Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 18 of 25
Found at i:2615479 original size:13 final size:13
Alignment explanation
Indices: 2615459--2615493 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
2615449 TAATGATTAT
2615459 ATATTTTTAATTAA
1 ATATTTTTAA-TAA
2615473 ATATTTTTAATAA
1 ATATTTTTAATAA
*
2615486 TTATTTTT
1 ATATTTTT
2615494 GTTATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATTTTTAATAA
Found at i:2615916 original size:7 final size:6
Alignment explanation
Indices: 2615864--2615923 Score: 61
Period size: 6 Copynumber: 9.7 Consensus size: 6
2615854 ATGAGTAATG
*
2615864 ATTTAA ATTTAA ATAAATAA ATTT-A ATTT-A ATTTAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA AT--TTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
2615913 ATTTAA TATTT
1 ATTTAA -ATTT
2615924 TTAAAAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
5 10 0.21
6 22 0.47
7 10 0.21
8 5 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:2616271 original size:18 final size:18
Alignment explanation
Indices: 2616248--2616282 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2616238 AAAATATGAT
*
2616248 ACATAAAATATAAATATG
1 ACATAAAATACAAATATG
*
2616266 ACATAATATACAAATAT
1 ACATAAAATACAAATAT
2616283 TTTTAAATTT
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:0.60, C:0.09, G:0.03, T:0.29
Consensus pattern (18 bp):
ACATAAAATACAAATATG
Found at i:2617223 original size:27 final size:25
Alignment explanation
Indices: 2617170--2617227 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
2617160 TAAATTTAAT
2617170 TATAAAAATAATTAAAAATAATAAA
1 TATAAAAATAATTAAAAATAATAAA
* * *
2617195 TATATAAATATATTAAAATTTATATAA
1 TATAAAAATA-ATTAAAAATAATA-AA
2617222 TATAAA
1 TATAAA
2617228 TTATTATTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 11 0.41
27 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
TATAAAAATAATTAAAAATAATAAA
Found at i:2617224 original size:25 final size:25
Alignment explanation
Indices: 2617161--2617233 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
2617151 TAAATTTTTT
* *
2617161 AAATTTA-ATTATAAAAATA-ATTA
1 AAATTTATATAATATAAATATATTA
* * *
2617184 AAAATAATAAATATATAAATATATTA
1 AAATTTATATA-ATATAAATATATTA
2617210 AAATTTATATAATATAAAT-TATTA
1 AAATTTATATAATATAAATATATTA
2617234 TTATATTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
23 5 0.13
24 6 0.15
25 16 0.41
26 12 0.31
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATTTATATAATATAAATATATTA
Found at i:2617240 original size:32 final size:34
Alignment explanation
Indices: 2617203--2617267 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
2617193 AATATATAAA
*
2617203 TATATTAAAATTTATAT-AATATA-AATTATTAT
1 TATATTAAAATTTATATAAATATATAATAATTAT
**
2617235 TATATTAATTTTTATATAAATATATAATAATTA
1 TATATTAAAATTTATATAAATATATAATAATTA
2617268 AATATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 15 0.54
33 6 0.21
34 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (34 bp):
TATATTAAAATTTATATAAATATATAATAATTAT
Found at i:2617401 original size:33 final size:31
Alignment explanation
Indices: 2617327--2617402 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 31
2617317 TTTTATTTTA
*
2617327 TTATTTATATATAAAATAATTATTTAAAAAAAT
1 TTATTAATATATAAAATAATTATTT--AAAAAT
2617360 TTATTAATATATAAAATAATTATTT-AAAAT
1 TTATTAATATATAAAATAATTATTTAAAAAT
*
2617390 TTAATAATA-ATAA
1 TTATTAATATATAA
2617403 GATATTAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 13 0.32
33 24 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (31 bp):
TTATTAATATATAAAATAATTATTTAAAAAT
Found at i:2617645 original size:4 final size:4
Alignment explanation
Indices: 2617626--2617666 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
2617616 TGTTCGGGAA
* * *
2617626 AGAG CGAG ATAG AGAG AGAG AGAG AGAG AGAG AGAC AGAG A
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG A
2617667 AGGCATTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02
Consensus pattern (4 bp):
AGAG
Found at i:2617645 original size:6 final size:6
Alignment explanation
Indices: 2617626--2617666 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
2617616 TGTTCGGGAA
* * *
2617626 AGAGCG AGATAG AGAGAG AGAGAG AGAGAG AGAGAC AGAGA
1 AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGAG AGAGA
2617667 AGGCATTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.44, T:0.02
Consensus pattern (6 bp):
AGAGAG
Found at i:2626313 original size:2 final size:2
Alignment explanation
Indices: 2626306--2626338 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2626296 TCAGGCCTTC
2626306 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
2626339 AGGGGTAGTT
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:2630667 original size:17 final size:17
Alignment explanation
Indices: 2630641--2630674 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2630631 GAAAAAGAGG
2630641 TTCCTCTTTTTT-TTTT
1 TTCCTCTTTTTTGTTTT
2630657 TTCCTTCTTTTTTGTTTT
1 TTCC-TCTTTTTTGTTTT
2630675 ATATGATCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 8 0.50
18 4 0.25
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTCCTCTTTTTTGTTTT
Found at i:2636360 original size:41 final size:37
Alignment explanation
Indices: 2636315--2636396 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 37
2636305 ATAAAAAGTT
2636315 TAATAATTTAATTTATTTATTGATATATATCATAAATTATA
1 TAATAATTTAA-TTATTT-TTGATAT-TATCAT-AATTATA
* * * *
2636356 TAATATTTTAATTATTTTTTATATTATTATTATTATA
1 TAATAATTTAATTATTTTTGATATTATCATAATTATA
2636393 TAAT
1 TAAT
2636397 TAAAATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 10 0.27
38 5 0.14
39 6 0.16
40 6 0.16
41 10 0.27
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (37 bp):
TAATAATTTAATTATTTTTGATATTATCATAATTATA
Found at i:2636418 original size:29 final size:28
Alignment explanation
Indices: 2636386--2636441 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
2636376 ATATTATTAT
2636386 TATT-ATATAATTAAAATATTTTATCATAA
1 TATTCATATAA-TAAAATA-TTTATCATAA
*
2636415 TATTCATATCATAAAATATTTATCATA
1 TATTCATATAATAAAATATTTATCATA
2636442 TCTAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 9 0.36
29 11 0.44
30 5 0.20
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (28 bp):
TATTCATATAATAAAATATTTATCATAA
Found at i:2636774 original size:2 final size:2
Alignment explanation
Indices: 2636767--2636795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2636757 CCCACCCTGG
2636767 AC 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 AC A
2636796 TATATGTGTT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2645028 original size:4 final size:4
Alignment explanation
Indices: 2645019--2645061 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
2645009 AGTGAAGGGA
2645019 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
2645062 TATGGGCTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2650172 original size:2 final size:2
Alignment explanation
Indices: 2650165--2650194 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2650155 GAATAATCTA
2650165 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
2650195 CCATTCTTTA
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:2652061 original size:24 final size:25
Alignment explanation
Indices: 2651980--2652083 Score: 117
Period size: 24 Copynumber: 4.3 Consensus size: 25
2651970 AATATCATGC
2651980 TTAAAAATTATATTTAATGCATTAT
1 TTAAAAATTATATTTAATGCATTAT
* * * *
2652005 TTCAAAA-TATATGTATTG-ATT-G
1 TTAAAAATTATATTTAATGCATTAT
* *
2652027 TAAAAAATTATATTTAAT-TATTAT
1 TTAAAAATTATATTTAATGCATTAT
2652051 TTAAAAATTATATTTAATGCATTAT
1 TTAAAAATTATATTTAATGCATTAT
*
2652076 TTCAAAAT
1 TTAAAAAT
