Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold510
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: 507550
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 4 of 4
Found at i:427247 original size:20 final size:20
Alignment explanation
Indices: 427222--427292 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
427212 GCCAATGTCC
*
427222 TGTATCGATACATATTTATG
1 TGTATCGATACATATTAATG
* *
427242 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
427262 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
427282 TGTATCGATAC
1 TGTATCGATAC
427293 TTTTCAGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 3 0.07
20 39 0.91
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:427358 original size:21 final size:21
Alignment explanation
Indices: 427332--427372 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
427322 GTCAACCTTG
427332 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
427353 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
427373 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:428392 original size:20 final size:21
Alignment explanation
Indices: 428367--428415 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
428357 TATCTCTCCC
428367 TCTTTTCGT-TTTCGAAATAA
1 TCTTTTCGTATTTCGAAATAA
**
428387 TCTTTTTTTTTATTTCGAAATAA
1 TC--TTTTCGTATTTCGAAATAA
428410 TCTTTT
1 TCTTTT
428416 TTTTGTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 5 0.21
23 13 0.54
ACGTcount: A:0.22, C:0.12, G:0.06, T:0.59
Consensus pattern (21 bp):
TCTTTTCGTATTTCGAAATAA
Found at i:428402 original size:23 final size:23
Alignment explanation
Indices: 428376--428434 Score: 93
Period size: 22 Copynumber: 2.6 Consensus size: 23
428366 CTCTTTTCGT
428376 TTTCGAAATAATCTTTTTTTTTA
1 TTTCGAAATAATCTTTTTTTTTA
*
428399 TTTCGAAATAATC-TTTTTTTTG
1 TTTCGAAATAATCTTTTTTTTTA
*
428421 TTTCAAAATAATCT
1 TTTCGAAATAATCT
428435 CCCCTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (23 bp):
TTTCGAAATAATCTTTTTTTTTA
Found at i:430368 original size:13 final size:13
Alignment explanation
Indices: 430332--430368 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
430322 ATAGTACCTT
*
430332 TGTATCGATACAA
1 TGTATCGATATAA
430345 TGTATCGATATAA
1 TGTATCGATATAA
430358 TGTATCGATAT
1 TGTATCGATAT
430369 TAAGATCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:430721 original size:19 final size:21
Alignment explanation
Indices: 430678--430729 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
430668 TTCAATAATT
*
430678 TGTATCGATACATTTAGTAAA
1 TGTATCGATACATTAAGTAAA
430699 TGTATCGATACA-TAAGT-AA
1 TGTATCGATACATTAAGTAAA
430718 TGTATCGATACA
1 TGTATCGATACA
430730 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 4 0.13
21 12 0.40
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTAAGTAAA
Found at i:430803 original size:13 final size:13
Alignment explanation
Indices: 430785--430841 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
430775 TGTAGAATGC
430785 ATCGATACATTGT
1 ATCGATACATTGT
430798 ATCGATACATTTGT
1 ATCGATACA-TTGT
*
430812 A--G--A-A-TGC
1 ATCGATACATTGT
430819 ATCGATACATTGT
1 ATCGATACATTGT
430832 ATCGATACAT
1 ATCGATACAT
430842 CGATCTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
7 3 0.09
9 2 0.06
10 1 0.03
11 1 0.03
12 2 0.06
13 21 0.60
14 5 0.14
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (13 bp):
ATCGATACATTGT
Found at i:430804 original size:34 final size:34
Alignment explanation
Indices: 430761--430841 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
430751 GCCAAGGAAA
430761 TGTATCGATACATTTGTAGAATGCATCGATACAT
1 TGTATCGATACATTTGTAGAATGCATCGATACAT
430795 TGTATCGATACATTTGTAGAATGCATCGATACAT
1 TGTATCGATACATTTGTAGAATGCATCGATACAT
430829 TGTATCGATACAT
1 TGTATCGATACAT
430842 CGATCTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (34 bp):
TGTATCGATACATTTGTAGAATGCATCGATACAT
Found at i:430851 original size:20 final size:21
Alignment explanation
Indices: 430818--430862 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
430808 TTGTAGAATG
430818 CATCGATACATTGTATCGATA
1 CATCGATACATTGTATCGATA
*
430839 CATCGAT-CTTTGTATCGATA
1 CATCGATACATTGTATCGATA
430859 CATC
1 CATC
430863 TAGGAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (21 bp):
CATCGATACATTGTATCGATA
Found at i:431735 original size:13 final size:13
Alignment explanation
Indices: 431717--431741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
431707 CATAAAGTGT
431717 TGTATCGATACAA
1 TGTATCGATACAA
431730 TGTATCGATACA
1 TGTATCGATACA
431742 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:431752 original size:32 final size:33
Alignment explanation
Indices: 431697--431760 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 33
431687 TTCAATGATT
431697 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
431730 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACA
431761 TAAGTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:431754 original size:19 final size:19
Alignment explanation
Indices: 431696--431779 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
431686 TTTCAATGAT
431696 TTGTATCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
431716 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
431730 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
431748 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
431767 TTGTATCGATACA
1 TTGTATCGATACA
431780 ATATAAGCTA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 11 0.19
15 2 0.04
17 2 0.04
19 30 0.53
20 12 0.21
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:431961 original size:51 final size:52
Alignment explanation
Indices: 431855--431982 Score: 240
Period size: 51 Copynumber: 2.5 Consensus size: 52
431845 CACTGATCTT
