Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold452
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: 589716
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
File 4 of 5
Found at i:334680 original size:26 final size:26
Alignment explanation
Indices: 334651--334702 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
334641 TGTTGTTTTG
*
334651 TGCATAATTAGTTTGAATATATATAT
1 TGCATAATTAGATTGAATATATATAT
334677 TGCATAATTAGATTGAATATATATAT
1 TGCATAATTAGATTGAATATATATAT
334703 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (26 bp):
TGCATAATTAGATTGAATATATATAT
Found at i:336491 original size:15 final size:15
Alignment explanation
Indices: 336471--336522 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
336461 ATAATATAAA
336471 TATAATATAAAATTT
1 TATAATATAAAATTT
336486 TATAATA-AAAA--T
1 TATAATATAAAATTT
* *
336498 TATTATATAATATTT
1 TATAATATAAAATTT
336513 TA-AATATAAA
1 TATAATATAAA
336523 TATGATATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 10 0.33
15 10 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAATATAAAATTT
Found at i:336512 original size:27 final size:26
Alignment explanation
Indices: 336461--336534 Score: 96
Period size: 26 Copynumber: 2.8 Consensus size: 26
336451 TTGTAAAAAA
336461 ATAATATAAATATAATATAAAATTTT
1 ATAATATAAATATAATATAAAATTTT
* * *
336487 ATAATAAAAATTATTATATAATATTTT
1 ATAATATAAA-TATAATATAAAATTTT
*
336514 A-AATATAAATATGATATAAAA
1 ATAATATAAATATAATATAAAA
336535 AATATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 10 0.24
26 16 0.39
27 15 0.37
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
ATAATATAAATATAATATAAAATTTT
Found at i:341262 original size:2 final size:2
Alignment explanation
Indices: 341253--341322 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
341243 AGAAGAGAGA
* *
341253 AT AT -T AT AT A- AT AC AT AA 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
341293 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
341323 TGGACGAGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
1 2 0.03
2 60 0.97
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:341828 original size:19 final size:18
Alignment explanation
Indices: 341783--341824 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
341773 TAATATTATG
341783 TATAATATAA-AAAAATA
1 TATAATATAATAAAAATA
*
341800 -AAAATATAATAAAAATA
1 TATAATATAATAAAAATA
341817 TATAATAT
1 TATAATAT
341825 TAATTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TATAATATAATAAAAATA
Found at i:342856 original size:32 final size:34
Alignment explanation
Indices: 342799--342898 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 34
342789 GTATAATTAT
*
342799 TTAATATATTATATATTTATATAAATTTTTACT-TA
1 TTAATATATT-TATA-TTATATAAATTTTTAATATA
342834 TTAATA-ATTTATATTATATAAA-TTTTAATATA
1 TTAATATATTTATATTATATAAATTTTTAATATA
* *
342866 TTCATATATTTATATTCATAT-TATTTTTAATAT
1 TTAATATATTTATATT-ATATAAATTTTTAATAT
342899 CAATATTATG
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
31 6 0.10
32 16 0.28
33 14 0.24
34 16 0.28
35 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (34 bp):
TTAATATATTTATATTATATAAATTTTTAATATA
Found at i:342879 original size:14 final size:15
Alignment explanation
Indices: 342862--342891 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
342852 TAAATTTTAA
342862 TATATTCATA-TATT
1 TATATTCATATTATT
342876 TATATTCATATTATT
1 TATATTCATATTATT
342891 T
1 T
342892 TTAATATCAA
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:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTCATATTATT
Found at i:349241 original size:18 final size:18
Alignment explanation
Indices: 349218--349325 Score: 58
Period size: 21 Copynumber: 5.3 Consensus size: 18
349208 ATCTTCTTCT
349218 CTCCTCCTCCTATCATCC
1 CTCCTCCTCCTATCATCC
*
349236 CTCCT-CTCTCTATTATCTCTC
1 CTCCTCCTC-CTATCA--TC-C
349257 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
*
349278 CTCCTATCTCTACTATC-TCTC
1 CTCC--TC-CTCCTATCATC-C
349299 CTGTCTCTCCTCCTATCATCC
1 C--TC-CTCCTCCTATCATCC
349320 CTCCTC
1 CTCCTC
349326 TCTCTTCTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 32
0.66 0.04 0.30
Matches are distributed among these distances:
17 3 0.04
18 14 0.20
19 4 0.06
20 6 0.09
21 22 0.31
22 6 0.09
23 4 0.06
24 8 0.11
25 3 0.04
ACGTcount: A:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (18 bp):
CTCCTCCTCCTATCATCC
Found at i:349273 original size:42 final size:42
Alignment explanation
Indices: 349221--349339 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
349211 TTCTTCTCTC
*
349221 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
349263 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
349305 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
349340 TTGAGGGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.09, C:0.46, G:0.02, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:349280 original size:12 final size:11
Alignment explanation
Indices: 349254--349329 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
349244 TCTATTATCT
*
349254 CTCCTGTCTCTC
1 CTCCTATCTC-C
349266 CTCCTATCATCC
1 CTCCTATC-TCC
349278 CTCCTATCT--
1 CTCCTATCTCC
*
349287 CTACTATCT--
1 CTCCTATCTCC
*
349296 CTCCTGTCTCTC
1 CTCCTATCTC-C
349308 CTCCTATCATCC
1 CTCCTATC-TCC
*
349320 CTCCTCTCTC
1 CTCCTATCTC
349330 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:353510 original size:30 final size:30
Alignment explanation
Indices: 353474--353533 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
353464 GTTGGTTAAG
353474 TACATTTTATTTATGTATTAGATTATGATA
1 TACATTTTATTTATGTATTAGATTATGATA
*
353504 TACATTTTATTTATGTATTATATTATGATA
1 TACATTTTATTTATGTATTAGATTATGATA
353534 CACTCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.55
Consensus pattern (30 bp):
TACATTTTATTTATGTATTAGATTATGATA
Found at i:353697 original size:22 final size:22
Alignment explanation
Indices: 353671--353715 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
353661 TTAAATGAAA
353671 TTATTAATATAATTTTATAATT
1 TTATTAATATAATTTTATAATT
* * *
353693 TTATTACTTTTATTTTATAATT
1 TTATTAATATAATTTTATAATT
353715 T
1 T
353716 GATTTTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTAATATAATTTTATAATT
Found at i:354072 original size:26 final size:26
Alignment explanation
Indices: 354037--354088 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
354027 TAAATTTATA
*
354037 TATTATAAAT-AAATTAGATGATATTT
1 TATTAAAAATAAAATTAGAT-ATATTT
*
354063 TATTAAAAATAAAATTATATATATTT
1 TATTAAAAATAAAATTAGATATATTT
354089 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TATTAAAAATAAAATTAGATATATTT
Found at i:354935 original size:26 final size:25
Alignment explanation
Indices: 354883--354928 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
354873 ATTTTGATAA
354883 TATATAA-AATAATTATTTAAAATT
1 TATATAATAATAATTATTTAAAATT
*
354907 TATATAATAAT-ATTTTTTAAAA
1 TATATAATAATAATTATTTAAAA
354929 ATTTTATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATAATAATAATTATTTAAAATT
Found at i:356052 original size:26 final size:27
Alignment explanation
Indices: 356025--356123 Score: 96
Period size: 26 Copynumber: 3.6 Consensus size: 27
356015 TAATATTAAA
*
356025 ATATAATATAAAT-TATTAAT-TTTTAA
1 ATATAATATAAATATA-AAATATTTTAA
*
356051 ATTTAATATAAATATAAAATATTTTAA
1 ATATAATATAAATATAAAATATTTTAA
* *
356078 ATATGATTTATAACATAATAAAATA-TATAA
1 ATAT-A-ATATAA-AT-ATAAAATATTTTAA
356108 ATATAATATAAATATA
1 ATATAATATAAATATA
356124 TGAATAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
26 18 0.30
27 13 0.21
28 6 0.10
29 6 0.10
30 10 0.16
31 8 0.13
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
ATATAATATAAATATAAAATATTTTAA
Found at i:356399 original size:23 final size:23
Alignment explanation
Indices: 356348--356418 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
356338 TAAAACTTAA
*
356348 AAAATA-TAAT-TAAT-TTATTT
1 AAAATATTAATATAATATAATTT
*
356368 -AAATTTTAATATAATATAATTT
1 AAAATATTAATATAATATAATTT
*
356390 AAAATATTAATA-ATTAATAATTT
