Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_14 ID=scaffold_14-JGI_221_v2.0
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: 2042280
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64439 characters in sequence are not A, C, G, or T
File 3 of 7
Found at i:468951 original size:76 final size:75
Alignment explanation
Indices: 468786--468956 Score: 254
Period size: 75 Copynumber: 2.3 Consensus size: 75
468776 AAGGAAAACC
* * * * * *
468786 AGGATTATTCCTTTATTAATAGAGAATGCAAATGGAAAGTTAGAAAATGAATTATATTCTTTCCC
1 AGGATTATTCCCTTATTAATAAAGAAGGCAAACGAAAAGTTAGAAAAGGAATTATATTCTTTCCC
*
468851 AAAAGAATTT
66 AAAAGAATAT
468861 AGGATTATTCCCTTATTAATAAAGAAGGCAAACGAAAAGTTAGAAAAAAGGAATTATATTCTTT-
1 AGGATTATTCCCTTATTAATAAAGAAGGCAAACGAAAAGTTAG--AAAAGGAATTATATTCTTTC
468925 CCAAAAGAATAT
64 CCAAAAGAATAT
468937 AGGATTATTCCCTTATTAAT
1 AGGATTATTCCCTTATTAAT
468957 GAAAAGTAAG
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
75 38 0.44
76 31 0.36
77 18 0.21
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.33
Consensus pattern (75 bp):
AGGATTATTCCCTTATTAATAAAGAAGGCAAACGAAAAGTTAGAAAAGGAATTATATTCTTTCCC
AAAAGAATAT
Found at i:472479 original size:19 final size:19
Alignment explanation
Indices: 472455--472496 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
472445 TAATAAACTT
472455 TTAAAT-AATTAAGGTTTAA
1 TTAAATAAATTAAGG-TTAA
*
472474 TTAAATAAATTATGGTTAA
1 TTAAATAAATTAAGGTTAA
472493 TTAA
1 TTAA
472497 GTTTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (19 bp):
TTAAATAAATTAAGGTTAA
Found at i:487714 original size:464 final size:463
Alignment explanation
Indices: 487018--487931 Score: 1605
Period size: 464 Copynumber: 2.0 Consensus size: 463
487008 CTTGTCCATG
487018 TTACTTTGCATAAATTCTAATAAATCCGTTAAATGTTGACATAAAAATATGCACATTTTTCTAAG
1 TTACTTTGCATAAATTCTAATAAATCCGTTAAATGTTGACATAAAAATATGCACATTTTTCTAAG
* *
487083 TGATAAATATAAGATCTCGGAAGAGCTTATGATTTTAGATTTCAAGTTCATAAATAATCGAGTTG
66 TGATAAATATAAGATCTCGAAAGAGCTTATGATTTTAGATTTCAAGTTCATAAATAATCAAGTTG
* * *
487148 CCATGAAAAATTTTCGTAATGTTCGCTAAGCATGATGATGAATGAATTGAATTAAGAGTTGTAAT
131 CCATGAAAAATTTTCGTAACGTTCGCTAAGCATAATGATGAATGAATCGAATTAAGAGTTGTAAT
487213 TGTTCTAGCTTAATCATGTTATTGCTGTTAAATCTTGTGAATTGCTGCTAAACATTCCATTGCAT
196 TGTTCTAGCTTAATCATGTTATTGCTGTTAAATCTTGTGAATTGCTGCTAAACATTCCATTGCAT
* *
487278 TTTATTTTATCTTATTTGCATATTAGTTGTCAATTTAATTAGGACATTTATCACCATCAAATATT
261 TTTATTCTATCTCATTTGCATATTAGTTGTCAATTTAATTAGGACATTTATCACCATCAAATATT
487343 TTATTTTCATAACAAACTTGTAAAACATTAATTTTACAATTGTTGTTTATCAATACAGTCCCTAT
326 TTATTTTCATAACAAACTTGTAAAACATTAATTTTACAATTGTTGTTTATCAATACAGTCCCTAT
* *
487408 GGAGACTATACTCTTTTTACTCACTTATTACTTGATAGTGACTGTGTATACTTGCATATTCTTGA
391 GGAGACTATACTCTTTTTACTCACTTATTACTTAATAGTGACT-TGTATACTTGCACATTCTTGA
487473 CCTGTCCTA
455 CCTGTCCTA
**
487482 TTACTTTGCATAAATTCTAATAAATCCGTTAAATGTTGACATAAAAATATGCATGTTTTTCTAAG
1 TTACTTTGCATAAATTCTAATAAATCCGTTAAATGTTGACATAAAAATATGCACATTTTTCTAAG
*
487547 TGATAAATATATGATCTCGAAAGAGCTTATGATTTTAGATTTCAAGTTCATAAATAATCAAGTTG
66 TGATAAATATAAGATCTCGAAAGAGCTTATGATTTTAGATTTCAAGTTCATAAATAATCAAGTTG
** * *
487612 CCATGAAATTTTTTCAG-AACGTTTGCTAAGCATAATGATGAATGAATCGAATTAAGTGTTGTAA
131 CCATGAAAAATTTTC-GTAACGTTCGCTAAGCATAATGATGAATGAATCGAATTAAGAGTTGTAA
* *
487676 TTGTTCTAGCTTAATCATGTTATTGTTGTTAAATCTTGTGAATTGCTGTTAAACATTCCATTGCA
195 TTGTTCTAGCTTAATCATGTTATTGCTGTTAAATCTTGTGAATTGCTGCTAAACATTCCATTGCA
*
487741 TTTTATTCTATCTCATTTGCATATTAGTTGTCAATTTAATTTGGACATTTATCACCATCAAATAT
260 TTTTATTCTATCTCATTTGCATATTAGTTGTCAATTTAATTAGGACATTTATCACCATCAAATAT
* *
487806 TTTATTTTCATAACCAACTTGTCAAACATTAATTTTACAATTGTTGTTTATCAATACAGTCCCTA
325 TTTATTTTCATAACAAACTTGTAAAACATTAATTTTACAATTGTTGTTTATCAATACAGTCCCTA
*
487871 TGGAGACTATACTCTTTTTACTCACTTATTACTTAATAGTGACTTGTATGCTTGCACATTC
390 TGGAGACTATACTCTTTTTACTCACTTATTACTTAATAGTGACTTGTATACTTGCACATTC
487932 CATCGCGAAC
Statistics
Matches: 427, Mismatches: 22, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
463 15 0.04
464 411 0.96
465 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (463 bp):
TTACTTTGCATAAATTCTAATAAATCCGTTAAATGTTGACATAAAAATATGCACATTTTTCTAAG
TGATAAATATAAGATCTCGAAAGAGCTTATGATTTTAGATTTCAAGTTCATAAATAATCAAGTTG
CCATGAAAAATTTTCGTAACGTTCGCTAAGCATAATGATGAATGAATCGAATTAAGAGTTGTAAT
TGTTCTAGCTTAATCATGTTATTGCTGTTAAATCTTGTGAATTGCTGCTAAACATTCCATTGCAT
TTTATTCTATCTCATTTGCATATTAGTTGTCAATTTAATTAGGACATTTATCACCATCAAATATT
TTATTTTCATAACAAACTTGTAAAACATTAATTTTACAATTGTTGTTTATCAATACAGTCCCTAT
GGAGACTATACTCTTTTTACTCACTTATTACTTAATAGTGACTTGTATACTTGCACATTCTTGAC
CTGTCCTA
Found at i:488005 original size:19 final size:20
Alignment explanation
Indices: 487981--488018 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
487971 TGGTAGAATT
*
487981 TTTATTC-TAGAAGATATAA
1 TTTATTCTTAGAAAATATAA
488000 TTTATTCTTAGAAAATATA
1 TTTATTCTTAGAAAATATA
488019 TTCTCACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (20 bp):
TTTATTCTTAGAAAATATAA
Found at i:490427 original size:15 final size:15
Alignment explanation
Indices: 490400--490438 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
490390 ATGAAAGTTT
*
490400 TTAATATAATATTGGA
1 TTAATA-AATATTAGA
490416 TTAATAAATATTAGA
1 TTAATAAATATTAGA
490431 TGTAATAA
1 T-TAATAA
490439 TGTAATATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (15 bp):
TTAATAAATATTAGA
Found at i:495091 original size:18 final size:18
Alignment explanation
Indices: 495065--495101 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
495055 CCTGGGAAAC
*
495065 TCTATATCCTTCAGGGAT
1 TCTAAATCCTTCAGGGAT
*
495083 TCTAAATCCTTCTGGGAT
1 TCTAAATCCTTCAGGGAT
495101 T
1 T
495102 GTTATATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (18 bp):
TCTAAATCCTTCAGGGAT
Found at i:500822 original size:49 final size:49
Alignment explanation
Indices: 500769--500930 Score: 198
Period size: 49 Copynumber: 3.3 Consensus size: 49
500759 CAACGATGAC
500769 TTTTAGTATTTGTTTATTCTGCCATCTCGGGTTGCCCGACAATGATGGT
1 TTTTAGTATTTGTTTATTCTGCCATCTCGGGTTGCCCGACAATGATGGT
* * *
500818 TTTTAGTATTTGTTTATTCTACCATCTCGGGTTGCCCAAGAATGATGGCT
1 TTTTAGTATTTGTTTATTCTGCCATCTCGGGTTGCCCGACAATGATGG-T
* * * * ** * ***
500868 TTTTAGTATTTGATTATTCTGTCATCCCAGGTTGTTCGGCAATGATACC
1 TTTTAGTATTTGTTTATTCTGCCATCTCGGGTTGCCCGACAATGATGGT
500917 TTTTAGTATTTGTT
1 TTTTAGTATTTGTT
500931 CATACTATCT
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 58 0.61
50 37 0.39
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.45
Consensus pattern (49 bp):
TTTTAGTATTTGTTTATTCTGCCATCTCGGGTTGCCCGACAATGATGGT
Found at i:500901 original size:50 final size:49
Alignment explanation
Indices: 500754--500893 Score: 199
Period size: 49 Copynumber: 2.8 Consensus size: 49
500744 TCCCAATTTA
* **
500754 CCCAACAACGATGACTTTTAGTATTTGTTTATTCTGCCATCTCGGGTTG
1 CCCAACAATGATGGTTTTTAGTATTTGTTTATTCTGCCATCTCGGGTTG
* *
500803 CCCGACAATGATGGTTTTTAGTATTTGTTTATTCTACCATCTCGGGTTG
1 CCCAACAATGATGGTTTTTAGTATTTGTTTATTCTGCCATCTCGGGTTG
* * *
500852 CCCAAGAATGATGGCTTTTTAGTATTTGATTATTCTGTCATC
1 CCCAACAATGATGG-TTTTTAGTATTTGTTTATTCTGCCATC
500894 CCAGGTTGTT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
49 56 0.70
50 24 0.30
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (49 bp):
CCCAACAATGATGGTTTTTAGTATTTGTTTATTCTGCCATCTCGGGTTG
Found at i:505058 original size:64 final size:64
Alignment explanation
Indices: 504984--505106 Score: 183
Period size: 64 Copynumber: 1.9 Consensus size: 64
504974 ATCCCGATCA
* * * * * *
504984 GTATTAATCCTGCATGTGTTGCAGACATACCGCAGCTCTTTGTGAGCATCCTGTTATATAATCG
1 GTATTAATCCTGCATCTATTGCAGACATACCACAGCTCTTTATAAGCATCCTGATATATAATCG
*
505048 GTATTGATCCTGCATCTATTGCAGACATACCACAGCTCTTTATAAGCATCCTGATATAT
1 GTATTAATCCTGCATCTATTGCAGACATACCACAGCTCTTTATAAGCATCCTGATATAT
505107 TGCGTTTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (64 bp):
GTATTAATCCTGCATCTATTGCAGACATACCACAGCTCTTTATAAGCATCCTGATATATAATCG
Found at i:508203 original size:50 final size:52
Alignment explanation
Indices: 508147--508244 Score: 155
Period size: 50 Copynumber: 1.9 Consensus size: 52
508137 ATCTAAACTG
* **
508147 CATAATAATTAACTATTTAAATTTAAAT-ATTTAATAA-ATTTTCTTAACAT
1 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTAACAT
508197 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTA
1 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTA
508245 CCATTTGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 25 0.58
51 9 0.21
52 9 0.21
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (52 bp):
CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTAACAT
Found at i:508426 original size:14 final size:14
Alignment explanation
Indices: 508390--508440 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
508380 AAGAATTGAC
*
508390 AATTGAGAATAA-A
1 AATTGAGAACAAGA
* *
508403 ACATTAAGAACAAGC
1 A-ATTGAGAACAAGA
508418 AATTGAGAACAAGA
1 AATTGAGAACAAGA
508432 AATTGAGAA
1 AATTGAGAA
508441 TCAAATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.18
Consensus pattern (14 bp):
AATTGAGAACAAGA
Found at i:511388 original size:76 final size:75
Alignment explanation
Indices: 511262--511459 Score: 279
Period size: 76 Copynumber: 2.6 Consensus size: 75
511252 TAACAAAGTT
*
511262 TTGCACCCAACTCTAGTCGGATAAATCGAAGGTATCAAATGTGTGCTTAGCACTAGTAAGATAAA
1 TTGCACCCAACGCTAGTCGGATAAATC-AAGGTATCAAATGTGTGCTTAGCACTAGTAAGATAAA
511327 CCGACAATGAG
65 CCGACAATGAG
* **
511338 TTGCACCCAGCGCTAGTCGGATAAATTCAAGGTATCAAATGTGTGCTTAGCACTAGTTGGATAAA
1 TTGCACCCAACGCTAGTCGGATAAA-TCAAGGTATCAAATGTGTGCTTAGCACTAGTAAGATAAA
*
511403 CTGACAATGAG
65 CCGACAATGAG
* * * * *
511414 TTGCGCCCAACGCTAGTTGGATAAACTGACGATATCAAATGTGTGC
1 TTGCACCCAACGCTAGTCGGATAAA-TCAAGGTATCAAATGTGTGC
511460 CTATCACTGT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
76 107 0.98
77 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (75 bp):
TTGCACCCAACGCTAGTCGGATAAATCAAGGTATCAAATGTGTGCTTAGCACTAGTAAGATAAAC
CGACAATGAG
Found at i:515237 original size:76 final size:75
Alignment explanation
Indices: 515087--515295 Score: 220
Period size: 76 Copynumber: 2.7 Consensus size: 75
515077 GTGTCTAGAA
* * **
515087 GATAAATCATAACAAAGTTTTGCGCCCAACGCTAGTCAAATAAACCAATGATATCAAATGTGTGC
1 GATAAA-CA-AACAAAGATTTGCGCCCAATGCTAGTCGGATAAA-CAATGATATCAAATGTGTGC
* *
