Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008547.1 Hibiscus syriacus cultivar Beakdansim tig00111438_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: 134269
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:267 original size:52 final size:52
Alignment explanation
Indices: 156--333 Score: 144
Period size: 52 Copynumber: 3.3 Consensus size: 52
146 TGACGAGCCT
* * * * * * *
156 GCTCCCTATTCCTTCAGGAAGTATAAG-ACTCGACACATCTTCATAAAACGTGTCT
1 GCTCTCTATTCATTCA-G-AGTA-AAGAACTCGAAAAATCTTAAT-AAACGGGTCC
* *
211 GCTCTCTATTCATTCAGAGTAAAG-ACTTGAACAATCTTTAATAAACGGGTCC
1 GCTCTCTATTCATTCAGAGTAAAGAACTCGAAAAATC-TTAATAAACGGGTCC
* * * *
263 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCATAAACAGGTCC
1 GCTCTCTATTCATTC--AGAGTAAAGAACTCGAAAAATCTTAATAAACGGGTCC
* *
317 GCTCCCTATTCTTTCAG
1 GCTCTCTATTCATTCAG
334 GGAGTATAGG
Statistics
Matches: 102, Mismatches: 17, Indels: 11
0.78 0.13 0.08
Matches are distributed among these distances:
52 35 0.34
53 8 0.08
54 35 0.34
55 24 0.24
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (52 bp):
GCTCTCTATTCATTCAGAGTAAAGAACTCGAAAAATCTTAATAAACGGGTCC
Found at i:483 original size:50 final size:51
Alignment explanation
Indices: 259--608 Score: 523
Period size: 50 Copynumber: 6.9 Consensus size: 51
249 TAATAAACGG
* * **
259 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCATA--AACAG
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCA-ACGAACTT
* * *
313 GTCCGCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
364 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
415 GTCCGCTCTCTATT-ATTCAGAGAGTATA-GACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
*
464 GTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
515 G-CCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
565 GTCCGCTCCCTATT-CTTCAGAGAGTATAGGACTCAATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
609 AAACAATTTG
Statistics
Matches: 278, Mismatches: 13, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
49 35 0.13
50 114 0.41
51 98 0.35
54 31 0.11
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:1960 original size:45 final size:47
Alignment explanation
Indices: 1911--2023 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 47
1901 CTTTTATTTA
*
1911 TCTTTTTTCAT-TTTTCTCTTTTCCTTC-CTTTTTCCATTTTTCTC-T
1 TCTTTTTTC-TCTTTTCTCTTTTCCATCACTTTTTCCATTTTTCTCAT
* * * *
1956 TCTTTTTT-TCTTTTCGTTTTTTCCATCATTTTTTTCGTTTTTCTCAT
1 TCTTTTTTCTCTTTTC-TCTTTTCCATCACTTTTTCCATTTTTCTCAT
2003 T-TTTTTTCTCTTTTCTCTTTT
1 TCTTTTTTCTCTTTTCTCTTTT
2024 ATTTCTTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
43 1 0.02
44 5 0.09
45 17 0.30
46 25 0.44
47 9 0.16
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (47 bp):
TCTTTTTTCTCTTTTCTCTTTTCCATCACTTTTTCCATTTTTCTCAT
Found at i:1969 original size:26 final size:27
Alignment explanation
Indices: 1911--2023 Score: 83
Period size: 26 Copynumber: 4.2 Consensus size: 27
1901 CTTTTATTTA
* **
1911 TCTTTTTTCATTTTTCTCTT-TTCCTT
1 TCTTTTTCCATTTTTCTCTTCTTTTTT
*
1937 CCTTTTTCCATTTTTCTCTTCTTTTTT
1 TCTTTTTCCATTTTTCTCTTCTTTTTT
** *
1964 TC-TTTTCGTTTTTTC-CATCATTTTTT
1 TCTTTTTCCATTTTTCTCTTC-TTTTTT
*
1990 TCGTTTTTCTCATTTTT-T-TTCTCTTTTC
1 TC-TTTTTC-CATTTTTCTCTTCT-TTTTT
2018 TCTTTT
1 TCTTTT
2024 ATTTCTTCTT
Statistics
Matches: 68, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
25 3 0.04
26 37 0.54
27 10 0.15
28 13 0.19
29 5 0.07
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.72
Consensus pattern (27 bp):
TCTTTTTCCATTTTTCTCTTCTTTTTT
Found at i:2002 original size:18 final size:18
Alignment explanation
Indices: 1913--2008 Score: 60
Period size: 18 Copynumber: 5.3 Consensus size: 18
1903 TTTATTTATC
*
1913 TTTTTTCATTTTTCTC-T
1 TTTTTTCGTTTTTCTCAT
* *
1930 TTTCCTTCCTTTTTC-CAT
1 TTT-TTTCGTTTTTCTCAT
*
1948 TTTTCTC-TTCTTT-T--T
1 TTTTTTCGTT-TTTCTCAT
1963 TTCTTTTCGTTTTTTCCATCAT
1 TT-TTTTCG-TTTTT-C-TCAT
1985 TTTTTTCGTTTTTCTCAT
1 TTTTTTCGTTTTTCTCAT
2003 TTTTTT
1 TTTTTT
2009 TCTCTTTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 23
0.69 0.06 0.26
Matches are distributed among these distances:
15 3 0.05
16 6 0.10
17 12 0.19
18 25 0.40
19 1 0.02
20 6 0.10
21 6 0.10
22 3 0.05
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTTCGTTTTTCTCAT
Found at i:2009 original size:21 final size:21
Alignment explanation
Indices: 1959--2009 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1949 TTTCTCTTCT
1959 TTTTTTCTTTTCGTTTTTTCCA
1 TTTTTT-TTTTCGTTTTTTCCA
**
1981 TCATTTTTTTCG-TTTTTCTCA
1 TTTTTTTTTTCGTTTTTTC-CA
2002 TTTTTTTT
1 TTTTTTTT
2010 CTCTTTTCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 6 0.25
21 14 0.58
22 4 0.17
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.75
Consensus pattern (21 bp):
TTTTTTTTTTCGTTTTTTCCA
Found at i:2023 original size:18 final size:18
Alignment explanation
Indices: 1913--2030 Score: 68
Period size: 19 Copynumber: 6.5 Consensus size: 18
1903 TTTATTTATC
1913 TTTTTTCATTTTTCTC-TT
1 TTTTTTC-TTTTTCTCATT
* *
1931 TTCCTTCCTTTTTC-CATT
1 TT-TTTTCTTTTTCTCATT
*
1949 TTTCTCTTCTTTTTTTC-TT
1 TTT-T-TTCTTTTTCTCATT
** *
1968 TTCGTT-TTTTCCATCA-T
1 TTTTTTCTTTTTC-TCATT
1985 TTTTTTCGTTTTTCTCATT
1 TTTTTTC-TTTTTCTCATT
2004 TTTTTTCTCTTTTCTC-TT
1 TTTTTTCT-TTTTCTCATT
*
2022 TTATTTCTT
1 TTTTTTCTT
2031 CTTCAAGCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 23
0.68 0.12 0.21
Matches are distributed among these distances:
16 4 0.05
17 11 0.14
18 26 0.34
19 34 0.45
20 1 0.01
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTTCTTTTTCTCATT
Found at i:2033 original size:19 final size:19
Alignment explanation
Indices: 1981--2029 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1971 GTTTTTTCCA
1981 TCATTTT-TTTCGT-TTTTC
1 TCATTTTATTTC-TCTTTTC
*
1999 TCATTTTTTTTCTCTTTTC
1 TCATTTTATTTCTCTTTTC
2018 TC-TTTTATTTCT
1 TCATTTTATTTCT
2030 TCTTCAAGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (19 bp):
TCATTTTATTTCTCTTTTC
Found at i:11714 original size:44 final size:46
Alignment explanation
Indices: 11650--11747 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 46
11640 TTGTTATTCA
11650 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATG-TTTATT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGATTTATT
*
11695 CAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATT
1 CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATG-ATTTATT
11741 CGAAAAA
1 C-AAAAA
11748 ACGAAAATAA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
44 27 0.55
45 10 0.20
46 7 0.14
47 5 0.10
ACGTcount: A:0.40, C:0.20, G:0.10, T:0.30
Consensus pattern (46 bp):
CAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGATTTATT
Found at i:27048 original size:21 final size:21
Alignment explanation
Indices: 27024--27087 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
27014 GCAAATTCGC
27024 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
27045 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
27065 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
27086 GT
1 GT
27088 CTACAGTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:27104 original size:22 final size:22
Alignment explanation
Indices: 27076--27128 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
27066 TTCCATTTCG
27076 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
27098 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
