Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004733.1 Hibiscus syriacus cultivar Beakdansim tig00010685_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: 62944
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1888 original size:21 final size:20
Alignment explanation
Indices: 1844--1891 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 20
1834 CTCTTGATAG
1844 GTATCGATACACCTT-AA-A
1 GTATCGATACACCTTGAATA
1862 -TATCGATACACCTTGAATA
1 GTATCGATACACCTTGAATA
1881 TGTATCGATAC
1 -GTATCGATAC
1892 CTAGATGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 14 0.54
18 2 0.08
19 1 0.04
21 9 0.35
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (20 bp):
GTATCGATACACCTTGAATA
Found at i:1933 original size:37 final size:37
Alignment explanation
Indices: 1891--1964 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
1881 TGTATCGATA
1891 CCTAGATGGGTACCGATACCCCCTATCGGGTTTAGGC
1 CCTAGATGGGTACCGATACCCCCTATCGGGTTTAGGC
* *
1928 CCTAGATGGGTCCCGATACCTCCTATCGGGTTTAGGC
1 CCTAGATGGGTACCGATACCCCCTATCGGGTTTAGGC
1965 TTTAAATCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.26
Consensus pattern (37 bp):
CCTAGATGGGTACCGATACCCCCTATCGGGTTTAGGC
Found at i:7950 original size:111 final size:115
Alignment explanation
Indices: 7675--7983 Score: 375
Period size: 111 Copynumber: 2.7 Consensus size: 115
7665 CATCATAATC
* * * *
7675 AGAATATATAAGCACACACATTGCTATCATATCA-AATCGTAATGTGCACACAAAGTGTAATCAT
1 AGAAAATATAAGAACACACAGTGCTATCATATCATAATCATAATGTGCACA-AAAGTGT-ATCAT
* * *
7739 ATCAG--GATATATACTAGCGCACCCACCGGTAGACCACAATATATCAGAATT
64 ATCAGAATATATATACTAGTGCACCCACCGGTACACCACAATATA-CAGAATT
* * * *
7790 AGAACATATAAGGACACACGGTGCTATCATATCATAATCATAATGTGCACAAAAGTGTACCATAT
1 AGAAAATATAAGAACACACAGTGCTATCATATCATAATCATAATGTGCACAAAAGTGTATCATAT
*
7855 CAGAATATATATACTAGTGCACCCATCGGTACACC-C-ATATA-AGAATT
66 CAGAATATATATACTAGTGCACCCACCGGTACACCACAATATACAGAATT
* *
7902 -GAAAATATAAGAACACACAGTGCTATCATATCATAATCATAATATGCAC-AAAGTGCAATCATA
1 AGAAAATATAAGAACACACAGTGCTATCATATCATAATCATAATGTGCACAAAAGTG-TATCATA
* *
7965 TCAAAATATAGATA-TAGTG
65 TCAGAATATATATACTAGTG
7984 TACCTTTAGG
Statistics
Matches: 172, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
110 11 0.06
111 62 0.36
112 6 0.03
114 14 0.08
115 38 0.22
116 41 0.24
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (115 bp):
AGAAAATATAAGAACACACAGTGCTATCATATCATAATCATAATGTGCACAAAAGTGTATCATAT
CAGAATATATATACTAGTGCACCCACCGGTACACCACAATATACAGAATT
Found at i:10924 original size:30 final size:29
Alignment explanation
Indices: 10890--10972 Score: 87
Period size: 33 Copynumber: 2.7 Consensus size: 29
10880 TAAAATTTAT
10890 AACTTTTAAAAATTACATTTTTAGTCCC-TA
1 AACTTTTAAAAATTACATTTTT--TCCCTTA
*
10920 AACTTTTACAAAAAATTAAATTTTTTCCCTTA
1 AACTTTT---AAAAATTACATTTTTTCCCTTA
* *
10952 AACTTTCAAAACTTACATTTT
1 AACTTTTAAAAATTACATTTT
10973 AATCACTAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
29 12 0.27
30 7 0.16
31 4 0.09
32 8 0.18
33 14 0.31
ACGTcount: A:0.39, C:0.17, G:0.01, T:0.43
Consensus pattern (29 bp):
AACTTTTAAAAATTACATTTTTTCCCTTA
Found at i:11307 original size:138 final size:138
Alignment explanation
Indices: 11122--11989 Score: 1233
Period size: 138 Copynumber: 6.3 Consensus size: 138
11112 ATTTTCTAGT
* * * * *
11122 AATAATTGATTAAAATTAATTAGGACTAATATTGGAG-CTTCATTCTTAGGCCTAATTTCATATT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCA-CCTTAGGCCTAATTTCACATT
* * *
11186 TAGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCGTTGCTTATGCTTGAAGTTCTAAATTAATT
65 TAGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAAGTTCCAAATTAATT
11251 ATTCGATTC
130 ATTCGATTC
* * *
11260 AATAATTGATTAACATTAATTAGGATTAATATTATAGCCTCCATCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
** * * *
11325 AGTCCTTAAAATTAAAAGAATTCTTAATTTGGTCCTCGCTTTTGCTCGAGGTTCCAAATTAATTA
66 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAAGTTCCAAATTAATTA
11390 TTCGATTC
131 TTCGATTC
*
11398 AATAATTGATTAAAATTAATTAGTATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
* * *
11463 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCGTTGCTTATGCTTGAAGTTCTAAATTAATTA
66 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAAGTTCCAAATTAATTA
11528 TTCGATTC
131 TTCGATTC
* * *
11536 AATAATTGATTAACATTAATTAGGATTAATATTATAGCCTCCATCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
* * *
11601 AGTCCTTAAAATTAGAAGAATTCTTAATTTGGTCCTCGCTT-TAGCTCGAGGTTCCAAATTAATT
66 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTAT-GCTTGAAGTTCCAAATTAATT
11665 ATTCGATTC
130 ATTCGATTC
**
11674 AATAATTGATTAAAATTAATTAATATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
* * * * *
11739 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTC-ATTTTTCCTCAAGGTTCCAAATTAATT
66 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAA-GTTCCAAATTAATT
11803 ATTCGATTC
130 ATTCGATTC
* * *
11812 AATAATCGAATAAAA-TAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACCTTT
1 AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
* * * * * * *
11876 AGTCCTTAAAATTAGGAGAATTTTTTACTTGGTCCTCACTTATGCTTGAGGTTCCAATTTAATTT
66 AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAAGTTCCAAATTAATTA
* * *
11941 TTTGAATA
131 TTCGATTC
*
11949 ACATAATTGATTAAAATTAATTTAAG-TTAATATTAGAGCCT
1 A-ATAATTGATTAAAATTAA-TTAGGATTAATATTAGAGCCT
11990 ACATTTTTAG
Statistics
Matches: 652, Mismatches: 70, Indels: 15
0.88 0.09 0.02
Matches are distributed among these distances:
137 104 0.16
138 522 0.80
139 22 0.03
140 4 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (138 bp):
AATAATTGATTAAAATTAATTAGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
AGTCCTTAAAATTAGGAGAATTCTTAATTTGGTCCTCGCTTATGCTTGAAGTTCCAAATTAATTA
TTCGATTC
Found at i:14978 original size:22 final size:21
Alignment explanation
Indices: 14927--14987 Score: 63
Period size: 22 Copynumber: 3.0 Consensus size: 21
14917 TATTGATACC
* *
14927 GGTAAGGGATATCGATACCCT
1 GGTAAGGTATATCGATACCAT
* *
14948 AGTAGGGTAGTATCGATACCAT
1 GGTAAGGTA-TATCGATACCAT
14970 GGTAAGG--TATCGATACCA
1 GGTAAGGTATATCGATACCA
14988 GGCAACATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 11 0.33
21 6 0.18
22 16 0.48
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (21 bp):
GGTAAGGTATATCGATACCAT
Found at i:15045 original size:94 final size:95
Alignment explanation
Indices: 14857--15060 Score: 214
Period size: 94 Copynumber: 2.1 Consensus size: 95
14847 ATACCGATGA
* *
14857 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCAAATATAATTTTGGTATTG
1 GGTAGTATCGATACCATGATAA-GGGTATCGATACCAAGAAACATCAAACATAATTTTGGTATCG
* * *
14922 ATACCGGTAAGGGATATCGATACCCTAGTAG
65 ATACCAGTAAGGGATATAGATACCATAGTAG
* * * * * *
14953 GGTAGTATCGATACCATGGTAA-GGTATCGATACCAGGCAACATCGAACCTATTTTTGGTATCGA
1 GGTAGTATCGATACCATGATAAGGGTATCGATACCAAGAAACATCAAACATAATTTTGGTATCGA
* * * * *
15017 TGCCCAG-AGGGGGTATAGGTACCATAGTAT
66 T-ACCAGTAAGGGATATAGATACCATAGTAG
* *
15047 AGAAGTATCGATAC
1 GGTAGTATCGATAC
15061 TAGGGAAGTA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
94 65 0.73
95 3 0.03
96 21 0.24
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (95 bp):
GGTAGTATCGATACCATGATAAGGGTATCGATACCAAGAAACATCAAACATAATTTTGGTATCGA
TACCAGTAAGGGATATAGATACCATAGTAG
Found at i:15499 original size:59 final size:58
Alignment explanation
Indices: 15400--15565 Score: 221
Period size: 59 Copynumber: 2.9 Consensus size: 58
15390 ATTACCAAAT
* * * *
15400 GGCACTTCGTGTGCAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATAG
1 GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAG
* * *
15458 GGCACTTCGTGTGCTAACATGATAAGAAATTCATAATAAGTGTAAGAATTTCTATATTG
1 GGCACTTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAG
*
15517 GGCACCTT-GTGTGCT-AAGGATAAG-AATTCATACTAAGTGTATGAATTTC
1 GGCA-CTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
15566 CGTATGGGAA
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
56 23 0.24
57 7 0.07
58 17 0.18
59 46 0.48
60 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.34
Consensus pattern (58 bp):
GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTATATAG
