Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold221
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: 2539808
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 19
Found at i:341847 original size:12 final size:12
Alignment explanation
Indices: 341832--341862 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
341822 ATTTTCTTAG
*
341832 TTATTTTAGTAT
1 TTATATTAGTAT
341844 TTATATTAGTAT
1 TTATATTAGTAT
341856 TTATATT
1 TTATATT
341863 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (12 bp):
TTATATTAGTAT
Found at i:342028 original size:17 final size:17
Alignment explanation
Indices: 342008--342040 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
341998 AGCATCTAAA
342008 TATTTAATTATAAAATT
1 TATTTAATTATAAAATT
*
342025 TATTTAATTATTAAAT
1 TATTTAATTATAAAAT
342041 AAAAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTTAATTATAAAATT
Found at i:344495 original size:35 final size:35
Alignment explanation
Indices: 344456--344562 Score: 160
Period size: 35 Copynumber: 3.1 Consensus size: 35
344446 AGCTAATTTG
* * **
344456 CTATCTTTCAATGTGTTCATATTGTTCGGTTACAT
1 CTATCTTTCAATGTGGTCATATCGTTCAATTACAT
*
344491 CTATCTTTCAATGTGGTCATGTCGTTCAATTACAT
1 CTATCTTTCAATGTGGTCATATCGTTCAATTACAT
*
344526 CTATCTTTCAATGTGGTCATGTCGTTCAATTACAT
1 CTATCTTTCAATGTGGTCATATCGTTCAATTACAT
344561 CT
1 CT
344563 TTTCTCTCAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 67 1.00
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (35 bp):
CTATCTTTCAATGTGGTCATATCGTTCAATTACAT
Found at i:344520 original size:18 final size:18
Alignment explanation
Indices: 344497--344555 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
344487 ACATCTATCT
344497 TTCAATGTGGTCATGTCG
1 TTCAATGTGGTCATGTCG
** * *
344515 TTCAAT-TACATC-TATCT
1 TTCAATGT-GGTCATGTCG
344532 TTCAATGTGGTCATGTCG
1 TTCAATGTGGTCATGTCG
344550 TTCAAT
1 TTCAAT
344556 TACATCTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.42
Consensus pattern (18 bp):
TTCAATGTGGTCATGTCG
Found at i:348250 original size:20 final size:21
Alignment explanation
Indices: 348203--348250 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
348193 TTAATTTAAA
* * *
348203 TTATTTGATTTAAATTATTAT
1 TTATTTAATATAAAATATTAT
348224 TTA-TTAATATAAAATATT-T
1 TTATTTAATATAAAATATTAT
348243 TTATTTAA
1 TTATTTAA
348251 ATTTAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTATTTAATATAAAATATTAT
Found at i:348276 original size:17 final size:16
Alignment explanation
Indices: 348254--348285 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
348244 TATTTAAATT
348254 TAATTATAAATAATATA
1 TAATTATAAA-AATATA
348271 TAATTATAAAAATAT
1 TAATTATAAAAATAT
348286 TTTTATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTATAAAAATATA
Found at i:348307 original size:17 final size:17
Alignment explanation
Indices: 348281--348318 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
348271 TAATTATAAA
* *
348281 AATA-TTTTTATATTTT
1 AATATTTTTTAAATATT
348297 AATATTTTTTAAATATT
1 AATATTTTTTAAATATT
348314 AATAT
1 AATAT
348319 AAATTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATTTTTTAAATATT
Found at i:352151 original size:22 final size:22
Alignment explanation
Indices: 352123--352166 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
352113 TGCTCATAAC
*
352123 TATGTTACTCAGATTCAAGTGT
1 TATGTTACTCAGACTCAAGTGT
*
352145 TATGTTATTCAGACTCAAGTGT
1 TATGTTACTCAGACTCAAGTGT
352167 AAGTATCGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (22 bp):
TATGTTACTCAGACTCAAGTGT
Found at i:353578 original size:29 final size:29
Alignment explanation
Indices: 353539--353650 Score: 74
Period size: 29 Copynumber: 3.9 Consensus size: 29
353529 ATTTTTATAC
353539 ATTTTATATTAATTATTATATTATAATTAT
1 ATTTTA-ATTAATTATTATATTATAATTAT
*
353569 ATTTTAATTAACTT-TTA-ATATATAATAAT
1 ATTTTAATTAA-TTATTATAT-TATAATTAT
** * * *
353598 ATTATATAAAAAAATA-AATA-TATAATTAA
1 ATT-T-TAATTAATTATTATATTATAATTAT
*
353627 ATATT-ATT-ATTATTATATTATAAT
1 ATTTTAATTAATTATTATATTATAAT
353651 AAAAAATTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 19
0.67 0.13 0.20
Matches are distributed among these distances:
25 3 0.05
26 4 0.06
27 7 0.11
28 3 0.05
29 28 0.45
30 11 0.18
31 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTTAATTAATTATTATATTATAATTAT
Found at i:353706 original size:19 final size:20
Alignment explanation
Indices: 353679--353741 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 20
353669 AAATTTAATA
* *
353679 ATTTATATAT-TTTTTTTAT
1 ATTTATATATGTTATATTAT
*
353698 ATTTTTATATGTTATATTAT
1 ATTTATATATGTTATATTAT
* * *
353718 ATTTAAAATATTTTATATTTT
1 ATTT-ATATATGTTATATTAT
353739 ATT
1 ATT
353742 AATTTTAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
19 9 0.26
20 11 0.31
21 15 0.43
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTATATATGTTATATTAT
Found at i:353723 original size:47 final size:45
Alignment explanation
Indices: 353666--353792 Score: 121
Period size: 47 Copynumber: 2.6 Consensus size: 45
353656 ATTTTAAAAA
* *
353666 ATTAAATTTAATAAT-TTATATATTTTTTTTATATTTTTATATGTTAT
1 ATTAAATTTAA-AATATTATATA-TTTTATTA-ATTTTAATATGTTAT
* *
353713 ATTATATTTAAAATATTTTATATTTTATTAATTTTAATATGTTAATAGT
1 ATTAAATTTAAAATATTATATATTTTATTAATTTTAATATG-T--TA-T
353762 ATTATAATTTTAAAATATTAATATATTTTAT
1 ATTA-AA-TTTAAAATATT-ATATATTTTAT
353793 AGAAAATTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
45 10 0.15
46 11 0.17
47 16 0.24
48 2 0.03
49 5 0.08
50 1 0.02
51 11 0.17
52 10 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (45 bp):
ATTAAATTTAAAATATTATATATTTTATTAATTTTAATATGTTAT
Found at i:353769 original size:25 final size:24
Alignment explanation
Indices: 353710--353788 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
353700 TTTTATATGT
*
353710 TATATTAT-A-TTTAAAATATTTTA
1 TATATTATAATTTTAAAATA-TTAA
* * *
353733 TATTTTATTAATTTTAATATGTTAA
1 TATATTA-TAATTTTAAAATATTAA
353758 TAGTATTATAATTTTAAAATATTAA
1 TA-TATTATAATTTTAAAATATTAA
353783 TATATT
1 TATATT
353789 TTATAGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
23 6 0.13
24 5 0.11
25 23 0.51
26 11 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (24 bp):
TATATTATAATTTTAAAATATTAA
Found at i:353856 original size:24 final size:25
Alignment explanation
Indices: 353796--353856 Score: 58
Period size: 24 Copynumber: 2.6 Consensus size: 25
353786 ATTTTATAGA
353796 AAATT-AT-ATTTTATGTTATATTT
1 AAATTGATAATTTTATGTTATATTT
* **
353819 AAATTGTTTTTTTTATGTTA-ATTT
1 AAATTGATAATTTTATGTTATATTT
353843 -AATTAGATAATTTT
1 AAATT-GATAATTTT
353857 TTTTTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
23 9 0.30
24 11 0.37
25 10 0.33
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (25 bp):
AAATTGATAATTTTATGTTATATTT
Found at i:369141 original size:30 final size:27
Alignment explanation
Indices: 369105--369171 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 27
369095 TTATATTTGT
369105 ATATTATTATATATCATAATAATGTTTAAA
1 ATATTATTATAT-TCAT-ATAAT-TTTAAA
* *
369135 ATATTA-TATATTTATATAATTTTAAT
1 ATATTATTATATTCATATAATTTTAAA
369161 ATATTAATTAT
1 ATATT-ATTAT
369172 TTGTGTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 10 0.30
27 6 0.18
28 6 0.18
29 5 0.15
30 6 0.18
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
ATATTATTATATTCATATAATTTTAAA
Found at i:369173 original size:26 final size:27
Alignment explanation
Indices: 369109--369166 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
369099 ATTTGTATAT
*
369109 TATTATATA-TCATAATAATGTTTAAAA