1 AAAATATTAATATAAT-ATAATTT
356413 AAAATA
1 AAAATA
356419 AAAAATTACG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 4 0.10
22 7 0.17
23 23 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATATTAATATAATATAATTT
Found at i:356479 original size:17 final size:17
Alignment explanation
Indices: 356441--356477 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
356431 AAATAATCAT
356441 AATTT-AAATTAATTTA
1 AATTTAAAATTAATTTA
356457 AATTTAAAATT-ATTTA
1 AATTTAAAATTAATTTA
356473 AATTT
1 AATTT
356478 TATTCCTCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTAAAATTAATTTA
Found at i:360298 original size:15 final size:14
Alignment explanation
Indices: 360262--360304 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
360252 TTGACTTCGT
360262 TTTTAATTATTTTA
1 TTTTAATTATTTTA
360276 TTTT-ATTATTGTT-
1 TTTTAATTATT-TTA
360289 TCTTTAATTATTTTA
1 T-TTTAATTATTTTA
360304 T
1 T
360305 GATGTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 7 0.28
14 11 0.44
15 7 0.28
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTTAATTATTTTA
Found at i:360985 original size:19 final size:19
Alignment explanation
Indices: 360961--361000 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
360951 TTTACTGTCT
360961 GAACTGATCTTGTTAACTG
1 GAACTGATCTTGTTAACTG
360980 GAACTGATCTTGTTAACTG
1 GAACTGATCTTGTTAACTG
360999 GA
1 GA
361001 CTACAAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.35
Consensus pattern (19 bp):
GAACTGATCTTGTTAACTG
Found at i:362892 original size:2 final size:2
Alignment explanation
Indices: 362885--362912 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
362875 CTGCATCAAC
362885 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
362913 TCAAAAACAA
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):
AT
Found at i:365506 original size:18 final size:18
Alignment explanation
Indices: 365485--365521 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
365475 TGGATGGCTT
365485 TTATGTGATTATTACAGA
1 TTATGTGATTATTACAGA
365503 TTATGTGATTATTACAGA
1 TTATGTGATTATTACAGA
365521 T
1 T
365522 GTGAGTAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (18 bp):
TTATGTGATTATTACAGA
Found at i:366803 original size:28 final size:29
Alignment explanation
Indices: 366757--366829 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 29
366747 GGATTATTTT
366757 TTAAATAAT-T-ATACAAATT-ATTATTAAA
1 TTAAATAATATAATA-AAATTAATT-TTAAA
366785 -TAAACTAATA-AATAAAATTAATTTTAAA
1 TTAAA-TAATATAATAAAATTAATTTTAAA
366813 TTAAATAATATAATAAA
1 TTAAATAATATAATAAA
366830 TAAAAATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
27 4 0.10
28 19 0.49
29 16 0.41
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAATAATATAATAAAATTAATTTTAAA
Found at i:366832 original size:7 final size:7
Alignment explanation
Indices: 366816--366850 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
366806 TTTTAAATTA
366816 AATAATAT
1 AATAA-AT
366824 AATAAAT
1 AATAAAT
366831 AA-AAAT
1 AATAAAT
366837 AATAAAT
1 AATAAAT
366844 AATAAAT
1 AATAAAT
366851 CGTGTACTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 15 0.58
8 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:366840 original size:13 final size:14
Alignment explanation
Indices: 366816--366850 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
366806 TTTTAAATTA
366816 AATAATATAATAAAT
1 AATAA-ATAATAAAT
366831 AA-AAATAATAAAT
1 AATAAATAATAAAT
366844 AATAAAT
1 AATAAAT
366851 CGTGTACTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 11 0.58
14 6 0.32
15 2 0.11
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATAATAAAT
Found at i:367837 original size:67 final size:65
Alignment explanation
Indices: 367727--367871 Score: 247
Period size: 67 Copynumber: 2.2 Consensus size: 65
367717 AATATATGTA
*
367727 ATATATATATATAAAATATATTAATGCATCGAAACATTAATCTGTCCATATGTACATGCATATAT
1 ATATATATATATATAATATATTAATGCATCGAAACATTAATCTGTCCATATGTACATGCATATAT
*
367792 ATATATATATATATAATATTATTAATGCATCGAAACGATTGATCTGTCCATATGTACATGCATAT
1 ATATATATATATATAATA-TATTAATGCATCGAAAC-ATTAATCTGTCCATATGTACATGCATAT
367857 AT
64 AT
367859 ATATATATA-ATAT
1 ATATATATATATAT
367872 TAATGCATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
65 17 0.22
66 21 0.28
67 38 0.50
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (65 bp):
ATATATATATATATAATATATTAATGCATCGAAACATTAATCTGTCCATATGTACATGCATATAT
Found at i:368721 original size:6 final size:6
Alignment explanation
Indices: 368710--368734 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
368700 ATTGCTAATT
368710 AATTTA AATTTA AATTTA AATTTA A
1 AATTTA AATTTA AATTTA AATTTA A
368735 TTAATTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:375698 original size:21 final size:21
Alignment explanation
Indices: 375672--375718 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
375662 CAAATGAAGA
*
375672 AGCTAG-AAAGAGCTAATATTG
1 AGCTAGAAAAG-GCTAAAATTG
375693 AGCTAGAAAAGGCTAAAATTG
1 AGCTAGAAAAGGCTAAAATTG
375714 AGCTA
1 AGCTA
375719 AAGCAGCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (21 bp):
AGCTAGAAAAGGCTAAAATTG
Found at i:376732 original size:39 final size:39
Alignment explanation
Indices: 376678--376762 Score: 125
Period size: 39 Copynumber: 2.2 Consensus size: 39
376668 AGTTATCCTA
* * *
376678 TCAAATCTATAATCATATTATTCAACCTTAAAACAAAAC
1 TCAAACCTAAAATCATATTACTCAACCTTAAAACAAAAC
*
376717 TCAAACCTAAAATCATATTACTCAATCTTAAAACAAAAC
1 TCAAACCTAAAATCATATTACTCAACCTTAAAACAAAAC
*
376756 CCAAACC
1 TCAAACC
376763 CACGTACTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (39 bp):
TCAAACCTAAAATCATATTACTCAACCTTAAAACAAAAC
Found at i:376740 original size:21 final size:21
Alignment explanation
Indices: 376678--376741 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
376668 AGTTATCCTA
* * *
376678 TCAAATCTATAATCATATTAT
1 TCAAACCTAAAATCATATTAC
*
376699 TC-AACCTTAAAA-CA-A-AAC
1 TCAAACC-TAAAATCATATTAC
376717 TCAAACCTAAAATCATATTAC
1 TCAAACCTAAAATCATATTAC
376738 TCAA
1 TCAA
376742 TCTTAAAACA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
18 8 0.24
19 7 0.21
20 6 0.18
21 12 0.36
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (21 bp):
TCAAACCTAAAATCATATTAC
Found at i:376748 original size:21 final size:21
Alignment explanation
Indices: 376688--376749 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
376678 TCAAATCTAT
* *
376688 AATCATATTATTCAACCTTAA
1 AATCATATTACTCAAACTTAA
* *
376709 AA-CA-A-AACTCAAACCTAA
1 AATCATATTACTCAAACTTAA
*
376727 AATCATATTACTCAATCTTAA
1 AATCATATTACTCAAACTTAA
376748 AA
1 AA
376750 CAAAACCCAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 11 0.35
19 3 0.10
20 3 0.10
21 14 0.45
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (21 bp):
AATCATATTACTCAAACTTAA
Found at i:377184 original size:13 final size:13
Alignment explanation
Indices: 377166--377190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
377156 ACTTCAGATT
377166 AAATATTAAATTA
1 AAATATTAAATTA
377179 AAATATTAAATT
1 AAATATTAAATT
377191 TTTAAATTAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATATTAAATTA
Found at i:378441 original size:3 final size:3
Alignment explanation
Indices: 378433--378465 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
378423 ATCAAATCTG
378433 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
378466 ATTTTATGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:378900 original size:3 final size:3
Alignment explanation
Indices: 378892--378926 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
378882 CCTCAGAGTC
378892 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
378927 GGCTCATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:379370 original size:19 final size:19
Alignment explanation
Indices: 379346--379413 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
379336 TAGTTTAACT
*
379346 TTTAAATTATTTAATTTAA
1 TTTAAATTATTTATTTTAA
379365 TTTAAATTA-TTATTCATTAA
1 TTTAAATTATTTATT--TTAA
*
379385 TTAAAATTATATT-TTTTAA
1 TTTAAATTAT-TTATTTTAA
379404 TTT-AATTATT
