Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000837.1 Hibiscus syriacus cultivar Beakdansim tig00001618_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: 96872
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4622 original size:77 final size:78
Alignment explanation
Indices: 4472--4709 Score: 365
Period size: 78 Copynumber: 3.0 Consensus size: 78
4462 GGGGCCTATA
4472 GGCCTACCCAAGGATACCCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
1 GGCCTACCCAAGGATA-CCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
4537 TAAGATATACCTTG
65 TAAGATATACCTTG
* * *
4551 GGCTTA-CCAAGGATATCCTTAGATCCGTA-GGTTACCTTAAGCATACAACAAA-GAAACCAACC
1 GGCCTACCCAAGGATA-CCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
4613 TAAGTATATACCTTG
65 TAAG-ATATACCTTG
4628 GGCCTACCCAAGGATACCATTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
1 GGCCTACCCAAGGATACC-TTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACC
* *
4693 TAAAAATATGCCTTG
65 T-AAGATATACCTTG
4708 GG
1 GG
4710 TGCTATAAGC
Statistics
Matches: 144, Mismatches: 9, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
76 14 0.10
77 39 0.27
78 40 0.28
79 27 0.19
80 22 0.15
81 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.21
Consensus pattern (78 bp):
GGCCTACCCAAGGATACCTTAGATCCATAGGGTTACCTTAAGCACACAACAAAGGAAACCAACCT
AAGATATACCTTG
Found at i:7296 original size:22 final size:22
Alignment explanation
Indices: 7270--7320 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
7260 AGTCAACGCC
7270 GGTCAACGCCTGTCAAAGTTCT
1 GGTCAACGCCTGTCAAAGTTCT
*
7292 GGTCAAAGCCTGTCAAAGTTCT
1 GGTCAACGCCTGTCAAAGTTCT
7314 GGTCAAC
1 GGTCAAC
7321 AGTGGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (22 bp):
GGTCAACGCCTGTCAAAGTTCT
Found at i:7298 original size:12 final size:12
Alignment explanation
Indices: 7281--7319 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
7271 GTCAACGCCT
7281 GTCAAAGTTCTG
1 GTCAAAGTTCTG
*
7293 GTCAAAG-CCT-
1 GTCAAAGTTCTG
7303 GTCAAAGTTCTG
1 GTCAAAGTTCTG
7315 GTCAA
1 GTCAA
7320 CAGTGGTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 7 0.30
11 4 0.17
12 12 0.52
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (12 bp):
GTCAAAGTTCTG
Found at i:8868 original size:42 final size:43
Alignment explanation
Indices: 8816--8927 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 43
8806 AAAAACGCCA
* * *
8816 CAAAAGGTGAAGACCTTTAGTGG-CGTTTTTATACAAATGTGG
1 CAAAAGGTGAAGACCTATAGCGGAAGTTTTTATACAAATGTGG
* *
8858 CAAAAGGTGAAGATCTATAGCGGAATTTTTTATACAAA--T-G
1 CAAAAGGTGAAGACCTATAGCGGAAGTTTTTATACAAATGTGG
* * *
8898 CAAAAGGTCAAGATCTATAGC-GACGTTTTT
1 CAAAAGGTGAAGACCTATAGCGGAAGTTTTT
8928 GTTAAAAACA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
39 7 0.11
40 21 0.34
41 1 0.02
42 20 0.33
43 12 0.20
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.30
Consensus pattern (43 bp):
CAAAAGGTGAAGACCTATAGCGGAAGTTTTTATACAAATGTGG
Found at i:8927 original size:40 final size:42
Alignment explanation
Indices: 8841--8919 Score: 126
Period size: 40 Copynumber: 1.9 Consensus size: 42
8831 TTTAGTGGCG
*
8841 TTTTTATACAAATGTGGCAAAAGGTGAAGATCTATAGCGGAAT
1 TTTTTATACAAA-GTGGCAAAAGGTCAAGATCTATAGCGGAAT
8884 TTTTTATACAAA-T-GCAAAAGGTCAAGATCTATAGCG
1 TTTTTATACAAAGTGGCAAAAGGTCAAGATCTATAGCG
8920 ACGTTTTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
40 22 0.63
41 1 0.03
43 12 0.34
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (42 bp):
TTTTTATACAAAGTGGCAAAAGGTCAAGATCTATAGCGGAAT
Found at i:13088 original size:20 final size:20
Alignment explanation
Indices: 13059--13113 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
13049 CTAACATAAC
13059 CCTT-GGTATCGATACCAAG
1 CCTTCGGTATCGATACCAAG
13078 CCTTCGGTATCGATACCAAG
1 CCTTCGGTATCGATACCAAG
13098 CCTTCGGTATCGATAC
1 CCTTCGGTATCGATAC
13114 TACTCTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.11
20 31 0.89
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (20 bp):
CCTTCGGTATCGATACCAAG
Found at i:13303 original size:20 final size:20
Alignment explanation
Indices: 13278--13326 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
13268 GTGATCCCGA
13278 TATCGATACC-ACCCTA-TAGG
1 TATCGATACCAACCC-AGTA-G
13298 TATCGATACCAACCCAGTAG
1 TATCGATACCAACCCAGTAG
13318 TATCGATAC
1 TATCGATAC
13327 TCTTTTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (20 bp):
TATCGATACCAACCCAGTAG
Found at i:14859 original size:22 final size:22
Alignment explanation
Indices: 14831--14873 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
14821 GTAAGATGAT
*
14831 AAGTCCTCCAAGCTATCTATAC
1 AAGTCCTCCAAGCCATCTATAC
*
14853 AAGTCCTCCGAGCCATCTATA
1 AAGTCCTCCAAGCCATCTATA
14874 AGACATCCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.33, G:0.12, T:0.26
Consensus pattern (22 bp):
AAGTCCTCCAAGCCATCTATAC
Found at i:15052 original size:44 final size:44
Alignment explanation
Indices: 14984--15143 Score: 135
Period size: 44 Copynumber: 3.6 Consensus size: 44
14974 CAAAAGATTC
* ** * *
14984 GATTCCATCATAGAAGTTGGTGGATCAACATTCCCTTTTTGCTA
1 GATTCCATCACAGAAGGAGATGGATCAACATTCCCTTTTTACTA
* * * * *
15028 GATTCCATCACATAAGGAGTTGGATCAACA-TCACCATTTTATTC
1 GATTCCATCACAGAAGGAGATGGATCAACATTC-CCTTTTTACTA
* * * *
15072 GATTCCATCACAGAAGGAGATGAATCAACATTCCTTTTTTTCTT
1 GATTCCATCACAGAAGGAGATGGATCAACATTCCCTTTTTACTA
* * *
15116 GCA-GCCATCACAGAAGGAGGTGAATCAA
1 G-ATTCCATCACAGAAGGAGATGGATCAA
15144 TATTTCAATA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
