Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold101
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: 827217
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.34
Warning! 25308 characters in sequence are not A, C, G, or T
File 4 of 6
Found at i:424304 original size:6 final size:6
Alignment explanation
Indices: 424293--424350 Score: 57
Period size: 6 Copynumber: 9.3 Consensus size: 6
424283 ATATTAAAGG
*
424293 AAATAA AAATAA AAATAA AAA-AA AGAATAC AAATAAGA AAATAA AGAAT-A
1 AAATAA AAATAA AAATAA AAATAA A-AATAA AAAT-A-A AAATAA A-AATAA
424343 AAATAA AA
1 AAATAA AA
424351 TGGTTATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
5 6 0.14
6 27 0.61
7 7 0.16
8 4 0.09
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:424321 original size:18 final size:19
Alignment explanation
Indices: 424293--424350 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
424283 ATATTAAAGG
424293 AAATAAA-AATAAAAATAA
1 AAATAAAGAATAAAAATAA
*
424311 AAA-AAAGAATACAAATAAGA
1 AAATAAAGAATAAAAAT-A-A
424331 AAATAAAGAAT-AAAATAA
1 AAATAAAGAATAAAAATAA
424349 AA
1 AA
424351 TGGTTATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
17 3 0.09
18 14 0.41
19 2 0.06
20 8 0.24
21 7 0.21
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (19 bp):
AAATAAAGAATAAAAATAA
Found at i:426957 original size:16 final size:16
Alignment explanation
Indices: 426936--426986 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
426926 GAATTAAATT
*
426936 ATTTAATTATAAATAA
1 ATTTAAATATAAATAA
426952 ATTTAAATATTAAATAA
1 ATTTAAATA-TAAATAA
*
426969 GTATTAAATAT-AATAA
1 AT-TTAAATATAAATAA
426985 AT
1 AT
426987 ACTAAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 14 0.47
17 9 0.30
18 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTTAAATATAAATAA
Found at i:427794 original size:4 final size:4
Alignment explanation
Indices: 427785--427821 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
427775 ATAAGTATGC
427785 AATT AATT AATT AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT AATT AATT AATT A
427822 CAGAGATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
AATT
Found at i:429887 original size:20 final size:21
Alignment explanation
Indices: 429851--429889 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
429841 TCATTTTTAA
*
429851 TTAATTTTATTAATTATAATT
1 TTAATTTTATAAATTATAATT
429872 TTAATTTT-TAAATTATAA
1 TTAATTTTATAAATTATAA
429890 CGCTAGGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAATTTTATAAATTATAATT
Found at i:432098 original size:8 final size:7
Alignment explanation
Indices: 432079--432127 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
432069 TAAAGGAGAT
432079 AAAAATA
1 AAAAATA
*
432086 AAAATTA
1 AAAAATA
432093 AAAAATGAA
1 AAAAAT--A
432102 TAAAAATA
1 -AAAAATA
432110 AGAAAATA
1 A-AAAATA
432118 AAAAATA
1 AAAAATA
432125 AAA
1 AAA
432128 TAAAATGGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 21 0.58
8 8 0.22
9 1 0.03
10 6 0.17
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:432133 original size:25 final size:24
Alignment explanation
Indices: 432077--432132 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
432067 ATTAAAGGAG
* *
432077 ATAAAAATAAAAATTAAAAAATGA
1 ATAAAAATAAAAAATAAAAAATAA
432101 ATAAAAATAAGAAAATAAAAAATAAA
1 ATAAAAATAA-AAAATAAAAAAT-AA
432127 ATAAAA
1 ATAAAA
432133 TGGGTATGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 10 0.36
25 11 0.39
26 7 0.25
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.18
Consensus pattern (24 bp):
ATAAAAATAAAAAATAAAAAATAA
Found at i:432794 original size:4 final size:4
Alignment explanation
Indices: 432785--432826 Score: 66
Period size: 4 Copynumber: 10.2 Consensus size: 4
432775 ATCAGTATGC
*
432785 AATT AATT AATT AATT AATTT GATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AA-TT AATT AATT AATT AATT AATT A
432827 CAGAGATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 32 0.91
5 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (4 bp):
AATT
Found at i:432812 original size:21 final size:21
Alignment explanation
Indices: 432786--432825 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
432776 TCAGTATGCA
432786 ATTAATTAATTAATTAATTTG
1 ATTAATTAATTAATTAATTTG
432807 ATTAATTAATTAATTAATT
1 ATTAATTAATTAATTAATT
432826 ACAGAGATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATTAATTAATTAATTAATTTG
Found at i:433124 original size:20 final size:20
Alignment explanation
Indices: 433079--433117 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
433069 AAAAATTGAA
433079 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
433099 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
433118 GAAGGGAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:433262 original size:27 final size:27
Alignment explanation
Indices: 433201--433271 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
433191 AAACAAGCCT
* *
433201 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
433229 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
433256 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
433272 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:435193 original size:21 final size:22
Alignment explanation
Indices: 435155--435200 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
435145 ATCTGTTGAA
* **
435155 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
435176 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
435198 ACT
1 ACT
435201 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:437678 original size:20 final size:20
Alignment explanation
Indices: 437653--437698 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
437643 AAGAATTGAA
*
437653 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
437673 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
437693 GAGGGA
1 GAGGGA
437699 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:437849 original size:24 final size:27
Alignment explanation
Indices: 437775--437843 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
437765 AAACAAGTCT
* *
437775 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
437803 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
*
437830 CCATTTTTTACAAA
1 CCATTTTTGACAAA
437844 AAAATAGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 18 0.49
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:438437 original size:3 final size:3
