Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1532
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 192937 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:533327 original size:2 final size:2
Alignment explanation
Indices: 533320--533389 Score: 113
Period size: 2 Copynumber: 35.0 Consensus size: 2
533310 TAAATTATAT
* * *
533320 TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TG TC TG TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
533362 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
533390 AAGGTAAAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50
Consensus pattern (2 bp):
TC
Found at i:538380 original size:17 final size:17
Alignment explanation
Indices: 538358--538393 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
538348 CTGTCCTTCT
538358 TACCTTTTAAGGAGAAC
1 TACCTTTTAAGGAGAAC
538375 TACCTTTTAAGGAGAAC
1 TACCTTTTAAGGAGAAC
538392 TA
1 TA
538394 TCCCATAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (17 bp):
TACCTTTTAAGGAGAAC
Found at i:538551 original size:2 final size:2
Alignment explanation
Indices: 538544--538625 Score: 155
Period size: 2 Copynumber: 41.0 Consensus size: 2
538534 TGCACATGCA
*
538544 TC TC TC TC TC TC TC TC GC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
538586 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
538626 ACACACACAC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.00, C:0.50, G:0.01, T:0.49
Consensus pattern (2 bp):
TC
Found at i:538630 original size:2 final size:2
Alignment explanation
Indices: 538625--538664 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
538615 CTCTCTCTCT
** *
538625 CA CA CA CA CA CA CA CA CA CA CA TG CA CG CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
538665 AACCAGGTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.47, G:0.05, T:0.03
Consensus pattern (2 bp):
CA
Found at i:540483 original size:2 final size:2
Alignment explanation
Indices: 540476--540514 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
540466 TGGGATCCTT
540476 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
540515 GATAAATATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:551884 original size:1 final size:1
Alignment explanation
Indices: 551878--551906 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
551868 TAGGCTTTGA
551878 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
551907 TGCGCACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:553304 original size:21 final size:21
Alignment explanation
Indices: 553280--553345 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
553270 GTTTTGGCAG
553280 AAGTATTAAGTTTCCGCTAAA
1 AAGTATTAAGTTTCCGCTAAA
* * ** *
553301 AAGTA-CACACTTTTGGC--AG
1 AAGTATTA-AGTTTCCGCTAAA
553320 AAGTATTAAGTTTCCGCTAAA
1 AAGTATTAAGTTTCCGCTAAA
553341 AAGTA
1 AAGTA
553346 CACACTAGCC
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
21 17 0.55
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
AAGTATTAAGTTTCCGCTAAA
Found at i:553315 original size:40 final size:40
Alignment explanation
Indices: 553271--553351 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
553261 CATTTCTACG
553271 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC
1 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC
553311 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC
1 TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC
553351 T
1 T
553352 AGCCATTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (40 bp):
TTTTGGCAGAAGTATTAAGTTTCCGCTAAAAAGTACACAC
Found at i:558778 original size:60 final size:60
Alignment explanation
Indices: 558710--558893 Score: 332
Period size: 60 Copynumber: 3.1 Consensus size: 60
558700 CATATAAATC
* *
558710 AGCATCAGGACGATTAACACAGTTCTGGAAAAATCTCCTCCACGACCCTCGTTATAATGT
1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
558770 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
**
558830 AGCATCAGGACGATTATTACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
1 AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
558890 AGCA
1 AGCA
558894 ATGTCCTTTT
Statistics
Matches: 120, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 120 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (60 bp):
AGCATCAGGACGATTAACACAGCTCTGGAAAAATCTCCTCCACGAGCCTCGTTATAATGT
Found at i:571657 original size:18 final size:18
Alignment explanation
Indices: 571636--571677 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
571626 CTCTTGATTT
571636 AGCTATATAGCTTGAAAA
1 AGCTATATAGCTTGAAAA
* *
571654 AGCTATATAGCTTTATAA
1 AGCTATATAGCTTGAAAA
571672 AGCTAT
1 AGCTAT
571678 TCAAACTAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (18 bp):
AGCTATATAGCTTGAAAA
Found at i:575806 original size:19 final size:19
Alignment explanation
Indices: 575782--575818 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
575772 CTCATGAAAT
575782 TTTTTTTTCAAAGTGCGTA
1 TTTTTTTTCAAAGTGCGTA
*
575801 TTTTTTTTCAAGGTGCGT
1 TTTTTTTTCAAAGTGCGT
575819 TAGCACACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.11, G:0.19, T:0.54
Consensus pattern (19 bp):
TTTTTTTTCAAAGTGCGTA
Found at i:576115 original size:2 final size:2
Alignment explanation
Indices: 576071--576095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
576061 CATCACTTCA
576071 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
576096 NNNNNNNNNN
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:578213 original size:20 final size:20
Alignment explanation
Indices: 578188--578228 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
578178 GTTGTGTTTT
*
578188 TAAAATACGTGTGAAGATTG
1 TAAAATACGTGTGAAAATTG
578208 TAAAATACGTGTGAAAATTG
1 TAAAATACGTGTGAAAATTG
578228 T
1 T
578229 CTCTTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (20 bp):
TAAAATACGTGTGAAAATTG
Found at i:581915 original size:229 final size:228
Alignment explanation
Indices: 581513--581944 Score: 855
Period size: 229 Copynumber: 1.9 Consensus size: 228
581503 TGTAAATTTC
581513 ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA
1 ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA
581578 ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC
66 ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC
581643 CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG
131 CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG
581708 TTTTGTTATAAAAAAAATGTTGTTGTTTATACT
196 TTTTGTTATAAAAAAAATGTTGTTGTTTATACT
581741 ANTGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTG
1 A-TGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTG
581806 AATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTT
65 AATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTT
581871 CCAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTT
130 CCAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTT
581936 GTTTTGTTA
195 GTTTTGTTA
581945 ATGTTGTTGT
Statistics
Matches: 203, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
228 1 0.00
229 202 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (228 bp):
ATGCAGACGACGCAATGGATGACACGAACTCTATTTATTTTGGTAAATGTTTTCATACAGTTTGA
ATTGAAAAAAATTACATGGGTATCAATTCTAAATGGCTTGTATTATAAACCAGATATTCTTTTTC
CAACAGAAATTATATCTAAGTAAGAATTTTTTCCAACTTCTTTTCTTATTTGTTATCTCGTGTTG
TTTTGTTATAAAAAAAATGTTGTTGTTTATACT
Found at i:582045 original size:2 final size:2
Alignment explanation
Indices: 582038--582110 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
582028 TGATGAATAA
582038 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
582080 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
582111 GTGACATATG
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:583169 original size:21 final size:23
Alignment explanation
Indices: 583109--583167 Score: 118
Period size: 23 Copynumber: 2.6 Consensus size: 23
583099 AAACGAGACA
583109 TCGCGCTAACACACAACACGCCG
1 TCGCGCTAACACACAACACGCCG
583132 TCGCGCTAACACACAACACGCCG
1 TCGCGCTAACACACAACACGCCG
583155 TCGCGCTAACACA
1 TCGCGCTAACACA
583168 ACTTTGCACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.31, C:0.42, G:0.17, T:0.10
Consensus pattern (23 bp):
TCGCGCTAACACACAACACGCCG
Found at i:583178 original size:31 final size:31
Alignment explanation
Indices: 583143--583206 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
583133 CGCGCTAACA
583143 CACAACACGCCGTCGCGCTAACACAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
*
583174 CACAACACGCCGTCGCGCTAACGCAACTTTG
1 CACAACACGCCGTCGCGCTAACACAACTTTG
583205 CA
1 CA
583207 AGTTTCACAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.39, G:0.17, T:0.16
Consensus pattern (31 bp):
CACAACACGCCGTCGCGCTAACACAACTTTG
Found at i:584371 original size:31 final size:31
Alignment explanation
Indices: 584333--584620 Score: 354
Period size: 31 Copynumber: 10.1 Consensus size: 31
584323 CTGTGAAACT
*
584333 TGCAAAGTTGCGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584364 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584395 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
*
584426 TGCAAAGTTGTGTTAGCGCAACGGCGTG-T-
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
* *
584455 T------TTATGTTAGTGCGACGGCGTG-T-
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
* *
584478 TGC------GTGTTAGCGCGATGGCATGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584503 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584534 TGCAAAGTTGTGTTAGCGCGACGGCGTG-T-
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584563 T-----G-TGTGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584588 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584619 TG
1 TG
584621 TGTTAGCGCG
Statistics
Matches: 228, Mismatches: 11, Indels: 36
0.83 0.04 0.13
