Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015324.1 Kokia drynarioides strain JFW-HI SEQ_130370, whole genome shotgun sequence
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: 507159
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 280 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:333241 original size:73 final size:73
Alignment explanation
Indices: 333102--333245 Score: 225
Period size: 73 Copynumber: 2.0 Consensus size: 73
333092 TTAATCAAAC
* *
333102 TCTGATTAGTTTAAATTATTTTATTATTATTTAACATAAGAATTTAGCTTATAAATAGGCTCTTT
1 TCTGATTAGTTTAAATTATTTTACTATTATTTAACATAAGAATTTAGCTTATAAATAGACTCTTT
333167 TACAACCT
66 TACAACCT
* * * * *
333175 TCTGATTAGTTTAAATTATTTTACTATTATTTGACCTAAGAATTTAGTTTATAAATAGATTTTTT
1 TCTGATTAGTTTAAATTATTTTACTATTATTTAACATAAGAATTTAGCTTATAAATAGACTCTTT
333240 TACAAC
66 TACAAC
333246 ATTGGAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 64 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (73 bp):
TCTGATTAGTTTAAATTATTTTACTATTATTTAACATAAGAATTTAGCTTATAAATAGACTCTTT
TACAACCT
Found at i:334064 original size:20 final size:20
Alignment explanation
Indices: 334041--334083 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
334031 TAAAATATAA
*
334041 ATATATTTCAAA-AAATAATT
1 ATATAATTCAAATAAAT-ATT
*
334061 ATATAATTGAAATAAATATT
1 ATATAATTCAAATAAATATT
334081 ATA
1 ATA
334084 AAAATATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATAATTCAAATAAATATT
Found at i:336290 original size:6 final size:6
Alignment explanation
Indices: 336274--336303 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
336264 ACCCACCAAG
*
336274 TCACCA CCACCA TCACCA TCACCA TCACCA
1 TCACCA TCACCA TCACCA TCACCA TCACCA
336304 CCCGCCAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.53, G:0.00, T:0.13
Consensus pattern (6 bp):
TCACCA
Found at i:336435 original size:39 final size:38
Alignment explanation
Indices: 336392--336551 Score: 162
Period size: 39 Copynumber: 4.4 Consensus size: 38
336382 AGTTTATCCA
*
336392 CCACCCAAATCACCAAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACC-AGCAAGCCGCCAACTTACGCTCCT
*
336431 CCACCCAAGTCACCCAGCAAGCCGCCTACTTACGCTCCT
1 CCACCCAAGTCA-CCAGCAAGCCGCCAACTTACGCTCCT
*
336470 -----C----CACC--CAAGCCGCCAACTCACGCTCCT
1 CCACCCAAGTCACCAGCAAGCCGCCAACTTACGCTCCT
* *
336497 CCACCCAAGTCACCGACCAAGCCACCAACTTACGCTCCT
1 CCACCCAAGTCACC-AGCAAGCCGCCAACTTACGCTCCT
*
336536 CCACCCAAGCCACCAG
1 CCACCCAAGTCACCAG
336552 TTTATCCTCC
Statistics
Matches: 100, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
27 20 0.20
29 2 0.02
30 2 0.02
32 1 0.01
34 1 0.01
36 4 0.04
38 1 0.01
39 67 0.67
40 2 0.02
ACGTcount: A:0.27, C:0.50, G:0.11, T:0.12
Consensus pattern (38 bp):
CCACCCAAGTCACCAGCAAGCCGCCAACTTACGCTCCT
Found at i:336482 original size:27 final size:27
Alignment explanation
Indices: 336448--336505 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
336438 AGTCACCCAG
* *
336448 CAAGCCGCCTACTTACGCTCCTCCACC
1 CAAGCCGCCAACTCACGCTCCTCCACC
336475 CAAGCCGCCAACTCACGCTCCTCCACC
1 CAAGCCGCCAACTCACGCTCCTCCACC
336502 CAAG
1 CAAG
336506 TCACCGACCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.22, C:0.52, G:0.12, T:0.14
Consensus pattern (27 bp):
CAAGCCGCCAACTCACGCTCCTCCACC
Found at i:336482 original size:66 final size:66
Alignment explanation
Indices: 336409--336546 Score: 231
Period size: 66 Copynumber: 2.1 Consensus size: 66
336399 AATCACCAAG
* * * *
336409 CAAGCCGCCAACTTACGCTCCTCCACCCAAGTCACCCAGCAAGCCGCCTACTTACGCTCCTCCAC
1 CAAGCCGCCAACTCACGCTCCTCCACCCAAGTCACCCACCAAGCCACCAACTTACGCTCCTCCAC
336474 C
66 C
*
336475 CAAGCCGCCAACTCACGCTCCTCCACCCAAGTCACCGACCAAGCCACCAACTTACGCTCCTCCAC
1 CAAGCCGCCAACTCACGCTCCTCCACCCAAGTCACCCACCAAGCCACCAACTTACGCTCCTCCAC
336540 C
66 C
336541 CAAGCC
1 CAAGCC
336547 ACCAGTTTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.25, C:0.51, G:0.12, T:0.13
Consensus pattern (66 bp):
CAAGCCGCCAACTCACGCTCCTCCACCCAAGTCACCCACCAAGCCACCAACTTACGCTCCTCCAC
C
Found at i:350222 original size:17 final size:17
Alignment explanation
Indices: 350191--350242 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
350181 TAAGTTTATA
350191 TTAATTT-TATTTTGTTT
1 TTAATTTAT-TTTTGTTT
* **
350208 TTAGTTTATTTTTGTAA
1 TTAATTTATTTTTGTTT
*
350225 TTAATTTATTTTTCTTT
1 TTAATTTATTTTTGTTT
350242 T
1 T
350243 GTGTGTTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 26 0.96
18 1 0.04
ACGTcount: A:0.19, C:0.02, G:0.06, T:0.73
Consensus pattern (17 bp):
TTAATTTATTTTTGTTT
Found at i:351622 original size:21 final size:21
Alignment explanation
Indices: 351598--351647 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
351588 CAAACTTTAT
351598 GATTCTTGGTTATTTGATACC
1 GATTCTTGGTTATTTGATACC
351619 GATTCTTGGTTATTTGATACC
1 GATTCTTGGTTATTTGATACC
351640 GATTCTTG
1 GATTCTTG
351648 CATGCATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.20, T:0.48
Consensus pattern (21 bp):
GATTCTTGGTTATTTGATACC
Found at i:359443 original size:5 final size:5
Alignment explanation
Indices: 359429--359470 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
359419 TCATTTTAAG
* *
359429 TTATA ATATA TTATA TTATA TTATA TTAT- TTTTA -TATA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT
359471 GTAATTTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
4 6 0.19
5 25 0.81
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:362026 original size:82 final size:83
Alignment explanation
Indices: 361896--362057 Score: 186
Period size: 82 Copynumber: 2.0 Consensus size: 83
361886 ATGATAGTAT
* * ** * * **
361896 AAATATAATTTCATCATTTTAATAATTTATATATTTATTATTTTTAAAATGT-TAAATTAAATTT
1 AAATATAATTTCATCA-TTTAATAATTTAAATATTTATAAACTATAAAAGGTCTAAATTAAAAGT
*
361960 TTATTATTTTTAAGGGATAA
65 TTATCA-TTTTAAGGGATAA
*
361980 AAATATAATTTTATCA-TTAATAATTTAAA-ATTTTATAAACTATAAAAGGTCTAAATTAAAAGT
1 AAATATAATTTCATCATTTAATAATTTAAATA-TTTATAAACTATAAAAGGTCTAAATTAAAAGT
362043 TTATCATTTTAAGGG
65 TTATCATTTTAAGGG
362058 GTTATAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
81 1 0.02
82 35 0.53
83 15 0.23
84 15 0.23
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (83 bp):
AAATATAATTTCATCATTTAATAATTTAAATATTTATAAACTATAAAAGGTCTAAATTAAAAGTT
TATCATTTTAAGGGATAA
Found at i:363313 original size:16 final size:17
Alignment explanation
Indices: 363292--363324 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
363282 TCAAATTAAT
*
363292 TTAAATTAATTT-TCAA
1 TTAAATAAATTTCTCAA
363308 TTAAATAAATTTCTCAA
1 TTAAATAAATTTCTCAA
363325 ACCAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAATAAATTTCTCAA
Found at i:366276 original size:21 final size:21
Alignment explanation
Indices: 366252--366298 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
366242 AGTTAAATTG
*
366252 TATAAT-ATTTAAATAATTTAA
1 TATAATGATATAAATAA-TTAA
*
366273 TATAATGATATAAGTAATTAA
1 TATAATGATATAAATAATTAA
366294 TATAA
1 TATAA
366299 ATTATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
TATAATGATATAAATAATTAA
Found at i:366352 original size:27 final size:27
Alignment explanation
Indices: 366293--366356 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
366283 TAAGTAATTA
* * *
366293 ATATAAATTATTTTTAAATTTGATGAT
1 ATATAAAATATTTTAAAATTTGATAAT
