Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007748.1 Hibiscus syriacus cultivar Beakdansim tig00110013_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: 4568288
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 24
Found at i:197359 original size:14 final size:14
Alignment explanation
Indices: 197340--197373 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
197330 CATCAATTAA
197340 ACAAATCAACTTTT
1 ACAAATCAACTTTT
197354 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
197368 ATAAAT
1 ACAAAT
197374 AAATTAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:197412 original size:78 final size:78
Alignment explanation
Indices: 197276--197440 Score: 251
Period size: 78 Copynumber: 2.1 Consensus size: 78
197266 ATTTAAAACA
*
197276 ACAAATCAACTTTTACAAATCAATTAAACAAGTAAAAAATAAGAATTATTTACACATCAATTAAA
1 ACAAATCAACTTTTACAAATAAATTAAACAAGTAAAAAATAAGAATTATTTACACATCAATTAAA
197341 CAAATCAACTTTT
66 CAAATCAACTTTT
* *** * *
197354 ACAAATCAACTTTTATAAATAAATTAAACAA-TCAAAAAATAATTCTTATTTCCTCATCAATTAA
1 ACAAATCAACTTTTACAAATAAATTAAACAAGT-AAAAAATAAGAATTATTTACACATCAATTAA
197418 ACAAATCAACTTTT
65 ACAAATCAACTTTT
197432 ACAAATCAA
1 ACAAATCAA
197441 TTAAACAAGC
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
77 1 0.01
78 78 0.99
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.31
Consensus pattern (78 bp):
ACAAATCAACTTTTACAAATAAATTAAACAAGTAAAAAATAAGAATTATTTACACATCAATTAAA
CAAATCAACTTTT
Found at i:200131 original size:59 final size:59
Alignment explanation
Indices: 200032--200153 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
200022 CAGCAGGCTG
* *
200032 CATATTCGGGAATACACTAAAGGATACCTAGTCTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTCTAGATGGTGGACACGACCTTATGTGT
* ** *
200091 CATATTCGGGACTGTACTTAAGGATACCTAGTAC-AGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGT-CTAGATGGTGGACACGACCTTATGTGT
200150 CATA
1 CATA
200154 CTCGAGATAG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 55 0.98
60 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTCTAGATGGTGGACACGACCTTATGTGT
Found at i:200809 original size:23 final size:23
Alignment explanation
Indices: 200783--200847 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
200773 AAATTATTAA
* **
200783 AGGGGTACCGATTCCCCTGCTAC
1 AGGGGAACCGATTCCCCCACTAC
*
200806 A-GGGAATCGATTCCCCCACTAC
1 AGGGGAACCGATTCCCCCACTAC
*
200828 A-GGGAATCGATTCCCCCACT
1 AGGGGAACCGATTCCCCCACT
200848 GTTCACTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
22 37 0.97
23 1 0.03
ACGTcount: A:0.23, C:0.35, G:0.22, T:0.20
Consensus pattern (23 bp):
AGGGGAACCGATTCCCCCACTAC
Found at i:200816 original size:22 final size:22
Alignment explanation
Indices: 200791--200847 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
200781 AAAGGGGTAC
**
200791 CGATTCCCCTGCTACAGGGAAT
1 CGATTCCCCCACTACAGGGAAT
200813 CGATTCCCCCACTACAGGGAAT
1 CGATTCCCCCACTACAGGGAAT
200835 CGATTCCCCCACT
1 CGATTCCCCCACT
200848 GTTCACTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.23, C:0.39, G:0.18, T:0.21
Consensus pattern (22 bp):
CGATTCCCCCACTACAGGGAAT
Found at i:202050 original size:42 final size:42
Alignment explanation
Indices: 201979--202072 Score: 129
Period size: 42 Copynumber: 2.2 Consensus size: 42
201969 GTGAATCGGG
*
201979 CTCTTGAACGGTGGGAGGGACCTCCTGAACGAT-GAGAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCCTGAACGATAG-GAGAGGC
* *
202021 CTCTTGAATGGTGGGAAGGG-CCTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGG-AGGGACCTCCTGAACGATAGGAGAGGC
202063 CTCTTGAACG
1 CTCTTGAACG
202073 ATGACAGGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 41 0.89
43 5 0.11
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCCTGAACGATAGGAGAGGC
Found at i:202073 original size:21 final size:21
Alignment explanation
Indices: 201979--202075 Score: 99
Period size: 21 Copynumber: 4.6 Consensus size: 21
201969 GTGAATCGGG
*
201979 CTCTTGAACGGTGGGAG-GGAC
1 CTCTTGAACGATGGGAGAGG-C
* * *
202000 CTCCTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGAGGC
* *
202021 CTCTTGAATGGTGGGA-AGGGC
1 CTCTTGAACGATGGGAGA-GGC
*
202042 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGATGGGAGAGGC
202063 CTCTTGAACGATG
1 CTCTTGAACGATG
202076 ACAGGTGCTT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
21 58 0.95
22 3 0.05
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGAGGC
Found at i:204161 original size:29 final size:29
Alignment explanation
Indices: 204119--204177 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
204109 CTTATATAAA
*
204119 CGTTGCGATTGTTGCGAAAGTCAAATTCG
1 CGTTGCAATTGTTGCGAAAGTCAAATTCG
204148 CGTTGCAATTGTTGCGAAAGTCAAATTCG
1 CGTTGCAATTGTTGCGAAAGTCAAATTCG
204177 C
1 C
204178 AACGCGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (29 bp):
CGTTGCAATTGTTGCGAAAGTCAAATTCG
Found at i:204186 original size:20 final size:20
Alignment explanation
Indices: 204161--204200 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
204151 TGCAATTGTT
*
204161 GCGAAAGTCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
204181 GCGAAAATCAAATTCGCAAC
1 GCGAAAATCAAATTCGCAAC
204201 ACAAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
GCGAAAATCAAATTCGCAAC
Found at i:204207 original size:20 final size:20
Alignment explanation
Indices: 204168--204209 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
204158 GTTGCGAAAG
* *
204168 TCAAATTCGCAACGCGAAAA
1 TCAAATTCGCAACACAAAAA
204188 TCAAATTCGCAACACAAAAA
1 TCAAATTCGCAACACAAAAA
204208 TC
1 TC
204210 GCAACGCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.26, G:0.10, T:0.17
Consensus pattern (20 bp):
TCAAATTCGCAACACAAAAA
Found at i:205728 original size:21 final size:21
Alignment explanation
Indices: 205704--205778 Score: 105
Period size: 21 Copynumber: 3.6 Consensus size: 21
205694 GTGAATCGGG
* *
205704 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
205725 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
* *
205746 CTCTTGAATGATGAGAGGGTC
1 CTCTTGAACGATGAGAGGGGC
*
205767 CTTTTGAACGAT
1 CTCTTGAACGAT
205779 AGGAAGGACA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:206232 original size:21 final size:21
Alignment explanation
Indices: 206208--206258 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
206198 CACCATTGTT
* *
206208 ATCACGTAAAGTACCGATCTC
1 ATCACGTAAAGCACCGACCTC
*
206229 ATCACGTAAAGCACTGACCTC
1 ATCACGTAAAGCACCGACCTC
206250 ATCACGTAA
1 ATCACGTAA
206259 CTCCCCTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (21 bp):
ATCACGTAAAGCACCGACCTC
Found at i:208267 original size:22 final size:22
Alignment explanation
Indices: 208241--208287 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
208231 GAGATAGACA
*
208241 GATTTCGTCAGAGATGGGGATG
1 GATTTCGTCAGAGATGGGGACG
*
208263 GATTTCGTCGGAGATGGGGACG
1 GATTTCGTCAGAGATGGGGACG
208285 GAT
1 GAT
208288 GTCGCCGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.26
Consensus pattern (22 bp):
GATTTCGTCAGAGATGGGGACG
Found at i:208447 original size:20 final size:20
Alignment explanation
Indices: 208422--208470 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
208412 TAAAAGCGCT
208422 TTGTGAATTTGACTTCTGTG
1 TTGTGAATTTGACTTCTGTG
208442 TTGTGAATTTGACTTCTGTG
1 TTGTGAATTTGACTTCTGTG
*
208462 TTGCGAATT
1 TTGTGAATT
208471 ACAGATTCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.10, G:0.24, T:0.49
Consensus pattern (20 bp):
TTGTGAATTTGACTTCTGTG
Found at i:208498 original size:20 final size:20
Alignment explanation
Indices: 208461--208500 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
208451 TGACTTCTGT
*
208461 GTTGCGAATTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
* *
208481 GTTGCGATTTTCAAATTCGC
1 GTTGCGAATTACAAATTCGC
208501 AACCAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:208913 original size:106 final size:106
Alignment explanation
Indices: 208728--208940 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
208718 CTCCTTCCCA
208728 TATATTTGTGTTGAATTAGCCATGATAGGTGCACTTATAGGAAATCTGCTCGTTAAACCCGTCGC
1 TATATTTGTGTTGAATTAGCCATGATAGGTGCACTTATAGGAAATCTGCTCGTTAAACCCGTCGC
208793 AGATTGAGATCCCATTAAAGTTATCTCTCTCAGCCAGATAG
66 AGATTGAGATCCCATTAAAGTTATCTCTCTCAGCCAGATAG
208834 TATATTTGTGTTGAATTAGCCATGATAGGTGCACTTATAGGAAATCTGCTCGTTAAACCCGTCGC
1 TATATTTGTGTTGAATTAGCCATGATAGGTGCACTTATAGGAAATCTGCTCGTTAAACCCGTCGC
208899 AGATTGAGATCCCATTAAAGTTATCTCTCTCAGCCAGATAG
66 AGATTGAGATCCCATTAAAGTTATCTCTCTCAGCCAGATAG
208940 T
1 T
208941 CGTCGGAGGA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (106 bp):
TATATTTGTGTTGAATTAGCCATGATAGGTGCACTTATAGGAAATCTGCTCGTTAAACCCGTCGC
AGATTGAGATCCCATTAAAGTTATCTCTCTCAGCCAGATAG
Found at i:211476 original size:37 final size:38
Alignment explanation
Indices: 211411--211482 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
211401 TAATTTTTTG
*
211411 AAAATGTTTTTGAAAAATATAATATATATAGTTTTCAA
1 AAAATATTTTTGAAAAATATAATATATATAGTTTTCAA
*
211449 AAAATATTTTTCGAAATATAT-AT-TATATAGTTTT
1 AAAATATTTTT-GAAAAATATAATATATATAGTTTT
211483 TTTAAAACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 11 0.35
38 12 0.39
39 8 0.26
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
AAAATATTTTTGAAAAATATAATATATATAGTTTTCAA
Found at i:211496 original size:37 final size:38
Alignment explanation
Indices: 211391--211502 Score: 111
Period size: 37 Copynumber: 2.9 Consensus size: 38
211381 TTTATTTTAG
* *
211391 TAATATAGTATAATTTTTTGAAAATGTTTTTGAAAAATA
1 TAATATA-TATAGTTTTTTAAAAATGTTTTTGAAAAATA
** * *
211430 TAATATATATAGTTTTCAAAAAATATTTTTCGAAATATA
1 TAATATATATAGTTTTTTAAAAATGTTTTT-GAAAAATA
* * *
211469 T-AT-TATATAGTTTTTTTAAAACGTTTTTAAAAAA
1 TAATATATATAGTTTTTTAAAAATGTTTTTGAAAAA
211503 CTTATATCTT
Statistics
Matches: 59, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
36 4 0.07
37 20 0.34
38 20 0.34
39 15 0.25
