Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A12
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: 103038859
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4950000 characters in sequence are not A, C, G, or T
File 2 of 320
Found at i:308600 original size:17 final size:19
Alignment explanation
Indices: 308567--308601 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
308557 ATTATTTGGA
308567 TATTGTATAACTTTTGTTT
1 TATTGTATAACTTTTGTTT
308586 TATTGT-TAA-TTTTGTT
1 TATTGTATAACTTTTGTT
308602 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (19 bp):
TATTGTATAACTTTTGTTT
Found at i:309423 original size:3 final size:3
Alignment explanation
Indices: 309417--309441 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
309407 AGCAGCGGGC
309417 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
309442 AAGAAGGACA
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:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:322700 original size:6 final size:7
Alignment explanation
Indices: 322685--322709 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
322675 CACTACTTGT
322685 AAAATAA
1 AAAATAA
322692 AAAATAA
1 AAAATAA
322699 AAAATAA
1 AAAATAA
322706 AAAA
1 AAAA
322710 AAGTTTTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:324621 original size:21 final size:23
Alignment explanation
Indices: 324597--324641 Score: 67
Period size: 21 Copynumber: 2.0 Consensus size: 23
324587 TTGAACTAAC
324597 TGCTACTAACAACC-ATTA-TTA
1 TGCTACTAACAACCTATTAGTTA
*
324618 TGCTACTAACGACCTATTAGTTA
1 TGCTACTAACAACCTATTAGTTA
324641 T
1 T
324642 CTTAACAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 4 0.19
23 4 0.19
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (23 bp):
TGCTACTAACAACCTATTAGTTA
Found at i:326210 original size:21 final size:21
Alignment explanation
Indices: 326165--326212 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
326155 AGATATATTT
*
326165 TAAATAAATTTATACATTTTT
1 TAAATAAATTTATACATTTTA
*
326186 TAAATAAATTTATTC-TTTTAA
1 TAAATAAATTTATACATTTT-A
326207 TAAATA
1 TAAATA
326213 GTATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATAAATTTATACATTTTA
Found at i:326997 original size:25 final size:26
Alignment explanation
Indices: 326963--327012 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
326953 TATTTTGATC
*
326963 ATTAAGATAA-TATGAAAGTTTAAAA
1 ATTAAGATAATTATAAAAGTTTAAAA
* *
326988 ATTAATATAATTTTAAAAGTTTAAA
1 ATTAAGATAATTATAAAAGTTTAAA
327013 TGAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (26 bp):
ATTAAGATAATTATAAAAGTTTAAAA
Found at i:327059 original size:18 final size:17
Alignment explanation
Indices: 327036--327079 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
327026 AATTTAAAAT
*
327036 ATTTTAATTTGAATTTGA
1 ATTTTAATTTAAATTT-A
*
327054 ATTTTAAATTAAATTTA
1 ATTTTAATTTAAATTTA
*
327071 TTTTTAATT
1 ATTTTAATT
327080 ATTTCACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAATTTAAATTTA
Found at i:327165 original size:21 final size:21
Alignment explanation
Indices: 327124--327165 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
327114 TAAATAATAA
* *
327124 TTTATTATTAAATTTTCTTTT
1 TTTATTATTAAATTATATTTT
327145 TTTATTATTAAATTATATTTT
1 TTTATTATTAAATTATATTTT
327166 AAATATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTATTATTAAATTATATTTT
Found at i:342955 original size:44 final size:44
Alignment explanation
Indices: 342892--342979 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
342882 AACAAAAAAA
342892 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
342936 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
1 AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
342980 CTTAATTCCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.36
Consensus pattern (44 bp):
AACTTCAATATCATGATTACAATCTTCATCTATGACTAGCCTAT
Found at i:352373 original size:9 final size:9
Alignment explanation
Indices: 352359--352390 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
352349 ATAAGTATAA
352359 AATTAACCG
1 AATTAACCG
352368 AATTAACCG
1 AATTAACCG
352377 AATTAACCG
1 AATTAACCG
352386 AATTA
1 AATTA
352391 TTTGTACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:352425 original size:5 final size:6
Alignment explanation
Indices: 352410--352450 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
352400 AATTATATGT
*
352410 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
352451 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:352491 original size:13 final size:13
Alignment explanation
Indices: 352475--352499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352465 AATTTTTATG
352475 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
352488 ATTGGGTTGGGT
1 ATTGGGTTGGGT
352500 TGAGTTGAGT
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:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:357566 original size:14 final size:14
Alignment explanation
Indices: 357547--357573 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
357537 TCTGAAAATT
357547 AAAAATATATATTA
1 AAAAATATATATTA
357561 AAAAATATATATT
1 AAAAATATATATT
357574 TATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATATATATTA
Found at i:357774 original size:21 final size:22
Alignment explanation
Indices: 357728--357785 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 22
357718 AATATTTACG
*
357728 ATTTTTTTAT-AATTTTAAGTT
1 ATTTTATTATAAATTTTAAGTT
* *
357749 TTTTTATTATAAATTTTATG-T
1 ATTTTATTATAAATTTTAAGTT
*
357770 ATTTTCTTA-AAATTTT
1 ATTTTATTATAAATTTT
357786 TAGATGATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 7 0.23
21 16 0.52
22 8 0.26
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (22 bp):
ATTTTATTATAAATTTTAAGTT
Found at i:357774 original size:22 final size:20
Alignment explanation
Indices: 357728--357785 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
357718 AATATTTACG
357728 ATTTTTTTATAATTTTAAGT
1 ATTTTTTTATAATTTTAAGT
* *
357748 TTTTTTATTATAAATTTTATGT
1 ATTTTT-TTAT-AATTTTAAGT
* *
357770 ATTTTCTTAAAATTTT
1 ATTTTTTTATAATTTT
357786 TAGATGATGC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 11 0.35
21 7 0.23
22 13 0.42
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (20 bp):
ATTTTTTTATAATTTTAAGT
Found at i:362646 original size:28 final size:26
Alignment explanation
Indices: 362615--362683 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
362605 AAAACTTCAG
362615 AAAATTATAAAAAAATATTAAAAATTAT
1 AAAATTA-AAAAAAA-ATTAAAAATTAT
* * *
362643 AAAATGTAGATAAAAAATTCAAATTTAT
1 AAAAT-TA-AAAAAAAATTAAAAATTAT
*
362671 AAACTTAAAAAAA
1 AAAATTAAAAAAA
362684 TATGATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
26 5 0.15
27 2 0.06
28 19 0.56
29 8 0.24
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (26 bp):
AAAATTAAAAAAAAATTAAAAATTAT
Found at i:363991 original size:8 final size:8
Alignment explanation
Indices: 363978--364012 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
363968 ATTCAACTCC
363978 AAAAAGAA
1 AAAAAGAA
363986 AAAAAGAA
1 AAAAAGAA
363994 AAAAAGAA
1 AAAAAGAA
364002 AAAAAGAA
1 AAAAAGAA
364010 AAA
1 AAA
364013 GACCCTGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:367399 original size:28 final size:28
Alignment explanation
Indices: 367366--367427 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
367356 TTGATAAGGG
**
367366 TTATATTTAATGTGGCGTATGCTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
* *
367394 TTATATTTAATGTAATGTATGGTTTTAT
1 TTATATTTAATGTAACGTATGCTTTTAT
367422 TTATAT
1 TTATAT
367428 ATAAGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.15, T:0.56
Consensus pattern (28 bp):
TTATATTTAATGTAACGTATGCTTTTAT
Found at i:369532 original size:29 final size:29
Alignment explanation
Indices: 369480--369535 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