43 2 0.02
44 89 0.95
45 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
GATTCCATCACAGAAGGAGATGGATCAACATTCCCTTTTTACTA
Found at i:15133 original size:88 final size:88
Alignment explanation
Indices: 14980--15143 Score: 204
Period size: 88 Copynumber: 1.9 Consensus size: 88
14970 TTTTCAAAAG
* ** * * * *
14980 ATTCGATTCCATCATAGAAGTTGGTGGATCAACATTCCCTTTTTGCTAGATTCCATCACATAAGG
1 ATTCGATTCCATCACAGAAGGAGATGAATCAACATTCCCTTTTTGCTAGATGCCATCACAGAAGG
* *
15045 AGTTGGATCAACATCACCATTTT
66 AGGTGAATCAACATCACCATTTT
* * *
15068 ATTCGATTCCATCACAGAAGGAGATGAATCAACATTCCTTTTTTTCTTGCA-GCCATCACAGAAG
1 ATTCGATTCCATCACAGAAGGAGATGAATCAACATTCCCTTTTTGCTAG-ATGCCATCACAGAAG
15132 GAGGTGAATCAA
65 GAGGTGAATCAA
15144 TATTTCAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
88 62 0.98
89 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (88 bp):
ATTCGATTCCATCACAGAAGGAGATGAATCAACATTCCCTTTTTGCTAGATGCCATCACAGAAGG
AGGTGAATCAACATCACCATTTT
Found at i:15321 original size:118 final size:118
Alignment explanation
Indices: 15178--15596 Score: 423
Period size: 118 Copynumber: 3.6 Consensus size: 118
15168 AGAAGGATGT
* * * * **
15178 AACTCGTCCACAGAGGAAGAAGAAGTTCATAATAATAAGAACTTTTTTGACCTTTTGCTCAAATC
1 AACTCGTCCACGGAGGAAGAAGAAGTTCATAATGATAAAAACTTTTTCGACCTTTCACTCAAATC
* * **
15243 TATCACAGAATGAGGTAGATTAACATTTCAAATGAG-GTGTTCATAATGGGA-A
66 TATCACAGAAAGAGGTAGATTAACATTTCAAATG-GTGAGTTCATAATAAGAGA
* * * *
15295 GAACTCGTCCACGGAGAAAGAAGAAGTTCATAATGAGAATAACTTTTTCGTCCTTTCACTCAAAT
1 -AACTCGTCCACGGAGGAAGAAGAAGTTCATAATGATAAAAACTTTTTCGACCTTTCACTCAAAT
* * *
15360 CCATCACAGAAAGAGGTTGATTAACATTTCAAATGGTGAGTTCATACTAAGAGA
65 CTATCACAGAAAGAGGTAGATTAACATTTCAAATGGTGAGTTCATAATAAGAGA
** * *
15414 AACTCGTCCACGGAGGGGGGAA-AAGTTCATAATGATAAAAACTTGTTCAACCTTTCACTCAAAT
1 AACTCGTCCACGGA-GGAAGAAGAAGTTCATAATGATAAAAACTTTTTCGACCTTTCACTCAAAT
* * * * * * * *
15478 CTAGCACATAAGGAAGTGGATTAACATTTCAAATGG-GAAGTTTATAGTAAGAGG
65 CTATCACAGAAAGAGGTAGATTAACATTTCAAATGGTG-AGTTCATAATAAGAGA
* * * * * * * * * *
15532 AACTCATCAATGGAGGAATAAGAAGTTTATAATGAGAAGAATTTTTTCGACTTTTCACTAAAATC
1 AACTCGTCCACGGAGGAAGAAGAAGTTCATAATGATAAAAACTTTTTCGACCTTTCACTCAAATC
15597 CATTATAAAA
Statistics
Matches: 249, Mismatches: 47, Indels: 10
0.81 0.15 0.03
Matches are distributed among these distances:
117 6 0.02
118 238 0.96
119 5 0.02
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (118 bp):
AACTCGTCCACGGAGGAAGAAGAAGTTCATAATGATAAAAACTTTTTCGACCTTTCACTCAAATC
TATCACAGAAAGAGGTAGATTAACATTTCAAATGGTGAGTTCATAATAAGAGA
Found at i:18676 original size:4 final size:4
Alignment explanation
Indices: 18669--18696 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
18659 GCTTGCTTAC
18669 TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT
18697 AGATTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:21832 original size:3 final size:3
Alignment explanation
Indices: 21826--21885 Score: 90
Period size: 3 Copynumber: 20.7 Consensus size: 3
21816 TAATATTTAT
21826 TAA TAA TAA -AA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
21872 TAA T-A TAAA TAA TA
1 TAA TAA T-AA TAA TA
21886 TTTAAATGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.11
3 45 0.85
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:22200 original size:38 final size:38
Alignment explanation
Indices: 22125--22223 Score: 171
Period size: 38 Copynumber: 2.6 Consensus size: 38
22115 TTGAATAAGC
22125 TCTTCTCATTATGAACTTCTTCTTTCTTTTTCAGATGAGT
1 TCTTCTCATTATGAAC-T-TTCTTTCTTTTTCAGATGAGT
*
22165 TCTTCTCATTATGAACTTTCTTTCTTTTTCTGATGAGT
1 TCTTCTCATTATGAACTTTCTTTCTTTTTCAGATGAGT
22203 TCTTCTCATTATGAACTTTCT
1 TCTTCTCATTATGAACTTTCT
22224 CTGGAAAGGT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
38 41 0.71
39 1 0.02
40 16 0.28
ACGTcount: A:0.17, C:0.20, G:0.09, T:0.54
Consensus pattern (38 bp):
TCTTCTCATTATGAACTTTCTTTCTTTTTCAGATGAGT
Found at i:22292 original size:162 final size:158
Alignment explanation
Indices: 22020--22343 Score: 438
Period size: 162 Copynumber: 2.0 Consensus size: 158
22010 GTTTAATAAA
* *
22020 TTCTTCTCTTTCTTCTGATGAGTTCTTCTCATTATGAACTTTCCGCTCGGGATGATGTTGACCTA
1 TTCTTCTCTTTCTTCTGATGAGTTCTTCTCATTATGAACTTTCCGCTCGGGATGATGCTAACCTA
* * * * *
22085 TTTCCTTCTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTT
66 TCTCCTTATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC-TT
22150 CTTTTTCAGATGAGTTCTTCTCATTATGAACT
130 C---TTCAGATGAGTTCTTCTCATTATGAACT
* * * *
22182 TTCTT-TCTTT-TTCTGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGTTGATGCTAAT
1 TTCTTCTCTTTCTTCTGATGAGTTCTTCTCATTATGAACTTTCCGCTCG---GGATGATGCTAAC
* * *
22244 CTATCTCTTTATGTGATAGAATTATGCAAAAGGTTGAACAAGCTCTTCTCATTGTGAACTTCTTC
63 CTATCTCCTTATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTC
22309 TTCTTCAGATGAGTTCTTCTCATTATGAACT
128 TTCTTCAGATGAGTTCTTCTCATTATGAACT
22340 TTCT
1 TTCT
22344 CTGGAAAATC
Statistics
Matches: 145, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
158 32 0.22
159 4 0.03
160 30 0.21
161 8 0.06
162 71 0.49
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (158 bp):
TTCTTCTCTTTCTTCTGATGAGTTCTTCTCATTATGAACTTTCCGCTCGGGATGATGCTAACCTA
TCTCCTTATGTGATAGAATCATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
TTCAGATGAGTTCTTCTCATTATGAACT
Found at i:22473 original size:115 final size:112
Alignment explanation
Indices: 22269--22567 Score: 383
Period size: 116 Copynumber: 2.7 Consensus size: 112
