Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001892.1 Hibiscus syriacus cultivar Beakdansim tig00003838_pilon, 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: 101142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:469 original size:251 final size:249
Alignment explanation
Indices: 106--717 Score: 688
Period size: 249 Copynumber: 2.4 Consensus size: 249
96 GACATACTAG
* * * *
106 TTTGAAAATAGTTTACTAGGTAAGAAGCTTTAGAAATCACTTTTTTACTTTTCAAAAATTTCATT
1 TTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCAC-TTTTTACTTTTCAAAAATTTCATT
* * * * * *
171 TTCATAGAATTTTAAATGAGAAGCTTTGAAAATCACTTTCATTTTTCATAAATATCATATAAAAA
65 TTCAGAAAATATTAAATGA-AAACTTTG-AAATCGCTTTCTTTTTTC--AAATATCATATAAAAA
* * * * * *
236 AATTATGCCAAATGTCT-TATATGACCCTAAGGACTTATCACCCTGTTC-GA-AAGAATGA-AGA
126 AATCATACCAAAGGT-TATATAT-ACCCGAACGACTTATCA-CCT-TTCTAAGAAGAATGATAGA
* * *
297 T-AACCATAAGGATTTAATTATTATGCTCAAAAGCCTTACTGATGA-CTCAGA-GATTTAATTGT
187 TGAACCAT-AGGATTTAATCATTATGCTCAAAAGACTTACTGATGACCT-AGAGGATTTAATCG-
359 T
249 T
*
360 TTTGGAAATAGATTA-TA-GTAAAAAACTTTGGAAATCACTTTCTTACTTTTC-AAAATTTCATT
1 TTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCACTTT-TTACTTTTCAAAAATTTCATT
* * * *
422 TTCAGAAAAGATTAAATGATAAACTTTGCAAATCGCTTTCTTTTTTCAAATGTCATATGAAAACA
65 TTCAGAAAATATTAAATGA-AAACTTTG-AAATCGCTTTCTTTTTTCAAATATCATATAAAAAAA
* * * * * * *
487 TCCTACCGAAGGTTATATATCCCCGAACGACTTATCATCTTTCTAAGAAGACTTATAGATGACCC
128 TCATACCAAAGGTTATATATACCCGAACGACTTATCACCTTTCTAAGAAGAATGATAGATGAACC
*
552 ATAGGATTTAATCATTATGCTCAAAAGACTTATTGATGACCTAGAGGATTTAATCGT
193 ATAGGATTTAATCATTATGCTCAAAAGACTTACTGATGACCTAGAGGATTTAATCGT
609 TTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCACTTTTTACTTTTCAAAAATTTCATTT
1 TTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCACTTTTTACTTTTCAAAAATTTCATTT
* *
674 T-AGAAAATATTAAATGAGAACTTTGAAATTTGCTTTCTTATTTT
66 TCAGAAAATATTAAATGAAAACTTTGAAA-TCGCTTTCTT-TTTT
718 TTTAAAATAT
Statistics
Matches: 307, Mismatches: 38, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
246 3 0.01
247 3 0.01
248 24 0.08
249 101 0.33
250 46 0.15
251 88 0.29
252 27 0.09
253 2 0.01
254 13 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.37
Consensus pattern (249 bp):
TTTGGAAATAGATTACTAGGTAAGAAACTTTGGAAATCACTTTTTACTTTTCAAAAATTTCATTT
TCAGAAAATATTAAATGAAAACTTTGAAATCGCTTTCTTTTTTCAAATATCATATAAAAAAATCA
TACCAAAGGTTATATATACCCGAACGACTTATCACCTTTCTAAGAAGAATGATAGATGAACCATA
GGATTTAATCATTATGCTCAAAAGACTTACTGATGACCTAGAGGATTTAATCGT
Found at i:3701 original size:2 final size:2
Alignment explanation
Indices: 3694--3733 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3684 TAACACATTC
3694 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3734 CGATTTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8264 original size:12 final size:12
Alignment explanation
Indices: 8247--8271 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8237 GATGGTTAAG
8247 TATTTTTCCTAA
1 TATTTTTCCTAA
8259 TATTTTTCCTAA
1 TATTTTTCCTAA
8271 T
1 T
8272 GAGCTTCCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTTCCTAA
Found at i:9686 original size:95 final size:94
Alignment explanation
Indices: 9551--9729 Score: 240
Period size: 95 Copynumber: 1.9 Consensus size: 94
9541 ACAAAGGGAC
* *
9551 GTATCGATACCATGAATCCAGAATGTCAAAATAGTATCGATACT-GAAAGGGAGTAT-CGATACC
1 GTATCGATACCATGAATACAGAATATCAAAATAGTATCGATA-TGGAAAGGGAGTATCCG-TACC
9614 ATAGTATA-ATAGTATCGATACTGAGAGAAGG
64 ATAGTATAGA-AGTATCGATACTGAGAGAAGG
* * *
9645 GTATCGATACCATGCACTACAGAATAT-AGAAATGGTATCGATATGGAAAGGGGGTATCCGTACC
1 GTATCGATACCATG-AATACAGAATATCA-AAATAGTATCGATATGGAAAGGGAGTATCCGTACC
9709 ATAGTATAGAAGTATCGATAC
64 ATAGTATAGAAGTATCGATAC
9730 CAGGGTAGTT
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
94 16 0.21
95 56 0.75
96 3 0.04
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.25
Consensus pattern (94 bp):
GTATCGATACCATGAATACAGAATATCAAAATAGTATCGATATGGAAAGGGAGTATCCGTACCAT
AGTATAGAAGTATCGATACTGAGAGAAGG
Found at i:10220 original size:20 final size:20
Alignment explanation
Indices: 10148--10228 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 20
10138 AACTAAAAAT
*
10148 GCATGAATGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
10168 GCATGAAAGAATGTCATAATTAAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
10195 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
10215 GCATGAAAGGATGC
1 GCATGAAAGGATGC
10229 CATAACTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
20 27 0.55
21 1 0.02
23 3 0.06
24 3 0.06
26 1 0.02
27 14 0.29
ACGTcount: A:0.42, C:0.10, G:0.26, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:10261 original size:49 final size:47
Alignment explanation
Indices: 10134--10559 Score: 615
Period size: 47 Copynumber: 9.0 Consensus size: 47
10124 TAAACCGAAT
* *
10134 CCATAACTAAAAATGCATGAATGGATGCATTAAGGCATGAAAGAATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
10181 TCATAATTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
10228 CCATAACTAAAAAAATGCATGAAATGATGCATTAAGGCATGTAAGGATG
