Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167893.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_16, 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: 22157061
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 74000 characters in sequence are not A, C, G, or T
File 3 of 113
Found at i:696949 original size:2 final size:2
Alignment explanation
Indices: 696942--696976 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
696932 TAATTTAGAA
696942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
696977 AAACAATCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:723818 original size:21 final size:20
Alignment explanation
Indices: 723776--723820 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
723766 TTATTATGCG
*
723776 ATTTAAATTAATATATTAAA
1 ATTTAAATTAATATAATAAA
723796 ATTTAAATTTAAT-TAATATAA
1 ATTTAAA-TTAATATAATA-AA
723817 ATTT
1 ATTT
723821 TTTTTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTAAATTAATATAATAAA
Found at i:725246 original size:2 final size:2
Alignment explanation
Indices: 725196--725230 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
725186 AAATAAATAA
725196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
725231 CACACACATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:725358 original size:3 final size:3
Alignment explanation
Indices: 725350--725384 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
725340 AATTTTCTTT
725350 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
725385 CTTCTTCTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:726107 original size:12 final size:12
Alignment explanation
Indices: 726086--726133 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
726076 GTTTCGTAAG
*
726086 TTTTTCTTTTTC
1 TTTTTATTTTTC
726098 TTTTTATTTTTC
1 TTTTTATTTTTC
* **
726110 GTTTTGATTTTGA
1 -TTTTTATTTTTC
726123 TTTTTATTTTT
1 TTTTTATTTTT
726134 TTATGTTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 20 0.69
13 9 0.31
ACGTcount: A:0.08, C:0.06, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTTC
Found at i:726134 original size:20 final size:20
Alignment explanation
Indices: 726111--726149 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
726101 TTATTTTTCG
*
726111 TTTTGATTTTGATTTTTATT
1 TTTTGATGTTGATTTTTATT
*
726131 TTTTTATGTTGATTTTTAT
1 TTTTGATGTTGATTTTTAT
726150 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.74
Consensus pattern (20 bp):
TTTTGATGTTGATTTTTATT
Found at i:726159 original size:22 final size:22
Alignment explanation
Indices: 726119--726182 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
726109 CGTTTTGATT
*
726119 TTGATTTTTAT-T-TTTTTATG
1 TTGATTTTTATATATTTTTATA
726139 TTGATTTTTATATATTTTTATA
1 TTGATTTTTATATATTTTTATA
*
726161 TT-ATTTTTTATGATATTGTTAT
1 TTGA-TTTTTAT-ATATTTTTAT
726183 TATTATTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 11 0.29
21 2 0.05
22 16 0.42
23 9 0.24
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.70
Consensus pattern (22 bp):
TTGATTTTTATATATTTTTATA
Found at i:726168 original size:12 final size:12
Alignment explanation
Indices: 726130--726205 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
726120 TGATTTTTAT
*
726130 TTTTTTATGTTGA
1 TTTTTTATATT-A
726143 -TTTTTATA-TA
1 TTTTTTATATTA
726153 -TTTTTATATTA
1 TTTTTTATATTA
726164 TTTTTTATGA-TA
1 TTTTTTAT-ATTA
*
726176 TTGTTATTATTATTG
1 TT-TT-TTA-TATTA
726191 TTATTTTATATTA
1 TT-TTTTATATTA
726204 TT
1 TT
726206 ACTAATAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
10 9 0.17
11 3 0.06
12 18 0.35
13 9 0.17
14 7 0.13
15 6 0.12
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTTTATATTA
Found at i:726169 original size:23 final size:24
Alignment explanation
Indices: 726143--726202 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
726133 TTTATGTTGA
*
726143 TTTTTATATATTTTTA-TATTAT-
1 TTTTTATATATTGTTATTATTATG
726165 TTTTTATGATATTGTTATTATTATTG
1 TTTTTAT-ATATTGTTATTATTA-TG
726191 TTATTT-TATATT
1 TT-TTTATATATT
726203 ATTACTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.22
23 8 0.25
24 5 0.16
25 6 0.19
26 3 0.09
27 3 0.09
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (24 bp):
TTTTTATATATTGTTATTATTATG
Found at i:727915 original size:66 final size:66
Alignment explanation
Indices: 727837--727962 Score: 234
Period size: 66 Copynumber: 1.9 Consensus size: 66
727827 ACCATCGTTC
*
727837 CTCATTTTTTGTCGTTACAAAGCACATGTTTTTAATGAACTCCACATATATTACTGGTATAGTTG
1 CTCATTTCTTGTCGTTACAAAGCACATGTTTTTAATGAACTCCACATATATTACTGGTATAGTTG
727902 T
66 T
*
727903 CTCATTTCTTGTCGTTACAAAGCACATGTTTTTAATGGACTCCACATATATTACTGGTAT
1 CTCATTTCTTGTCGTTACAAAGCACATGTTTTTAATGAACTCCACATATATTACTGGTAT
727963 CGACTTGAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.41
Consensus pattern (66 bp):
CTCATTTCTTGTCGTTACAAAGCACATGTTTTTAATGAACTCCACATATATTACTGGTATAGTTG
T
Found at i:729789 original size:19 final size:19
Alignment explanation
Indices: 729765--729804 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
729755 CTTAAAGCCC
729765 ACCAAAAAAAAAAAAAAAA
1 ACCAAAAAAAAAAAAAAAA
* *
729784 ACCAAACAAAAAACAAAAA
1 ACCAAAAAAAAAAAAAAAA
729803 AC
1 AC
729805 AGAAAAGGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.00
Consensus pattern (19 bp):
ACCAAAAAAAAAAAAAAAA
Found at i:731051 original size:3 final size:3
Alignment explanation
Indices: 731043--731076 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
731033 AAAATACATC
731043 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
731077 GTTTATTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:731412 original size:13 final size:13
Alignment explanation
Indices: 731396--731420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
731386 AAGCTTTTAT
731396 TTTTTTCTTTCCC
1 TTTTTTCTTTCCC
731409 TTTTTTCTTTCC
1 TTTTTTCTTTCC
731421 TCCTTCTCCC
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTCTTTCCC
Found at i:731835 original size:3 final size:3
Alignment explanation
Indices: 731827--731851 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
731817 TCACTTTACC
731827 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
731852 CATTCTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:733531 original size:30 final size:30
Alignment explanation
Indices: 733497--733555 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
733487 TTTTTTTGTT
* *
733497 TGTTTTAGTTATTGCATGTGTAGGATCAAA
1 TGTTTTAGTTACTACATGTGTAGGATCAAA
*
733527 TGTTTTAGTTACTACATGTGTATGATCAA
1 TGTTTTAGTTACTACATGTGTAGGATCAA
733556 TTTAGATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.20, T:0.44
Consensus pattern (30 bp):
TGTTTTAGTTACTACATGTGTAGGATCAAA
Found at i:735962 original size:134 final size:134
Alignment explanation
Indices: 735749--736015 Score: 507
Period size: 134 Copynumber: 2.0 Consensus size: 134
735739 ATGAAGTTGC
735749 CACCAATCTTTTTTGGCTAGGTGCGATTGACCACTTATTAAAATTTATCTTTTTAACAAAATTTT
1 CACCAATCTTTTTTGGCTAGGTGCGATTGACCACTTATTAAAATTTATCTTTTTAACAAAATTTT
735814 AAAATTAATTAAAATTTATTAAAAATATAATTTTATGATCTGTAAAACAGTCTAGATGCGAGAGT
66 AAAATTAATTAAAATTTATTAAAAATATAATTTTATGATCTGTAAAACAGTCTAGATGCGAGAGT
735879 CGAA
131 CGAA
*
735883 CACCAATCTTTTTTTGCTAGGTGCGATTGACCACTTATTAAAATTTATCTTTTTAACAAAATTTT
1 CACCAATCTTTTTTGGCTAGGTGCGATTGACCACTTATTAAAATTTATCTTTTTAACAAAATTTT
**
735948 AAAATTAATTAAAATTTATTAAAAATATAATTTTATGATCTGTAAAACAGTCTAGATTTGAGAGT
66 AAAATTAATTAAAATTTATTAAAAATATAATTTTATGATCTGTAAAACAGTCTAGATGCGAGAGT
736013 CGA
131 CGA
736016 TTACTCGTGA
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 130 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (134 bp):
CACCAATCTTTTTTGGCTAGGTGCGATTGACCACTTATTAAAATTTATCTTTTTAACAAAATTTT
AAAATTAATTAAAATTTATTAAAAATATAATTTTATGATCTGTAAAACAGTCTAGATGCGAGAGT
CGAA
Found at i:738134 original size:21 final size:20
Alignment explanation
Indices: 738095--738151 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
738085 CATCAGCCAC
738095 TTTTG-TTTTTTTTTATATT
1 TTTTGTTTTTTTTTTATATT
*
738114 TTTTGTTTTTTTCTTTCTATT
1 TTTTGTTTTTTT-TTTATATT
*
738135 TTTTGTATTTTTGTTTA
1 TTTTGT-TTTTTTTTTA
738152 ATTAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 16 0.50
22 5 0.16