22259 ATAGAATTAT
** *
22269 GCAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTC-TTCTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
* * * * *
22331 TTATGAACTTTCTCTGGAAAATCTGATCCATTAAGTGATGGATT-TA
66 TTATGAACTTTCCCTGGAAAATCTGATCCATCAAATGATGAATTCAA
*
22377 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTGTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGAT---GAGTTCTT
* *
22442 CTCATTATGAACTTTCCCTGG-CAATGTTGATCCATCAAATGATGAATTCAA
62 CTCATTATGAACTTTCCCTGGAAAAT-CTGATCCATCAAATGATGAATTCAA
* * *
22493 ACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTTTCTTCTTCAGATGAGTTCTTCTC
22558 ATTATGAACT
65 ATTATGAACT
22568 CGAACTGGAA
Statistics
Matches: 166, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
108 30 0.18
111 3 0.02
112 13 0.08
113 21 0.13
114 3 0.02
115 46 0.28
116 50 0.30
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTTCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCCCTGGAAAATCTGATCCATCAAATGATGAATTCAA
Found at i:22541 original size:116 final size:110
Alignment explanation
Indices: 22270--22567 Score: 377
Period size: 115 Copynumber: 2.7 Consensus size: 110
22260 TAGAATTATG
** *
22270 CAAAAGGTTGAACAAGCTCTTCTCATTGTGAA--CTTCTTCTTCTTCAGATGAGTTCTTCTCATT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
22333 ATGAACTTTCTCTGGAAAATCTGATCCATTAAGTGATGGATTTAG
66 ATGAACTTTCCCTGGAAAATCTGATCCATCAAATGATGAATTAAA
*
22378 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTGTTCTTTCTTCTTCAGATGACGAGTTCTTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTC-TTCTTCTTCAGAT---GAGTTCTTC
* *
22443 TCATTATGAACTTTCCCTGG-CAATGTTGATCCATCAAATGATGAATTCAAA
61 TCATTATGAACTTTCCCTGGAAAAT-CTGATCCATCAAATGATGAATT-AAA
*
22494 CAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAA-TTCTTCTT-CTTCTTCAGATGAGTTCTTCTCA
22559 TTATGAACT
64 TTATGAACT
22568 CGAACTGGAA
Statistics
Matches: 165, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
108 29 0.18
111 3 0.02
112 13 0.08
113 21 0.13
114 3 0.02
115 48 0.29
116 48 0.29
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (110 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAATTCTTCTTCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCCCTGGAAAATCTGATCCATCAAATGATGAATTAAA
Found at i:23740 original size:114 final size:115
Alignment explanation
Indices: 23540--23991 Score: 759
Period size: 114 Copynumber: 4.0 Consensus size: 115
23530 GATCATGCAG
* * * * *
23540 TTCATCTTTCAATTCTAATGATTGG-TTCTAT-GGTTCCTACCAAATCAGATCAGATAACTCAAA
1 TTCATCTTTCAAATCCAATGATTGGCTT-TTTGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
23603 GAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
65 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
*
23654 TTCATCTTTCAAATCCAATGATTGG-TTTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGCTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
23718 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* * *
23768 TTCATCTTTTAAATCCAATGATTGGCTTTTAGGGTTTATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGCTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
23833 AACACTTCCA-AAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* *
23882 TTCATCTTTTAAATCCAATGATTGGCTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGGCTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
23947 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGA
66 AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGA
23992 TAACGTGGTA
Statistics
Matches: 324, Mismatches: 11, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
113 2 0.01
114 242 0.75
115 80 0.25
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (115 bp):
TTCATCTTTCAAATCCAATGATTGGCTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:23939 original size:229 final size:228
Alignment explanation
Indices: 23540--23991 Score: 771
Period size: 229 Copynumber: 2.0 Consensus size: 228
23530 GATCATGCAG
* * * * *
23540 TTCATCTTTCAATTCTAATGATTGGTTCTATGGTTCCTACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
23605 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
* *
23670 AATGATTGGTTTTTGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
23735 CTATTGGGTCTTCTTATTTCTACTATGAGCAAA
196 CTATTGGGTCTTCTTATTTCTACTATGAGCAAA
* * *
23768 TTCATCTTTTAAATCCAATGATTGGCTTTTAGGGTTTATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAG
* *
23833 AACACTTCCA-AAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTCATCTTTTAAATC
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATC
23897 CAATGATTGGCTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
130 CAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGA
23962 TGCTATTGGGTCTTCTTATTTCTACTATGA
194 TGCTATTGGGTCTTCTTATTTCTACTATGA
23992 TAACGTGGTA
Statistics
Matches: 210, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
228 84 0.40
229 126 0.60
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (228 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTAGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAATTCATCTTTCAAATCC
AATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTATTGGGTCTTCTTATTTCTACTATGAGCAAA
Found at i:24309 original size:19 final size:17
Alignment explanation
Indices: 24285--24333 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 17
24275 AAAATAAAAG
24285 AATAAATTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
24304 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