1 CCATAACT--AAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
10277 CCATAACTAAAAAAATACATGAACGGATGCATTAAGGCATGAAATGATG
1 CCATAACT--AAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
10326 CCATAACTAAAAAATACATGAAAGGATACATTAAGGCATGAAAGGATG
1 CCATAACT-AAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
10374 CCATAACTAAAAATGCATGAACGGATACATTAAGGCATGAAATGATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
10421 CCATAACTAAAAATGCATG-AACGATTCATTAAGGCACG-AACGATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
10466 CCATAACTAAAAATGCATG-AAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
10512 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATAAAAGGATG
1 CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
10559 C
1 C
10560 ATTAAGGCAT
Statistics
Matches: 346, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
45 41 0.12
46 40 0.12
47 131 0.38
48 45 0.13
49 89 0.26
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.21
Consensus pattern (47 bp):
CCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:10510 original size:20 final size:20
Alignment explanation
Indices: 10480--10579 Score: 112
Period size: 20 Copynumber: 4.7 Consensus size: 20
10470 AACTAAAAAT
10480 GCATG-AAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
10499 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATG-CAT---T---AAG
10526 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
10546 GCATAAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
10566 GCATGAAAGGATGC
1 GCATGAAAGGATGC
10580 CATAATTAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 15
0.78 0.05 0.17
Matches are distributed among these distances:
19 5 0.07
20 41 0.59
21 3 0.04
23 1 0.01
24 1 0.01
26 3 0.04
27 15 0.22
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:10664 original size:47 final size:47
Alignment explanation
Indices: 10546--10680 Score: 153
Period size: 47 Copynumber: 2.9 Consensus size: 47
10536 ATGCATTAAG
* *
10546 GCATAAAAGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAAAT
1 GCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
* ** * * * * *
10593 GCATGAAAATATACTTTAAAGCATGAAAGTATGCCATAGCTAAAAAT
1 GCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
* * *
10640 GCATCAACGGATGCATTAAGGCATGAAAAGAGGCCATAACT
1 GCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACT
10681 GAAATTAAAT
Statistics
Matches: 68, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.21
Consensus pattern (47 bp):
GCATCAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAAT
Found at i:16031 original size:21 final size:21
Alignment explanation
Indices: 16007--16059 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
15997 AGCTAGAAGG
*
16007 ATCGATCACTTTTAAAAAAGA
1 ATCGATTACTTTTAAAAAAGA
16028 ATCGATTACTTTTAAAAAAGA
1 ATCGATTACTTTTAAAAAAGA
16049 ATCGATTACTT
1 ATCGATTACTT
16060 GGCTAGAAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCGATTACTTTTAAAAAAGA
Found at i:20498 original size:21 final size:21
Alignment explanation
Indices: 20472--20515 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20462 AGCTTGAATT
*
20472 ATTCAAGGAGTATCGATACTG
1 ATTCAAGCAGTATCGATACTG
*
20493 ATTCAATCAGTATCGATACTG
1 ATTCAAGCAGTATCGATACTG
20514 AT
1 AT
20516 GAGGTAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (21 bp):
ATTCAAGCAGTATCGATACTG
Found at i:20645 original size:95 final size:95
Alignment explanation
Indices: 20519--20741 Score: 295
Period size: 95 Copynumber: 2.3 Consensus size: 95
20509 TACTGATGAG
** * * * *
20519 GTAGTATCGATAATATGGTGAGGGTATCGATACCAGGTAACGTC-AAACCTAATTTTGATATCGA
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAAA-CTAATTTTGATATCGA
* * * *
20583 TAGCAGAAGGGGGTATCGGTACCCTAGTATA
65 TACCAGAAGGGGGTATCGATACCATAGTAGA
* *
20614 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCCACATCGAAACTAATTTTGGTATCGAT
1 GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAAACTAATTTTGATATCGAT
*
20679 ACCGGAAGGGGGTATCGATACCATAGTAGA
66 ACCAGAAGGGGGTATCGATACCATAGTAGA
* *
20709 GTAATATCGATACCATGGTAGGGGTATCGATAC
1 GTAGTATCGATACCATGGTAAGGGTATCGATAC
20742 TGAAGGGCCA
Statistics
Matches: 112, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
95 109 0.97
96 3 0.03
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (95 bp):
GTAGTATCGATACCATGGTAAGGGTATCGATACCAAGCAACATCGAAACTAATTTTGATATCGAT
ACCAGAAGGGGGTATCGATACCATAGTAGA
Found at i:21143 original size:59 final size:59
Alignment explanation
Indices: 21072--21469 Score: 593
Period size: 59 Copynumber: 6.8 Consensus size: 59
21062 ATGGCACTAA
* * * * *
21072 GTGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGAATTTCTACATAGAGCATTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
21131 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTT
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * *
21190 GTGTGCTAAAATGGTAAGGAAATTATACTAAGTGTATGAATTTCCAAATAGGACACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * * *
21249 TTGTTCTAAAATGGTAATGAAATTATACTAAGTGTATGAATTTCCAGATAGGGCATTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
