Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007088.1 Hibiscus syriacus cultivar Beakdansim tig00018503_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: 69940
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:2625 original size:29 final size:29
Alignment explanation
Indices: 2583--2667 Score: 127
Period size: 29 Copynumber: 3.0 Consensus size: 29
2573 AGTTAAGATT
2583 TTTAAGATAAGAATAAAATATATTTTTAA
1 TTTAAGATAAGAATAAAATATATTTTTAA
* *
2612 TTTAAAATAAGAATAGAATATATTTTTAA
1 TTTAAGATAAGAATAAAATATATTTTTAA
* *
2641 GTGAAGATAAGAA-AAAATATATTTTTA
1 TTTAAGATAAGAATAAAATATATTTTTA
2668 TATTAAATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 13 0.26
29 37 0.74
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (29 bp):
TTTAAGATAAGAATAAAATATATTTTTAA
Found at i:2683 original size:28 final size:27
Alignment explanation
Indices: 2584--2684 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 27
2574 GTTAAGATTT
*
2584 TTAAGATAAGAATAAAATATATTTTTAAT
1 TTAA-ATAAGAA-AAAATATATTTTTAAG
*
2613 TTAAAATAAGAATAGAATATATTTTTAAG
1 TT-AAATAAGAA-AAAATATATTTTTAAG
*
2642 TGAAGATAAGAAAAAATATATTTTTATA-
1 TTAA-ATAAGAAAAAATATATTTTTA-AG
*
2670 TTAAATTAATAAAAA
1 TTAAA-TAAGAAAAA
2685 TATTTAAATA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
27 1 0.02
28 26 0.42
29 33 0.53
30 2 0.03
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (27 bp):
TTAAATAAGAAAAAATATATTTTTAAG
Found at i:2697 original size:92 final size:94
Alignment explanation
Indices: 2602--2768 Score: 211
Period size: 90 Copynumber: 1.8 Consensus size: 94
2592 AGAATAAAAT
* *
2602 ATATTTTTAATTTAAAATAAGAATAGAAT-ATA-T-TTTTAAGTGAAGAT-AAGA-AAAA-ATAT
1 ATATATTTAAGTTAAAAT-AGAATA-AATAATATTATTTTAAGTGAAGATAAAGATAAAATATAT
*
2661 ATTTTTATATTAAATTAATAAAAATATTTAA
64 ATTTTTACATTAAATTAATAAAAATATTTAA
*** *
2692 ATATATTTAAGTTAAAATATTTTAAATAATATTATTTTAAGTGATGATAAAGATAAAATATATAT
1 ATATATTTAAGTTAAAATAGAATAAATAATATTATTTTAAGTGAAGATAAAGATAAAATATATAT
2757 TTTTACATTAAA
66 TTTTACATTAAA
2769 ATAAAATAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
88 3 0.05
89 6 0.09
90 17 0.27
91 13 0.20
92 4 0.06
93 4 0.06
94 17 0.27
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.43
Consensus pattern (94 bp):
ATATATTTAAGTTAAAATAGAATAAATAATATTATTTTAAGTGAAGATAAAGATAAAATATATAT
TTTTACATTAAATTAATAAAAATATTTAA
Found at i:5591 original size:13 final size:13
Alignment explanation
Indices: 5558--5592 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
5548 AAAATATTTT
5558 AAAATTGTTTATA
1 AAAATTGTTTATA
5571 ACAAATTGTTTATA
1 A-AAATTGTTTATA
5585 AAAATTGT
1 AAAATTGT
5593 GGAATGCAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (13 bp):
AAAATTGTTTATA
Found at i:7405 original size:28 final size:30
Alignment explanation
Indices: 7374--7440 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
7364 TAATTACCCA
*
7374 TTCATACATGAA-A-TATAAAATTTTC-AGT
1 TTCATACATGAATATTATAAAATTCTCGA-T
*
7402 TTCATACAT-AATATTTTAAAATTCTCGAT
1 TTCATACATGAATATTATAAAATTCTCGAT
7431 TTCATACATG
1 TTCATACATG
7441 GTGTTTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 2 0.06
28 10 0.30
29 20 0.61
30 1 0.03
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (30 bp):
TTCATACATGAATATTATAAAATTCTCGAT
Found at i:7777 original size:11 final size:11
Alignment explanation
Indices: 7761--7794 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
7751 GGTATAAGGA
7761 TGGGTAGGTGG
1 TGGGTAGGTGG
7772 TGGGTAGGTGG
1 TGGGTAGGTGG
7783 TGGGTAGGTGG
1 TGGGTAGGTGG
7794 T
1 T
7795 AGATACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.00, G:0.62, T:0.29
Consensus pattern (11 bp):
TGGGTAGGTGG
Found at i:8546 original size:2 final size:2
Alignment explanation
Indices: 8539--8634 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
8529 ATTGTAAGTA
