Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold77
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: 1374688
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.34
Warning! 47366 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:322513 original size:28 final size:28
Alignment explanation
Indices: 322476--322556 Score: 81
Period size: 34 Copynumber: 2.7 Consensus size: 28
322466 CGTATCAAAA
*
322476 TTAAATTAAAAAAATTTAAATTTAAATT
1 TTAAAATAAAAAAATTTAAATTTAAATT
322504 TTAAAATAAATTTAAAAAATTTTAAATTTAAATT
1 TTAAAAT--A---AAAAAA-TTTAAATTTAAATT
* *
322538 TTAAAATAATAAATTTTAA
1 TTAAAATAAAAAAATTTAA
322557 TGGATAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 11 0.25
29 4 0.09
30 1 0.02
32 1 0.02
33 6 0.14
34 21 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAAAATAAAAAAATTTAAATTTAAATT
Found at i:322514 original size:33 final size:34
Alignment explanation
Indices: 322472--322546 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
322462 CCATCGTATC
322472 AAAATTAAA-TTAAAAAAATTTAAATTTAAATTTT
1 AAAA-TAAATTTAAAAAAATTTAAATTTAAATTTT
*
322506 AAAATAAATTTAAAAAATTTTAAATTTAAATTTT
1 AAAATAAATTTAAAAAAATTTAAATTTAAATTTT
322540 AAAATAA
1 AAAATAA
322547 TAAATTTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATAAATTTAAAAAAATTTAAATTTAAATTTT
Found at i:323065 original size:17 final size:16
Alignment explanation
Indices: 323039--323070 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
323029 TTTTGAAATT
323039 TTTTAATTTAAATTAA
1 TTTTAATTTAAATTAA
323055 TTTTAAGTTTAAATTA
1 TTTTAA-TTTAAATTA
323071 TGTTGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTTTAATTTAAATTAA
Found at i:323740 original size:16 final size:16
Alignment explanation
Indices: 323687--323745 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
323677 AATATCGATT
*
323687 AATATATATTAATTTTAA
1 AATA-ATATTAA-TATAA
* *
323705 AATAA-AATAAAATAA
1 AATAATATTAATATAA
323720 AATAATATTAATATAA
1 AATAATATTAATATAA
*
323736 TATAATATTA
1 AATAATATTA
323746 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 8 0.24
16 21 0.62
17 1 0.03
18 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATATTAATATAA
Found at i:323805 original size:21 final size:19
Alignment explanation
Indices: 323761--323798 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
323751 TTTTAATTTG
*
323761 ATATTATTTTATATGGATC
1 ATATAATTTTATATGGATC
*
323780 ATATAATTTTATATTGATC
1 ATATAATTTTATATGGATC
323799 TCATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (19 bp):
ATATAATTTTATATGGATC
Found at i:324831 original size:19 final size:20
Alignment explanation
Indices: 324788--324831 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
324778 AAAAAAATTA
* * *
324788 AAAAAATTAATAATTTTTTT
1 AAAAAATAAAAAATTATTTT
324808 AAAAAATAAAAAATTATTTT
1 AAAAAATAAAAAATTATTTT
324828 AAAA
1 AAAA
324832 CATTTTAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATAAAAAATTATTTT
Found at i:324866 original size:29 final size:27
Alignment explanation
Indices: 324811--324879 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 27
324801 TTTTTTTAAA
*
324811 AAATAAAAAATTATTTTAAAACA-TTTT
1 AAAT-AAAAATTATCTTAAAACATTTTT
*
324838 AAGATAAAAATTATCTTAATAATTATTTTT
1 AA-ATAAAAATTATCTTAA-AA-CATTTTT
*
324868 AAATAATAATTA
1 AAATAAAAATTA
324880 AATAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 15 0.43
28 4 0.11
29 10 0.29
30 6 0.17
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (27 bp):
AAATAAAAATTATCTTAAAACATTTTT
Found at i:329688 original size:2 final size:2
Alignment explanation
Indices: 329675--329715 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
329665 CATATTGGAA
*
329675 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
329716 GATAGATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:333285 original size:28 final size:28
Alignment explanation
Indices: 333253--333317 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
333243 GATAAGTGTT
** *
333253 AGACAATATGGATAAGTTTATTTTAATA
1 AGACAATATGGATAAGACTATCTTAATA
333281 AGACAATATGGATAAGACTATCTTAATA
1 AGACAATATGGATAAGACTATCTTAATA
*
333309 AGATAATAT
1 AGACAATAT
333318 CTAAAGTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (28 bp):
AGACAATATGGATAAGACTATCTTAATA
Found at i:336813 original size:19 final size:20
Alignment explanation
Indices: 336774--336813 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
336764 ACAACACTTA
*
336774 TGTATCGATACAGTTATTGTT
1 TGTATCGATACAG-AATTGTT
336795 TGTATCGATACA-AATTGTT
1 TGTATCGATACAGAATTGTT
336814 GAAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAGAATTGTT
Found at i:339160 original size:21 final size:21
Alignment explanation
Indices: 339136--339191 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
339126 TTTTTGTCCA
339136 AATGTATCGATACATTGTTAG
1 AATGTATCGATACATTGTTAG
339157 AATGTATCGATACATTGTTAG
1 AATGTATCGATACATTGTTAG
339178 AATGTATCGATACA
1 AATGTATCGATACA
339192 AGGTCCCAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTGTTAG
Found at i:339267 original size:13 final size:13
Alignment explanation
Indices: 339249--339273 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
339239 CATAAAGTGT
339249 TGTATCGATACAA
1 TGTATCGATACAA
339262 TGTATCGATACA
1 TGTATCGATACA
339274 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:339271 original size:33 final size:33
Alignment explanation
Indices: 339229--339295 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
339219 TTCAACGATT
339229 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
339262 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
339295 T
1 T
339296 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:339333 original size:13 final size:13
Alignment explanation
Indices: 339315--339342 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
339305 TGCCAAAAAA
339315 TGTATCGATACAT
1 TGTATCGATACAT
339328 TGTATCGATACAT
1 TGTATCGATACAT
339341 TG
1 TG
339343 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:339406 original size:52 final size:52
Alignment explanation
Indices: 339348--339472 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
339338 CATTGATCTT
*
339348 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
339400 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
339452 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
339473 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:345367 original size:30 final size:31
Alignment explanation
Indices: 345309--345367 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
345299 TATTTCGGTC
* * *
345309 ACTTAACTTTTTAAAAGATTTTATTTTGATG
1 ACTTAACTTTTTAAAAAATTATAATTTGATG
345340 ACTTAAC-TTTTAAAAAATTATAATTTGA
1 ACTTAACTTTTTAAAAAATTATAATTTGA
345368 AAATTTTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (31 bp):
ACTTAACTTTTTAAAAAATTATAATTTGATG
Found at i:345648 original size:16 final size:16
Alignment explanation
Indices: 345624--345658 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
345614 AAGAACAAAA
*
345624 AAATATAAATTTTTTT
1 AAATATAAATTTATTT
*
345640 AAATTTAAATTTATTT
1 AAATATAAATTTATTT
345656 AAA
1 AAA
345659 AAATATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATAAATTTATTT
Found at i:346905 original size:23 final size:23
Alignment explanation
Indices: 346855--346912 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 23
346845 TTTTAAGGTG
*
346855 AATATAAATAAATAATATGAATAT
1 AATATAAA-ATATAATATGAATAT
*
346879 AATATAAAATATAATTTG-ATAT
1 AATATAAAATATAATATGAATAT
346901 AAATATATAAAT
1 -AATATA-AAAT
346913 GTATAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.13
23 14 0.47
24 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (23 bp):
AATATAAAATATAATATGAATAT
Found at i:346947 original size:21 final size:21
Alignment explanation
Indices: 346914--346954 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