369470 TAGCTATTTG
* * *
369480 AACTAATTAATTACACTGTTAAAATATTA
1 AACTAATTAATAACACTATAAAAATATTA
*
369509 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACACTATAAAAATAT
369536 AGAGACCAAA
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:0.54, C:0.09, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACACTATAAAAATATTA
Found at i:376802 original size:81 final size:81
Alignment explanation
Indices: 376664--376829 Score: 260
Period size: 81 Copynumber: 2.0 Consensus size: 81
376654 TGATCACACA
* **
376664 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCGAGGTGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
* *
376729 CGATGTTGCTTATACG
66 CGATGCTGCTCATACG
* *
376745 AGCTGTGACTGTAACATGTAACTGTATATGCTCACATGAGTTGTGGGTCAAAATGTTAAGCTACA
1 AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
*
376810 TGATGCTGCTCATACG
66 CGATGCTGCTCATACG
376826 AGCT
1 AGCT
376830 ATGAAAAATC
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (81 bp):
AGCTGTGACTGTAACATGTAACCGTATATGCTCACATGAGTTGTGGGCCAAAATGTTAAGCTACA
CGATGCTGCTCATACG
Found at i:378666 original size:19 final size:19
Alignment explanation
Indices: 378629--378668 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
378619 TTATTGTTTC
* * *
378629 TTGTTGTTTTTTTATTATT
1 TTGTTGTTTTCTCAGTATT
378648 TTGTTGTTTTCTCAGTATT
1 TTGTTGTTTTCTCAGTATT
378667 TT
1 TT
378669 ACTATTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.10, C:0.05, G:0.12, T:0.72
Consensus pattern (19 bp):
TTGTTGTTTTCTCAGTATT
Found at i:383148 original size:18 final size:18
Alignment explanation
Indices: 383125--383160 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
383115 TTAAAAAAAA
383125 TCATGATAGGTTCTAGTT
1 TCATGATAGGTTCTAGTT
383143 TCATGATAGGTTCTAGTT
1 TCATGATAGGTTCTAGTT
383161 CCAACTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
TCATGATAGGTTCTAGTT
Found at i:386390 original size:12 final size:12
Alignment explanation
Indices: 386373--386397 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
386363 GATTTACAGC
386373 AAAAAAAGAAAG
1 AAAAAAAGAAAG
386385 AAAAAAAGAAAG
1 AAAAAAAGAAAG
386397 A
1 A
386398 GGCACGTCAA
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAG
Found at i:390047 original size:24 final size:24
Alignment explanation
Indices: 389988--390057 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 24
389978 AATAATAAAA
*
389988 TATATTGTTTTTAAAAAATATTTT
1 TATATTATTTTTAAAAAATATTTT
390012 TATATTAATTTTTAAAAATATTCATTTTT
1 TATATT-ATTTTTAAAAA-A-T-A-TTTT
*
390041 TATTTTTATTTTTAAAA
1 TA-TATTATTTTTAAAA
390058 TAGAAATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
24 6 0.16
25 10 0.26
26 1 0.03
27 1 0.03
28 1 0.03
29 16 0.42
30 3 0.08
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (24 bp):
TATATTATTTTTAAAAAATATTTT
Found at i:392379 original size:13 final size:13
Alignment explanation
Indices: 392361--392386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
392351 TGTACCTTAA
392361 AACTCAAGTTTAC
1 AACTCAAGTTTAC
392374 AACTCAAGTTTAC
1 AACTCAAGTTTAC
392387 TAAATTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
AACTCAAGTTTAC
Found at i:398372 original size:16 final size:17
Alignment explanation
Indices: 398341--398373 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
398331 TTTATAAGTA
398341 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
398358 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
398374 GCTTCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:398719 original size:46 final size:47
Alignment explanation
Indices: 398659--398885 Score: 302
Period size: 46 Copynumber: 4.9 Consensus size: 47
398649 TTTGACATGA
* * * * *
398659 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
398705 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* * *
398751 TGCCATGGTATCTTTCAACCATGGTATTATTC-GTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* *
398797 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
398843 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCA
398886 AAGAGCACAC
Statistics
Matches: 167, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 5 0.03
46 162 0.97
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
Found at i:401038 original size:3 final size:3
Alignment explanation
Indices: 401024--401072 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
401014 CTTTTATACA
401024 AAT AATT AAT AAT AA- AAT AAT AAT AA- AAT AAT AAT AA- AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
401067 AA- AAT A
1 AAT AAT A
401073 TCTCATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:401044 original size:8 final size:8
Alignment explanation
Indices: 401031--401072 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
401021 ACAAATAATT
401031 AATAATAA
1 AATAATAA
401039 AATAAT--
1 AATAATAA
401045 AATAA-AA
1 AATAATAA
401052 TAATAATAA
1 -AATAATAA
401061 AATAATAA
1 AATAATAA
401069 AATA
1 AATA
401073 TCTCATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.17
8 23 0.77
9 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:401046 original size:11 final size:11
Alignment explanation
Indices: 401030--401068 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
401020 TACAAATAAT
401030 TAATAATAAAA
1 TAATAATAAAA
401041 TAATAATAAAA
1 TAATAATAAAA
401052 TAATAATAAAA
1 TAATAATAAAA
401063 TAATAA
1 TAATAA
401069 AATATCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:401055 original size:19 final size:19
Alignment explanation
Indices: 401031--401072 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
401021 ACAAATAATT
401031 AATAATAAAATAATAATAA
1 AATAATAAAATAATAATAA
401050 AATAATAATAA-AATAATAA
1 AATAATAA-AATAATAATAA
401069 AATA
1 AATA
401073 TCTCATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAATAAAATAATAATAA
Found at i:401095 original size:20 final size:21
Alignment explanation
Indices: 401042--401117 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 21
401032 ATAATAAAAT
*
401042 AATAATAAAATA-ATAA-TAA
1 AATAATAAAATATCTAATTAA
*
401061 AATAATAAAATATCTCATTAA
1 AATAATAAAATATCTAATTAA
*
401082 AATAAT-ATATATCTAATTAAA
1 AATAATAAAATATCTAATT-AA
*
401103 TAATCATAAAATATC
1 -AATAATAAAATATC
401118 ATCAACATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.26
20 12 0.26
21 11 0.24
22 5 0.11
23 6 0.13
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.33
Consensus pattern (21 bp):
AATAATAAAATATCTAATTAA
Found at i:401363 original size:29 final size:30
Alignment explanation
Indices: 401313--401370 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
401303 CACCCTTAAA
* * *
401313 ATATTTGCACTATTAGTCCTTTAACTTTTC
1 ATATTTACACTATTAATCCTTTAAATTTTC
401343 ATATTTACACT-TTAATCCTTTAAATTTT
1 ATATTTACACTATTAATCCTTTAAATTTT
401371 GAGCATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTTAAATTTTC
Found at i:402285 original size:310 final size:310
Alignment explanation
Indices: 401723--402346 Score: 1230
Period size: 310 Copynumber: 2.0 Consensus size: 310
401713 AATTCAATAT
401723 TTCACATTTGCCTCTCAGAACTTTTACCAACAGAAATAGAAGATAATATCATATGAATCTTATTA
1 TTCACATTTGCCTCTCAGAACTTTTACCAACAGAAATAGAAGATAATATCATATGAATCTTATTA
401788 TCAAGTGTTTTATCACATGTATTGGCTTGAAAAACCAAAGAAAGATAGAGTAGTACCATTTGTGA
66 TCAAGTGTTTTATCACATGTATTGGCTTGAAAAACCAAAGAAAGATAGAGTAGTACCATTTGTGA
*
401853 ATCAATCAGACTTGTGATAATTTCTATCTATTAGCATATTTATCCAACCTTTCCATATATTGATT
131 ATCAACCAGACTTGTGATAATTTCTATCTATTAGCATATTTATCCAACCTTTCCATATATTGATT
401918 ATAGCATCCAAACATGAACAGTTGTATATACCTCTGAAAATATCAGTACATATAAAATACCCGTA
196 ATAGCATCCAAACATGAACAGTTGTATATACCTCTGAAAATATCAGTACATATAAAATACCCGTA
401983 CAAAATCCCCAAAAATTTTTACTGTAATATACTTATTTATAACAGCTATA
261 CAAAATCCCCAAAAATTTTTACTGTAATATACTTATTTATAACAGCTATA
402033 TTCACATTTGCCTCTCAGAACTTTTACCAACAGAAATAGAAGATAATATCATATGAATCTTATTA
