Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold363
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: 552799
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
File 2 of 4
Found at i:211238 original size:18 final size:17
Alignment explanation
Indices: 211193--211243 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
211183 TATTTATATT
211193 TTAAATTAAAA-ATTTAA
1 TTAAA-TAAAATATTTAA
*
211210 TTAAATAAAATATTTTA
1 TTAAATAAAATATTTAA
*
211227 TTAATATGAAAT-TTTAA
1 TTAA-ATAAAATATTTAA
211244 GTTCAACCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 5 0.17
17 18 0.62
18 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAAATAAAATATTTAA
Found at i:211761 original size:4 final size:4
Alignment explanation
Indices: 211752--211794 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
211742 TTTTATAGTG
* * *
211752 TTTC TTTC TTGC TTTC TTTA TTTC TTTC TTCC TCTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TT
211795 CCAGAACCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
4 29 0.91
5 3 0.09
ACGTcount: A:0.02, C:0.26, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:214997 original size:16 final size:18
Alignment explanation
Indices: 214976--215018 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
214966 TTAGGAGTTG
214976 AATTTTAAATT-TA-TTA
1 AATTTTAAATTATATTTA
*
214992 AATTTT-TATTATATTTA
1 AATTTTAAATTATATTTA
215009 AATTTTAAAT
1 AATTTTAAAT
215019 ATGTTGGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 9 0.41
18 2 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTTAAATTATATTTA
Found at i:216842 original size:21 final size:21
Alignment explanation
Indices: 216818--216896 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
216808 TGGTGACACT
*
216818 GAGGATGATGATGATGAAGAG
1 GAGGATGATGAAGATGAAGAG
* *
216839 GAGGAAGACGAAGATGAAGCAG
1 GAGGATGATGAAGATGAAG-AG
* *
216861 CA-GATGATCAAGATGAAGATG
1 GAGGATGATGAAGATGAAGA-G
*
216882 GAGG-TGAGGAAGATG
1 GAGGATGATGAAGATG
216897 GATCTGGTGA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 1 0.02
21 40 0.89
22 4 0.09
ACGTcount: A:0.41, C:0.05, G:0.41, T:0.14
Consensus pattern (21 bp):
GAGGATGATGAAGATGAAGAG
Found at i:216985 original size:3 final size:3
Alignment explanation
Indices: 216971--217019 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
216961 TGGCAGTGGA
* * *
216971 GAT GAG GAT GAT GAT GAT GAT GAT GAT GAC GAT GAT GAC GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
217019 G
1 G
217020 GCGATGAGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.04, G:0.37, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:217043 original size:9 final size:9
Alignment explanation
Indices: 217031--217069 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
217021 CGATGAGGAG
217031 GAGGAAGAA
1 GAGGAAGAA
*
217040 GAGGAAGAG
1 GAGGAAGAA
* *
217049 GAGGAGGAG
1 GAGGAAGAA
217058 GAGGAAGAA
1 GAGGAAGAA
217067 GAG
1 GAG
217070 CTTCAGCCAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (9 bp):
GAGGAAGAA
Found at i:226234 original size:17 final size:17
Alignment explanation
Indices: 226214--226334 Score: 68
Period size: 17 Copynumber: 6.8 Consensus size: 17
226204 TATAATATAA
*
226214 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
*
226231 ATATCATATTTTATATT
1 ATATTATATTTTATATT
* * *
226248 ATATTTTAATTTTTTA-A
1 ATATTAT-ATTTTATATT
*
226265 AAATT-TATTTATATCATAT
1 ATATTATATTT-TAT-AT-T
* *
226284 ATATATATATATATATTTT
1 ATAT-TATAT-TTTATATT
226303 ATATTATATTTTA-ATT
1 ATATTATATTTTATATT
*
226319 ATTTTTTATATTTTAT
1 A--TATTATATTTTAT
226335 TTACATCGAG
Statistics
Matches: 78, Mismatches: 15, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
15 4 0.05
16 6 0.08
17 28 0.36
18 23 0.29
19 8 0.10
20 2 0.03
21 6 0.08
22 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:226272 original size:72 final size:72
Alignment explanation
Indices: 226196--226332 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 72
226186 AATATAATTT
* * *
226196 TTTATTTTTATAATATAAATAT-TATTTTTTATATTATATCATATTTTATATTATATTTTA-ATT
1 TTTATTTATATAATATAAATATATA-TATATATATTATATCATATTTTA-ATTATATTTTATATT
226259 TTTTAAAAA
64 TTTTAAAAA
* * * * *
226268 TTTATTTATATCATATATATATATATATATATTTTATATTATATTTTAATTATTTTTTATATTTT
1 TTTATTTATATAATATAAATATATATATATATATTATATCATATTTTAATTATATTTTATATTTT
226333 ATTTACATCG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
71 10 0.18
72 43 0.78
73 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (72 bp):
TTTATTTATATAATATAAATATATATATATATATTATATCATATTTTAATTATATTTTATATTTT
TTAAAAA
Found at i:228290 original size:7 final size:7
Alignment explanation
Indices: 228269--228310 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
228259 AGAGCGAAAT
228269 TAATAAA
1 TAATAAA
228276 TAATTAAA
1 TAA-TAAA
228284 TAATAAA
1 TAATAAA
228291 TAA-AAA
1 TAATAAA
228297 T-ATGAAA
1 TAAT-AAA
228304 TAATAAA
1 TAATAAA
228311 AGAGGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 1 0.03
6 4 0.13
7 17 0.55
8 9 0.29
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (7 bp):
TAATAAA
Found at i:228345 original size:13 final size:13
Alignment explanation
Indices: 228327--228353 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
228317 AAAAATAAAA
228327 TAATTAATTTTTT
1 TAATTAATTTTTT
228340 TAATTAATTTTTT
1 TAATTAATTTTTT
228353 T
1 T
228354 CACAGTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TAATTAATTTTTT
Found at i:228563 original size:14 final size:16
Alignment explanation
Indices: 228536--228568 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
228526 TTAATCTAAA
228536 ATATTTATTAATATAT
1 ATATTTATTAATATAT
228552 ATATTT-TT-ATATAT
1 ATATTTATTAATATAT
228566 ATA
1 ATA
228569 ATACTGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATATTTATTAATATAT
Found at i:228954 original size:15 final size:15
Alignment explanation
Indices: 228934--228967 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
228924 TTAATATATC
*
228934 AAATATAAATTTTAT
1 AAATATAAATTTAAT
*
228949 AAATATGAATTTAAT
1 AAATATAAATTTAAT
228964 AAAT
1 AAAT
228968 TTGATAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
AAATATAAATTTAAT
Found at i:229054 original size:17 final size:18
Alignment explanation
Indices: 229026--229060 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
229016 TAACGTAATG
*
229026 TAAAATTTTTAAATATAA
1 TAAAATTTTTAAAAATAA
229044 TAAAA-TTTTAAAAATAA
1 TAAAATTTTTAAAAATAA
229061 ATATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTTTAAAAATAA
Found at i:229063 original size:18 final size:18
Alignment explanation
Indices: 229026--229060 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
229016 TAACGTAATG
*
229026 TAAAATTTTTAAATATAA
1 TAAAATTTTAAAATATAA
229044 TAAAATTTTAAAA-ATAA
1 TAAAATTTTAAAATATAA
229061 ATATAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAAATTTTAAAATATAA
Found at i:235975 original size:21 final size:21
Alignment explanation
Indices: 235951--235990 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
235941 AACCAAATGA
* *
235951 TATGGAATCTAAATTTATTGG
1 TATGAAATCTAAATATATTGG
*
235972 TATGAAATTTAAATATATT
1 TATGAAATCTAAATATATT
235991 AAATATTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (21 bp):
TATGAAATCTAAATATATTGG
Found at i:236334 original size:21 final size:21
Alignment explanation
