Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold348
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: 1216543
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.31
Warning! 64198 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:425707 original size:42 final size:42
Alignment explanation
Indices: 425661--425749 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
425651 TCATGTTTAA
* *
425661 GAGCATCATCATTTTGGATGAACTGTTTAGGCTTGTGCTTAG
1 GAGCATCAACATTTTGGATGAACTGCTTAGGCTTGTGCTTAG
*
425703 GAGCATCAACATTTTGGATGAATTGCTTAGGCTTGTGCTTAG
1 GAGCATCAACATTTTGGATGAACTGCTTAGGCTTGTGCTTAG
425745 GAGCA
1 GAGCA
425750 ATGTGACAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.35
Consensus pattern (42 bp):
GAGCATCAACATTTTGGATGAACTGCTTAGGCTTGTGCTTAG
Found at i:430000 original size:50 final size:49
Alignment explanation
Indices: 429886--430011 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 49
429876 TTCCAAAGCT
*
429886 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTACTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGCC
* * * *
429935 ATATCCCAAATATGGTCTTACATGGGA-GTTCTCATATCG-A-TGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGATGTT-TC-T-T-GTACTGCCAATGCC
429985 ATGTCCCAGACATGGTCTTACATGGGA
1 ATGTCCCAGACATGGTCTTACATGGGA
430012 CCTCATTCCT
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
48 3 0.05
49 25 0.38
50 34 0.52
51 2 0.03
52 1 0.02
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (49 bp):
ATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGCC
Found at i:432356 original size:17 final size:17
Alignment explanation
Indices: 432334--432369 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
432324 AATAGATAAC
432334 ATAGATAAAATTAATAT
1 ATAGATAAAATTAATAT
432351 ATAGATAAAATTAATAT
1 ATAGATAAAATTAATAT
432368 AT
1 AT
432370 GAATTTGATT
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:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAGATAAAATTAATAT
Found at i:436627 original size:12 final size:12
Alignment explanation
Indices: 436604--436640 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 12
436594 AAATGTGATC
436604 AATTACACTAAAT
1 AATTA-ACTAAAT
436617 AATTAACTAAAT
1 AATTAACTAAAT
436629 AATTAAACTAAA
1 AATT-AACTAAA
436641 AATATGTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTAACTAAAT
Found at i:436687 original size:12 final size:13
Alignment explanation
Indices: 436669--436701 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
436659 AGTGATCTAA
436669 AAACTAAATAATT
1 AAACTAAATAATT
436682 -AACTAAATAATT
1 AAACTAAATAATT
436694 AAACTAAA
1 AAACTAAA
436702 AATAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (13 bp):
AAACTAAATAATT
Found at i:443217 original size:18 final size:18
Alignment explanation
Indices: 443184--443248 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
443174 TAAAAAAAAC
443184 ATTTGAAAATTGAATAACG
1 ATTTGAAAA-TGAATAACG
* *
443203 ATTTGTAAATGAATAATG
1 ATTTGAAAATGAATAACG
* * *
443221 TTTTGGAAATGAACGACACG
1 ATTTGAAAATGAA-TA-ACG
443241 ATTTGAAA
1 ATTTGAAA
443249 TTAGCATAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
18 19 0.53
19 9 0.25
20 8 0.22
ACGTcount: A:0.43, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
ATTTGAAAATGAATAACG
Found at i:443442 original size:14 final size:14
Alignment explanation
Indices: 443423--443453 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
443413 TGGGTTTTTT
443423 TAAGAACTGATTTC
1 TAAGAACTGATTTC
443437 TAAGAACTGATTTC
1 TAAGAACTGATTTC
443451 TAA
1 TAA
443454 ATGTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (14 bp):
TAAGAACTGATTTC
Found at i:449681 original size:18 final size:18
Alignment explanation
Indices: 449637--449681 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
449627 GCAATAAAAA
449637 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
449655 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
449673 AATGTTTTG
1 AACGTTTTG
449682 GGAACGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:450359 original size:34 final size:34
Alignment explanation
Indices: 450295--450364 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
450285 TTAAGAAAAA
*
450295 AATATCTTGCAACCTTTGTAAAAATATTAATAAG
1 AATATCTTGCAACCTTCGTAAAAATATTAATAAG
450329 AATATCTTGCAACCTTCGTAAAAATATTAATAAG
1 AATATCTTGCAACCTTCGTAAAAATATTAATAAG
450363 AA
1 AA
450365 CTTAAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.33
Consensus pattern (34 bp):
AATATCTTGCAACCTTCGTAAAAATATTAATAAG
Found at i:450907 original size:3 final size:3
Alignment explanation
Indices: 450899--450943 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
450889 AAACTATACG
450899 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
450944 ATACTATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:455076 original size:14 final size:14
Alignment explanation
Indices: 455057--455088 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
455047 TCTAGGGTGT
455057 GAATCAGGTTTATA
1 GAATCAGGTTTATA
455071 GAATCAGGTTTATA
1 GAATCAGGTTTATA
455085 -AATC
1 GAATC
455089 GAGAGAGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (14 bp):
GAATCAGGTTTATA
Found at i:467629 original size:16 final size:17
Alignment explanation
Indices: 467601--467639 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
467591 TGGAGTTGAA
467601 TGAG-ATGGAAAAATTT
1 TGAGCATGGAAAAATTT
467617 TGAGCATGGAAAAATTT
1 TGAGCATGGAAAAATTT
*
467634 CGAGCA
1 TGAGCA
467640 CAAGCCTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.26
Consensus pattern (17 bp):
TGAGCATGGAAAAATTT
Found at i:471926 original size:34 final size:34
Alignment explanation
Indices: 471888--471957 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
471878 AACACACTAG
* * *
471888 ATGCTTGTATGAGCCAGCCCATCCAGCACACCAA
1 ATGCTCGTATGAGCAAACCCATCCAGCACACCAA
*
471922 ATGCTCGTATGAGCAAATCCATCCAGCACACCAA
1 ATGCTCGTATGAGCAAACCCATCCAGCACACCAA
471956 AT
1 AT
471958 AACACTGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.19
Consensus pattern (34 bp):
ATGCTCGTATGAGCAAACCCATCCAGCACACCAA
Found at i:473573 original size:17 final size:17
Alignment explanation
Indices: 473553--473606 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
473543 TATAAACATA
473553 ACATAAATCATTAATTC
1 ACATAAATCATTAATTC
* * *
473570 ACAT--A-CATAAACATA
1 ACATAAATCATTAA-TTC
473585 ACATAAATCATTAATTC
1 ACATAAATCATTAATTC
473602 ACATA
1 ACATA
473607 CATATTACCT
Statistics
Matches: 27, Mismatches: 6, Indels: 8
0.66 0.15 0.20
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 11 0.41
18 5 0.19
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.30
Consensus pattern (17 bp):
ACATAAATCATTAATTC
Found at i:473581 original size:32 final size:32
Alignment explanation
Indices: 473544--473610 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
473534 ATACATTAAT
473544 ATAAACATAACATAAATCATTAATTCACATAC
1 ATAAACATAACATAAATCATTAATTCACATAC
473576 ATAAACATAACATAAATCATTAATTCACATAC
1 ATAAACATAACATAAATCATTAATTCACATAC
473608 ATA
1 ATA
473611 TTACCTCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.28
Consensus pattern (32 bp):
ATAAACATAACATAAATCATTAATTCACATAC
Found at i:478312 original size:32 final size:32
Alignment explanation
Indices: 478271--478339 Score: 79
Period size: 32 Copynumber: 2.1 Consensus size: 32
478261 TGGATAAGTT
478271 TTAATGTAATTATGAAAATTT-TTAAAAGGTTAA
1 TTAATGTAATT-TGAAAATTTATT-AAAGGTTAA
* *
478304 TTAA-GTAATTTGATAATTTAGTTAAATGTTAA
1 TTAATGTAATTTGAAAATTTA-TTAAAGGTTAA
478336 TTAA
1 TTAA
478340 ATAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 8 0.25
32 18 0.56
33 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (32 bp):
TTAATGTAATTTGAAAATTTATTAAAGGTTAA
Found at i:478667 original size:40 final size:40
Alignment explanation
Indices: 478623--478805 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
478613 AATTATTGTA
*
478623 TGAATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
478663 TGAATGCACATA-GATGCCCTTATTTGTAC-TCTGGTACCCA
1 TGAATGCACATACG-TGCCCCTGTTTGTACTTC-GGTACCCC
* **
478703 TAAATGCACATTTGTGCCCCTGTTTG-ACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
478742 TAAATGCACATACTTG-CCCTGATTTGTACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTG-TTTGTACTTCGGTACCCC
* *
478782 TGAATGCACATGCATG-CCCTGTTT
1 TGAATGCACATACGTGCCCCTGTTT
478806 AAACTCCGGT
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
38 5 0.04
39 31 0.25
40 85 0.70
41 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:478760 original size:79 final size:80
Alignment explanation
Indices: 478625--478805 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 80
478615 TTATTGTATG
* * * *
478625 AATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGAATGCACATAGATGCCCTTATTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATGCACATACATGCCCTGATTTGT
478690 AC-TCTGGTACCCATA
66 ACTTC-GGTACCCATA
** *
478705 AATGCACATTTGTGCCCCTGTTTG-ACTTCGGTACCCCTAAATGCACATACTTGCCCTGATTTGT
1 AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATGCACATACATGCCCTGATTTGT
* *
478769 ACTTCGGTACCCCTG
66 ACTTCGGTACCCATA
* *
478784 AATGCACATGCATG-CCCTGTTT
1 AATGCACATACGTGCCCCTGTTT
478806 AAACTCCGGT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
78 8 0.09
79 56 0.64
80 24 0.27
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.33
Consensus pattern (80 bp):
AATGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTAAATGCACATACATGCCCTGATTTGT
ACTTCGGTACCCATA
Found at i:485368 original size:19 final size:21
Alignment explanation
Indices: 485346--485384 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
485336 GAATAAACCA
485346 AGTG-GAG-GGTCAACACACC
1 AGTGTGAGAGGTCAACACACC
*
485365 AGTGTGGGAGGTCAACACAC
1 AGTGTGAGAGGTCAACACAC
485385 TCGTGTAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 2 0.12
21 11 0.65
ACGTcount: A:0.31, C:0.23, G:0.33, T:0.13
Consensus pattern (21 bp):
AGTGTGAGAGGTCAACACACC
Found at i:490545 original size:17 final size:17
Alignment explanation
Indices: 490520--490553 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
490510 AAAGTAGTTC
490520 AAAACAAAAATAATAAT
1 AAAACAAAAATAATAAT
* *
490537 AAAATAAAACTAATAAT
1 AAAACAAAAATAATAAT
490554 TATTTTTTAA
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:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAACAAAAATAATAAT
Found at i:504811 original size:33 final size:33
Alignment explanation
Indices: 504758--504822 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
504748 TATTTATGCC
*
504758 TTAAATTGAAAATATTTTTTA-TATAGGGGGAGT
1 TTAAATTGAAAATATATTTTATTA-AGGGGGAGT
504791 TTAAATTGAAAATGA-ATTTTATTAAGGGGGAG
1 TTAAATTGAAAAT-ATATTTTATTAAGGGGGAG
504823 CAATTTATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (33 bp):
TTAAATTGAAAATATATTTTATTAAGGGGGAGT
Found at i:506939 original size:14 final size:14
Alignment explanation
Indices: 506920--506953 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
506910 TCATCATTTG
506920 CCTATAACCAAAAC
1 CCTATAACCAAAAC
*
506934 CCTATAACTAAAAC
1 CCTATAACCAAAAC
506948 CC-ATAA
1 CCTATAA
506954 ACCCATACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:508465 original size:18 final size:18
Alignment explanation
Indices: 508432--508483 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
508422 TCGTAAATCG
* * *
508432 GATTCCGATTCTGGTTCG
1 GATTCGGATTCAGGTTCC
* *
508450 GGTTCGGGTTCAGGTTCC
1 GATTCGGATTCAGGTTCC
508468 GATTCGGATTCAGGTT
1 GATTCGGATTCAGGTT
508484 AGGGAACTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.12, C:0.19, G:0.33, T:0.37
Consensus pattern (18 bp):
GATTCGGATTCAGGTTCC
Found at i:515991 original size:71 final size:71
Alignment explanation
Indices: 515879--516014 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 71
515869 AATTGTGAAG
* * * *
515879 GAGATTGGTTGATATGTTAGAGCTCGAATGCTTTAGATGGTAAGATGAATGTTGTTGTCGGACAA
1 GAGATTGATTGATATGTTAGAGCTCAAATGCTTTAGATGGTAAAAGGAATGTTGTTGTCGGACAA
515944 ATTTGT
66 ATTTGT
* *
515950 GAGATTGATTGATATGTTAGAGCTCAAATGCTTTATATGGTAAAAGGAATTTTGTTGTCGGACAA
1 GAGATTGATTGATATGTTAGAGCTCAAATGCTTTAGATGGTAAAAGGAATGTTGTTGTCGGACAA
516015 GCCTATCAAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.29, C:0.07, G:0.27, T:0.36
Consensus pattern (71 bp):
GAGATTGATTGATATGTTAGAGCTCAAATGCTTTAGATGGTAAAAGGAATGTTGTTGTCGGACAA
ATTTGT
Found at i:518083 original size:20 final size:20
Alignment explanation
Indices: 518058--518115 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 20
518048 CATGGCATTG
518058 ACTACCAACATTGTTAAAAT
1 ACTACCAACATTGTTAAAAT
* *
518078 ACTACCAAC-TTGGTATAAT
1 ACTACCAACATTGTTAAAAT
518097 ACT---AACATTGTTAAAAT
1 ACTACCAACATTGTTAAAAT
518114 AC
1 AC
518116 GTTGACACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 3 0.09
17 10 0.30
19 11 0.33
20 9 0.27
ACGTcount: A:0.43, C:0.19, G:0.07, T:0.31
Consensus pattern (20 bp):
ACTACCAACATTGTTAAAAT
Found at i:523173 original size:88 final size:88
Alignment explanation
Indices: 523080--523345 Score: 532
Period size: 88 Copynumber: 3.0 Consensus size: 88
523070 CTCTCATCAA
523080 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
1 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
523145 ATGAATTTTTCTTACTAGTATAT
66 ATGAATTTTTCTTACTAGTATAT
523168 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
1 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
523233 ATGAATTTTTCTTACTAGTATAT
66 ATGAATTTTTCTTACTAGTATAT
523256 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
1 AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
523321 ATGAATTTTTCTTACTAGTATAT
66 ATGAATTTTTCTTACTAGTATAT
523344 AA
1 AA
523346 TTGTTTTATT
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 178 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (88 bp):
AACAAAAATTAATGCAGGGAAAACAAAGTGGGAAAAACAACTTTTTTCTTCTTTTCCTACACAAC
ATGAATTTTTCTTACTAGTATAT
Found at i:523756 original size:17 final size:17
Alignment explanation
Indices: 523736--523772 Score: 51
Period size: 15 Copynumber: 2.2 Consensus size: 17
523726 GAATAATGAA
523736 GTTTTAGGAATAACTA-T
1 GTTTTA-GAATAACTATT
523753 G-TTTAGAATAACTATT
1 GTTTTAGAATAACTATT
523769 GTTT
1 GTTT
523773 GGAACAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 9 0.50
16 6 0.33
17 3 0.17
ACGTcount: A:0.32, C:0.05, G:0.16, T:0.46
Consensus pattern (17 bp):
GTTTTAGAATAACTATT
Found at i:523757 original size:16 final size:16
Alignment explanation
Indices: 523738--523786 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
523728 ATAATGAAGT
523738 TTTAGGAATAACTATG
1 TTTAGGAATAACTATG
523754 TTTA-GAATAACTATTG
1 TTTAGGAATAACTA-TG
*
523770 TTT-GGAACAACT-TG
1 TTTAGGAATAACTATG
523784 TTT
1 TTT
523787 TTAGAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 5 0.17
15 9 0.30
16 16 0.53
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (16 bp):
TTTAGGAATAACTATG
Found at i:523763 original size:15 final size:15
Alignment explanation
Indices: 523720--523786 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
523710 GAACAATTAT
523720 TGTTTAGAATAA-TGA
1 TGTTTAGAATAACT-A
*
523735 AGTTTTAGGAATAACTA
1 TG-TTTA-GAATAACTA
523752 TGTTTAGAATAACTA
1 TGTTTAGAATAACTA
* *
523767 TTGTTTGGAACAACT-
1 -TGTTTAGAATAACTA
523782 TGTTT
1 TGTTT
523787 TTAGAATAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.11
15 10 0.23
16 20 0.45
17 8 0.18
18 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.42
Consensus pattern (15 bp):
TGTTTAGAATAACTA
Found at i:525810 original size:20 final size:20
Alignment explanation
Indices: 525782--525825 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
525772 ATTGTACTTC
525782 GGTGACTCTATTTGCACTCT
1 GGTGACTCTATTTGCACTCT
* *
525802 GGTGTCTCTGTTTGCACTCT
1 GGTGACTCTATTTGCACTCT
525822 GGTG
1 GGTG
525826 CCTTTGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.23, G:0.27, T:0.41
Consensus pattern (20 bp):
GGTGACTCTATTTGCACTCT
Found at i:525836 original size:20 final size:20
Alignment explanation
Indices: 525793--525839 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
525783 GTGACTCTAT
* *
525793 TTGCACTCTGGTGTCTCTGT
1 TTGCACTCTGGTGCCTCTGA
*
525813 TTGCACTCTGGTGCCTTTGA
1 TTGCACTCTGGTGCCTCTGA
525833 TTGCACT
1 TTGCACT
525840 ATCGTACCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (20 bp):
TTGCACTCTGGTGCCTCTGA
Found at i:528063 original size:18 final size:18
Alignment explanation
Indices: 528028--528062 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
528018 TATAAAATGC
*
528028 AAACTTTATATATATTTT
1 AAACTTAATATATATTTT
528046 AAACTTAATATAT-TTTT
1 AAACTTAATATATATTTT
528063 TGAAAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (18 bp):
AAACTTAATATATATTTT
Found at i:530313 original size:24 final size:23
Alignment explanation
Indices: 530286--530333 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
530276 AAAAATATTT
530286 AAAAAGAAAATATAAATTATAAAA
1 AAAAAGAAAATATAAATT-TAAAA
***
530310 AAAATTTAAATATAAATTTAAAA
1 AAAAAGAAAATATAAATTTAAAA
530333 A
1 A
530334 CATTTTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAAAGAAAATATAAATTTAAAA
Found at i:530323 original size:17 final size:19
Alignment explanation
Indices: 530287--530325 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
530277 AAAATATTTA
530287 AAAAGAAAATATAAATTAT
1 AAAAGAAAATATAAATTAT
*
530306 AAAA-AAAATTTAAA-TAT
1 AAAAGAAAATATAAATTAT
530323 AAA
1 AAA
530326 TTTAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 9 0.47
19 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
AAAAGAAAATATAAATTAT
Found at i:530326 original size:12 final size:12
Alignment explanation
Indices: 530293--530331 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
530283 TTTAAAAAGA
530293 AAATATAAATTAT
1 AAATATAAATT-T
*
530306 AAA-AAAAATTT
1 AAATATAAATTT
530317 AAATATAAATTT
1 AAATATAAATTT
530329 AAA
1 AAA
530332 AACATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 16 0.70
13 3 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATATAAATTT
Found at i:532186 original size:87 final size:87
Alignment explanation
