Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006835.1 Hibiscus syriacus cultivar Beakdansim tig00017374_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: 88386
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Found at i:1807 original size:22 final size:21
Alignment explanation
Indices: 1765--1817 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1755 ATTCTAACTA
1765 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
1786 TCGCGTTGCGATTTTCCTAAA-
1 TCGCATTGCGA-TTTCCCAAAT
*
1807 TCGCAATGCGA
1 TCGCATTGCGA
1818 ATCTGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.70
22 8 0.30
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1842 original size:20 final size:20
Alignment explanation
Indices: 1803--1842 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1793 GCGATTTTCC
* *
1803 TAAATCGCAATGCGAATCTG
1 TAAATCGCAACGAGAATCTG
*
1823 TAAATCGCAACGAGATTCTG
1 TAAATCGCAACGAGAATCTG
1843 ACTATCGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
TAAATCGCAACGAGAATCTG
Found at i:2724 original size:23 final size:24
Alignment explanation
Indices: 2694--2746 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2684 GTATTCGAAA
2694 TTTGATCTTGGT-AATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
2717 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
2741 TTTGAT
1 TTTGAT
2747 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:5185 original size:20 final size:20
Alignment explanation
Indices: 5160--5248 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
5150 CAACGAGGAA
5160 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
5180 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
5200 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
5220 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCGGAAATGACT
5240 ATCGCAACG
1 ATCGCAACG
5249 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.25, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:5308 original size:34 final size:33
Alignment explanation
Indices: 5220--5315 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
5210 GGAATTGACT
* **
5220 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
5254 ATCGCAATGCGAAATGAAAATTGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
5287 ATCGTAATTCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
5316 CGAAATTAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.53
34 25 0.47
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.17
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:5350 original size:20 final size:19
Alignment explanation
Indices: 5325--5411 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 19
5315 GCGAAATTAG
5325 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
5344 TTTTCGCATTGCGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
5362 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* **
5378 TTTCGCATTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
5397 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
5412 ATCTGTTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
14 8 0.15
16 4 0.08
18 4 0.08
19 15 0.28
20 22 0.42
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:5412 original size:20 final size:19
Alignment explanation
Indices: 5364--5412 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
5354 GCGATTCACT
**
5364 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
5383 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
5403 CGTTGCGATA
1 CGTTGCGATA
5413 TCTGTTTTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:5611 original size:33 final size:34
Alignment explanation
Indices: 5549--5612 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 34
5539 ATTAGTTTCG
**
5549 CGTTGCGATTTTCATTTTTGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
5583 CGTTGCGATTTTCA-TTTCACATTGCGATTC
1 CGTTGCGATTTTCATTTTCACATTGCGATTC
5613 TCGTTGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCACATTGCGATTCACT
Found at i:7206 original size:42 final size:42
Alignment explanation
Indices: 7127--7219 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
7117 CCTCTTCAAC
* * *
7127 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
7169 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
7211 GATGACAGG
1 GATGACAGG
7220 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:7723 original size:20 final size:20
Alignment explanation
Indices: 7700--7768 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 20
7690 GAAACTTAAA
7700 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
7720 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
7740 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
7760 ATCGCAACG
1 ATCGCAACG
