Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold72
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: 5928628
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 261288 characters in sequence are not A, C, G, or T
File 33 of 39
Found at i:4744169 original size:10 final size:11
Alignment explanation
Indices: 4744137--4744175 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
4744127 TCAATAATTT
*
4744137 TAAATATAATA
1 TAAATATTATA
4744148 TAAATATTATA
1 TAAATATTATA
4744159 TAAAT-TTATA
1 TAAATATTATA
4744169 TATAATA
1 TA-AATA
4744176 AATTATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATATTATA
Found at i:4745450 original size:23 final size:22
Alignment explanation
Indices: 4745419--4745514 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 22
4745409 TATTGATAAT
*
4745419 AATTTTATTTTATATTTTTTAAA
1 AATTATATTTTATATTTTTT-AA
4745442 AATTATA-TTTA-A-TTTTTAA
1 AATTATATTTTATATTTTTTAA
**
4745461 AA-T-T-TTTTATATATTTAAAA
1 AATTATATTTTATAT-TTTTTAA
*
4745481 AATTATATTTTGTATTTATATTAA
1 AATTATATTTTATATTT-T-TTAA
4745505 AATATATATT
1 AAT-TATATT
4745515 AAATAAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
17 5 0.09
18 2 0.04
19 4 0.07
20 12 0.21
21 2 0.04
22 7 0.12
23 14 0.25
24 5 0.09
25 6 0.11
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (22 bp):
AATTATATTTTATATTTTTTAA
Found at i:4745459 original size:20 final size:21
Alignment explanation
Indices: 4745423--4745490 Score: 74
Period size: 20 Copynumber: 3.4 Consensus size: 21
4745413 GATAATAATT
4745423 TTAT-TTTATATTTTTTAAAAA
1 TTATATTTATA-TTTTTAAAAA
4745444 TTATATTTA-ATTTTT-AAAA
1 TTATATTTATATTTTTAAAAA
*
4745463 TT-T-TTTATATATTTAAAAAA
1 TTATATTTATAT-TTTTAAAAA
4745483 TTATATTT
1 TTATATTT
4745491 TGTATTTATA
Statistics
Matches: 40, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
17 4 0.10
18 3 0.08
19 9 0.22
20 11 0.28
21 6 0.15
22 7 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATATTTATATTTTTAAAAA
Found at i:4745490 original size:25 final size:25
Alignment explanation
Indices: 4745462--4745514 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4745452 AATTTTTAAA
*
4745462 ATTTTTTATATAT-TTAAAAAATTAT
1 ATTTTGTATATATATTAAAAAA-TAT
* *
4745487 ATTTTGTATTTATATTAAAATATAT
1 ATTTTGTATATATATTAAAAAATAT
4745512 ATT
1 ATT
4745515 AAATAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTGTATATATATTAAAAAATAT
Found at i:4746589 original size:13 final size:13
Alignment explanation
Indices: 4746573--4746607 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
4746563 ATGTATTAAT
4746573 TAAATTAAAATTA
1 TAAATTAAAATTA
*
4746586 TAAATTAAAATTT
1 TAAATTAAAATTA
*
4746599 TAATTTAAA
1 TAAATTAAA
4746608 TAAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAATTAAAATTA
Found at i:4746856 original size:4 final size:4
Alignment explanation
Indices: 4746847--4746871 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4746837 GGTTGAGAAA
4746847 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4746872 TCTCAATGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4747138 original size:8 final size:8
Alignment explanation
Indices: 4747097--4747250 Score: 55
Period size: 8 Copynumber: 17.4 Consensus size: 8
4747087 AAATATATAA
4747097 ATATTTAT
1 ATATTTAT
*
4747105 ATGAATT-T
1 AT-ATTTAT
*
4747113 ATATTAAT
1 ATATTTAT
4747121 ATGAATTTAT
1 AT--ATTTAT
4747131 ATATTTATATT
1 ATA-TT-TA-T
4747142 ATATTTAT
1 ATATTTAT
4747150 ATATTTTATT
1 ATA-TTTA-T
*
4747160 ATAATATAATT
1 AT-AT-TTA-T
4747171 ATATTTAT
1 ATATTTAT
4747179 AATATTTAT
1 -ATATTTAT
4747188 ATAAATTT-T
1 AT--ATTTAT
4747197 GATATATTA-
1 -ATAT-TTAT
4747206 ATGATTTAT
1 AT-ATTTAT
*
4747215 AT-TATAT
1 ATATTTAT
* *
4747222 AAATTTTAAA
1 ATA-TTT-AT
4747232 ATATTTAT
1 ATATTTAT
4747240 ATATTTAT
1 ATATTTAT
4747248 ATA
1 ATA
4747251 ATATTTTTTA
Statistics
Matches: 112, Mismatches: 12, Indels: 44
0.67 0.07 0.26
Matches are distributed among these distances:
7 7 0.06
8 35 0.31
9 33 0.29
10 26 0.23
11 11 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (8 bp):
ATATTTAT
Found at i:4747151 original size:29 final size:29
Alignment explanation
Indices: 4747111--4747191 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 29
4747101 TTATATGAAT
* *
4747111 TTATATTAATATGAATTTA-TAT-ATTTATA
1 TTATATTTATAT-AATTTATTATAATATA-A
*
4747140 TTATATTTATATATTTTATTATAATATAA
1 TTATATTTATATAATTTATTATAATATAA
4747169 TTATATTTATA-ATATTTA-TATAA
1 TTATATTTATATA-ATTTATTATAA
4747192 ATTTTGATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 11 0.24
29 30 0.67
30 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (29 bp):
TTATATTTATATAATTTATTATAATATAA
Found at i:4747189 original size:15 final size:15
Alignment explanation
Indices: 4747140--4747189 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 15
4747130 TATATTTATA
4747140 TTATATTTAT-ATAT
1 TTATATTTATAATAT
4747154 TT-TA-TTATAATAT
1 TTATATTTATAATAT
4747167 AATTATATTTATAATAT
1 --TTATATTTATAATAT
4747184 TTATAT
1 TTATAT
4747190 AAATTTTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
12 4 0.13
13 6 0.19
14 2 0.06
15 8 0.26
16 2 0.06
17 9 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATATTTATAATAT
Found at i:4747225 original size:32 final size:33
Alignment explanation
Indices: 4747184--4747254 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
4747174 TTTATAATAT
* *
4747184 TTATATAAATTTTGATATA-TTA-ATGATTTATA
1 TTATATAAATTTTAAAATATTTATAT-ATTTATA
4747216 TTATATAAATTTTAAAATATTTATATATTTATA
1 TTATATAAATTTTAAAATATTTATATATTTATA
*
4747249 TAATAT
1 TTATAT
4747255 TTTTTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 17 0.50
33 15 0.44
34 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (33 bp):
TTATATAAATTTTAAAATATTTATATATTTATA
Found at i:4748671 original size:2 final size:2
Alignment explanation
Indices: 4748664--4748703 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
4748654 TCTTCTCCAT
4748664 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4748704 GAATTAGTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:4748818 original size:17 final size:17
Alignment explanation
Indices: 4748793--4748826 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4748783 ATTTATAATA
*
4748793 TTTAGATTTAAATTATT
1 TTTAAATTTAAATTATT
*
4748810 TTTAAATTTAATTTATT
1 TTTAAATTTAAATTATT
4748827 GGTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TTTAAATTTAAATTATT
Found at i:4749126 original size:18 final size:17
Alignment explanation
Indices: 4749101--4749138 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
4749091 TTATTGAAGG
4749101 ATAAAATTAAAAAATAA
1 ATAAAATTAAAAAATAA
*
4749118 ATAATAATTTAAAAATAA
1 ATAA-AATTAAAAAATAA
4749136 ATA
1 ATA
4749139 TAAGATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATTAAAAAATAA
Found at i:4749149 original size:236 final size:235
Alignment explanation
Indices: 4748891--4749396 Score: 827
Period size: 236 Copynumber: 2.1 Consensus size: 235
4748881 AGGATAAAAA
* * *
4748891 TAAAAATAAAAATAATATTATAATATATATAAATTTTCATATTAAATTCTGATCATTTCTAATTT
1 TAAAAATAAATATAATATTATAATATATATAAATTTTCATATTAAATTCCGATCACTTCTAATTT
* * *
4748956 AAATTATTTTAGATTTGAATCGGATGATTCGAGTTTAATATTCAGATTATTTAGATTCAAATTAT
66 AAATTATTTTAGATTTGAATCGGATGATTCAAATTTAATATTCAGAATATTTAGATTCAAATTAT
*
4749021 TTTTAAATTTAATTTATTGATTTTTAAAATTAAATTAGACTAAATTTCATTTTCATATTTTATTA
131 TTTTAAATTTAATTTATTGAATTTTAAAATTAAATTAGACTAAATTTCATTTTCATATTTTATTA
*