27120 CGTTGCGAT
1 CGTTGCGAT
27129 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:27280 original size:5 final size:6
Alignment explanation
Indices: 27241--27277 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
27231 GACACGTATT
27241 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
27278 CGAGACGGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.30, C:0.54, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:27785 original size:12 final size:12
Alignment explanation
Indices: 27777--27801 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27767 CTCGTGGTCG
27777 TGGTCGTGGTAA
1 TGGTCGTGGTAA
27789 TGGTCGTGGTAA
1 TGGTCGTGGTAA
27801 T
1 T
27802 ACGTGTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (12 bp):
TGGTCGTGGTAA
Found at i:27921 original size:20 final size:20
Alignment explanation
Indices: 27893--27966 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
27883 ACTGTAGACT
27893 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
27913 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
27934 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
27954 ATCGCAACGCGAA
1 ATCGCAACGCGAA
27967 TTTGCGATAG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.39, C:0.23, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:28386 original size:60 final size:61
Alignment explanation
Indices: 28273--28425 Score: 147
Period size: 60 Copynumber: 2.5 Consensus size: 61
28263 ATATATATGT
* * * * *
28273 ATAGTTTG-GGATGAAACTGAAATGTTCAAAAAGTTTGAGGATCAATTTTGAATGA-AGGTC
1 ATAGTTTGAGGGTGAAATTGAAATGTTCAAAAAGTGTGAAGATCAATTTAGAATGATA-GTC
* *
28333 ATAGTTTGAGGGTGAAATTAAAATGTTC-AAATGTGTGAAGA-CTAATTTAGAATGATAGTC
1 ATAGTTTGAGGGTGAAATTGAAATGTTCAAAAAGTGTGAAGATC-AATTTAGAATGATAGTC
* *
28393 AAAATTT-AGGGATGAAATTGAAATGATT-AAAAA
1 ATAGTTTGAGGG-TGAAATTGAAATG-TTCAAAAA
28426 TTTAGGGACT
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
59 5 0.07
60 49 0.64
61 22 0.29
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (61 bp):
ATAGTTTGAGGGTGAAATTGAAATGTTCAAAAAGTGTGAAGATCAATTTAGAATGATAGTC
Found at i:30513 original size:88 final size:93
Alignment explanation
Indices: 30407--30584 Score: 217
Period size: 88 Copynumber: 2.0 Consensus size: 93
30397 AATACTCTTT
* * * **
30407 ACGTTTGAGTAAATAGTCATTTTGGTCCC-T-ATTATTTT-T-T-TGGAGCATTTTGGCTCCCGT
1 ACGTTTGACTAAATAGTCACTTT-GACCCTTGATTATTTTGTGTGTGGAGCATTTTGGCTCCCCA
30467 AC-TTTCATTTT-GAGGCAAAAAGGCCGTA
65 ACATTTCATTTTAG-GGCAAAAAGGCCGTA
* *
30495 ACGTTTGACTAAATAGTCACTTTGACCCTTGCTTTTTTTGTGTGTGGAGCATTTTGGCTCCCCAA
1 ACGTTTGACTAAATAGTCACTTTGACCCTTGATTATTTTGTGTGTGGAGCATTTTGGCTCCCCAA
*
30560 CATTTCATTTTAGGGCAAAAGGGCC
66 CATTTCATTTTAGGGCAAAAAGGCC
30585 CTATTTTGAT
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
87 4 0.05
88 22 0.29
89 6 0.08
90 1 0.01
91 1 0.01
92 20 0.27
93 20 0.27
94 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (93 bp):
ACGTTTGACTAAATAGTCACTTTGACCCTTGATTATTTTGTGTGTGGAGCATTTTGGCTCCCCAA
CATTTCATTTTAGGGCAAAAAGGCCGTA
Found at i:32604 original size:3 final size:3
Alignment explanation
Indices: 32596--32633 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
32586 AATTTTAATT
*
32596 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTT TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
32634 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:32638 original size:9 final size:8
Alignment explanation
Indices: 32593--32641 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
32583 TTTAATTTTA
32593 ATTTTATT
1 ATTTTATT
32601 A--TTATT
1 ATTTTATT
32607 ATTATTATT
1 ATT-TTATT
32616 A-TTTATT
1 ATTTTATT
32623 ATTTTTATT
1 A-TTTTATT
32632 ATGTTTATT
1 AT-TTTATT
32641 A
1 A
32642 ATTACATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.17
7 6 0.17
8 3 0.09
9 20 0.57
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
ATTTTATT
Found at i:32645 original size:22 final size:22
Alignment explanation
Indices: 32598--32645 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
32588 TTTTAATTTT
*
32598 ATTATTATTATTATTATTATTT
1 ATTATTATTATTATTATTATTA
*
32620 ATTATTTTTATTATGT-TTATTA
1 ATTATTATTATTAT-TATTATTA
32642 ATTA
1 ATTA
32646 CATATTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTATTATTATTATTA
Found at i:39045 original size:12 final size:12
Alignment explanation
Indices: 39021--39069 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
39011 GAGCAAAGAG
39021 CAAAGAGAAAAAT
1 CAAAGA-AAAAAT
*
39034 CAAAGCAAAAAT
1 CAAAGAAAAAAT
*
39046 CAAAGAAAAAAG
1 CAAAGAAAAAAT
39058 CAAAGAACAAAA
1 CAAAGAA-AAAA
39070 AGAGGACAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.71, C:0.12, G:0.12, T:0.04
Consensus pattern (12 bp):
CAAAGAAAAAAT
Found at i:39061 original size:24 final size:24
Alignment explanation
Indices: 38993--39071 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
38983 AGATCATATT
* *
38993 AAAGCGAAGAGAAAAG-AAGAGCAA
1 AAAGCAAAGAAAAAAGCAA-AGCAA
* *
39017 AGAGCAAAGAGAAAAATCAAAGCAA
1 AAAGCAAAGA-AAAAAGCAAAGCAA
*
39042 AAATCAAAGAAAAAAGCAAAGAACAA
1 AAAGCAAAGAAAAAAGCAAAG--CAA
39068 AAAG
1 AAAG
39072 AGGACAAAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 18 0.42
25 17 0.40
26 8 0.19
ACGTcount: A:0.67, C:0.10, G:0.20, T:0.03
Consensus pattern (24 bp):
AAAGCAAAGAAAAAAGCAAAGCAA
Found at i:40271 original size:16 final size:16
Alignment explanation
Indices: 40244--40289 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
40234 AGAAAAGTAT
*
40244 ACACAAACATACATCA
1 ACACATACATACATCA
* **
40260 ACTCATACATACATGT
1 ACACATACATACATCA
40276 ACACATACATACAT
1 ACACATACATACAT
40290 AATATATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.22
Consensus pattern (16 bp):
ACACATACATACATCA
Found at i:40747 original size:34 final size:34
Alignment explanation
Indices: 40648--40753 Score: 90
Period size: 34 Copynumber: 3.1 Consensus size: 34
40638 AAACAAATTT
** **
40648 TTGTCTCGCTTT-AGACAATTTCTTTCAAAGCAAATT
1 TTGTCTCG-TTTGAGACAATTTC-TT-AAAAAAAAAA
* *
40684 TTGTCTCGATTGAGACAGCTTTC-TAAAAAAAAAA
1 TTGTCTCGTTTGAGACA-ATTTCTTAAAAAAAAAA
* *
40718 TTGTCTCGTTTGAGACAATTTCTTGAAAAACAAA
1 TTGTCTCGTTTGAGACAATTTCTTAAAAAAAAAA
40752 TT
1 TT
40754 CCGCCTCACT
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
33 4 0.07
34 33 0.58
35 3 0.05
36 13 0.23
37 4 0.07
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (34 bp):
TTGTCTCGTTTGAGACAATTTCTTAAAAAAAAAA
Found at i:40857 original size:105 final size:105
Alignment explanation
Indices: 40744--40933 Score: 249
Period size: 105 Copynumber: 1.8 Consensus size: 105
40734 AATTTCTTGA
*
40744 AAAACAAATTCCGCCTCACTGGAGACATTTTTCCTTTGAGATACAAACCTT-GAATTTGATTCAC
1 AAAACAAATTCCGCCTCACTGGAGACATTTTCCCTTTGAGATACAAA-CTTCGAATTTGATTCAC
40808 -TTAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
65 ATT-AAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * * * * * * *
40849 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTCCGCCTCACTGGAGACATTTTCCCTTTGAGATACAAACTTCGAATTTGATTCACA
* *
40914 TTAAACAAAGTTGATCTCAC
66 TTAAACAAAATTAATCTCAC
40934 TTGAGAATGT
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
104 2 0.03
105 68 0.94
106 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.36
Consensus pattern (105 bp):
AAAACAAATTCCGCCTCACTGGAGACATTTTCCCTTTGAGATACAAACTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:40990 original size:36 final size:36
Alignment explanation
