Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003033.1 Hibiscus syriacus cultivar Beakdansim tig00006313_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: 68792
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:11849 original size:238 final size:235
Alignment explanation
Indices: 11385--11870 Score: 702
Period size: 238 Copynumber: 2.1 Consensus size: 235
11375 GAAGAATATT
* ** *
11385 TTCAATTCTGCCAGCCGATTTTCATGAAGAAACAAACTGCTTTTTGTGAAGAGGTTCTCCACCAC
1 TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACTTTTTGTAAAGAGGTTCTCCACCAC
* *
11450 CGACTGACTCATCTTCCACACCAATTTCCCACTGACGGCCTCATTTCCCATTATTTTCTTCCGCC
66 CGACTGACACATCTTCCACACCAATTTCCCACTGACGGCCTCATTTCCCATTATTCTCTTCCGCC
* *
11515 GTTGATCACCGGATCTTCTAGATTTGCTTGCCTGACACCAACATCAAGGATATGCTTCGTTTCTT
131 GTTGATCACCGGATCTTCCAGATTTGCTTGCCTGACACCAACATCAAGGATATACTTCGTTTCTT
*
11580 GAGGGAGATCCTCATCTTAATGAACCTAAGCCAAGTGTTC
196 GAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
* * *
11620 TTCAAATCTGCCAGTCGATTTTCATGAAGAAACAAGCAATTGTTTTGTAAAGAGGTTCTCCACCA
1 TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACT-TTTTGTAAAGAGGTTCTCCACCA
* * * * * * *
11685 CCGACTGACACATCTTCCATAGCCGATTTCTCACTGACGGCCTCTTTTCCCGTTCTTCTCTTCTG
65 CCGACTGACACATCTTCCACA-CCAATTTCCCACTGACGGCCTCATTTCCCATTATTCTCTTCCG
* * **
11750 TCGTTGATCACCGGATCTTCCAGATTTGCTTGCCTCGACGCCAGTATCAAGGATATACTTCGTTT
129 CCGTTGATCACCGGATCTTCCAGATTTGCTTGCCT-GACACCAACATCAAGGATATACTTCGTTT
* * * *
11815 CTTGAGGGAGATCCTCATCTCAGTGGATCTAAGCCGAGTGTTC
193 CTTGAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
11858 TTCAAATCTGCCA
1 TTCAAATCTGCCA
11871 CCGTCGTCGG
Statistics
Matches: 221, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
235 35 0.16
236 41 0.19
237 69 0.31
238 76 0.34
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (235 bp):
TTCAAATCTGCCAGCCGATTTTCATGAAGAAACAAACAACTTTTTGTAAAGAGGTTCTCCACCAC
CGACTGACACATCTTCCACACCAATTTCCCACTGACGGCCTCATTTCCCATTATTCTCTTCCGCC
GTTGATCACCGGATCTTCCAGATTTGCTTGCCTGACACCAACATCAAGGATATACTTCGTTTCTT
GAGGGAGATCCTCATCTCAATGAACCTAAGCCAAGTGTTC
Found at i:24065 original size:32 final size:36
Alignment explanation
Indices: 24029--24093 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
24019 GTATTTGGTT
24029 AGAAGAAA-G-GAG-TTTGT-TGTGTAAGAGATTAA
1 AGAAGAAATGAGAGTTTTGTGTGTGTAAGAGATTAA
*
24061 AGAAGAAATGAGTGTTTTGTGTGTGTAAGAGAT
1 AGAAGAAATGAGAGTTTTGTGTGTGTAAGAGAT
24094 GAAAAGAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 8 0.29
33 1 0.04
34 2 0.07
35 5 0.18
36 12 0.43
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.31
Consensus pattern (36 bp):
AGAAGAAATGAGAGTTTTGTGTGTGTAAGAGATTAA
Found at i:24640 original size:21 final size:21
Alignment explanation
Indices: 24589--24641 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
24579 ATTATGACTA
*
24589 TCGCAATGCAATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
24610 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
24631 TCGCAATGCGA
1 TCGCAATGCGA
24642 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:24656 original size:20 final size:20
Alignment explanation
Indices: 24631--24702 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
24621 TTTTCCCAAT
24631 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
24651 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
** *
24671 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
24692 TCGCAATGCGA
1 TCGCAATGCGA
24703 TACTGACTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:24716 original size:20 final size:20
Alignment explanation
Indices: 24691--24805 Score: 124
Period size: 20 Copynumber: 5.7 Consensus size: 20
24681 AATTTGGAAA
*
24691 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
24711 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
24732 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
24752 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
24772 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
24792 ATCGCAACGAGATA
1 ATCGCAACGCGATA
24806 ATATAGAATC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 63 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:25406 original size:19 final size:19
Alignment explanation
Indices: 25382--25435 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
25372 ATCGCAACGA
*
25382 GAAAATTGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
25401 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
