Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2119
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: 54676
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:73 original size:28 final size:28
Alignment explanation
Indices: 8--87 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
1 CATCCTC
*
8 ACCTTCAAAAG-CCATAAGTTAGTGGCA
1 ACCTTCAAAAGCCCATAAGTCAGTGGCA
* * **
35 TCTTTTTAAAGCCCATAAGTCAGTGGCA
1 ACCTTCAAAAGCCCATAAGTCAGTGGCA
* *
63 ACCTTCAAAAGCCCATGACTCAGTG
1 ACCTTCAAAAGCCCATAAGTCAGTG
88 ATCTCTTCTC
Statistics
Matches: 41, Mismatches: 11, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
27 7 0.17
28 34 0.83
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (28 bp):
ACCTTCAAAAGCCCATAAGTCAGTGGCA
Found at i:132 original size:30 final size:31
Alignment explanation
Indices: 65--597 Score: 549
Period size: 30 Copynumber: 17.4 Consensus size: 31
55 CAGTGGCAAC
* * *
65 CTTCAAAAGCCCATGACTCAGT-G-ATCTCTT
1 CTTC-AAAGTCCACGACTCAGTGGCATCTTTT
* *
95 C-TCAAAGTCAATGACTCAGTGGCAT-TTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
124 CTTCAAAGTCCACAACTCAGTGGCATCTCTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
155 -TTCTAAGTCCACGACTCGGTGGCATCCTTTT
1 CTTCAAAGTCCACGACTCAGTGGCAT-CTTTT
* *
186 CTTTC-AAGTCCATGACTCAGTGGCATATTTT
1 C-TTCAAAGTCCACGACTCAGTGGCATCTTTT
*
217 CTTCAAA-TCCACAACTCAGTGGCATCTCTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCT-TTT
* *
248 C-T--AAGTCCACGAATTAGTGGCATCCTTTT
1 CTTCAAAGTCCACGACTCAGTGGCAT-CTTTT
* * *
277 CTCCCAAAGTCTACGACTCAATGGCATCTTTT
1 CT-TCAAAGTCCACGACTCAGTGGCATCTTTT
*
309 CTTCAAAGTCCACAACTCAGTGGCATCTTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
340 CTTCAAAGTCCATGACTCAGTGGAAAT-TTCTT
1 CTTCAAAGTCCACGACTCAGTGG-CATCTT-TT
* * *
372 C-TC-AAGTCCCCGACTTAGTGGCATCTTGT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
401 C-CCAAAGTCCACGATTCAGTGGCATCTTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
431 CTTCAAAGTCCACAACTCAGTGGCATCTCTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
462 -TTCTAAGTCCACGACTCAGTGGCATCCTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
492 CTTCCAAGTCCATGACTCAGTGGCATCTTTTTT
1 CTTCAAAGTCCACGACTCAGTGGCATC--TTTT
**
525 CTTCAAAGTCCACGACTCAGTGGCATCCCTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
* *
556 C-CCAAAGTCCACAACTCAGTGGCATCTTTT
1 CTTCAAAGTCCACGACTCAGTGGCATCTTTT
586 CTTCAAAGTCCA
1 CTTCAAAGTCCA
598 TGCAATCTTT
Statistics
Matches: 417, Mismatches: 62, Indels: 47
0.79 0.12 0.09
Matches are distributed among these distances:
28 17 0.04
29 31 0.07
30 161 0.39
31 129 0.31
32 31 0.07
33 48 0.12
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (31 bp):
CTTCAAAGTCCACGACTCAGTGGCATCTTTT
Found at i:228 original size:92 final size:92
Alignment explanation
Indices: 107--597 Score: 545
Period size: 92 Copynumber: 5.3 Consensus size: 92
97 CAAAGTCAAT
*
107 GACTCAGTGGCAT-TTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACT
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACT
* *
171 CGGTGGCATCCTTTTCTTTCAAGTCCAT
66 CAGTGGCATCCTTTTC-TTCAAGTCCAC
* * *
199 GACTCAGTGGCATATTTTCTTCAAA-TCCACAACTCAGTGGCATC-TCTTTCTAAGTCCACGAAT
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACT
* * *
262 TAGTGGCATCCTTTTCTCCCAAAGTCTAC
66 CAGTGGCATCCTTTTCT-TC-AAGTCCAC
* * *
291 GACTCAATGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGAC
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTT-TTCTAAGTCCACGAC
* *
356 TCAGTGGAAAT--TTCTTC-TCAAGTCCCC
65 TCAGTGG-CATCCTT-TTCTTCAAGTCCAC
* * * * * * *
383 GACTTAGTGGCATCTTGTC-CCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCACAAC
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTT-TTCTAAGTCCACGAC
447 TCAGTGGCATCTCTTTTC-T-AAGTCCAC
65 TCAGTGGCATC-CTTTTCTTCAAGTCCAC
* * **
474 GACTCAGTGGCATCCTTTCTTCCAAGTCCATGACTCAGTGGCATCTTTTTTCTTCAAAGTCCACG
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTTTC-T--AAGTCCACG
* *
539 ACTCAGTGGCATCC-CTTC-CCAAAGTCCAC
63 ACTCAGTGGCATCCTTTTCTTC-AAGTCCAC
*
568 AACTCAGTGGCATCTTTTCTTCAAAGTCCA
1 GACTCAGTGGCATCTTTTCTTCAAAGTCCA
598 TGCAATCTTT
Statistics
Matches: 339, Mismatches: 43, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
90 3 0.01
91 104 0.31
92 115 0.34
93 34 0.10
94 60 0.18
95 21 0.06
96 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.15, T:0.32
Consensus pattern (92 bp):
GACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTTTCTAAGTCCACGACT
CAGTGGCATCCTTTTCTTCAAGTCCAC
Found at i:394 original size:61 final size:61
Alignment explanation
Indices: 80--597 Score: 476
Period size: 61 Copynumber: 8.5 Consensus size: 61
70 AAAGCCCATG
* * *
80 ACTCAGT-G-ATCTCTTC-TCAAAGTCAATGACTCAGTGGCATTT-TTCTTCAAAGTCCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTCTTC-TCAAAGTCCACA
* * * **
138 ACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCGGTGGCATCCTT-TTCTTTC-AAGTCCATG
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCAT--TTCTTC--TCAAAGTCCACA
* * * *
200 ACTCAGTGGCATATTTTCTTCAAA-TCCACAACTCAGTGGCATCTCTT-TCTAAGTCCACGA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTCTTCTCAAAGTCCAC-A
* * * *
260 A-TTAGTGGCATCCTTTTCTCCCAAAGTCTACGACTCAATGGCATCTT-TTCTTCAAAGTCCACA
1 ACTCAGTGGCAT-CTTTTCT-TCAAAGTCCACGACTCAGTGGCAT-TTCTTC-TCAAAGTCCACA
* * * *
323 ACTCAGTGGCATCTTTTCTTCAAAGTCCATGACTCAGTGGAAATTTCTTCTC-AAGTCCCCG
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGG-CATTTCTTCTCAAAGTCCACA
* * * *
384 ACTTAGTGGCATCTTGTC-CCAAAGTCCACGATTCAGTGGCATCTT-TTCTTCAAAGTCCACA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCAT-TTCTTC-TCAAAGTCCACA
* * **
445 ACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGCATCCTTTCTTC-C-AAGTCCATG
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCA---TTTCTTCTCAAAGTCCACA
** *
506 ACTCAGTGGCATCTTTTTTCTTCAAAGTCCACGACTCAGTGGCATCCCTTCCCAAAGTCCACA
1 ACTCAGTGGCATC--TTTTCTTCAAAGTCCACGACTCAGTGGCATTTCTTCTCAAAGTCCACA
569 ACTCAGTGGCATCTTTTCTTCAAAGTCCA
1 ACTCAGTGGCATCTTTTCTTCAAAGTCCA
598 TGCAATCTTT
Statistics
Matches: 376, Mismatches: 52, Indels: 61
0.77 0.11 0.12
Matches are distributed among these distances:
58 9 0.02
59 22 0.06
60 57 0.15