2652084 ATTACCTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
22 5 0.08
23 14 0.22
24 26 0.41
25 18 0.29
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (25 bp):
TTAAAAATTATATTTAATGCATTAT
Found at i:2652518 original size:14 final size:13
Alignment explanation
Indices: 2652472--2652523 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 13
2652462 GTAATAATAT
*
2652472 AATTTAAAATTAA
1 AATTTAAATTTAA
**
2652485 AAAAT-AATTT-A
1 AATTTAAATTTAA
2652496 AATTTAAATTTAA
1 AATTTAAATTTAA
2652509 AATATTAAATTTAA
1 AAT-TTAAATTTAA
2652523 A
1 A
2652524 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 4 0.13
12 9 0.29
13 7 0.23
14 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTAAATTTAA
Found at i:2652529 original size:18 final size:18
Alignment explanation
Indices: 2652475--2652530 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
2652465 ATAATATAAT
* *
2652475 TTAAAATTAAAAAATAAT-
1 TTAAATTTAAATAA-AATA
2652493 TTAAATTTAAATTTAAAATA
1 TTAAATTTAAA--TAAAATA
2652513 TTAAATTTAAATAAAATA
1 TTAAATTTAAATAAAATA
2652531 AATACTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 17 0.52
19 3 0.09
20 13 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATTTAAATAAAATA
Found at i:2653181 original size:21 final size:22
Alignment explanation
Indices: 2653152--2653196 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2653142 TAATTTTTAA
2653152 ATTTAAATT-TATTTATATTAT
1 ATTTAAATTATATTTATATTAT
* *
2653173 ATTTTAATTAATTTTTATATTAT
1 ATTTAAATT-ATATTTATATTAT
2653196 A
1 A
2653197 ATTATTTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
23 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTAAATTATATTTATATTAT
Found at i:2655046 original size:15 final size:15
Alignment explanation
Indices: 2655011--2655063 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
2655001 CTCTCAATGG
*
2655011 TTAAATTAAATTGAGT
1 TTAAATTAAATT-AAT
2655027 TTAAATTAAATTAAT
1 TTAAATTAAATTAAT
* *
2655042 TTAAATTGAGTTAAT
1 TTAAATTAAATTAAT
2655057 TTAAATT
1 TTAAATT
2655064 TTAAAATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 22 0.65
16 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (15 bp):
TTAAATTAAATTAAT
Found at i:2655047 original size:26 final size:25
Alignment explanation
Indices: 2655011--2655063 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
2655001 CTCTCAATGG
2655011 TTAAATTAAATTGAGTTTAAATTAAA
1 TTAAATTAAATTGAG-TTAAATTAAA
* *
2655037 TTAATTTAAATTGAGTTAATTTAAA
1 TTAAATTAAATTGAGTTAAATTAAA
2655062 TT
1 TT
2655064 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.44
26 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (25 bp):
TTAAATTAAATTGAGTTAAATTAAA
Found at i:2657405 original size:17 final size:19
Alignment explanation
Indices: 2657379--2657422 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
2657369 AACTTTGGCA
*
2657379 ATAAAAAAAATAATAAGAT
1 ATAAAAAATATAATAAGAT
*
2657398 ATAAAAAATATAATAATAT
1 ATAAAAAATATAATAAGAT
2657417 ATAAAA
1 ATAAAA
2657423 TATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
ATAAAAAATATAATAAGAT
Found at i:2657470 original size:20 final size:20
Alignment explanation
Indices: 2657445--2657482 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2657435 ATAAATTATT
2657445 AATATATTAA-AATTTAAATA
1 AATATA-TAATAATTTAAATA
2657465 AATATATAATAATTTAAA
1 AATATATAATAATTTAAA
2657483 ATTATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATATAATAATTTAAATA
Found at i:2657474 original size:27 final size:27
Alignment explanation
Indices: 2657380--2657486 Score: 89
Period size: 26 Copynumber: 4.1 Consensus size: 27
2657370 ACTTTGGCAA
* * * *
2657380 TAAAAAAAATA-ATAAGATATAAAAAA
1 TAAAATAAATATATAATATATTAAAAT
* * *
2657406 TATAAT-AATATATAAAATATTTAAA-
1 TAAAATAAATATATAATATATTAAAAT
2657431 TAAAATAAAT-TATTAATATATTAAAAT
1 TAAAATAAATATA-TAATATATTAAAAT
*
2657458 TTAAATAAATATATAATA-ATTTAAAAT
1 TAAAATAAATATATAATATA-TTAAAAT
2657485 TA
1 TA
2657487 TTATAATATA
Statistics
Matches: 65, Mismatches: 10, Indels: 11
0.76 0.12 0.13
Matches are distributed among these distances:
25 11 0.17
26 30 0.46
27 22 0.34
28 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.36
Consensus pattern (27 bp):
TAAAATAAATATATAATATATTAAAAT
Found at i:2662541 original size:21 final size:21
Alignment explanation
Indices: 2662491--2662535 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2662481 TTTATTTATG
2662491 AAAAAT-AATTT--GATTAAT
1 AAAAATAAATTTGAGATTAAT
2662509 AAAAATAAATTTGAGATTAAT
1 AAAAATAAATTTGAGATTAAT
*
2662530 GAAAAT
1 AAAAAT
2662536 TTATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 5 0.22
21 12 0.52
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAAATAAATTTGAGATTAAT
Found at i:2663841 original size:15 final size:16
Alignment explanation
Indices: 2663815--2663844 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2663805 ATAGATGAAA
2663815 AAATATTTTTTAAAAT
1 AAATATTTTTTAAAAT
2663831 AAATA-TTTTTAAAA
1 AAATATTTTTTAAAA
2663845 AATAATCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTTTTTAAAAT
Found at i:2663849 original size:17 final size:16
Alignment explanation
Indices: 2663815--2663845 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2663805 ATAGATGAAA
*
2663815 AAATATTTTTTAAAAT
1 AAATATTTTTAAAAAT
2663831 AAATATTTTTAAAAA
1 AAATATTTTTAAAAA
2663846 ATAATCTATC
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTTTTAAAAAT
Found at i:2667919 original size:2 final size:2
Alignment explanation
Indices: 2667912--2667948 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2667902 AGATAAGATC
*
2667912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2667949 AATAAAATCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2669172 original size:17 final size:17
Alignment explanation
Indices: 2669138--2669172 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2669128 ATTAAATTTA
*
2669138 ATTAATTATATTTTTAT
1 ATTAATTATATTTATAT
*
2669155 ATTAATTATGTTTATAT
1 ATTAATTATATTTATAT
2669172 A
1 A
2669173 ATATTTTTAA
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:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTAATTATATTTATAT
Found at i:2674523 original size:34 final size:33
Alignment explanation
Indices: 2674477--2674593 Score: 148
Period size: 34 Copynumber: 3.5 Consensus size: 33
2674467 GTAAAAACCA
*
2674477 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATC-C
*
2674511 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATC-C
* *
2674545 CCATTTAATCAACAATGGTAAA-CTACTAAATCA
1 CCATTTAATCAACAATGG-AAACCTACCAAATCC
2674578 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2674594 TCTCCCACTT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
33 17 0.23
34 54 0.72
35 4 0.05
ACGTcount: A:0.42, C:0.27, G:0.06, T:0.25
Consensus pattern (33 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCC
Found at i:2678895 original size:34 final size:34
Alignment explanation
Indices: 2678849--2678945 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
2678839 GTAAAAACCA
* *
2678849 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGAAACCTACCAAATCAC
*
2678883 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-AAACCTACCAAATCAC
* * *
2678917 CCATTTAATCAATAATGGTAAGCTACCAA
1 CCATTTAATCAACAATGGAAACCTACCAA
2678946 CATGTCGTCC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.06
34 47 0.87
35 4 0.07
ACGTcount: A:0.40, C:0.28, G:0.08, T:0.24
Consensus pattern (34 bp):
CCATTTAATCAACAATGGAAACCTACCAAATCAC
Found at i:2679069 original size:34 final size:34
Alignment explanation
Indices: 2679022--2679096 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2679012 AGGGTCTGAT
*
2679022 TAAATGGGTGATTTGGT-GGTTTACCATTGTTGAC
