Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold350
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: 1036165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 8
Found at i:9817 original size:1 final size:1
Alignment explanation
Indices: 9811--9909 Score: 99
Period size: 1 Copynumber: 99.0 Consensus size: 1
9801 CGTCCTCCAC
* * * * * *
9811 AAAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAAAAACAAAAAAAAAACAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
9876 ACAAACAAAAAACAAACAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9910 GGGTCCGGAT
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 76 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:9827 original size:10 final size:10
Alignment explanation
Indices: 9812--9909 Score: 146
Period size: 10 Copynumber: 9.8 Consensus size: 10
9802 GTCCTCCACA
9812 AAAAAAAAAC
1 AAAAAAAAAC
9822 AAAAAAAAAC
1 AAAAAAAAAC
*
9832 AAAACAAAAC
1 AAAAAAAAAC
9842 AAAAAAAAAC
1 AAAAAAAAAC
9852 AAAAAAAAAAC
1 -AAAAAAAAAC
9863 AAAAAAAAA-
1 AAAAAAAAAC
*
9872 AAAAACAAAC
1 AAAAAAAAAC
9882 AAAAAACAAAC
1 AAAAAA-AAAC
9893 -AAAAAAAAC
1 AAAAAAAAAC
9902 AAAAAAAA
1 AAAAAAAA
9910 GGGTCCGGAT
Statistics
Matches: 80, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
9 12 0.15
10 54 0.68
11 14 0.17
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:9835 original size:15 final size:15
Alignment explanation
Indices: 9811--9906 Score: 119
Period size: 15 Copynumber: 6.4 Consensus size: 15
9801 CGTCCTCCAC
9811 AAAAAA-AAAACAAA
1 AAAAAACAAAACAAA
9825 AAAAAACAAAACAAA
1 AAAAAACAAAACAAA
9840 ACAAAAA-AAAACAAAA
1 A-AAAAACAAAAC-AAA
*
9856 AAAAAACAAAAAAAA
1 AAAAAACAAAACAAA
9871 AAAAAAC-AAACAAA
1 AAAAAACAAAACAAA
9885 AAACAAACAAAA-AAA
1 AAA-AAACAAAACAAA
9900 ACAAAAA
1 A-AAAAA
9907 AAAGGGTCCG
Statistics
Matches: 73, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 15 0.21
15 40 0.55
16 18 0.25
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAACAAAACAAA
Found at i:9854 original size:41 final size:41
Alignment explanation
Indices: 9809--9909 Score: 163
Period size: 41 Copynumber: 2.5 Consensus size: 41
9799 GGCGTCCTCC
*
9809 ACAAAAAAAAAACAAAAAAAAACAAAACAAAACAAAAAA-AA
1 ACAAAAAAAAAACAAAAAAAAAAAAAAC-AAACAAAAAACAA
9850 ACAAAAAAAAAACAAAAAAAAAAAAAACAAACAAAAAACAA
1 ACAAAAAAAAAACAAAAAAAAAAAAAACAAACAAAAAACAA
9891 AC--AAAAAAAACAAAAAAAA
1 ACAAAAAAAAAACAAAAAAAA
9910 GGGTCCGGAT
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
39 17 0.29
40 10 0.17
41 31 0.53
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (41 bp):
ACAAAAAAAAAACAAAAAAAAAAAAAACAAACAAAAAACAA
Found at i:11351 original size:33 final size:33
Alignment explanation
Indices: 11314--11380 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
11304 TTCAACGATT
11314 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
11347 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
11380 T
1 T
11381 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:11352 original size:13 final size:13
Alignment explanation
Indices: 11334--11358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11324 CATAAAATGT
11334 TGTATCGATACAA
1 TGTATCGATACAA
11347 TGTATCGATACA
1 TGTATCGATACA
11359 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:11442 original size:13 final size:13
Alignment explanation
Indices: 11424--11448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11414 ATTACTCACA
11424 TGTATCGATACAT
1 TGTATCGATACAT
11437 TGTATCGATACA
1 TGTATCGATACA
11449 CTGATCTTTG
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:11513 original size:52 final size:52
Alignment explanation
Indices: 11457--11581 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
11447 CACTGATCTT
*
11457 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
11509 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
11561 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
11582 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:14944 original size:29 final size:30
Alignment explanation
Indices: 14905--15194 Score: 181
Period size: 30 Copynumber: 9.6 Consensus size: 30
14895 TCACCCTTCA
* *
14905 AAAGTCCACAAGTCAGTGGCA-TATTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* *
14934 AAAGCCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
14964 AAAAGCCCACAAGTCAGTGGCAAC-C---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* * *
14992 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
15022 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
15051 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
15081 TTTTGTAAA-CTCACAACTCTA-TAGCACTCTTTTTC
1 ------AAAGCCCACAAGTC-AGTGGCACTCTTTTTC
* * *
15116 TTTTTAAGCCCACAAGTTAGTGGCAC-CCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCACTCTTTTTC
*
15149 AAAAGCCCACAAGTCAGTGGCAAC-C--TTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
15178 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
15195 AGCAACCTTC
Statistics
Matches: 213, Mismatches: 30, Indels: 37
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.01
27 20 0.09
28 20 0.09
29 47 0.22
30 52 0.24
31 23 0.11
32 1 0.00
33 12 0.06
34 12 0.06
35 21 0.10
36 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.27
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:14972 original size:31 final size:30
Alignment explanation
Indices: 14901--15080 Score: 154
Period size: 29 Copynumber: 6.1 Consensus size: 30
14891 TTCCTCACCC
*
14901 TTCAAAAGTCCACAAGTCAGTGGCATATTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATTT
*
14931 TTC-AAAGCCCACAAGTCAGTGGCATTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TATTT
**
14961 TTCAAAAGCCCACAAGTCAGTGGCA-A-CC
1 TTCAAAAGCCCACAAGTCAGTGGCATATTT
* ***
14989 TTC-AAAGCCCACAAATCAGTGGCACCCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATTT
** * *
15018 TTCCGAAGCCCACAAGTCGGTGGCAT-CTT
1 TTCAAAAGCCCACAAGTCAGTGGCATATTT
* * * * *
15047 TTCCAAAGTCCACAACTCCGTGGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TATTT
15078 TTC
1 TTC
15081 TTTTGTAAAC
Statistics
Matches: 125, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
27 20 0.16
28 3 0.02
29 47 0.38
30 29 0.23
31 26 0.21
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATATTT
Found at i:15147 original size:34 final size:36
Alignment explanation
Indices: 15056--15147 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 36
15046 TTTCCAAAGT
*
15056 CCACAACTC-CGTGGCACTCTTTTTCTTTTGTAAAC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
* * *
15091 TCACAACTCTA-TAGCACTCTTTTTCTTTT-TAAGC
1 CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
* *
15125 CCACAAGT-TAGTGGCACCCTTTT
1 CCACAACTCTAGTGGCACTCTTTT
15148 CAAAAGCCCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
33 2 0.04
34 20 0.43
35 25 0.53
ACGTcount: A:0.22, C:0.29, G:0.11, T:0.38
Consensus pattern (36 bp):
CCACAACTCTAGTGGCACTCTTTTTCTTTTGTAAAC
Found at i:15155 original size:30 final size:29
Alignment explanation
Indices: 15121--15244 Score: 139
Period size: 28 Copynumber: 4.3 Consensus size: 29
15111 TTTTCTTTTT
* *
15121 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
15151 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
15179 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* * *
15207 AAGCACACAAGT-TGAT-GCAAACCTCTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
15236 AAGCCCACA
1 AAGCCCACA
15245 CAAGTTGGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.06
28 42 0.51
29 15 0.18
30 21 0.25
ACGTcount: A:0.37, C:0.31, G:0.15, T:0.17
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:15421 original size:43 final size:43
Alignment explanation
Indices: 15360--15449 Score: 162
Period size: 43 Copynumber: 2.1 Consensus size: 43
15350 GCATCTTCAT
* *
15360 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
15403 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
15446 CTTT
1 CTTT
15450 TCCATCTTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
Found at i:15444 original size:92 final size:95
Alignment explanation
Indices: 15264--15502 Score: 331
Period size: 92 Copynumber: 2.5 Consensus size: 95
15254 GGCGTCTCCT
* * * * *
15264 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATT-G-A-CAT-CCTTTAAGTCCAATATAGC
15329 TGGCCTTGAATCAGCATATTGGCA-TCTT-CATC
62 TGGCCTTGAATCAGCATATTGGCACTCTTCCATC
*
15361 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
*
15425 CTTGAATCAGCATATTGGCACCTTTTCCATC
66 CTTGAATCAGCATATTGGCA-CTCTTCCATC
* *
15456 TTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
15503 TTCTCATCTT
Statistics
Matches: 128, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
92 42 0.33
94 4 0.03
95 42 0.33
96 6 0.05
97 34 0.27
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTAAGTCCAATATAGCTGGC
CTTGAATCAGCATATTGGCACTCTTCCATC
Found at i:15481 original size:52 final size:53
Alignment explanation
Indices: 15403--15556 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
15393 ACATTGGCAC
*
15403 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
15455 CTTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
15510 CTTTAAGCCCAATATCGTTGGTCGTGAATCAACATATTGGCATCTTT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTT
15557 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 37 0.44
53 5 0.06
54 6 0.07
55 36 0.43
