Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006513.1 Hibiscus syriacus cultivar Beakdansim tig00015867_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 291456
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
File 1 of 2
Found at i:7536 original size:24 final size:24
Alignment explanation
Indices: 7504--7562 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
7494 CGTAAAAGTA
7504 ATCGAGACAGAAGATATTCACGCT
1 ATCGAGACAGAAGATATTCACGCT
7528 ATCGAGACAGAAGATATTCACGCT
1 ATCGAGACAGAAGATATTCACGCT
7552 ATCGAGACAGA
1 ATCGAGACAGA
7563 TAAATCAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (24 bp):
ATCGAGACAGAAGATATTCACGCT
Found at i:10521 original size:15 final size:16
Alignment explanation
Indices: 10501--10552 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
10491 ATATTACTTA
10501 TTCAAGTCATTT-AAG
1 TTCAAGTCATTTCAAG
*
10516 TTCAAGTCAATTTGAA-
1 TTCAAGTC-ATTTCAAG
* *
10532 TTCAGGTCTTTTCAAG
1 TTCAAGTCATTTCAAG
10548 TTCAA
1 TTCAA
10553 ATTGAATAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 13 0.43
16 15 0.50
17 2 0.07
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.40
Consensus pattern (16 bp):
TTCAAGTCATTTCAAG
Found at i:11879 original size:60 final size:59
Alignment explanation
Indices: 11770--11901 Score: 142
Period size: 60 Copynumber: 2.2 Consensus size: 59
11760 TTGAATGAAT
* * * * **
11770 ATTTTGTAATTTTTAATAGTTAGGAGACTCAACAAAACATTGTTTTATAGTCTAACAACC
1 ATTTTGTAACTTTTAATAGTCAGGAGACTCAACAAAACAATATCCTATAGT-TAACAACC
* * *
11830 ATTTTGTAACTTTTAATAGTCAGTG-GACTCGACAAAACAATATCCTATAGTTGAGAACC
1 ATTTTGTAACTTTTAATAGTCAG-GAGACTCAACAAAACAATATCCTATAGTTAACAACC
11889 ATTTGTGT-ACTTT
1 ATTT-TGTAACTTT
11902 ACCCTATTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 15 0.25
60 45 0.74
61 1 0.02
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTCAGGAGACTCAACAAAACAATATCCTATAGTTAACAACC
Found at i:12753 original size:16 final size:17
Alignment explanation
Indices: 12728--12779 Score: 72
Period size: 16 Copynumber: 3.1 Consensus size: 17
12718 TAAAAATATA
12728 ATTA-TTTTTATATTAT
1 ATTATTTTTTATATTAT
12744 ATT-TTTTTTATATTAT
1 ATTATTTTTTATATTAT
*
12760 ATTATATTTTATATATAT
1 ATTATTTTTTATAT-TAT
12778 AT
1 AT
12780 GATATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 18 0.56
17 9 0.28
18 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTATTTTTTATATTAT
Found at i:12759 original size:21 final size:23
Alignment explanation
Indices: 12735--12787 Score: 74
Period size: 21 Copynumber: 2.4 Consensus size: 23
12725 ATAATTATTT
*
12735 TTATATTATATTTT-T-TTTATA
1 TTATATTATATTTTATATATATA
12756 TTATATTATATTTTATATATATA
1 TTATATTATATTTTATATATATA
*
12779 TGATATTAT
1 TTATATTAT
12788 TTATTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 14 0.50
22 1 0.04
23 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATATTATATTTTATATATATA
Found at i:13249 original size:28 final size:27
Alignment explanation
Indices: 13218--13288 Score: 115
Period size: 28 Copynumber: 2.6 Consensus size: 27
13208 AAATACAAAA
13218 TTATTATAAAAATCAAAATCGAAATAAT
1 TTATTA-AAAAATCAAAATCGAAATAAT
*
13246 TTATTAAAAAAATCTAAATCGAAATAAT
1 TTATT-AAAAAATCAAAATCGAAATAAT
13274 TTATTAAAAAATCAA
1 TTATTAAAAAATCAA
13289 CCGAATTGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 9 0.22
28 30 0.75
29 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (27 bp):
TTATTAAAAAATCAAAATCGAAATAAT
Found at i:13656 original size:29 final size:29
Alignment explanation
Indices: 13624--13684 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
13614 GGTGACCAAT
13624 TTTTA-AGAATTTAAATATGCAAATATTTA
1 TTTTACAGAATTTAAA-ATGCAAATATTTA
** **
13653 TTTTACATCATTTAAAATTTAAATATTTA
1 TTTTACAGAATTTAAAATGCAAATATTTA
13682 TTT
1 TTT
13685 GACAACTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (29 bp):
TTTTACAGAATTTAAAATGCAAATATTTA
Found at i:18943 original size:19 final size:19
Alignment explanation
Indices: 18919--18956 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18909 AACAAGACAA
18919 GAACACCAAGGAACCGCAC
1 GAACACCAAGGAACCGCAC
18938 GAACACCAAGGAACCGCAC
1 GAACACCAAGGAACCGCAC
18957 ACGAAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.37, G:0.21, T:0.00
Consensus pattern (19 bp):
GAACACCAAGGAACCGCAC
Found at i:26040 original size:28 final size:28
Alignment explanation
Indices: 25990--26046 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
25980 AAAAAAATTG
* *
25990 AATACTTTATGGATTTATATTGACAAAA
1 AATACTTTAAGGATCTATATTGACAAAA
* * *
26018 AATACTTTAAGTATCTATTTTGATAAAA
1 AATACTTTAAGGATCTATATTGACAAAA
26046 A
1 A
26047 TAAATAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (28 bp):
AATACTTTAAGGATCTATATTGACAAAA
Found at i:26797 original size:3 final size:3
Alignment explanation
Indices: 26789--26857 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
26779 CTAATTCCAT
26789 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
26837 ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC
26858 GGGCTACCCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:28220 original size:26 final size:25
Alignment explanation
Indices: 28191--28247 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
28181 ACTTTATTAT
* *
28191 TTTAAATTTATATATTTTTAATAAAA
1 TTTAAATATACAT-TTTTTAATAAAA
* *
28217 TTTATATATACATTTTTTTATAAAA
1 TTTAAATATACATTTTTTAATAAAA
28242 TTTAAA
1 TTTAAA
28248 AGATAAATGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAAATATACATTTTTTAATAAAA
Found at i:28688 original size:31 final size:31
Alignment explanation
Indices: 28653--28721 Score: 129
Period size: 31 Copynumber: 2.2 Consensus size: 31
28643 ATGAGAACAA
*
28653 AACAACATACAAAACAGATTCATTTTATTTC
1 AACAACATACAAAACAAATTCATTTTATTTC
28684 AACAACATACAAAACAAATTCATTTTATTTC
1 AACAACATACAAAACAAATTCATTTTATTTC
28715 AACAACA
1 AACAACA
28722 ACCTATTGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.29
Consensus pattern (31 bp):
AACAACATACAAAACAAATTCATTTTATTTC
Found at i:32253 original size:22 final size:22
Alignment explanation
Indices: 32226--32289 Score: 64
Period size: 21 Copynumber: 3.0 Consensus size: 22
32216 TTTCATCCCC
32226 TATATATATTTTTTATTTAT-T
1 TATATATATTTTTTATTTATAT
**
32247 TACTATAT-TCCTTTATTTATAT
1 TA-TATATATTTTTTATTTATAT
32269 TATAT-TA-TTTTTATTATATAT
1 TATATATATTTTTTATT-TATAT
32290 ATCTTATATC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 7 0.20
21 20 0.57
22 8 0.23
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (22 bp):
TATATATATTTTTTATTTATAT
Found at i:32276 original size:14 final size:14
Alignment explanation
Indices: 32259--32298 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
32249 CTATATTCCT
32259 TTATTTATATTATA
1 TTATTTATATTATA
*
32273 TTATTTTTATTATA
1 TTATTTATATTATA
32287 TATATCTTATAT
1 T-TAT-TTATAT
32299 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:32460 original size:44 final size:42
Alignment explanation
Indices: 32386--32474 Score: 106
Period size: 44 Copynumber: 2.1 Consensus size: 42
32376 TTTATACGTT
* * *
32386 TTTATATATATATTTTCTTAAAATTCTATTTTTGTTTTCATTTA
1 TTTATATATATATTATATTAAAATTCTA-TTTTATTTT-ATTTA
* * *
32430 TTTATATATATATTATATTATATTTTTATTTTATTTTATTTA
1 TTTATATATATATTATATTAAAATTCTATTTTATTTTATTTA
32472 TTT
1 TTT
32475 TTTCTATTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 8 0.21
43 8 0.21
44 23 0.59
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (42 bp):
TTTATATATATATTATATTAAAATTCTATTTTATTTTATTTA
Found at i:37150 original size:13 final size:13
Alignment explanation
Indices: 37120--37168 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
37110 ATCAGAACAT
37120 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
37134 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
37147 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
37160 AAAG-GAAAA
1 AAAGAGAAAA
37169 TTGAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:37155 original size:27 final size:25
Alignment explanation
Indices: 37120--37169 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
37110 ATCAGAACAT
37120 AAAGAGAAAAAAGCAAAGAGAAAATAA
1 AAAGAGAAAAAA-CAAAG-GAAAATAA
37147 AAAGAGAAAAAACAAAGGAAAAT
1 AAAGAGAAAAAACAAAGGAAAAT
37170 TGAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 6 0.26
26 5 0.22
27 12 0.52
ACGTcount: A:0.74, C:0.04, G:0.18, T:0.04
Consensus pattern (25 bp):
AAAGAGAAAAAACAAAGGAAAATAA
Found at i:37359 original size:69 final size:69
Alignment explanation
Indices: 37241--37375 Score: 225
Period size: 69 Copynumber: 2.0 Consensus size: 69
37231 GATTTAAACT
* * *
37241 ATGAGATTGATCAAGCACAATCATTTCTGAATCACTGAACCACTTCACTCGAAGATCCTAGAGCA
1 ATGAGATTGATCAAGAACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
37306 TGAA
66 TGAA
* *
37310 ATGAGATTGATCAAGAACAATCATTTCTGAATCATTGAATCACTCCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGAACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
37375 T
66 T
37376 CAAGAGAGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (69 bp):
ATGAGATTGATCAAGAACAATCATTTCTGAATCACTGAACCACTCCACTCGAAGATCATAGAGCA
TGAA
Found at i:38985 original size:37 final size:37
