Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001819.1 Hibiscus syriacus cultivar Beakdansim tig00003683_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: 76741
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:748 original size:30 final size:29
Alignment explanation
Indices: 710--768 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
700 GTGGACCCTA
710 ATGTTTTGTTTGATTCAT-TCATATTTCTT
1 ATGTTTTGTTTGATTCATGT-ATATTTCTT
739 ATGTGTTTGTTTGATTCATGTATATTTCTT
1 ATGT-TTTGTTTGATTCATGTATATTTCTT
769 CTATTTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 4 0.14
30 23 0.82
31 1 0.04
ACGTcount: A:0.17, C:0.08, G:0.14, T:0.61
Consensus pattern (29 bp):
ATGTTTTGTTTGATTCATGTATATTTCTT
Found at i:5383 original size:26 final size:25
Alignment explanation
Indices: 5352--5405 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
5342 AAAAAGAATG
5352 AATTTATAAA-ATTTTA-AAGAAATAAA
1 AATTTA-AAATATTTTATAAG--ATAAA
5378 AATTTAAAATATTTTATAAGATAAA
1 AATTTAAAATATTTTATAAGATAAA
5403 AAT
1 AAT
5406 AAAATTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 11 0.42
26 12 0.46
27 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (25 bp):
AATTTAAAATATTTTATAAGATAAA
Found at i:6882 original size:9 final size:9
Alignment explanation
Indices: 6870--6900 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
6860 ATAAAAAAAT
6870 GAAAATAAA
1 GAAAATAAA
6879 GAAAATAAA
1 GAAAATAAA
6888 GAAAATAAA
1 GAAAATAAA
6897 -AAAA
1 GAAAA
6901 CAACCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.81, C:0.00, G:0.10, T:0.10
Consensus pattern (9 bp):
GAAAATAAA
Found at i:6977 original size:23 final size:23
Alignment explanation
Indices: 6937--6984 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6927 AGTAAAGATA
* * *
6937 AAAATGAATACAATAAGAAAAAT
1 AAAATGAAGAAAAAAAGAAAAAT
*
6960 AAAATGAAGAAAAAAAGAATAAT
1 AAAATGAAGAAAAAAAGAAAAAT
6983 AA
1 AA
6985 TGATAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAATGAAGAAAAAAAGAAAAAT
Found at i:7307 original size:2 final size:2
Alignment explanation
Indices: 7302--7365 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
7292 GGAAAAAATG
7302 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7343 TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
7366 GATAAATAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:7958 original size:37 final size:36
Alignment explanation
Indices: 7908--7981 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 36
7898 ATGTTTGTGG
7908 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGT-AAACTCT
*
7945 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAACTCT
7981 A
1 A
7982 ACGTTATGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 8 0.22
37 28 0.78
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (36 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAACTCT
Found at i:8761 original size:35 final size:36
Alignment explanation
Indices: 8717--8810 Score: 154
Period size: 35 Copynumber: 2.6 Consensus size: 36
8707 CGGAAAACAG
8717 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGG-T
1 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
**
8752 TTTTTTTGTGTTTCAAGAGAAATGATTTCAAAGGTT
1 TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
*
8788 TTTTTTTGTGTTTTAAGAGAAAC
1 TTTTTTTGTGTTTCAAGAGAAAC
8811 TGTCTCAAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 32 0.59
36 22 0.41
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (36 bp):
TTTTTTTGTGTTTCAAGAGAAACAATTTCAAAGGTT
Found at i:8873 original size:73 final size:73
Alignment explanation
Indices: 8796--9128 Score: 282
Period size: 73 Copynumber: 4.7 Consensus size: 73
8786 TTTTTTTTTG
*
8796 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
8861 ACAAAATT
66 ACAAAATT
* * * * * *
8869 TGTTTCAAGAGAAACTGACTCAAGAGATACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
** *
8934 ATGAATTT
66 ACAAAATT
* * * *
8942 TGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATTTTGTTTCAAGGGAAACTGCCTCAAGAG
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAG
8997 AGACAAAATT
64 AGACAAAATT
* * *** * * *
9007 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAAAAT-TTTC-AAGAAAAATTGTCTCAAGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAG-GAAACTGTCTCAAGAGA