Alignment explanation
Indices: 438429--438463 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
438419 GTATAAAAAC
438429 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
438464 GAATTGATGA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:438530 original size:17 final size:16
Alignment explanation
Indices: 438508--438548 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
438498 TTCTATATTA
438508 TTATTTTTTATTAATTT
1 TTATTTTTTA-TAATTT
*
438525 TTATTTATTATAATTT
1 TTATTTTTTATAATTT
*
438541 TAATTTTT
1 TTATTTTT
438549 AAATTATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTTTATAATTT
Found at i:438541 original size:25 final size:26
Alignment explanation
Indices: 438487--438542 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
438477 TAATATTCTT
*
438487 TTTTATTTAAATTCTATATTATTATT
1 TTTTATTTAAATTCTATATTATTATA
* *
438513 TTTTA-TTAATTTTTAT-TTATTATAA
1 TTTTATTTAAATTCTATATTATTAT-A
438538 TTTTA
1 TTTTA
438543 ATTTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 7 0.27
25 14 0.54
26 5 0.19
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATTTAAATTCTATATTATTATA
Found at i:441069 original size:18 final size:17
Alignment explanation
Indices: 441020--441086 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
441010 ATACATATTT
*
441020 TAAAATTAATAT-AATA
1 TAAAATTCATATAAATA
441036 T-AAATT-AT-TAATATA
1 TAAAATTCATATAA-ATA
441051 TAAAAATTCATATAAATA
1 T-AAAATTCATATAAATA
*
441069 TAAAATATCTTATAAATA
1 TAAAAT-TCATATAAATA
441087 AATATGACAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.02
14 3 0.07
15 9 0.21
16 1 0.02
17 10 0.23
18 16 0.37
19 3 0.07
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATTCATATAAATA
Found at i:442530 original size:2 final size:2
Alignment explanation
Indices: 442523--442547 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
442513 GCAAATATGC
442523 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 A
442548 ATTAAGGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:442952 original size:19 final size:21
Alignment explanation
Indices: 442928--442972 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
442918 ATTATTTAAA
442928 ATATTAAAAATT-TAT-TTTT
1 ATATTAAAAATTATATATTTT
* *
442947 ATATTAATATTTATATATTTT
1 ATATTAAAAATTATATATTTT
442968 ATATT
1 ATATT
442973 TTTATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 10 0.45
20 3 0.14
21 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTAAAAATTATATATTTT
Found at i:443261 original size:23 final size:23
Alignment explanation
Indices: 443230--443273 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
443220 ATTTTTTTAA
* *
443230 ATATTTATATTTAACATATATAT
1 ATATATATATTTAACACATATAT
443253 ATATATATATTTAACACATAT
1 ATATATATATTTAACACATAT
443274 TTTTTATGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATATATTTAACACATATAT
Found at i:444960 original size:4 final size:4
Alignment explanation
Indices: 444951--444984 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
444941 TATTTAACTA
444951 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT-T TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA
444985 CAAATATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:445259 original size:23 final size:23
Alignment explanation
Indices: 445233--445277 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
445223 CGACTATCTA
445233 TGATGATAATATATCCTATAAAT
1 TGATGATAATATATCCTATAAAT
* *
445256 TGATGATGATGTATCCTATAAA
1 TGATGATAATATATCCTATAAA
445278 AAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (23 bp):
TGATGATAATATATCCTATAAAT
Found at i:449407 original size:8 final size:8
Alignment explanation
Indices: 449396--449477 Score: 57
Period size: 7 Copynumber: 10.5 Consensus size: 8
449386 ATTAAAATAT
449396 TATATAAA
1 TATATAAA
*
449404 TATATGAA
1 TATATAAA
449412 TATATTAAA
1 TATA-TAAA
*
449421 -ATATATA
1 TATATAAA
*
449428 TCATATAAT
1 T-ATATAAA
*
449437 TAT-TAAT
1 TATATAAA
449444 TAT-TAAA
1 TATATAAA
449451 -ATATAAA
1 TATATAAA
*
449458 AATAT-AA
1 TATATAAA
449465 TATATTAAA
1 TATA-TAAA
449474 TATA
1 TATA
449478 ATTATAACAC
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
6 2 0.03
7 22 0.37
8 21 0.35
9 15 0.25
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:449525 original size:33 final size:34
Alignment explanation
Indices: 449378--449525 Score: 88
Period size: 38 Copynumber: 4.1 Consensus size: 34
449368 TAATATGATA
* * *
449378 TAAAAATAATTAAAATATTATATAAATATATGAATATAT
1 TAAAAAT-A-TAATATATAATATAAAT-TATTAA-AT-T
* *
449417 T-AAAATATATATCATATAATTATTAATTATTAAAATA
1 TAAAAATATA-AT-ATATAA-TATAAATTATT-AAATT
*
449454 TAAAAATATAATATATTAA-ATATAATTA-TAACACT
1 TAAAAATATAATATA-TAATATA-AATTATTAA-ATT
* *
449489 TAAAAATAT-GTGTATAATATAAATTATTAAATT
1 TAAAAATATAATATATAATATAAATTATTAAATT
449522 TAAA
1 TAAA
449526 TTTAATTAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
33 14 0.16
34 11 0.12
35 13 0.15
36 10 0.11
37 8 0.09
38 23 0.26
39 9 0.10
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (34 bp):
TAAAAATATAATATATAATATAAATTATTAAATT
Found at i:450399 original size:13 final size:12
Alignment explanation
Indices: 450381--450410 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
450371 TTTTAAAAAT
450381 ATTTATATTTAAA
1 ATTTATATTT-AA
450394 ATTTATATTTAA
1 ATTTATATTTAA
450406 ATTTA
1 ATTTA
450411 AATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTTATATTTAA
Found at i:450781 original size:22 final size:22
Alignment explanation
Indices: 450750--450794 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
450740 TTTTCTTTTT
450750 AAAATAAAAATA-TTTTTTTAA
1 AAAATAAAAATAGTTTTTTTAA
450771 AAAATATAAAATAGTTTTTTTAA
1 AAAATA-AAAATAGTTTTTTTAA
450794 A
1 A
450795 CCCTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATAAAAATAGTTTTTTTAA
Found at i:450904 original size:19 final size:18
Alignment explanation
Indices: 450873--450917 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
450863 AAACATCAAA
450873 ATATT-TTTTATTTTATT
1 ATATTATTTTATTTTATT
450890 ATATTATTTTCATTTTATT
1 ATATTATTTT-ATTTTATT
*
450909 TTATTATTT
1 ATATTATTT
450918 AATAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.20
18 4 0.16
19 16 0.64
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (18 bp):
ATATTATTTTATTTTATT
Found at i:455245 original size:17 final size:17
Alignment explanation
Indices: 455223--455255 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
