Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold301
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: 562684
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 4 of 4
Found at i:512565 original size:22 final size:22
Alignment explanation
Indices: 512518--512574 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
512508 CTGGACATGT
512518 TAAAAAAA--CATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
512538 TAAAAAAAATGCATGAAACATAA
1 T-AAAAAAATGCATGAAACATAA
512561 TAAAAAAATGCATG
1 TAAAAAAATGCATG
512575 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.03
21 7 0.21
22 13 0.38
23 13 0.38
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
TAAAAAAATGCATGAAACATAA
Found at i:513514 original size:20 final size:19
Alignment explanation
Indices: 513485--513559 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
513475 AAAAAGACAT
513485 AATGTATCGATACATTGTA
1 AATGTATCGATACATTGTA
* *
513504 GAATATATCGATACATTCATA
1 -AATGTATCGATACATT-GTA
* *
513525 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTG-TA
513545 AATGTATCGATACAT
1 AATGTATCGATACAT
513560 CAGGGTATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGTA
Found at i:513541 original size:40 final size:39
Alignment explanation
Indices: 513482--513559 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
513472 GGTAAAAAGA
* *
513482 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
*
513521 CATACATGTATCGATACATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
513560 CAGGGTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:516499 original size:9 final size:9
Alignment explanation
Indices: 516471--516508 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
516461 AGTCAAAAGT
516471 AAACAAAAA
1 AAACAAAAA
*
516480 AAA-AAACA
1 AAACAAAAA
516488 AAACAAAAA
1 AAACAAAAA
516497 AAACAGAAAA
1 AAACA-AAAA
516507 AA
1 AA
516509 GGTGCAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (9 bp):
AAACAAAAA
Found at i:516767 original size:16 final size:16
Alignment explanation
Indices: 516746--516796 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 16
516736 TGTTCTTTTC
516746 CAAAAAAGAAACAAAA
1 CAAAAAAGAAACAAAA
*
516762 CAAAAAAG-GA-AAAA
1 CAAAAAAGAAACAAAA
*
516776 -AAAGAAGAAAC-AAA
1 CAAAAAAGAAACAAAA
516790 CAAAAAA
1 CAAAAAA
516797 ACAATCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 6 0.21
14 8 0.29
15 6 0.21
16 8 0.29
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (16 bp):
CAAAAAAGAAACAAAA
Found at i:516811 original size:28 final size:28
Alignment explanation
Indices: 516747--516812 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
516737 GTTCTTTTCC
**
516747 AAAAAAGAAACAAAACAAAAAAGGAAAA
1 AAAAAAGAAACAAAACAAAAAAACAAAA
*
516775 AAAAGAAGAAAC-AAACAAAAAAACAATCA
1 AAAA-AAGAAACAAAACAAAAAAACAA-AA
516804 AAAAAAGAA
1 AAAAAAGAA
516813 GAGAGGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 21 0.64
29 12 0.36
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.02
Consensus pattern (28 bp):
AAAAAAGAAACAAAACAAAAAAACAAAA
Found at i:517804 original size:34 final size:34
Alignment explanation
Indices: 517761--517888 Score: 109
Period size: 31 Copynumber: 3.8 Consensus size: 34
517751 CTTCAAATAC
*
517761 CTTTTTAAAGTCCACGACTCCATGGCACCTTCTT
1 CTTTTTAAAGCCCACGACTCCATGGCACCTTCTT
**
517795 CTTTTTAAAGCCCACGACTCTGTGGCA-C--CTT
1 CTTTTTAAAGCCCACGACTCCATGGCACCTTCTT
* * * ** * *
517826 CTTTTCAAAGGCCACAACTCTGTGGCATCTTTTT
1 CTTTTTAAAGCCCACGACTCCATGGCACCTTCTT
* * *
517860 CCTTTTTAAAGCCTACAACTCCGTGGCAC
1 -CTTTTTAAAGCCCACGACTCCATGGCAC
517889 TCTTTTTCCT
Statistics
Matches: 78, Mismatches: 12, Indels: 7
0.80 0.12 0.07
Matches are distributed among these distances:
31 27 0.35
32 1 0.01
33 1 0.01
34 26 0.33
35 23 0.29
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (34 bp):
CTTTTTAAAGCCCACGACTCCATGGCACCTTCTT
Found at i:517936 original size:27 final size:27
Alignment explanation
Indices: 517896--518011 Score: 90
Period size: 28 Copynumber: 4.0 Consensus size: 27
517886 CACTCTTTTT
*
517896 CCTTCTAAGTCCACAACTCTGTGGCACC
1 CCTT-TAAGCCCACAACTCTGTGGCACC
*
517924 CGTTTAAGCCCACAACTCTGTGGCACTC
1 CCTTTAAGCCCACAACTCTGTGGCAC-C
*
517952 TTTTTCCTTCTAAGTCCACAACT-TCGTGGCACC
1 -----CCTT-TAAGCCCACAACTCT-GTGGCACC