4749086 AAATTTTATTGAAGGATAAAATTAAAAAATAAATAATAATT
196 AAATTTTATTGAAGGATAAAAAT-AAAAATAAATAATAATT
* *
4749127 TAAAAATAAATATAAGATTATAATATATATAAATTTTCATATTAGATTCCGATCACTTCTAATTT
1 TAAAAATAAATATAATATTATAATATATATAAATTTTCATATTAAATTCCGATCACTTCTAATTT
* * * *
4749192 ATATTTTTTTAGATTTGAATTGGATGATTCAAATTTAATATTTAGAATATTTAGATTCAAATTAT
66 AAATTATTTTAGATTTGAATCGGATGATTCAAATTTAATATTCAGAATATTTAGATTCAAATTAT
*
4749257 TTTTAAATTTAATTTATTGAATTTTAAAATTAAATTAGACTAAATTTGATTTTCATATTTTATTA
131 TTTTAAATTTAATTTATTGAATTTTAAAATTAAATTAGACTAAATTTCATTTTCATATTTTATTA
*
4749322 AAATTTTATTGAAGGATAAAAATAAAAATAAATAATATTT
196 AAATTTTATTGAAGGATAAAAATAAAAATAAATAATAATT
4749362 TAAAAA-ATAATATAATATTATAATATA-AGTAAATT
1 TAAAAATA-AATATAATATTATAATATATA-TAAATT
4749397 AATTTTAATC
Statistics
Matches: 251, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
234 2 0.01
235 46 0.18
236 203 0.81
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (235 bp):
TAAAAATAAATATAATATTATAATATATATAAATTTTCATATTAAATTCCGATCACTTCTAATTT
AAATTATTTTAGATTTGAATCGGATGATTCAAATTTAATATTCAGAATATTTAGATTCAAATTAT
TTTTAAATTTAATTTATTGAATTTTAAAATTAAATTAGACTAAATTTCATTTTCATATTTTATTA
AAATTTTATTGAAGGATAAAAATAAAAATAAATAATAATT
Found at i:4750597 original size:15 final size:15
Alignment explanation
Indices: 4750579--4750630 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
4750569 AATTTATATA
4750579 ATATAAATTATTAAT
1 ATATAAATTATTAAT
4750594 ATATTAAAATTTATATAA-
1 ATA-T-AAA-TTAT-TAAT
4750612 ATATAAATTATTAAT
1 ATATAAATTATTAAT
4750627 ATAT
1 ATAT
4750631 TAAAATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.09
15 11 0.34
16 4 0.12
17 4 0.12
18 7 0.22
19 3 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATAAATTATTAAT
Found at i:4750601 original size:16 final size:16
Alignment explanation
Indices: 4750582--4750634 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
4750572 TTATATAATA
4750582 TAAATTATTAATATAT
1 TAAATTATTAATATAT
4750598 TAAAATTTATATAA-ATA-
1 T-AAA-TTAT-TAATATAT
4750615 TAAATTATTAATATAT
1 TAAATTATTAATATAT
4750631 TAAA
1 TAAA
4750635 ATTTATATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.09
15 7 0.22
16 8 0.25
17 4 0.12
18 7 0.22
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTATTAATATAT
Found at i:4750607 original size:18 final size:18
Alignment explanation
Indices: 4750563--4750650 Score: 77
Period size: 18 Copynumber: 5.2 Consensus size: 18
4750553 TACATAAATT
4750563 TATTAAAATTTA-T-ATA
1 TATTAAAATTTATTAATA
4750579 -A-TATAAA-TTATTAATA
1 TATTA-AAATTTATTAATA
4750595 TATTAAAATTTATATAA-A
1 TATTAAAATTTAT-TAATA
4750613 TA-T-AAA-TTATTAATA
1 TATTAAAATTTATTAATA
4750628 TATTAAAATTTATATAAATA
1 TATTAAAATTTAT-T-AATA
4750648 TAT
1 TAT
4750651 AATAAAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
14 8 0.14
15 12 0.20
16 7 0.12
17 8 0.14
18 13 0.22
19 4 0.07
20 7 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAAATTTATTAATA
Found at i:4750620 original size:33 final size:33
Alignment explanation
Indices: 4750563--4750649 Score: 167
Period size: 33 Copynumber: 2.7 Consensus size: 33
4750553 TACATAAATT
4750563 TATTAAAATTTATAT-AATATAAATTATTAATA
1 TATTAAAATTTATATAAATATAAATTATTAATA
4750595 TATTAAAATTTATATAAATATAAATTATTAATA
1 TATTAAAATTTATATAAATATAAATTATTAATA
4750628 TATTAAAATTTATATAAATATA
1 TATTAAAATTTATATAAATATA
4750650 TAATAAAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
32 15 0.28
33 39 0.72
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
TATTAAAATTTATATAAATATAAATTATTAATA
Found at i:4753069 original size:2 final size:2
Alignment explanation
Indices: 4753064--4753090 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4753054 AAGTGAAAAG
4753064 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
4753091 GGTAGTGACC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4753323 original size:21 final size:20
Alignment explanation
Indices: 4753275--4753324 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
4753265 CCAAAAGATC
4753275 AAATTT-AAT-ATTTTTATT
1 AAATTTAAATAATTTTTATT
* **
4753293 CAATAAAAATAATTTTTAATT
1 AAATTTAAATAATTTTT-ATT
4753314 AAATTTAAATA
1 AAATTTAAATA
4753325 TAAAAATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
18 3 0.13
19 3 0.13
20 6 0.26
21 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATTTAAATAATTTTTATT
Found at i:4753346 original size:22 final size:22
Alignment explanation
Indices: 4753313--4753354 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
4753303 AATTTTTAAT
4753313 TAAATTTAAATATAAAAATATA
1 TAAATTTAAATATAAAAATATA
4753335 TAAATATT-AATATAAAAATA
1 TAAAT-TTAAATATAAAAATA
4753355 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAATTTAAATATAAAAATATA
Found at i:4753812 original size:2 final size:2
Alignment explanation
Indices: 4753805--4753833 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4753795 GTTCTAACTC
4753805 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4753834 TTTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:4754457 original size:2 final size:2
Alignment explanation
Indices: 4754452--4754482 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4754442 GTGTGTGTGC
4754452 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
4754483 ATACTAAATC
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:4755044 original size:18 final size:17
Alignment explanation
Indices: 4755003--4755044 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
4754993 ATATTAAATT
4755003 AATTTAA-TATATAATA
1 AATTTAATTATATAATA
* *
4755019 AATATAATTATATTATTA
1 AATTTAATTATA-TAATA
4755037 AATTTAAT
1 AATTTAAT
4755045 ACTAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 6 0.29
17 4 0.19
18 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAATTATATAATA
Found at i:4756137 original size:15 final size:15
Alignment explanation
Indices: 4756119--4756160 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
4756109 ATTTAAAATA
*
4756119 ATATTAAAAATTAAT
1 ATATTATAAATTAAT
* *
4756134 ATATTTTATATTAAT
1 ATATTATAAATTAAT
4756149 AT-TTATAAATTA
1 ATATTATAAATTA
4756161 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATAAATTAAT
Found at i:4756421 original size:21 final size:21
Alignment explanation
Indices: 4756395--4756439 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4756385 GATAATTATT
4756395 TTTAAAAATTAAAATTTATAA
1 TTTAAAAATTAAAATTTATAA
** *
4756416 TTTAAATTTTAATATTTATAA
1 TTTAAAAATTAAAATTTATAA
4756437 TTT
1 TTT
4756440 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTAAAAATTAAAATTTATAA
Found at i:4759920 original size:104 final size:104
Alignment explanation
Indices: 4759737--4759944 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
4759727 CAGTGACTTC
*
4759737 AACAGCAACAACTCCCGCAAGCTGAAAATGAAAACGATACAATCATGGATCATTCAACATCCTTC
1 AACAGCAACAACTCCCGCAAGCTGAAAATGAAAACAATACAATCATGGATCATTCAACATCCTTC
4759802 ATAGTCAACAACACTGGATTTAATCTATGTGCAGTCATT
66 ATAGTCAACAACACTGGATTTAATCTATGTGCAGTCATT
*
4759841 AACAGCAACAACTCCCGCAAGCTGAAAATGAAAACAATACAGTCATGGATCATTCAACATCCTTC
1 AACAGCAACAACTCCCGCAAGCTGAAAATGAAAACAATACAATCATGGATCATTCAACATCCTTC
*
4759906 ATAGTCAACGACACTGGATTTAATCTATGTGCAGTCATT
66 ATAGTCAACAACACTGGATTTAATCTATGTGCAGTCATT
4759945 TGTGTGGTGT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (104 bp):
AACAGCAACAACTCCCGCAAGCTGAAAATGAAAACAATACAATCATGGATCATTCAACATCCTTC
ATAGTCAACAACACTGGATTTAATCTATGTGCAGTCATT
Found at i:4762744 original size:6 final size:6
Alignment explanation
