Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold449
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: 225422
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 7766 characters in sequence are not A, C, G, or T
Found at i:2156 original size:24 final size:24
Alignment explanation
Indices: 2129--2209 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 24
2119 TAGCTCAAAA
*
2129 GAGCATCCCGTTATTAGCTCTTAT
1 GAGCATCCCGTTATTAGCTCTTAC
* * * *
2153 GAGCTTCCCG-TATGTAGTTTTTGC
1 GAGCATCCCGTTAT-TAGCTCTTAC
*
2177 GAGCTTCCCGTTA-TAGCTCTT-C
1 GAGCATCCCGTTATTAGCTCTTAC
2199 GGAGCATCCCG
1 -GAGCATCCCG
2210 ATAAGTTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
22 1 0.02
23 18 0.39
24 25 0.54
25 2 0.04
ACGTcount: A:0.16, C:0.27, G:0.22, T:0.35
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTTAC
Found at i:5207 original size:44 final size:44
Alignment explanation
Indices: 5110--5230 Score: 138
Period size: 44 Copynumber: 2.8 Consensus size: 44
5100 GAAGATGGCA
* *
5110 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTAT
1 AATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
* * * *
5154 AATCCTATCTCACTGAAGTTGTAGTGGAGCGGATTAAAATC-AC
1 AATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
** *
5197 AGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGAT
1 A-ATCTTATCTCACTGAAGTTGCAGTGGAGCAGAT
5231 CGTATCTGGT
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 9 0.14
44 55 0.86
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCACTGAAGTTGCAGTGGAGCAGATTAAAACCTAC
Found at i:6806 original size:7 final size:7
Alignment explanation
Indices: 6796--6829 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
6786 TTAGTAATTT
6796 TTTTATA
1 TTTTATA
6803 TTTTATA
1 TTTTATA
6810 TTTTATA
1 TTTTATA
6817 TTTCTCATA
1 TTT-T-ATA
6826 TTTT
1 TTTT
6830 TCGTATTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 17 0.68
8 2 0.08
9 6 0.24
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:6828 original size:9 final size:8
Alignment explanation
Indices: 6795--6845 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
6785 ATTAGTAATT
*
6795 TTTTTATA
1 TTTTCATA
6803 TTTT-ATA
1 TTTTCATA
6810 TTTT-ATA
1 TTTTCATA
6817 TTTCTCATA
1 TTT-TCATA
*
6826 TTTTTCGTA
1 -TTTTCATA
6835 TTTTCATA
1 TTTTCATA
6843 TTT
1 TTT
6846 AATTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
7 13 0.34
8 15 0.39
9 7 0.18
10 3 0.08
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTCATA
Found at i:6968 original size:27 final size:28
Alignment explanation
Indices: 6911--6968 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
6901 ATTTTTTTTA
*
6911 ATATAATGTAATTATTTTTTAAAATTTT
1 ATATAATGTAATTATTTTTTAAAATTCT
*
6939 ATAT-ATGTAATTATATTTTTATAA-TCT
1 ATATAATGTAATTAT-TTTTTAAAATTCT
6966 ATA
1 ATA
6969 CGTATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 15 0.56
28 12 0.44
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (28 bp):
ATATAATGTAATTATTTTTTAAAATTCT
Found at i:8776 original size:29 final size:28
Alignment explanation
Indices: 8733--8804 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 28
8723 TAAAAATTCA
*
8733 AAAAAATTATAAAAAGTCATTTTAAAA-AT
1 AAAAAATCATAAAAA-TCA-TTTAAAAGAT
* *
8762 AAAAAATCATTAAAATGATTTAAAAGTAT
1 AAAAAATCATAAAAATCATTTAAAAG-AT
8791 AAAAAAT-ATAAAAA
1 AAAAAATCATAAAAA
8805 ATTAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.19
28 8 0.22
29 22 0.59
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAAAATCATAAAAATCATTTAAAAGAT
Found at i:14449 original size:44 final size:44
Alignment explanation
Indices: 14358--14480 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 44
14348 ATTTCTTTTT
* * *
14358 TTTCTTTCTTCCCAATTTCCTTTTTTCTTTCTTTTTCTCTGTTACC
1 TTTC-TTCTTCCCAATTTCCTTTTCT-TTTCTTTTTCTCCGTGACC
14404 TTTCTTCTTCCCAATTTCCTTTTCTTTTCTTTTTC-CCGATGACC
1 TTTCTTCTTCCCAATTTCCTTTTCTTTTCTTTTTCTCCG-TGACC
* * * *
14448 TTTCTTCTTCCTAATGTCTTTTTCTCTTCTTTT
1 TTTCTTCTTCCCAATTTCCTTTTCTTTTCTTTT
14481 CTTTGCTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.03
44 43 0.62
45 20 0.29
46 4 0.06
ACGTcount: A:0.07, C:0.28, G:0.03, T:0.61
Consensus pattern (44 bp):
TTTCTTCTTCCCAATTTCCTTTTCTTTTCTTTTTCTCCGTGACC
Found at i:20570 original size:16 final size:17
Alignment explanation
Indices: 20538--20571 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
20528 ACATTAATTT
*
20538 ATAATTGATATATTTAA
1 ATAATTGATATAATTAA
20555 ATAATT-ATATAATTAA
1 ATAATTGATATAATTAA
20571 A
1 A
20572 AGAAAAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAATTGATATAATTAA
Found at i:22548 original size:13 final size:14
Alignment explanation
Indices: 22527--22555 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
22517 GTATTTGCAA
22527 TATATATATATAAG
1 TATATATATATAAG
22541 TATA-ATATATAAG
1 TATATATATATAAG
22554 TA
1 TA
22556 AATCTTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:22820 original size:13 final size:12
Alignment explanation
