment explanation
Indices: 9287--9328 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9277 ATACTACCAC
9287 CATTCCA-TTT-CCACATCATT
1 CATTCCATTTTACCACATCATT
*
9307 CATTTCATTTTACCACATCATT
1 CATTCCATTTTACCACATCATT
9329 ATCATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 3 0.16
22 10 0.53
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (22 bp):
CATTCCATTTTACCACATCATT
Found at i:9904 original size:21 final size:21
Alignment explanation
Indices: 9878--9929 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
9868 ACTATTTTTT
9878 TAGTTAA-AAGTTATTTATGAA
1 TAGTTAACAA-TTATTTATGAA
9899 TAGTTAACAATTATTTATGAA
1 TAGTTAACAATTATTTATGAA
*
9920 AAGTTAACAA
1 TAGTTAACAA
9930 AAGTTGGTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (21 bp):
TAGTTAACAATTATTTATGAA
Found at i:13065 original size:128 final size:132
Alignment explanation
Indices: 12829--13071 Score: 332
Period size: 128 Copynumber: 1.9 Consensus size: 132
12819 TAGAAATTTC
* *
12829 TCAGTGATATATCAAACCATTGAATGATGTTTTTTTTTACTAATGCTTTAATGAAAAACATCATT
1 TCAGTGATATATCAAACAATTGAATGATG--TTTTTTGACTAATGCTTTAATGAAAAACATCATT
* * *
12894 TTCTCAGTGACCATTTAGTGCATAATGACAAAAACCTTGCAGTGCTCAATAACATCATTTTTAAA
64 TTCTCAGTGACCATTTAATGAACAATGACAAAAACCTTGCAGTGCTCAATAACATCATTTTTAAA
12959 CTTT
129 CTTT
* * **
12963 TCAGTGATATATCAAACAATTGAATGATG-TTTTTGAC-CAT-TTTTAATGAAAAATGTCA-TTT
1 TCAGTGATATATCAAACAATTGAATGATGTTTTTTGACTAATGCTTTAATGAAAAACATCATTTT
* * *
13024 CTCAGTGACCATTTAATGAACAGTGACAAAAACTTTTCAGTGCTCAAT
66 CTCAGTGACCATTTAATGAACAATGACAAAAACCTTGCAGTGCTCAAT
13072 CACTTCAATT
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
128 45 0.46
129 15 0.15
130 2 0.02
131 7 0.07
134 28 0.29
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (132 bp):
TCAGTGATATATCAAACAATTGAATGATGTTTTTTGACTAATGCTTTAATGAAAAACATCATTTT
CTCAGTGACCATTTAATGAACAATGACAAAAACCTTGCAGTGCTCAATAACATCATTTTTAAACT
TT
Found at i:13178 original size:112 final size:112
Alignment explanation
Indices: 12981--13188 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 112
12971 ATATCAAACA
**
12981 ATTGAATGATGTTTTTGACCATTTTTAATGAAAAATGTCATTTCTCAGTGACCATTTAATGAACA
1 ATTGAATGATGTTTTTGACCATTTTTAATGAAAAACATCATTTCTCAGTGACCATTTAATGAACA
* *
13046 GTGACAAAAACTTTTCAGTGCTCAATCACTTCAATTCAATTAAATAT
66 ATGACAAAAACTTTTCAGTGCCCAATCACTTCAATTCAATTAAATAT
* *
13093 ATTGAATGATGTTTTTGACCATTTTTAATGAAAAACATCTTTTCTCATTGACCATTTAATGAACA
1 ATTGAATGATGTTTTTGACCATTTTTAATGAAAAACATCATTTCTCAGTGACCATTTAATGAACA
* * * *
13158 ATGACATAAGCTTTTTAGTGCCCAATTACTT
66 ATGACAAAAACTTTTCAGTGCCCAATCACTT
13189 TATTTCTGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
112 86 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (112 bp):
ATTGAATGATGTTTTTGACCATTTTTAATGAAAAACATCATTTCTCAGTGACCATTTAATGAACA
ATGACAAAAACTTTTCAGTGCCCAATCACTTCAATTCAATTAAATAT
Found at i:13945 original size:26 final size:26
Alignment explanation
Indices: 13915--13979 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
13905 TTATTGTACT
*
13915 TAATGTAATGTAAGAATTACTGTTTC
1 TAATGTAATGTAAGAATTAATGTTTC
* *
13941 TAATGTAATGTAGGAGTTAATGTTTC
1 TAATGTAATGTAAGAATTAATGTTTC
*
13967 TAATATAATGTAA
1 TAATGTAATGTAA
13980 TGTAATGTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.42
Consensus pattern (26 bp):
TAATGTAATGTAAGAATTAATGTTTC
Found at i:20499 original size:25 final size:27
Alignment explanation
Indices: 20443--20505 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
