Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 2 of 33
Found at i:116059 original size:9 final size:9
Alignment explanation
Indices: 115979--116061 Score: 61
Period size: 9 Copynumber: 9.7 Consensus size: 9
115969 AATTTTTTTA
115979 TAATATATT
1 TAATATATT
*
115988 TAAATATAAT
1 T-AATATATT
*
115998 TAATATAAT
1 TAATATATT
*
116007 TGATATAATT
1 TAATAT-ATT
116017 T-AT-TATT
1 TAATATATT
*
116024 TATTATA-T
1 TAATATATT
116032 T--TATATT
1 TAATATATT
*
116039 TAAAAT-TT
1 TAATATATT
116047 TAATATATT
1 TAATATATT
116056 TAATAT
1 TAATAT
116062 TTATATTATG
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
6 4 0.07
7 6 0.10
8 11 0.18
9 28 0.47
10 11 0.18
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
TAATATATT
Found at i:119175 original size:2 final size:2
Alignment explanation
Indices: 119168--119201 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
119158 TATCATTGCA
* *
119168 AT AT AT AT AT AT AT AT AT AA AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119202 GTTTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:119898 original size:24 final size:25
Alignment explanation
Indices: 119851--119898 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
119841 TCTCTTTTTA
119851 ATTTAATTATCATAAGAATATAATGT
1 ATTTAATTA-CATAAGAATATAATGT
*
119877 ATTTAATTA-ATAGGAATATAAT
1 ATTTAATTACATAAGAATATAAT
119899 TTTATAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
26 9 0.43
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTTAATTACATAAGAATATAATGT
Found at i:120054 original size:400 final size:399
Alignment explanation
Indices: 119247--120064 Score: 864
Period size: 400 Copynumber: 2.0 Consensus size: 399
119237 CTTATAATGC
* *
119247 TTTTAATTGTTTGATAACTAATTAGATTTATTTGATAAACTTAAATAAATTTAAAAAATAAAATT
1 TTTTAATTGTTTGATAACTAATTAGATTCATTTGATAAACTTAAATAAACTTAAAAAATAAAATT
* *
119312 TTATATTTAGACATTGATTGAATAACATATGTTTATATTTATTTATTAAAATAAATGAATTGATT
66 TTATATTTAGACATTGATTGAATAACA-A---TTATATTCATTTATTAAAATAAATAAATTGATT
* * *
119377 CGCATGTGAGATAAGAATATATTTACATTTATATGTAAACAATATAAAGTTTAAGCTTGATAAGT
127 CGCATGTCAAATAAGAATATATTTACATTTATATATAAACAATATAAAGTTTAAGCTTGATAAGT
* * * *
119442 CTTTTTTTAATTTAATTATCATAGGAATATAATGAATTTAATTGATAGAAATATGTTTTGATAAA
192 CTCTTTTTAATTTAATTATCATAAGAATATAATGAATTTAATTAATAGAAATATATTTTGATAAA
* *
119507 AAAAAAATGAAGAAACTTATAAATACTTTAGCATTCTACATTAACAAATTACAATGAACTAAACA
257 AAAAAAATGAAGAAACTTATAAATACTTTAGAACTCTACATTAACAAATTACAATGAACTAAACA
* ** * ** * *** * * * ** * * ** *
119572 TATAGTTTGAATTATTTCACTCATTTTTTTTTTTATATTTTTAATATTAGTTATTTATTTATTCA
322 TAGAGAATAAAGGATTTCAC-AATTAAATATTTAAAAAGTATAATATAAACTATTTATCTATT-A
* * **
119637 ATCTTTTACTTATTG
385 ATCTATAACCAATTG
*
119652 TTTTTAATTGTTTGATAACTAATTAGATTCATTTGATAAACTTAAATAAACTTGAAAAATAAAAT
1 -TTTTAATTGTTTGATAACTAATTAGATTCATTTGATAAACTTAAATAAACTTAAAAAATAAAAT
* *
119717 TTTATATTTAGACATTGATTGAATAAC-A-TATATTCATTTATTAAAATGAATAAATTGATTTGC
65 TTTATATTTAGACATTGATTGAATAACAATTATATTCATTTATTAAAATAAATAAATTGATTCGC
* *
119780 ATGTCAAATTAGAATATATTTACATTTATATATAAATAATATAAAGTTTAAGCTTGATAAGTCTC
130 ATGTCAAATAAGAATATATTTACATTTATATATAAACAATATAAAGTTTAAGCTTGATAAGTCTC
* * **
119845 TTTTTAATTTAATTATCATAAGAATATAATGTATTTAATTAATAGGAATATAATTTT-AT-AAGG
195 TTTTTAATTTAATTATCATAAGAATATAATGAATTTAATTAATAGAAATAT-ATTTTGATAAAAA
* * * * * ** ** * *
119908 AAATATTAAGAAATTTATAAATATTTTAGAACTCTACGTTAACAACTAATTATTATTTA-TTAAG
259 AAAAATGAAGAAACTTATAAATACTTTAGAACTCTACATTAAC-A--AATTACAATGAACTAAAC
* * *
119972 TTAGGAGAAAATAAAGGA-TTCA-AATTAAATATTTAAGGAAAGTATAATCCTAAACT-TTTCTC
321 ATA-GAG--AATAAAGGATTTCACAATTAAATATTTAA--AAAGTATAAT-ATAAACTATTTATC
120034 TATT-AT-TATAACCAATTG
380 TATTAATCTATAACCAATTG
*
120052 TTTTATTTGTTTG
1 TTTTAATTGTTTG
120065 TTATTATCTT
Statistics
Matches: 341, Mismatches: 61, Indels: 27
0.79 0.14 0.06
Matches are distributed among these distances:
399 50 0.15
400 148 0.43
401 19 0.06
402 10 0.03
403 18 0.05
404 8 0.02
406 88 0.26
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.43
Consensus pattern (399 bp):
TTTTAATTGTTTGATAACTAATTAGATTCATTTGATAAACTTAAATAAACTTAAAAAATAAAATT
TTATATTTAGACATTGATTGAATAACAATTATATTCATTTATTAAAATAAATAAATTGATTCGCA
TGTCAAATAAGAATATATTTACATTTATATATAAACAATATAAAGTTTAAGCTTGATAAGTCTCT
TTTTAATTTAATTATCATAAGAATATAATGAATTTAATTAATAGAAATATATTTTGATAAAAAAA
AAATGAAGAAACTTATAAATACTTTAGAACTCTACATTAACAAATTACAATGAACTAAACATAGA
GAATAAAGGATTTCACAATTAAATATTTAAAAAGTATAATATAAACTATTTATCTATTAATCTAT
AACCAATTG
Found at i:122431 original size:18 final size:18
Alignment explanation
Indices: 122405--122445 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
122395 GTTTTACGAC
*
122405 TAAAATTTATTGATCAAA-
1 TAAAGTTTATTGAT-AAAG
122423 TAAAGTTTATTGATAAAG
1 TAAAGTTTATTGATAAAG
122441 TAAAG
1 TAAAG
122446 AGTAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (18 bp):
TAAAGTTTATTGATAAAG
Found at i:123162 original size:4 final size:4
Alignment explanation
Indices: 123136--123197 Score: 97
Period size: 4 Copynumber: 15.5 Consensus size: 4
123126 ACCATGGTAT
* * *
123136 TATA TACA TACA TATA TACA TATA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
123184 TATA TATA TATA TA
1 TATA TATA TATA TA
123198 CAAATTTTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:123716 original size:21 final size:20
Alignment explanation
Indices: 123692--123744 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
123682 AACTAGTAAA
123692 ATAAAAT-TACTAACTATTATT
1 ATAAAATATA-TAACTA-TATT
*
123713 ATAAAATATATAATTATATT
1 ATAAAATATATAACTATATT
123733 ATAAAA-ATATAA
1 ATAAAATATATAA
123745 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 6 0.20
20 10 0.33
21 12 0.40
22 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATATATAACTATATT
Found at i:123760 original size:21 final size:21
Alignment explanation
Indices: 123715--123760 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
123705 CTATTATTAT
*
123715 AAAATATATAATTATATTATA
1 AAAATATATAATTATATAATA
*
123736 AAAATATA-AATTTTATAATA
1 AAAATATATAATTATATAATA
123756 GAAAA
1 -AAAA
123761 ACATTATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATATATAATTATATAATA
Found at i:124384 original size:15 final size:15
Alignment explanation
Indices: 124354--124440 Score: 59
Period size: 15 Copynumber: 5.7 Consensus size: 15
124344 ATATTGCTTA
124354 AAACTTGAAATTATTT
1 AAACTT-AAATTATTT
*
124370 AAACTTAAATAATTT
1 AAACTTAAATTATTT
* * * *
124385 GAGCTCAAA-TATATC
1 AAACTTAAATTAT-TT
124400 AAACTTAAATTATTT
1 AAACTTAAATTATTT
* * *
124415 AAATCTAAAAATACTT
1 AAA-CTTAAATTATTT
*
124431 AAATTTAAAT
1 AAACTTAAAT
124441 AACATAAATC
Statistics
Matches: 52, Mismatches: 16, Indels: 7
0.69 0.21 0.09
Matches are distributed among these distances:
14 2 0.04
15 29 0.56
16 21 0.40
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (15 bp):
AAACTTAAATTATTT
Found at i:126720 original size:16 final size:15
Alignment explanation
Indices: 126699--126728 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
126689 TTTATCAATG
126699 TAATATAATATTATTT
1 TAATATAA-ATTATTT
126715 TAATATAAATTATT
1 TAATATAAATTATT
126729 AATCTTATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATATAAATTATTT
Found at i:128489 original size:4 final size:4
Alignment explanation
Indices: 128482--128508 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
128472 TCTATGTATA
128482 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
128509 GACATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:129554 original size:17 final size:17
Alignment explanation
Indices: 129534--129567 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
129524 TTTTCTCCTT
*
129534 TTTATTTTTATATTTTA
1 TTTATATTTATATTTTA
129551 TTTATATTTATATTTTA
1 TTTATATTTATATTTTA
129568 CATAAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATATTTATATTTTA
Found at i:134310 original size:29 final size:30
Alignment explanation
Indices: 134278--134334 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
134268 CGTTGTTGCC
*
134278 AAAAGTACCTAT-ACCAAAATACATGTGTT
1 AAAAGTACCTATGACAAAAATACATGTGTT
* *
134307 AAAAGTACCTTTGTCAAAAATACATGTG
1 AAAAGTACCTATGACAAAAATACATGTG
134335 ACAAAGTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAAGTACCTATGACAAAAATACATGTGTT
Found at i:134356 original size:14 final size:15
Alignment explanation
Indices: 134337--134374 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
134327 TACATGTGAC
134337 AAAGTACTTATATT-
1 AAAGTACTTATATTA
*
134351 AAAGTATTTATATTA
1 AAAGTACTTATATTA
134366 AAAGTACTT
1 AAAGTACTT
134375 GTACCAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (15 bp):
AAAGTACTTATATTA
Found at i:134395 original size:14 final size:14
Alignment explanation
Indices: 134376--134405 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
134366 AAAGTACTTG
134376 TACCAAAATATTTA
1 TACCAAAATATTTA
*
134390 TACCAAAGTATTTA
1 TACCAAAATATTTA
134404 TA
1 TA
134406 TAAAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
TACCAAAATATTTA
Found at i:136752 original size:28 final size:27
Alignment explanation
Indices: 136691--136752 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
136681 AGATCAAAAT
* *
136691 ATATTTAAATATAAATATAAAATATAA
1 ATATTTAAATAAAAATATAAAAGATAA
* *
136718 TTTTTTAAATAAAAA-ATTAAAAAGATAA
1 ATATTTAAATAAAAATA-T-AAAAGATAA
136746 ATATTTA
1 ATATTTA
136753 CATCTCGGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.04
27 13 0.48
28 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATTTAAATAAAAATATAAAAGATAA
Found at i:142082 original size:24 final size:24
Alignment explanation
Indices: 142055--142100 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
142045 TGCTTTTTTG
* *
142055 ATTATGTAATATTTTATTTATATA
1 ATTATATAATATTTAATTTATATA
*
142079 ATTATATATTATTTAATTTATA
1 ATTATATAATATTTAATTTATA
142101 GAATATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
ATTATATAATATTTAATTTATATA
Found at i:142201 original size:23 final size:24
Alignment explanation
Indices: 142169--142216 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
142159 TATTATATTT
*
142169 TAAAATTTAATA-AAATAAAAATA
1 TAAAAATTAATATAAATAAAAATA
142192 TAAAAATTAATATTAAATAAAAATA
1 TAAAAATTAATA-TAAATAAAAATA
142217 ATATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
25 11 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAAAATTAATATAAATAAAAATA
Found at i:142934 original size:2 final size:2
Alignment explanation
Indices: 142927--142975 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
142917 TGTTGTTGAA
*
142927 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
142969 AT -T AT AT
1 AT AT AT AT
142976 CTGCACAACG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:145974 original size:20 final size:18
Alignment explanation
Indices: 145946--145988 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
145936 GTTAGAAAAG
145946 TTTAAAAAATTTAAATATAT
1 TTTAAAAAA-TTAAA-ATAT
*
145966 TTTATAAAATTAAAATAT
1 TTTAAAAAATTAAAATAT
145984 TTTAA
1 TTTAA
145989 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTAAAAAATTAAAATAT
Found at i:145999 original size:27 final size:28
Alignment explanation
Indices: 145947--146022 Score: 70
Period size: 28 Copynumber: 2.8 Consensus size: 28
145937 TTAGAAAAGT
* *
145947 TTAAAAAATTTAAATATATTTT-ATAA-AA
1 TTAAAATATTTTAAT-T-TTTTAATAATAA
145975 TTAAAATATTTTAATTTTTTAATAATAA
1 TTAAAATATTTTAATTTTTTAATAATAA
*
146003 TT-AATTACTTTT-ATTTTTTA
1 TTAAAATA-TTTTAATTTTTTA
146023 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 4 0.10
27 17 0.40
28 21 0.50
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAAATATTTTAATTTTTTAATAATAA
Found at i:148913 original size:28 final size:28
Alignment explanation
Indices: 148881--148935 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
148871 GTTAATATTT
*
148881 AATTA-AAAATAACAAATTTTTTATTATA
1 AATTATAAAATAA-AAAATTTTTATTATA
* *
148909 AATTATTATATAAAAAATTTTTATTAT
1 AATTATAAAATAAAAAATTTTTATTAT
148936 CGTATTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTATAAAATAAAAAATTTTTATTATA
Found at i:159142 original size:34 final size:34
Alignment explanation
Indices: 159096--159280 Score: 257
Period size: 34 Copynumber: 5.5 Consensus size: 34
159086 GTAAAAACCA
*
159096 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
159130 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
159164 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
159198 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
159232 CCATTTAGTCAACAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
159265 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
159281 TCTCCCACTT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.26, G:0.08, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:163409 original size:19 final size:20
Alignment explanation
Indices: 163354--163410 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 20
163344 ACAGTAACCG
* *
163354 TATACTTGAATAGTA-CTCG
1 TATACGTGAATAGTACCTCA
163373 TATACGTGAATAGTACCT-A
1 TATACGTGAATAGTACCTCA
163392 TATACGTGAATAGTACCTC
1 TATACGTGAATAGTACCTC
163411 GACAACCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 32 0.94
20 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (20 bp):
TATACGTGAATAGTACCTCA
Found at i:163759 original size:34 final size:34
Alignment explanation
Indices: 163713--163897 Score: 248
Period size: 34 Copynumber: 5.5 Consensus size: 34
163703 GTAAAAACCA
*
163713 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
163747 CCATTTAGTCAACAATGGTAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGGT-AACCTACCAAATCTC
* *
163781 CCATTTAATCAATAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
163815 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
163849 CCATTTAGTCAACAATGGTAAACTACCAAAT-TA
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
163882 CCATTTAATTAACAAT
1 CCATTTAATCAACAAT
163898 ATATATATAT
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
33 18 0.13
34 113 0.84
35 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:163903 original size:2 final size:2
Alignment explanation
Indices: 163896--163928 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
163886 TTAATTAACA
163896 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
163929 GTATGGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:164147 original size:2 final size:2
Alignment explanation
Indices: 164140--164171 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
164130 AAAGGCCAGA
164140 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
164172 TAATCCAGAA
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:167141 original size:2 final size:2
Alignment explanation
Indices: 167099--167126 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
167089 TATTGAAGTA
167099 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
167127 TGGTGAGATT
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:168834 original size:2 final size:2
Alignment explanation
Indices: 168827--168868 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
168817 CCTTTTAATT
168827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
168869 AACCATTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:168988 original size:28 final size:27
Alignment explanation
Indices: 168923--168995 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
168913 AAAGTCATTT
* *
168923 TTTGTTTTTGTCAAAAATGATGGTTCC
1 TTTGTATTTGTAAAAAATGATGGTTCC
*
168950 TTTGTGTTTGTAAAAAATGATGGTTCC
1 TTTGTATTTGTAAAAAATGATGGTTCC
*
168977 TTTTTTATTTGTAAAAAAT
1 -TTTGTATTTGTAAAAAAT
