Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold250
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: 1171037
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 53818 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:748123 original size:15 final size:15
Alignment explanation
Indices: 748075--748126 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
748065 AATTTATGGT
*
748075 TTTCAGAATCTTAAAG
1 TTTCACAATC-TAAAG
* * *
748091 TTTTCACAGTTTATAG
1 -TTTCACAATCTAAAG
748107 TTTCACAATCTAAAG
1 TTTCACAATCTAAAG
748122 TTTCA
1 TTTCA
748127 GTGCGTAACG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
15 17 0.61
16 4 0.14
17 7 0.25
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTCACAATCTAAAG
Found at i:749420 original size:35 final size:35
Alignment explanation
Indices: 749379--749474 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
749369 AATTTCAGTG
* * * *
749379 GGCATGCTTTACATGCGATTTAGAATCAGTATAGT
1 GGCATGCTTAACATGCGAATCAGAATCAGTATAAT
* *
749414 GGCATGCTTAACATACGAATCAGAATTAGTATAAT
1 GGCATGCTTAACATGCGAATCAGAATCAGTATAAT
* *
749449 GACATGCTTAACATGTGAATCAGAAT
1 GGCATGCTTAACATGCGAATCAGAAT
749475 ACCAACAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 52 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (35 bp):
GGCATGCTTAACATGCGAATCAGAATCAGTATAAT
Found at i:750523 original size:32 final size:32
Alignment explanation
Indices: 750487--750550 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
750477 AGGAGGAGGG
* *
750487 GCGGCAAAAAGAGAGGTGAAGAATAGAATGAA
1 GCGGCAAAAAGAGAGATGAAGAATAAAATGAA
* *
750519 GCGGCTAAAAGAGAGATGGAGAATAAAATGAA
1 GCGGCAAAAAGAGAGATGAAGAATAAAATGAA
750551 CAAAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.33, T:0.11
Consensus pattern (32 bp):
GCGGCAAAAAGAGAGATGAAGAATAAAATGAA
Found at i:754297 original size:24 final size:24
Alignment explanation
Indices: 754265--754312 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
754255 TCGAGACCCT
754265 CGAAGCCCCACTTATCCGTGCCTA
1 CGAAGCCCCACTTATCCGTGCCTA
754289 CGAAGCCCCACTTATCCGTGCCTA
1 CGAAGCCCCACTTATCCGTGCCTA
754313 TTCGAGCGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.21
Consensus pattern (24 bp):
CGAAGCCCCACTTATCCGTGCCTA
Found at i:755974 original size:21 final size:21
Alignment explanation
Indices: 755949--755994 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
755939 GGACTAATTT
*
755949 AAAAT-AACTTGGAAATTTTGG
1 AAAATAAACTTGAAAATTTT-G
*
755970 AAAATAAAGTTGAAAATTTTG
1 AAAATAAACTTGAAAATTTTG
755991 AAAA
1 AAAA
755995 CAAGGGTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.52, C:0.02, G:0.15, T:0.30
Consensus pattern (21 bp):
AAAATAAACTTGAAAATTTTG
Found at i:761634 original size:11 final size:9
Alignment explanation
Indices: 761618--761649 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
761608 CGAAATAAAT
*
761618 TATATATAG
1 TATATATAA
761627 TATATATAA
1 TATATATAA
761636 TATATATAA
1 TATATATAA
761645 TATAT
1 TATAT
761650 TTTTTAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (9 bp):
TATATATAA
Found at i:763203 original size:58 final size:60
Alignment explanation
Indices: 763113--763237 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 60
763103 AAATAAAAGA
*
763113 ATTACATGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATAC-C-CCC
1 ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCCC
*
763171 ATTACTTGTTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCCC
1 ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCCC
763231 -TTACTTG
1 ATTACTTG
763238 ATGCATATCT
Statistics
Matches: 63, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
58 52 0.83
59 8 0.13
60 3 0.05
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (60 bp):
ATTACTTGCTAAGGATAATTCAATAAAATCACAAGCAATTCCTATTTCTAATACTCTCCC
Found at i:768521 original size:23 final size:23
Alignment explanation
Indices: 768493--768544 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
768483 TAATGTAAAT
* * *
768493 TTATTTTTAGCAATTACAAATCA
1 TTATTTTCAACAATTACAAACCA
*
768516 TTATTTCCAACAATTACAAACCA
1 TTATTTTCAACAATTACAAACCA
768539 TT-TTTT
1 TTATTTT
768545 ACTATTACAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (23 bp):
TTATTTTCAACAATTACAAACCA
Found at i:779646 original size:80 final size:82
Alignment explanation
Indices: 779508--779666 Score: 304
Period size: 80 Copynumber: 2.0 Consensus size: 82
779498 TAATGATCAC
779508 ATCTCTTAAACATAAACGTAAAACAAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATG
1 ATCTCTTAAACATAAACGTAAAACAAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATG
779573 CAGAGAATATCCTTAAT
66 CAGAGAATATCCTTAAT
779590 ATCTCTTAAACATAAACGTAAAAC-AAAAAAAA-CATGCTTACGATACAAGATTCAAAGGTAATG
1 ATCTCTTAAACATAAACGTAAAACAAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATG
779653 CAGAGAATATCCTT
66 CAGAGAATATCCTT
779667 TCTTTTTTTC
Statistics
Matches: 77, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
80 45 0.58
81 8 0.10
82 24 0.31
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (82 bp):
ATCTCTTAAACATAAACGTAAAACAAAAAAAAAGCATGCTTACGATACAAGATTCAAAGGTAATG
CAGAGAATATCCTTAAT
Found at i:788841 original size:35 final size:34
Alignment explanation
Indices: 788775--788841 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
788765 ATGTTTATTG
*
788775 TTTGTATTAAAGTGTATGCCAAATTTTGATTTCT
1 TTTGTATTAAAGTGTATGCCAAATTTGGATTTCT
* **
788809 TTTGTTATTAAAGTGTATGGCAGGTTTGGATTT
1 TTTG-TATTAAAGTGTATGCCAAATTTGGATTT
788842 TTCTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.24, C:0.06, G:0.21, T:0.49
Consensus pattern (34 bp):
TTTGTATTAAAGTGTATGCCAAATTTGGATTTCT
Found at i:790794 original size:26 final size:26
Alignment explanation
Indices: 790755--790813 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
790745 CCGAATATAA
* * *
790755 TAAATATATATTTTTATTTTTTATTTT
1 TAAA-ATAAATTTTTAATGTTTATTTT
790782 TAAAATAAATTTTTAATGTTTATTTT
1 TAAAATAAATTTTTAATGTTTATTTT
*
790808 AAAAAT
1 TAAAAT
790814 GGGCCGGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 24 0.86
27 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TAAAATAAATTTTTAATGTTTATTTT
Found at i:791310 original size:4 final size:4
Alignment explanation
Indices: 791301--791358 Score: 54
Period size: 4 Copynumber: 15.2 Consensus size: 4
791291 AACGAAACAG
*
791301 GAAA GAAA GAAA GAAA G-AA -AAA GAAA -AAG GAAA GAAA -AAGA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A GAAA
791346 -AGAA GAAA GAAA G
1 GA-AA GAAA GAAA G
791359 CCAGTGCCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
3 9 0.20
4 33 0.73
5 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:791321 original size:29 final size:29
Alignment explanation
Indices: 791283--791357 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 29
791273 AAATAGCAAC
*
791283 AAAGCAAAAACGAAACAGGAAAGAAAGAA-AG
1 AAAG-AAAAA-GAAAAAGGAAAGAAA-AAGAG
791314 AAAGAAAAAGAAAAAGGAAAGAAAAAGAG
1 AAAGAAAAAGAAAAAGGAAAGAAAAAGAG
791343 AAAAGAAGAAAGAAA
1 -AAAGAA-AAAGAAA
791358 GCCAGTGCCT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 2 0.05
29 16 0.40
30 11 0.28
31 11 0.28
ACGTcount: A:0.73, C:0.04, G:0.23, T:0.00
Consensus pattern (29 bp):
AAAGAAAAAGAAAAAGGAAAGAAAAAGAG
Found at i:791335 original size:17 final size:17
Alignment explanation
Indices: 791302--791357 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
791292 ACGAAACAGG
*
791302 AAAGAAAGAAAGAAAGAA
1 AAAGAAA-AAGGAAAGAA
791320 AAAGAAAAAGGAAAGAA
1 AAAGAAAAAGGAAAGAA
791337 AAAGAGAAAAGAAGAAAGAA
1 AAAGA-AAAAG--GAAAGAA
791357 A
1 A
791358 GCCAGTGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 14 0.41
18 12 0.35
20 8 0.24
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGGAAAGAA
Found at i:792298 original size:41 final size:39
Alignment explanation
Indices: 792238--792376 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 39
792228 GACTTTGAGT
* * *
792238 CGATGAAACACTGGATGCCAATTTACTACTTCAGATTAATT
1 CGATGAGACACTGGGTGCCAATTTA-TACTTCAGATT-ATC
* * *
792279 CGATGAGGCACTGGGTGCCAA-TT-TACTTCAGTTTAGC
1 CGATGAGACACTGGGTGCCAATTTATACTTCAGATTATC
* * *
792316 CGATGAGACATTGTGTGTCAATTTATTACTTC-GAATTATC
1 CGATGAGACACTGGGTGCCAATTTA-TACTTCAG-ATTATC
* *
792356 CGATGAGGCATTGGGTGCCAA
1 CGATGAGACACTGGGTGCCAA
792377 ACTGGTGTGT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
37 18 0.23
38 12 0.15
39 1 0.01
40 30 0.38
41 18 0.23
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (39 bp):
CGATGAGACACTGGGTGCCAATTTATACTTCAGATTATC
Found at i:793479 original size:11 final size:11
Alignment explanation
Indices: 793460--793494 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
793450 AGCTTCTTTG
793460 GATTCAAATAT
1 GATTCAAATAT
*
793471 GATTTAAATAT
1 GATTCAAATAT
*
793482 GAATCAAATAT
1 GATTCAAATAT
793493 GA
1 GA
793495 CAAATCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (11 bp):
GATTCAAATAT
Found at i:793722 original size:44 final size:44
Alignment explanation
Indices: 793592--793725 Score: 108
Period size: 46 Copynumber: 3.0 Consensus size: 44
793582 ATTTATTTGG
* * * *
793592 TTATTGTCTGCCATGTGCATGACAGAAACAAATTTGTTTGTATT
1 TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATT
** **** * ** *
793636 AAATTGT-TTGGTTATTGTACATGACATAAATGAATTTCTTTGTATT
1 TTATTGTCTACCATA-TGT--ATGACAAAAACAAATTTGTTTGTATT
793682 TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATT
1 TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATT
793726 AAATTGTTTG
Statistics
Matches: 64, Mismatches: 22, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
43 2 0.03
44 29 0.45
46 30 0.47
47 3 0.05
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (44 bp):
TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATT
Found at i:793732 original size:44 final size:44
Alignment explanation
Indices: 793594--793732 Score: 118
Period size: 44 Copynumber: 3.1 Consensus size: 44
793584 TTATTTGGTT
* * * *
793594 ATTGTCTGCCATGTGCATGACAGAAACAAATTTGTTTGTATTAA
1 ATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAA
**** * ** * **
793638 ATTGT-TTGGTTATTGTACATGACATAAATGAATTTCTTTGTATTTT
1 ATTGTCTACCATA-TGT--ATGACAAAAACAAATTTGTTTGTATTAA
793684 ATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAA
1 ATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAA
793728 ATTGT
1 ATTGT
793733 TTGGTTATTG
Statistics
