Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001241.1 Hibiscus syriacus cultivar Beakdansim tig00002442_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: 165807
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3768 original size:23 final size:21
Alignment explanation
Indices: 3740--3782 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3730 TAACGTTACG
3740 AATTATTGAGTATAACATACTAA
1 AATTATT-A-TATAACATACTAA
*
3763 AATTATTATTTAACATACTA
1 AATTATTATATAACATACTA
3783 TATATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (21 bp):
AATTATTATATAACATACTAA
Found at i:9802 original size:31 final size:31
Alignment explanation
Indices: 9767--9828 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
9757 TATAACCCCC
*
9767 CAACATTTAGTCCATTTTCAATATGGTCCCT
1 CAACATTTAGTCCATTTGCAATATGGTCCCT
*
9798 CAACATTTAGTCCGTTTGCAATATGGTCCCT
1 CAACATTTAGTCCATTTGCAATATGGTCCCT
9829 GACATAACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.24, C:0.26, G:0.13, T:0.37
Consensus pattern (31 bp):
CAACATTTAGTCCATTTGCAATATGGTCCCT
Found at i:10228 original size:15 final size:16
Alignment explanation
Indices: 10201--10230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
10191 ATTCGAAACA
10201 ATTTAATAAATTTAAT
1 ATTTAATAAATTTAAT
10217 ATTTAA-AAATTTAA
1 ATTTAATAAATTTAA
10231 AAAGCTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAATAAATTTAAT
Found at i:11854 original size:31 final size:31
Alignment explanation
Indices: 11813--11873 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
11803 AAGTTACGTC
*
11813 AGGGACCATATTGCAAATGGACTAAATGTTG
1 AGGGACCATATTGCAAATAGACTAAATGTTG
*
11844 AGGGATCATATTGCAAATAGACTAAATGTT
1 AGGGACCATATTGCAAATAGACTAAATGTT
11874 AGAGAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (31 bp):
AGGGACCATATTGCAAATAGACTAAATGTTG
Found at i:11886 original size:31 final size:31
Alignment explanation
Indices: 11819--11886 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
11809 CGTCAGGGAC
* *
11819 CATATTGCAAATGGACTAAATGTTGAGGGAT
1 CATATTGCAAATAGACTAAATGTTGAGGAAT
11850 CATATTGCAAATAGACTAAATGTT-AGAGAAT
1 CATATTGCAAATAGACTAAATGTTGAG-GAAT
*
11881 TATATT
1 CATATT
11887 ACAAGTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (31 bp):
CATATTGCAAATAGACTAAATGTTGAGGAAT
Found at i:15445 original size:24 final size:23
Alignment explanation
Indices: 15418--15464 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
15408 ATGAAAGGAA
15418 AAAGAAAAA-AATAATAAGAAAAAT
1 AAAGAAAAAGAA-AATAA-AAAAAT
15442 AAAGAAAAAGAAAATAAAAAAAT
1 AAAGAAAAAGAAAATAAAAAAAT
15465 TACAATAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.27
24 14 0.64
25 2 0.09
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (23 bp):
AAAGAAAAAGAAAATAAAAAAAT
Found at i:16584 original size:2 final size:2
Alignment explanation
Indices: 16579--16615 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
16569 TATTTAAGTA
16579 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16616 GGACGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:17291 original size:84 final size:84
Alignment explanation
Indices: 17161--18397 Score: 1230
Period size: 84 Copynumber: 14.7 Consensus size: 84
17151 AACTCGATAA
* * * * * * *
17161 TTTTATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCT-GAGCTG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATATGCCT-TGGAGCTG
*
17225 AGTGTAATCGAACTCGAAGCTC
63 AGTGTAATCGAACTCGAAGGTC
* * * * * * ** * * *
17247 -TTTGATGACAGATGACCCTTCTCGACTTAAGTTATGCTATAATTTGATATGCCTTTGAGCTGAA
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAA-ATGATATGCCTTGGAGCTGAG
17311 TGTAATCGAACTCGAAGGT-
65 TGTAATCGAACTCGAAGGTC
* * * * * * *
17330 ATTTATTGACAGATAACCCTTCTAGCCTTTAGTTATGTTGTAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
* * * *
17395 GTAGTCAAACTTGAAGGTT
66 GTAATCGAACTCGAAGGTC
* * * * * **
17414 TTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAAC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
17479 G-AAGTCGAACTCGAAGGTC
66 GTAA-TCGAACTCGAAGGTC
* * * * * * * * *
17498 GTTTGTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCTTTGAGCTGAG
1 TTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
*
17563 TGTAATCGAAATCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * *
17583 -TTTGATTGGTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTGGGGCAGAG
1 TTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
** *
17647 CATAGTCGAACTCGAAGGTC
65 TGTAATCGAACTCGAAGGTC
* * * * * * **
17667 TTTTGCTGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGCAAATGTTGTGCCTTTGAGCTGAAA
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
* *
17732 GTAATCGATCTCGAAGATC
66 GTAATCGAACTCGAAGGTC
* * * * *
17751 TTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATATGCATTAGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
* *
17816 GTAGTCAAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * *
17835 TTTTGGTGGTAGATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAG-
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
**
17899 CAAACTCGAACTCGAAGGTC
66 GTAA-TCGAACTCGAAGGTC
* * * * * * * **
17919 TTTTGTTTGGCAGATAACCCTTCTCGACTTAAGATATGTTGCAAATGATGTGGCTTTAAGCTGAG
1 TTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
17984 TGTAATCGAACTCGAAGGT-
65 TGTAATCGAACTCGAAGGTC
* * * *** * *
18003 TTTTGATTGACTGATAACCTTTCTAGCCTTGAGTTATGGAACAAATGATATACCTTAGG-GCAGA
1 TTTTG-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT-GGAGCTGA
* * *
18067 GAGTAGTCAAACTCGAAGGTC
64 GTGTAATCGAACTCGAAGGTC
* * * * * * *
18088 TTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGTTATGCCTTTGAGCTGAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
18153 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
18172 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTAGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
*
18237 GTAGTCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * * * * * *
18256 TTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAAT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