Indices: 236292--236350 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
236282 ATAATATATA
*
236292 AAATTAA-AAATT-TTTGATT
1 AAATTAATAAATTATTTAATT
236311 AAATTAATAAATTATTTAATT
1 AAATTAATAAATTATTTAATT
* * *
236332 AAAATATTAAAATATTTAA
1 AAATTAATAAATTATTTAA
236351 ATTTAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.21
20 5 0.15
21 22 0.65
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAATTAATAAATTATTTAATT
Found at i:236962 original size:2 final size:2
Alignment explanation
Indices: 236955--236987 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
236945 GTGTCATTTA
236955 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 A
236988 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:236992 original size:2 final size:2
Alignment explanation
Indices: 236987--237025 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
236977 ATATATATAT
236987 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
237026 ACAATAGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:242701 original size:12 final size:12
Alignment explanation
Indices: 242684--242709 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
242674 TTAGAAGATG
242684 TAGTAATAATAA
1 TAGTAATAATAA
242696 TAGTAATAATAA
1 TAGTAATAATAA
242708 TA
1 TA
242710 CCTTAATAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (12 bp):
TAGTAATAATAA
Found at i:244517 original size:3 final size:3
Alignment explanation
Indices: 244509--244543 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
244499 CAAAACAGAA
* *
244509 AAT AAT AAT AAT AAT AAC AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
244544 AAGAGAACCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:244530 original size:12 final size:12
Alignment explanation
Indices: 244509--244543 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
244499 CAAAACAGAA
*
244509 AATAATAATAAT
1 AATAACAATAAT
244521 AATAACAATAAT
1 AATAACAATAAT
244533 AATAACAATAA
1 AATAACAATAA
244544 AAGAGAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (12 bp):
AATAACAATAAT
Found at i:246826 original size:18 final size:19
Alignment explanation
Indices: 246790--246830 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
246780 TACTGTTTAA
* *
246790 AAAAATTATTTAAATTATT
1 AAAAAGTATATAAATTATT
246809 AAAAAGTATATAAA-TATT
1 AAAAAGTATATAAATTATT
246827 AAAA
1 AAAA
246831 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAGTATATAAATTATT
Found at i:252650 original size:21 final size:21
Alignment explanation
Indices: 252567--252665 Score: 62
Period size: 21 Copynumber: 4.9 Consensus size: 21
252557 TTTATTTTGA
*
252567 ATTTAAA-AATTTAAATATAAT
1 ATTTAAATAATTTATAT-TAAT
* * *
252588 AATTAATTAATTTATAAT-AT
1 ATTTAAATAATTTATATTAAT
** * *
252608 ATTTTTAT-A-TTATAATCAT
1 ATTTAAATAATTTATATTAAT
* *
252627 ATTTAAATTATTTTTATTAAT
1 ATTTAAATAATTTATATTAAT
*
252648 ATTTTAATAATTTATATT
1 ATTTAAATAATTTATATT
252666 TTATAAATTT
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
18 7 0.12
19 9 0.16
20 7 0.12
21 28 0.48
22 7 0.12
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTAAATAATTTATATTAAT
Found at i:252656 original size:8 final size:8
Alignment explanation
Indices: 252643--252753 Score: 51
Period size: 8 Copynumber: 14.0 Consensus size: 8
252633 ATTATTTTTA
252643 TTAATATT
1 TTAATATT
*
252651 TTAATAAT
1 TTAATATT
252659 TT-ATATT
1 TTAATATT
*
252666 TTATAAATT
1 TTA-ATATT
*
252675 TTAAAATAT
1 TTAATAT-T
252684 TT-ATATAT
1 TTAATAT-T
252692 TT-ATATTT
1 TTAATA-TT
252700 TATAATATT
1 T-TAATATT
252709 TTAATTATAT
1 TTAA-TAT-T
*
252719 TT--TCATA
1 TTAAT-ATT
252726 TT-ATATT
1 TTAATATT
252733 TTAATA-T
1 TTAATATT
252740 TT-ATA-T
1 TTAATATT
252746 TTAATATT
1 TTAATATT
252754 ATAAATTTAT
Statistics
Matches: 84, Mismatches: 6, Indels: 26
0.72 0.05 0.22
Matches are distributed among these distances:
6 6 0.07
7 19 0.23
8 35 0.42
9 18 0.21
10 6 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (8 bp):
TTAATATT
Found at i:252659 original size:24 final size:24
Alignment explanation
Indices: 252632--252735 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 24
252622 ATCATATTTA
252632 AATTATTTTTATTAATATTTTAAT
1 AATTATTTTTATTAATATTTTAAT
252656 AATTTATATTTTA-TAA-ATTTTAA-
1 AA-TTAT-TTTTATTAATATTTTAAT
*
252679 AA-TATTTATATATTTATATTTT-AT
1 AATTATTT-T-TATTAATATTTTAAT
* *
252703 AA-TATTTTAATT-ATATTTTCAT
1 AATTATTTTTATTAATATTTTAAT
252725 -ATTATATTTTA
1 AATTAT-TTTTA
252736 ATATTTATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
20 2 0.03
21 12 0.18
22 10 0.15
23 10 0.15
24 21 0.31
25 7 0.10
26 5 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (24 bp):
AATTATTTTTATTAATATTTTAAT
Found at i:252667 original size:26 final size:26
Alignment explanation
Indices: 252634--252695 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
252624 CATATTTAAA
*
252634 TTAT-TTTTATTAATATTTTAATA-AT
1 TTATATTTTATTAA-ATTTTAAAATAT
252659 TTATATTTTA-TAAATTTTAAAATAT
1 TTATATTTTATTAAATTTTAAAATAT
252684 TTATATATTTAT
1 TTATAT-TTTAT
252696 ATTTTATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 8 0.25
25 15 0.47
26 9 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTTTATTAAATTTTAAAATAT
Found at i:252699 original size:33 final size:35
Alignment explanation
Indices: 252638--252735 Score: 123
Period size: 34 Copynumber: 2.9 Consensus size: 35
252628 TTTAAATTAT
* *
252638 TTTTATTAATATTTTAATAATTTATATTTTATAA-A
1 TTTTAATAATATTTTCAT-ATTTATATTTTATAATA
252673 TTTTAA-AATATTTAT-ATATTTATATTTTATAATA
1 TTTTAATAATATTT-TCATATTTATATTTTATAATA
*
252707 TTTTAATTATATTTTCATA-TTATATTTTA
1 TTTTAATAATATTTTCATATTTATATTTTA
252736 ATATTTATAT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
33 15 0.26
34 27 0.47
35 15 0.26
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (35 bp):
TTTTAATAATATTTTCATATTTATATTTTATAATA
Found at i:252730 original size:13 final size:12
Alignment explanation
Indices: 252635--252756 Score: 82
Period size: 13 Copynumber: 10.2 Consensus size: 12
252625 ATATTTAAAT
252635 TATTTT-TATTAA
1 TATTTTATATT-A
252647 TATTTTAATAATTTA
1 TATTTT-AT-A-TTA
252662 TATTTTATA--A
1 TATTTTATATTA
*
252672 -ATTTTA-A-AA
1 TATTTTATATTA
252681 TATTTATATATTTA
1 TATTT-TATA-TTA
252695 TATTTTATA--A
1 TATTTTATATTA
252705 TATTTTA-ATTA
1 TATTTTATATTA
252716 TATTTTCATATTA
1 TATTTT-ATATTA
252729 TATTTTAATATTTA
1 TATTTT-ATA-TTA
*
252743 TATTTAATATTA
1 TATTTTATATTA
252755 TA
1 TA
252757 AATTTATAAA
Statistics
Matches: 92, Mismatches: 3, Indels: 30
0.74 0.02 0.24
Matches are distributed among these distances:
8 1 0.01
9 8 0.09
10 13 0.14
11 9 0.10
12 13 0.14
13 21 0.23
14 17 0.18
15 8 0.09
16 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTTTATATTA
Found at i:252734 original size:58 final size:55
Alignment explanation
Indices: 252634--252753 Score: 131
Period size: 58 Copynumber: 2.1 Consensus size: 55
252624 CATATTTAAA
*
252634 TTAT-TTTTATTAATATTTTAATAATTTATATTTTATAAATTTTAAAATATTTATATAT
1 TTATATTTTATTAATATTTTAATAATTTATATATTAT-AATTTT--AATATTTATAT-T
252692 TTATATTTTA-TAATATTTTAATTATATTT-TCATATTAT-ATTTTAATATTTATATT
1 TTATATTTTATTAATATTTTAA-TA-ATTTAT-ATATTATAATTTTAATATTTATATT
*
252747 TAATATT
1 TTATATT
252754 ATAAATTTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
55 7 0.12
56 11 0.20
58 20 0.36
59 8 0.14
60 10 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (55 bp):