Matches: 69, Mismatches: 22, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
43 2 0.03
44 34 0.49
46 30 0.43
47 3 0.04
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (44 bp):
ATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAA
Found at i:793745 original size:90 final size:90
Alignment explanation
Indices: 793592--793910 Score: 449
Period size: 90 Copynumber: 3.5 Consensus size: 90
793582 ATTTATTTGG
*
793592 TTATTGTCTGCCATGTGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
1 TTATTGTCTGCCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
*
793657 TGACATAAATGAATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
* * *
793682 TTATTGTCTACCATATGTATGACAAAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
1 TTATTGTCTGCCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
793747 TGACATAAATGGATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
* ** * * *
793772 TTATTGTCTGTCATATGCATGACAGAAATGAATTTATTTGTATTAAATTGTTTGGTTATTGAACT
1 TTATTGTCTGCCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
*
793837 TGACAAAAATGGATTTCTTTGTATT
66 TGACATAAATGGATTTCTTTGTATT
** * * * * ** *
793862 AAAGTGTATGGCATGTGCATGACAGAAATGAATTTGTTTGTGTTAAATT
1 TTATTGTCTGCCATATGCATGACAGAAACAAATTTGTTTGTATTAAATT
793911 ATTTTTTGTA
Statistics
Matches: 206, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 206 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.44
Consensus pattern (90 bp):
TTATTGTCTGCCATATGCATGACAGAAACAAATTTGTTTGTATTAAATTGTTTGGTTATTGTACA
TGACATAAATGGATTTCTTTGTATT
Found at i:796250 original size:41 final size:41
Alignment explanation
Indices: 796178--796276 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
796168 ATCGGCTTTT
* * * * *
796178 AGCCTGCTAGACTTATAGTCCGAATTGTTTCACCGGCATTA
1 AGCCTGCTAGACATAAAGTCCGAAATATTTCACCGGCATCA
796219 AGCCTGCTAGACATAAAG-CCTGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCC-GAAATATTTCACCGGCATCA
* *
796260 AACCTGCTAGACGTAAA
1 AGCCTGCTAGACATAAA
796277 TTCTGAAACA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 2 0.04
41 48 0.96
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCCGAAATATTTCACCGGCATCA
Found at i:796801 original size:12 final size:13
Alignment explanation
Indices: 796784--796819 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
796774 ATTTGAGCAT
796784 TATATACATAT-A
1 TATATACATATAA
796796 TATATACATATACA
1 TATATACATATA-A
796810 TATATACATA
1 TATATACATA
796820 CTCATACCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (13 bp):
TATATACATATAA
Found at i:796826 original size:18 final size:18
Alignment explanation
Indices: 796785--796820 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
796775 TTTGAGCATT
*
796785 ATATACATATATATATAC
1 ATATACATATATACATAC
796803 ATATACATATATACATAC
1 ATATACATATATACATAC
796821 TCATACCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATACATATATACATAC
Found at i:803314 original size:50 final size:49
Alignment explanation
Indices: 803198--803426 Score: 243
Period size: 48 Copynumber: 4.7 Consensus size: 49
803188 ATAGCAACAT
*
803198 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGATGTT-TCATGTAC-
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATCT-CG
* * * *
803246 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCTG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTC-G
* * **
803296 TGCCCATGCCATGTCCCAGACATGGTCTTAC--GGGGGACCTCATCTCG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTCG
* * **
803343 ATGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTC-G
* *
803394 TGCCAACGCCATGTCCCAGGCATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
803427 AGGACCTCAT
Statistics
Matches: 152, Mismatches: 21, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
47 1 0.01
48 73 0.48
49 8 0.05
50 69 0.45
51 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATCTCG
Found at i:803432 original size:50 final size:50
Alignment explanation
Indices: 803198--803434 Score: 250
Period size: 50 Copynumber: 4.8 Consensus size: 50
803188 ATAGCAACAT
** * *
803198 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * ** * *
803246 TGCCAATGCCATATCCCAGATATGGTTTTACATGGGAGTTCTCATATCTG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ** *
803296 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGA-C-CTCATCTCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
803344 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
803394 TGCCAACGCCATGTCCCAGGCATGGTCTTACATAGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
803435 ATCCTCTTAA
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
48 70 0.44
49 10 0.06
50 78 0.49
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:803432 original size:98 final size:99
Alignment explanation
Indices: 803198--803437 Score: 272
Period size: 98 Copynumber: 2.4 Consensus size: 99
803188 ATAGCAACAT
** * *
803198 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGATGT-TTCATGTACTGCCAATGCCATATCC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGACCTCATCATGTACTGCCAACGCCATATCC
* * ** *
803262 CAGATATGGTTTTACATGGGAGTTCTCATATCTG
66 CAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
803296 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCATC-TCG-A-TGCCAACGCCATGT
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGACCTCATCAT-GTACTGCCAACGCCATAT
* *
803358 CCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
64 CCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
803394 TGCCAACGCCATGTCCCAGGCATGGTCTTACATAGGACCTCATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGACCTCATC
803438 CTCTTAATGT
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
98 109 0.92
99 6 0.05
100 3 0.03
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.28
Consensus pattern (99 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGACCTCATCATGTACTGCCAACGCCATATCC
CAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:809754 original size:85 final size:85
Alignment explanation
Indices: 809611--809780 Score: 277
Period size: 85 Copynumber: 2.0 Consensus size: 85
809601 CCCTATTCCG
* * *
809611 GCAACAGAGACGGGTTAGGGGTGTTACACCAACTCACCAGGAAATAGCCCCAACTTACCAAGAAG
1 GCAACAGAGACGGATTAGGAGTGTTACACCAACTCACCAAGAAATAGCCCCAACTTACCAAGAAG
*
809676 TTGTCCCAAGAGAAAAGCTT
66 CTGTCCCAAGAGAAAAGCTT
* * *
809696 GCAACGGAGACGGATTAGGAGTGTTACACCAACTCACTAAGAAATATCCCCAACTTACCAAGAAG
1 GCAACAGAGACGGATTAGGAGTGTTACACCAACTCACCAAGAAATAGCCCCAACTTACCAAGAAG
809761 CTGTCCCAAGAGAAAAGCTT
66 CTGTCCCAAGAGAAAAGCTT
809781 TCATTCAAGA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (85 bp):
GCAACAGAGACGGATTAGGAGTGTTACACCAACTCACCAAGAAATAGCCCCAACTTACCAAGAAG
CTGTCCCAAGAGAAAAGCTT
Found at i:816019 original size:29 final size:29
Alignment explanation
Indices: 815954--816020 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
815944 TATTTTTTTA
* *
815954 AATGTATAATTAAATTAAATTAAAAATTT
1 AATGTATATTTAAACTAAATTAAAAATTT
* ** *
815983 TACATATATTTAAACTAAATTCAAAATTT
1 AATGTATATTTAAACTAAATTAAAAATTT
816012 AATGTATAT
1 AATGTATAT
816021 AATTACAAAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (29 bp):
AATGTATATTTAAACTAAATTAAAAATTT
Found at i:816380 original size:27 final size:26
Alignment explanation
Indices: 816326--816385 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 26
816316 TATTTTTTTC
*
816326 CAAAATCTATAAAAATTAAAACAAATT
1 CAAAATATATAAAAATTAAAAC-AATT
816353 CAAAATATATAAAATATTCAAAAC-ATT
1 CAAAATATATAAAA-ATT-AAAACAATT
816380 CTAAAA
1 C-AAAA
816386 AATTCTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 17 0.59
28 7 0.24
29 5 0.17
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (26 bp):
CAAAATATATAAAAATTAAAACAATT
Found at i:816390 original size:19 final size:18
Alignment explanation
Indices: 816348--816390 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
816338 AAATTAAAAC
*
816348 AAATTCAAAATATATAAA
1 AAATTCAAAACATATAAA
* *
816366 ATATTCAAAACATTCTAAA
1 AAATTCAAAACA-TATAAA
816385 AAATTC
1 AAATTC
816391 TATATAGATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (18 bp):
AAATTCAAAACATATAAA
Found at i:818482 original size:21 final size:21
Alignment explanation
Indices: 818458--818501 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
818448 GAATCTTTAG
*
818458 TATTTATTGTATCATTT-TATT
1 TATTTAAT-TATCATTTCTATT
818479 TATTTAATTATCATTTCTATT
1 TATTTAATTATCATTTCTATT
818500 TA
1 TA
818502 ATTAGGTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTAATTATCATTTCTATT
Found at i:818839 original size:27 final size:27
Alignment explanation
Indices: 818801--818856 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
818791 AAAATATGTC
*
818801 ATAAGTGCTAACGAAAGTGTTCTTTCA
1 ATAAGTGCTAACGAAAGTGTTATTTCA
818828 ATAAGTGCTAACGAAAGTGTTATTTCA
1 ATAAGTGCTAACGAAAGTGTTATTTCA
818855 AT
1 AT
818857 TACAATCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (27 bp):
ATAAGTGCTAACGAAAGTGTTATTTCA
Found at i:819731 original size:23 final size:24
Alignment explanation
Indices: 819670--819732 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 24
819660 CTCAAAACTT
*
819670 TTTTATATATATTTAGATTTTTATTA
1 TTTTATA-AT-TTTAGATTTTGATTA
* *
819696 TTTT-TAAAATTTA-ATTTTGATTC
1 TTTTAT-AATTTTAGATTTTGATTA
819719 TTTTATAATTTTAG
1 TTTTATAATTTTAG
819733 GATCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
23 18 0.60
24 5 0.17
25 2 0.07
26 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (24 bp):
TTTTATAATTTTAGATTTTGATTA
Found at i:820041 original size:19 final size:19
Alignment explanation
Indices: 820017--820054 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
820007 AATGCATTCA
820017 CCAAAGTTTGTAGTTCTTT
1 CCAAAGTTTGTAGTTCTTT
820036 CCAAAGTTTGTAGTTCTTT
1 CCAAAGTTTGTAGTTCTTT
820055 TTTACCCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
CCAAAGTTTGTAGTTCTTT
Found at i:821886 original size:41 final size:42
Alignment explanation
Indices: 821815--821904 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 42
821805 GATTCACTGG
* *
821815 CACTTAGCCCTGTTAGGCTTAAAGCTTGATTCAGATCACCGA
1 CACTTAGCCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGA
* *
821857 CACTTAG-CCTGCTAGGCTTATAA-CCTGATTTAGATCACCGG
1 CACTTAGCCCTGCTAGGCTTA-AAGCCTGATTCAGATCACCGA
821898 CACTTAG
1 CACTTAG
821905 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 34 0.79
42 9 0.21
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (42 bp):