1 TTCACATTTGCCTCTCAGAACTTTTACCAACAGAAATAGAAGATAATATCATATGAATCTTATTA
402098 TCAAGTGTTTTATCACATGTATTGGCTTGAAAAACCAAAGAAAGATAGAGTAGTACCATTTGTGA
66 TCAAGTGTTTTATCACATGTATTGGCTTGAAAAACCAAAGAAAGATAGAGTAGTACCATTTGTGA
*
402163 ATCAACCAGACTTGTGATAATTTCTGTCTATTAGCATATTTATCCAACCTTTCCATATATTGATT
131 ATCAACCAGACTTGTGATAATTTCTATCTATTAGCATATTTATCCAACCTTTCCATATATTGATT
402228 ATAGCATCCAAACATGAACAGTTGTATATACCTCTGAAAATATCAGTACATATAAAATACCCGTA
196 ATAGCATCCAAACATGAACAGTTGTATATACCTCTGAAAATATCAGTACATATAAAATACCCGTA
402293 CAAAATCCCCAAAAATTTTTACTGTAATATACTTATTTATAACAGCTATA
261 CAAAATCCCCAAAAATTTTTACTGTAATATACTTATTTATAACAGCTATA
402343 TTCA
1 TTCA
402347 AATATTTAAT
Statistics
Matches: 312, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
310 312 1.00
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.34
Consensus pattern (310 bp):
TTCACATTTGCCTCTCAGAACTTTTACCAACAGAAATAGAAGATAATATCATATGAATCTTATTA
TCAAGTGTTTTATCACATGTATTGGCTTGAAAAACCAAAGAAAGATAGAGTAGTACCATTTGTGA
ATCAACCAGACTTGTGATAATTTCTATCTATTAGCATATTTATCCAACCTTTCCATATATTGATT
ATAGCATCCAAACATGAACAGTTGTATATACCTCTGAAAATATCAGTACATATAAAATACCCGTA
CAAAATCCCCAAAAATTTTTACTGTAATATACTTATTTATAACAGCTATA
Found at i:403845 original size:29 final size:30
Alignment explanation
Indices: 403808--403865 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
403798 GTAAATGCTC
* * *
403808 AAAATTTAAAGGATTAA-AGTGTAAATATG
1 AAAAGTTAAAGGACTAATAGTGCAAATATG
403837 AAAAGTTAAAGGACTAATAGTGCAAATAT
1 AAAAGTTAAAGGACTAATAGTGCAAATAT
403866 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.52, C:0.03, G:0.17, T:0.28
Consensus pattern (30 bp):
AAAAGTTAAAGGACTAATAGTGCAAATATG
Found at i:404101 original size:20 final size:21
Alignment explanation
Indices: 404067--404120 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
404057 TGATGATATT
*
404067 TTATGATTA-TTTAATTAGATA
1 TTAT-ATTATTTTAATGAGATA
404088 -TATATTATTTTAATGAGATA
1 TTATATTATTTTAATGAGATA
*
404108 TTTTATTATTTTA
1 TTATATTATTTTA
404121 TTATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.14
20 14 0.48
21 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TTATATTATTTTAATGAGATA
Found at i:404119 original size:8 final size:8
Alignment explanation
Indices: 404106--404147 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
404096 TTTAATGAGA
404106 TATTTTAT
1 TATTTTAT
404114 TATTTTAT
1 TATTTTAT
404122 TA--TTAT
1 TATTTTAT
404128 T-TTATTAT
1 TATT-TTAT
404136 TATTTTAT
1 TATTTTAT
404144 TATT
1 TATT
404148 AATTATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 5 0.17
8 23 0.77
9 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTTTAT
Found at i:404124 original size:3 final size:3
Alignment explanation
Indices: 404106--404154 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
404096 TTTAATGAGA
404106 TAT T-T TAT TAT T-T TAT TAT TAT T-T TAT TAT TAT T-T TAT TAT TAAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
404151 TAT T
1 TAT T
404155 TGGTATAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 8 0.20
3 30 0.73
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:404126 original size:11 final size:11
Alignment explanation
Indices: 404110--404148 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
404100 ATGAGATATT
404110 TTATTATTTTA
1 TTATTATTTTA
404121 TTATTATTTTA
1 TTATTATTTTA
404132 TTATTATTTTA
1 TTATTATTTTA
404143 TTATTA
1 TTATTA
404149 ATTATTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:404130 original size:19 final size:19
Alignment explanation
Indices: 404106--404147 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
404096 TTTAATGAGA
404106 TATTTTATTATTTTATTAT
1 TATTTTATTATTTTATTAT
404125 TATTTTATTATTATT-TTAT
1 TATTTTATTATT-TTATTAT
404144 TATT
1 TATT
404148 AATTATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TATTTTATTATTTTATTAT
Found at i:406345 original size:46 final size:46
Alignment explanation
Indices: 406297--406611 Score: 445
Period size: 46 Copynumber: 6.8 Consensus size: 46
406287 GCTCTTTGAT
** * *
406297 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** *
406343 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
406389 ATGAAACGAATAATACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
406435 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
406481 A-GAAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
406527 ATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * * *
406573 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAATAAGACCATGGTTGAAAGATACCATGGCA
406612 TCATGTCAAA
Statistics
Matches: 248, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
45 2 0.01
46 245 0.99
47 1 0.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:406918 original size:16 final size:17
Alignment explanation
Indices: 406897--406929 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
406887 ATGATGAAGC
406897 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
406913 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
406930 TACTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:408053 original size:46 final size:46
Alignment explanation
Indices: 407993--408267 Score: 406
Period size: 46 Copynumber: 6.0 Consensus size: 46
407983 TTTCTGTCAT
* * *
407993 GTTGCCATGTTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
*
408039 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
* *
408085 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
* **
408131 GTTGCCATGGTATCTTTAAACCATGGTCTTACACATTTCATATCAC
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
** * *
408177 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATTAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
* **
408223 GTTGCCATCGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCA
408268 AAGAGCACAC
Statistics
Matches: 212, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 212 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (46 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATATCAC
Found at i:408161 original size:138 final size:138
Alignment explanation
Indices: 407945--408253 Score: 440
Period size: 138 Copynumber: 2.2 Consensus size: 138
407935 TTTGACATGA
* * * *
407945 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTCATTTTCTGTCATGTTGCCATGTTATCTTT
1 TGCCATAGTATCTTTCAACCATGGTC-T--T-ATTCATTTTCTGTCACGTTGCCATGGTATCTTT
* ** * * **
408010 CAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCAT
62 AAACCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACAT
408075 TTCATATCAGGT
127 TTCATATCAGGT
*
408087 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTTCATGTCACGTTGCCATGGTATCTTTAAA
1 TGCCATAGTATCTTTCAACCATGGTCTTATTCATTTTC-TGTCACGTTGCCATGGTATCTTTAAA
408151 CCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
65 CCATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTC
*
408216 ATATTAGGT
130 ATATCAGGT
*
408225 TGCCATCGTATCTTTCAACCATGGTCTTA
1 TGCCATAGTATCTTTCAACCATGGTCTTA
408254 CACATTTCAT
Statistics
Matches: 152, Mismatches: 14, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
137 5 0.03
138 122 0.80
139 1 0.01
141 1 0.01
142 23 0.15
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (138 bp):
TGCCATAGTATCTTTCAACCATGGTCTTATTCATTTTCTGTCACGTTGCCATGGTATCTTTAAAC
CATGGTCTTACACATTTCATATCACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
TATCAGGT
Found at i:410190 original size:16 final size:16
Alignment explanation
Indices: 410171--410209 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
410161 AATTTTTCCC
*
410171 TTTTTCCTTCTTTCTT
1 TTTTTCCTTCCTTCTT
*
410187 TTTTCCCTTCCTTCTT
1 TTTTTCCTTCCTTCTT
*
410203 TCTTTCC
1 TTTTTCC
410210 CCTACTCTCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTCCTTCCTTCTT
Found at i:410283 original size:2 final size:2
Alignment explanation