9070 GACAAAACTT
65 GACAAAA-TT
* * * *
9080 AGTTCCAAAAGAAACTGTCTCAAG-GAAGACGAAA-TTTGTTTC-AAGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAACTTTGTTTCAAAGGAAA
9129 ACATATTTAA
Statistics
Matches: 204, Mismatches: 40, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
64 3 0.01
65 45 0.22
66 2 0.01
67 1 0.00
68 2 0.01
70 1 0.00
71 3 0.01
72 31 0.15
73 115 0.56
74 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (73 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
ACAAAATT
Found at i:8876 original size:21 final size:21
Alignment explanation
Indices: 8815--8880 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
8805 AGAAACTGTC
8815 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
* *
8837 TCAA-AG-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
8852 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
8873 TCAAGAGA
1 TCAAGAGA
8881 AACTGACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
15 7 0.21
16 2 0.06
17 4 0.12
20 4 0.12
21 13 0.38
22 4 0.12
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:8883 original size:36 final size:36
Alignment explanation
Indices: 8796--9193 Score: 282
Period size: 36 Copynumber: 11.4 Consensus size: 36
8786 TTTTTTTTTG
*
8796 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
8833 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* *
8869 TGTTTCAAGAGAAACTGACTCAAGAGATACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * ** *
8906 AGTTCCAAAAGAAACTGTCTCAAGGGAGATGAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
8942 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
8971 TGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * **
9007 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATT
* * *
9044 T-TTTCAAGAAAAATTGTCTCAAGAAAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
9080 AGTTCCAAAAGAAACTGTCTCAAG-GAAGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAG-AGACAAAATT
* * *
9116 TGTTTCAAG-GAAAACATAT-T-TA-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* *
9145 TGTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
9181 TGTTTCAAG-GAAA
1 TGTTTCAAGAGAAA
9194 ACATATTCAA
Statistics
Matches: 284, Mismatches: 47, Indels: 62
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.01
29 36 0.13
30 4 0.01
31 2 0.01
32 4 0.01
33 4 0.01
35 12 0.04
36 126 0.44
37 93 0.33
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:9067 original size:174 final size:174
Alignment explanation
Indices: 8796--9203 Score: 613
Period size: 174 Copynumber: 2.3 Consensus size: 174
8786 TTTTTTTTTG
* * * *
8796 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGAG
** * * *
8861 ACAAAATTTGTTTCAAGAGAAACTGACTCAAGAGATACAAAACTTAGTTCCAAAAGAAACTGTCT
65 ACAAAAAATGTTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCT
* * *
8926 CAAGGGAGATGAATTTTGTTTCAAGGAAAACATATTCAAAGATTT
130 CAAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
*
8971 TGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
* *
9036 CAAAAAAAT-TTTCAAGAAAAATTGTCTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCT
66 C-AAAAAATGTTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCT
*
9100 CAAGGAAGACGAAATTTGTTTCAAGGAAAACATATTTAAAGATTT
130 CAAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
* *
9145 TGTTTCAAGGGAAACTGTCTCAAGAGAGGCAAAATTTGTTTCAAGGAAAACATAT-TCAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-TATCTCAA
9204 AGATTTTGTT
Statistics
Matches: 212, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
174 173 0.82
175 39 0.18
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (174 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAGA
CAAAAAATGTTTCAAGAAAAACTGACTCAAGAAAGACAAAACTTAGTTCCAAAAGAAACTGTCTC
AAGGAAGACGAAATTTGTTTCAAGGAAAACATATTCAAAGATTT
Found at i:9154 original size:29 final size:29
Alignment explanation
Indices: 9114--9224 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
9104 GAAGACGAAA
*
9114 TTTGTTTCAAGGAAAACATATTTAAAGAT
1 TTTGTTTCAAGGAAAACATATTAAAAGAT
* * *
9143 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGGCAAAA
1 TTTGTTTCAAGGAAAACATAT-T-AA-A-A-G---AT
*
9179 TTTGTTTCAAGGAAAACATATTCAAAGAT
1 TTTGTTTCAAGGAAAACATATTAAAAGAT
*
