Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005326.1 Hibiscus syriacus cultivar Beakdansim tig00012057_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: 92809
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1104 original size:20 final size:20
Alignment explanation
Indices: 1049--1104 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
1039 AAGATTTTAA
1049 AAAAAATATATAATAATGAAT
1 AAAAAATATAT-ATAATGAAT
*
1070 AAAAAATGA-AAATAAT-AAT
1 AAAAAAT-ATATATAATGAAT
1089 AAAATAATATATATAA
1 AAAA-AATATATATAA
1105 AGTTATAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 8 0.27
20 13 0.43
21 8 0.27
22 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAAATATATATAATGAAT
Found at i:1322 original size:16 final size:16
Alignment explanation
Indices: 1293--1333 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1283 TATAATATAT
*
1293 ATATAATAATAATAAA
1 ATATAATAAAAATAAA
*
1309 ATATAGTAAAAATAAA
1 ATATAATAAAAATAAA
*
1325 ATAAAATAA
1 ATATAATAA
1334 TTTAATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
ATATAATAAAAATAAA
Found at i:1382 original size:17 final size:16
Alignment explanation
Indices: 1354--1390 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1344 ATATATATGT
*
1354 ATAATAATATAACATGA
1 ATAATAAAATAA-ATGA
1371 ATAATAAAATAAATGA
1 ATAATAAAATAAATGA
1387 ATAA
1 ATAA
1391 AATATTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (16 bp):
ATAATAAAATAAATGA
Found at i:2118 original size:21 final size:21
Alignment explanation
Indices: 2092--2137 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
2082 AGGCTCTTAA
*
2092 AACGGTAGGAGGGACCCATTG
1 AACGGTAGGAGGAACCCATTG
2113 AACGGTAGGAGGAACCCATTG
1 AACGGTAGGAGGAACCCATTG
2134 AACG
1 AACG
2138 ATGACAGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.35, T:0.13
Consensus pattern (21 bp):
AACGGTAGGAGGAACCCATTG
Found at i:2155 original size:21 final size:21
Alignment explanation
Indices: 2131--2207 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
2121 GAGGAACCCA
2131 TTGAACGATGACAGGGGCCTC
1 TTGAACGATGACAGGGGCCTC
* **
2152 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGACAGGGGCCTC
* * *
2173 TTGAACGATGAAATGAGCCTC
1 TTGAACGATGACAGGGGCCTC
2194 TTGAACGATGACAG
1 TTGAACGATGACAG
2208 ATGAATCAGG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
TTGAACGATGACAGGGGCCTC
Found at i:4373 original size:19 final size:19
Alignment explanation
Indices: 4322--4376 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
4312 AGTAGTTTCT
*
4322 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
4342 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
4362 GAAACTAAAATCGCA
1 GAAACTAAAATCGCA
4377 TAGTGGAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.47, C:0.22, G:0.16, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:7287 original size:26 final size:27
Alignment explanation
Indices: 7228--7299 Score: 94
Period size: 26 Copynumber: 2.7 Consensus size: 27
7218 GGTTTTACTT
* *
7228 TTTTTAATATTTATTATTTTGGGCTTA
1 TTTTTAATATTTATTATTTAGGGCCTA
*
7255 TTATTAATATTTATTA-TTAGGGCCTA
1 TTTTTAATATTTATTATTTAGGGCCTA
*
7281 TTTTTAAAATTTATT-TTTA
1 TTTTTAATATTTATTATTTA
7300 TAATATTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
26 24 0.62
27 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.60
Consensus pattern (27 bp):
TTTTTAATATTTATTATTTAGGGCCTA
Found at i:8731 original size:143 final size:141
Alignment explanation
Indices: 8438--8817 Score: 482
Period size: 143 Copynumber: 2.7 Consensus size: 141
8428 TCAACAACTT
8438 TTTATCCTCGGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCTCCTCAATTCGAT--ACAA
1 TTTATCCTC-GCCTTCTTTTCCTCTACATTTTCATCAACCTTC-T-TCCTCAATTCGATCCACAA
* *
8501 CCTTGTCATCTTGAGCTTCACTGATCTTTTGGTTTTCTCTTTGACAACTTTCGAAGTTTGTGATG
63 CCTTGTCATCTTGAGCTTCACTGATC---T--TCTTCTCTTTGACAACTTTCGAAATTTGTGATG
* *
8566 CACTTGGTGGTTCAACACA
123 CACTTAGTCGTTCAACACA
*
8585 TTTATCCTCAGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCACTCGATTCGATCCACAAC
1 TTTATCCTC-GCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTC-CTCAATTCGATCCACAAC
*
8650 CTTGTCATCTTGAGCTTCGCTGATCTTCTTCTCTTTGACAACTTTCGAAATTTGTGATGCACTTA
64 CTTGTCATCTTGAGCTTCACTGATCTTCTTCTCTTTGACAACTTTCGAAATTTGTGATGCACTTA
*
8715 GTCGTTCAACATA
129 GTCGTTCAACACA
* * * * * * * *
8728 TTTATCCTCGGC--CTTATCTTCTACGTTTTCGTCAACCTTC-ACCTCAATTTGGTCCACAACCT
1 TTTATCCTCGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCCTCAATTCGATCCACAACCT
* *
8790 TGTTATCTAGAGCTTCACTGATCTTCTT
66 TGTCATCTTGAGCTTCACTGATCTTCTT
8818 GTTGTTCTTC
Statistics
Matches: 210, Mismatches: 20, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
138 42 0.20
139 1 0.00
140 24 0.11
142 2 0.01
143 56 0.27
145 3 0.01
146 11 0.05
147 42 0.20
148 29 0.14
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (141 bp):
TTTATCCTCGCCTTCTTTTCCTCTACATTTTCATCAACCTTCTTCCTCAATTCGATCCACAACCT
TGTCATCTTGAGCTTCACTGATCTTCTTCTCTTTGACAACTTTCGAAATTTGTGATGCACTTAGT
CGTTCAACACA
Found at i:14872 original size:12 final size:12
Alignment explanation
Indices: 14851--14884 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
14841 ATCACATTTC
*
14851 CAATACCAAACA
1 CAATATCAAACA
14863 CAATATCAAACA
1 CAATATCAAACA
*
14875 CAATCTCAAA
1 CAATATCAAA
14885 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:17677 original size:20 final size:20
Alignment explanation
Indices: 17652--17715 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
17642 AATCATAGCA
17652 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* * ***
17672 CGAATTTGACTATCTCAACG
1 CGAATTTGACTTTCGCGTTG
17692 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
17712 CGAA
1 CGAA
17716 AGTGTACATT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:17849 original size:64 final size:64
Alignment explanation
Indices: 17770--17927 Score: 244
Period size: 64 Copynumber: 2.5 Consensus size: 64
17760 TTGAATAAAC
* * *
17770 AACAAATCAACTTTTACAAATCAATTAAACAATCAAAAAATAATTCTTATTTACACATCAGTTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAATTATTATTTACACATCAATTA
* * *
