Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004412.1 Hibiscus syriacus cultivar Beakdansim tig00009674_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: 100983
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:345 original size:54 final size:53
Alignment explanation
Indices: 204--347 Score: 171
Period size: 54 Copynumber: 2.6 Consensus size: 53
194 GTAATGGTAG
* * * * *
204 TATCGATACCTGAAGGATGGTATCGATACCCTTAAAACATCGAATGCCAGATTGG
1 TATCGGTACCTG-AGGA-GGTATCGATACCCTTGAAACATCAAATGCCAGATCGA
* * * *
259 TATCAGTACCTGGAGGAGGTATTGATACCCTTGAAACATCAAATGCTATATCGA
1 TATCGGTACCT-GAGGAGGTATCGATACCCTTGAAACATCAAATGCCAGATCGA
313 TATCGGTACCATGAGGAGGTATCGATACCCTTGAA
1 TATCGGTACC-TGAGGAGGTATCGATACCCTTGAA
348 GGGAAGTATC
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
54 61 0.80
55 14 0.18
56 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (53 bp):
TATCGGTACCTGAGGAGGTATCGATACCCTTGAAACATCAAATGCCAGATCGA
Found at i:830 original size:13 final size:15
Alignment explanation
Indices: 812--843 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
802 AAATACTTTG
812 AATAATGAT-TGA-T
1 AATAATGATGTGATT
825 AATAATGATGTGATT
1 AATAATGATGTGATT
840 AATA
1 AATA
844 GCCCAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
AATAATGATGTGATT
Found at i:925 original size:21 final size:21
Alignment explanation
Indices: 901--950 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
891 ATTCGAGGGT
*
901 TTATGTGGTCTTTCGGGATAA
1 TTATGTGGTCTTTCGGGACAA
922 TTATGTGGTCTTTCGGGACAA
1 TTATGTGGTCTTTCGGGACAA
*
943 ATATGTGG
1 TTATGTGG
951 CACTTCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.10, G:0.30, T:0.40
Consensus pattern (21 bp):
TTATGTGGTCTTTCGGGACAA
Found at i:957 original size:21 final size:22
Alignment explanation
Indices: 933--1024 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 22
923 TATGTGGTCT
933 TTCGG-GACAAATATGTGGCAC
1 TTCGGTGACAAATATGTGGCAC
*
954 TTCGGTG-CAAAACTATGTGACAC
1 TTCGGTGAC-AAA-TATGTGGCAC
*
977 TTCGGTGTA-AACCTATGTGGTC-C
1 TTCGGTG-ACAA-ATATGTGG-CAC
* *
1000 TTCGG-GACAATTATGTGGTAC
1 TTCGGTGACAAATATGTGGCAC
1021 TTCG
1 TTCG
1025 ATGGAAATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
21 19 0.33
22 7 0.12
23 30 0.53
24 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (22 bp):
TTCGGTGACAAATATGTGGCAC
Found at i:1002 original size:23 final size:23
Alignment explanation
Indices: 944--1004 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
934 TCGGGACAAA
944 TATGTGGCACTTCGGTGCAAAAC
1 TATGTGGCACTTCGGTGCAAAAC
* * *
967 TATGTGACACTTCGGTGTAAACC
1 TATGTGGCACTTCGGTGCAAAAC
990 TATGTGGTC-CTTCGG
1 TATGTGG-CACTTCGG
1005 GACAATTATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (23 bp):
TATGTGGCACTTCGGTGCAAAAC
Found at i:3859 original size:27 final size:27
Alignment explanation
Indices: 3829--3881 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3819 GATAGTAGAG
*
3829 TTGTTCTACACATCCCTTATCATACAT
1 TTGTTCAACACATCCCTTATCATACAT
3856 TTGTTCAACACATCCCTTATCATACA
1 TTGTTCAACACATCCCTTATCATACA
3882 CTTATTCGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.38
Consensus pattern (27 bp):
TTGTTCAACACATCCCTTATCATACAT
Found at i:5138 original size:15 final size:16
Alignment explanation
Indices: 5113--5144 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5103 TATTCAATTT
5113 ACAAGTCCAAATTACA
1 ACAAGTCCAAATTACA
5129 ACAA-TCCAAATTACA
1 ACAAGTCCAAATTACA
5144 A
1 A
5145 AAGACACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (16 bp):
ACAAGTCCAAATTACA
Found at i:7331 original size:23 final size:23
Alignment explanation
Indices: 7305--7365 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
7295 TGCACTAAAA
*
7305 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
7328 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
7351 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
7366 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:7544 original size:103 final size:103
Alignment explanation
Indices: 7381--7598 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
7371 TAATGTCCAT
* * *
7381 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATTAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
7446 GACTTTACACATGTTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
7484 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
7549 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
7587 AAGGACCACATA
1 AAGGACCACATA
7599 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:12449 original size:23 final size:23
Alignment explanation
Indices: 12411--12467 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
12401 CTCATATAAA
* *
12411 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTTCCACATAGAAT
* * *
12434 TGTACTGTAGTTCCACGTAGAAT
