Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008079.1 Hibiscus syriacus cultivar Beakdansim tig00110581_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: 86585
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:175 original size:75 final size:75
Alignment explanation
Indices: 12--154 Score: 218
Period size: 74 Copynumber: 1.9 Consensus size: 75
2 TATAAGCCCT
*
12 CAGTACAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTGATATTTTCAAAACCTTCAAGTCATCT
1 CAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTGATATTTTCAAAACCTTCAAGTCATCT
77 GTAAAACTTG
66 GTAAAACTTG
* * **
87 CAGTGCAGGATG-TTTCAAAAAGCCTTCAGGAGTTTTTTGATA-TTTCAAAGCCTTCGGGTCATC
1 CAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAG-CTTTTGATATTTTCAAAACCTTCAAGTCATC
150 TGTAA
65 TGTAA
155 GCCCTTTAGG
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 43 0.69
75 19 0.31
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (75 bp):
CAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTGATATTTTCAAAACCTTCAAGTCATCT
GTAAAACTTG
Found at i:288 original size:88 final size:90
Alignment explanation
Indices: 129--358 Score: 333
Period size: 88 Copynumber: 2.6 Consensus size: 90
119 TTTTTTGATA
* * * *
129 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGGTGCATGATGTTTTCAAAGCCTTCGGGTCA
1 TTTCAAAACCTTCGGGTCATCTATAAGCCC-TTAAGTGCATGATGTTTGCAAAGCCTTCGGGTCA
194 TCTGTAAACCCTTCAGTGCATGATGT
65 TCTGTAAACCCTTCAGTGCATGATGT
*
220 TTTCAAAACCTT-GGGTCATCTATAAGCCCTTAAGTGCATGAT-TTTGCAAAGTCTTCGGGTCAT
1 TTTCAAAACCTTCGGGTCATCTATAAGCCCTTAAGTGCATGATGTTTGCAAAGCCTTCGGGTCAT
* *
283 TTGTAAGCCCTTCAGTGCATGATGT
66 CTGTAAACCCTTCAGTGCATGATGT
* *
308 TTTCAAAACCTTCGGGTCATCCATAAGCCC-TACAGTGCA-GATGTTTTCAAA
1 TTTCAAAACCTTCGGGTCATCTATAAGCCCTTA-AGTGCATGATGTTTGCAAA
359 AAGCTTCGGG
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
88 59 0.46
89 41 0.32
90 16 0.13
91 11 0.09
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (90 bp):
TTTCAAAACCTTCGGGTCATCTATAAGCCCTTAAGTGCATGATGTTTGCAAAGCCTTCGGGTCAT
CTGTAAACCCTTCAGTGCATGATGT
Found at i:336 original size:45 final size:45
Alignment explanation
Indices: 129--368 Score: 315
Period size: 45 Copynumber: 5.4 Consensus size: 45
119 TTTTTTGATA
* *
129 TTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCA-GTGCATGATGT
* *
175 TTTCAAAGCCTTCGGGTCATCTGTAAACCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* *
220 TTTCAAAACCTT-GGGTCATCTATAAGCCCTTAAGTGCATGAT-T
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
* ** *
263 TTGCAAAGTCTTCGGGTCATTTGTAAGCCCTTCAGTGCATGATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
** *
308 TTTCAAAACCTTCGGGTCATCCATAAGCCCTACAGTGCA-GATGT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
*
352 TTTCAAAAAGCTTCGGG
1 TTTC-AAAACCTTCGGG
369 AGCTTTTTGA
Statistics
Matches: 171, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
43 10 0.06
44 63 0.37
45 66 0.39
46 32 0.19
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.33
Consensus pattern (45 bp):
TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGT
Found at i:443 original size:43 final size:44
Alignment explanation
Indices: 376--466 Score: 150
Period size: 43 Copynumber: 2.1 Consensus size: 44
366 GGGAGCTTTT
*
376 TGATATTTCAAAACCTTCGAGTCATCTGTAAGACCT-CAGTGCA
1 TGATGTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
*