TTATATTTTATTAATATTTTAATAATTTATATATTATAATTTTAATATTTATATT
Found at i:252752 original size:21 final size:19
Alignment explanation
Indices: 252687--252764 Score: 58
Period size: 20 Copynumber: 4.2 Consensus size: 19
252677 AAAATATTTA
*
252687 TATATTTATATTTTATA-A
1 TATATTTATATTTTATATT
*
252705 TAT-TTTA-ATTATAT-TT
1 TATATTTATATTTTATATT
252721 TCATA-TTATATTTTAATATT
1 T-ATATTTATATTTT-ATATT
* *
252741 TATATTTAATATTATAAATT
1 TATATTT-ATATTTTATATT
252761 TATA
1 TATA
252765 AAGTTACATC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
16 7 0.15
17 9 0.19
18 7 0.15
19 5 0.11
20 13 0.28
21 6 0.13
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTTATATTTTATATT
Found at i:252762 original size:27 final size:26
Alignment explanation
Indices: 252687--252765 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
252677 AAAATATTTA
*
252687 TATATTTATATTTTATAATATTT-TAAT
1 TATATTTA-ATATTATAA-ATTTATAAT
* * *
252714 TATATTTTCATATTAT-ATTTTAATATT
1 TATA-TTTAATATTATAAATTT-ATAAT
252741 TATATTTAATATTATAAATTTATAA
1 TATATTTAATATTATAAATTTATAA
252766 AGTTACATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
25 3 0.07
26 14 0.34
27 21 0.51
28 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
TATATTTAATATTATAAATTTATAAT
Found at i:255513 original size:16 final size:16
Alignment explanation
Indices: 255482--255523 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
255472 TTTGATATGA
255482 ATATATTTAATTTTTT
1 ATATATTTAATTTTTT
*
255498 TTAT-TTTAAGTTTTTT
1 ATATATTTAA-TTTTTT
255514 ATATATTTAA
1 ATATATTTAA
255524 AATGTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 5 0.23
16 12 0.55
17 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
ATATATTTAATTTTTT
Found at i:256386 original size:2 final size:2
Alignment explanation
Indices: 256375--256413 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
256365 AACATTACTC
256375 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
256414 TCCAACACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:265157 original size:20 final size:19
Alignment explanation
Indices: 265125--265172 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 19
265115 ATTTTTTTCG
*
265125 TATTATAATTTTATTTAAAA
1 TATTATAATTTTATAT-AAA
265145 TATTAT-ATATTTATATAAA
1 TATTATAAT-TTTATATAAA
265164 TATTGATAA
1 TATT-ATAA
265173 ATTAATAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 14 0.58
21 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TATTATAATTTTATATAAA
Found at i:266009 original size:2 final size:2
Alignment explanation
Indices: 266004--266062 Score: 73
Period size: 2 Copynumber: 29.0 Consensus size: 2
265994 AATATATTTC
* * *
266004 AT AT AT AT AT AT AT AT AC AA AT AT AT TT CAT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
*
266047 AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT
266063 CAAAAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
2 48 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:266011 original size:25 final size:25
Alignment explanation
Indices: 265975--266041 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 25
265965 AAAGTACCAC
*
265975 TTTCATACATATACACACAAATATA
1 TTTCATATATATACACACAAATATA
* *
266000 TTTCATATATATATATATATACAAATATA
1 TTTC----ATATATATACACACAAATATA
266029 TTTCATATATATA
1 TTTCATATATATA
266042 TATATATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
25 13 0.37
29 22 0.63
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (25 bp):
TTTCATATATATACACACAAATATA
Found at i:266018 original size:31 final size:30
Alignment explanation
Indices: 265983--266047 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
265973 ACTTTCATAC
265983 ATATACACACAAATATATTTCATATATATAT
1 ATATA-ACACAAATATATTTCATATATATAT
*
266014 ATAT-ATACAAATATATTTCATATATATAT
1 ATATAACACAAATATATTTCATATATATAT
266043 ATATA
1 ATATA
266048 TATATATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 28 0.88
31 4 0.12
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (30 bp):
ATATAACACAAATATATTTCATATATATAT
Found at i:266023 original size:29 final size:29
Alignment explanation
Indices: 265991--266049 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
265981 ACATATACAC
265991 ACAAATATATTTCATATATATATATATAT
1 ACAAATATATTTCATATATATATATATAT
266020 ACAAATATATTTCATATATATATATATAT
1 ACAAATATATTTCATATATATATATATAT
266049 A
1 A
266050 TATATGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (29 bp):
ACAAATATATTTCATATATATATATATAT
Found at i:266515 original size:3 final size:3
Alignment explanation
Indices: 266501--266538 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
266491 TCAAGTTTCA
*
266501 ATT ATT -TT ATT ATT ATT ATT GTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
266539 TTTGGAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:271153 original size:27 final size:27
Alignment explanation
Indices: 271112--271189 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
271102 TTTTTTATAT
* *
271112 AAAAAAATAATAATTCAAAGATAGAAG
1 AAAAAAATTATAATTCAAAGATAAAAG
* *
271139 AAAAAAATTACAATTCAAGGATAAAAG
1 AAAAAAATTATAATTCAAAGATAAAAG
* * *
271166 AAAGAAATTATAATTGAAGGATAA
1 AAAAAAATTATAATTCAAAGATAA
271190 GAGTAAGAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.63, C:0.04, G:0.13, T:0.21
Consensus pattern (27 bp):
AAAAAAATTATAATTCAAAGATAAAAG
Found at i:271197 original size:27 final size:27
Alignment explanation
Indices: 271116--271207 Score: 87
Period size: 27 Copynumber: 3.4 Consensus size: 27
271106 TTATATAAAA
* * * * *
271116 AAATAATAATTCAAAGATAGAAGAAAA
1 AAATTATAATTGAAGGATAAAAGAAAG
* *
271143 AAATTACAATTCAAGGATAAAAGAAAG
1 AAATTATAATTGAAGGATAAAAGAAAG
* *
271170 AAATTATAATTGAAGGATAAGAGTAAG
1 AAATTATAATTGAAGGATAAAAGAAAG
*
271197 AGATT-TAATTG
1 AAATTATAATTG
271208 TTAAAATTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 6 0.11
27 49 0.89
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (27 bp):
AAATTATAATTGAAGGATAAAAGAAAG
Found at i:272082 original size:2 final size:2
Alignment explanation
Indices: 272077--272103 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
272067 ATATATATAT
272077 AC 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 AC A
272104 TTTGGAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:272097 original size:41 final size:41
Alignment explanation
Indices: 272020--272100 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
272010 AAAACAAACA
* * *
272020 CATAATATATATATACACACACTCCAGTAGAAACACACACC
1 CATAATATATATATACACACACACCAGCACAAACACACACC
* *
272061 CATAATATATATATATACACACACACA-CACACACACACAC
1 CATAATATATATATACACACACAC-CAGCACAAACACACAC
272101 ACATTTGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (41 bp):
CATAATATATATATACACACACACCAGCACAAACACACACC
Found at i:273072 original size:2 final size:2
Alignment explanation
Indices: 273065--273096 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
273055 GCGAAAAACT
273065 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
273097 GATGATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:273512 original size:23 final size:22
Alignment explanation
Indices: 273486--273544 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
273476 TAAAAAAGAA
273486 TTAAAAATATTATAAT-TTAAGTT
1 TTAAAAATATTATAATATTAA--T
*
273509 TTAAATATATTA-AATATTAAT