18321 GTAATCGAACTCGAAGGTC
66 GTAATCGAACTCGAAGGTC
* * *
18340 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAACGATATGCCTTGGA
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGA
18398 CGGAGTCTCA
Statistics
Matches: 939, Mismatches: 198, Indels: 30
0.80 0.17 0.03
Matches are distributed among these distances:
83 37 0.04
84 731 0.78
85 167 0.18
86 4 0.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
GTAATCGAACTCGAAGGTC
Found at i:17816 original size:421 final size:418
Alignment explanation
Indices: 17165--18362 Score: 1668
Period size: 421 Copynumber: 2.8 Consensus size: 418
17155 CGATAATTTT
* * * * * * * *
17165 ATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATTTGCCTCTGAGCTGAGTGT
1 ATTGGTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAA--TGATATGCCT-TGGGCAGAG-AT
* * * * * * *
17230 AATCGAACTCGAAGCTC-TTTGATGACAGAT-GACCCTTCTCGACTTAAGTTATGCTATAATTTG
62 AGTCGAACTCGAAGGTCTTTTGATGGCAGATAG-CCCTTCTCGCCTTGAGTTATGCTGTAA-ATG
* * * *
17293 ATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGT-ATTTATTGACAGATAACCCTTCTAGCC
125 TTATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCC
* * * * *
17357 TTTAGTTATGTTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTTTTTTGGTG
190 TTGAGTTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTG
*
17422 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAACGAAGTCGA
255 GCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGAA-TCGA
* * * *
17487 ACTCGAAGGTCGTTTGTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTC
319 ACTCGAAGGTCTTTTGTTTGGCAGATAACCCTTCTCGACTTAAGATATGCTGCAAATGATGTGGC
*
17552 TTTGAGCTGAGTGTAATCGAAATCGAAGGTCTTTG
384 TTTAAGCTGAGTGTAATCGAAATCGAAGGTCTTTG
17587 ATTGGTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTGGGGCAGAGCATAG
1 ATTGGTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTT-GGGCAGAG-ATAG
* * *
17652 TCGAACTCGAAGGTCTTTTGCTGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGCAAATGTTGT
64 TCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATGTTAT
* * * *
17717 GCCTTTGAGCTGAAAGTAATCGATCTCGAAGATCTTTTGTTGGTAGATAACCCTTCTAGCCTTGA
129 GCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGA
* * * *
17782 GTTATGCTACAAATGATATGCATTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGTAG
194 GTTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCAG
* * * * *
17847 ATAACCCTTTTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCAAACTCGAACTC
259 ATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGAA-TCGAACTC
*
17912 GAAGGTCTTTTGTTTGGCAGATAACCCTTCTCGACTTAAGATATGTTGCAAATGATGTGGCTTTA
323 GAAGGTCTTTTGTTTGGCAGATAACCCTTCTCGACTTAAGATATGCTGCAAATGATGTGGCTTTA
* *
17977 AGCTGAGTGTAATCGAACTCGAAGGTTTTTG
388 AGCTGAGTGTAATCGAAATCGAAGGTCTTTG
* * **** *
18008 ATTGACT-GATAACCTTTCTAGCCTTGAGTTATGGAACAAATGATATACCTTAGGGCAGAGAGTA
1 ATTG-GTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTT-GGGCAGAGA-TA
* * *
18072 GTCAAACTCGAAGGTCTTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATGTTA
63 GTCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATGTTA
18137 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
128 TGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTG
*
18202 AGTTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCA
193 AGTTATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCA
* * *
18267 GATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGTTGTGCCTTTGAGCTGAATGTAATCGAACT
258 GATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACG-AATCGAACT
18332 CGAAGGTCTTTTG-TTGGCAGATAACCCTTCT
322 CGAAGGTCTTTTGTTTGGCAGATAACCCTTCT
18363 AGCCTTGAGT
Statistics
Matches: 688, Mismatches: 81, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
419 1 0.00
420 84 0.12
421 563 0.82
422 40 0.06
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (418 bp):
ATTGGTAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCTTGGGCAGAGATAGTC
GAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGTAAATGTTATGC
CTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGT
TATGTTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTGGCAGAT
AGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGAATCGAACTCGAA
GGTCTTTTGTTTGGCAGATAACCCTTCTCGACTTAAGATATGCTGCAAATGATGTGGCTTTAAGC
TGAGTGTAATCGAAATCGAAGGTCTTTG
Found at i:19227 original size:95 final size:95
Alignment explanation
Indices: 19033--19292 Score: 389
Period size: 95 Copynumber: 2.7 Consensus size: 95
19023 GGCTAGCTGA
* * * * *
19033 ATCCAT-AAGCCGGGGTGTTTAACCAATTGCTCTAGAGGGATAACTTAATATCATTATATAG-AT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
19096 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTGAATATT
19130 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
19195 TAATCGCCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTGAATATT
*
19225 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
19290 ATA
65 ATA
19293 TAATTATAAT
Statistics
Matches: 152, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
94 4 0.03
95 98 0.64
96 6 0.04
97 8 0.05
98 36 0.24
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:21876 original size:23 final size:23
Alignment explanation
Indices: 21850--21896 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
21840 AATTAATATT
*
21850 AAATAA-ATGAAAGGAAAAAGAAA
1 AAATAATAAGAAA-GAAAAAGAAA
21873 AAATAATAAGAAAGAAAAAGAAA
1 AAATAATAAGAAAGAAAAAGAAA
21896 A
1 A
21897 TAAAAAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.09
Consensus pattern (23 bp):
AAATAATAAGAAAGAAAAAGAAA
Found at i:21909 original size:29 final size:29
Alignment explanation
Indices: 21865--21930 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
21855 AATGAAAGGA
*
21865 AAAAG-AAAAAATAATAAG-AAAGAAAAAG
1 AAAAGAAAAAAACAAT-AGTAAAGAAAAAG
* *
21893 AAAATAAAAAAACAATAGTAAAGAAAATG
1 AAAAGAAAAAAACAATAGTAAAGAAAAAG
21922 AAAAGAAAA
1 AAAAGAAAA
21931 CATATTGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (29 bp):
AAAAGAAAAAAACAATAGTAAAGAAAAAG
