Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 113 of 163
Found at i:31651735 original size:17 final size:18
Alignment explanation
Indices: 31651702--31651746 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
31651692 TTGAACTATT
*
31651702 TCATTGATATGGAAAATG
1 TCATTGAAATGGAAAATG
31651720 TCATTGAAAT-GAAAATG
1 TCATTGAAATGGAAAATG
31651737 -CTATTGAAAT
1 TC-ATTGAAAT
31651747 AGTGAGTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 15 0.60
18 9 0.36
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (18 bp):
TCATTGAAATGGAAAATG
Found at i:31653025 original size:15 final size:13
Alignment explanation
Indices: 31652993--31653029 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
31652983 TCTTTGGTGA
31652993 ACTCTCTTTCATT
1 ACTCTCTTTCATT
31653006 ACTCTCTTTCATT
1 ACTCTCTTTCATT
**
31653019 GTTCTCTTTCA
1 ACTCTCTTTCA
31653030 GCCTTGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.30, G:0.03, T:0.54
Consensus pattern (13 bp):
ACTCTCTTTCATT
Found at i:31663498 original size:17 final size:18
Alignment explanation
Indices: 31663456--31663498 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31663446 AAAATATTTA
*
31663456 TGTATTTATATCATGTGT
1 TGTATTTATATCATGTAT
* *
31663474 TGTTTTTATATCGT-TAT
1 TGTATTTATATCATGTAT
31663491 TGTATTTA
1 TGTATTTA
31663499 AGGTATTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.21, C:0.05, G:0.14, T:0.60
Consensus pattern (18 bp):
TGTATTTATATCATGTAT
Found at i:31663902 original size:23 final size:23
Alignment explanation
Indices: 31663876--31663926 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
31663866 TTATGGCATC
** *
31663876 TTTTTCCTCTGTCTTGTGACACG
1 TTTTTCCTCTACCTTGTCACACG
*
31663899 TTTTTTCTCTACCTTGTCACACG
1 TTTTTCCTCTACCTTGTCACACG
31663922 TTTTT
1 TTTTT
31663927 GTCTAGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.25, G:0.12, T:0.53
Consensus pattern (23 bp):
TTTTTCCTCTACCTTGTCACACG
Found at i:31666641 original size:27 final size:26
Alignment explanation
Indices: 31666587--31666679 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 26
31666577 AGCCCTAACA
* * *
31666587 AACTTCCTCATTTAAGACAGTCTTGACG
1 AACTTCCACA-TTAAGATAG-CCTGACG
31666615 AACTTCCACATTAAGATAGCCTCGACG
1 AACTTCCACATTAAGATAGCCT-GACG
*
31666642 AACTTCCACATTAAGATAATCCTGACG
1 AACTTCCACATTAAGAT-AGCCTGACG
*
31666669 GACTTCCACAT
1 AACTTCCACAT
31666680 CATGTGACTT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.03
27 43 0.74
28 13 0.22
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.27
Consensus pattern (26 bp):
AACTTCCACATTAAGATAGCCTGACG
Found at i:31671972 original size:23 final size:23
Alignment explanation
Indices: 31671937--31671984 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
31671927 AAATAATTTT
**
31671937 AAAATTTTTAAAATATT-TATAAA
1 AAAATTTCCAAAA-ATTATATAAA
31671960 AAAATTTCCAAAAATTATATAAA
1 AAAATTTCCAAAAATTATATAAA
31671983 AA
1 AA
31671985 TTTAATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAATTTCCAAAAATTATATAAA
Found at i:31673258 original size:24 final size:24
Alignment explanation
Indices: 31673225--31673275 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
31673215 AGAAATAATC
* * *
31673225 TTTCAGTTAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
31673249 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
31673273 TTT
1 TTT
31673276 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:31673284 original size:24 final size:24
Alignment explanation
Indices: 31673233--31673287 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
31673223 TCTTTCAGTT
* * *
31673233 AAACTTTGTTTATTTGTTTCAATT
1 AAACTCTGTTTAGTTGTTTCAATC
* *
31673257 AAACTCTGTTTAGTTGTTTGAGTC
1 AAACTCTGTTTAGTTGTTTCAATC
31673281 AAACTCT
1 AAACTCT
31673288 TATTAGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (24 bp):
AAACTCTGTTTAGTTGTTTCAATC
Found at i:31675229 original size:24 final size:24
Alignment explanation
Indices: 31675201--31675263 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
31675191 AGAAAGAATC
*
31675201 TTTCAGTTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* *
31675225 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAGTTAAACTCTATTTAGTTG
* *
31675249 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
31675264 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAGTTG
Found at i:31681530 original size:40 final size:38
Alignment explanation
Indices: 31681476--31681604 Score: 104
Period size: 34 Copynumber: 3.4 Consensus size: 38
31681466 AGTCTAGTAG
* * * *
31681476 TGTTTACAGTGTCACTACTGCTTCAGTATAGCATCGCGA
1 TGTTTATAGTGTCACTACAG-TTCAATATAGCATCGCAA
* * *
31681515 TGTTTTATAGTGTCACCTCCAGTTTAATATAGCATTGCAA
1 TG-TTTATAGTGTCA-CTACAGTTCAATATAGCATCGCAA
* * *
31681555 TGTTTATAGTGTCACTAC----CAATATATCATTGCAG
1 TGTTTATAGTGTCACTACAGTTCAATATAGCATCGCAA
*
31681589 TGTTTACAGTGTCACT
1 TGTTTATAGTGTCACT
31681605 GCCATTTCAG
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
34 28 0.37
38 3 0.04
39 14 0.18
40 27 0.36
41 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (38 bp):
TGTTTATAGTGTCACTACAGTTCAATATAGCATCGCAA
Found at i:31681703 original size:39 final size:39
Alignment explanation
Indices: 31681474--31681702 Score: 184
Period size: 39 Copynumber: 6.0 Consensus size: 39
31681464 ATAGTCTAGT
* *** * *
31681474 AGTGTTTACAGTGTCACTACTGCTTCAGTATAGCATCGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTGC
* * * * *
31681513 -GATGTTTTATAGTGTCACCT-CCAGTTTAATATAGCATTGC
1 AG-TG-TTTACAGTGTCA-CTGCCAATTCAGTATATCATTGC
* * *
31681553 AATGTTTATAGTGTCACTACC-A---A-TATATCATTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTGC
* *
31681587 AGTGTTTACAGTGTCACTGCCATTTCAGGATATCATTGC
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTGC
* *
31681626 AGTGTTTACAGTGTCACTGCTAATTCAGTATATCATTGT
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTGC
* * * *
31681665 AGTGTTTGCAATGTCACTACCAGTTCAGTATATCATTG
1 AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTG
31681703 TTAATCAATC
Statistics
Matches: 156, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
34 28 0.18
35 1 0.01
38 4 0.03
39 94 0.60
40 27 0.17
41 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTGCCAATTCAGTATATCATTGC
Found at i:31687648 original size:39 final size:39
Alignment explanation
Indices: 31687595--31687689 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 39
31687585 TCACCGTCAG
* * * * * *
31687595 TTCAATATAACATTGCAGTGTTTATAGTGTTACTACCAA
1 TTCAGTATATCATTGCAGTGTTTACAATGTCACCACCAA
* *
31687634 TTCAGTATATCATTGCAGTGTTTACAATGTCACCGCCAG
1 TTCAGTATATCATTGCAGTGTTTACAATGTCACCACCAA
31687673 TTCAGTATATCATTGCA
1 TTCAGTATATCATTGCA
31687690 AATCAGTCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (39 bp):
TTCAGTATATCATTGCAGTGTTTACAATGTCACCACCAA
Found at i:31689604 original size:14 final size:16
Alignment explanation
Indices: 31689573--31689604 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31689563 TATATTGATT
31689573 TTTTAGCACAATATGG
1 TTTTAGCACAATATGG
31689589 TTTTAGCA-AA-ATGG
1 TTTTAGCACAATATGG
31689603 TT
1 TT
31689605 CGTTGCGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (16 bp):
TTTTAGCACAATATGG
Found at i:31692477 original size:14 final size:14
Alignment explanation
Indices: 31692455--31692488 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31692445 TTGAGACGAG
*
31692455 AATAGATTTAATTA
1 AATAAATTTAATTA
31692469 AATAAATTTAATTA
1 AATAAATTTAATTA
*
31692483 ATTAAA
1 AATAAA
31692489 AATTTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATAAATTTAATTA
Found at i:31693686 original size:3 final size:3
Alignment explanation
Indices: 31693678--31693708 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31693668 CCATTCTCTT
31693678 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31693709 AAGACAAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31694126 original size:2 final size:2
Alignment explanation
Indices: 31694119--31694146 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
31694109 ATTAATGTAA
31694119 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
31694147 TAGAATTGAT
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):
AT
Found at i:31710551 original size:30 final size:30
Alignment explanation
Indices: 31710517--31710573 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
31710507 TTTGTTTCAG
*
31710517 GTTCT-ATATTATTATTATCTTCTAATACTT
1 GTTCTAAT-TTATTATTAACTTCTAATACTT
*
31710547 GTTCTAATTTTTTATTAACTTCTAATA
1 GTTCTAATTTATTATTAACTTCTAATA
31710574 GCATACCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.28, C:0.12, G:0.04, T:0.56
Consensus pattern (30 bp):
GTTCTAATTTATTATTAACTTCTAATACTT
Found at i:31710906 original size:5 final size:5
Alignment explanation
Indices: 31710874--31710905 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
31710864 TTCTCTGTTG
31710874 TTTTC TTTTC TTTTC TTTTC TTTT- TTTT- TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
31710906 TGATGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 8 0.30
5 19 0.70
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (5 bp):
TTTTC
Found at i:31725643 original size:17 final size:18
Alignment explanation
Indices: 31725609--31725655 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
31725599 AGTATTATTG
*
31725609 ATATTTTTTATAATATTTA
1 ATATTTTTTA-GATATTTA
31725628 ATATTTTTTAGA-ATTTA
1 ATATTTTTTAGATATTTA
* *
31725645 AAATTATTTAG
1 ATATTTTTTAG
31725656 TTGTGTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.56
18 1 0.04
19 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (18 bp):
ATATTTTTTAGATATTTA
Found at i:31726392 original size:19 final size:19
Alignment explanation
Indices: 31726370--31726433 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 19
31726360 AAAATATTAA
31726370 AAAATTAAAAATATTTATT
1 AAAATTAAAAATATTTATT
**
31726389 AAAATTTCAAAT-TTTA-T
1 AAAATTAAAAATATTTATT
***
31726406 ATTTTTAAAAATA-TT-TT
1 AAAATTAAAAATATTTATT
31726423 AAAATTAAAAA
1 AAAATTAAAAA
31726434 AACTAAAGTA
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
17 19 0.58
18 4 0.12
19 10 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATTAAAAATATTTATT
Found at i:31726430 original size:17 final size:17
Alignment explanation
Indices: 31726359--31726433 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 17
31726349 TCTCAAAACA
**
31726359 AAAAATATTAAAAAATT
1 AAAAATATTTTAAAATT
31726376 AAAAATATTTATTAAAATT
1 AAAAATA-TT-TTAAAATT
** ***
31726395 TCAAAT-TTTATATTTTT
1 AAAAATATTT-TAAAATT
31726412 AAAAATATTTTAAAATT
1 AAAAATATTTTAAAATT
31726429 AAAAA
1 AAAAA
31726434 AACTAAAGTA
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
16 1 0.02
17 26 0.62
18 5 0.12
19 10 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (17 bp):
AAAAATATTTTAAAATT
Found at i:31728968 original size:17 final size:16
Alignment explanation
Indices: 31728947--31728987 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
31728937 ATATTAAAAA
31728947 TATAATTTTAT-TATT
1 TATAATTTTATATATT
31728962 T-TAATAATTTATATATT
1 TATAAT--TTTATATATT
31728979 TATAATTTT
1 TATAATTTT
31728988 TAAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 4 0.18
15 1 0.05
16 8 0.36
17 5 0.23
18 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATATATT
Found at i:31729070 original size:78 final size:82
Alignment explanation
Indices: 31728915--31729089 Score: 189
Period size: 80 Copynumber: 2.1 Consensus size: 82
31728905 TAACGGTCAG
* * * * *
31728915 AATTAAATTGTATATTTTTATTATATTAAAAATATAATTTTATTATTTTAATAATTTATATATTT
1 AATTAAATTTTATATTTTTA-TATAGTAAAAATATAATTTTATCATTTTAAT-ATTAAAATATTT
* *
31728980 ATAATTTTTAAAAAAT-TA
64 ATAAATTATAAAAAATCTA
*
31728998 AATTAAATTTTATATTTTTA-A-AGTAAAAATATATTTTTATCATTATTAAT-TTAAAAT-TTTA
1 AATTAAATTTTATATTTTTATATAGTAAAAATATAATTTTATCATT-TTAATATTAAAATATTTA
*
31729059 TAAATTATAAAATATCTA
65 TAAATTATAAAAAATCTA
*
31729077 AACTAAAATTTTA
1 AA-TTAAATTTTA
31729090 CCATTTTACT
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
78 16 0.20
79 9 0.11
80 29 0.37
81 6 0.08
83 19 0.24
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (82 bp):
AATTAAATTTTATATTTTTATATAGTAAAAATATAATTTTATCATTTTAATATTAAAATATTTAT
AAATTATAAAAAATCTA
Found at i:31731274 original size:30 final size:31
Alignment explanation
Indices: 31731240--31731310 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
31731230 CATTTAACAC
31731240 AACAGTCACTCAAC-TT-T-GAAAATGTGACAA
1 AACAGTCACT-AACGTTATCGAAAA-GTGACAA
31731270 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCGAAAAGTGACAA
*
31731301 AACAATCACT
1 AACAGTCACT
31731311 GAAATTATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.32
31 17 0.46
32 5 0.14
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCGAAAAGTGACAA
Found at i:31731929 original size:30 final size:30
Alignment explanation
Indices: 31731862--31731931 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
31731852 ACAATTAATC
* *
31731862 AGTGACTGTTTTGTCACTTTTCGATAACGTT
1 AGTGACTGTCTTGTCACTTTTC-ATAAAGTT
31731893 AGTGACTGTCTTGTCACATTTT-A-AAAGTT
1 AGTGACTGTCTTGTCAC-TTTTCATAAAGTT
31731922 GAGTGACTGT
1 -AGTGACTGT
31731932 TGTGTTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 5 0.14
30 10 0.29
31 16 0.46
32 4 0.11
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (30 bp):
AGTGACTGTCTTGTCACTTTTCATAAAGTT
Found at i:31734044 original size:5 final size:5
Alignment explanation
Indices: 31734015--31734067 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
31734005 TCCATTTCCT
* * * * *
31734015 TTCTT TTCTT TTCTC TTCTTT TTCCC TTCCC TTCTC TTCTC TTCTC TTCTC
1 TTCTC TTCTC TTCTC TTC-TC TTCTC TTCTC TTCTC TTCTC TTCTC TTCTC
31734066 TT
1 TT
31734068 TGTTTGGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
5 38 0.90
6 4 0.10
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (5 bp):
TTCTC
Found at i:31740839 original size:23 final size:23
Alignment explanation
Indices: 31740813--31740857 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31740803 TTACTGTTGG
31740813 ATTGAAAT-TTCTTAATGTTTTAT
1 ATTGAAATGTT-TTAATGTTTTAT
*
31740836 ATTGGAATGTTTTAATGTTTTA
1 ATTGAAATGTTTTAATGTTTTA
31740858 CTTAATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.29, C:0.02, G:0.13, T:0.56
Consensus pattern (23 bp):
ATTGAAATGTTTTAATGTTTTAT
Found at i:31742181 original size:21 final size:21
Alignment explanation
Indices: 31742157--31742199 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31742147 TAGGGATAAA
31742157 GAGAAGAAGAAGAAAAAGAAG
1 GAGAAGAAGAAGAAAAAGAAG
* *
31742178 GAGAAGAAGAAGGAAGAGAAG
1 GAGAAGAAGAAGAAAAAGAAG
31742199 G
1 G
31742200 CAAAGGCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (21 bp):
GAGAAGAAGAAGAAAAAGAAG
Found at i:31742182 original size:15 final size:16
Alignment explanation
Indices: 31742158--31742198 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
31742148 AGGGATAAAG
*
31742158 AGAAGAAGAAGAA-AA
1 AGAAGGAGAAGAAGAA
31742173 AGAAGGAGAAGAAGAA
1 AGAAGGAGAAGAAGAA
*
31742189 GGAA-GAGAAG
1 AGAAGGAGAAG
31742199 GCAAAGGCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (16 bp):
AGAAGGAGAAGAAGAA
Found at i:31742197 original size:12 final size:13
Alignment explanation
Indices: 31742158--31742198 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
31742148 AGGGATAAAG
31742158 AGAAGAA-GAAGA
1 AGAAGAAGGAAGA
*
31742170 AAAAGAAGG-AGA
1 AGAAGAAGGAAGA
31742182 AGAAGAAGGAAG-
1 AGAAGAAGGAAGA
31742194 AGAAG
1 AGAAG
31742199 GCAAAGGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 22 0.88
13 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (13 bp):
AGAAGAAGGAAGA
Found at i:31746106 original size:45 final size:45
Alignment explanation
Indices: 31746055--31746144 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
31746045 ATGATTAAAA
*
31746055 TAGAAATATTATTATAAATGTTATTTATCCAACATAATAAAGAGC
1 TAGAAATATTATTATAAATGTTATTTATCCAAAATAATAAAGAGC
31746100 TAGAAATATTATTATAAATGTTATTTATCCAAAATAATAAAGAGC
1 TAGAAATATTATTATAAATGTTATTTATCCAAAATAATAAAGAGC
31746145 AATGTTGTTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.36
Consensus pattern (45 bp):
TAGAAATATTATTATAAATGTTATTTATCCAAAATAATAAAGAGC
Found at i:31750649 original size:42 final size:42
Alignment explanation
Indices: 31750569--31750654 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
31750559 GAGACCTCCT
* *
31750569 CCTTCGCCTATAGCTGATTGGTGATCTTGACATGGACCTTGA
1 CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
* *
31750611 CCTTCGCCTATAACTGATTGGTGATCTAGACTTTGACCTTGA
1 CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
31750653 CC
1 CC
31750655 GTCTTCGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.21, T:0.34
Consensus pattern (42 bp):
CCTTCGCCTATAACTGATTGGTGATCTAGACATGGACCTTGA
Found at i:31750666 original size:42 final size:42
Alignment explanation
Indices: 31750572--31750666 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
31750562 ACCTCCTCCT
* * * *
31750572 TCGCCTATAGCTGATTGGTGATCTTGACATGGACCTTGACCT
1 TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
* * *
31750614 TCGCCTATAACTGATTGGTGATCTAGACTTTGACCTTGACCG
1 TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
**
31750656 TCTTCGATAAC
1 TCGCCGATAAC
31750667 CAAGGGGTGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (42 bp):
TCGCCGATAACTGATTGGTGATCTAGACATGGACCTTGACCG
Found at i:31758774 original size:18 final size:18
Alignment explanation
Indices: 31758732--31758774 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
31758722 CGATCGATCG
*
31758732 CGACCACGATCATGGCCA
1 CGACCACGACCATGGCCA
* * *
31758750 CGGCCACGACCATGTCCT
1 CGACCACGACCATGGCCA
31758768 CGACCAC
1 CGACCAC
31758775 AACTACTAGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.44, G:0.21, T:0.12
Consensus pattern (18 bp):
CGACCACGACCATGGCCA
Found at i:31759496 original size:33 final size:35
Alignment explanation
Indices: 31759453--31759524 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 35
31759443 TAATATAAAT
* * *
31759453 ATAAGTAATCCTTTAAC-AAACTTTCAAGCA-AAC
1 ATAAGCAATCCCTTAACAAAACTTGCAAGCATAAC
31759486 ATAAGCAATCCCTTAACAAAACTTGCAAGCATAAC
1 ATAAGCAATCCCTTAACAAAACTTGCAAGCATAAC
31759521 ATAA
1 ATAA
31759525 CAGAAAAACA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 15 0.44
34 12 0.35
35 7 0.21
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.24
Consensus pattern (35 bp):
ATAAGCAATCCCTTAACAAAACTTGCAAGCATAAC
Found at i:31760025 original size:70 final size:70
Alignment explanation
Indices: 31759941--31760085 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 70
31759931 TAGTTACAAG
*
31759941 AATATAAAAAGTTTAAGGAAGATGGAAGGTTAAAGGTCAAGGGAGATGAAAGATTGAACATACAT
1 AATATAAAAAGTTTAAGGAAGATGGAAGGTTAAAGATCAAGGGAGATGAAAGATTGAACATACAT
31760006 TTAAT
66 TTAAT
* *
31760011 AATATAAAAGGTTTAAGGAAGATGGAAGGTTAAAGATCAAGGGAGATGAAAGATTGAACATCCAT
1 AATATAAAAAGTTTAAGGAAGATGGAAGGTTAAAGATCAAGGGAGATGAAAGATTGAACATACAT
31760076 TTAAT
66 TTAAT
31760081 AATAT
1 AATAT
31760086 TCATAATATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.47, C:0.05, G:0.23, T:0.25
Consensus pattern (70 bp):
AATATAAAAAGTTTAAGGAAGATGGAAGGTTAAAGATCAAGGGAGATGAAAGATTGAACATACAT
TTAAT
Found at i:31760961 original size:17 final size:17
Alignment explanation
Indices: 31760921--31760962 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
31760911 AAAGTTTATG
*
31760921 TAAATATCTTAAAAAAT
1 TAAATATTTTAAAAAAT
31760938 T-AA-ATTTTAAAAAAT
1 TAAATATTTTAAAAAAT
31760953 TAAATATTTT
1 TAAATATTTT
31760963 GAGAATTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 12 0.55
16 4 0.18
17 6 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATATTTTAAAAAAT
Found at i:31761577 original size:24 final size:24
Alignment explanation
Indices: 31761550--31761607 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
31761540 AAGCCTAATT
* *
31761550 CTAATCAATATCAAATATATTATA
1 CTAATAAATATCAAAAATATTATA
* * *
31761574 CTAATAAATGTTAAAAATATTGTA
1 CTAATAAATATCAAAAATATTATA
*
31761598 CTAAAAAATA
1 CTAATAAATA
31761608 CTAAATCTTC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.34
Consensus pattern (24 bp):
CTAATAAATATCAAAAATATTATA
Found at i:31761612 original size:24 final size:24
Alignment explanation
Indices: 31761566--31761612 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
31761556 AATATCAAAT
* **
31761566 ATATTATACTAATAAATGTTAAAA
1 ATATTATACTAAAAAATACTAAAA
*
31761590 ATATTGTACTAAAAAATACTAAA
1 ATATTATACTAAAAAATACTAAA
31761613 TCTTCTAGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.34
Consensus pattern (24 bp):
ATATTATACTAAAAAATACTAAAA
Found at i:31764979 original size:24 final size:24
Alignment explanation
Indices: 31764952--31764999 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
31764942 CAACATGAGC
31764952 ACCAGACCATACGTCTTGTGGAGT
1 ACCAGACCATACGTCTTGTGGAGT
31764976 ACCAGACCATACGTCTTGTGGAGT
1 ACCAGACCATACGTCTTGTGGAGT
31765000 CTTTTTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (24 bp):
ACCAGACCATACGTCTTGTGGAGT
Found at i:31767190 original size:24 final size:24
Alignment explanation
Indices: 31767163--31767218 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
31767153 AAGCTTAATT
* *
31767163 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAATATATTATA
*
31767187 CTAATAAATGTTAAATATATTATA
1 CTAATAAATGTCAAATATATTATA
31767211 CTAATAAA
1 CTAATAAA
31767219 ATTAAATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATA
Found at i:31774711 original size:25 final size:25
Alignment explanation
Indices: 31774662--31774712 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
31774652 TTTATTATTT
**
31774662 AGAAAAAGAGAAAAAAAAGTCGAAA
1 AGAAAAAGAGAAAAAAAAGGAGAAA
**
31774687 AGAAAAATTGAAAAAAAAGGAGAAA
1 AGAAAAAGAGAAAAAAAAGGAGAAA
31774712 A
1 A
31774713 TTGAGGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.06
Consensus pattern (25 bp):
AGAAAAAGAGAAAAAAAAGGAGAAA
Found at i:31775791 original size:23 final size:25
Alignment explanation
Indices: 31775765--31775810 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
31775755 CCAATTAGGG
31775765 AATTAT-TGTTT-AAATTTAATTCA
1 AATTATCTGTTTAAAATTTAATTCA
*
31775788 AATTATCTTTTTAAAATTTAATT
1 AATTATCTGTTTAAAATTTAATT
31775811 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 4 0.20
25 10 0.50
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAAAATTTAATTCA
Found at i:31779783 original size:35 final size:35
Alignment explanation
Indices: 31779744--31779812 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
31779734 AAGATAATAT
**
31779744 ATTTTGTTTAACTTGGTTTGAAAGCAATAGCTTAG
