Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012601.1 Corchorus capsularis cultivar CVL-1 contig12622, whole genome shotgun sequence
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: 184842
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:11368 original size:13 final size:13
Alignment explanation
Indices: 11350--11377 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
11340 ATTTTCATTA
11350 ATTAATATGTTAT
1 ATTAATATGTTAT
11363 ATTAATATGTTAT
1 ATTAATATGTTAT
11376 AT
1 AT
11378 AATCTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTAATATGTTAT
Found at i:11917 original size:53 final size:53
Alignment explanation
Indices: 11837--11943 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
11827 CAACCTAGCC
11837 TCTAAATGATAATTTGTTTTGGAATAGCCATTTTGCCCCCTAAACTTTACATA
1 TCTAAATGATAATTTGTTTTGGAATAGCCATTTTGCCCCCTAAACTTTACATA
11890 TCTAAATGATAATTTGTTTTGGAATAGCCATTTTGCCCCCTAAACTTTACATA
1 TCTAAATGATAATTTGTTTTGGAATAGCCATTTTGCCCCCTAAACTTTACATA
11943 T
1 T
11944 TTAAGACAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (53 bp):
TCTAAATGATAATTTGTTTTGGAATAGCCATTTTGCCCCCTAAACTTTACATA
Found at i:16780 original size:27 final size:27
Alignment explanation
Indices: 16744--16807 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 27
16734 ATTTCTGGAA
16744 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
16771 AACAAGGGAAATGGACAATTAAAAAGG
1 AACAAGGGAAATGGACAATTAAAAAGG
16798 AACAGAGGGA
1 AACA-AGGGA
16808 GTAATTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 31 0.86
28 5 0.14
ACGTcount: A:0.55, C:0.08, G:0.28, T:0.09
Consensus pattern (27 bp):
AACAAGGGAAATGGACAATTAAAAAGG
Found at i:25756 original size:15 final size:15
Alignment explanation
Indices: 25736--25765 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25726 TAAAAAATTC
25736 TCTCTCTCTCTCTTT
1 TCTCTCTCTCTCTTT
25751 TCTCTCTCTCTCTTT
1 TCTCTCTCTCTCTTT
25766 CTTTCTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (15 bp):
TCTCTCTCTCTCTTT
Found at i:25887 original size:14 final size:14
Alignment explanation
Indices: 25865--25899 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25855 TTTTTCTACT
*
25865 TTTAT-TTTATTTA
1 TTTATATTTATATA
25878 TTTATATTTATATA
1 TTTATATTTATATA
25892 TTTATATT
1 TTTATATT
25900 ATCAATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:25919 original size:24 final size:25
Alignment explanation
Indices: 25883--25929 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
25873 ATTTATTTAT
25883 ATTTATATATTTATATTA-TCAATGG
1 ATTTATATATTTAT-TTATTCAATGG
*
25908 ATTTTTAT-TTTATTTATTCAAT
1 ATTTATATATTTATTTATTCAAT
25930 TTCTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 10 0.50
25 7 0.35
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (25 bp):
ATTTATATATTTATTTATTCAATGG
Found at i:31051 original size:210 final size:210
Alignment explanation
Indices: 30672--31097 Score: 536
Period size: 210 Copynumber: 2.0 Consensus size: 210
30662 CTGAGCAAGA
* * *
30672 TACCAGACTTTACAATGGCCCCAAATCTCCAAAGCTTGGTTTTGACAGGTTGTATCAAGATGGTA
1 TACCAGACTTTACAATGGCCCCAAACCTCCAAAGCTTGATTTTGACAGGTTGTATCAAGATAGTA
* * * *
30737 GATATTCATCCGTCTATCAGACTTCTAAGGAGACTTAAACTTCTTGATTTAAGAGACTGCAGAAG
66 GATATTCATCCATCCATCAGACTTCTAAGGAGACTTAAAATTCTTGATTTAAGAGACTGCAAAAG
* * ** * * *
30802 TCTTAGGAGTCTTCCTACCAAATTTGAAACATTATCTCTTGAGACATTGATTCTTTCAGGTTGCA
131 TCTTAGGAGTCTTCCAACCAAAATTGAAACAGAATCTCTTGAAACATTAATTCTTTCAGGCTGCA
30867 CAAATCTCAAAAGGT
196 CAAATCTCAAAAGGT
** *
30882 TACCAGACTTTACAATGGCCCCAAACCT-CAAA-CATTTGATTTCTG-TTGGTTGTGTCAAGATA
1 TACCAGACTTTACAATGGCCCCAAACCTCCAAAGC--TTGATTT-TGACAGGTTGTATCAAGATA
* * *
30944 GTAGATGTTCATCCATCCATCGGACTTCTAAGGAGTCTTAAAATTC-TGAATTTAAGAGACTGCA
63 GTAGATATTCATCCATCCATCAGACTTCTAAGGAGACTTAAAATTCTTG-ATTTAAGAGACTGCA
* ** *
31008 AAAGTCTTAGGAGTCTTCCAACCAAAATTGGAATGGAATCTCTTGAAATATTAATTCTTTCAGGC
127 AAAGTCTTAGGAGTCTTCCAACCAAAATTGAAACAGAATCTCTTGAAACATTAATTCTTTCAGGC
* * **
31073 TGCTCGAATCTTGAAAGGT
192 TGCACAAATCTCAAAAGGT
31092 TACCAG
1 TACCAG
31098 CTCAGATGGA
Statistics
Matches: 184, Mismatches: 28, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
208 1 0.01
209 6 0.03
210 175 0.95
211 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (210 bp):
TACCAGACTTTACAATGGCCCCAAACCTCCAAAGCTTGATTTTGACAGGTTGTATCAAGATAGTA
GATATTCATCCATCCATCAGACTTCTAAGGAGACTTAAAATTCTTGATTTAAGAGACTGCAAAAG
TCTTAGGAGTCTTCCAACCAAAATTGAAACAGAATCTCTTGAAACATTAATTCTTTCAGGCTGCA
CAAATCTCAAAAGGT
Found at i:32721 original size:7 final size:7
Alignment explanation
Indices: 32709--32733 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
32699 CATGTCTATG
32709 AGGAGGC
1 AGGAGGC
32716 AGGAGGC
1 AGGAGGC
32723 AGGAGGC
1 AGGAGGC
32730 AGGA
1 AGGA
32734 CCAAGTGGGA
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:0.32, C:0.12, G:0.56, T:0.00
Consensus pattern (7 bp):
AGGAGGC
Found at i:43339 original size:74 final size:74
Alignment explanation
Indices: 43249--43400 Score: 286
Period size: 74 Copynumber: 2.1 Consensus size: 74
43239 ACAAAAACAG
43249 TAGACAAAGAAAAAGAATTAATTGTCACTAAGCTATTTAGGAAATTGCAGACACTTGTTTCTTCA
1 TAGACAAAGAAAAAGAATTAATTGTCACTAAGCTATTTAGGAAATTGCAGACACTTGTTTCTTCA
43314 ACCTTCCAA
66 ACCTTCCAA
*
43323 TAGACAAAGAAAAAGAATTAATTGTCACTAAGCTATTTTGGAAATTGCAGACACTTGTTTCTTCA
1 TAGACAAAGAAAAAGAATTAATTGTCACTAAGCTATTTAGGAAATTGCAGACACTTGTTTCTTCA