515152 CTAGCACTAGTGG
63 CCAACACTAGTGG
** * *
515165 GATAAACCGACAATGATTTGCGCCCAATGCTAGTCGGATAAACAGATGCTATCAAATGTGTGCCC
1 GATAAACAAACAAAGATTTGCGCCCAATGCTAGTCGGATAAACA-ATGATATCAAATGTGTGCCC
* *
515230 AATACTAGTTG
65 AACACTAGTGG
* * ** *
515241 GATATACAAACAAAGATTTGCGCCCAGTAATAGTCGGATAAACCAACGATATCAA
1 GATAAACAAACAAAGATTTGCGCCCAATGCTAGTCGGATAAA-CAATGATATCAA
515296 TCACTCATTT
Statistics
Matches: 108, Mismatches: 21, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
75 2 0.02
76 97 0.90
77 3 0.03
78 6 0.06
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (75 bp):
GATAAACAAACAAAGATTTGCGCCCAATGCTAGTCGGATAAACAATGATATCAAATGTGTGCCCA
ACACTAGTGG
Found at i:525562 original size:50 final size:52
Alignment explanation
Indices: 525502--525599 Score: 155
Period size: 50 Copynumber: 1.9 Consensus size: 52
525492 ATCTAAACCG
* **
525502 CATAATAATTAACTATTTAAATTTAAAT-ATTTAATAA-ATTTTCTTAACAT
1 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTAACAT
525552 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTA
1 CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTA
525600 CCATTTGTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
50 25 0.58
51 9 0.21
52 9 0.21
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (52 bp):
CATAATAATTAACTAATTAAAACTAAATAATTTAATAATATTTTCTTAACAT
Found at i:525780 original size:14 final size:14
Alignment explanation
Indices: 525744--525794 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
525734 AAGAATTGAC
*
525744 AATTGAGAATAA-A
1 AATTGAGAACAAGA
* *
525757 ACATTAAGAACAAGC
1 A-ATTGAGAACAAGA
525772 AATTGAGAACAAGA
1 AATTGAGAACAAGA
525786 AATTGAGAA
1 AATTGAGAA
525795 TCAAATTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
13 1 0.03
14 29 0.94
15 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.18, T:0.18
Consensus pattern (14 bp):
AATTGAGAACAAGA
Found at i:531665 original size:16 final size:15
Alignment explanation
Indices: 531626--531667 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
531616 AGATGATAAT
531626 TATTAATATATAATTA
1 TATTAAT-TATAATTA
*
531642 TATCAATTATAATATA
1 TATTAATTATAAT-TA
531658 TATTAATTAT
1 TATTAATTAT
531668 TATCAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:531839 original size:84 final size:84
Alignment explanation
Indices: 531749--531917 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
531739 AAATTAATAG
*
531749 CAAATAATAATTTAATATGCATTATATTAATTATTAATTGTTATTTACTTTGAGTAGAATTAAAA
1 CAAATAATAAATTAATATGCATTATATTAATTATTAATTGTTATTTACTTTGAGTAGAATTAAAA
531814 CTTAGAATTTTTAAGAACT
66 CTTAGAATTTTTAAGAACT
* *
531833 CAAATAATAAATTAATATGCGTTATATTAATTATTAATTGTTATTTACTTTGAGTAGAATTAGAA
1 CAAATAATAAATTAATATGCATTATATTAATTATTAATTGTTATTTACTTTGAGTAGAATTAAAA
531898 CTTAGAATTTTTAAGAACT
66 CTTAGAATTTTTAAGAACT
531917 C
1 C
531918 TACTTTAGCT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (84 bp):
CAAATAATAAATTAATATGCATTATATTAATTATTAATTGTTATTTACTTTGAGTAGAATTAAAA
CTTAGAATTTTTAAGAACT
Found at i:532344 original size:25 final size:25
Alignment explanation
Indices: 532308--532368 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
532298 CTCCTAAATT
*
532308 TTAATTTAATTATCTAAT-TTTTCA-A
1 TTAATTAAATTAT-TAATATTTT-ATA
*
532333 TTTATTAAATTATTAATATTTTATA
1 TTAATTAAATTATTAATATTTTATA
532358 TTAATTAAATT
1 TTAATTAAATT
532369 TTTGACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATTAAATTATTAATATTTTATA
Found at i:541200 original size:27 final size:27
Alignment explanation
Indices: 541157--541393 Score: 320
Period size: 27 Copynumber: 8.8 Consensus size: 27
541147 TGCGATTCGT
* *
541157 GGGT-AAATGACCAAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
541183 GGGTAAAATGATCGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
541210 GGGTAAAATGATCGAAATACCCTCAAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
541237 AGGTAAAATGATCGAAATACCCTCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
* * *
541264 GGGTAAAATGACCAAAATACCC-CTAAA
1 GGGTAAAATGATCGAAATACCCTC-GAA
*
541291 GGGTAAAATGACCGAAATACCCAT-GAA
1 GGGTAAAATGATCGAAATACCC-TCGAA
* *
541318 GGGTAAAATGATCGAAATACCCCCAAA
1 GGGTAAAATGATCGAAATACCCTCGAA
*
541345 GGGTAAAATGATCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATACCCTCGAA
541372 GGGTAAAATGA-CTGAAATACCC
1 GGGTAAAATGATC-GAAATACCC
541394 CATTGGGTAA
Statistics
Matches: 190, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
26 6 0.03
27 184 0.97
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.16
Consensus pattern (27 bp):
GGGTAAAATGATCGAAATACCCTCGAA
Found at i:544188 original size:17 final size:18
Alignment explanation
Indices: 544148--544189 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
544138 CCATTATGCT
544148 ATTAAATAGACATTTAAA
1 ATTAAATAGACATTTAAA
* *
544166 AATAAATATA-ATTTAAA
1 ATTAAATAGACATTTAAA
*
544183 TTTAAAT
1 ATTAAAT
544190 TATTAGTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
ATTAAATAGACATTTAAA
Found at i:547233 original size:196 final size:196
Alignment explanation
Indices: 546897--547292 Score: 630
Period size: 196 Copynumber: 2.0 Consensus size: 196
546887 ATGATGAGAG
* * *
546897 GACACTATCAAGGATTGCCAATTGTATTAACGAAAATATGAACAGGGTGTTAACAGAGGAATTTT
1 GACACTATCAAGGATTACCAATTGTATTAACGAAAATATGAACAGGGCGTTAACAGAGGAATTTC
* * *
546962 GAATTGAAGAAATCACAAAGGCAGTAAAGAATATAGCACTTTTAAAGGCTTCTAGTGTGGGCAAC
66 GAATTGAAGAAATCACAAAGGCAGTAAAGAATATAGCACCTTTAAAGGCTTCTAGAGTGGACAAC
* ** *
547027 TACCCCACTTTGTTTTAGCAAAAGTATTGGCATATTGCGGTGGAAGAAATAGCGAGTTTCTGCTT
131 TACCCCACTTTGTTTTACCAAAAGTATTGGCATATTGCGAAGGAAGAAATAGCGAGTTTCTACTT
547092 T
196 T
* *
547093 GACACTATCAGGGATTACCAATTGTATTAACGAAAATATGAACAGGGCGTTAATAGAGGAATTTC
1 GACACTATCAAGGATTACCAATTGTATTAACGAAAATATGAACAGGGCGTTAACAGAGGAATTTC
* * *
547158 GAATTGAAGAAATCACAACGGCAGTAAAGAATATAGCACCTTTAAAGGCTTTTAGAGTGGACAGC
66 GAATTGAAGAAATCACAAAGGCAGTAAAGAATATAGCACCTTTAAAGGCTTCTAGAGTGGACAAC
* * *
547223 TACTCCACTTTGTTTTACCAAAAGTATTGGCATATTGTGAAGGAAGAAATAGTGAGTTTCTACTT
131 TACCCCACTTTGTTTTACCAAAAGTATTGGCATATTGCGAAGGAAGAAATAGCGAGTTTCTACTT
547288 T
196 T
547289 GACA
1 GACA
547293 TATTAAACAC
Statistics
Matches: 182, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
196 182 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (196 bp):
GACACTATCAAGGATTACCAATTGTATTAACGAAAATATGAACAGGGCGTTAACAGAGGAATTTC
GAATTGAAGAAATCACAAAGGCAGTAAAGAATATAGCACCTTTAAAGGCTTCTAGAGTGGACAAC
TACCCCACTTTGTTTTACCAAAAGTATTGGCATATTGCGAAGGAAGAAATAGCGAGTTTCTACTT
T
Found at i:549357 original size:23 final size:23
Alignment explanation
Indices: 549308--549357 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
549298 ATGTCTAACT
* * * *
549308 GTAATATCTCGAAAATTACTATT
1 GTAATACCCCGAAAATTACAATA
549331 GTAATACCCCGAAAATTACAATA
1 GTAATACCCCGAAAATTACAATA
549354 GTAA
1 GTAA
549358 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (23 bp):
GTAATACCCCGAAAATTACAATA
Found at i:557961 original size:39 final size:39
Alignment explanation
Indices: 557916--558134 Score: 307
Period size: 39 Copynumber: 5.6 Consensus size: 39
557906 AACATATTTT
557916 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * * *
557955 TAAGTATTATGATATATGCTTGAATGTTATGCGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
557994 TGAGTATTATGATATATGCTTAAATGCTATGTGATTAAA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
558033 TGATTATTGTGATATAT-CTTTGAAA-GTTATGTGATTATA
1 TGAGTATTGTGATATATGC-TT-AAATGTTATGTGATTATA
558072 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
558111 TGTGTAATGTGATATACGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
558135 AGTGAATATG
Statistics
Matches: 159, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
38 4 0.03
39 151 0.95
40 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.19, T:0.44
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:567045 original size:17 final size:18
Alignment explanation
Indices: 567014--567047 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
567004 CTACAAAGTA
*
567014 AAAAAAAATATTAAATTG
1 AAAAAAAAGATTAAATTG
567032 AAAAAAAAGA-TAAATT
1 AAAAAAAAGATTAAATT
567048 TAATAACTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAAAAAAGATTAAATTG
Found at i:569307 original size:18 final size:18
Alignment explanation
Indices: 569286--569330 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 18
569276 GATAAAATTT
569286 TGTCATCATACAAAATAC
1 TGTCATCATACAAAATAC
569304 TG---TCA-ACAAAATAC
1 TGTCATCATACAAAATAC
569318 TGTCATCATACAA
1 TGTCATCATACAA
569331 CGCTGAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
14 11 0.48
15 3 0.13
17 3 0.13
18 6 0.26
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (18 bp):
TGTCATCATACAAAATAC
Found at i:580449 original size:18 final size:18
Alignment explanation
Indices: 580411--580449 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
580401 GAATTAAAAT
*
580411 ATTAATTAAACTAATTAA
1 ATTAATTAAACTAATGAA
* *
580429 ATTAATTAACCTAATGGA
1 ATTAATTAAACTAATGAA
580447 ATT
1 ATT
580450 TCCTATTCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (18 bp):
ATTAATTAAACTAATGAA
Found at i:583406 original size:54 final size:54
Alignment explanation
Indices: 583348--583453 Score: 149
Period size: 54 Copynumber: 2.0 Consensus size: 54
583338 TCGTCACTCG
* * *
583348 TGTAACTCACTGAGTTGCCCCACACGCCTGTGTGCCAAGCCGTGTGCTAGGCTA
1 TGTAACTCACTGAGTTGCCACACACGCCAGTGTGCCAAGCCGTGTGCCAGGCTA
* * * *
583402 TGTAACTCTCTTAGTTGCCACACACGCCAGTGTGCTAGGCCGTGTGCCAGGC
1 TGTAACTCACTGAGTTGCCACACACGCCAGTGTGCCAAGCCGTGTGCCAGGC
583454 CGTATGCTAG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.18, C:0.31, G:0.26, T:0.25
Consensus pattern (54 bp):
TGTAACTCACTGAGTTGCCACACACGCCAGTGTGCCAAGCCGTGTGCCAGGCTA
Found at i:583448 original size:12 final size:12
Alignment explanation
Indices: 583431--583470 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
583421 ACACACGCCA
583431 GTGTGCTAGGCC
1 GTGTGCTAGGCC
*
583443 GTGTGCCAGGCC
1 GTGTGCTAGGCC
*
583455 GTATGCTAGGCC
1 GTGTGCTAGGCC
583467 GTGT
1 GTGT
583471 AACTCGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (12 bp):
GTGTGCTAGGCC
Found at i:597947 original size:64 final size:63
Alignment explanation
Indices: 597878--598004 Score: 152
Period size: 63 Copynumber: 2.0 Consensus size: 63
597868 AGAAATGGTG
