Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 7 of 21
Found at i:654902 original size:46 final size:47
Alignment explanation
Indices: 654812--654909 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 47
654802 TATATTATAA
* * *
654812 AAATTTAAAACTAATATAATAGTACATATTATAATATATTTAAATAT
1 AAATATAAAAATAATATAATAGTACATAATATAATATATTTAAATAT
* *
654859 AAATATAAAAATAATATAATA-TTCATAATATAATATTTTTAAATAT
1 AAATATAAAAATAATATAATAGTACATAATATAATATATTTAAATAT
654905 AAATA
1 AAATA
654910 ATAGGAAGAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
46 27 0.59
47 19 0.41
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (47 bp):
AAATATAAAAATAATATAATAGTACATAATATAATATATTTAAATAT
Found at i:656200 original size:18 final size:19
Alignment explanation
Indices: 656163--656201 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
656153 CGTTGGAGCC
*
656163 TTTTTAATTTTTTATAATA
1 TTTTTAATTTTATATAATA
*
656182 TTTTTAA-TTTATATTATA
1 TTTTTAATTTTATATAATA
656200 TT
1 TT
656202 AGGTTATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTAATTTTATATAATA
Found at i:657116 original size:12 final size:12
Alignment explanation
Indices: 657099--657142 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
657089 ACTACTTTTT
657099 TCTCTCTTTCTC
1 TCTCTCTTTCTC
*
657111 TCTCTCTTTCTT
1 TCTCTCTTTCTC
*
657123 TTTCT-TTTCTC
1 TCTCTCTTTCTC
*
657134 TTTCTCTTT
1 TCTCTCTTT
657143 TTTTCCTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.36
12 18 0.64
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (12 bp):
TCTCTCTTTCTC
Found at i:657119 original size:23 final size:22
Alignment explanation
Indices: 657071--657145 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
657061 AAAATACAAT
657071 TTTTTTCTCTTTTCT-TTTACTAC
1 TTTTTTCTCTTTTCTCTTT-CT-C
*
657094 TTTTTTCTCTCTTTCTCTCTCTC
1 TTTTTTCTCT-TTTCTCTTTCTC
*
657117 TTTCTTTTTCTTTTCTCTTTCTC
1 TTT-TTTCTCTTTTCTCTTTCTC
657140 TTTTTT
1 TTTTTT
657146 TCCTTTTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
22 3 0.07
23 28 0.61
24 13 0.28
25 2 0.04
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTTCTCTTTTCTCTTTCTC
Found at i:657153 original size:9 final size:10
Alignment explanation
Indices: 657070--657155 Score: 50
Period size: 12 Copynumber: 7.7 Consensus size: 10
657060 AAAAATACAA
657070 TTTTTTTCTC
1 TTTTTTTCTC
657080 TTTTCTTTTACTAC
1 -TTT-TTTT-CT-C
657094 TTTTTTCTCTC
1 TTTTTT-TCTC
*
657105 TTTCTCTCTCTC
1 TTT-T-TTTCTC
657117 TTTCTTTT-TC
1 TTT-TTTTCTC
657127 TTTTCTCTTTCTC
1 -TTT-T-TTTCTC
657140 TTTTTTTC-C
1 TTTTTTTCTC
657149 TTTTTTT
1 TTTTTTT
657156 TCCCTGCTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
9 8 0.12
10 6 0.09
11 15 0.23
12 25 0.39
13 9 0.14
14 1 0.02
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:657257 original size:12 final size:12
Alignment explanation
Indices: 657240--657273 Score: 61
Period size: 11 Copynumber: 2.9 Consensus size: 12
657230 CTCATTTCTC
657240 TTTTTCCTTTTT
1 TTTTTCCTTTTT
657252 TTTTT-CTTTTT
1 TTTTTCCTTTTT
657263 TTTTTCCTTTT
1 TTTTTCCTTTT
657274 CCTTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTCCTTTTT
Found at i:658196 original size:22 final size:21
Alignment explanation
Indices: 658160--658204 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
658150 TTATGTTTGG
658160 ATGAAAGGGAAATAGAGGAAGA
1 ATGAAAGGGAAATAG-GGAAGA
* * *
658182 ATGAAAGTGAGATAGGTAAGA
1 ATGAAAGGGAAATAGGGAAGA
658203 AT
1 AT
658205 CTTTTCTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.51, C:0.00, G:0.33, T:0.16
Consensus pattern (21 bp):
ATGAAAGGGAAATAGGGAAGA
Found at i:659525 original size:2 final size:2
Alignment explanation
Indices: 659518--659560 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
659508 CTTGTCTAAT
659518 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
659560 T
1 T
659561 TGGCATGCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:659948 original size:15 final size:17
Alignment explanation
Indices: 659924--659964 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
659914 TTTATAAATT
*
659924 TTTATATAATTT-A-TA
1 TTTATTTAATTTGACTA
659939 TTTATTTAATTTGACTA
1 TTTATTTAATTTGACTA
659956 TTATATTTA
1 TT-TATTTA
659965 TAATCTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 11 0.50
16 1 0.05
17 4 0.18
18 6 0.27
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (17 bp):
TTTATTTAATTTGACTA
Found at i:661677 original size:10 final size:10
Alignment explanation
Indices: 661662--661744 Score: 59
Period size: 10 Copynumber: 8.3 Consensus size: 10
661652 TTAGATCATG
661662 TTTATATATT
1 TTTATATATT
661672 TTTATATATT
1 TTTATATATT
*
661682 TCTATTATATT
1 TTTA-TATATT
661693 TATT-T-TATT
1 T-TTATATATT
661702 TTTA-AT-TT
1 TTTATATATT
*
661710 TATATTATATT
1 TTTA-TATATT
661721 TTATAATATATT
1 TT-T-ATATATT
*
661733 TTAAT-TATT
1 TTTATATATT
661742 TTT
1 TTT
661745 TAATTTTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
8 7 0.12
9 12 0.21
10 18 0.31
11 10 0.17
12 10 0.17
13 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATATT
Found at i:661721 original size:12 final size:12
Alignment explanation
Indices: 661686--661766 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
661676 TATATTTCTA
661686 TTATATT-TATT
1 TTATATTATATT
*
661697 TTAT-TTTTAATT
1 TTATATTAT-ATT
661709 TTATATTATATT
1 TTATATTATATT
*
661721 TTATAATATATT
1 TTATATTATATT
*
661733 TTA-ATTATTTT
1 TTATATTATATT
* *
661744 TTA-ATTTTAAAT
1 TTATATTAT-ATT
661756 TTATATTATAT
1 TTATATTATAT
661767 CTAAAATTAT
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 2 0.04
11 18 0.32
12 29 0.52
13 7 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTATATT
Found at i:662017 original size:27 final size:26
Alignment explanation
Indices: 661987--662068 Score: 73
Period size: 27 Copynumber: 3.2 Consensus size: 26
661977 AATTATTTTA
*
661987 AAAAATAATTAAAATATAATAT-GAT
1 AAAAATAATTAAAATATAATATAAAT
662012 ATAAAA-AATATATAAATATAATATAAAT
1 A-AAAATAAT-TA-AAATATAATATAAAT
* *
662040 ATAAATATATTAAAAT-TTATAT-AAT
1 AAAAATA-ATTAAAATATAATATAAAT
662065 AAAA
1 AAAA
662069 TTATTAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
25 10 0.21
26 11 0.23
27 18 0.38
28 6 0.13
29 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (26 bp):
AAAAATAATTAAAATATAATATAAAT
Found at i:662027 original size:28 final size:28
Alignment explanation
Indices: 661985--662044 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
661975 ATAATTATTT
*
661985 TAAAAAATAATTAAAATATAATAT-GATA
1 TAAAAAATAATT-AAATATAATATAAATA
662013 TAAAAAAT-ATATAAATATAATATAAATA
1 TAAAAAATAAT-TAAATATAATATAAATA
662041 TAAA
1 TAAA
662045 TATATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (28 bp):
TAAAAAATAATTAAATATAATATAAATA
Found at i:662030 original size:17 final size:17
Alignment explanation
Indices: 661991--662079 Score: 58
Period size: 17 Copynumber: 5.2 Consensus size: 17
661981 ATTTTAAAAA
*
661991 ATAATTAAAATATAATAT
1 ATAATAAAAATATAA-AT
*
662009 GATATAAAAAATATATAAAT
1 -ATA-ATAAAA-ATATAAAT
*
662029 ATAATATAAATATAAAT
1 ATAATAAAAATATAAAT
* *
662046 AT-ATTAAAAT-T-TAT
1 ATAATAAAAATATAAAT
* *
662060 ATAATAAAATTATTAAT
1 ATAATAAAAATATAAAT
662077 ATA
1 ATA
662080 TCAAATTTTA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
14 4 0.07
15 7 0.13
16 7 0.13
17 15 0.27
18 4 0.07
19 6 0.11
20 6 0.11
21 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (17 bp):
ATAATAAAAATATAAAT
Found at i:662065 original size:31 final size:30
Alignment explanation
Indices: 662027--662111 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
662017 AAATATATAA
662027 ATATAATATAAATATAAATATATTAAAATTT
1 ATATAATA-AAATATAAATATATTAAAATTT
* *
662058 ATATAATAAAATTATTAATATA-TCAAATTT
1 ATATAATAAAA-TATAAATATATTAAAATTT
662088 -TAT-A-AAAATATAAAATATATTAAA
1 ATATAATAAAATAT-AAATATATTAAA
662112 TACGATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
26 3 0.06
27 10 0.21
28 4 0.09
29 3 0.06
30 10 0.21
31 17 0.36
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATAATAAAATATAAATATATTAAAATTT
Found at i:662078 original size:37 final size:41
Alignment explanation
Indices: 661988--662104 Score: 97
Period size: 37 Copynumber: 3.0 Consensus size: 41
