Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005517.1 Hibiscus syriacus cultivar Beakdansim tig00012749_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: 144552
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1437 original size:15 final size:15
Alignment explanation
Indices: 1414--1446 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1404 TCAGATCAAA
*
1414 ATTTGGATATATGTT
1 ATTTAGATATATGTT
1429 ATTTAGATATATGTT
1 ATTTAGATATATGTT
1444 ATT
1 ATT
1447 CGAATGTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (15 bp):
ATTTAGATATATGTT
Found at i:2666 original size:15 final size:16
Alignment explanation
Indices: 2639--2668 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2629 TTATATTTAT
2639 GTACTTAGGAGAATCG
1 GTACTTAGGAGAATCG
2655 GTACTT-GGAGAATC
1 GTACTTAGGAGAATC
2669 ACAATCAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (16 bp):
GTACTTAGGAGAATCG
Found at i:4547 original size:37 final size:37
Alignment explanation
Indices: 4506--4588 Score: 166
Period size: 37 Copynumber: 2.2 Consensus size: 37
4496 AGCCTGCAAG
4506 TAAATCAAATCTCCACTACTAATAAGAACACGATGCA
1 TAAATCAAATCTCCACTACTAATAAGAACACGATGCA
4543 TAAATCAAATCTCCACTACTAATAAGAACACGATGCA
1 TAAATCAAATCTCCACTACTAATAAGAACACGATGCA
4580 TAAATCAAA
1 TAAATCAAA
4589 GGGTCTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.22
Consensus pattern (37 bp):
TAAATCAAATCTCCACTACTAATAAGAACACGATGCA
Found at i:4794 original size:25 final size:22
Alignment explanation
Indices: 4757--4810 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
4747 GCATTTGATT
* *
4757 TTTTTTTTTTTTTCTTTTTTCACA
1 TTTTTTTTGTTTT-TGTTTTC-CA
4781 CTTTTTTTTGTTTTTGTTTTCCA
1 -TTTTTTTTGTTTTTGTTTTCCA
4804 TTTTTTT
1 TTTTTTT
4811 CATGTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 6 0.22
25 12 0.44
ACGTcount: A:0.06, C:0.11, G:0.04, T:0.80
Consensus pattern (22 bp):
TTTTTTTTGTTTTTGTTTTCCA
Found at i:15529 original size:69 final size:69
Alignment explanation
Indices: 15418--15561 Score: 252
Period size: 69 Copynumber: 2.1 Consensus size: 69
15408 AGTTTCATCT
*
15418 TCTGTTCCAATTTCTCAAGGATGGTTAGCTCTTCTGCTAAATGATACTCTGGTTTCCTACAAGGT
1 TCTGTTCCAATTTCTCAAGGATGGTTAGCTCTTCTGCTAAATGATACCCTGGTTTCCTACAAGGT
15483 ATCA
66 ATCA
* * *
15487 TCTGTTCCAATTTCTCAAGGTTGGTTAGCTCTTCTGCTAAATGATTCCCTGGTTTCCTACATGGT
1 TCTGTTCCAATTTCTCAAGGATGGTTAGCTCTTCTGCTAAATGATACCCTGGTTTCCTACAAGGT
15552 ATCA
66 ATCA
15556 TCTGTT
1 TCTGTT
15562 AAAGAAGGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.40
Consensus pattern (69 bp):
TCTGTTCCAATTTCTCAAGGATGGTTAGCTCTTCTGCTAAATGATACCCTGGTTTCCTACAAGGT
ATCA
Found at i:24888 original size:23 final size:23
Alignment explanation
Indices: 24862--24923 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
24852 AATTAATTAT
24862 ATTTAATAATAAATTTAGGTTGA
1 ATTTAATAATAAATTTAGGTTGA
24885 ATTTAATAATAAATTTAGGTTGA
1 ATTTAATAATAAATTTAGGTTGA
*
24908 ATTTAAAAATAAATTT
1 ATTTAATAATAAATTT
24924 GGGATTATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
ATTTAATAATAAATTTAGGTTGA
Found at i:30563 original size:13 final size:14
Alignment explanation
Indices: 30534--30573 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
30524 TTTCTATCTA
*
30534 TTTGCAGAGATTTT
1 TTTGCAGGGATTTT
*
30548 TTTGTAGGGATTTT
1 TTTGCAGGGATTTT
30562 TTTGCAGGGATT
1 TTTGCAGGGATT
30574 ACTTCCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.17, C:0.05, G:0.28, T:0.50
Consensus pattern (14 bp):
TTTGCAGGGATTTT
Found at i:31715 original size:24 final size:23
Alignment explanation
Indices: 31687--31740 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
31677 ATTTTTATAC
31687 TTATAATGTATA-TTTTATTATTTT
1 TTATAATGTATAGTTTTA--ATTTT
* * *
31711 TTATATTTTATAGTTTTAGTTTT
1 TTATAATGTATAGTTTTAATTTT
31734 TTATAAT
1 TTATAAT
31741 TTTTTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 10 0.40
24 10 0.40
25 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (23 bp):
TTATAATGTATAGTTTTAATTTT
Found at i:33513 original size:23 final size:23
Alignment explanation
Indices: 33485--33550 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
33475 CCGATCTGAC
33485 CATTGATCGTTGACTTTGACTAG
1 CATTGATCGTTGACTTTGACTAG
**
33508 TGTTGA-CTGTTGACTTTGACTAG
1 CATTGATC-GTTGACTTTGACTAG
*
33531 CATTAATCGTTGACTTTGAC
1 CATTGATCGTTGACTTTGAC
33551 CAAAAAGTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (23 bp):
CATTGATCGTTGACTTTGACTAG