* * *
597878 AAATGGAGAAATAGGAAA-CATTTGGAAA-AAAT-TAAGGTTTTCTCCAAGATAAAAATGAAAAT
1 AAATGGAG-AA-ACGAAATCATTTGGAAATAAATGT--GGTTTTCTCCAAAATAAAAATAAAAAT
597940 GA
62 GA
* *
597942 AAATGGAGAAACGAAATTATTTGGAAATAAATGTGGTTTTCTCCAAAATGAAAATAAAAATGA
1 AAATGGAGAAACGAAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATAAAAATAAAAATGA
598005 CCTAAAAAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
62 5 0.09
63 37 0.67
64 12 0.22
65 1 0.02
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.25
Consensus pattern (63 bp):
AAATGGAGAAACGAAATCATTTGGAAATAAATGTGGTTTTCTCCAAAATAAAAATAAAAATGA
Found at i:612025 original size:41 final size:41
Alignment explanation
Indices: 611961--612039 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
611951 ACTTGCTTCA
*
611961 ATTGGTTAAAGGCCCTCTCACATTGAGGATCTCAATCTCAT
1 ATTGGTTAAAGGCCCTCTCACATTAAGGATCTCAATCTCAT
* * *
612002 ATTGGTTAAAGGCCTTCTTACATTAAGGATCTTAATCT
1 ATTGGTTAAAGGCCCTCTCACATTAAGGATCTCAATCT
612040 TATACCTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (41 bp):
ATTGGTTAAAGGCCCTCTCACATTAAGGATCTCAATCTCAT
Found at i:625619 original size:34 final size:34
Alignment explanation
Indices: 625557--625624 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
625547 TACACAGTTC
* *
625557 AACAGTCTTGAGCCTAAGCCCTTTTCAGTATCAGT
1 AACAGTCTTGAGCCTAAGCCCATCTCAGTA-CAGT
* *
625592 AACAGT-TTGGGCCTTAGCCCATCTCAGTACAGT
1 AACAGTCTTGAGCCTAAGCCCATCTCAGTACAGT
625625 GTCAAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.14
34 19 0.66
35 6 0.21
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.29
Consensus pattern (34 bp):
AACAGTCTTGAGCCTAAGCCCATCTCAGTACAGT
Found at i:635191 original size:2 final size:2
Alignment explanation
Indices: 635184--635230 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
635174 GATTGGTAAT
635184 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
635226 TG TG T
1 TG TG T
635231 TTATATTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:640960 original size:3 final size:3
Alignment explanation
Indices: 640954--640981 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
640944 TATTAATGAA
640954 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
640982 GGACTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:642673 original size:142 final size:142
Alignment explanation
Indices: 642424--642689 Score: 426
Period size: 142 Copynumber: 1.9 Consensus size: 142
642414 GACCTGATAC
* **
642424 GATCCACTCTACTGTAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCTGCTGTAACTCC
1 GATCCACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTCC
*
642489 AGGGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCT
66 AGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCT
642554 TCAATCTGATGT
131 TCAATCTGATGT
* * *
642566 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCT-TTATTTTAATCCGCTCCACTGTAACTT
1 GATCCACTCTACTGTAACTTCAGAGAGATAAGAT-CTGTGATTTTAATCCGCTCCACTGTAACTC
* * *
642630 TAGAGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
65 CAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT
642690 GAAATTCTTC
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
142 111 0.98
143 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (142 bp):
GATCCACTCTACTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGTAACTCC
AGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCT
TCAATCTGATGT
Found at i:642943 original size:95 final size:96
Alignment explanation
Indices: 642693--642974 Score: 476
Period size: 96 Copynumber: 2.9 Consensus size: 96
642683 AAGATCTGAA
* * *
642693 ATTCTTCAATCTATTCCACTGCCAACTAGGGAGATAGAATTATCGGATTCAATGTACTCCACTGT
1 ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTGT
* *
642758 AGTCACAGGAAGGTAAAATCTGCCATCTTCG
66 AGTCACAGGGAGGTAAAATTTGCCATCTTCG
642789 ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTGT
1 ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTGT
642854 AGTCACAGGGAGGTAAAATTTGCCATCTTCG
66 AGTCACAGGGAGGTAAAATTTGCCATCTTCG
* * *
642885 ATT-TTCAATCCATTCTACTGCCAACCAGGGAGATAGAATTATTGGCTTCAATGTACTCTACTGT
1 ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTGT
*
642949 AGTCACAAGGAGGTAAAATTTGCCAT
66 AGTCACAGGGAGGTAAAATTTGCCAT
642975 ATTTGATCTG
Statistics
Matches: 177, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
95 83 0.47
96 94 0.53
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (96 bp):
ATTCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTATCGGCTTCAATGTACTCTACTGT
AGTCACAGGGAGGTAAAATTTGCCATCTTCG
Found at i:643777 original size:88 final size:88
Alignment explanation
Indices: 642990--643769 Score: 1319
Period size: 88 Copynumber: 8.9 Consensus size: 88
642980 ATCTGCCCCA
* * * ** * *
642990 CTGTCGATGCAGGAGGGCAATATCTACTGTCTTCAACCAGCTTCACCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
* *
643055 GTTTGTGTTTTCGACCTGTTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * *
643078 CTGTCAATGCAAGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGGGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643143 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
643166 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACC-AGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
* * *
643230 GTTTGTGTCTTTGACCTTCTTCA
66 GTTTGTGTCTTCGACCTGCTTCG
*
643253 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCATCCAGCTCCATCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643318 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
643341 CTGTCAATGCAGGAAGGCAAGATCTTTGGTCTTCAACCAGCTCCATCACAACCGAGAGATGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643406 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
643429 CTGTCAATACAGGAAGGCAAGATCTTTTATCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643494 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* *
643517 CTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGATGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643582 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
* * *
643605 CTGTCAATACAGGAAGGCAAGATCTTTTGTCTTCAACCAGATCCATCACAACCAAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643670 GTTTGTGTCTTCGACCTGCTTCG
66 GTTTGTGTCTTCGACCTGCTTCG
*
643693 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCAAGAGAGGCAAG
1 CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
643758 GTTTGTGTCTTC
66 GTTTGTGTCTTC
643770 AATCTGCTCC
Statistics
Matches: 652, Mismatches: 39, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
87 82 0.13
88 570 0.87
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (88 bp):
CTGTCAATGCAGGAAGGCAAGATCTTTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAG
GTTTGTGTCTTCGACCTGCTTCG
Found at i:644045 original size:44 final size:44
Alignment explanation
Indices: 643766--644327 Score: 196
Period size: 44 Copynumber: 12.8 Consensus size: 44
643756 AGGTTTGTGT
**
643766 CTTCAATCTGCTCCGTTGTAA-TCTCAGGGAGATAAGA-C-CT-G
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAG
* * * * ** *
643807 ATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTTA-
1 CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCAC--TAG
* * * * * *
643851 TTTTAATCTGCTCCACTATAACTTCAGGGAGATAGGATTAC-CG
1 CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
** * * *
643894 ACTTTGATCTACTCCGCTGTAAGC-TCAGGGAGATAAGAT-A-TGAAATT
1 -CTTCAATCTGCTCCACTGTAA-CTTCAGGGAGATAAGATCACT---A-G
* * *
643941 CTTCAGTCTGTTCCACTGTAA-TCTCAGGGAAATAAGA-C-CT-G
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAG
* * * * * * * * *
643982 GTGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCATTGG
1 CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
* * * *
644026 TTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAG
1 CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
* * * *
644070 CTTCAATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTGCAATT
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATC-ACTA-G
* *** * * *
644116 TTTTGGTCTGTTCCACCGTAA-TCTCAGGGAAATAAGA-C-CT-G
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCACTAG
* * * * * ** *
644157 GTGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATC-CTTG
1 CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
* * * * *
644200 ATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTAG
1 -CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
* * *
644245 CTTCAATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTACAATT
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATC-ACTA-G
** * *
644291 CTTCGGTCTGTTCCACTGTAA-TCTCAGGGAAATAAGA
1 CTTCAATCTGCTCCACTGTAACT-TCAGGGAGATAAGA
644328 CCTGTATAAT
Statistics
Matches: 376, Mismatches: 112, Indels: 61
0.68 0.20 0.11
Matches are distributed among these distances:
41 77 0.20
42 9 0.02
43 6 0.02
44 183 0.49
45 11 0.03
46 90 0.24
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCACTAG
Found at i:644086 original size:175 final size:175
Alignment explanation
Indices: 643782--644331 Score: 879
Period size: 175 Copynumber: 3.1 Consensus size: 175
643772 TCTGCTCCGT
* * *
643782 TGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCC
1 TGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC
* * * ** *
643847 TTTATTTTAATCTGCTCCACTATAACTTCAGGGAGATAGGATTAC-CGACTTTGATCTACTCCGC
66 TTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAG-CTTCAATCTGCTCCGC
* * *
643911 TGTAAGCTCAGGGAGATAAGATATGAAATTCTTCAGTCTGTTCCAC
130 TGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCAC
* *
643957 TGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTTAGAGAGATAAGATCA
1 TGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC
*
644022 TTGGTTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
66 TTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
* * *
644087 GTAATCTCAGGGAGATAAGATCTGCAATTTTTTGGTCTGTTCCAC
131 GTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCAC
* *
644132 CGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAAAGAGATAAGATCC
1 TGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC
*
644197 TTGATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
66 TTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
644262 GTAATCTCAGGGAGATAAGATCT-ACAATTCTTCGGTCTGTTCCAC