1 TGCACCGTAGTTCCACATAGAAT
12457 TGCACCGTAGT
1 TGCACCGTAGT
12468 GCCATATAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (23 bp):
TGCACCGTAGTTCCACATAGAAT
Found at i:12663 original size:102 final size:103
Alignment explanation
Indices: 12482--12703 Score: 383
Period size: 102 Copynumber: 2.2 Consensus size: 103
12472 TATAATAATG
* * * *
12482 TCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCT
1 TCCAGAAGGACCACATACCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCT
12547 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
* *
12585 TTC-GAAGGACCACATACCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCT
1 TCCAGAAGGACCACATACCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCT
12649 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
66 CACCAGACTTCACACATGTTCCAAAGAATACATATATA
12687 TCCAGAAGGACCACATA
1 TCCAGAAGGACCACATA
12704 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
102 96 0.86
103 15 0.14
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
TCCAGAAGGACCACATACCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCT
CACCAGACTTCACACATGTTCCAAAGAATACATATATA
Found at i:20234 original size:42 final size:42
Alignment explanation
Indices: 20187--20266 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
20177 CCACCTTAAT
* *
20187 TTTAATTACGATTCGAATTAAGTAATAATATATAAAAAAATA
1 TTTAATTACGATTCAAATTAAGTAACAATATATAAAAAAATA
*
20229 TTTAATTATGATTCAAATTAAGTAACAATATATAAAAA
1 TTTAATTACGATTCAAATTAAGTAACAATATATAAAAA
20267 CATAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.53, C:0.05, G:0.06, T:0.36
Consensus pattern (42 bp):
TTTAATTACGATTCAAATTAAGTAACAATATATAAAAAAATA
Found at i:21416 original size:28 final size:28
Alignment explanation
Indices: 21384--21441 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
21374 GAGTCCATGA
*
21384 TTATATTATGTATTTGATTTGCCTCTGC
1 TTATATTATGTATTTCATTTGCCTCTGC
*
21412 TTATATTATGTATTTCATTTGCCTTTGC
1 TTATATTATGTATTTCATTTGCCTCTGC
21440 TT
1 TT
21442 CTGATGTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (28 bp):
TTATATTATGTATTTCATTTGCCTCTGC
Found at i:25279 original size:9 final size:9
Alignment explanation
Indices: 25265--25330 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 9
25255 GGCTGCTGGA
25265 AACCGGTTT
1 AACCGGTTT
25274 AACCGGTTTT
1 AACCGG-TTT
25284 CAACCGGTTCT
1 -AACCGGTT-T
*
25295 GACCGGTTT
1 AACCGGTTT
*
25304 CAACCGGTTCG
1 -AACCGGTT-T
25315 AACCGGTTT
1 AACCGGTTT
*
25324 GACCGGT
1 AACCGGT
25331 CTGAATCGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 13 0.28
10 27 0.57
11 7 0.15
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:25290 original size:20 final size:21
Alignment explanation
Indices: 25265--25323 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
25255 GGCTGCTGGA
25265 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
*
25285 AACCGGTTCTGACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
*
25305 AACCGGTTCGAACCGGTTT
1 AACCGGTTCTAACCGGTTT
25324 GACCGGTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 26 0.76
21 8 0.24
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:25301 original size:10 final size:10
Alignment explanation
Indices: 25286--25374 Score: 59
Period size: 10 Copynumber: 9.3 Consensus size: 10
25276 CCGGTTTTCA
25286 ACCGGTTCTG
1 ACCGGTTCTG
*
25296 ACCGGTT-TCA
1 ACCGGTTCT-G
25306 ACCGGTTC-G
1 ACCGGTTCTG
25315 AACCGGTT-TG
1 -ACCGGTTCTG
25325 ACCGG-TCTG
1 ACCGGTTCTG
*
25334 AATCGGTT-TG
1 -ACCGGTTCTG
*
25344 ACCAG-TCTG
1 ACCGGTTCTG
25353 AGCCGGTT-TG
1 A-CCGGTTCTG
25363 ACCGG-TCTG
1 ACCGGTTCTG
25372 ACC
1 ACC
25375 CGACCCGACC
Statistics
Matches: 62, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
8 3 0.05
9 23 0.37
10 34 0.55
11 2 0.03
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.27
Consensus pattern (10 bp):
ACCGGTTCTG
Found at i:25302 original size:30 final size:29
Alignment explanation
Indices: 25266--25330 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
25256 GCTGCTGGAA
25266 ACCGGTTT-AACCGGTTTTC-AACCGGTTCTG
1 ACCGGTTTCAACCGG--TTCGAACCGGTT-TG
25296 ACCGGTTTCAACCGGTTCGAACCGGTTTG
1 ACCGGTTTCAACCGGTTCGAACCGGTTTG
25325 ACCGGT
1 ACCGGT
25331 CTGAATCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
29 11 0.33
30 16 0.48
31 6 0.18
ACGTcount: A:0.17, C:0.28, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTCAACCGGTTCGAACCGGTTTG
Found at i:25330 original size:19 final size:20
Alignment explanation
Indices: 25286--25372 Score: 94
Period size: 19 Copynumber: 4.5 Consensus size: 20
25276 CCGGTTTTCA
*
25286 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTTCTGAACCGGTTT-G
25306 ACCGGTTC-GAACCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
*
25325 ACCGG-TCTGAATCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
