Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001213.1 Hibiscus syriacus cultivar Beakdansim tig00002395_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: 68785
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1191 original size:40 final size:40
Alignment explanation
Indices: 1127--1240 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 40
1117 TTTCCCCGAA
* *
1127 TTTT-CGTGTTTGTTTACGTAATTCGTTTTCCGGAAAATG
1 TTTTCCGTGTTTGTTCACGTAATTCGTTTTCCGGAAAACG
* *
1166 TTTTCCCTTGTTTGTTCA-GTAATTCGTTTTTCGGAAAACG
1 TTTT-CCGTGTTTGTTCACGTAATTCGTTTTCCGGAAAACG
*
1206 TTTTCCGTGTGT-TTCACGTAATTCGTTTTCCGGAA
1 TTTTCCGTGTTTGTTCACGTAATTCGTTTTCCGGAA
1241 TGTAATTCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
38 4 0.06
39 27 0.42
40 24 0.37
41 10 0.15
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.47
Consensus pattern (40 bp):
TTTTCCGTGTTTGTTCACGTAATTCGTTTTCCGGAAAACG
Found at i:1240 original size:39 final size:40
Alignment explanation
Indices: 1137--1240 Score: 142
Period size: 40 Copynumber: 2.6 Consensus size: 40
1127 TTTTCGTGTT
* *
1137 TGTTT-ACGTAATTCGTTTTCCGGAAAATGTTTTCCCTTG
1 TGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCCGTG
* *
1176 TTTGTTCA-GTAATTCGTTTTTCGGAAAACGTTTT-CCGTG
1 TGT-TTCACGTAATTCGTTTTCCGGAAAACGTTTTCCCGTG
1215 TGTTTCACGTAATTCGTTTTCCGGAA
1 TGTTTCACGTAATTCGTTTTCCGGAA
1241 TGTAATTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
38 4 0.07
39 25 0.45
40 26 0.46
41 1 0.02
ACGTcount: A:0.18, C:0.17, G:0.19, T:0.45
Consensus pattern (40 bp):
TGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCCGTG
Found at i:1568 original size:26 final size:26
Alignment explanation
Indices: 1493--1587 Score: 70
Period size: 26 Copynumber: 3.5 Consensus size: 26
1483 AAATAATCAA
* *
1493 TTATATTATAATAATATAAGACATTATATT
1 TTATATT-TAATAATAT-ATA-A-TATTTT
1523 TTAT-TTTAATAAATATATAA-ATTTTT
1 TTATATTTAAT-AATATATAATA-TTTT
*
1549 TTATATTTAATAATGA-ATAATATTAT
1 TTATATTTAATAAT-ATATAATATTTT
1575 TTATATTTCAATA
1 TTATATTT-AATA
1588 TTTAGTAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
25 1 0.02
26 25 0.45
27 13 0.23
28 6 0.11
29 7 0.12
30 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTATATTTAATAATATATAATATTTT
Found at i:1799 original size:20 final size:19
Alignment explanation
Indices: 1759--1818 Score: 95
Period size: 20 Copynumber: 3.1 Consensus size: 19
1749 GATGTTTTCC
1759 AAATGTAATTCA-TTTCAG
1 AAATGTAATTCATTTTCAG
1777 AAATGTAATTCATTTTACAG
1 AAATGTAATTCATTTT-CAG
1797 AAATGTAATTCATTTTCCAG
1 AAATGTAATTCATTTT-CAG
1817 AA
1 AA
1819 TTCAAATTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
18 12 0.31
19 3 0.08
20 24 0.62
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (19 bp):
AAATGTAATTCATTTTCAG
Found at i:1826 original size:20 final size:20
Alignment explanation
Indices: 1765--1827 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
1755 TTCCAAATGT
**
1765 AATTCA-TTT-CAGAAATGT
1 AATTCATTTTACAGAAATCA
**
1783 AATTCATTTTACAGAAATGT
1 AATTCATTTTACAGAAATCA
* *
1803 AATTCATTTTCCAGAATTCA
1 AATTCATTTTACAGAAATCA
1823 AATTC
1 AATTC
1828 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.15
19 3 0.08
20 30 0.77
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (20 bp):
AATTCATTTTACAGAAATCA
Found at i:1837 original size:15 final size:15
Alignment explanation
Indices: 1801--1881 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
1791 TTACAGAAAT
**
1801 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1816 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1830 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1845 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1860 GT-ATTCAAATTCCA
1 GTAATTCAAATTCCA
1874 GTAATTCA
1 GTAATTCA
1882 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
14 26 0.45
15 32 0.55
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1843 original size:29 final size:30
Alignment explanation
Indices: 1801--1881 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 30
1791 TTACAGAAAT
1801 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1830 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1860 GT-ATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1882 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 34 0.69
30 15 0.31
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1859 original size:44 final size:44
Alignment explanation
Indices: 1801--1886 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
1791 TTACAGAAAT
**
1801 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