1 TATTATATATTTAT-ATAATGTTTAAAA
*
369136 TATTATATATTTATATAAT-TTTAATA
1 TATTATATATTTATATAATGTTTAAAA
369162 TATTA
1 TATTA
369167 ATTATTTGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 11 0.39
27 14 0.50
28 3 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TATTATATATTTATATAATGTTTAAAA
Found at i:369254 original size:27 final size:28
Alignment explanation
Indices: 369185--369254 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
369175 TGTTAATGTA
**
369185 AAATTTAAT-GATAAAAATATTTTTATTT
1 AAATTTAATAG-TAAAAATATTTTTATAC
369213 AAATTTAATTA-TAAAAATATTTTTA-AC
1 AAATTTAA-TAGTAAAAATATTTTTATAC
*
369240 ATATTTAATAGTAAA
1 AAATTTAATAGTAAA
369255 TTTTGATGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 22 0.61
29 1 0.03
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (28 bp):
AAATTTAATAGTAAAAATATTTTTATAC
Found at i:369770 original size:47 final size:49
Alignment explanation
Indices: 369673--369780 Score: 120
Period size: 47 Copynumber: 2.3 Consensus size: 49
369663 ATGATACGAT
*
369673 ATAA-ATAAATATTTTAAATGAATTATTAATATATTAAAATTAAAATAA
1 ATAATATAAATATTTTAAATGAATTATTAATATAGTAAAATTAAAATAA
**
369721 AT-ATA-AAATATTTTAAACATG-ATTA-TAATATAGTAAAATATACGA-AA
1 ATAATATAAATATTTT-AA-ATGAATTATTAATATAGTAAAAT-TAAAATAA
369768 ATAATATAAATAT
1 ATAATATAAATAT
369781 ATAAATTATC
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
47 27 0.53
48 15 0.29
49 9 0.18
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (49 bp):
ATAATATAAATATTTTAAATGAATTATTAATATAGTAAAATTAAAATAA
Found at i:373521 original size:22 final size:22
Alignment explanation
Indices: 373496--373537 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
373486 ATTTTTTTAT
373496 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
373518 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
373538 ATATTTGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:381868 original size:11 final size:11
Alignment explanation
Indices: 381854--381900 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
381844 AAAATATTTA
381854 TATATTTATAT
1 TATATTTATAT
*
381865 TATATTTTTAT
1 TATATTTATAT
*
381876 TATTTTTATAT
1 TATATTTATAT
*
381887 GATA-TTATAT
1 TATATTTATAT
381897 TATA
1 TATA
381901 AAATAAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:381872 original size:30 final size:32
Alignment explanation
Indices: 381838--381900 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
381828 AAATTAAATA
381838 ATTTTTAAAATATTTATAT-AT-TTATATTAT
1 ATTTTTAAAATATTTATATGATATTATATTAT
** *
381868 ATTTTTATTATTTTTATATGATATTATATTAT
1 ATTTTTAAAATATTTATATGATATTATATTAT
381900 A
1 A
381901 AAATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 16 0.57
31 2 0.07
32 10 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
ATTTTTAAAATATTTATATGATATTATATTAT
Found at i:382417 original size:37 final size:35
Alignment explanation
Indices: 382361--382432 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 35
382351 TCCATTACAT
*** *
382361 TATTTTATAATTTTTTAAAATTGATTTTATATTAATA
1 TATTTTATAATTAAATAAAAAT-ATTTT-TATTAATA
382398 TATTTTATAATTAAATAAAAATATTTTTATTAATA
1 TATTTTATAATTAAATAAAAATATTTTTATTAATA
382433 AATAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 8 0.26
36 5 0.16
37 18 0.58
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (35 bp):
TATTTTATAATTAAATAAAAATATTTTTATTAATA
Found at i:382434 original size:22 final size:23
Alignment explanation
Indices: 382394--382437 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
382384 ATTTTATATT
382394 AATATATTTTATAATTAAATAAA
1 AATATATTTTATAATTAAATAAA
382417 AATAT-TTTTATTAA-TAAATAA
1 AATATATTTTA-TAATTAAATAA
382438 TAATTTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATATATTTTATAATTAAATAAA
Found at i:382439 original size:19 final size:21
Alignment explanation
Indices: 382397--382452 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
382387 TTATATTAAT
382397 ATATTTTATAATTAAATAAAA
1 ATATTTTATAATTAAATAAAA
382418 ATATTTT-T-ATT-AATAAATA
1 ATATTTTATAATTAAATAAA-A
* *
382437 ATAATTTA-AATCAAAT
1 ATATTTTATAATTAAAT
382453 TAACTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 3 0.10
21 10 0.34
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATTTTATAATTAAATAAAA
Found at i:383380 original size:31 final size:30
Alignment explanation
Indices: 383293--383383 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 30
383283 TTTTTATTTG
* * **
383293 ATTAAATTTTACAATTAAATTTTAATTTTTT
1 ATTAAATTTTACCATTAAA-TTTGATTTTCA
*
383324 ATTAAATTTTACCACTAAACTTTGATTTTCA
1 ATTAAATTTTACCATTAAA-TTTGATTTTCA
*
383355 ATTAAATTTTACCATTCAATATTGATTTT
1 ATTAAATTTTACCATTAAAT-TTGATTTT
383384 GAATGGTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.02
31 50 0.98
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (30 bp):
ATTAAATTTTACCATTAAATTTGATTTTCA
Found at i:383533 original size:21 final size:21
Alignment explanation
Indices: 383494--383534 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
383484 TTTTCATTTT
* **
383494 ATAAAATAAAAACTTAAAAAA
1 ATAAAAGAAAAACCCAAAAAA
383515 ATAAAAGAAAAACCCAAAAA
1 ATAAAAGAAAAACCCAAAAA
383535 GTTTTAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (21 bp):
ATAAAAGAAAAACCCAAAAAA
Found at i:383598 original size:26 final size:26
Alignment explanation
Indices: 383565--383619 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
383555 AAATTCTATT
*
383565 TTATTTTTAATT-TTATAAATTAATATA
1 TTATTTTTAATTATTA-AAA-TAAAATA
383592 TTATTTTTAATTATTAAAATAAAATA
1 TTATTTTTAATTATTAAAATAAAATA
383618 TT
1 TT
383620 TGAAAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 8 0.31
27 15 0.58
28 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTTTTAATTATTAAAATAAAATA
Found at i:389132 original size:16 final size:16
Alignment explanation
Indices: 389113--389144 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
389103 ATATTTTTAT
*
389113 TATAATTTATTAAATA
1 TATAAATTATTAAATA
389129 TATAAATTATTAAATA
1 TATAAATTATTAAATA
389145 AATCTTAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATTATTAAATA
Found at i:389913 original size:28 final size:25
Alignment explanation
Indices: 389860--389914 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
389850 TTTATTATTA
*
389860 AATATTTATTATAATTAATAATGAT
1 AATATTTATTATAATTAATAACGAT
389885 AATATTTATTATAATATAATATAACGAT
1 AATATTTATTATAAT-T-A-ATAACGAT
389913 AA
1 AA
389915 AGATATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 15 0.58
26 1 0.04
27 1 0.04
28 9 0.35
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (25 bp):
AATATTTATTATAATTAATAACGAT
Found at i:390222 original size:15 final size:15
Alignment explanation
Indices: 390191--390237 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
390181 TCGATCTAGG
390191 TAATATTTAAACT-TAA
1 TAATA-TTAAA-TATAA
390207 TAATATTAAATATAA
1 TAATATTAAATATAA
*
390222 TTATA-TAAATATAA
1 TAATATTAAATATAA
390236 TA
1 TA
390238 TAAAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 11 0.39
15 12 0.43
16 5 0.18
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATTAAATATAA
Found at i:390232 original size:14 final size:13
Alignment explanation
Indices: 390206--390272 Score: 61
Period size: 12 Copynumber: 5.2 Consensus size: 13
390196 TTTAAACTTA
390206 ATAATAT-TAAAT
1 ATAATATATAAAT
390218 ATAATTATATAAAT
1 ATAA-TATATAAAT
390232 ATAATATA-AAAT
1 ATAATATATAAAT
* *
390244 AATTAAAATAT-GAT
1 -A-TAATATATAAAT
390258 ATAATATA-AAAT
1 ATAATATATAAAT
390270 ATA
1 ATA
390273 TGATTATCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 19 0.42
