Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 23
Found at i:313 original size:24 final size:24
Alignment explanation
Indices: 273--319 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
263 ACAGTTATTC
*
273 CACTTGAAGTTCAAAAAGATATGT
1 CACTTGAAGTGCAAAAAGATATGT
* *
297 CACTTGAAGTGCCAAAAGTTATG
1 CACTTGAAGTGCAAAAAGATATG
320 ATCATGAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (24 bp):
CACTTGAAGTGCAAAAAGATATGT
Found at i:1381 original size:29 final size:31
Alignment explanation
Indices: 1348--1406 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1338 CTTAGCTTTA
*
1348 TATTATGTTTACATAT-GTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
1377 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
1407 GGCAGCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 7 0.27
31 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2323 original size:19 final size:21
Alignment explanation
Indices: 2299--2350 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2289 CAGCCAAGAG
*
2299 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
2318 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
2339 CATGTATTTTCA
1 CATGTATTTTCA
2351 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:2788 original size:19 final size:18
Alignment explanation
Indices: 2760--2797 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
2750 CCTTTCTTTA
2760 TTCATTCATT-CTTAATAT
1 TTCATTCATTACTT-ATAT
2778 TTCATTTCATTACTTATAT
1 TTCA-TTCATTACTTATAT
2797 T
1 T
2798 ATTATCCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 11 0.61
20 3 0.17
ACGTcount: A:0.26, C:0.16, G:0.00, T:0.58
Consensus pattern (18 bp):
TTCATTCATTACTTATAT
Found at i:3798 original size:19 final size:21
Alignment explanation
Indices: 3754--3806 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 21
3744 GAAACCCCTT
3754 TGAAAATACATGATTTTTTAAA
1 TGAAAATACATGA-TTTTTAAA
3776 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
3795 TGAAGATACATG
1 TGAAAATACATG
3807 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
22 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:7726 original size:19 final size:20
Alignment explanation
Indices: 7683--7736 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
7673 GAAACCCCTT
7683 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
7704 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
7723 TGAAGATACATGAT
1 TGAAAATACATGAT
7737 CTTGGCCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:10088 original size:24 final size:24
Alignment explanation
Indices: 10061--10128 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
10051 GACATGTTCT
* *
10061 TTGACGTTCCAACAGTTATGCCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
* * *
10085 TTGAAGTTCAAAAAGATATGTCAC
1 TTGAAGTTCCAAAAGTTATGCCAC
*
10109 TTGAAGTGCCAAAAGTTATG
1 TTGAAGTTCCAAAAGTTATG
10129 ATCATTGAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (24 bp):
TTGAAGTTCCAAAAGTTATGCCAC
Found at i:10144 original size:24 final size:23
Alignment explanation
Indices: 10068--10144 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 23
10058 TCTTTGACGT
* *
10068 TCCAACAGTTATGCCACTTGAAG
1 TCCAAAAGTTATGTCACTTGAAG
* *
10091 TTCAAAAAGATATGTCACTTGAAG
1 -TCCAAAAGTTATGTCACTTGAAG
10115 TGCCAAAAGTTATGATCA-TTGAAG
1 T-CCAAAAGTTATG-TCACTTGAAG
10139 CTCCAA
1 -TCCAA
10145 GTTCATTACA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.02
24 39 0.89
25 4 0.09
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (23 bp):
TCCAAAAGTTATGTCACTTGAAG
Found at i:11208 original size:30 final size:31
Alignment explanation
Indices: 11172--11231 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
11162 CTTAGCTTTA
11172 TATTATGTTTACATAT-ATTTTAGAT-TCATT
1 TATTATGTTTACATATCA-TTTAGATATCATT
*
11202 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
11232 GGCAGCATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:20582 original size:13 final size:13
Alignment explanation
Indices: 20564--20602 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
20554 TTGTATTTTG
20564 CTTTCTTTGTTTC
1 CTTTCTTTGTTTC
20577 CTTTCTTTGTTTC
1 CTTTCTTTGTTTC
20590 CTTTCTTTAGTTT
1 CTTTCTTT-GTTT
20603 TTCTTCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (13 bp):
CTTTCTTTGTTTC
Found at i:27356 original size:22 final size:20
Alignment explanation
Indices: 27331--27370 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
27321 ATGTTTGTTT
27331 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
27353 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
27371 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:31622 original size:22 final size:20
Alignment explanation
Indices: 31597--31636 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31587 ATGTTTGTTT
31597 ATGGTAATGGGAGCTAAGTATG
1 ATGGTAAT--GAGCTAAGTATG
*
31619 ATGGTCATGAGCTAAGTA
1 ATGGTAATGAGCTAAGTA
31637 CATCATCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
22 7 0.41
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (20 bp):
ATGGTAATGAGCTAAGTATG
Found at i:35552 original size:25 final size:30
Alignment explanation
Indices: 35518--35582 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
35508 CCTTGGCTTG
35518 CTTTCTCTTTT-TGAA-CTTC-TC-TTTT-T
1 CTTT-TCTTTTCTGAATCTTCTTCTTTTTGT
*
35544 CTTTTCTTTTCTGAATTTTCTTCTTTTTGT
1 CTTTTCTTTTCTGAATCTTCTTCTTTTTGT
35574 CTTTTCTTT
1 CTTTTCTTT
35583 CTTTTTGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.18
26 8 0.24
27 3 0.09
28 2 0.06
29 4 0.12
30 10 0.30
ACGTcount: A:0.06, C:0.20, G:0.05, T:0.69
Consensus pattern (30 bp):
CTTTTCTTTTCTGAATCTTCTTCTTTTTGT
Found at i:35584 original size:17 final size:17
Alignment explanation
Indices: 35540--35589 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
35530 GAACTTCTCT
35540 TTTTCTTTTCTTTTCTGAA
1 TTTTC-TTTCTTTT-TGAA
**
35559 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGAA
35575 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
35590 CACTCCAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.25
17 16 0.57
19 5 0.18
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGAA
Found at i:39492 original size:19 final size:19
Alignment explanation
Indices: 39465--39523 Score: 51
Period size: 19 Copynumber: 3.5 Consensus size: 19
39455 GAAAAATCAG
39465 AAAACAAAGTGAAGCACTC
1 AAAACAAAGTGAAGCACTC
*
39484 AAAAGAAA--GAAG-----
1 AAAACAAAGTGAAGCACTC
39496 AAAACAAAGTGAAGCACTC
1 AAAACAAAGTGAAGCACTC
*
39515 AAAAGAAAG
1 AAAACAAAG
39524 AAAAAATCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
12 7 0.23
14 4 0.13
17 4 0.13
19 15 0.50
ACGTcount: A:0.61, C:0.14, G:0.19, T:0.07
Consensus pattern (19 bp):
AAAACAAAGTGAAGCACTC
Found at i:39501 original size:31 final size:31
Alignment explanation
Indices: 39463--39529 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
39453 AAGAAAAATC
39463 AGAAAACAAAGTGAAGCACTCAAAAGAAAGA
1 AGAAAACAAAGTGAAGCACTCAAAAGAAAGA
39494 AGAAAACAAAGTGAAGCACTCAAAAGAAAGA
1 AGAAAACAAAGTGAAGCACTCAAAAGAAAGA
39525 A-AAAA
1 AGAAAA
39530 TCCAGCACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.64, C:0.12, G:0.18, T:0.06
Consensus pattern (31 bp):
AGAAAACAAAGTGAAGCACTCAAAAGAAAGA
Found at i:43454 original size:35 final size:37
Alignment explanation
Indices: 43385--43464 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
43375 ATACTATTTC
* *
43385 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAG
*
43422 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAG
1 CATCACCATAATCCATCTACCATTATCACGCCTATAG
43457 CATCACCA
1 CATCACCA
43465 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.31, C:0.38, G:0.05, T:0.26
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAG
Found at i:44745 original size:11 final size:11