455213 AAAAGAATTA
455223 AATTCAAACAAATATTG
1 AATTCAAACAAATATTG
*
455240 AATTCAAATAAATATT
1 AATTCAAACAAATATT
455256 TAAATCAGTT
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:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
AATTCAAACAAATATTG
Found at i:467635 original size:6 final size:6
Alignment explanation
Indices: 467624--467661 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
467614 ATTGCATGAG
* *
467624 ATCATT ATCATT ATCATT ATTATC ATCATT ATCATT AT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT AT
467662 TTAATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
ATCATT
Found at i:467647 original size:9 final size:9
Alignment explanation
Indices: 467633--467662 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
467623 GATCATTATC
467633 ATTATCATT
1 ATTATCATT
*
467642 ATTATCATC
1 ATTATCATT
467651 ATTATCATT
1 ATTATCATT
467660 ATT
1 ATT
467663 TAATAAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.53
Consensus pattern (9 bp):
ATTATCATT
Found at i:469978 original size:3 final size:3
Alignment explanation
Indices: 469970--470002 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
469960 GTAAGTGATT
469970 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
470003 AAGGATCAAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:473999 original size:2 final size:2
Alignment explanation
Indices: 473983--474019 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
473973 ACATGCTGGA
*
473983 AT AT AT A- AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
474020 TTCAGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:478229 original size:6 final size:6
Alignment explanation
Indices: 478218--478243 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
478208 TTAATTTAAA
478218 AATTAT AATTAT AATTAT AATTAT AA
1 AATTAT AATTAT AATTAT AATTAT AA
478244 AATAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AATTAT
Found at i:478385 original size:31 final size:31
Alignment explanation
Indices: 478347--478408 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
478337 AAATTTTAAC
* *
478347 TTATTTTTTAAATACAATTACTTTCTAATAA
1 TTATTTTTAAAACACAATTACTTTCTAATAA
* * *
478378 TTATTTTTAAAACACTATTATTTTTTAATAA
1 TTATTTTTAAAACACAATTACTTTCTAATAA
478409 GTTGGTAGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (31 bp):
TTATTTTTAAAACACAATTACTTTCTAATAA
Found at i:481188 original size:33 final size:34
Alignment explanation
Indices: 481124--481189 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
481114 AAGTTTGTTC
*
481124 TTTTGATGGATTATACTTCTTAAAAGATAAGAAG
1 TTTTGATGGACTATACTTCTTAAAAGATAAGAAG
481158 TTTTGATGGACTATACTTCTT-AAAGATAAGAA
1 TTTTGATGGACTATACTTCTTAAAAGATAAGAA
481190 AGATAAACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (34 bp):
TTTTGATGGACTATACTTCTTAAAAGATAAGAAG
Found at i:481481 original size:2 final size:2
Alignment explanation
Indices: 481474--481499 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
481464 GTACTACTGC
481474 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
481500 GTATTATTAA
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:482373 original size:25 final size:26
Alignment explanation
Indices: 482328--482380 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
482318 TGAAATAATT
*
482328 TAATTATTATTTATTTAATAAAA-AA
1 TAATTATTATTTAATTAATAAAATAA
*
482353 TAATTTTTATTTGAATT-ATAAAATAA
1 TAATTATTATTT-AATTAATAAAATAA
482379 TA
1 TA
482381 TTTAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TAATTATTATTTAATTAATAAAATAA
Found at i:482379 original size:23 final size:21
Alignment explanation
Indices: 482335--482384 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 21
482325 ATTTAATTAT
482335 TATTTATTTAATAAAAAATAA
1 TATTTATTTAATAAAAAATAA
* *
482356 TTTTTATTTGAATTATAAAATAA
1 TATTTATTT-AA-TAAAAAATAA
482379 TATTTA
1 TATTTA
482385 AATATATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 2 0.08
23 14 0.58
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TATTTATTTAATAAAAAATAA
Found at i:485978 original size:3 final size:3
Alignment explanation
Indices: 485970--485996 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
485960 ATTGATCACC
485970 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
485997 CATGACATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:489277 original size:19 final size:21
Alignment explanation
Indices: 489241--489288 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
489231 CCTTTTGAAA
*
489241 AAATA-AATTTTGTAATAT-T
1 AAATATAATTTTATAATATAT
489260 AAATATAATTTTAT-ATATAT
1 AAATATAATTTTATAATATAT
489280 AAA-ATAATT
1 AAATATAATT
489289 AAAATATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AAATATAATTTTATAATATAT
Found at i:489279 original size:21 final size:19
Alignment explanation
Indices: 489241--489288 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
489231 CCTTTTGAAA
*
489241 AAATA-AATTTTGTAATATT
1 AAATATAATTTTATAATA-T
489260 AAATATAATTTTATATATAT
1 AAATATAATTTTATA-ATAT
489280 AAA-ATAATT
1 AAATATAATT
489289 AAAATATATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 11 0.42
20 12 0.46
21 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AAATATAATTTTATAATAT
Found at i:489436 original size:21 final size:21
Alignment explanation
Indices: 489401--489444 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
489391 TTATAATAAA
489401 TAAAAAAATAGTT-AACAATAT
1 TAAAAAAATAGTTAAAC-ATAT
* *
489422 TAAAAAATTATTTAAACATAT
1 TAAAAAAATAGTTAAACATAT
489443 TA
1 TA
489445 TCATTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAAAATAGTTAAACATAT
Found at i:489525 original size:14 final size:14
Alignment explanation
Indices: 489508--489537 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
489498 TTAAAATTTA
489508 AAAATATAAAAATT
1 AAAATATAAAAATT
*
489522 AAAATATAAAATTT
1 AAAATATAAAAATT
489536 AA
1 AA
489538 TAGTATTGAT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:490462 original size:22 final size:22
Alignment explanation
Indices: 490422--490463 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
490412 AATGTTGATA
*
490422 AACAATTAAACATACATTAATT
1 AACAATTAAACAAACATTAATT
490444 AACAA-TAAACAAACAATTAA
1 AACAATTAAACAAAC-ATTAA
490464 GATTTAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (22 bp):
AACAATTAAACAAACATTAATT
Found at i:490539 original size:13 final size:13
Alignment explanation