431855 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
431907 TGTATCGATACATGCAGGCAAATTTGCCC-GATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
431958 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
431983 TCATATTTCG
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
51 46 0.61
52 29 0.39
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:440148 original size:53 final size:54
Alignment explanation
Indices: 440086--440192 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 54
440076 AAATCTCTTT
* *
440086 TCAAAGCCCACGACTGAGTGGCATTTTGT-C-TCAAAGTCCATGACTCAGTGGCA
1 TCAAAGCCCACGACTCAGTGGCATTTT-TCCTTCAAAGTCCACGACTCAGTGGCA
* * *
440139 TCAAAGCCCATGACTCAGTGGCATTTTTCCTTCTAAGTCCACGACTCCGTGGCA
1 TCAAAGCCCACGACTCAGTGGCATTTTTCCTTCAAAGTCCACGACTCAGTGGCA
440193 CCTTTTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
52 1 0.02
53 26 0.55
54 20 0.43
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (54 bp):
TCAAAGCCCACGACTCAGTGGCATTTTTCCTTCAAAGTCCACGACTCAGTGGCA
Found at i:440149 original size:23 final size:23
Alignment explanation
Indices: 440116--440162 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
440106 GCATTTTGTC
*
440116 TCAAAGTCCATGACTCAGTGGCA
1 TCAAAGCCCATGACTCAGTGGCA
440139 TCAAAGCCCATGACTCAGTGGCA
1 TCAAAGCCCATGACTCAGTGGCA
440162 T
1 T
440163 TTTTCCTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (23 bp):
TCAAAGCCCATGACTCAGTGGCA
Found at i:440253 original size:34 final size:33
Alignment explanation
Indices: 440162--440578 Score: 286
Period size: 31 Copynumber: 13.0 Consensus size: 33
440152 CTCAGTGGCA
*
440162 TTTTTCCTTCTAAGTCCACGACTCCGTGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* * *
440195 TTTTT--TT-TAAAGCCCACAATTCCGTGGTACTC
1 TTTTTCCTTCT-AAGTCCACAACTCCGTGGCAC-C
440227 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* *
440260 -----CGTT-TAAGCCCACAACTCCGTGGCACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-C
440288 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* * *
440321 -----CGTT-TAAGCCCACAACTCCATGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* * *
440348 TTGTTCCTTTTAAGTCCACGACTCCGTGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* * *
440381 TTCTT--TTCAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-C
* *
440413 TTTTTCCCTTTTAAAGTCCACAAC-CTTGTGGCACC
1 TTTTT-CCTTCT-AAGTCCACAACTC-CGTGGCACC
* **
440448 TTGTTCCTTCTAAGTCCATGACTCCGTGGCACC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
* * * * * * *
440481 ---TTCCTTTCAAAGTTCGCGACTCTGTGGGAGC
1 TTTTTCC-TTCTAAGTCCACAACTCCGTGGCACC
* * *
440512 TTCTT--TTCAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCAC-C
* *
440544 TTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACC
1 TTTTT-CCTTCT-AAGTCCACAACTCCGTGGCACC
440579 CGTTTAAGTC
Statistics
Matches: 300, Mismatches: 50, Indels: 66
0.72 0.12 0.16
Matches are distributed among these distances:
27 42 0.14
28 7 0.02
30 5 0.02
31 77 0.26
32 19 0.06
33 51 0.17
34 49 0.16
35 12 0.04
36 38 0.13
ACGTcount: A:0.19, C:0.35, G:0.15, T:0.31
Consensus pattern (33 bp):
TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC
Found at i:440267 original size:27 final size:27
Alignment explanation
Indices: 440237--440410 Score: 123
Period size: 27 Copynumber: 5.8 Consensus size: 27
440227 TTTTTCCTTC
*
440237 TAAGTCCACAACTCCGTGGCACCCGTT
1 TAAGCCCACAACTCCGTGGCACCCGTT
*
440264 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 TAAGCCCACAACTCCGTGGCAC-C-----CGTT
*
440297 CTAAGTCCACAACTCCGTGGCACCCGTT
1 -TAAGCCCACAACTCCGTGGCACCCGTT
* *
440325 TAAGCCCACAACTCCATGGCACCTTGTTCCTTT
1 TAAGCCCACAACTCCGTGGCA-C-----CCGTT
* * *
440358 TAAGTCCACGACTCCGTGGCACCTTCTTT
1 TAAGCCCACAACTCCGTGGCACC--CGTT
440387 TCAAAGCCCACAACTCCGTGGCAC
1 T--AAGCCCACAACTCCGTGGCAC
440411 TCTTTTTCCC
Statistics
Matches: 118, Mismatches: 12, Indels: 30
0.74 0.08 0.19
Matches are distributed among these distances:
27 41 0.35
28 5 0.04
29 5 0.04
31 19 0.16
32 1 0.01
33 26 0.22
34 21 0.18
ACGTcount: A:0.21, C:0.37, G:0.16, T:0.26
Consensus pattern (27 bp):
TAAGCCCACAACTCCGTGGCACCCGTT
Found at i:440298 original size:61 final size:61
Alignment explanation
Indices: 440162--440608 Score: 368
Period size: 61 Copynumber: 7.0 Consensus size: 61
440152 CTCAGTGGCA
* ** * *
440162 TTTTTCCTTCTAAGTCCACGACTCCGTGGCACCTTTTTTTTAAAGCCCACAATTCCGTGGTACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC---CGTTT-AAGCCCACAACTCCGTGGCACTC
440227 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTC
*
440288 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCATGGCAC-C
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTC
* * * *
440348 TTGTTCCTTTTAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTC
1 TTTTTCCTTCTAAGTCCACAACTCCGTGGCACC--CGTTT--AAGCCCACAACTCCGTGGCACTC
* * * * **
440413 TTTTTCCCTTTTAAAGTCCACAAC-CTTGTGGCACCTTGTTCCTTCTAAGTCCATGACTCCGTGG
1 TTTTT-CCTTCT-AAGTCCACAACTC-CGTGGCACC-----CGTT-TAAGCCCACAACTCCGTGG
440477 CAC-C
57 CACTC
* * * * * * * *
440481 ---TTCCTTTCAAAGTTCGCGACTCTGTGGGAGCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
1 TTTTTCC-TTCTAAGTCCACAACTCCGTGGCA-C-CCGTTT--AAGCCCACAACTCCGTGGCACT
440543 C
61 C
* * * * *
440544 TTTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCCGTTTAAGTCCACAACTTCATGGCA-TC
1 TTTTT-CCTTCT-AAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTC
440606 TTT
1 TTT
440609 CACCCTTCTC
Statistics
Matches: 316, Mismatches: 42, Indels: 51
0.77 0.10 0.12
Matches are distributed among these distances:
60 32 0.10
61 82 0.26
62 30 0.09
63 18 0.06
64 36 0.11
65 47 0.15
66 12 0.04
67 34 0.11
68 1 0.00
69 18 0.06
70 5 0.02
71 1 0.00
ACGTcount: A:0.19, C:0.34, G:0.15, T:0.32
Consensus pattern (61 bp):
TTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCGTGGCACTC
Found at i:440646 original size:32 final size:33
Alignment explanation
Indices: 440610--440714 Score: 178
Period size: 33 Copynumber: 3.2 Consensus size: 33
440600 GGCATCTTTC
440610 ACCCTTCTC-AAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
440642 ACCC-TCTCTAAAGCCCACACAAGTTGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
*
440674 ACCATTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
440707 ACCCTTCT
1 ACCCTTCT
440715 AAGCCCAATA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 4 0.06
32 29 0.43
33 34 0.51
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (33 bp):
ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:440660 original size:131 final size:125
Alignment explanation
Indices: 440229--440609 Score: 429
Period size: 131 Copynumber: 3.0 Consensus size: 125
440219 TGGTACTCTT
* * *
440229 TTTCC-TTCTAAGTCCACAACTCCGTGGCACC--CGTTT--AAGCCCACAACTCCGTGGCACTCT
1 TTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
* *
440289 TTTT-CCTTCT-AAGTCCACAACTCCGTGGCACCCGTTTAAGCCCACAACTCCATGGCACC
66 TTTTCCCTTTTAAAGTCCACAACTCCGTGGCACCCGTTTAAGTCCACAACTCCATGGCA-C
*
440348 TTGTTCCTTT-TAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
1 -T-TTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACT
* * ** *
440412 CTTTTTCCCTTTTAAAGTCCACAAC-CTTGTGGCACCTTGTTCCTTCTAAGTCCATGACTCCGTG
64 CTTTTTCCCTTTTAAAGTCCACAACTC-CGTGGCACC-----CGTT-TAAGTCCACAACTCCATG
440476 GCAC
122 GCAC
* * * * * *
440480 CTTCCTTTCAAAGTTCGCGACTCTGTGGGAGCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
1 TTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
* *
440545 TTTTCCCTTTTAAAGCCCACAACTCCGTGGCACCCGTTTAAGTCCACAACTTCATGGCATC
66 TTTTCCCTTTTAAAGTCCACAACTCCGTGGCACCCGTTTAAGTCCACAACTCCATGGCA-C
440606 TTTC
1 TTTC
440610 ACCCTTCTCA
Statistics
Matches: 219, Mismatches: 24, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
120 1 0.00
121 26 0.12
122 2 0.01
123 4 0.02
125 45 0.21
126 13 0.06
127 19 0.09
130 7 0.03
131 80 0.37
132 5 0.02
133 17 0.08
ACGTcount: A:0.20, C:0.35, G:0.15, T:0.30
Consensus pattern (125 bp):
TTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTCT
TTTTCCCTTTTAAAGTCCACAACTCCGTGGCACCCGTTTAAGTCCACAACTCCATGGCAC
Found at i:440782 original size:49 final size:49
Alignment explanation
Indices: 440729--440980 Score: 280
Period size: 43 Copynumber: 5.4 Consensus size: 49
440719 CCAATATCGT
* *
440729 TGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAATCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
*
440778 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
*
440821 TGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
* *
440870 TGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCGATATAGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
** * * ** *
440913 TGGCCTTGCCTCAGCACATTGGCA--TTTTTCTTCAAGTTAAATGTCGC
1 TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
*
440960 TGGCCATGAATCAGCACATTG
1 TGGCCTTGAATCAGCACATTG
440981 TCATTTTTGC
Statistics
Matches: 173, Mismatches: 20, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
43 77 0.45
45 2 0.01
47 31 0.18
49 63 0.36
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (49 bp):
TGGCCTTGAATCAGCACATTGGCACCTTCTTCTTTAAGTCCAATGTAGC
Found at i:440876 original size:92 final size:92
Alignment explanation
Indices: 440709--440980 Score: 395
Period size: 92 Copynumber: 3.0 Consensus size: 92
440699 CGGTGGCAAC
* * * *
440709 CCTTCTAAGCCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAATCCAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
440774 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
440802 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
440867 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* ** * * * **
440894 CCTTTAAGTCCGATATAGCTGGCCTTGCCTCAGCACATTGGCA--TTTTTCTTCAAGTTAAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
* *
440957 CGCTGGCCATGAATCAGCACATTG
66 AGCTGGCCTTGAATCAGCACATTG
440981 TCATTTTTGC
Statistics
Matches: 165, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
90 38 0.23
92 123 0.75
93 4 0.02
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:441183 original size:43 final size:43
Alignment explanation
Indices: 441115--441387 Score: 285
Period size: 43 Copynumber: 6.1 Consensus size: 43
441105 CCTCATCATA
* * *
441115 TTTAAGTCCAATGTAGCTGGTCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCACC
* * *
441158 TTTAAGTCCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCA----C--C
* * *
441207 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCACC
* * *
441250 TTTAAGTCCAATATTGCTAGCCTTGAATCATCATATTGGCACCTTCTTC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCA----C--C
* *
441299 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCACC
* * *
441342 TTTAAGTCTAATATAGCTACCCTTGAATCAGCATATTGGCACC
1 TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCACC
441385 TTT
1 TTT
441388 TCCATCTTTA
Statistics
Matches: 190, Mismatches: 28, Indels: 24
0.79 0.12 0.10
Matches are distributed among these distances:
43 113 0.59
45 2 0.01
47 2 0.01
49 73 0.38
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.33
Consensus pattern (43 bp):
TTTAAGTCCAATATAGCTAGCCTTGAATCAGCACATTGGCACC
Found at i:441272 original size:92 final size:92
Alignment explanation
Indices: 441115--441431 Score: 481
Period size: 92 Copynumber: 3.4 Consensus size: 92
441105 CCTCATCATA
* * *
441115 TTTAAGTCCAATGTAGCTGGTCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTAGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
* *
441180 TTGAATTAGCATATTGGCACCTTCATC
66 TTGAATCAGCATATTGGCACCTTCTTC
* * *
441207 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTAAGTCCAATATTGCTAGCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
*
