Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007155.1 Hibiscus syriacus cultivar Beakdansim tig00018734_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: 91243
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:24291 original size:22 final size:22
Alignment explanation
Indices: 24266--24366 Score: 85
Period size: 22 Copynumber: 4.5 Consensus size: 22
24256 TTAAAATAAA
*
24266 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
24288 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
24312 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
24335 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
*
24357 TTAATTTAAA
1 TTATTTTAAA
24367 TAATTTATTA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 32 0.55
23 12 0.21
24 12 0.21
25 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:24315 original size:14 final size:15
Alignment explanation
Indices: 24204--24321 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
24194 TAATAAGGTT
24204 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
24219 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
24234 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
24249 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
24264 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
24283 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
24301 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
24315 ATTTATT
1 ATTTATT
24322 AGTATGGATT
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 58 0.64
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.07
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:24338 original size:18 final size:18
Alignment explanation
Indices: 24315--24394 Score: 53
Period size: 18 Copynumber: 4.4 Consensus size: 18
24305 ATTTTAAATA
24315 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
*
24333 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AGTATGGATTG
* *
24355 ATTTAATT--TA---AATA
1 ATTT-ATTAGTATGGATTG
24369 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
24387 ATTTATTA
1 ATTTATTA
24395 TTGTAGTTGT
Statistics
Matches: 47, Mismatches: 5, Indels: 20
0.65 0.07 0.28
Matches are distributed among these distances:
13 3 0.06
14 6 0.13
15 2 0.04
17 2 0.04
18 15 0.32
20 2 0.04
21 2 0.04
22 14 0.30
23 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:24366 original size:54 final size:54
Alignment explanation
Indices: 24301--24784 Score: 616
Period size: 54 Copynumber: 8.8 Consensus size: 54
24291 TTTTAAAATA
24301 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* ***
24355 ATTTAATTTAAATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
24413 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTACTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
24467 ATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
24521 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AAATA--AATT-
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
24571 ATTTGTATGGATTAATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
**
24633 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
24687 ATTTAGTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
24741 ATTTATTTTAAATAATTTATTATTATGGATTGATTTATTTTAAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
24785 TAATTTATTT
Statistics
Matches: 372, Mismatches: 42, Indels: 32
0.83 0.09 0.07
Matches are distributed among these distances:
50 14 0.04
51 3 0.01
52 2 0.01
53 5 0.01
54 250 0.67
55 6 0.02
56 8 0.02
57 4 0.01
58 59 0.16
59 2 0.01
60 2 0.01
61 3 0.01
62 14 0.04
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:24461 original size:22 final size:22
Alignment explanation
Indices: 24436--24478 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
24426 AATTTATTAG
24436 TATGGATTGATTTACTTTAAAA
1 TATGGATTGATTTACTTTAAAA
*
24458 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTACTTTAAA
24479 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (22 bp):
TATGGATTGATTTACTTTAAAA
Found at i:24494 original size:166 final size:163
Alignment explanation
Indices: 24301--24786 Score: 621
Period size: 166 Copynumber: 3.0 Consensus size: 163
24291 TTTTAAAATA
24301 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAATTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAATTTAA
24366 ATAATTTATTAGTATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTT
66 ATAATTTATTAGTATGGATTGATTTATTATT-TA-TTGTATGGATTGATTTATTTTAAATAATTT
24431 ATTAGTATGGATTGATTTACTTTAAAATATGGATTG
129 ATTAGTATGGATTGATTTA-TTTAAAATATGGATTG
* * *
24467 ATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATAGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAATTTAA
* *
24532 ATAATTTATTAGTATGAATTGATTTATTTTAAATAAATTATTTGTATGGATTAATTTATTTT-AA
66 ATAATTTATTAGTATGGATTGATTTA--TT--AT---TTA-TTGTATGGATTGATTTATTTTAAA
* * ***
24596 -AA--TA-TAG-ATTGATTTA-TTATTGTAGTTGTATGGATTG
123 TAATTTATTAGTATGGATTGATTTATT-TA-AAATATGGATTG
** *
24633 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATTGATTTAGTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAATTTAA
* ***
24698 ATAATTTATTAGTATAGATTGATTTA-T-TTTAAAATATGGATTGATTTATTTTAAATAATTTAT
66 ATAATTTATTAGTATGGATTGATTTATTATTTATTGTATGGATTGATTTATTTTAAATAATTTAT
* *
24761 TATTATGGATTGATTTATTTTAAATA
131 TAGTATGGATTGATTTATTTAAAATA
24787 ATTTATTTGT
Statistics
Matches: 275, Mismatches: 29, Indels: 37
0.81 0.09 0.11
Matches are distributed among these distances:
156 17 0.06
157 5 0.02
158 2 0.01
160 3 0.01
161 4 0.01
162 8 0.03
163 6 0.02
164 2 0.01
165 5 0.02
166 187 0.68
167 3 0.01
168 4 0.01
170 4 0.01
171 2 0.01
172 22 0.08
173 1 0.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (163 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTAATTTAA
ATAATTTATTAGTATGGATTGATTTATTATTTATTGTATGGATTGATTTATTTTAAATAATTTAT
TAGTATGGATTGATTTATTTAAAATATGGATTG
Found at i:24509 original size:86 final size:82
Alignment explanation
Indices: 24301--24730 Score: 330
Period size: 86 Copynumber: 5.1 Consensus size: 82
24291 TTTTAAAATA
* *