Found at i:32652 original size:13 final size:14
Alignment explanation
Indices: 32613--32654 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
32603 CCGTAGAATG
*
32613 ATGAACAAAATTAA
1 ATGAATAAAATTAA
**
32627 ATTTATAAAATTAA
1 ATGAATAAAATTAA
32641 ATGAAT-AAATTAA
1 ATGAATAAAATTAA
32654 A
1 A
32655 AAATTAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (14 bp):
ATGAATAAAATTAA
Found at i:33574 original size:27 final size:29
Alignment explanation
Indices: 33512--33596 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 29
33502 TTTATATATC
* * *
33512 TTTAAAGTATATTTTATTTTTATCTTAACT
1 TTTAAA-TATATTTTATTATTATATTAACG
33542 TATTAAATATATTTTATTATTA-ATTAA-G
1 T-TTAAATATATTTTATTATTATATTAACG
*
33570 TTTAAAAATATTTTATTATTATTATTA
1 TTTAAATATATTTTATTATTA-TATTA
33597 TTTTAATTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
27 19 0.40
28 1 0.02
29 8 0.17
30 15 0.31
31 5 0.10
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTTAAATATATTTTATTATTATATTAACG
Found at i:33579 original size:29 final size:30
Alignment explanation
Indices: 33519--33682 Score: 129
Period size: 29 Copynumber: 5.4 Consensus size: 30
33509 ATCTTTAAAG
* * * *
33519 TATATTTTATTTTTATCTTAA-CTTATTAAA
1 TATATTTTATTATTATATTAAGTTTA-AAAA
33549 TATATTTTATTATTA-ATTAAGTTTAAAAA
1 TATATTTTATTATTATATTAAGTTTAAAAA
* *
33578 TATTTTATTATTATTATTATTTTAATTTTAAAATA
1 TA---TATT-TTATTATTATATTAAGTTTAAAA-A
* *
33613 TATATTTTATTCTTATATT-AGTTTAAATA
1 TATATTTTATTATTATATTAAGTTTAAAAA
* * * *
33642 TATATTTTATTCTTATTTTAA-CTTAGAAA
1 TATATTTTATTATTATATTAAGTTTAAAAA
*
33671 TATTTTTTATTA
1 TATATTTTATTA
33683 AATTTATTTT
Statistics
Matches: 110, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
29 43 0.39
30 25 0.23
31 11 0.10
32 8 0.07
33 9 0.08
34 11 0.10
35 3 0.03
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (30 bp):
TATATTTTATTATTATATTAAGTTTAAAAA
Found at i:52960 original size:2 final size:2
Alignment explanation
Indices: 52921--52947 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52911 TAAGTCATGC
52921 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52948 AAACATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53119 original size:2 final size:2
Alignment explanation
Indices: 53112--53147 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
53102 TTTTCTTCTG
*
53112 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53148 AATTTCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:53320 original size:266 final size:267
Alignment explanation
Indices: 52841--53379 Score: 981
Period size: 266 Copynumber: 2.0 Consensus size: 267
52831 AATACAAAAT
52841 TATATATATATATATATATATATAACATGTATAAATTTCTTAAGTAATTAATATAAGAAAGTGAA
1 TATATATATATATATATATATATAACATGTATAAATTTCTTAAGTAATTAATATAAGAAAGTGAA
52906 GTTAATAAGTCATGCATATATATATATATATATATATATATAAAACATGTATATAATTACACAAA
66 GTTAATAAGTCATGC------A-ATATATATATATATATATAAAACATGTATATAATTACACAAA
52971 ATCAAAGTTCATATATAAAATTACATATTTGATAAAAATTCATGTATAACTCTGATATTTGTTTC
124 ATCAAAGTTCATATATAAAATTACATATTTGATAAAAATTCATGTATAACTCTGATATTTGTTTC
53036 AATAAAATATTATACATAATTATATAGTTACCAAGTTATATACAGGACCCTCTACTTCTTAAATT
189 AATAAAATATTATACATAATTATATAGTTACCAAGTTATATACAGGACCCTCTACTTCTTAAATT
53101 GTTTTCTTCTGATA
254 GTTTTCTTCTGATA
*
53115 TATATATATATATATATATATATAATATGTATAAATTTCTTAAGTAATTAATATAAGAAAGTGAA
1 TATATATATATATATATATATATAACATGTATAAATTTCTTAAGTAATTAATATAAGAAAGTGAA
53180 GTTAATAAGTCATGC-ATATATATATATATATATAAAACATGTATATAATTACACAAAATCAAAG
66 GTTAATAAGTCATGCAATATATATATATATATATAAAACATGTATATAATTACACAAAATCAAAG
53244 TTCATATATAAAATTACATATTTGATAAAAATTCATGTATAACTCTGATATTTGTTTCAATAAAA
131 TTCATATATAAAATTACATATTTGATAAAAATTCATGTATAACTCTGATATTTGTTTCAATAAAA
*
53309 TATTATACATAATTATATAGTTACCAAGTTATATACATGACCCTCTACTTCTTAAATTGTTTTCT
196 TATTATACATAATTATATAGTTACCAAGTTATATACAGGACCCTCTACTTCTTAAATTGTTTTCT
*
53374 TTTGAT
261 TCTGAT
53380 CCAAGTAAGG
Statistics
Matches: 262, Mismatches: 3, Indels: 8
0.96 0.01 0.03
Matches are distributed among these distances:
266 183 0.70
274 79 0.30
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (267 bp):
TATATATATATATATATATATATAACATGTATAAATTTCTTAAGTAATTAATATAAGAAAGTGAA
GTTAATAAGTCATGCAATATATATATATATATATAAAACATGTATATAATTACACAAAATCAAAG
TTCATATATAAAATTACATATTTGATAAAAATTCATGTATAACTCTGATATTTGTTTCAATAAAA
TATTATACATAATTATATAGTTACCAAGTTATATACAGGACCCTCTACTTCTTAAATTGTTTTCT
TCTGATA
Found at i:53888 original size:33 final size:33
Alignment explanation
Indices: 53846--53913 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
53836 CTAAATTAAA
* * *
53846 CCTTAGCCTGCAGATATATTGATTAACCTTATG
1 CCTTAGCCTGCAGATATATTAAATAACATTATG
*
53879 CCTTAGCCTGCAGATATGTTAAATAACATTATG
1 CCTTAGCCTGCAGATATATTAAATAACATTATG
53912 CC
1 CC
53914 AAATATATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (33 bp):
CCTTAGCCTGCAGATATATTAAATAACATTATG
Found at i:73093 original size:13 final size:13
Alignment explanation
Indices: 73075--73117 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
73065 TGAACTTAGG
73075 AATTTATATTAAA
1 AATTTATATTAAA
**
73088 AA-TT-TATTAGG
1 AATTTATATTAAA
73099 AATTTATATTAAA
1 AATTTATATTAAA
73112 AATTTA
1 AATTTA
73118 AAGGTGTGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 7 0.29
12 4 0.17
13 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (13 bp):
AATTTATATTAAA
Found at i:73099 original size:24 final size:24
Alignment explanation
Indices: 73070--73117 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
73060 AGGGGTGAAC
73070 TTAGGAATTTATATTAAAAATTTA
1 TTAGGAATTTATATTAAAAATTTA
73094 TTAGGAATTTATATTAAAAATTTA
1 TTAGGAATTTATATTAAAAATTTA
73118 AAGGTGTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (24 bp):
TTAGGAATTTATATTAAAAATTTA
Found at i:73591 original size:36 final size:36
Alignment explanation
Indices: 73544--73614 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
73534 ATTGATTTTT
*
73544 TGAAAAATAAATTACTGTAATTTAAATTACTGAAAC
1 TGAAAAATAAATTACTGGAATTTAAATTACTGAAAC
* *
73580 TGAAAAATAAATTATTGGAATTTGAATTACTGAAA