Alignment explanation
Indices: 44729--44784 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
44719 ATTAGAGTGC
44729 AAAAAGAAAAG
1 AAAAAGAAAAG
44740 AAAAAGACAAA-
1 AAAAAGA-AAAG
* *
44751 AAGAAGAATCAGAA
1 AAAAAGAA--A-AG
44765 AAAAAGAAAAG
1 AAAAAGAAAAG
44776 AAAAAGAAA
1 AAAAAGAAA
44785 TTCAAAAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
10 1 0.03
11 23 0.62
12 5 0.14
13 1 0.03
14 7 0.19
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:55472 original size:24 final size:24
Alignment explanation
Indices: 55426--55477 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
55416 TCTTGGCACT
* * *
55426 TCAAGTGGCATATCTTTTTGAACA
1 TCAAGTGGCATAGCTGTTGGAACA
*
55450 TCAAGTGGCATAGCTGTTGGAACG
1 TCAAGTGGCATAGCTGTTGGAACA
55474 TCAA
1 TCAA
55478 AGGACATGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (24 bp):
TCAAGTGGCATAGCTGTTGGAACA
Found at i:58051 original size:35 final size:35
Alignment explanation
Indices: 58001--58075 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
57991 CATTTTCACA
58001 CCTATAACATCACCATC-TTCTATTACCATTGCACG
1 CCTATAACATCACCATCTTTC-ATTACCATTGCACG
* * *
58036 CCTATATCATTACCATCTTTCATTACCATTTCACG
1 CCTATAACATCACCATCTTTCATTACCATTGCACG
58071 CCTAT
1 CCTAT
58076 GTAACCACCA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 33 0.92
36 3 0.08
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.36
Consensus pattern (35 bp):
CCTATAACATCACCATCTTTCATTACCATTGCACG
Found at i:58481 original size:11 final size:11
Alignment explanation
Indices: 58467--58501 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
58457 CAAAAGCAAC
58467 AAAAAAAAAAG
1 AAAAAAAAAAG
58478 AAAAACAAAAAG
1 AAAAA-AAAAAG
*
58490 AAAAGAAAAAG
1 AAAAAAAAAAG
58501 A
1 A
58502 CTCCTACATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:58486 original size:17 final size:17
Alignment explanation
Indices: 58464--58499 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
58454 CAACAAAAGC
58464 AACAAAAAAAAAAGAAA
1 AACAAAAAAAAAAGAAA
*
58481 AACAAAAAGAAAAGAAA
1 AACAAAAAAAAAAGAAA
58498 AA
1 AA
58500 GACTCCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.86, C:0.06, G:0.08, T:0.00
Consensus pattern (17 bp):
AACAAAAAAAAAAGAAA
Found at i:58548 original size:16 final size:16
Alignment explanation
Indices: 58525--58563 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
58515 TTTGGAGTGC
58525 AAAAGAAT-AAAAGAA
1 AAAAGAATCAAAAGAA
*
58540 AAGAAGAATCAAAAGCA
1 AA-AAGAATCAAAAGAA
58557 AAAAGAA
1 AAAAGAA
58564 AATTGAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 11 0.52
17 8 0.38
ACGTcount: A:0.74, C:0.05, G:0.15, T:0.05
Consensus pattern (16 bp):
AAAAGAATCAAAAGAA
Found at i:58802 original size:26 final size:26
Alignment explanation
Indices: 58773--58830 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
58763 TTCTTAACAT
58773 TTTCTATGC-TACCCCTATCATAACCA
1 TTTCTAT-CTTACCCCTATCATAACCA
*
58799 TTTCTATCTTACCCCTATCATAACTA
1 TTTCTATCTTACCCCTATCATAACCA
58825 TTTCTA
1 TTTCTA
58831 GACCCTAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (26 bp):
TTTCTATCTTACCCCTATCATAACCA
Found at i:64954 original size:6 final size:6
Alignment explanation
Indices: 64943--64985 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
64933 CAAAAGCAAC
* *
64943 AAAAAG AAAAAG TAAGAAG AAAAAT AAAAAG -AAAAG AAAAAG A
1 AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
64986 CTCCTACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:64972 original size:20 final size:17
Alignment explanation
Indices: 64943--64983 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
64933 CAAAAGCAAC
*
64943 AAAAAGAAAAAGTAAGAAG
1 AAAAATAAAAAG-AA-AAG
64962 AAAAATAAAAAGAAAAG
1 AAAAATAAAAAGAAAAG
64979 AAAAA
1 AAAAA
64984 GACTCCTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (17 bp):
AAAAATAAAAAGAAAAG
Found at i:74719 original size:54 final size:54
Alignment explanation
Indices: 74638--74745 Score: 189
Period size: 54 Copynumber: 2.0 Consensus size: 54
74628 GGATACATGG
* *
74638 TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGTTAAATGA
1 TGGTTCGGCCAGCCCTTGTACCTCTATAAAATGACATAATTAAATGCTAAATGA
*
74692 TGGTTCGGCCATCCCTTGTACCTCTATAAAATGACATAATTAAATGCTAAATGA
1 TGGTTCGGCCAGCCCTTGTACCTCTATAAAATGACATAATTAAATGCTAAATGA
74746 CATAATGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.31
Consensus pattern (54 bp):
TGGTTCGGCCAGCCCTTGTACCTCTATAAAATGACATAATTAAATGCTAAATGA
Found at i:78782 original size:24 final size:24
Alignment explanation
Indices: 78748--78795 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
78738 AAAAAGGAAT
*
78748 TAGAACTTGTTTGGTAACATTTAA
1 TAGAACCTGTTTGGTAACATTTAA
78772 TAGAACCTGTTTGGTAACATTTAA
1 TAGAACCTGTTTGGTAACATTTAA
78796 CTCACCTCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (24 bp):
TAGAACCTGTTTGGTAACATTTAA
Found at i:80234 original size:11 final size:11
Alignment explanation
Indices: 80209--80248 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
80199 AAAAAAAACA
80209 AAAAAAAAGGC
1 AAAAAAAAGGC
80220 -AAAAAAAGGC
1 AAAAAAAAGGC
*
80230 AAAAAAAGGGC
1 AAAAAAAAGGC
80241 AAAAAAAA
1 AAAAAAAA
80249 AAGCCAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.75, C:0.07, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGGC
Found at i:80237 original size:10 final size:10
Alignment explanation
Indices: 80210--80247 Score: 67
Period size: 10 Copynumber: 3.7 Consensus size: 10
80200 AAAAAAACAA
80210 AAAAAAAGGC
1 AAAAAAAGGC
80220 AAAAAAAGGC
1 AAAAAAAGGC
80230 AAAAAAAGGGC
1 AAAAAAA-GGC
80241 AAAAAAA
1 AAAAAAA
80248 AAAGCCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 17 0.63
11 10 0.37
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAAAGGC
Found at i:98515 original size:8 final size:8
Alignment explanation
Indices: 98504--98543 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
98494 TCTTTTTCTT
98504 TTCTTTTC
1 TTCTTTTC
98512 TTCTTTTC
1 TTCTTTTC
98520 TTCTTTT-
1 TTCTTTTC
98527 TGTCTTTTC
1 T-TCTTTTC
98536 TTTCTTTT
1 -TTCTTTT
98544 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 6 0.21
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:98523 original size:16 final size:17
Alignment explanation
Indices: 98497--98545 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
98487 GAACTTCTCT
98497 TTTTCTTTTCTTTTCT-TC
1 TTTTC-TTTCTTTT-TGTC
98515 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
98531 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
98546 CACTCCAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 9 0.31
18 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:103513 original size:35 final size:36
Alignment explanation
Indices: 103428--103513 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
103418 TAAGATACTA
*
103428 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* *
103463 CCTATAACATCACCATCTTCCATTATCA-TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* *
103498 CCTATATCATTACCAT
1 CCTATAACATCACCAT
103514 TGCATGCCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 24 0.53
36 21 0.47
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.31
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTGCACG
Found at i:103549 original size:22 final size:22
Alignment explanation
Indices: 103484--103550 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
103474 ACCATCTTCC
* *
103484 ATTATCATTGCACGCCTATATC
1 ATTACCATTGCACGCCTATATA
*
103506 ATTACCATTGCATGCCTATATA
1 ATTACCATTGCACGCCTATATA
* *
103528 ATTACCATTTCACGCGTATATA
1 ATTACCATTGCACGCCTATATA
103550 A
1 A
103551 CCACCAATCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (22 bp):
ATTACCATTGCACGCCTATATA
Found at i:107726 original size:16 final size:16
Alignment explanation
Indices: 107705--107737 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