441272 TTGAATCATCATATTGGCACCTTCTTC
66 TTGAATCAGCATATTGGCACCTTCTTC
* **
441299 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCTAATATAGCTACCC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
*
441364 TTGAATCAGCATATTGGCACCTTTTCCATC
66 TTGAATCAGCATATTGGCACC--TT-CTTC
*
441394 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
441432 ACATCTTTTT
Statistics
Matches: 209, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
92 167 0.80
94 2 0.01
95 40 0.19
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (92 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCC
TTGAATCAGCATATTGGCACCTTCTTC
Found at i:442376 original size:13 final size:13
Alignment explanation
Indices: 442358--442382 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
442348 CATAAAGTGT
442358 TGTATCGATACAA
1 TGTATCGATACAA
442371 TGTATCGATACA
1 TGTATCGATACA
442383 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:442437 original size:32 final size:32
Alignment explanation
Indices: 442340--442438 Score: 144
Period size: 32 Copynumber: 3.1 Consensus size: 32
442330 CAACGATTTG
*
442340 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATA
*
442373 TATCGATACATAAGTGTTGTATCAATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
* * *
442405 TATTGATACATAAGTTTTGTATCGATAAAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
442437 TA
1 TA
442439 AGCTACTGCC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:442554 original size:52 final size:50
Alignment explanation
Indices: 442491--442637 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 50
442481 CGATACATTA
442491 TATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGATG
1 TATCGATACACTGATC--TGTATCGATACATGCAGGCAAATTTGCCCAGATG
* *
442543 TATCGATACACT-ATAAAATGTATCGATACATGTAGGCAAATTTGCCCAGATG
1 TATCGATACACTGAT---CTGTATCGATACATGCAGGCAAATTTGCCCAGATG
*
442595 TATCGATACACTATGAACTGTATCGATACATGCAGGCAAATTT
1 TATCGATACAC--TGATCTGTATCGATACATGCAGGCAAATTT
442638 TCATATTTCG
Statistics
Matches: 84, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
51 2 0.02
52 80 0.95
54 1 0.01
55 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (50 bp):
TATCGATACACTGATCTGTATCGATACATGCAGGCAAATTTGCCCAGATG
Found at i:447295 original size:27 final size:28
Alignment explanation
Indices: 447265--447340 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 28
447255 ATTTTTCACA
*
447265 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTCACATC
*
447292 ATCGGGGATACTCCAACCCCGTCACTTC
1 ATCGGGGATACTCCAACCCCGTCACATC
***
447320 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
447341 ACTTTATTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.53
28 20 0.47
ACGTcount: A:0.24, C:0.37, G:0.21, T:0.18
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTCACATC
Found at i:447425 original size:79 final size:79
Alignment explanation
Indices: 447292--447498 Score: 342
Period size: 79 Copynumber: 2.6 Consensus size: 79
447282 CCCGTTAATC
* * *
447292 ATCGGGGATACTCCAACCCCGTCACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
447357 ATTGATTTCTCACA
66 ATTGATTTCTCACA
* *
447371 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
*
447436 ATTGATTTCTCGCA
66 ATTGATTTCTCACA
* *
447450 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCTAACCCCG
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
447499 TTATTATCTC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 119 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
ATTGATTTCTCACA
Found at i:447514 original size:79 final size:78
Alignment explanation
Indices: 447292--447527 Score: 339
Period size: 79 Copynumber: 3.0 Consensus size: 78
447282 CCCGTTAATC
* * *
447292 ATCGGGGATACTCCAACCCCGTCACTTCCGAGGGGATACTCCAACCCCGACTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG-CTTTATTCCTAAAAT
447357 ATTGATTTCTCACA
65 ATTGATTTCTCACA
*
447371 ATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC-GCTTTATTCCTAAAAT
*
447436 ATTGATTTCTCGCA
65 ATTGATTTCTCACA
* * *
447450 ATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGATACTCTAACCCCGTTATTATCTCC-AAAA
1 ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGCT-TTAT-TCCTAAAA
*
447514 TATTAAATTTCTCA
64 TATT-GATTTCTCA
447528 TCGGGAGATG
Statistics
Matches: 142, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
78 2 0.01
79 129 0.91
80 11 0.08
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.31
Consensus pattern (78 bp):
ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGCTTTATTCCTAAAATA
TTGATTTCTCACA
Found at i:449561 original size:4 final size:4
Alignment explanation
Indices: 449552--449582 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
449542 TTTTGAGGTG
*
449552 TTTA TTTA TTTA TTTA TTTA TTGA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
449583 GTTTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:459490 original size:5 final size:5
Alignment explanation
Indices: 459482--459539 Score: 59
Period size: 5 Copynumber: 11.6 Consensus size: 5
459472 CTCTTCTAAA
*
459482 AAAAC AAAAAC AAAAGC -AAA- AAAA- AAAAC AAAAAA AAAAC AAAAC
1 AAAAC -AAAAC AAAA-C AAAAC AAAAC AAAAC -AAAAC AAAAC AAAAC
459527 AAAAC AAAAC AAA
1 AAAAC AAAAC AAA
459540 GAAAAAAGAG
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
4 7 0.15
5 29 0.63
6 10 0.22
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:459492 original size:6 final size:6
Alignment explanation
Indices: 459481--459539 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
459471 TCTCTTCTAA
* *
459481 AAAAAC AAAAAC AAAAGC AAAAAA AAAAAC AAAAA- AAAAAC -AAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
459527 -AAAAC -AAAAC AAA
1 AAAAAC AAAAAC AAA
459540 GAAAAAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 20 0.43
6 27 0.57