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
TAATATATATAGTTTTTTAAAAATGTTTTTGAAAAATA
Found at i:211576 original size:35 final size:37
Alignment explanation
Indices: 211521--211593 Score: 107
Period size: 35 Copynumber: 2.0 Consensus size: 37
211511 TTATATACAA
*
211521 TATATAAGTTTTTAAACATTTTGAAAAT-T-ATATAG
1 TATATAAGTTTTGAAACATTTTGAAAATATAATATAG
211556 TATAT-AGTTTTGAAATCATTTTGAAAATATAATATAG
1 TATATAAGTTTTGAAA-CATTTTGAAAATATAATATAG
211593 T
1 T
211594 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
34 9 0.26
35 17 0.50
36 1 0.03
37 7 0.21
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (37 bp):
TATATAAGTTTTGAAACATTTTGAAAATATAATATAG
Found at i:211654 original size:72 final size:70
Alignment explanation
Indices: 211521--211696 Score: 174
Period size: 72 Copynumber: 2.6 Consensus size: 70
211511 TTATATACAA
*
211521 TATATAA-GTTTTT--AAACA-TTTTGAAAA-TTATAT-AGTATATAGTTTTGAAATCATTTTGA
1 TATATAATGTTTTTAAAAACATTTTTGAAAATTTATATAAATATATAGTTTTGAAATCATTTTGA
211580 AAA--
66 AAACT
**
211583 TATA-ATATAGTTTTTAAAAAACATTTTTGGAAAATTTATATAATATATATAGTTTT-AAATTTT
1 TATATA-AT-GTTTTT-AAAAACATTTTT-GAAAATTTATATAA-ATATATAGTTTTGAAATCAT
211646 TTTGGAAAACT
61 TTT-GAAAACT
* *
211657 TATATAATGTTTTTAAAATCATTTTTGAAAACTATATATA
1 TATATAATGTTTTTAAAAACATTTTTGAAAA-TTTATATA
211697 GTTTTGAAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 22
0.77 0.04 0.18
Matches are distributed among these distances:
61 1 0.01
62 5 0.05
64 6 0.06
67 5 0.05
68 4 0.04
69 5 0.05
70 6 0.06
71 14 0.15
72 34 0.37
73 6 0.06
74 6 0.06
75 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (70 bp):
TATATAATGTTTTTAAAAACATTTTTGAAAATTTATATAAATATATAGTTTTGAAATCATTTTGA
AAACT
Found at i:211693 original size:32 final size:34
Alignment explanation
Indices: 211626--211707 Score: 95
Period size: 32 Copynumber: 2.6 Consensus size: 34
211616 ATTTATATAA
*
211626 TATATATAGTTTT--AAAT-TTTTTTGGAAAACT
1 TATATATAGTTTTGAAAATCATTTTTGGAAAACT
*
211657 TATATA-ATGTTTTTAAAATCATTTTT-GAAAAC-
1 TATATATA-GTTTTGAAAATCATTTTTGGAAAACT
211689 TATATATAGTTTTGAAAAT
1 TATATATAGTTTTGAAAAT
211708 GTTTTTAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
30 1 0.02
31 11 0.25
32 16 0.36
33 11 0.25
34 5 0.11
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (34 bp):
TATATATAGTTTTGAAAATCATTTTTGGAAAACT
Found at i:211790 original size:5 final size:5
Alignment explanation
Indices: 211780--211840 Score: 54
Period size: 5 Copynumber: 12.6 Consensus size: 5
211770 ATTATTAATA
* * * *
211780 TTTAT TTTAT TTTAT TTTAT TTCAT TTTA- -TTAA TTTAA TTTAA TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT
* *
211828 TTTGT TTTGT TTT
1 TTTAT TTTAT TTT
211841 GTGATCTAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 3 0.06
5 47 0.94
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:212068 original size:16 final size:15
Alignment explanation
Indices: 212047--212077 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
212037 ACCGGTCGAA
212047 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
212063 CATCCCGGGATGACC
1 CATCCCGGGATGACC
212078 GGTCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:214909 original size:18 final size:18
Alignment explanation
Indices: 214883--214917 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
214873 TCGAAAGGAC
*
214883 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
214901 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
214918 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:220135 original size:18 final size:18
Alignment explanation
Indices: 220109--220143 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
220099 TCGAAAGGAC
*
220109 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
220127 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
220144 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:222751 original size:21 final size:22
Alignment explanation
Indices: 222727--222768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
222717 TTTTATTATT
222727 GTTTTTCTATT-TTTCTTTTTG
1 GTTTTTCTATTATTTCTTTTTG
* *
222748 GTTTTTTTATTATTTGTTTTT
1 GTTTTTCTATTATTTCTTTTT
222769 TTACATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.07, C:0.05, G:0.10, T:0.79
Consensus pattern (22 bp):
GTTTTTCTATTATTTCTTTTTG
Found at i:222755 original size:35 final size:33
Alignment explanation
Indices: 222687--222768 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
222677 ATGTATATAC
* *
222687 TTATT-TTATTTTACTATTTTCATTTTGGCTTT
1 TTATTATTGTTTTTCTATTTTCATTTTGGCTTT
* *
222719 TTATTATTGTTTTTCTATTTTTCTTTTTGGTTTTT
1 TTATTATTGTTTTTCTA-TTTTCATTTTGG-CTTT
222754 TTATTATTTGTTTTT
1 TTATTA-TTGTTTTT
222769 TTACATTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 5 0.12
33 9 0.21
34 11 0.26
35 9 0.21
36 8 0.19
ACGTcount: A:0.12, C:0.06, G:0.07, T:0.74
Consensus pattern (33 bp):
TTATTATTGTTTTTCTATTTTCATTTTGGCTTT
Found at i:223001 original size:19 final size:18
Alignment explanation
Indices: 222950--222997 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
222940 TTTATTTTTG
222950 TTTATTTTATCA-TTCTA
1 TTTATTTTATCATTTCTA
*
222967 TTTATTTTGTTCATTTCTA
1 TTTATTTT-ATCATTTCTA
*
222986 TTTACTTTATCA
1 TTTATTTTATCA
222998 ATTTTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 6 0.23
19 12 0.46
ACGTcount: A:0.21, C:0.12, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTTATCATTTCTA
Found at i:228388 original size:143 final size:152
Alignment explanation
Indices: 228052--228659 Score: 916
Period size: 149 Copynumber: 4.1 Consensus size: 152
228042 AACTTAAGTC
228052 GAAGGGTTATCTGCCAAAAGACCTTCGAGTTCGATACACTCAACTCGA-GG--CATCATTTACAG
1 GAAGGGTTATCTGCC-AAAGACC-TCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACAG
*
228114 CATAACTTAAGTAGAAGGGTTATATGTACCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGT
64 CATAACTTAAGTAGAAGGGTTATCTG--CCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGT
*
228179 A-ATCGTTTGCAGTATAGCTTAAGGA
127 ATATCGTTTACAGTATAGCTTAAGGA
*
228204 GAAGGGTTAGC--CCAAAGACCTC-AG-TCGATACACTCAACTCGAGGGCACATCATTTACAGCA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACAGCA
* * *
228265 TAACTCAAGTAGAAGGGTT-TCTGCC-AAGACC-TCAAGTTC-A-ACACTCAGCTCCAGGTATAT
66 TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGTATAT
228325 CGTTTACAGTATAGCTTAAGGA
131 CGTTTACAGTATAGCTTAAGGA
* *
228347 -AAGGGTTATCTGCCAAAGACCTC-AGTTC-A-ACACTCAGCTCGAGGGCACATCATTTATAGCA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACAGCA
*
228408 TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTTGAGTTCGATACGCTCAGCTCCAGGTATAT
66 TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGTATAT
228473 CGTTTACAGTATAGCTTAAGGA
131 CGTTTACAGTATAGCTTAAGGA
228495 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTT--A-CA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACAGCA
* * *
228557 TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTTGAGTTCGATACGCTCAGCTCCAGGCACAT
66 TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGTATAT
*
228622 CATTTACAGTATAGC-TAAGGA
131 CGTTTACAGTATAGCTTAAGGA
228643 GAAGGGTTATCTGCCAA
1 GAAGGGTTATCTGCCAA
228660 CCAGAGACTC
Statistics
Matches: 423, Mismatches: 17, Indels: 36
0.89 0.04 0.08
Matches are distributed among these distances:
142 25 0.06
143 72 0.17
144 27 0.06
145 14 0.03
146 26 0.06
147 5 0.01
148 69 0.16
149 141 0.33
150 8 0.02
151 1 0.00
152 35 0.08
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (152 bp):
GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACAGCA
TAACTTAAGTAGAAGGGTTATCTGCCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGTATAT
CGTTTACAGTATAGCTTAAGGA
Found at i:228509 original size:76 final size:75
Alignment explanation
Indices: 228052--228659 Score: 669
Period size: 76 Copynumber: 8.2 Consensus size: 75
228042 AACTTAAGTC
* * *
228052 GAAGGGTTATCTGCCAAAAGACCTTCGAGTTCGATACACTCAACTCGAGG--CATCATTTACAGC
1 GAAGGGTTATCTGCC-AAAGACC-TCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAGT
* *
228115 ATAACTTAAGTA
64 ATAGCTTAAGGA
* * * * *
228127 GAAGGGTTATATGTACCAAAGACCTTCGAGTTCGATACGCTCAGCTCCAGGTA-ATCGTTTGCAG
1 GAAGGGTTATCTG--CCAAAGACC-TCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAG
228191 TATAGCTTAAGGA
63 TATAGCTTAAGGA
* * * *
228204 GAAGGGTTAGC--CCAAAGACCTC-AG-TCGATACACTCAACTCGAGGGCACATCATTTACAGCA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAGCTCCA-GGCACATCATTTACAGTA
* * *
228265 TAACTCAAGTA
65 TAGCTTAAGGA
* * * *
228276 GAAGGGTT-TCTGCC-AAGACCTCAAGTTC-A-ACACTCAGCTCCAGGTATATCGTTTACAGTAT
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAGTAT
228337 AGCTTAAGGA
66 AGCTTAAGGA
* * *
228347 -AAGGGTTATCTGCCAAAGACCTC-AGTTC-A-ACACTCAGCTCGAGGGCACATCATTTATAGCA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAGCTCCA-GGCACATCATTTACAGTA
* *
228408 TAACTTAAGTA
65 TAGCTTAAGGA
* * * * *
228419 GAAGGGTTATCTGCCAAAGACCTTTGAGTTCGATACGCTCAGCTCCAGGTATATCGTTTACAGTA
1 GAAGGGTTATCTGCCAAAGACC-TCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAGTA
228484 TAGCTTAAGGA
65 TAGCTTAAGGA
* *
228495 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAACTCGAGGGCACATCATTTACA-TA
1 GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAGCTCCA-GGCACATCATTTACAGTA
*
228559 -A-CTTAAGTA
65 TAGCTTAAGGA
* *
228568 GAAGGGTTATCTGCCAAAGACCTTTGAGTTCGATACGCTCAGCTCCAGGCACATCATTTACAGTA
1 GAAGGGTTATCTGCCAAAGACC-TCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAGTA
228633 TAGC-TAAGGA
65 TAGCTTAAGGA
228643 GAAGGGTTATCTGCCAA
1 GAAGGGTTATCTGCCAA
228660 CCAGAGACTC
Statistics
Matches: 448, Mismatches: 62, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
70 22 0.05
71 52 0.12
72 77 0.17
73 79 0.18
74 26 0.06
75 62 0.14
76 89 0.20
77 41 0.09
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (75 bp):