CACTTAGCCCTGCTAGGCTTAAAGCCTGATTCAGATCACCGA
Found at i:824640 original size:21 final size:21
Alignment explanation
Indices: 824578--824642 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
824568 TGTAAAATAC
* * *
824578 TTTTTTGTCATAATTTTAGAA
1 TTTTTTGTTAAAATTTTATAA
* * *
824599 TTTTTAAGATTTAAATATTATAA
1 TTTTT-TG-TTAAAATTTTATAA
824622 TTTTTTGTTAAAATTTTATAA
1 TTTTTTGTTAAAATTTTATAA
824643 ATACACATAA
Statistics
Matches: 33, Mismatches: 9, Indels: 4
0.72 0.20 0.09
Matches are distributed among these distances:
21 17 0.52
22 2 0.06
23 14 0.42
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTTGTTAAAATTTTATAA
Found at i:824958 original size:10 final size:10
Alignment explanation
Indices: 824943--824971 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
824933 CCACTTTTGT
824943 GCAATTACAA
1 GCAATTACAA
824953 GCAATTACAA
1 GCAATTACAA
824963 GCAATTACA
1 GCAATTACA
824972 CCTAAATCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.21, G:0.10, T:0.21
Consensus pattern (10 bp):
GCAATTACAA
Found at i:830784 original size:15 final size:15
Alignment explanation
Indices: 830750--830784 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
830740 TATATATGCC
830750 ACAATAATAAATACA
1 ACAATAATAAATACA
* *
830765 TCAATAATAAATATA
1 ACAATAATAAATACA
830780 ACAAT
1 ACAAT
830785 GGCATAGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:831063 original size:11 final size:11
Alignment explanation
Indices: 831047--831083 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
831037 ACGTATATAT
831047 ATAAAATAATA
1 ATAAAATAATA
831058 ATAAAATAA-A
1 ATAAAATAATA
831068 ATAAAA-AATA
1 ATAAAATAATA
831078 AGTAAA
1 A-TAAA
831084 TATTTACTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.08
10 9 0.38
11 13 0.54
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (11 bp):
ATAAAATAATA
Found at i:831175 original size:23 final size:24
Alignment explanation
Indices: 831120--831182 Score: 83
Period size: 26 Copynumber: 2.6 Consensus size: 24
831110 ATATACGTAT
*
831120 AAATATAAAAATATTCATTTAAAA
1 AAATAGAAAAATATTCATTTAAAA
831144 AAATGTAGAAAAATATTCA-TTAAAA
1 AAA--TAGAAAAATATTCATTTAAAA
*
831169 AAATAGAAATATAT
1 AAATAGAAAAATAT
831183 ATGCATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 10 0.29
24 3 0.09
25 9 0.26
26 13 0.37
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (24 bp):
AAATAGAAAAATATTCATTTAAAA
Found at i:831211 original size:21 final size:21
Alignment explanation
Indices: 831186--831230 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
831176 AATATATATG
831186 CATATATAG-ATAAAATAATTA
1 CATATAT-GTATAAAATAATTA
831207 CATATATGTATAAAATAATTA
1 CATATATGTATAAAATAATTA
831228 CAT
1 CAT
831231 TATCAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (21 bp):
CATATATGTATAAAATAATTA
Found at i:835287 original size:22 final size:19
Alignment explanation
Indices: 835207--835318 Score: 59
Period size: 20 Copynumber: 5.6 Consensus size: 19
835197 TTTTATCTAA
*
835207 AAAATAAATATTTAA-TATT
1 AAAAT-AATATTAAACTATT
* *
835226 AAGATAATCAATTCAA-TATT
1 AAAATAAT--ATTAAACTATT
* *
835246 AAATTAATA-AAATACTATT
1 AAAATAATATTAA-ACTATT
*
835265 AAAATAAGTATTAAATTAAATT
1 AAAATAA-TATTAAACT--ATT
* *
835287 AAATTAAATTTTAAACTATT
1 AAAAT-AATATTAAACTATT
835307 AAAATAATATTA
1 AAAATAATATTA
835319 TTTTTGGAAT
Statistics
Matches: 70, Mismatches: 14, Indels: 18
0.69 0.14 0.18
Matches are distributed among these distances:
17 1 0.01
18 5 0.07
19 20 0.29
20 26 0.37
21 2 0.03
22 14 0.20
23 2 0.03
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAATATTAAACTATT
Found at i:838129 original size:26 final size:26
Alignment explanation
Indices: 838100--838173 Score: 105
Period size: 27 Copynumber: 2.8 Consensus size: 26
838090 TCTCATCCCT
838100 ATTTTACCCCTGGTAAAATTTTGACA
1 ATTTTACCCCTGGTAAAATTTTGACA
*
838126 ATTTTA-CCCTCGGTGAAAATTTTGACG
1 ATTTTACCCCT-GGT-AAAATTTTGACA
*
838153 ATTTTACCTCTGGTAAAATTT
1 ATTTTACCCCTGGTAAAATTT
838174 CGAGAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.09
26 16 0.37
27 20 0.47
28 3 0.07
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (26 bp):
ATTTTACCCCTGGTAAAATTTTGACA
Found at i:838149 original size:27 final size:27
Alignment explanation
Indices: 838100--838173 Score: 109
Period size: 26 Copynumber: 2.8 Consensus size: 27
838090 TCTCATCCCT
838100 ATTTTACCC-CTGGTAAAATTTTGACA
1 ATTTTACCCTCTGGTAAAATTTTGACA
*
838126 ATTTTACCCTC-GGTGAAAATTTTGACG
1 ATTTTACCCTCTGGT-AAAATTTTGACA
838153 ATTTTA-CCTCTGGTAAAATTT
1 ATTTTACCCTCTGGTAAAATTT
838174 CGAGAAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 23 0.52
27 21 0.48
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTCTGGTAAAATTTTGACA
Found at i:849774 original size:16 final size:17
Alignment explanation
Indices: 849742--849776 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
849732 ATTTAATCTT
*
849742 TATATAACATAACATAA
1 TATATAACATAAAATAA
849759 TATATAA-ATAAAATAA
1 TATATAACATAAAATAA
849775 TA
1 TA
849777 AGTTACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TATATAACATAAAATAA
Found at i:854192 original size:29 final size:31
Alignment explanation
Indices: 854144--854201 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
854134 AAAATTTTAG
* *
854144 AATTTAATTCTTATAGTTTT-ATTTTCAATA
1 AATTTAATTCCTATAGTTTTCAGTTTCAATA
*
854174 AATTTAA-TCCTATATTTTTCAGTTTCAA
1 AATTTAATTCCTATAGTTTTCAGTTTCAA
854202 AATTCAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.53
Consensus pattern (31 bp):
AATTTAATTCCTATAGTTTTCAGTTTCAATA
Found at i:855994 original size:19 final size:19
Alignment explanation
Indices: 855972--856014 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
855962 AATTTTGATA
855972 AAATAAAATAAAATAAAAT
1 AAATAAAATAAAATAAAAT
* * *
855991 AAATCAAATCAATTAAAAT
1 AAATAAAATAAAATAAAAT
*
856010 TAATA
1 AAATA
856015 TGATATTTTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAATAAAATAAAAT
Found at i:856002 original size:5 final size:5
Alignment explanation
Indices: 855969--855993 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
855959 AATAATTTTG
855969 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
855994 TCAAATCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:874399 original size:7 final size:7
Alignment explanation
Indices: 874387--874446 Score: 75
Period size: 7 Copynumber: 8.4 Consensus size: 7
874377 ATTTCTTCTC
874387 ATTTTAA
1 ATTTTAA
874394 ATTTTAA
1 ATTTTAA
874401 ATTTTAA
1 ATTTTAA
**
874408 ATTTTTT
1 ATTTTAA
* *
874415 GTGTTATA
1 ATTTTA-A
874423 ATTTTAA
1 ATTTTAA
874430 ATTTTAA
1 ATTTTAA
874437 ATTTTAA
1 ATTTTAA
874444 ATT
1 ATT
874447 ATAGTTTGTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
7 40 0.91
8 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:874434 original size:36 final size:38
Alignment explanation
Indices: 874387--874473 Score: 151
Period size: 36 Copynumber: 2.3 Consensus size: 38
874377 ATTTCTTCTC
874387 ATTTTAAATTTTAAATTTTAAATT-T-TTTGTGTTATA
1 ATTTTAAATTTTAAATTTTAAATTATATTTGTGTTATA
874423 ATTTTAAATTTTAAATTTTAAATTATAGTTTGTGTTATA
1 ATTTTAAATTTTAAATTTTAAATTATA-TTTGTGTTATA
874462 ATTTTAAATTTT
1 ATTTTAAATTTT
874474 TTGTGGTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 24 0.50
37 1 0.02
39 23 0.48
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (38 bp):
ATTTTAAATTTTAAATTTTAAATTATATTTGTGTTATA
Found at i:875949 original size:91 final size:91
Alignment explanation
Indices: 875804--876009 Score: 313
Period size: 91 Copynumber: 2.3 Consensus size: 91
875794 GATTTTAGTT
* *
875804 AATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
1 AATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
* * * *
875869 TTAATATTAATTATTTTAAATTGTATA
65 GTAATAATAATTATTTTAAATTATACA
*
875896 AATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATATG
1 AATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATG
875961 TAATAATAATTATTTTAAATTATACA
66 TAATAATAATTATTTTAAATTATACA
* * *
875987 AATTCATAAAATATAATTTATTA
1 AATTCATATAAGAAAATTTATTA
876010 GTTATAATTA
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
91 90 0.87
92 14 0.13
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
AATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATG
TAATAATAATTATTTTAAATTATACA
Found at i:875978 original size:26 final size:28
Alignment explanation
Indices: 875924--875984 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
875914 TATTATCAAG
* *
875924 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
875952 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
875978 AATTATA
1 AATTATA
875985 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:875984 original size:44 final size:43
Alignment explanation
Indices: 875842--875984 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
875832 GAATTTTATG
* *
875842 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
875886 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
875933 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
875977 AAATTATA
1 AAATTATA
875985 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:882614 original size:3 final size:3
Alignment explanation
Indices: 882600--882664 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
882590 CAAAATTTGG
*
882600 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
882648 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
882665 CACTTTTAAC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:882748 original size:29 final size:27
Alignment explanation
Indices: 882716--882770 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
882706 CATTTGCTTA
882716 TTTTCAATT-TTTATTTAAACTTTTTTTAG
1 TTTT-AATTGTTTATTT--ACTTTTTTTAG
*
882745 TTTTATTTGTTTATTTACTTTTTTTA
1 TTTTAATTGTTTATTTACTTTTTTTA
882771 ATTAGTTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (27 bp):
TTTTAATTGTTTATTTACTTTTTTTAG
Found at i:887395 original size:13 final size:13
Alignment explanation
Indices: 887377--887401 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
887367 TTTTTAAAAT
887377 TATTATTTTAATG
1 TATTATTTTAATG
887390 TATTATTTTAAT
1 TATTATTTTAAT
887402 TGAAATAAAT
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:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
TATTATTTTAATG
Found at i:889135 original size:94 final size:94
Alignment explanation
Indices: 889017--889190 Score: 258