Indices: 410278--410306 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
410268 CCTTTTACTT
410278 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
410307 ATAACTTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:427510 original size:161 final size:162
Alignment explanation
Indices: 427244--427725 Score: 896
Period size: 161 Copynumber: 3.0 Consensus size: 162
427234 GACGAGTGTA
*
427244 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
427309 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
427374 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGATT
*
427406 AAGTGATGATCTATGTTACAGTGAATCC-CCTACAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
427470 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGC
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
427535 GTAATAATC-TTTCCTACCAATTAAATTTGCTT
131 GTAATAATCTTTTCC-ACCAATTAAATTTGATT
427567 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
427632 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
427697 GTAATAATCTTTTCCACCAATTAAATTTG
131 GTAATAATCTTTTCCACCAATTAAATTTG
427726 CTTACTTTTA
Statistics
Matches: 310, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
160 5 0.02
161 150 0.48
162 150 0.48
163 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGATT
Found at i:427677 original size:162 final size:162
Alignment explanation
Indices: 427244--427729 Score: 904
Period size: 162 Copynumber: 3.0 Consensus size: 162
427234 GACGAGTGTA
*
427244 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGAAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
427309 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGGTTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
*
427374 GTAATAATCTTTTCCACCAATTAAATTTGATT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
*
427406 AAGTGATGATCTATGTTACAGTGAATCC-CCTACAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
*
427470 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGC
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
427535 GTAATAATC-TTTCCTACCAATTAAATTTGCTT
131 GTAATAATCTTTTCC-ACCAATTAAATTTGCTT
427567 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
1 AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
427632 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
66 AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
427697 GTAATAATCTTTTCCACCAATTAAATTTGCTT
131 GTAATAATCTTTTCCACCAATTAAATTTGCTT
427729 A
1 A
427730 CTTTTAAAAC
Statistics
Matches: 314, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
160 5 0.02
161 150 0.48
162 154 0.49
163 5 0.02
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (162 bp):
AAGTGATGATCTATGTTACAGTGAATCCACCTTCAACATATGTGGAAACAGATGCCGACTAGGCT
AGGATAACGATCCTTCAGACAATCTTCAATCTAAGACACAGATTGCAAGTCAGTCCAAAACTAGG
GTAATAATCTTTTCCACCAATTAAATTTGCTT
Found at i:428853 original size:18 final size:18
Alignment explanation
Indices: 428830--428900 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
428820 CGTTTACGGT
428830 ACTATTCACGTATACAGC
1 ACTATTCACGTATACAGC
*
428848 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGC
** *
428866 ACTATTCACGTATATGGT
1 ACTATTCACGTATACAGC
*
428884 ACTGTTCACGTATACAG
1 ACTATTCACGTATACAG
428901 TAGTTGGGAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (18 bp):
ACTATTCACGTATACAGC
Found at i:435865 original size:8 final size:9
Alignment explanation
Indices: 435853--435877 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
435843 GAAAAAGTAA
435853 AAAAAAAAG
1 AAAAAAAAG
435862 AAAAAAAAG
1 AAAAAAAAG
435871 AAAAAAA
1 AAAAAAA
435878 CTAGATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:436194 original size:3 final size:3
Alignment explanation
Indices: 436186--436220 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
436176 TACCTTGTGC
436186 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
436221 GGCGGCTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:436758 original size:4 final size:4
Alignment explanation
Indices: 436749--436774 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
436739 CCCTTTAACC
436749 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
436775 TAAAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:437798 original size:111 final size:111
Alignment explanation
Indices: 437665--437882 Score: 328
Period size: 111 Copynumber: 2.0 Consensus size: 111
437655 TTCTTCCAAT
* * * * *
437665 TTGGAATGATGAGAGGATAGAAAATAAGAGAGAAATATATGTTAGTTCAAAATTATGAATTTTTA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
* * *
437730 AATTTTTTATTTTATTTTCTTTCATTTTTCAATTCTACCAAGTAAA
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
* * *
437776 TTGGAATCATGAGATGAGAGAAAATAAAAGAGAAGTGGATGTTAGTTCAAAATTATGAATTTTCA
1 TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
*
437841 GATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
66 AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAG
437883 CAACGAAGAA
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
111 95 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.40
Consensus pattern (111 bp):
TTGGAATCATGAGAGGAGAGAAAATAAAAGAGAAATAGATGTTAGTTCAAAATTATGAATTTTCA
AATGTTTTATTTTATCTTCTTTCATTTTTCAACTCTACCAAGTAAA
Found at i:444941 original size:29 final size:28
Alignment explanation
Indices: 444908--444965 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
444898 CAATAAAAGC
*
444908 CCATTTCTTACTTTATTTA-CGGAAATAGG
1 CCATTT-TTACATTATTTACCGG-AATAGG
*
444937 CCATTTTTTCATTATTTACCGGAATAGG
1 CCATTTTTACATTATTTACCGGAATAGG
444965 C
1 C
444966 TGAAAACACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (28 bp):
CCATTTTTACATTATTTACCGGAATAGG
Found at i:474610 original size:30 final size:30
Alignment explanation
Indices: 474575--474634 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
474565 AAATTTCGAG
*
474575 TTAGTCGAGTTGACGAATCCTATTTTAGCA
1 TTAGTCCAGTTGACGAATCCTATTTTAGCA
474605 TTAGTCCAGTTGACGAATCCTATTTTAGCA
1 TTAGTCCAGTTGACGAATCCTATTTTAGCA
474635 ACCTAACTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (30 bp):
TTAGTCCAGTTGACGAATCCTATTTTAGCA
Found at i:476938 original size:39 final size:40
Alignment explanation
Indices: 476852--476942 Score: 102
Period size: 39 Copynumber: 2.3 Consensus size: 40
476842 CTTACGTATT
*
476852 TTTAA-ATATATATATGTCTTATTGTTATCATATAAGTGC
1 TTTAATATATATATATGTCATATTGTTATCATATAAGTGC
*
476891 TTGT-ATATATATATATGTACATATT-TTA-CATATAACTTG-
1 TT-TAATATATATATATGT-CATATTGTTATCATATAA-GTGC
476930 TTTAATATATATA
1 TTTAATATATATA
476943 CGTATACTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
38 1 0.02
39 21 0.47
40 18 0.40
41 5 0.11
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (40 bp):
TTTAATATATATATATGTCATATTGTTATCATATAAGTGC
Found at i:480066 original size:46 final size:46
Alignment explanation
Indices: 480014--480379 Score: 473
Period size: 46 Copynumber: 8.0 Consensus size: 46
480004 GCTTTCTGAA
* *
480014 ATGAAATGTGTAAGAACATGGTTGAAAGACACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
480060 ATGAAATGTGTAAGACCATAGTTGAAAGATACCATGGCAACAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* *
480106 ATGAAAGGTGTAAGATCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * *
480152 ATGAAATGTGTAAGACCACGGTTGAAAGATACCATGGCAATAGGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * *
480198 ATAAAATGTGTAAGATCATGGTTAAAAGATACCATAGCAACATGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* ** * *
480244 ATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTAAC
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
*** *
480290 ATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
* * * * *
480336 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATG
480380 TCAAAGATAA
Statistics