ACGTcount: A:0.85, C:0.14, G:0.02, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:459502 original size:11 final size:11
Alignment explanation
Indices: 459481--459539 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
459471 TCTCTTCTAA
459481 AAAAACAAAAAC
1 AAAAAC-AAAAC
* *
459493 AAAAGCAAAAAA
1 AAAAAC-AAAAC
*
459505 AAAAACAAAAA
1 AAAAACAAAAC
459516 AAAAACAAAAC
1 AAAAACAAAAC
459527 -AAAACAAAAC
1 AAAAACAAAAC
459537 AAA
1 AAA
459540 GAAAAAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
10 10 0.24
11 17 0.40
12 15 0.36
ACGTcount: A:0.85, C:0.14, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:459514 original size:10 final size:10
Alignment explanation
Indices: 459479--459546 Score: 68
Period size: 10 Copynumber: 6.7 Consensus size: 10
459469 CTTCTCTTCT
459479 AAAAAAACAA
1 AAAAAAACAA
459489 AAACAAAAGCAA
1 AAA-AAAA-CAA
459501 AAAAAAA-AA
1 AAAAAAACAA
*
459510 CAAAAAA-AA
1 AAAAAAACAA
*
459519 AACAAAACAA
1 AAAAAAACAA
*
459529 AACAAAACAA
1 AAAAAAACAA
459539 AGAAAAAA
1 A-AAAAAA
459547 GAGAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
9 15 0.30
10 16 0.32
11 13 0.26
12 6 0.12
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:459521 original size:29 final size:30
Alignment explanation
Indices: 459481--459546 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 30
459471 TCTCTTCTAA
459481 AAAAACAAAAACAAAAGCAAAA-AAAA-AAAC
1 AAAAA-AAAAACAAAA-CAAAACAAAACAAAC
*
459511 AAAAAAAAAACAAAACAAAACAAAACAAAG
1 AAAAAAAAAACAAAACAAAACAAAACAAAC
459541 AAAAAA
1 AAAAAA
459547 GAGAGAAAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 5 0.15
29 14 0.42
30 14 0.42
ACGTcount: A:0.85, C:0.12, G:0.03, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAACAAAACAAAACAAAACAAAC
Found at i:460602 original size:55 final size:55
Alignment explanation
Indices: 460518--460712 Score: 230
Period size: 55 Copynumber: 3.5 Consensus size: 55
460508 CTCCTTCAGC
*
460518 TTTTC-AGTCCTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
460572 TTTTCTAATCCTCAAAGAGCAAGACACCTTTTCATTTTAAAGCCCACACAGGTTGGTGGCA
1 TTTTCTAGTCCTCAAAGAGCAGGACA-C----C-TTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
460633 TTTTCCAGTCTTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
460688 CTTCCTCGTCCTCAAAGAGCAGGAC
1 TTTTCTAGTCCTCAAAGAGCAGGAC
460713 GCTCTCTCCT
Statistics
Matches: 118, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
54 5 0.04
55 62 0.53
56 2 0.02
60 2 0.02
61 47 0.40
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (55 bp):
TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:460826 original size:60 final size:59
Alignment explanation
Indices: 460753--460933 Score: 237
Period size: 55 Copynumber: 3.1 Consensus size: 59
460743 GAGCAGGATG
*
460753 CCTTTTAAAGCCCACACAAGTCGGTGGCACTTTCAGTCCTCAAAGAGCAGGATGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATG-CTTCT
* *
460813 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTTAAAGAGCAGGA-----CT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCAGTCCTCAAAGAGCAGGATGCTTCT
* * *
460868 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCTAGTCCTCAAAAAGCAGGATGCTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-AGTCCTCAAAGAGCAGGATGCT-TCT
460929 CCTTT
1 CCTTT
460934 CGCCTTTTTG
Statistics
Matches: 105, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
54 2 0.02
55 47 0.45
60 29 0.28
61 27 0.26
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (59 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCAGTCCTCAAAGAGCAGGATGCTTCT
Found at i:460878 original size:209 final size:208
Alignment explanation
Indices: 460524--461135 Score: 845
Period size: 209 Copynumber: 2.9 Consensus size: 208
460514 CAGCTTTTCA
* *
460524 GTCCTCAAAGAGCAGGACT-CCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTAATCCTCAAA
1 GTCCTCAAAGAGCAGGA-TGCCTTTTAAAGCCCACACAAGTCGGTGGCA-TTTC-AGTCCTCAAA
* ** * *
460588 GAGCAAGACACCTTTTCATTTTAAAGCCCACACAGGTTGGTGGCA-TTTTCCAGTCTTCAAAGAG
63 GAGCAGGATGCCTTCTCATTTTAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCTTCAAAGAG
* * *
460652 CAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCACTTCCTCGTCCTCAAAGAGCAGGACGCTC
127 CAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTC
460717 TCTCCTTTCGCCTTTTT
192 TCTCCTTTCGCCTTTTT
*
460734 GTCTTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTCGGTGGCACTTTCAGTCCTCAAAGA
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTCGGTGGCA-TTTCAGTCCTCAAAGA
* *
460799 GCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTTAAAGAGCAG
65 GCAGGATGCCTTCTCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAG
* * *
460864 GACTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCTAGTCCTCAAAAAGCAGGATGCTCTCT
130 GACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCT
460929 CCTTTCGCCTTTTT
195 CCTTTCGCCTTTTT
* * *
460943 GTCCTCAAATAGTAGGATGCCTTTTAAAGCCCACACAAG-CTGGTGGCATCTTCAGTCCTCAAAC
1 GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTC-GGTGGCAT-TTCAGTCCTCAAAG
* *
461007 AGCAGGATGCCTTCTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCA
64 AGCAGGATGCCTTCTCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCA
* * * *
461072 GGATGCTTTTTCTTTTCAAAGCCTAGACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGA
129 GGA--C---TCCTTTT-AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGA
461136 TGCTTTTTCT
Statistics
Matches: 361, Mismatches: 30, Indels: 17
0.88 0.07 0.04
Matches are distributed among these distances:
208 2 0.01
209 259 0.72
210 52 0.14
211 1 0.00
214 6 0.02
215 38 0.11
216 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (208 bp):
GTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGTCGGTGGCATTTCAGTCCTCAAAGAG
CAGGATGCCTTCTCATTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCTTCAAAGAGCAGG
ACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTC
CTTTCGCCTTTTT
Found at i:460893 original size:55 final size:54
Alignment explanation
Indices: 460734--460920 Score: 223
Period size: 55 Copynumber: 3.3 Consensus size: 54
460724 TCGCCTTTTT
*
460734 GTCTTCAAAGAGCAGGA-TGCCTTTTAAAGCCCACACAAGTCGGTGGCACTTTCA
1 GTCTTCAAAGAGCAGGACT-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCA
*
460788 GTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
1 GTCTTCAAAGAGCAGGA------CTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCA
* * *
460849 GTCTTTAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTCCTA
1 GTCTTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC-A
* *
460904 GTCCTCAAAAAGCAGGA
1 GTCTTCAAAGAGCAGGA
460921 TGCTCTCTCC
Statistics
Matches: 115, Mismatches: 9, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
54 18 0.16
55 47 0.41
60 29 0.25
61 21 0.18
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.25
Consensus pattern (54 bp):
GTCTTCAAAGAGCAGGACTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCA
Found at i:461086 original size:61 final size:60
Alignment explanation
Indices: 460964--461257 Score: 390
Period size: 61 Copynumber: 4.8 Consensus size: 60
460954 GTAGGATGCC
* * *
460964 TTTTAAAGCCCACACAAGCTGGTGGCATCTTCAGTCCTCAAACAGCAGGATGCCTTCTCT
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGATGCCTTCTCT
* *
461024 TTTTAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAAGAGCAGGATGCTTTTTCT
1 TTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCAGTCCTCAAAGAGCAGGATGCCTTCTCT
* * * * *
461085 TTTCAAAGCCTAGACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCT
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGATGCCTTCTCT
* * * * *
461146 TTTCAAAGCCTAAACAAGTTGGTGGCATTTTCCAATCCTCAAAGAGCAGGATGCCTTCTCC
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTT-CAGTCCTCAAAGAGCAGGATGCCTTCTCT
* * *
461207 TTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTTAAAGAGCAGGA
1 TTTTAAAGCCCACACAAGTTGGTGGCATTTTC-AGTCCTCAAAGAGCAGGA
461258 CGCTCTCTCC
Statistics
Matches: 211, Mismatches: 20, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
60 31 0.15
61 180 0.85
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (60 bp):
TTTTAAAGCCCACACAAGTTGGTGGCATTTTCAGTCCTCAAAGAGCAGGATGCCTTCTCT
Found at i:461406 original size:59 final size:60
Alignment explanation
Indices: 461325--461532 Score: 212
Period size: 61 Copynumber: 3.5 Consensus size: 60
461315 CAAGCCAGTG
461325 GCAC-TTTCAGTCCTCAAAGAGCAAGG-CGCCTTCTACTTTT-AAAGCCCACACAAGTTGGT
1 GCACTTTTCAGTCCTCAAAGAGC-AGGACGCCTTCT-CTTTTCAAAGCCCACACAAGTTGGT
* * * *
461384 -CACTTTTCAGTCTTCAAAGAGCAGGATGCTTTCT-TTTTGCAAAGCCCACAGAAGTTGGT
1 GCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTT-CAAAGCCCACACAAGTTGGT
* * * * * *
461443 GGCAC-CTTCTAGTCCTCAGAGGGCAGGACACCTTTTCTTTTCAAAGCCCACACGAGTTGGT
1 -GCACTTTTC-AGTCCTCAAAGAGCAGGACGCCTTCTCTTTTCAAAGCCCACACAAGTTGGT
* *
461504 GGCACTTTTCAGTCCTCAAAAAGTAGGAC
1 -GCACTTTTCAGTCCTCAAAGAGCAGGAC
461533 ACACTTCCTT
Statistics
Matches: 121, Mismatches: 19, Indels: 16
0.78 0.12 0.10
Matches are distributed among these distances:
57 4 0.03
58 6 0.05
59 41 0.34
60 3 0.02
61 60 0.50
62 7 0.06
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (60 bp):
GCACTTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCTTTTCAAAGCCCACACAAGTTGGT
Found at i:461636 original size:42 final size:42
Alignment explanation
Indices: 461515--461648 Score: 126
Period size: 42 Copynumber: 3.1 Consensus size: 42
461505 GCACTTTTCA
* * ** *
461515 GTCCTCAAAAAGTAGGACACACTTCCTTCTCTTCTTTTCTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATT-TC-CCTTTT-TCTTTT
* *
461560 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTTCTTTT
1 GTCCTCAAAGAGCAGGACACACTTTATTTCCCTTTTTCTTTT
* * * *
461602 GTCCTCAAAGTGCAGGACATA-TTTCGTTTCCCTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACACACTTT-ATTTCCCTTTTTCTTTT
461644 GTCCT
1 GTCCT
461649 TGAAAAACAT
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
41 3 0.04
42 43 0.57
43 5 0.07
44 1 0.01
45 23 0.31
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.43
Consensus pattern (42 bp):
GTCCTCAAAGAGCAGGACACACTTTATTTCCCTTTTTCTTTT
Found at i:461721 original size:42 final size:40
Alignment explanation
Indices: 461675--461768 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 40
461665 CTCTTTTCCA
* *
461675 CTTTGTCCTTAAGAAGCAGGACACT-TTCCTATTCTTCTCTTC
1 CTTTGTCCTCAAGAAGCAAGAC-CTATTCC-ATTCTT-TCTTC
* * *
461717 CTTTGTCCTCAAGGAGCAAGACCTATTTCATTCTTTTTTC
1 CTTTGTCCTCAAGAAGCAAGACCTATTCCATTCTTTCTTC
461757 CTTTGTCCTCAA
1 CTTTGTCCTCAA
461769 AAAGTGGGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
40 16 0.35
41 8 0.17
42 22 0.48
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (40 bp):
CTTTGTCCTCAAGAAGCAAGACCTATTCCATTCTTTCTTC
Found at i:463597 original size:21 final size:22
Alignment explanation
Indices: 463562--463605 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
463552 AAAATCACAT
*
463562 ATTTGTCGAAATGTATCGATAC
1 ATTTGTAGAAATGTATCGATAC
463584 ATTTGTAG-AATGTATCGATAC
1 ATTTGTAGAAATGTATCGATAC
463605 A
1 A
463606 AGGCCCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (22 bp):
ATTTGTAGAAATGTATCGATAC
Found at i:466221 original size:28 final size:28
Alignment explanation
Indices: 466185--466257 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
466175 GTTAATCATC
466185 GGGGATACTCCAACCCCATCACTTCCGA
1 GGGGATACTCCAACCCCATCACTTCCGA
466213 GGGGATACTCCAACCCCATCACTTCCGA
1 GGGGATACTCCAACCCCATCACTTCCGA
466241 GGGGATACTCCAACCCC
1 GGGGATACTCCAACCCC
466258 GGCTTTATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.25, C:0.40, G:0.19, T:0.16
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATCACTTCCGA
Found at i:466353 original size:79 final size:80
Alignment explanation
Indices: 466215--466365 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 80
466205 ACTTCCGAGG
*
466215 GGATACTCCAACCCCATCACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT-G
1 GGATACTCCAACCCCATCACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTAA
466279 ATTTCTCACAATCGA
66 ATTTCTCACAATCGA
* * * * *
466294 GGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCCC-GTTATTATCTCC-AAAATATT
1 GGATACTCCAACCCCATCACTTCCGAGGGGATACTCCAACCCCGGCT-TTAT-TCCTAAAATATT
466357 AAATTTCTC
64 AAATTTCTC
466366 GTCGGGAGAT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
78 2 0.03
79 51 0.81
80 10 0.16
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.29
Consensus pattern (80 bp):
GGATACTCCAACCCCATCACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTAA
ATTTCTCACAATCGA
Found at i:468801 original size:13 final size:13
Alignment explanation
Indices: 468783--468807 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
468773 CAATTGTGTA
468783 TGTATCGATACAG
1 TGTATCGATACAG
468796 TGTATCGATACA
1 TGTATCGATACA
468808 AAGCATGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:477415 original size:21 final size:21
Alignment explanation
Indices: 477369--477423 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
477359 TTTTTACTTA
*
477369 AAAACATTCAGTTTAAAGCTCG
1 AAAACATTTA-TTTAAAGCTCG
*
477391 AAAACATTTATTTATAA-CTCT
1 AAAACATTTATTTA-AAGCTCG
477412 AAAACATTTATT
1 AAAACATTTATT
477424 AATATTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAACATTTATTTAAAGCTCG
Found at i:488986 original size:13 final size:13
Alignment explanation
Indices: 488968--488993 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
488958 CAATTTTTTG
488968 TGTATCGATACAT
1 TGTATCGATACAT
488981 TGTATCGATACAT
1 TGTATCGATACAT
488994 ACTTGATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:489057 original size:20 final size:20
Alignment explanation
Indices: 489032--489105 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
489022 CTGCCAAGAA
489032 ATGTATCGATACAACTTTTT
1 ATGTATCGATACAACTTTTT
***
489052 ATGTATCGATAC-A-TTGCAAC
1 ATGTATCGATACAACTT--TTT
*
489072 ATGTATCGATACATCTTTTT
1 ATGTATCGATACAACTTTTT
489092 CATGTATCGATACA
1 -ATGTATCGATACA
489106 TTGCAACATG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 24 0.57
21 13 0.31
22 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAACTTTTT
Found at i:489109 original size:41 final size:40
Alignment explanation
Indices: 489032--489124 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 40
489022 CTGCCAAGAA
489032 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
*
489072 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTT-ATGTATCGATACATTGCAAC
489113 ATGTATCGATAC
1 ATGTATCGATAC
489125 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (40 bp):
ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
Found at i:489117 original size:20 final size:20
Alignment explanation
Indices: 489052--489124 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
489042 ACAACTTTTT
489052 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
489072 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
489093 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
489113 ATGTATCGATAC
1 ATGTATCGATAC
489125 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:489478 original size:32 final size:33
Alignment explanation
Indices: 489416--489478 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
489406 GATCCTAACA
** * *
489416 GTATCGATACAATTTTTTGTGTATCGATACATT
1 GTATCGATACAATACTTGGTGTATCAATACATT
489449 GTATCGATA-AATACTTGGTGTATCAATACA
1 GTATCGATACAATACTTGGTGTATCAATACA
489479 AGTTTGGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (33 bp):
GTATCGATACAATACTTGGTGTATCAATACATT
Found at i:492020 original size:13 final size:13
Alignment explanation
Indices: 492002--492040 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
491992 ATAATCACCC
*
492002 TGTATCGATACAG
1 TGTATCGATACAA
492015 TGTATCGATACAA
1 TGTATCGATACAA
492028 TGTATCGATACAA
1 TGTATCGATACAA
492041 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:492051 original size:20 final size:20
Alignment explanation
Indices: 492026--492104 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
492016 GTATCGATAC
492026 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
492046 AATGTATCGATACATAGAATTTTCA
1 AATGTATCGATACAAAGAA-----A
*
492071 GATGTATCGATACACAA-AAA
1 AATGTATCGATACA-AAGAAA
*
492091 CATGTATCGATACA
1 AATGTATCGATACA
492105 TTTTGGACAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
20 32 0.65
25 16 0.33
26 1 0.02
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:498220 original size:13 final size:13
Alignment explanation
Indices: 498202--498227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
498192 CAATTTTTTG
498202 TGTATCGATACAT
1 TGTATCGATACAT
498215 TGTATCGATACAT
1 TGTATCGATACAT
498228 ACTTGATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:498291 original size:20 final size:20
Alignment explanation
Indices: 498266--498339 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
498256 CTGCCAAGAA
498266 ATGTATCGATACAACTTTTT
1 ATGTATCGATACAACTTTTT
***
498286 ATGTATCGATAC-A-TTGCAAC
1 ATGTATCGATACAACTT--TTT
*
498306 ATGTATCGATACATCTTTTT
1 ATGTATCGATACAACTTTTT
498326 CATGTATCGATACA
1 -ATGTATCGATACA
498340 TTGCAACATG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 24 0.57
21 13 0.31
22 2 0.05
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAACTTTTT
Found at i:498343 original size:41 final size:40
Alignment explanation
Indices: 498266--498358 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 40
498256 CTGCCAAGAA
498266 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