* *
517985 CTTTTAAAGCTCACAACTCTGTGGCAC
1 CCTTT-AAGCCCACAACTCTGTGGCAC
518012 TCTTTTTCCC
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
27 22 0.31
28 24 0.34
29 1 0.01
33 5 0.07
34 19 0.27
ACGTcount: A:0.22, C:0.34, G:0.15, T:0.29
Consensus pattern (27 bp):
CCTTTAAGCCCACAACTCTGTGGCACC
Found at i:517939 original size:61 final size:62
Alignment explanation
Indices: 517864--518048 Score: 266
Period size: 61 Copynumber: 3.0 Consensus size: 62
517854 CTTTTTCCTT
* *
517864 TTTAAAGCCTACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCG
1 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCG
*
517926 TTT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACT-TCGTGGCACCCT
1 TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCT-GTGGCACCCG
* * * *
517987 TTTAAAGCTCACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGTCCACAACCCCGTGGCACC
1 TTTAAAGCCCACAACTCTGTGGCACTCTTTTT-CCTTCT-AAGTCCACAACTCTGTGGCACC
518049 TTGTTCCTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
60 1 0.01
61 56 0.50
62 30 0.27
63 5 0.05
64 19 0.17
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCG
Found at i:518124 original size:100 final size:100
Alignment explanation
Indices: 517933--518277 Score: 479
Period size: 97 Copynumber: 3.5 Consensus size: 100
517923 CCGTTTAAGC
* * * * *
517933 CCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACC--CTTTT-AAAGC
1 CCACAACCCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGC
*
517995 TCACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGT
65 CCACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGT
518031 CCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCC
1 CCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCC
*
518096 CACAA-TTTCGTGGCACTCTTTTTCCCTTTTAAAGT
66 CACAACTCT-GTGGCACTCTTTTTCCCTTTTAAAGT
* * *
518131 CCACAACCCTGTGG---CTTGTTCCTTTTAAGTCCACGACTCCGTGACACCTTCTTTTCAAAGCC
1 CCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCC
*
518193 CACAACTCTGTGGCACTCTTTTTTCCCATTTAAAGT
66 CACAACTCTGTGGCACTC-TTTTTCCCTTTTAAAGT
** * *
518229 CCACAACTTCATGGCACCTTGTTCCTTTTAAGTCCACAACTTCGTGGCA
1 CCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCA
518278 TCTTTAACCC
Statistics
Matches: 219, Mismatches: 19, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
97 91 0.42
98 43 0.20
99 7 0.03
100 49 0.22
101 29 0.13
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (100 bp):
CCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTCTTTTCAAAGCC
CACAACTCTGTGGCACTCTTTTTCCCTTTTAAAGT
Found at i:518384 original size:32 final size:32
Alignment explanation
Indices: 518283--518385 Score: 163
Period size: 32 Copynumber: 3.2 Consensus size: 32
518273 TGGCATCTTT
*
518283 AACCCTTCTCAAAGCCCACACAAGTTGGTGGC
1 AACCCTTCTCAAAGCCCACACAAGTCGGTGGC
* *
518315 AATCCCCTCT-AAAGCCCACACAAGTCGATGGC
1 AA-CCCTTCTCAAAGCCCACACAAGTCGGTGGC
518347 AACCCTTCTCAAAGCCCACACAAGTCGGTGGC
1 AACCCTTCTCAAAGCCCACACAAGTCGGTGGC
518379 AACCCTT
1 AACCCTT
518386 TTAAGTCCAA
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
31 6 0.09
32 52 0.81
33 6 0.09
ACGTcount: A:0.29, C:0.37, G:0.17, T:0.17
Consensus pattern (32 bp):
AACCCTTCTCAAAGCCCACACAAGTCGGTGGC
Found at i:518500 original size:43 final size:43
Alignment explanation
Indices: 518437--519259 Score: 791
Period size: 43 Copynumber: 18.0 Consensus size: 43
518427 CTTCATTTTT
*
518437 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* * *
518480 AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C
* **
518526 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* **
518572 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATTTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C---TCC
* *
518621 AAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCACCTCC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* *
518664 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C
* **
518710 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* **
518756 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATTTTT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C--C---TCC
* *
518805 AAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCACCTCC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