Indices: 40944--41047 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
40934 TTGAGAATGT
*
40944 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
40979 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* *
41015 TATCT-T-AAAGCAAATTTTGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
41048 TCATTTTCTC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 23 0.39
35 7 0.12
36 29 0.49
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:41329 original size:27 final size:27
Alignment explanation
Indices: 41288--41522 Score: 258
Period size: 29 Copynumber: 8.5 Consensus size: 27
41278 TCTTGAGACA
*
41288 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTTTTG-AAAAAATCTTTGAGTTT
*
41316 GTTTCTTTTGAAAAAAATCTTTGAGTTA
1 GTTTCTTTTG-AAAAAATCTTTGAGTTT
*
41344 GTTTCTCTTGAAAAAAAATCTTTGAGTTT
1 GTTTCTTTTG--AAAAAATCTTTGAGTTT
*
41373 GTTTCTCTTGAAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAATCTTTGAGTTT
* *
41400 GTTCCTCTTGAAAAAATCTTTGAGTTT
1 GTTTCTTTTGAAAAAATCTTTGAGTTT
* * *
41427 GCTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTTTTG-A-AAAAATCTTTGAGTTT
*
41456 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTTTTGAA-AAA-ATCTTTGAGTTT
* *
41484 GTTTCTTTTG-AAAAATTTTTGAGTCT
1 GTTTCTTTTGAAAAAATCTTTGAGTTT
* *
41510 ATTTATTTTGAAA
1 GTTTCTTTTGAAA
41523 CAAAGTTTTG
Statistics
Matches: 185, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.04
26 12 0.06
27 55 0.30
28 51 0.28
29 59 0.32
ACGTcount: A:0.28, C:0.10, G:0.14, T:0.47
Consensus pattern (27 bp):
GTTTCTTTTGAAAAAATCTTTGAGTTT
Found at i:41349 original size:56 final size:56
Alignment explanation
Indices: 41287--41498 Score: 286
Period size: 56 Copynumber: 3.8 Consensus size: 56
41277 CTCTTGAGAC
*
41287 AGTTTCTCTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTT
1 AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTT
* *
41343 AGTTTCTCTTGAAAAAAAATCTTTGAGTTTGTTTCTCTTG-AAAAAATCTTTGAGTT
1 AGTTCCTCTTG-AAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTT
* * * *
41399 TGTTCCTCTTG-AAAAAATCTTTGAGTTTGCTCCTTTTGAATAAAAATCTTGGAGTT
1 AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAA-AAAAATCTTTGAGTT
* * *
41455 TGTTCCTTTTGAATAAATATCTTTGAG-TTGTTTCTTTTGAAAAA
1 AGTTCCTCTTGAA-AAAAATCTTTGAGTTTGTTTCTTTTGAAAAA
41499 TTTTTGAGTC
Statistics
Matches: 140, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
54 24 0.17
55 1 0.01
56 63 0.45
57 40 0.29
58 12 0.09
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.46
Consensus pattern (56 bp):
AGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTT
Found at i:41358 original size:29 final size:28
Alignment explanation
Indices: 41288--41498 Score: 275
Period size: 29 Copynumber: 7.5 Consensus size: 28
41278 TCTTGAGACA
41288 GTTTCTCTTGAAAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
* *
41316 GTTTCTTTTGAAAAAAATCTTTGAGTTA
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
41344 GTTTCTCTTGAAAAAAAATCTTTGAGTTT
1 GTTTCTCTTG-AAAAAAATCTTTGAGTTT
41373 GTTTCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
*
41400 GTTCCTCTTG-AAAAAATCTTTGAGTTT
1 GTTTCTCTTGAAAAAAATCTTTGAGTTT
* * * *
41427 GCTCCTTTTGAATAAAAATCTTGGAGTTT
1 GTTTCTCTTGAA-AAAAATCTTTGAGTTT
* * *
41456 GTTCCTTTTGAATAAATATCTTTGAG-TT
1 GTTTCTCTTGAA-AAAAATCTTTGAGTTT
*
41484 GTTTCTTTTGAAAAA
1 GTTTCTCTTGAAAAA
41499 TTTTTGAGTC
Statistics
Matches: 168, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
27 54 0.32
28 49 0.29
29 65 0.39
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (28 bp):
GTTTCTCTTGAAAAAAATCTTTGAGTTT
Found at i:41519 original size:83 final size:82
Alignment explanation
Indices: 41292--41522 Score: 279
Period size: 83 Copynumber: 2.8 Consensus size: 82
41282 GAGACAGTTT
*
41292 CTCTTGAAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAAATCTTTGAGTTAGTTTCTCTTGAAA
1 CTCTTG-AAAAAATCTTTGAGTTTGTTTCTTTTG-AAAAAATCTTTGAGTTA-TTTCTTTTGAAA
* *
41357 AAAAATCTTTGAGTTTGTTT
63 AAAAATCTTGGAGTTTGTTC
* * * *
41377 CTCTTGAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAATCTTTGAGTT-TGCTCCTTTTGAATA
1 CTCTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAATCTTTGAGTTAT--TTCTTTTGAAAA
41441 AAAATCTTGGAGTTTGTTC
64 AAAATCTTGGAGTTTGTTC
* * *
41460 CTTTTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATTTTTGAGTCTATTTATTTTGAAA
1 CTCTTGAA-AAA-ATCTTTGAGTTTGTTTCTTTTGAAAAAATCTTTGAGT-TATTTCTTTTGAAA
41523 CAAAGTTTTG
Statistics
Matches: 126, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
81 1 0.01
83 70 0.56
84 39 0.31
85 16 0.13
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (82 bp):
CTCTTGAAAAAATCTTTGAGTTTGTTTCTTTTGAAAAAATCTTTGAGTTATTTCTTTTGAAAAAA
AATCTTGGAGTTTGTTC
Found at i:41641 original size:28 final size:28
Alignment explanation
Indices: 41610--41678 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
41600 TTTTGTGAAA
*
41610 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
41638 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
41666 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
41679 TCTCTCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:41715 original size:68 final size:65
Alignment explanation
Indices: 41629--41794 Score: 242
Period size: 68 Copynumber: 2.5 Consensus size: 65
41619 TTTGAGATTG
**
41629 TTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAG
1 TTTCTTTAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA-
*
41694 T
65 A
41695 TTTCTTTAAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTT-AAAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
41760 AA
64 AA
** * *
41762 TTTCTTTTGAAAAAAATCTTTGAATCTGTTTCT
1 TTTCTTTAAAAAAAAATCTTTGAGTTTGTTTCT
41795 CTTAAAATGA
Statistics
Matches: 91, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
65 20 0.22
66 9 0.10
67 9 0.10
68 53 0.58
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (65 bp):
TTTCTTTAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:41729 original size:96 final size:94
Alignment explanation
Indices: 41571--41746 Score: 246
Period size: 96 Copynumber: 1.9 Consensus size: 94
41561 CTTTGAGTCT
* *
41571 GAAACAAATTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAAAAATCTTTGAGATTGTTTCTTT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAAATCTTTGAGATTGTTTCTTT
*
41636 TGAAA-AAAATCTTTGAGTTTGTTTCTTTG
66 GGAAACAAAAT-TTTGAGTTTGTTTCTTTG
* * * * *
41665 GAAACAAAATTTTGTCTCTCTTAAGATAGTTTTCTTTAAAAACAAAAATCTTTGAGTTTGTTTCT
1 GAAACAAAATTTTGTCTCTCTTAAGACAATTTT-GTGAAAAA-AAAAATCTTTGAGATTGTTTCT
41730 TTGGAAACAAAATTTTG
64 TTGGAAACAAAATTTTG
41747 TCTCTCTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
94 29 0.41
95 6 0.08
96 31 0.44
97 5 0.07
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.43
Consensus pattern (94 bp):
GAAACAAAATTTTGTCTCTCTTAAGACAATTTTGTGAAAAAAAAAATCTTTGAGATTGTTTCTTT
GGAAACAAAATTTTGAGTTTGTTTCTTTG
Found at i:42033 original size:120 final size:119
Alignment explanation
Indices: 41895--42118 Score: 276
Period size: 120 Copynumber: 1.9 Consensus size: 119
41885 TTAACAAAAT
* * *
41895 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
41958 ACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGTGATC
64 A--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
* ** **
42015 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * *
42080 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