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.37
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:15729 original size:169 final size:173
Alignment explanation
Indices: 15403--15789 Score: 455
Period size: 169 Copynumber: 2.2 Consensus size: 173
15393 ACATTGGCAC
*
15403 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAAT
* * * *
15468 GTAGTTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGTC
65 ATAGCTAGCC-TGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCGTTGGTC
* *
15533 GTGAATCAACATATTGGCATCTTTATCACT-TTTCTCATCTTCAT
129 GTGAATCAACATATTGGCATCTTTATCACTCTTTATCATCATCAT
*
15577 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTT-ATCTTTAAGTCCAATA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAATA
* ** * ** *
15640 TCGCTAGCC-GCATATTGGC-TATT-TTATCCTTTTTCTCATCTTTAAACCCAATATTGTTGGTC
66 TAGCTAGCCTG-A-ATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCGTTGGTC
* * *
15702 GTGAATCAACGTATTGGTCCT-TTTATCACTCTTTATCCTCATCAT
129 GTGAATCAACATATTGG-CATCTTTATCACTCTTTATCATCATCAT
* * * * * * *
15747 CTTTAAGACCAGTGTTGCAGGCCTTGAATCTGCATAGTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
15790 ATTGCAAAAT
Statistics
Matches: 184, Mismatches: 25, Indels: 12
0.83 0.11 0.05
Matches are distributed among these distances:
169 61 0.33
170 53 0.29
171 24 0.13
173 3 0.02
174 43 0.23
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (173 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAATA
TAGCTAGCCTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAACCCAATATCGTTGGTCGT
GAATCAACATATTGGCATCTTTATCACTCTTTATCATCATCAT
Found at i:16377 original size:13 final size:13
Alignment explanation
Indices: 16359--16396 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
16349 CATAAAGTGT
16359 TGTATCGATACAA
1 TGTATCGATACAA
16372 TGTATCGATACAA
1 TGTATCGATACAA
16385 TGTATCGATACA
1 TGTATCGATACA
16397 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:16479 original size:13 final size:13
Alignment explanation
Indices: 16461--16485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16451 ATCACTTCAA
16461 TGTATCGATACAT
1 TGTATCGATACAT
16474 TGTATCGATACA
1 TGTATCGATACA
16486 CTAATCTTTG
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:16623 original size:52 final size:52
Alignment explanation
Indices: 16474--16624 Score: 212
Period size: 52 Copynumber: 2.9 Consensus size: 52
16464 ATCGATACAT
* ** * * *
16474 TGTATCGATACACTAATCTTTGTATCGATACATGTAGGCAAATTTACCCATA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTTCCCAGA
* ** *
16526 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTTCCCCGA
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTTCCCAGA
16578 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTTC
1 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTTC
16625 ATATTTCGGG
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (52 bp):
TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTTTCCCAGA
Found at i:21639 original size:29 final size:30
Alignment explanation
Indices: 21597--21655 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
21587 AGGATCACCC
21597 CCCACATTGGGGGGG-AAAACAAGAAAACT
1 CCCACATTGGGGGGGCAAAACAAGAAAACT
* *
21626 CCCACATTTGGGGGGCCAAACAAGAAAACT
1 CCCACATTGGGGGGGCAAAACAAGAAAACT
21656 TGTCCAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (30 bp):
CCCACATTGGGGGGGCAAAACAAGAAAACT
Found at i:21639 original size:30 final size:29
Alignment explanation
Indices: 21597--21655 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
21587 AGGATCACCC
*
21597 CCCACATTGGGGGGGAAAACAAGAAAACT
1 CCCACATTGGGGGGCAAAACAAGAAAACT
*
21626 CCCACATTTGGGGGGCCAAACAAGAAAACT
1 CCCACA-TTGGGGGGCAAAACAAGAAAACT
21656 TGTCCAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.39, C:0.24, G:0.25, T:0.12
Consensus pattern (29 bp):
CCCACATTGGGGGGCAAAACAAGAAAACT
Found at i:23155 original size:63 final size:62
Alignment explanation
Indices: 23038--23563 Score: 707
Period size: 63 Copynumber: 8.4 Consensus size: 62
23028 CTTCTTTTAG
* * * *
23038 CCTTTTAGTCCTCAAAAAGCATGACGTCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * *
23100 CCATTTAGTCCTCAAA-ATGTAGGACGTCTTTGTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGA-GCAGGACGCCTTT-TTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * *
23163 CCCTTTTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCA
1 -CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * *
23226 CCATTTAGTCCTCAAAGAGCAAGACGTCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACG-CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * *
23289 CCCTTTTAGTCATCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 -CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * * *
23352 CC-TTTAGTCCTCAAAGAGCAAGACACTTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* *
23413 CCCTTCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCAAACGAGTTGGTGGCA
1 -CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* * *
23476 CCTTTTAGTCCTCAAAGAGCAGGACACTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGACGC-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
* *
23539 -TTTCTTAGTCCTCAAAGAGTAGGAC
1 CCTT-TTAGTCCTCAAAGAGCAGGAC
23564 ACCCTTTATT
Statistics
Matches: 416, Mismatches: 38, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
61 55 0.13
62 79 0.19
63 232 0.56
64 49 0.12
65 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (62 bp):
CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
Found at i:23485 original size:250 final size:252
Alignment explanation
Indices: 23038--23538 Score: 767
Period size: 250 Copynumber: 2.0 Consensus size: 252
23028 CTTCTTTTAG
* * * *
23038 CCTTTTAGTCCTCAAAAAGCATGACGTCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCA
1 CCTTTTAGTCATCAAAAAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCA
* * * *
23103 TTTAGTCCTCAAAATGTAGGACGTCTTTGTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTT
66 TTTAGTCCTCAAAATGCAAGACGACTTTGTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTT
* * * * *
23168 TTAGTCCTCAAAGAGTAGGACACCTTTTTCTTTTTAAAGCCCACATGAGTTGGTGGCACCATTTA
131 CTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCAAACGAGTTGGTGGCACCATTTA
* *
23233 GTCCTCAAAGAGCAAGAC-GTCTTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC
196 GTCCTCAAAGAGCAAGACACT-TTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
* *
23290 CCTTTTAGTCATCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-
1 CCTTTTAGTCATCAAAAAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCA
*
23354 TTTAGTCCTCAAAGA-GCAAGAC-ACTTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCT
66 TTTAGTCCTCAAA-ATGCAAGACGACTTTGTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCT
* *
23417 TCTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCAAACGAGTTGGTGGCACCTTTT
130 TCTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCAAACGAGTTGGTGGCACCATTT
*
23482 AGTCCTCAAAGAGCAGGACACTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
195 AGTCCTCAAAGAGCAAGACACTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
23539 TTTCTTAGTC
Statistics
Matches: 226, Mismatches: 21, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
250 148 0.65
251 19 0.08
252 59 0.26
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (252 bp):
CCTTTTAGTCATCAAAAAGCAAGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCA
TTTAGTCCTCAAAATGCAAGACGACTTTGTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTT
CTAGTCCTCAAAGAGCAGGACACCTTTTTCTTTTCAAAGCCCAAACGAGTTGGTGGCACCATTTA
GTCCTCAAAGAGCAAGACACTTTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:23640 original size:43 final size:42
Alignment explanation
Indices: 23539--23641 Score: 145
Period size: 42 Copynumber: 2.4 Consensus size: 42
23529 GTTGGTGGCA
* * *
23539 TTTCTTAGTCCTCAAAGAGTAGGACACCCTTTATTCTCTTTT
1 TTTCTTTGTCCTCAAAGAGTAGGACACACTTAATTCTCTTTT
*
23581 TTTCTTTATCCTCAAAGAGTAGGACACACTTAACTTC-CTTCTT
1 TTTCTTTGTCCTCAAAGAGTAGGACACACTTAA-TTCTCTT-TT
23624 TTTCTTTGTCCTCAAAGA
1 TTTCTTTGTCCTCAAAGA
23642 ACAGGGCACG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 32 0.59
43 22 0.41
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (42 bp):
TTTCTTTGTCCTCAAAGAGTAGGACACACTTAATTCTCTTTT
Found at i:23725 original size:46 final size:45
Alignment explanation
Indices: 23589--23777 Score: 153
Period size: 46 Copynumber: 4.4 Consensus size: 45
23579 TTTTTCTTTA
* * * * *
23589 TCCTCAAAGAGTAGGACACACTTAACTTCCTTCTTTT-TC-TTTG
1 TCCTCAAAGAGCAAGACACACTTCATTTCCTTCTTTTCCCTTTTG
* ** * * * *
23632 TCCTCAAAGAAC-AG-GGCACGTCATGT-CTT-TTTTTCC-TCTG
1 TCCTCAAAGAGCAAGACACACTTCATTTCCTTCTTTTCCCTTTTG
23672 TCCTCAAAGAGCAAGACACA-TTCAATTTCCTTCTTTTCCCCTTTTG
1 TCCTCAAAGAGCAAGACACACTTC-ATTTCCTTCTTTT-CCCTTTTG
* * * *
23718 TCTTCAAAGAGCAATACACACTTCATTTCTTTCTTTTCCTTTTTG
1 TCCTCAAAGAGCAAGACACACTTCATTTCCTTCTTTTCCCTTTTG
23763 TCCTCAAAGAG-AAGA
1 TCCTCAAAGAGCAAGA
23778 ACGCGTTTTA
Statistics
Matches: 113, Mismatches: 24, Indels: 17
0.73 0.16 0.11
Matches are distributed among these distances:
39 4 0.04
40 18 0.16
41 10 0.09
42 6 0.05
43 13 0.12
44 7 0.06
45 19 0.17
46 33 0.29
47 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (45 bp):
TCCTCAAAGAGCAAGACACACTTCATTTCCTTCTTTTCCCTTTTG
Found at i:23838 original size:39 final size:40
Alignment explanation
Indices: 23757--23840 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