20433 TCATTTTCGA
** *
20443 ATTAACCGAACTTTTTTTTCTTTAATT
1 ATTAACCGAACTTTTTTTTCTGAAAAT
*
20470 GTTAACCGAAC-TTTTTTTC-GAAAAT
1 ATTAACCGAACTTTTTTTTCTGAAAAT
*
20495 ATTAATCGAAC
1 ATTAACCGAAC
20506 CGAATAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
25 12 0.40
26 8 0.27
27 10 0.33
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (27 bp):
ATTAACCGAACTTTTTTTTCTGAAAAT
Found at i:20623 original size:17 final size:17
Alignment explanation
Indices: 20596--20634 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
20586 AATTTACAAT
*
20596 TAATT-TAAATAATATC
1 TAATTATAAATAATATA
20612 TAATTATAAATAATATA
1 TAATTATAAATAATATA
20629 TAATTA
1 TAATTA
20635 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATA
Found at i:21667 original size:178 final size:178
Alignment explanation
Indices: 21368--21719 Score: 614
Period size: 178 Copynumber: 2.0 Consensus size: 178
21358 TGGAGAACGC
* * *
21368 AACAATAATTCAATTTAATAGAATCTCAGAGTAAAACATGCACGGTCAGAAAATCAATATAAATT
1 AACAATAATTCAATTTAATAAAATCTCAGAGTAAAACATGCACCGTCAAAAAATCAATATAAATT
* *
21433 CATAAATAGAAATAAGATTTCATAATACATATTATAATACGAGTTTAAAATTCAAAGCAGATAAA
66 CATAAATAGAAATAAGAGTTCATAATACATATTATAATACGAGTTTAAAATTCAAAGAAGATAAA
21498 ATAATTTAACATCCCAAAATGTCACAGATAAATATAAAGTTAACAAAA
131 ATAATTTAACATCCCAAAATGTCACAGATAAATATAAAGTTAACAAAA
*
21546 AACAATAATTTAATTTAATAAAATCTCAGAGTAAAACATGCACCGTCAAAAAATCAATATAAATT
1 AACAATAATTCAATTTAATAAAATCTCAGAGTAAAACATGCACCGTCAAAAAATCAATATAAATT
* * *
21611 CATAAATAGAAATAAGAGTTCATAATACATATTATGATACTAGTTTAAAGTTCAAAGAAGATAAA
66 CATAAATAGAAATAAGAGTTCATAATACATATTATAATACGAGTTTAAAATTCAAAGAAGATAAA
*
21676 ATAATTTAATATCCCAAAATGTCACAGATAAATATAAAGTTAAC
131 ATAATTTAACATCCCAAAATGTCACAGATAAATATAAAGTTAAC
21720 GGGAAAAAAA
Statistics
Matches: 164, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
178 164 1.00
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (178 bp):
AACAATAATTCAATTTAATAAAATCTCAGAGTAAAACATGCACCGTCAAAAAATCAATATAAATT
CATAAATAGAAATAAGAGTTCATAATACATATTATAATACGAGTTTAAAATTCAAAGAAGATAAA
ATAATTTAACATCCCAAAATGTCACAGATAAATATAAAGTTAACAAAA
Found at i:22181 original size:29 final size:29
Alignment explanation
Indices: 22129--22225 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 29
22119 CCAAGACAAG
*
22129 GATTTAATCT-ATGCAGAATTAGGATGGA
1 GATTTAATCTCATGAAGAATTAGGATGGA
*
22157 GATTTAATCTCATAAAGAATTAGGACATGGA
1 GATTTAATCTCATGAAGAATTAGG--ATGGA
* * * *
22188 G--TTACTCTCATGTAGAATCAGGATGGG
1 GATTTAATCTCATGAAGAATTAGGATGGA
*
22215 GATATAATCTC
1 GATTTAATCTC
22226 GGGCAGAATC
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
27 5 0.09
28 10 0.18
29 34 0.62
31 6 0.11
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (29 bp):
GATTTAATCTCATGAAGAATTAGGATGGA
Found at i:25895 original size:2 final size:2
Alignment explanation
Indices: 25888--25915 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25878 AACTATTTAA
25888 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
25916 TTAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26009 original size:32 final size:31
Alignment explanation
Indices: 25959--26037 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
25949 TGTCTTTAAG
* *
25959 AAATCAATC-AATTCCTCAATCTTTCTAAAATA
1 AAATCATTCAAATT-CTCAAACTTT-TAAAATA
*
25991 AAATCATTCAAATTCTCAAACTTTTTAAATA
1 AAATCATTCAAATTCTCAAACTTTTAAAATA
** *
26022 AGGTCATTCAAGTTCT
1 AAATCATTCAAATTCT