9208 TTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGAAAAC
9225 TGTCTCAAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
28 2 0.03
29 34 0.53
30 1 0.02
31 1 0.02
32 2 0.03
33 2 0.03
34 1 0.02
35 1 0.02
36 18 0.28
37 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (29 bp):
TTTGTTTCAAGGAAAACATATTAAAAGAT
Found at i:9165 original size:65 final size:66
Alignment explanation
Indices: 9090--9246 Score: 257
Period size: 65 Copynumber: 2.4 Consensus size: 66
9080 AGTTCCAAAA
* *
9090 GAAACTGTCTCAAGGA-AGACGAAATTTGTTTCAAGGAAAACATATTTAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
9154 G
66 G
*
9155 GAAACTGTCTCAA-GAGAGGCAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
1 GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
9219 G
66 G
*
9220 GAAACTGTCTCAA-GAGAGAGAAAATTT
1 GAAACTGTCTCAAGGAGAGACAAAATTT
9247 TAATTTGAGT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
64 2 0.02
65 84 0.98
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
GAAACTGTCTCAAGGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAG
G
Found at i:16827 original size:22 final size:22
Alignment explanation
Indices: 16801--16860 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
16791 TTAGTGCAGA
*
16801 GGGAATCGATACCCCCTTGA-AG
1 GGGAATCGATACCCCC-TCACAG
* * *
16823 GGGAACCGATTCCCCC-CACAT
1 GGGAATCGATACCCCCTCACAG
16844 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
16861 GAGGGTTCTG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.50
22 14 0.47
ACGTcount: A:0.25, C:0.35, G:0.23, T:0.17
Consensus pattern (22 bp):
GGGAATCGATACCCCCTCACAG
Found at i:18454 original size:18 final size:18
Alignment explanation
Indices: 18416--18461 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
18406 TTGACGACAC
*
18416 GAGGAACAAACACGAGCA
1 GAGGAACAAACACGAACA
18434 GAGGAACAAACAC-AACTA
1 GAGGAACAAACACGAAC-A
*
18452 GAGGATCAAA
1 GAGGAACAAA
18462 TGCCTCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.52, C:0.20, G:0.24, T:0.04
Consensus pattern (18 bp):
GAGGAACAAACACGAACA
Found at i:19141 original size:37 final size:37
Alignment explanation
Indices: 19097--19167 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
19087 CATTTTTAAA
19097 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTCAAAGAG
1 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTCAAAGAG
19134 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTCAAA
1 GAGTAGTGTTAGAGTAAGGGGGAGTAATTTCAAA
19168 CTTGAAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.37, T:0.25
Consensus pattern (37 bp):
GAGTAGTGTTAGAGTAAGGGGGAGTAATTTCAAAGAG
Found at i:19159 original size:21 final size:21
Alignment explanation
Indices: 19097--19159 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
19087 CATTTTTAAA
19097 GAGTAGTGTTAGAGTAAGGGG
1 GAGTAGTGTTAGAGTAAGGGG
* * *
19118 GAGTAAT-TT-CA--AA-GAG
1 GAGTAGTGTTAGAGTAAGGGG
19134 GAGTAGTGTTAGAGTAAGGGG
1 GAGTAGTGTTAGAGTAAGGGG
19155 GAGTA
1 GAGTA
19160 ATTTCAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
16 8 0.26
17 4 0.13
18 1 0.03
19 1 0.03
20 4 0.13
21 13 0.42
ACGTcount: A:0.33, C:0.02, G:0.41, T:0.24
Consensus pattern (21 bp):
GAGTAGTGTTAGAGTAAGGGG
Found at i:22851 original size:6 final size:6
Alignment explanation
Indices: 22840--22868 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
22830 TAATCCGCAA
22840 AAATTT AAATTT AAATTT AAATTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATT
22869 ATTCGATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AAATTT
Found at i:23003 original size:25 final size:27
Alignment explanation
Indices: 22964--23018 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
22954 TAAATAGAAT
22964 AAAGAAAATAAAAAACGACTGAA-ATA
1 AAAGAAAATAAAAAACGACTGAAGATA
* * *
22990 AAAGAATA-AAAAAAGGAGTGAAGATA
1 AAAGAAAATAAAAAACGACTGAAGATA
23016 AAA
1 AAA
23019 ATGAATACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.11
Consensus pattern (27 bp):
AAAGAAAATAAAAAACGACTGAAGATA
Found at i:23599 original size:20 final size:19
Alignment explanation
Indices: 23567--23604 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
23557 AAAACATATA
23567 AAATATAATAATAATAATG
1 AAATATAATAATAATAATG
23586 AAATATATATAATAATAAT
1 AAATATA-ATAATAATAAT
23605 AGTAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (19 bp):