42119 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (119 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGTGATC
Found at i:42095 original size:64 final size:63
Alignment explanation
Indices: 42016--42140 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
42006 GATGTGATCC
* *
42016 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
42080 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
42141 TACCCACATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:42185 original size:40 final size:40
Alignment explanation
Indices: 42122--42201 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
42112 TTGTCTCTCG
42122 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
42162 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
42202 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:42617 original size:36 final size:34
Alignment explanation
Indices: 42577--42672 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 34
42567 TTTGAGAAAA
* *
42577 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAGTTTGTTTCTTT-GAAACAAAA-TAAAC
* * *
42613 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAGTTTGTTT-CTTTGAAACAAAATAAAC
* *
42648 ATCTTTGAGATCGTTTCTCTTGAAA
1 ATCTTTGAGTTTGTTTCT-TTGAAA
42673 TGAATTTTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
34 1 0.02
35 21 0.44
36 23 0.48
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTTGAGTTTGTTTCTTTGAAACAAAATAAAC
Found at i:42664 original size:35 final size:36
Alignment explanation
Indices: 42598--42672 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
42588 TGTTTCTTTG
* *
42598 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
42634 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
42669 GAAA
1 GAAA
42673 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:42881 original size:28 final size:28
Alignment explanation
Indices: 42830--42926 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 28
42820 GAGACAGTTG
*
42830 CTTTTGAAACACATTATCATTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
*
42861 -TTCTTGAAACACATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
* *
42889 CTTTTGAAACAAATCTTTGAATCGGTTT
1 CTTTTGAAACAAATCTTTGAGTCTGTTT
*
42917 CTCTTGAAAC
1 CTTTTGAAAC
42927 CATAATCCCT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
28 44 0.77
29 3 0.05
30 2 0.04
31 8 0.14
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:43141 original size:40 final size:41
Alignment explanation
Indices: 43079--43191 Score: 142
Period size: 40 Copynumber: 2.7 Consensus size: 41
43069 CTAAAGATGG
43079 CCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCC-T-CAA
1 CCAGCCGTCCTCATCACGTAGGAACCGTGTCA-CCCTTACAA
* *
43119 CCAGACC-TCCTCATCACGTAGGAGCCGTGTCACCCTTAGATAA
1 CCAG-CCGTCCTCATCACGTAGGAACCGTGTCACCCTT--ACAA
*
43162 CCAGCCGTCCTCATCATGTAGGAACCGTGT
1 CCAGCCGTCCTCATCACGTAGGAACCGTGT
43192 TATCACCTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
39 3 0.05
40 29 0.46
41 2 0.03
42 2 0.03
43 27 0.43
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (41 bp):
CCAGCCGTCCTCATCACGTAGGAACCGTGTCACCCTTACAA
Found at i:43174 original size:134 final size:134
Alignment explanation
Indices: 42934--43198 Score: 442
Period size: 134 Copynumber: 2.0 Consensus size: 134
42924 AACCATAATC
* * *
42934 CCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAGCCGTGTCATCCCCTGACCAGATCTCCTCAT
1 CCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCAT
42999 CACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCAC
66 CACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCAC
43064 CACT
131 CACT
43068 CCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCAT-CCCTCAACCAGACCTCCTCA
1 CCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCT-AACCAGACCTCCTCA
* * * **
43132 TCACGTAGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCATGTAGGAACCGTGTTATCA
65 TCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCA
43197 CC
130 CC
43199 TTTAGATGGC
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
133 4 0.03
134 118 0.97
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (134 bp):
CCTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCAT
CACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCAAGTTATCAC
CACT
Found at i:43504 original size:3 final size:3
Alignment explanation
Indices: 43496--43533 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
43486 AATTTTAATT
*
43496 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTT TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
43534 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:43538 original size:9 final size:8
Alignment explanation
Indices: 43493--43541 Score: 50
Period size: 9 Copynumber: 6.1 Consensus size: 8
43483 TTTAATTTTA
43493 ATTTTATT
1 ATTTTATT
43501 A--TTATT
1 ATTTTATT
43507 ATTATTATT
1 ATT-TTATT
43516 A-TTTATT
1 ATTTTATT
43523 ATTTTTATT
1 A-TTTTATT
43532 ATGTTTATT
1 AT-TTTATT
43541 A
1 A
43542 ATTACATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
6 6 0.17
7 6 0.17
8 3 0.09
9 20 0.57
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (8 bp):
ATTTTATT
Found at i:43545 original size:22 final size:22
Alignment explanation
Indices: 43498--43545 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43488 TTTTAATTTT
*
43498 ATTATTATTATTATTATTATTT
1 ATTATTATTATTATTATTATTA
*
43520 ATTATTTTTATTATGT-TTATTA
1 ATTATTATTATTAT-TATTATTA
43542 ATTA
1 ATTA
43546 CATATTACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTATTATTATTATTA
Found at i:56559 original size:23 final size:24
Alignment explanation
Indices: 56515--56561 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
56505 ATACATTGAC
** *
56515 AAATTATATAAATGCAATAACATT
1 AAATTATATAAAAACAAAAACATT
56539 AAATTAT-TAAAAACAAAAACATT
1 AAATTATATAAAAACAAAAACATT
56562 CATTTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTATATAAAAACAAAAACATT
Found at i:57228 original size:8 final size:8
Alignment explanation
Indices: 57215--57255 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
57205 CTCATTTTCA
57215 GAGAATTT
1 GAGAATTT
57223 GAGAATTT
1 GAGAATTT
*
57231 -AGAGTTT
1 GAGAATTT
*
57238 GGGAATTT
1 GAGAATTT
57246 GAGAATTT
1 GAGAATTT
57254 GA
1 GA
57256 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:57556 original size:128 final size:128
Alignment explanation
Indices: 57328--57826 Score: 883
Period size: 128 Copynumber: 3.9 Consensus size: 128
57318 ATCGGAGTAT
*
57328 TATTCACATGAAGGCGCGTTTCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
57393 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
57456 TATTCATATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
57521 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATACCAGTACCTATTATTTCAC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*
57584 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATGTGTTATCA
1 TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
*
57649 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCTC
66 TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
*** * * *
57712 -AGGGGACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCATAGAATATGTTATC
1 TA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATC
57776 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
65 ATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
57827 AATCAGGTAA
Statistics