Alignment explanation
Indices: 38926--39007 Score: 121
Period size: 37 Copynumber: 2.2 Consensus size: 37
38916 TTTGAAAACA
** *
38926 TTTCCCTT-GAAACGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAG
38962 TTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAG
1 TTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAG
*
38999 TTTCTCTTG
1 TTTCCCTTG
39008 AAACATAAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 8 0.20
37 33 0.80
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (37 bp):
TTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAG
Found at i:39015 original size:102 final size:101
Alignment explanation
Indices: 38839--39081 Score: 360
Period size: 102 Copynumber: 2.4 Consensus size: 101
38829 TAAAAAGAAG
* * * *
38839 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAAAATATTGTCTCCCTTGAGGCAATTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAA-AAAATTTTGTCTCCCTTGAGACAATTTCTCT
* *
38904 TGAAACATAAACTTTGAAAACATTTCCCTTGAAACGA
65 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* *
38941 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAGTTTCTCT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTT-GAAAAAAATTTTGTCTCCCTTGAGACAATTTCTCT
*
39006 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
65 TGAAACATAAACATTGAAAACATTTCCCTTGAAACAA
* * *
39043 ATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
1 ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATT
39082 ATTTGAATAT
Statistics
Matches: 128, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
101 9 0.07
102 115 0.90
103 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (101 bp):
ATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGACAATTTCTCTT
GAAACATAAACATTGAAAACATTTCCCTTGAAACAA
Found at i:39067 original size:65 final size:63
Alignment explanation
Indices: 38961--39200 Score: 195
Period size: 65 Copynumber: 3.8 Consensus size: 63
38951 TCTTGAGATA
* * * *
38961 GTTTCCCTTGGAAAAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 GTTTCCCTT-GAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAA-ATTG-AAA
39026 C
63 C
* * * *
39027 ATTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AATTATTTGAATA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACATAA--AATTGAA-A
*
39091 T
63 C
*** * ** * * *
39092 GTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC-T-AAGTT---TC
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAAATTGAAAC
* * *
39150 GTCTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACA
39201 AAATCTTTGA
Statistics
Matches: 139, Mismatches: 30, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
58 41 0.29
62 3 0.02
64 5 0.04
65 81 0.58
66 9 0.06
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (63 bp):
GTTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAAATTGAAAC
Found at i:40178 original size:110 final size:110
Alignment explanation
Indices: 39980--40237 Score: 303
Period size: 110 Copynumber: 2.4 Consensus size: 110
39970 GCTTCCCAGT
* * * * *
39980 TTCAGAGCCAATTTCAACTTCACATCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTTA
1 TTCAGAGCCAATTTCAACGTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* *
40045 CAACGAAGGGGCGACTGATTGTCAACAAATAACTTTC-CAGTTTCA
66 CAACGAAGGGGCGACTGACTGTCAACAAACAA-TTTCACAGTTTCA
* * *
40090 TTCAGAGTCAATTTCAACGTCACAGCGAATGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACGTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * * *
40155 CAGCGAAGGGGCGGCTGGCTGTCAATAAACAATTTCACAG-TTC-
66 CAACGAAGGGGCGACTGACTGTCAACAAACAATTTCACAGTTTCA
* * *
40198 --CAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACGTCACAG-CGAAGGATATTGAACTC
40238 GGAATAATAC
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
105 1 0.01
106 33 0.26
109 7 0.06
110 86 0.68
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACGTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGACTGTCAACAAACAATTTCACAGTTTCA
Found at i:41611 original size:14 final size:15
Alignment explanation
Indices: 41592--41621 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41582 ATTCCTTTTT
41592 TTATTTATAT-TATA
1 TTATTTATATATATA
41606 TTATTTATATATATA
1 TTATTTATATATATA
41621 T
1 T
41622 ATATATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTATATATATA
Found at i:41713 original size:2 final size:2
Alignment explanation
Indices: 41706--41738 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41696 TTTATACATT
41706 TA 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 TA T
41739 TCTTAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41946 original size:18 final size:18
Alignment explanation
Indices: 41919--41953 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41909 TTTTTATTCA
41919 TTTTTAATTTCTTTTACC
1 TTTTTAATTTCTTTTACC
* *
41937 TTTTTTATTTTTTTTAC
1 TTTTTAATTTCTTTTAC
41954 TCCATTAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTAATTTCTTTTACC
Found at i:42035 original size:11 final size:11
Alignment explanation
Indices: 42019--42071 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
42009 TTGTTTATTT
42019 TTATTATTTTA
1 TTATTATTTTA
42030 TTATTATTTTA
1 TTATTATTTTA
*
42041 TTTTTCATTTT-
1 TTATT-ATTTTA
* *
42052 TTCTTGTTTTA
1 TTATTATTTTA
42063 TTTATTATT
1 -TTATTATT
42072 CTCACGTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 4 0.12
11 19 0.56
12 11 0.32
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:45336 original size:43 final size:43
Alignment explanation
Indices: 45288--45377 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
45278 TTCGCTCGTC
** *
45288 TAATTATTATTATTTTTTTAAAATCATATTTACCATTACGTTT
1 TAATTATTATTATTTTTAAAAAATCATATTTAACATTACGTTT
45331 TAATTATTATTATTTTTAAAAAATCATATTTAACATTACGTTT
1 TAATTATTATTATTTTTAAAAAATCATATTTAACATTACGTTT
45374 TAAT
1 TAAT
45378 ATCTCTTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (43 bp):
TAATTATTATTATTTTTAAAAAATCATATTTAACATTACGTTT
Found at i:47587 original size:8 final size:8
Alignment explanation
Indices: 47574--47612 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
47564 TAATAAACTT
47574 AAATAAAA
1 AAATAAAA
47582 AAATAAAA
1 AAATAAAA
*
47590 CAATAAAA
1 AAATAAAA
47598 AAAT-AAA
1 AAATAAAA
47605 AAATAAAA
1 AAATAAAA
47613 TAAACCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATAAAA
Found at i:47599 original size:15 final size:15
Alignment explanation
Indices: 47574--47612 Score: 69
Period size: 16 Copynumber: 2.5 Consensus size: 15
47564 TAATAAACTT
47574 AAATAAAAAAATAAA
1 AAATAAAAAAATAAA
47589 ACAATAAAAAAATAAA
1 A-AATAAAAAAATAAA
47605 AAATAAAA
1 AAATAAAA
47613 TAAACCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAAAAATAAA
Found at i:49670 original size:233 final size:233
Alignment explanation
Indices: 49263--49735 Score: 811
Period size: 233 Copynumber: 2.0 Consensus size: 233
49253 AAGTCGTAGG
* * * * *
49263 TTCTTCTCATCGTGATTTTTCTTCTGGAAATGTTGATCCCTTTAGTGAGGTGTTGCTGATTCGAA
1 TTCTTCTCATCGTGATTTTTCTTCTGGAAATATTAATCCCTTAAGTGAGGTGTTACTGATTAGAA
*
49328 GTGTTGTGAATTTAGCAATAGGTCAAACAAGTTATTCTCATTATGAACTTCTTCTCCCCCTGTCG
66 GTGTTGTGAATCTAGCAATAGGTCAAACAAGTTATTCTCATTATGAACTTCTTCTCCCCCTGTCG
*
49393 GATGAGTTTTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTG
131 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTG
49458 ATTCAAAATGTCGTGAATCGAGTGATAGGTCAAACAAA
196 ATTCAAAATGTCGTGAATCGAGTGATAGGTCAAACAAA
*
49496 TTCTTCTCATCGTGATTTTTCTTCTGGAAATATTAATCCGTTAAGTGAGGTGTTACTGATTAGAA
1 TTCTTCTCATCGTGATTTTTCTTCTGGAAATATTAATCCCTTAAGTGAGGTGTTACTGATTAGAA
* * *
49561 GTGTTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCG
66 GTGTTGTGAATCTAGCAATAGGTCAAACAAGTTATTCTCATTATGAACTTCTTCTCCCCCTGTCG
**
49626 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGTGAGGCGTCACTG
131 GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTG
* *
49691 ATTCGAAATGTCGTGAATCGAGTGATAGGTCAAACAAG
196 ATTCAAAATGTCGTGAATCGAGTGATAGGTCAAACAAA
49729 TTCTTCT
1 TTCTTCT
49736 TATTAAGAAC
Statistics
Matches: 225, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
233 225 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (233 bp):
TTCTTCTCATCGTGATTTTTCTTCTGGAAATATTAATCCCTTAAGTGAGGTGTTACTGATTAGAA
GTGTTGTGAATCTAGCAATAGGTCAAACAAGTTATTCTCATTATGAACTTCTTCTCCCCCTGTCG
GATGAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGCAAGGCGTCACTG
ATTCAAAATGTCGTGAATCGAGTGATAGGTCAAACAAA
Found at i:50079 original size:136 final size:136
Alignment explanation
Indices: 49566--50210 Score: 835
Period size: 136 Copynumber: 4.7 Consensus size: 136
49556 TAGAAGTGTT
* *
49566 GTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
1 GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
* * * *
49631 GTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGTGAGGCGTCACTGATTCG
66 GTTCTTCTCATTATGAACTCTCCATTTG-AAATGTTAATCCCTCAAGCGAGGCATCACTGATTCA
*
49696 AAATGTC
130 AAATATC
* * * * * *
49703 GTGAATCGAGTGATAGGTCAAACAAGTTCTTCTTATTAAGAACTTCCTCTCCCTCTGTCGGAGGA
1 GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
* * * * * **
49768 GTTCCTCTCATTATGAACTCTCCATTGGAAATATCAATCCCTCAGGCGAGGCATTGCTGATTCAA
66 GTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCATCACTGATTCAA
*
49833 AATATT
131 AATATC
* *
49839 GTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCA-TATGAACCTCTTCTCCCTCTGTCGGATGA
1 GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
* * **
49903 GTTTTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTAAAGTAAGGCATCACTGATTCAA
66 GTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCATCACTGATTCAA
49968 AATATC
131 AATATC
* * * * *
49974 GTGAATCAAGCGATAGGTCGAACAAGCTCTTCTCATTATAAACTTCTTCTCCCACTTTCGGATGA
1 GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
* * **
50039 GTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCGTCACTAATTTGA
66 GTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCATCACTGATTCAA
*
50104 AATGTC
131 AATATC
* ** * * * * *
50110 GTGAATCGAGTGATAAATTGAACAAGCTATTCTCATTATGAACTTCTTTTCCCCTTTGTCTGG-T
1 GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCCTCTGTC-GGAT
*
50174 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTT
64 GAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTT
50211 GATCAGTTCA
Statistics
Matches: 438, Mismatches: 67, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
135 116 0.26
136 194 0.44
137 126 0.29
138 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (136 bp):
GTGAATCGAGCGATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGA
GTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCATCACTGATTCAA
AATATC
Found at i:50080 original size:271 final size:272
Alignment explanation
Indices: 49564--50210 Score: 868
Period size: 271 Copynumber: 2.4 Consensus size: 272
49554 ATTAGAAGTG
*
49564 TTGTGAATCTAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGAT
1 TTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGAT
* * * *
49629 GAGTTCTTCTCATTATGAACTCTCCATTTGAAAATGTCAATCCCTCAAGTGAGGCGTCACTGATT
66 GAGTTCTTCTCATTATGAACTCTCCATTTG-AAATGTTAATCCCTAAAGTAAGGCATCACTGATT
* * * * * * *
49694 CGAAATGTCGTGAATCGAGTGATAGGTCAAACAAGTTCTTCTTATTAAGAACTTCCTCTCCCTCT
130 CAAAATATCGTGAATCAAGCGATAGGTCAAACAAGCTCTTCTCATTAAGAACTTCCTCTCCCACT
* **
49759 GTCGGAGGAGTTCCTCTCATTATGAACTCTCCATTGGAAATATCAATCCCTCAGGCGAGGCATTG
195 GTCGGAGGAGTTCCTCTCATTATGAACTCTCCATTGGAAATATCAATCCCTCAAGCGAGGCATCA
*
49824 CTGATTCAAAATA
260 CTAATTCAAAATA
*
49837 TTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCA-TATGAACCTCTTCTCCCTCTGTCGGAT
1 TTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGAT
*
49901 GAGTTTTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTAAAGTAAGGCATCACTGATTC
66 GAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTAAAGTAAGGCATCACTGATTC
* *
49966 AAAATATCGTGAATCAAGCGATAGGTCGAACAAGCTCTTCTCATTATA-AACTTCTTCTCCCACT
131 AAAATATCGTGAATCAAGCGATAGGTCAAACAAGCTCTTCTCATTA-AGAACTTCCTCTCCCACT
* * * * * * *
50030 TTCGGATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTCAAGCGAGGCGTCA
195 GTCGGAGGAGTTCCTCTCATTATGAACTCTCCATTGGAAATATCAATCCCTCAAGCGAGGCATCA
** *
50095 CTAATTTGAAATG
260 CTAATTCAAAATA
* ** ** * * * * *
50108 TCGTGAATCGAGTGATAAATTGAACAAGCTATTCTCATTATGAACTTCTTTTCCCCTTTGTCTGG
1 TTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCCTCTGTC-GG
*
50173 -TGAGTTCTTCTCATTATGAACTCTCCATTGGAAATGTT
64 ATGAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTT
50211 GATCAGTTCA
Statistics
Matches: 327, Mismatches: 43, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
271 177 0.54
272 68 0.21
273 80 0.24
274 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (272 bp):
TTGTGAATCGAGCAATAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGAT
GAGTTCTTCTCATTATGAACTCTCCATTTGAAATGTTAATCCCTAAAGTAAGGCATCACTGATTC
AAAATATCGTGAATCAAGCGATAGGTCAAACAAGCTCTTCTCATTAAGAACTTCCTCTCCCACTG
TCGGAGGAGTTCCTCTCATTATGAACTCTCCATTGGAAATATCAATCCCTCAAGCGAGGCATCAC
TAATTCAAAATA
Found at i:51169 original size:14 final size:15
Alignment explanation
Indices: 51145--51182 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
51135 AACCTCTCAT
*
51145 TTTCTTTTCTTTTTC
1 TTTCTTTTCTTTTTA
51160 TTTC-TTTCTTTTTA
1 TTTCTTTTCTTTTTA
51174 TTTCATTTT
1 TTTC-TTTT
51183 TCCTTTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 13 0.65
15 4 0.20
16 3 0.15
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTCTTTTTA
Found at i:51177 original size:24 final size:24
Alignment explanation
Indices: 51150--51197 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
51140 CTCATTTTCT
* *
51150 TTTC-TTTTTCTTTCTTTCTTTTTA
1 TTTCATTTTTCCTT-TTTCCTTTTA
51174 TTTCATTTTTCCTTTTTCCTTTTA
1 TTTCATTTTTCCTTTTTCCTTTTA
51198 GGCGTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTCATTTTTCCTTTTTCCTTTTA
Found at i:68864 original size:24 final size:24
Alignment explanation
Indices: 68837--68888 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
68827 TACCCTGGCG
68837 GCCAACCTCTCTCGAGGACTGACC
1 GCCAACCTCTCTCGAGGACTGACC
* * *
68861 GCCAGCCTTTCTCGAGGCCTGACC
1 GCCAACCTCTCTCGAGGACTGACC
68885 GCCA
1 GCCA
68889 TTCTGCTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.17, C:0.42, G:0.23, T:0.17
Consensus pattern (24 bp):
GCCAACCTCTCTCGAGGACTGACC
Found at i:71913 original size:34 final size:33
Alignment explanation
Indices: 71846--71916 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
71836 CTTTACAAAC
*
71846 TCCCTAGTTTTTCACGGGCTAAACTAGAACATT
1 TCCCTAGTTTTACACGGGCTAAACTAGAACATT
* * * *
71879 TCCCTAGCTTTTACACTGGCTTAGCTATAACATT
1 TCCCTAG-TTTTACACGGGCTAAACTAGAACATT
71913 TCCC
1 TCCC
71917 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGCTAAACTAGAACATT
Found at i:72604 original size:18 final size:18
Alignment explanation
Indices: 72557--72614 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 18
72547 ATGTTTAATG
72557 AAAAAGATA-CTAATTGTT
1 AAAAAGATATC-AATTGTT
72575 AATAAAAGGATATCAATTGTT
1 -A-AAAA-GATATCAATTGTT
72596 AAAAAGATATCAATTGTT
1 AAAAAGATATCAATTGTT
72614 A
1 A
72615 CCAATTATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 14 0.39
19 5 0.14
20 5 0.14
21 11 0.31
22 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (18 bp):
AAAAAGATATCAATTGTT
Found at i:74688 original size:34 final size:33
Alignment explanation
Indices: 74636--74706 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 33
74626 CTTTACAAAC
*
74636 TCCCTAGTTTTTCACGGGC-TAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGCTTAAA-TAGAACCTT
74669 TCCCTAGCTTTTACACGGGCTTAAATAGAACCTT
1 TCCCTAG-TTTTACACGGGCTTAAATAGAACCTT
74703 TCCC
1 TCCC
74707 CTTTATAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
33 7 0.20
34 24 0.69
35 4 0.11
ACGTcount: A:0.24, C:0.30, G:0.14, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGCTTAAATAGAACCTT
Found at i:75027 original size:22 final size:22
Alignment explanation
Indices: 74986--75027 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
74976 TGCCCATAAC
*
74986 AGGGAGTATCGGTATCCCTTCA
1 AGGGAGTATCGGTATACCTTCA
75008 AGGG-GTATCGGTATTACCTT
1 AGGGAGTATCGGTA-TACCTT
75028 TTTTAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.31
Consensus pattern (22 bp):
AGGGAGTATCGGTATACCTTCA
Found at i:76203 original size:22 final size:20
Alignment explanation
Indices: 76160--76206 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
76150 TAGTCACATT
*
76160 AGAATAATTCATAAAATCAA
1 AGAATAATTCAAAAAATCAA
*
76180 AGAATAATTAGCAAAAAATTAA
1 AGAATAATT--CAAAAAATCAA
76202 AGAAT
1 AGAAT
76207 CAGATGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 9 0.39
22 14 0.61
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (20 bp):
AGAATAATTCAAAAAATCAA
Found at i:82129 original size:35 final size:35
Alignment explanation
Indices: 82083--82156 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
82073 CTTTTTCAAT
82083 TTTACAATCTTTCATACCAAGGTCTAGGAGCTTGC
1 TTTACAATCTTTCATACCAAGGTCTAGGAGCTTGC
82118 TTTACAATCTTTCATACCAAGGTCTAGGAGCTTGC
1 TTTACAATCTTTCATACCAAGGTCTAGGAGCTTGC
82153 TTTA
1 TTTA
82157 AACCATAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (35 bp):
TTTACAATCTTTCATACCAAGGTCTAGGAGCTTGC
Found at i:87007 original size:2 final size:2
Alignment explanation
Indices: 87000--87085 Score: 172
Period size: 2 Copynumber: 43.0 Consensus size: 2
86990 TGAATCATTG
87000 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
87084 AT
1 AT
87086 GTGTGTGTGT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 84 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:87090 original size:2 final size:2
Alignment explanation
Indices: 87085--87116 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
87075 TATATATATA
87085 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
87117 AACATAAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:88213 original size:23 final size:23
Alignment explanation
Indices: 88145--88205 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
88135 ACATTTTATA
* *
88145 TGGCAATTTGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
88168 CGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
88191 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
88206 TTTATACGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:93215 original size:19 final size:19
Alignment explanation
