Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007229.1 Hibiscus syriacus cultivar Beakdansim tig00019138_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: 83028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2618 original size:2 final size:2
Alignment explanation
Indices: 2578--2608 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2568 AATAATTTAT
*
2578 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2609 CTTAATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:8849 original size:18 final size:18
Alignment explanation
Indices: 8822--8857 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
8812 TTTCATTCCG
* *
8822 ATTTCCTCCCTTTTTCTT
1 ATTTCATCCCTTCTTCTT
8840 ATTTCATCCCTTCTTCTT
1 ATTTCATCCCTTCTTCTT
8858 CTTCAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTCATCCCTTCTTCTT
Found at i:11238 original size:18 final size:19
Alignment explanation
Indices: 11215--11250 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
11205 AAAATAAGTT
11215 TATAATATAT-ATAATTTA
1 TATAATATATAATAATTTA
*
11233 TATAATATTTAATAATTT
1 TATAATATATAATAATTT
11251 CGGTTAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAATATATAATAATTTA
Found at i:12683 original size:16 final size:15
Alignment explanation
Indices: 12664--12693 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12654 GTAATGTGGA
12664 TAAAAATGATTTTGAT
1 TAAAAATG-TTTTGAT
12680 TAAAAATGTTTTGA
1 TAAAAATGTTTTGA
12694 GAGTCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAAAAATGTTTTGAT
Found at i:13021 original size:2 final size:2
Alignment explanation
Indices: 13014--13041 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13004 AGTAAAGTAA
13014 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
13042 TTAAGTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15075 original size:122 final size:123
Alignment explanation
Indices: 14869--15649 Score: 975
Period size: 122 Copynumber: 6.6 Consensus size: 123
14859 ATGGATTCGA
*
14869 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
14933 ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
66 ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
*
14991 GCAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
* ** *
15056 ATTATGAACACTTCT-GAAATATTGATGCCGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
* *
15113 GCAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTC-TCATTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
* *
15177 ATTATGAACACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
* *
15235 GCAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
* * * * * * *
15299 ATTATGAACTCTACCTGG-CA-----ATGTTGATC-A-AT-C--AAGTGAT-GAATTCAA
66 ATTATGAACACT-TCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAG-AGTCAT
* * *
15347 GCAAAAGGTTGAACAAGTTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTTATTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
* *
15412 ATTATGAACACTTTTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT
66 ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
* * *
15470 GCAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
* * * * * * *
15534 ATTATGAACTCTACCT-GACA-----ATGTTGATCCA--T-C--AAGTGAT-GAATTCAA
66 ATTATGAACACT-TCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAG-AGTCAT
15582 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAA--T-TTCTTC---CTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
15641 ATTATGAAC
66 ATTATGAAC
15650 TCCTTCTGTG
Statistics
Matches: 584, Mismatches: 55, Indels: 55
0.84 0.08 0.08
Matches are distributed among these distances:
107 27 0.05
109 3 0.01
110 3 0.01
111 2 0.00
112 90 0.15
113 33 0.06
114 2 0.00
115 2 0.00
116 1 0.00
117 19 0.03
118 9 0.02
119 1 0.00
120 1 0.00
121 39 0.07
122 265 0.45
123 86 0.15
124 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (123 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
ATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCAT
Found at i:15463 original size:235 final size:234
Alignment explanation
Indices: 14863--15649 Score: 1187
Period size: 235 Copynumber: 3.3 Consensus size: 234
14853 TCTGCAATGG
* *
14863 ATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTC
1 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTA
*
14928 TTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTATGTGATAGAGTCATGC
66 TTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC
*
14993 AAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
131 AAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCATTCTTCAGATGAGTTCTTCTTAT
* * * * **
15058 TATGAACACT-TCT-GAAATATTGATGCCGATCTATCTCCTTCTGTGAT-A
195 TATGAACTCTACCTGGCAATGTTGAT--C-A---A--T-C--AAGTGATGA
* * * *