17834 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATTATTATTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAATTATTATTTACACATCAATTA
*
17898 AACAAATCAATTTTTACAAATCAATGTAAA
1 AACAAATCAACTTTTACAAATCAAT-TAAA
17928 ATTCAATTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 82 0.95
65 4 0.05
ACGTcount: A:0.51, C:0.16, G:0.01, T:0.32
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAATAATTATTATTTACACATCAATTA
Found at i:19318 original size:21 final size:21
Alignment explanation
Indices: 19292--19388 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
19282 GTGAATCGGG
*
19292 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
** *
19313 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGGGAGGGAC
*
19334 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
* *
19355 ATCTTGAACGATTGGAGGGAC
1 CTCTTGAACGATGGGAGGGAC
19376 CTCTTGAACGATG
1 CTCTTGAACGATG
19389 AAAGGGGCCT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGAC
Found at i:19351 original size:42 final size:42
Alignment explanation
Indices: 19292--19385 Score: 145
Period size: 42 Copynumber: 2.2 Consensus size: 42
19282 GTGAATCGGG
* *
19292 CTCTTGAACGGTGGGAGGGACCTCTTGAACGA-TGACAGGGGC
1 CTCTTGAACGGTGGGAGGGACATCTTGAACGATTG-CAGGGAC
*
19334 CTCTTGAACGGTGGGAGGGACATCTTGAACGATTGGAGGGAC
1 CTCTTGAACGGTGGGAGGGACATCTTGAACGATTGCAGGGAC
19376 CTCTTGAACG
1 CTCTTGAACG
19386 ATGAAAGGGG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
42 46 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACATCTTGAACGATTGCAGGGAC
Found at i:19394 original size:21 final size:21
Alignment explanation
Indices: 19292--19431 Score: 124
Period size: 21 Copynumber: 6.7 Consensus size: 21
19282 GTGAATCGGG
* *
19292 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGAC
* *
19313 CTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATGAGAGGGAC
* *
19334 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGAC
*
19355 ATCTTGAACGATTG-GAGGGAC
1 CTCTTGAACGA-TGAGAGGGAC
* *
19376 CTCTTGAACGATGAAAGGGGC
1 CTCTTGAACGATGAGAGGGAC
* * *
19397 CTCCTGAATGAT-AG-GAGAC
1 CTCTTGAACGATGAGAGGGAC
19416 GCTTCTTGAACGATGA
1 -C-TCTTGAACGATGA
19432 CAGGTGCATC
Statistics
Matches: 94, Mismatches: 20, Indels: 9
0.76 0.16 0.07
Matches are distributed among these distances:
19 3 0.03
20 4 0.04
21 84 0.89
22 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGAC
Found at i:19423 original size:63 final size:63
Alignment explanation
Indices: 19293--19430 Score: 179
Period size: 63 Copynumber: 2.2 Consensus size: 63
19283 TGAATCGGGC
* * * * * *
19293 TCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGACA
1 TCTTGAACGATGGGAGGGACCTCTTGAACGATGAAAGGGGCCTCCTGAACGATAGGAGCGACA
* * *
19356 TCTTGAACGATTGGAGGGACCTCTTGAACGATGAAAGGGGCCTCCTGAATGATAGGAGACG-CT
1 TCTTGAACGATGGGAGGGACCTCTTGAACGATGAAAGGGGCCTCCTGAACGATAGGAG-CGACA
19419 TCTTGAACGATG
1 TCTTGAACGATG
19431 ACAGGTGCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 63 0.98
64 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.22
Consensus pattern (63 bp):
TCTTGAACGATGGGAGGGACCTCTTGAACGATGAAAGGGGCCTCCTGAACGATAGGAGCGACA
Found at i:19605 original size:23 final size:23
Alignment explanation
Indices: 19575--19618 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19565 GGGCCGCTGA
* *
19575 AAATAAATTAATACATAAATAGT
1 AAATAAATAAATAAATAAATAGT
19598 AAATAAATAAATAAATAAATA
1 AAATAAATAAATAAATAAATA
19619 ATGCCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAATAAATAAATAAATAGT
Found at i:19606 original size:4 final size:4
Alignment explanation
Indices: 19575--19619 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
19565 GGGCCGCTGA
* * *
19575 AAAT AAAT TAAT ACAT AAAT -AGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
19620 TGCCGAAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 2 0.06
4 32 0.94
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:19606 original size:19 final size:19
Alignment explanation
Indices: 19578--19614 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19568 CCGCTGAAAA
* *
19578 TAAATTAATACATAAATAG
1 TAAATAAATAAATAAATAG
19597 TAAATAAATAAATAAATA
1 TAAATAAATAAATAAATA
19615 AATAATGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (19 bp):
TAAATAAATAAATAAATAG
Found at i:21644 original size:14 final size:14
Alignment explanation
Indices: 21627--21657 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
21617 CGAAACTAAA
21627 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
*
21641 TTCGTGTTGCGATT
1 TTCGCGTTGCGATT
21655 TTC
1 TTC
21658 ATTTTCGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.48
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:21683 original size:20 final size:20
Alignment explanation
Indices: 21640--21683 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
21630 GCGTTGCGAT
* * *
21640 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGAATTTAAG
*
21660 TTTCGTGTTGGGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
21680 TTTC
1 TTTC
21684 AAAAACTATT
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:0.14, C:0.11, G:0.23, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:22264 original size:20 final size:20
Alignment explanation
Indices: 22241--22287 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22231 GGAATCTGGT
* *
22241 TTGCGAAATTAGAGTTCGCG
1 TTGCGAAATTAGAATTCACG
*
22261 TTGCGAAATTGGAATTCACG
1 TTGCGAAATTAGAATTCACG
22281 TTGCGAA
1 TTGCGAA
22288 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TTGCGAAATTAGAATTCACG
Found at i:24092 original size:37 final size:37
Alignment explanation
Indices: 24049--24132 Score: 123
Period size: 37 Copynumber: 2.3 Consensus size: 37
24039 GAACGCGATT
**
24049 TAAAATGTTACATTTCCCAAACATTTTTTGTTGAACC
1 TAAAATGTTACATTTCCCAAACATTTTTCATTGAACC
* **
24086 TAAAATGTTACATTTCCCTAACATTTTTCATTGGTCC
1 TAAAATGTTACATTTCCCAAACATTTTTCATTGAACC
24123 TAAAATGTTA
1 TAAAATGTTA
24133 TGTCTTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (37 bp):
TAAAATGTTACATTTCCCAAACATTTTTCATTGAACC
Found at i:25283 original size:2 final size:2
Alignment explanation