*
518848 AAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACCTCC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* *
518891 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C
* **
518937 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
*
518983 AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C
* * *
519029 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC----TC--C
* * * **
519081 TTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* * *
519127 AAGTCCAATATAGCTGGCATTGAATCAGCATATTGGTACCTTCTTC
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC-TC--C
* **
519173 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTT
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
*
519219 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCT
1 AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCT
519260 TTTCCATCTT
Statistics
Matches: 663, Mismatches: 72, Indels: 90
0.80 0.09 0.11
Matches are distributed among these distances:
43 335 0.51
44 10 0.02
46 7 0.01
48 7 0.01
49 260 0.39
52 44 0.07
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTCC
Found at i:518545 original size:92 final size:92
Alignment explanation
Indices: 518388--519305 Score: 1221
Period size: 92 Copynumber: 9.9 Consensus size: 92
518378 CAACCCTTTT
* ** *
518388 AAGTCCAATATCGCTCACCTTGAATCAGCATATTGGCACCTTCATTTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
518453 GCCTTGAATCAGCACATTGGCACCTCC
66 GCCTTGAATCAGCACATTGGCACCTCC
* *
518480 AAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
**
518545 GCCTTGAATCAGCACATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTCC
* * *
518572 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATTTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
518637 GCCTTGAATTAGCACATTGGCACCTCC
66 GCCTTGAATCAGCACATTGGCACCTCC
*
518664 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
**
518729 GCCTTGAATCAGCACATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTCC
* * *
518756 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCATCATTTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
518821 GCCTTGAATCAACACATTGGCACCTCC
66 GCCTTGAATCAGCACATTGGCACCTCC
* * * *
518848 AAGTCCAATATTGCTGGCCTTGAATCAGCACATTGGCACC-TC--C---AAGTCCAATATCGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
*
518907 GCCTTGAATCAGCATATTGGCACCTTCATC
66 GCCTTGAATCAGCACATTGGCACC-TC--C
* * * *
518937 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCG
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
518996 CTGGCCTTGAATCAGCACATTGGCACCTTCATC
63 CTGGCCTTGAATCAGCACATTGGCACC-TC--C
* *
519029 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATG
1 ---AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
* * **
519094 TCGCTGGCCTTGAATCAACACATTGGCACCTTT
60 TAGCTGGCCTTGAATCAGCACATTGGCACCTCC
* * *
519127 AAGTCCAATATAGCTGGCATTGAATCAGCATATTGGTACCTTCTTCTTTAAGTCCAATGTAGCTG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
**
519192 GCCTTGAATCAGCACATTGGCACCTTT
66 GCCTTGAATCAGCACATTGGCACCTCC
*
519219 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAG
1 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTAG
*
519284 CCGGCCTTGAATCAGCACATTG
63 CTGGCCTTGAATCAGCACATTG
519306 ACATCCTTTT
Statistics
Matches: 747, Mismatches: 58, Indels: 39
0.89 0.07 0.05
Matches are distributed among these distances:
86 36 0.05
87 2 0.00
89 3 0.00
91 2 0.00
92 582 0.78
93 1 0.00
94 2 0.00
95 75 0.10
99 1 0.00
100 1 0.00
101 42 0.06
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTG
GCCTTGAATCAGCACATTGGCACCTCC
Found at i:518981 original size:21 final size:21
Alignment explanation
Indices: 518957--519024 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
518947 ATGTAGCTGG
518957 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
518978 CCTTTAAGTC--CA-ATATCGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
519000 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
519021 CCTT
1 CCTT
519025 CATCTTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 12 0.35
22 8 0.24
23 5 0.15
24 2 0.06
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:519351 original size:56 final size:52
Alignment explanation
