Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 32
Found at i:1438283 original size:32 final size:32
Alignment explanation
Indices: 1438235--1438297 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1438225 ATTATATTTA
* *
1438235 AATATTTTATATTTATATTAATTTTAATAAATT
1 AATAATTTATATTTATATAAATTTTAA-AAATT
1438268 AATAATTTATA-TTATATAAATTTTAAAAAT
1 AATAATTTATATTTATATAAATTTTAAAAAT
1438298 ATTTTATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 14 0.50
33 10 0.36
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATAATTTATATTTATATAAATTTTAAAAATT
Found at i:1438320 original size:27 final size:27
Alignment explanation
Indices: 1438213--1438320 Score: 85
Period size: 27 Copynumber: 3.8 Consensus size: 27
1438203 TTATTTATTT
* *
1438213 TTTTATATTATAATTATATT-TAAATA
1 TTTTATATTATAATTTTATTAAAAATA
*
1438239 TTTTATATTTATATTAATTTTAATAAATTAATA
1 TTTTATA--T-TA-TAATTTTATTAAA--AATA
* **
1438272 ATTTATATTATATAAATT-TTAAAAATA
1 TTTTATATTATA-ATTTTATTAAAAATA
1438299 TTTTATATTATAATTTTATTAA
1 TTTTATATTATAATTTTATTAA
1438321 TTTATATAAA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
26 10 0.16
27 19 0.30
28 1 0.02
29 8 0.13
30 13 0.21
31 2 0.03
33 10 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
TTTTATATTATAATTTTATTAAAAATA
Found at i:1438340 original size:15 final size:14
Alignment explanation
Indices: 1438316--1438353 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1438306 TTATAATTTT
1438316 ATTA-ATTTATATAA
1 ATTATATTTATAT-A
1438330 ATTATATTTATATA
1 ATTATATTTATATA
*
1438344 ATCATATTTA
1 ATTATATTTA
1438354 ATATTATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTATATTTATATA
Found at i:1438345 original size:33 final size:30
Alignment explanation
Indices: 1438236--1438343 Score: 90
Period size: 33 Copynumber: 3.3 Consensus size: 30
1438226 TTATATTTAA
1438236 ATATTTTATATTTATATTAATTTTAATAAATT
1 ATATTTTATATTT-TATTAATTTT-ATAAATT
* * * *
1438268 AATAATTTATATTATATAAATTTTAAAAATATT
1 -ATATTTTATATTTTATTAATTTT-ATAA-ATT
* *
1438301 TTATATTATAATTTTATTAATTTATATAAATT
1 ATATTTTAT-ATTTTATTAATTT-TATAAATT
1438333 ATATTTATATA
1 ATATTT-TATA
1438344 ATCATATTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
32 27 0.46
33 31 0.53
34 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATTTTATATTTTATTAATTTTATAAATT
Found at i:1438357 original size:15 final size:15
Alignment explanation
Indices: 1438320--1438353 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1438310 AATTTTATTA
*
1438320 ATTTATATAAATTAT
1 ATTTATATAAATCAT
1438335 ATTTATAT-AATCAT
1 ATTTATATAAATCAT
1438349 ATTTA
1 ATTTA
1438354 ATATTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTTATATAAATCAT
Found at i:1439023 original size:5 final size:5
Alignment explanation
Indices: 1438965--1439069 Score: 51
Period size: 5 Copynumber: 21.4 Consensus size: 5
1438955 AATTTATTTT
* * * * * **
1438965 TTATA TTATG TTATG TTATA -TATT TTATT TTA-A TTTTA AAATA -TATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
1439012 TTTATA TTATA TTATA TTTTAA TTAT- TTTTA TATATA TTATA TT-TA
1 -TTATA TTATA TTATA TTAT-A TTATA TTATA T-TATA TTATA TTATA
1439058 -TATA CTTATA TT
1 TTATA -TTATA TT
1439070 TAAAATAACC
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
3 1 0.01
4 15 0.19
5 45 0.58
6 16 0.21
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1439024 original size:11 final size:11
Alignment explanation
Indices: 1439008--1439060 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
1438998 TTTTAAAATA
1439008 TATATTTATAT
1 TATATTTATAT
1439019 TATA-TTATAT
1 TATATTTATAT
* *
1439029 TTTAATTAT-T
1 TATATTTATAT
* *
1439039 TTTATATATAT
1 TATATTTATAT
1439050 TATATTTATAT
1 TATATTTATAT
1439061 ACTTATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1439049 original size:31 final size:30
Alignment explanation
Indices: 1438980--1439060 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
1438970 TTATGTTATG
* *
1438980 TTATATATTTTATTTTA-ATTTTAAAATAT
1 TTATATATATTATATTATATTTTAAAATAT
* * * *
1439009 ATATTTATATTATATTATATTTTAATTATTT
1 TTATATATATTATATTATATTTTAA-AATAT
1439040 TTATATATATTATATTTATAT
1 TTATATATATTATA-TTATAT
1439061 ACTTATATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
29 13 0.32
30 7 0.17
31 15 0.37
32 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
TTATATATATTATATTATATTTTAAAATAT
Found at i:1439053 original size:36 final size:37
Alignment explanation
Indices: 1438983--1439060 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 37
1438973 TGTTATGTTA
*
1438983 TATATTTTATTTTAATTTTAAAATATATATTTATA-T
1 TATATTATATTTTAATTTTAAAATATATATTTATATT
***
1439019 TATATTATATTTTAATTATTTTTATATATA-TTATATT
1 TATATTATATTTTAATT-TTAAAATATATATTTATATT
1439056 TATAT
1 TATAT
1439061 ACTTATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 21 0.58
37 15 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (37 bp):
TATATTATATTTTAATTTTAAAATATATATTTATATT
Found at i:1439070 original size:31 final size:28
Alignment explanation
Indices: 1439004--1439056 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1438994 TTAATTTTAA
*
1439004 AATATATATTTATATTATATTATATTTT
1 AATATATTTTTATATTATATTATATTTT
1439032 AAT-TATTTTTATA-TATATTATATTT
1 AATATATTTTTATATTATATTATATTT
1439057 ATATACTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 9 0.38
28 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
AATATATTTTTATATTATATTATATTTT
Found at i:1439465 original size:31 final size:30
Alignment explanation
Indices: 1439424--1439495 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1439414 ATTTATTATA
* *
1439424 ATTTTGATTTAAATAAATTTAAT-ATTTTAAT
1 ATTTTAATTTAAATAAA--TAATAAATTTAAT
*
1439455 ATTTTAATTTAAATAGATAATAAATTTAAT
1 ATTTTAATTTAAATAAATAATAAATTTAAT
*
1439485 ATTTAAATTTA
1 ATTTTAATTTA
1439496 TTATTTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 4 0.11
30 17 0.47
31 15 0.42
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTTTAATTTAAATAAATAATAAATTTAAT
Found at i:1439491 original size:13 final size:13
Alignment explanation
Indices: 1439437--1439502 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
1439427 TTGATTTAAA
1439437 TAAATTTAATATTT
1 TAAATTTAATA-TT
*
1439451 TAATATTTTA-ATT
1 TAA-ATTTAATATT
*
1439464 TAAA--TAGATA-A
1 TAAATTTA-ATATT
1439475 TAAATTTAATATT
1 TAAATTTAATATT
*
1439488 TAAATTTATTATT
1 TAAATTTAATATT
1439501 TA
1 TA
1439503 TTAATTATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
10 1 0.02
11 5 0.12
12 5 0.12
13 21 0.51
14 4 0.10
15 5 0.12
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (13 bp):
TAAATTTAATATT
Found at i:1439784 original size:26 final size:26
Alignment explanation
Indices: 1439732--1439785 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
1439722 ATAAAAATAA
* *
1439732 TAAATGAATTTTAATATTATATAAAT
1 TAAATGAATTTGAATATTATAGAAAT
* * *
1439758 TAAATTAATTTGAATATTTTAGGAAT
1 TAAATGAATTTGAATATTATAGAAAT
1439784 TA
1 TA
1439786 TAAATATACG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (26 bp):
TAAATGAATTTGAATATTATAGAAAT
Found at i:1444503 original size:21 final size:20
Alignment explanation
Indices: 1444453--1444503 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1444443 TATATATTTT
* * *
1444453 TTAAAATTTTTTTAAATATA
1 TTAAAATATTTTAAAAAATA
1444473 TTAAAA-ATTTTAAAAAATA
1 TTAAAATATTTTAAAAAATA
1444492 TTAAATATATTT
1 TTAAA-ATATTT
1444504 ATATTCACGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 15 0.58