1 TGAAAAATAAATTACTGGAATTTAAATTACTGAAA
73615 TTTGAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (36 bp):
TGAAAAATAAATTACTGGAATTTAAATTACTGAAAC
Found at i:73629 original size:15 final size:15
Alignment explanation
Indices: 73598--73639 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
73588 AAATTATTGG
73598 AATTTGAATTACT-GA
1 AATTTGAATTA-TAGA
73613 AATTTGAATTATAGA
1 AATTTGAATTATAGA
*
73628 AA-ATGAATTATA
1 AATTTGAATTATA
73640 TTTCTGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (15 bp):
AATTTGAATTATAGA
Found at i:73860 original size:49 final size:50
Alignment explanation
Indices: 73763--73861 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
73753 TACAAATATT
*
73763 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
73813 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
73862 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:73906 original size:32 final size:30
Alignment explanation
Indices: 73840--73908 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
73830 ATTTATTATT
*
73840 AAATATT-ATTTTTATAATTTTATTAATAA
1 AAATATTAATTTTTATAATTTTATAAATAA
*
73869 AAATATTAATTTTTGTATATTTTAGTGAAAT-A
1 AAATATTAATTTTTATA-ATTTTA-T-AAATAA
73901 AAATATTA
1 AAATATTA
73909 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 7 0.21
30 8 0.24
31 6 0.18
32 10 0.29
33 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATATTAATTTTTATAATTTTATAAATAA
Found at i:73992 original size:23 final size:23
Alignment explanation
Indices: 73943--74005 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
73933 GTGTTATATT
* **
73943 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
73966 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
73989 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
74006 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:74029 original size:28 final size:28
Alignment explanation
Indices: 73989--74088 Score: 109
Period size: 28 Copynumber: 3.5 Consensus size: 28
73979 CTTTATTAAA
73989 ATATTATTTAAATATATAAATAATATTAT
1 ATATTA-TTAAATATATAAATAATATTAT
**
74018 -TCATTATTAAATATATAAATTTTATTAT
1 AT-ATTATTAAATATATAAATAATATTAT
74046 ATATTATTAAATA-A-AATATAATATCT-T
1 ATATTATTAAATATATAA-ATAATAT-TAT
74073 ATATTATTATAATATA
1 ATATTATTA-AATATA
74089 ATTGATTATT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 2 0.03
27 16 0.26
28 37 0.61
29 6 0.10
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (28 bp):
ATATTATTAAATATATAAATAATATTAT
Found at i:74033 original size:19 final size:20
Alignment explanation
Indices: 73981--74033 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
73971 TTAAATATCT
73981 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
74000 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
74021 TTATTAAATATAT
1 TTATTAAATATAT
74034 AAATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:74042 original size:25 final size:26
Alignment explanation
Indices: 73990--74126 Score: 92
Period size: 28 Copynumber: 5.2 Consensus size: 26
73980 TTTATTAAAA
73990 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAATATATAAAT-ATATTAT
*
74018 TCATTATTAAATATATAAATTTTATTAT
1 T-ATTATTAAATATATAAA-TATATTAT
* *
74046 ATATTATTAAATAAAATATAATATCTTA-
1 -TATTATTAAAT-ATATA-AATATATTAT
*
74074 TATTATTATA-ATAT-AAT-TGATTAT
1 TATTATTAAATATATAAATAT-ATTAT
*
74098 T-TTA-TATAATAT-TAAAAATATTA-
1 TATTATTA-AATATATAAATATATTAT
74121 TATTAT
1 TATTAT
74127 ATTATTATAA
Statistics
Matches: 87, Mismatches: 9, Indels: 29
0.70 0.07 0.23
Matches are distributed among these distances:
22 3 0.03
23 12 0.14
24 12 0.14
25 4 0.05
27 9 0.10
28 30 0.34
29 15 0.17
30 2 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (26 bp):
TATTATTAAATATATAAATATATTAT
Found at i:74390 original size:42 final size:42
Alignment explanation
Indices: 74338--74452 Score: 167
Period size: 42 Copynumber: 2.7 Consensus size: 42
74328 ATGAATTACA
* * *
74338 TTCCGGAAAACCAATTACGTGAAACAAACACGGAAAAATATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAAACATT
*
74380 TTCCGAAAAACGAATTACGTAAAACAAACACGGAAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAAACATT
* * *
74422 TTTCGAAAAATGAATTACGTGAAATAAACAC
1 TTCCGAAAAACGAATTACGTGAAACAAACAC
74453 ATAATTTCAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGGAAAAACATT
Found at i:77048 original size:17 final size:18
Alignment explanation
Indices: 77012--77052 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
77002 ATATTATGTA
*
77012 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
77030 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
77047 TTTACT
1 TTTACT
77053 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:78688 original size:18 final size:18
Alignment explanation
Indices: 78665--78704 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
78655 ACAGTAGCCA
*
78665 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
78683 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
78701 CCGC
1 CCGC
78705 CGCCTTTCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:80268 original size:20 final size:20
Alignment explanation
Indices: 80243--80285 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
80233 TCTAAGAGCC
*
80243 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
80263 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
80283 CAT
1 CAT
80286 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:89515 original size:20 final size:20
Alignment explanation
Indices: 89490--89532 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
89480 TCTAAGAGCC
*
89490 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
89510 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
89530 CAT
1 CAT
89533 GTGGTGGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:98868 original size:11 final size:11
Alignment explanation
Indices: 98852--98886 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
98842 TGACTTTGTT
98852 TATCATTTTAC
1 TATCATTTTAC
*
98863 TATCATTTCAC
1 TATCATTTTAC
98874 TATCATTTTAC