107695 TCTTCAAGTA
*
107705 ATGGCTAAGTGGAGAC
1 ATGGCTAAGTAGAGAC
107721 ATGGCTAAGTAGAGAC
1 ATGGCTAAGTAGAGAC
107737 A
1 A
107738 ACTCTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (16 bp):
ATGGCTAAGTAGAGAC
Found at i:111102 original size:19 final size:20
Alignment explanation
Indices: 111078--111117 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
111068 TATCCCATCC
111078 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
111097 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
111117 T
1 T
111118 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:113501 original size:54 final size:54
Alignment explanation
Indices: 113420--113527 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
113410 GGATACATGG
113420 TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
1 TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
113474 TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
1 TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
113528 CATAATGTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (54 bp):
TGGTTCGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
Found at i:115535 original size:24 final size:25
Alignment explanation
Indices: 115499--115546 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
115489 CACAATGATC
* *
115499 TGCATTTTCTTCAGTTTCATCATCT
1 TGCATTGTCTTCAGGTTCATCATCT
*
115524 TGCATTGT-TTCAGGTTCTTCATC
1 TGCATTGTCTTCAGGTTCATCATC
115547 AAAAATAGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.15, C:0.23, G:0.12, T:0.50
Consensus pattern (25 bp):
TGCATTGTCTTCAGGTTCATCATCT
Found at i:116976 original size:22 final size:26
Alignment explanation
Indices: 116951--117004 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
116941 AAAATCAGTA
116951 AAGAAA-TTG-AAGCACTC-AAAA-G
1 AAGAAATTTGTAAGCACTCAAAAAGG
116973 AAGAAATTTGTAAGCACTCAAAAAGG
1 AAGAAATTTGTAAGCACTCAAAAAGG
116999 AAGAAA
1 AAGAAA
117005 AGAAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.21
23 3 0.11
24 8 0.29
25 4 0.14
26 7 0.25
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.15
Consensus pattern (26 bp):
AAGAAATTTGTAAGCACTCAAAAAGG
Found at i:118282 original size:12 final size:12
Alignment explanation
Indices: 118265--118290 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
118255 GGAAAGAAGA
118265 CTATGGTTATGG
1 CTATGGTTATGG
118277 CTATGGTTATGG
1 CTATGGTTATGG
118289 CT
1 CT
118291 TATGAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.12, G:0.31, T:0.42
Consensus pattern (12 bp):
CTATGGTTATGG
Found at i:126236 original size:35 final size:36
Alignment explanation
Indices: 126151--126236 Score: 113
Period size: 35 Copynumber: 2.4 Consensus size: 36
126141 TAAGATACTA
*
126151 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* *
126186 CCTATAACATCACCATCTTCCATTATCA-TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTGCACG
* *
126221 CCTATATCATTACCAT
1 CCTATAACATCACCAT
126237 TGCACGCCTA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
35 24 0.53
36 21 0.47
ACGTcount: A:0.29, C:0.36, G:0.03, T:0.31
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTGCACG
Found at i:126272 original size:22 final size:22
Alignment explanation
Indices: 126207--126273 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
126197 ACCATCTTCC
* *
126207 ATTATCATTGCACGCCTATATC
1 ATTACCATTGCACGCCTATATA
126229 ATTACCATTGCACGCCTATATA
1 ATTACCATTGCACGCCTATATA
* *
126251 ATTACCATTTCACGCATATATA
1 ATTACCATTGCACGCCTATATA
126273 A
1 A
126274 CCACCAATCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.34
Consensus pattern (22 bp):
ATTACCATTGCACGCCTATATA
Found at i:130440 original size:16 final size:16
Alignment explanation
Indices: 130419--130451 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
130409 TCTTCAAGTA
130419 ATGGCTAAGTGGAGAC
1 ATGGCTAAGTGGAGAC
130435 ATGGCTAAGTGGAGAC
1 ATGGCTAAGTGGAGAC
130451 A
1 A
130452 ACTCTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.36, T:0.18
Consensus pattern (16 bp):
ATGGCTAAGTGGAGAC
Found at i:133820 original size:19 final size:20
Alignment explanation
Indices: 133796--133835 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
133786 TATCCCATCC
133796 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
133815 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
133835 T
1 T
133836 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:134134 original size:21 final size:22
Alignment explanation
Indices: 134103--134160 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 22
134093 AAATTAGAGT
134103 GAAAA-AAGAAAAGAAAATATA
1 GAAAAGAAGAAAAGAAAATATA
* *
134124 -AAAAGAAG-AAA-CAAATTTA
1 GAAAAGAAGAAAAGAAAATATA
134143 GAAAAGAAGAAAAGAAAA
1 GAAAAGAAGAAAAGAAAA
134161 AGAAGTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 6 0.20
20 15 0.50
21 6 0.20
22 3 0.10
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.09
Consensus pattern (22 bp):
GAAAAGAAGAAAAGAAAATATA
Found at i:135982 original size:54 final size:54
Alignment explanation
Indices: 135901--136008 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
135891 GGATACATGG
*
135901 TGGTTTGGCCAGCCCTTGTGCCTCTATAAAATGACATAATTAAATGCTAAATGA
1 TGGTTTGGCCAGCCCTTGTGCCACTATAAAATGACATAATTAAATGCTAAATGA
135955 TGGTTTGGCCAGCCCTTGTGCCACTATAAAATGACATAATTAAATGCTAAATGA
1 TGGTTTGGCCAGCCCTTGTGCCACTATAAAATGACATAATTAAATGCTAAATGA
136009 CATAATGTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (54 bp):
TGGTTTGGCCAGCCCTTGTGCCACTATAAAATGACATAATTAAATGCTAAATGA
Found at i:140869 original size:17 final size:17
Alignment explanation
Indices: 140847--140896 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
140837 AATTGGAGTG
140847 CAAAAAGAAAGAAAAGA
1 CAAAAAGAAAGAAAAGA
140864 CAAAAA-AGAAGAAAAGA
1 CAAAAAGA-AAGAAAAGA
140881 -AGAAAAGAAAAGAAAA
1 CA-AAAAG-AAAGAAAA
140897 AGAGAAGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.07
17 19 0.66
18 7 0.24
19 1 0.03
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (17 bp):
CAAAAAGAAAGAAAAGA
Found at i:140871 original size:18 final size:17
Alignment explanation
Indices: 140848--140896 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
140838 ATTGGAGTGC
140848 AAAAAGAAAGAAAAGACA
1 AAAAAGAAAGAAAAGA-A
140866 AAAAAG-AAGAAAAGAA
1 AAAAAGAAAGAAAAGAA
*
140882 GAAAAGAAAAGAAAA
1 AAAAAG-AAAGAAAA
140897 AGAGAAGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 6 0.21
17 9 0.32
18 13 0.46
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAAAAGAA
Found at i:140878 original size:8 final size:8
Alignment explanation
Indices: 140849--140889 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
140839 TTGGAGTGCA
140849 AAAAGAAAG
1 AAAAG-AAG
*
140858 AAAAGACAA
1 AAAAGA-AG
140867 AAAAGAAG
1 AAAAGAAG
140875 AAAAGAAG
1 AAAAGAAG
140883 AAAAGAA
1 AAAAGAA
140890 AAGAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 17 0.59
9 12 0.41
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:140902 original size:18 final size:17
Alignment explanation
Indices: 140849--140902 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 17
140839 TTGGAGTGCA
*
140849 AAAAG-AAAGAAAAGAC
1 AAAAGAAAAGAAAAGAG
140865 AAAA-AAGAAGAAAAGAAG
1 AAAAGAA-AAGAAAAG-AG
140883 AAAAGAAAAGAAAAAGAG
1 AAAAGAAAAG-AAAAGAG
140901 AA
1 AA
140903 GTTCAAAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
16 5 0.16
17 8 0.25
18 12 0.38
19 7 0.22
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAAAAGAG
Found at i:143832 original size:23 final size:23
Alignment explanation
Indices: 143787--143832 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
143777 TTATACCTAT
*
143787 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
143810 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