Indices: 519215--519353 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
519205 ACATTGGCAC
* *
519215 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
519267 CTTTAAGTTCAATGTAGCCGGCCTTGAATCAGCACATTGACATCCTTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC--TTTTC-CAT
* * * *
519323 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
519354 ACATATTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
52 37 0.52
53 2 0.03
55 5 0.07
56 27 0.38
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:519427 original size:67 final size:68
Alignment explanation
Indices: 519319--519445 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
519309 TCCTTTTTTC
* * *
519319 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
519383 TCT
66 TCT
* * * *
519386 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
519446 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:520204 original size:13 final size:13
Alignment explanation
Indices: 520186--520274 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
520176 CATAAAGTGT
520186 TGTATCGATACAA
1 TGTATCGATACAA
520199 TGTATCGATACATAA
1 TGTATCGATAC--AA
520214 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
520231 TGTATCGATACATAA
1 TGTATCGATAC--AA
520246 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
520263 TGTATCGATACA
1 TGTATCGATACA
520275 TAAGTTTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:520221 original size:32 final size:32
Alignment explanation
Indices: 520166--520298 Score: 239
Period size: 32 Copynumber: 4.1 Consensus size: 32
520156 TTCAACGATT
520166 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
520199 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
520231 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
520263 TGTATCGATACATAAGTTTTGTATCGCTACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
520295 TGTA
1 TGTA
520299 AGCTACTGCC
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 85 0.87
33 13 0.13
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:529241 original size:13 final size:13
Alignment explanation
Indices: 529223--529274 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
529213 AGCTTCATAG
529223 CGATACATTGTAT
1 CGATACATTGTAT
529236 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
529255 CGATACATTGTAT
1 CGATACATTGTAT
529268 CGATACA
1 CGATACA
529275 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:529255 original size:19 final size:19
Alignment explanation
Indices: 529231--529312 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
529221 AGCGATACAT
*
529231 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
529250 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
529263 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
529282 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
529301 TGTATCGATACA
1 TGTATCGATACA
529313 TTGTATCAAT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 40 0.71
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:529264 original size:32 final size:32
Alignment explanation
Indices: 529223--529293 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
529213 AGCTTCATAG
529223 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
529255 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
529287 CGATACA
1 CGATACA
529294 ACACTTATGT
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:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:532213 original size:14 final size:14
Alignment explanation
Indices: 532194--532220 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
532184 CGGACGAGAT
532194 CTTCATCAATCAAA
1 CTTCATCAATCAAA
532208 CTTCATCAATCAA
1 CTTCATCAATCAA
532221 GCAAAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTCATCAATCAAA
Found at i:534750 original size:13 final size:13
Alignment explanation
Indices: 534729--534758 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
534719 CGATAAATGG
*
534729 TACATTGTATCGA
1 TACAATGTATCGA
534742 TACAATGTATCGA
1 TACAATGTATCGA
534755 TACA
1 TACA
534759 TGGACAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:534756 original size:33 final size:33
Alignment explanation
Indices: 534714--534778 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