1 TTAAAAATATTATAATATTAAT
*
273530 TTGAAAATAATTATA
1 TTAAAAAT-ATTATA
273545 TAAACTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 16 0.53
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (22 bp):
TTAAAAATATTATAATATTAAT
Found at i:277099 original size:2 final size:2
Alignment explanation
Indices: 277092--277116 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277082 ATAAACAAAT
277092 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 T
277117 GTCAATTGTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:277839 original size:2 final size:2
Alignment explanation
Indices: 277832--277856 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
277822 TCTCATTCAA
277832 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
277857 AAACCAATTA
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:280861 original size:17 final size:17
Alignment explanation
Indices: 280839--280887 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
280829 ATATTTACAT
280839 ATAAATATATATTAAAA
1 ATAAATATATATTAAAA
*
280856 ATAAATAT-TTTTAAAAA
1 ATAAATATATATT-AAAA
* *
280873 ATAAAAAAATATTAA
1 ATAAATATATATTAA
280888 CTTCCAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 20 0.77
18 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAAATATATATTAAAA
Found at i:281274 original size:18 final size:18
Alignment explanation
Indices: 281251--281305 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 18
281241 TATTAAAAAT
281251 ATAATTTTTTAAATATAA
1 ATAATTTTTTAAATATAA
* *
281269 ATAA-TTTTAAAAAATAA
1 ATAATTTTTTAAATATAA
281286 ATAAATTTATTTTAAATATA
1 AT-AA-TT-TTTTAAATATA
281306 TATTCATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 13 0.45
18 6 0.21
20 1 0.03
21 9 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAATTTTTTAAATATAA
Found at i:284321 original size:2 final size:2
Alignment explanation
Indices: 284308--284343 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
284298 TCGAATATTC
*
284308 TA TA TC 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
284344 AGATTATCCT
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:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:287579 original size:17 final size:16
Alignment explanation
Indices: 287563--287606 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
287553 AATTTTTTTA
287563 AATATTAAATATATTT
1 AATATTAAATATATTT
*
287579 -ATATTAAAAATATATT
1 AATATTAAATATAT-TT
*
287595 AATATTTAATAT
1 AATATTAAATAT
287607 TTATTCAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 12 0.52
16 2 0.09
17 9 0.39
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTAAATATATTT
Found at i:287584 original size:15 final size:15
Alignment explanation
Indices: 287563--287606 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 15
287553 AATTTTTTTA
287563 AATATTAAATATATT
1 AATATTAAATATATT
*
287578 TATATTAAAAATATATT
1 AATATT--AAATATATT
*
287595 AATATTTAATAT
1 AATATTAAATAT
287607 TTATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 10 0.42
17 14 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATATTAAATATATT
Found at i:289097 original size:27 final size:28
Alignment explanation
Indices: 289043--289098 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
289033 GATAGTGGAT
*
289043 AAATTTATTAATTTTAATTTGGACTTAA
1 AAATTTATTAATTTTAATTTGAACTTAA
*
289071 AAATTTAATTAA-TTT-ATTTGAATTTAA
1 AAATTT-ATTAATTTTAATTTGAACTTAA
289098 A
1 A
289099 TTCGATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.44
28 9 0.36
29 5 0.20
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (28 bp):
AAATTTATTAATTTTAATTTGAACTTAA
Found at i:289189 original size:16 final size:16
Alignment explanation
Indices: 289170--289222 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
289160 AAATGACTAA
289170 AATTTAAAATGATTTG
1 AATTTAAAATGATTTG
* *
289186 AATTTATAATGATCTG
1 AATTTAAAATGATTTG
* *
289202 AA-TCAAAAT-AATTG
1 AATTTAAAATGATTTG
289216 AATTTAA
1 AATTTAA
289223 TAAATTTAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
14 5 0.17
15 8 0.28
16 16 0.55
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (16 bp):
AATTTAAAATGATTTG
Found at i:291142 original size:2 final size:2
Alignment explanation
Indices: 291135--291159 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
291125 CTGTTTTATT
291135 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 T
291160 GCATTAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:293646 original size:2 final size:2
Alignment explanation
Indices: 293639--293683 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
293629 AACAAGAAAA
293639 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
293681 AG A
1 AG A
293684 TGGAAGGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:295508 original size:39 final size:34
Alignment explanation
Indices: 295436--295501 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
295426 TATAATTTCG
*
295436 AAAATA-TAAAT-TTTTTAAATTTTTTAAATATA
1 AAAATATTAAATATATTTAAATTTTTTAAATATA
295468 AAAATATTAAATATATTTAAATTTGGTTTAAATA
1 AAAATATTAAATATATTTAAATTT--TTTAAATA
295502 ACATAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.21
33 5 0.17
34 10 0.34
36 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (34 bp):
AAAATATTAAATATATTTAAATTTTTTAAATATA
Found at i:296249 original size:22 final size:23
Alignment explanation
Indices: 296212--296258 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
296202 TTGAGTTATT
*
296212 ATTTAATTAATAAAAATATTTAA
1 ATTTAATTAATAAAAATATATAA
296235 ATTTAATT-ATAAAAATATATAA
1 ATTTAATTAATAAAAATATATAA
296257 AT
1 AT
296259 ATAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAATTAATAAAAATATATAA
Found at i:298201 original size:20 final size:20
Alignment explanation
Indices: 298176--298262 Score: 70
Period size: 20 Copynumber: 4.2 Consensus size: 20
298166 ATTTTTTTAA
*
298176 AAAATTATATATATATATAT
1 AAAATTATATATATATAAAT
298196 AAAATTATAGT-TATATAAAT
1 AAAATTATA-TATATATAAAT
* * * *
298216 ATATTTAAAAATATATTAAAT
1 AAAATTATATATATA-TAAAT
*
298237 ATAAATTTTATATATA-AATAT
1 A-AAATTATATATATATAA-AT
298258 AAAAT
1 AAAAT
298263 ATCGAAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
20 33 0.63
21 10 0.19
22 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (20 bp):
AAAATTATATATATATAAAT
Found at i:298217 original size:26 final size:26
Alignment explanation
Indices: 298180--298258 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
298170 TTTTAAAAAA
* *
298180 TTATATATATATATATAAAATTATAG
1 TTATATAAATATATATAAAAATATAG
*
298206 TTATATAAATATATTTAAAAATATA-
1 TTATATAAATATATATAAAAATATAG
* *
298231 TTAAATATAAATTTTATATATAAATATA
1 TT--ATATAAA-TATATATAAAAATATA
298259 AAATATCGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
25 2 0.05
26 22 0.50
27 7 0.16
28 13 0.30
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (26 bp):
TTATATAAATATATATAAAAATATAG
Found at i:298912 original size:18 final size:18
Alignment explanation
Indices: 298879--298913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
298869 TTAAAAAAAA
*
298879 TATTTATATCTAAATATT
1 TATTTATATATAAATATT
*
298897 TATTTATATATGAATAT
1 TATTTATATATAAATAT
298914 AAGAATATAA
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:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TATTTATATATAAATATT