Indices: 532016--532178 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 87
532006 TTAAATTCGG
* *
532016 TGAATTCATCAAGTCCATCTCATTAGGACCACCCAAACTTTAGGATATGAACTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAGAGTAA
532081 GAAACTTAACCTCACATGTCGA
66 GAAACTTAACCTCACATGTCGA
* * * * * * *
532103 TGAATTCATTAAGTTCATCTCAATATGACCATCTAAACTCTGGGATATGAATTCATTAAGAGTAA
1 TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAGAGTAA
532168 G-AACTTAACCT
66 GAAACTTAACCT
532179 TAGCATGTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
86 10 0.15
87 57 0.85
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (87 bp):
TGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTAGGATATGAACTCATTAAGAGTAA
GAAACTTAACCTCACATGTCGA
Found at i:535871 original size:22 final size:22
Alignment explanation
Indices: 535846--535897 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
535836 CAGGATGTCA
*
535846 TGTCGCGACATCGAGTGTATGT
1 TGTCGCGACATCGAATGTATGT
** *
535868 TGTCATGACATTGAATGTATGT
1 TGTCGCGACATCGAATGTATGT
*
535890 CGTCGCGA
1 TGTCGCGA
535898 TGAGATTAGG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.33
Consensus pattern (22 bp):
TGTCGCGACATCGAATGTATGT
Found at i:537360 original size:12 final size:12
Alignment explanation
Indices: 537343--537367 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
537333 TATCTTTAGT
537343 TGGAAAAGTGAA
1 TGGAAAAGTGAA
537355 TGGAAAAGTGAA
1 TGGAAAAGTGAA
537367 T
1 T
537368 TCGTTTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (12 bp):
TGGAAAAGTGAA
Found at i:538600 original size:21 final size:21
Alignment explanation
Indices: 538565--538634 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 21
538555 TAAGTAATAC
* *
538565 TAACTTGTTTTAAAACAGTTT
1 TAACTTGATTGAAAACAGTTT
*
538586 TAACTTGATTGAAAA-TG-TT
1 TAACTTGATTGAAAACAGTTT
** *
538605 TAACTCAATTGAAACCA-TTT
1 TAACTTGATTGAAAACAGTTT
*
538625 TAACCTGATT
1 TAACTTGATT
538635 TTATCATTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
19 14 0.38
20 10 0.27
21 13 0.35
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (21 bp):
TAACTTGATTGAAAACAGTTT
Found at i:538795 original size:46 final size:46
Alignment explanation
Indices: 538728--538911 Score: 368
Period size: 46 Copynumber: 4.0 Consensus size: 46
538718 GCTAGGTATA
538728 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
1 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
538774 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
1 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
538820 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
1 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
538866 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
1 ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
538912 GGTGATCGGT
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 138 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (46 bp):
ACATAGTTGCTCCAACAACAGATGTGGCAATCCGTTGCTCAAACCT
Found at i:555385 original size:357 final size:357
Alignment explanation
Indices: 554726--555416 Score: 938
Period size: 357 Copynumber: 1.9 Consensus size: 357
554716 AAATAAAGTA
** * *
554726 GTTTTCAGGATCCACACGGCCTAGGCATTTCCATACGGGCTGCATACATGCCCATGTGCCAACCT
1 GTTTTCAGGATCCACACAACCTAGGCATTTCCACACGGGCTGCATACATGCCCATGTGCCAACCG
* * * * *
554791 GTGCCGATTTCGCACCCTACTTCCTAAAGACACGAAAAAACCTAATTTTTACGGTTTCTGAGAAT
66 GTGCCGATTTCACACCCTACTTCCCAAAGACACGAAAAAACCCAATTTTTACGGTCTCTAAGAAT
* * *
554856 TCTAAAGTCTATAAATACAAATTAAAATAAGACATAAGGGGCAATCAGAGAATATTGAAGAAAAC
131 TCTAAAGTCTATAAATACAAATTAAAAGAAGACATAAGGGGCAATCAGAGAAGATCGAAGAAAAC
* * * * * *
554921 ACTAGAAAAACACCATCGGAATCAACTTGGAAGTAGATCTTCATTAAGATTGAAGACCTTCTTTT
196 ACTAGAAAAACACCATCAGAATCAACTCGGAAGCAGATCTCCATCAAGATTGAAGACCTCCTTTT
* * * *
554986 AATTTCATTTGAAGTTTTATTGAGTTTCTTTATGTCTTGTGGTTTTTCTGACTTTTAGATGTTTC
261 AATTTCATTTAAAATTTTATTGAGTTTCTTTATGTCTTGTGGTTTTTCTGACTATGAGATGTTTC
*
555051 TATTCAGGATTTCAAACTTATTCCCTAGAGTT
326 TAATCAGGATTTCAAACTTATTCCCTAGAGTT
* * *
555083 GTTTTCAGGATCCACACAACCTGGGCATTTCCACACGGGCTAG-ATACATGCCCATGTGCTAGCC
1 GTTTTCAGGATCCACACAACCTAGGCATTTCCACACGGGCT-GCATACATGCCCATGTGCCAACC
* * *** * * *
555147 GGTGCTGATTTCACACCCTACTTCCCAAATATGTG-GAAAACCCAATTTTTAGGGTCTCTAAGCA
65 GGTGCCGATTTCACACCCTACTTCCCAAAGACACGAAAAAACCCAATTTTTACGGTCTCTAAGAA
* * ** *
555211 TTCTAAATTCTATTAATACCCATTAAAAGAAGACATAAGGGGACAATCAGAGAAGATCGGAGAAA
130 TTCTAAAGTCTATAAATACAAATTAAAAGAAGACATAAGGGG-CAATCAGAGAAGATCGAAGAAA
* * * *
555276 ACACTCGAAGAAGACCATCAGAATCAACTCGGAAGCGGATCTCCATCAAGATTGAAGACCTCCTT
194 ACACTAGAAAAACACCATCAGAATCAACTCGGAAGCAGATCTCCATCAAGATTGAAGACCTCCTT
*
555341 TTAATTTC-TTTCAAAATTTTATTGAGTTTCTTTATGTGTTGTGGTTTTTCTGACTATGAGATGT
259 TTAATTTCATTT-AAAATTTTATTGAGTTTCTTTATGTCTTGTGGTTTTTCTGACTATGAGATGT
555405 TTCTAATCAGGA
323 TTCTAATCAGGA
555417 CTATGAACTA
Statistics
Matches: 287, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
356 63 0.22
357 223 0.78
358 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (357 bp):
GTTTTCAGGATCCACACAACCTAGGCATTTCCACACGGGCTGCATACATGCCCATGTGCCAACCG
GTGCCGATTTCACACCCTACTTCCCAAAGACACGAAAAAACCCAATTTTTACGGTCTCTAAGAAT
TCTAAAGTCTATAAATACAAATTAAAAGAAGACATAAGGGGCAATCAGAGAAGATCGAAGAAAAC
ACTAGAAAAACACCATCAGAATCAACTCGGAAGCAGATCTCCATCAAGATTGAAGACCTCCTTTT
AATTTCATTTAAAATTTTATTGAGTTTCTTTATGTCTTGTGGTTTTTCTGACTATGAGATGTTTC
TAATCAGGATTTCAAACTTATTCCCTAGAGTT
Found at i:558931 original size:16 final size:16
Alignment explanation
Indices: 558912--558944 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
558902 TTTATTTCAT
*
558912 ATTATTTTTAAAAATA
1 ATTAATTTTAAAAATA
558928 ATTAATTTTAAAAATA
1 ATTAATTTTAAAAATA
558944 A
1 A
558945 AAAAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAATTTTAAAAATA
Found at i:559807 original size:9 final size:9
Alignment explanation
Indices: 559795--559828 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
559785 CCCTTTTCCC
*
559795 TATTTTCTT
1 TATTTTATT
559804 TATTTTATT
1 TATTTTATT
559813 TA-TTTATT
1 TATTTTATT
559821 TATTTTAT
1 TATTTTAT
559829 ATTTCCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TATTTTATT
Found at i:561790 original size:21 final size:21
Alignment explanation
Indices: 561766--561805 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
561756 CGGCAGTTGC
561766 TTTCTTTTATGCCAATTTTAT
1 TTTCTTTTATGCCAATTTTAT
*
561787 TTTCTTTTATGCCAGTTTT
1 TTTCTTTTATGCCAATTTT
561806 TTGGTGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTCTTTTATGCCAATTTTAT
Found at i:562616 original size:19 final size:18
Alignment explanation
Indices: 562582--562635 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
562572 TGGGCTGTTC
562582 TGGGCCTTGTTGGGCCGAAA
1 TGGGCCTTG-TGGGCC-AAA
* *
562602 TGGGCCGTGTGGGCCCAA
1 TGGGCCTTGTGGGCCAAA
562620 TGGG-CTTGTGGGCCAA
1 TGGGCCTTGTGGGCCAA
562636 CACGGGTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 10 0.33
18 6 0.20
19 6 0.20
20 8 0.27
ACGTcount: A:0.13, C:0.22, G:0.43, T:0.22
Consensus pattern (18 bp):
TGGGCCTTGTGGGCCAAA
Found at i:562879 original size:27 final size:27
Alignment explanation
Indices: 562849--563086 Score: 200
Period size: 27 Copynumber: 8.8 Consensus size: 27
562839 AAAATTATTG
*
562849 AAATACCCTCGATGGGTAAAATTACCA
1 AAATACCCTCAATGGGTAAAATTACCA
* * *
562876 AAATACCCT-AGATGGGAAAAATTATCG
1 AAATACCCTCA-ATGGGTAAAATTACCA
* * *
562903 AAATACCCTTAATAGGTAAAATTACCG
1 AAATACCCTCAATGGGTAAAATTACCA
* * * *
562930 AAATACCCCCGATGGGAAAAATTATCA
1 AAATACCCTCAATGGGTAAAATTACCA
*
562957 AAATACTCC-CAATGGGTAAAATTACCG
1 AAATAC-CCTCAATGGGTAAAATTACCA
* * *
562984 AAATA-CCTCCGATGGGTAAAGTTATCA
1 AAATACCCT-CAATGGGTAAAATTACCA
*
563011 AAATACTCC-CAATGGGTAAAATTACCG
1 AAATAC-CCTCAATGGGTAAAATTACCA
* *
563038 AAATACCC-CTATAGGGTAAAATGACCGA
1 AAATACCCTCAAT-GGGTAAAATTACC-A
* *
563066 AAA-ACCCCCAAAGGGTAAAAT
1 AAATACCCTCAATGGGTAAAAT
563087 AACTATAATG
Statistics
Matches: 170, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
25 2 0.01
26 5 0.03
27 153 0.90
28 8 0.05
29 2 0.01
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.21
Consensus pattern (27 bp):
AAATACCCTCAATGGGTAAAATTACCA
Found at i:563055 original size:54 final size:53
Alignment explanation
Indices: 562860--563086 Score: 269
Period size: 54 Copynumber: 4.2 Consensus size: 53
562850 AATACCCTCG
* * * *
562860 ATGGGTAAAATTACCAAAATACCCTAGATGGGAAAAATTATCGAAATAC-CCTTA
1 ATGGGTAAAATTACCGAAATACCC-CGATGGGAAAAATTATCAAAATACTCC-CA
*
562914 ATAGGTAAAATTACCGAAATACCCCCGATGGGAAAAATTATCAAAATACTCCCA
1 ATGGGTAAAATTACCGAAATA-CCCCGATGGGAAAAATTATCAAAATACTCCCA
* *
562968 ATGGGTAAAATTACCGAAATACCTCCGATGGGTAAAGTTATCAAAATACTCCCA
1 ATGGGTAAAATTACCGAAATACC-CCGATGGGAAAAATTATCAAAATACTCCCA
* * * * *
563022 ATGGGTAAAATTACCGAAATACCCCTATAGGGTAAAATGACCGAAAA-ACCCCCA
1 ATGGGTAAAATTACCGAAATACCCCGAT-GGGAAAAATTATC-AAAATACTCCCA
*
563076 AAGGGTAAAAT
1 ATGGGTAAAAT
563087 AACTATAATG
Statistics
Matches: 154, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
53 6 0.04
54 139 0.90
55 9 0.06
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (53 bp):