21308 GTCTGCTAAAAT-GTAAGGAAATCATACTAAGTGTATGAATTTCCATATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * *
21366 GTGTTCTAAAATGTTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGTACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
21425 GTGTGCTAAAATGATAAGGAAATCATACTAA-TGATATGAATTTCC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTG-TATGAATTTCC
21470 TATTGAATTT
Statistics
Matches: 307, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
58 54 0.18
59 253 0.82
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (59 bp):
GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
Found at i:26396 original size:228 final size:226
Alignment explanation
Indices: 25995--26442 Score: 797
Period size: 228 Copynumber: 2.0 Consensus size: 226
25985 GTAAATTATC
* * *
25995 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
26060 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 GAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
26125 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
26190 AAACATAAATTACATAACTTTCAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAGTATA
*
26222 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
26287 TGAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TGAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* *
26352 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
26417 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
26443 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
227 40 0.19
228 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
GAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAGTATA
Found at i:26532 original size:20 final size:19
Alignment explanation
Indices: 26509--26554 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
26499 CGATATACCA
26509 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
26529 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
26549 GGTAAA
1 GGTAAA
26555 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:26699 original size:20 final size:19
Alignment explanation
Indices: 26676--26722 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
26666 CGATATAACA
26676 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
26696 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
26716 GGTAAAA
1 GGTAAAA
26723 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:26724 original size:17 final size:19
Alignment explanation
Indices: 26685--26727 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
26675 AGGTAAAAAT
26685 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
26705 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
26722 ATGATA
1 ATGATA
26728 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:29003 original size:21 final size:21
Alignment explanation
Indices: 28957--29021 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
28947 AAGACAATCA
** *
28957 AGAGTCGAAGAGAAACTTAAT
1 AGAGTCGAAGAGAAACTCGAG
* *
28978 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
28999 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
29020 AG
1 AG
29022 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:29097 original size:33 final size:33
Alignment explanation
Indices: 29055--29120 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
29045 AAATAGATGG
*
29055 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
29088 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
29121 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:30935 original size:19 final size:19
Alignment explanation
Indices: 30911--30959 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
30901 AATGTAGGGT
30911 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
30930 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
30949 TATTTTTGTAT
1 TAATTTTGTAT
30960 GTGAATATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:31492 original size:199 final size:199
Alignment explanation
Indices: 31078--32133 Score: 1947
Period size: 199 Copynumber: 5.3 Consensus size: 199
31068 CAATATGGCC
* *
31078 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAAACATCGAAA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCG-AA
* * * * *
31143 ACCAAAGGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTCTACCGGTTTTAAGAG
64 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAG
*
31208 AGAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGA
129 AGAATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGA
31272 ATGGAA
194 ATGGAA
*
31278 AACAGTGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
31343 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
31408 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
31473 GGAA
196 GGAA
*
31477 AACAGGGTACACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
31542 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
31607 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
31672 GGAA
196 GGAA
31676 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