15106 GAGTCATGCAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTC-TCATTCTTCAGATGAGT
1 -ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGT
*
15170 TATTCTCATTATGAACACTTCTGGAAATATTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT
64 TATTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAT
15235 GCAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTTA
129 GCAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTTA
15300 TTATGAACTCTACCTGGCAATGTTGATCAATCAAGTGATGA
194 TTATGAACTCTACCTGGCAATGTTGATCAATCAAGTGATGA
*
15341 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGGACTTCTTCTTCCTTCTTCAGATGAGTT
1 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTT
*
15406 ATTCTCATTATGAACACTTTTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATG
65 ATTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATG
*
15471 CAAAGGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTTAT
130 CAAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTTAT
* *
15536 TATGAACTCTACCTGACAATGTTGATCCATCAAGTGATGA
195 TATGAACTCTACCTGGCAATGTTGATCAATCAAGTGATGA
*
15576 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA--T-TTCTT-C-CTTCAGATGAGTTC
1 ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTA
15636 TTCTCATTATGAAC
66 TTCTCATTATGAAC
15650 TCCTTCTGTG
Statistics
Matches: 510, Mismatches: 27, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
229 27 0.05
231 1 0.00
232 5 0.01
233 1 0.00
234 47 0.09
235 220 0.43
236 1 0.00
237 1 0.00
239 1 0.00
242 1 0.00
243 37 0.07
244 159 0.31
245 9 0.02
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (234 bp):
ATTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTA
TTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGC
AAAGGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTTATT
ATGAACTCTACCTGGCAATGTTGATCAATCAAGTGATGA
Found at i:15621 original size:17 final size:17
Alignment explanation
Indices: 15596--15648 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
15586 AAGGTTGAAC
15596 AAGTTCTTCTCATTATG
1 AAGTTCTTCTCATTATG
* *
15613 AATTTCTTCCTTCA-GATG
1 AAGTTCTT-C-TCATTATG
15631 -AGTTCTTCTCATTATG
1 AAGTTCTTCTCATTATG
15647 AA
1 AA
15649 CTCCTTCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 3 0.11
16 4 0.14
17 14 0.50
18 4 0.14
19 3 0.11
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (17 bp):
AAGTTCTTCTCATTATG
Found at i:15818 original size:73 final size:72
Alignment explanation
Indices: 15664--15990 Score: 424
Period size: 73 Copynumber: 4.5 Consensus size: 72
15654 TCTGTGGTTA
* * *
15664 TTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCTTGTTTCGAGTGAAACTGTCTCAAGCGAG
1 TTTTAAGAAAAACAATCTCAAGTGAGAT-AAA-TTGTTGTTTCGAGTGAAACTTTCTCAAGCGAG
15729 ACAAAGTTTG
64 ACAAA-TTTG
* * * *
15739 TTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTGTTTCGAGGGAAACTTTCTCCAGTGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTTTCTCAAGCGAG-A
* *
15804 CTAGTTTG
65 CAAATTTG
* *
15812 TTTTAAG-AAAACAATCTCAAGTGAAATAAATTATTGTTTCGAGTGAAA-TTGTCTCAAGCGAGA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTT-TCTCAAGCGAGA
*
15875 CGCAATTTG
65 C-AAATTTG
* * * * *
15884 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAGAA
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTTTCTCAAGCGAGAC
15949 ACAATTTG
66 A-AATTTG
15957 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
15991 CTATTTGAAA
Statistics
Matches: 221, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
71 4 0.02
72 58 0.26
73 125 0.57
74 8 0.04
75 26 0.12
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (72 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTTTCTCAAGCGAGAC
AAATTTG
Found at i:15937 original size:145 final size:146
Alignment explanation
Indices: 15664--15989 Score: 487
Period size: 145 Copynumber: 2.2 Consensus size: 146
15654 TCTGTGGTTA
* *
15664 TTTTAAGAAAAACAATCTCGAGTGAGATAAAATTTCTTGTTTCGAGTGAAACTGTCTCAAGCGAG
1 TTTTAAGAAAAACAATCTCAAGTGAGAT-AAA-TTATTGTTTCGAGTGAAACTGTCTCAAGCGAG
* * * *
15729 ACAAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTGTTTCGAGGGAAACTTTCT
64 ACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAACTTTCT
* *
15794 CCAGTGAG-AACTAGTTTG
129 CCAGCGAGAAAC-AATTTG
* *
15812 TTTTAAG-AAAACAATCTCAAGTGAAATAAATTATTGTTTCGAGTGAAATTGTCTCAAGCGAGAC
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTGTTTCGAGTGAAACTGTCTCAAGCGAGAC
* *
15876 GCAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTC
66 -AAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAACTTTCTC
15940 CAGCGAGAAACAATTTG
130 CAGCGAGAAACAATTTG
15957 TTTTAAGAAAAACAATCTCAAGTGAGATAAATT
1 TTTTAAGAAAAACAATCTCAAGTGAGATAAATT
15990 GCTATTTGAA
Statistics
Matches: 162, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
145 105 0.65