Indices: 22790--22823 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
22780 AAACTATGAG
22790 AATAAAATA-AT
1 AATAAAATATAT
22801 AATAAAATATAT
1 AATAAAATATAT
22813 ATATAAAATAT
1 A-ATAAAATAT
22824 GCACATGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAAATATAT
Found at i:22865 original size:23 final size:22
Alignment explanation
Indices: 22807--22867 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 22
22797 TAATAATAAA
*
22807 ATATA-TATATAAAATATGCAC
1 ATATATTATAAAAAATATGCAC
* *
22828 ATGTATTTATAAAAAATATATGCAT
1 ATATA-TTAT-AAAAA-ATATGCAC
22853 ATATATTATAAAAAA
1 ATATATTATAAAAAA
22868 ATACGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 4 0.12
22 1 0.03
23 8 0.25
24 8 0.25
25 11 0.34
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
ATATATTATAAAAAATATGCAC
Found at i:22870 original size:25 final size:25
Alignment explanation
Indices: 22820--22867 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
22810 TATATATAAA
*
22820 ATATGCACATGTATTTATAAAAAAT
1 ATATGCACATATATTTATAAAAAAT
*
22845 ATATGCATATATA-TTATAAAAAA
1 ATATGCACATATATTTATAAAAAA
22868 ATACGTGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (25 bp):
ATATGCACATATATTTATAAAAAAT
Found at i:22896 original size:3 final size:3
Alignment explanation
Indices: 22884--22943 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
22874 GTGTAAATGT
*
22884 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA A-A TATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT-A
22929 ATA AT- ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
22944 GCATACAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 5 0.10
3 41 0.82
4 4 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:24325 original size:85 final size:84
Alignment explanation
Indices: 24216--24380 Score: 231
Period size: 85 Copynumber: 2.0 Consensus size: 84
24206 ATCTACTCGT
* * * *
24216 AATCTGCTCTCTGTAACCTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCATTGCAACTTCA
1 AATCTACTCTCTGCAACCTCAGAGAAATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCA
24281 GAAAAATAGGATTGGATGC
66 GAAAAATAGGATTGGATGC
* * *
24300 AATCTACTCTACTGCAACTTCAGAGAAATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACTTC
1 AATCTACTCT-CTGCAACCTCAGAGAAATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTC
** *
24365 AGGGAGATAGGATTGG
65 AGAAAAATAGGATTGG
24381 TACCTTCAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
84 9 0.13
85 61 0.87
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (84 bp):
AATCTACTCTCTGCAACCTCAGAGAAATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCA
GAAAAATAGGATTGGATGC
Found at i:24364 original size:44 final size:43
Alignment explanation
Indices: 24234--24366 Score: 135
Period size: 44 Copynumber: 3.1 Consensus size: 43
24224 CTCTGTAACC
* *
24234 TCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCATTGCAACT
1 TCAGAGAAATAAGATCT-TGGTTTTAATCCGCTCCACTGCAACT
* * * ** ** *
24278 TCAGAAAAATAGGA--TTGGATGCAATCTACTCTACTGCAACT
1 TCAGAGAAATAAGATCTTGGTTTTAATCCGCTCCACTGCAACT
*
24319 TCAGAGAAATAAGATCTGTGGTTTTAATCCGCTCCACTGTAACT
1 TCAGAGAAATAAGATCT-TGGTTTTAATCCGCTCCACTGCAACT
24363 TCAG
1 TCAG
24367 GGAGATAGGA
Statistics
Matches: 67, Mismatches: 19, Indels: 6
0.73 0.21 0.07
Matches are distributed among these distances:
41 31 0.46
42 1 0.01
43 1 0.01
44 34 0.51
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (43 bp):
TCAGAGAAATAAGATCTTGGTTTTAATCCGCTCCACTGCAACT
Found at i:24807 original size:167 final size:167
Alignment explanation
Indices: 24508--25044 Score: 664
Period size: 167 Copynumber: 3.2 Consensus size: 167
24498 ATTGAAATGT
* * * * * * * *
24508 CAGGGAAACAAGATTCAACATCGTGACTTCAATCTGTTCCCCTACACCGCCAGGGAAGTAAGATT
1 CAGGGAGATAAGATTCACCATCGTGGCTTCAATCTGCTCCACTGCAACGCCAGGGAAGTAAGATT
* *
24573 CGCTGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCATGGCTT
66 CGCCGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACGGCTT
*
24638 TAATCTGCTCCACTTCAGCCAATCCAAGTCTTAATGC
131 TAATCTGCTCCACTTCAGCCAATCCAAGTCTTAACGC
* * ** *
24675 TAGGAAGATAAGATTCACCATCGTGGCTTCAATCTGCTCTGCTGCAATGCCAGGGAAGTAAGATT
1 CAGGGAGATAAGATTCACCATCGTGGCTTCAATCTGCTCCACTGCAACGCCAGGGAAGTAAGATT
* * * ** *
24740 CGCCGTTGTGGCTTCAATCCGTTCCACCGTAAAGCCAAAGAGATAGGATTTGCTATCCACAGCTT
66 CGCCGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACGGCTT
* * *
24805 TAAT-TCGCTTCACTTCATCCAATCCAAGTCTTAACAC
131 TAATCT-GCTCCACTTCAGCCAATCCAAGTCTTAACGC
*** * * * * *
24842 CAGGGAGATAAGATTTGTCGTCATGGTTTCAATCTACTCCACTGCAACGCTAGGGAAGTAAGATT
1 CAGGGAGATAAGATTCACCATCGTGGCTTCAATCTGCTCCACTGCAACGCCAGGGAAGTAAGATT
* * ** *
24907 CACCATTACGACTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACGGCTT
66 CGCCGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACGGCTT
* *
24972 TAATCCT-TTCCACTTCAGCCAATCTAAGTCTTAACGC
131 TAAT-CTGCTCCACTTCAGCCAATCCAAGTCTTAACGC
* *
25009 CAGGGAGATAAGATTCGCCGTCGTGGCTTCAATCTG
1 CAGGGAGATAAGATTCACCATCGTGGCTTCAATCTG
25045 TTTAACTGCA
Statistics