Indices: 93191--93300 Score: 85
Period size: 19 Copynumber: 5.5 Consensus size: 19
93181 TTTCTATTTC
93191 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
93210 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
93231 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
* * **
93251 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
*
93272 GTTGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
93292 TCGTTGCGA
1 TCGTTGCGA
93301 AAATTCGTTG
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
19 28 0.42
20 10 0.15
21 10 0.15
22 19 0.28
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:93236 original size:41 final size:41
Alignment explanation
Indices: 93191--93300 Score: 211
Period size: 41 Copynumber: 2.7 Consensus size: 41
93181 TTTCTATTTC
93191 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
93232 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
*
93273 TTGTTGCGATTTTCCAAATTCGTTGCGA
1 TCGTTGCGATTTTCCAAATTCGTTGCGA
93301 AAATTCGTTG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (41 bp):
TCGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTG
Found at i:93238 original size:22 final size:22
Alignment explanation
Indices: 93210--93282 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
93200 TTTTCCAAAT
93210 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
* * **
93232 TCGTTGCGAT--TTTCCAAAT-
1 TCGTTGCGATAGTCTACAGTTG
93251 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
93273 TTGTTGCGAT
1 TCGTTGCGAT
93283 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.40
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:93903 original size:5 final size:5
Alignment explanation
Indices: 93893--93941 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
93883 CCGCCGCCGT
*
93893 TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTA TCGTC TCGT
1 TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGTC TCGT
93942 GGTCGTGGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.02, C:0.37, G:0.20, T:0.41
Consensus pattern (5 bp):
TCGTC
Found at i:95432 original size:25 final size:25
Alignment explanation
Indices: 95386--95447 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
95376 GCATAAAGTG
95386 TAAAATACTATA---TTTTTATTAA
1 TAAAATACTATATTTTTTTTATTAA
95408 TAAAATACTATATTTTTTTTATTAA
1 TAAAATACTATATTTTTTTTATTAA
*
95433 TAAAATACTACATTT
1 TAAAATACTATATTT
95448 AAACACTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 12 0.33
25 24 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (25 bp):
TAAAATACTATATTTTTTTTATTAA
Found at i:95471 original size:2 final size:2
Alignment explanation
Indices: 95464--95491 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
95454 TTTAAAACTT
95464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
95492 ATGAGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:107073 original size:4 final size:4
Alignment explanation
Indices: 107064--107104 Score: 66
Period size: 4 Copynumber: 10.2 Consensus size: 4
107054 AGGAAAGGTA
107064 ACAT ACAT ACAT ACAT ACAT ACAT A-ATT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACA-T ACAT ACAT ACAT A
107105 TAAATCATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 1 0.03
4 33 0.94
5 1 0.03
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:114983 original size:65 final size:66
Alignment explanation
Indices: 114876--115007 Score: 212
Period size: 65 Copynumber: 2.0 Consensus size: 66
114866 AGTTATTTTA
114876 ACAAATAATTACTTTTAAAAAAAATTAAAATAAAAATCAACATGCAGCAACATCTTAGGATATCA
1 ACAAATAATTACTTTTAAAAAAAATTAAAATAAAAATCAACATGCAGCAACATCTTAGGATATCA
114941 T
66 T
* * * * *
114942 ACAAATAATTA-TTTTTAAAAAAATTACAATAAAAATTAACATGCAGCAACATCTTATGCTATCA
1 ACAAATAATTACTTTTAAAAAAAATTAAAATAAAAATCAACATGCAGCAACATCTTAGGATATCA
115006 T
66 T
115007 A
1 A
115008 TGATAAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 50 0.82
66 11 0.18
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.30
Consensus pattern (66 bp):
ACAAATAATTACTTTTAAAAAAAATTAAAATAAAAATCAACATGCAGCAACATCTTAGGATATCA
T
Found at i:116656 original size:3 final size:3
Alignment explanation
Indices: 116648--116727 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
116638 ATATTATAAA
* *
116648 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
116696 TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
116728 AATATATTAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:116735 original size:9 final size:10
Alignment explanation
Indices: 116723--116761 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
116713 TTATTATTAT
116723 TATTAAAT-A
1 TATTAAATAA
116732 TATTAAATACA
1 TATTAAATA-A
116743 TATATAAATAA
1 TAT-TAAATAA
116754 TATTAAAT
1 TATTAAAT
116762 TACAAGCCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 5 0.19
11 8 0.30
12 6 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
TATTAAATAA
Found at i:116868 original size:16 final size:16
Alignment explanation
Indices: 116847--116915 Score: 131
Period size: 16 Copynumber: 4.4 Consensus size: 16
116837 CCTAATCCCT
116847 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
116863 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
116879 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
116895 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
116911 A-CCGC
1 AGCCGC
116916 TGCCACGTCC
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
15 4 0.08
16 49 0.92
ACGTcount: A:0.07, C:0.57, G:0.19, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:118855 original size:29 final size:30
Alignment explanation
Indices: 118781--118856 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 30
118771 AGATTAAAAA
* * *
118781 TTCAT-ATATTTAATTTTTAATTCTTTCTT
1 TTCATAATATTTAATATTTAATTCATTATT
* * *
118810 TTCAAAAT-TTTTATATTTACTT-ATTATT
1 TTCATAATATTTAATATTTAATTCATTATT
118838 TTCATAATATTTAATATTT
1 TTCATAATATTTAATATTT
118857 TATTTGCAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 11 0.30
29 24 0.65
30 2 0.05
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (30 bp):
TTCATAATATTTAATATTTAATTCATTATT
Found at i:129519 original size:7 final size:7
Alignment explanation
Indices: 129507--129569 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
129497 ATTATGCTTG
129507 AAGAAAA
1 AAGAAAA
129514 AAG--AA
1 AAGAAAA
129519 AA-AAAA
1 AAGAAAA
*
129525 ACGAAAA
1 AAGAAAA
129532 AAGAAAA
1 AAGAAAA
129539 AA-AAACGA
1 AAGAAA--A
129547 AA-AAAA
1 AAGAAAA
129553 AAGAAAA
1 AAGAAAA
*
129560 AAGGAAA
1 AAGAAAA
129567 AAG
1 AAG
129570 GGGGGTCAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
5 4 0.09
6 9 0.19
7 28 0.60
8 6 0.13
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:129530 original size:11 final size:10
Alignment explanation
Indices: 129510--129561 Score: 65
Period size: 10 Copynumber: 5.3 Consensus size: 10
129500 ATGCTTGAAG
129510 AAAAAAGAAA
1 AAAAAAGAAA
129520 AAAAAACG---
1 AAAAAA-GAAA
129528 AAAAAAGAAA
1 AAAAAAGAAA
129538 AAAAAACGAAA
1 AAAAAA-GAAA
129549 AAAAAAGAAA
1 AAAAAAGAAA
129559 AAA
1 AAA
129562 GGAAAAAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
7 1 0.03
8 6 0.16
10 19 0.51
11 11 0.30
ACGTcount: A:0.87, C:0.04, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:129532 original size:18 final size:18
Alignment explanation
Indices: 129509--129568 Score: 95
Period size: 18 Copynumber: 3.3 Consensus size: 18
129499 TATGCTTGAA
129509 GAAAAAAGAAAAAAAAAC
1 GAAAAAAGAAAAAAAAAC
129527 GAAAAAAGAAAAAAAAAC
1 GAAAAAAGAAAAAAAAAC
*
129545 GAAAAAA-AAAGAAAAAAG
1 GAAAAAAGAAA-AAAAAAC
129563 GAAAAA
1 GAAAAA
129569 GGGGGGTCAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 3 0.08
18 37 0.93
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (18 bp):
GAAAAAAGAAAAAAAAAC
Found at i:129549 original size:29 final size:27
Alignment explanation
Indices: 129510--129568 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
129500 ATGCTTGAAG
129510 AAAAAAGAAAAAAAAACGAAAAAAGAAA
1 AAAAAAGAAAAAAAAA-GAAAAAAGAAA
*
129538 AAAAAACGAAAAAAAAAGAAAAAAGGAA
1 AAAAAA-GAAAAAAAAAGAAAAAAGAAA
129566 AAA
1 AAA
129569 GGGGGGTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAAAAAAGAAAAAAGAAA
Found at i:131111 original size:83 final size:83
Alignment explanation
Indices: 130691--131104 Score: 783
Period size: 83 Copynumber: 5.0 Consensus size: 83
130681 TGTAATGTAT
*
130691 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAA
1 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
130756 TTTGGAAGATGAATTTGC
66 TTTGGAAGATGAATTTGC
130774 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
130839 TTTGGAAGATGAATTTGC
66 TTTGGAAGATGAATTTGC
130857 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
1 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
130922 TTTGGAAGATGAATTTGC
66 TTTGGAAGATGAATTTGC
*
130940 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAGAACCAATCATTGAA
1 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
*
131005 TTTGGAAGATGAATGTGC
66 TTTGGAAGATGAATTTGC
* *
131023 TCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGACAGAACCAATCATTGAA
1 TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
131088 TTTGGAAGATGAATTTG
66 TTTGGAAGATGAATTTG
131105 TTCATAGTAG
Statistics
Matches: 324, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 324 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (83 bp):
TAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAA
TTTGGAAGATGAATTTGC
Found at i:132273 original size:113 final size:112
Alignment explanation
Indices: 131892--132642 Score: 914
Period size: 113 Copynumber: 6.7 Consensus size: 112
131882 CAAAGATTCA
* * *
131892 AATCTATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAA-AACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
131956 AGGAAGAAGAAG-TCATAATGAGAAGAACTTGTTCAACCCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CCTTTTA-CTG
* * * *
132004 AATTCATCAATTG-TGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
132068 A-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTA-CTG
*
132112 AATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
132177 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TG
*
132225 AATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
132290 AGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACT-G
* * *
132338 AATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
132402 AGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGCAT-
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTAC-TG
* * * * * *
132449 AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTCTAGAGAAAGTTCATAATGAGAAGAA
1 AA-TCCAT--C------A-TTTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA
* * * * *
132514 CTCATCTGAAGAAGGAAGAAAAAGTTCATAAT--GAAGAGCTTATTCAACCTTTTGCTC
54 CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTG
* * * * *
132571 AATCCATCA-CTGATGGAGCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
132635 AGGAAGAA
66 AGGAAGAA
132643 CTCATCTGAA
Statistics
Matches: 567, Mismatches: 48, Indels: 51
0.85 0.07 0.08
Matches are distributed among these distances:
108 19 0.03
109 111 0.20
110 25 0.04
111 39 0.07
112 135 0.24
113 142 0.25
114 1 0.00
119 1 0.00
120 1 0.00
121 8 0.01
122 22 0.04
123 14 0.02
124 49 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACTG
Found at i:132435 original size:112 final size:113
Alignment explanation
Indices: 131889--132642 Score: 899
Period size: 112 Copynumber: 6.7 Consensus size: 113
131879 TAGCAAAGAT
* * * *
131889 TCAAATCTATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATAAGAA-AACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
131953 AGAAGGAAGAAGAAG-TCATAATGAGAAGAACTTGTTCAACCCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CCTTTTGC
* * * * *
132001 -CTGAATTCATCAATTG-TGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TC-AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* **
132064 AAGAA-G--GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTACC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
132110 T-GAATCCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
132174 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * *
132222 AT-GAATTCATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 -TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* *
132286 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* *
132335 TCAAATCCATCACTTGATGGAGCAGCTTTTCCAGAG-AAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
132399 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * * *
132447 AT-AATTCTATCACAGAAGGAGATAGATTAGCATCAGCCTTTCTAGAGAAAGTTCATAATGAGAA
1 -TCAAATCCATCAC---------TTGA-T-GGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAA
* * *
132511 GAACTCATCTGAAGAAGGAAGAAAAAGTTCATAAT--GAAGAGCTTATTCAACCTTTTGC
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * *
132569 TC-AATCCATCAC-TGATGGAGCAACTTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
132632 AGAAGGAAGAA
66 AGAAGGAAGAA
132643 CTCATCTGAA
Statistics
Matches: 565, Mismatches: 53, Indels: 51
0.84 0.08 0.08
Matches are distributed among these distances:
108 12 0.02
109 115 0.20
110 25 0.04
111 38 0.07
112 143 0.25
113 137 0.24
121 12 0.02
122 20 0.04
123 14 0.02
124 49 0.09
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:132642 original size:20 final size:19
Alignment explanation
Indices: 132615--132661 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
132605 AGTTCATAAT
132615 AAGAAGAACTCATCTGAAG
1 AAGAAGAACTCATCTGAAG
*
132634 AAGGAAGAACTCATCTGAAT
1 AA-GAAGAACTCATCTGAAG
132654 AAGAAGAA
1 AAGAAGAA
132662 TTTATTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (19 bp):
AAGAAGAACTCATCTGAAG
Found at i:132799 original size:3 final size:3
Alignment explanation
Indices: 132791--132868 Score: 99
Period size: 3 Copynumber: 26.7 Consensus size: 3
132781 CATATTATAA
* *
132791 TAT TAT TAT TAT TA- TATT TAT TAT TAT TAC TAT AAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
132835 TAT TA- TAT TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
132869 AATATATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
2 6 0.09
3 57 0.88
4 2 0.03
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:132888 original size:46 final size:46
Alignment explanation
Indices: 132783--132888 Score: 123
Period size: 46 Copynumber: 2.3 Consensus size: 46
132773 TTTTTACCCA
132783 TATTATAAT-AT-TATTATTATTATATTTATTATTATTACTATAAT
1 TATTATAATAATATATTATTATTATATTTATTATTATTACTATAAT
* * *
132827 TATTATATTATTATATTATTATTATCA-TTATTATTATTATTA-AAT
1 TATTATAATAATATATTATTATTAT-ATTTATTATTATTACTATAAT
132872 ATATTA-AATACATATAT
1 -TATTATAATA-ATATAT
132889 AATAATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
44 8 0.15
45 7 0.13
46 36 0.69
47 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (46 bp):
TATTATAATAATATATTATTATTATATTTATTATTATTACTATAAT
Found at i:133008 original size:16 final size:16
Alignment explanation
Indices: 132987--133023 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
132977 CCTAATCCCT
132987 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
133003 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
133019 A-CCGC
1 AGCCGC
133024 TGCCACGTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.08, C:0.57, G:0.19, T:0.16
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:141889 original size:19 final size:17
Alignment explanation
Indices: 141855--141906 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
141845 CTTTCCTTTC
*
141855 TCTTTTTTTTTGTTTCGAA
1 TCTTCTTTTTT-TTTC-AA
*
141874 TCTCTCTTTTTTTTTCTA
1 TCT-TCTTTTTTTTTCAA
141892 TCTTCTGTTTTTTTT
1 TCTTCT-TTTTTTTT
141907 TTGTTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 3 0.10
18 12 0.41
19 7 0.24
20 7 0.24
ACGTcount: A:0.06, C:0.15, G:0.06, T:0.73
Consensus pattern (17 bp):
TCTTCTTTTTTTTTCAA
Found at i:141915 original size:18 final size:18
Alignment explanation
Indices: 141880--141922 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
141870 CGAATCTCTC
141880 TTTTTTTTTCTATCTTCT
1 TTTTTTTTTCTATCTTCT
* *
141898 GTTTTTTTTT-TGTTTTCT
1 -TTTTTTTTTCTATCTTCT
141916 TTTTTTT
1 TTTTTTT
141923 CTTTTCTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 6 0.27
19 9 0.41
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (18 bp):
TTTTTTTTTCTATCTTCT
Found at i:142416 original size:3 final size:3
Alignment explanation
Indices: 142408--142471 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
142398 CAAAAAATTG
* * **
142408 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
142452 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
142472 CGAAAAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:142878 original size:46 final size:46
Alignment explanation
Indices: 142671--142886 Score: 184
Period size: 46 Copynumber: 4.8 Consensus size: 46
142661 TCTACGGGTG
*
142671 ACACGGCTCCTACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGTTC-TGGCCATCTAAAGGTGATA
* * ** * *
142718 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
1 ACACGGCTCCTACGTGATGAGGA-GTTCTGGCCATCTAAAGGTGATA
* * * *
142761 GCACGGCTCCTACGTGATGAGGAGATCTGG---TCT---GGGGAATG
1 ACACGGCTCCTACGTGATGAGGAGTTCTGGCCATCTAAAGGTG-ATA
* *
142802 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAGTTCTGGCCATCTAAAGGTGATA
* *
142848 ACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCTAAA
1 ACACGGCTCCTACGTGATGAGGA-GTTCTGGCCATCTAAA
142887 AGTTATGGTT
Statistics
Matches: 136, Mismatches: 21, Indels: 25
0.75 0.12 0.14
Matches are distributed among these distances:
38 2 0.01
40 3 0.02
41 28 0.21
42 1 0.01
43 26 0.19
44 3 0.02
45 4 0.03
46 42 0.31
47 26 0.19
48 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (46 bp):
ACACGGCTCCTACGTGATGAGGAGTTCTGGCCATCTAAAGGTGATA
Found at i:143127 original size:69 final size:67
Alignment explanation
Indices: 143040--143230 Score: 305
Period size: 66 Copynumber: 2.8 Consensus size: 67
143030 TGTCTCAAAT
* **
143040 GAGACAAAATTTTGTTTCCAAAGAAA-CAGACTCAAAGATTTTTTTTTTTCAAAAGAAATTATCT
1 GAGACAAAATTTTATTTCCAAAGAAACCA-ACTCAAAGA--TTTTTTTTTCAAAAGAAAGCATCT
143104 TAAGA
63 TAAGA
*
143109 GAGACAAAATTTTATTTCCAAAGAAACCAACTCAAAGATTTTTGTTTCAAAAG-AAGCATCTTAA