Period size: 94 Copynumber: 1.9 Consensus size: 94
889007 CACATTTATA
* * *
889017 CTCACACTTACCCTATAAATAAGTGTCAACTTCTTCACTATTTTTATTAAAATGATAATTTTAAT
1 CTCACACTTACCCTATAAATAAGTGACAACTTCTTCACTATTTTCATTAAAAAGATAATTTTAAT
* *
889082 CCCACGTTGATTAGAGAATACTCTCATAT
66 CCCACATTGACTAGAGAATACTCTCATAT
* * * * *
889111 CTCACATTTACCTTATAAATAAGTGACAATTTCTTCTCTATTTTCATTAAAAAGCTAATTTTAAT
1 CTCACACTTACCCTATAAATAAGTGACAACTTCTTCACTATTTTCATTAAAAAGATAATTTTAAT
889176 CCCACATTGACTAGA
66 CCCACATTGACTAGA
889191 AAAATATTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 70 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (94 bp):
CTCACACTTACCCTATAAATAAGTGACAACTTCTTCACTATTTTCATTAAAAAGATAATTTTAAT
CCCACATTGACTAGAGAATACTCTCATAT
Found at i:889412 original size:77 final size:76
Alignment explanation
Indices: 889260--889415 Score: 217
Period size: 77 Copynumber: 2.0 Consensus size: 76
889250 AAAAAGTTAA
* * *
889260 TTTTAATCTCACATTGGCCAGAGAACACTCACATGCTCACATTAACCTTATAAATAAGTGTAAAT
1 TTTTAATCCCACATTGACCAGAGAACACTCACATGCTCAAATTAACCTTATAAATAAGTGTAAAT
889325 TTCTTCATTAT
66 TTCTTCATTAT
* * *
889336 TTTTAATCCCACATTGACCAGAGAACACTC-CTATATCTCAAATTTATCTTATAAATAAGTG-AT
1 TTTTAATCCCACATTGACCAGAGAACACTCAC-AT-GCTCAAATTAACCTTATAAATAAGTGTA-
889399 AATTTCTTCATTAT
63 AATTTCTTCATTAT
889413 TTT
1 TTT
889416 CGTTAAAAAG
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
75 1 0.01
76 31 0.44
77 39 0.55
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (76 bp):
TTTTAATCCCACATTGACCAGAGAACACTCACATGCTCAAATTAACCTTATAAATAAGTGTAAAT
TTCTTCATTAT
Found at i:889542 original size:19 final size:19
Alignment explanation
Indices: 889518--889554 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
889508 AATACAATAC
889518 TAGTACTAAAATTTTGCAG
1 TAGTACTAAAATTTTGCAG
889537 TAGTACTAAAATTTTGCA
1 TAGTACTAAAATTTTGCA
889555 AATAAATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
TAGTACTAAAATTTTGCAG
Found at i:897080 original size:24 final size:24
Alignment explanation
Indices: 897048--897094 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
897038 CTAAATTTAG
*
897048 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
897072 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
897095 ATTTCCCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:898494 original size:18 final size:18
Alignment explanation
Indices: 898457--898494 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
898447 TTCGTTTTTG
*
898457 TTTTCTTTTTTGTTGTTT
1 TTTTCTTTTTTGTTGCTT
898475 TTTTCTTTTTT-TCTGCTT
1 TTTTCTTTTTTGT-TGCTT
898493 TT
1 TT
898495 GTTTGTTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTGTTGCTT
Found at i:899133 original size:44 final size:44
Alignment explanation
Indices: 899019--899150 Score: 140
Period size: 45 Copynumber: 3.0 Consensus size: 44
899009 CTGTAATTTA
* *
899019 TAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCAC
1 TAGCTTCAATCTGATCCACTGCAACTTCAGGGAGATAAGATT-AC
* * * * ** *
899064 TATCTTCAGTCTGCTCCACTACAACTTCAAAGAGATAAGACTT-G
1 TAGCTTCAATCTGATCCACTGCAACTTCAGGGAGATAAGA-TTAC
*
899108 TGGCTTCAATCTGATCCACTGCAACTTCAGGGAGATAATGATT
1 TAGCTTCAATCTGATCCACTGCAACTTCAGGGAGATAA-GATT
899151 TTGTTACGGT
Statistics
Matches: 70, Mismatches: 15, Indels: 5
0.78 0.17 0.06
Matches are distributed among these distances:
44 33 0.47
45 35 0.50
46 2 0.03
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (44 bp):
TAGCTTCAATCTGATCCACTGCAACTTCAGGGAGATAAGATTAC
Found at i:899300 original size:44 final size:42
Alignment explanation
Indices: 899252--899368 Score: 105
Period size: 44 Copynumber: 2.8 Consensus size: 42
899242 TATTAATAGC
*
899252 TTCAATCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCAAT
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTG--AT
* * * *
899296 TTCAAACTGC-CTCACTGTAATTTTAGGG-GATAAGGTTTGAT
1 TTCAATCTGCTC-CACTGCAACTTCAGGGAGATAAGGTTTGAT
* * * *
899337 AT-GATCTGCTCTACTGCAACTTCAGAGAGATA
1 TTCAATCTGCTCCACTGCAACTTCAGGGAGATA
899369 GGATCTGTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 9
0.72 0.16 0.11
Matches are distributed among these distances:
40 16 0.28
41 8 0.14
43 12 0.21
44 21 0.37
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGAT
Found at i:899530 original size:44 final size:44
Alignment explanation
Indices: 899397--899574 Score: 142
Period size: 44 Copynumber: 4.0 Consensus size: 44
899387 TTCAATCTAT
* * * * *
899397 TCCACTACAACTTCATAGAAATAAGA-TTCGCTATCTTTAGTCTGC
1 TCCACTGCAACTTCAGAGAGATAAGACTT-G-TAGCTTTAATCTGC
* * * * * * *
899442 TTCTCTGCAACTTTAGAGAGATAAGACTTGCATCTTCAACCTGC
1 TCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTTAATCTGC
* *
899486 TCCACTGCAACTTCAGAGAGATAAGATTTGTGGCTTTAATCTGC
1 TCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTTAATCTGC
* * * * * * *
899530 TCCATTGTAACTTCAGGGAGATAACACTGGTGGCTTAAATCTGC
1 TCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTTAATCTGC
899574 T
1 T
899575 TCCCTACTAC
Statistics
Matches: 106, Mismatches: 26, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
44 83 0.78
45 21 0.20
46 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
TCCACTGCAACTTCAGAGAGATAAGACTTGTAGCTTTAATCTGC
Found at i:900000 original size:50 final size:50
Alignment explanation
Indices: 899932--900282 Score: 360
Period size: 50 Copynumber: 7.0 Consensus size: 50
899922 CAATTTGGGA
*
899932 AAGCAAGATTCGTTGTTGTAGCTTTAATATGTTCCACTACACTGCCAGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* * ** * * * *
899982 AAGTAAGATTCGTTGTTGTAGCTTTAATCTATTTAACTGCAATGTCGGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* * *
900032 AAGCAAGATTCGCTGTAGTAGCTTCAATCTGTTCCACTACACTGCCAGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* * ** * * ***
900082 AAGTAAGATTCGTTGTTGTAGCTTTAATCTATTTAACTGCAATGTTGGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* * *
900132 AAGCAAGATTCGTTGTTGTAGCTTCAATCTGTTCCACTACACCGCCAAGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* ** * ** * * ** *
900182 AAGTAAGATTCACTGTTGTAGCTTTAATCTTTTTAACTGCAATATCGGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
* * *
900232 AAGCAAGATTTGCTGTTGTAGCTTCAATCTGTTCCACTACACTGCCAGGG
1 AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
900282 A
1 A
900283 TATGGGGAAC
Statistics
Matches: 231, Mismatches: 70, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 231 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (50 bp):
AAGCAAGATTCGTTGTTGTAGCTTTAATCTGTTCCACTACACTGCCAGGG
Found at i:900071 original size:100 final size:100
Alignment explanation
Indices: 899851--900282 Score: 616
Period size: 100 Copynumber: 4.3 Consensus size: 100
899841 TCGCTACCTT
* * * * * * *
899851 TAGCTTTAATCTGTTCCATTTCCAC-GCCAAGGAAATAAGATTCACTATTGTAGCTTCAATCTAT
1 TAGCTTCAATCTGTTCCA-CTACACTGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTAT
* * * *
899915 TTAACTACAAT-TTGGGAAAGCAAGATTCGTTGTTG
65 TTAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* * **
899950 TAGCTTTAATATGTTCCACTACACTGCCAGGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTATT
1 TAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTATT
*
900015 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTAG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
**
900050 TAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCGTTGTTGTAGCTTTAATCTATT
1 TAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTATT
* *
900115 TAACTGCAATGTTGGGGAAGCAAGATTCGTTGTTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
* * *
900150 TAGCTTCAATCTGTTCCACTACACCGCCAAGGAAGTAAGATTCACTGTTGTAGCTTTAATCTTTT
1 TAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTATT
* *
900215 TAACTGCAATATCGGGGAAGCAAGATTTGCTGTTG
66 TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
900250 TAGCTTCAATCTGTTCCACTACACTGCCAGGGA
1 TAGCTTCAATCTGTTCCACTACACTGCCAGGGA
900283 TATGGGGAAC
Statistics
Matches: 301, Mismatches: 30, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
98 4 0.01
99 60 0.20
100 237 0.79
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (100 bp):
TAGCTTCAATCTGTTCCACTACACTGCCAGGGAAGTAAGATTCACTGTTGTAGCTTTAATCTATT
TAACTGCAATGTCGGGGAAGCAAGATTCGCTGTTG
Found at i:906544 original size:14 final size:14
Alignment explanation
Indices: 906525--906552 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
906515 CATTCATATC
906525 TTATTCATACCTAA
1 TTATTCATACCTAA
906539 TTATTCATACCTAA
1 TTATTCATACCTAA
906553 CATGTTGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
TTATTCATACCTAA
Found at i:924025 original size:25 final size:24
Alignment explanation
Indices: 923961--924029 Score: 84
Period size: 24 Copynumber: 2.8 Consensus size: 24
923951 AGCGTCCCGT
* * *
923961 TATTAGCTCTCACGAGCATCTTGA
1 TATTGGCTCTCATGAGCTTCTTGA
* *
923985 TATTGGCTCTCTTGAGCTTTTTGA
1 TATTGGCTCTCATGAGCTTCTTGA
924009 TATATGGCTCTCATGAGCTTC
1 TAT-TGGCTCTCATGAGCTTC
924030 CCATTAACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 22 0.59
25 15 0.41
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.41
Consensus pattern (24 bp):
TATTGGCTCTCATGAGCTTCTTGA
Found at i:924211 original size:24 final size:23
Alignment explanation
Indices: 924153--924234 Score: 67
Period size: 24 Copynumber: 3.4 Consensus size: 23
924143 AGGCTTTTAC
* *
924153 ATGAGCTTTTCGATTAATGGCTCT
1 ATGAGCTTCTCGA-TATTGGCTCT
* *
924177 CTGGAGTTTCTCGATATTGGCTCGT
1 AT-GAGCTTCTCGATATTGGCTC-T
*
924202 ATGAGCTTCTTGAT-TATGGCTCTT
1 ATGAGCTTCTCGATAT-TGGCTC-T
924226 ATGAGCTTC
1 ATGAGCTTC
924235 CCGTTATACA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.02
24 35 0.74
25 11 0.23
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.41
Consensus pattern (23 bp):
ATGAGCTTCTCGATATTGGCTCT
Found at i:924614 original size:19 final size:19
Alignment explanation
Indices: 924590--924627 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
924580 TATGGCCAAG
924590 TTGATTGGATATTTCTTGT
1 TTGATTGGATATTTCTTGT
924609 TTGATTGGATATTTCTTGT
1 TTGATTGGATATTTCTTGT
924628 ATACTTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (19 bp):
TTGATTGGATATTTCTTGT
Found at i:925469 original size:73 final size:73
Alignment explanation
Indices: 925350--925530 Score: 308
Period size: 73 Copynumber: 2.5 Consensus size: 73
925340 TTTCAAACAC
* *
925350 CCTAGAACACGAGCGTGTGGCTTGGCCATGTGACCCCTGCACTTATTTATTGCGAGTCAGTATGC
1 CCTAGCACACGGGCGTGTGGCTTGGCCATGTGACCCCTGCACTTATTTATTGCGAGTCAGTATGC
