Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014039.1 Kokia drynarioides strain JFW-HI SEQ_129070, 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: 50039
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--42 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1 AT AT AT AT AT AT 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 AT AT AT AT AT AT
43 GATCGGACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:909 original size:15 final size:15
Alignment explanation
Indices: 891--921 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
881 GATTTAAACT
891 CTATACATTTTTATC
1 CTATACATTTTTATC
906 CTATACATTTTTATC
1 CTATACATTTTTATC
921 C
1 C
922 CTTAGGATTT
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:0.26, C:0.23, G:0.00, T:0.52
Consensus pattern (15 bp):
CTATACATTTTTATC
Found at i:1002 original size:123 final size:119
Alignment explanation
Indices: 782--1093 Score: 475
Period size: 123 Copynumber: 2.7 Consensus size: 119
772 GGATTTAAAC
782 TCTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCATT
1 TCTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCATT
847 AATATCTTTGTATTTACAATTGAGAGCCCTAAGGGATTTAAACTCTATACATTTTT
66 AATATCTTTGTATTTACAATTGAGAGCCCTAAGGGATTTAAACTCTATACA--TTT
903 ATCCTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCA
1 -T-CTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCA
* *
968 TTAATATCTTTGTATTTATAATTGAGAGTCCTAAGGGATTTAAACTCTATACATTT
64 TTAATATCTTTGTATTTACAATTGAGAGCCCTAAGGGATTTAAACTCTATACATTT
* *
1024 T-TAT-C-------T--CTTAGGATTTACATTAATTACTCTGGTAACTTTATACATTCATTCATT
1 TCTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCATT
1078 AATATCTTTGTATTTA
66 AATATCTTTGTATTTA
1094 GCAAATGTTT
Statistics
Matches: 185, Mismatches: 4, Indels: 16
0.90 0.02 0.08
Matches are distributed among these distances:
108 62 0.34
110 1 0.01
117 1 0.01
118 3 0.02
120 1 0.01
121 3 0.02
122 1 0.01
123 113 0.61
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.45
Consensus pattern (119 bp):
TCTATACATTTTTATCCCTTAGGATTTACATTAATTACCCTGGTAACTCTATACATTCATTCATT
AATATCTTTGTATTTACAATTGAGAGCCCTAAGGGATTTAAACTCTATACATTT
Found at i:2741 original size:63 final size:65
Alignment explanation
Indices: 2651--2832 Score: 245
Period size: 63 Copynumber: 2.9 Consensus size: 65
2641 TTTGTTATTT
2651 ATTTATTTATTTATATTCAT-AAAAT-AATAAATAAATAATAAAATAAAATAAATATTATTTTAC
1 ATTTATTTATTTATATTCATAAAAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTAC
2714 ATTTATTTATTTATATTCATACAATAATAAATAAATAAATAATAAAATAAAATAAATATTATTTT
1 ATTTATTTATTTATATTCATA-AA-AATAAATAAATAAATAATAAAATAAAATAAATATTATTTT
2779 --
64 AC
* * *
2779 A--TATTTATTTATATTTATAAAAAT-ATTAAATAAATAAAAATAATAAGAA-AAATA
1 ATTTATTTATTTATATTCATAAAAATAAATAAATAAATAATAA-AATAA-AATAAATA
2833 AAATAAGGTT
Statistics
Matches: 110, Mismatches: 3, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
60 14 0.13
61 13 0.12
62 4 0.04
63 37 0.34
65 3 0.03
66 3 0.03
67 36 0.33
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (65 bp):
ATTTATTTATTTATATTCATAAAAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTAC
Found at i:2817 original size:17 final size:18
Alignment explanation
Indices: 2795--2835 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2785 ATTTATATTT
* *
2795 ATAAAAATATTAA-ATAA
1 ATAAAAATAATAAGAAAA
2812 ATAAAAATAATAAGAAAA
1 ATAAAAATAATAAGAAAA
2830 ATAAAA
1 ATAAAA
2836 TAAGGTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (18 bp):
ATAAAAATAATAAGAAAA
Found at i:3527 original size:39 final size:39
Alignment explanation
Indices: 3484--3817 Score: 206
Period size: 39 Copynumber: 8.4 Consensus size: 39
3474 CCTCTGGTTA
* *
3484 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATAATTG
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGATCG
*
3523 GGGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGATCG
* * *** * **
3562 GGGTAAAAGATTGGATGGTCTTCAATCTTGCCTTTTGGTTA
1 GGGTAAAAGATTGGATTG-CTTCAATC-TACCCCATGATCG
** *
3603 GGGTAAAAGATTGGATTTTTTCAATCTGCCCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGATCG
* * * * * * * **
3642 AGGTAAAAGATCGAATGGTCTTCAATTTTGCCCTC-TGGTTA
1 GGGTAAAAGATTGGATTG-CTTCAA-TCTACCC-CATGATCG
* * ** *
3683 AGGTAAAATATTGGATTTTTTTCAATCTGCCCCATGATCG
1 GGGTAAAAGATTGGA-TTGCTTCAATCTACCCCATGATCG
* * * * **
3723 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTC-TGGTTA
1 GGGTAAAAGATTGGATTG-CTTCAATC-TACCC-CATGATCG
* * * * *
3764 GGATAAAAGATTGAATTTCTTCAATTTTCCCCATGATCG
1 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGATCG
*
3803 GGGT-AAAGATCGGAT
1 GGGTAAAAGATTGGAT
3818 GGTTTTCAAT
Statistics
Matches: 221, Mismatches: 63, Indels: 23
0.72 0.21 0.07
Matches are distributed among these distances:
38 10 0.05
39 84 0.38
40 55 0.25
41 69 0.31
42 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (39 bp):
GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGATCG
Found at i:3627 original size:80 final size:80
Alignment explanation
Indices: 3523--3857 Score: 501
Period size: 80 Copynumber: 4.2 Consensus size: 80
3513 CCCATAATTG
* *
3523 GGGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* *
3588 CTTGCCTTTTGGTTA
66 CTTGCCCTCTGGTTA
* * *
3603 GGGTAAAAGATTGGATTTTTTCAATCTGCCCCATGATCGAGGTAAAAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
3668 TTTGCCCTCTGGTTA
66 CTTGCCCTCTGGTTA
* * *
3683 AGGTAAAATATTGGATTTTTTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
1 GGGTAAAAGATTGGA-TTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAA
3748 TCTTGCCCTCTGGTTA
65 TCTTGCCCTCTGGTTA
* * * * *
3764 GGATAAAAGATTGAATTTCTTCAATTTTCCCCATGATCGGGGT-AAAGATCGGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
*
3828 CTTGCCCTTTGGTTA
66 CTTGCCCTCTGGTTA