7769 AAGAGAATCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:7839 original size:20 final size:20
Alignment explanation
Indices: 7814--7937 Score: 152
Period size: 20 Copynumber: 6.5 Consensus size: 20
7804 GATTCTTTCG
**
7814 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
7834 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
7854 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
7874 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
7894 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
7908 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
7928 TTGCAATAGT
1 TTGCGATAGT
7938 AAACTATTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 6 0.07
20 72 0.79
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:9865 original size:20 final size:20
Alignment explanation
Indices: 9807--9876 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
9797 GAAACTTTAA
* **
9807 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
9827 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
9847 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
9867 ATCGCAACGC
1 ATCGCAACGC
9877 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:9945 original size:20 final size:20
Alignment explanation
Indices: 9920--9966 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
9910 GATTCTCTCG
*
9920 TTGCGATAGTCAAATTCGCA
1 TTGCGATAATCAAATTCGCA
** *
9940 TTGCGATAATCATTTTCGCG
1 TTGCGATAATCAAATTCGCA
9960 TTGCGAT
1 TTGCGAT
9967 TCACTCGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
TTGCGATAATCAAATTCGCA
Found at i:10576 original size:20 final size:20
Alignment explanation
Indices: 10555--10679 Score: 205
Period size: 20 Copynumber: 6.2 Consensus size: 20
10545 ATAGTCAGAT
* *
10555 TCGCATTACGATTTACGTAT
1 TCGCATTGCGATTTACGTAA
10575 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
10595 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
10615 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
10635 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGTAA
* * *
10655 TCGCATTACGATTTAGGAAA
1 TCGCATTGCGATTTACGTAA
10675 TCGCA
1 TCGCA
10680 ACGCGAATTT
Statistics
Matches: 100, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 100 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAA
Found at i:10694 original size:21 final size:21
Alignment explanation
Indices: 10665--10706 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
10655 TCGCATTACG
10665 ATTTAGGAAATCGCAACGCGA
1 ATTTAGGAAATCGCAACGCGA
* *
10686 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
10707 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:14634 original size:9 final size:9
Alignment explanation
Indices: 14620--14644 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
14610 GATCCCTCAT
14620 AAGACCTCC
1 AAGACCTCC
14629 AAGACCTCC
1 AAGACCTCC
14638 AAGACCT
1 AAGACCT
14645 GATTCCTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (9 bp):
AAGACCTCC
Found at i:23704 original size:22 final size:23
Alignment explanation
Indices: 23673--23716 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
23663 TCTCGATCGA
23673 GTCATGAGAGAAAGGGAGAGAGT
1 GTCATGAGAGAAAGGGAGAGAGT
23696 GTCA-GAGAGAAAGGGAGAGAG
1 GTCATGAGAGAAAGGGAGAGAG
23717 AGAGAGAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.41, C:0.05, G:0.45, T:0.09
Consensus pattern (23 bp):
GTCATGAGAGAAAGGGAGAGAGT
Found at i:23724 original size:22 final size:22
Alignment explanation
Indices: 23678--23724 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
23668 ATCGAGTCAT
* *
23678 GAGAGAAAGGGAGAGAGTGTCA
1 GAGAGAAAGGGAGAGAGAGACA
*
23700 GAGAGAAAGGGAGAGAGAGAGA
1 GAGAGAAAGGGAGAGAGAGACA
23722 GAG
1 GAG
23725 TGCCATAGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.49, T:0.04
Consensus pattern (22 bp):
GAGAGAAAGGGAGAGAGAGACA
Found at i:37610 original size:16 final size:16
Alignment explanation
Indices: 37588--37660 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 16
37578 TGGTTTAGTA
37588 GTTTTTTT-TTTCTCT
1 GTTTTTTTCTTTCTCT
37603 GTTTTTTTCTTTCTCT
1 GTTTTTTTCTTTCTCT
* * * *
37619 GGTTCTGTCTCTCTCT
1 GTTTTTTTCTTTCTCT
* * *
37635 -CTTTTTTCTGTCTCC
1 GTTTTTTTCTTTCTCT
37650 G-TTTTTTCTTT
1 GTTTTTTTCTTT
37661 TTTTTCAGGT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
15 27 0.59
16 19 0.41
ACGTcount: A:0.00, C:0.22, G:0.10, T:0.68
Consensus pattern (16 bp):
GTTTTTTTCTTTCTCT
Found at i:38117 original size:17 final size:15
Alignment explanation
Indices: 38074--38114 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
38064 GGTCTGTAAT
38074 TATTTATTT-ATATA
1 TATTTATTTAATATA
38088 TATTTATTTAATATA
1 TATTTATTTAATATA
38103 TATTTA-TTAATA
1 TATTTATTTAATA
38115 ATAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:38118 original size:3 final size:3