ATGGGTAAAATTACCGAAATACCCCGATGGGAAAAATTATCAAAATACTCCCA
Found at i:563082 original size:81 final size:79
Alignment explanation
Indices: 562849--563167 Score: 230
Period size: 81 Copynumber: 3.9 Consensus size: 79
562839 AAAATTATTG
* * * * * **
562849 AAATACCCTCGATGGGTAAAATTACCAAAATA-CCCTAGATGGGAAAAATTATCGAAATACCCTT
1 AAATACCC-CAATGGGTAAAATTACCAAAATACCCCTATA-GGGTAAAATGACCGAAATACCCCC
* *
562913 AATA-GGTAAAATTACCG
64 AA-AGGGT-AAATTAACA
* * * * * *
562930 AAATACCCCCGATGGGAAAAATTATCAAAATACTCCCAAT-GGGTAAAATTACCGAAATACCTCC
1 AAATA-CCCCAATGGGTAAAATTACCAAAATAC-CCCTATAGGGTAAAATGACCGAAATACCCCC
* * *
562994 GATGGGTAAAGTTATCA
64 AAAGGGTAAA-TTAACA
* *
563011 AAATACTCCCAATGGGTAAAATTACCGAAATACCCCTATAGGGTAAAATGACCGAAAAACCCCCA
1 AAATAC-CCCAATGGGTAAAATTACCAAAATACCCCTATAGGGTAAAATGACCGAAATACCCCCA
*
563076 AAGGGTAAAATAACTA
65 AAGGGTAAATTAAC-A
* * ** * ** * * *
563092 TAATGCCCCCGTAGGGTAAAATGACCGTAATGCCTCTATAGGGTAAAATGACCGTAATACCCCCA
1 AAATACCCCAAT-GGGTAAAATTACCAAAATACCCCTATAGGGTAAAATGACCGAAATACCCCCA
*
563157 TAAGGTTAAAT
65 -AAGGGTAAAT
563168 AACCGTAATA
Statistics
Matches: 191, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
80 16 0.08
81 160 0.84
82 11 0.06
83 4 0.02
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (79 bp):
AAATACCCCAATGGGTAAAATTACCAAAATACCCCTATAGGGTAAAATGACCGAAATACCCCCAA
AGGGTAAATTAACA
Found at i:563135 original size:54 final size:54
Alignment explanation
Indices: 563012--563181 Score: 162
Period size: 54 Copynumber: 3.1 Consensus size: 54
563002 AAGTTATCAA
* * * * *
563012 AATACTCCCAATGGGTAAAATTACCGA-AATACCCCTATAGGGTAAAATGACCGA
1 AATACCCCCAAAGGGTAAAATAACC-ATAATACCCCCATAGGGTAAAATGACCGT
* * * *
563066 AAAACCCCCAAAGGGTAAAATAACTATAATGCCCCCGTAGGGTAAAATGACCGT
1 AATACCCCCAAAGGGTAAAATAACCATAATACCCCCATAGGGTAAAATGACCGT
* * * * * * * * *
563120 AATGCCTCTATAGGGTAAAATGACCGTAATACCCCCATAAGGTTAAATAACCGT
1 AATACCCCCAAAGGGTAAAATAACCATAATACCCCCATAGGGTAAAATGACCGT
563174 AATACCCC
1 AATACCCC
563182 TGTAAGTTAA
Statistics
Matches: 91, Mismatches: 24, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
53 1 0.01
54 90 0.99
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.20
Consensus pattern (54 bp):
AATACCCCCAAAGGGTAAAATAACCATAATACCCCCATAGGGTAAAATGACCGT
Found at i:563168 original size:81 final size:81
Alignment explanation
Indices: 563024--563223 Score: 224
Period size: 81 Copynumber: 2.5 Consensus size: 81
563014 TACTCCCAAT
* * *
563024 GGGTAAAATTACCGAAATACCCCTATAGGGTAAAATGACCGAAAAACCCCCAAAGGGTAAAATAA
1 GGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAAAAACCCCCAAAGGGTAAAATAA
* *
563089 CTATAATGCCCCCGTA
66 CCATAATACCCCCGTA
* * * *
563105 GGGTAAAATGACCGTAATGCCTCTATAGGGTAAAATGACCGTAATACCCCCATAA-GGTTAAATA
1 GGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAAAAACCCCCA-AAGGGTAAAATA
* *
563169 ACCGTAATACCCCTGTA
65 ACCATAATACCCCCGTA
* * * * **
563186 AGTTAAAATGATCATAATGCCCCTGGAGGGT-AAATGAC
1 GGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGAC
563224 TATTTTACCC
Statistics
Matches: 100, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
80 7 0.07
81 91 0.91
82 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (81 bp):
GGGTAAAATGACCGTAATGCCCCTATAGGGTAAAATGACCGAAAAACCCCCAAAGGGTAAAATAA
CCATAATACCCCCGTA
Found at i:563219 original size:27 final size:27
Alignment explanation
Indices: 563024--563223 Score: 141
Period size: 27 Copynumber: 7.4 Consensus size: 27
563014 TACTCCCAAT
* * * *
563024 GGGTAAAATTACCGAAATACCCCTATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* ** ***
563051 GGGTAAAATGACCGAAAAACCCCCAAA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* ** *
563078 GGGTAAAATAACTATAATGCCCCCGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* *
563105 GGGTAAAATGACCGTAATGCCTCTATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* **
563132 GGGTAAAATGACCGTAATACCCCCATA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* * * *
563159 AGGTTAAATAACCGTAATACCCCTGTA
1 GGGTAAAATGACCGTAATGCCCCTGTA
* * * * *
563186 AGTTAAAATGATCATAATGCCCCTGGA
1 GGGTAAAATGACCGTAATGCCCCTGTA
563213 GGGT-AAATGAC
1 GGGTAAAATGAC
563224 TATTTTACCC
Statistics
Matches: 137, Mismatches: 36, Indels: 1
0.79 0.21 0.01
Matches are distributed among these distances:
26 6 0.04
27 131 0.96
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (27 bp):
GGGTAAAATGACCGTAATGCCCCTGTA
Found at i:563323 original size:24 final size:24
Alignment explanation
Indices: 563250--563350 Score: 96
Period size: 24 Copynumber: 4.2 Consensus size: 24
563240 TGTAAATGGT
* **
563250 TGATTTGTCCGTGATGTAAATGAC
1 TGATTTGTCTGTGATGTGTATGAC
* * * **
563274 TGATTTGTCTATTATTTAAATGAC
1 TGATTTGTCTGTGATGTGTATGAC
*
563298 TGATTTGTCTGTGAT-TGGTATTAC
1 TGATTTGTCTGTGATGT-GTATGAC
*
563322 TGATTTGTTTGTGATGTGTATGAC
1 TGATTTGTCTGTGATGTGTATGAC
563346 TGATT
1 TGATT
563351 CTGAGCATGG
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 1 0.02
24 62 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.08, G:0.23, T:0.48
Consensus pattern (24 bp):
TGATTTGTCTGTGATGTGTATGAC
Found at i:563518 original size:32 final size:32
Alignment explanation
Indices: 563468--563576 Score: 105
Period size: 32 Copynumber: 3.4 Consensus size: 32
563458 TTGCTGCGAT
563468 GCTACTGATGGCTTTGTGCCGATCATATTACC
1 GCTACTGATGGCTTTGTGCCGATCATATTACC
* * * ** *
563500 GTTACTGATGG-TTGTGTGCAGTTCATACCACT
1 GCTACTGATGGCTT-TGTGCCGATCATATTACC
* * *
563532 GCTACTGATGGCTTTATGCCAATCATATTACT
1 GCTACTGATGGCTTTGTGCCGATCATATTACC
*
563564 G-TACTTATGGCTT
1 GCTACTGATGGCTT
563577 GTAGCCATTC
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
31 13 0.21
32 46 0.75
33 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (32 bp):
GCTACTGATGGCTTTGTGCCGATCATATTACC
Found at i:563598 original size:22 final size:22
Alignment explanation
Indices: 563568--563614 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
563558 ATTACTGTAC
* * *
563568 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTTATAGCCATCCTGT
*
563590 TTATAGCTTATAGCTATCCTGT
1 TTATAGCTTATAGCCATCCTGT
563612 TTA
1 TTA
563615 CTACTCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (22 bp):
TTATAGCTTATAGCCATCCTGT
Found at i:582129 original size:229 final size:229
Alignment explanation
Indices: 581723--582182 Score: 875
Period size: 229 Copynumber: 2.0 Consensus size: 229
581713 TCCCAAATCT
*
581723 TGTGAAAATGTTCTTGTGTAGAAACTTTAGCACTGACTTGGCATCATTTGTAGCTAGGGATATCA
1 TGTGAAAATGTTCTTGTGTAGAAACTTTAGCACTGACTTGGAATCATTTGTAGCTAGGGATATCA
581788 CCTCGACCCACTTAAAGACATTGTCCACTACCACAAGTATGTAGATATTGTCAAATGATGGTGGA
66 CCTCGACCCACTTAAAGACATTGTCCACTACCACAAGTATGTAGATATTGTCAAATGATGGTGGA
* * *
581853 AATGGACCCATAAAGTCGATTCCCCAAACATCAAACAAATTAATCTCCAAAATATTTTACAATGG
131 AATGGACCCAAAAAGTCAATTCCCCAAACATCAAACAAATCAATCTCCAAAATATTTTACAATGG
581918 CATTTCGTGTCTCTTAGATAAATTGCATGTCCTC
196 CATTTCGTGTCTCTTAGATAAATTGCATGTCCTC
581952 TGTGAAAATGTTCTTGTGTAGAAACTTTAGCACTGACTTGGAATCATTTGTAGCTAGGGATATCA
1 TGTGAAAATGTTCTTGTGTAGAAACTTTAGCACTGACTTGGAATCATTTGTAGCTAGGGATATCA
582017 CCTCGACCCACTTAAAGACATTGTCCACTACCACAAGTATGTAGATATTGTCAAATGATGGTGGA
66 CCTCGACCCACTTAAAGACATTGTCCACTACCACAAGTATGTAGATATTGTCAAATGATGGTGGA
582082 AATGGACCCAAAAAGTCAATTCCCCAAACATCAAACAAATCAATCTCCAAAATATTTTACAATGG
131 AATGGACCCAAAAAGTCAATTCCCCAAACATCAAACAAATCAATCTCCAAAATATTTTACAATGG
*
582147 CATTTCGTGTCTCTTAGATAAATTGCATGTTCTC
196 CATTTCGTGTCTCTTAGATAAATTGCATGTCCTC
582181 TG
1 TG
582183 ACAATGATCA
Statistics
Matches: 226, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
229 226 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (229 bp):
TGTGAAAATGTTCTTGTGTAGAAACTTTAGCACTGACTTGGAATCATTTGTAGCTAGGGATATCA
CCTCGACCCACTTAAAGACATTGTCCACTACCACAAGTATGTAGATATTGTCAAATGATGGTGGA
AATGGACCCAAAAAGTCAATTCCCCAAACATCAAACAAATCAATCTCCAAAATATTTTACAATGG
CATTTCGTGTCTCTTAGATAAATTGCATGTCCTC
Found at i:587764 original size:19 final size:19
Alignment explanation
Indices: 587736--587782 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
587726 AAATGCAACT
* * *
587736 CAATTCACCTGAATATAGA
1 CAATTAACCTAAATACAGA
587755 CAATTAACCTAAATACAGA
1 CAATTAACCTAAATACAGA
587774 CAATTAACC
1 CAATTAACC
587783 AAGTCTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.47, C:0.23, G:0.06, T:0.23
Consensus pattern (19 bp):
CAATTAACCTAAATACAGA
Found at i:602241 original size:9 final size:9
Alignment explanation
Indices: 602227--602266 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
602217 TTTGGTTAAA
602227 AATTAACCG
1 AATTAACCG
602236 AATTAACCG
1 AATTAACCG
*
602245 AATTACCCG
1 AATTAACCG
*
602254 AATTATCCG
1 AATTAACCG
602263 AATT
1 AATT
602267 GAATCAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:602521 original size:16 final size:16
Alignment explanation
Indices: 602500--602531 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
602490 GGTAGACTTT
602500 AGTTTTAGTTTTATTG
1 AGTTTTAGTTTTATTG
602516 AGTTTTAGTTTTATTG
1 AGTTTTAGTTTTATTG
602532 GGTTGGGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (16 bp):
AGTTTTAGTTTTATTG