1 ATTTTGTTTAACTTGACTTGAAAGCAATAGCTTAG
* *
31779779 ATTTTGTTTAACTTGACTTGCAAGCAATATCTTA
1 ATTTTGTTTAACTTGACTTGAAAGCAATAGCTTA
31779813 TTTGACTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGAAAGCAATAGCTTAG
Found at i:31783022 original size:326 final size:326
Alignment explanation
Indices: 31782429--31783080 Score: 1277
Period size: 326 Copynumber: 2.0 Consensus size: 326
31782419 CATTGTTATC
31782429 AGGATCAATGACCCCAATAACTCAAAAGACTAATAGGGATAGACCAAATTAGAGAAGGTTTCGAC
1 AGGATCAATGACCCCAATAACTCAAAAGACTAATAGGGATAGACCAAATTAGAGAAGGTTTCGAC
31782494 GTGTTAGGAGTGCTCCTTTTGCAGATTTTGTTCCTAGTGATGGTTATACAAAAGCAAATTACATG
66 GTGTTAGGAGTGCTCCTTTTGCAGATTTTGTTCCTAGTGATGGTTATACAAAAGCAAATTACATG
*
31782559 TTATGAGTCTGTTTTACGGTTCATGTTTGTGTTCAGTAGGATTCAAGTTCTGTTGAACATCTATT
131 TTATGAGTCTGTTTTACGGTTCATGTTTGTGTTCAATAGGATTCAAGTTCTGTTGAACATCTATT
*
31782624 TTTATTCTATTTGTGTTTTTATTCTTGATGATGATGCAGTTGTTGGGTAAGTATTTGTAGATTAT
196 TTTATTCTATTTGTGTTTTTATTCTTGATGATGATACAGTTGTTGGGTAAGTATTTGTAGATTAT
31782689 TAACTCAGATTCTGTGATATGATCTCCTGTTTGCAAATTCTCATTTCCTAATGCTTTGATTTTGT
261 TAACTCAGATTCTGTGATATGATCTCCTGTTTGCAAATTCTCATTTCCTAATGCTTTGATTTTGT
31782754 A
326 A
31782755 AGGATCAATGACCCCAATAACTCAAAAGACTAATAGGGATAGACCAAATTAGAGAAGGTTTCGAC
1 AGGATCAATGACCCCAATAACTCAAAAGACTAATAGGGATAGACCAAATTAGAGAAGGTTTCGAC
*
31782820 GTGTTATGAGTGCTCCTTTTGCAGATTTTGTTCCTAGTGATGGTTATACAAAAGCAAATTACATG
66 GTGTTAGGAGTGCTCCTTTTGCAGATTTTGTTCCTAGTGATGGTTATACAAAAGCAAATTACATG
31782885 TTATGAGTCTGTTTTACGGTTCATGTTTGTGTTCAATAGGATTCAAGTTCTGTTGAACATCTATT
131 TTATGAGTCTGTTTTACGGTTCATGTTTGTGTTCAATAGGATTCAAGTTCTGTTGAACATCTATT
31782950 TTTATTCTATTTGTGTTTTTATTCTTGATGATGATACAGTTGTTGGGTAAGTATTTGTAGATTAT
196 TTTATTCTATTTGTGTTTTTATTCTTGATGATGATACAGTTGTTGGGTAAGTATTTGTAGATTAT
31783015 TAACTCAGATTCTGTGATATGATCTCCTGTTTGCAAATTCTCATTTCCTAATGCTTTGATTTTGT
261 TAACTCAGATTCTGTGATATGATCTCCTGTTTGCAAATTCTCATTTCCTAATGCTTTGATTTTGT
31783080 A
326 A
31783081 GAGCGGTTGA
Statistics
Matches: 323, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 323 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (326 bp):
AGGATCAATGACCCCAATAACTCAAAAGACTAATAGGGATAGACCAAATTAGAGAAGGTTTCGAC
GTGTTAGGAGTGCTCCTTTTGCAGATTTTGTTCCTAGTGATGGTTATACAAAAGCAAATTACATG
TTATGAGTCTGTTTTACGGTTCATGTTTGTGTTCAATAGGATTCAAGTTCTGTTGAACATCTATT
TTTATTCTATTTGTGTTTTTATTCTTGATGATGATACAGTTGTTGGGTAAGTATTTGTAGATTAT
TAACTCAGATTCTGTGATATGATCTCCTGTTTGCAAATTCTCATTTCCTAATGCTTTGATTTTGT
A
Found at i:31784366 original size:8 final size:8
Alignment explanation
Indices: 31784349--31784378 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
31784339 AAATTTTTTA
*
31784349 AAAATTAT
1 AAAATAAT
31784357 AAAATAAT
1 AAAATAAT
31784365 AAAATAAT
1 AAAATAAT
31784373 AAAATA
1 AAAATA
31784379 TATTTACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAATAAT
Found at i:31789582 original size:2 final size:2
Alignment explanation
Indices: 31789575--31789599 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31789565 CATTTTGGAA
31789575 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
31789600 CCATATGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:31797204 original size:69 final size:69
Alignment explanation
Indices: 31797075--31797212 Score: 195
Period size: 69 Copynumber: 2.0 Consensus size: 69
31797065 AATGTCAGTT
*** * ** *
31797075 AACTAGTAAACTAAGATGGCTATCTTTTGTCTTCTTTCCTCAAGACCTTAAGACTGCATTGGTAG
1 AACTAGTAAACTAAGACAACCATCTTTTGTCTTCTTTCCTCAAGACCTTAAGACCACATTGGTAA
31797140 CAAA
66 CAAA
* *
31797144 AACTAGTAAACTAAGACAACCATCTTTTGTCTTCTTTCCTCAAGACCTTAGGTCCACATTGGTAA
1 AACTAGTAAACTAAGACAACCATCTTTTGTCTTCTTTCCTCAAGACCTTAAGACCACATTGGTAA
31797209 CAAA
66 CAAA
31797213 CCTCTTTTTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (69 bp):
AACTAGTAAACTAAGACAACCATCTTTTGTCTTCTTTCCTCAAGACCTTAAGACCACATTGGTAA
CAAA
Found at i:31810206 original size:45 final size:45
Alignment explanation
Indices: 31810112--31810208 Score: 113
Period size: 45 Copynumber: 2.1 Consensus size: 45
31810102 TAGAAAAAAA
* * * *
31810112 AAGAAGAAACAAATTCCTAAAAACTAGTTTTAAAATGTGGATGGTT
1 AAGAA-AAACAAATCCCTAAAAACTAGCTTAAAAATGTGGATGGCT
* * * *
31810158 AAGAAAAACAAATCCCTCATAACTAGCTTAAAAATGTGGGTTGCT
1 AAGAAAAACAAATCCCTAAAAACTAGCTTAAAAATGTGGATGGCT
31810203 AAGAAA
1 AAGAAA
31810209 GGAACTCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 38 0.88
46 5 0.12
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.25
Consensus pattern (45 bp):
AAGAAAAACAAATCCCTAAAAACTAGCTTAAAAATGTGGATGGCT
Found at i:31822380 original size:51 final size:51
Alignment explanation
Indices: 31822307--31822444 Score: 197
Period size: 51 Copynumber: 2.7 Consensus size: 51
31822297 AAACGAAAAG
* *
31822307 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATACTTTACGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATACATGACGGATTAAA
* *
31822358 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATACATGACGGATTAAA
* * *
31822409 GGTCTGATGACTCAA-TGTCATCGTGATTATATGAAT
1 GGTCCGATGACT-AAGTGTCATCGTGAGTAAATGAAT
31822445 TCCTATATGG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 77 0.97
52 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (51 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATACATGACGGATTAAA
Found at i:31823868 original size:30 final size:31
Alignment explanation
Indices: 31823826--31823889 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
31823816 ATAATAAAAC
*
31823826 AAAATAAAAGGAT-TAATTTAAAAAGGATAAA
1 AAAATAAAAGGATCTAA-TTAAAAAAGATAAA
*
31823857 AAAAT-AAAGGATCTAATTAAAAAAGATACA
1 AAAATAAAAGGATCTAATTAAAAAAGATAAA
31823887 AAA
1 AAA
31823890 GGATTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 22 0.73
31 8 0.27
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (31 bp):
AAAATAAAAGGATCTAATTAAAAAAGATAAA
Found at i:31823992 original size:26 final size:26
Alignment explanation
Indices: 31823933--31823984 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
31823923 AATTTTAAAG
31823933 AAATAAAATTAAAAGGATTAAATTTT
1 AAATAAAATTAAAAGGATTAAATTTT
* * *
31823959 AAAAAAAATTAAAAGGGTTTAATTTT
1 AAATAAAATTAAAAGGATTAAATTTT
31823985 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.35
Consensus pattern (26 bp):
AAATAAAATTAAAAGGATTAAATTTT
Found at i:31824145 original size:24 final size:24
Alignment explanation
Indices: 31824100--31824145 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31824090 GATTTAAGGG
* *
31824100 TTAAATTAAAATAAAAATAAAGTT
1 TTAAAGTAAAATAAAAAAAAAGTT
31824124 TTAAAGTAAAA-AAAATAAAAAG
1 TTAAAGTAAAATAAAA-AAAAAG
31824146 GAAAAAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (24 bp):
TTAAAGTAAAATAAAAAAAAAGTT
Found at i:31825482 original size:3 final size:3
Alignment explanation
Indices: 31825474--31825503 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
31825464 TATTTTGTTC
*
31825474 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31825504 GGATTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:31825675 original size:75 final size:75
Alignment explanation
Indices: 31825584--31825989 Score: 501
Period size: 75 Copynumber: 5.4 Consensus size: 75
31825574 ACATTTAGTA
* *
31825584 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCCGACTATTGTTGGGCACA
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCTGACTAGTGTTGGGCACA
31825649 CTTTTTATAT
66 CTTTTTATAT
* * * *
31825659 TCGTCAATTATCCGACTAGCGCTGGGCGTAACCTTTGTCAATTTATCTGACTAGTGTTGGGCACA
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCTGACTAGTGTTGGGCACA
*
31825724 CTTCTTATAT
66 CTTTTTATAT
* * * * * * * *
31825734 TCGTTGGTTATCCGACTAGTGTTTGACGCAACCTTT-TTCAGTTTATTTGACTAGTGCTGGGCAC
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTT-AGTTTATCTGACTAGTGTTGGGCAC
*
31825798 ACTTCTTATAT
65 ACTTTTTATAT
* * * * * *
31825809 TCGTCGGTTATCCAACTAGCGCTGGGAGCAATCTTTCTTAGTTTATCTGACTAGTGCTGGGCACA
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCTGACTAGTGTTGGGCACA
31825874 CTTTTTATAT
66 CTTTTTATAT
* * * * * *
31825884 TCATTGGTTATTCGACTAGCGCTGGGTGCAACCTTTGTTAGTTTATCTTACTAGTGTTGGGCACA
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCTGACTAGTGTTGGGCACA
31825949 -TTTCTTATAT
66 CTTT-TTATAT
* * *
31825959 TCGTCGATTATCTGACTAGTGCTGGGTGCAA
1 TCGTCGATTATCCGACTAGCGCTGGGCGCAA
31825990 AAACTTAATA
Statistics
Matches: 284, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
74 4 0.01
75 278 0.98
76 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (75 bp):
TCGTCGATTATCCGACTAGCGCTGGGCGCAACCTTTGTTAGTTTATCTGACTAGTGTTGGGCACA
CTTTTTATAT
Found at i:31825756 original size:40 final size:40
Alignment explanation
Indices: 31825701--31825984 Score: 133
Period size: 40 Copynumber: 7.5 Consensus size: 40
31825691 CTTTGTCAAT
* *
31825701 TTATCTGACTAGTGTTGGGCACACTTCTTATATTCGTTGG
1 TTATCCGACTAGTGCTGGGCACACTTCTTATATTCGTTGG
* *
31825741 TTATCCGACTAGTGTTTGACGCA-AC--CTT-T-TTCAG-T--
1 TTATCCGACTAGTG-CTG-GGCACACTTCTTATATTC-GTTGG
** *
31825776 TTATTTGACTAGTGCTGGGCACACTTCTTATATTCGTCGG
1 TTATCCGACTAGTGCTGGGCACACTTCTTATATTCGTTGG
* * * * *
31825816 TTATCCAACTAGCGCTGGG-AGCA-ATCTT-TCTTAG-T--
1 TTATCCGACTAGTGCTGGGCA-CACTTCTTATATTCGTTGG
* * *
31825851 TTATCTGACTAGTGCTGGGCACACTTTTTATATTCATTGG
1 TTATCCGACTAGTGCTGGGCACACTTCTTATATTCGTTGG
* * * *
31825891 TTATTCGACTAGCGCTGGGTGCA-AC--CTT-TGTTAG-T--
1 TTATCCGACTAGTGCT-GG-GCACACTTCTTATATTCGTTGG
** * * * *
31825926 TTATCTTACTAGTGTTGGGCACATTTCTTATATTCGTCGA
1 TTATCCGACTAGTGCTGGGCACACTTCTTATATTCGTTGG
*
31825966 TTATCTGACTAGTGCTGGG
1 TTATCCGACTAGTGCTGGG
31825985 TGCAAAAACT
Statistics
Matches: 176, Mismatches: 41, Indels: 54
0.65 0.15 0.20
Matches are distributed among these distances:
33 6 0.03
34 7 0.04
35 41 0.23
36 10 0.06
37 14 0.08
38 13 0.07
39 10 0.06
40 60 0.34
41 9 0.05
42 6 0.03
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (40 bp):
TTATCCGACTAGTGCTGGGCACACTTCTTATATTCGTTGG
Found at i:31826383 original size:3 final size:3
Alignment explanation
Indices: 31826370--31826415 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
31826360 AAAAGCCCAG
31826370 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
31826416 TCTTTCCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:31829297 original size:15 final size:14
Alignment explanation
Indices: 31829277--31829308 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
31829267 TAACATTCAG
31829277 TTCGAACATAAATCA
1 TTCGAACATAAA-CA
31829292 TTCGAACATAAACA
1 TTCGAACATAAACA
31829306 TTC
1 TTC
31829309 CATTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (14 bp):
TTCGAACATAAACA
Found at i:31832677 original size:21 final size:21
Alignment explanation
Indices: 31832634--31832678 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31832624 AAAGAAAGTT
*
31832634 GGAAGAAAGAGAAAAGGGGAG
1 GGAAGAAAGAGAAAAGGCGAG
* *
31832655 GGAAGAAAGAGAGAAGGCTAG
1 GGAAGAAAGAGAAAAGGCGAG
31832676 GGA
1 GGA
31832679 GAAGCTGAGA
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:0.49, C:0.02, G:0.47, T:0.02
Consensus pattern (21 bp):
GGAAGAAAGAGAAAAGGCGAG
Found at i:31837580 original size:20 final size:20
Alignment explanation
Indices: 31837553--31837737 Score: 127
Period size: 20 Copynumber: 9.2 Consensus size: 20
31837543 AGTACGAAAT
31837553 CCCTGTATACACTTCGGTGC
1 CCCTGTATACACTTCGGTGC
* *
31837573 CTCTGTATGCACTTCGGTGC
1 CCCTGTATACACTTCGGTGC