* *
925415 TTACATGG
66 TTACACGA
*
925423 CCTAGCACACGGGCGTGTGGTTTGGCCATGTGACCCCTGCACTTATTTATTGCGAGTCAGTATGC
1 CCTAGCACACGGGCGTGTGGCTTGGCCATGTGACCCCTGCACTTATTTATTGCGAGTCAGTATGC
925488 TTACACGA
66 TTACACGA
*
925496 CCTAGCACACGGGCGTGTGGCTTGGCCGTGTGACC
1 CCTAGCACACGGGCGTGTGGCTTGGCCATGTGACC
925531 TAAGTCAGAG
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 101 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (73 bp):
CCTAGCACACGGGCGTGTGGCTTGGCCATGTGACCCCTGCACTTATTTATTGCGAGTCAGTATGC
TTACACGA
Found at i:927409 original size:27 final size:27
Alignment explanation
Indices: 927367--927617 Score: 278
Period size: 27 Copynumber: 9.3 Consensus size: 27
927357 ATTCGTGGGC
*
927367 AAATGACAGAAATACCCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
927394 AAATGA-CTAAAGTACCCTC-AATGGGTA
1 AAATGACCGAAA-TACCCTCGAA-GGGTA
* *
927421 AAATGATCGAAATACCCTCGATGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
*
927448 AAATGACCGAAATACCCT-TAATGGGTA
1 AAATGACCGAAATACCCTCGAA-GGGTA
* ** *
927475 AATTGACAAAAATACCCTCGAAAGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
**
927502 AAATGACCGAAATAATCTCGAAGGGTA
1 AAATGACCGAAATACCCTCGAAGGGTA
* *
927529 AAATGATCGAAATACCCCTCGAATGGTA
1 AAATGACCGAAATA-CCCTCGAAGGGTA
*
927557 AAATGACCGAAATACCC-CTAAAGGGTA
1 AAATGACCGAAATACCCTC-GAAGGGTA
*
927584 AAATGACCGAAATACCC-CTATAGGGTA
1 AAATGACCGAAATACCCTCGA-AGGGTA
927611 AAATGAC
1 AAATGAC
927618 TGTTATACCC
Statistics
Matches: 189, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
26 8 0.04
27 151 0.80
28 30 0.16
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGAAGGGTA
Found at i:928017 original size:28 final size:28
Alignment explanation
Indices: 927974--928065 Score: 130
Period size: 28 Copynumber: 3.2 Consensus size: 28
927964 ACTGCATTGT
927974 ACTGATTACTGTATTGGGCTAAGGCCCAC
1 ACTG-TTACTGTATTGGGCTAAGGCCCAC
*
928003 ACTGTTATTGTATTGGGCTAAGGCCCACAC
1 ACTGTTACTGTATTGGGCTAAGG-CC-CAC
* *
928033 ACTATTACTGTAATGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
928061 ACTGT
1 ACTGT
928066 ACTACTACTG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
28 25 0.45
29 8 0.14
30 23 0.41
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:928050 original size:30 final size:30
Alignment explanation
Indices: 927978--928062 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
927968 CATTGTACTG
927978 ATTACTGTATTGGGCTAAGG-CC-CACACT
1 ATTACTGTATTGGGCTAAGGCCCACACACT
* *
928006 GTTATTGTATTGGGCTAAGGCCCACACACT
1 ATTACTGTATTGGGCTAAGGCCCACACACT
*
928036 ATTACTGTAATGGGCTAAGGCCCACAC
1 ATTACTGTATTGGGCTAAGGCCCACAC
928063 TGTACTACTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 18 0.36
29 2 0.04
30 30 0.60
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (30 bp):
ATTACTGTATTGGGCTAAGGCCCACACACT
Found at i:946782 original size:84 final size:84
Alignment explanation
Indices: 946681--946835 Score: 213
Period size: 84 Copynumber: 1.8 Consensus size: 84
946671 ATTAAATCCC
* * * *
946681 GAAACAAAATTATATCAAAATAAAAT-ATGTTAAACGGTGAGAATAAATCCCAAAAAATATTTTA
1 GAAACAAAATAAAATC-AAATAAAATCATATTAAACGGCGAGAATAAATCCCAAAAAATATTTTA
*
946745 TTTAATTGAATTCTAATTTG
65 ATTAATTGAATTCTAATTTG
* * * *
946765 GAAACAAAATAAAATCAAATAAAATCTTATTAAACGGCGGGAATAAATCCCGAAATATATTTTAA
1 GAAACAAAATAAAATCAAATAAAATCATATTAAACGGCGAGAATAAATCCCAAAAAATATTTTAA
946830 TTAATT
66 TTAATT
946836 TTAATTTCTC
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 9 0.15
84 52 0.85
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (84 bp):
GAAACAAAATAAAATCAAATAAAATCATATTAAACGGCGAGAATAAATCCCAAAAAATATTTTAA
TTAATTGAATTCTAATTTG
Found at i:946939 original size:87 final size:87
Alignment explanation
Indices: 946797--947059 Score: 334
Period size: 86 Copynumber: 3.0 Consensus size: 87
946787 AATCTTATTA
* *
946797 AACGGCGGGAATAAATCCCGAAATATATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAA
1 AACGGCGGGAATAAATCCCGAAACAAATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAA
946862 TCAAAATGTAATAAATCCGTTG
66 TCAAAATGTAATAAATCCGTTG
* ** * * *
946884 AACGGTGGGAATAAATCTTGAAA-AAAATTTATTTAATTTTAATTTCTCATTTTTTGCAACAAAA
1 AACGGCGGGAATAAATCCCGAAACAAATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAA
946948 TCAAAATGTAATAAATCCGTTG
66 TCAAAATGTAATAAATCCGTTG
* * * * * * *
946970 AATGGCAGGAATAAATCCCGAAACAGATTTTAAATTAATTTTAA-TACTCAGTTTTGGAAATAAA
1 AACGGCGGGAATAAATCCCGAAACAAATTTT-AATTAATTTTAATTTCTCATTTTTGGCAACAAA
*
947034 ATCAAAATTGGAATAAAAT-CGTTG
65 ATCAAAA-TGTAAT-AAATCCGTTG
947058 AA
1 AA
947060 TGGTGAGAAT
Statistics
Matches: 151, Mismatches: 21, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
86 77 0.51
87 47 0.31
88 23 0.15
89 4 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (87 bp):
AACGGCGGGAATAAATCCCGAAACAAATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAA
TCAAAATGTAATAAATCCGTTG
Found at i:947087 original size:88 final size:85
Alignment explanation
Indices: 946805--947089 Score: 297
Period size: 86 Copynumber: 3.3 Consensus size: 85
946795 TAAACGGCGG
* *
946805 GAATAAATCCCGAAATATATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAATCAAAATG
1 GAATAAAT-CCTAAA-AGATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAATCAAAATG
* *
946870 TAATAAATCCGTTGAACGGTGG
64 TAATAAATCCGTTGAATGGTGA
* * * * *
946892 GAATAAATCTTGAAAAAAATTTATTTAATTTTAATTTCTCATTTTTTGCAACAAAATCAAAATGT
1 GAATAAATCCT-AAAAGATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAATCAAAATGT
*
946957 AATAAATCCGTTGAATGG-CA
65 AATAAATCCGTTGAATGGTGA
* * * * *
946977 GGAATAAATCCCGAAACAGATTTTAAATTAATTTTAA-TACTCAGTTTTGGAAATAAAATCAAAA
1 -GAATAAAT-CCTAAA-AGATTTT-AATTAATTTTAATTTCTCATTTTTGGCAACAAAATCAAAA
*
947041 TTGGAATAAAAT-CGTTGAATGGTGA
62 -TGTAAT-AAATCCGTTGAATGGTGA
*
947066 GAATCAATCCTAAAATGGATTTTA
1 GAATAAATCCTAAAA--GATTTTA
947090 TTTTACTCAT
Statistics
Matches: 165, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
86 76 0.46
87 45 0.27
88 39 0.24
89 5 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (85 bp):
GAATAAATCCTAAAAGATTTTAATTAATTTTAATTTCTCATTTTTGGCAACAAAATCAAAATGTA
ATAAATCCGTTGAATGGTGA
Found at i:947319 original size:79 final size:79
Alignment explanation
Indices: 947021--947324 Score: 389
Period size: 79 Copynumber: 3.8 Consensus size: 79
947011 TAATACTCAG
* * * * * *
947021 TTTTGGAAATAAAATCAAAA-TTGGAATAAAATCGTTGAATGG-TGAGAATCAATCCTAAAATGG
1 TTTTGGAAATAAAA-CAAAATTTGGAATAAAATCGTTGAACGGCAGA-AACCAATCCCAAAACGA
947084 ATTTTATTTTACTCA-T
64 ATTTTATTTTACT-AGT
* * * * * *
947100 TTTTGGCAATAAAACAAAATTTGGAATAAAATCGTTGAACAGCAAAAATCAATCCCTAAACAAAT
1 TTTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGCAGAAACCAATCCCAAAACGAAT
*
947165 TTTATTTTACTTGT
66 TTTATTTTACTAGT
* * * *
947179 TTTTGGAAATAAAACAAAATTTGGAATAAAATCGGTGAACGGCAGAAACCAATTCCGAAACGGAT
1 TTTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGCAGAAACCAATCCCAAAACGAAT
947244 TTTATTTTACTAGT
66 TTTATTTTACTAGT
* *
947258 TTTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGTAGGAACCAATCCCAAAACGAAT
1 TTTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGCAGAAACCAATCCCAAAACGAAT
947323 TT
66 TT
947325 CGTTTACCTT
Statistics
Matches: 195, Mismatches: 27, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
78 5 0.03
79 189 0.97
80 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (79 bp):
TTTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGCAGAAACCAATCCCAAAACGAAT
TTTATTTTACTAGT
Found at i:947408 original size:89 final size:86
Alignment explanation
Indices: 947259--947429 Score: 207
Period size: 89 Copynumber: 2.0 Consensus size: 86
947249 TTTACTAGTT
* * * * *
947259 TTTGGAAATAAAACAAAATTTGGAATAAAATCGTTGAACGGTAGGAACCAATCCCAAAACGAATT
1 TTTGGAAATAAAAAAAAATATGAAATAAAATCGTTGAACGGGAGGAACAAATCCCAAAACGAATT
*
947324 TCGTTTACCTTTAATTTCCCG
66 TCATTTACCTTTAATTTCCCG
* * * *
947345 TTTGGAAATAAAATAAAAATAATGAAATAAAATCCGTTGAACGGGGGGAATAAATCCCGAAACGG
1 TTTGGAAATAAAA-AAAAAT-ATGAAATAAAAT-CGTTGAACGGGAGGAACAAATCCCAAAACGA
* *
947410 ATTTTATTTACTTTTAATTT
63 ATTTCATTTACCTTTAATTT
947430 TAAAACAAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
86 13 0.19
87 5 0.07
88 10 0.14
89 42 0.60
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (86 bp):
TTTGGAAATAAAAAAAAATATGAAATAAAATCGTTGAACGGGAGGAACAAATCCCAAAACGAATT
TCATTTACCTTTAATTTCCCG
Found at i:950005 original size:69 final size:69
Alignment explanation
Indices: 949909--950080 Score: 186
Period size: 69 Copynumber: 2.5 Consensus size: 69
949899 ACGAAAGAAT
* * *
949909 TTGCGCCCAGTGCTAGTCAGATAAACCGATAG-ATGTGTGCCTAGCACTAGTCAGATAAACTGAC
1 TTGCACCCAGCGCTAGTCAGATAAACCGA-AGAATGTGTGCCCAGCACTAGTCAGATAAACTGAC
949973 GGAGG
65 GGAGG
* * * * *
949978 TTGCACCCAGCGCTAGTCGGTTCAACCGACGAATGTGTGCCCAGCACTAGTCAGATAAACTGATG
1 TTGCACCCAGCGCTAGTCAGATAAACCGAAGAATGTGTGCCCAGCACTAGTCAGATAAACTGACG
* *
950043 AAAG
66 GAGG
** * *
950047 TTGGGCCCAGTGCTAGTC-GAATAAACCGACGAAT
1 TTGCACCCAGCGCTAGTCAG-ATAAACCGAAGAAT
950081 AATTAGTGAG
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
68 2 0.02
69 84 0.98
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (69 bp):
TTGCACCCAGCGCTAGTCAGATAAACCGAAGAATGTGTGCCCAGCACTAGTCAGATAAACTGACG
GAGG
Found at i:950056 original size:35 final size:35
Alignment explanation
Indices: 949921--950079 Score: 110
Period size: 35 Copynumber: 4.6 Consensus size: 35
949911 GCGCCCAGTG
* * *
949921 CTAGTCAGATAAACCGA-TAGA-TGTGTGCCTAGCA
1 CTAGTCAGATAAACCGACGAAAGT-TGTGCCCAGCA
* * * ** *
949955 CTAGTCAGATAAACTGACGGAGGTTGCACCCAGCG
1 CTAGTCAGATAAACCGACGAAAGTTGTGCCCAGCA
* * * *
949990 CTAGTCGGTTCAACCGACGAATG-TGTGCCCAGCA
1 CTAGTCAGATAAACCGACGAAAGTTGTGCCCAGCA
* * * **
950024 CTAGTCAGATAAACTGATGAAAGTTGGGCCCAGTG
1 CTAGTCAGATAAACCGACGAAAGTTGTGCCCAGCA
950059 CTAGTC-GAATAAACCGACGAA
1 CTAGTCAG-ATAAACCGACGAA
950080 TAATTAGTGA
Statistics
Matches: 92, Mismatches: 29, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
34 42 0.46
35 49 0.53
36 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (35 bp):
CTAGTCAGATAAACCGACGAAAGTTGTGCCCAGCA
Found at i:954885 original size:2 final size:2
Alignment explanation
Indices: 954878--954907 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
954868 NNNNNNNNNN
954878 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
954908 TATTCTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:958453 original size:23 final size:23