* *
25344 ACCAG-TCTGAGCCGGTTTG
1 ACCGGTTCTGAACCGGTTTG
25363 ACCGG-TCTGA
1 ACCGGTTCTGA
25373 CCCGACCCGA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
18 2 0.03
19 41 0.69
20 16 0.27
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (20 bp):
ACCGGTTCTGAACCGGTTTG
Found at i:25373 original size:9 final size:9
Alignment explanation
Indices: 25316--25374 Score: 55
Period size: 9 Copynumber: 6.3 Consensus size: 9
25306 ACCGGTTCGA
*
25316 ACCGGTTTG
1 ACCGGTCTG
25325 ACCGGTCTG
1 ACCGGTCTG
* *
25334 AATCGGTTTG
1 -ACCGGTCTG
*
25344 ACCAGTCTG
1 ACCGGTCTG
*
25353 AGCCGGTTTG
1 A-CCGGTCTG
25363 ACCGGTCTG
1 ACCGGTCTG
25372 ACC
1 ACC
25375 CGACCCGACC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
9 25 0.64
10 14 0.36
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:25397 original size:22 final size:22
Alignment explanation
Indices: 25371--25413 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
25361 TGACCGGTCT
25371 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
25393 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
25414 GTTGACCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:25415 original size:7 final size:7
Alignment explanation
Indices: 25403--25433 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
25393 GACCCGACCC
25403 GACCGTT
1 GACCGTT
25410 GACCGTT
1 GACCGTT
25417 GACCGTT
1 GACCGTT
25424 GACCGTT
1 GACCGTT
25431 GAC
1 GAC
25434 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:32590 original size:9 final size:9
Alignment explanation
Indices: 32576--32650 Score: 69
Period size: 10 Copynumber: 7.8 Consensus size: 9
32566 GGCTGCTGGA
32576 AACCGGTTT
1 AACCGGTTT
32585 AACCGGTTTT
1 AACCGG-TTT
32595 CAACCGGTTCT
1 -AACCGGTT-T
*
32606 GACCGGTTT
1 AACCGGTTT
*
32615 GACCGGTTT
1 AACCGGTTT
*
32624 CAACCGGTTCG
1 -AACCGGTT-T
32635 AACCGGTTT
1 AACCGGTTT
*
32644 GACCGGT
1 AACCGGT
32651 CTGAATCGGT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
9 22 0.39
10 27 0.48
11 7 0.12
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:32621 original size:19 final size:18
Alignment explanation
Indices: 32597--32694 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 18
32587 CCGGTTTTCA
*
32597 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TGACCGGTCTG
*
32616 ACCGGTTTCAACCGGT-TCG
1 ACCGGTTT-GACCGGTCT-G
32635 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGTCTG
* *
32654 AATCGGTTTGACCAGTCTG
1 -ACCGGTTTGACCGGTCTG
32673 AGCCGGTTTGACCGGTCTG
1 A-CCGGTTTGACCGGTCTG
32692 ACC
1 ACC
32695 CGACCCAACC
Statistics
Matches: 68, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.07
19 54 0.79
20 9 0.13
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.28
Consensus pattern (18 bp):
ACCGGTTTGACCGGTCTG
Found at i:32639 original size:29 final size:30
Alignment explanation
Indices: 32576--32650 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
32566 GGCTGCTGGA
*
32576 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
32607 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
32635 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
32651 CTGAATCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:36952 original size:19 final size:19
Alignment explanation
Indices: 36927--37022 Score: 99
Period size: 19 Copynumber: 5.1 Consensus size: 19
36917 AGTTAACTTT
36927 GGTCAAAGTCAATGGGTCA
1 GGTCAAAGTCAATGGGTCA
* *
36946 TGTCAAAGTCAACGGGTCA
1 GGTCAAAGTCAATGGGTCA
*
36965 GGTCAAAGTCAACGGGTC-
1 GGTCAAAGTCAATGGGTCA
*
36983 GGATC-AAGTCAATGGG-CC
1 GG-TCAAAGTCAATGGGTCA
*
37001 GATTCAAAGTCAATGGTGTCA
1 G-GTCAAAGTCAATGG-GTCA
37022 G
1 G
37023 ATCAGTTTGG
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
17 1 0.02
18 15 0.23
19 46 0.71
20 1 0.02
21 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.21
Consensus pattern (19 bp):
GGTCAAAGTCAATGGGTCA
Found at i:37051 original size:20 final size:20
Alignment explanation
Indices: 37019--37083 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
37009 GTCAATGGTG
*
37019 TCAGATCAGTTTGGGTTGAC
1 TCAGATCAGTTTGAGTTGAC
*
37039 TCAGATC-GATTTGAGTTGCC
1 TCAGATCAG-TTTGAGTTGAC
* * * *
37059 TTAGTTCGGTCTGAGTTGAC
1 TCAGATCAGTTTGAGTTGAC
37079 TCAGA
1 TCAGA
37084 CCGGTTCAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (20 bp):
TCAGATCAGTTTGAGTTGAC
Found at i:42226 original size:36 final size:36
Alignment explanation
Indices: 42145--42308 Score: 206
Period size: 36 Copynumber: 4.6 Consensus size: 36
42135 CGAAAGAAAA
*
42145 CATCGGCACTTCCGATT-AAGTCGAACAGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * *
42180 CATCGACACTTTCGATTCAAGTTGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
*
42216 TATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * * *
42252 CATCGACACTTCCGATTCAAGTTGAACGGAATGATG