24320 AATAAATTGAATTT
1 AATAAATTGAATTT
24334 AAAGAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 3 0.11
19 11 0.41
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:35328 original size:26 final size:28
Alignment explanation
Indices: 35298--35355 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
35288 AAACATTAAT
*
35298 AAAATAAT-A-TACATATAAATATTATG
1 AAAATAATAAGTACATATAAAAATTATG
* *
35324 AAAATAATAAGTATATATAAAAATTTTG
1 AAAATAATAAGTACATATAAAAATTATG
35352 AAAA
1 AAAA
35356 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 8 0.30
27 1 0.04
28 18 0.67
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AAAATAATAAGTACATATAAAAATTATG
Found at i:35868 original size:28 final size:29
Alignment explanation
Indices: 35837--35892 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
35827 ATTTCAAAAT
35837 TATAATTATAAA-AAAATATTAATTTATA
1 TATAATTATAAATAAAATATTAATTTATA
* *
35865 TATATTTATAAATAAAATATTTATTTAT
1 TATAATTATAAATAAAATATTAATTTAT
35893 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (29 bp):
TATAATTATAAATAAAATATTAATTTATA
Found at i:36590 original size:34 final size:34
Alignment explanation
Indices: 36552--36616 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
36542 AATAAATAAA
* *
36552 ATTTAGAGACCAAATTGAAAGGATTATAAATTTG
1 ATTTAGAGACCAAAATGAAAGGATTACAAATTTG
* * *
36586 ATTTAGTGACTAAAATGTAAGGATTACAAAT
1 ATTTAGAGACCAAAATGAAAGGATTACAAAT
36617 CTAAGGGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (34 bp):
ATTTAGAGACCAAAATGAAAGGATTACAAATTTG
Found at i:37585 original size:3 final size:3
Alignment explanation
Indices: 37572--37629 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
37562 TTATATCTAT
*
37572 TAA TAA T-A TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37619 T-A TAAA TAA TA
1 TAA T-AA TAA TA
37630 TTTAAATGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.88
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:42795 original size:18 final size:18
Alignment explanation
Indices: 42773--42808 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42763 CTAACATGAC
*
42773 ATTTTT-AATTATTTTTT
1 ATTTTTAAATTATTATTT
42790 ATTTTTAAATTATTATTT
1 ATTTTTAAATTATTATTT
42808 A
1 A
42809 ATTAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTAAATTATTATTT
Found at i:44801 original size:20 final size:20
Alignment explanation
Indices: 44773--44827 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
44763 ACCTGCACAT
*
44773 TTGGCATCGATACCGGAAAG
1 TTGGTATCGATACCGGAAAG
44793 TTGGTATCGATACCGGAAAG
1 TTGGTATCGATACCGGAAAG
44813 TTGGTATCGATACCG
1 TTGGTATCGATACCG
44828 ACCATCCTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGGTATCGATACCGGAAAG
Found at i:45834 original size:17 final size:18
Alignment explanation
Indices: 45800--45834 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
45790 AAACATATTT
45800 GAACAAAATTCATTATGAC
1 GAACAAAATT-ATTATGAC
45819 GAACAAAATT-TTATGA
1 GAACAAAATTATTATGA
45835 AAAATCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
GAACAAAATTATTATGAC
Found at i:50875 original size:45 final size:44
Alignment explanation
Indices: 50746--50887 Score: 142
Period size: 45 Copynumber: 3.2 Consensus size: 44
50736 TAAAAAATCC
* *
50746 TTTGATTTTAATTTTCGCAACCCAATAATAAAAATTAACTAATCA
1 TTTGATTTTAATTTT-GCAACCCAATAATAAAAATGAACTAATAA
* * * * * *
50791 TTTGATTTTAATTTCT-AAATCCGAGTAATTAAAAGGAACTGATAA
1 TTTGATTTTAATTT-TGCAA-CCCAATAATAAAAATGAACTAATAA
* **
50836 TTTGATTTTAATTTTGGCAACCCAATAATCAAAATGAACTAATCC
1 TTTGATTTTAATTTT-GCAACCCAATAATAAAAATGAACTAATAA
50881 TTTGATT
1 TTTGATT
50888 CTTTTGGCAA
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
44 3 0.04
45 71 0.92
46 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (44 bp):
TTTGATTTTAATTTTGCAACCCAATAATAAAAATGAACTAATAA
Found at i:54620 original size:29 final size:29
Alignment explanation
Indices: 54585--54666 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
54575 AAACTAAATT
* *
54585 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
54614 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
54643 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
54667 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:59387 original size:29 final size:29
Alignment explanation
Indices: 59352--59438 Score: 129
Period size: 29 Copynumber: 3.0 Consensus size: 29
59342 AAACTAAATT
59352 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTACTTACATCATTTAATTAAA
* *
59381 GATGTCATTACTTACATCATTTAAGTAAT
1 GATGTCATTACTTACATCATTTAATTAAA
* *
59410 GATGTCATTGCTTACATCAATTTAGTTAA
1 GATGTCATTACTTACATC-ATTTAATTAA
59439 GAGAGAGTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
29 44 0.85
30 8 0.15
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTACTTACATCATTTAATTAAA
Found at i:61208 original size:54 final size:52
Alignment explanation
Indices: 61120--61260 Score: 194
Period size: 54 Copynumber: 2.7 Consensus size: 52
61110 TCAGTTTTTT
* * *
61120 CATTTCAGTCATTA-TTTATTTCTGATTTGACTACTGCTCTTTTATTTTATG
1 CATTTTAGTCATTATTTTATTTCTGATTTGGCTACTGCTATTTTATTTTATG
* * *
61171 CATTTTAGTCACTATTTTTTATTTCTTATTTGGCTACTGTTATTTTATTTTATG
1 CATTTTAGTCA-T-TATTTTATTTCTGATTTGGCTACTGCTATTTTATTTTATG
*
61225 CATTTTAGTCATTATTTTGTTTCTGATTTGGCTACT
1 CATTTTAGTCATTATTTTATTTCTGATTTGGCTACT
61261 ATTTTTTGTT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
51 10 0.13
52 22 0.28
53 2 0.03