61 111 0.30
62 83 0.22
63 48 0.13
64 46 0.12
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (61 bp):
ACTCAGTGGCATCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTCTTCTCAAAGTCCACA
Found at i:465 original size:155 final size:150
Alignment explanation
Indices: 79--597 Score: 611
Period size: 155 Copynumber: 3.4 Consensus size: 150
69 AAAAGCCCAT
* * * *
79 GACTCAGT-G-ATCTCTTCTCAAAGTCAATGACTCAGTGGCAT-TTTTCTTCAAAGTCCACAACT
1 GACTCAGTGGCATCT-TTCCCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCACAACT
*
141 CAGTGGCATCTCTTTTCTAAGTCCACGACTCGGTGGCATCCTTTTCTTTCAAGTCCATGACTCAG
65 CAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCAT-CTTTTC-TTCAAGTCCATGACTCAG
* *
206 TGG-CATATTTTCTTCAAATCCAC
128 TGGAAAT-TTTTCTTCAAGTCCAC
* * * * * *
229 AACTCAGTGGCATCTCTT-TCTAAGTCCACGAATT-AGTGGCATCCTTTTCTCCCAAAGTCTACG
1 GACTCAGTGGCATCT-TTCCCAAAGTCCACG-ATTCAGTGGCAT-CTTTTCT-TCAAAGTCCACA
* * * *
292 ACTCAATGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCATGACT
62 ACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGCATCTTTTCTTC-AAGTCCATGACT
*
357 CAGTGGAAATTTCTTC-TCAAGTCCCC
125 CAGTGGAAATTT-TTCTTCAAGTCCAC
*
383 GACTTAGTGGCATCTTGTCCCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCACAACT
1 GACTCAGTGGCATCTT-TCCCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCACAACT
*
448 CAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCCTTTCTTCCAAGTCCATGACTCAGT
65 CAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCTTTTCTT-CAAGTCCATGACTCAGT
**
513 GGCATCTTTTTTCTTCAAAGTCCAC
129 GG-A-AATTTTTCTTC-AAGTCCAC
* * *
538 GACTCAGTGGCATCCCTTCCCAAAGTCCACAACTCAGTGGCATCTTTTCTTCAAAGTCCA
1 GACTCAGTGGCAT-CTTTCCCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCA
598 TGCAATCTTT
Statistics
Matches: 315, Mismatches: 35, Indels: 33
0.82 0.09 0.09
Matches are distributed among these distances:
150 7 0.02
151 18 0.06
152 57 0.18
153 39 0.12
154 87 0.28
155 105 0.33
156 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (150 bp):
GACTCAGTGGCATCTTTCCCAAAGTCCACGATTCAGTGGCATCTTTTCTTCAAAGTCCACAACTC
AGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCATCTTTTCTTCAAGTCCATGACTCAGTGG
AAATTTTTCTTCAAGTCCAC
Found at i:755 original size:33 final size:33
Alignment explanation
Indices: 669--859 Score: 187
Period size: 33 Copynumber: 5.9 Consensus size: 33
659 TCTGTTGCAC
* ***
669 CCTTTTAAGTCCACAATTTTGTGGCACCTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * * *
702 CTTTTTAATGCCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAA-GTCCACAACTCCATGGCACCTTTTT
*
736 CCTTTTAAGTCCACAACTCCATGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* *
769 CCTTTTAAGTCCACAACTCAATAGCA-C-----
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* *
796 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
* * *
829 TCATTTAAGTCTACAACTCCATGGCACCTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTT
860 ATCTTTAAGA
Statistics
Matches: 130, Mismatches: 21, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
27 23 0.18
28 1 0.01
32 1 0.01
33 78 0.60
34 27 0.21
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.37
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCATGGCACCTTTTT
Found at i:801 original size:67 final size:67
Alignment explanation
Indices: 669--801 Score: 151
Period size: 67 Copynumber: 2.0 Consensus size: 67
659 TCTGTTGCAC
* *** * * ** * *
669 CCTTTTAAGTCCACAATTTTGTGGCACCTTTTTCTTTTTAATGCCCACAACTCCGTGGCATCTTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAATGCCCACAACTCAATAGCACCTTT
734 TT
66 TT
* *
736 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAA-GTCCACAACTCAATAGCACCCTT
1 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAATGCCCACAACTCAATAGCACCTTT
800 TT
66 TT
802 AAGTCCACAA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
66 19 0.35
67 35 0.65
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (67 bp):
CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAATGCCCACAACTCAATAGCACCTTT
TT
Found at i:836 original size:60 final size:60
Alignment explanation
Indices: 736--856 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 60
726 GCATCTTTTT
*
736 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCTTTTAAGTCCACAACTCAATAGCAC
1 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCATTTAAGTCCACAACTCAATAGCAC
* * * * * * *
796 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTTTCATTTAAGTCTACAACTCCATGGCAC
1 CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCATTTAAGTCCACAACTCAATAGCAC
856 C
1 C
857 TTTATCTTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.25, C:0.32, G:0.11, T:0.32
Consensus pattern (60 bp):
CCTTTTAAGTCCACAACTCCATGGCACCTTGTTCCATTTAAGTCCACAACTCAATAGCAC
Found at i:929 original size:43 final size:43
Alignment explanation
Indices: 862--952 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
852 GCACCTTTAT
* * *
862 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGACCAATATCGCTAGCCTTGAATAAGCACATTGGCAC
* * *
905 CTTTAAGTCCAATATTGCTAGCCTTGAATAAGCATATTGGCAC
1 CTTTAAGACCAATATCGCTAGCCTTGAATAAGCACATTGGCAC
948 CTTTA
1 CTTTA
953 CCATCTTGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (43 bp):
CTTTAAGACCAATATCGCTAGCCTTGAATAAGCACATTGGCAC
Found at i:1124 original size:39 final size:39
Alignment explanation
Indices: 1024--1124 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
1014 AATGCTGCTA
* *
1024 GCCTTGAATCAACACATTGGCAAAAGCCCAATATCACTG
1 GCCTTGAATCAACATATTGGCACAAGCCCAATATCACTG
* *
1063 GCCTTGAATCAGCATATTGGCACAAGCCCAATATCCCTG
1 GCCTTGAATCAACATATTGGCACAAGCCCAATATCACTG
*
1102 GCCTTGAATAAACATATTGGCAC
1 GCCTTGAATCAACATATTGGCAC
1125 CTTCATCTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.23
Consensus pattern (39 bp):
GCCTTGAATCAACATATTGGCACAAGCCCAATATCACTG
Found at i:1342 original size:274 final size:268
Alignment explanation
Indices: 850--1358 Score: 666
Period size: 274 Copynumber: 1.9 Consensus size: 268
840 TACAACTCCA
* *
850 TGGCACCTTTATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCC
1 TGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCC
** * * * * *
915 AATATTGCTAGCCTTGAATAAGCATATTGGCACCTTTACCATCTTGAGTCCAATATCGTTGGCCT
66 AATATACCGAGCCTTGAATAAGCACATTGGCA-CTCTACCATCTTGAGTCCAATATCATAGGCCT
* * *
980 TGAATCAGCATGTTAGCACCTTGTCTTTAAGACCAATGCTGCTAGCCTTGAATCAACACATTGGC
130 TGAATCAGCATATTAGCACCTTGTCTCTAAGACCAATGCTGCTAGCCCTGAATCAACACATTGGC
*
1045 AAAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACAAGCCCAATATCCCTGGCCTTGAA
195 AAAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCACAAGCCCAATATCCCTGGCCTTGAA
1110 TAAACATAT
260 TAAACATAT
* *
1119 TGGCACCTTCATCTTTAAGACCGATGTCATTGGCCTTGAATCAGCACATTGGCACATTAACCATG
1 TGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGG--C----ACC---
* *
1184 TTTAAGTCCAATGTCACCGA-CCTTGAATCAGCACATTGGCA-TCT-CCATCTTGAGTCCAATAT
57 TTTAAGTCCAATAT-ACCGAGCCTTGAATAAGCACATTGGCACTCTACCATCTTGAGTCCAATAT
* * * * * *
1246 CATAGTCCTTGAATCAGCATATTGGCACTTTGTCTCTAAGA-CAATGCTGTTGGCCCTGAATCAG
121 CATAGGCCTTGAATCAGCATATTAGCACCTTGTCTCTAAGACCAATGCTGCTAGCCCTGAATCAA
* *
1310 CACATTGGCATAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCA
186 CACATTGGCAAAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCA
1359 TCTTGTCTTT
Statistics
Matches: 205, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
269 48 0.23
271 1 0.00
274 65 0.32
275 55 0.27
276 2 0.01
278 32 0.16
279 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (268 bp):
TGGCACCTTCATCTTTAAGACCAATGTCACTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCC
AATATACCGAGCCTTGAATAAGCACATTGGCACTCTACCATCTTGAGTCCAATATCATAGGCCTT
GAATCAGCATATTAGCACCTTGTCTCTAAGACCAATGCTGCTAGCCCTGAATCAACACATTGGCA
AAAGCCCAATATCACTGGCCTTGAATCAACATATTGGCACAAGCCCAATATCCCTGGCCTTGAAT
AAACATAT
Found at i:1428 original size:87 final size:87
Alignment explanation
Indices: 1252--1789 Score: 636
Period size: 87 Copynumber: 6.3 Consensus size: 87
1242 ATATCATAGT
* * * * *
1252 CCTTGAATCAGCATATTGGCACTTTGTCTCTAAGA-CAATG-CTGTTGGCCCTGAATCAGCACAT
1 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTC-GCTGGCCTTGAATCAGCACAT
*
1315 TGGCATAAGCCCAATATCGCTGG
65 TGGCACAAGCCCAATATCGCTGG
* * * * * *
1338 CCTTGAATCAACATATTGGCATCTTGTCTTTAAAACCAATGTCGCTAGCTTTGAATCAGCACATT
1 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
* * * *
1403 GGCACAAGCTCAATACCACTAG
66 GGCACAAGCCCAATATCGCTGG
* *
1425 CCTTGAATCAGCATATTGGCACCGTGCCTTTAAGGCCAATGTCGCTGGCCTTGAATCAGCACA-T
1 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
*
1489 ---ACAAGCCTAATATCGCTGG
66 GGCACAAGCCCAATATCGCTGG
1508 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAATTCAGCACAT
1 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAA-TCAGCACAT
*
1573 TGGCAGAAGCCCAATATCGCTGG
65 TGGCACAAGCCCAATATCGCTGG
* * *
1596 CCTTGAATCAGCATATCGGCACCTT-CAGTTTAAGACGCAAT-TCGCTGGCCTT-AATCAGCATA
1 CCTTGAATCAGCATATTGGCACCTTGC-CTTTAAGAC-CAATGTCGCTGGCCTTGAATCAGCACA
*
1658 TGGGCAACAAGCCCAATATCGCTGG
64 TTGGC-ACAAGCCCAATATCGCTGG
* * ** * *
1683 CCGTG-ATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTTGC-CACCTTCAATCAACACATT
1 CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
*
1746 GGCACCAAGCCC-A-ATCGGTGG
66 GGCA-CAAGCCCAATATCGCTGG
1767 CCTTGAATCAGCCATA-TGGCACC
1 CCTTGAATCAG-CATATTGGCACC
1790 CCCCCCCCCT
Statistics
Matches: 389, Mismatches: 47, Indels: 33
0.83 0.10 0.07
Matches are distributed among these distances:
83 67 0.17
84 19 0.05
85 23 0.06
86 94 0.24
87 121 0.31
88 61 0.16
89 4 0.01
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (87 bp):
CCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATT
GGCACAAGCCCAATATCGCTGG
Found at i:1771 original size:171 final size:169
Alignment explanation
Indices: 1252--1789 Score: 590
Period size: 171 Copynumber: 3.1 Consensus size: 169
1242 ATATCATAGT
** * * * *
1252 CCTTGAATCAGCATATTGGCACTTTGTCTCTAAGA-CAATG-CTGTTGGCCCTGAATCAGCACAT
1 CCTTGAATCAGCATA-TGGCACCGTGCCTTTAAGACCAATGTC-GCTGGCCTTGAATCAGCACA-
* * * * *
1315 TGGCATAAGCCCAATATCGCTGGCCTTGAATCAACATATTGGCATCTTGTCTTTAAAACCAATGT
63 TGGCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGT
* * * * *
1380 CGCTAGCTTTGAATCAGCACATTGGCACAAGCTCAATACCACTAG
128 CGCCA-CCTTGAATCAGCACATTGGCACAAGCCCAAT--CGCTGG
*
1425 CCTTGAATCAGCATATTGGCACCGTGCCTTTAAGGCCAATGTCGCTGGCCTTGAATCAGCACAT-
1 CCTTGAATCAGCATA-TGGCACCGTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATG
*
1489 --ACAAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCG
65 GCACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCG
** *
1552 CTGGCCTTGAATTCAGCACATTGGCAGAAGCCCAATATCGCTGG
130 C-CACCTTGAA-TCAGCACATTGGCACAAGCCC-A-ATCGCTGG
* * *
1596 CCTTGAATCAGCATATCGGCACC-TTCAGTTTAAGACGCAAT-TCGCTGGCCTT-AATCAGCATA
1 CCTTGAATCAGCATAT-GGCACCGTGC-CTTTAAGAC-CAATGTCGCTGGCCTTGAATCAGCACA
*
1658 TGGGCAACAAGCCCAATATCGCTGGCCGTG-ATCAGCATATTGGCACCTTGCCTTTAAGACCAAT
63 T-GGC-ACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAAT
* * * *
1722 GTTGCCACCTTCAATCAACACATTGGCACCAAGCCCAATCGGTGG
126 GTCGCCACCTTGAATCAGCACATTGGCA-CAAGCCCAATCGCTGG
1767 CCTTGAATCAGCCATATGGCACC
1 CCTTGAATCAG-CATATGGCACC
1790 CCCCCCCCCT
Statistics
Matches: 316, Mismatches: 33, Indels: 34
0.83 0.09 0.09
Matches are distributed among these distances:
170 77 0.24
171 86 0.27
172 24 0.08
173 45 0.14
174 61 0.19
175 23 0.07
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (169 bp):
CCTTGAATCAGCATATGGCACCGTGCCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATGG
CACAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGACCAATGTCGC
CACCTTGAATCAGCACATTGGCACAAGCCCAATCGCTGG
Found at i:1880 original size:50 final size:49
Alignment explanation
Indices: 1797--2041 Score: 220
Period size: 50 Copynumber: 5.0 Consensus size: 49
1787 ACCCCCCCCC
* * * *
1797 CCTT-CATCTTTATGACCATGTCGTTGGCCTTGAATCAGCACATTGGCA
1 CCTTACATCTTTAAGTCCAAGTCGCTGGCCTTGAATCAGCACATTGGCA
*
1845 CCTTAACCATCTTTAAGTCCAAGTCGC-CGCCTTGAATCAGCAC-TTGGCA
1 CCTT-A-CATCTTTAAGTCCAAGTCGCTGGCCTTGAATCAGCACATTGGCA
* *
1894 TCTT-CATCTTTTAAGTCCCATA-TCGCTGGCCTTGAATCAGCATATTGGCAA
1 CCTTACATC-TTTAAGT-CCA-AGTCGCTGGCCTTGAATCAGCACATTGGC-A
* * * *
1945 CCTT-TATCTTTTAAGACCATGTCACTGGCCTTGAATCAGCACATTGGCA
1 CCTTACATC-TTTAAGTCCAAGTCGCTGGCCTTGAATCAGCACATTGGCA
* * *
1994 CCTT-CATCTTT-AGTCCGATA-TCGTTGGCCTTGAATCAACATATTGGCA
