Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003180.1 Hibiscus syriacus cultivar Beakdansim tig00006695_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: 64678
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1348 original size:134 final size:134
Alignment explanation
Indices: 1084--1440 Score: 468
Period size: 134 Copynumber: 2.7 Consensus size: 134
1074 CGGGTCATCC
* * * * * * * * *
1084 AAGGGTGACACGGTTCTTACGTGATGAGAAAATCTGATCGAGG-GATGACACTACTCATGCATGA
1 AAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCG-GGAGATGACACGACTCATACGTGA
* *
1148 TGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACCCGGTTCCTACGTGATGAGGACGGTTGG
65 TGAAGAGTTC-TGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGTTGG
1213 TTATCT
129 TTATCT
*
1219 AGGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACGTGAT
1 AAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACGTGAT
* * * *
1284 AAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAATACGGTTCTTATGTGATGAGGAC-GTCTGGT
66 GAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGT-TGGT
1348 TATCT
130 TATCT
* * * *
1353 AAGGGTGACATGGCTCCTACGCGATG-GAGAGATCGGGTCAGGAGATGACACGGCTCATACGTGA
1 AAGGGTGACACGGCTCCTACGCGATGAG-GAGATCTGGTCGGGAGATGACACGACTCATACGTGA
*
1417 TGAAGAGTTATGGCCATCTTTAGG
65 TGAAGAGTTCTGGCCATCTTTAGG
1441 GATAACGATT
Statistics
Matches: 196, Mismatches: 23, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
133 3 0.02
134 133 0.68
135 60 0.31
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (134 bp):
AAGGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTCGGGAGATGACACGACTCATACGTGAT
GAAGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGTTGGTT
ATCT
Found at i:1775 original size:29 final size:30
Alignment explanation
Indices: 1726--1783 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1716 ACAAAACTTT
1726 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
1756 GTTTCAAAAGAAA-TGACTCAAAGATTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTT
1784 TTCACGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:1866 original size:91 final size:93
Alignment explanation
Indices: 1662--1875 Score: 270
Period size: 91 Copynumber: 2.3 Consensus size: 93
1652 CTCAAAGATT
* *
1662 TTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTTG
1 TTTCAAAAGAAACA-ACTCAAAGATTTTTCTCAAG-AAAACTGTCTCAAGAGAAACAAAACTTTG
* *
1727 TTTCAAAAGAAACAAACTCAAAGATTTTGG
64 GTTCAAAAGAAACAAACTCAAAGATTTTGA
** * * *
1757 TTTCAAAAGAAATGACTCAAAGATTTTT-TCACG-AAATTGTCTTAAGAGAAACAAAACTTTGGT
1 TTTCAAAAGAAACAACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGGT
** *
1820 TCAAAAGAAACAGGCTCAAAGATTTTTA
66 TCAAAAGAAACAAACTCAAAGATTTTGA
* *
1848 TTTCAAAAGAAACAACTCACAGACTTTT
1 TTTCAAAAGAAACAACTCAAAGATTTTT
1876 GTTTTAAGAG
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
91 74 0.72
93 4 0.04
94 14 0.14
95 11 0.11
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (93 bp):
TTTCAAAAGAAACAACTCAAAGATTTTTCTCAAGAAAACTGTCTCAAGAGAAACAAAACTTTGGT
TCAAAAGAAACAAACTCAAAGATTTTGA
Found at i:1910 original size:33 final size:32
Alignment explanation
Indices: 1872--1946 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
1862 ACTCACAGAC
*
1872 TTTTGTTTTAAGAGAAATAAACTCAAAGATAGG
1 TTTTG-TTTAAGAGAAACAAACTCAAAGATAGG
* *
1905 TTTTGTTTAAGGGAAACAATCTCAAAGATA--
1 TTTTGTTTAAGAGAAACAAACTCAAAGATAGG
1935 TTTT-TTTAAGAG
1 TTTTGTTTAAGAG
1947 GAATTGTCTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 7 0.18
30 4 0.11
32 22 0.58
33 5 0.13
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (32 bp):
TTTTGTTTAAGAGAAACAAACTCAAAGATAGG