54 44 0.56
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.57
Consensus pattern (52 bp):
CATTTTAGTCATTATTTTATTTCTGATTTGGCTACTGCTATTTTATTTTATG
Found at i:61239 original size:26 final size:26
Alignment explanation
Indices: 61159--61242 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
61149 ACTACTGCTC
*
61159 TTTTATTTTATGCATTTTAGTCACTA
1 TTTTATTTTATGCATTTTAGTCATTA
* * *
61185 TTTT-TTATT-T-CTTATTTGGCTACTGTTA
1 TTTTATT-TTATGCAT-TTTAG-T-C-ATTA
61213 TTTTATTTTATGCATTTTAGTCATTA
1 TTTTATTTTATGCATTTTAGTCATTA
61239 TTTT
1 TTTT
61243 GTTTCTGATT
Statistics
Matches: 43, Mismatches: 7, Indels: 16
0.65 0.11 0.24
Matches are distributed among these distances:
24 2 0.05
25 7 0.16
26 14 0.33
27 2 0.05
28 9 0.21
29 7 0.16
30 2 0.05
ACGTcount: A:0.19, C:0.10, G:0.08, T:0.63
Consensus pattern (26 bp):
TTTTATTTTATGCATTTTAGTCATTA
Found at i:61371 original size:2 final size:2
Alignment explanation
Indices: 61364--61475 Score: 224
Period size: 2 Copynumber: 56.0 Consensus size: 2
61354 TAGTCCATTA
61364 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
61406 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
61448 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
61476 GCATGTTTCA
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 110 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63770 original size:24 final size:24
Alignment explanation
Indices: 63735--63792 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
63725 TATTCTTTCG
*
63735 CTTCAATTGAGCTCAAATTTTAGA
1 CTTCAATCGAGCTCAAATTTTAGA
*
63759 CTTCAATCGAGCTCAAATTTTAGG
1 CTTCAATCGAGCTCAAATTTTAGA
63783 CTTCAATCGA
1 CTTCAATCGA
63793 ACTTCTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (24 bp):
CTTCAATCGAGCTCAAATTTTAGA
Found at i:67762 original size:50 final size:52
Alignment explanation
Indices: 67690--67827 Score: 154
Period size: 59 Copynumber: 2.6 Consensus size: 52
67680 CACACTCCAA
** *
67690 TTTGCCTTTTCATCACGGCTAGGAGGGTT-GG-TTAGAGCCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
*
67740 TTTTCCTTTTCATTGCGACTAGGAGGGTTTGATAGGACACTTAGAGCCATATTATCGAG
1 TTTGCCTTTTCATTGCGACTAGGAGGG--T--TAGG--A-TTAGAGCCATATTATCGAG
*
67799 TTTGCCTTTTCATTGCAACTAGGAGGGTT
1 TTTGCCTTTTCATTGCGACTAGGAGGGTT
67828 CGATAGGACA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
50 23 0.32
52 1 0.01
54 1 0.01
55 3 0.04
57 1 0.01
59 44 0.60
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.36
Consensus pattern (52 bp):
TTTGCCTTTTCATTGCGACTAGGAGGGTTAGGATTAGAGCCATATTATCGAG
Found at i:67813 original size:59 final size:59
Alignment explanation
Indices: 67721--67841 Score: 215
Period size: 59 Copynumber: 2.1 Consensus size: 59
67711 GGAGGGTTGG
* * *
67721 TTAGAGCCATATTATCGAGTTTTCCTTTTCATTGCGACTAGGAGGGTTTGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
67780 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
67839 TTA
1 TTA
67842 TCCATCTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCAACTAGGAGGGTTCGATAGGACAC
Found at i:72252 original size:50 final size:54
Alignment explanation
Indices: 72182--72314 Score: 141
Period size: 59 Copynumber: 2.4 Consensus size: 54
72172 CACACTCCAA
* * *
72182 TTTGCCTTTTCATCGTGACTAGGAGGG-T-T-GG-TTAGAGCCATATTATCGAG
1 TTTGTCTTTTCATTGCGACTAGGAGGGTTATAGGATTAGAGCCATATTATCGAG
72232 TTTGTCTTTTCATTGCGACTAGGAGGGTTAGATAGGACACTTAGAGCCATATTATCGAG
1 TTTGTCTTTTCATTGCGACTAGGAGGGTT--ATAGG--A-TTAGAGCCATATTATCGAG
*
72291 TTT-TCCTTTTCATTGCGATTAGGA
1 TTTGT-CTTTTCATTGCGACTAGGA
72315 TAGTTCGATA
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
50 24 0.35
51 1 0.01
54 1 0.01
55 2 0.03
58 1 0.01
59 40 0.58
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (54 bp):
TTTGTCTTTTCATTGCGACTAGGAGGGTTATAGGATTAGAGCCATATTATCGAG
Found at i:72305 original size:59 final size:59
Alignment explanation
Indices: 72213--72333 Score: 181
Period size: 59 Copynumber: 2.1 Consensus size: 59
72203 GGAGGGTTGG
*
72213 TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGGGTTAGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGAGTTAGATAGGACAC
* * * *
72272 TTAGAGCCATATTATCGAGTTT-TCCTTTTCATTGCGATTAGGATAGTTCGATAGTACAC
1 TTAGAGCCATATTATCGAGTTTGT-CTTTTCATTGCGACTAGGAGAGTTAGATAGGACAC
72331 TTA
1 TTA
72334 TCCATCTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 1 0.02
59 55 0.98
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGTCTTTTCATTGCGACTAGGAGAGTTAGATAGGACAC
Found at i:73252 original size:22 final size:21
Alignment explanation
Indices: 73199--73244 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
73189 GGTTTTTGTT
73199 ATTTAGTAAAACTCTTTCGTG
1 ATTTAGTAAAACTCTTTCGTG
*
73220 ATTTAGTAAAACTCTTTCTTG
1 ATTTAGTAAAACTCTTTCGTG
73241 ATTT
1 ATTT
73245 TAGAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.11, T:0.48
Consensus pattern (21 bp):
ATTTAGTAAAACTCTTTCGTG
Found at i:73392 original size:19 final size:18
Alignment explanation
Indices: 73373--73421 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
73363 GTTGTTTTTA
73373 AAATAAAAAATAAGAATT
1 AAATAAAAAATAAGAATT
* *
73391 AAATAAAAGAAAAATAATT
1 AAATAAAA-AATAAGAATT
73410 AAATAAACAAAT
1 AAATAAA-AAAT
73422 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.20
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:74156 original size:2 final size:2
Alignment explanation
Indices: 74149--74214 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
74139 TTTAATTTTG