Matches are distributed among these distances:
23 55 0.24
24 3 0.01
25 4 0.02
29 2 0.01
30 3 0.01
31 161 0.71
ACGTcount: A:0.15, C:0.16, G:0.39, T:0.30
Consensus pattern (31 bp):
TGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
Found at i:584470 original size:54 final size:54
Alignment explanation
Indices: 584403--584631 Score: 276
Period size: 54 Copynumber: 4.2 Consensus size: 54
584393 TGTGCAAAGT
* *
584403 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCAACGGCGTGTTT
1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
* * * *
584457 TATGTTAGTGCGACGGCGTG-T-TGC------GTGTTAGCGCGATGGCATGTTGTGCAAAG
1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGC--G-TGT----TG
584510 TTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 -TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584565 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
1 TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
584619 TGTGTTAGCGCGA
1 TGTGTTAGCGCGA
584632 TGTCTCGTTT
Statistics
Matches: 149, Mismatches: 10, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
46 14 0.09
48 1 0.01
49 3 0.02
52 3 0.02
53 1 0.01
54 103 0.69
55 2 0.01
56 3 0.02
59 3 0.02
60 1 0.01
62 15 0.10
ACGTcount: A:0.14, C:0.16, G:0.39, T:0.31
Consensus pattern (54 bp):
TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTG
Found at i:584485 original size:23 final size:23
Alignment explanation
Indices: 584435--584502 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 23
584425 GTGCAAAGTT
* **
584435 GTGTTAGCGCAACGGCGTGTTTT
1 GTGTTAGCGCGACGGCGTGTTGC
* *
584458 ATGTTAGTGCGACGGCGTGTTGC
1 GTGTTAGCGCGACGGCGTGTTGC
* *
584481 GTGTTAGCGCGATGGCATGTTG
1 GTGTTAGCGCGACGGCGTGTTG
584503 TGCAAAGTTG
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.38, T:0.32
Consensus pattern (23 bp):
GTGTTAGCGCGACGGCGTGTTGC
Found at i:584548 original size:85 final size:85
Alignment explanation
Indices: 584459--584620 Score: 288
Period size: 85 Copynumber: 1.9 Consensus size: 85
584449 GCGTGTTTTA
* *
584459 TGTTAGTGCGACGGCGTGTTGCGTGTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGA
1 TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA
584524 CGGCGTGTTGTGCAAAGTTG
66 CGGCGTGTTGTGCAAAGTTG
* *
584544 TGTTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGA
1 TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA
584609 CGGCGTGTTGTG
66 CGGCGTGTTGTG
584621 TGTTAGCGCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 73 1.00
ACGTcount: A:0.14, C:0.16, G:0.40, T:0.30
Consensus pattern (85 bp):
TGTTAGCGCGACGGCGTGTTGCGTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGA
CGGCGTGTTGTGCAAAGTTG
Found at i:584562 original size:108 final size:108
Alignment explanation
Indices: 584373--584587 Score: 376
Period size: 108 Copynumber: 2.0 Consensus size: 108
584363 GTGCAAAGTT
*
584373 GTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG
1 GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG
* *
584438 TTAGCGCAACGGCGTGTTTTATGTTAGTGCGACGGCGTGTTGC
66 TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTGC
*
584481 GTGTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG
1 GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG
* *
584546 TTAGCGCGACGGCGTGTTGTGTGTTAGCGCGACGGCGTGTTG
66 TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTG
584588 TGCAAAGTTG
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 101 1.00
ACGTcount: A:0.14, C:0.16, G:0.39, T:0.30
Consensus pattern (108 bp):
GTGTTAGCGCGACGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTG
TTAGCGCAACGGCGTGTTGTATGTTAGCGCGACGGCGTGTTGC
Found at i:584571 original size:23 final size:23
Alignment explanation
Indices: 584542--584589 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
584532 TGTGCAAAGT
584542 TGTGTTAGCGCGACGGCGTGTTG
1 TGTGTTAGCGCGACGGCGTGTTG
584565 TGTGTTAGCGCGACGGCGTGTTG
1 TGTGTTAGCGCGACGGCGTGTTG
584588 TG
1 TG
584590 CAAAGTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.08, C:0.17, G:0.44, T:0.31
Consensus pattern (23 bp):
TGTGTTAGCGCGACGGCGTGTTG
Found at i:584602 original size:139 final size:135
Alignment explanation
Indices: 584344--584633 Score: 390
Period size: 139 Copynumber: 2.1 Consensus size: 135
584334 GCAAAGTTGC
* *
584344 GTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT
1 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT
*
584409 AGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGTGCGACGGC
66 AGCGCGACGGCGTGTTGT----AGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGCGCGACGGC
584474 GTGTTGCGT
127 GTGTTGCGT
584483 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT
1 GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT
* *
584548 AGCGCGACGGCGTG-T-T-G-TGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTTAGCGCGA
66 AGCGCGACGGCGTGTTGTAGTTGTGTTAGCGCAACGGCGTG-T-T------TTATGTTAGCGCGA
*
584609 CGGCGTGTTGTGT
123 CGGCGTGTTGCGT
584622 GTTAGCGCGATG
1 GTTAGCGCGATG
584634 TCTCGTTTAT
Statistics
Matches: 137, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
131 19 0.14
132 2 0.01
133 1 0.01
137 1 0.01
138 1 0.01
139 113 0.82
ACGTcount: A:0.15, C:0.16, G:0.39, T:0.30
Consensus pattern (135 bp):
GTTAGCGCGATGGCATGTTGTGCAAAGTTGTGTTAGCGCGACGGCGTGTTGTGCAAAGTTGTGTT
AGCGCGACGGCGTGTTGTAGTTGTGTTAGCGCAACGGCGTGTTTTATGTTAGCGCGACGGCGTGT
TGCGT
Found at i:586765 original size:21 final size:22
Alignment explanation
Indices: 586726--586775 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
586716 AAAAGAAGTC
586726 ATTTTCACACATTGATGCATGA
1 ATTTTCACACATTGATGCATGA
* *
586748 ATTTTC-CATATTGGTGCATGA
1 ATTTTCACACATTGATGCATGA
586769 ATTTTCA
1 ATTTTCA
586776 AGAACAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (22 bp):
ATTTTCACACATTGATGCATGA
Found at i:589576 original size:16 final size:16
Alignment explanation
Indices: 589555--589586 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
589545 TTCTACAACA
*
589555 ACATAGCTTTGCACAT
1 ACATAGCTTTACACAT
589571 ACATAGCTTTACACAT
1 ACATAGCTTTACACAT
589587 TGTCTTTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (16 bp):
ACATAGCTTTACACAT
Found at i:591893 original size:12 final size:12
Alignment explanation
Indices: 591876--591903 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
591866 CATTAAGACA
591876 ACAACTACACTG
1 ACAACTACACTG
591888 ACAACTACACTG
1 ACAACTACACTG
591900 ACAA
1 ACAA
591904 GGAATATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.32, G:0.07, T:0.14
Consensus pattern (12 bp):
ACAACTACACTG
Found at i:595077 original size:1 final size:1
Alignment explanation
Indices: 595073--595119 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
595063 TTTTTGTGGG
** *
595073 TTTTTTTTGGTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
595120 GGGGGGGGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:595088 original size:10 final size:10
Alignment explanation
Indices: 595059--595121 Score: 65
Period size: 10 Copynumber: 6.3 Consensus size: 10
595049 TTTGTTGTGG
595059 TGGTTTTTTGT
1 TGGTTTTTT-T
*
595070 GGGTTTTTTT
1 TGGTTTTTTT
595080 TGGTTTTTTT
1 TGGTTTTTTT
*
595090 TTGTTTTTTT
1 TGGTTTTTTT
*
595100 T-TTTTTTTT
1 TGGTTTTTTT
**
595109 TTTTTTTTTT
1 TGGTTTTTTT
595119 TGG
1 TGG
595122 GGGGGGGGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
9 8 0.18
10 29 0.64
11 8 0.18
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (10 bp):
TGGTTTTTTT
Found at i:596854 original size:18 final size:17
Alignment explanation
Indices: 596831--596866 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
596821 TAATATTTAT
596831 ATCTATTAAATCTTATTA
1 ATCTATTAAATC-TATTA
*
596849 ATCTATTATATCTATTA
1 ATCTATTAAATCTATTA
596866 A
1 A
596867 ACCTTACAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (17 bp):
ATCTATTAAATCTATTA
Found at i:598276 original size:21 final size:21
Alignment explanation
Indices: 598250--598346 Score: 126
Period size: 21 Copynumber: 4.7 Consensus size: 21
598240 TACACCATAG
598250 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
598271 CATAGCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
* *
598292 CATAGCATAACATTGGAATCT
1 CATAGCATAGCATTGAAATCT
598313 CATAGCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
598333 CATAGAATCGCATT
1 CATAGCATAGCATT
598347 CGTCATATCA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.24
21 52 0.76
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:598534 original size:5 final size:5
Alignment explanation
Indices: 598521--598554 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
598511 GTTCAAATCT
* *
598521 CATAG CATAC CATAG CATAG CATAG CATAC CATA
1 CATAG CATAG CATAG CATAG CATAG CATAG CATA
598555 TCATTAAGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (5 bp):
CATAG
Found at i:598536 original size:10 final size:10
Alignment explanation
Indices: 598521--598554 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
598511 GTTCAAATCT
598521 CATAGCATAC
1 CATAGCATAC
*
598531 CATAGCATAG
1 CATAGCATAC
598541 CATAGCATAC
1 CATAGCATAC
598551 CATA
1 CATA
598555 TCATTAAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.21
Consensus pattern (10 bp):
CATAGCATAC
Found at i:598604 original size:21 final size:21
Alignment explanation
Indices: 598578--598631 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
598568 CATTTCAATT
*
598578 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATACCATACAAA
598599 TCTCATAGCATACCATACAAA
1 TCTCATAGCATACCATACAAA
*
598620 TCTCATACCATA
1 TCTCATAGCATA
598632 TCATTAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATACCATACAAA
Found at i:627568 original size:445 final size:441
Alignment explanation
Indices: 626428--627764 Score: 2162
Period size: 441 Copynumber: 3.0 Consensus size: 441
626418 CCTAGACCCA