*
366320 ATATAAAATATTTTAAAATTTTA-AAT
1 ATATAAAATATTTTAAAATTTGATAAT
366346 ATAATAAAATA
1 AT-ATAAAATA
366357 AGATTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATAAAATATTTTAAAATTTGATAAT
Found at i:380665 original size:2 final size:2
Alignment explanation
Indices: 380658--380693 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
380648 TCTAATTATT
380658 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
380694 AACCTTTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:381869 original size:15 final size:16
Alignment explanation
Indices: 381851--381880 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
381841 AAAAATATCG
381851 AAATTAAAAT-TAAAT
1 AAATTAAAATATAAAT
381866 AAATTAAAATATAAA
1 AAATTAAAATATAAA
381881 AATTAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATTAAAATATAAAT
Found at i:382082 original size:22 final size:23
Alignment explanation
Indices: 382045--382087 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
382035 AAAACCTTCT
*
382045 TTCTTTCCTTTTTAATGTAAAGC
1 TTCTTTCCGTTTTAATGTAAAGC
*
382068 TTCTTT-CGTTTTAATTTAAA
1 TTCTTTCCGTTTTAATGTAAA
382088 ATTTTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (23 bp):
TTCTTTCCGTTTTAATGTAAAGC
Found at i:395311 original size:29 final size:29
Alignment explanation
Indices: 395223--395311 Score: 72
Period size: 30 Copynumber: 3.0 Consensus size: 29
395213 TTCTAGGATA
*
395223 TTCACTTCTTTACAATTTAGTCAAAACTTT
1 TTCACTTCTTTACAATTTAGTCAATAC-TT
* * * * ** *
395253 TTTA-TTATTCACACTTTAACCCCATCACTT
1 TTCACTTCTTTACAATTT-AGTCAAT-ACTT
395283 TTCACTTCTTTACAATTTAGTCAATACTT
1 TTCACTTCTTTACAATTTAGTCAATACTT
395312 CGGATTTATT
Statistics
Matches: 41, Mismatches: 15, Indels: 7
0.65 0.24 0.11
Matches are distributed among these distances:
29 14 0.34
30 15 0.37
31 12 0.29
ACGTcount: A:0.28, C:0.24, G:0.02, T:0.46
Consensus pattern (29 bp):
TTCACTTCTTTACAATTTAGTCAATACTT
Found at i:396981 original size:220 final size:222
Alignment explanation
Indices: 396591--397034 Score: 748
Period size: 220 Copynumber: 2.0 Consensus size: 222
396581 ATGAGGAGTG
396591 ACTCCAAGTTTTCTAGTTGATGTAATTTTATAGTTATCTCTTCACCAAAAAAAAAAAAGAGTATT
1 ACTCCAAGTTTTCTAGTTGATGTAATTTTATAGTTATCTCTTCA-CAAAAAAAAAAAAGAGTATT
396656 CCTTTTACTTTTCACTTTTAGATAGAATCCATATATTCAATTGATTATAATATCTCCAAGACACC
65 CCTTTTACTTTTCACTTTTAGATAGAATCCATATATTCAATTGATTATAATATCTCCAAGACACC
* *
396721 CTATATTTAAAAAAAAATTCCTTTCATCTCTATTGAAAAAGAAAATGTGAA-TTTTCAATTACGA
130 CAATATTTAAAAAAAAATTCCTTTCATCTCTATTGAAAAAGAAAACGTGAATTTTTCAATTACGA
396785 AAGTTCAAATTCAGGACAAATAAATTGA
195 AAGTTCAAATTCAGGACAAATAAATTGA
* * * * * *
396813 ACTCCGAGTTTTCTCGTTGATGTAATTTTATAGTTATTTTTTTA-ACAAAAAAAAAAGAGTATTC
1 ACTCCAAGTTTTCTAGTTGATGTAATTTTATAGTTATCTCTTCACAAAAAAAAAAAAGAGTATTC
* *
396877 CTTTTACTTTTCACTTTTAGATAGAATCCATATATTCAATTGATTATAATATCTCTAAGACACTC
66 CTTTTACTTTTCACTTTTAGATAGAATCCATATATTCAATTGATTATAATATCTCCAAGACACCC
* *
396942 AATATTTTAAAAAAAATTCCTTTCGTCTCTATTGAAAAAGAAAACGTGAATTTTTCAATTACGAA
131 AATATTTAAAAAAAAATTCCTTTCATCTCTATTGAAAAAGAAAACGTGAATTTTTCAATTACGAA
*
397007 AGTTCAAATTCAGGACAAATAAGTTGA
196 AGTTCAAATTCAGGACAAATAAATTGA
397034 A
1 A
397035 ATAATTAACT
Statistics
Matches: 208, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
220 128 0.62
221 41 0.20
222 39 0.19
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (222 bp):
ACTCCAAGTTTTCTAGTTGATGTAATTTTATAGTTATCTCTTCACAAAAAAAAAAAAGAGTATTC
CTTTTACTTTTCACTTTTAGATAGAATCCATATATTCAATTGATTATAATATCTCCAAGACACCC
AATATTTAAAAAAAAATTCCTTTCATCTCTATTGAAAAAGAAAACGTGAATTTTTCAATTACGAA
AGTTCAAATTCAGGACAAATAAATTGA
Found at i:397148 original size:14 final size:15
Alignment explanation
Indices: 397129--397158 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
397119 ATCAGTATTG
397129 TTTTTTCTC-AAATT
1 TTTTTTCTCTAAATT
397143 TTTTTTCTCTAAATT
1 TTTTTTCTCTAAATT
397158 T
1 T
397159 CAAGTATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTCTCTAAATT
Found at i:403681 original size:129 final size:126
Alignment explanation
Indices: 403435--403692 Score: 317
Period size: 129 Copynumber: 2.0 Consensus size: 126
403425 CAGACGGGGT
* * *
403435 TGGTGACAAAAATGATTCTGAAGTGAATCGAGAATCCTTGGGTGTATCTGCTGCACTTAGTCCCT
1 TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTGTATCTGCAGCACTTAGGCCCT
* * * *
403500 CAGAAAGGCTTCACTTGGGAGCAAGTGGTATTCGCAGTCACACAGCACATGGCAGTTTGAG
66 CAGAAAGGCTTCACTTGGGAGCAAGCGGCATGCGCAGTAACACAGCACATGGCAGTTTGAG
* * *
403561 TGGTGACGAAAATGATTCTGAAGTTAATAGAGAATCCTTGGGCTTGT-T-TGCAGCTCTTAATGG
1 TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGG--TGTATCTGCAGCACTT-A-GG
* *
403624 CCTCTCCGAAAGGCTTCA-TTGGGGAGCAGGCGGCATGCGCAGTAACACAAG-ACATGGCAGTTT
62 CC-CTCAGAAAGGCTTCACTT-GGGAGCAAGCGGCATGCGCAGTAACAC-AGCACATGGCAGTTT
403687 GAG
124 GAG
403690 TGG
1 TGG
403693 CGGAAATGGA
Statistics
Matches: 113, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
126 47 0.42
127 2 0.02
128 8 0.07
129 54 0.48
130 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (126 bp):
TGGTGACAAAAATGATTCTGAAGTGAATAGAGAATCCTTGGGTGTATCTGCAGCACTTAGGCCCT
CAGAAAGGCTTCACTTGGGAGCAAGCGGCATGCGCAGTAACACAGCACATGGCAGTTTGAG
Found at i:408516 original size:15 final size:15
Alignment explanation
Indices: 408492--408525 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
408482 TCTGTGTATG
*
408492 TATTTATTTATTGTT
1 TATTTATTTATTATT
*
408507 TATTTGTTTATTATT
1 TATTTATTTATTATT
408522 TATT
1 TATT
408526 AATATTTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:411734 original size:20 final size:20
Alignment explanation
Indices: 411692--411736 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
411682 AAAGATGTTA
* * *
411692 AAACTTTTTTTCTTACTAGT
1 AAACTTTTATTCTTAATACT
*
411712 AAACTTTTATTCTTAATCCT
1 AAACTTTTATTCTTAATACT
411732 AAACT
1 AAACT
411737 AGAGCAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.18, G:0.02, T:0.49
Consensus pattern (20 bp):
AAACTTTTATTCTTAATACT
Found at i:412456 original size:3 final size:3
Alignment explanation
Indices: 412448--412475 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
412438 CACTCTCCAC
412448 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
412476 CATTTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:417815 original size:86 final size:86
Alignment explanation
Indices: 417612--417982 Score: 554
Period size: 86 Copynumber: 4.3 Consensus size: 86
417602 GTTTTCACCG
* * * *
417612 ATTATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCA
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTAT-T
* * *
417677 AATTTT-CATATTTGAAGT-ACA
65 AATTTTAAATATTT-AAATAAAA
* * * *
417698 A--ATTAGTATTATATTACAATTTTTATCAAATAATATGTTGATTTGGCAATATATTATTTATTA
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTA
417761 ATTTTAAATATTTAAATAAAA
66 ATTTTAAATATTTAAATAAAA
*
417782 ATTATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTA
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTA
417847 A-TTTAAATATTTAAATAAAA
66 ATTTTAAATATTTAAATAAAA
* * *
417867 ATTATTACTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGATAATACATTATTTATTT
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTA
417932 ATTTTAAATATTTAAATAAAA