1 CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
* * *
42288 TATC-GCACTTTCGTTTCAAGT
1 CATCGGCACTTCCGATTCAAGT
42309 ATTCGTCTTT
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 29 0.26
36 82 0.74
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (36 bp):
CATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAG
Found at i:42255 original size:72 final size:72
Alignment explanation
Indices: 42146--42308 Score: 258
Period size: 72 Copynumber: 2.3 Consensus size: 72
42136 GAAAGAAAAC
*
42146 ATCGGCACTTCCGATT-AAGTCGAACAGAAGGAAGCATCGACACTTTCGATTCAAGTTGAACGGA
1 ATCGGCACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTCCGATTCAAGTTGAACGGA
42210 AGGAAGT
66 AGGAAGT
*
42217 ATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGACACTTCCGATTCAAGTTGAACGGA
1 ATCGGCACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTCCGATTCAAGTTGAACGGA
* *
42282 ATGATGT
66 AGGAAGT
* *
42289 ATC-GCACTTTCGTTTCAAGT
1 ATCGGCACTTCCGATTCAAGT
42309 ATTCGTCTTT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
71 31 0.36
72 54 0.64
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (72 bp):
ATCGGCACTTCCGATTCAAGTCGAACAGAAGGAAGCATCGACACTTCCGATTCAAGTTGAACGGA
AGGAAGT
Found at i:47045 original size:23 final size:23
Alignment explanation
Indices: 46978--47032 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
46968 CGTTTATATG
*
46978 TTCACGAACATATCCATTTAGCA
1 TTCACGAACATATCCATTTAGTA
47001 TTCACGAACATATCCATTTAGTA
1 TTCACGAACATATCCATTTAGTA
47024 TTCACGAAC
1 TTCACGAAC
47033 GTGTTCGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (23 bp):
TTCACGAACATATCCATTTAGTA
Found at i:55421 original size:39 final size:39
Alignment explanation
Indices: 55375--55452 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
55365 TTAATTAAGT
* *
55375 TTGGTTCTAGTTTCCACCATCTAAATGTGTGTCTAGTTC
1 TTGGTTCTAGTTTCCACCATCTAAATATGTGGCTAGTTC
*
55414 TTGGTTCTAGTTTCTACCATCTAAATATGTGGCTAGTTC
1 TTGGTTCTAGTTTCCACCATCTAAATATGTGGCTAGTTC
55453 CCAAAAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (39 bp):
TTGGTTCTAGTTTCCACCATCTAAATATGTGGCTAGTTC
Found at i:58118 original size:82 final size:82
Alignment explanation
Indices: 57981--58142 Score: 270
Period size: 82 Copynumber: 2.0 Consensus size: 82
57971 TATTCTAACT
* * * *
57981 ATTGCCATCCTTTCCTGATTGCTTACTGCTTTTCTTTCACTGCTTTGACCGGAGACATGCATCTC
1 ATTGCCATCCTTTCCTGATTGCTTACTGCTTTACTTTCACCGCTTTAACAGGAGACATGCATCTC
58046 AAATCCAATTGAATAAA
66 AAATCCAATTGAATAAA
*
58063 ATTGCCATCTTTTCCTGATTGCTTACTGCTTTACTTTCACCGCTTTAACAGGAGACATGCATCTC
1 ATTGCCATCCTTTCCTGATTGCTTACTGCTTTACTTTCACCGCTTTAACAGGAGACATGCATCTC
*
58128 GAATCCAATTGAATA
66 AAATCCAATTGAATA
58143 TTGTGAAGGA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (82 bp):
ATTGCCATCCTTTCCTGATTGCTTACTGCTTTACTTTCACCGCTTTAACAGGAGACATGCATCTC
AAATCCAATTGAATAAA
Found at i:64029 original size:3 final size:3
Alignment explanation
Indices: 64021--64068 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
64011 TCTACTTTTG
*
64021 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTT TTA CTT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
64066 TTA
1 TTA
64069 ATGTTGTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:69038 original size:77 final size:79
Alignment explanation
Indices: 68895--69047 Score: 204
Period size: 77 Copynumber: 2.0 Consensus size: 79
68885 ATATAGTAAG
* *
68895 TAAACATTAAATGAATGTAATTTTGATTACAACTCTTTTAATTGATATTTAATTCGAAATAATTA
1 TAAACATTAAATGAATGTAATTTAGATTACAACTCATTTAATTGATATTTAATTCGAAATAATTA
68960 AATAATATTTTAAA
66 AATAATATTTTAAA
* * * * * *
68974 TAAACATT-AATGATTGTAATTTAGATTATAAGT-ATTTGA-TGTATATTTAATTTGAATTAATT
1 TAAACATTAAATGAATGTAATTTAGATTACAACTCATTTAATTG-ATATTTAATTCGAAATAATT
69036 AAATAATATTTT
65 AAATAATATTTT
69048 TATTAATTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
76 2 0.03
77 34 0.52
78 21 0.32
79 8 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (79 bp):
TAAACATTAAATGAATGTAATTTAGATTACAACTCATTTAATTGATATTTAATTCGAAATAATTA
AATAATATTTTAAA
Found at i:69816 original size:102 final size:102
Alignment explanation
Indices: 69665--69876 Score: 239
Period size: 102 Copynumber: 2.1 Consensus size: 102
69655 TTTGAAATTT
* * *
69665 TTGAAACAAAATTGATCTTACATGAGATAGTTATCCTAAAAACAAATTTCGTCTTACTTGAGACA
1 TTGAAACAAAATTGATCTCACATGAGATAGTTATCCTAAAAACAAATTTCATCTCACTTGAGACA
* ** * *
69730 ATTTTCCCTT-GAGATGCAAATTTTGAATTTGTTTAAC
66 ATTTT-CCTTCGAAACACAAATTTGGAAATTGTTTAAC
* * * * * * *
69767 TTGAAACAAAGTTGATCTCACTTGAGATTGTTTTTCTTAAAAA-ACATTTCATCTCCCTTGAGAC
1 TTGAAACAAAATTGATCTCACATGAGATAG-TTATCCTAAAAACAAATTTCATCTCACTTGAGAC
* *
69831 AGTTTTCCTTCGAAACACAAATTTGGAAATTGTTTATC
65 AATTTTCCTTCGAAACACAAATTTGGAAATTGTTTAAC
69869 TTGAAACA
1 TTGAAACA
69877 TAAAACCTTA
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