626428 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA
1 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA
* * * *
626493 ATCAATAGTACAACTAAGTGTATAATTATTGTTCTTTGTTTAAAGTTTTAAGTCCTTCTGTCTAA
66 ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA
* *
626558 GTATATTCAAGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCT
131 GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA
*
626623 AGGTCACAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATG-TCACAAGTTAAAA
196 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGAT-ACAAGTTAAAA
* * *
626687 GTCTGTATATTAAAGGAGTCTTGTGTTATGGCCCAGACAATATTTTTTATGAAAAGCTTGACCTT
260 GTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGACCTT
* *
626752 GAAGAACAAAATAAGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATGTACC
325 GAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCTACC
* * *
626817 TATGTTCCAAGTTTTAAGTCTTAATGTCAAAGGGTATTAAAGTTAC-GACTCA
390 TATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCT-G
626869 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA
1 GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA
*
626934 ATCAATAGTACACCTGAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA
66 ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA
* * * *
626999 GTAAATTCAGGACTTGAACAATGAAGTTTTTTCAAATTTGACCTTGAAATAAAATTTTTAGGTCA
131 GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA
*
627064 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGACACAAGTTAAAAG
196 AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTAAAAG
*
627129 TCTGTATGTTAAAAGAGTCTTGTGTTATGGTCCGGACAATATTTTTTTATG-AAAGCTTGA-CTT
261 TCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATA-TTTTTTATGAAAAGCTTGACCTT
* *
627192 CGAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCGC-GCACTCTTTCTAAATACCATCTA
325 -GAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGC-CTGCACTCCTTCTCAATACCATCTA
*
627256 CCTATGTTCCAAATTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG
388 CCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG
* *
627310 GACAAAATTTTATTATTTTTTTTCTTAATTTGACCTTGAGTAAAACAAGGTCAAGGTCAAATAAT
1 GACAAAATTTTATTA-TCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTC--AT-AT
* * * *
627375 ATTATTCAATAGTACACCTAAGTGTATTATTATTGTCCTTTGTTTAAGGTTTGAAGTCCTTCTGT
62 ATAAATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGT
* * ***
627440 CAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTCCTAATATGACCTTGAAATTTTTTTTTTAG
127 CAAAGTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAG
*
627505 GTCAAGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCTATGATACAAGTTA
192 GTCAAGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTA
* * *
627570 AAAGTCTGTAAGTTAAAGGAGTCTTGTGTTATGGTCCGGATAATATTTTTTATGAAAAGCCTGAC
257 AAAGTCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGAC
* *
627635 CTTGAAAAACAAAATAGGTCAAGGTCAAAACTGTTGGTGGCCTGCACTCCTTCTCAATACCATCT
322 CTTGAAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCT
* *
627700 ACCTATCTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTTAAGTTACGGCCTG
387 ACCTATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG
627755 GACAAAATTT
1 GACAAAATTT
627765 GGATGAAGAA
Statistics
Matches: 830, Mismatches: 54, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
440 3 0.00
441 410 0.49
442 53 0.06
444 12 0.01
445 349 0.42
446 3 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (441 bp):
GACAAAATTTTATTATCTTTTTCTTAATTTGACCTTGAGTAAAACATGGTCAAGGTCATATATAA
ATCAATAGTACACCTAAGTGTATTATTATTGTTCTTTGTTTAAAGTTTGAAGTCCTTCTGTCAAA
GTATATTCAGGAGTTGAACAATGAAGTTTTTTCTAATTTGACCTTGAAATAAATTTTTTAGGTCA
AGGTCAAAAATTTTGGTAAGGTTCAACTAGGTTATATACCATCTATCCATGATACAAGTTAAAAG
TCTGTATGTTAAAGGAGTCTTGTGTTATGGTCCGGACAATATTTTTTATGAAAAGCTTGACCTTG
AAGAACAAAATAGGTCAAGGTCAAAACTTTTGGTGGCCTGCACTCCTTCTCAATACCATCTACCT
ATGTTCCAAGTTTGAAGTCTTAATGTCAAAGGGTATTAAAGTTACGGCCTG
Found at i:628530 original size:17 final size:17
Alignment explanation
Indices: 628505--628537 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
628495 CTGGTACTGT
*
628505 ACCAGTTATCGGCTAAG
1 ACCAATTATCGGCTAAG
628522 ACCAATTATCGGCTAA
1 ACCAATTATCGGCTAA
628538 ACTGAGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
ACCAATTATCGGCTAAG
Found at i:633116 original size:165 final size:167
Alignment explanation
Indices: 632595--633308 Score: 881
Period size: 165 Copynumber: 4.2 Consensus size: 167
632585 AAAGAATCAT
* * *
632595 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGCTTTACTCTGA-ATATTCCTTTGTTTAAC
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCT-ATATATTCCTATGTTAAAC
* * * * * *
632659 TTTGACCCCCCCCCCATTTTGGCCCCACCCTACCCCTGGGGATCATGATTTTCACAACTATGAAT
65 TTCGA---CCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAA
* **
632724 CTACACTACCTGAGGATGCTTCCACACAAGAATCAGCTTTC
127 ATACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* **
632765 CTGACTGATTAGTTTCT--GAA-AAGATTTTTAAAGATTTACTCTATATATTCAAATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* * * **
632827 TC-AACCCCCTATTGTGGCCCAACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAATCTAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC
* * * *
632891 ACTATCTAAGGTTGCTTCCACACAAGTGTCAGCTTTC
131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * *
632928 CTGGCTGATTAGTTTCCGAGAAGAAGATTTTTAAAGATTTACTCTATACATACCTATGTAAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* *
632993 TCGA-CCCCCCATTGTGGCCCCATCCTACCCCCGGGGGT-ATGATTTTCACAACATTGAAAATAC
66 TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC
* *
633056 ACTACCTGAGGATGCTTCCACACTAGTTTCAGCTTTG
131 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
633093 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
* *
633158 TCGACCCCCCCCCCGTTGTGGCCCCACCCTTCCCCCGGGGGTCATGATTTTCACAACTTTGAATC
66 TCGA---CCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAA--
*
633223 TACACTACATGTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
126 -A-A-TACA-CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* *
633269 CTGG-T-CTTATGGTTCATGAGAAGAAGATTTTTGAAA-ATTT
1 CTGGCTGATTA-GTTTC-TGAGAAGAAGATTTTT-AAAGATTT
633309 CTCGAAAATT
Statistics
Matches: 474, Mismatches: 51, Indels: 32
0.85 0.09 0.06
Matches are distributed among these distances:
163 101 0.21
165 121 0.26
166 72 0.15
167 37 0.08
168 3 0.01
169 31 0.07
170 35 0.07
173 1 0.00
174 4 0.01
175 9 0.02
176 57 0.12
177 3 0.01
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (167 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTTAAACT
TCGACCCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTGAAAATAC
ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:635433 original size:21 final size:21
Alignment explanation
Indices: 635407--635503 Score: 135
Period size: 21 Copynumber: 4.7 Consensus size: 21
635397 TACACCATAG
635407 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
635428 CATAGCATAGCATTGAAATCT
1 CATAGCATAGCATTGAAATCT
*
635449 CATAGCATAGCATTGGAATCT
1 CATAGCATAGCATTGAAATCT
*
635470 CATACCATAGCA-T-ACAATCT
1 CATAGCATAGCATTGA-AATCT
* *
635490 CATAGAATCGCATT
1 CATAGCATAGCATT
635504 CGTCATATCA
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 15 0.22
21 53 0.78
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (21 bp):
CATAGCATAGCATTGAAATCT
Found at i:635469 original size:42 final size:41
Alignment explanation
Indices: 635407--635525 Score: 141
Period size: 42 Copynumber: 2.9 Consensus size: 41
635397 TACACCATAG
*
635407 CATAGCATAGCATTGAAATCTCATAGCATAGCATTGA-AATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCA-T-ACAATCT
*
635449 CATAGCATAGCATTGGAATCTCATACCATAGCATACAATCT
1 CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
* * ** *
635490 CATAGAATCGCATTCGTCATATCATACCATAGCATA
1 CATAGCATAGCATT-GAAATCTCATACCATAGCATA
635526 GCATACAACA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.01
41 18 0.26
42 49 0.72
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (41 bp):
CATAGCATAGCATTGAAATCTCATACCATAGCATACAATCT
Found at i:635698 original size:15 final size:15
Alignment explanation
Indices: 635678--635706 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
635668 GTTCAAATCT
635678 CATAGCATACCATAG
1 CATAGCATACCATAG
635693 CATAGCATACCATA
1 CATAGCATACCATA
635707 TCATTAAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (15 bp):
CATAGCATACCATAG
Found at i:635756 original size:21 final size:21
Alignment explanation
Indices: 635730--635809 Score: 108
Period size: 21 Copynumber: 3.8 Consensus size: 21
635720 CATTTCAATT
635730 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
635751 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
* *
635772 TCTCATAGCATATCATTA-ACA
1 TCTCATAGCATAGCA-TACAAA
* *
635793 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
635810 GCATAAATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 2 0.04
21 49 0.92
22 2 0.04
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:636580 original size:163 final size:168
Alignment explanation
Indices: 636303--636724 Score: 656
Period size: 163 Copynumber: 2.5 Consensus size: 168
636293 TCACACTTTT
** *
636303 TTGTAAGCGCTCTCATGCCTACAAATTTTGACATATTTTCATTAAATGTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCC-AC--A-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
* * *
636368 CTACTATTACCTTGATCAAGTTCGAAAATCAGAATTGGTCGATAC-TTTT-TTGGAGTTATGGGA
62 CCACTATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGA
636431 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
127 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
636473 TTGTAAGCGCTCTCATG-C-C-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
1 TTGTAAGCGCTCTCATGCCACATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