1 TAAATGGGAGATTTGGTAGG-TTACCATTGTTGAC
* *
2679056 TAAATGGGAGATTTGGTAGGTTGCCATTGTTGAT
1 TAAATGGGAGATTTGGTAGGTTACCATTGTTGAC
2679090 TAAATGG
1 TAAATGG
2679097 TGGTTTTTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 35 0.95
35 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.31, T:0.39
Consensus pattern (34 bp):
TAAATGGGAGATTTGGTAGGTTACCATTGTTGAC
Found at i:2681183 original size:17 final size:17
Alignment explanation
Indices: 2681163--2681200 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2681153 TAATATAATA
2681163 TATAAAAATATATT-TTT
1 TATAAAAATA-ATTATTT
*
2681180 TATAAATATAATTATTT
1 TATAAAAATAATTATTT
2681197 TATA
1 TATA
2681201 TATTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAAAAATAATTATTT
Found at i:2681186 original size:15 final size:17
Alignment explanation
Indices: 2681168--2681200 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2681158 TAATATATAA
2681168 AAATAT-ATT-TTTTAT
1 AAATATAATTATTTTAT
2681183 AAATATAATTATTTTAT
1 AAATATAATTATTTTAT
2681200 A
1 A
2681201 TATTTTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AAATATAATTATTTTAT
Found at i:2681501 original size:21 final size:21
Alignment explanation
Indices: 2681489--2681528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2681479 ATATAATTTT
*
2681489 AATATTATAAAATATATATTA
1 AATATAATAAAATATATATTA
*
2681510 AATATAATAAAAAATATAT
1 AATATAATAAAATATATAT
2681529 ATCAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATATAATAAAATATATATTA
Found at i:2681865 original size:15 final size:13
Alignment explanation
Indices: 2681822--2681870 Score: 62
Period size: 15 Copynumber: 3.5 Consensus size: 13
2681812 TTTTAAAAAA
2681822 ATTATTTTATTAT
1 ATTATTTTATTAT
2681835 ATTCATATTTATTAT
1 ATT-AT-TTTATTAT
2681850 ATCTATTTTATCTAT
1 AT-TATTTTAT-TAT
2681865 ATTATT
1 ATTATT
2681871 ATATGTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.09
14 11 0.34
15 17 0.53
16 1 0.03
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTATTTTATTAT
Found at i:2682082 original size:23 final size:23
Alignment explanation
Indices: 2682053--2682098 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2682043 ATTTAAATCC
2682053 TAATTTAATTTAGGGCTTAGTTT
1 TAATTTAATTTAGGGCTTAGTTT
*
2682076 TAATTTAATTTAGGGTTTAGTTT
1 TAATTTAATTTAGGGCTTAGTTT
2682099 CATAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.26, C:0.02, G:0.17, T:0.54
Consensus pattern (23 bp):
TAATTTAATTTAGGGCTTAGTTT
Found at i:2683106 original size:13 final size:13
Alignment explanation
Indices: 2683087--2683131 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
2683077 AAATATATTT
2683087 TTATTTAAATTTAA
1 TTATTT-AATTTAA
2683101 -TATTTAATTTAA
1 TTATTTAATTTAA
* *
2683113 TTATTTTATATAA
1 TTATTTAATTTAA
2683126 TTATTT
1 TTATTT
2683132 TTAAAGACTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTTAATTTAA
Found at i:2683905 original size:17 final size:18
Alignment explanation
Indices: 2683878--2683924 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
2683868 ACAAAATATT
*
2683878 ATTTTTAATTTTTATA-AA
1 ATTTTT-ATTTTTAAATAA
2683896 ATTTTTA-TTTTAAATAA
1 ATTTTTATTTTTAAATAA
2683913 ATTTATTATTTT
1 ATTT-TTATTTT
2683925 CTTCCTAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 9 0.36
19 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTATTTTTAAATAA
Found at i:2684020 original size:8 final size:8
Alignment explanation
Indices: 2684007--2684036 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2683997 TAAAACATAA
2684007 TTTTTTAT
1 TTTTTTAT
2684015 TTTTTTAT
1 TTTTTTAT
*
2684023 TATTTTAT
1 TTTTTTAT
2684031 TTTTTT
1 TTTTTT
2684037 TGGATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTAT
Found at i:2688265 original size:23 final size:23
Alignment explanation
Indices: 2688239--2688287 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2688229 TTAAATAATT
2688239 TTTTATATTTAATATATTATTA-A
1 TTTTATATTTAATATA-TATTATA
* *
2688262 TTTTATGTTTATTATATATTATA
1 TTTTATATTTAATATATATTATA
2688285 TTT
1 TTT
2688288 ACAATTATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTATATTTAATATATATTATA
Found at i:2688757 original size:16 final size:15
Alignment explanation
Indices: 2688730--2688764 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
2688720 ATTTGATATG
2688730 TTTAAAAAAATTAAA
1 TTTAAAAAAATTAAA
*
2688745 TTTAAAAATAATTTAA
1 TTTAAAAA-AATTAAA
2688761 TTTA
1 TTTA
2688765 TACTATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTAAAAAAATTAAA
Found at i:2689150 original size:16 final size:17
Alignment explanation
Indices: 2689125--2689158 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2689115 TTTTTAAATA
*
2689125 TTAAATATTTATA-ATT
1 TTAAAAATTTATATATT
2689141 TTAAAAATTTATATATT
1 TTAAAAATTTATATATT
2689158 T
1 T
2689159 ATCATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAAAAATTTATATATT
Found at i:2689156 original size:24 final size:23
Alignment explanation
Indices: 2689116--2689160 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2689106 TTGTATATTT
*
2689116 TTTTAAATATTAAATATTTATAA
1 TTTTAAAAATTAAATATTTATAA
*
2689139 TTTTAAAAATTTATATATTTAT
1 TTTTAAAAA-TTAAATATTTAT
2689161 CATAAACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTAAAAATTAAATATTTATAA
Found at i:2696644 original size:15 final size:15
Alignment explanation
Indices: 2696620--2696737 Score: 61
Period size: 15 Copynumber: 8.3 Consensus size: 15
2696610 AGTACCTGTG
*
2696620 TAAAATTATTTATGT
1 TAAAAATATTTATGT
*
2696635 TAAAAATATTTAT-A
1 TAAAAATATTTATGT
* *
2696649 TCAAAATATTTGA-AT
1 TAAAAATATTT-ATGT
* *
2696664 TAAAAGTATCTATG-
1 TAAAAATATTTATGT
* *
2696678 TGAAAATATCTATGT
1 TAAAAATATTTATGT
*
2696693 T-AAAATA--TGTGT
1 TAAAAATATTTATGT
* **
2696705 T-AAAATATCTATAC
1 TAAAAATATTTATGT
*
2696719 TAAAAATATTTATAT
1 TAAAAATATTTATGT
2696734 TAAA
1 TAAA
2696738 TTACTTCAGT
Statistics
Matches: 80, Mismatches: 16, Indels: 14
0.73 0.15 0.13
Matches are distributed among these distances:
12 11 0.14
14 32 0.40
15 37 0.46
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (15 bp):
TAAAAATATTTATGT
Found at i:2696656 original size:14 final size:14
Alignment explanation
Indices: 2696637--2696737 Score: 64
Period size: 14 Copynumber: 7.2 Consensus size: 14
2696627 ATTTATGTTA
* *
2696637 AAAATATTTATATC
1 AAAATATCTATATT
*
2696651 AAAATATTTGA-ATT
1 AAAATATCT-ATATT
* *
2696665 AAAAGTATCTATGTG
1 AAAA-TATCTATATT
*
2696680 AAAATATCTATGTT
1 AAAATATCTATATT
* *
2696694 AAAATA--TGTGTT
1 AAAATATCTATATT
*
2696706 AAAATATCTATACTA
1 AAAATATCTATA-TT
*
2696721 AAAATATTTATATT
1 AAAATATCTATATT
2696735 AAA
1 AAA
2696738 TTACTTCAGT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
12 11 0.16
14 37 0.53
15 22 0.31
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (14 bp):
AAAATATCTATATT
Found at i:2696684 original size:43 final size:41
Alignment explanation
Indices: 2696635--2696733 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 41
2696625 TTATTTATGT
* *
2696635 TAAAAATATTTATATCAAAATATTTGAATTAAAAGTATCTAT-G
1 TAAAAATATTTATATCAAAATATGTG--TTAAAA-TATCTATAC
* * * *
2696678 TGAAAATATCTATGTTAAAATATGTGTTAAAATATCTATAC
1 TAAAAATATTTATATCAAAATATGTGTTAAAATATCTATAC
2696719 TAAAAATATTTATAT
1 TAAAAATATTTATAT
2696734 TAAATTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
40 7 0.15
41 18 0.39
43 21 0.46
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (41 bp):
TAAAAATATTTATATCAAAATATGTGTTAAAATATCTATAC
Found at i:2696725 original size:41 final size:42
Alignment explanation
Indices: 2696635--2696737 Score: 120
Period size: 41 Copynumber: 2.5 Consensus size: 42
2696625 TTATTTATGT
* * *
2696635 TAAAAATATTTATATCAAAATATTTGAATTAAAAGTATCTATG