1 CCTTACATCTTTAAGTCC-A-AGTCGCTGGCCTTGAATCAGCACATTGGCA
2042 TCTTTAAAAC
Statistics
Matches: 164, Mismatches: 21, Indels: 24
0.78 0.10 0.11
Matches are distributed among these distances:
46 4 0.02
47 11 0.07
48 39 0.24
49 32 0.20
50 48 0.29
51 30 0.18
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (49 bp):
CCTTACATCTTTAAGTCCAAGTCGCTGGCCTTGAATCAGCACATTGGCA
Found at i:2036 original size:98 final size:97
Alignment explanation
Indices: 1797--2041 Score: 298
Period size: 98 Copynumber: 2.5 Consensus size: 97
1787 ACCCCCCCCC
* * *
1797 CCTTCATCTTTATGACCATGTCGTTGGCCTTGAATCAGCACATTGGC-ACCTTAACCATCTTTAA
1 CCTTCATCTTTA-GTCCATATCGTTGGCCTTGAATCAGCATATTGGCAACCTTAACCATCTTTAA
* *
1861 GTCCAAGTCGCCGCCTTGAATCAGCACTTGGCA
65 GACCAAGTCACCGCCTTGAATCAGCACTTGGCA
* * * *
1894 TCTTCATCTTTTAAGTCCCATATCGCTGGCCTTGAATCAGCATATTGGCAACCTTTATC-T-TTT
1 CCTTCATC-TTT-AGT-CCATATCGTTGGCCTTGAATCAGCATATTGGCAACCTTAACCATCTTT
* *
1957 AAGACCATGTCACTGGCCTTGAATCAGCACATTGGCA
63 AAGACCAAGTCAC-CGCCTTGAATCAGCAC-TTGGCA
*
1994 CCTTCATCTTTAGTCCGATATCGTTGGCCTTGAATCAACATATTGGCA
1 CCTTCATCTTTAGTCC-ATATCGTTGGCCTTGAATCAGCATATTGGCA
2042 TCTTTAAAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 13
0.82 0.09 0.08
Matches are distributed among these distances:
97 9 0.07
98 49 0.39
99 49 0.39
100 20 0.16
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (97 bp):
CCTTCATCTTTAGTCCATATCGTTGGCCTTGAATCAGCATATTGGCAACCTTAACCATCTTTAAG
ACCAAGTCACCGCCTTGAATCAGCACTTGGCA
Found at i:7461 original size:18 final size:17
Alignment explanation
Indices: 7434--7471 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
7424 AAACTCGGAG
7434 AAAAAAAAAA-GAGAAAA
1 AAAAAAAAAATG-GAAAA
7451 AAAAGAAAAAATGGAAAA
1 AAAA-AAAAAATGGAAAA
7469 AAA
1 AAA
7472 GTAGGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 14 0.74
19 1 0.05
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAATGGAAAA
Found at i:8229 original size:156 final size:156
Alignment explanation
Indices: 7925--8217 Score: 408
Period size: 156 Copynumber: 1.9 Consensus size: 156
7915 GATTATTGAT
* * * **
7925 GTGTTTTTATGAGATTTTAGTAATTGGGGACTAAAATGCAAATATGTAAAAGTTTAGGGACTTGG
1 GTGTTTGTATGAGATTTTAGTAATTAGGGACTAAAATGCAAATATATAAAAGTTTAGGGACACGG
* * * * * *
7990 TTGCAAAGATTTATCCCATGAAATTTTTGCTTGCCGAAACATGCTAAATCATTTTTCCATGTTTC
66 TTGCAAAAATTTATCCCATGAAATTTTTGCTGGCCAAAACATGCTAAACCATTTTGCCATATTTC
8055 CCTTGCGGATTTGAAGGTTTGAAGGA
131 CCTTGCGGATTTGAAGGTTTGAAGGA
* * *
8081 GTGTTTGTATGTGATTTTAGTAATTAGGGACTAAAATGCAAATATATTAAAGTTTGGGGACACGG
1 GTGTTTGTATGAGATTTTAGTAATTAGGGACTAAAATGCAAATATATAAAAGTTTAGGGACACGG
* *
8146 TTGCAAAAATTTGTCCCATGAAATTTTTGCTAGGCCAAAACATAG-TGAACCATTTTGCCATATT
66 TTGCAAAAATTTATCCCATGAAATTTTTGCT-GGCCAAAACAT-GCTAAACCATTTTGCCATATT
*
8210 TTCCTTGC
129 TCCCTTGC
8218 TTATTTGAGG
Statistics
Matches: 118, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
156 86 0.73
157 31 0.26
158 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.37
Consensus pattern (156 bp):
GTGTTTGTATGAGATTTTAGTAATTAGGGACTAAAATGCAAATATATAAAAGTTTAGGGACACGG
TTGCAAAAATTTATCCCATGAAATTTTTGCTGGCCAAAACATGCTAAACCATTTTGCCATATTTC
CCTTGCGGATTTGAAGGTTTGAAGGA
Found at i:13061 original size:10 final size:8
Alignment explanation
Indices: 13040--13066 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
13030 GTCCCTACAA
13040 ATATATTC
1 ATATATTC
13048 ATATATTC
1 ATATATTC
13056 ATATATTC
1 ATATATTC
13064 ATA
1 ATA
13067 CCATGCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (8 bp):
ATATATTC
Found at i:20235 original size:17 final size:17
Alignment explanation
Indices: 20215--20289 Score: 105
Period size: 17 Copynumber: 4.2 Consensus size: 17
20205 ATGAATGAAA
20215 GAAAGTTGTGAAAGCAT
1 GAAAGTTGTGAAAGCAT
*
20232 GAAAGTTTTGAAAGCAT
1 GAAAGTTGTGAAAGCAT
*
20249 GAAATGATGATGCAAAGCAT
1 GAAA-GTTG-TG-AAAGCAT
20269 GAAAGTTGTGAAAGCAT
1 GAAAGTTGTGAAAGCAT
20286 GAAA
1 GAAA
20290 TGATGATGCA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
17 31 0.61
18 4 0.08
19 5 0.10
20 11 0.22
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.23
Consensus pattern (17 bp):
GAAAGTTGTGAAAGCAT
Found at i:20267 original size:20 final size:20
Alignment explanation
Indices: 20242--20304 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
20232 GAAAGTTTTG
20242 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
*
20262 AAAGCATGAAA-GTTG-TG-
1 AAAGCATGAAATGATGATGC
20279 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
20299 AAAGCA
1 AAAGCA
20305 AGTAACGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 11 0.29
18 5 0.13
19 5 0.13
20 17 0.45
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:20267 original size:37 final size:37
Alignment explanation
Indices: 20225--20304 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
20215 GAAAGTTGTG
*
20225 AAAGCATGAAAGTTTTGAAAGCATGAAATGATGATGC
1 AAAGCATGAAAGTTGTGAAAGCATGAAATGATGATGC
20262 AAAGCATGAAAGTTGTGAAAGCATGAAATGATGATGC
1 AAAGCATGAAAGTTGTGAAAGCATGAAATGATGATGC
20299 AAAGCA
1 AAAGCA
20305 AGTAACGTGG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (37 bp):
AAAGCATGAAAGTTGTGAAAGCATGAAATGATGATGC
Found at i:26485 original size:17 final size:17
Alignment explanation
Indices: 26432--26478 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
26422 TCTCTAAATA
26432 AAAAATAAAAAAGAAAG
1 AAAAATAAAAAAGAAAG
26449 AAAAATAAAAAAGAAAG
1 AAAAATAAAAAAGAAAG
26466 AAAAATAAAAAAG
1 AAAAATAAAAAAG
26479 TATGAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAATAAAAAAGAAAG
Found at i:26486 original size:15 final size:16
Alignment explanation
Indices: 26468--26497 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26458 AAAGAAAGAA
26468 AAATA-AAAAAGTATG
1 AAATAGAAAAAGTATG
26483 AAATAGAAAAAGTAT
1 AAATAGAAAAAGTAT
26498 AGATAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (16 bp):
AAATAGAAAAAGTATG
Found at i:28871 original size:42 final size:42
Alignment explanation
Indices: 28690--30493 Score: 501
Period size: 42 Copynumber: 42.9 Consensus size: 42
28680 ACCCTTATCT
* * * * * * *
28690 AAAGTCGGCTTGTCAGCTTTGACCCTGGAAACTTTCTTACCC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