131 GTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTGTTCCAC
644307 TGTAATCTCAGGGAAATAAGACCTG
1 TGTAATCTCAGGGAAATAAGACCTG
644332 TATAATGAAC
Statistics
Matches: 345, Mismatches: 28, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
175 344 1.00
176 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (175 bp):
TGTAATCTCAGGGAAATAAGACCTGGTGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC
TTGATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCT
GTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTGTTCCAC
Found at i:645543 original size:7 final size:7
Alignment explanation
Indices: 645531--645592 Score: 83
Period size: 7 Copynumber: 9.0 Consensus size: 7
645521 TTAGCCTCTC
645531 CATTTTT
1 CATTTTT
645538 CATTTTT
1 CATTTTT
645545 CATTTTT
1 CATTTTT
645552 -ATTTTT
1 CATTTTT
645558 CATTTTT
1 CATTTTT
*
645565 CA-TTCT
1 CATTTTT
645571 CATTTTT
1 CATTTTT
645578 CATTTATT
1 CATTT-TT
*
645586 TATTTTT
1 CATTTTT
645593 TGACTCAGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
6 11 0.22
7 32 0.65
8 6 0.12
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:645555 original size:13 final size:14
Alignment explanation
Indices: 645531--645592 Score: 83
Period size: 13 Copynumber: 4.5 Consensus size: 14
645521 TTAGCCTCTC
645531 CATTTTTCATTTTT
1 CATTTTTCATTTTT
645545 CATTTTT-ATTTTT
1 CATTTTTCATTTTT
*
645558 CATTTTTCA-TTCT
1 CATTTTTCATTTTT
645571 CATTTTTCATTTATT
1 CATTTTTCATTT-TT
*
645586 TATTTTT
1 CATTTTT
645593 TGACTCAGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
13 25 0.60
14 10 0.24
15 7 0.17
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:645555 original size:20 final size:20
Alignment explanation
Indices: 645532--645592 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
645522 TAGCCTCTCC
645532 ATTTTTCATTTTTCATTTTT
1 ATTTTTCATTTTTCATTTTT
* *
645552 ATTTTTCATTTTTCATTCTC
1 ATTTTTCATTTTTCATTTTT
*
645572 ATTTTTCATTTATTTATTTTT
1 ATTTTTCATTT-TTCATTTTT
645593 TGACTCAGAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 29 0.83
21 6 0.17
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.72
Consensus pattern (20 bp):
ATTTTTCATTTTTCATTTTT
Found at i:646490 original size:26 final size:27
Alignment explanation
Indices: 646454--646525 Score: 67
Period size: 26 Copynumber: 2.6 Consensus size: 27
646444 TCTCATTTTC
*
646454 TTTTTCTTTTTCTTT-TATTTTTGATTT
1 TTTTTCTTTTT-TTTCTACTTTTGATTT
*
646481 TTTTTC-TTTTTTTCTGCTTTTGATTT
1 TTTTTCTTTTTTTTCTACTTTTGATTT
*
646507 TGATTTTTTTATTTTTTCT
1 T--TTTTCTT-TTTTTTCT
646526 TTTCCTTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.08
26 15 0.41
27 6 0.16
28 4 0.11
29 1 0.03
30 8 0.22
ACGTcount: A:0.07, C:0.08, G:0.06, T:0.79
Consensus pattern (27 bp):
TTTTTCTTTTTTTTCTACTTTTGATTT
Found at i:646508 original size:32 final size:33
Alignment explanation
Indices: 646449--646550 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 33
646439 TGGCCTCTCA
* *
646449 TTTTCTTTTTCTTTTTCTTTTATTTTTGATTTT
1 TTTTCTTTTTCTTCTGCTTTTATTTTTGATTTT
646482 TTTTCTTTTT-TTCTGCTTTTGA-TTTTGATTTT
1 TTTTCTTTTTCTTCTGCTTTT-ATTTTTGATTTT
* * *
646514 TTTAT-TTTTTCTTTTCCTTCTT-TTTTTGCTTTT
1 TTT-TCTTTTTCTTCTGCTT-TTATTTTTGATTTT
646547 TTTT
1 TTTT
646551 TTTGGAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
32 27 0.46
33 30 0.51
34 2 0.03
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.79
Consensus pattern (33 bp):
TTTTCTTTTTCTTCTGCTTTTATTTTTGATTTT
Found at i:646541 original size:39 final size:36
Alignment explanation
Indices: 646480--646553 Score: 85
Period size: 39 Copynumber: 2.0 Consensus size: 36
646470 ATTTTTGATT
*
646480 TTTTTTCTTTTTTTCTGCTTTTGATTTTGATTTTTTTA
1 TTTTTTCTTTTCTTCTGCTTTTGATTTT--TTTTTTTA
** *
646518 TTTTTTCTTTTCCTTCTTTTTTTGCTTTTTTTTTTT
1 TTTTTTCTTTT-CTTCTGCTTTTGATTTTTTTTTTT
646554 GGAATTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 7 0.23
38 11 0.35
39 13 0.42
ACGTcount: A:0.04, C:0.11, G:0.05, T:0.80
Consensus pattern (36 bp):
TTTTTTCTTTTCTTCTGCTTTTGATTTTTTTTTTTA
Found at i:650312 original size:109 final size:108
Alignment explanation
Indices: 650006--650413 Score: 590
Period size: 109 Copynumber: 3.7 Consensus size: 108
649996 ATTTGGTTAG
* * *
650006 ACGAGAAATCGAAACCCAGCACTTTA-GAGCACGTTCCTCAAATTTCCAAACGCAAAACATTGCC
1 ACGAGAAATCGAAACCCAGTACCTTAGGA-CACGTTCCTCGAATTTCCAAACGCAAAACATTGCC
*
650070 TTATTTTG-AAATTTTTGAAAAGGATATTTAGCTATTTGGTTGA
65 TTATTTTGAAAATTTTTGAAAAGGATATTTAGCTATTTGGTCGA
* * * * **
650113 ACGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTCGAATTTCCAAACATAAAACATTG
1 ACGAG--AAATCGAAACCCAGTACCTTAGGACACG-TTCCTCGAATTTCCAAACGCAAAACATTG
*
650178 CCTTATTTTGAAAATTTTTGAAAAGGATATTAAG-TCATTTGGTCGA
63 CCTTATTTTGAAAATTTTTGAAAAGGATATTTAGCT-ATTTGGTCGA
*
650224 ACGAGAAATCGAAACCCAGTACCTTAGGACACGTTCCTCGAATTTCAAAACGCAAAACATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGACACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
650289 TATTTTTGAAAAGTTTTT-AAAAGGATATTTAGCTATTTGGTCGA
66 TA-TTTTGAAAA-TTTTTGAAAAGGATATTTAGCTATTTGGTCGA
* *
650333 ACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCT
1 ACGAGAAATCGAAACCCAGTACCTTAGGACACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
650398 TATTTTGAAATATTTT
66 TATTTTGAAA-ATTTT
650414 CCTTTTTTGA
Statistics
Matches: 269, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
107 5 0.02
108 42 0.16
109 143 0.53
110 43 0.16
111 36 0.13
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Consensus pattern (108 bp):
ACGAGAAATCGAAACCCAGTACCTTAGGACACGTTCCTCGAATTTCCAAACGCAAAACATTGCCT
TATTTTGAAAATTTTTGAAAAGGATATTTAGCTATTTGGTCGA
Found at i:650410 original size:18 final size:17
Alignment explanation
Indices: 650387--650428 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
650377 TCCAAACGCA
650387 AAATATTGCCTTATTTTG
1 AAATATTGCCTT-TTTTG
*
650405 AAATATTTTCCTTTTTTG
1 AAATA-TTGCCTTTTTTG
650423 AAATAT
1 AAATAT
650429 GAAGTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 15 0.68
19 6 0.27
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (17 bp):
AAATATTGCCTTTTTTG
Found at i:650766 original size:21 final size:20
Alignment explanation
Indices: 650740--650779 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
650730 TAAATATGCA
*
650740 TATATATATATATATAAAATT
1 TATATATAT-TAGATAAAATT
650761 TATATATATTAGATAAAAT
1 TATATATATTAGATAAAAT
650780 ATATGTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATATATATTAGATAAAATT
Found at i:650869 original size:3 final size:3
Alignment explanation
Indices: 650863--650902 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
650853 TATTAATGAA
650863 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
650903 GGACTAAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:662397 original size:22 final size:22
Alignment explanation
Indices: 662335--662404 Score: 113
Period size: 22 Copynumber: 3.2 Consensus size: 22
662325 CTAGTTCAAA
* **
662335 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
662357 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
662379 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
662401 CATG
1 CATG
662405 TCAAGTAATC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:664729 original size:16 final size:17
Alignment explanation
Indices: 664695--664736 Score: 61
Period size: 16 Copynumber: 2.5 Consensus size: 17
664685 CAAAAGAAAC
664695 ATAT-AATATTCATATAA
1 ATATAAATATTCA-ATAA
664712 ATATAAATATTC-ATAA
1 ATATAAATATTCAATAA
664728 ATATAAATA
1 ATATAAATA
664737 AATATCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.54
17 4 0.17
18 7 0.29
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATTCAATAA
Found at i:668485 original size:103 final size:103
Alignment explanation
Indices: 668306--668522 Score: 425
Period size: 103 Copynumber: 2.1 Consensus size: 103
668296 AATGTAAACA
668306 AAACTAAGACAACTTGATTAAAACAAAATAAAAATATGCTACACTGAATTACGGTAGATCAAACT
1 AAACTAAGACAACTTGATTAAAACAAAATAAAAATATGCTACACTGAATTACGGTAGATCAAACT
668371 CCCCCACACTGAATTCATTGTTTGTCCTCAAGCAATGC
66 CCCCCACACTGAATTCATTGTTTGTCCTCAAGCAATGC
668409 AAACTAAGACAACTTGATTAAAACAAAATAAAAATATGCTACACTGAATTACGGTAGATCAAACT
1 AAACTAAGACAACTTGATTAAAACAAAATAAAAATATGCTACACTGAATTACGGTAGATCAAACT
668474 CCCCCACACTGAATTCATTGTTTGTCCTCAAGCAATGC
66 CCCCCACACTGAATTCATTGTTTGTCCTCAAGCAATGC
*
668512 AAACAAAGACA
1 AAACTAAGACA
668523 GTAATTAAAA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.24
Consensus pattern (103 bp):
AAACTAAGACAACTTGATTAAAACAAAATAAAAATATGCTACACTGAATTACGGTAGATCAAACT
CCCCCACACTGAATTCATTGTTTGTCCTCAAGCAATGC
Found at i:686892 original size:35 final size:35
Alignment explanation
Indices: 686853--686923 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
686843 AATAAAAGAA
686853 AAAATAAAATTAAAATCAGTGATTTTCATCGTTGG
1 AAAATAAAATTAAAATCAGTGATTTTCATCGTTGG
686888 AAAATAAAATTAAAATCAGTGATTTTCATCGTTGG
1 AAAATAAAATTAAAATCAGTGATTTTCATCGTTGG
686923 A
1 A
686924 GGCTTCGTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (35 bp):
AAAATAAAATTAAAATCAGTGATTTTCATCGTTGG
Found at i:695680 original size:34 final size:35
Alignment explanation
Indices: 695636--695702 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
695626 CAGTAAAATG
* *
695636 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
695670 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
695703 CTGGTGTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:695706 original size:14 final size:15
Alignment explanation
Indices: 695630--695706 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
695620 GATTGGCAGT
* *
695630 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
695644 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
*
695658 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
695678 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
695693 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
695707 TGTTTAATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:696908 original size:27 final size:27
Alignment explanation
Indices: 696878--696946 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
696868 AATAATCAAT
*
696878 TCAATATACAACAAGGTT-AAGACATA-A
1 TCAATAT-CAACAA-ATTCAAGACATATA