146 32 0.20
147 18 0.11
148 7 0.04
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.32
Consensus pattern (146 bp):
TTTTAAGAAAAACAATCTCAAGTGAGATAAATTATTGTTTCGAGTGAAACTGTCTCAAGCGAGAC
AAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAACTTTCTCC
AGCGAGAAACAATTTG
Found at i:17199 original size:52 final size:54
Alignment explanation
Indices: 17130--17235 Score: 153
Period size: 52 Copynumber: 2.0 Consensus size: 54
17120 ATAATCACTG
* *
17130 GTTCATAAAACATTTGACAACACATTCATCC-AAC-TGTGGCTTCTGCTCAGAT
1 GTTCATAAAACACTTGACAACACATTCATCCTAACATGTGGCTTCTGCCCAGAT
* **
17182 GTTCGTAAAACACTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGAT
1 GTTCATAAAACACTTGACAACACATTCATCCTAACATGTGGCTTCTGCCCAGAT
17236 TTCTGGTCAG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
52 29 0.62
53 1 0.02
54 17 0.36
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.31
Consensus pattern (54 bp):
GTTCATAAAACACTTGACAACACATTCATCCTAACATGTGGCTTCTGCCCAGAT
Found at i:22891 original size:21 final size:21
Alignment explanation
Indices: 22866--22905 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
22856 TAAAAATACG
22866 AATGTAAAATGAAAATGCAAA
1 AATGTAAAATGAAAATGCAAA
* *
22887 AATGTGAAATGCAAATGCA
1 AATGTAAAATGAAAATGCA
22906 TGTATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGTAAAATGAAAATGCAAA
Found at i:24599 original size:7 final size:7
Alignment explanation
Indices: 24587--24613 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
24577 AGAGCAACAT
24587 ATAAAAA
1 ATAAAAA
24594 ATAAAAA
1 ATAAAAA
24601 ATAAAAA
1 ATAAAAA
24608 ATAAAA
1 ATAAAA
24614 TAAAATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:25259 original size:27 final size:25
Alignment explanation
Indices: 25229--25297 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
25219 ATGAAATTTA
25229 AATAAAATACAAAATATTAATAAAAAT
1 AATAAAATA-AAAATATT-ATAAAAAT
* * *
25256 AATATACATATAAATATTATGAAAAT
1 AATA-AAATAAAAATATTATAAAAAT
25282 AATAAGTAATAAAAAT
1 AATAA--AATAAAAAT
25298 TTTGAAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.03
26 11 0.32
27 18 0.53
28 4 0.12
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (25 bp):
AATAAAATAAAAATATTATAAAAAT
Found at i:25490 original size:16 final size:15
Alignment explanation
Indices: 25471--25500 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
25461 GTAATGTGGA
25471 TAAAAATGATTTTGAT
1 TAAAAATG-TTTTGAT
25487 TAAAAATGTTTTGA
1 TAAAAATGTTTTGA
25501 GAGTCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAAAAATGTTTTGAT
Found at i:26153 original size:13 final size:13
Alignment explanation
Indices: 26135--26166 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
26125 AAATAAAAAT
26135 AATAATAAAGAGA
1 AATAATAAAGAGA
*
26148 AATAATAAAGAGC
1 AATAATAAAGAGA
26161 AATAAT
1 AATAAT
26167 TAAAATACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.19
Consensus pattern (13 bp):
AATAATAAAGAGA
Found at i:27056 original size:2 final size:2
Alignment explanation
Indices: 27049--27073 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27039 TTTATTTTGA
27049 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
27074 AAGCTGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30274 original size:118 final size:118
Alignment explanation
Indices: 30136--30375 Score: 444
Period size: 118 Copynumber: 2.0 Consensus size: 118
30126 AAAATTTAAA
* *
30136 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAATAAGTCTTGTACTCTTGTCATTCTT
1 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
*
30201 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTACATTTAATAGGGGTT
66 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTACATTTAAGAGGGGTT
30254 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
1 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
*
30319 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTACATTTACGAGGGGTT
66 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTACATTTAAGAGGGGTT
30372 AAGG
1 AAGG
30376 CTTGGTACTT
Statistics
Matches: 118, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 118 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.29
Consensus pattern (118 bp):
AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTACATTTAAGAGGGGTT
Found at i:34926 original size:2 final size:2
Alignment explanation
Indices: 34919--34949 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34909 TATATTAAAT
34919 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34950 GGGAAAGTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35778 original size:3 final size:3
Alignment explanation
Indices: 35765--35801 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
35755 TAGTTTGAAA
35765 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