24301 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATT-GATTTAATTTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA-AT-TATTAGA-TTGATTT-
* *
24365 AATAATTTATTAGTATGGATTG
62 -ATTATTTAGTAGTATGGATTG
* * *
24387 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAA-AA-TTATTAG-ATTGATTT
* *
24445 ATTTACTTTA-AAATATGGATTG
62 A-TTA-TTTAGTAGTATGGATTG
* * *
24467 ATTTATTTTAAATAATTTATTAGTATGGATCGATTTATTTTAAAATATAGATT-GATTTATTTTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA-AT-TATTAGATTGA-TTT-
* * *
24531 AATAATTTATTAGTATGAATTG
62 -ATTATTTAGTAGTATGGATTG
* * *
24553 ATTTATTTTAAATAAATTATTTGTATGGATTAATTTATTTT-AAAA-TA-TAGATTGATTTATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAATTATTAGATTGATTTATTA
*
24615 TTGTAGTTGTATGGATTG
66 TT-TAGTAGTATGGATTG
** * *
24633 ATTTATTTTAAATAATTTATTAGTATAAATTGATTTATTTTAAAATATGGATT-GATTTAGTTTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA-AT-TATTAGATTGA-TTT-
* * *
24697 AATAATTTATTAGTATAGATTG
62 -ATTATTTAGTAGTATGGATTG
24719 ATTTATTTTAAA
1 ATTTATTTTAAA
24731 ATATGGATTG
Statistics
Matches: 275, Mismatches: 39, Indels: 60
0.74 0.10 0.16
Matches are distributed among these distances:
79 6 0.02
80 94 0.34
81 20 0.07
82 12 0.04
84 14 0.05
85 18 0.07
86 105 0.38
87 6 0.02
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (82 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAATTATTAGATTGATTTATTA
TTTAGTAGTATGGATTG
Found at i:24670 original size:18 final size:18
Alignment explanation
Indices: 24647--24725 Score: 65
Period size: 18 Copynumber: 4.4 Consensus size: 18
24637 ATTTTAAATA
24647 ATTTATTAGTATAAATTG
1 ATTTATTAGTATAAATTG
*
24665 ATTTATT-TTA-AAATATGG
1 ATTTATTAGTATAAAT-T-G
* * *
24683 ATTGATTTAGTTTAAA-TA
1 ATTTA-TTAGTATAAATTG
*
24701 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAAATTG
24719 ATTTATT
1 ATTTATT
24726 TTAAAATATG
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
16 4 0.09
17 11 0.24
18 24 0.52
19 3 0.07
20 1 0.02
21 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (18 bp):
ATTTATTAGTATAAATTG
Found at i:24778 original size:18 final size:17
Alignment explanation
Indices: 24732--24814 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 17
24722 TATTTTAAAA
24732 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
* *
24749 TA---AATAATTTATTAT
1 TATGGATTGATTTATT-T
24764 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
* *
24781 TA---AATAATTTATTT
1 TATGGATTGATTTATTT
24795 GTATGGATTGATTTATTT
1 -TATGGATTGATTTATTT
24813 TA
1 TA
24815 AAATATAGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 16
0.68 0.11 0.22
Matches are distributed among these distances:
14 19 0.38
15 5 0.10
17 7 0.14
18 19 0.38
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (17 bp):
TATGGATTGATTTATTT
Found at i:24872 original size:14 final size:14
Alignment explanation
Indices: 24853--24879 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24843 GTATGGATTG
24853 ATTTATTTTAAATA
1 ATTTATTTTAAATA
24867 ATTTATTTTAAAT
1 ATTTATTTTAAAT
24880 TTCAGTATTG