Indices: 4762733--4762791 Score: 66
Period size: 6 Copynumber: 9.3 Consensus size: 6
4762723 AAAAAATAAA
*
4762733 TTTAAT TTTAAT TTTAAT TTT-AT ATTTAAT TATTTAT GTTTAAAT TTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT -TTTAAT T-TTAAT -TTT-AAT TTTAAT
4762784 TTTAAT TT
1 TTTAAT TT
4762792 ATATTAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
5 2 0.04
6 30 0.65
7 11 0.24
8 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (6 bp):
TTTAAT
Found at i:4762759 original size:38 final size:38
Alignment explanation
Indices: 4762717--4762796 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
4762707 TAAATTTATT
4762717 TATTTAAAAAAATAAATTT-AATTTTAATTTTAATTTTA
1 TATTTAAAAAAATAAATTTAAATTTTAATTTTAA-TTTA
** ** **
4762755 TATTTAATTATTTATGTTTAAATTTTAATTTTAATTTA
1 TATTTAAAAAAATAAATTTAAATTTTAATTTTAATTTA
4762793 TATT
1 TATT
4762797 AAATTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 21 0.60
39 14 0.40
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (38 bp):
TATTTAAAAAAATAAATTTAAATTTTAATTTTAATTTA
Found at i:4762805 original size:12 final size:13
Alignment explanation
Indices: 4762732--4762806 Score: 70
Period size: 12 Copynumber: 6.1 Consensus size: 13
4762722 AAAAAAATAA
4762732 ATTT-AATTTTA-
1 ATTTAAATTTTAT
*
4762743 ATTTTAATTTTAT
1 ATTTAAATTTTAT
*
4762756 ATTTAATTATTTAT
1 ATTTAAAT-TTTAT
*
4762770 GTTTAAATTTTA-
1 ATTTAAATTTTAT
*
4762782 ATTTTAA-TTTAT
1 ATTTAAATTTTAT
4762794 A-TTAAATTTTAT
1 ATTTAAATTTTAT
4762806 A
1 A
4762807 ATATTAATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
11 12 0.23
12 19 0.37
13 10 0.19
14 11 0.21
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (13 bp):
ATTTAAATTTTAT
Found at i:4763367 original size:2 final size:2
Alignment explanation
Indices: 4763360--4763389 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4763350 CTCCTAAGCA
4763360 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
4763390 TTTCTATAAT
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):
CT
Found at i:4763527 original size:5 final size:5
Alignment explanation
Indices: 4763512--4763572 Score: 52
Period size: 5 Copynumber: 11.4 Consensus size: 5
4763502 GGAAAAAATA
*
4763512 AATTT AA-TT AATTT AAATTT AATTT AATTT AAATAT AATAATT AATTT
1 AATTT AATTT AATTT -AATTT AATTT AATTT -AATTT AAT--TT AATTT
*
4763560 ATAATT AATTT AA
1 A-ATTT AATTT AA
4763573 AATAATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
4 4 0.09
5 25 0.54
6 13 0.28
7 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
AATTT
Found at i:4763535 original size:11 final size:11
Alignment explanation
Indices: 4763519--4763573 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
4763509 ATAAATTTAA
4763519 TTAATTTAAAT
1 TTAATTTAAAT
4763530 TTAATTT-AAT
1 TTAATTTAAAT
* *
4763540 TTAAATATAATAA
1 TT-AATTTAA-AT
4763553 TTAATTTATAA-
1 TTAATTTA-AAT
4763564 TTAATTTAAA
1 TTAATTTAAA
4763574 ATAATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 7 0.19
11 19 0.51
12 7 0.19
13 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:4763606 original size:23 final size:23
Alignment explanation
Indices: 4763564--4763630 Score: 91
Period size: 23 Copynumber: 2.9 Consensus size: 23
4763554 TAATTTATAA
4763564 TTAATTTAAAATAATATAAATA-T
1 TTAATTTAAAATAAT-TAAATACT
*
4763587 TTAAATTTAAAATAATTAAAAACT
1 TT-AATTTAAAATAATTAAATACT
*
4763611 TTAATATAAAATAATTAAAT
1 TTAATTTAAAATAATTAAAT
4763631 TTAAAAAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
23 23 0.59
24 16 0.41
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TTAATTTAAAATAATTAAATACT
Found at i:4763606 original size:33 final size:36
Alignment explanation
Indices: 4763575--4763648 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 36
4763565 TAATTTAAAA
*
4763575 TAATATAAATATTTAAATTTAAAATAA-TTAAAAACTT
1 TAATATAAATAATTAAATTTAAAATAATTTAAAAA--T
4763612 TAATATAAAATAATTAAATTTAAAA-AAGTTTAAAAAT
1 TAATAT-AAATAATTAAATTTAAAATAA-TTTAAAAAT
4763649 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 9 0.27
38 17 0.52
39 7 0.21
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (36 bp):
TAATATAAATAATTAAATTTAAAATAATTTAAAAAT
Found at i:4766186 original size:15 final size:15
Alignment explanation
Indices: 4766166--4766195 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4766156 TATTAACTCC
4766166 TGGTTCTAGTATCAG
1 TGGTTCTAGTATCAG
4766181 TGGTTCTAGTATCAG
1 TGGTTCTAGTATCAG
4766196 ATTATGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (15 bp):
TGGTTCTAGTATCAG
Found at i:4774465 original size:12 final size:12
Alignment explanation
Indices: 4774448--4774481 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
4774438 CAATATTTCC
*
4774448 TGTATATGTATA
1 TGTATATATATA
4774460 TGTATATATATA
1 TGTATATATATA
*
4774472 TATATATATA
1 TGTATATATA
4774482 GTAAAAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (12 bp):
TGTATATATATA
Found at i:4784308 original size:2 final size:2
Alignment explanation
Indices: 4784301--4784335 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4784291 ATTTTGATTC
4784301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4784336 TCCTTTTCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4786715 original size:2 final size:2
Alignment explanation
Indices: 4786704--4786742 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
4786694 TGATAATGAC
4786704 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4786743 ATCTGCAGGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4787771 original size:24 final size:25
Alignment explanation
Indices: 4787723--4787773 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
4787713 ATTTGTATTC
* *
4787723 AATATTAATATTTAATATATTTTTA
1 AATATGAATATATAATATATTTTTA
4787748 AATATGAATATATAA-ATATTTTTA
1 AATATGAATATATAATATATTTTTA
4787772 AA
1 AA
4787774 GATCTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATGAATATATAATATATTTTTA
Found at i:4788635 original size:2 final size:2
Alignment explanation
Indices: 4788628--4788663 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4788618 TCTGCCATGG
4788628 TC TC TC 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 TC TC TC
4788664 GGTTTGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4790869 original size:2 final size:2
Alignment explanation
Indices: 4790862--4790890 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4790852 TAGCTAGTTA
4790862 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 A
4790891 GAGAGAGAGA
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4792232 original size:13 final size:13
Alignment explanation
Indices: 4792214--4792238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4792204 TCTAAAGATC
4792214 AGATTATCATTTT
1 AGATTATCATTTT
4792227 AGATTATCATTT
1 AGATTATCATTT
4792239 AAAGTTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (13 bp):
AGATTATCATTTT
Found at i:4796505 original size:14 final size:14
Alignment explanation
Indices: 4796486--4796514 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4796476 TTATTTAATT
4796486 ATTTAATATTATAA
1 ATTTAATATTATAA
4796500 ATTTAATATTATAA
1 ATTTAATATTATAA
4796514 A
1 A
4796515 AATAATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAATATTATAA
Found at i:4805455 original size:14 final size:14
Alignment explanation
Indices: 4805436--4805464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4805426 TAAAAAACTG
4805436 TATATACACAAATA
1 TATATACACAAATA
4805450 TATATACACAAATA
1 TATATACACAAATA