20 7 0.27
21 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAAATATTTTAAAAAATA
Found at i:1452440 original size:3 final size:3
Alignment explanation
Indices: 1452432--1452464 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1452422 TAATTAGGAC
1452432 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1452465 GTTGCTGTTG
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1453380 original size:2 final size:2
Alignment explanation
Indices: 1453373--1453412 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1453363 ATTGATTCTT
1453373 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
1453413 AATTAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1453617 original size:47 final size:44
Alignment explanation
Indices: 1453563--1453673 Score: 107
Period size: 47 Copynumber: 2.4 Consensus size: 44
1453553 GATAATTTTA
1453563 ATATTTATATTATTTTTTATATTATAATAATAATTATAATATCA-TAT
1 ATATTTATATTATTTTTTATATTAT-AT-A-AATTATAATAT-ATTAT
* ** * *
1453610 ATTTTTATAAAATTTAATATATATTATATAAATTTTAATATATTTAT
1 ATATTTATATTATTT--TTTATATTATATAAATTATAATATA-TTAT
1453657 ATATTTATATTATTTTT
1 ATATTTATATTATTTTT
1453674 ATTTATTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
45 2 0.04
46 10 0.20
47 28 0.55
48 2 0.04
49 9 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (44 bp):
ATATTTATATTATTTTTTATATTATATAAATTATAATATATTAT
Found at i:1453619 original size:27 final size:24
Alignment explanation
Indices: 1453580--1453652 Score: 71
Period size: 27 Copynumber: 3.0 Consensus size: 24
1453570 TATTATTTTT
1453580 TATATTATAATAATAATTATAATATCA
1 TATATTATAATAA-AATT-TAATAT-A
* *
1453607 TATATTTTTATAAAATTT-A-ATA
1 TATATTATAATAAAATTTAATATA
*
1453629 TATATTAT-ATAAATTTTAATATA
1 TATATTATAATAAAATTTAATATA
1453652 T
1 T
1453653 TTATATATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 8 0.20
22 9 0.22
23 6 0.15
24 1 0.03
25 1 0.03
26 4 0.10
27 11 0.28
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTATAATAAAATTTAATATA
Found at i:1453641 original size:21 final size:20
Alignment explanation
Indices: 1453606--1453659 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
1453596 TTATAATATC
*
1453606 ATATATTTTTATAAAATTTA
1 ATATATTTATATAAAATTTA
*
1453626 ATATATATTATATAAATTTTA
1 ATATAT-TTATATAAAATTTA
1453647 ATATATTTATATA
1 ATATATTTATATA
1453660 TTTATATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATATTTATATAAAATTTA
Found at i:1453650 original size:19 final size:21
Alignment explanation
Indices: 1453606--1453659 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1453596 TTATAATATC
*
1453606 ATATATTTTTATA-AAATTTA
1 ATATATATTTATATAAATTTA
*
1453626 ATATATA-TTATATAAATTTT
1 ATATATATTTATATAAATTTA
1453646 A-ATATATTTATATA
1 ATATATATTTATATA
1453660 TTTATATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTTATATAAATTTA
Found at i:1453843 original size:19 final size:20
Alignment explanation
Indices: 1453819--1453866 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
1453809 ATATGTTTTT
1453819 ATAATTAATTTAT-ATAAAA
1 ATAATTAATTTATAATAAAA
*
1453838 ATAATT--TTTATAATATAA
1 ATAATTAATTTATAATAAAA
1453856 ATAA-TAATTTA
1 ATAATTAATTTA
1453867 ACTTTGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.24
18 9 0.36
19 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTAATTTATAATAAAA
Found at i:1453859 original size:18 final size:17
Alignment explanation
Indices: 1453827--1453860 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1453817 TTATAATTAA
1453827 TTTATATAAAAATAATT
1 TTTATATAAAAATAATT
*
1453844 TTTATAATATAAATAAT
1 TTTAT-ATAAAAATAAT
1453861 AATTTAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTATATAAAAATAATT
Found at i:1464101 original size:34 final size:34
Alignment explanation
Indices: 1464037--1464219 Score: 260
Period size: 34 Copynumber: 5.4 Consensus size: 34
1464027 AAGAACAAGA
* *
1464037 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1464070 TGTTGACTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1464104 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1464138 TGTTGATTAAATGGGTGATTTGGTGGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
1464172 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
1464206 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1464220 TGGTTTTTAC
Statistics
Matches: 132, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 11 0.08
34 121 0.92
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1464212 original size:102 final size:101
Alignment explanation
Indices: 1464037--1464219 Score: 312
Period size: 102 Copynumber: 1.8 Consensus size: 101
1464027 AAGAACAAGA
1464037 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTACC
1464102 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
66 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * *
1464138 TGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTAC
1464203 CATTGTTGATTAAATGG
65 CATTGTTGATTAAATGG
1464220 TGGTTTTTAC
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 12 0.16
102 64 0.84
ACGTcount: A:0.26, C:0.08, G:0.27, T:0.40
Consensus pattern (101 bp):
TGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTACC
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:1464580 original size:19 final size:19
Alignment explanation
Indices: 1464524--1464586 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1464514 TGGTTGTCGA
**
1464524 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1464543 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1464562 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1464581 GTTACT
1 GGTACT
1464587 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1467883 original size:34 final size:34
Alignment explanation
Indices: 1467817--1468001 Score: 264
Period size: 34 Copynumber: 5.5 Consensus size: 34
1467807 AAGTGGGAGA
* *
1467817 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1467850 ATTGTTGACTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1467884 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1467918 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
1467952 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
1467986 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1468002 TGGTTTTTAC
Statistics
Matches: 134, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 13 0.10
34 121 0.90
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1467992 original size:102 final size:101
Alignment explanation
Indices: 1467817--1468001 Score: 316
Period size: 102 Copynumber: 1.8 Consensus size: 101
1467807 AAGTGGGAGA
1467817 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTA
1467882 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
1467918 ATTGTTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTT
*
1467983 GCCATTGTTGATTAAATGG
65 ACCATTGTTGATTAAATGG
1468002 TGGTTTTTAC
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
101 14 0.18
102 64 0.82
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGACTAAATGAGAAATTTGGTAGCTTA
CCATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:1471029 original size:24 final size:22
Alignment explanation
Indices: 1471002--1471052 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
1470992 AAAATAGTAT
*
1471002 ATAAATATTAAAAATTAAATTTAA
1 ATAAATATAAAAAATTAAA--TAA
*
1471026 ATAATTATAAAAAATTAAATAA
1 ATAAATATAAAAAATTAAATAA
1471048 ATAAA
1 ATAAA