346904 TATATAAATG
*
346914 TATAAAAATTTTACATAAAAA
1 TATAAAAATTTTAAATAAAAA
346935 TATAATAAA-TTTAAATAAAA
1 TATAA-AAATTTTAAATAAAA
346955 TTAAAATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TATAAAAATTTTAAATAAAAA
Found at i:346962 original size:21 final size:21
Alignment explanation
Indices: 346923--346962 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
346913 GTATAAAAAT
* *
346923 TTTACATAAAAATATAATAAA
1 TTTAAATAAAAATAAAATAAA
*
346944 TTTAAATAAAATTAAAATA
1 TTTAAATAAAAATAAAATA
346963 CATAAAAATA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTAAATAAAAATAAAATAAA
Found at i:346979 original size:36 final size:37
Alignment explanation
Indices: 346925--346997 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 37
346915 ATAAAAATTT
* *
346925 TACATAAAAATATAATAAA-TTTAAATAAAATTAAAA
1 TACATAAAAATATAATAAACATTAAATAAAATAAAAA
*
346961 TACATAAAAATA-ATATAAACATTATATAAAATAAAAA
1 TACATAAAAATATA-ATAAACATTAAATAAAATAAAAA
346998 ATTAGCAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 1 0.03
36 17 0.53
37 14 0.44
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (37 bp):
TACATAAAAATATAATAAACATTAAATAAAATAAAAA
Found at i:347354 original size:20 final size:19
Alignment explanation
Indices: 347329--347410 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 19
347319 ATATAATATG
347329 ATATAAAATTAATAAAAAAT
1 ATATAAAATT-ATAAAAAAT
* ***
347349 ATATAAATATAATAAATTTT
1 ATATAAA-ATTATAAAAAAT
* * *
347369 ATATAATATTATTAATAAT
1 ATATAAAATTATAAAAAAT
*
347388 ATATCAAAATTTTAAAAAAT
1 ATAT-AAAATTATAAAAAAT
347408 ATA
1 ATA
347411 AAATATTTTG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
19 12 0.26
20 33 0.70
21 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (19 bp):
ATATAAAATTATAAAAAAT
Found at i:347358 original size:26 final size:28
Alignment explanation
Indices: 347293--347360 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
347283 AGGATGTACA
347293 ATATAAATA-AAATATTAAAAATTAAAAT
1 ATATAAATATAAATATTAAAAA-TAAAAT
* *
347321 ATAATATGATATAAA-ATTAATAA-AAAAT
1 AT-ATA-AATATAAATATTAAAAATAAAAT
347349 ATATAAATATAA
1 ATATAAATATAA
347361 TAAATTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
26 6 0.18
27 3 0.09
28 9 0.26
29 3 0.09
30 10 0.29
31 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (28 bp):
ATATAAATATAAATATTAAAAATAAAAT
Found at i:347418 original size:19 final size:20
Alignment explanation
Indices: 347368--347424 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 20
347358 TAATAAATTT
* *
347368 TATATAATATTATTAATAATA
1 TATAAAATATT-TTAATAAAA
*
347389 TATCAAA-ATTTTAA-AAAA
1 TATAAAATATTTTAATAAAA
347407 TATAAAATATTTTGAATA
1 TATAAAATATTTT-AATA
347425 CAATTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 9 0.31
19 9 0.31
20 5 0.17
21 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATTTTAATAAAA
Found at i:348571 original size:19 final size:19
Alignment explanation
Indices: 348547--348614 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
348537 AATTCAACAA
348547 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
348566 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
348581 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
348598 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
348615 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:348586 original size:13 final size:13
Alignment explanation
Indices: 348568--348592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348558 ACATAAGTTT
348568 TGTATCGATACAA
1 TGTATCGATACAA
348581 TGTATCGATACA
1 TGTATCGATACA
348593 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:348590 original size:32 final size:32
Alignment explanation
Indices: 348549--348611 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
348539 TTCAACAATT
*
348549 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
348581 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
348612 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:348672 original size:13 final size:13
Alignment explanation
Indices: 348654--348679 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
348644 CATTTTTCTA
348654 TGTATCGATACAT
1 TGTATCGATACAT
348667 TGTATCGATACAT
1 TGTATCGATACAT
348680 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:348676 original size:33 final size:33
Alignment explanation
Indices: 348634--348700 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
348624 GCCAAGGAAA
***
348634 TGTATCGATACATTTTTCTATGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
*
348667 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTATGTATCGATACAT
348700 T
1 T
348701 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTATGTATCGATACAT
Found at i:351167 original size:53 final size:50
Alignment explanation
Indices: 351047--351171 Score: 151
Period size: 51 Copynumber: 2.4 Consensus size: 50
351037 CTCAATTCTC
* * * *
351047 CACAATCGGGGATAGTCCAACTCCGATTTTATTTTCAAGACAATAATTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAACAATTTT
* *
351097 CTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTTT
1 C-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACAACAA-TTTT
*
351151 CACAATCGAGGATACTCCAAC
1 CACAATCGGGGATACTCCAAC
351172 CTCGTTATCT
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
50 1 0.02
51 32 0.51
53 25 0.40
54 5 0.08
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (50 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACAACAATTTT
Found at i:351217 original size:28 final size:28
Alignment explanation
Indices: 351160--351231 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
351150 TCACAATCGA
* **
351160 GGATACTCCAACCTCGTTATCTCATTGG
1 GGATACTCCAACCCCGTTATCTCAGAGG
*
351188 GGATACTCCAACCCCGTTA-CTTCCGAGG
1 GGATACTCCAACCCCGTTATC-TCAGAGG
*
351216 GGATACTCTAACCCCG
1 GGATACTCCAACCCCG
351232 GCTTTATTCC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 37 0.97
ACGTcount: A:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTATCTCAGAGG
Found at i:353837 original size:20 final size:20
Alignment explanation
Indices: 353759--353837 Score: 63
Period size: 20 Copynumber: 3.9 Consensus size: 20
353749 CTAATTCGAC
*
353759 TTATAATATTTATTTATATTA
1 TTATAAAATTTATTT-TATTA
*
353780 TTA-AAAATTAAATTTTATT-
1 TTATAAAATT-TATTTTATTA
* * *
353799 TTTTAAAAATATATATTATTA
1 TTAT-AAAATTTATTTTATTA
*
353820 TTATAATATTTATTTTAT
1 TTATAAAATTTATTTTAT
353838 CATATACATT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 27 0.61
21 15 0.34
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATAAAATTTATTTTATTA
Found at i:354322 original size:30 final size:30
Alignment explanation
Indices: 354261--354321 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
354251 ATTATATAAA
354261 TATTAATATAAAAATAACTTTTAAAATTTT
1 TATTAATATAAAAATAACTTTTAAAATTTT
354291 TATTAATATTTAAATAATAA-TTTT-AAATTTT
1 TATTAATA--TAAA-AATAACTTTTAAAATTTT
354322 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 8 0.29
31 7 0.25
32 8 0.29
33 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTAATATAAAAATAACTTTTAAAATTTT
Found at i:354353 original size:6 final size:7
Alignment explanation
Indices: 354309--354333 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
354299 TTTAAATAAT
354309 AATTTTA
1 AATTTTA
354316 AATTTTA
1 AATTTTA
354323 AATTTTA
1 AATTTTA
354330 AATT
1 AATT
354334 AAATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:355273 original size:18 final size:18
Alignment explanation
Indices: 355222--355274 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
355212 ATAAATTTAA
*
355222 AATAATATATTT-TTATT
1 AATAATATATTTATTTTT
* *
355239 -AT-ATATATTCATATTT
1 AATAATATATTTATTTTT
355255 AATAATATATTTATTTTT
1 AATAATATATTTATTTTT
355273 AA
1 AA
355275 ATTTAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 7 0.25
16 5 0.18
17 2 0.07