*
43388 ACCTTCCCA
66 ACCTTCCAA
43397 TAGA
1 TAGA
43401 TTATTAGCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 76 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (74 bp):
TAGACAAAGAAAAAGAATTAATTGTCACTAAGCTATTTAGGAAATTGCAGACACTTGTTTCTTCA
ACCTTCCAA
Found at i:49917 original size:104 final size:106
Alignment explanation
Indices: 49745--50005 Score: 395
Period size: 104 Copynumber: 2.5 Consensus size: 106
49735 AGTTTAGCCT
* *
49745 TAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATT-AAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
49810 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
*
49852 TAATTTCACTAAGTTTAGCCCCAAATTAAA-TTT-TTTTTATTTTAAGGGTAAATTCCATAATTA
1 TAATTTCACTAAGTTTAGCCCCAAATTAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
* * *
49915 ATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAT
66 ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
49956 TAA-TTCACTAAGTTTAG-CCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATT-AAATTTTATTTTTATTTTAAGGGT
50006 TAGAAAATTA
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
102 8 0.06
103 17 0.12
104 70 0.49
105 18 0.13
106 3 0.02
107 26 0.18
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.42
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:53318 original size:16 final size:16
Alignment explanation
Indices: 53297--53328 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53287 GCTTGACTTA
53297 TACTGCGTCATGATAT
1 TACTGCGTCATGATAT
53313 TACTGCGTCATGATAT
1 TACTGCGTCATGATAT
53329 ACCGGAAAAA
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:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
TACTGCGTCATGATAT
Found at i:54011 original size:108 final size:108
Alignment explanation
Indices: 53872--54090 Score: 393
Period size: 108 Copynumber: 2.0 Consensus size: 108
53862 ATTTCAATCT
*
53872 CTAATGTTTTAATTAATCCTCCCAGCAGTTAAATCTTGTGACTTTTTGTGGGAGGTCTTGGGTTC
1 CTAATGTTTTAATTAATCCTCCCAGCAGTTAAACCTTGTGACTTTTTGTGGGAGGTCTTGGGTTC
*
53937 GAATTCTGTGATGGACGAGGTGGGATCATGGAAAAGGAAAGAG
66 GAATTCTGGGATGGACGAGGTGGGATCATGGAAAAGGAAAGAG
* *
53980 CTAATGTTTTAATTAATCCTCCCAGCGGTTAAACCTTGTGACTTTTTGTGGGAGGTCTTGGGTTT
1 CTAATGTTTTAATTAATCCTCCCAGCAGTTAAACCTTGTGACTTTTTGTGGGAGGTCTTGGGTTC
*
54045 GAATTCTGGGATGGACGGGGTGGGATCATGGAAAAGGAAAGAG
66 GAATTCTGGGATGGACGAGGTGGGATCATGGAAAAGGAAAGAG
54088 CTA
1 CTA
54091 TCTCCTATTG
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.25, C:0.13, G:0.30, T:0.32
Consensus pattern (108 bp):
CTAATGTTTTAATTAATCCTCCCAGCAGTTAAACCTTGTGACTTTTTGTGGGAGGTCTTGGGTTC
GAATTCTGGGATGGACGAGGTGGGATCATGGAAAAGGAAAGAG
Found at i:54776 original size:15 final size:15
Alignment explanation
Indices: 54756--54790 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54746 AGATTTAGAA
* *
54756 TTTTTCGGGTTTAAG
1 TTTTTCGAGTTCAAG
54771 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
54786 TTTTT
1 TTTTT
54791 TTTTGAGTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.09, G:0.20, T:0.57
Consensus pattern (15 bp):
TTTTTCGAGTTCAAG
Found at i:54798 original size:18 final size:18
Alignment explanation
Indices: 54771--54810 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
54761 CGGGTTTAAG
54771 TTTTTCGAGTTCAAGTTT
1 TTTTTCGAGTTCAAGTTT
* *
54789 TTTTTTGAGTTCAGGTTT
1 TTTTTCGAGTTCAAGTTT
54807 TTTT
1 TTTT
54811 GGGTTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.07, G:0.17, T:0.62
Consensus pattern (18 bp):
TTTTTCGAGTTCAAGTTT
Found at i:54807 original size:16 final size:16
Alignment explanation
Indices: 54788--54830 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
54778 AGTTCAAGTT
**
54788 TTTTTTTGAGTTCAGG
1 TTTTTTTGAGTTCAAA
*
54804 TTTTTTTGGGTTCAAA
1 TTTTTTTGAGTTCAAA
54820 TTTTTTTGAGT
1 TTTTTTTGAGT
54831 CGAGTGGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTTTTTGAGTTCAAA
Found at i:54807 original size:17 final size:18
Alignment explanation
Indices: 54771--54830 Score: 56
Period size: 16 Copynumber: 3.6 Consensus size: 18
54761 CGGGTTTAAG
*
54771 TTTTTCGAGTTCAAGTTT
1 TTTTTCGAGTTCAAGGTT
*
54789 TTTTTTGAGTTC-AGGTT
1 TTTTTCGAGTTCAAGGTT
* *
54806 TTTTT-GGGTTCAA-ATT
1 TTTTTCGAGTTCAAGGTT
54822 TTTTT-GAGT
1 TTTTTCGAGT
54831 CGAGTGGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 15 0.42
17 10 0.28
18 11 0.31
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.58
Consensus pattern (18 bp):
TTTTTCGAGTTCAAGGTT
Found at i:59393 original size:73 final size:74
Alignment explanation
Indices: 59316--59454 Score: 244
Period size: 74 Copynumber: 1.9 Consensus size: 74
59306 ACTTTTCGGG
* *
59316 TGACTAAAAAGCCCCTCTATGAGTTT-CCCTATTCCTTTTCTTTCTACCATTTTTCGTAATTACA
1 TGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCATTTTTCGTAATTACA
59380 CTTTTAGAA
66 CTTTTAGAA
*
59389 TGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTTTTCGTAATTACA
1 TGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCATTTTTCGTAATTACA
59454 C
66 C
59455 ATTTCCCTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
73 26 0.42
74 36 0.58
ACGTcount: A:0.24, C:0.28, G:0.08, T:0.40
Consensus pattern (74 bp):
TGACTAAAAAGCCCCTCTATGAGTTTCCCCAATTCCTTTTCCTTCTACCATTTTTCGTAATTACA
CTTTTAGAA
Found at i:61856 original size:540 final size:541
Alignment explanation
Indices: 60838--61919 Score: 2148