534704 TTCCACTGTT
*
534714 TGTATCGATAAATGGTAC-ATTGTATCGATACAA
1 TGTATCGATAAATGG-ACAACTGTATCGATACAA
*
534747 TGTATCGATACATGGACAACTGTATCGATACA
1 TGTATCGATAAATGGACAACTGTATCGATACA
534779 TGAAACTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (33 bp):
TGTATCGATAAATGGACAACTGTATCGATACAA
Found at i:534772 original size:20 final size:19
Alignment explanation
Indices: 534743--534780 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
534733 TTGTATCGAT
534743 ACAATGTATCGATACATGG
1 ACAATGTATCGATACATGG
534762 ACAACTGTATCGATACATG
1 ACAA-TGTATCGATACATG
534781 AAACTGGCAG
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:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:534799 original size:96 final size:96
Alignment explanation
Indices: 534622--534875 Score: 413
Period size: 96 Copynumber: 2.7 Consensus size: 96
534612 TACATTATGC
* * * *
534622 ATCGATACAT-GTTCATTGTACCGATACATTGTATCGATACATGGACAACTGTATCGATACATGA
1 ATCGATAAATGGTACATTGTATCGATACAATGTATCGATACATGGACAACTGTATCGATACATGA
534686 AACTGGCAACAGCTACCCTTCCACTGTTTGT
66 AACTGGCAACAGCTACCCTTCCACTGTTTGT
534717 ATCGATAAATGGTACATTGTATCGATACAATGTATCGATACATGGACAACTGTATCGATACATGA
1 ATCGATAAATGGTACATTGTATCGATACAATGTATCGATACATGGACAACTGTATCGATACATGA
*
534782 AACTGGCAGCAGCTACCCTTCCACTGTTTGT
66 AACTGGCAACAGCTACCCTTCCACTGTTTGT
* * *
534813 ATCGATAAATGGTACATTATATCGATACAATGTATCGATACAT-GATAAATTGTATCGATACAT
1 ATCGATAAATGGTACATTGTATCGATACAATGTATCGATACATGGA-CAACTGTATCGATACAT
534876 TGCTTTAAAC
Statistics
Matches: 149, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
95 11 0.07
96 138 0.93
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (96 bp):
ATCGATAAATGGTACATTGTATCGATACAATGTATCGATACATGGACAACTGTATCGATACATGA
AACTGGCAACAGCTACCCTTCCACTGTTTGT
Found at i:534852 original size:33 final size:33
Alignment explanation
Indices: 534810--534874 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
534800 TTCCACTGTT
* *
534810 TGTATCGATAAATGGTACATTATATCGATACAA
1 TGTATCGATAAATGATAAATTATATCGATACAA
* *
534843 TGTATCGATACATGATAAATTGTATCGATACA
1 TGTATCGATAAATGATAAATTATATCGATACA
534875 TTGCTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATAAATGATAAATTATATCGATACAA
Found at i:542864 original size:37 final size:38
Alignment explanation
Indices: 542760--542865 Score: 139
Period size: 38 Copynumber: 2.8 Consensus size: 38
542750 AACAGAAAAA
* *
542760 GGGAGAAATATTGTTT-TGAAAATAAATTTTTATCAAAG
1 GGGAGAAAT-TTTTTTATGAAAATAATTTTTTATCAAAG
*
542798 GGGAGAAATTTTTTTATGAAAATAATTTTTTATCAAGG
1 GGGAGAAATTTTTTTATGAAAATAATTTTTTATCAAAG
542836 GGGAGAAA-TTTTTTATGGAAAAT--TTTTTTA
1 GGGAGAAATTTTTTTAT-GAAAATAATTTTTTA
542866 ATGAGAGCCT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
36 7 0.11
37 13 0.21
38 43 0.68
ACGTcount: A:0.38, C:0.02, G:0.19, T:0.42
Consensus pattern (38 bp):
GGGAGAAATTTTTTTATGAAAATAATTTTTTATCAAAG
Found at i:543464 original size:19 final size:19
Alignment explanation
Indices: 543421--543493 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
543411 CATACCTAGA
*
543421 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
543441 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
543460 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
543480 TGTATCGATACATG
1 TGTATCGATACATG
543494 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 17 0.35
20 30 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:545368 original size:23 final size:22
Alignment explanation
Indices: 545326--545372 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
545316 ATATTTTTAA
545326 GAGAAAAATTTTTATTAAGGGG
1 GAGAAAAATTTTTATTAAGGGG
* *
545348 GAGAAAATTTTTTATTAAAGGG
1 GAGAAAAATTTTTATTAAGGGG
545370 GAG
1 GAG
545373 TTATAATTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (22 bp):
GAGAAAAATTTTTATTAAGGGG
Found at i:547781 original size:13 final size:13
Alignment explanation
Indices: 547763--547788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
547753 ACATTTTGTG
547763 ATGTATCGATACA
1 ATGTATCGATACA
547776 ATGTATCGATACA
1 ATGTATCGATACA
547789 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:547783 original size:33 final size:32
Alignment explanation
Indices: 547741--547808 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