GAAGGGTTATCTGCCAAAGACCTCGAGTTCGATACACTCAGCTCCAGGCACATCATTTACAGTAT
AGCTTAAGGA
Found at i:229380 original size:14 final size:14
Alignment explanation
Indices: 229347--229380 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
229337 AAAAATATAT
229347 ATATATTTTTCAAA
1 ATATATTTTTCAAA
* *
229361 AAATATTTTTCGAA
1 ATATATTTTTCAAA
229375 ATATAT
1 ATATAT
229381 ATTATAGGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (14 bp):
ATATATTTTTCAAA
Found at i:229621 original size:35 final size:35
Alignment explanation
Indices: 229429--229621 Score: 149
Period size: 34 Copynumber: 5.5 Consensus size: 35
229419 CTTATATACA
*
229429 ATATATA-AGTTTTAAAA-CA-TTTTGAAAATTAT
1 ATATATATAGTTTTAAAATCATTTTTGAAAACTAT
*
229461 ATAGTATATAGTTTTGAAATCA-TTTTGAAAA-TAT
1 ATA-TATATAGTTTTAAAATCATTTTTGAAAACTAT
* *
229495 A-ATATATAGTTTTTTAAAAACATTTTTGGAAAATTTATAT
1 ATATATATAG--TTTTAAAATCATTTTT-GAAAA---CTAT
**
229535 AATATATATAGTTTT--AATTTTTTTTGGAAAACT-T
1 -ATATATATAGTTTTAAAATCATTTTT-GAAAACTAT
229569 ATATA-AT-GTTTTTAAAATCATTTTTGAAAACTAT
1 ATATATATAG-TTTTAAAATCATTTTTGAAAACTAT
229603 ATA-ATATAGTTTTGAAAAT
1 ATATATATAGTTTT-AAAAT
229622 GTTTTTAAAT
Statistics
Matches: 132, Mismatches: 9, Indels: 37
0.74 0.05 0.21
Matches are distributed among these distances:
31 1 0.01
32 16 0.12
33 18 0.14
34 41 0.31
35 22 0.17
36 5 0.04
38 13 0.10
40 7 0.05
41 1 0.01
42 8 0.06
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (35 bp):
ATATATATAGTTTTAAAATCATTTTTGAAAACTAT
Found at i:229627 original size:34 final size:34
Alignment explanation
Indices: 229555--229621 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 34
229545 GTTTTAATTT
*
229555 TTTTTGGAAAACTTATATAATGTTTTTAAAATCA
1 TTTTTGGAAAACTTATATAATGTTTTGAAAATCA
229589 TTTTT-GAAAAC-TATATAATATAGTTTTGAAAAT
1 TTTTTGGAAAACTTATAT-A-AT-GTTTTGAAAAT
229622 GTTTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 5 0.17
33 7 0.24
34 7 0.24
35 10 0.34
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (34 bp):
TTTTTGGAAAACTTATATAATGTTTTGAAAATCA
Found at i:229695 original size:5 final size:5
Alignment explanation
Indices: 229685--229743 Score: 82
Period size: 5 Copynumber: 11.6 Consensus size: 5
229675 ATTATTAATA
* * *
229685 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TATTAA TTTAA TTTAT TTTGT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT TTTAT TTTAT
229736 TTTAT TTT
1 TTTAT TTT
229744 GTGATCCAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
5 45 0.92
6 4 0.08
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:229971 original size:16 final size:15
Alignment explanation
Indices: 229950--229980 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
229940 GTCGGCCGAA
229950 CATCCCGGGACTGACC
1 CATCCCGGGA-TGACC
229966 CATCCCGGGATGACC
1 CATCCCGGGATGACC
229981 GGTCACACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.19, C:0.42, G:0.26, T:0.13
Consensus pattern (15 bp):
CATCCCGGGATGACC
Found at i:230956 original size:2 final size:2
Alignment explanation
Indices: 230951--230987 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
230941 ATACATTTCT
230951 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
230988 TTTTTTCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:231103 original size:26 final size:27
Alignment explanation
Indices: 231055--231105 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
231045 TTCATTTGTT
* * *
231055 TTTTTTTTTTTTGTTTTTGTTTATTAC
1 TTTTTTTATTTTGTATGTGTTTATTAC
231082 TTTTTTTATTTTGTATGT-TTTATT
1 TTTTTTTATTTTGTATGTGTTTATT
231106 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.10, C:0.02, G:0.08, T:0.80
Consensus pattern (27 bp):
TTTTTTTATTTTGTATGTGTTTATTAC
Found at i:231156 original size:18 final size:18
Alignment explanation
Indices: 231108--231167 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
231098 GTTTTATTTT
231108 TTTATTTTATCA-TTCTA
1 TTTATTTTATCATTTCTA
*
231125 TTTATTTTGTTCATTTCTA
1 TTTATTTT-ATCATTTCTA
*
231144 TTTACTTTATCATTT-T-
1 TTTATTTTATCATTTCTA
231160 TTTATTTT
1 TTTATTTT
231168 TATGTTGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 7 0.19
17 9 0.24
18 9 0.24
19 12 0.32
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTTTATCATTTCTA
Found at i:238335 original size:23 final size:23
Alignment explanation
Indices: 238288--238336 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
238278 AATAACATAT
* **
238288 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCACTTATATAATAAAA
*
238311 TAGGTAGCACTTGTATAATAAAA
1 TAGGTAGCACTTATATAATAAAA
238334 TAG
1 TAG
238337 ACATTTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATAAAA
Found at i:238825 original size:199 final size:200
Alignment explanation
Indices: 238482--238883 Score: 567
Period size: 199 Copynumber: 2.0 Consensus size: 200
238472 TGTTTTTGGG
* * * * *
238482 CACTTTATGTGTGCACCTCATTTGGCATTCATTCTAGACAAAATGTATCGACACAAATTTAAAAA
1 CACTTTATGCGTGCACCTCATTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATTCAAAAA
* *
238547 GTGTCGATACATTATATTGACCGCTTTTCTAATTAAACCAGTATATTTATACCGGTTATATTGTA
66 GTGTCGATACATTATATTGACCGCTTTTCGAATTAAACCAGTATATTTATACCGGTTACATTGTA
*
238612 AATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATGCTTTTAT-AAATGT
131 AATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTATAAAATGT
238676 ATCGA
196 ATCGA
* * * *
238681 CACTTTATGCGTGCACCTCGGTTGGGCTTTCATTCTGGACAAAAAGTATCAACACAAATTCCAAA
1 CACTTTATGCGTGCACCTC-ATTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATTCAAAA
* * * * *
238746 TGTGTCGATACATTATGTTGACATG-TTTTCGAATT-AACCGGTATATTTATACTGGTTACATTG
65 AGTGTCGATACATTATATTGAC-CGCTTTTCGAATTAAACCAGTATATTTATACCGGTTACATTG
* * * *
238809 TTAATTTACTTATTACATTATAATTATTGGTTTCGATGTTTTTGGGGTCGATACTTTTATAAAAT
129 TAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTATAAAAT
*
238874 GTATTGA
194 GTATCGA
238881 CAC
1 CAC
238884 ATATGTTTAC
Statistics
Matches: 178, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
199 98 0.55
200 79 0.44
201 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.40
Consensus pattern (200 bp):
CACTTTATGCGTGCACCTCATTGGGCATTCATTCTAGACAAAAAGTATCAACACAAATTCAAAAA
GTGTCGATACATTATATTGACCGCTTTTCGAATTAAACCAGTATATTTATACCGGTTACATTGTA
AATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTATAAAATGT
ATCGA
Found at i:241628 original size:19 final size:19
Alignment explanation
Indices: 241604--241651 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
241594 TTACATTGAC
241604 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
241623 ATACAAAATTATGAATCGT
1 ATACAAAATTATAAATCGT
241642 ATACAAAATT
1 ATACAAAATT
241652 TCCCCTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.52, C:0.10, G:0.06, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:241929 original size:20 final size:20
Alignment explanation
Indices: 241904--241948 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
241894 GGTCCAAATA
241904 GTAAGCTAGGAATTGGTAAG
1 GTAAGCTAGGAATTGGTAAG
241924 GTAAGCTAGGAATTGGTAAG
1 GTAAGCTAGGAATTGGTAAG
241944 GTAAG
1 GTAAG
241949 ATTTCTTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.36, T:0.24
Consensus pattern (20 bp):
GTAAGCTAGGAATTGGTAAG
Found at i:243234 original size:25 final size:20
Alignment explanation
Indices: 243175--243225 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
243165 TTTCTACCGG
*
243175 TTACATTGTAAAGTTACCTA
1 TTACATTATAAAGTTACCTA
243195 TTACATTATAAAGTTACCTA
1 TTACATTATAAAGTTACCTA
243215 TTACATTATAA
1 TTACATTATAA
243226 TTATCAGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (20 bp):
TTACATTATAAAGTTACCTA
Found at i:243655 original size:197 final size:198
Alignment explanation
Indices: 243195--243820 Score: 878
Period size: 199 Copynumber: 3.2 Consensus size: 198
243185 AAGTTACCTA
* * *
243195 TTACATTATAAAGTTACCTATTACATTATAATTATCAGTTTCGATATTTTTGGGATCGATACAAT
1 TTACATTTTAAAGTTACCTATTACATTATAATTATCAGTTTTGATGTTTTTGGGATCGATACAAT
* * * *
243260 TTTAAATGTATCGACACTTTATGCGTGCACCTCATTGGGCATTTATTATGGGCAGAAAGTATCGA
66 TTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAGAAAGTATCGA
* *
243325 CACATATTTAGAAAGTGTCGATACATTGTGTAGACCTATTTTCTCATAAAATTGGTATATTTATA
131 CACA-ATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGGTATATTTATA
*
243390 CCGG
195 TCGG
*
243394 TTACATTGTT-AATTTACCTATTACATTATAATTATCAGTTTTGATGTTTTTGGGATCGATACAA
1 TTACATT-TTAAAGTTACCTATTACATTATAATTATCAGTTTTGATGTTTTTGGGATCGATACAA
* * * *
243458 TTTTACATGTATCGACACTTTATACGTGCACCTCGTTTGGCATTCATTCTGGACAAAAAGTATCG
65 TTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAGAAAGTATCG
* * * * * * * *
243523 ACACAATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAAT-TAACCGGTATATTTATG
130 ACACAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGGTATATTTATA
243587 TCGG
195 TCGG
* * *
243591 TTACATTTTAAAGTTGCCTATTACATTATAATTATCGGTTTTGATGTTTTTGGGATCAATACAAT
1 TTACATTTTAAAGTTACCTATTACATTATAATTATCAGTTTTGATGTTTTTGGGATCGATACAAT
* * * *
243656 TTTAAATGTATCGACACTTTATGCGTACAGCTCGTTGGGTATTCATTCTGGACAGAAAGTATCAA
66 TTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAGAAAGTATCGA
* * * * *
243721 CATAAATTTAGAAAGTGTCGGTACATTATGTAAACCTATTTTCTCATAAAACTGGTATATATCTA
131 CA-CAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGGTATATTTATA
243786 TCGG
195 TCGG
* *
243790 TTACATTGTAAATTTACCTATTACATTATAA
1 TTACATTTTAAAGTTACCTATTACATTATAA
243821 ATTTACCTAT
Statistics
Matches: 372, Mismatches: 51, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
196 2 0.01
197 133 0.36
198 72 0.19
199 164 0.44
200 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (198 bp):
TTACATTTTAAAGTTACCTATTACATTATAATTATCAGTTTTGATGTTTTTGGGATCGATACAAT
TTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGGACAGAAAGTATCGA
CACAATTTAGAAAGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACTGGTATATTTATAT
CGG