26038 TTATTGCATT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 19 0.47
32 17 0.43
33 4 0.10
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (31 bp):
AAATCATTCAAATTCTCAAACTTTTAAAATA
Found at i:32532 original size:19 final size:19
Alignment explanation
Indices: 32505--32545 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
32495 AGTTCGGGTT
* * *
32505 TTTTTGAGTTTTAGTTGAG
1 TTTTCGAGTTTGAGTAGAG
32524 TTTTCGAGTTTGAGTAGAG
1 TTTTCGAGTTTGAGTAGAG
32543 TTT
1 TTT
32546 AGTAATACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.02, G:0.27, T:0.54
Consensus pattern (19 bp):
TTTTCGAGTTTGAGTAGAG
Found at i:33728 original size:17 final size:15
Alignment explanation
Indices: 33687--33729 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
33677 GTTTGTTAAA
*
33687 ACTGAATGGTTTAGC
1 ACTGAATGATTTAGC
*
33702 ACTAAATGATTTAGC
1 ACTGAATGATTTAGC
33717 AGTCTGAATGATT
1 A--CTGAATGATT
33730 AAGAGGCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 14 0.61
17 9 0.39
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (15 bp):
ACTGAATGATTTAGC
Found at i:39925 original size:22 final size:21
Alignment explanation
Indices: 39898--39942 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
39888 ACAACTGATT
39898 TACTAACTAATTGCTAACTAAC
1 TACTAACTAATTGCTAAC-AAC
*
39920 TACTAACTAATTGTTAACAAC
1 TACTAACTAATTGCTAACAAC
39941 TA
1 TA
39943 ACAAACTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (21 bp):
TACTAACTAATTGCTAACAAC
Found at i:39949 original size:22 final size:22
Alignment explanation
Indices: 39902--39949 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
39892 CTGATTTACT
*
39902 AACTAATTGCTAACTAACTACT
1 AACTAATTGCTAACTAACTACA
*
39924 AACTAATTGTTAAC-AACTAACA
1 AACTAATTGCTAACTAACT-ACA
39946 AACT
1 AACT
39950 TTCCAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.29
Consensus pattern (22 bp):
AACTAATTGCTAACTAACTACA
Found at i:45312 original size:14 final size:14
Alignment explanation
Indices: 45293--45319 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45283 AGTTAGTAAG
45293 TTAGTTAGTTTGTT
1 TTAGTTAGTTTGTT
45307 TTAGTTAGTTTGT
1 TTAGTTAGTTTGT
45320 GAGTCAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.22, T:0.63
Consensus pattern (14 bp):
TTAGTTAGTTTGTT
Found at i:45837 original size:16 final size:17
Alignment explanation
Indices: 45807--45839 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
45797 TCAATTATAT
45807 TTTTTTATAAAATTTAA
1 TTTTTTATAAAATTTAA
*
45824 TTTTTTA-AATATTTAA
1 TTTTTTATAAAATTTAA
45840 ATAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTTATAAAATTTAA
Found at i:46662 original size:22 final size:22
Alignment explanation
Indices: 46605--46668 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
46595 AATAACTATT
* *
46605 ATAAAATAAAAT-AA-TTTTGA
1 ATAAAATAATATAAATTTTTAA
*
46625 ATGAAATAATCA-AAATTTTTAA
1 ATAAAATAAT-ATAAATTTTTAA
*
46647 ATAAAATAATATAAATATTTAA
1 ATAAAATAATATAAATTTTTAA
46669 TATTATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 8 0.23
21 4 0.11
22 23 0.66
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (22 bp):
ATAAAATAATATAAATTTTTAA
Found at i:52749 original size:16 final size:16
Alignment explanation
Indices: 52725--52756 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52715 CAATGGAATT
52725 ATGAAACATGACACCA
1 ATGAAACATGACACCA
*
52741 ATGACACATGACACCA
1 ATGAAACATGACACCA
52757 TTCGATTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.12