13 9 0.20
14 17 0.38
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (13 bp):
ATAATATATAAAT
Found at i:390236 original size:26 final size:28
Alignment explanation
Indices: 390206--390272 Score: 79
Period size: 26 Copynumber: 2.5 Consensus size: 28
390196 TTTAAACTTA
*
390206 ATAATATTAAATATAATT-ATATA-AAT
1 ATAATATTAAATATAATTAAAATATAAT
*
390232 ATAATA-TAAA-ATAATTAAAATATGAT
1 ATAATATTAAATATAATTAAAATATAAT
*
390258 ATAATATAAAATATA
1 ATAATATTAAATATA
390273 TGATTATCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 6 0.18
25 8 0.24
26 14 0.41
27 3 0.09
28 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (28 bp):
ATAATATTAAATATAATTAAAATATAAT
Found at i:393466 original size:20 final size:21
Alignment explanation
Indices: 393441--393498 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
393431 ACTGTAGCAA
393441 AATAATAT-TAATATATATTT
1 AATAATATATAATATATATTT
*
393461 AATAAT-TATAAT-TATAATT
1 AATAATATATAATATATATTT
393480 ACATAA-ATATAATATATAT
1 A-ATAATATATAATATATAT
393499 AAAATTATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
19 8 0.25
20 20 0.62
21 4 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAATATATAATATATATTT
Found at i:393504 original size:25 final size:24
Alignment explanation
Indices: 393462--393526 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 24
393452 TATATATTTA
*
393462 ATAATTATAATTATAATTACAT-AAAT
1 ATAA-TATAA-TAAAATTA-ATAAAAT
*
393488 ATAATATATATAAAATTATTAAAAT
1 ATAATATA-ATAAAATTAATAAAAT
*
393513 ATAGTATAATAAAA
1 ATAATATAATAAAA
393527 ATATTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 7 0.21
25 22 0.65
26 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATAATATAATAAAATTAATAAAAT
Found at i:393510 original size:24 final size:24
Alignment explanation
Indices: 393484--393531 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
393474 ATAATTACAT
*
393484 AAATATAATATATATAAAATTATTA
1 AAATATAATATA-ATAAAAATATTA
*
393509 AAATATAGTATAATAAAAATATT
1 AAATATAATATAATAAAAATATT
393532 TATTTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATAATATAATAAAAATATTA
Found at i:393592 original size:16 final size:16
Alignment explanation
Indices: 393571--393604 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
393561 TAATTTATTA
393571 AAATTA-ATATAAATAT
1 AAATTATAT-TAAATAT
393587 AAATTATATTAAATAT
1 AAATTATATTAAATAT
393603 AA
1 AA
393605 TTAGTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATTATATTAAATAT
Found at i:398375 original size:15 final size:15
Alignment explanation
Indices: 398355--398386 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
398345 TGATTTCACG
398355 AATATGATATGTAAA
1 AATATGATATGTAAA
398370 AATATGATATGTAAA
1 AATATGATATGTAAA
398385 AA
1 AA
398387 ATTATTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (15 bp):
AATATGATATGTAAA
Found at i:398504 original size:30 final size:29
Alignment explanation
Indices: 398470--398563 Score: 90
Period size: 30 Copynumber: 3.3 Consensus size: 29
398460 TTATATAAAA
398470 ATAAAATATCTTAAATAATTTTATGATATG
1 ATAAAATAT-TTAAATAATTTTATGATATG
* * **
398500 AT-AAA-ATTT--ATAATTATAAT-AAAAA
1 ATAAAATATTTAAATAATT-TTATGATATG
398525 ATAAAATATTTTAAATAATTTTATGATATG
1 ATAAAATA-TTTAAATAATTTTATGATATG
398555 ATAAAATAT
1 ATAAAATAT
398564 ATAATTATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
25 10 0.20
26 6 0.12
27 3 0.06
28 5 0.10
29 7 0.14
30 18 0.37
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.41
Consensus pattern (29 bp):
ATAAAATATTTAAATAATTTTATGATATG
Found at i:398527 original size:55 final size:55
Alignment explanation
Indices: 398466--398576 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
398456 AAATTTATAT
*
398466 AAAAATAAAATATCTTAAATAATTTTATGATATGATAAAATTTATAATTATAATA
1 AAAAATAAAATATCTTAAATAATTTTATGATATGATAAAATATATAATTATAATA
*
398521 AAAAATAAAATATTTTAAATAATTTTATGATATGATAAAATATATAATTATAATA
1 AAAAATAAAATATCTTAAATAATTTTATGATATGATAAAATATATAATTATAATA
398576 A
1 A
398577 GAATGAATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (55 bp):
AAAAATAAAATATCTTAAATAATTTTATGATATGATAAAATATATAATTATAATA
Found at i:398991 original size:17 final size:17
Alignment explanation
Indices: 398971--399029 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
398961 TATTTATTAA
398971 ATATAAATATATATTTT
1 ATATAAATATATATTTT
398988 ATATAAATATTATAATTTT
1 ATATAAATA-TAT-ATTTT
* * *
399007 -TA-AAATGTTTATTTA
1 ATATAAATATATATTTT
399022 ATATAAAT
1 ATATAAAT
399030 TTAATAATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 4 0.11
16 4 0.11
17 17 0.49
18 5 0.14
19 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATAAATATATATTTT
Found at i:399043 original size:15 final size:14
Alignment explanation
Indices: 399020--399116 Score: 59
Period size: 14 Copynumber: 7.4 Consensus size: 14
399010 AATGTTTATT
*
399020 TAATATAAATTTAA
1 TAATATAAATATAA
*
399034 TAATATTAA-AT-A
1 TAATATAAATATAA
*
399046 TAATATAAATATGA
1 TAATATAAATATAA
399060 TAA-A-AAAT-TAA
1 TAATATAAATATAA
399071 -AATAT-AATATAA
1 TAATATAAATATAA
** *
399083 TTTTAAAAATA-ATA
1 TAATATAAATATA-A
399097 TAATAT-AATATATA
1 TAATATAAATATA-A
399111 TAATAT
1 TAATAT
399117 TTTAAATTTA
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
10 2 0.03
11 6 0.09
12 16 0.25
13 11 0.17
14 29 0.45
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (14 bp):
TAATATAAATATAA
Found at i:399052 original size:5 final size:5
Alignment explanation
Indices: 399020--399116 Score: 51
Period size: 5 Copynumber: 19.2 Consensus size: 5
399010 AATGTTTATT
* *
399020 TAATA TAAATT TAATAA TATTA -AATA TAATA TAA-A T-ATGA TAA-A
1 TAATA T-AATA TAAT-A TAATA TAATA TAATA TAATA TAAT-A TAATA
* * * *
399064 AAATTA AAATA TAATA TAATTT TAAAAA TAATA TAATA TAATA T-ATA
1 TAA-TA TAATA TAATA TAA-TA T-AATA TAATA TAATA TAATA TAATA
399111 TAATA T
1 TAATA T
399117 TTTAAATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
3 1 0.01
4 12 0.17
5 41 0.58
6 15 0.21
7 2 0.03
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:399096 original size:17 final size:18
Alignment explanation
Indices: 399067--399100 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
399057 TGATAAAAAA
399067 TTAAAATATAATATAATT
1 TTAAAATATAATATAATT
399085 TTAAAA-ATAATATAAT
1 TTAAAATATAATATAAT
399101 ATAATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAATATAATATAATT
Found at i:399109 original size:29 final size:29
Alignment explanation
Indices: 399022--399110 Score: 71
Period size: 27 Copynumber: 3.2 Consensus size: 29
399012 TGTTTATTTA
* * *
399022 ATATAAATTTAATAATATTA-AATATAAT
1 ATATAATTTTAAAAATAATATAATATAAT
* * *
399050 ATA-AATATGATAAAA-AAT-TAAAAT-AT
1 ATATAATTTTA-AAAATAATATAATATAAT
399076 AATATAATTTTAAAAATAATATAATATAAT
1 -ATATAATTTTAAAAATAATATAATATAAT
399106 ATATA
1 ATATA
399111 TAATATTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
26 2 0.04
27 17 0.38
28 14 0.31
29 10 0.22
30 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
ATATAATTTTAAAAATAATATAATATAAT
Found at i:399668 original size:14 final size:14
Alignment explanation
Indices: 399649--399678 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
399639 AAAAATTTTC
*
399649 TTTTTCTTTTCATT
1 TTTTTCTTTTAATT
399663 TTTTTCTTTTAATT
1 TTTTTCTTTTAATT
399677 TT
1 TT
399679 CCTTTGATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTAATT
Found at i:401253 original size:8 final size:8
Alignment explanation
Indices: 401232--401271 Score: 64
Period size: 8 Copynumber: 5.1 Consensus size: 8
401222 TGCTATTCCC
*