696905 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATC-AACAAATTCAAGACATATA
*
696933 TCAAAATCCAACAA
1 TCAATAT-CAACAA
696947 TCTAAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 3 0.08
27 20 0.56
28 12 0.33
29 1 0.03
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (27 bp):
TCAATATCAACAAATTCAAGACATATA
Found at i:701970 original size:43 final size:42
Alignment explanation
Indices: 701923--702063 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 42
701913 TTTTAAGTGT
*
701923 TGATTCCACCATATATTTGATTGTAAAAGAGGTTGCTATGTGC
1 TGATTCCACCGTATATTTGATTGTAAAAG-GGTTGCTATGTGC
* * * * *
701966 TGATTCC-CCGTATCA-CTGAATATAAAGGTGGTTGCTAAGTGC
1 TGATTCCACCGTAT-ATTTGATTGTAAAAG-GGTTGCTATGTGC
* * ** *
702008 AGATTCCATCGTACCTTTGATTGTGAAAGGGATTGCTATGTGC
1 TGATTCCACCGTATATTTGATTGTAAAAGGG-TTGCTATGTGC
702051 TGATTCC-CCGTAT
1 TGATTCCACCGTAT
702064 CACTAAATTT
Statistics
Matches: 74, Mismatches: 20, Indels: 9
0.72 0.19 0.09
Matches are distributed among these distances:
42 38 0.51
43 36 0.49
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.35
Consensus pattern (42 bp):
TGATTCCACCGTATATTTGATTGTAAAAGGGTTGCTATGTGC
Found at i:702013 original size:85 final size:84
Alignment explanation
Indices: 701903--702091 Score: 254
Period size: 85 Copynumber: 2.2 Consensus size: 84
701893 TTATTGATTC
** ** *
701903 TAAAGGTGGTTTTTAAGTGTTGATTCCACCATATATTTGATTGTAAAAGAGG-TTGCTATGTGCT
1 TAAAGGTGGTTGCTAAGTGCAGATTCCACCATACATTTGATTGTAAAAG-GGATTGCTATGTGCT
*
701967 GATTCCCCGTATCACTGAAT
65 GATTCCCCGTATCACTAAAT
* * * *
701987 ATAAAGGTGGTTGCTAAGTGCAGATTCCATCGTACCTTTGATTGTGAAAGGGATTGCTATGTGCT
1 -TAAAGGTGGTTGCTAAGTGCAGATTCCACCATACATTTGATTGTAAAAGGGATTGCTATGTGCT
702052 GATTCCCCGTATCACTAAAT
65 GATTCCCCGTATCACTAAAT
*
702072 TTAAGGTGGTTGCTAAGTGC
1 TAAAGGTGGTTGCTAAGTGC
702092 TGAATCTACT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
84 21 0.23
85 71 0.77
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (84 bp):
TAAAGGTGGTTGCTAAGTGCAGATTCCACCATACATTTGATTGTAAAAGGGATTGCTATGTGCTG
ATTCCCCGTATCACTAAAT
Found at i:707718 original size:25 final size:25
Alignment explanation
Indices: 707683--707732 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
707673 TTGGATAAAA
707683 AGGGGTCGCTAAGTGCAGATTCCCG
1 AGGGGTCGCTAAGTGCAGATTCCCG
* **
707708 AGGGGTTGCTAAGTGTTGATTCCCG
1 AGGGGTCGCTAAGTGCAGATTCCCG
707733 GAATTATTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.26
Consensus pattern (25 bp):
AGGGGTCGCTAAGTGCAGATTCCCG
Found at i:707855 original size:85 final size:84
Alignment explanation
Indices: 707744--707945 Score: 269
Period size: 85 Copynumber: 2.4 Consensus size: 84
707734 AATTATTGAT
* * * *
707744 TATAAACGTGGTAGCTAAGTGCTGATTCTACCGTATATTTGATTGTGAAAGGGGTTGCTATGTGC
1 TATAAA-GTGGTTGCTAAGTGTTGATTCCACCGCATATTTGATTGTGAAAGGGGTTGCTATGTGC
*
707809 TAATTCCCCGTATCACTGAA
65 TAATTCCCCGTATCACTAAA
* * * * *
707829 TATAATGGTGGTTGCTAAGTGTTGATTCCACGGCATCTTTTATTGTGAAAGGGGTTGCTATGTGT
1 TATAA-AGTGGTTGCTAAGTGTTGATTCCACCGCATATTTGATTGTGAAAGGGGTTGCTATGTGC
*
707894 TGATTCCCCGTATCACTAAA
65 TAATTCCCCGTATCACTAAA
* *
707914 TTTAAAGTGGTTGCTAAGTGTTGAATCCACCG
1 TATAAAGTGGTTGCTAAGTGTTGATTCCACCG
707946 AGTAACGGAA
Statistics
Matches: 101, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
84 24 0.24
85 77 0.76
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (84 bp):
TATAAAGTGGTTGCTAAGTGTTGATTCCACCGCATATTTGATTGTGAAAGGGGTTGCTATGTGCT
AATTCCCCGTATCACTAAA
Found at i:707857 original size:42 final size:42
Alignment explanation
Indices: 707711--707937 Score: 167
Period size: 43 Copynumber: 5.4 Consensus size: 42
707701 ATTCCCGAGG
* * * *
707711 GGTTGCTAAGTGTTGATTCCCGGAATTATTGATTATAAACGT
1 GGTTGCTAAGTGTTGATTCCCCGTATCATTGATTATAAAGGT
* * * *
707753 GGTAGCTAAGTGCTGATTCTACCGTAT-ATTTGATTGTGAAAGG-
1 GGTTGCTAAGTGTTGATTC-CCCGTATCA-TTGATTAT-AAAGGT
* * * * * *
707796 GGTTGCTATGTGCTAATTCCCCGTATCACTGAATATAATGGT
1 GGTTGCTAAGTGTTGATTCCCCGTATCATTGATTATAAAGGT
* * * * *
707838 GGTTGCTAAGTGTTGATTCCACGGCATCTTTTATTGTGAAAGG-
1 GGTTGCTAAGTGTTGATTCC-CCGTATCATTGATTAT-AAAGGT
* **
707881 GGTTGCTATGTGTTGATTCCCCGTATCACTAAATT-TAAA-GT
1 GGTTGCTAAGTGTTGATTCCCCGTATCA-TTGATTATAAAGGT
707922 GGTTGCTAAGTGTTGA
1 GGTTGCTAAGTGTTGA
707938 ATCCACCGAG
Statistics
Matches: 143, Mismatches: 33, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
40 1 0.01
41 22 0.15
42 52 0.36
43 60 0.42
44 8 0.06
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (42 bp):
GGTTGCTAAGTGTTGATTCCCCGTATCATTGATTATAAAGGT
Found at i:711361 original size:39 final size:39
Alignment explanation
Indices: 711318--711562 Score: 217
Period size: 39 Copynumber: 6.3 Consensus size: 39
711308 CAGGGATATT
* * * *
711318 GAAGTACAACAGCGACACGTATATGTATTCAAGGGTACC
1 GAAGTACAACAGCGGCACGTATGTGCAATCAAGGGTACC
**
711357 GAAGTACAACAAAGGCACGTATGTGCAATC-AGGCGTACC
1 GAAGTACAACAGCGGCACGTATGTGCAATCAAGG-GTACC
* * * * *
711396 AAAGTACAATAG-GGCCACATATGTGCATTCAGGGGTACC
1 GAAGTACAACAGCGG-CACGTATGTGCAATCAAGGGTACC
* * * *
711435 GAAGTACTACAGTGGCACGTATGTACAATCAGGGGTACC
1 GAAGTACAACAGCGGCACGTATGTGCAATCAAGGGTACC
* * ** * *
711474 GACGTACAACAGCGGCACATATGTGC-ATTTAGCAGTACT
1 GAAGTACAACAGCGGCACGTATGTGCAATCAAG-GGTACC
* * * *
711513 GAAGTACAATAGGGGCACGTATCTGCAATCAAGGGTATC
1 GAAGTACAACAGCGGCACGTATGTGCAATCAAGGGTACC
711552 GAAGTACAACA
1 GAAGTACAACA
711563 TTTAACTTCT
Statistics
Matches: 161, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
38 8 0.05
39 145 0.90
40 8 0.05
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (39 bp):
GAAGTACAACAGCGGCACGTATGTGCAATCAAGGGTACC
Found at i:711426 original size:78 final size:77
Alignment explanation
Indices: 711318--711562 Score: 260
Period size: 78 Copynumber: 3.1 Consensus size: 77
711308 CAGGGATATT
* * * * *
711318 GAAGTACAACAGCGACACGTATATGTATTCAAGGGTACCGAAGTACAACAAAGGCACGTATGTGC
1 GAAGTACAACAGCGGCACATATGTGCATTCAAGGGTACCGAAGTACAACAGAGGCACGTATGTGC
711383 AATCAGGCGTACC
66 AATCAGG-GTACC
* * * * * *
711396 AAAGTACAATAG-GGCCACATATGTGCATTCAGGGGTACCGAAGTACTACAGTGGCACGTATGTA
1 GAAGTACAACAGCGG-CACATATGTGCATTCAAGGGTACCGAAGTACAACAGAGGCACGTATGTG
711460 CAATCAGGGGTACC
65 CAATCA-GGGTACC
* * * * * * *
711474 GACGTACAACAGCGGCACATATGTGCATT-TAGCAGTACTGAAGTACAATAGGGGCACGTATCTG
1 GAAGTACAACAGCGGCACATATGTGCATTCAAG-GGTACCGAAGTACAACAGAGGCACGTATGTG
*
711538 CAATCAAGGGTATC
65 CAATC-AGGGTACC
711552 GAAGTACAACA
1 GAAGTACAACA
711563 TTTAACTTCT
Statistics
Matches: 137, Mismatches: 25, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
77 2 0.01
78 130 0.95
79 5 0.04
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (77 bp):
GAAGTACAACAGCGGCACATATGTGCATTCAAGGGTACCGAAGTACAACAGAGGCACGTATGTGC
AATCAGGGTACC
Found at i:729839 original size:2 final size:2
Alignment explanation
Indices: 729832--729856 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
729822 ACAAATATTC
729832 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
729857 ATAATTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:736218 original size:44 final size:46
Alignment explanation
Indices: 736126--736211 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
736116 TCAAAGTTGT
*
736126 AATGGAATAGAGCTGTAATCAGTAATTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTATAATCAGTAATTCAATTGTTTGGTTGAATGG
*
736172 AATGGAATAGAGCTATAAT-AG-AATTC-TTGTGTTTGGTTGA
1 AATGGAATAGAGCTATAATCAGTAATTCAAT-TGTTTGGTTGA
736212 TCGGAATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
43 1 0.03
44 16 0.43
45 2 0.05
46 18 0.49
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (46 bp):
AATGGAATAGAGCTATAATCAGTAATTCAATTGTTTGGTTGAATGG
Found at i:741585 original size:163 final size:164
Alignment explanation
Indices: 741388--741717 Score: 468
Period size: 163 Copynumber: 2.0 Consensus size: 164
741378 ATTTAATAAT
* * *
741388 ATAAATAGTAGATCTAAATAAAATTATTACTATTTATATTTAGGGATTTTTTTTGATGATCTTTT
1 ATAAACAGTAGATATAAATAAAATTATTACTATTTATATTTAAGGATTTTTTTTGATGATCTTTT
* * *
741453 ATTTGGGGTAAAGGGTGAAAAGTAAAAATTTAGGGGGAAAATAATAAGTTTTGAAGGTTG-GGAG
66 ATTTAGGGTAAAGGGTGAAAAGTAAAAATTTAGGGGGAAAATAAAAAGTTTTG-AGGGTGAGGAG
* *
741517 AATAAAA-TTTGAGAGGG-AAAGTAAATGGGGGTAA
130 AATAAAATTTTG-GAGGGAAAAGTAAATAGGGGAAA
* * * *
741551 ATAAACAGTATATATAAATAAAATTATTACTATTTATGTTTAAGGATTTTTTTTTATGATTTTTT
1 ATAAACAGTAGATATAAATAAAATTATTACTATTTATATTTAAGGATTTTTTTTGATGATCTTTT
* * * *
741616 ATTTATGGTAAAGGGTGAAAAGTAAAAGTTTAGGGGGGAAATAAAAAGTTTTGAGGGTGAGGGGA
66 ATTTAGGGTAAAGGGTGAAAAGTAAAAATTTAGGGGGAAAATAAAAAGTTTTGAGGGTGAGGAGA
*
741681 ATAAAATTTTGGGGGGAAAAGTAAATAGGGGAAA
131 ATAAAATTTTGGAGGGAAAAGTAAATAGGGGAAA
741715 ATA
1 ATA
741718 TTCAAAAAAC
Statistics
Matches: 147, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
162 5 0.03
163 120 0.82
164 22 0.15
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35
Consensus pattern (164 bp):
ATAAACAGTAGATATAAATAAAATTATTACTATTTATATTTAAGGATTTTTTTTGATGATCTTTT
ATTTAGGGTAAAGGGTGAAAAGTAAAAATTTAGGGGGAAAATAAAAAGTTTTGAGGGTGAGGAGA
ATAAAATTTTGGAGGGAAAAGTAAATAGGGGAAA
Found at i:741809 original size:29 final size:30
Alignment explanation
Indices: 741765--741821 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
741755 GGGGTGCGAC
*
741765 GGGAGGGAAGTAAAAGTCTTAGGGGGAAGT
1 GGGAGGGAAGTAAAAGTATTAGGGGGAAGT
* *
741795 GGGAGGG-TGTAAAAGTATTGGGGGGAA
1 GGGAGGGAAGTAAAAGTATTAGGGGGAA
741822 ATTAAAAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.49, T:0.18
Consensus pattern (30 bp):
GGGAGGGAAGTAAAAGTATTAGGGGGAAGT
Found at i:753059 original size:11 final size:11
Alignment explanation
Indices: 753037--753072 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
753027 AACAAATCCT
753037 CTCTCAAATTTC
1 CTCTC-AATTTC
753049 CTCTCAATTTC
1 CTCTCAATTTC
753060 CTCTCAATTTC
1 CTCTCAATTTC
753071 CT
1 CT
753073 TCCAAATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 19 0.79
12 5 0.21
ACGTcount: A:0.19, C:0.36, G:0.00, T:0.44
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:753089 original size:11 final size:11
Alignment explanation
Indices: 753036--753091 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
753026 AAACAAATCC
753036 TCTCTCAAATT
1 TCTCTCAAATT
753047 TCCTCTC-AATT
1 T-CTCTCAAATT
753058 TCCTCTC-AATT
1 T-CTCTCAAATT
753069 TC-CTTCCAAATT
1 TCTC-T-CAAATT
753081 TCTCTCAAATT
1 TCTCTCAAATT