Found at i:1929 original size:32 final size:30
Alignment explanation
Indices: 1834--1949 Score: 87
Period size: 29 Copynumber: 3.8 Consensus size: 30
1824 AAGAAACAGG
* **
1834 CTCAAAGAT-TTTTATTTCAAAAGAAAC-AA
1 CTCAAAGATATTTTGTTT-AAGGGAAACAAA
* * * *
1863 CTCACAGA-CTTTTGTTTTAAGAGAAATAAA
1 CTCAAAGATATTTTG-TTTAAGGGAAACAAA
*
1893 CTCAAAGATAGGTTTTGTTTAAGGGAAACAAT
1 CTCAAAGATA--TTTTGTTTAAGGGAAACAAA
1925 CTCAAAGATATTTT-TTTAAGAGGAA
1 CTCAAAGATATTTTGTTTAAG-GGAA
1950 TTGTCTTAAA
Statistics
Matches: 71, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
29 24 0.34
30 20 0.28
32 22 0.31
33 5 0.07
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (30 bp):
CTCAAAGATATTTTGTTTAAGGGAAACAAA
Found at i:1998 original size:66 final size:66
Alignment explanation
Indices: 1917--2133 Score: 209
Period size: 66 Copynumber: 3.3 Consensus size: 66
1907 TTGTTTAAGG
* * * ** *
1917 GAAACA-ATCTCAAAGATATTTT-TTTAAGAGGAATTGTCTT-AAAAGAGACAAACCTTTGTTTT
1 GAAACAGA-CTCAAAGAT-TTTTCTTCAAAAGGAACTGT-TTCAAAAGAGACAAAAATTTGTTTC
1979 CATAA
63 CA-AA
*
1984 -AAACAGACTTAAAGATTTTTCTTCAAAAGGAACTGTTTCAAAAGAGACAAAAATTTGTTTCCAA
1 GAAACAGACTCAAAGATTTTTCTTCAAAAGGAACTGTTTCAAAAGAGACAAAAATTTGTTTCCAA
2048 A
66 A
* * * *
2049 GAAACATACTCAAAGA-TTCT-TTCAAAAGAAACT-TTCTCAAAAGAGACAAAATTTTGTTAT-C
1 GAAACAGACTCAAAGATTTTTCTTCAAAAGGAACTGTT-TCAAAAGAGACAAAAATTTGTT-TCC
2110 AAA
64 AAA
2113 GAAAC-GTACTCAAAGATTTTT
1 GAAACAG-ACTCAAAGATTTTT
2134 TCATTTTGTT
Statistics
Matches: 128, Mismatches: 14, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
63 2 0.02
64 51 0.40
65 15 0.12
66 59 0.46
67 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (66 bp):
GAAACAGACTCAAAGATTTTTCTTCAAAAGGAACTGTTTCAAAAGAGACAAAAATTTGTTTCCAA
A
Found at i:2105 original size:64 final size:63
Alignment explanation
Indices: 1957--2136 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 63
1947 GAATTGTCTT
** * * *
1957 AAAAGAGACAAACCTTTGTTTTCATAA-AAACAGACTTAAAGATTTTTCTTCAAAAGGAACTGTT
1 AAAAGAGACAAAAATTTG-TTTCA-AAGAAACATACTCAAAGA-TTTT-TTCAAAAGAAACTGTT
2021 TC
62 TC
*
2023 AAAAGAGACAAAAATTTGTTTCCAAAGAAACATACTCAAAGATTCTTTCAAAAGAAACT-TTCTC
1 AAAAGAGACAAAAATTTGTTT-CAAAGAAACATACTCAAAGATTTTTTCAAAAGAAACTGTT-TC
* *
2087 AAAAGAGACAAAATTTTGTTATCAAAGAAACGTACTCAAAGATTTTTTCA
1 AAAAGAGACAAAAATTTGTT-TCAAAGAAACATACTCAAAGATTTTTTCA
2137 TTTTGTTTTG
Statistics
Matches: 101, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
63 2 0.02
64 59 0.58
65 9 0.09
66 31 0.31
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.29
Consensus pattern (63 bp):
AAAAGAGACAAAAATTTGTTTCAAAGAAACATACTCAAAGATTTTTTCAAAAGAAACTGTTTC
Found at i:2204 original size:100 final size:101
Alignment explanation
Indices: 2049--2229 Score: 246
Period size: 100 Copynumber: 1.8 Consensus size: 101
2039 TGTTTCCAAA
* *
2049 GAAACATACTCAAAGATTCTTTCAAAAGAAACTTTCTCAAAAGAGACAAAATTTTGTTATC-AAA
1 GAAACAGACTCAAAGATTCTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTT-TCAAAA
*
2113 GAAA-CGTACTCAAAGATTTTTTCATTTTGTTTTGGGT
65 GAAATAG-ACTCAAAGATTTTTTCATTTTGTTTTGGGT
* *
2150 GAAACAGACTCAAAGATT-TTTCAATAA-AATA-TGTCTCAAGAGAGACAAAGTTTTGTTTCAAA
1 GAAACAGACTCAAAGATTCTTTCAA-AAGAA-ACTGTCTCAAAAGAGACAAAATTTTGTTTCAAA
2212 AGAAATAGACTCAAAGAT
64 AGAAATAGACTCAAAGAT
2230 CCTTTGTTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
99 2 0.03
100 48 0.68
101 21 0.30
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (101 bp):
GAAACAGACTCAAAGATTCTTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTTGTTTCAAAAG
AAATAGACTCAAAGATTTTTTCATTTTGTTTTGGGT
Found at i:2255 original size:30 final size:31
Alignment explanation