3843 GGGTAAAAGATTGGA
1 GGGTAAAAGATTGGA
3858 GGTTGTAACT
Statistics
Matches: 230, Mismatches: 24, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
79 47 0.20
80 110 0.48
81 73 0.32
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
CTTGCCCTCTGGTTA
Found at i:3726 original size:161 final size:159
Alignment explanation
Indices: 3524--3857 Score: 497
Period size: 161 Copynumber: 2.1 Consensus size: 159
3514 CCATAATTGG
*
3524 GGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATTGGATGGTCTTCAATC
1 GGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATC
* * * * *
3589 TTGCCTTTTGGTTAGGGTAAAAGATTGGATTTTTTCAATCTGCCCCATGATCGAGGTAAAAGATC
66 TTGCCCTCTGGTTAGGATAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGAGGT-AAAGATC
*
3654 GAATGGTCTTCAATTTTGCCCTCTGGTTAA
130 GAATGGTCTTCAATCTTGCCCTCTGGTTAA
* * *
3684 GGTAAAATATTGGATTTTTTTCAATCTGCCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
1 GGTAAAAGATTGGA-TTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAAT
* * *
3749 CTTGCCCTCTGGTTAGGATAAAAGATTGAATTTCTTCAATTTTCCCCATGATCGGGGTAAAGATC
65 CTTGCCCTCTGGTTAGGATAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGAGGTAAAGATC
* * * *
3814 GGATGGTTTTCAATCTTGCCCTTTGGTTAG
130 GAATGGTCTTCAATCTTGCCCTCTGGTTAA
3844 GGTAAAAGATTGGA
1 GGTAAAAGATTGGA
3858 GGTTGTAACT
Statistics
Matches: 155, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
160 58 0.37
161 97 0.63
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (159 bp):
GGTAAAAGATTGGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGGATGGTCTTCAATC
TTGCCCTCTGGTTAGGATAAAAGATTGAATTTCTTCAATCTGCCCCATGATCGAGGTAAAGATCG
AATGGTCTTCAATCTTGCCCTCTGGTTAA
Found at i:4014 original size:50 final size:50
Alignment explanation
Indices: 3924--4102 Score: 152
Period size: 50 Copynumber: 3.6 Consensus size: 50
3914 CAATCTTCTC
* * * * *
3924 CTCTACAGCTTTAAGTGAATGAGATTTGCCATTACAGTTTCATTCTGCCT
1 CTCTACAGCTTTAGGTGTATAAGATTTGTCATTGCAGTTTCATTCTGCCT
* *
3974 CTCTACAGCTTTAGGTGTATAAGATTTGTCTTTGCGGTTTCAATT-TGCAC-
1 CTCTACAGCTTTAGGTGTATAAGATTTGTCATTGCAGTTTC-ATTCTGC-CT
* * * *
4024 CTCCACAGTTTTAGGTGTATCAGATTT-TCCATTGCAGTTTCAGTCTGTACCT
1 CTCTACAGCTTTAGGTGTATAAGATTTGT-CATTGCAGTTTCATTCTG--CCT
* * *
4076 C-C-ACAACTTTAGGAGTAAAAGATTTGT
1 CTCTACAGCTTTAGGTGTATAAGATTTGT
4103 TGTTATATCG
Statistics
Matches: 103, Mismatches: 18, Indels: 15
0.76 0.13 0.11
Matches are distributed among these distances:
49 3 0.03
50 91 0.88
51 7 0.07
52 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (50 bp):
CTCTACAGCTTTAGGTGTATAAGATTTGTCATTGCAGTTTCATTCTGCCT
Found at i:5035 original size:12 final size:13
Alignment explanation
Indices: 5004--5046 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
4994 GACCTCCCCT
* *
5004 TTTTCTTTCTCTT
1 TTTTCTTTTTCTC
5017 TTCTTCTTTTTC-C
1 TT-TTCTTTTTCTC
5030 TTTTCTTTTTCTC
1 TTTTCTTTTTCTC
5043 TTTT
1 TTTT
5047 TCTCTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 9 0.35
13 9 0.35
14 8 0.31
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTTTCTC
Found at i:5044 original size:28 final size:27
Alignment explanation
Indices: 5001--5055 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
4991 CTCGACCTCC
5001 CCTTTTTCTTTCTC-TTTTCTTCTTTTT
1 CCTTTTTCTTTCTCTTTTTC-TCTTTTT
*
5028 CCTTTTCTTTTTCTCTTTTTCTCTTTTT
1 CCTTTT-TCTTTCTCTTTTTCTCTTTTT
5056 TTTTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 14 0.56
29 5 0.20
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (27 bp):
CCTTTTTCTTTCTCTTTTTCTCTTTTT
Found at i:5059 original size:20 final size:20
Alignment explanation
Indices: 5002--5078 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
4992 TCGACCTCCC
* *
5002 CTTTTTCT-TTCTCTTTTCTT
1 CTTTTTCTCTTTTTTTTTC-T
5022 CTTTTTC-CTTTTCTTTTTCT
1 CTTTTTCTCTTTT-TTTTTCT
5042 CTTTTTCTCTTTTTTTTT-T
1 CTTTTTCTCTTTTTTTTTCT
** *
5061 AATTTTGTCTTTTTTTTT
1 CTTTTTCTCTTTTTTTTT
5079 GAAATTTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
19 16 0.33
20 23 0.47
21 10 0.20
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (20 bp):
CTTTTTCTCTTTTTTTTTCT
Found at i:5066 original size:28 final size:29
Alignment explanation
Indices: 5001--5074 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 29
4991 CTCGACCTCC
*
5001 CCTTTT-TCTTTCTC-TTTTCTTCTTTTT
1 CCTTTTATTTTTCTCTTTTTCTTCTTTTT
*
5028 CCTTTTCTTTTTCTCTTTTTC-TCTTTTT
1 CCTTTTATTTTTCTCTTTTTCTTCTTTTT
* * *
5056 -TTTTTAATTTTGTCTTTTT
1 CCTTTTATTTTTCTCTTTTT
5075 TTTTGAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 21 0.52
28 14 0.35
29 5 0.12
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (29 bp):
CCTTTTATTTTTCTCTTTTTCTTCTTTTT
Found at i:5074 original size:8 final size:8
Alignment explanation
Indices: 5009--5055 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
4999 CCCCTTTTTC
5009 TTTCTC-T
1 TTTCTCTT
5016 TTTCTTCTT
1 TTTC-TCTT
5025 TTTC-C--
1 TTTCTCTT
5030 TTT-TCTT
1 TTTCTCTT
5037 TTTCTCTT
1 TTTCTCTT
5045 TTTCTCTT
1 TTTCTCTT
5053 TTT
1 TTT
5056 TTTTTAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
5 4 0.12
7 8 0.24
8 17 0.50
9 5 0.15
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTCTCTT
Found at i:5084 original size:20 final size:19
Alignment explanation
Indices: 5044--5085 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
5034 CTTTTTCTCT
*
5044 TTTTCTCTTTTTTTTTTAA
1 TTTTCTCTTTTTTTTTAAA
*
5063 TTTTGTCTTTTTTTTTGAAA
1 TTTTCTCTTTTTTTTT-AAA
5083 TTT
1 TTT
5086 CTTCCTCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTCTCTTTTTTTTTAAA
Found at i:5959 original size:11 final size:11
Alignment explanation
Indices: 5945--5974 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5935 TCATCTTGAC
5945 TTTTTCTTTCT
1 TTTTTCTTTCT
*
5956 TTTTTCTTTTT
1 TTTTTCTTTCT