1 GAGACAAAATTTTATTTCCAAAGAAACCAACTCAAAGATTTTTTTTTCAAAAGAAAGCATCTTAA
143173 GA
66 GA
143175 GAGACAAAATTTTATTTCCAAAGAAACCAACTCAAAGATTTTTTTTTCAAAAGAAA
1 GAGACAAAATTTTATTTCCAAAGAAACCAACTCAAAGATTTTTTTTTCAAAAGAAA
143231 CAATCTCAAA
Statistics
Matches: 115, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
66 63 0.55
67 16 0.14
69 34 0.30
70 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (67 bp):
GAGACAAAATTTTATTTCCAAAGAAACCAACTCAAAGATTTTTTTTTCAAAAGAAAGCATCTTAA
GA
Found at i:143230 original size:30 final size:30
Alignment explanation
Indices: 143184--143249 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
143174 AGAGACAAAA
* *
143184 TTTTATTTCCAAAGAAACCAA-CTCAAAGAT
1 TTTTTTTTCAAAAGAAA-CAATCTCAAAGAT
143214 TTTTTTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTTTTTCAAAAGAAACAATCTCAAAGAT
143244 TTTTTT
1 TTTTTT
143250 CACAAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.39
Consensus pattern (30 bp):
TTTTTTTTCAAAAGAAACAATCTCAAAGAT
Found at i:143310 original size:52 final size:53
Alignment explanation
Indices: 143235--143338 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
143225 AAGAAACAAT
143235 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
143289 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
143339 AAATAAATAG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:143420 original size:29 final size:28
Alignment explanation
Indices: 143349--143504 Score: 217
Period size: 28 Copynumber: 5.6 Consensus size: 28
143339 AAATAAATAG
* *
143349 ACTCAAAGATATTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
143376 ACTC-AAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
* *
143404 ACTCCAAGATTTTTATTCAAAAGGAGCAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAA
*
143433 ACTCAAAGATTTTTTTCAAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
* *
143461 ACTCAAAGATTTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAA
143489 ACTCAAAGATTTTTTT
1 ACTCAAAGATTTTTTT
143505 TTTCTCAAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
26 8 0.07
27 15 0.13
28 60 0.50
29 36 0.30
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAA
Found at i:143842 original size:36 final size:36
Alignment explanation
Indices: 143758--143861 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
143748 GAGAAAATGA
* * *
143758 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
143792 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
143828 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
143862 CGATTTCAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:144015 original size:105 final size:100
Alignment explanation
Indices: 143829--144060 Score: 259
Period size: 105 Copynumber: 2.3 Consensus size: 100
143819 TAGAGAAATT
* * **
143829 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAACGATTTCAAGTGAGATCAACTTTGTTTAATGT
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGT
* *
143894 GAAACAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 GAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
143930 GTCTCAAGCGAGACAAAATTTGTTTTGCAAGAAACAACAATCTAAGGTGAGATTAATTTTGTTT-
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AGAAACAA-AATC-AA-GTGAGATCAACTTTGTTTA
* * * * *
143994 TTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AT-GTGAAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
**
144035 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
144061 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
100 5 0.05
101 21 0.19
102 7 0.06
103 2 0.02
104 3 0.03
105 72 0.65
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAACAAAATCAAGTGAGATCAACTTTGTTTAATGTG
AAACAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:144162 original size:36 final size:36
Alignment explanation
Indices: 144080--144163 Score: 114
Period size: 36 Copynumber: 2.3 Consensus size: 36
144070 AAAATTTGTG
*
144080 GAAAAATGTCTCAAGCGAGACATAATATGTTTTAAA
1 GAAAAATGTCTCAAGCGAGACAAAATATGTTTTAAA
** * *
144116 GAAAGTTGTCTCAAGCGAGACAAAATTTGTTTTTAA
1 GAAAAATGTCTCAAGCGAGACAAAATATGTTTTAAA
*
144152 GAAAACTGTCTC
1 GAAAAATGTCTC
144164 TAGTGAAACG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (36 bp):
GAAAAATGTCTCAAGCGAGACAAAATATGTTTTAAA
Found at i:144521 original size:4 final size:4
Alignment explanation
Indices: 144512--144561 Score: 86
Period size: 4 Copynumber: 13.0 Consensus size: 4
144502 TTTATGTATC
144512 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
144558 ATGT
1 ATGT
144562 GTATACTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.05
4 42 0.95
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:145756 original size:12 final size:11
Alignment explanation
Indices: 145728--145765 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
145718 TCCTCTTTTG
*
145728 TTCTTTGCTTT
1 TTCTTTGATTT
145739 TTCTTTGATTT
1 TTCTTTGATTT
145750 TTGCTTTGATTT
1 TT-CTTTGATTT
145762 TTCT
1 TTCT
145766 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:145770 original size:18 final size:17
Alignment explanation
Indices: 145749--145795 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
145739 TTCTTTGATT
145749 TTTGCTTTGATTTTTCTC
1 TTTGCTTTGATTTTT-TC
145767 TTTGCTCTTTG-TTTTTTC
1 TTTG--CTTTGATTTTTTC
*
145785 TTTGGTTTGAT
1 TTTGCTTTGAT
145796 CTTTGCACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 4 0.16
17 1 0.04
18 10 0.40
19 5 0.20
20 5 0.20
ACGTcount: A:0.04, C:0.13, G:0.15, T:0.68
Consensus pattern (17 bp):
TTTGCTTTGATTTTTTC
Found at i:146467 original size:46 final size:45
Alignment explanation
Indices: 146375--146468 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
146365 ATAAATGCAG
* * * *
146375 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
146420 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
146466 TGT
1 TGT
146469 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:152102 original size:18 final size:20
Alignment explanation
Indices: 152066--152113 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
152056 CGAATCTCTC
152066 TTTTTTTTTGCTATCTTCTGT
1 TTTTTTTTTGCTATCTTCT-T
152087 TTTTTTTTTG-T-T-TTCTT
1 TTTTTTTTTGCTATCTTCTT
152104 TTTTTCTTTT
1 TTTTT-TTTT
152114 TCTCTGAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 1 0.04
20 1 0.04
21 10 0.38
ACGTcount: A:0.02, C:0.10, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTTTTTGCTATCTTCTT
Found at i:152604 original size:3 final size:3
Alignment explanation
Indices: 152596--152659 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
152586 CAAAAAATTG
* * **
152596 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
152640 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
152660 CGAAAAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:154767 original size:13 final size:13
Alignment explanation
Indices: 154732--154802 Score: 67
Period size: 13 Copynumber: 5.7 Consensus size: 13
154722 AAACGAACAC
*
154732 GAACGAACAAAAT
1 GAACGAACACAAT
*
154745 AAACGAACACAAT
1 GAACGAACACAAT
154758 GAACGAACAC---
1 GAACGAACACAAT
* *
154768 GAGCGAACAAAAT
1 GAACGAACACAAT
* *
154781 AAACGAATACAAT
1 GAACGAACACAAT
154794 GAACGAACA
1 GAACGAACA
154803 TAAACGAACA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
10 8 0.18
13 36 0.82
ACGTcount: A:0.58, C:0.20, G:0.15, T:0.07
Consensus pattern (13 bp):
GAACGAACACAAT
Found at i:154775 original size:36 final size:36
Alignment explanation
Indices: 154723--154813 Score: 146
Period size: 36 Copynumber: 2.5 Consensus size: 36
154713 TTAAATAATA
154723 AACGAACACGAACGAACAAAATAAACGAACACAATG
1 AACGAACACGAACGAACAAAATAAACGAACACAATG
* *
154759 AACGAACACGAGCGAACAAAATAAACGAATACAATG
1 AACGAACACGAACGAACAAAATAAACGAACACAATG
**
154795 AACGAACATAAACGAACAA
1 AACGAACACGAACGAACAA
154814 CACAAACACA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.58, C:0.21, G:0.14, T:0.07
Consensus pattern (36 bp):
AACGAACACGAACGAACAAAATAAACGAACACAATG
Found at i:155239 original size:46 final size:40
Alignment explanation
Indices: 155147--155249 Score: 161
Period size: 40 Copynumber: 2.6 Consensus size: 40
155137 AACGAGCCCT
* ***
155147 TTGTTCGTGTTCGTTCATTTAATTAAACGAATGTAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATC
155187 TTGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATC
1 TTGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATC
*
155227 TTGTTCATGTTCATTCATTTAAT
1 TTGTTCATGTTCGTTCATTTAAT
155250 AAATAAACGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (40 bp):
TTGTTCATGTTCGTTCATTTAATTAAACGAACACAAAATC
Found at i:156560 original size:17 final size:16
Alignment explanation
Indices: 156540--156587 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
156530 TATTTTGTTT
156540 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAA-TA
156557 TTTAAATTT-TTTAATA
1 TTT-AATTTATTTAATA
* *
156573 TTTTATTTAATTAAT
1 TTTAATTTATTTAAT
156588 TTTTTTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 10 0.37
17 8 0.30
18 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTAATTTATTTAATA
Found at i:158559 original size:64 final size:64
Alignment explanation