1 TAAAAATATTTATATTAAAATATGTG-ATTAAAAGTATCTATC
* * *
2696678 TGAAAATATCTATGTTAAAATATGTG-TTAAAA-TATCTATAC
1 TAAAAATATTTATATTAAAATATGTGATTAAAAGTATCTAT-C
2696719 TAAAAATATTTATATTAAA
1 TAAAAATATTTATATTAAA
2696738 TTACTTCAGT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
40 7 0.14
41 22 0.44
43 21 0.42
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (42 bp):
TAAAAATATTTATATTAAAATATGTGATTAAAAGTATCTATC
Found at i:2699976 original size:2 final size:2
Alignment explanation
Indices: 2699971--2699995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2699961 TTTATCTGGC
2699971 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
2699996 CTCATGTTTA
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:2700952 original size:16 final size:15
Alignment explanation
Indices: 2700921--2700971 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
2700911 TTAATATCAA
2700921 TAATTATATTAAATT
1 TAATTATATTAAATT
*
2700936 TAATTATTTTAAAATT
1 TAATTATATT-AAATT
2700952 TAAATTGA-ATTAAATT
1 T-AATT-ATATTAAATT
2700968 TAAT
1 TAAT
2700972 ATTTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 12 0.39
16 12 0.39
17 6 0.19
18 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TAATTATATTAAATT
Found at i:2702165 original size:10 final size:10
Alignment explanation
Indices: 2702150--2702175 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2702140 GGATAAATAA
2702150 TAGAACATGG
1 TAGAACATGG
2702160 TAGAACATGG
1 TAGAACATGG
2702170 TAGAAC
1 TAGAAC
2702176 TAGAAGACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (10 bp):
TAGAACATGG
Found at i:2706037 original size:23 final size:23
Alignment explanation
Indices: 2706011--2706055 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2706001 ATCATGCATT
*
2706011 AATTTAATTA-AAATATAAATAAA
1 AATTAAATTACAAA-ATAAATAAA
2706034 AATTAAATTACAAAATAAATAA
1 AATTAAATTACAAAATAAATAA
2706056 TATATAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AATTAAATTACAAAATAAATAAA
Found at i:2707094 original size:2 final size:2
Alignment explanation
Indices: 2707055--2707152 Score: 57
Period size: 2 Copynumber: 52.0 Consensus size: 2
2707045 ATACACGTAC
* * * * * *
2707055 AT AT TT AT AA AT AT TT AT AT AT TT AT AT CAT AT TT AT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
* * *
2707098 AT -T TT A- AT AT AT TT AT AT AT AT AT AT -T AT AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2707136 AT AT A- AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT
2707153 CCAAAAATAT
Statistics
Matches: 71, Mismatches: 17, Indels: 16
0.68 0.16 0.15
Matches are distributed among these distances:
1 7 0.10
2 62 0.87
3 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:2707108 original size:33 final size:33
Alignment explanation
Indices: 2707055--2707152 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
2707045 ATACACGTAC
2707055 ATATT-TATAAATATTTATATATTTATATCATAT
1 ATATTATATAAATATTTATATATTTATAT-ATAT
*
2707088 TTA-TATATAAAT-TTTAATATATTTATATATAT
1 ATATTATATAAATATTT-ATATATTTATATATAT
** *
2707120 ATATTATATTTATA-TTATATAATTATAT-TAT
1 ATATTATATAAATATTTATATATTTATATATAT
2707151 AT
1 AT
2707153 CCAAAAATAT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
31 5 0.09
32 21 0.38
33 30 0.54
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
ATATTATATAAATATTTATATATTTATATATAT
Found at i:2707110 original size:41 final size:43
Alignment explanation
Indices: 2707057--2707152 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 43
2707047 ACACGTACAT
*
2707057 ATTTATAA-ATATTTATATATTTATATCATATTTATA-TATA-A
1 ATTT-TAATATATTTATATATATATATCATATTTATATTATATA
*
2707098 ATTTTAATATATTTATATATATATATTATATTTATATTATATA
1 ATTTTAATATATTTATATATATATATCATATTTATATTATATA
* *
2707141 ATTATATTATAT
1 ATTTTAATATAT
2707153 CCAAAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 3 0.06
41 30 0.62
42 4 0.08
43 11 0.23
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (43 bp):
ATTTTAATATATTTATATATATATATCATATTTATATTATATA
Found at i:2707145 original size:13 final size:13
Alignment explanation
Indices: 2707105--2707152 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2707095 TAAATTTTAA
2707105 TATATT-TATATAT
1 TATATTATATA-AT
2707118 ATATATTATAT--T
1 -TATATTATATAAT
2707130 TATATTATATAAT
1 TATATTATATAAT
2707143 TATATTATAT
1 TATATTATAT
2707153 CCAAAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.32
12 1 0.03
13 11 0.35
14 6 0.19
15 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
TATATTATATAAT
Found at i:2707269 original size:29 final size:31
Alignment explanation
Indices: 2707227--2707290 Score: 87
Period size: 29 Copynumber: 2.1 Consensus size: 31
2707217 TTGTGAAGAA
* *
2707227 AATATTTTAGTTTTTGTATTATT-AAA-TTT
1 AATATTTTAATTTTTATATTATTAAAATTTT
*
2707256 AATATTTTAATTTTTATATTTTTAAAATTTT
1 AATATTTTAATTTTTATATTATTAAAATTTT
2707287 AATA
1 AATA
2707291 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 20 0.67
30 3 0.10
31 7 0.23
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (31 bp):
AATATTTTAATTTTTATATTATTAAAATTTT
Found at i:2708117 original size:20 final size:20
Alignment explanation
Indices: 2708089--2708132 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
2708079 AACAAAATAT
* *
2708089 ATATTTTTATTAATAATTTA
1 ATATATTTAATAATAATTTA
* *
2708109 ATATATTTAATATTTATTTA
1 ATATATTTAATAATAATTTA
2708129 ATAT
1 ATAT
2708133 CAAAATTCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATATTTAATAATAATTTA
Found at i:2708170 original size:20 final size:20
Alignment explanation
Indices: 2708104--2708171 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
2708094 TTTATTAATA
2708104 ATTTAATATATTTAATAT-TT
1 ATTTAA-ATATTTAATATCTT
* *
2708124 ATTT-AATA-TCAAAATTCTT
1 ATTTAAATATTTAATA-TCTT
2708143 -TTTAAAATATTTAATATCTT
1 ATTT-AAATATTTAATATCTT
2708163 ATTTAAATA
1 ATTTAAATA
2708172 AATTGATCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
17 4 0.11
18 7 0.18
19 3 0.08
20 17 0.45
21 7 0.18
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTTAAATATTTAATATCTT
Found at i:2709928 original size:31 final size:30
Alignment explanation
Indices: 2709893--2709960 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2709883 AGACAGGCAG
* *
2709893 TAAATTAAATTTTTATAATT-TTTATAATATT
1 TAAATTAAA-TTTTAAAATTATTT-TAAAATT
*
2709924 TAAATTTTAATTTTAAAATTATTTTAAAATT
1 TAAA-TTAAATTTTAAAATTATTTTAAAATT
2709955 TAAATT
1 TAAATT
2709961 CATTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.06
31 23 0.72
32 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TAAATTAAATTTTAAAATTATTTTAAAATT
Found at i:2710355 original size:21 final size:21
Alignment explanation
Indices: 2710328--2710397 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2710318 AATTTTTTAA
2710328 TAAATTTTAA-TTAAATTATT
1 TAAATTTTAATTTAAATTATT
* *
2710348 TAAAATTTAAATTTAATTTATT
1 T-AAATTTTAATTTAAATTATT
*
2710370 T-TATTTTAAATTTAAATTATTT
1 TAAATTTT-AATTTAAATTA-TT
2710392 TAAATT
1 TAAATT
2710398 AAGATCATTC
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
20 5 0.13
21 18 0.46
22 13 0.33
23 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAATTTTAATTTAAATTATT
Found at i:2710359 original size:16 final size:16
Alignment explanation
Indices: 2710338--2710397 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
2710328 TAAATTTTAA
*
2710338 TTAAATTATTTAAAAT
1 TTAAATTATTTTAAAT
2710354 TT-AA--A-TTT-AAT
1 TTAAATTATTTTAAAT
**
2710365 TTATTTTATTTTAAAT
1 TTAAATTATTTTAAAT
2710381 TTAAATTATTTTAAAT
1 TTAAATTATTTTAAAT
2710397 T
1 T
2710398 AAGATCATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
11 5 0.15
12 2 0.06
13 1 0.03
14 1 0.03
15 5 0.15
16 20 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAAATTATTTTAAAT
Found at i:2710360 original size:27 final size:28
Alignment explanation
Indices: 2710328--2710387 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
2710318 AATTTTTTAA
2710328 TAAATTTTAA-TTAAATTATTTAAAATT
1 TAAATTTTAATTTAAATTATTTAAAATT
** *
2710355 TAAA-TTTAATTTATTTTATTTTAAATT
1 TAAATTTTAATTTAAATTATTTAAAATT
2710382 TAAATT
1 TAAATT
2710388 ATTTTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 5 0.18
27 22 0.79
28 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (28 bp):
TAAATTTTAATTTAAATTATTTAAAATT
Found at i:2710399 original size:21 final size:21
Alignment explanation
Indices: 2710338--2710399 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
2710328 TAAATTTTAA
*
2710338 TTAAATTATTTAAAATTTAAAT
1 TTAAATTATTTTAAA-TTAAAT
* **
2710360 TTAATTTATTTTATTTTAAAT
1 TTAAATTATTTTAAATTAAAT
2710381 TTAAATTATTTTAAATTAA
1 TTAAATTATTTTAAATTAA
2710400 GATCATTCAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 22 0.67
22 11 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAATTATTTTAAATTAAAT
Found at i:2710448 original size:15 final size:15
Alignment explanation
Indices: 2710428--2710478 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
2710418 AACTTTTGAG
2710428 TTATTTTAGTTTAAA
1 TTATTTTAGTTTAAA
*
2710443 TTA-TTTAGATTCAAA
1 TTATTTTAG-TTTAAA
* *
2710458 TTATTTTGAATTTAAT
1 TTATTTT-AGTTTAAA
2710474 TTATT
1 TTATT
2710479 AAATTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 5 0.17
15 11 0.38
16 12 0.41
17 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (15 bp):
TTATTTTAGTTTAAA
Found at i:2711302 original size:2 final size:2
Alignment explanation
Indices: 2711295--2711325 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2711285 ACTTGGACCC
2711295 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 A
2711326 ATGATGAAGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2711544 original size:2 final size:2
Alignment explanation
Indices: 2711537--2711564 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2711527 GCTTCAAACT
2711537 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
2711565 AGAAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2714493 original size:17 final size:18
Alignment explanation
Indices: 2714471--2714505 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2714461 AATCAGCCAC
*
2714471 GGAAAA-AAAAGCCAAAA
1 GGAAAATAAAACCCAAAA
2714488 GGAAAATAAAACCCAAAA
1 GGAAAATAAAACCCAAAA
2714506 ACTGAAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.14, G:0.14, T:0.03
Consensus pattern (18 bp):
GGAAAATAAAACCCAAAA
Found at i:2716406 original size:2 final size:2
Alignment explanation
Indices: 2716401--2716430 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2716391 ATAAGTAAAA
*
2716401 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2716431 TAGCCAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2716723 original size:19 final size:18
Alignment explanation
Indices: 2716628--2716725 Score: 56
Period size: 18 Copynumber: 5.2 Consensus size: 18
2716618 TTTGAGTGAA
* *
2716628 TATTTTTTTAAATTAAAG
1 TATTTTTTAAAATAAAAG
*
2716646 TAGTTTTTTAAGGAA-CAAA-
1 TA-TTTTTTAA--AATAAAAG
*
2716665 TATTTTTTGAAAAGAAGTAAG
1 TATTTTTT-AAAATAA--AAG
* **
2716686 TAATTTTTAAAATTTAAG
1 TATTTTTTAAAATAAAAG
2716704 TATTTTTTAAATATAAAAG
1 TATTTTTTAAA-ATAAAAG
2716723 TAT
1 TAT
2716726 ATAAATATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
17 2 0.03
18 22 0.36
19 19 0.31
20 9 0.15
21 9 0.15
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (18 bp):
TATTTTTTAAAATAAAAG
Found at i:2716870 original size:20 final size:18
Alignment explanation
Indices: 2716841--2716896 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
2716831 TTTTGTTTTC
2716841 AAAATGATAATTTTTTCACAT
1 AAAAT-ATAATTTTTT-A-AT
* *
2716862 AAAATATAAATTTCTAAT
1 AAAATATAATTTTTTAAT
*
2716880 AAAATTTAATTTTTTAA
1 AAAATATAATTTTTTAA
2716897 AATAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 16 0.53
19 1 0.03
20 8 0.27
21 5 0.17
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (18 bp):
AAAATATAATTTTTTAAT
Found at i:2718110 original size:28 final size:27
Alignment explanation
Indices: 2718064--2718129 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
2718054 AAAATATATT
* *
2718064 TATATTTTTATTTTATTATTTAATATAAA
1 TATATTTTAATTATATTA-TT-ATATAAA
*
2718093 TATATTTTAATTAT-TTATTATATATA
1 TATATTTTAATTATATTATTATATAAA
*
2718119 CATATTTTAAT
1 TATATTTTAAT
2718130 ATAATACCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 16 0.48
27 2 0.06
28 3 0.09
29 12 0.36
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TATATTTTAATTATATTATTATATAAA
Found at i:2718114 original size:24 final size:26
Alignment explanation
Indices: 2718072--2718129 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
2718062 TTTATATTTT
*
2718072 TATTTT-ATTATTTAATATA-A-ATA
1 TATTTTAATTATTTAATATATATACA
*
2718095 TATTTTAATTATTTATTATATATACA
1 TATTTTAATTATTTAATATATATACA
2718121 TATTTTAAT
1 TATTTTAAT
2718130 ATAATACCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 6 0.20
24 12 0.40
25 1 0.03
26 11 0.37
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTTTAATTATTTAATATATATACA
Found at i:2718123 original size:26 final size:24
Alignment explanation
Indices: 2718072--2718129 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
2718062 TTTATATTTT
*
2718072 TATTTT-ATTATTTAATATAAATA
1 TATTTTAATTATTTAATATAAACA
*
2718095 TATTTTAATTATTTATTATATATACA
1 TATTTTAATTATTTA--ATATAAACA
2718121 TATTTTAAT
1 TATTTTAAT
2718130 ATAATACCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 6 0.20
24 8 0.27
26 16 0.53
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
TATTTTAATTATTTAATATAAACA
Found at i:2718714 original size:20 final size:19
Alignment explanation
Indices: 2718659--2718715 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
2718649 TTTTTTATTT
* *
2718659 AAATTTAATTAAAATTT-A
1 AAATTTATTTAATATTTAA
*
2718677 AAATTTATTTTATCATTTAA
1 AAATTTATTTAAT-ATTTAA
2718697 AAATATTATTTAATATTTA
1 AAAT-TTATTTAATATTTA
2718716 TATAATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.31
19 4 0.12
20 10 0.31
21 8 0.25
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATTTATTTAATATTTAA
Found at i:2718726 original size:21 final size:21
Alignment explanation
Indices: 2718672--2718726 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
2718662 TTTAATTAAA
*
2718672 ATTT-AAAA-TTTATTTTATC
1 ATTTAAAAATTTTATTTAATC
*
2718691 ATTTAAAAATATTATTTAAT-
1 ATTTAAAAATTTTATTTAATC
*
2718711 ATTTATATAATTTTAT
1 ATTTA-AAAATTTTAT
2718727 AATTAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 4 0.14
20 9 0.31
21 16 0.55
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAAAAATTTTATTTAATC
Found at i:2719166 original size:16 final size:15
Alignment explanation
Indices: 2719122--2719169 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
2719112 TAATAATTTT
*
2719122 TTATTATT-T-ATTG
1 TTATTATTATAATTA
2719135 TTATTATTATAATTA
1 TTATTATTATAATTA
*
2719150 TTATTATTTTCAATTA
1 TTATTATTAT-AATTA
2719166 TTAT
1 TTAT
2719170 ACTCTGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 8 0.27
14 1 0.03
15 12 0.40
16 9 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTATTATTATAATTA
Found at i:2723485 original size:25 final size:24
Alignment explanation
Indices: 2723439--2723485 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
2723429 TATATTTTAC
*
2723439 TTTTATTATTTTTATTTTATTATA
1 TTTTATTATTTTTATTTGATTATA
2723463 TTTTAATTATTTTT-TATTGATTA
1 TTTT-ATTATTTTTAT-TTGATTA
2723486 GAATTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTTATTATTTTTATTTGATTATA
Found at i:2723663 original size:19 final size:18