Alignment explanation
Indices: 958427--958470 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
958417 CCTAGGCGCA
*
958427 TGTAATATACCAAAAATTACTAC
1 TGTAATACACCAAAAATTACTAC
* *
958450 TGTAATACCCCGAAAATTACT
1 TGTAATACACCAAAAATTACT
958471 GCAGTAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (23 bp):
TGTAATACACCAAAAATTACTAC
Found at i:968938 original size:19 final size:19
Alignment explanation
Indices: 968914--968951 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
968904 ATAGAGATAA
968914 CTCCATTTAAGATCATTTG
1 CTCCATTTAAGATCATTTG
*
968933 CTCCATTTGAGATCATTTG
1 CTCCATTTAAGATCATTTG
968952 TTTAATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (19 bp):
CTCCATTTAAGATCATTTG
Found at i:971286 original size:84 final size:83
Alignment explanation
Indices: 971174--971616 Score: 629
Period size: 84 Copynumber: 5.2 Consensus size: 83
971164 TACGTTTTTG
* *
971174 TTTGGAAACAAAA-AAATATCGAATAAAATCTTGTTCAACGGCGGGAATAAATCCCGAAACAGAT
1 TTTGGAAACAAAATAAA-ATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGAT
971238 TTTATTTAATTCAATTC-ACA
65 TTTATTTAATT-AATTCTA-A
* ** *
971258 TTTGTAAACAAAATAAAATCAAATAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATT
1 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATT
* *
971323 TTATGTAATTCAATTCAAA
66 TTATTTAATT-AATTCTAA
* *
971342 TTTGGAAACAAAATAAAATCAAATAAAATCTTATTAAACGGCAGGAATAAATCCCGAAACAGATT
1 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATT
971407 TTATTTAATTATATTCTAA
66 TTATTTAATTA-ATTCTAA
* *
971426 TTTGGAAACAAAATAAAATCAAAAAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATT
1 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATT
971491 TTATTTAATTATATTCTAA
66 TTATTTAATTA-ATTCTAA
* *
971510 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGGGAATAAATTCCGAAACAGATT
1 TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATT
*
971575 TTATTTAATTTAATTTCTCATT
66 TTATTTAA-TTAA-TTCT-A-A
*
971597 TTTGGCAACAAAATTAAAAT
1 TTTGGAAACAAAA-TAAAAT
971617 GTAATAAATC
Statistics
Matches: 328, Mismatches: 23, Indels: 12
0.90 0.06 0.03
Matches are distributed among these distances:
83 1 0.00
84 297 0.91
85 11 0.03
86 1 0.00
87 12 0.04
88 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (83 bp):
TTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACAGATT
TTATTTAATTAATTCTAA
Found at i:971397 original size:168 final size:167
Alignment explanation
Indices: 971106--971616 Score: 647
Period size: 168 Copynumber: 3.0 Consensus size: 167
971096 TTATATCATT
* * * * *
971106 AAATCAAATTAAAAT-TTGTTAAACGATGAGAATAAATCCCAAAATAGA-ATTA-GTTGATTACG
1 AAATCAAA-TAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATTTTATG-TAATTACA
* ** * *
971168 TTTTTGTTTGGAAACAAAA-AAATATCGAATAAAATCTTGTTCAACGGCGGGAATAAATCCCGAA
64 TTCTAATTTGGAAACAAAATAAA-ATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAA
*
971232 ACAGATTTTATTTAATTCAATTC-ACATTTGTAAACAAAATA
128 ACAGATTTTATTTAATT-AATTCTA-ATTTGGAAACAAAATA
971273 AAATCAAATAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATTTTATGTAATT-CAAT
1 AAATCAAATAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATTTTATGTAATTAC-AT
* * *
971337 TCAAATTTGGAAACAAAATAAAATCAAATAAAATCTTATTAAACGGCAGGAATAAATCCCGAAAC
65 TCTAATTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAAC
971402 AGATTTTATTTAATTATATTCTAATTTGGAAACAAAATA
130 AGATTTTATTTAATTA-ATTCTAATTTGGAAACAAAATA
* *** * * *
971441 AAATCAAAAAAAATCTTGTTAAACGGCAGGAATAAATCCCGAAACAGATTTTATTTAATTATATT
1 AAATCAAATAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATTTTATGTAATTACATT
* *
971506 CTAATTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAATGGCGGGAATAAATTCCGAAACA
66 CTAATTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACA
* *
971571 GATTTTATTTAATTTAATTTCTCATTTTTGGCAACAAAATTA
131 GATTTTATTTAA-TTAA-TTCT-A-ATTTGGAAACAAAA-TA
971613 AAAT
1 AAAT
971617 GTAATAAATC
Statistics
Matches: 303, Mismatches: 28, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
166 6 0.02
167 41 0.14
168 225 0.74
169 12 0.04
170 1 0.00
171 12 0.04
172 6 0.02
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (167 bp):
AAATCAAATAAAATCTTGTTAAACGATGGGAATAAATCCCAAAACAGATTTTATGTAATTACATT
CTAATTTGGAAACAAAATAAAATCAAATAAAATCTTGTTAAACGGCGGGAATAAATCCCGAAACA
GATTTTATTTAATTAATTCTAATTTGGAAACAAAATA
Found at i:971710 original size:79 final size:77
Alignment explanation
Indices: 971622--971877 Score: 280
Period size: 79 Copynumber: 3.2 Consensus size: 77
971612 AAAATGTAAT
* *
971622 AAATCCATTGAACGGCAGGAATTAAAT-TTGAAATGAATTTTATTTTACTCGTTTTTGGAAATAA
1 AAAT-CATTGAACGGC-GGAA-TCAATCTCGAAA-GAATTTTATTTTACTCGTTTTTGGAAATAA
* *
971686 AACAAAATTTAGAATA
62 AACAAAATGTGGAATA
* * * *
971702 AAATCATTGAACGGCGAGAATCAATCCCAAAACGGATTTTATTTTACTCGTTTTTGAAAAATAAA
1 AAATCATTGAACGGCG-GAATCAATCTCGAAA-GAATTTTATTTTACTCGTTTTTG-GAAATAAA
*
971767 ACAAAATGTGGAACA
63 ACAAAATGTGGAATA
** * * *
971782 AAATTGTTGAACGGTGGGAATCAATCTGGAAACAGATTTTATTTTACTCGTTTTTGGAAATAAAA
1 AAATCATTGAACGG-CGGAATCAATCTCGAAAGA-ATTTTATTTTACTCGTTTTTGGAAATAAAA
971847 CAAAATGTGGAATA
64 CAAAATGTGGAATA
* *
971861 AAATCGTTAAACGGCGG
1 AAATCATTGAACGGCGG
971878 GAGCCACTCT
Statistics
Matches: 148, Mismatches: 23, Indels: 12
0.81 0.13 0.07
Matches are distributed among these distances:
78 7 0.05
79 72 0.49
80 68 0.46
81 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (77 bp):
AAATCATTGAACGGCGGAATCAATCTCGAAAGAATTTTATTTTACTCGTTTTTGGAAATAAAACA
AAATGTGGAATA
Found at i:971795 original size:80 final size:79
Alignment explanation
Indices: 971658--971876 Score: 312
Period size: 80 Copynumber: 2.8 Consensus size: 79
971648 TTTGAAATGA
* * *
971658 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATTTAGAATAAAATCATTGAACGGCGAGAAT
1 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGAGAAT
*
971723 CAATCCCAAAACGG
66 CAATCCCAAAACAG
* * * * *
971737 ATTTTATTTTACTCGTTTTTGAAAAATAAAACAAAATGTGGAACAAAATTGTTGAACGGTGGGAA
1 ATTTTATTTTACTCGTTTTTG-GAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGAGAA
***
971802 TCAATCTGGAAACAG
65 TCAATCCCAAAACAG
*
971817 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTAAACGGCG
1 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCG
971877 GGAGCCACTC
Statistics
Matches: 122, Mismatches: 17, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
79 55 0.45
80 67 0.55
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (79 bp):
ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGAGAAT
CAATCCCAAAACAG
Found at i:971899 original size:79 final size:79
Alignment explanation
Indices: 971658--971904 Score: 325
Period size: 79 Copynumber: 3.1 Consensus size: 79
971648 TTTGAAATGA
* * * *
971658 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATTTAGAATAAAATCATTGAACGGCGAGAAT
1 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGGGAAT
*
971723 CAATCCCA-AAACGG
66 CAAT-CTAGAAACGG
* * * *
971737 ATTTTATTTTACTCGTTTTTGAAAAATAAAACAAAATGTGGAACAAAATTGTTGAACGGTGGGAA
1 ATTTTATTTTACTCGTTTTTG-GAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGGGAA
* *
971802 TCAATCTGGAAACAG
65 TCAATCTAGAAACGG
* **
971817 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTAAACGGCGGGAGC
1 ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGGGAAT
* *
971882 CACTCTAGAAATGG
66 CAATCTAGAAACGG
971896 ATTTTATTT
1 ATTTTATTT
971905 ACCTTTAATT
Statistics
Matches: 144, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
79 78 0.54
80 66 0.46
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (79 bp):
ATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATGTGGAATAAAATCGTTGAACGGCGGGAAT
CAATCTAGAAACGG
Found at i:972194 original size:18 final size:18
Alignment explanation
Indices: 972154--972193 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
972144 ATTTATTTAA
* *
972154 TTTTTAAAAGAAAATGGT
1 TTTTTAAAAAAAAATAGT
972172 TTTTTAAAAAAAAATA-T
1 TTTTTAAAAAAAAATAGT
972189 TTTTT
1 TTTTT
972194 TCTTCGCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTTTAAAAAAAAATAGT
Found at i:973883 original size:31 final size:31
Alignment explanation
Indices: 973847--973927 Score: 105
Period size: 31 Copynumber: 2.6 Consensus size: 31
973837 AACATCCCAA
973847 TGACTTAAATGTAAACTTTTGAATAAG-TCAG
1 TGACTTAAATGTAAACTTTTGAAT-AGTTCAG
* *
973878 TGACTTAAATGAAAAATTTTGAATAGTTCAG
1 TGACTTAAATGTAAACTTTTGAATAGTTCAG
973909 TGAC-TAAATTGT-AACTTTT
1 TGACTTAAA-TGTAAACTTTT
973928 TTTAGTTAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 12 0.27
31 32 0.73
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (31 bp):
TGACTTAAATGTAAACTTTTGAATAGTTCAG
Found at i:976796 original size:17 final size:16
Alignment explanation
Indices: 976759--976811 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
976749 ACATTCTAGA
*
976759 AAATTTGTAATAAATTTT
1 AAATTTCTAA-AAA-TTT
*
976777 AAATTTTTAAAAATTAT
1 AAATTTCTAAAAATT-T
976794 AAA-TTCTAAAAATTT
1 AAATTTCTAAAAATTT
976809 AAA
1 AAA
976812 ATAATAGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 4 0.12
16 12 0.38
17 7 0.22
18 9 0.28
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
AAATTTCTAAAAATTT
Found at i:978023 original size:12 final size:12
Alignment explanation
Indices: 978006--978032 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
977996 ATTGTTGGAA
978006 TTGCGTATTAGC
1 TTGCGTATTAGC
978018 TTGCGTATTAGC
1 TTGCGTATTAGC
978030 TTG
1 TTG
978033 ATTGGCATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.26, T:0.44
Consensus pattern (12 bp):
TTGCGTATTAGC
Found at i:978371 original size:11 final size:11
Alignment explanation
Indices: 978357--978381 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
978347 AATTACAATT
978357 AATCAAATCAC
1 AATCAAATCAC
978368 AATCAAATCAC
1 AATCAAATCAC
978379 AAT
1 AAT
978382 AAACAGAGTT
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:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (11 bp):
AATCAAATCAC
Found at i:979371 original size:70 final size:70
Alignment explanation
Indices: 979258--979563 Score: 373
Period size: 70 Copynumber: 4.4 Consensus size: 70
979248 GTAATAATCT
* * * * *
979258 TTTTGCGCCCATCACTAGTTGGATAGACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATTGA
1 TTTTGCGCCCAACGCTAGTCGGATAAACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATCGA
979323 CAATG
66 CAATG
* * *
979328 TTTTGGGCCCAGCGCTAGTCGGATAAACCGACGAATAGTGTGCCCTA-CACTAGT-AGAATAATC