Found at i:33583 original size:16 final size:17
Alignment explanation
Indices: 33551--33583 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
33541 TGACTTTGAC
33551 CAAAAAGTCAAATTTTT
1 CAAAAAGTCAAATTTTT
*
33568 CAAAAAGTCATATTTT
1 CAAAAAGTCAAATTTT
33584 ATGTTTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
CAAAAAGTCAAATTTTT
Found at i:38604 original size:10 final size:9
Alignment explanation
Indices: 38576--38613 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
38566 TAAGAAAACA
38576 AAAAG-AAG
1 AAAAGAAAG
38584 AAAA-AAAG
1 AAAAGAAAG
38592 AAAAGAAATG
1 AAAAGAAA-G
38602 AAAAGAAAG
1 AAAAGAAAG
38611 AAA
1 AAA
38614 GTTGAAGCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 11 0.41
9 7 0.26
10 9 0.33
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:39183 original size:26 final size:26
Alignment explanation
Indices: 39150--39203 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
39140 TTGGGTAACC
39150 GAAGGATAATTCGCCCTAGAATGGAA
1 GAAGGATAATTCGCCCTAGAATGGAA
39176 GAAGGATAATTCGCCCTAGAATGGAA
1 GAAGGATAATTCGCCCTAGAATGGAA
39202 GA
1 GA
39204 GGAATTTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.19
Consensus pattern (26 bp):
GAAGGATAATTCGCCCTAGAATGGAA
Found at i:43460 original size:16 final size:16
Alignment explanation
Indices: 43439--43476 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
43429 TCCACGGTGG
*
43439 AGGACTTGCCTGACGA
1 AGGACTTGCCTAACGA
*
43455 AGGACTTGCCTAACGG
1 AGGACTTGCCTAACGA
43471 AGGACT
1 AGGACT
43477 ATCTGACAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (16 bp):
AGGACTTGCCTAACGA
Found at i:43500 original size:16 final size:16
Alignment explanation
Indices: 43438--43500 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
43428 TTCCACGGTG
*
43438 GAGGACTTGCCTGAC-
1 GAGGACATGCCTGACA
* * *
43453 GAAGGACTTGCCTAACG
1 G-AGGACATGCCTGACA
43470 GAGGACTAT--CTGACA
1 GAGGAC-ATGCCTGACA
43485 GAGGACATGCCTGACA
1 GAGGACATGCCTGACA
43501 TAAGACTTCC
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.05
15 11 0.28
16 24 0.62
17 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.30, T:0.17
Consensus pattern (16 bp):
GAGGACATGCCTGACA
Found at i:44177 original size:38 final size:38
Alignment explanation
Indices: 44135--44238 Score: 102
Period size: 38 Copynumber: 2.7 Consensus size: 38
44125 CCATGCAAGG
* *
44135 TTGTCTGATGTTGTGTGGTCTAGACATTGTACGCTCTT
1 TTGTCTGATGTTGTGTAGTCTAGACATTGTACGCTCTA
* * * ** *
44173 TTGTCTAATATTGTATTA-TCTAGACACCGTACGTTCTA
1 TTGTCTGATGTTGT-GTAGTCTAGACATTGTACGCTCTA
* *
44211 ATGTATGATGTTGTGTAGTCTAGACATT
1 TTGTCTGATGTTGTGTAGTCTAGACATT
44239 AAATTTCATC
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
37 2 0.04
38 46 0.94
39 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.43
Consensus pattern (38 bp):
TTGTCTGATGTTGTGTAGTCTAGACATTGTACGCTCTA
Found at i:52845 original size:8 final size:8
Alignment explanation
Indices: 52832--52863 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
52822 TTAGGGTTAG
52832 AATAAAAA
1 AATAAAAA
52840 AATAAAAA
1 AATAAAAA
52848 AATAAAAAA
1 AAT-AAAAA
52857 AATAAAA
1 AATAAAA
52864 TAACATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:52849 original size:9 final size:9
Alignment explanation
Indices: 52835--52863 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
52825 GGGTTAGAAT
52835 AAAAAAAT-
1 AAAAAAATA
52843 AAAAAAATA
1 AAAAAAATA
52852 AAAAAAATA
1 AAAAAAATA
52861 AAA
1 AAA
52864 TAACATTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:53105 original size:160 final size:162
Alignment explanation
Indices: 52923--53245 Score: 632
Period size: 160 Copynumber: 2.0 Consensus size: 162
52913 TCCAATTGAT
52923 ATTATTTGAAAGCTACAAGAAATAATATAGAGTTAGGAGGGGCTAATTTTTAAAATATAAGAATT
1 ATTATTTGAAAGCTACAAGAAATAATATAGAGTTAGGAGGGGCTAATTTTTAAAATATAAGAATT
52988 TTAAATATGGATTAAATTGAAAGAATTCAAATTTTAAAGGCAAAATTACAATAGGTGACCAAAAT
66 TTAAATATGGATTAAATTGAAAGAATTCAAATTTTAAAGGCAAAATTACAATAGGTGACCAAAAT
53053 GAATTACACTTCG-AAGTGCA-GGATTGTAAA
131 GAATTACACTTCGAAAGTGCAGGGATTGTAAA
53083 ATTATTTGAAAGCTACAAGAAATAATATAGAGTTAGGAGGGGCTAATTTTTAAAATATAAGAATT
1 ATTATTTGAAAGCTACAAGAAATAATATAGAGTTAGGAGGGGCTAATTTTTAAAATATAAGAATT
53148 TTAAATATGGATTAAATTGAAAGAATTCAAATTTTAAAGGCAAAATTACAATAGGTGACCAAAAT
66 TTAAATATGGATTAAATTGAAAGAATTCAAATTTTAAAGGCAAAATTACAATAGGTGACCAAAAT
53213 GAATTACACTTCGAAAGTGCAGGGATTGTAAA
131 GAATTACACTTCGAAAGTGCAGGGATTGTAAA
53245 A
1 A
53246 ATAATTTAAG
Statistics