18 14 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
AATAATATATTTATTTTT
Found at i:355515 original size:21 final size:20
Alignment explanation
Indices: 355491--355530 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
355481 AAATTTTAAA
355491 AAATTATAAATATTAAAACTC
1 AAATTATAAAT-TTAAAACTC
* *
355512 AAATTTTAAATTTATAACT
1 AAATTATAAATTTAAAACT
355531 TCATAAATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
AAATTATAAATTTAAAACTC
Found at i:358576 original size:24 final size:25
Alignment explanation
Indices: 358540--358589 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
358530 TTCAGTTTAA
358540 ATTACTATTTAATTATAAAAATATT
1 ATTACTATTTAATTATAAAAATATT
*
358565 ATTACT-TTTAATTATAAAACTATT
1 ATTACTATTTAATTATAAAAATATT
358589 A
1 A
358590 ATATAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTACTATTTAATTATAAAAATATT
Found at i:359979 original size:2 final size:2
Alignment explanation
Indices: 359972--360017 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
359962 TGGCCATTTG
359972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
360014 AT AT
1 AT AT
360018 TCTTGAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360586 original size:21 final size:19
Alignment explanation
Indices: 360559--360616 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
360549 TAATAATAAA
360559 AATATTATTTTTTATTTTT
1 AATATTATTTTTTATTTTT
**
360578 ATCATATTA-TAATTATTTTT
1 A--ATATTATTTTTTATTTTT
*
360598 AATATTATATTTATATTTT
1 AATATTAT-TTTTTATTTT
360617 ATGATGGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 6 0.20
19 1 0.03
20 17 0.57
21 6 0.20
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
AATATTATTTTTTATTTTT
Found at i:360595 original size:20 final size:19
Alignment explanation
Indices: 360570--360618 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
360560 ATATTATTTT
360570 TTATTTTTATCATATTATAA
1 TTATTTTTAT-ATATTATAA
*
360590 TTATTTTTA-ATATTATAT
1 TTATTTTTATATATTATAA
360608 TTATATTTTAT
1 TTAT-TTTTAT
360619 GATGGTGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 12 0.46
19 5 0.19
20 9 0.35
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTTTTATATATTATAA
Found at i:360968 original size:22 final size:21
Alignment explanation
Indices: 360943--360983 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
360933 TATTAAAAAT
*
360943 TATTTTATTATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
360965 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
360984 AATAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:362020 original size:17 final size:18
Alignment explanation
Indices: 361998--362032 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
361988 ATTAAAGATG
361998 TAATTATATT-TTTATTT
1 TAATTATATTATTTATTT
362015 TAATTATATTATTTATTT
1 TAATTATATTATTTATTT
362033 ATTTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
TAATTATATTATTTATTT
Found at i:362033 original size:17 final size:17
Alignment explanation
Indices: 361998--362050 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
361988 ATTAAAGATG
361998 TAATTATATT-TTTATTT
1 TAATTATATTATTTA-TT
362015 TAATTATATTATTTATT
1 TAATTATATTATTTATT
*
362032 T-ATT-TATTA-ATATT
1 TAATTATATTATTTATT
362046 TAATT
1 TAATT
362051 CAAAATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
16 3 0.09
17 13 0.39
18 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TAATTATATTATTTATT
Found at i:363585 original size:2 final size:2
Alignment explanation
Indices: 363570--363613 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
363560 TCACCAACCA
* *
363570 AT AT AT AG AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
363612 AT
1 AT
363614 CAAAATAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:369256 original size:22 final size:22
Alignment explanation
Indices: 369231--369273 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
369221 TAATCTGATT
*
369231 AAATG-ATTTAAATAATTATTTA
1 AAATGTATTAAAAT-ATTATTTA
369253 AAATGTATTAAAATATTATTT
1 AAATGTATTAAAATATTATTT
369274 TTATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
AAATGTATTAAAATATTATTTA
Found at i:370322 original size:15 final size:15
Alignment explanation
Indices: 370280--370327 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
370270 AATATATAAA
370280 AATTTAT-ATAAAAAT
1 AATTTATAAT-AAAAT
* *
370295 AATATTTTAATAATAT
1 AAT-TTATAATAAAAT
370311 AATTTATAATAAAAT
1 AATTTATAATAAAAT
370326 AA
1 AA
370328 ATTTCAGATC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 15 0.56
16 10 0.37
17 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTATAATAAAAT
Found at i:370330 original size:16 final size:16
Alignment explanation
Indices: 370279--370331 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
370269 AAATATATAA
370279 AAATTTAT-ATAAAAAT
1 AAATTTATAAT-AAAAT
*
370295 AATATTT-TAATAATAT
1 AA-ATTTATAATAAAAT
370311 -AATTTATAATAAAAT
1 AAATTTATAATAAAAT
370326 AAATTT
1 AAATTT
370332 CAGATCAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 9 0.29
16 12 0.39
17 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTATAATAAAAT
Found at i:370453 original size:15 final size:14
Alignment explanation
Indices: 370429--370458 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
370419 AAAAATTCAT
370429 ATTTTAATAAAATA
1 ATTTTAATAAAATA
370443 ATTTATAATAAAATA
1 ATTT-TAATAAAATA
370458 A
1 A
370459 AATTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTTAATAAAATA
Found at i:373553 original size:15 final size:15
Alignment explanation
Indices: 373506--373553 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
373496 CATTTATCCA
*
373506 TTAACATATCAATAG
1 TTAACATATAAATAG
*
373521 TT-ACATATACAACA-
1 TTAACATATA-AATAG
373535 TTAACATATAAATAG
1 TTAACATATAAATAG
373550 TTAA
1 TTAA
373554 AAATCCATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.33
Consensus pattern (15 bp):
TTAACATATAAATAG
Found at i:374119 original size:34 final size:33
Alignment explanation
Indices: 374071--374291 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
374061 TGGTAAAAAC
*
374071 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
374104 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
374138 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
374172 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
374206 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
* *
374240 CACCCATTTAATCAACAATGGTAAACTATCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
374274 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
374292 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:374187 original size:68 final size:67
Alignment explanation
Indices: 374073--374291 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
374063 GTAAAAACCA
* * *
374073 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
374138 CAC
65 CAC
* * * *
374141 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
374206 CTC
65 CAC
* * * * *
374209 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTATCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
374274 CA-
65 CAC
374276 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
374292 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:374215 original size:102 final size:101
Alignment explanation
Indices: 374071--374291 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
374061 TGGTAAAAAC
* *
374071 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
374136 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * * *
374172 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
374237 AATCACCCATTTAATCAACAATGGTAAACTATCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
374274 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
374292 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:378386 original size:19 final size:19
Alignment explanation