Period size: 540 Copynumber: 2.0 Consensus size: 541
60828 ATCTCTATGC
60838 CCATAAGTAAACTACCTACCTACCAAATACATAAATAAACAAATTACAAATAAACTCACATTTCG
1 CCATAAGTAAACTACCTACCTACCAAATACATAAATAAACAAATTACAAATAAACTCACATTTCG
60903 TGAGAGTTGAACCTAAGACCCCATGGTTTAGGTAGGCTGCAACTAAGAGTCAAGTACTCTACAAC
66 TGAGAGTTGAACCTAAGACCCCATGGTTTAGGTAGGCTGCAACTAAGAGTCAAGTACTCTACAAC
60968 CAGACTAAATGCATTTAATTCAGAATGGTAAAAATATTGAAACTAATCCATTTAAATAATTGCAT
131 CAGACTAAATGCATTTAATTCAGAATGGTAAAAATATTGAAACTAATCCATTTAAATAATTGCAT
*
61033 TTTTACTGCAACCTTATATAATCCAATCAATTAATCAATCAAGCACCACTCTAGAATAAAAAAAT
196 TTTTACTGCAACCTTATATAATCCAATCAATTAATCAATCAAGCACCACTCTAGAACAAAAAAAT
61098 ATTCTTGGCCCTTATATAATTGATTATATTAATATCCTTATTCAATTAGTTAATCAAGTATCACT
261 ATTCTTGGCCCTTATATAATTGATTATATTAATATCCTTATTCAATTAGTTAATCAAGTATCACT
61163 CTAAAATAAAGAACGCCCGTAGCGCCAGTGCGGGCTAATATAACTTGTTATATATGGATAGCATA
326 CTAAAATAAAGAACGCCCGTAGCGCCAGTGCGGGCTAATATAACTTGTTATATATGGATAGCATA
61228 TGTCATCTCCTCCTAATTTTAGAATTTTGTAAATAAAAGCTATATATTTAATAATAATATATACT
391 TGTCATCTCCTCCTAATTTTAGAATTTTGTAAATAAAAGCTATATATTTAATAATAATATATACT
61293 ATACATTATTTGAATAAACATATGGAAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCG
456 ATACATTATTTGAATAAACATATGGAAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCG
61358 AGAGAACTAA-TTTTTTTCGT
521 AGAGAACTAATTTTTTTTCGT
61378 CCATAAGTAAACTACCTACCTACCAAATACATAAATAAACAAATTACAAATAAACTCACATTTCG
1 CCATAAGTAAACTACCTACCTACCAAATACATAAATAAACAAATTACAAATAAACTCACATTTCG
61443 TGAGAGTTGAACCTAAGACCCCATGGTTTAGGTAGGCTGCAACTAAGAGTCAAGTACTCTACAAC
66 TGAGAGTTGAACCTAAGACCCCATGGTTTAGGTAGGCTGCAACTAAGAGTCAAGTACTCTACAAC
61508 CAGACTAAATGCATTTAATTCAGAATGGTAAAAATATTGAAACTAATCCATTTAAATAATTGCAT
131 CAGACTAAATGCATTTAATTCAGAATGGTAAAAATATTGAAACTAATCCATTTAAATAATTGCAT
61573 TTTTACTGCAACCTTATATAATCCAATCAATTAATCAATCAAGCACCACTCTAGAACAAAAAAAT
196 TTTTACTGCAACCTTATATAATCCAATCAATTAATCAATCAAGCACCACTCTAGAACAAAAAAAT
61638 ATTCTTGGCCCTTATATAATTGATTATATTAATATCCTTATTCAATTAGTTAATCAAGTATCACT
261 ATTCTTGGCCCTTATATAATTGATTATATTAATATCCTTATTCAATTAGTTAATCAAGTATCACT
61703 CTAAAATAAAGAACGCCCGTAGCGCCAGTGCGGGCTAATATAACTTGTTATATATGGATAGCATA
326 CTAAAATAAAGAACGCCCGTAGCGCCAGTGCGGGCTAATATAACTTGTTATATATGGATAGCATA
61768 TGTCATCTCCTCCTAATTTTAGAATTTTGTAAATAAAAGCTATATATTTAATAATAATATATACT
391 TGTCATCTCCTCCTAATTTTAGAATTTTGTAAATAAAAGCTATATATTTAATAATAATATATACT
61833 ATACATTATTTGAATAAACATATGGAAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCG
456 ATACATTATTTGAATAAACATATGGAAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCG
61898 AGAGAACTAATTTTTTTTCGT
521 AGAGAACTAATTTTTTTTCGT
61919 C
1 C
61920 TTTTCTCACT
Statistics
Matches: 540, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
540 529 0.98
541 11 0.02
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (541 bp):
CCATAAGTAAACTACCTACCTACCAAATACATAAATAAACAAATTACAAATAAACTCACATTTCG
TGAGAGTTGAACCTAAGACCCCATGGTTTAGGTAGGCTGCAACTAAGAGTCAAGTACTCTACAAC
CAGACTAAATGCATTTAATTCAGAATGGTAAAAATATTGAAACTAATCCATTTAAATAATTGCAT
TTTTACTGCAACCTTATATAATCCAATCAATTAATCAATCAAGCACCACTCTAGAACAAAAAAAT
ATTCTTGGCCCTTATATAATTGATTATATTAATATCCTTATTCAATTAGTTAATCAAGTATCACT
CTAAAATAAAGAACGCCCGTAGCGCCAGTGCGGGCTAATATAACTTGTTATATATGGATAGCATA
TGTCATCTCCTCCTAATTTTAGAATTTTGTAAATAAAAGCTATATATTTAATAATAATATATACT
ATACATTATTTGAATAAACATATGGAAATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCG
AGAGAACTAATTTTTTTTCGT
Found at i:62077 original size:45 final size:45
Alignment explanation
Indices: 62026--62111 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
62016 AGAGTAATGG
62026 AATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGGTGA
1 AATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGGTGA
* ** *
62071 AATTACTAAAAGATCCCTATCCCGGGTTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
62112 AGAAGTAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (45 bp):
AATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGGGTGA
Found at i:63905 original size:2 final size:2
Alignment explanation
Indices: 63898--63927 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
63888 CTCATACTTT
63898 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
63928 TATTTCTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:64695 original size:12 final size:13
Alignment explanation
Indices: 64672--64697 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64662 CTGTTTCTGG
64672 TCTTTAAAAAAAT
1 TCTTTAAAAAAAT
64685 TCTTTAAAAAAAT
1 TCTTTAAAAAAAT
64698 GACAGCAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TCTTTAAAAAAAT
Found at i:65670 original size:45 final size:45
Alignment explanation
Indices: 65619--65708 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
65609 GATTAGTTCT
65619 CCAGCTCATCATTAATCCGGGGTAGGAATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGAATCTTTTAGTAATTCCAC
* *
65664 CCAGCTCATCATTAATCTGGGGTAGGGATCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAATCCGGGGTAGGAATCTTTTAGTAATTCCAC
65709 AGCTCTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (45 bp):
CCAGCTCATCATTAATCCGGGGTAGGAATCTTTTAGTAATTCCAC
Found at i:71715 original size:3 final size:3
Alignment explanation
Indices: 71709--71738 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
71699 ACTTTATTAT
71709 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