*
1845 GTAATTCAAATTCCAGTATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTC
1887 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:3793 original size:30 final size:29
Alignment explanation
Indices: 3708--3887 Score: 102
Period size: 30 Copynumber: 6.1 Consensus size: 29
3698 CCAGAATGGG
* *
3708 AAAAACA-AAACTTAAAGAATCAAAATAGT
1 AAAAACAGAAACTTAAAGACT-AAAATAGA
* * * * *
3737 ACAAACAGGAATTTAAAGGTCCAAAATAGA
1 AAAAACAGAAACTTAAA-GACTAAAATAGA
*
3767 AAAAACAGAAACTTAAGAGACTAAAATAGC
1 AAAAACAGAAACTTAA-AGACTAAAATAGA
*
3797 AAAAATAGAAAAC-TAAAGGGACT-AAATAG-
1 AAAAACAG-AAACTTAAA--GACTAAAATAGA
* * * *
3826 AAATACATACATTTAAAGGACTAAAATA-A
1 AAAAACAGAAACTTAAA-GACTAAAATAGA
* *
3855 CAAAAATAGAAACTTAAGGGACT-AAATAGA
1 -AAAAACAGAAACTTAA-AGACTAAAATAGA
3885 AAA
1 AAA
3888 TAAAAATAAT
Statistics
Matches: 114, Mismatches: 25, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
28 7 0.06
29 29 0.25
30 68 0.60
31 10 0.09
ACGTcount: A:0.60, C:0.11, G:0.13, T:0.17
Consensus pattern (29 bp):
AAAAACAGAAACTTAAAGACTAAAATAGA
Found at i:5487 original size:17 final size:18
Alignment explanation
Indices: 5457--5502 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
5447 TTTGTATCTC
*
5457 TCTCTGTTTCTGTTGT-T
1 TCTCTGTCTCTGTTGTGT
5474 TC-CTCGTCTCTGTTGTGT
1 TCTCT-GTCTCTGTTGTGT
5492 TCTCTGTCTCT
1 TCTCTGTCTCT
5503 CCGTTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 12 0.48
18 9 0.36
19 2 0.08
ACGTcount: A:0.00, C:0.26, G:0.17, T:0.57
Consensus pattern (18 bp):
TCTCTGTCTCTGTTGTGT
Found at i:6685 original size:223 final size:226
Alignment explanation
Indices: 6253--7099 Score: 1332
Period size: 223 Copynumber: 3.8 Consensus size: 226
6243 TCTTGATGAG
*
6253 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
6317 AG-AAAGTTGATCCATCAAGTGATGGATT-TGAGCAAAA--TCTGAACAAA-T-TT-TCATTATG
65 GGAAAAGCTGATCCATCAAGTGATGAATTCAG-GCAAAAGGT-TGAACAAATTCTTCTCATTATG
* * **** * *
6375 AACTTCTTCATCCTTCTTCAGATGAGTTCTT-TTATTATGAACTCGAACTGGAAAAGCTAATCTA
128 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCA
* * *
6439 TCAAGTGATAGATTTGA-GCAAAAGTTTGAACAAA
193 TCAAGTGAT-GAATTCAGGCAAAAGGTTGAACAAA
* *
6473 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
6538 GAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTG-A-AAGTTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
6601 TTCTTCTTCCTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
6665 AGTGATGAATTCAGGCAAAAGGTTGAACAAA
196 AGTGATGAATTCAGGCAAAAGGTTGAACAAA
6696 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
6761 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAA-
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
6825 --CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG-AAAGCTGATCCATCA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
6887 AGTGATGAATTCAGGCAAAAGGTTGAACAAA
196 AGTGATGAATTCAGGCAAAAGGTTGAACAAA
6918 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
6983 GAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
7048 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
131 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
7100 TGTCAATCCA
Statistics
Matches: 581, Mismatches: 29, Indels: 28
0.91 0.05 0.04
Matches are distributed among these distances:
219 3 0.01
220 60 0.10
221 29 0.05
222 209 0.36
223 212 0.36
224 1 0.00
225 65 0.11
226 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (226 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCA
AGTGATGAATTCAGGCAAAAGGTTGAACAAA
Found at i:7113 original size:113 final size:113
Alignment explanation
Indices: 6253--7099 Score: 1332
Period size: 113 Copynumber: 7.6 Consensus size: 113
6243 TCTTGATGAG
*
6253 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
6317 AG-AAAGTTGATCCATCAAGTGATGGATT-TGAGCAAAA--TCTGAACAAA
65 GGAAAAGCTGATCCATCAAGTGATGAATTCAG-GCAAAAGGT-TGAACAAA
* * ****
6364 -T-TT-TCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTT-TTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
6425 GAAAAGCTAATCTATCAAGTGATAGATTTGA-GCAAAAGTTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGAT-GAATTCAGGCAAAAGGTTGAACAAA
* *
6473 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTTTCATTATGAACTTTTTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
6538 GAAAGGCTGATCCATCAATTGATGAATTCAGGTAAAAGGTTG-A-AAG
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
6584 TTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
6648 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