Indices: 25276--25306 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25266 ACAATAGAAC
25276 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
25307 CAGTGACGGG
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:27131 original size:154 final size:149
Alignment explanation
Indices: 26949--27226 Score: 414
Period size: 154 Copynumber: 1.8 Consensus size: 149
26939 ATCAACTCAC
* *
26949 TTTTTTCAACCAAAATTGCTCAAATTTAAAAAGTAAACAACATGGGCGTAATCAAACAAAAACAT
1 TTTTTTCAACCAAAATTGCTCAAATTTAAAAAATAAACAACAAGGGCG---T-AAA-AAAAACAT
* *
27014 TTTAAGGTCAAAA-CAACAAGTAAACATTGAGGGGGCATCAATTGGAATTATACCAAAAGTACAA
61 TTTAAGGTCAAAAGAAACAAGTAAACATT-AGGGGGCAACAATTGGAATTATACCAAAAGTACAA
27078 TTTTTATTGATAGTTAACCAATTGG
125 TTTTTATTGATAGTTAACCAATTGG
*
27103 TTTTTTCGACCAAAATTGCTCAAATTTAAAAAATAAACAACAAGGGCGTAAAAAAAACATTTTAA
1 TTTTTTCAACCAAAATTGCTCAAATTTAAAAAATAAACAACAAGGGCGTAAAAAAAACATTTTAA
*
27168 GGTCAAAATTGGAAATAAGTAAACATTAGGGGGCAACAATTGGAATTATACCAAAAGTA
66 GGTCAAAA---GAAACAAGTAAACATTAGGGGGCAACAATTGGAATTATACCAAAAGTA
27227 AAAAATAAAT
Statistics
Matches: 114, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
149 21 0.18
150 3 0.03
151 1 0.01
152 31 0.27
153 13 0.11
154 45 0.39
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (149 bp):
TTTTTTCAACCAAAATTGCTCAAATTTAAAAAATAAACAACAAGGGCGTAAAAAAAACATTTTAA
GGTCAAAAGAAACAAGTAAACATTAGGGGGCAACAATTGGAATTATACCAAAAGTACAATTTTTA
TTGATAGTTAACCAATTGG
Found at i:39485 original size:8 final size:7
Alignment explanation
Indices: 39463--39492 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
39453 CATGCATTCA
39463 TGCATTT
1 TGCATTT
39470 TGCATTT
1 TGCATTT
39477 TGCATTTT
1 TGCA-TTT
39485 TGCATTT
1 TGCATTT
39492 T
1 T
39493 CATCTACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (7 bp):
TGCATTT
Found at i:39491 original size:15 final size:14
Alignment explanation
Indices: 39463--39492 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
39453 CATGCATTCA
39463 TGCATTTTGCATTT
1 TGCATTTTGCATTT
39477 TGCATTTTTGCATTT
1 TGCA-TTTTGCATTT
39492 T
1 T
39493 CATCTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:40663 original size:24 final size:24
Alignment explanation
Indices: 40636--40715 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
40626 AGATCCAATC
40636 AAGAACAAAAAAGAAAAGAAGCAA
1 AAGAACAAAAAAGAAAAGAAGCAA
*
40660 AAGAAGAAAAAA-ACAAAGAA-CAA
1 AAGAACAAAAAAGA-AAAGAAGCAA
* *
40683 AGAGAA-ACAAAAGAAAAAAAG--A
1 A-AGAACAAAAAAGAAAAGAAGCAA
40705 AAGAACAAAAA
1 AAGAACAAAAA
40716 TCAAAAAGGG
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
21 4 0.09
22 6 0.13
23 15 0.32
24 22 0.47
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (24 bp):
AAGAACAAAAAAGAAAAGAAGCAA
Found at i:40695 original size:33 final size:31
Alignment explanation
Indices: 40639--40702 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
40629 TCCAATCAAG
* *
40639 AACAAAAAAGAAAAGAAGCAAAAGAAGAAAAA
1 AACAAAAAACAAAAGAAACAAAAGAA-AAAAA
*
40671 AACAAAGAACAAAGAGAAACAAAAGAAAAAAA
1 AACAAAAAACAAA-AGAAACAAAAGAAAAAAA
40703 GAAAGAACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.78, C:0.08, G:0.14, T:0.00
Consensus pattern (31 bp):
AACAAAAAACAAAAGAAACAAAAGAAAAAAA
Found at i:40698 original size:9 final size:9
Alignment explanation
Indices: 40649--40706 Score: 54
Period size: 8 Copynumber: 6.9 Consensus size: 9
40639 AACAAAAAAG
*
40649 AAAAGAAGC
1 AAAAGAAAC
*
40658 AAAAG-AAG
1 AAAAGAAAC
40666 AAAA-AAAC
1 AAAAGAAAC
40674 -AAAG-AAC
1 AAAAGAAAC
40681 AAAGAGAAAC
1 AAA-AGAAAC
40691 AAAAGAAA-
1 AAAAGAAAC
40699 AAAAGAAA
1 AAAAGAAA
40707 GAACAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
7 6 0.15
8 17 0.41
9 12 0.29
10 6 0.15
ACGTcount: A:0.78, C:0.07, G:0.16, T:0.00
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:42420 original size:106 final size:106
Alignment explanation
Indices: 42258--43347 Score: 1511
Period size: 106 Copynumber: 10.3 Consensus size: 106
42248 GGGCCATCCG
* * * *
42258 CAATTTCAACTCCAC-GACGGAGGATATTGTGCTACTCGAGACAACACAAGTTCAACTTCACGAC
1 CAATTTCAACTTCACAG-CGAAGGATATTG-G--ACTCCAGACAACGCAAGTTCAACTTCACGAC
* *
42322 GAAGGGACGGTTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
62 GAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * *
42367 CAATTTAAACTTCACAGCGAATGATATTGGACTCTAGACAACGCAAGTTCAACTTTACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
42432 GGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
*
42473 CAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* *
42538 GGACTGCTGGTTGTCAATAAACAA-TTCCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTT-CCCAATTTCAGAGC
42579 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
42644 GGACCGCTGATTGTCAATAAATAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
42685 CAATTTCAACATCACAGC-AAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAA
1 CAATTTCAACTTCACAGCGAA-GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
42749 GGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGC
65 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
42791 CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
42856 GGACGGCTGGTTGTCAAC-AATAATTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * *
42896 CAGTTTCAACTTCGCAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
42961 GGACCGCTGGTTGTCAATAAACAATTTTCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
43002 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * *
43067 GGACCGTTGGTTTTCAATAAACAACTTCCCAATTTCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * **
43108 CAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCCCAACTTCACGACGAA
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAA
* * * * *
43172 GGGGCGGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGT
65 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* * * *
43208 CAATTTCAACTTCATAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
* * ** *
43273 GGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGC
66 GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
* *
43314 CAATTTCAACTTCAC-GACGGAGGATATTAGACTC
1 CAATTTCAACTTCACAG-CGAAGGATATTGGACTC
43348 GGAACAATGC