Found at i:16013 original size:68 final size:68
Alignment explanation
Indices: 15940--16539 Score: 932
Period size: 68 Copynumber: 8.8 Consensus size: 68
15930 AAAAGATCAA
* * *
15940 GAGGCCTAACTGTACATATGATAGAAATGTGTCATTTATGCCAGTTAGATGAAAGAATAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16005 TTT
66 TTT
* * * *
16008 GAGGCCTAACTGTGCATATGACAG-AAGGTGTCATTTATGCCAGTTAAATGAAAGACTAAATTTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16072 TTT
66 TTT
* *
16075 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGTCAGTTAGATAAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16140 TTT
66 TTT
* * *
16143 GAGGCCTAACTGTGCATATGACATAAATGTGTCATTTATGCCAATTAGATGAAATACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16208 TTT
66 TTT
* *
16211 GAGTCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAATTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16276 TTT
66 TTT
* *
16279 GAGGCCTAACTGTGCATATGACAGAAATATGCCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16344 TTT
66 TTT
* *
16347 GAGGCCTAACTGTGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
16412 TTT
66 TTT
* * *
16415 GAGACCTAACTGTACATATGACAGAAAGGTGTCAATTATGTATGCCAGTTAGATGAAAGACTAAG
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTC-A-T-T-TATGCCAGTTAGATGAAAGACTAAG
16480 TGTCTTT
62 TGTCTTT
* * * *
16487 GAGACCTAACTGTACATATGACAGAAATGTGTCAATTATGCCTGTTAGATGAA
1 GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAA
16540 CGGTTATGTA
Statistics
Matches: 492, Mismatches: 35, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
67 62 0.13
68 361 0.73
69 2 0.00
70 1 0.00
71 2 0.00
72 64 0.13
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (68 bp):
GAGGCCTAACTGTGCATATGACAGAAATGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTC
TTT
Found at i:16207 original size:32 final size:32
Alignment explanation
Indices: 16171--16275 Score: 74
Period size: 32 Copynumber: 3.2 Consensus size: 32
16161 TGACATAAAT
16171 GTGTCATTTATGCCAATTAGATGAAATACTAA
1 GTGTCATTTATGCCAATTAGATGAAATACTAA
* * *
16203 GTGTC-TTTGA-GTCCTAACT-G-TGCATATGACAGAAA
1 GTGTCATTT-ATG-CC-AATTAGATG-AAAT-AC--TAA
*
16238 TGTGTCATTTATGCCAATTAGATGAAAGACTAA
1 -GTGTCATTTATGCCAATTAGATGAAATACTAA
16271 GTGTC
1 GTGTC
16276 TTTGAGGCCT
Statistics
Matches: 54, Mismatches: 7, Indels: 24
0.64 0.08 0.28
Matches are distributed among these distances:
31 6 0.11
32 17 0.31
33 7 0.13
35 7 0.13
36 11 0.20
37 6 0.11
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (32 bp):
GTGTCATTTATGCCAATTAGATGAAATACTAA
Found at i:16640 original size:81 final size:81
Alignment explanation
Indices: 16505--16947 Score: 635
Period size: 81 Copynumber: 5.5 Consensus size: 81
16495 ACTGTACATA
* *
16505 TGACAGAAATGTGTCAATTATGCCTGTTAGATGAACGGTTATGTACCGTTGAGTAAAAGAAAAAT
1 TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
*
16570 GGCCTAGCTGTGCAAT
66 GGCCTAGTTGTGCAAT
* * *
16586 TGACAGAAATGTGTCAATTAAGCCAGTTAGATGAACGGTTAAGTACCATTGAGT--AA-AACAAT
1 TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
* *
16648 GGCCTAGCTATGCAAT
66 GGCCTAGTTGTGCAAT
* * *
16664 TGATAGAAAGGTGTTAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
1 TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
16729 GGCCTAGTTGTGCAAT
66 GGCCTAGTTGTGCAAT
** * *
16745 TGACAGAAAAATGTCAATTATGTCAGTTGGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
1 TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
*
16810 GGCTTAGTTGTGCAAT
66 GGCCTAGTTGTGCAAT
* * * *
16826 TGGA-AAAAAGGTGTCAATTATGCTAGTTAGATGAACGGTTAAGTACAGTTGAGTAAAAGAAAAA
1 T-GACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAA
16890 TGGCCTAGTTGTGCAAT
65 TGGCCTAGTTGTGCAAT
* * *
16907 TGGCAGAAATGTGTCAATTATGCTAGTTAGACGAAC-GTTAA
1 TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAA
16948 ACACTTTTGA
Statistics
Matches: 324, Mismatches: 33, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
78 69 0.21
79 2 0.01
80 8 0.02
81 243 0.75
82 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.28
Consensus pattern (81 bp):
TGACAGAAATGTGTCAATTATGCCAGTTAGATGAACGGTTAAGTACCGTTGAGTAAAAGAAAAAT
GGCCTAGTTGTGCAAT
Found at i:23329 original size:162 final size:161
Alignment explanation
Indices: 22922--23540 Score: 1000
Period size: 162 Copynumber: 3.9 Consensus size: 161
22912 ATATGATTTG
*
22922 TGAGAAATTGATTTTCAAAGTTTCTCACTTAATATTTCCCAAAATTGAAATTTTTGAAAAGTAAG
1 TGAGAAATTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAAG
*
22987 CAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGCA
66 AAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGCA
* **
23052 TGATATTTTTCATATGATATTTTTTTTAAAAA
131 TGATA-TTTTCATTTGATATTTTTTGAAAAAA
*
23084 TGAGAAATTTGATTTTCAAATTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAA
1 TGAGAAA-TTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAA
*
23149 GAAAACAATTTTCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGC
65 GAAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGC
23214 ATGATATTTTCATTTGATATTTTTTGGAAAAAA
130 ATGATATTTTCATTTGATATTTTTT-GAAAAAA
23247 TGAGAAATTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAAG
1 TGAGAAATTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAAG
* * *
23312 AAAACGATTTCCAAAGTTTCTTACGTAGTAAATTATTTTCATGAAATCAGTAAGACCTTCAGGCA
66 AAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGCA
*
23377 TAATATTTTCATTTGATA-TTTTTGAAAAACA
131 TGATATTTTCATTTGATATTTTTTGAAAAA-A
* * *
23408 TGAGAAATCGATTTTCAAAGTTTCTCATTTAATCTTTCCTAAAATTGAAATTTTTGAAAAGTAAG
1 TGAGAAATTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAAG
* * *
23473 AAAACGATTTCCAAAG--TC---CTTAGTAAATTAATTCCAA-AAATCAGTAAGACCTTCAGGCA
66 AAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGCA
23532 TGATATTTT
131 TGATATTTT
23541 TGGGAAAATG
Statistics
Matches: 433, Mismatches: 21, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
155 30 0.07
156 15 0.03
159 2 0.00
160 6 0.01
161 84 0.19
162 160 0.37
163 136 0.31
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (161 bp):
TGAGAAATTGATTTTCAAAGTTTCTCACTTAATCTTTCCCAAAATTGAAATTTTTGAAAAGTAAG
AAAACAATTTCCAAAGTTTCTTACTTAGTAAATTATTTTCAAGAAATCAGTAAGACCTTCAGGCA
TGATATTTTCATTTGATATTTTTTGAAAAAA
Found at i:23866 original size:101 final size:102
Alignment explanation
Indices: 23649--23866 Score: 323
Period size: 102 Copynumber: 2.1 Consensus size: 102
23639 CTTAAAACAA
** * *
23649 TTCCCTTGAAACACAAATTTTGTAATTGTTTAACTCGAAACAAAAATTCATCTCACTTGAAATTG
1 TTCCCTTGAAACACAAAACTTGAAATAGTTTAACTCGAAACAAAAATTCATCTCACTTGAAATTG
*
23714 TTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGT
66 TTTTTCTTAAAATCAATTTCGTCTCACTTGAGATAGT
* * *
23751 TTCCCTTGGAACACAAAACTTGAAATAGTTTCACTCGAAACAAAATTTCATCTCACTTGAAATTG
1 TTCCCTTGAAACACAAAACTTGAAATAGTTTAACTCGAAACAAAAATTCATCTCACTTGAAATTG
* *
23816 TTTTT-TTTAAATCAATCTT-GTCTCACTTGAGATATT
66 TTTTTCTTAAAATCAAT-TTCGTCTCACTTGAGATAGT
23852 TTCCCTTGAAACACA
1 TTCCCTTGAAACACA
23867 CAAGTTAAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 39 0.38
102 65 0.62
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (102 bp):
TTCCCTTGAAACACAAAACTTGAAATAGTTTAACTCGAAACAAAAATTCATCTCACTTGAAATTG
TTTTTCTTAAAATCAATTTCGTCTCACTTGAGATAGT
Found at i:23894 original size:102 final size:102
Alignment explanation
Indices: 23649--23904 Score: 315
Period size: 102 Copynumber: 2.5 Consensus size: 102
23639 CTTAAAACAA
** ** * *
23649 TTCCCTTGAAACACAAATTTTGTAATTGTTTAACTCGAAACAAAAATTCATCTCACTTGAAATTG
1 TTCCCTTGAAACACAAAACTTAAAATAGTTTCACTCGAAACAAAAATTCATCTCACTTGAAATTG
*
23714 TTTTTCTTAAAATCAATTTCGTCTCGCTTGAGATAGT
66 TTTTTCTTAAAATCAATTTCGTCTCACTTGAGATAGT
* * *
23751 TTCCCTTGGAACACAAAACTTGAAATAGTTTCACTCGAAACAAAATTTCATCTCACTTGAAATTG
1 TTCCCTTGAAACACAAAACTTAAAATAGTTTCACTCGAAACAAAAATTCATCTCACTTGAAATTG
* *
23816 TTTTT-TTTAAATCAATCTT-GTCTCACTTGAGATATT
66 TTTTTCTTAAAATCAAT-TTCGTCTCACTTGAGATAGT
* * * * *
23852 TTCCCTTGAAACACACAAGTTAAAATTG-TTCATTCGAAA-AACAATT-ATCTCAC
1 TTCCCTTGAAACACAAAACTTAAAATAGTTTCACTCGAAACAAAAATTCATCTCAC
23905 CTAAGATAGA
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