419 TGATGTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
463 -GATG
1 TGATG
467 ATAGACCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 38 0.84
44 7 0.16
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
TGATGTTTCAAAACCTTCGAGTCATCTGTAAGACCTACAGTGCA
Found at i:650 original size:3 final size:3
Alignment explanation
Indices: 635--677 Score: 52
Period size: 3 Copynumber: 14.0 Consensus size: 3
625 TCATTTCATT
*
635 TTA TTA ATA TTA TTA TTA -TA TTA TATA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA TTA TTA TTA
678 AATAAATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 27 0.77
4 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:650 original size:12 final size:12
Alignment explanation
Indices: 635--678 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
625 TCATTTCATT
635 TTATTAATATTA
1 TTATTAATATTA
647 TTATT-ATATTA
1 TTATTAATATTA
658 TATATTATATATTA
1 T-TATTA-ATATTA
672 TTATTAA
1 TTATTAA
679 ATAAATAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.24
12 10 0.34
13 5 0.17
14 7 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:663 original size:7 final size:7
Alignment explanation
Indices: 645--677 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
635 TTATTAATAT
645 TATTATTA
1 TATTA-TA
653 TATTATA
1 TATTATA
660 TATTATA
1 TATTATA
667 TATTAT-
1 TATTATA
673 TATTA
1 TATTA
678 AATAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 5 0.20
7 15 0.60
8 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TATTATA
Found at i:689 original size:25 final size:24
Alignment explanation
Indices: 636--682 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
626 CATTTCATTT
* *
636 TATTAATATTATTATTATATTATA
1 TATTAATATTATTATTAAATAATA
660 TATTATATATTATTATTAAATAA
1 TATTA-ATATTATTATTAAATAA
683 ATAATTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
TATTAATATTATTATTAAATAATA
Found at i:2572 original size:2 final size:2
Alignment explanation
Indices: 2567--2670 Score: 169
Period size: 2 Copynumber: 53.5 Consensus size: 2
2557 TCTTTTTTAA
2567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
*
2650 AT AT AT AT -T AT A- AT CT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
2671 ATTAATATTT
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
1 3 0.03
2 92 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10415 original size:21 final size:21
Alignment explanation
Indices: 10389--10428 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10379 CAGAACCCCA
*
10389 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
10410 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
10429 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:10463 original size:20 final size:21
Alignment explanation
Indices: 10409--10471 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
10399 GATTCCCCTG
10409 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
10433 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
10453 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
10472 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:14316 original size:22 final size:21
Alignment explanation
Indices: 14274--14313 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
14264 GAGTTTGTTT
*
14274 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
14295 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