* * *
31837593 CCCTATATGCACTTTGGTGC
1 CCCTGTATACACTTCGGTGC
* ** *
31837613 CCCTGTATACATTTTTGTGT
1 CCCTGTATACACTTCGGTGC
* **
31837633 CCCTGTATGCACTTCAATGC
1 CCCTGTATACACTTCGGTGC
** **
31837653 CCCTGTATGTACTTTTGTGC
1 CCCTGTATACACTTCGGTGC
* ****
31837673 CCTTGTATGTGTTTCGGTGC
1 CCCTGTATACACTTCGGTGC
* * *
31837693 TCTTGTATGCACTTCGGTGC
1 CCCTGTATACACTTCGGTGC
* *
31837713 CCCTGTATGCACTTTGGTGC
1 CCCTGTATACACTTCGGTGC
*
31837733 TCCTG
1 CCCTG
31837738 AAAATAAATT
Statistics
Matches: 132, Mismatches: 33, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 132 1.00
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (20 bp):
CCCTGTATACACTTCGGTGC
Found at i:31837619 original size:40 final size:40
Alignment explanation
Indices: 31837553--31837737 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 40
31837543 AGTACGAAAT
* * *
31837553 CCCTGTATACACTTCGGTGCCTCTGTATGCACTTCGGTGC
1 CCCTGTATGCACTTTGGTGCCCCTGTATGCACTTCGGTGC
* * * ** *
31837593 CCCTATATGCACTTTGGTGCCCCTGTATACATTTTTGTGT
1 CCCTGTATGCACTTTGGTGCCCCTGTATGCACTTCGGTGC
*** * **
31837633 CCCTGTATGCACTTCAATGCCCCTGTATGTACTTTTGTGC
1 CCCTGTATGCACTTTGGTGCCCCTGTATGCACTTCGGTGC
* ** * *
31837673 CCTTGTATG-TGTTTCGGTGCTCTTGTATGCACTTCGGTGC
1 CCCTGTATGCACTTT-GGTGCCCCTGTATGCACTTCGGTGC
*
31837713 CCCTGTATGCACTTTGGTGCTCCTG
1 CCCTGTATGCACTTTGGTGCCCCTG
31837738 AAAATAAATT
Statistics
Matches: 111, Mismatches: 32, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
39 2 0.02
40 106 0.95
41 3 0.03
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (40 bp):
CCCTGTATGCACTTTGGTGCCCCTGTATGCACTTCGGTGC
Found at i:31837639 original size:60 final size:59
Alignment explanation
Indices: 31837553--31837737 Score: 217
Period size: 60 Copynumber: 3.1 Consensus size: 59
31837543 AGTACGAAAT
* *
31837553 CCCTGTATACACTTCGGTGCCTCTGTATGCACTTCGGTGCCCCTATATGCACTTTGGTGC
1 CCCTGTATACATTTCGGTGCC-CTGTATGCACTTCGGTGCCCCTGTATGCACTTTGGTGC
** ** * *
31837613 CCCTGTATACATTTTTGTGTCCCTGTATGCACTTCAATGCCCCTGTATGTACTTTTGTGC
1 CCCTGTATACATTTCGGTG-CCCTGTATGCACTTCGGTGCCCCTGTATGCACTTTGGTGC
* *** *
31837673 CCTTGTATGTGTTTCGGTGCTCTTGTATGCACTTCGGTGCCCCTGTATGCACTTTGGTGC
1 CCCTGTATACATTTCGGTGC-CCTGTATGCACTTCGGTGCCCCTGTATGCACTTTGGTGC
*
31837733 TCCTG
1 CCCTG
31837738 AAAATAAATT
Statistics
Matches: 102, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 1 0.01
60 99 0.97
61 2 0.02
ACGTcount: A:0.12, C:0.28, G:0.22, T:0.38
Consensus pattern (59 bp):
CCCTGTATACATTTCGGTGCCCTGTATGCACTTCGGTGCCCCTGTATGCACTTTGGTGC
Found at i:31845622 original size:3 final size:3
Alignment explanation
Indices: 31845599--31845647 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
31845589 TTACCACCAG
31845599 AGA AG- AGA AG- AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
31845644 AGA A
1 AGA A
31845648 ATGGACGCAC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:31846491 original size:20 final size:20
Alignment explanation
Indices: 31846478--31846515 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31846468 TAAAAAATAT
31846478 AAAATTCAAATAAATATAAA
1 AAAATTCAAATAAATATAAA
*
31846498 AAAATTCAAATATATATA
1 AAAATTCAAATAAATATA
31846516 CTCTAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATTCAAATAAATATAAA
Found at i:31846905 original size:27 final size:26
Alignment explanation
Indices: 31846872--31846925 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
31846862 TTGAGTGTAC
* *
31846872 TTTAAGTACTAAATTGAACAAAAAAAA
1 TTTAAGTACCAAAATGAA-AAAAAAAA
31846899 TTTAAGTACCAAAATGAAAAAAAAAA
1 TTTAAGTACCAAAATGAAAAAAAAAA
31846925 T
1 T
31846926 ATACTGCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 9 0.36
27 16 0.64
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (26 bp):
TTTAAGTACCAAAATGAAAAAAAAAA
Found at i:31859862 original size:24 final size:23
Alignment explanation
Indices: 31859824--31859868 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
31859814 CTATTAAGAG
31859824 TTTAATGAAACAAATAAACAGAA
1 TTTAATGAAACAAATAAACAGAA
*
31859847 TTTAATTGAAATAAATAAACAG
1 TTTAA-TGAAACAAATAAACAG
31859869 GGCTTAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.27
Consensus pattern (23 bp):
TTTAATGAAACAAATAAACAGAA
Found at i:31859875 original size:24 final size:24
Alignment explanation
Indices: 31859825--31859878 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
31859815 TATTAAGAGT
*
31859825 TTAA-TGAAACAAATAAACAGAAT
1 TTAATTGAAACAAATAAACAGAAC
* **
31859848 TTAATTGAAATAAATAAACAGGGC
1 TTAATTGAAACAAATAAACAGAAC
31859872 TTAATTG
1 TTAATTG
31859879 GAAGATTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (24 bp):
TTAATTGAAACAAATAAACAGAAC
Found at i:31875520 original size:15 final size:15
Alignment explanation
Indices: 31875497--31875526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31875487 TTGCTACGGT
*
31875497 TTTTCAAAATTGAAA
1 TTTTAAAAATTGAAA
31875512 TTTTAAAAATTGAAA
1 TTTTAAAAATTGAAA
31875527 AGTATAAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (15 bp):
TTTTAAAAATTGAAA
Found at i:31877566 original size:15 final size:17
Alignment explanation
Indices: 31877546--31877584 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
31877536 AACCCTTTAA
31877546 AAATTATTAAAAT-AT-
1 AAATTATTAAAATGATG
31877561 AAATTATTAAAATGATG
1 AAATTATTAAAATGATG
31877578 AAATTAT
1 AAATTAT
31877585 ATTTTTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 13 0.59
16 2 0.09
17 7 0.32
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
AAATTATTAAAATGATG
Found at i:31881287 original size:2 final size:2
Alignment explanation
Indices: 31881280--31881311 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31881270 TCTACCATAA
31881280 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
31881312 TAAAGTGGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31885168 original size:11 final size:12
Alignment explanation
Indices: 31885152--31885184 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
31885142 ATTTTTTATC
31885152 TAAATATTTAA-
1 TAAATATTTAAT
31885163 TAAATATGTTAAT
1 TAAATAT-TTAAT
31885176 TAAATATTT
1 TAAATATTT
31885185 TTCACCAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 7 0.35
12 6 0.30
13 7 0.35
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (12 bp):
TAAATATTTAAT
Found at i:31886867 original size:15 final size:15
Alignment explanation
Indices: 31886847--31886892 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
31886837 TGTTACATAA
31886847 TTTTATATTATTTAT
1 TTTTATATTATTTAT
*
31886862 TTTTATATCA-TTAT
1 TTTTATATTATTTAT
* *
31886876 TTTTCTCTTATTT-T
1 TTTTATATTATTTAT
31886890 TTT
1 TTT
31886893 AATTTACGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTATATTATTTAT
Found at i:31886875 original size:14 final size:15
Alignment explanation
Indices: 31886847--31886879 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31886837 TGTTACATAA
*
31886847 TTTTATATTATTTAT
1 TTTTATATCATTTAT
31886862 TTTTATATCA-TTAT
1 TTTTATATCATTTAT
31886876 TTTT
1 TTTT
31886880 CTCTTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTATATCATTTAT
Found at i:31888173 original size:25 final size:24
Alignment explanation
Indices: 31888126--31888174 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
31888116 ATAATTTTAT
*
31888126 CATATTTTTAAATAAACATAAATA
1 CATATTTTTAAATAAACAAAAATA
*
31888150 CATATTTTTAAAATAAATAAAAATA
1 CATATTTTT-AAATAAACAAAAATA
31888175 TAAAAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (24 bp):
CATATTTTTAAATAAACAAAAATA
Found at i:31890408 original size:22 final size:22
Alignment explanation
Indices: 31890378--31890422 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
31890368 GTCCAACTTT
*
31890378 AAGTATTATGTCATATAATTTC
1 AAGTATTATGTAATATAATTTC
*
31890400 AAGTGTTATGTAATATAATTTC
1 AAGTATTATGTAATATAATTTC
31890422 A
1 A
31890423 CTAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (22 bp):
AAGTATTATGTAATATAATTTC
Found at i:31891659 original size:143 final size:143
Alignment explanation
Indices: 31891401--31891674 Score: 521
Period size: 143 Copynumber: 1.9 Consensus size: 143
31891391 TCAATACGGA
31891401 GAACTCGTTACCTTAAATATGCAACCTACGTTCAAGACTATACACATCATCGATATATTGTTCGA
1 GAACTCGTTACCTTAAATATGCAACCTACGTTCAAGACTATACACATCATCGATATATTGTTCGA
*
31891466 CATTTAAATTGAATGTTGCGGATGCTGCAACCACATGTATACATGAATATCTTAGTGTTTGCAAC
66 CATTAAAATTGAATGTTGCGGATGCTGCAACCACATGTATACATGAATATCTTAGTGTTTGCAAC
31891531 CACATGTATACGT
131 CACATGTATACGT
*
31891544 GAACTCGTTACCTTAAATATGCAACGTACGTTCAAGACTATACACATCATCGATATATTGTTCGA
1 GAACTCGTTACCTTAAATATGCAACCTACGTTCAAGACTATACACATCATCGATATATTGTTCGA
*
31891609 CATTAAAATTGAATGTTGCGGATGCTGCAACCACATGTATACATGAATATCTTAGTGTTTGGAAC
66 CATTAAAATTGAATGTTGCGGATGCTGCAACCACATGTATACATGAATATCTTAGTGTTTGCAAC
31891674 C
131 C
31891675 TCTCGCACTC
Statistics
Matches: 128, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
143 128 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (143 bp):
GAACTCGTTACCTTAAATATGCAACCTACGTTCAAGACTATACACATCATCGATATATTGTTCGA
CATTAAAATTGAATGTTGCGGATGCTGCAACCACATGTATACATGAATATCTTAGTGTTTGCAAC
CACATGTATACGT
Found at i:31894191 original size:7 final size:7
Alignment explanation
Indices: 31894179--31894216 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
31894169 AAATAATATT
31894179 TTTAAAA
1 TTTAAAA
31894186 TTTAAAA
1 TTTAAAA
31894193 TTTAAAA
1 TTTAAAA
31894200 --T-AAA
1 TTTAAAA
31894204 TTTAAAA
1 TTTAAAA
31894211 TTTAAA
1 TTTAAA
31894217 TAATAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
4 3 0.11
5 1 0.04
6 1 0.04
7 23 0.82
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTTAAAA
Found at i:31894223 original size:25 final size:25
Alignment explanation
Indices: 31894163--31894227 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 25
31894153 TGGCTCCACC
31894163 AAAATAAAATAATATTTTTAAAATTTA
1 AAAATAAAATAA-A-TTTTAAAATTTA
*
31894190 AAATTTAAAATAAA-TTTAAAATTTA
1 AAA-ATAAAATAAATTTTAAAATTTA
31894215 AATAAT-AAATAAA
1 AA-AATAAAATAAA
31894228 AAATTTCATC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
24 7 0.21
25 14 0.41
26 1 0.03
27 4 0.12
28 8 0.24
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATAAAATAAATTTTAAAATTTA
Found at i:31894230 original size:20 final size:18
Alignment explanation
Indices: 31894189--31894233 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
31894179 TTTAAAATTT
**
31894189 AAAATTTAAAATAAATTT
1 AAAATTTAAAATAAATAA
31894207 AAAATTTAAATAATAAATAA
1 AAAATTT-AA-AATAAATAA
31894227 AAAATTT
1 AAAATTT
31894234 CATCGGGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 14 0.61
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTTAAAATAAATAA
Found at i:31894845 original size:3 final size:3
Alignment explanation
Indices: 31894837--31894868 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31894827 CTACCCTAAA
31894837 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31894869 AAATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:31895514 original size:3 final size:3
Alignment explanation
Indices: 31895508--31895548 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
31895498 AATAATATAA
31895508 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
31895549 AAAATCTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:31896372 original size:21 final size:20
Alignment explanation