168996 AGTGACTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 25 0.61
28 16 0.39
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (27 bp):
TTTGTATTTGTAAAAAATGATGGTTCC
Found at i:173449 original size:27 final size:27
Alignment explanation
Indices: 173416--173484 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
173406 ACAATTTATA
173416 TTTGTCAAAAATGGTTATTCCTTTGTG
1 TTTGTCAAAAATGGTTATTCCTTTGTG
*
173443 TTTGTCAACAATGGTTATTCCTTTGTG
1 TTTGTCAAAAATGGTTATTCCTTTGTG
*
173470 TTTCTCAAAAATGGT
1 TTTGTCAAAAATGGT
173485 GGCTTGTTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTTATTCCTTTGTG
Found at i:174932 original size:22 final size:22
Alignment explanation
Indices: 174885--174983 Score: 78
Period size: 19 Copynumber: 4.4 Consensus size: 22
174875 TAAGCCTGGG
*
174885 TTTTATTATATAAAT-TAT-T-
1 TTTTATAATATAAATATATATA
174904 TTTTATAATATAAATATATATA
1 TTTTATAATATAAATATATATA
* * *
174926 TTTTATAAGAATGTTATAAAATTTATA
1 TTTTAT---AAT-ATA-AATATATATA
*
174953 TTTTTATAATATAACTATATATA
1 -TTTTATAATATAAATATATATA
174976 TTTTATAA
1 TTTTATAA
174984 GAATAAATCT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
19 14 0.22
20 3 0.05
21 1 0.02
22 14 0.22
23 7 0.11
24 2 0.03
25 6 0.10
26 2 0.03
27 8 0.13
28 6 0.10
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTATAATATAAATATATATA
Found at i:174959 original size:50 final size:49
Alignment explanation
Indices: 174890--174987 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 49
174880 CTGGGTTTTA
174890 TTATATAAATTATTTTTTATAATATAAATATATATATTTTATAAGAATG
1 TTATATAAATTATTTTTTATAATATAAATATATATATTTTATAAGAATG
*
174939 TTATA-AAATTTATATTTTTATAATATAACTATATATATTTTATAAGAAT
1 TTATATAAA-TTAT-TTTTTATAATATAAATATATATATTTTATAAGAAT
174988 AAATCTAACT
Statistics
Matches: 46, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 3 0.07
49 9 0.20
50 34 0.74
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (49 bp):
TTATATAAATTATTTTTTATAATATAAATATATATATTTTATAAGAATG
Found at i:174989 original size:28 final size:27
Alignment explanation
Indices: 174908--174989 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
174898 ATTATTTTTT
174908 ATAATATAAATATATATATTTTATAAGA
1 ATAATAT-AATATATATATTTTATAAGA
** * *
174936 ATGTTATAAAATTTATATTTT-T----
1 ATAATATAATATATATATTTTATAAGA
174958 ATAATATAACTATATATATTTTATAAGA
1 ATAATATAA-TATATATATTTTATAAGA
174986 ATAA
1 ATAA
174990 ATCTAACTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
22 7 0.17
23 10 0.25
24 1 0.03
26 1 0.03
27 12 0.30
28 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (27 bp):
ATAATATAATATATATATTTTATAAGA
Found at i:178462 original size:25 final size:26
Alignment explanation
Indices: 178406--178464 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
178396 AAATTATATT
* *
178406 TAAATTTA-ATTCGTTTAATAATAGA
1 TAAATTTATATTCATTTAATAATAAA
* *
178431 TATATTTATATTCATTTAA-ATTAAA
1 TAAATTTATATTCATTTAATAATAAA
178456 TAAATTTAT
1 TAAATTTAT
178465 TCATAAATAC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
25 19 0.68
26 9 0.32
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (26 bp):
TAAATTTATATTCATTTAATAATAAA
Found at i:179156 original size:15 final size:15
Alignment explanation
Indices: 179136--179164 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
179126 ATTGATATTC
179136 GAATTTAATTTGATT
1 GAATTTAATTTGATT
179151 GAATTTAATTTGAT
1 GAATTTAATTTGAT
179165 AAATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
GAATTTAATTTGATT
Found at i:180256 original size:18 final size:19
Alignment explanation
Indices: 180233--180268 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
180223 GATTGAATTA
*
180233 ATTGATTTTTTA-AGTTGT
1 ATTGATATTTTATAGTTGT
180251 ATTGATATTTTATAGTTG
1 ATTGATATTTTATAGTTG
180269 AAAATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (19 bp):
ATTGATATTTTATAGTTGT
Found at i:180804 original size:17 final size:17
Alignment explanation
Indices: 180753--180807 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
180743 ATAATGTTTC
180753 AAAATTTATAT-AATAT
1 AAAATTTATATAAATAT
180769 -AAA-TTAT-TAATATATT
1 AAAATTTATATAA-ATA-T
180785 AAAATTTATATAAATAT
1 AAAATTTATATAAATAT
180802 AAAATT
1 AAAATT
180808 AAATTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 6 0.18
16 1 0.03
17 10 0.30
18 7 0.21
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAATTTATATAAATAT
Found at i:181540 original size:19 final size:19
Alignment explanation
Indices: 181516--181556 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
181506 ATACAAGTTA
* *
181516 TATATATGTATGTATGATT
1 TATATATATATATATGATT
181535 TATATATATATATATGATT
1 TATATATATATATATGATT
181554 TAT
1 TAT
181557 TGGTTAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (19 bp):
TATATATATATATATGATT
Found at i:186470 original size:20 final size:21
Alignment explanation
Indices: 186445--186486 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
186435 TTAAATTTAA
*
186445 TATTTATTTTATA-TTAAAAT
1 TATTTATTTAATACTTAAAAT
186465 TATTTATTTAATACTTAAAAT
1 TATTTATTTAATACTTAAAAT
186486 T
1 T
186487 TTAATACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTTATTTAATACTTAAAAT
Found at i:186539 original size:20 final size:20
Alignment explanation
Indices: 186502--186540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
186492 ACAAATTAAC
* *
186502 TAATTAAATTAATTATAAAT
1 TAATTAAATCAATAATAAAT
*
186522 TAATTAAATCGATAATAAA
1 TAATTAAATCAATAATAAA
186541 AAATCCCAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TAATTAAATCAATAATAAAT
Found at i:188338 original size:18 final size:18
Alignment explanation
Indices: 188315--188350 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
188305 AACTAAGATG
188315 CCATGCATAATTTTGGTT
1 CCATGCATAATTTTGGTT
188333 CCATGCATAATTTTGGTT
1 CCATGCATAATTTTGGTT
188351 TTCACAGGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
CCATGCATAATTTTGGTT
Found at i:191411 original size:25 final size:25
Alignment explanation
Indices: 191359--191448 Score: 71
Period size: 25 Copynumber: 3.6 Consensus size: 25
191349 ATTTAAAATT
* * * *
191359 TTAAAATATTTAATTTATATTAAATA
1 TTAAATTATTTAATTAAAATT-ATTA
*
191385 TTAAATTATTTAATT-AACTATATTA
1 TTAAATTATTTAATTAAAAT-TATTA
191410 TTAAA-TA-TTATATTAAAATTATTAA
1 TTAAATTATTTA-ATTAAAATTATT-A
191435 TT-AATTATTTAATT
1 TTAAATTATTTAATT
191449 TAATTAATTC
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
23 3 0.06
24 11 0.21
25 21 0.40
26 18 0.34
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAAATTATTTAATTAAAATTATTA
Found at i:191423 original size:12 final size:12
Alignment explanation
Indices: 191364--191431 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
191354 AAATTTTAAA
*
191364 ATATTTAAT-TT
1 ATATTAAATATT
191375 ATATTAAATATT
1 ATATTAAATATT
*
191387 AAATT--AT-TT
1 ATATTAAATATT
*
191396 A-ATTAACTA-T
1 ATATTAAATATT
191406 ATTATTAAATATT
1 A-TATTAAATATT
191419 ATATTAAA-ATT
1 ATATTAAATATT
191430 AT
1 AT
191432 TAATTAATTA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 5 0.11
11 13 0.28
12 20 0.43
13 2 0.04
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (12 bp):
ATATTAAATATT
Found at i:191446 original size:21 final size:21
Alignment explanation
Indices: 191359--191434 Score: 63
Period size: 24 Copynumber: 3.6 Consensus size: 21
191349 ATTTAAAATT
*
191359 TTAAAA-TATTTAAT-TTATA
1 TTAAAATTATTAAATATTATA
191378 TT-AAA-TATTAAATTATT-TAA
1 TTAAAATTATTAAA-TATTAT-A
191398 TTAACTATATTATTAAATATTATA
1 TTAA--A-ATTATTAAATATTATA
191422 TTAAAATTATTAA
1 TTAAAATTATTAA
191435 TTAATTATTT
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
18 9 0.19
19 4 0.09
20 5 0.11
21 9 0.19
22 1 0.02
23 1 0.02
24 10 0.21
25 8 0.17
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAAATTATTAAATATTATA
Found at i:191448 original size:12 final size:12