1 TTTAAATTATT
379414 AAAAATATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
17 1 0.02
18 10 0.24
19 15 0.36
20 12 0.29
21 2 0.05
22 2 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTAAATTATTTATTTTAA
Found at i:379452 original size:24 final size:24
Alignment explanation
Indices: 379380--379454 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
379370 ATTATTATTC
379380 ATTAATTAAAATTATATTTTTTAAT
1 ATTAATTAAAA-TATATTTTTTAAT
* * *
379405 -TTAATTATTAAA-A-ATATATAAAT
1 ATTAATTA--AAATATATTTTTTAAT
379428 ATTAATTAAAATATATTTTTTAAT
1 ATTAATTAAAATATATTTTTTAAT
379452 ATT
1 ATT
379455 TTATTATATT
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
22 3 0.08
23 8 0.21
24 25 0.64
26 3 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTAATTAAAATATATTTTTTAAT
Found at i:379490 original size:20 final size:20
Alignment explanation
Indices: 379346--379494 Score: 54
Period size: 19 Copynumber: 8.0 Consensus size: 20
379336 TAGTTTAACT
*
379346 TTTAAATTATTTAAT-TTAA
1 TTTAAATTATTAAATATTAA
*
379365 TTTAAATTATT-ATTCATTAA
1 TTTAAATTATTAAAT-ATTAA
* ** *
379385 TTAAAATTA-TATTTTTTAA
1 TTTAAATTATTAAATATTAA
*
379404 TTT-AATTATTAAA-AAT-A
1 TTTAAATTATTAAATATTAA
*
379421 TATAAA-TATT--A-ATTAA
1 TTTAAATTATTAAATATTAA
** * * * *
379437 AATATATTTTTTAATATT-T
1 TTTAAATTATTAAATATTAA
*
379456 TATTATATT-TTAAATATTAA
1 T-TTAAATTATTAAATATTAA
379476 TTTAAATTATTAAAT-TTAA
1 TTTAAATTATTAAATATTAA
379495 GCGTAAGGAG
Statistics
Matches: 97, Mismatches: 20, Indels: 26
0.68 0.14 0.18
Matches are distributed among these distances:
15 3 0.03
16 5 0.05
17 10 0.10
18 10 0.10
19 39 0.40
20 30 0.31
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTATTAAATATTAA
Found at i:387694 original size:16 final size:16
Alignment explanation
Indices: 387670--387709 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
387660 TATATTTATA
*
387670 TAAT-TTTTTATATAAT
1 TAATATTTTAATA-AAT
387686 TAATATTTTAATAAAT
1 TAATATTTTAATAAAT
387702 TAATATTT
1 TAATATTT
387710 AAATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATATTTTAATAAAT
Found at i:389114 original size:207 final size:207
Alignment explanation
Indices: 388759--389173 Score: 751
Period size: 207 Copynumber: 2.0 Consensus size: 207
388749 CCTACATCGG
*
388759 CAACTCCTGCGACTTCCCCATCCACATCATCGCTTCCACCTACTATAACTAGTCCGACTGCTATG
1 CAACTCCTGCGACTTCCCCATCCACATCATCGCTTCCACCTACTACAACTAGTCCGACTGCTATG
*
388824 CCCCCACTGGCTCAATCCCCTGCTGTGATTCCGCCTGCTTCTTCCAGCCCCCCGTTTCAATCTCC
66 CCCCCACTGGCTCAATCCCCTGCTGTGATTCCGCCTGCTTCTTCCAGCCCCCAGTTTCAATCTCC
388889 AGAGGCTGCTCCATCAATAGCTACGCCTCCGGCATTCACACCCGCAAGTTCCCCTCCGTCACTGA
131 AGAGGCTGCTCCATCAATAGCTACGCCTCCGGCATTCACACCCGCAAGTTCCCCTCCGTCACTGA
388954 CACCAACAGGTT
196 CACCAACAGGTT
* *
388966 CAACTCCTGCGACTTCCCCATCCACATCATCGCTTCCGCCTGCTACAACTAGTCCGACTGCTATG
1 CAACTCCTGCGACTTCCCCATCCACATCATCGCTTCCACCTACTACAACTAGTCCGACTGCTATG
*
389031 CCCCCACTGGCTCAATCCCCTGCTGTGATTCCGCCTGCTTCTTCGAGGCCCCCAG-TTCAATCTC
66 CCCCCACTGGCTCAATCCCCTGCTGTGATTCCGCCTGCTTCTTCCA-GCCCCCAGTTTCAATCTC
* *
389095 CAGAGGCTGCTCCATCAATAGCTACGCCTCCGGCATTCACACCCGCAAGTTCCTCTCCGTCATTG
130 CAGAGGCTGCTCCATCAATAGCTACGCCTCCGGCATTCACACCCGCAAGTTCCCCTCCGTCACTG
389160 ACACCAACAGGTT
195 ACACCAACAGGTT
389173 C
1 C
389174 TTCCCCAACA
Statistics
Matches: 200, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
207 193 0.96
208 7 0.04
ACGTcount: A:0.19, C:0.41, G:0.15, T:0.24
Consensus pattern (207 bp):
CAACTCCTGCGACTTCCCCATCCACATCATCGCTTCCACCTACTACAACTAGTCCGACTGCTATG
CCCCCACTGGCTCAATCCCCTGCTGTGATTCCGCCTGCTTCTTCCAGCCCCCAGTTTCAATCTCC
AGAGGCTGCTCCATCAATAGCTACGCCTCCGGCATTCACACCCGCAAGTTCCCCTCCGTCACTGA
CACCAACAGGTT
Found at i:389784 original size:21 final size:22
Alignment explanation
Indices: 389745--389787 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
389735 CTAAAAACCA
389745 TTAATTTTTTTAACAATTAAAT
1 TTAATTTTTTTAACAATTAAAT
*
389767 TTAATTTTTTTAA-TATTAAAT
1 TTAATTTTTTTAACAATTAAAT
389788 ATATAAAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTTTTTAACAATTAAAT
Found at i:389906 original size:19 final size:19
Alignment explanation
Indices: 389879--389951 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
389869 TGATCACGAC
*
389879 ATATTTAATAAATATTAAA
1 ATATATAATAAATATTAAA
389898 ATATATAATAAATATAATATAA
1 ATATATAATAAATAT--TA-AA
*
389920 TATATTTAAATAAA-ATTAAA
1 -ATATAT-AATAAATATTAAA
389940 ATA-ATAA-AAATA
1 ATATATAATAAATA
389952 CATATATTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
16 3 0.07
17 3 0.07
18 1 0.02
19 17 0.38
20 2 0.04
21 4 0.09
22 2 0.04
23 7 0.16
24 6 0.13
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATAATAAATATTAAA
Found at i:389916 original size:24 final size:23
Alignment explanation
Indices: 389885--389956 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 23
389875 CGACATATTT
389885 AATAAATATTAAAATATATAATA
1 AATAAATATTAAAATATATAATA
*
389908 AATATAATA-T--AATATAT-TTA
1 AATA-AATATTAAAATATATAATA
389928 AATAAA-ATTAAAATA-ATAA-A
1 AATAAATATTAAAATATATAATA
*
389948 AATACATAT
1 AATAAATAT
389957 ATTGTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 14 0.35
21 13 0.32
23 5 0.12
24 4 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAATATTAAAATATATAATA
Found at i:390713 original size:20 final size:20
Alignment explanation
Indices: 390690--390729 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
390680 AATATATTTT
390690 TATATAAAT-TTAAATATAAA
1 TATATAAATATT-AATATAAA
*
390710 TATATAACTATTAATATAAA
1 TATATAAATATTAATATAAA
390730 AATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (20 bp):
TATATAAATATTAATATAAA
Found at i:393093 original size:22 final size:22
Alignment explanation
Indices: 393065--393107 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
393055 AAGTAGGACT
393065 GCATTCAGTCGTCCAATTTGTG
1 GCATTCAGTCGTCCAATTTGTG
*
393087 GCATTCAGTCTTCCAATTTGT
1 GCATTCAGTCGTCCAATTTGT
393108 ATGAAGCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.40
Consensus pattern (22 bp):
GCATTCAGTCGTCCAATTTGTG
Found at i:396994 original size:33 final size:33
Alignment explanation
Indices: 396947--397014 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
396937 CCAATCCCAG
*
396947 TTCTTCGACCCAGCATCAAACGAGCTTTCTGGT
1 TTCTTCGACCCAGCATCAAACGAGCTTTCAGGT
* * *
396980 TTCTTGGACTCAGCATCTAACGAGCTTTCAGGT
1 TTCTTCGACCCAGCATCAAACGAGCTTTCAGGT
397013 TT
1 TT
397015 TGTCACCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (33 bp):
TTCTTCGACCCAGCATCAAACGAGCTTTCAGGT
Found at i:397806 original size:77 final size:77
Alignment explanation
Indices: 397676--397821 Score: 231
Period size: 77 Copynumber: 1.9 Consensus size: 77
397666 GGAGGCATTT
* * *
397676 GTGACTTTCATGTTCTTCTTATCAGGCAACTCATCACTTTGATCCATAGGCATGACATTGTTGTG
1 GTGACTTGCATGTTCTTCTCATCAGGCAACTCATCACTGTGATCCATAGGCATGACATTGTTGTG
397741 ATGTTGCGTATA
66 ATGTTGCGTATA
* *
397753 GTGACTTGCATGTTCTTCTCATCACGG-AACTCATCACTGTGATCCATATGCATGACTTTGTTGT
1 GTGACTTGCATGTTCTTCTCATCA-GGCAACTCATCACTGTGATCCATAGGCATGACATTGTTGT
397817 GATGT
65 GATGT
397822 AGAGCCAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 61 0.97
78 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (77 bp):
GTGACTTGCATGTTCTTCTCATCAGGCAACTCATCACTGTGATCCATAGGCATGACATTGTTGTG
ATGTTGCGTATA
Found at i:399350 original size:99 final size:99
Alignment explanation
Indices: 399229--399429 Score: 248
Period size: 101 Copynumber: 2.0 Consensus size: 99
399219 TTATTTTCTC
* ** *
399229 CACATAAATTTTGACAATTGCTCTACCCCCT-AA-AATTAAAAATATAAATAGA-TGTTTTATCT
1 CACATAAATTTTGACAACTGCTCTACCCCCTAAATAAAAAAAAATACAAATA-ACTGTTTTATCT
** *
399291 -TAGAATATTTTTTATTAATTTTTTAATAATAATCAT
65 CT-GAATATTTTTTATTAA-CATGTAATAATAATCAT
*
399327 CACATTAAATTTTGACAACTGCTCTACCCTCTAAATAAAAAAAAATACAAATAACTGTTTTATCT
1 CACA-TAAATTTTGACAACTGCTCTACCCCCTAAATAAAAAAAAATACAAATAACTGTTTTATCT
* *
399392 CTTAATTTTTTTTATTAACATGTAATAATAATCAT
65 CTGAATATTTTTTATTAACATGTAATAATAATCAT
399427 CAC
1 CAC
399430 CTGATTCTAA
Statistics