5967 TTTTTCTT
1 TTTTTCTT
5975 AGGTTTCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:10165 original size:71 final size:73
Alignment explanation
Indices: 10086--10260 Score: 225
Period size: 71 Copynumber: 2.4 Consensus size: 73
10076 TATATTCATA
* * *
10086 AAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTA-TT-TATTTATATTCAT-
1 AAATAATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTTATAATAATA
10148 ACAATAAT
66 ACAATAAT
* *
10156 AAATAAATAAATAAATAATAAAATAAAATAAATATTATTTTATATTTATTTATATTTATAATAAT
1 AAAT-AATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTTATAATAAT
*
10221 AATAATAAT
65 AACAATAAT
*
10230 -AATAATAAATAAACATAATAAGA-AAAATAAA
1 AAATAATAAAT-AA-ATAATAAAACAAAATAAA
10261 ATGAAGTTTC
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
70 4 0.04
71 40 0.43
72 9 0.10
73 24 0.26
74 15 0.16
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.38
Consensus pattern (73 bp):
AAATAATAAATAAATAATAAAACAAAATAAATATTATTTTACATTTATTTATATTTATAATAATA
ACAATAAT
Found at i:10202 original size:63 final size:61
Alignment explanation
Indices: 10063--10234 Score: 179
Period size: 63 Copynumber: 2.7 Consensus size: 61
10053 TGTTATTTAT
* * *
10063 TTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATTAATATTATT
1 TTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATAATA
* *
10124 TTACATTTATTTATTTATATTCATACAATAATAAATAAATAAATAAATAATAAAATAAA-ATAAA
1 TT--ATTTATTTATTTATATTCATAAAATAATAAATAAAT-AAT-AA-AACAAAATAAATAT-AA
10188 TA
60 TA
*
10190 TTATTTTATATTTATTTATATTTATAATAATAAT-AAT-AATAATAA
1 TTA--TT-TATTTATTTATATTCATAA-AATAATAAATAAATAATAA
10235 TAAATAAACA
Statistics
Matches: 94, Mismatches: 7, Indels: 17
0.80 0.06 0.14
Matches are distributed among these distances:
61 2 0.02
63 35 0.37
64 6 0.06
65 7 0.07
66 18 0.19
67 20 0.21
68 6 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (61 bp):
TTATTTATTTATTTATATTCATAAAATAATAAATAAATAATAAAACAAAATAAATATAATA
Found at i:10221 original size:3 final size:3
Alignment explanation
Indices: 10213--10250 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
10203 ATTTATATTT
10213 ATA ATA ATA ATA ATA ATA ATA ATAA ATA A-A CATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA -ATA ATA A
10251 GAAAAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 1 0.03
3 27 0.84
4 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:13964 original size:28 final size:28
Alignment explanation
Indices: 13918--13979 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
13908 AAATGAGACT
13918 TTTTGGATACCCGACGGTAAAATGGTAA
1 TTTTGGATACCCGACGGTAAAATGGTAA
* * *
13946 TTTTGGATTCTCGAGGGTAAAATGGTAA
1 TTTTGGATACCCGACGGTAAAATGGTAA
13974 TTTTGG
1 TTTTGG
13980 GAAATTTTGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGATACCCGACGGTAAAATGGTAA
Found at i:14091 original size:28 final size:28
Alignment explanation
Indices: 14004--14151 Score: 79
Period size: 28 Copynumber: 5.1 Consensus size: 28
13994 TAAAAATGAA
* *
14004 TTTTAGACATCCGAGGGT-AAACGGTAAT
1 TTTTAGACATTCGA-GGTAAAATGGTAAT
* * * *
14032 TTTTAGAAAAATCGAGATAAAAAAT-ATAAT
1 TTTTAG-ACATTCGAGGT--AAAATGGTAAT
*
14062 TTTTGGACATTCGAGGTAAAATGGTAAT
1 TTTTAGACATTCGAGGTAAAATGGTAAT
**
14090 TTTTAGAGTTTCGAGGTCAAAAATGG--AT
1 TTTTAGACATTCGAGGT--AAAATGGTAAT
* * * *
14118 TTTTTGACATTTGGGGGGTAAAGTGGTAAT
1 TTTTAGACA-TT-CGAGGTAAAATGGTAAT
14148 TTTT
1 TTTT
14152 TAAAGTTTTG
Statistics
Matches: 89, Mismatches: 20, Indels: 20
0.69 0.16 0.16
Matches are distributed among these distances:
27 5 0.06
28 40 0.45
29 15 0.17
30 26 0.29
31 3 0.03
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (28 bp):
TTTTAGACATTCGAGGTAAAATGGTAAT
Found at i:14172 original size:59 final size:58
Alignment explanation
Indices: 14079--14386 Score: 182
Period size: 59 Copynumber: 5.3 Consensus size: 58
14069 CATTCGAGGT
* * * * *
14079 AAAATGGTAA-TTTTTAGAGTTTCGAGGTCAAAAATGGATTTTTTGACATTTGGGGGGT-
1 AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAATGGATTTTTAGA-ATTT-GGGGGTA
* * * *
14137 AAAGTGGTAATTTTTTAAAGTTTTGGGGTTAAAAATAGAATTTTTAGAGGTTTGGAGGTA
1 AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAAT-GGATTTTTAGA-ATTTGGGGGTA
* ** * *
14197 AAAAT-GTGATTTTCAAAAGTTTTAGGGTTAAAAATGGAATTTTTAGAAGTTCGGGGGTA
1 AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAATGG-ATTTTTAGAA-TTTGGGGGTA
* ** * * * *
14256 AAAATAG-AATTTTTGGAAGTTTAGGGG-TAAAAATGTGATTTTCAAAAGTTTTGGGGTCA
1 AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAATG-GATTTTTAGAA-TTTGGGGGT-A
* * * ** ** * **
14315 TAAATTG-AATTTGTGGAAGTTCAGGGG-TAAAAATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAATGG-ATTTTTAGAA-TTTGGGGGTA
14373 AAAATGG-AATTTTT
1 AAAATGGTAATTTTT
14387 GGAAGTTCGG
Statistics
Matches: 200, Mismatches: 41, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
58 47 0.23
59 136 0.68
60 17 0.09
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (58 bp):
AAAATGGTAATTTTTTAAAGTTTTGGGGTTAAAAATGGATTTTTAGAATTTGGGGGTA
Found at i:14305 original size:58 final size:58
Alignment explanation
Indices: 14161--14428 Score: 236
Period size: 59 Copynumber: 4.6 Consensus size: 58
14151 TTAAAGTTTT
* * * *** *
14161 GGGGTTAAAAATAGAATTTTTAGAGGTTT-GGAGGTAAAAAT-GTGATTTTCAAAAGTTTTA
1 GGGG-TAAAAATGGAATTTTTAGAAGTTTAGG-GGTAAAAATAG-AATTTTTGGAAG-TTCA
* ** *
14221 GGGTTAAAAATGGAATTTTTAGAAGTTCGGGGGTAAAAATAGAATTTTTGGAAGTTTA
1 GGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGTTCA
* * * * * *
14279 GGGGTAAAAATGTG-ATTTTCAAAAGTTTTGGGGTCATAAATTGAATTTGTGGAAGTTCA
1 GGGGTAAAAATG-GAATTTTTAGAAGTTTAGGGGT-AAAAATAGAATTTTTGGAAGTTCA
* * * *
14338 GGGGTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGTTCA
** *
14396 GGGGTAAAAATATAATTTTTGGACAGTTTAGGG
1 GGGGTAAAAATGGAATTTTTAGA-AGTTTAGGG