Alignment explanation
Indices: 191388--191454 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
191378 TTAAATATTA
191388 AATTATTTAATT
1 AATTATTTAATT
*
191400 AACTATATT-ATT
1 AATTAT-TTAATT
*
191412 AAATA-TTATATT
1 AATTATTTA-ATT
191424 AAAATTA-TTAATT
1 --AATTATTTAATT
191437 AATTATTTAATTT
1 AATTATTTAA-TT
191450 AATTA
1 AATTA
191455 ATTCAACAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
10 2 0.04
11 5 0.11
12 19 0.42
13 12 0.27
14 7 0.16
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (12 bp):
AATTATTTAATT
Found at i:196807 original size:18 final size:18
Alignment explanation
Indices: 196784--196819 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
196774 AATCGATCGA
196784 AATCGATCAAATTTGGTT
1 AATCGATCAAATTTGGTT
196802 AATCGATCAAATTTGGTT
1 AATCGATCAAATTTGGTT
196820 TATCTAGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
AATCGATCAAATTTGGTT
Found at i:197274 original size:3 final size:3
Alignment explanation
Indices: 197266--197290 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
197256 ATCGATCAGT
197266 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
197291 TCATACTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:204153 original size:17 final size:19
Alignment explanation
Indices: 204119--204158 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
204109 TTTTTAAAAA
*
204119 AATAAATATATCTATGTTG
1 AATAAATATATCTATGTTC
204138 AATAAATA-AT-TATGTTC
1 AATAAATATATCTATGTTC
204155 AATA
1 AATA
204159 CTTATATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 10 0.50
18 2 0.10
19 8 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (19 bp):
AATAAATATATCTATGTTC
Found at i:205093 original size:2 final size:2
Alignment explanation
Indices: 205086--205120 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
205076 GTTTGGTGAC
*
205086 TA TA TA TA TA TA TA TA TA TA TA TA CA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
205121 GGATTTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:205243 original size:2 final size:2
Alignment explanation
Indices: 205236--205260 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
205226 CATTAAATAC
205236 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
205261 TTGCGTGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:208010 original size:4 final size:4
Alignment explanation
Indices: 207990--208048 Score: 73
Period size: 4 Copynumber: 14.8 Consensus size: 4
207980 ATATTAACGA
* * * * *
207990 ATAT ATGT ATCT ATAT ATAT ATAT CTAT ATAT GTAT CTAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
208038 ATAT ATAT ATA
1 ATAT ATAT ATA
208049 CCTTATTGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:208019 original size:26 final size:26
Alignment explanation
Indices: 207990--208047 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
207980 ATATTAACGA
*
207990 ATATATGTATCTATATATATATATCT
1 ATATATGTATCTATATATATATATAT
208016 ATATATGTATCTATATATATATATAT
1 ATATATGTATCTATATATATATATAT
208042 ATATAT
1 ATATAT
208048 ACCTTATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (26 bp):
ATATATGTATCTATATATATATATAT
Found at i:212487 original size:25 final size:24
Alignment explanation
Indices: 212440--212485 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
212430 GACTGTCCAG
212440 TTTATTTTTCTAAATTATTTTATT
1 TTTATTTTTCTAAATTATTTTATT
212464 TTTATTTTT-TAAA-TA-TTTATT
1 TTTATTTTTCTAAATTATTTTATT
212485 T
1 T
212486 ATAACCTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 2 0.09
23 4 0.18
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTATTTTTCTAAATTATTTTATT
Found at i:214524 original size:21 final size:23
Alignment explanation
Indices: 214498--214546 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
214488 CTTGTTTTGC
*
214498 TATTTAAT-TTTTTTAT-ATTAA
1 TATTTAATATATTTTATAATTAA
214519 TATTT-ATATATTTTATAATTAA
1 TATTTAATATATTTTATAATTAA
214541 -ATTTAA
1 TATTTAA
214547 ATAAAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 16 0.67
22 6 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTAATATATTTTATAATTAA
Found at i:215812 original size:22 final size:20
Alignment explanation
Indices: 215774--215816 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
215764 TTAAAGTTTA
*
215774 AATTTAAAAATCAAAAAAGT
1 AATTTAAAAATAAAAAAAGT
215794 AATTTAAAAAATAAGAAAAAGT
1 AATTT-AAAAATAA-AAAAAGT
215816 A
1 A
215817 TAGCTCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.23
Consensus pattern (20 bp):
AATTTAAAAATAAAAAAAGT
Found at i:216729 original size:27 final size:29
Alignment explanation
Indices: 216670--216730 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
216660 ATATTTAAAG
216670 TTTTATAAATTTATTATATAAAAAAATTA
1 TTTTATAAATTTATTATATAAAAAAATTA
* *
216699 --TTATAAATTT-TTATA-AAATAATTTA
1 TTTTATAAATTTATTATATAAAAAAATTA
216724 TTTTATA
1 TTTTATA
216731 TTGATGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
25 8 0.29
26 5 0.18
27 15 0.54
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
TTTTATAAATTTATTATATAAAAAAATTA
Found at i:216963 original size:32 final size:30
Alignment explanation
Indices: 216927--217009 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 30
216917 AAATATTATA
216927 TATATAAATTTTTATATATTAATAATTTATTT
1 TATATAAATTTTTATATATTAAT-ATTT-TTT
* * *
216959 TATATAAATTTTAATTTTTTAATATTTTTT
1 TATATAAATTTTTATATATTAATATTTTTT
*
216989 AAT-TAAATTTATTATTATATT
1 TATATAAATTT-TTA-TATATT
217010 TTAAATTTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 7 0.17
30 7 0.17
31 8 0.19
32 20 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATATAAATTTTTATATATTAATATTTTTT
Found at i:216995 original size:29 final size:32
Alignment explanation
Indices: 216903--216998 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 32
216893 TTCATATTAT
* *
216903 TTTTAATATATTTGA-AATATTATAT-ATATAAA
1 TTTTAATATA-TTAATAAT-TTATTTAATATAAA
* *
216935 TTTTTATATATTAATAATTTATTTTATATAAA
1 TTTTAATATATTAATAATTTATTTAATATAAA
* *
216967 TTTTAATTTTTTAAT-ATTT-TTTAAT-TAAA
1 TTTTAATATATTAATAATTTATTTAATATAAA
216996 TTT
1 TTT
216999 ATTATTATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.13
30 5 0.09
31 12 0.22
32 31 0.56
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (32 bp):
TTTTAATATATTAATAATTTATTTAATATAAA
Found at i:217018 original size:42 final size:41
Alignment explanation
Indices: 216966--217052 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
216956 TTTTATATAA
* *
216966 ATTTTAATTTTTTAATATT-TTTTAATT-AAATT-TATTATTAT
1 ATTTTAA--TTTT-ATATTATTATAATTAAAATTAAATTATTAT
217007 ATTTTAAATTTTATATTATTATAATTAAAATTAAATTATTAT
1 ATTTT-AATTTTATATTATTATAATTAAAATTAAATTATTAT
217049 ATTT
1 ATTT
217053 ATTATATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
39 5 0.12
40 11 0.28
41 10 0.25
42 14 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (41 bp):
ATTTTAATTTTATATTATTATAATTAAAATTAAATTATTAT
Found at i:217026 original size:22 final size:21
Alignment explanation
Indices: 216993--217052 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
216983 TTTTTTAATT
216993 AAATT-TATTATTATATTTTA
1 AAATTATATTATTATATTTTA
* *
217013 AATTTTATATTATTATA-ATTA
1 AA-ATTATATTATTATATTTTA
*
217034 AAATTAAATTATTATATTT
1 AAATTATATTATTATATTT
217053 ATTATATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
20 14 0.44
21 8 0.25
22 10 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATTATATTATTATATTTTA
Found at i:217048 original size:28 final size:29
Alignment explanation
Indices: 217010--217079 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 29
217000 TTATTATATT
217010 TTAAATT-TTATATTATTATA-ATTAAAA
1 TTAAATTATTATATTATTATATATTAAAA
* *
217037 TTAAATTATTATATTTATTATATATTTATA
1 TTAAATTATTATA-TTATTATATATTAAAA
217067 -TAAA-TATTATATT
1 TTAAATTATTATATT