Matches: 309, Mismatches: 58, Indels: 6
0.83 0.16 0.02
Matches are distributed among these distances:
166 1 0.00
167 307 0.99
169 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (167 bp):
CAGGGAGATAAGATTCACCATCGTGGCTTCAATCTGCTCCACTGCAACGCCAGGGAAGTAAGATT
CGCCGTTGTGGCTTCAATCCGTTCCACTGTAATGCCAAAGAGATAGGATTCGCTGCCCACGGCTT
TAATCTGCTCCACTTCAGCCAATCCAAGTCTTAACGC
Found at i:25287 original size:88 final size:88
Alignment explanation
Indices: 25122--25300 Score: 243
Period size: 88 Copynumber: 2.0 Consensus size: 88
25112 GGCGATAAGA
* * * *
25122 CTGGTGTCTTCGATCTGCTTCCCTGCCAGTACAGGAAGGCAAGATCTGCCATTTTCAACCTACTC
1 CTGGTATCTTCGATCTACTTCCCTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTC
* *
25187 CCCTGCTACTCA-GAGAGACAAGG
66 CACTACTACTCAGGA-AGACAAGG
* * *
25210 CTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATTTTCAGCCTACTC
1 CTGGTATCTTCGATCTACTTCCCTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTC
* *
25275 CACTACTGCTCAGGAAGATAAGG
66 CACTACTACTCAGGAAGACAAGG
25298 CTG
1 CTG
25301 AAGTTTCACC
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
88 77 0.97
89 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (88 bp):
CTGGTATCTTCGATCTACTTCCCTGCCAATACAGGAAGACAAGATCTGCCATTTTCAACCTACTC
CACTACTACTCAGGAAGACAAGG
Found at i:26579 original size:21 final size:20
Alignment explanation
Indices: 26555--26603 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
26545 TTAGCCTCTC
26555 TATTTTT-ACTTTTCTATTTTT
1 TATTTTTCA-TTTTC-ATTTTT
26576 TATTTTTCATTTTCATTTTT
1 TATTTTTCATTTTCATTTTT
26596 TCATTTTT
1 T-ATTTTT
26604 TTCATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.27
21 18 0.69
22 1 0.04
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (20 bp):
TATTTTTCATTTTCATTTTT
Found at i:26615 original size:10 final size:9
Alignment explanation
Indices: 26585--26614 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
26575 TTATTTTTCA
26585 TTTTCA-TT
1 TTTTCATTT
26593 TTTTCATTT
1 TTTTCATTT
26602 TTTTCATTT
1 TTTTCATTT
26611 TTTT
1 TTTT
26615 TACAACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.29
9 15 0.71
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCATTT
Found at i:27131 original size:13 final size:12
Alignment explanation
Indices: 27099--27129 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
27089 CCCGGTAGAG
*
27099 TTTTTTCATTCT
1 TTTTTTTATTCT
27111 TTTTTTTATTCT
1 TTTTTTTATTCT
27123 TTTTTTT
1 TTTTTTT
27130 TAGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTTATTCT
Found at i:28634 original size:24 final size:24
Alignment explanation
Indices: 28598--28643 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
28588 AGGGCTCTGA
*
28598 TGGCTAGTAGTAACCGTCTTTGGC
1 TGGCTAGTAGTAACCGACTTTGGC
* * *
28622 TGGCTTGTTGTAATCGACTTTG
1 TGGCTAGTAGTAACCGACTTTG
28644 AATAACCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.17, G:0.28, T:0.39
Consensus pattern (24 bp):
TGGCTAGTAGTAACCGACTTTGGC
Found at i:29189 original size:20 final size:21
Alignment explanation
Indices: 29146--29192 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
29136 TGTATTTGTA
29146 TTTGCTCTAGTTTCTCTAACC
1 TTTGCTCTAGTTTCTCTAACC
* **
29167 TTTGGTCTA-TTTCTCTAGTC
1 TTTGCTCTAGTTTCTCTAACC
29187 TTTGCT
1 TTTGCT
29193 TGGGTGCCGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.11, C:0.23, G:0.13, T:0.53
Consensus pattern (21 bp):
TTTGCTCTAGTTTCTCTAACC
Found at i:30727 original size:20 final size:20
Alignment explanation
Indices: 30670--30727 Score: 53
Period size: 26 Copynumber: 2.6 Consensus size: 20
30660 TATTCGATTG
*
30670 TTTAAGTCTGTTCTTCTTTC
1 TTTAAATCTGTTCTTCTTTC
30690 TTTAAATTATTTTCTGTTCTTCTTTC
1 TTT-AA--A---TCTGTTCTTCTTTC
30716 TTTAAATCTGTT
1 TTTAAATCTGTT
30728 TCAAATACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
20 9 0.29
21 2 0.06
23 1 0.03
25 2 0.06
26 17 0.55
ACGTcount: A:0.16, C:0.16, G:0.07, T:0.62
Consensus pattern (20 bp):
TTTAAATCTGTTCTTCTTTC
Found at i:37207 original size:12 final size:12
Alignment explanation
Indices: 37192--37216 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37182 GCACCAAACT
37192 ATAAAACAAATA
1 ATAAAACAAATA
37204 ATAAAACAAATA
1 ATAAAACAAATA
37216 A
1 A
37217 AGGACAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAACAAATA
Found at i:37224 original size:23 final size:23
Alignment explanation
Indices: 37197--37241 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
37187 AAACTATAAA
*
37197 ACAAATAATAAAAC-AAATAAAGG
1 ACAAATAAAAAAACTAAA-AAAGG
37220 ACAAATAAAAAAACTAAAAAAG
1 ACAAATAAAAAAACTAAAAAAG
37242 TAAATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.11
Consensus pattern (23 bp):
ACAAATAAAAAAACTAAAAAAGG
Found at i:37265 original size:20 final size:21
Alignment explanation
Indices: 37237--37276 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
37227 AAAAAACTAA
*
37237 AAAAGTAAATAAA-GAAAAAC
1 AAAAGTAAAAAAACGAAAAAC
*
37257 AAAATTAAAAAAACGAAAAA
1 AAAAGTAAAAAAACGAAAAA