Found at i:602546 original size:13 final size:13
Alignment explanation
Indices: 602528--602565 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
602518 TTTTAGTTTT
602528 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
602541 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
602554 ATTAGGTTGGGT
1 ATTGGGTTGGGT
602566 TGAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:604486 original size:12 final size:12
Alignment explanation
Indices: 604469--604494 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
604459 TTTGTGAATT
604469 TTTTAGAAGATA
1 TTTTAGAAGATA
604481 TTTTAGAAGATA
1 TTTTAGAAGATA
604493 TT
1 TT
604495 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:605737 original size:9 final size:9
Alignment explanation
Indices: 605723--605753 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
605713 GTTAAACGAA
605723 TCGAGTTAT
1 TCGAGTTAT
*
605732 TCGAGTTAA
1 TCGAGTTAT
605741 TCGAGTTAT
1 TCGAGTTAT
605750 TCGA
1 TCGA
605754 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:605823 original size:9 final size:9
Alignment explanation
Indices: 605806--605842 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
605796 TGAGTTTTCA
605806 AATTCGAAT
1 AATTCGAAT
*
605815 AACTCGAAT
1 AATTCGAAT
605824 AATTCGAAT
1 AATTCGAAT
*
605833 CATTCGAAT
1 AATTCGAAT
605842 A
1 A
605843 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:605926 original size:29 final size:31
Alignment explanation
Indices: 605890--605950 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
605880 AAACCTTTTT
* *
605890 ACTTTTCCCTCAAAACTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
605920 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
605951 CTCCCAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:607655 original size:6 final size:6
Alignment explanation
Indices: 607638--607685 Score: 60
Period size: 6 Copynumber: 8.0 Consensus size: 6
607628 GCATCATGCA
* * * *
607638 CCAGAG CTAGAG CCAGAG CCAGAG CCAGAG CCAGTG CTAGTG CCAGAG
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG
607686 ATGAAACTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.08
Consensus pattern (6 bp):
CCAGAG
Found at i:611416 original size:14 final size:14
Alignment explanation
Indices: 611375--611419 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
611365 GCACACAAAC
*
611375 AAACAACAAAAGAA
1 AAACAAAAAAAGAA
*
611389 AAGCAGAGAAAAAGAA
1 AAACA-A-AAAAAGAA
611405 AAACAAAAAAAGAA
1 AAACAAAAAAAGAA
611419 A
1 A
611420 TTTGTATTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 13 0.50
15 2 0.08
16 11 0.42
ACGTcount: A:0.78, C:0.09, G:0.13, T:0.00
Consensus pattern (14 bp):
AAACAAAAAAAGAA
Found at i:613621 original size:27 final size:27
Alignment explanation
Indices: 613546--613623 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
613536 GAAAAATCAG
613546 ACCATTGGCGCCTCTCAGGAT-GACACC
1 ACCATTGGCGCCTCTCA-GATAGACACC
* * * * *
613573 ACTAATGGCGCCTCTCACATAGGCACT
1 ACCATTGGCGCCTCTCAGATAGACACC
*
613600 ACCATTGGCGCCTCTGAGATAGAC
1 ACCATTGGCGCCTCTCAGATAGAC
613624 GCCAATACTA
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.05
27 38 0.95
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.21
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAGATAGACACC
Found at i:613794 original size:28 final size:29
Alignment explanation
Indices: 613750--613815 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
613740 AATAACCCAT
613750 TTTC-GTAAATAATTTTTTTGAC-ACCCTA
1 TTTCAGTAAATAATTTTTTT-ACTACCCTA
*
613778 TTTCAGTACATAATTTTTTT-CTACCCTA
1 TTTCAGTAAATAATTTTTTTACTACCCTA
*
613806 TTTGAGTAAA
1 TTTCAGTAAA
613816 AAACCCTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 1 0.03
28 18 0.55
29 14 0.42
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTCAGTAAATAATTTTTTTACTACCCTA
Found at i:613948 original size:18 final size:18
Alignment explanation
Indices: 613927--613988 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 18
613917 TTTGATGTCC
613927 TTTTATATTTAAAATAAA
1 TTTTATATTTAAAATAAA
613945 TTTTATTATTTAAAAGTATTTTAA
1 TTTTA-TATTTAAAA-TA----AA
*
613969 TTTTTTATTTAAAATAAA
1 TTTTATATTTAAAATAAA
613987 TT
1 TT
613989 AACAAAAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
18 9 0.24
19 9 0.24
20 2 0.05
22 2 0.05
23 9 0.24
24 6 0.16
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTATATTTAAAATAAA
Found at i:616139 original size:15 final size:16
Alignment explanation
Indices: 616119--616152 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
616109 ACTACTTTTA
616119 TTATTTA-TTAATATT
1 TTATTTATTTAATATT
*
616134 TTATTTATTTATTATT
1 TTATTTATTTAATATT
616150 TTA
1 TTA
616153 AGTATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTATTTAATATT
Found at i:617175 original size:25 final size:23
Alignment explanation
Indices: 617145--617206 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 23
617135 TACATTTAAA
*
617145 ATAATTATAATTTAGTAAAATTGTG
1 ATAATTATAATTTA--AAAATAGTG
* *
617170 ATAATTACACATTTAAAAATAGTT
1 ATAATTATA-ATTTAAAAATAGTG
617194 ATAATT-TAATTTA
1 ATAATTATAATTTA
617207 CATTTGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.16
23 1 0.03
24 13 0.41
25 8 0.25
26 5 0.16
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (23 bp):
ATAATTATAATTTAAAAATAGTG
Found at i:617302 original size:13 final size:13
Alignment explanation
Indices: 617284--617308 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
617274 TGTACTTTAT
617284 TGATCAAAAGGGG
1 TGATCAAAAGGGG
617297 TGATCAAAAGGG
1 TGATCAAAAGGG
617309 ACCAAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (13 bp):
TGATCAAAAGGGG
Found at i:620208 original size:22 final size:23
Alignment explanation
Indices: 620182--620234 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
620172 TAATTAGTTT
620182 AAATATA-TATTT-GAAATTATAA
1 AAATATATTATTTAGAAATTA-AA
*
620204 AAATATATTATTTAATAAATTAAA
1 AAATATATTATTT-AGAAATTAAA
620228 AAATATA
1 AAATATA
620235 AAATCACGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 5 0.19
24 9 0.33
25 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATATATTATTTAGAAATTAAA
Found at i:625462 original size:13 final size:13
Alignment explanation
Indices: 625444--625487 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
625434 CTGCGATACA
*
625444 ATATGCAAACCCG
1 ATATGCAAACCCT
625457 ATATGCAAACCCT
1 ATATGCAAACCCT
* *
625470 ATGTGCGAACCCT
1 ATATGCAAACCCT
625483 ATATG
1 ATATG
625488 GAAGCATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (13 bp):
ATATGCAAACCCT
Found at i:628685 original size:40 final size:40
Alignment explanation
Indices: 628640--628731 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 40
628630 TGGTAATGCT
* * *
628640 ATCGAAATTGGGTAAACCGGGATGATAGTTTAAAAAGGCC
1 ATCGAAATCGGGTAAACCAGGATGATAATTTAAAAAGGCC
* *
628680 ATCGAAATCGGGTAAACCAGGATGGTAATTTAATAAGGCC
1 ATCGAAATCGGGTAAACCAGGATGATAATTTAAAAAGGCC
*
628720 AACGAAATCGGG
1 ATCGAAATCGGG
628732 CTACTCGAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (40 bp):
ATCGAAATCGGGTAAACCAGGATGATAATTTAAAAAGGCC
Found at i:631924 original size:37 final size:37
Alignment explanation
Indices: 631873--631943 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
631863 TTCTTTTGAA
631873 CATTTTCATACACATATCAAATAACCATATACTTATT
1 CATTTTCATACACATATCAAATAACCATATACTTATT
*
631910 CATTTTCATTCACATATCAAATAACCATATACTT
1 CATTTTCATACACATATCAAATAACCATATACTT
631944 GAAATTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.38
Consensus pattern (37 bp):
CATTTTCATACACATATCAAATAACCATATACTTATT
Found at i:639672 original size:26 final size:26
Alignment explanation
Indices: 639642--639703 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
639632 ACACAACGCC
* * *
639642 ACAAAATAGGACAAAT-ACTAAGGATT
1 ACAAAATA-AACAAATAAATAAGAATT
*
639668 ACAAAATAAACAAATAAATAATAATT
1 ACAAAATAAACAAATAAATAAGAATT
639694 ACAAAATAAA
1 ACAAAATAAA
639704 AATAAAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.65, C:0.10, G:0.06, T:0.19
Consensus pattern (26 bp):
ACAAAATAAACAAATAAATAAGAATT
Found at i:639806 original size:118 final size:114
Alignment explanation
Indices: 639640--639936 Score: 404
Period size: 114 Copynumber: 2.6 Consensus size: 114
639630 CAACACAACG
*
639640 CCACAAAATAGGACAAATACTAAGGATTACAAAATAAACAAATAAATAATAATTACAAAATAAAA
1 CCACAAAATAGGACAAATAATAAGGATTA-AAAATAAACAAATAAATAATAATTACAAAATAAAA
* * * *
639705 ATAAAAATGTACCTTTAAACCTTAATAAGCTGCTGCCTCCTC-TCTTTCCAAAC
65 ATAAAAATGCACCTCTAAACCTTAAT-A--TGCTACCTCCTCTTC-TTCCAAAA
* *
639758 CCACAAAATAGGATAAATAATAAGGATTATAAAATAAATAAATAAATAATAATTAC--AATAAAA
1 CCACAAAATAGGACAAATAATAAGGATTA-AAAATAAACAAATAAATAATAATTACAAAATAAAA
*
639821 ATTAAAAATGCATCTCTAAACCTTAATATGCTACCTCCTCTTCTTCCAAAA
65 A-TAAAAATGCACCTCTAAACCTTAATATGCTACCTCCTCTTCTTCCAAAA
* * *
639872 CCACAAAATAGGACAAATAATAAGGATTACAAACAAACAAA-AAATAATAATTAAAAAATAAAAA
1 CCACAAAATAGGACAAATAATAAGGATTAAAAATAAACAAATAAATAATAATTACAAAATAAAAA
639936 T
66 T
639937 GTACCTTGAA
Statistics
Matches: 161, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