Alignment explanation
Indices: 38110--38167 Score: 100
Period size: 3 Copynumber: 19.7 Consensus size: 3
38100 ATATATTTAT
*
38110 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38158 TAA TAA -AA TA
1 TAA TAA TAA TA
38168 TGGATAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38673 original size:117 final size:116
Alignment explanation
Indices: 38392--38822 Score: 582
Period size: 117 Copynumber: 3.7 Consensus size: 116
38382 TAGAATTATG
* * * *
38392 CAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCATATGAGGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
* * * * *
38457 TCATTATGAACTTTCTCTGG-AA-GAAATAATCCATCCAGTGATGAATTCAGA-
66 TCATTATGAACTTTC-CTGGCAATG--TTGATCCATCAAATGATGAATTCAAAC
* * * *
38508 TAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
38573 TCATTATGAACTCTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* * *
38625 CAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTCTTCAGATGATGAGTTCTTC
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
*
38690 TCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 TCATTATGAACT-TTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
* * ***
38742 CAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTTTCAT-ATGAGTTCTT
1 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGATGAGTTCTT
38806 CTCATTATGAACTTTCC
65 CTCATTATGAACTTTCC
38823 GCTGGGGATG
Statistics
Matches: 283, Mismatches: 27, Indels: 10
0.88 0.08 0.03
Matches are distributed among these distances:
116 98 0.35
117 180 0.64
118 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (116 bp):
CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTC
TCATTATGAACTTTCCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:38902 original size:95 final size:93
Alignment explanation
Indices: 38796--38970 Score: 242
Period size: 94 Copynumber: 1.9 Consensus size: 93
38786 TCTTTTTCAT
** * * * *
38796 ATGAGTTCTTCTCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAAGTAATGGATTCATGTA
1 ATGAGTTCTTCTCATTATGAACTTT-CGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTA
*
38861 AAAGGTTTGAACAAATTCTTCCTTCTTTAG
65 AAAGG-TTGAAAAAATTCTTCCTTCTTTAG
* * *
38891 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAAGTAA
1 ATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTAA
38956 AAGGTTGAAAAAATT
66 AAGGTTGAAAAAATT
38971 ATTCTCATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
93 10 0.14
94 35 0.50
95 25 0.36
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (93 bp):
ATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAAGATGATCCATCAAATAATGGATTCAAGTAA
AAGGTTGAAAAAATTCTTCCTTCTTTAG
Found at i:38996 original size:113 final size:113
Alignment explanation
Indices: 38876--39083 Score: 380
Period size: 113 Copynumber: 1.8 Consensus size: 113
38866 TTTGAACAAA
* *
38876 TTCTTCCTTCTTTAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
38941 GATGGATTCAAGTAAAAGGTTGAAAAAATTATTCTCATTATGAACTTC
66 GATGGATTCAAGTAAAAGGTTGAAAAAATTATTCTCATTATGAACTTC
38989 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
1 TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
* *
39054 GATGGATTCAGGTAAAAGGTTGAACAAATT
66 GATGGATTCAAGTAAAAGGTTGAAAAAATT
39084 CTTCCTTCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 91 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (113 bp):
TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAACTGATCCATCAAAT
GATGGATTCAAGTAAAAGGTTGAAAAAATTATTCTCATTATGAACTTC
Found at i:39113 original size:206 final size:210
Alignment explanation
Indices: 38678--39144 Score: 633
Period size: 206 Copynumber: 2.2 Consensus size: 210
38668 TTCTTCAGAT
* * * *
38678 GATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
1 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAAC
* * * * *
38742 CAAAAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTTCTTTTTCATATGAGTTCTTC
65 CAAAAAATTGAAAAAATTATTCTCATTATGAACTTCTTCTTC--TCTTCTTCAGATGAGTTCTTC
* ** * * *
38807 TCATTATGAACTTTCCGCTGGGGATGATGCTCCATCAAGTAATGGATTCATGTAAAAGGTTTGAA
128 TCATTATGAACTTTCCGCTGGGAAAAATGATCCATCAAATAATGGATTCAGGTAAAAGGTTTGAA
38872 CAAATTCTTCCTTCTTTA
193 CAAATTCTTCCTTCTTTA
* * **
38890 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTC-AAGT
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAACC
**
38954 AAAAGGTTGAAAAAATTATTCTCATTATGAACTTCTTCTTC-CTTCTTCAGATGAGTTCTTCTCA
66 AAAAAATTGAAAAAATTATTCTCATTATGAACTTCTTCTTCTCTTCTTCAGATGAGTTCTTCTCA
* *
39018 TTATGAACTTT-CTCT-GGAAAAACTGATCCATCAAATGATGGATTCAGGTAAAAGG-TTGAACA
131 TTATGAACTTTCCGCTGGGAAAAA-TGATCCATCAAATAATGGATTCAGGTAAAAGGTTTGAACA
39080 AATTCTTCCTTCTTTA
195 AATTCTTCCTTCTTTA
39096 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAGAA-ATGATCCATCAA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAA-AAGATGATCCATCAA