*
636535 TATTACCTTGGTCAAGTTCGAAAATCAGCATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT
66 TATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT
*
636600 GACCACAATAATGACTTCGTTTTATCCAAAAATTGACC
131 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
636638 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCC-AC--A-TTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA
*
636703 CCACTATAACCTTGGTCAAGTT
62 CCACTATTACCTTGGTCAAGTT
636725 TCTAAATTAG
Statistics
Matches: 234, Mismatches: 9, Indels: 16
0.90 0.03 0.06
Matches are distributed among these distances:
163 77 0.33
164 4 0.02
165 72 0.31
166 1 0.00
167 1 0.00
168 1 0.00
169 1 0.00
170 17 0.07
172 60 0.26
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (168 bp):
TTGTAAGCGCTCTCATGCCACATTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCAC
TATTACCTTGGTCAAGTTCGAAAATCAGAATTGGTCAATACTTTTTGTTGGAGTTATGGGACTTT
GACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:637999 original size:4 final size:4
Alignment explanation
Indices: 637992--638044 Score: 54
Period size: 4 Copynumber: 13.0 Consensus size: 4
637982 TGATGATTGG
* * *
637992 ATGA ATGA ATGGA ATGA ATGA ATGA ATG- ATAGA TTGA TTGA ATGA ATAA
1 ATGA ATGA AT-GA ATGA ATGA ATGA ATGA AT-GA ATGA ATGA ATGA ATGA
638041 ATGA
1 ATGA
638045 TTGTTTTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 35 0.83
5 5 0.12
ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28
Consensus pattern (4 bp):
ATGA
Found at i:640555 original size:26 final size:26
Alignment explanation
Indices: 640526--640585 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
640516 CAAGGGAGAT
*
640526 TGGCATTCTTTGTATGGCCACCAAAA
1 TGGCATTCTTTGAATGGCCACCAAAA
640552 TGGCATTCTTTGAATGGCCACCAAAA
1 TGGCATTCTTTGAATGGCCACCAAAA
640578 TGGCATTC
1 TGGCATTC
640586 ACCTGACATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (26 bp):
TGGCATTCTTTGAATGGCCACCAAAA
Found at i:648789 original size:21 final size:21
Alignment explanation
Indices: 648763--648804 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
648753 GGAGCTGCCA
*
648763 TCAAAGAAGAAGGTTCCAACG
1 TCAAAGAAGAAGGGTCCAACG
*
648784 TCAAAGAAGACGGGTCCAACG
1 TCAAAGAAGAAGGGTCCAACG
648805 ATGAAGAAGA
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:0.40, C:0.21, G:0.26, T:0.12
Consensus pattern (21 bp):
TCAAAGAAGAAGGGTCCAACG
Found at i:648811 original size:21 final size:21
Alignment explanation
Indices: 648787--648845 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
648777 TCCAACGTCA
*
648787 AAGAAGACGGGTCCAACGATG
1 AAGAAGACGGGTCCAACGAGG
* *
648808 AAGAAGACTGTTCCAACGAGG
1 AAGAAGACGGGTCCAACGAGG
*
648829 AAAAAGACGGGTCCAAC
1 AAGAAGACGGGTCCAAC
648846 TCGGGAGAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.41, C:0.20, G:0.29, T:0.10
Consensus pattern (21 bp):
AAGAAGACGGGTCCAACGAGG
Found at i:648812 original size:42 final size:42
Alignment explanation
Indices: 648766--648845 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
648756 GCTGCCATCA
*
648766 AAGAAGAAGGTTCCAACG-TCAAAGAAGACGGGTCCAACGATG
1 AAGAAGAAGGTTCCAACGAGCAAA-AAGACGGGTCCAACGATG
** *
648808 AAGAAGACTGTTCCAACGAGGAAAAAGACGGGTCCAAC
1 AAGAAGAAGGTTCCAACGAGCAAAAAGACGGGTCCAAC
648846 TCGGGAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 30 0.91
43 3 0.09
ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11
Consensus pattern (42 bp):
AAGAAGAAGGTTCCAACGAGCAAAAAGACGGGTCCAACGATG
Found at i:649754 original size:166 final size:166
Alignment explanation
Indices: 649479--650937 Score: 2061
Period size: 166 Copynumber: 8.8 Consensus size: 166
649469 GTGAATATGC
*
649479 AAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* *
649543 AATATGGCATGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTAAG
65 AATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
**
649608 AAATT-TTTGACGGAAATTTGTTTGAAAATTTTGGCTA
130 -AATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
* *
649645 AAAATAAACAAAGTAC-TCA-TTACACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCCCA
1 AAAATAAACAAAGT-CGTCATTTA-ACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCA
* ** ** * * * *
649708 CGATAAAGCATGCTTATACAAATACTGTGTAAAAATTTCGAGCATCTGCGATGAACAGTTGCTGA
64 CAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGA
649773 GAATTCTTTGACAAAAATTTGTTTGAAAATGTTT-GCTA
129 GAATTCTTTGACAAAAATTTGTTTGAAAAT-TTTGGCTA
* * * *
649811 AAAATAAATAAAGTCGTCATTTAACAGGAAGTTGACATCTGATTGGTACAAAAACATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * * * * *
649876 ATTTGGCATACCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGTGATTAATAGCTGCTGAGA
66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* **
649941 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
* * * *
649977 AAAATAAATAAAGTCGTCATTTAACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCTCA-A
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
*
650041 GATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
66 -ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
650106 AATTCTTTGACAAAAATTTGTTTGAAAATGTTT-GCTA
130 AATTCTTTGACAAAAATTTGTTTGAAAAT-TTTGGCTA
** *
650143 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGATATCTGATTGGTACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * *
650208 ATATGGCATGCCATAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
650273 ATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA
131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
* *
650309 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACATCTGATTGGTACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * *
650374 ATATGGCATGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGA
66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* **
650439 AATCTTTGACGGAAATTTGTTTGAAAATTTTGGCTA
131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
* * *
650475 AAAATAAACAAAGTAC-TCATATAACAGGAAGTTGACGTCCAATTGGTACAAAAATACATCCCAC
1 AAAATAAACAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * ** * * *
650539 GATATAGCATGCTTATACAAATACTGTGTAAAAATTTCAAGCATCTGCTATAAACAGTTGCTGAG
65 AATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
650604 AATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTA
130 AATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
*
650641 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACA
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
* * * * * *
650706 ATATGGCATGCCTATACAAATATTGTGTAAAATTTTTAAGCATCTGCGATAGATAGTTGCTGAGA
66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* * *
650771 ATTCTTTGACGAAAATTTGTTTGAAAATTTTAGTTAA
131 ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCT-A
* * * *
650808 AAAATAAGCAAAGTCATCATTTAAGAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
** * *
650873 ATATGGCATGCCTTAACAAACACTGTGTAAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
650938 TAAATGCGAC
Statistics
Matches: 1157, Mismatches: 123, Indels: 25
0.89 0.09 0.02
Matches are distributed among these distances:
165 16 0.01
166 1012 0.87
167 129 0.11
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (166 bp):
AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACA
ATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
ATTCTTTGACAAAAATTTGTTTGAAAATTTTGGCTA
Found at i:650973 original size:4 final size:4
Alignment explanation
Indices: 650964--651007 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
650954 TTTTGTTACG
* *
650964 GACA GACA GACA GACA GACA GACT GACG GACA GACA GACA GACA
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
651008 CACAAGGGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.45, C:0.25, G:0.27, T:0.02
Consensus pattern (4 bp):
GACA
Found at i:652969 original size:21 final size:21
Alignment explanation
Indices: 652945--653227 Score: 326
Period size: 21 Copynumber: 13.6 Consensus size: 21
652935 TTTTTATAAA
652945 TTCCAACTTTAAAGTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
**
652966 TTCCAACTTTAATCTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
* *
652987 TTCCAACTTTAATGTTAGAAT
1 TTCCAACTTTAAAGTTGGAAT
*
653008 TTCCAACTTTAAAGGTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
*
653029 TTCCAACTTTAAAGTT-GATTT
1 TTCCAACTTTAAAGTTGGA-AT
**
653050 TTCCAA-TTTAAAAGTTAAAAT
1 TTCCAACTTT-AAAGTTGGAAT
* *
653071 TACAAAC-TTAACAGTTGGAAT
1 TTCCAACTTTAA-AGTTGGAAT
**
653092 TTCCAACTTTAATCTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
*
653113 TTCCAACTTTCAAGTT-G-AT
1 TTCCAACTTTAAAGTTGGAAT
* *
653132 TTCCAACTTTCAAGTT-GATTT
1 TTCCAACTTTAAAGTTGGA-AT
653153 TTCCAACTTTAAAGTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
**
653174 TTCCAACTTTAATCTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
*
653195 TTCCAACTTTCAAGTTGGAAT
1 TTCCAACTTTAAAGTTGGAAT
653216 TTCCAACTTTAA
1 TTCCAACTTTAA
653228 TATTGGGATT
Statistics
Matches: 222, Mismatches: 31, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
19 19 0.09
20 8 0.04
21 188 0.85
22 7 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (21 bp):
TTCCAACTTTAAAGTTGGAAT
Found at i:656057 original size:22 final size:23
Alignment explanation
Indices: 656014--656070 Score: 107
Period size: 22 Copynumber: 2.5 Consensus size: 23
656004 CCACCTAAGA
656014 TTAAGGCGGATTCCTTTTTTGTT
1 TTAAGGCGGATTCCTTTTTTGTT
656037 TTAAGGCGGATTCC-TTTTTGTT
1 TTAAGGCGGATTCCTTTTTTGTT
656059 TTAAGGCGGATT
1 TTAAGGCGGATT
656071 TTTATTACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.16, C:0.12, G:0.25, T:0.47
Consensus pattern (23 bp):
TTAAGGCGGATTCCTTTTTTGTT
Found at i:661443 original size:74 final size:74
Alignment explanation
Indices: 661322--661468 Score: 294
Period size: 74 Copynumber: 2.0 Consensus size: 74
661312 TACAGGATCA