35802 CAGATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:36620 original size:134 final size:136
Alignment explanation
Indices: 36441--36800 Score: 435
Period size: 139 Copynumber: 2.6 Consensus size: 136
36431 ATCTAATAAG
* * *
36441 AGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGGTGAGTTCTTCTCATTAT
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-TTCAGATGAGTTCTTCTCATTAT
* * * *
36505 GAACTCCTTCTGGAAATGATGATCCTCAAAAGAGG-T-GTTGATTCAACTTCATATGTGATGAAT
65 GAACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTTCGTTCATTCAACTCCATAGGTGATGAAT
*
36568 TAAGGC-A
130 CAA-GCTA
* * *
36575 AGGTTGAATAAGTTCTTGTCATTATGAACTTCTTCTTCCTTTTCAGACGAGTTCTTCTCATTATG
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATG
* ** *
36640 AACTTCC-TCTGAAAATGTTGATCCTCAAGTGAGGTTCTTCTTTCATTCAACTCCATAGGTGATG
66 AAC-TCCTTCTGGAAATGTTGATCCTCAAAAGAGG---TTCGTTCATTCAACTCCATAGGTGATG
36704 AATCAAGCTA
127 AATCAAGCTA
* * * *
36714 AAGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATG
1 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATG
*
36779 AACT-TTATCTGGAAATGTTGAT
66 AACTCCT-TCTGGAAATGTTGAT
36801 GCTGATCTAT
Statistics
Matches: 192, Mismatches: 24, Indels: 15
0.83 0.10 0.06
Matches are distributed among these distances:
134 79 0.41
135 8 0.04
138 4 0.02
139 101 0.53
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (136 bp):
AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATGAGTTCTTCTCATTATG
AACTCCTTCTGGAAATGTTGATCCTCAAAAGAGGTTCGTTCATTCAACTCCATAGGTGATGAATC
AAGCTA
Found at i:37040 original size:113 final size:113
Alignment explanation
Indices: 36834--37379 Score: 702
Period size: 113 Copynumber: 4.8 Consensus size: 113
36824 AGAGTCAAGC
** * * * *
36834 AAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTTAGATAAGTTCTTCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
36898 TATGAACTTTCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCGAGA
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGA
* * * * *
36946 AAAATGTTAAACAAAATTTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
37011 TATGAACTCTAC-CTGGCAATGATGATCCATCAAATGATGAATTC-AAA
66 TATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGA
* *
37058 CAAAATGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 -AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * * *
37123 TTATGAACTTTCTCTAGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
65 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGA
** *
37172 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
37237 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGC
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGA
** * *
37285 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCCTCTCAT
1 AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
37350 TATGAACTTTCTTTGGAAATGTTGATCCAT
66 TATGAACTTTCTCTGGAAAAGCTGATCCAT
37380 TGTGATGGAT
Statistics
Matches: 385, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
112 34 0.09
113 348 0.90
114 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGAATTCGAGA
Found at i:37267 original size:339 final size:342
Alignment explanation
Indices: 36719--37357 Score: 874
Period size: 339 Copynumber: 1.9 Consensus size: 342
36709 AGCTAAAGTC
*
36719 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
* * ***
36784 TATCTGGAAATGTTGATGCTGATCTATATCCTTCTTTGATAGAGTCAAGCAAAAGGTTGAACAAG
66 TATCTAGAAA---T-ATGCTGATC-ACATCC-TAAGTGATAGAGTCAAGCAAAAGGTTGAACAAG
* * * * *
36849 TTCTTCTTATTATGAACTTCTTTTTCTTCTTTAGATAAGTTCTTCTCATTATGAACTTTCTCTGG
125 CTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTGG
* * * * *
36914 AAAAGTTAATCCATCGAGTGATGAATTCGAGAAAAATGTTAAACAAAATTTTCTCATTATGAATT
190 AAAAGCTAATCCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAAATCTTCTCATTATGAACT
* *
36979 TCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCTACCTGGCAATGATGATCCATCAA
255 TCTTCTTCCTTCTTCAGATGAGTTCCTCTCATTATGAACTCTACCTGGCAATGATGATCCATCAA
37044 ATGATGAATTCAAACAAAATGTT
320 ATGATGAATTCAAACAAAATGTT
*
37067 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT
* * * **
37132 TTCTCTAGAAA-A-GCTGATC-CAT-C-AAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTT
65 TTATCTAGAAATATGCTGATCACATCCTAAGTGATAGAGTCAAGCAAAAGGTTGAACAAGCTCTT
*
37192 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACTTTCTCTGGAAAA
130 CTCATTATGAACTTCTT-TTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTGGAAAA
* * * * * **
37257 GCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT
194 GCTAATCCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAAATCTTCTCATTATGAACTTCTT
*
37322 CTTCCTTCTTCATATGAGTTCCTCTCATTATGAACT
259 CTTCCTTCTTCAGATGAGTTCCTCTCATTATGAACT
37358 TTCTTTGGAA
Statistics