547731 CGTTACAAGC
*
547741 CAATGTATCGATACATTTTGTGATGTATCGATA
1 CAATGTATCGATACATATTGTG-TGTATCGATA
547774 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGTGTGTATCGATA
547806 CAA
1 CAA
547809 ATTTAGCTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 13 0.38
33 21 0.62
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
CAATGTATCGATACATATTGTGTGTATCGATA
Found at i:547867 original size:20 final size:20
Alignment explanation
Indices: 547842--547893 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
547832 CAATGACTTC
**
547842 TATCGATACATTTTTTCAAG
1 TATCGATACATTTAGTCAAG
*
547862 TATCGATACATTTAGTCATG
1 TATCGATACATTTAGTCAAG
547882 TATCGATACATT
1 TATCGATACATT
547894 GTATCGATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTAGTCAAG
Found at i:549078 original size:89 final size:89
Alignment explanation
Indices: 548941--549406 Score: 659
Period size: 89 Copynumber: 5.2 Consensus size: 89
548931 TTCCTTTCTG
* * * *
548941 TTTGACATATGGTTACCGCCTTGGTCAAACTCTTCTCATTTTAGGTCTGACGTATGGTTACCACC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTCTGACGTATGGTTACCACC
* * *
549006 ATGGTTAGATTCTTTCTATTTTAA
66 CTGGTCAGATTCTTTCTATTTTGA
**
549030 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTCTGACGTATAATTACCACC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTCTGACGTATGGTTACCACC
*
549095 CTGGTTAGATTCTTTCTATTTTGA
66 CTGGTCAGATTCTTTCTATTTTGA
* * * *
549119 TTTGATGTATGGTTACCACCCTGGTCAGACTCTTCTTATTTCAGGTTTGACGTATGGTTACCACC
1 TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTCTGACGTATGGTTACCACC
*
549184 CTGGTCAGATTCTTTCCATTTTGA
66 CTGGTCAGATTCTTTCTATTTTGA
*
549208 TTTAACGTATGGTTACCACCCTGGTCAAAACTCTTCTCAGTTT-AGGTCTGACGTATGGTTACCA
1 TTTGACGTATGGTTACCACCCTGGTC-AAACTCTTCTCA-TTTCAGGTCTGACGTATGGTTACCA
*
549272 CCCTCGTCAGATTCTTTCTATTTTGA
64 CCCTGGTCAGATTCTTTCTATTTTGA
* * * *
549298 TTTGACATATGGTTACCACCCTGG-CGAAACTTTTCTCATTTCAAGTC-GAACGTATGGTAACCA
1 TTTGACGTATGGTTACCACCCTGGTC-AAACTCTTCTCATTTCAGGTCTG-ACGTATGGTTACCA
* * *
549361 CCCTAGTCAAATTCTTTCCATTTTGA
64 CCCTGGTCAGATTCTTTCTATTTTGA
549387 TTTGACGTATGGTTACCACC
1 TTTGACGTATGGTTACCACC
549407 TTCCAATTTG
Statistics
Matches: 340, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
88 4 0.01
89 257 0.76
90 76 0.22
91 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (89 bp):
TTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTCTGACGTATGGTTACCACC
CTGGTCAGATTCTTTCTATTTTGA
Found at i:549313 original size:179 final size:178
Alignment explanation
Indices: 548941--549406 Score: 668
Period size: 179 Copynumber: 2.6 Consensus size: 178
548931 TTCCTTTCTG
* * * *
548941 TTTGACATATGGTTACCGCCTTGGTCAAACTCTTCTCATTTTAGGTCTGACGTATGGTTACCACC
1 TTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTTTGACGTATGGTTACCACC
* * * *
549006 ATGGTTAGATTCTTTCTATTTTAATTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTT
66 CTGGTCAGATTCTTTCCATTTTGATTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTT
* *
549071 CAGGTCTGACGTATAATTACCACCCTGGTTAGATTCTTTCTATTTTGA
131 CAGGTCTGACGTATAATTACCACCCTCGTCAGATTCTTTCTATTTTGA
** * *
549119 TTTGATGTATGGTTACCACCCTGGTCAGACTCTTCTTATTTCAGGTTTGACGTATGGTTACCACC
1 TTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTTTGACGTATGGTTACCACC
*
549184 CTGGTCAGATTCTTTCCATTTTGATTTAACGTATGGTTACCACCCTGGTCAAAACTCTTCTCAGT
66 CTGGTCAGATTCTTTCCATTTTGATTTGACGTATGGTTACCACCCTGGTC-AAACTCTTCTCA-T
**
549249 TT-AGGTCTGACGTATGGTTACCACCCTCGTCAGATTCTTTCTATTTTGA
129 TTCAGGTCTGACGTATAATTACCACCCTCGTCAGATTCTTTCTATTTTGA
* * * *
549298 TTTGACATATGGTTACCACCCTGG-CGAAACTTTTCTCATTTCAAG-TCGAACGTATGGTAACCA
1 TTTGACATATGGTTACCACCCTGGTC-AAACTCTTCTCATTTCAGGTTTG-ACGTATGGTTACCA
* *
549361 CCCTAGTCAAATTCTTTCCATTTTGATTTGACGTATGGTTACCACC
64 CCCTGGTCAGATTCTTTCCATTTTGATTTGACGTATGGTTACCACC
549407 TTCCAATTTG
Statistics
Matches: 256, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
178 105 0.41
179 148 0.58
180 3 0.01
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (178 bp):
TTTGACATATGGTTACCACCCTGGTCAAACTCTTCTCATTTCAGGTTTGACGTATGGTTACCACC
CTGGTCAGATTCTTTCCATTTTGATTTGACGTATGGTTACCACCCTGGTCAAACTCTTCTCATTT
CAGGTCTGACGTATAATTACCACCCTCGTCAGATTCTTTCTATTTTGA
Found at i:549634 original size:43 final size:43
Alignment explanation