Found at i:243766 original size:396 final size:396
Alignment explanation
Indices: 242697--243820 Score: 1460
Period size: 416 Copynumber: 2.8 Consensus size: 396
242687 GCATGATTTA
* * * * * *
242697 AAAAAATATCGATACAAATTTTAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTATATC
1 AAAAAGTATCGACAC-AATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAATTA-ACC
* * ** * * * * **
242762 GGTATGTTTCTACCGGTTACATTGTAAATTTACTTATTACATTATAATTATGGGTTTCGATGCCT
64 GGTATATTTATGTCGGTTACATTTTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
242827 TTGGGATCGATA-AATTTAATATATGTATCGACACTTTATGCGTGCACCTCGTTTGGCT-TTCAT
129 TTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCG-TTGGGTATTCAT
* * *
242890 TCTGGACAAAAAGTATCGACATAAATTTACAAAGTGTCGATACATTGTGTAGGCCTATTTTCTCA
191 TCTGGACAGAAAGTATCGACATAAATTTAGAAAGTGTCGATACATTGTGTAGACCTATTTTCTCA
* * *
242955 TAAAACCGATATATTTATACCGGTTACATTGTTAATTTACCTATTACATTGTAATTATCAGTTTC
256 TAAAACTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATCAGTTTC
*
243020 GATGTTTTAAGCATCAATACAATTTTAAATATATCGACACTTTATGCGTGCACCTCGTTTGGCAT
321 GATGTTTTAAGCATCAATACAATTTTAAATATATCGACACTTTATACGTGCACCTCGTTTGGCAT
243085 TCATTATGGAC
386 TCATTATGGAC
* * * *
243096 AAAAAGTTTCGTCACAATTTAAAAAGTATAGATACATTATATTGACTTATTTTCTAATTAACCGG
1 AAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAATTAACCGG
*
243161 TATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAAAGTTACCTATTACATTATAA
66 TATA-TT-TA--TG-T-C---G----GTTA-C-A-T---TT-TAAAGTTACCTATTACATTATAA
* *
243226 TTATCAGTTTCGATATTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACC
111 TTATCGGTTTCGATGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACC
* * * * * * *
243291 TCATTGGGCATTTATTATGGGCAGAAAGTATCGACACATATTTAGAAAGTGTCGATACATTGTGT
176 TCGTTGGGTATTCATTCTGGACAGAAAGTATCGACATAAATTTAGAAAGTGTCGATACATTGTGT
*
243356 AGACCTATTTTCTCATAAAATTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATT
241 AGACCTATTTTCTCATAAAACTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATT
* ** * * * *
243421 ATAATTATCAGTTTTGATGTTTTTGGGATCGATACAATTTTACATGTATCGACACTTTATACGTG
306 ATAATTATCAGTTTCGATGTTTTAAGCATCAATACAATTTTAAATATATCGACACTTTATACGTG
*
243486 CACCTCGTTTGGCATTCATTCTGGAC
371 CACCTCGTTTGGCATTCATTATGGAC
243512 AAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAATTAACCGG
1 AAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAATTAACCGG
* *
243577 TATATTTATGTCGGTTACATTTTAAAGTTGCCTATTACATTATAATTATCGGTTTTGATGTTTTT
66 TATATTTATGTCGGTTACATTTTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * *
243642 GGGATCAATACAATTTTAAATGTATCGACACTTTATGCGTACAGCTCGTTGGGTATTCATTCTGG
131 GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGTATTCATTCTGG
* * * *
243707 ACAGAAAGTATCAACATAAATTTAGAAAGTGTCGGTACATTATGTAAACCTATTTTCTCATAAAA
196 ACAGAAAGTATCGACATAAATTTAGAAAGTGTCGATACATTGTGTAGACCTATTTTCTCATAAAA
* * * *
243772 CTGGTATATATCTATCGGTTACATTGTAAATTTACCTATTACATTATAA
261 CTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAA
243821 ATTTACCTAT
Statistics
Matches: 627, Mismatches: 76, Indels: 47
0.84 0.10 0.06
Matches are distributed among these distances:
396 199 0.32
397 9 0.01
398 42 0.07
399 12 0.02
400 1 0.00
401 1 0.00
402 1 0.00
403 5 0.01
406 1 0.00
407 1 0.00
410 5 0.01
411 2 0.00
412 2 0.00
413 1 0.00
414 2 0.00
415 6 0.01
416 286 0.46
417 46 0.07
418 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (396 bp):
AAAAAGTATCGACACAATTTAAAAAGTATCGATACATTATATTGACCTATTTTCTAATTAACCGG
TATATTTATGTCGGTTACATTTTAAAGTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
GGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGTATTCATTCTGG
ACAGAAAGTATCGACATAAATTTAGAAAGTGTCGATACATTGTGTAGACCTATTTTCTCATAAAA
CTGGTATATTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATCAGTTTCGATGT
TTTAAGCATCAATACAATTTTAAATATATCGACACTTTATACGTGCACCTCGTTTGGCATTCATT
ATGGAC
Found at i:243815 original size:20 final size:20
Alignment explanation
Indices: 243790--243840 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
243780 TATCTATCGG
*
243790 TTACATTGTAAATTTACCTA
1 TTACATTATAAATTTACCTA
243810 TTACATTATAAATTTACCTA
1 TTACATTATAAATTTACCTA
243830 TTACATTATAA
1 TTACATTATAA
243841 TTATGTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (20 bp):
TTACATTATAAATTTACCTA
Found at i:248682 original size:199 final size:197
Alignment explanation
Indices: 248222--249296 Score: 1107
Period size: 199 Copynumber: 5.4 Consensus size: 197
248212 CGTAATTTCA
*
248222 AAAAAGTATCGACACAAATTTATAAA-GTGTCGATACTTTATGTAGACCTATTTTCTCATAAAAC
1 AAAAAGTATCGACAC--ATTTA-AAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
* * * *
248286 TGGCATATTTCTACCGAG-TACATCGTAAATTTACCTATTACATTGTAATTATAGGTTTCGATGT
63 CGGTATATTTATACCG-GTTACATTGTAAATTTACCTATTACATTGTAATTATA-GTTTCGATGT
* * * *
248350 TTTTAGGATCGATACT-TTTAATAAATGTATCAACACTTTATTCGTGCACCTCG-TTGGGCATTC
126 TTTTAGGATCGATA-TATTT-ATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTC
*
248413 ATTCTGGAT
189 ATTCTGGAC
* * * *
248422 AAAAAGTATCGACAC-TTTCGAAATTTGTGTCGATACTTTATGTAGACCTACTTCCTCATAAAAC
1 AAAAAGTATCGACACATTT--AAA-ATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
* * *
248486 TGGTATATTTATACTGGTTACATTGTAATTTTACCTATTACATTGTAATTATTAGTTTCGATGTT
63 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTA-TAGTTTCGATGTT
* *
248551 TTTAGGATCGATATAATTT-TAAATGTATCGACACTTTATGCGTGTACTTAGTTTTGGCA-TCAT
127 TTTAGGATCGATAT-ATTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTCAT
*
248614 TGTGGAC
191 TCTGGAC
* * * *
248621 AAAAA-TGATCGACACTTTCTAAATTTGTGTTGATACATTATGTAGACCTATTTTTTCATAAAAC
1 AAAAAGT-ATCGACACATT-TAAA-ATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAAC
** * * * * * *
248685 CAATAGATTTCTACCGGTTACATTGTTAATTTACCTATTACATTGTAATTATCGATTTTGATATT
63 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATAG-TTTCGATGTT
* * * *
248750 TTTGGGATCGATATAATTT-TAAATGTATCGACACTTTATGCGTGCGCCTTGTTTT-TCATTCAT
127 TTTAGGATCGATAT-ATTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTCAT
*
248813 TCTGGAT
191 TCTGGAC
* * * * * * *
248820 AAAAAGTTTCGACAAAAAATAAAAAAGTATCGATACATTATGTAGACTTATTTTCTCATAAAACC
1 AAAAAGTATCGAC--ACATTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * * *
248885 GATGTATTTATATCGGTTACATTGCAAAATTACCTATTACATTATAATTATGTGTTTCGATGTTT
64 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTAT-AGTTTCGATGTTT
* * * * *
248950 TT-GTGATCGATACTTTTTATAAATGTATCGACCCTTTATGCGTGCACCTCGTTTGGGCACTCAT
128 TTAG-GATCGATA-TATTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTCAT
*
249014 TATGGAC
191 TCTGGAC
* * * * * *
249021 AAAAAGTATCGACACAAATTTAAAAAGTGTCGATACATTATGTTGACTTGTTTTCTAATTAAACC
1 AAAAAGTATCGACAC--ATTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
* * * * * *
249086 GTTATATTTATACCGGTTACATCGTAAAATTACCTATTATATTATAATTA-AGGTTCGATGTTTT
64 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATAGTTTCGATGTTTT
* * *
249150 TAGGATCGATATGTTTTATAAATATATCGACACTTTATGCGTGCACCTAG-TTTGACATTCATTC
129 TAGGATCGATAT-ATTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTCATTC
249214 TGGAC
193 TGGAC
* * * * *
249219 AAAATGTATCGACACAAATTTAAAATGTCTCGATACATTATGTAGACCTATTTTGTCATTAAACA
1 AAAAAGTATCGACAC--ATTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACC
*
249284 TGTATATTT-TACC
64 GGTATATTTATACC
249297 TATTACTTTA
Statistics
Matches: 742, Mismatches: 107, Indels: 55
0.82 0.12 0.06
Matches are distributed among these distances:
197 7 0.01
198 87 0.12
199 366 0.49
200 166 0.22
201 116 0.16
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (197 bp):
AAAAAGTATCGACACATTTAAAATGTGTCGATACATTATGTAGACCTATTTTCTCATAAAACCGG
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTGTAATTATAGTTTCGATGTTTTTA
GGATCGATATATTTATAAATGTATCGACACTTTATGCGTGCACCTAGTTTTGGCATTCATTCTGG
AC
Found at i:249770 original size:117 final size:118
Alignment explanation
Indices: 249557--249784 Score: 363
Period size: 117 Copynumber: 1.9 Consensus size: 118
249547 AATAAACATG
*
249557 TACAACAACCTATTGCTATATTTTCTCATCTCATACATAATTACTCCGACTATGTATAAGAAACA
1 TACAACAACCTATTGCTATATTTTCTCATCTCATACATAATTACTCCGAATATGTATAAGAAACA
* *
249622 TGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAGA
66 TGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAGA
*
249675 TACAACAATCTATTGCTA-ACTTTTCTCATCTCATACATAATTACAT-C-AATATGTATAAGAAA
1 TACAACAACCTATTGCTATA-TTTTCTCATCTCATACATAATTAC-TCCGAATATGTATAAGAAA
* *
249737 CATGTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC
64 CATGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTAC
249785 TCCGACTATA
Statistics
Matches: 102, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
117 59 0.58
118 42 0.41
119 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (118 bp):
TACAACAACCTATTGCTATATTTTCTCATCTCATACATAATTACTCCGAATATGTATAAGAAACA
TGTACAACAACCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCAGA
Found at i:249781 original size:66 final size:67
Alignment explanation
Indices: 249675--249853 Score: 238
Period size: 67 Copynumber: 2.7 Consensus size: 67
249665 TACATTCAGA
* *
249675 TACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACAT-C-AATATGTATAAGAAAC
1 TACAA-AACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCGAATATATATAAGAAAC
249738 ATG
65 ATG
*
249741 TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC-TCCGACTATATATAAGAAAC
1 TACAA-AACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCGAATATATATAAGAAAC
249805 ATG
65 ATG
* * * * *
249808 TAGAACACTATATTGCTAATTTTTCTCATCTCACACATAATTACAT
1 TACAAAAC-CTATTGCTAACTTTTCTCATCTCATACATAATTACAT
249854 TTAGATACAA
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 45 0.45
67 53 0.53
68 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (67 bp):
TACAAAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCCGAATATATATAAGAAACA
TG