Matches: 161, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
160 143 0.89
161 7 0.04
162 11 0.07
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (162 bp):
ATTATTTGAAAGCTACAAGAAATAATATAGAGTTAGGAGGGGCTAATTTTTAAAATATAAGAATT
TTAAATATGGATTAAATTGAAAGAATTCAAATTTTAAAGGCAAAATTACAATAGGTGACCAAAAT
GAATTACACTTCGAAAGTGCAGGGATTGTAAA
Found at i:54251 original size:40 final size:38
Alignment explanation
Indices: 54144--54419 Score: 241
Period size: 39 Copynumber: 7.3 Consensus size: 38
54134 TTTTTATAAA
* * *
54144 ATATATTATATATATTTTCCAAAAACGTTTT-AAAACT
1 ATATATTATATATATTTTTCAAAAATGTTTTCAAAAAT
** *
54181 ATATATTATACGTA-ATTTCGAAAAATGTTTTCAAAAAAT
1 ATATATTATATATATTTTTC-AAAAATGTTTTC-AAAAAT
** **
54220 ATATATTATATATATTTTTTCAAAAATGTTTTTTAAACC
1 ATATATTATATATA-TTTTTCAAAAATGTTTTCAAAAAT
*
54259 ATATATTATATAT-TTTTT--AAAATGTTTTC-CAAAT
1 ATATATTATATATATTTTTCAAAAATGTTTTCAAAAAT
* ** *
54293 -TATA-TAT-TATATTTTTAAAAAACATTTTCAAAACTT
1 ATATATTATATATATTTTTCAAAAATGTTTTCAAAA-AT
*
54329 ATATATTATATAT-GTTTTCGAAAAATGTTTTCAAAAAT
1 ATATATTATATATATTTTTC-AAAAATGTTTTCAAAAAT
* *
54367 ATATA-TATTATATATATTTTCGAAAATTGTTTTCAAAATT
1 ATATATTA-TATATAT-TTTTC-AAAAATGTTTTCAAAAAT
54407 ATATATTATATAT
1 ATATATTATATAT
54420 TATGTATATA
Statistics
Matches: 192, Mismatches: 29, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
31 3 0.02
32 8 0.04
33 4 0.02
34 11 0.06
35 12 0.06
36 4 0.02
37 33 0.17
38 18 0.09
39 50 0.26
40 43 0.22
41 6 0.03
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (38 bp):
ATATATTATATATATTTTTCAAAAATGTTTTCAAAAAT
Found at i:54304 original size:148 final size:148
Alignment explanation
Indices: 54150--54420 Score: 381
Period size: 148 Copynumber: 1.9 Consensus size: 148
54140 TAAAATATAT
** * *
54150 TATA-TATATTTTCCAAAAACGTTTT-AAAAC-TATATATTATACGTAATTTCGAAAAATGTTTT
1 TATATTATATTTTTAAAAAACATTTTCAAAACTTATATATTATACATAATTTCGAAAAATGTTTT
**
54212 CAAAAA-ATATATATTATATATATTTTTTC-AAAAATGTTTTTTAAACCATATATTATATATTTT
66 CAAAAATATATATATTATATATA--TTTTCGAAAAATGTTTTCAAAACCATATATTATATATTTT
54275 TTAAAATGTTTTCCAAATTA
129 TTAAAATGTTTTCCAAATTA
* **
54295 TATATTATATTTTTAAAAAACATTTTCAAAACTTATATATTATATATGTTTTCGAAAAATGTTTT
1 TATATTATATTTTTAAAAAACATTTTCAAAACTTATATATTATACATAATTTCGAAAAATGTTTT
* **
54360 CAAAAATATATATATTATATATATTTTCGAAAATTGTTTTCAAAATTATATATTATATATT
66 CAAAAATATATATATTATATATATTTTCGAAAAATGTTTTCAAAACCATATATTATATATT
54421 ATGTATATAT
Statistics
Matches: 109, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
145 4 0.04
146 18 0.17
147 10 0.09
148 61 0.56
149 16 0.15
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (148 bp):
TATATTATATTTTTAAAAAACATTTTCAAAACTTATATATTATACATAATTTCGAAAAATGTTTT
CAAAAATATATATATTATATATATTTTCGAAAAATGTTTTCAAAACCATATATTATATATTTTTT
AAAATGTTTTCCAAATTA
Found at i:56508 original size:19 final size:20
Alignment explanation
Indices: 56469--56510 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
56459 ATTTTCATAA
* *
56469 CATTTAGAGTCATTTAGTTG
1 CATTTAGAGTCATGTAATTG
56489 CATTTAG-GTCATGTAATTG
1 CATTTAGAGTCATGTAATTG
56508 CAT
1 CAT
56511 ATGGTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (20 bp):
CATTTAGAGTCATGTAATTG
Found at i:57703 original size:46 final size:46
Alignment explanation
Indices: 57643--57782 Score: 133
Period size: 45 Copynumber: 3.1 Consensus size: 46
57633 ATTATTCTTT
* *
57643 ATTTTC-ATTAATAACATCCATTCATGTTTATAATGCA-CCATTATGC
1 ATTTTCAATT-ATAACATCCATTCATGTTGATAATGCACCCA-TAAGC
* *
57689 ATTTTCAATTATAACATCCTTTTATGTTGATAATGCACCCATAAGC
1 ATTTTCAATTATAACATCCATTCATGTTGATAATGCACCCATAAGC
** * **** *
57735 A-TTTCAATTATGGCATCCTTTCATACCAATAATGCACCCATATGC
1 ATTTTCAATTATAACATCCATTCATGTTGATAATGCACCCATAAGC
57780 ATT
1 ATT
57783 ATTATTTTGG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
45 37 0.47
46 36 0.46
47 6 0.08
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (46 bp):
ATTTTCAATTATAACATCCATTCATGTTGATAATGCACCCATAAGC
Found at i:57755 original size:45 final size:45
Alignment explanation
Indices: 57703--58059 Score: 474
Period size: 45 Copynumber: 8.0 Consensus size: 45
57693 TCAATTATAA
* * * * *
57703 CATCCTTTTATGTTGATAATGCACCCATAAGCATT-TCAATTATGG
1 CATCCTTTCATGCTGATAATGCACCCATATGCATTAT-TATTTTGG
* **
57748 CATCCTTTCATACCAATAATGCACCCATATGCATTATTATTTTGG
1 CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTGG
* *
57793 CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGG
1 CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTGG
*
57838 CATCCTTTCATGCCT-ATAATGCACCCATATTCATTATTATTTTGG
1 CATCCTTTCATG-CTGATAATGCACCCATATGCATTATTATTTTGG
* * *
57883 CAT-CTTTCATGCCGAT-ATACACCCATATGCACTATTATTTTGG
1 CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTGG
57926 CATCCTTTCATGCCT-ATAATGCACCCATATGCATTATTATTTTGG
1 CATCCTTTCATG-CTGATAATGCACCCATATGCATTATTATTTTGG
* **
57971 CTTATTTTCATGCCT-ATAATGCACCCATATGCATTATTATTTTGG
1 CATCCTTTCATG-CTGATAATGCACCCATATGCATTATTATTTTGG
*
58016 CATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTTTG
1 CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTG
58060 TTCATTCGTT
Statistics
Matches: 277, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
43 28 0.10
44 21 0.08
45 226 0.82
46 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (45 bp):
CATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTTTGG
Found at i:57839 original size:90 final size:90
Alignment explanation
Indices: 57703--58059 Score: 531
Period size: 90 Copynumber: 4.0 Consensus size: 90
57693 TCAATTATAA
* ** * * * * * *
57703 CATCCTTTTATGTTGATAATGCACCCATAAGCATT-TCAATTATGGCATCCTTTCATACCAATAA
1 CATCCTTTCATGCCGATAATACACCCATATGCATTAT-TATTTTGGCATCCTTTCATGCCTATAA
57767 TGCACCCATATGCATTATTATTTTGG
65 TGCACCCATATGCATTATTATTTTGG
57793 CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTATAAT
1 CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTATAAT
*
57858 GCACCCATATTCATTATTATTTTGG
66 GCACCCATATGCATTATTATTTTGG
*
57883 CAT-CTTTCATGCCGAT-ATACACCCATATGCACTATTATTTTGGCATCCTTTCATGCCTATAAT
1 CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTATAAT
57946 GCACCCATATGCATTATTATTTTGG
66 GCACCCATATGCATTATTATTTTGG
* ** * * *
57971 CTTATTTTCATGCCTATAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGATAAT
1 CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTATAAT
58036 GCACCCATATGCATTATTATTTTG
66 GCACCCATATGCATTATTATTTTG
58060 TTCATTCGTT
Statistics
Matches: 246, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
88 72 0.29
89 24 0.10
90 149 0.61
91 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (90 bp):
CATCCTTTCATGCCGATAATACACCCATATGCATTATTATTTTGGCATCCTTTCATGCCTATAAT
GCACCCATATGCATTATTATTTTGG
Found at i:66096 original size:19 final size:20
Alignment explanation
Indices: 66057--66098 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
66047 ATTTTCATAA
* *
66057 CATTTAGAGTCATTTAGTTG
1 CATTTAGAGTCATGTAATTG
66077 CATTTAG-GTCATGTAATTG
1 CATTTAGAGTCATGTAATTG
66096 CAT
1 CAT
66099 GTGGTGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.43
Consensus pattern (20 bp):
CATTTAGAGTCATGTAATTG
Found at i:66824 original size:31 final size:31
Alignment explanation
Indices: 66786--66848 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
66776 AATACCAACA
66786 TGAAGAAGAAGAAGAGTAGGAAATGCTTTAC
1 TGAAGAAGAAGAAGAGTAGGAAATGCTTTAC
66817 TGAAGAAGAAGAAGAGTAGGAAATGCTTTAC
1 TGAAGAAGAAGAAGAGTAGGAAATGCTTTAC
66848 T
1 T
66849 TTCTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.44, C:0.06, G:0.29, T:0.21
Consensus pattern (31 bp):
TGAAGAAGAAGAAGAGTAGGAAATGCTTTAC
Found at i:72254 original size:90 final size:89
Alignment explanation
Indices: 72138--72314 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
72128 TAATCCATAA
* *
72138 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATAAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAAT-AAAACCCTAATATAAT
72203 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
*
72228 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATAATT
*
72293 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
72315 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 37 0.45
90 46 0.55
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATAATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:72944 original size:30 final size:29
Alignment explanation
Indices: 72910--72968 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
72900 GGAAAAAATG
*
72910 TAGGGACTAAAAAAGTAATTTTCAAAAGTT
1 TAGGGACCAAAAAAGTAATTTT-AAAAGTT
**
72940 TAGGGACCAAAAGTGTAATTTTAAAAGTT
1 TAGGGACCAAAAAAGTAATTTTAAAAGTT
72969 AGGTGTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.31
Consensus pattern (29 bp):
TAGGGACCAAAAAAGTAATTTTAAAAGTT
Found at i:74413 original size:19 final size:19
Alignment explanation
Indices: 74389--74430 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
74379 CTACACACAA
**
74389 AAAGTTTCGGAACTCTTTG