1 TATCATTTTAC
98885 TA
1 TA
98887 AAAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (11 bp):
TATCATTTTAC
Found at i:99717 original size:21 final size:21
Alignment explanation
Indices: 99688--99727 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
99678 TTTTTATTAT
* *
99688 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
99709 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
99728 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:101448 original size:44 final size:44
Alignment explanation
Indices: 101387--101472 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
101377 TTTTAAGTTG
101387 AGCTTTAGGGGAAGAGTGGATTTGTGGGTCTGCAAATATTTAAA
1 AGCTTTAGGGGAAGAGTGGATTTGTGGGTCTGCAAATATTTAAA
**
101431 AGCTTTAGGGGGGGAGTGGATTTGTGGGTCTGCAAATATTTA
1 AGCTTTAGGGGAAGAGTGGATTTGTGGGTCTGCAAATATTTA
101473 CTGTTGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.07, G:0.35, T:0.33
Consensus pattern (44 bp):
AGCTTTAGGGGAAGAGTGGATTTGTGGGTCTGCAAATATTTAAA
Found at i:101983 original size:16 final size:16
Alignment explanation
Indices: 101964--102012 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
101954 TAAATAATTT
101964 AAATGTTGAATGATTC
1 AAATGTTGAATGATTC
*
101980 AAATGTTGAATAATTC
1 AAATGTTGAATGATTC
101996 AAATGTTGAATGATTC
1 AAATGTTGAATGATTC
102012 A
1 A
102013 GAGGCTCTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (16 bp):
AAATGTTGAATGATTC
Found at i:104834 original size:2 final size:2
Alignment explanation
Indices: 104827--104852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
104817 TCAAATAATT
104827 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
104853 AAAGAACTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:106996 original size:136 final size:135
Alignment explanation
Indices: 106623--107113 Score: 752
Period size: 136 Copynumber: 3.6 Consensus size: 135
106613 TTGTTAGATT
* * * * *
106623 GAACAAGTTCTTCGCATTATGAAATTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * * *
106687 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCAAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
106751 TAGGTC
130 TAGGTC
*
106757 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
*
106822 TCCATTGAAAATGTTGATCCCTCAAGTGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
106887 AGGTC
131 AGGTC
*
106892 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
106957 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
107022 TAGGTC
130 TAGGTC
*
107028 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACT
*
107093 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
107114 ACCTATTTTT
Statistics
Matches: 325, Mismatches: 28, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
134 31 0.10
135 124 0.38
136 169 0.52
137 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:120082 original size:2 final size:2
Alignment explanation
Indices: 120075--120142 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
120065 TCAAATAATT
120075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
120117 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
120143 AAGAACTTGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:122813 original size:125 final size:127
Alignment explanation
Indices: 122631--122877 Score: 306
Period size: 126 Copynumber: 2.0 Consensus size: 127
122621 TAAACTACAT
* * *
122631 CATTCATCACTGAACTTTACTCTCTCTATTTTTATCACTCACTGTACTTTCAATTTTTT-AATTT
1 CATTCATCACTGAACTTTACTCTCTCTATTATTATCACTAACTGCACTTTCAATTTTTTCAATTT
* *
122695 ACTCACTT-AACTTTT-AAAT-TACTTATGTTTTGGTCACTCTAAATTATTTTATTATTAGAGAA
66 ACTCA-TTGAACTTTTGAAATGTAC-T-TGTTTTGGCCAATCTAAATTATTTTATTATTAGAGAA
* * * * * *
122757 CATTCCTCATTGAACTTTACTCTTTTTCTTATT-TCACTAACTGCACTTTCAATTTTTTCAGTTT
1 CATTCATCACTGAACTTTACTCTCTCTATTATTATCACTAACTGCACTTTCAATTTTTTCAATTT
* * *
122821 ACTCATTGAACTTTTGAAATGTTCTTGTTTTGGCCAATTTGAATTATTTTATTATTA
66 ACTCATTGAACTTTTGAAATGTACTTGTTTTGGCCAATCTAAATTATTTTATTATTA
122878 TTTTGGTATG
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
125 25 0.24
126 71 0.69
127 5 0.05
128 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (127 bp):
CATTCATCACTGAACTTTACTCTCTCTATTATTATCACTAACTGCACTTTCAATTTTTTCAATTT
ACTCATTGAACTTTTGAAATGTACTTGTTTTGGCCAATCTAAATTATTTTATTATTAGAGAA
Found at i:124279 original size:23 final size:23
Alignment explanation
Indices: 124250--124310 Score: 122
Period size: 23 Copynumber: 2.7 Consensus size: 23
124240 TGTGAATTCA
124250 GCTGCATTATTGCAGCACTTATT
1 GCTGCATTATTGCAGCACTTATT
124273 GCTGCATTATTGCAGCACTTATT
1 GCTGCATTATTGCAGCACTTATT
124296 GCTGCATTATTGCAG
1 GCTGCATTATTGCAG
124311 TCCTTCAGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (23 bp):
GCTGCATTATTGCAGCACTTATT
Found at i:124284 original size:11 final size:11
Alignment explanation
Indices: 124250--124308 Score: 82
Period size: 11 Copynumber: 5.2 Consensus size: 11
124240 TGTGAATTCA
124250 GCTGCATTATT
1 GCTGCATTATT
*
124261 GCAGCACTTATT
1 GCTGCA-TTATT
124273 GCTGCATTATT
1 GCTGCATTATT
*
124284 GCAGCACTTATT
1 GCTGCA-TTATT
124296 GCTGCATTATT
1 GCTGCATTATT
124307 GC
1 GC
124309 AGTCCTTCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
11 22 0.52
12 20 0.48
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:124710 original size:35 final size:31
Alignment explanation
Indices: 124647--124739 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 31
124637 TGAATTTATA
124647 TTATATAAAAAAATTAGTTAATTAGTTTAAG
1 TTATATAAAAAAATTAGTTAATTAGTTTAAG
*
124678 TTATATAAAAGAATAATTATTTAAATTAGTTT-A-
1 TTATAT-AAA-AA-AATTAGTT-AATTAGTTTAAG
* **
124711 TTGT-TATAAATTATTAGTTAATTAGTTTA
1 TTATATA-AAAAAATTAGTTAATTAGTTTA
124740 TTATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 8 0.16
32 6 0.12
33 5 0.10
34 8 0.16
35 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATATAAAAAAATTAGTTAATTAGTTTAAG
Found at i:124722 original size:18 final size:18
Alignment explanation
Indices: 124699--124753 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
124689 AATAATTATT