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:27565 original size:15 final size:15
Alignment explanation
Indices: 27531--27581 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
27521 CGCCCCGCAT
* *
27531 CCGCACCGCATCCAC
1 CCGCCCCGCATCCGC
*
27546 CCGCCTCGCATCCGC
1 CCGCCCCGCATCCGC
* *
27561 ACGCCCCACATCCGC
1 CCGCCCCGCATCCGC
27576 CCGCCC
1 CCGCCC
27582 AACTAAATAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.14, C:0.63, G:0.16, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:27576 original size:26 final size:26
Alignment explanation
Indices: 27518--27569 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
27508 TTGAGACTTT
*
27518 ACCCGCCCCGCATCCGCACCGCATCC
1 ACCCGCCCCGCATCCGCACCGCACCC
*
27544 ACCCGCCTCGCATCCGCA-CGC-CCC
1 ACCCGCCCCGCATCCGCACCGCACCC
27568 AC
1 AC
27570 ATCCGCCCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 3 0.12
26 17 0.71
ACGTcount: A:0.15, C:0.62, G:0.15, T:0.08
Consensus pattern (26 bp):
ACCCGCCCCGCATCCGCACCGCACCC
Found at i:33628 original size:30 final size:31
Alignment explanation
Indices: 33592--33650 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
33582 TCGATACTTT
33592 ATCTAAAATTTAGA-GTCAAAATAATATTTC
1 ATCTAAAATTTAGATGTCAAAATAATATTTC
* *
33622 ATCTAAAGTTTAGATGTCAAATTAATATT
1 ATCTAAAATTTAGATGTCAAAATAATATT
33651 GAATCAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
ATCTAAAATTTAGATGTCAAAATAATATTTC
Found at i:33648 original size:31 final size:30
Alignment explanation
Indices: 33592--33675 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
33582 TCGATACTTT
* * **
33592 ATCTAAAATTTAGAGTCAAAATAATATTTC
1 ATCTAAAGTTTAGAGTCAAATTAATATTGA
33622 ATCTAAAGTTTAGATGTCAAATTAATATTGA
1 ATCTAAAGTTTAGA-GTCAAATTAATATTGA
*
33653 ATC--AAGTTTAGGGGTCAAATTAA
1 ATCTAAAGTTTA-GAGTCAAATTAA
33676 AACGTAACTC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.36
30 14 0.30
31 16 0.34
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (30 bp):
ATCTAAAGTTTAGAGTCAAATTAATATTGA
Found at i:36649 original size:17 final size:17
Alignment explanation
Indices: 36627--36664 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
36617 ACCATTAAGC
*
36627 TTTATTCTTTATTCTAT
1 TTTATTCTTTATTATAT
*
36644 TTTATTTTTTATTATAT
1 TTTATTCTTTATTATAT
36661 TTTA
1 TTTA
36665 AATTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTCTTTATTATAT
Found at i:37078 original size:15 final size:15
Alignment explanation
Indices: 37058--37087 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37048 CCATGAGTCT
37058 GTCGTTTCATCCTCC
1 GTCGTTTCATCCTCC
*
37073 GTCGTTTCATGCTCC
1 GTCGTTTCATCCTCC
37088 TCAGAGATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.37, G:0.17, T:0.40
Consensus pattern (15 bp):
GTCGTTTCATCCTCC
Found at i:40185 original size:18 final size:18
Alignment explanation
Indices: 40163--40376 Score: 268
Period size: 18 Copynumber: 11.7 Consensus size: 18
40153 CTTGTTTGCC
*
40163 TATTAATAATTCAGCGTC-
1 TATTAATAATTCTGC-TCG
40181 TATTAATAATAATTCTGCTCG
1 TATT-A-A-TAATTCTGCTCG