74149 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
74191 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
74215 GCACGAACTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75137 original size:28 final size:30
Alignment explanation
Indices: 75104--75170 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
75094 TAAAAAAATA
* *
75104 TAAGATATAATTATTTT-TTT-TATTTAAT
1 TAAGATATAATCATTTTCTTTATATTCAAT
*
75132 TAAGATATGATCATTTTCGTTTATATTCAAT
1 TAAGATATAATCATTTTC-TTTATATTCAAT
75163 TAAGATAT
1 TAAGATAT
75171 GTTCACCCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 15 0.45
30 3 0.09
31 15 0.45
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.52
Consensus pattern (30 bp):
TAAGATATAATCATTTTCTTTATATTCAAT
Found at i:75167 original size:31 final size:28
Alignment explanation
Indices: 75104--75171 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
75094 TAAAAAAATA
* * *
75104 TAAGATATAATTATTTTTTTTATTTAAT
1 TAAGATATGATCATTTTTTTTATTCAAT
75132 TAAGATATGATCATTTTCGTTTATATTCAAT
1 TAAGATATGATCATTTT--TTT-TATTCAAT
75163 TAAGATATG
1 TAAGATATG
75172 TTCACCCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 15 0.44
30 3 0.09
31 16 0.47
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.51
Consensus pattern (28 bp):
TAAGATATGATCATTTTTTTTATTCAAT
Found at i:75968 original size:22 final size:22
Alignment explanation
Indices: 75934--75999 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 22
75924 AAATAATATA
*
75934 ATTTTATATATTAAGTTAAAAAT
1 ATTTT-TATATTAACTTAAAAAT
*
75957 ATTTTTATATTAACTTATTAAAT
1 ATTTTTATATTAACTTA-AAAAT
75980 ATATTTTATGATTAACTTAA
1 AT-TTTTAT-ATTAACTTAA
76000 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 11 0.30
23 11 0.30
24 6 0.16
25 9 0.24
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (22 bp):
ATTTTTATATTAACTTAAAAAT
Found at i:75983 original size:25 final size:23
Alignment explanation
Indices: 75928--75999 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 23
75918 GATTATAAAT
*
75928 AATATAATTTTATATATTAAGTTAA
1 AATAT-ATTTT-TATATTAACTTAA
75953 AA-ATATTTTTATATTAACTTATTA
1 AATATATTTTTATATTAACTTA--A
75977 AATATA-TTTTATGATTAACTTAA
1 AATATATTTTTAT-ATTAACTTAA
76000 TTTTAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 11 0.26
23 6 0.14
24 11 0.26
25 14 0.33
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (23 bp):
AATATATTTTTATATTAACTTAA
Found at i:76038 original size:21 final size:21
Alignment explanation
Indices: 75999--76038 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
75989 GATTAACTTA
* * *
75999 ATTTTAAAATATTTTATTTTC
1 ATTTAAAAATATATAATTTTC
76020 ATTTAAAAATATATAATTT
1 ATTTAAAAATATATAATTT
76039 ATTTTAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAAAATATATAATTTTC
Found at i:82847 original size:3 final size:3
Alignment explanation
Indices: 82839--82868 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
82829 TAAAAATAAA
82839 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
82869 TCAGAGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:83109 original size:31 final size:31
Alignment explanation
Indices: 83056--83134 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
83046 TATAAGAGTT
* * * *
83056 AAATTAATATTTCA-TCAAATTTTAATAATG
1 AAATTGATATTTCATTTATATTTTAAGAATG
*
83086 AAATTGATATCTT-ATTTATATTTTAAGAATT
1 AAATTGATAT-TTCATTTATATTTTAAGAATG
83117 AAATTGATATTTCATTTA
1 AAATTGATATTTCATTTA
83135 AAATTAAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
30 12 0.29
31 29 0.71
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (31 bp):
AAATTGATATTTCATTTATATTTTAAGAATG
Found at i:83150 original size:30 final size:30
Alignment explanation
Indices: 83054--83151 Score: 85
Period size: 30 Copynumber: 3.2 Consensus size: 30
83044 AATATAAGAG
* * *
83054 TTAAATTAATATTTCA-TCAAATTTTAATAA
1 TTAAATTGATATTTCATTTAAATTTAAAT-A
* *
83084 TGAAATTGATATCTT-ATTTATATTTTAAGA-A
1 TTAAATTGATAT-TTCATTTA-AATTTAA-ATA
*
83115 TTAAATTGATATTTCATTTAAAATTAAATA
1 TTAAATTGATATTTCATTTAAATTTAAATA
83145 TTAAATT
1 TTAAATT
83152 AAAAAATGTC
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
29 1 0.02
30 26 0.48
31 21 0.39
32 5 0.09
33 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (30 bp):
TTAAATTGATATTTCATTTAAATTTAAATA
Found at i:84038 original size:16 final size:18
Alignment explanation
Indices: 84013--84055 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
84003 TAATATGGTG
84013 TTTTTGAAAT-TTATT-TA
1 TTTTT-AAATATTATTATA
84030 TTTTTAAATATTATTATA
1 TTTTTAAATATTATTATA
*
84048 TTTATAAA
1 TTTTTAAA
84056 AAAACTAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 10 0.43
18 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTAAATATTATTATA
Found at i:85256 original size:38 final size:38
Alignment explanation
Indices: 85187--85322 Score: 150
Period size: 38 Copynumber: 3.6 Consensus size: 38
85177 AATGTATTTT
* *
85187 TTTTCGAAAACGTATAATATATAGCTTTTTTTAAAAAATAG
1 TTTT-GAAAACGTATAATATATA--ATTTTTTAAAAAACAG
* * *
85228 TTTTGAAAACGCATAATATATAATTTTTTTAAAAACGG
1 TTTTGAAAACGTATAATATATAATTTTTTAAAAAACAG
* * * *
85266 TTTCGAAAACGTATAATTTAT-A-GTTTAAAAAAACAG
1 TTTTGAAAACGTATAATATATAATTTTTTAAAAAACAG
85302 TTTTGAAAACGTATAATATAT
1 TTTTGAAAACGTATAATATAT
85323 GGTTTTGAAA
Statistics
Matches: 81, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
36 29 0.36
37 1 0.01
38 30 0.37
40 17 0.21
41 4 0.05
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.39