Alignment explanation
Indices: 2723628--2723663 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2723618 CTTTTTTCTT
*
2723628 AAAAAAATAATTTATTGA
1 AAAAAAATAATTGATTGA
2723646 AAAAAAATATATTGATTG
1 AAAAAAATA-ATTGATTG
2723664 TATTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (18 bp):
AAAAAAATAATTGATTGA
Found at i:2723778 original size:18 final size:18
Alignment explanation
Indices: 2723755--2723815 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 18
2723745 TAAATTTTAA
2723755 TATATTTATATTTTATAT
1 TATATTTATATTTTATAT
*
2723773 TATATTTATATTTAAAATAT
1 TATATTTATATTT--TATAT
*
2723793 TATA-TCATATTTTA-AT
1 TATATTTATATTTTATAT
2723809 TATATTT
1 TATATTT
2723816 TTATGTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
16 6 0.17
17 2 0.06
18 13 0.36
19 7 0.19
20 8 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATTTATATTTTATAT
Found at i:2723816 original size:11 final size:12
Alignment explanation
Indices: 2723755--2723816 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 12
2723745 TAAATTTTAA
2723755 TATATTTATATTT
1 TATA-TTATATTT
2723768 TATATTATA-TT
1 TATATTATATTT
* *
2723779 TATATTTAAAATAT
1 TATA-TT-ATATTT
*
2723793 TATATCATATTT
1 TATATTATATTT
2723805 TA-ATTATATTT
1 TATATTATATTT
2723816 T
1 T
2723817 TATGTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 15 0.38
12 13 0.32
13 7 0.17
14 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
TATATTATATTT
Found at i:2724316 original size:3 final size:3
Alignment explanation
Indices: 2724308--2724350 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2724298 TTATGATATC
2724308 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2724351 CTATTATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2728030 original size:19 final size:18
Alignment explanation
Indices: 2727988--2728030 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
2727978 AAAACTCTCC
2727988 TTATCTGTTTTTAAGTAAA
1 TTAT-TGTTTTTAAGTAAA
* *
2728007 ATATTGTTTTTACTGTAAA
1 TTATTGTTTTTA-AGTAAA
2728026 TTATT
1 TTATT
2728031 TGTTGTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (18 bp):
TTATTGTTTTTAAGTAAA
Found at i:2733884 original size:20 final size:20
Alignment explanation
Indices: 2733859--2733901 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2733849 TTTAATGTTA
2733859 AAAACCATATTCTATGATAG
1 AAAACCATATTCTATGATAG
2733879 AAAACCATATTCTATGATAG
1 AAAACCATATTCTATGATAG
2733899 AAA
1 AAA
2733902 CACGTTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (20 bp):
AAAACCATATTCTATGATAG
Found at i:2735891 original size:31 final size:30
Alignment explanation
Indices: 2735840--2735897 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
2735830 AAATTATAAT
*
2735840 AAAAAATAATTATTAAATAATATTAAATTA
1 AAAAAATAATTATTAAATAATAATAAATTA
2735870 AAAAATATATATTA-TAAATAATAATAAA
1 AAAAA-ATA-ATTATTAAATAATAATAAA
2735898 ATATTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 5 0.20
31 16 0.64
32 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAAAATAATTATTAAATAATAATAAATTA
Found at i:2735950 original size:15 final size:15
Alignment explanation
Indices: 2735930--2735972 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2735920 AAAAATAAAA
2735930 TAAAAATAAAAGAAT
1 TAAAAATAAAAGAAT
* *
2735945 TAAAAATATATATGACT
1 TAAAAATA-A-AAGAAT
2735962 TAAAAATAAAA
1 TAAAAATAAAA
2735973 AGATGGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.39
16 2 0.09
17 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (15 bp):
TAAAAATAAAAGAAT
Found at i:2735965 original size:43 final size:42
Alignment explanation
Indices: 2735885--2735972 Score: 108
Period size: 43 Copynumber: 2.1 Consensus size: 42
2735875 TATATATTAT
* * *
2735885 AAATAATAATAAAATATTAAAATCATATTTGTATTAAAAATA
1 AAATAAAAATAAAAAATTAAAATCATATATGTATTAAAAATA
2735927 AAATAAAAATAAAAGAATTAAAAAT-ATATATG-ACTTAAAAATA
1 AAATAAAAATAAAA-AATT-AAAATCATATATGTA-TTAAAAATA
2735970 AAA
1 AAA
2735973 AGATGGAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
42 14 0.35
43 21 0.52
44 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (42 bp):
AAATAAAAATAAAAAATTAAAATCATATATGTATTAAAAATA
Found at i:2736101 original size:24 final size:24
Alignment explanation
Indices: 2736070--2736138 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 24
2736060 TAGTATATGT
2736070 TTATTAATTTATA-TAATAATAAAA
1 TTATTAATTTATATTAA-AATAAAA
*
2736094 TTATTAA-TTATATTAAATTAAAA
1 TTATTAATTTATATTAAAATAAAA
* *
2736117 -T-TTAATTTATTTTTAAATAAAA
1 TTATTAATTTATATTAAAATAAAA
2736139 AATCATGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.10
22 14 0.36
23 11 0.28
24 10 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTAATTTATATTAAAATAAAA
Found at i:2736115 original size:23 final size:24
Alignment explanation
Indices: 2736070--2736126 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
2736060 TAGTATATGT
2736070 TTATTAATTTATATAATAATAAAA
1 TTATTAATTTATATAATAATAAAA
*
2736094 TTATTAA-TTATATTAA-ATTAAAA
1 TTATTAATTTATA-TAATAATAAAA
2736117 -T-TTAATTTAT
1 TTATTAATTTAT
2736127 TTTTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 5 0.17
23 11 0.37
24 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TTATTAATTTATATAATAATAAAA
Found at i:2736454 original size:2 final size:2
Alignment explanation
Indices: 2736447--2736476 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2736437 ATACACGTTA
2736447 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
2736477 CTCCTTAAAA
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:2751373 original size:47 final size:47
Alignment explanation
Indices: 2751298--2751388 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
2751288 TTTATACCTT
*
2751298 AATCAACTTCTCAAATGTAAACCATATATATGAATACTTCAATGGTC
1 AATCAACTTCTCAAATGCAAACCATATATATGAATACTTCAATGGTC
* ** *
2751345 AATCAACTTTTCAAATGCAAACTGTATATTTGAATACTTCAATG
1 AATCAACTTCTCAAATGCAAACCATATATATGAATACTTCAATG
2751389 ACCATAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (47 bp):
AATCAACTTCTCAAATGCAAACCATATATATGAATACTTCAATGGTC
Found at i:2760778 original size:22 final size:21
Alignment explanation
Indices: 2760735--2760774 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
2760725 AAATTGTATT
2760735 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
2760756 TAAATATTAA-TATAAAATA
1 TAAAT-TTAATTATAAAATA
2760775 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:2762410 original size:22 final size:22
Alignment explanation
Indices: 2762367--2762411 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2762357 ATTTATATCT
* *
2762367 TTCAATTTTAATATTTTTAAAA
1 TTCAATTTTAATATTATAAAAA
2762389 TTCACATTTTAATA-TATAAAAA
1 TTCA-ATTTTAATATTATAAAAA
2762411 T
1 T
2762412 ATATTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
TTCAATTTTAATATTATAAAAA
Found at i:2768881 original size:18 final size:17
Alignment explanation
Indices: 2768842--2768882 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
2768832 AAAATATTTA
*
2768842 ATATTTTTATAATAATT
1 ATATTTTTATAATAAAT
*
2768859 TTATTTTTATAAATAAAT
1 ATATTTTTAT-AATAAAT
2768877 ATATTT
1 ATATTT
2768883 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTTTTATAATAAAT
Found at i:2772301 original size:13 final size:13
Alignment explanation
Indices: 2772285--2772318 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2772275 CTCTTATTTT
2772285 TTTAATATTTATA
1 TTTAATATTTATA
*
2772298 TTTAATTTTTATA
1 TTTAATATTTATA
*
2772311 TTCAATAT
1 TTTAATAT
2772319 AATTTTTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAATATTTATA
Found at i:2772330 original size:19 final size:20
Alignment explanation
Indices: 2772283--2772337 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