1 AAAGTTTCAAAACTCTTTG
74408 AAAGTTTCAAAACTCTTTG
1 AAAGTTTCAAAACTCTTTG
74427 AAAG
1 AAAG
74431 AGCTATTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (19 bp):
AAAGTTTCAAAACTCTTTG
Found at i:75451 original size:19 final size:21
Alignment explanation
Indices: 75418--75456 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
75408 TAGAAATTAA
*
75418 TGTTAGAGTGATG-AATTTGG
1 TGTTAGAATGATGAAATTTGG
75438 TGTTAGAATG-TGAAATTTG
1 TGTTAGAATGATGAAATTTG
75457 ACTATTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (21 bp):
TGTTAGAATGATGAAATTTGG
Found at i:77121 original size:19 final size:19
Alignment explanation
Indices: 77097--77144 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
77087 ATATGCATTG
77097 AGCTATGAACT-TGAAAATA
1 AGCTATGAA-TATGAAAATA
*
77116 AGCTATGAATATGAAATTA
1 AGCTATGAATATGAAAATA
*
77135 AGTTATGAAT
1 AGCTATGAAT
77145 CTCAAATAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (19 bp):
AGCTATGAATATGAAAATA
Found at i:77156 original size:18 final size:18
Alignment explanation
Indices: 77111--77156 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
77101 ATGAACTTGA
* *
77111 AAATAAGCTATGAATATG
1 AAATAAGTTATGAATATC
*
77129 AAATTAAGTTATGAATCTC
1 AAA-TAAGTTATGAATATC
77148 AAATAAGTT
1 AAATAAGTT
77157 TTGAGTCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.33
Consensus pattern (18 bp):
AAATAAGTTATGAATATC
Found at i:77228 original size:6 final size:6
Alignment explanation
Indices: 77217--77264 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
77207 AGTACAAATT
* * *
77217 ATGAAA ATGAAA TATGAAA GTGAAT ATGAAA GTGAAA GATGAAA ATGA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA -ATGAAA ATGA
77265 GATATGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 23 0.68
7 11 0.32
ACGTcount: A:0.56, C:0.00, G:0.23, T:0.21
Consensus pattern (6 bp):
ATGAAA
Found at i:77234 original size:13 final size:13
Alignment explanation
Indices: 77216--77273 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
77206 AAGTACAAAT
77216 TATGAAAATGAAA
1 TATGAAAATGAAA
*
77229 TATGAAAGTG-AA
1 TATGAAAATGAAA
*
77241 TATGAAAGTGAAA
1 TATGAAAATGAAA
* *
77254 GATGAAAATGAGA
1 TATGAAAATGAAA
77267 TATGAAA
1 TATGAAA
77274 GTTTTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
12 12 0.31
13 27 0.69
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.22
Consensus pattern (13 bp):
TATGAAAATGAAA
Found at i:81650 original size:24 final size:24
Alignment explanation
Indices: 81617--81668 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
81607 AGGCGAATAT
*
81617 TCAGGGGTCTCAGAATGGTGCGGA
1 TCAGGGGTCTCAGAACGGTGCGGA
* *
81641 TCAGGTGTCTCAGAACGGTGCTGA
1 TCAGGGGTCTCAGAACGGTGCGGA
81665 TCAG
1 TCAG
81669 TAGTCGGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (24 bp):
TCAGGGGTCTCAGAACGGTGCGGA
Found at i:90955 original size:22 final size:23
Alignment explanation
Indices: 90928--90974 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
90918 AAGACGTAAT
90928 TTTTGAAATTTT-TATTTAT-TTA
1 TTTTGAAATTTTAT-TTTATGTTA
*
90950 TTTTGATATTTTATTTTATGTTA
1 TTTTGAAATTTTATTTTATGTTA
90973 TT
1 TT
90975 GTAATTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.70
Consensus pattern (23 bp):
TTTTGAAATTTTATTTTATGTTA
Found at i:90983 original size:22 final size:20
Alignment explanation
Indices: 90934--90983 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
90924 TAATTTTTGA
*
90934 AATTTTTATTTATTTATTTT
1 AATTTTTATTTATTTATTGT
*
90954 GATATTTTATTTTATGTTATTGT
1 AAT-TTTTA-TTTAT-TTATTGT
90977 AATTTTT
1 AATTTTT
90984 TATGATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 5 0.21
22 9 0.38
23 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (20 bp):
AATTTTTATTTATTTATTGT
Found at i:90984 original size:23 final size:22
Alignment explanation
Indices: 90936--90986 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
90926 ATTTTTGAAA
* *
90936 TTTTTA-TTTATTTATTTTGAT
1 TTTTTATTTTATTTATTGTAAT
*
90957 ATTTTATTTTATGTTATTGTAAT
1 TTTTTATTTTAT-TTATTGTAAT
90980 TTTTTAT
1 TTTTTAT
90987 GATAATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 5 0.21
22 5 0.21
23 14 0.58
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.73
Consensus pattern (22 bp):
TTTTTATTTTATTTATTGTAAT
Found at i:92209 original size:57 final size:57
Alignment explanation
Indices: 92121--92242 Score: 244
Period size: 57 Copynumber: 2.1 Consensus size: 57
92111 TCACCTGTAT