Matches: 356, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
127 1 0.00
128 355 1.00
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (128 bp):
TATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTATCA
TTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCAC
Found at i:58288 original size:33 final size:34
Alignment explanation
Indices: 58227--58399 Score: 197
Period size: 34 Copynumber: 5.0 Consensus size: 34
58217 AAATTTAATG
*
58227 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * * *
58261 TTAAATTT-GAATAATATTATTTTTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
58294 TTAAATTTCGAATAATATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
58328 TTAAATTT-GAATAATATTATTTTTATTTTTATTTTTATT
1 TTAAATTTCGAATAATA-TA-----ATTTATATTTTAAAT
*
58367 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
58400 AACATTTATC
Statistics
Matches: 116, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
33 36 0.31
34 50 0.43
39 22 0.19
40 8 0.07
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:58303 original size:67 final size:71
Alignment explanation
Indices: 58227--58399 Score: 282
Period size: 73 Copynumber: 2.5 Consensus size: 71
58217 AAATTTAATG
*
58227 TTAAATTTCGAATACTATAATTTATATTTTAAATTTAAATTTGAAT-A-A-TA-TTATTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAATTTAAATTTGAATAATATTATTTATTTTTATT
58288 TTTATT
66 TTTATT
58294 TTAAATTTCGAATAATATAATTTATATTTTAAATTTAAATTTGAATAATATTATTTTTATTTTTA
1 TTAAATTTCGAATAATATAATTTATATTTTAAATTTAAATTTGAATAATATTA--TTTATTTTTA
58359 TTTTTATT
64 TTTTTATT
*
58367 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
58400 AACATTTATC
Statistics
Matches: 98, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
67 45 0.46
68 1 0.01
69 1 0.01
70 2 0.02
73 49 0.50
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.56
Consensus pattern (71 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAATTTAAATTTGAATAATATTATTTATTTTTATT
TTTATT
Found at i:58369 original size:5 final size:6
Alignment explanation
Indices: 58344--58368 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
58334 TTGAATAATA
58344 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
58369 AAATTTCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:58380 original size:40 final size:39
Alignment explanation
Indices: 58246--58396 Score: 144
Period size: 39 Copynumber: 4.1 Consensus size: 39
58236 GAATACTATA
* * *
58246 ATTTATATTTTAAATTTAAATTTGAATAATATTATTTTT
1 ATTTTTATTTTAAATTTAAATTTGAATAATATAATTTGT
*
58285 ATTTTTATTTTAAA--T---TTCGAATAATATAA-TT-T
1 ATTTTTATTTTAAATTTAAATTTGAATAATATAATTTGT
* *
58317 A----TATTTTAAATTTAAATTTGAATAATATTATTTTT
1 ATTTTTATTTTAAATTTAAATTTGAATAATATAATTTGT
* *
58352 ATTTTTATTTTTATTTTAAATTTCGAATAATATAATTTGT
1 ATTTTTATTTTAAATTTAAATTT-GAATAATATAATTTGT
58392 ATTTT
1 ATTTT
58397 AAAAACATTT
Statistics
Matches: 91, Mismatches: 9, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
28 9 0.10
30 1 0.01
32 2 0.02
33 14 0.15
34 14 0.15
35 2 0.02
37 1 0.01
39 29 0.32
40 19 0.21
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (39 bp):
ATTTTTATTTTAAATTTAAATTTGAATAATATAATTTGT
Found at i:58948 original size:21 final size:21
Alignment explanation
Indices: 58918--59011 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
58908 TATGGTATAA
*
58918 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
58939 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
58960 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
*
58981 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
59002 AACCCTGCGG
1 AACCCTGCGG
59012 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.28, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:59041 original size:21 final size:21
Alignment explanation
Indices: 59015--59062 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
59005 CCTGCGGAGA
*
59015 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
59036 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
59057 GGGCAT
1 TGGCAT
59063 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:60825 original size:17 final size:19
Alignment explanation
Indices: 60803--60846 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
60793 ATAATATTAT
60803 AAATATTAT-TTTA-ATAA
1 AAATATTATATTTACATAA
*
60820 AAATATAATATTTACATAA
1 AAATATTATATTTACATAA
*
60839 ATATATTA
1 AAATATTA
60847 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATATTATATTTACATAA
Found at i:60838 original size:19 final size:18
Alignment explanation
Indices: 60803--60877 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
60793 ATAATATTAT
*
60803 AAATATTAT-TTTAATAA
1 AAATATAATATTTAATAA
60820 AAATATAATATTTACATAA
1 AAATATAATATTTA-ATAA
*
60839 ATATATTAATA--T-A-AA
1 AAATA-TAATATTTAATAA
60854 AAATAATAACTATTTAA-AA
1 AAAT-ATAA-TATTTAATAA
60873 AAATA
1 AAATA
60878 CTAACATAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
15 8 0.17
16 4 0.09
17 8 0.17
18 7 0.15
19 15 0.32
20 5 0.11
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATATAATATTTAATAA
Found at i:60887 original size:34 final size:34
Alignment explanation
Indices: 60818--60889 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
60808 TTATTTTAAT
* * *
60818 AAAAATATAATATTTACATAAATATATTAATATA
1 AAAAATATAATATTTACATAAAAATACTAACATA
60852 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAAT-ATAA-TATTTACATAAAAATACTAACATA
60886 AAAA
1 AAAA
60890 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 22 0.67
35 5 0.15
36 6 0.18
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (34 bp):
AAAAATATAATATTTACATAAAAATACTAACATA
Found at i:66903 original size:23 final size:25
Alignment explanation
Indices: 66872--66918 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
66862 AATAAAAATT
66872 AAAATATAATATA-AGATGA-AATAC
1 AAAATATAAT-TAGAGATGATAATAC
66896 AAAA-ATAATTAGAGATGATAATA
1 AAAATATAATTAGAGATGATAATA
66919 TATTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.10
23 11 0.52
24 8 0.38
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.26
Consensus pattern (25 bp):
AAAATATAATTAGAGATGATAATAC
Found at i:67634 original size:15 final size:16
Alignment explanation
Indices: 67611--67649 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
67601 GAATTCGAAG
*
67611 ATTAATATAA-TTAAA
1 ATTATTATAATTTAAA
67626 ATTATTATAATTTAAA
1 ATTATTATAATTTAAA
*
67642 AATATTAT
1 ATTATTAT
67650 TTAAATACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATTATAATTTAAA
Found at i:80856 original size:30 final size:31
Alignment explanation
Indices: 80791--80864 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
80781 TTCAAAAAAA
* * *
80791 TAATATTTTATTTAAAGTTTATGAGTTAAAT
1 TAATATTTTATCTAAAATTTAAGAGTTAAAT
*
80822 TAATATTTTATCTAAAATTTAAGA-TTATAT
1 TAATATTTTATCTAAAATTTAAGAGTTAAAT
80852 TAATATTTT-TCTA
1 TAATATTTTATCTA
80865 CGAATTCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 4 0.10
30 14 0.36
31 21 0.54
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (31 bp):
TAATATTTTATCTAAAATTTAAGAGTTAAAT
Found at i:81231 original size:28 final size:29
Alignment explanation
Indices: 81190--81244 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
81180 ACTTTGTTGA
81190 GTCCTCTAACTATTAATA-GTTACAAAATG
1 GTCCTCTAACTATTAATATGTT-CAAAATG
* *
81219 GTCC-CTAGCTATTCATATGTTCAAAA
1 GTCCTCTAACTATTAATATGTTCAAAA
81245 CTTGTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (29 bp):