Indices: 158506--158669 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
158496 CGGTGCACCA
* *
158506 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGCGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
** * **
158570 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
** *
158635 AGAATGCATCGGTGCATGAAATGCATTCGATGTTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTT
158670 CAATTAATTC
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
64 32 0.37
65 54 0.63
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:158659 original size:17 final size:19
Alignment explanation
Indices: 158620--158666 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
158610 ATATTCAGAG
158620 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
158639 TGCATCGGTGCAT-GA-AA
1 TGCATCGATGCATGGAGAA
158656 TGCATTCGATG
1 TGCA-TCGATG
158667 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 12 0.48
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:158689 original size:65 final size:62
Alignment explanation
Indices: 158510--158716 Score: 204
Period size: 65 Copynumber: 3.2 Consensus size: 62
158500 GCACCAAGTG
* * *
158510 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGCGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGG--AG
158574 -
62 A
* *
158574 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
158638 A
62 A
* * * *
158639 TGCATCGGTGCATGAAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
158704 TGCATCGGTGCAT
1 TGCATCGATGCAT
158717 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
63 3 0.02
64 35 0.29
65 77 0.63
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:167164 original size:45 final size:45
Alignment explanation
Indices: 167100--167204 Score: 210
Period size: 45 Copynumber: 2.3 Consensus size: 45
167090 TGCACCAAGT
167100 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
167145 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
1 GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
167190 GTGCATCGATGCATG
1 GTGCATCGATGCATG
167205 GCTTGTGCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (45 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGC
Found at i:167279 original size:65 final size:65
Alignment explanation
Indices: 167146--167305 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 65
167136 ATAGCCTGCG
* * ****
167146 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
167210 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
167275 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
167306 CAATTAATTC
Statistics
Matches: 83, Mismatches: 12, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
64 27 0.33
65 56 0.67
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:167294 original size:17 final size:19
Alignment explanation
Indices: 167256--167302 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
167246 ATATTCAGAG
167256 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
167275 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
167292 TGCATTCGATG
1 TGCA-TCGATG
167303 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:174578 original size:43 final size:43
Alignment explanation
Indices: 174512--174696 Score: 230
Period size: 43 Copynumber: 4.3 Consensus size: 43
174502 CGGTTTGATG
* * *
174512 TTTAGCGGCGTTTTTC-CTACAAACGCCGCAATATATGTCGAGA
1 TTTAGCGGCGTTTTTCTC-ACAAACGCCACAATAGATGTTGAGA
* ** * *
174555 TTTAACGGCGTTTTTCTCACAAACGATACAATAGGTTTTGAGA
1 TTTAGCGGCGTTTTTCTCACAAACGCCACAATAGATGTTGAGA
*
174598 TTTAGCGGCGTTTTTATCACAAACGCCACAATAGATGTTGAGA
1 TTTAGCGGCGTTTTTCTCACAAACGCCACAATAGATGTTGAGA
* * *
174641 TTTAGCAGCATTTTTCTCACAAACGCCGCAATA-AGTGTTGAGA
1 TTTAGCGGCGTTTTTCTCACAAACGCCACAATAGA-TGTTGAGA
174684 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
174697 GTAACAAAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
42 1 0.01
43 118 0.98
44 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTCTCACAAACGCCACAATAGATGTTGAGA
Found at i:174782 original size:44 final size:45
Alignment explanation
Indices: 174728--174848 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 45
174718 TACCATATAT
* * *
174728 TTAGCGGCGTTTTTTTGATACAAACACCGCTAAAGGTCTGGTATA
1 TTAGCGGCGTTTTTTTGATACAAACGCCGCTAAAGGTATGGCATA
** * *
174773 -TAGCGGCGTTTTTAGGATACAAACGCCACTAAATGTATGGCATA
1 TTAGCGGCGTTTTTTTGATACAAACGCCGCTAAAGGTATGGCATA
174817 TTA-CGGCG-TTTTTT-ATTACAAACGCCGCTAAA
1 TTAGCGGCGTTTTTTTGA-TACAAACGCCGCTAAA
174849 TAACACAGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 19 0.30
44 42 0.66
45 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (45 bp):
TTAGCGGCGTTTTTTTGATACAAACGCCGCTAAAGGTATGGCATA
Found at i:175194 original size:21 final size:21
Alignment explanation
Indices: 175170--175220 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
175160 GTTGATATGA
175170 TGCTTCTCTCTGTGCTGCCGT
1 TGCTTCTCTCTGTGCTGCCGT
175191 TGCTTCTCTCTGTGCTGCCGT
1 TGCTTCTCTCTGTGCTGCCGT
*
175212 TGCTGCTCT
1 TGCTTCTCT
175221 GGCTGCTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.00, C:0.33, G:0.24, T:0.43
Consensus pattern (21 bp):
TGCTTCTCTCTGTGCTGCCGT
Found at i:175227 original size:21 final size:21
Alignment explanation
Indices: 175170--175242 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
175160 GTTGATATGA
* *
175170 TGCTTCTCTCTGTGCTGCCGT
1 TGCTGCTCTCGGTGCTGCCGT
* *
175191 TGCTTCTCTCTGTGCTGCCGT
1 TGCTGCTCTCGGTGCTGCCGT
* **
175212 TGCTGCTCT-GGCTGCTTCCAC
1 TGCTGCTCTCGG-TGCTGCCGT
175233 TGCTGCTCTC
1 TGCTGCTCTC
175243 TCTATTTCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.98
ACGTcount: A:0.01, C:0.36, G:0.23, T:0.40
Consensus pattern (21 bp):
TGCTGCTCTCGGTGCTGCCGT
Found at i:180818 original size:23 final size:25
Alignment explanation
Indices: 180781--180828 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
180771 TTTTCAGAAG
180781 TTATTATTTTCCTATTCGAAAGCAA
1 TTATTATTTTCCTATTCGAAAGCAA
180806 TTATT-TTTT-CTATTCGAAAGCAA
1 TTATTATTTTCCTATTCGAAAGCAA
180829 AAAACACTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 14 0.61
24 4 0.17
25 5 0.22
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (25 bp):
TTATTATTTTCCTATTCGAAAGCAA
Found at i:190354 original size:23 final size:23
Alignment explanation
Indices: 190302--190356 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
190292 ATGTAATGAC
190302 TCAAACCCAGAATGACCAAAACA
1 TCAAACCCAGAATGACCAAAACA
*** *
190325 AGTAACCC-GAGATGACCCAAACA
1 TCAAACCCAGA-ATGACCAAAACA
190348 TCAAACCCA
1 TCAAACCCA
190357 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 3
0.70 0.21 0.09
Matches are distributed among these distances:
22 2 0.09
23 21 0.91
ACGTcount: A:0.47, C:0.33, G:0.11, T:0.09
Consensus pattern (23 bp):
TCAAACCCAGAATGACCAAAACA
Found at i:195190 original size:14 final size:14
Alignment explanation
Indices: 195145--195192 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
195135 ATCTAGAGTA
195145 AATACAATATATTAT
1 AATA-AATATATTAT
**
195160 AGATAAATATAAGAT
1 A-ATAAATATATTAT
*
195175 AATAAATATTTTAT
1 AATAAATATATTAT
195189 AATA
1 AATA
195193 TTAAATAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 14 0.52
15 10 0.37
16 3 0.11
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (14 bp):
AATAAATATATTAT
Found at i:196913 original size:17 final size:17
Alignment explanation
Indices: 196887--196942 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
196877 ATATTTACAT
*
196887 ATAA-AATATTAAGTAAA
1 ATAATAATATTAA-AAAA
196904 A-AATAATATTAAAAAA
1 ATAATAATATTAAAAAA
* *
196920 ATAATAATAATAATAAA
1 ATAATAATATTAAAAAA
*
196937 GTAATA
1 ATAATA
196943 TATACGTACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 6 0.18
17 27 0.82
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
ATAATAATATTAAAAAA
Found at i:196985 original size:5 final size:5
Alignment explanation
Indices: 196953--197031 Score: 53
Period size: 5 Copynumber: 16.2 Consensus size: 5
196943 TATACGTACT
* *
196953 AAAT- AAAT- AAATA AAAGTAA AAAGA AAATA AAA-A TAGAT- AAAT-
1 AAATA AAATA AAATA AAA-T-A AAATA AAATA AAATA -AAATA AAATA
*
196996 AAATA AAAT- AGATA TAAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA -AAATA AAATA AAATA AAATA A
197032 TAAAACTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
4 19 0.31
5 33 0.54
6 5 0.08
7 4 0.07
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:197014 original size:15 final size:16
Alignment explanation
Indices: 196978--197020 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 16
196968 AGTAAAAAGA
196978 AAATAAAAATAGATAAAT
1 AAAT-AAAATAGAT-AAT
196996 AAATAAAATAGAT-AT
1 AAATAAAATAGATAAT
197011 AAATAAAATA
1 AAATAAAATA
197021 AAATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
17 9 0.36
18 4 0.16
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (16 bp):
AAATAAAATAGATAAT
Found at i:197014 original size:19 final size:18
Alignment explanation
Indices: 196955--197025 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 18
196945 TACGTACTAA
196955 ATAAAT-AAATAAAAGTA-
1 ATAAATAAAATAAAA-TAG
*
196972 A-AAAGAAAATAAAAATAG
1 ATAAATAAAAT-AAAATAG
196990 ATAAAT-AAATAAAATAG