66 ATTTTAAATATTTAAATAAAA
417953 ATTATTATTATTATATTACAATTTTTATCA
1 ATTATTATTATTATATTACAATTTTTATCA
417983 TAATTTAAAT
Statistics
Matches: 259, Mismatches: 21, Indels: 10
0.89 0.07 0.03
Matches are distributed among these distances:
83 9 0.03
84 62 0.24
85 81 0.31
86 107 0.41
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (86 bp):
ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTATTA
ATTTTAAATATTTAAATAAAA
Found at i:417930 original size:171 final size:170
Alignment explanation
Indices: 417612--417982 Score: 566
Period size: 171 Copynumber: 2.2 Consensus size: 170
417602 GTTTTCACCG
* *
417612 ATTATTATTATTATATTACAATTTATATCAAATATTGTGTTAATTTGACAATACATTATTTATCA
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTATCA
** * * *
417677 AATTTTCATATTTGAAGTACAAATTAGTATTATATTACAATTTTTATCAAATAATATGTTGATTT
66 AATTTAAATATTTGAAATAAAAATTACTATTATATTACAATTTTTATCAAATAATATGTTGATTT
* *
417742 GGCAATATATTATTTATTAATTTTAAATATTTAAATAAAA
131 GACAATACATTATTTATTAATTTTAAATATTTAAATAAAA
* * *
417782 ATTATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATACATTATTTAT-T
1 ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTATCA
*
417846 AATTTAAATATTT-AAATAAAAATTATTACTATTATATTACAATTTTTATCAAATAATGTGTTGA
66 AATTTAAATATTTGAAAT-AAAA--ATTACTATTATATTACAATTTTTATCAAATAATATGTTGA
* *
417910 TTTGATAATACATTATTTATTTATTTTAAATATTTAAATAAAA
128 TTTGACAATACATTATTTATTAATTTTAAATATTTAAATAAAA
417953 ATTATTATTATTATATTACAATTTTTATCA
1 ATTATTATTATTATATTACAATTTTTATCA
417983 TAATTTAAAT
Statistics
Matches: 182, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
168 3 0.02
169 14 0.08
170 59 0.32
171 106 0.58
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (170 bp):
ATTATTATTATTATATTACAATTTTTATCAAATAATGTGTTAATTTGACAATACATTATTTATCA
AATTTAAATATTTGAAATAAAAATTACTATTATATTACAATTTTTATCAAATAATATGTTGATTT
GACAATACATTATTTATTAATTTTAAATATTTAAATAAAA
Found at i:420436 original size:30 final size:30
Alignment explanation
Indices: 420385--420476 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
420375 TCCGTTTACT
** * *
420385 TTTTAAATTTAATTTGAAATTTCATTTTTA
1 TTTTAAATTTAATTTCTAATTTCATGTATA
*
420415 TTTTAAATTTAATTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCATGTATA
* ** *
420445 TTTTAATTTTTTTTTCTAATTTCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCATGTATA
420475 TT
1 TT
420477 CTAATTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCATGTATA
Found at i:420453 original size:17 final size:18
Alignment explanation
Indices: 420426--420483 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
420416 TTTAAATTTA
420426 ATTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
420444 ATTT-TAATTT--T-T-T
1 ATTTCTAATTTCCTGTAT
420457 -TTTCTAATTTCCTGTAT
1 ATTTCTAATTTCCTGTAT
420474 A-TTCTAATTT
1 ATTTCTAATTT
420484 TTTTTTAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
12 3 0.09
13 7 0.21
14 1 0.03
15 2 0.06
16 1 0.03
17 16 0.47
18 4 0.12
ACGTcount: A:0.22, C:0.12, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTCTAATTTCCTGTAT
Found at i:420494 original size:28 final size:30
Alignment explanation
Indices: 420427--420489 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
420417 TTAAATTTAA
*
420427 TTTCTAATTTCCTGTATATTTTAATTTTTT
1 TTTCTAATTTCCTGTATATTCTAATTTTTT
420457 TTTCTAATTTCCTGTATATTCTAATTTTTT
1 TTTCTAATTTCCTGTATATTCTAATTTTTT
420487 TTT
1 TTT
420490 AATTTATATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.11, G:0.03, T:0.67
Consensus pattern (30 bp):
TTTCTAATTTCCTGTATATTCTAATTTTTT
Found at i:421451 original size:61 final size:61
Alignment explanation
Indices: 421352--421625 Score: 306
Period size: 61 Copynumber: 4.5 Consensus size: 61
421342 ATAAAAGGGG
* * *
421352 GTGTCAGCCATTGCATGGCCAACACCAAAAAAATTGAAATTTTTTTATCCAAGAAAAAGGA
1 GTGTCGGCCATTGCATGACCAACACCAAAAAAATTGAAATTTTTTTATCCGAGAAAAAGGA
* * * *
421413 GTGT-GGCCATTGCATGACTAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAGGGG
1 GTGTCGGCCATTGCATGACCAACACC-AAAAAAATTGAAATTTTTTTATCCGAGAAAAAGGA
* * *
421474 GTGTCAGCCATTGCATGACCAACACCAAAAAAATTTGAAATTTTTTTATCTGA-AAAAGGGA
1 GTGTCGGCCATTGCATGACCAACACCAAAAAAA-TTGAAATTTTTTTATCCGAGAAAAAGGA
* * * * * * *
421535 GTGTCGGCTATTGCTTGGCCAACACC-CAAAAA-TGTAATTTTTTTATCCGAGAAAAGGGG
1 GTGTCGGCCATTGCATGACCAACACCAAAAAAATTGAAATTTTTTTATCCGAGAAAAAGGA
* * *
421594 GTGTCGACCA-TGCAATGACCTACACCCAAAAA
1 GTGTCGGCCATTGC-ATGACCAACACCAAAAAA
421626 TGCATTTTTT
Statistics
Matches: 181, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
58 19 0.10
59 24 0.13
60 27 0.15
61 74 0.41
62 37 0.20
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (61 bp):
GTGTCGGCCATTGCATGACCAACACCAAAAAAATTGAAATTTTTTTATCCGAGAAAAAGGA
Found at i:421619 original size:120 final size:119
Alignment explanation
Indices: 421313--421625 Score: 377
Period size: 120 Copynumber: 2.6 Consensus size: 119
421303 ATTACATGGT
* * * *
421313 CAACACCAAAAAATTTAA-TTTTTTA-CCAAATAAAAGGGGGTGTCAGCCATTGCATGGCCAACA
1 CAACACCAAAAAATGTAATTTTTTTATCC-GAGAAAAGGGGGTGTCAGCCATTGCATGACCAACA
421376 CCAAAAAAATTGAAATTTTTTTATCCAAGAAAAAGGAGTGTGGCCATTGCATGAC
65 CCAAAAAAATTGAAATTTTTTTATCCAAGAAAAAGGAGTGTGGCCATTGCATGAC
* * *
421431 TAACACCAAAAAAAATTGAAATTTTTTTATCCGAGAACAGGGGGTGTCAGCCATTGCATGACCAA
1 CAACACC--AAAAAA-TGTAATTTTTTTATCCGAGAAAAGGGGGTGTCAGCCATTGCATGACCAA
* * * *
421496 CACCAAAAAAATTTGAAATTTTTTTAT-C-TGAAAAAGGGAGTGTCGGCTATTGCTTGGC
63 CACCAAAAAAA-TTGAAATTTTTTTATCCAAGAAAAA-GGAGTGT-GGCCATTGCATGAC
* *
421554 CAACACCCAAAAATGTAATTTTTTTATCCGAGAAAAGGGGGTGTC-GACCA-TGCAATGACCTAC
1 CAACACCAAAAAATGTAATTTTTTTATCCGAGAAAAGGGGGTGTCAG-CCATTGC-ATGACCAAC
*
421617 ACCCAAAAA
64 ACCAAAAAA
421626 TGCATTTTTT
Statistics
Matches: 168, Mismatches: 17, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
118 6 0.04
119 4 0.02
120 55 0.33
121 14 0.08
122 55 0.33
123 34 0.20
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (119 bp):
CAACACCAAAAAATGTAATTTTTTTATCCGAGAAAAGGGGGTGTCAGCCATTGCATGACCAACAC
CAAAAAAATTGAAATTTTTTTATCCAAGAAAAAGGAGTGTGGCCATTGCATGAC
Found at i:422577 original size:31 final size:30
Alignment explanation
Indices: 422541--422634 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 30
422531 TTAACATCCT
* *
422541 AGTGACTTAAATAATAACTTTTCAATAATTC
1 AGTGACTTAAATAA-AACTTTTGAATAGTTC
*
422572 AGTGACTTAAATAAAAATTTTAGAATAGTTC
1 AGTGACTTAAATAAAACTTTT-GAATAGTTC
422603 AGTGACTTAAAATAAAACTTTTGAATAGTTC
1 AGTGACTT-AAATAAAACTTTTGAATAGTTC
422634 A
1 A
422635 ATGATCATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 6 0.11
31 39 0.68
32 12 0.21
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.36
Consensus pattern (30 bp):
AGTGACTTAAATAAAACTTTTGAATAGTTC
Found at i:423395 original size:28 final size:30
Alignment explanation
Indices: 423339--423396 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
423329 TTCAAAAAAT
423339 AAAAATATTAGGTTTAACATATATTAATTAA
1 AAAAATATTAGGTTTAACA-ATATTAATTAA
*
423370 AAAAATATTATGTTTAAC-ATA-TAATTA
1 AAAAATATTAGGTTTAACAATATTAATTA
423397 TGTAATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 6 0.23
29 3 0.12
31 17 0.65
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAAATATTAGGTTTAACAATATTAATTAA
Found at i:424054 original size:18 final size:20