6696 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
6761 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
6809 TTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
6871 G-AAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
6918 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
6983 GAAAAGCTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
7031 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
7096 GAAA
66 GAAA
7100 TGTCAATCCA
Statistics
Matches: 684, Mismatches: 34, Indels: 34
0.91 0.05 0.05
Matches are distributed among these distances:
107 17 0.02
108 59 0.09
109 75 0.11
110 122 0.18
111 34 0.05
112 122 0.18
113 255 0.37
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAA
Found at i:8224 original size:165 final size:165
Alignment explanation
Indices: 7908--8423 Score: 928
Period size: 165 Copynumber: 3.1 Consensus size: 165
7898 CTTATTTCTA
*
7908 CTATGAGCAAATTCATCTTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATC-TTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
7973 AGAACACTTTTCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAA
65 AGAACAC--TTCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAA
8038 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
128 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
8076 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
8141 GAACACTTCCAGAAGATGCTATGAGCACA-TCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
66 GAACACTT-CAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAC
8205 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
8241 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
* *
8306 GAACACTTCAAAAGATGCTATTAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
66 GAACACTTCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
8371 AGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 AGATCAGATAACTCAAAGAACACTTCCAGAAGATG
8406 CTATTG-GCAAATTCATCT
1 CTA-TGAGCAAATTCATCT
8424 ATTCCAGTTA
Statistics
Matches: 340, Mismatches: 5, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
164 18 0.05
165 231 0.68
166 22 0.06
167 53 0.16
168 16 0.05
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (165 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACC
AGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:8225 original size:82 final size:83
Alignment explanation
Indices: 7908--8423 Score: 930
Period size: 83 Copynumber: 6.2 Consensus size: 83
7898 CTTATTTCTA
* *
7908 CTATGAGCAAATTCATCTTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATTAGATAACTCAA
1 CTATGAGCACATTCATC-TTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAA
*
7973 AGAACACTTTTCAGAAGATG
65 AGAACAC-TTCCAGAAGATG
7993 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
8058 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
8076 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
8141 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
8159 CTATGAGCACA-TCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
8223 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
8241 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
8306 GAACACTT-CAAAAGATG
66 GAACACTTCCAGAAGATG
*
8323 CTATTAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
8388 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
8406 CTATTG-GCAAATTCATCT
1 CTA-TGAGCACATTCATCT
8424 ATTCCAGTTA
Statistics
Matches: 420, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
82 162 0.39
83 188 0.45
84 54 0.13
85 16 0.04
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:9584 original size:12 final size:12
Alignment explanation
Indices: 9562--9616 Score: 60
Period size: 13 Copynumber: 4.5 Consensus size: 12
9552 TGACCTCCCC
9562 TTTTC-CTTTTT
1 TTTTCTCTTTTT
9573 TTTTCTCTTTTT
1 TTTTCTCTTTTT
9585 TCTTT-TCTTTTTT
1 T-TTTCTC-TTTTT
*
9598 CTTTTTTCTTTTT
1 -TTTTCTCTTTTT
9611 TTTTCT
1 TTTTCT
9617 TCTTCAAGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
11 5 0.13
12 14 0.37
13 16 0.42
14 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTCTTTTT
Found at i:9584 original size:19 final size:19
Alignment explanation
Indices: 9562--9616 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
9552 TGACCTCCCC
*
9562 TTTTCCTTTTTTTTTCTCT
1 TTTTTCTTTTTTTTTCTCT
9581 TTTTTCTTTTCTTTTT-TCT
1 TTTTTCTTTT-TTTTTCTCT
9600 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTTTTCT
9617 TCTTCAAGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 5 0.15
19 23 0.70
20 5 0.15
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTTTTTTCTCT
Found at i:9590 original size:14 final size:13
Alignment explanation
Indices: 9561--9620 Score: 63
Period size: 12 Copynumber: 4.7 Consensus size: 13
9551 TTGACCTCCC
*
9561 CTTTTCCTTTTTT
1 CTTTTTCTTTTTT
*
9574 -TTTCTCTTTTTT
1 CTTTTTCTTTTTT
9586 C-TTTTCTTTTTT
1 CTTTTTCTTTTTT
9598 CTTTTTTCTTTTTT
1 C-TTTTTCTTTTTT
9612 -TTTCTTCTT
1 CTTT-TTCTT
9621 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 24 0.60
13 5 0.12
14 11 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:9610 original size:7 final size:7
Alignment explanation
Indices: 9562--9620 Score: 63
Period size: 7 Copynumber: 9.0 Consensus size: 7
9552 TGACCTCCCC
*
9562 TTTTCCT
1 TTTTCTT
9569 TTTT-TT
1 TTTTCTT
*
9575 TTCTCTT
1 TTTTCTT
9582 TTTTC--
1 TTTTCTT
9587 TTTTCTT
1 TTTTCTT
9594 TTTTCTT
1 TTTTCTT
9601 TTTTCTT
1 TTTTCTT
9608 TTTT-TT
1 TTTTCTT
*
9614 TCTTCTT
1 TTTTCTT
9621 CAAGCATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 5 0.11
6 9 0.20
7 30 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:18081 original size:24 final size:23
Alignment explanation
Indices: 18054--18118 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
18044 ATGAAATATT
*
18054 AATAATATATATAAATACTATAAA
1 AATAATATATATAAATA-TAAAAA
* *
18078 AATAATATGTATATATATAAAAA
1 AATAATATATATAAATATAAAAA
* *
18101 AATTATAAAT-TAAATATA
1 AATAATATATATAAATATA
18119 TGAAATTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 7 0.21
23 12 0.35
24 15 0.44
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
AATAATATATATAAATATAAAAA
Found at i:20238 original size:3 final size:3
Alignment explanation
Indices: 20230--20287 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
20220 GGCCTGGTTG
* *
20230 TAA TAA TAA TAT TAA TAA TAA -AA AAA T-A TAA TAAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
*
20273 TAA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA
20288 ATAAAACCGG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:22551 original size:130 final size:131
Alignment explanation
Indices: 22369--22634 Score: 342
Period size: 130 Copynumber: 2.0 Consensus size: 131
22359 ATCTTTAGGA
** ** **
22369 AGGG-TGATAACATGGTTCCTTCGGGATGAGGACGGTTGGTTATCTAAAGGTGACACGGCTCCTA
1 AGGGATGATAACATGGTTCCTTCGGGATGAGGACGACTAATTATCTAAAGGTGACAAAGCTCCTA
* * * *
22433 TGTGATGAGAAGGTCTGGTC-GGGGATGACACAGTTCCTATGTGATGAGGACGATA-AGCCATCT
66 CGTGATGAGAAGGTCTGGTCGGGGGATGACACAGTTCCTACGCGATGAGGACGACATA-CCATCT
22496 TT
130 TT
* * **
22498 AGGGATGATAACATGGTTCCTAT-GTGATGAGGTCGACTAATTATCTAGGGGTGACAAAGCTCCT
1 AGGGATGATAACATGGTTCCT-TCGGGATGAGGACGACTAATTATCTAAAGGTGACAAAGCTCCT
* *
22562 ACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGTTCCTACGCGATGAGGACGACATACCATCT
65 ACGTGATGAGAAGGTCTGGTCGGGGGATGACACAGTTCCTACGCGATGAGGACGACATACCATCT
22627 TT
130 TT
22629 AGGGAT
1 AGGGAT
22635 TTTGGTTTCA
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
129 4 0.03
130 66 0.56
131 46 0.39
132 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (131 bp):
AGGGATGATAACATGGTTCCTTCGGGATGAGGACGACTAATTATCTAAAGGTGACAAAGCTCCTA
CGTGATGAGAAGGTCTGGTCGGGGGATGACACAGTTCCTACGCGATGAGGACGACATACCATCTT
T
Found at i:22775 original size:66 final size:66
Alignment explanation
Indices: 22687--22925 Score: 325
Period size: 66 Copynumber: 3.6 Consensus size: 66
22677 GAAGCTGTCG
* * * * * *
22687 CAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGGGTGTTTCATGGGAAACTGTC
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATGGGAAACTATC
22752 T
66 T
* ** * *
22753 CAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTTAATGTTTCATGAGAAATTATC
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATGGGAAACTATC
22818 T
66 T
* * *
22819 CAAGGGAGACAAAATTTGTTTAAAGGGAAACAATCTCACAGGTTGGTGTTTTATGGGAAACTATC
1 CAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATGGGAAACTATC
22884 T
66 T
* *
22885 CAAGGGAGACAAAATTTTTTTTCAAGGGAAACAAACTCAAA
1 CAAGGGAGACAAAA-TTTGTTTCAAGGGAAACAATCTCAAA
22926 TATTTTTGTT
Statistics
Matches: 149, Mismatches: 23, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
66 127 0.85
67 22 0.15
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (66 bp):
CAAGGGAGACAAAATTTGTTTCAAGGGAAACAATCTCAAAGGTTGGTGTTTCATGGGAAACTATC
T
Found at i:22777 original size:21 final size:20
Alignment explanation
Indices: 22744--22785 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
22734 GTTTCATGGG
*
22744 AAACTGTCTCAAGGGAGACA
1 AAACTGTCTCAAGGGAAACA
*
22764 AAACTTGTTTCAAGGGAAACA
1 AAAC-TGTCTCAAGGGAAACA
22785 A
1 A
22786 TCTCAAAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (20 bp):