124699 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
124717 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
124729 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
124746 TAAATTAG
1 TAAATTAG
124754 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:125054 original size:29 final size:29
Alignment explanation
Indices: 125017--125094 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 29
125007 TAGTAATAAA
125017 TTATAATTAAAAATCA-TTTATTAGTTTAA-G
1 TTAT-ATTAAAAAT-AGTTTATTAG-TTAACG
125047 TTATATTAAAAAATAGTTTATTAGTTAACG
1 TTATATT-AAAAATAGTTTATTAGTTAACG
125077 TTATATTAAAGAATAGTT
1 TTATATTAAA-AATAGTT
125095 AAAGTTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.45
Consensus pattern (29 bp):
TTATATTAAAAATAGTTTATTAGTTAACG
Found at i:125063 original size:22 final size:22
Alignment explanation
Indices: 125038--125118 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
125028 AATCATTTAT
125038 TAGTTTAAGTTATATTAAAAAA
1 TAGTTTAAGTTATATTAAAAAA
*
125060 TAGTTTATTAGTTAACGTTATATTAAAGAA
1 TAG-----T--TTAA-GTTATATTAAAAAA
* *
125090 TAGTTAAAGTTATATTAAATAA
1 TAGTTTAAGTTATATTAAAAAA
125112 TAGTTTA
1 TAGTTTA
125119 TTAGTTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
22 22 0.47
23 3 0.06
25 1 0.02
27 1 0.02
29 4 0.09
30 16 0.34
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.43
Consensus pattern (22 bp):
TAGTTTAAGTTATATTAAAAAA
Found at i:125423 original size:28 final size:28
Alignment explanation
Indices: 125392--125458 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
125382 TTTTATATAA
125392 TATAATATATAACTTAAACTAACAAACT
1 TATAATATATAACTTAAACTAACAAACT
*
125420 TAT-ATAATATAACTTAAACTAGCAAACT
1 TATAAT-ATATAACTTAAACTAACAAACT
* *
125448 AATAATTTATA
1 TATAATATATA
125459 CTAACAAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.06
28 30 0.88
29 2 0.06
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (28 bp):
TATAATATATAACTTAAACTAACAAACT
Found at i:125461 original size:21 final size:21
Alignment explanation
Indices: 125428--125476 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
125418 CTTATATAAT
*
125428 ATAACTTAAACTAGCAAACTA
1 ATAACTTAAACTAACAAACTA
* *
125449 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
125470 ATTAACT
1 A-TAACT
125477 AGATTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.16, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:125863 original size:21 final size:21
Alignment explanation
Indices: 125838--125903 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
125828 GCAATAATGT
125838 AGCTATGGATGCAACGCATGC
1 AGCTATGGATGCAACGCATGC
* * * *
125859 AGCTACGGATGC-AGGAATCTCCC
1 AGCTATGGATGCAACGCA--T-GC
125882 AGCTATGGATGCAACGCATGC
1 AGCTATGGATGCAACGCATGC
125903 A
1 A
125904 TTCCAAAGCT
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
20 3 0.09
21 13 0.39
22 2 0.06
23 12 0.36
24 3 0.09
ACGTcount: A:0.29, C:0.26, G:0.27, T:0.18
Consensus pattern (21 bp):
AGCTATGGATGCAACGCATGC
Found at i:135969 original size:15 final size:15
Alignment explanation
Indices: 135949--135982 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
135939 TTTAGCTGGA
*
135949 CGGGCGGATGTGGGG
1 CGGGCGGATGCGGGG
135964 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGG
135979 CGGG
1 CGGG
135983 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.18, G:0.68, T:0.09
Consensus pattern (15 bp):
CGGGCGGATGCGGGG
Found at i:143815 original size:20 final size:19
Alignment explanation
Indices: 143792--143837 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
143782 CGATATACCA
143792 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
143812 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
143832 GGTAAA
1 GGTAAA
143838 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:144002 original size:19 final size:20
Alignment explanation
Indices: 143959--144004 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
143949 CGATATAACA
143959 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
143979 GGTAACAAA-ATGATAAAA-C
1 GGTAA-AAATATGATAAAACC
143998 GGTAAAA
1 GGTAAAA
144005 TGATACCGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 14 0.56
21 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:146287 original size:21 final size:21
Alignment explanation
Indices: 146240--146304 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
146230 AAGACAATCA
* *
146240 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
146262 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
146282 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
146303 AG
1 AG
146305 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:146380 original size:33 final size:33
Alignment explanation
Indices: 146338--146403 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
146328 AAATAGATGG
*
146338 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
146371 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
146404 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:148219 original size:19 final size:19
Alignment explanation
Indices: 148195--148243 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
148185 AATGTCGAGT
148195 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
148214 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
148233 TATTTTTGTAT
1 TAATTTTGTAT
148244 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:148713 original size:199 final size:199
Alignment explanation
Indices: 148371--149532 Score: 2247
Period size: 199 Copynumber: 5.8 Consensus size: 199
148361 CAACAGGGTG
*
148371 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATA
1 CCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
148436 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
65 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
148501 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
130 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
148566 GTGCA
195 GTGCA
148571 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