*
40202 TATTAATAATTCTGCTCC
1 TATTAATAATTCTGCTCG
*
40220 TGTTAATAATTCTGCTCG
1 TATTAATAATTCTGCTCG
40238 TATTAATAATTCTGCTCG
1 TATTAATAATTCTGCTCG
* *
40256 TATTAATAATTCTGCGCC
1 TATTAATAATTCTGCTCG
40274 TATTAATAATTCTGCTCG
1 TATTAATAATTCTGCTCG
*
40292 TATTAATAATTTTGCTCG
1 TATTAATAATTCTGCTCG
* * *
40310 TATTGATGATTCTGCTTG
1 TATTAATAATTCTGCTCG
*
40328 TATTAATAATTCTGTTCG
1 TATTAATAATTCTGCTCG
* *
40346 TGTTAATAATTCTGCTCA
1 TATTAATAATTCTGCTCG
*
40364 TATTAATGATTCT
1 TATTAATAATTCT
40377 ACTAATAATT
Statistics
Matches: 169, Mismatches: 23, Indels: 8
0.85 0.12 0.04
Matches are distributed among these distances:
18 151 0.89
19 2 0.01
20 4 0.02
21 12 0.07
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (18 bp):
TATTAATAATTCTGCTCG
Found at i:41595 original size:3 final size:3
Alignment explanation
Indices: 41587--41642 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
41577 CTTCCATTAT
* *
41587 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CTC CAC CTC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
*
41635 TAC CAC CA
1 CAC CAC CA
41643 TCACGAGTAG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.64, G:0.00, T:0.05
Consensus pattern (3 bp):
CAC
Found at i:46942 original size:32 final size:32
Alignment explanation
Indices: 46918--46998 Score: 117
Period size: 32 Copynumber: 2.5 Consensus size: 32
46908 GGTCCGGTTC
*
46918 GAACGGTTCAACGGTTCTGGCCGGTTCACTAA
1 GAACGGTTCAACGGTTCTGGCCGGTCCACTAA
* *
46950 TAACGGTTCAACGGTTCTGGCCGGTTCACTAA
1 GAACGGTTCAACGGTTCTGGCCGGTCCACTAA
*
46982 TAACGGTTCAACCGGTT
1 GAACGGTTCAA-CGGTT
46999 TAGATTGAAC
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 42 0.89
33 5 0.11
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (32 bp):
GAACGGTTCAACGGTTCTGGCCGGTCCACTAA
Found at i:52773 original size:3 final size:3
Alignment explanation
Indices: 52765--52931 Score: 217
Period size: 3 Copynumber: 55.7 Consensus size: 3
52755 TCTCAAACAT
* * * *
52765 TTC TTC TTC TTC TTC TTC TTC TTC TCC TTC TTC TTC TTC TCC TCC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * *
52813 TTC TTC TTC TTC TCC TTC TCC TTC TTC TTC TTA TCC TTC TTC TCC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * *
52861 TTC TTC TTC TCC TTC TTC TTC TTC TCC TTC TCC TTC TTC TCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
52909 TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TT
52932 GGATTCCGTG
Statistics
Matches: 142, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 142 1.00
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:53017 original size:3 final size:3
Alignment explanation
Indices: 53009--53036 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52999 CCATCAGTGC
53009 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
53037 GCTGCCACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:61019 original size:2 final size:2
Alignment explanation
Indices: 61012--61039 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61002 TTGCTTTGAA
61012 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