217080 CAAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 9 0.24
28 12 0.32
29 12 0.32
30 5 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (29 bp):
TTAAATTATTATATTATTATATATTAAAA
Found at i:217387 original size:21 final size:20
Alignment explanation
Indices: 217361--217402 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
217351 TTAAAAGCAA
*
217361 AATATATATATTTATATTTAT
1 AATATATAAATTTAT-TTTAT
217382 AATATATAAATTTATTTTAT
1 AATATATAAATTTATTTTAT
217402 A
1 A
217403 CATTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATATATAAATTTATTTTAT
Found at i:217531 original size:8 final size:8
Alignment explanation
Indices: 217510--217566 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
217500 AATTTTTATA
217510 TAAAA-AT
1 TAAAATAT
*
217517 TATAATAT
1 TAAAATAT
217525 TAAAATA-
1 TAAAATAT
217532 -AAAATAAT
1 TAAAAT-AT
217540 TAAAAATAT
1 T-AAAATAT
217549 TAAAATA-
1 TAAAATAT
*
217556 TAAAATTT
1 TAAAATAT
217564 TAA
1 TAA
217567 TTTATTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
6 5 0.12
7 11 0.27
8 17 0.41
9 3 0.07
10 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAAATAT
Found at i:217560 original size:15 final size:16
Alignment explanation
Indices: 217510--217566 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
217500 AATTTTTATA
*
217510 TAAAA-ATTATAATAT
1 TAAAATATTAAAATAT
217525 TAAAATA--AAAATAAT
1 TAAAATATTAAAAT-AT
217540 TAAAAATATTAAAATA-
1 T-AAAATATTAAAATAT
*
217556 TAAAATTTTAA
1 TAAAATATTAA
217567 TTTATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 4 0.11
15 17 0.49
16 8 0.23
17 1 0.03
18 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAATATTAAAATAT
Found at i:218480 original size:28 final size:28
Alignment explanation
Indices: 218432--218490 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
218422 ATTTAATTAT
* *
218432 ATTTATATATTTTTTATATAATAAATAA
1 ATTTATATATTATATATATAATAAATAA
* *
218460 ATTTATATAATTATATA-ATAATTAATTA
1 ATTTATAT-ATTATATATATAATAAATAA
218488 ATT
1 ATT
218491 AAGATATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTATATATTATATATATAATAAATAA
Found at i:218956 original size:20 final size:21
Alignment explanation
Indices: 218931--218969 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
218921 AACCTATTTT
*
218931 TATAATTCA-AATTTAATACA
1 TATAATTCATAACTTAATACA
218951 TATAATTCATAACTTAATA
1 TATAATTCATAACTTAATA
218970 TTTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAATTCATAACTTAATACA
Found at i:223942 original size:2 final size:2
Alignment explanation
Indices: 223935--223974 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
223925 ATCAAGTAGC
*
223935 AT AT AT AT AT AT AT AT AT AT -T GCT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT
223975 TGCTTCAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223963 original size:20 final size:20
Alignment explanation
Indices: 223938--223978 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
223928 AAGTAGCATA
223938 TATATATATATATATATTGC
1 TATATATATATATATATTGC
223958 TATATATATATATATATTGC
1 TATATATATATATATATTGC
223978 T
1 T
223979 TCAAGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (20 bp):
TATATATATATATATATTGC
Found at i:225773 original size:21 final size:21
Alignment explanation
Indices: 225749--225845 Score: 76
Period size: 21 Copynumber: 4.6 Consensus size: 21
225739 TTAAAAATTT
225749 TATTTTTAATTAATATTTATA
1 TATTTTTAATTAATATTTATA
*
225770 TATTTTATAATTAA-ATTTAAA
1 TATTTT-TAATTAATATTTATA
* *
225791 TATTTTATATTTTATTATTTA-A
1 TATTTT-TA-ATTAATATTTATA
* *
225813 TATTTTTTATT-ATGCTTTATA
1 TATTTTTAATTAAT-ATTTATA
225834 T-TTTATTAATTA
1 TATTT-TTAATTA
225846 TGTAATATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
19 1 0.02
20 9 0.15
21 29 0.48
22 17 0.28
23 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (21 bp):
TATTTTTAATTAATATTTATA
Found at i:225782 original size:22 final size:21
Alignment explanation
Indices: 225749--225818 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
225739 TTAAAAATTT
225749 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAATATTTA-A
225770 TATTTTATAATTAA-ATTTAAA
1 TATTTTATAATTAATATTT-AA
* *
225791 TATTTTATATTTTATTATTTAA
1 TATTTTATA-ATTAATATTTAA
225813 TATTTT
1 TATTTT
225819 TTATTATGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
21 20 0.47
22 19 0.44
23 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTATAATTAATATTTAA
Found at i:225822 original size:17 final size:17
Alignment explanation
Indices: 225800--225853 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
225790 ATATTTTATA
225800 TTTTATTATTTAATATT
1 TTTTATTATTTAATATT
*
225817 TTTTATTATGCTTTATATT
1 TTTTATTAT--TTAATATT
*
225836 TTATTAATTATGTAATAT
1 TT-TT-ATTATTTAATAT
225854 AAATAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.30
19 14 0.47
20 2 0.07
21 5 0.17
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTTATTATTTAATATT
Found at i:226909 original size:20 final size:21
Alignment explanation
Indices: 226872--226911 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
226862 ACTTGTTTTA
226872 TAAAAAATAATTTATAAAAAG
1 TAAAAAATAATTTATAAAAAG
226893 TAAAAAA-AAGTTT-TAAAAA
1 TAAAAAATAA-TTTATAAAAA
226912 ATTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (21 bp):
TAAAAAATAATTTATAAAAAG
Found at i:228008 original size:20 final size:19
Alignment explanation
Indices: 227967--228008 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
227957 TTCGGATGGT
* *
227967 TAAATTTTATATTTTAATA
1 TAAAATTTATATTTTAACA
227986 TAAAATTTATATTTTAAACA
1 TAAAATTTATATTTT-AACA
228006 TAA
1 TAA
228009 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAATTTATATTTTAACA
Found at i:240247 original size:20 final size:21
Alignment explanation
Indices: 240222--240264 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
240212 TAAAAAATAA
*
240222 TAAAAATTT-TATTTTGATTC
1 TAAAAATTTATATTTTAATTC
240242 TAAAAATTTATATTTTAATTC
1 TAAAAATTTATATTTTAATTC
240263 TA
1 TA
240265 CTACCAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (21 bp):
TAAAAATTTATATTTTAATTC
Found at i:242267 original size:13 final size:13
Alignment explanation
Indices: 242251--242275 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242241 TCAATAAAAT
242251 TATAAAATAATAG
1 TATAAAATAATAG
242264 TATAAAATAATA
1 TATAAAATAATA
242276 AAATTGTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
TATAAAATAATAG
Found at i:243056 original size:11 final size:11
Alignment explanation
Indices: 243037--243141 Score: 78
Period size: 11 Copynumber: 10.0 Consensus size: 11
243027 TTAATAATTT
*
243037 TAAAAATAATA
1 TAAATATAATA
243048 TAAATATAATA
1 TAAATATAATA
243059 T-AA-AT-ATA
1 TAAATATAATA
*
243067 CAAATAT-ATA
1 TAAATATAATA
* *
243077 AAAAT-TTATA
1 TAAATATAATA
*
243087 TAAATATAAAA
1 TAAATATAATA
*
243098 TAACT-TAAATA
1 TAAATAT-AATA
* *
243109 TGATTATAATA
1 TAAATATAATA
*
243120 TAAAAATAATA
1 TAAATATAATA
243131 TAAATATAATA
1 TAAATATAATA
243142 ATTTTCATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
8 3 0.04
9 5 0.07
10 19 0.26
11 46 0.62
12 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (11 bp):
TAAATATAATA
Found at i:243071 original size:28 final size:27
Alignment explanation
Indices: 243039--243141 Score: 113
Period size: 28 Copynumber: 3.7 Consensus size: 27
243029 AATAATTTTA
243039 AAAATAATATAAATATAATATAAATAT
1 AAAATAATATAAATATAATATAAATAT
* *
243066 ACAAAT-ATATAAAAATTTATATAAATAT
1 A-AAATAATATAAATA-TAATATAAATAT
*
243094 AAAATAACT-TAAATATGAT-TATAATAT
1 AAAATAA-TATAAATATAATATA-AATAT
243121 AAAAATAATATAAATATAATA
1 -AAAATAATATAAATATAATA
243142 ATTTTCATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
26 2 0.03
27 22 0.35
28 38 0.60
29 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (27 bp):