8539 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
8581 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
8623 AT AT AT AT AT AT
1 AT AT AT AT AT AT
8635 GGAACATGTT
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9314 original size:15 final size:14
Alignment explanation
Indices: 9284--9351 Score: 73
Period size: 15 Copynumber: 4.6 Consensus size: 14
9274 TGATATGAAA
9284 ATGTGAAATAAGCT
1 ATGTGAAATAAGCT
*
9298 ATGTGACAATGAGCT
1 ATGTGA-AATAAGCT
* *
9313 ATGTGATTATATGTCT
1 ATGTGA-AATAAG-CT
*
9329 ATGTGATATAAGCT
1 ATGTGAAATAAGCT
9343 ATGTGAAAT
1 ATGTGAAAT
9352 GTGTAAATGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
14 16 0.36
15 21 0.47
16 8 0.18
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (14 bp):
ATGTGAAATAAGCT
Found at i:9315 original size:42 final size:42
Alignment explanation
Indices: 9219--9319 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 42
9209 TATATGATAT
* * *
9219 TGACCTATGTGATTACATGAAAAAGGTGATATAAGCTATGTGGCAT
1 TGACCTATGTGA-T--ATG-AAAAGGTGAAATAAGCTATGTGACAA
*
9265 TGACCTATGTGATATGAAAATGTGAAATAAGCTATGTGACAA
1 TGACCTATGTGATATGAAAAGGTGAAATAAGCTATGTGACAA
*
9307 TGAGCTATGTGAT
1 TGACCTATGTGAT
9320 TATATGTCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
42 34 0.68
43 3 0.06
45 1 0.02
46 12 0.24
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (42 bp):
TGACCTATGTGATATGAAAAGGTGAAATAAGCTATGTGACAA
Found at i:9332 original size:16 final size:14
Alignment explanation
Indices: 9244--9348 Score: 72
Period size: 15 Copynumber: 7.3 Consensus size: 14
9234 CATGAAAAAG
9244 GTGATATAAGCTAT
1 GTGATATAAGCTAT
* *
9258 GTGGCAT-TGACCTAT
1 GT-G-ATATAAGCTAT
*
9273 GTGATATGAA--AAT
1 GTGATAT-AAGCTAT
*
9286 GTGAAATAAGCTAT
1 GTGATATAAGCTAT
* *
9300 GTGACAATGAGCTAT
1 GTGA-TATAAGCTAT
*
9315 GTGATTATATGTCTAT
1 GTGA-TATAAG-CTAT
9331 GTGATATAAGCTAT
1 GTGATATAAGCTAT
9345 GTGA
1 GTGA
9349 AATGTGTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
12 2 0.03
13 10 0.14
14 18 0.25
15 31 0.44
16 10 0.14
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.34
Consensus pattern (14 bp):
GTGATATAAGCTAT
Found at i:9459 original size:23 final size:23
Alignment explanation
Indices: 9424--9514 Score: 92
Period size: 23 Copynumber: 4.0 Consensus size: 23
9414 GAGTTGAGGG
**
9424 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
*
9447 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAA
* * *
9470 TTCCACGTTGTCTTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAA
* * * *
9493 TACAATGTGGTCCTTCTGGACA
1 TTCTACGTGGTCCTTCGGGACA
9515 TTTTTATGTG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAA
Found at i:10037 original size:24 final size:23
Alignment explanation
Indices: 9985--10037 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
9975 ACTCTTATAT
* *
9985 TTATGTAAATTATTGAACTTCTA
1 TTATTTAAATTATTGAACTTCCA
10008 TT-TTTAAATTAAGTTGAA-TTCCA
1 TTATTTAAATT-A-TTGAACTTCCA
10031 TTATTTA
1 TTATTTA
10038 TTTTTGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 7 0.28
23 9 0.36
24 9 0.36
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.51
Consensus pattern (23 bp):
TTATTTAAATTATTGAACTTCCA
Found at i:15395 original size:58 final size:58
Alignment explanation
Indices: 15302--15416 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
15292 TAAAGTACAC
* * * * * *
15302 AAATATTCCCCGACTATAGGATACTACTTTTTTAAGTCCCTCGATTATTAAAAGTTAT
1 AAATAATCACCGACTATAGAATACTACTTTGTTAAGTCCATCGACTATTAAAAGTTAT
** *
15360 AAATAATCACCGACTATAGAATGTTACTTTGTTAAGTTCATCGACTATTAAAAGTTA
1 AAATAATCACCGACTATAGAATACTACTTTGTTAAGTCCATCGACTATTAAAAGTTA
15417 CAAAATGGTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.37
Consensus pattern (58 bp):
AAATAATCACCGACTATAGAATACTACTTTGTTAAGTCCATCGACTATTAAAAGTTAT
Found at i:15873 original size:55 final size:55