98 7 0.05
99 5 0.04
100 10 0.07
101 48 0.36
102 65 0.48
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (102 bp):
TTCCCTTGAAACACAAAACTTAAAATAGTTTCACTCGAAACAAAAATTCATCTCACTTGAAATTG
TTTTTCTTAAAATCAATTTCGTCTCACTTGAGATAGT
Found at i:24651 original size:14 final size:14
Alignment explanation
Indices: 24632--24673 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
24622 ATACCCTATC
24632 ATTATTTTATTAAT
1 ATTATTTTATTAAT
*
24646 ATTATTTTATTAGT
1 ATTATTTTATTAAT
24660 ATTTATTATTATTA
1 A-TTATT-TTATTA
24674 TTTTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 14 0.56
15 5 0.20
16 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
ATTATTTTATTAAT
Found at i:24668 original size:3 final size:3
Alignment explanation
Indices: 24632--24751 Score: 88
Period size: 3 Copynumber: 40.0 Consensus size: 3
24622 ATACCCTATC
* *
24632 ATT ATT -TT ATT AAT ATT ATT -TT ATT AGT ATTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* * * * *
24676 TTT ATT ATT ATA ATT AAT ATTT ATT ATT -TT CATT -TT ATCT TTT TTT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT -ATT ATT AT-T ATT ATT
*
24722 ATT ATT ACT A-T ATT ATT ATT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
24752 TCAAATATAT
Statistics
Matches: 94, Mismatches: 13, Indels: 20
0.74 0.10 0.16
Matches are distributed among these distances:
2 10 0.11
3 73 0.78
4 11 0.12
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:24699 original size:28 final size:25
Alignment explanation
Indices: 24645--24713 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 25
24635 ATTTTATTAA
* *
24645 TATTA-TTTTATTAGTATTTATTAT
1 TATTATTTTTATTATTATTTAATAT
24669 TATTATTTTTATTATTATAATTAATATT
1 TATTATTTTTATTATTAT--TTAATA-T
*
24697 TATTATTTTCATT-TTAT
1 TATTATTTTTATTATTAT
24714 CTTTTTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 5 0.13
25 11 0.29
27 9 0.24
28 13 0.34
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (25 bp):
TATTATTTTTATTATTATTTAATAT
Found at i:28064 original size:138 final size:138
Alignment explanation
Indices: 27887--28459 Score: 808
Period size: 138 Copynumber: 4.2 Consensus size: 138
27877 ATTTTCTAGT
*
27887 AATAATTGATTAAAATTAATTAGGACTAATATTATAGCCTCCATCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACATTT
** *
27952 AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTTAAGGTTCCAAATTAATTA
66 AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTCGAGATTCCAAATTAATTA
28017 TTTGATTC
131 TTTGATTC
*
28025 AATAATTGATTAAAATTAATTAGGACTAATATTATAGCCTCCATCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACATTT
* * *
28090 AGTCCTTAAAATTAGGACAATTCTTAACTTGGTCCTCGTTTATGCTCGAGGTTCCAAATTAATTA
66 AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTCGAGATTCCAAATTAATTA
28155 TTTGATTC
131 TTTGATTC
* * * *
28163 AATAATTGATTAAAATTAATTAGGATTAATACTAGAGACT-CATCTTAGGCTTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACATTT
* * * * * * **
28227 AGTCCTTAAAATTAGGAGAATTATTAATTTGGTACTTGCTTTTGCTCGAGAATCTGAATTAATTA
66 AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTCGAGATTCCAAATTAATTA
*
28292 TTCGATTC
131 TTTGATTC
* * *
28300 AATAATTGATTAAAATTAATTTGGATTAATATTAGAGCCTCCACCTTAGGCCTAATTTCACATTT
1 AATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACATTT
* * * * * * * *
28365 AGTCCTTAAAATTAAGATAATTTTTTACTTGATCCTCGCTTATGCTCGAGACTCCAATTTAATGA
66 AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTCGAGATTCCAAATTAATTA
*
28430 TTTGAAT-
131 TTTGATTC
*
28437 AGCATAATTAATTAAAATTAATT
1 A--ATAATTGATTAAAATTAATT
28460 TAATTTAATA
Statistics
Matches: 389, Mismatches: 43, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
137 122 0.31
138 248 0.64
139 19 0.05
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (138 bp):
AATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCATCTTAGGCCTAATTTCACATTT
AGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTCGAGATTCCAAATTAATTA
TTTGATTC
Found at i:28308 original size:275 final size:275
Alignment explanation
Indices: 27886--28459 Score: 817
Period size: 275 Copynumber: 2.1 Consensus size: 275
27876 AATTTTCTAG
* * *
27886 TAATAATTGATTAAAATTAATTAGGACTAATATTATAGCCTCCATCTTAGGCCTAATTTCACATT
1 TAATAATTGATTAAAATTAATTAGGACTAATACTAGAGACTCCATCTTAGGCCTAATTTCACATT
* * * **
27951 TAGTCCTTAAAATTAGGAGAATTCTTAACTTGGTCCTCGCTTATGCTTAAGGTTCCAAATTAATT
66 TAGTCCTTAAAATTAGGAGAATTATTAACTTGGTACTCGCTTATGCTCAAGAATCCAAATTAATT
* * *
28016 ATTTGATTCAATAATTGATTAAAATTAATTAGGACTAATATTATAGCCTCCATCTTAGGCCTAAT
131 ATTCGATTCAATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCACCTTAGGCCTAAT
* * * **
28081 TTCACATTTAGTCCTTAAAATTAGGACAATTCTTAACTTGGTCCTCGTTTATGCTCGAGGTTCCA
196 TTCACATTTAGTCCTTAAAATTAAGACAATTCTTAACTTGATCCTCGCTTATGCTCGAGACTCCA
* *
28146 AATTAATTATTTGAT
261 AATTAATGATTTGAA
* *
28161 TCAATAATTGATTAAAATTAATTAGGATTAATACTAGAGACT-CATCTTAGGCTTAATTTCACAT
1 T-AATAATTGATTAAAATTAATTAGGACTAATACTAGAGACTCCATCTTAGGCCTAATTTCACAT
* * * * **
28225 TTAGTCCTTAAAATTAGGAGAATTATTAATTTGGTACTTGCTTTTGCTCGAGAATCTGAATTAAT
65 TTAGTCCTTAAAATTAGGAGAATTATTAACTTGGTACTCGCTTATGCTCAAGAATCCAAATTAAT
* *
28290 TATTCGATTCAATAATTGATTAAAATTAATTTGGATTAATATTAGAGCCTCCACCTTAGGCCTAA
130 TATTCGATTCAATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCACCTTAGGCCTAA
* * *
28355 TTTCACATTTAGTCCTTAAAATTAAGATAATTTTTTACTTGATCCTCGCTTATGCTCGAGACTCC
195 TTTCACATTTAGTCCTTAAAATTAAGACAATTCTTAACTTGATCCTCGCTTATGCTCGAGACTCC
*
28420 AATTTAATGATTTGAA
260 AAATTAATGATTTGAA
*
28436 TAGCATAATTAATTAAAATTAATT
1 TA--ATAATTGATTAAAATTAATT
28460 TAATTTAATA
Statistics
Matches: 263, Mismatches: 33, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
274 1 0.00
275 207 0.79
276 55 0.21
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (275 bp):
TAATAATTGATTAAAATTAATTAGGACTAATACTAGAGACTCCATCTTAGGCCTAATTTCACATT
TAGTCCTTAAAATTAGGAGAATTATTAACTTGGTACTCGCTTATGCTCAAGAATCCAAATTAATT
ATTCGATTCAATAATTGATTAAAATTAATTAGGACTAATATTAGAGCCTCCACCTTAGGCCTAAT
TTCACATTTAGTCCTTAAAATTAAGACAATTCTTAACTTGATCCTCGCTTATGCTCGAGACTCCA
AATTAATGATTTGAA
Found at i:31411 original size:183 final size:183
Alignment explanation
Indices: 31103--31468 Score: 732
Period size: 183 Copynumber: 2.0 Consensus size: 183
31093 CGCGACAGCC
31103 GTAACACCGTCCGCGACGGCTGCAATCACGGTAAACCAAATGGATGCATCATGCTTGTATTGGTT
1 GTAACACCGTCCGCGACGGCTGCAATCACGGTAAACCAAATGGATGCATCATGCTTGTATTGGTT
31168 TTCATTAGTGTCTCCCTTCGATTCTATCAGGTGCTTCCTGTTTGAAGTTGCTCGATCGACCCGAA
66 TTCATTAGTGTCTCCCTTCGATTCTATCAGGTGCTTCCTGTTTGAAGTTGCTCGATCGACCCGAA
31233 ACGTCCTCGAATTCGGTCTTTATCTAACTATAGTTTCTGCATAACATCCAGGA
131 ACGTCCTCGAATTCGGTCTTTATCTAACTATAGTTTCTGCATAACATCCAGGA
31286 GTAACACCGTCCGCGACGGCTGCAATCACGGTAAACCAAATGGATGCATCATGCTTGTATTGGTT
1 GTAACACCGTCCGCGACGGCTGCAATCACGGTAAACCAAATGGATGCATCATGCTTGTATTGGTT
31351 TTCATTAGTGTCTCCCTTCGATTCTATCAGGTGCTTCCTGTTTGAAGTTGCTCGATCGACCCGAA
66 TTCATTAGTGTCTCCCTTCGATTCTATCAGGTGCTTCCTGTTTGAAGTTGCTCGATCGACCCGAA
31416 ACGTCCTCGAATTCGGTCTTTATCTAACTATAGTTTCTGCATAACATCCAGGA
131 ACGTCCTCGAATTCGGTCTTTATCTAACTATAGTTTCTGCATAACATCCAGGA
31469 ATATGGCAGT
Statistics
Matches: 183, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
183 183 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (183 bp):
GTAACACCGTCCGCGACGGCTGCAATCACGGTAAACCAAATGGATGCATCATGCTTGTATTGGTT
TTCATTAGTGTCTCCCTTCGATTCTATCAGGTGCTTCCTGTTTGAAGTTGCTCGATCGACCCGAA
ACGTCCTCGAATTCGGTCTTTATCTAACTATAGTTTCTGCATAACATCCAGGA
Found at i:35497 original size:21 final size:21
Alignment explanation
Indices: 35447--35504 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
35437 AATCAGTTCC
35447 CAGAATCGCAATGCGATAGTA
1 CAGAATCGCAATGCGATAGTA
* ** *
35468 CA-AATTCGCATTGCGATTTTT
1 CAGAA-TCGCAATGCGATAGTA
*
35489 CAGAATCGCAACGCGA
1 CAGAATCGCAATGCGA
35505 ATATGAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (21 bp):
CAGAATCGCAATGCGATAGTA
Found at i:35517 original size:20 final size:20
Alignment explanation
Indices: 35492--35767 Score: 161
Period size: 20 Copynumber: 13.7 Consensus size: 20
35482 GATTTTTCAG
*
35492 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