143833 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:145687 original size:22 final size:26
Alignment explanation
Indices: 145662--145715 Score: 80
Period size: 24 Copynumber: 2.2 Consensus size: 26
145652 AAAATCAGTA
145662 AAGAAA-TTG-AAGCACTC-AAAA-G
1 AAGAAATTTGTAAGCACTCAAAAAGG
145684 AAGAAATTTGTAAGCACTCAAAAAGG
1 AAGAAATTTGTAAGCACTCAAAAAGG
145710 AAGAAA
1 AAGAAA
145716 AGAAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.21
23 3 0.11
24 8 0.29
25 4 0.14
26 7 0.25
ACGTcount: A:0.56, C:0.11, G:0.19, T:0.15
Consensus pattern (26 bp):
AAGAAATTTGTAAGCACTCAAAAAGG
Found at i:153021 original size:18 final size:19
Alignment explanation
Indices: 152975--153024 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
152965 GAAACCCCTT
*
152975 TGAAAATACATGATTTTTGA
1 TGAAAATACATGA-TTTTAA
152995 TGAAAATACATGA-TTTAA
1 TGAAAATACATGATTTTAA
*
153013 TGAAGATACATG
1 TGAAAATACATG
153025 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
20 13 0.46
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:155003 original size:7 final size:6
Alignment explanation
Indices: 154984--155025 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
154974 CAAAAGCAAC
* *
154984 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AGAAAG AAAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAA
155026 TACTCCTACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:155012 original size:19 final size:18
Alignment explanation
Indices: 154984--155025 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
154974 CAAAAGCAAC
*
154984 AAAAAGAAAAAGAAAGAAG
1 AAAAACAAAAAGAAA-AAG
*
155003 AAAAACAAAAAGAGAAAG
1 AAAAACAAAAAGAAAAAG
155021 AAAAA
1 AAAAA
155026 TACTCCTACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:159784 original size:27 final size:28
Alignment explanation
Indices: 159729--159798 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
159719 AAAGAAAATC
* *
159729 AGAAAAAAAGAAATTGAAGCACTCCAAA
1 AGAAAGAAAGAAATTGAAGCACTCAAAA
* *
159757 AGAAAGAAAGAAATT-CAGCATTCAAAA
1 AGAAAGAAAGAAATTGAAGCACTCAAAA
*
159784 AGAAGGAAAGCAAAT
1 AGAAAGAAAG-AAAT
159799 AAAAGAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
27 18 0.50
28 18 0.50
ACGTcount: A:0.60, C:0.11, G:0.17, T:0.11
Consensus pattern (28 bp):
AGAAAGAAAGAAATTGAAGCACTCAAAA
Found at i:164563 original size:13 final size:13
Alignment explanation
Indices: 164545--164570 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
164535 TACTATATAT
164545 TTTCATCACCATC
1 TTTCATCACCATC
164558 TTTCATCACCATC
1 TTTCATCACCATC
164571 CTCCATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTCATCACCATC
Found at i:170618 original size:28 final size:25
Alignment explanation
Indices: 170563--170618 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
170553 TTTTTTGCTT
**
170563 TTTCTTCTTTTGAGTGCTGGATTTC
1 TTTCTTCTTTTGAGTGCTCAATTTC
170588 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTC
170616 TTT
1 TTT
170619 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 6 0.23
28 9 0.35
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGCTCAATTTC
Found at i:179399 original size:806 final size:806
Alignment explanation
Indices: 177847--179460 Score: 2924
Period size: 806 Copynumber: 2.0 Consensus size: 806
177837 ATGTCTCAAA
* * * *
177847 GTCCATGGAATGAAGATAGGTAACAACTAGGCGTGAATTAGCTTCCAACATGGATCTAGGTGACA
1 GTCCATGGAATAAAGATAGGCAACAACTAGGCGTGAATTAGCTTCCAACATGCATCTAGGTAACA
*
177912 TGGCATCCATTGGGCAGCCTATAGATGAACTAGCTTCAAGGTAAGCTAGGTGAGTGTCTTGGTAG
66 TGGCATCCATTGGGCAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGGTGAGTGTCTTGGTAG
*
177977 CTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTTCTCAACTCCTCAG
131 CTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTGCTCAACTCCTCAG
178042 CTACTCTCCCAGCTACTTCCAGCTACCTCTAGTCCACTTTTCAGTAATTTGGTCTAAAGCTCTCC
196 CTACTCTCCCAGCTACTTCCAGCTACCTCTAGTCCACTTTTCAGTAATTTGGTCTAAAGCTCTCC
*
178107 TCCAGCTATGTTTAGCTACATGCTAGCTCCTCCAGCTAAGTTTAAGCTCCTTATGTGATGAAATG
261 TCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAGCTAAGTTTAAGCTCCTTATGTGATGAAATG
* * *
178172 AGCTGCCATAATGTTCATGAGCTAGTGTGAGTTGCTATGCTTTTCCTTTTAGCTAGCCAAGCTAC
326 AGCTGCCATAATGTTCATGAGCTAGTGTGAGCTGCTATCCTTGTCCTTTTAGCTAGCCAAGCTAC
*
178237 CATAATATGTCTTGTTTTGTGTTTCACCTATAGGAATCACCAAACAAATAAAATAAGCAATGTGT
391 CATAATATGCCTTGTTTTGTGTTTCACCTATAGGAATCACCAAACAAATAAAATAAGCAATGTGT
178302 GAGCTCATTTAAGGTAAAATGCATGCCGACGTGAGGTGTTTGAGTGATATGAGCTATGAATGCAT
456 GAGCTCATTTAAGGTAAAATGCATGCCGACGTGAGGTGTTTGAGTGATATGAGCTATGAATGCAT
* * *
178367 GTCATGAGCTAGGTACATAACGATATAACATATATTAGCTAATGTATAAGACCTAGGAGCTGGAA
521 GTCATGAGCTAAGTACATAACGATATAACATATATAAGCTAATGTATAAGACCTAGGAGCTAGAA
* * *
178432 TGATTGCACGTGAGCTAACAAATGAATGATTAAGCATTCTTCCATTTCACGAATGAATTAAATCA
586 TGAATGCACGTGAGCTAACAAATGAATGATTAAGCATTATGCCATTTCACGAATGAATTAAATCA
*
178497 TGCTTAAATGAATGCAAGACTAATATAACATACTTAACATACTTGAAATAACATTTTACATCAAT
651 TGCTTAAATGAATGCAAGACTAATATAACATACTTAACATACTTGAAATAACATTGTACATCAAT
*
178562 TATAAAGATGTGAATGCATGAATATCATATAATATGGTAGTCATAAATGATAAATGGAAATATGT
716 TATAAAGATGTGAATGCATGAATATCATATAATATGGTAGTCATAAATGATAAATGGAAACATGT
178627 AATAATAATATCCTAAGAAATGATAT
781 AATAATAATATCCTAAGAAATGATAT
178653 GTCCATGGAATAAAGATAGGCAACAACTAGGCGTGAATTAGCTTCCAACATGCATCTAGGTAACA
1 GTCCATGGAATAAAGATAGGCAACAACTAGGCGTGAATTAGCTTCCAACATGCATCTAGGTAACA
*
178718 TGGCATCCATTGGGCAGCCTAGAGATGAACTAGCTTCAAGTTAAGCTAGGTGAGTGTCTTGGTAG
66 TGGCATCCATTGGGCAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGGTGAGTGTCTTGGTAG
178783 CTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTGCTCAACTCCTCAG
131 CTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTGCTCAACTCCTCAG
* *
178848 CTACTCTCCCATCTATTTCCAGCTACCTCTAGTCCACTTTTCAGTAATTTGGTCTAAAGCTCTCC
196 CTACTCTCCCAGCTACTTCCAGCTACCTCTAGTCCACTTTTCAGTAATTTGGTCTAAAGCTCTCC
*
178913 TCCAGCTAAGTTTAGCTACATGCTAGCTTCTCCAGCTAAGTTTAAGCTCCTTATGTGATGAAATG
261 TCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAGCTAAGTTTAAGCTCCTTATGTGATGAAATG
178978 AGCTGCCATAATGTTCATGAGCTAGTGTGAGCTGCTATCCTTGTCCTTTTAGCTAGCCAAGCTAC
326 AGCTGCCATAATGTTCATGAGCTAGTGTGAGCTGCTATCCTTGTCCTTTTAGCTAGCCAAGCTAC
179043 CATAATATGCCTTGTTTTGTGTTTCACCTATAGGAATCACCAAACAAATAAAATAAGCAATGTGT
391 CATAATATGCCTTGTTTTGTGTTTCACCTATAGGAATCACCAAACAAATAAAATAAGCAATGTGT
* * *
179108 GAGCTTATTTAAGGTAAAATGCATG-CTACCGTGAGGTTTTTGAGTGATATGAGCTATGAATGCA
456 GAGCTCATTTAAGGTAAAATGCATGCCGA-CGTGAGGTGTTTGAGTGATATGAGCTATGAATGCA
* *
179172 TGTCATGAGCTAAGTACATAATGATATAACATATGTAAGCTAATGTATAAGACCTAGGAGCTAGA
520 TGTCATGAGCTAAGTACATAACGATATAACATATATAAGCTAATGTATAAGACCTAGGAGCTAGA
* *
179237 ATGAATGCACGTGAGCTAACAAATGAATGATTAAGCATTATGCCATTTCACGAATTAATTGAATC
585 ATGAATGCACGTGAGCTAACAAATGAATGATTAAGCATTATGCCATTTCACGAATGAATTAAATC
*
179302 ATGCTTAAATGAATGCAAGACTAATATAACATACTTAACATACTTGAAATAACATTGTGCATCAA
650 ATGCTTAAATGAATGCAAGACTAATATAACATACTTAACATACTTGAAATAACATTGTACATCAA
*
179367 TTATAAAGATGTGAATGCATGAATATCATATAATATGGTATTCATAAATGATAAATGGAAACATG
715 TTATAAAGATGTGAATGCATGAATATCATATAATATGGTAGTCATAAATGATAAATGGAAACATG
179432 TAATAATAATATCCTAAGAAATGATAT
780 TAATAATAATATCCTAAGAAATGATAT
179459 GT
1 GT
179461 AATCATAACA
Statistics
Matches: 775, Mismatches: 32, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
805 2 0.00
806 773 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (806 bp):
GTCCATGGAATAAAGATAGGCAACAACTAGGCGTGAATTAGCTTCCAACATGCATCTAGGTAACA
TGGCATCCATTGGGCAGCCTAGAGATGAACTAGCTTCAAGGTAAGCTAGGTGAGTGTCTTGGTAG
CTAACTAGGTGAGTTATAGCTTGATGAACTCAAGCTAGTTAGCTTTGGTCTGCTCAACTCCTCAG
CTACTCTCCCAGCTACTTCCAGCTACCTCTAGTCCACTTTTCAGTAATTTGGTCTAAAGCTCTCC
TCCAGCTAAGTTTAGCTACATGCTAGCTCCTCCAGCTAAGTTTAAGCTCCTTATGTGATGAAATG
AGCTGCCATAATGTTCATGAGCTAGTGTGAGCTGCTATCCTTGTCCTTTTAGCTAGCCAAGCTAC