Consensus pattern (16 bp):
ATGAAACATGACACCA
Found at i:52946 original size:31 final size:31
Alignment explanation
Indices: 52908--52971 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52898 TGACGACCAC
* *
52908 ATCTTAATTAAATAAAAACGAAAGTGATCGT
1 ATCTTAATTAAATAAAAACAAAAGTGACCGT
52939 ATCTTAATTAAATAAAAACAAAAGTGACCGT
1 ATCTTAATTAAATAAAAACAAAAGTGACCGT
52970 AT
1 AT
52972 ATTATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTGACCGT
Found at i:54602 original size:42 final size:42
Alignment explanation
Indices: 54556--54652 Score: 185
Period size: 42 Copynumber: 2.3 Consensus size: 42
54546 AATGCGATAG
54556 TCGACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACT
1 TCGACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACT
*
54598 TCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACT
1 TCGACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACT
54640 TCGACTATCGCAA
1 TCGACTATCGCAA
54653 TGCGAATATG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
TCGACTATCGCAACGAATTTGGAATAAATCGAAACGCGAACT
Found at i:54649 original size:21 final size:21
Alignment explanation
Indices: 54509--54658 Score: 89
Period size: 21 Copynumber: 7.2 Consensus size: 21
54499 ATATATAACA
54509 CGAACTTCGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
* *
54530 CGAA-TACGTA-AATCGCAATG
1 CGAACTTCG-ACTATCGCAATG
*
54550 CGATA-GTCGACTATCGCAA--
1 CGA-ACTTCGACTATCGCAATG
* * * * *
54569 CGAATTTGGAATAAATCGAAACG
1 CGAACTTCGACT--ATCGCAATG
54592 CGAACTTCGACTATCGCAA--
1 CGAACTTCGACTATCGCAATG
* * * *
54611 CGAATTTGGAATAAATCGCAACG
1 CGAACTTCGACT--ATCGCAATG
54634 CGAACTTCGACTATCGCAATG
1 CGAACTTCGACTATCGCAATG
54655 CGAA
1 CGAA
54659 TATGTAAATC
Statistics
Matches: 97, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
18 1 0.01
19 16 0.16
20 16 0.16
21 46 0.47
23 18 0.19
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (21 bp):
CGAACTTCGACTATCGCAATG
Found at i:55281 original size:12 final size:11
Alignment explanation
Indices: 55239--55296 Score: 84
Period size: 12 Copynumber: 5.3 Consensus size: 11
55229 TCTCGTCTCG
55239 GGTCGGGTCG-
1 GGTCGGGTCGT
55249 GGTCGGGTCG-
1 GGTCGGGTCGT
55259 GGTCGGGTCGT
1 GGTCGGGTCGT
55270 GGTCGTGGTCGT
1 GGTCG-GGTCGT
55282 GGTCGTGGTCGT
1 GGTCG-GGTCGT
55294 GGT
1 GGT
55297 AATACATGTC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.43
11 5 0.11
12 21 0.46
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (11 bp):
GGTCGGGTCGT
Found at i:55296 original size:6 final size:5
Alignment explanation
Indices: 55236--55292 Score: 78
Period size: 5 Copynumber: 10.6 Consensus size: 5
55226 CCGTCTCGTC
55236 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG
55284 TCGTGG TCG
1 TCG-GG TCG
55293 TGGTAATACA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 28 0.55
6 23 0.45
ACGTcount: A:0.00, C:0.19, G:0.54, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:57136 original size:21 final size:21
Alignment explanation
Indices: 57078--57137 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
57068 GTTGCGATAG
*
57078 TCGACTATCGCAACGCGAACT
1 TCGACTATCGCAATGCGAACT
57099 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
*
57120 TCGACTATCGCATTGCGA
1 TCGACTATCGCAATGCGA
57138 TTTACATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGACTATCGCAATGCGAACT
Found at i:57172 original size:21 final size:21
Alignment explanation