Found at i:300362 original size:2 final size:2
Alignment explanation
Indices: 300355--300396 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
300345 AAAGTTTAAA
*
300355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
300397 TTGAACCTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:307788 original size:2 final size:2
Alignment explanation
Indices: 307781--307810 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
307771 AGAAATGAAA
307781 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
307811 CTGGAAAAGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:310130 original size:16 final size:16
Alignment explanation
Indices: 310105--310135 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
310095 ACAACCAAAA
310105 AGTTCCACCTTCAATC
1 AGTTCCACCTTCAATC
*
310121 AGTTCTACCTTCAAT
1 AGTTCCACCTTCAAT
310136 TAATACGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.32, G:0.06, T:0.35
Consensus pattern (16 bp):
AGTTCCACCTTCAATC
Found at i:319322 original size:10 final size:10
Alignment explanation
Indices: 319307--319428 Score: 60
Period size: 10 Copynumber: 12.4 Consensus size: 10
319297 ATTTGATTTT
*
319307 TATATTTTAA
1 TATATTATAA
319317 TATATTATAA
1 TATATTATAA
*
319327 TATAATATCAA
1 TATATTAT-AA
*
319338 TAGA-TA-AA
1 TATATTATAA
319346 TATATTA-AA
1 TATATTATAA
* *
319355 TTTTATGTAAAA
1 -TATAT-TATAA
*
319367 TTTATTATTAA
1 TATATTA-TAA
*
319378 TATTTTATAA
1 TATATTATAA
*
319388 TTTA-TATAA
1 TATATTATAA
319397 -ATA-TATAA
1 TATATTATAA
*
319405 TATTTTAATAA
1 TATATT-ATAA
*
319416 TA-ATTTTAA
1 TATATTATAA
319425 TATA
1 TATA
319429 AAAAAGAATA
Statistics
Matches: 88, Mismatches: 14, Indels: 20
0.72 0.11 0.16
Matches are distributed among these distances:
8 12 0.14
9 16 0.18
10 33 0.38
11 25 0.28
12 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.50
Consensus pattern (10 bp):
TATATTATAA
Found at i:319786 original size:19 final size:18
Alignment explanation
Indices: 319756--319843 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
319746 ATATGATGTT
319756 ATATAAA-A-ATAAATATA
1 ATATAAATATATAAA-ATA
* *
319773 ATATAAATATATAAATTT
1 ATATAAATATATAAAATA
319791 AT-TAAAATTATATAAAATA
1 ATAT-AAA-TATATAAAATA
* *
319810 ATATTAATATATTAAAATTT
1 ATATAAATATA-TAAAA-TA
319830 ATATAAATATATAA
1 ATATAAATATATAA
319844 TATTTTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.14
18 11 0.19
19 26 0.46
20 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATAAATATATAAAATA
Found at i:319842 original size:10 final size:10
Alignment explanation
Indices: 319764--319842 Score: 53
Period size: 10 Copynumber: 8.1 Consensus size: 10
319754 TTATATAAAA
319764 ATAAATATA-
1 ATAAATATAT
319773 ATATAA-ATAT
1 ATA-AATATAT
*
319783 ATAAATTTAT
1 ATAAATATAT
319793 -TAAA-ATTAT
1 ATAAATA-TAT
319802 ATAAA-ATAAT
1 ATAAATAT-AT
*
319812 ATTAATATAT
1 ATAAATATAT
*
319822 -TAAAATTTAT
1 AT-AAATATAT
319832 ATAAATATAT
1 ATAAATATAT
319842 A
1 A
319843 ATATTTTAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
9 17 0.31
10 35 0.64
11 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
ATAAATATAT
Found at i:322364 original size:74 final size:74
Alignment explanation
Indices: 322215--322363 Score: 228
Period size: 74 Copynumber: 2.0 Consensus size: 74
322205 ACTCCGACTC
* * * * *
322215 AAGTGTGATTGTTAGATATGAGTATATGACTTTATTTTTTAAAGTTTTTTTTATATATTTAAAAG
1 AAGTGTGATTATCAGATATGAGTATATGACTTTATTTTTTAAAGATTTTTTCATATATTTAAAAA
*
322280 ATTTTTAAA
66 ATTTTAAAA
*
322289 AAGTGTGATTATCAGATATGAGTATGTGACTTTATTTTTTAAA-ATTTTTTCATATATTTAAAAA
1 AAGTGTGATTATCAGATATGAGTATATGACTTTATTTTTTAAAGATTTTTTCATATATTTAAAAA
322353 ATTTTAAAA
66 ATTTTAAAA
322362 AA
1 AA
322364 AAATTATATT
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
73 28 0.41
74 40 0.59
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (74 bp):
AAGTGTGATTATCAGATATGAGTATATGACTTTATTTTTTAAAGATTTTTTCATATATTTAAAAA
ATTTTAAAA
Found at i:324756 original size:2 final size:2
Alignment explanation
Indices: 324749--324779 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
324739 ATACAGGGAA
324749 TC TC TC TC TC TC TC 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 T
324780 TTATGATTTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:335094 original size:10 final size:10
Alignment explanation
Indices: 335024--335096 Score: 55
Period size: 10 Copynumber: 7.3 Consensus size: 10
335014 ATATTTGTGC
335024 ATTTATATATT
1 ATTT-TATATT
*
335035 -TTTTATGTT
1 ATTTTATATT
*
335044 AATTTTTATCTT
1 -A-TTTTATATT
335056 A-TTT-TA-T
1 ATTTTATATT
335063 ATTTTATATT
1 ATTTTATATT
335073 ATATTTATATT
1 AT-TTTATATT
*
335084 ATTTAATATT
1 ATTTTATATT
335094 ATT
1 ATT
335097 AGATTTAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 10 0.20
10 16 0.31
11 11 0.22
12 8 0.16
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (10 bp):
ATTTTATATT
Found at i:335308 original size:1 final size:1
Alignment explanation
Indices: 335302--335332 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
335292 TTCGAAAATG
335302 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
335333 GTTGACAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:337723 original size:23 final size:23
Alignment explanation
Indices: 337693--337736 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
337683 AGGCAAAAAG
337693 TTGAGAGATCCATGCAGATCTTC
1 TTGAGAGATCCATGCAGATCTTC
337716 TTGAGAGATCCATGCAGATCT
1 TTGAGAGATCCATGCAGATCT
337737 CAGACAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (23 bp):
TTGAGAGATCCATGCAGATCTTC
Found at i:353783 original size:36 final size:34
Alignment explanation
Indices: 353715--353792 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 34
353705 AATTTGTACC
*
353715 TAAAATT-TATTATTTTTAATAATAATATAAAAT
1 TAAAATTATATTATTTTTAATAATAATAAAAAAT
353748 TAAAATTATATTTATTTCTTAA-AATTAATAAAAAAT
1 TAAAATTATA-TTATTT-TTAATAA-TAATAAAAAAT
353784 TAAAATTAT
1 TAAAATTAT
353793 TAGATACAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
33 7 0.17
34 2 0.05
35 8 0.20
36 23 0.57
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
TAAAATTATATTATTTTTAATAATAATAAAAAAT
Found at i:357552 original size:14 final size:14
Alignment explanation
Indices: 357509--357544 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
357499 TAAAATTTAT
*
357509 ATTTTATAAAAAAA
1 ATTTTATTAAAAAA
357523 ATTTTATTAAAAAA
1 ATTTTATTAAAAAA
357537 ATTTTATT
1 ATTTTATT
357545 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATTTTATTAAAAAA
Found at i:357570 original size:20 final size:21
Alignment explanation
Indices: 357545--357592 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
357535 AAATTTTATT
* *
357545 TTTAAAATAAATTGATT-TAA
1 TTTAAAATAAATTAATTAAAA
*
357565 TTTAAATTAAATTAATTAAAA
1 TTTAAAATAAATTAATTAAAA
357586 TTTAAAA
1 TTTAAAA
357593 AATTTCGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TTTAAAATAAATTAATTAAAA
Found at i:358246 original size:28 final size:27
Alignment explanation
Indices: 358206--358258 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
358196 TTTTAAAATT
* *
358206 TTTATATATTTAATTATTTTTATTACA
1 TTTATATATTTAATAATTTTAATTACA
*
358233 TTTATATTTATTAATAATTTTAATTA
1 TTTATATAT-TTAATAATTTTAATTA
358259 TAATATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTTATATATTTAATAATTTTAATTACA
Found at i:360787 original size:22 final size:22