661978 ATTATTTTAA
* *
661988 AAAATAATTAAAATATAATATGATATAAAAAATATATAAAT
1 AAAATTATTAATATATAATATGATATAAAAAATATATAAAT
* * **
662029 ATAA-TATAAATATA-AATAT-AT-TAAAATTTATAT-AAT
1 AAAATTATTAATATATAATATGATATAAAAAATATATAAAT
**
662065 AAAATTATTAATATATCAA-ATTTTAT-AAAAATATA-AAAT
1 AAAATTATTAATATAT-AATATGATATAAAAAATATATAAAT
662104 A
1 A
662105 TATTAAATAC
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
36 6 0.10
37 19 0.32
38 4 0.07
39 19 0.32
40 8 0.14
41 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.37
Consensus pattern (41 bp):
AAAATTATTAATATATAATATGATATAAAAAATATATAAAT
Found at i:662685 original size:31 final size:31
Alignment explanation
Indices: 662622--662685 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
662612 TGATACGAAA
*
662622 AATAAAATTATTAATATATCATAATTTTTAT
1 AATAAAATTATTAATATATCATAATTTATAT
* *
662653 AATATAAATTATTAATATTTTA-AATTTATAT
1 AATA-AAATTATTAATATATCATAATTTATAT
662684 AA
1 AA
662686 AAATATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (31 bp):
AATAAAATTATTAATATATCATAATTTATAT
Found at i:663137 original size:30 final size:30
Alignment explanation
Indices: 663103--663198 Score: 122
Period size: 30 Copynumber: 3.2 Consensus size: 30
663093 TTTTTAAAGT
* *
663103 TTATTTAAGTATAAATTAAAAATTAAAAAA
1 TTATTTAAGTACAAATTAAAAATTAAAAAC
* **
663133 TTATTTAAATACAAATTAATGATTAAAAAC
1 TTATTTAAGTACAAATTAAAAATTAAAAAC
*
663163 TTATTT-AGATACAAATTAAAAGTTAAAAAC
1 TTATTTAAG-TACAAATTAAAAATTAAAAAC
663193 TTATTT
1 TTATTT
663199 CACTACAATA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 1 0.02
30 55 0.98
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (30 bp):
TTATTTAAGTACAAATTAAAAATTAAAAAC
Found at i:665231 original size:8 final size:8
Alignment explanation
Indices: 665205--665252 Score: 59
Period size: 7 Copynumber: 6.5 Consensus size: 8
665195 TAATATTACT
665205 TATATTTA
1 TATATTTA
665213 T-TATTTA
1 TATATTTA
*
665220 TATATTTT
1 TATATTTA
665228 TATA-TTA
1 TATATTTA
665235 -ATATTTA
1 TATATTTA
665242 TATATTT-
1 TATATTTA
665249 TATA
1 TATA
665253 ATTAAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
6 3 0.09
7 16 0.46
8 16 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TATATTTA
Found at i:665239 original size:22 final size:21
Alignment explanation
Indices: 665204--665262 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
665194 TTAATATTAC
665204 TTATAT-TTATTATTTATATAT
1 TTATATATTA-TATTTATATAT
*
665225 TTTTATATTAATATTTATATAT
1 TTATATATT-ATATTTATATAT
*
665247 TT-TATAATTAAATTTA
1 TTATAT-ATTATATTTA
665263 AATAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 14 0.42
22 18 0.55
23 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATATTATATTTATATAT
Found at i:665279 original size:23 final size:22
Alignment explanation
Indices: 665214--665279 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
665204 TTATATTTAT
* *
665214 TATTTATATATTTTTATATTAA
1 TATTTATAAATTTTTTTATTAA
* * *
665236 TATTTATATATTTTATAATTAA
1 TATTTATAAATTTTTTTATTAA
665258 -ATTTAAATAAATTTTTTTATTA
1 TATTT--ATAAATTTTTTTATTA
665280 TAAAATATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 4 0.11
22 19 0.53
23 13 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTTATAAATTTTTTTATTAA
Found at i:667860 original size:21 final size:23
Alignment explanation
Indices: 667836--667882 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
667826 CAATAATATA
667836 ATAT-TTAT-TAATTTTGTATT-T
1 ATATATTATATAATTTT-TATTAT
667857 ATATATTATATAATTTTTATTAT
1 ATATATTATATAATTTTTATTAT
667880 ATA
1 ATA
667883 AATAGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 8 0.35
23 11 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATATATTATATAATTTTTATTAT
Found at i:668332 original size:2 final size:2
Alignment explanation
Indices: 668325--668354 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
668315 TTTCATGGAT
668325 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
668355 AACCCTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:668641 original size:3 final size:3
Alignment explanation
Indices: 668633--668679 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
668623 TGATTAGAAT
668633 ATA ATA ATA ATA ATA ATA ATA ATA ATA ACT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
668678 AT
1 AT
668680 TTATATTCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 1 0.02
3 40 0.95
4 1 0.02
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:671350 original size:334 final size:334
Alignment explanation
Indices: 670741--671398 Score: 1316
Period size: 334 Copynumber: 2.0 Consensus size: 334
670731 AGTCTGAAGA
670741 CTTAGATGTATTAGCAAGTAAGCCTTAAGGAACAGAAAGAAATAGTCAAGCCTTTATAATTTGTA
1 CTTAGATGTATTAGCAAGTAAGCCTTAAGGAACAGAAAGAAATAGTCAAGCCTTTATAATTTGTA
670806 TATTTAAAACAGGAAAATAAGTCATTTCTAACCTGAGAAGCCCATTTACATAGTGCAGAAGCCAG
66 TATTTAAAACAGGAAAATAAGTCATTTCTAACCTGAGAAGCCCATTTACATAGTGCAGAAGCCAG
670871 ACCAGAGAGTACAGAAGCAGCCAAAACAGGGACAATTCCGAAAAATAGAATTTGCTTGGGGTCAC
131 ACCAGAGAGTACAGAAGCAGCCAAAACAGGGACAATTCCGAAAAATAGAATTTGCTTGGGGTCAC
670936 CACTGCTAGAAGCTTTGCTAGGACCTTCACCAATGCTTAGAAGAACAGCTGCTATGATCAACAAA
196 CACTGCTAGAAGCTTTGCTAGGACCTTCACCAATGCTTAGAAGAACAGCTGCTATGATCAACAAA
671001 AACAGAGCCCCAATTTGTTGAATTGATAGCCTCTGCCGGCAAGAAACACCACAAATTAAGCCAAG
261 AACAGAGCCCCAATTTGTTGAATTGATAGCCTCTGCCGGCAAGAAACACCACAAATTAAGCCAAG
671066 GAACAGCTG
326 GAACAGCTG
671075 CTTAGATGTATTAGCAAGTAAGCCTTAAGGAACAGAAAGAAATAGTCAAGCCTTTATAATTTGTA
1 CTTAGATGTATTAGCAAGTAAGCCTTAAGGAACAGAAAGAAATAGTCAAGCCTTTATAATTTGTA
671140 TATTTAAAACAGGAAAATAAGTCATTTCTAACCTGAGAAGCCCATTTACATAGTGCAGAAGCCAG
66 TATTTAAAACAGGAAAATAAGTCATTTCTAACCTGAGAAGCCCATTTACATAGTGCAGAAGCCAG
671205 ACCAGAGAGTACAGAAGCAGCCAAAACAGGGACAATTCCGAAAAATAGAATTTGCTTGGGGTCAC
131 ACCAGAGAGTACAGAAGCAGCCAAAACAGGGACAATTCCGAAAAATAGAATTTGCTTGGGGTCAC
671270 CACTGCTAGAAGCTTTGCTAGGACCTTCACCAATGCTTAGAAGAACAGCTGCTATGATCAACAAA
196 CACTGCTAGAAGCTTTGCTAGGACCTTCACCAATGCTTAGAAGAACAGCTGCTATGATCAACAAA
671335 AACAGAGCCCCAATTTGTTGAATTGATAGCCTCTGCCGGCAAGAAACACCACAAATTAAGCCAA
261 AACAGAGCCCCAATTTGTTGAATTGATAGCCTCTGCCGGCAAGAAACACCACAAATTAAGCCAA
671399 ATAAGCTCAC
Statistics
Matches: 324, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 324 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (334 bp):
CTTAGATGTATTAGCAAGTAAGCCTTAAGGAACAGAAAGAAATAGTCAAGCCTTTATAATTTGTA
TATTTAAAACAGGAAAATAAGTCATTTCTAACCTGAGAAGCCCATTTACATAGTGCAGAAGCCAG
ACCAGAGAGTACAGAAGCAGCCAAAACAGGGACAATTCCGAAAAATAGAATTTGCTTGGGGTCAC
CACTGCTAGAAGCTTTGCTAGGACCTTCACCAATGCTTAGAAGAACAGCTGCTATGATCAACAAA
AACAGAGCCCCAATTTGTTGAATTGATAGCCTCTGCCGGCAAGAAACACCACAAATTAAGCCAAG
GAACAGCTG
Found at i:673489 original size:29 final size:29
Alignment explanation
Indices: 673457--673512 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
673447 ATAAAATTAA
673457 TTTT-TAATTTAATTTATAAATAATTTTAT
1 TTTTATAATTT-ATTTATAAATAATTTTAT
* *
673486 TTTTATAATTTATTTTTTAATAATTTT
1 TTTTATAATTTATTTATAAATAATTTT
673513 TTATTAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (29 bp):
TTTTATAATTTATTTATAAATAATTTTAT
Found at i:673495 original size:14 final size:16
Alignment explanation
Indices: 673461--673512 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
673451 AATTAATTTT
* * *
673461 TAATTTAATTTATAAA
1 TAATTTTATTTTTTAA
673477 TAATTTTA-TTTTT-A
1 TAATTTTATTTTTTAA
673491 TAA-TTTATTTTTTAA
1 TAATTTTATTTTTTAA
673506 TAATTTT
1 TAATTTT
673513 TTATTAAACT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 4 0.13
14 9 0.30
15 7 0.23
16 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTTTATTTTTTAA
Found at i:673519 original size:14 final size:14
Alignment explanation
Indices: 673469--673519 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
673459 TTTAATTTAA
*
673469 TTTATAAATAATTT
1 TTTATTAATAATTT
*
673483 TATT-TTTATAATTT
1 T-TTATTAATAATTT
*
673497 ATTTTTTAATAATTT
1 -TTTATTAATAATTT
673512 TTTATTAA
1 TTTATTAA
673520 ACTCAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.60
15 12 0.40
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTATTAATAATTT
Found at i:674039 original size:2 final size:2
Alignment explanation