ACGTcount: A:0.09, C:0.04, G:0.07, T:0.81
Consensus pattern (20 bp):
TTTTGTTTTTTTTTTATATT
Found at i:741205 original size:3 final size:3
Alignment explanation
Indices: 741197--741226 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
741187 AAGTAGAAGG
741197 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
741227 GCATGCTGCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:745322 original size:42 final size:42
Alignment explanation
Indices: 745263--745349 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
745253 TATATGGATC
745263 TCAGGGAATTTTTTAGTTTTTTATGATGAATACCTCATTACA
1 TCAGGGAATTTTTTAGTTTTTTATGATGAATACCTCATTACA
745305 TCAGGGAATTTTTTAGTTTTTTATGATGAATACCTCATTACA
1 TCAGGGAATTTTTTAGTTTTTTATGATGAATACCTCATTACA
745347 TCA
1 TCA
745350 TCAAATACTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.45
Consensus pattern (42 bp):
TCAGGGAATTTTTTAGTTTTTTATGATGAATACCTCATTACA
Found at i:750546 original size:2 final size:2
Alignment explanation
Indices: 750539--750568 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
750529 TGATTTAATA
750539 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
750569 CCACCAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:763411 original size:2 final size:2
Alignment explanation
Indices: 763404--763444 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
763394 TCCATGTTGA
763404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
763445 CCATTTGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:764869 original size:12 final size:12
Alignment explanation
Indices: 764849--764891 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
764839 TATTTAATTA
764849 TAAAATTTTTAT
1 TAAAATTTTTAT
*
764861 TAAAGTTTTTAT
1 TAAAATTTTTAT
*
764873 TAAAAATATTTATT
1 T-AAAATTTTTA-T
764887 TAAAA
1 TAAAA
764892 AATATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 12 0.46
13 12 0.46
14 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
TAAAATTTTTAT
Found at i:764884 original size:13 final size:13
Alignment explanation
Indices: 764839--764913 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
764829 GTATAATGTT
764839 TATTTAATTATAAAA
1 TATTT-ATTA-AAAA
* *
764854 TTTTTATT-AAAG
1 TATTTATTAAAAA
*
764866 TTTTTATTAAAAA
1 TATTTATTAAAAA
764879 TATTTATTTAAAAA
1 TATTTA-TTAAAAA
*
764893 -ATATATT-AAAA
1 TATTTATTAAAAA
764904 TATATTATTA
1 TAT-TTATTA
764914 TTTTTTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
11 4 0.08
12 15 0.31
13 16 0.33
14 10 0.20
15 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (13 bp):
TATTTATTAAAAA
Found at i:768251 original size:22 final size:23
Alignment explanation
Indices: 768226--768294 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
768216 AATATCTTTT
*
768226 AATTTAATTAATATTA-ATAAAA
1 AATTTAATAAATATTATATAAAA
* * *
768248 AATTTCATAAATTTTATTTAAAA
1 AATTTAATAAATATTATATAAAA
* * *
768271 AATTTCATAAATTTTATTTAAAA
1 AATTTAATAAATATTATATAAAA
768294 A
1 A
768295 TTTTTATCTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 13 0.31
23 29 0.69
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (23 bp):
AATTTAATAAATATTATATAAAA
Found at i:768297 original size:22 final size:23
Alignment explanation
Indices: 768243--768294 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
768233 TTAATATTAA
768243 TAAAAAATTTCATAAATTTTATT
1 TAAAAAATTTCATAAATTTTATT
768266 TAAAAAATTTCATAAATTTTATT
1 TAAAAAATTTCATAAATTTTATT
768289 TAAAAA
1 TAAAAA
768295 TTTTTATCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAAAAATTTCATAAATTTTATT
Found at i:771441 original size:21 final size:20
Alignment explanation
Indices: 771415--771474 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
771405 ATCAAATTAA
771415 ATTTAAATATTTTTATATTT
1 ATTTAAATATTTTTATATTT
* * *
771435 GATTTAAGTAATTTATAAATTT
1 -ATTTAAAT-ATTTTTATATTT
*
771457 AATTAAA-A-TTTTATATTT
1 ATTTAAATATTTTTATATTT
771475 TAATATATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 8 0.26
19 1 0.03
21 12 0.39
22 10 0.32
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTTAAATATTTTTATATTT
Found at i:771476 original size:19 final size:21
Alignment explanation
Indices: 771454--771500 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
771444 AATTTATAAA
771454 TTTAATTAAAATTTT-A-TAT
1 TTTAATTAAAATTTTAATTAT
*
771473 TTTAA-T-ATATTTTAATTAT
1 TTTAATTAAAATTTTAATTAT
771492 TTTAATTAA
1 TTTAATTAA
771501 TAAAATATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 13 0.57
20 1 0.04
21 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTAATTAAAATTTTAATTAT
Found at i:771481 original size:10 final size:10
Alignment explanation
Indices: 771468--771497 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
771458 ATTAAAATTT
771468 TATATTTTAA
1 TATATTTTAA
771478 TATATTTTAA
1 TATATTTTAA
771488 T-TATTTTAA
1 TATATTTTAA
771497 T
1 T
771498 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:771494 original size:9 final size:9
Alignment explanation
Indices: 771470--771499 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
771460 TAAAATTTTA
771470 TATTTTAAT
1 TATTTTAAT
771479 ATATTTTAAT
1 -TATTTTAAT
771489 TATTTTAAT
1 TATTTTAAT
771498 TA
1 TA
771500 ATAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTTTAAT
Found at i:774967 original size:20 final size:20
Alignment explanation
Indices: 774926--774967 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
774916 AAAAATAATA
*
774926 TAAAAAATTATATATATTTT
1 TAAAAAATTATATATATATT
*
774946 TAAAAAA-TATATTTAATATT
1 TAAAAAATTATATAT-ATATT
774966 TA
1 TA
774968 TTCACGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TAAAAAATTATATATATATT
Found at i:775381 original size:13 final size:12
Alignment explanation
Indices: 775359--775394 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
775349 TAGTTTTGTA
775359 ATATATTTAAAT
1 ATATATTTAAAT
775371 ATATATATTAAAT
1 ATATAT-TTAAAT
775384 ATATA-TTAAAT
1 ATATATTTAAAT
775395 GAGTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 6 0.26
12 6 0.26
13 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTTAAAT
Found at i:775539 original size:29 final size:29
Alignment explanation
Indices: 775507--775583 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
775497 TAGTCATGTT
* * *
775507 TTTATATATATTCGTATTACTTATGCCTA
1 TTTATGTATATTCGTATTAATTATGCCAA
* *
775536 TTTATGTATATAT-GTGTTAATTATGTCAA
1 TTTATGTATAT-TCGTATTAATTATGCCAA
*
775565 TTCATGTATATTCGTATTA
1 TTTATGTATATTCGTATTA
775584 TTCGTATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
28 1 0.03
29 37 0.95
30 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.10, T:0.52
Consensus pattern (29 bp):
TTTATGTATATTCGTATTAATTATGCCAA
Found at i:782448 original size:145 final size:145
Alignment explanation
Indices: 782179--782469 Score: 510
Period size: 145 Copynumber: 2.0 Consensus size: 145
782169 CTATGCCATT
782179 GATAAACTGAATAATAACTGTCCCATTTCCACAATTATCTTATAATTTTGCTTTATAAGCAGAAA
1 GATAAACTGAATAATAACTGTCCCATTTCCACAATTATCTTATAATTTTGCTTTATAAGCAGAAA
* *
782244 CAAATAATCACTCCCAATAATTCTGTTTCCAGTTTATCTTTCAGGTTAAATGTTGGGCACCACCC
66 CAAATAATCACTCCCAATAATTCTGTTTCCAGTTTATCTTTCAGGTTAAAGGTTAGGCACCACCC
782309 TTGTTAATTGAGATA
131 TTGTTAATTGAGATA
* * **
782324 GATAAATTGAATAATAACTGTCCCATTTCCACTATTATCTTATGCTTTTGCTTTATAAGCAGAAA
1 GATAAACTGAATAATAACTGTCCCATTTCCACAATTATCTTATAATTTTGCTTTATAAGCAGAAA
* *
782389 CAAATAATCACTCCCAATAATTCTGTTTCTAGTTTATCTTTCAGGTTAAAGGTTAGGCACTACCC
66 CAAATAATCACTCCCAATAATTCTGTTTCCAGTTTATCTTTCAGGTTAAAGGTTAGGCACCACCC
782454 TTGTTAATTGAGATA
131 TTGTTAATTGAGATA
782469 G
1 G
782470 CTTCCTCAAC
Statistics
Matches: 138, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
145 138 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (145 bp):
GATAAACTGAATAATAACTGTCCCATTTCCACAATTATCTTATAATTTTGCTTTATAAGCAGAAA
CAAATAATCACTCCCAATAATTCTGTTTCCAGTTTATCTTTCAGGTTAAAGGTTAGGCACCACCC
TTGTTAATTGAGATA
Found at i:795482 original size:2 final size:2
Alignment explanation
Indices: 795475--795510 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
795465 TTTCAGGAGC
*
795475 AT AT AT AT GT 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