Alignment explanation
Indices: 15779--15957 Score: 232
Period size: 56 Copynumber: 3.2 Consensus size: 55
15769 GGTCTCGAAA
* * *
15779 GGGCCTCGAAATCGAGTATATATATCAGTTGTTGCCATTAATAAGCATAAAAATAG
1 GGGCC-CGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGTATAAAAATAG
* * * **
15835 GGGGCCGAAATTGAGTATATCTATCAGTTATTTTCATTAAGAAGTATAAAAATAG
1 GGGCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGTATAAAAATAG
* *
15890 GGGCTCCAAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAATATAAAAATAG
1 GGGC-CCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGTATAAAAATAG
*
15946 AGGCCCCGAAAT
1 -GGGCCCGAAAT
15958 TAAATATATC
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
55 46 0.44
56 55 0.53
57 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (55 bp):
GGGCCCGAAATCGAGTATATCTATCAGTTGTTGCCATTAAGAAGTATAAAAATAG
Found at i:16768 original size:22 final size:22
Alignment explanation
Indices: 16731--16795 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
16721 TTATCATTAT
16731 AGGTCCAATTTTTTTTCAATAAA
1 AGGTCCAA-TTTTTTTCAATAAA
*
16754 ATGTCCAATTTTTTTCAATAAA
1 AGGTCCAATTTTTTTCAATAAA
*
16776 AGGTCCAATTTTTATCAATA
1 AGGTCCAATTTTTTTCAATA
16796 CTTATTATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 32 0.82
23 7 0.18
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (22 bp):
AGGTCCAATTTTTTTCAATAAA
Found at i:16831 original size:30 final size:30
Alignment explanation
Indices: 16775--16833 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
16765 TTTTCAATAA
16775 AAGGTCCAATTTTTATCAATACTTATTATC
1 AAGGTCCAATTTTTATCAATACTTATTATC
*
16805 AAGGATCCAATTTTT-TCAATATTTATTAT
1 AAGG-TCCAATTTTTATCAATACTTATTAT
16834 TAGGGGCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.46
Consensus pattern (30 bp):
AAGGTCCAATTTTTATCAATACTTATTATC
Found at i:16914 original size:30 final size:31
Alignment explanation
Indices: 16874--16951 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
16864 TTCTAATATT
16874 TATTTGTTATTATGAGTCTAA-TTTTTTCAA
1 TATTTGTTATTATGAGTCTAATTTTTTTCAA
16904 TACTTT-TTATTAT-ATGTCTAATTTTTTTCAA
1 TA-TTTGTTATTATGA-GTCTAATTTTTTTCAA
16935 TATTTGTTATTATGAGT
1 TATTTGTTATTATGAGT
16952 ACTCTTAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
29 1 0.02
30 18 0.42
31 23 0.53
32 1 0.02
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (31 bp):
TATTTGTTATTATGAGTCTAATTTTTTTCAA
Found at i:18854 original size:12 final size:12
Alignment explanation
Indices: 18833--18861 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18823 AACATTACCC
18833 ATGT-ATGAACA
1 ATGTCATGAACA
18844 ATGTCATGAACA
1 ATGTCATGAACA
18856 ATGTCA
1 ATGTCA
18862 AATAGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (12 bp):
ATGTCATGAACA
Found at i:18915 original size:11 final size:11
Alignment explanation
Indices: 18899--18935 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
18889 TTTTAAAAAG
18899 TTTTAAACACA
1 TTTTAAACACA
18910 TTTTAAACAC-
1 TTTTAAACACA
*
18920 -TTTAAACATA
1 TTTTAAACACA
18930 TTTTAA
1 TTTTAA
18936 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTTAAACACA
Found at i:27847 original size:19 final size:19
Alignment explanation
Indices: 27812--27861 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
27802 ATAATTCTAT
27812 TAAAATAATATTTAAAAACA-A
1 TAAAATAA-A-TT-AAAACATA
27833 TAAAATAAATTAAAACATA
1 TAAAATAAATTAAAACATA
27852 TAAAATAAAT
1 TAAAATAAAT
27862 GACTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 1 0.04
21 8 0.29
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAATAAATTAAAACATA
Found at i:29179 original size:3 final size:3
Alignment explanation
Indices: 29171--29268 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
29161 TTAATATATT
* * *
29171 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29219 TAA TAA TAA TAA TAA TAA 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