Alignment explanation
Indices: 360729--360790 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
360719 TAATTCAAAT
* *
360729 ATATTAAAATAATATTTTTATTA
1 ATATTTAAATAAT-TTTTAATTA
360752 ATATTTATAA-AATTTTATAATTA
1 ATATTTA-AATAATTTT-TAATTA
360775 A-ATTTAAATAATTTTT
1 ATATTTAAATAATTTTT
360791 TTATATTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
21 3 0.09
22 14 0.41
23 15 0.44
24 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTAAATAATTTTTAATTA
Found at i:360803 original size:22 final size:25
Alignment explanation
Indices: 360764--360808 Score: 69
Period size: 22 Copynumber: 1.9 Consensus size: 25
360754 ATTTATAAAA
360764 TTTTATAATTAAATTTAAATAATTT
1 TTTTATAATTAAATTTAAATAATTT
360789 TTTTAT-ATT-AA-TTAAATAAT
1 TTTTATAATTAAATTTAAATAAT
360809 AGTTTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 2 0.10
24 3 0.15
25 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTATAATTAAATTTAAATAATTT
Found at i:362307 original size:17 final size:16
Alignment explanation
Indices: 362240--362307 Score: 63
Period size: 17 Copynumber: 4.2 Consensus size: 16
362230 AATATTGTTT
*
362240 TATT-AAATAATAGTTT
1 TATTAAAATAATA-TTA
362256 TATTAAAATAATAATTA
1 TATTAAAATAAT-ATTA
362273 TATT--AATAAT-TTA
1 TATTAAAATAATATTA
362286 TTATTACAAATAATATTA
1 -TATTA-AAATAATATTA
362304 TATT
1 TATT
362308 TTTAAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 6 0.14
16 4 0.09
17 23 0.52
18 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
TATTAAAATAATATTA
Found at i:362369 original size:15 final size:14
Alignment explanation
Indices: 362331--362373 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
362321 TAGTAAGTTT
362331 AATA-ATATTCAAAA
1 AATATATATT-AAAA
362345 AATATATATTAAAA
1 AATATATATTAAAA
*
362359 ATTATATTATTAAAA
1 AATATA-TATTAAAA
362374 TAATTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
AATATATATTAAAA
Found at i:362374 original size:14 final size:14
Alignment explanation
Indices: 362335--362373 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
362325 AAGTTTAATA
*
362335 ATATTCAAAAAATAT
1 ATATT-AAAAATTAT
362350 ATATTAAAAATTAT
1 ATATTAAAAATTAT
362364 ATTATTAAAA
1 A-TATTAAAA
362374 TAATTTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATTAAAAATTAT
Found at i:366883 original size:28 final size:28
Alignment explanation
Indices: 366851--366957 Score: 82
Period size: 25 Copynumber: 4.0 Consensus size: 28
366841 CTTGAATTGT
*
366851 TATTTATAATAATAAATATTATAAATAA
1 TATTTATAATAATAAATATTATAATTAA
* **
366879 TATTTTATATTAATATTTA-TATAATTAA
1 TA-TTTATAATAATAAATATTATAATTAA
*
366907 T-TTTA-AATAA-AAATATTTTAATTAA
1 TATTTATAATAATAAATATTATAATTAA
** **
366932 T-TAAATAATAATTTATATTA-AATTAA
1 TATTTATAATAATAAATATTATAATTAA
366958 ATTAATTCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
24 3 0.05
25 15 0.24
26 15 0.24
27 5 0.08
28 11 0.18
29 13 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TATTTATAATAATAAATATTATAATTAA
Found at i:366892 original size:13 final size:15
Alignment explanation
Indices: 366851--366916 Score: 63
Period size: 13 Copynumber: 4.7 Consensus size: 15
366841 CTTGAATTGT
*
366851 TATTTATAATAATAAA
1 TATTTAT-ATAATTAA
366867 TA-TTATA-AA-TAA
1 TATTTATATAATTAA
366879 TATTT-TAT-ATTAA
1 TATTTATATAATTAA
366892 TATTTATATAATTAA
1 TATTTATATAATTAA
*
366907 T-TTTAAATAA
1 TATTTATATAA
366917 AAATATTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 7 0.16
13 12 0.28
14 12 0.28
15 10 0.23
16 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTTATATAATTAA
Found at i:366898 original size:41 final size:39
Alignment explanation
Indices: 366851--366932 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 39
366841 CTTGAATTGT
366851 TATTTATAATAATAAATATT-ATAAATAATATTTTATATTAA
1 TATTTAT-ATAATAAATATTAATAAA-AATATTTTA-ATTAA
* *
366892 TATTTATATAATTAATTTTAAATAAAAATATTTTAATTAA
1 TATTTATATAATAAATATT-AATAAAAATATTTTAATTAA
366932 T
1 T
366933 TAAATAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
40 16 0.43
41 16 0.43
42 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (39 bp):
TATTTATATAATAAATATTAATAAAAATATTTTAATTAA
Found at i:366943 original size:15 final size:15
Alignment explanation
Indices: 366925--366971 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
366915 AAAAATATTT
366925 TAATTAATTAAATAA
1 TAATTAATTAAATAA
*
366940 TAATTTATATTAAATTA
1 TAA-TTA-ATTAAATAA
366957 -AATTAATTCAAATAA
1 TAATTAATT-AAATAA
366972 AAAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 11 0.41
16 5 0.19
17 8 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTAATTAAATAA
Found at i:368062 original size:22 final size:22
Alignment explanation
Indices: 368037--368083 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
368027 GATTAAATGG
*
368037 TGATTTGATAGTTTATTATTGT
1 TGATTTGATAGTTTATCATTGT
* *
368059 TGATTTGATGGTTTGTCATTGT
1 TGATTTGATAGTTTATCATTGT
368081 TGA
1 TGA
368084 CTAAATGTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.55
Consensus pattern (22 bp):
TGATTTGATAGTTTATCATTGT
Found at i:368188 original size:34 final size:34
Alignment explanation
Indices: 368150--368217 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
368140 GATGGTTTAC
368150 CATTGTTAACTAAATGAAAGATTTGGTAGTTTTT
1 CATTGTTAACTAAATGAAAGATTTGGTAGTTTTT
* * **
368184 CATTGTTGATTAAATGAGTGATTTGGTAGTTTTT
1 CATTGTTAACTAAATGAAAGATTTGGTAGTTTTT
368218 ATCAAAACCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (34 bp):
CATTGTTAACTAAATGAAAGATTTGGTAGTTTTT
Found at i:368598 original size:18 final size:18
Alignment explanation
Indices: 368564--368599 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
368554 GAGTATTACC
**
368564 AGCGAATCAGTTGGTTTT
1 AGCGAATCAGTAAGTTTT
368582 AGCGAATCAGTAAGTTTT
1 AGCGAATCAGTAAGTTTT
368600 GGTCTTGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (18 bp):
AGCGAATCAGTAAGTTTT
Found at i:371646 original size:2 final size:2
Alignment explanation
Indices: 371639--371668 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
371629 ATTTCATGGT
371639 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
371669 ACACACACAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:371673 original size:2 final size:2
Alignment explanation
Indices: 371668--371697 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
371658 CTCTCTCTCT
371668 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
371698 TTGATGTATT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:378693 original size:28 final size:26
Alignment explanation
Indices: 378657--378731 Score: 96
Period size: 28 Copynumber: 2.8 Consensus size: 26
378647 AAAGCCACCC
378657 TTTTTGTTTGTCAAAAATGGTGGTTCCT
1 TTTTTGTTTGTCAAAAATGGTGGTT--T
* *
378685 TTTTTGTTTATAAAAAATGGTGGTTT
1 TTTTTGTTTGTCAAAAATGGTGGTTT
* *
378711 TTGTTGTTTGTCAAAATTGGT
1 TTTTTGTTTGTCAAAAATGGT
378732 AACTATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 18 0.44
28 23 0.56
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.52
Consensus pattern (26 bp):
TTTTTGTTTGTCAAAAATGGTGGTTT
Found at i:380288 original size:6 final size:6
Alignment explanation
Indices: 380263--380300 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
380253 ATTTTCTTAG
*
380263 AGAAAA AGCTAAA A-AAAA AGAAAA AGAAAA AGAAAA AG
1 AGAAAA AG-AAAA AGAAAA AGAAAA AGAAAA AGAAAA AG