Indices: 674034--674059 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
674024 ATACACACAC
674034 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
674060 TAAATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674933 original size:16 final size:16
Alignment explanation
Indices: 674914--674947 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
674904 GAACCAAAAT
*
674914 ATTACTGAATTCGATA
1 ATTACTAAATTCGATA
*
674930 ATTACTAAATTCTATA
1 ATTACTAAATTCGATA
674946 AT
1 AT
674948 AAAACATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACTAAATTCGATA
Found at i:675139 original size:14 final size:14
Alignment explanation
Indices: 675120--675147 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
675110 AAGCATTAAA
675120 TAGCCAACCACCAC
1 TAGCCAACCACCAC
675134 TAGCCAACCACCAC
1 TAGCCAACCACCAC
675148 AATTACCTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.50, G:0.07, T:0.07
Consensus pattern (14 bp):
TAGCCAACCACCAC
Found at i:679547 original size:19 final size:19
Alignment explanation
Indices: 679512--679571 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
679502 GTGAATTGTG
**
679512 ATTTTTTTATTTTGTTTTA
1 ATTTTTTTATTAAGTTTTA
679531 ATTTTTTTATTAAGTTTT-
1 ATTTTTTTATTAAGTTTTA
* * *
679549 GTATTTTTAGTTGAGTTTTA
1 ATTTTTTTA-TTAAGTTTTA
679569 ATT
1 ATT
679572 GAGTTTGGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
18 7 0.22
19 24 0.75
20 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (19 bp):
ATTTTTTTATTAAGTTTTA
Found at i:679678 original size:47 final size:45
Alignment explanation
Indices: 679551--679685 Score: 164
Period size: 45 Copynumber: 3.0 Consensus size: 45
679541 TAAGTTTTGT
* * * *
679551 ATTTTTAGTTGAGTTTTAATTGAGTTTGGATTTAAGTTTATATAG
1 ATTTTTAGTAGGGTTTTAATTGAGTTTGAATTTAAATTTATATAG
*
679596 ATTTTTAGTAGGGTTTTAATTTGA-TTTGAGTTTAAATTTATATAG
1 ATTTTTAGTAGGGTTTTAA-TTGAGTTTGAATTTAAATTTATATAG
* **
679641 ATTTTTAATTATGTTTTTTAATTGAGTTTGAATTTAAATTTATAT
1 ATTTTT-AGTA-GGGTTTTAATTGAGTTTGAATTTAAATTTATAT
679686 TTTATTAAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
45 41 0.53
46 11 0.14
47 25 0.32
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (45 bp):
ATTTTTAGTAGGGTTTTAATTGAGTTTGAATTTAAATTTATATAG
Found at i:679732 original size:22 final size:22
Alignment explanation
Indices: 679674--679734 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 22
679664 GAGTTTGAAT
*
679674 TTAAATTTATATTTTATTAAATA
1 TTAAATTTA-ATTTTTTTAAATA
* **
679697 -T-ATTTTAA-AATTTTAAATA
1 TTAAATTTAATTTTTTTAAATA
679716 TTAAATTTAATTTTTTTAA
1 TTAAATTTAATTTTTTTAA
679735 TTTATTTAAT
Statistics
Matches: 28, Mismatches: 7, Indels: 7
0.67 0.17 0.17
Matches are distributed among these distances:
19 8 0.29
20 2 0.07
21 11 0.39
22 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTAAATTTAATTTTTTTAAATA
Found at i:680007 original size:19 final size:18
Alignment explanation
Indices: 679985--680140 Score: 78
Period size: 18 Copynumber: 8.7 Consensus size: 18
679975 TATTTTTATT
679985 TAATTATTTAATATAAGTA
1 TAATTATTTAATATAA-TA
*
680004 TAATT-TTTAATATATATT
1 TAATTATTTAATATA-ATA
*
680022 TTATTATTTAATATAAATA
1 TAATTATTTAATAT-AATA
680041 TAA-T-TTT-A-ATAAT-
1 TAATTATTTAATATAATA
*
680054 TTATT-TTTAATATAAATA
1 TAATTATTTAATAT-AATA
* * *
680072 TAATTA-ATAATTTAACA
1 TAATTATTTAATATAATA
* * *
680089 TAAATATAATTTTATTTATATT
1 T-AAT-T-ATTTAATATA-ATA
*
680111 TTATTATTTAATATAAATA
1 TAATTATTTAATAT-AATA
680130 TAATT-TTTAAT
1 TAATTATTTAAT
680141 TATTTATTTT
Statistics
Matches: 104, Mismatches: 18, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 3 0.03
16 3 0.03
17 10 0.10
18 33 0.32
19 32 0.31
20 4 0.04
21 8 0.08
22 2 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TAATTATTTAATATAATA
Found at i:680022 original size:37 final size:34
Alignment explanation
Indices: 679981--680148 Score: 150
Period size: 29 Copynumber: 5.2 Consensus size: 34
679971 ATTTTATTTT
*
679981 TATTTAATTATTTAATATAAGTATAATTTTTAATATA
1 TATTT-ATTATTTAATATAAATATAATTTTT-A-ATA
680018 TATTTTATTATTTAATATAAATATAA-TTTTAATA
1 TA-TTTATTATTTAATATAAATATAATTTTTAATA
680052 -ATTTATT-TTTAATATAAATATAA---TTAATA
1 TATTTATTATTTAATATAAATATAATTTTTAATA
** *
680081 -ATTTAACA-TAAATAT-AAT-T--TTATTT-ATA
1 TATTTATTATTTAATATAAATATAATT-TTTAATA
680109 T-TTTATTATTTAATATAAATATAATTTTTAAT-
1 TATTTATTATTTAATATAAATATAATTTTTAATA
680141 TATTTATT
1 TATTTATT
680149 TTATATATAT
Statistics
Matches: 110, Mismatches: 7, Indels: 32
0.74 0.05 0.21
Matches are distributed among these distances:
27 1 0.01
28 11 0.10
29 25 0.23
30 3 0.03
31 17 0.15
32 10 0.09
33 11 0.10
34 3 0.03
35 1 0.01
36 4 0.04
37 21 0.19
38 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
TATTTATTATTTAATATAAATATAATTTTTAATA
Found at i:680040 original size:25 final size:24
Alignment explanation
Indices: 680012--680104 Score: 80
Period size: 31 Copynumber: 3.6 Consensus size: 24
680002 TATAATTTTT
680012 AATATATATTTTATTATTTAATATA
1 AATATA-ATTTTATTATTTAATATA
680037 AATATAATTTTAATAATTTATTTTTAATATA
1 AATATAA-TTT--T-A-TTA--TTTAATATA
* * *
680068 AATATAA-TTAATAATTTAACATA
1 AATATAATTTTATTATTTAATATA
680091 AATATAATTTTATT
1 AATATAATTTTATT
680105 TATATTTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 17
0.71 0.06 0.22
Matches are distributed among these distances:
23 15 0.27
24 5 0.09
25 11 0.20
26 1 0.02
27 1 0.02
28 1 0.02
29 5 0.09
31 16 0.29
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATAATTTTATTATTTAATATA
Found at i:680041 original size:21 final size:20
Alignment explanation
Indices: 679981--680140 Score: 72
Period size: 19 Copynumber: 8.8 Consensus size: 20
679971 ATTTTATTTT
679981 TATTTAATTATTTAATATAA
1 TATTTAATTATTTAATATAA
680001 GTA--TAATT-TTTAATAT-A
1 -TATTTAATTATTTAATATAA
*
680018 TATTTTATTATTTAATATAA
1 TATTTAATTATTTAATATAA
*
680038 -ATATAA-T-TTT-A-AT-A
1 TATTTAATTATTTAATATAA
680052 -ATTT-ATT-TTTAATATAAA
1 TATTTAATTATTTAATAT-AA
* *
680070 TATAATTAATAATTTAACATAA
1 TAT--TTAATTATTTAATATAA
* *
680092 -ATATAA-T-TTT-AT-TTA
1 TATTTAATTATTTAATATAA
*
680107 TATTTTATTATTTAATATAA
1 TATTTAATTATTTAATATAA
*
680127 -ATATAATT-TTTAAT
1 TATTTAATTATTTAAT
680141 TATTTATTTT
Statistics
Matches: 105, Mismatches: 15, Indels: 41
0.65 0.09 0.25
Matches are distributed among these distances:
13 1 0.01
14 8 0.08
15 5 0.05
16 10 0.10
17 8 0.08
18 23 0.22
19 30 0.29
20 3 0.03
21 6 0.06
22 4 0.04
23 7 0.07
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (20 bp):
TATTTAATTATTTAATATAA
Found at i:680058 original size:29 final size:29
Alignment explanation
Indices: 680025--680170 Score: 106
Period size: 30 Copynumber: 4.9 Consensus size: 29
680015 ATATATTTTA
680025 TTATTTAATATAAATATAATTTTAATAAT
1 TTATTTAATATAAATATAATTTTAATAAT
680054 TTATTTTTAATATAAATATAA--TTAAT-A-
1 TTA--TTTAATATAAATATAATTTTAATAAT
* *
680081 --ATTTAACATAAATATAATTTTATTTATATTTT
1 TTATTTAATATAAATATAATTTTA---ATA--AT
*
680113 ATTATTTAATATAAATATAATTTTTAATTAT
1 -TTATTTAATATAAATATAA-TTTTAATAAT
* * *
680144 TTATTTTATATATATACACATTTTAAT
1 TTATTTAATATAAATATA-ATTTTAAT
680171 TAAATATTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 31
0.70 0.06 0.23
Matches are distributed among these distances:
23 15 0.16
25 4 0.04
28 3 0.03
29 8 0.09
30 22 0.24
31 18 0.19
33 2 0.02
35 16 0.17
36 5 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
TTATTTAATATAAATATAATTTTAATAAT
Found at i:680085 original size:54 final size:56
Alignment explanation
Indices: 680027--680134 Score: 166
Period size: 54 Copynumber: 1.9 Consensus size: 56
680017 ATATTTTATT
*
680027 ATTTAATATAAATATAATTTTA-ATAATTTATT-TTTAATATAAATATAATTAATA
1 ATTTAACATAAATATAATTTTATATAATTTATTATTTAATATAAATATAATTAATA
*
680081 ATTTAACATAAATATAATTTTATTTATATTTTATTATTTAATATAAATATAATT
1 ATTTAACATAAATATAATTTTA--TATAATTTATTATTTAATATAAATATAATT
680135 TTTAATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
54 21 0.44
57 9 0.19
58 18 0.38
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (56 bp):
ATTTAACATAAATATAATTTTATATAATTTATTATTTAATATAAATATAATTAATA
Found at i:680129 original size:89 final size:94
Alignment explanation
Indices: 679984--680159 Score: 272