Statistics
Matches: 885, Mismatches: 81, Indels: 33
0.89 0.08 0.03
Matches are distributed among these distances:
100 79 0.09
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 103 0.12
106 660 0.75
107 4 0.00
108 1 0.00
109 23 0.03
110 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (106 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGC
Found at i:44136 original size:37 final size:37
Alignment explanation
Indices: 44046--44150 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
44036 CCTTTTCGTC
* * *
44046 CTACTAGAATTCAAACTCCTAAAAATAGAATATAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* ** *
44083 TTGTTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
44120 CTACTATGATTTAAACTCCTAAATATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
44151 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:44758 original size:2 final size:2
Alignment explanation
Indices: 44751--44801 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
44741 GTATTATTAC
*
44751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA 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
44793 TA TA TA TA T
1 TA TA TA TA T
44802 TGTAATTATC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45956 original size:20 final size:19
Alignment explanation
Indices: 45931--45984 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
45921 GCGAAATAAA
45931 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
45951 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
45971 AATCGCAACGCGAT
1 AATCGCAACGCGAT
45985 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:46139 original size:20 final size:20
Alignment explanation
Indices: 46095--46227 Score: 151
Period size: 20 Copynumber: 6.5 Consensus size: 20
46085 GATTCTGACT
*
46095 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
46116 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
46136 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
46156 ATTGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
46176 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
46196 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
46217 ATCGCAACGCG
1 ATCGCAACGCG
46228 ATTTTTAAAG
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
20 65 0.69
21 29 0.31
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:46175 original size:40 final size:40
Alignment explanation
Indices: 46095--46227 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
46085 GATTCTGACT
* * * *
46095 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGT-AAATCGCAACGAGAATACGTAA
* *
46136 ATCGCAACGCGTATCTGTAAATTGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
* *
46176 ATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAA
1 ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT-AA
46217 ATCGCAACGCG
1 ATCGCAACGCG
46228 ATTTTTAAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 52 0.65
41 28 0.35
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAA
Found at i:46180 original size:101 final size:101
Alignment explanation
Indices: 46034--46227 Score: 221
Period size: 101 Copynumber: 1.9 Consensus size: 101
46024 GATTTTCCAG
* * * * * *
46034 AATCGCAACTCGAATATGAAAATTGCAACGCGAACATATAGATCGCAACGCG-ATTC-TGACTAT
1 AATCGCAACGCGAATATGAAAATTGCAACGAGAACACATAAATCGCAACGCGTATCCGT-A-AAT
** *
46097 CGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
64 CGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
* * * * * *
46135 AATCGCAACGCGTATCTGTAAATTGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGAATATGAAAATTGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
46200 CAACGACAATACGTAAAATCGCAACGCG
66 CAACGACAATACGTAAAATCGCAACGCG
46228 ATTTTTAAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
101 71 0.93
102 4 0.05
103 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (101 bp):
AATCGCAACGCGAATATGAAAATTGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATCG
CAACGACAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:46216 original size:60 final size:62
Alignment explanation
Indices: 46095--46225 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 62
46085 GATTCTGACT
* * *
46095 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCTGT-AA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCATATCTGTAAA
* *
46156 ATTGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATCGCAACGACA-ATAC-GTAAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACG-CATAT-CTGTAAA
46217 ATCGCAACG
1 ATCGCAACG
46226 CGATTTTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
60 34 0.56
61 27 0.44
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (62 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCATATCTGTAAA
Found at i:46847 original size:21 final size:21
Alignment explanation
Indices: 46786--46864 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
46776 TTCTAAACTT
46786 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
46806 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
46826 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
46847 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
46865 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:46887 original size:19 final size:19
Alignment explanation
Indices: 46786--46907 Score: 92
Period size: 20 Copynumber: 6.5 Consensus size: 19
46776 TTCTAAACTT
**
46786 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
46806 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
** *
46826 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC--GCGAAATG
46847 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
46861 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
46880 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
46899 AAAATCGCA
1 AAAATCGCA
46908 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 26 0.31
20 28 0.34
21 13 0.16
22 1 0.01
ACGTcount: A:0.49, C:0.21, G:0.19, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:46950 original size:33 final size:33
Alignment explanation
Indices: 46908--46999 Score: 121