Indices: 57146--57220 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
57136 GATTTACATA
57146 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
57167 TTCGCATTGCGATAATCTAAG
1 TTCGCATTGCGATAGTCCAAG
*
57188 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
57209 TTCGCGTTGCGA
1 TTCGCATTGCGA
57221 ATCTGGAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:57414 original size:19 final size:19
Alignment explanation
Indices: 57388--57461 Score: 60
Period size: 19 Copynumber: 3.9 Consensus size: 19
57378 TTTAATTTGA
57388 AATAATTTAATATTAATAT
1 AATAATTTAATATTAATAT
* * *
57407 ATTAATTTACT-TATAATTT
1 AATAATTTAATAT-TAATAT
* *
57426 AATAATTTATTATTAATTT
1 AATAATTTAATATTAATAT
** *
57445 AATGGTTTCATATTAAT
1 AATAATTTAATATTAAT
57462 TTATTGTTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
18 1 0.02
19 42 0.95
20 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
AATAATTTAATATTAATAT
Found at i:57425 original size:30 final size:30
Alignment explanation
Indices: 57389--57445 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
57379 TTAATTTGAA
57389 ATAATTTAAT-ATTAATATATTAATTTACTT
1 ATAATTTAATAATTAAT-TATTAATTTACTT
*
57419 ATAATTTAATAATTTATTATTAATTTA
1 ATAATTTAATAATTAATTATTAATTTA
57446 ATGGTTTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (30 bp):
ATAATTTAATAATTAATTATTAATTTACTT
Found at i:57807 original size:38 final size:38
Alignment explanation
Indices: 57736--57816 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
57726 TAATATGTAC
* * * * *
57736 CAAGTACCCATGTATTGAAGTCCAATTGGCCCAAGTAA
1 CAAGTACCCAAGCATTGAAGTCCAATCGACCCAAATAA
* *
57774 CAAGTACCCAAGCATTGAGGTCCAATCGACCCAAATAC
1 CAAGTACCCAAGCATTGAAGTCCAATCGACCCAAATAA
57812 CAAGT
1 CAAGT
57817 TTGAATACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (38 bp):
CAAGTACCCAAGCATTGAAGTCCAATCGACCCAAATAA
Found at i:59140 original size:187 final size:186
Alignment explanation
Indices: 58863--59277 Score: 507
Period size: 187 Copynumber: 2.2 Consensus size: 186
58853 TAGGTTGCCT
* * *
58863 CTAAAATGTTATTAGAGTTTAAGATGAT-GAGGTCTTAGA-TTTTCTCACGATAAAAAAATTAGT
1 CTAAAATGTTATCAGAGTTTAAGCTGATGGA-GTCTTAGATTTTTCTCACGATAAAAAAATAAGT
* * * * * * *
58926 TATAAGCTAAAAATGTTATAGATATCTATAATAAATGCAGTTGCA-CACAATAATGTTATGGTTC
65 TAAAAGCCAAAAATATTATAGATATCTATAATAAATACAGTTG-AGCACAAAAATGTCATGGTTA
* ** * ** *
58990 ACTAATAAAGTAAGTTGTGATTTGAAATGTTAATATTTTTATTAATAAAATGGATTGCGC
129 ACTAAGAAAGTAAGTTGCAATATGAAACATTAATA--TTTATTAATAAAATGGATTGCAC
* * *
59050 CTAAAATATTATCAGAGTTTAAGCTGATGGAGCCTTAGATTTTTC-CACGATAACAAAATAAGTT
1 CTAAAATGTTATCAGAGTTTAAGCTGATGGAGTCTTAGATTTTTCTCACGATAAAAAAATAAGTT
* *
59114 AAAAGCCAAAAATATTAT-GAATATCTATAATAAATACGGTTGAGCCCAAAAATGTCATGGTTAA
66 AAAAGCCAAAAATATTATAG-ATATCTATAATAAATACAGTTGAGCACAAAAATGTCATGGTTAA
* *
59178 CTAAGAAAGTAGGTTGCAATATGAAACATTAATATTTATTAATAAAATGGGTTGCAC
130 CTAAGAAAGTAAGTTGCAATATGAAACATTAATATTTATTAATAAAATGGATTGCAC
* * *
59235 CTAAAATGTTACCAGAATTTAGGCTGATGGAGTCTTAGATTTT
1 CTAAAATGTTATCAGAGTTTAAGCTGATGGAGTCTTAGATTTT
59278 CAGTAATCCC
Statistics
Matches: 195, Mismatches: 29, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
185 59 0.30
186 2 0.01
187 127 0.65
188 7 0.04
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (186 bp):
CTAAAATGTTATCAGAGTTTAAGCTGATGGAGTCTTAGATTTTTCTCACGATAAAAAAATAAGTT
AAAAGCCAAAAATATTATAGATATCTATAATAAATACAGTTGAGCACAAAAATGTCATGGTTAAC
TAAGAAAGTAAGTTGCAATATGAAACATTAATATTTATTAATAAAATGGATTGCAC
Done.