AAACTGTCTCAAGGGAAACA
Found at i:22790 original size:36 final size:35
Alignment explanation
Indices: 22733--22856 Score: 96
Period size: 36 Copynumber: 3.6 Consensus size: 35
22723 CAAAGATGGG
* **
22733 TGTTTCATGGGAAACTGTCTCAAGGGAGACAAAACT
1 TGTTTCAAGGGAAACAATCTCAAGGGAGACAAAA-T
***
22769 TGTTTCAAGGGAAACAATCTCAA---AG-GTTAA-
1 TGTTTCAAGGGAAACAATCTCAAGGGAGACAAAAT
* * **
22799 TGTTTCATGAGAAATTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACAATCTCAAGGGAGACAAAA-T
*
22835 TGTTTAAAGGGAAACAATCTCA
1 TGTTTCAAGGGAAACAATCTCA
22857 CAGGTTGGTG
Statistics
Matches: 64, Mismatches: 18, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
30 19 0.30
32 2 0.03
33 4 0.06
34 2 0.03
36 37 0.58
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (35 bp):
TGTTTCAAGGGAAACAATCTCAAGGGAGACAAAAT
Found at i:22875 original size:132 final size:133
Alignment explanation
Indices: 22687--22925 Score: 363
Period size: 132 Copynumber: 1.8 Consensus size: 133
22677 GAAGCTGTCG
* * *
22687 CAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGGGTGTTTCATGGGAAACTGTC
1 CAAGAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
*
22752 TCAAGGGAGACAAAA-CTTGTTTCAAGGGAAACAATCTCAAAGGTTAATGTTTCATGAGAAATTA
66 TCAAGGGAGACAAAATCTTGTTTCAAGGGAAACAAACTCAAAGGTTAATGTTTCATGAGAAATTA
22816 TCT
131 TCT
* * * * * *
22819 CAAGGGAGACAAAATTTGTTTAAAGGGAAACAATCTCACAGGTTGGTGTTTTATGGGAAACTATC
1 CAAGAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
* *
22884 TCAAGGGAGACAAAATTTTTTTTCAAGGGAAACAAACTCAAA
66 TCAAGGGAGACAAAATCTTGTTTCAAGGGAAACAAACTCAAA
22926 TATTTTTGTT
Statistics
Matches: 94, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
132 71 0.76
133 23 0.24
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (133 bp):
CAAGAGAGACAAAATTCGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
TCAAGGGAGACAAAATCTTGTTTCAAGGGAAACAAACTCAAAGGTTAATGTTTCATGAGAAATTA
TCT
Found at i:22944 original size:132 final size:133
Alignment explanation
Indices: 22687--22973 Score: 353
Period size: 132 Copynumber: 2.2 Consensus size: 133
22677 GAAGCTGTCG
* * * *
22687 CAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATGGGTGTTTCATGGGAAACTGTC
1 CAAGAGAGACAAAATTTGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
* * * *
22752 TCAAGGGAGACAAAACTTGTTTCAAGGGAAACAATCTCAAAGGTTAATGTTTCATGAG-AAATTA
66 TCAAGGGAGACAAAACTTGTTTCAAGGGAAACAAACTCAAAGATTAATGTTTCATAAGAAAAATA
22816 TCT
131 TCT
* * * * *
22819 CAAGGGAGACAAAATTTGTTTAAAGGGAAACAATCTCACAGGTTGGTGTTTTATGGGAAACTATC
1 CAAGAGAGACAAAATTTGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
* * * **
22884 TCAAGGGAGACAAAATTTTTTTTCAAGGGAAACAAACTCAAATATTTTTGTTTCA-AAGAAAAAA
66 TCAAGGGAGACAAAA-CTTGTTTCAAGGGAAACAAACTCAAAGATTAATGTTTCATAAG-AAAAA
*
22948 TGTCT
129 TATCT
* *
22953 CAAGTGAGACGAAATTTGTTT
1 CAAGAGAGACAAAATTTGTTT
22974 TGATAGAAAT
Statistics
Matches: 131, Mismatches: 21, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
132 73 0.56
133 32 0.24
134 26 0.20
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (133 bp):
CAAGAGAGACAAAATTTGTTTAAAGGGAAACAATCTCAAAGATGGGTGTTTCATGGGAAACTATC
TCAAGGGAGACAAAACTTGTTTCAAGGGAAACAAACTCAAAGATTAATGTTTCATAAGAAAAATA
TCT
Found at i:23018 original size:36 final size:40
Alignment explanation
Indices: 22934--23048 Score: 107
Period size: 36 Copynumber: 3.0 Consensus size: 40
22924 AATATTTTTG
* ** * *
22934 TTTCAAAGAAAAAATGTCTCAAGTGAGACGAAA-TTTG-T
1 TTTCATAGAAAAGTTGTCTCAAGCGAGACAAAATTTTGTT
*
22972 TTTGATAG-AAA-TTGTCTCAAGCGAGA-AAAATTTTGTT
1 TTTCATAGAAAAGTTGTCTCAAGCGAGACAAAATTTTGTT
* * *
23009 TTTCA-AGAAAAGTTGTTTCTAGCGAGACAACATTTTGTT
1 TTTCATAGAAAAGTTGTCTCAAGCGAGACAAAATTTTGTT
23048 T
1 T
23049 CGAGAGAAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
35 3 0.05
36 19 0.30
37 11 0.17
38 19 0.30
39 11 0.17
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (40 bp):
TTTCATAGAAAAGTTGTCTCAAGCGAGACAAAATTTTGTT
Found at i:24253 original size:15 final size:14
Alignment explanation
Indices: 24229--24279 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
24219 TCCCCTTTTA
24229 TTTGTTTTTTTTCT
1 TTTGTTTTTTTTCT
24243 TTTGATTTTTTTTCT
1 TTTG-TTTTTTTTCT
* * *
24258 TTTCTCTTTTCTCT
1 TTTGTTTTTTTTCT
24272 TTTGTTTT
1 TTTGTTTT
24280 GCTCTTTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (14 bp):
TTTGTTTTTTTTCT
Found at i:24310 original size:26 final size:26
Alignment explanation
Indices: 24276--24343 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
24266 TTCTCTTTTG
*
24276 TTTTGCTCTTTGTTTTTTCTTTACTTC
1 TTTT-CTCTTTGTTTTTTCTTTACTTA