Indices: 2201--2259 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2191 GAGACAAAGT
2201 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAATAGACTCAAAGATCC
*
2232 TTTGTTTCAAAAGAAA-CGACTCAAAGAT
1 TTTGTTTCAAAAGAAATAGACTCAAAGAT
2260 GATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAATAGACTCAAAGATCC
Found at i:2337 original size:36 final size:37
Alignment explanation
Indices: 2296--2401 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 37
2286 CATAATTTGG
*
2296 AAAATTGTCTCAAGTGAGACAACATTTGTTTTT-AGA
1 AAAATTGTCTCAAGTGAGACAAAATTTGTTTTTGAGA
* ** *
2332 GAAATTGTCTCAAACGAGACAAAAATTGTTTTTGAGA
1 AAAATTGTCTCAAGTGAGACAAAATTTGTTTTTGAGA
*
2369 AAAATTATCTCAAGTGAGACAAAAATTTGTTTT
1 AAAATTGTCTCAAGTGAGAC-AAAATTTGTTTT
2402 AAAATTCTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 28 0.48
37 19 0.33
38 11 0.19
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (37 bp):
AAAATTGTCTCAAGTGAGACAAAATTTGTTTTTGAGA
Found at i:3849 original size:22 final size:22
Alignment explanation
Indices: 3823--3865 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3813 AGTTTTATTA
*
3823 AAGTTTACTCTTTTTACTTTTC
1 AAGTTTACCCTTTTTACTTTTC
* *
3845 AAGTTTTCCCTTTTTTCTTTT
1 AAGTTTACCCTTTTTACTTTT
3866 ATTTTCAAGC
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:0.14, C:0.19, G:0.05, T:0.63
Consensus pattern (22 bp):
AAGTTTACCCTTTTTACTTTTC
Found at i:10370 original size:18 final size:18
Alignment explanation
Indices: 10335--10377 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
10325 TCTTATTATT
* *
10335 TTTACTTTAATTATTTTTA
1 TTTA-TTTAATCACTTTTA
10354 TTTATTTAATCACTTTTA
1 TTTATTTAATCACTTTTA
10372 -TTATTT
1 TTTATTT
10378 TAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:10387 original size:18 final size:18
Alignment explanation
Indices: 10335--10388 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
10325 TCTTATTATT
10335 TTTACTTTAATTAT-TTTTA
1 TTTA-TTTAA-TATCTTTTA
10354 TTTATTTAATCA-CTTTTA
1 TTTATTTAAT-ATCTTTTA
10372 -TTATTTTAATATCTTTT
1 TTTA-TTTAATATCTTTT
10389 TACCAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 5 0.16
18 22 0.71
19 4 0.13
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTATTTAATATCTTTTA
Found at i:15267 original size:14 final size:14
Alignment explanation
Indices: 15250--15284 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
15240 AAAGGAACCA
15250 AAATAAAAAAACAT
1 AAATAAAAAAACAT
* *
15264 AAATTAAAATACAT
1 AAATAAAAAAACAT
15278 AAATAAA
1 AAATAAA
15285 TATGTACATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (14 bp):
AAATAAAAAAACAT
Found at i:16807 original size:23 final size:23
Alignment explanation
Indices: 16777--16826 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
16767 AGGGGATTAG
16777 GGTTAAAACCCTAATCTATTTAA
1 GGTTAAAACCCTAATCTATTTAA
*
16800 GGTTAAAACCCTAATCTATTTAG
1 GGTTAAAACCCTAATCTATTTAA
16823 GGTT
1 GGTT
16827 TGACAAATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (23 bp):
GGTTAAAACCCTAATCTATTTAA
Found at i:19195 original size:13 final size:13
Alignment explanation
Indices: 19177--19201 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19167 TATTCTCATG
19177 TGTTAAAAAAAGA
1 TGTTAAAAAAAGA
19190 TGTTAAAAAAAG
1 TGTTAAAAAAAG
19202 TTAACAGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
TGTTAAAAAAAGA
Found at i:30265 original size:34 final size:34
Alignment explanation
Indices: 30222--30320 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
30212 TTTCATCCTA
*
30222 TTAGGATTCAAATTCCTAAAAATAGGATAGAATT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
30256 TTAGGATTCAAACTCCTAAAAGTAGGATAGAGTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