1 ATAAATAAAATAAAATAG
197007 ATATAAATAAAATAAAATA
1 --ATAAATAAAATAAAATA
197026 AAATAATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
16 3 0.07
17 14 0.31
18 9 0.20
19 9 0.20
20 10 0.22
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
ATAAATAAAATAAAATAG
Found at i:197138 original size:3 final size:3
Alignment explanation
Indices: 197130--197176 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
197120 TATTTAAATA
197130 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
197177 ACATATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:199262 original size:114 final size:107
Alignment explanation
Indices: 199128--199388 Score: 283
Period size: 117 Copynumber: 2.4 Consensus size: 107
199118 TTACTCCGAC
* * * * * * *
199128 TCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTG-GAACTAG-GAATTTGTTTGTTGACAGT
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGAAATAGAAAAGTT-TTTGTTGACAAT
* *
199191 CAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGCTGTTGTGCTGGCTTGAG
65 CAGCCGCCCCTTCATCGTGAAGTTGAGC-T-TG-TG-T-TG-T--CTTGAG
* * * *
199242 TCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTGAAAAGTTTTTGTTGATAA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-A-GAAATAGAAAAGTTTTTGTTGACAA
*
199307 TCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGGG
64 TCAGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGAG
199351 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
1 TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
199389 AATTGGGAAG
Statistics
Matches: 127, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
108 1 0.01
109 40 0.31
111 1 0.01
112 2 0.02
113 1 0.01
114 34 0.27
115 2 0.02
116 1 0.01
117 41 0.32
118 4 0.03
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (107 bp):
TCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGAAATAGAAAAGTTTTTGTTGACAATC
AGCCGCCCCTTCATCGTGAAGTTGAGCTTGTGTTGTCTTGAG
Found at i:200504 original size:17 final size:15
Alignment explanation
Indices: 200478--200521 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
200468 ACCCACCTTA
200478 TTTTTCTTCTCTTTTT
1 TTTTTCTTCT-TTTTT
*
200494 TCTTTTGTTCTTTTTT
1 T-TTTTCTTCTTTTTT
200510 TTTTTC-TCTTTT
1 TTTTTCTTCTTTT
200522 CAATTTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
15 4 0.16
16 7 0.28
17 8 0.32
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (15 bp):
TTTTTCTTCTTTTTT
Found at i:200571 original size:78 final size:78
Alignment explanation
Indices: 200477--200634 Score: 185
Period size: 78 Copynumber: 2.0 Consensus size: 78
200467 AACCCACCTT
** * * *
200477 ATTTTTCTTCTCTTTTTT-CTTTTGTTCTTT-TTTTTTTTCTCTTTTCAATTTAGGGCGCCCTTT
1 ATTTTTC-TCT-TTTTTTGCTTTT-TT-TTTGTTTTTTTT-TCGCTTCAACTTAGGACGCCCTCT
*
200540 CGGGTTTTCACCCTAAGC
61 CGGGTTATCACCCTAAGC
*
200558 ATTTTTCTCTTTTTTTGCTTTTTTTTTGTTTTTTTTTCGCTTCGACTTAGGACGCCCTCTCGGGT
1 ATTTTTCTCTTTTTTTGCTTTTTTTTTGTTTTTTTTTCGCTTCAACTTAGGACGCCCTCTCGGGT
*
200623 TATCATCCTAAG
66 TATCACCCTAAG
200635 AGAAGTACTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
78 36 0.54
79 16 0.24
80 8 0.12
81 7 0.10
ACGTcount: A:0.09, C:0.22, G:0.13, T:0.56
Consensus pattern (78 bp):
ATTTTTCTCTTTTTTTGCTTTTTTTTTGTTTTTTTTTCGCTTCAACTTAGGACGCCCTCTCGGGT
TATCACCCTAAGC
Found at i:200581 original size:11 final size:11
Alignment explanation
Indices: 200567--200599 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
200557 CATTTTTCTC
200567 TTTTTTTGCTT
1 TTTTTTTGCTT
200578 TTTTTTTG-TT
1 TTTTTTTGCTT
200588 TTTTTTTCGCTT
1 TTTTTTT-GCTT
200600 CGACTTAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 9 0.45
12 2 0.10
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:204568 original size:2 final size:2
Alignment explanation
Indices: 204561--204616 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
204551 TGCACCTTTC
204561 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
204603 AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT
204617 CCACGCATAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:204942 original size:30 final size:30
Alignment explanation
Indices: 204886--205015 Score: 217
Period size: 30 Copynumber: 4.3 Consensus size: 30
204876 GAAGGACCTA
* *
204886 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
204915 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
204945 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
204975 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
*
205006 TCCATAGGTC
1 TCCAGAGGTC
205016 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 16 0.17
30 66 0.69
31 14 0.15
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:205032 original size:31 final size:31
Alignment explanation
Indices: 204910--205064 Score: 102
Period size: 30 Copynumber: 5.1 Consensus size: 31
204900 AGACCCCGGT
* ** * *
204910 AACTGTCCAGAGGTCATAAAGATCCTCGGT-
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* ** * *
204940 AACTGTCCAGAGGTCATAAAGATCCTCGGT-
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* ** * *
204970 AACTGTCCAGAGGTCATAAAGATCCTCGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
*
205001 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCACGAAGAACCTAGGTA
* * *
205032 AACT-TCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTCACGAAGA-ACCTAGGTA
205062 AAC
1 AAC
205065 CCTCGACTCT
Statistics
Matches: 114, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
29 1 0.01
30 84 0.74
31 29 0.25
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCACGAAGAACCTAGGTA
Found at i:206232 original size:21 final size:21
Alignment explanation
Indices: 206202--206246 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
206192 ATTCTGTCGT
* *
206202 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
206223 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
206244 TTG
1 TTG
206247 CCCAGAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:206544 original size:41 final size:41
Alignment explanation
Indices: 206498--206580 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
206488 ATTTAACTTC
206498 AAATTCTACTTATCAATTCCTTTCCAAAATTTCATAAAAAA
1 AAATTCTACTTATCAATTCCTTTCCAAAATTTCATAAAAAA
*
206539 AAATTCTACTTATCAATTCCTTTCCAAAATTTCATATAAAA
1 AAATTCTACTTATCAATTCCTTTCCAAAATTTCATAAAAAA
206580 A
1 A
206581 CTCCAAATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.37
Consensus pattern (41 bp):
AAATTCTACTTATCAATTCCTTTCCAAAATTTCATAAAAAA
Found at i:207456 original size:2 final size:2
Alignment explanation
Indices: 207449--207487 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
207439 TGCACCTTTC
207449 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
207488 CATTCCACGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:207820 original size:30 final size:30
Alignment explanation
Indices: 207764--208034 Score: 451
Period size: 30 Copynumber: 9.1 Consensus size: 30
207754 GAAGGACCTA
* *
207764 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
207793 TCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
207823 TCC-GAGGTCAT-AAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
207851 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
207881 TCCATAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
207911 TCCAAAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
207941 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
207971 TCCA-AGGTCATAAAGATCCTTGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
208000 TCCAGAGGTCATAAAGATCCTCGGTACACTG
1 TCCAGAGGTCATAAAGATCCTCGGTA-ACTG
208031 TCCA
1 TCCA
208035 TAGTCTCGAA
Statistics
Matches: 228, Mismatches: 9, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
28 20 0.09
29 58 0.25
30 142 0.62
31 8 0.04
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:208063 original size:30 final size:31
Alignment explanation
Indices: 208027--208087 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
208017 TCCTCGGTAC
208027 ACTGTCCATA-GTCTCGAAG-ACATAGGTAAA
1 ACTGTCCATATGT-TCGAAGAACATAGGTAAA
*
208057 ACTGTCCATATGTTCGTAGAACATAGGTAAA
1 ACTGTCCATATGTTCGAAGAACATAGGTAAA
208088 CCCTCGACTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (31 bp):
ACTGTCCATATGTTCGAAGAACATAGGTAAA
Found at i:209242 original size:21 final size:20
Alignment explanation
Indices: 209203--209246 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
209193 ATTCTGTCGT
* *
209203 TTGAAGGGGTATCGTTTCCTC
1 TTGAAGGGGTACCGATTCC-C
*
209224 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
209244 TTG
1 TTG
209247 CCCAGAATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.36
Consensus pattern (20 bp):
TTGAAGGGGTACCGATTCCC
Found at i:209475 original size:30 final size:30
Alignment explanation
Indices: 209439--209499 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
209429 TTTCCTTAAG
209439 CTTAGTTATCATCTAATAATCAAAACCCAA
1 CTTAGTTATCATCTAATAATCAAAACCCAA
209469 CTTAGTTATCATCTAATAATCAAAACCCAA
1 CTTAGTTATCATCTAATAATCAAAACCCAA
209499 C
1 C
209500 CTTAAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.30
Consensus pattern (30 bp):
CTTAGTTATCATCTAATAATCAAAACCCAA
Done.