29267 TA
1 TA
29269 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:29845 original size:113 final size:113
Alignment explanation
Indices: 29563--30569 Score: 1766
Period size: 113 Copynumber: 8.9 Consensus size: 113
29553 GATATCAAAC
*
29563 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * *
29628 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAA
66 -ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGC-A
*
29678 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
29743 ATGAACTTTCTCTGGAAAATATGATCCACCGAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
*
29791 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
29856 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
29904 AAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
29968 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
30016 AAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
30080 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
30128 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
30193 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
30241 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
30306 ATGAATTTTCTCTGGAAATGTTGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
30354 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
30419 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
30467 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * *
30532 ATGAATTTTCTCTGGAAATGTTGATCCATCAAGTGATG
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATG
30570 AATTTGAATC
Statistics
Matches: 857, Mismatches: 33, Indels: 6
0.96 0.04 0.01
Matches are distributed among these distances:
112 224 0.26
113 536 0.63
114 34 0.04
115 63 0.07
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
Found at i:31208 original size:52 final size:52
Alignment explanation
Indices: 31130--31951 Score: 1382
Period size: 52 Copynumber: 15.7 Consensus size: 52
31120 CACTTCTTCG
* * *
31130 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
31182 GATCAGATAACTCAAAGAACACTTCCAGAAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCA
*
31237 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31289 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
31341 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
31393 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31445 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
31497 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31549 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31601 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31653 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31705 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
* *
31757 GATCAGATAACTCAAAGAAACAGTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31810 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31862 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
31914 GATTAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
31952 TGAGCACATA
Statistics
Matches: 737, Mismatches: 23, Indels: 20
0.94 0.03 0.03
Matches are distributed among these distances:
51 2 0.00
52 634 0.86
53 51 0.07
55 50 0.07
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:32900 original size:1 final size:1
Alignment explanation
Indices: 32894--33004 Score: 87
Period size: 1 Copynumber: 111.0 Consensus size: 1
32884 CCTTGACCCC
* * * * ** * * * * * * * *
32894 TTTTTTTCTTTTTCTTTTTCTTCTTTTCCTTTCTTTTTTCTTTTCTTTTCTTTCTCTTCTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
32959 TTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
33005 CAAGCATAAT
Statistics
Matches: 82, Mismatches: 28, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:32952 original size:36 final size:36