Matches: 88, Mismatches: 10, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
98 4 0.05
99 25 0.28
100 20 0.23
101 38 0.43
102 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (99 bp):
CACATAAATTTTGACAACTGCTCTACCCCCTAAATAAAAAAAAATACAAATAACTGTTTTATCTC
TGAATATTTTTTATTAACATGTAATAATAATCAT
Found at i:401154 original size:6 final size:6
Alignment explanation
Indices: 401140--401173 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
401130 TTTGCTACAT
* *
401140 AGGCAC AGGCTC AGGCTC AGGCTC AGGCAC AGGC
1 AGGCTC AGGCTC AGGCTC AGGCTC AGGCTC AGGC
401174 AAAATTCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.24, C:0.32, G:0.35, T:0.09
Consensus pattern (6 bp):
AGGCTC
Found at i:401160 original size:12 final size:12
Alignment explanation
Indices: 401140--401173 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
401130 TTTGCTACAT
401140 AGGCACAGGCTC
1 AGGCACAGGCTC
*
401152 AGGCTCAGGCTC
1 AGGCACAGGCTC
401164 AGGCACAGGC
1 AGGCACAGGC
401174 AAAATTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.32, G:0.35, T:0.09
Consensus pattern (12 bp):
AGGCACAGGCTC
Found at i:401624 original size:2 final size:2
Alignment explanation
Indices: 401617--401647 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
401607 CTGTCGCTCT
401617 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
401648 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:401652 original size:2 final size:2
Alignment explanation
Indices: 401647--401681 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
401637 ACACACACAC
* *
401647 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
401682 ATTTAAAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:405003 original size:71 final size:71
Alignment explanation
Indices: 404887--405029 Score: 277
Period size: 71 Copynumber: 2.0 Consensus size: 71
404877 TTTAGCTTAA
404887 GATAGTTTCCTCTTTGAAGGTTTTGCAACCTAAAGAGTTGCATATGCAGGAATTGACTTCATAAA
1 GATAGTTTCCTCTTTGAAGGTTTTGCAACCTAAAGAGTTGCATATGCAGGAATTGACTTCATAAA
404952 AATGCT
66 AATGCT
*
404958 GATAGTTTCCTCTTTGAAGGTTTTGCAACCTAAAGAGTTGCATATGCAGGAATTGACTTTATAAA
1 GATAGTTTCCTCTTTGAAGGTTTTGCAACCTAAAGAGTTGCATATGCAGGAATTGACTTCATAAA
405023 AATGCT
66 AATGCT
405029 G
1 G
405030 GTCTTCTAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 71 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (71 bp):
GATAGTTTCCTCTTTGAAGGTTTTGCAACCTAAAGAGTTGCATATGCAGGAATTGACTTCATAAA
AATGCT
Found at i:410491 original size:129 final size:128
Alignment explanation
Indices: 410346--410600 Score: 431
Period size: 129 Copynumber: 2.0 Consensus size: 128
410336 TTGTTGAAGT
* * *
410346 TTTTAACTTATTATAGATGTATTTTTTACTTATACTTGACATTTGAAATTTTGTTAGGATGATTA
1 TTTTAACTTATTATAGATGTATCTTTTACTTATACTTGAAATTTAAAATTTTGTT-GGATGATTA
*
410411 TCCT-TATTTGAATTATAAAAAAATTTAAAATTTTAAAATGTAATTTTAATTTATTGATGTAAGG
65 TCCTGTATTTGAATTATAAAAAAA-TTAAAATTTTAAAATGTAATTTTAACTTATTGATGTAAGG
*
410475 TTTTGACTTATTATAGATGTATCTTTTACTTATACTTGAAATTTAAAATTTTGTTGGATGATTAT
1 TTTTAACTTATTATAGATGTATCTTTTACTTATACTTGAAATTTAAAATTTTGTTGGATGATTAT
*
410540 CCTGTATTTGAATTATAAAAAAATTAGAATTTTAAAATGTAATTTTAACTTATTGATGTAA
66 CCTGTATTTGAATTATAAAAAAATTAAAATTTTAAAATGTAATTTTAACTTATTGATGTAA
410601 AACAATTAAA
Statistics
Matches: 119, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
128 49 0.41
129 70 0.59
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (128 bp):
TTTTAACTTATTATAGATGTATCTTTTACTTATACTTGAAATTTAAAATTTTGTTGGATGATTAT
CCTGTATTTGAATTATAAAAAAATTAAAATTTTAAAATGTAATTTTAACTTATTGATGTAAGG
Found at i:412417 original size:23 final size:23
Alignment explanation
Indices: 412391--412435 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
412381 TTCATTGGTA
412391 ACATATAAATAT-ATATATATATT
1 ACAT-TAAATATAATATATATATT
*
412414 ACATTAAATATAATTTATATAT
1 ACATTAAATATAATATATATAT
412436 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
ACATTAAATATAATATATATATT
Found at i:412664 original size:19 final size:20
Alignment explanation
Indices: 412634--412671 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
412624 TTTTAAAAAT
*
412634 TAATATAAATAATTTTATTA
1 TAATATAAATAATATTATTA
412654 TAATA-AAATAATATTATT
1 TAATATAAATAATATTATT
412672 TATTTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATATAAATAATATTATTA
Found at i:413060 original size:2 final size:2
Alignment explanation
Indices: 413053--413083 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
413043 AGATTCGTTT
413053 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
413084 CTCTACAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:413886 original size:2 final size:2
Alignment explanation
Indices: 413881--413905 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
413871 TATATGTGTG
413881 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 T
413906 CTTGCATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:418540 original size:16 final size:16
Alignment explanation
Indices: 418519--418573 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
418509 TCTAACCATT
418519 AAAAAAAAT-AAAATG
1 AAAAAAAATAAAAATG
418534 AAAAAAAATAAAAATG
1 AAAAAAAATAAAAATG
418550 AAAAATAAACTAATAAAT-
1 AAAAA-AAA-TAA-AAATG
418568 AAAAAA
1 AAAAAA
418574 GAAAAAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.25
16 11 0.31
17 4 0.11
18 8 0.22
19 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.15
Consensus pattern (16 bp):
AAAAAAAATAAAAATG
Found at i:419235 original size:2 final size:2
Alignment explanation
Indices: 419228--419261 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
419218 AAGAACCTAC
419228 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
419262 GCGACTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:420331 original size:2 final size:2
Alignment explanation
Indices: 420324--420357 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
420314 TGTGGAAGCT
420324 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
420358 CCCTGCCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:428513 original size:28 final size:24
Alignment explanation
Indices: 428455--428516 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
428445 AATTAATTAA
428455 ATATAATATAATAATATAAAAAAT
1 ATATAATATAATAATATAAAAAAT
* *
428479 A-AAAATATAATATATATATTAAAATTT
1 ATATAATATAATA-ATATA--AAAA-AT
428506 ATATAATATAA
1 ATATAATATAA
428517 ATTATTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 10 0.33
24 6 0.20
26 4 0.13
27 2 0.07
28 8 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAATATAATAATATAAAAAAT
Found at i:429317 original size:21 final size:21
Alignment explanation
Indices: 429291--429337 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
429281 GAACAAAAGA
* * *
429291 AGCTAGAAAGAGCTGATATTG
1 AGCTAGAAAAAGCTAAAATTG
429312 AGCTAGAAAAAGCTAAAATTG
1 AGCTAGAAAAAGCTAAAATTG
429333 AGCTA
1 AGCTA
429338 AGGCAGCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.21
Consensus pattern (21 bp):
AGCTAGAAAAAGCTAAAATTG
Found at i:434187 original size:19 final size:19
Alignment explanation
Indices: 434153--434189 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
434143 AGTTGTCAGG
**
434153 TTTCTTAAATTTGTTTTAT
1 TTTCTTAAATCAGTTTTAT
434172 TTTCTTAAATCAGTTTTA
1 TTTCTTAAATCAGTTTTA
434190 ACTTTTCATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.62
Consensus pattern (19 bp):
TTTCTTAAATCAGTTTTAT
Found at i:437060 original size:3 final size:3
Alignment explanation
Indices: 437052--437077 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
437042 ATTAAGAAAG
437052 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
437078 AGCAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:444521 original size:14 final size:14
Alignment explanation
Indices: 444477--444522 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
444467 CTGCAATATT
*
444477 AGATTTCCAATGAA
1 AGATTTCCAAAGAA
* *
444491 AGAATTACCAAAAAA
1 AG-ATTTCCAAAGAA
444506 AGATTTCCAAAGAA
1 AGATTTCCAAAGAA
444520 AGA
1 AGA
444523 GAAGAAGAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (14 bp):