92121 AGTCAGCAACAGAGCATCAGATATCAATGTCACAACCTACATTCACACACTCGAATC
1 AGTCAGCAACAGAGCATCAGATATCAATGTCACAACCTACATTCACACACTCGAATC
92178 AGTCAGCAACAGAGCATCAGATATCAATGTCACAACCTACATTCACACACTCGAATC
1 AGTCAGCAACAGAGCATCAGATATCAATGTCACAACCTACATTCACACACTCGAATC
92235 AGTCAGCA
1 AGTCAGCA
92243 TTTCAACATA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.19
Consensus pattern (57 bp):
AGTCAGCAACAGAGCATCAGATATCAATGTCACAACCTACATTCACACACTCGAATC
Found at i:93221 original size:30 final size:30
Alignment explanation
Indices: 93176--93232 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
93166 AAGTAAATTT
*
93176 GAAGAAGAGAATAAGAAG-ATGGAAATGGA
1 GAAGAAGAGAATAAGAAGTATGAAAATGGA
*
93205 GAAGAAGAATAATAAGAAGTATGAAAAT
1 GAAGAAG-AGAATAAGAAGTATGAAAAT
93233 TTACCAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.29
30 10 0.42
31 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.28, T:0.14
Consensus pattern (30 bp):
GAAGAAGAGAATAAGAAGTATGAAAATGGA
Found at i:95356 original size:28 final size:28
Alignment explanation
Indices: 95274--95400 Score: 148
Period size: 29 Copynumber: 4.4 Consensus size: 28
95264 GAAAATTATA
* * *
95274 AAAATATCACATTTATTAAAAATTATTACC
1 AAAATATCAC-TTT-TTCAAAATAATTCCC
*
95304 AAAATATCACCGTTTT-ACAAATAATTCCC
1 AAAATATCA-CTTTTTCA-AAATAATTCCC
95333 AAAATATCACTTTTTCAAAATAATTCCC
1 AAAATATCACTTTTTCAAAATAATTCCC
*
95361 AAAATGTCACCTTTTTCAAAATAATTCCC
1 AAAATATCA-CTTTTTCAAAATAATTCCC
*
95390 AAAATGTCACT
1 AAAATATCACT
95401 GGGTCGAGTC
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
28 27 0.31
29 49 0.56
30 11 0.12
31 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATATCACTTTTTCAAAATAATTCCC
Found at i:95364 original size:57 final size:58
Alignment explanation
Indices: 95274--95400 Score: 168
Period size: 57 Copynumber: 2.2 Consensus size: 58
95264 GAAAATTATA
*
95274 AAAATATCACATTTATTAAAAATTATTACCAAAATATCACCGTTTTAC-AAATAATTCCC
1 AAAATATCAC-TTTATTAAAAATAATTACCAAAATATCACC-TTTTACAAAATAATTCCC
* * * *
95333 AAAATATCACTTT-TTCAAAATAATTCCCAAAATGTCACCTTTTTCAAAATAATTCCC
1 AAAATATCACTTTATTAAAAATAATTACCAAAATATCACCTTTTACAAAATAATTCCC
*
95390 AAAATGTCACT
1 AAAATATCACT
95401 GGGTCGAGTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
56 5 0.08
57 43 0.70
58 3 0.05
59 10 0.16
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (58 bp):
AAAATATCACTTTATTAAAAATAATTACCAAAATATCACCTTTTACAAAATAATTCCC
Found at i:95434 original size:17 final size:17
Alignment explanation
Indices: 95395--95457 Score: 90
Period size: 17 Copynumber: 3.6 Consensus size: 17
95385 TTCCCAAAAT
* *
95395 GTCACTGGGTCGAGTCGG
1 GTCAATGGGTCGGGTC-G
*
95413 GTCAACGGGTCGGGTCG
1 GTCAATGGGTCGGGTCG
95430 GTCAATGGGTCGGGTCG
1 GTCAATGGGTCGGGTCG
95447 GTCAATGGGTC
1 GTCAATGGGTC
95458 AACCCGGTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
17 28 0.68
18 13 0.32
ACGTcount: A:0.13, C:0.21, G:0.44, T:0.22
Consensus pattern (17 bp):
GTCAATGGGTCGGGTCG
Found at i:98914 original size:19 final size:18
Alignment explanation
Indices: 98887--98923 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
98877 TTATGTCATT
*
98887 TGAATATGAAAAATAAAAA
1 TGAAAATGAAAAA-AAAAA
98906 TGAAAATGAAAAAAAAAA
1 TGAAAATGAAAAAAAAAA
98924 CATTTATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
TGAAAATGAAAAAAAAAA
Found at i:99577 original size:199 final size:202
Alignment explanation
Indices: 99117--99643 Score: 534
Period size: 199 Copynumber: 2.6 Consensus size: 202
99107 TTTGAACGTT
* * * * * * * *
99117 ATTTT-ACACTGCTTAGAATATCTCGTATGTGTCGACACTAGCCTCAATTGAAACATAAG-TACA
1 ATTTTAACA-TGCTTACAATGTCTCATATGTATCGATATTACCCTCAATTGAAAGATAAGTTAC-
* *
99180 AATATTACACCTCTAATCTTATAAATTACGAAAATTTTCAGATGAACTACCCGAAAATACCCCGC
64 AATATTACGCCTCTAATCTTATAAATTACGAAAATTTTCAGATGAACTACACGAAAATA--CCGC
* * * * *
99245 CTTGAACATGTCTATAAAGCCATTTTAGCTTCTTCTTTATGTAGAAAACCAAGCTTTGGAATCAT
127 CTTGAACATGCCTATAAAGCCATTTTAGCTTCTTCTTCATGCACAAAACCAAGCTTTGGAACCAT
* * *
99310 TTTGAACGTGA
192 TTTCAAAGCGA
* * * *
99321 TTTTTACCCTGCTTACAATGTCTCATATGTGTCGATATTACCCTCAATTGAAAGATAAGTTACAA
1 ATTTTAACATGCTTACAATGTCTCATATGTATCGATATTACCCTCAATTGAAAGATAAGTTACAA
* * * * *
99386 TATTACGCCTCTAATCTTATAAATTACG-AAATTGTTTAGATTAACTGCATGAAAA-A-TGCCTT
66 TATTACGCCTCTAATCTTATAAATTACGAAAATT-TTCAGATGAACTACACGAAAATACCGCCTT
*
99448 GAATATGCCTATCAAAG-CATTTTAGCATT-TTCTTCATGCACAAAA-CAAGCTTTGGAACCATT
130 GAACATGCCTAT-AAAGCCATTTTAGC-TTCTTCTTCATGCACAAAACCAAGCTTTGGAACCATT
99510 TTCAAAGCGA
193 TTCAAAGCGA