71739 AATCAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:78862 original size:31 final size:31
Alignment explanation
Indices: 78824--79021 Score: 160
Period size: 31 Copynumber: 6.5 Consensus size: 31
78814 GTTGGCTAAT
78824 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * **
78855 TGCTCAAATAAGGGCCTGACATTT-T-AATT
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * *
78884 TGGC-CAAATAAGGACCTAACATTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * * **
78915 TACTCAAATAAGGGCCCGATC-TTTG--AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
*
78944 TGGC-CAAATAAGGGCCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * *
78975 TGCTCAAATAAGTGCCTAAAG-TTATCGAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTC-AAAA
79006 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
79022 CGATTTCAGT
Statistics
Matches: 131, Mismatches: 25, Indels: 22
0.74 0.14 0.12
Matches are distributed among these distances:
28 4 0.03
29 38 0.29
30 10 0.08
31 75 0.57
32 4 0.03
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:78921 original size:60 final size:60
Alignment explanation
Indices: 78828--78991 Score: 249
Period size: 60 Copynumber: 2.7 Consensus size: 60
78818 GCTAATTGCT
* *
78828 CAAATAAGGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGCCTGA-CATTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATC-TTTGAATTTGGC
* * * *
78888 CAAATAAGGACCTAACATTTGCCAAAATACTCAAATAAGGGCCCGATCTTTGAATTTGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
*
78948 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGTGCCT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCT
78992 AAAGTTATCG
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
60 91 0.99
61 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCTGATCTTTGAATTTGGC
Found at i:79084 original size:31 final size:31
Alignment explanation
Indices: 79049--79217 Score: 181
Period size: 31 Copynumber: 5.6 Consensus size: 31
79039 ACGTATGAGA
79049 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
** *
79080 TAGGCCCTTATTTG-GCCAAATT--CAAA-GA
1 TAGGCCCTTATTTGAG-CATTTTGGCAAACGT
*
79108 TCGAGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAG-GCCCTTATTTGAGCATTTTGGCAAACGT
* * * *
79140 TAGGCACTTATTTGACCAATTT---AAAAGAT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACG-T
*
79169 CAGGCCCTTATTTGAGCATTTTGGCAAACGT
1 TAGGCCCTTATTTGAGCATTTTGGCAAACGT
79200 TAGGCCCTTATTTGAGCA
1 TAGGCCCTTATTTGAGCA
79218 ATGATAAATA
Statistics
Matches: 110, Mismatches: 18, Indels: 20
0.74 0.12 0.14
Matches are distributed among these distances:
28 7 0.06
29 38 0.35
30 2 0.02
31 56 0.51
32 7 0.06
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (31 bp):
TAGGCCCTTATTTGAGCATTTTGGCAAACGT
Found at i:79120 original size:60 final size:60
Alignment explanation
Indices: 79046--79214 Score: 279
Period size: 60 Copynumber: 2.8 Consensus size: 60
79036 ATGACGTATG
* *
79046 AGAT-AGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAA
1 AGATCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAA
* *
79105 AGATC-GAGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCACTTATTTGACCAATTTAAA
1 AGATCAG-GCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAA
79165 AGATCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
1 AGATCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
79215 GCAATGATAA
Statistics
Matches: 102, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
59 5 0.05
60 96 0.94
61 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (60 bp):
AGATCAGGCCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAA
Found at i:79179 original size:29 final size:29
Alignment explanation
Indices: 79081--79183 Score: 84
Period size: 29 Copynumber: 3.5 Consensus size: 29
79071 GGCAAACGTT
* * *
79081 AGGCCCTTATTTGGCCAAATTCAAAGATC
1 AGGCCCTTATTTGACCAATTTAAAAGATC
* * * *
79110 -GAGCCCTTATTTGAGCATTTTGGCAAACG-TT
1 AG-GCCCTTATTTGACCAATTT---AAAAGATC
*
79141 AGGCACTTATTTGACCAATTTAAAAGATC
1 AGGCCCTTATTTGACCAATTTAAAAGATC
79170 AGGCCCTTATTTGA
1 AGGCCCTTATTTGA
79184 GCATTTTGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
28 5 0.09
29 29 0.53
31 17 0.31
32 4 0.07
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGACCAATTTAAAAGATC
Found at i:84556 original size:29 final size:30
Alignment explanation
Indices: 84479--84563 Score: 111
Period size: 30 Copynumber: 2.9 Consensus size: 30
84469 CGTTTGAGAG
**
84479 GGGGCAAAACAACCAAAATTGAGAGTTCAT
1 GGGGCAAAACGTCCAAAATTGAGAGTTCAT
*
84509 TGGGCAAAACGTCCAAAATTGAGAGTTCA-
1 GGGGCAAAACGTCCAAAATTGAGAGTTCAT
* *
84538 GGGGTAAAATGTCCAAAATTGA-AGTT
1 GGGGCAAAACGTCCAAAATTGAGAGTT
84564 TAGAGGGCTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.08
29 19 0.39
30 26 0.53
ACGTcount: A:0.40, C:0.14, G:0.25, T:0.21
Consensus pattern (30 bp):
GGGGCAAAACGTCCAAAATTGAGAGTTCAT
Found at i:84576 original size:29 final size:29
Alignment explanation
Indices: 84491--84578 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
84481 GGCAAAACAA
* * *
84491 CCAAAATTGAGAGTTCATTGGGCAAAACGT
1 CCAAAATTGAGAGTTCA-GGGGCTAAATGT
84521 CCAAAATTGAGAGTTCAGGGG-TAAAATGT
1 CCAAAATTGAGAGTTCAGGGGCT-AAATGT
*
84550 CCAAAATTGA-AGTTTAGAGGGCTAAATGT
1 CCAAAATTGAGAGTTCAG-GGGCTAAATGT
84579 GTTAGAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
28 6 0.12
29 27 0.53
30 18 0.35