AGATTTCCAAAGAA
Found at i:446388 original size:56 final size:56
Alignment explanation
Indices: 446321--446434 Score: 176
Period size: 56 Copynumber: 2.0 Consensus size: 56
446311 TGGTAGTTGA
* * *
446321 TACCTTTTTTACTTCT-GCAGCTTGGAATTTTAGCAAATTAAGTACCCAAGTCAAAT
1 TACCCTTTTTACTT-TAGCAGCTTGGAATTTAAGCAAATTAAGCACCCAAGTCAAAT
*
446377 TACCCTTTTTACTTTAGTAGCTTGGAATTTAAGCAAATTAAGCACCCAAGTCAAAT
1 TACCCTTTTTACTTTAGCAGCTTGGAATTTAAGCAAATTAAGCACCCAAGTCAAAT
446433 TA
1 TA
446435 ATTAATGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 1 0.02
56 52 0.98
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.36
Consensus pattern (56 bp):
TACCCTTTTTACTTTAGCAGCTTGGAATTTAAGCAAATTAAGCACCCAAGTCAAAT
Found at i:449856 original size:15 final size:15
Alignment explanation
Indices: 449836--449865 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
449826 TTTTGGCATA
449836 TATATATATATATAT
1 TATATATATATATAT
449851 TATATATATATATAT
1 TATATATATATATAT
449866 AAGAATACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:449856 original size:17 final size:17
Alignment explanation
Indices: 449834--449866 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
449824 TATTTTGGCA
449834 TATATATATATATATAT
1 TATATATATATATATAT
449851 TATATATATATATATA
1 TATATATATATATATA
449867 AGAATACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:449880 original size:2 final size:2
Alignment explanation
Indices: 449833--449866 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
449823 ATATTTTGGC
449833 AT AT AT AT AT AT AT AT AT -T 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 A
449867 AGAATACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:451052 original size:50 final size:50
Alignment explanation
Indices: 450985--451237 Score: 337
Period size: 50 Copynumber: 5.1 Consensus size: 50
450975 TAGAGCCAAT
* * *
450985 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAAC
1 AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAAC
* * * *
451035 AATTATGACCACATCTCTCAATTGTCAAAGATTGGTGAAGAATCA-TCAAC
1 AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT-AGTCAAC
* * *
451085 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAAC
1 AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAAC
* * * *
451135 AATTACGACCACCTTTCTCGATTATCAAAGGTTGGTGAAGAATAATCAAT
1 AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAAC
* * *
451185 AATTACGACCATCTCTCTTGATTGTCAAAGGTTAGTGAAGAATAGTCAAC
1 AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAAC
451235 AAT
1 AAT
451238 GGCAACACCT
Statistics
Matches: 173, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 171 0.99
51 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (50 bp):
AATTACGACCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAAC
Found at i:451163 original size:100 final size:100
Alignment explanation
Indices: 450985--451237 Score: 380
Period size: 100 Copynumber: 2.5 Consensus size: 100
450975 TAGAGCCAAT
*
450985 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAACAATTATGACCACATC
1 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAACAATTACGACCACATC
* *
451050 TCTCAATTGTCAAAGATTGGTGAAGAATCATCAAC
66 TCTCAATTATCAAAGATTGGTGAAGAATAATCAAC
* * * *
451085 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTGGTGAAAAATAGTCAACAATTACGACCACCTT
1 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAACAATTACGACCACATC
* * *
451150 TCTCGATTATCAAAGGTTGGTGAAGAATAATCAAT
66 TCTCAATTATCAAAGATTGGTGAAGAATAATCAAC
* * * *
451185 AATTACGACCATCTCTCTTGATTGTCAAAGGTTAGTGAAGAATAGTCAACAAT
1 AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAACAAT
451238 GGCAACACCT
Statistics
Matches: 137, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 137 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (100 bp):
AATTACGGCTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTCAACAATTACGACCACATC
TCTCAATTATCAAAGATTGGTGAAGAATAATCAAC
Found at i:455471 original size:50 final size:50
Alignment explanation
Indices: 455400--455602 Score: 223
Period size: 50 Copynumber: 4.0 Consensus size: 50
455390 GCTTAGAGTC
* *
455400 AACAATTATG-TCCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAGTC
1 AACAATTATGAT-CACATCTCTCGATTATCAAAGGTTGGTGAAGAATAGTT
* * * *
455450 AATAATTATGATCACATCTCTCAATTGTCAAAGGTTGGTGAAGAATCGTT
1 AACAATTATGATCACATCTCTCGATTATCAAAGGTTGGTGAAGAATAGTT
* * * * *
455500 AACAATTACGGTCACCTCTCTCGATTGTCAAAAGTTGGTGAAGAATAGTT
1 AACAATTATGATCACATCTCTCGATTATCAAAGGTTGGTGAAGAATAGTT
* * *
455550 AACAGTTACTGA-CA-ATCTTTCTAGATTATCAAAGGTTGATGAAGAATAGTT
1 AACAATTA-TGATCACATC--TCTCGATTATCAAAGGTTGGTGAAGAATAGTT
455601 AA
1 AA
455603 TAATGACAAC
Statistics
Matches: 128, Mismatches: 21, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
49 2 0.02
50 94 0.73
51 32 0.25
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (50 bp):
AACAATTATGATCACATCTCTCGATTATCAAAGGTTGGTGAAGAATAGTT
Found at i:466722 original size:3 final size:3
Alignment explanation
Indices: 466708--466751 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
466698 TGCCCTTTAT
*
466708 TTA TTG TTA TTA TTAA TTA TTA -TA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
466752 AATTATCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:466742 original size:14 final size:14
Alignment explanation
Indices: 466715--466751 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
466705 TATTTATTGT
466715 TATTATTAATTATTA
1 TATTATT-ATTATTA
466730 TATTATTATTATTA
1 TATTATTATTATTA
*
466744 TTTTATTA
1 TATTATTA
466752 AATTATCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:470106 original size:2 final size:2
Alignment explanation
Indices: 470101--470135 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
470091 TATATATATA
470101 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
470136 ATATATATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:471321 original size:4 final size:4
Alignment explanation
Indices: 471312--471342 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
471302 AATGTGATCT
471312 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
471343 TTGGTGGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:471465 original size:3 final size:3
Alignment explanation
Indices: 471457--471482 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
471447 ATAGAAACAA
471457 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
471483 AAGCTATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:471882 original size:2 final size:2
Alignment explanation
Indices: 471875--471900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
471865 GTAGTCATTC
471875 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
471901 TATTCATGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:475577 original size:13 final size:14
Alignment explanation
Indices: 475556--475584 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
475546 AATATTGTTA
475556 TAATAATAATATTT
1 TAATAATAATATTT
475570 TAAT-ATAATATTT
1 TAATAATAATATTT
475583 TA
1 TA
475585 TTAAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATAATAATATTT
Found at i:475949 original size:9 final size:10
Alignment explanation
Indices: 475928--475956 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
475918 TAGTAATTTT
475928 AATTAATAAA
1 AATTAATAAA
475938 AATTAA-AAA
1 AATTAATAAA
475947 AATTAATAAA
1 AATTAATAAA
475957 TTATAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AATTAATAAA
Found at i:476364 original size:21 final size:21
Alignment explanation
Indices: 476333--476382 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
476323 AAAACAATAA
* *
476333 TAATGATAAAATTAATTATTAG
1 TAATAATAAAATTAA-AATTAG
476355 -AATAATAAAATTAAAATTAG
1 TAATAATAAAATTAAAATTAG
476375 TAATAATA
1 TAATAATA
476383 TATATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
TAATAATAAAATTAAAATTAG
Found at i:476492 original size:23 final size:22
Alignment explanation
Indices: 476466--476559 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 22