661322 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT
1 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT
661387 AGCTCGCTT
66 AGCTCGCTT
661396 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT
1 AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT
661461 AGCTCGCT
66 AGCTCGCT
661469 GATATCTAGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (74 bp):
AGAAGACACAAAGAATTGGGCTTAACATTTCTACCTCCTCCTTTGTCAATGTTTTTGAGGTGTCT
AGCTCGCTT
Found at i:663005 original size:172 final size:172
Alignment explanation
Indices: 662719--663345 Score: 961
Period size: 172 Copynumber: 3.6 Consensus size: 172
662709 TCACACTTTT
* *
662719 TTGTAAGCGCTCTCATGCCTACAAATTTTTACGGATTTTCATTAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA
* *
662784 CCACTATTACCTTGGTCAAGTTCGAAAATCAACATTGGTCGATACTTTTTGTTGGAGTTATGGGA
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
**
662849 CTTTGACCACAATAATGACTTTGTTTTATCCAAAAATTGACC
131 CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
* * *
662891 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTTATGAAATCTATACCAAATGTGTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA
* *
662956 CCACTAATA-CTTCGGTCAAGTTCGAAAATCAGCTTTGGTCAATACTTTTTGTTGGAGTTATGGG
66 CCACTAATACCTT-GGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
*
663020 ACTTTGACCACAATAATGACTCCGTTTTATCCTAAAATTGACC
130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
* * * *
663063 TTGTAAGCGCTCTAATGCCTACAAATTTTGACGGATTTTCAAT-TAATTTATAACAAATGTTTGT
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTC-ATGAAATTTATACCAAATGTTTAT
* * *
663127 ACCACTAATACTTTGGTCAAGTTCGTAAATCAGCATTGGTCGATGCTTTTTGTTGGAGTTATGGG
65 ACCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGG
* *
663192 ACTTTGACCACAATAATGACTCCGTTTTATCCCATAATTGACC
130 ACTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
* * *
663235 TTGTAAGTGCTCTCATGCCTACAAATTTTGTCGGATTTACATGAAATTTATACCAAATGTTTATA
1 TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA
* * ** *
663300 TCACTAATACCGTGGTCAAGTTCCTAAATCAGCCTTGGTCGATACT
66 CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACT
663346 AGTATACTGC
Statistics
Matches: 412, Mismatches: 39, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
171 5 0.01
172 403 0.98
173 4 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (172 bp):
TTGTAAGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATGAAATTTATACCAAATGTTTATA
CCACTAATACCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGA
CTTTGACCACAATAATGACTCCGTTTTATCCAAAAATTGACC
Found at i:668305 original size:11 final size:11
Alignment explanation
Indices: 668289--668313 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
668279 AGTTTTCGTT
668289 GTTTTGGGTCA
1 GTTTTGGGTCA
668300 GTTTTGGGTCA
1 GTTTTGGGTCA
668311 GTT
1 GTT
668314 AGCCCAATAC
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:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (11 bp):
GTTTTGGGTCA
Found at i:696504 original size:2 final size:2
Alignment explanation
Indices: 696497--696555 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
696487 NNNNNNNNNN
696497 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
696539 CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT C
696556 CTTTTTCCTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:697334 original size:17 final size:17
Alignment explanation
Indices: 697312--697379 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 17
697302 CCCATTGGCC
*
697312 TGGCCTGGCCTCAAAGT
1 TGGCCTGGCCTCAAAAT
*
697329 TGGCCTGGCCTC--ACT
1 TGGCCTGGCCTCAAAAT
*
697344 T---TTGGCCTCAAAAT
1 TGGCCTGGCCTCAAAAT
*
697358 TGGCCTGGCCTCAAATT
1 TGGCCTGGCCTCAAAAT
697375 TGGCC
1 TGGCC
697380 ACTACAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
12 7 0.17
14 3 0.07
15 3 0.07
17 28 0.68
ACGTcount: A:0.16, C:0.31, G:0.25, T:0.28
Consensus pattern (17 bp):
TGGCCTGGCCTCAAAAT
Found at i:697349 original size:29 final size:29
Alignment explanation
Indices: 697317--697379 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
697307 TGGCCTGGCC
* **
697317 TGGCCTCAAAGTTGGCCTGGCCTCACTTT
1 TGGCCTCAAAATTGGCCTGGCCTCAAATT
697346 TGGCCTCAAAATTGGCCTGGCCTCAAATT
1 TGGCCTCAAAATTGGCCTGGCCTCAAATT
697375 TGGCC
1 TGGCC
697380 ACTACAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.30, G:0.24, T:0.29
Consensus pattern (29 bp):
TGGCCTCAAAATTGGCCTGGCCTCAAATT
Found at i:697452 original size:11 final size:11
Alignment explanation
Indices: 697430--697459 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
697420 CTTTACATAT
697430 TTGATGTTTTTA
1 TTGAT-TTTTTA
697442 TTGATTTTTTA
1 TTGATTTTTTA
697453 TTGATTT
1 TTGATTT
697460 ATTTTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (11 bp):
TTGATTTTTTA
Found at i:700812 original size:3 final size:3
Alignment explanation
Indices: 700804--700855 Score: 86
Period size: 3 Copynumber: 17.3 Consensus size: 3
700794 TGGCACGATT
* *
700804 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATT ATC ATC ATC ATC ATT ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
700852 ATC A
1 ATC A
700856 ATCTAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:702802 original size:2 final size:2
Alignment explanation
Indices: 702795--702848 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
702785 CTGAAACAAA
702795 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
702837 TC TC TC TC TC TC
1 TC TC TC TC TC TC
702849 ATGTATTTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:703958 original size:15 final size:15
Alignment explanation
Indices: 703938--703972 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
703928 ATTTTTTCTG
703938 CAATGATCAATGAAC
1 CAATGATCAATGAAC
703953 CAATGATCAATGAAC
1 CAATGATCAATGAAC
703968 CAATG
1 CAATG
703973 GCACAGTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (15 bp):
CAATGATCAATGAAC
Found at i:704542 original size:18 final size:18
Alignment explanation
Indices: 704519--704556 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
704509 TGGTCCCAAA
704519 TCAAATTTTGGCCTGGCC
1 TCAAATTTTGGCCTGGCC
*
704537 TCAAATTTTGGCCTTGCC
1 TCAAATTTTGGCCTGGCC
704555 TC
1 TC
704557 TACTTTGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.29, G:0.18, T:0.37
Consensus pattern (18 bp):
TCAAATTTTGGCCTGGCC
Found at i:705657 original size:18 final size:18
Alignment explanation
Indices: 705626--705697 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
705616 ATGTTTATAG
705626 AGGCCAAA-TTTGAGGCC
1 AGGCCAAATTTTGAGGCC
705643 AGGCCAAATTTTGAGGCC
1 AGGCCAAATTTTGAGGCC
* *
705661 AGGACAAAATTTG-GAGCC
1 AGGCCAAATTTTGAG-GCC
*
705679 AGGCCTAATTTTGAGGCC
1 AGGCCAAATTTTGAGGCC
705697 A
1 A
705698 AACGTGAGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.19
18 37 0.79
19 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGCCAAATTTTGAGGCC
Found at i:705802 original size:65 final size:65
Alignment explanation
Indices: 705707--705836 Score: 244
Period size: 65 Copynumber: 2.0 Consensus size: 65
705697 AAACGTGAGG
705707 CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA
1 CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA
705772 NCAAGACCAAC-TTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAA
1 -CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAA
705836 A
65 A
705837 GAATGCACAC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
65 54 0.84
66 10 0.16
ACGTcount: A:0.34, C:0.25, G:0.26, T:0.15
Consensus pattern (65 bp):
CAAGACCAACTTTGAGGACAGACCAGGCCAATGCGGCCAGGCCAGGTTTTAGAGTATGCCAAAAA
Found at i:706455 original size:2 final size:2
Alignment explanation
Indices: 706448--706472 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
706438 TATGGTCGGC
706448 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
706473 NNNNNNNNNN
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:708401 original size:2 final size:2
Alignment explanation
Indices: 708394--708452 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
708384 TAAGTTTATC
708394 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
708436 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
708453 TCAATGTTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:715384 original size:3 final size:3
Alignment explanation
Indices: 715376--715442 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
715366 TGTGAAATTA
* * *
715376 ATC ATC ATC ATC ATC ACC ACC ATC ATC GATAC ATGT ATC ATC ATC A-C
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC -AT-C AT-C ATC ATC ATC ATC
*
715423 AATC ATC TTC ATC ATC ATC A
1 -ATC ATC ATC ATC ATC ATC A
715443 CTGTCAAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 1 0.02
3 44 0.83
4 7 0.13
5 1 0.02
ACGTcount: A:0.34, C:0.33, G:0.03, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:721221 original size:41 final size:41
Alignment explanation
Indices: 721176--721320 Score: 272
Period size: 41 Copynumber: 3.5 Consensus size: 41
721166 ATACTGATAT
721176 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
*
721217 ACGTATACGTCTCTGGTACTGTTTGGTTGGTACTGTCAGGG
1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
721258 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
1 ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
*
721299 ACGTATATGTCCCTGGTACTGT
1 ACGTATACGTCCCTGGTACTGT
721321 ATACATGTAC
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 101 1.00
ACGTcount: A:0.15, C:0.19, G:0.30, T:0.35
Consensus pattern (41 bp):
ACGTATACGTCCCTGGTACTGTTTGGTTGGTACTGTCAGGG
Found at i:728309 original size:22 final size:22
Alignment explanation
Indices: 728283--728882 Score: 1092
Period size: 22 Copynumber: 27.3 Consensus size: 22
728273 CTGTTTTTCG
728283 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728305 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728327 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