Indices: 378362--378401 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
378352 TGTACAATAA
*
378362 CTGTATACTTGAATAGTAC
1 CTGTATACGTGAATAGTAC
378381 CTGTATACGTGAATAGTAC
1 CTGTATACGTGAATAGTAC
378400 CT
1 CT
378402 CGACAACCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (19 bp):
CTGTATACGTGAATAGTAC
Found at i:378736 original size:34 final size:33
Alignment explanation
Indices: 378692--378915 Score: 236
Period size: 34 Copynumber: 6.6 Consensus size: 33
378682 AGGTTTGATA
*
378692 AAATCCACCATTTAATCAACAATGGCAACCTACC
1 AAAT-CACCATTTAATCAACAATGGTAACCTACC
*
378726 AAATCTACCATTTAGTCAACAATGGTAAGCC-ACC
1 AAATC-ACCATTTAATCAACAATGGTAA-CCTACC
* *
378760 AAATCACCCATTTAATCAATAATGGTAAACTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
** *
378794 AAATTTCTCATTTAATCAACAATGGTAAGCTACC
1 AAATCAC-CATTTAATCAACAATGGTAACCTACC
* * *
378828 AAATCTCCCATTTAGTCAACAATGGCAAACC-ACC
1 AAATC-ACCATTTAATCAACAATGG-TAACCTACC
* **
378862 AAATCACCCATTTAATCAACAATAGTAAATTACC
1 AAATCA-CCATTTAATCAACAATGGTAACCTACC
*
378896 AAATCATCATTTAATCAACA
1 AAATCACCATTTAATCAACA
378916 GAATAAAAAC
Statistics
Matches: 160, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
33 19 0.12
34 135 0.84
35 6 0.04
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (33 bp):
AAATCACCATTTAATCAACAATGGTAACCTACC
Found at i:378806 original size:68 final size:67
Alignment explanation
Indices: 378699--378915 Score: 274
Period size: 68 Copynumber: 3.2 Consensus size: 67
378689 ATAAAATCCA
* * *
378699 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
378764 CAC
65 CAC
* * *
378767 CCATTTAATCAATAATGGTAAACTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
378832 CTC
65 CAC
* * * * **
378835 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATAGTAAATTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
378900 CA-
65 CAC
*
378902 TCATTTAATCAACA
1 CCATTTAATCAACA
378916 GAATAAAAAC
Statistics
Matches: 128, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
67 14 0.11
68 113 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.26
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:378876 original size:102 final size:101
Alignment explanation
Indices: 378700--378915 Score: 335
Period size: 102 Copynumber: 2.1 Consensus size: 101
378690 TAAAATCCAC
* *
378700 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
* *
378765 ACCCATTTAATCAATAATGGTAAACTACCAAATTTC-T
66 ACCCATTTAATCAACAATAGTAAACTACCAAA--TCAT
* * *
378802 CATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
*
378867 ACCCATTTAATCAACAATAGTAAATTACCAAATCAT
66 ACCCATTTAATCAACAATAGTAAACTACCAAATCAT
378903 CATTTAATCAACA
1 CATTTAATCAACA
378916 GAATAAAAAC
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
100 2 0.02
101 14 0.13
102 89 0.85
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAAATC
ACCCATTTAATCAACAATAGTAAACTACCAAATCAT
Found at i:380445 original size:19 final size:19
Alignment explanation
Indices: 380403--380445 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
380393 TTAAAAAAAT
* *
380403 TTTAAATTTTTTATTTAGA
1 TTTAAATTATTTATTTAAA
380422 TTTAAATTATTT-TTTAAA
1 TTTAAATTATTTATTTAAA
380440 TATTAA
1 T-TTAA
380446 TAGAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTAAATTATTTATTTAAA
Found at i:382123 original size:13 final size:13
Alignment explanation
Indices: 382105--382129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
382095 AATATTAAAC
382105 ATATTTATATTTG
1 ATATTTATATTTG
382118 ATATTTATATTT
1 ATATTTATATTT
382130 AAATTTAAAT
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:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:386091 original size:11 final size:11
Alignment explanation
Indices: 386075--386100 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
386065 TTTATTTCAA
386075 AAAATTAAAAT
1 AAAATTAAAAT
386086 AAAATTAAAAT
1 AAAATTAAAAT
386097 AAAA
1 AAAA
386101 ATAATTACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:386617 original size:14 final size:14
Alignment explanation
Indices: 386600--386627 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
386590 TTTTTTAATT
386600 TTAAATATATTTTA
1 TTAAATATATTTTA
386614 TTAAATATATTTTA
1 TTAAATATATTTTA
386628 AATATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATATATTTTA
Found at i:386655 original size:22 final size:23
Alignment explanation
Indices: 386606--386660 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
386596 AATTTTAAAT
* *
386606 ATATTTTATTAAATATATTTTAA
1 ATATTTAATTAAATATACTTTAA
386629 ATA-TTAATTAAAT-TACTTTAA
1 ATATTTAATTAAATATACTTTAA
*
386650 TTTATTTAATT
1 -ATATTTAATT
386661 TTATATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.26
22 11 0.41
23 9 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTAATTAAATATACTTTAA
Found at i:386778 original size:28 final size:28
Alignment explanation
Indices: 386735--386789 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
386725 ATTTAAATTA
*
386735 AATTAAATCAAATTTAATCAATTTTTTT
1 AATTAAATCAAATTTAATCAACTTTTTT
* *
386763 AATTAAATTAATTTTAATCAACTTTTT
1 AATTAAATCAAATTTAATCAACTTTTT
386790 ATCTCCCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTAAATCAAATTTAATCAACTTTTTT
Found at i:387394 original size:18 final size:17
Alignment explanation
Indices: 387352--387397 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
387342 ATAAAATTAC
387352 ATATTATTTTTATAATA
1 ATATTATTTTTATAATA
* *
387369 ATATTTATTTTTTTATTCA
1 ATA-TTATTTTTATAAT-A
387388 ATATTATTTT
1 ATATTATTTT
387398 GTGGGGGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
ATATTATTTTTATAATA
Found at i:387729 original size:16 final size:16
Alignment explanation
Indices: 387704--387740 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
387694 TTTAAATTAA
387704 ATAA-TATATAATTT-T
1 ATAATTATAT-ATTTAT
387719 ATAATTATATATTTAT
1 ATAATTATATATTTAT
387735 ATAATT
1 ATAATT
387741 TTTACCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATAATTATATATTTAT
Found at i:387740 original size:24 final size:22
Alignment explanation
Indices: 387690--387742 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
387680 TAATTTAATT
387690 TAATTTTAAATTAAATAATATA
1 TAATTTTAAATTAAATAATATA
* *
387712 TAATTTTATAATTATATATTTATA
1 TAATTTTA-AATTAAATA-ATATA
387736 TAATTTT
1 TAATTTT
387743 TACCATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 8 0.30
23 8 0.30
24 11 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTTTAAATTAAATAATATA
Found at i:388063 original size:15 final size:15
Alignment explanation
Indices: 388045--388102 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 15
388035 ATATTCAAAT
388045 ATATTTTAAATATAA
1 ATATTTTAAATATAA
*
388060 ATA--TTAAACATAA
1 ATATTTTAAATATAA
388073 ATATTTTAAAAATATAA
1 ATATTTT--AAATATAA
* *
388090 AAAATTTAAATAT
1 ATATTTTAAATAT
388103 TTTTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 12 0.34
15 11 0.31
17 12 0.34
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATATTTTAAATATAA
Found at i:388360 original size:31 final size:29
Alignment explanation
Indices: 388261--388363 Score: 109
Period size: 30 Copynumber: 3.4 Consensus size: 29
388251 GAAAAAATAA
* * *
388261 AAAATTAATTTTGGTATAAATTTAAAATT
1 AAAATTTATTTTGATATAAATTAAAAATT
*
388290 AATAACTTATTTTGATAATAAATT-AAAATT
1 AA-AATTTATTTTGAT-ATAAATTAAAAATT
*
388320 AAAATTTTATATTGATACTAAATTAAAAATAT
1 AAAA-TTTATTTTGATA-TAAATTAAAAAT-T
388352 AAAATTTATTTT
1 AAAATTTATTTT
388364 AACCTCCATA
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
29 5 0.08
30 33 0.53
31 19 0.31
32 5 0.08
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (29 bp):
AAAATTTATTTTGATATAAATTAAAAATT
Found at i:388551 original size:16 final size:16
Alignment explanation
Indices: 388530--388581 Score: 63
Period size: 15 Copynumber: 3.3 Consensus size: 16
388520 TCTACGAAAT
388530 AATTATATAATAAAAA