61040 TAGAATGTTG
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:61434 original size:455 final size:456
Alignment explanation
Indices: 60580--61494 Score: 1609
Period size: 455 Copynumber: 2.0 Consensus size: 456
60570 TCTAACCATG
60580 ATATTAGAATGTTGATTTTGAGGTTAGGATGTTGAATTGGATCAAATTGTAAGTTTGCTAAAGTT
1 ATATTAGAATGTTGATTTTGAGGTTAGGATGTTGAATTGGATCAAATTGTAAGTTTGCTAAAGTT
** *
60645 TGGGAATTAAATCATGAATATTGGAAAGTGTTTGAGTTAAATGGCAATTATGCAAGTGTGAAGGC
66 TGGGAATTAAATCATGAATATTGGAAAGTGTGAGAGTTAAATGGCAATTATGCAAGTGTAAAGGC
*
60710 ACTAGTTTGAATACATTGTTAAGATTCTGGAAATTTGGCTTTTGGAATTTAATTTAAAGTGAAAT
131 ACTAGTTTGAATACATTGTTAAGATTCTGGAAATTTGGCGTTTGGAATTTAATTTAAAGTGAAAT
*
60775 GGCAAATGACCATTTTGAATGAATTGGAAAAGTTAGGATAGATTCTAAAAGAATTCATAAATGGT
196 GACAAATGACCATTTTGAATGAATTGGAAAAGTTAGGATAGATTCTAAAAGAATTCATAAATGGT
60840 GGTTGAAATGTAAAGTTGTGAAAATTATGTGGATTAGTGATGAATATGAATACTAAAGGAATTAA
261 GGTTGAAATGTAAAGTTGTGAAAATTATGTGGATTAGTGATGAATATGAATACTAAAGGAATTAA
60905 AGTGTCATTTTGGAATGTTAAGGTTGATATTGAGCTGTGAAATGACATCTGTATCGAACAAGTAT
326 AGTGTCATTTTGGAATGTTAAGGTTGATATTGAGCTGTGAAATGACATCTGTATCGAACAAGTAT
* *
60970 CATAAGAATTTTATTGATTTATTTATTAAATTTTGCTTTGAAATATATATATATATATATATATA
391 CAAAAGAATTTTATGGATTTATTTATTAAATTTTGCTTTGAAATATATATATATATATATATATA
61035 T
456 T
* *
61036 ATATTAGAATGTTGATTTTGAGGTTAGGATGTTGATTTGGATCAAATTTTAAGTTTG-TAAAGTT
1 ATATTAGAATGTTGATTTTGAGGTTAGGATGTTGAATTGGATCAAATTGTAAGTTTGCTAAAGTT
* * *
61100 TGGGAATTAAATCATGAATATTGGAAAGTGTGAGAGTTAAATGGCAATTATGTAATTGTAAAGGT
66 TGGGAATTAAATCATGAATATTGGAAAGTGTGAGAGTTAAATGGCAATTATGCAAGTGTAAAGGC
* *
61165 ACTAGTTTGAATACATTGTTAGGATTCTGGAAATTTGGCGTTTGGAATTTAATTTAAATTGAAAT
131 ACTAGTTTGAATACATTGTTAAGATTCTGGAAATTTGGCGTTTGGAATTTAATTTAAAGTGAAAT
61230 GACAAA-GTACCATTTTGAATGAATTGGAAAAGTTAGGATAGATTCTAAAAGAATTCATAAATGG
196 GACAAATG-ACCATTTTGAATGAATTGGAAAAGTTAGGATAGATTCTAAAAGAATTCATAAATGG
* *
61294 TGGTTGAAATGTAAAGTTGTGGAAATTATGTGGATTAGTGGTGAATATGAATACTAAAGGAATTA
260 TGGTTGAAATGTAAAGTTGTGAAAATTATGTGGATTAGTGATGAATATGAATACTAAAGGAATTA
* * * *
61359 AAGTGTCATTTTGGAATGTTAAGGTTGATATTTAGTTGTGAAATGATATTTGTATCGAACAAGTA
325 AAGTGTCATTTTGGAATGTTAAGGTTGATATTGAGCTGTGAAATGACATCTGTATCGAACAAGTA
* *
61424 TCAAAAGAATTTTATGGATTTATTTATTATATTTTGCTTTGATATATATATATATATATATATAT
390 TCAAAAGAATTTTATGGATTTATTTATTAAATTTTGCTTTGAAATATATATATATATATATATAT
61489 AT
455 AT
61491 ATAT
1 ATAT
61495 ATATATATAT
Statistics
Matches: 436, Mismatches: 22, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
454 1 0.00
455 380 0.87
456 55 0.13
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (456 bp):
ATATTAGAATGTTGATTTTGAGGTTAGGATGTTGAATTGGATCAAATTGTAAGTTTGCTAAAGTT
TGGGAATTAAATCATGAATATTGGAAAGTGTGAGAGTTAAATGGCAATTATGCAAGTGTAAAGGC
ACTAGTTTGAATACATTGTTAAGATTCTGGAAATTTGGCGTTTGGAATTTAATTTAAAGTGAAAT
GACAAATGACCATTTTGAATGAATTGGAAAAGTTAGGATAGATTCTAAAAGAATTCATAAATGGT
GGTTGAAATGTAAAGTTGTGAAAATTATGTGGATTAGTGATGAATATGAATACTAAAGGAATTAA
AGTGTCATTTTGGAATGTTAAGGTTGATATTGAGCTGTGAAATGACATCTGTATCGAACAAGTAT