AAAATAATATAAATATAATATAAATAT
Found at i:243350 original size:14 final size:14
Alignment explanation
Indices: 243329--243365 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
243319 AAAATAAAAG
243329 ATTATAAATATTAAA
1 ATTATAAAT-TTAAA
243344 ATT-TAAATTTAAA
1 ATTATAAATTTAAA
243357 ATTATAAAT
1 ATTATAAAT
243366 GGTTAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.38
14 10 0.48
15 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTATAAATTTAAA
Found at i:248091 original size:2 final size:2
Alignment explanation
Indices: 248086--248120 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
248076 ATATATATAT
248086 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
248121 AATTTTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:249561 original size:16 final size:16
Alignment explanation
Indices: 249540--249571 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
249530 ATATTAAAAT
249540 TTAAATATTAAATTTA
1 TTAAATATTAAATTTA
*
249556 TTAAATATTATATTTA
1 TTAAATATTAAATTTA
249572 AAAAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATTAAATTTA
Found at i:250190 original size:24 final size:22
Alignment explanation
Indices: 250142--250198 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 22
250132 CTTTAGATTA
250142 TTATTTAATTAATAAAAAAATT
1 TTATTTAATTAATAAAAAAATT
*
250164 TTATTTAAATTTAATAATAAATATT
1 TTATTT-AA-TTAATAA-AAAAATT
250189 TAATATTTAA
1 T--TATTTAA
250199 ATATATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 6 0.21
23 2 0.07
24 7 0.24
25 7 0.24
26 2 0.07
27 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATTTAATTAATAAAAAAATT
Found at i:250195 original size:27 final size:24
Alignment explanation
Indices: 250142--250200 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 24
250132 CTTTAGATTA
250142 TTATTT-AA-TTAATAAAAAAATT
1 TTATTTAAATTTAATAAAAAAATT
*
250164 TTATTTAAATTTAATAATAAATATT
1 TTATTTAAATTTAATAA-AAAAATT
250189 TAATATTTAAAT
1 T--TATTTAAAT
250201 ATATTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 6 0.19
23 2 0.06
24 7 0.23
25 7 0.23
27 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATTTAAATTTAATAAAAAAATT
Found at i:250209 original size:38 final size:37
Alignment explanation
Indices: 250166--250275 Score: 111
Period size: 38 Copynumber: 3.0 Consensus size: 37
250156 AAAAAATTTT
250166 ATTTAAAT-TTAATAATAAATATTTAATATTTAAATA
1 ATTTAAATATTAATAATAAATATTTAATATTTAAATA
* *
250202 TATTTTAAATAATAA-AATAAATTTTTAA-ATTTAAA-A
1 -A-TTTAAATATTAATAATAAATATTTAATATTTAAATA
* * *
250238 AATTAAATCTTAATAAATAAATATTTTATTATTTAAAT
1 ATTTAAATATTAAT-AATAAATA-TTTAATATTTAAAT
250276 TTAATTCGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
34 9 0.15
35 1 0.02
36 8 0.14
37 12 0.20
38 26 0.44
39 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTAAATATTAATAATAAATATTTAATATTTAAATA
Found at i:250212 original size:19 final size:19
Alignment explanation
Indices: 250179--250241 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
250169 TAAATTTAAT
250179 AATAAATATTT-AATATTTA
1 AATAAAT-TTTAAATATTTA
* * *
250198 AATATATTTTAAATAATAA
1 AATAAATTTTAAATATTTA
*
250217 AATAAATTTTTAA-ATTTA
1 AATAAATTTTAAATATTTA
250235 AA-AAATT
1 AATAAATT
250242 AAATCTTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
17 5 0.14
18 8 0.22
19 23 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATAAATTTTAAATATTTA
Found at i:250261 original size:59 final size:59
Alignment explanation
Indices: 250145--250261 Score: 132
Period size: 59 Copynumber: 2.0 Consensus size: 59
250135 TAGATTATTA
* * * **
250145 TTTAATTAATAAAAAAATTTTATTTAAATTTAATAATAAATATTTAATATTTAAATATAT
1 TTTAAATAATAAAAAAA-TTTATTTAAATTTAAAAATAAATACTTAATAAATAAATATAT
250205 TTTAAATAATAAAATAAA-TT-TTTAAATTTAAAAAATTAAAT-CTTAATAAATAAATAT
1 TTTAAATAATAAAA-AAATTTATTTAAATTT-AAAAA-TAAATACTTAATAAATAAATAT
250262 TTTATTATTT
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
58 9 0.18
59 19 0.39
60 18 0.37
61 3 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (59 bp):
TTTAAATAATAAAAAAATTTATTTAAATTTAAAAATAAATACTTAATAAATAAATATAT
Found at i:253060 original size:12 final size:12
Alignment explanation
Indices: 253043--253068 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
253033 TATTATTGCC
253043 AAAAAATATTTT
1 AAAAAATATTTT
253055 AAAAAATATTTT
1 AAAAAATATTTT
253067 AA
1 AA
253069 TTGCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAAAATATTTT
Found at i:253101 original size:35 final size:37
Alignment explanation
Indices: 253056--253168 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 37
253046 AAATATTTTA
*
253056 AAAAATATTTTAATTGCAT-T-ATAA-TTAAATAAAAT
1 AAAAATATTTTAATT-AATATAATAATTTAAATAAAAT
*
253091 AAAAATATTTTTATTAATAAATAATAATTTAAATAAAAT
1 AAAAATATTTTAATTAAT--ATAATAATTTAAATAAAAT
*
253130 AAAAATAGTTTT-ATTAATAAATAATAATTTAAGTAAAAT
1 AAAAATA-TTTTAATTAAT--ATAATAATTTAAATAAAAT
253169 CTAATTAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
34 2 0.03
35 14 0.20
37 1 0.01
38 4 0.06
39 44 0.64
40 4 0.06
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.40
Consensus pattern (37 bp):
AAAAATATTTTAATTAATATAATAATTTAAATAAAAT
Found at i:253108 original size:39 final size:40
Alignment explanation
Indices: 253076--253168 Score: 147
Period size: 39 Copynumber: 2.4 Consensus size: 40
253066 TAATTGCATT
*
253076 ATAA-TTAAATAAAATAAAAATATTTTTATTAA-TAAATA
1 ATAATTTAAATAAAATAAAAATAGTTTTATTAATTAAATA
253114 ATAATTTAAATAAAATAAAAATAGTTTTATTAA-TAAATA
1 ATAATTTAAATAAAATAAAAATAGTTTTATTAATTAAATA
*
253153 ATAATTTAAGTAAAAT
1 ATAATTTAAATAAAAT
253169 CTAATTAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
38 4 0.08
39 48 0.92
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (40 bp):
ATAATTTAAATAAAATAAAAATAGTTTTATTAATTAAATA
Found at i:253114 original size:22 final size:21
Alignment explanation
Indices: 253087--253153 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
253077 TAATTAAATA
253087 AAATAAAAATATTTTTATTAAT
1 AAATAAAAATA-TTTTATTAAT
*
253109 AAAT---AATAATTTA--AAT
1 AAATAAAAATATTTTATTAAT
253125 AAAATAAAAATAGTTTTATTAAT
1 -AAATAAAAATA-TTTTATTAAT
253148 AAATAA
1 AAATAA
253154 TAATTTAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 3 0.08
17 4 0.11
18 4 0.11
19 4 0.11
20 4 0.11
21 4 0.11
22 10 0.28
23 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (21 bp):
AAATAAAAATATTTTATTAAT
Found at i:254764 original size:96 final size:96
Alignment explanation
Indices: 254646--254827 Score: 337
Period size: 96 Copynumber: 1.9 Consensus size: 96
254636 TATAACATTA
*
254646 CTTGATCAATCTCTAATTAGATTGAAATTTTGGTGATTCAATGATTTCATATTTTCAAATTTCTG
1 CTTGATCAATCTCTAATTAGATTGAAATTTTGGTGATTCAATGATTTCATATTTCCAAATTTCTG
*
254711 CATTACGTCAGATTCTTGCAGCATAGCGTTG
66 CATTACATCAGATTCTTGCAGCATAGCGTTG
*
254742 CTTGATCAATCTTTAATTAGATTGAAATTTTGGTGATTCAATGATTTCATATTTCCAAATTTCTG
1 CTTGATCAATCTCTAATTAGATTGAAATTTTGGTGATTCAATGATTTCATATTTCCAAATTTCTG
254807 CATTACATCAGATTCTTGCAG
66 CATTACATCAGATTCTTGCAG
254828 GAAGCTACTT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.42
Consensus pattern (96 bp):
CTTGATCAATCTCTAATTAGATTGAAATTTTGGTGATTCAATGATTTCATATTTCCAAATTTCTG
CATTACATCAGATTCTTGCAGCATAGCGTTG
Found at i:257563 original size:23 final size:23
Alignment explanation
Indices: 257533--257587 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
257523 AAACTTTCAT
257533 AAAAAAATTATACTATTTTTTTA
1 AAAAAAATTATACTATTTTTTTA
*
257556 AAAAAAATTATACTATTTTTTTT
1 AAAAAAATTATACTATTTTTTTA
257579 AAAAAAATT
1 AAAAAAATT
257588 TATTTTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAAAATTATACTATTTTTTTA
Found at i:257786 original size:38 final size:37
Alignment explanation
Indices: 257708--257819 Score: 104
Period size: 38 Copynumber: 2.9 Consensus size: 37
257698 TGAATTTTGA
257708 TTTAGTTTAAATTTATATTTAATAATTAAAAATAATTT