753092 CATATTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
9 1 0.03
10 2 0.05
11 24 0.60
12 12 0.30
13 1 0.03
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:753091 original size:23 final size:22
Alignment explanation
Indices: 753036--753091 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
753026 AAACAAATCC
753036 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAATTTCCTCTCAATT
753058 TCCTCTC-AATTTCCT-TCCAAATT
1 T-CTCTCAAATTTCCTCT-C-AATT
753081 TCTCTCAAATT
1 TCTCTCAAATT
753092 CATATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.03
22 15 0.50
23 14 0.47
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:753105 original size:51 final size:51
Alignment explanation
Indices: 753050--753149 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
753040 TCAAATTTCC
**
753050 TCTCAATTTCCTCTCAATTTCCTTCCAAATTTCTCTCAAAT-TCATATTTAA
1 TCTCAATTAACTCTCAATTTCCTTCCAAATTTCTCTCAAATCTC-TATTTAA
* ** *
753101 TCTCAATTAACTCTCGATTTCCTTTTAAATTTCTCTTAAATCTCTATTT
1 TCTCAATTAACTCTCAATTTCCTTCCAAATTTCTCTCAAATCTCTATTT
753150 TTAAATAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 40 0.95
52 2 0.05
ACGTcount: A:0.26, C:0.25, G:0.01, T:0.48
Consensus pattern (51 bp):
TCTCAATTAACTCTCAATTTCCTTCCAAATTTCTCTCAAATCTCTATTTAA
Found at i:761086 original size:13 final size:13
Alignment explanation
Indices: 761060--761102 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
761050 TTAATTCTAG
* *
761060 TTAATTTAAATAA
1 TTAATATAATTAA
*
761073 TTAATATTATTAA
1 TTAATATAATTAA
*
761086 TTATTATAATTAA
1 TTAATATAATTAA
761099 TTAA
1 TTAA
761103 AATTGATGTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TTAATATAATTAA
Found at i:763080 original size:41 final size:41
Alignment explanation
Indices: 763023--763106 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
763013 GCCGGTGAAT
763023 TTAGTTGGGGGTCTACCATCTTGGCAACATTATATCGGAGG
1 TTAGTTGGGGGTCTACCATCTTGGCAACATTATATCGGAGG
763064 TTAGTTGGGGGTCTACCATCTTGGCAACATTATATCGGAGG
1 TTAGTTGGGGGTCTACCATCTTGGCAACATTATATCGGAGG
763105 TT
1 TT
763107 GTCTGTCACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (41 bp):
TTAGTTGGGGGTCTACCATCTTGGCAACATTATATCGGAGG
Found at i:764677 original size:29 final size:29
Alignment explanation
Indices: 764618--765093 Score: 727
Period size: 29 Copynumber: 15.9 Consensus size: 29
764608 GTAAAAAAAT
*
764618 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
764648 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
764677 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
764706 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
764735 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
764764 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
764793 CTTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
764822 CCTAATTTAATTAAAAACACTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
764851 CTTAATTTAATTAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
764880 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
764910 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
764939 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
764968 CCTAATTTAATTAAAAACCTATTTTAAAACCCTAAACCTTAA
1 CCTAATTTAATTAAAAACC----CT--AACCC-------TAA
765010 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
765039 CCTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
765069 CTTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
765094 ATTAACAAAA
Statistics
Matches: 418, Mismatches: 13, Indels: 31
0.90 0.03 0.07
Matches are distributed among these distances:
29 306 0.73
30 78 0.19
33 1 0.00
35 5 0.01
36 5 0.01
38 1 0.00
42 22 0.05
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:765015 original size:71 final size:70
Alignment explanation
Indices: 764923--765057 Score: 252
Period size: 71 Copynumber: 1.9 Consensus size: 70
764913 AATTTAATTA
764923 AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCT
1 AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCT
764988 ATTTT
66 ATTTT
*
764993 AAAACCCTAAACCTTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
1 AAAACCCT-AACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACC
765058 CTAAACCCTA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
70 8 0.13
71 55 0.87
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (70 bp):
AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCT
ATTTT
Found at i:768331 original size:125 final size:125
Alignment explanation
Indices: 768104--768383 Score: 476
Period size: 125 Copynumber: 2.3 Consensus size: 125
768094 CCACGAGGGC
* *
768104 GCGATTTTATACTATTTGCTCAGAAACGTC--AAAAAATTTATTTCTTACATGACCAACTGTAGT
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGTAGC
*
768167 GAAATCGCGTCCACGAGGGCATGATTTCACAATTCCTTCTCAAATAGCATCCTGGTAGAA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTGGTAGAA
*
768227 GTGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGTAGC
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGTAGC
* *
768292 GAAATCGCGTCCACGAGGGCACGATTTCACAATTTCTTCTTAAATAGCATCCTGGTAGAA
66 GAAATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTGGTAGAA
768352 GCGATTTTATACTATTTGACT-AGAAACGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
768384 CTCGAAATAA
Statistics
Matches: 147, Mismatches: 7, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
123 29 0.20
125 116 0.79
126 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (125 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAAATTATTTCTTACATGACCAACTGTAGC
GAAATCGCGTCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTGGTAGAA
Found at i:769608 original size:29 final size:27
Alignment explanation
Indices: 769534--769609 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 27
769524 CCAGGAAATC
769534 TTTTTAA-TAATTTGA-TTTAAAATTA
1 TTTTTAATTAATTTGATTTTAAAATTA
*
769559 TTTTTAATTAGTATTCGATTTTAAAATTA
1 TTTTTAATTA--ATTTGATTTTAAAATTA
*
769588 TTATTTAATTTAATTTAATTTT
1 TT-TTTAA-TTAATTTGATTTT
769610 TATTATTGTG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
28 5 0.12
29 20 0.48
30 5 0.12
31 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.59
Consensus pattern (27 bp):
TTTTTAATTAATTTGATTTTAAAATTA
Found at i:775876 original size:33 final size:31
Alignment explanation
Indices: 775810--775876 Score: 73
Period size: 33 Copynumber: 2.1 Consensus size: 31
775800 GAAATTTTAA
**
775810 TAAATAAAAAATATATAAATTTATTAAGTAT
1 TAAATAAAAAATATATAAATTTATTAAAAAT
*
775841 TAAATTAAAATAATATA-AATATTTTTTAAAAAT
1 TAAA-TAAAA-AATATATAA-ATTTATTAAAAAT
775874 TAA
1 TAA
775877 TATGGGCGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 4 0.13
32 7 0.23
33 19 0.63
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (31 bp):
TAAATAAAAAATATATAAATTTATTAAAAAT
Found at i:780783 original size:16 final size:16
Alignment explanation
Indices: 780762--780792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
780752 CTATGCATGC
*
780762 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
780778 AAAATACAAAAGACA
1 AAAATACAAAAGACA
780793 TAATAGTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:786675 original size:22 final size:21
Alignment explanation
Indices: 786624--786676 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
786614 GAACATAATC
786624 AAAACATCAT-CTAGACAAATT
1 AAAACA-CATACTAGACAAATT
*
786645 AAATA-ACATACTAGGAGAAATT
1 AAA-ACACATACTA-GACAAATT
786667 AAAACACATA
1 AAAACACATA
786677 ATTAGGGACT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 8 0.30
22 16 0.59
ACGTcount: A:0.57, C:0.15, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAACACATACTAGACAAATT
Found at i:791448 original size:45 final size:43
Alignment explanation
Indices: 791399--791482 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 43
791389 GCTAGTACGA
* * *
791399 TGTGGTTAAACTACTCAAAAGGTGCAGATAAAGCTGTTCAAACGG
1 TGTGGATAAACAACTC-AAAGGTGCAGATAAA-CTGCTCAAACGG
* *
791444 TGTGGATAAACAACTCAACGGTGTAGATAAACTGCTCAA
1 TGTGGATAAACAACTCAAAGGTGCAGATAAACTGCTCAA
791483 CTTCCTCCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 7 0.21
44 13 0.38
45 14 0.41
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (43 bp):
TGTGGATAAACAACTCAAAGGTGCAGATAAACTGCTCAAACGG
Found at i:791483 original size:21 final size:22
Alignment explanation
Indices: 791405--791482 Score: 77
Period size: 21 Copynumber: 3.5 Consensus size: 22
791395 ACGATGTGGT
* *
791405 TAAACTACTCAAAAGGTGCAGA
1 TAAACTACTCAAACGGTGTAGA
** *
791427 TAAAGCTGTTCAAACGGTGTGGA
1 TAAA-CTACTCAAACGGTGTAGA
*
791450 TAAACAACTC-AACGGTGTAGA
1 TAAACTACTCAAACGGTGTAGA
*
791471 TAAACTGCTCAA
1 TAAACTACTCAA
791483 CTTCCTCCAT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 18 0.42
22 8 0.19
23 17 0.40
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (22 bp):
TAAACTACTCAAACGGTGTAGA
Found at i:797106 original size:62 final size:62
Alignment explanation
Indices: 797031--797151 Score: 224
Period size: 62 Copynumber: 2.0 Consensus size: 62
797021 CAATGAGTTT
*
797031 AAATATAACCATGAGTAGCTAAATTCTAAGTGGTTAGTTGGTGGAAATGATGGGTAACTCTG
1 AAATATAACCATGAGCAGCTAAATTCTAAGTGGTTAGTTGGTGGAAATGATGGGTAACTCTG
*
797093 AAATATAACCATGAGCAGCTAAATTCTAAGTGGTTGGTTGGTGGAAATGATGGGTAACT
1 AAATATAACCATGAGCAGCTAAATTCTAAGTGGTTAGTTGGTGGAAATGATGGGTAACT
797152 ATGATTTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (62 bp):
AAATATAACCATGAGCAGCTAAATTCTAAGTGGTTAGTTGGTGGAAATGATGGGTAACTCTG
Found at i:803695 original size:12 final size:12
Alignment explanation
Indices: 803678--803732 Score: 53
Period size: 12 Copynumber: 4.6 Consensus size: 12
803668 TTAATAAAAT
803678 ACTATTAAATTA
1 ACTATTAAATTA
803690 ACTATTAAATTTA
1 ACTATTAAA-TTA
803703 A-T-TTAATATTAA
1 ACTATTAA-ATT-A
*
803715 ACTATTAAAATA
1 ACTATTAAATTA
803727 A-TATTA
1 ACTATTA
803733 TTTTTAGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 11 0.30
12 15 0.41
13 7 0.19
14 4 0.11
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (12 bp):
ACTATTAAATTA
Found at i:803710 original size:37 final size:36
Alignment explanation
Indices: 803663--803732 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
803653 TGCTTTAATA
*
803663 TTAAATTAATA-AAATACTATTAAATTAACTATTAAAT
1 TTAAATTAATATAAA-ACTATTAAAATAA-TATTAAAT
* *