101 4 0.04
102 77 0.85
103 10 0.11
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGAAACAAAATTGATCTCACATGAGATAGTTATCCTAAAAACAAATTTCATCTCACTTGAGACA
ATTTTCCTTCGAAACACAAATTTGGAAATTGTTTAAC
Found at i:69975 original size:68 final size:67
Alignment explanation
Indices: 69862--70045 Score: 244
Period size: 68 Copynumber: 2.7 Consensus size: 67
69852 TTTGGAAATT
* * * * * *
69862 GTTTATCTTGAAACATAAAACCTTAGAGATTGTTTCTCTTGAAACAAGTTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACATAAAAACTTTGAGATCGTTTATCTTGAAACAAATTTTGTCTCCCTTGAGA
69927 CA
66 CA
* *
69929 GTTTCTCTTGAAACATAAAAAATATTGAGATCGTTTATCTTGAAACAAATTTTGTCTCTCTTGAG
1 GTTTCTCTTGAAACATAAAAACT-TTGAGATCGTTTATCTTGAAACAAATTTTGTCTCCCTTGAG
69994 ACA
65 ACA
* ** *
69997 ATTTCTCTTGAAACATAAAAACTTTGAGATTATTT-TCTTTAAACAAATT
1 GTTTCTCTTGAAACATAAAAACTTTGAGATCGTTTATCTTGAAACAAATT
70046 ATCCCTAAAG
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
66 13 0.13
67 30 0.29
68 60 0.58
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (67 bp):
GTTTCTCTTGAAACATAAAAACTTTGAGATCGTTTATCTTGAAACAAATTTTGTCTCCCTTGAGA
CA
Found at i:70389 original size:139 final size:137
Alignment explanation
Indices: 70043--70729 Score: 935
Period size: 137 Copynumber: 5.0 Consensus size: 137
70033 CTTTAAACAA
* **
70043 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACTAGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGATCT
* * * * * *
70108 CCTCATCACGTAGGAGCAACGTCGTCCTTAGATAGCCAGATTTCCTCATCACCTAGGAACCGTGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCTCATCACGTAGGAACCGTGT
70173 TATCTAC
131 TATCTAC
* *
70180 ATAATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCAATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGATCT
* * * * *
70245 ACTCATAACGTAGGAGCAGCGTCATCCTTAGATAACTAGACTTCCTCATCATGTAGGAACCGAGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCTCATCACGTAGGAACC--GT
70310 GTTATCTAC
129 GTTATCTAC
* * * * * *
70319 ATTATCCCTAAAGATGGCTAGACGTCCTTATCATGTAAGAACAATGTCATCAACGGACCTGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGATCT
*
70384 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACTATACTTCCTCATCACGTAGGAACCGTGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCTCATCACGTAGGAACCGTGT
70449 TATCTAC
131 TATCTAC
* * * **
70456 ATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTTATCCGTCGACCCGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGATCT
* * * *
70521 CCTCATCACATAGGAGCAGCTTCATCCTTAGATAACCATACTTGCTCATCACGTAGGAACCATGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCTCATCACGTAGGAACCGTGT
*
70586 TATCTCC
131 TATCTAC
* * * * * *
70593 AATTTATCCTTAAAGATGGCTAGACATCCTCATCACATAGGAACAATGTCATCCGCCAACCAGAT
1 -A-TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGAT
* * * *
70658 CTCCTCATCACGTAGGAGCAACGTCA-CCATTAGATAAACATATTTTCTCATCACGTAGGAACCG
64 CTCCTCATCACGTAGGAGCAGCGTCATCC-TTAGATAACCATACTTCCTCATCACGTAGGAACCG
70722 TGTTATCT
128 TGTTATCT
70730 CCAATTTTAC
Statistics
Matches: 490, Mismatches: 55, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
137 245 0.50
138 3 0.01
139 242 0.49
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCGATCT
CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACCATACTTCCTCATCACGTAGGAACCGTGT
TATCTAC
Found at i:70537 original size:276 final size:274
Alignment explanation
Indices: 70042--70729 Score: 977
Period size: 276 Copynumber: 2.5 Consensus size: 274
70032 TCTTTAAACA
70042 AATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGA-CTAGAT
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACCT-GAT
* * * *
70106 CTCCTCATCACGTAGGAGCAACGTCGTCCTTAGATAGCCAGATTTCCTCATCACCTAGGAACCGT
65 CTCCTCATCACGTAGGAGCAACGTCATCCTTAGATA-ACATATTTCCTCATCACGTAGGAACCGT
* *
70171 GTTATCTACATAATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCG
129 GTTATCTACATAATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTCATCCACCG
* * *
70236 ACCCAATCTACTCATAACGTAGGAGCAGCGTCATCCTTAGATAACTAGACTTCCTCATCATGTAG
194 ACCCAATCTACTCATAACATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAG
70301 GAACCGAGTGTTATCTAC
259 GAACC-A-TGTTATCTAC
* ** * * *
70319 -ATTATCCCTAAAGATGGCTAGACGTCCTTATCATGTAAGAACAATGTCATCAACGGACCTGATC
1 AATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACCTGATC
* *
70383 TCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAACTATACTTCCTCATCACGTAGGAACCGTG
66 TCCTCATCACGTAGGAGCAACGTCATCCTTAGATAAC-ATATTTCCTCATCACGTAGGAACCGTG
* * **
70448 TTATCTACATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTTATCCGTCGA
130 TTATCTACATAATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTCATCCACCGA
* * * * * *
70513 CCCGATCTCCTCATCACATAGGAGCAGCTTCATCCTTAGATAACCATACTTGCTCATCACGTAGG
195 CCCAATCTACTCATAACATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGG
*
70578 AACCATGTTATCTCC
260 AACCATGTTATCTAC
* * * * *
70593 AATTTATCCTTAAAGATGGCTAGACATCCTCATCACATAGGAACAATGTCATCCGCCAACCAGAT
1 AA-TTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACCTGAT
*
70658 CTCCTCATCACGTAGGAGCAACGTCA-CCATTAGATAAACATATTTTCTCATCACGTAGGAACCG
65 CTCCTCATCACGTAGGAGCAACGTCATCC-TTAGAT-AACATATTTCCTCATCACGTAGGAACCG
70722 TGTTATCT
128 TGTTATCT
70730 CCAATTTTAC
Statistics
Matches: 363, Mismatches: 42, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
274 9 0.02
275 5 0.01
276 344 0.95
277 5 0.01
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (274 bp):
AATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACCTGATC
TCCTCATCACGTAGGAGCAACGTCATCCTTAGATAACATATTTCCTCATCACGTAGGAACCGTGT
TATCTACATAATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTCATCCACCGAC
CCAATCTACTCATAACATAGGAGCAGCGTCATCCTTAGATAACCAGACTTCCTCATCACGTAGGA
ACCATGTTATCTAC
Found at i:70736 original size:139 final size:137
Alignment explanation
Indices: 70043--70729 Score: 914
Period size: 139 Copynumber: 5.0 Consensus size: 137
70033 CTTTAAACAA
* *
70043 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACATAGGAACAATGTCATCCACCGACTAGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT
* * ** * * *
70108 CCTCATCACGTAGGAGCAACGTCGTCCTTAGATAGCCAGATTTCCTCATCACCTAGGAACCGTGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAAACATACTTCCTCATCACGTAGGAACCGTGT
70173 TATCTAC
131 TATCTAC
*
70180 ATAATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCCA-ATC
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGA-CCAGATC
* * * *
70244 TACTCATAACGTAGGAGCAGCGTCATCCTTAGAT-AACTAGACTTCCTCATCATGTAGGAACCGA
65 TCCTCATCACGTAGGAGCAGCGTCATCCTTAGATAAAC-ATACTTCCTCATCACGTAGGAACC--
70308 GTGTTATCTAC
127 GTGTTATCTAC
* * * * * *
70319 ATTATCCCTAAAGATGGCTAGACGTCCTTATCATGTAAGAACAATGTCATCAACGGACCTGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT
70384 CCTCATCACGTAGGAGCAGCGTCATCCTTAGAT-AACTATACTTCCTCATCACGTAGGAACCGTG
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAAAC-ATACTTCCTCATCACGTAGGAACCGTG
70448 TTATCTAC
130 TTATCTAC
* * * ** *
70456 ATTATCCCTAAAGATGGCTAGACATCCTCATCACGTAAGAACAATGTTATCCGTCGACCCGATCT
1 ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT
* * * * *
70521 CCTCATCACATAGGAGCAGCTTCATCCTTAGATAACCATACTTGCTCATCACGTAGGAACCATGT
66 CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAAACATACTTCCTCATCACGTAGGAACCGTGT
*
70586 TATCTCC
131 TATCTAC
* * * * *
70593 AATTTATCCTTAAAGATGGCTAGACATCCTCATCACATAGGAACAATGTCATCCGCCAACCAGAT
1 -A-TTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGAT
* * *
70658 CTCCTCATCACGTAGGAGCAACGTCA-CCATTAGATAAACATATTTTCTCATCACGTAGGAACCG
64 CTCCTCATCACGTAGGAGCAGCGTCATCC-TTAGATAAACATACTTCCTCATCACGTAGGAACCG
70722 TGTTATCT
128 TGTTATCT
70730 CCAATTTTAC
Statistics
Matches: 489, Mismatches: 52, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
136 1 0.00
137 239 0.49
138 9 0.02
139 240 0.49
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (137 bp):
ATTATCCCTAAAGATGGCTAGACGTCCTCATCACGTAGGAACAATGTCATCCACCGACCAGATCT
CCTCATCACGTAGGAGCAGCGTCATCCTTAGATAAACATACTTCCTCATCACGTAGGAACCGTGT
TATCTAC
Found at i:70932 original size:3 final size:3
Alignment explanation
Indices: 70924--70986 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
70914 TCTACTTTTG
70924 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA CTT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA TTA TTA
* *
70970 TTA TTA ATA TTT TTA TT
1 TTA TTA TTA TTA TTA TT
70987 TCATTTTTCC
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:70993 original size:28 final size:28
Alignment explanation
Indices: 70924--70987 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
70914 TCTACTTTTG
*
70924 TTATTA-TTA-TTATTATTATTATTATTA
1 TTATTATTTACTT-TTATTATTATTAATA
70951 TTATTATTTACTTTTATTATTATTAATA
1 TTATTATTTACTTTTATTATTATTAATA
*
70979 TTTTTATTT
1 TTATTATTT
70988 CATTTTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 6 0.18
28 25 0.76
29 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (28 bp):
TTATTATTTACTTTTATTATTATTAATA
Found at i:74336 original size:95 final size:94
Alignment explanation
Indices: 74224--74413 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 94
74214 GAGACAGAAA
74224 GAGAGTTTTTTTTATTAATATAAAATAAATAATATTTGTTTAAAAATAACTTTTAATTATTTGAT
1 GAGAGTTTTTTTTATTAATATAAAATAAATAATATTTGTTTAAAAATAACTTTTAATTATTTGAT
74289 ATTAAATATTTAAATTTCTAACATTCATC
66 ATTAAATATTTAAATTTCTAACATTCATC
74318 GAGAGTTTTTTTTTATTAATATAAAATAAATAATATTTGTTTAAAAATAACTTTTAATTATTTGA
1 GAGAG-TTTTTTTTATTAATATAAAATAAATAATATTTGTTTAAAAATAACTTTTAATTATTTGA
74383 TATTAAATATTTAAATTTCTAACATTCATC
65 TATTAAATATTTAAATTTCTAACATTCATC
74413 G
1 G
74414 TGCTCGAAAT
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 5 0.05