14314 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:16331 original size:22 final size:23
Alignment explanation
Indices: 16293--16348 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 23
16283 AACTATTCAT
16293 GGGGAATCGGTACCCCCCTTGGG
1 GGGGAATCGGTACCCCCCTTGGG
16316 GGGGAATCGGTA-CCCCCTTGGG
1 GGGGAATCGGTACCCCCCTTGGG
16338 GGGGAATCGGT
1 GGGGAATCGGT
16349 TCCCTCTGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.64
23 12 0.36
ACGTcount: A:0.14, C:0.25, G:0.43, T:0.18
Consensus pattern (23 bp):
GGGGAATCGGTACCCCCCTTGGG
Found at i:20823 original size:14 final size:15
Alignment explanation
Indices: 20806--20838 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
20796 GATGTTGTTC
*
20806 AAAAAAGAGA-GAAA
1 AAAAAAGACATGAAA
20820 AAAAAAGACATGAAA
1 AAAAAAGACATGAAA
20835 AAAA
1 AAAA
20839 TGGAAAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAGACATGAAA
Found at i:25453 original size:21 final size:21
Alignment explanation
Indices: 25414--25453 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25404 AAAGGGGACA
* * *
25414 AAATGTTGTACCTCTAGAGTC
1 AAATATTGTACATCAAGAGTC
25435 AAATATTGTACATCAAGAG
1 AAATATTGTACATCAAGAG
25454 CTATTCGTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
AAATATTGTACATCAAGAGTC
Found at i:26313 original size:24 final size:24
Alignment explanation
Indices: 26286--26332 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26276 TTTTATTTAG
*
26286 ATATTTAAAATATT-TTTAAAATAA
1 ATATTTAAAA-ATTGATTAAAATAA
26310 ATATTTAAAAATTGATTAAAATA
1 ATATTTAAAAATTGATTAAAATA
26333 TATTCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATTTAAAAATTGATTAAAATAA
Found at i:26443 original size:15 final size:16
Alignment explanation
Indices: 26423--26456 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
26413 TTAATCCTAC
26423 AAATAAGA-ATTTAAA
1 AAATAAGATATTTAAA
*
26438 AAATAATATATTTAAA
1 AAATAAGATATTTAAA
26454 AAA
1 AAA
26457 ATTTATGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAATAAGATATTTAAA
Found at i:28901 original size:14 final size:14
Alignment explanation
Indices: 28882--28913 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
28872 AACCAATTGA
*
28882 TAAAAATAATATAT
1 TAAAAATAAAATAT
28896 TAAAAATAAAATAT
1 TAAAAATAAAATAT
28910 TAAA
1 TAAA
28914 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAATAAAATAT
Found at i:28908 original size:19 final size:18
Alignment explanation
Indices: 28884--28925 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28874 CCAATTGATA
*
28884 AAAATAATATATTAAAAAT
1 AAAATAATA-AATAAAAAT
*
28903 AAAATATTAAATAAAAAT
1 AAAATAATAAATAAAAAT
28921 AAAAT
1 AAAAT
28926 TTAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATAATAAATAAAAAT
Found at i:28929 original size:17 final size:18
Alignment explanation
Indices: 28896--28932 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28886 AATAATATAT
28896 TAAAAATAAAATATTAAA
1 TAAAAATAAAATATTAAA
28914 TAAAAATAAAAT-TTAAA
1 TAAAAATAAAATATTAAA
28931 TA
1 TA
28933 TTTGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAAAATATTAAA
Found at i:29143 original size:24 final size:24
Alignment explanation
Indices: 29111--29157 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29101 GGGCGAGAGT
29111 GGGAGGGGAAGGGGCGAGAAAAGG
1 GGGAGGGGAAGGGGCGAGAAAAGG
* *
29135 GGGAGGGGAGGGGGCGGGAAAAG
1 GGGAGGGGAAGGGGCGAGAAAAG