CAAAAGAATTTTATGGATTTATTTATTAAATTTTGCTTTGAAATATATATATATATATATATATA
T
Found at i:61472 original size:2 final size:2
Alignment explanation
Indices: 61465--61525 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
61455 TTTTGCTTTG
61465 AT AT AT 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 AT AT AT
* *
61507 AT AT TT AT A- AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
61526 GATTTTGTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62950 original size:602 final size:602
Alignment explanation
Indices: 61790--62978 Score: 2175
Period size: 602 Copynumber: 2.0 Consensus size: 602
61780 TATAAAATGA
*
61790 ATTGATACCTAGTTTATATATGATGTTATACCATGAATGTTATTTCGGGTATGAACTGTCTAATG
1 ATTGATACCTAGTTTATATATGATGTTATACCATGAATGTTATTTCGGGTATGAACTGTCCAATG
61855 TTAAATTATATTGATATACATTGTCATGGATGAAATAAATATAGACTATATGTCCAAGTATGTCA
66 TTAAATTATATTGATATACATTGTCATGGATGAAATAAATATAGACTATATGTCCAAGTATGTCA
61920 TTGAGGGACAATGGTATAGTTGGCATGCCACAGAGTCTAGCAGTAAGGCTACATATTCGGTTTAG
131 TTGAGGGACAATGGTATAGTTGGCATGCCACAGAGTCTAGCAGTAAGGCTACATATTCGGTTTAG
* *
61985 CACTATAGTGTATATAAAGGACATTTAGTGCATATGATGGGCAAGACCTTATGCATATTGACACT
196 CACTATAGTGTATATAAAAGACATTTAGTGCATATGATGGGCAAGACCATATGCATATTGACACT
62050 TCAATGCATATTTGACTCGTGTACCCAAGGTCCTCATAGGTTTATATTTGAGTTTTGGTTTATTG
261 TCAATGCATATTTGACTCGTGTACCCAAGGTCCTCATAGGTTTATATTTGAGTTTTGGTTTATTG
* *
62115 GTTAATAAATGATATACAAGTGAATAAGAATTTGAGATTATGGAATAAATGACAAGTATATTGGT
326 GTTAATAAATGATATACAAATGAATAAGAATGTGAGATTATGGAATAAATGACAAGTATATTGGT
62180 AATAAATTTTATATGTAGATTATATCATGTTAATATATAGTAACATACTTGAAATTATAGGTAAA
391 AATAAATTTTATATGTAGATTATATCATGTTAATATATAGTAACATACTTGAAATTATAGGTAAA
62245 ATGATCATAATGCATTAAACATTGTTATTTATATTTATGTGTTGCATTGCCTAGAATATTTCTAT
456 ATGATCATAATGCATTAAACATTGTTATTTATATTTATGTGTTGCATTGCCTAGAATATTTCTAT
*
62310 GTTTGTCTCACTAAGTGAAAACTTAGCGTGTAATTGTTTCACACGTAGGTACTAATAAGAAAGCA
521 GTTTGTCTCACTAAGTGAAAACTTAGCGTGTAATTGTTTCACACGTAGGTACTAATAAAAAAGCA
62375 TATTCAGTTTAGTTGGC
586 TATTCAGTTTAGTTGGC
62392 ATTGAT-CACTAGTTTATATATGATGTTATACCATGAATGTTATTTCGGGTATGAACTGTCCAAT
1 ATTGATAC-CTAGTTTATATATGATGTTATACCATGAATGTTATTTCGGGTATGAACTGTCCAAT
* *
62456 GTTAAATTATATTGATATACATTGTCATGGATGAAATAAGTATATACTATATGTCCAAGTATGTC
65 GTTAAATTATATTGATATACATTGTCATGGATGAAATAAATATAGACTATATGTCCAAGTATGTC
62521 ATTGAGGGACAATGGTATAGTTGGCATGCCACAGAGTCTAGCAGTAAGGCTACATATTCGGTTTA
130 ATTGAGGGACAATGGTATAGTTGGCATGCCACAGAGTCTAGCAGTAAGGCTACATATTCGGTTTA
* **
62586 GCACTATAGTGTATATAAAAGACATTTAGTGCATATGATGGGCACGACCATATGTGTATTGACAC
195 GCACTATAGTGTATATAAAAGACATTTAGTGCATATGATGGGCAAGACCATATGCATATTGACAC
*
62651 TTCAATGCATATTTGACTCGTGTACCCAAGGTCCTCATAGGTTTATATTTGGGTTTTGGTTTATT
260 TTCAATGCATATTTGACTCGTGTACCCAAGGTCCTCATAGGTTTATATTTGAGTTTTGGTTTATT
*
62716 GGTTAATAAATGATATACAAATGAATAAGAATGTGAGCTTATGGAATAAATGACAAGTATATTGG
325 GGTTAATAAATGATATACAAATGAATAAGAATGTGAGATTATGGAATAAATGACAAGTATATTGG
62781 TAATAAATTTTATATGTAGATTATATCATGTTAATATATAGTAACATGA-TTGAAATTATAGGTA
390 TAATAAATTTTATATGTAGATTATATCATGTTAATATATAGTAACAT-ACTTGAAATTATAGGTA