* * ** * * *
99520 ATTTTAACATGTTTACAATTTCTTGTATGTATCGATATTGA-CCTCAACTGAAAGATAAATTTCA
1 ATTTTAACATGCTTACAATGTCTCATATGTATCGATATT-ACCCTCAATTGAAAGATAAGTTACA
* * * * * *
99584 ATACTACGCCTCTAATCTTATAAATCATGAAAAAATTT-AGATTAACTACCCGAAAATACC
65 ATATTACGCCTCTAATCTTATAAATTACG-AAAATTTTCAGATGAACTACACGAAAATACC
99644 TCTCGAACGT
Statistics
Matches: 268, Mismatches: 45, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
199 115 0.43
200 41 0.15
201 10 0.04
203 6 0.02
204 92 0.34
205 4 0.01
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (202 bp):
ATTTTAACATGCTTACAATGTCTCATATGTATCGATATTACCCTCAATTGAAAGATAAGTTACAA
TATTACGCCTCTAATCTTATAAATTACGAAAATTTTCAGATGAACTACACGAAAATACCGCCTTG
AACATGCCTATAAAGCCATTTTAGCTTCTTCTTCATGCACAAAACCAAGCTTTGGAACCATTTTC
AAAGCGA
Found at i:100915 original size:28 final size:28
Alignment explanation
Indices: 100883--100937 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
100873 ATAATAGGTC
* *
100883 ATATAAATAA-ACTATTAAAAGTATAAAT
1 ATATAAATAACAATAATAAAA-TATAAAT
*
100911 ATATATATAACAATAATAAAATATAAA
1 ATATAAATAACAATAATAAAATATAAA
100938 AATTATAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (28 bp):
ATATAAATAACAATAATAAAATATAAAT
Found at i:101028 original size:3 final size:3
Alignment explanation
Indices: 100996--101057 Score: 74
Period size: 3 Copynumber: 20.3 Consensus size: 3
100986 TTATAGGTGA
*
100996 AAT ATT AAT ATAT ATAT ATAT AAT -AT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
101043 AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT A
101058 TAAAATTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 39 0.72
4 11 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:101117 original size:2 final size:2
Alignment explanation
Indices: 101112--101145 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
101102 ACATACATAC
101112 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
101146 TTACAATGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102316 original size:21 final size:21
Alignment explanation
Indices: 102290--102333 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
102280 ATAGTTTGTA
102290 ATAATAATTATATAAAATAAT
1 ATAATAATTATATAAAATAAT
102311 ATAATAATTATATAAAATAAT
1 ATAATAATTATATAAAATAAT
102332 AT
1 AT
102334 CCACGGTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATAATTATATAAAATAAT
Found at i:103178 original size:110 final size:110
Alignment explanation
Indices: 103037--103240 Score: 309
Period size: 110 Copynumber: 1.9 Consensus size: 110
103027 TGGGAAATTG
** * *
103037 TTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCC
1 TTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCC
*
103102 TTCATTGTGAAGTTGAGATTGACTCTGAATGAAACTGAAAAGTTA
66 TTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
* * * *
103147 TTTGTTGACAACCAGTCGCCCCTTCATTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCT
1 TTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCC
* *
103212 TTCGTTGTGAAGTTGAAATTGGCTCTGAA
66 TTCATTGTGAAGTTGAAATTGACTCTGAA
103241 ATTGGGAAGC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
110 83 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (110 bp):
TTTGTTGACAACCAGTCGCCCCTTCACTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATATCC
TTCATTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTA
Found at i:104393 original size:8 final size:7
Alignment explanation
Indices: 104372--104412 Score: 57
Period size: 8 Copynumber: 5.7 Consensus size: 7
104362 CTTATTTTTC
104372 TTTTC-T
1 TTTTCTT
104378 TTTTCTT
1 TTTTCTT
104385 TTGTTCTT
1 TT-TTCTT
104393 TTTTCTCT
1 TTTTCT-T
104401 TTTTCTT
1 TTTTCTT
104408 TTTTC
1 TTTTC
104413 AATTTAGGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.16
7 13 0.41
8 14 0.44
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTCTT
Found at i:104397 original size:15 final size:15
Alignment explanation
Indices: 104372--104412 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
104362 CTTATTTTTC
104372 TTTTC-TTTTTCT-T
1 TTTTCTTTTTTCTCT
104385 TTGTTCTTTTTTCTCT
1 TT-TTCTTTTTTCTCT
104401 TTTTCTTTTTTC
1 TTTTCTTTTTTC
104413 AATTTAGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.08
14 3 0.12
15 17 0.68
16 3 0.12
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTTCTCT
Found at i:111562 original size:17 final size:19
Alignment explanation
Indices: 111531--111568 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