803700 TTAATTTAATATTAAACTATTAAAATAATATTA
1 TTAAATTAATATAAAACTATTAAAATAATATTA
803733 TTTTTAGAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 5 0.17
37 22 0.76
38 2 0.07
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (36 bp):
TTAAATTAATATAAAACTATTAAAATAATATTAAAT
Found at i:809501 original size:39 final size:39
Alignment explanation
Indices: 809456--809535 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
809446 ATGGCTTGAA
809456 AATGGTTACTTGTGACATGTTTTGGTACATATTTGAACT
1 AATGGTTACTTGTGACATGTTTTGGTACATATTTGAACT
809495 AATGGTTACTTGTGACATGTTTTGGTACATATTTGAACT
1 AATGGTTACTTGTGACATGTTTTGGTACATATTTGAACT
809534 AA
1 AA
809536 GGCATTATGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (39 bp):
AATGGTTACTTGTGACATGTTTTGGTACATATTTGAACT
Found at i:812946 original size:16 final size:15
Alignment explanation
Indices: 812925--812979 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
812915 TCTAGGTATG
812925 TGAAGAGACTTGAAGA
1 TGAAGAGACTTGAA-A
812941 TGAAGAG--TTAGAAA
1 TGAAGAGACTT-GAAA
812955 TGTGAAGAGACTTGAATA
1 --TGAAGAGACTTGAA-A
812973 TGAAGAG
1 TGAAGAG
812980 TTACACACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
14 3 0.09
15 3 0.09
16 21 0.64
17 3 0.09
18 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.31, T:0.22
Consensus pattern (15 bp):
TGAAGAGACTTGAAA
Found at i:812963 original size:32 final size:32
Alignment explanation
Indices: 812922--812982 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
812912 GTTTCTAGGT
812922 ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
1 ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
*
812954 ATGTGAAGAGACTTGAATATGAAGAGTTA
1 ATGTGAAGAGACTTGAAGATGAAGAGTTA
812983 CACACATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.43, C:0.03, G:0.30, T:0.25
Consensus pattern (32 bp):
ATGTGAAGAGACTTGAAGATGAAGAGTTAGAA
Found at i:813050 original size:39 final size:39
Alignment explanation
Indices: 812996--813087 Score: 166
Period size: 39 Copynumber: 2.4 Consensus size: 39
812986 ACATGCATGT
*
812996 AGATGAATAGTCACAACTCCTATAGCATTTAAGTGATGA
1 AGATGAATAGTCACAACTCCTATAGCACTTAAGTGATGA
*
813035 AGATGAATAGTCACAACTCCTATAGCACTTAAGTGATGT
1 AGATGAATAGTCACAACTCCTATAGCACTTAAGTGATGA
813074 AGATGAATAGTCAC
1 AGATGAATAGTCAC
813088 TTACAACTCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 51 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.27
Consensus pattern (39 bp):
AGATGAATAGTCACAACTCCTATAGCACTTAAGTGATGA
Found at i:818576 original size:16 final size:16
Alignment explanation
Indices: 818526--818568 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
818516 GGTTGGGGGG
*
818526 AATGAAATAGAGCTGT
1 AATGGAATAGAGCTGT
818542 AATGGAATAGAGCTGT
1 AATGGAATAGAGCTGT
818558 AATGGAATAGA
1 AATGGAATAGA
818569 ACCGTAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.44, C:0.05, G:0.28, T:0.23
Consensus pattern (16 bp):
AATGGAATAGAGCTGT
Found at i:818645 original size:44 final size:46
Alignment explanation
Indices: 818558--818646 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 46
818548 ATAGAGCTGT
*
818558 AATGGAATAGAACCGTAATCAGTAATTCAGTTGTTTGGTTGAATGG
1 AATGGAATAGAACCGCAATCAGTAATTCAGTTGTTTGGTTGAATGG
* *
818604 AATGGAATAGAACTGCAAT-AGT-ATTC-TTGTGTTTGGTTGAATG
1 AATGGAATAGAACCGCAATCAGTAATTCAGT-TGTTTGGTTGAATG
818647 TAATATGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 1 0.03
44 18 0.46
45 3 0.08
46 17 0.44
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (46 bp):
AATGGAATAGAACCGCAATCAGTAATTCAGTTGTTTGGTTGAATGG
Found at i:818778 original size:26 final size:26
Alignment explanation
Indices: 818748--818797 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
818738 GTTATTAAAT
* **
818748 TTTAATAAGATTATTATTAAATATAA
1 TTTAATAAAATTAAAATTAAATATAA
818774 TTTAATAAAATTAAAATTAAATAT
1 TTTAATAAAATTAAAATTAAATAT
818798 TTTAGTCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTAATAAAATTAAAATTAAATATAA
Found at i:819238 original size:26 final size:27
Alignment explanation
Indices: 819203--819277 Score: 89
Period size: 31 Copynumber: 2.6 Consensus size: 27
819193 TAAAAAAATC
819203 AAAACTCATAGTTCTTTATGTTATTCA
1 AAAACTCATAGTTCTTTATGTTATTCA
*
819230 AAAAC-CATAGTCCTTGATTTTATGTTATTCA
1 AAAACTCATAG---TT--CTTTATGTTATTCA
819261 AAAACTCATAGTTCTTT
1 AAAACTCATAGTTCTTT
819278 GTATTATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
26 5 0.12
27 8 0.20
29 4 0.10
31 18 0.45
32 5 0.12
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (27 bp):
AAAACTCATAGTTCTTTATGTTATTCA
Found at i:823385 original size:56 final size:50
Alignment explanation
Indices: 823319--823664 Score: 313
Period size: 50 Copynumber: 6.8 Consensus size: 50
823309 ATTTGGGTAA
* * * *
823319 AGAGATCCCATGTAAGACCATGTCTAGGACATGGCATTGACATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
823375 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
823425 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
823475 AGAGGTCCCCTGTAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** ** * * * * *
823525 AGAACTCTAAGGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * * * * *
823574 AAACATCTCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
823623 AAACATCCCATGTAAGACCATGTCTGGGATATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
823665 TGTTATTATC
Statistics
Matches: 259, Mismatches: 30, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
48 1 0.00
49 86 0.33
50 129 0.50
53 3 0.01
55 1 0.00
56 39 0.15
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:823596 original size:49 final size:49
Alignment explanation
Indices: 823536--823664 Score: 231
Period size: 49 Copynumber: 2.6 Consensus size: 49
823526 GAACTCTAAG
*
823536 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCTCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCCCAT
823585 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCCCAT
1 GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCCCAT
* *
823634 GTAAGACCATGTCTGGGATATGGCTTTGGCA
1 GTAAGACCATATCTGGGATATGGCATTGGCA
823665 TGTTATTATC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 77 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (49 bp):
GTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGAAACATCCCAT
Found at i:825734 original size:26 final size:26
Alignment explanation
Indices: 825698--825748 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
825688 CTGAGTATGA
825698 ACGTGAATTTGTCAGACTCTGCAAGC
1 ACGTGAATTTGTCAGACTCTGCAAGC
825724 ACGTGAATTTGTCAGACTCTGCAAG
1 ACGTGAATTTGTCAGACTCTGCAAG
825749 TATGCTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (26 bp):
ACGTGAATTTGTCAGACTCTGCAAGC
Found at i:829851 original size:50 final size:50
Alignment explanation
Indices: 829797--829973 Score: 221
Period size: 50 Copynumber: 3.5 Consensus size: 50
829787 GGTCCAATGC
829797 AAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTTCATAT
1 AAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTTCATAT
* * **
829847 AAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCTTC-CGT
1 AAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGT-TTCATAT
* * * ** **
829897 AAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCCATAT
1 AAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTTCATAT
* *
829947 AAGACCATATATGGGAAATGGCATTGG
1 AAGACCATATCTGGGACATGGCATTGG
829974 TAGTACAAGA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.01
50 104 0.96
51 3 0.03
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (50 bp):
AAGACCATATCTGGGACATGGCATTGGCACCGAGATGAGAGGTTTCATAT
Found at i:830004 original size:49 final size:49
Alignment explanation
Indices: 829939--830073 Score: 207
Period size: 49 Copynumber: 2.8 Consensus size: 49
829929 ATATGAGAAC
* * * *
829939 TCCCATATAAGACCATATATGGGAAATGGCATTGGTAGTACAAGAAACA
1 TCCCATGTAAGACCATATTTGGGATATGGCATTGGCAGTACAAGAAACA
*
829988 TCCCATGTAAAACCATATTTGGGATATGGCATTGGCAGTACAAGAAACA
1 TCCCATGTAAGACCATATTTGGGATATGGCATTGGCAGTACAAGAAACA
* *
830037 TCCCATGTAAGACCATGTTTGGGATATGGCTTTGGCA
1 TCCCATGTAAGACCATATTTGGGATATGGCATTGGCA
830074 TGTTATTATC
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 78 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (49 bp):
TCCCATGTAAGACCATATTTGGGATATGGCATTGGCAGTACAAGAAACA
Found at i:833730 original size:130 final size:128
Alignment explanation
Indices: 833587--833834 Score: 379
Period size: 130 Copynumber: 1.9 Consensus size: 128
833577 TGTTGTGCAG
* * ** *
833587 TTTGCCAATAGCTAAAAACAGTAAAATCAACAAAATGAGCAATCAATAAGAATCAAACAGTACAA
1 TTTGCAAAGAGCTAAAAACAACAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTAC-A
*
833652 AAAAAAGTAAAAACAGACAAACCCATTTAAATTTGAACTGAAAGAACACAAAAGCAAAACTGTAA
65 AAAAAAGTAAAAACAAACAAACCCATTTAAA-TTGAACTGAAAGAACACAAAAGCAAAACTGTAA
* * * *
833717 TTTGCAAAGAGCTAAGAACAACAAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAGTACAG
1 TTTGCAAAGAGCTAAAAACAACAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTACAA
*
833782 AAAAAGTAAAAACAAACAAACCCATTTTAATTGAACTGAAAGAACACAAAAGC
66 AAAAAGTAAAAACAAACAAACCCATTTAAATTGAACTGAAAGAACACAAAAGC
833835 GAAGACCGTA
Statistics
Matches: 107, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
128 23 0.21
129 29 0.27
130 55 0.51
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (128 bp):
TTTGCAAAGAGCTAAAAACAACAAAATCAACAAAAGGAGCAATCAATAAGAATCAAACAGTACAA
AAAAAGTAAAAACAAACAAACCCATTTAAATTGAACTGAAAGAACACAAAAGCAAAACTGTAA
Found at i:833898 original size:130 final size:129
Alignment explanation
Indices: 833609--833883 Score: 369
Period size: 129 Copynumber: 2.1 Consensus size: 129
833599 TAAAAACAGT
*
833609 AAAATCAACAAAATG-AGCAATCAATAAGAATCAAACAGTACAAAAAAAAGTAAAAACAGACAAA
1 AAAATCAACAAAA-GAAGCAATCAATAAGAATCAAACAGTACAAAAAAAAGTAAAAACAAACAAA
* *
833673 CCCATTTAAATTTGAACTGAAAGAACACAAAAGCAAAACTGTAATTTGCAAAGAGCTAAGAACAA
65 CCCATTTAAATTTGAACTGAAAGAACACAAAAGCAAAACCGTAATTT-CAAAGAACTAAGAACAA
833738 C
129 C
** * *
833739 AAAATCAACAAAAGGGGCAATCAATAAGAATCAAATAGTAC-AGAAAAAGTAAAAACAAACAAAC
1 AAAATCAACAAAAGAAGCAATCAATAAGAATCAAACAGTACAAAAAAAAGTAAAAACAAACAAAC
* * * *
833803 CCATTTTAA-TTGAACTGAAAGAACACAAAAGCGAAGACCGTAGTTT-AAAGAACTAAGAACAGC
66 CCATTTAAATTTGAACTGAAAGAACACAAAAGC-AAAACCGTAATTTCAAAGAACTAAGAACAAC
*