35512 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
35532 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
35552 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* *
35573 AATCGCAACGC-ATATCCGTA
1 AATCGCAACGCGA-ATACGAA
35593 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
35614 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
35634 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
35654 AATCGCAATGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
35674 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * *
35694 AATCGCAATGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
*
35714 AATCGCAACGAC-ATTACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
35735 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
35755 AATCGCAACGCGA
1 AATCGCAACGCGA
35768 TCGATAATTC
Statistics
Matches: 198, Mismatches: 42, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.02
20 140 0.71
21 53 0.27
22 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:35668 original size:40 final size:41
Alignment explanation
Indices: 35553--35764 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
35543 GATTCTGACT
* * *
35553 ATCGCAACGAGTATCCGTAAAATCGCAACGCATATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
35594 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
35635 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
35675 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
35715 ATCGCAACGACATTACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
35756 ATCGCAACG
1 ATCGCAACG
35765 CGATCGATAA
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 74 0.47
41 83 0.53
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:35865 original size:21 final size:20
Alignment explanation
Indices: 35836--35890 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
35826 ATTCTGACTA
35836 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTT-CCAAAT
* *
35857 TCGCGTTGCGAATTTCCTAAT
1 TCGCATTGCG-ATTTCCAAAT
*
35878 TCGCAATGCGATT
1 TCGCATTGCGATT
35891 ACGTAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 3 0.10
21 22 0.76
22 4 0.14
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATTTCCAAAT
Found at i:35903 original size:20 final size:20
Alignment explanation
Indices: 35878--36009 Score: 180
Period size: 20 Copynumber: 6.7 Consensus size: 20
35868 ATTTCCTAAT
35878 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
35898 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
35918 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
* *
35938 TCACAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
*
35958 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGATTAC-GTAAA
*
35978 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGATTAC-GTAAA
*
35998 T-GCAATGAGATT
1 TCGCAATGCGATT
36010 CTGACTATCG
Statistics
Matches: 106, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
19 10 0.09
20 96 0.91
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:36914 original size:24 final size:24
Alignment explanation
Indices: 36863--36916 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36853 GTATTCGAAA
*
36863 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
36887 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
36911 TTTGAT
1 TTTGAT
36917 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:39353 original size:20 final size:20
Alignment explanation
Indices: 39328--39601 Score: 151
Period size: 20 Copynumber: 14.7 Consensus size: 20
39318 GACATTCATT
*
39328 TGACTATTGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
39348 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
39368 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
* *
39388 TGACTATCACAACGCAGAAA
1 TGACTATCGCAACGCGGAAA
*
39408 TGACTATCGCAA--C-GAGA
1 TGACTATCGCAACGCGGAAA
*
39425 -GA--ATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
** * *
39441 TGAAAATCGTAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
** *
39460 TGAAAATCGCAA--C-G-AG
1 TGACTATCGCAACGCGGAAA
* *
39476 TGA--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGGAAA
**
39494 TGAAAATCGCAACGC-G-AA
1 TGACTATCGCAACGCGGAAA
*
39512 --A--ATCACAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
* *
39528 TGACTATCGCAACACAGAAA
1 TGACTATCGCAACGCGGAAA
* *
39548 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
*
39568 TGACTATCGTAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
39588 TGACTATCGCAACG
1 TGACTATCGCAACG
39602 AGTTTCGCGT
Statistics
Matches: 205, Mismatches: 30, Indels: 38
0.75 0.11 0.14
Matches are distributed among these distances:
14 24 0.12
15 1 0.00
16 13 0.06
17 7 0.03
18 8 0.04
19 24 0.12
20 122 0.60
21 6 0.03
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:39392 original size:40 final size:38
Alignment explanation
Indices: 39328--39599 Score: 171
Period size: 40 Copynumber: 7.3 Consensus size: 38
39318 GACATTCATT
* * *
39328 TGACTATTGCAACGCGAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAATGCGAAT-TGACTATCGCAACGC-GAAA
*
39368 TGACTATCGCAATGCGGAATTGACTATCACAACGCAGAAA
1 TGACTATCGCAATGC-GAATTGACTATCGCAACGC-GAAA
*
39408 TGACTATCGCAA--CGAGA--GA--ATCGCAATGCGAAA
1 TGACTATCGCAATGCGA-ATTGACTATCGCAACGCGAAA
** * * ** *
39441 TGAAAATCGTAATGCGAAATGAAAATCGCAA--CG-AG
1 TGACTATCGCAATGCGAATTGACTATCGCAACGCGAAA
* **
39476 TGA--ATCGCAATGCGAAAATGAAAATCGCAACGCG-AA
1 TGACTATCGCAATGCG-AATTGACTATCGCAACGCGAAA
* * *
39512 --A--ATCACAACGCGAATATGACTATCGCAACACAGAAA
1 TGACTATCGCAATGCGAAT-TGACTATCGCAACGC-GAAA
*
39548 TGACTATCGCAATGCGGAATTGACTATCGTAACGCGGAAA
1 TGACTATCGCAATGC-GAATTGACTATCGCAACGC-GAAA
39588 TGACTATCGCAA
1 TGACTATCGCAA
39600 CGAGTTTCGC
Statistics
Matches: 189, Mismatches: 24, Indels: 38
0.75 0.10 0.15
Matches are distributed among these distances:
33 25 0.13
34 46 0.24
35 8 0.04
36 11 0.06
37 2 0.01
38 10 0.05
40 79 0.42
41 8 0.04
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.18
Consensus pattern (38 bp):
TGACTATCGCAATGCGAATTGACTATCGCAACGCGAAA
Found at i:39454 original size:19 final size:19
Alignment explanation
Indices: 39426--39512 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
39416 GCAACGAGAG
39426 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39445 AATCGTAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
39464 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
39478 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
39498 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
39513 ATCACAACGC
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 8 0.14
16 5 0.09
17 2 0.04
18 3 0.05
19 28 0.49
20 11 0.19
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:39469 original size:52 final size:53
Alignment explanation
Indices: 39373--39512 Score: 174
Period size: 53 Copynumber: 2.6 Consensus size: 53
39363 GGAAATGACT
* * ** * **
39373 ATCGCAATGCGGAATTGACTATCACAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
* * *
39427 ATCGCAATGCG-AAATGAAAATCGTAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
39479 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAA
1 ATCGCAATGCGAAAATGAAAATCGCAACGCGAAA
39513 ATCACAACGC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
52 31 0.42
53 32 0.43
54 11 0.15
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (53 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:39514 original size:14 final size:14
Alignment explanation
Indices: 39495--39525 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39485 ATGCGAAAAT
*
39495 GAAAATCGCAACGC
1 GAAAATCACAACGC
39509 GAAAATCACAACGC
1 GAAAATCACAACGC
39523 GAA
1 GAA
39526 TATGACTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.26, G:0.19, T:0.06
Consensus pattern (14 bp):
GAAAATCACAACGC
Found at i:39525 original size:34 final size:34
Alignment explanation
Indices: 39457--39540 Score: 96
Period size: 34 Copynumber: 2.5 Consensus size: 34
39447 TCGTAATGCG
** * *
39457 AAATGAAAATCGCAACGAGTGAATCGCAATGCGA
1 AAATGAAAATCGCAACGAGAAAATCACAACGCGA
*
39491 AAATGAAAATCGCAACGCGAAAATCACAACGCGA