31741 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACC-GTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
31805 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTATCGATATTTTTTTCCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
31870 GGAA
196 GGAA
31874 AACA-GGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
31938 CAAAAGTATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
32003 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
131 AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
32068 GGAA
196 GGAA
*
32072 AACATGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
1 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
32134 GAGTGTTTCA
Statistics
Matches: 837, Mismatches: 16, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
197 97 0.12
198 312 0.37
199 394 0.47
200 34 0.04
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (199 bp):
AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTATAAATAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAAT
GGAA
Found at i:32840 original size:6 final size:6
Alignment explanation
Indices: 32816--32913 Score: 61
Period size: 6 Copynumber: 16.3 Consensus size: 6
32806 AGCGGTCGCA
* * * * * * *
32816 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAC GACGAT GAAGCT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
** * * * * * *
32864 GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
32912 GA
1 GA
32914 TGATCCAAAC
Statistics
Matches: 72, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
6 72 1.00
ACGTcount: A:0.37, C:0.08, G:0.35, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:32851 original size:9 final size:9
Alignment explanation
Indices: 32837--32916 Score: 70
Period size: 9 Copynumber: 8.6 Consensus size: 9
32827 TGACGATGAA
32837 GATGACGAT
1 GATGACGAT
*
32846 GATGACGAC
1 GATGACGAT
**
32855 GATGAAGCTGGC
1 GATG-A-C-GAT
*
32867 GATGAAGAT
1 GATGACGAT
32876 GATGACGAT
1 GATGACGAT
*
32885 GATGATGAT
1 GATGACGAT
*
32894 GATGATGAT
1 GATGACGAT
*
32903 GATGAAGAT
1 GATGACGAT
32912 GATGA
1 GATGA
32917 TCCAAACAAG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
9 51 0.85
10 1 0.02
11 2 0.03
12 6 0.10
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (9 bp):
GATGACGAT
Found at i:32888 original size:3 final size:3
Alignment explanation
Indices: 32867--32917 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
32857 TGAAGCTGGC
* * *
32867 GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
32915 GAT
1 GAT
32918 CCAAACAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.37, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:32917 original size:12 final size:12
Alignment explanation
Indices: 32819--32913 Score: 91
Period size: 12 Copynumber: 7.9 Consensus size: 12
32809 GGTCGCAGAA
*
32819 GATGAAGCTGAC
1 GATGAAGATGAC
32831 GATGAAGATGAC
1 GATGAAGATGAC
* *
32843 GATGATGACGAC
1 GATGAAGATGAC
* *
32855 GATGAAGCTGGC
1 GATGAAGATGAC
*
32867 GATGAAGATGAT
1 GATGAAGATGAC
* * *
32879 GACGATGATGAT
1 GATGAAGATGAC
* *
32891 GATGATGATGAT
1 GATGAAGATGAC
32903 GATGAAGATGA
1 GATGAAGATGA
32914 TGATCCAAAC
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 69 1.00
ACGTcount: A:0.36, C:0.08, G:0.35, T:0.21
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:34795 original size:183 final size:183
Alignment explanation
Indices: 34418--35089 Score: 1183
Period size: 183 Copynumber: 3.7 Consensus size: 183
34408 GCAATGCTAT
* *
34418 CGGTATAAATATACCGGTTTTATGCGCGAATAGGCCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
34483 GTGTCGGTAC-TT-TGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTGT-TAAAAGTGTCGAC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATT-TAAAAAAGTGTCGAC
34544 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
34598 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* *
34663 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAACTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
34728 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
34781 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* *
34846 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
** *
34911 TTTACACATCGGAACCCGGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
* *
34964 CGGTATAAATATACCGGTTTTATGAGCG-ATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
35028 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCG
35090 GTAATTTTAA
Statistics
Matches: 473, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
180 73 0.15
181 2 0.00
182 125 0.26
183 273 0.58
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGACA
TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:35055 original size:365 final size:363
Alignment explanation
Indices: 34418--35089 Score: 1177
Period size: 365 Copynumber: 1.8 Consensus size: 363
34408 GCAATGCTAT
*
34418 CGGTATAAATATACCGGTTTTATGCGCGAATAGGCCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGCCTACAACCTATATCGACACTTTTTAATATT
* *
34483 GTGTCGGTACTTTGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTTAAAAGTGTCGACATTT
66 GTGTCGGTACTTTGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTAAAAAGTATCGACATTT
*
34548 ACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACC
131 ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACC
* *
34613 GGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTAT
196 GGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTAT
* *
34678 GTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAACTGTCGACATTTACACATCGGAAC
261 GTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAACTGTCGACATTTACACATCGGAAC
34743 CCATAATTATAATGTAATAGATAATTTTGTAATATAAC
326 CCATAATTATAATGTAATAGATAATTTTGTAATATAAC
*
34781 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGCCTACAACCTATATCGACACTTTTTAATATT
*
34846 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATT-TAAAAAAGTATCGAC
66 GTGTCGGTAC-TT-TGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTGT-AAAAAGTATCGAC
* *
34910 ATTTACACATCGGAACCCGGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATA
127 ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATA
34975 TACCGGTTTTATGAGCG-ATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACT
192 TACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACT
*
35039 TTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
257 TTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAACTGTCG
35090 GTAATTTTAA
Statistics
Matches: 292, Mismatches: 13, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
363 73 0.25
364 2 0.01
365 125 0.43
366 92 0.32
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (363 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGCCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTGTCCAGATTGGAAGAAAAATGTGTCGATACATTGTAAAAAGTATCGACATTT
ACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACC
GGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTAT
GTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAACTGTCGACATTTACACATCGGAAC
CCATAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:37586 original size:25 final size:25
Alignment explanation
Indices: 37558--37622 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
37548 TTATCATTAA
37558 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
37583 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
37608 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
37623 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:37996 original size:23 final size:23
Alignment explanation
Indices: 37965--38113 Score: 217
Period size: 23 Copynumber: 6.5 Consensus size: 23
37955 ATAGGTAAAC
*
37965 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
37988 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
38011 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
38034 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
38057 ATATAATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
38080 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
38103 ATATATTGTAA
1 ATATAATGTAA
38114 AGTATCTATC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 112 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:38024 original size:46 final size:46
Alignment explanation
Indices: 37965--38113 Score: 271
Period size: 46 Copynumber: 3.2 Consensus size: 46
37955 ATAGGTAAAC
*
37965 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
38011 ATATAATGTAATAGGTAGTGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
38057 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
*
38103 ATATATTGTAA
1 ATATAATGTAA
38114 AGTATCTATC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 99 1.00
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.40
Consensus pattern (46 bp):
ATATAATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTT
Found at i:38553 original size:18 final size:18
Alignment explanation
Indices: 38532--38568 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38522 GTAATTGGAG
38532 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
38550 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
38568 T
1 T
38569 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:38576 original size:24 final size:24
Alignment explanation
Indices: 38524--38570 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
38514 TTTCATATGT
* *
38524 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
38548 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
38571 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:38867 original size:39 final size:39
Alignment explanation
Indices: 38824--38910 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
38814 TCTGATGCTC
*
38824 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
38863 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
38902 ATCAAAATC
1 ATCAAAATC
38911 TACAACTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:39360 original size:23 final size:23
Alignment explanation
Indices: 39329--39401 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
39319 ATAGGTAAAA
*
39329 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