Period size: 33 Copynumber: 2.8 Consensus size: 33
46898 CAAAATCGCA
46908 TTGCGATTTTCATTTCGCGTTGCGAATCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGAATCTCTCG
* *
46941 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGAATCTCTCG
* ** *
46974 TTGTGATAGTCATTCTCTCGTTGCGA
1 TTGCGATTTTCATT-TCGCGTTGCGA
47000 TTTTCATTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 41 0.80
34 10 0.20
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGAATCTCTCG
Found at i:46963 original size:19 final size:19
Alignment explanation
Indices: 46903--46967 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 19
46893 GAAACCAAAA
* *
46903 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATT
*
46922 TCGCGTTGCG-----AATC
1 TCGCGTTGCGATTTTAATT
*
46936 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
46955 TCGCGTTGCGATT
1 TCGCGTTGCGATT
46968 CTCTCGTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
14 11 0.31
19 24 0.69
ACGTcount: A:0.14, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:48820 original size:82 final size:83
Alignment explanation
Indices: 48681--49025 Score: 377
Period size: 94 Copynumber: 3.9 Consensus size: 83
48671 TAGATTGCTT
* * *
48681 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
48746 ATTTGTCTTTTGGTTGAA
66 ATTTGTCTTTTGGTTGAA
* *
48764 A-TAAATTTATTCGGTTGTTGCCGATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
48828 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 A-----------TTTGTCTTTTGGTTGAA
*
48857 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAG-
48922 ATTTATCTTTGTTTTATCTTTTGGTTGAA
65 ---TA--TTTG-----TCTTTTGGTTGAA
* * * * * *
48951 ATTAAATTTGTTTGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
49016 ATTTGTCTTT
66 ATTTGTCTTT
49026 GTTTTGTCTT
Statistics
Matches: 226, Mismatches: 15, Indels: 42
0.80 0.05 0.15
Matches are distributed among these distances:
82 59 0.26
83 6 0.03
88 4 0.02
89 4 0.02
90 2 0.01
93 18 0.08
94 131 0.58
98 2 0.01
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (83 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTTGGTTGAA
Found at i:48907 original size:94 final size:93
Alignment explanation
Indices: 48747--49041 Score: 491
Period size: 94 Copynumber: 3.2 Consensus size: 93
48737 GAAGTTAGTA
* * *
48747 TTTGTCTTTTGGTTGAAATAAATTTATTCGGTTGTTGCCGATTCTGCTAAACTGTGTATTCTTTA
1 TTTGTCTTTTGGTTGAAATAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
48812 ACACTGTGAAGTTAGTATTTGTCTTTGT
66 ACACTGTGAAGTTAGTATTTGTCTTTGT
48840 TTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAA-TAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
*
48905 AACACTGTGAAGTTAGTATTTATCTTTGT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
* * *
48934 TTTATCTTTTGGTTGAAATTAAATTTGTTTGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTT
1 TTTGTCTTTTGGTTGAAA-TAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTT
* *
48999 AATACTCTGAAGTTAGTATTTGTCTTTGT
65 AACACTGTGAAGTTAGTATTTGTCTTTGT
49028 TTTGTCTTTTGGTT
1 TTTGTCTTTTGGTT
49042 TAAGTAATAC
Statistics
Matches: 189, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
93 18 0.10
94 171 0.90
ACGTcount: A:0.20, C:0.12, G:0.19, T:0.49
Consensus pattern (93 bp):
TTTGTCTTTTGGTTGAAATAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTA
ACACTGTGAAGTTAGTATTTGTCTTTGT
Found at i:49141 original size:17 final size:18
Alignment explanation
Indices: 49119--49160 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
49109 AATGACTATT
49119 GCAACGCGAAATG-AATC
1 GCAACGCGAAATGAAATC
*
49136 GCAACGTGAAATGAAAATC
1 GCAACGCGAAATG-AAATC
49155 GCAACG
1 GCAACG
49161 AGAGAATCGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
19 10 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:49156 original size:19 final size:18
Alignment explanation
Indices: 49096--49160 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
49086 TAGTTTACTT
*
49096 TCGCAACGTGAAAAATGACTA
1 TCGCAACGTG--AAATGA-AA
* *
49117 TTGCAACGCGAAATG-AA
1 TCGCAACGTGAAATGAAA
49134 TCGCAACGTGAAATGAAAA
1 TCGCAACGTGAAATG-AAA
49153 TCGCAACG
1 TCGCAACG
49161 AGAGAATCGC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 14 0.38
19 15 0.41
21 8 0.22
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (18 bp):
TCGCAACGTGAAATGAAA
Found at i:49170 original size:14 final size:14
Alignment explanation
Indices: 49149--49188 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
49139 ACGTGAAATG
*
49149 AAAATCGCAACGAG
1 AAAATCGCAACGAC
*
49163 AGAATCGCAACGAC
1 AAAATCGCAACGAC
49177 AAAATCGCAACG
1 AAAATCGCAACG
49189 CGAAACTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.25, G:0.20, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:49222 original size:19 final size:19
Alignment explanation
Indices: 49200--49320 Score: 91
Period size: 19 Copynumber: 6.8 Consensus size: 19
49190 GAAACTATAA
49200 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
49219 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
49233 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTCATT
49252 TCGCGTTGCG--TTTC---
1 TCGCGTTGCGATTTTCATT
*
49266 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
49285 TCGCGTTGCGATAGTCATTTT
1 TCGCGTTGCGATTTTCA--TT
*
49306 TCACGTTGCGATTTT
1 TCGCGTTGCGATTTT
49321 AAGTTCCAGA
Statistics
Matches: 77, Mismatches: 13, Indels: 22
0.69 0.12 0.20
Matches are distributed among these distances:
14 17 0.22
16 7 0.09
17 7 0.09
19 32 0.42
21 14 0.18
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:49250 original size:33 final size:33
Alignment explanation
Indices: 49203--49296 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
49193 ACTATAATCG
*
49203 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
49236 CGTTACGATTTTCATTTCGCGTTGCGTTTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
49269 CGTTGCGATTTTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
49297 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:49286 original size:21 final size:20
Alignment explanation
Indices: 49269--49320 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
49259 GCGTTTCTCT