Alignment explanation
Indices: 32897--32978 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
32887 TGACCCCTTT
*
32897 TTTTCTTTTTCTTTTTCTTCTTTTCCTTTCTTTTTTC
1 TTTTC-TTTTCTTTCTCTTCTTTTCCTTTCTTTTTTC
* *
32934 TTTTCTTTTCTTTCTCTTCTTTTTCTTTCTTTTTTT
1 TTTTCTTTTCTTTCTCTTCTTTTCCTTTCTTTTTTC
*
32970 TTTTTTTTT
1 TTTTCTTTT
32979 TTTTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 36 0.88
37 5 0.12
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (36 bp):
TTTTCTTTTCTTTCTCTTCTTTTCCTTTCTTTTTTC
Found at i:40670 original size:17 final size:17
Alignment explanation
Indices: 40631--40672 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
40621 ATACTTGCAA
40631 ATAAAACATATAAATATT
1 ATAAAA-ATATAAATATT
40649 ATAAAAATAATAAATA-T
1 ATAAAAAT-ATAAATATT
40666 ATAAAAA
1 ATAAAAA
40673 AAATTTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAAATATAAATATT
Found at i:41439 original size:19 final size:18
Alignment explanation
Indices: 41428--41461 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41418 AATATATTTA
41428 AAACA-ATAAAATAAATT
1 AAACATATAAAATAAATT
41445 AAACATATAAAATAAAT
1 AAACATATAAAATAAAT
41462 GACTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (18 bp):
AAACATATAAAATAAATT
Found at i:42777 original size:3 final size:3
Alignment explanation
Indices: 42769--42878 Score: 193
Period size: 3 Copynumber: 36.7 Consensus size: 3
42759 TTAATATATT
* * *
42769 TAA TAA TAA AAA TAA TAA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42817 TAA TAA TAA TAA TAA TAA 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
42865 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
42879 TGGATAAAAA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:44961 original size:2 final size:2
Alignment explanation
Indices: 44954--45003 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
44944 TTAGAAGAGT
44954 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44996 TA TA TA TA
1 TA TA TA TA
45004 GTAAATTCAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60063 original size:23 final size:23
Alignment explanation
Indices: 60037--60093 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
60027 AACAAATATT
60037 AAAACGTCATATAAACCAAAACC
1 AAAACGTCATATAAACCAAAACC
*
60060 AAAACGTCATATAAATCAAAACC
1 AAAACGTCATATAAACCAAAACC
60083 AAAACGTCATA
1 AAAACGTCATA
60094 AAATATCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.56, C:0.23, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAACGTCATATAAACCAAAACC
Found at i:65231 original size:27 final size:27
Alignment explanation
Indices: 65201--65252 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
65191 GTTTTAGATC
*
65201 AATTATCCATTCAATAAATGTATGACA
1 AATTATCCATTCAATAAATGAATGACA
* * *
65228 AATTATTCTTTCAATATATGAATGA
1 AATTATCCATTCAATAAATGAATGA
65253 TATATAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (27 bp):
AATTATCCATTCAATAAATGAATGACA
Found at i:65325 original size:27 final size:27
Alignment explanation
Indices: 65295--65348 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
65285 TATTTTATCG
65295 ATTATAAGATGTTATTCTATAAAGTTT
1 ATTATAAGATGTTATTCTATAAAGTTT
* *
65322 ATTATAAGGTGTTATTTTATAAAGTTT
1 ATTATAAGATGTTATTCTATAAAGTTT
65349 TTTGATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (27 bp):
ATTATAAGATGTTATTCTATAAAGTTT
Found at i:67147 original size:21 final size:20
Alignment explanation
Indices: 67123--67161 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
67113 TCACACCTCA
67123 TCTCCCTTCCTTTAATTCGTC
1 TCTCCCTT-CTTTAATTCGTC
* *
67144 TCTCTCTTCTTTACTTCG
1 TCTCCCTTCTTTAATTCG
67162 AATCATTCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.08, C:0.36, G:0.05, T:0.51
Consensus pattern (20 bp):
TCTCCCTTCTTTAATTCGTC
Done.