1471053 AAATTATATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 7 0.29
24 17 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAAATATAAAAAATTAAATAA
Found at i:1471051 original size:16 final size:17
Alignment explanation
Indices: 1471022--1471058 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1471012 AAAATTAAAT
1471022 TTAAATAATTATAAAAAA
1 TTAAATAA-TATAAAAAA
1471040 TTAAATAA-ATAAAAAA
1 TTAAATAATATAAAAAA
1471056 TTA
1 TTA
1471059 TATGTACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TTAAATAATATAAAAAA
Found at i:1471438 original size:20 final size:21
Alignment explanation
Indices: 1471400--1471438 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1471390 CTCGTTTTTT
* *
1471400 TTTTTTTTTGTGTTTTTATGA
1 TTTTTTTTTATGTTCTTATGA
1471421 TTTTTTTTTAT-TTCTTAT
1 TTTTTTTTTATGTTCTTAT
1471439 TCTTTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTATGTTCTTATGA
Found at i:1472535 original size:14 final size:14
Alignment explanation
Indices: 1472502--1472539 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1472492 ATACTTTATG
*
1472502 TATTA-ATATTATA
1 TATTATATATTTTA
1472515 T-TTATATATTTTA
1 TATTATATATTTTA
1472528 TATTATATATTT
1 TATTATATATTT
1472540 AAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 3 0.14
13 9 0.41
14 10 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATATATTTTA
Found at i:1472550 original size:23 final size:23
Alignment explanation
Indices: 1472511--1472582 Score: 85
Period size: 23 Copynumber: 3.1 Consensus size: 23
1472501 GTATTAATAT
1472511 TATATTT-ATATATTTTATATTA
1 TATATTTAATATATTTTATATTA
*
1472533 TATATTTAAAATATTTTATA-TA
1 TATATTTAATATATTTTATATTA
* *
1472555 TAAATTTTAATATATTATTAAATTA
1 TATA-TTTAATATATT-TTATATTA
1472580 TAT
1 TAT
1472583 TATATAAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 12 0.29
23 21 0.51
24 4 0.10
25 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATATTTAATATATTTTATATTA
Found at i:1472568 original size:32 final size:33
Alignment explanation
Indices: 1472532--1472621 Score: 105
Period size: 32 Copynumber: 2.8 Consensus size: 33
1472522 ATTTTATATT
*
1472532 ATATATTTA-AAATATTTTATATATAAATTTTA
1 ATATATTTATTAATATTTTATATATAAATTTTA
*
1472564 ATATA-TTATTAA-ATTATATTATATAAATTTTA
1 ATATATTTATTAATATTTTA-TATATAAATTTTA
* *
1472596 AAAAATTTATTAATATTTTATCATAT
1 ATATATTTATTAATATTTTAT-ATAT
1472622 TTTAATTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 8 0.17
32 23 0.48
33 8 0.17
34 9 0.19
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
ATATATTTATTAATATTTTATATATAAATTTTA
Found at i:1472569 original size:34 final size:34
Alignment explanation
Indices: 1472506--1472596 Score: 98
Period size: 36 Copynumber: 2.7 Consensus size: 34
1472496 TTTATGTATT
* *
1472506 AATATTATATTTATATATTTTATATTATATATTTAA
1 AATATTATATATATAAATTTTA-A-TATATATTTAA
*
1472542 AATATTTTATATATAAATTTTAATATAT-TATTAA
1 AATATTATATATATAAATTTTAATATATAT-TTAA
*
1472576 ATTA-TAT-TATATAAATTTTAA
1 AATATTATATATATAAATTTTAA
1472597 AAAATTTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 14 0.29
33 3 0.06
34 12 0.24
35 1 0.02
36 19 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (34 bp):
AATATTATATATATAAATTTTAATATATATTTAA
Found at i:1476479 original size:13 final size:13
Alignment explanation
Indices: 1476461--1476485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1476451 TTATCGATTC
1476461 AATTAATTTAATT
1 AATTAATTTAATT
1476474 AATTAATTTAAT
1 AATTAATTTAAT
1476486 ATGATTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTAATTTAATT
Found at i:1477343 original size:36 final size:37
Alignment explanation
Indices: 1477286--1477361 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
1477276 ACTTATTATT
**
1477286 ATTTAAAAATTTTATATTTAATAAT-TACTTTTATAAA
1 ATTTAAAAATAATATATTTAATAATATA-TTTTATAAA
* *
1477323 ATTTAAAAATAATATA-TTAATTATATATTTTTTAAA
1 ATTTAAAAATAATATATTTAATAATATATTTTATAAA
1477359 ATT
1 ATT
1477362 ATTATTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 18 0.53
37 16 0.47
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAAAAATAATATATTTAATAATATATTTTATAAA
Found at i:1477370 original size:28 final size:29
Alignment explanation
Indices: 1477324--1477378 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1477314 TTTTATAAAA
1477324 TTTAAAAATAATATATT-AATTATATATTT
1 TTTAAAAATAATATATTAAATTA-ATATTT
* *
1477353 TTTAAAATTATTAT-TTAAATTAATAT
1 TTTAAAAATAATATATTAAATTAATAT
1477379 CATTAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAAAAATAATATATTAAATTAATATTT
Found at i:1478204 original size:18 final size:17
Alignment explanation
Indices: 1478170--1478211 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1478160 TATAATTTAA
1478170 AAATAAATTTAAATATT
1 AAATAAATTTAAATATT
*
1478187 AAATAAATATTTAATATT
1 AAATAAAT-TTAAATATT
*
1478205 TAATAAA
1 AAATAAA
1478212 AATGTACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAAATTTAAATATT
Found at i:1478898 original size:59 final size:59
Alignment explanation
Indices: 1478799--1478916 Score: 218
Period size: 59 Copynumber: 2.0 Consensus size: 59
1478789 CTGGGAGCTA
*
1478799 AGCTCAACCAAGGAAGCCACCAGACGAGAAAGAATTATACAGGGAAGATTATAGGCACG
1 AGCTCAACCAAGGAAGCCACCAGACGAGAAAGAATCATACAGGGAAGATTATAGGCACG
*
1478858 AGCTCAACCAAGGAAGCCACCAGACGAGAAAGAGTCATACAGGGAAGATTATAGGCACG
1 AGCTCAACCAAGGAAGCCACCAGACGAGAAAGAATCATACAGGGAAGATTATAGGCACG
1478917 GGCTACGAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.42, C:0.21, G:0.26, T:0.11
Consensus pattern (59 bp):
AGCTCAACCAAGGAAGCCACCAGACGAGAAAGAATCATACAGGGAAGATTATAGGCACG
Found at i:1480682 original size:22 final size:22
Alignment explanation
Indices: 1480639--1480682 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1480629 TATGAGTTCG
* * *
1480639 ATTTTTATATATTATTATTAAA
1 ATTTTTAAATATTATAAATAAA
*
1480661 ATTTTTAAATTTTATAAATAAA
1 ATTTTTAAATATTATAAATAAA
1480683 TTAAAATTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTTTTAAATATTATAAATAAA
Found at i:1482251 original size:22 final size:22
Alignment explanation
Indices: 1482226--1482270 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1482216 TAATAAAAAA
1482226 TTAAA-AATATTTTTTATTTAAT
1 TTAAATAAT-TTTTTTATTTAAT
*
1482248 TTAAATAATTTTTTTTTTTAAT
1 TTAAATAATTTTTTTATTTAAT
1482270 T
1 T
1482271 ATTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTAAATAATTTTTTTATTTAAT
Found at i:1484308 original size:31 final size:31
Alignment explanation
Indices: 1484273--1484341 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1484263 TGATTCAAAC
*
1484273 ATAAAATAATTAAAA-TAAATTAAATTTAAAT
1 ATAAAATAATTAAAATTAAA-AAAATTTAAAT
* * *
1484304 ATAAATTATTTAAAATTAAAAAAATTTTAAT
1 ATAAAATAATTAAAATTAAAAAAATTTAAAT
*
1484335 TTAAAAT
1 ATAAAAT
1484342 GAGTCAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
31 27 0.87
32 4 0.13
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
ATAAAATAATTAAAATTAAAAAAATTTAAAT
Found at i:1484314 original size:15 final size:15
Alignment explanation
Indices: 1484273--1484319 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1484263 TGATTCAAAC
*
1484273 ATAAAATAA-TTAAA
1 ATAAATTAATTTAAA
1484287 ATAAATTAAATTTAAA
1 ATAAATT-AATTTAAA
1484303 TATAAATT-ATTTAAA
1 -ATAAATTAATTTAAA
1484318 AT
1 AT
1484320 TAAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 8 0.28
15 9 0.31
16 5 0.17
17 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAATTAATTTAAA
Found at i:1485458 original size:24 final size:25