401232 TTATTTGT
1 TTATTGGT
401240 TT-TTGGT
1 TTATTGGT
401247 TTATTGGT
1 TTATTGGT
401255 TTATTGGT
1 TTATTGGT
401263 TTATTGGT
1 TTATTGGT
401271 T
1 T
401272 ATCTTTCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.10, C:0.00, G:0.23, T:0.68
Consensus pattern (8 bp):
TTATTGGT
Found at i:401995 original size:2 final size:2
Alignment explanation
Indices: 401988--402017 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
401978 TCCTGTCTTC
401988 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
402018 GATAACCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:404344 original size:2 final size:2
Alignment explanation
Indices: 404337--404363 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
404327 AATATGATTT
404337 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
404364 TAAGGTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406794 original size:27 final size:28
Alignment explanation
Indices: 406764--406817 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
406754 TAGTAGATTG
406764 TTAA-GTCTAACTACAAGTATGTAAAAA
1 TTAAGGTCTAACTACAAGTATGTAAAAA
406791 TTAAGGTCTAACTACAAGTATGTAAAA
1 TTAAGGTCTAACTACAAGTATGTAAAA
406818 GTTAGAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (28 bp):
TTAAGGTCTAACTACAAGTATGTAAAAA
Found at i:407429 original size:2 final size:2
Alignment explanation
Indices: 407422--407457 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
407412 CTTTGTTGGT
407422 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
407458 ATGATCAAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:407589 original size:13 final size:13
Alignment explanation
Indices: 407571--407603 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
407561 ATAGTAATTA
407571 TTAATAA-TTAGAT
1 TTAATAACTTA-AT
407584 TTAATAACTTAAT
1 TTAATAACTTAAT
407597 TTAATAA
1 TTAATAA
407604 AAATATTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (13 bp):
TTAATAACTTAAT
Found at i:409125 original size:5 final size:5
Alignment explanation
Indices: 409115--409146 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
409105 TAATTTTTAT
409115 AAAA- AAAA- AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
409147 TTGAGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:411777 original size:11 final size:11
Alignment explanation
Indices: 411760--411791 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
411750 TTATTAAAAA
411760 AATATATATTT
1 AATATATATTT
*
411771 TATATATATTT
1 AATATATATTT
411782 AATATATATT
1 AATATATATT
411792 AAACATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATATATATTT
Found at i:412022 original size:2 final size:2
Alignment explanation
Indices: 412015--412046 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
412005 ATATTTTAAG
412015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412047 GCAATTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:412644 original size:16 final size:16
Alignment explanation
Indices: 412619--412678 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
412609 TTTATTGATT
412619 AAAATAAATTTTAAAA
1 AAAATAAATTTTAAAA
* *
412635 AAAATTAATTATAAAA
1 AAAATAAATTTTAAAA
* * *
412651 TATATAAATATTAAATA
1 AAAATAAATTTTAAA-A
412668 AAAATAAATTT
1 AAAATAAATTT
412679 GTAATATTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
16 24 0.73
17 9 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAAATTTTAAAA
Found at i:416295 original size:54 final size:54
Alignment explanation
Indices: 416221--416325 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
416211 TTGAGCGCTA
* * *
416221 TTATCATCTGTTTTCGTATTAGCCTTTGAATTTATTTTCTTTTTAATTTCTGAT
1 TTATCATCTGGTTTCATATTAGCCTTTGAATTTATTTTCCTTTTAATTTCTGAT
* * *
416275 TTATCTTCTGGTTTCATATTATCCTTTGAATTTTTTTTCCTTTTAATTTCT
1 TTATCATCTGGTTTCATATTAGCCTTTGAATTTATTTTCCTTTTAATTTCT
416326 TATCTTTATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.08, T:0.61
Consensus pattern (54 bp):
TTATCATCTGGTTTCATATTAGCCTTTGAATTTATTTTCCTTTTAATTTCTGAT
Found at i:419409 original size:21 final size:22
Alignment explanation
Indices: 419376--419419 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
419366 TATTTAACAG
*
419376 AAATGATTAATTA-AATTTTAT
1 AAATAATTAATTATAATTTTAT
*
419397 AAATAATTTATTATTAATTTTAT
1 AAATAATTAATTA-TAATTTTAT
419420 TTTGAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAATAATTAATTATAATTTTAT
Found at i:421464 original size:16 final size:18
Alignment explanation
Indices: 421432--421473 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
421422 TATCATGATT
421432 AATTATAATAAATATTAA
1 AATTATAATAAATATTAA
*
421450 TATTA-AATAAA-ATTAA
1 AATTATAATAAATATTAA
421466 AATTATAA
1 AATTATAA
421474 AATAATGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 9 0.43
17 8 0.38
18 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATTATAATAAATATTAA
Found at i:427719 original size:2 final size:2
Alignment explanation
Indices: 427712--427737 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
427702 CATTATCCTT
427712 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
427738 TATATATATA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:432979 original size:14 final size:14
Alignment explanation
Indices: 432960--432994 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
432950 AACTTCGAGT
432960 TAATTTATAAATAA
1 TAATTTATAAATAA
*
432974 TAATTTAAAAATAA
1 TAATTTATAAATAA
432988 -AATTTAT
1 TAATTTAT
432995 TTTTATTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTTATAAATAA
Found at i:433269 original size:21 final size:20
Alignment explanation
Indices: 433250--433286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
433240 TTATTAAATT
433250 TAATTATA-AAAAATAAAAA
1 TAATTATATAAAAATAAAAA
*
433269 TATTTATATAAAAATAAA
1 TAATTATATAAAAATAAA
433287 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATTATATAAAAATAAAAA
Found at i:433296 original size:17 final size:18
Alignment explanation
Indices: 433266--433299 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
433256 TAAAAAATAA
*
433266 AAATATTTATATAAAAAT
1 AAATATTTAAATAAAAAT
433284 AAAT-TTTAAATAAAAA
1 AAATATTTAAATAAAAA
433300 CGAGCTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATATTTAAATAAAAAT
Found at i:439069 original size:2 final size:2
Alignment explanation
Indices: 439062--439092 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
439052 TCACCATCTT
*
439062 TA TA TA TA TA TA TG TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
439093 CCAATTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:439762 original size:16 final size:16
Alignment explanation
Indices: 439708--439754 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 16
439698 ATTATATTCG
439708 TATTATTTTTTATATTA
1 TATT-TTTTTTATATTA
*
439725 TATTTTTTTTATATTT
1 TATTTTTTTTATATTA
439741 TAATTTTTTTTATA
1 T-ATTTTTTTTATA
439755 ATCTATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTTTTATATTA
Found at i:439774 original size:18 final size:18
Alignment explanation
Indices: 439751--439785 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
439741 TAATTTTTTT
439751 TATAATCTAT-TTATATTA
1 TATAAT-TATATTATATTA
439769 TATAATTATATTATATT
1 TATAATTATATTATATT
439786 CAAAATTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATTATATTATATTA
Found at i:440096 original size:49 final size:48
Alignment explanation
Indices: 440039--440136 Score: 112
Period size: 49 Copynumber: 2.0 Consensus size: 48
440029 ATTTAGAATG
* * *
440039 ATTTAATTTGATTCA-AATTAATATATAATAATT-TTA-AAAAATATTTTT