1 TTTA-TTTAAATTTATATTTAATAATTAAAAATAATTT
*
257746 TTTATTTAAATTT-TATTATAA-AATATATAAATATTATTT
1 TTTATTTAAATTTATATT-TAATAAT-TA-AAA-ATAATTT
* * *
257785 TTTA-TTAAATATAAATTAAATTAAATTAAAAATAA
1 TTTATTTAAATTTATATTTAA-T-AATTAAAAATAA
257820 ACTTAAATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
36 7 0.11
37 14 0.23
38 19 0.31
39 16 0.26
40 2 0.03
41 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (37 bp):
TTTATTTAAATTTATATTTAATAATTAAAAATAATTT
Found at i:257809 original size:10 final size:11
Alignment explanation
Indices: 257788--257834 Score: 60
Period size: 11 Copynumber: 4.3 Consensus size: 11
257778 ATTATTTTTT
257788 ATTAAATATAA
1 ATTAAATATAA
257799 ATTAAAT-TAA
1 ATTAAATATAA
*
257809 ATTAAAAATAA
1 ATTAAATATAA
*
257820 ACTTAAATAAAA
1 A-TTAAATATAA
257832 ATT
1 ATT
257835 TTGAAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
10 9 0.29
11 13 0.42
12 9 0.29
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
ATTAAATATAA
Found at i:257809 original size:16 final size:16
Alignment explanation
Indices: 257788--257834 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
257778 ATTATTTTTT
257788 ATTAAATATAAATTAA
1 ATTAAATATAAATTAA
*
257804 ATTAAAT-TAAAAATAA
1 ATTAAATAT-AAATTAA
*
257820 ACTTAAATAAAAATT
1 A-TTAAATATAAATT
257835 TTGAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 14 0.56
17 10 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTAAATATAAATTAA
Found at i:266625 original size:21 final size:21
Alignment explanation
Indices: 266586--266625 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
266576 CATTAATTAG
* **
266586 ATGAAAAAATGTATTTTTTGA
1 ATGAAAAAATATAACTTTTGA
266607 ATGAAAAAATATAACTTTT
1 ATGAAAAAATATAACTTTT
266626 AATAACCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGAAAAAATATAACTTTTGA
Found at i:269065 original size:23 final size:21
Alignment explanation
Indices: 269017--269065 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
269007 TTTAATAATA
* *
269017 TATAATATAATATTATTTATT
1 TATAATAAAATATTATATATT
269038 T-TAATAAAATATTAATATAGTT
1 TATAATAAAATATT-ATATA-TT
269060 TATAAT
1 TATAAT
269066 TTTAATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.48
21 5 0.22
22 3 0.13
23 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATAATAAAATATTATATATT
Found at i:269197 original size:23 final size:21
Alignment explanation
Indices: 269151--269198 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
269141 ATAGTATTTT
* *
269151 AATAATATTTATATTAATTGA
1 AATAATATTTATAATAATTAA
269172 AATAATATTTTAATAATAATTAA
1 AATAATA-TTT-ATAATAATTAA
269195 AATA
1 AATA
269199 TTTTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 7 0.30
22 3 0.13
23 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATAATATTTATAATAATTAA
Found at i:269371 original size:22 final size:23
Alignment explanation
Indices: 269341--269401 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
269331 TAGTTTAATG
*
269341 ATAAATAGTTTTTAATATTT-TA
1 ATAATTAGTTTTTAATATTTATA
*
269363 ATAATTAGTATTTAATATTTATA
1 ATAATTAGTTTTTAATATTTATA
* *
269386 AAAATATTGTTTTTAA
1 ATAAT-TAGTTTTTAA
269402 AAAATGTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 18 0.56
23 6 0.19
24 8 0.25
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (23 bp):
ATAATTAGTTTTTAATATTTATA
Found at i:269447 original size:18 final size:19
Alignment explanation
Indices: 269424--269475 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
269414 AACGTTTTAA
269424 AAATAATTATATTAATA-T
1 AAATAATTATATTAATATT
*
269442 AAATAATCT-TATAAATATT
1 AAATAAT-TATATTAATATT
269461 AATATAATTAATATT
1 AA-ATAATT-ATATT
269476 TTAATAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 14 0.52
19 5 0.19
20 5 0.19
21 3 0.11
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATAATTATATTAATATT
Found at i:269860 original size:22 final size:22
Alignment explanation
Indices: 269830--269871 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
269820 TAGTTTAATG
*
269830 ATAAATAGTTTTTAATATTTTA
1 ATAAATAGTATTTAATATTTTA
*
269852 ATAATTAGTATTTAATATTT
1 ATAAATAGTATTTAATATTT
269872 ATAACAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAAATAGTATTTAATATTTTA
Found at i:270231 original size:32 final size:32
Alignment explanation
Indices: 270180--270253 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
270170 AAATAACGTG
* * **
270180 AATTTAAAATGACTCGATATCAAAATGATTTA
1 AATTCAAAATGACTCGATATCAAAACGACCTA
* * *
270212 AATTCAAAATGATTTGATATCGAAACGACCTA
1 AATTCAAAATGACTCGATATCAAAACGACCTA
270244 AATTCAAAAT
1 AATTCAAAAT
270254 AATTCAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AATTCAAAATGACTCGATATCAAAACGACCTA
Found at i:276587 original size:18 final size:19
Alignment explanation
Indices: 276566--276606 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
276556 TTTGTAAATA
*
276566 TAATA-AAATTTTTTATTT
1 TAATATAAATTTATTATTT
*
276584 TAATATATATTTATTATTT
1 TAATATAAATTTATTATTT
276603 TAAT
1 TAAT
276607 TAGTAATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TAATATAAATTTATTATTT
Found at i:277053 original size:21 final size:20
Alignment explanation
Indices: 277006--277054 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
276996 ACTTTATTTT
*
277006 ATCATA-ATAATTTTATTAA
1 ATCATATATAATTTTAATAA
**
277025 ATTTTATATATATTTTAATAA
1 ATCATATATA-ATTTTAATAA
277046 ATCATATAT
1 ATCATATAT
277055 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 16 0.70
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (20 bp):
ATCATATATAATTTTAATAA
Found at i:280249 original size:2 final size:2
Alignment explanation
Indices: 280242--280274 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
280232 GATCAAACCA
280242 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
280275 ATTGTGGACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:280363 original size:2 final size:2
Alignment explanation
Indices: 280318--280344 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
280308 GATCAAACCA
280318 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
280345 ATTGAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:280834 original size:30 final size:30
Alignment explanation
Indices: 280798--280859 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
280788 ATTTATACAT
280798 ATATTTTATAGATTATAGATAACAATAGTA
1 ATATTTTATAGATTATAGATAACAATAGTA
* *
280828 ATATTTTATAGATTATAGATGATAATAGTA
1 ATATTTTATAGATTATAGATAACAATAGTA
280858 AT
1 AT
280860 TACAGCTCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.42
Consensus pattern (30 bp):
ATATTTTATAGATTATAGATAACAATAGTA
Found at i:281105 original size:11 final size:11
Alignment explanation
Indices: 281089--281231 Score: 64
Period size: 11 Copynumber: 13.8 Consensus size: 11
281079 TGAATACATG
281089 ATATAAATAAT
1 ATATAAATAAT
281100 ATATAAA-AAT
1 ATATAAATAAT
*
281110 ATAATTAA-AAT
1 AT-ATAAATAAT
*
281121 ATA-ATATCAA-
1 ATATAAAT-AAT
281131 ATAT-AATAAT
1 ATATAAATAAT
*
281141 ATATAAAAAAT
1 ATATAAATAAT
281152 A-ATACGAAT-AT
1 ATATA--AATAAT
*
281163 A-ATATA-AAT
1 ATATAAATAAT
281172 ATATAAAT-AT
1 ATATAAATAAT
*
281182 AT-TAAATATTT
1 ATATAAATA-AT
281193 ATATAATATAAT
1 ATATAA-ATAAT
*
281205 -TATTAAT-AT
1 ATATAAATAAT
*
281214 AT-TAAAT-TT
1 ATATAAATAAT
281223 ATATAAATA
1 ATATAAATA
281232 GATAATATAT
Statistics
Matches: 101, Mismatches: 13, Indels: 36
0.67 0.09 0.24
Matches are distributed among these distances:
9 21 0.21
10 34 0.34
11 37 0.37
12 6 0.06
13 3 0.03
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
ATATAAATAAT
Found at i:281136 original size:31 final size:28
Alignment explanation
Indices: 281100--281178 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 28
281090 TATAAATAAT
*
281100 ATATAAAAATATAATTAAAATATAATATCAA