95 90 0.95
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (94 bp):
GAGAGTTTTTTTTATTAATATAAAATAAATAATATTTGTTTAAAAATAACTTTTAATTATTTGAT
ATTAAATATTTAAATTTCTAACATTCATC
Found at i:74854 original size:2 final size:2
Alignment explanation
Indices: 74834--74877 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
74824 TTAATATGCG
74834 TA TA T- TA TA TA GTA T- 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
74875 TA T
1 TA T
74878 TTGTATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76027 original size:16 final size:16
Alignment explanation
Indices: 76006--76050 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
75996 AATTTGGTCC
76006 GTTTTAGTTAATTAAT
1 GTTTTAGTTAATTAAT
*
76022 GTTTTATTTAATT-AT
1 GTTTTAGTTAATTAAT
* *
76037 TTTTTAGTTTATTA
1 GTTTTAGTTAATTA
76051 TATTTTATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.27, C:0.00, G:0.09, T:0.64
Consensus pattern (16 bp):
GTTTTAGTTAATTAAT
Found at i:76050 original size:15 final size:15
Alignment explanation
Indices: 76007--76057 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
75997 ATTTGGTCCG
* *
76007 TTTTAGTTAATTAATG
1 TTTTAGTTTATT-ATA
*
76023 TTTTA-TTTAATTATT
1 TTTTAGTTT-ATTATA
76038 TTTTAGTTTATTATA
1 TTTTAGTTTATTATA
76053 TTTTA
1 TTTTA
76058 TGAATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (15 bp):
TTTTAGTTTATTATA
Found at i:76056 original size:16 final size:16
Alignment explanation
Indices: 76007--76056 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
75997 ATTTGGTCCG
*
76007 TTTTAGTTAATTA-AT
1 TTTTAGTTTATTATAT
76022 GTTTTA-TTTAATTAT-T
1 -TTTTAGTTT-ATTATAT
76038 TTTTAGTTTATTATAT
1 TTTTAGTTTATTATAT
76054 TTT
1 TTT
76057 ATGAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTTTAGTTTATTATAT
Found at i:76127 original size:18 final size:18
Alignment explanation
Indices: 76085--76137 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
76075 TTCCTATTTA
76085 TTTATCTATTTATTTTTATC
1 TTTAT-TATTTA-TTTTATC
*
76105 TTTATTTTTTATTTTAT-
1 TTTATTATTTATTTTATC
76122 TATTATTATTT-TTTTA
1 T-TTATTATTTATTTTA
76138 ATTTAACTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 5 0.17
20 5 0.17
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTATTTATTTTATC
Found at i:86087 original size:18 final size:18
Alignment explanation
Indices: 86064--86101 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
86054 CTAGGAAGAG
*
86064 AATAAAGATTGCTCTAGC
1 AATAAAGATTCCTCTAGC
*
86082 AATAAAGATTCCTCTTGC
1 AATAAAGATTCCTCTAGC
86100 AA
1 AA
86102 CTATTCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (18 bp):
AATAAAGATTCCTCTAGC
Found at i:86293 original size:37 final size:37
Alignment explanation
Indices: 86252--86339 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
86242 AAACTATTTT
86252 GTCATTCTTAGGATCATTTTTCTAGAAAAT-T-ATATGA
1 GTCATTCTTAGGATCATTTTT-TAG-AAATGTCATATGA
* * * *
86289 GTCATTCTTAGGACCATTTTTTTGAGATGTCATTTGA
1 GTCATTCTTAGGATCATTTTTTAGAAATGTCATATGA
86326 GTCATTCTTAGGAT
1 GTCATTCTTAGGAT
86340 TGTCTCCCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
35 3 0.07
36 3 0.07
37 38 0.86
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.44
Consensus pattern (37 bp):
GTCATTCTTAGGATCATTTTTTAGAAATGTCATATGA
Found at i:87243 original size:118 final size:118
Alignment explanation
Indices: 87019--87365 Score: 420
Period size: 118 Copynumber: 3.0 Consensus size: 118
87009 TCACTTTGTT
* * * *
87019 CGATTCCATCACAGAAGGAGGTGGATCAACAGTTCCAAATCA-AGAGTTCATAAT--G-AGAACT
1 CGATTCCATCATAGAAGAAGGTGGATCAACA-TTTCAAATGAGAGAGTTCATAATGAGAAGAACT
* * * *
87080 CATCCGATGAGGGAGAAGAAATTTATAATGAGAAGAACTTGTTCAACCTTAGCA
65 CATCCAATGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCA
* * *
87134 TGGTTCCATCATAGAAGAAGGTGGATCAACATTTCTAATGAGAGAGTTCATAATGAGAAGAACTC
1 CGATTCCATCATAGAAGAAGGTGGATCAACATTTCAAATGAGAGAGTTCATAATGAGAAGAACTC
* *
87199 ATCCAATAAGGGAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTAGCA
66 ATCCAATGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCA
* * * * *
87252 CGATTCCATCACT-GAA-AGAGGTGAAACAACATTTCCAATGCGAGAGTTCATAATGAGAATAAC
1 CGATTCCATCA-TAGAAGA-AGGTGGATCAACATTTCAAATGAGAGAGTTCATAATGAGAAGAAC
* * *
87315 TCAACAAATGAGGGAGAAA-AAGTTCATAATGAGAAGAACTTGTTAAACCTT
64 TCATCCAATGAGGGA-AAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
87366 GGCTCATCCA
Statistics
Matches: 200, Mismatches: 25, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
114 7 0.04
115 39 0.19
117 2 0.01
118 148 0.74
119 4 0.02
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.23
Consensus pattern (118 bp):
CGATTCCATCATAGAAGAAGGTGGATCAACATTTCAAATGAGAGAGTTCATAATGAGAAGAACTC
ATCCAATGAGGGAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCA
Found at i:87819 original size:118 final size:117