** * * * *
28732 TTCAGTCTGCCTGCCGGCTTTGATCCTAGAGA-TTGCCTCACTT
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT-CCTCACTC
* ** * * *
28775 AAAGTCTGCCTATCGGCTTTGACTTTTGAGACTTTTCTACCCTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
* * * *
28819 --AGTGTGCCTATCGGCTTTGACCTTGGAGACTACCTCACTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * *
28859 AAAGTCTACCTATCGGCTTTAACCCT--AGACATTTCT-ACCTTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCA-C-TC
* * * * * * *
28901 -AA-TCTACCTGT-GGACTTTAACCCTAGAGACTACCTTATTT
1 AAAGTCTGCCTGTCGG-CTTTGACCCTGGAGACTTCCTCACTC
* * * * *
28941 AAAGTTTGCCTATCAGCTTTAACCCTAGAGACTTTCCTTC-CTTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCC-TCAC-TC
** * *
28985 --AGTCT-CCTTGTCAACTTTGACCTTGGAGACTACCTCA-TC
1 AAAGTCTGCC-TGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * *
29024 TAAAGTCTGTCC-GTCGGCTTTGACCCTAGAGACTTTTCTACCCTC
1 -AAAGTCTG-CCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
* * *
29069 --AGTCTGCTTGTCGGCTTTGACCTTGGAGACTACCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* **
29108 TAAAGTCTACCTGTCAACTTTGACCCTGGAGACTTTCCTTC-CTTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCC-TCAC-TC
* * * * *
29153 --AGTTTGCCTATCGGCTTTGACCCTAGAGACTT-TTCTACCC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-ACTC
** * * * * *
29193 TTAGTCTGCCTGTTGACTTTGACCTTGAAGACTACCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* *
29234 TAAAGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCT-ACCC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCACTC
* * * * * ** * * *
29277 TTAA-TCTACTTGTCGACTTTAACCCTAAAGACTGCCTTACTT
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * *
29319 AAAGTCT-ACTGTCGGCTTTAACCCTGGAGACTTTCTTAC-C
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
** * * *
29359 CTAGTCTGCCTATCGGCTTTGACCCTAGAGACTGCCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * ** * * *
29400 TAAAGTCTTCCTATTGAATTTGACCTTAGAGACTTTCCTACCCTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
** * * *
29445 -AA-TCTGGTTGTCAGCTTTGACCTTAGAGACTGT-CTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACT-TCCTCACTC
* ** *
29484 TAAAGTCTGCCTGTCGGCTTTGACCTTAAAGACATTCCTACCCTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
* * ** * *
29529 --AGTC-ACCTATCAACTTTGACCCTTGAGACTACCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * ** * *
29567 TAAAGTTTGCCTATTAGCTTTGACCTTGGAGACTTTCCTACCCTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
* * *
29612 --AGTCTACTTGTCGGCTTTGACCCTGGAGACTGCC-CTA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTC-ACTC
* * *
29651 TAAAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTTCTTC-C-C
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC--TTCCTCACTC
** * * * * * *
29694 TTAGTTTGCCTATCGACTTTGACTCTAGAGACTGCCTCACTTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCAC-TC
* * * * *
29737 -AAGTTTGCTTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
*
29780 -AA-TCTGCCTGTCGGCTTTGACCCTAGAGA-TTGCCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTT-CCTCACTC
* * * * * *
29819 TAAAGTCTGCCAGTCGACTTTGACCTTGGAGACTTTCTTACCC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
** * * ** * * * * *
29862 TTCAGTTTACCTGTCAACTTTGACACTAGAGACTGCCTTACTT
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * ** * * * *
29905 AAAGTCTGCATATTAGCTTTGACCTTAGAGACTTTTCTACCCTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CACTC
* * * * *
29949 --AGTCTGCTTGTCAGCTTTGACCCTGGAGACTGCCTCCCTT
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* *
29989 AAAGTCTGCCTGTCGGCTTTGACCCTAGAGATTTTCCT-ACTC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTCACTC
** * * * ** *
30031 TCAGTCTGCCTGTCAGTTTTGACCTTAAAGACTGCCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * *
30072 TAAAGTTTGCGTGTCAGCTTTGACCCTGGAGACTTTCCT-AC-C
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCTCACTC
** * * * * *
30114 TTTAGTGTACCTGTCAGCTTTGACCCTAGAGACTACCTCA-TC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * * * *
30156 TAAAGTTTGCCTGTCGGCTTTAACCCTAGATATTTTCCT-ACCC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGA-CTTCCTCACTC
** * * * * *
30199 TTAGTCTACCTGTTC-ACTTTGACTCTTAGAGACTTTCCTACCCTTC
1 AAAGTCTGCCTG-TCGGCTTTGAC-CCTGGAGAC-TTCCT-CAC-TC
* * *
30245 --AGTCTGCTTGTCAGCTTTGA-CCTCGGAGACTGCCTCA-TC
1 AAAGTCTGCCTGTCGGCTTTGACCCT-GGAGACTTCCTCACTC
* * *
30284 AAAAGTCTGCTTGTCGACTTTGACCCTGGAGACTTTCCTACCCTTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGAC-TTCCT-CAC-TC
* * * * * * *
30330 -AA-TCTACTTATCAGCTTTGACCCTTGAGACTGCCTCACTT
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * * * ** ** * *
30370 AAAGTTTGCTTATCGACTTTGATCCTAAAGACTTTTTTACCC
1 AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * * * * *
30412 TTAAGTCTGCATGTCGGCTTTGACTCTGGAGACTTCTTCGCCC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
* * ** * *
30455 TTAAGTTTGCCTACCGACTTTGACCCTGGAGACTACCTC
1 -AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTC
30494 GTCTTAAGTT
Statistics
Matches: 1284, Mismatches: 358, Indels: 238
0.68 0.19 0.13
Matches are distributed among these distances:
38 2 0.00
39 18 0.01
40 54 0.04
41 136 0.11
42 790 0.62
43 231 0.18
44 38 0.03
45 12 0.01
46 3 0.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (42 bp):
AAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTCCTCACTC
Found at i:29199 original size:84 final size:83
Alignment explanation
Indices: 29069--30275 Score: 892
Period size: 84 Copynumber: 14.4 Consensus size: 83
29059 TTCTACCCTC
* ** * *
29069 AGTCTGCTTGTCGGCTTTGACCTTGGAGAC-TACCT-CATCTAAAGTCTACCTGTCAACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTAC-CCT-TAGTCTACCTGTCAACTTTGAC
* * **
29132 CCTGGAGACTTTCCTTC-CTTC
64 CCTAGAGAC-TGCC-TCACTAA
* * * * * **
29153 AGTTTGCCTATCGGCTTTGACCCTAGAGACTTTTCTACCCTTAGTCTGCCTGTTGACTTTGA-CC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
* *
29217 TTGAAGACTACCTCATCTAA
66 TAG-AGACTGCCTCA-CTAA
* * * * * * *
29237 AGTCTGCCTGTCAGCTTTGACCCTGGAGACTTTCCTACCCTTAATCTACTTGTCGACTTTAACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