4805464 T
1 T
4805465 GTATCAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (14 bp):
TATATACACAAATA
Found at i:4806250 original size:2 final size:2
Alignment explanation
Indices: 4806243--4806282 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4806233 CTCTGAATCG
4806243 TC TC TC TC TC 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 TC TC TC TC TC
4806283 GGTTTGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4806880 original size:17 final size:17
Alignment explanation
Indices: 4806860--4806910 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
4806850 ATATATTTTA
4806860 TTAAATTATAATTATAT
1 TTAAATTATAATTATAT
* **
4806877 TTAAAATATTTTTATA-
1 TTAAATTATAATTATAT
*
4806893 TTATAATTAAAATTATAT
1 TTA-AATTATAATTATAT
4806911 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 3
0.71 0.20 0.09
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTATAATTATAT
Found at i:4806901 original size:28 final size:29
Alignment explanation
Indices: 4806841--4806901 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
4806831 ACGAATTCAT
*
4806841 ATTATATTTATATATTTTATTAAATTATA
1 ATTATATTTAAATATTTTATTAAATTATA
*
4806870 ATTATATTTAAA-ATATTT-TTATATTATA
1 ATTATATTTAAATAT-TTTATTAAATTATA
4806898 ATTA
1 ATTA
4806902 AAATTATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.52
29 14 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTATATTTAAATATTTTATTAAATTATA
Found at i:4808744 original size:5 final size:5
Alignment explanation
Indices: 4808734--4808765 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
4808724 TTGATACTAA
4808734 AAAAG AAAAG AAAAG AAAAG AAAAAG AAAAG A
1 AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG A
4808766 GCAGAGCAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4809789 original size:10 final size:11
Alignment explanation
Indices: 4809772--4809801 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
4809762 AATTTTTTTA
4809772 TAAATTTAAGT
1 TAAATTTAAGT
4809783 T-AATTTAAGT
1 TAAATTTAAGT
4809793 TAAATTTAA
1 TAAATTTAA
4809802 ATAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (11 bp):
TAAATTTAAGT
Found at i:4818701 original size:2 final size:2
Alignment explanation
Indices: 4818689--4818722 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
4818679 AACATTTGGA
*
4818689 AT AT TT 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
4818723 TCGTTCATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4819641 original size:18 final size:18
Alignment explanation
Indices: 4819614--4819648 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4819604 ACATATTGAG
* *
4819614 AAAAATAAAATTAAAAAT
1 AAAAAAAAAAGTAAAAAT
4819632 AAAAAAAAAAGTAAAAA
1 AAAAAAAAAAGTAAAAA
4819649 AGAGACAACT
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:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (18 bp):
AAAAAAAAAAGTAAAAAT
Found at i:4821725 original size:46 final size:46
Alignment explanation
Indices: 4821658--4821793 Score: 254
Period size: 46 Copynumber: 3.0 Consensus size: 46
4821648 TCGAAGGTTA
4821658 GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACATGC
1 GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACATGC
4821704 GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACATGC
1 GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACATGC
* *
4821750 GAGTTAAATCATAAACTGCTGCATGGCAATCAATGTATATACAT
1 GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACAT
4821794 ACATACATAC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 88 1.00
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (46 bp):
GAGTTAAATCATAAACTGCTGCATGGCAATCAAAGTATACACATGC
Found at i:4821795 original size:4 final size:4
Alignment explanation
Indices: 4821788--4821819 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
4821778 ATCAATGTAT
*
4821788 ATAC ATAC ATAC ATAC CTAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
4821820 GTGTGCGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:4821810 original size:16 final size:16
Alignment explanation
Indices: 4821789--4821819 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4821779 TCAATGTATA
4821789 TACATACATACATACC
1 TACATACATACATACC
4821805 TACATACATACATAC
1 TACATACATACATAC
4821820 GTGTGCGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (16 bp):
TACATACATACATACC
Found at i:4828193 original size:19 final size:19
Alignment explanation
Indices: 4828169--4828228 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
4828159 AATGCAAAAC
4828169 TTATTAAATTATGAACATT
1 TTATTAAATTATGAACATT
* *
4828188 TTATT-AA--ATGCAAGA-C
1 TTATTAAATTATG-AACATT
4828204 TTATTAAATTATGAACATT
1 TTATTAAATTATGAACATT
4828223 TTATTA
1 TTATTA
4828229 CACTCGTACA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 8 0.25
17 5 0.16
18 5 0.16
19 14 0.44
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (19 bp):
TTATTAAATTATGAACATT
Found at i:4828206 original size:35 final size:35
Alignment explanation
Indices: 4828157--4828228 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
4828147 AAAAGAACAA
4828157 TAAATGCAAAACTTATTAAATTATGAACATTTTAT
1 TAAATGCAAAACTTATTAAATTATGAACATTTTAT
*
4828192 TAAATGCAAGACTTATTAAATTATGAACATTTTAT
1 TAAATGCAAAACTTATTAAATTATGAACATTTTAT
4828227 TA
1 TA
4828229 CACTCGTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.40
Consensus pattern (35 bp):
TAAATGCAAAACTTATTAAATTATGAACATTTTAT
Found at i:4829661 original size:18 final size:17
Alignment explanation
Indices: 4829628--4829661 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4829618 GAAAAATAAT
*
4829628 AAAATTAATTTTTTTGA
1 AAAATTAATGTTTTTGA
4829645 AAAATTAATAGTTTTTG
1 AAAATTAAT-GTTTTTG
4829662 TTTGAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
AAAATTAATGTTTTTGA
Found at i:4830828 original size:2 final size:2
Alignment explanation
Indices: 4830823--4830848 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4830813 ACACACACAC
4830823 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
4830849 GTATGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4830954 original size:2 final size:2
Alignment explanation
Indices: 4830947--4830980 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4830937 AAGAAGGGGA
4830947 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
4830981 TCAATGAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4831221 original size:2 final size:2
Alignment explanation
Indices: 4831214--4831240 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4831204 TTGAAAAAGA
4831214 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 A
4831241 ACTTAATATT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4831361 original size:2 final size:2
Alignment explanation
Indices: 4831348--4831383 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4831338 TATTTTAGTT
* *
4831348 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4831384 ACTCAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4832651 original size:35 final size:39
Alignment explanation
Indices: 4832576--4832654 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 39
4832566 AATTTACATA
**
4832576 ATAAAAATTATTTTTATTTAAAATTTTATAAATATTAAT
1 ATAAAAATTATTTTTATTTAAAATTTTATAAATACAAAT
*
4832615 ATAAAAA-TA-TTTT-TTTAATATTTT-TAAATACAAAT
1 ATAAAAATTATTTTTATTTAAAATTTTATAAATACAAAT
4832650 ATAAA
1 ATAAA
4832655 CTTTGAGATC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 14 0.38