795511 TTTGAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:796460 original size:37 final size:37
Alignment explanation
Indices: 796423--796494 Score: 103
Period size: 37 Copynumber: 1.9 Consensus size: 37
796413 AATTTAAATT
*
796423 TTTTAAAA-ATAATTTAATAAAATTT-TTTAAAAAAA
1 TTTTAAAACATAAATTAATAAAATTTATTTAAAAAAA
796458 TTTTAAAACGATAAATTAATAAAATTTAATTTAAAAA
1 TTTTAAAAC-ATAAATTAATAAAATTT-ATTTAAAAA
796495 TCAATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
35 8 0.25
37 16 0.50
39 8 0.25
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (37 bp):
TTTTAAAACATAAATTAATAAAATTTATTTAAAAAAA
Found at i:796495 original size:37 final size:35
Alignment explanation
Indices: 796413--796495 Score: 89
Period size: 37 Copynumber: 2.3 Consensus size: 35
796403 TTTTAAGTGA
** *
796413 AATTTAAATTTTTTAAAAATAATTTAATAAAATTT
1 AATTTAAAAATTTTAAAAATAAATTAATAAAATTT
796448 --TTTAAAAAAATTTTAAAACGATAAATTAATAAAATTT
1 AATTT--AAAAATTTTAAAA--ATAAATTAATAAAATTT
796485 AATTTAAAAAT
1 AATTTAAAAAT
796496 CAATAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
33 3 0.08
35 11 0.28
37 22 0.56
39 3 0.08
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (35 bp):
AATTTAAAAATTTTAAAAATAAATTAATAAAATTT
Found at i:797157 original size:2 final size:2
Alignment explanation
Indices: 797152--797183 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
797142 ATATACATTC
*
797152 AT AT AT GT 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
797184 GCAAAGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:797229 original size:15 final size:15
Alignment explanation
Indices: 797209--797242 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
797199 TATTTTCAAT
797209 TGTTTCAC-AGCATCA
1 TGTTTCACAAG-ATCA
797224 TGTTTCACAAGATCA
1 TGTTTCACAAGATCA
797239 TGTT
1 TGTT
797243 CGTTTTTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (15 bp):
TGTTTCACAAGATCA
Found at i:805576 original size:21 final size:20
Alignment explanation
Indices: 805556--805595 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
805546 TTTTTTTTTG
805556 GGTATATTGCTTATA-AATTT
1 GGTATA-TGCTTATATAATTT
*
805576 GGTATATGCTTTTATAATTT
1 GGTATATGCTTATATAATTT
805596 TGATTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.28, C:0.05, G:0.15, T:0.53
Consensus pattern (20 bp):
GGTATATGCTTATATAATTT
Found at i:806171 original size:15 final size:16
Alignment explanation
Indices: 806148--806181 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
806138 CTTGATGACA
*
806148 TATCTTTAACAA-TGG
1 TATCCTTAACAATTGG
806163 TATCCTTAACAATTGG
1 TATCCTTAACAATTGG
806179 TAT
1 TAT
806182 GAGCTTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (16 bp):
TATCCTTAACAATTGG
Found at i:806342 original size:198 final size:197
Alignment explanation
Indices: 806004--806392 Score: 726
Period size: 198 Copynumber: 2.0 Consensus size: 197
805994 TTTATGTACC
806004 TATCCTTGATATAGCTTATACCTTTCAAGCAAAATTGTGTGTGCCTTAAATTGATTAATCTTTAT
1 TATCCTTGATATAGCTTATACCTTTCAAGCAAAATTGTGTGTGCCTTAAATTGATTAATCTTTAT
* * *
806069 TTTGAAATGAAGAGCAATATTAGAATACAATTTTGCTTGATTTATTTTGTGATAACAATTGGTAC
66 TTTGAAATGAAGAGCAATATTAGAATACAATTTTACTTAATTTATTTTGTGATAACAATTGATAC
806134 GCTTCTTGATGACATATCTTTAACAATGGTATCCTTAACAATTGGTATGAGCTTGTATGCATATG
131 GCTTCTTGATGACATATCTTTAACAATGGTATCCTTAA-AATTGGTATGAGCTTGTATGCATATG
806199 TTA
195 TTA
806202 TATCCTTGATATAGCTTATACCTTTCAAGCAAAATTGTGTGTGCCTTAAATTGATTAATCTTTAT
1 TATCCTTGATATAGCTTATACCTTTCAAGCAAAATTGTGTGTGCCTTAAATTGATTAATCTTTAT
806267 TTTGAAATG-AGAAGCAATATTAGAATACAATTTTACTTAATTTATTTTGTGATAACAATTGATA
66 TTTGAAATGAAG-AGCAATATTAGAATACAATTTTACTTAATTTATTTTGTGATAACAATTGATA
806331 CGCTTCTTGATGACATATCTTTAACAATGGTATCCTTAAAATTGGTATGAGCTTGTATGCAT
130 CGCTTCTTGATGACATATCTTTAACAATGGTATCCTTAAAATTGGTATGAGCTTGTATGCAT
806393 GTGCTTGAAT
Statistics
Matches: 187, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
197 25 0.13
198 162 0.87
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.41
Consensus pattern (197 bp):
TATCCTTGATATAGCTTATACCTTTCAAGCAAAATTGTGTGTGCCTTAAATTGATTAATCTTTAT
TTTGAAATGAAGAGCAATATTAGAATACAATTTTACTTAATTTATTTTGTGATAACAATTGATAC
GCTTCTTGATGACATATCTTTAACAATGGTATCCTTAAAATTGGTATGAGCTTGTATGCATATGT
TA
Found at i:809782 original size:16 final size:16
Alignment explanation
Indices: 809761--809793 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
809751 GTTCAATCAA
809761 TTTTCTCT-TTTTCTTT
1 TTTTCTCTATTTT-TTT
809777 TTTTCTCTATTTTTTT
1 TTTTCTCTATTTTTTT
809793 T
1 T
809794 GCTATTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTCTATTTTTTT
Found at i:815387 original size:25 final size:23
Alignment explanation
Indices: 815340--815387 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
815330 TTGGACATAA
*
815340 TTTATATGATATATTTAAAAATT
1 TTTATATGATATATTCAAAAATT
815363 TTTATATGATATATTACAAATAATT
1 TTTATATGATATATT-CAAA-AATT
815388 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.68
24 3 0.14
25 4 0.18
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTATATGATATATTCAAAAATT
Found at i:815887 original size:15 final size:15
Alignment explanation
Indices: 815867--815920 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
815857 CTATAAAATA
815867 TTAAATATTAATAAT
1 TTAAATATTAATAAT
*
815882 TTAAATATT-TTAAT
1 TTAAATATTAATAAT
* * *
815896 GATAAATATTACTATT
1 -TTAAATATTAATAAT
815912 TTAAATATT
1 TTAAATATT
815921 TTATTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 4 0.12
15 25 0.78
16 3 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAAATATTAATAAT
Found at i:815942 original size:15 final size:16
Alignment explanation
Indices: 815922--815952 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
815912 TTAAATATTT
815922 TATTTTAATA-TAAAA
1 TATTTTAATAGTAAAA
815937 TATTTTAATAGTAAAA
1 TATTTTAATAGTAAAA
815953 CAATATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (16 bp):
TATTTTAATAGTAAAA
Found at i:815976 original size:19 final size:18
Alignment explanation
Indices: 815930--815978 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
815920 TTTATTTTAA
815930 TATAAAATATTTTAATAG
1 TATAAAATATTTTAATAG
* *
815948 TAAAACAATATTTTAAATAT
1 TATAA-AATATTTT-AATAG
*
815968 TTTAAAATATT
1 TATAAAATATT
815979 AATAATAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TATAAAATATTTTAATAG
Found at i:815999 original size:54 final size:49
Alignment explanation
Indices: 815867--816026 Score: 144
Period size: 54 Copynumber: 3.1 Consensus size: 49
815857 CTATAAAATA
* * * *
815867 TTAAATATTAATAATTTAAATATTTTAATGATAAATATTACTATTTTAAATATT
1 TTAAATATTAAT-A-TAAAATATGTTAATAATAAACA--A-TATTTTAAATATT
* * *
815921 TT--ATTTTAATATAAAATATTTTAATAGTAAAACAATATTTTAAATATT
1 TTAAATATTAATATAAAATATGTTAATAAT-AAACAATATTTTAAATATT
815969 TTAAAATATTAATAATAAATATGATGTTAATAATAAACAATATTTGTAAATATT
1 TT-AAATATTAAT-ATAAA-AT-ATGTTAATAATAAACAATATTT-TAAATATT
816023 TTAA
1 TTAA
816027 TGCTAAAATA
Statistics
Matches: 90, Mismatches: 8, Indels: 17
0.78 0.07 0.15
Matches are distributed among these distances:
48 15 0.17
49 1 0.01
50 14 0.16
51 12 0.13
52 12 0.13
53 15 0.17
54 21 0.23
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (49 bp):
TTAAATATTAATATAAAATATGTTAATAATAAACAATATTTTAAATATT
Found at i:816380 original size:35 final size:35
Alignment explanation
Indices: 816313--816380 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
816303 AAAATTTTAA
*
816313 AAATTAACCAAATAACAAAACAAAATATTTTTATT
1 AAATTAACCAAATAACAAAACAAAATACTTTTATT
* * *
816348 AAATTATCCAAATAACGGAAA-ATAATACTTTTA
1 AAATTAACCAAATAAC-AAAACAAAATACTTTTA
816381 AAAAAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 25 0.89
36 3 0.11
ACGTcount: A:0.54, C:0.12, G:0.03, T:0.31
Consensus pattern (35 bp):
AAATTAACCAAATAACAAAACAAAATACTTTTATT
Found at i:820081 original size:21 final size:21
Alignment explanation
Indices: 820055--820107 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
820045 TGGGCTCGTC
820055 TTGTTCTGGCTATTGCCAGGT
1 TTGTTCTGGCTATTGCCAGGT
820076 TTGTTCTGGCTATTGCCAGGT
1 TTGTTCTGGCTATTGCCAGGT
*
820097 CTGTTCTGGCT
1 TTGTTCTGGCT
820108 TTGGGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.08, C:0.21, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGTTCTGGCTATTGCCAGGT
Found at i:823199 original size:24 final size:24
Alignment explanation
Indices: 823150--823203 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
823140 AATAATTTTT
**
823150 ATAAATTTATTAAATCTAACGTAA
1 ATAAATTTATTAAATCTAACAAAA
*
823174 ATAAATTTATTTAAATC-AATAAAA
1 ATAAATTTA-TTAAATCTAACAAAA
823198 ATAAAT
1 ATAAAT
823204 AAATAAACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAAATTTATTAAATCTAACAAAA
Found at i:825310 original size:6 final size:6
Alignment explanation
Indices: 825301--825331 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
825291 TTTTTTTATA
*
825301 AAAAAT AAAAAT AAAAAT AAAAAT AAGAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
825332 TTTTTTATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:825481 original size:2 final size:2
Alignment explanation
Indices: 825474--825508 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
825464 CTCAAAATTT
*
825474 TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
825509 TTTTCTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:827120 original size:188 final size:188
Alignment explanation
Indices: 826803--827166 Score: 611
Period size: 188 Copynumber: 1.9 Consensus size: 188
826793 ATCTCTACCT
* * *
826803 GTCAACTTTGATGTTTATTTGCGCATTTCACATGTAATGTATAACTTCTTATCCTCTAAGAAATA
1 GTCAACTTTGATGTTTATTTGCCCATTTCACATGTAATGTATAACTCCCTATCCTCTAAGAAATA
* *
826868 GAAATATGATGATAGGATCTCTCATGCCCTTTCCCTGCTACTTGGTATGCCATTAATTGCTTTAA
66 GAAATATGATGACAGGATCTCTCATGCCCTTTCCCTGCTACTTGGTATGCCATTAATCGCTTTAA
826933 CTAATGATATTTCCCAAGTTGTTTAATGCTAACATCTGATCCCAAACTTTCTAACCCA
131 CTAATGATATTTCCCAAGTTGTTTAATGCTAACATCTGATCCCAAACTTTCTAACCCA
** *
826991 GTCAACTTTGATGTTTATTTGCCCATTTCATGTGTAATTTATAACTCCCTATCCTCTAAGAAATA
1 GTCAACTTTGATGTTTATTTGCCCATTTCACATGTAATGTATAACTCCCTATCCTCTAAGAAATA
* * * *
827056 GAAATATGATGACAGGATCTCTCATGTCCTTTCCCTGCTCCTTGGTATGCTATTGATCGCTTTAA
66 GAAATATGATGACAGGATCTCTCATGCCCTTTCCCTGCTACTTGGTATGCCATTAATCGCTTTAA
*
827121 CTAATGATGTTTCCCAAGTTGTTTAATGCTAACATCTGATCCCAAA
131 CTAATGATATTTCCCAAGTTGTTTAATGCTAACATCTGATCCCAAA
827167 TTTTGTGTTT
Statistics
Matches: 163, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 163 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.38
Consensus pattern (188 bp):
GTCAACTTTGATGTTTATTTGCCCATTTCACATGTAATGTATAACTCCCTATCCTCTAAGAAATA
GAAATATGATGACAGGATCTCTCATGCCCTTTCCCTGCTACTTGGTATGCCATTAATCGCTTTAA
CTAATGATATTTCCCAAGTTGTTTAATGCTAACATCTGATCCCAAACTTTCTAACCCA
Found at i:835311 original size:31 final size:31
Alignment explanation
Indices: 835273--835340 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
835263 TATATTTAAT
* * *
835273 TTTTTATGTAGATATAAATTAT-AATACGTAA
1 TTTTTATGTA-AAATAAAATATGAATACATAA
835304 TTTTTATGTAAAATAAAATATGAATACATAA
1 TTTTTATGTAAAATAAAATATGAATACATAA
*
835335 ATTTTA
1 TTTTTA
835341 ATATTTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (31 bp):
TTTTTATGTAAAATAAAATATGAATACATAA
Found at i:837099 original size:2 final size:2
Alignment explanation
Indices: 837092--837120 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
837082 AATATCTGGC
837092 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 T
837121 TGATTAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:838102 original size:2 final size:2
Alignment explanation
Indices: 838095--838119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
838085 AAACTTGAAA
838095 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
838120 AATGATTTGG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:838484 original size:2 final size:2
Alignment explanation
Indices: 838477--838512 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
838467 CTCCTCATTT
* *
838477 TA TA TA TA AA TA TA AA 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
838513 ATGAGAAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:844739 original size:78 final size:78
Alignment explanation
Indices: 844610--844770 Score: 322
Period size: 78 Copynumber: 2.1 Consensus size: 78
844600 TCTAATGAGG
844610 TTTATTGGCAACTAAAGCATGGTAAAATTTTAGTTCGAATACTTCAAGACTTTATAAACCTTTTC
1 TTTATTGGCAACTAAAGCATGGTAAAATTTTAGTTCGAATACTTCAAGACTTTATAAACCTTTTC
844675 CATTATGACTTTT
66 CATTATGACTTTT
844688 TTTATTGGCAACTAAAGCATGGTAAAATTTTAGTTCGAATACTTCAAGACTTTATAAACCTTTTC
1 TTTATTGGCAACTAAAGCATGGTAAAATTTTAGTTCGAATACTTCAAGACTTTATAAACCTTTTC
844753 CATTATGACTTTT
66 CATTATGACTTTT
844766 TTTAT
1 TTTAT
844771 AAGCAAGATG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 83 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (78 bp):
TTTATTGGCAACTAAAGCATGGTAAAATTTTAGTTCGAATACTTCAAGACTTTATAAACCTTTTC
CATTATGACTTTT
Found at i:845936 original size:26 final size:26
Alignment explanation
Indices: 845889--845938 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
845879 GAGGTGCAAA
*
845889 ATTTTACTGAGTGACAATTATAATTT
1 ATTTTACTGAGTGACAAATATAATTT
845915 ATTTTACTGAGTG-CAAAATATAAT
1 ATTTTACTGAGTGAC-AAATATAAT
845939 AATGACAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTACTGAGTGACAAATATAATTT
Found at i:847368 original size:21 final size:21
Alignment explanation
Indices: 847342--847384 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
847332 TTTTTGGGTA
847342 AATTATATAAATATATCTTAT
1 AATTATATAAATATATCTTAT
847363 AATTATATAAATATATCTTAT
1 AATTATATAAATATATCTTAT
847384 A
1 A
847385 GTTAAATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (21 bp):
AATTATATAAATATATCTTAT
Found at i:850509 original size:18 final size:18
Alignment explanation
Indices: 850486--850520 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
850476 AAGCTAGTCA
850486 ATGGGAACCGATTGGTTT
1 ATGGGAACCGATTGGTTT
*
850504 ATGGGAATCGATTGGTT
1 ATGGGAACCGATTGGTT
850521 ATATAATCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.09, G:0.34, T:0.34
Consensus pattern (18 bp):
ATGGGAACCGATTGGTTT
Found at i:850909 original size:3 final size:3
Alignment explanation
Indices: 850901--850957 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
850891 TGATCTCCTT
*
850901 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
850949 TAA TAA TAA
1 TAA TAA TAA
850958 AGTTAAGGAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:851042 original size:3 final size:3
Alignment explanation
Indices: 851034--851061 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
851024 TGTGACAAAC
851034 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
851062 TAGATTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:851412 original size:16 final size:16
Alignment explanation
Indices: 851356--851445 Score: 74
Period size: 16 Copynumber: 5.6 Consensus size: 16
851346 AATCAATCCC
*
851356 AATTTAAATTAATTCA
1 AATTTAAAATAATTCA
* * *
851372 AATTTGAAATGATTTGA
1 AATTTAAAAT-AATTCA
851389 AA-TTAAAATAATTCA
1 AATTTAAAATAATTCA
** *
851404 AATTTAAAATGGTCCA
1 AATTTAAAATAATTCA
* *
851420 AATTCAAAATGATTCA
1 AATTTAAAATAATTCA
*
851436 AAATTAAAAT
1 AATTTAAAAT
851446 TGCCCAAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
15 6 0.11
16 45 0.79
17 6 0.11
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (16 bp):
AATTTAAAATAATTCA
Found at i:851429 original size:32 final size:32
Alignment explanation
Indices: 851354--851445 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 32
851344 GAAATCAATC
* * * *
851354 CCAATTTAAATTAATTCAAATTTGAAATGATT
1 CCAAATTAAAATAATTCAAATTTAAAATGAGT
**
851386 TGAAATTAAAATAATTCAAATTTAAAATG-GT
1 CCAAATTAAAATAATTCAAATTTAAAATGAGT
* *
851417 CCAAATTCAAAATGATTCAAAATTAAAAT
1 CCAAATT-AAAATAATTCAAATTTAAAAT
851446 TGCCCAAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
31 6 0.12
32 43 0.88
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (32 bp):
CCAAATTAAAATAATTCAAATTTAAAATGAGT
Found at i:851453 original size:32 final size:31
Alignment explanation
Indices: 851388--851453 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
851378 AAATGATTTG
* *
851388 AAATTAAAATAATTCAAATTTAAAATGGTCC
1 AAATTAAAATAATTCAAAATTAAAATGGCCC
* *
851419 AAATTCAAAATGATTCAAAATTAAAATTGCCC
1 AAATT-AAAATAATTCAAAATTAAAATGGCCC
851451 AAA
1 AAA
851454 AAATTAACCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 5 0.17
32 25 0.83
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.29