Period size: 89 Copynumber: 1.9 Consensus size: 94
679974 TTATTTTTAT
* * *
679984 TTAATTATTTAATATAAGTATAATTTTTAATATATATTTTATTATTTAATATAAATATAA-TTTT
1 TTAATAATTTAACATAAATATAATTTTTAATATATATTTTATTATTTAATATAAATATAATTTTT
680048 AATAATTTATTTT-TA-ATATAAATATAA
66 AATAATTTATTTTATATATATAAATATAA
*
680075 TTAATAATTTAACATAAATATAA-TTTT-ATTTATATTTTATTATTTAATATAAATATAATTTTT
1 TTAATAATTTAACATAAATATAATTTTTAATATATATTTTATTATTTAATATAAATATAATTTTT
*
680138 AATTATTTATTTTATATATATA
66 AATAATTTATTTTATATATATA
680160 CACATTTTAA
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
89 30 0.39
90 20 0.26
91 22 0.29
92 5 0.06
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.55
Consensus pattern (94 bp):
TTAATAATTTAACATAAATATAATTTTTAATATATATTTTATTATTTAATATAAATATAATTTTT
AATAATTTATTTTATATATATAAATATAA
Found at i:680156 original size:26 final size:24
Alignment explanation
Indices: 680097--680157 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
680087 CATAAATATA
*
680097 ATTTTATTTAT-ATTTTATTATTT
1 ATTTTATATATAATTTTATTATTT
* * *
680120 AATATAAATATAATTTTTAATTATTT
1 ATTTTATATATAA-TTTT-ATTATTT
680146 ATTTTATATATA
1 ATTTTATATATA
680158 TACACATTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
23 7 0.25
24 1 0.04
25 4 0.14
26 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATATATAATTTTATTATTT
Found at i:680277 original size:21 final size:21
Alignment explanation
Indices: 680253--680310 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
680243 TGTACTAATT
* *
680253 TTAATCTCACTCTTATAATAC
1 TTAATCTCACTATTATAATAA
* * *
680274 TTAATTTTATTATTATAATAA
1 TTAATCTCACTATTATAATAA
680295 TTAATCTCACTATTAT
1 TTAATCTCACTATTAT
680311 CGTTATTTTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAATCTCACTATTATAATAA
Found at i:681135 original size:6 final size:6
Alignment explanation
Indices: 681124--681149 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
681114 TTCACAGCCA
681124 TCGTAT TCGTAT TCGTAT TCGTAT TC
1 TCGTAT TCGTAT TCGTAT TCGTAT TC
681150 TTCTTCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.50
Consensus pattern (6 bp):
TCGTAT
Found at i:682259 original size:11 final size:11
Alignment explanation
Indices: 682240--682266 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
682230 TTTATATAAA
682240 ATTTTATACAT
1 ATTTTATACAT
682251 ATTTTATACAT
1 ATTTTATACAT
682262 ATTTT
1 ATTTT
682267 TGTTGTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTATACAT
Found at i:683853 original size:25 final size:24
Alignment explanation
Indices: 683823--683881 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 24
683813 ATTAATTTTG
*
683823 ATATATTTATATATTCATATCATATT
1 ATAT-TTTATATA-TAATATCATATT
*
683849 AATATTTTTTATATAATATCATATT
1 -ATATTTTATATATAATATCATATT
683874 ATATTTTA
1 ATATTTTA
683882 ATTATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 7 0.24
25 11 0.38
26 7 0.24
27 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (24 bp):
ATATTTTATATATAATATCATATT
Found at i:683906 original size:21 final size:19
Alignment explanation
Indices: 683872--683912 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
683862 TAATATCATA
*
683872 TTATATTTTAATTATTTTT
1 TTATATTTTAATTATATTT
683891 TTATATTATATAATTATATTT
1 TTATATT-T-TAATTATATTT
683912 T
1 T
683913 ATTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATATTTTAATTATATTT
Found at i:684492 original size:21 final size:21
Alignment explanation
Indices: 684413--684515 Score: 74
Period size: 21 Copynumber: 5.0 Consensus size: 21
684403 TGACTTAACT
684413 TAAAATATTATTTAAAT-A-A
1 TAAAATATTATTTAAATAATA
684432 TAAAA-ATTATTTAAATTTAATTA
1 TAAAATATTATTTAAA--TAA-TA
**
684455 TAAAATA-TATAAATAATAATA
1 TAAAATATTATTTA-AATAATA
* * *
684476 TAAAATATTATTTTAATATTT
1 TAAAATATTATTTAAATAATA
*
684497 TAATATA-T-TTTAAATAATA
1 TAAAATATTATTTAAATAATA
684516 AAATAATTTT
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
18 10 0.15
19 13 0.20
20 2 0.03
21 21 0.32
22 6 0.09
23 10 0.15
24 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATATTATTTAAATAATA
Found at i:684520 original size:19 final size:18
Alignment explanation
Indices: 684447--684525 Score: 52
Period size: 19 Copynumber: 4.2 Consensus size: 18
684437 ATTATTTAAA
*
684447 TTTAATTATAAAATATAT
1 TTTAATAATAAAATATAT
**
684465 AAATAATAATATAAAATATTAT
1 -TTTAAT-A-ATAAAATA-TAT
* **
684487 TTTAATATTTTAATATAT
1 TTTAATAATAAAATATAT
684505 TTTAAATAATAAAATA-AT
1 TTT-AATAATAAAATATAT
684523 TTT
1 TTT
684526 TTAATTCGAT
Statistics
Matches: 45, Mismatches: 11, Indels: 9
0.69 0.17 0.14
Matches are distributed among these distances:
18 11 0.24
19 18 0.40
20 1 0.02
21 12 0.27
22 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTAATAATAAAATATAT
Found at i:685987 original size:18 final size:20
Alignment explanation
Indices: 685950--686001 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
685940 TATGATATGT
685950 AATATAATATAATATTAAAA
1 AATATAATATAATATTAAAA
*
685970 AATATAA-AT-ATGTTAAAA
1 AATATAATATAATATTAAAA
**
685988 TTTATAATA-AATAT
1 AATATAATATAATAT
686002 ATAATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
18 13 0.50
19 6 0.23
20 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATATAATATAATATTAAAA
Found at i:686678 original size:20 final size:20
Alignment explanation
Indices: 686655--686692 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
686645 ATTAACCTAC
686655 TGATGTGGACGTTGACTTGT
1 TGATGTGGACGTTGACTTGT
**
686675 TGATGTGGTTGTTGACTT
1 TGATGTGGACGTTGACTT
686693 TATTGAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.08, G:0.34, T:0.45
Consensus pattern (20 bp):
TGATGTGGACGTTGACTTGT
Found at i:688012 original size:21 final size:20
Alignment explanation
Indices: 687983--688039 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
687973 TCCATTTTAT
*
687983 TTATCTTATTTTTTAAAATTA
1 TTATATTATTTTTTAAAA-TA
* *
688004 TTATATTATCTCTTAAAATA
1 TTATATTATTTTTTAAAATA
*
688024 TTATTTTATATTTTTA
1 TTATATTAT-TTTTTA
688040 TTATATATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATTATTTTTTAAAATA
Found at i:690793 original size:28 final size:28
Alignment explanation
Indices: 690753--690824 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
690743 AAAAAAAAAT
* ** *
690753 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
690781 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
690809 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
690825 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:690944 original size:52 final size:52
Alignment explanation
Indices: 690813--691151 Score: 153
Period size: 52 Copynumber: 6.4 Consensus size: 52
690803 AAATAACGAG
* * * * **
690813 GTTGGAGTATCCTCGATTGT-GAAAAATTGGTATTTTTGGAAATAGAATTGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGG-AGTTTTGAAAATAAAACCGGA
* * ** *
690865 GTTGAAATATCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCGG-
1 GTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
* * **
690916 GATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTT-AGCGATAAAACCGGA
1 G-TTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGA-AAATAAAACCGGA
** ** ** * *
690969 GTTGGAGTATCCCC---T-CAGAAATAACGGGGTTGGAGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGGAAA-AA-----TTGGAGT-T--TTGAAAATAAAACCGGA
* * *
691024 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAA-AAATTGGAG-TTTTGA-AAATAAAACCGGA
* * * * * *
691078 GTTAGAGTATCCCCGATTATAG-AAAATTAGTGTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
*
691129 GTTGGAATATCCCCGATTGTGGA
1 GTTGGAGTATCCCCGATTGTGGA
691152 GAATTGATAA
Statistics
Matches: 215, Mismatches: 45, Indels: 54
0.68 0.14 0.17
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
51 36 0.17
52 86 0.40
53 25 0.12
54 29 0.13
55 19 0.09
56 2 0.01
57 3 0.01
58 7 0.03
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCGGA
Found at i:691009 original size:28 final size:27
Alignment explanation
Indices: 690969--691037 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
690959 TAAAACCGGA
690969 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
690997 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