Indices: 490518--490570 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
490508 TTTAATACTA
*
490518 AATATAAAATAAT
1 AATAAAAAATAAT
490531 AATAAAAAATATTAT
1 AATAAAAAATA--AT
*
490546 TATAAATAAATAA-
1 AATAAA-AAATAAT
490559 AATAAAAAATAA
1 AATAAAAAATAA
490571 AACATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 6 0.18
13 15 0.44
14 1 0.03
15 7 0.21
16 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AATAAAAAATAAT
Found at i:490643 original size:22 final size:23
Alignment explanation
Indices: 490598--490644 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
490588 TTATTATTAC
*
490598 TTTAAACAAATTAATATATAAAA
1 TTTAAACAAATTAATAAATAAAA
*
490621 TTTAAATAAATT-ATAAATAAAA
1 TTTAAACAAATTAATAAATAAAA
490643 TT
1 TT
490645 CACGAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TTTAAACAAATTAATAAATAAAA
Found at i:491965 original size:20 final size:22
Alignment explanation
Indices: 491926--491967 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
491916 AAATTATTTA
491926 TTTATGTTTATTAAATTTAAAAG
1 TTTATGTTTATT-AATTTAAAAG
491949 TTTAT-TTTATT-ATTTAAAA
1 TTTATGTTTATTAATTTAAAA
491968 TATATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
22 6 0.32
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTATGTTTATTAATTTAAAAG
Found at i:492513 original size:16 final size:15
Alignment explanation
Indices: 492491--492532 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
492481 AATATCTAAT
492491 AATTAATTTATTAAA
1 AATTAATTTATTAAA
492506 ATATTAATTATATTAAA
1 A-ATTAATT-TATTAAA
492523 AATTAATTTA
1 AATTAATTTA
492533 ATTTTACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.12
16 14 0.56
17 8 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATTTATTAAA
Found at i:493466 original size:24 final size:24
Alignment explanation
Indices: 493417--493466 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
493407 AAACTTATTT
**
493417 AAATTTATAAAAAAAATCTATCTA
1 AAATTTATAAAAAAAATAAATCTA
*
493441 AAATTTAATAAAAAAATTAAAT-TA
1 AAATTT-ATAAAAAAAATAAATCTA
493465 AA
1 AA
493467 TAAATAATTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATTTATAAAAAAAATAAATCTA
Found at i:493467 original size:23 final size:24
Alignment explanation
Indices: 493415--493467 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
493405 CGAAACTTAT
**
493415 TTAAATTTATAAAAAAAATCTATC
1 TTAAATTTATAAAAAAAATCTAAA
*
493439 TAAAATTTA-ATAAAAAAAT-TAAA
1 TTAAATTTATA-AAAAAAATCTAAA
493462 TTAAAT
1 TTAAAT
493468 AAATAATTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (24 bp):
TTAAATTTATAAAAAAAATCTAAA
Found at i:493906 original size:25 final size:25
Alignment explanation
Indices: 493878--493939 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 25
493868 TAATTATTGA
493878 TTAAATAATAAA-AAATT-TAATATTT
1 TTAAATAA-AAATAAATTCTAA-ATTT
493903 TTAAATAAAAATTAAATTCTAAATTT
1 TTAAATAAAAA-TAAATTCTAAATTT
493929 TATAAATAAAA
1 T-TAAATAAAA
493940 TATTAAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.09
25 8 0.24
26 10 0.30
27 12 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAATAAAAATAAATTCTAAATTT
Found at i:498033 original size:19 final size:19
Alignment explanation
Indices: 497999--498078 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 19
497989 TGCTTATTTA
**
497999 TTTATATATTCGTATTATT
1 TTTATATATTTTTATTATT
498018 TTTATATATTTTTATTTATT
1 TTTATATATTTTTA-TTATT
* * * *
498038 ATAAT-TATATTTA-AATT
1 TTTATATATTTTTATTATT
* **
498055 ATTATATATTTAAATTATT
1 TTTATATATTTTTATTATT
498074 TTTAT
1 TTTAT
498079 GTAATATTTA
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
17 7 0.15
18 5 0.11
19 26 0.57
20 8 0.17
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTATATATTTTTATTATT
Found at i:498064 original size:16 final size:16
Alignment explanation
Indices: 498043--498073 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
498033 TTATTATAAT
498043 TATATTTAAATTATTA
1 TATATTTAAATTATTA
498059 TATATTTAAATTATT
1 TATATTTAAATTATT
498074 TTTATGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTAAATTATTA
Found at i:498245 original size:7 final size:7
Alignment explanation
Indices: 498233--498262 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
498223 TATATTCATC
498233 TTTTTCT
1 TTTTTCT
498240 TTTTTCT
1 TTTTTCT
498247 TTTTT-T
1 TTTTTCT
498253 TTTTTCT
1 TTTTTCT
498260 TTT
1 TTT
498263 GTTCCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (7 bp):
TTTTTCT
Found at i:498249 original size:13 final size:13
Alignment explanation
Indices: 498231--498262 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
498221 CCTATATTCA
498231 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
*
498244 TCTTTTTTTTTTT
1 TCTTTTTCTTTTT
498257 TCTTTT
1 TCTTTT
498263 GTTCCTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TCTTTTTCTTTTT
Found at i:501206 original size:20 final size:20
Alignment explanation
Indices: 501174--501212 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
501164 ATTTTTATTT
501174 AAATTTAATTATAAAAATAA
1 AAATTTAATTATAAAAATAA
*
501194 AAATATTAA-TATAACAATA
1 AAAT-TTAATTATAAAAATA
501213 TTTTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAATTATAAAAATAA
Found at i:501230 original size:18 final size:19
Alignment explanation
Indices: 501209--501245 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
501199 TTAATATAAC
*
501209 AATATTTTTTAATA-TTTT
1 AATATTTTTAAATAGTTTT
501227 AATATTTTTAAATAGTTTT
1 AATATTTTTAAATAGTTTT
501246 TGCTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
AATATTTTTAAATAGTTTT
Found at i:501692 original size:22 final size:24
Alignment explanation
Indices: 501667--501712 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
501657 TTATTAATTC
* *
501667 ATTTTT-T-ATATTATATTTATAT
1 ATTTTTATCATATCATAATTATAT
501689 ATTTTTATCATATCATAATTATAT
1 ATTTTTATCATATCATAATTATAT
501713 TTAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (24 bp):
ATTTTTATCATATCATAATTATAT
Found at i:503056 original size:31 final size:31
Alignment explanation
Indices: 502999--503059 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
502989 ATTATTTATA
** *
502999 GGTCAAATTATTTGTTTGATCTAATAAATTC
1 GGTCAAATTATTTACTGGATCTAATAAATTC
503030 GGTCAAATTATTTACTGGAT-TCAATAAATT
1 GGTCAAATTATTTACTGGATCT-AATAAATT
503060 TAATCTGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (31 bp):
GGTCAAATTATTTACTGGATCTAATAAATTC
Found at i:506348 original size:2 final size:2
Alignment explanation