30290 CTACTATGATTTAAACTCTTAAAAATAGGAT
1 -T--TAGGATTCAAACTCCTAAAAATAGGAT
30321 TCACAAGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
34 31 0.56
35 1 0.02
37 23 0.42
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (34 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:30809 original size:18 final size:18
Alignment explanation
Indices: 30788--30841 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
30778 TTGATTTTTT
30788 TTATTATTATTATTTTAC
1 TTATTATTATTATTTTAC
**
30806 TTA-TATATATGCTTTTAC
1 TTATTAT-TATTATTTTAC
30824 TT-TT-TTATATATTTTAC
1 TTATTATTAT-TATTTTAC
30841 T
1 T
30842 CATTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
16 3 0.10
17 11 0.38
18 15 0.52
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (18 bp):
TTATTATTATTATTTTAC
Found at i:32161 original size:5 final size:5
Alignment explanation
Indices: 32151--32183 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
32141 TCTTTTCATC
32151 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
32184 CATCACTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:34056 original size:25 final size:25
Alignment explanation
Indices: 34028--34091 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 25
34018 AATCAAAAAC
34028 AAAGAAAAAAGAGAAAT-AAAAGAAA
1 AAAGAAAAAAGA-AAATAAAAAGAAA
* *
34053 AAAGAAAGAACAAAATCAAAAAGAAA
1 AAAGAAAAAAGAAAAT-AAAAAGAAA
34079 AAGAGACAAAAAG
1 AA-AGA-AAAAAG
34092 CACATGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 10 0.32
26 10 0.32
27 3 0.10
28 4 0.13
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAAGAAAATAAAAAGAAA
Found at i:34067 original size:19 final size:18
Alignment explanation
Indices: 34022--34080 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
34012 AGATCCAATC
34022 AAAAAC-AAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
* *
34039 AGAAATAAAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
**
34057 AAAGAACAAAATCAAAAAG
1 AAA-AACAAAAGAAAAAAG
34076 AAAAA
1 AAAAA
34081 GAGACAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 4 0.12
18 15 0.44
19 15 0.44
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAAG
Found at i:34711 original size:22 final size:22
Alignment explanation
Indices: 34683--34759 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
34673 GCTACCCCAT
34683 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
*
34705 CAAACCTTTGAACATCAAAT-A
1 CAAACCTTTGAGCATCAAATGA
* *
34726 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
34749 CAAACCTTTGA
1 CAAACCTTTGA
34760 CCAAACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:35561 original size:37 final size:35
Alignment explanation
Indices: 35512--35645 Score: 142
Period size: 37 Copynumber: 3.7 Consensus size: 35
35502 TTTCCAATAT
* * *
35512 AAATTTTTTCTCGCTTGAGACAGTCTCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTC-TTTGAAAC
* * * *
35548 AATATTTTATCTCGCTTGAGATAGTTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGACAG--TCTCTTTGAAAC
* *
35586 AAATTTCGTCTCCCTTGAGACAGTCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTC-TCTTTGAAAC
35622 AAATTTTGTCTCCCTTGAGACAGT
1 AAATTTTGTCTCCCTTGAGACAGT
35646 TTCTCTCCAG
Statistics
Matches: 83, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 1 0.01
36 34 0.41
37 36 0.43
38 9 0.11
39 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
AAATTTTGTCTCCCTTGAGACAGTCTCTTTGAAAC
Found at i:35621 original size:36 final size:36
Alignment explanation
Indices: 35512--35649 Score: 154
Period size: 36 Copynumber: 3.8 Consensus size: 36
35502 TTTCCAATAT
* * *