36 10 0.27
37 4 0.11
38 2 0.05
39 7 0.19
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (39 bp):
ATAAAAATTATTTTTATTTAAAATTTTATAAATACAAAT
Found at i:4833034 original size:24 final size:26
Alignment explanation
Indices: 4833002--4833049 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
4832992 GATTTAAATT
* *
4833002 ATTATTTATATAATT-T-TTTTAAAA
1 ATTAATTATAAAATTATATTTTAAAA
4833026 ATTAATTATAAAATTATATTTTAA
1 ATTAATTATAAAATTATATTTTAA
4833050 TATTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 13 0.65
25 1 0.05
26 6 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTAATTATAAAATTATATTTTAAAA
Found at i:4833293 original size:12 final size:12
Alignment explanation
Indices: 4833276--4833316 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
4833266 GGGTGCAGAA
*
4833276 ATATATATATAT
1 ATATATGTATAT
*
4833288 ATATATGTATCT
1 ATATATGTATAT
4833300 ATATATGTATAT
1 ATATATGTATAT
4833312 ATATA
1 ATATA
4833317 AAATATATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:4833324 original size:2 final size:2
Alignment explanation
Indices: 4833276--4833316 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
4833266 GGGTGCAGAA
* * *
4833276 AT AT AT AT AT AT AT AT AT GT AT CT AT AT AT GT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4833317 AAATATATTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4834169 original size:36 final size:36
Alignment explanation
Indices: 4834083--4834173 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 36
4834073 ATATGATTTG
* *
4834083 ATTTATATTAAAT-TAAAATTTAATTTTTAATATTA
1 ATTTAAATTAAATATAAAATTTAATATTTAATATTA
* *
4834118 TTTTAAATGATAATATAAAATTTTAA-ATTTAAT-TTA
1 ATTTAAATTA-AATATAAAA-TTTAATATTTAATATTA
4834154 ATTTAAATTTAAATATAAAA
1 ATTTAAA-TTAAATATAAAA
4834174 AAAATTAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
35 7 0.15
36 21 0.46
37 13 0.28
38 5 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (36 bp):
ATTTAAATTAAATATAAAATTTAATATTTAATATTA
Found at i:4835173 original size:22 final size:20
Alignment explanation
Indices: 4835152--4835190 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
4835142 TTAATATATT
4835152 TTAAATAATAATTTAAATTA
1 TTAAATAATAATTTAAATTA
*
4835172 TTAAATTA-AATTTAAATTA
1 TTAAATAATAATTTAAATTA
4835191 AAACTTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAAATAATAATTTAAATTA
Found at i:4835756 original size:20 final size:20
Alignment explanation
Indices: 4835733--4835776 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
4835723 TATAATATAA
4835733 TAAATATGATAAAATATATT
1 TAAATATGATAAAATATATT
* *
4835753 TAAATATGATTAAATTTATT
1 TAAATATGATAAAATATATT
4835773 TAAA
1 TAAA
4835777 GTCAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (20 bp):
TAAATATGATAAAATATATT
Found at i:4842583 original size:23 final size:22
Alignment explanation
Indices: 4842549--4842609 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
4842539 TTTAATTAAT
* *
4842549 TAATATATTTAATTTTAAAAAA
1 TAATATTTTTAAATTTAAAAAA
*
4842571 TAATATTTATTAAATTTAAAATA
1 TAATATTT-TTAAATTTAAAAAA
* *
4842594 TAAAATTTGT-AATTTA
1 TAATATTTTTAAATTTA
4842610 CGATTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 6 0.18
22 8 0.24
23 19 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAATATTTTTAAATTTAAAAAA
Found at i:4842586 original size:24 final size:23
Alignment explanation
Indices: 4842557--4842601 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4842547 ATTAATATAT
* *
4842557 TTAATTTTAAAAAATAATATTTA
1 TTAAATTTAAAAAATAAAATTTA
*
4842580 TTAAATTTAAAATATAAAATTT
1 TTAAATTTAAAAAATAAAATTT
4842602 GTAATTTACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAATTTAAAAAATAAAATTTA
Found at i:4842961 original size:27 final size:25
Alignment explanation
Indices: 4842900--4842961 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
4842890 CATAATATTG
4842900 ATATATATATTTTTTATATATTTAA
1 ATATATATATTTTTTATATATTTAA
* *
4842925 A-AAATAATATTTTATATTTATATTTAA
1 ATATAT-ATATTTT-T-TATATATTTAA
4842952 ATATATATAT
1 ATATATATAT
4842962 GAAATACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 3 0.10
25 8 0.27
26 1 0.03
27 15 0.50
28 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATATATTTTTTATATATTTAA
Found at i:4858372 original size:17 final size:19
Alignment explanation
Indices: 4858341--4858378 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
4858331 AATTTGATTA
4858341 TTTTAAGGTT-TTTTTAAT
1 TTTTAAGGTTATTTTTAAT
4858359 TTTTAA-GTTATTTTTAAT
1 TTTTAAGGTTATTTTTAAT
4858377 TT
1 TT
4858379 CAGATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (19 bp):
TTTTAAGGTTATTTTTAAT
Found at i:4858402 original size:16 final size:16
Alignment explanation
Indices: 4858352--4858411 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
4858342 TTTAAGGTTT
*
4858352 TTTTAATTTTTAAGTTA
1 TTTTAA-TTTTAAGTCA
*
4858369 TTTTTAA-TTTCAGATCA
1 -TTTTAATTTTAAG-TCA
4858386 TTTTAATTTTAAGTCA
1 TTTTAATTTTAAGTCA
4858402 TTTT-ATTTTA
1 TTTTAATTTTA
4858412 TTTTAAGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.16
16 18 0.49
17 7 0.19
18 6 0.16
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTAATTTTAAGTCA
Found at i:4858589 original size:21 final size:20
Alignment explanation
Indices: 4858565--4858623 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
4858555 GATTCGAATC
4858565 ATTTTTAAATTTAAATTAAT
1 ATTTTTAAATTTAAATTAAT
4858585 GA-TTTTAAATTATTAAATT-AT
1 -ATTTTTAAA-T-TTAAATTAAT
4858606 -TTATTTAAA-TTAAATTAA
1 ATT-TTTAAATTTAAATTAA
4858624 AATAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 8 0.24
21 10 0.30
22 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTTAAATTTAAATTAAT
Found at i:4858621 original size:26 final size:26
Alignment explanation
Indices: 4858589--4858652 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
4858579 ATTAATGATT
*
4858589 TTAAATTATTAAATTATT-TATTTAAA
1 TTAAATTA-TAAATAATTATATTTAAA
4858615 TTAAATTA-AAATAATTAATATTTAAA
1 TTAAATTATAAATAATT-ATATTTAAA
4858641 -TAAATTAATAAA
1 TTAAATT-ATAAA
4858653 ATTTTTTAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
24 7 0.21
25 6 0.18
26 17 0.52
27 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
TTAAATTATAAATAATTATATTTAAA
Found at i:4858646 original size:16 final size:16
Alignment explanation
Indices: 4858611--4858650 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
4858601 ATTATTTATT
4858611 TAAATTAA-ATTAAAA
1 TAAATTAATATTAAAA
*
4858626 T-AATTAATATTTAAA
1 TAAATTAATATTAAAA
4858641 TAAATTAATA
1 TAAATTAATA
4858651 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 8 0.36
16 8 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTAATATTAAAA
Found at i:4859144 original size:18 final size:18
Alignment explanation
Indices: 4859121--4859163 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
4859111 CTTGCAATTA
*
4859121 ATATATTTTTATTATTTT
1 ATATATTTTTATTATGTT
4859139 ATATA-TTTTATTATGTT
1 ATATATTTTTATTATGTT
4859156 ATA-ATTTT
1 ATATATTTT
4859164 GTTTAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 17 0.74
18 5 0.22
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
ATATATTTTTATTATGTT
Found at i:4863222 original size:10 final size:10
Alignment explanation
Indices: 4863207--4863277 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 10
4863197 AATTTGTTCG
4863207 AATTTAAATT
1 AATTTAAATT
* *
4863217 ATTTTAAAAT
1 AATTTAAATT
*
4863227 AATTTAATTT
1 AATTTAAATT
4863237 AATTTAAATT
1 AATTTAAATT
* **