23747 TTTCTTTTCC
* * *
23757 TTTTTGTCCTCAAAGAGAAGAACGCGTTTTATTTTCCTTT
1 TTTTTATCCTCAAAGAGAAGAACGCATTTCATTTTCCTTT
* * *
23797 TTTTTATCCTCAAAGAGCAGGACGTATTTCATTTTCCTTT
1 TTTTTATCCTCAAAGAGAAGAACGCATTTCATTTTCCTTT
23837 TTTT
1 TTTT
23841 CTTTTGTCCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (40 bp):
TTTTTATCCTCAAAGAGAAGAACGCATTTCATTTTCCTTT
Found at i:24872 original size:59 final size:59
Alignment explanation
Indices: 24742--24857 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
24732 ACACCTTACG
**
24742 ACTCCCATGCAACCTTGTGGTTTTTGTTTGTGGTAGTTTAGGACTTTTTTGTTCCTTGA
1 ACTCCCATGCATTCTTGTGGTTTTTGTTTGTGGTAGTTTAGGACTTTTTTGTTCCTTGA
24801 ACTCCCATGCATTCTTGTGGTTTTTGTTTGTGGTAGTTTAGGACTTTTTTGTTCCTT
1 ACTCCCATGCATTCTTGTGGTTTTTGTTTGTGGTAGTTTAGGACTTTTTTGTTCCTT
24858 AGTTTTGTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (59 bp):
ACTCCCATGCATTCTTGTGGTTTTTGTTTGTGGTAGTTTAGGACTTTTTTGTTCCTTGA
Found at i:26119 original size:10 final size:10
Alignment explanation
Indices: 26104--26128 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
26094 TAATTACTTC
26104 TTTTTTAATT
1 TTTTTTAATT
26114 TTTTTTAATT
1 TTTTTTAATT
26124 TTTTT
1 TTTTT
26129 ATTTTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:27455 original size:104 final size:104
Alignment explanation
Indices: 27344--27555 Score: 264
Period size: 104 Copynumber: 2.0 Consensus size: 104
27334 TATTTTAATT
* * * * **
27344 AAATTAAATTTTTTAGTTATAAATTATATAAACATTATTAATGTAAAGATA-TATAACGGTAATT
1 AAATTAAATTTTTTAGTTATAAATTAGATAAACATCATTAATATAAAAATATTATAACAATAATT
*
27408 TAAAAATAAAATAAAAAATAAACACTATTTTCATCTATTC
66 TAAAAATAAAAT-AAAAATAAACACTATTTTCATATATTC
* * *
27448 AAATTAAATTTTTTATTTATAAATTAGATAAGCATCATTAATATAAAAATATTTATAATAATAAT
1 AAATTAAATTTTTTAGTTATAAATTAGATAAACATCATTAATATAAAAATA-TTATAACAATAAT
* * ** *
27513 TTAAGAATAGAATAAAAATAATGACTATTTTCATATGTTC
65 TTAAAAATAAAATAAAAATAAACACTATTTTCATATATTC
27553 AAA
1 AAA
27556 AGTTTATCTG
Statistics
Matches: 91, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
104 45 0.49
105 26 0.29
106 20 0.22
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.39
Consensus pattern (104 bp):
AAATTAAATTTTTTAGTTATAAATTAGATAAACATCATTAATATAAAAATATTATAACAATAATT
TAAAAATAAAATAAAAATAAACACTATTTTCATATATTC
Found at i:29998 original size:18 final size:18
Alignment explanation
Indices: 29975--30028 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
29965 ATACTAAGTT
29975 AATTTTTTTTAAATTCAAA
1 AATTTTTTTTAAATT-AAA
*
29994 ATTTTTTATTTAAATTAAA
1 AATTTTT-TTTAAATTAAA
* *
30013 AAATTATTTT-AATTAA
1 AATTTTTTTTAAATTAA
30029 TTAAATCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.20
18 3 0.10
19 13 0.43
20 8 0.27
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTTTTAAATTAAA
Found at i:30013 original size:19 final size:19
Alignment explanation
Indices: 29977--30013 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
29967 ACTAAGTTAA
29977 TTTTTTTTAAATTCAAAAT
1 TTTTTTTTAAATTCAAAAT
29996 TTTTTATTTAAATT-AAAA
1 TTTTT-TTTAAATTCAAAA
30014 AATTATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTTTTAAATTCAAAAT
Found at i:30017 original size:21 final size:21
Alignment explanation
Indices: 29977--30033 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
29967 ACTAAGTTAA
*
29977 TTTTT-TTTAAATT-CAAAAT
1 TTTTTATTTAAATTAAAAAAT
29996 TTTTTATTTAAATTAAAAAAT
1 TTTTTATTTAAATTAAAAAAT
*
30017 TATTTTAATT-AATTAAA
1 T-TTTTATTTAAATTAAA
30034 TCATATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.15
20 8 0.24
21 13 0.39
22 7 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTATTTAAATTAAAAAAT
Found at i:41557 original size:9 final size:9
Alignment explanation
Indices: 41533--41570 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
41523 TAAACTAGTG
41533 AAGAAAAACA
1 AAGAAAAA-A
41543 AA-AAAAAA
1 AAGAAAAAA
41551 AAGAAAAAA
1 AAGAAAAAA
41560 AAGAAAAAA
1 AAGAAAAAA
41569 AA
1 AA
41571 AATTAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 3 0.11
9 22 0.81
10 2 0.07
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:48903 original size:19 final size:19
Alignment explanation
Indices: 48879--48915 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48869 CGTATTATAA
*
48879 TTTCTAATATTTTGTACAG
1 TTTCTAATATTATGTACAG
48898 TTTCTAATATTATGTACA
1 TTTCTAATATTATGTACA
48916 ATAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTCTAATATTATGTACAG
Found at i:50359 original size:20 final size:20
Alignment explanation
Indices: 50307--50388 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 20
50297 AAAAAAAAAA
50307 ATTC-CAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
***
50326 ATTTGTAGAATGTATCGATAC
1 ATTCACA-AATGTATCGATAC
50347 ATTCACAAATGTATCGATAC
1 ATTCACAAATGTATCGATAC
50367 ATTCTACAAATGTATCGATAC
1 ATTC-ACAAATGTATCGATAC
50388 A
1 A
50389 GGGTCCCAAC
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 3 0.05
20 18 0.33
21 34 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (20 bp):
ATTCACAAATGTATCGATAC
Found at i:50368 original size:41 final size:40
Alignment explanation
Indices: 50307--50388 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
50297 AAAAAAAAAA
* *
50307 ATTCCAAATGTATCGATACATTTGTA-GAATGTATCGATAC
1 ATTCCAAATGTATCGATACA-TTCTACAAATGTATCGATAC
50347 ATTCACAAATGTATCGATACATTCTACAAATGTATCGATAC
1 ATTC-CAAATGTATCGATACATTCTACAAATGTATCGATAC
50388 A
1 A
50389 GGGTCCCAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
ATTCCAAATGTATCGATACATTCTACAAATGTATCGATAC
Found at i:50448 original size:19 final size:19
Alignment explanation
Indices: 50424--50491 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
50414 AATTCAACGA
50424 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
50443 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
50458 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
50475 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
50492 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:50462 original size:32 final size:32
Alignment explanation
Indices: 50426--50488 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
50416 TTCAACGATT
*
50426 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
50458 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
50489 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:50463 original size:13 final size:13
Alignment explanation
Indices: 50445--50469 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50435 ACATAAGTTT
50445 TGTATCGATACAA
1 TGTATCGATACAA
50458 TGTATCGATACA
1 TGTATCGATACA
50470 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50549 original size:13 final size:13
Alignment explanation
Indices: 50531--50556 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50521 CATTTTTCTG
50531 TGTATCGATACAT
1 TGTATCGATACAT
50544 TGTATCGATACAT
1 TGTATCGATACAT
50557 GGATCTTTGT
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:50553 original size:33 final size:33
Alignment explanation
Indices: 50511--50577 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
50501 GCCAAGGAAA
***
50511 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
50544 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
50577 T
1 T
50578 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:53099 original size:28 final size:27
Alignment explanation
Indices: 53032--53104 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
53022 CTTCACAATC
* *
53032 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
53059 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
53087 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
53105 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:53149 original size:51 final size:51
Alignment explanation
Indices: 53087--53257 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
53077 TTATTTCTGA
* * *
53087 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
53138 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
53191 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
53243 GAGGATACTCCAACC
1 GGGGATACTCCAACC
53258 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:53277 original size:28 final size:27
Alignment explanation
Indices: 53242--53321 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
53232 TTTTCACAAT
53242 CGAG-GATACTCCAACCTCGTTATTTC
1 CGAGAGATACTCCAACCTCGTTATTTC
* *
53268 ATCG-GAGATACTCCAACCCCGTTACTTC
1 --CGAGAGATACTCCAACCTCGTTATTTC
* *
53296 CGAGGGAACACTCCAACCTCGTTATT
1 CGAGAG-ATACTCCAACCTCGTTATT
53322 ATCTCCAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 38 0.88
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (27 bp):
CGAGAGATACTCCAACCTCGTTATTTC
Found at i:56401 original size:13 final size:13
Alignment explanation
Indices: 56383--56407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56373 CAAAGATCAG
56383 TGTATCGATACAA
1 TGTATCGATACAA
56396 TGTATCGATACA
1 TGTATCGATACA
56408 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:56470 original size:13 final size:13
Alignment explanation
Indices: 56452--56503 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
56442 AGCTTCGTAG
56452 CGATACATTGTAT
1 CGATACATTGTAT
56465 CGATACAACACTTGTGTAT
1 CGAT---ACA-TT--GTAT
56484 CGATACATTGTAT
1 CGATACATTGTAT
56497 CGATACA
1 CGATACA
56504 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:56484 original size:19 final size:18