1 ATTTAATTTAATT-ATAATAAATATA-AAT-ATTATTATAAAAATAATTTT
440087 ATTTAAATTTAATTATAATAAATATAAATATTATTATAAAAATAATTTT
1 ATTT-AATTTAATTATAATAAATATAAATATTATTATAAAAATAATTTT
440136 A
1 A
440137 AATTTTAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
47 3 0.07
48 11 0.26
49 29 0.67
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (48 bp):
ATTTAATTTAATTATAATAAATATAAATATTATTATAAAAATAATTTT
Found at i:451921 original size:32 final size:33
Alignment explanation
Indices: 451822--451915 Score: 102
Period size: 32 Copynumber: 2.9 Consensus size: 33
451812 ACTTTGAGGA
*
451822 ATTAGACATAATTACTCAAAAATTTGA-AGAAT
1 ATTAGACATAATTACTCATAAATTTGATAGAAT
* * * * * *
451854 ATTAAACAAAACTACACGTAAATTTAAT-GAAT
1 ATTAGACATAATTACTCATAAATTTGATAGAAT
*
451886 ATTAGACATAATTACTCCTAAATTTGATAG
1 ATTAGACATAATTACTCATAAATTTGATAG
451916 TTATTAAAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 3
0.75 0.21 0.05
Matches are distributed among these distances:
32 46 0.98
33 1 0.02
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.32
Consensus pattern (33 bp):
ATTAGACATAATTACTCATAAATTTGATAGAAT
Found at i:452843 original size:147 final size:148
Alignment explanation
Indices: 452576--452872 Score: 551
Period size: 147 Copynumber: 2.0 Consensus size: 148
452566 TTCCTTTCTC
*
452576 CTTTACTTCTCTCCTGTCAGACATAAAGCATCGATTTCCTTCCTACATGCATACCCATGGTATCG
1 CTTTACTTCTCTCCTGTCAGACATAAAGCATCGATTTCCTTCCTACATGCATACCCATGATATCG
*
452641 TTTCCTGGACAAAACTCACTATCAGTTGTCTTACATAATGAATATCCAATAGAAAGGCTCCAATG
66 TTTCCTGGACAAAACTCACTATCAGTTGTCTTACACAATGAATATCCAATAGAAAGGCTCCAATG
452706 CCT-ACATCTATCACCCA
131 CCTAACATCTATCACCCA
* *
452723 CTTTACTTCTCTCCTGTCAGACATAAAGCATCGATTTCCTTCCTACGTGCATACCCATGATATCT
1 CTTTACTTCTCTCCTGTCAGACATAAAGCATCGATTTCCTTCCTACATGCATACCCATGATATCG
452788 TTTCCTGGACAAAACTCACTATCAGTTGTCTTACACAATGAATATCCAATAGAAAGGCTCCAATG
66 TTTCCTGGACAAAACTCACTATCAGTTGTCTTACACAATGAATATCCAATAGAAAGGCTCCAATG
452853 CCTAACATCTATCACCCA
131 CCTAACATCTATCACCCA
452871 CT
1 CT
452873 AAAGGCAACT
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
147 129 0.89
148 16 0.11
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (148 bp):
CTTTACTTCTCTCCTGTCAGACATAAAGCATCGATTTCCTTCCTACATGCATACCCATGATATCG
TTTCCTGGACAAAACTCACTATCAGTTGTCTTACACAATGAATATCCAATAGAAAGGCTCCAATG
CCTAACATCTATCACCCA
Found at i:453784 original size:19 final size:20
Alignment explanation
Indices: 453762--453809 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
453752 AATATTAAAT
*
453762 TATTAAAATATTATTT-TTA
1 TATTAAAATAATATTTATTA
*
453781 TATTAATATTAATATTTATTA
1 TATTAA-AATAATATTTATTA
453802 TAATTAAA
1 T-ATTAAA
453810 TTTAAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 5 0.21
22 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TATTAAAATAATATTTATTA
Found at i:453814 original size:28 final size:28
Alignment explanation
Indices: 453783--453848 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
453773 TATTTTTATA
*
453783 TTAATATTAATA-TTTATTATAATTAAAT
1 TTAATATTAATATTTTAAT-TAATTAAAT
453811 TTAA-ATTAAATATTTTAATTAATTAAAT
1 TTAATATT-AATATTTTAATTAATTAAAT
453839 TATAAT-TTAA
1 T-TAATATTAA
453849 ATTAAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 3 0.09
28 20 0.61
29 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
TTAATATTAATATTTTAATTAATTAAAT
Found at i:453850 original size:12 final size:12
Alignment explanation
Indices: 453803--453866 Score: 64
Period size: 12 Copynumber: 5.6 Consensus size: 12
453793 TATTTATTAT
453803 AATT-AAATTTA
1 AATTAAAATTTA
*
453814 AATTAAATATTTT
1 AATTAAA-ATTTA
453827 AATT--AA-TTA
1 AATTAAAATTTA
*
453836 AATTATAATTTA
1 AATTAAAATTTA
*
453848 AATTAAAAATTA
1 AATTAAAATTTA
453860 AATTAAA
1 AATTAAA
453867 TAAAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
9 6 0.14
10 1 0.02
11 7 0.16
12 22 0.50
13 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAAATTTA
Found at i:453865 original size:17 final size:18
Alignment explanation
Indices: 453803--453887 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
453793 TATTTATTAT
453803 AATTAAATTTAAATTAAA
1 AATTAAATTTAAATTAAA
* *
453821 TATTTTAA-TT-AATT--A
1 -AATTAAATTTAAATTAAA
453836 AATTATAATTTAAATTAAA
1 AATTA-AATTTAAATTAAA
*
453855 AATTAAA-TTAAATAAAA
1 AATTAAATTTAAATTAAA
*
453872 ATATTATATTTAAATT
1 A-ATTAAATTTAAATT
453888 TAACTCAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 3 0.06
15 3 0.06
16 2 0.04
17 18 0.35
18 9 0.17
19 17 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAAATTTAAATTAAA
Found at i:453986 original size:15 final size:16
Alignment explanation
Indices: 453966--453996 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
453956 TTAATATTTT
453966 TTATAAAT-TAAAATA
1 TTATAAATCTAAAATA
453981 TTATAAATCTAAAATA
1 TTATAAATCTAAAATA
453997 AATTTAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
TTATAAATCTAAAATA
Found at i:454118 original size:15 final size:17
Alignment explanation
Indices: 454098--454131 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
454088 ATTAAATATC
454098 TAAATTCA-TA-TTATT
1 TAAATTCATTATTTATT
454113 TAAATTCATTATTTATT
1 TAAATTCATTATTTATT
454130 TA
1 TA
454132 TTATTAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 2 0.12
17 7 0.41
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTCATTATTTATT
Found at i:454256 original size:14 final size:15
Alignment explanation
Indices: 454220--454260 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
454210 TTTTAACATA
454220 TATATTATAAATAATT
1 TATATT-TAAATAATT
454236 TGA-ATTTAAAT-ATT
1 T-ATATTTAAATAATT
454250 TATATTTAAAT
1 TATATTTAAAT
454261 TTAATATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 12 0.52
15 5 0.22
16 4 0.17
17 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATTTAAATAATT
Found at i:455039 original size:25 final size:25
Alignment explanation
Indices: 455011--455059 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
455001 AATATTTTAT
455011 TTTAAATTAATAAAATTTAAAAAAA
1 TTTAAATTAATAAAATTTAAAAAAA
* **
455036 TTTATATTTTTAAAATTTAAAAAA
1 TTTAAATTAATAAAATTTAAAAAA
455060 TCAATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTAAATTAATAAAATTTAAAAAAA
Found at i:455057 original size:32 final size:30
Alignment explanation
Indices: 454987--455057 Score: 72
Period size: 32 Copynumber: 2.2 Consensus size: 30
454977 TTAATTAATT
*
454987 TTTATAATATAAAAAATATTTTATTTTAAA
1 TTTAAAATATAAAAAATATTTTATTTTAAA
*
455017 TTAATAAAATTTAAAAAA-ATTTATATTTTTAAAA
1 TT--TAAAATATAAAAAATATTT-TA-TTTT-AAA
455051 TTTAAAA
1 TTTAAAA
455058 AATCAATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
30 2 0.06
31 4 0.12
32 19 0.56
33 4 0.12
34 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (30 bp):
TTTAAAATATAAAAAATATTTTATTTTAAA
Found at i:456990 original size:32 final size:31
Alignment explanation
Indices: 456949--457054 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
456939 TTAACAATTG
456949 TCAAATTTACGAGTAATTATGTCTAATATTTA
1 TCAAATTTACGAGTAATTATGT-TAATATTTA
* *
456981 TCAAATTTACGAGTAATTTTGTTCAATATTCA
1 TCAAATTTACGAGTAATTATGTT-AATATTTA
** * * *
457013 TCAAATTTGTGAGAAATTATATTTA-ATTTA
1 TCAAATTTACGAGTAATTATGTTAATATTTA
*
457043 TTAAATTTACGA
1 TCAAATTTACGA
457055 TCAATATCTG
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
30 13 0.21
31 2 0.03
32 46 0.75
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.44
Consensus pattern (31 bp):
TCAAATTTACGAGTAATTATGTTAATATTTA
Found at i:458960 original size:22 final size:23
Alignment explanation