Indices: 31896347--31896421 Score: 53
Period size: 21 Copynumber: 3.5 Consensus size: 20
31896337 TTCATCGTAT
31896347 AACATATCAAATTGCGATATA
1 AACAT-TCAAATTGCGATATA
* * *
31896368 AACATTTAACA-TGAAGTTATCAA
1 AACATTCAA-ATTG-CGATAT--A
31896391 TAACATATCAAATTGCGATATA
1 -AACAT-TCAAATTGCGATATA
31896413 AACATTCAA
1 AACATTCAA
31896422 CTATATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 15
0.66 0.10 0.24
Matches are distributed among these distances:
20 9 0.22
21 15 0.37
22 1 0.02
23 1 0.02
24 10 0.24
25 5 0.12
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (20 bp):
AACATTCAAATTGCGATATA
Found at i:31896551 original size:22 final size:22
Alignment explanation
Indices: 31896495--31896603 Score: 87
Period size: 22 Copynumber: 5.0 Consensus size: 22
31896485 ACAATCCATT
*
31896495 AGAGAGCATCGAAGTGCTAA-A
1 AGAGAGCATAGAAGTGCTAATA
* * *
31896516 CAAAGAGAAAAGAAGTGCTAATA
1 -AGAGAGCATAGAAGTGCTAATA
* * *
31896539 AGGGAGCATAGAAGTCCTAATC
1 AGAGAGCATAGAAGTGCTAATA
* *
31896561 AGAGAGCATTGAAGTGCTGAACA
1 AGAGAGCATAGAAGTGCT-AATA
* *
31896584 A-AGAGCACAAAAGTGCTAAT
1 AGAGAGCATAGAAGTGCTAAT
31896604 CAGTTAATAG
Statistics
Matches: 66, Mismatches: 19, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
21 2 0.03
22 60 0.91
23 4 0.06
ACGTcount: A:0.45, C:0.14, G:0.26, T:0.16
Consensus pattern (22 bp):
AGAGAGCATAGAAGTGCTAATA
Found at i:31897740 original size:20 final size:21
Alignment explanation
Indices: 31897705--31897744 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
31897695 TACTTATGTA
*
31897705 TTTAGTTTAACTTTTAATTAG
1 TTTAGTTTAACCTTTAATTAG
31897726 TTTAG-TTAACCTTTAATTA
1 TTTAGTTTAACCTTTAATTA
31897745 ACTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTAGTTTAACCTTTAATTAG
Found at i:31910883 original size:16 final size:17
Alignment explanation
Indices: 31910856--31910890 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
31910846 AATCTGTACC
31910856 ATTTAGTAAAAATAAAT
1 ATTTAGTAAAAATAAAT
31910873 ATTTA-TAAAAATAAAT
1 ATTTAGTAAAAATAAAT
31910889 AT
1 AT
31910891 AATTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
ATTTAGTAAAAATAAAT
Found at i:31914125 original size:7 final size:6
Alignment explanation
Indices: 31914110--31914148 Score: 60
Period size: 6 Copynumber: 6.2 Consensus size: 6
31914100 CAGAATTCAA
31914110 TTTTAT TTTTAT TTTTAT TTTTAT CTTTTAT CTTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT -TTTTAT -TTTTAT T
31914149 CTCTTCAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 19 0.59
7 13 0.41
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:31922493 original size:14 final size:14
Alignment explanation
Indices: 31922474--31922500 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31922464 CAAGGCAGGG
31922474 AAGCGGACCAAGAA
1 AAGCGGACCAAGAA
31922488 AAGCGGACCAAGA
1 AAGCGGACCAAGA
31922501 GTATCATGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.22, G:0.30, T:0.00
Consensus pattern (14 bp):
AAGCGGACCAAGAA
Found at i:31926730 original size:80 final size:80
Alignment explanation
Indices: 31926613--31926902 Score: 404
Period size: 80 Copynumber: 3.6 Consensus size: 80
31926603 AGTTTAACTG
* * * * **
31926613 ACTAAAGCTGGACTCATTTTTGCGGTTTATCCACTAGGCACTAGGTATCAGAATTTGACGGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGAATTTGACGGATAT
*
31926678 TTGTTGCTTAATCCA
66 TTGTTGGTTAATCCA
* * *
31926693 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACT-GTGTGCCA-AGATTTGATGAAC
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAG-GTGCCAGA-ATTTGACGGAT
31926756 ATTTGTTGGTTAATCCA
64 ATTTGTTGGTTAATCCA
* * * * * *
31926773 ACTAGAGCTGGGCTCACTTTTGCGATTTATCCGTTAAGCACTGGGTGCCAGGATTTGACAGATAT
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGAATTTGACGGATAT
31926838 TTGTTGGTTAATCCA
66 TTGTTGGTTAATCCA
31926853 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCA
1 ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCA
31926903 AGATCGTTGG
Statistics
Matches: 184, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.01
80 181 0.98
81 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCAGAATTTGACGGATAT
TTGTTGGTTAATCCA
Found at i:31926894 original size:160 final size:160
Alignment explanation
Indices: 31926613--31926906 Score: 455
Period size: 160 Copynumber: 1.8 Consensus size: 160
31926603 AGTTTAACTG
* * * * *
31926613 ACTAAAGCTGGACTCATTTTTGCGGTTTATCCACTAGGCACTAGGTATCAGAATTTGACGGATAT
1 ACTAAAGCTGGACTCACTTTTGCGATTTATCCACTAAGCACTAGGTACCAGAATTTGACAGATAT
31926678 TTGTTGCTTAATCCAACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACT-GTGTGCC
66 TTGTTGCTTAATCCAACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAG-GTGCC
31926742 AAGATTTGATGAACATTTGTTGGTTAATCCA
130 AAGATTTGATGAACATTTGTTGGTTAATCCA
* * ** * * *
31926773 ACTAGAGCTGGGCTCACTTTTGCGATTTATCCGTTAAGCACTGGGTGCCAGGATTTGACAGATAT
1 ACTAAAGCTGGACTCACTTTTGCGATTTATCCACTAAGCACTAGGTACCAGAATTTGACAGATAT
*
31926838 TTGTTGGTTAATCCAACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCA
66 TTGTTGCTTAATCCAACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCA
31926903 AGAT
131 AGAT
31926907 CGTTGGTTTA
Statistics
Matches: 120, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
160 119 0.99
161 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (160 bp):
ACTAAAGCTGGACTCACTTTTGCGATTTATCCACTAAGCACTAGGTACCAGAATTTGACAGATAT
TTGTTGCTTAATCCAACTAGAGCTGGGCTCACTTTTGCGGTTTATCCGCTAGGCACTAGGTGCCA
AGATTTGATGAACATTTGTTGGTTAATCCA
Found at i:31930684 original size:58 final size:60
Alignment explanation
Indices: 31930612--31930744 Score: 175
Period size: 58 Copynumber: 2.3 Consensus size: 60
31930602 AAAATCGGGA
* *
31930612 TCAAAAATAAAATTTTTTAGACATTCGGGGGTAAAAGGGTAA-TTTTGAAAG-TTTGGGG
1 TCAAAAATGAAATTTTTTAGACATTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGG
* * * *
31930670 TCAAAAATGAAA-TTTTTGGATATTTGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGG
1 TCAAAAATGAAATTTTTTAGACATTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGG
*
31930729 TC-AAAATGTAATTTTT
1 TCAAAAATGAAATTTTT
31930745 GGAAGTTTCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
57 24 0.37
58 28 0.43
59 13 0.20
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (60 bp):
TCAAAAATGAAATTTTTTAGACATTCGAGGGTAAAAGGGTAATTTTTGAAAGTTTTGGGG
Found at i:31930687 original size:29 final size:28
Alignment explanation
Indices: 31930639--31930832 Score: 148
Period size: 29 Copynumber: 6.8 Consensus size: 28
31930629 TAGACATTCG
**
31930639 GGGGTAAAAGGGTAA-TTTTGAAAGTTT
1 GGGGTAAAAATGTAATTTTTGAAAGTTT
* *
31930666 GGGGTCAAAAATGAAATTTTTGGATA-TTT
1 GGGGT-AAAAATGTAATTTTT-GAAAGTTT
31930695 GAGGGT-AAAATGGTAATTTTTGAAAGTTTT
1 G-GGGTAAAAAT-GTAATTTTTGAAAG-TTT
* *
31930725 GGGGTCAAAATGTAATTTTTGGAAGTTT
1 GGGGTAAAAATGTAATTTTTGAAAGTTT
** *
31930753 CAAGGTAAAAATCG-AGATTTTT-AGAATTTT
1 -GGGGTAAAAAT-GTA-ATTTTTGA-AAGTTT
**
31930783 AAGGTAAAAATGTAATTTTT-AAAGTTTT
1 GGGGTAAAAATGTAATTTTTGAAAG-TTT
31930811 GGGGTTAAAAATGTAATTTTTG
1 GGGG-TAAAAATGTAATTTTTG
31930833 GGGTCAAAAA
Statistics
Matches: 136, Mismatches: 15, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.05
28 31 0.23
29 70 0.51
30 28 0.21
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (28 bp):
GGGGTAAAAATGTAATTTTTGAAAGTTT
Found at i:31930760 original size:58 final size:57
Alignment explanation
Indices: 31930641--31930762 Score: 167
Period size: 58 Copynumber: 2.1 Consensus size: 57
31930631 GACATTCGGG
* *
31930641 GGTAAAAGGGTAATTTTGAAAGTTTGGGGTCAAAAATGAAATTTTTGGATATTTGAG
1 GGTAAAAGGGTAATTTTGAAAGTTTGGGGTCAAAAATGAAATTTTTGGATATTTCAA
* *
31930698 GGTAAAATGGTAATTTTTGAAAGTTTTGGGGTC-AAAATGTAATTTTTGGA-AGTTTCAA
1 GGTAAAAGGGTAA-TTTTGAAAG-TTTGGGGTCAAAAATGAAATTTTTGGATA-TTTCAA
31930756 GGTAAAA
1 GGTAAAA
31930763 ATCGAGATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
57 13 0.22
58 36 0.62
59 9 0.16
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.36
Consensus pattern (57 bp):
GGTAAAAGGGTAATTTTGAAAGTTTGGGGTCAAAAATGAAATTTTTGGATATTTCAA
Found at i:31930763 original size:87 final size:87
Alignment explanation
Indices: 31930672--31930833 Score: 231
Period size: 87 Copynumber: 1.9 Consensus size: 87
31930662 GTTTGGGGTC
* * *
31930672 AAAAAT-GAAATTTTTGGATATTTGAGGGT-AAAATGGTAATTTTTGAAAGTTTTGGGG-TCAAA
1 AAAAATCGAAATTTTTAGA-ATTTGAAGGTAAAAAT-GTAATTTTT-AAAGTTTTGGGGTTAAAA
31930734 ATGTAATTTTTGGAAGTTTCAAGGT
63 ATGTAATTTTTGGAAGTTTCAAGGT
* *
31930759 AAAAATCGAGATTTTTAGAATTTTAAGGTAAAAATGTAATTTTTAAAGTTTTGGGGTTAAAAATG
1 AAAAATCGAAATTTTTAGAATTTGAAGGTAAAAATGTAATTTTTAAAGTTTTGGGGTTAAAAATG
31930824 TAATTTTTGG
66 TAATTTTTGG
31930834 GGTCAAAAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
86 12 0.18
87 40 0.60
88 15 0.22
ACGTcount: A:0.36, C:0.02, G:0.22, T:0.40
Consensus pattern (87 bp):
AAAAATCGAAATTTTTAGAATTTGAAGGTAAAAATGTAATTTTTAAAGTTTTGGGGTTAAAAATG
TAATTTTTGGAAGTTTCAAGGT
Found at i:31930849 original size:20 final size:20
Alignment explanation
Indices: 31930807--31930854 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
31930797 ATTTTTAAAG
*
31930807 TTTTGGGGTTAAAAATGTAAT
1 TTTTGGGGTCAAAAATG-AAT
*
31930828 TTTTGGGGTCAAAAATAGATT
1 TTTTGGGGTCAAAAAT-GAAT
31930849 TTTTGG
1 TTTTGG
31930855 AAGTTCGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.25, T:0.44
Consensus pattern (20 bp):
TTTTGGGGTCAAAAATGAAT
Found at i:31930880 original size:29 final size:29
Alignment explanation
Indices: 31930838--31930940 Score: 125
Period size: 29 Copynumber: 3.5 Consensus size: 29
31930828 TTTTGGGGTC
*
31930838 AAAAATAGATTTTTTGGAAGTTCGAAGGT
1 AAAAATAGAATTTTTGGAAGTTCGAAGGT
* **
31930867 AAAAATATAATTTTTGGAAGTTTTAAGGT
1 AAAAATAGAATTTTTGGAAGTTCGAAGGT
**
31930896 CAAAAATAGAATTTTTGGAAGTTCGGGGGT
1 -AAAAATAGAATTTTTGGAAGTTCGAAGGT
* *
31930926 AAAACTATAATTTTT
1 AAAAATAGAATTTTT
31930941 AGATAGTTTA
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
29 38 0.61
30 24 0.39
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAAATAGAATTTTTGGAAGTTCGAAGGT
Found at i:31930901 original size:30 final size:30
Alignment explanation
Indices: 31930834--31930920 Score: 131
Period size: 29 Copynumber: 2.9 Consensus size: 30
31930824 TAATTTTTGG
*
31930834 GGTCAAAAATAGATTTTTTGGAAGTTCGAA
1 GGTCAAAAATAGAATTTTTGGAAGTTCGAA
* **
31930864 GGT-AAAAATATAATTTTTGGAAGTTTTAA
1 GGTCAAAAATAGAATTTTTGGAAGTTCGAA
31930893 GGTCAAAAATAGAATTTTTGGAAGTTCG
1 GGTCAAAAATAGAATTTTTGGAAGTTCG
31930921 GGGGTAAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 25 0.51
30 24 0.49
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.36
Consensus pattern (30 bp):
GGTCAAAAATAGAATTTTTGGAAGTTCGAA
Found at i:31930927 original size:59 final size:60
Alignment explanation
Indices: 31930834--31930949 Score: 180
Period size: 59 Copynumber: 1.9 Consensus size: 60
31930824 TAATTTTTGG
* *
31930834 GGTCAAAAATAGATTTTTTGGAAGTTCGAAGGTAAAAATATAATTTTTGGA-AGTTTTAA
1 GGTCAAAAATAGAATTTTTGGAAGTTCGAAGGTAAAAATATAATTTTTAGATAGTTTTAA
** *
31930893 GGTCAAAAATAGAATTTTTGGAAGTTCGGGGGTAAAACTATAATTTTTAGATAGTTT
1 GGTCAAAAATAGAATTTTTGGAAGTTCGAAGGTAAAAATATAATTTTTAGATAGTTT
31930950 AGGGACCTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 46 0.90
60 5 0.10
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (60 bp):
GGTCAAAAATAGAATTTTTGGAAGTTCGAAGGTAAAAATATAATTTTTAGATAGTTTTAA