1 TTTTGCGCCCAACGCTAGTCGGATAAACCAACGAATAGTGTGCCC-AGCACTAGTCA-AATAATC
979391 GACAATG
64 GACAATG
* * ** * * * *
979398 TCTTGCGCTCAGTGCTAGTTGGATAAACCAACGAATAGTGTGCCTAGCACTAGCCGAATAATCGA
1 TTTTGCGCCCAACGCTAGTCGGATAAACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATCGA
979463 CAATG
66 CAATG
** * * * *
979468 TTTTATGCCCAACGCTAATCGGATAAACCAACGAATAGTGTGCCTAGCACTAGTCGAATAACCGA
1 TTTTGCGCCCAACGCTAGTCGGATAAACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATCGA
979533 CAATG
66 CAATG
*
979538 TTTTGCACCCAACGCTAGTCGGATAA
1 TTTTGCGCCCAACGCTAGTCGGATAA
979564 TCAAAAATAT
Statistics
Matches: 202, Mismatches: 30, Indels: 8
0.84 0.12 0.03
Matches are distributed among these distances:
69 2 0.01
70 199 0.99
71 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (70 bp):
TTTTGCGCCCAACGCTAGTCGGATAAACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATCGA
CAATG
Found at i:979381 original size:35 final size:34
Alignment explanation
Indices: 979342--979533 Score: 83
Period size: 35 Copynumber: 5.5 Consensus size: 34
979332 GGGCCCAGCG
*
979342 CTAGTCGGATAAACCGACGAATAGTGTGCCCTACA
1 CTAGTCGAAT-AACCGACGAATAGTGTGCCCTACA
* * * *
979377 CTAGTAGAATAATCGAC-AAT-GTCTTGCGCT-CA
1 CTAGTCGAATAACCGACGAATAGT-GTGCCCTACA
* * *
979409 GTGCTAGTTGGATAAACCAACGAATAGTGTG-CCTAGCA
1 ---CTAGTCGAAT-AACCGACGAATAGTGTGCCCTA-CA
* * * * *
979447 CTAGCCGAATAATCGAC-AAT-GTTTTATGCCCAACG
1 CTAGTCGAATAACCGACGAATAG---TGTGCCCTACA
* * *
979482 CTAATCGGATAAACCAACGAATAGTGTG-CCTAGCA
1 CTAGTCGAAT-AACCGACGAATAGTGTGCCCTA-CA
979517 CTAGTCGAATAACCGAC
1 CTAGTCGAATAACCGAC
979534 AATGTTTTGC
Statistics
Matches: 110, Mismatches: 30, Indels: 35
0.63 0.17 0.20
Matches are distributed among these distances:
32 5 0.05
33 11 0.10
34 20 0.18
35 46 0.42
36 15 0.14
37 8 0.07
38 5 0.05
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (34 bp):
CTAGTCGAATAACCGACGAATAGTGTGCCCTACA
Found at i:979555 original size:140 final size:140
Alignment explanation
Indices: 979258--979563 Score: 416
Period size: 140 Copynumber: 2.2 Consensus size: 140
979248 GTAATAATCT
* * * * *
979258 TTTTGCGCCCATCACTAGTTGGATAGACCAACGAATAGTGTGCCCAGCACTAGTCAAATAATTGA
1 TTTTGCGCCCAACGCTAGTTGGATAAACCAACGAATAGTGTGCCCAGCACTAGCCAAATAATCGA
* * * *
979323 CAATGTTTTGGGCCCAGCGCTAGTCGGATAAACCGACGAATAGTGTGCCCTACACTAGTAGAATA
66 CAATGTTTTAGGCCCAACGCTAATCGGATAAACCAACGAATAGTGTGCCCTACACTAGTAGAATA
*
979388 ATCGACAATG
131 ACCGACAATG
* * ** * *
979398 TCTTGCGCTCAGTGCTAGTTGGATAAACCAACGAATAGTGTGCCTAGCACTAGCCGAATAATCGA
1 TTTTGCGCCCAACGCTAGTTGGATAAACCAACGAATAGTGTGCCCAGCACTAGCCAAATAATCGA
* *
979463 CAATGTTTTATGCCCAACGCTAATCGGATAAACCAACGAATAGTGTG-CCTAGCACTAGTCGAAT
66 CAATGTTTTAGGCCCAACGCTAATCGGATAAACCAACGAATAGTGTGCCCTA-CACTAGTAGAAT
979527 AACCGACAATG
130 AACCGACAATG
* *
979538 TTTTGCACCCAACGCTAGTCGGATAA
1 TTTTGCGCCCAACGCTAGTTGGATAA
979564 TCAAAAATAT
Statistics
Matches: 142, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
139 4 0.03
140 138 0.97
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (140 bp):
TTTTGCGCCCAACGCTAGTTGGATAAACCAACGAATAGTGTGCCCAGCACTAGCCAAATAATCGA
CAATGTTTTAGGCCCAACGCTAATCGGATAAACCAACGAATAGTGTGCCCTACACTAGTAGAATA
ACCGACAATG
Found at i:982039 original size:13 final size:12
Alignment explanation
Indices: 981995--982117 Score: 61
Period size: 12 Copynumber: 9.8 Consensus size: 12
981985 AAAAACGAAA
* *
981995 TGATTAAAAATT
1 TGATGAAAAACT
* *
982007 TGATGGAAAATT
1 TGATGAAAAACT
*
982019 TTATGAAAAGACT
1 TGATGAAAA-ACT
982032 TGATGAAAAACT
1 TGATGAAAAACT
*
982044 T--TAAAAGGAACT
1 TGATGAAA--AACT
* *
982056 TGCTGCAAAACT
1 TGATGAAAAACT
*
982068 TGATAAAAAACT
1 TGATGAAAAACT
*
982080 TGGTAATTAAAAACT
1 T-G--ATGAAAAACT
*
982095 TGATAAAAGAACT
1 TGATGAAA-AACT
*
982108 AGATGAAAAA
1 TGATGAAAAA
982118 TACTTGAAGA
Statistics
Matches: 86, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
10 4 0.05
12 47 0.55
13 21 0.24
14 4 0.05
15 10 0.12
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:982077 original size:12 final size:12
Alignment explanation
Indices: 982062--982124 Score: 54
Period size: 12 Copynumber: 4.8 Consensus size: 12
982052 AACTTGCTGC
982062 AAAACTTGATAA
1 AAAACTTGATAA
*
982074 AAAACTTGGTAATTA
1 AAAACTT-G--ATAA
982089 AAAACTTGATAA
1 AAAACTTGATAA
*
982101 AAGAACTAGATGAA
1 AA-AACTTGAT-AA
982115 AAATACTTGA
1 AAA-ACTTGA
982125 AGAAAGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 12 0.29
13 9 0.22
14 10 0.24
15 10 0.24
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.25
Consensus pattern (12 bp):
AAAACTTGATAA
Found at i:982135 original size:18 final size:18
Alignment explanation
Indices: 982112--982149 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
982102 AGAACTAGAT
*
982112 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
982130 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
982148 GA
1 GA
982150 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:982811 original size:27 final size:27
Alignment explanation
Indices: 982781--982835 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
982771 GGACATTTCG
*
982781 AATTTTTTTACGTGAGACATAATGACA
1 AATTTTTTTACGCGAGACATAATGACA
982808 AATTTTTTTACGCGAGACATAATGACA
1 AATTTTTTTACGCGAGACATAATGACA
982835 A
1 A
982836 CCGAAGCACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (27 bp):
AATTTTTTTACGCGAGACATAATGACA
Found at i:987141 original size:24 final size:24
Alignment explanation
Indices: 987114--987231 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 24
987104 CGAAATAATT
* *
987114 AAAAACTTGATGGAAAATTTTATGA
1 AAAAACTTGATGAAAAACTTTAT-A
*
987139 AAAGACTTGATGAAAAACTTTA-A
1 AAAAACTTGATGAAAAACTTTATA
* * *
987162 AAAGAACTTGCTGCAAAACTTGATA
1 AAA-AACTTGATGAAAAACTTTATA
* *
987187 AAAAACTTGGTAATTAAAAACTTGATA
1 AAAAACTT-G--ATGAAAAACTTTATA
*
987214 AAAGAACTAGATGAAAAA
1 AAA-AACTTGATGAAAAA
987232 TACTTGAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
23 4 0.05
24 20 0.27
25 31 0.41
27 16 0.21
28 4 0.05
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.25
Consensus pattern (24 bp):
AAAAACTTGATGAAAAACTTTATA
Found at i:987191 original size:12 final size:12
Alignment explanation
Indices: 987114--987238 Score: 63
Period size: 12 Copynumber: 9.8 Consensus size: 12
987104 CGAAATAATT
*
987114 AAAAACTTGATG
1 AAAAACTTGATA
* * *
987126 GAAAATTTTATGA
1 AAAAACTTGAT-A
* *
987139 AAAGACTTGATG
1 AAAAACTTGATA
*
987151 AAAAACTTTA-A
1 AAAAACTTGATA
* *
987162 AAAGAACTTGCTG
1 AAA-AACTTGATA
*
987175 CAAAACTTGATA
1 AAAAACTTGATA
*
987187 AAAAACTTGGTAATT
1 AAAAACTT-G--ATA
987202 AAAAACTTGATA
1 AAAAACTTGATA
*
987214 AAAGAACTAGATGA
1 AAA-AACTTGAT-A
987228 AAAATACTTGA
1 AAAA-ACTTGA
987239 AGAAAGAAAA
Statistics
Matches: 81, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
11 3 0.04
12 40 0.49
13 18 0.22
14 10 0.12
15 10 0.12
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.26
Consensus pattern (12 bp):
AAAAACTTGATA
Found at i:987249 original size:18 final size:18
Alignment explanation
Indices: 987226--987263 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
987216 AGAACTAGAT
*
987226 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
987244 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
987262 GA
1 GA
987264 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:990697 original size:12 final size:12
Alignment explanation
Indices: 990680--990709 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
990670 TCAGTAAGTT
990680 ACACGGCCTAGC
1 ACACGGCCTAGC
990692 ACACGGCCTAGC
1 ACACGGCCTAGC
990704 ACACGG
1 ACACGG
990710 GCGTGTGGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.40, G:0.27, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:1007093 original size:23 final size:22
Alignment explanation
Indices: 1007065--1007110 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 22
1007055 TAACATCATG
1007065 TTAATGATTATAATATTATAATA
1 TTAATGATTATAA-ATTATAATA
*
1007088 TTAATGATTATAAATTTTAATA
1 TTAATGATTATAAATTATAATA
1007110 T
1 T
1007111 GTTATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TTAATGATTATAAATTATAATA
Found at i:1007123 original size:16 final size:17
Alignment explanation
Indices: 1007079--1007124 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
1007069 TGATTATAAT
1007079 ATTATAATATT-A-ATG
1 ATTATAATATTAATATG
*
1007094 ATTATAAATTTTAATATG
1 ATTAT-AATATTAATATG
1007112 -TTATAATATTAAT
1 ATTATAATATTAAT
1007125 GATTTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 13 0.50
17 5 0.19
18 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
ATTATAATATTAATATG
Found at i:1009202 original size:63 final size:63
Alignment explanation
Indices: 1009112--1009236 Score: 169
Period size: 63 Copynumber: 2.0 Consensus size: 63
1009102 TGACAAGCGT
* * * *
1009112 GTAACTTACTGTTTATGAATCAGAGTCACACGGGCCAGGGAAACAGGTCTGTGTCCAGGCCAA
1 GTAACTCACTATTTATGAAACAGAGTCACACGGGCCAGAGAAACAGGTCTGTGTCCAGGCCAA
* * * * *
1009175 GTAACTCACTATTTGTGAAACAGAGTCACATGGGTCAGAGACACAGGTGTGTGTCCAGGCCA
1 GTAACTCACTATTTATGAAACAGAGTCACACGGGCCAGAGAAACAGGTCTGTGTCCAGGCCA
1009237 TGTGAGAGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (63 bp):
GTAACTCACTATTTATGAAACAGAGTCACACGGGCCAGAGAAACAGGTCTGTGTCCAGGCCAA
Found at i:1011120 original size:61 final size:61
Alignment explanation
Indices: 1010987--1011572 Score: 406
Period size: 61 Copynumber: 9.6 Consensus size: 61
1010977 CAACAATATA
* * * * * * *
1010987 TATATTCATATACGAATCAAATTCCGCAATGTATAATCATATAAAAATCAATTCGGCAATG
1 TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAATTCGGCAATG
* * ** * * *
1011048 TATAACTATATATGAATCAAGTTCGGCAATGTATAATCATATACAAATTAATTCGGCAACT-
1 TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAATTCGGCAA-TG
* * * *
1011109 TATATCCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAGCAAAG
1 TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAA-TTCGGCAATG
* *** * * **
1011171 TATAAT-CATATACAAATCAATTT-GGCAACT-TATCTTCATATACAAATCAATTTTGTTAATG
1 TAT-ATCCATATACAAATCAATTTCAGCAA-TGTATAACCATATACAAATTAA-TTCGGCAATG
* * * * *
1011232 TATAACCATATACAAATAAATTTCAGCAACGTACAACCATATACAAATTAATTCAGCAACT-
1 TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAATTCGGCAA-TG
* * ***
1011293 TATATCCATATACAATTCAATTTCAACAATGTATAACCATATACAAATTAATTTCAAAAATG
1 TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAA-TTCGGCAATG
* ** * * *** * **