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (29 bp):
CCAAAATTGAGAGTTCAGGGGCTAAATGT
Found at i:87755 original size:31 final size:31
Alignment explanation
Indices: 87720--87794 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
87710 CTTTATTGAT
*
87720 TGGACTCAATTGAC-CGAATCTTATGAGTACA
1 TGGACTAAATTGACTC-AATCTTATGAGTACA
** *
87751 TGGACTGGATTGACTCAATCTTGTGAGTACA
1 TGGACTAAATTGACTCAATCTTATGAGTACA
*
87782 TGAACTAAATTGA
1 TGGACTAAATTGA
87795 TTGCTTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (31 bp):
TGGACTAAATTGACTCAATCTTATGAGTACA
Found at i:95558 original size:15 final size:15
Alignment explanation
Indices: 95538--95568 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
95528 ATTCCTTATT
95538 AGGTGAGTAATAATA
1 AGGTGAGTAATAATA
95553 AGGTGAGTAATAATA
1 AGGTGAGTAATAATA
95568 A
1 A
95569 TCTGCTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (15 bp):
AGGTGAGTAATAATA
Found at i:96248 original size:36 final size:36
Alignment explanation
Indices: 96203--96290 Score: 97
Period size: 39 Copynumber: 2.4 Consensus size: 36
96193 TGCAAAAATA
**
96203 GCTACTGAAACAGTTTATA-TTCCTTTAAAACTCTCT
1 GCTACTGAAACAGTGGATAGTTCCTTT-AAACTCTCT
*
96239 GCTATTGAAACATAGTGGATAGGTTCCTTTAAACTCTCT
1 GCTACTGAAAC--AGTGGATA-GTTCCTTTAAACTCTCT
*
96278 GCTACTAAAACAG
1 GCTACTGAAACAG
96291 ATTCACATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
36 10 0.23
37 2 0.05
38 6 0.14
39 18 0.42
40 7 0.16
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (36 bp):
GCTACTGAAACAGTGGATAGTTCCTTTAAACTCTCT
Found at i:98625 original size:39 final size:39
Alignment explanation
Indices: 98549--98625 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
98539 TTTATATTTC
* * * *
98549 CTACTTTTCTGCTGGTCTATAATTTGAACCATGTGTTTT
1 CTACTTTTCTACTGGTATACAATTTGAACAATGTGTTTT
*
98588 CTACTTTTCTACTGGTATGCAATTTGAACTAAT-TGTTT
1 CTACTTTTCTACTGGTATACAATTTGAAC-AATGTGTTT
98626 GCTTTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (39 bp):
CTACTTTTCTACTGGTATACAATTTGAACAATGTGTTTT
Found at i:101936 original size:36 final size:37
Alignment explanation
Indices: 101895--101984 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 37
101885 GGTGCAAAAT
101895 AGCTACTGAAACAGAGT-ATA-TTCCTTTAAAAATCTC
1 AGCTACTGAAACAGAGTGATAGTTCCTTT-AAAATCTC
* * *
101931 TGCTACTAAAACAGAGTGGATAGGTTCCTTTAAACTCTC
1 AGCTACTGAAACAGAGT-GATA-GTTCCTTTAAAATCTC
101970 AGCTACTGAAACAGA
1 AGCTACTGAAACAGA
101985 TTCAAATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 15 0.33
38 3 0.07
39 20 0.44
40 7 0.16
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (37 bp):
AGCTACTGAAACAGAGTGATAGTTCCTTTAAAATCTC
Found at i:104355 original size:186 final size:187
Alignment explanation
Indices: 104016--104361 Score: 509
Period size: 186 Copynumber: 1.9 Consensus size: 187
104006 TCAAATGGTA
* * *
104016 AAATTAAAGAATGGTCCTCGGATATTTATATTTTAAGATATTTAGTTCTTGTACTATTTTTATTT
1 AAATTAAAGAATGGTCCTCAGACATTTATATTTTAAGATATTTAGTTCTTGTACTATTCTTATTT
* * * *
104081 AACTTGATTTAGCCCTTCAATATTATTTATTTTATATAAAGTCCTCAAATATTTTCAAACTATAC
66 AACTT-ATTTAACCCTTCAACATTATTTATTTCATATAAAGTCCTCAAACATTTTCAAACTATAC
* **
104146 GGTTTAATCCCTAAAACATTTGATTCTATGTTGATTTAGTCCTCACATTTTCATTTTC
130 AGTTTAATAACTAAAACATTTGATTCTATGTTGATTTAGTCCTCACATTTTCATTTTC
* *
104204 AAATTAAAGAATGGTCCTCAGACATTTATATTTTATGCTATTTAGTTCTT-TCACTA-TCTTATT
1 AAATTAAAGAATGGTCCTCAGACATTTATATTTTAAGATATTTAGTTCTTGT-ACTATTCTTATT
** *
104267 TAACTT-TTTAACCCTTCAACATTATTTATTTCATATAAAAGTCCTCTCACATTTTCAAACTATG
65 TAACTTATTTAACCCTTCAACATTATTTATTTCATAT-AAAGTCCTCAAACATTTTCAAACTATA
104331 CAGTTTAATAACTAAAACATTTGATTCTATG
129 CAGTTTAATAACTAAAACATTTGATTCTATG
104362 CAATTTAGTC
Statistics
Matches: 141, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
185 27 0.19
186 51 0.36
187 13 0.09
188 50 0.35
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (187 bp):
AAATTAAAGAATGGTCCTCAGACATTTATATTTTAAGATATTTAGTTCTTGTACTATTCTTATTT
AACTTATTTAACCCTTCAACATTATTTATTTCATATAAAGTCCTCAAACATTTTCAAACTATACA
GTTTAATAACTAAAACATTTGATTCTATGTTGATTTAGTCCTCACATTTTCATTTTC
Found at i:104594 original size:134 final size:132
Alignment explanation
Indices: 104428--104722 Score: 316
Period size: 135 Copynumber: 2.2 Consensus size: 132
104418 CTGATTAATC
* *
104428 CTTCACCTTAGTTTCTTTTATCTTTATTATA-T-TTTTTAAGTTTTGT-T-GATTAATATATTCT
1 CTTCACCTT-TTTTCTTTTATCTTTATTATATTCTTTTTAAGTTTT-TCTCG-TT-A-AGATTCT
* * * * *
104489 ATAAATATGATAC-CAGATACTTTTT-AATTAGTTGATTTAGTCTCTCAAGCATTTGATTCTATG
61 ATAAATAAGAT-CTCAAATA-TTTTTCAATTAGTCGATTTAGTCCCTCAAACATTTGATTCTATG
104552 CAATTTAGTT
124 CAATTTAG-T
* * *
104562 CTTCACCTTTTTTCTTTTATCTTTCTTAATATTTCTTTTTTAGTTTTTCTCGTTACGATTCTATA
1 CTTCACCTTTTTTCTTTTATCTTTATT-ATA-TTCTTTTTAAGTTTTTCTCGTTAAGATTCTATA
* *
104627 AATAAGATCTCAAATATTTTTCTATTAGTCGATTTAGTCCCTCAAACATTTGATTTTATGCAATT
64 AATAAGATCTCAAATATTTTTCAATTAGTCGATTTAGTCCCTCAAACATTTGATTCTATGCAATT
104692 TAGT
129 TAGT
* *
104696 CATTCACCTTTTTCCTTTT-TATTTATT
1 C-TTCACCTTTTTTCTTTTATCTTTATT
104723 TTGCTTATTA
Statistics
Matches: 137, Mismatches: 15, Indels: 18
0.81 0.09 0.11
Matches are distributed among these distances:
133 16 0.12
134 26 0.19
135 77 0.56
136 3 0.02
137 14 0.10
138 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.08, T:0.53
Consensus pattern (132 bp):
CTTCACCTTTTTTCTTTTATCTTTATTATATTCTTTTTAAGTTTTTCTCGTTAAGATTCTATAAA