Indices: 506343--506368 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
506333 CTATATATAT
506343 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
506369 CAATACATTA
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):
AC
Found at i:507038 original size:19 final size:19
Alignment explanation
Indices: 507004--507040 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
506994 ATTAAATGAT
**
507004 AATATTTATATTATATTTA
1 AATATTTATAAAATATTTA
507023 AATATTTATAAAATATTT
1 AATATTTATAAAATATTT
507041 TTAAAAAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTTATAAAATATTTA
Found at i:507434 original size:28 final size:28
Alignment explanation
Indices: 507372--507434 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
507362 TTATAAAATT
**
507372 TTAATAATATTTATATATCAAATATAAA
1 TTAATAATATTTATATAAAAAATATAAA
507400 -TACATAATTATTTATATAAAAAAT-TAAA
1 TTA-ATAA-TATTTATATAAAAAATATAAA
507428 TTAATAA
1 TTAATAA
507435 AAATATTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 2 0.07
28 12 0.40
29 16 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (28 bp):
TTAATAATATTTATATAAAAAATATAAA
Found at i:508154 original size:13 final size:13
Alignment explanation
Indices: 508138--508178 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
508128 ATTATATCAT
*
508138 TAAATTTTTATTA
1 TAAACTTTTATTA
*
508151 TAAACCTTTATTA
1 TAAACTTTTATTA
508164 TTAAACTTTTATTA
1 -TAAACTTTTATTA
508178 T
1 T
508179 TAATAAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TAAACTTTTATTA
Found at i:508174 original size:14 final size:14
Alignment explanation
Indices: 508136--508181 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
508126 AAATTATATC
*
508136 ATTAAATTTTTATT
1 ATTAAACTTTTATT
*
508150 A-TAAACCTTTATT
1 ATTAAACTTTTATT
508163 ATTAAACTTTTATT
1 ATTAAACTTTTATT
508177 ATTAA
1 ATTAA
508182 TAAACTTAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTAAACTTTTATT
Found at i:511924 original size:3 final size:3
Alignment explanation
Indices: 511916--511963 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
511906 GTAGTGGAAT
511916 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
511964 ATTAGATTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:512175 original size:18 final size:20
Alignment explanation
Indices: 512148--512191 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
512138 TAATTAGGTT
512148 TAATAATTTTA-GATA-AAA
1 TAATAATTTTATGATATAAA
*
512166 TAATATTTTTATGATATAAA
1 TAATAATTTTATGATATAAA
512186 T-ATAAT
1 TAATAAT
512192 AAAAAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
19 8 0.36
20 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (20 bp):
TAATAATTTTATGATATAAA
Found at i:512492 original size:2 final size:2
Alignment explanation
Indices: 512485--512509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
512475 TATAGATTTT
512485 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
512510 CAAAACAAGG
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:512997 original size:21 final size:21
Alignment explanation
Indices: 512971--513016 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
512961 AATTTCATTA
512971 AAAAATATGAATTAAATTTTT
1 AAAAATATGAATTAAATTTTT
* * *
512992 AAAAATATTAGTTAATTTTTT
1 AAAAATATGAATTAAATTTTT
513013 AAAA
1 AAAA
513017 GAGATGAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
AAAAATATGAATTAAATTTTT
Found at i:513262 original size:2 final size:2
Alignment explanation
Indices: 513255--513288 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
513245 CTCTGTATCC
513255 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
513289 TTGAAATCAA
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):
CT
Found at i:513536 original size:16 final size:16
Alignment explanation
Indices: 513511--513545 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
513501 TCTCTACTAC
513511 ATATAAATATAGATAT
1 ATATAAATATAGATAT
*
513527 ATATAGATATAGATAT
1 ATATAAATATAGATAT
513543 ATA
1 ATA
513546 GATTCATTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
ATATAAATATAGATAT
Found at i:514560 original size:14 final size:14
Alignment explanation
Indices: 514543--514570 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
514533 ATTATACTTG
514543 TAATTTTATAATTT
1 TAATTTTATAATTT
514557 TAATTTTATAATTT
1 TAATTTTATAATTT
514571 ATTATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATTTTATAATTT
Found at i:514583 original size:13 final size:13
Alignment explanation
Indices: 514566--514601 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
514556 TTAATTTTAT
514566 AATTTATTATTAA
1 AATTTATTATTAA
* *
514579 TATTTATGATTAA
1 AATTTATTATTAA
514592 AATTTATTAT
1 AATTTATTAT
514602 AATTAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
AATTTATTATTAA
Found at i:514990 original size:13 final size:13
Alignment explanation
Indices: 514969--515002 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
514959 ATGTAACATC
*
514969 ATAATAAATATTA
1 ATAATAAATATCA
*
514982 ATTATAAATATCA
1 ATAATAAATATCA
514995 ATAATAAA
1 ATAATAAA
515003 AAAATCAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAATAAATATCA
Found at i:515643 original size:27 final size:27
Alignment explanation
Indices: 515587--515652 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
515577 AGCTTCCATA
*
515587 TTTGACAAATACAAAGGAAACCACTATT
1 TTTGACAAACACAAA-GAAACCACTATT
*
515615 TTTGACAAACACAAA-ATAACCATTATT
1 TTTGACAAACACAAAGA-AACCACTATT
515642 TTTGACAAACA
1 TTTGACAAACA
515653 AATGGGTGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.57
28 14 0.40
ACGTcount: A:0.47, C:0.18, G:0.08, T:0.27
Consensus pattern (27 bp):
TTTGACAAACACAAAGAAACCACTATT
Found at i:520222 original size:27 final size:28
Alignment explanation
Indices: 520162--520227 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 28
520152 AGCCTCTATA
* *
520162 TTTGACAAATACAAAGAAAACTACCATT
1 TTTGACAAACACAAAGAAAACCACCATT
*
520190 TTTGACAAACACAAA-ATAACCACCATT
1 TTTGACAAACACAAAGAAAACCACCATT
520217 TTTGACAAACA
1 TTTGACAAACA
520228 AATGGGTGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (28 bp):
TTTGACAAACACAAAGAAAACCACCATT
Found at i:524492 original size:22 final size:22
Alignment explanation
Indices: 524457--524542 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
524447 TTTTAGAAGC
* *
524457 TAATTTATTCAAAAATCAAATT
1 TAATTTTTTCAAAAATAAAATT
*
524479 TAATTTTTTGAAAAATAAAATT
1 TAATTTTTTCAAAAATAAAATT
* * **