14429 TCCTCTAGTG
Statistics
Matches: 173, Mismatches: 29, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
58 73 0.42
59 94 0.54
60 6 0.03
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (58 bp):
GGGGTAAAAATGGAATTTTTAGAAGTTTAGGGGTAAAAATAGAATTTTTGGAAGTTCA
Found at i:14393 original size:88 final size:88
Alignment explanation
Indices: 14161--14378 Score: 312
Period size: 88 Copynumber: 2.5 Consensus size: 88
14151 TTAAAGTTTT
* *
14161 GGGGTTAAAAATAGAATTTTTAGAGGTTT-GGAGGTAAAAATGTGATTTTCAAAAGTTTTAGGGT
1 GGGG-TAAAAATAGAATTTTTGGAAGTTTAGG-GGTAAAAATGTGATTTTCAAAAGTTTTAGGGT
* * *
14225 TAAAAATGGAATTTTTAGAAGTTCG
64 CAAAAATGGAATTTGTAGAAGTTCA
*
14250 GGGGTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTCAAAAGTTTTGGGGTCA
1 GGGGTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTCAAAAGTTTTAGGGTCA
* * *
14315 TAAATTGAATTTGTGGAAGTTCA
66 AAAATGGAATTTGTAGAAGTTCA
* *
14338 GGGGTAAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATG
1 GGGGTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATG
14379 GAATTTTTGG
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
88 111 0.95
89 6 0.05
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (88 bp):
GGGGTAAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGTGATTTTCAAAAGTTTTAGGGTCA
AAAATGGAATTTGTAGAAGTTCA
Found at i:14416 original size:29 final size:29
Alignment explanation
Indices: 14220--14428 Score: 213
Period size: 29 Copynumber: 7.1 Consensus size: 29
14210 CAAAAGTTTT
* *
14220 AGGGTTAAAAATGGAATTTTTAGAAGTTC
1 AGGGGTAAAAATGGAATTTTTGGAAGTTC
* * *
14249 GGGGGTAAAAATAGAATTTTTGGAAGTTT
1 AGGGGTAAAAATGGAATTTTTGGAAGTTC
*** *
14278 AGGGGTAAAAATGTG-ATTTTCAAAAGTTT
1 AGGGGTAAAAATG-GAATTTTTGGAAGTTC
* * * *
14307 TGGGGTCATAAATTGAATTTGTGGAAGTTC
1 AGGGGT-AAAAATGGAATTTTTGGAAGTTC
*
14337 AGGGGTAAAAATGGAATTTTTGGAAGTTT
1 AGGGGTAAAAATGGAATTTTTGGAAGTTC
*
14366 AAGGGTAAAAATGGAATTTTTGGAAGTTC
1 AGGGGTAAAAATGGAATTTTTGGAAGTTC
* ** *
14395 GGGGGTAAAAATATAATTTTTGGACAGTTT
1 AGGGGTAAAAATGGAATTTTTGGA-AGTTC
14425 AGGG
1 AGGG
14429 TCCTCTAGTG
Statistics
Matches: 145, Mismatches: 31, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
29 118 0.81
30 27 0.19
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
AGGGGTAAAAATGGAATTTTTGGAAGTTC
Found at i:14429 original size:29 final size:28
Alignment explanation
Indices: 14166--14429 Score: 190
Period size: 29 Copynumber: 9.0 Consensus size: 28
14156 GTTTTGGGGT
* * * *
14166 TAAAAATAGAATTTTTAGAGGTTTGGAGG
1 TAAAAATGGAATTTTTGGAAGTTTAG-GG
***
14195 TAAAAATGTG-ATTTTCAAAAGTTTTAGGG
1 TAAAAATG-GAATTTTTGGAAG-TTTAGGG
* **
14224 TTAAAAATGGAATTTTTAGAAGTTCGGGGG
1 -TAAAAATGGAATTTTTGGAAGTT-TAGGG
*
14254 TAAAAATAGAATTTTTGGAAGTTTAGGGG
1 TAAAAATGGAATTTTTGGAAGTTTA-GGG
*** *
14283 TAAAAATGTG-ATTTTCAAAAGTTTTGGGG
1 TAAAAATG-GAATTTTTGGAAG-TTTAGGG
* * * *
14312 TCATAAATTGAATTTGTGGAAGTTCAGGGG
1 T-AAAAATGGAATTTTTGGAAGTTTA-GGG
14342 TAAAAATGGAATTTTTGGAAGTTTAAGGG
1 TAAAAATGGAATTTTTGGAAGTTT-AGGG
**
14371 TAAAAATGGAATTTTTGGAAGTTCGGGGG
1 TAAAAATGGAATTTTTGGAAGTT-TAGGG
**
14400 TAAAAATATAATTTTTGGACAGTTTAGGG
1 TAAAAATGGAATTTTTGGA-AGTTTAGGG
14429 T
1 T
14430 CCTCTAGTGT
Statistics
Matches: 185, Mismatches: 36, Indels: 28
0.74 0.14 0.11
Matches are distributed among these distances:
29 135 0.73
30 50 0.27
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:15498 original size:9 final size:9
Alignment explanation
Indices: 15474--15518 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
15464 TTTTATTTAA
*
15474 TATTAATAC
1 TATTATTAC
15483 TATTTATTAC
1 TA-TTATTAC
*
15493 TATTATTAT
1 TATTATTAC
*
15502 TATTATTAT
1 TATTATTAC
15511 TATTATTA
1 TATTATTA
15519 TTAACCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
9 25 0.76
10 8 0.24
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (9 bp):
TATTATTAC
Found at i:15501 original size:3 final size:3
Alignment explanation
Indices: 15486--15521 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
15476 TTAATACTAT
*
15486 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15522 ACCATTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:16287 original size:17 final size:17
Alignment explanation
Indices: 16265--16322 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
16255 AATTAACCTT
*
16265 AATTTACAATGAATTTA
1 AATTTAAAATGAATTTA
*
16282 AATTTAAAATAAATTTA
1 AATTTAAAATGAATTTA
**
16299 AACTCAAAAATGAATTTA
1 AA-TTTAAAATGAATTTA
16317 AATTTA
1 AATTTA
16323 GAAAAAAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAAATGAATTTA
Found at i:16332 original size:18 final size:17
Alignment explanation
Indices: 16276--16342 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
16266 ATTTACAATG
*
16276 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAAAA
* * *
16293 AATTTAAACTCAAAAATG
1 AATTTAAATTTAAAAA-A
16311 AATTTAAATTTAGAAAAA
1 AATTTAAATTTA-AAAAA
* *
16329 AATTCAAACTTAAA
1 AATTTAAATTTAAA
16343 GTAAATTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
17 15 0.38
18 20 0.51
19 4 0.10
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (17 bp):
AATTTAAATTTAAAAAA
Found at i:17064 original size:206 final size:206
Alignment explanation
Indices: 16700--17707 Score: 1318
Period size: 206 Copynumber: 4.9 Consensus size: 206
16690 TCTGGTTCTA
* * * ** ** **
16700 TTGACTTGGCCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* * * * *
16765 CTCTGTGTTTCATCAGGAAGACGAATTTGGTTCACTTCTCCGTATCTCATCAGGAAGCTAA-CAT
66 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA-
* * * * **
16829 TTTTATTGCTTCGCCCTACTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGATTTACTCGCA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAA
* *
16894 TTGAGCGTGGGT
195 TCGAGAGTGGGT
* *