TAAGATCTCAAATATTTTTCAATTAGTCGATTTAGTCCCTCAAACATTTGATTCTATGCAATTTA
GT
Found at i:111292 original size:37 final size:35
Alignment explanation
Indices: 111208--111276 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
111198 TTGAGATCAT
* *
111208 AAGAAAAGGTATTTTAACCAAAAAAAAAAAAAAAA
1 AAGAAAAGGAATTCTAACCAAAAAAAAAAAAAAAA
* *
111243 AAGAAAAGGAATTCTGACCAAAAAATAAAAAAAA
1 AAGAAAAGGAATTCTAACCAAAAAAAAAAAAAAA
111277 GTTGAGAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (35 bp):
AAGAAAAGGAATTCTAACCAAAAAAAAAAAAAAAA
Found at i:118135 original size:33 final size:33
Alignment explanation
Indices: 118098--118161 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
118088 TAGAATTTTA
*
118098 TTAGTACAATT-CAAATTACATTTTACGGGTTTC
1 TTAGTACAATTGC-AATTACATATTACGGGTTTC
* *
118131 TTAGTCCAATTGCAATTATATATTACGGGTT
1 TTAGTACAATTGCAATTACATATTACGGGTT
118162 AAGTGTAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TTAGTACAATTGCAATTACATATTACGGGTTTC
Found at i:118275 original size:28 final size:27
Alignment explanation
Indices: 118210--118277 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 27
118200 TTTTGGAAGT
* *
118210 AATGTTGAAGAGATTGGTTGAGATTAA
1 AATGTTTAAGAGTTTGGTTGAGATTAA
**
118237 AA---TTGGGAGTTTGGTTGAGATTAAA
1 AATGTTTAAGAGTTTGGTTGAGATT-AA
118262 AATGTTTAAGAGTTTG
1 AATGTTTAAGAGTTTG
118278 TCTAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
24 16 0.52
25 4 0.13
27 2 0.06
28 9 0.29
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (27 bp):
AATGTTTAAGAGTTTGGTTGAGATTAA
Found at i:123691 original size:62 final size:62
Alignment explanation
Indices: 123615--123741 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
123605 AACAAAGGTC
123615 AAATCTTAATACTTGCAATCCTTTATGTTTTCTTTTGTGTGTTGAGATTTGAGAATGACCCA
1 AAATCTTAATACTTGCAATCCTTTATGTTTTCTTTTGTGTGTTGAGATTTGAGAATGACCCA
123677 AAATCTTAATACTTGCAATCCTTTATGTTTTCTTTTGTGTGTTGAGATTTGAGAATGACCCA
1 AAATCTTAATACTTGCAATCCTTTATGTTTTCTTTTGTGTGTTGAGATTTGAGAATGACCCA
123739 AAA
1 AAA
123742 AGAAAAAGAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.43
Consensus pattern (62 bp):
AAATCTTAATACTTGCAATCCTTTATGTTTTCTTTTGTGTGTTGAGATTTGAGAATGACCCA
Found at i:125817 original size:55 final size:57
Alignment explanation
Indices: 125720--125830 Score: 154
Period size: 55 Copynumber: 2.0 Consensus size: 57
125710 TAGATCAGAA
* * *
125720 TTTTTATAAAGAAAAGACCACGGTATAACAATACTACTGGATTATTACAAAGAATTG
1 TTTTTATAAAGAAAAGACCACGGTAAAACAATACTACCGGATTATTACAAAAAATTG
* * *
125777 TTTTTATAAA-AAAA-ACCATGGTAAAACGATACTACCGGATTATTATAAAAAATT
1 TTTTTATAAAGAAAAGACCACGGTAAAACAATACTACCGGATTATTACAAAAAATT
125831 ATAAAGAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
55 34 0.71
56 4 0.08
57 10 0.21
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (57 bp):
TTTTTATAAAGAAAAGACCACGGTAAAACAATACTACCGGATTATTACAAAAAATTG
Found at i:131203 original size:6 final size:7
Alignment explanation
Indices: 131171--131202 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
131161 TTTCATTTTC
131171 TTTTTGT
1 TTTTTGT
131178 TTTTTGT
1 TTTTTGT
131185 TTTTTGT
1 TTTTTGT
131192 TTTTTGT
1 TTTTTGT
131199 TTTT
1 TTTT
131203 GAACATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (7 bp):
TTTTTGT
Found at i:132958 original size:32 final size:34
Alignment explanation
Indices: 132884--132959 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
132874 AAACCCTAAA
* *
132884 CTTCATTTCTAACAACTTCTTCAAACTTCATTTTT
1 CTTCATTT-TAACAACATCTTCAAACTTCATTTTC
*
132919 ATT--TTTTAACAA-ATCTTCAAA-TTCATTTTC
1 CTTCATTTTAACAACATCTTCAAACTTCATTTTC
132949 CTTCATTTTAA
1 CTTCATTTTAA
132960 TCATAAACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
30 10 0.29
31 8 0.23
32 12 0.34
33 3 0.09
35 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (34 bp):
CTTCATTTTAACAACATCTTCAAACTTCATTTTC
Found at i:132985 original size:26 final size:26
Alignment explanation
Indices: 132956--133035 Score: 112
Period size: 26 Copynumber: 3.2 Consensus size: 26
132946 TTCCTTCATT
132956 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
132982 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
133008 TTAAACATAAACTAA-T-AA-ACTAA
1 TTAATCATAAACTAATTAAATACTAA
133031 TTAAT
1 TTAAT
133036 TTTTAGTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
23 9 0.19
24 1 0.02
25 1 0.02
26 37 0.77
ACGTcount: A:0.55, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:133118 original size:10 final size:10
Alignment explanation
Indices: 133103--133132 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
133093 CTAATTAATA
133103 TTAAAAAATT
1 TTAAAAAATT
133113 TTAAAAAATT
1 TTAAAAAATT
*
133123 TAAAAAAATT
1 TTAAAAAATT
133133 AAATTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:133335 original size:20 final size:20
Alignment explanation
Indices: 133296--133338 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
133286 TAAAAATTAT
**
133296 AAAAGGGGACGGTATTTAGC
1 AAAAGGGGACGGTAAATAGC
*
133316 AAAAGGGGGCGGTAAATAGC
1 AAAAGGGGACGGTAAATAGC
133336 AAA
1 AAA
133339 CCCTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.35, T:0.14
Consensus pattern (20 bp):
AAAAGGGGACGGTAAATAGC
Found at i:143731 original size:80 final size:80
Alignment explanation
Indices: 143627--143786 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
143617 CATTGCAATC