Found at i:31932974 original size:17 final size:17
Alignment explanation
Indices: 31932949--31932985 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31932939 CTTTAATTTT
*
31932949 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
31932966 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
31932983 ATT
1 ATT
31932986 CAAACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:31933709 original size:206 final size:206
Alignment explanation
Indices: 31933349--31934753 Score: 1752
Period size: 206 Copynumber: 6.9 Consensus size: 206
31933339 TCTGGTTTTA
* * ** **
31933349 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCAACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* * * * * * ** *
31933414 CTCTGTGTTTCATCAGGAAAAAGGATTTGGTTCACTTCTTTGTATCTCATCAGGAAGTTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
31933479 TTTATTGCTTCGACCTACTTCTCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
31933544 CGAGCGTGGGT
196 CGAGCGTGGGT
** *
31933555 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTTGTTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* * *
31933620 CTCAGTATCTCATTAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
31933685 TTTATTACTTCGACTTGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
31933750 CGAGCGTGGGT
196 CGAGCGTGGGT
* * * *
31933761 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
*
31933826 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
31933891 TTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCGCAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
** *
31933955 TAAGC-----C
196 CGAGCGTGGGT
* * * * * * * * ** **
31933961 TTGAGTTAGTATACTTCTCTGTACCTCATCAGGAAGATAACCGCCCCGTTTGTTTCAATATGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* * * * *
31934026 CTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATTAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * * *
31934091 TTTATTGCTTCAACCCGCTTTTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
*
31934156 CGAGCGTGAGT
196 CGAGCGTGGGT
* ** ** *
31934167 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGAGTCGTTTGTTTCAATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* * *
31934232 CTCTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * *
31934297 TTTATTGTTTCGACCCGCTTTTTAGTATCTCATCTGGAAGCTGGGGTTCGAAGATTTGCTCACAT
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
*
31934362 CGAGCATGGGT
196 CGAGCGTGGGT
* * * *
31934373 TTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACTGCGTC-GTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* *
31934437 CTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
31934502 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAG-TAGGGGTTCGAAGATTTGTTCGCA
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCACA
* * *
31934566 T-TA-AGTTGG-
195 TCGAGCGTGGGT
* * * * *
31934575 -T-A--T--ACTTCTT-T--GTATCTCATCAAGAAGATGATCGTCTCACTTGTTTCTATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
* * * **
31934631 CTCTGTACCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTGTCTCATCAATAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
31934696 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTTGAAGATTTG
131 TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
31934754 TTCGCATTGA
Statistics
Matches: 1048, Mismatches: 142, Indels: 30
0.86 0.12 0.02
Matches are distributed among these distances:
193 21 0.02
194 129 0.12
195 2 0.00
196 6 0.01
198 1 0.00
200 149 0.14
201 23 0.02
203 3 0.00
204 2 0.00
205 154 0.15
206 558 0.53
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
CGAGCGTGGGT
Found at i:31934178 original size:406 final size:405
Alignment explanation
Indices: 31933349--31934753 Score: 1717
Period size: 406 Copynumber: 3.5 Consensus size: 405
31933339 TCTGGTTTTA
* * ** *
31933349 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGATCAACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-TGCATCACTTGTTTCAATCCACTT
* * * * * * ** *
31933414 CTCTGTGTTTCATCAGGAAAAAGGATTTGGTTCACTTCTTTGTATCTCATCAGGAAGTTAACCAT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * *
31933479 TTTATTGCTTCGACCTACTTCTCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
130 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
** *
31933544 CGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTT
195 TAAGC-----TTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-GTTGTT
* * * * * *
31933609 TCAATTTGTTTCTCAGTATCTCATTAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGG
254 TCAATATGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAG
* * * *
31933674 AAGCTAACCATTTTATTACTTCGACTTGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGA
319 AAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGA
*
31933739 TTTGCTCACATCGAGCGTGGGT
384 TTTGCTCACATCGAGCGTGAGT
* * *
31933761 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGA-TGCATCACTTGTTTCAATCCACTT
*
31933826 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCCT
65 CTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* *
31933891 TTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCGCAT
130 TTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACAT
* * * * * * * * *
31933955 TAAGCCTTGAGTTAGTATACTTCTCTGTACCTCATCAGGAAGATAACCGCCCCGTTTGTTTCAAT
195 TAAGCTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCG-TTGTTTCAAT
* * * *
31934020 ATGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATTAAGAAGCT
259 ATGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCT
* * * * *
31934085 AACCATTTTATTGCTTCAACCCGCTTTTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTGC
324 AACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGC
31934150 TCACATCGAGCGTGAGT
389 TCACATCGAGCGTGAGT
**
31934167 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAT-CGAGTCGTTTGTTTCAATCCACT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATGC-A-TCACTTGTTTCAATCCACT
* * *
31934231 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCA
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * * *
31934296 TTTTATTGTTTCGACCCGCTTTTTAGTATCTCATCTGGAAGCTGGGGTTCGAAGATTTGCTCACA
129 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
* * * * *
31934361 TCGAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACTGCGTCGTTGTT
194 T-TA--A--GCTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCGTTGTT
** *
31934426 TCAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAG
254 TCAATATGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAG
31934491 AAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAG-TAGGGGTTCGAAG
319 AAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCT-GGGGTTCGAAG
31934555 ATTTG-T----TC--GC---A--
383 ATTTGCTCACATCGAGCGTGAGT
* * * * ** * * *
31934566 TTAAGTTGGTATACTTCTTTGTATCTCATCAAGAAGATGATCGTC-TCACTTGTTTCTATCCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAT-G-CATCACTTGTTTCAATCCACT
* * * **
31934630 TCTCTGTACCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTGTCTCATCAATAAGCTAACCA
64 TCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* *
31934695 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTTGAAGATTTG
129 TTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
31934754 TTCGCATTGA
Statistics
Matches: 859, Mismatches: 121, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
399 159 0.19
401 1 0.00
402 1 0.00
404 3 0.00
405 2 0.00
406 331 0.39
407 21 0.02
408 1 0.00
410 3 0.00
411 149 0.17
412 188 0.22
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (405 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATGCATCACTTGTTTCAATCCACTTC
TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
TTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATT
AAGCTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTTCAATAT
GCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAA
CCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTC
ACATCGAGCGTGAGT
Found at i:31934551 original size:612 final size:605
Alignment explanation
Indices: 31933362--31934753 Score: 1926
Period size: 612 Copynumber: 2.3 Consensus size: 605
31933352 ATTTGGTCTT
* * * ** ** * ***
31933362 CTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTGAT-CAACTTCTCTGTGTTTCA
1 CTTCTCTGTACCTCATCAAGAAGATAACCGCCCCACTTGTTTCAATAC-GCTTCTCTGTACCTCA
* * * * *** * * * *
31933426 TCAGGAAAAAGGATTTGGTTCACTTCTTTGTATCTCATCAGGAAGTTAACCATTTTATTGCTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATCAAGAAGCTAACCATTTTATTGCTTCA
* * * *
31933491 ACCTACTTCTCAGTATCTCACCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGGGTT
130 ACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTT
* ****
31933556 TGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATTTGTTTC
195 TGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGACTCACTTGTTTCAATCCACTTC
* * *
31933621 TCAGTATCTCATTAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATT
260 TCAGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
**
31933686 TTATTACTTCGACTTGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
325 TTATTACTTCGACCCGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
*
31933751 GAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTT
390 GAGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTT
* *
31933816 CAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGA
455 CAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGA
* *
31933881 AGCTAACCCTTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAGGAAGCTGGGTTCGAAGATT
520 AGCTAACCATTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAAGAAGCTGGGTTCGAAGATT
31933946 TGCTCGCATTAAGCCTTGAGTTAGTATA
585 TGCTCGCATTAAG--TT--G---GTATA
* ** *
31933974 CTTCTCTGTACCTCATCAGGAAGATAACCGCCCCGTTTGTTTCAATATGCTTCTCTGTACCTCAT
1 CTTCTCTGTACCTCATCAAGAAGATAACCGCCCCACTTGTTTCAATACGCTTCTCTGTACCTCAT
*
31934039 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATTAAGAAGCTAACCATTTTATTGCTTCAA
66 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATCAAGAAGCTAACCATTTTATTGCTTCAA
* * * *
31934104 CCCGCTTTTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTGCTCACATCGAGCGTGAGTTT
131 CCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTT
* * **
31934169 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGAGTCGTTTGTTTCAATCCACTTCT
196 GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGACTCACTTGTTTCAATCCACTTCT
* * *
31934234 CTGTATCTCATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCATTT
261 CAGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
** * * * *
31934299 TATTGTTTCGACCCGCTTTTTAGTATCTCATCTGGAAGCTGGGGTTCGAAGATTTGCTCACATCG
326 TATTACTTCGACCCGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCG
* * *
31934364 AGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACTGCGTCG-TTGTTTC
391 AGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTTC
31934428 AATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
456 AATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
* *
31934493 GCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAG-TAGGGGTTCGAAGAT
521 GCTAACCATTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAAGAAGCT--GGGTTCGAAGAT
*
31934557 TTGTTCGCATTAAGTTGGTATA
584 TTGCTCGCATTAAGTTGGTATA
* * * * * * * *