4863247 ATTTTATTTTT
1 AATTTA-AATT
* *
4863258 AATTTAGATA
1 AATTTAAATT
4863268 AATTTAAATT
1 AATTTAAATT
4863278 TATCGATTTT
Statistics
Matches: 45, Mismatches: 15, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
10 38 0.84
11 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
AATTTAAATT
Found at i:4863273 original size:21 final size:21
Alignment explanation
Indices: 4863234--4863273 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4863224 AATAATTTAA
* *
4863234 TTTAATTTAAATTATTTTATT
1 TTTAATTTAAATAAATTTATT
*
4863255 TTTAATTTAGATAAATTTA
1 TTTAATTTAAATAAATTTA
4863274 AATTTATCGA
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:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTAATTTAAATAAATTTATT
Found at i:4863805 original size:4 final size:4
Alignment explanation
Indices: 4863798--4863831 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
4863788 TATATATATA
4863798 TATG TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TA
4863832 AATAAACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:4863944 original size:2 final size:2
Alignment explanation
Indices: 4863939--4863966 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4863929 GTAGTGTGTG
4863939 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
4863967 GATGCTTCTT
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:4864626 original size:34 final size:34
Alignment explanation
Indices: 4864587--4864660 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
4864577 TAACTTAATT
4864587 AATTCACCTAATCATTCAATAAATTCGAGATTTA
1 AATTCACCTAATCATTCAATAAATTCGAGATTTA
*
4864621 AATTCAGCTAATCATTCAATAAATTCGAGATTTA
1 AATTCACCTAATCATTCAATAAATTCGAGATTTA
4864655 AATTCA
1 AATTCA
4864661 ATATTTATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (34 bp):
AATTCACCTAATCATTCAATAAATTCGAGATTTA
Found at i:4865296 original size:21 final size:21
Alignment explanation
Indices: 4865243--4865296 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
4865233 TCTTCAGTGC
* *
4865243 CATCATCGCCATTATCATCAA
1 CATCATCGTCATTATAATCAA
** **
4865264 CATCATTATCATTATAATCGT
1 CATCATCGTCATTATAATCAA
4865285 CATCATCGTCAT
1 CATCATCGTCAT
4865297 CATCATCATT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (21 bp):
CATCATCGTCATTATAATCAA
Found at i:4869216 original size:3 final size:3
Alignment explanation
Indices: 4869208--4869249 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
4869198 TAAAAGCAAT
4869208 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4869250 GTTATCCAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4882828 original size:2 final size:2
Alignment explanation
Indices: 4882775--4882808 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4882765 GCATACATAC
4882775 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
4882809 TTGTTGTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4885387 original size:2 final size:2
Alignment explanation
Indices: 4885380--4885414 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4885370 ATTTGTTCGT
4885380 TC TC 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 TC TC T
4885415 GACTGTAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4885835 original size:31 final size:30
Alignment explanation
Indices: 4885760--4885835 Score: 75
Period size: 31 Copynumber: 2.5 Consensus size: 30
4885750 GATTATTTAA
* *
4885760 ATAAT-AATTTTTTAAATTTAATTATAAAT
1 ATAATAAAATTTTTAAATATAATTATAAAT
* *
4885789 ATACATATAATTTTTAAATAT-ATTTTAAAT
1 ATA-ATAAAATTTTTAAATATAATTATAAAT
4885819 AATAATAAAATCTTTTA
1 -ATAATAAAAT-TTTTA
4885836 GATCAACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 3 0.08
30 16 0.42
31 19 0.50
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAATAAAATTTTTAAATATAATTATAAAT
Found at i:4888973 original size:117 final size:117
Alignment explanation
Indices: 4888766--4888978 Score: 311
Period size: 117 Copynumber: 1.8 Consensus size: 117
4888756 CCCCAACTAG
* * * * * *
4888766 TCCATCTTTATGTTTAATGTATTAACGAATATTTCCTTATATCTTTCACTAATCTTTTACACCTT
1 TCCATCTTTAGGTTCAATGTATTAACAAAAAGTTCCTTATATCTTTCACTAATCTTTCACACCTT
*
4888831 TTCCTCATTCATTACTTTCAGAAATAAGCCTACAACTAAATCGCTAATCAGT
66 TTCCTCATTCATTACTTTCACAAATAAGCCTACAACTAAATCGCTAATCAGT
* *
4888883 TCCATCTTTAGGTTCAATTTATTAACAAAAAGTTCCTT-TAATCTTTCATTAATCTTTCACACCT
1 TCCATCTTTAGGTTCAATGTATTAACAAAAAGTTCCTTAT-ATCTTTCACTAATCTTTCACACCT
* *
4888947 TTTTCTTATTCATTACTTTCACAAATAAGCCT
65 TTTCCTCATTCATTACTTTCACAAATAAGCCT
4888979 TACTTCTAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
116 1 0.01
117 83 0.99
ACGTcount: A:0.30, C:0.22, G:0.05, T:0.43
Consensus pattern (117 bp):
TCCATCTTTAGGTTCAATGTATTAACAAAAAGTTCCTTATATCTTTCACTAATCTTTCACACCTT
TTCCTCATTCATTACTTTCACAAATAAGCCTACAACTAAATCGCTAATCAGT
Found at i:4891443 original size:2 final size:2
Alignment explanation
Indices: 4891436--4891464 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4891426 AATGATTCTC
4891436 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 A
4891465 GGCACTACTG
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4891831 original size:20 final size:20
Alignment explanation
Indices: 4891808--4891887 Score: 51
Period size: 20 Copynumber: 4.2 Consensus size: 20
4891798 TTCATAAAAA
4891808 ATATTAAATTATTAAAGATT
1 ATATTAAATTATTAAAGATT
* * *
4891828 ATATT--TTTA-AAAATATT
1 ATATTAAATTATTAAAGATT
* ** * *
4891845 -TTTTAAAAAAATAAAAAATT
1 ATATTAAATTATTAAAGA-TT
4891865 ATATTAAATTATTAAAGATT
1 ATATTAAATTATTAAAGATT
4891885 ATA
1 ATA
4891888 CTTTTAAAAA
Statistics
Matches: 41, Mismatches: 14, Indels: 10
0.63 0.22 0.15
Matches are distributed among these distances:
16 3 0.07
17 6 0.15
18 4 0.10
19 4 0.10
20 12 0.29
21 12 0.29
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
ATATTAAATTATTAAAGATT
Found at i:4891911 original size:55 final size:56
Alignment explanation
Indices: 4891808--4891923 Score: 207
Period size: 57 Copynumber: 2.1 Consensus size: 56
4891798 TTCATAAAAA
*
4891808 ATATTAAATTATTAAAGATTATATTTTTAAAAATATTTTTTAAAAAAATAAAAAATT
1 ATATTAAATTATTAAAGATTATACTTTTAAAAATA-TTTTTAAAAAAATAAAAAATT
4891865 ATATTAAATTATTAAAGATTATACTTTTAAAAATA-TTTTAAAAAAATAAAAAATT
1 ATATTAAATTATTAAAGATTATACTTTTAAAAATATTTTTAAAAAAATAAAAAATT
4891920 ATAT
1 ATAT
4891924 AAACGGTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 24 0.41
57 34 0.59
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (56 bp):
ATATTAAATTATTAAAGATTATACTTTTAAAAATATTTTTAAAAAAATAAAAAATT
Found at i:4892339 original size:27 final size:29
Alignment explanation
Indices: 4892274--4892341 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
4892264 AATTTATTTA
* *
4892274 TTAACATAATTTTAATATATATTTTTAATT
1 TTAACA-AATATTAATATATATTATTAATT
*
4892304 ATATA-AAATATTAATATATA-TATT-ATT
1 TTA-ACAAATATTAATATATATTATTAATT
4892331 TTAACAAATAT
1 TTAACAAATAT
4892342 ATCAAACATA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
26 1 0.03
27 11 0.34
28 3 0.09
29 13 0.41
30 3 0.09
31 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
TTAACAAATATTAATATATATTATTAATT
Found at i:4894486 original size:81 final size:81
Alignment explanation
Indices: 4894401--4894552 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 81
4894391 TAGGGTCAAG
* * * *
4894401 TTTATACCATTAA-TGTTCAAATCAATTGATCATAAAACTTTCATATTAATCATGTGTTTTACTT
1 TTTATACCATTAATTG-CCAAATAAATTGATCATAAAACTTTCATATTAAACATGTGATTTACTT
4894465 TATATATTATTGTTTTA
65 TATATATTATTGTTTTA