Alignment explanation
Indices: 424012--424062 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
424002 GAATAAACCT
*
424012 TAAAAATATATAAAACTGTA
1 TAAAAATATTTAAAACTGTA
*
424032 AAAAAATATTTAAAA-T-TA
1 TAAAAATATTTAAAACTGTA
424050 TAAAAA-ATTTAAA
1 TAAAAATATTTAAA
424063 TAATTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 1 0.04
20 13 0.46
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAATATTTAAAACTGTA
Found at i:424081 original size:26 final size:26
Alignment explanation
Indices: 424035--424089 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
424025 AACTGTAAAA
*
424035 AAATATTTAAAATTATAAAAAATT-T
1 AAATATTGAAAATTATAAAAAATTGT
424060 AAATAATTGAAAATTA-ATAAAAATTGT
1 AAAT-ATTGAAAATTATA-AAAAATTGT
424087 AAA
1 AAA
424090 AAAATATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (26 bp):
AAATATTGAAAATTATAAAAAATTGT
Found at i:424092 original size:20 final size:20
Alignment explanation
Indices: 424023--424196 Score: 110
Period size: 20 Copynumber: 8.8 Consensus size: 20
424013 AAAAATATAT
* * *
424023 AAAACTGTAAAAAAATATTT
1 AAAATTGTAAAAAATTATTA
*
424043 AAAATTATAAAAAA-T-TTA
1 AAAATTGTAAAAAATTATTA
*
424061 AATAATTG---AAAATTAATA
1 AA-AATTGTAAAAAATTATTA
* *
424079 AAAATTGTAAAAAAATATTG
1 AAAATTGTAAAAAATTATTA
* **
424099 AAAATGGTAAAAACGTATTTA
1 AAAATTGTAAAAAATTA-TTA
*
424120 AAAATTGTAAAAAAGTTAATA
1 AAAATTGTAAAAAA-TTATTA
* *
424141 AAAATTATAAAACATTATTTA
1 AAAATTGTAAAAAATTA-TTA
* *
424162 AAATTTGT-AAAACTTATT-
1 AAAATTGTAAAAAATTATTA
* *
424180 AAAATAGTAAATAATTA
1 AAAATTGTAAAAAATTA
424197 ACAAATCAAA
Statistics
Matches: 117, Mismatches: 27, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
16 4 0.03
17 6 0.05
18 14 0.12
19 13 0.11
20 42 0.36
21 36 0.31
22 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (20 bp):
AAAATTGTAAAAAATTATTA
Found at i:424102 original size:21 final size:20
Alignment explanation
Indices: 424013--424173 Score: 100
Period size: 21 Copynumber: 8.1 Consensus size: 20
424003 AATAAACCTT
*
424013 AAAAATA-TATAAAACTGTAA
1 AAAAATATTA-AAAATTGTAA
* *
424033 AAAAATATTTAAAATTAT-A
1 AAAAATATTAAAAATTGTAA
424052 AAAAAT-TTAAATAATTG---
1 AAAAATATTAAA-AATTGTAA
* *
424069 AAAATTAATAAAAATTGTAA
1 AAAAATATTAAAAATTGTAA
* *
424089 AAAAATATTGAAAATGGTAA
1 AAAAATATTAAAAATTGTAA
**
424109 AAACGTATTTAAAAATTGTAA
1 AAAAATA-TTAAAAATTGTAA
* * *
424130 AAAAGTTAATAAAAATTATAA
1 AAAA-ATATTAAAAATTGTAA
* * *
424151 AACATTATTTAAAATTTGTAA
1 AAAAATA-TTAAAAATTGTAA
424172 AA
1 AA
424174 CTTATTAAAA
Statistics
Matches: 109, Mismatches: 23, Indels: 17
0.73 0.15 0.11
Matches are distributed among these distances:
17 10 0.09
18 8 0.07
19 11 0.10
20 37 0.34
21 41 0.38
22 2 0.02
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (20 bp):
AAAAATATTAAAAATTGTAA
Found at i:424174 original size:62 final size:60
Alignment explanation
Indices: 424069--424197 Score: 145
Period size: 62 Copynumber: 2.1 Consensus size: 60
424059 TAAATAATTG
*
424069 AAAATTAATAAAAATTGTAAAAAAATATTGAAAATGGTAAAAACGTATTTAAAAATTGTAA
1 AAAATTAATAAAAATTATAAAAAAATATTGAAAATGGTAAAAACGTA-TTAAAAATTGTAA
* * * * * *
424130 AAAAGTTAATAAAAATTATAAAACATTATTTAAAATTTGT-AAAACTTATT-AAAATAGTAA
1 AAAA-TTAATAAAAATTATAAAAAAATATTGAAAA-TGGTAAAAACGTATTAAAAATTGTAA
*
424190 ATAATTAA
1 AAAATTAA
424198 CAAATCAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 4 0.07
60 12 0.21
61 6 0.10
62 33 0.57
63 3 0.05
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (60 bp):
AAAATTAATAAAAATTATAAAAAAATATTGAAAATGGTAAAAACGTATTAAAAATTGTAA
Found at i:431960 original size:21 final size:22
Alignment explanation
Indices: 431918--431961 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
431908 ATTTTTCCTA
* *
431918 TTTTTGGATTTTTACTTTTTTT
1 TTTTTGGATTTTTACATATTTT
*
431940 TTTTTGTA-TTTTACATATTTT
1 TTTTTGGATTTTTACATATTTT
431961 T
1 T
431962 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTGGATTTTTACATATTTT
Found at i:431960 original size:22 final size:22
Alignment explanation
Indices: 431918--431961 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
431908 ATTTTTCCTA
*
431918 TTTTTGGATTTTTACTTTTTTT
1 TTTTTGGATTTTTACTATTTTT
*
431940 TTTTTGTA-TTTTACATATTTTT
1 TTTTTGGATTTTTAC-TATTTTT
431962 AAGAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.75
Consensus pattern (22 bp):
TTTTTGGATTTTTACTATTTTT
Found at i:432022 original size:24 final size:24
Alignment explanation
Indices: 431991--432048 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
431981 TTTAAAGTTT
431991 TTGAAAATATTTATATTTTTCTAA
1 TTGAAAATATTTATATTTTTCTAA
*
432015 TTGAAAATATTTATATTTTTTTAA
1 TTGAAAATATTTATATTTTTCTAA
*
432039 TTTAAAATAT
1 TTGAAAATAT
432049 ATATTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (24 bp):
TTGAAAATATTTATATTTTTCTAA
Found at i:435398 original size:58 final size:59
Alignment explanation
Indices: 435281--435774 Score: 262
Period size: 59 Copynumber: 8.4 Consensus size: 59
435271 ATTGTGGATT
* * ** *
435281 TTCGGGGGTAAAATGGTAATTTTGGGAAAATTCGAGGTTAAAAATGAAATTTTTAGACA
1 TTCGAGGGTAAAATGGTAATTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
* * * *
435340 TTCGGGGGTAAAAGGGTAATTTTGAG-AGTTTCGAGGTTAAAAATGGAGTTTTTGGACA
1 TTCGAGGGTAAAATGGTAATTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
* * * * * * * **
435398 TCCGAGGGTAAAATGATAATTTTCAAAAGTTT-TAGGGTCAAAAATGGAAATTTTAGAGG
1 TTCGAGGGTAAAATGGTAATTTTGAGAAGTTTCGA-GGTTAAAAATGGAATTTTTAGACA
*
435457 TTCGAGGGTAAAAATGG-AATTTTTG-GAAGTTTCGAGGTT-AAAATGGAATTTTTGGA-A
1 TTCGAGGGT-AAAATGGTAA-TTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
* *
435514 GCTTCGA-GGTCAAAAATGG-AATTTTTG-GAAG-TTCGAGGGTAAAAATGGAATTTTTGGA-A
1 --TTCGAGGGT--AAAATGGTAA-TTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
* * * *
435573 GTTTTGA-GGTAAAAAATGG-AATTTCTGA-AAGTTTAG-GGGTAAAAATGTAATTTTTAGA-A
1 --TTCGAGGGT--AAAATGGTAATTT-TGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
* * * * * * *
435632 GTTTTG-GGGTCAAAAATAG-AATTTTTAGGAGTTT-GAGGGGTAAAAATGGATTTTTTGGA-A
1 --TTCGAGGGT--AAAATGGTAATTTTGAGAAGTTTCGA-GGTTAAAAATGGAATTTTTAGACA
* * * * * *
435692 GTTTTG-TGGTAAAAATGG-AATTTTTAGAAGTTTCGAGGTCAAAAATTGAATTTTTTGA-A
1 --TTCGAGGGT-AAAATGGTAATTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
*
435751 GTTCGGGGGTAAAAAT-GTAATTTT
1 -TTCGAGGGT-AAAATGGTAATTTT
435775 TGGACAGTTT
Statistics
Matches: 362, Mismatches: 54, Indels: 38
0.80 0.12 0.08
Matches are distributed among these distances:
58 84 0.23
59 233 0.64
60 45 0.12
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (59 bp):
TTCGAGGGTAAAATGGTAATTTTGAGAAGTTTCGAGGTTAAAAATGGAATTTTTAGACA
Found at i:435474 original size:88 final size:87
Alignment explanation
Indices: 435357--435774 Score: 260
Period size: 88 Copynumber: 4.7 Consensus size: 87
435347 GTAAAAGGGT
* * * *
435357 AATTTTGAGAGTTTCGAGGTTAAAAATGGAGTTTTTGGACA-TCCGAGGGTAAAATGATAATTTT
1 AATTTT-AGAGGTTCGAGGGTAAAAATGGAATTTTTGGA-AGTCCGAGGGTAAAATG-GAATTTT
*
435421 CAAAAGTTTTAG-GGTCAAAAATGGA
63 CAAAAG-CTTAGAGGTCAAAAATGGA
* * **
435446 AATTTTAGAGGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTTAAAATGGAATTTTTG
1 AATTTTAGAGGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TCCGAGGGTAAAATGGAATTTTCA
* *