*
498306 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTT-ATGTATCGATACATTGCAAC
498347 ATGTATCGATAC
1 ATGTATCGATAC
498359 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 19 0.37
41 32 0.63
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (40 bp):
ATGTATCGATACAACTTTTTATGTATCGATACATTGCAAC
Found at i:498351 original size:20 final size:20
Alignment explanation
Indices: 498286--498358 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
498276 ACAACTTTTT
498286 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
498306 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
498327 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
498347 ATGTATCGATAC
1 ATGTATCGATAC
498359 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:498712 original size:32 final size:33
Alignment explanation
Indices: 498650--498712 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
498640 GATCCTAACA
** * *
498650 GTATCGATACAATTTTTTGTGTATCGATACATT
1 GTATCGATACAATACTTGGTGTATCAATACATT
498683 GTATCGATA-AATACTTGGTGTATCAATACA
1 GTATCGATACAATACTTGGTGTATCAATACA
498713 AGTTTGGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (33 bp):
GTATCGATACAATACTTGGTGTATCAATACATT
Found at i:499183 original size:427 final size:424
Alignment explanation
Indices: 498306--499073 Score: 1342
Period size: 427 Copynumber: 1.8 Consensus size: 424
498296 ACATTGCAAC
*
498306 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
1 ATGTATCGATA-ATCTATTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
*
498371 ATCGATACTTTTAGGGGTTTTGACAATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
65 ATCGATACTTTTAAGGGTTTTGACAATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
*
498436 CTATGTATCGATACTTTGATACATTTTAACTTAAAAATTAATCATTTTAAGCCTTGAAAACATTT
130 CTATGTATCGATACTTTGATACATTTTAACTTAAAAATCAATCATTTTAAGCCTTGAAAACATTT
*
498501 GTACTTAACTAGAAAACATTTAGTGAATCAAAAATCATTTGGTACAAAATTTATAAAGCATCTAA
195 ATACTTAACTAGAAAACATTTAGTGAATCAAAAATCATTTGGTACAAAATTTATAAAGCATCTAA
498566 TTGAATAAAACATATTATTGTTATTTTCAAAATAATTTCCGGTTTTATTCAATCCTTTGTTATAT
260 TTGAATAAAACATATTATTGTTATTTTCAAAATAATTTCCGGTTTTATTCAATCCTTTGTTATAT
* * * * * **
498631 CAAAACCAAGATCCTAACAGTATCGATACAATTTTTTGTGTATCGATACATTGTATCGATAAATA
325 CAAAACCAAGATCCTAACAG-ATC-ATACAACTTTTTGTATAACAAAACATTGTATAAATAAATA
498696 CTTGGTGTATCAATACAAGTTTGGCTACTGCCAAGAA
388 CTTGGTGTATCAATACAAGTTTGGCTACTGCCAAGAA
*
498733 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
1 ATGTATCGATA-ATCTATTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGT
498798 ATCGATACTTTTAAGGGTTTTGACAATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
65 ATCGATACTTTTAAGGGTTTTGACAATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATAC
*
498863 CTATGTATCGATACTTTGATATATTTTAACTTAAAAATCAATCATTTTAAGCCTTGAAAACATTT
130 CTATGTATCGATACTTTGATACATTTTAACTTAAAAATCAATCATTTTAAGCCTTGAAAACATTT
* *
498928 ATCCTTAACTAGAAAACATTTGGTGAATCAAAAATCATTTGGTACAAAATTTATAAAGCA-CTTA
195 ATACTTAACTAGAAAACATTTAGTGAATCAAAAATCATTTGGTACAAAATTTATAAAGCATC-TA
498992 ATTGAATAAAACATATTATTGTTATTTTC-AAATAATTTCCGGTTTTATTCAATCCTTTGTTATA
259 ATTGAATAAAACATATTATTGTTATTTTCAAAATAATTTCCGGTTTTATTCAATCCTTTGTTATA
499056 TCAAAACCAAGATCCTAA
324 TCAAAACCAAGATCCTAA
499074 TAATCTCCCC
Statistics
Matches: 334, Mismatches: 6, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
426 54 0.16
427 280 0.84
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (424 bp):
ATGTATCGATAATCTATTTCATGTATCGATACATTGCAACATGTATCGATACTTTGAATTGTGTA
TCGATACTTTTAAGGGTTTTGACAATTTTAGCCTAAGTCAACCTTAATGTATCGATACAAATACC
TATGTATCGATACTTTGATACATTTTAACTTAAAAATCAATCATTTTAAGCCTTGAAAACATTTA
TACTTAACTAGAAAACATTTAGTGAATCAAAAATCATTTGGTACAAAATTTATAAAGCATCTAAT
TGAATAAAACATATTATTGTTATTTTCAAAATAATTTCCGGTTTTATTCAATCCTTTGTTATATC
AAAACCAAGATCCTAACAGATCATACAACTTTTTGTATAACAAAACATTGTATAAATAAATACTT
GGTGTATCAATACAAGTTTGGCTACTGCCAAGAA
Found at i:501254 original size:13 final size:13
Alignment explanation
Indices: 501236--501273 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
501226 ATAATCACCC
501236 TGTATCGATACAA
1 TGTATCGATACAA
501249 TGTATCGATACAA
1 TGTATCGATACAA
501262 TGTATCGATACA
1 TGTATCGATACA
501274 TTGAATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:503351 original size:15 final size:15
Alignment explanation
Indices: 503331--503361 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
503321 ATTTCGTTTG
*
503331 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
503346 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
503361 G
1 G
503362 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:505190 original size:20 final size:21
Alignment explanation
Indices: 505155--505205 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
505145 TATGCAAGTT
505155 TTCATT-TTTC-TTAGCTAAC
1 TTCATTATTTCATTAGCTAAC
505174 -TCATTATTTCATTAGCTAAC
1 TTCATTATTTCATTAGCTAAC
505194 TTC-TTATTTCAT
1 TTCATTATTTCAT
505206 CTTGCAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.17
19 4 0.14
20 18 0.62
21 2 0.07
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTCATTATTTCATTAGCTAAC
Found at i:507437 original size:13 final size:13
Alignment explanation
Indices: 507419--507444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
507409 CAATTTTTTG
507419 TGTATCGATACAT
1 TGTATCGATACAT
507432 TGTATCGATACAT
1 TGTATCGATACAT
507445 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:507459 original size:32 final size:33
Alignment explanation
Indices: 507399--507462 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
507389 AACAAGCCAA
** *
507399 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
507432 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
507463 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Done.