39145 GTGGATTCGA
Statistics
Matches: 229, Mismatches: 23, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
206 72 0.31
207 33 0.14
208 32 0.14
211 40 0.17
212 52 0.23
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (210 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGAATTCAAACC
AAAAAATTGAAAAAATTATTCTCATTATGAACTTCTTCTTCTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCCGCTGGGAAAAATGATCCATCAAATAATGGATTCAGGTAAAAGGTTTGAACAA
ATTCTTCCTTCTTTA
Found at i:40102 original size:82 final size:82
Alignment explanation
Indices: 39887--40434 Score: 942
Period size: 82 Copynumber: 6.7 Consensus size: 82
39877 CCTACTGAAT
** *
39887 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
39952 TGATTGGTTCTG-CCAAAC
66 TGATT-GTTCTGTCC-AAC
*
39970 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40034 ATGATTGTTCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
** *
40052 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
40117 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
*
40134 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTACTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40198 ATGATTGTTCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
*
40216 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCTAAACTCA
40280 ATGATTGTTCTGTCCAAC
65 ATGATTGTTCTGTCCAAC
40298 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
40363 TGATTGTTCTGTCCAAC
66 TGATTGTTCTGTCCAAC
40380 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTT
40435 TCATTTAATT
Statistics
Matches: 446, Mismatches: 14, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
81 4 0.01
82 373 0.84
83 67 0.15
84 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCTAAACTCAA
TGATTGTTCTGTCCAAC
Found at i:41237 original size:16 final size:18
Alignment explanation
Indices: 41197--41242 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
41187 ATCATAGAAG
*
41197 AATAAATTGAATTTCCCAA
1 AATAAATTGAATCTCCC-A
41216 AATAAATTGAATCT-CC-
1 AATAAATTGAATCTCCCA
41232 AATAAATTGAA
1 AATAAATTGAA
41243 CTTGAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 11 0.42
18 2 0.08
19 13 0.50
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (18 bp):
AATAAATTGAATCTCCCA
Found at i:53893 original size:16 final size:16
Alignment explanation
Indices: 53872--53902 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53862 TTTAGTAGTT
53872 TTTTTTTCTTTCTCTA
1 TTTTTTTCTTTCTCTA
53888 TTTTTTTCTTTCTCT
1 TTTTTTTCTTTCTCT
53903 GGTTCTGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTCTTTCTCTA
Found at i:53940 original size:19 final size:20
Alignment explanation
Indices: 53905--53945 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
53895 CTTTCTCTGG
53905 TTCTGTCTCTCTCTTTT-TT
1 TTCTGTCTCTCTCTTTTCTT
*
53924 TTCTGTCTC-CGTTTTTTCTT
1 TTCTGTCTCTC-TCTTTTCTT
53944 TT
1 TT
53946 TTTTCAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 1 0.05
19 14 0.74
20 4 0.21
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.68
Consensus pattern (20 bp):
TTCTGTCTCTCTCTTTTCTT
Found at i:54401 original size:17 final size:15
Alignment explanation
Indices: 54358--54398 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
54348 GGTCTGTAAT
54358 TATTTATTT-ATATA
1 TATTTATTTAATATA
54372 TATTTATTTAATATA
1 TATTTATTTAATATA
54387 TATTTA-TTAATA
1 TATTTATTTAATA
54399 ATAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TATTTATTTAATATA
Found at i:54402 original size:3 final size:3
Alignment explanation
Indices: 54394--54443 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
54384 ATATATTTAT
* *
54394 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
54442 TA
1 TA
54444 TGGATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:61048 original size:24 final size:24
Alignment explanation
Indices: 61016--61098 Score: 141
Period size: 24 Copynumber: 3.5 Consensus size: 24
61006 TACACCTTGT
61016 ATCGATGCA-TCCCTTGACGGGTGC
1 ATCGATGCACT-CCTTGACGGGTGC
*
61040 ATCGATGCACTCCTTGACGGGTGT
1 ATCGATGCACTCCTTGACGGGTGC
61064 ATCGATGCACTCCTTGACGGGTGC
1 ATCGATGCACTCCTTGACGGGTGC
61088 ATCGATGCACT
1 ATCGATGCACT
61099 ATCTATGCAT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
24 55 0.98
25 1 0.02
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.27
Consensus pattern (24 bp):
ATCGATGCACTCCTTGACGGGTGC
Found at i:69762 original size:18 final size:18
Alignment explanation
Indices: 69739--69773 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
69729 GTCAACCACC
*
69739 TCCCCAACCTGTTGGGCA
1 TCCCCAACCTGGTGGGCA
*
69757 TCCCCATCCTGGTGGGC
1 TCCCCAACCTGGTGGGC
69774 CTCCACACCC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.40, G:0.26, T:0.23
Consensus pattern (18 bp):
TCCCCAACCTGGTGGGCA
Done.