35512 AAATTTTTTCTCGCTTGAGACAGTC-TCATTTAAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTC-TTTGAAAC
* * * *
35548 AATATTTTATCTCGCTTGAGATAGTTTTTCTTTGAAAC
1 AA-ATTTTGTCTCCCTTGAGACAG-TCTTCTTTGAAAC
* *
35586 AAATTTCGTCTCCCTTGAGACAGTCTTCCTTGAAAC
1 AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
35622 AAATTTTGTCTCCCTTGAGACAGT-TTCT
1 AAATTTTGTCTCCCTTGAGACAGTCTTCT
35650 CTCCAGACAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
35 3 0.03
36 36 0.41
37 36 0.41
38 10 0.11
39 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
AAATTTTGTCTCCCTTGAGACAGTCTTCTTTGAAAC
Found at i:35839 original size:106 final size:106
Alignment explanation
Indices: 35650--36606 Score: 1432
Period size: 106 Copynumber: 9.0 Consensus size: 106
35640 GACAGTTTCT
* *
35650 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
35715 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * *** ** * *
35756 CTCAAGACAGCACAAGCTCAACTTCAC-AGCGAAGGGGTGGCTGACTGTCAACAAACAACTTCTC
1 CTCCAGACAACGCAAGTTCAACTTCACGA-CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
35820 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGA
65 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
35862 CTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* *
35927 ATTTCAGAGCCAATTTCAACTTCACAGTGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
35968 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
*
36033 ATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * *
36074 CTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* * *
36139 ATTTCAGAGCAAATTTCAACTTCACAACGAAAGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
36180 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGATTGTCAACAAACAATTTACCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* * *
36245 ATTTCGGAGCCACTTTCTACTTCACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * *
36286 CTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* *
36351 ATTTCAGAGCCAATTTTAACTTCACAGCGAAGGAAATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* *
36392 CTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTA
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* *
36457 ATTTCGGAGCCAATTTCAACTTTACAGCGAAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
* * * * * * * *
36498 TTCGAGACAACACAAGTTCAACTTCACAAAGAAGGGACGGTTGGTTGTCAACAAACAATTTCCCG
1 CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
* *
36563 ATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGA
66 ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGA
36604 CTC
1 CTC
36607 GGAAAAATCC
Statistics
Matches: 767, Mismatches: 81, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
105 2 0.00
106 764 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
CTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGA
Found at i:37456 original size:37 final size:37
Alignment explanation
Indices: 37356--37458 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 37
37346 CATTTTCGTC
* *
37356 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTATGATTCAAACTCTTAAAAATAGGATAGAATT
* *
37393 -T--TAGGATTCAAACTCCTTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACT-CTTAAAAATAGGATAGAATT
* *
37428 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTATGATTCAAACTCTTAAAAATAGGAT
37459 TCACAAGCAT
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
34 12 0.22
35 17 0.31
36 2 0.04
37 13 0.24
38 11 0.20
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.33
Consensus pattern (37 bp):
CTACTATGATTCAAACTCTTAAAAATAGGATAGAATT
Found at i:37977 original size:20 final size:20
Alignment explanation