1 AATTATATAATAAAAA
388546 AATTATATAAT-AAAA
1 AATTATATAATAAAAA
* *
388561 TATAATATAA-AAAAA
1 AATTATATAATAAAAA
388576 TAATTA
1 -AATTA
388582 AAATTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 16 0.53
16 14 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATTATATAATAAAAA
Found at i:388564 original size:26 final size:25
Alignment explanation
Indices: 388534--388603 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 25
388524 CGAAATAATT
388534 ATATAATAAAAAAATTATATAATAAA
1 ATATAATAAAAAAATTATA-AATAAA
*
388560 ATATAATATAAAAAA--ATAATTAAA
1 ATATAATA-AAAAAATTATAAATAAA
*
388584 ATTTAAATAATAAAAATTAT
1 ATAT-AATAA-AAAAATTAT
388604 TAACATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
24 9 0.24
25 12 0.32
26 8 0.22
27 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAATAAAAAAATTATAAATAAA
Found at i:388570 original size:28 final size:25
Alignment explanation
Indices: 388533--388603 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 25
388523 ACGAAATAAT
388533 TATATAATAAAAAAATTATATAATAAAA
1 TATA-AATAAAAAAATTATAT--TAAAA
388561 TATAATATAAAAAAA-TA-ATTAAAA
1 TATAA-ATAAAAAAATTATATTAAAA
*
388585 TTTAAATAATAAAAATTAT
1 TATAAATAA-AAAAATTAT
388604 TAACATATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
23 4 0.11
24 14 0.37
25 2 0.05
26 2 0.05
27 3 0.08
28 13 0.34
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (25 bp):
TATAAATAAAAAAATTATATTAAAA
Found at i:388578 original size:13 final size:13
Alignment explanation
Indices: 388539--388584 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
388529 TAATTATATA
*
388539 ATAAAAAAATTAT
1 ATAAAAAAATAAT
388552 ATAATAAAATATAAT
1 ATAA-AAAA-ATAAT
388567 ATAAAAAAATAAT
1 ATAAAAAAATAAT
388580 -TAAAA
1 ATAAAA
388585 TTTAAATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 9 0.30
14 8 0.27
15 8 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
ATAAAAAAATAAT
Found at i:388598 original size:24 final size:24
Alignment explanation
Indices: 388534--388611 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
388524 CGAAATAATT
*
388534 ATATAATA-AAAAAATTATATAATAAA
1 ATATAATATAAAAAA--ATA-ATTAAA
388560 ATATAATATAAAAAAATAATTAAA
1 ATATAATATAAAAAAATAATTAAA
* * *
388584 ATTTAA-ATAATAAAAATTATTAAC
1 ATATAATATAA-AAAAATAATTAAA
388608 ATAT
1 ATAT
388612 TATAATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 4 0.09
24 24 0.53
25 3 0.07
26 8 0.18
27 6 0.13
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATAATATAAAAAAATAATTAAA
Found at i:388808 original size:29 final size:28
Alignment explanation
Indices: 388762--388816 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
388752 TTATATTATC
*
388762 ATAAATAAAATATATTTTTAAATTTTTTT
1 ATAAATAAAATA-ATTTTTAAAGTTTTTT
* * *
388791 ATAATTAATATATTTTTTAAAGTTTT
1 ATAAATAAAATAATTTTTAAAGTTTT
388817 GTATGTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 12 0.55
29 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATAAATAAAATAATTTTTAAAGTTTTTT
Found at i:388979 original size:26 final size:27
Alignment explanation
Indices: 388950--389002 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 27
388940 ATCTGACTCA
*
388950 AAAAATTATTATTA-TTT-ATTATATTT
1 AAAAATT-TTATCATTTTAATTATATTT
388976 -AAAATTTTATCATTTTAATTATATTT
1 AAAAATTTTATCATTTTAATTATATTT
389002 A
1 A
389003 TTAATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
24 5 0.22
25 9 0.39
26 9 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
AAAAATTTTATCATTTTAATTATATTT
Found at i:389359 original size:21 final size:18
Alignment explanation
Indices: 389334--389383 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
389324 CTCATTATAG
389334 ATTTATATTATATGAGATAT
1 ATTTATATTATAT-A-ATAT
389354 ATTT-TATTATATAATAT
1 ATTTATATTATATAATAT
389371 ATCTTAT-TTATAT
1 AT-TTATATTATAT
389384 TCTATATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.21
18 9 0.32
19 9 0.32
20 4 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTATATTATATAATAT
Found at i:389452 original size:20 final size:20
Alignment explanation
Indices: 389423--389465 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
389413 AAATATTTAT
389423 ATTTTATATACA-ATTATATA
1 ATTTTATATACATATTAT-TA
* *
389443 ATTTTTTATATATATTATTA
1 ATTTTATATACATATTATTA
389463 ATT
1 ATT
389466 ATATTATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTATATACATATTATTA
Found at i:389717 original size:31 final size:31
Alignment explanation
Indices: 389662--389756 Score: 118
Period size: 32 Copynumber: 3.0 Consensus size: 31
389652 ATTTAATTAC
389662 TTTAAAATTAAAAATATTAATCATAAATTTAA
1 TTTAAAATTAAAAATA-TAATCATAAATTTAA
*
389694 TTTAAAATTAAAAATATAATCATAAATTTAC
1 TTTAAAATTAAAAATATAATCATAAATTTAA
* * * * *
389725 TTCAATATTGAAAATTATAATAATAAAATTAA
1 TTTAAAATT-AAAAATATAATCATAAATTTAA
389757 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
31 21 0.38
32 34 0.62
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (31 bp):
TTTAAAATTAAAAATATAATCATAAATTTAA
Found at i:390148 original size:43 final size:48
Alignment explanation
Indices: 390095--390188 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 48
390085 ATTCATATTT
390095 TTATAATTCATGATATA-AAA-ATTAATATA-TT-TATAA-ATTTATA
1 TTATAATTCATGATATATAAATATTAATATATTTATATAATATTTATA
* * * *
390138 TTATAGTTCATTATATATAAATTTTTATATATTTATATAATATTTATA
1 TTATAATTCATGATATATAAATATTAATATATTTATATAATATTTATA
390186 TTA
1 TTA
390189 ATTATTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 15 0.36
44 3 0.07
45 7 0.17
46 2 0.05
47 5 0.12
48 10 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (48 bp):
TTATAATTCATGATATATAAATATTAATATATTTATATAATATTTATA
Found at i:390166 original size:10 final size:11
Alignment explanation
Indices: 390153--390230 Score: 70
Period size: 11 Copynumber: 7.0 Consensus size: 11
390143 GTTCATTATA
390153 TATAA-ATTTT
1 TATAATATTTT
*
390163 TAT-ATATTTA
1 TATAATATTTT
*
390173 TATAATATTTA
1 TATAATATTTT
390184 TATTAATTATTTT
1 TA-TAA-TATTTT
390197 TATAATATTTT
1 TATAATATTTT
*
390208 ATATTATATTTT
1 -TATAATATTTT
* *
390220 AATTATATTTT
1 TATAATATTTT
390231 ATTTTATAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
9 1 0.02
10 10 0.17
11 25 0.42
12 16 0.27
13 7 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATAATATTTT
Found at i:390166 original size:37 final size:33
Alignment explanation
Indices: 390115--390250 Score: 106
Period size: 37 Copynumber: 4.0 Consensus size: 33
390105 TGATATAAAA
*
390115 ATTAATATATTTATAAATTTATATTATAGTTCATTAT
1 ATTAATATTTTTATAAATTTATATTATA--T--TTAT
* *
390152 ATATAA-ATTTTTATATATTTATATAATATTTAT
1 AT-TAATATTTTTATAAATTTATATTATATTTAT
390185 ATTAATTATTTTTATAATATTTTATATTATATTT-T
1 ATTAA-TATTTTTATAA-A-TTTATATTATATTTAT
390220 AATT-ATA-TTTTAT---TTTATAATTATATTTAT
1 -ATTAATATTTTTATAAATTTAT-ATTATATTTAT
390250 A
1 A
390251 CGATATAATC
Statistics
Matches: 86, Mismatches: 5, Indels: 24
0.75 0.04 0.21
Matches are distributed among these distances:
28 5 0.06
29 10 0.12
30 1 0.01
32 3 0.03
33 12 0.14
34 11 0.13
35 4 0.05
36 16 0.19
37 21 0.24
38 3 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.60
Consensus pattern (33 bp):
ATTAATATTTTTATAAATTTATATTATATTTAT
Found at i:390193 original size:20 final size:20
Alignment explanation
Indices: 390151--390193 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
390141 TAGTTCATTA
* *
390151 TATATAAATTTTTATATATT
1 TATATAAATTTATATATAAT
390171 TATATAATATTTATAT-TAAT
1 TATATAA-ATTTATATATAAT
390191 TAT
1 TAT
390194 TTTTATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATATAAATTTATATATAAT
Found at i:390225 original size:16 final size:18
Alignment explanation
Indices: 390160--390246 Score: 60
Period size: 16 Copynumber: 4.8 Consensus size: 18
390150 ATATATAAAT
*
390160 TTTTATATATTTATATAATA
1 TTTTATA-A-TTATATTATA
390180 -TTTAT-ATTA-ATTAT-
1 TTTTATAATTATATTATA
390194 TTTTATAATATTTTATATTATA