Found at i:249862 original size:184 final size:183
Alignment explanation
Indices: 249544--250166 Score: 865
Period size: 184 Copynumber: 3.3 Consensus size: 183
249534 CATACCTAAA
*
249544 TATAATAAACATGTACAACAACCTATTGCTATA-TTTTCTCATCTCATACATAATTACTCCGACT
1 TATAAGAAACATGTACAACAACCTATTGCTA-ACTTTTCTCATCTCATACATAATTACTCCGACT
*
249608 ATGTATAAGAAACATGTAGAACACCCTATTGCTAACTTTTCTCATCTCACACATAATTACATTCA
65 ATGTATAAGAAACATGTAGAACA-CCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTA
*
249673 GATACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAATATG
129 GATACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATG
*
249728 TATAAGAAACATGTACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
1 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
* * *
249793 TATATAAGAAACATGTAGAACACTATATTGCTAATTTTTCTCATCTCACACATAATTACATTTAG
66 TGTATAAGAAACATGTAGAACAC-CTATTGCTAACTTTTCTCATCTCACACATAATTACATTTAG
* *
249858 ATACAACAATCTATTGCTAGCTTTTCTCATCTCATTCATAATTACATCAACATG
130 ATACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATG
* * *
249912 TATAAGAAACATGTACAACAATCTATTGCTAACTTGTCTCATCTCATACATAATTACAT-CAAC-
1 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC-TCCGACT
* * *
249975 ATGTATAAGAAATATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAA
65 ATGTATAAGAAACATGTAGAAC-ACCTATTGCTAACTTTTCTCATCTCACACATAA-T---T--A
* *
250040 CATGTATAAGAAATATGTACAACAACCTATTGCTAACTTTTCTAATCTCATACATAATTACATCA
123 CAT-T-T-AG----A--TACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCA
250105 ACATG
179 ACATG
* * *
250110 TATAAGAAACATGTACAACAACCTGTTGCTAACTTTTCTCACCTCAAACATAATTAC
1 TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC
250167 ATTTAGATAC
Statistics
Matches: 392, Mismatches: 28, Indels: 24
0.88 0.06 0.05
Matches are distributed among these distances:
183 49 0.12
184 231 0.59
185 1 0.00
187 1 0.00
189 4 0.01
190 1 0.00
191 1 0.00
192 2 0.01
196 1 0.00
198 101 0.26
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.34
Consensus pattern (183 bp):
TATAAGAAACATGTACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTA
TGTATAAGAAACATGTAGAACACCTATTGCTAACTTTTCTCATCTCACACATAATTACATTTAGA
TACAACAATCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATG
Found at i:249963 original size:117 final size:118
Alignment explanation
Indices: 249741--249970 Score: 329
Period size: 117 Copynumber: 2.0 Consensus size: 118
249731 AAGAAACATG
* *
249741 TACAATAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCGACTATATATAAGAAACA
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCAACTATATATAAGAAACA
* * * *
249806 TGTAGAACACTATATTGCTAATTTTTCTCATCTCACACATAATTACATTTAGA
66 TGTACAACAATATATTGCTAACTTGTCTCATCTCACACATAATTACATTTAGA
* * * *
249859 TACAACAATCTATTGCTAGCTTTTCTCATCTCATTCATAATTACAT-CAAC-ATGTATAAGAAAC
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTAC-TCCAACTATATATAAGAAAC
* *
249922 ATGTACAACAATCTATTGCTAACTTGTCTCATCTCATACATAATTACAT
65 ATGTACAACAATATATTGCTAACTTGTCTCATCTCACACATAATTACAT
249971 CAACATGTAT
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
117 55 0.56
118 43 0.43
119 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (118 bp):
TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACTCCAACTATATATAAGAAACA
TGTACAACAATATATTGCTAACTTGTCTCATCTCACACATAATTACATTTAGA
Found at i:249965 original size:66 final size:66
Alignment explanation
Indices: 249859--250168 Score: 521
Period size: 66 Copynumber: 4.7 Consensus size: 66
249849 TACATTTAGA
* * *
249859 TACAACAATCTATTGCTAGCTTTTCTCATCTCATTCATAATTACATCAACATGTATAAGAAACAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
249924 G
66 G
* * *
249925 TACAACAATCTATTGCTAACTTGTCTCATCTCATACATAATTACATCAACATGTATAAGAAATAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
249990 G
66 G
*
249991 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAATAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
250056 G
66 G
*
250057 TACAACAACCTATTGCTAACTTTTCTAATCTCATACATAATTACATCAACATGTATAAGAAACAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
250122 G
66 G
* * *
250123 TACAACAACCTGTTGCTAACTTTTCTCACCTCAAACATAATTACAT
1 TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACAT
250169 TTAGATACAA
Statistics
Matches: 232, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 232 1.00
ACGTcount: A:0.38, C:0.22, G:0.06, T:0.33
Consensus pattern (66 bp):
TACAACAACCTATTGCTAACTTTTCTCATCTCATACATAATTACATCAACATGTATAAGAAACAT
G
Found at i:251912 original size:20 final size:21
Alignment explanation
Indices: 251883--251956 Score: 98
Period size: 20 Copynumber: 3.6 Consensus size: 21
251873 GCAGCCTTCG
*
251883 TGCATGGATGCACA-ACAGGA
1 TGCATCGATGCACAGACAGGA
* **
251903 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGACAGGA
251924 TGCATCGATGCACAGA-AGGA
1 TGCATCGATGCACAGACAGGA
251944 TGCATCGATGCAC
1 TGCATCGATGCAC
251957 TAATTGCATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
20 28 0.61
21 18 0.39
ACGTcount: A:0.30, C:0.24, G:0.27, T:0.19
Consensus pattern (21 bp):
TGCATCGATGCACAGACAGGA
Found at i:251919 original size:41 final size:41
Alignment explanation
Indices: 251874--251956 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
251864 CTAGCCGTTG
*
251874 CAGCCTTCG-TGCATGGATGCACA-ACAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAGA-AGGATGCATCGATGCA
251915 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
251956 C
1 C
251957 TAATTGCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 1 0.03
41 37 0.95
42 1 0.03
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (41 bp):
CAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:252026 original size:42 final size:41
Alignment explanation
Indices: 251980--252070 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
251970 TGTTTGAGGA
*
251980 ATGCACTGC-ATGATGCATCGATGCACTAGTGCA-GGTGCATGG
1 ATGCACTGCAAGGATGCATCGATGCAC---TGCAGGGTGCATGG
*
252022 ATGCACTGCAAGGATGCATGGATGCACTGCAGGGGTGCATGG
1 ATGCACTGCAAGGATGCATCGATGCACTGCA-GGGTGCATGG
252064 ATGCACT
1 ATGCACT
252071 TTAACACCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
40 4 0.09
42 25 0.57
43 15 0.34
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (41 bp):
ATGCACTGCAAGGATGCATCGATGCACTGCAGGGTGCATGG
Found at i:252041 original size:21 final size:20
Alignment explanation
Indices: 251980--252070 Score: 103
Period size: 21 Copynumber: 4.3 Consensus size: 20
251970 TGTTTGAGGA
* *
251980 ATGCACTGCATGATGCATCG
1 ATGCACTGCAGGATGCATGG
252000 ATGCACTAGTGCAGG-TGCATGG
1 ATGCAC---TGCAGGATGCATGG
252022 ATGCACTGCAAGGATGCATGG
1 ATGCACTGC-AGGATGCATGG
*
252043 ATGCACTGCAGGGGTGCATGG
1 ATGCACTGCA-GGATGCATGG
252064 ATGCACT
1 ATGCACT
252071 TTAACACCCT
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
19 3 0.05
20 10 0.16
21 32 0.52
22 12 0.19
23 5 0.08
ACGTcount: A:0.24, C:0.21, G:0.33, T:0.22
Consensus pattern (20 bp):
ATGCACTGCAGGATGCATGG
Found at i:252197 original size:30 final size:30
Alignment explanation
Indices: 252150--252209 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
252140 AAACTTTGAA
*
252150 TAAATTTAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
252179 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
252210 CCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:254416 original size:34 final size:32
Alignment explanation
Indices: 254356--254425 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
254346 CCTTACAAAC
* *
254356 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
* *
254388 TCCCTAGATTTTACACGGGATTAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
254422 TCCC
1 TCCC
254426 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:254806 original size:21 final size:21
Alignment explanation
Indices: 254782--254844 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
254772 ACTAGCCGTT
* *
254782 ACAGCCTTTATGCATGGATGC
1 ACAGCCTTGATGCATCGATGC
**
254803 ACAG-CAGGATGCATCGATGC
1 ACAGCCTTGATGCATCGATGC
254823 ACAGCCTTGATGCATCGATGC
1 ACAGCCTTGATGCATCGATGC
254844 A
1 A
254845 TAGAAGGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (21 bp):
ACAGCCTTGATGCATCGATGC
Found at i:254816 original size:20 final size:20
Alignment explanation
Indices: 254791--254865 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
254781 TACAGCCTTT
*
254791 ATGCATGGATGCACAGCAGG
1 ATGCATCGATGCACAGCAGG
**
254811 ATGCATCGATGCACAGCCTTG
1 ATGCATCGATGCACAG-CAGG
* *
254832 ATGCATCGATGCATAGAAGG
1 ATGCATCGATGCACAGCAGG
254852 ATGCATCGATGCAC
1 ATGCATCGATGCAC
254866 TAATTGTATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (20 bp):
ATGCATCGATGCACAGCAGG
Found at i:254843 original size:41 final size:41
Alignment explanation
Indices: 254782--254865 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
254772 ACTAGCCGTT
* * *
254782 ACAGCCTTTATGCATGGATGCACAGCAGGATGCATCGATGC
1 ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGC
*
254823 ACAGCCTTGATGCATCGATGCATAGAAGGATGCATCGATGC
1 ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGC
254864 AC
1 AC
254866 TAATTGTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (41 bp):
ACAGCCTTGATGCATCGATGCACAGAAGGATGCATCGATGC
Found at i:254932 original size:42 final size:41
Alignment explanation
Indices: 254886--254984 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
254876 CGGTGTTTGA
*
254886 GTGCATGGATGCACTGCA-TGATGCATCGATGCACTAGTGCA-G
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCAC---TGCAGG
*
254928 GTGCATGGATGCACTGCAGGGATGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGGATGCATCGATGCACTGCA-GG
254970 GTGCATGGATGCACT
1 GTGCATGGATGCACT
254985 TTGACACCCT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
40 4 0.08
42 34 0.65
43 14 0.27
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (41 bp):
GTGCATGGATGCACTGCAGGGATGCATCGATGCACTGCAGG