Indices: 458935--458979 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
458925 GTCATTTAAA
* *
458935 TTATATATTATTAT-AATAATTT
1 TTATATAATAATATAAATAATTT
458957 TTATATAATAATATAAATAATTT
1 TTATATAATAATATAAATAATTT
458980 ATTTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTATATAATAATATAAATAATTT
Found at i:460590 original size:20 final size:21
Alignment explanation
Indices: 460565--460607 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
460555 CGGAAACTTC
460565 TTAAAAAAATAC-TAAAATAT
1 TTAAAAAAATACTTAAAATAT
*
460585 TT-AAAAAATCCTTAAAATAT
1 TTAAAAAAATACTTAAAATAT
460605 TTA
1 TTA
460608 TTTTTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TTAAAAAAATACTTAAAATAT
Found at i:460714 original size:26 final size:23
Alignment explanation
Indices: 460685--460754 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 23
460675 ATAAAAAATT
460685 AATTAAATTAAAAGATTATATATATA
1 AATTAAATTAAAA-ATTATAT-T-TA
*
460711 AATTAAACATAAAAAATT-TATTTA
1 AATT-AA-ATTAAAAATTATATTTA
460735 AATATAAATTAAAAATTATA
1 AAT-TAAATTAAAAATTATA
460755 AAATATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 9 0.24
24 9 0.24
25 2 0.05
26 7 0.18
27 5 0.13
28 6 0.16
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (23 bp):
AATTAAATTAAAAATTATATTTA
Found at i:460740 original size:30 final size:31
Alignment explanation
Indices: 460706--460766 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
460696 AAGATTATAT
* *
460706 ATATAAATTAAACA-TAAAAAATTTATTTAA
1 ATATAAATTAAAAATTAAAAAATATATTTAA
*
460736 ATATAAATTAAAAATTATAAAATATATTTAA
1 ATATAAATTAAAAATTAAAAAATATATTTAA
460767 TAATTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
ATATAAATTAAAAATTAAAAAATATATTTAA
Found at i:460787 original size:6 final size:6
Alignment explanation
Indices: 460778--460914 Score: 61
Period size: 6 Copynumber: 22.3 Consensus size: 6
460768 AATTTTATTT
* * *
460778 TTTATA TTTATA TTTATA TATTATA ATTATA TTTA-A ATTAT- TTTTTA
1 TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA TTTATA TTTATA
* * * *
460825 TTTATAA TATAAATT TTTATA TATTATAA TTTATA TTTAAAA ATT-T-
1 TTTAT-A T-T-TATA TTTATA T-TTAT-A TTTATA TTT-ATA TTTATA
* * *
460871 TGTATA ATTATA -TTAT- TTTATA TTATATT TTTATA TTTAATA TT
1 TTTATA TTTATA TTTATA TTTATA TT-TATA TTTATA TTT-ATA TT
460915 ATAATTTTAC
Statistics
Matches: 97, Mismatches: 19, Indels: 29
0.67 0.13 0.20
Matches are distributed among these distances:
4 1 0.01
5 16 0.16
6 44 0.45
7 30 0.31
8 4 0.04
9 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (6 bp):
TTTATA
Found at i:460819 original size:28 final size:28
Alignment explanation
Indices: 460788--460865 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 28
460778 TTTATATTTA
460788 TATTTATATATTATAATTATATTTAAAT
1 TATTTATATATTATAATTATATTTAAAT
* *
460816 TATTT-TTTATT-T-A-TA-ATATAAAT
1 TATTTATATATTATAATTATATTTAAAT
460839 T-TTTATATATTATAATTTATATTTAAA
1 TATTTATATATTATAA-TTATATTTAAA
460866 AATTTTGTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
22 3 0.08
23 13 0.32
24 3 0.08
25 2 0.05
26 1 0.03
27 7 0.17
28 11 0.28
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TATTTATATATTATAATTATATTTAAAT
Found at i:460856 original size:29 final size:30
Alignment explanation
Indices: 460824--460882 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
460814 ATTATTTTTT
*
460824 ATTTATA-ATATAAATTTT-TATATATTATA
1 ATTTATATATAAAAATTTTGTATA-ATTATA
*
460853 ATTTATATTTAAAAATTTTGTATAATTATA
1 ATTTATATATAAAAATTTTGTATAATTATA
460883 TTATTTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTATATATAAAAATTTTGTATAATTATA
Found at i:460899 original size:50 final size:50
Alignment explanation
Indices: 460790--460883 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
460780 TATATTTATA
* * *
460790 TTTATATATTATAATTATATTTAAATTATTTTTTATTTATAATATAAATT
1 TTTATATATTATAATTATATTTAAATAATTTTGTATTAATAATATAAATT
*
460840 TTTATATATTATAATTTATATTTAAA-AATTTTGTA-TAATTATAT
1 TTTATATATTATAA-TTATATTTAAATAATTTTGTATTAATAATAT
460884 TATTTTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
49 7 0.18
50 21 0.54
51 11 0.28
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (50 bp):
TTTATATATTATAATTATATTTAAATAATTTTGTATTAATAATATAAATT
Found at i:461061 original size:2 final size:2
Alignment explanation
Indices: 461054--461090 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
461044 TATCTTTCAT
461054 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
461091 TTTTAATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:461197 original size:9 final size:9
Alignment explanation
Indices: 461183--461207 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
461173 TAAAAAATCA
461183 AATTAAATT
1 AATTAAATT
461192 AATTAAATT
1 AATTAAATT
461201 AATTAAA
1 AATTAAA
461208 AATTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:461451 original size:12 final size:12
Alignment explanation
Indices: 461434--461486 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 12
461424 CAAAGATTGA
461434 TTAATTTAATTT
1 TTAATTTAATTT
461446 TTAATTTAATTATGT
1 TTAATTTAA-T-T-T
461461 TTAATTTTAATTT
1 TTAA-TTTAATTT
461474 TTATATTATAATT
1 TTA-ATT-TAATT
461487 ATATCATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 9 0.26
13 7 0.20
14 8 0.23
15 6 0.17
16 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
TTAATTTAATTT
Found at i:461457 original size:21 final size:21
Alignment explanation
Indices: 461433--461486 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
461423 TCAAAGATTG
461433 ATTA-ATTTAATTTTTAATTTA
1 ATTATATTTAA-TTTTAATTTA
*
461454 ATTATGTTTAATTTTAATTT-
1 ATTATATTTAATTTTAATTTA
461474 -TTATATTATAATT
1 ATTATATT-TAATT
461487 ATATCATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 5 0.17
21 13 0.45
22 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTATATTTAATTTTAATTTA
Found at i:461864 original size:28 final size:25
Alignment explanation
Indices: 461817--461867 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
461807 GTTAGAATTT
*
461817 TTTAATATTTATAATATTTAATTAA
1 TTTAATATTTATAAAATTTAATTAA
461842 TTTAATAATTATATAAAAGTTTAATT
1 TTTAAT-ATT-TATAAAA-TTTAATT
461868 TTAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 6 0.27
28 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTAATATTTATAAAATTTAATTAA
Found at i:461901 original size:19 final size:18
Alignment explanation
Indices: 461872--461912 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
461862 TTAATTTTAA
461872 ATTTATTAAATAAGTTTT
1 ATTTATTAAATAAGTTTT
**
461890 ATTTATTTAAATATTTTTT
1 ATTTA-TTAAATAAGTTTT
461909 ATTT
1 ATTT
461913 TAAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTATTAAATAAGTTTT
Found at i:461981 original size:5 final size:5
Alignment explanation
Indices: 461971--462020 Score: 55
Period size: 5 Copynumber: 9.4 Consensus size: 5
461961 AAAAATTTAA
* *
461971 AATAT AATAT AAATAT AATAT AAAAAT AATTAA AATAT AATAT AATAT
1 AATAT AATAT -AATAT AATAT -AATAT AA-TAT AATAT AATAT AATAT
462019 AA
1 AA
462021 AAATAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 26 0.68
6 12 0.32
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (5 bp):
AATAT
Found at i:461986 original size:11 final size:11
Alignment explanation
Indices: 461970--462020 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
461960 AAAAAATTTA
461970 AAATATAATAT
1 AAATATAATAT
461981 AAATATAATAT
1 AAATATAATAT
*
461992 AAAAATAAT-T
1 AAATATAATAT
462002 AAAATATAATAT
1 -AAATATAATAT
462014 -AATATAA
1 AAATATAA