37277 GGACAAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.78, C:0.05, G:0.07, T:0.10
Consensus pattern (21 bp):
AAAAGTAAAAAAACGAAAAAC
Found at i:37284 original size:7 final size:7
Alignment explanation
Indices: 37274--37298 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37264 AAAAAACGAA
37274 AAAGGAC
1 AAAGGAC
37281 AAAGGAC
1 AAAGGAC
37288 AAAGGAC
1 AAAGGAC
37295 AAAG
1 AAAG
37299 AAATGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.28, T:0.00
Consensus pattern (7 bp):
AAAGGAC
Found at i:38340 original size:17 final size:17
Alignment explanation
Indices: 38318--38351 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38308 TTTTCTCTAT
*
38318 TTTTTAAATATTTATAA
1 TTTTTAAATATATATAA
38335 TTTTTAAATATATATAA
1 TTTTTAAATATATATAA
38352 CAATACTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTAAATATATATAA
Found at i:39493 original size:13 final size:13
Alignment explanation
Indices: 39475--39507 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39465 GGTTACGAGT
39475 TTAATTATAATGA
1 TTAATTATAATGA
*
39488 TTAATTATAATTA
1 TTAATTATAATGA
39501 -TAATTAT
1 TTAATTAT
39508 TCGAATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
TTAATTATAATGA
Found at i:47713 original size:21 final size:21
Alignment explanation
Indices: 47677--47731 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
47667 AATCATATCT
47677 TCCAAGATTG--TATATCATA
1 TCCAAGATTGCATATATCATA
47696 TCCAAGATTGCATATATCATA
1 TCCAAGATTGCATATATCATA
*
47717 TCTAAGATTGCATAT
1 TCCAAGATTGCATAT
47732 CCTTGAAGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 10 0.30
21 23 0.70
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.36
Consensus pattern (21 bp):
TCCAAGATTGCATATATCATA
Found at i:48165 original size:44 final size:44
Alignment explanation
Indices: 48105--48491 Score: 535
Period size: 44 Copynumber: 8.8 Consensus size: 44
48095 ACCAGTATGG
48105 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
48149 GAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
*
48193 GAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * ***
48235 GAAGACAAGATCTACTTTCTTCGATCTACTTCGCCACCAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
48280 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* *
48324 GAAGACAAGATCTGCTATCTTTGATCTACTTCGCGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * *
48368 GAAGATAAGATCTGTTATCTTTGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
* * * * * ***
48412 GAAGACAAGATCTGCTTTCTTCGATTTACTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACAT
*
48457 GAAAACAAGATCTGCTATCTTCGATCTACTTCACG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACG
48492 ACAACCCAGG
Statistics
Matches: 303, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
42 41 0.14
44 190 0.63
45 72 0.24
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
Found at i:48368 original size:175 final size:176
Alignment explanation
Indices: 48077--48491 Score: 735
Period size: 175 Copynumber: 2.4 Consensus size: 176
48067 AAGACTTGTA
48077 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
48142 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
66 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
48207 CTT-TCTTCGATCTACTT-CGCCAATACATGAAGACAAGATCTACTT
131 -TTATCTTCGATCTACTTACGCCAATACATGAAGACAAGATCTACTT
*
48252 TCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
* *
48317 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCGCGCCAATACATGAAGATAAGATCTG
66 AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
* *
48382 TTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
131 TTATCTTCGATCTACTT-ACGCCAATACATGAAGACAAGATCTACTT
* *
48429 TCTTCGATTTACTTCGCCACCAGTATGGGAAAACAAGATCTGCTATCTTCGATCTACTTCACG
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACG
48492 ACAACCCAGG
Statistics
Matches: 229, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
174 2 0.01
175 140 0.61
177 87 0.38
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (176 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCC
AATACATGAAGACAAGATCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTG
TTATCTTCGATCTACTTACGCCAATACATGAAGACAAGATCTACTT
Found at i:48614 original size:88 final size:88
Alignment explanation
Indices: 48462--49480 Score: 1543
Period size: 88 Copynumber: 11.6 Consensus size: 88
48452 TATGGGAAAA
* * * * * *
48462 CAAGATCTGCTATCTTCGATCTACTTCACGACAACCCAGGGAGGCAAGGCTGGTATCTTTGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* * **
48527 GCTTCACTGTCGGTATAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
*
48550 CAAGATCTACTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* * *
48615 GCTTCACTGTCGGTACAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* * * * * *
48638 CAAGATCTGCTATCATAAACCTGCTCCACTACGACCCAGGGAGACAAGTCTGGTATATTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* * *
48703 GCTTCACTGTCGGTACAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