112 12 0.07
113 10 0.06
114 54 0.34
115 2 0.01
116 9 0.06
117 22 0.14
118 52 0.32
ACGTcount: A:0.54, C:0.16, G:0.06, T:0.24
Consensus pattern (114 bp):
CCACAAAATAGGACAAATAATAAGGATTAAAAATAAACAAATAAATAATAATTACAAAATAAAAA
TAAAAATGCACCTCTAAACCTTAATATGCTACCTCCTCTTCTTCCAAAA
Found at i:639890 original size:114 final size:115
Alignment explanation
Indices: 639640--639989 Score: 398
Period size: 118 Copynumber: 3.1 Consensus size: 115
639630 CAACACAACG
*
639640 CCACAAAATAGGACAAATACTAAGGATTACAAAATAAACAAATAAATAATAATTACAAAATAAAA
1 CCACAAAATAGGACAAATAATAAGGATTA-AAAATAAACAAATAAATAATAATTAC-AAATAAAA
* * * *
639705 ATAAAAATGTACCTTTAAACCTTAATAAGCTGCTGCCTCCTCTCTTTCCAAAC
64 ATAAAAATGCACCTCTAAACCTTAATAA-CTGCTACCTCCTCTCTTTCCAAAA
* *
639758 CCACAAAATAGGATAAATAATAAGGATTATAAAATAAATAAATAAATAATAATTAC-AATAAAAA
1 CCACAAAATAGGACAAATAATAAGGATTA-AAAATAAACAAATAAATAATAATTACAAATAAAAA
*
639822 TTAAAAATGCATCTCTAAACCTTAAT-A-TGCTACCTCCTCT-TCTTCCAAAA
65 -TAAAAATGCACCTCTAAACCTTAATAACTGCTACCTCCTCTCT-TTCCAAAA
* *
639872 CCACAAAATAGGACAAATAATAAGGATTACAAACAAACAAA-AAATAATAATT----A-AAAAAT
1 CCACAAAATAGGACAAATAATAAGGATTAAAAATAAACAAATAAATAATAATTACAAATAAAAAT
* * ** * * *
639931 AAAAATGTACCT-TGAAACCCTAATATACTATTGCCTCCTCTCCTTCCAACA
66 AAAAATGCACCTCT-AAACCTTAATA-ACTGCTACCTCCTCTCTTTCCAAAA
639982 CCACAAAA
1 CCACAAAA
639990 CCTTCTTCTA
Statistics
Matches: 204, Mismatches: 21, Indels: 22
0.83 0.09 0.09
Matches are distributed among these distances:
106 1 0.00
107 20 0.10
108 5 0.02
109 2 0.01
110 25 0.12
112 11 0.05
113 10 0.05
114 47 0.23
116 9 0.04
117 22 0.11
118 52 0.25
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (115 bp):
CCACAAAATAGGACAAATAATAAGGATTAAAAATAAACAAATAAATAATAATTACAAATAAAAAT
AAAAATGCACCTCTAAACCTTAATAACTGCTACCTCCTCTCTTTCCAAAA
Found at i:640418 original size:22 final size:22
Alignment explanation
Indices: 640393--640462 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
640383 AAATTCAATA
640393 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
640415 TCAATTCCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
640437 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
640459 TCAA
1 TCAA
640463 ACTCTCAAAT
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:0.31, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:640468 original size:30 final size:30
Alignment explanation
Indices: 640434--640492 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
640424 TTCAAAAATT
* *
640434 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
640464 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
640493 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:640478 original size:52 final size:51
Alignment explanation
Indices: 640412--640514 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 51
640402 TTCAAAAATT
* * *
640412 CTCTCAATTCCCTTCAAAAATTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
*
640464 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
640515 TCCATATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
51 4 0.09
52 38 0.83
53 4 0.09
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAATTCCCTTCAAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:640503 original size:21 final size:22
Alignment explanation
Indices: 640464--640505 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
640454 TTCTCTCAAA
640464 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
640486 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
640506 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:640732 original size:14 final size:15
Alignment explanation
Indices: 640703--640736 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
640693 AAATTTTAAA
640703 TTTTATTTAAGATAT
1 TTTTATTTAAGATAT
*
640718 TTTTATTTATG-TAT
1 TTTTATTTAAGATAT
640732 TTTTA
1 TTTTA
640737 GATATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TTTTATTTAAGATAT
Found at i:641457 original size:7 final size:7
Alignment explanation
Indices: 641445--641469 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
641435 AGTGGATTGA
641445 TATTTAG
1 TATTTAG
641452 TATTTAG
1 TATTTAG
641459 TATTTAG
1 TATTTAG
641466 TATT
1 TATT
641470 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:642656 original size:23 final size:23
Alignment explanation
Indices: 642629--642703 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 23
642619 AAAACCCTAA
642629 CCTAACTTAATATAATTAAAAAC
1 CCTAACTTAATATAATTAAAAAC
642652 CCTAAC----T-TAATTAAAAAC
1 CCTAACTTAATATAATTAAAAAC
642670 CCTAACCTTAATTAATTTAATTAAAAAC
1 CCTAA-CTTAA-T-A--TAATTAAAAAC
642698 CCTAAC
1 CCTAAC
642704 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
18 16 0.38
19 2 0.05
23 6 0.14
24 1 0.02
27 1 0.02
28 16 0.38
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (23 bp):
CCTAACTTAATATAATTAAAAAC
Found at i:642664 original size:18 final size:19
Alignment explanation
Indices: 642641--642684 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
642631 TAACTTAATA
642641 TAATTAAAAACCCTAA-CT
1 TAATTAAAAACCCTAACCT
642659 TAATTAAAAACCCTAACCT
1 TAATTAAAAACCCTAACCT
642678 TAATTAA
1 TAATTAA
642685 TTTAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATTAAAAACCCTAACCT
Found at i:642685 original size:46 final size:46
Alignment explanation
Indices: 642615--642703 Score: 153
Period size: 46 Copynumber: 1.9 Consensus size: 46
642605 ACATTATTTG
642615 ATTAAAAACCCTAACCTAACTTAATATAATTAAAAACCCTAACTTA
1 ATTAAAAACCCTAACCTAACTTAATATAATTAAAAACCCTAACTTA
*
642661 ATTAAAAACCCTAACCTTAA-TTAATTTAATTAAAAACCCTAAC
1 ATTAAAAACCCTAACC-TAACTTAATATAATTAAAAACCCTAAC
642704 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
46 38 0.93
47 3 0.07
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.29
Consensus pattern (46 bp):
ATTAAAAACCCTAACCTAACTTAATATAATTAAAAACCCTAACTTA
Found at i:644423 original size:122 final size:125
Alignment explanation
Indices: 644161--644426 Score: 335
Period size: 122 Copynumber: 2.1 Consensus size: 125
644151 CCACGAGGGC
* *
644161 GCGATTTGACACTATTTGCTCAGAAACGTCAAAAAAAAAATATTTCCTACATGACCAACTGTAGC
1 GCGATTTCACACTATTTGCTCAGAAAAGTC-AAAAAAAAATATTTCCTACATGACCAACTGTAGC
* * * * **
644226 GAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTACCCAATATAGCATCCTTGTATCA
65 GAAATCGAGTCCACGAGGCCACGATTTCACAATTTCTACCCAATATAGCATCCTGGTAGAA
* * * *
644287 GCGATTTTATACTATTTGCTCAGTAAAAGTC-AAAAAAATTATTTCTTACATGACC-ACTGTAGC
1 GCGATTTCACACTATTTGCTCAG-AAAAGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGC
* *
644350 GAAATCGAGT-CACGAGGCCACGATTTCGCAATTTC-ATCTCAA-ATAGCATCCTGGTAGAA
65 GAAATCGAGTCCACGAGGCCACGATTTCACAATTTCTA-CCCAATATAGCATCCTGGTAGAA
*
644409 GCGATTTCCCACTATTTG
1 GCGATTTCACACTATTTG
644427 ACCAGATACA
Statistics
Matches: 122, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
122 30 0.25
123 26 0.21
124 17 0.14
125 22 0.18
126 21 0.17
127 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (125 bp):
GCGATTTCACACTATTTGCTCAGAAAAGTCAAAAAAAAATATTTCCTACATGACCAACTGTAGCG
AAATCGAGTCCACGAGGCCACGATTTCACAATTTCTACCCAATATAGCATCCTGGTAGAA
Found at i:647179 original size:13 final size:13
Alignment explanation
Indices: 647158--647191 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
647148 TCTTTGATTT
647158 ATTATTTTATTTTA
1 ATTA-TTTATTTTA
*
647172 GTTATTTATTTTA
1 ATTATTTATTTTA
647185 ATTATTT
1 ATTATTT
647192 TATCTGACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
ATTATTTATTTTA
Found at i:650796 original size:11 final size:11
Alignment explanation
Indices: 650780--650804 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
650770 TTTTCAGATC
650780 TTATTATTTTA
1 TTATTATTTTA
650791 TTATTATTTTA
1 TTATTATTTTA
650802 TTA
1 TTA
650805 AAAATTTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:651203 original size:18 final size:18
Alignment explanation
Indices: 651163--651203 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
651153 TTAATCTTTG
651163 ATTTA-TTATTTTATTTT
1 ATTTATTTATTTTATTTT
*
651180 AGTTATTTATTTTAATTTT
1 ATTTATTTATTTT-ATTTT
651199 -TTTAT
1 ATTTAT
651204 CTAACTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTATTTATTTTATTTT
Found at i:653955 original size:12 final size:12
Alignment explanation
Indices: 653940--653969 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
653930 AACCATAATT
*
653940 AATATATTATTA
1 AATAAATTATTA
653952 AATAAATTATTA
1 AATAAATTATTA
653964 AATAAA
1 AATAAA
653970 GTATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAATTATTA
Found at i:662623 original size:19 final size:19
Alignment explanation
Indices: 662599--662690 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
662589 AATCATATAT
*
662599 TCTAAGATTGCATATCGTA
1 TCTAAGATTGCATATCATA
**
662618 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
662637 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
662656 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
662675 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
662691 CTCAAAAATT