Alignment explanation
Indices: 1485431--1485480 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1485421 TTGACATGTC
1485431 AATTTATTAATATCATATTTA-ATT
1 AATTTATTAATATCATATTTATATT
* * *
1485455 AATTTTTTTATATTATATTTATATT
1 AATTTATTAATATCATATTTATATT
1485480 A
1 A
1485481 TGTAATTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
AATTTATTAATATCATATTTATATT
Found at i:1486123 original size:23 final size:21
Alignment explanation
Indices: 1486076--1486136 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
1486066 TTAATTGGAC
1486076 TTTTAGTTTAAGTTTAAATAAG
1 TTTTAGTTTAA-TTTAAATAAG
**
1486098 TTTTTAGTTTAGATTTAAATGGG
1 -TTTTAGTTTA-ATTTAAATAAG
*
1486121 TTTAAGTTTAAATTTA
1 TTTTAGTTT-AATTTA
1486137 TATTTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 13 0.39
23 19 0.58
24 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (21 bp):
TTTTAGTTTAATTTAAATAAG
Found at i:1486519 original size:3 final size:3
Alignment explanation
Indices: 1486511--1486542 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1486501 AATCTAACTT
1486511 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1486543 TCTCAACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1486753 original size:20 final size:21
Alignment explanation
Indices: 1486728--1486768 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1486718 ACTCATTTTT
*
1486728 ATTTTATATTA-AAAATAATG
1 ATTTTAAATTATAAAATAATG
1486748 ATTTTAAATTATTAAAATAAT
1 ATTTTAAATTA-TAAAATAAT
1486769 TTAATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
ATTTTAAATTATAAAATAATG
Found at i:1486882 original size:4 final size:4
Alignment explanation
Indices: 1486867--1486897 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1486857 TACCGTTCAC
*
1486867 ATAA AAAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1486898 CGGGGAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAA
Found at i:1488211 original size:15 final size:15
Alignment explanation
Indices: 1488191--1488288 Score: 51
Period size: 15 Copynumber: 6.4 Consensus size: 15
1488181 CCATGTATTA
1488191 ATTTTATATTTATAT
1 ATTTTATATTTATAT
*
1488206 ATTTTAT-TATAT-T
1 ATTTTATATTTATAT
* *
1488219 ATATTTATGTTTAAAAT
1 AT-TTTATATTT-ATAT
* *
1488236 AATTTT-TATATATAA
1 -ATTTTATATTTATAT
1488251 ATTTTTATATTT-TATT
1 A-TTTTATATTTATA-T
* *
1488267 AATTTATATTATATAA
1 ATTTTATATT-TATAT
1488283 ATTTTA
1 ATTTTA
1488289 AAAAAATTAT
Statistics
Matches: 61, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
13 3 0.05
14 10 0.16
15 25 0.41
16 15 0.25
17 6 0.10
18 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
ATTTTATATTTATAT
Found at i:1488258 original size:32 final size:32
Alignment explanation
Indices: 1488192--1488287 Score: 92
Period size: 32 Copynumber: 3.1 Consensus size: 32
1488182 CATGTATTAA
* *
1488192 TTTTATATTTATAT-ATTT-TATTATAT-TAT
1 TTTTATATTTAAATAATTTATATTATATAAAT
* * *
1488221 ATTTATGTTTAAAATAATTTTTA-TATATAAAT
1 TTTTATATTT-AAATAATTTATATTATATAAAT
* *
1488253 TTTTATATTTTATTAATTTATATTATATAAAT
1 TTTTATATTTAAATAATTTATATTATATAAAT
1488285 TTT
1 TTT
1488288 AAAAAAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
29 8 0.15
30 3 0.06
31 18 0.34
32 24 0.45
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (32 bp):
TTTTATATTTAAATAATTTATATTATATAAAT
Found at i:1488706 original size:50 final size:50
Alignment explanation
Indices: 1488652--1488836 Score: 167
Period size: 50 Copynumber: 3.7 Consensus size: 50
1488642 TAGGTAGCTG
* * * *
1488652 TAATTATTAATTATTTTTTATCAACCTTTGACAGTCGAGAGAGGTGGTCA
1 TAATTATTAATTATTTCTCACCAACCTTTGACAATCGAGAGAGGTGGTCA
* * *
1488702 TAATTATTGATTGTTTCTCACCAACCTTTGACAATCGAGAGAGGT-GACTA
1 TAATTATTAATTATTTCTCACCAACCTTTGACAATCGAGAGAGGTGGTC-A
* * * * * * * * **
1488752 TAATTGTTGACTATTCCTCACCAATCTTTTACAATCGAGATATGTGACCA
1 TAATTATTAATTATTTCTCACCAACCTTTGACAATCGAGAGAGGTGGTCA
* *
1488802 TAATTGTTGATTA-TTCTTCACCAACCTTTGACAAT
1 TAATTATTAATTATTTC-TCACCAACCTTTGACAAT
1488837 AAAGAAAGGT
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
49 4 0.04
50 106 0.95
51 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (50 bp):
TAATTATTAATTATTTCTCACCAACCTTTGACAATCGAGAGAGGTGGTCA
Found at i:1488790 original size:100 final size:100
Alignment explanation
Indices: 1488677--1488863 Score: 234
Period size: 100 Copynumber: 1.9 Consensus size: 100
1488667 TTTTATCAAC
* ** * **
1488677 CTTTGACAGTCGAGAGAGGTGGTCATAATTATTGATTGTT-TCTCACCAACCTTTGACAATCGAG
1 CTTTGACAATCGAGAGAGGTGACCATAATTATTGATTATTCT-TCACCAACCTTTGACAATAAAG
*
1488741 AGAGGTGA-CTATAATTGTTGACTATTCCTCACCAAT
65 AAAGGTGATC-ATAATTGTTGACTATTCCTCACCAAT
* * * *
1488777 CTTTTACAATCGAGATATGTGACCATAATTGTTGATTATTCTTCACCAACCTTTGACAATAAAGA
1 CTTTGACAATCGAGAGAGGTGACCATAATTATTGATTATTCTTCACCAACCTTTGACAATAAAGA
*
1488842 AAGGTGATCGTAATTGTTGACT
66 AAGGTGATCATAATTGTTGACT
1488864 TTAAGCATCT
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
100 71 0.97
101 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (100 bp):
CTTTGACAATCGAGAGAGGTGACCATAATTATTGATTATTCTTCACCAACCTTTGACAATAAAGA
AAGGTGATCATAATTGTTGACTATTCCTCACCAAT
Found at i:1488856 original size:50 final size:50
Alignment explanation
Indices: 1488673--1488861 Score: 211
Period size: 50 Copynumber: 3.8 Consensus size: 50
1488663 TATTTTTTAT
* * * *
1488673 CAACCTTTGACAGTCGAGAGAGGTGGTCATAATTATTGATTGTT-TCTCAC
1 CAACCTTTGACAATCGAGAGAGGTGATCATAATTGTTGATTATTCT-TCAC
* *
1488723 CAACCTTTGACAATCGAGAGAGGTGA-CTATAATTGTTGACTATTCCTCAC
1 CAACCTTTGACAATCGAGAGAGGTGATC-ATAATTGTTGATTATTCTTCAC
* * * * *
1488773 CAATCTTTTACAATCGAGATATGTGACCATAATTGTTGATTATTCTTCAC
1 CAACCTTTGACAATCGAGAGAGGTGATCATAATTGTTGATTATTCTTCAC
** * *
1488823 CAACCTTTGACAATAAAGAAAGGTGATCGTAATTGTTGA
1 CAACCTTTGACAATCGAGAGAGGTGATCATAATTGTTGA
1488862 CTTTAAGCAT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
49 1 0.01
50 114 0.98
51 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (50 bp):
CAACCTTTGACAATCGAGAGAGGTGATCATAATTGTTGATTATTCTTCAC
Found at i:1493304 original size:50 final size:50
Alignment explanation
Indices: 1493244--1493398 Score: 247
Period size: 50 Copynumber: 3.1 Consensus size: 50
1493234 AGAGGTGGTG
*
1493244 TTGTTAACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTGGCCGTAA
1 TTGTTAACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTAA
* * * * *
1493294 TTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGATGGTCATAA
1 TTGTTAACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTAA
*
1493344 TTGTTAACTATTTCTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTAA
1 TTGTTAACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTAA
1493394 TTGTT
1 TTGTT
1493399 GACTCTAAGC
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 93 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (50 bp):
TTGTTAACTATTTTTCACCAACCTTTGACAATCAAGAGAGGTGGTCGTAA
Found at i:1493819 original size:2 final size:2
Alignment explanation
Indices: 1493812--1493838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1493802 CAACAGCTTG
1493812 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 A
1493839 CATAGTCGTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1496524 original size:21 final size:20
Alignment explanation
Indices: 1496477--1496525 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1496467 TAGATGAATA
1496477 TTAA-ATAAA-AATAAAATT
1 TTAATATAAATAATAAAATT
*
1496495 TTAAT-TAAATAATATAATTT
1 TTAATATAAATAATA-AAATT