691024 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
691038 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:691105 original size:212 final size:212
Alignment explanation
Indices: 690758--691151 Score: 589
Period size: 212 Copynumber: 1.9 Consensus size: 212
690748 AAAATCGGGA
* *
690758 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT
* * * *
690823 CCTCGATTGTGAAAAATTGGTATTTTTGGAAATAGAATTGGAGTTGAAATATCCCCGATTAAAGG
66 CCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATCGGAGTTGAAATATCCCCGATTAAAGG
* *
690888 AAAATTGGCGTTTTGAAAATAAAACCGG-GATTGGAGTATCCCCGATTGTGGAAAAATTAGTGTT
131 AAAATTAGCGTTTTGAAAATAAAACCGGAG-TTGGAATATCCCCGATTGTGGAAAAATTAGTGTT
690952 TTAGCGATAAAACCGGAG
195 TTAGCGATAAAACCGGAG
* *
690970 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTAT
1 TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT
* * *
691034 CCCCGATTGTGAAGAAATTGGTGTTTTTTAGAAATAAAATCGGAGTT-AGAGTATCCCCGATTAT
66 CCCCGATTGTGAA-AAATTGGT-ATTTTTAGAAATAAAATCGGAGTTGA-AATATCCCCGATTAA
* *
691098 A-GAAAATTAGTGTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
128 AGGAAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
691152 GAATTGATAA
Statistics
Matches: 163, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
211 29 0.18
212 99 0.61
213 35 0.21
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (212 bp):
TTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTAT
CCCCGATTGTGAAAAATTGGTATTTTTAGAAATAAAATCGGAGTTGAAATATCCCCGATTAAAGG
AAAATTAGCGTTTTGAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTT
TAGCGATAAAACCGGAG
Found at i:691129 original size:51 final size:54
Alignment explanation
Indices: 691028--691146 Score: 156
Period size: 51 Copynumber: 2.3 Consensus size: 54
691018 AACGGGGTTG
* * *
691028 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTAGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAGAAATAAAATCGGAGTTA
*
691082 GAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGA-AAATAAAATCGGAGTTG
1 GAGTATCCCCGATTATGAAG-AAATTAGTGTTTTTGAGAAATAAAATCGGAGTTA
*
691133 GAATATCCCCGATT
1 GAGTATCCCCGATT
691147 GTGGAGAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 29 0.49
52 7 0.12
53 8 0.14
54 15 0.25
ACGTcount: A:0.34, C:0.12, G:0.22, T:0.32
Consensus pattern (54 bp):
GAGTATCCCCGATTATGAAGAAATTAGTGTTTTTGAGAAATAAAATCGGAGTTA
Found at i:693529 original size:13 final size:13
Alignment explanation
Indices: 693511--693536 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
693501 ACAAAGATCC
693511 ATGTATCGATACA
1 ATGTATCGATACA
693524 ATGTATCGATACA
1 ATGTATCGATACA
693537 CCGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:693600 original size:19 final size:18
Alignment explanation
Indices: 693576--693643 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
693566 CAGTAGCTAA
693576 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
693595 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
693610 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
693627 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
693644 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:693616 original size:13 final size:13
Alignment explanation
Indices: 693598--693622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
693588 ACAATACTTA
693598 TGTATCGATACAT
1 TGTATCGATACAT
693611 TGTATCGATACA
1 TGTATCGATACA
693623 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:693620 original size:32 final size:32
Alignment explanation
Indices: 693579--693641 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
693569 TAGCTAATTA
*
693579 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
693611 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
693642 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:697662 original size:22 final size:22
Alignment explanation
Indices: 697619--697668 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
697609 AAAATATTAA
* *
697619 AAATTATTTTTAATTTATATTT
1 AAATAATTTTTAATTTAAATTT
*
697641 ATATAATTTTATAA-TTAAATTT
1 AAATAATTTT-TAATTTAAATTT
697663 AAATAA
1 AAATAA
697669 AAATATTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AAATAATTTTTAATTTAAATTT
Found at i:697868 original size:2 final size:2
Alignment explanation
Indices: 697861--697893 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
697851 TCCGGCACAT
697861 TA TA TA TA TA TA 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 TA T
697894 CATAAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:702337 original size:13 final size:13
Alignment explanation
Indices: 702319--702346 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
702309 TGGAGCTATT
702319 TAAAAATTTTAAA
1 TAAAAATTTTAAA
702332 TAAAAATTTTAAA
1 TAAAAATTTTAAA
702345 TA
1 TA
702347 TTTAAAAGTT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAAAAATTTTAAA
Found at i:702505 original size:24 final size:26
Alignment explanation
Indices: 702478--702525 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
702468 AAAATCTGTC
*
702478 AAATTAATTT-TTTATT-TTTTTATT
1 AAATCAATTTATTTATTATTTTTATT
*
702502 AAATCAATTTATTTTTTATTTTTA
1 AAATCAATTTATTTATTATTTTTA
702526 CCCATTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 5 0.25
26 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
AAATCAATTTATTTATTATTTTTATT
Found at i:702763 original size:18 final size:18
Alignment explanation
Indices: 702740--702781 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
702730 TCTGATTTGA
702740 TAAAAAA-AATTTATAATT
1 TAAAAAATAATTTA-AATT
702758 TAAAAAATTAATTTAAATT
1 TAAAAAA-TAATTTAAATT
702777 TAAAA
1 TAAAA
702782 TAATCTTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAAATAATTTAAATT
Found at i:702785 original size:16 final size:17
Alignment explanation
Indices: 702740--702790 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
702730 TCTGATTTGA
*
702740 TAAAAAAAATTTATAATT
1 TAAAAATAATTTA-AATT
702758 TAAAAAATTAATTTAAATT
1 T-AAAAA-TAATTTAAATT
702777 T-AAAATAATCTTAA
1 TAAAAATAAT-TTAA
702791 CGATTCTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 1 0.03
19 10 0.34
20 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATAATTTAAATT
Found at i:702982 original size:15 final size:15
Alignment explanation
Indices: 702962--702993 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
702952 CTATTTTTTA
702962 AAAATATTAATATCC
1 AAAATATTAATATCC
702977 AAAATATTAATATCC
1 AAAATATTAATATCC
702992 AA
1 AA
702994 CCTATATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAATATTAATATCC
Found at i:703610 original size:12 final size:13
Alignment explanation
Indices: 703593--703626 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
703583 TAAAAAAATA
703593 TTAATTTTTT-AG
1 TTAATTTTTTCAG
*
703605 TTAATTTTTTCAT
1 TTAATTTTTTCAG
703618 TTAATTTTT
1 TTAATTTTT
703627 AAAAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (13 bp):
TTAATTTTTTCAG
Found at i:704300 original size:20 final size:19
Alignment explanation
Indices: 704277--704326 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
704267 GTCTAACCCC
704277 ATTAAAATTAATATTTAATA
1 ATTAAAATTAATATTT-ATA
* *
704297 ATTAAAA-AAATATTTTTA
1 ATTAAAATTAATATTTATA
*
704315 TTTAAAATTAAT
1 ATTAAAATTAAT
704327 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 8 0.32
19 10 0.40
20 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTAAAATTAATATTTATA
Found at i:704841 original size:12 final size:13
Alignment explanation
Indices: 704824--704878 Score: 71
Period size: 12 Copynumber: 4.4 Consensus size: 13
704814 ATAAATTTTA
704824 ATTTAT-TTATAT
1 ATTTATATTATAT
*
704836 ATTTATATTATTT
1 ATTTATATTATAT
704849 ATATTATATTATAT
1 AT-TTATATTATAT
704863 -TTTATATTATAT
1 ATTTATATTATAT
704875 -TTTA
1 ATTTA
704879 ATTTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
12 21 0.54
13 8 0.21
14 10 0.26
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTATATTATAT
Found at i:704846 original size:5 final size:5
Alignment explanation
Indices: 704826--704875 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
704816 AAATTTTAAT
704826 TTAT- TTATA -TAT- TTATA TTAT- TTATA TTATA TTATA TTTTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA --TTATA TTATA