Alignment explanation
Indices: 56459--56523 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
56449 TAGCGATACA
56459 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
56477 TGTGTATCGAT---ACA--
1 T-TGTATCGATACAACACT
56491 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
56509 TATGTATCGATACAA
1 T-TGTATCGATACAA
56524 TTTCTGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 2 0.05
19 22 0.55
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:56493 original size:32 final size:32
Alignment explanation
Indices: 56452--56522 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
56442 AGCTTCGTAG
*
56452 CGATACATTGTATCGATACAACACTTGTGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
56484 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
56516 CGATACA
1 CGATACA
56523 ATTTCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:56833 original size:19 final size:19
Alignment explanation
Indices: 56809--56876 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
56799 AATTCAACAA
56809 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
56828 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
56843 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
56860 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
56877 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:56848 original size:13 final size:13
Alignment explanation
Indices: 56830--56854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56820 ACATAAGTTT
56830 TGTATCGATACAA
1 TGTATCGATACAA
56843 TGTATCGATACA
1 TGTATCGATACA
56855 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:56852 original size:32 final size:32
Alignment explanation
Indices: 56811--56873 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
56801 TTCAACAATT
*
56811 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
56843 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
56874 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:56934 original size:13 final size:13
Alignment explanation
Indices: 56916--56941 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56906 CATTTTTCTG
56916 TGTATCGATACAT
1 TGTATCGATACAT
56929 TGTATCGATACAT
1 TGTATCGATACAT
56942 GGATCTTTGT
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:56938 original size:33 final size:33
Alignment explanation
Indices: 56896--56962 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
56886 GCCAAGGAAA
***
56896 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
56929 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
56962 T
1 T
56963 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:60762 original size:52 final size:52
Alignment explanation
Indices: 60622--60742 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
60612 TGAAAAGTTA
60622 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
60674 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
60726 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
60743 AAAATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:60859 original size:13 final size:13
Alignment explanation
Indices: 60841--60865 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60831 CAAAAAAATA
60841 TGTATCGATACAT
1 TGTATCGATACAT
60854 TGTATCGATACA
1 TGTATCGATACA
60866 ACATTTTATG
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:60861 original size:33 final size:33
Alignment explanation
Indices: 60819--60885 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
60809 AGTAGCTTAA
60819 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
60852 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
60885 A
1 A
60886 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:60964 original size:21 final size:21
Alignment explanation
Indices: 60923--60964 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
60913 GTTGGGACCT
*
60923 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
60944 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
60965 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:62823 original size:51 final size:52
Alignment explanation
Indices: 62760--63096 Score: 208
Period size: 51 Copynumber: 6.4 Consensus size: 52
62750 TCAATTCTCC
* * *
62760 ACAATCGTGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAATTT-TCT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTCT-T
* * *
62811 ATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACACCAATTTCTT
* * ** ** * * ***
62864 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTT
1 -ACAATCGGGGATACTCCAACTCCGATTTTATTTTC--AAAAACACCAATTTC-TT
** * ** * *
62918 A-TTTCCGAGGAGATACTCCAACTCCGGTTTTA-TCGCTAAAACACTAATTT-TT
1 ACAAT-CG-GG-GATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTCTT
* * *
62970 CCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAGACACTAATTT-TCT
1 --ACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAAACACCAATTTCT-T
* *
63023 ATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 ACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACACCAATTTCTT
63076 CACAATCGGGGATACTCCAAC
1 -ACAATCGGGGATACTCCAAC
63097 CCCGTTATTT
Statistics
Matches: 217, Mismatches: 47, Indels: 41
0.71 0.15 0.13
Matches are distributed among these distances:
51 61 0.28
52 41 0.19
53 41 0.19
54 55 0.25
55 15 0.07
56 1 0.00
57 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.31
Consensus pattern (52 bp):
ACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACACCAATTTCTT
Found at i:63084 original size:105 final size:104
Alignment explanation
Indices: 62754--63095 Score: 338
Period size: 105 Copynumber: 3.2 Consensus size: 104
62744 AGTTTATCAA
* * * * *
62754 TTCTCCACAATCGTGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTTCACAATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGG
*
62819 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
65 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
* * * ** ** * *** *
62859 TTCTTCACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA-CCCCGT-TATT
1 TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTC-AAGACACT--AATTTTC-TATA-A
* * *
62921 TCCGAGGAGATACTCCAACTCCGGTTTTA--TCGC-TAAAACACTAAT
61 T-CG-GG-GATACTCCAACTCCGATTTTATTTC-CAAAAAACACCAAT
62966 TT-TTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAGACACTAATTTTCTATAATCG
1 TTCTT-CACAATCGGGGATACTCCAATCC-GGTTTTATTTTCAAGACACTAATTTTCTATAATCG
63030 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
64 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
63071 TTCTTCACAATCGGGGATACTCCAA
1 TTCTTCACAATCGGGGATACTCCAA
63096 CCCCGTTATT
Statistics
Matches: 183, Mismatches: 36, Indels: 36
0.72 0.14 0.14
Matches are distributed among these distances:
103 26 0.14
104 9 0.05
105 61 0.33
106 12 0.07
107 41 0.22
108 9 0.05
109 25 0.14
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (104 bp):
TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGGG
GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
Found at i:63196 original size:80 final size:82
Alignment explanation
Indices: 63026--63204 Score: 281
Period size: 80 Copynumber: 2.2 Consensus size: 82
63016 ATTTTCTATA
*
63026 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
63091 TCCAACCCCGTTATTTC
66 TCCAACCCCGTTATTTC
*** * *
63108 CGAGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
*
63171 TCCAACCTCGTTATTTC
66 TCCAACCCCGTTATTTC
63188 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
63205 CCTGTTACTT
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 45 0.52
81 13 0.15
82 29 0.33
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (82 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
TCCAACCCCGTTATTTC
Found at i:63197 original size:28 final size:28
Alignment explanation
Indices: 63165--63231 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
63155 TCACAGTCGA
* **
63165 GGATACTCCAA-CCTCGTTATTTCATCGG
1 GGATACTCCAACCCT-GTTACTTCAGAGG
*
63193 GGATACTCCAACCCTGTTACTTCCGAGG
1 GGATACTCCAACCCTGTTACTTCAGAGG
63221 GGATACTCCAA
1 GGATACTCCAA
63232 TCCCGATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 31 0.91
29 3 0.09
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (28 bp):
GGATACTCCAACCCTGTTACTTCAGAGG
Found at i:69495 original size:36 final size:36
Alignment explanation
Indices: 69454--69556 Score: 84
Period size: 36 Copynumber: 3.2 Consensus size: 36
69444 CCTTTTTCTT
69454 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
* * * *
69490 TCAAAG---A-GCAA---GAT-GCTTTTTCT--T-T
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
*
69515 TCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCC
1 TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
69551 TCAAAG
1 TCAAAG
69557 AGCAGGACAC
Statistics
Matches: 47, Mismatches: 9, Indels: 22
0.60 0.12 0.28
Matches are distributed among these distances:
25 6 0.13
26 1 0.02
28 9 0.19
29 5 0.11
32 5 0.11
33 8 0.17
35 1 0.02
36 12 0.26
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (36 bp):
TCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCC
Found at i:69599 original size:55 final size:55
Alignment explanation
Indices: 69451--71018 Score: 1705
Period size: 55 Copynumber: 27.6 Consensus size: 55
69441 ACGCCTTTTT
* * *