AAATATAATAATAATAATG
Found at i:24007 original size:37 final size:37
Alignment explanation
Indices: 23957--24027 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
23947 TTGTGGATCC
23957 TATTTTAAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTAAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
23994 TATTTTTAGGAGTTTGAATCTTAGTAAAACTCTA
1 TATTTTAAGGAGTTTGAATCATAGTAAAACTCTA
24028 ACGTTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (37 bp):
TATTTTAAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:24327 original size:19 final size:19
Alignment explanation
Indices: 24303--24366 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
24293 TAAATACTTA
24303 AAATATATAATTTTTATTT
1 AAATATATAATTTTTATTT
24322 AAATATATAATTTTTTTATTT
1 AAATATATAA--TTTTTATTT
* *
24343 AAATATATTATTTTCATTT
1 AAATATATAATTTTTATTT
24362 AAATA
1 AAATA
24367 GTTTAACTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 23 0.56
21 18 0.44
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATATATAATTTTTATTT
Found at i:24337 original size:21 final size:21
Alignment explanation
Indices: 24303--24356 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
24293 TAAATACTTA
24303 AAATATATAA--TTTTTATTT
1 AAATATATAATTTTTTTATTT
24322 AAATATATAATTTTTTTATTT
1 AAATATATAATTTTTTTATTT
*
24343 AAATATATTATTTT
1 AAATATATAATTTT
24357 CATTTAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 10 0.31
21 22 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
AAATATATAATTTTTTTATTT
Found at i:28072 original size:16 final size:16
Alignment explanation
Indices: 28048--28091 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
28038 TGGATGAAAC
28048 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
*
28064 TGTATAAAACAGAC--
1 TGTAGAAAACAGACTG
28078 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
28092 AAGTCTGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:30393 original size:51 final size:51
Alignment explanation
Indices: 30317--30417 Score: 175
Period size: 51 Copynumber: 2.0 Consensus size: 51
30307 TAAGGAAAGG
*
30317 ATAGGCTGTAAAGAAATATAGGTTTGAACAAGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATAGGTTTGAACAAGCTGAAATTCCTTGTAACTA
* *
30368 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATAGGTTTGAACAAGCTGAAATTCCTTGTAACT
30418 CTCCCCCTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATAGGTTTGAACAAGCTGAAATTCCTTGTAACTA
Found at i:32218 original size:14 final size:15
Alignment explanation
Indices: 32183--32226 Score: 72
Period size: 14 Copynumber: 2.9 Consensus size: 15
32173 CCTGATACCA
32183 TGTAGAAAACAGACTG
1 TGTAGAAAACAGAC-G
32199 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
32213 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
32227 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
16 14 0.50
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:32953 original size:25 final size:25
Alignment explanation
Indices: 32908--32956 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
32898 TGGCAGAGGC
*
32908 AAGAAATTAACATACTGTATTGTTA
1 AAGAAATTAACATACTATATTGTTA
*
32933 AAGAGATTAACATGA-TATATTGTT
1 AAGAAATTAACAT-ACTATATTGTT
32957 TCCAATGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (25 bp):
AAGAAATTAACATACTATATTGTTA
Found at i:37483 original size:28 final size:28
Alignment explanation
Indices: 37443--37499 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
37433 AAGTCATAAG
**
37443 AAGCATGAGCATTCCTTCCAGGGAAAAA
1 AAGCATGAGCATTCCTTAAAGGGAAAAA
37471 AAGCATGAGCATTCCTTAAAGGGAAAAA
1 AAGCATGAGCATTCCTTAAAGGGAAAAA
37499 A
1 A
37500 CCCAACAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.18
Consensus pattern (28 bp):
AAGCATGAGCATTCCTTAAAGGGAAAAA
Found at i:41437 original size:41 final size:41
Alignment explanation
Indices: 41378--41536 Score: 282
Period size: 41 Copynumber: 3.9 Consensus size: 41
41368 TAGTTACTGA
* **
41378 AACTATACGATAAGTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGATATCTATTAATTTGAATCACATGAATGTCTG
41419 AACTATATGATATCTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGATATCTATTAATTTGAATCACATGAATGTCTG
*
41460 AACTATATGATACCTATTAATTTGAATCACATGAATGTCTG
1 AACTATATGATATCTATTAATTTGAATCACATGAATGTCTG