704874 TT
1 TT
704876 TTAATTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 14 0.35
5 21 0.52
7 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
TTATA
Found at i:704846 original size:17 final size:19
Alignment explanation
Indices: 704826--704875 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 19
704816 AAATTTTAAT
704826 TTATTTATA-TAT-TTATA
1 TTATTTATATTATATTATA
704843 TTATTTATATTATATTATA
1 TTATTTATATTATATTATA
704862 -T-TTTATATTATATT
1 TTATTTATATTATATT
704876 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 22 0.71
18 4 0.13
19 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATATTATATTATA
Found at i:706060 original size:20 final size:21
Alignment explanation
Indices: 706028--706089 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 21
706018 ATGTTTACAG
*
706028 ATTATGTTT-ATATATTTTAT
1 ATTATATTTAATATATTTTAT
* *
706048 TTTAT-TTTAATATATTATA-
1 ATTATATTTAATATATTTTAT
*
706067 ATTATATTTAAAATATTTTAT
1 ATTATATTTAATATATTTTAT
706088 AT
1 AT
706090 AAATTTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 7 0.21
20 25 0.74
21 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTATATTTAATATATTTTAT
Found at i:706063 original size:10 final size:10
Alignment explanation
Indices: 706037--706100 Score: 58
Period size: 10 Copynumber: 6.3 Consensus size: 10
706027 GATTATGTTT
706037 ATATATTTTA
1 ATATATTTTA
* *
706047 TTTTATTTTA
1 ATATATTTTA
*
706057 ATATATTATA
1 ATATATTTTA
706067 AT-TATATTTA
1 ATATAT-TTTA
*
706077 AAATATTTTA
1 ATATATTTTA
*
706087 TATAAATTTTA
1 -ATATATTTTA
706098 ATA
1 ATA
706101 AATTAATAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
9 3 0.07
10 28 0.67
11 11 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
ATATATTTTA
Found at i:708525 original size:3 final size:3
Alignment explanation
Indices: 708504--708537 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
708494 ATGAATTGGG
* *
708504 TGA TGA GGA TGA GGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
708538 AGCAAATGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.38, T:0.29
Consensus pattern (3 bp):
TGA
Found at i:710910 original size:6 final size:6
Alignment explanation
Indices: 710899--710927 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
710889 ATTAAATTAA
710899 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
710928 AGTTGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:711340 original size:16 final size:17
Alignment explanation
Indices: 711319--711350 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
711309 GCTTTATTTT
711319 TTATAATTT-TAATAAA
1 TTATAATTTATAATAAA
711335 TTATAATTTATAATAA
1 TTATAATTTATAATAA
711351 TTTCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TTATAATTTATAATAAA
Found at i:711940 original size:14 final size:14
Alignment explanation
Indices: 711899--711956 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
711889 GTCCATCTAC
*
711899 ATTTTTTTAAATTT
1 ATTTTTTAAAATTT
*
711913 -TTTTTAAAATATTT
1 ATTTTTTAAA-ATTT
711927 ATTTTTTAAAATTT
1 ATTTTTTAAAATTT
*
711941 AATTTTTAATAATTT
1 ATTTTTTAA-AATTT
711956 A
1 A
711957 ATATTTGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
13 7 0.19
14 16 0.43
15 14 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTTAAAATTT
Found at i:711945 original size:15 final size:15
Alignment explanation
Indices: 711912--711958 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
711902 TTTTTAAATT
*
711912 TTTTTTAAAATATTTA
1 TTTTTTAAAAT-TTAA
711928 TTTTTTAAAATTTAA
1 TTTTTTAAAATTTAA
711943 -TTTTTAATAATTTAA
1 TTTTTTAA-AATTTAA
711958 T
1 T
711959 ATTTGTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 11 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTAAAATTTAA
Found at i:712027 original size:19 final size:19
Alignment explanation
Indices: 712000--712041 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
711990 ATATTTTTTA
*
712000 ATATTTATAT-TATAATATT
1 ATATATATATGTATAAT-TT
*
712019 ATATATATATGTATTATTT
1 ATATATATATGTATAATTT
712038 ATAT
1 ATAT
712042 GATAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
ATATATATATGTATAATTT
Found at i:712052 original size:18 final size:18
Alignment explanation
Indices: 712031--712068 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
712021 ATATATATGT
712031 ATTATTT-ATATGATAAAA
1 ATTATTTAATAT-ATAAAA
712049 ATTATTTAATATATAAAA
1 ATTATTTAATATATAAAA
712067 AT
1 AT
712069 ATAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTATTTAATATATAAAA
Found at i:712948 original size:11 final size:11
Alignment explanation
Indices: 712932--712961 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
712922 TTATTTATGA
712932 ATTTATATTAT
1 ATTTATATTAT
712943 ATTTATATTAT
1 ATTTATATTAT
712954 A-TTATATT
1 ATTTATATT
712962 TTATACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.37
11 12 0.63
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:712953 original size:28 final size:28
Alignment explanation
Indices: 712922--712976 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
712912 AAATTTTAAC
* *
712922 TTAT-TTATGAATTTATATTATATTTATA
1 TTATATTAT-AATTTATACTAAATTTATA
*
712950 TTATATTATATTTTATACTAAATTTAT
1 TTATATTATAATTTATACTAAATTTAT
712977 TTTTTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATATTATAATTTATACTAAATTTATA
Found at i:717959 original size:26 final size:27
Alignment explanation
Indices: 717923--718014 Score: 84
Period size: 26 Copynumber: 3.4 Consensus size: 27
717913 TGTACTCTAA
* *
717923 ATTTTTTTATTTTAAATTAAAATT-TT
1 ATTTTATTATTTTAAATTAAAATTAAT
*
717949 ATTTTATTATTTTAAA-TAATATTAAT
1 ATTTTATTATTTTAAATTAAAATTAAT
*
717975 ATTTTTATT-TTTTATAATTAAATTTAAAT
1 A-TTTTATTATTTTA-AATTAAAATT-AAT
718004 ATATTT-TTATT
1 AT-TTTATTATT
718015 AATAAATAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 6 0.11
26 22 0.41
27 9 0.17
28 8 0.15
29 9 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTTATTATTTTAAATTAAAATTAAT
Found at i:718367 original size:5 final size:6
Alignment explanation
Indices: 718352--718379 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
718342 AAAAGGGGAA
718352 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
718380 CAAAACAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:719496 original size:2 final size:2
Alignment explanation
Indices: 719489--719513 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
719479 CATGCTGCAT
719489 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
719514 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:723127 original size:18 final size:18
Alignment explanation
Indices: 723100--723134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
723090 TAATAAAAGT
723100 TAAAAATAATAATTATAG
1 TAAAAATAATAATTATAG
* *
723118 TAAAATTAATTATTATA
1 TAAAAATAATAATTATA
723135 ATATTAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAAATAATAATTATAG
Found at i:723334 original size:37 final size:37
Alignment explanation
Indices: 723292--723370 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 37
723282 AATTTAATAA
723292 AATAATATTT-AA--TTATTTATTATATTTTATAAATTTT
1 AATAATATTTCAATTTTATTTA--ATATTTTA-AAATTTT
*
723329 TATAATATTTCAATTTTATTTAATATTTTAAAATTTT
1 AATAATATTTCAATTTTATTTAATATTTTAAAATTTT
723366 AATAA
1 AATAA
723371 ATTATTGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 20 0.54
38 10 0.27
40 7 0.19
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (37 bp):
AATAATATTTCAATTTTATTTAATATTTTAAAATTTT
Found at i:723343 original size:17 final size:18
Alignment explanation
Indices: 723323--723356 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
723313 ATATTTTATA
723323 AATTTT-TATAATATTTC
1 AATTTTATATAATATTTC
*
723340 AATTTTATTTAATATTT
1 AATTTTATATAATATTT
723357 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTTATATAATATTTC
Found at i:723363 original size:20 final size:20
Alignment explanation
Indices: 723313--723370 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
723303 ATTATTTATT
723313 ATATTTTATAAATTTT-TATA
1 ATATTTTA-AAATTTTATATA
* *
723333 ATA-TTT-CAATTTTATTTA
1 ATATTTTAAAATTTTATATA