Matches: 277, Mismatches: 42, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 1 0.00
46 276 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (46 bp):
ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
Found at i:480156 original size:25 final size:25
Alignment explanation
Indices: 480082--480157 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
480072 AGACCATAGT
*
480082 TGAAAGATACCATGGCAACAGGATA
1 TGAAAGATACCATGGCAACATGATA
* ** * * *
480107 TGAAAGGT-GTA-AG-ATCATGGT-
1 TGAAAGATACCATGGCAACATGATA
480128 TGAAAGATACCATGGCAACATGATA
1 TGAAAGATACCATGGCAACATGATA
480153 TGAAA
1 TGAAA
480158 TGTGTAAGAC
Statistics
Matches: 34, Mismatches: 13, Indels: 8
0.62 0.24 0.15
Matches are distributed among these distances:
21 7 0.21
22 6 0.18
23 2 0.06
24 7 0.21
25 12 0.35
ACGTcount: A:0.42, C:0.12, G:0.25, T:0.21
Consensus pattern (25 bp):
TGAAAGATACCATGGCAACATGATA
Found at i:480679 original size:16 final size:17
Alignment explanation
Indices: 480660--480692 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
480650 ATGATGGAGC
480660 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
480676 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
480693 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:489648 original size:19 final size:20
Alignment explanation
Indices: 489621--489658 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
489611 TTTTATATTA
489621 TTAAAAAAATTAA-ATTTTT
1 TTAAAAAAATTAATATTTTT
*
489640 TTAACAAAATTAATATTTT
1 TTAAAAAAATTAATATTTT
489659 AAAATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTAAAAAAATTAATATTTTT
Found at i:491614 original size:29 final size:30
Alignment explanation
Indices: 491582--491640 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
491572 CTTATAATGA
491582 ACATTTTA-AATAAATAA-TTATTTTAATTT
1 ACATTTTATAAT-AATAATTTATTTTAATTT
*
491611 ACATTTTATAATAATAATTTTTTTTAATTT
1 ACATTTTATAATAATAATTTATTTTAATTT
491641 TTTCAACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (30 bp):
ACATTTTATAATAATAATTTATTTTAATTT
Found at i:499931 original size:87 final size:86
Alignment explanation
Indices: 499777--499968 Score: 201
Period size: 88 Copynumber: 2.2 Consensus size: 86
499767 CTTTAAAAAG
* * * * * * *
499777 AAAAAAG-AATTAAACTCTTTTTTTTTGCACTTAATTGAGTACTTTAACTTTCAGAATGTATAAA
1 AAAAAAGCAATTAAACCCTTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
* *
499841 AAAAGGC-CTTCAAATTTTTTC
66 AAAAGACACTT-AAAATTTTTC
* * *
499862 AAAAAAAGCAATTAAGCCCATTTTTTTTTCCACTTAACTGGGTAATTGAGCTTTCAAAATATAT-
1 -AAAAAAGCAATTAAACCC-TTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATA
*
499926 TAAAAAGACACTTAAAATTTTTC
64 AAAAAAGACACTTAAAATTTTTC
*
499949 AAAAAAGCTATTAAAACCCT
1 AAAAAAGCAATT-AAACCCT
499969 ACTCTTATTA
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
86 19 0.22
87 29 0.33
88 39 0.45
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (86 bp):
AAAAAAGCAATTAAACCCTTTTTTTTTCCACTTAACTGAGTAATTGAACTTTCAAAATATATAAA
AAAAGACACTTAAAATTTTTC
Found at i:500037 original size:17 final size:18
Alignment explanation
Indices: 500002--500041 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
499992 AATATAAAAA
500002 TAAATTTTAGAAAAATTAT
1 TAAATTTTA-AAAAATTAT
*
500021 TAAATTTT-AAAATTTAT
1 TAAATTTTAAAAAATTAT
500038 TAAA
1 TAAA
500042 AATAGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAAAATTAT
Found at i:500148 original size:20 final size:19
Alignment explanation
Indices: 500123--500170 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
500113 GATTTTTGAT
500123 ATAAAATGATAAAAAAATCA
1 ATAAAATGATAAAAAAAT-A
* * *
500143 ATAAAAGTTATAGAAAAATT
1 ATAAAA-TGATAAAAAAATA
500163 ATAAAATG
1 ATAAAATG
500171 TTTCTTATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 1 0.04
20 12 0.52
21 10 0.43
ACGTcount: A:0.65, C:0.02, G:0.08, T:0.25
Consensus pattern (19 bp):
ATAAAATGATAAAAAAATA
Found at i:500299 original size:10 final size:10
Alignment explanation
Indices: 500286--500375 Score: 50
Period size: 9 Copynumber: 9.5 Consensus size: 10
500276 CTTCTATATA
500286 TTTTATAATT
1 TTTTATAATT
*
500296 TTTTACAA-T
1 TTTTATAATT
**
500305 TTTTATAAAA
1 TTTTATAATT
* *
500315 GTTTACAATT
1 TTTTATAATT
500325 TTTTAT-ATT
1 TTTTATAATT
500334 TTTTACT-A--
1 TTTTA-TAATT
500342 TTTTAT-ATT
1 TTTTATAATT
*
500351 TTTTCTAA-T
1 TTTTATAATT
*
500360 TGTTATTAATT
1 TTTTA-TAATT
500371 TTTTA
1 TTTTA
500376 ATATTTGAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
7 2 0.03
8 5 0.08
9 25 0.42
10 23 0.38
11 5 0.08
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:500308 original size:19 final size:19
Alignment explanation
Indices: 500286--500375 Score: 80
Period size: 19 Copynumber: 4.8 Consensus size: 19
500276 CTTCTATATA
500286 TTTTATAATTTTTTACAAT
1 TTTTATAATTTTTTACAAT
***
500305 TTTTATAAAAGTTTACAAT
1 TTTTATAATTTTTTACAAT
*
500324 TTTT-TATATTTTTTACTA-
1 TTTTATA-ATTTTTTACAAT
500342 TTTTAT-ATTTTTT-CTAAT
1 TTTTATAATTTTTTAC-AAT
*
500360 TGTTATTAATTTTTTA
1 TTTTA-TAATTTTTTA
500376 ATATTTGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 8 0.15
18 10 0.18
19 29 0.53
20 7 0.13
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTACAAT
Found at i:500310 original size:56 final size:55
Alignment explanation
Indices: 500233--500354 Score: 140
Period size: 56 Copynumber: 2.2 Consensus size: 55
500223 TTACATTTTG
* * * *
500233 TATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTTATACTTCTATA-TATTT
1 TATAATTTT-TTACAACTTTATAAAAGTTTACAATTTTTTATA-TTCTATACTATTT
* * *
500289 TATAATTTTTTACAATTTTTATAAAAGTTTACAATTTTTTATATTTTTTACTATTT
1 TATAATTTTTTACAA-CTTTATAAAAGTTTACAATTTTTTATATTCTATACTATTT
500345 TAT-ATTTTTT
1 TATAATTTTTT
500355 CTAATTGTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
55 17 0.30
56 40 0.70
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (55 bp):
TATAATTTTTTACAACTTTATAAAAGTTTACAATTTTTTATATTCTATACTATTT
Found at i:500347 original size:17 final size:17
Alignment explanation
Indices: 500325--500391 Score: 66
Period size: 17 Copynumber: 3.8 Consensus size: 17
500315 GTTTACAATT
500325 TTTTATATTTTTTACTA
1 TTTTATATTTTTTACTA
500342 TTTTATATTTTTT-CTAA
1 TTTTATATTTTTTACT-A
*
500359 TTGTTATTAATTTTTTAATA
1 TT-TTA-T-ATTTTTTACTA
*
500379 TTTGA-ATTTTTTA
1 TTTTATATTTTTTA
500392 TTAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
16 10 0.23
17 16 0.37
18 3 0.07
19 3 0.07
20 10 0.23
21 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTTTACTA
Found at i:506803 original size:18 final size:18
Alignment explanation
Indices: 506760--506827 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
506750 TTAGTAACAT
* *
506760 TCAATCATTCAGTAGCAA
1 TCAATTATTCAGTAGCAG
*
506778 TTAATTATTCAGTAGCAG
1 TCAATTATTCAGTAGCAG
* *
506796 TCATTTATTCAATAGCAG
1 TCAATTATTCAGTAGCAG
506814 TCAGA-TATTCAGTA
1 TCA-ATTATTCAGTA
506828 CCTTTATTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TCAATTATTCAGTAGCAG
Found at i:507047 original size:51 final size:53
Alignment explanation
Indices: 506943--507057 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 53
506933 CCGTAATGGT
*
506943 AATAGAAACAGTAACAGTAACGGTACACAGAATACCTCATCGGAACAAATCCGG
1 AATAGTAACAGTAACAGTAACGGTA-ACAGAATACCTCATCGGAACAAATCCGG
* * * **
506997 AATAGTAACAGTAACAGTAA-GGT-ACGGAGTACCTCTTCGGAATGAATCCGG
1 AATAGTAACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGG
*
507048 AACAGTAACA
1 AATAGTAACA
507058 ATAAGGCGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
51 32 0.59
53 3 0.06
54 19 0.35
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (53 bp):
AATAGTAACAGTAACAGTAACGGTAACAGAATACCTCATCGGAACAAATCCGG
Found at i:508369 original size:20 final size:21
Alignment explanation
Indices: 508346--508393 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
508336 TATAATTATT
*
508346 TAATTAATAAATATCT-TTTA