Indices: 549574--549714 Score: 144
Period size: 43 Copynumber: 3.3 Consensus size: 43
549564 CTCATTGTTT
* * * *
549574 ACCTGTCGGCTCAGTCCTCGATAAACCTCTTATCCCCTCGGTG
1 ACCTGTCAGCTTAGTCCTCGGTAAACCTCTTATCCCCTTGGTG
* ** *
549617 ACTTGTCAGCTTAGTCCTCGGGT-AACC-CTTCAT-CCCTTATTT
1 ACCTGTCAGCTTAGTCCTC-GGTAAACCTCTT-ATCCCCTTGGTG
*
549659 ACCTGTCAGCTTAGTCCTTGGTAAACCTCTTATCCCCTTGGTG
1 ACCTGTCAGCTTAGTCCTCGGTAAACCTCTTATCCCCTTGGTG
* *
549702 ACCTATCGGCTTA
1 ACCTGTCAGCTTA
549715 ATTCTTGGTC
Statistics
Matches: 78, Mismatches: 15, Indels: 10
0.76 0.15 0.10
Matches are distributed among these distances:
41 3 0.04
42 31 0.40
43 42 0.54
44 2 0.03
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (43 bp):
ACCTGTCAGCTTAGTCCTCGGTAAACCTCTTATCCCCTTGGTG
Found at i:549694 original size:42 final size:42
Alignment explanation
Indices: 549571--549694 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
549561 TATCTCATTG
* * * *
549571 TTTACCTGTCGGCTCAGTCCTCGATAAACCTCTTATCCCCTCG
1 TTTACCTGTCAGCTTAGTCCTCGGTAAACCTCTTAT-CCCTCA
* * * *
549614 GTGACTTGTCAGCTTAGTCCTCGGGT-AACC-CTTCATCCCTTA
1 TTTACCTGTCAGCTTAGTCCTC-GGTAAACCTCTT-ATCCCTCA
*
549656 TTTACCTGTCAGCTTAGTCCTTGGTAAACCTCTTATCCC
1 TTTACCTGTCAGCTTAGTCCTCGGTAAACCTCTTATCCC
549695 CTTGGTGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.05
42 34 0.52
43 26 0.40
44 2 0.03
ACGTcount: A:0.17, C:0.33, G:0.15, T:0.35
Consensus pattern (42 bp):
TTTACCTGTCAGCTTAGTCCTCGGTAAACCTCTTATCCCTCA
Found at i:551483 original size:164 final size:164
Alignment explanation
Indices: 550753--551794 Score: 1232
Period size: 166 Copynumber: 6.3 Consensus size: 164
550743 ATTTTTCATG
* * ** *
550753 TTTTC-AAATTACGAAGTTTTCTTCTCTATAAATTTTTTCAGAGG-GATTTTTCATT-GTTTTTA
1 TTTTCGAAA-TACGGAGTTTTCTACTCCGTAAATTTTTTC-GAGGAGATTTTTC-TTGGTTTTTG
* * *
550815 ATTTTTAAAATTAATAAAATATTATTATTTATTTCATATTAATTCACTTTTCAAAAATTCATTCA
63 ATTTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCA
* *
550880 TTTCTATAAATTTTGAATTTTTTT-CTTGAAATTTTTCTT
128 TTTCCATAAA-TTT-AATTTTTTTCCTTGAAA-TTCTCTT
* * * *
550919 TTTCCGAAATACGGAGTTTTCTACTTCGTAAATTTTTTCAAGGGGATTTTTCTTGGTTTTTGATT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTGATT
550984 TTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTTCATTCATT
66 TTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAA-TTCATTCATT
* *
551049 TCTATAAATTTTAA-TTTTTTCCTTGAAATTTTCTTT
130 TCCATAAA-TTTAATTTTTTTCCTTGAAATTCTC-TT
* * *
551085 TTTTCGAAATACGGAGTTTTCTACTCCATAAATTTTTTCG-GGAGACTTTTTCTCGGTTTTTTAT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGA-TTTTTCTTGGTTTTTGAT
* * * * * *
551149 CTTTAAGATTTATCAAATATTATTATCTATTTCGTATTAATTCAGTTTTCAAAAATTCATTGATT
65 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATT
* *
551214 TTCATAAATTTTAA-ATTTTTCCTTGAAATTCTCTTTT
130 TCCATAAA-TTTAATTTTTTTCCTTGAAATTCTC--TT
* * * *
551251 TTTTCGAAATACAGAGTTTTCTACTCCGTAATTTTTTTCAAGG-GTATTTTTCTTGGTTTTTCAT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAG-ATTTTTCTTGGTTTTTGAT
* *
551315 TTTTAAAATTCATAAAATATTATTATTTATTTCATATTAATTCTGTTTTCAAAAATTCATTCATT
65 TTTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATT
*
551380 TCCATAAA-TTAATTTTTTTCCTTGAAACTCCTCTT
130 TCCATAAATTTAATTTTTTTCCTTGAAA-TTCTCTT
** * * *
551415 TTTTCGAAATACTTAGTTTTCTACTCCGTAAATTTTTTCGAGCAGATTTTTCATGGTTTTTTATT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTGATT
* * * * *
551480 TTTAGAATTCATCAAATATTGTTATTTATTTCAGATTAATTCAATTTTCAAAAATTCTTTCATTT
66 TTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTT
*
551545 CCATAAATTTTGAA--TTTTTCCTTTAAATTCTCCTT
131 CCATAAA-TTT-AATTTTTTTCCTTGAAATTCT-CTT
* * * * * *
551580 TTTTCAAAATACGAATTTTTCTACTCCGTAATTTTTTTTGGGGAGATTTTTCTTGG-TTTTGATT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTGATT
*
551644 TTTAAAATTCATCAAATATTATTATTTATTT-TTATTAATTCAGTTTTCAAAAATTCATTCATTT
66 TTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTT
* * *
551708 ACATGAATTTTGAATTTTTTTCCTT-AAAATCTCCTT
131 CCAT-AAATTT-AATTTTTTTCCTTGAAATTCT-CTT
* * * ** *
551744 TCTCCGAAAAATTGAGTTTTCTACTCCATAAATTTTTTCGGAGGA-ATTTTT
1 TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTC-GAGGAGATTTTT
551795 TTCGATTTAA
Statistics
Matches: 763, Mismatches: 92, Indels: 44
0.85 0.10 0.05