1 AAATGAAAATCGCAACGAGAAAATCACAACGCGA
* **
39525 ATATGACTATCGCAAC
1 AAATGAAAATCGCAAC
39541 ACAGAAATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.14
Consensus pattern (34 bp):
AAATGAAAATCGCAACGAGAAAATCACAACGCGA
Found at i:39647 original size:34 final size:34
Alignment explanation
Indices: 39609--39704 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
39599 ACGAGTTTCG
39609 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
39643 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
39676 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
39705 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:39825 original size:14 final size:14
Alignment explanation
Indices: 39806--39842 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
39796 CATCAATTAA
39806 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
39820 ACAAATCATCTTTT
1 ACAAATCAACATTT
39834 ACAAATCAA
1 ACAAATCAA
39843 TTAAACAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:41241 original size:21 final size:21
Alignment explanation
Indices: 41217--41295 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
41207 CAACGATGAC
41217 AGTGGCCTCTTGAACGGTGGG
1 AGTGGCCTCTTGAACGGTGGG
* * **
41238 AGTGGACTCTTG-AGGGATGAT
1 AGTGGCCTCTTGAACGG-TGGG
* *
41259 AGGGGCCTCTTGAACGATAGGG
1 AGTGGCCTCTTGAACGGT-GGG
*
41281 -GAGGCCTCTTGAACG
1 AGTGGCCTCTTGAACG
41296 ATGATAGGTG
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
20 3 0.07
21 38 0.86
22 3 0.07
ACGTcount: A:0.20, C:0.18, G:0.39, T:0.23
Consensus pattern (21 bp):
AGTGGCCTCTTGAACGGTGGG
Found at i:41290 original size:42 final size:42
Alignment explanation
Indices: 41192--41303 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
41182 TCTAGAATGT
* * * *
41192 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACGA
* **
41234 TGGGAGTGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
41276 TAGGG-GAGGCCTCTTGAACGATGATAGG
1 T-GGGAGAGGACTCTTGAACGATGATAGG
41304 TGAGTCGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:41806 original size:20 final size:20
Alignment explanation
Indices: 41783--41831 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
41773 GAAACTTAAA
41783 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
41803 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
41823 ATCGCAACG
1 ATCGCAACG
41832 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:41887 original size:19 final size:19
Alignment explanation
Indices: 41874--42015 Score: 109
Period size: 19 Copynumber: 7.7 Consensus size: 19
41864 GCGATTATAG
**
41874 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
*
41893 TTTCGCGTTGTGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
41909 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
41926 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
41945 TTTCTCGTTGCGA--TTCA
1 TTTCGCGTTGCGATTTTCA
* **
41962 TTTTGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
* *
41981 TTTTTCACGTTGCGATTTTAA
1 --TTTCGCGTTGCGATTTTCA
*
42002 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
42016 AAGTAAACTA
Statistics
Matches: 98, Mismatches: 16, Indels: 17
0.75 0.12 0.13
Matches are distributed among these distances:
14 7 0.07
15 3 0.03
16 2 0.02
17 17 0.17
18 3 0.03
19 41 0.42
20 11 0.11
21 14 0.14
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:41921 original size:33 final size:33
Alignment explanation
Indices: 41879--41942 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
41869 TATAGTTTCG
** *
41879 CGTTGCGATTTTGGTTTCGCGTTGTGATTTTGT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
41912 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTTT
41943 CATTTCTCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.08, C:0.16, G:0.27, T:0.50
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTTTGT
Found at i:42210 original size:94 final size:94
Alignment explanation
Indices: 42063--42442 Score: 647
Period size: 94 Copynumber: 4.1 Consensus size: 94
42053 ATGGATTACA
* *
42063 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
42127 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
42156 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGCTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
42221 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
42250 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
42315 TTAGCATAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
42344 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
42408 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
42438 TTACT
1 TTACT
42443 AAGTAATCTA
Statistics
Matches: 271, Mismatches: 13, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
93 23 0.08
94 248 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:44166 original size:20 final size:20
Alignment explanation
Indices: 44143--44186 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
44133 ATGAAAATCA
44143 CAACG-AGATAATGACTATCG
1 CAACGTAGA-AATGACTATCG
*
44163 CAACGTGGAAATGACTATCG
1 CAACGTAGAAATGACTATCG
44183 CAAC
1 CAAC
44187 AATAGAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
CAACGTAGAAATGACTATCG
Found at i:44216 original size:33 final size:33
Alignment explanation
Indices: 44159--44284 Score: 180
Period size: 33 Copynumber: 3.8 Consensus size: 33
44149 GATAATGACT
* ** * *
44159 ATCGCAACGTGGAAATGACTATCGCAACAATAGA
1 ATCGCAACG-CGAAATGAAAATCGCAACGAGAGA
*
44193 ATCGCAACACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
44226 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
44259 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
44285 TGCGATTTTG
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 76 0.90
34 8 0.10
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:44230 original size:14 final size:14
Alignment explanation
Indices: 44211--44267 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
44201 ACGAAATGAA
44211 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
44225 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
44244 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
44258 AATCGTAACG
1 AATCGCAACG
44268 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:44289 original size:19 final size:19
Alignment explanation
Indices: 44192--44289 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
44182 GCAACAATAG
*
44192 AATCGCAACACGAAATGAA
1 AATCGCAACGCGAAATGAA
*
44211 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
44225 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
44244 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
*
44258 AATCGTAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
44277 AATCGCAATGCGA
1 AATCGCAACGCGA
44290 TTTTGGTTTC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:44333 original size:33 final size:33
Alignment explanation
Indices: 44285--44377 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
44275 AAAATCGCAA
**
44285 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
44318 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
** *
44351 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGCGTTGCGATT
44378 TTCATTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:44397 original size:20 final size:20
Alignment explanation
Indices: 44349--44399 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44339 CGATTCTCTC
** *
44349 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
*
44369 GTTGCGATTTTCATTTTTAT
1 GTTGCGATTTTCATTTTCAT
44389 GTTGCGATTTT
1 GTTGCGATTTT
44400 AAGTTTAGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.22, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:45044 original size:40 final size:40
Alignment explanation
Indices: 44962--45130 Score: 248
Period size: 40 Copynumber: 4.2 Consensus size: 40
44952 AAAAATCGTA
* *
44962 TTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGTCG
1 TTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCTCG
*
45003 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCG
* *
45043 TTGTGATTTACAGATACGCGTTGCGATTTACGTATTCTCG