1011355 TATAAT-TATATATGAATTAA-TTCGGCAACT-TATCTTCATATACAAATCAATTTCGATAATG
1 TAT-ATCCATATACAAATCAATTTCAGCAA-TGTATAACCATATACAAATTAA-TTCGGCAATG
* * * * *
1011416 TATAAT-CATATCCAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAACT-
1 TAT-ATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAATTCGGCAA-TG
* * * *
1011477 TATATCCATATACAATTCAATGTT-AACAACGTATAACCATATACAAATTAATTTCAGCAATG
1 TATATCCATATACAAATCAAT-TTCAGCAATGTATAACCATATACAAATTAA-TTCGGCAATG
* * * *
1011539 TATAAT-TATATACGAATTAA-TTCAGCAATATATA
1 TAT-ATCCATATACAAATCAATTTCAGCAATGTATA
1011573 TATCTATAAC
Statistics
Matches: 409, Mismatches: 94, Indels: 44
0.75 0.17 0.08
Matches are distributed among these distances:
60 5 0.01
61 286 0.70
62 112 0.27
63 6 0.01
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (61 bp):
TATATCCATATACAAATCAATTTCAGCAATGTATAACCATATACAAATTAATTCGGCAATG
Found at i:1011301 original size:184 final size:184
Alignment explanation
Indices: 1011023--1011566 Score: 806
Period size: 184 Copynumber: 3.0 Consensus size: 184
1011013 CAATGTATAA
* ** * ** * * * * *
1011023 TCATATAAAAATCAA-TTCGGCAATGTATAACTATATATGAATCAAGTTCGGCAATGTATAATCA
1 TCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAGCAATGTACAACCA
*
1011087 TATACAAATTAATTCGGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATATA
66 TATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATATA
* * * *
1011152 CAAATTAATTTCAGCAAAGTATAATCATATACAAATCAATTTGGCAACTTATCT
131 CAAATTAATTTCAGCAAAGTATAATTATATACGAATTAATTCGGCAACTTATCT
* * *
1011206 TCATATACAAATCAATTTTGTTAATGTATAACCATATACAAATAAATTTCAGCAACGTACAACCA
1 TCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAGCAATGTACAACCA
1011271 TATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATATA
66 TATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATATA
* *
1011336 CAAATTAATTTCA-AAAATGTATAATTATATATGAATTAATTCGGCAACTTATCT
131 CAAATTAATTTCAGCAAA-GTATAATTATATACGAATTAATTCGGCAACTTATCT
* *
1011390 TCATATACAAATCAATTTCGATAATGTATAATCATATCCAAATAAATTTCAGCAATGTACAACCA
1 TCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAGCAATGTACAACCA
* *
1011455 TATACGAATTAATTCAGCAACTTATATCCATATACAATTCAATGTT-AACAACGTATAACCATAT
66 TATACAAATTAATTCAGCAACTTATATCCATATACAATTCAAT-TTCAACAATGTATAACCATAT
* *
1011519 ACAAATTAATTTCAGCAATGTATAATTATATACGAATTAATTCAGCAA
130 ACAAATTAATTTCAGCAAAGTATAATTATATACGAATTAATTCGGCAA
1011567 TATATATATC
Statistics
Matches: 326, Mismatches: 31, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
183 17 0.05
184 305 0.94
185 4 0.01
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.33
Consensus pattern (184 bp):
TCATATACAAATCAATTTCGATAATGTATAACCATATACAAATAAATTTCAGCAATGTACAACCA
TATACAAATTAATTCAGCAACTTATATCCATATACAATTCAATTTCAACAATGTATAACCATATA
CAAATTAATTTCAGCAAAGTATAATTATATACGAATTAATTCGGCAACTTATCT
Found at i:1011573 original size:92 final size:92
Alignment explanation
Indices: 1011043--1011566 Score: 654
Period size: 92 Copynumber: 5.7 Consensus size: 92
1011033 ATCAATTCGG
* ** * * * *
1011043 CAATGTATAACTATATATGAATCAAGTTCGGCAATGTATAATCATATACAAATTAATTCGGCAAC
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
1011108 TTATATCCATATACAATTCAATTTCAA
66 TTATATCCATATACAATTCAATTTCAA
* * **
1011135 CAATGTATAACCATATACAAATTAATTTCAGCAAAGTATAATCATATACAAATCAATTTGGCAAC
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
* * * ***
1011200 TTATCTTCATATACAAATCAATTTTGT
66 TTATATCCATATACAATTCAATTTCAA
* * * * *
1011227 TAATGTATAACCATATACAAATAAATTTCAGCAACGTACAACCATATACAAATTAATTCAGCAAC
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
1011292 TTATATCCATATACAATTCAATTTCAA
66 TTATATCCATATACAATTCAATTTCAA
** * ** *
1011319 CAATGTATAACCATATACAAATTAATTTCAAAAATGTATAATTATATATGAATTAATTCGGCAAC
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
* * * *
1011384 TTATCTTCATATACAAATCAATTTCGA
66 TTATATCCATATACAATTCAATTTCAA
* * * * * * *
1011411 TAATGTATAATCATATCCAAATAAATTTCAGCAATGTACAACCATATACGAATTAATTCAGCAAC
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
1011476 TTATATCCATATACAATTCAATGTT-AA
66 TTATATCCATATACAATTCAAT-TTCAA
* * *
1011503 CAACGTATAACCATATACAAATTAATTTCAGCAATGTATAATTATATACGAATTAATTCAGCAA
1 CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAA
1011567 TATATATATC
Statistics
Matches: 364, Mismatches: 67, Indels: 2
0.84 0.15 0.00
Matches are distributed among these distances:
92 362 0.99
93 2 0.01
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.33
Consensus pattern (92 bp):
CAATGTATAACCATATACAAATTAATTTCAGCAATGTATAATCATATACAAATTAATTCAGCAAC
TTATATCCATATACAATTCAATTTCAA
Found at i:1023788 original size:15 final size:15
Alignment explanation
Indices: 1023757--1023814 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
1023747 CCGTATACAA
1023757 TTTTTT-TTC-AATTT
1 TTTTTTCTTCGAA-TT
1023771 TTTTTTCTTTTCG-ATT
1 TTTTTTC--TTCGAATT
1023787 TTTTTTCTTCGAATT
1 TTTTTTCTTCGAATT
1023802 TTTTTTCTTCGAA
1 TTTTTTCTTCGAA
1023815 ACTACAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
14 10 0.26
15 16 0.41
16 9 0.23
17 4 0.10
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.71
Consensus pattern (15 bp):
TTTTTTCTTCGAATT
Found at i:1023788 original size:16 final size:17
Alignment explanation
Indices: 1023757--1023810 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
1023747 CCGTATACAA
1023757 TTTT-TTTTC-AATTTTT
1 TTTTCTTTTCGAA-TTTT
1023773 TTTTCTTTTCG-ATTTT
1 TTTTCTTTTCGAATTTT
1023789 TTTTC--TTCGAATTTT
1 TTTTCTTTTCGAATTTT
1023804 TTTTCTT
1 TTTTCTT
1023811 CGAAACTACA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.12
15 10 0.30
16 13 0.39
17 6 0.18
ACGTcount: A:0.09, C:0.11, G:0.04, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTCGAATTTT
Found at i:1034018 original size:21 final size:20
Alignment explanation
Indices: 1034002--1034070 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
1033992 GATGTTTATA
1034002 TGAATCGATTGTTTGTTGTTT
1 TGAATCGATTGTTTGTT-TTT
* * *
1034023 TAAATCAATTTTTTGTTTCTT
1 TGAATCGATTGTTTGTTT-TT
1034044 TGAATCGATTGTTT-TTTGTT
1 TGAATCGATTGTTTGTTT-TT
1034064 TGAATCG
1 TGAATCG
1034071 GTTCATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
20 13 0.32
21 27 0.68
ACGTcount: A:0.19, C:0.07, G:0.17, T:0.57
Consensus pattern (20 bp):
TGAATCGATTGTTTGTTTTT
Found at i:1034067 original size:20 final size:20
Alignment explanation
Indices: 1034002--1034093 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
1033992 GATGTTTATA
*
1034002 TGAATCGATTGTTTGTTGTTT
1 TGAATCGATTGTTTTTTG-TT
* * * *
1034023 TAAATCAATTTTTTGTTTCTT
1 TGAATCGATTGTTT-TTTGTT
1034044 TGAATCGATTGTTTTTTGTT
1 TGAATCGATTGTTTTTTGTT
* ** *
1034064 TGAATCGGTTCATTATTGTT
1 TGAATCGATTGTTTTTTGTT
*
1034084 TAAATCGATT
1 TGAATCGATT
1034094 CAAACTCCAA
Statistics
Matches: 55, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 29 0.53
21 24 0.44
22 2 0.04
ACGTcount: A:0.21, C:0.08, G:0.16, T:0.55
Consensus pattern (20 bp):
TGAATCGATTGTTTTTTGTT
Found at i:1036928 original size:4 final size:4
Alignment explanation
Indices: 1036921--1036946 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1036911 TAAATAAAAC
1036921 TCTT TCTT TCTT TCTT TCTT TCTT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TC
1036947 CAATCAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
TCTT
Found at i:1036991 original size:13 final size:13
Alignment explanation
Indices: 1036956--1036984 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1036946 CCAATCAATG
1036956 GTAATTAATTATT
1 GTAATTAATTATT
1036969 GTAATTAATTATT
1 GTAATTAATTATT
1036982 GTA
1 GTA
1036985 TGTAATTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (13 bp):
GTAATTAATTATT
Found at i:1043292 original size:20 final size:21
Alignment explanation
Indices: 1043267--1043309 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1043257 TTAAAAATAT
*
1043267 TAATTTTGTT-AAATAGTAAA
1 TAATTTTGTTAAAACAGTAAA
*
1043287 TAATTTTTTTAAAACAGTAAA
1 TAATTTTGTTAAAACAGTAAA
1043308 TA
1 TA
1043310 TTAACTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (21 bp):
TAATTTTGTTAAAACAGTAAA
Found at i:1043376 original size:29 final size:29
Alignment explanation
Indices: 1043343--1043398 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1043333 TATTTAATTT
*
1043343 TTTAATAGTATAAGG-ACTAAATTAATCTA
1 TTTAATAATA-AAGGAACTAAATTAATCTA
*
1043372 TTTAATAATAAAGGAACTAATTTAATC
1 TTTAATAATAAAGGAACTAAATTAATC
1043399 AGGACCCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (29 bp):
TTTAATAATAAAGGAACTAAATTAATCTA
Found at i:1046614 original size:29 final size:29
Alignment explanation
Indices: 1046555--1046613 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
1046545 ATCAATCCTT
1046555 AATCCTTGCATTCAAATGTTATAAAATAA
1 AATCCTTGCATTCAAATGTTATAAAATAA
1046584 AATCCTTGCATTCAAATGTTAT-AAATAA
1 AATCCTTGCATTCAAATGTTATAAAATAA
1046612 AA
1 AA
1046614 ACAAAAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 8 0.27
29 22 0.73
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.34
Consensus pattern (29 bp):
AATCCTTGCATTCAAATGTTATAAAATAA
Found at i:1050187 original size:42 final size:42
Alignment explanation
Indices: 1050058--1050369 Score: 213
Period size: 43 Copynumber: 7.4 Consensus size: 42
1050048 CTCGGTGGAT
** * *
1050058 TCAGCACTTAGCAACCAC-CATAAATTTAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACTTTTAAATTCAATGATACGGGGAA
* * * * * *
1050099 TCAACACATAGCAACCCCTTTCACAATT-AAGGATTCGGTGGAA
1 TCAGCACTTAGCAACCACTTTTA-AATTCAATGATACGG-GGAA
* *
1050142 TCAGCACTTAGCAACCACTTTTATATTCAGTGATACGGGGAA
1 TCAGCACTTAGCAACCACTTTTAAATTCAATGATACGGGGAA
* * * ** *
1050184 TCAGCACTTAGCAACCCCATTCACAATT-AAAAATACGGTGGAT
1 TCAGCACTTAGCAACCACTTTTA-AATTCAATGATACGG-GGAA
* * *
1050227 TCAGCACATAGCAACCA-TCTTTATATTCAACGATACGGGGAA
1 TCAGCACTTAGCAACCACT-TTTAAATTCAATGATACGGGGAA
* * * ** *
1050269 TCAACATTTAGCAACC-CATTTCACAATT-AAAAATACGGTGGGA
1 TCAGCACTTAGCAACCAC-TTTTA-AATTCAATGATACGG-GGAA
* * * * * *
1050312 TCAGCACTTAGCAACCACCTTTAGAGTCAATAATTCAGGGAA
1 TCAGCACTTAGCAACCACTTTTAAATTCAATGATACGGGGAA
1050354 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
1050370 CTTCGGGGAA
Statistics
Matches: 206, Mismatches: 51, Indels: 27
0.73 0.18 0.10
Matches are distributed among these distances:
41 15 0.07
42 93 0.45
43 97 0.47
44 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (42 bp):
TCAGCACTTAGCAACCACTTTTAAATTCAATGATACGGGGAA
Done.