435511 GAAGCTTCGAGGTCAAAAATGGA
65 AAAGCTTAGAGGTCAAAAATGGA
* * * **
435534 ATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGA-GGTAAAAAATGGAA-TTT
1 AATTTTAGAGGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TCCGAGGGT--AAAATGGAATTTT
* * * *
435597 CTGAAAGTTTAGGGGT-AAAAATGTA
63 C-AAAAGCTTAGAGGTCAAAAATGGA
* * * * ** *
435622 ATTTTTAGAAGTTTTG-GGGTCAAAAATAGAATTTTTAGG-AGTTTGAGGGGTAAAAATGGATTT
1 AATTTTAG-AGGTTCGAGGGT-AAAAATGGAATTTTT-GGAAGTCCGA-GGGT-AAAATGGAATT
*** * * *
435685 TTTGGAAGTTTTGTGGT-AAAAATGGA
61 TTCAAAAGCTTAGAGGTCAAAAATGGA
* * * * * * *
435711 ATTTTTAGAAGTTTCGA-GGTCAAAAATTGAATTTTTTGAAGTTCGGGGGTAAAAATGTAATTTT
1 AATTTTAG-AGGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTCCGAGGGT-AAAATGGAATTTT
435775 TGGACAGTTT
Statistics
Matches: 275, Mismatches: 40, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
87 6 0.02
88 137 0.50
89 124 0.45
90 8 0.03
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.35
Consensus pattern (87 bp):
AATTTTAGAGGTTCGAGGGTAAAAATGGAATTTTTGGAAGTCCGAGGGTAAAATGGAATTTTCAA
AAGCTTAGAGGTCAAAAATGGA
Found at i:435569 original size:29 final size:29
Alignment explanation
Indices: 435281--435783 Score: 352
Period size: 29 Copynumber: 17.1 Consensus size: 29
435271 ATTGTGGATT
* * *
435281 TTCGGGGGT-AAAATGGTAATTTTGGGAAAA
1 TTCGAGGGTAAAAATGG-AATTTTTGG-AAG
* * *
435311 TTCGAGGTTAAAAATGAAATTTTTAGACA-
1 TTCGAGGGTAAAAATGGAATTTTTGGA-AG
* *
435340 TTCGGGGGT-AAAAGGGTAA-TTTT-GAGAG
1 TTCGAGGGTAAAAATGG-AATTTTTGGA-AG
* *
435368 TTTCGAGGTTAAAAATGGAGTTTTTGGACA-
1 -TTCGAGGGTAAAAATGGAATTTTTGGA-AG
* * ***
435398 TCCGAGGGT-AAAATGATAATTTTCAAAAG
1 TTCGAGGGTAAAAATG-GAATTTTTGGAAG
** * * *
435427 TTTTAGGGTCAAAAATGGAAATTTTAGAGG
1 TTCGAGGGT-AAAAATGGAATTTTTGGAAG
435457 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
*
435486 TTTCGA-GGTTAAAATGGAATTTTTGGAAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAG
435515 CTTCGA-GGTCAAAAATGGAATTTTTGGAAG
1 -TTCGAGGGT-AAAAATGGAATTTTTGGAAG
435545 TTCGAGGGTAAAAATGGAATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTGGAAG
* * *
435574 TTTTGA-GGTAAAAAATGGAATTTCTGAAAG
1 -TTCGAGGGT-AAAAATGGAATTTTTGGAAG
* * *
435604 TT-TAGGGGTAAAAATGTAATTTTTAGAAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGAAG
* *
435633 TTTTG-GGGTCAAAAATAGAATTTTTAGG-AG
1 -TTCGAGGGT-AAAAATGGAATTTTT-GGAAG
* *
435663 TTTGAGGGGTAAAAATGGATTTTTTGGAAG
1 TTCGA-GGGTAAAAATGGAATTTTTGGAAG
* * *
435693 TTTTG-TGGTAAAAATGGAATTTTTAGAAG
1 -TTCGAGGGTAAAAATGGAATTTTTGGAAG
* *
435722 TTTCGA-GGTCAAAAATTGAATTTTTTGAAG
1 -TTCGAGGGT-AAAAATGGAATTTTTGGAAG
* *
435752 TTCGGGGGTAAAAATGTAATTTTTGGACAG
1 TTCGAGGGTAAAAATGGAATTTTTGGA-AG
435782 TT
1 TT
435784 TAGAGACCTC
Statistics
Matches: 380, Mismatches: 62, Indels: 62
0.75 0.12 0.12
Matches are distributed among these distances:
27 3 0.01
28 17 0.04
29 187 0.49
30 149 0.39
31 24 0.06
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (29 bp):
TTCGAGGGTAAAAATGGAATTTTTGGAAG
Found at i:435569 original size:59 final size:58
Alignment explanation
Indices: 435431--435783 Score: 340
Period size: 59 Copynumber: 6.0 Consensus size: 58
435421 CAAAAGTTTT
* * *
435431 AGGGTCAAAAATGGAAATTTTAG-AGGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCG
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTCGA-GGTAAAAATGGAATTTTTGGAAG-TTCG
* *
435491 A-GGTTAAAATGGAATTTTTGGAAGCTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCG
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTCG
* * * *
435549 AGGGTAAAAATGGAATTTTTGGAAGTTTTGAGGTAAAAAATGGAATTTCTGAAAGTT-T
1 AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTTGGAAGTTCG
* * * * * *
435607 AGGGGTAAAAATGTAATTTTTAGAAGTTTTGGGGTCAAAAATAGAATTTTTAGG-AGTTTG
1 A-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGT-AAAAATGGAATTTTT-GGAAGTTCG
* * * *
435667 AGGGGTAAAAATGGATTTTTTGGAAGTTTTGTGGTAAAAATGGAATTTTTAGAAGTTTCG
1 A-GGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAG-TTCG
* * * *
435727 A-GGTCAAAAATTGAATTTTTTGAAG-TTCGGGGGTAAAAATGTAATTTTTGGACAGTT
1 AGGGT-AAAAATGGAATTTTTGGAAGTTTC-GAGGTAAAAATGGAATTTTTGGA-AGTT
435784 TAGAGACCTC
Statistics
Matches: 249, Mismatches: 33, Indels: 23
0.82 0.11 0.08
Matches are distributed among these distances:
58 29 0.12
59 181 0.73
60 39 0.16
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
AGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTAAAAATGGAATTTTTGGAAGTTCG
Found at i:435605 original size:30 final size:29
Alignment explanation
Indices: 435437--435784 Score: 355
Period size: 29 Copynumber: 11.8 Consensus size: 29
435427 TTTTAGGGTC
* * *
435437 AAAAATGGAAATTTTAG-AGGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGT
435466 AAAAATGGAATTTTTGGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
* *
435495 TAAAATGGAATTTTTGGAAGCTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
435524 CAAAAATGGAATTTTTGGAAG-TTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGA-GGT
*
435554 AAAAATGGAATTTTTGGAAGTTTTGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
* * * *
435583 AAAAAATGGAATTTCTGAAAGTTTAGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTCGAGGT
* * * *
435613 AAAAATGTAATTTTTAGAAGTTTTGGGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
435642 CAAAAATAGAATTTTTAGG-AGTTT-GAGGGGT
1 -AAAAATGGAATTTTT-GGAAGTTTCGA--GGT
* * *
435673 AAAAATGGATTTTTTGGAAGTTTTGTGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
*
435702 AAAAATGGAATTTTTAGAAGTTTCGAGGT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGT
* * *
435731 CAAAAATTGAATTTTTTGAAG-TTCGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTC-GAGGT
*
435761 AAAAATGTAATTTTTGGACAGTTT
1 AAAAATGGAATTTTTGGA-AGTTT
435785 AGAGACCTCT
Statistics
Matches: 271, Mismatches: 33, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
29 146 0.54
30 118 0.44
31 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGT
Found at i:437435 original size:15 final size:15
Alignment explanation
Indices: 437411--437443 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
437401 TGAGCAACTA
437411 GGCTGCTGACGTGGT
1 GGCTGCTGACGTGGT
*
437426 GGCTGTTGACGTGGT
1 GGCTGCTGACGTGGT
437441 GGC
1 GGC
437444 CTCTGATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.48, T:0.27
Consensus pattern (15 bp):
GGCTGCTGACGTGGT
Found at i:437641 original size:17 final size:17
Alignment explanation
Indices: 437621--437730 Score: 150
Period size: 17 Copynumber: 6.4 Consensus size: 17
437611 CTTTATTTAT
* *
437621 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
437638 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
*
437656 TTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAA
437673 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
*
437690 TTTAAATTTTAAAACAAA
1 TTTAAA-TTTAAAATAAA
437708 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
437725 TTTAAA
1 TTTAAA
437731 ATAAGTTATT
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
16 1 0.01
17 53 0.64
18 29 0.35
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:437671 original size:35 final size:34
Alignment explanation
Indices: 437621--437730 Score: 150
Period size: 35 Copynumber: 3.2 Consensus size: 34
437611 CTTTATTTAT