41501 AACTATATGATATCTATTAATTTGAATCACATGAAT
1 AACTATATGATATCTATTAATTTGAATCACATGAAT
41537 ACAATTAAAA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (41 bp):
AACTATATGATATCTATTAATTTGAATCACATGAATGTCTG
Found at i:42300 original size:21 final size:21
Alignment explanation
Indices: 42275--42327 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42265 ATTCTGACTA
42275 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
42296 TCGCATTGTGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
42317 TCGCAATGCGA
1 TCGCATTGCGA
42328 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:42342 original size:20 final size:20
Alignment explanation
Indices: 42317--42390 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
42307 TTTTCCTAAT
42317 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * ** *
42337 TCGCAACGCAAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
42358 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
42378 TCGCAATGCGAAT
1 TCGCAATGCGAAT
42391 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:42601 original size:22 final size:22
Alignment explanation
Indices: 42576--42651 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
42566 TCACTTCTAA
* *
42576 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
42598 GACGAAATCAGTCCCCATCGCC
1 GACGAAATCAGTCCCCATCTCC
* *
42620 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
42642 GGCAAAATCA
1 GACGAAATCA
42652 TTCACGGTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.26, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:43013 original size:33 final size:34
Alignment explanation
Indices: 42976--43048 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
42966 ACTATCGCAA
** *
42976 TGCGATTCTAT-CGTTGCGATTTTC-ATTTCGCGT
1 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
43009 TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
43043 TGCGAT
1 TGCGAT
43049 AGTCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 20 0.57
34 14 0.40
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (34 bp):
TGCGATTCTTGCGTTGCGATAGTCAAATTCGCGT
Found at i:43044 original size:20 final size:20
Alignment explanation
Indices: 43019--43068 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
43009 TGCGATTCTT
43019 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
43039 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
43059 GTGTTGCGAT
1 GCGTTGCGAT
43069 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:43074 original size:20 final size:20
Alignment explanation
Indices: 43036--43090 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
43026 GATAGTCAAA
* **
43036 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
43056 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
43076 TTCGTATTGCGATTT
1 TTCGTGTTGCGATTT
43091 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:43098 original size:20 final size:20
Alignment explanation
Indices: 43055--43098 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
43045 CGATAGTCAT
* ** *
43055 TTTCGTGTTGCGATTTTCAT
1 TTTCGTATTGCGATTTAAAG
43075 TTTCGTATTGCGATTTAAAG
1 TTTCGTATTGCGATTTAAAG
43095 TTTC
1 TTTC
43099 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTATTGCGATTTAAAG
Found at i:44994 original size:20 final size:20
Alignment explanation
Indices: 44969--45145 Score: 184
Period size: 20 Copynumber: 9.5 Consensus size: 20
44959 AGAATAGTTT
44969 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
44989 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
45009 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
45029 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
45045 A--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
45062 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
45078 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
45096 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
45116 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
45136 ACTATCGCAA
1 ACTATCGCAA
45146 CGAAAGAATC
Statistics
Matches: 136, Mismatches: 7, Indels: 28
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.10
16 10 0.07
17 8 0.06
18 5 0.04
19 7 0.05
20 93 0.68
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:45024 original size:40 final size:37