* * *
24303 TTTTCTCTTTGCTCTTTCTTTGCTTA
1 TTTTCTCTTTGTTTTTTCTTTACTTA
24329 TTTTCTCTTTGTTTT
1 TTTTCTCTTTGTTTT
24344 GATTTGATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 31 0.89
27 4 0.11
ACGTcount: A:0.03, C:0.19, G:0.07, T:0.71
Consensus pattern (26 bp):
TTTTCTCTTTGTTTTTTCTTTACTTA
Found at i:24338 original size:33 final size:31
Alignment explanation
Indices: 24264--24338 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
24254 TTCTTTTCTC
* * * *
24264 TTTTCTCTTTTGTTTTGCTCTTTGTTTTTTC
1 TTTTCTCTTTTCTTTTGCTCTTTCTTTCTTA
*
24295 TTTACTTCTTTTCTCTTTGCTCTTTCTTTGCTTA
1 TTTTC-TCTTTTCT-TTTGCTCTTTCTTT-CTTA
24329 TTTTCTCTTT
1 TTTTCTCTTT
24339 GTTTTGATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 4 0.11
32 7 0.20
33 18 0.51
34 6 0.17
ACGTcount: A:0.03, C:0.20, G:0.07, T:0.71
Consensus pattern (31 bp):
TTTTCTCTTTTCTTTTGCTCTTTCTTTCTTA
Found at i:28079 original size:30 final size:30
Alignment explanation
Indices: 28045--28166 Score: 108
Period size: 30 Copynumber: 4.1 Consensus size: 30
28035 CAAAATAGAA
28045 AAAATTGAAAAAATAGAAACTTAAGGGACT
1 AAAATTGAAAAAATAGAAACTTAAGGGACT
* * *
28075 AAAATATCAAAAACTA-AAACTAAAGGGACT
1 AAAAT-TGAAAAAATAGAAACTTAAGGGACT
* * * **
28105 -AAATAGAAAATAA-AGATATTTAAATGACT
1 AAAATTGAAAA-AATAGAAACTTAAGGGACT
*
28134 AAAA-TAACAAAAATAGAAACTTAAGGGACT
1 AAAATTGA-AAAAATAGAAACTTAAGGGACT
28164 AAA
1 AAA
28167 TAGAAAATAA
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
28 5 0.07
29 17 0.25
30 39 0.57
31 8 0.12
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (30 bp):
AAAATTGAAAAAATAGAAACTTAAGGGACT
Found at i:29657 original size:3 final size:3
Alignment explanation
Indices: 29649--29692 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
29639 GTAATTATGC
* *
29649 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29693 TTTTTGTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:30354 original size:158 final size:159
Alignment explanation
Indices: 30066--30385 Score: 633
Period size: 158 Copynumber: 2.0 Consensus size: 159
30056 TCCAAGGCTT
30066 TTTGTTGATAGTTTGCCTAAATTAATTTCAGGATAAACGTCGGGCTGTTAAACAACTTGTTTATC
1 TTTGTTGATAGTTTGCCTAAATTAATTTCAGGATAAACGTCGGGCTGTTAAACAACTTGTTTATC
30131 ATACTCTTCCTGACAATGGTTCTTTTACTTGTTGATTGGTGTGGATGGAAAATTTTGAGGCTACC
66 ATACTCTTCCTGACAATGGTTCTTTTACTTGTTGATTGGTGTGGATGGAAAATTTTGAGGCTACC
30196 CTTGGCACCAATTTTACTTGACCT-CCCA
131 CTTGGCACCAATTTTACTTGACCTCCCCA
30224 TTTGTTGATAGTTTGCCTAAATTAATTTCAGGATAAACGTCGGGCTGTTAAACAACTTGTTTATC
1 TTTGTTGATAGTTTGCCTAAATTAATTTCAGGATAAACGTCGGGCTGTTAAACAACTTGTTTATC
30289 ATACTCTTCCTGACAATGGTTCTTTTACTTGTTGATTGGTGTGGATGGAAAATTTTGAGGCTACC
66 ATACTCTTCCTGACAATGGTTCTTTTACTTGTTGATTGGTGTGGATGGAAAATTTTGAGGCTACC
30354 CTTGGCACCAATTTTACTTGACCTCCCCA
131 CTTGGCACCAATTTTACTTGACCTCCCCA
30383 TTT
1 TTT
30386 ACCATATCTT
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 154 0.96
159 7 0.04
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (159 bp):
TTTGTTGATAGTTTGCCTAAATTAATTTCAGGATAAACGTCGGGCTGTTAAACAACTTGTTTATC
ATACTCTTCCTGACAATGGTTCTTTTACTTGTTGATTGGTGTGGATGGAAAATTTTGAGGCTACC
CTTGGCACCAATTTTACTTGACCTCCCCA
Found at i:38162 original size:21 final size:21
Alignment explanation
Indices: 38059--38163 Score: 135
Period size: 21 Copynumber: 5.0 Consensus size: 21
38049 ATTACGATAG
*
38059 TCCAAGTTCACGTTGCGAT--TT
1 TCCAAGTT--CGTTGCGATAGTC
38080 TCCAAGTTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
*
38101 TCCAAGTGCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
38122 TCCAAGTTCGTTGC-ATTAGTC
1 TCCAAGTTCGTTGCGA-TAGTC
*
38143 TCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
38164 CAAAACCGCA
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.12
20 1 0.01
21 65 0.86
22 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
TCCAAGTTCGTTGCGATAGTC
Found at i:38287 original size:5 final size:5
Alignment explanation
Indices: 38277--38309 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
38267 AACCACGACC
38277 ACGAG ACGAG ACGAG ACGAG ACG-G ACGACG ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGA-G ACG
38310 GCGGCGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.36, C:0.24, G:0.39, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:38297 original size:15 final size:15
Alignment explanation
Indices: 38271--38309 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
38261 GACCACAACC
*
38271 ACGACCACGAGACGAG
1 ACGACGACGAGACG-G
38287 ACGA-GACGAGACGG
1 ACGACGACGAGACGG
38301 ACGACGACG
1 ACGACGACG