723351 ATATTTTAAAATTTTA-ATA
1 ATATTTTAAAATTTTATATA
723370 A
1 A
723371 ATTATTGGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 6 0.19
18 6 0.19
19 9 0.29
20 10 0.32
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTTTAAAATTTTATATA
Found at i:723758 original size:66 final size:64
Alignment explanation
Indices: 723629--723779 Score: 171
Period size: 67 Copynumber: 2.3 Consensus size: 64
723619 CAAAAGATTT
* * * *
723629 AATTAAATTAAAAAATTTATATTACAATGAATATAATAATTTTTAATTTTTAATAAAATT-AAA
1 AATTAAATTAAAAAAATTATATTAAAATGAAAATAATAATTTTGAATTTTTAATAAAATTAAAA
* * *
723692 AATTAAATTTAAAAAAATTATATTGAAAAATTAAAATATTAATTATTGAGTTTTTAATAAAA-TA
1 AATTAAA-TTAAAAAAATTATATT--AAAATGAAAATAATAATT-TTGAATTTTTAATAAAATTA
723756 AAA
62 AAA
723759 AATTTTAAATTAAAAAAATTA
1 AA--TTAAATTAAAAAAATTA
723780 ATTTAAGTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
63 7 0.09
64 15 0.20
66 15 0.20
67 20 0.27
68 12 0.16
69 5 0.07
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (64 bp):
AATTAAATTAAAAAAATTATATTAAAATGAAAATAATAATTTTGAATTTTTAATAAAATTAAAA
Found at i:724238 original size:20 final size:22
Alignment explanation
Indices: 724200--724250 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
724190 ATGTTTTTTT
*
724200 CTTAAAAA-CACATGAAAAT-C
1 CTTAAAAATTACATGAAAATCC
724220 CTTAAAAATTACATG-AAATCC
1 CTTAAAAATTACATGAAAATCC
*
724241 CCTAAAAATT
1 CTTAAAAATT
724251 TCAAGATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (22 bp):
CTTAAAAATTACATGAAAATCC
Found at i:725887 original size:39 final size:37
Alignment explanation
Indices: 725844--725959 Score: 100
Period size: 39 Copynumber: 3.1 Consensus size: 37
725834 AACTTTTAAA
725844 AAAAATTAAACTTCTACAAATAAAAATAAATAATACACT
1 AAAAATTAAA-TTCTACAAATAAAAATAAATAATACA-T
* *
725883 AAAAATTTAAATTCATA-TAATAAATAT-AA-AA-A-AT
1 AAAAA-TTAAATTC-TACAAATAAAAATAAATAATACAT
* *
725917 -AAATTTAAATTTCTACAAATAAAAATAAATTATATCAT
1 AAAAATTAAA-TTCTACAAATAAAAATAAATAATA-CAT
725955 AAAAA
1 AAAAA
725960 ATATAAATAC
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
32 7 0.12
33 14 0.23
34 3 0.05
35 2 0.03
36 2 0.03
37 2 0.03
38 4 0.07
39 19 0.32
40 7 0.12
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (37 bp):
AAAAATTAAATTCTACAAATAAAAATAAATAATACAT
Found at i:726014 original size:73 final size:72
Alignment explanation
Indices: 725841--726002 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 72
725831 CGTAACTTTT
* * *
725841 AAAAA-AAA-TTAAACTTCTACAAATAAAAATAAATAATACACTAAAAATTTAAATTCATATAAT
1 AAAAACAAATTTAAATTTCTACAAATAAAAATAAATAATACACTAAAAATATAAATACATATAAT
725904 AAATATA
66 AAATATA
* *
725911 AAAAATAAATTTAAATTTCTACAAATAAAAATAAATTATATCA-TAAAAAATATAAATACATATA
1 AAAAACAAATTTAAATTTCTACAAATAAAAATAAATAATA-CACT-AAAAATATAAATACATATA
*
725975 AT-TATACCTA
64 ATAAATA--TA
*
725985 AAAAACACATTTAAATTT
1 AAAAACAAATTTAAATTT
726003 TATTAAAAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
70 5 0.06
71 3 0.04
72 32 0.41
73 21 0.27
74 18 0.23
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (72 bp):
AAAAACAAATTTAAATTTCTACAAATAAAAATAAATAATACACTAAAAATATAAATACATATAAT
AAATATA
Found at i:727179 original size:16 final size:16
Alignment explanation
Indices: 727160--727194 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
727150 TAAAATTTTT
*
727160 AATTATTTTTAATTTA
1 AATTATTTTAAATTTA
727176 AATTATTTTAAATTTA
1 AATTATTTTAAATTTA
727192 AAT
1 AAT
727195 CACTTTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:727769 original size:25 final size:27
Alignment explanation
Indices: 727735--727785 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
727725 TATCTACATT
*
727735 ATGTAATAAAATATTAT-TAAAATATC
1 ATGTAATAAAACATTATATAAAATATC
727761 ATGT-ATAAAACATTATGATAAAATA
1 ATGTAATAAAACATTAT-ATAAAATA
727786 CATATATCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 11 0.50
26 4 0.18
27 7 0.32
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (27 bp):
ATGTAATAAAACATTATATAAAATATC
Found at i:727879 original size:27 final size:27
Alignment explanation
Indices: 727827--727879 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
727817 ATTTTATTTT
* * *
727827 AAATTACATATTATATTTTTAAAATAA
1 AAATAACATATTATACTTTAAAAATAA
727854 AAATAACATATT-TACTTTAAATAATA
1 AAATAACATATTATACTTTAAA-AATA
727880 TGTACATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAACATATTATACTTTAAAAATAA
Found at i:728250 original size:11 final size:11
Alignment explanation
Indices: 728234--728258 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
728224 AAATATGATT
728234 ATATAAATATA
1 ATATAAATATA
728245 ATATAAATATA
1 ATATAAATATA
728256 ATA
1 ATA
728259 ATTAATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAAATATA
Found at i:730821 original size:125 final size:125
Alignment explanation
Indices: 730599--730849 Score: 484
Period size: 125 Copynumber: 2.0 Consensus size: 125
730589 CCCAAGGAAA
730599 GTAGAGCAAAAGCTAACTATTCATGTTACCAGCTAATCGACCCTTGGTATCCTGATAATGAAGGT
1 GTAGAGCAAAAGCTAACTATTCATGTTACCAGCTAATCGACCCTTGGTATCCTGATAATGAAGGT
*
730664 CTGACCAAATGTAAGCAGCTGATTATCAGTGTAAAACAAGCGTAACACATTAGAATACAC
66 CTGACCAAATGTAAGCAGCTGATTATCAGTGTAAAACAAGAGTAACACATTAGAATACAC
*
730724 GTAGAGCAAAAGCTATCTATTCATGTTACCAGCTAATCGACCCTTGGTATCCTGATAATGAAGGT
1 GTAGAGCAAAAGCTAACTATTCATGTTACCAGCTAATCGACCCTTGGTATCCTGATAATGAAGGT
730789 CTGACCAAATGTAAGCAGCTGATTATCAGTGTAAAACAAGAGTAACACATTAGAATACAC
66 CTGACCAAATGTAAGCAGCTGATTATCAGTGTAAAACAAGAGTAACACATTAGAATACAC
730849 G
1 G
730850 ACAAGATAAA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 124 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (125 bp):
GTAGAGCAAAAGCTAACTATTCATGTTACCAGCTAATCGACCCTTGGTATCCTGATAATGAAGGT
CTGACCAAATGTAAGCAGCTGATTATCAGTGTAAAACAAGAGTAACACATTAGAATACAC
Found at i:732252 original size:16 final size:17
Alignment explanation
Indices: 732224--732267 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
732214 TTTTATTTTA
732224 ATTTAATTTAAAATAAT
1 ATTTAATTTAAAATAAT
732241 ATTTAA-TTAAAATAAT
1 ATTTAATTTAAAATAAT
*
732257 ATTTTATTTAA
1 ATTTAATTTAA
732268 TTTTAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTTAAAATAAT
Found at i:732262 original size:44 final size:45
Alignment explanation
Indices: 732214--732306 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 45
732204 TTTTTTTATT
732214 TTTTATTTTAA-TTTAA-TTTAAAATAATATTTAAT-T-AAAATAATA
1 TTTTA-TTTAATTTTAATTTTAAAATAATA-TTAATATAAAAATAA-A
*
732258 TTTTATTTAATTTTAATTTTAAAATATTATTAATATAAAAATAAA
1 TTTTATTTAATTTTAATTTTAAAATAATATTAATATAAAAATAAA
732303 TTTT
1 TTTT
732307 TAATACTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
43 5 0.11
44 15 0.34
45 17 0.39
46 7 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (45 bp):
TTTTATTTAATTTTAATTTTAAAATAATATTAATATAAAAATAAA
Found at i:732317 original size:45 final size:44
Alignment explanation
Indices: 732225--732326 Score: 106
Period size: 45 Copynumber: 2.3 Consensus size: 44
732215 TTTATTTTAA
*
732225 TTTAATTTAAAATAATATTTAATTAAAATAATATTTTATTTAAT
1 TTTAATTTAAAATAATATTTAATTAAAATAATATTTTATATAAT
* *
732269 TTTAATTTTAAAATATTA-TTAATATAAAAATAA-ATTTT-TAATACT
1 TTTAA-TTTAAAATAATATTTAAT-T-AAAATAATATTTTAT-ATAAT
732314 TTT-A-TTAAAATAA
1 TTTAATTTAAAATAA
732327 ATAATATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
42 8 0.16
44 12 0.24
45 23 0.46
46 7 0.14
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (44 bp):
TTTAATTTAAAATAATATTTAATTAAAATAATATTTTATATAAT
Found at i:732582 original size:23 final size:25
Alignment explanation
Indices: 732531--732582 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
732521 TATACTTATA
732531 ATATAAAAAATAATATGAGATAATG
1 ATATAAAAAATAATATGAGATAATG
* *
732556 ATATAACATATAATATGA-A-AATG
1 ATATAAAAAATAATATGAGATAATG
732579 ATAT
1 ATAT
732583 GAATATATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.32
24 1 0.04
25 16 0.64
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.31
Consensus pattern (25 bp):
ATATAAAAAATAATATGAGATAATG
Found at i:733395 original size:18 final size:19
Alignment explanation
Indices: 733369--733404 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
733359 AATTATTTTC