1 TTTTAT-A-A--TTATATTATA
*
390216 -TTT-TAATTATATTTTA
1 TTTTATAATTATATTATA
390232 TTTTATAATTATATT
1 TTTTATAATTATATT
390247 TATACGATAT
Statistics
Matches: 55, Mismatches: 2, Indels: 22
0.70 0.03 0.28
Matches are distributed among these distances:
15 9 0.16
16 12 0.22
17 4 0.07
18 12 0.22
19 6 0.11
20 4 0.07
21 8 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATAATTATATTATA
Found at i:390227 original size:23 final size:23
Alignment explanation
Indices: 390162--390238 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 23
390152 ATATAAATTT
390162 TTATATATTTATATAATA-TTTATA
1 TTATAT-TTTA-ATAATATTTTATA
*
390186 TTAATTATTTTTATAATATTTTATA
1 TT-A-TATTTTAATAATATTTTATA
* *
390211 TTATATTTTAATTATATTTTATT
1 TTATATTTTAATAATATTTTATA
390234 TTATA
1 TTATA
390239 ATTATATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 22 0.48
24 9 0.20
25 12 0.26
26 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATATTTTAATAATATTTTATA
Found at i:390240 original size:18 final size:16
Alignment explanation
Indices: 390206--390247 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 16
390196 TTATAATATT
*
390206 TTATATTATATTTTAA
1 TTATATTTTATTTTAA
390222 TTATATTTTATTTTATAA
1 TTATATTTTA-TTT-TAA
390240 TTATATTT
1 TTATATTT
390248 ATACGATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 9 0.39
17 3 0.13
18 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTTTATTTTAA
Found at i:390733 original size:16 final size:17
Alignment explanation
Indices: 390685--390740 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
390675 ATTGATTTGG
*
390685 TATTGATTT-AAATTAT
1 TATTTATTTAAAATTAT
390701 TATTTATGTAATAAAATTAT
1 TATTTAT-T--TAAAATTAT
390721 T-TTTATTTAAAATTAAT
1 TATTTATTTAAAATT-AT
390738 TAT
1 TAT
390741 AAAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 13 0.39
17 4 0.12
18 2 0.06
19 6 0.18
20 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
TATTTATTTAAAATTAT
Found at i:391637 original size:12 final size:12
Alignment explanation
Indices: 391620--391657 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
391610 GATTAAAAAT
*
391620 TTTATTTTATTA
1 TTTATTATATTA
391632 TTTATTATATTA
1 TTTATTATATTA
*
391644 -TTAATATATTA
1 TTTATTATATTA
391655 TTT
1 TTT
391658 TATAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTATATTA
Found at i:392888 original size:11 final size:11
Alignment explanation
Indices: 392872--393018 Score: 88
Period size: 11 Copynumber: 13.0 Consensus size: 11
392862 AAATAATTTA
392872 TATATTTATAT
1 TATATTTATAT
*
392883 TATATTTTTA-
1 TATATTTATAT
*
392893 TATTTTTATAT
1 TATATTTATAT
*
392904 TATAATTATATT
1 TATATTTATA-T
* * *
392916 TAAAATAAT-T
1 TATATTTATAT
392926 TATATTTATATAT
1 TATA-TT-TATAT
392939 TAATAATTTATAT
1 T-AT-ATTTATAT
** *
392952 TATATAAATTT
1 TATATTTATAT
*
392963 TAAAATATT-T-T
1 T-ATAT-TTATAT
392974 TATATTTATAT
1 TATATTTATAT
392985 TATATTTATAT
1 TATATTTATAT
392996 TATA-TTATATT
1 TATATTTATA-T
393007 TATATATTATAT
1 TATAT-TTATAT
393019 AATCATATTA
Statistics
Matches: 105, Mismatches: 17, Indels: 27
0.70 0.11 0.18
Matches are distributed among these distances:
9 2 0.02
10 21 0.20
11 47 0.45
12 17 0.16
13 13 0.12
14 4 0.04
15 1 0.01
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTATAT
Found at i:392928 original size:48 final size:46
Alignment explanation
Indices: 392873--393008 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 46
392863 AATAATTTAT
*
392873 ATATTTATATTATATTTTTATATTTTTATATTATAATTATATTTAAA
1 ATATTTATATTATATTTTTATATATTTATATTAT-ATTATATTTAAA
* * *
392920 ATAATTTATATTTATATATTAATA-ATTTATATTATA-TAAATTTTAAA
1 AT-ATTTATA-TTATATTTTTATATATTTATATTATATTATA-TTTAAA
*
392967 ATA-TT-T-TTATATTTATATTATATTTATATTATATTATATTTA
1 ATATTTATATTATATTTTTA-TATATTTATATTATATTATATTTA
393009 TATATTATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
42 8 0.11
43 2 0.03
44 17 0.23
45 5 0.07
46 4 0.05
47 11 0.15
48 17 0.23
49 11 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (46 bp):
ATATTTATATTATATTTTTATATATTTATATTATATTATATTTAAA
Found at i:392931 original size:35 final size:34
Alignment explanation
Indices: 392889--393017 Score: 118
Period size: 35 Copynumber: 3.6 Consensus size: 34
392879 ATATTATATT
*
392889 TTTATATTTTTATATTATAATTATATTTAAAATAA
1 TTTATATTTATATATTATAATTATATTTAAAAT-A
392924 TTTATATTTATATATTAATAATTTATATTATATAAAT-
1 TTTATATTTATATATT-ATAA-TTATATT-TA-AAATA
* * *
392961 TTTAAAATATTTTTATATT-TATATTATATTTATATTA
1 TTT---ATATTTATATATTATA-ATTATATTTAAAATA
392998 TATTATATTTATATATTATA
1 T-TTATATTTATATATTATA
393018 TAATCATATT
Statistics
Matches: 78, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
35 27 0.35
36 8 0.10
37 13 0.17
38 13 0.17
39 5 0.06
40 12 0.15
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TTTATATTTATATATTATAATTATATTTAAAATA
Found at i:392977 original size:75 final size:75
Alignment explanation
Indices: 392892--393030 Score: 203
Period size: 75 Copynumber: 1.9 Consensus size: 75
392882 TTATATTTTT
*
392892 ATATTTTTATA-TTATAATTATATTTAAAATAAT-TTATATTTATATATTA-ATAATTTATATTA
1 ATATTTTTATATTTAT-ATTATATTT-AAATAATATTATATTTATATATTATATAA-TCATATTA
392954 TATAAATTTTAAA
63 TATAAATTTTAAA
* *
392967 ATATTTTTATATTTATATTATATTTATATTATATTATATTTATATATTATATAATCATATTATA
1 ATATTTTTATATTTATATTATATTTAAATAATATTATATTTATATATTATATAATCATATTATA
393031 GTTAAAATTA
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
74 5 0.09
75 45 0.78
76 8 0.14
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (75 bp):
ATATTTTTATATTTATATTATATTTAAATAATATTATATTTATATATTATATAATCATATTATAT
AAATTTTAAA
Found at i:393484 original size:32 final size:34
Alignment explanation
Indices: 393448--393519 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 34
393438 CATTTTTTAA
393448 TTTTATAAAAAT-AATTAATT-TAATATA-AAAAT
1 TTTTATAAAAATAAATTAATTATAAT-TAGAAAAT
*
393480 TTTTA-AAAAATAAATTTATTATAATTAGAAAAT
1 TTTTATAAAAATAAATTAATTATAATTAGAAAAT
*
393513 ATTTATA
1 TTTTATA
393520 GGCATTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 6 0.18
32 14 0.41
33 13 0.38
34 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (34 bp):
TTTTATAAAAATAAATTAATTATAATTAGAAAAT
Found at i:393485 original size:20 final size:18
Alignment explanation
Indices: 393441--393485 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
393431 ACTGTTACAT
393441 TTTTTAATTTTATAAAAA
1 TTTTTAATTTTATAAAAA
**
393459 TAATTAATTTAATATAAAAA
1 TTTTTAATTT--TATAAAAA
393479 TTTTTAA
1 TTTTTAA
393486 AAAATAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.38
20 13 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTTAATTTTATAAAAA
Found at i:393781 original size:13 final size:14
Alignment explanation
Indices: 393765--393796 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
393755 ATAAAAAGAT
393765 TTTAT-AAATAAAA
1 TTTATAAAATAAAA
393778 TTTATAAAATAAAA
1 TTTATAAAATAAAA
393792 TTTAT
1 TTTAT
393797 TTTATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTATAAAATAAAA
Found at i:393911 original size:32 final size:33
Alignment explanation
Indices: 393873--393951 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 33
393863 ATATAATTCT
393873 TTATATTTTTATAATT-CATTATATATAAATT-
1 TTATATTTTTATAATTACATTATATATAAATTA
* * *
393904 TTAATATTTTTATATATTATATTATATTTATATTA
1 TT-ATATTTTTATA-ATTACATTATATATAAATTA
393939 TT-TATTTTTATAA
1 TTATATTTTTATAA
393952 ATATTTTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 2 0.05
32 12 0.29
33 13 0.32
34 12 0.29
35 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (33 bp):
TTATATTTTTATAATTACATTATATATAAATTA
Found at i:393912 original size:60 final size:59
Alignment explanation
Indices: 393830--393943 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
393820 AATTTATTTT
* * *
393830 ATTATATATATATGTCATTATTTTTAATATATAATATAATTCTTTATATT-TTTATAATTC
1 ATTATATATAAATGTCAATATTTTT-ATATATAATATAA-TATTTATATTATTTATAATTC