69451 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGTCCTCAAAGAGCAAGATGCTTTTTC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----AC
*
69512 TTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
69567 CTCTCAAAGCCCACATAAGTTGGTGGTATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
69622 CTCTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTAAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * *
69677 CTTTTAAAGCCCACACAAGTTGGTGGTATTTTTCAGTCCTCAAAGAGCAGGACAT
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * *
69732 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-C-GTCCCCAAAGAGCAGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* **
69786 CTTCTCCTTTTAAAGCCCACACAAGTTAGTGGCATCCTCCAGTCCTCAAAGAGCAGGACAC
1 CTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
69847 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * * *
69902 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-C-GTCCCCAAAGAGTAGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
**
69956 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCCTCCAGTCCTCAAAGAGCAGGACAC
1 CTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
*
70017 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
70072 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTTT---GTCCCCAAAGAGCAGGACGC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
70126 CTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAAGAGTAGGATGCCTTC
1 CTT-T-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA------C
70191 AC
54 AC
*
70193 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * *
70248 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAAGATAC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
70303 TTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
1 -----C-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* *
70364 CTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* *
70419 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAATCCTCAAAGAGCAGGACAC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* * ** * *
70474 CTTTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGTCCTCAAAGAACAGGATGCTTTTTC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----AC
* * *
70535 TTTTCAAAGCCCACATAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
* * * *
70590 CTTTCAAAGCCCACACAAGATGGTGGTA-TTTACAGTCCTCAAAGAGCAGGGCAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * * *
70644 CTTTTAAAGCCCATACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----AC
* * * * *
70705 TTTTCAAAGCCTACACAGGTTGGTGGCACCTTT-CAGTCCCCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
*
70760 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
* * * *
70815 CTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTC
1 CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGA--C----AC
* * * *
70876 TTTTCAAAGCCCACACAAGTTGGTGACACCTTT-CAGTCCCCAAAGAGCAGGACAC
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
*
70931 CTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACAC
1 CT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACAC
*
70986 CTTTCAAAGCCCACACGAGTTGGTGGCACTTTT
1 CTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
71019 TACTCCTCAA
Statistics
Matches: 1301, Mismatches: 131, Indels: 156
0.82 0.08 0.10
Matches are distributed among these distances:
53 3 0.00
54 111 0.09
55 735 0.56
56 21 0.02
57 7 0.01
58 2 0.00
59 8 0.01
60 78 0.06
61 320 0.25
62 9 0.01
65 1 0.00
66 1 0.00
67 5 0.00
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (55 bp):
CTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACAC
Found at i:69867 original size:170 final size:172
Alignment explanation
Indices: 69423--71018 Score: 1854
Period size: 170 Copynumber: 9.3 Consensus size: 172
69413 TAGCCCTTCC
* * * * * *
69423 CAGTCCTCAAAAAGCAAGACGCCTTTTTCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCTAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* * * *
69488 CCTCAAAGAGCAAGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTC
66 CCTCAAAGAGCAGGAT-C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC
* * *
69553 AAAGAGCAGGACACCTCTCAAAGCCCACATAAGTTGGTGGTA-TTTT
126 AAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
*
69599 CCAGTCCTCAAAGAGCAGGACACC-TCT-C----AAAGCCCACACAAGTTGGTGGCATTTTCCAG
1 -CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAG
* * *
69658 TCCTAAAAGAGCAGGA-CACCTTTTAAAGCCCACACAAGTTGGTGGTATTTTTCAGTCCTCAAAG
65 TCCTCAAAGAGCAGGATCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAG
*
69722 AGCAGGACATCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
130 AGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * **
69765 C-GTCCCCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTAGTGGCATCCTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
*
69829 CCTCAAAGAGCAGGA-CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
66 CCTCAAAGAGCAGGATCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGA
69893 GCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
131 GCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * **
69935 C-GTCCCCAAAGAGTAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATCCTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
*
69999 CCTCAAAGAGCAGGA-CACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGA
66 CCTCAAAGAGCAGGATCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGA
*
70063 GTAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
131 GCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
70105 -TGTCCCCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* * *
70169 CCTCAAAGAGTAGGATGCCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAATCCTC
66 CCTCAAAGAGCAGGA-----TCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC
*
70234 AAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT
126 AAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* ** * *
70281 CAGTCCTCAAAGAGCAAGA-TACTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAG
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCATTTTCCAG
* **
70345 TCCTCAAAGAGCAGGA-CACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAG
65 TCCTCAAAGAGCAGGATCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAG
*
70409 AGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT
130 AGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * **
70452 CAATCCTCAAAGAGCAGGA------CACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTTAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
* * * * **
70511 CCTCAAAGAACAGGATGCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTCAGTCCTC
66 CCTCAAAGAGCAGGAT-C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTC
* * *
70576 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGATGGTGGTA--TTT
126 AAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
70621 ACAGTCCTCAAAGAGCAGG--G----CACCTTTTAAAGCCCATACAGGTTGGTGGCATTTTTCAG
1 -CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAG
* * * * ** *
70680 TCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCTACACAGGTTGGTGGCACCTTTCAGTCCC
65 TCCTCAAAGAGCAGGAT-C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
* *
70745 CAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTT
125 CAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* * * *
70792 CCAGTCCTCAAAAAGCAGGA------CACCTTTTAAAGCCCACACAGGTTGGTGGCATTTTTCAG
1 -CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAG
* * * ** *
70851 TCCTCAAAGAGCAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGACACCTTTCAGTCCC
65 TCCTCAAAGAGCAGGAT-C----ACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCT
*
70916 CAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT
125 CAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
* *
70964 CAGTCCTCAAAGAGCAGGACACCTT-T-C----AAAGCCCACACGAGTTGGTGGCACTTTT
1 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTT
71019 TACTCCTCAA
Statistics
Matches: 1292, Mismatches: 93, Indels: 73
0.89 0.06 0.05
Matches are distributed among these distances:
164 19 0.01
165 124 0.10
166 9 0.01
167 1 0.00
169 4 0.00
170 524 0.41
171 424 0.33
172 7 0.01
175 2 0.00
176 99 0.08
177 79 0.06
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.24
Consensus pattern (172 bp):
CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
CCTCAAAGAGCAGGATCACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAAAGA
GCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT
Found at i:70420 original size:26 final size:26
Alignment explanation
Indices: 70390--70477 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
70380 AAGTTGGTGG
70390 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * * **
70416 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCTCA-AAG-AGCAGGA
*
70445 CACCTTTCAATCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
70471 CACCTTT
1 CACCTTT
70478 TAAAGCCCAC
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 15 0.34
27 7 0.16
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:70987 original size:26 final size:26
Alignment explanation
Indices: 70900--70991 Score: 78
Period size: 26 Copynumber: 3.4 Consensus size: 26
70890 ACAAGTTGGT
*
70900 GACACCTTTCAGTCCCCAAAGAGCAG
1 GACACCTTTCAGTCCACAAAGAGCAG
* * * **
70926 GACACCTCTTAAAGCCCACACAAGTTGGTG
1 GACACCT-TT-CAGTCCACA-AAG-AGCAG
*
70956 G-CACCTTTCAGTCCTCAAAGAGCAG