Matches: 256, Mismatches: 33, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
338 45 0.18
339 129 0.50
340 1 0.00
341 2 0.01
343 7 0.03
344 1 0.00
348 33 0.13
349 38 0.15
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (342 bp):
GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
TATCTAGAAATATGCTGATCACATCCTAAGTGATAGAGTCAAGCAAAAGGTTGAACAAGCTCTTC
TCATTATGAACTTCTTTTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTGGAAAAGC
TAATCCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAAATCTTCTCATTATGAACTTCTTCT
TCCTTCTTCAGATGAGTTCCTCTCATTATGAACTCTACCTGGCAATGATGATCCATCAAATGATG
AATTCAAACAAAATGTT
Found at i:40654 original size:114 final size:114
Alignment explanation
Indices: 40459--40685 Score: 409
Period size: 114 Copynumber: 2.0 Consensus size: 114
40449 AGACTATCAT
*
40459 CAAATTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCGAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
** *
40524 AAGAACACTTTTAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAG
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
*
40573 CAAATTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCA
1 CAAATTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
40638 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
66 AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA
40686 AAACGTGGCA
Statistics
Matches: 108, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 108 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (114 bp):
CAAATTCATCTTTCAAATCTAATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAACTCA
AAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
Found at i:42357 original size:32 final size:32
Alignment explanation
Indices: 42316--42377 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
42306 GAAGAAATGA
**
42316 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTCATAGAGATACTTCTCG
42348 TTGTTATGCTCATCTCATAGAGATACTTCT
1 TTGTTATGCTCATCTCATAGAGATACTTCT
42378 TGTGTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTCATAGAGATACTTCTCG
Found at i:42874 original size:8 final size:8
Alignment explanation
Indices: 42861--42917 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
42851 CTTGGTTCAA
42861 TTTTTCTT
1 TTTTTCTT
*
42869 TTTTTCCT
1 TTTTTCTT
42877 TTTTTCTT
1 TTTTTCTT
*
42885 CTTTTCCTTTT
1 -TTTT--TCTT
*
42896 TTTTTCCT
1 TTTTTCTT
42904 TTTTTCTAT
1 TTTTTCT-T
42913 TTTTT
1 TTTTT
42918 TCAAGCATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
8 22 0.56
9 10 0.26
10 4 0.10
11 3 0.08
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTCTT
Found at i:42882 original size:16 final size:16
Alignment explanation
Indices: 42861--42897 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
42851 CTTGGTTCAA
*
42861 TTTTTCTTTTTTTCCT
1 TTTTTCTTCTTTTCCT
42877 TTTTTCTTCTTTTCCT
1 TTTTTCTTCTTTTCCT
42893 TTTTT
1 TTTTT
42898 TTTCCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTCTTTTCCT
Found at i:42915 original size:16 final size:15
Alignment explanation
Indices: 42861--42916 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
42851 CTTGGTTCAA
42861 TTTTTCTTTTTTTCCT
1 TTTTTC-TTTTTTCCT
42877 TTTTTCTTCTTTTCC-
1 TTTTTCTT-TTTTCCT
42892 --TTT-TTTTTTCCT
1 TTTTTCTTTTTTCCT
42904 TTTTTCTATTTTT
1 TTTTTCT-TTTTT
42917 TTCAAGCATA
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
11 6 0.18
12 2 0.06
13 3 0.09
14 3 0.09
15 3 0.09
16 17 0.50
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTTCCT
Found at i:42915 original size:19 final size:19
Alignment explanation
Indices: 42876--42919 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42866 CTTTTTTTCC
42876 TTTTTTCTTCTTTTCCTTT
1 TTTTTTCTTCTTTTCCTTT
*
42895 TTTTTTCCTT-TTTT-CTAT
1 TTTTTT-CTTCTTTTCCTTT
42913 TTTTTTC
1 TTTTTTC
42920 AAGCATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 9 0.39
19 10 0.43
20 3 0.13
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTTCTTCTTTTCCTTT
Found at i:43513 original size:165 final size:163
Alignment explanation
Indices: 43110--43570 Score: 681
Period size: 165 Copynumber: 2.8 Consensus size: 163
43100 TAGATCGCTC
** * ** * *
43110 TCTTGGAACTCTCTCAGATGTACTTTCTTGTTGTGATCTTTCATCATCCACTTCTGATACATCTG
1 TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
* * **
43175 CCCATGGCAAATAACTTTCAAT-ACATTCCCATCAATAAACCTTAATTGATCAAATCAAGCTTGG
66 -CCATGGCAAATAACTTTCAATCTCA-TCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGG
43239 ATCTATTCAGTCTCCTTTTTAGCACTAGATAAACA
129 ATCTATTCAGTCTCCTTTTTAGCACTAGATAAACA
* * *
43274 TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATCCTTCATCATCCGTTTTTTATATATATG
1 TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
43339 CCTATGGCAAATAACTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