* * * *
393890 ATTATATATAAATTTTAATATTTTTATATATTATATTATATTTATATTATTTAT
1 ATTATATATAAATGTCAATATTTTTATATATAATATAATATTTATATTATTTAT
393944 TTTTATAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 9 0.20
59 16 0.35
60 21 0.46
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.59
Consensus pattern (59 bp):
ATTATATATAAATGTCAATATTTTTATATATAATATAATATTTATATTATTTATAATTC
Found at i:393944 original size:18 final size:18
Alignment explanation
Indices: 393873--393944 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
393863 ATATAATTCT
* * *
393873 TTATATTTTTATAATTCA
1 TTATATTTATATTATTTA
* *
393891 TTATATATA-AAT-TTTA
1 TTATATTTATATTATTTA
* *
393907 ATATTTTTATA-TATTATA
1 TTATATTTATATTATT-TA
393925 TTATATTTATATTATTTA
1 TTATATTTATATTATTTA
393943 TT
1 TT
393945 TTTATAAATA
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
16 10 0.25
17 4 0.10
18 22 0.55
19 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATATTTATATTATTTA
Found at i:395045 original size:12 final size:12
Alignment explanation
Indices: 395025--395053 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
395015 TTTTCATAAT
395025 TAAAA-TTTAAA
1 TAAAATTTTAAA
395036 TAAAATTTTAAA
1 TAAAATTTTAAA
395048 TAAAAT
1 TAAAAT
395054 AAAATAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAAATTTTAAA
Found at i:396271 original size:42 final size:42
Alignment explanation
Indices: 396174--396266 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
396164 ATTTTGCTAA
* *
396174 AAATTT-TTATAAAATTTTTAATTAAATAACATTATAATTATT
1 AAATTTATTATAAAATATTTAATTAAATAACATTAAAATTA-T
396216 AAATTTATT-TAAAATATTTAA-TAAATAA-ATTAAAATTA-
1 AAATTTATTATAAAATATTTAATTAAATAACATTAAAATTAT
396254 AAATTTAATTATA
1 AAATTT-ATTATA
396267 TAAAAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
38 6 0.13
39 3 0.07
40 11 0.24
41 7 0.15
42 17 0.37
43 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (42 bp):
AAATTTATTATAAAATATTTAATTAAATAACATTAAAATTAT
Found at i:396287 original size:7 final size:7
Alignment explanation
Indices: 396275--396357 Score: 57
Period size: 7 Copynumber: 12.3 Consensus size: 7
396265 TATAAAAATT
396275 ATATAAA
1 ATATAAA
396282 ATATAAA
1 ATATAAA
**
396289 ATACTTCA
1 ATA-TAAA
* *
396297 AGATATA
1 ATATAAA
*
396304 ATATAAT
1 ATATAAA
*
396311 ATATAAT
1 ATATAAA
396318 AT-TAAA
1 ATATAAA
*
396324 ATATTAA
1 ATATAAA
396331 A-ATAAA
1 ATATAAA
*
396337 ATAT-AT
1 ATATAAA
396343 ATA-AAA
1 ATATAAA
396349 ATATAAA
1 ATATAAA
396356 AT
1 AT
396358 TTTATAAATA
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
6 18 0.31
7 36 0.62
8 4 0.07
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (7 bp):
ATATAAA
Found at i:396375 original size:35 final size:35
Alignment explanation
Indices: 396274--396386 Score: 103
Period size: 35 Copynumber: 3.3 Consensus size: 35
396264 ATATAAAAAT
* * *
396274 TATAT-AAAATATAAAATACT-TCAAGATATAATA
1 TATATAAAAATATAAAATATTATAAATATATAATA
*
396307 TA-ATATATAATATTAAAATATTA-AAATA-A-AATA
1 TATATA-AAAATA-TAAAATATTATAAATATATAATA
*
396340 TATATAAAAATATAAAATTTTATAAATATATAATA
1 TATATAAAAATATAAAATATTATAAATATATAATA
* *
396375 TTTATTAAAATA
1 TATATAAAAATA
396387 AATTATTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
32 11 0.17
33 18 0.28
34 10 0.16
35 25 0.39
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (35 bp):
TATATAAAAATATAAAATATTATAAATATATAATA
Found at i:396393 original size:17 final size:17
Alignment explanation
Indices: 396325--396404 Score: 65
Period size: 17 Copynumber: 4.6 Consensus size: 17
396315 AATATTAAAA
* *
396325 TATTAAAATAAAATATA
1 TATTAAAATATAATATT
* *
396342 TATAAAAATATAAAATT
1 TATTAAAATATAATATT
396359 T-TATAAATATATAATATT
1 TAT-TAAA-ATATAATATT
396377 TATTAAAATA-AATTATT
1 TATTAAAATATAA-TATT
* *
396394 AATTTAAATAT
1 TATTAAAATAT
396405 TTAATAAATT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
16 3 0.06
17 32 0.64
18 14 0.28
19 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATTAAAATATAATATT
Found at i:396423 original size:18 final size:18
Alignment explanation
Indices: 396350--396424 Score: 56
Period size: 18 Copynumber: 4.6 Consensus size: 18
396340 TATATAAAAA
* * *
396350 TATAAAATTTTATAAATA
1 TATAATATTTAATAAATT
*
396368 TATAATATTTATTAAA--
1 TATAATATTTAATAAATT
*
396384 -ATAA-A-TT-ATTAATT
1 TATAATATTTAATAAATT
396398 TA-AATATTTAATAAATT
1 TATAATATTTAATAAATT
396415 TATAATATTT
1 TATAATATTT
396425 TGTACAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
12 3 0.07
13 2 0.05
14 3 0.07
15 6 0.14
16 2 0.05
17 8 0.18
18 20 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATATTTAATAAATT
Found at i:397276 original size:17 final size:17
Alignment explanation
Indices: 397239--397286 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
397229 GAATACATGA
397239 ATTTTTTTCTC--TTTT
1 ATTTTTTTCTCATTTTT
*
397254 -TCTTTTTCTCATTTTT
1 ATTTTTTTCTCATTTTT
397270 ATTTTTTTCTCATTTTT
1 ATTTTTTTCTCATTTTT
397287 TTCTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.32
16 4 0.14
17 15 0.54
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTTTTCTCATTTTT
Found at i:397293 original size:17 final size:17
Alignment explanation
Indices: 397250--397294 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 17
397240 TTTTTTTCTC
397250 TTTTTCTTTTTCTCATT
1 TTTTTCTTTTTCTCATT
397267 TTTATT-TTTTTCTCATT
1 TTT-TTCTTTTTCTCATT
397284 TTTTTCTTTTT
1 TTTTTCTTTTT
397295 TTTAGCCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTCTTTTTCTCATT
Found at i:397295 original size:8 final size:8
Alignment explanation
Indices: 397240--397296 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
397230 AATACATGAA
397240 TTTTTTTC
1 TTTTTTTC
*
397248 TCTTTTTC
1 TTTTTTTC
*
397256 TTTTTCTC
1 TTTTTTTC
397264 ATTTTTATT-
1 -TTTTT-TTC
*
397273 TTTTTCTC
1 TTTTTTTC
397281 ATTTTTTTC
1 -TTTTTTTC
397290 TTTTTTT
1 TTTTTTT
397297 TAGCCATGCC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
7 1 0.03
8 25 0.64
9 12 0.31
10 1 0.03
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTTC
Found at i:397949 original size:9 final size:9
Alignment explanation
Indices: 397935--398017 Score: 52
Period size: 9 Copynumber: 9.7 Consensus size: 9
397925 ACGAATATAT
397935 ATATATAAA
1 ATATATAAA
397944 ATATATAAA
1 ATATATAAA
397953 A-A-ATAAA
1 ATATATAAA
* *
397960 ATAAATTATTA
1 ATATA-TA-AA
397971 ATATATAAA
1 ATATATAAA
397980 A-A-ATAAA
1 ATATATAAA
* * *
397987 ATGTCTTAA
1 ATATATAAA
*
397996 ATATAAAAA
1 ATATATAAA
398005 ATA-ATAAA
1 ATATATAAA
398013 A-ATAT
1 ATATAT
398018 GAATCCATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 15
0.68 0.13 0.18
Matches are distributed among these distances:
7 13 0.23
8 10 0.18
9 24 0.43
10 4 0.07
11 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
ATATATAAA
Found at i:397981 original size:21 final size:23
Alignment explanation
Indices: 397946--398008 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 23
397936 TATATAAAAT
*
397946 ATATAAAAAATAAAATAAATTATTAA
1 ATATAAAAAATAAAAT---GTATTAA
*
397972 TATATAAAAAATAAAATGTCTTAA
1 -ATATAAAAAATAAAATGTATTAA
397996 ATATAAAAAATAA
1 ATATAAAAAATAA
398009 TAAAAATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 13 0.38
24 5 0.15
27 16 0.47
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
ATATAAAAAATAAAATGTATTAA
Found at i:397985 original size:22 final size:22
Alignment explanation
Indices: 397957--398008 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
397947 TATAAAAAAT
397957 AAAATAAAT-TATTAATATATAA
1 AAAATAAATGTATTAA-ATATAA
*
397979 AAAATAAAATGTCTTAAATATAA
1 AAAAT-AAATGTATTAAATATAA
398002 AAAATAA
1 AAAATAA
398009 TAAAAATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 15 0.56
24 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAATAAATGTATTAAATATAA
Found at i:398014 original size:27 final size:25
Alignment explanation