16906 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCTCGTCGTTTATTTCAATCTGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* * * * * *
16971 CTTTATATCTCATTAGGAAGACAAATTTGGTCCACTTCTCAATATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
17036 TTTATTGCTTTGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAAT
17101 CGAGAGTGGGT
196 CGAGAGTGGGT
* * *
17112 TTGATTTGGTCTTCTTCTTAGTATCTCATCAAGAAGATGACCGCGTCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* *
17177 CTCTGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAATCAT
66 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* ** * ** *
17242 TTTATTGCTTCGACCTGCTTCTCAATGCCTCATTAGGAAGCTGGAATTCGAAGATTTTCTCAAAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAAT
*
17307 CGAGCGTGGGT
196 CGAGAGTGGGT
* *
17318 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACGTCGTTTGTTTCAATCTACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* * * *
17383 CTCTGTGTCTCATCAAGAAGAC-AGATTTGGTCCATTTCTCAGTATCTCATTAGAAAGCTAACCA
66 CTCTGTATCTCATCAAGAAGACGA-ATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
** * * **
17447 TTTTATTGCTTCGACCTGCTTCTCAGTGCCTCATTAGAAAGCTGGGGTTCGAAGATTTGCTCGTA
130 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAA
* *
17512 TTGAGAGTGAGT
195 TCGAGAGTGGGT
*
17524 TTGATTTGGTCTTCTTCTCAGTATCTCATTAGGAAGATGACCGCGTCGTTTGTTTCAATCTG-TT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
* *
17588 -TC----TCT--TCATGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * *
17646 TTTATTGATTCGA-CTCGCTTCTTAGTATCTCATCAGGAAGTTGGGATTCGAAGATTTGCTCA
131 TTTATTGCTTCGACCT-GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
17708 CCTTTTGAGT
Statistics
Matches: 707, Mismatches: 91, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
197 2 0.00
198 96 0.14
199 1 0.00
200 3 0.00
204 2 0.00
205 2 0.00
206 599 0.85
207 2 0.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATCTGCTT
CTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAAAT
CGAGAGTGGGT
Found at i:17916 original size:78 final size:79
Alignment explanation
Indices: 17792--18078 Score: 395
Period size: 78 Copynumber: 3.7 Consensus size: 79
17782 TACCCCGTGA
* * * * * *
17792 TCGGGGTAGGAGTTTGGTTGACGATGATCTGCCCCAAGCCCGGGGTAAGAGATCGAATGGC-TCT
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTTC-
*
17856 AATCTGCCTCT-GAC
65 AATCTGCCTCTAGGC
* * *
17870 TCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAAACTCAGGGTAA-ATGATCAAATGACTTC
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGA-GATCAAATGACTTC
17934 AATCTGCC-CTAGGC
65 AATCTGCCTCTAGGC
* * *
17948 TCGAGGTAAGAGATTGGTTGATTATGATCTGCCCCAAGCTCGGGGTAAAAGATCAAATGACTTCA
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTTCA
18013 ATCTG-CTCTAGGC
66 ATCTGCCTCTAGGC
*
18026 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGCTCGGGGTAAGAGAT
1 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGAT
18079 TGGTTAACGA
Statistics
Matches: 185, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
77 4 0.02
78 178 0.96
79 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (79 bp):
TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAAGCTCGGGGTAAGAGATCAAATGACTTCA
ATCTGCCTCTAGGC
Found at i:18056 original size:39 final size:38
Alignment explanation
Indices: 17792--18083 Score: 167
Period size: 39 Copynumber: 7.5 Consensus size: 38
17782 TACCCCGTGA
* * * *
17792 TCGGGGTAGGAGTTTGGTTGACGATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGA-TATGATCTGCCCCAGGC
* * * * * * * * * *
17831 CCGGGGTAAGAGATCGAATGGCTCTAATCTGCCTCTGAC
1 TCGGGGTAAGAGATTG-GTTGATATGATCTGCCCCAGGC
* **
17870 TCGGGGTAAGAGATTGGTTGATGATGATTTGCCCCAAAC
1 TCGGGGTAAGAGATTGGTTGAT-ATGATCTGCCCCAGGC
* **** * *
17909 TCAGGGTAA-ATGATCAAATGACT-TCAATCTGCCCTAGGC
1 TCGGGGTAAGA-GATTGGTTGA-TAT-GATCTGCCCCAGGC
* *
17948 TCGAGGTAAGAGATTGGTTGATTATGATCTGCCCCAAGC
1 TCGGGGTAAGAGATTGGTTGA-TATGATCTGCCCCAGGC
* **** * * *
17987 TCGGGGTAAAAGATCAAATGACT-TCAATCTGCTCTAGGC
1 TCGGGGTAAGAGATTGGTTGA-TAT-GATCTGCCCCAGGC
18026 TCGGGGTAAGAGATTGGTTGATGATGATCTGCCCCAGGC
1 TCGGGGTAAGAGATTGGTTGAT-ATGATCTGCCCCAGGC
18065 TCGGGGTAAGAGATTGGTT
1 TCGGGGTAAGAGATTGGTT
18084 AACGATGTAA
Statistics
Matches: 179, Mismatches: 64, Indels: 20
0.68 0.24 0.08
Matches are distributed among these distances:
38 7 0.04
39 166 0.93
40 6 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (38 bp):
TCGGGGTAAGAGATTGGTTGATATGATCTGCCCCAGGC
Found at i:18230 original size:51 final size:51
Alignment explanation
Indices: 18157--18331 Score: 142
Period size: 51 Copynumber: 3.5 Consensus size: 51
18147 TTATTCCAAC
* *
18157 TTTACTGTAACTTCAG-GAAGATAGGATTTGATGTTGAAGCTTCATCTTACT
1 TTTACTGCAACTTCAGAG-AGATAGGAATTGATGTTGAAGCTTCATCTTACT
* * * * * *** * **
18208 TTTACTACAACTTCAGAGAGATAAAGACTTGCTATTG-TTTTTAATCAAAC-
1 TTTACTGCAACTTCAGAGAGAT-AGGAATTGATGTTGAAGCTTCATCTTACT
* * *
18258 TTTACTGCAACTTCA-AGAGGATAGGAATTGACGTTAAAGCTTCATCTTGCT
1 TTTACTGCAACTTCAGAGA-GATAGGAATTGATGTTGAAGCTTCATCTTACT
*
18309 CTTACTGCAACTTCAGAGAGATA
1 TTTACTGCAACTTCAGAGAGATA
18332 AAGACTTGCT
Statistics
Matches: 91, Mismatches: 27, Indels: 12
0.70 0.21 0.09
Matches are distributed among these distances:
49 11 0.12
50 23 0.25
51 43 0.47
52 14 0.15
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (51 bp):
TTTACTGCAACTTCAGAGAGATAGGAATTGATGTTGAAGCTTCATCTTACT
Found at i:18298 original size:101 final size:101
Alignment explanation
Indices: 18145--18343 Score: 299
Period size: 101 Copynumber: 2.0 Consensus size: 101
18135 GCTGCTGTAG
* * * * * * * *
18145 TTTTATTCCAACTTTACTGTAACTTCAGGAAGATAGGATTTGATGTTGAAGCTTCATCTTACTTT
1 TTTTAATCAAACTTTACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTACTCT
18210 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