39352 ATATAATGTAATATGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
39375 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
39398 ATAT
1 ATAT
39402 TGTAAAGTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:42029 original size:95 final size:95
Alignment explanation
Indices: 41806--42029 Score: 236
Period size: 95 Copynumber: 2.4 Consensus size: 95
41796 GTACTGATGA
* * * * * *
41806 GGTAGTATCGATACCATAGT-GAGGGTATTAATACCAGATAATATCGAACCTGATTTTGGTATCG
1 GGTAGTATCGATACCATGGTAG-GGGTATTGATACCAGACAACATCAAACCTAATTTTGGTATCG
* * * * *
41870 ATATCGGAAGGGGGTATTGGTACCCTAACAT
65 ATACCGGAAGGGGGTACTGATACCATAACAG
* * * * * * *
41901 AGTAGTATCGATACCATGGTAAGGGCATCGATACCA-AGCCACATCAAAGCTAATTTTGGTATTG
1 GGTAGTATCGATACCATGGTAGGGGTATTGATACCAGA-CAACATCAAACCTAATTTTGGTATCG
**
41965 ATACCGGAAGGGGGTACTGATACCATAGTAG
65 ATACCGGAAGGGGGTACTGATACCATAACAG
41996 GGTAGTATCGATACCATGGTAGGGGTATTGATAC
1 GGTAGTATCGATACCATGGTAGGGGTATTGATAC
42030 TGAATGGCCA
Statistics
Matches: 103, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
94 1 0.01
95 102 0.99
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAGGGGTATTGATACCAGACAACATCAAACCTAATTTTGGTATCGA
TACCGGAAGGGGGTACTGATACCATAACAG
Found at i:42608 original size:117 final size:117
Alignment explanation
Indices: 42351--42683 Score: 522
Period size: 117 Copynumber: 2.8 Consensus size: 117
42341 ATTACCAAAT
* * *
42351 GGCACTAAGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTATAGATAGGGCACT
1 GGCACTACGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACT
*
42416 TCGTGTGCTACAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
66 TCGTGTGCTAAAAT-GTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * * * * * *
42469 GGCACTTCATGTGCTAAAATGGTAAGGAAATTATACCAAGTGTATGAATTTCCAGATAGTGTACT
1 GGCACTACGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACT
* * *
42534 TCGTGTGCTAAAATGTAAGAAAATCACACTAAGTGTATGAATTTCCATATAG
66 TCGTGTGCTAAAATGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
42586 GGCACTACGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACT
1 GGCACTACGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACT
42651 TCGTGTGCTAAAATGATAAGGAAATCATACTAA
66 TCGTGTGCTAAAATG-TAAGGAAATCATACTAA
42684 TGAAATGAAT
Statistics
Matches: 192, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
117 108 0.56
118 84 0.44
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (117 bp):
GGCACTACGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACT
TCGTGTGCTAAAATGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:42694 original size:176 final size:177
Alignment explanation
Indices: 42359--42695 Score: 525
Period size: 176 Copynumber: 1.9 Consensus size: 177
42349 ATGGCACTAA
* * * *
42359 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTATAGATAGGGCACTTCGTGTGC
1 GTGTGCTAAAATGGTAAGAAAATCACACTAAGTGTATGAATTTACAGATAGGGCACTACGTGTGC
* *
42424 TACAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTCATGTGCTAAAAT
66 TAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGAACTTCATGTGCTAAAAT
* * *
42489 GGTAAGGAAATTATACCAAGTGTATGAATTTCCAGATAGTGTACTTC
131 GATAAGGAAATCATACCAAGTGAATGAATTTCCAGATAGTGTACTTC
* *
42536 GTGTGCTAAAAT-GTAAGAAAATCACACTAAGTGTATGAATTTCCATATAGGGCACTACGTGTGC
1 GTGTGCTAAAATGGTAAGAAAATCACACTAAGTGTATGAATTTACAGATAGGGCACTACGTGTGC
* *
42600 TAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACTTCGTGTGCTAAAAT
66 TAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGAACTTCATGTGCTAAAAT
*
42665 GATAAGGAAATCATACTAA-TGAAATGAATTT
131 GATAAGGAAATCATACCAAGTG-AATGAATTT
42696 TCTATTGAAT
Statistics
Matches: 145, Mismatches: 14, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
175 2 0.01
176 131 0.90
177 12 0.08
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (177 bp):
GTGTGCTAAAATGGTAAGAAAATCACACTAAGTGTATGAATTTACAGATAGGGCACTACGTGTGC
TAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGAACTTCATGTGCTAAAAT
GATAAGGAAATCATACCAAGTGAATGAATTTCCAGATAGTGTACTTC
Found at i:42695 original size:59 final size:59
Alignment explanation
Indices: 42359--42683 Score: 508
Period size: 59 Copynumber: 5.5 Consensus size: 59
42349 ATGGCACTAA
**
42359 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTATAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
42418 GTGTGCTACAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * * *
42477 ATGTGCTAAAATGGTAAGGAAATTATACCAAGTGTATGAATTTCCAGATAGTGTACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* * * *
42536 GTGTGCTAAAAT-GTAAGAAAATCACACTAAGTGTATGAATTTCCATATAGGGCACTAC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
* *
42594 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAGGGAACTTC
1 GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
*
42653 GTGTGCTAAAATGATAAGGAAATCATACTAA
1 GTGTGCTAAAATGGTAAGGAAATCATACTAA
42684 TGAAATGAAT
Statistics
Matches: 240, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 50 0.21
59 190 0.79
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (59 bp):
GTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAGGGCACTTC
Found at i:44590 original size:54 final size:54
Alignment explanation
Indices: 44134--44582 Score: 607
Period size: 54 Copynumber: 8.3 Consensus size: 54
44124 TTTAATTTCA
* * * *
44134 TGGGTTGCATACTTAGTACCGATATGGTCGTTCATAAACTTATTATGAATTATG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
* * *
44188 TGGGCTGCACACTTAGTGTCGATACGGTTGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
* * *
44242 TGGGTTGCACACGTAGTGCCGACACGGTTGTTCATAAACTTATTATGAATTGTT-
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATT-TTG
* ** * **
44296 TGGGTTGCACACTTAGTGCCAATATAGTCATTCATAAACTTATTATGAATTTCA
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
*
44350 TAGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
*
44404 TGGGTTGCACACTTAGTGCCGATACGATCGTTCATAAACTTATTATGAATTATT-
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATT-TTG
* *
44458 TGGGTTGCACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAA-TTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
* * * * **
44511 TGGGTTGTACACTTAGTGCTGATATGGTTGTTCATAAACTTATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
* *
44565 TGGGCTGTACACTTAGTG
1 TGGGTTGCACACTTAGTG
44583 TTGATATGTA
Statistics
Matches: 352, Mismatches: 38, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
52 1 0.00
53 46 0.13
54 301 0.86
55 4 0.01
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACTTATTATGAATTTTG
Found at i:50592 original size:54 final size:54
Alignment explanation
Indices: 50460--50600 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 54
50450 TTTAATTTAA
* * * * * * *
50460 TGGGTTTCAAACTTAGTGCCAATACAGTCGTTCATAAACTTATTATGAATTCTG
1 TGGGTTACACACTTAGTGTCGATACGGTCGTTCATAAAATTATTATGAATTCCG
50514 TGGGTTACACACTTAGTGTCGATACGGTCGTTCATAAAATTATTATGAATTCCG
1 TGGGTTACACACTTAGTGTCGATACGGTCGTTCATAAAATTATTATGAATTCCG
* * *
50568 TGGGTTGCACACTTGGTGAT-GATACGGTTGTTC
1 TGGGTTACACACTTAGTG-TCGATACGGTCGTTC
50601 GCTCTTGTGG
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 75 0.99
55 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (54 bp):
TGGGTTACACACTTAGTGTCGATACGGTCGTTCATAAAATTATTATGAATTCCG
Found at i:52786 original size:15 final size:16
Alignment explanation
Indices: 52758--52787 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52748 CGAGGGGAGT
52758 CAGCCCATCACTCTAC
1 CAGCCCATCACTCTAC
52774 CAGCCCA-CACTCTA
1 CAGCCCATCACTCTA
52788 GGTGAAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.50, G:0.07, T:0.17
Consensus pattern (16 bp):
CAGCCCATCACTCTAC
Found at i:62917 original size:54 final size:54
Alignment explanation
Indices: 62827--63531 Score: 930
Period size: 54 Copynumber: 13.1 Consensus size: 54
62817 GGAGTTATCA
* * *
62827 ACGGTCGATCATAAACTTATTATGAATTTTGTGGGTTGCACAATTAGTGCCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * * *
62881 ACAGTCATTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTACCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * * * *
62935 ACGATCATTCATAAACTTATTATGAATTCCGTGGGTTACACACTTAGTGTCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * * * *
62989 ACAGTCGTTCATACACTTATTATGAATTATGTGGGTTGCACACTTATTGCTGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
*
63043 ACGGTCGTTCATAAACTTATTATGAATTCCGTGGGTTGCACACTTAGTGCCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * * *
63097 ACGGTCGTTCATAAACTTATTATGAATTATGTGGGTTGTACACTTAGTACTGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * *
63151 ACGGTCCTTCATAAACTTATTATGAATTCTGTGGGTTACACATTTAGTGCCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* ** *
63205 ACAGTTATTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGTC-ATT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGA-T
* * * **
63259 ACGGTCGTTCATAAACTTATTATAAATTAC-GTGGGTTACAGACTTAGTGTTGAT
1 ACGGTCGTTCATAAACTTATTATGAATT-CTGTGGGTTGCACACTTAGTGCCGAT
* * *
63313 ACGGTCGTTCATAAACTTATTAAGAATTCTGTGGGTTACACACTTAGTGTCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* *
63367 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGAACACTTAGTACCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
* * **
63421 ACGGTCATTCATAAACTTATTATGAATTATGTGGGTTGCACACTTAGTGTTGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
*** * *
63475 ATAATCGTTCATAAAATTATTATGAATT-TCGTGGGTTGCCCACTTAGTGCCGAT
1 ACGGTCGTTCATAAACTTATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGAT
63529 ACG
1 ACG
63532 TAAAAATGCA
Statistics
Matches: 567, Mismatches: 79, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
53 3 0.01
54 562 0.99
55 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (54 bp):
ACGGTCGTTCATAAACTTATTATGAATTCTGTGGGTTGCACACTTAGTGCCGAT
Found at i:62979 original size:27 final size:27
Alignment explanation
Indices: 62949--63088 Score: 72
Period size: 27 Copynumber: 5.2 Consensus size: 27
62939 TCATTCATAA
62949 ACTTATTATGAATTCCGTGGGTTACAC
1 ACTTATTATGAATTCCGTGGGTTACAC
* * * * * *
62976 ACTTAGTGTCG-ATACAGT-CGTTCATAC
1 ACTTATTAT-GAATTCCGTGGGTT-ACAC
** *
63003 ACTTATTATGAATTATGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTACAC
* * * * * *
63030 ACTTATTGCTG-ATACGGT-CGTTCATAA