CATAATATGCCTTGTTTTGTGTTTCACCTATAGGAATCACCAAACAAATAAAATAAGCAATGTGT
GAGCTCATTTAAGGTAAAATGCATGCCGACGTGAGGTGTTTGAGTGATATGAGCTATGAATGCAT
GTCATGAGCTAAGTACATAACGATATAACATATATAAGCTAATGTATAAGACCTAGGAGCTAGAA
TGAATGCACGTGAGCTAACAAATGAATGATTAAGCATTATGCCATTTCACGAATGAATTAAATCA
TGCTTAAATGAATGCAAGACTAATATAACATACTTAACATACTTGAAATAACATTGTACATCAAT
TATAAAGATGTGAATGCATGAATATCATATAATATGGTAGTCATAAATGATAAATGGAAACATGT
AATAATAATATCCTAAGAAATGATAT
Found at i:185793 original size:35 final size:35
Alignment explanation
Indices: 185714--185819 Score: 124
Period size: 35 Copynumber: 3.0 Consensus size: 35
185704 ACTACCTAAA
* * * *
185714 CATCACCATATTCCATCACCATTTTCACGCCTATAA
1 CATCACCATCTTCTATCACCA-TTGCACGCCTATAT
*
185750 CATCACCATCTT-TCATTACCATTGCACGCCTATAT
1 CATCACCATCTTCT-ATCACCATTGCACGCCTATAT
* *
185785 CATTACCATCTTCTATCACCATTTCACGCCTATAT
1 CATCACCATCTTCTATCACCATTGCACGCCTATAT
185820 AACCACCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 42 0.70
36 18 0.30
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.34
Consensus pattern (35 bp):
CATCACCATCTTCTATCACCATTGCACGCCTATAT
Found at i:186338 original size:23 final size:23
Alignment explanation
Indices: 186293--186338 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
186283 TTATACCTAT
*
186293 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
186316 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
186339 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:187971 original size:8 final size:8
Alignment explanation
Indices: 187943--187990 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
187933 TTGGAGTGCA
187943 AAAAGAAAG
1 AAAAG-AAG
187952 AAAAGACA-
1 AAAAGA-AG
187960 AAAAGAAG
1 AAAAGAAG
*
187968 AAAAGAAT
1 AAAAGAAG
187976 AAAAGAAG
1 AAAAGAAG
187984 AAAAGAA
1 AAAAGAA
187991 AAGAAAAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
7 1 0.03
8 28 0.80
9 6 0.17
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:187973 original size:5 final size:5
Alignment explanation
Indices: 187943--187997 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
187933 TTGGAGTGCA
187943 AAAAG -AAAG AAAAG ACAAA- AAGAAG AAAAG AATAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AA-AAG AA-AAG AAAAG
187989 AAAAG AAAA
1 AAAAG AAAA
187998 AGAGAAGTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
4 5 0.12
5 29 0.67
6 9 0.21
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:187990 original size:16 final size:15
Alignment explanation
Indices: 187942--187992 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 15
187932 ATTGGAGTGC
187942 AAAAAGAAAGAAAAGA
1 AAAAAG-AAGAAAAGA
187958 CAAAAAGAAGAAAAGA
1 -AAAAAGAAGAAAAGA
187974 ATAAAAGAAGAAAAGA
1 A-AAAAGAAGAAAAGA
187990 AAA
1 AAA
187993 GAAAAAGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.09
16 24 0.73
17 6 0.18
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (15 bp):
AAAAAGAAGAAAAGA
Found at i:188000 original size:16 final size:15
Alignment explanation
Indices: 187942--188000 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
187932 ATTGGAGTGC
*
187942 AAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAAG
*
187957 ACAAAAAGAAGAAAAG
1 A-AAAAAAAAGAAAAG
*
187973 AATAAAAGAAGAAAAG
1 AA-AAAAAAAGAAAAG
187989 AAAAGAAAAAGA
1 AAAA-AAAAAGA
188001 GAAGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 4 0.11
16 34 0.89
ACGTcount: A:0.78, C:0.02, G:0.19, T:0.02
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:188013 original size:14 final size:14
Alignment explanation
Indices: 187994--188023 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
187984 AAAAGAAAAG
187994 AAAAAGAGAAGTTC
1 AAAAAGAGAAGTTC
188008 AAAAAGAGAAGTTC
1 AAAAAGAGAAGTTC
188022 AA
1 AA
188024 CCATTTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (14 bp):
AAAAAGAGAAGTTC
Found at i:190760 original size:23 final size:23
Alignment explanation
Indices: 190711--190760 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
190701 ATCCTTATAC
190711 ATAT-AGATACTTATTTCATATG
1 ATATAAGATACTTATTTCATATG
* *
190733 TTATAAGATAGTTATTTTCATAT-
1 ATATAAGATACTTA-TTTCATATG
190756 ATATA
1 ATATA
190761 TATATATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 3 0.13
23 12 0.52
24 8 0.35
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (23 bp):
ATATAAGATACTTATTTCATATG
Found at i:191866 original size:19 final size:20
Alignment explanation
Indices: 191850--191886 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
191840 ATTTATTTCA
191850 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
191869 TTTCATTACTTA-TATTTA
1 TTTCATTACTTATTATTTA
191887 CCCTTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:196093 original size:36 final size:36
Alignment explanation
Indices: 196042--196152 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 36
196032 TAAGATACTA
196042 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * * *
196077 CCTATAACATCACCATCTTCCATTACC-GTTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * * *
196112 CCTATATCATTACCATATTCTATCACCATTTT-ACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
196147 CCTATA
1 CCTATA
196153 TAACCACCAA
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
35 39 0.63
36 23 0.37
ACGTcount: A:0.28, C:0.34, G:0.05, T:0.33
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTTCACG
Found at i:196812 original size:18 final size:18
Alignment explanation
Indices: 196789--196827 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
196779 ATGCAAAATT
196789 ATGTCCTTTTGTTGCTCA
1 ATGTCCTTTTGTTGCTCA
196807 ATGTCCTTTTGTTGCTCA
1 ATGTCCTTTTGTTGCTCA
196825 ATG
1 ATG
196828 GATATGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (18 bp):
ATGTCCTTTTGTTGCTCA
Found at i:201462 original size:26 final size:26
Alignment explanation
Indices: 201426--201496 Score: 124
Period size: 26 Copynumber: 2.7 Consensus size: 26
201416 TCCTAGAACA
201426 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
201452 CCCATGTGCCTTGCATATGACCAGCC
1 CCCATGTGCCTTGCATATGACCAGCC
* *
201478 CCCTTGTGCCTTGTATATG
1 CCCATGTGCCTTGCATATG
201497 GATCATTTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.17, C:0.35, G:0.20, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGCC
Found at i:204930 original size:24 final size:21
Alignment explanation
Indices: 204895--204937 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
204885 GGCTCATTCT
*
204895 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
204918 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
204938 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:212609 original size:91 final size:91
Alignment explanation
Indices: 212454--212627 Score: 303
Period size: 91 Copynumber: 1.9 Consensus size: 91
212444 CCCATGTGCC
*
212454 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
212519 CTCCCTATTCGGCCAAGCCATATGTT
66 CTCCCTATTCGGCCAAGCCATATGTT
* * * *
212545 TTGCATGTGATCAGCCCCCATGTGCCTTGCTTGTGGTTCATTTAGGCGCCAAGATAAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
212610 CTCCCTATTCGGCCAAGC
66 CTCCCTATTCGGCCAAGC
212628 ATCAACTACC
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.21, C:0.28, G:0.22, T:0.29
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATAAAGAGTTCT
CTCCCTATTCGGCCAAGCCATATGTT
Found at i:213463 original size:28 final size:28
Alignment explanation
Indices: 213401--213463 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
213391 AAAAAAAATC
* * * *
213401 AGAAAAGAAATTGAAGCACTCCAAAATA
1 AGAAAAGAAAATCAAGCACTCAAAAAGA
*
213429 A-ATAAAGAAAATCCAGCACTCAAAAAGA
1 AGA-AAAGAAAATCAAGCACTCAAAAAGA
213457 AGAAAAG
1 AGAAAAG
213464 CAAAGAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
27 1 0.04
28 26 0.93
29 1 0.04
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.11