* *
18246 TTTTAATCAAACTTTACTGCAACTTCAAGAGGATAGGAATTGACGTTAAAGCTTCATCTTGCTCT
1 TTTTAATCAAACTTTACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTACTCT
*
18311 TACTGCAACTTCAGAGAGATAAAGACTTGCTAT
66 TACTACAACTTCAGAGAGATAAAGACTTGCTAT
18344 AGTAGTTTTG
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (101 bp):
TTTTAATCAAACTTTACTGCAACTTCAAGAAGATAGGAATTGACGTTAAAGCTTCATCTTACTCT
TACTACAACTTCAGAGAGATAAAGACTTGCTATTGT
Found at i:18619 original size:100 final size:100
Alignment explanation
Indices: 18432--18996 Score: 499
Period size: 100 Copynumber: 5.7 Consensus size: 100
18422 CAAGGTATCG
* * * *** * * *
18432 GGTTCACCATTACGACTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTGGA-CTCGCCGTTGCG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATC-CGCCATTGCG
* * *
18496 G-CTTAAATATTTCTC-TTCTTGTCTTCTGAGGTTCACA
65 GTCTTAAATCTTTCCCGTT-ATGTCTTCTGAGGTT-A-A
* ** * * * * *
18533 -GTCCGTCATTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
* *
18597 TC-TAGATCTTTCCCTTTATGTCTT-TGAGG-TACTA
66 TCTTAAATCTTTCCCGTTATGTCTTCTGAGGTTA--A
* * * * *** * * *
18631 GGTCCGCCATTGCGACTTAAACCTTTCCC--TTGTGTCTTCATGATACTGGATCCACCATTG-TG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
* * * *
18693 ACTTAGATCTTTCCAGTTATGTC-TCTGAGGTAAAA
66 TCTTAAATCTTTCCCGTTATGTCTTCTGAGGT-TAA
* * * * *
18728 GGTTCACCGTTGCTACTTAAACCCTTCCCTTTTGTATCTTTGCGATATTGGATCCGCTATTGCGG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
* * * *
18793 TCTTAAATCTTTCCAGTCATGT-TTCTAATGTATAA
66 TCTTAAATCTTTCCCGTTATGTCTTCTGAGGT-TAA
*
18828 GGTTCACCGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
* * *
18893 TATTAAATCTTTCTCGTCATGTC-TCTGAGGTATAA
66 TCTTAAATCTTTCCCGTTATGTCTTCTGAGGT-TAA
* *
18928 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTATTGGATCCGCCGTTGCGG
1 GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
18993 TCTT
66 TCTT
18997 GGATCCTTCC
Statistics
Matches: 388, Mismatches: 62, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
96 3 0.01
97 73 0.19
98 2 0.01
99 56 0.14
100 250 0.64
101 4 0.01
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (100 bp):
GGTTCACCATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGG
TCTTAAATCTTTCCCGTTATGTCTTCTGAGGTTAA
Found at i:19014 original size:100 final size:100
Alignment explanation
Indices: 18539--19014 Score: 539
Period size: 100 Copynumber: 4.8 Consensus size: 100
18529 CACAGTCCGT
* * * * *
18539 CATTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGATCCGCCGTTACGGTC-TAGA
1 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * * * *
18603 TCTTTCCCTTTATGTCTTTGAGGTACT-AGGTCCGC
66 TCTTTCCCGTCATGTCTCTGAGGTA-TAAGGTTCAC
* * *** * * * *
18638 CATTGCGACTTAAACCTTTCCC--TTGTGTCTTCATGATACTGGATCCACCATTG-TGACTTAGA
1 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * *
18700 TCTTTCCAGTTATGTCTCTGAGGTAAAAGGTTCAC
66 TCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCAC
* * * * * *
18735 CGTTGCTACTTAAACCCTTCCCTTTTGTATCTTTGCGATATTGGATCCGCTATTGCGGTCTTAAA
1 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* * * *
18800 TCTTTCCAGTCATGTTTCTAATGTATAAGGTTCAC
66 TCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCAC
* * *
18835 CGTTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTATTAAA
1 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
*
18900 TCTTTCTCGTCATGTCTCTGAGGTATAAGGTTCAC
66 TCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCAC
* * *
18935 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTATTGGATCCGCCGTTGCGGTCTTGGA
1 CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
* *
19000 TCCTTCCCGCCATGT
66 TCTTTCCCGTCATGT
19015 TTCATGGTGC
Statistics
Matches: 319, Mismatches: 53, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
96 2 0.01
97 75 0.24
99 45 0.14
100 197 0.62
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (100 bp):
CATTGCGACTTAAACCCTTCCCTTTTGTATCTTTGCGGTACTGGATCCGCCATTGCGGTCTTAGA
TCTTTCCCGTCATGTCTCTGAGGTATAAGGTTCAC
Found at i:20227 original size:17 final size:16
Alignment explanation
Indices: 20205--20252 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 16
20195 GACCTCTCCC
20205 TTTTTCTATTTTTTTTG
1 TTTTTCT-TTTTTTTTG
20222 TTTTTCTTCTTGTTTTTG
1 TTTTTCTT-TT-TTTTTG
20240 CTTTTCTCTTTTT
1 -TTTT-TCTTTTT
20253 CTTTCTATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 9 0.33
18 7 0.26
19 6 0.22
20 4 0.15
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.79
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTG
Found at i:20234 original size:12 final size:12
Alignment explanation
Indices: 20222--20285 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
20212 ATTTTTTTTG
*
20222 TTTTTCTTCTTG
1 TTTTTCTTCTTC
20234 TTTTTGCTT-TTC
1 TTTTT-CTTCTTC
*
20246 TCTTT-TTCTT-
1 TTTTTCTTCTTC
*
20256 TCTATTCTTCTTC
1 T-TTTTCTTCTTC
*
20269 TTCTTCTTCTTC
1 TTTTTCTTCTTC
20281 TTTTT
1 TTTTT
20286 ATTGTATCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
10 3 0.07
11 4 0.10
12 30 0.73
13 4 0.10
ACGTcount: A:0.02, C:0.22, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:20272 original size:18 final size:19
Alignment explanation
Indices: 20225--20273 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
20215 TTTTTTGTTT
* *
20225 TTCTTCTTGTT-TTTGCTT
1 TTCTTCTTCTTCTTTGCTA
*
20243 TTC-TCTTTTTCTTT-CTA
1 TTCTTCTTCTTCTTTGCTA
20260 TTCTTCTTCTTCTT
1 TTCTTCTTCTTCTT
20274 CTTCTTCTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.02, C:0.22, G:0.04, T:0.71
Consensus pattern (19 bp):
TTCTTCTTCTTCTTTGCTA
Found at i:25149 original size:29 final size:30
Alignment explanation
Indices: 25117--25178 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
25107 AAAATGAGAC
25117 TTTTTGGATAC-CCAGGGGCAAAATGGTAA