* * *
62845 AAATGATCATAATGCATTAAACATTGTTATTTATATTTTTGTGTTGCATTGCTTTGAATATTTCT
454 AAATGATCATAATGCATTAAACATTGTTATTTATATTTATGTGTTGCATTGCCTAGAATATTTCT
* * *
62910 ATGTTTGTCTCACTAAGTGAAAACTTAGTGTGTGATTGTTTTACACGTAGGTACTAATAAAAAAG
519 ATGTTTGTCTCACTAAGTGAAAACTTAGCGTGTAATTGTTTCACACGTAGGTACTAATAAAAAAG
62975 CATA
584 CATA
62979 ATAAGAAGCG
Statistics
Matches: 566, Mismatches: 19, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
601 1 0.00
602 564 1.00
603 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (602 bp):
ATTGATACCTAGTTTATATATGATGTTATACCATGAATGTTATTTCGGGTATGAACTGTCCAATG
TTAAATTATATTGATATACATTGTCATGGATGAAATAAATATAGACTATATGTCCAAGTATGTCA
TTGAGGGACAATGGTATAGTTGGCATGCCACAGAGTCTAGCAGTAAGGCTACATATTCGGTTTAG
CACTATAGTGTATATAAAAGACATTTAGTGCATATGATGGGCAAGACCATATGCATATTGACACT
TCAATGCATATTTGACTCGTGTACCCAAGGTCCTCATAGGTTTATATTTGAGTTTTGGTTTATTG
GTTAATAAATGATATACAAATGAATAAGAATGTGAGATTATGGAATAAATGACAAGTATATTGGT
AATAAATTTTATATGTAGATTATATCATGTTAATATATAGTAACATACTTGAAATTATAGGTAAA
ATGATCATAATGCATTAAACATTGTTATTTATATTTATGTGTTGCATTGCCTAGAATATTTCTAT
GTTTGTCTCACTAAGTGAAAACTTAGCGTGTAATTGTTTCACACGTAGGTACTAATAAAAAAGCA
TATTCAGTTTAGTTGGC
Found at i:70544 original size:15 final size:14
Alignment explanation
Indices: 70524--70561 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
70514 AATTGTTCCC
70524 TTATTATTTATTTAT
1 TTATTATTT-TTTAT
70539 TTATTATATTTTTAT
1 TTATTAT-TTTTTAT
70554 TTATTATT
1 TTATTATT
70562 GTTAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.86
16 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTATTTTTTAT
Found at i:70752 original size:6 final size:6
Alignment explanation
Indices: 70738--70787 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
70728 CATAGAAGAA
*
70738 GAAGAG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG
70786 GA
1 GA
70788 GGAGGAGGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:70793 original size:3 final size:3
Alignment explanation
Indices: 70785--70828 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
70775 AAGGGGAAGG
70785 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
70829 GAGTAATAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:82942 original size:29 final size:29
Alignment explanation
Indices: 82887--82942 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
82877 CAAATTTTGG
* * * * *
82887 TTAGTGACCAAAGTGTATATTTTGAAAGT
1 TTAGTAACCAAAGTATAAACTTGGAAAGT
82916 TTAGTAACCAAAGTATAAACTTGGAAA
1 TTAGTAACCAAAGTATAAACTTGGAAA
82943 ACTTTAGGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (29 bp):
TTAGTAACCAAAGTATAAACTTGGAAAGT
Found at i:87756 original size:20 final size:19
Alignment explanation
Indices: 87718--87768 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
87708 CGTTTATTTG
* *
87718 GTATGGAGACAAATTTTTC
1 GTATGGAGACCAATCTTTC
*
87737 AGTATGGAGACCAGTCTTTC
1 -GTATGGAGACCAATCTTTC
87757 GTTATGGAGACC
1 G-TATGGAGACC
87769 GAGCAGTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (19 bp):
GTATGGAGACCAATCTTTC
Done.