Found at i:254955 original size:21 final size:20
Alignment explanation
Indices: 254887--254984 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
254877 GGTGTTTGAG
*
254887 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
254907 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
254929 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
254950 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCA-GGA
254971 TGCATGGATGCACT
1 TGCATGGATGCACT
254985 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 34 0.49
22 12 0.17
23 5 0.07
ACGTcount: A:0.22, C:0.20, G:0.35, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:255120 original size:30 final size:29
Alignment explanation
Indices: 255064--255122 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
255054 AAACTTTGAA
255064 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
255093 TAAATTCAATTCAAGT-CAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
255123 CTTAAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:256044 original size:24 final size:24
Alignment explanation
Indices: 256017--256088 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
256007 AAACGGAGAT
* *
256017 ATCAAAAATCAAAACAGAATTTAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
256041 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
256065 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
256089 GTAATGTATC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:256099 original size:48 final size:48
Alignment explanation
Indices: 256017--256108 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
256007 AAACGGAGAT
* * *
256017 ATCAAAAATCAAAACAGAATTTAGATCAGATATCATAACAGAATCCAG
1 ATCAAAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
* *
256065 ATCAGAAATCAAAACAGAATTCAGGTAATG-TATCAGAACAGAAT
1 ATCAAAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAAT
256109 TCAAGTCGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
48 37 0.97
49 1 0.03
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (48 bp):
ATCAAAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCCAG
Found at i:256121 original size:48 final size:48
Alignment explanation
Indices: 256017--256123 Score: 119
Period size: 48 Copynumber: 2.2 Consensus size: 48
256007 AAACGGAGAT
* * * * *
256017 ATCAAAAATCAAAACAGAATTTAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
*
256065 ATCAGAAATCAAAACAGAATTCAGGTAATG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAAAACAGAATTCAGATAA-GATATCAGAACAGAA-TCAAG
*
256114 -TCGGAAATCA
1 ATCAGAAATCA
256124 GATAAAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
48 45 0.90
49 5 0.10
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.21
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATAAGATATCAGAACAGAATCAAG
Found at i:260486 original size:66 final size:63
Alignment explanation
Indices: 260347--260486 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 63
260337 ACTCCCTTCA
* * * *
260347 CCCCCGTAAGTTCACCCCTCAAATCCATAACTTCTTCACCACTCCATCAATTTTTCCACCCAT
1 CCCCCTTAACTTCACCCCTCAAATCCATAACTTCTTCACCAATACATCAATTTTTCCACCCAT
* * *
260410 CACCATCTTAACTTCACCCCTCAACTCCATAACTTCTTTCACCAATACATCTATTTTTCCACCCA
1 C-CC-CCTTAACTTCACCCCTCAAATCCATAACTTC-TTCACCAATACATCAATTTTTCCACCCA
260475 CTT
63 --T
260478 CCCCCTTAA
1 CCCCCTTAA
260487 GCCTCTCCAT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.02
64 2 0.03
65 27 0.42
66 30 0.47
67 2 0.03
68 2 0.03
ACGTcount: A:0.26, C:0.42, G:0.01, T:0.31
Consensus pattern (63 bp):
CCCCCTTAACTTCACCCCTCAAATCCATAACTTCTTCACCAATACATCAATTTTTCCACCCAT
Found at i:262996 original size:70 final size:69
Alignment explanation
Indices: 262892--263047 Score: 258
Period size: 70 Copynumber: 2.2 Consensus size: 69
262882 TACATTTTTA
* ** * *
262892 TAAAATATCGACACTTTATAGGCCTATTACTGCTTCTCTTTTAAATTCTAAAAGTGTCGATACTT
1 TAAAGTATCGACACTTTATAAACCTATTAATGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTT
262957 ATAT
66 ATAT
262961 TAAAGTATCGACACTTTATAAACGCTATTAATGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
1 TAAAGTATCGACACTTTATAAAC-CTATTAATGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
263026 TATAT
65 TATAT
263031 TAAAGTATCGACACTTT
1 TAAAGTATCGACACTTT
263048 CAACATATCC
Statistics
Matches: 81, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
69 20 0.25
70 61 0.75
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.39
Consensus pattern (69 bp):
TAAAGTATCGACACTTTATAAACCTATTAATGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTT
ATAT
Found at i:263275 original size:182 final size:181
Alignment explanation
Indices: 262961--263872 Score: 1283
Period size: 182 Copynumber: 5.0 Consensus size: 181
262951 ATACTTATAT
** *
262961 TAAAGTATCGACACTTTATAAACGCTATTAATGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
* * *
263026 TATATTAAAGTATCGACACTTTCAACATATCCGATAACGCTTTACCGGTTTTATCATTTCGAGAC
66 TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTT-GAGAC
* *
263091 CGATTTTGTCATATTGTTACCTGTTATATTGTTATAGGTCGATATATTTTTA
130 CGATTTTGTCATATTTTTACCTGTTATATTGTTATAGGTCGATACATTTTTA
* * *
263143 TAAAGTTTCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCATAAGTGTCAATACT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
*
263208 TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCACTTTACCGGTTTTGTCATTTGAAGAC
66 TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTG-AGAC
*
263273 CGATTTTGTGATATTTTTACCTGTTATATTGTTAT-GGATCGATACATTTTTA
130 CGATTTTGTCATATTTTTACCTGTTATATTGTTATAGG-TCGATACATTTTTA
* * * *
263325 TAAAGTATCGATACTTTATAGACGCTATTAATGCTTCTCTTTTAAATTCCATAAGTGTCGATACT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
* * *
263390 TTTATTAAAGTATTGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTGGAGAC
66 TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTT-GAGAC
* *
263455 CGATTTTGTCATATTTTTACTTGTTATATTGTTAT-GGATTGATACATTTTTA
130 CGATTTTGTCATATTTTTACCTGTTATATTGTTATAGG-TCGATACATTTTTA
* *
263507 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTATTTTAAATTCCAAAAGTGTCGATAGT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
* * * *
263572 TATATTAAAGTATCGACACTTTCAACATATCTGGTAACGCTTTACCGTTTTTGTCATTTCGAGAT
66 TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTT-GAGAC
* * * *
263637 CGGTTTTGTCATATTTTTACCTGTTATATTATTATAGATCAATACATTTTTA
130 CGATTTTGTCATATTTTTACCTGTTATATTGTTATAGGTCGATACATTTTTA
*
263689 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTTTCGATACT
1 TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
* * * * ** * * * *
263754 TAT-TTCAATGGAATCGATACTTTAAACATATTAGGTAGCGCTTTACCGTTTTTGTCATAATAAA
66 TATATT-AA-AGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCAT-TTGAG
* * * *
263818 ACCG-GTTTGATCATATTTTTACATGTTATACTGTTATAGATCGATACATTTTTA
128 ACCGATTTTG-TCATATTTTTACCTGTTATATTGTTATAGGTCGATACATTTTTA
263872 T
1 T
263873 TTGTATCAAT
Statistics
Matches: 658, Mismatches: 64, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
181 5 0.01
182 563 0.86
183 89 0.14
184 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (181 bp):
TAAAGTATCGACACTTTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACT
TATATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTGAGACC
GATTTTGTCATATTTTTACCTGTTATATTGTTATAGGTCGATACATTTTTA
Found at i:264923 original size:182 final size:182
Alignment explanation
Indices: 264610--265084 Score: 679
Period size: 182 Copynumber: 2.6 Consensus size: 182
264600 ACCGCCAAAT
* * * * *
264610 TAAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATCGATAAAACTGATCA-CGAAAAG
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATAT-GATAAAACTGGT-ATCGAAATG
* * * *
264674 ACAATATCGGTAAAGCCCTACC-AGATATATTGAACGTGTCGATACTTTAATATAAGGATCAACA
64 ATAAAATCGGTAAAGCACTACCGA-ATATATTGAAAGTGTCGATACTTTAATATAAGGATCAACA
*
264738 CTTTATGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTTTCGATACTTTA
128 CTTTATGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
264793 TAAAAATGTATCGATCCACAACGATATAATAGGTAAAAATATGACAAAACCGGTATCGAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCGAAATGAT
* * * *
264858 AAAACCGGTAAAGCACTACCGAATATATTTAAAGTGTCGATACTTTAATATAAGTATCGACACTT
66 AAAATCGGTAAAGCACTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGGATCAACACTT
* *
264923 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTA
131 TATGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
264975 TAAAAATATATCGATCCACAACGATATAACAGGTAAAAA-ATGATAAAAATGGTATCAAAATGAT
1 TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCGAAATGAT
*
265039 AAAATCGGTAAAG-AGCTACCGGATATATTGAAAGTGTCGATACTTT
66 AAAATCGGTAAAGCA-CTACCGAATATATTGAAAGTGTCGATACTTT
265085 CATAAGTACG
Statistics
Matches: 261, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
180 1 0.00
181 63 0.24
182 158 0.61
183 39 0.15
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCGAAATGAT
AAAATCGGTAAAGCACTACCGAATATATTGAAAGTGTCGATACTTTAATATAAGGATCAACACTT
TATGAATTTAAAAGAGAAGCAGTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:266894 original size:22 final size:24
Alignment explanation
Indices: 266849--266899 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
266839 TTTTGTGTTT
*
266849 TTATATAAAATGATAGTATATTTA
1 TTATATAAAATGATAGAATATTTA
*
266873 TTATATAAAATTATA-AAT-TTTA
1 TTATATAAAATGATAGAATATTTA
266895 TTATA
1 TTATA
266900 AATGCAGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.36
23 2 0.08
24 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
TTATATAAAATGATAGAATATTTA
Found at i:267198 original size:15 final size:15
Alignment explanation
Indices: 267178--267210 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
267168 TGGTTGTATT
*
267178 GGGGGATGACGGTGA
1 GGGGGATGACAGTGA
267193 GGGGGATGACAGTGA
1 GGGGGATGACAGTGA
267208 GGG
1 GGG
267211 AAAATAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.06, G:0.61, T:0.12