462021 AAATAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 8 0.22
11 27 0.75
12 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:462006 original size:22 final size:23
Alignment explanation
Indices: 461968--462097 Score: 75
Period size: 22 Copynumber: 5.9 Consensus size: 23
461958 ATAAAAAATT
461968 TAAAATATAATATAAATATAATA
1 TAAAATATAATATAAATATAATA
461991 TAAAA-ATAAT-TAAAATATAATA
1 TAAAATATAATAT-AAATATAATA
* * *
462013 TAATATA-AAAAT-AACA-AA-A
1 TAAAATATAATATAAATATAATA
*
462032 -AAAATATAAATATAAAAATAA-A
1 TAAAATAT-AATATAAATATAATA
* *
462054 TTAAAAT-TTATATAAAATAAAATA
1 -TAAAATATAATAT-AAATATAATA
*
462078 CTAACATATAA-A-AAATATAA
1 -TAAAATATAATATAAATATAA
462098 ATTTATAATA
Statistics
Matches: 82, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
18 5 0.06
19 1 0.01
20 6 0.07
21 7 0.09
22 35 0.43
23 14 0.17
24 12 0.15
25 2 0.02
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAATATAATATAAATATAATA
Found at i:462012 original size:27 final size:27
Alignment explanation
Indices: 461976--462075 Score: 116
Period size: 27 Copynumber: 3.7 Consensus size: 27
461966 TTTAAAATAT
461976 AATATAAATATAATATAAAAATAATTAA
1 AATAT-AATATAATATAAAAATAATTAA
*
462004 AATATAATATAATATAAAAATAA-CAA
1 AATATAATATAATATAAAAATAATTAA
*
462030 AA-AAAATATAAATATAAAAATAAATTAA
1 AATATAATAT-AATATAAAAAT-AATTAA
* *
462058 AAT-TTATATAAAATAAAA
1 AATATAATATAATATAAAA
462076 TACTAACATA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
25 6 0.10
26 15 0.24
27 28 0.45
28 13 0.21
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (27 bp):
AATATAATATAATATAAAAATAATTAA
Found at i:462018 original size:38 final size:37
Alignment explanation
Indices: 461971--462123 Score: 109
Period size: 38 Copynumber: 4.0 Consensus size: 37
461961 AAAAATTTAA
461971 AATATAATATAAATATAATATAAAAATAATTAAAATAT
1 AATATAATATAAATATAATATAAAAA-AATTAAAATAT
* *
462009 AATATAATATAAAAATAACA-AAAAAAA-TATAAATAT
1 AATATAATATAAATATAATATAAAAAAATTA-AAATAT
* * *
462045 AAAAATAA-ATTAAA-ATTTATATAAAATAAAATACTAACATAT
1 -AATATAATA-TAAATA-TAATAT-AAA-AAAAT--TAAAATAT
* *
462087 AA-AAAATATAAATTTATAATATTAAAAAATTAAAATA
1 AATATAATATAAA--TATAATATAAAAAAATTAAAATA
462124 AATTTAAATT
Statistics
Matches: 91, Mismatches: 10, Indels: 28
0.71 0.08 0.22
Matches are distributed among these distances:
35 2 0.02
36 10 0.11
37 18 0.20
38 24 0.26
39 3 0.03
40 16 0.18
41 5 0.05
42 10 0.11
43 3 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (37 bp):
AATATAATATAAATATAATATAAAAAAATTAAAATAT
Found at i:462026 original size:11 final size:11
Alignment explanation
Indices: 461940--462015 Score: 63
Period size: 11 Copynumber: 7.0 Consensus size: 11
461930 AATTTAAATT
461940 AAATAACTATAA
1 AAATAA-TATAA
461952 TAAAT--TAT-A
1 -AAATAATATAA
*
461961 AAA-AATTTAA
1 AAATAATATAA
461971 AATATAATATAA
1 AA-ATAATATAA
*
461983 ATATAATATAA
1 AAATAATATAA
461994 AAATAAT-TAA
1 AAATAATATAA
462004 AATATAATATAA
1 AA-ATAATATAA
462016 TATAAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 11 0.21
11 21 0.40
12 10 0.19
13 4 0.08
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATATAA
Found at i:462091 original size:58 final size:56
Alignment explanation
Indices: 461972--462099 Score: 151
Period size: 53 Copynumber: 2.3 Consensus size: 56
461962 AAAATTTAAA
* *
461972 ATATAATATAAATAT-AATATAAAAATAATTAAAATATAATATAATATAAAAATAAC
1 ATATAA-AAAAATATAAATATAAAAATAATTAAAATATAATATAAAATAAAAATAAC
*
462028 --A-AAAAAAATATAAATATAAAAATAAATTAAAAT-TTATATAAAATAAAATACTAAC
1 ATATAAAAAAATATAAATATAAAAAT-AATTAAAATATAATATAAAATAAAA-A-TAAC
462083 ATAT-AAAAAATATAAAT
1 ATATAAAAAAATATAAAT
462100 TTATAATATT
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
52 7 0.11
53 26 0.42
54 11 0.18
55 4 0.06
57 14 0.23
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (56 bp):
ATATAAAAAAATATAAATATAAAAATAATTAAAATATAATATAAAATAAAAATAAC
Found at i:462826 original size:158 final size:160
Alignment explanation
Indices: 462529--462835 Score: 431
Period size: 158 Copynumber: 1.9 Consensus size: 160
462519 TGCTGATCAC
* *
462529 AATTCCAAATCAATTTTATGTTTCGTTTCGCTGCTGAGAAAATGCAAGAAAAGAAAACGAATTGA
1 AATTCCAAATCAATTTTATGTTTCGTTTCGCTGCTGAGAAAACGCAAGAAAAGAAAACGAATTAA
* * * *
462594 TTAGAAAATTTCGAGTGAATTTTTTGACCTTCAGGACTGTTATTCAACTGATTTTGAATTACTTA
66 TTAGAAAATTTCGAGTGAA-TTTTTGACCGTCAGGACTGTTATGCAACTGAGTTTGAAGTACTTA
* *
462659 TCAATTAAAATCAATTTGGATTCCTGATAGT
130 TCAACTAAAACCAATTTGGATTCCTGATAGT
* * * ** *
462690 AATTCCAAATCAATTTTATGTTTCGTTTGGCTGCTGAGAAAACGGAAGGAAA-AAAGGGTATTAA
1 AATTCCAAATCAATTTTATGTTTCGTTTCGCTGCTGAGAAAACGCAAGAAAAGAAAACGAATTAA
*
462754 TTAG-AAATTTCGAGTGACA-TTTTGACCGTCAGGACTGTTATGCATCTGAGTTTGAAGTACTTA
66 TTAGAAAATTTCGAGTGA-ATTTTTGACCGTCAGGACTGTTATGCAACTGAGTTTGAAGTACTTA
*
462817 TCACCTAAAACCAATTTGG
130 TCAACTAAAACCAATTTGG
462836 GACAGAAACC
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
158 55 0.43
159 13 0.10
160 13 0.10
161 48 0.37
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.35
Consensus pattern (160 bp):
AATTCCAAATCAATTTTATGTTTCGTTTCGCTGCTGAGAAAACGCAAGAAAAGAAAACGAATTAA
TTAGAAAATTTCGAGTGAATTTTTGACCGTCAGGACTGTTATGCAACTGAGTTTGAAGTACTTAT
CAACTAAAACCAATTTGGATTCCTGATAGT
Found at i:468082 original size:18 final size:18
Alignment explanation
Indices: 468061--468095 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
468051 AATTTTTCTC
468061 ATTAATTCAATTGATTTT
1 ATTAATTCAATTGATTTT
* *
468079 ATTAATTTATTTGATTT
1 ATTAATTCAATTGATTT
468096 AATCAATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (18 bp):
ATTAATTCAATTGATTTT
Found at i:468343 original size:18 final size:18
Alignment explanation
Indices: 468320--468355 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
468310 CTTTATTGTT
468320 CATTATATTATTGAAATA
1 CATTATATTATTGAAATA
468338 CATTATATTATTGAAATA
1 CATTATATTATTGAAATA
468356 TTATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (18 bp):
CATTATATTATTGAAATA
Found at i:471961 original size:27 final size:27
Alignment explanation
Indices: 471929--472021 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 27
471919 TAGAATAATA
471929 AAAATATAATAAAATATTATATATTAT
1 AAAATATAATAAAATATTATATATTAT
471956 AAAATAT-ATAAAATAAATTAT-TAATATAT
1 AAAATATAATAAAAT--ATTATAT-AT-TAT
*
471985 TAAATATAATATAAATTATTA-A-ATT-T
1 AAAATATAATA-AAA-TATTATATATTAT
*
472011 AAAAAATAATA
1 AAAATATAATA
472022 TGACAAATGA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
26 17 0.31
27 9 0.16
28 9 0.16
29 9 0.16
30 7 0.13
31 3 0.05
32 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
AAAATATAATAAAATATTATATATTAT
Found at i:472345 original size:14 final size:14
Alignment explanation
Indices: 472326--472382 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
472316 AAATATTAAA
472326 AATATTTTTATATT
1 AATATTTTTATATT
472340 AATATTTTTATATT
1 AATATTTTTATATT
*
472354 --T-TTATTATAATT
1 AATATTTTTAT-ATT
472366 ATATTATTTTTATATT
1 A-A-TATTTTTATATT
472382 A
1 A
472383 TTTTTAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
14 14 0.40
16 5 0.14
17 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
AATATTTTTATATT
Found at i:472355 original size:22 final size:22
Alignment explanation
Indices: 472327--472382 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
472317 AATATTAAAA
* *
472327 ATATTTTTATATTAATATTTTT
1 ATATTTTTATATTAATAATTAT
472349 ATA-TTTT-TATT-ATAATTAT
1 ATATTTTTATATTAATAATTAT
472368 ATTATTTTTATATTA
1 A-TATTTTTATATTA
472383 TTTTTAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 7 0.25
20 6 0.21
21 8 0.29