*
48726 CAAGATCTGCTATCTTCAACCTGTTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
48791 GCTTCGCTGTCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
48814 AAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGTTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* *
48879 GCTTCGCTGTCGGTACAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* * *
48902 AAAGATCTGCTATCTTCAACCTGCTCCACTACGACCCATGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* * *
48967 GCTTCACTGTCGGTACAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* * * * *
48990 CAAGATCTGTTATCTTCAACTTGCTCCACTACAACTCAGTGAGGGAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* *
49055 GCTTCGCTGTCGATGTAGGAATG
66 GCTTCGCTGTCGATGCAGGAAGG
*
49078 CAAGATCTGCTATCTTCAACCTGCTCTACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
*
49143 GCTTCGCTATCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
49166 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCTGGGAGGCAAGGCTTGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
*
49231 GCTTCGTTGTCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
49254 CAAGATCTGTTATCTTCAACCTGCTCCACTACAACCTAGGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
*
49319 GCTTCGCTATCGATGCAGGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
49342 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCTAAGGAGGCAAGGCTGGTATCTTCGATCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
* *
49407 GCTTCACTGTCGATGCATGAAGG
66 GCTTCGCTGTCGATGCAGGAAGG
* *
49430 CAAGATCTGCTATATTCAACCTGCTTCACTACAACCCAGGGAGGCAAGGCT
1 CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCT
49481 TTGTGATTTC
Statistics
Matches: 855, Mismatches: 76, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 855 1.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (88 bp):
CAAGATCTGCTATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGGTATCTTCGATCT
GCTTCGCTGTCGATGCAGGAAGG
Found at i:56095 original size:4 final size:4
Alignment explanation
Indices: 56078--56109 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
56068 TTTAAAATTG
*
56078 TAAA TAAG TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
56110 AACAGTAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:56859 original size:5 final size:5
Alignment explanation
Indices: 56840--56875 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
56830 TTGTCTCGTT
56840 TTTTA TTTT- TCTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA T
56876 CGTTTATTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 27 0.93
6 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:58881 original size:20 final size:20
Alignment explanation
Indices: 58853--58891 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58843 CGAACTTGAG
58853 CTTCCTCTTCTCTTTTTCTC
1 CTTCCTCTTCTCTTTTTCTC
* *
58873 CTTCTTCTTCTTTTTTTCT
1 CTTCCTCTTCTCTTTTTCT
58892 TTTTTACTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (20 bp):
CTTCCTCTTCTCTTTTTCTC
Found at i:67531 original size:42 final size:41
Alignment explanation
Indices: 67453--67541 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 41
67443 TTACAAATTG
*
67453 TTAATTATATAAATTCGATTATTTAAATTTGGTTTT-GGTATA
1 TTAATTATATAAATTCGATTATGTAAATTT-GTTTTGGGTA-A
67495 TTAATTATATAAATTCGATTATCGTAATATTT-TTTTGGGTAA
1 TTAATTATATAAATTCGATTAT-GTAA-ATTTGTTTTGGGTAA
67537 TTAAT
1 TTAAT
67542 AACAAAGTCC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 32 0.74
43 7 0.16
44 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (41 bp):
TTAATTATATAAATTCGATTATGTAAATTTGTTTTGGGTAA
Found at i:79164 original size:31 final size:31
Alignment explanation
Indices: 79126--79184 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
79116 TTGGACATTC
79126 TCATAATGCTCAATTGAGTCACGAACATATT
1 TCATAATGCTCAATTGAGTCACGAACATATT
79157 TCATAATGCTCAATTGAGTCACGAACAT
1 TCATAATGCTCAATTGAGTCACGAACAT
79185 TAGCAGGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (31 bp):
TCATAATGCTCAATTGAGTCACGAACATATT
Found at i:79962 original size:102 final size:102
Alignment explanation
Indices: 79786--79995 Score: 366
Period size: 102 Copynumber: 2.1 Consensus size: 102
79776 TTAACTAGAT
*
79786 ATTAATCCTTAAACTTTATTCAAGACTGTTGCTAAGCCATTATGTAACATCTATTGTCTATAAAC
1 ATTAAACCTTAAACTTTATTCAAGACTGTTGCTAAGCCATTATGTAACATCTATTGTCTATAAAC
*
79851 CTTATAAGATCTTTACTACAATAAATAATTTAATTTA
66 CTTATAAGATCTTTACGACAATAAATAATTTAATTTA
* * *
79888 ATTAAACCTTAAACTTTATTCATGATTGTTGCTAAGTCATTATGTAACATCTATTGTCTATAAAC
1 ATTAAACCTTAAACTTTATTCAAGACTGTTGCTAAGCCATTATGTAACATCTATTGTCTATAAAC
*
79953 CTTATAAGATCTTTACGACAATAAATAATTTCATTTA
66 CTTATAAGATCTTTACGACAATAAATAATTTAATTTA
79990 ATTAAA
1 ATTAAA
79996 GTTGTTGTGG
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 102 1.00
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (102 bp):
ATTAAACCTTAAACTTTATTCAAGACTGTTGCTAAGCCATTATGTAACATCTATTGTCTATAAAC
CTTATAAGATCTTTACGACAATAAATAATTTAATTTA
Found at i:92477 original size:84 final size:84