Indices: 397946--398015 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
397936 TATATAAAAT
397946 ATATAAAAAATAA-AATAAATTATTA
1 ATATAAAAAATAATAA-AAATTATTA
* *
397971 ATATATAAAA-AAT-AAAATGTCTTAA
1 ATATAAAAAATAATAAAAAT-TATT-A
397996 ATATAAAAAATAATAAAAAT
1 ATATAAAAAATAATAAAAAT
398016 ATGAATCCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
23 4 0.11
24 6 0.16
25 19 0.51
26 3 0.08
27 5 0.14
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
ATATAAAAAATAATAAAAATTATTA
Found at i:398311 original size:17 final size:17
Alignment explanation
Indices: 398268--398315 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
398258 GTTAATTTTG
398268 ATTTGAATTTAA--AAA
1 ATTTGAATTTAATTAAA
*
398283 ATTTGATTATTTAATTTAA
1 ATTTGA--ATTTAATTAAA
398302 ATTTGAATTTAATT
1 ATTTGAATTTAATT
398316 CAATTTGAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
17 14 0.50
19 8 0.29
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (17 bp):
ATTTGAATTTAATTAAA
Found at i:398395 original size:16 final size:16
Alignment explanation
Indices: 398371--398430 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
398361 TTAAACCCGA
*
398371 AAATGATCTAAACACG
1 AAATAATCTAAACACG
* *
398387 AAATAATCTGAACTCG
1 AAATAATCTAAACACG
* *
398403 AAATAA-CTCAAACCCA
1 AAATAATCT-AAACACG
*
398419 AAATGATCTAAA
1 AAATAATCTAAA
398431 TCTGAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
15 2 0.06
16 31 0.89
17 2 0.06
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (16 bp):
AAATAATCTAAACACG
Found at i:398951 original size:297 final size:296
Alignment explanation
Indices: 398418--398994 Score: 1100
Period size: 297 Copynumber: 1.9 Consensus size: 296
398408 ACTCAAACCC
*
398418 AAAATGATCTAAATCTGAAATAACTAGAACAATTAACTCAAAATAACCCAAACTTAAATTTAAGT
1 AAAATGATCTAAATCTGAAATAACTAGAACAATTAACCCAAAATAACCCAAACTTAAATTTAAGT
398483 ATCATTTTATTTAAAAATATTAAGTTAATAAAAATAATAATTATAAATTATAACATAAATTATTA
66 ATCATTTTATTTAAAAATATTAAGTTAATAAAAATAATAATTATAAATTATAACATAAATTATTA
*
398548 ATTTATTTTATTTCACTATTTATAATTATATTAGATTATGATAAAGTATGCAAATAGCATTTGGT
131 ATTTATTTTATTTCACTATTTATAATTATATTAGATTATGATAAAGCATGCAAATAGCATTTGGT
398613 ATACATAAATTAATTATATTTCTATTTTTGTTCTCTTATTTTTATGTAAAATAATGTAATAATTA
196 ATACATAAATTAATTATATTTCTATTTTTGTTCTCTTATTTTTATGTAAAATAATGTAATAATTA
398678 TATATGTGCTTATTATAACATAAATTGGTATACATA
261 TATATGTGCTTATTATAACATAAATTGGTATACATA
* *
398714 AAAATGATCTAAATCTGAAATAATTAGAACAATTAACCCAAAATGACCCAAACTTAAATTTAAGT
1 AAAATGATCTAAATCTGAAATAACTAGAACAATTAACCCAAAATAACCCAAACTTAAATTTAAGT
398779 ATCATTTTATTTAAAAAATATTAAGTTAATAAAAATAATAATTATAAATTATAACATAAATTATT
66 ATCATTTTATTT-AAAAATATTAAGTTAATAAAAATAATAATTATAAATTATAACATAAATTATT
398844 AATTTATTTTATTTCACTATTTATAATTATATTAGATTATGATAAAGCATGCAAATAGCATTTGG
130 AATTTATTTTATTTCACTATTTATAATTATATTAGATTATGATAAAGCATGCAAATAGCATTTGG
*
398909 TATACATAAATTGATTATATTTCTATTTTTGTTCTCTTATTTTTATGTAAAATAATGTAATAATT
195 TATACATAAATTAATTATATTTCTATTTTTGTTCTCTTATTTTTATGTAAAATAATGTAATAATT
398974 ATATATGTGCTTATTATAACA
260 ATATATGTGCTTATTATAACA
398995 ATTTTAAATT
Statistics
Matches: 275, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
296 74 0.27
297 201 0.73
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.42
Consensus pattern (296 bp):
AAAATGATCTAAATCTGAAATAACTAGAACAATTAACCCAAAATAACCCAAACTTAAATTTAAGT
ATCATTTTATTTAAAAATATTAAGTTAATAAAAATAATAATTATAAATTATAACATAAATTATTA
ATTTATTTTATTTCACTATTTATAATTATATTAGATTATGATAAAGCATGCAAATAGCATTTGGT
ATACATAAATTAATTATATTTCTATTTTTGTTCTCTTATTTTTATGTAAAATAATGTAATAATTA
TATATGTGCTTATTATAACATAAATTGGTATACATA
Found at i:399909 original size:27 final size:27
Alignment explanation
Indices: 399872--399952 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
399862 ATATACGATA
**
399872 ATTTATATATTTATATCATATTTATTAT
1 ATTT-TATATTTATATCATATTTAAAAT
* *
399900 ATTTTTTA-TTATAATTATATTTAAAAT
1 ATTTTATATTTAT-ATCATATTTAAAAT
* *
399927 ATTTTATATTTATATTATAATTAAAA
1 ATTTTATATTTATATCATATTTAAAA
399953 AAAATTTACT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.09
27 33 0.73
28 8 0.18
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (27 bp):
ATTTTATATTTATATCATATTTAAAAT
Found at i:400409 original size:5 final size:5
Alignment explanation
Indices: 400399--400462 Score: 73
Period size: 5 Copynumber: 13.4 Consensus size: 5
400389 CATTTATTTT
* *
400399 TTATA TTATA TTTTA TTATA TTATTT TTATA TTATA TT-TA -TATA TTATA
1 TTATA TTATA TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA
400448 -TA-A TTATA TTATA TT
1 TTATA TTATA TTATA TT
400463 TAAAATTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
3 2 0.04
4 8 0.16
5 36 0.72
6 4 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:400423 original size:13 final size:13
Alignment explanation
Indices: 400392--400464 Score: 64
Period size: 13 Copynumber: 5.6 Consensus size: 13
400382 TCGGCCTCAT
400392 TTATTTT-TTATA
1 TTATTTTATTATA
400404 TTATATTTTATTATA
1 -T-TATTTTATTATA
400419 TTA-TTT-TTATA
1 TTATTTTATTATA
400430 TTATATTTA-TATA
1 TTAT-TTTATTATA
* *
400443 TTATATAATTATA
1 TTATTTTATTATA
400456 TTATATTTA
1 TTAT-TTTA
400465 AAATTACTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
11 8 0.16
12 5 0.10
13 22 0.45
14 9 0.18
15 5 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTTTATTATA
Found at i:400429 original size:26 final size:25
Alignment explanation
Indices: 400396--400463 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 25
400386 CCTCATTTAT
400396 TTTTTATATTATATTTTATTATATTA
1 TTTTTATATTATATTTTA-TATATTA
400422 TTTTTATATTATA-TTTATATATTA
1 TTTTTATATTATATTTTATATATTA
*
400446 TATAATTATATTATATTT
1 T-T-TTTATATTATATTT
400464 AAAATTACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
24 8 0.21
25 5 0.13
26 23 0.61
27 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTTATATTATATTTTATATATTA
Found at i:400430 original size:11 final size:11
Alignment explanation
Indices: 400404--400446 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
400394 ATTTTTTATA
*
400404 TTATATT-TTA
1 TTATATTATTT
400414 TTATATTATTT
1 TTATATTATTT
400425 TTATATTATATT
1 TTATATTAT-TT
400437 TATATATTAT
1 T-TATATTAT
400447 ATAATTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 7 0.24
11 11 0.38
12 3 0.10
13 8 0.28
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATATTATTT
Found at i:400442 original size:8 final size:7
Alignment explanation
Indices: 400400--400461 Score: 62
Period size: 7 Copynumber: 9.4 Consensus size: 7
400390 ATTTATTTTT
400400 TATATTA
1 TATATTA
*
400407 TATTTTA
1 TATATTA
400414 TTATATTA
1 -TATATTA
400422 T-T-TT-
1 TATATTA
400426 TATATTA
1 TATATTA
400433 TAT-TTA
1 TATATTA
400439 TATATTA
1 TATATTA
*
400446 TATAAT-
1 TATATTA
400452 TATATTA
1 TATATTA
400459 TAT
1 TAT
400462 TTAAAATTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 14 0.31
7 21 0.47
8 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
TATATTA
Found at i:400704 original size:31 final size:32
Alignment explanation
Indices: 400654--400713 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
400644 TTACTTACTT
400654 TAAAATATAAAATATTAATCATAAATTTAGTC
1 TAAAATATAAAATATTAATCATAAATTTAGTC
400686 TAAAAT-TAAAA-ATATAATCATAAATTTA
1 TAAAATATAAAATAT-TAATCATAAATTTA
400714 CTCTGATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 2 0.07
31 19 0.70
32 6 0.22
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.37
Consensus pattern (32 bp):
TAAAATATAAAATATTAATCATAAATTTAGTC
Found at i:400763 original size:16 final size:15
Alignment explanation
Indices: 400724--400765 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
400714 CTCTGATATT
400724 ATTAAAAATTATAATA
1 ATTAAAAATTA-AATA
400740 A-T-AAAATTAAATTA
1 ATTAAAAATTAAA-TA
400754 ATTAAAAATTAA
1 ATTAAAAATTAA
400766 TAAATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 10 0.43
15 2 0.09
16 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATTAAAAATTAAATA
Done.