Consensus pattern (38 bp):
TTTTGAAAACGTATAATATATAATTTTTTAAAAAACAG
Found at i:85310 original size:36 final size:36
Alignment explanation
Indices: 85188--85327 Score: 127
Period size: 36 Copynumber: 3.7 Consensus size: 36
85178 ATGTATTTTT
* *
85188 TTTCGAAAACGTATAATATATAGCTTTTTTTAAAAAATAG
1 TTTCGAAAACGTATAATATATAG----TTTAAAAAAACAG
* * * ** *
85228 TTTTGAAAACGCATAATATATAATTTTTTTAAAAACGG
1 TTTCGAAAACGTATAATATAT-A-GTTTAAAAAAACAG
*
85266 TTTCGAAAACGTATAATTTATAGTTTAAAAAAACAG
1 TTTCGAAAACGTATAATATATAGTTTAAAAAAACAG
* *
85302 TTTTGAAAACGTATAATATATGGTTT
1 TTTCGAAAACGTATAATATATAGTTT
85328 TGAAAACATT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
36 33 0.40
37 1 0.01
38 28 0.34
40 19 0.23
41 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTCGAAAACGTATAATATATAGTTTAAAAAAACAG
Found at i:85346 original size:35 final size:36
Alignment explanation
Indices: 85271--85360 Score: 92
Period size: 36 Copynumber: 2.5 Consensus size: 36
85261 AACGGTTTCG
* *
85271 AAAACGTATAATTTATAGTTTAAAAAAACAGTTTTG
1 AAAACGTATAATATATAGTTTAAAAAAACAGTTTTA
* ** *
85307 AAAACGTATAATATATGGTTT-TGAAAACATTTTTA
1 AAAACGTATAATATATAGTTTAAAAAAACAGTTTTA
*
85342 AAAACATATATAATATATA
1 AAAAC--GTATAATATATA
85361 TAATCTTTGA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
35 15 0.34
36 19 0.43
37 10 0.23
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (36 bp):
AAAACGTATAATATATAGTTTAAAAAAACAGTTTTA
Found at i:85453 original size:24 final size:22
Alignment explanation
Indices: 85419--85465 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
85409 TTCATACATA
* *
85419 TATTTTATATTTCTTTTTATTT
1 TATTTTATATTTATTTTCATTT
85441 TATTTTATTTATTTATTTTCATTT
1 TATTTTA--TATTTATTTTCATTT
85465 T
1 T
85466 GGTTTAGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (22 bp):
TATTTTATATTTATTTTCATTT
Found at i:85471 original size:24 final size:24
Alignment explanation
Indices: 85426--85471 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
85416 ATATATTTTA
* * *
85426 TATTTCTTTTTATTTTATTTTATT
1 TATTTATTTTCATTTTAGTTTATT
*
85450 TATTTATTTTCATTTTGGTTTA
1 TATTTATTTTCATTTTAGTTTA
85472 GGTCCAAGTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (24 bp):
TATTTATTTTCATTTTAGTTTATT
Found at i:86519 original size:10 final size:10
Alignment explanation
Indices: 86489--86538 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 10
86479 ATCCTTTAAA
86489 TTTTTATTT-
1 TTTTTATTTC
86498 TTATTT-TTTC
1 TT-TTTATTTC
86508 TTTTTATTTC
1 TTTTTATTTC
86518 TTTTTTATTCTC
1 -TTTTTATT-TC
*
86530 TTTTAATTT
1 TTTTTATTT
86539 TGACATGTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 8 0.23
10 10 0.29
11 15 0.43
12 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTATTTC
Found at i:86531 original size:12 final size:11
Alignment explanation
Indices: 86489--86533 Score: 51
Period size: 10 Copynumber: 4.3 Consensus size: 11
86479 ATCCTTTAAA
86489 TTTTTATTT-T
1 TTTTTATTTCT
*
86499 TATTT-TTTC-
1 TTTTTATTTCT
86508 TTTTTATTTCT
1 TTTTTATTTCT
86519 TTTTTATTCTCT
1 TTTTTATT-TCT
86531 TTT
1 TTT
86534 AATTTTGACA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
9 7 0.24
10 8 0.28
11 8 0.28
12 6 0.21
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTCT
Found at i:86616 original size:14 final size:14
Alignment explanation
Indices: 86597--86629 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
86587 CTCCTTTTAA
86597 TATTTTTTATATTT
1 TATTTTTTATATTT
86611 TATTTTTTATATTT
1 TATTTTTTATATTT
*
86625 AATTT
1 TATTT
86630 CTTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTTATATTT
Found at i:88297 original size:31 final size:31
Alignment explanation
Indices: 88238--88319 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 31
88228 TATTTTCAAT
* *
88238 TTAATGATTAAATTT-TTAAAAATTAT-AAA
1 TTAATTATTAAATTTATCAAAAATTATAAAA
88267 TTAATTATTAAATTTATCAAAATATTATAAAA
1 TTAATTATTAAATTTATCAAAA-ATTATAAAA
88299 TT-ATTATTAAAATTTATCAAA
1 TTAATTATT-AAATTTATCAAA
88320 CTATAAGAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 14 0.30
30 5 0.11
31 11 0.23
32 17 0.36
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (31 bp):
TTAATTATTAAATTTATCAAAAATTATAAAA
Found at i:88312 original size:32 final size:32
Alignment explanation
Indices: 88247--88350 Score: 101
Period size: 31 Copynumber: 3.4 Consensus size: 32
88237 TTTAATGATT
*
88247 AAATTT-TTAAAA-ATTAT-AAATTAATTATT-
1 AAATTTATCAAAATATTATAAAATT-ATTATTA
88276 AAATTTATCAAAATATTATAAAATTATTATTA
1 AAATTTATCAAAATATTATAAAATTATTATTA
* * * *
88308 AAATTTATCAAACTATAAGAAAA-TATCATTA
1 AAATTTATCAAAATATTATAAAATTATTATTA
**
88339 ATCTTTATCAAA
1 AAATTTATCAAA
88351 TAATGATCAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
29 6 0.09
30 5 0.08
31 28 0.44
32 25 0.39
ACGTcount: A:0.52, C:0.06, G:0.01, T:0.41
Consensus pattern (32 bp):
AAATTTATCAAAATATTATAAAATTATTATTA
Found at i:88339 original size:31 final size:32
Alignment explanation
Indices: 88276--88350 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 32
88266 ATTAATTATT
* * *
88276 AAATTTATCAAAATATTATAAAATTATTATTA
1 AAATTTATCAAAATATAAGAAAATTATCATTA
*
88308 AAATTTATCAAACTATAAGAAAA-TATCATTA
1 AAATTTATCAAAATATAAGAAAATTATCATTA
**
88339 ATCTTTATCAAA
1 AAATTTATCAAA
88351 TAATGATCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 17 0.46
32 20 0.54
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (32 bp):
AAATTTATCAAAATATAAGAAAATTATCATTA
Found at i:88439 original size:20 final size:20