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 66 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:674178 original size:25 final size:24
Alignment explanation
Indices: 674144--674193 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
674134 TCAACGGCTG
674144 AGATTAAAGGGTATCTACAAATTAA
1 AGATTAAAGGGTATCTA-AAATTAA
674169 AGATTAAAGGGTATCTAAAATTAA
1 AGATTAAAGGGTATCTAAAATTAA
674193 A
1 A
674194 TCATATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (24 bp):
AGATTAAAGGGTATCTAAAATTAA
Found at i:674224 original size:19 final size:19
Alignment explanation
Indices: 674193--674312 Score: 186
Period size: 19 Copynumber: 6.2 Consensus size: 19
674183 CTAAAATTAA
674193 ATCATATTCTAAGATTGCAT
1 ATCATA-TCTAAGATTGCAT
**
674213 ATCATATCTAAGATTATAT
1 ATCATATCTAAGATTGCAT
674232 ATCATATCTAAGATTGCATAT
1 ATCATATCTAAGATTGC--AT
674253 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
*
674272 ATCATATCTAGGATTGCAT
1 ATCATATCTAAGATTGCAT
674291 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
674310 ATC
1 ATC
674313 CTCAAAAATT
Statistics
Matches: 92, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
19 67 0.73
20 6 0.07
21 19 0.21
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:674265 original size:40 final size:37
Alignment explanation
Indices: 674180--674305 Score: 173
Period size: 40 Copynumber: 3.3 Consensus size: 37
674170 GATTAAAGGG
*
674180 TATCTAAAATTAA-ATCATATTCTAAGATTGCATATCA
1 TATCTAAGATTAATATCATA-TCTAAGATTGCATATCA
674217 TATCTAAGATTATATATCATATCTAAGATTGCATATATCA
1 TATCTAAGATTA-ATATCATATCTAAGATTGC--ATATCA
* *
674257 TATCTAAGATTGCATATCATATCTAGGATTGCATATCA
1 TATCTAAGATT-AATATCATATCTAAGATTGCATATCA
674295 TATCTAAGATT
1 TATCTAAGATT
674306 GCATATCCTC
Statistics
Matches: 81, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
37 11 0.14
38 29 0.36
39 6 0.07
40 35 0.43
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (37 bp):
TATCTAAGATTAATATCATATCTAAGATTGCATATCA
Found at i:674268 original size:59 final size:60
Alignment explanation
Indices: 674193--674311 Score: 204
Period size: 59 Copynumber: 2.0 Consensus size: 60
674183 CTAAAATTAA
*
674193 ATCATATTCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATAT
1 ATCATATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATAT
* *
674253 ATCATA-TCTAAGATTGCATATCATATCTAGGATTGCATATCATATCTAAGATTGCATAT
1 ATCATATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATAT
674312 CCTCAAAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 50 0.89
60 6 0.11
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (60 bp):
ATCATATTCTAAGATTGCATATCATATCTAAGATTACATATCATATCTAAGATTGCATAT
Found at i:684049 original size:3 final size:3
Alignment explanation
Indices: 684041--684077 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
684031 CTCTGATCTC
684041 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
684078 CTCTCACTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:693755 original size:22 final size:21
Alignment explanation
Indices: 693720--693796 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
693710 AAATGGTATC
* *
693720 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
693741 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
693764 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
693783 TGCATATCATATCT
1 TACAAATCATATCT
693797 AATATTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 19 0.40
21 4 0.08
22 15 0.31
23 10 0.21
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:693763 original size:23 final size:22
Alignment explanation
Indices: 693720--693777 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
693710 AAATGGTATC
* *
693720 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
693741 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
693764 TGCATATCATATCT
1 TACAAATCATATCT
693778 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:693780 original size:19 final size:19
Alignment explanation
Indices: 693756--693809 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
693746 AATCATATCT
693756 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
693775 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
693794 TCTAATATTGCATATC
1 TCTAAGATTGCATATC
693810 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:704240 original size:19 final size:20
Alignment explanation
Indices: 704197--704249 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
704187 TGCATGCTGG
*
704197 CACACGAAGCGCATCTTAGT
1 CACACGAAACGCATCTTAGT
*
704217 -GCACGAAACGCATCTT-GT
1 CACACGAAACGCATCTTAGT
*
704235 CACACGAAATGCATC
1 CACACGAAACGCATC
704250 CTAACACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (20 bp):
CACACGAAACGCATCTTAGT
Found at i:710324 original size:21 final size:19
Alignment explanation
Indices: 710300--710360 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
710290 TCTAAAATTT
710300 AAAATAAAGTATTTAAAAATAA
1 AAAATAAA-TA-TTAAAAAT-A
*
710322 AAAATAAATA-TAAAATTA
1 AAAATAAATATTAAAAATA
* *
710340 TAAATAAATATTATAAATA
1 AAAATAAATATTAAAAATA
710359 AA
1 AA
710361 TGAATACCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 10 0.30
19 13 0.39
21 2 0.06
22 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATAAATATTAAAAATA
Found at i:710352 original size:13 final size:13
Alignment explanation
Indices: 710325--710361 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
710315 AAAATAAAAA
*
710325 ATAAATATAAAATT
1 ATAAATA-AATATT
710339 ATAAATAAATATT
1 ATAAATAAATATT
710352 ATAAATAAAT
1 ATAAATAAAT
710362 GAATACCTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATAAATAAATATT
Found at i:710929 original size:81 final size:81
Alignment explanation
Indices: 710792--710999 Score: 346
Period size: 81 Copynumber: 2.6 Consensus size: 81
710782 GCACTAGGAC
* * * *
710792 CGTGAACTTCCCTTGCGAGCCCTTCT-AGCGAACCCCCACTACAAGGTCTGTACACAATCAATTG
1 CGTGAACTTCTCTTGCGAGCCCTTTTGA-CGAGCCCCCACTACAAGGTCTATACACAATCAATTG
710856 GTAGGGCCCAATCGGGT
65 GTAGGGCCCAATCGGGT
*
710873 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTATTCACAATCAATTGG
1 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTATACACAATCAATTGG
710938 TAGGGCCCAATCGGGT
66 TAGGGCCCAATCGGGT
*
710954 CGTGAACTTCTCTTACGAGCCCTTTTGACGAGCCCCCACTACAAGG
1 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGG
711000 CCTTAATGCA
Statistics
Matches: 120, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
81 119 0.99
82 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.22, T:0.24
Consensus pattern (81 bp):
CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTATACACAATCAATTGG
TAGGGCCCAATCGGGT
Found at i:711035 original size:81 final size:80
Alignment explanation
Indices: 710792--711024 Score: 321
Period size: 81 Copynumber: 2.9 Consensus size: 80
710782 GCACTAGGAC
* * *
710792 CGTGAACTTCCCTTGCGAGCCCTTCT-AGCGAACCCCCACTACAAGGTCTGTACA-CAATCAATT
1 CGTGAACTTCTCTTGCGAGCCCTTTTGA-CGAGCCCCCACTACAAGGTCT-TA-ATCAATCAATT
710855 GGTAGGGCCCAATCGGGT
63 GGTAGGGCCCAATCGGGT
*
710873 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTC-TATTCACAATCAATTG
1 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTTAAT--CAATCAATTG
710937 GTAGGGCCCAATCGGGT
64 GTAGGGCCCAATCGGGT
* *
710954 CGTGAACTTCTCTTACGAGCCCTTTTGACGAGCCCCCACTACAAGGCCTTAATGC-ATCCAATTG
1 CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTTAAT-CAAT-CAATTG
711018 GTAGGGC
64 GTAGGGC
711025 TCAACTGGGT
Statistics
Matches: 138, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
79 2 0.01
80 2 0.01
81 130 0.94
82 4 0.03
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (80 bp):
CGTGAACTTCTCTTGCGAGCCCTTTTGACGAGCCCCCACTACAAGGTCTTAATCAATCAATTGGT
AGGGCCCAATCGGGT
Found at i:713395 original size:137 final size:137
Alignment explanation
Indices: 713141--713397 Score: 327
Period size: 137 Copynumber: 1.9 Consensus size: 137
713131 TATGTTGGAT
* * * * * *
713141 CTGCGAGCTTAACTCCCCAAGCTCTTATAATGTCAATTGGGAGCGTAGATCCTTTAGTTGCTTTG
1 CTGCGAGCTTAACTCCACAAGCTCTTATAATGTCAATTGAGACCGCAGATCCTCTAGCTGCTTTG
* * * * *
713206 GAGGTTGTGATCTTAAACTGACAAACCTTTATGGCATCAGTTGGGAGCGTAGGTCTGCTAACTGT
66 GAGATTGCGATCTTAAACTGACAAACCTTTATGACATAAGTTAGGAGCGTAGGTCTGCTAACTGT
713271 GTTAGAG
131 GTTAGAG
** * * *
713278 CTGCGAGCTTAACTTTACGAGCTCTTGTAATGTCAATTGAGACCGCAGGT-CTGCTAGCTGCTTT
1 CTGCGAGCTTAACTCCACAAGCTCTTATAATGTCAATTGAGACCGCAGATCCT-CTAGCTGCTTT
* * *
713342 GGAGATTGCGATCTTAAATTGACAAACCTTTATGACATAATTTAGGAGTGTAGGTC
65 GGAGATTGCGATCTTAAACTGACAAACCTTTATGACATAAGTTAGGAGCGTAGGTC
713398 CACTGGTTGT
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
136 2 0.02
137 98 0.98
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CTGCGAGCTTAACTCCACAAGCTCTTATAATGTCAATTGAGACCGCAGATCCTCTAGCTGCTTTG
GAGATTGCGATCTTAAACTGACAAACCTTTATGACATAAGTTAGGAGCGTAGGTCTGCTAACTGT
GTTAGAG
Found at i:713519 original size:123 final size:123
Alignment explanation
Indices: 713295--713519 Score: 281
Period size: 123 Copynumber: 1.8 Consensus size: 123
713285 CTTAACTTTA
* * * *
713295 CGAGCTCTTGTAATGTCAATTGAGACCGCAGGTCTGCTAGCTGCTTTGGAGATTGCGATCTTAAA