*
49269 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCA
**
49288 CGTTGCGATAGTCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCA
49309 CGTTGCGATTTT
1 CGTTGCGATTTT
49321 AAGTTCCAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 12 0.46
21 14 0.54
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCA
Found at i:49778 original size:42 final size:42
Alignment explanation
Indices: 49717--49809 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
49707 GTCCGACTCG
* * * *
49717 CCTATTATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
49759 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* *
49801 ACTGTCATC
1 CCTATCATC
49810 GTTGAAGAGG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.25
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:51226 original size:14 final size:14
Alignment explanation
Indices: 51190--51226 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
51180 GATTGTTTAA
*
51190 TTGATTTGCAAAAG
1 TTGATTTGTAAAAG
*
51204 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
51218 TTGATTTGT
1 TTGATTTGT
51227 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:51355 original size:19 final size:19
Alignment explanation
Indices: 51333--51424 Score: 69
Period size: 19 Copynumber: 5.4 Consensus size: 19
51323 AAAAATGACT
51333 ATCGCAATACGAAATGAAA
1 ATCGCAATACGAAATGAAA
* *
51352 ATCG-TA-ACG--A-GATA
1 ATCGCAATACGAAATGAAA
*
51366 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
*
51385 ATCGC-A-ACG--A-GAGA
1 ATCGCAATACGAAATGAAA
*
51399 ATCGCAATGCGAAATGAAA
1 ATCGCAATACGAAATGAAA
51418 ATCGCAA
1 ATCGCAA
51425 CGACAAAATC
Statistics
Matches: 54, Mismatches: 9, Indels: 20
0.65 0.11 0.24
Matches are distributed among these distances:
14 15 0.28
15 4 0.07
16 4 0.07
17 5 0.09
18 4 0.07
19 22 0.41
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATACGAAATGAAA
Found at i:51379 original size:33 final size:33
Alignment explanation
Indices: 51333--51445 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
51323 AAAAATGACT
* * *
51333 ATCGCAATACGAAATGAAAATCGTAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
51366 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
51399 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
51432 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
51446 CTAAATTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:51505 original size:33 final size:33
Alignment explanation
Indices: 51458--51621 Score: 166
Period size: 33 Copynumber: 4.8 Consensus size: 33
51448 AAATTCGCAA
*
51458 TGCGATTTTCATTTCGCTTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* * *
51491 TGTGATTTTTATTTCGCATTGCGATAGTCATTTCCGAGT
1 TGCGATTTTCATTTCGCATTGCGAT--TC-TCT-C--GT
* * * **
51530 TGCGATATTCATATTCGCGTTGCGATTTTAACGT
1 TGCGATTTTCAT-TTCGCATTGCGATTCTCTCGT
* *
51564 TGCAATTTTCATTTCGCATTGTGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
51597 TGCGATTTTCATTTCGCATTGCGAT
1 TGCGATTTTCATTTCGCATTGCGAT
51622 AGACATTAAG
Statistics
Matches: 104, Mismatches: 20, Indels: 14
0.75 0.14 0.10
Matches are distributed among these distances:
33 61 0.59
34 12 0.12
35 2 0.02
36 3 0.03
37 2 0.02
38 1 0.01
39 11 0.11
40 12 0.12
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:51534 original size:20 final size:20
Alignment explanation
Indices: 51509--51555 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
51499 TTATTTCGCA
51509 TTGCGATAGTCAT-TTCCGAG
1 TTGCGATAGTCATATT-CGAG
* *
51529 TTGCGATATTCATATTCGCG
1 TTGCGATAGTCATATTCGAG
51549 TTGCGAT
1 TTGCGAT
51556 TTTAACGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATATTCGAG
Found at i:54179 original size:24 final size:24
Alignment explanation
Indices: 54152--54198 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
54142 CAAAATCCGA
54152 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
54176 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
54199 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:54207 original size:24 final size:24
Alignment explanation
Indices: 54156--54207 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
54146 ATCCGAGTAT
** *
54156 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
54180 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
54204 TGAC
1 TGAC
54208 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:55081 original size:20 final size:20
Alignment explanation
Indices: 55058--55108 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
55048 GAATCTCGTT
55058 GCGATTTAC-TAAATCGCAAC
1 GCGA-TTACGTAAATCGCAAC
*
55078 GCGATTACGTAAATCGCAAT
1 GCGATTACGTAAATCGCAAC
*
55098 GCGAATACGTA
1 GCGATTACGTA
55109 TTCGCATTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
GCGATTACGTAAATCGCAAC
Found at i:55126 original size:20 final size:20
Alignment explanation
Indices: 55103--55285 Score: 113
Period size: 20 Copynumber: 9.0 Consensus size: 20
55093 GCAATGCGAA
*
55103 TACGTATTCGCATTGCGATT
1 TACGTATTCGCGTTGCGATT
* *
55123 TACGGATACGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
* * *
55143 TACGGATACACGTTGCGATTT
1 TACGTATTCGCGTTGCGA-TT
55164 TACGTATT-GTCGTTGCGATT
1 TACGTATTCG-CGTTGCGATT
* *
55184 TACGAATACGCGTTGCGATTT
1 TACGTATTCGCGTTGCGA-TT
* * *
55205 TACAG-ATACTCGTTGCGATAG
1 TAC-GTATTCGCGTTGCGAT-T
* *
55226 T-CAG-AATCGCGTTGCAATT
1 TAC-GTATTCGCGTTGCGATT
** *
55245 TATATGTTCGCGTTGCGATTT
1 TACGTATTCGCGTTGCGA-TT
* *
55266 TTCATATTCGCGTTGCGATT
1 TACGTATTCGCGTTGCGATT
55286 CTGGAAAATT
Statistics
Matches: 130, Mismatches: 24, Indels: 18
0.76 0.14 0.10
Matches are distributed among these distances:
19 1 0.01
20 76 0.58
21 52 0.40
22 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (20 bp):
TACGTATTCGCGTTGCGATT
Found at i:55167 original size:21 final size:20
Alignment explanation
Indices: 55115--55223 Score: 130
Period size: 20 Copynumber: 5.3 Consensus size: 20
55105 CGTATTCGCA
55115 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGGATACGCG
*
55135 TTGCGATTTACGGATACACG
1 TTGCGATTTACGGATACGCG
* *
55155 TTGCGATTTTACGTAT-TGTCG
1 TTGCGA-TTTACGGATACG-CG
*
55176 TTGCGATTTACGAATACGCG