476456 GTAAGAGTAT
*
476466 ATTTATTATTATATATTTTAATA
1 ATTTATT-TTATATATTTAAATA
*
476489 ATTT-TTTTGAAATATTTAAATTA
1 ATTTATTTT-ATATATTTAAA-TA
*
476512 A-TTATTTTATA-A-TTATATAA
1 ATTTATTTTATATATTTAAAT-A
*
476532 ATATATGTATTATAT-TTTAAATA
1 ATTTAT-T-TTATATATTTAAATA
476555 ATTTA
1 ATTTA
476560 AAACTTTTTT
Statistics
Matches: 55, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
19 1 0.02
20 6 0.11
21 6 0.11
22 16 0.29
23 21 0.38
24 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATTTTATATATTTAAATA
Found at i:477760 original size:26 final size:27
Alignment explanation
Indices: 477714--477787 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 27
477704 TTTATTATAG
*
477714 TATAAATTTTTTAATA-T-TTTTA-TT
1 TATAAATATTTTAATATTATTTTATTT
477738 TATAAATATTTTAATATTATTTTATTT
1 TATAAATATTTTAATATTATTTTATTT
477765 TATAATAATTATTTTATATATTA
1 TAT-A-AA-TATTTTA-ATATTA
477788 ATAATAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 15 0.36
25 1 0.02
26 5 0.12
27 5 0.12
28 1 0.02
29 2 0.05
30 7 0.17
31 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (27 bp):
TATAAATATTTTAATATTATTTTATTT
Found at i:477789 original size:19 final size:19
Alignment explanation
Indices: 477743--477792 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
477733 TTATTTATAA
477743 ATATTTTAAT-ATTATTTT
1 ATATTTTAATAATTATTTT
477761 AT-TTTATAATAATTATTTT
1 ATATTT-TAATAATTATTTT
*
477780 ATATATTAATAAT
1 ATATTTTAATAAT
477793 AAAAAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 6 0.21
19 17 0.61
20 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTTTAATAATTATTTT
Found at i:479017 original size:26 final size:26
Alignment explanation
Indices: 478987--479037 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
478977 TTTAATGCCT
478987 TAAACACTACAATGTTTAAATTGTAA
1 TAAACACTACAATGTTTAAATTGTAA
* *
479013 TAAACACTGCATTGTTTAAATTGTA
1 TAAACACTACAATGTTTAAATTGTA
479038 GTTTGCATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (26 bp):
TAAACACTACAATGTTTAAATTGTAA
Found at i:487805 original size:15 final size:16
Alignment explanation
Indices: 487785--487833 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
487775 TTTGACCACC
487785 GACGAGA-AGAGAAG-A
1 GACGAGACA-AGAAGAA
487800 GACGAGACAAGAAGAA
1 GACGAGACAAGAAGAA
487816 GACGAGACAAGAA-AA
1 GACGAGACAAGAAGAA
487831 GAC
1 GAC
487834 AAAGACAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 17 0.53
16 15 0.47
ACGTcount: A:0.55, C:0.12, G:0.33, T:0.00
Consensus pattern (16 bp):
GACGAGACAAGAAGAA
Found at i:487839 original size:16 final size:15
Alignment explanation
Indices: 487794--487859 Score: 69
Period size: 16 Copynumber: 4.2 Consensus size: 15
487784 CGACGAGAAG
* *
487794 AGAAGAGACGAGACA
1 AGAAAAGACAAGACA
*
487809 AGAAGAAGACGAGACA
1 AGAA-AAGACAAGACA
487825 AGAAAAGACAAAGACAA
1 AGAAAAGAC-AAGAC-A
*
487842 AGACAAGACAAGACA
1 AGAAAAGACAAGACA
487857 AGA
1 AGA
487860 CAGCAATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
15 13 0.29
16 23 0.51
17 9 0.20
ACGTcount: A:0.61, C:0.14, G:0.26, T:0.00
Consensus pattern (15 bp):
AGAAAAGACAAGACA
Found at i:487848 original size:22 final size:21
Alignment explanation
Indices: 487820--487861 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
487810 GAAGAAGACG
487820 AGACAAGAAAAGACAAAGACAA
1 AGACAAGAAAAGAC-AAGACAA
*
487842 AGACAAGACAAGACAAGACA
1 AGACAAGAAAAGACAAGACA
487862 GCAATTCACG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.64, C:0.17, G:0.19, T:0.00
Consensus pattern (21 bp):
AGACAAGAAAAGACAAGACAA
Found at i:487860 original size:5 final size:5
Alignment explanation
Indices: 487799--487861 Score: 63
Period size: 5 Copynumber: 12.0 Consensus size: 5
487789 AGAAGAGAAG
* * * *
487799 AGACG AGACA AGAAGA AGACG AGACA AGAAA AGACAA AGACAA AGACA
1 AGACA AGACA AG-ACA AGACA AGACA AGACA AGAC-A AGAC-A AGACA
487847 AGACA AGACA AGACA
1 AGACA AGACA AGACA
487862 GCAATTCACG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
5 34 0.69
6 15 0.31
ACGTcount: A:0.60, C:0.16, G:0.24, T:0.00
Consensus pattern (5 bp):
AGACA
Found at i:488337 original size:17 final size:17
Alignment explanation
Indices: 488317--488356 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
488307 AAGTTTGCCC
* *
488317 AACAATAAGTGAATAAA
1 AACAATAAATAAATAAA
488334 AACAATAAATAAATAAA
1 AACAATAAATAAATAAA
488351 ATACAA
1 A-ACAA
488357 ACTTTGAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.70, C:0.07, G:0.05, T:0.17
Consensus pattern (17 bp):
AACAATAAATAAATAAA
Found at i:494090 original size:2 final size:2
Alignment explanation
Indices: 494083--494118 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
494073 ACACTACCTG
494083 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
494119 TCTTCCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:494975 original size:10 final size:10
Alignment explanation
Indices: 494960--494993 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
494950 TTATGAAATC
*
494960 ATATATATAT
1 ATATATATGT
494970 ATATATATGT
1 ATATATATGT
*
494980 ATGTATATGT
1 ATATATATGT
494990 ATAT
1 ATAT
494994 TAGTCAAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (10 bp):
ATATATATGT
Found at i:495744 original size:2 final size:2
Alignment explanation
Indices: 495737--495765 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
495727 TTTAACAATC
495737 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 A
495766 GTCAATACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:503543 original size:2 final size:2
Alignment explanation
Indices: 503538--503581 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
503528 AGTGTGTGTG
503538 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
503578 TA TA
1 TA TA
503582 AATAATTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:503593 original size:14 final size:16
Alignment explanation
Indices: 503538--503593 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 16
503528 AGTGTGTGTG
*
503538 TATATATATATATATAT
1 TATA-ATATAAATATAT
*
503555 ATATATATATATATATAT
1 -TATA-ATATAAATATAT
503573 TATAATATAAATA-AT
1 TATAATATAAATATAT
503588 TA-AATA
1 TATAATA
503594 AATAAACAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
14 4 0.11
15 4 0.11
16 8 0.22
17 4 0.11
18 17 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATAATATAAATATAT
Found at i:503741 original size:4 final size:4
Alignment explanation
Indices: 503734--503760 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
503724 AAGAAAGGAA
503734 ATTT ATTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATT
503761 AATTCAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:504287 original size:3 final size:3
Alignment explanation
Indices: 504279--504303 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
504269 GTTATAACCG
504279 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
504304 ACTGTTGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:506015 original size:36 final size:38
Alignment explanation
Indices: 505961--506044 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 38
505951 TAGTAGGTTC
** *
505961 AATTAATTAATTAATTTAAATATT-AT-TAATTAAATT
1 AATTAATTTTTTAATTTAAATATTAATAAAATTAAATT
* *
505997 AATTAATTTTTTATTTTAATTATTAATAAAATTAAATT
1 AATTAATTTTTTAATTTAAATATTAATAAAATTAAATT
*
506035 AA-AAATTTTT
1 AATTAATTTTT
506045 ATTATATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
36 20 0.50
37 9 0.22
38 11 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
AATTAATTTTTTAATTTAAATATTAATAAAATTAAATT
Found at i:506066 original size:38 final size:37
Alignment explanation
Indices: 505988--506066 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 37
505978 AAATATTATT
* *
505988 AATTAAATTAATTAATTTTTTATTTTAATTATTAATAA
1 AATTAAATTAATAAATTTTTTATATTAATTA-TAATAA
506026 AATTAAATTAA-AAATTTTTATTATATTAATTA-AATCAA
1 AATTAAATTAATAAA-TTTT-TTATATTAATTATAAT-AA
506064 AAT
1 AAT
506067 AATTTTGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
37 5 0.14
38 20 0.56