1496515 TTAATATAAAT
1 TTAATATAAAT
1496526 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.31
19 4 0.15
20 9 0.35
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAATATAAATAATAAAATT
Found at i:1496533 original size:20 final size:20
Alignment explanation
Indices: 1496477--1496525 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
1496467 TAGATGAATA
*
1496477 TTAAATAAA-AATAAAA-TT
1 TTAATTAAATAATAAAATTT
*
1496495 TTAATTAAATAATATAATTT
1 TTAATTAAATAATAAAATTT
1496515 TTAATATAAAT
1 TTAAT-TAAAT
1496526 TTAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 8 0.31
19 6 0.23
20 7 0.27
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAATTAAATAATAAAATTT
Found at i:1498100 original size:12 final size:13
Alignment explanation
Indices: 1498059--1498135 Score: 86
Period size: 13 Copynumber: 6.0 Consensus size: 13
1498049 TTTTAAATTA
1498059 TTAAATTAATAAAT
1 TTAAA-TAATAAAT
* *
1498073 TTAAATATTTAAT
1 TTAAATAATAAAT
1498086 TTAAA-AATAAAT
1 TTAAATAATAAAT
* *
1498098 TTAAATATTTAAT
1 TTAAATAATAAAT
1498111 TTAAA-AATAAAT
1 TTAAATAATAAAT
*
1498123 TTAAATATTAAAT
1 TTAAATAATAAAT
1498136 ATAATAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
12 20 0.38
13 27 0.52
14 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATAATAAAT
Found at i:1498100 original size:25 final size:25
Alignment explanation
Indices: 1498066--1498145 Score: 133
Period size: 25 Copynumber: 3.2 Consensus size: 25
1498056 TTATTAAATT
1498066 AATAAATTTAAATATTTAATTTAAA
1 AATAAATTTAAATATTTAATTTAAA
1498091 AATAAATTTAAATATTTAATTTAAA
1 AATAAATTTAAATATTTAATTTAAA
* *
1498116 AATAAATTTAAATATTAAATATAATA
1 AATAAATTTAAATATTTAATTTAA-A
1498142 AATA
1 AATA
1498146 TTTAATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
25 47 0.90
26 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAATTTAAATATTTAATTTAAA
Found at i:1498167 original size:17 final size:17
Alignment explanation
Indices: 1498147--1498182 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1498137 TAATAAATAT
1498147 TTAATAAAAACATATAA
1 TTAATAAAAACATATAA
* *
1498164 TTAATTAAAAGATATAA
1 TTAATAAAAACATATAA
1498181 TT
1 TT
1498183 TTTAATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (17 bp):
TTAATAAAAACATATAA
Found at i:1500490 original size:20 final size:20
Alignment explanation
Indices: 1500444--1500495 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
1500434 AAAATTTTAT
1500444 TTTATTAT--TTAAAAAATA
1 TTTATTATAATTAAAAAATA
**
1500462 -TTAAAATAATTAAAAAATA
1 TTTATTATAATTAAAAAATA
1500481 TTTATTATAATTAAA
1 TTTATTATAATTAAA
1500496 TTTAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 5 0.19
19 10 0.37
20 12 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTATTATAATTAAAAAATA
Found at i:1500911 original size:22 final size:22
Alignment explanation
Indices: 1500855--1500911 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
1500845 AGTTTAATAT
** *
1500855 TTTTATGAATTCAATTTTTACA
1 TTTTATGAATAAAATTTTTAAA
* * *
1500877 TATTATTATTAAAATTTTTAAA
1 TTTTATGAATAAAATTTTTAAA
1500899 TTTTATGAATAAA
1 TTTTATGAATAAA
1500912 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTATGAATAAAATTTTTAAA
Found at i:1501671 original size:23 final size:26
Alignment explanation
Indices: 1501643--1501695 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 26
1501633 TTTTTATGAT
*
1501643 TAATGTA-AATTA-AAAATTTT-AAA
1 TAATGTATAAATATAAAATTTTCAAA
*
1501666 TAATGTATAAATATAATATTTTCAAA
1 TAATGTATAAATATAAAATTTTCAAA
1501692 TAAT
1 TAAT
1501696 AAAAATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.28
24 4 0.16
25 7 0.28
26 7 0.28
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (26 bp):
TAATGTATAAATATAAAATTTTCAAA
Found at i:1502467 original size:2 final size:2
Alignment explanation
Indices: 1502462--1502500 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1502452 CTAAATGTTA
1502462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1502501 ATCTCCTAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1506148 original size:2 final size:2
Alignment explanation
Indices: 1506141--1506166 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1506131 GAAAACAAGG
1506141 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
1506167 TAAAGCAACT
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:1511193 original size:28 final size:27
Alignment explanation
Indices: 1511138--1511203 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
1511128 GCCACCCATT
* *
1511138 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGATAGTTATTTTG
1511165 TGTTTGTCAAAAATGATAGTT-TCCTTTG
1 TGTTTGTCAAAAATGATAGTTAT--TTTG
*
1511193 TATTTGTCAAA
1 TGTTTGTCAAA
1511204 TATGGAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.56
28 14 0.41
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGATAGTTATTTTG
Found at i:1511335 original size:20 final size:20
Alignment explanation
Indices: 1511286--1511339 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
1511276 AATAGAGGCC
1511286 CCCTCCTCCCTCTCAAACAT
1 CCCTCCTCCCTCTCAAACAT
** *
1511306 TTCTCCTCCCTCTCAAGCAT
1 CCCTCCTCCCTCTCAAACAT
*
1511326 CCCTCATCCCTCTC
1 CCCTCCTCCCTCTC
1511340 TTGTATCCCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.15, C:0.54, G:0.02, T:0.30
Consensus pattern (20 bp):
CCCTCCTCCCTCTCAAACAT
Found at i:1512048 original size:2 final size:2
Alignment explanation
Indices: 1512036--1512064 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1512026 TCATCACCTC
1512036 AT AT A- 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
1512065 TTAACTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1512712 original size:16 final size:16
Alignment explanation
Indices: 1512691--1512736 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
1512681 TGAATGATAT
*
1512691 TTAAAATAATTCAAAC
1 TTAAAATTATTCAAAC
*
1512707 TTAAAATTATTTAAAC
1 TTAAAATTATTCAAAC
*
1512723 TCAAAATTATTCAA
1 TTAAAATTATTCAA
1512737 TAATTAACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATTATTCAAAC
Found at i:1513198 original size:2 final size:2
Alignment explanation
Indices: 1513193--1513228 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1513183 TGTGTGTGTG
*
1513193 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1513229 TTCAAGCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1514202 original size:28 final size:30
Alignment explanation
Indices: 1514170--1514231 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1514160 AATAAGTGTG
*
1514170 TATTTAAA-TTATTTAAAATT-T-TTTTATA
1 TATTTAAATTTATATAAAATTATATTTTA-A
1514198 TATTTAAATTTATATAAAATTATATTTTAA
1 TATTTAAATTTATATAAAATTATATTTTAA
1514228 TATT
1 TATT
1514232 AATATTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 6 0.20
31 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TATTTAAATTTATATAAAATTATATTTTAA
Found at i:1514874 original size:2 final size:2
Alignment explanation
Indices: 1514867--1514894 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1514857 TATCTTTTGG
1514867 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
1514895 GTATTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1515089 original size:39 final size:39
Alignment explanation
Indices: 1515041--1515116 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
1515031 AAAAAATATT
* *
1515041 ATAAGATATA-AATACAATATAAAAATATATTAAAATAAA
1 ATAAAATATATAATACAATATAAAAA-ATAATAAAATAAA
* *
1515080 ATAAAATATATGATATAATATAAAAAATAATAAAATA