Alignment explanation
Indices: 44969--45166 Score: 193
Period size: 40 Copynumber: 5.5 Consensus size: 37
44959 AGAATAGTTT
44969 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA--CGAAAA-G
* *
45009 ACTATCGCAACGCGAAAATGACTATCGCAACG-AGAG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAAG
**
45045 A--ATCGCAATGCG-AAATGAAAATCGCAAC-AACAA-
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAA-AAG
*
45078 A--ATCACAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA--CGAAAA-G
**
45116 ACTATCGCAATGCGAATTTGACTATCGCAACG-AAAG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAAG
45152 A--ATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
45167 TGAAAATCGC
Statistics
Matches: 135, Mismatches: 13, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
33 26 0.19
34 37 0.27
36 7 0.05
37 7 0.05
38 5 0.04
40 53 0.39
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.17
Consensus pattern (37 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAAG
Found at i:45197 original size:107 final size:107
Alignment explanation
Indices: 44976--45177 Score: 368
Period size: 107 Copynumber: 1.9 Consensus size: 107
44966 TTTACTATCG
44976 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
1 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
*
45041 AGAGAATCGCAATGCGAAATGAAAATCGCAACAACAAAATCA
66 AAAGAATCGCAATGCGAAATGAAAATCGCAACAACAAAATCA
* **
45083 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACG
1 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
45148 AAAGAATCGCAATGCGAAATGAAAATCGCA
66 AAAGAATCGCAATGCGAAATGAAAATCGCA
45178 TTGCGATTCT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 91 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (107 bp):
CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACG
AAAGAATCGCAATGCGAAATGAAAATCGCAACAACAAAATCA
Found at i:45233 original size:20 final size:20
Alignment explanation
Indices: 45205--45345 Score: 152
Period size: 20 Copynumber: 7.4 Consensus size: 20
45195 CGATAGTCAA
45205 ATTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
* *
45225 ATTGTGATAGTCATTTTCTC
1 ATTGCGATAGTCATTTTCGC
*
45245 ATTGTGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
* **
45265 GTTGCGATTTTCA-TTTCGC
1 ATTGCGATAGTCATTTTCGC
*
45284 ATTGCGAT--TC--TCTCG-
1 ATTGCGATAGTCATTTTCGC
45299 -TTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
*
45318 GTTGCGATAGTCATTTTCGC
1 ATTGCGATAGTCATTTTCGC
*
45338 GTTGCGAT
1 ATTGCGAT
45346 TTTAAGTTTC
Statistics
Matches: 105, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
17 2 0.02
18 4 0.04
19 13 0.12
20 73 0.70
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.43
Consensus pattern (20 bp):
ATTGCGATAGTCATTTTCGC
Found at i:45355 original size:20 final size:20
Alignment explanation
Indices: 45297--45355 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
45287 GCGATTCTCT
* *
45297 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
45317 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
45337 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
45356 AGATTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:45920 original size:21 final size:21
Alignment explanation
Indices: 45852--45920 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
45842 GGCTTCCCTT
*
45852 ATCGTTCAAGAGGCCTCTATC
1 ATCGTTCAAGAGGCCACTATC
** * * **
45873 ATCCCTCAAGAGTCCCCTCCC
1 ATCGTTCAAGAGGCCACTATC
* *
45894 ACCGTTCAAGAGGCCACTGTC
1 ATCGTTCAAGAGGCCACTATC
45915 ATCGTT
1 ATCGTT
45921 GGAGAGGTCC
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCACTATC
Found at i:47334 original size:14 final size:14
Alignment explanation
Indices: 47315--47350 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47305 ATTGTTTAAT
47315 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
47329 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
47343 TGATTTGT
1 TGATTTGT
47351 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:47550 original size:20 final size:20
Alignment explanation
Indices: 47521--47614 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
47511 GCGATTCTCT
47521 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
47541 CGTTGTGATAGTTAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