39 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
AATTAAATTAATAAATTTTTTATATTAATTATAATAA
Found at i:506178 original size:17 final size:17
Alignment explanation
Indices: 506156--506203 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
506146 TTATAATTCA
*
506156 AATAAATATAATTATAT
1 AATAAATATAATTAAAT
506173 AATAAATAT--TTAAAT
1 AATAAATATAATTAAAT
* *
506188 ATTAAATATAAGTAAA
1 AATAAATATAATTAAA
506204 AATTACATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.50
17 13 0.50
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAAATATAATTAAAT
Found at i:509930 original size:166 final size:164
Alignment explanation
Indices: 509752--510221 Score: 574
Period size: 166 Copynumber: 2.8 Consensus size: 164
509742 AAAGGATACG
* *
509752 AAAAGTCTTGAAAATTTTTATACCTCTATAGAAGGCCATATGAATAATAAAAATCTTTAAAAATG
1 AAAAGTCTTGAAAATTTCTATACCTCTA-AGAAGGCCATAGGAATAATAAAAATCTTTAAAAATG
* * *
509817 ACTAAAATAATGATTTTAGCTCTAAAAAATAAAATTTGATATTTAATCTCTAACCTTTTGAA-AA
65 ACTAAAATGATGATTTTAGCTCTAAAAACTAAAATTTGATATTTAATC-CTAA-ATTTTGAATAA
** ***
509881 TTTCATTTCATACTTGATGGAAAAA-TAAGAAAATAAA
128 TTTCATTTCATAC-CCAACAAAAAATTAAGAAAATAAA
509918 AAAAGTCTTGAAAATTTCTATACCTCTACAGAAGAG-CATAGGAATAATAAAAATCTTTAAAAAT
1 AAAAGTCTTGAAAATTTCTATACCTCTA-AGAAG-GCCATAGGAATAATAAAAATCTTTAAAAAT
*
509982 GACTAAAATGATGATTTTAGCTCTAAAAACTAAAATTT-ACTATTTAATCCTTAAATTTTTAATA
64 GACTAAAATGATGATTTTAGCTCTAAAAACTAAAATTTGA-TATTTAATCC-TAAATTTTGAATA
* * * **
510046 ATTTCATTTTATACCCAACAAAAAATTGAGAAGATACG
127 ATTTCATTTCATACCCAACAAAAAATTAAGAAAATAAA
* * *
510084 AAAAGTCTTGAAAATTTCTATA-CTCCTACGAAAGACCATAGGAATAATAGAAATCTTTAAAAAT
1 AAAAGTCTTGAAAATTTCTATACCT-CTAAG-AAGGCCATAGGAATAATAAAAATCTTTAAAAAT
* * * *
510148 GACTAAGATGATGATTTTACCTCTAAAAACTAAAATTTGCTATTTAATCCCTAAATCTTT-AAAA
64 GACTAAAATGATGATTTTAGCTCTAAAAACTAAAATTTGATATTTAAT-CCTAAAT-TTTGAATA
510212 ATTTTCATTT
127 A-TTTCATTT
510222 TAGTCCCTAC
Statistics
Matches: 268, Mismatches: 24, Indels: 23
0.85 0.08 0.07
Matches are distributed among these distances:
165 17 0.06
166 237 0.88
167 14 0.05
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (164 bp):
AAAAGTCTTGAAAATTTCTATACCTCTAAGAAGGCCATAGGAATAATAAAAATCTTTAAAAATGA
CTAAAATGATGATTTTAGCTCTAAAAACTAAAATTTGATATTTAATCCTAAATTTTGAATAATTT
CATTTCATACCCAACAAAAAATTAAGAAAATAAA
Found at i:510956 original size:21 final size:21
Alignment explanation
Indices: 510895--510956 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
510885 ATAGCTAATA
*
510895 ATAACTTTTGTAATAATTTTG
1 ATAACTTCTGTAATAATTTTG
* *
510916 ATAGC-CCT-TAATATAGTTTTG
1 ATAACTTCTGTAATA-A-TTTTG
510937 ATAACTTCTGTAATAATTTT
1 ATAACTTCTGTAATAATTTT
510957 TTTATGATCT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 5 0.16
20 2 0.06
21 17 0.53
22 3 0.09
23 5 0.16
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (21 bp):
ATAACTTCTGTAATAATTTTG
Found at i:511115 original size:21 final size:21
Alignment explanation
Indices: 511078--511117 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
511068 ATAAATTTTT
*
511078 ATATAATTTTGTTTATAATGG
1 ATATAATTTTGTATATAATGG
511099 ATATAACTTTTG-ATATAAT
1 ATATAA-TTTTGTATATAAT
511118 TTTAATAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (21 bp):
ATATAATTTTGTATATAATGG
Found at i:511510 original size:20 final size:20
Alignment explanation
Indices: 511482--511556 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
511472 TTTTACCCAG
*
511482 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
* *** *
511502 ATATATCGATACATGGATGA
1 ATGTATCGATACATTCTTCA
*
511522 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTCTTCA
511542 ATGTATCGATACATT
1 ATGTATCGATACATT
511557 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:512535 original size:22 final size:21
Alignment explanation
Indices: 512489--512536 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
512479 GTCCAGCATC
512489 TCATTGAATGTTATCCATTAGT
1 TCATTGAATGTTATCCATTA-T
*
512511 TCATTGTATGATTATCACATT-T
1 TCATTGAATG-TTATC-CATTAT
512533 TCAT
1 TCAT
512537 GTCAAGATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 14 0.61
23 5 0.22
24 4 0.17
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (21 bp):
TCATTGAATGTTATCCATTAT
Found at i:516401 original size:26 final size:27
Alignment explanation
Indices: 516347--516402 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
516337 TTGTTTATAA
*
516347 AATTTTCAATTAATTAATAATAATTTT
1 AATTTTCAATTAATTAATAATAATATT
*
516374 AATTTTTAATTAAATT-A-AATAATATT
1 AATTTTCAATT-AATTAATAATAATATT
516400 AAT
1 AAT
516403 ATAATTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 11 0.42
27 11 0.42
28 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
AATTTTCAATTAATTAATAATAATATT
Found at i:521462 original size:55 final size:55
Alignment explanation
Indices: 521390--521499 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
521380 ATCATAAATA
521390 AGATCATTCAAAAAAGGGTAAGATCAACCTTATACCATTATAGATCATCCAAAAC
1 AGATCATTCAAAAAAGGGTAAGATCAACCTTATACCATTATAGATCATCCAAAAC
521445 AGATCATTCAAAAAAGGGTAAGATCAACCTTATACCATTATAGATCATCCAAAAC
1 AGATCATTCAAAAAAGGGTAAGATCAACCTTATACCATTATAGATCATCCAAAAC
521500 TTTTTTCCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (55 bp):
AGATCATTCAAAAAAGGGTAAGATCAACCTTATACCATTATAGATCATCCAAAAC
Found at i:522865 original size:40 final size:41
Alignment explanation
Indices: 522820--522897 Score: 149
Period size: 40 Copynumber: 1.9 Consensus size: 41
522810 TGCTTTAAAA
522820 AATCATGAAGCATGAAATTATTTGAACATA-TAAAAAAGGT
1 AATCATGAAGCATGAAATTATTTGAACATATTAAAAAAGGT
522860 AATCATGAAGCATGAAATTATTTGAACATATTAAAAAA
1 AATCATGAAGCATGAAATTATTTGAACATATTAAAAAA
522898 AAGTAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 30 0.81
41 7 0.19
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (41 bp):
AATCATGAAGCATGAAATTATTTGAACATATTAAAAAAGGT
Found at i:523707 original size:58 final size:58
Alignment explanation
Indices: 523638--523757 Score: 231
Period size: 58 Copynumber: 2.1 Consensus size: 58
523628 TAAAAATAGC
523638 TAAAAAAAGAATACAACATGAAATGATAACACTAACATGAACGAATACACAAATATGT
1 TAAAAAAAGAATACAACATGAAATGATAACACTAACATGAACGAATACACAAATATGT
*
523696 TAAAAAAAGAATACAACATGAAATGATAACACTAACATGAATGAATACACAAATATGT
1 TAAAAAAAGAATACAACATGAAATGATAACACTAACATGAACGAATACACAAATATGT
523754 TAAA
1 TAAA
523758 GTTATTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (58 bp):
TAAAAAAAGAATACAACATGAAATGATAACACTAACATGAACGAATACACAAATATGT
Found at i:523943 original size:17 final size:17
Alignment explanation
Indices: 523913--523951 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
523903 GCATTATAAT
523913 TATTTATCATTTAATTA
1 TATTTATCATTTAATTA
*
523930 TATTATATCA-TTAATTT
1 TATT-TATCATTTAATTA
523947 TATTT
1 TATTT
523952 TTATAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTATCATTTAATTA
Found at i:524533 original size:13 final size:13
Alignment explanation
Indices: 524515--524571 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
524505 TTCAACGATT
524515 TGTATCGATACAA
1 TGTATCGATACAA
524528 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
524543 GTGTTGTATCGATATAA
1 ----TGTATCGATACAA
524560 TGTATCGATACA
1 TGTATCGATACA
524572 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:524552 original size:19 final size:18
Alignment explanation
Indices: 524528--524590 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
524518 ATCGATACAA
524528 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
524547 TGTATCGAT--ATAA---
1 TGTATCGATACATAAGTT
524560 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
524579 TGTATCGATACA
1 TGTATCGATACA
524591 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
15 4 0.11
17 4 0.11
19 21 0.55
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:524555 original size:32 final size:32
Alignment explanation
Indices: 524514--524598 Score: 152
Period size: 32 Copynumber: 2.7 Consensus size: 32
524504 TTTCAACGAT
524514 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
* *