Alignment explanation
Indices: 87612--87845 Score: 292
Period size: 118 Copynumber: 2.0 Consensus size: 117
87602 TCATCATTTT
* * *
87612 GTTCGATTCCATCACAGAAGAAGGAGGATCAACATTTCCAGTGAAGAGTTCATACTGAGAAGAAC
1 GTTCGATTCCATCACAAAAGAAGGAGAATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAAC
*
87677 TCATCCAACGAGGGAGAAGAAGTTCATAACG-GAAAGAAATTATTCAACCTTG
66 TCATCCAACAAGGGAGAAGAAGTTCATAACGAGAAA-AAATTATTCAACCTTG
* ** *
87729 GTTCGATTCCATCATAAAATG-AGGAGAATCAACATTTCCAAGTGGGGAGTTCATAATGAGAATA
1 GTTCGATTCCATCACAAAA-GAAGGAGAATCAACATTTCC-AGTGAAGAGTTCATAATGAGAAGA
* * * * * * *
87793 ACTCGTTCGATAAGGGAGAAGAAGTTCATAATGAGAAAAACTTGTTCAACCTT
64 ACTCATCCAACAAGGGAGAAGAAGTTCATAACGAGAAAAAATTATTCAACCTT
87846 AGCTCGATCC
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
117 34 0.34
118 61 0.62
119 4 0.04
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (117 bp):
GTTCGATTCCATCACAAAAGAAGGAGAATCAACATTTCCAGTGAAGAGTTCATAATGAGAAGAAC
TCATCCAACAAGGGAGAAGAAGTTCATAACGAGAAAAAATTATTCAACCTTG
Found at i:87948 original size:40 final size:40
Alignment explanation
Indices: 87891--87967 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
87881 TTATCATTTT
* *
87891 GCTCGTCCATCACATAAGGCGTTGGATCAACATCACCATG
1 GCTCGTCCATCACATAAGGAGTTAGATCAACATCACCATG
** * *
87931 GCTCGTCCATCGTATAAGGAGTTAGATTAATATCACC
1 GCTCGTCCATCACATAAGGAGTTAGATCAACATCACC
87968 TTGGGACAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (40 bp):
GCTCGTCCATCACATAAGGAGTTAGATCAACATCACCATG
Found at i:91482 original size:17 final size:17
Alignment explanation
Indices: 91460--91531 Score: 108
Period size: 17 Copynumber: 4.2 Consensus size: 17
91450 ATTAAACTCA
*
91460 CCCGGTTTTTATAGTGT
1 CCCGGTTTTTATGGTGT
91477 CCCGGTTTTTATGGTGT
1 CCCGGTTTTTATGGTGT
*
91494 CCCCGTTTTTATGGTGT
1 CCCGGTTTTTATGGTGT
**
91511 CCCCATTTTTATGGTGT
1 CCCGGTTTTTATGGTGT
91528 CCCG
1 CCCG
91532 ATCGCATTGA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 51 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.44
Consensus pattern (17 bp):
CCCGGTTTTTATGGTGT
Found at i:92101 original size:3 final size:3
Alignment explanation
Indices: 92093--92118 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
92083 TTTTTGCACT
92093 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
92119 TCCTTACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:95825 original size:13 final size:13
Alignment explanation
Indices: 95807--95849 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
95797 TTTTCTCTTA
*
95807 AAAAAAAGAAAAG
1 AAAAAAAGAGAAG
95820 AAAAAAA-ATGAAG
1 AAAAAAAGA-GAAG
*
95833 AAAAAATGAGAAG
1 AAAAAAAGAGAAG
95846 AAAA
1 AAAA
95850 GGAAGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (13 bp):
AAAAAAAGAGAAG
Found at i:95856 original size:12 final size:12
Alignment explanation
Indices: 95812--95860 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
95802 TCTTAAAAAA
95812 AAGAAAA-GAA-
1 AAGAAAATGAAG
95822 AA-AAAATGAAG
1 AAGAAAATGAAG
95833 AA-AAAATG-AG
1 AAGAAAATGAAG
*
95843 AAGAAAAGGAAG
1 AAGAAAATGAAG
95855 AAGAAA
1 AAGAAA
95861 GGGGCTTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
9 4 0.12
10 9 0.26
11 13 0.38
12 8 0.24
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (12 bp):
AAGAAAATGAAG
Found at i:100242 original size:16 final size:14
Alignment explanation
Indices: 100197--100248 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
100187 TGACATAGAG
*
100197 AAAAAAAGAAGATAT
1 AAAAAAAGAA-AAAT
100212 AACAAAAAGAAAAAT
1 AA-AAAAAGAAAAAT
100227 ACAAAAAAGAGAAAAT
1 A-AAAAAAGA-AAAAT
100243 AAAAAA
1 AAAAAA
100249 GAATAGAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 18 0.55
16 15 0.45
ACGTcount: A:0.79, C:0.04, G:0.10, T:0.08
Consensus pattern (14 bp):
AAAAAAAGAAAAAT
Found at i:100272 original size:26 final size:25
Alignment explanation
Indices: 100243--100309 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 25
100233 AAGAGAAAAT
*
100243 AAAAAAGAATAGAGATAAAAGAAAGC
1 AAAAAAGAA-AGAGAGAAAAGAAAGC
*
100269 -AAAAAG--AGAGAGAAAGGAAAGC
1 AAAAAAGAAAGAGAGAAAAGAAAGC
*
100291 AAAAAAGAAAAAGAAGAAA
1 AAAAAAGAAAGAG-AGAAA
100310 TAAATCATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
22 14 0.41
23 6 0.18
25 9 0.26
26 5 0.15
ACGTcount: A:0.72, C:0.03, G:0.22, T:0.03
Consensus pattern (25 bp):
AAAAAAGAAAGAGAGAAAAGAAAGC
Found at i:100305 original size:23 final size:22
Alignment explanation
Indices: 100263--100305 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
100253 AGAGATAAAA
* *
100263 GAAAGCAAAAAGAGAGAGAAAG
1 GAAAGCAAAAAGAAAAAGAAAG
100285 GAAAGCAAAAAAGAAAAAGAA
1 GAAAGC-AAAAAGAAAAAGAA
100306 GAAATAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.70, C:0.05, G:0.26, T:0.00
Consensus pattern (22 bp):
GAAAGCAAAAAGAAAAAGAAAG
Done.