733369 TTTTGTATTTTTATAAATA
1 TTTTGTATTTTTATAAATA
733388 TTTT-TATTTTTATAAAT
1 TTTTGTATTTTTATAAAT
733405 TGAAACATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTTGTATTTTTATAAATA
Found at i:737789 original size:2 final size:2
Alignment explanation
Indices: 737784--737814 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
737774 TCTCTCTCTC
737784 TA TA TA TA TA 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
737815 TTATTGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:740094 original size:45 final size:44
Alignment explanation
Indices: 740045--740176 Score: 117
Period size: 45 Copynumber: 3.2 Consensus size: 44
740035 TTTAAAATTT
740045 TAAAAAATTTTCAACTACTCTTAAAGAAACTTAGAAAGAAAATAA
1 TAAAAAATTTTCAACTA-TCTTAAAGAAACTTAGAAAGAAAATAA
* **
740090 TAAAAAATATTT--A-GA---T-AAG-AA--T-G-AAGAAAAATTT
1 TAAAAAAT-TTTCAACTATCTTAAAGAAACTTAGAAAG-AAAATAA
740124 TAAAAAATTTTCAACTATTCTTAAAGAAACTTAGAAAGAAAATAA
1 TAAAAAATTTTCAACTA-TCTTAAAGAAACTTAGAAAGAAAATAA
740169 TAAAAAAT
1 TAAAAAAT
740177 ATTTAGATAA
Statistics
Matches: 66, Mismatches: 6, Indels: 30
0.65 0.06 0.29
Matches are distributed among these distances:
33 6 0.09
34 14 0.21
35 2 0.03
36 1 0.02
37 2 0.03
38 3 0.05
39 1 0.02
40 1 0.02
41 3 0.05
42 2 0.03
43 1 0.02
44 2 0.03
45 22 0.33
46 6 0.09
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.28
Consensus pattern (44 bp):
TAAAAAATTTTCAACTATCTTAAAGAAACTTAGAAAGAAAATAA
Found at i:740129 original size:79 final size:79
Alignment explanation
Indices: 740038--740203 Score: 314
Period size: 79 Copynumber: 2.1 Consensus size: 79
740028 AGAAAATTTT
740038 AAAATTTTAAAAAATTTTCAACTACTCTTAAAGAAACTTAGAAAGAAAATAATAAAAAATATTTA
1 AAAATTTTAAAAAATTTTCAACTACTCTTAAAGAAACTTAGAAAGAAAATAATAAAAAATATTTA
*
740103 GATAAGAATGAAGA
66 GATAAAAATGAAGA
*
740117 AAAATTTTAAAAAATTTTCAACTATTCTTAAAGAAACTTAGAAAGAAAATAATAAAAAATATTTA
1 AAAATTTTAAAAAATTTTCAACTACTCTTAAAGAAACTTAGAAAGAAAATAATAAAAAATATTTA
740182 GATAAAAATGAAGA
66 GATAAAAATGAAGA
740196 AAAATTTT
1 AAAATTTT
740204 GGAAAAAACG
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.57, C:0.05, G:0.08, T:0.30
Consensus pattern (79 bp):
AAAATTTTAAAAAATTTTCAACTACTCTTAAAGAAACTTAGAAAGAAAATAATAAAAAATATTTA
GATAAAAATGAAGA
Found at i:740737 original size:21 final size:21
Alignment explanation
Indices: 740711--740787 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
740701 AAAAAATTCA
740711 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
740732 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
* *
740753 AATGTATCGATACA-TTCTACA
1 AATGTATCGATACATTTGTA-G
740774 AATGTATCGATACA
1 AATGTATCGATACA
740788 GGGTCCCAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 3 0.06
21 48 0.94
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:740862 original size:13 final size:13
Alignment explanation
Indices: 740844--740868 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
740834 GCATAAGTTT
740844 TGTATCGATACAA
1 TGTATCGATACAA
740857 TGTATCGATACA
1 TGTATCGATACA
740869 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:740871 original size:32 final size:32
Alignment explanation
Indices: 740825--740887 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
740815 TTCAACAATT
* *
740825 TGTATCGATGCATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
740857 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
740888 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:740881 original size:19 final size:19
Alignment explanation
Indices: 740824--740890 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
740814 ATTCAACAAT
* *
740824 TTGTATCGATGCATAAGTT
1 TTGTATCGATACATAAGTA
740843 TTGTATCGATAC---A--A
1 TTGTATCGATACATAAGTA
740857 -TGTATCGATACATAAGTA
1 TTGTATCGATACATAAGTA
740875 TTGTATCGATACATAA
1 TTGTATCGATACATAA
740891 TTAGCTACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
13 11 0.28
16 2 0.05
18 1 0.03
19 26 0.65
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATAAGTA
Found at i:740948 original size:13 final size:13
Alignment explanation
Indices: 740930--740955 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
740920 CATTTTTCTG
740930 TGTATCGATACAT
1 TGTATCGATACAT
740943 TGTATCGATACAT
1 TGTATCGATACAT
740956 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:740967 original size:33 final size:33
Alignment explanation
Indices: 740910--740976 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
740900 GCCAAGGAAA
***
740910 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
* *
740943 TGTATCGATACATGGATCTTTGTATTGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
740976 T
1 T
740977 TGAAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.13, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:741013 original size:15 final size:15
Alignment explanation
Indices: 740993--741021 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
740983 TTTTACCCAG
740993 ATGTATCGATACATA
1 ATGTATCGATACATA
741008 ATGTATCGATACAT
1 ATGTATCGATACAT
741022 TCAGGCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (15 bp):
ATGTATCGATACATA
Found at i:743441 original size:17 final size:17
Alignment explanation
Indices: 743419--743451 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
743409 CTTCACAATC
743419 GGGGATACTCCAACCCT
1 GGGGATACTCCAACCCT
*
743436 GGGGATATTCCAACCC
1 GGGGATACTCCAACCC
743452 CGTTATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (17 bp):
GGGGATACTCCAACCCT
Found at i:743521 original size:52 final size:52
Alignment explanation
Indices: 743464--743687 Score: 157
Period size: 52 Copynumber: 4.3 Consensus size: 52
743454 TTATTTCTGA
* ** * * * * *
743464 GGGGATACTCCAACCCATACTTTATTTTTAAAATATTGATTTTTTCATAATC
1 GGGGATACTCCAACCCAGACTTTATTGCTAAAACACTAATTTTTCCACAATC
* **
743516 GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCAGACTTTATTGCTAAAACACTAATTTTTCCACAATC
* ** * * * **
743568 GGGGATACTCCAACCCCGGTTTTATT-TTCAAAACACCAATTTTCCCTTTAATC
1 GGGGATACTCCAACCCAGACTTTATTGCT-AAAACACTAATTTTTCC-ACAATC
* * * * * *
743621 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAATACCAATTTCT-CACAATC
1 GGGGATACTCCAAC-CCAGACTTTA-TTGCTAAAACACTAATTTTTCCACAATC
*
743673 GAGGATACTCCAACC
1 GGGGATACTCCAACC
743688 TCGTTATTTC
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 2 0.01
52 99 0.70
53 25 0.18
54 16 0.11
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACCCAGACTTTATTGCTAAAACACTAATTTTTCCACAATC
Found at i:743644 original size:53 final size:53
Alignment explanation
Indices: 743509--743687 Score: 211
Period size: 52 Copynumber: 3.4 Consensus size: 53
743499 TTGATTTTTT
* * * *
743509 CATAATCGGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTTC
1 CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTCC
* *
743561 CACAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCC
1 CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTCC
* * * * *
743613 CTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAA-TTTCT
1 C-ATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTCC
* *
743666 CACAATCGAGGATACTCCAACC
1 CATAATCGGGGATACTCCAACC
743688 TCGTTATTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
52 62 0.57
53 38 0.35
54 9 0.08
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (53 bp):
CATAATCGGGGATACTCCAACCCCGGTTTTATTTCCAAAAACACCAATTTTCC
Found at i:743706 original size:28 final size:28
Alignment explanation
Indices: 743670--743744 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
743660 ATTTCTCACA
* * *
743670 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
743698 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
743726 CGAGGGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
743745 TGGCTTTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:747247 original size:33 final size:33
Alignment explanation
Indices: 747210--747276 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
747200 TTCAACGATT
747210 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
747243 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
747276 T
1 T
747277 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Done.