25420 GAAAATCGCATTGCGA
1 GAAAATCGCAATGCGA
25436 TTTTCTCGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.19
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:25449 original size:14 final size:14
Alignment explanation
Indices: 25430--25483 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
25420 GAAAATCGCA
25430 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
25444 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
25461 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
25477 TTGCGAT
1 TTGCGAT
25484 AGTCAGTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:27098 original size:41 final size:42
Alignment explanation
Indices: 27053--27140 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 42
27043 CCTCTTCAAC
* *
27053 GATGACAGTGGCCTCTTGAACG-GCGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGCGGAGGGGACTCTTGAGG
* ** *
27094 GATGATAGGGGCCTCTTGAACGATTGGAGGGGATTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGCGGAGGGGACTCTTGAGG
27136 GATGA
1 GATGA
27141 TAGGTGAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 20 0.50
42 20 0.50
ACGTcount: A:0.20, C:0.15, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGCGGAGGGGACTCTTGAGG
Found at i:27109 original size:21 final size:21
Alignment explanation
Indices: 27080--27144 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
27070 GAACGGCGGG
27080 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
* ** *
27101 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGATA
*
27122 GGGGATTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
27143 GG
1 GG
27145 TGAGTCGGGC
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGATA
Found at i:27139 original size:42 final size:41
Alignment explanation
Indices: 27053--27144 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 41
27043 CCTCTTCAAC
* * *
27053 GATGACAGTGGCCTCTTGAACGGCGGGGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGGCGGAGGGGACTCTTGAGG
** *
27094 GATGATAGGGGCCTCTTGAACGATTGGAGGGGATTCTTGAGG
1 GATGATAGGGGCCTCTTGAACG-GCGGAGGGGACTCTTGAGG
27136 GATGATAGG
1 GATGATAGG
27145 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (41 bp):
GATGATAGGGGCCTCTTGAACGGCGGAGGGGACTCTTGAGG
Found at i:27507 original size:20 final size:20
Alignment explanation
Indices: 27482--27557 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
27472 GAATAGTTTG
* *
27482 CTTTCGCAACACGAAACTTA
1 CTTTCGCAACACGAAAATGA
*
27502 CTTTCGCAACGCGAAAATGA
1 CTTTCGCAACACGAAAATGA
* * * *
27522 CTATCGCAACGCGGAAATGG
1 CTTTCGCAACACGAAAATGA
*
27542 CTATCGCAACACGAAA
1 CTTTCGCAACACGAAA
27558 TGAAAATCGT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (20 bp):
CTTTCGCAACACGAAAATGA
Found at i:27566 original size:19 final size:19
Alignment explanation
Indices: 27544--27589 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
27534 GGAAATGGCT
27544 ATCGCAACACGAAATGAAA
1 ATCGCAACACGAAATGAAA
* **
27563 ATCGTAATGCGAAATGAAA
1 ATCGCAACACGAAATGAAA
27582 ATCGCAAC
1 ATCGCAAC
27590 GACAAAATAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.17, T:0.15
Consensus pattern (19 bp):
ATCGCAACACGAAATGAAA
Found at i:27605 original size:33 final size:33
Alignment explanation
Indices: 27568--27642 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
27558 TGAAAATCGT
27568 AATGCGAAATGAAAATCGCAACGACAAAATAGC
1 AATGCGAAATGAAAATCGCAACGACAAAATAGC
* *
27601 AATGCGAAATGAAAATTGCAACGACAAAATCGC
1 AATGCGAAATGAAAATCGCAACGACAAAATAGC
*
27634 AACGCGAAA
1 AATGCGAAA
27643 CACAAATCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.12
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGACAAAATAGC
Found at i:27621 original size:19 final size:19
Alignment explanation
Indices: 27553--27621 Score: 67
Period size: 19 Copynumber: 3.9 Consensus size: 19
27543 TATCGCAACA
*
27553 CGAAATGAAAATCGTAATG
1 CGAAATGAAAATCGCAATG
27572 CGAAATGAAAATCGCAA--
1 CGAAATGAAAATCGCAATG
* *
27589 CG--A-CAAAATAGCAATG
1 CGAAATGAAAATCGCAATG
*
27605 CGAAATGAAAATTGCAA
1 CGAAATGAAAATCGCAA
27622 CGACAAAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.22
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.51, C:0.14, G:0.19, T:0.16
Consensus pattern (19 bp):
CGAAATGAAAATCGCAATG
Found at i:27671 original size:19 final size:19
Alignment explanation
Indices: 27649--27765 Score: 92
Period size: 19 Copynumber: 6.6 Consensus size: 19
27639 GAAACACAAA