66 CC-ATGGCAAATAACTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
* *
43404 TCTATTCAGTCTCCTTTTTTAGCACTATATCAACA
130 TCTATTCAGTCTCC-TTTTTAGCACTAGATAAACA
*
43439 TCTTGGAACTCTCTTGGATGTACGTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
1 TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
* * * *
43504 CTCATGGCAAATAGCTTTCAATCTTATCTCATCAATAAGGTTTAATTGATCAAATCGAGCTTGGA
66 C-CATGGCAAATAACTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGA
43569 TC
130 TC
43571 CCTTCAGCCT
Statistics
Matches: 269, Mismatches: 24, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
163 2 0.01
164 124 0.46
165 142 0.53
166 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.39
Consensus pattern (163 bp):
TCTTGGAACTCTCTTGGATGTACTTTCTTGTTATGATCTTTCATCATCCGTTTTTGATATATCTG
CCATGGCAAATAACTTTCAATCTCATCTCATCAATAAGGCTTAATTGATCAAATCAAGCTTGGAT
CTATTCAGTCTCCTTTTTAGCACTAGATAAACA
Found at i:49707 original size:3 final size:3
Alignment explanation
Indices: 49689--49724 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
49679 TAGTTTGAAA
49689 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49725 CAGATTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:50665 original size:139 final size:134
Alignment explanation
Indices: 50369--50839 Score: 413
Period size: 139 Copynumber: 3.6 Consensus size: 134
50359 ATAAGAGGTT
* *
50369 GAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGGTGAGTTCTTCTCATTATGAAC-
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTT-TTCAGATGAGTTCTTCTCATTATGAACT
* * * * *
50432 TCCTTCTGGAAATGA-TGATCCTCAAAAGAGGTGTTGATTCAACTTCATATGTGATGAATTAAGG
65 TTC-TCTGGAAAT-ATTGATCCTCAAAAGAGGTGTTCATTCAACTCCATAGGTGATGAATCAAGG
* *
50496 CAAGGTT
128 CAAAGTC
* * * * *
50503 GAATAAGTTCTTGTCATTATGAACTTCTTCTTCCTTTTTAGACGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTTTCAGATGAGTTCTTCTCATTATGAACTT
* ** *
50568 TCTCTGAAAATATTGATCCTCAAGTGAGGTTCTTCTTTCATTCAACTCCATAGGTGATGAATCAA
66 TCTCTGGAAATATTGATCCTCAAAAGAGG----T-GTTCATTCAACTCCATAGGTGATGAATCAA
50633 -GCTAAAGTC
126 GGC-AAAGTC
* *
50642 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * * * **
50707 TATCTGGAAATGTTGATGCT-----GA--T-CT-ATATC--CTTC-T--GTGATAGAGTCAAGAA
66 TCTCTGGAAATATTGATCCTCAAAAGAGGTGTTCAT-TCAACTCCATAGGTGAT-GAATCAAGGC
*
50758 AAAGGTT
129 AAA-GTC
* *
50765 GAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGATAAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTT-TTCAGATGAGTTCTTCTCATTATGAACT
50829 TTCTCTGGAAA
65 TTCTCTGGAAA
50840 AGTTAATCCA
Statistics
Matches: 285, Mismatches: 38, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
121 5 0.02
122 14 0.05
123 69 0.24
124 3 0.01
125 2 0.01
126 3 0.01
128 1 0.00
133 1 0.00
134 74 0.26
135 7 0.02
138 3 0.01
139 103 0.36
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (134 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTTTTCAGATGAGTTCTTCTCATTATGAACTT
TCTCTGGAAATATTGATCCTCAAAAGAGGTGTTCATTCAACTCCATAGGTGATGAATCAAGGCAA
AGTC
Found at i:50963 original size:113 final size:113
Alignment explanation
Indices: 50754--51429 Score: 986
Period size: 113 Copynumber: 6.0 Consensus size: 113
50744 GATAGAGTCA
* * * *
50754 AGAAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTT-TTTCTTCTTCAGATAAGTTCTTCT
1 AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
50818 CATTATGAACTTTCTCTGGAAAAGTTAATCCATCGAGTGATGAATTCG
66 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* * ** *
50866 AGAAAAATGTTAAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * * *
50931 CATTATGAACTCTAC-CTGGCAATGCTGATCCATCAAATGAT-GAATTC
66 CATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* **
50978 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AGA-AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
51043 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
65 TCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* *
51092 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCT
1 AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
51157 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
66 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* *
51205 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCT
1 AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
51270 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
66 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
* *
51318 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCC
1 AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
51383 CATTCTGAACTTTCTTTGGAAATA-TTGATCCAT--TGTGATGGATTTG
66 CATTATGAACTTTCTCTGGAAA-AGCTGATCCATCAAGTGATGGATTTG
51429 A
1 A
51430 ATCTTTGCTA
Statistics
Matches: 519, Mismatches: 39, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