380301 CATTGACCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 4 0.14
6 20 0.71
7 4 0.14
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (6 bp):
AGAAAA
Found at i:382980 original size:25 final size:26
Alignment explanation
Indices: 382945--383004 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
382935 GAAAATAATG
*
382945 AAGAAG-TTTTCAACAAGGAGGAGCA
1 AAGAAGATTTCCAACAAGGAGGAGCA
* *
382970 AAGAAGATTTCCCAACAAGGGGGAGTA
1 AAGAAGATTT-CCAACAAGGAGGAGCA
*
382997 AAAAAGAT
1 AAGAAGAT
383005 CAAGCCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 6 0.21
26 3 0.10
27 20 0.69
ACGTcount: A:0.47, C:0.12, G:0.27, T:0.15
Consensus pattern (26 bp):
AAGAAGATTTCCAACAAGGAGGAGCA
Found at i:388904 original size:19 final size:19
Alignment explanation
Indices: 388847--388907 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
388837 TTTAAAATTT
*
388847 TTAAATATATAAA-AAAAT-
1 TTAAATATA-AAATAATATC
* *
388865 TTAAAAATTAAATATATTATC
1 TTAAATA-TAAA-ATAATATC
388886 TTAAATATAAAATAATATC
1 TTAAATATAAAATAATATC
388905 TTA
1 TTA
388908 TGACTAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 8 0.24
19 13 0.38
20 7 0.21
21 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATATAAAATAATATC
Found at i:389270 original size:20 final size:20
Alignment explanation
Indices: 389209--389279 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
389199 ATAATTGATA
* * *
389209 AATTTAATTTATATTAAATAA
1 AATTTAAATTAAATT-AATAT
* **
389230 AATTTAAATAAAATTTTTAT
1 AATTTAAATTAAATTAATAT
389250 AATTTAAATTAAATTAATAT
1 AATTTAAATTAAATTAATAT
*
389270 -ATATAAATTA
1 AATTTAAATTA
389280 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 9 0.22
20 19 0.47
21 12 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAATTAAATTAATAT
Found at i:397260 original size:9 final size:9
Alignment explanation
Indices: 397236--397288 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
397226 AATTTAATAA
397236 TTTATATATT
1 TTTAT-TATT
*
397246 TATATTATT
1 TTTATTATT
*
397255 TTTATTATA
1 TTTATTATT
*
397264 TTTATTATA
1 TTTATTATT
397273 TTTA-TATAT
1 TTTATTAT-T
397282 TTTATTA
1 TTTATTA
397289 ATTATATTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
8 3 0.08
9 28 0.76
10 6 0.16
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTATT
Found at i:397264 original size:22 final size:23
Alignment explanation
Indices: 397237--397350 Score: 65
Period size: 22 Copynumber: 4.8 Consensus size: 23
397227 ATTTAATAAT
397237 TTATATATTTATATTAT-TTTTA
1 TTATATATTTATATTATATTTTA
*
397259 TTATATTTATTATATTTATATATTTTA
1 TTATA--TATT-TATAT-TATATTTTA
** *
397286 TTAATTATATTTATATT-TAAAATAA
1 TT-A-TATATTTATATTAT-ATTTTA
*
397311 TT-TATATTTATA-TAAATTTTA
1 TTATATATTTATATTATATTTTA
* *
397332 ATATTATAATTATATTATA
1 TTA-TATATTTATATTATA
397351 ATAGAAGATG
Statistics
Matches: 68, Mismatches: 12, Indels: 22
0.67 0.12 0.22
Matches are distributed among these distances:
21 5 0.07
22 15 0.22
23 9 0.13
24 8 0.12
25 10 0.15
26 7 0.10
27 11 0.16
28 1 0.01
29 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTATATATTTATATTATATTTTA
Found at i:397271 original size:18 final size:18
Alignment explanation
Indices: 397248--397304 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
397238 TATATATTTA
397248 TATTATTTTTATTATATT
1 TATTATTTTTATTATATT
*
397266 TATTATATTTA-TATATTT
1 TATTATTTTTATTATA-TT
* *
397284 TATTAATTATATTTATATT
1 TATTATTTTTA-TTATATT
397303 TA
1 TA
397305 AAATAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 4 0.12
18 20 0.62
19 4 0.12
20 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTATTTTTATTATATT
Found at i:397281 original size:31 final size:31
Alignment explanation
Indices: 397237--397299 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 31
397227 ATTTAATAAT
*
397237 TTATATATTTATATTATT-TTTATTATATTTA
1 TTATATATTTATATT-TTATTAATTATATTTA
397268 TTATAT-TTATATATTTTATTAATTATATTTA
1 TTATATATT-TATATTTTATTAATTATATTTA
397299 T
1 T
397300 ATTTAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
TTATATATTTATATTTTATTAATTATATTTA
Found at i:397823 original size:26 final size:25
Alignment explanation
Indices: 397774--397825 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 25
397764 CTCAATCGAA
* *
397774 TTTGTATTTTAAGAAAAAATATTTT
1 TTTGTATTTTAAAAAAAAAGATTTT
397799 TTTGTATTTTAAAAAAAAAAGATTTT
1 TTTGTATTTT-AAAAAAAAAGATTTT
397825 T
1 T
397826 ACTGTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTGTATTTTAAAAAAAAAGATTTT
Found at i:397824 original size:25 final size:25
Alignment explanation
Indices: 397774--397825 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
397764 CTCAATCGAA
* *
397774 TTTGTATTTTAAGAAAAAATATTTT
1 TTTGTATTTTAAGAAAAAAAAATTT
397799 TTTGTATTTTAA-AAAAAAAAGATTT
1 TTTGTATTTTAAGAAAAAAAA-ATTT
397824 TT
1 TT
397826 ACTGTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (25 bp):
TTTGTATTTTAAGAAAAAAAAATTT
Found at i:398746 original size:27 final size:27
Alignment explanation
Indices: 398686--398747 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
398676 TGCATTAGCA
* * *
398686 TATATTTTTCTAAATTTTAAATATTTT
1 TATATTTTTCTAAATTATAAAAATGTT
*
398713 TATATTTTTTTAAATTATAAAAATAGTT
1 TATATTTTTCTAAATTATAAAAAT-GTT
398741 TA-ATTTT
1 TATATTTT
398748 ATAAATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TATATTTTTCTAAATTATAAAAATGTT
Found at i:399558 original size:39 final size:38
Alignment explanation
Indices: 399474--399558 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
399464 TTGTGCTACC
* ** *
399474 GATTAAAAATAGTGATTTTTGTTTTGAACCATTTCATCG
1 GATT-AAAATAGTGATTTTTATTTTGAACCATACCAACG
399513 GATTAAAATAGTGATTTTTATTTT-AACCTATACCACACG
1 GATTAAAATAGTGATTTTTATTTTGAACC-ATACCA-ACG
*
399552 GGTTAAA
1 GATTAAA
399559 TGTAGTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
37 4 0.10
38 23 0.59
39 12 0.31
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (38 bp):
GATTAAAATAGTGATTTTTATTTTGAACCATACCAACG
Found at i:402179 original size:27 final size:27
Alignment explanation
Indices: 402149--402207 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
402139 AAGGTTACGG
402149 CGGAGGTGACATTGCAGGAACTTCTGA
1 CGGAGGTGACATTGCAGGAACTTCTGA
* * *
402176 CGGAGGTGATATTGCAGGAAGTTCTGG
1 CGGAGGTGACATTGCAGGAACTTCTGA
402203 CGGAG
1 CGGAG
402208 ATAATTGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (27 bp):
CGGAGGTGACATTGCAGGAACTTCTGA
Found at i:402304 original size:30 final size:30
Alignment explanation
Indices: 402243--402304 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
402233 ATTATTATTG
* ** *
402243 TAATTTCTACAAATGATATATTTGATTACT
1 TAATTTCTACAAATGACATATTCAATAACT
*
402273 TAATTTCTACAGATGACATATTCAATAACT
1 TAATTTCTACAAATGACATATTCAATAACT
402303 TA
1 TA
402305 TCTGAAATCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (30 bp):
TAATTTCTACAAATGACATATTCAATAACT
Found at i:404171 original size:16 final size:16
Alignment explanation
Indices: 404150--404183 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
404140 AATCCGCATC
404150 AACATAAGTGGAAGAT
1 AACATAAGTGGAAGAT
404166 AACATAAGTGGAAGAT
1 AACATAAGTGGAAGAT
404182 AA
1 AA
404184 GATACGATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (16 bp):
AACATAAGTGGAAGAT
Found at i:410380 original size:18 final size:18
Alignment explanation
Indices: 410359--410408 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