1 ATAAAATATATAATACAATATAAAAAATAATAAAATA
1515117 TGATATGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (39 bp):
ATAAAATATATAATACAATATAAAAAATAATAAAATAAA
Found at i:1515095 original size:27 final size:27
Alignment explanation
Indices: 1515065--1515127 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
1515055 CAATATAAAA
* *
1515065 ATATATTAAAATAAAATAA-AATATATG
1 ATATAATAAAA-AAAATAATAAAATATG
*
1515092 ATATAATATAAAAAATAATAAAATATG
1 ATATAATAAAAAAAATAATAAAATATG
1515119 ATATGAATA
1 ATAT-AATA
1515128 TATAAATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.23
27 20 0.65
28 4 0.13
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
ATATAATAAAAAAAATAATAAAATATG
Found at i:1515113 original size:29 final size:28
Alignment explanation
Indices: 1515071--1515135 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 28
1515061 AAAAATATAT
1515071 TAAAATAAAATAAAATATATGATAT-AATA
1 TAAAATAAAAT-AAA-ATATGATATGAATA
1515100 TAAAA-AATAATAAAATATGATATGAATA
1 TAAAATAA-AATAAAATATGATATGAATA
1515128 TATAAATA
1 TA-AAATA
1515136 TATAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 9 0.28
28 11 0.34
29 11 0.34
30 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.31
Consensus pattern (28 bp):
TAAAATAAAATAAAATATGATATGAATA
Found at i:1515117 original size:22 final size:22
Alignment explanation
Indices: 1515050--1515122 Score: 57
Period size: 22 Copynumber: 3.5 Consensus size: 22
1515040 TATAAGATAT
* *
1515050 AAATACAATATAAAAATATATTA
1 AAATATAATATAAAAA-ATAATA
1515073 AAATA-AA-AT--AAAAT-ATA
1 AAATATAATATAAAAAATAATA
**
1515090 TGATATAATATAAAAAATAATA
1 AAATATAATATAAAAAATAATA
*
1515112 AAATATGATAT
1 AAATATAATAT
1515123 GAATATATAA
Statistics
Matches: 39, Mismatches: 6, Indels: 11
0.70 0.11 0.20
Matches are distributed among these distances:
17 5 0.13
18 4 0.10
19 5 0.13
21 7 0.18
22 13 0.33
23 5 0.13
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (22 bp):
AAATATAATATAAAAAATAATA
Found at i:1515134 original size:27 final size:27
Alignment explanation
Indices: 1515077--1515156 Score: 81
Period size: 27 Copynumber: 2.8 Consensus size: 27
1515067 ATATTAAAAT
*
1515077 AAAATAA-AATATATGATATAATATAA
1 AAAATAATAAAATATGATATAATATAA
1515103 AAAATAATAAAATATGATATGAATATATA
1 AAAATAATAAAATATGATAT-AATATA-A
* *
1515132 AATATATAATTTAAATTTGATATAA
1 AA-A-ATAA-TAAAATATGATATAA
1515157 CATGAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
26 7 0.16
27 11 0.24
28 6 0.13
29 3 0.07
30 1 0.02
31 6 0.13
32 11 0.24
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (27 bp):
AAAATAATAAAATATGATATAATATAA
Found at i:1515425 original size:2 final size:2
Alignment explanation
Indices: 1515418--1515448 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1515408 GTTCTTTAAT
1515418 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 T
1515449 TCAGAAGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1515851 original size:2 final size:2
Alignment explanation
Indices: 1515844--1515886 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1515834 TTGATGCTTT
1515844 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
1515886 T
1 T
1515887 TAAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1516612 original size:3 final size:3
Alignment explanation
Indices: 1516604--1516628 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1516594 CTCATGTTTA
1516604 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
1516629 TCATATCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:1517210 original size:2 final size:2
Alignment explanation
Indices: 1517203--1517232 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1517193 TCCTCTGGCC
*
1517203 AG AG AG AG AG AT 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
1517233 GGAGGGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1520159 original size:11 final size:11
Alignment explanation
Indices: 1520138--1520168 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1520128 TCATAATACT
1520138 ATATAAAATAAA
1 ATAT-AAATAAA
1520150 ATATAAATAAA
1 ATATAAATAAA
1520161 ATATAAAT
1 ATATAAAT
1520169 GAATGAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:1520247 original size:20 final size:20
Alignment explanation
Indices: 1520219--1520272 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
1520209 CATGTCAAAA
*
1520219 TTTATATAAATATATAATAT
1 TTTAAATAAATATATAATAT
1520239 TTTAAATAAA-AT-T-ATAT
1 TTTAAATAAATATATAATAT
*
1520256 TATAAA-AAATAATATAA
1 TTTAAATAAAT-ATATAA
1520273 ATATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.11
17 9 0.32
18 3 0.11
19 3 0.11
20 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTAAATAAATATATAATAT
Found at i:1520277 original size:23 final size:21
Alignment explanation
Indices: 1520243--1520292 Score: 50
Period size: 23 Copynumber: 2.3 Consensus size: 21
1520233 TAATATTTTA
1520243 AATA-AAATTATATTATAAAAAAT
1 AATATAAATTATA--AT-AAAAAT
1520266 AATATAAA-TATAATAAAAAT
1 AATATAAATTATAATAAAAAT
1520286 ACATATA
1 A-ATATA
1520293 TTCACTGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
23 8 0.32
24 3 0.12
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AATATAAATTATAATAAAAAT
Found at i:1521314 original size:30 final size:31
Alignment explanation
Indices: 1521278--1521336 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
1521268 CTTTAAAAAT
*
1521278 TTGAAAAA-TTATTTATATATTATTATTTGA
1 TTGAAAAAGTTAATTATATATTATTATTTGA
*
1521308 TTGAAAAATGTTAATTATATATTTTTATT
1 TTGAAAAA-GTTAATTATATATTATTATT
1521337 ATATATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 8 0.32
32 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (31 bp):
TTGAAAAAGTTAATTATATATTATTATTTGA
Found at i:1523043 original size:14 final size:14
Alignment explanation
Indices: 1522993--1523045 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1522983 ATAACATAAA
1522993 TATATAATAAAATT
1 TATATAATAAAATT
* *
1523007 TATTTGATACAAATTAT
1 TATATAATA-AAA-T-T
1523024 TAATATAATAAAATT
1 T-ATATAATAAAATT
1523039 TATATAA
1 TATATAA
1523046 ATATAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 13 0.42
15 5 0.16
16 2 0.06
17 5 0.16
18 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (14 bp):
TATATAATAAAATT
Found at i:1523051 original size:17 final size:16
Alignment explanation
Indices: 1523017--1523063 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1523007 TATTTGATAC
1523017 AAAT-TATTAATATAATA
1 AAATATATTAA-AT-ATA
*
1523034 AAATTTATATAAATATA
1 AAATATAT-TAAATATA
1523051 AAATATATTAAAT
1 AAATATATTAAAT
1523064 TTAATAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.19
17 14 0.52
18 5 0.19
19 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATATTAAATATA
Found at i:1524801 original size:15 final size:16
Alignment explanation
Indices: 1524767--1524807 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
1524757 GACCGATCCA
1524767 TAATT-ATATATAATT
1 TAATTAATATATAATT
*
1524782 GAATTAATATAT-ATT
1 TAATTAATATATAATT
1524797 TAATTAA-ATAT
1 TAATTAATATAT
1524808 TTATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 13 0.57
16 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (16 bp):
TAATTAATATATAATT
Found at i:1524835 original size:16 final size:17
Alignment explanation
Indices: 1524814--1524847 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1524804 ATATTTATAT
1524814 ATATTATATT-AATTAA
1 ATATTATATTAAATTAA
*
1524830 ATATTATTTTAAATTAA