* *
29302 TAAAGACTGCCTTACTTAA
66 TAGAGACTGCCTCAC-TAA
* * * * * **
29321 AGTCT-ACTGTCGGCTTTAACCCTGGAGAC-TTTCTTACCC-TAGTCTGCCTATCGGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC-TACCCTTAGTCTACCTGTCAACTTTGACC
29383 CTAGAGACTGCCTCATCTAA
65 CTAGAGACTGCCTCA-CTAA
* * * ** * * * * *** * *
29403 AGTCTTCCTATTGAATTTGACCTTAGAGACTTTCCTACCCTCAATCTGGTTGTCAGCTTTGACCT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
*
29468 TAGAGACTGTCTCATCTAA
66 TAGAGACTGCCTCA-CTAA
** * * * *
29487 AGTCTGCCTGTCGGCTTTGACCTTAAAGACATTCCTACCCTCAGTC-ACCTATCAACTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
* *
29551 TTGAGACTACCTCATCTAA
66 TAGAGACTGCCTCA-CTAA
* * ** * * * **
29570 AGTTTGCCTATTAGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTACTTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
*
29635 TGGAGACTGCC-CTATCTAA
66 TAGAGACTGCCTC-A-CTAA
* * * * * * *
29654 AGTCTGCCTGTCGACTTTGACCTTGGAGACTTTTCTTCCCTTAGTTTGCCTATCGACTTTGACTC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
*
29719 TAGAGACTGCCTCACTTCA
66 TAGAGACTGCCTCAC-TAA
* * * * * * * **
29738 AGTTTGCTTGTCAGCTTTGACCTTGGAGACTTTCCTACCCTCAATCTGCCTGTCGGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
*
29803 TAGAGATTGCCTCATCTAA
66 TAGAGACTGCCTCA-CTAA
* * *
29822 AGTCTGCCAGTCGACTTTGACCTTGGAGAC-TTTCTTACCCTTCAGTTTACCTGTCAACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTC-TACCCTT-AGTCTACCTGTCAACTTTGAC
* *
29886 ACTAGAGACTGCCTTACTTAA
64 CCTAGAGACTGCCTCAC-TAA
* * ** * * * * *
29907 AGTCTGCATATTAGCTTTGACCTTAGAGACTTTTCTACCCTCAGTCTGCTTGTCAGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
* *
29972 TGGAGACTGCCTCCCTTAA
66 TAGAGACTGCCTCAC-TAA
* * * * * **
29991 AGTCTGCCTGTCGGCTTTGACCCTAGAGA-TTTTCCTACTCTCAGTCTGCCTGTCAGTTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTT-CTACCCTTAGTCTACCTGTCAACTTTGACC
* *
30055 TTAAAGACTGCCTCATCTAA
65 CTAGAGACTGCCTCA-CTAA
* * * * * * * *
30075 AGTTTGCGTGTCAGCTTTGACCCTGGAGACTTTCCTACCTTTAGTGTACCTGTCAGCTTTGACCC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
*
30140 TAGAGACTACCTCATCTAA
66 TAGAGACTGCCTCA-CTAA
* * * * *
30159 AGTTTGCCTGTCGGCTTTAACCCTAGATA-TTTTCCTACCCTTAGTCTACCTGTTC-ACTTTGAC
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTT-CTACCCTTAGTCTACCTG-TCAACTTTGAC
* * * **
30222 TCTTAGAGACTTTCCTACCCTTC
64 -CCTAGAGAC-TGCCT-CACTAA
* * *
30245 AGTCTGCTTGTCAGCTTTGACCTCGGAGACT
1 AGTCTGCCTGTCGGCTTTGACCTTGGAGACT
30276 GCCTCATCAA
Statistics
Matches: 895, Mismatches: 198, Indels: 57
0.78 0.17 0.05
Matches are distributed among these distances:
82 43 0.05
83 135 0.15
84 598 0.67
85 85 0.09
86 32 0.04
87 2 0.00
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.35
Consensus pattern (83 bp):
AGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTTAGTCTACCTGTCAACTTTGACCC
TAGAGACTGCCTCACTAA
Found at i:30329 original size:85 final size:86
Alignment explanation
Indices: 30214--30445 Score: 274
Period size: 85 Copynumber: 2.7 Consensus size: 86
30204 CTACCTGTTC
*
30214 ACTTTGACTCTTAGAGACTTTCCTACCCTTCAGTCTGCTTGTCAGCTTTGACCTC-GGAGACTGC
1 ACTTTGAC-CCTAGAGACTTTCCTACCCTTCAGTCTGCTTGTCAGCTTTGACCTCTGGAGACTGC
*
30278 CTCA-TCAAAAGTCTGCTTGTCG
65 CTCACT-AAAAGTCTGCTTATCG
* * * * *
30300 ACTTTGACCCTGGAGACTTTCCTACCCTTCAATCTACTTATCAGCTTTGACC-CTTGAGACTGCC
1 ACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCTTGTCAGCTTTGACCTCTGGAGACTGCC
* *
30364 TCACTTAAAGTTTGCTTATCG
66 TCACTAAAAGTCTGCTTATCG
* * ** * * *
30385 ACTTTGATCCTAAAGACTTTTTTACCCTTAAGTCTGCATGTCGGCTTTGA-CTCTGGAGACT
1 ACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCTTGTCAGCTTTGACCTCTGGAGACT
30446 TCTTCGCCCT
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
84 2 0.02
85 111 0.91
86 9 0.07
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (86 bp):
ACTTTGACCCTAGAGACTTTCCTACCCTTCAGTCTGCTTGTCAGCTTTGACCTCTGGAGACTGCC
TCACTAAAAGTCTGCTTATCG
Found at i:30904 original size:43 final size:44
Alignment explanation
Indices: 30844--31091 Score: 174
Period size: 44 Copynumber: 5.8 Consensus size: 44
30834 TAACTTGTTG
* * **
30844 GCTTTATCCCC-AGTCAACCTTTCTTA-CCTTTGGTGACCTATTG
1 GCTTTGTCCCCGA-TCAACCTTTCTTACCCTTTGGTGACCTGTCA
* * *
30887 GCTTTGTCCCCGATCAACCATTCTTACCCTTTGTTTACCTGTCA
1 GCTTTGTCCCCGATCAACCTTTCTTACCCTTTGGTGACCTGTCA
* * * * *
30931 GCTATGTCCCTGGT-AAAC-TTCTTACCCCTTGGTGACCTGTCA
1 GCTTTGTCCCCGATCAACCTTTCTTACCCTTTGGTGACCTGTCA
* * * * *
30973 GCTTTGTCCCCGGTCAACCTTTCTTACCCTTTGTTTACATGT-T
1 GCTTTGTCCCCGATCAACCTTTCTTACCCTTTGGTGACCTGTCA
* * * * *
31016 GACTATATCCCCGGT-AAACTTT-TT-CTCTATTGGTGACCTGTC-
1 G-CTTTGTCCCCGATCAACCTTTCTTACCCT-TTGGTGACCTGTCA
*
31058 GACTTTGTCCCC-AGTCAACCTTTTTTACCCTTTG
1 G-CTTTGTCCCCGA-TCAACCTTTCTTACCCTTTG
31092 TTTCCCTGTT
Statistics
Matches: 160, Mismatches: 34, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
41 3 0.02
42 55 0.34
43 41 0.26
44 58 0.36
45 3 0.02
ACGTcount: A:0.16, C:0.31, G:0.15, T:0.39
Consensus pattern (44 bp):
GCTTTGTCCCCGATCAACCTTTCTTACCCTTTGGTGACCTGTCA
Found at i:30969 original size:42 final size:44
Alignment explanation
Indices: 30850--31143 Score: 142
Period size: 44 Copynumber: 6.8 Consensus size: 44
30840 GTTGGCTTTA
* * * * ** *
30850 TCCCCAGTCAACCTTTCTTA-CCTTTGGTGACCTATTGGCTTTG
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAGCTATG
* * * * * *
30893 TCCCCGATCAACCATTCTTACCCTTTGTTTACCTGTCAGCTATG
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAGCTATG
* *
30937 TCCCTGGT-AAAC-TTCTTACCCCTTGGTGACCTGTCAGCTTTG
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAGCTATG
* * * * * * *
30979 TCCCCGGTCAACCTTTCTTACCCTTTGTTTACATGT-TGACTATA
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAG-CTATG
** *
31023 TCCCCGGT-AAACTTT-TT-CTCTATTGGTGACCTGTC-GACTTTG
1 TCCCCGGTCAAACTTTCTTAC-CCCTTGGTGACCTGTCAG-CTATG
* * * * * ** *
31065 TCCCCAGTCAACCTTTTTTACCCTTTGTTTCCCTGT-TGACTATG
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAG-CTATG
* * * *
31109 TCCCCAGT-AAA-TTTCTTACTCCTAGGTGGCCTGTC
1 TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTC
31144 GACTTTATCT
Statistics