111 13 0.03
112 41 0.08
113 457 0.88
114 8 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
AGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTG
Found at i:51190 original size:339 final size:338
Alignment explanation
Indices: 50642--51429 Score: 1046
Period size: 339 Copynumber: 2.3 Consensus size: 338
50632 AGCTAAAGTC
* *
50642 GAACAAGTTCTTCTCATTATGAACTTCTTCTTTC-TCTTCAGATAAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* * * * **
50706 TTATCTGGAAATGTTGATGCTGATCTATATCCTTCTGTGATAGAGTCAAGAAAAAGGTTGAACAA
66 TTCTCTGGAAA---T-A-GCTG------ATCCATCTGTGATGGATTTGAGAAAAAGGTTGAACAA
* * * *
50771 GTTCTTCTTATTATGAACTTCTTTTTCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTG
120 GCTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTG
* * * * *
50836 GAAAAGTTAATCCATCGAGTGATGAATTCGAGAAAAATGTTAAACAAATTCTTCTCATTATGAAT
185 GAAAAGCTAATCCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAACTCTTCTCATTATGAAC
* * *
50901 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGCTGATCCATC
250 TTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACT-TACTCTGGAAAAGCTGATCCATC
50965 AAATGATGAATTCAAACAAAAGGTT
314 AAATGATGAATTCAAACAAAAGGTT
*
50990 GAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* *
51055 TTCTCTGGAAA-AGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCA
66 TTCTCTGGAAATAGCTGATCCATC-TGTGATGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCA
* *
51119 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCATCTCATTATGAACTTTCTCTGGAAAAGCTG
130 TTATGAACTTCTT-TTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTGGAAAAGCTA
* * * * *
51184 ATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTC
194 ATCCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAACTCTTCTCATTATGAACTTCTTCTTC
* * *
51249 CTTCTTCAGATGAGTTCATCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGA
259 CTTCTTCAGATGAGTTCATCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAA
** *
51314 TTTGAGCAAAAGGTT
324 TTCAAACAAAAGGTT
* * *
51329 GAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCCCATTCTGAACT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
* *
51394 TTCTTTGGAAATA-TTGATCCAT-TGTGATGGATTTGA
66 TTCTCTGGAAATAGCTGATCCATCTGTGATGGATTTGA
51430 ATCTTTGCTA
Statistics
Matches: 392, Mismatches: 43, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
337 19 0.05
338 47 0.12
339 249 0.64
340 1 0.00
343 4 0.01
344 1 0.00
348 32 0.08
349 39 0.10
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (338 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
TTCTCTGGAAATAGCTGATCCATCTGTGATGGATTTGAGAAAAAGGTTGAACAAGCTCTTCTCAT
TATGAACTTCTTTTCCTTCTTCAGATAAGTTCATCTCATTATGAACTTTCTCTGGAAAAGCTAAT
CCATCAAGTGATGAATTCGAGAAAAAGGTTAAACAAACTCTTCTCATTATGAACTTCTTCTTCCT
TCTTCAGATGAGTTCATCTCATTATGAACTTACTCTGGAAAAGCTGATCCATCAAATGATGAATT
CAAACAAAAGGTT
Found at i:52727 original size:11 final size:12
Alignment explanation
Indices: 52709--52737 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
52699 AGAGCAACAT
52709 ATAAAAAATAAA
1 ATAAAAAATAAA
52721 A-AAAAAATAAA
1 ATAAAAAATAAA
52732 ATAAAA
1 ATAAAA
52738 TGAAATGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:53415 original size:27 final size:25
Alignment explanation
Indices: 53330--53422 Score: 73
Period size: 27 Copynumber: 3.6 Consensus size: 25
53320 TCTGACAAAC
* * *
53330 AAAATAATATGAAATTTAAATAAAATA
1 AAAATATTATGAAA-AT-AATATAATA
*
53357 AAAATATTAATAAAAATAATATACATA
1 AAAATATT-ATGAAAATAATATA-ATA
*
53384 TAAATATTATGAAAATAATAAGTAATA
1 AAAATATTATGAAAATAAT-A-TAATA
53411 AAAAT-TT-TGAAA
1 AAAATATTATGAAA
53423 GAAAAGAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
25 5 0.09
26 17 0.31
27 26 0.47
28 7 0.13
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAATATTATGAAAATAATATAATA
Found at i:53608 original size:16 final size:15
Alignment explanation
Indices: 53589--53618 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
53579 GTAATGTGGA
53589 TAAAAATGATTTTGAT
1 TAAAAATG-TTTTGAT
53605 TAAAAATGTTTTGA
1 TAAAAATGTTTTGA
53619 GAGTCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAAAAATGTTTTGAT
Found at i:54278 original size:13 final size:13
Alignment explanation
Indices: 54260--54291 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
54250 AAATAAAAAT
54260 AATAATAAAGAGA
1 AATAATAAAGAGA
*
54273 AATAATAAAGAGC
1 AATAATAAAGAGA
54286 AATAAT
1 AATAAT
54292 TAAAATACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.66, C:0.03, G:0.12, T:0.19
Consensus pattern (13 bp):
AATAATAAAGAGA
Found at i:58479 original size:118 final size:118
Alignment explanation
Indices: 58343--58582 Score: 417
Period size: 118 Copynumber: 2.0 Consensus size: 118
58333 AAAATTTAAA
* * *