524501 GAACTTTTTCAAAAATTTAATT
1 TAATTTTTTCAAAAATAAAATT
524523 TAATTTTTGT--AAAATAAAAT
1 TAATTTTT-TCAAAAATAAAAT
524543 GATTTTAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 8 0.16
22 42 0.82
23 1 0.02
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (22 bp):
TAATTTTTTCAAAAATAAAATT
Found at i:526001 original size:16 final size:17
Alignment explanation
Indices: 525972--526007 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
525962 AAGAGAACGC
*
525972 AAAAGTGATTTAAATTT
1 AAAAGTGATATAAATTT
525989 AAAA-TGATATAAATTT
1 AAAAGTGATATAAATTT
526005 AAA
1 AAA
526008 TAAAGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
AAAAGTGATATAAATTT
Found at i:526027 original size:21 final size:20
Alignment explanation
Indices: 526001--526052 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 20
525991 AATGATATAA
526001 ATTTAAATAAAGTAT-AATTTT
1 ATTTAAA-AAA-TATCAATTTT
526022 ATTTAAAAAATATCAA-TTT
1 ATTTAAAAAATATCAATTTT
*
526041 A-ATAAAAAATAT
1 ATTTAAAAAATAT
526053 AACTATAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.34
19 7 0.24
20 5 0.17
21 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAAAAATATCAATTTT
Found at i:531118 original size:2 final size:2
Alignment explanation
Indices: 531113--531138 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
531103 ATACAAACAA
531113 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
531139 GCAAATCATT
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:531323 original size:28 final size:28
Alignment explanation
Indices: 531292--531355 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 28
531282 ATAGGGCTTG
*
531292 TAATATAAAAAATAATATAATATAA-ATA
1 TAATATAAAAAATAATA-AAAATAATATA
531320 TAATATAAAAAATAATAAAAATAATATA
1 TAATATAAAAAATAATAAAAATAATATA
531348 TATATATA
1 TA-ATATA
531356 TATAAATATC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 6 0.18
28 22 0.67
29 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (28 bp):
TAATATAAAAAATAATAAAAATAATATA
Found at i:531334 original size:23 final size:22
Alignment explanation
Indices: 531308--531364 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
531298 AAAAAATAAT
531308 ATAATATAAATATAATATAAAAA
1 ATAATATAAATATAATAT-AAAA
* *
531331 ATAATA-AAA-ATAATATATAT
1 ATAATATAAATATAATATAAAA
531351 ATATATATAAATAT
1 ATA-ATATAAATAT
531365 CATGAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 5 0.17
21 10 0.34
22 6 0.21
23 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATATAAATATAATATAAAA
Found at i:531362 original size:21 final size:20
Alignment explanation
Indices: 531294--531363 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
531284 AGGGCTTGTA
*
531294 ATATAAAAAATA-ATATAAT
1 ATATAAATAATATATATAAT
* *
531313 ATA-AATATAATATAAAAAAT
1 ATATAA-ATAATATATATAAT
*
531333 AATAAAAATAATATATATATAT
1 -ATATAAATAATATATATA-AT
531355 ATATAAATA
1 ATATAAATA
531364 TCATGAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.05
19 8 0.20
20 5 0.12
21 21 0.52
22 4 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATATAAATAATATATATAAT
Found at i:531376 original size:32 final size:33
Alignment explanation
Indices: 531298--531386 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 33
531288 CTTGTAATAT
531298 AAAA-AAT-AATATAATATAAATATA-ATATAA
1 AAAATAATAAATATAATATAAATATATATATAA
* *
531328 AAAATAATAAAAATAATATATATATATATAT-A
1 AAAATAATAAATATAATATAAATATATATATAA
* * * *
531360 AATATCATGAATATAATGTAAATATAT
1 AAAATAATAAATATAATATAAATATAT
531387 GAAAATCTTA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 4 0.08
31 3 0.06
32 37 0.77
33 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (33 bp):
AAAATAATAAATATAATATAAATATATATATAA
Found at i:532302 original size:54 final size:55
Alignment explanation
Indices: 532210--532325 Score: 180
Period size: 54 Copynumber: 2.1 Consensus size: 55
532200 TTAAATAGTA
**
532210 AAAAAAATATTTATTCAAAAATATGTTCAAATGAGTTGAAAAATCTATTTTATTT
1 AAAAAAATATTTATTCAAAAATATGTTCAAAAAAGTTGAAAAATCTATTTTATTT
* * *
532265 AAAAAGATATTTATTCAAAATTATGTT-AAAAAAGTTGAAAAGTCTATTTTATTT
1 AAAAAAATATTTATTCAAAAATATGTTCAAAAAAGTTGAAAAATCTATTTTATTT
532319 AAAAAAA
1 AAAAAAA
532326 AGTTGAAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
54 30 0.55
55 25 0.45
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (55 bp):
AAAAAAATATTTATTCAAAAATATGTTCAAAAAAGTTGAAAAATCTATTTTATTT
Found at i:533223 original size:15 final size:17
Alignment explanation
Indices: 533192--533225 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
533182 AAATTCTCAT
533192 TATTTTATAATTAAAAA
1 TATTTTATAATTAAAAA
533209 TATTTTA-AA-TAAAAA
1 TATTTTATAATTAAAAA
533224 TA
1 TA
533226 ATAAAAAATT
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATTTTATAATTAAAAA
Found at i:533438 original size:20 final size:19
Alignment explanation
Indices: 533399--533443 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
533389 GATAAATATC
*
533399 ATAAA-AATAATTTTATAA
1 ATAAATAATAATTTAATAA
533417 ATAAATAATAATTTGAATAA
1 ATAAATAATAATTT-AATAA
533437 ATAAATA
1 ATAAATA
533444 TCCTTAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
ATAAATAATAATTTAATAA
Found at i:534368 original size:20 final size:20
Alignment explanation
Indices: 534343--534384 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
534333 AAGAAGGTAG
*
534343 TTGTTTTTTATG-AATATGTT
1 TTGTTTTTAATGCAA-ATGTT
534363 TTGTTTTTAATGCAAATGTT
1 TTGTTTTTAATGCAAATGTT
534383 TT
1 TT
534385 TATCTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 18 0.90
21 2 0.10
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.62
Consensus pattern (20 bp):
TTGTTTTTAATGCAAATGTT
Found at i:539491 original size:81 final size:81
Alignment explanation
Indices: 539351--539504 Score: 254
Period size: 81 Copynumber: 1.9 Consensus size: 81
539341 GCCAGAAACT
* **
539351 GGGTAACATAGCTGCACCTGATAGGTTGTTGTCTGATATATTAGCAAATTTGTCACATCAGCTTA
1 GGGTAACATAGCTACACCTGATAGGTCATTGTCTGATATATTAGCAAATTTGTCACATCAGCTTA
539416 ACTGAGCCAGCAGGCC
66 ACTGAGCCAGCAGGCC
* * *
539432 GGGTAACATAGGTACACCTGATAGGTCATTGTCTGATATATTGGCAAATTTGTCTCATCAGCTTA
1 GGGTAACATAGCTACACCTGATAGGTCATTGTCTGATATATTAGCAAATTTGTCACATCAGCTTA
539497 ACTGAGCC
66 ACTGAGCC
539505 TGGCCATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (81 bp):
GGGTAACATAGCTACACCTGATAGGTCATTGTCTGATATATTAGCAAATTTGTCACATCAGCTTA
ACTGAGCCAGCAGGCC
Found at i:546118 original size:12 final size:12
Alignment explanation