Alignment explanation
Indices: 88416--88453 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
88406 TTATATATAA
*
88416 TTTAAAATTTTAATAATTAT
1 TTTAAAATTTTAAAAATTAT
*
88436 TTTATAATTTTAAAAATT
1 TTTAAAATTTTAAAAATT
88454 TAATAATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAAAATTTTAAAAATTAT
Found at i:88441 original size:29 final size:28
Alignment explanation
Indices: 88397--88460 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
88387 TATAATATCA
*
88397 TAATAATTATTATATATAATTTAAAATTT
1 TAATAATTATTATATA-AATTTAAAAATT
* *
88426 TAATAATTATTTTATAATTTTAAAAATT
1 TAATAATTATTATATAAATTTAAAAATT
88454 TAATAAT
1 TAATAAT
88461 AAAAAACTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TAATAATTATTATATAAATTTAAAAATT
Found at i:88942 original size:8 final size:8
Alignment explanation
Indices: 88929--88956 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
88919 TTTCGCTTCT
88929 TTTCTACA
1 TTTCTACA
88937 TTTCTACA
1 TTTCTACA
88945 TTTCTACA
1 TTTCTACA
88953 TTTC
1 TTTC
88957 AACAGCTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.25, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTCTACA
Found at i:89613 original size:31 final size:32
Alignment explanation
Indices: 89578--89641 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
89568 ATAGTGTTGT
*
89578 TTTGGTTTATGAAGGTGG-AGAGAGGGATTGA
1 TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
* * *
89609 TTTGGTGTATGGAGGTGGAAGCGTGGGATTGA
1 TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
89641 T
1 T
89642 GGGTCTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.22, C:0.02, G:0.44, T:0.33
Consensus pattern (32 bp):
TTTGGTGTATGAAGGTGGAAGAGAGGGATTGA
Found at i:92272 original size:23 final size:23
Alignment explanation
Indices: 92245--92317 Score: 128
Period size: 23 Copynumber: 3.2 Consensus size: 23
92235 AGGAAAAAAA
92245 CCTAACCCATTATTTAAAGTAAC
1 CCTAACCCATTATTTAAAGTAAC
*
92268 CCTAACCTATTATTTAAAGTAAC
1 CCTAACCCATTATTTAAAGTAAC
*
92291 CCTAACCCATTATTTAAAGTAGC
1 CCTAACCCATTATTTAAAGTAAC
92314 CCTA
1 CCTA
92318 TTCTAAAACC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (23 bp):
CCTAACCCATTATTTAAAGTAAC
Found at i:92332 original size:46 final size:46
Alignment explanation
Indices: 92245--92333 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
92235 AGGAAAAAAA
** **
92245 CCTAACCCATTATTTAAAGTAACCCTAACCTATTATTTAAAGTAAC
1 CCTAACCCATTATTTAAAGTAACCCTAACCTAAAACCTAAAGTAAC
* **
92291 CCTAACCCATTATTTAAAGTAGCCCTATTCTAAAACCTAAAGT
1 CCTAACCCATTATTTAAAGTAACCCTAACCTAAAACCTAAAGT
92334 GGTTGCTGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 36 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (46 bp):
CCTAACCCATTATTTAAAGTAACCCTAACCTAAAACCTAAAGTAAC
Found at i:92932 original size:20 final size:20
Alignment explanation
Indices: 92901--92946 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
92891 AAGAAAGAAA
92901 GCATTC-AAAAAATATCATT
1 GCATTCAAAAAAATATCATT
92920 GCATTCAAAAAAATATCATT
1 GCATTCAAAAAAATATCATT
92940 GCATTCA
1 GCATTCA
92947 TTTCTAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.46, C:0.17, G:0.07, T:0.30
Consensus pattern (20 bp):
GCATTCAAAAAAATATCATT
Found at i:93167 original size:25 final size:25
Alignment explanation
Indices: 93098--93180 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
93088 ATAGAACAAG
* * * *
93098 TTCATAGAATCAGTTAACAATTTTA
1 TTCATATAATCAGTAAACAAATCTA
* **
93123 TTCATATAATCCGTGGACAAATCTA
1 TTCATATAATCAGTAAACAAATCTA
*
93148 TTCATATAATTAGTAAACAAATCTA
1 TTCATATAATCAGTAAACAAATCTA
*
93173 GTCATATA
1 TTCATATA
93181 TACTATACCA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.36
Consensus pattern (25 bp):
TTCATATAATCAGTAAACAAATCTA
Found at i:93226 original size:27 final size:27
Alignment explanation
Indices: 93187--93273 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
93177 TATATACTAT
*
93187 ACCATTTTTAACAGAAGAAACTCTTAA
1 ACCATTTTCAACAGAAGAAACTCTTAA
93214 ACCATTTTCAACAGAAGAAA-TCTTTAA
1 ACCATTTTCAACAGAAGAAACTC-TTAA
* * *
93241 ACCATTTTC-ACATAAGAAACCCCTAA
1 ACCATTTTCAACAGAAGAAACTCTTAA
93267 A-CATTTT
1 ACCATTTT
93274 TACTAAACTA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.11
26 15 0.28
27 33 0.61
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.30
Consensus pattern (27 bp):
ACCATTTTCAACAGAAGAAACTCTTAA
Found at i:93237 original size:26 final size:28
Alignment explanation
Indices: 93187--93260 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
93177 TATATACTAT
*
93187 ACCATTTTTAACAGAAGAAACTC-TTAA
1 ACCATTTTCAACAGAAGAAACTCTTTAA
93214 ACCATTTTCAACAGAAGAAA-TCTTTAA
1 ACCATTTTCAACAGAAGAAACTCTTTAA
*
93241 ACCATTTTC-ACATAAGAAAC
1 ACCATTTTCAACAGAAGAAAC
93261 CCCTAAACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.26
27 32 0.74
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (28 bp):
ACCATTTTCAACAGAAGAAACTCTTTAA
Found at i:94246 original size:32 final size:30
Alignment explanation
Indices: 94210--94282 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
94200 GTTCCTTAGA
*
94210 ACATAGGTAATC-CTGTCCATATGTCTCGAATG
1 ACATAGGTAA-CACTGTCC--ATGTCTCGAAAG
*
94242 ACATATGTAACACTGTCCATGTCTCGAAAG
1 ACATAGGTAACACTGTCCATGTCTCGAAAG
94272 ACATAGGTAAC
1 ACATAGGTAAC
94283 CCTCGACTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 21 0.57
31 1 0.03
32 15 0.41
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (30 bp):
ACATAGGTAACACTGTCCATGTCTCGAAAG
Done.