1 TTGCGATTTACGGATACGCG
* *
55196 TTGCGATTTTACAGATACTCG
1 TTGCGA-TTTACGGATACGCG
55217 TTGCGAT
1 TTGCGAT
55224 AGTCAGAATC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
20 42 0.55
21 34 0.45
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGGATACGCG
Found at i:55218 original size:41 final size:40
Alignment explanation
Indices: 55115--55223 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 40
55105 CGTATTCGCA
* *
55115 TTGCGA-TTTACGGATACGCGTTGCGATTTACGGATACACG
1 TTGCGATTTTAC-GATACTCGTTGCGATTTACGAATACACG
** *
55155 TTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCG
1 TTGCGATTTTACG-ATACTCGTTGCGATTTACGAATACACG
55196 TTGCGATTTTACAGATACTCGTTGCGAT
1 TTGCGATTTTAC-GATACTCGTTGCGAT
55224 AGTCAGAATC
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 7 0.12
41 51 0.86
42 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTACGATACTCGTTGCGATTTACGAATACACG
Found at i:55237 original size:41 final size:41
Alignment explanation
Indices: 55115--55245 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 41
55105 CGTATTCGCA
* * * * *
55115 TTGCGA-TTTACGGATACGCGTTGCGATTTACGGATACACG
1 TTGCGATTTTACGTATACTCGTTGCGATTCACGAATACGCG
** *
55155 TTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACGCG
1 TTGCGATTTTACGTATACTCGTTGCGATTCACGAATACGCG
55196 TTGCGATTTTACAG-ATACTCGTTGCGATAGTCA-GAAT-CGCG
1 TTGCGATTTTAC-GTATACTCGTTGCGAT--TCACGAATACGCG
*
55237 TTGCAATTT
1 TTGCGATTT
55246 ATATGTTCGC
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 6 0.08
41 64 0.83
42 5 0.06
43 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
TTGCGATTTTACGTATACTCGTTGCGATTCACGAATACGCG
Found at i:55239 original size:61 final size:60
Alignment explanation
Indices: 55110--55246 Score: 159
Period size: 61 Copynumber: 2.2 Consensus size: 60
55100 GAATACGTAT
* * * * * *
55110 TCGCATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGATTTTACGTA
1 TCGCGTTGCGATTTACGAATACGCGTTGCGATTTACAGATACACGTTGCGATGTCACGAA
* *
55170 TTGTCGTTGCGATTTACGAATACGCGTTGCGATTTTACAGATACTCGTTGCGATAGTCA-GAA
1 TCG-CGTTGCGATTTACGAATACGCGTTGCGA-TTTACAGATACACGTTGCGAT-GTCACGAA
*
55232 TCGCGTTGCAATTTA
1 TCGCGTTGCGATTTA
55247 TATGTTCGCG
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
60 2 0.03
61 37 0.58
62 23 0.36
63 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGAATACGCGTTGCGATTTACAGATACACGTTGCGATGTCACGAA
Found at i:60077 original size:12 final size:12
Alignment explanation
Indices: 60062--60101 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
60052 ATGTTTTGAT
60062 TTCTGATCTGAA
1 TTCTGATCTGAA
* *
60074 TTCTGTTCTGAT
1 TTCTGATCTGAA
*
60086 TTCTGATCTGGA
1 TTCTGATCTGAA
60098 TTCT
1 TTCT
60102 ATTATGATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (12 bp):
TTCTGATCTGAA
Found at i:60100 original size:24 final size:23
Alignment explanation
Indices: 60036--60140 Score: 102
Period size: 24 Copynumber: 4.4 Consensus size: 23
60026 ATTTTATCTA
* * *
60036 ATTTCTGATTTGAAATATGTTTTG
1 ATTTCTGATCTGAATTCTG-TTTG
60060 ATTTCTGATCTGAATTCTGTTCTG
1 ATTTCTGATCTGAATTCTGTT-TG
* *
60084 ATTTCTGATCTGGATTCTATTATG
1 ATTTCTGATCTGAATTCTGTT-TG
* * *
60108 ATATATGATATGAATTCTGCTTTG
1 ATTTCTGATCTGAATTCTG-TTTG
60132 ATTTCTGAT
1 ATTTCTGAT
60141 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
23 2 0.03
24 62 0.94
25 2 0.03
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.50
Consensus pattern (23 bp):
ATTTCTGATCTGAATTCTGTTTG
Found at i:61334 original size:24 final size:22
Alignment explanation
Indices: 61307--61356 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
61297 ATTATTTGAT
*
61307 TAAAAATATTTTTTTATAAAAAAC
1 TAAAAATA-TTATTTA-AAAAAAC
*
61331 TAAAAATATTATTTAAAAAAAT
1 TAAAAATATTATTTAAAAAAAC
61353 TAAA
1 TAAA
61357 TTCAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 10 0.42
23 6 0.25
24 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAAAATATTATTTAAAAAAAC
Found at i:62203 original size:13 final size:13
Alignment explanation
Indices: 62185--62211 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
62175 CACCTCGAGT
62185 CGTTTCTTCTAGG
1 CGTTTCTTCTAGG
62198 CGTTTCTTCTAGG
1 CGTTTCTTCTAGG
62211 C
1 C
62212 ATGGGTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (13 bp):
CGTTTCTTCTAGG
Found at i:64093 original size:81 final size:82
Alignment explanation
Indices: 63997--64146 Score: 212
Period size: 81 Copynumber: 1.8 Consensus size: 82
63987 ACTTTAGCGG
* * * *
63997 CGTTTCTTAAACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCCGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
64062 AGGTACATATGTAATGA
66 AGGTACATATGTAATGA
* * * * *
64079 CGTTT-TTCAACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAAT
1 CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
64143 AGGT
66 AGGT
64147 CCATCTATAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 54 0.92
82 5 0.08
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (82 bp):
CGTTTCTTAAACAAACGCCACAACAGAGTAGTACTATAGCGGCATTTTTATACAAACGCCGCAAT
AGGTACATATGTAATGA
Found at i:64126 original size:41 final size:41
Alignment explanation
Indices: 63986--64334 Score: 172
Period size: 41 Copynumber: 8.4 Consensus size: 41
63976 CACAAAATGA
* *
63986 TACTTTAGCGGCGTTTCTTAAACAAACGCCGCTATAGAGTAG
1 TACTTTAGCGGCGTTT-TTATACAAACGCCGCAATAGAGTAG
* * * *
64028 TACTATAGCGGCATTTTTATATAAACGCCGCAATAG-GTACA
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
* ** * * *
64069 TA-TGTAATGACGTTTTTCA-ACAAACGCCACAACAGAGTAG
1 TACTTTAGCGGCGTTTTT-ATACAAACGCCGCAATAGAGTAG
* *
64109 TACTTTAGCGGCGTTTTTATACAAACTCTGCAATAG-GTCCA-
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGT--AG
* * * * * * * *
64150 T-CTATAGTGGCATTTTTTTCTGACAAACGTCGCAAAAGATTTG
1 TACTTTAGCGGC--GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * * **
64193 TACTTTAGCGGCGTTTTTATAAAAATGCCACAATAGAGTTC
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
* * * * * * * * * * *
64234 TCCTATAGTGGCTTTTTTTCTAATAAATGCTGCAACATATTAG
1 TACTTTAGCGGC-GTTTTTAT-ACAAACGCCGCAATAGAGTAG
* * *
64277 AACTTTAGCGGCGTTTTTATACAAACGCCGCAA-AAAATATG
1 TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTA-G