* *
728349 TCGATTTTTACCTGGTTTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728371 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728393 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728415 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728437 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728459 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728481 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728503 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728525 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728547 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728569 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728591 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728613 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728635 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728657 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728679 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728701 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728723 TAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
*
728745 TAGATTTTTACCTTGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
*
728767 TAGATTTTTACCTGGTTTTTGT
1 TAGATTTTTACCTGGTCTTTGT
*
728789 AAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
*
728811 CAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
* * * * *
728833 TAAATCTTAACCTTGTTTTTGT
1 TAGATTTTTACCTGGTCTTTGT
*
728855 AAGATTTTTACCTGGTCTTTGT
1 TAGATTTTTACCTGGTCTTTGT
728877 TAGATT
1 TAGATT
728883 CGTTATCCTC
Statistics
Matches: 555, Mismatches: 23, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 555 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (22 bp):
TAGATTTTTACCTGGTCTTTGT
Found at i:729801 original size:45 final size:46
Alignment explanation
Indices: 729737--729847 Score: 181
Period size: 45 Copynumber: 2.5 Consensus size: 46
729727 GCATCTCATT
*
729737 GTGTGTTTAAGCATGCATGTACCTTTTTTGTGGTGAAGTGTTGA-A
1 GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA
* *
729782 GTGTGTTTAGGCATGCATGTACCTTTTTTGGGGTGAAGTGTTTACA
1 GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA
729828 -TGTGTTTAAGCATGCATGTA
1 GTGTGTTTAAGCATGCATGTA
729848 GTACTACCTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 60 0.98
46 1 0.02
ACGTcount: A:0.20, C:0.10, G:0.29, T:0.41
Consensus pattern (46 bp):
GTGTGTTTAAGCATGCATGTACCTTTTTTGGGGTGAAGTGTTGACA
Found at i:729926 original size:55 final size:55
Alignment explanation
Indices: 729858--730004 Score: 258
Period size: 55 Copynumber: 2.7 Consensus size: 55
729848 GTACTACCTT
* * *
729858 TTTTTAGTGGTGAAGTGTTTAAGCGTACCTTATTGGTAAAGTGTTTGAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC
*
729913 TTTTTGGTGGTGAAGTGTTTGAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC
729968 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGT
1 TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGT
730005 GGTGAAGTGT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 87 1.00
ACGTcount: A:0.18, C:0.13, G:0.27, T:0.43
Consensus pattern (55 bp):
TTTTTGGTGGTGAAGTGTTTAAGCCTACCTTTTTGGTAAAGTGTTTGAGCCTACC
Found at i:729931 original size:29 final size:29
Alignment explanation
Indices: 729858--730020 Score: 221
Period size: 29 Copynumber: 5.8 Consensus size: 29
729848 GTACTACCTT
* * *
729858 TTTTTAGTGGTGAAGTGTTTAAGCGTACC
1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
* *
729887 -TTAT--TGGTAAAGTGTTTGAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
729913 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
*
729942 -TTTT--TGGTAAAGTGTTTGAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
*
729968 TTTTTGGTGGTGAAGTGTTTAAGCCTACC
1 TTTTTGGTGGTGAAGTGTTTGAGCCTACC
729997 TTTTTGGTGGTGAAGTGTTTGAGC
1 TTTTTGGTGGTGAAGTGTTTGAGC
730021 ATGTCCTGGG
Statistics
Matches: 118, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
26 40 0.34
27 7 0.06
28 7 0.06
29 64 0.54
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.42
Consensus pattern (29 bp):
TTTTTGGTGGTGAAGTGTTTGAGCCTACC
Found at i:733582 original size:3 final size:3
Alignment explanation
Indices: 733574--733607 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
733564 AGTTGGATGA
733574 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
733608 ATAACAAGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:734258 original size:93 final size:93
Alignment explanation
Indices: 734099--734321 Score: 383
Period size: 93 Copynumber: 2.4 Consensus size: 93
734089 TAATGGAGCG
*
734099 GTACCACCAAACACCCTGGATATGAAGTAAAACAACAGAGGTTATTATATCAGTGATTTATCCTT
1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT
734164 GTCACATGTATAGAAAACTGATGAAGCA
66 GTCACATGTATAGAAAACTGATGAAGCA
*
734192 GTACCACCAAACACCCCGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT
1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT
734257 GTCACATGTATAGAAAACTGATGAAGCA
66 GTCACATGTATAGAAAACTGATGAAGCA
* * * * *
734285 GTTCCATCAGACACCCTGGATGTGAAGTTAAACAACA
1 GTACCACCAAACACCCTGGATATGAAGTAAAACAACA
734322 GACACTATTT
Statistics
Matches: 122, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 122 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (93 bp):
GTACCACCAAACACCCTGGATATGAAGTAAAACAACACAGGTTATTATATCAGTGATTTATCCTT
GTCACATGTATAGAAAACTGATGAAGCA
Found at i:739032 original size:11 final size:11
Alignment explanation
Indices: 739016--739040 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
739006 TTGAGAACGT
739016 TGTCAAAAAAG
1 TGTCAAAAAAG
739027 TGTCAAAAAAG
1 TGTCAAAAAAG
739038 TGT
1 TGT
739041 ACTAATTTGA
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:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (11 bp):
TGTCAAAAAAG
Found at i:739151 original size:1 final size:1
Alignment explanation
Indices: 739145--739172 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
739135 AGCACCACTA
739145 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCC
739173 GACCTTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:747332 original size:11 final size:12
Alignment explanation
Indices: 747314--747341 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
747304 AATTGAATGC
747314 ATTTTTTTTTTT
1 ATTTTTTTTTTT
747326 ATTTTTTTTTTT
1 ATTTTTTTTTTT
747338 ATTT
1 ATTT
747342 AAATACAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (12 bp):
ATTTTTTTTTTT
Found at i:749639 original size:2 final size:2
Alignment explanation
Indices: 749632--749697 Score: 78
Period size: 2 Copynumber: 33.0 Consensus size: 2
749622 AGGGTTAACG
* ** ** *
749632 AT AT AT AT AT AT AT AT AT AT AT AN NN NN NT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
749674 AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
749698 CCCTTCTAGT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:750619 original size:2 final size:2
Alignment explanation
Indices: 750612--750710 Score: 130
Period size: 2 Copynumber: 50.5 Consensus size: 2
750602 TGATGTTTGA
750612 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
750652 AG GG GG AG GG AG GG GG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
750694 AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG A
750711 AACCAGCTTG
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
1 2 0.02
2 85 0.98
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
AG
Found at i:754651 original size:3 final size:3
Alignment explanation
Indices: 754643--754670 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
754633 AAACGTACAA
754643 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
754671 TTCTTCTTCT
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:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:754675 original size:3 final size:3
Alignment explanation
Indices: 754669--754730 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
754659 CTCCTCCTCC
754669 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
754717 TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TC
754731 CTGCTCCTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:754771 original size:12 final size:15
Alignment explanation
Indices: 754741--754779 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
754731 CTGCTCCTCA
754741 TCGTCCTCAATCTCG
1 TCGTCCTCAATCTCG
*
754756 TCGTCCTCATTCTCG
1 TCGTCCTCAATCTCG
*
754771 TCATCCTCA
1 TCGTCCTCA
754780 TCCCAATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.41, G:0.10, T:0.36
Consensus pattern (15 bp):
TCGTCCTCAATCTCG
Found at i:764973 original size:2 final size:2
Alignment explanation
Indices: 764966--765027 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
764956 GTAGACGTGT
** **
764966 TA TA TA TA TA TA TA TA TA NN NN TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
765008 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
765028 ATTTTAAGCT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:769194 original size:14 final size:14
Alignment explanation
Indices: 769175--769209 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
769165 ATTCAAGATT
*
769175 CGAGATTGGAAATA
1 CGAGATTCGAAATA
*
769189 CGAGATTCGAAGTA
1 CGAGATTCGAAATA
769203 CGAGATT
1 CGAGATT
769210 TGAGATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (14 bp):
CGAGATTCGAAATA
Found at i:770005 original size:2 final size:2
Alignment explanation
Indices: 770000--770046 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
769990 TTTTTTTTAT
770000 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
770042 TC TC T
1 TC TC T
770047 GAGATGTCAA
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:772011 original size:2 final size:2