1 ATATTATATTAAATTAA
1524847 A
1 A
1524848 CTAATATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTATATTAAATTAA
Found at i:1524852 original size:26 final size:26
Alignment explanation
Indices: 1524797--1524859 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
1524787 AATATATATT
* * *
1524797 TAATTAAATATTTATATATATTATAT
1 TAATTAAATATTTATATAAATTAAAC
*
1524823 TAATTAAATA-TTATTTTAAATTAAAC
1 TAATTAAATATTTA-TATAAATTAAAC
1524849 TAATATAAATA
1 TAAT-TAAATA
1524860 AAAAATATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 22 0.71
27 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TAATTAAATATTTATATAAATTAAAC
Found at i:1526267 original size:24 final size:24
Alignment explanation
Indices: 1526239--1526286 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1526229 TTTTATTTTA
* *
1526239 TTTTTATTTTCTTTATTTTTTATTG
1 TTTTTA-TATCTTTACTTTTTATTG
1526264 TTTTTATATCTTTACTTTTTATT
1 TTTTTATATCTTTACTTTTTATT
1526287 TTAATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (24 bp):
TTTTTATATCTTTACTTTTTATTG
Found at i:1526269 original size:16 final size:15
Alignment explanation
Indices: 1526234--1526288 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
1526224 TATCCTTTTA
1526234 TTTTA-TTTTTATTT
1 TTTTATTTTTTATTT
1526248 TCTTTATTTTTTATTGT
1 T-TTTATTTTTTATT-T
* *
1526265 TTTTATATCTTTA-CT
1 TTTTAT-TTTTTATTT
1526280 TTTTATTTT
1 TTTTATTTT
1526289 AATTATAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 3 0.09
15 11 0.32
16 13 0.38
17 7 0.21
ACGTcount: A:0.15, C:0.05, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTATTTTTTATTT
Found at i:1526294 original size:24 final size:23
Alignment explanation
Indices: 1526234--1526295 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
1526224 TATCCTTTTA
*
1526234 TTTTATTTTTATT-T-TCTTTATT
1 TTTTA-TTTTATTATATCTTTACT
*
1526256 TTTTATTGTTTTTATATCTTTACT
1 TTTTATT-TTATTATATCTTTACT
1526280 TTTTATTTTAATTATA
1 TTTTATTTT-ATTATA
1526296 ATATAAAACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 9 0.27
23 3 0.09
24 19 0.58
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTATTTTATTATATCTTTACT
Found at i:1526327 original size:24 final size:22
Alignment explanation
Indices: 1526299--1526356 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 22
1526289 AATTATAATA
* *
1526299 TAAAACAAAAAATTAAAAAATT
1 TAAAACAAAAAAATAAAAAATC
*
1526321 TGAAAAAATAAAAAATAAAAAATC
1 T-AAAACA-AAAAAATAAAAAATC
1526345 TAAAACAAAAAA
1 TAAAACAAAAAA
1526357 GAAATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 6 0.20
23 10 0.33
24 14 0.47
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAAACAAAAAAATAAAAAATC
Found at i:1527486 original size:2 final size:2
Alignment explanation
Indices: 1527479--1527524 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1527469 TTTCACCTCA
* *
1527479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1527521 AT AT
1 AT AT
1527525 CTAAGTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1528508 original size:18 final size:20
Alignment explanation
Indices: 1528473--1528516 Score: 74
Period size: 18 Copynumber: 2.3 Consensus size: 20
1528463 TTATATTTAA
1528473 TAATATAAAAATATAATTTT
1 TAATATAAAAATATAATTTT
1528493 TAATAT-AAAA-ATAATTTT
1 TAATATAAAAATATAATTTT
1528511 TAATAT
1 TAATAT
1528517 TTTAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 14 0.58
19 4 0.17
20 6 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAATATAAAAATATAATTTT
Found at i:1528512 original size:51 final size:49
Alignment explanation
Indices: 1528441--1528538 Score: 119
Period size: 51 Copynumber: 2.0 Consensus size: 49
1528431 TCACAATTAA
* *
1528441 TTAATTTAAATAATATTTTTATTTATATTTAATAATATAAAAAT-ATAATTT
1 TTAATATAAATAATATTTTTA-ATAT-TTTAAT-ATATAAAAATAATAATTT
*
1528492 TTAATATAAA-AATAATTTTTAATATTTTAATATATTAAAATAATAAT
1 TTAATATAAATAAT-ATTTTTAATATTTTAATATATAAAAATAATAAT
1528539 ATAAATCATC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
48 9 0.21
49 11 0.26
50 6 0.14
51 16 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (49 bp):
TTAATATAAATAATATTTTTAATATTTTAATATATAAAAATAATAATTT
Found at i:1529875 original size:23 final size:22
Alignment explanation
Indices: 1529834--1529915 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 22
1529824 TATTTGTTTG
*
1529834 AATTTATTTATTTAAATTAAATA
1 AATTTATTTA-TGAAATTAAATA
*
1529857 AATTTATTTATGAATATTAAACA
1 AATTTATTTATGAA-ATTAAATA
* * *
1529880 AATGTATTAATAAACATATAAATA
1 AATTTATTTATGAA-AT-TAAATA
* *
1529904 AATATGTTTATG
1 AATTTATTTATG
1529916 TATAAATAAA
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.07
23 30 0.65
24 13 0.28
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
AATTTATTTATGAAATTAAATA
Found at i:1529902 original size:47 final size:45
Alignment explanation
Indices: 1529851--1529952 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 45
1529841 TTATTTAAAT
* * * *
1529851 TAAATAAATTTATTTATGAATATTAA-ACAAATGTATTAATAAACATA
1 TAAATAAATATATTTATG--TATAAATAAAAATATATTAATAAACA-A
* *
1529898 TAAATAAATATGTTTATGTATAAATAAAAATATATTCATAAACAA
1 TAAATAAATATATTTATGTATAAATAAAAATATATTAATAAACAA
1529943 TAAATAAATA
1 TAAATAAATA
1529953 AATAAAATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
45 16 0.33
46 16 0.33
47 16 0.33
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (45 bp):
TAAATAAATATATTTATGTATAAATAAAAATATATTAATAAACAA
Found at i:1530659 original size:16 final size:15
Alignment explanation
Indices: 1530627--1530669 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1530617 TAATAATTTA
1530627 ATAATTTATATTATATTT
1 ATAATTT-TA-TATA-TT
*
1530645 ATATTTTTATATATT
1 ATAATTTTATATATT
1530660 ATAATTTTAT
1 ATAATTTTAT
1530670 TTAAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 11 0.48
16 4 0.17
17 2 0.09
18 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATAATTTTATATATT
Found at i:1530670 original size:27 final size:26
Alignment explanation
Indices: 1530632--1530691 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
1530622 ATTTAATAAT
* * *
1530632 TTATATTATATTTATATTTTTATATA
1 TTATATTATATTTAAAATATTATATA
*
1530658 TTATAATTTTATTTAAAATATTATATA
1 TTAT-ATTATATTTAAAATATTATATA
1530685 TTTATAT
1 -TTATAT
1530692 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.14
27 20 0.71
28 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATATTATATTTAAAATATTATATA
Found at i:1530688 original size:20 final size:20
Alignment explanation
Indices: 1530655--1530694 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1530645 ATATTTTTAT
*
1530655 ATATTATAATTTTATTTAAA
1 ATATTATAATTTTATATAAA
1530675 ATATTAT-ATATTTATATAAA
1 ATATTATAAT-TTTATATAAA
1530695 TTTTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATTATAATTTTATATAAA
Found at i:1530709 original size:23 final size:24
Alignment explanation
Indices: 1530683--1530736 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
1530673 AAATATTATA
* *
1530683 TATTTATATAAATTTTAATAAA-T
1 TATTTATATAAATTATAAAAAATT
* * *
1530706 TATTAATTTATATTATAAAAAATT
1 TATTTATATAAATTATAAAAAATT
1530730 TATTTAT
1 TATTTAT
1530737 TTTTTATACC
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTTATATAAATTATAAAAAATT
Found at i:1530723 original size:30 final size:33
Alignment explanation
Indices: 1530654--1530724 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 33
1530644 TATATTTTTA
*
1530654 TATATTAT-AATTTTATTTAAAATATTATATAT
1 TATATTATAAATTTTATATAAAATATTATATAT
*