1 GACACCTTTCAGTCCACAAAGAGCAG
70981 GACACCTTTCA
1 GACACCTTTCA
70992 AAGCCCACAC
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 19 0.39
27 8 0.16
28 8 0.16
29 8 0.16
30 3 0.06
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.20
Consensus pattern (26 bp):
GACACCTTTCAGTCCACAAAGAGCAG
Found at i:72028 original size:19 final size:19
Alignment explanation
Indices: 72004--72040 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
71994 CGTATTATAA
*
72004 TTTCTAATATTTTGTACAG
1 TTTCTAATATTATGTACAG
72023 TTTCTAATATTATGTACA
1 TTTCTAATATTATGTACA
72041 ATAATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTCTAATATTATGTACAG
Found at i:75394 original size:13 final size:13
Alignment explanation
Indices: 75376--75400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75366 CAAAGATCAG
75376 TGTATCGATACAA
1 TGTATCGATACAA
75389 TGTATCGATACA
1 TGTATCGATACA
75401 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:75463 original size:13 final size:13
Alignment explanation
Indices: 75445--75496 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
75435 AGCTTCGTAG
75445 CGATACATTGTAT
1 CGATACATTGTAT
75458 CGATACAACACTTGTGTAT
1 CGAT---ACA-TT--GTAT
75477 CGATACATTGTAT
1 CGATACATTGTAT
75490 CGATACA
1 CGATACA
75497 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 15 0.45
15 2 0.06
16 6 0.18
17 2 0.06
19 8 0.24
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:75477 original size:19 final size:18
Alignment explanation
Indices: 75452--75516 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
75442 TAGCGATACA
75452 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
75470 TGTGTATCGAT---ACA--
1 T-TGTATCGATACAACACT
75484 TTGTATCGATACAACACT
1 TTGTATCGATACAACACT
75502 TATGTATCGATACAA
1 T-TGTATCGATACAA
75517 TTTCTGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 9 0.22
14 1 0.03
16 6 0.15
18 2 0.05
19 22 0.55
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAACACT
Found at i:75486 original size:32 final size:32
Alignment explanation
Indices: 75445--75515 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
75435 AGCTTCGTAG
*
75445 CGATACATTGTATCGATACAACACTTGTGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
75477 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
75509 CGATACA
1 CGATACA
75516 ATTTCTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:75847 original size:19 final size:19
Alignment explanation
Indices: 75823--75890 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
75813 AATTCAACAA
75823 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
75842 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
75857 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
75874 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
75891 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:75862 original size:13 final size:13
Alignment explanation
Indices: 75844--75868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75834 ACATAAGTTT
75844 TGTATCGATACAA
1 TGTATCGATACAA
75857 TGTATCGATACA
1 TGTATCGATACA
75869 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:75866 original size:32 final size:32
Alignment explanation
Indices: 75825--75887 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
75815 TTCAACAATT
*
75825 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
75857 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
75888 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:75948 original size:13 final size:13
Alignment explanation
Indices: 75930--75956 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
75920 CATTTTTCTG
75930 TGTATCGATACAT
1 TGTATCGATACAT
75943 TGTATCGATACAT
1 TGTATCGATACAT
75956 T
1 T
75957 TGGAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:78363 original size:51 final size:52
Alignment explanation
Indices: 78291--78636 Score: 217
Period size: 51 Copynumber: 6.6 Consensus size: 52
78281 TTGAGTTTAT
* * * *
78291 CAATTCTCCACAATCGTGGATATTCCAACTCCGATTTTATTTTC-AAAACAC
1 CAATTTTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACAC
* * * *
78342 TAATTTTCTATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACAC
* * ** ** * *
78395 CAA-TTTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTC
1 CAATTTTC-T-ACAATCGGGGATACTCCAACTCCGATTTTATTTTC--AAAAACAC
* * * ** *
78448 CAACCCCGTTATT-TCCGA--GGGGATACTCCAACTCCGGTTTTA-TCGCTAAAACAC
1 CAA-----TT-TTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACAC
* * * *
78502 TAATTTTTCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAGACAC
1 CAA-TTTTCTACAATCGGGGATACTCCAACTCC-GATTTTATTTTCAAAAACAC
* * *
78554 TAATTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACAC
1 CAATTTTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTC-AAAAACAC
*
78607 CAATTTCTTTACAATCGGGGATACTCCAAC
1 CAATTT-TCTACAATCGGGGATACTCCAAC
78637 CCCGTTATTT
Statistics
Matches: 224, Mismatches: 48, Indels: 43
0.71 0.15 0.14
Matches are distributed among these distances:
49 2 0.01
50 4 0.02
51 72 0.32
52 41 0.18
53 30 0.13
54 48 0.21
55 17 0.08
56 1 0.00
57 5 0.02
58 1 0.00
59 1 0.00
60 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
CAATTTTCTACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAAACAC
Found at i:78478 original size:28 final size:27
Alignment explanation
Indices: 78411--78479 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 27
78401 CTTCACAATC
**
78411 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* *
78438 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
78466 GGGGATACTCCAAC
1 GGGGATACTCCAAC
78480 TCCGGTTTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.22
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:78628 original size:105 final size:104
Alignment explanation
Indices: 78294--78635 Score: 329
Period size: 105 Copynumber: 3.2 Consensus size: 104
78284 AGTTTATCAA
* * * * *
78294 TTCTCCACAATCGTGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGG
1 TTCTTCACAATCGGGGATACTCCAA-TCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGG
*
78359 GGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAAT
65 GGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
* * * ** ** * *** *
78399 TTCTTCACAATCGGGGATACTCCAACCCCG-TTAATCATCGGGGATACTCCAA-CCCCGT-TATT
1 TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTC-AAGACACT--AATTTTC-TATA-A
* * *
78461 TCCGAGGGGATACTCCAACTCCGGTTTTA--TCGC-TAAAACACTAAT
61 T-C--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAAACACCAAT
78506 TT-TTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAAGACACTAATTTTCTATAATCG
1 TTCTT-CACAATCGGGGATACTCCAATCC-GGTTTTATTTTCAAGACACTAATTTTCTATAATCG
78570 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
64 GGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
*
78611 TTCTTTACAATCGGGGATACTCCAA
1 TTCTTCACAATCGGGGATACTCCAA
78636 CCCCGTTATT
Statistics
Matches: 182, Mismatches: 37, Indels: 36
0.71 0.15 0.14
Matches are distributed among these distances:
103 29 0.16
104 7 0.04
105 59 0.32
106 12 0.07
107 40 0.22
108 7 0.04
109 28 0.15
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.32
Consensus pattern (104 bp):
TTCTTCACAATCGGGGATACTCCAATCCGGTTTTATTTTCAAGACACTAATTTTCTATAATCGGG
GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
Found at i:78737 original size:28 final size:28
Alignment explanation
Indices: 78705--78776 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
78695 TCACAGTCGA
* * **
78705 GGATACTCCAACCTCGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
78733 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
78761 GGATACTCCAATCCCG
1 GGATACTCCAACCCCG
78777 ATTTTTTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:78742 original size:80 final size:82
Alignment explanation
Indices: 78566--78744 Score: 272
Period size: 80 Copynumber: 2.2 Consensus size: 82
78556 ATTTTCTATA
* *
78566 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTTACAATCGGGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
78631 TCCAACCCCGTTATTTC
66 TCCAACCCCGTTATTTC
*** * *
78648 CGAGGGGATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATAC
1 ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
*
78711 TCCAACCTCGTTATTTC
66 TCCAACCCCGTTATTTC
78728 ATCGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
78745 CCCGTTACTT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 44 0.51
81 13 0.15
82 29 0.34
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (82 bp):
ATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATAC
TCCAACCCCGTTATTTC
Found at i:80864 original size:14 final size:14
Alignment explanation
Indices: 80845--80872 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
80835 TGGAATTTGA
80845 TTGGTAATCAAATT
1 TTGGTAATCAAATT
80859 TTGGTAATCAAATT
1 TTGGTAATCAAATT
80873 CCTCATTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (14 bp):
TTGGTAATCAAATT
Found at i:81505 original size:2 final size:2
Alignment explanation
Indices: 81498--81528 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
81488 TTTAAAACTT
81498 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
81529 CAACCTCCCT
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:81570 original size:18 final size:18
Alignment explanation
Indices: 81544--81584 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
81534 TCCCTTATCA
*