1 TAATTAATAAATATCTATTAA
508366 TAATTAATAAATATCTATTAA
1 TAATTAATAAATATCTATTAA
508387 TAATTAA
1 TAATTAA
508394 ATACATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTAATAAATATCTATTAA
Found at i:515816 original size:17 final size:17
Alignment explanation
Indices: 515769--515810 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
515759 TTATCATTTA
* *
515769 TTAAATAAAA-ATAATT
1 TTAATTAAAACATTATT
515785 TTAATTAAAACATTATT
1 TTAATTAAAACATTATT
515802 TT-ATTAAAA
1 TTAATTAAAA
515811 TGATTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAACATTATT
Found at i:516705 original size:20 final size:20
Alignment explanation
Indices: 516680--516729 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
516670 TGGCTTAAAA
516680 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
516700 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
516717 GTGGTAGTGGATT
1 TTGGTAGTGGATT
516730 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:521265 original size:20 final size:20
Alignment explanation
Indices: 521240--521289 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
521230 TGGCTTAAAA
521240 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
521260 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
521277 GTGGTAGTGGATT
1 TTGGTAGTGGATT
521290 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:523214 original size:22 final size:19
Alignment explanation
Indices: 523169--523218 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
523159 TTTGTTTCAT
*
523169 GAAAAATAATTTAGTCAAT
1 GAAAAATAATTTAGTCAAC
*
523188 AAAAAATAACTTATAGATCAAC
1 GAAAAATAA-TT-TAG-TCAAC
523210 GAAAAATAA
1 GAAAAATAA
523219 ATTCATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 2 0.08
21 3 0.12
22 12 0.48
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
GAAAAATAATTTAGTCAAC
Found at i:523363 original size:19 final size:17
Alignment explanation
Indices: 523333--523375 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
523323 TAATATTACT
*
523333 ATATTAATAATAATTTTAA
1 ATATTAAAAAT-A-TTTAA
*
523352 ATTTTAAAAATATTTAA
1 ATATTAAAAATATTTAA
523369 ATATTAA
1 ATATTAA
523376 GATCAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 11 0.52
18 1 0.05
19 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATTAAAAATATTTAA
Found at i:528170 original size:24 final size:22
Alignment explanation
Indices: 528127--528170 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
528117 AGAAAATTGA
**
528127 TTTTTTTTTCAAATTTTTAAGT
1 TTTTTTTTTCAAATGATTAAGT
528149 TTTTTTTTTCAAGAATGATTAA
1 TTTTTTTTTC-A-AATGATTAA
528171 ATATAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 1 0.06
24 7 0.39
ACGTcount: A:0.27, C:0.05, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTTTTTTTCAAATGATTAAGT
Found at i:535263 original size:27 final size:27
Alignment explanation
Indices: 535215--535373 Score: 166
Period size: 27 Copynumber: 5.9 Consensus size: 27
535205 GTGAGGCTGC
* *
535215 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
535242 CAGATATTGTTGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
*
535268 CAGATATATGTAGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
535295 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
535322 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
535349 CAGATAATTGTGGTATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
535374 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:535315 original size:54 final size:54
Alignment explanation
Indices: 535233--535373 Score: 221
Period size: 54 Copynumber: 2.6 Consensus size: 54
535223 GTGACGAAGT
* *
535233 CACCAGATACAGAT-ATTGTTGCAGAGCCACCAGAACAGATATATGTAGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTAGCAGAGC
* *
535287 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTAGCAGAGC
*
535341 CACCAGATCAGATAATTGTGGTATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
535374 GACGCTTCCT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 5 0.06
54 75 0.94
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTAGCAGAGC
Found at i:537012 original size:26 final size:26
Alignment explanation
Indices: 536981--537088 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
536971 TGAAATGCCC
*
536981 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
537007 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
537033 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
537059 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
537085 ATCA
1 ATCA
537089 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:543082 original size:12 final size:12
Alignment explanation
Indices: 543067--543092 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
543057 TGGGTTTCTA
543067 TGGACCTTACGG
1 TGGACCTTACGG
543079 TGGACCTTACGG
1 TGGACCTTACGG
543091 TG
1 TG
543093 AGAATCTAAG
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:0.15, C:0.23, G:0.35, T:0.27
Consensus pattern (12 bp):
TGGACCTTACGG
Found at i:553563 original size:6 final size:6
Alignment explanation
Indices: 553553--553586 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
553543 TTAAATTATA
* *
553553 TTTTAA TTTTAT TTTTAG TTTTAG TTTTAG TTTT
1 TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTT
553587 TGAAATTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (6 bp):
TTTTAG
Found at i:553568 original size:12 final size:12
Alignment explanation
Indices: 553548--553586 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
553538 GAAAGTTAAA
*
553548 TTATATTTTAATT
1 TTAT-TTTTAGTT
553561 TTATTTTTAGTT
1 TTATTTTTAGTT
*
553573 TTAGTTTTAGTT
1 TTATTTTTAGTT
553585 TT
1 TT
553587 TGAAATTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (12 bp):
TTATTTTTAGTT
Found at i:558311 original size:14 final size:14
Alignment explanation
Indices: 558289--558318 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
558279 TAGACTCGCA
*
558289 GACATACAAGATGC
1 GACACACAAGATGC
558303 GACACACAAGATGC
1 GACACACAAGATGC
558317 GA
1 GA
558319 GCTATCTTGA
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:0.43, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
GACACACAAGATGC
Found at i:558354 original size:29 final size:29
Alignment explanation
Indices: 558312--558374 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
558302 CGACACACAA
*
558312 GATGCGAGCTATCTTGACACGCGAATTAC
1 GATGCGAGCTATCTTGACACGCGAACTAC
* * *
558341 GATGTGAGCTATCTTGACATGTGAACTAC
1 GATGCGAGCTATCTTGACACGCGAACTAC
558370 GATGC
1 GATGC
558375 TGTGAACTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (29 bp):
GATGCGAGCTATCTTGACACGCGAACTAC
Found at i:559082 original size:13 final size:13
Alignment explanation
Indices: 559066--559094 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
559056 CTTTTTTACC
559066 GCACTTTTCAAAA
1 GCACTTTTCAAAA
559079 GCACTTTTCAAAA
1 GCACTTTTCAAAA
559092 GCA
1 GCA
559095 ATGAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.24, G:0.10, T:0.28
Consensus pattern (13 bp):
GCACTTTTCAAAA
Found at i:560215 original size:8 final size:8
Alignment explanation
Indices: 560202--560241 Score: 80
Period size: 8 Copynumber: 5.0 Consensus size: 8
560192 TTAGCTCTTG
560202 TTATTTTA
1 TTATTTTA
560210 TTATTTTA
1 TTATTTTA
560218 TTATTTTA
1 TTATTTTA
560226 TTATTTTA
1 TTATTTTA
560234 TTATTTTA
1 TTATTTTA
560242 AATTTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TTATTTTA
Found at i:560249 original size:16 final size:16
Alignment explanation
Indices: 560202--560247 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
560192 TTAGCTCTTG
*
560202 TTATTTTATTATTTTA
1 TTATTTTAATATTTTA
*
560218 TTATTTTATTATTTTA
1 TTATTTTAATATTTTA
560234 TTATTTTAA-ATTTT
1 TTATTTTAATATTTT
560248 TAATAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
15 5 0.17
16 24 0.83