1530686 T-TA-TATAAATTTTA-ATAAATTATTA-AT-T
1 TATATTATAAATTTTATATAAAATATTATATAT
1530714 TATATTATAAA
1 TATATTATAAA
1530725 AAATTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 2 0.06
29 4 0.12
30 18 0.53
31 9 0.26
32 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATATTATAAATTTTATATAAAATATTATATAT
Found at i:1530762 original size:7 final size:7
Alignment explanation
Indices: 1530752--1530788 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
1530742 ATACCATATA
1530752 ATATTTT
1 ATATTTT
1530759 ATATTTT
1 ATATTTT
1530766 ATA-TTT
1 ATATTTT
1530772 AT-TTTT
1 ATATTTT
1530778 AATATTTT
1 -ATATTTT
1530786 ATA
1 ATA
1530789 ACGATAATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
6 8 0.30
7 15 0.56
8 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATATTTT
Found at i:1531223 original size:34 final size:34
Alignment explanation
Indices: 1531185--1531250 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1531175 AATTTATCAA
1531185 TATTTACTTAAATCGATCAATCTTATCTTTATTT
1 TATTTACTTAAATCGATCAATCTTATCTTTATTT
*
1531219 TATTTATTTAAATCGATCAATCTTATCTTTAT
1 TATTTACTTAAATCGATCAATCTTATCTTTAT
1531251 ACTAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.03, T:0.53
Consensus pattern (34 bp):
TATTTACTTAAATCGATCAATCTTATCTTTATTT
Found at i:1531690 original size:21 final size:20
Alignment explanation
Indices: 1531655--1531696 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1531645 AAATTAAAAT
**
1531655 ATAAAAAATTTAAAAATCAAA
1 ATAAAAAATAGAAAAAT-AAA
1531676 ATAAAAAATAGAAAAATAAA
1 ATAAAAAATAGAAAAATAAA
1531696 A
1 A
1531697 GAGGAAGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.19
Consensus pattern (20 bp):
ATAAAAAATAGAAAAATAAA
Found at i:1532753 original size:11 final size:10
Alignment explanation
Indices: 1532733--1532766 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
1532723 CCATCTTTCA
1532733 ATATATATTT
1 ATATATATTT
1532743 ATATCATATTT
1 ATAT-ATATTT
1532754 ATATAT-TTT
1 ATATATATTT
1532763 ATAT
1 ATAT
1532767 TATAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 6 0.26
11 10 0.43
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (10 bp):
ATATATATTT
Found at i:1532759 original size:21 final size:21
Alignment explanation
Indices: 1532733--1532775 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
1532723 CCATCTTTCA
1532733 ATATATATTTATATCAT-ATTT
1 ATATAT-TTTATATCATAATTT
*
1532754 ATATATTTTATATTATAATTT
1 ATATATTTTATATCATAATTT
1532775 A
1 A
1532776 ACTTTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTTTATATCATAATTT
Found at i:1533089 original size:21 final size:21
Alignment explanation
Indices: 1533065--1533108 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1533055 AATTTAATTT
* *
1533065 AATTAATTTATTTATTTTTTA
1 AATTAATGTATTTAATTTTTA
*
1533086 AATTTATGTATTTAATTTTTA
1 AATTAATGTATTTAATTTTTA
1533107 AA
1 AA
1533109 AATAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
AATTAATGTATTTAATTTTTA
Found at i:1533222 original size:15 final size:16
Alignment explanation
Indices: 1533202--1533238 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
1533192 GACTTTTGAA
1533202 TTATTTTTAA-AATTT
1 TTATTTTTAATAATTT
1533217 TTA-TTTTAATAATTT
1 TTATTTTTAATAATTT
1533232 TTATTTT
1 TTATTTT
1533239 AAATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.30
15 11 0.55
16 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTTAATAATTT
Found at i:1533239 original size:15 final size:14
Alignment explanation
Indices: 1533206--1533245 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
1533196 TTTGAATTAT
1533206 TTTTAAAATTTTTA
1 TTTTAAAATTTTTA
1533220 TTTTAATAATTTTTA
1 TTTTAA-AATTTTTA
1533235 TTTT-AAATTTT
1 TTTTAAAATTTT
1533246 AAATTAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.24
14 7 0.28
15 12 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAAAATTTTTA
Found at i:1533252 original size:12 final size:12
Alignment explanation
Indices: 1533237--1533261 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1533227 AATTTTTATT
1533237 TTAAATTTTAAA
1 TTAAATTTTAAA
1533249 TTAAATTTTAAA
1 TTAAATTTTAAA
1533261 T
1 T
1533262 GATTTATTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAATTTTAAA
Found at i:1533922 original size:31 final size:31
Alignment explanation
Indices: 1533886--1533965 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
1533876 ATTTGTTTAC
*
1533886 ATCCAAATAAGTTCTTGATTTTTTAA-TTTGT
1 ATCCAAATAAGTTCTTAATTTTTTAACTTT-T
* *
1533917 ATCCAAATTAACTT-TAAATTTTTTAACTTTT
1 ATCCAAA-TAAGTTCTTAATTTTTTAACTTTT
*
1533948 ATCGAAATAAGTTCTTAA
1 ATCCAAATAAGTTCTTAA
1533966 CTTTAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
30 5 0.12
31 27 0.68
32 8 0.20
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.47
Consensus pattern (31 bp):
ATCCAAATAAGTTCTTAATTTTTTAACTTTT
Found at i:1534592 original size:29 final size:29
Alignment explanation
Indices: 1534550--1534605 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1534540 ATTTTTTTCA
* *
1534550 AGTTCAGTTAGTTAGATATAAATTAATCG
1 AGTTCAATTAGTTAGATACAAATTAATCG
* *
1534579 AGTTCAATTGGTTAGATGCAAATTAAT
1 AGTTCAATTAGTTAGATACAAATTAAT
1534606 TCAATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.38
Consensus pattern (29 bp):
AGTTCAATTAGTTAGATACAAATTAATCG
Found at i:1534654 original size:21 final size:21
Alignment explanation
Indices: 1534630--1534680 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1534620 TATTATTTTA
*
1534630 AAATATAAAAATATTATGATT
1 AAATTTAAAAATATTATGATT
* * *
1534651 AAATTTATATATTTTATGATT
1 AAATTTAAAAATATTATGATT
1534672 AAATTTAAA
1 AAATTTAAA
1534681 TAAAATAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AAATTTAAAAATATTATGATT
Found at i:1535228 original size:15 final size:15
Alignment explanation
Indices: 1535207--1535245 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1535197 GATATAATAA
1535207 TTAAATTAAATAAA-
1 TTAAATTAAATAAAG
*
1535221 TATAAATTATATAAAG
1 T-TAAATTAAATAAAG
1535237 TTAAATTAA
1 TTAAATTAA
1535246 TTTTATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAATTAAATAAAG
Found at i:1535487 original size:21 final size:21
Alignment explanation
Indices: 1535463--1535502 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1535453 TTGCTCGAGG
* *
1535463 TAATTAAATATTATATAAAAA
1 TAATTAAAAATAATATAAAAA
1535484 TAATTAAAAATAATATAAA
1 TAATTAAAAATAATATAAA
1535503 TTATTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAATTAAAAATAATATAAAAA
Found at i:1535493 original size:11 final size:11
Alignment explanation
Indices: 1535475--1535526 Score: 52
Period size: 10 Copynumber: 4.5 Consensus size: 11
1535465 ATTAAATATT
1535475 ATATAAAAATA
1 ATATAAAAATA
1535486 AT-TAAAAATA
1 ATATAAAAATA
*
1535496 ATATAAATTATTA
1 ATATAAA--AATA
1535509 ATATATAAAATA
1 ATATA-AAAATA
*
1535521 TTATAA
1 ATATAA
1535527 TATAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 10 0.29
11 7 0.21
12 7 0.21
13 8 0.24
14 2 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:1535529 original size:15 final size:15
Alignment explanation
Indices: 1535493--1535531 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1535483 ATAATTAAAA
*
1535493 ATAATATAAATTATT
1 ATAATATAAAATATT
1535508 A-ATATATAAAATATT
1 ATA-ATATAAAATATT
1535523 ATAATATAA
1 ATAATATAA
1535532 TTTTTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 19 0.90
16 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATATAAAATATT
Done.