1 CGAGCTCTTATAATGTCAACTGAGACCGCAGGTCCGCTAGCTGCTTTGGAGATTACGATCTTAAA
* * **
713360 TTGACAAACCTTTATGACATAATTTAGGAGTGTAGGTCCACTGGTTGTGCCGGAGCTG
66 TCGACAAACCTTTATAACATAATTTAGGAGCCTAGGTCCACTGGTTGTGCCGGAGCTG
* * * * * * *
713418 CGAGCTCTTATAATGTCAGCTGGGAGCGTAGGTCCGGTAGTTGCTTTGGAGGTTACGATCTTAAA
1 CGAGCTCTTATAATGTCAACTGAGACCGCAGGTCCGCTAGCTGCTTTGGAGATTACGATCTTAAA
* *
713483 TCGATAAACCTTTATAACATCAA-TTGGGAGCCTAGGT
66 TCGACAAACCTTTATAACAT-AATTTAGGAGCCTAGGT
713520 TCGCTAGCTA
Statistics
Matches: 84, Mismatches: 17, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
123 82 0.98
124 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (123 bp):
CGAGCTCTTATAATGTCAACTGAGACCGCAGGTCCGCTAGCTGCTTTGGAGATTACGATCTTAAA
TCGACAAACCTTTATAACATAATTTAGGAGCCTAGGTCCACTGGTTGTGCCGGAGCTG
Found at i:713680 original size:134 final size:134
Alignment explanation
Indices: 713420--713816 Score: 361
Period size: 134 Copynumber: 2.9 Consensus size: 134
713410 CGGAGCTGCG
* * ** ** * * *
713420 AGCTCTTATAATGTCAGCTGGGAGCGTAGGTCCGGTAGTTGCTTTGGAGGTTACGATCTTAAATC
1 AGCTCTTGTAATGTCAACTGGGAGCACAGGTCC-ACAG-TACTTTGGAGGTTGCGATCTTAAACC
* * * * * * *
713485 GATAAACCTTTATAACATCAATTGGGAGCCTAGGTTCGCTAGCTATGTC-AAATCTGAGAGCTAA
64 GACAAACCTTTATGACATCAACTGGGAGCATAGGTTCGCTAGCTGTGTCGAAGT-TGTGAGCTAA
713549 AC-TCCA
128 ACTTCCA
* * ** *
713555 TGAGCTCTTGTAATGTCAGCTGGGAGTACAGGTCTGCTAG-A-TTTGGAGGTTGTGATCTTAAAC
1 --AGCTCTTGTAATGTCAACTGGGAGCACAGGTCCAC-AGTACTTTGGAGGTTGCGATCTTAAAC
* * * * *
713618 CGACAAACCTTTATGACATCAACTGGGAGCGTAGGCTCGCTAGTTGTGTCGGAGTTGTGAGCTTA
63 CGACAAACCTTTATGACATCAACTGGGAGCATAGGTTCGCTAGCTGTGTCGAAGTTGTGAGCTAA
713683 ACTTTCCA
128 AC-TTCCA
* * ** * * *
713691 AGCTCTTGTAATGTCAATTGGTAGCGTAGGTCCACAGTTACTTTAGAGGTTGCAATCTTAAACTG
1 AGCTCTTGTAATGTCAACTGGGAGCACAGGTCCACAG-TACTTTGGAGGTTGCGATCTTAAACCG
* * * *
713756 ACAAACCTTTATGACATCAGCTAGGAGCATAGGTTCGCTAGCTGTGTTGAAGCTGTGAGCT
65 ACAAACCTTTATGACATCAACTGGGAGCATAGGTTCGCTAGCTGTGTCGAAGTTGTGAGCT
713817 CTTGTAATGC
Statistics
Matches: 212, Mismatches: 41, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
133 2 0.01
134 99 0.47
135 3 0.01
136 78 0.37
137 30 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (134 bp):
AGCTCTTGTAATGTCAACTGGGAGCACAGGTCCACAGTACTTTGGAGGTTGCGATCTTAAACCGA
CAAACCTTTATGACATCAACTGGGAGCATAGGTTCGCTAGCTGTGTCGAAGTTGTGAGCTAAACT
TCCA
Found at i:722195 original size:16 final size:16
Alignment explanation
Indices: 722176--722206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
722166 TGCAATGACA
722176 TAGGTTCACATAACAT
1 TAGGTTCACATAACAT
*
722192 TAGGTTCGCATAACA
1 TAGGTTCACATAACA
722207 CAATATAATG
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:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (16 bp):
TAGGTTCACATAACAT
Found at i:722301 original size:38 final size:36
Alignment explanation
Indices: 722259--722343 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
722249 TGCTTGCATT
*
722259 CAACATATGGGTTCGAACATATATTCATGG-TCCCCATA
1 CAACATATGGGTTC--ACAGATATTCATGGCT-CCCATA
* * *
722297 CAACATATGGATTCTCAGATATTCATGGCTCGCATA
1 CAACATATGGGTTCACAGATATTCATGGCTCCCATA
722333 CAACATATGGG
1 CAACATATGGG
722344 CTCGCATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 27 0.66
37 1 0.02
38 13 0.32
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (36 bp):
CAACATATGGGTTCACAGATATTCATGGCTCCCATA
Found at i:725856 original size:43 final size:43
Alignment explanation
Indices: 725769--725966 Score: 195
Period size: 43 Copynumber: 4.6 Consensus size: 43
725759 ACACGTGTAC
* * * * * *
725769 CATTGGACAAGTCGAAGTAATT-TACTGGCACACGTAGTGTAT
1 CATTGGATAAATCGAAGAAATTATATTGGCACACATAGTGCAT
* * * *
725811 CATTGGATAAATTGAA-ACAATTATACTAGTC-CAAATAGTGCAT
1 CATTGGATAAATCGAAGA-AATTATA-TTGGCACACATAGTGCAT
* * * *
725854 CATTGGGTAAACCGAAGAAATTATATTGGCACGCGTAGTGCAT
1 CATTGGATAAATCGAAGAAATTATATTGGCACACATAGTGCAT
** * *
725897 CATCCGATAAATTGAAGCAATTATATTGGCACACATAGTGCAT
1 CATTGGATAAATCGAAGAAATTATATTGGCACACATAGTGCAT
725940 CATTGGATAAATCGAAGAAATTATATT
1 CATTGGATAAATCGAAGAAATTATATT
725967 TGAAAAACAG
Statistics
Matches: 121, Mismatches: 30, Indels: 9
0.76 0.19 0.06
Matches are distributed among these distances:
42 20 0.17
43 98 0.81
44 3 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (43 bp):
CATTGGATAAATCGAAGAAATTATATTGGCACACATAGTGCAT
Found at i:725918 original size:86 final size:86
Alignment explanation
Indices: 725781--725966 Score: 241
Period size: 86 Copynumber: 2.2 Consensus size: 86
725771 TTGGACAAGT
* * * ** *
725781 CGAAGTAATT-TACTGGCACACGTAGTGTATCATTGGATAAATTGAAACAATTATACTAGTC-CA
1 CGAAGAAATTATATTGGCACACGTAGTGCATCATCCGATAAATTGAAACAATTATA-TAGGCACA
*
725844 AATAGTGCATCATTGGGTAAAC
65 AATAGTGCATCATTGGATAAAC
* * * *
725866 CGAAGAAATTATATTGGCACGCGTAGTGCATCATCCGATAAATTGAAGCAATTATATTGGCACAC
1 CGAAGAAATTATATTGGCACACGTAGTGCATCATCCGATAAATTGAAACAATTATATAGGCACAA
*
725931 ATAGTGCATCATTGGATAAAT
66 ATAGTGCATCATTGGATAAAC
725952 CGAAGAAATTATATT
1 CGAAGAAATTATATT
725967 TGAAAAACAG
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
85 12 0.14
86 75 0.86
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (86 bp):
CGAAGAAATTATATTGGCACACGTAGTGCATCATCCGATAAATTGAAACAATTATATAGGCACAA
ATAGTGCATCATTGGATAAAC
Found at i:734628 original size:47 final size:47
Alignment explanation
Indices: 734574--734672 Score: 171
Period size: 47 Copynumber: 2.1 Consensus size: 47
734564 TGAACAAGTC
*
734574 TGATGCTCCCATATCAACAAGATCACTCATTCTCTGGCCTACGCTGT
1 TGATGCTCCCATATCAACAAGATCACTCATTCTCTGGCCTACGATGT
* *
734621 TGATGCTCCCATATCAACAAGATCACTCATTCTCTGGGCTGCGATGT
1 TGATGCTCCCATATCAACAAGATCACTCATTCTCTGGCCTACGATGT
734668 TGATG
1 TGATG
734673 TCCACAAAAC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.30
Consensus pattern (47 bp):
TGATGCTCCCATATCAACAAGATCACTCATTCTCTGGCCTACGATGT
Found at i:735584 original size:120 final size:120
Alignment explanation
Indices: 735371--735613 Score: 416
Period size: 120 Copynumber: 2.0 Consensus size: 120
735361 TATAGAAGTT
735371 TATTTCAACTAGAAAAACGGAATCCTAGTTCAACTAGGTTGTAGAAGGTGACAACCCTAGTTAAT
1 TATTTCAACTAGAAAAACGGAATCCTAGTTCAACTAGGTTGTAGAAGGTGACAACCCTAGTTAAT
* *
735436 TATACTAGGGTTTGTCATCCCCCTTATTAAATAAGGGGCTATTGGACTTCTTCCA
66 TATACTAGGGTTTGTCATCCCCCTTATTAAATAAGGGGCTATTAGACCTCTTCCA
*
735491 TATTTCAACTAGAAAAACGGAATCCTAGTTCAACTAGGTTGTA-AGGGGTGACAACCCTAGTTAA
1 TATTTCAACTAGAAAAACGGAATCCTAGTTCAACTAGGTTGTAGA-AGGTGACAACCCTAGTTAA
* * *
735555 TTTTACTAGGGTTTGTCGTCCCCCTTATTAAATAAGGGGCTATTAGACCTCTTTCA
65 TTATACTAGGGTTTGTCATCCCCCTTATTAAATAAGGGGCTATTAGACCTCTTCCA
735611 TAT
1 TAT
735614 CTGGTCCAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
119 1 0.01
120 115 0.99
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (120 bp):
TATTTCAACTAGAAAAACGGAATCCTAGTTCAACTAGGTTGTAGAAGGTGACAACCCTAGTTAAT
TATACTAGGGTTTGTCATCCCCCTTATTAAATAAGGGGCTATTAGACCTCTTCCA
Found at i:745711 original size:8 final size:8
Alignment explanation
Indices: 745698--745722 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
745688 ATTATTTTTA
745698 TTTATTAT
1 TTTATTAT
745706 TTTATTAT
1 TTTATTAT
745714 TTTATTAT
1 TTTATTAT
745722 T
1 T
745723 ATTTTAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTATTAT
Found at i:745912 original size:14 final size:14
Alignment explanation
Indices: 745893--745921 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
745883 GTGTAAGTGG
745893 ACAAAGATAGAAAT
1 ACAAAGATAGAAAT
745907 ACAAAGATAGAAAT
1 ACAAAGATAGAAAT
745921 A
1 A
745922 AGATTAAGTA
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:0.66, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAAAGATAGAAAT
Found at i:746806 original size:41 final size:41
Alignment explanation
Indices: 746735--746839 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 41
746725 TTATTTTATG
* * *
746735 AATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCCTA
1 AATTACACATACGTGCCCCTGTTGGGACTTCGGTACCCCTA
* * *
746776 AATTTCACATACGTGCCCTTGTTGGGACTTCGGTACCTCTA
1 AATTACACATACGTGCCCCTGTTGGGACTTCGGTACCCCTA
*
746817 AATTACACATATGTGCCCCTGTT
1 AATTACACATACGTGCCCCTGTT
746840 TACACTCTGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (41 bp):
AATTACACATACGTGCCCCTGTTGGGACTTCGGTACCCCTA
Found at i:758064 original size:26 final size:26
Alignment explanation
Indices: 758035--758087 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
758025 CCAATCTGAC
*
758035 ATATCTACCCTATTCTGAGTTCTCAA
1 ATATCTACCCTATTCTGAGTCCTCAA
** *
758061 ATATCTTGCCTCTTCTGAGTCCTCAA
1 ATATCTACCCTATTCTGAGTCCTCAA
758087 A
1 A
758088 ATCCAAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.28, G:0.09, T:0.38
Consensus pattern (26 bp):
ATATCTACCCTATTCTGAGTCCTCAA
Found at i:768909 original size:13 final size:13
Alignment explanation
Indices: 768891--768915 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
768881 GATATTAGTA
768891 AAATTATTTACAC
1 AAATTATTTACAC
768904 AAATTATTTACA
1 AAATTATTTACA
768916 GTTAAGTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTATTTACAC
Done.