1 TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCG
* * *
45083 TTGCGATTTACGGATACGCGTTGCGATTTTCATATTCGCG
1 TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCG
*
45123 TTACGATT
1 TTGCGATT
45131 CTGGAAAATC
Statistics
Matches: 116, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
40 92 0.79
41 24 0.21
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (40 bp):
TTGCGATTTACGGATACGCGTTGCGATTTACGTATTCTCG
Found at i:45122 original size:20 final size:20
Alignment explanation
Indices: 44962--45130 Score: 164
Period size: 20 Copynumber: 8.4 Consensus size: 20
44952 AAAAATCGTA
*
44962 TTGCGATTTACGGATAT-GCG
1 TTGCGATTTACGTAT-TCGCG
44982 TTGCGATTTTACGTATT-GTCG
1 TTGCGA-TTTACGTATTCG-CG
* * *
45003 TTGCGATTTACGGATACGCA
1 TTGCGATTTACGTATTCGCG
*
45023 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCG
* *
45043 TTGTGATTTACAG-ATACGCG
1 TTGCGATTTAC-GTATTCGCG
*
45063 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCG
* *
45083 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCG
* *
45103 TTGCGATTTTCATATTCGCG
1 TTGCGATTTACGTATTCGCG
*
45123 TTACGATT
1 TTGCGATT
45131 CTGGAAAATC
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
19 1 0.01
20 103 0.84
21 18 0.15
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCG
Found at i:45229 original size:20 final size:19
Alignment explanation
Indices: 45180--45233 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
45170 ATTCTTCATA
45180 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
45199 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
45220 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
45234 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:46630 original size:2 final size:2
Alignment explanation
Indices: 46623--46665 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
46613 CTAAGTTTTC
46623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46665 A
1 A
46666 ACTTAGGATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47877 original size:6 final size:6
Alignment explanation
Indices: 47868--47927 Score: 52
Period size: 6 Copynumber: 10.2 Consensus size: 6
47858 TTAGGTCTGT
* * *
47868 AAAATA AAAATA ATAATGA AAGATC AAAAT- AAAATA AAAAT- AAAATA
1 AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA
* *
47915 ATAATA ATAATA A
1 AAAATA AAAATA A
47928 TATACAAAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 10 0.22
6 31 0.69
7 4 0.09
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:48442 original size:24 final size:25
Alignment explanation
Indices: 48392--48454 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
48382 GCTGTAATTG
48392 TTGGGGGGAGAAAGAAGAAAAGTTT
1 TTGGGGGGAGAAAGAAGAAAAGTTT
48417 TTGGGGGGAGAAAGAAGAAAAGTTT
1 TTGGGGGGAGAAAGAAGAAAAGTTT
48442 TTGGGGGGA-AAAG
1 TTGGGGGGAGAAAG
48455 GGAGAGAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.11
25 34 0.89
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.19
Consensus pattern (25 bp):
TTGGGGGGAGAAAGAAGAAAAGTTT
Found at i:49533 original size:9 final size:9
Alignment explanation
Indices: 49515--49617 Score: 56
Period size: 9 Copynumber: 11.6 Consensus size: 9
49505 AAATAGTAAG
49515 TAAAATAAA
1 TAAAATAAA
49524 T-AAATAAA
1 TAAAATAAA
**
49532 -ATATGTAAA
1 TA-AAATAAA
*
49541 TAATATAAA
1 TAAAATAAA
49550 -AAAATAAA
1 TAAAATAAA
*
49558 GAAAA-AGAA
1 TAAAATA-AA
* *
49567 GAAAATATA
1 TAAAATAAA
49576 TATAAATAAA
1 TA-AAATAAA
49586 -ACAAATAAA
1 TA-AAATAAA
49595 TAAAAT-AA
1 TAAAATAAA
*
49603 TAAAAAAAA
1 TAAAATAAA
49612 GTAAAA
1 -TAAAA
49618 ATATATATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
8 22 0.29
9 39 0.52
10 14 0.19
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (9 bp):
TAAAATAAA
Found at i:49533 original size:13 final size:13
Alignment explanation
Indices: 49502--49639 Score: 79
Period size: 13 Copynumber: 10.5 Consensus size: 13
49492 GAAAGCAAAG
*
49502 ATAAAAT-AGTAA
1 ATAAAATAAATAA
*
49514 GTAAAATAAATAA
1 ATAAAATAAATAA
**
49527 ATAAAATATGTAA
1 ATAAAATAAATAA
* *
49540 ATAATATAAAAAA
1 ATAAAATAAATAA
49553 ATAAAGA-AAA-AGA
1 ATAAA-ATAAATA-A
*
49566 AGAAAATATATATAA
1 ATAAAATA-A-ATAA
*
49581 ATAAAACAAATAA
1 ATAAAATAAATAA
49594 ATAAAAT-AATAA
1 ATAAAATAAATAA
*
49606 AAAAAAGTAAA-AA
1 ATAAAA-TAAATAA
* *
49619 TATATATATAAATTA
1 -ATA-AAATAAATAA
49634 ATAAAA
1 ATAAAA
49640 CAGATAATAA
Statistics
Matches: 95, Mismatches: 19, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
12 18 0.19
13 51 0.54
14 14 0.15
15 11 0.12
16 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (13 bp):
ATAAAATAAATAA
Found at i:49622 original size:45 final size:45
Alignment explanation
Indices: 49545--49630 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 45
49535 TGTAAATAAT
49545 ATAAAAAAATAAAGAAAAAGAAGAAAATATATATAAATAAAACAA
1 ATAAAAAAATAAAGAAAAAGAAGAAAATATATATAAATAAAACAA
*
49590 ATAAATAAAATAATA-AAAAA-AAGTAAAA-ATATATATATAAA
1 ATAAA-AAAATAA-AGAAAAAGAAG-AAAATATATATAAATAAA
49631 TTAATAAAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
45 20 0.54
46 16 0.43
47 1 0.03
ACGTcount: A:0.74, C:0.01, G:0.05, T:0.20
Consensus pattern (45 bp):
ATAAAAAAATAAAGAAAAAGAAGAAAATATATATAAATAAAACAA
Found at i:49639 original size:40 final size:38
Alignment explanation
Indices: 49588--49687 Score: 98
Period size: 40 Copynumber: 2.6 Consensus size: 38
49578 TAAATAAAAC
*
49588 AAATAAATAAAATAATAAAAAAAAGTAAAAATATATATAT
1 AAATTAATAAAATAATAAAAAAAA-T-AAAATATATATAT
* * *
49628 AAATTAATAAAACAGATAATAAAAAATAACATATATATGT
1 AAATTAATAAAATA-ATAA-AAAAAATAAAATATATATAT
49668 -AATCTAA-AAAATAA-AAAAAA
1 AAAT-TAATAAAATAATAAAAAA
49688 TATACTAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
36 4 0.08
37 2 0.04
38 1 0.02
39 8 0.15
40 26 0.50
41 5 0.10
42 6 0.12
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (38 bp):
AAATTAATAAAATAATAAAAAAAATAAAATATATATAT
Found at i:50319 original size:37 final size:37
Alignment explanation
Indices: 50209--50320 Score: 188
Period size: 37 Copynumber: 3.0 Consensus size: 37
50199 ATGCTTGTGG
* * *
50209 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCC
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
*
50246 ATCCTATTTTTAGGAGTTTGAATTCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
50283 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
50320 A
1 A
50321 ACATTATGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:50920 original size:39 final size:39
Alignment explanation
Indices: 50846--50922 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
50836 AATAGTAAGT
* *
50846 AAAATAAGAAAAATATATATAAAAAATAAAGAAATAAAG
1 AAAAGAAGAAAAATATATATAAAAAACAAAGAAATAAAG
*
50885 AAAAGAAGAAAAA-A-ATATAAATTAAACAAATAAATAAA
1 AAAAGAAGAAAAATATATATAAA--AAACAAAGAAATAAA
50923 ATAATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 7 0.21
38 1 0.03
39 25 0.76
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.17
Consensus pattern (39 bp):
AAAAGAAGAAAAATATATATAAAAAACAAAGAAATAAAG
Found at i:50978 original size:77 final size:77
Alignment explanation
Indices: 50907--51050 Score: 170
Period size: 77 Copynumber: 1.9 Consensus size: 77
50897 AAATATAAAT
* *
50907 TAAACAAATAAATAAAATA-ATAATAAA-AAAGTAAAA-ATAT-ATATATATATACATATATATA
1 TAAA-AAAT-AATAAAATATAT-ATAAATAAA-TAAAACATATAATA-AAAAATACATATATATA
50968 TATAATAAATAAAAACA
61 TATAATAAATAAAAACA
* * *
50985 TAAAAAATAGTAAAATATATATAAATTAATAAAACATATAATAAAAAATACATATATATATGTAA
1 TAAAAAATAATAAAATATATATAAATAAATAAAACATATAATAAAAAATACATATATATATATAA
51050 T
66 T
51051 CTAAAAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
76 18 0.32
77 32 0.56
78 7 0.12
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (77 bp):
TAAAAAATAATAAAATATATATAAATAAATAAAACATATAATAAAAAATACATATATATATATAA
TAAATAAAAACA
Found at i:51023 original size:19 final size:19
Alignment explanation
Indices: 50963--51029 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
50953 ATATACATAT
*
50963 ATATATATAATAAATAAAAAC
1 ATATATA-AATTAAT-AAAAC
* * *
50984 ATA-A-AAAATAGTAAAAT
1 ATATATAAATTAATAAAAC
51001 ATATATAAATTAATAAAAC
1 ATATATAAATTAATAAAAC