Consensus pattern (28 bp):
AGAAAAGAAAATCAAGCACTCAAAAAGA
Found at i:220496 original size:3 final size:3
Alignment explanation
Indices: 220488--220535 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
220478 TCATTTCGTT
*
220488 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
220536 AATAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:222712 original size:18 final size:18
Alignment explanation
Indices: 222691--222759 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 18
222681 TTTTATATAC
222691 TTATTATTTTCATAGTAT
1 TTATTATTTTCATAGTAT
*
222709 TTATATAATTTTCTTATTAATAT
1 TTAT-T-ATTTTC--A-TAGTAT
*
222732 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAGTA-T
222751 TTATTATTT
1 TTATTATTT
222760 ACTTTTCTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
18 14 0.34
19 4 0.10
20 7 0.17
22 6 0.15
23 8 0.20
24 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (18 bp):
TTATTATTTTCATAGTAT
Found at i:225047 original size:7 final size:7
Alignment explanation
Indices: 225012--225052 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
225002 TTTTCCTACA
225012 TGCATTT
1 TGCATTT
225019 T-CATTT
1 TGCATTT
225025 TGCATCTT
1 TGCAT-TT
225033 TGCATTT
1 TGCATTT
*
225040 TTCATTT
1 TGCATTT
225047 TGCATT
1 TGCATT
225053 CATACTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.20
7 17 0.57
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.10, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:227651 original size:17 final size:17
Alignment explanation
Indices: 227620--227666 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
227610 AAGAAAGAAG
227620 AAAAA-AAAAACAAAA-C
1 AAAAAGAAAAA-AAAAGC
*
227636 AAAACAGAAAAAAAAAGG
1 AAAA-AGAAAAAAAAAGC
227654 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
227667 TTGAATCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 14 0.52
18 9 0.33
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAGC
Found at i:229784 original size:114 final size:115
Alignment explanation
Indices: 229475--229792 Score: 514
Period size: 115 Copynumber: 2.8 Consensus size: 115
229465 AAGTGCTATG
*
229475 TGCTCATAGTAGAAATAAGAAGACTCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
229540 TGATTTGGTATGAACTCCAAAATCAATCATTGAATTTGAAAGATGAATTT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGAATTTAAAAGATGAATTT
*
229590 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATA
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
229655 TGGTTTGGTATGAACCCCAAAACCAATCATT-AGATTTAAAAGATGAA-TT
66 TGATTTGGTATGAACCCCAAAACCAATCATTGA-ATTTAAAAGATGAATTT
* *
229704 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
229769 TGATTCGGTAGGAACCCCAGAACC
66 TGATTTGGTATGAACCCCAAAACC
229793 GATTTATGGA
Statistics
Matches: 189, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
114 85 0.45
115 104 0.55
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.32
Consensus pattern (115 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACCCCAAAACCAATCATTGAATTTAAAAGATGAATTT
Found at i:229812 original size:114 final size:113
Alignment explanation
Indices: 229475--229815 Score: 470
Period size: 114 Copynumber: 3.0 Consensus size: 113
229465 AAGTGCTATG
*
229475 TGCTCATAGTAGAAATAAGAAGACTCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
229540 TGATTTGGTATGAACTCCAAAATCAATCATTGAATTTGAAAGATGAATTT
66 TGATTTGGTATGAACCCCAAAACCATTTA-TGAA-TTGAAAGATGAATTT
*
229590 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATA
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
229655 TGGTTTGGTATGAACCCCAAAACCAATCATTA-GATTTAAAAGATGAA-TT
66 TGATTTGGTATGAACCCCAAAACC-AT--TTATGAATTGAAAGATGAATTT
* *
229704 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * *
229769 TGATTCGGTAGGAACCCCAGAACCGATTTATGGAATTGGAAGATGAA
66 TGATTTGGTATGAACCCCAAAACC-ATTTAT-GAATTGAAAGATGAA
229816 CTGCATGATC
Statistics
Matches: 201, Mismatches: 20, Indels: 11
0.87 0.09 0.05
Matches are distributed among these distances:
112 3 0.01
114 98 0.49
115 95 0.47
116 3 0.01
118 2 0.01
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (113 bp):
TGCTCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGATTTGGTATGAACCCCAAAACCATTTATGAATTGAAAGATGAATTT
Found at i:232201 original size:22 final size:22
Alignment explanation
Indices: 232175--232217 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
232165 TACACTCTTC
232175 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAGATTCTCTTTTT
232197 AAAGATGATAGATTCTCTTTT
1 AAAGATGATAGATTCTCTTTT
232218 CAAAAATAAA
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:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTT
Found at i:232799 original size:76 final size:76
Alignment explanation
Indices: 232673--233543 Score: 1616
Period size: 76 Copynumber: 11.5 Consensus size: 76
232663 CTATTTCCCA
*
232673 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGTCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
232738 AGCCTCAGGGT
66 AGCCTTAGGGT
232749 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
232814 AGCCTCAGGGT
66 AGCCTTAGGGT
232825 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
232890 AGACTAAGGGT
66 AGCCTTAGGGT
232901 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
232966 AGCCTTAGGGT
66 AGCCTTAGGGT
232977 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
233042 AGCCTTAGGGT
66 AGCCTTAGGGT
233053 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
233118 AGCCTTAGGGT
66 AGCCTTAGGGT
233129 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
233194 AGCCTAAGGGT
66 AGCCTTAGGGT
233205 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
233270 AGCCTTAGGAT
66 AGCCTTAGGGT
* *
233281 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
233346 AGCCTTAAGGT
66 AGCCTTAGGGT
233357 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
233422 AGCCTTAGGGT
66 AGCCTTAGGGT
233433 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
233498 AGCCTTCGGGT
66 AGCCTTAGGGT
* * *
233509 CATATGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
233544 CATTTCCATC
Statistics
Matches: 776, Mismatches: 19, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 776 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:233678 original size:3 final size:3
Alignment explanation
Indices: 233670--233714 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
233660 TCATTTCGTT
*
233670 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
233715 AATAAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:242003 original size:24 final size:22
Alignment explanation
Indices: 241964--242018 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
241954 GTTGATCCAC
* *
241964 AAGACATGTCCTTTGACATTTCA
1 AAGA-ATGTCCTTTGAAATTTAA
*
241987 AAGGATGTACCTCTTGAAATTTAA
1 AAGAATGT-CCT-TTGAAATTTAA
242011 AAGAATGT
1 AAGAATGT
242019 TCCAATTGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTTAA
Found at i:243480 original size:30 final size:30
Alignment explanation
Indices: 243439--243544 Score: 169
Period size: 30 Copynumber: 3.5 Consensus size: 30
243429 AAGGAGCTTC
*
243439 AACTTAACTGGAGGAGTTAGCATGTAGCTA
1 AACTTAGCTGGAGGAGTTAGCATGTAGCTA
*
243469 AACTTAGCTGGAGGAGCTAGCATGTAGCTA
1 AACTTAGCTGGAGGAGTTAGCATGTAGCTA
243499 AACTTAGCTGGAGGA-TCTAGCATGTAGCTA
1 AACTTAGCTGGAGGAGT-TAGCATGTAGCTA
*
243529 AACATAGCTGGAGGAG
1 AACTTAGCTGGAGGAG
243545 AACTTTGGAC
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (30 bp):
AACTTAGCTGGAGGAGTTAGCATGTAGCTA
Found at i:247978 original size:19 final size:18
Alignment explanation
Indices: 247956--248002 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
247946 AGTGAATAAT
247956 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
* *
247975 AATAATAAGAATGATATGA
1 AAT-ATAAGAATGAAAAGA
247994 AATA-AAGAA