** *
4894482 TTTATAGTATTAATTGCCAAATAAATTGATTATAAAACTTTCATATTAAACATGTGATTTACTTT
1 TTTATACCATTAATTGCCAAATAAATTGATCATAAAACTTTCATATTAAACATGTGATTTACTTT
4894547 ATATAT
66 ATATAT
4894553 ATATATATAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
81 61 0.97
82 2 0.03
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (81 bp):
TTTATACCATTAATTGCCAAATAAATTGATCATAAAACTTTCATATTAAACATGTGATTTACTTT
ATATATTATTGTTTTA
Found at i:4894487 original size:19 final size:21
Alignment explanation
Indices: 4894455--4894493 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
4894445 ATTAATCATG
4894455 TGTTTTACTTTATA-TATTAT
1 TGTTTTACTTTATAGTATTAT
4894475 TGTTTTA-TTTATAGTATTA
1 TGTTTTACTTTATAGTATTA
4894494 ATTGCCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (21 bp):
TGTTTTACTTTATAGTATTAT
Found at i:4894553 original size:2 final size:2
Alignment explanation
Indices: 4894546--4894572 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4894536 TGATTTACTT
4894546 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
4894573 TTTCTGTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4894856 original size:17 final size:16
Alignment explanation
Indices: 4894834--4894879 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
4894824 TATTTAATTT
4894834 AATTTAAATTTTTTATA
1 AATTTAAATTTTTTA-A
*
4894851 AATTTAAAATTTTTAA
1 AATTTAAATTTTTTAA
*
4894867 AATATTATATTTT
1 AAT-TTAAATTTT
4894880 AATAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATTTAAATTTTTTAA
Found at i:4894908 original size:25 final size:25
Alignment explanation
Indices: 4894866--4894933 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
4894856 AAAATTTTTA
* * *
4894866 AAATATTATATTTTAATAATTATATCT
1 AAATA-TATA-TTAAATAAATATATAT
4894893 AAATATATATTAAATAAATATATAT
1 AAATATATATTAAATAAATATATAT
4894918 AAATAT-T-TTAAATAAA
1 AAATATATATTAAATAAA
4894934 ATAAAAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 9 0.24
24 1 0.03
25 19 0.50
26 4 0.11
27 5 0.13
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATATATTAAATAAATATATAT
Found at i:4894912 original size:15 final size:14
Alignment explanation
Indices: 4894892--4894922 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4894882 TAATTATATC
4894892 TAAATATATATTAAA
1 TAAATATATA-TAAA
4894907 TAAATATATATAAA
1 TAAATATATATAAA
4894921 TA
1 TA
4894923 TTTTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATATATATAAA
Found at i:4895398 original size:21 final size:20
Alignment explanation
Indices: 4895374--4895415 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4895364 ATATAAAAAA
*
4895374 AATTAATATAAAATATATAAT
1 AATTAAGATAAAAT-TATAAT
*
4895395 AATTTAGATAAAATTATAAT
1 AATTAAGATAAAATTATAAT
4895415 A
1 A
4895416 CAAAAATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTAAGATAAAATTATAAT
Found at i:4899011 original size:115 final size:117
Alignment explanation
Indices: 4898816--4899029 Score: 301
Period size: 115 Copynumber: 1.8 Consensus size: 117
4898806 ATCCCAAACT
* * * * * *
4898816 AGTTCCATCTTTACGTTTAATGTAGTAACGAATATTTCCTTATATCTTTCAGTAATCTTTTACAC
1 AGTTCCACCTTTACGGTTAATGTAGTAACCAAAAGTTCCTTATATCTTTCAGTAATCTTTCACAC
4898881 CTTTTTCTCATTCATTACTTTCAGAAATAAGCCTACAACTAAATCGCTAATC
66 CTTTTTCTCATTCATTACTTTCAGAAATAAGCCTACAACTAAATCGCTAATC
4898933 AGTTCCACCTTTA-GGTTAATGT-GTTAACCAAAAGTTCCTT-TAATCTTTCA-TAATCTTTCAC
1 AGTTCCACCTTTACGGTTAATGTAG-TAACCAAAAGTTCCTTAT-ATCTTTCAGTAATCTTTCAC
* * *
4898994 AGCTTTTTCTTATTCATTACTTTCAGTAATAAGCCT
64 ACCTTTTTCTCATTCATTACTTTCAGAAATAAGCCT
4899030 TACTTCTAAT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
115 45 0.52
116 29 0.34
117 12 0.14
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (117 bp):
AGTTCCACCTTTACGGTTAATGTAGTAACCAAAAGTTCCTTATATCTTTCAGTAATCTTTCACAC
CTTTTTCTCATTCATTACTTTCAGAAATAAGCCTACAACTAAATCGCTAATC
Found at i:4902184 original size:19 final size:19
Alignment explanation
Indices: 4902162--4902211 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4902152 ATTTTTTTAT
*
4902162 TATATATAATATTAGTGTA
1 TATATATAATATTAATGTA
* *
4902181 TATATATTATTTTAATGTA
1 TATATATAATATTAATGTA
*
4902200 TATATCTAATAT
1 TATATATAATAT
4902212 ATATTAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (19 bp):
TATATATAATATTAATGTA
Found at i:4903622 original size:23 final size:23
Alignment explanation
Indices: 4903596--4903668 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
4903586 AAATAATTTT
4903596 TATTTAAATTAAATTATAAAATA
1 TATTTAAATTAAATTATAAAATA
4903619 TA-TTAATATT-AA-TATAAAAATAA
1 TATTTAA-ATTAAATTAT-AAAAT-A
* *
4903642 TATTTTAA-TAAATAATAAAATA
1 TATTTAAATTAAATTATAAAATA
*
4903664 AATTT
1 TATTT
4903669 TTATATCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
21 3 0.07
22 17 0.41
23 16 0.39
24 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
TATTTAAATTAAATTATAAAATA
Found at i:4904669 original size:17 final size:17
Alignment explanation
Indices: 4904629--4904671 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
4904619 TAAAATATAT
*
4904629 TATAT-TTAGATTTAAA
1 TATATATTAAATTTAAA
4904645 TA-AGTATTAAATTTAAA
1 TATA-TATTAAATTTAAA
4904662 TATATATTAA
1 TATATATTAA
4904672 GTATGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 3 0.13
17 18 0.78
18 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (17 bp):
TATATATTAAATTTAAA
Found at i:4907111 original size:2 final size:2
Alignment explanation
Indices: 4907104--4907136 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4907094 TAATTTACTT
4907104 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4907137 TTAATTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4908265 original size:2 final size:2
Alignment explanation
Indices: 4908258--4908306 Score: 55
Period size: 2 Copynumber: 25.0 Consensus size: 2
4908248 AATTTTATTT
* * * *
4908258 TA TA TA TA TT TA TA TA TA TA TA TA TG TA CA T- TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4908299 TA TA TA TA
1 TA TA TA TA
4908307 AAAAACAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4908271 original size:43 final size:43
Alignment explanation
Indices: 4908189--4908282 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
4908179 AAGAAAAAAA
* * * *
4908189 TTATATATTTATATTTATATTTTTTATTTAAAATATTATATTT
1 TTATATATTAATAATTATATTTTATATTTAAAATATTATATAT
*
4908232 TTATATATTAATAATTA-ATTTTAT-TTTATATATATTTATATAT
1 TTATATATTAATAATTATATTTTATATTTA-AAATA-TTATATAT
*
4908275 ATATATAT
1 TTATATAT
4908283 GTACATTATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.23
43 29 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
TTATATATTAATAATTATATTTTATATTTAAAATATTATATAT
Found at i:4908547 original size:21 final size:19
Alignment explanation
Indices: 4908513--4908556 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
4908503 ATATATTTTA
*
4908513 TTAAATATATTTAAATATT
1 TTAAATATATTTAAATAAT
*
4908532 TTAAATATTAATTTAATTAAT
1 TTAAATA-T-ATTTAAATAAT
4908553 TTAA
1 TTAA
4908557 TTTTATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 7 0.33
20 1 0.05
21 13 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAAATATATTTAAATAAT
Found at i:4908558 original size:14 final size:14
Alignment explanation
Indices: 4908539--4908632 Score: 54
Period size: 14 Copynumber: 6.9 Consensus size: 14
4908529 ATTTTAAATA
4908539 TTAATTTAATTAAT
1 TTAATTTAATTAAT
* *
4908553 TTAATTTTA-TATT
1 TTAATTTAATTAAT
* * *
4908566 TTAATAATAA-AAAA
1 TTAAT-TTAATTAAT
* * *
4908580 TTAATAT-ATAAAA
1 TTAATTTAATTAAT
*