51020 ATATAATAAA
1 ATAT-ATAAA
51030 AAATACATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
17 7 0.19
18 5 0.14
19 15 0.42
20 6 0.17
21 3 0.08
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.28
Consensus pattern (19 bp):
ATATATAAATTAATAAAAC
Found at i:51669 original size:36 final size:37
Alignment explanation
Indices: 51578--51688 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
51568 ATGCTTGTGG
* *
51578 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
51615 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
51652 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
51688 A
1 A
51689 ACATTATGTT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
36 31 0.43
37 41 0.57
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAACTCT
Found at i:51710 original size:73 final size:73
Alignment explanation
Indices: 51578--51719 Score: 171
Period size: 73 Copynumber: 1.9 Consensus size: 73
51568 ATGCTTGTGG
* * * *
51578 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAACCTATGTTTA-GAGTTTGAATCCTAC
51643 TAAAACTCT
65 TAAAACTCT
* * **
51652 ATCCTA-TTTTAGGAGTTTGAATCCTAGTAAAACTCTAACATTATGTTTA-TTTTCTGAATCCTA
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAAC-CTATGTTTAGAGTT-TGAATCCTA
51715 CTAAA
64 CTAAA
51720 TCTGGGTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
72 2 0.03
73 43 0.74
74 13 0.22
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (73 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCTAACCTATGTTTAGAGTTTGAATCCTACT
AAAACTCT
Found at i:52314 original size:90 final size:81
Alignment explanation
Indices: 52158--52450 Score: 257
Period size: 83 Copynumber: 3.5 Consensus size: 81
52148 ATAGTGTGAT
* * * * * * *
52158 TGATGTGTCATCGAGTTGGATGGAATCGAACTCGACAATTTTGTTGACAGATAGCCCTTCTTGCC
1 TGATGTGTCTTTGAGTTGAATGTAATCGAACTCGA-AGTTTTGTTGACAGATAACCCTTCTAGCC
* *
52223 TTGAGCTATATTGTAAA
65 TTGAGCTATACTGCAAA
* *
52240 TTTGATTTGCCTCTGAGTTGAGTTGAATGTAATCGAACTCGAAGGTATTTGATGACAGATAACCC
1 --TGATGTG--TCT---TTGAGTTGAATGTAATCGAACTCGAA-GT-TTTGTTGACAGATAACCC
*
52305 TTCTAGCCTTGAGTTATACTGCAAA
57 TTCTAGCCTTGAGCTATACTGCAAA
* * *
52330 TGATGTGTCTTTGAGCTGAATGTAGTCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTAGC
1 TGATGTGTCTTTGAGTTGAATGTAATCGAACTCGAA-GT-TTTGTTGACAGATAACCCTTCTAGC
*
52395 CTTGAGTTATGA-TGCAAA
64 CTTGAGCTAT-ACTGCAAA
* * * *
52413 TGATGTGCCCTCGAAGCT-AAGTGTAATCGAACTCGAAG
1 TGATGTGTCTTTG-AGTTGAA-TGTAATCGAACTCGAAG
52451 GTCTTTCAAG
Statistics
Matches: 176, Mismatches: 23, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
83 78 0.44
84 26 0.15
86 5 0.03
88 7 0.04
89 23 0.13
90 37 0.21
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (81 bp):
TGATGTGTCTTTGAGTTGAATGTAATCGAACTCGAAGTTTTGTTGACAGATAACCCTTCTAGCCT
TGAGCTATACTGCAAA
Found at i:52359 original size:83 final size:83
Alignment explanation
Indices: 52257--52452 Score: 270
Period size: 83 Copynumber: 2.3 Consensus size: 83
52247 TGCCTCTGAG
* *
52257 TTGAGTTGAATGTAATCGAACTCGAAGGTATTTGATGACAGATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTATTGGATGACAGATAACCCTTCTAGCCTTGAGTTAT
* *
52322 -ACTGCAAATGATGTGTCT
66 GA-TGCAAATGATGTGCCC
* * * *
52340 TTGAGCTGAATGTAGTCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTAGCCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTATTGGATGACAGATAACCCTTCTAGCCTTGAGTTAT
52405 GATGCAAATGATGTGCCC
66 GATGCAAATGATGTGCCC
*
52423 TCGAAGCT-AAGTGTAATCGAACTCGAAGGT
1 TTG-AGCTGAA-TGTAATCGAACTCGAAGGT
52453 CTTTCAAGAG
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
83 77 0.78
84 22 0.22
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.31
Consensus pattern (83 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTATTGGATGACAGATAACCCTTCTAGCCTTGAGTTAT
GATGCAAATGATGTGCCC
Found at i:52586 original size:67 final size:66
Alignment explanation
Indices: 52454--52670 Score: 249
Period size: 67 Copynumber: 3.2 Consensus size: 66
52444 CTCGAAGGTC
* * * * * * * *
52454 TTTCAAGAGAAACATTTTCAAAGGTTTTTTTGTGTTTCAAGAGAAAAAATTTCAAAGGTGGCAAA
1 TTTCAAGAGAAACATATTCAAA-G---ATTTGTGTTTCAAGAGAAACAGTCTCAAGGGAGACAAA
52519 ATTTTG
62 A-TTTG
*
52525 TTTCAAGAGAAACATATTCAAAGATTTGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTT
1 TTTCAAGAGAAACATATTCAAAGATTTGTGTTTCAAGAGAAACAGTCTCAAGGGAGACAAAA-TT
52590 TG
65 TG
* * *
52592 TTTCAA-AGAAAACAGATTCAAAGATTT-TGTTTCAAGGGAAACAGTCTCAAGAGAGACAAAATT
1 TTTCAAGAG-AAACATATTCAAAGATTTGTGTTTCAAGAGAAACAGTCTCAAGGGAGACAAAATT
52655 TG
65 TG
52657 TTTCAAGAGAAACA
1 TTTCAAGAGAAACA
52671 AAACTTAGTT
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
65 15 0.12
66 35 0.27
67 58 0.45
70 1 0.01
71 21 0.16
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (66 bp):
TTTCAAGAGAAACATATTCAAAGATTTGTGTTTCAAGAGAAACAGTCTCAAGGGAGACAAAATTT
G
Found at i:52691 original size:22 final size:21
Alignment explanation
Indices: 52647--52691 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
52637 CTCAAGAGAG
* * *
52647 ACAAAATTTGTTTCAAGAGAA
1 ACAAAATTAGTTCCAAAAGAA
52668 ACAAAACTTAGTTCCAAAAGAA
1 ACAAAA-TTAGTTCCAAAAGAA
52690 AC
1 AC
52692 TGTCTCAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.51, C:0.16, G:0.11, T:0.22
Consensus pattern (21 bp):
ACAAAATTAGTTCCAAAAGAA
Found at i:52782 original size:123 final size:124
Alignment explanation
Indices: 52562--52792 Score: 419
Period size: 123 Copynumber: 1.9 Consensus size: 124
52552 GTGTTTCAAG
*
52562 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGAAAACAGATTCAAAGATTTTGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAA
52627 GGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAAACTTAGTTCCAAA
66 GGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAAACTTAGTTCCAAA
* *
52686 AGAAACTGTCTCAAGGGAGACGAAA-TTTGTTTCAAGGAAAACAAATTCAAAGATTTTGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAA
*
52750 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
66 GGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAC
52793 TGTCTTAAGG
Statistics
Matches: 103, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
123 79 0.77
124 24 0.23
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (124 bp):
AGAAACTGTCTCAAGGGAGACAAAACTTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAA
GGGAAACAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAAACTTAGTTCCAAA
Found at i:52792 original size:36 final size:36
Alignment explanation
Indices: 52740--53029 Score: 382
Period size: 36 Copynumber: 8.2 Consensus size: 36
52730 ATTCAAAGAT
52740 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * **
52776 TTTGTTTCAAGAGAAACTGTCTTAAGGGAGATGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
52812 TTTGTTTCAA-GGAAAATAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACT-G-TCTCAAGAGAGACAAAA
*
52841 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
52877 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
52913 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
52949 CTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
52986 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
53022 CTTTGTTT
1 -TTTGTTT
53030 TAAGTAAATT
Statistics
Matches: 223, Mismatches: 18, Indels: 25
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.00
29 13 0.06
30 7 0.03
31 1 0.00
32 2 0.01
33 2 0.01
35 6 0.03
36 148 0.66
37 43 0.19
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:52804 original size:101 final size:101
Alignment explanation
Indices: 52659--53029 Score: 465
Period size: 101 Copynumber: 3.6 Consensus size: 101
52649 AAAATTTGTT
* * * * * *
52659 TCAAGAGAAACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGA
1 TCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA
52724 AAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTC
65 AAACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTC
* * **
52761 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTTAAGGGAGATGAAATTTGTTTCAAGGAA
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAA
* * *
52826 AATAGATTCAAAGATTTTGTTTCAAGGGAAACTATC
66 AACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTC
*
52862 TCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGA
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GA
* ** *
52927 AACTGTCTCAAGAGAGACAAA-ACTTTGTTTCAAGGGAAACTGTC
65 AA-----AC-A-A-ATTCAAAGATTTTGTTTCAAGGGAAACTGTC
*
52971 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTT
1 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTT
53030 TAAGTAAATT
Statistics
Matches: 236, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
101 135 0.57
102 18 0.08
108 1 0.00
109 70 0.30
110 12 0.05
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (101 bp):
TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAA
AACAAATTCAAAGATTTTGTTTCAAGGGAAACTGTC
Found at i:53083 original size:73 final size:73
Alignment explanation
Indices: 52841--53029 Score: 353
Period size: 73 Copynumber: 2.6 Consensus size: 73
52831 ATTCAAAGAT
*
52841 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
52905 AGACAAAA
66 AGACAAAA
*
52913 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
52978 AGACAAAA
66 AGACAAAA
52986 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTT
53030 TAAGTAAATT
Statistics
Matches: 113, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
72 34 0.30
73 79 0.70
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (73 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAG
AGACAAAA
Found at i:56506 original size:218 final size:218
Alignment explanation
Indices: 56119--56555 Score: 784
Period size: 218 Copynumber: 2.0 Consensus size: 218
56109 TATTTAAAGG
* * *
56119 TACATTCGGACTAAATCTTTTAAACCAGAAACAAGTTGACTAGTCTTATCCCTTCATCTGTCACT
1 TACATCCGAACTAAATCTTTTAAACCAGAAACAAGTTGACTAGTCTTATCCCTTCATCTGTCACC
*
56184 GGTCGAATACCCTGCCGAACTGCTCCGGCTTCTCTGGCCAAACCGTGCAAGTGACGAGCTGTTTT
66 GGTCGAATACCCTGCCGAACCGCTCCGGCTTCTCTGGCCAAACCGTGCAAGTGACGAGCTGTTTT
*
56249 TTGTACATGTTTCCAGAAGTATCGAATGACTGCATCTCTAGCTTTTATCATTTGCTGAACCTATT
131 TTGTACATGTTTCCAGAAGTATCGAATGACTACATCTCTAGCTTTTATCATTTGCTGAACCTATT
56314 CTATAACGGAAACACCATTGAAA
196 CTATAACGGAAACACCATTGAAA
56337 TACATCCGAACTAAATCTTTTAAACCAGAAACAAGTTGACTAGTCTTATCCCTTCATCTGTCACC
1 TACATCCGAACTAAATCTTTTAAACCAGAAACAAGTTGACTAGTCTTATCCCTTCATCTGTCACC
* *
56402 GGTCGAATACCCTGCCGAACCGCTCTGGCTTCTCTGGCCAAACCGTGCAAGTGACGAGTTGTTTT
66 GGTCGAATACCCTGCCGAACCGCTCCGGCTTCTCTGGCCAAACCGTGCAAGTGACGAGCTGTTTT
* * *
56467 TTGTACATGTTTCCAGAAGTATCGAATGACTACATCTCTAGCTTTTATCTTTTGTTGAACCTGTT
131 TTGTACATGTTTCCAGAAGTATCGAATGACTACATCTCTAGCTTTTATCATTTGCTGAACCTATT
56532 CTATAACGGAAACACCATTGAAA
196 CTATAACGGAAACACCATTGAAA
56555 T
1 T
56556 CCTCCATCAA
Statistics
Matches: 209, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 209 1.00
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (218 bp):
TACATCCGAACTAAATCTTTTAAACCAGAAACAAGTTGACTAGTCTTATCCCTTCATCTGTCACC
GGTCGAATACCCTGCCGAACCGCTCCGGCTTCTCTGGCCAAACCGTGCAAGTGACGAGCTGTTTT
TTGTACATGTTTCCAGAAGTATCGAATGACTACATCTCTAGCTTTTATCATTTGCTGAACCTATT
CTATAACGGAAACACCATTGAAA
Found at i:58151 original size:4 final size:4
Alignment explanation
Indices: 58144--58297 Score: 56
Period size: 4 Copynumber: 38.8 Consensus size: 4
58134 ATAGTAAGTA
* * * *
58144 AAAT AAAT AAAT AAAT ATAT AAA- AAAT AAAG AAAA AGAAG AAA- AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT
* * * *
58191 ATAT AAAT AAAAC AAAT -AAT -AAT -AAT -AAT AAAGT AAAAT TAAT ATAT
1 AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA-T -AAAT AAAT AAAT
* * *
58238 ATAT ATAT AAAAT AAAT AAA- AACAT AAA- AAAT -AGT AAAT ATATAT
1 AAAT AAAT -AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT A-A-AT
* *
58283 ATAT AAAT TAAT AAA
1 AAAT AAAT AAAT AAA
58298 ACAGATAATA
Statistics
Matches: 117, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
3 25 0.21
4 72 0.62
5 14 0.12
6 6 0.05
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:58240 original size:47 final size:49
Alignment explanation
Indices: 58189--58315 Score: 131
Period size: 47 Copynumber: 2.7 Consensus size: 49
58179 AGAAGAAAAA
*
58189 ATATATAAATAAAACAAATAATAATAATAATAAAGTA-AAAT-TA-ATAT
1 ATATATAAATAAAACAAATAATAA-AATAATAAAATAGAAATATATATAT
* *
58236 ATATATATATAAAATAAATAA-AAACATAA-AAAATAGTAAATATATATAT
1 ATATATAAATAAAACAAATAATAAA-ATAATAAAATAG-AAATATATATAT
* * *
58285 ATAAATTAATAAAACAGATAATAAAA-AATAA
1 ATATATAAATAAAACAAATAATAAAATAATAA
58316 CATATAATCT
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
45 6 0.09
46 6 0.09
47 23 0.35
48 4 0.06
49 23 0.35
50 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (49 bp):
ATATATAAATAAAACAAATAATAAAATAATAAAATAGAAATATATATAT
Found at i:58247 original size:26 final size:23
Alignment explanation
Indices: 58188--58256 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
58178 AAGAAGAAAA
58188 AATATATAAATAAAACAAATAAT
1 AATATATAAATAAAACAAATAAT
58211 AATA-AT-AATAAAGTA-AAATTAAT
1 AATATATAAATAAA--ACAAA-TAAT
* *
58234 ATATATATATATAAAATAAATAA
1 A-ATATATAAATAAAACAAATAA
58257 AAACATAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
21 6 0.16
22 5 0.13
23 10 0.26
24 7 0.18
25 5 0.13
26 5 0.13
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (23 bp):
AATATATAAATAAAACAAATAAT
Found at i:58251 original size:43 final size:40
Alignment explanation
Indices: 58143--58298 Score: 117
Period size: 41 Copynumber: 3.8 Consensus size: 40
58133 AATAGTAAGT
* * *
58143 AAAATAAATAAATAAATATATAAAA-AATAAAGAAAAAGAAG
1 AAAATTAATATATAAATATATAAAATAATAAA-AAATA-AAG
*
58184 AAAA--AATATATAAATA-AAACAAATAATAATAATAATAAAG
1 AAAATTAATATATAAATATATA-AAATAATAA-AA-AATAAAG
*
58224 TAAAATTAATATATATATATATAAAATAAATAAAAACATAAA-
1 -AAAATTAATATATAAATATATAAAAT-AATAAAAA-ATAAAG
* * *
58266 AAATAGTAA-ATATATATATATAAATTAATAAAA
1 AAA-ATTAATATATAAATATATAAAATAATAAAA
58299 CAGATAATAA
Statistics
Matches: 97, Mismatches: 7, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
38 2 0.02
39 14 0.14
40 16 0.16
41 31 0.32
42 5 0.05
43 22 0.23
44 7 0.07
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (40 bp):
AAAATTAATATATAAATATATAAAATAATAAAAAATAAAG
Found at i:58350 original size:20 final size:20
Alignment explanation
Indices: 58306--58359 Score: 51
Period size: 20 Copynumber: 2.7 Consensus size: 20
58296 AAACAGATAA
*
58306 TAAAAAAT-AACATATAATC
1 TAAAAAATAAAAATATAATC
58325 TAAAAAAATAAAAATAT-ATAC
1 T-AAAAAATAAAAATATAAT-C
58346 TAAAATAA-AAAAAT
1 TAAAA-AATAAAAAT
58360 GCATAAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.03
20 19 0.63
21 10 0.33
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAAAAATAAAAATATAATC
Found at i:58943 original size:39 final size:39
Alignment explanation
Indices: 58852--58962 Score: 172
Period size: 39 Copynumber: 2.9 Consensus size: 39
58842 CTTGTGGATT
* * *
58852 CTATTTTTAGGAGTTTAAATCATAGTAGAACTC--TATC
1 CTATTTTTAGGAGTTTAAATCCTAATAAAACTCTATATC
58889 CTATTTTTAGGAGTTTAAATCCTAATAAAACTCTATATC
1 CTATTTTTAGGAGTTTAAATCCTAATAAAACTCTATATC
*
58928 CTATTTTTAGAAGTTTAAATCCTAATAAAACTCTA
1 CTATTTTTAGGAGTTTAAATCCTAATAAAACTCTA
58963 ACATTATGTT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
37 30 0.44
39 38 0.56
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (39 bp):
CTATTTTTAGGAGTTTAAATCCTAATAAAACTCTATATC
Found at i:58951 original size:21 final size:21
Alignment explanation
Indices: 58886--58951 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
58876 GTAGAACTCT
*
58886 ATCCTATTTTTAGGAGTTTAA
1 ATCCTATTTTTAGAAGTTTAA
* * * * *
58907 ATCCTA---ATAAAACTCTAT
1 ATCCTATTTTTAGAAGTTTAA
58925 ATCCTATTTTTAGAAGTTTAA
1 ATCCTATTTTTAGAAGTTTAA
58946 ATCCTA
1 ATCCTA
58952 ATAAAACTCT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 12 0.39
21 19 0.61
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (21 bp):
ATCCTATTTTTAGAAGTTTAA
Found at i:59785 original size:2 final size:2
Alignment explanation
Indices: 59778--59835 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
59768 TACAAAGAAA
59778 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59820 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
59836 TAGATCTACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.