* *
437621 TTTAAATTTATAATAATTTTAAATTTGAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTT-AAAATAAA
*
437656 TTTAAACTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
*
437690 TTTAAATTTTAAAACAAATTT-AATCTTAAAATAAA
1 TTTAAA-TTTAAAATAAATTTAAAT-TTAAAATAAA
437725 TTTAAA
1 TTTAAA
437731 ATAAGTTATT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
34 17 0.25
35 51 0.75
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
Found at i:437688 original size:52 final size:52
Alignment explanation
Indices: 437621--437730 Score: 175
Period size: 52 Copynumber: 2.1 Consensus size: 52
437611 CTTTATTTAT
* * *
437621 TTTAAATTTATAATAATTTTAAATTTGAAAATAAATTTAAACTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
* *
437673 TTTAAATTTAAAATAAATTTAAATTTTAAAACAAATTTAATCTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
437725 TTTAAA
1 TTTAAA
437731 ATAAGTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (52 bp):
TTTAAATTTAAAATAAATTTAAATTTGAAAACAAATTTAAACTTAAAATAAA
Found at i:437702 original size:7 final size:6
Alignment explanation
Indices: 437621--437698 Score: 58
Period size: 6 Copynumber: 13.5 Consensus size: 6
437611 CTTTATTTAT
* * *
437621 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* *
437668 -ATAAA TTTAAA TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
437699 TAAAACAAAT
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
4 1 0.02
5 13 0.23
6 37 0.66
7 5 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:440605 original size:25 final size:24
Alignment explanation
Indices: 440549--440605 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
440539 ATTTAAGTAT
440549 ATGTTTTTA-AAAATTTATTTTCA
1 ATGTTTTTAGAAAATTTATTTTCA
*
440572 AT-TTATTAGGAAATATTTATTTT-A
1 ATGTTTTTA-GAAA-ATTTATTTTCA
440596 ATGTTTTTAG
1 ATGTTTTTAG
440606 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 5 0.18
23 2 0.07
24 7 0.25
25 14 0.50
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (24 bp):
ATGTTTTTAGAAAATTTATTTTCA
Found at i:441346 original size:39 final size:39
Alignment explanation
Indices: 441248--441336 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
441238 TTAAAAATTA
* * * *
441248 TTTAATACAATAAAAT-ATTTATTATATTTATTTGTGTTT
1 TTTAATATAAT-AAATGTTTTATTATATTTATTAGTGCTT
441287 TTTAATATAATAAATGTTTTATTATATTTATGATAGTGCTT
1 TTTAATATAATAAATGTTTTATTATATTTAT--TAGTGCTT
441328 TTT-ATATAA
1 TTTAATATAA
441337 ATACTTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 4 0.09
39 24 0.56
40 6 0.14
41 9 0.21
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (39 bp):
TTTAATATAATAAATGTTTTATTATATTTATTAGTGCTT
Found at i:441429 original size:17 final size:17
Alignment explanation
Indices: 441403--441453 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
441393 CATTTAGTGT
*
441403 ATTATATTTAAAAAAAA
1 ATTATTTTTAAAAAAAA
441420 ATTATTTTTAAATAAAAA
1 ATTATTTTTAAA-AAAAA
* *
441438 CTAATTTTTAAAAAAA
1 ATTATTTTTAAAAAAA
441454 TCATATATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTATTTTTAAAAAAAA
Found at i:441444 original size:18 final size:17
Alignment explanation
Indices: 441409--441453 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
441399 GTGTATTATA
*
441409 TTTAAAAAAAAATTATT
1 TTTAAAAAAAAATAATT
*
441426 TTTAAATAAAAACTAATT
1 TTTAAA-AAAAAATAATT
441444 TTTAAAAAAA
1 TTTAAAAAAA
441454 TCATATATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
TTTAAAAAAAAATAATT
Found at i:446173 original size:9 final size:9
Alignment explanation
Indices: 446136--446205 Score: 54
Period size: 10 Copynumber: 7.7 Consensus size: 9
446126 TCATGTGACA
*
446136 AAAAATTAT
1 AAAAATAAT
446145 AAAAA-AAT
1 AAAAATAAT
446153 AAAAATCAAT
1 AAAAAT-AAT
*
446163 AAAAATGAT
1 AAAAATAAT
*
446172 AAAAATTATT
1 AAAAA-TAAT
**
446182 AAATTTTAAT
1 AAA-AATAAT
446192 AAAAAT-AT
1 AAAAATAAT
446200 AAAAAT
1 AAAAAT
446206 TAAAATTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
8 15 0.31
9 13 0.27
10 20 0.42
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (9 bp):
AAAAATAAT
Found at i:446221 original size:26 final size:27
Alignment explanation
Indices: 446163--446230 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 27
446153 AAAAATCAAT
** *
446163 AAAAATGATAAAAATTATTAAATTTTAAT
1 AAAAAT-ATAAAAATTA-TAAATTAAAAA
446192 AAAAATATAAAAATTA-AAATTAAAAA
1 AAAAATATAAAAATTATAAATTAAAAA
446218 AAAAATTATAAAA
1 AAAAA-TATAAAA
446231 TGCATCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.34
27 7 0.20
28 10 0.29
29 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAAATATAAAAATTATAAATTAAAAA
Found at i:446222 original size:12 final size:13
Alignment explanation
Indices: 446189--446231 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
446179 ATTAAATTTT
446189 AATAAAAATATAAA
1 AATAAAAAT-TAAA
*
446203 AATTAAAATTAAA
1 AATAAAAATTAAA
446216 AA-AAAAATTATAA
1 AATAAAAATTA-AA
446229 AAT
1 AAT
446232 GCATCAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 7 0.28
13 10 0.40
14 8 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAAAATTAAA
Found at i:448399 original size:45 final size:45
Alignment explanation
Indices: 448349--448438 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
448339 CGATTACATC
448349 TTGTCGTCCTAAAATAAAACTCTTATTAATTGACGTGTCAAAATA
1 TTGTCGTCCTAAAATAAAACTCTTATTAATTGACGTGTCAAAATA
448394 TTGTCGTCCTAAAATAAAACTCTTATTAATTGACGTGTCAAAATA
1 TTGTCGTCCTAAAATAAAACTCTTATTAATTGACGTGTCAAAATA
448439 GAAATACAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (45 bp):
TTGTCGTCCTAAAATAAAACTCTTATTAATTGACGTGTCAAAATA
Found at i:454595 original size:43 final size:43
Alignment explanation
Indices: 454542--454652 Score: 168
Period size: 43 Copynumber: 2.6 Consensus size: 43
454532 ATCTATTAAT
* *
454542 TTTAGTGGCGTTTGTGGGGAAAGCGCCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
* * *
454585 TTTAGCGGCGTTTGTGTGGAAAACGCCGCTGAAGACCATGTTC
1 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
*
454628 TTCAGCGGCGTTTGTGGGGAAAGCG
1 TTTAGCGGCGTTTGTGGGGAAAGCG
454653 TAGTAAAGGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCATGTTC
Found at i:457884 original size:22 final size:22
Alignment explanation
Indices: 457859--457903 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
457849 TATTTAAAAA
457859 TTAAAAATAAT-TAAAAATAATT
1 TTAAAAATAATAT-AAAATAATT
* *
457881 TTAAATATTATATAAAATAATT
1 TTAAAAATAATATAAAATAATT
457903 T
1 T
457904 ATAATAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 19 0.95
23 1 0.05
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAATAATATAAAATAATT
Found at i:463511 original size:80 final size:80
Alignment explanation
Indices: 463210--463505 Score: 350
Period size: 80 Copynumber: 3.7 Consensus size: 80
463200 ACAATTATGG
* * *
463210 CACCCAGTGCCTAGCGGA-ATAACCGCGAAAGTGATCCCAGCTCTAGTTGGATT-AACCAACAAA
1 CACCCAGTGCCTAGCGGATA-AACCGCGAATGTGAGCCCAGCTCTAGTCGG-TTAAACCAACAAA
* *
463273 TATCCGTCAAGTCCT-A
64 TATCCGTCAAATCTTGA
* * * *
463289 GCACCCAGTGCTTAGCGGATAAACTGCGAATGTGAACCAAGCTCTAGTCGGTTAAACCAACAAAT
1 -CACCCAGTGCCTAGCGGATAAACCGCGAATGTGAGCCCAGCTCTAGTCGGTTAAACCAACAAAT
*
463354 ATCCGTCAAATCTTGG
65 ATCCGTCAAATCTTGA
* * ** * * *
463370 CACCCAGTGCATAGTGGATAAAATGC-AATTGTGAGCCCAACTCTAGTCGGTTAGACCGACAAAT