27649 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
27668 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
27684 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
27701 TCGTATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
27717 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
27734 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
27753 TCCGCGTTGCGAT
1 T-CGCATTGCGAT
27766 AGCCATTTTC
Statistics
Matches: 79, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
14 12 0.15
15 6 0.08
16 8 0.10
17 8 0.10
18 6 0.08
19 29 0.37
20 10 0.13
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:27690 original size:14 final size:14
Alignment explanation
Indices: 27671--27729 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
27661 TTTCATTTCG
27671 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
27685 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
27702 CGTATTGCGATTTTGT
1 CG--TTGCGATTTTGT
27718 CGTTGCGATTTT
1 CGTTGCGATTTT
27730 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:27696 original size:33 final size:33
Alignment explanation
Indices: 27654--27745 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
27644 ACAAATCGCA
*
27654 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
27687 TTGCGATTTTCATTTCGTATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
27720 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
27746 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:27764 original size:20 final size:19
Alignment explanation
Indices: 27718--27784 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
27708 GCGATTTTGT
**
27718 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
27737 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
27757 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGTCA-TTTCG
*
27777 TGTTGCGA
1 CGTTGCGA
27785 AAGTAAACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.35
20 23 0.57
21 3 0.08
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:29747 original size:20 final size:20
Alignment explanation
Indices: 29689--29747 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
29679 AATAGTTTCT
* *
29689 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
29709 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
* *
29729 GAATATGACTATCGCAACG
1 GAAAATGACAATCGCAACG
29748 AGAGAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.14
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:30027 original size:20 final size:21
Alignment explanation
Indices: 30002--30051 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
29992 CTCTGAGAGA
30002 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
30022 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
30043 TCGGAGATG
1 T-GGAGATG
30052 GGTGAGAGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 2 0.08
22 17 0.65
ACGTcount: A:0.22, C:0.12, G:0.42, T:0.24
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:30038 original size:22 final size:22
Alignment explanation
Indices: 30010--30053 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
30000 GATGGAGATA
30010 GACGGATTTCG-CTGGAGATGGG
1 GACGGATTTCGTC-GGAGATGGG
30032 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
30054 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:30268 original size:20 final size:20
Alignment explanation
Indices: 30240--30324 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
30230 GATTATGTAT
*
30240 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
30260 TATCGCGTTGCGAAAGACAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
30280 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
30301 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
30321 TATC
1 TATC
30325 ACATTGCGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
19 3 0.06
20 35 0.67
21 13 0.25
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:30305 original size:41 final size:41
Alignment explanation
Indices: 30260--30337 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
30250 CGAAAGTCAG
*
30260 TATCGCGTTGCGAAAGACAGTATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGAAAGACAGTATCACATTGCGATTTTGTAT
* *
30301 TATCGCGTTGCGATAGTCAGTATCACATTGCGATTTT
1 TATCGCGTTGCGAAAGACAGTATCACATTGCGATTTT
30338 CCCAATTCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGAAAGACAGTATCACATTGCGATTTTGTAT
Found at i:30331 original size:20 final size:20