2772273 TCCTCTTATT
* *
2772283 TTTTTAATATTTATATTTAA
1 TTTTTAATATTCATATATAA
2772303 TTTTT-ATATTCA-ATATAA
1 TTTTTAATATTCATATATAA
*
2772321 TTTTTAATATACATATA
1 TTTTTAATATTCATATA
2772338 AAAATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 10 0.33
19 12 0.40
20 8 0.27
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTTAATATTCATATATAA
Found at i:2772336 original size:18 final size:18
Alignment explanation
Indices: 2772300--2772338 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2772290 TATTTATATT
*
2772300 TAATTTTTATATTCAATA
1 TAATTTTTATATACAATA
2772318 TAATTTTTAATATAC-ATA
1 TAATTTTT-ATATACAATA
2772336 TAA
1 TAA
2772339 AAATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTTTATATACAATA
Found at i:2772366 original size:26 final size:26
Alignment explanation
Indices: 2772314--2772368 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
2772304 TTTTATATTC
* *
2772314 AATATAATTTTTAATATACATATAAA
1 AATATAATTTCTAATATACATAAAAA
*
2772340 AATATAATTCTCTAA-ATATATAAAAA
1 AATATAATT-TCTAATATACATAAAAA
2772366 AAT
1 AAT
2772369 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (26 bp):
AATATAATTTCTAATATACATAAAAA
Found at i:2772625 original size:5 final size:5
Alignment explanation
Indices: 2772594--2772642 Score: 68
Period size: 5 Copynumber: 10.2 Consensus size: 5
2772584 TATTATTTTA
2772594 AATAT AATTAT AATAT AA-A- AATA- AATAT AATAT AATAT AATAT AATAT
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
2772642 A
1 A
2772643 CAAATTATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.05
4 6 0.15
5 28 0.68
6 5 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AATAT
Found at i:2772668 original size:32 final size:31
Alignment explanation
Indices: 2772592--2772682 Score: 94
Period size: 32 Copynumber: 2.8 Consensus size: 31
2772582 TATATTATTT
* * *
2772592 TAAATATAATTATAATATAAAAATAAATATAA
1 TAAA-ATAAATATAATATAAAATTAAACATAA
*
2772624 TATAATATAATATAATATACAAATTATAACATAA
1 TAAAATA-AATATAATATA-AAATTA-AACATAA
2772658 -AAAATAAATATAATATATAAATTAA
1 TAAAATAAATATAATATA-AAATTAA
2772683 CTAAAATTTA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 4 0.08
32 30 0.60
33 10 0.20
34 6 0.12
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (31 bp):
TAAAATAAATATAATATAAAATTAAACATAA
Found at i:2773796 original size:47 final size:47
Alignment explanation
Indices: 2773702--2773798 Score: 108
Period size: 49 Copynumber: 2.0 Consensus size: 47
2773692 ATCCATTACT
* **
2773702 ATTATTATTTTTAATTTATATATTTTTAAAAATTGATAAAAAATATAAA
1 ATTAATATTTTTAATACATATATTTTTAAAAA-T-ATAAAAAATATAAA
*
2773751 ATTAATATTTTTAATACATAT-TTTTTACAAAA-ATAATAAATTATAAA
1 ATTAATATTTTTAATACATATATTTTTA-AAAATATAA-AAAATATAAA
2773798 A
1 A
2773799 AACAAAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
46 4 0.10
47 10 0.24
48 6 0.14
49 22 0.52
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (47 bp):
ATTAATATTTTTAATACATATATTTTTAAAAATATAAAAAATATAAA
Found at i:2774052 original size:33 final size:32
Alignment explanation
Indices: 2774015--2774078 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
2774005 CCTTTCTCCT
2774015 TTTTCT-TTACTCT-CTCCTTCTTTCTCTCCACCA
1 TTTTCTCTT-CTCTCCT-CTTC-TTCTCTCCACCA
*
2774048 TTTTCTCTTTTCTCCTCTTCTTCTCTCCACC
1 TTTTCTCTTCTCTCCTCTTCTTCTCTCCACC
2774079 CACCCTGTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
32 11 0.39
33 13 0.46
34 4 0.14
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.53
Consensus pattern (32 bp):
TTTTCTCTTCTCTCCTCTTCTTCTCTCCACCA
Found at i:2774077 original size:32 final size:34
Alignment explanation
Indices: 2774014--2774078 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
2774004 TCCTTTCTCC
2774014 TTTTTCTTTACTCTCTCCTTCTTTCTCTCCACCA
1 TTTTTCTTTACTCTCTCCTTCTTTCTCTCCACCA
*
2774048 TTTTCTCTTTTCTC-CT-CTTC-TTCTCTCCACC
1 TTTT-TCTTTACTCTCTCCTTCTTTCTCTCCACC
2774079 CACCCTGTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 11 0.38
33 4 0.14
34 6 0.21
35 8 0.28
ACGTcount: A:0.06, C:0.40, G:0.00, T:0.54
Consensus pattern (34 bp):
TTTTTCTTTACTCTCTCCTTCTTTCTCTCCACCA
Found at i:2775010 original size:118 final size:120
Alignment explanation
Indices: 2774742--2775037 Score: 334
Period size: 118 Copynumber: 2.5 Consensus size: 120
2774732 AACAATTATG
* * *
2774742 TTGGCGTTTCCATTTATAAGATGCCATCCATTCTAGTGCTTTCAAGTAATTAAT-ACTTCGGCGC
1 TTGGCGTTTCCATTTATAAAACGCCATCCATTCTAGTGCTTTCAAGTAATTAATGCCTTCGGCGC
* * *
2774806 TTACTATTAGAAACACTAACATGCCAGCCATTGCCATTTAGGTGGCATCAGCTATG
66 TTACTATTAGAAACACCAACATGCAAGCCATTGCCATTTAGGTGGCA-CAGCTATA
* ** * *
2774862 CTGGCGTTTCCATTTATAAAGGGTCATCCATTCTAGTGCTTTCAGGTAATTAATGCCTT-GGCGC
1 TTGGCGTTTCCATTTATAAAACGCCATCCATTCTAGTGCTTTCAAGTAATTAATGCCTTCGGCGC
* * ** *
2774926 TTA-TATT-GAAACGCCAATATGCAAGCCATTTTCATTTAGGAAAT-GC-CAGGTATA
66 TTACTATTAGAAACACCAACATGCAAGCCATTGCCATTTAGG---TGGCACAGCTATA
* * * *
2774980 TTGGCATTTTCATTTATAAAACGCCATCCATTCTTGTACTTTCAAGTAATTAATGCCT
1 TTGGCGTTTCCATTTATAAAACGCCATCCATTCTAGTGCTTTCAAGTAATTAATGCCT
2775038 AGGCTTTTAG
Statistics
Matches: 148, Mismatches: 24, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
118 82 0.55
119 4 0.03
120 58 0.39
121 4 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (120 bp):
TTGGCGTTTCCATTTATAAAACGCCATCCATTCTAGTGCTTTCAAGTAATTAATGCCTTCGGCGC
TTACTATTAGAAACACCAACATGCAAGCCATTGCCATTTAGGTGGCACAGCTATA
Found at i:2775866 original size:11 final size:11
Alignment explanation
Indices: 2775838--2775876 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2775828 TATTCGACTC
2775838 AAATTTTAATTA
1 AAATTTT-ATTA
*
2775850 AAATTTTATTT
1 AAATTTTATTA
2775861 AAATTTT-TTA
1 AAATTTTATTA
2775871 AAATTT
1 AAATTT
2775877 AAAAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.32
11 10 0.40
12 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AAATTTTATTA
Found at i:2779614 original size:34 final size:34
Alignment explanation
Indices: 2779583--2779707 Score: 146
Period size: 34 Copynumber: 3.7 Consensus size: 34
2779573 GTGGTTTGTC
*
2779583 ATTGTTGACTAAATGAGAGATTTAGTAGTTTGCA
1 ATTGTTGACTAAATGGGAGATTTAGTAGTTTGCA
* * * * *
2779617 ACTT-TTGATTAAATGGGTGATTTAATGGTTTGCT
1 A-TTGTTGACTAAATGGGAGATTTAGTAGTTTGCA
2779651 ATTGTTGACTAAATGGGAGATTTAGTAGTTTGTC-
1 ATTGTTGACTAAATGGGAGATTTAGTAGTTTG-CA
* *
2779685 ATTGTTGATTAAATGGGTGATTT
1 ATTGTTGACTAAATGGGAGATTT
2779708 GGTGGTTTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
33 2 0.03
34 71 0.93
35 3 0.04
ACGTcount: A:0.27, C:0.05, G:0.25, T:0.43
Consensus pattern (34 bp):
ATTGTTGACTAAATGGGAGATTTAGTAGTTTGCA
Found at i:2779714 original size:68 final size:68
Alignment explanation
Indices: 2779566--2779715 Score: 225
Period size: 68 Copynumber: 2.2 Consensus size: 68
2779556 TTACCATTGT
2779566 TGATTTGGTGGTTTGTCATTGTTGACTAAATGAGAGATTTAGTAGTTTGCAACTTTTGATTAAAT
1 TGATTTGGTGGTTTGTCATTGTTGACTAAATGAGAGATTTAGTAGTTTGCAACTTTTGATTAAAT
2779631 GGG
66 GGG
** *
2779634 TGATTTAATGGTTTG-CTATTGTTGACTAAATGGGAGATTTAGTAGTTTGTC-A-TTGTTGATTA
1 TGATTTGGTGGTTTGTC-ATTGTTGACTAAATGAGAGATTTAGTAGTTTG-CAACTT-TTGATTA
2779696 AATGGG
63 AATGGG
2779702 TGATTTGGTGGTTT
1 TGATTTGGTGGTTT
2779716 TTACCAAACC
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
67 3 0.04
68 70 0.95
69 1 0.01
ACGTcount: A:0.23, C:0.05, G:0.27, T:0.45
Consensus pattern (68 bp):
TGATTTGGTGGTTTGTCATTGTTGACTAAATGAGAGATTTAGTAGTTTGCAACTTTTGATTAAAT
GGG
Found at i:2782725 original size:19 final size:19
Alignment explanation
Indices: 2782698--2782752 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
2782688 CACAGTACTA
*
2782698 TATATGTGAATAGTACCCG
1 TATACGTGAATAGTACCCG
*
2782717 TATACGTGAATAGTACCTG
1 TATACGTGAATAGTACCCG
*
2782736 TATACATGAATAGTACC
1 TATACGTGAATAGTACC