Consensus pattern (15 bp):
GGGGGATGACAGTGA
Found at i:267316 original size:21 final size:21
Alignment explanation
Indices: 267292--267335 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
267282 AAGACAATCA
267292 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
267313 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
267334 AG
1 AG
267336 GCATAAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:267406 original size:33 final size:33
Alignment explanation
Indices: 267369--267434 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
267359 AAATAGATGG
*
267369 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
267402 AGTGGTGAAAGAAGTTGATGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
267435 TCTTAAGATG
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:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:269242 original size:19 final size:19
Alignment explanation
Indices: 269218--269266 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
269208 AATGTAGGGT
*
269218 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
269237 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
269256 TAATTTTGTAT
1 TAATTTTGTAT
269267 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:269277 original size:18 final size:19
Alignment explanation
Indices: 269218--269289 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
269208 AATGTAGGGT
* * *
269218 TAATTTTTTATAAGATTTA
1 TAATTTTGTATGAGATATA
* *
269237 TAATTTTGTATAAGATTTA
1 TAATTTTGTATGAGATATA
*
269256 TAATTTTGTATGTGA-ATA
1 TAATTTTGTATGAGATATA
*
269274 TAATTATGTATGAGAT
1 TAATTTTGTATGAGAT
269290 GAGAAAAGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.33
19 31 0.67
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TAATTTTGTATGAGATATA
Found at i:271397 original size:12 final size:12
Alignment explanation
Indices: 271351--271396 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
271341 GTCAATGAAT
271351 ATGAAGATGACG
1 ATGAAGATGACG
*
271363 ATGAAGATGACA
1 ATGAAGATGACG
* *
271375 ATGATGATGATG
1 ATGAAGATGACG
*
271387 ATGATGATGA
1 ATGAAGATGA
271397 TCCAAACAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.41, C:0.04, G:0.30, T:0.24
Consensus pattern (12 bp):
ATGAAGATGACG
Found at i:272903 original size:51 final size:53
Alignment explanation
Indices: 272848--272957 Score: 120
Period size: 51 Copynumber: 2.1 Consensus size: 53
272838 ATAATGGATG
* *
272848 CCAAAAAGGG-TGAATGCACAAAGTGTCGATACATTT-TCATAGAGTGTCGAT-
1 CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCA-AAAGTGTCGATC
* * * * *
272899 CC-AAATGGGTTGCACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGATC
1 CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
272951 CCAAAAA
1 CCAAAAA
272958 CATCGAAACC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
50 6 0.13
51 34 0.72
52 4 0.09
53 3 0.06
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (53 bp):
CCAAAAAGGGTTGAACGCACAAAGTGTCGATACATTTATCAAAAGTGTCGATC
Found at i:273088 original size:250 final size:249
Alignment explanation
Indices: 272666--273150 Score: 713
Period size: 250 Copynumber: 1.9 Consensus size: 249
272656 TAAAGTTTCC
*
272666 CATAAAGTGTCGATCCATATATAAAAAGTAACGACCCAAAAACATCAAAACCCATAATTATAATG
1 CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAACATCAAAACCCATAATTATAATG
* *
272731 TAATGAGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATAGAAAATAGGTCTACAAC
66 TAATAAGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATAGAAAATAGGTCTACAAC
* * * * * *
272796 ATTTATCGACACTTATTAGTATTGTGTCGATACTTTTTGTCCATAATGGATGCCAAAAAGGGTGA
131 ATGTATCGACACTTATTAATATTGTGTCAATAATTTTTGTCCAGAATGGATGCCAAAAAAGGTGA
* * *
272861 ATGCACAAAGTGTCGATACATTTTCATAGAGTGTCGATCCAAATGGGTTGCACG
196 ACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCAAATGGGTTGCACG
* * * ** *
272915 CATAAAGTTTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAAT
1 CATAAAGTGTCGATACATATATAAAAAGTAACGA-CCCAAAAACATCAAAACCCATAATTATAAT
* *
272980 GTAATAAGTAATTTTGT-AATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTAT
65 GTAATAAGTAATTTT-TCAATATAACCGGTATAAATATACCGGTTTTAT-AGAAAATAGGTCTAC
* *
273044 AAGATGTATCGACACTTCTTAATATTGTG-CAATAATTTTTGTCCAGAATGGATGCCAAAAAAGG
128 AACATGTATCGACACTTATTAATATTGTGTCAATAATTTTTGTCCAGAATGGATGCCAAAAAAGG
* *
273108 TGAACGCATAAAGTGTCGATACATTTTCAAAAAGTGTTGATCC
193 TGAACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCC
273151 CAAAAACATC
Statistics
Matches: 209, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
249 28 0.13
250 142 0.68
251 39 0.19
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (249 bp):
CATAAAGTGTCGATACATATATAAAAAGTAACGACCCAAAAACATCAAAACCCATAATTATAATG
TAATAAGTAATTTTTCAATATAACCGGTATAAATATACCGGTTTTATAGAAAATAGGTCTACAAC
ATGTATCGACACTTATTAATATTGTGTCAATAATTTTTGTCCAGAATGGATGCCAAAAAAGGTGA
ACGCACAAAGTGTCGATACATTTTCAAAAAGTGTCGATCCAAATGGGTTGCACG
Found at i:273258 original size:199 final size:200
Alignment explanation
Indices: 272912--273432 Score: 762
Period size: 199 Copynumber: 2.6 Consensus size: 200
272902 AATGGGTTGC
*
272912 ACGCATAAAGTTTCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTATCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
* * * *
272977 AATGTAATAAGTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
66 AATGTAATAGGTAATTTTATAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGATCT
* * *
273042 ATAAGATGTATCGACACTTCTT-AATATTGTG-CAATAATTTTTGTCCAGAATGGATGCCAAAAA
131 ATAACATGTAGCGACACTTCTTAAAT-TTGTGTCAATAATTTTTGTCCAAAATGGATGCC-AAAA
273105 AGG-TGA
194 AGGATGA
* * *
273111 ACGCATAAAGTGTCGATACATTT-TCAAAAAGTGTTGATCCCAAAAACATCGAAACCCATAATTA
1 ACGCATAAAGTATCGATACATTTAT-TAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTA
* *
273175 TAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGATC
65 TAATGTAATAGGTAATTTTATAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGATC
* * * *
273240 TATAACATGTAGCGACACTTGTTAAATTTGTGTCGATACTTTTTTTCCAAAATGGATGCCAAAAA
130 TATAACATGTAGCGACACTTCTTAAATTTGTGTCAATAATTTTTGTCCAAAATGGATGCCAAAAA
273305 GGATGA
195 GGATGA
* * * *
273311 AAGCACAAAGTATCGATACATTTATTAAAAGTGTCGATACCGAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTATCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
* * * *
273376 AATATAATAGGTAATTTTATAATATAATCAGTATAAATATATTGGTTTTATGAGAGA
66 AATGTAATAGGTAATTTTATAATATAACCGGTATAAATATATCGGTTTTATGAGAGA
273433 TATCGACACT
Statistics
Matches: 288, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
198 1 0.00
199 150 0.52
200 136 0.47
201 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (200 bp):
ACGCATAAAGTATCGATACATTTATTAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTAT
AATGTAATAGGTAATTTTATAATATAACCGGTATAAATATATCGGTTTTATGAGAGAATAGATCT
ATAACATGTAGCGACACTTCTTAAATTTGTGTCAATAATTTTTGTCCAAAATGGATGCCAAAAAG
GATGA
Found at i:276543 original size:200 final size:197
Alignment explanation
Indices: 276152--276876 Score: 818
Period size: 200 Copynumber: 3.6 Consensus size: 197
276142 ACCTAAATAT
* * *
276152 GTGTCGATACATTT-TCTACAAGTATCGA-CCCAAAAACATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAAT
* * * * * *
276215 AGGTAAATTAACAATGTAACCGATATAAATATACCAGTTAATTAGAAAACAGGTCAACATAATGT
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTATGAGAAAATAGGTC-ACATAATGT
* * * *
276280 ATCGACACTTGTGGAATTTGTGTCGATAC-TTATTGTCCAGAATGAATGCCCAAACGAGGTGCAC
129 ATCGACAATTGT-TAATTTGTGTCGATACATT-TTGTTCATAATGAATG-CCAAACGAGGTGCAC
276344 GCATAAA
191 GCATAAA
* *
276351 GTGTCGCTACATTTATTAAAAGTATCGATCCCAAAAACATCAAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAATA
* *
276416 AGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAGCATAAAGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGG-TTTATGAGAAAATAGGTCA-CATAATGT
* *
276481 ATCGACAATTGTTAAATTTGTGTCGATACATTTTGTTCATAATGAATGTCAAACGGGGTGCACGC
129 ATCGACAATTGTT-AATTTGTGTCGATACATTTTGTTCATAATGAATGCCAAACGAGGTGCACGC
*
276546 ATAGA
193 ATAAA
* * * *
276551 GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCGAAA-CGAAAATTACAATGTGATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAATA
* * *
276615 GGTAAATTTTACAATGTACCCGGTATAAATATACCGATTTTATGAGAAAATAGGTCTAAATAATG
66 GGTAAA-TTTACAATGTAACCGGTATAAATATACCG-GTTTATGAGAAAATAGGTC-ACATAATG
* * * *
276680 TATCGACACTTTGTTAGTTTGTGTCGAT--ATTTTTTTCCAGGATGAAATATGAATGCCCAACGA
128 TATCGACA-ATTGTTAATTTGTGTCGATACATTTTGTT-C---AT---A-ATGAATGCCAAACGA
*
276743 GGTGCAAGCATAAA
184 GGTGCACGCATAAA
* * ** *
276757 GTGTCGATACATTTA--AAATTGTATCGATCTAAAAAACATTGAAACCGATAATAATAATGTAAT
1 GTGTCGATACATTTATTAAA-AGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAAT
** * **
276820 AGGTAAATTTGTAATGTTACCGGTATAAATATACCGGTTTACTTCGAAAATAGGTCA
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTA-TGAGAAAATAGGTCA
276877 ATATAAGCGC
Statistics
Matches: 454, Mismatches: 51, Indels: 37
0.84 0.09 0.07
Matches are distributed among these distances:
198 7 0.02
199 46 0.10
200 201 0.44
201 68 0.15
202 4 0.01
204 8 0.02
205 60 0.13
206 60 0.13
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (197 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTATGAGAAAATAGGTCACATAATGTAT
CGACAATTGTTAATTTGTGTCGATACATTTTGTTCATAATGAATGCCAAACGAGGTGCACGCATA
AA
Found at i:277099 original size:11 final size:11
Alignment explanation
Indices: 277083--277107 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
277073 ACCGTTCACG
277083 CCGTTTTTTAA
1 CCGTTTTTTAA
277094 CCGTTTTTTAA
1 CCGTTTTTTAA
277105 CCG
1 CCG
277108 CCGCACACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.12, T:0.48
Consensus pattern (11 bp):
CCGTTTTTTAA
Found at i:281207 original size:22 final size:23
Alignment explanation
Indices: 281182--281230 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
281172 ATGTATCTTC
281182 AAATA-ATAATTAAATGAAAT-AA