1 CACCCAGTGCCTAGCGGATAAACCGCGAA-TGTGAGCCCAGCTCTAGTCGGTTAAACCAACAAAT
463434 ATCCGTCAAATCTTGA
65 ATCCGTCAAATCTTGA
*
463450 CACCCAGTGCCTAGCGGATAAACCGC-AATTGTGAGCCCAGCTCTAGTCAGTTAAAC
1 CACCCAGTGCCTAGCGGATAAACCGCGAA-TGTGAGCCCAGCTCTAGTCGGTTAAAC
463506 TGACAACATA
Statistics
Matches: 187, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
79 4 0.02
80 182 0.97
81 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (80 bp):
CACCCAGTGCCTAGCGGATAAACCGCGAATGTGAGCCCAGCTCTAGTCGGTTAAACCAACAAATA
TCCGTCAAATCTTGA
Found at i:464750 original size:20 final size:21
Alignment explanation
Indices: 464716--464755 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
464706 ACATTAATTT
*
464716 AAAATGAATTTATAATTTAAC
1 AAAATGAATTAATAATTTAAC
464737 AAAA-GAATTAATAATTTAA
1 AAAATGAATTAATAATTTAA
464756 TTTTCTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAATGAATTAATAATTTAAC
Found at i:466269 original size:23 final size:24
Alignment explanation
Indices: 466225--466274 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
466215 AAGTTCCACC
* *
466225 AAAATTTAAGATAATTCCTT-AAT
1 AAAATTTAAGAAAATTCATTAAAT
466248 AAAATTTAA-AAAATCTCATTAAAT
1 AAAATTTAAGAAAAT-TCATTAAAT
466272 AAA
1 AAA
466275 TAAATAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 13 0.57
24 6 0.26
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAATTTAAGAAAATTCATTAAAT
Found at i:467198 original size:15 final size:14
Alignment explanation
Indices: 467174--467204 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
467164 CATGGATTTC
467174 ATATAATATATATT
1 ATATAATATATATT
467188 ATATAAATATATATT
1 ATAT-AATATATATT
467203 AT
1 AT
467205 TTGCTGGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAATATATATT
Found at i:474416 original size:19 final size:19
Alignment explanation
Indices: 474389--474427 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
474379 ATCAAATGTG
474389 TAAAGAGTGGTAATAGTGA
1 TAAAGAGTGGTAATAGTGA
*
474408 TAAATAGTGGTAATAGTGA
1 TAAAGAGTGGTAATAGTGA
474427 T
1 T
474428 GTGTGAACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
TAAAGAGTGGTAATAGTGA
Found at i:478105 original size:3 final size:3
Alignment explanation
Indices: 478097--478139 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
478087 CGAATTTGGC
478097 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
478140 TTGTTCTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:482702 original size:41 final size:41
Alignment explanation
Indices: 482627--482706 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
482617 GCTTATTGTA
* *
482627 TTTTCAATTTGTTTGTTGTTTTACGAATTATTTTAATATCG
1 TTTTCAATTTGTTTGTTATTTTAAGAATTATTTTAATATCG
* * * *
482668 TTTTTAATTTGTTTGTTATTTTAATATTTGTTTTAATAT
1 TTTTCAATTTGTTTGTTATTTTAAGAATTATTTTAATAT
482707 TTTTAAGTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.64
Consensus pattern (41 bp):
TTTTCAATTTGTTTGTTATTTTAAGAATTATTTTAATATCG
Found at i:483266 original size:22 final size:22
Alignment explanation
Indices: 483221--483267 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
483211 AATTTTCTCA
*
483221 ATTCTCTCAATTTTATTCATCT
1 ATTCTCTCAATTTTATTCAACT
483243 ATTCTCTCAATTTCTA-TCAACT
1 ATTCTCTCAATTT-TATTCAACT
483265 ATT
1 ATT
483268 TAGTTCTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTCTCTCAATTTTATTCAACT
Found at i:483444 original size:30 final size:30
Alignment explanation
Indices: 483410--483470 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
483400 TACATTTCTG
483410 ACATTCAATTATAAATGATAAGAAAATACT
1 ACATTCAATTATAAATGATAAGAAAATACT
483440 ACATTCAATTATAAATGATAAGAAAATACT
1 ACATTCAATTATAAATGATAAGAAAATACT
483470 A
1 A
483471 TTATTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.54, C:0.10, G:0.07, T:0.30
Consensus pattern (30 bp):
ACATTCAATTATAAATGATAAGAAAATACT
Found at i:484335 original size:21 final size:20
Alignment explanation
Indices: 484303--484341 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
484293 AAATATTTTC
484303 AAAAAAATTATAATAAATTT
1 AAAAAAATTATAATAAATTT
* *
484323 AAAAATATATATAGTAAAT
1 AAAAAAAT-TATAATAAAT
484342 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAAAATTATAATAAATTT
Found at i:485431 original size:16 final size:16
Alignment explanation
Indices: 485406--485444 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
485396 TGTTTAATAT
*
485406 TTCACCACTCAACATG
1 TTCACTACTCAACATG
485422 TTCACTACTCAACATG
1 TTCACTACTCAACATG
485438 TTCACTA
1 TTCACTA
485445 TGAGCGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.31
Consensus pattern (16 bp):
TTCACTACTCAACATG
Found at i:485644 original size:45 final size:46
Alignment explanation
Indices: 485566--485663 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 46
485556 CATTTTCATT
* * *
485566 TCCATTT-TGAGAAAACCATATTTATTTTCAAATGATT-TAATTTC
1 TCCATTTCGGAGAAAACCATAATCATTTTCAAATGATTCTAATTTC
* *
485610 TCCATTTCGGAGAAAACCATAATCA-TTTCTAAATGTTTCTCATTTC
1 TCCATTTCGGAGAAAACCATAATCATTTTC-AAATGATTCTAATTTC
*
485656 TCTATTTC
1 TCCATTTC
485664 TATTCATTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
44 11 0.24
45 21 0.47
46 13 0.29
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (46 bp):
TCCATTTCGGAGAAAACCATAATCATTTTCAAATGATTCTAATTTC
Found at i:486177 original size:33 final size:35
Alignment explanation
Indices: 486103--486177 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 35
486093 TGGATTTATG
* *
486103 TATTTTTGTATTTTTTGAAATTTTAATTAATTTTC
1 TATTTTTATATTTTTTGAAATTTTAATTAAATTTC
* *
486138 TTTTTTTATATTTTTT-ATATTTT-A-TAAATTTC
1 TATTTTTATATTTTTTGAAATTTTAATTAAATTTC
486170 ATATTTTT
1 -TATTTTT
486178 TTAAATTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
32 7 0.21
33 7 0.21
34 6 0.18
35 14 0.41
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (35 bp):
TATTTTTATATTTTTTGAAATTTTAATTAAATTTC
Found at i:489927 original size:24 final size:23
Alignment explanation
Indices: 489878--489927 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
489868 TAAAATAGGT
* *
489878 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
489901 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
489925 TAT
1 TAT
489928 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:490066 original size:58 final size:58
Alignment explanation
Indices: 489905--490071 Score: 221
Period size: 58 Copynumber: 2.9 Consensus size: 58
489895 ATATTATATA
* * *
489905 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATTTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATTTAATTAAATTAT
* * * *
489965 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATTTAATTAAATTAT
*
490022 TTATTATTTTTATTAAATTATATTTAATAATAATTTTATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATTTAAT
490072 AACAATAATC
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
57 21 0.23
58 56 0.60
59 8 0.09
60 8 0.09
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATTTAATTAAATTAT
Found at i:492597 original size:21 final size:18
Alignment explanation
Indices: 492566--492604 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 18
492556 TAATTTTTAA
492566 TAAGAATTTTTATTTATTTT
1 TAAGAATTTTT-TTT-TTTT
492586 TAAGACATTTTTTTTTTTT