Indices: 37952--37989 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37942 ATTATTATTA
37952 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
37972 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
37990 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:42274 original size:2 final size:2
Alignment explanation
Indices: 42267--42297 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
42257 CATAACTTGC
42267 AT AT AT 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 AT AT AT A
42298 GTTTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44361 original size:14 final size:14
Alignment explanation
Indices: 44307--44362 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
44297 ATATAAATTA
*
44307 TTAAATAATTCATAT
1 TTAAATAATTTAT-T
* *
44322 TTAAATATATTAATA
1 TTAAATA-ATTTATT
*
44337 TT-AATATTTTATT
1 TTAAATAATTTATT
44350 TTAAATAATTTAT
1 TTAAATAATTTAT
44363 AAATATGTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 6 0.18
14 13 0.39
15 9 0.27
16 5 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATAATTTATT
Found at i:47159 original size:3 final size:3
Alignment explanation
Indices: 47151--47176 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47141 TGTTCCATCG
47151 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
47177 TTGATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:48096 original size:35 final size:35
Alignment explanation
Indices: 48057--48124 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
48047 TAAACGCAAA
48057 TACCCGTACAAAATGAGTACATTTTCATTGTTTAT
1 TACCCGTACAAAATGAGTACATTTTCATTGTTTAT
48092 TACCCGTACAAAATGAGTACATTTTCATTGTTT
1 TACCCGTACAAAATGAGTACATTTTCATTGTTT
48125 GTTCTCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.40
Consensus pattern (35 bp):
TACCCGTACAAAATGAGTACATTTTCATTGTTTAT
Found at i:48604 original size:28 final size:28
Alignment explanation
Indices: 48564--48622 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
48554 CAGAATATGC
48564 TCAACATCCTCCCTGCTGCTTCAACTCT
1 TCAACATCCTCCCTGCTGCTTCAACTCT
48592 TCAACATCCTCCCTGCTGCTTCAACTCT
1 TCAACATCCTCCCTGCTGCTTCAACTCT
48620 TCA
1 TCA
48623 GTGCGAGCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.19, C:0.42, G:0.07, T:0.32
Consensus pattern (28 bp):
TCAACATCCTCCCTGCTGCTTCAACTCT
Found at i:58770 original size:45 final size:47
Alignment explanation
Indices: 58705--58807 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 47
58695 TGTTATTCAC
* *
58705 AAAAAGAAATCCTAACCGCATGATATCTAATTCGTATGC-TTGTTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
* *
58751 AAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
58798 AAAAACGAAA
1 AAAAA-GAAA
58808 ATAAATGACT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 27 0.55
46 8 0.16
47 11 0.22
48 3 0.06
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (47 bp):
AAAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:62063 original size:55 final size:52
Alignment explanation
Indices: 62029--62161 Score: 149
Period size: 55 Copynumber: 2.5 Consensus size: 52
62019 GATGGGTCTG
* *
62029 CTCCCTATTCTTTCAAGGAGTATAAGACTCGAAAAATATTCGGCAAACGTGTCCA
1 CTCCCTATTCATTCAAGGAGTATAAGACTCGAAAAATCTT---CAAACGTGTCCA
* * **
62084 CTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAATAAATGGTCCA
1 CTCCCTATTCATTCAAGGAGTATAAGACTCGAAAAATCTTCAA-ACGT-GTCCA
* *
62138 CTCCATATTCATTCAGGGAGTATA
1 CTCCCTATTCATTCAAGGAGTATA
62162 GAACTTAAAC
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
52 3 0.04
53 2 0.03
54 28 0.41
55 36 0.52
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (52 bp):