GTCCTCTAACTATTAATATGTTCAAAATG
Found at i:82209 original size:21 final size:21
Alignment explanation
Indices: 82179--82231 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
82169 TGCTTTTTGG
*
82179 ATCGATACTTTTAATAAATGT
1 ATCGACACTTTTAATAAATGT
82200 ATCGACACTTTTAATAAATGT
1 ATCGACACTTTTAATAAATGT
82221 ATCGACACTTT
1 ATCGACACTTT
82232 ATGCGTGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
ATCGACACTTTTAATAAATGT
Found at i:82380 original size:221 final size:220
Alignment explanation
Indices: 81994--82428 Score: 588
Period size: 221 Copynumber: 2.0 Consensus size: 220
81984 GATACAATTT
*
81994 TAAATGTATCGACACTTTATGCGGGCACCTTGTTGGACATTCATTCTGGAAAAAAGTATCGACAC
1 TAAATGTATCGACACTTTATGCGGGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACAC
* * * *
82059 AAGGTTAAAACGGGTCGATACATTATGTAAACCTATTTTCTCATAAAACCAGTATATTTCTACCG
66 AAGGTTAAAACGGGTCGATACATTATGTAAACCTATTCTATCATAAAACCAGTATATTTATACCA
* *
82124 GGTACATTGTAAATTTACTTATTACATTGTAATTATCAATTTCGATGCTTTTT-GGATCGATACT
131 GGTACATTGTAAATTTACCTATTACATTATAATTATCAATTTCGATG-TTTTTGGGATCGATACT
82188 TTTA-ATAAATGTATCGACACTTTTAA
195 TTTAGA-AAATGTATCGACACTTTTAA
* * *
82214 TAAATGTATCGACACTTTATGCGTGCACCTCGTTTGG-CATTCATTCTTGACAAAATGTATCGAC
1 TAAATGTATCGACACTTTATGCGGGCACCTCG-TTGGACATTCATTCTGGA-AAAAAGTATCGAC
**** *** ** ***
82278 ACTTTTTTAAGTTGTTTCGATACATTATGTTGGCCTATTCTATCATAAAACCAGTATATTTATAC
64 ACAAGGTTAAAACGGGTCGATACATTATGTAAACCTATTCTATCATAAAACCAGTATATTTATAC
* * *
82343 CAGTTACATTGTAAATTTACCTATTACATTATAATTATCGATTTCGATGTTTTTGGGGTCGATAC
129 CAGGTACATTGTAAATTTACCTATTACATTATAATTATCAATTTCGATGTTTTTGGGATCGATAC
82408 TTTTAGAAAATGTATCGACAC
194 TTTTAGAAAATGTATCGACAC
82429 ATATGTTTAC
Statistics
Matches: 186, Mismatches: 25, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
220 47 0.25
221 138 0.74
222 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (220 bp):
TAAATGTATCGACACTTTATGCGGGCACCTCGTTGGACATTCATTCTGGAAAAAAGTATCGACAC
AAGGTTAAAACGGGTCGATACATTATGTAAACCTATTCTATCATAAAACCAGTATATTTATACCA
GGTACATTGTAAATTTACCTATTACATTATAATTATCAATTTCGATGTTTTTGGGATCGATACTT
TTAGAAAATGTATCGACACTTTTAA
Found at i:82863 original size:80 final size:79
Alignment explanation
Indices: 82723--82872 Score: 194
Period size: 80 Copynumber: 1.9 Consensus size: 79
82713 TTTAACATTT
* *
82723 CCGGTAAAATACCAAACAATAACAAAACCGATAAAAAAATAACAAAATCGGTAGCGTTTTTACCG
1 CCGGTAAAATACCAAACAATAACAAAACCGATAAAAAAATAACAAAATCGATA-CATTTTTACCG
82788 GTTTTATTAAGAAAA
65 GTTTTATTAAGAAAA
* * * ***
82803 CCGGTAAAATACCAAAATAATAACAAAACCGGTAAAAATAATAATATTTTCGATA-ATTTTTACC
1 CCGGTAAAATACC-AAACAATAACAAAACCGATAAAAA-AATAACAAAATCGATACATTTTTACC
82867 GGTTTT
64 GGTTTT
82873 GTTATGCACA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
80 27 0.45
81 22 0.37
82 11 0.18
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (79 bp):
CCGGTAAAATACCAAACAATAACAAAACCGATAAAAAAATAACAAAATCGATACATTTTTACCGG
TTTTATTAAGAAAA
Found at i:82935 original size:125 final size:125
Alignment explanation
Indices: 82760--83019 Score: 333
Period size: 125 Copynumber: 2.1 Consensus size: 125
82750 CCGATAAAAA
* * * * * *
82760 AATAACAAAATCGGTAGCGTTTTTACCGGTTTTATTAAGAAAACCGGTAAAATACCAAAATAATA
1 AATAACAAAACCGATTGCGCTTTTACCGATTTTATTAAGAAAACCAGTAAAATACCAAAATAATA
* * *
82825 ACAAAACCGGTAAAAATAATAATATTTTCGATAATTTTTACCGGTTTTGTTATGCACAAC
66 ACAAAACCGATAAAAATAATAATATTTTCGATAATTTTTACCGATTTTATTATGCACAAC
* * *
82885 AATAATAAAACCGATTGCGCTTTTACCGATTTTATTAAG-AAACCAAGTAAAATATCAAATTAAT
1 AATAACAAAACCGATTGCGCTTTTACCGATTTTATTAAGAAAACC-AGTAAAATACCAAAATAAT
* * ** * * *
82949 AATAAAACCGATAGAAATAATAATATTTTTTATAATTTTTACTGATTTTATTATGTATAAC
65 AACAAAACCGATAAAAATAATAATATTTTCGATAATTTTTACCGATTTTATTATGCACAAC
83010 AATAACAAAA
1 AATAACAAAA
83020 ATATTTTTTT
Statistics
Matches: 114, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
124 5 0.04
125 109 0.96
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (125 bp):
AATAACAAAACCGATTGCGCTTTTACCGATTTTATTAAGAAAACCAGTAAAATACCAAAATAATA
ACAAAACCGATAAAAATAATAATATTTTCGATAATTTTTACCGATTTTATTATGCACAAC
Found at i:84542 original size:22 final size:24
Alignment explanation
Indices: 84517--84561 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
84507 CTAATTATTA
*
84517 TTTAAAAAT-TAA-ATTTTAAAAC
1 TTTAAAAATATAATAATTTAAAAC
84539 TTTAAAAATATAATAATTTAAAA
1 TTTAAAAATATAATAATTTAAAA
84562 ATAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 3 0.15
24 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTAAAAATATAATAATTTAAAAC
Found at i:91857 original size:3 final size:3
Alignment explanation
Indices: 91849--91895 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
91839 TTTTTATTGA
* *
91849 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
91894 TA
1 TA
91896 CAAACAGGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:91857 original size:12 final size:11
Alignment explanation
Indices: 91842--91893 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
91832 TACCCATTTT
91842 TTATTGATATTA
1 TTATT-ATATTA
91854 TTATTATTATT-
1 TTATTA-TATTA
91865 TTATT-TATTA
1 TTATTATATTA
*
91875 TTATTAAAATTA
1 TTATT-ATATTA
91887 TTATTAT
1 TTATTAT
91894 TACAAACAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 4 0.12
10 5 0.15
11 7 0.21
12 18 0.53
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TTATTATATTA
Found at i:93189 original size:15 final size:15
Alignment explanation
Indices: 93169--93198 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
93159 TGAGCTTTTA
93169 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
93184 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
93199 TAATAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:96471 original size:19 final size:19
Alignment explanation
Indices: 96447--96485 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
96437 TCGAATGCAT
96447 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
96466 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
96485 T
1 T
96486 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:96501 original size:65 final size:64
Alignment explanation
Indices: 96405--96593 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 64
96395 GCATCAGTCA
** * * ***
96405 ATGCATCGATGCATCGATGAAT-TAATT-AAACATCGAATGCATTCCATGCACCGATGCACTCTC
1 ATGCATCGATGCATC-A-GAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAGC
96468 C
64 C
* * *
96469 ATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATTCATTTGATGCATCGATGCACAAGC
1 ATGCATCGATGCA-TCAGAATATTTTTC-AAACATCGAATGCATTTCATGCATCGATGCACAAGC
96533 C
64 C
**
96534 ATGCATCGATGCATCAGGCTATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
1 ATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACA
96594 CTTGGTGCAC
Statistics
Matches: 105, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
63 6 0.06
64 49 0.47
65 50 0.48
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (64 bp):
ATGCATCGATGCATCAGAATATTTTTCAAACATCGAATGCATTTCATGCATCGATGCACAAGCC
Found at i:96608 original size:64 final size:64
Alignment explanation
Indices: 96384--96613 Score: 216
Period size: 64 Copynumber: 3.6 Consensus size: 64
96374 TATTCAAAGG
* * * *
96384 CATGCACCGATGCATCAGTCAATGCATCGATGCATCGATGAAT-TAATT--AAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
96446 TTC
62 TTT
* * * *
96449 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATTCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