2782753 TCGACAACCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (19 bp):
TATACGTGAATAGTACCCG
Found at i:2784348 original size:22 final size:22
Alignment explanation
Indices: 2784313--2784359 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2784303 GATTAAATGG
*
2784313 TGATTTGGTAGTTTGCCATTGT
1 TGATTTCGTAGTTTGCCATTGT
*
2784335 TGATTTCGTGGTTTGCCATTGT
1 TGATTTCGTAGTTTGCCATTGT
2784357 TGA
1 TGA
2784360 CTAAATAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.11, G:0.28, T:0.49
Consensus pattern (22 bp):
TGATTTCGTAGTTTGCCATTGT
Found at i:2784383 original size:34 final size:34
Alignment explanation
Indices: 2784336--2784594 Score: 277
Period size: 34 Copynumber: 7.4 Consensus size: 34
2784326 TGCCATTGTT
* * **
2784336 GATTTCGTGGTTTGCCATTGTTGACTAAATAAGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
* * * *
2784370 GATTTGGTAGTTTGCCATTATTGATTAAATGAGT
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
*
2784404 GATTTGGTGGTTTGCCATTGTTGACTAAATGGGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
* * * *
2784438 GATTTAGTAGTTTGCCATTGTTGATTAAATTGGT
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
*
2784472 GATTTGGTGGTTTGCCATTGTTGACTAAATGGGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
*
2784506 GATTTGGTAGTTTGGTGGTTTGCAATTGTTGACTAAATGGGA
1 GATTTGGTA--------GTTTGCCATTGTTGACTAAATGGGA
* *
2784548 GATTTGGTAGTTTGCCATTATTGATTAAAT-GGA
1 GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
2784581 TGATTTGGTAGTTT
1 -GATTTGGTAGTTT
2784595 TTACCAAACC
Statistics
Matches: 190, Mismatches: 26, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
33 3 0.02
34 154 0.81
42 33 0.17
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (34 bp):
GATTTGGTAGTTTGCCATTGTTGACTAAATGGGA
Found at i:2784448 original size:68 final size:68
Alignment explanation
Indices: 2784330--2784519 Score: 310
Period size: 68 Copynumber: 2.8 Consensus size: 68
2784320 GTAGTTTGCC
* * **
2784330 ATTGTTGATTTCGTGGTTTGCCATTGTTGACTAAATAAGAGATTTGGTAGTTTGCCATTATTGAT
1 ATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGAT
2784395 TAA
66 TAA
* *
2784398 A-TGAGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTAGTAGTTTGCCATTGTTGA
1 ATTG-GTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGA
2784462 TTAA
65 TTAA
2784466 ATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGTTTG
1 ATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGTTTG
2784520 GTGGTTTGCA
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
67 2 0.02
68 109 0.96
69 2 0.02
ACGTcount: A:0.23, C:0.07, G:0.27, T:0.43
Consensus pattern (68 bp):
ATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGAT
TAA
Found at i:2784526 original size:42 final size:42
Alignment explanation
Indices: 2784474--2784561 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
2784464 AAATTGGTGA
*
2784474 TTTGGTGGTTTGCCATTGTTGACTAAATGGGAGATTTGGTAG
1 TTTGGTGGTTTGCAATTGTTGACTAAATGGGAGATTTGGTAG
2784516 TTTGGTGGTTTGCAATTGTTGACTAAATGGGAGATTTGGTAG
1 TTTGGTGGTTTGCAATTGTTGACTAAATGGGAGATTTGGTAG
2784558 TTTG
1 TTTG
2784562 CCATTATTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.19, C:0.06, G:0.33, T:0.42
Consensus pattern (42 bp):
TTTGGTGGTTTGCAATTGTTGACTAAATGGGAGATTTGGTAG
Found at i:2784577 original size:76 final size:76
Alignment explanation
Indices: 2784447--2784594 Score: 217
Period size: 76 Copynumber: 1.9 Consensus size: 76
2784437 AGATTTAGTA
* * * * * *
2784447 GTTTGCCATTGTTGATTAAATTGGTGATTTGGTGGTTTGCCATTGTTGACTAAATGGGA-GATTT
1 GTTTGCAATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGACTAAAT-GGATGATTT
2784511 GGTAGTTTGGTG
65 GGTAGTTTGGTG
*
2784523 GTTTGCAATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGATTAAATGGATGATTTG
1 GTTTGCAATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGACTAAATGGATGATTTG
2784588 GTAGTTT
66 GTAGTTT
2784595 TTACCAAACC
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
75 3 0.05
76 61 0.95
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (76 bp):
GTTTGCAATTGTTGACTAAATGGGAGATTTGGTAGTTTGCCATTATTGACTAAATGGATGATTTG
GTAGTTTGGTG
Found at i:2784806 original size:19 final size:19
Alignment explanation
Indices: 2784774--2784834 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
2784764 TTTTACGTAC
2784774 ATAGTACC-GTATACATGA
1 ATAGTACCTGTATACATGA
*
2784792 ATAGTACCTGTATACATAA
1 ATAGTACCTGTATACATGA
* **
2784811 ATTGTACCTGTATATGTGA
1 ATAGTACCTGTATACATGA
2784830 ATAGT
1 ATAGT
2784835 GCCACGATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 8 0.22
19 28 0.78
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (19 bp):
ATAGTACCTGTATACATGA
Found at i:2785115 original size:19 final size:20
Alignment explanation
Indices: 2785091--2785151 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
2785081 AGTTGTCGAT
2785091 GTACTATTCACGTCTATA-G-
1 GTACTATTCACGT-TATACGA
2785110 GTACTATTCAC-TTATACGA
1 GTACTATTCACGTTATACGA
2785129 GTACTATTCACG-TATACG-
1 GTACTATTCACGTTATACGA
2785147 GTACT
1 GTACT
2785152 GTGCACGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.10
18 7 0.18
19 28 0.72
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (20 bp):
GTACTATTCACGTTATACGA
Found at i:2785158 original size:18 final size:19
Alignment explanation
Indices: 2785110--2785160 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
2785100 ACGTCTATAG
* *
2785110 GTACTATTCACTTATACGA
1 GTACTATGCACGTATACGA
*
2785129 GTACTATTCACGTATACG-
1 GTACTATGCACGTATACGA
*
2785147 GTACTGTGCACGTA
1 GTACTATGCACGTA
2785161 AAACAGTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (19 bp):
GTACTATGCACGTATACGA
Found at i:2785238 original size:34 final size:34
Alignment explanation
Indices: 2785197--2785287 Score: 119
Period size: 34 Copynumber: 2.7 Consensus size: 34
2785187 GTGAAGGAAA
2785197 AACAATGGCAAACCACTAAATCACCCATTTAATC
1 AACAATGGCAAACCACTAAATCACCCATTTAATC
* * * *** *
2785231 AATAATGGCAAACTACCAAATCTTTCATTTAGTC
1 AACAATGGCAAACCACTAAATCACCCATTTAATC
2785265 AACAATGGCAAACCACTAAATCA
1 AACAATGGCAAACCACTAAATCA
2785288 ACAATGGCAA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (34 bp):
AACAATGGCAAACCACTAAATCACCCATTTAATC
Found at i:2785307 original size:22 final size:22
Alignment explanation
Indices: 2785263--2785307 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2785253 TTTCATTTAG
*
2785263 TCAACAATGGCAAACCACTAAA
1 TCAACAATGGCAAACCACCAAA
*
2785285 TCAACAATGGCAAACTACCAAA
1 TCAACAATGGCAAACCACCAAA
2785307 T
1 T
2785308 TACCATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.27, G:0.09, T:0.16
Consensus pattern (22 bp):
TCAACAATGGCAAACCACCAAA
Found at i:2788035 original size:117 final size:117
Alignment explanation
Indices: 2787826--2788066 Score: 430
Period size: 117 Copynumber: 2.1 Consensus size: 117
2787816 TGCTGAACTT
* *
2787826 CAATCTATTTTGCTTACTAAAACACAATGCTCACAGAAAGGTAGACTTACTGTTTTGAGTCCAAA
1 CAATCTATTTTGCTTACTAAAACACAATACTCACAGAAAGGTAGACTTACTATTTTGAGTCCAAA
2787891 AAAGCAATCTACTATCAGATAGAATCTTTATACCTCGTTCTGACATATGACC
66 AAAGCAATCTACTATCAGATAGAATCTTTATACCTCGTTCTGACATATGACC
2787943 CAATCTATTTTGCTTACTTAAAACACAATACTCACAGAAAGGTAGACTTACTATTTTGAGTCC-A
1 CAATCTATTTTGCTTAC-TAAAACACAATACTCACAGAAAGGTAGACTTACTATTTTGAGTCCAA
* *
2788007 AGAAGCAATCTACTATCAGATAGAATCTTTATACCTCGTTCTGACATATGGCC
65 AAAAGCAATCTACTATCAGATAGAATCTTTATACCTCGTTCTGACATATGACC
2788060 CAATCTA
1 CAATCTA
2788067 CGATGCCACA
Statistics
Matches: 119, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
117 76 0.64
118 43 0.36
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (117 bp):
CAATCTATTTTGCTTACTAAAACACAATACTCACAGAAAGGTAGACTTACTATTTTGAGTCCAAA
AAAGCAATCTACTATCAGATAGAATCTTTATACCTCGTTCTGACATATGACC
Done.