1 ACTTATT-ATGAATTCCGTGGGTT-ACAC
*
63057 ACTTATTATGAATTCCGTGGGTTGCAC
1 ACTTATTATGAATTCCGTGGGTTACAC
63084 ACTTA
1 ACTTA
63089 GTGCCGATAC
Statistics
Matches: 76, Mismatches: 29, Indels: 16
0.63 0.24 0.13
Matches are distributed among these distances:
26 9 0.12
27 58 0.76
28 9 0.12
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (27 bp):
ACTTATTATGAATTCCGTGGGTTACAC
Found at i:63914 original size:18 final size:18
Alignment explanation
Indices: 63880--63913 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
63870 CTATACTATG
*
63880 GTATTGATACTCCTTTTA
1 GTATCGATACTCCTTTTA
63898 GTATCGATAC-CCTTTT
1 GTATCGATACTCCTTTT
63914 TTGCATTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.47
Consensus pattern (18 bp):
GTATCGATACTCCTTTTA
Found at i:65723 original size:18 final size:20
Alignment explanation
Indices: 65683--65728 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
65673 TTATCTCAAG
65683 TAAAACTATCATATGATATT
1 TAAAACTATCATATGATATT
65703 TAAAAC-AT-ATATGTATATT
1 TAAAACTATCATATG-ATATT
*
65722 AAAAACT
1 TAAAACT
65729 TCTTAGAGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (20 bp):
TAAAACTATCATATGATATT
Found at i:86579 original size:16 final size:16
Alignment explanation
Indices: 86558--86590 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
86548 GAGCACCATT
*
86558 AATTTTAAATTTATAA
1 AATTTTAAAATTATAA
86574 AATTTTAAAATTATAA
1 AATTTTAAAATTATAA
86590 A
1 A
86591 GTACTCAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTTTAAAATTATAA
Found at i:86652 original size:22 final size:23
Alignment explanation
Indices: 86610--86652 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
86600 GTGTAATTAT
**
86610 AAATTAGTTTAAAATCTAAATGC
1 AAATTAGTTTAAAATAAAAATGC
86633 AAATTA-TTTAAAATAAAAAT
1 AAATTAGTTTAAAATAAAAAT
86653 ATTACATTAT
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:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (23 bp):
AAATTAGTTTAAAATAAAAATGC
Found at i:87355 original size:15 final size:17
Alignment explanation
Indices: 87329--87360 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
87319 TAAAATAATG
87329 TTTAATATTTAT-TTAT
1 TTTAATATTTATATTAT
87345 TTTAA-ATTTATATTAT
1 TTTAATATTTATATTAT
87361 ATGATCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATATTTATATTAT
Found at i:87400 original size:23 final size:24
Alignment explanation
Indices: 87373--87422 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
87363 GATCATAAAT
* *
87373 AAATATTTTAA-ATTTATTTTTTA
1 AAATAGTTTAATATTGATTTTTTA
87396 AAATAGTTTAATATTGATTTTTTA
1 AAATAGTTTAATATTGATTTTTTA
87420 AAA
1 AAA
87423 ACATATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
AAATAGTTTAATATTGATTTTTTA
Found at i:88096 original size:43 final size:43
Alignment explanation
Indices: 88048--88132 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
88038 TGTAGAAAAA
* *
88048 TCATCCTTAAGTTTTTTGATACTTATTATTGGGAGTCTAATTT
1 TCATCCATAAGTTTTTTGATACTTATTATTGAGAGTCTAATTT
* **
88091 TCATCCATAAGTTTTTTTATTTTTATTATTGAGAGTCTAATT
1 TCATCCATAAGTTTTTTGATACTTATTATTGAGAGTCTAATT
88133 CTATGTTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.53
Consensus pattern (43 bp):
TCATCCATAAGTTTTTTGATACTTATTATTGAGAGTCTAATTT
Found at i:88157 original size:3 final size:3
Alignment explanation
Indices: 88145--88183 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
88135 ATGTTCACTA
88145 TAT TATT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT T
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T
88184 GTTGTTGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:88163 original size:13 final size:13
Alignment explanation
Indices: 88145--88183 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
88135 ATGTTCACTA
88145 TATTATTTATTAT
1 TATTATTTATTAT
88158 TATTATTTATTAT
1 TATTATTTATTAT
88171 TATTA-TTATTAT
1 TATTATTTATTAT
88183 T
1 T
88184 GTTGTTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:88188 original size:3 final size:3
Alignment explanation
Indices: 88182--88213 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
88172 ATTATTATTA
88182 TTG TTG TTG TTG TTG -TG TTG TTG -TG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
88214 GATAAACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:88202 original size:8 final size:8
Alignment explanation
Indices: 88182--88214 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
88172 ATTATTATTA
88182 TTGTTGTTG
1 TTGTTG-TG
88191 TTGTTGTG
1 TTGTTGTG
88199 TTGTTGTG
1 TTGTTGTG
88207 TTGTTGTG
1 TTGTTGTG
88215 ATAAACACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.75
9 6 0.25
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (8 bp):
TTGTTGTG
Found at i:89291 original size:22 final size:22
Alignment explanation
Indices: 89261--89302 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
89251 AAAAAAATCA
* * *
89261 GATATTAAAATGAATTAAAACG
1 GATAGTAAAATAAAATAAAACG
89283 GATAGTAAAATAAAATAAAA
1 GATAGTAAAATAAAATAAAA
89303 AATTAAACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.24
Consensus pattern (22 bp):
GATAGTAAAATAAAATAAAACG
Done.