Alignment explanation
Indices: 92351--92523 Score: 337
Period size: 84 Copynumber: 2.1 Consensus size: 84
92341 AACTAATTCC
*
92351 AATAATGCTAATAATACTTAGACAAAAACTAGGATAAATCAATTGAAGGCACTCATATGTTTCTT
1 AATAATGATAATAATACTTAGACAAAAACTAGGATAAATCAATTGAAGGCACTCATATGTTTCTT
92416 TCCCAAAACCTTAATGTAA
66 TCCCAAAACCTTAATGTAA
92435 AATAATGATAATAATACTTAGACAAAAACTAGGATAAATCAATTGAAGGCACTCATATGTTTCTT
1 AATAATGATAATAATACTTAGACAAAAACTAGGATAAATCAATTGAAGGCACTCATATGTTTCTT
92500 TCCCAAAACCTTAATGTAA
66 TCCCAAAACCTTAATGTAA
92519 AATAA
1 AATAA
92524 AGGAAAAGAA
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (84 bp):
AATAATGATAATAATACTTAGACAAAAACTAGGATAAATCAATTGAAGGCACTCATATGTTTCTT
TCCCAAAACCTTAATGTAA
Found at i:101294 original size:17 final size:17
Alignment explanation
Indices: 101272--101306 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
101262 ATGTGTACTT
101272 ATATAGAGGTTAGGTTA
1 ATATAGAGGTTAGGTTA
101289 ATATAGAGGTTAGGTTA
1 ATATAGAGGTTAGGTTA
101306 A
1 A
101307 CACCGGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (17 bp):
ATATAGAGGTTAGGTTA
Found at i:110057 original size:12 final size:12
Alignment explanation
Indices: 110040--110071 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
110030 GTTTATCTGT
110040 TATCTGTATTTG
1 TATCTGTATTTG
110052 TATCTGTATTTG
1 TATCTGTATTTG
110064 TATCTGTA
1 TATCTGTA
110072 AAGGACTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (12 bp):
TATCTGTATTTG
Found at i:110059 original size:6 final size:6
Alignment explanation
Indices: 110033--110071 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
110023 TTGTTTTGTT
* *
110033 TATCTG TTATCTG TATTTG TATCTG TATTTG TATCTG TA
1 TATCTG -TATCTG TATCTG TATCTG TATCTG TATCTG TA
110072 AAGGACTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.18, C:0.10, G:0.15, T:0.56
Consensus pattern (6 bp):
TATCTG
Found at i:125277 original size:7 final size:7
Alignment explanation
Indices: 125265--125343 Score: 140
Period size: 7 Copynumber: 11.0 Consensus size: 7
125255 TATTTTAGGC
125265 AAACCCT
1 AAACCCT
125272 AAACCCT
1 AAACCCT
125279 AAACCCT
1 AAACCCT
125286 AAACCCT
1 AAACCCT
125293 AAACCCT
1 AAACCCT
125300 AAACCCCT
1 AAA-CCCT
125308 AAACCCT
1 AAACCCT
125315 AAACCCT
1 AAACCCT
125322 AAACCCT
1 AAACCCT
125329 AAAACCCT
1 -AAACCCT
125337 AAACCCT
1 AAACCCT
125344 GGATAGAGGA
Statistics
Matches: 70, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
7 56 0.80
8 14 0.20
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:125316 original size:29 final size:28
Alignment explanation
Indices: 125265--125343 Score: 140
Period size: 29 Copynumber: 2.8 Consensus size: 28
125255 TATTTTAGGC
125265 AAACCCTAAACCCTAAACCCTAAACCCT
1 AAACCCTAAACCCTAAACCCTAAACCCT
125293 AAACCCTAAACCCCTAAACCCTAAACCCT
1 AAACCCTAAA-CCCTAAACCCTAAACCCT
125322 AAACCCTAAAACCCTAAACCCT
1 AAACCCT-AAACCCTAAACCCT
125344 GGATAGAGGA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 10 0.20
29 36 0.73
30 3 0.06
ACGTcount: A:0.43, C:0.43, G:0.00, T:0.14
Consensus pattern (28 bp):
AAACCCTAAACCCTAAACCCTAAACCCT
Found at i:126898 original size:51 final size:51
Alignment explanation
Indices: 126839--126979 Score: 183
Period size: 55 Copynumber: 2.7 Consensus size: 51
126829 TCATATACTA
*
126839 ATATATTAGCTATTCTGGAGCTTTCATCTAATTTTGTAGTACCAAATATTG
1 ATATATTAGCTATTTTGGAGCTTTCATCTAATTTTGTAGTACCAAATATTG
* *
126890 ATATATTAGCTAGCTCGTTTGGAGCTTTTATCTAATTTCGTAGTACCAAATATTG
1 ATATATTAGCTA--T--TTTGGAGCTTTCATCTAATTTTGTAGTACCAAATATTG
* * * *
126945 ATATATTAGCTCTTTTGTAGCTTTCAACTATTTTT
1 ATATATTAGCTATTTTGGAGCTTTCATCTAATTTT
126980 CATATCACTT
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
51 29 0.38
53 2 0.03
55 46 0.60
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (51 bp):
ATATATTAGCTATTTTGGAGCTTTCATCTAATTTTGTAGTACCAAATATTG
Found at i:131664 original size:51 final size:50
Alignment explanation
Indices: 131538--131762 Score: 256
Period size: 51 Copynumber: 4.4 Consensus size: 50
131528 TCGATACGTG
* * * *
131538 TAGTAGCCTTCACATAGTACTACACACGTAATCAAG-TTTTACGGTTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTT-CGGTACACA
131588 TAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTTTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACA
* * * * * * *
131639 TAGTAGCATTCACTTAGTACTACACATGTGACC-ATCATTTATCGATTCACG
1 TAGTAGCCTTCACATAGTACTACACACGTGACCAAGC-TTT-TCGGTACACA
* *
131690 TAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACA
1 TAGTAGCCTTCACATAGTACTACACACGTGACC-AAGCTTTTCGGTACACA
* *
131741 TTGTAGCCTTCACTTAGTACTA
1 TAGTAGCCTTCACATAGTACTA
131763 NNNNNNNNNN
Statistics
Matches: 146, Mismatches: 23, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.01
50 34 0.23
51 102 0.70
52 6 0.04
53 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (50 bp):
TAGTAGCCTTCACATAGTACTACACACGTGACCAAGCTTTTCGGTACACA
Found at i:131713 original size:102 final size:101
Alignment explanation
Indices: 131538--131762 Score: 333