1 ATATAAAAATAT-A-TAAAAAATAATA-CAA
*
281131 ATATAATAATATATAAAAAATAATACGAA
1 ATATAAAAATATATAAAAAATAATAC-AA
*
281160 TATAATATAAATATATAAA
1 -AT-ATAAAAATATATAAA
281179 TATATTAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 1 0.02
29 13 0.32
30 3 0.07
31 24 0.59
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.32
Consensus pattern (28 bp):
ATATAAAAATATATAAAAAATAATACAA
Found at i:281177 original size:8 final size:8
Alignment explanation
Indices: 281164--281263 Score: 62
Period size: 8 Copynumber: 11.9 Consensus size: 8
281154 TACGAATATA
281164 ATATAAAT
1 ATATAAAT
281172 ATATAAAT
1 ATATAAAT
281180 ATATTAAAT
1 ATA-TAAAT
* *
281189 ATTTATAT
1 ATATAAAT
281197 A-ATATAAT
1 ATATA-AAT
*
281205 -TATTAAT
1 ATATAAAT
281212 ATATTAAATTT
1 ATA-TAAA--T
281223 ATATAAAT
1 ATATAAAT
*
281231 AGAT-AAT
1 ATATAAAT
281238 ATATTAAAT
1 ATA-TAAAT
*
281247 ACGTAAAAAT
1 A--TATAAAT
281257 ATATAAA
1 ATATAAA
281264 AAAATACACT
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
7 10 0.14
8 32 0.45
9 14 0.20
10 9 0.13
11 6 0.08
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:281187 original size:17 final size:17
Alignment explanation
Indices: 281167--281247 Score: 65
Period size: 17 Copynumber: 4.4 Consensus size: 17
281157 GAATATAATA
281167 TAAATATATAAATATAT
1 TAAATATATAAATATAT
281184 TAAATATTTATATAATATAAT
1 TAAATA--TATA-AATAT-AT
*
281205 TATTAATATATTAAATTTAT
1 TA--AATATA-TAAATATAT
*
281225 ATAAATAGAT-AATATAT
1 -TAAATATATAAATATAT
281242 TAAATA
1 TAAATA
281248 CGTAAAAATA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
16 6 0.11
17 12 0.23
18 1 0.02
19 9 0.17
20 7 0.13
21 12 0.23
22 2 0.04
23 4 0.08
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATATATAAATATAT
Found at i:281202 original size:34 final size:32
Alignment explanation
Indices: 281159--281247 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 32
281149 AATAATACGA
281159 ATATAATATAAATATATAAATATATTAAATATTT
1 ATATAATATAAATATATAAATATATT-AA-ATTT
*
281193 ATATAATAT-AAT-TATTAATATATTAAATTT
1 ATATAATATAAATATATAAATATATTAAATTT
*
281223 ATATAAATAGATAATATATTAAATA
1 ATAT-AATATA-AATATA-TAAATA
281248 CGTAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 8 0.17
31 6 0.13
32 11 0.23
33 6 0.13
34 11 0.23
35 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATATATAAATATATTAAATTT
Found at i:281206 original size:21 final size:18
Alignment explanation
Indices: 281089--281247 Score: 70
Period size: 19 Copynumber: 8.7 Consensus size: 18
281079 TGAATACATG
* *
281089 ATATAAATAATATATAAAA
1 ATATAATTAA-ATATATAA
281108 ATATAATTAAA-ATAT--
1 ATATAATTAAATATATAA
*
281123 A-AT-ATCAAATATAATAA
1 ATATAATTAAATAT-ATAA
*
281140 TATATAA-AAAATA-ATACGA
1 -ATATAATTAAATATATA--A
281159 ATATAATATAAATATATAA
1 ATATAAT-TAAATATATAA
281178 ATAT-ATTAAATATTTATATA
1 ATATAATTAAATA--TATA-A
281198 ATATAATTATTAATATATTAA
1 ATATAATTA--AATATA-TAA
* *
281219 AT-TTATATAAATAGAT-A
1 ATATAAT-TAAATATATAA
281236 ATAT-ATTAAATA
1 ATATAATTAAATA
281248 CGTAAAAATA
Statistics
Matches: 112, Mismatches: 7, Indels: 45
0.68 0.04 0.27
Matches are distributed among these distances:
13 5 0.04
14 4 0.04
15 3 0.03
16 6 0.05
17 17 0.15
18 12 0.11
19 31 0.28
20 14 0.12
21 14 0.12
22 2 0.02
23 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (18 bp):
ATATAATTAAATATATAA
Found at i:281241 original size:26 final size:26
Alignment explanation
Indices: 281164--281246 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 26
281154 TACGAATATA
281164 ATATAAATATATAAATATATTAAATATTT
1 ATATAAATATAT-AATATATT-AA-ATTT
281193 ATATAATATAATTATTAATATATTAAATTT
1 ATATAA-AT-A-TA-TAATATATTAAATTT
*
281223 ATATAAATAGATAATATATTAAAT
1 ATATAAATATATAATATATTAAAT
281247 ACGTAAAAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
26 13 0.27
27 1 0.02
28 1 0.02
29 8 0.16
30 12 0.24
31 3 0.06
32 10 0.20
33 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATAAATATATAATATATTAAATTT
Found at i:281256 original size:26 final size:26
Alignment explanation
Indices: 281208--281262 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
281198 ATATAATTAT
** *
281208 TAATATATTAAATTTATATAAATAGA
1 TAATATATTAAATACATAAAAATAGA
* *
281234 TAATATATTAAATACGTAAAAATATA
1 TAATATATTAAATACATAAAAATAGA
281260 TAA
1 TAA
281263 AAAAATACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (26 bp):
TAATATATTAAATACATAAAAATAGA
Found at i:283079 original size:21 final size:20
Alignment explanation
Indices: 283045--283087 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
283035 ATTTTTTATT
283045 TAAATTTAATTATAAAATTAA
1 TAAATTTAATTATAAAA-TAA
283066 TAAATATTAA-TATAAAATAA
1 TAAAT-TTAATTATAAAATAA
283086 TA
1 TA
283088 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.24
21 12 0.57
22 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATTTAATTATAAAATAA
Found at i:283099 original size:36 final size:36
Alignment explanation
Indices: 283054--283172 Score: 123
Period size: 36 Copynumber: 3.2 Consensus size: 36
283044 TTAAATTTAA
283054 TTATAAAATTAATAAATATTAATATAAAATAATATT
1 TTATAAAATTAATAAATATTAATATAAAATAATATT
* ** * * * * *
283090 TTATTAAATTTTTAAATAATAATTTAAATTACTATAA
1 TTATAAAATTAATAAATATTAATATAAAATAATAT-T
283127 TTATAAAATATAA-AAATATTAATATAAAAATAATATT
1 TTATAAAAT-TAATAAATATTAATAT-AAAATAATATT
*
283164 TTTTAAAAT
1 TTATAAAAT
283173 AGTAATTTTG
Statistics
Matches: 63, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
36 28 0.44
37 26 0.41
38 9 0.14
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (36 bp):
TTATAAAATTAATAAATATTAATATAAAATAATATT
Found at i:283171 original size:37 final size:36
Alignment explanation
Indices: 283057--283173 Score: 103
Period size: 37 Copynumber: 3.2 Consensus size: 36
283047 AATTTAATTA
283057 TAAAAT-TAATAAATATTAATATAAAATAATATTTTAT
1 TAAAATATAA-AAATATTAATATAAAATAATATTTT-T
* ** * * * * * *
283094 T-AAATTTTTAAATAATAATTTAAATTACTATAATTA
1 TAAAATATAAAAATATTAATATAAAATAATAT-TTTT
283130 TAAAATATAAAAATATTAATATAAAAATAATATTTTT
1 TAAAATATAAAAATATTAATAT-AAAATAATATTTTT
283167 TAAAATA
1 TAAAATA
283174 GTAATTTTGA
Statistics
Matches: 59, Mismatches: 17, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
36 23 0.39
37 28 0.47
38 8 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (36 bp):
TAAAATATAAAAATATTAATATAAAATAATATTTTT
Found at i:286398 original size:17 final size:16
Alignment explanation
Indices: 286366--286414 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
286356 AATGACAGAT
* *
286366 TTTTAAAATAAGATTA
1 TTTTAAATTAAAATTA
286382 CTTTTAAATTAAAATTA
1 -TTTTAAATTAAAATTA
*
286399 TTTGAAATT-AAATTA
1 TTTTAAATTAAAATTA
286414 T
1 T
286415 GGTACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 7 0.24
16 8 0.28
17 14 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (16 bp):
TTTTAAATTAAAATTA
Found at i:286979 original size:10 final size:10
Alignment explanation
Indices: 286944--287097 Score: 51
Period size: 10 Copynumber: 16.1 Consensus size: 10
286934 TAGATCTAAT
286944 TATTTTTATA
1 TATTTTTATA
* *
286954 AATTTGTATCA
1 TATTTTTAT-A
286965 -A-TTTTATA
1 TATTTTTATA
*
286973 TATTTTTAAA
1 TATTTTTATA
* *
286983 TATTATAAT-
1 TATTTTTATA
*
286992 TATATTTA-A
1 TATTTTTATA
* *
287001 -AATATTATA
1 TATTTTTATA
287010 TA--TTTATA
1 TATTTTTATA
*
287018 TATTTTAATA
1 TATTTTTATA
**
287028 TATTAATA-A
1 TATTTTTATA
* *
287037 TTAATATTATA
1 -TATTTTTATA
*
287048 TAAATTTTA-A
1 T-ATTTTTATA
*
287058 TATATTTATA
1 TATTTTTATA
287068 TATTTTTATCA
1 TATTTTTAT-A
287079 TA--TTTATA
1 TATTTTTATA
*
287087 TTTTTTTATA
1 TATTTTTATA
287097 T
1 T
287098 TATGTCATAT
Statistics
Matches: 104, Mismatches: 25, Indels: 30
0.65 0.16 0.19
Matches are distributed among these distances:
8 14 0.13
9 23 0.22
10 56 0.54
11 11 0.11
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (10 bp):
TATTTTTATA
Done.