29158 CAAAATTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.04, G:0.66, T:0.00
Consensus pattern (24 bp):
GGGAGGGGAAGGGGCGAGAAAAGG
Found at i:47543 original size:27 final size:27
Alignment explanation
Indices: 47513--47565 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
47503 CACATATATG
* * *
47513 TATATATACTTTTGTTTTTCATAAAAT
1 TATATAAACTATTGTTTTTCAAAAAAT
47540 TATATAAACTATTGTTTTTCAAAAAA
1 TATATAAACTATTGTTTTTCAAAAAA
47566 ACTTTTGGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (27 bp):
TATATAAACTATTGTTTTTCAAAAAAT
Found at i:49608 original size:19 final size:19
Alignment explanation
Indices: 49586--49641 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
49576 ACCATGGCAA
49586 CGATTCCTCAAAATGGTAC
1 CGATTCCTCAAAATGGTAC
* * *
49605 CGA-TAC-C---ATGGCAA
1 CGATTCCTCAAAATGGTAC
49619 CGATTCCTCAAAATGGTAC
1 CGATTCCTCAAAATGGTAC
49638 CGAT
1 CGAT
49642 ACCATGCATG
Statistics
Matches: 26, Mismatches: 6, Indels: 10
0.62 0.14 0.24
Matches are distributed among these distances:
14 8 0.31
15 2 0.08
16 1 0.04
17 1 0.04
18 2 0.08
19 12 0.46
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (19 bp):
CGATTCCTCAAAATGGTAC
Found at i:49610 original size:33 final size:33
Alignment explanation
Indices: 49568--49647 Score: 160
Period size: 33 Copynumber: 2.4 Consensus size: 33
49558 TGCTAAGGCA
49568 GTACCGATACCATGGCAACGATTCCTCAAAATG
1 GTACCGATACCATGGCAACGATTCCTCAAAATG
49601 GTACCGATACCATGGCAACGATTCCTCAAAATG
1 GTACCGATACCATGGCAACGATTCCTCAAAATG
49634 GTACCGATACCATG
1 GTACCGATACCATG
49648 CATGTTATCG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (33 bp):
GTACCGATACCATGGCAACGATTCCTCAAAATG
Found at i:62140 original size:45 final size:44
Alignment explanation
Indices: 62050--62141 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 44
62040 TGAAGTATAG
62050 GGCCATGAGGAAGTAGTTTGGAAAAATTGTAGAAAAGTTCATAT
1 GGCCATGAGGAAGTAGTTTGGAAAAATTGTAGAAAAGTTCATAT
*
62094 GGCCATGAGGAAGTAGTTTTGGAAAAATTGTAGAACAA-TTCCTAT
1 GGCCATGAGGAAGTAG-TTTGGAAAAATTGTAGAA-AAGTTCATAT
62139 GGC
1 GGC
62142 TTAGAAATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
44 16 0.36
45 27 0.60
46 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (44 bp):
GGCCATGAGGAAGTAGTTTGGAAAAATTGTAGAAAAGTTCATAT
Found at i:63921 original size:18 final size:18
Alignment explanation
Indices: 63886--63930 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
63876 TTCTCTTATT
*
63886 TTTATTTAAATTGCTTTTA
1 TTTATTT-AATTGATTTTA
63905 TTTATTTAATTGATTTTA
1 TTTATTTAATTGATTTTA
63923 -TTATTTAA
1 TTTATTTAA
63931 ATATCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (18 bp):
TTTATTTAATTGATTTTA
Found at i:73119 original size:21 final size:20
Alignment explanation
Indices: 73095--73143 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
73085 CTCTATTCTC
*
73095 TTATTTTTATTTAAATTGCTT
1 TTATTTTTATTT-AATCGCTT
73116 TTA--TTTATTTAATCGCTT
1 TTATTTTTATTTAATCGCTT
73134 TTATTATTTA
1 TTATT-TTTA
73144 AATATCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
21 7 0.29
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.65
Consensus pattern (20 bp):
TTATTTTTATTTAATCGCTT
Found at i:73135 original size:18 final size:18
Alignment explanation
Indices: 73100--73144 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
73090 TTCTCTTATT
*
73100 TTTATTTAAATTGCTTTTA
1 TTTATTT-AATCGCTTTTA