1 TTTTTGGATACTCCAGGGGCAAAATGGTAA
* ** *
25146 -TTTTGGATTCTCGGGGGGTAAAATGGTAA
1 TTTTTGGATACTCCAGGGGCAAAATGGTAA
25175 TTTT
1 TTTT
25179 GGGAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
28 9 0.33
29 15 0.56
30 3 0.11
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.35
Consensus pattern (30 bp):
TTTTTGGATACTCCAGGGGCAAAATGGTAA
Found at i:25284 original size:29 final size:29
Alignment explanation
Indices: 25252--25731 Score: 327
Period size: 29 Copynumber: 16.5 Consensus size: 29
25242 AATCGAGATA
*
25252 AAAAATAGAATTTTTGGACA-TTCGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGT
* **
25281 -AAAATGGTAATTTTTAG-AGTTTC-GGCCT
1 AAAAATGG-AATTTTTGGAAG-TTCGGGGGT
* * *
25309 TAAAATGG-ATTTTTGGACA-TTTGGGGGG
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGT
* * * *
25337 CAAAGTGGTAATTTTTGAAAGTTTCGGGGTT
1 AAAAATGG-AATTTTTGGAAG-TTCGGGGGT
*
25368 AAAAATGGAATTTTTGGAGGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
** * *
25397 AAAAATGTG-ATTTTTAAAAGTTTTGGGGTT
1 AAAAATG-GAATTTTTGGAAG-TTCGGGGGT
* *
25427 AAAATTAGAATTTTTGGAAGTTCGGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* * * *
25456 AAAATTAGAATTTTTGGAAGTTTGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
** **
25485 AAAAATGTG-ATTTTTAAAAGTTTC-GATGT
1 AAAAATG-GAATTTTTGGAAG-TTCGGGGGT
*
25514 CAAAAAAT-TAATTTTTGGAAGTTCGGGGGT
1 --AAAAATGGAATTTTTGGAAGTTCGGGGGT
**
25544 AAAAATGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* **
25573 TAAAATGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* **
25602 TAAAATGGAATTTTTGGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *
25631 TAAAATGGAATTTTTGGAAGTT-TGGGGT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
* *** * * *
25659 TAAAATGTG-ATTTTCAAAAGTTTTGAGGTT
1 AAAAATG-GAATTTTTGGAAG-TTCGGGGGT
* *
25689 AAAAATGGAATTTTTGGAAGTTTGGGGAT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGT
*
25718 AAAAATGTAATTTT
1 AAAAATGGAATTTT
25732 CGAATAATTT
Statistics
Matches: 363, Mismatches: 63, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
27 10 0.03
28 44 0.12
29 219 0.60
30 72 0.20
31 18 0.05
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGT
Found at i:25506 original size:58 final size:59
Alignment explanation
Indices: 25259--25731 Score: 344
Period size: 59 Copynumber: 8.1 Consensus size: 59
25249 ATAAAAAATA
* ** *
25259 GAATTTTTGGACA--TTCGGGGGTAAAA-TGGTAATTTTTAG-AGTTTCGGCCTTAAAATG-
1 GAATTTTTGGA-AGTTTCGGGGGTAAAATTGG-AATTTTTGGAAGTTT-GGGGTAAAAATGT
** * *
25316 G-ATTTTTGGACA-TTT-GGGGGGCAAAGTGGTAATTTTTGAAAGTTTCGGGGTTAAAAATG-
1 GAATTTTTGGA-AGTTTCGGGGGTAAAATTGG-AATTTTTGGAAGTTT-GGGG-TAAAAATGT
* * ** *
25375 GAATTTTTGG-AGGTTCGGGGGTAAAAATGTG-ATTTTTAAAAGTTTTGGGGTTAAAAT-T
1 GAATTTTTGGAAGTTTCGGGGGTAAAATTG-GAATTTTTGGAAG-TTTGGGGTAAAAATGT
*
25433 AGAATTTTTGGAAG-TTCGGGGGTAAAATTAGAATTTTTGGAAGTTTGAGGGTAAAAATGT
1 -GAATTTTTGGAAGTTTCGGGGGTAAAATTGGAATTTTTGGAAGTTTG-GGGTAAAAATGT
** ** *
25493 G-ATTTTTAAAAGTTTC-GATGTCAAAAAATT--AATTTTTGGAAGTTCGGGGGTAAAAATG-
1 GAATTTTTGGAAGTTTCGGGGGT---AAAATTGGAATTTTTGGAAGTT-TGGGGTAAAAATGT
* * *
25551 GAATTTTTGGAAGTTTTGGGGTTAAAA-TGGAATTTTTGGAAGTTTTGGGGTTAAAATG-
1 GAATTTTTGGAAGTTTCGGGGGTAAAATTGGAATTTTTGGAAG-TTTGGGGTAAAAATGT
* * *
25609 GAATTTTTGGAAGTTTTGGGGTTAAAA-TGGAATTTTTGGAAGTTTGGGGTTAAAATGT
1 GAATTTTTGGAAGTTTCGGGGGTAAAATTGGAATTTTTGGAAGTTTGGGGTAAAAATGT
*** * * * *
25667 G-ATTTTCAAAAGTTTTGAGGTTAAAAATGGAATTTTTGGAAGTTTGGGGATAAAAATGT
1 GAATTTTTGGAAGTTTCGGGGGTAAAATTGGAATTTTTGGAAGTTTGGGG-TAAAAATGT
25726 -AATTTT
1 GAATTTT
25732 CGAATAATTT
Statistics
Matches: 351, Mismatches: 36, Indels: 56
0.79 0.08 0.13
Matches are distributed among these distances:
56 20 0.06
57 54 0.15
58 121 0.34
59 122 0.35
60 27 0.08
61 7 0.02
ACGTcount: A:0.31, C:0.03, G:0.28, T:0.38
Consensus pattern (59 bp):
GAATTTTTGGAAGTTTCGGGGGTAAAATTGGAATTTTTGGAAGTTTGGGGTAAAAATGT
Found at i:26434 original size:17 final size:17
Alignment explanation
Indices: 26412--26469 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
26402 AATTAACCTT
*
26412 AATTTACAATGAATTTA
1 AATTTAAAATGAATTTA
*
26429 AATTTAAAATAAATTTA
1 AATTTAAAATGAATTTA
**
26446 AACTCAAAAATGAATTTA
1 AA-TTTAAAATGAATTTA
26464 AATTTA
1 AATTTA
26470 GAAAAAATTC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AATTTAAAATGAATTTA
Found at i:26461 original size:18 final size:17
Alignment explanation
Indices: 26419--26466 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
26409 CTTAATTTAC
**
26419 AATGAATTTAAATTTAA
1 AATGAATTTAAATCAAA
*
26436 AATAAATTTAAACTCAAA
1 AATGAATTTAAA-TCAAA
26454 AATGAATTTAAAT
1 AATGAATTTAAAT
26467 TTAGAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (17 bp):
AATGAATTTAAATCAAA
Found at i:27081 original size:30 final size:29
Alignment explanation
Indices: 27045--27159 Score: 94
Period size: 30 Copynumber: 4.0 Consensus size: 29
27035 CCAACTTTAA
*
27045 AAAAAAAATATAAAGTTTAAGTATCAAATT
1 AAAAAAAATATAAA-TTTAAATATCAAATT
* *
27075 AAAAAAAATGTCAAATTTAAATATTAAATT
1 AAAAAAAATAT-AAATTTAAATATCAAATT
** *
27105 GGACAAAA-A-AAA-TTAAATA-CTAAATT
1 AAAAAAAATATAAATTTAAATATC-AAATT
* *
27131 AAAAAAAATATTAAGTTAAAATATCAAAT
1 AAAAAAAATA-TAAATTTAAATATCAAAT
27160 ATTATATTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
26 17 0.26
27 4 0.06
29 2 0.03
30 38 0.58
31 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (29 bp):
AAAAAAAATATAAATTTAAATATCAAATT
Found at i:30252 original size:30 final size:30
Alignment explanation
Indices: 30192--30316 Score: 173
Period size: 30 Copynumber: 4.2 Consensus size: 30
30182 ATGTAGGACA
30192 ATATCAAAGAACAACCACAAAGGC-TTCAC
1 ATATCAAAGAACAACCACAAAGGCTTTCAC
30221 ATATCAAAGAACAACCACAAAGGCTTTCAC
1 ATATCAAAGAACAACCACAAAGGCTTTCAC
*