Alignment explanation
Indices: 30220--30334 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
30210 TGCTTTGAAA
*
30220 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
30241 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
30261 ATCGCGTTGCGAAAGACAGT
1 ATCGCATTGCGATAGTCAGT
* *
30281 ATCGCATTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
30302 ATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
*
30322 ATCACATTGCGAT
1 ATCGCATTGCGAT
30335 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.07
20 45 0.61
21 23 0.31
22 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:30348 original size:41 final size:41
Alignment explanation
Indices: 30260--30355 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
30250 CGAAAGTCAG
* * ** *
30260 TATCGCGTTGCGAAAGACAGTATCGCATTGCGATTTTGTAT
1 TATCGCGTTGCGATAGACAGTATCACATTGCGATTTTCCAA
*
30301 TATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGACAGTATCACATTGCGATTTT-CCAA
30343 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
30356 TTACTTATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
41 46 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
TATCGCGTTGCGATAGACAGTATCACATTGCGATTTTCCAA
Found at i:30416 original size:21 final size:22
Alignment explanation
Indices: 30364--30416 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
30354 ATTTACTTAT
30364 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
30385 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
30406 TCGCATTGCGA
1 TCGCATTGCGA
30417 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:34668 original size:11 final size:12
Alignment explanation
Indices: 34651--34727 Score: 59
Period size: 12 Copynumber: 6.4 Consensus size: 12
34641 TATAGTTTTT
*
34651 TATTTATTTATA
1 TATTTATATATA
34663 -ATTTATATATA
1 TATTTATATATA
*
34674 TATTTA-ATAAA
1 TATTTATATATA
* * *
34685 AATTGTATACAAA
1 TATT-TATATATA
*
34698 TAATTATATATA
1 TATTTATATATA
*
34710 TATATATATATA
1 TATTTATATATA
34722 TCATTT
1 T-ATTT
34728 TTAATTTTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
11 17 0.34
12 24 0.48
13 9 0.18
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (12 bp):
TATTTATATATA
Found at i:35558 original size:2 final size:2
Alignment explanation
Indices: 35553--35582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35543 AAAAATTAAA
35553 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
35583 GTATGATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36485 original size:23 final size:24
Alignment explanation
Indices: 36441--36492 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
36431 TGACTAATTG
* * *
36441 GAATTGTAAAATTTAATCCAACTT
1 GAATTGAAAAAATTAATACAACTT
36465 GAATTGAAAAAATTAA-ACAACTT
1 GAATTGAAAAAATTAATACAACTT
*
36488 AAATT
1 GAATT
36493 AATCAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (24 bp):
GAATTGAAAAAATTAATACAACTT
Found at i:50113 original size:2 final size:2
Alignment explanation
Indices: 50106--50130 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50096 CAACAGCCTG
50106 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
50131 TTTTCACGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:53521 original size:18 final size:18
Alignment explanation
Indices: 53498--53544 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
53488 ATGTAAAGTA
*
53498 GTATCGATACCACTTTGG
1 GTATCGATACCACTTAGG
53516 GTATCGATACCACTTAGG
1 GTATCGATACCACTTAGG
*
53534 ATATCGATACC
1 GTATCGATACC
53545 TGTAACACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (18 bp):
GTATCGATACCACTTAGG
Found at i:53878 original size:24 final size:24
Alignment explanation
Indices: 53851--53902 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
53841 TGTTAAGTGA
53851 TTATTCATTAAATTTTAATTTGGT
1 TTATTCATTAAATTTTAATTTGGT
53875 TTATTCATTAAATTTTAATTTGGT
1 TTATTCATTAAATTTTAATTTGGT
53899 TTAT
1 TTAT
53903 GTTCTTTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.08, T:0.60
Consensus pattern (24 bp):
TTATTCATTAAATTTTAATTTGGT
Found at i:63569 original size:20 final size:20
Alignment explanation
Indices: 63517--63570 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
63507 ACAAACTGGT
* *
63517 AGTATCGGTACTACCTTGAG
1 AGTATCGATACTTCCTTGAG
63537 AGTATCGATACTTCCTTGAG
1 AGTATCGATACTTCCTTGAG
63557 AGTATCGATACTTC
1 AGTATCGATACTTC
63571 TCTTACCTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTTCCTTGAG
Done.