73119 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
73137 -TTATTTAA
1 TTTATTTAA
73145 ATATCTCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 10 0.40
19 7 0.28
ACGTcount: A:0.27, C:0.07, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:74698 original size:19 final size:20
Alignment explanation
Indices: 74653--74699 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
74643 TCAAACGACC
74653 GAAAACATGTCATAAAGACAG
1 GAAAA-ATGTCATAAAGACAG
*
74674 GAAAAATGTTATAAAGACA-
1 GAAAAATGTCATAAAGACAG
74693 GAAAAAT
1 GAAAAAT
74700 ACGTGTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.28
20 13 0.52
21 5 0.20
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GAAAAATGTCATAAAGACAG
Found at i:74713 original size:23 final size:21
Alignment explanation
Indices: 74660--74718 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 21
74650 ACCGAAAACA
74660 TGTCATAAAGACAGGAAAAATG
1 TGTCATAAAGACA-GAAAAATG
74682 T-T-ATAAAGACAGAAAAATACG
1 TGTCATAAAGACAGAAAAAT--G
*
74703 TGTCATAAAGATAGAA
1 TGTCATAAAGACAGAA
74719 TTAATAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
19 7 0.22
20 9 0.28
21 3 0.09
22 2 0.06
23 11 0.34
ACGTcount: A:0.53, C:0.08, G:0.19, T:0.20
Consensus pattern (21 bp):
TGTCATAAAGACAGAAAAATG
Found at i:75230 original size:12 final size:13
Alignment explanation
Indices: 75215--75246 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
75205 AATTTCGAAT
75215 TAAAATAAA-TTA
1 TAAAATAAATTTA
75227 TAAAATAAATTTA
1 TAAAATAAATTTA
75240 TAAAATA
1 TAAAATA
75247 TAAGATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAAAATAAATTTA
Found at i:79556 original size:15 final size:15
Alignment explanation
Indices: 79536--79567 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
79526 AGTTTTGCTC
79536 CTAGTGAAGATGCAT
1 CTAGTGAAGATGCAT
79551 CTAGTGAAGATGCAT
1 CTAGTGAAGATGCAT
79566 CT
1 CT
79568 GCTGTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (15 bp):
CTAGTGAAGATGCAT
Found at i:80227 original size:43 final size:43
Alignment explanation
Indices: 80161--80555 Score: 340
Period size: 43 Copynumber: 9.3 Consensus size: 43
80151 CAGAGTGCAT
* * ** *
80161 ATTTGGCGGCGTTTGT-TCTAAAAACAACGCTATAGGTCTGAC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * *
80203 ATTTTTCGGCGTTTGTATCCAAAAACGTCGCTATAGATATGTC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * *
80246 ATTTTTCGGTGTTTGTATTCAAAAACGTCGCTATAGATCTGAC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * *
80289 CTTTTGCGGCGTTTGT-TCCAAAAATGTCACTATAGATCTGAC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * * * *
80331 CTTTTGCGGCGTTTGTA-CCAAAAAATGCCGCTATATAACTGAC
1 ATTTTGCGGCGTTTGTATCC-AAAAACGTCGCTATAGATCTGAC
* * * *
80374 CTTTTGCGGCGTTTGT-TCC-AAAATGCCGCTATAGATCTGAT
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * * ** *
80415 A-TTTGCGGCGTTTGTATCAAAAAATGCCGCTATAGAAATTAC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
* * * *
80457 CTTTTGCGGCGTTTGT-TCTAAAAACG-CTGGTATAGATCTCTAC
1 ATTTTGCGGCGTTTGTATCCAAAAACGTC-GCTATAGATCT-GAC
* * * * *
80500 CTTTTGCGGCGTTTGT-TCCGAAAACGCCGCAATAGATCTTGAT
1 ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATC-TGAC
*
80543 TTTTTGCGGCGTT
1 ATTTTGCGGCGTT
80556 CTTTTGTTCT
Statistics
Matches: 298, Mismatches: 44, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
40 14 0.05
41 22 0.07
42 89 0.30
43 171 0.57