96514 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
96578 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
96614 AGTGTTCCAA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 67 0.49
65 64 0.47
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:102408 original size:20 final size:21
Alignment explanation
Indices: 102379--102434 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
102369 TTTGTGCTTC
*
102379 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
102399 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
102421 ATGCATCGATGCAT
1 ATGCATCGATGCAT
102435 AAGAACATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:104003 original size:21 final size:21
Alignment explanation
Indices: 103961--104004 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
103951 ACCCCGGGAG
*
103961 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
103982 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
104003 CT
1 CT
104005 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:105068 original size:19 final size:19
Alignment explanation
Indices: 105044--105082 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
105034 TCGAATGCAT
105044 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
105063 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
105082 T
1 T
105083 GAATATTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:105076 original size:64 final size:64
Alignment explanation
Indices: 104981--105189 Score: 230
Period size: 65 Copynumber: 3.2 Consensus size: 64
104971 TATTCAAAGG
*
104981 CATGCACCGATGCA-TCAGTCCATGCATCGATGCATCGATGAATTAATT-AAACATCGAATGCAT
1 CATGCACCGATGCACTC--TCCATGCATCGATGCATC-ATGAATTATTTCAAACATCGAATGCAT
*
105044 TC
63 TT
105046 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGAA-TATTTTCAAAACATCGAATGCAT
1 CATGCACCGATGCACTCTCCATGCATCGATGCA-TCATGAATTA-TTTC-AAACATCGAATGCAT
105109 TT
63 TT
* * *** * *
105111 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATT-TTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCATCATG-AATTATTTCAAACATCGAATGCATTT
*
105175 CATGCATCGATGCAC
1 CATGCACCGATGCAC
105190 ACTTGGTGCA
Statistics
Matches: 126, Mismatches: 10, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
62 2 0.02
63 6 0.05
64 49 0.39
65 65 0.52
66 3 0.02
67 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCATCATGAATTATTTCAAACATCGAATGCATTT
Found at i:105205 original size:64 final size:64
Alignment explanation
Indices: 104981--105210 Score: 234
Period size: 64 Copynumber: 3.6 Consensus size: 64
104971 TATTCAAAGG
* * *
104981 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--AAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
105043 TTC
62 TTT
* * *
105046 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
105111 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAAAACATCGAATGCATTT
*** *
105175 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
105211 AGTGTTCCAA
Statistics
Matches: 140, Mismatches: 20, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 69 0.49
65 65 0.46
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:109391 original size:9 final size:9
Alignment explanation
Indices: 109377--109431 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
109367 AAGAAGAAGG
109377 AAAAAAGAA
1 AAAAAAGAA
109386 AAAAAAGAAA
1 AAAAAAG-AA
*
109396 AAGGAAAAAAA
1 AA--AAAAGAA
*
109407 ACAAAAAGGA
1 A-AAAAAGAA
109417 AAAAAAGAA
1 AAAAAAGAA
109426 AAAAAA
1 AAAAAA
109432 AGGAAAATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 20 0.53
10 10 0.26
11 3 0.08
12 5 0.13
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:109397 original size:16 final size:16
Alignment explanation
Indices: 109362--109429 Score: 75
Period size: 16 Copynumber: 4.2 Consensus size: 16
109352 CTCATCTAGC
*
109362 AAAGAAAGAAGAAGGAAA
1 AAAGAAA-AA-AAAGAAA
109380 AAAGAAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
* *
109396 AAGGAAAAAAAA-CAA
1 AAAGAAAAAAAAGAAA
*
109411 AAAGGAAAAAAAGAAA
1 AAAGAAAAAAAAGAAA
109427 AAA
1 AAA
109430 AAAGGAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
15 12 0.28
16 22 0.51
17 2 0.05
18 7 0.16
ACGTcount: A:0.81, C:0.01, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAGAAA
Found at i:109399 original size:23 final size:23
Alignment explanation
Indices: 109361--109431 Score: 81
Period size: 23 Copynumber: 3.0 Consensus size: 23
109351 ACTCATCTAG
*
109361 CAAAGAAAGAAGAAGGAAAAAAGAA
1 CAAA-AAAGAAAAAGGAAAAAA-AA
109386 -AAAAAAGAAAAAGGAAAAAAAA
1 CAAAAAAGAAAAAGGAAAAAAAA
* *
109408 CAAAAAGGAAAAAAAGAAAAAAAA
1 CAAAAAAG-AAAAAGGAAAAAAAA
109432 AGGAAAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.05
23 22 0.54
24 17 0.41
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (23 bp):
CAAAAAAGAAAAAGGAAAAAAAA
Found at i:109438 original size:9 final size:9
Alignment explanation
Indices: 109373--109438 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
109363 AAGAAAGAAG
109373 AAGG-AAAA
1 AAGGAAAAA
109381 AA-GAAAAA
1 AAGGAAAAA
*
109389 AA--AGAAA
1 AAGGAAAAA
109396 AAGGAAAAA
1 AAGGAAAAA
*
109405 AA--ACAAA
1 AAGGAAAAA
109412 AAGGAAAAA
1 AAGGAAAAA
*
109421 AAGAAAAAAA
1 AAG-GAAAAA
109431 AAGGAAAA
1 AAGGAAAA
109439 TTGAATCAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
7 13 0.28
8 8 0.17
9 17 0.37
10 8 0.17
ACGTcount: A:0.82, C:0.02, G:0.17, T:0.00
Consensus pattern (9 bp):
AAGGAAAAA
Found at i:114857 original size:113 final size:113
Alignment explanation
Indices: 114645--115207 Score: 812
Period size: 113 Copynumber: 5.0 Consensus size: 113
114635 TAGCAAAGAT
* *
114645 TCAAATCCATCAC--AATGGATCAA-TCTTTCCAGA-AAGAGTTCATAATGAGAACAACTCATCT
1 TCAAATCCATCACTTGATGGATCAACT-TTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCT
114706 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
*
114756 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
114821 AGAAGGAAGAAGAAGTTCATAATGGGAAGAGCTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
* * *
114869 TCAAATCTATCAATTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
** *
114934 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * * * * * *
114982 TTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCTG
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
* ** * *
115046 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
** * *
115095 TTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
115160 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
115208 ATGACTCTAT
Statistics
Matches: 412, Mismatches: 34, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
111 13 0.03
112 1 0.00
113 394 0.96
114 4 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
Found at i:116069 original size:11 final size:11
Alignment explanation
Indices: 116043--116082 Score: 66
Period size: 10 Copynumber: 3.8 Consensus size: 11
116033 GAACGCTGGA
116043 AACCGGTTTT-
1 AACCGGTTTTG
116053 AACCGGTTTTG
1 AACCGGTTTTG
116064 AACCGGTTTTG
1 AACCGGTTTTG
116075 -ACCGGTTT
1 AACCGGTTT
116083 GACCGGTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 18 0.62
11 11 0.38
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (11 bp):
AACCGGTTTTG
Found at i:116069 original size:21 final size:20
Alignment explanation
Indices: 116043--116089 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
116033 GAACGCTGGA
116043 AACCGGTTTTAACCGGTTTTG