38310 GCGGCGGCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 12 0.57
16 4 0.19
ACGTcount: A:0.36, C:0.28, G:0.36, T:0.00
Consensus pattern (15 bp):
ACGACGACGAGACGG
Found at i:38795 original size:12 final size:11
Alignment explanation
Indices: 38765--38798 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
38755 CCGTCTCGTC
38765 TCGGGTCG-GG
1 TCGGGTCGTGG
38775 TCGGGTCGTGG
1 TCGGGTCGTGG
38786 TCGTGGTCGTGG
1 TCG-GGTCGTGG
38798 T
1 T
38799 AATACGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (11 bp):
TCGGGTCGTGG
Found at i:39270 original size:21 final size:21
Alignment explanation
Indices: 38872--39266 Score: 565
Period size: 21 Copynumber: 19.0 Consensus size: 21
38862 ATACAATAAT
38872 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
38893 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
38914 GAACTTTGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
* * *
38935 GAAGTTGAAGAGTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
38956 GAAGTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
38977 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
38998 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
* *
39019 GAAGTTAGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
39040 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
39061 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
39082 G-A--TGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
39100 GAATTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
39121 AAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
39142 GAACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
39163 GCACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
*
39184 GTACTTGGAGACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
* *
39205 GCACTTGGA-A-AATCGCAACGC
1 GAACTTGGAGACTATCGCAA--C
*
39226 GAACTTGGA-A-AATCGCAACGC
1 GAACTTGGAGACTATCGCAA--C
39247 GAACTT-G-GACTATCGCAAC
1 GAACTTGGAGACTATCGCAAC
39266 G
1 G
39267 CGAATATGTA
Statistics
Matches: 346, Mismatches: 21, Indels: 16
0.90 0.05 0.04
Matches are distributed among these distances:
18 17 0.05
19 10 0.03
20 4 0.01
21 315 0.91
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.19
Consensus pattern (21 bp):
GAACTTGGAGACTATCGCAAC
Found at i:42161 original size:20 final size:21
Alignment explanation
Indices: 42136--42179 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
42126 TTTGGTAATA
42136 ATACCCAAAAGA-CAATATCG
1 ATACCCAAAAGACCAATATCG
*
42156 ATACCCAAGAGACCAATATCG
1 ATACCCAAAAGACCAATATCG
42177 ATA
1 ATA
42180 TTATATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.48, C:0.25, G:0.11, T:0.16
Consensus pattern (21 bp):
ATACCCAAAAGACCAATATCG
Found at i:50334 original size:17 final size:17
Alignment explanation
Indices: 50312--50349 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
50302 CTATTCTTCG
*
50312 AGTGGTCAAAATAATGA
1 AGTGGTCAAAATAATAA
50329 AGTGGTCAAAATAATAA
1 AGTGGTCAAAATAATAA
50346 AGTG
1 AGTG
50350 TTCTAGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (17 bp):
AGTGGTCAAAATAATAA
Found at i:53870 original size:47 final size:47
Alignment explanation
Indices: 53797--54007 Score: 205
Period size: 47 Copynumber: 4.5 Consensus size: 47
53787 CTAGCACTTT
* *
53797 ATGTGCGATATT-TTACTAGCAGTTTATACTGTATACTGTGCATTGA
1 ATGTGCCATATTGTTACTAGCAGTTTATACTGTATACTGTGCACTGA
* *
53843 ATGTGCCATATTGTTACTAGCAATTTATACT-TCATACTAG-GTACTGA
1 ATGTGCCATATTGTTACTAGCAGTTTATACTGT-ATACT-GTGCACTGA
* * * * * *
53890 ATGTGCCATACTGTTAAT-GACAGTTTATAATGCATACCGGGCACTGA
1 ATGTGCCATATTGTTACTAG-CAGTTTATACTGTATACTGTGCACTGA
* * * * * * *
53937 ATGTGACATACTATTACTGGCAGTTTATACTGTATATTGTGTACTAA
1 ATGTGCCATATTGTTACTAGCAGTTTATACTGTATACTGTGCACTGA
*
53984 ATGTGCCATATCGTTACTAGCAGT
1 ATGTGCCATATTGTTACTAGCAGT
54008 AATGTTGCAT
Statistics
Matches: 132, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
46 14 0.11
47 116 0.88
48 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.37
Consensus pattern (47 bp):
ATGTGCCATATTGTTACTAGCAGTTTATACTGTATACTGTGCACTGA
Found at i:54474 original size:17 final size:17
Alignment explanation
Indices: 54390--54479 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
54380 AAAATGAAAT
*
54390 TAAAAGAAATA-ACACAG
1 TAAAAGATATATA-ACAG
* * *
54407 TAAAAGATACATTACAA
1 TAAAAGATATATAACAG
* *
54424 TTAAAGATATAGTAA-AA
1 TAAAAGATATA-TAACAG
* *
54441 TAAAGGACATAGT-ACAG
1 TAAAAGATATA-TAACAG
54458 TAAAAGATATATAACAG
1 TAAAAGATATATAACAG
54475 TAAAA
1 TAAAA
54480 AGAGCAGTAC
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
16 2 0.04