410349 AAAATAATTT
410359 ATATAATATTAATATTAA
1 ATATAATATTAATATTAA
*
410377 ATATTAATA-T-ATTTTAA
1 ATA-TAATATTAATATTAA
410394 A-AT-ATATTAATATTA
1 ATATAATATTAATATTA
410409 TGTTATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 6 0.22
17 7 0.26
18 4 0.15
19 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAATATTAATATTAA
Found at i:410427 original size:22 final size:23
Alignment explanation
Indices: 410399--410453 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
410389 TTTAAAATAT
410399 ATTAATAT-TATGTTATATTTTA
1 ATTAATATATATGTTATATTTTA
410421 ATTAATATATATGTTATA-TTT-
1 ATTAATATATATGTTATATTTTA
410442 ATTAATTATATA
1 ATTAA-TATATA
410454 AAATATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 5 0.16
22 17 0.55
23 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
ATTAATATATATGTTATATTTTA
Found at i:410593 original size:23 final size:24
Alignment explanation
Indices: 410525--410594 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
410515 CAATTTATGT
*
410525 TATATTTTTAGCAATTTTTAATTAA
1 TATATATTTAGCAATTTTTAA-TAA
* ** *
410550 TA-ATGTTTATGTTATTATTAA-AA
1 TATATATTTA-GCAATTTTTAATAA
410573 TATATATTTAGCAATTTTTAAT
1 TATATATTTAGCAATTTTTAAT
410595 TTTATCTTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
23 12 0.35
24 12 0.35
25 10 0.29
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (24 bp):
TATATATTTAGCAATTTTTAATAA
Found at i:410733 original size:17 final size:17
Alignment explanation
Indices: 410711--410745 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
410701 TTTTACTATA
*
410711 ATTTTAAATTATATTTT
1 ATTTTAAATGATATTTT
*
410728 ATTTTATATGATATTTT
1 ATTTTAAATGATATTTT
410745 A
1 A
410746 ATTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
ATTTTAAATGATATTTT
Found at i:411015 original size:15 final size:17
Alignment explanation
Indices: 410976--411016 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
410966 AAACTATGAG
410976 TTTTATAAATATATAGTA
1 TTTTA-AAATATATAGTA
*
410994 TTATAAAATA-ATA-TA
1 TTTTAAAATATATAGTA
411009 TTTTAAAA
1 TTTTAAAA
411017 ATTAGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 9 0.43
16 3 0.14
17 5 0.24
18 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TTTTAAAATATATAGTA
Found at i:411377 original size:93 final size:93
Alignment explanation
Indices: 411266--411439 Score: 271
Period size: 93 Copynumber: 1.9 Consensus size: 93
411256 TATAATTTTG
* * **
411266 CAAAATATTATAATTTTTAAAA-TTTTAATAAAATAAAATAATAAATATTCGT-ATATATCATAT
1 CAAAATATAATAATTTTTAAAATTTTTAA-AAAATAAAATAATAAATATTCGTGA-ACAAAATAT
411329 AATTAAATAAATAATATTAATTTTATATAA
64 AATTAAATAAATAATATTAATTTTATATAA
*
411359 CAAAATATAATAATTTTTAAAATTTTTAAAAAATAAAATGATAAATATTCGTGAACAAAATATAA
1 CAAAATATAATAATTTTTAAAATTTTTAAAAAATAAAATAATAAATATTCGTGAACAAAATATAA
411424 TTAAATAAATAATATT
66 TTAAATAAATAATATT
411440 TACAATTATT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
93 67 0.91
94 7 0.09
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (93 bp):
CAAAATATAATAATTTTTAAAATTTTTAAAAAATAAAATAATAAATATTCGTGAACAAAATATAA
TTAAATAAATAATATTAATTTTATATAA
Found at i:411534 original size:24 final size:24
Alignment explanation
Indices: 411474--411555 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 24
411464 TGAATGTTAC
*
411474 AAATTATAAAAAATATTTTTTTTATA
1 AAATTATAAAAAATA--ATTTTTATA
411500 AAATCTTTATACAAAAATTAA-TTTTA-A
1 AAA---TTATA-AAAAA-TAATTTTTATA
*
411527 AAATTATAGAAAATAATTTTTATA
1 AAATTATAAAAAATAATTTTTATA
411551 AAATT
1 AAATT
411556 TTTATACAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
22 3 0.06
23 9 0.19
24 11 0.23
26 3 0.06
27 4 0.09
28 5 0.11
29 5 0.11
30 5 0.11
31 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (24 bp):
AAATTATAAAAAATAATTTTTATA
Found at i:412296 original size:21 final size:22
Alignment explanation
Indices: 412272--412312 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
412262 GATAAAGATT
412272 TTTTTATTTAT-TTATTTTTTG
1 TTTTTATTTATATTATTTTTTG
*
412293 TTTTTATTTTTATTATTTTT
1 TTTTTATTTATATTATTTTT
412313 AAAAAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (22 bp):
TTTTTATTTATATTATTTTTTG
Found at i:412304 original size:23 final size:22
Alignment explanation
Indices: 412270--412312 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
412260 TAGATAAAGA
412270 TTTTTTTATTTATTTATTTTTTG
1 TTTTTTTATTTA-TTATTTTTTG
412293 TTTTTATT-TTTATTATTTTT
1 TTTTT-TTATTTATTATTTTT
412313 AAAAAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 9 0.47
24 2 0.11
ACGTcount: A:0.14, C:0.00, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTTTTATTTATTATTTTTTG
Found at i:415227 original size:7 final size:7
Alignment explanation
Indices: 415215--415246 Score: 50
Period size: 6 Copynumber: 4.9 Consensus size: 7
415205 ATTTTGTTAT
415215 TTATTTA
1 TTATTTA
415222 TTATTTA
1 TTATTTA
415229 TT-TTTA
1 TTATTTA
415235 TT-TTTA
1 TTATTTA
415241 TTATTT
1 TTATTT
415247 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.50
7 12 0.50
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TTATTTA
Found at i:415227 original size:11 final size:11
Alignment explanation
Indices: 415211--415251 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
415201 AAAGATTTTG
415211 TTATTTATTTA
1 TTATTTATTTA
415222 TTATTTATTT-
1 TTATTTATTTA
415232 TTA-TT-TTTA
1 TTATTTATTTA
*
415241 TTATTTTTTTA
1 TTATTTATTTA
415252 AAAAATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 5 0.19
11 14 0.52
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:415249 original size:16 final size:17
Alignment explanation
Indices: 415214--415248 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
415204 GATTTTGTTA
415214 TTTATTTATTATTTATT
1 TTTATTTATTATTTATT
415231 TTTATTT-TTA-TTATT
1 TTTATTTATTATTTATT
415246 TTT
1 TTT
415249 TTAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTATTTATTATTTATT
Found at i:415259 original size:91 final size:91
Alignment explanation
Indices: 415036--415222 Score: 286
Period size: 91 Copynumber: 2.1 Consensus size: 91
415026 TAATATATAA
** * * *
415036 ATTTATCATAATTTGCACACATATTATATTTATACAAAATTACTTATGCTTTTGAAGAGAAGTAT
1 ATTTATCATAATTTATATAGATATTATATTTATACAAAATTACTTATGCTTTTGAAAAGAAGTAT
*
415101 AACGTATATAAAAATTTTGTTAATTT
66 AACGGATATAAAAATTTTGTTAATTT
* *
415127 ATTTATCATAATTTATATAGATAATATATTTATACAAAATTACTTATGTTTTTGAAAAGAAGTAT
1 ATTTATCATAATTTATATAGATATTATATTTATACAAAATTACTTATGCTTTTGAAAAGAAGTAT
*
415192 AACGGATATAAAGATTTTGTT-ATTT
66 AACGGATATAAAAATTTTGTTAATTT
415217 ATTTAT
1 ATTTAT
415223 TATTTATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
90 10 0.11
91 77 0.89
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.44
Consensus pattern (91 bp):
ATTTATCATAATTTATATAGATATTATATTTATACAAAATTACTTATGCTTTTGAAAAGAAGTAT
AACGGATATAAAAATTTTGTTAATTT
Found at i:415434 original size:20 final size:18
Alignment explanation
Indices: 415409--415466 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 18
415399 GAAACAAAAG
415409 TTTTGTTATTTATTTATTTT
1 TTTTGTTA-TTA-TTATTTT
415429 TTTTGTTATTATTATTTT
1 TTTTGTTATTATTATTTT
*
415447 TATT-TTATTATTATTTT
1 TTTTGTTATTATTATTTT
415464 TTT
1 TTT
415467 AAATGGGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 15 0.42
18 10 0.28
19 3 0.08
20 8 0.22
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTGTTATTATTATTTT
Done.