Matches are distributed among these distances:
163 38 0.05
164 212 0.28
165 147 0.19
166 336 0.44
167 30 0.04
ACGTcount: A:0.28, C:0.12, G:0.08, T:0.52
Consensus pattern (164 bp):
TTTTCGAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTGATT
TTTAAAATTCATCAAATATTATTATTTATTTCATATTAATTCAGTTTTCAAAAATTCATTCATTT
CCATAAATTTAATTTTTTTCCTTGAAATTCTCTT
Found at i:552040 original size:11 final size:10
Alignment explanation
Indices: 552017--552062 Score: 53
Period size: 9 Copynumber: 4.9 Consensus size: 10
552007 GGTTTCAGCC
552017 TTTTATTT-T
1 TTTTATTTAT
*
552026 TTTAATTTAT
1 TTTTATTTAT
552036 TTTTATTTAT
1 TTTTATTTAT
*
552046 TTAT-TTTA-
1 TTTTATTTAT
552054 TTTTATTTA
1 TTTTATTTA
552063 GTCATTCACC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
8 3 0.10
9 15 0.48
10 13 0.42
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:552041 original size:19 final size:18
Alignment explanation
Indices: 552017--552062 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
552007 GGTTTCAGCC
*
552017 TTTTATTTTTTTAATTTA
1 TTTTATTTATTTAATTTA
*
552035 TTTTTATTTATTTATTTTA
1 -TTTTATTTATTTAATTTA
552054 TTTTATTTA
1 TTTTATTTA
552063 GTCATTCACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTATTTAATTTA
Found at i:552047 original size:14 final size:14
Alignment explanation
Indices: 552018--552062 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
552008 GTTTCAGCCT
*
552018 TTTATTTTT-TTAA
1 TTTATTTTTATTTA
552031 TTTATTTTTATTTA
1 TTTATTTTTATTTA
552045 TTTA-TTTTATTTTA
1 TTTATTTTTA-TTTA
552059 TTTA
1 TTTA
552063 GTCATTCACC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 14 0.48
14 15 0.52
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:552357 original size:22 final size:23
Alignment explanation
Indices: 552323--552373 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
552313 TGATTCAGCT
*
552323 GAAAAA-AGAGAGAGAATAAAG-A
1 GAAAAATAGAGAGAAAAT-AAGTA
552345 GAAAAATAG-GAGAAAATAAGTA
1 GAAAAATAGAGAGAAAATAAGTA
552367 GAAAAAT
1 GAAAAAT
552374 TAGAAAAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 21 0.81
23 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.10
Consensus pattern (23 bp):
GAAAAATAGAGAGAAAATAAGTA
Found at i:553287 original size:19 final size:20
Alignment explanation
Indices: 553242--553292 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
553232 ATTTCAACGA
*
553242 TTTGTATTGATACATAAAGT
1 TTTGTATCGATACATAAAGT
* *
553262 GTTGTATCGATACAT-ATGT
1 TTTGTATCGATACATAAAGT
553281 TTTGTATCGATA
1 TTTGTATCGATA
553293 TAATGTAAGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (20 bp):
TTTGTATCGATACATAAAGT
Found at i:553414 original size:52 final size:52
Alignment explanation
Indices: 553370--553498 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
553360 CACTGATCTT
553370 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
553422 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
553474 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
553499 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:559042 original size:18 final size:18
Alignment explanation
Indices: 559021--559058 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
559011 TTACCTTCAG
*
559021 ATTAATGTCACACAACAA
1 ATTAATGTCAAACAACAA
559039 ATTAATGTCAAACAACAA
1 ATTAATGTCAAACAACAA
559057 AT
1 AT
559059 GTTTCACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.18, G:0.05, T:0.24
Consensus pattern (18 bp):
ATTAATGTCAAACAACAA
Found at i:561225 original size:20 final size:20
Alignment explanation
Indices: 561189--561226 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
561179 TATCATATCA
*
561189 TATTTATTGTTTTTTTTAAT
1 TATTTATTGTTTATTTTAAT
561209 TATTTATT-TTATATTTTA
1 TATTTATTGTT-TATTTTA
561227 TAATTTCATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TATTTATTGTTTATTTTAAT
Found at i:561395 original size:16 final size:16
Alignment explanation
Indices: 561371--561427 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
561361 AATGGTGGTT
*
561371 TAAATTTTATTTTATA
1 TAAAATTTATTTTATA
* *
561387 TAAAATTTAATATAT-
1 TAAAATTTATTTTATA
*
561402 TAAAAATTTATATTATA
1 T-AAAATTTATTTTATA
*
561419 TAAATTTTA
1 TAAAATTTA
561428 AAAATGTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAATTTATTTTATA
Done.