17 52 0.93
18 2 0.04
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.21
Consensus pattern (17 bp):
TAAAAGATATATAACAG
Found at i:57064 original size:23 final size:23
Alignment explanation
Indices: 57038--57087 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
57028 AATAACGTAT
* *
57038 TAGGTAGAATTTATATAATATAA
1 TAGGTAGAACTTATATAATAAAA
**
57061 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAACTTATATAATAAAA
57084 TAGG
1 TAGG
57088 CATTTAACCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (23 bp):
TAGGTAGAACTTATATAATAAAA
Found at i:57139 original size:87 final size:87
Alignment explanation
Indices: 56914--57140 Score: 310
Period size: 87 Copynumber: 2.6 Consensus size: 87
56904 TATATTATAT
* * * *
56914 CATTTAATCGAAAATATTATTAAGTACAATAACATATGAGGTAACACTTATATAATGTAATAAAT
1 CATTTAACCGAAAATATTATTAAGTACAATAACATATTAGGTAGCACTTATATAATATAATAAAT
*
56979 AGCGCTTATATAATAAAATATA
66 AGCGCTTATATAATAAAATAGA
* * * * **
57001 TATTTAACCGAAAATATTATTAAGTACAATAACGTATTAGGTAGAATTTATATAATATAATAGGT
1 CATTTAACCGAAAATATTATTAAGTACAATAACATATTAGGTAGCACTTATATAATATAATAAAT
*
57066 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGA
* * * *
57088 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGATAGCGCTTATAT
1 CATTTAACCGAAAATATTATTAAGTACAATAACATATTAGGTAGCACTTATAT
57141 TAACATATTT
Statistics
Matches: 120, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 120 1.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.33
Consensus pattern (87 bp):
CATTTAACCGAAAATATTATTAAGTACAATAACATATTAGGTAGCACTTATATAATATAATAAAT
AGCGCTTATATAATAAAATAGA
Found at i:57593 original size:200 final size:199
Alignment explanation
Indices: 57158--57659 Score: 636
Period size: 200 Copynumber: 2.5 Consensus size: 199
57148 TTTTCTAACT
* * *
57158 AAACAGGTATACTTATACCGGTAATATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGA
1 AAACAGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
57223 TGTTTTTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCATTGGATAT
66 TGTTTTTGAGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACAT
* * *
57286 TCATTCTGGAAAAAAATATCGACGCAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTC
130 TCATTCTGGAAAAAAATATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTCTA
57351 TCATA
195 TCATA
* * * * * *
57356 AAACCGGTATATTTCTACTGGGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGA
1 AAACAGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
57421 TGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGACATT
66 TGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACATT
** *** ** * *
57486 CATTCTGGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACATTATGTTGACTTATTCT
131 CATTCTGGA-AAAAAATATCGACACAAACTTAAA-ACGTGTCGATACATTATGTAGACCTATTCT
57550 ATCATA
194 ATCATA
* * *
57556 AAACTGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGATTTCGT
1 AAACAGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
57621 TATTTTT-AGGGTCGATACTTTTAGA-AAATATATCGACAC
66 TGTTTTTGA-GATCGATACTTTTA-ATAAATGTATCGACAC
57660 ATATGTTTAC
Statistics
Matches: 261, Mismatches: 37, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
197 3 0.01
198 73 0.28
199 53 0.20
200 131 0.50
201 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (199 bp):
AAACAGGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGAGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCATTGGACATT
CATTCTGGAAAAAAATATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTCTAT
CATA
Found at i:58165 original size:60 final size:60
Alignment explanation
Indices: 58092--58226 Score: 270
Period size: 60 Copynumber: 2.2 Consensus size: 60
58082 TCGGTAATTA
58092 TTACCGGTTTTGTTATGCATAACAATAACAAAACCGGTCATAACAAAATCGATAATGTTT
1 TTACCGGTTTTGTTATGCATAACAATAACAAAACCGGTCATAACAAAATCGATAATGTTT
58152 TTACCGGTTTTGTTATGCATAACAATAACAAAACCGGTCATAACAAAATCGATAATGTTT
1 TTACCGGTTTTGTTATGCATAACAATAACAAAACCGGTCATAACAAAATCGATAATGTTT
58212 TTACCGGTTTTGTTA
1 TTACCGGTTTTGTTA
58227 AAAAACCCGA
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (60 bp):
TTACCGGTTTTGTTATGCATAACAATAACAAAACCGGTCATAACAAAATCGATAATGTTT
Found at i:68089 original size:24 final size:24
Alignment explanation
Indices: 68057--68104 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
68047 TAAACTTAAT
68057 TTTTTTTATTTTATTTGGTTGCTC
1 TTTTTTTATTTTATTTGGTTGCTC
68081 TTTTTTTATTTTATTTGGTTGCTC
1 TTTTTTTATTTTATTTGGTTGCTC
68105 ATTTATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.08, G:0.12, T:0.71
Consensus pattern (24 bp):
TTTTTTTATTTTATTTGGTTGCTC
Done.