833866 TAAATCAATCAACAAGAA
1 AAAATCAA-CAA-AAGAA
833884 TCAAATAGTA
Statistics
Matches: 128, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
127 22 0.17
128 26 0.20
129 43 0.34
130 37 0.29
ACGTcount: A:0.56, C:0.16, G:0.13, T:0.15
Consensus pattern (129 bp):
AAAATCAACAAAAGAAGCAATCAATAAGAATCAAACAGTACAAAAAAAAGTAAAAACAAACAAAC
CCATTTAAATTTGAACTGAAAGAACACAAAAGCAAAACCGTAATTTCAAAGAACTAAGAACAAC
Found at i:839890 original size:7 final size:7
Alignment explanation
Indices: 839878--839914 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
839868 ATTAACCATG
839878 AATATTT
1 AATATTT
839885 AATATTT
1 AATATTT
839892 AATATTT
1 AATATTT
839899 AATATTT
1 AATATTT
839906 AATATTT
1 AATATTT
839913 AA
1 AA
839915 AAGTCTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
AATATTT
Found at i:842897 original size:37 final size:35
Alignment explanation
Indices: 842804--842897 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 35
842794 TTCTCCAAAT
* *
842804 TCACATTTCAATTCAATTTCACTTTTTCACTTTCAA
1 TCACAATTCAATTCAA-TTCACTTTTCCACTTTCAA
*
842840 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAA
1 TCACAATTCAATTC--AATTCACTTTTCCA-CTTTCAA
842878 GTCA-ATATTCAATTCAATTC
1 -TCACA-ATTCAATTCAATTC
842898 TACACATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
36 13 0.26
37 16 0.32
38 9 0.18
39 12 0.24
ACGTcount: A:0.32, C:0.23, G:0.01, T:0.44
Consensus pattern (35 bp):
TCACAATTCAATTCAATTCACTTTTCCACTTTCAA
Found at i:843264 original size:22 final size:24
Alignment explanation
Indices: 843222--843266 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
843212 CTACTAAGTT
843222 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
843246 TACTT-CTTTTCT-ACTTAATTC
1 TACTTACTTTTCTAACTTAATTC
843267 TTTGCCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.43
23 7 0.33
24 5 0.24
ACGTcount: A:0.24, C:0.22, G:0.00, T:0.53
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:844020 original size:7 final size:7
Alignment explanation
Indices: 844004--844032 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
843994 TCTTTTAATT
844004 TAAT-AA
1 TAATAAA
844010 TAATAAA
1 TAATAAA
844017 TAATAAA
1 TAATAAA
844024 TAATAAA
1 TAATAAA
844031 TA
1 TA
844033 TCTTATGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:861354 original size:24 final size:24
Alignment explanation
Indices: 861327--861378 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
861317 AATCAAAGTC
* *
861327 AAATATATTATGCT-ACTAAATGCT
1 AAATATATTATACTCA-TAAATACT
861351 AAATATATTATACTCATAAATACT
1 AAATATATTATACTCATAAATACT
861375 AAAT
1 AAAT
861379 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTCATAAATACT
Found at i:865720 original size:24 final size:24
Alignment explanation
Indices: 865678--865729 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
865668 AATCAAAGTC
** *
865678 AAATATATTATGTTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
865702 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
865726 AAAT
1 AAAT
865730 CTTCAAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:866970 original size:2 final size:2
Alignment explanation
Indices: 866965--867004 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
866955 ATGTGTGTGT
866965 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
867005 ACTCTGAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:868139 original size:3 final size:3
Alignment explanation
Indices: 868133--868162 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
868123 TAACATCATC
*
868133 TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
868163 CATTGTTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:869762 original size:21 final size:21
Alignment explanation
Indices: 869726--869767 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
869716 AAAATTATTA
869726 AAAACTATAAAAAATAAAAAT
1 AAAACTATAAAAAATAAAAAT
869747 AAAA-TATAAAATAATAAAAAT
1 AAAACTATAAAA-AATAAAAAT
869768 TACATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAACTATAAAAAATAAAAAT
Found at i:870174 original size:28 final size:28
Alignment explanation
Indices: 870143--870204 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
870133 GTTTTATCAT
870143 TTTTATACTCTTT-TTTAATTTTTAATAA
1 TTTTATACT-TTTATTTAATTTTTAATAA
* **
870171 TTTTATAGTTTTATTTAATTTTTTGTAA
1 TTTTATACTTTTATTTAATTTTTAATAA
870199 TTTTAT
1 TTTTAT
870205 TTTTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 3 0.10
28 27 0.90
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (28 bp):
TTTTATACTTTTATTTAATTTTTAATAA
Found at i:870257 original size:15 final size:15
Alignment explanation
Indices: 870239--870278 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
870229 ATTTTTGCAA
*
870239 TTTTCTATTTTCTAT
1 TTTTTTATTTTCTAT
*
870254 TTTTTTATTTTTTAT
1 TTTTTTATTTTCTAT
870269 TTTTTTATTT
1 TTTTTTATTT
870279 ATAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTATTTTCTAT
Found at i:870272 original size:7 final size:7
Alignment explanation
Indices: 870238--870312 Score: 51
Period size: 7 Copynumber: 9.7 Consensus size: 7
870228 TATTTTTGCA
*
870238 ATTTTCT
1 ATTTTTT
*
870245 ATTTTCT
1 ATTTTTT
870252 ATTTTTTT
1 A-TTTTTT
870260 ATTTTTT
1 ATTTTTT
870267 ATTTTTTT
1 A-TTTTTT
*
870275 ATTTATAAT
1 ATTT-T-TT
870284 ATTTTTAT
1 ATTTTT-T
*
870292 AATTATTAT
1 -ATT-TTTT
870301 ATTTTTT
1 ATTTTTT
870308 ATTTT
1 ATTTT
870313 GTAACTTTTC
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
7 26 0.46
8 19 0.34
9 9 0.16
10 2 0.04
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (7 bp):
ATTTTTT
Found at i:870288 original size:15 final size:15
Alignment explanation
Indices: 870255--870311 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
870245 ATTTTCTATT
* *
870255 TTTTTATTTTTTATT
1 TTTTTATTTATTATA
*
870270 TTTTTATTTATAATA
1 TTTTTATTTATTATA
870285 TTTTTATAATTATTATA
1 TTTTTAT--TTATTATA
870302 TTTTTTATTT
1 -TTTTTATTT
870312 TGTAACTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 19 0.54
16 2 0.06
17 7 0.20
18 7 0.20
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTTATTTATTATA
Found at i:870951 original size:39 final size:39
Alignment explanation
Indices: 870863--870997 Score: 208
Period size: 38 Copynumber: 3.6 Consensus size: 39
870853 ATTTTAAAAA
870863 TTAAAA-T-AAAAATTAAAAAAAGTATTTTAAAA-ATATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAGA-ATT
870900 TTAAAATTAAAAAATT-AAAAAAGTATTTTAAAAGAATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAGAATT
*
870938 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAGTATT
1 TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAGAATT
*
870977 TTAAAGTTAAAAAA-TAAAAAA
1 TTAAAATTAAAAAATTAAAAAA
870998 TAAAAATAAA
Statistics
Matches: 92, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
37 6 0.07
38 44 0.48
39 42 0.46
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (39 bp):
TTAAAATTAAAAAATTAAAAAAAGTATTTTAAAAGAATT
Found at i:870971 original size:11 final size:11
Alignment explanation
Indices: 870957--870981 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
870947 AAAAATTAAA
870957 AAAAGTATTTT
1 AAAAGTATTTT
870968 AAAAGTATTTT
1 AAAAGTATTTT
870979 AAA
1 AAA
870982 GTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:872823 original size:36 final size:38
Alignment explanation
Indices: 872743--872824 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 38
872733 CCCTACCTGC
*
872743 AAAATGTTTGGTTATTGGGCTTGGAGCCTGAATGCTCTGGAG
1 AAAATGTTTGGTTATTGGGCTTGGAGCCTG-A-G--CAGGAG
872785 AAAATGTTTGGTTATTGGGCTTGGAGCCTG-G-AGGAG
1 AAAATGTTTGGTTATTGGGCTTGGAGCCTGAGCAGGAG
872821 AAAA
1 AAAA
872825 ATAAATTGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
36 8 0.21
39 1 0.03
42 30 0.77
ACGTcount: A:0.26, C:0.10, G:0.34, T:0.30
Consensus pattern (38 bp):
AAAATGTTTGGTTATTGGGCTTGGAGCCTGAGCAGGAG
Found at i:875295 original size:21 final size:22
Alignment explanation
Indices: 875266--875307 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
875256 TTTCTTGTTG
875266 CCTCTGCTGCTGCCTCTACTTC
1 CCTCTGCTGCTGCCTCTACTTC
*
875288 CCTC-GCTGTTGCCTCTACTT
1 CCTCTGCTGCTGCCTCTACTT
875308 TAAGTTGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.05, C:0.43, G:0.14, T:0.38
Consensus pattern (22 bp):
CCTCTGCTGCTGCCTCTACTTC
Found at i:883470 original size:2 final size:2
Alignment explanation
Indices: 883456--883495 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
883446 GTAACCTTAT
*
883456 TA TA TA TG T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
883496 GTAAAGGTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:884027 original size:17 final size:17
Alignment explanation
Indices: 883994--884027 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
883984 TTGTGTTTTG
*
883994 TGCAAAAAGGGCTAAAT
1 TGCAAAAAGGGCAAAAT
*
884011 TGCAAAAAGTGCAAAAT
1 TGCAAAAAGGGCAAAAT
884028 GTTAGGGGCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (17 bp):
TGCAAAAAGGGCAAAAT
Found at i:884467 original size:2 final size:2
Alignment explanation
Indices: 884429--884459 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
884419 ATAAGCATGA
884429 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 A
884460 CGTATATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:884894 original size:42 final size:42
Alignment explanation
Indices: 884831--885030 Score: 287
Period size: 42 Copynumber: 4.8 Consensus size: 42
884821 GAATGTAATA
884831 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
1 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
* *
884873 CAGACTTTACGTCTAGTAGGCTTAATGCCGATGAAATAATTT
1 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
* * *
884915 CAGACTTTACGTCTAGCAGGCTTAATGTCGGTGAAACAATAT
1 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
** *
884957 CAGACTTTACGTCTAGCAGGCTTAATGCCACTGAAA-CATTT
1 CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
* *
884998 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTTTACGTCTAGCAGGCTTAA-TGCCGGTG
885031 TACTGAATCA
Statistics
Matches: 141, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
40 3 0.02
41 28 0.20
42 110 0.78
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (42 bp):
CAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAATTT
Done.