1 TAAGA-ATTTTTTTTTTTT
492605 GCAATTATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 8 0.44
21 6 0.33
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (18 bp):
TAAGAATTTTTTTTTTTT
Found at i:496630 original size:21 final size:22
Alignment explanation
Indices: 496606--496663 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
496596 AAAAATACAA
496606 ATTTTGAATTTTTTTATAAA-T
1 ATTTTGAATTTTTTTATAAATT
*
496627 ATTTTGAA---TTTTAAAAATT
1 ATTTTGAATTTTTTTATAAATT
496646 ATTTTG-ATTTTTTTATAA
1 ATTTTGAATTTTTTTATAA
496664 TTTTTGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 9 0.29
19 7 0.23
21 15 0.48
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTGAATTTTTTTATAAATT
Found at i:496644 original size:18 final size:18
Alignment explanation
Indices: 496617--496656 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
496607 TTTTGAATTT
*
496617 TTTTATAAA-TATTTTGAA
1 TTTTAAAAATTATTTTG-A
496635 TTTTAAAAATTATTTTGA
1 TTTTAAAAATTATTTTGA
496653 TTTT
1 TTTT
496657 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTTAAAAATTATTTTGA
Found at i:496748 original size:9 final size:9
Alignment explanation
Indices: 496734--496764 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
496724 CACCAATAAG
496734 TTATTCGAA
1 TTATTCGAA
*
496743 TTATTCGAG
1 TTATTCGAA
496752 TTATTCGAA
1 TTATTCGAA
496761 TTAT
1 TTAT
496765 AAAATTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (9 bp):
TTATTCGAA
Found at i:499929 original size:16 final size:16
Alignment explanation
Indices: 499908--499938 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
499898 GCCTCTTGTC
499908 TAAAAGATGAAATTTA
1 TAAAAGATGAAATTTA
499924 TAAAAGATGAAATTT
1 TAAAAGATGAAATTT
499939 TACCTTCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
TAAAAGATGAAATTTA
Found at i:500329 original size:2 final size:2
Alignment explanation
Indices: 500316--500354 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
500306 TTCGACATTC
*
500316 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
500355 TCGTTTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:502314 original size:17 final size:18
Alignment explanation
Indices: 502291--502351 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 18
502281 CCAAACTCAT
**
502291 TTTAAATTTATTTTACGA
1 TTTAAATTTATTTTAAAA
502309 -TTAAATTTATTTTAAAA
1 TTTAAATTTATTTTAAAA
502326 TTTAAATTTATTTT-AAA
1 TTTAAATTTATTTTAAAA
502343 TTT-AATTTA
1 TTTAAATTTA
502352 AGTTTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.15
17 21 0.52
18 13 0.32
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:502323 original size:11 final size:11
Alignment explanation
Indices: 502309--502357 Score: 52
Period size: 11 Copynumber: 4.8 Consensus size: 11
502299 TATTTTACGA
502309 TTAAATTTATT
1 TTAAATTTATT
502320 TTAAA---A-T
1 TTAAATTTATT
502327 TTAAATTTATT
1 TTAAATTTATT
*
502338 TTAAATTTAAT
1 TTAAATTTATT
*
502349 TTAAGTTTA
1 TTAAATTTA
502358 AATTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
7 6 0.19
8 1 0.03
10 1 0.03
11 24 0.75
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:502339 original size:46 final size:46
Alignment explanation
Indices: 502289--502393 Score: 147
Period size: 46 Copynumber: 2.3 Consensus size: 46
502279 GCCCAAACTC
* * * *
502289 ATTTTAAATTTATTTTACGATTAAATTTATTTTAAAATTTAAATTT
1 ATTTTAAATTTAATTTAAGATTAAATTCATTTTAAAATTTAAAATT
* *
502335 ATTTTAAATTTAATTTAAGTTTAAATTCATTTTCAAATTTAAAATT
1 ATTTTAAATTTAATTTAAGATTAAATTCATTTTAAAATTTAAAATT
*
502381 ATTATAAATTTAA
1 ATTTTAAATTTAA
502394 AATAAATTAC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (46 bp):
ATTTTAAATTTAATTTAAGATTAAATTCATTTTAAAATTTAAAATT
Found at i:502341 original size:29 final size:28
Alignment explanation
Indices: 502309--502376 Score: 91
Period size: 29 Copynumber: 2.4 Consensus size: 28
502299 TATTTTACGA
* *
502309 TTAAATTTATTTTAAAATTTAAATTTATT
1 TTAAATTTAATTT-AAATTTAAATTCATT
*
502338 TTAAATTTAATTTAAGTTTAAATTCATT
1 TTAAATTTAATTTAAATTTAAATTCATT
502366 TTCAAATTTAA
1 TT-AAATTTAA
502377 AATTATTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 15 0.43
29 20 0.57
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAAATTTAATTTAAATTTAAATTCATT
Found at i:502357 original size:17 final size:17
Alignment explanation
Indices: 502291--502361 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 17
502281 CCAAACTCAT
* *
502291 TTTAAATTTATTTTACGA
1 TTTAAATTTAGTTTA-AA
*
502309 -TTAAATTTATTTTAAAA
1 TTTAAATTTAGTTT-AAA
*
502326 TTTAAATTTATTTTAAA
1 TTTAAATTTAGTTTAAA
502343 TTT-AATTTAAGTTTAAA
1 TTTAAATTT-AGTTTAAA
502360 TT
1 TT
502362 CATTTTCAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 5 0.10
17 29 0.60
18 14 0.29
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAGTTTAAA
Found at i:502358 original size:35 final size:35
Alignment explanation
Indices: 502291--502359 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
502281 CCAAACTCAT
* *
502291 TTTAAATTTATTTTACGATTAAATTTATTTTAAAA
1 TTTAAATTTATTTTACAATTAAATTTAGTTTAAAA
*
502326 TTTAAATTTATTTTA-AATTTAATTTAAGTTTAAA
1 TTTAAATTTATTTTACAATTAAATTT-AGTTTAAA
502360 TTCATTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 8 0.27
35 22 0.73
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTACAATTAAATTTAGTTTAAAA
Found at i:503048 original size:3 final size:3
Alignment explanation
Indices: 503040--503068 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
503030 GTTAAATAGT
503040 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
503069 TTAGTGCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:504308 original size:30 final size:30
Alignment explanation
Indices: 504235--504444 Score: 134
Period size: 29 Copynumber: 7.1 Consensus size: 30
504225 TAGGAGGTCT
* *
504235 CGAAACTGCCAAAAATTCTATTTTT-ACCC
1 CGAAACTTCCAAAAATTCCATTTTTAACCC
* *
504264 CTG-AACTTCTAAAAATTCCATTTTTAACCT
1 C-GAAACTTCCAAAAATTCCATTTTTAACCC
*
504294 CGAAACTTCCAAAAATTCCATTTTTTACCCC
1 CGAAACTTCCAAAAATTCCA-TTTTTAACCC
* * *
504325 CTAAACTTCCAAAAATTATCA-TTTT-CCCC
1 CGAAACTTCCAAAAATT-CCATTTTTAACCC
* * * *
504354 CG-GA-TGTCCAAAAACTCCATTTTCAACCA
1 CGAAACT-TCCAAAAATTCCATTTTTAACCC
* * * *
504383 CAAAAC-TCTAAAAATTACC-CTTTTACCCC
1 CGAAACTTCCAAAAATT-CCATTTTTAACCC
* *
504412 CG-AA-TATCTAAAAATTCCATTTTTAACTC
1 CGAAACT-TCCAAAAATTCCATTTTTAACCC
504441 CGAA
1 CGAA
504445 TTTTCCCAAA
Statistics
Matches: 138, Mismatches: 28, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
27 3 0.02
28 17 0.12
29 63 0.46
30 29 0.21
31 24 0.17
32 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTAACCC
Found at i:504331 original size:31 final size:29
Alignment explanation
Indices: 504237--504341 Score: 129
Period size: 31 Copynumber: 3.5 Consensus size: 29
504227 GGAGGTCTCG
* *
504237 AAACTGCCAAAAATTCTATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCT
* * * *
504266 GAACTTCTAAAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCT
504296 AAACTTCCAAAAATTCCATTTTTTACCCCCT
1 AAACTTCCAAAAATTCCA-TTTTTA-CCCCT
504327 AAACTTCCAAAAATT
1 AAACTTCCAAAAATT
504342 ATCATTTTCC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
29 19 0.30
30 21 0.33
31 23 0.37
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCT
Done.