Matches: 191, Mismatches: 49, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
41 1 0.01
42 73 0.38
43 38 0.20
44 78 0.41
45 1 0.01
ACGTcount: A:0.16, C:0.31, G:0.15, T:0.39
Consensus pattern (44 bp):
TCCCCGGTCAAACTTTCTTACCCCTTGGTGACCTGTCAGCTATG
Found at i:30981 original size:86 final size:85
Alignment explanation
Indices: 30864--31149 Score: 310
Period size: 86 Copynumber: 3.3 Consensus size: 85
30854 CAGTCAACCT
* * * *
30864 TTCTTA-CCTTTGGTGACCTATTGGCTTTGTCCCCGATCAACCATTCTTACCCTTTGTTTACCTG
1 TTCTTACCCCTTGGTGACCT-GTCGCTTTGTCCCCGATCAACCTTTCTTACCCTTTGTTTACCTG
* *
30928 -TCAGCTATGTCCCTGGTAAAC
65 TTGA-CTATGTCCCCGGTAAAC
* *
30949 TTCTTACCCCTTGGTGACCTGTCAGCTTTGTCCCCGGTCAACCTTTCTTACCCTTTGTTTACATG
1 TTCTTACCCCTTGGTGACCTGTC-GCTTTGTCCCCGATCAACCTTTCTTACCCTTTGTTTACCTG
*
31014 TTGACTATATCCCCGGTAAAC
65 TTGACTATGTCCCCGGTAAAC
* ** * *
31035 TT-TTTCTCTATTGGTGACCTGTCGACTTTGTCCCC-AGTCAACCTTTTTTACCCTTTGTTTCCC
1 TTCTTAC-CCCTTGGTGACCTGTCG-CTTTGTCCCCGA-TCAACCTTTCTTACCCTTTGTTTACC
* *
31098 TGTTGACTATGTCCCCAGTAAAT
63 TGTTGACTATGTCCCCGGTAAAC
* * *
31121 TTCTTACTCCTAGGTGGCCTGTCGACTTT
1 TTCTTACCCCTTGGTGACCTGTCG-CTTT
31150 ATCTCCGGGT
Statistics
Matches: 169, Mismatches: 25, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
85 11 0.07
86 153 0.91
87 5 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (85 bp):
TTCTTACCCCTTGGTGACCTGTCGCTTTGTCCCCGATCAACCTTTCTTACCCTTTGTTTACCTGT
TGACTATGTCCCCGGTAAAC
Found at i:31731 original size:17 final size:17
Alignment explanation
Indices: 31711--31756 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
31701 GGAAAATTCA
31711 AAAAAATAAAAAATAAT
1 AAAAAATAAAAAATAAT
* *
31728 AAAAAAT-CAAAATTAT
1 AAAAAATAAAAAATAAT
*
31744 CAAAAATAAAAAA
1 AAAAAATAAAAAA
31757 ATTCTTCAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.17
Consensus pattern (17 bp):
AAAAAATAAAAAATAAT
Found at i:31738 original size:26 final size:25
Alignment explanation
Indices: 31703--31757 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
31693 ATTTGTTTGG
*
31703 AAAATTCAAAAAAATAAAAAATAATA
1 AAAAATCAAAAAAATAAAAAATAA-A
** *
31729 AAAAATCAAAATTATCAAAAATAAA
1 AAAAATCAAAAAAATAAAAAATAAA
31754 AAAA
1 AAAA
31758 TTCTTCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 5 0.20
26 20 0.80
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (25 bp):
AAAAATCAAAAAAATAAAAAATAAA
Found at i:31844 original size:20 final size:20
Alignment explanation
Indices: 31819--31883 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
31809 TAAAGTTGTG
*
31819 AAAGCATGAAATGAAGATGC
1 AAAGCATGAAATGATGATGC
*
31839 AAAGCATGAAA-GTTG-TG-
1 AAAGCATGAAATGATGATGC
31856 AAAGCATGAAATGATGATGC
1 AAAGCATGAAATGATGATGC
31876 AAAGCATG
1 AAAGCATG
31884 TAACGTGGAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.28
18 5 0.13
19 4 0.10
20 19 0.49
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.18
Consensus pattern (20 bp):
AAAGCATGAAATGATGATGC
Found at i:31852 original size:37 final size:37
Alignment explanation
Indices: 31810--31883 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
31800 TGAATAAATT
31810 AAAGTTGTGAAAGCATGAAATGAAGATGCAAAGCATG
1 AAAGTTGTGAAAGCATGAAATGAAGATGCAAAGCATG
*
31847 AAAGTTGTGAAAGCATGAAATGATGATGCAAAGCATG
1 AAAGTTGTGAAAGCATGAAATGAAGATGCAAAGCATG
31884 TAACGTGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.45, C:0.08, G:0.27, T:0.20
Consensus pattern (37 bp):
AAAGTTGTGAAAGCATGAAATGAAGATGCAAAGCATG
Found at i:34249 original size:13 final size:13
Alignment explanation
Indices: 34231--34256 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34221 ACATTTTGGG
34231 ATGTATCGATACA
1 ATGTATCGATACA
34244 ATGTATCGATACA
1 ATGTATCGATACA
34257 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:34251 original size:33 final size:32
Alignment explanation
Indices: 34209--34276 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
34199 CGTTACAAGC
*
34209 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
34242 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
34274 CAA
1 CAA
34277 ATTTGGCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:34973 original size:22 final size:22
Alignment explanation
Indices: 34930--34974 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34920 TTTTCTTTTC
* *
34930 TCTCCCCCTTAATTAGAAAATT
1 TCTCCCCCTTAAGTAAAAAATT
34952 TCTCCCCCTT-AGTAAAATAATT
1 TCTCCCCCTTAAGTAAAA-AATT
34974 T
1 T
34975 AGCAGTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (22 bp):
TCTCCCCCTTAAGTAAAAAATT
Found at i:36672 original size:20 final size:21
Alignment explanation
Indices: 36643--36683 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
36633 TGTTTTTGTT
36643 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
36662 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
36684 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:42952 original size:13 final size:13
Alignment explanation
Indices: 42934--42959 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42924 ACATTTTGGG
42934 ATGTATCGATACA
1 ATGTATCGATACA
42947 ATGTATCGATACA
1 ATGTATCGATACA
42960 TATTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:42959 original size:33 final size:32
Alignment explanation
Indices: 42912--42978 Score: 98
Period size: 33 Copynumber: 2.1 Consensus size: 32
42902 TGTTACAAGC
*
42912 CAATGTATCAATACATTTTGGGATGTATCGATA
1 CAATGTATCAATACATATTGGG-TGTATCGATA
* *
42945 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCAATACATATTGGGTGTATCGATA
42977 CA
1 CA
42979 TATTTGGCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 12 0.39
33 19 0.61
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
CAATGTATCAATACATATTGGGTGTATCGATA
Found at i:46310 original size:19 final size:20
Alignment explanation
Indices: 46267--46317 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
46257 TACAAGCCAA
**
46267 TGTATCGATACATTTTATGG
1 TGTATCGATACATACTATGG
46287 TGTATCGATACATACTAT-G
1 TGTATCGATACATACTATGG
46306 TGTATCGATACA
1 TGTATCGATACA
46318 AGTTTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATACTATGG
Found at i:46414 original size:20 final size:20
Alignment explanation