31934579 CTTCTTTGTATCTCATCAAGAAGATGATCGTCTCACTTGTTTCTATCCGCTTCTCTGTACCTCAT
1 CTTCTCTGTACCTCATCAAGAAGATAACCGCCCCACTTGTTTCAATACGCTTCTCTGTACCTCAT
* * * * *
31934644 CAGGAAGACGAATTTGGTCTACTTCTCAGTGTCTCATCAATAAGCTAACCATTTTATTGCTTCAA
66 CAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATCAAGAAGCTAACCATTTTATTGCTTCAA
*
31934709 CCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTTGAAGATTTG
131 CCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTG
31934754 TTCGCATTGA
Statistics
Matches: 687, Mismatches: 90, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
605 157 0.23
608 1 0.00
610 3 0.00
611 115 0.17
612 411 0.60
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (605 bp):
CTTCTCTGTACCTCATCAAGAAGATAACCGCCCCACTTGTTTCAATACGCTTCTCTGTACCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAATATCTAATCAAGAAGCTAACCATTTTATTGCTTCAA
CCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGTGAGTTT
GATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGACTCACTTGTTTCAATCCACTTCT
CAGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTT
TATTACTTCGACCCGATTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCG
AGCATGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAAATGACTGCATCGCTTGTTTC
AATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAAGAA
GCTAACCATTTTATTGCTTCAACCTGCTTCTCAATATCTCATCAAGAAGCTGGGTTCGAAGATTT
GCTCGCATTAAGTTGGTATA
Found at i:31934751 original size:194 final size:194
Alignment explanation
Indices: 31934421--31934795 Score: 626
Period size: 194 Copynumber: 1.9 Consensus size: 194
31934411 GACTGCGTCG
*
31934421 TTGTTTCAATCCGCTTCTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCA
1 TTGTTTCAATCCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCA
*
31934486 TCAAGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGTAGGGGTTC
66 TCAAGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTAGGGGTTC
*
31934551 GAAGATTTGTTCGCATTAAGTTGGTATACTTCTTTGTATCTCATCAAGAAGATGATCGTCTCAC
131 GAAGATTTGTTCGCATTAAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGATCGTCTCAC
* * * *
31934615 TTGTTTCTATCCGCTTCTCTGTACCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTGTCTCA
1 TTGTTTCAATCCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCA
*
31934680 TCAATAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGCT-GGGGTT
66 TCAAGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAG-TAGGGGTT
* * * *
31934744 TGAAGATTTGTTCGCATTGAGTTGGTATACTTCTCTGTATCTTATCAGGAAG
130 CGAAGATTTGTTCGCATTAAGTTGGTATACTTCTCTGTATCTCATCAAGAAG
31934796 CTGGGGTTCG
Statistics
Matches: 168, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
194 167 0.99
195 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (194 bp):
TTGTTTCAATCCGCTTCTCTGTACCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCA
TCAAGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAAGAAGTAGGGGTTC
GAAGATTTGTTCGCATTAAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGATCGTCTCAC
Found at i:31934809 original size:60 final size:60
Alignment explanation
Indices: 31934713--31934855 Score: 250
Period size: 60 Copynumber: 2.4 Consensus size: 60
31934703 CTTCAACCTG
* * *
31934713 CTTCTCAGTATCTCATCAAGAAGCTGGGGTTTGAAGATTTGTTCGCATTGAGTTGGTATA
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATA
*
31934773 CTTCTCTGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATA
1 CTTCTCTGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATA
31934833 CTTCTCTGTATCTCATCAGGAAG
1 CTTCTCTGTATCTCATCAGGAAG
31934856 ATGACCGCCT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 78 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (60 bp):
CTTCTCTGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCGCATTGAGTTGGTATA
Found at i:31935339 original size:92 final size:92
Alignment explanation
Indices: 31935049--31935780 Score: 1015
Period size: 92 Copynumber: 7.9 Consensus size: 92
31935039 TCCAAACTCC
* * * * * * *
31935049 ACTGCATCTTCATGAAGATAGGATTTGGTG-TCGAAGCTTCATCTTGCTCTTACTGCAACTTCAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
* *****
31935113 AGAGATAAAGACTTGTTTATTTGTTTTT
66 AGAGATAAAGACTTG-CTATCCAACTTT
* * * * * *
31935141 AATCCAACTTCAAGAAGATAGGAA-TGAT-ATTGAAGCTTTATCTTGCTCTTACTACAACTTTAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
*
31935204 AGAGAT-AAGACTTGCTATCCATCTTT
66 AGAGATAAAGACTTGCTATCCAACTTT
*
31935230 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTCAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
31935295 AGAGATAAAGACTTGCTATCCAACTTT
66 AGAGATAAAGACTTGCTATCCAACTTT
*
31935322 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTTTTACTACAACTTCAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
*
31935387 ATAGATAAAGACTTGCTATTGTTTTTAATCCAACTTT
66 AGAGATAAAGACTTGC---------T-ATCCAACTTT
* * *
31935424 ACTGCAACTTCAAGAGGATAGGAATTGGTGTTTGAAGCTTCATCTTGCTATTACTACAACTTGAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
31935489 AGAGATAAAGACTTGCTATCCAACTTT
66 AGAGATAAAGACTTGCTATCCAACTTT
* *
31935516 ACTGTAACTTCAAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTGCTCTTACTACAACTTCA
1 ACTGCAACTTC-AAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCA
31935581 GAGAGATAAAGACTTGCTATCCAACTTT
65 GAGAGATAAAGACTTGCTATCCAACTTT
* * *
31935609 ACTGCAACTTCAAAAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTTAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
*
31935674 AAAGATAAAGACTTGCTATCCAACTTT
66 AGAGATAAAGACTTGCTATCCAACTTT
* *
31935701 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTTTTACTAC-ACTTCAG
1 ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
31935765 AGAGATAAAGACTTGC
66 AGAGATAAAGACTTGC
31935781 CATTGTATTT
Statistics
Matches: 580, Mismatches: 45, Indels: 31
0.88 0.07 0.05
Matches are distributed among these distances:
89 28 0.05
90 12 0.02
91 97 0.17
92 267 0.46
93 88 0.15
101 1 0.00
102 87 0.15
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (92 bp):
ACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAG
AGAGATAAAGACTTGCTATCCAACTTT
Found at i:31935484 original size:52 final size:51
Alignment explanation
Indices: 31935318--31935768 Score: 172
Period size: 52 Copynumber: 9.4 Consensus size: 51
31935308 TGCTATCCAA
*
31935318 CTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
1 CTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
* * * * * *** * ***
31935369 CTTTTACTACAACTTC-AGATAGATAAAGACTTGCT-ATTG-TTTTTAATCCAA
1 C-TTTACTACAACTTCAAGA-GGAT-AGGAATTGATGTTTGAAGCTTCATCTTG
* *
31935420 CTTTACTGCAACTTCAAGAGGATAGGAATTGGTGTTTGAAGCTTCATCTTG
1 CTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
* * ***
31935471 CTATTACTACAACTT-GAGAGAGATA--AA--GA--CTT---GC-T-ATCCAA
1 CT-TTACTACAACTTCAAGAG-GATAGGAATTGATGTTTGAAGCTTCATCTTG
** *
31935512 CTTTACTGTAACTTCAAAGAGGATAGGAATTGATGTTTGAAGCTTTATCTTG
1 CTTTACTACAACTTC-AAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
* ***
31935564 CTCTTACTACAACTTC-AGAGAGATA--AA--GA--CTT---GC-T-ATCCAA
1 CT-TTACTACAACTTCAAGAG-GATAGGAATTGATGTTTGAAGCTTCATCTTG
* * *
31935605 CTTTACTGCAACTTCAAAAGGATAGGAATTGATGTTTAAAGCTTCATCTTG
1 CTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
* * * ***
31935656 CTCTTACTACAACTT-TAGAAAGATA--AA--GA--CTT---GC-T-ATCCAA
1 CT-TTACTACAACTTCAAG-AGGATAGGAATTGATGTTTGAAGCTTCATCTTG
* *
31935697 CTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTG
1 CTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
31935748 CTTTTACTAC-ACTTCAGAGAG
1 C-TTTACTACAACTTCA-AGAG
31935769 ATAAAGACTT
Statistics
Matches: 281, Mismatches: 68, Indels: 101
0.62 0.15 0.22
Matches are distributed among these distances:
40 42 0.15
41 24 0.09
42 11 0.04
43 8 0.03
44 4 0.01
45 2 0.01
46 10 0.04
47 2 0.01
48 5 0.02
49 11 0.04
50 29 0.10
51 45 0.16
52 70 0.25
53 18 0.06
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
CTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTG
Found at i:31935684 original size:287 final size:282
Alignment explanation
Indices: 31935082--31935780 Score: 1023
Period size: 287 Copynumber: 2.5 Consensus size: 282
31935072 TTTGGTGTCG
* * * * *
31935082 AAGCTTCATCTTGCTCTTACTGCAACTTCAGAGAGATAAAGACTTG-TTTATTTGT----TTTTA
1 AAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGCTTTTTTTATCCAACTTTA
* * * * * * *
31935142 ATCCAACTTCAAGAAGATAGGAA-TGAT-ATTGAAGCTTTATCTTGCTCTTACTACAACTTTAGA
66 CTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTATTACTACAACTTCAGA
*
31935205 GAGAT-AAGACTTGCTATCCATCTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCT
131 GAGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCT
31935269 TCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACTTCA
196 TCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACTTCA
* *
31935334 AGAGGATAGGAATTGATGTTTG
261 AAAGGATAGGAATTGATGTTTA
* *
31935356 AAGCTTCATCTTGCTTTTACTACAACTTCAGATAGATAAAGACTTGCTATTGTTTTTAATCCAAC
1 AAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGC--TT-TTTTT-ATCCAAC
*
31935421 TTTACTGCAACTTCAAGAGGATAGGAATTGGTGTTTGAAGCTTCATCTTGCTATTACTACAACTT
62 TTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTATTACTACAACTT
* * *
31935486 GAGAGAGATAAAGACTTGCTATCCAACTTTACTGTAACTTCAAAGAGGATAGGAATTGATGTTTG
127 CAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACTTC-AAGAGGATAGGAATTGATGTTTA
*
31935551 AAGCTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAA
191 AAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAA
31935616 CTTCAAAAGGATAGGAATTGATGTTTA
256 CTTCAAAAGGATAGGAATTGATGTTTA
*
31935643 AAGCTTCATCTTGCTCTTACTACAACTTTAGAAAGATAAAGACTTGC------TATCCAACTTTA
1 AAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGCTTTTTTTATCCAACTTTA
* *
31935702 CTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTTTTACTAC-ACTTCAGA
66 CTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTATTACTACAACTTCAGA
31935766 GAGATAAAGACTTGC
131 GAGATAAAGACTTGC
31935781 CATTGTATTT
Statistics
Matches: 385, Mismatches: 27, Indels: 24
0.88 0.06 0.06
Matches are distributed among these distances:
274 43 0.11
276 22 0.06
277 66 0.17
278 5 0.01
279 1 0.00
283 24 0.06
284 3 0.01
285 37 0.10
286 29 0.08
287 155 0.40
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (282 bp):
AAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTTGCTTTTTTTATCCAACTTTA
CTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTATTACTACAACTTCAGA
GAGATAAAGACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCT
TCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACTTCA
AAAGGATAGGAATTGATGTTTA
Found at i:31935733 original size:379 final size:375
Alignment explanation
Indices: 31935049--31935791 Score: 1175
Period size: 379 Copynumber: 2.0 Consensus size: 375
31935039 TCCAAACTCC
* * * * *
31935049 ACTGCATCTTCATGAAGATAGGATTTGGTGTCGAAGCTTCATCTTGCTCTTACTGCAACTTCAGA
1 ACTGCAACTTCAAGAAGATAGGAATTGGTGTCGAAGCTTCATCTTGCTATTACTACAACTTCAGA
* *****
31935114 GAGATAAAGACTTGTTTATTTGTTTTTAATCCAACTTCAAGAAGATAGGAATGATATTGAAGCTT
66 GAGATAAAGACTTGTCTATCCAACTTTAATCCAACTTCAAGAAGATAGGAATGATATTGAAGCTT
* * *
31935179 TATCTTGCTCTTACTACAACTTTAGAGAGATAAGACTTGCTATCCATCTTTACTGCAACTTCAAG
131 TATCTTGCTCTTACTACAACTTCAGAGAGATAAGACTTGCTATCCAACTTTACTGCAACTTCAAA
*
31935244 AGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTT
196 AGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTT
*