1 AATATAAGAA
248003 ATGATAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 5 0.20
18 1 0.04
19 14 0.56
20 5 0.20
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:248454 original size:19 final size:21
Alignment explanation
Indices: 248411--248462 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
248401 GAAACCCCTT
248411 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
248432 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
248451 TGAAGATACATG
1 TGAAAATACATG
248463 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:249267 original size:30 final size:31
Alignment explanation
Indices: 249226--249285 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
249216 ACATGTTGCC
**
249226 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
249257 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
249286 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:251726 original size:13 final size:13
Alignment explanation
Indices: 251710--251753 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
251700 TTTTTGAATT
251710 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
251723 TTTTTTTCTTTTC
1 TTTTTTTCTTTTC
* *
251736 TGATTTTTCTCTTC
1 T-TTTTTTCTTTTC
251750 TTTT
1 TTTT
251754 GACTTTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTTTCTTTTC
Found at i:252531 original size:19 final size:21
Alignment explanation
Indices: 252488--252539 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
252478 GAAACCCCTT
252488 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
252509 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
252528 TGAAGATACATG
1 TGAAAATACATG
252540 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:253328 original size:30 final size:31
Alignment explanation
Indices: 253287--253346 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
253277 ACATGTTGCC
**
253287 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
253318 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
253347 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:256092 original size:17 final size:17
Alignment explanation
Indices: 256070--256103 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
256060 CGGCTTAAAA
256070 AAATGGTTAGGGTATAG
1 AAATGGTTAGGGTATAG
*
256087 AAATGGTTATGGTATAG
1 AAATGGTTAGGGTATAG
256104 GGGTAGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (17 bp):
AAATGGTTAGGGTATAG
Found at i:261349 original size:17 final size:16
Alignment explanation
Indices: 261280--261351 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
261270 ATTCATGCAT
261280 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
* *
261297 GTTGGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
261315 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
261332 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
261349 CTA
1 CTA
261352 ACTCTTAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
16 1 0.02
17 27 0.61
18 16 0.36
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:274885 original size:13 final size:13
Alignment explanation
Indices: 274867--274901 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
274857 TGTTCTAGGA
274867 AGCCTTGTGGTGC
1 AGCCTTGTGGTGC
274880 AGCCTTGTGGTGC
1 AGCCTTGTGGTGC
274893 AGCCTTGTG
1 AGCCTTGTG
274902 CATGGAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.37, T:0.31
Consensus pattern (13 bp):
AGCCTTGTGGTGC
Found at i:286511 original size:5 final size:5
Alignment explanation
Indices: 286501--286531 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
286491 CTTCAACTTC
286501 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
286532 CTTTTTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:288516 original size:2 final size:2
Alignment explanation
Indices: 288505--288558 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
288495 TAACTATAGG
288505 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
288546 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
288559 GAAAATAACT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:291500 original size:8 final size:8
Alignment explanation
Indices: 291489--291528 Score: 55
Period size: 8 Copynumber: 4.9 Consensus size: 8
291479 TCTTTTTCTT
291489 TTCTTTTC
1 TTCTTTTC
291497 TTCTTTTC
1 TTCTTTTC
291505 TTCTTTT-
1 TTCTTTTC
291512 TGTCTTTTC
1 T-TCTTTTC
291521 TTTCTTTT
1 -TTCTTTT
291529 TGCACTCCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.03
8 21 0.72
9 6 0.21
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.78
Consensus pattern (8 bp):
TTCTTTTC
Found at i:291508 original size:16 final size:17
Alignment explanation
Indices: 291482--291530 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
291472 GAACTTCTCT
291482 TTTTCTTTTCTTTTCT-TC
1 TTTTC-TTTCTTTT-TGTC
291500 TTTTC-TTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
291516 TTTTCTTTCTTTTTG
1 TTTTCTTTCTTTTTG
291531 CACTCCAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.03
16 14 0.48
17 9 0.31
18 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.04, T:0.78
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:295368 original size:24 final size:22
Alignment explanation
Indices: 295331--295375 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
295321 TTGCCCCATT
* *
295331 CTTTTGAATTTCAAGAGGTACATC
1 CTTTTAAATGTCAA-AGG-ACATC
295355 CTTTTAAATGTCAAAGGACAT
1 CTTTTAAATGTCAAAGGACAT
295376 ATCTTGTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
CTTTTAAATGTCAAAGGACATC
Found at i:296540 original size:5 final size:5
Alignment explanation
Indices: 296530--296560 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
296520 CTTCAACTTC
*
296530 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
296561 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:300179 original size:24 final size:22
Alignment explanation
Indices: 300143--300186 Score: 52
Period size: 24 Copynumber: 1.9 Consensus size: 22
300133 TGCCTCATTC
* *
300143 TTTTGAATTTCAAGAGGTACATCA
1 TTTTAAATGTCAA-AGG-ACATCA
300167 TTTTAAATGTCAAAGGACAT
1 TTTTAAATGTCAAAGGACAT
300187 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 3 0.17
24 11 0.61
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
TTTTAAATGTCAAAGGACATCA
Found at i:301351 original size:5 final size:5
Alignment explanation
Indices: 301341--301371 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
301331 CTTCAACTTC
*
301341 TTTCT TTTCT TTTCT TTTCT TTGCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
301372 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:309896 original size:24 final size:22
Alignment explanation
Indices: 309859--309903 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
309849 TTGGCTCATT
* *
309859 CTTTTGAATTTCAAGAGGTACATC
1 CTTTTAAATGTCAA-AGG-ACATC
309883 CTTTTAAATGTCAAAGGACAT
1 CTTTTAAATGTCAAAGGACAT
309904 ATCTTGTGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
CTTTTAAATGTCAAAGGACATC
Found at i:311147 original size:15 final size:15
Alignment explanation
Indices: 311112--311140 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
311102 GTGCTTCAAC
311112 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
311126 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
311141 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:315493 original size:17 final size:16
Alignment explanation
Indices: 315424--315495 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
315414 ATTCATGCAT
315424 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
* * *
315441 GTTGGTTAATTAATTAAA
1 -CTAGTTCATTAA-TAAA
* *
315459 GTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
315476 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
315493 CTA
1 CTA