Indices: 46372--46421 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
46362 TCTTTTTCAA
*
46372 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
46392 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
46412 GTATCGATAC
1 GTATCGATAC
46422 TTTTTAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:46757 original size:34 final size:35
Alignment explanation
Indices: 46719--46785 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
46709 CCTTACAACA
46719 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
46753 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
46786 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:47263 original size:13 final size:13
Alignment explanation
Indices: 47245--47270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47235 CAATTTTTTG
47245 TGTATCGATACAT
1 TGTATCGATACAT
47258 TGTATCGATACAT
1 TGTATCGATACAT
47271 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:47285 original size:32 final size:33
Alignment explanation
Indices: 47225--47288 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
47215 TACAAGCCAA
** *
47225 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
47258 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
47289 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:48030 original size:12 final size:12
Alignment explanation
Indices: 48013--48038 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48003 TAATTCACAC
48013 ATATCAAAATTT
1 ATATCAAAATTT
48025 ATATCAAAATTT
1 ATATCAAAATTT
48037 AT
1 AT
48039 TTGCATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATCAAAATTT
Found at i:49214 original size:13 final size:13
Alignment explanation
Indices: 49196--49220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49186 ACTGAAGTAA
49196 TGTATCGATACAT
1 TGTATCGATACAT
49209 TGTATCGATACA
1 TGTATCGATACA
49221 ATCTGGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50826 original size:84 final size:84
Alignment explanation
Indices: 50736--50901 Score: 212
Period size: 84 Copynumber: 2.0 Consensus size: 84
50726 TCATTTTCCA
* * *
50736 TTTGCAACTCATTTC-TTTTCTCCTCTAATTCATTTACTTTCTTTTTAAAAGAAT-T-ATTTTCT
1 TTTGCAACTC-TTTCATATTCTCCTCTAATTCACTTAATTTC-TTTT-AAAGAATATCATTTTCT
50798 AAACTCATTGATTTACTTTCAT
63 AAACTCATTGATTTACTTTCAT
* * *
50820 TTTGCAACTCTTTCATATTCTTCTCTAATTCACTTAATTTCTTTTCAAGAATATCATTTTCTACA
1 TTTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTTTCTAAA
* *
50885 CTTATTGATTTATTTTC
66 CTCATTGATTTACTTTC
50902 TTCTTTGAGT
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
82 6 0.08
83 9 0.13
84 56 0.79
ACGTcount: A:0.25, C:0.19, G:0.04, T:0.52
Consensus pattern (84 bp):
TTTGCAACTCTTTCATATTCTCCTCTAATTCACTTAATTTCTTTTAAAGAATATCATTTTCTAAA
CTCATTGATTTACTTTCAT
Found at i:52463 original size:34 final size:35
Alignment explanation
Indices: 52425--52491 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
52415 CCTTACAACA
52425 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCT
52459 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAGAACCTCTC
52492 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 12 0.40
37 13 0.43
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCT
Found at i:52969 original size:13 final size:13
Alignment explanation
Indices: 52951--52976 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52941 CAATTTTTTG
52951 TGTATCGATACAT
1 TGTATCGATACAT
52964 TGTATCGATACAT
1 TGTATCGATACAT
52977 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:52991 original size:32 final size:33
Alignment explanation
Indices: 52931--52994 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
52921 TACAAGCCAA
** *
52931 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
52964 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
52995 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:53540 original size:230 final size:230
Alignment explanation
Indices: 53137--53590 Score: 809
Period size: 230 Copynumber: 2.0 Consensus size: 230
53127 ATGTATCGAT
53137 ACAAATACCTATGTATCGATACTTTGATATATTTTAACTTAAAAATCAATCATTTTAAGCCTTGA
1 ACAAATACCTATGTATCGATACTTTGATATATTTTAACTTAAAAATCAATCATTTTAAGCCTTGA
* *
53202 AAACATTTATCCTTAACTAGAAAATATTTGGTGAATCAAAAATCATTTGGTACAAAATTTATAAA
66 AAACATTTATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTTATAAA
* * *
53267 GCACTTAGTTGAATAAAACATATTATTGTTATTTTCAAAATAATTTCCGGTTTTATTCAATCCTT
131 GCACTTAATTGAATAAAACATATTATTGGTATTTTCAAAATAATTCCCGGTTTTATTCAATCCTT
53332 TGTTATATCAAAACCAAGATCCTAACAGTATCAAA
196 TGTTATATCAAAACCAAGATCCTAACAGTATCAAA
*
53367 ACAAATACCTATGTATCGATACTTTGATATATTTTATCTTAAAAATCAATCATTTTAAGCCTTGA
1 ACAAATACCTATGTATCGATACTTTGATATATTTTAACTTAAAAATCAATCATTTTAAGCCTTGA
*
53432 AAACATTTATACTTAACTAGAAAACATTTGGTGAATCAAAAATTATTTGGTACAAAATTTATAAA
66 AAACATTTATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTTATAAA
** * *
53497 TTACTTAATTGAATAAAACATATTTTTGGTATTTTTAAAATAATTCCCGGTTTTATTCAATCCTT
131 GCACTTAATTGAATAAAACATATTATTGGTATTTTCAAAATAATTCCCGGTTTTATTCAATCCTT
53562 TGTTATATCAAAACCAAGATCCTAACAGT
196 TGTTATATCAAAACCAAGATCCTAACAGT
53591 CTCCCCCTTT
Statistics
Matches: 213, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
230 213 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (230 bp):
ACAAATACCTATGTATCGATACTTTGATATATTTTAACTTAAAAATCAATCATTTTAAGCCTTGA
AAACATTTATACTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTTATAAA
GCACTTAATTGAATAAAACATATTATTGGTATTTTCAAAATAATTCCCGGTTTTATTCAATCCTT
TGTTATATCAAAACCAAGATCCTAACAGTATCAAA
Found at i:53940 original size:35 final size:34
Alignment explanation
Indices: 53894--53982 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 34
53884 AATTCGCGCA
*
53894 TTCTCCCCCTTAAT-TAATCATAAGCACTTATCTCT
1 TTCTCCCCCTTAATAAAAT-ATAA-CACTTATCTCT
* * *
53929 TTCTCCTCCTTAATCAAAATTTTACACTTATCTCT
1 TTCTCCCCCTTAAT-AAAATATAACACTTATCTCT
53964 TTCTCCCCCTTAATCAAAA
1 TTCTCCCCCTTAAT-AAAA
53983 ATTTATTTGC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
35 42 0.89
36 2 0.04
37 3 0.06
ACGTcount: A:0.27, C:0.31, G:0.01, T:0.40
Consensus pattern (34 bp):
TTCTCCCCCTTAATAAAATATAACACTTATCTCT
Done.