CTCCCTATTCATTCAAGGAGTATAAGACTCGAAAAATCTTCAAACGTGTCCA
Found at i:62150 original size:54 final size:54
Alignment explanation
Indices: 62023--62433 Score: 346
Period size: 54 Copynumber: 7.7 Consensus size: 54
62013 TCAAATGATG
* * * * * **
62023 GGTCTGCTCCCTATTCTTTCAAGGAGTATA-AGACTCGAAAAATATTCGGCAAAC
1 GGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC
* * *
62077 GTGTCCACTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAAT
1 G-GTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC
* * ** *
62132 GGTCCACTCCATATTCATTCAGGGAGTATAGAACTTAAACAATTTTCATA-AAAC
1 GGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCA-ACAAAC
** * * *
62186 --TCCGCTTTCTATTCCTTCA--GAGTATAGAACTCGAACAATCTTCAGCAAAT
1 GGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC
* * *
62236 GTTTCGGTCCCTATTCATTCAGGGAGTATA-AGACTCGAACAATCTTCAACAAAC
1 GGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC
* * * *
62290 GGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAAC
1 GGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC
* * * *
62344 GGGTTCGCTCTCTATTCCA-TCAGAGAGTATAGAACTCG----ATCTTCAACAAATG
1 -GGTCCGCTCCCTATT-CATTCAGGGAGTATAGAACTCGAACAATCTTCAACAAA-C
* *
62396 GGTCCGCTCTCTATTACA-TCAGAGAGTATAGAACTCGA
1 GGTCCGCTCCCTATT-CATTCAGGGAGTATAGAACTCGA
62434 TCTTCATAAA
Statistics
Matches: 298, Mismatches: 45, Indels: 30
0.80 0.12 0.08
Matches are distributed among these distances:
50 25 0.08
51 47 0.16
52 28 0.09
53 1 0.00
54 117 0.39
55 79 0.27
56 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (54 bp):
GGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC
Found at i:62219 original size:104 final size:106
Alignment explanation
Indices: 62029--62342 Score: 307
Period size: 104 Copynumber: 2.9 Consensus size: 106
62019 GATGGGTCTG
* * * * ** * *
62029 CTCCCTATTCTTTCAAGGAGTATAAGACTCGAAA-AATATTCGGCAAACGTGTCCACTCCCTATT
1 CTCCATATTCATTCAGGGAGTATAAGACTC-AAACAATCTTCAACAAAC--GTCCGCTCTCTATT
* * *
62093 CATTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAATGGTCCA
63 CCTTCA-AGAGTATAGA-ACTCGAACAATCTTCAACAAATGGTCCA
* * *
62138 CTCCATATTCATTCAGGGAGTAT-AGAACTTAAACAATTTTCATA-AAAC-TCCGCTTTCTATTC
1 CTCCATATTCATTCAGGGAGTATAAG-ACTCAAACAATCTTCA-ACAAACGTCCGCTCTCTATTC
* * * *
62200 CTTC-AGAGTATAGAACTCGAACAATCTTCAGCAAATGTTTCG
64 CTTCAAGAGTATAGAACTCGAACAATCTTCAACAAATGGTCCA
* * * *
62242 GTCCCTATTCATTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGTCTGCTCTCTATTCC
1 CTCCATATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAAC-GTCCGCTCTCTATTCC
62307 TTCAGAGAGTATAGAACTCGAACAATCTTCAACAAA
65 TTCA-AGAGTATAGAACTCGAACAATCTTCAACAAA
62343 CGGGTTCGCT
Statistics
Matches: 170, Mismatches: 25, Indels: 21
0.79 0.12 0.10
Matches are distributed among these distances:
103 1 0.01
104 68 0.40
105 3 0.02
106 30 0.18
108 35 0.21
109 33 0.19
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (106 bp):
CTCCATATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTCCGCTCTCTATTCCT
TCAAGAGTATAGAACTCGAACAATCTTCAACAAATGGTCCA
Found at i:62407 original size:51 final size:50
Alignment explanation
Indices: 62277--62439 Score: 227
Period size: 51 Copynumber: 3.1 Consensus size: 50
62267 GACTCGAACA
* * *
62277 ATCTTCAACAAACGGTCTGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
1 ATCTTCAACAAAGGGTCCGCTCTCTATTCCATCAGAGAGTATAGAACTCG
*
62327 AACAATCTTCAACAAACGGGTTCGCTCTCTATTCCATCAGAGAGTATAGAACTCG
1 ----ATCTTCAACAAA-GGGTCCGCTCTCTATTCCATCAGAGAGTATAGAACTCG
*
62382 ATCTTCAACAAATGGGTCCGCTCTCTATTACATCAGAGAGTATAGAACTCG
1 ATCTTCAACAAA-GGGTCCGCTCTCTATTCCATCAGAGAGTATAGAACTCG
62433 ATCTTCA
1 ATCTTCA
62440 TAAATGAATT