4908593 TTAAATTAATTAAAT
1 TTAATTTAATT-AAT
4908608 TTAATTTAATTAAT
1 TTAATTTAATTAAT
4908622 TT--TTTAATTAA
1 TTAATTTAATTAA
4908633 AACAATTTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
12 10 0.16
13 19 0.30
14 23 0.36
15 12 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATTTAATTAAT
Found at i:4908566 original size:21 final size:22
Alignment explanation
Indices: 4908518--4908573 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
4908508 TTTTATTAAA
*
4908518 TATATTTAAATATTTTAAATAT
1 TATATTTAAATAATTTAAATAT
* *
4908540 TA-ATTTAATTAATTT-AATTT
1 TATATTTAAATAATTTAAATAT
*
4908560 TATATTTTAATAAT
1 TATATTTAAATAAT
4908574 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 20 0.71
22 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTAAATAATTTAAATAT
Found at i:4909456 original size:25 final size:26
Alignment explanation
Indices: 4909419--4909472 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
4909409 TAAATATTAA
* **
4909419 AAAATATATTAAATTATTAAATT-TT
1 AAAATATAATAAAAAATTAAATTATT
*
4909444 AAAATTTAATAAAAAATTAAATTATT
1 AAAATATAATAAAAAATTAAATTATT
4909470 AAA
1 AAA
4909473 TATTATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AAAATATAATAAAAAATTAAATTATT
Found at i:4909962 original size:23 final size:20
Alignment explanation
Indices: 4909936--4909984 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 20
4909926 AATTATATAA
4909936 TAAAAGAAAAATATATGATATTT
1 TAAAAGAAAAATA-AT-A-ATTT
*
4909959 TAAAGAGTAAAATAATAATTT
1 TAAA-AGAAAAATAATAATTT
4909980 TAAAA
1 TAAAA
4909985 TGTAAATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.33
22 1 0.04
23 6 0.25
24 8 0.33
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (20 bp):
TAAAAGAAAAATAATAATTT
Found at i:4912408 original size:17 final size:17
Alignment explanation
Indices: 4912363--4912411 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
4912353 TAAAATATAT
*
4912363 TATATTTAAATTTAAGTA
1 TATATTT-AATTTAAATA
* **
4912381 AATATCAAATTTAAATA
1 TATATTTAATTTAAATA
4912398 TATATTTAATTTAA
1 TATATTTAATTTAA
4912412 TTTGTATTGT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
17 20 0.83
18 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
TATATTTAATTTAAATA
Found at i:4912433 original size:34 final size:34
Alignment explanation
Indices: 4912395--4912471 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
4912385 TCAAATTTAA
* *
4912395 ATATATATTTAATTTAAT-TTGTATTGTTTATTTT
1 ATATATATTTAA-ATAATATTGTATTGTTTATTAT
* * *
4912429 ATATATTTTTAAATAATATTTTATTTTTTATTAT
1 ATATATATTTAAATAATATTGTATTGTTTATTAT
4912463 AT-TATATTT
1 ATATATATTT
4912472 TTAAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 10 0.28
34 26 0.72
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (34 bp):
ATATATATTTAAATAATATTGTATTGTTTATTAT
Found at i:4912474 original size:35 final size:36
Alignment explanation
Indices: 4912411--4912500 Score: 105
Period size: 35 Copynumber: 2.5 Consensus size: 36
4912401 ATTTAATTTA
* * *
4912411 ATTTGTATTGTTTATTTTA-TATATTTTT-AAATAAT
1 ATTT-TATTTTTTATTATATTATATTTTTAAAAAAAT
4912446 ATTTTATTTTTTATTATATTATATTTTTAAAAAAAT
1 ATTTTATTTTTTATTATATTATATTTTTAAAAAAAT
*
4912482 ATTTT-TTTATTATTGATAT
1 ATTTTATTTTTTATT-ATAT
4912501 CAAAAATAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
34 12 0.25
35 21 0.44
36 15 0.31
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (36 bp):
ATTTTATTTTTTATTATATTATATTTTTAAAAAAAT
Found at i:4913406 original size:27 final size:27
Alignment explanation
Indices: 4913345--4913443 Score: 98
Period size: 27 Copynumber: 3.8 Consensus size: 27
4913335 AATAAAAATT
* *
4913345 AACCACCAATTTTGACAAAC-AACAAG
1 AACCACCATTTTTGACAAACAAAAAAG
* *
4913371 --CCACAATTTTTAACAAACAAAAAAG
1 AACCACCATTTTTGACAAACAAAAAAG
* *
4913396 AACCACCATTTTTGACAAA-TACAAAG
1 AACCACCATTTTTGACAAACAAAAAAG
*
4913422 TAACCACCATTTTTTACAAACA
1 -AACCACCATTTTTGACAAACA
4913444 CAAAGGATGG
Statistics
Matches: 58, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 15 0.26
25 5 0.09
26 5 0.09
27 33 0.57
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.22
Consensus pattern (27 bp):
AACCACCATTTTTGACAAACAAAAAAG
Found at i:4918542 original size:27 final size:27
Alignment explanation
Indices: 4918476--4918542 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
4918466 TCGAATTATC
*
4918476 ATAAAATTTT-AAATTTTATTAACAGA
1 ATAAAATTTTAAAATTATATTAACAGA
** * **
4918502 ATAAAATTAAAAAATTATATTAAGATT
1 ATAAAATTTTAAAATTATATTAACAGA
*
4918529 TTAAAATTTTAAAA
1 ATAAAATTTTAAAA
4918543 CAATCTACTA
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
26 8 0.26
27 23 0.74
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.40
Consensus pattern (27 bp):
ATAAAATTTTAAAATTATATTAACAGA
Found at i:4919081 original size:39 final size:41
Alignment explanation
Indices: 4919018--4919121 Score: 101
Period size: 41 Copynumber: 2.5 Consensus size: 41
4919008 ATACTTTTTT
4919018 TATTGAATTATTAAA-ATTTATTATACTAA-A-ATTTAAGTAAA
1 TATTGAA-T-TTAAATATTT-TTATACTAATATATTTAAGTAAA
* * *
4919059 TATTGAATTTAAATATTTTTATATTAATATATTTAATTTAA
1 TATTGAATTTAAATATTTTTATACTAATATATTTAAGTAAA
4919100 T-TT-AATTTAAATAATATTTTAT
1 TATTGAATTTAAAT-AT-TTTTAT
4919122 TTTTTAAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
39 22 0.40
40 10 0.18
41 23 0.42
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (41 bp):
TATTGAATTTAAATATTTTTATACTAATATATTTAAGTAAA
Found at i:4921020 original size:50 final size:50
Alignment explanation
Indices: 4920758--4921040 Score: 397
Period size: 50 Copynumber: 5.7 Consensus size: 50
4920748 TACACTTAGA
* * * *
4920758 GTCAACAATTATGGTCACCT-TTTTTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
4920807 GTCAACAATTATGACCACATCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
4920857 ATCAACAATTACGGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
** * *
4920907 GTCAACAATTACAGCTACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
*
4920957 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
4921007 GTCAACAATTATGGCTATCTTTATCTATTGTCAA
1 GTCAACAATTATGGCCACCTCTCTCTATTGTCAA
4921041 GGGTACTTTC
Statistics
Matches: 209, Mismatches: 24, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
49 17 0.08
50 192 0.92
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:4925518 original size:50 final size:50
Alignment explanation
Indices: 4925426--4925708 Score: 322
Period size: 50 Copynumber: 5.7 Consensus size: 50
4925416 TATACTTAGG
* ** * *
4925426 GTCAACAATTATGGCCACCT-TTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATC
** * *
4925475 GTCAACAATTATAACCACCTCTCTATATTGTCAAAGATTGGTGAAGAATC
1 GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATC
* * * *
4925525 GTCAACAATTACGGTCATCTCTTTCTATTGTCAAAGTTTGGTGAAGAATC
1 GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATC
* *
4925575 GTCAACAATTACGATCATCTCTCTCTATTATCAAA-AGTTGGTGAA-AATC
1 GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGA-TTGGTGAAGAATC
* **
4925624 ATCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTAATGAAGAATC
1 GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATC
* * * *
4925674 ATCAACAATTATGATCA-CTTTCTTCTATTATCAAA
1 GTCAACAATTACGATCACCTCTC-TCTATTGTCAAA
4925709 AGTACTTTCC
Statistics
Matches: 204, Mismatches: 25, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
49 64 0.31
50 140 0.69
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (50 bp):
GTCAACAATTACGATCACCTCTCTCTATTGTCAAAGATTGGTGAAGAATC
Done.