Consensus pattern (31 bp):
AAATTAAAATAATTCAAAATTAAAATGGCCC
Found at i:852082 original size:50 final size:55
Alignment explanation
Indices: 851966--852084 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 55
851956 AAATAATTGC
*
851966 AATTAAA-TGTGTATCATAATTAAATATTTAAAATAATTTGTATATAATTATATT
1 AATTAAATTATGTATCATAATTAAATATTTAAAATAATTTGTATATAATTATATT
* * *
852020 AAATATGTAATTATGTATTATAATTAAA-ATTTAAAATAATCTT-TATATATTTATATT
1 -AAT-T-AAATTATGTATCATAATTAAATATTTAAAATAAT-TTGTATATAATTATATT
852077 AAATTAAA
1 -AATTAAA
852085 ATAAATAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
55 5 0.09
56 2 0.04
57 31 0.56
58 17 0.31
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (55 bp):
AATTAAATTATGTATCATAATTAAATATTTAAAATAATTTGTATATAATTATATT
Found at i:852420 original size:21 final size:21
Alignment explanation
Indices: 852385--852425 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
852375 AATATTTATA
*
852385 TTTATTTTTAAAATATAATTT
1 TTTATTTTTAAAATAAAATTT
**
852406 TTTATTTTTTTAATAAAATT
1 TTTATTTTTAAAATAAAATT
852426 AGAATAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTTTTAAAATAAAATTT
Found at i:852424 original size:26 final size:26
Alignment explanation
Indices: 852368--852416 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
852358 TTAAATATAC
852368 AAAATACAATATTTATATTTATTTTT
1 AAAATACAATATTTATATTTATTTTT
* *
852394 AAAATATAAT-TTTTTATTT-TTTT
1 AAAATACAATATTTATATTTATTTT
852417 AATAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 8 0.38
26 9 0.43
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
AAAATACAATATTTATATTTATTTTT
Found at i:854061 original size:15 final size:14
Alignment explanation
Indices: 854043--854097 Score: 83
Period size: 14 Copynumber: 3.9 Consensus size: 14
854033 GTTTTTAGAA
854043 TTTTGGATTTTAAGG
1 TTTTGGATTTT-AGG
854058 TTTTGGATTTTAGG
1 TTTTGGATTTTAGG
*
854072 ATTTGGATTTTAGG
1 TTTTGGATTTTAGG
*
854086 GTTTGGATTTTA
1 TTTTGGATTTTA
854098 TGGGGTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
14 27 0.71
15 11 0.29
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (14 bp):
TTTTGGATTTTAGG
Found at i:854078 original size:29 final size:29
Alignment explanation
Indices: 854035--854097 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 29
854025 AATTTGGGGT
*
854035 TTTTAGAATTTTGGATTTTAAGGTTTTGGA
1 TTTTAGAATTTTGGATTTT-AGGGTTTGGA
*
854065 TTTTAGGA-TTTGGATTTTAGGGTTTGGA
1 TTTTAGAATTTTGGATTTTAGGGTTTGGA
854093 TTTTA
1 TTTTA
854098 TGGGGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 14 0.45
29 10 0.32
30 7 0.23
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (29 bp):
TTTTAGAATTTTGGATTTTAGGGTTTGGA
Found at i:854113 original size:17 final size:16
Alignment explanation
Indices: 854050--854136 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 16
854040 GAATTTTGGA
* *
854050 TTTTAAGGTTTTGGA-
1 TTTTAGGGTTTTAGAT
* *
854065 TTTTA-GGATTTGGA-
1 TTTTAGGGTTTTAGAT
*
854079 TTTTAGGG-TTTGGAT
1 TTTTAGGGTTTTAGAT
*
854094 TTTATGGGGTTTTAGAT
1 TTT-TAGGGTTTTAGAT
* *
854111 TTTTAGGGTTTTAAAA
1 TTTTAGGGTTTTAGAT
854127 TTTT-GGGTTT
1 TTTTAGGGTTT
854137 AGGTTTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
14 19 0.31
15 16 0.26
16 18 0.29
17 9 0.15
ACGTcount: A:0.18, C:0.00, G:0.28, T:0.54
Consensus pattern (16 bp):
TTTTAGGGTTTTAGAT
Found at i:854147 original size:21 final size:23
Alignment explanation
Indices: 854112--854155 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
854102 GTTTTAGATT
*
854112 TTTAGGGTTTTAAAA-TTTTGGG
1 TTTAGGGTTTCAAAAGTTTTGGG
854134 TTTA-GGTTTCAAAAGTTTTGGG
1 TTTAGGGTTTCAAAAGTTTTGGG
854156 GTTTGGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.23, C:0.02, G:0.27, T:0.48
Consensus pattern (23 bp):
TTTAGGGTTTCAAAAGTTTTGGG
Found at i:854723 original size:37 final size:36
Alignment explanation
Indices: 854653--854723 Score: 83
Period size: 37 Copynumber: 1.9 Consensus size: 36
854643 TTTATCATGC
*
854653 ATAAATATAAAAGAAATACTCAAAATAACAAAAATA
1 ATAAATATAAAAGAAATACTCAAAATAAAAAAAATA
*
854689 ATAATATATAAAA-AAA-ATTCAAAAATTAAAAAAAA
1 ATAA-ATATAAAAGAAATACTC-AAAA-TAAAAAAAA
854724 AAGTTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
35 3 0.10
36 11 0.37
37 16 0.53
ACGTcount: A:0.72, C:0.06, G:0.01, T:0.21
Consensus pattern (36 bp):
ATAAATATAAAAGAAATACTCAAAATAAAAAAAATA
Found at i:855802 original size:19 final size:19
Alignment explanation
Indices: 855778--855816 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
855768 TTAAACCAAT
*
855778 ATTATTATTATTATTAAAA
1 ATTATTATTATTACTAAAA
855797 ATTATTATTATTACTAAAA
1 ATTATTATTATTACTAAAA
855816 A
1 A
855817 AAAAATGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTATTATTATTACTAAAA
Found at i:855818 original size:22 final size:22
Alignment explanation
Indices: 855777--855819 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
855767 ATTAAACCAA
* **
855777 TATTATTATTATTATTAAAAAT
1 TATTATTATTACTAAAAAAAAT
855799 TATTATTATTACTAAAAAAAA
1 TATTATTATTACTAAAAAAAA
855820 AATGTAGACC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TATTATTATTACTAAAAAAAAT
Found at i:856064 original size:22 final size:22
Alignment explanation
Indices: 856045--856126 Score: 94
Period size: 22 Copynumber: 3.7 Consensus size: 22
856035 AATTATGTTC
856045 AGAGGTCTTAAAAATCATGTCA
1 AGAGGTCTTAAAAATCATGTCA
* * *
856067 AGAGGTCTTAGAAATCATGCCT
1 AGAGGTCTTAAAAATCATGTCA
* *
856089 AGAGGTCTTAGAAATCATATTC-
1 AGAGGTCTTAAAAATCAT-GTCA
*
856111 GGAGGTCTTAAAAATC
1 AGAGGTCTTAAAAATC
856127 TCAAAATCTT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
22 51 0.98
23 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.28
Consensus pattern (22 bp):
AGAGGTCTTAAAAATCATGTCA
Found at i:856221 original size:22 final size:22
Alignment explanation
Indices: 856191--856247 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
856181 AAATCTTTTA
*
856191 CCCGAAGGTCTTGAAAG-TTATG
1 CCCGGAGGTCTT-AAAGATTATG
*
856213 CCCGGAGGTCTTAGAGATTATG
1 CCCGGAGGTCTTAAAGATTATG
*
856235 CTCGGAGGTCTTA
1 CCCGGAGGTCTTA
856248 CAAATCTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (22 bp):
CCCGGAGGTCTTAAAGATTATG
Found at i:856353 original size:128 final size:127
Alignment explanation
Indices: 856109--856371 Score: 341
Period size: 128 Copynumber: 2.1 Consensus size: 127
856099 GAAATCATAT
*
856109 TCGGAGGTCTTAAAAATCTCAAAATCTTTGAATGTACCTCTAATAAGAGGTAATAAAACTTTAAA
1 TCGGAGGTCTTAAAAATCTCAAAATCTTTGAATGTACCTCTAATAAGAGGCAATAAAACTTTAAA
* * **
856174 AATTTGAAAATCTTTTACCCGAAGGTCTTGAAAGTTATGCCCGGAGGTCTTAGAGATTATGC
66 AATTTAAAAATCTTTTACCCGAAGGTCTTGAAAGTTATGCCCGAAAATCTTAGAGATTATGC
* * *
856236 TCGGAGGTCTTACAAATCTCAAAATCTTTGAATGCT-CATTCTAATCAA-AGGCAATGAAACTTT
1 TCGGAGGTCTTAAAAATCTCAAAATCTTTGAATG-TAC-CTCTAAT-AAGAGGCAATAAAACTTT
** * * ** *
856299 AAAAATTTAAAAATCTTTTATTCGGAGGTCTTGAAAGTTGTGCCTTAAAATCTTAGATATTATGC
63 AAAAATTTAAAAATCTTTTACCCGAAGGTCTTGAAAGTTATGCCCGAAAATCTTAGAGATTATGC
*
856364 TTGGAGGT
1 TCGGAGGT
856372 TTTAGAGATT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
127 34 0.29
128 81 0.69
129 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (127 bp):
TCGGAGGTCTTAAAAATCTCAAAATCTTTGAATGTACCTCTAATAAGAGGCAATAAAACTTTAAA
AATTTAAAAATCTTTTACCCGAAGGTCTTGAAAGTTATGCCCGAAAATCTTAGAGATTATGC
Found at i:856404 original size:22 final size:22
Alignment explanation
Indices: 856379--856421 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
856369 GGTTTTAGAG
856379 ATTATGCCCGAAGGTCTTAAAA
1 ATTATGCCCGAAGGTCTTAAAA
* *
856401 ATTATGTCCGGAGGTCTTAAA
1 ATTATGCCCGAAGGTCTTAAA
856422 GAATCGACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (22 bp):
ATTATGCCCGAAGGTCTTAAAA
Found at i:856561 original size:22 final size:22
Alignment explanation
Indices: 856486--856561 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
856476 ACCGTAAATC
* * *
856486 AAAATTATACCCAGAGATCTTA
1 AAAATTATGCCCGGAGGTCTTA
* * * *
856508 GAAATTATGCCTGGAAGTTTTA
1 AAAATTATGCCCGGAGGTCTTA
* *
856530 AAACTCATGCCCGGAGGTCTTA
1 AAAATTATGCCCGGAGGTCTTA
856552 AAAATTATGC
1 AAAATTATGC
856562 TTAGAGGTCT
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (22 bp):
AAAATTATGCCCGGAGGTCTTA