1 AACCGGTTTTAACCGG-TTTG
*
116064 AACCGGTTTTGACCGGTTTG
1 AACCGGTTTTAACCGGTTTG
116084 -ACCGGT
1 AACCGGT
116090 CACGACCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 15 0.60
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (20 bp):
AACCGGTTTTAACCGGTTTG
Found at i:116123 original size:17 final size:18
Alignment explanation
Indices: 116092--116133 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
116082 TGACCGGTCA
116092 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
116110 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
116127 CGACCCG
1 CGACCCG
116134 TTGATCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.17, C:0.50, G:0.24, T:0.10
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:116128 original size:12 final size:13
Alignment explanation
Indices: 116093--116137 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
116083 GACCGGTCAC
116093 GACCCGACCCGTT
1 GACCCGACCCGTT
116106 GACCCGACCCGACCGTT
1 GACCCGA--C--CCGTT
116123 GACCCGACCCGTT
1 GACCCGACCCGTT
116136 GA
1 GA
116138 TCGGTGCTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 14 0.50
15 2 0.07
17 12 0.43
ACGTcount: A:0.18, C:0.44, G:0.24, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:116201 original size:29 final size:29
Alignment explanation
Indices: 116169--116236 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
116159 ATTTAGTTTT
*
116169 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * *
116198 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
*
116227 CGTGCTATTT
1 GGTGCTATTT
116237 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:123333 original size:22 final size:23
Alignment explanation
Indices: 123296--123342 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
123286 TGACCGGTCA
123296 CGACCCGACCCGTTGACCCGACC
1 CGACCCGACCCGTTGACCCGACC
123319 CGACCCGA-CCGTTGACCCGACC
1 CGACCCGACCCGTTGACCCGACC
123341 CG
1 CG
123343 TTAACCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.17, C:0.51, G:0.23, T:0.09
Consensus pattern (23 bp):
CGACCCGACCCGTTGACCCGACC
Found at i:123410 original size:29 final size:29
Alignment explanation
Indices: 123378--123445 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
123368 ATTTGGTTTT
*
123378 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
* * * *
123407 GGTGCTATATTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAG
123436 GGTGCTATTT
1 GGTGCTATTT
123446 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.06, G:0.25, T:0.40
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAG
Found at i:125078 original size:3 final size:3
Alignment explanation
Indices: 125070--125119 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
125060 TTTTTATTGA
* *
125070 TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
125115 TAT TA
1 TAT TA
125120 CAAATAGGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:125110 original size:15 final size:16
Alignment explanation
Indices: 125092--125124 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
125082 TATTTTATTT
125092 ATTATTATTATTA-AA
1 ATTATTATTATTACAA
125107 ATTATTATTATTACAA
1 ATTATTATTATTACAA
125123 AT
1 AT
125125 AGGCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
ATTATTATTATTACAA
Found at i:126423 original size:15 final size:15
Alignment explanation
Indices: 126403--126432 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
126393 GGAGCTTTTA
126403 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
126418 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
126433 TAATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:127875 original size:7 final size:7
Alignment explanation
Indices: 127863--127947 Score: 50
Period size: 7 Copynumber: 12.3 Consensus size: 7
127853 TAGATTACAC
127863 CCTAAAT
1 CCTAAAT
127870 CCTAAA-
1 CCTAAAT
*
127876 CTTAAA-
1 CCTAAAT
127882 CCTTAAAT
1 CC-TAAAT
**
127890 TATAAAT
1 CCTAAAT
* *
127897 TCTAAAC
1 CCTAAAT
127904 CCTAAA-
1 CCTAAAT
127910 CTCTAAAT
1 C-CTAAAT
*
127918 CTTAAAT
1 CCTAAAT
*
127925 CTTAAAT
1 CCTAAAT
*
127932 CCTAAAC
1 CCTAAAT
*
127939 CCTTAAT
1 CCTAAAT
127946 CC
1 CC
127948 GATTATGTGA
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
6 7 0.11
7 54 0.87
8 1 0.02
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (7 bp):
CCTAAAT
Found at i:127936 original size:21 final size:21
Alignment explanation
Indices: 127865--127937 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
127855 GATTACACCC
127865 TAAATCCTAAA-CTTAAACCT
1 TAAATCCTAAATCTTAAACCT
** *
127885 TAAATTATAAAT-TCTAAACCC
1 TAAATCCTAAATCT-TAAACCT
*
127906 TAAA-CTCTAAATCTTAAATCT
1 TAAATC-CTAAATCTTAAACCT
127927 TAAATCCTAAA
1 TAAATCCTAAA
127938 CCCTTAATCC
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
20 10 0.24
21 29 0.71
22 2 0.05
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAATCCTAAATCTTAAACCT
Found at i:129209 original size:35 final size:35
Alignment explanation
Indices: 129165--129240 Score: 91
Period size: 35 Copynumber: 2.2 Consensus size: 35
129155 TAAAACCCGA
*
129165 CGAGCTTGAATCAAACTCAAAATCGAGCTTCAATT
1 CGAGTTTGAATCAAACTCAAAATCGAGCTTCAATT
* * * * *
129200 CGAGTTTGAATCGAGCTTAAAATCGAGTTTGAATT
1 CGAGTTTGAATCAAACTCAAAATCGAGCTTCAATT
129235 -GAGTTT
1 CGAGTTT
129241 AAAATTGAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 6 0.17
35 29 0.83
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (35 bp):
CGAGTTTGAATCAAACTCAAAATCGAGCTTCAATT
Found at i:129211 original size:23 final size:23
Alignment explanation
Indices: 129185--129260 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 23
129175 TCAAACTCAA
* *
129185 AATCGAGCTTCAATTCGAGTTTG
1 AATCGAGCTTAAAATCGAGTTTG
129208 AATCGAGCTTAAAATCGAGTTTG
1 AATCGAGCTTAAAATCGAGTTTG
* * * * *
129231 AATTGAGTTTAAAATTGAGCTTC
1 AATCGAGCTTAAAATCGAGTTTG
129254 AATCGAG
1 AATCGAG
129261 TTCGAGTCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (23 bp):
AATCGAGCTTAAAATCGAGTTTG
Found at i:129251 original size:35 final size:35
Alignment explanation
Indices: 129183--129262 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
129173 AATCAAACTC
* *
129183 AAAATCGAGCTTCAATTCGAGTTTGAATCGAGCTT
1 AAAATCGAGTTTCAATTCGAGTTTAAATCGAGCTT
* *
129218 AAAATCGAGTTTGAATT-GAGTTTAAAATTGAGCTT
1 AAAATCGAGTTTCAATTCGAGTTT-AAATCGAGCTT
*
129253 -CAATCGAGTT
1 AAAATCGAGTT
129263 CGAGTCTCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 15 0.38
35 24 0.62
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (35 bp):
AAAATCGAGTTTCAATTCGAGTTTAAATCGAGCTT
Found at i:130455 original size:21 final size:21
Alignment explanation
Indices: 130416--130457 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
130406 AATCCTTATA
*
130416 TTTTAATTTAATATTTTTAAT
1 TTTTAATTTAATAATTTTAAT
130437 TTTTAATTTTAA-AATTTTAAT
1 TTTTAA-TTTAATAATTTTAAT
130458 ATTGATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTAATTTAATAATTTTAAT
Found at i:133778 original size:9 final size:9
Alignment explanation
Indices: 133764--133804 Score: 55
Period size: 9 Copynumber: 4.2 Consensus size: 9
133754 GCCTGCCGGT
133764 AAAGAGAAA
1 AAAGAGAAA
133773 AAAGAGAAA
1 AAAGAGAAA
133782 AAAGAGAAGA
1 AAAGAGAA-A
133792 AGAAGAAGAAA
1 A-AAG-AGAAA
133803 AA
1 AA
133805 GAAGGCTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 17 0.59
10 3 0.10
11 5 0.17
12 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (9 bp):
AAAGAGAAA
Done.