524546 TTGTATCGATATAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
524578 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
524599 CTACGAAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:529352 original size:17 final size:15
Alignment explanation
Indices: 529332--529371 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
529322 AAATGATGAA
529332 AAAAAAAACAAACAAAC
1 AAAAAAAAC--ACAAAC
*
529349 AAAAAAAACACACAC
1 AAAAAAAACACAAAC
529364 AAAAAAAA
1 AAAAAAAA
529372 TGCAAAGGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAACACAAAC
Found at i:530720 original size:31 final size:30
Alignment explanation
Indices: 530648--530770 Score: 126
Period size: 31 Copynumber: 4.1 Consensus size: 30
530638 TTCAAATACC
530648 TTCTT-AAAGTCCACAACTCAGTGGCAT-T
1 TTCTTCAAAGTCCACAACTCAGTGGCATCT
* *
530676 TTGTCCCAAAGTCCACAACTCAGTGGCAATCT
1 TTCT-TCAAAGTCCACAACTCAGTGGC-ATCT
*
530708 CTT-TTCAAAGTCCACGACTCAGTGGCATCTT
1 -TTCTTCAAAGTCCACAACTCAGTGGCATC-T
* * * *
530739 TTCTTCAAAGCCCACGACTCCGTGGCACCT
1 TTCTTCAAAGTCCACAACTCAGTGGCATCT
530769 TT
1 TT
530771 TTCTTTTCAA
Statistics
Matches: 81, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
28 3 0.04
30 28 0.35
31 46 0.57
32 2 0.02
33 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.15, T:0.29
Consensus pattern (30 bp):
TTCTTCAAAGTCCACAACTCAGTGGCATCT
Found at i:530818 original size:35 final size:34
Alignment explanation
Indices: 530707--531028 Score: 418
Period size: 34 Copynumber: 9.5 Consensus size: 34
530697 AGTGGCAATC
* * * * *
530707 TCTTTTCAAAGTCCACGACTCAGTGGCATC-TTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
* *
530740 TC--TTCAAAGCCCACGACTCCGTGGCACCTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
* * *
530772 TCTTTTCAAAGCCCACAATTCCGTAGCACCTTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACC-TTTT
*
530807 TCTTTTTAAAGCCCACCACTCCGTGGCACTCTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTT
530842 TCTTTTTAAAGCCCACAACTCCGTGGCACC-TTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
*
530875 TCTTTTTAAAGCCCACAACTCCGTGACACCTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
*
530909 TCTTTTTAAAGCTCACAACTCCGTGGCACCTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
* *
530943 TCTTTTCAAAGTCCACAACTCCGTGGCACCTTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
* * * *
530977 TCTTTTTAAAGCCCACAAATTCGTGGAACATTTT
1 TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
531011 TCTTTTCTAAAGCCCACA
1 TCTTTT-TAAAGCCCACA
531029 CAAGTCGGTG
Statistics
Matches: 259, Mismatches: 23, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
31 23 0.09
32 5 0.02
33 34 0.13
34 124 0.48
35 72 0.28
36 1 0.00
ACGTcount: A:0.22, C:0.31, G:0.11, T:0.35
Consensus pattern (34 bp):
TCTTTTTAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:531053 original size:33 final size:33
Alignment explanation
Indices: 531016--531214 Score: 344
Period size: 33 Copynumber: 6.0 Consensus size: 33
531006 ATTTTTCTTT
*
531016 TCTAAAGCCCACACAAGTCGGTGGCAAACATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
531049 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
*
531082 TCTAAAGCCTACACAAGTCGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
*
531115 TCTAAAGCCCACACAAGTCGGTGGCAAACATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
*
531148 TCTAAAGCCCACACAAGTTGGTGGCAACCATTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
* *
531181 TCTAAAGCCCACACAAGTTGGTGGCAACCCTTC
1 TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
531214 T
1 T
531215 AAGCCTAATA
Statistics
Matches: 159, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 159 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (33 bp):
TCTAAAGCCCACACAAGTCGGTGGCAACCATTC
Found at i:531348 original size:21 final size:20
Alignment explanation
Indices: 531280--531348 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 20
531270 AATGTAGCTG
531280 ACCTTGAATCAGCATATTGGC
1 ACCTTGAATCAGCA-ATTGGC
* *
531301 ACCTTTAAGTC--CAATGTAGC
1 ACCTTGAA-TCAGCAAT-TGGC
531321 TGACCTTGAATCAGCACATTGGC
1 --ACCTTGAATCAGCA-ATTGGC
531344 ACCTT
1 ACCTT
531349 TAAGTCCAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 14
0.67 0.07 0.25
Matches are distributed among these distances:
19 2 0.05
20 5 0.14
21 14 0.38
22 9 0.24
23 5 0.14
24 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (20 bp):
ACCTTGAATCAGCAATTGGC
Found at i:531398 original size:135 final size:135
Alignment explanation
Indices: 531221--531715 Score: 660
Period size: 135 Copynumber: 3.6 Consensus size: 135
531211 TTCTAAGCCT
* * *
531221 AATATCGCTGGCCTTGAATTAACATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGACCTTG
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
* *
531286 AATCAGCATATTGGCACCTTTAAGTCCAATGTAGCTGACCTTGAATCAGCACATTGGCACCTTTA
66 AATCAGCATATTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTA
531351 AGTCC
131 AGTCC
* *
531356 AATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
* *
531421 AATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACACCTTTA
66 AATCAGCATATTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-C----
531486 TCTTTAAGTCC
126 -CTTTAAGTCC
* * * *
531497 AATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTTAAGTCCAATATCGCTGGCCTTG
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
* *
531556 AATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGACAC
66 AATCAGCATATTGGCA-C----CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
* *
531621 CTTCAAGTCT
126 CTTTAAGTCC
* * *
531631 AATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTCGCTGGCCTTG
1 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
*
531696 AATCAGCACATTGGCACCTT
66 AATCAGCATATTGGCACCTT
531716 CAACTTGAAG
Statistics
Matches: 319, Mismatches: 24, Indels: 34
0.85 0.06 0.09
Matches are distributed among these distances:
134 37 0.12
135 161 0.50
136 2 0.01
139 2 0.01
140 79 0.25
141 38 0.12
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (135 bp):
AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTG
AATCAGCATATTGGCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTA
AGTCC
Found at i:531408 original size:92 final size:92
Alignment explanation
Indices: 531260--531715 Score: 710
Period size: 92 Copynumber: 5.0 Consensus size: 92
531250 GCACCTTTAT
* * *
531260 CTTTAAGTCCAATGTAGCTGACCTTGAATCAGCATATTGGCA-C-----CTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
531319 GCTGACCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* *
531346 CTTTAAGTCCAATATAGCTGGCCTTGAATTAGCATATTGGCACCTTTATCTTTAAGTCCAATGTA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
531411 GCTGGCCTTGAATCAGCATATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
*
531438 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGACACCTTTATCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
531503 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * *
531530 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
*
531594 GCTGGCCTTGAATCAGCACATTGACAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
* * * * *
531621 CTTCAAGTCTAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
531686 GCTGGCCTTGAATCAGCACATTGGCAC
66 GCTGGCCTTGAATCAGCACATTGGCAC
531713 CTT
1 CTT
531716 CAACTTGAAG
Statistics
Matches: 342, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
86 39 0.11
87 1 0.00
91 85 0.25
92 217 0.63
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCAC
Found at i:531440 original size:21 final size:21
Alignment explanation
Indices: 531416--531483 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
531406 ATGTAGCTGG
531416 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* ** *
531437 CCTTTAAGTCCAATATAGCTGG--
1 CCTTGAA-T-CAGCATA-TTGGCA
*
531459 CCTTGAATCAGCATATTGACA
1 CCTTGAATCAGCATATTGGCA
531480 CCTT
1 CCTT
531484 TATCTTTAAG
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 11 0.33
22 7 0.21
23 5 0.15
24 3 0.09
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Done.