30251 ATATCATAA-AACAGCCACAAAGGCTTTCAC
1 ATATCA-AAGAACAACCACAAAGGCTTTCAC
*** * *
30281 ATATTGGAGAACAGCCATAAAGGCTTTCAC
1 ATATCAAAGAACAACCACAAAGGCTTTCAC
30311 ATATCA
1 ATATCA
30317 CATTCTGCCA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
29 25 0.29
30 59 0.69
31 2 0.02
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (30 bp):
ATATCAAAGAACAACCACAAAGGCTTTCAC
Found at i:35382 original size:473 final size:478
Alignment explanation
Indices: 34469--35411 Score: 1486
Period size: 473 Copynumber: 2.0 Consensus size: 478
34459 CATCGACTTA
*
34469 AAATTGATATATAATATTACAAATTGTATCAAAATTTACGAATAATTTTAATATTTATCATATTA
1 AAATTGATATATAACATTACAAATTGTATCAAAATTTACGAATAATTTTAATATTTATCATATTA
*
34534 TATTAAGCTCAATCCACTATATTTTTTAAAACTATCATTGACATGTATAAAGATAGTCTAAAAAT
66 TATTAAGCTCAATCCACTATATTTTTTAAAACTATCATTGACATGTATAAAGAGAGTC-----A-
34599 TATATATATATATATATTAAAAAATCTAAAATATAAATTCTATCAAATAAATTTTAAAAGTTATT
125 TATATATATATATATATT---AAATCTAAAATATAAATTCTATCAAATAAATTTTAAAAGTTATT
* * * *
34664 TATTGTTAAAAAATATAATTGCAGCATTGTGCGGGCACGCCCAACCCTAGGGTAGTTTGGGAGTG
187 TATTGTTAAAAAATATAATTACAACATTGTGCGAGCACGCCCAACCCTAGGATAGTTTGGGAGTG
* * * *
34729 TAGCCATCTAGACCCCAGGATTGGAAGGGGTCCAAAAAAATTTCTTTAGTTTTAAGGTGGACATT
252 TAGCCATCCAGAACCCAGGATTGAAAGGGGCCCAAAAAAATTTCTTTAGTTTTAAGGTGGACATT
* * *
34794 CTTTTTCAACCTTTCAAATTTTATGATTGACGTTTCATTGCAGGTAAAAAAATAATAAAATAAAA
317 CTTTTTCAACCTTTCAAATTTTATGATTGACGCTTCATTGCAAGAAAAAAAATAATAAAATAAAA
*
34859 TAAAAAAGTCTCAATTTTTTATTTGATTATATTACATTTTATAATTTTTTTTAAAAGATCCCAAT
382 TAAAAAAGTCTCAAGTTTTTATTTGATTATATTACATTTTATAATTTTTTTTAAAAGATCCCAAT
34924 TTATTGTTTCACCTAAAACCCAAAAATGTATC
447 TTATTGTTTCACCTAAAACCCAAAAATGTATC
34956 AAATTGATATATAACATTACAAATTGTATCAAAATTTACGAATAATTTTAATATTTATCATATTA
1 AAATTGATATATAACATTACAAATTGTATCAAAATTTACGAATAATTTTAATATTTATCATATTA
35021 -ATTAAGCTCAATCCACTATATTTTTTAAAACTATCATTGACATGTATAAAGAGAGTC-TA-ATA
66 TATTAAGCTCAATCCACTATATTTTTTAAAACTATCATTGACATGTATAAAGAGAGTCATATATA
35083 TATATATATA-T-AATCTAAAATATAAATTCTATCAAATAAATTTTAAAAGTTATTTATTGTTAA
131 TATATATATATTAAATCTAAAATATAAATTCTATCAAATAAATTTTAAAAGTTATTTATTGTTAA
* **** * * *
35146 AAAATATAATTACAACATTGTGCGAGCAGGTTTGACTCTAGGATAGTTTGGGAGTGTGGCCGTCC
196 AAAATATAATTACAACATTGTGCGAGCACGCCCAACCCTAGGATAGTTTGGGAGTGTAGCCATCC
*
35211 AGAACCCAGGGTTGAAAGGGGCCCAAAAAAATTTCTTTAGTTTTTAAGGTGGACATTCTTTTTCA
261 AGAACCCAGGATTGAAAGGGGCCCAAAAAAATTTCTTTAG-TTTTAAGGTGGACATTCTTTTTCA
** * *
35276 ACCTTTCAAATTTTATGATTGGTGCTTCATTGCAAGAAAAAAAATAATAAAATAAAGTAAAAGAG
325 ACCTTTCAAATTTTATGATTGACGCTTCATTGCAAGAAAAAAAATAATAAAATAAAATAAAAAAG
* *
35341 T-T-AAGTTTTTATTTGATTATATTATATTTTATAATTTTTTTTAAAAGATCTCAATTTATTGTT
390 TCTCAAGTTTTTATTTGATTATATTACATTTTATAATTTTTTTTAAAAGATCCCAATTTATTGTT
35404 TCACCTAA
455 TCACCTAA
35412 GGCCTAAAAA
Statistics
Matches: 426, Mismatches: 29, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
472 66 0.15
473 141 0.33
474 83 0.19
477 1 0.00
478 13 0.03
479 2 0.00
486 56 0.13
487 64 0.15
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (478 bp):
AAATTGATATATAACATTACAAATTGTATCAAAATTTACGAATAATTTTAATATTTATCATATTA
TATTAAGCTCAATCCACTATATTTTTTAAAACTATCATTGACATGTATAAAGAGAGTCATATATA
TATATATATATTAAATCTAAAATATAAATTCTATCAAATAAATTTTAAAAGTTATTTATTGTTAA
AAAATATAATTACAACATTGTGCGAGCACGCCCAACCCTAGGATAGTTTGGGAGTGTAGCCATCC
AGAACCCAGGATTGAAAGGGGCCCAAAAAAATTTCTTTAGTTTTAAGGTGGACATTCTTTTTCAA
CCTTTCAAATTTTATGATTGACGCTTCATTGCAAGAAAAAAAATAATAAAATAAAATAAAAAAGT
CTCAAGTTTTTATTTGATTATATTACATTTTATAATTTTTTTTAAAAGATCCCAATTTATTGTTT
CACCTAAAACCCAAAAATGTATC
Found at i:38640 original size:36 final size:36
Alignment explanation
Indices: 38593--38669 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
38583 TAATAGTAAA
** *
38593 AATAATAATAAAATAATAGTTATATAATATCCAAAT
1 AATAATAATAAAATAATAGCAATATAATAACCAAAT
*
38629 AATAATAATAAAATAGTAGCAATATAATAACCAAAT
1 AATAATAATAAAATAATAGCAATATAATAACCAAAT
*
38665 TATAA
1 AATAA
38670 CAAATTAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (36 bp):
AATAATAATAAAATAATAGCAATATAATAACCAAAT
Found at i:45965 original size:22 final size:22
Alignment explanation
Indices: 45938--45983 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
45928 ATAGGAAGGT
45938 TAACTAATAGATATAAATTACA
1 TAACTAATAGATATAAATTACA
45960 TAACTAATAGATATAAATTACA
1 TAACTAATAGATATAAATTACA
45982 TA
1 TA
45984 CTTATCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (22 bp):
TAACTAATAGATATAAATTACA
Found at i:49520 original size:4 final size:4
Alignment explanation
Indices: 49507--49545 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
49497 AAAATTGAAG
*
49507 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAA
49546 GAAGAAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:49537 original size:21 final size:20
Alignment explanation
Indices: 49507--49547 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
49497 AAAATTGAAG
49507 GAAAAAAGAAAGAAAAAAGA
1 GAAAAAAGAAAGAAAAAAGA
*
49527 GAAAGAAAGAAAGAAAGAAGA
1 GAAA-AAAGAAAGAAAAAAGA
49548 AGAAGGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
GAAAAAAGAAAGAAAAAAGA
Found at i:49557 original size:25 final size:25
Alignment explanation
Indices: 49503--49587 Score: 74
Period size: 25 Copynumber: 3.6 Consensus size: 25
49493 AACGAAAATT
*
49503 GAAGGAAAAAAGAAAG-AA-AA-AA
1 GAAGGAAGAAAGAAAGAAAGAAGAA
*
49525 G-AGAAAGAAAGAAAGAAAGAAGAA
1 GAAGGAAGAAAGAAAGAAAGAAGAA
* * *
49549 GAAGGAAGAATGAGAAGAACG-GGAA
1 GAAGGAAGAAAGA-AAGAAAGAAGAA
49574 GAAGG-AGAAAGAAA
1 GAAGGAAGAAAGAAA
49588 AAAAAAAGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
21 12 0.24
22 3 0.06
23 4 0.08
24 9 0.18
25 17 0.33
26 6 0.12
ACGTcount: A:0.66, C:0.01, G:0.32, T:0.01
Consensus pattern (25 bp):
GAAGGAAGAAAGAAAGAAAGAAGAA
Done.