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTAATATTTTA
Found at i:561041 original size:16 final size:15
Alignment explanation
Indices: 561015--561045 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
561005 ACATTTATTC
561015 AAAATATTAAAAATT
1 AAAATATTAAAAATT
561030 AAAATAATTAAAAATT
1 AAAAT-ATTAAAAATT
561046 TTAGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:563742 original size:29 final size:30
Alignment explanation
Indices: 563701--563757 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
563691 TACAGATAGT
* *
563701 CACCCAACTATAAAAAATTTTCAATTTAGG
1 CACCCAACAATAAAAAATTTCCAATTTAGG
563731 CACCCAA-AATAAAAAATTTCCAATTTA
1 CACCCAACAATAAAAAATTTCCAATTTA
563758 AGTTTCACGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.28
Consensus pattern (30 bp):
CACCCAACAATAAAAAATTTCCAATTTAGG
Found at i:564075 original size:15 final size:16
Alignment explanation
Indices: 564057--564090 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
564047 AAATAGTTTG
*
564057 AAAT-TTAATATTTTA
1 AAATATTAATATTGTA
564072 AAATATTAATATTGTA
1 AAATATTAATATTGTA
564088 AAA
1 AAA
564091 ATCTCCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATATTAATATTGTA
Found at i:569385 original size:24 final size:24
Alignment explanation
Indices: 569357--569403 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
569347 TTCAACTTTG
569357 AGTTAGGTGACAAAACAATCACTT
1 AGTTAGGTGACAAAACAATCACTT
* *
569381 AGTTAGTTGATAAAACAATCACT
1 AGTTAGGTGACAAAACAATCACT
569404 CAGGTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (24 bp):
AGTTAGGTGACAAAACAATCACTT
Found at i:586528 original size:61 final size:61
Alignment explanation
Indices: 586433--586557 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 61
586423 TATCTCTCTT
586433 TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTAAAAAAGTTAAATATTA
1 TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTAAAAAAGTTAAATATTA
*
586494 TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTTAAAAAGTTAAATATTA
1 TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTAAAAAAGTTAAATATTA
586555 TTT
1 TTT
586558 ATTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (61 bp):
TTTTTAATGGGAAATATTAACCAGACACTGATATTTTAATTTTTAAAAAAGTTAAATATTA
Found at i:587091 original size:28 final size:28
Alignment explanation
Indices: 587060--587117 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 28
587050 TAAAATAAAA
* *
587060 AAATTTT-ATTAATATTTTTATAATTTAT
1 AAATTTTAATTAATAATTATA-AATTTAT
587088 AAATTTTAAATTAATAATTATAAATTTAT
1 AAATTTT-AATTAATAATTATAAATTTAT
587117 A
1 A
587118 TTTTATCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 7 0.27
29 8 0.31
30 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
AAATTTTAATTAATAATTATAAATTTAT
Found at i:589834 original size:18 final size:18
Alignment explanation
Indices: 589811--589913 Score: 80
Period size: 18 Copynumber: 5.4 Consensus size: 18
589801 ACATTGTGAT
589811 CTGAAGCCCGAAGTCTAA
1 CTGAAGCCCGAAGTCTAA
**
589829 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
589850 CAGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
**
589868 CTGAAGCACATAAGTGCTAAA
1 CTGAAGC-CCGAAGT-CT-AA
* *
589889 CGGAAGCCCGAAGGCTAA
1 CTGAAGCCCGAAGTCTAA
589907 CTGAAGC
1 CTGAAGC
589914 ACACCAGAGC
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
18 23 0.36
19 13 0.20
20 12 0.19
21 16 0.25
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (18 bp):
CTGAAGCCCGAAGTCTAA
Found at i:589855 original size:21 final size:21
Alignment explanation
Indices: 589831--589895 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
589821 AAGTCTAACT
589831 GAAGCACATAAGTGCTAAACA
1 GAAGCACATAAGTGCTAAACA
** *
589852 GAAGC-CCGAAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACA
*
589870 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACA
589891 GAAGC
1 GAAGC
589896 CCGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
20 7 0.20
21 13 0.37
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACA
Found at i:589868 original size:39 final size:39
Alignment explanation
Indices: 589813--589916 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
589803 ATTGTGATCT
*
589813 GAAGCCCGAAGTCTAACTGAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
*
589852 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
589891 GAAGCCCGAAGGCTAACTGAAGCACA
1 GAAGCCCGAAGGCTAACTGAAGCACA
589917 CCAGAGCTGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.39, C:0.24, G:0.24, T:0.12
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
Found at i:593566 original size:16 final size:15
Alignment explanation
Indices: 593545--593582 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
593535 ATAAATCAAA
593545 TTAATTAATTTATTAT
1 TTAATTAATTTATT-T
*
593561 TTAATTATTTTATTT
1 TTAATTAATTTATTT
593576 TTAATTA
1 TTAATTA
593583 GTGATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTAATTAATTTATTT
Found at i:593760 original size:29 final size:30
Alignment explanation
Indices: 593713--593801 Score: 108
Period size: 31 Copynumber: 3.0 Consensus size: 30
593703 TTGATTTAAT
* * *
593713 GTGCAATTATACACATG-AATTTTAATTTG
1 GTGCAATTATATACTTGAAACTTTAATTTG
593742 GTGCAATTATATACTTGAAACTTTAATTATG
1 GTGCAATTATATACTTGAAACTTTAATT-TG
* * *
593773 GTTCAAATGTATACTTGAAACTTTAATTT
1 GTGCAATTATATACTTGAAACTTTAATTT
593802 TAATTTAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 15 0.29
30 10 0.19
31 27 0.52
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (30 bp):
GTGCAATTATATACTTGAAACTTTAATTTG
Found at i:597427 original size:18 final size:19
Alignment explanation
Indices: 597406--597441 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
597396 TAAAAAATAA
597406 ATAAAT-TTTAGAATTTTC
1 ATAAATATTTAGAATTTTC
597424 ATAAATATTTAGAATTTT
1 ATAAATATTTAGAATTTT
597442 TCGTAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (19 bp):
ATAAATATTTAGAATTTTC
Found at i:599607 original size:14 final size:14
Alignment explanation
Indices: 599579--599612 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
599569 TCCTATGAAA
599579 ATTAAATATATAAT
1 ATTAAATATATAAT
599593 ATTATAATATA-AAT
1 ATTA-AATATATAAT
599607 ATTAAA
1 ATTAAA
599613 AGAATATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 11 0.58
15 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAATATATAAT
Found at i:607539 original size:15 final size:16
Alignment explanation
Indices: 607515--607544 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
607505 GTAATTTCGC
607515 AAAATATTATAATTTA
1 AAAATATTATAATTTA
607531 AAAAT-TTATAATTT
1 AAAATATTATAATTT
607545 CTAATTTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATATTATAATTTA
Found at i:613892 original size:80 final size:82
Alignment explanation
Indices: 613802--613963 Score: 238
Period size: 80 Copynumber: 2.0 Consensus size: 82
613792 TACTTTTTTA
* * * * *
613802 TCTTTAAATTTTAATGATGTGGCATTATTTTATTGGTTCGTAAAAA-TAT-TTTTTTAGGATAAT
1 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAACTATACTTTTTAAGATAAT
*
613865 CCTAATAGAATTTATTC
66 CCGAATAGAATTTATTC
*
613882 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAACTATACTTTTTAAGATCAT
1 TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAACTATACTTTTTAAGATAAT
*
613947 CCGAATATAATTTATTC
66 CCGAATAGAATTTATTC
613964 CCTATTTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 43 0.60
81 3 0.04
82 26 0.36
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.46
Consensus pattern (82 bp):
TCTTTAAATTTTAATGATGTGGCACTATTTTATTGGTGCATAAAAACTATACTTTTTAAGATAAT
CCGAATAGAATTTATTC
Found at i:615768 original size:4 final size:4
Alignment explanation
Indices: 615759--615790 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
615749 ACAACTAGGA
615759 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG
1 TGAG TGAG TGAG TGAG TGAG TGAG TGAG TGAG
615791 ACAAGGCAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
TGAG
Found at i:619897 original size:20 final size:19
Alignment explanation
Indices: 619872--619910 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
619862 TCCTATGCAA
619872 TGATGGATGGCATTAATTTC
1 TGATGG-TGGCATTAATTTC
* *
619892 TGATGGTGGGATTCATTTC
1 TGATGGTGGCATTAATTTC
619911 ATAAGCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (19 bp):
TGATGGTGGCATTAATTTC
Found at i:621371 original size:17 final size:17
Alignment explanation
Indices: 621345--621382 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
621335 GTTATATATT
*
621345 TATTTCAAATTATTTTA
1 TATTTCAAATTATTGTA
*
621362 TATTTTAAATTATTGTA
1 TATTTCAAATTATTGTA
621379 TATT
1 TATT
621383 ATGTATTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TATTTCAAATTATTGTA
Found at i:626414 original size:23 final size:22
Alignment explanation
Indices: 626371--626415 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
626361 AATGTAATAA
**
626371 ATATTTTTAATAATGTCTACAT
1 ATATTTTTAATAAAATCTACAT
*
626393 ATATATTTTAATAAAATTTACAT
1 ATAT-TTTTAATAAAATCTACAT
626416 TTAAAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
ATATTTTTAATAAAATCTACAT
Found at i:626558 original size:12 final size:12
Alignment explanation
Indices: 626543--626567 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
626533 AAAAAGATTT
626543 AAAAAAAACAAA
1 AAAAAAAACAAA
626555 AAAAAAAACAAA
1 AAAAAAAACAAA
626567 A
1 A
626568 TTAAAGAAAA
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:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAA
Found at i:626577 original size:16 final size:16
Alignment explanation
Indices: 626554--626595 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
626544 AAAAAAACAA
*
626554 AAAAAAAAACAAAATT
1 AAAAAAAAACAAAATG
* *
626570 AAAGAAAAATAAAATG
1 AAAAAAAAACAAAATG
626586 AAAAAAAAAC
1 AAAAAAAAAC
626596 TCCAAACTGA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.10
Consensus pattern (16 bp):
AAAAAAAAACAAAATG
Found at i:626928 original size:22 final size:22
Alignment explanation
Indices: 626903--626946 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
626893 AAACAACGTA
* *
626903 AAATTAAGGATTAAAAAAAATT
1 AAATGAAGGACTAAAAAAAATT
* *
626925 AAATGAATGACTAAAATAAATT
1 AAATGAAGGACTAAAAAAAATT
626947 TATTTTTATA
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:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (22 bp):
AAATGAAGGACTAAAAAAAATT
Found at i:638939 original size:20 final size:21
Alignment explanation
Indices: 638902--638947 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
638892 AAAACAAAGT
*
638902 AAAATTATCAAAATAATTCAA
1 AAAATTATCAAAATAATTAAA
638923 AAAATATAT-AAAA-AATTAAA
1 AAAAT-TATCAAAATAATTAAA
638943 AAAAT
1 AAAAT
638948 GAATGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 11 0.48
21 9 0.39
22 3 0.13
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATTATCAAAATAATTAAA
Found at i:640105 original size:24 final size:24
Alignment explanation
Indices: 640058--640107 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
640048 TTTGGGTTAG
*
640058 TTGGGTTAGACTTAGTATTCGGGC
1 TTGGGTTAGACTTAATATTCGGGC
* * *
640082 TTGGGTTAGATTTAATGTTTGGGC
1 TTGGGTTAGACTTAATATTCGGGC
640106 TT
1 TT
640108 TTAATTTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (24 bp):
TTGGGTTAGACTTAATATTCGGGC
Found at i:640459 original size:14 final size:14
Alignment explanation
Indices: 640436--640465 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
640426 TTGAAAATAT
640436 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
640450 GTTGATTTGGATTG
1 GTTGAATTGGATTG
640464 GT
1 GT
640466 CTCGGTTTAA
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:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:641674 original size:5 final size:5
Alignment explanation
Indices: 641664--641703 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
641654 CTTGGTTGGA
641664 GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGGAAG GGGA
1 GGGAG GGGAG GGGAG GGGAG GGGAG GGGAG GGG-AG GGGA
641704 AAAGAGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.78, T:0.00
Consensus pattern (5 bp):
GGGAG
Found at i:643094 original size:47 final size:47
Alignment explanation
Indices: 642985--643095 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
642975 CCGAGATAAG
* * * *
642985 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAATATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
* * *
643032 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TAGTA
643079 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
643096 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 50 0.94
48 2 0.04
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATAGTA
Found at i:650061 original size:21 final size:21
Alignment explanation
Indices: 650020--650103 Score: 72
Period size: 18 Copynumber: 4.3 Consensus size: 21
650010 AGAGGTAACC
*
650020 GAAGAAGATGAAGT--TGT-T
1 GAAGAAGATGAAGTACTTTAT
*
650038 GAAGAAGGTGAAGTACTTTAT
1 GAAGAAGATGAAGTACTTTAT
* * *
650059 GAAGAAAATGATGT--TGTA-
1 GAAGAAGATGAAGTACTTTAT
650077 GAAGAAGATGAAGTACTTTAT
1 GAAGAAGATGAAGTACTTTAT
*
650098 GGAGAA
1 GAAGAA
650104 AATGGTGTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
18 25 0.50
19 3 0.06
20 5 0.10
21 17 0.34
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (21 bp):
GAAGAAGATGAAGTACTTTAT
Found at i:650113 original size:39 final size:39
Alignment explanation
Indices: 650020--650115 Score: 138
Period size: 39 Copynumber: 2.5 Consensus size: 39
650010 AGAGGTAACC
* * * *
650020 GAAGAAGATGAAGTTGTTGAAGAAGGTGAAGTACTTTAT
1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
650059 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
1 GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
* *
650098 GGAGAAAATGGTGTTGTA
1 GAAGAAAATGATGTTGTA
650116 CAGGATGAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.40, C:0.02, G:0.30, T:0.28
Consensus pattern (39 bp):
GAAGAAAATGATGTTGTAGAAGAAGATGAAGTACTTTAT
Found at i:650127 original size:21 final size:21
Alignment explanation
Indices: 650101--650145 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
650091 ACTTTATGGA
* *
650101 GAAAATGGTGTTGTACAGGAT
1 GAAAATGATGTTGTACAAGAT
*
650122 GAAAATGATGTTGTAGAAGAT
1 GAAAATGATGTTGTACAAGAT
650143 GAA
1 GAA
650146 GTACTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27
Consensus pattern (21 bp):
GAAAATGATGTTGTACAAGAT
Found at i:650225 original size:33 final size:34
Alignment explanation
Indices: 650122--650228 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 34
650112 TGTACAGGAT
650122 GAAAATGATGTTGTAGAAGATGAAGTACTTTG-TGAA
1 GAAAATGATGTTGTAGAAGATGAAG-A--TTGATGAA
* *
650158 GAAAATGATATTTTAGAAGAT-ATAGATT-ATGAA
1 GAAAATGATGTTGTAGAAGATGA-AGATTGATGAA
* *
650191 GAAAATGGTGTTGTAGAAGATGAAG-TTGAAGAA
1 GAAAATGATGTTGTAGAAGATGAAGATTGATGAA
650224 GAAAA
1 GAAAA
650229 GTGTTATTGG
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 2 0.03
33 35 0.57
34 1 0.02
35 2 0.03
36 21 0.34
ACGTcount: A:0.45, C:0.01, G:0.26, T:0.28
Consensus pattern (34 bp):
GAAAATGATGTTGTAGAAGATGAAGATTGATGAA
Found at i:656958 original size:30 final size:32
Alignment explanation
Indices: 656914--656976 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
656904 TAGTAAAGGT
*
656914 AAAATTGTACTTTAA-CCTCCTAAAATTGATAA
1 AAAATTGTACTTTAATCCTCCAAAAATT-ATAA
*
656946 AAAATTG-A-TTTAATCCTTCAAAAATTATAA
1 AAAATTGTACTTTAATCCTCCAAAAATTATAA
656976 A
1 A
656977 GATATAGGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.36
31 11 0.39
32 7 0.25
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.35
Consensus pattern (32 bp):
AAAATTGTACTTTAATCCTCCAAAAATTATAA
Done.