Period size: 102 Copynumber: 2.2 Consensus size: 101
131528 TCGATACGTG
* * ** * *
131538 TAGTAGCCTTCACATAGTACTACACACGTAATCAAGTTTTACGGTTCACGTAGTAGCCTTCACAT
1 TAGTAGCCTTCACTTAGTACTACACACGTAACCAACATTTACGATTCACGTAGTAGCCTTCACAC
*
131603 AGTACTACACACGTGACCAAAGCTTTTCGGTACACA
66 AGTACTACACACGTGACCAAAGCTTCTCGGTACACA
* * * *
131639 TAGTAGCATTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCCTTCACA
1 TAGTAGCCTTCACTTAGTACTACACACGTAACCAACATTTA-CGATTCACGTAGTAGCCTTCACA
131704 CAGTACTACACACGTGACCAAAGCTTCTCGGTACACA
65 CAGTACTACACACGTGACCAAAGCTTCTCGGTACACA
*
131741 TTGTAGCCTTCACTTAGTACTA
1 TAGTAGCCTTCACTTAGTACTA
131763 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 33 0.30
102 77 0.70
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (101 bp):
TAGTAGCCTTCACTTAGTACTACACACGTAACCAACATTTACGATTCACGTAGTAGCCTTCACAC
AGTACTACACACGTGACCAAAGCTTCTCGGTACACA
Found at i:135467 original size:10 final size:10
Alignment explanation
Indices: 135452--135485 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
135442 ATAAATAATT
135452 TTTTTTAAAA
1 TTTTTTAAAA
135462 TTTTTTAAAA
1 TTTTTTAAAA
*
135472 -TTTTTAATA
1 TTTTTTAAAA
135481 TTTTT
1 TTTTT
135486 AGTATATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:135475 original size:9 final size:9
Alignment explanation
Indices: 135453--135486 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
135443 TAAATAATTT
135453 TTTTTAAAA
1 TTTTTAAAA
135462 TTTTTTAAAA
1 -TTTTTAAAA
*
135472 TTTTTAATA
1 TTTTTAAAA
135481 TTTTTA
1 TTTTTA
135487 GTATATTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:143941 original size:19 final size:18
Alignment explanation
Indices: 143919--143957 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
143909 TGAAATTGAT
143919 AAAAATTGAA-AATTGAGAC
1 AAAAATT-AATAATTGA-AC
143938 AAAAATTAATAATTGAAC
1 AAAAATTAATAATTGAAC
143956 AA
1 AA
143958 GTTTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (18 bp):
AAAAATTAATAATTGAAC
Found at i:144565 original size:17 final size:17
Alignment explanation
Indices: 144535--144573 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
144525 ATTATAAACA
*
144535 TAAATAAGTGTTTTCTT
1 TAAATAAGTATTTTCTT
* *
144552 TAAATGAGTATTTTTTT
1 TAAATAAGTATTTTCTT
144569 TAAAT
1 TAAAT
144574 TATAAACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (17 bp):
TAAATAAGTATTTTCTT
Found at i:144837 original size:10 final size:10
Alignment explanation
Indices: 144822--144862 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
144812 TTTTAATCAA
144822 ATATATATTT
1 ATATATATTT
*
144832 ATATATATTAA
1 ATATATATT-T
*
144843 ATATATTTTT
1 ATATATATTT
144853 ATATATATTT
1 ATATATATTT
144863 TTAATCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATATTT
Found at i:144845 original size:21 final size:21
Alignment explanation
Indices: 144820--144861 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
144810 ATTTTTAATC
144820 AAATATATATTTATATATATT
1 AAATATATATTTATATATATT
*
144841 AAATATATTTTTATATATATT
1 AAATATATATTTATATATATT
144862 TTTAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAATATATATTTATATATATT
Found at i:145100 original size:11 final size:11
Alignment explanation
Indices: 145083--145120 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
145073 TTTTTAATCA
145083 AATATATATTT
1 AATATATATTT
* *
145094 TATATATATTA
1 AATATATATTT
145105 AATATATATTT
1 AATATATATTT
145116 AATAT
1 AATAT
145121 GGGACAGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
AATATATATTT
Found at i:165798 original size:29 final size:30
Alignment explanation
Indices: 165743--165808 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
165733 CTTTAATGTG
*
165743 TAATTGTATATATAAATTTTGATTTTG-TA
1 TAATTTTATATATAAATTTTGATTTTGATA
*
165772 TAATTTTATATATGAAATTTTGA-TTTGATC
1 TAATTTTATATAT-AAATTTTGATTTTGATA
165802 TAATTTT
1 TAATTTT
165809 TGTAAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (30 bp):
TAATTTTATATATAAATTTTGATTTTGATA
Found at i:167996 original size:45 final size:44
Alignment explanation
Indices: 167942--168027 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
167932 TTCGCTTTAT
* *
167942 TGGATTAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAATGTAA
* ***
167987 TGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAATG
1 TGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAATG
168028 GAATAGATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (44 bp):
TGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAATGTAA
Found at i:176453 original size:13 final size:13
Alignment explanation
Indices: 176435--176459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
176425 TTTTTTTGAA
176435 TTTTTAATTAATG
1 TTTTTAATTAATG
176448 TTTTTAATTAAT
1 TTTTTAATTAAT
176460 ACTTTTTTTT
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATG
Found at i:188374 original size:145 final size:146
Alignment explanation
Indices: 188194--188487 Score: 572
Period size: 145 Copynumber: 2.0 Consensus size: 146