143627 ACTATCGTCACAACTATCAAAATCTTCATCACCATCATCGTTGTCGTCCGAATCATCATCATCAA
1 ACTATCGTCACAACTATCAAAATCTTCATCACCATCATCGTTGTCGTCCGAATCATCATCATCAA
143692 ATTCATTCAGATCAT
66 ATTCATTCAGATCAT
143707 ACTATCGTCACAACTATCAAAATCTTCATCACCATCATCGTTGTCGTCCGAATCATCATCATCAA
1 ACTATCGTCACAACTATCAAAATCTTCATCACCATCATCGTTGTCGTCCGAATCATCATCATCAA
143772 ATTCATTCAGATCAT
66 ATTCATTCAGATCAT
143787 TGTAATAATC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (80 bp):
ACTATCGTCACAACTATCAAAATCTTCATCACCATCATCGTTGTCGTCCGAATCATCATCATCAA
ATTCATTCAGATCAT
Found at i:143825 original size:3 final size:3
Alignment explanation
Indices: 143819--143859 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
143809 TTCCTCATCA
* * *
143819 TCC TCC TCC TCC TCC TCC TCA TCC TCG TCC TCA TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
143860 ATCGTCATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.05, C:0.59, G:0.02, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:143834 original size:12 final size:12
Alignment explanation
Indices: 143810--143859 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
143800 AGAGTCGTCT
*
143810 TCCTCATCATCC
1 TCCTCATCCTCC
*
143822 TCCTCCTCCTCC
1 TCCTCATCCTCC
*
143834 TCCTCATCCTCG
1 TCCTCATCCTCC
143846 TCCTCATCCTCC
1 TCCTCATCCTCC
143858 TC
1 TC
143860 ATCGTCATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.08, C:0.56, G:0.02, T:0.34
Consensus pattern (12 bp):
TCCTCATCCTCC
Found at i:143860 original size:9 final size:9
Alignment explanation
Indices: 143810--143862 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 9
143800 AGAGTCGTCT
*
143810 TCCTCATCA
1 TCCTCATCC
*
143819 TCCTCCTCC
1 TCCTCATCC
*
143828 TCCTCCTCC
1 TCCTCATCC
* * *
143837 TCATCCTCG
1 TCCTCATCC
143846 TCCTCATCC
1 TCCTCATCC
143855 TCCTCATC
1 TCCTCATC
143863 GTCATCATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.09, C:0.55, G:0.02, T:0.34
Consensus pattern (9 bp):
TCCTCATCC
Found at i:146983 original size:23 final size:23
Alignment explanation
Indices: 146953--146998 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
146943 CATTTGTCAC
146953 CCATCATATATTTTCCAATCCCT
1 CCATCATATATTTTCCAATCCCT
146976 CCATCATATATTTTCCAATCCCT
1 CCATCATATATTTTCCAATCCCT
146999 TATTAATGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (23 bp):
CCATCATATATTTTCCAATCCCT
Found at i:155413 original size:23 final size:22
Alignment explanation
Indices: 155359--155461 Score: 79
Period size: 22 Copynumber: 4.6 Consensus size: 22
155349 TAATGTCCCT
*
155359 ATGAAATTTTGATCTA-CATACT-
1 ATGAAATTTTGAT-AACCAT-CTA
*
155381 ATGAAATTTTGATAACCCTCTA
1 ATGAAATTTTGATAACCATCTA
* * *
155403 ATGGAAATTTTGAAAACTAAACT-
1 AT-GAAATTTTGATAAC-CATCTA
*
155426 ATGAAATTTTGATAACCTTC-A
1 ATGAAATTTTGATAACCATCTA
155447 TATGAAATTTTGATA
1 -ATGAAATTTTGATA
155462 TCCTCCGTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 4 0.06
22 44 0.68
23 15 0.23
24 2 0.03
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (22 bp):
ATGAAATTTTGATAACCATCTA
Found at i:155474 original size:20 final size:20
Alignment explanation
Indices: 155427--155497 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
155417 AACTAAACTA
* *
155427 TGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATATCCTTC--C
155449 TGAAATTTTGATATCC-TCC
1 TGAAATTTTGATATCCTTCC
*
155468 GTGAAATTTTGATTTCCTTCC
1 -TGAAATTTTGATATCCTTCC
155489 TGAAATTTT
1 TGAAATTTT
155498 AATTACTCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
20 24 0.55
21 5 0.11
22 15 0.34
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.45
Consensus pattern (20 bp):
TGAAATTTTGATATCCTTCC
Found at i:156674 original size:22 final size:22
Alignment explanation
Indices: 156624--156675 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
156614 TCACATTTTG
156624 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
156645 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
156667 AAAATTTTG
1 AAAATTTTG
156676 TTGACCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 3 0.11
22 25 0.89
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:157100 original size:24 final size:21
Alignment explanation
Indices: 157039--157125 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 21
157029 TTGTTATAAT
157039 TAACC-ACCTTATGAAATTTCAA
1 TAACCAACC-TATGAAATTT-AA
*
157061 TAACCAACCTAGGAAATATTAA
1 TAACCAACCTATGAAAT-TTAA
* *
157083 TAACCTGATCCTATGAAATTTTAG
1 TAACC--AACCTATGAAA-TTTAA
157107 TAACC-ACACTATGAAATTT
1 TAACCAAC-CTATGAAATTT
157126 TGATAACTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
21 4 0.07
22 27 0.50
23 5 0.09
24 17 0.31
25 1 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (21 bp):
TAACCAACCTATGAAATTTAA
Found at i:157121 original size:22 final size:21
Alignment explanation
Indices: 157093--157190 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 21
157083 TAACCTGATC
157093 CTATGAAATTTTAGTAACCACA
1 CTATGAAATTTT-GTAACCACA
157115 CTATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTG-TAAC--CACA
157138 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTT-GTAACCACA
* *
157159 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTG-TAACCACA
157180 CTCATGAAATT
1 CT-ATGAAATT
157191 GTAATAACCA
Statistics
Matches: 65, Mismatches: 3, Indels: 16
0.77 0.04 0.19
Matches are distributed among these distances:
20 1 0.02
21 6 0.09
22 54 0.83
23 3 0.05