*
64318 TACTTTAGCGACGTTTT
1 TACTTTAGCGGCGTTTT
64335 CTTAAAAACG
Statistics
Matches: 221, Mismatches: 70, Indels: 33
0.68 0.22 0.10
Matches are distributed among these distances:
40 43 0.19
41 96 0.43
42 39 0.18
43 34 0.15
44 9 0.04
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (41 bp):
TACTTTAGCGGCGTTTTTATACAAACGCCGCAATAGAGTAG
Found at i:64166 original size:81 final size:82
Alignment explanation
Indices: 64006--64309 Score: 263
Period size: 84 Copynumber: 3.7 Consensus size: 82
63996 GCGTTTCTTA
* * * * * * *
64006 AACAAACGCCGCTATAGAGTAGTACTATAGCGGCATTTTTATATAAACGCCGCAATAGGTACATA
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
* * * *
64071 TGTAATGACGTTTTTC-
66 TATAGTGGCATTTTTCT
* * *
64087 AACAAACGCCACAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCTGCAATAGGTCCATC
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
64152 TATAGTGGCATTTTTTTCT
66 TATAGTGGCA--TTTTTCT
* * * * * * * *
64171 GACAAACGTCGCAAAAGATTTGTACTTTAGCGGCGTTTTTATA-AAAATGCCACAATAGAGTTC-
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACT-CCGCAATAG-GTACA
*
64234 TCCTATAGTGGCTTTTTTTCT
64 T-CTATAGTGGC-ATTTTTCT
* * * * * * *
64255 AATAAATGCTGCAACATATTAGAACTTTAGCGGCGTTTTTATACAAACGCCGCAA
1 AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAA
64310 AAAATATGTA
Statistics
Matches: 178, Mismatches: 37, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
81 61 0.34
83 10 0.06
84 91 0.51
85 16 0.09
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (82 bp):
AACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACTCCGCAATAGGTACATC
TATAGTGGCATTTTTCT
Found at i:68812 original size:21 final size:21
Alignment explanation
Indices: 68788--68846 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
68778 TGATTTATTA
**
68788 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
68809 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
*
68830 TTATGGATGTCAAGTTT
1 TTATGGATTTCAAGTTT
68847 ATTGAAAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.05, G:0.20, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:69089 original size:43 final size:43
Alignment explanation
Indices: 68994--69228 Score: 292
Period size: 43 Copynumber: 5.5 Consensus size: 43
68984 TATAGATATG
* ** * * *
68994 ACCTTTTGCGGCGTTTGTTCTAAAAAACGCCGCTATATA-CCAG
1 ACCTATTGCGGCGTTTGTT-GGAAAAACGCCGCTAAATATCAAC
* * * * * *
69037 ATCTTTTGCGGTGTTTGTAGGAAAAACGCCGTTAAATCTCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAC
* *
69080 ACCTATTGCGGCGTTTGTGGGAAAAACGCCGCTAAATCTCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAC
* *
69123 ACCTATTACGGCATTTGTTGGAAAAACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAC
* *
69166 ACCTATTGCGGTGTTTGTTGGACAAACGCCGCTAAATATCAAC
1 ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAC
69209 ACCTATTGCGGCGTTTGTTG
1 ACCTATTGCGGCGTTTGTTG
69229 TCGTTACCTA
Statistics
Matches: 167, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
42 14 0.08
43 153 0.92
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAAC
Found at i:73203 original size:29 final size:29
Alignment explanation
Indices: 73170--73236 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
73160 GGTATAGTTT
*
73170 TGAAACAAATGAAAATTT-AGATACTAAAA
1 TGAAACAAATAAAAATTTAAG-TACTAAAA
**
73199 TGAAATTAATAAAAATTTAAGTACTAAAA
1 TGAAACAAATAAAAATTTAAGTACTAAAA
*
73228 CGAAACAAA
1 TGAAACAAA
73237 ATTAATAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (29 bp):
TGAAACAAATAAAAATTTAAGTACTAAAA
Found at i:73437 original size:2 final size:2
Alignment explanation
Indices: 73430--73519 Score: 180
Period size: 2 Copynumber: 45.0 Consensus size: 2
73420 CCAAATTTTA
73430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73472 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
73514 AT AT AT
1 AT AT AT
73520 TGGATTTTGA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74433 original size:36 final size:37
Alignment explanation
Indices: 74361--74434 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
74351 GTTGGAAAAT
* * *
74361 ATTTATATATTTTCTTTTAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTTAAAAATTGAAAATCATAAA
74398 ATTTATATAATTT-TTTTATAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTCTTTTA-AAAATTGAAAATCATAAA
74434 A
1 A
74435 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.33
37 22 0.67
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTTATATAATTTCTTTTAAAAATTGAAAATCATAAA
Found at i:78234 original size:15 final size:15
Alignment explanation
Indices: 78214--78247 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
78204 ACATTACCCG
78214 CCCCGCATCCGCCCA
1 CCCCGCATCCGCCCA
*
78229 CCCCGCATCCGCCCG
1 CCCCGCATCCGCCCA
78244 CCCC
1 CCCC
78248 ACATAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.71, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCCGCATCCGCCCA
Found at i:86753 original size:72 final size:75
Alignment explanation
Indices: 86636--86772 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 75
86626 CAAGTATAGT
* *
86636 AATAAATAATAGTATTAATCTCATCTTCTTTTCCCAATATGCTATTTAATATATTATCTTTTCCC
1 AATAAATAATAGTATTAATCTCATCTTCTTTTCCCAATATACTATTTAATACATTATCTTTTCCC
86701 CATATATAAC
66 CATATATAAC
* * * *
86711 AATAACTAATAGTATT-AT-T-ATCTTCTTTTCCTAATCTACTATTTATTACATTATCTTTTCCC
1 AATAAATAATAGTATTAATCTCATCTTCTTTTCCCAATATACTATTTAATACATTATCTTTTCCC
86773 AAATTATACT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
72 38 0.68
73 1 0.02
74 2 0.04
75 15 0.27
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (75 bp):
AATAAATAATAGTATTAATCTCATCTTCTTTTCCCAATATACTATTTAATACATTATCTTTTCCC
CATATATAAC
Found at i:87838 original size:32 final size:32
Alignment explanation
Indices: 87802--87867 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
87792 TATGATATGT
* * *
87802 ATATCATTTAAAACGATTATGTGATATATATC
1 ATATCACTTAAAACAATAATGTGATATATATC
* *
87834 ATATCACTTAAAATAATAATGTGATATATGTC
1 ATATCACTTAAAACAATAATGTGATATATATC
87866 AT
1 AT
87868 GTCAGTAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (32 bp):
ATATCACTTAAAACAATAATGTGATATATATC
Done.