188184 CCTTGGAATT
188194 TTTAGATTTTTGAATTTTATATATAAATTATCATGTATTTTAGATCCGATGTCCATATTGTATAA
1 TTTAGATTTTTGAATTTTATATATAAATTATCATGTATTTTAGATCCGATGTCCATATTGTATAA
188259 CAGTCAATCCCCTTAGCCAAATTGTTTTTCATATGATACGTCCTTTTAAGCCATAAGGTTATACT
66 CAGTCAATCCCCTTAGCCAAATTGTTTTTCATATGATACGTCCTTTTAAGCCATAAGGTTATACT
188324 TTATATTAACAAAGTA
131 TTATATTAACAAAGTA
188340 TTTAGATTTTTG-ATTTTATATATAAATTATCATGTATTTTAGATCCGATGTCCATATTGTATAA
1 TTTAGATTTTTGAATTTTATATATAAATTATCATGTATTTTAGATCCGATGTCCATATTGTATAA
*
188404 CAGTCAATCCCCTTAGCCAAATTGTTTTTCCTATGATACGTCCTTTTAAGCCATAAGGTTATACT
66 CAGTCAATCCCCTTAGCCAAATTGTTTTTCATATGATACGTCCTTTTAAGCCATAAGGTTATACT
188469 TTATATTAACAAAGTA
131 TTATATTAACAAAGTA
188485 TTT
1 TTT
188488 TTTAGTTTTT
Statistics
Matches: 147, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
145 135 0.92
146 12 0.08
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (146 bp):
TTTAGATTTTTGAATTTTATATATAAATTATCATGTATTTTAGATCCGATGTCCATATTGTATAA
CAGTCAATCCCCTTAGCCAAATTGTTTTTCATATGATACGTCCTTTTAAGCCATAAGGTTATACT
TTATATTAACAAAGTA
Found at i:188918 original size:20 final size:20
Alignment explanation
Indices: 188862--188918 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
188852 TTTATTATTT
*
188862 TTTTCTTTTTCCTAATATG-
1 TTTTCTTTTTCATAATATGA
* *
188881 TTGT-TGTTTCAT-ATATGA
1 TTTTCTTTTTCATAATATGA
*
188899 TTTTCTTTTTCTTAATATGA
1 TTTTCTTTTTCATAATATGA
188919 GTTTGATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 9 0.31
20 6 0.21
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTCTTTTTCATAATATGA
Found at i:190396 original size:20 final size:20
Alignment explanation
Indices: 190340--190396 Score: 57
Period size: 18 Copynumber: 3.0 Consensus size: 20
190330 TTTATTATTT
*
190340 TTTTCTTTTTCCTAATATG-
1 TTTTCTTTTTCATAATATGA
* *
190359 TTGT-TGTTTCAT-ATATGA
1 TTTTCTTTTTCATAATATGA
*
190377 TTTTCTTTTTCTTAATATGA
1 TTTTCTTTTTCATAATATGA
190397 GTTTGATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
17 5 0.17
18 9 0.31
19 9 0.31
20 6 0.21
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTTCTTTTTCATAATATGA
Found at i:199158 original size:20 final size:20
Alignment explanation
Indices: 199130--199169 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
199120 GTCAATAAAT
* *
199130 AATTTAAAATTTATAAAAAA
1 AATTCAAAAATTATAAAAAA
199150 AATTCAAAAATTATAAAAAA
1 AATTCAAAAATTATAAAAAA
199170 TTAAAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AATTCAAAAATTATAAAAAA
Found at i:199175 original size:17 final size:18
Alignment explanation
Indices: 199146--199187 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
199136 AAATTTATAA
199146 AAAAAATTCAAAAATTA-T
1 AAAAAATTC-AAAATTATT
199164 AAAAAATT-AAAATTATT
1 AAAAAATTCAAAATTATT
199181 AAAAAAT
1 AAAAAAT
199188 AGTATAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 8 0.35
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAAATTCAAAATTATT
Found at i:203565 original size:13 final size:13
Alignment explanation
Indices: 203547--203574 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
203537 ACAAATTTGG
203547 AAAGATGATAAAT
1 AAAGATGATAAAT
203560 AAAGATGATAAAT
1 AAAGATGATAAAT
203573 AA
1 AA
203575 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:203905 original size:11 final size:11
Alignment explanation
Indices: 203891--203918 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
203881 ATGAAATTGT
203891 AAAATTCATGG
1 AAAATTCATGG
203902 AAAATTCATGG
1 AAAATTCATGG
203913 AAAATT
1 AAAATT
203919 TCTGAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (11 bp):
AAAATTCATGG
Found at i:204700 original size:73 final size:73
Alignment explanation
Indices: 204564--204701 Score: 161
Period size: 73 Copynumber: 1.9 Consensus size: 73
204554 GATCTTTGTG
* * * * *
204564 AGCTTCTTGATTAATGGCTCTCCAGAGCTACCTGATATGGCTCTCTTGAACTTCCTGATATATGG
1 AGCTTCTCGATTAATGGCTCTCCAGAGCTACCCGATATGACTCACATGAACTTCCTGATATATGG
204629 TTATCCGA
66 TTATCCGA
* * * * * *
204637 AGCTTCTCGATTAATGGCTTTTCGGAGCTACCCGTTATTGACTCACATGAGCTTCTTGA-ATATG
1 AGCTTCTCGATTAATGGCTCTCCAGAGCTACCCGATA-TGACTCACATGAACTTCCTGATATATG
204701 G
65 G
204702 CTCTTATGAG
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
73 37 0.70
74 16 0.30
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (73 bp):
AGCTTCTCGATTAATGGCTCTCCAGAGCTACCCGATATGACTCACATGAACTTCCTGATATATGG
TTATCCGA
Found at i:221387 original size:59 final size:59
Alignment explanation
Indices: 221311--221428 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
221301 AGTTAGTTAC
*
221311 TTATTACTTAATTTTGAAAATTTTAAGTTGAAACCTACATTCGTTTGGTTGAGAGGTAA
1 TTATTACTTAATATTGAAAATTTTAAGTTGAAACCTACATTCGTTTGGTTGAGAGGTAA
*
221370 TTATTACTTAATATTGAAAATTTTAAGTTGAAACCTACATTTGTTTGGTTGAGAGGTAA
1 TTATTACTTAATATTGAAAATTTTAAGTTGAAACCTACATTCGTTTGGTTGAGAGGTAA
221429 GGAGTTTGAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (59 bp):
TTATTACTTAATATTGAAAATTTTAAGTTGAAACCTACATTCGTTTGGTTGAGAGGTAA
Done.