315496 ACTCTTAATT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
16 1 0.02
17 26 0.62
18 15 0.36
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:320479 original size:51 final size:51
Alignment explanation
Indices: 320423--320522 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
320413 AAGTACCTTC
320423 ATAAAAAGATTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTTT
1 ATAAAAAGATTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTTT
* *
320474 ATAAAAAGGTTCATATCTTTTGAAAGAATGCCTTGTAAGTTCTTGATCT
1 ATAAAAAGATTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCT
320523 GAAAAAAAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (51 bp):
ATAAAAAGATTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTTT
Found at i:320531 original size:51 final size:51
Alignment explanation
Indices: 320425--320533 Score: 173
Period size: 51 Copynumber: 2.1 Consensus size: 51
320415 GTACCTTCAT
* ** *
320425 AAAAAGATTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTTTAT
1 AAAAAGGTTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTGAAA
*
320476 AAAAAGGTTCATATCTTTTGAAAGAATGCCTTGTAAGTTCTTGATCTGAAA
1 AAAAAGGTTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTGAAA
320527 AAAAAGG
1 AAAAAGG
320534 AAACTTTCAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (51 bp):
AAAAAGGTTCATATCTTTTGAAAGAATACCTTGTAAGTTCTTGATCTGAAA
Found at i:332599 original size:22 final size:21
Alignment explanation
Indices: 332566--332613 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
332556 GGAGTGCAAA
332566 AAGAAAAGAAAAATACCAAAAG
1 AAGAAAAGAAAAA-ACCAAAAG
*
332588 AAGAATAA-AAAAAATCAAAAG
1 AAGAA-AAGAAAAAACCAAAAG
332609 -AGAAA
1 AAGAAA
332614 GCAAGCCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 7 0.29
22 10 0.42
23 2 0.08
ACGTcount: A:0.75, C:0.06, G:0.12, T:0.06
Consensus pattern (21 bp):
AAGAAAAGAAAAAACCAAAAG
Found at i:354601 original size:17 final size:17
Alignment explanation
Indices: 354579--354612 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
354569 TATCCTCCCC
354579 CTATACCATAACCATTT
1 CTATACCATAACCATTT
* *
354596 CTATACCCTAACTATTT
1 CTATACCATAACCATTT
354613 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:357535 original size:19 final size:21
Alignment explanation
Indices: 357511--357562 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
357501 CGGCCAAGAG
*
357511 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
357530 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
357551 CATGTATTTTCA
1 CATGTATTTTCA
357563 AAGGAGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:358293 original size:10 final size:9
Alignment explanation
Indices: 358278--358335 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 9
358268 ATTGGAGTGC
358278 AAAAAGAAA
1 AAAAAGAAA
358287 GAAAAAGACAA
1 -AAAAAGA-AA
358298 AAGAAGAGAAA
1 AA-AA-AGAAA
358309 AATCAAA-AAA
1 AA--AAAGAAA
358319 AAAAAGAAA
1 AAAAAGAAA
358328 AAAAAGAA
1 AAAAAGAA
358336 GAATTTCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 3 0.07
9 11 0.26
10 14 0.33
11 9 0.21
12 5 0.12
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:358317 original size:18 final size:16
Alignment explanation
Indices: 358277--358335 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 16
358267 AATTGGAGTG
358277 CAAAAAGAAAGAAAAA
1 CAAAAAGAAAGAAAAA
*
358293 GACAAAAGAAGAGAAAAA
1 CA-AAAAGAA-AGAAAAA
358311 TCAAAAA-AAA-AAAGAA
1 -CAAAAAGAAAGAAA-AA
*
358327 AAAAAAGAA
1 CAAAAAGAA
358336 GAATTTCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 9 0.26
18 11 0.31
19 1 0.03
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (16 bp):
CAAAAAGAAAGAAAAA
Found at i:358328 original size:12 final size:12
Alignment explanation
Indices: 358278--358338 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
358268 ATTGGAGTGC
*
358278 AAAAAGAAAGAA
1 AAAAAAAAAGAA
*
358290 AAAGACAAAAGAA
1 AAA-AAAAAAGAA
* * **
358303 GAGAAAAATCAA
1 AAAAAAAAAGAA
358315 AAAAAAAAAGAA
1 AAAAAAAAAGAA
*
358327 AAAAAAGAAGAA
1 AAAAAAAAAGAA
358339 TTTCAAAAAG
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
12 28 0.78
13 8 0.22
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:362820 original size:11 final size:10
Alignment explanation
Indices: 362804--362836 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
362794 TATTTTTTTC
362804 AAAAAAACAA
1 AAAAAAACAA
362814 AAAAAAACAA
1 AAAAAAACAA
*
362824 AAAAAAATAA
1 AAAAAAACAA
362834 AAA
1 AAA
362837 CAAAGCCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.91, C:0.06, G:0.00, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:362835 original size:16 final size:17
Alignment explanation
Indices: 362805--362840 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
362795 ATTTTTTTCA
362805 AAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAAC
*
362822 AAAAAA-AAATAAAAAC
1 AAAAAACAAAAAAAAAC
362838 AAA
1 AAA
362841 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.03
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAC
Found at i:368075 original size:22 final size:22
Alignment explanation
Indices: 368041--368083 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
368031 AAATCCAGCA
368041 AAGAAAATCAAAGCACTCAAAG
1 AAGAAAATCAAAGCACTCAAAG
* *
368063 AAGAAATTGAAAGCACTCAAA
1 AAGAAAATCAAAGCACTCAAA
368084 AAGGAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.16, G:0.14, T:0.12
Consensus pattern (22 bp):
AAGAAAATCAAAGCACTCAAAG
Found at i:371038 original size:24 final size:22
Alignment explanation
Indices: 370999--371053 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
370989 GGTGATCCAC
* *
370999 AAGACATGTCCTTTGACATTTCA
1 AAGA-ATGTCCTTTGAAATTTAA
*
371022 AAGGATGTACCTCTTGAAATTTAA
1 AAGAATGT-CCT-TTGAAATTTAA
371046 AAGAATGT
1 AAGAATGT
371054 GCCAATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 4 0.15
23 6 0.23
24 16 0.62
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (22 bp):
AAGAATGTCCTTTGAAATTTAA
Found at i:377200 original size:36 final size:35
Alignment explanation
Indices: 377153--377264 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
377143 TAAGATACTA
*
377153 CCTATAACATCACCATCTTCCATCACCAATGTCACG
1 CCTATAACATCACCATCTTCCATCACCATTG-CACG
*
377189 CCTATAACATCACCATATTCCATCACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTGCACG
** ** *
377224 CCTATATTATCTTCAACTTCCATCACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTGCACG
377259 CCTATA
1 CCTATA
377265 TTATCTTCAA
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.29, C:0.37, G:0.05, T:0.29
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTGCACG
Found at i:377245 original size:35 final size:35
Alignment explanation
Indices: 377169--377300 Score: 167
Period size: 35 Copynumber: 3.7 Consensus size: 35
377159 ACATCACCAT
* ** **
377169 CTTCCATCACCAATGTCACGCCTATAACATCACCATA
1 CTTCCATCACCATTG-CACGCCTATATTATCTTCA-A
377206 -TTCCATCACCATTGCACGCCTATATTATCTTCAA
1 CTTCCATCACCATTGCACGCCTATATTATCTTCAA
377240 CTTCCATCACCATTGCACGCCTATATTATCTTCAA
1 CTTCCATCACCATTGCACGCCTATATTATCTTCAA
* **
377275 CTTCTATCACCATTTTACGCCTATAT
1 CTTCCATCACCATTGCACGCCTATAT
377301 AACCACCAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
34 1 0.01
35 72 0.84
36 13 0.15
ACGTcount: A:0.27, C:0.34, G:0.05, T:0.33
Consensus pattern (35 bp):
CTTCCATCACCATTGCACGCCTATATTATCTTCAA
Found at i:377723 original size:6 final size:6
Alignment explanation
Indices: 377694--377737 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
377684 AAAAGCAATA
*
377694 AAAAGAG AAAAAG AAAGAAG AAAAAT AAAAAG -AAAAG AAAAAG A
1 AAAA-AG AAAAAG AAA-AAG AAAAAG AAAAAG AAAAAG AAAAAG A
377738 CTTCTACATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 5 0.15
6 18 0.55
7 10 0.30
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAAG
Done.