148636 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
*
148701 ATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
148766 TGCA
196 TGCA
148770 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
148835 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
148900 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
148964 TGCA
196 TGCA
148968 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATCATCGAACCCAAAAGTATA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAATCATCGAACCCAAAAGTATA
149033 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
65 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
*
149098 AATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAG
130 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
*
149162 ATGCA
195 GTGCA
*
149167 CTCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
149232 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
149297 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
149362 TGCA
196 TGCA
149366 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
149431 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
149496 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
149533 AATTTAAATA
Statistics
Matches: 951, Mismatches: 9, Indels: 5
0.99 0.01 0.01
Matches are distributed among these distances:
198 197 0.21
199 730 0.77
200 24 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (199 bp):
CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
TGCA
Found at i:149292 original size:397 final size:398
Alignment explanation
Indices: 148371--149532 Score: 2247
Period size: 397 Copynumber: 2.9 Consensus size: 398
148361 CAACAGGGTG
*
148371 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATA
1 CCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
148436 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
65 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
148501 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
130 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
148566 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
195 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
148631 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
260 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
*
148696 TCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
325 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
*
148761 CAAGGTGCA
390 CAAGATGCA
148770 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
148835 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
148900 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAAGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
148964 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAATCATCGAACCCAAAAG
196 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAATCATCGAACCCAAAAG
149029 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
260 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
*
149094 TCTAAATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAA
325 TCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
149158 CAAGATGCA
390 CAAGATGCA
*
149167 CTCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
1 CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
149232 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
66 TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
149297 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
131 ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
149362 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
196 TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
149427 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
261 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
149492 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
326 CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
149533 AATTTAAATA
Statistics
Matches: 755, Mismatches: 6, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
397 374 0.50
398 357 0.47
399 24 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (398 bp):
CCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAA
TGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAA
ATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAGG
TGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
CTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAAC
AAGATGCA
Found at i:149504 original size:596 final size:597
Alignment explanation
Indices: 148371--149532 Score: 2256
Period size: 596 Copynumber: 1.9 Consensus size: 597
148361 CAACAGGGTG
148371 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATA
1 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATA
148436 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
66 ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
*
148501 AATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
131 AATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
*
148566 GTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
196 ATGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
148631 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
261 TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
148696 TCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
326 TCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
148761 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
391 CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
148826 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
456 AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
148891 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
521 TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
148956 AAACAAGGTGCA
586 AAACAAGGTGCA
*
148968 CCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAAATCATCGAACCCAAAAGTAT
1 CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCC-AAAATCATCGAACCCAAAAGTAT
149032 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