Found at i:858179 original size:22 final size:22
Alignment explanation
Indices: 858135--858179 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
858125 ATTGCTAAGG
* * *
858135 AATTATGAAATTAGCAATAAGA
1 AATTAAGAAATTAGAAAGAAGA
*
858157 AATTAAGAAATTAGAAAGCAGA
1 AATTAAGAAATTAGAAAGAAGA
858179 A
1 A
858180 TCCCCAAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (22 bp):
AATTAAGAAATTAGAAAGAAGA
Found at i:862125 original size:19 final size:20
Alignment explanation
Indices: 862101--862168 Score: 77
Period size: 19 Copynumber: 3.3 Consensus size: 20
862091 TGTTTGGATG
862101 AAAAATTTTATTTGTAAAA-
1 AAAAATTTTATTTGTAAAAT
862120 AAAAATTTTAATTT-TAAAAT
1 AAAAATTTT-ATTTGTAAAAT
*
862140 AAAATTACTTTATTTGATAAAAT
1 AAAA--ATTTTATTTG-TAAAAT
862163 AAAAAT
1 AAAAAT
862169 GAAATATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
19 14 0.34
20 8 0.20
21 5 0.12
22 4 0.10
23 10 0.24
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAAATTTTATTTGTAAAAT
Found at i:864769 original size:27 final size:26
Alignment explanation
Indices: 864720--864774 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
864710 GATACACAAA
* *
864720 ATTATAATAAAATTGAATAAAATGAT
1 ATTATAATAAAATTAAATAAAATAAT
* *
864746 ATTATAGATATAATTAAATTAAATAAT
1 ATTATA-ATAAAATTAAATAAAATAAT
864773 AT
1 AT
864775 CATCATATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
ATTATAATAAAATTAAATAAAATAAT
Found at i:867218 original size:13 final size:12
Alignment explanation
Indices: 867199--867236 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
867189 AAAATTCAAG
867199 AAAAA-AAAAT-
1 AAAAATAAAATA
867209 AAAAATAAAATA
1 AAAAATAAAATA
867221 AAGAAATAAAATA
1 AA-AAATAAAATA
867234 AAA
1 AAA
867237 TAATGATTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.20
11 5 0.20
12 3 0.12
13 12 0.48
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:867374 original size:18 final size:18
Alignment explanation
Indices: 867351--867388 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
867341 AAAAATTATT
867351 TTCAAAGAAAATTGATAC
1 TTCAAAGAAAATTGATAC
867369 TTCAAAGAAAATTGATAC
1 TTCAAAGAAAATTGATAC
867387 TT
1 TT
867389 TCAACTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
TTCAAAGAAAATTGATAC
Found at i:867399 original size:77 final size:78
Alignment explanation
Indices: 867299--867448 Score: 232
Period size: 77 Copynumber: 1.9 Consensus size: 78
867289 TTGTACAAGA
* *
867299 AAAATTGATACTTTCAACTTTTCCTAAAAAAATTTTTTTTTG-AAAAA-TTATTTTCAAAGAAAA
1 AAAATTGATACTTTCAACTTTTCCT-AAAAAATATTTTTTAGAAAAAACTTATTTTCAAAGAAAA
867362 TTGATACTTCAAAG
65 TTGATACTTCAAAG
** *
867376 AAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAGAAAAAACTTATTTTCAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGAAAAAACTTATTTTCAAAGAAAAT
867441 TGATACTT
66 TGATACTT
867449 TCAACTTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
76 12 0.18
77 30 0.45
78 24 0.36
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.40
Consensus pattern (78 bp):
AAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTAGAAAAAACTTATTTTCAAAGAAAAT
TGATACTTCAAAG
Found at i:867412 original size:60 final size:59
Alignment explanation
Indices: 867341--867472 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 59
867331 TTTTTTTTTG
867341 AAAAATTATTTTCA-AAGAAAA-TTGATACTTCAAAGAAAATTGATACTTTCAACTTTTCCTC
1 AAAAA-TATTTTCAGAA-AAAACTT-AT-CTTCAAAGAAAATTGATACTTTCAACTTTTCCTC
* * * * *
867402 GAAAATATTTTTTAGAAAAAACTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTT
1 AAAAATA-TTTTCAGAAAAAACTTATCTTCAAAGAAAATTGATACTTTCAACTTTTCCTC
867462 AAAAATATTTT
1 AAAAATATTTT
867473 TTTAAAAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
59 4 0.06
60 39 0.63
61 15 0.24
62 4 0.06
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (59 bp):
AAAAATATTTTCAGAAAAAACTTATCTTCAAAGAAAATTGATACTTTCAACTTTTCCTC
Found at i:867581 original size:10 final size:10
Alignment explanation
Indices: 867495--867598 Score: 53
Period size: 10 Copynumber: 10.5 Consensus size: 10
867485 ATTTAAAGAA
867495 AATAAA-AAT
1 AATAAATAAT
867504 AAATAAATAAAT
1 -AATAAAT-AAT
867516 AA-AAATAA-
1 AATAAATAAT
867524 AGATAAAATAA-
1 A-AT-AAATAAT
867535 AATAAGA-AAT
1 AATAA-ATAAT
*
867545 ATTAAATAAT
1 AATAAATAAT
** *
867555 TCTAATCTAATT
1 AATAA-ATAA-T
867567 AATAAATAAT
1 AATAAATAAT
867577 AAT-AAT-A-
1 AATAAATAAT
867584 AATAAATAAT
1 AATAAATAAT
867594 AATAA
1 AATAA
867599 TAAATGAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
7 3 0.04
8 5 0.07
9 12 0.16
10 32 0.43
11 15 0.20
12 7 0.09
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:867587 original size:17 final size:17
Alignment explanation
Indices: 867562--867603 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
867552 AATTCTAATC
*
867562 TAATTAATAAATAATAA
1 TAATAAATAAATAATAA
867579 TAATAAATAAATAATAA
1 TAATAAATAAATAATAA
867596 TAATAAAT
1 TAATAAAT
867604 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAATAAATAAATAATAA
Found at i:868390 original size:8 final size:7
Alignment explanation
Indices: 868372--868409 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
868362 CGAGTAATCA
*
868372 AAAAAAG
1 AAAAAAT
868379 AAAAAAT
1 AAAAAAT
*
868386 AAAAATT
1 AAAAAAT
868393 AAAAAAT
1 AAAAAAT
868400 AAAAAAT
1 AAAAAAT
868407 AAA
1 AAA
868410 GATAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:868454 original size:20 final size:16
Alignment explanation
Indices: 868416--868446 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
868406 TAAAGATAAT
868416 ATATTAATAGATAAAA
1 ATATTAATAGATAAAA
868432 ATATTAATAGATAAA
1 ATATTAATAGATAAA
868447 TAACAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATTAATAGATAAAA
Found at i:868466 original size:47 final size:44
Alignment explanation
Indices: 868403--868570 Score: 129
Period size: 43 Copynumber: 3.8 Consensus size: 44
868393 AAAAAATAAA
868403 AAATAAAG-ATAATATATTAATAGATAAA-AATATTAATAGATAA-AT
1 AAATAAAGTAT-ATATATTAATAGATAAATAATA--AATA-ATAATAT
*
868448 AACAATAAAGTATATATATCAATAGATAAATAATAAATAATAATAT
1 -A-AATAAAGTATATATATTAATAGATAAATAATAAATAATAATAT
* * *
868494 AAAT-AA-TAATATATGTTAATAGATAAATAA-ATATATATGTATAT
1 AAATAAAGT-ATATATATTAATAGATAAATAATAAATA-AT-AATAT
* *
868538 TAATAAA-TA-ATAATAGTAATA-ATAAATAATAAA
1 AAATAAAGTATAT-ATATTAATAGATAAATAATAAA
868571 AATTTAGAAT
Statistics
Matches: 103, Mismatches: 9, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 5 0.05
43 34 0.33
44 20 0.19
45 8 0.08
46 7 0.07
47 23 0.22
48 6 0.06
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (44 bp):
AAATAAAGTATATATATTAATAGATAAATAATAAATAATAATAT
Found at i:868497 original size:12 final size:12
Alignment explanation
Indices: 868480--868506 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
868470 TAGATAAATA
868480 ATAAATAATAAT
1 ATAAATAATAAT
868492 ATAAATAATAAT
1 ATAAATAATAAT
868504 ATA
1 ATA
868507 TGTTAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAAATAATAAT
Found at i:868607 original size:23 final size:24
Alignment explanation
Indices: 868565--868613 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
868555 AATAATAAAT
868565 AATAAAAATTT-AGAATAAAATAA
1 AATAAAAATTTAAGAATAAAATAA
868588 AATAAAAATAATTAA-AA-AAAATAA
1 AATAAAAAT--TTAAGAATAAAATAA
868612 AA
1 AA
868614 ATAGGCCCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 9 0.39
24 9 0.39
25 4 0.17
26 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (24 bp):
AATAAAAATTTAAGAATAAAATAA
Found at i:868941 original size:41 final size:41
Alignment explanation
Indices: 868793--869186 Score: 318
Period size: 41 Copynumber: 9.4 Consensus size: 41
868783 TTTGATTAAA
* * *
868793 GCTCCTCTAAGCAGAGGTTCAACGACTTTGAGAAATATAAACAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTT-AGAAA-AT-AA-AAT
* *
868838 GCTCCTCTAATCAGAAGCTCAACAACTTT-GAAAAT-AAAT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAGAAAATAAAAT
* * * * * * *
868877 GACTCATCTAAGCAGAAGTTCAACCACTTTAGAAAGTAAATT
1 G-CTCCTCTAATCAGAGGCTCAACGACTTTAGAAAATAAAAT
* *
868919 GCTCCTCTAATCAGAGGCTCAACGA-TTTTGAAAAATAAAAG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAG-AAAATAAAAT
* * * *
868960 GCTCATCGAATCAGAGGCTCAACGACTTTGGAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAGAAAATAAAAT
* * *
869001 GCTCCTCTAATCAGAGGCTCAATGACTTTTAAAAAAATAAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGAC-TTT-AGAAAAT-AA-AAT
* *
869046 GCTCCTCTAAAT-AGAGGTTTAACGACTTTTA-AAAATAAAAT
1 GCTCCTCT-AATCAGAGGCTCAACGAC-TTTAGAAAATAAAAT
* * * *
869087 GCTCCTTTAAAT-AGAGGCTTAATGACTTTTA-AAAATAAAAG
1 GCTCCTCT-AATCAGAGGCTCAACGAC-TTTAGAAAATAAAAT
* *
869128 GCTCCTCTAATCAGAGGCTCAACGACTTT-GAAAAATAGATT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTAG-AAAATAAAAT
* *
869169 ACTCCTCTAAACAGAGGC
1 GCTCCTCTAATCAGAGGC
869187 ATCACAACTT
Statistics
Matches: 288, Mismatches: 48, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
39 3 0.01
40 35 0.12
41 166 0.58
42 15 0.05
43 14 0.05
44 3 0.01
45 49 0.17
46 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTAGAAAATAAAAT
Found at i:869000 original size:82 final size:83
Alignment explanation
Indices: 868793--869207 Score: 378
Period size: 82 Copynumber: 5.0 Consensus size: 83
868783 TTTGATTAAA
* * ** *
868793 GCTCCTCTAAGCAGAGGTTCAACGACTTTGAGAAATATAAACAAAGCTCCTCTAATCAGAAGCTC
1 GCTCATCTAATCAGAGGTTCAACGACTTTG-GAAA-AT-AA-ATTGCTCCTCTAATCAGAGGCTC
* *
868858 AACAAC-TTTG-AAAATAAATG
62 AACGACTTTTGAAAAATAAAAG
* * * * * *
868878 ACTCATCTAAGCAGAAGTTCAACCACTTTAGAAAGTAAATTGCTCCTCTAATCAGAGGCTCAACG
1 GCTCATCTAATCAGAGGTTCAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGCTCAACG
868943 A-TTTTGAAAAATAAAAG
66 ACTTTTGAAAAATAAAAG
* * *
868960 GCTCATCGAATCAGAGGCTCAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGCTCAATG
1 GCTCATCTAATCAGAGGTTCAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGCTCAACG
* *
869025 ACTTTTAAAAAAATAAATAAA
66 ACTTTT-GAAAAAT-AA-AAG
* * ** * * *
869046 GCTCCTCTAAAT-AGAGGTTTAACGACTTTTAAAAATAAAATGCTCCTTTAAAT-AGAGGCTTAA
1 GCTCATCT-AATCAGAGGTTCAACGACTTTGGAAAATAAATTGCTCCTCT-AATCAGAGGCTCAA
*
869109 TGACTTTT-AAAAATAAAAG
64 CGACTTTTGAAAAATAAAAG
* * * * * *
869128 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAGATTACTCCTCTAAACAGAGGCATC-AC
1 GCTCATCTAATCAGAGGTTCAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGC-TCAAC
* *
869192 AAC-TTCGAAAAATAAA
65 GACTTTTGAAAAATAAA
869208 TTGCTCCTTG
Statistics
Matches: 274, Mismatches: 44, Indels: 27
0.79 0.13 0.08
Matches are distributed among these distances:
81 35 0.13
82 126 0.46
83 8 0.03
84 16 0.06
85 27 0.10
86 56 0.20
87 6 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.26
Consensus pattern (83 bp):
GCTCATCTAATCAGAGGTTCAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGCTCAACG
ACTTTTGAAAAATAAAAG
Found at i:869070 original size:127 final size:125
Alignment explanation
Indices: 868789--869162 Score: 339
Period size: 127 Copynumber: 3.0 Consensus size: 125
868779 AAAATTTGAT
** * * * *
868789 TAAAGCTCCTCTAAGCAGAGGTTCAACGACTTTGAGAAATATAAACAAAGCTCCTCTAATCAGAA
1 TAAAGCTCCTCTAAATAGAGGTTCAACGATTTTGA-AAA-AT-AA-AAAGCTCATCAAATCAGAG
* * * * * * * *
868854 GCTCAACAACTTTGAAAATAAATGACTCATCTAAGCAGAAGTTCAACCAC-TTT-AGAAAGTAAA
62 GCTCAACGACTTTGAAAATAAATG-CTCCTCTAATCAGAGGCTCAACGACTTTTAAAAAAATAAA
* * * *
868917 T--TGCTCCTCT-AATCAGAGGCTCAACGATTTTGAAAAATAAAAGGCTCATCGAATCAGAGGCT
1 TAAAGCTCCTCTAAAT-AGAGGTTCAACGATTTTGAAAAATAAAAAGCTCATCAAATCAGAGGCT
*
868979 CAACGACTTTGGAAAATAAATTGCTCCTCTAATCAGAGGCTCAATGACTTTTAAAAAAATAAA
65 CAACGACTTT-GAAAATAAA-TGCTCCTCTAATCAGAGGCTCAACGACTTTTAAAAAAATAAA
* * * *
869042 TAAAGCTCCTCTAAATAGAGGTTTAACGACTTTT-AAAAATAAAATGCTCCTTTAAAT-AGAGGC
1 TAAAGCTCCTCTAAATAGAGGTTCAACGA-TTTTGAAAAATAAAAAGCT-CATCAAATCAGAGGC
* * * * *
869105 TTAATGACTTTTAAAAATAAAAGGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAA
64 TCAACGAC-TTTGAAAAT-AAATGCTCCTCTAATCAGAGGCTCAACGACTTTTAAAAA
869163 TAGATTACTC
Statistics
Matches: 203, Mismatches: 31, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
122 27 0.13
123 30 0.15
124 7 0.03
125 13 0.06
126 25 0.12
127 82 0.40
128 19 0.09
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (125 bp):
TAAAGCTCCTCTAAATAGAGGTTCAACGATTTTGAAAAATAAAAAGCTCATCAAATCAGAGGCTC
AACGACTTTGAAAATAAATGCTCCTCTAATCAGAGGCTCAACGACTTTTAAAAAAATAAA
Found at i:870248 original size:13 final size:13
Alignment explanation
Indices: 870232--870278 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
870222 TCATTCATTT
870232 TTTTTTCTTTTCA
1 TTTTTTCTTTTCA
870245 TTTTTT-TCTTTCA
1 TTTTTTCT-TTTCA
* *
870258 TTTTTTCATTTCG
1 TTTTTTCTTTTCA
870271 TTTTTTCT
1 TTTTTTCT
870279 CTTTTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTTCA
Found at i:870248 original size:14 final size:14
Alignment explanation
Indices: 870231--870283 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
870221 TTCATTCATT
870231 TTTTTTTCTTTTCA
1 TTTTTTTCTTTTCA
870245 TTTTTTTC-TTTCA
1 TTTTTTTCTTTTCA
* *
870258 -TTTTTTCATTTCG
1 TTTTTTTCTTTTCA
870271 TTTTTTCTCTTTT
1 TTTTTT-TCTTTT
870284 TTTGAAGCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 7 0.21
13 9 0.26
14 13 0.38
15 5 0.15
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTTTTCTTTTCA
Found at i:870261 original size:26 final size:27
Alignment explanation
Indices: 870232--870282 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
870222 TCATTCATTT
*
870232 TTTTTTCTTTTCATTTTTT-TCTTTCA
1 TTTTTTCATTTCATTTTTTCTCTTTCA
*
870258 TTTTTTCATTTCGTTTTTTCTCTTT
1 TTTTTTCATTTCATTTTTTCTCTTT
870283 TTTTGAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.76
Consensus pattern (27 bp):
TTTTTTCATTTCATTTTTTCTCTTTCA
Found at i:870283 original size:21 final size:21
Alignment explanation
Indices: 870217--870284 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
870207 TTGAGTCCTC
870217 CTTTTTCA-TTCATTTTTT-T
1 CTTTTTCATTTCATTTTTTCT
* *
870236 TTCTTTTCATTT-TTTTCTTTCAT
1 CT-TTTTCATTTCATTT-TTTC-T
*
870259 -TTTTTCATTTCGTTTTTTCT
1 CTTTTTCATTTCATTTTTTCT
870279 CTTTTT
1 CTTTTT
870285 TTGAAGCATA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 1 0.03
20 10 0.26
21 23 0.59
22 4 0.10
23 1 0.03
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.75
Consensus pattern (21 bp):
CTTTTTCATTTCATTTTTTCT
Found at i:880138 original size:22 final size:22
Alignment explanation
Indices: 880096--880138 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
880086 GCATATGAAT
* *
880096 AACATAATTAATAAAGTAAATA
1 AACATAATGAATAAAGAAAATA
880118 AACATGAATGAATAAA-AAAAT
1 AACAT-AATGAATAAAGAAAAT
880139 CTATACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.65, C:0.05, G:0.07, T:0.23
Consensus pattern (22 bp):
AACATAATGAATAAAGAAAATA
Found at i:880992 original size:56 final size:57
Alignment explanation
Indices: 880740--881017 Score: 264
Period size: 57 Copynumber: 4.8 Consensus size: 57
880730 TGCTTTTATA
* * ** * *
880740 CAAGAAAAATTTATACTTTCAATTTTTCCCCAAAATATTTTTTTA-AAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCTTCAAAATA-TTTTTTAGAAAATTTATTTT
* * * *
880797 CGAA-AAAAATTGATACTTTCAATTTTTCCTCAAAAAAAAACATTTTTTGGAAAA-TTATTTT
1 C-AAGAAAAATTGATACTTTCAACTTTTCTTC-----AAAATATTTTTTAGAAAATTTATTTT
*
880858 CAA-AGAAAATTGATA-TCTTCAACTTTT-TCTCAAAAATATTTTTTAGAAAAAACTTATTTT
1 CAAGA-AAAATTGATACT-TTCAACTTTTCT-TC-AAAATATTTTTTAG--AAAATTTATTTT
*
880918 CAAGGAAAATTGATACTTTCAACTTTTCTTCAAAA-ATTTTTTAGAAAATTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCTTCAAAATATTTTTTAGAAAATTTATTTT
*
880974 CAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTT
1 CAAGAAAAATTGATACTTTCAACTTTT-CTTCAAAATATTTTTT
881018 TTGGAATTTT
Statistics
Matches: 189, Mismatches: 14, Indels: 35
0.79 0.06 0.15
Matches are distributed among these distances:
56 37 0.20
57 46 0.24
58 18 0.10
59 8 0.04
60 36 0.19
61 36 0.19
62 8 0.04
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (57 bp):
CAAGAAAAATTGATACTTTCAACTTTTCTTCAAAATATTTTTTAGAAAATTTATTTT
Found at i:881044 original size:4 final size:4
Alignment explanation
Indices: 881037--881095 Score: 57
Period size: 4 Copynumber: 13.8 Consensus size: 4
881027 TATTTAAAGA
*
881037 AAAT AAAT AAAT AAAT AAAT AAAT AATAT AAAG ATAA- AAAT ATAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT A-AAT AAAT A-AAT -AAAT
881088 AAAAT AAA
1 -AAAT AAA
881096 ACAAAATAAG
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
3 2 0.04
4 29 0.59
5 17 0.35