22 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
ATATTTTTATATTAATAATTAT
Found at i:472368 original size:31 final size:31
Alignment explanation
Indices: 472334--472400 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
472324 AAAATATTTT
472334 TATATTAATATTTT-TA-TATTTTT-ATTATAAT
1 TATATT-AT-TTTTATATTATTTTTAATTAT-AT
472365 TATATTATTTTTATATTATTTTTAATTATAT
1 TATATTATTTTTATATTATTTTTAATTATAT
472396 TATAT
1 TATAT
472401 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 4 0.12
30 4 0.12
31 20 0.61
32 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TATATTATTTTTATATTATTTTTAATTATAT
Found at i:472369 original size:17 final size:16
Alignment explanation
Indices: 472347--472400 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
472337 ATTAATATTT
472347 TTATATTTTTATTATAA
1 TTATATTTTTATTAT-A
472364 TTATATTATTT-TTATA
1 TTATATT-TTTATTATA
*
472380 TTAT-TTTTAATTATA
1 TTATATTTTTATTATA
472395 TTATAT
1 TTATAT
472401 ATAAAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 2 0.06
15 11 0.33
16 6 0.18
17 11 0.33
18 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTTTTATTATA
Found at i:472383 original size:22 final size:21
Alignment explanation
Indices: 472328--472383 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
472318 ATATTAAAAA
472328 TATTTTTATATTA-ATATTTT
1 TATTTTTATATTATATATTTT
472348 TATATTTT-TATTATA-ATTATAT
1 TAT-TTTTATATTATATATT-T-T
472370 TATTTTTATATTAT
1 TATTTTTATATTAT
472384 TTTTAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
20 11 0.35
21 10 0.32
22 10 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTATATTATATATTTT
Found at i:472419 original size:30 final size:30
Alignment explanation
Indices: 472385--472447 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
472375 TTATATTATT
*
472385 TTTAATT-ATATTATATATAA-AATTATTAAA
1 TTTAATTAATACTATATA-AAGAATT-TTAAA
*
472415 TTTAATTAATACTATTTAAAGAATTTTAAA
1 TTTAATTAATACTATATAAAGAATTTTAAA
472445 TTT
1 TTT
472448 TATATAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTAATTAATACTATATAAAGAATTTTAAA
Found at i:472608 original size:18 final size:18
Alignment explanation
Indices: 472574--472626 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
472564 ATAATCATAA
*
472574 TAATTTA-ATTTTAATTTT
1 TAATTTATATTAT-ATTTT
472592 TAATTTATATTATA-TTT
1 TAATTTATATTATATTTT
*
472609 TATTTTATAATTATATTT
1 TAATTTAT-ATTATATTT
472627 AATTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 10 0.33
18 14 0.47
19 6 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTTATATTATATTTT
Found at i:472615 original size:17 final size:18
Alignment explanation
Indices: 472589--472631 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
472579 TAATTTTAAT
*
472589 TTTTAATTTAT-ATTATA
1 TTTTATTTTATAATTATA
472606 TTTTATTTTATAATTATA
1 TTTTATTTTATAATTATA
*
472624 TTTAATTT
1 TTTTATTT
472632 ATTATCAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTTTATAATTATA
Found at i:472632 original size:17 final size:17
Alignment explanation
Indices: 472589--472633 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
472579 TAATTTTAAT
472589 TTTTAATTTATATTATA
1 TTTTAATTTATATTATA
*
472606 TTTTATTTTATAATTATA
1 TTTTAATTTAT-ATTATA
472624 -TTTAATTTAT
1 TTTTAATTTAT
472634 TATCAACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTAATTTATATTATA
Found at i:475159 original size:19 final size:18
Alignment explanation
Indices: 475124--475196 Score: 63
Period size: 17 Copynumber: 4.4 Consensus size: 18
475114 ATAGATAACT
475124 TTAA-TTTTTAT-TGTAT-
1 TTAATTTTTTATAT-TATA
475140 TTAATTTTTTATATTATA
1 TTAATTTTTTATATTATA
*
475158 TT-ATATTTTAT-TT-TA
1 TTAATTTTTTATATTATA
475173 --AATTTTTTATATTATA
1 TTAATTTTTTATATTATA
475189 TTCAATTT
1 TT-AATTT
475197 AATATCTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
14 8 0.17
15 4 0.09
16 8 0.17
17 18 0.39
18 3 0.07
19 5 0.11
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
TTAATTTTTTATATTATA
Found at i:475330 original size:15 final size:16
Alignment explanation
Indices: 475312--475348 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
475302 AAGTTATAAA
475312 AATAATTTT-TATATT
1 AATAATTTTATATATT
*
475327 AAT-ATTTTATATTTT
1 AATAATTTTATATATT
475342 AATAATT
1 AATAATT
475349 AAATTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 11 0.58
16 3 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
AATAATTTTATATATT
Found at i:480782 original size:26 final size:27
Alignment explanation
Indices: 480746--480800 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
480736 CAGTGGCTTC
480746 TACTTGAATTGTCATC-AATAATAAAA
1 TACTTGAATTGTCATCTAATAATAAAA
480772 TACTTGAATTGTCATCTAATAATAAAA
1 TACTTGAATTGTCATCTAATAATAAAA
480799 TA
1 TA
480801 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (27 bp):
TACTTGAATTGTCATCTAATAATAAAA
Found at i:481057 original size:22 final size:21
Alignment explanation
Indices: 481021--481068 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 21
481011 TTATATTTTA
481021 TATATAATATCATTTAAATATATT
1 TATATAATA-CATTTAAA-AT-TT
481045 TATATAATA-ATTTAAAATTT
1 TATATAATACATTTAAAATTT
481065 TATA
1 TATA
481069 ATATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.25
21 2 0.08
22 7 0.29
24 9 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATAATACATTTAAAATTT
Found at i:481087 original size:19 final size:19
Alignment explanation
Indices: 481063--481101 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
481053 AATTTAAAAT
481063 TTTATAATATAATATATTA
1 TTTATAATATAATATATTA
* *
481082 TTTATATTATATTATATTA
1 TTTATAATATAATATATTA
481101 T
1 T
481102 ATTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTATAATATAATATATTA
Found at i:481098 original size:21 final size:21
Alignment explanation
Indices: 481039--481132 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
481029 ATCATTTAAA
481039 TATATTTATAT-A-ATAAT-T
1 TATATTTATATAATATAATAT
*
481057 TAAAATTT-TATAATATAATA-
1 T-ATATTTATATAATATAATAT
* *
481077 TATTATTTATATTATATTATAT
1 TA-TATTTATATAATATAATAT
* *
481099 TATATTTATGTAATACAATA-
1 TATATTTATATAATATAATAT
*
481119 TA-ATATATATAATA
1 TATATTTATATAATA
481133 AAAACATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
18 4 0.07
19 17 0.29
20 12 0.20
21 24 0.41
22 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTTATATAATATAATAT
Found at i:484832 original size:36 final size:36
Alignment explanation
Indices: 484783--484855 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
484773 AACCAATTGT
* *
484783 AGACAAAACTGTCTGCATGCTCCATTTAACTCTTGA
1 AGACAAAACTGTCTGCAGGCTCCACTTAACTCTTGA
* *
484819 AGACAAAATTGTCTGTAGGCTCCACTTAACTCTTGA
1 AGACAAAACTGTCTGCAGGCTCCACTTAACTCTTGA
484855 A
1 A
484856 AACACCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (36 bp):
AGACAAAACTGTCTGCAGGCTCCACTTAACTCTTGA
Found at i:485816 original size:2 final size:2
Alignment explanation
Indices: 485809--485857 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
485799 CAGCCAATAA
* *
485809 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT AA 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
485851 AT AT AT A
1 AT AT AT A
485858 GATGAACAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:488070 original size:14 final size:13
Alignment explanation
Indices: 488042--488069 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
488032 AAAAATTGTC
488042 AATTTATTTTTAA
1 AATTTATTTTTAA
488055 AATTTATTTTTAA
1 AATTTATTTTTAA
488068 AA
1 AA
488070 AAATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTTATTTTTAA
Done.