65 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCT
149097 AAATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG-AAACAA
130 AAATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAA
*
149161 GATGCACTCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
195 GATGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA
149226 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
260 GTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAT
*
149291 GTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
325 GTCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAA
149356 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
390 ACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC
149421 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
455 AAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGA
149486 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
520 ATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
149533 AATTTAAATA
Statistics
Matches: 559, Mismatches: 5, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
596 390 0.70
597 169 0.30
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (597 bp):
CCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAACCCAAAAGTATA
ATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTA
AATAATGTATCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAACAAG
ATGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAG
TATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATG
TCTAAATAATATGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGGAAAA
CAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCA
AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAA
TATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAATGG
AAACAAGGTGCA
Found at i:151013 original size:3 final size:3
Alignment explanation
Indices: 151005--151078 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
150995 TGAAGCTGAC
* * * ** * *
151005 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
151053 GAT G-T GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
151079 CCAAACAAGT
Statistics
Matches: 55, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.34, C:0.05, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:152841 original size:182 final size:183
Alignment explanation
Indices: 152268--152956 Score: 1178
Period size: 182 Copynumber: 3.8 Consensus size: 183
152258 CAAAGTTTTC
* ** * *
152268 ACACTTTTTAATATTGTGTTTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
152333 -AAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
152395 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
152451 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
152516 AAAAAAGTGTCGACATTT--ACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
152579 AA-CGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
152631 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
152696 AAAAAAGTGTCGACATTTACACATCGGAACCCATA-TTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
* * *
152760 AATCGGTATAAAAATACCGGTTTTATGAGTGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
152813 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
152878 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGT-ATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
152942 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
152957 GTGTCGATAC
Statistics
Matches: 486, Mismatches: 13, Indels: 15
0.95 0.03 0.03
Matches are distributed among these distances:
180 132 0.27
181 78 0.16
182 193 0.40
183 69 0.14
184 11 0.02
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:152988 original size:22 final size:23
Alignment explanation
Indices: 152952--152994 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
152942 AACCGGTATA
152952 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
* *
152975 AAAA-GTGTCTATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
152995 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:154073 original size:23 final size:23
Alignment explanation
Indices: 154042--154105 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
154032 ATAGGTAAAC
*
154042 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
154065 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
154088 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
154106 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:154112 original size:23 final size:23
Alignment explanation
Indices: 154042--154114 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
154032 ATAGGTAAAC
* **
154042 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
154065 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
154088 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
154111 ATAT
1 ATAT
154115 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:154820 original size:18 final size:18
Alignment explanation
Indices: 154789--154825 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
154779 TTTTTTACTC
* *
154789 AAATATTATCAAAATAAA
1 AAATAATATAAAAATAAA
154807 AAATAATATAAAAATAAA
1 AAATAATATAAAAATAAA
154825 A
1 A
154826 TTTATTTTAA
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:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATAATATAAAAATAAA
Found at i:156388 original size:12 final size:12
Alignment explanation
Indices: 156373--156406 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
156363 GTTATTTAAA
156373 CGGGTATTGGGC
1 CGGGTATTGGGC
*
156385 CGGGTATTGGGT
1 CGGGTATTGGGC
156397 CGGGTATTGG
1 CGGGTATTGG
156407 CCTAGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.50, T:0.29
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:156617 original size:6 final size:6
Alignment explanation
Indices: 156606--156630 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
156596 AAATGGGTTT
156606 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
156631 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Done.