24 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (21 bp):
CTATGAAATTTTGTAACCACA
Found at i:157123 original size:46 final size:45
Alignment explanation
Indices: 157048--157221 Score: 155
Period size: 44 Copynumber: 3.9 Consensus size: 45
157038 TTAACCACCT
* * * * *
157048 TATGAAATTTCAATAACCA-ACCTAGGAAATATTAATAACCTGATCC-
1 TATGAAATTTTAGTAACCACA-CTATGAAATTTTGATAACCT--TCCA
157094 TATGAAATTTTAGTAACCACACTATGAAATTTTGATAA-CTTCCA
1 TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACCTTCCA
* *
157138 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCC-
1 TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACCTTCCA
* * *
157181 TCATGAAATTGTAATAACCATC-TTAT-AAATTTTTGATAACC
1 T-ATGAAATTTTAGTAACCA-CACTATGAAA-TTTTGATAACC
157222 ACATACAGAC
Statistics
Matches: 110, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
44 68 0.62
45 4 0.04
46 31 0.28
47 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (45 bp):
TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACCTTCCA
Found at i:157154 original size:44 final size:43
Alignment explanation
Indices: 157091--157221 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 43
157081 AATAACCTGA
*
157091 TCCTATGAAATTTTAGTAACCACACTATGAAATTTTGATAACT
1 TCCTATGAAATTTTAGTAACCACACTATGAAATTTTGATAACC
* *
157134 TCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC
1 TCC-TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACC
* * *
157178 TCCTCATGAAATTGTAATAACCATC-TTAT-AAATTTTTGATAACC
1 TCCT-ATGAAATTTTAGTAACCA-CACTATGAAA-TTTTGATAACC
157222 ACATACAGAC
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
43 6 0.08
44 69 0.91
45 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (43 bp):
TCCTATGAAATTTTAGTAACCACACTATGAAATTTTGATAACC
Found at i:161090 original size:23 final size:24
Alignment explanation
Indices: 161046--161093 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
161036 CCAAACAATC
161046 TTGAGCACTCTCGCTCGATCTCTAT
1 TTGAGCACTCTC-CTCGATCTCTAT
*
161071 TTGAGCACTCT-CTCGGTCTCTAT
1 TTGAGCACTCTCCTCGATCTCTAT
161094 AAATTAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
25 11 0.50
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.38
Consensus pattern (24 bp):
TTGAGCACTCTCCTCGATCTCTAT
Found at i:162418 original size:23 final size:24
Alignment explanation
Indices: 162375--162421 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
162365 CGAAACAATC
162375 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTC-CTCGGTCTCTAT
162400 TTGAGCACTCT-CTCGGTCTCTA
1 TTGAGCACTCTCCTCGGTCTCTA
162422 CAAATTAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.50
25 11 0.50
ACGTcount: A:0.13, C:0.32, G:0.19, T:0.36
Consensus pattern (24 bp):
TTGAGCACTCTCCTCGGTCTCTAT
Found at i:172003 original size:21 final size:20
Alignment explanation
Indices: 171953--172004 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
171943 CTAGCGCTGG
* *
171953 GCGCCCATGTGGTATGCTTG
1 GCGCCCATGTGGTATGCCTC
* *
171973 GCACCCCATGTGGTTTGCCTC
1 GC-GCCCATGTGGTATGCCTC
171994 GCGCCGCATGT
1 GCGCC-CATGT
172005 ACTCCAGTGC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.10, C:0.33, G:0.31, T:0.27
Consensus pattern (20 bp):
GCGCCCATGTGGTATGCCTC
Found at i:176782 original size:37 final size:38
Alignment explanation
Indices: 176740--176818 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
176730 ACATGATTAT
* * *
176740 TCATAAAGTTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTTATGTATATATGAAAAGACATGATGTTGA
176777 TCATAAAGTTATGTATATATGAAAAGACATGTATGTTGA
1 TCATAAAGTTATGTATATATGAAAAGACATG-ATGTTGA
176816 TCA
1 TCA
176819 AGTATATAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 28 0.76
39 9 0.24
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTATATATGAAAAGACATGATGTTGA
Found at i:178144 original size:31 final size:32
Alignment explanation
Indices: 178106--178167 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
178096 TGGGGGTGTC
178106 TTGGTTTCTTAAAGAAAC-AAAGAGATATATG
1 TTGGTTTCTTAAAGAAACAAAAGAGATATATG
* *
178137 TTGGTTTCTTAGAGAAACAAAAGAGTTATAT
1 TTGGTTTCTTAAAGAAACAAAAGAGATATAT
178168 CACTATGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (32 bp):
TTGGTTTCTTAAAGAAACAAAAGAGATATATG
Found at i:179400 original size:37 final size:38
Alignment explanation
Indices: 179358--179436 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 38
179348 ACATGATTAT
* *
179358 TCATAAAGTTATGTCTATTTGGAAAGACATG-TGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
179395 TCATAAAGTTATGTCTATATGAAAAGACATGTATGTTGA
1 TCATAAAGTTATGTCTATATGAAAAGACATG-ATGTTGA
179434 TCA
1 TCA
179437 AGTATATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 29 0.76
39 9 0.24
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (38 bp):
TCATAAAGTTATGTCTATATGAAAAGACATGATGTTGA
Found at i:181093 original size:48 final size:48
Alignment explanation
Indices: 181038--181134 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
181028 AAGTTGTTGC
*
181038 AGCATTATTTGAATTCAAATATCGAATCCTTCTGTCTCTGGTTTCCTT
1 AGCATTATTTGAATTCAAATATCGAATCCTTCTATCTCTGGTTTCCTT
181086 AGCATTATTTGAATTCAAATATCGAATCCTTCTATCTCTGGTTTCCTT
1 AGCATTATTTGAATTCAAATATCGAATCCTTCTATCTCTGGTTTCCTT
181134 A
1 A
181135 TTATAGGATG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (48 bp):
AGCATTATTTGAATTCAAATATCGAATCCTTCTATCTCTGGTTTCCTT
Done.