111521 ATATGAATGT
111531 AAAAACATGGAAAATATAA
1 AAAAACATGGAAAATATAA
111550 AAAAACAT-G-AAATATAA
1 AAAAACATGGAAAATATAA
111567 AA
1 AA
111569 TGCAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (19 bp):
AAAAACATGGAAAATATAA
Found at i:114788 original size:16 final size:15
Alignment explanation
Indices: 114765--114804 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
114755 AACGTGTTAG
114765 AAAAAAATAAAAATA
1 AAAAAAATAAAAATA
114780 AAAACAAATAAAAATA
1 AAAA-AAATAAAAATA
*
114796 AATAAAATA
1 AAAAAAATA
114805 GAGATGGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:115162 original size:17 final size:17
Alignment explanation
Indices: 115142--115188 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
115132 TTATAGGTGA
115142 AATATTAAT-ATATATAT
1 AATATTAATAATA-ATAT
*
115159 AATAATAATAATAATAT
1 AATATTAATAATAATAT
*
115176 AATATTAAAAATA
1 AATATTAATAATA
115189 TAATCAAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 23 0.88
18 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATTAATAATAATAT
Found at i:117344 original size:24 final size:24
Alignment explanation
Indices: 117317--117374 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
117307 GTTCGTGAAC
*
117317 GTTCGGTTATGTTGGTTCGATTAT
1 GTTCGTTTATGTTGGTTCGATTAT
* *
117341 GTTCGTTTATGTTTGTTCGGTTAT
1 GTTCGTTTATGTTGGTTCGATTAT
117365 GTTCGTTTAT
1 GTTCGTTTAT
117375 ATTCATTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.10, C:0.09, G:0.26, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTGGTTCGATTAT
Found at i:118396 original size:10 final size:10
Alignment explanation
Indices: 118381--118455 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
118371 GGGTCTCCAA
118381 CGTTTATGTT
1 CGTTTATGTT
118391 CGTTTATGTT
1 CGTTTATGTT
*
118401 TGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
118412 ATGTTCGTGTT
1 -CGTTTATGTT
118423 CGTTTATGTT
1 CGTTTATGTT
118433 CG----TGTT
1 CGTTTATGTT
118439 CGTTTATGTT
1 CGTTTATGTT
118449 CGTTTAT
1 CGTTTAT
118456 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.65
11 7 0.14
12 5 0.10
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:118406 original size:16 final size:16
Alignment explanation
Indices: 118387--118451 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
118377 CCAACGTTTA
*
118387 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
118403 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
118419 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
118435 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
118451 T
1 T
118452 TTATTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:118427 original size:26 final size:26
Alignment explanation
Indices: 118383--118433 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
118373 GTCTCCAACG
* *
118383 TTTATGTTCGTTTATGTTTGTGTTCA
1 TTTATGTTCGTTTACGTTTATGTTCA
118409 TTTATGTTCGTGTT-CGTTTATGTTC
1 TTTATGTTCGT-TTACGTTTATGTTC
118434 GTGTTCGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.10, C:0.10, G:0.20, T:0.61
Consensus pattern (26 bp):
TTTATGTTCGTTTACGTTTATGTTCA
Found at i:122111 original size:22 final size:22
Alignment explanation
Indices: 122082--122134 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
122072 GAAAAAAGAA
122082 CAGAAAAGCTATGAATTAATCC
1 CAGAAAAGCTATGAATTAATCC
* *
122104 TAGAAAAGCTATGATTTAATCC
1 CAGAAAAGCTATGAATTAATCC
122126 CAGAAAAGC
1 CAGAAAAGC
122135 ACAGGAACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.45, C:0.17, G:0.15, T:0.23
Consensus pattern (22 bp):
CAGAAAAGCTATGAATTAATCC
Found at i:124848 original size:37 final size:37
Alignment explanation
Indices: 124775--124849 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
124765 GTTAAAAAAT
* *
124775 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
124812 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTAAAAATCATAAA
124849 A
1 A
124850 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:125868 original size:38 final size:38
Alignment explanation
Indices: 125817--125890 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
125807 CCAAATTTGA
* *
125817 ACCACTAAAGAATATCTATGCAACTTCGGTTCTTATAT
1 ACCACTAAAGAATACCTATGCAACTTCAGTTCTTATAT
* *
125855 ACCACTATAGAATACCTATGTAACTTCAGTTCTTAT
1 ACCACTAAAGAATACCTATGCAACTTCAGTTCTTAT
125891 TTTTTTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.09, T:0.35
Consensus pattern (38 bp):
ACCACTAAAGAATACCTATGCAACTTCAGTTCTTATAT
Done.