31935309 GCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTTTT
261 GCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTTTT
* *
31935374 ACTACAACTTCAGATAGATAAAGACTTGCTATTGT-TTTTAATCCAACTTT
326 ACTAC-ACTTCAGAGAGATAAAGACTTGCCATTGTATTTTAATCCAACTTT
* * *
31935424 ACTGCAACTTCAAGAGGATAGGAATTGGTGTTTGAAGCTTCATCTTGCTATTACTACAACTTGAG
1 ACTGCAACTTCAAGAAGATAGGAATTGGTG-TCGAAGCTTCATCTTGCTATTACTACAACTTCAG
* ** * *
31935489 AGAGATAAAGACTTG-CTATCCAACTTTACTGTAACTTCAAAGAGGATAGGAATTGATGTTTGAA
65 AGAGATAAAGACTTGTCTATCCAACTTTAATCCAACTTC-AAGAAGATAGGAA-TGAT-ATTGAA
31935553 GCTTTATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATCCAACTTTACTGCAACT
127 GCTTTATCTTGCTCTTACTACAACTTCAGAGAGAT-AAGACTTGCTATCCAACTTTACTGCAACT
*
31935618 TCAAAAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTTAGAAAGATAAA
191 TCAAAAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAA
31935683 GACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTG
256 GACTTGCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTG
31935748 CTTTTACTACACTTCAGAGAGATAAAGACTTGCCATTGTATTTT
321 CTTTTACTACACTTCAGAGAGATAAAGACTTGCCATTGTATTTT
31935792 TGATCTGATC
Statistics
Matches: 335, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
375 40 0.12
376 57 0.17
377 4 0.01
378 66 0.20
379 168 0.50
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (375 bp):
ACTGCAACTTCAAGAAGATAGGAATTGGTGTCGAAGCTTCATCTTGCTATTACTACAACTTCAGA
GAGATAAAGACTTGTCTATCCAACTTTAATCCAACTTCAAGAAGATAGGAATGATATTGAAGCTT
TATCTTGCTCTTACTACAACTTCAGAGAGATAAGACTTGCTATCCAACTTTACTGCAACTTCAAA
AGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTCTTACTACAACTTCAGAAAGATAAAGACTT
GCTATCCAACTTTACTGCAACTTCAAGAGGATAGGAATTGATGTTTAAAGCTTCATCTTGCTTTT
ACTACACTTCAGAGAGATAAAGACTTGCCATTGTATTTTAATCCAACTTT
Found at i:31935949 original size:49 final size:49
Alignment explanation
Indices: 31935893--31935997 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
31935883 GCGACTAAAC
* *
31935893 CTTTCCCTTCAAATCTTTATAGTACTAGATCCGCCGTTGC-AGCTTAGAT
1 CTTTCCCTTC-AATCTTCATAGTACTAGATCCGCCGCTGCGAGCTTAGAT
** * * * *
31935942 CTTTCCCTTCTGTCTTCATGGTATTGGATCCGCCGCTGCGATCTTAGAT
1 CTTTCCCTTCAATCTTCATAGTACTAGATCCGCCGCTGCGAGCTTAGAT
31935991 CTTTCCC
1 CTTTCCC
31935998 GTCGGTTTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 22 0.47
49 25 0.53
ACGTcount: A:0.16, C:0.30, G:0.16, T:0.38
Consensus pattern (49 bp):
CTTTCCCTTCAATCTTCATAGTACTAGATCCGCCGCTGCGAGCTTAGAT
Found at i:31936013 original size:49 final size:49
Alignment explanation
Indices: 31935914--31936156 Score: 190
Period size: 49 Copynumber: 5.0 Consensus size: 49
31935904 AATCTTTATA
* * * *
31935914 GTACTAGATCCGCCGTTGC-AGCTTAGATCTTTCCCTTCTGTCTTCATG
1 GTACTGGATCCGCCGTTGCGATCTTAGATCTTTCCCGTCGGTCTTCATG
* * * *
31935962 GTATTGGATCCGCCGCTGCGATCTTAGATCTTTCCCGTCGGTTTTCGTG
1 GTACTGGATCCGCCGTTGCGATCTTAGATCTTTCCCGTCGGTCTTCATG
* * * **
31936011 GTACTGGATCCGCCATTGATG-TCTTAGATCTTTCCCTTATGTCTTCATG
1 GTACTGGATCCGCCGTTG-CGATCTTAGATCTTTCCCGTCGGTCTTCATG
** * * ** ** **
31936060 GTACTGGATCTACCGTCGCG-GCTTAGATCTTTCCTTTATGTCTTCGCG
1 GTACTGGATCCGCCGTTGCGATCTTAGATCTTTCCCGTCGGTCTTCATG
* * *
31936108 GTACCGGATCCGTCGTTGC-AGTCTTAGATCTTTCCCATCGTGT-TTCATG
1 GTACTGGATCCGCCGTTGCGA-TCTTAGATCTTTCCCGTCG-GTCTTCATG
31936157 AAGCTGAGAC
Statistics
Matches: 152, Mismatches: 38, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
48 55 0.36
49 94 0.62
50 3 0.02
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.38
Consensus pattern (49 bp):
GTACTGGATCCGCCGTTGCGATCTTAGATCTTTCCCGTCGGTCTTCATG
Found at i:31936021 original size:97 final size:97
Alignment explanation
Indices: 31935914--31936156 Score: 278
Period size: 97 Copynumber: 2.5 Consensus size: 97
31935904 AATCTTTATA
* * *
31935914 GTACTAGATCCGCCGTTGCAG-CTTAGATCTTTCCCTTCTGTCTTCATGGTATTGGATCCGCCG-
1 GTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTCTGTCTTCATGGTACTGGATCCACCGT
* * * *
31935977 CTGCGATCTTAGATCTTTCCCGTCGGTTTTCGTG
66 C-GCG-GCTTAGATCTTTCCCGTAGGTCTTCGCG
* * *
31936011 GTACTGGATCCGCCATTG-ATGTCTTAGATCTTTCCCTTATGTCTTCATGGTACTGGATCTACCG
1 GTACTGGATCCGCCGTTGCA-GTCTTAGATCTTTCCCTTCTGTCTTCATGGTACTGGATCCACCG
** *
31936075 TCGCGGCTTAGATCTTTCCTTTATGTCTTCGCG
65 TCGCGGCTTAGATCTTTCCCGTAGGTCTTCGCG
* * *
31936108 GTACCGGATCCGTCGTTGCAGTCTTAGATCTTTCCCATCGTGT-TTCATG
1 GTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTC-TGTCTTCATG
31936157 AAGCTGAGAC
Statistics
Matches: 123, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
96 1 0.01
97 76 0.62
98 45 0.37
99 1 0.01
ACGTcount: A:0.14, C:0.27, G:0.22, T:0.38
Consensus pattern (97 bp):
GTACTGGATCCGCCGTTGCAGTCTTAGATCTTTCCCTTCTGTCTTCATGGTACTGGATCCACCGT
CGCGGCTTAGATCTTTCCCGTAGGTCTTCGCG
Found at i:31937387 original size:12 final size:12
Alignment explanation
Indices: 31937353--31937387 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
31937343 CCTCGACCTC
31937353 TCTTTTCTTTTT
1 TCTTTTCTTTTT
31937365 TCTTCTT-TTTTT
1 TCTT-TTCTTTTT
31937377 TCTTTTCTTTT
1 TCTTTTCTTTT
31937388 ATTCATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 2 0.10
12 17 0.81
13 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TCTTTTCTTTTT
Found at i:31943056 original size:57 final size:58
Alignment explanation
Indices: 31942943--31943133 Score: 160
Period size: 57 Copynumber: 3.3 Consensus size: 58
31942933 TTAAAAAATC
* ** * * *
31942943 AGGATCAAAAATGAAATTTTTTGGACATTCAGGGGTAAAAGGATAA-TTTTGAAAGTTCG
1 AGGATCAAAAAT-AAAATTTTTGGGTATTCGGGGGCAAATGG-TAATTTTTGAAAGTTCG
31943002 -GGATCAAAAATAAAATTTTTGGGTATTCGGGGGCAAATGGTAATTTTTGAAAGTTCG
1 AGGATCAAAAATAAAATTTTTGGGTATTCGGGGGCAAATGGTAATTTTTGAAAGTTCG
* ** * * *
31943059 AGGGT-AAAAATGTAATTTTTGGAAGT-TTTGGGGTCAAAAATGG-AATTTTTGAAAGTTTG
1 AGGATCAAAAATAAAATTTTTGG--GTATTCGGGGGC--AAATGGTAATTTTTGAAAGTTCG
*
31943118 AGGGT-AAAAATTAAAA
1 AGGATCAAAAA-TAAAA
31943134 ATTTAATTTT
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
56 3 0.03
57 51 0.46
58 21 0.19
59 27 0.24
60 9 0.08
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (58 bp):
AGGATCAAAAATAAAATTTTTGGGTATTCGGGGGCAAATGGTAATTTTTGAAAGTTCG
Found at i:31943098 original size:30 final size:28
Alignment explanation
Indices: 31943036--31943268 Score: 189
Period size: 29 Copynumber: 7.8 Consensus size: 28
31943026 ATTCGGGGGC
* *
31943036 AAATGGTAATTTTTGAAAGTTCGAGGGTAA
1 AAAT-GTAATTTTTGGAAGTTTG-GGGTAA
31943066 AAATGTAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGTAATTTTTGGAAG-TTTGGGGT-AA
* *
31943096 AAATGGAATTTTTGAAAGTTTGAGGGTAAAAATTAA
1 AAATGTAATTTTTGGAAGTTTG-GGG-------TAA
* *
31943132 AAATTTAATTTTTGGAAGTTTTGGGGTCA
1 AAATGTAATTTTTGGAAG-TTTGGGGTAA
*
31943161 AAATGGAATTTTTGGAAGTTTGGGGT-A
1 AAATGTAATTTTTGGAAGTTTGGGGTAA
*
31943188 AAATGTAATTTTTGGAAGTTTTAGGGTTAA
1 AAATGTAATTTTTGGAAG-TTT-GGGGTAA
* **
31943218 AAATGGAATTTTTAAAAGTTTGTGGGTAA
1 AAATGTAATTTTTGGAAGTTTG-GGGTAA
* *
31943247 AAATGTATTTTTTAGATAGTTT
1 AAATGTAATTTTTGGA-AGTTT
31943269 AGGGACCTTC
Statistics
Matches: 168, Mismatches: 19, Indels: 32
0.77 0.09 0.15
Matches are distributed among these distances:
27 18 0.11
28 12 0.07
29 64 0.38
30 49 0.29
36 20 0.12
37 5 0.03
ACGTcount: A:0.34, C:0.01, G:0.24, T:0.40
Consensus pattern (28 bp):
AAATGTAATTTTTGGAAGTTTGGGGTAA
Found at i:31943198 original size:56 final size:59
Alignment explanation
Indices: 31943129--31943272 Score: 188
Period size: 57 Copynumber: 2.5 Consensus size: 59
31943119 GGGTAAAAAT
* * **
31943129 TAAAAATTTAATTTTTGGAAGTTTT-GGGGTCAAAATGGAATTTTTGGAAGTTTG-GGG
1 TAAAAATGTAATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTAAAAGTTTGTGGG
*
31943186 T-AAAATGTAATTTTTGGAAGTTTTAGGGTTAAAAATGGAATTTTTAAAAGTTTGTGGG
1 TAAAAATGTAATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTAAAAGTTTGTGGG
* *
31943244 TAAAAATGTATTTTTTAGATAG-TTTAGGG
1 TAAAAATGTAATTTTTGGA-AGTTTTAGGG
31943273 ACCTTCAGGG
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
56 22 0.29
57 26 0.34
58 4 0.05
59 22 0.29
60 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.25, T:0.42
Consensus pattern (59 bp):
TAAAAATGTAATTTTTGGAAGTTTTAGGGGTAAAAATGGAATTTTTAAAAGTTTGTGGG
Found at i:31944476 original size:12 final size:13
Alignment explanation
Indices: 31944456--31944489 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
31944446 ATTTAAAAAA
31944456 TATTTATTAATAT
1 TATTTATTAATAT
*
31944469 TA-TTATTACTAT
1 TATTTATTAATAT
31944481 TATTTATTA
1 TATTTATTA
31944490 TAAATGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATTAATAT
Found at i:31945333 original size:17 final size:17
Alignment explanation
Indices: 31945263--31945333 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 17
31945253 CCTTAATTTT
* *
31945263 ATTTTAATTTAAAAAAA
1 ATTTAAATTTAAAATAA
*
31945280 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * * *
31945297 ACTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
31945314 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
31945331 ATT
1 ATT
31945334 CAAACTTATT
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:31946227 original size:31 final size:31
Alignment explanation
Indices: 31946185--31946256 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
31946175 AAGGGGGCTT
31946185 AGCCCTCC-AAAATTTTGAAAAATTATAATTA
1 AGCCCTCCAAAAATTTT-AAAAATTATAATTA
* *
31946216 AGCCCTTCAAAAATTTTAAAAATTTTAATT-
1 AGCCCTCCAAAAATTTTAAAAATTATAATTA
*
31946246 AGACCTCCAAA
1 AGCCCTCCAAA
31946257 GTTTTATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 9 0.25
31 19 0.53
32 8 0.22
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (31 bp):
AGCCCTCCAAAAATTTTAAAAATTATAATTA
Found at i:31950443 original size:16 final size:16
Alignment explanation
Indices: 31950407--31950450 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
31950397 AACTTTTGAC
*
31950407 ATTTTTATTTAATAAT
1 ATTTTTATTTATTAAT
* *
31950423 CTTTTTATTTATTTAT
1 ATTTTTATTTATTAAT
*
31950439 ATTTTAATTTAT
1 ATTTTTATTTAT
31950451 ATTTCTTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTTATTTATTAAT
Found at i:31952340 original size:42 final size:42
Alignment explanation
Indices: 31952281--31952364 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
31952271 CAAATATTTT
*
31952281 TAAACCCAAATATAATTTCATTCTTCAAA-AACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCT-AAATAACACTCATAAAC
*
31952323 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
31952365 AACTCCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAATAACACTCATAAAC
Found at i:31952716 original size:69 final size:72
Alignment explanation
Indices: 31952643--31952783 Score: 173
Period size: 72 Copynumber: 2.0 Consensus size: 72
31952633 TTGTCGTGTA
* * *
31952643 GATTTTTACTGTATT-TTAAACTTTTGCTTATGTTT-TT-TTATAATCTTGTTATGTTATTGTTG
1 GATTTATACTGT-TTATTAAACTTTTACTTATGTTTGTTATTATAATCTTGTTATGTTATTATTG
31952705 -TTACTTT
65 TTTACTTT
* * * *
31952712 GATTTATATTGTTTACTTAAACTTTTACTTATTTTTGTTATTATAATCTTGTTGTGTTGTTATTG
1 GATTTATACTGTTTA-TTAAACTTTTACTTATGTTTGTTATTATAATCTTGTTATGTTATTATTG
31952777 TTTACTT
65 TTTACTT
31952784 GGGTTTTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
68 2 0.03
69 10 0.17
70 18 0.30
71 2 0.03
72 22 0.37
73 6 0.10
ACGTcount: A:0.20, C:0.07, G:0.11, T:0.62
Consensus pattern (72 bp):
GATTTATACTGTTTATTAAACTTTTACTTATGTTTGTTATTATAATCTTGTTATGTTATTATTGT
TTACTTT
Done.