Alignment explanation
Indices: 772004--772103 Score: 155
Period size: 2 Copynumber: 50.0 Consensus size: 2
771994 CAGTACCAGT
772004 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* * * * *
772046 TC TC TC TC TC TC TG TT TC TC TC GC TC TC TG TC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
772088 TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
772104 AACTGTTGGG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50
Consensus pattern (2 bp):
TC
Found at i:774247 original size:305 final size:304
Alignment explanation
Indices: 773692--774304 Score: 1003
Period size: 305 Copynumber: 2.0 Consensus size: 304
773682 CGTGCAGGTG
*
773692 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAATTTGCACCCCGAGAAAACCATT
1 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTGCACCCCGAGAAAACCATT
* *
773757 GTCAACCGACGCGAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT
66 GTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT
* ** *
773822 CCCAAACAGATACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAATTTTACTGCTT
131 CCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCTT
* * * *
773887 TTATATAGGAATAACTTTAATTCTACAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT
196 TTAGATAGGAATAACGTGAATTCTAAAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT
*
773952 TTGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT
261 TCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT
* * *
773996 AATATTATATAAATAGTGCCTGTTTGGGAGGGTAACAGTTGAAATTGACATCCCGAGAAAACCAT
1 AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTG-CACCCCGAGAAAACCAT
* * *
774061 TGTCAACCGACCCAAAGCGGAGGTTGACAATGTTTTTCGAGGGGTGTCAATTTTAACTGTTATCC
65 TGTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCC
* * *
774126 TCCCAAACAGGCACTATTTATTTTGTTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCT
130 TCCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCT
*
774191 TTTAGATAGGAATAACGTGAATTC-AAAGGCGAACCGTACGCGCATGATTTTCGCGCATGTAACA
195 TTTAGATAGGAATAACGTGAATTCTAAA-GCGAACCGTACGCGCATAATTTTCGCGCATGTAACA
774255 ATTCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT
259 ATTCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT
774301 AATA
1 AATA
774305 GGACAGATTA
Statistics
Matches: 285, Mismatches: 22, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
304 46 0.16
305 239 0.84
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (304 bp):
AATAATATATAAATAATGCCTGTTTGGGAGGGTAACAGTTGAAATTGCACCCCGAGAAAACCATT
GTCAACCGACCCAAAGCGGAGGTTGACAATGGTTTTCGAGGGGTGCCAATTTCAACTGTTATCCT
CCCAAACAGACACCATTTATTTTGCTATACTGAATGTCTTAATTTTAAAGAAAACATCACTGCTT
TTAGATAGGAATAACGTGAATTCTAAAGCGAACCGTACGCGCATAATTTTCGCGCATGTAACAAT
TCGTAATGTTACCCGTTGCTAAGTGCGTTGCTAACGCTGAGGGT
Found at i:774388 original size:62 final size:62
Alignment explanation
Indices: 774310--774433 Score: 203
Period size: 62 Copynumber: 2.0 Consensus size: 62
774300 TAATAGGACA
* *
774310 GATTATGAACTGCGTCTAAACCAATCATATTTAAGTATTTAACATGAAAGTATAACAAAACG
1 GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG
* * *
774372 GATTATGAACTACGTCTTAACCATTCAGATTTCAGTATTTAACATGAAAGTATAACAAAACG
1 GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG
774434 TTTTTTCTAG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (62 bp):
GATTATGAACTACGTCTAAACCAATCAGATTTAAGTATTTAACATGAAAGTATAACAAAACG
Found at i:776749 original size:17 final size:19
Alignment explanation
Indices: 776712--776749 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
776702 GGACATGGAG
*
776712 CTAAAATATTAACATGGAT
1 CTAAAATATTAACATGCAT
776731 CTAAAATA-T-ACATGCAT
1 CTAAAATATTAACATGCAT
776748 CT
1 CT
776750 TAGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.32
Consensus pattern (19 bp):
CTAAAATATTAACATGCAT
Found at i:780266 original size:14 final size:14
Alignment explanation
Indices: 780247--780276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
780237 ATCCCCAAAA
*
780247 CTCTCTTCCTCTCT
1 CTCTCTCCCTCTCT
780261 CTCTCTCCCTCTCT
1 CTCTCTCCCTCTCT
780275 CT
1 CT
780277 GGATTTTCTA
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:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (14 bp):
CTCTCTCCCTCTCT
Found at i:783909 original size:3 final size:3
Alignment explanation
Indices: 783901--783927 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
783891 ACCATCAGTT
783901 TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
783928 GTTTTCGCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:784588 original size:2 final size:2
Alignment explanation
Indices: 784581--784637 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
784571 TTTATATTCG
784581 GA 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 GA
784623 GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA G
784638 NNNNNNNNNN
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:790568 original size:2 final size:2
Alignment explanation
Indices: 790561--790627 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
790551 ATATTCTTCG
790561 GA 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 GA
790603 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
790628 TATAAACTCA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:794497 original size:59 final size:60
Alignment explanation
Indices: 794422--794581 Score: 207
Period size: 59 Copynumber: 2.6 Consensus size: 60
794412 GCAGGGAGGA
794422 ACAACTCACTAAAGGATTGCTGTAAACAAAAC-ACCAGCTGTAAATGGGCTGTTATACAT
1 ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTTATACAT
* *
794481 ACAACTCATTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGTGCTGTTAATA-AT
1 ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTT-ATACAT
* * * * * *
794541 ATAATTCACGACAATGATTGCTGTAAAAAAAAACAAACAGC
1 ACAACTCACTA-AAGGATTGCTGT-AAACAAAACAACCAGC
794582 AAGATGTGAA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
59 31 0.35
60 29 0.33
61 14 0.16
62 14 0.16
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (60 bp):
ACAACTCACTAAAGGATTGCTGTAAACAAAACAACCAGCTGTAAATGGGCTGTTATACAT
Found at i:794515 original size:30 final size:30
Alignment explanation
Indices: 794421--794515 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
794411 GGCAGGGAGG
*
794421 AACAACTCACTAAAGGATTGCTGTAAACAA
1 AACAACTCATTAAAGGATTGCTGTAAACAA
*
794451 AAC-AC-CAGCTGTAAATGG---GCTGTTATAC-A
1 AACAACTCA--T-TAAA-GGATTGCTG-TAAACAA
*
794480 TACAACTCATTAAAGGATTGCTGTAAACAA
1 AACAACTCATTAAAGGATTGCTGTAAACAA
794510 AACAAC
1 AACAAC
794516 CAGCTGTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 22
0.64 0.07 0.29
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 14 0.29
30 19 0.39
31 6 0.12
32 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (30 bp):
AACAACTCATTAAAGGATTGCTGTAAACAA
Found at i:794532 original size:30 final size:30
Alignment explanation
Indices: 794439--794533 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
794429 ACTAAAGGAT
794439 TGCTGTAAACAAAAC-ACCAGCTGTAAATG
1 TGCTGTAAACAAAACAACCAGCTGTAAATG
* * * *
794468 GGCTGTTATAC-ATACAACTCA--T-TAAAGG
1 TGCTG-TAAACAAAACAAC-CAGCTGTAAATG
794496 ATTGCTGTAAACAAAACAACCAGCTGTAAATG
1 --TGCTGTAAACAAAACAACCAGCTGTAAATG
794528 TGCTGT
1 TGCTGT
794534 TAATAATATA
Statistics
Matches: 49, Mismatches: 8, Indels: 17
0.66 0.11 0.23
Matches are distributed among these distances:
28 5 0.10
29 14 0.29
30 22 0.45
31 3 0.06
32 5 0.10
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (30 bp):
TGCTGTAAACAAAACAACCAGCTGTAAATG
Found at i:796216 original size:2 final size:2
Alignment explanation
Indices: 796209--796249 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
796199 TCTATTTGTC
796209 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
796250 TTTTCATGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:798771 original size:2 final size:2
Alignment explanation
Indices: 798764--798814 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
798754 GATTAGTTGA
798764 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
798805 -G AG AG AG AG A
1 AG AG AG AG AG A
798815 AGGGGGGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:799712 original size:3 final size:3
Alignment explanation
Indices: 799691--799787 Score: 88
Period size: 3 Copynumber: 32.3 Consensus size: 3
799681 GACGATGAAT
* *
799691 ATG ATG TTG ATG ATA ATG ATG ATG ACT- ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG A-TG ATG ATG ATG ATG ATG ATG
* * * ** * * *
799736 ACG ACG AAG AAA ATA ATA ATG ATG ATG ATG ATG ATG ATT ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
799784 ATG A
1 ATG A
799788 AACTAAATAA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
2 1 0.01
3 79 0.98
4 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:801169 original size:20 final size:21
Alignment explanation
Indices: 801139--801177 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
801129 TAAAAACTTT
801139 TTTTGAAAGATTTACCTGTAA
1 TTTTGAAAGATTTACCTGTAA
801160 TTTT-AAAGATTTACCTGT
1 TTTTGAAAGATTTACCTGT
801178 CGATAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTTGAAAGATTTACCTGTAA
Found at i:815133 original size:2 final size:2
Alignment explanation
Indices: 815120--815153 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
815110 ACTTTATTCT
* *
815120 AG AG AG AA AG AG AG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
815154 TGTGTTTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:815137 original size:12 final size:12
Alignment explanation
Indices: 815120--815150 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
815110 ACTTTATTCT
815120 AGAGAGAAAGAG
1 AGAGAGAAAGAG
815132 AGAGAGAAAGAG
1 AGAGAGAAAGAG
815144 AGAGAGA
1 AGAGAGA
815151 GAGTGTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (12 bp):
AGAGAGAAAGAG