6 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:881058 original size:16 final size:16
Alignment explanation
Indices: 881037--881095 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
881027 TATTTAAAGA
881037 AAATAAATAAATAAAT
1 AAATAAATAAATAAAT
*
881053 AAATAAATAATATAAAG
1 AAATAAATAA-ATAAAT
881070 ATAA-AAATATAATAAAAT
1 A-AATAAATA-AAT-AAAT
881088 AAAATAAA
1 -AAATAAA
881096 ACAAAATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 10 0.29
17 13 0.37
18 8 0.23
19 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAATAAATAAATAAAT
Found at i:881081 original size:27 final size:27
Alignment explanation
Indices: 881036--881095 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
881026 TTATTTAAAG
881036 AAAAT-AA-ATAAATAAATAA-ATAAAT
1 AAAATAAAGATAAATAAATAATA-AAAT
*
881061 AATATAAAGATAAA-AATATAATAAAAT
1 AAAATAAAGATAAATAA-ATAATAAAAT
881088 AAAATAAA
1 AAAATAAA
881096 ACAAAATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 4 0.14
26 4 0.14
27 20 0.69
28 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (27 bp):
AAAATAAAGATAAATAAATAATAAAAT
Found at i:881089 original size:22 final size:20
Alignment explanation
Indices: 881036--881096 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
881026 TTATTTAAAG
881036 AAAATAAAT-AAAT-AAAT-
1 AAAATAAATAAAATAAAATA
*
881053 -AAATAAATAATATAAAGATA
1 AAAATAAATAAAATAAA-ATA
881073 AAAATATAATAAAATAAAATA
1 AAAATA-AATAAAATAAAATA
881094 AAA
1 AAA
881097 CAAAATAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 8 0.22
17 3 0.08
18 2 0.06
19 2 0.06
21 11 0.31
22 10 0.28
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAAATAAAATAAAATA
Found at i:881094 original size:5 final size:5
Alignment explanation
Indices: 881036--881104 Score: 58
Period size: 5 Copynumber: 14.4 Consensus size: 5
881026 TTATTTAAAG
* *
881036 AAAAT -AAAT -AAAT -AAAT -AAAT -AAAT AATAT AAAGAT AAAAAT ATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT AAAAT
*
881083 AAAAT AAAAT AAAAC AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AA
881105 GAAATACTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
4 20 0.36
5 28 0.51
6 4 0.07
7 3 0.05
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:881144 original size:3 final size:3
Alignment explanation
Indices: 881136--881190 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
881126 CTAATCAATA
* *
881136 AAT AAT AAT AAT GAT AAG AAT AAT AAT AAT AAT AAT AAT AAAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT
*
881183 AAA AAT AA
1 AAT AAT AA
881191 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
3 38 0.84
4 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:881204 original size:17 final size:17
Alignment explanation
Indices: 881169--881204 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
881159 TAATAATAAT
* *
881169 AATAATAAATAAATAAA
1 AATAAAAAATAAAAAAA
881186 AATAAAAAATAAAAAAA
1 AATAAAAAATAAAAAAA
881203 AA
1 AA
881205 ACCTTGGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (17 bp):
AATAAAAAATAAAAAAA
Found at i:881962 original size:17 final size:17
Alignment explanation
Indices: 881942--882024 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 17
881932 AAAATAAAAA
881942 AATAAAGATAATATATT
1 AATAAAGATAATATATT
*
881959 AAT--AGATAAAAATATT
1 AATAAAGAT-AATATATT
*
881975 AAT--AGATAAATAATAAT
1 AATAAAGAT-AAT-ATATT
*
881992 AATAATAGATAA-ATAAT
1 AATAA-AGATAATATATT
882009 AATAAAGCAT-ATATAT
1 AATAAAG-ATAATATAT
882025 CAACAGATAA
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
15 4 0.07
16 20 0.36
17 25 0.45
19 2 0.04
20 4 0.07
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.31
Consensus pattern (17 bp):
AATAAAGATAATATATT
Found at i:881975 original size:16 final size:17
Alignment explanation
Indices: 881954--882009 Score: 78
Period size: 16 Copynumber: 3.2 Consensus size: 17
881944 TAAAGATAAT
881954 ATATTAATAGATAAA-A
1 ATATTAATAGATAAATA
881970 ATATTAATAGATAAATA
1 ATATTAATAGATAAATA
881987 ATAATAATAATAGATAAATA
1 AT-AT--TAATAGATAAATA
882007 ATA
1 ATA
882010 ATAAAGCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
16 15 0.42
17 3 0.08
18 2 0.06
19 1 0.03
20 15 0.42
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
ATATTAATAGATAAATA
Found at i:881991 original size:3 final size:3
Alignment explanation
Indices: 881949--882013 Score: 51
Period size: 3 Copynumber: 20.3 Consensus size: 3
881939 AAAAATAAAG
* * *
881949 ATA AT- ATA TTA ATA GATA AAA ATA TTA ATA GATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA
881996 ATA GATAA ATA ATA ATA A
1 ATA -AT-A ATA ATA ATA A
882014 AGCATATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
2 2 0.04
3 35 0.70
4 11 0.22
5 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:881992 original size:20 final size:20
Alignment explanation
Indices: 881949--882012 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
881939 AAAAATAAAG
881949 ATAAT-ATATTAATAGAT--
1 ATAATAATATTAATAGATAA
881966 A-AA-AATATTAATAGATAA
1 ATAATAATATTAATAGATAA
*
881984 ATAATAATAATAATAGATAA
1 ATAATAATATTAATAGATAA
882004 ATAATAATA
1 ATAATAATA
882013 AAGCATATAT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 14 0.34
17 1 0.02
18 1 0.02
19 2 0.05
20 23 0.56
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATAATAATATTAATAGATAA
Found at i:882154 original size:24 final size:23
Alignment explanation
Indices: 882117--882174 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 23
882107 TAATAGTAAT
882117 AATAAATAATAAAAAT-TTAGAAGAA
1 AATAAA-AATAAAAATATTA-AA-AA
882142 AATAAAAATAAAAATAATTAAAAA
1 AATAAAAATAAAAAT-ATTAAAAA
882166 AATAAAAAT
1 AATAAAAAT
882175 GAGCCTACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 20 0.65
25 8 0.26
26 3 0.10
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (23 bp):
AATAAAAATAAAAATATTAAAAA
Found at i:882380 original size:31 final size:31
Alignment explanation
Indices: 882345--882404 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
882335 ATATACTATT
*
882345 AGTGAATAAGATAATACAATTTTATTAATAA
1 AGTGAATAAGATAATACAATTTCATTAATAA
* *
882376 AGTGAATCAGATAATACCATTTCATTAAT
1 AGTGAATAAGATAATACAATTTCATTAAT
882405 GAGTAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (31 bp):
AGTGAATAAGATAATACAATTTCATTAATAA
Found at i:887936 original size:4 final size:4
Alignment explanation
Indices: 887927--887962 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
887917 CAAAAGATGA
*
887927 AAAT AAAT AAAT AAAT AAAT AAAT ACA- AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
887963 TCAGTAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 27 0.93
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:892537 original size:22 final size:22
Alignment explanation
Indices: 892512--892554 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
892502 TGTATATTTA
*
892512 TATTTGCATCTCTAGAATTAAG
1 TATTTGCATCCCTAGAATTAAG
*
892534 TATTTGTATCCCTAGAATTAA
1 TATTTGCATCCCTAGAATTAA
892555 TGACAGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.42
Consensus pattern (22 bp):
TATTTGCATCCCTAGAATTAAG
Found at i:895599 original size:150 final size:150
Alignment explanation
Indices: 895328--895628 Score: 593
Period size: 150 Copynumber: 2.0 Consensus size: 150
895318 ATGAAGACCT
895328 TAAAATGAGATAACATATAGAACTTGAGAACGTCACAATTCAAAACAGGATCAACTAACCCTTCG
1 TAAAATGAGATAACATATAGAACTTGAGAACGTCACAATTCAAAACAGGATCAACTAACCCTTCG
895393 GTGCGTCACAATTCTCTGGCTTCCAGGAACAAGTATCTGCCGATGTTGAAGACCCTGTATTTGTA
66 GTGCGTCACAATTCTCTGGCTTCCAGGAACAAGTATCTGCCGATGTTGAAGACCCTGTATTTGTA
895458 ACTGATTCAGGACCTACTTC
131 ACTGATTCAGGACCTACTTC
*
895478 TAAAATGAGATAACATGTAGAACTTGAGAACGTCACAATTCAAAACAGGATCAACTAACCCTTCG
1 TAAAATGAGATAACATATAGAACTTGAGAACGTCACAATTCAAAACAGGATCAACTAACCCTTCG
895543 GTGCGTCACAATTCTCTGGCTTCCAGGAACAAGTATCTGCCGATGTTGAAGACCCTGTATTTGTA
66 GTGCGTCACAATTCTCTGGCTTCCAGGAACAAGTATCTGCCGATGTTGAAGACCCTGTATTTGTA
895608 ACTGATTCAGGACCTACTTC
131 ACTGATTCAGGACCTACTTC
895628 T
1 T
895629 GCATCATTGT
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (150 bp):
TAAAATGAGATAACATATAGAACTTGAGAACGTCACAATTCAAAACAGGATCAACTAACCCTTCG
GTGCGTCACAATTCTCTGGCTTCCAGGAACAAGTATCTGCCGATGTTGAAGACCCTGTATTTGTA
ACTGATTCAGGACCTACTTC
Done.