44 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (43 bp):
ATTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGAC
Found at i:80363 original size:85 final size:84
Alignment explanation
Indices: 80166--80555 Score: 374
Period size: 85 Copynumber: 4.6 Consensus size: 84
80156 TGCATATTTG
* * ** * * *
80166 GCGGCGTTTGTTCTAAAAACAACGCTATAGGTCTGACATTTTTCGGCGTTTGTATCCAAAAACGT
1 GCGGCGTTTGTACCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGT-TCCAAAAACGT
* * *
80231 CGCTATAGATATGTCATTTT
65 CGCTATAGATCTGACCTTTT
* * * * *
80251 TCGGTGTTTGTATTCAAAAACGTCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGT
1 GCGGCGTTTGTA-CCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGT
*
80316 CACTATAGATCTGACCTTTT
65 CGCTATAGATCTGACCTTTT
* * * * *
80336 GCGGCGTTTGTACCAAAAAATGCCGCTATATAACTGACCTTTTGCGGCGTTTGTTCC-AAAATGC
1 GCGGCGTTTGTACC-AAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGT
80400 CGCTATAGATCTGA--TATTT
65 CGCTATAGATCTGACCT-TTT
* * ** * *
80419 GCGGCGTTTGTATCAAAAAATGCCGCTATAGAAATTACCTTTTGCGGCGTTTGTTCTAAAAACG-
1 GCGGCGTTTGTA-CCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGT
* *
80483 CTGGTATAGATCTCTACCTTTT
65 C-GCTATAGATCT-GACCTTTT
* * * **
80505 GCGGCGTTTGTTCCGAAAACGCCGCAATAGATCTTGATTTTTTGCGGCGTT
1 GCGGCGTTTGTACCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTT
80556 CTTTTGTTCT
Statistics
Matches: 253, Mismatches: 42, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
82 1 0.00
83 54 0.21
84 36 0.14
85 99 0.39
86 62 0.25
87 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (84 bp):
GCGGCGTTTGTACCAAAAACGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAACGTC
GCTATAGATCTGACCTTTT
Found at i:80459 original size:126 final size:126
Alignment explanation
Indices: 80267--80555 Score: 341
Period size: 126 Copynumber: 2.3 Consensus size: 126
80257 TTTGTATTCA
* * * **
80267 AAAACGTCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAATGTCACTATAGATCTGACC
1 AAAACGCCGCTATAGATCTGA-CTTTTGCGGCGTTTGTTCAAAAAATGCCACTATAGAAATGACC
* *
80332 TTTTGCGGCGTTTGTACCAAAAAATGCCGCTATATAACT-GACCTTTTGCGGCGTTTGTTCC-
65 TTTTGCGGCGTTTGT-CCAAAAAACGCCGCTATAGAACTCGACCTTTTGCGGCGTTTGTTCCG
* * *
80393 AAAATGCCGCTATAGATCTGA-TATTTGCGGCGTTTGTATCAAAAAATGCCGCTATAGAAATTAC
1 AAAACGCCGCTATAGATCTGACT-TTTGCGGCGTTTGT-TCAAAAAATGCCACTATAGAAATGAC
* * * * * *
80457 CTTTTGCGGCGTTTGTTCTAAAAACGCTGGTATAGATCTCTACCTTTTGCGGCGTTTGTTCCG
64 CTTTTGCGGCGTTTGTCCAAAAAACGCCGCTATAGAACTCGACCTTTTGCGGCGTTTGTTCCG
* *
80520 AAAACGCCGCAATAGATCTTGATTTTTTGCGGCGTT
1 AAAACGCCGCTATAGATC-TGA-CTTTTGCGGCGTT
80556 CTTTTGTTCT
Statistics
Matches: 138, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
124 1 0.01
125 30 0.22
126 76 0.55
127 16 0.12
128 3 0.02
129 11 0.08
130 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (126 bp):
AAAACGCCGCTATAGATCTGACTTTTGCGGCGTTTGTTCAAAAAATGCCACTATAGAAATGACCT
TTTGCGGCGTTTGTCCAAAAAACGCCGCTATAGAACTCGACCTTTTGCGGCGTTTGTTCCG
Found at i:85246 original size:24 final size:24
Alignment explanation
Indices: 85219--85267 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
85209 TGGCGTTCAC
85219 CTTGAGAAGGCTTATGATAGTGTT
1 CTTGAGAAGGCTTATGATAGTGTT
85243 CTTGAGAAGGCTTATGATAGTGTT
1 CTTGAGAAGGCTTATGATAGTGTT
85267 C
1 C
85268 CCCGCGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.37
Consensus pattern (24 bp):
CTTGAGAAGGCTTATGATAGTGTT
Done.