Found at i:815158 original size:2 final size:2
Alignment explanation
Indices: 815153--815196 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
815143 GAGAGAGAGA
* *
815153 GT GT GT TT GT TT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
815195 GT
1 GT
815197 ACTTCTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
GT
Found at i:816983 original size:11 final size:11
Alignment explanation
Indices: 816945--816988 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
816935 GGTCCACTCG
*
816945 GGGTTCACTTT
1 GGGTTTACTTT
*
816956 GGGTTTACTGT
1 GGGTTTACTTT
816967 GGGTTTACTTT
1 GGGTTTACTTT
* *
816978 GAGTTTCCTTT
1 GGGTTTACTTT
816989 TGAGAATTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.09, C:0.14, G:0.27, T:0.50
Consensus pattern (11 bp):
GGGTTTACTTT
Found at i:821249 original size:66 final size:66
Alignment explanation
Indices: 821143--821275 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
821133 ATATATTTGC
821143 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA
1 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA
821208 A
66 A
* *
821209 TACACTAAAAATAATTTTAATGAACATTTAAGTTAGAACATAATAGTTGATTAACAGATCAGAAA
1 TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA
821274 A
66 A
821275 T
1 T
821276 TGATTGAAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.50, C:0.10, G:0.11, T:0.29
Consensus pattern (66 bp):
TACACTAAAAATAATTTAAATGAACATTTAAGCTAGAACATAATAGTTGATTAACAGATCAGAAA
A
Found at i:830189 original size:8 final size:8
Alignment explanation
Indices: 830176--830267 Score: 94
Period size: 8 Copynumber: 11.5 Consensus size: 8
830166 TTTCCTGTGC
*
830176 GTCCGTCA
1 GTCCGTCT
830184 GTCCGTCT
1 GTCCGTCT
*
830192 GTCTGTCT
1 GTCCGTCT
*
830200 GTCCGCCT
1 GTCCGTCT
830208 GTCCGTCT
1 GTCCGTCT
*
830216 GTCCGTCC
1 GTCCGTCT
830224 GTCCGTCT
1 GTCCGTCT
*
830232 GTCTGTCT
1 GTCCGTCT
* *
830240 GGCTGTCT
1 GTCCGTCT
* *
830248 GTCTGTCC
1 GTCCGTCT
*
830256 GTCTGTCT
1 GTCCGTCT
830264 GTCC
1 GTCC
830268 CACTTCAGTT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 71 1.00
ACGTcount: A:0.01, C:0.36, G:0.26, T:0.37
Consensus pattern (8 bp):
GTCCGTCT
Found at i:830195 original size:4 final size:4
Alignment explanation
Indices: 830188--830266 Score: 86
Period size: 4 Copynumber: 19.8 Consensus size: 4
830178 CCGTCAGTCC
* * * * * *
830188 GTCT GTCT GTCT GTCC GCCT GTCC GTCT GTCC GTCC GTCC GTCT GTCT
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT
* *
830236 GTCT GGCT GTCT GTCT GTCC GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTC
830267 CCACTTCAGT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.00, C:0.34, G:0.27, T:0.39
Consensus pattern (4 bp):
GTCT
Found at i:831779 original size:21 final size:21
Alignment explanation
Indices: 831753--831796 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
831743 TTTTAGATTC
831753 GCACGAGCTCTCGCATACGTT
1 GCACGAGCTCTCGCATACGTT
* *
831774 GCACGAGCTCTCGGATTCGTT
1 GCACGAGCTCTCGCATACGTT
831795 GC
1 GC
831797 GTTTTAGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.27, T:0.25
Consensus pattern (21 bp):
GCACGAGCTCTCGCATACGTT
Found at i:834574 original size:2 final size:2
Alignment explanation
Indices: 834567--834591 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
834557 TTCTACAAAT
834567 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
834592 TTTTTTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:841362 original size:2 final size:2
Alignment explanation
Indices: 841355--841397 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
841345 NNNNNNNNNN
*
841355 GA GA GA GA GA AA 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 GA
841397 G
1 G
841398 GGGGGGGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:846577 original size:135 final size:134
Alignment explanation
Indices: 846299--846583 Score: 321
Period size: 134 Copynumber: 2.1 Consensus size: 134
846289 TGACCCCTAA
* * * * * *
846299 ACCATATATATTCATGTTTCTGATATCAAGGGGCATCAAATGTTTTGTAGGTCATGAGCCCTGTG
1 ACCATATATATTCTTGTTCCTGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAGCCCCGTG
* * * * *
846364 GGTGGTCCTGATCCCCTCAAACAGCAAGTCCCTTAATATCTTAAAATCAGTTGAGATCCCCACCC
66 GGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTGAAAATCAGTTGAGATCCCCACCC
846429 TTAC
131 TTAC
*
846433 ACCATATATATTCTTGTTCCTTG-TGTCAAGGGGCATCAAACGGTATGTAGGTCATG-GACCCCG
1 ACCATATATATTCTTGTTCC-TGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAG-CCCCG
* * * *
846496 -GGGATGGTCATGACCCCCCTCGAACAGGAAGTGCAC-GAATATCTCGAAAA-CGGTTGAGATTC
64 TGGG-TGGTCATGA-CCCCCTCAAACAGCAAGT-CACTGAATATCT-GAAAATCAGTTGAGATCC
846558 CCACCCCTT-C
125 CCA-CCCTTAC
846568 ACCATATATATTCTTG
1 ACCATATATATTCTTG
846584 ATCCAAAGGT
Statistics
Matches: 128, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
133 4 0.03
134 59 0.46
135 54 0.42
136 11 0.09
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (134 bp):
ACCATATATATTCTTGTTCCTGATATCAAGGGGCATCAAACGGTATGTAGGTCATGAGCCCCGTG
GGTGGTCATGACCCCCTCAAACAGCAAGTCACTGAATATCTGAAAATCAGTTGAGATCCCCACCC
TTAC
Found at i:852265 original size:19 final size:19
Alignment explanation
Indices: 852241--852293 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
852231 GGTGTGGCAG
* *
852241 ATCACGTAAATCACGCGAA
1 ATCACGTTAATCACGCCAA
**
852260 ATCACGTTAATCATACCAA
1 ATCACGTTAATCACGCCAA
852279 ATCACGTTAATCACG
1 ATCACGTTAATCACG
852294 GTATTGCTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.40, C:0.26, G:0.11, T:0.23
Consensus pattern (19 bp):
ATCACGTTAATCACGCCAA
Found at i:855003 original size:22 final size:22
Alignment explanation
Indices: 854979--855097 Score: 150
Period size: 22 Copynumber: 5.4 Consensus size: 22
854969 TACTTAACGA
* * *
854979 TTACTTAAAGGTGACGGAAATA
1 TTACTTAAATGTGACTGAAATG
*
855001 TTACTGAAATGTGACTGAAATG
1 TTACTTAAATGTGACTGAAATG
* *
855023 TTACTGAAATGTGACTGAAAGG
1 TTACTTAAATGTGACTGAAATG
*
855045 TTACTTAAATGTGACTGAAAGG
1 TTACTTAAATGTGACTGAAATG
*
855067 TTACTTAAATGTGACT-TAATGG
1 TTACTTAAATGTGACTGAAAT-G
855089 TTACTTAAA
1 TTACTTAAA
855098 GGTAACGGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
21 2 0.02
22 86 0.98
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (22 bp):
TTACTTAAATGTGACTGAAATG
Found at i:855085 original size:11 final size:11
Alignment explanation
Indices: 854989--855082 Score: 98
Period size: 11 Copynumber: 8.5 Consensus size: 11
854979 TTACTTAAAG
*
854989 GTGACGGAAAT
1 GTGACTGAAAT
* *
855000 ATTACTGAAAT
1 GTGACTGAAAT
855011 GTGACTGAAAT
1 GTGACTGAAAT
*
855022 GTTACTGAAAT
1 GTGACTGAAAT
*
855033 GTGACTGAAAG
1 GTGACTGAAAT
* *
855044 GTTACTTAAAT
1 GTGACTGAAAT
*
855055 GTGACTGAAAG
1 GTGACTGAAAT
* *
855066 GTTACTTAAAT
1 GTGACTGAAAT
855077 GTGACT
1 GTGACT
855083 TAATGGTTAC
Statistics
Matches: 65, Mismatches: 18, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 65 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (11 bp):
GTGACTGAAAT
Found at i:866349 original size:2 final size:2
Alignment explanation
Indices: 866342--866425 Score: 159
Period size: 2 Copynumber: 42.0 Consensus size: 2
866332 TATGTTGACA
*
866342 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
866384 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
866426 ATTGTTTACT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:867984 original size:4 final size:4
Alignment explanation
Indices: 867977--868071 Score: 79
Period size: 4 Copynumber: 24.2 Consensus size: 4
867967 ACTCTCTCTT
* * * * * * * *
867977 TCTG TCTG TCTG TCCG TCCG TCCG TCCG TCCG TCCG TCTG TCCG TCCG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
*
868025 T-TCG TCCG TCTG TCTG TCTG TCTG TCTG --TG TCTG TCTG TCTG TCTG
1 TCT-G TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
868071 T
1 T
868072 GTGTGTGTGT
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
2 2 0.02
4 79 0.98
ACGTcount: A:0.00, C:0.34, G:0.25, T:0.41
Consensus pattern (4 bp):
TCTG
Found at i:868047 original size:12 final size:12
Alignment explanation
Indices: 867977--868071 Score: 88
Period size: 12 Copynumber: 8.1 Consensus size: 12
867967 ACTCTCTCTT
*
867977 TCTGTCTGTCTG
1 TCTGTCCGTCTG
* *
867989 TCCGTCCGTCCG
1 TCTGTCCGTCTG
* *
868001 TCCGTCCGTCCG
1 TCTGTCCGTCTG
*
868013 TCTGTCCGTCCG
1 TCTGTCCGTCTG
868025 T-TCGTCCGTCTG
1 TCT-GTCCGTCTG
*
868037 TCTGTCTGTCTG
1 TCTGTCCGTCTG
868049 TCTGT--GTCTG
1 TCTGTCCGTCTG
*
868059 TCTGTCTGTCTG
1 TCTGTCCGTCTG
868071 T
1 T
868072 GTGTGTGTGT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
10 10 0.14
11 1 0.01
12 61 0.84
13 1 0.01
ACGTcount: A:0.00, C:0.34, G:0.25, T:0.41
Consensus pattern (12 bp):
TCTGTCCGTCTG
Found at i:868058 original size:14 final size:14
Alignment explanation
Indices: 868039--868067 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
868029 TCCGTCTGTC
868039 TGTCTGTCTGTCTG
1 TGTCTGTCTGTCTG
868053 TGTCTGTCTGTCTG
1 TGTCTGTCTGTCTG
868067 T
1 T
868068 CTGTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.28, T:0.52
Consensus pattern (14 bp):
TGTCTGTCTGTCTG
Found at i:868058 original size:18 final size:18
Alignment explanation
Indices: 868035--868083 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
868025 TTCGTCCGTC
868035 TGTCTGTCTGTCTGTCTG
1 TGTCTGTCTGTCTGTCTG
868053 TGTCTGTCTGTCTGTCTG
1 TGTCTGTCTGTCTGTCTG
* *
868071 TGTGTGTGTGTCT
1 TGTCTGTCTGTCT
868084 CTCTCTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.00, C:0.18, G:0.31, T:0.51
Consensus pattern (18 bp):
TGTCTGTCTGTCTGTCTG
Found at i:868086 original size:2 final size:2
Alignment explanation
Indices: 868081--868112 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
868071 TGTGTGTGTG
868081 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
868113 ACTCAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.