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
51 55 0.54
54 12 0.12
55 34 0.34
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (50 bp):
ATCTTCAACAAAGGGTCCGCTCTCTATTCCATCAGAGAGTATAGAACTCG
Found at i:62754 original size:17 final size:17
Alignment explanation
Indices: 62724--62758 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62714 TATCTTCATC
62724 TCAATGCTTCAATATCT
1 TCAATGCTTCAATATCT
62741 TCAAT-CTTCAAATATCT
1 TCAATGCTTC-AATATCT
62758 T
1 T
62759 TGGGAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (17 bp):
TCAATGCTTCAATATCT
Found at i:63802 original size:8 final size:8
Alignment explanation
Indices: 63779--63861 Score: 70
Period size: 8 Copynumber: 10.6 Consensus size: 8
63769 ACCCCCCTTT
63779 ATTTTTCTC
1 ATTTTT-TC
63788 TATTTTTTC
1 -ATTTTTTC
63797 A-TTTTTC
1 ATTTTTTC
63804 A-TTTTTC
1 ATTTTTTC
*
63811 TTTCTTTTTC
1 -AT-TTTTTC
*
63821 -TTCTTT-
1 ATTTTTTC
63827 -TTTTTTC
1 ATTTTTTC
63834 ATTTTTTC
1 ATTTTTTC
63842 ATTTTTTC
1 ATTTTTTC
63850 ATTTTTT-
1 ATTTTTTC
63857 ATTTT
1 ATTTT
63862 CACAAATTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.08
7 22 0.34
8 24 0.37
9 2 0.03
10 12 0.18
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (8 bp):
ATTTTTTC
Found at i:63833 original size:19 final size:19
Alignment explanation
Indices: 63790--63848 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
63780 TTTTTCTCTA
63790 TTTTTTCA-TTTTTCATTT
1 TTTTTTCATTTTTTCATTT
* *
63808 TTCTTTCTTTTTCTTC-TTT
1 TTTTTTCATTTT-TTCATTT
63827 TTTTTTCATTTTTTCATTT
1 TTTTTTCATTTTTTCATTT
63846 TTT
1 TTT
63849 CATTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
18 9 0.26
19 22 0.65
20 3 0.09
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTCATTTTTTCATTT
Found at i:63878 original size:7 final size:7
Alignment explanation
Indices: 63791--63861 Score: 55
Period size: 7 Copynumber: 10.6 Consensus size: 7
63781 TTTTCTCTAT
63791 TTTTTCA
1 TTTTTCA
63798 TTTTTCA
1 TTTTTCA
63805 TTTTTC-
1 TTTTTCA
63811 --TTTC-
1 TTTTTCA
63815 TTTTTC-
1 TTTTTCA
*
63821 TTCTTT-T
1 TT-TTTCA
63828 TTTTTCA
1 TTTTTCA
63835 TTTTTTCA
1 -TTTTTCA
63843 TTTTTTCA
1 -TTTTTCA
*
63851 TTTTTTA
1 TTTTTCA
63858 TTTT
1 TTTT
63862 CACAAATTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.07
6 9 0.16
7 28 0.50
8 15 0.27
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:63882 original size:10 final size:10
Alignment explanation
Indices: 63798--63856 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 10
63788 TATTTTTTCA
63798 TTTTTCATTT
1 TTTTTCATTT
63808 TTCTTTC-TTT
1 TT-TTTCATTT
* *
63818 TTCTTCTTTT
1 TTTTTCATTT
63828 TTTTTCA--T
1 TTTTTCATTT
63836 TTTTTCA--T
1 TTTTTCATTT
63844 TTTTTCATTT
1 TTTTTCATTT
63854 TTT
1 TTT
63857 ATTTTCACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
8 16 0.38
9 3 0.07
10 19 0.45
11 4 0.10
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:63907 original size:68 final size:68
Alignment explanation
Indices: 63799--63929 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 68
63789 ATTTTTTCAT
**
63799 TTTTCATTTTTCTTTCTTTTTCTTCTTTTTTTTTCATTTTTTCA-TTTTTTCATTTTTTATTTTC
1 TTTTCATTTTTCTTTCTTTTTCTTCTTTCCTTTTCATTTTTT-ATTTTTTTCATTTTTT-TTTTC
63863 ACAAA
64 ACAAA
*
63868 TTTTCATTTTT-TTTCTCATTTT-TT-TTTCCTTTTCCTTTTTTATTTTTTTCATTTTTTTTTTC
1 TTTTCATTTTTCTTTCT--TTTTCTTCTTTCCTTTTCATTTTTTATTTTTTTCATTTTTTTTTTC
63930 TTCTTCAAGC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
67 6 0.11
68 33 0.59
69 13 0.23
70 4 0.07
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.76
Consensus pattern (68 bp):
TTTTCATTTTTCTTTCTTTTTCTTCTTTCCTTTTCATTTTTTATTTTTTTCATTTTTTTTTTCAC
AAA
Done.