47561 CGTTGCGATAATCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
47581 TGTTGCGATAGTCATATT-CA
1 CGTTGCGATAGTCAT-TTCCG
47601 CGTTGCGATAGTCA
1 CGTTGCGATAGTCA
47615 AATGAATGTC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 60 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:50067 original size:24 final size:24
Alignment explanation
Indices: 50040--50086 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
50030 CAAAATCCGA
50040 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
50064 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
50087 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:50095 original size:24 final size:24
Alignment explanation
Indices: 50044--50095 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
50034 ATCCGAGTAT
** *
50044 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
50068 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
50092 TGAC
1 TGAC
50096 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:50772 original size:22 final size:21
Alignment explanation
Indices: 50733--50773 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
50723 TGCCGGATGG
**
50733 GGAAGGATGTCGTTGGATATA
1 GGAAGGATGTCGCCGGATATA
50754 GGAACGGATGTCGCCGGATA
1 GGAA-GGATGTCGCCGGATA
50774 GAGTGATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.27, C:0.12, G:0.39, T:0.22
Consensus pattern (21 bp):
GGAAGGATGTCGCCGGATATA
Found at i:50966 original size:20 final size:20
Alignment explanation
Indices: 50924--50970 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
50914 AAATTCAGTA
*
50924 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
*
50944 TTGCGATAGTCAGATTCGT-G
1 TTGCGATAGTCAGAATC-TCG
50964 TTGCGAT
1 TTGCGAT
50971 TTACATATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.21, C:0.15, G:0.28, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:50980 original size:20 final size:20
Alignment explanation
Indices: 50964--51070 Score: 133
Period size: 20 Copynumber: 5.3 Consensus size: 20
50954 CAGATTCGTG
*
50964 TTGCGATTTACATATTCGCA
1 TTGCGATTTACGTATTCGCA
*
50984 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTCGCA
* *
51004 TTGCGATTTACGTAATCGTA
1 TTGCGATTTACGTATTCGCA
* ** *
51024 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
51045 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
51065 TTGCGA
1 TTGCGA
51071 ATTAGGAAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 57 0.80
21 14 0.20
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:50988 original size:40 final size:38
Alignment explanation
Indices: 50944--51070 Score: 119
Period size: 40 Copynumber: 3.2 Consensus size: 38
50934 TAGAATCTCG
* *
50944 TTGCGATAGTCAGATTCGTGTTGCGATTTACATATTCGCA
1 TTGCGAT--TCAGATTCGCGTTGCGATTTACGTATTCGCA
* * * * *
50984 TTGCGATTTACGTATTTGCATTGCGATTTACGTAATCGTA
1 TTGCGATTCA-G-ATTCGCGTTGCGATTTACGTATTCGCA
*
51024 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGA--TT-CAGATTCGCGTTGCGATTTACGTATTCGCA
51065 TTGCGA
1 TTGCGA
51071 ATTAGGAAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 34 0.49
41 29 0.42
42 2 0.03
43 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (38 bp):
TTGCGATTCAGATTCGCGTTGCGATTTACGTATTCGCA
Found at i:51093 original size:21 final size:21
Alignment explanation
Indices: 51067--51112 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
51057 TATTCGCATT
*
51067 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
51088 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
51109 GCGA
1 GCGA
51113 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:57443 original size:2 final size:2
Alignment explanation
Indices: 57436--57495 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
57426 TTACAATTTA
* *
57436 AT AT AT AT AT AT AT AT AT -T CT AT -T A- AT -T AT A- AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57472 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
57496 TCTATTAATT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
1 6 0.12
2 43 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:57482 original size:42 final size:42
Alignment explanation
Indices: 57415--57519 Score: 159
Period size: 42 Copynumber: 2.6 Consensus size: 42