81544 TTACTTTTGGTTTCACCT
1 TTACATTTGGTTTCACCT
81562 TTACATTTGGTTTCACCT
1 TTACATTTGGTTTCACCT
81580 TTACA
1 TTACA
81585 GGCACATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.22, G:0.10, T:0.51
Consensus pattern (18 bp):
TTACATTTGGTTTCACCT
Found at i:88773 original size:2 final size:2
Alignment explanation
Indices: 88766--88790 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
88756 TTCACGTACA
88766 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
88791 ATTATCATAT
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:92609 original size:14 final size:14
Alignment explanation
Indices: 92582--92626 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
92572 GTACACTTAC
**
92582 ACAAAATTGAAAAA
1 ACAAAATTTTAAAA
*
92596 ACATAATTTTAAAA
1 ACAAAATTTTAAAA
92610 ACCAAAATTTTAAAA
1 A-CAAAATTTTAAAA
92625 AC
1 AC
92627 CAAAGCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.62, C:0.11, G:0.02, T:0.24
Consensus pattern (14 bp):
ACAAAATTTTAAAA
Found at i:92618 original size:15 final size:15
Alignment explanation
Indices: 92600--92630 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
92590 GAAAAAACAT
92600 AATTTTAAAAACCAA
1 AATTTTAAAAACCAA
92615 AATTTTAAAAACCAA
1 AATTTTAAAAACCAA
92630 A
1 A
92631 GCTAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (15 bp):
AATTTTAAAAACCAA
Found at i:94263 original size:144 final size:142
Alignment explanation
Indices: 93996--94267 Score: 508
Period size: 144 Copynumber: 1.9 Consensus size: 142
93986 AAACTCTCAA
*
93996 GTAAGTGAGGTTAAGGGAAAATATGTAGGCAATGAATCAAACTTGCATAAATCTAATGTTTGTTT
1 GTAAGTGAGGTTAAGGGAAAAGATGTAGGCAATGAATCAAACTTGCATAAATCTAATGTTTGTTT
*
94061 TTTTATCCCTTACTTATTTATTTGTTTATTTATTTATTAACTTACAACTCTAAGTTTTTTATTAT
66 CTTTATCCCTTACTTATTTATTTGTTTATTTATTTATTAACTTACAACTCTAAGTTTTTTATTAT
94126 TAGAACTCCTAG
131 TAGAACTCCTAG
94138 GTAAGTGAGGTTAAGGGAAAAGATGTAGGCAATGAATCAAACTTGCATAAATCTGAATGTTTGCT
1 GTAAGTGAGGTTAAGGGAAAAGATGTAGGCAATGAATCAAACTTGCATAAATCT-AATGTTTG-T
94203 TTCTTTATCCCTTACTTATTTATTTGTTTATTTATTTATTAACTTACAACTCTAAGTTTTTTATT
64 TTCTTTATCCCTTACTTATTTATTTGTTTATTTATTTATTAACTTACAACTCTAAGTTTTTTATT
94268 GTTTAGATTA
Statistics
Matches: 126, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
142 53 0.42
143 8 0.06
144 65 0.52
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (142 bp):
GTAAGTGAGGTTAAGGGAAAAGATGTAGGCAATGAATCAAACTTGCATAAATCTAATGTTTGTTT
CTTTATCCCTTACTTATTTATTTGTTTATTTATTTATTAACTTACAACTCTAAGTTTTTTATTAT
TAGAACTCCTAG
Found at i:95263 original size:20 final size:19
Alignment explanation
Indices: 95238--95275 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
95228 ATTTCAACGA
95238 TTTGTATCGATACATATTTT
1 TTTGTATCGATACA-ATTTT
95258 TTTGTATCGATACAATTT
1 TTTGTATCGATACAATTT
95276 AAGCTACTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTGTATCGATACAATTTT
Found at i:95332 original size:13 final size:13
Alignment explanation
Indices: 95314--95338 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95304 ATTACTCAAA
95314 TGTATCGATACAT
1 TGTATCGATACAT
95327 TGTATCGATACA
1 TGTATCGATACA
95339 CTGATCTTTG
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:95440 original size:52 final size:52
Alignment explanation
Indices: 95347--95474 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
95337 CACTGATCTT
*
95347 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
95398 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
95450 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
95475 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 19 0.26
52 52 0.70
53 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:99622 original size:22 final size:20
Alignment explanation
Indices: 99569--99615 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
99559 GCAATAGATC
*
99569 GATAC-ACTTATAATTGCATT
1 GATACAACTTTTAA-TGCATT
99589 GATACAATCTTTTAATGCATT
1 GATACAA-CTTTTAATGCATT
99610 GATACA
1 GATACA
99616 TGACTTTCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 5 0.21
21 13 0.54
22 6 0.25
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
GATACAACTTTTAATGCATT
Found at i:100522 original size:13 final size:12
Alignment explanation
Indices: 100477--100524 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
100467 TTATTTTATT
100477 TTTATTTTTTAA
1 TTTATTTTTTAA
* *
100489 TTTAGCTTTTTAG
1 TTTA-TTTTTTAA
100502 TTTCATTTTTTAAA
1 TTT-ATTTTTT-AA
100516 TTTATTTTT
1 TTTATTTTT
100525 AAGTGGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.14
13 20 0.69
14 5 0.17
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (12 bp):
TTTATTTTTTAA
Found at i:100524 original size:26 final size:25
Alignment explanation
Indices: 100465--100524 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
100455 CACGTGTGGG
* *
100465 TATTATTTTATTTTTATTTTTTAATT
1 TATT-TTTTAGTTTCATTTTTTAATT
*
100491 TAGCTTTTTAGTTTCATTTTTTAAATT
1 TA-TTTTTTAGTTTCATTTTTT-AATT
100518 TATTTTT
1 TATTTTT
100525 AAGTGGTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 21 0.75
27 7 0.25
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.72
Consensus pattern (25 bp):
TATTTTTTAGTTTCATTTTTTAATT
Found at i:100927 original size:18 final size:18
Alignment explanation
Indices: 100904--100950 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
100894 TAAGCAAGAA
100904 ATTTATTATTTTA-ATTAT
1 ATTTATTATTTTAGATT-T
100922 ATTTATT-TTTTAGATTT
1 ATTTATTATTTTAGATTT
*
100939 AATT-TTATTTTA
1 ATTTATTATTTTA
100951 TTTTATTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 14 0.54
18 10 0.38
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTATTATTTTAGATTT
Found at i:101752 original size:10 final size:10
Alignment explanation
Indices: 101720--101772 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
101710 ATACAATATG
101720 AATATGATACA
1 AATATGATA-A
*
101731 AAAATGATTAA
1 AATATGA-TAA
101742 AATATGATAA
1 AATATGATAA
* *
101752 AATAAGATAT
1 AATATGATAA
*
101762 AACATGATAA
1 AATATGATAA
101772 A
1 A
101773 TAATACGAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 19 0.56
11 13 0.38
12 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.26
Consensus pattern (10 bp):
AATATGATAA
Found at i:101768 original size:20 final size:23
Alignment explanation
Indices: 101745--101791 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
101735 TGATTAAAAT
101745 ATGAT-AA-AATAAG-ATATAAC
1 ATGATAAATAATAAGAATATAAC
*
101765 ATGATAAATAATACGAATATAAC
1 ATGATAAATAATAAGAATATAAC
101788 ATGA
1 ATGA
101792 ATATCTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 2 0.09
22 5 0.22
23 11 0.48
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.26
Consensus pattern (23 bp):
ATGATAAATAATAAGAATATAAC
Found at i:102291 original size:18 final size:19
Alignment explanation
Indices: 102246--102298 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 19
102236 GGGAAATGGG
*
102246 GGAGAAAGGAAGGAGAGAAA
1 GGAGAAAGG-AGAAGAGAAA
102266 GGAAAGAAAGGAGAAG-GAAA
1 GG--AGAAAGGAGAAGAGAAA
102286 GGAGAAAGAGAGA
1 GGAGAAAG-GAGA
102299 GGAGGGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 4 0.14
20 8 0.28
21 4 0.14
22 7 0.24
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (19 bp):
GGAGAAAGGAGAAGAGAAA
Found at i:102292 original size:22 final size:20
Alignment explanation
Indices: 102246--102294 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
102236 GGGAAATGGG
*
102246 GGAGAAAGGAAGGAGAGAAA
1 GGAGAAAGAAAGGAGAGAAA
102266 -G-GAAAGAAAGGAGAAGGAAA
1 GGAGAAAGAAAGGAG-A-GAAA
102286 GGAGAAAGA
1 GGAGAAAGA
102295 GAGAGGAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 11 0.46
19 2 0.08
20 4 0.17
21 1 0.04
22 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (20 bp):
GGAGAAAGAAAGGAGAGAAA
Found at i:102366 original size:16 final size:16
Alignment explanation
Indices: 102345--102396 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
102335 GAGGGGAAGG
*
102345 AAAGAAAGAG-GGAAA
1 AAAGAAAGAGACGAAA
102360 AAGAGAAAGAGACGAAA
1 AA-AGAAAGAGACGAAA
102377 AAAGAAAGA-A--AAA
1 AAAGAAAGAGACGAAA
102390 AAAGAAA
1 AAAGAAA
102397 AATACGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
13 10 0.29
15 3 0.09
16 15 0.44
17 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAGACGAAA
Found at i:102443 original size:16 final size:17
Alignment explanation
Indices: 102408--102444 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
102398 ATACGAGAAA
*
102408 ATTTTATTTTTGTGTTT
1 ATTTTATTTTTGTGTGT
102425 ATTTTATTTTT-TGTGT
1 ATTTTATTTTTGTGTGT
102441 ATTT
1 ATTT
102445 AAATTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.76
Consensus pattern (17 bp):
ATTTTATTTTTGTGTGT
Found at i:102531 original size:18 final size:16
Alignment explanation
Indices: 102508--102552 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
102498 ATAACTTTTT
102508 TATTTTTATATATTTA
1 TATTTTTATATATTTA
*
102524 TATATTTTTTCATATTTA
1 TAT-TTTTAT-ATATTTA
102542 TATTTTTATAT
1 TATTTTTATAT
102553 TGCTTTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTATATATTTA
Found at i:102541 original size:26 final size:26
Alignment explanation
Indices: 102487--102552 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
102477 TACATAAAAT
* *
102487 TTTATATATTAATA-ACTTTTTTATT
1 TTTATATATTTATATACTTTTTTATA
102512 TTTATATATTTATATA-TTTTTTCATA
1 TTTATATATTTATATACTTTTTT-ATA
*
102538 TTTATATTTTTATAT
1 TTTATATATTTATAT