Indices: 546103--546128 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
546093 TCCTAGCTGC
546103 AGTGTTCTTTTA
1 AGTGTTCTTTTA
546115 AGTGTTCTTTTA
1 AGTGTTCTTTTA
546127 AG
1 AG
546129 GAGGCTCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (12 bp):
AGTGTTCTTTTA
Found at i:549837 original size:21 final size:21
Alignment explanation
Indices: 549791--549875 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 21
549781 TATTATATAT
* * *
549791 TTAT-TTTTATATGATATATA
1 TTATATTTTATATAATAAAAA
549811 TT-TATTTTATATAATAAAAA
1 TTATATTTTATATAATAAAAA
*
549831 TTATATTATATA-AATATAAAA
1 TTATATTTTATATAATA-AAAA
*
549852 TTAATATATTATATAATTAAAAA
1 TT-ATATTTTATATAA-TAAAAA
549875 T
1 T
549876 AAGTAGAGTT
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
19 1 0.02
20 21 0.40
21 14 0.26
22 8 0.15
23 7 0.13
24 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TTATATTTTATATAATAAAAA
Found at i:550456 original size:2 final size:2
Alignment explanation
Indices: 550451--550482 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
550441 ATATATATAT
550451 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
550483 GGAGGTTGCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:551227 original size:18 final size:17
Alignment explanation
Indices: 551192--551232 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
551182 ATTATGTTGA
*
551192 TATTTTTAAAATTTTAT
1 TATTTTTAAAATTATAT
*
551209 TATTTTTTAAA-TATA-
1 TATTTTTAAAATTATAT
551224 TATTTTTAA
1 TATTTTTAA
551233 TATTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
15 8 0.38
16 3 0.14
17 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAATTATAT
Found at i:551463 original size:20 final size:21
Alignment explanation
Indices: 551430--551474 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
551420 ATATAATTTG
*
551430 ATTTGATTCTATTTTTATT-A
1 ATTTGATTCTATTTTAATTCA
551450 ATTTGATT-TGATTTTAATTCA
1 ATTTGATTCT-ATTTTAATTCA
551471 ATTT
1 ATTT
551475 TTGTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (21 bp):
ATTTGATTCTATTTTAATTCA
Found at i:560239 original size:13 final size:13
Alignment explanation
Indices: 560221--560245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560211 TTGATATTTA
560221 AAAAGATTTAAGT
1 AAAAGATTTAAGT
560234 AAAAGATTTAAG
1 AAAAGATTTAAG
560246 CTTAAAAAAT
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:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (13 bp):
AAAAGATTTAAGT
Found at i:562764 original size:2 final size:2
Alignment explanation
Indices: 562757--562785 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
562747 AAACATTATT
562757 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 T
562786 CAGCAAGCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:564901 original size:25 final size:26
Alignment explanation
Indices: 564873--564926 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
564863 AAAAAATAAG
* *
564873 TTTAATTA-TTATGATCGATTTTAAA
1 TTTAATTATTTATGATCAAATTTAAA
564898 TTTAATTATTTATGATCAAATTTAAA
1 TTTAATTATTTATGATCAAATTTAAA
564924 TTT
1 TTT
564927 GAGTTTACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTAATTATTTATGATCAAATTTAAA
Found at i:568838 original size:17 final size:18
Alignment explanation
Indices: 568816--568873 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
568806 CTTTTAAATT
568816 AAATTTATATTA-ATTTA
1 AAATTTATATTATATTTA
*
568833 AAATTTATGTTATTATTTAA
1 AAATTTATATTA-TATTT-A
* *
568853 AAAATTATAATTATAATTA
1 AAATTTAT-ATTATATTTA
568872 AA
1 AA
568874 TTAATTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 11 0.33
19 7 0.21
20 12 0.36
21 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTTATATTATATTTA
Found at i:570840 original size:11 final size:11
Alignment explanation
Indices: 570824--570885 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 11
570814 TGATTTTTTT
570824 TATTTTAAATA
1 TATTTTAAATA
570835 TATTTTATTAAATA
1 TA--TT-TTAAATA
570849 TATTTTAAATA
1 TATTTTAAATA
570860 TATTTTATTAAATA
1 TA--TT-TTAAATA
*
570874 TATTTTAGATA
1 TATTTTAAATA
570885 T
1 T
570886 TAATTTAGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
11 18 0.41
12 4 0.09
13 4 0.09
14 18 0.41
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTTTAAATA
Found at i:570847 original size:14 final size:14
Alignment explanation
Indices: 570828--570880 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
570818 TTTTTTTATT
570828 TTAAATATATTTTA
1 TTAAATATATTTTA
570842 TTAAATATA--TT-
1 TTAAATATATTTTA
570853 TTAAATATATTTTA
1 TTAAATATATTTTA
570867 TTAAATATATTTTA
1 TTAAATATATTTTA
570881 GATATTAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.25
12 2 0.06
13 2 0.06
14 23 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:570858 original size:25 final size:25
Alignment explanation
Indices: 570824--570885 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
570814 TGATTTTTTT
570824 TATTTTAAATATATTTTATTAAATA
1 TATTTTAAATATATTTTATTAAATA
570849 TATTTTAAATATATTTTATTAAATA
1 TATTTTAAATATATTTTATTAAATA
*
570874 TATTTTAGATAT
1 TATTTTAAATAT
570886 TAATTTAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (25 bp):
TATTTTAAATATATTTTATTAAATA
Found at i:570986 original size:29 final size:29
Alignment explanation
Indices: 570952--571008 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
570942 AATTAATTAA
*
570952 TTAAATCGATATT-TTAAACCGATTAAAAT
1 TTAAATCGA-ATTACTAAACCGATTAAAAT
570981 TTAAATCGAATTAACTAAACCGATTAAA
1 TTAAATCGAATT-ACTAAACCGATTAAA
571009 TCAAATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 9 0.36
30 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.33
Consensus pattern (29 bp):
TTAAATCGAATTACTAAACCGATTAAAAT
Found at i:571044 original size:27 final size:27
Alignment explanation
Indices: 571003--571054 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
570993 AACTAAACCG
*
571003 ATTAAATCAAATTTAATTAATTTTTTA
1 ATTAAATCAAATTTAATCAATTTTTTA
* *
571030 ATTAAATTAATTTTAATCAATTTTT
1 ATTAAATCAAATTTAATCAATTTTT
571055 GCTCGCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTAAATCAAATTTAATCAATTTTTTA
Found at i:572333 original size:12 final size:12
Alignment explanation
Indices: 572316--572341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
572306 AGCACTAAGG
572316 TAAACATATATA
1 TAAACATATATA
572328 TAAACATATATA
1 TAAACATATATA
572340 TA
1 TA
572342 TTTCAATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAACATATATA
Found at i:575206 original size:11 final size:11
Alignment explanation
Indices: 575192--575225 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
575182 AAATACAATT
575192 ATAATATAAAA
1 ATAATATAAAA
*
575203 ATAATATAAAT
1 ATAATATAAAA
*
575214 ATAAAATAAAA
1 ATAATATAAAA
575225 A
1 A
575226 CATAATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:575208 original size:22 final size:22
Alignment explanation
Indices: 575183--575225 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
575173 TATTATTTTA
* *
575183 AATACAATTATAATATAAAAAT
1 AATACAAATATAAAATAAAAAT
*
575205 AATATAAATATAAAATAAAAA
1 AATACAAATATAAAATAAAAA
575226 CATAATTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATACAAATATAAAATAAAAAT
Found at i:575420 original size:24 final size:24
Alignment explanation
Indices: 575393--575441 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
575383 AATATTAGAT
575393 AGCCTAATTCAATGAATCTATTTA
1 AGCCTAATTCAATGAATCTATTTA
575417 AGCCTAATTCAATGAATCTATTTA
1 AGCCTAATTCAATGAATCTATTTA
575441 A
1 A
575442 TTATTAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (24 bp):
AGCCTAATTCAATGAATCTATTTA
Found at i:575870 original size:19 final size:18
Alignment explanation
Indices: 575846--575922 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 18
575836 ATATATTAAA
* *
575846 AATAAATATTATTTAAATT
1 AATAAAAATTAATT-AATT
575865 AATAAAAATTAATTAATT
1 AATAAAAATTAATTAATT
575883 AATAATAAATAAATAAATTAAATT
1 AATAA-AAAT---T-AATT-AATT
575907 AATAAAAAATTAATTA
1 AAT-AAAAATTAATTA
575923 CATGTATATT
Statistics
Matches: 49, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 9 0.18
19 17 0.35
20 4 0.08
21 1 0.02
22 1 0.02
23 4 0.08
24 11 0.22
25 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AATAAAAATTAATTAATT
Found at i:575911 original size:24 final size:23
Alignment explanation
Indices: 575870--575916 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
575860 AAATTAATAA
* *
575870 AAATTAATTAATTAATAATAAAT
1 AAATAAATTAATTAATAAAAAAT
575893 AAATAAATTAAATTAATAAAAAAT
1 AAATAAATT-AATTAATAAAAAAT
575917 TAATTACATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATAAATTAATTAATAAAAAAT
Found at i:576066 original size:19 final size:18
Alignment explanation
Indices: 576040--576082 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
576030 TATATTTAAT
576040 ATTTATTTAATATTAAAA
1 ATTTATTTAATATTAAAA
576058 ATATTATTTAA-ATATAAAA
1 AT-TTATTTAATAT-TAAAA
576077 ATTTAT
1 ATTTAT
576083 CGAATCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTATTTAATATTAAAA
Found at i:576527 original size:2 final size:2
Alignment explanation
Indices: 576520--576545 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
576510 AAGTACTAAG
576520 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
576546 TTCAATACTA
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:576648 original size:16 final size:18
Alignment explanation
Indices: 576627--576662 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
576617 ATATTAAAAT
576627 TTTATA-TATTTTTT-TG
1 TTTATATTATTTTTTGTG
576643 TTTATATTATTTTTTGTG
1 TTTATATTATTTTTTGTG
576661 TT
1 TT
576663 ATAATAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 8 0.44
18 4 0.22
ACGTcount: A:0.17, C:0.00, G:0.08, T:0.75
Consensus pattern (18 bp):
TTTATATTATTTTTTGTG
Found at i:576778 original size:16 final size:16
Alignment explanation
Indices: 576752--576810 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
576742 TATATATTCG
*
576752 TATTATTTTATTTATAT
1 TATT-TTTTATTTATGT
576769 TATTTTTTATTTATGT
1 TATTTTTTATTTATGT
576785 TATTTTTT-TATTATGT
1 TATTTTTTAT-TTATGT
*
576801 TATATTTTAT
1 TATTTTTTAT
576811 ATTACGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
15 1 0.03
16 32 0.84
17 5 0.13
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TATTTTTTATTTATGT
Found at i:581862 original size:19 final size:18
Alignment explanation
Indices: 581838--581888 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
581828 TAAAAATTTT
581838 AATTTTCATTTTAACACAA
1 AATTTT-ATTTTAACACAA
* * *
581857 AATTTTTATATAAACACAT
1 AA-TTTTATTTTAACACAA
581876 AATTTTATTTTAA
1 AATTTTATTTTAA
581889 AATTTTGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 9 0.35
19 13 0.50
20 4 0.15
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTTATTTTAACACAA
Found at i:581988 original size:2 final size:2
Alignment explanation
Indices: 581981--582015 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
581971 AATGAAAAGA
581981 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
582016 ATCTTTCGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:582307 original size:16 final size:17
Alignment explanation
Indices: 582281--582316 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
582271 TAATGAATAT
*
582281 ATTTAATATTTTAAAAA
1 ATTTAATATTTAAAAAA
582298 ATTT-ATATTTAAAAAA
1 ATTTAATATTTAAAAAA
582314 ATT
1 ATT
582317 AATTTGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTAATATTTAAAAAA
Found at i:582380 original size:15 final size:15
Alignment explanation
Indices: 582351--582401 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
582341 ATATAAATAT
582351 TTTAAAAAATAATAAA
1 TTTAAAAAA-AATAAA
* *
582367 TTTAAATAACATAAA
1 TTTAAAAAAAATAAA
*
582382 TCTAAAAAAAATCAAA
1 TTTAAAAAAAAT-AAA
582398 TTTA
1 TTTA
582402 TTTTAAGAGG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TTTAAAAAAAATAAA
Found at i:584100 original size:2 final size:2
Alignment explanation
Indices: 584093--584136 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
584083 AAAATTCATT
584093 TA TA TA 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 TA TA TA
584135 TA
1 TA
584137 ACGAGGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:584267 original size:19 final size:18
Alignment explanation
Indices: 584229--584268 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
584219 TTTGTATGTC
*
584229 AAATTTTAAATAAATTAA
1 AAATATTAAATAAATTAA
* *
584247 AAATATTAAATTAATTTA
1 AAATATTAAATAAATTAA
584265 AAAT
1 AAAT
584269 TTTACGTACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATATTAAATAAATTAA
Found at i:584319 original size:2 final size:2
Alignment explanation
Indices: 584312--584336 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
584302 ACAATTTTTC
584312 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
584337 GCACGTGCTT
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
Done.