57405 AAAAGTTATG
57415 TATTCTATTAATTACAA--T--T-TA-ATATATATATATATA
1 TATTCTATTAATTACAATTTAATATATATATATATATATATA
*
57451 TATTCTATTAATTATAATTTAATATATATATATATATATATA
1 TATTCTATTAATTACAATTTAATATATATATATATATATATA
57493 TATTCTATTAATTACAATTTAATATAT
1 TATTCTATTAATTACAATTTAATATAT
57520 GTGTGTGCGC
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
36 16 0.26
38 1 0.02
40 1 0.02
41 2 0.03
42 41 0.67
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (42 bp):
TATTCTATTAATTACAATTTAATATATATATATATATATATA
Found at i:57543 original size:20 final size:20
Alignment explanation
Indices: 57518--57556 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57508 AATTTAATAT
57518 ATGTGTGTGCGCGTGTGTGC
1 ATGTGTGTGCGCGTGTGTGC
**
57538 ATGTGTGTTTGCGTGTGTG
1 ATGTGTGTGCGCGTGTGTG
57557 TGTCTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.10, G:0.44, T:0.41
Consensus pattern (20 bp):
ATGTGTGTGCGCGTGTGTGC
Found at i:57583 original size:25 final size:28
Alignment explanation
Indices: 57552--57607 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
57542 GTGTTTGCGT
57552 GTGTGTGT-C-TATTAATTACAATTTAA
1 GTGTGTGTACATATTAATTACAATTTAA
57578 TGTGTGTGTACTATATTAATTACAATTTAA
1 -GTGTGTGTAC-ATATTAATTACAATTTAA
57608 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 8 0.31
28 1 0.04
30 17 0.65
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.46
Consensus pattern (28 bp):
GTGTGTGTACATATTAATTACAATTTAA
Found at i:58916 original size:2 final size:2
Alignment explanation
Indices: 58909--58933 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58899 TTAACTTTTA
58909 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
58934 GGGTTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:60680 original size:22 final size:22
Alignment explanation
Indices: 60655--60697 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
60645 GCCTAGCTGT
* *
60655 TACTATCTCTAGCTTTTACTGA
1 TACTATCTCTAACTGTTACTGA
*
60677 TACTATTTCTAACTGTTACTG
1 TACTATCTCTAACTGTTACTG
60698 TTATTGTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (22 bp):
TACTATCTCTAACTGTTACTGA
Found at i:64689 original size:20 final size:20
Alignment explanation
Indices: 64664--64709 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
64654 GCTTGAAATT
*
64664 ACTGTAGCAGTATCGATACC
1 ACTGTAGCAGTATCAATACC
64684 ACTGTAGCAGTATCAATACC
1 ACTGTAGCAGTATCAATACC
*
64704 CCTGTA
1 ACTGTA
64710 ACATTCTGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (20 bp):
ACTGTAGCAGTATCAATACC
Found at i:68137 original size:20 final size:20
Alignment explanation
Indices: 68108--68155 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
68098 CTTGAAATTA
* *
68108 CTGTAACAGTATCGATACCC
1 CTGTAGCAGTATCAATACCC
68128 CTGTAGCAGTATCAATACCC
1 CTGTAGCAGTATCAATACCC
68148 CTGTAGCA
1 CTGTAGCA
68156 TTCTGGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (20 bp):
CTGTAGCAGTATCAATACCC
Found at i:68222 original size:20 final size:20
Alignment explanation
Indices: 68199--68237 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
68189 CTGTTAACAC
*
68199 AGTATCGGTACTATTCATAT
1 AGTATCAGTACTATTCATAT
*
68219 AGTATCAGTATTATTCATA
1 AGTATCAGTACTATTCATA
68238 CAACATAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (20 bp):
AGTATCAGTACTATTCATAT
Found at i:70859 original size:9 final size:9
Alignment explanation
Indices: 70845--70932 Score: 51
Period size: 9 Copynumber: 9.7 Consensus size: 9
70835 ATATTTGTAA
70845 ATATAATAT
1 ATATAATAT
70854 ATATAATTAAT
1 ATATAA-T-AT
*
70865 ATATTATAT
1 ATATAATAT
70874 ATATAA-AT
1 ATATAATAT
** *
70882 ATGCAAGAT
1 ATATAATAT
70891 A-ATAATA-
1 ATATAATAT
70898 ATAATAATA-
1 AT-ATAATAT
70907 ATAATAATA-
1 AT-ATAATAT
70916 ATAATAATAT
1 AT-ATAATAT
70926 ATTATAA
1 A-TATAA
70933 AAACTCAAAC
Statistics
Matches: 65, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
7 1 0.02
8 9 0.14
9 40 0.62
10 7 0.11
11 8 0.12
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (9 bp):
ATATAATAT
Found at i:70897 original size:3 final size:3
Alignment explanation
Indices: 70889--70924 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
70879 AATATGCAAG
70889 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
70925 TATTATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.