102553 TGCTTTTAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATATATTTATATACTTTTTTATA
Found at i:102553 original size:8 final size:8
Alignment explanation
Indices: 102503--102553 Score: 52
Period size: 8 Copynumber: 6.2 Consensus size: 8
102493 TATTAATAAC
102503 TTTTT-TA
1 TTTTTATA
102510 TTTTTATA
1 TTTTTATA
102518 TATTTATATA
1 T-TTT-TATA
102528 TTTTT-TCA
1 TTTTTAT-A
*
102536 TATTTATA
1 TTTTTATA
102544 TTTTTATA
1 TTTTTATA
102552 TT
1 TT
102554 GCTTTTAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 6 0.16
8 19 0.51
9 7 0.19
10 5 0.14
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTATA
Found at i:103710 original size:27 final size:29
Alignment explanation
Indices: 103679--103746 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 29
103669 TTTAAAACTT
103679 TAATTAATTTTTAATAAA-AATAATTATA
1 TAATTAATTTTTAATAAATAATAATTATA
* * *
103707 -AATTAAATTTTATTAAATAATATTTATA
1 TAATTAATTTTTAATAAATAATAATTATA
*
103735 TATTTAATTTTT
1 TAATTAATTTTT
103747 TTAATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
27 15 0.45
28 9 0.27
29 9 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATTAATTTTTAATAAATAATAATTATA
Found at i:103750 original size:28 final size:27
Alignment explanation
Indices: 103682--103750 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
103672 AAAACTTTAA
*
103682 TTAATTTTTAATAAAAATAATTATAAAT
1 TTAATTTTT-TTAAAAATAATTATAAAT
* * * *
103710 TAAATTTTATTAAATAATATTTATATAT
1 TTAATTTTTTTAAA-AATAATTATAAAT
103738 TTAATTTTTTTAA
1 TTAATTTTTTTAA
103751 TTTTTATTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
27 4 0.12
28 29 0.88
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTAATTTTTTTAAAAATAATTATAAAT
Found at i:103756 original size:24 final size:25
Alignment explanation
Indices: 103724--103772 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
103714 TTTTATTAAA
103724 TAATATTTA-TATATTTAATTTTTT
1 TAATATTTATTATATTTAATTTTTT
* * *
103748 TAATTTTTATTTTATTTTATTTTTT
1 TAATATTTATTATATTTAATTTTTT
103773 ATTATGTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (25 bp):
TAATATTTATTATATTTAATTTTTT
Found at i:107740 original size:104 final size:104
Alignment explanation
Indices: 107560--107750 Score: 382
Period size: 104 Copynumber: 1.8 Consensus size: 104
107550 AAATTTAAAC
107560 TTCTATTTGGTAATTACAACAGAAAACCAGATAAATTTTATTAGAGATAGTAATAACCTTTCTTG
1 TTCTATTTGGTAATTACAACAGAAAACCAGATAAATTTTATTAGAGATAGTAATAACCTTTCTTG
107625 TCTTAGTGTCAACATCTGAAGACCAGATAGTAATAACCT
66 TCTTAGTGTCAACATCTGAAGACCAGATAGTAATAACCT
107664 TTCTATTTGGTAATTACAACAGAAAACCAGATAAATTTTATTAGAGATAGTAATAACCTTTCTTG
1 TTCTATTTGGTAATTACAACAGAAAACCAGATAAATTTTATTAGAGATAGTAATAACCTTTCTTG
107729 TCTTAGTGTCAACATCTGAAGA
66 TCTTAGTGTCAACATCTGAAGA
107751 AAGACGAAGC
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.35
Consensus pattern (104 bp):
TTCTATTTGGTAATTACAACAGAAAACCAGATAAATTTTATTAGAGATAGTAATAACCTTTCTTG
TCTTAGTGTCAACATCTGAAGACCAGATAGTAATAACCT
Found at i:110756 original size:15 final size:15
Alignment explanation
Indices: 110736--110777 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
110726 ACATTGTTAA
110736 ACATGTGTTAGTGGT
1 ACATGTGTTAGTGGT
110751 ACATGTGTTAGTGGT
1 ACATGTGTTAGTGGT
*
110766 ACATATGTTAGT
1 ACATGTGTTAGT
110778 TTTATAAGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.24, C:0.07, G:0.29, T:0.40
Consensus pattern (15 bp):
ACATGTGTTAGTGGT
Found at i:118351 original size:32 final size:32
Alignment explanation
Indices: 118315--118417 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
118305 ATAAATTAAC
118315 TTAAATTTAAAATATTTTAAATTTGAAATAAT
1 TTAAATTTAAAATATTTTAAATTTGAAATAAT
118347 TTAAATTTAAAATATTTTAAATTTGAAATAAT
1 TTAAATTTAAAATATTTTAAATTTGAAATAAT
* ** *
118379 TTAAATTTAAAATAATTTAAATTCAAAATGAT
1 TTAAATTTAAAATATTTTAAATTTGAAATAAT
118411 TTAAATT
1 TTAAATT
118418 CAAATTAAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (32 bp):
TTAAATTTAAAATATTTTAAATTTGAAATAAT
Found at i:118421 original size:16 final size:16
Alignment explanation
Indices: 118293--118417 Score: 153
Period size: 16 Copynumber: 7.9 Consensus size: 16
118283 TTTAAAAAAT
**
118293 AAATAA-TTAAAAATA
1 AAATAATTTAAATTTA
* *
118308 AATTAACTTAAATTTA
1 AAATAATTTAAATTTA
* *
118324 AAATATTTTAAATTTG
1 AAATAATTTAAATTTA
118340 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
* *
118356 AAATATTTTAAATTTG
1 AAATAATTTAAATTTA
118372 AAATAATTTAAATTTA
1 AAATAATTTAAATTTA
*
118388 AAATAATTTAAATTCA
1 AAATAATTTAAATTTA
*
118404 AAATGATTTAAATT
1 AAATAATTTAAATT
118418 CAAATTAAAC
Statistics
Matches: 94, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
15 5 0.05
16 89 0.95
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (16 bp):
AAATAATTTAAATTTA
Found at i:118691 original size:16 final size:16
Alignment explanation
Indices: 118624--118710 Score: 61
Period size: 16 Copynumber: 5.4 Consensus size: 16
118614 TAAATTATTC
* *
118624 AAAACTAAAATAATTT
1 AAAATTAAAATAACTT
* *
118640 AAACTGAAAATAACTT
1 AAAATTAAAATAACTT
* * *
118656 AAAATTGAAGTGAA-TC
1 AAAATTAAAAT-AACTT
118672 AAAATTAAAATAACTT
1 AAAATTAAAATAACTT
* *
118688 AAAAATTTAAA-AATTT
1 -AAAATTAAAATAACTT
118704 AAAATTA
1 AAAATTA
118711 CTTAATCTAA
Statistics
Matches: 53, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
15 8 0.15
16 34 0.64
17 11 0.21
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAATTAAAATAACTT
Found at i:119110 original size:18 final size:19
Alignment explanation
Indices: 119070--119119 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
119060 GTACATTAAT
119070 TAAAATTTATATTAACATA
1 TAAAATTTATATTAACATA
* *
119089 TAAAATTTAT-TTTACATG
1 TAAAATTTATATTAACATA
119107 T-AAA-TTATATTAA
1 TAAAATTTATATTAA
119120 ATTAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 6 0.22
18 7 0.26
19 10 0.37
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (19 bp):
TAAAATTTATATTAACATA
Found at i:119138 original size:25 final size:25
Alignment explanation
Indices: 119110--119158 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
119100 TTACATGTAA
119110 ATTATATTAA-ATTAATATAAAATTT
1 ATTAT-TTAATATTAATATAAAATTT
* *
119135 ATTATTTAATGTTAATGTAAAATT
1 ATTATTTAATATTAATATAAAATT
119159 AAAATTACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
ATTATTTAATATTAATATAAAATTT
Found at i:119703 original size:1 final size:1
Alignment explanation
Indices: 119697--119721 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
119687 GTTGTCAAGG
119697 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
119722 GTCCTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:123521 original size:21 final size:21
Alignment explanation
Indices: 123497--123554 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
123487 AAAAGTATTT
123497 TTGGATGAAATG-ATGCATTGG
1 TTGGATGAAA-GAATGCATTGG
**
123518 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAGAATGCATTGG
*
123539 TTAGATGAAA-AATGCA
1 TTGGATGAAAGAATGCA
123555 ACTTTTATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 26 0.79
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (21 bp):
TTGGATGAAAGAATGCATTGG
Found at i:123560 original size:20 final size:21
Alignment explanation
Indices: 123521--123561 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
123511 GCATTGGTTG
**
123521 GATGAAAGAATGCATTTTTTA
1 GATGAAAGAATGCAACTTTTA
123542 GATGAAA-AATGCAACTTTTA
1 GATGAAAGAATGCAACTTTTA
123562 TAACCAAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (21 bp):
GATGAAAGAATGCAACTTTTA
Found at i:123560 original size:21 final size:21
Alignment explanation
Indices: 123521--123560 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
123511 GCATTGGTTG
*
123521 GATGAAAGAATGCATTTTTTA
1 GATGAAAGAATGCACTTTTTA
123542 GATGAAA-AATGCAACTTTT
1 GATGAAAGAATGC-ACTTTT
123561 ATAACCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (21 bp):
GATGAAAGAATGCACTTTTTA
Found at i:124054 original size:10 final size:10
Alignment explanation
Indices: 124013--124065 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
124003 CTGTACTTAC
124013 TTTATTTCAT
1 TTTATTTCAT
* *
124023 TTTGTTT-AC
1 TTTATTTCAT
*
124032 TTTATGCTCAT
1 TTTAT-TTCAT
124043 TTTATTTCAT
1 TTTATTTCAT
*
124053 TTCATTTCAT
1 TTTATTTCAT
124063 TTT
1 TTT
124066 TTTTACTTTA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 5 0.15
10 22 0.67
11 6 0.18
ACGTcount: A:0.17, C:0.13, G:0.04, T:0.66
Consensus pattern (10 bp):
TTTATTTCAT
Found at i:124454 original size:44 final size:44
Alignment explanation
Indices: 124379--124462 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
124369 AGCCAAAGGA
* * *
124379 AGTTAAGTGCTATATTATGAGAGTCACCTTTAGAATCCTACGAG
1 AGTTAAGTGCTACATAATAAGAGTCACCTTTAGAATCCTACGAG
*
124423 AGTTAAGTGCTACATAATAAGAG-CTATCTTTAGAATCCTA
1 AGTTAAGTGCTACATAATAAGAGTC-ACCTTTAGAATCCTA
124463 ATGCCTAGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 1 0.03
44 34 0.97
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (44 bp):
AGTTAAGTGCTACATAATAAGAGTCACCTTTAGAATCCTACGAG
Found at i:125944 original size:19 final size:19
Alignment explanation
Indices: 125920--125957 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
125910 ATTGACAATG
*
125920 ATTCTCAATTTTTCAATCA
1 ATTCTCAAATTTTCAATCA
125939 ATTCTCAAATTTTCAATCA
1 ATTCTCAAATTTTCAATCA
125958 TTTCATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTCTCAAATTTTCAATCA
Done.