58343 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAATAAGTCTTTTACTCTTGTCATTCTT
1 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
*
58408 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTAAATTTAATAGGGGTT
66 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTAAATTTAAGAGGGGTT
58461 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
1 AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
* * *
58526 GATAGAAGAGAATTAGTAATAGTTCGTCTAGCTAATTACATTTACGAGGGGTT
66 GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTAAATTTAAGAGGGGTT
58579 AAGG
1 AAGG
58583 CTTGGTACTT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 115 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (118 bp):
AAGGAAAAAGAAGAAAAAGAAACAGATTCTTCAGATGTAACAAGTCTTGTACTATTGTCATTCTT
GATAGAAGAGAATAAGTAATAGTTCGTCTAGCTAATTAAATTTAAGAGGGGTT
Found at i:63112 original size:2 final size:2
Alignment explanation
Indices: 63097--63135 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
63087 TAAAATAATT
*
63097 TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63136 GGGAAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63956 original size:3 final size:3
Alignment explanation
Indices: 63940--64005 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
63930 TAGTTTGAAA
63940 AAT AA- AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
63986 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
64006 CAGATTCAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:66227 original size:29 final size:30
Alignment explanation
Indices: 66189--66246 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
66179 TTTAGTAAAT
66189 ATTTTGAAAATAATGCTATATTGGTAATTA
1 ATTTTGAAAATAATGCTATATTGGTAATTA
** * *
66219 ATTTT-AAAATGGTGCTATTTTTGTAATT
1 ATTTTGAAAATAATGCTATATTGGTAATT
66247 TTGAAAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (30 bp):
ATTTTGAAAATAATGCTATATTGGTAATTA
Found at i:67020 original size:14 final size:14
Alignment explanation
Indices: 66986--67026 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
66976 ACATGATACA
66986 TGATACTTGA-TTCC
1 TGATA-TTGATTTCC
67000 TGAATATTGATTTCC
1 TG-ATATTGATTTCC
67015 TGATA-TGATTTC
1 TGATATTGATTTC
67027 TGTATTTCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.28
14 9 0.36
15 9 0.36
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (14 bp):
TGATATTGATTTCC
Found at i:73230 original size:7 final size:7
Alignment explanation
Indices: 73218--73249 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
73208 TTGACCCGAC
73218 CCGTTGA
1 CCGTTGA
73225 CCGTTGA
1 CCGTTGA
73232 CCGTTGA
1 CCGTTGA
*
73239 CTGTTGA
1 CCGTTGA
73246 CCGT
1 CCGT
73250 GATCGGGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.28, G:0.28, T:0.31
Consensus pattern (7 bp):
CCGTTGA
Found at i:77477 original size:64 final size:64
Alignment explanation
Indices: 77402--77575 Score: 210
Period size: 64 Copynumber: 2.7 Consensus size: 64
77392 TTGTATGAAT
* * ** *
77402 GTGCATTGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCGATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATT
77465 C
64 C
* * *
77466 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTAAAACATCGAATGCAATTG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
**
77530 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCAACAATAATA
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATA
77576 CTACATCTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
64 87 0.92
65 8 0.08
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTC
Found at i:77947 original size:24 final size:24
Alignment explanation
Indices: 77920--77969 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
77910 ACATGCATAA
*
77920 GATATAT-ATATGTTCATGTGATAT
1 GATATATGATATG-ACATGTGATAT
*
77944 GATATGTGATATGACATGTGATAT
1 GATATATGATATGACATGTGATAT
77968 GA
1 GA
77970 GAACATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (24 bp):
GATATATGATATGACATGTGATAT
Found at i:77952 original size:12 final size:12
Alignment explanation
Indices: 77934--77969 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
77924 TATATATGTT
77934 CATGTGATATGA
1 CATGTGATATGA
*
77946 TATGTGATATGA
1 CATGTGATATGA
77958 CATGTGATATGA
1 CATGTGATATGA
77970 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:78020 original size:29 final size:29
Alignment explanation
Indices: 77985--78058 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
77975 TGATATGAAG
77985 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
78014 TGACATGAGCTACATGATCACAAGAGAAA
1 TGACATGAGCTACATGATCACAAGAGAAA
*
78043 TAACATGAG-TACATGA
1 TGACATGAGCTACATGA
78059 ACATGTGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
TGACATGAGCTACATGATCACAAGAGAAA
Done.