1 AAATATATAATTAAAT-AAATGAA
* *
281204 AAATATATAGTTAACTAAATGAA
1 AAATATATAATTAAATAAATGAA
281227 AAAT
1 AAAT
281231 TAGACATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
AAATATATAATTAAATAAATGAA
Found at i:282184 original size:74 final size:74
Alignment explanation
Indices: 282095--282242 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
282085 CATCACCGTC
282095 GTCGCGGACCCATTCATCCCAAAACCGATGGATGCTAATGCCAGTTCTGTCACCCCCGTCGTTCT
1 GTCGCGGACCCATTCATCCCAAAACCGATGGATGCTAATGCCAGTTCTGTCACCCCCGTCGTTCT
282160 CTCCACCGA
66 CTCCACCGA
282169 GTCGCGGACCCATTCATCCCAAAACCGATGGATGCTAATGCCAGTTCTGTCACCCCCGTCGTTCT
1 GTCGCGGACCCATTCATCCCAAAACCGATGGATGCTAATGCCAGTTCTGTCACCCCCGTCGTTCT
282234 CTCCACCGA
66 CTCCACCGA
282243 TTCCGTGGTT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.20, C:0.38, G:0.19, T:0.23
Consensus pattern (74 bp):
GTCGCGGACCCATTCATCCCAAAACCGATGGATGCTAATGCCAGTTCTGTCACCCCCGTCGTTCT
CTCCACCGA
Found at i:284415 original size:30 final size:28
Alignment explanation
Indices: 284377--284444 Score: 100
Period size: 30 Copynumber: 2.4 Consensus size: 28
284367 ATGCACTAAC
284377 CAAAAGCAAATTGAAGTGAAAATCTAGAA
1 CAAAAGCAAATTGAAGTGAAAATC-AGAA
284406 CAAATAGCAAATTGAAGTGAAAATCAGAA
1 CAAA-AGCAAATTGAAGTGAAAATCAGAA
* *
284435 GAAAACCAAA
1 CAAAAGCAAA
284445 CTATGTCCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 5 0.14
29 11 0.31
30 20 0.56
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.15
Consensus pattern (28 bp):
CAAAAGCAAATTGAAGTGAAAATCAGAA
Found at i:284712 original size:54 final size:54
Alignment explanation
Indices: 284630--284738 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
284620 TAATCTTACC
*
284630 TTGCATGGCGATATTAATTAAAGTGGTAGGAATATCCAAAGAAGATGCAATTTG
1 TTGCAAGGCGATATTAATTAAAGTGGTAGGAATATCCAAAGAAGATGCAATTTG
*
284684 TTGCAAGGTGATATTAATTAAAGTGGTAGGAATATCCAAAGAAGATGCAATTTG
1 TTGCAAGGCGATATTAATTAAAGTGGTAGGAATATCCAAAGAAGATGCAATTTG
284738 T
1 T
284739 AACTGAGAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (54 bp):
TTGCAAGGCGATATTAATTAAAGTGGTAGGAATATCCAAAGAAGATGCAATTTG
Found at i:287989 original size:31 final size:31
Alignment explanation
Indices: 287950--288055 Score: 194
Period size: 31 Copynumber: 3.4 Consensus size: 31
287940 ATATTAACCA
287950 TAAGTAATTTAATTAATATTATTTAAATAGT
1 TAAGTAATTTAATTAATATTATTTAAATAGT
*
287981 TAACTAATTTAATTAATATTATTTAAATAGT
1 TAAGTAATTTAATTAATATTATTTAAATAGT
288012 TAAGTAATTTAATTAATATTATTTAAATAGT
1 TAAGTAATTTAATTAATATTATTTAAATAGT
*
288043 TAAGTGATTTAAT
1 TAAGTAATTTAAT
288056 AGATAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 72 1.00
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (31 bp):
TAAGTAATTTAATTAATATTATTTAAATAGT
Found at i:287997 original size:9 final size:10
Alignment explanation
Indices: 287954--288037 Score: 66
Period size: 9 Copynumber: 8.3 Consensus size: 10
287944 TAACCATAAG
287954 TAAT-TTAAT
1 TAATATTAAT
*
287963 TAATATTATT
1 TAATATTAAT
*
287973 TAAATAGTTAAC
1 T-AATA-TTAAT
287985 TAAT-TTAAT
1 TAATATTAAT
*
287994 TAATATTATT
1 TAATATTAAT
*
288004 TAAATAGTTAAG
1 T-AATA-TTAAT
288016 TAAT-TTAAT
1 TAATATTAAT
*
288025 TAATATTATT
1 TAATATTAAT
288035 TAA
1 TAA
288038 ATAGTTAAGT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
9 20 0.34
10 17 0.29
11 14 0.24
12 8 0.14
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (10 bp):
TAATATTAAT
Found at i:288054 original size:17 final size:17
Alignment explanation
Indices: 287970--288054 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 17
287960 AATTAATATT
*
287970 ATTTAAATAGTTAACTA
1 ATTTAAATAGTTAAGTA
* * *
287987 ATTTAATTA-AT-A-TT
1 ATTTAAATAGTTAAGTA
288001 ATTTAAATAGTTAAGTA
1 ATTTAAATAGTTAAGTA
* * *
288018 ATTTAATTA-AT-A-TT
1 ATTTAAATAGTTAAGTA
*
288032 ATTTAAATAGTTAAGTG
1 ATTTAAATAGTTAAGTA
288049 ATTTAA
1 ATTTAA
288055 TAGATAAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
14 18 0.36
15 4 0.08
16 4 0.08
17 24 0.48
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.47
Consensus pattern (17 bp):
ATTTAAATAGTTAAGTA
Found at i:289230 original size:29 final size:32
Alignment explanation
Indices: 289158--289235 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 32
289148 GGCATAACAT
*
289158 AAATTTAAAAGACTAGAATAATAAAAAAAATAT
1 AAATTTAAAAGACTA-AATAATAAAAAAAATAG
* * *
289191 AAATTT-GAAGACTAAAT-AT-TACAAAAT-G
1 AAATTTAAAAGACTAAATAATAAAAAAAATAG
289219 AAATTTAAAAGACTAAA
1 AAATTTAAAAGACTAAA
289236 ATGGCACAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 2 0.05
31 3 0.08
32 7 0.18
33 6 0.15
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (32 bp):
AAATTTAAAAGACTAAATAATAAAAAAAATAG
Found at i:289380 original size:31 final size:30
Alignment explanation
Indices: 289301--289391 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 30
289291 TGGTATTGAT
* *
289301 AAACATTTAAAACACTAAAATAACAAAAAA
1 AAACATTTAAAAGATTAAAATAACAAAAAA
* * * *
289331 ATAGAAAATTAAATGATTAAAATAACAAAAAC
1 A-A-ACATTTAAAAGATTAAAATAACAAAAAA
*
289363 AAACATTTAAAAGGATTAAAATAATAAAA
1 AAACATTTAAAA-GATTAAAATAACAAAA
289392 CAGAAAATTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
30 8 0.17
31 17 0.35
32 23 0.48
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (30 bp):
AAACATTTAAAAGATTAAAATAACAAAAAA
Found at i:290892 original size:3 final size:3
Alignment explanation
Indices: 290884--290908 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
290874 AAATATAAAT
290884 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
290909 CTTTAAAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:291339 original size:46 final size:42
Alignment explanation
Indices: 291279--291384 Score: 113
Period size: 46 Copynumber: 2.4 Consensus size: 42
291269 TGATGAAATA
* *
291279 GTTCCTTCGCGATGAGGACGACAAGTCATCTAAGGGTGATAACACG
1 GTTCCTACGTGATGAGGACGACAAGTCATCT--GGG-G-TAACACG
* ** * *
291325 GTTCCTACGTGATGAGGACGGCTGGTTATCTGGGGTGACACG
1 GTTCCTACGTGATGAGGACGACAAGTCATCTGGGGTAACACG
291367 GTTCCTACGTGATGAGGA
1 GTTCCTACGTGATGAGGA
291385 AATCTAGTCA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 24 0.45
43 1 0.02
44 3 0.06
46 25 0.47
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (42 bp):
GTTCCTACGTGATGAGGACGACAAGTCATCTGGGGTAACACG
Found at i:291685 original size:91 final size:91
Alignment explanation
Indices: 291530--291699 Score: 277
Period size: 91 Copynumber: 1.9 Consensus size: 91
291520 AAGCGTTGGA
* * * *
291530 TTGAACAAGTTTTTCTCATTGTGAACTTCTTCTCTCTTGTTGGATGAGTTCTTCTTATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
*
291595 TCTTCAATGGAAATACTGATGCAAGG
66 TCTCCAATGGAAATACTGATGCAAGG
*
291621 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
*
291686 TCTCCATTGGAAAT
66 TCTCCAATGGAAAT
291700 GTTGATCCAC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (91 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTCCAATGGAAATACTGATGCAAGG
Found at i:291758 original size:117 final size:114
Alignment explanation
Indices: 291616--291987 Score: 428
Period size: 117 Copynumber: 3.3 Consensus size: 114
291606 AATACTGATG
*
291616 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTT-AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTA
**
291681 TGAACTCTCCATTGGAAATGTTGATCCACCTCCTTCTGTGATGAAATCGAA
65 TGAACTCTCCATTGGAAATGTTGATCCACCTCCTTCTACGATGAAATCG-A
291732 CCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATT
1 -CAAGGTT-AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATT
* * * * * *
291797 ATAAACTCTCCATTGAAAATGTTGATCCACCTTCTTTTACGATGTACTCGA
64 ATGAACTCTCCATTGGAAATGTTGATCCACCTCCTTCTACGATGAAATCGA
* * *
291848 -AAGG--AACAAGTTCTTCTCATTATGAAC-T-TTCTTCCTCATTGGATGAATTATTCTCATTAT
1 CAAGGTTAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTAT
* * ** * *
291908 GAACTCTTC--TGGAAATGTT-AGTTCACCTCCTTCTTTGGTG-AATGTGA
66 GAACTCTCCATTGGAAATGTTGA-TCCACCTCCTTCTACGATGAAAT-CGA
*
291955 -AAGG--AATAAGTTCTTCTCATTATGAAC-TCTTCT
1 CAAGGTTAACAAGTTCTTCTCATTATGAACTTCTTCT
291988 GGAAATATTG
Statistics
Matches: 227, Mismatches: 25, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
106 3 0.01
107 51 0.22
108 4 0.02
109 36 0.16
110 1 0.00
111 23 0.10
114 4 0.02
116 1 0.00
117 104 0.46
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (114 bp):
CAAGGTTAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCATTGGAAATGTTGATCCACCTCCTTCTACGATGAAATCGA
Found at i:291881 original size:18 final size:18
Alignment explanation
Indices: 291858--291917 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
291848 AAGGAACAAG
291858 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
291876 TTCTTCCTCATTGGATGAA--
1 TTCTT-CTCATT--ATGAACT
*
291895 TTATTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
291913 CTTCT
1 -TTCT
291918 GGAAATGTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 5 0.15
18 11 0.32
19 13 0.38
21 5 0.15
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (18 bp):
TTCTTCTCATTATGAACT
Found at i:291917 original size:16 final size:16
Alignment explanation
Indices: 291859--291917 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
291849 AGGAACAAGT
291859 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
*
291875 TTTCTTCCTCATTGGATGAAT
1 --TCTT-CTCATT--ATGAAC
*
291896 TATTCTCATTATGAAC
1 TCTTCTCATTATGAAC
291912 TCTTCT
1 TCTTCT
291918 GGAAATGTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
16 10 0.29
18 10 0.29
19 9 0.26
21 5 0.15
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:292017 original size:70 final size:70
Alignment explanation
Indices: 291898--292052 Score: 256
Period size: 70 Copynumber: 2.2 Consensus size: 70
291888 GGATGAATTA
* * *
291898 TTCTCATTATGAACTCTTCTGGAAATGTTAGTTCACCTCCTTCTTTGGTGAATGTGAAAGGAATA
1 TTCTCATTATGAACTCTTCTGGAAATATTAGTTCACCTCCTTCTGTGGTGAATGTGAAAGGAACA
291963 AGTTC
66 AGTTC
* *
291968 TTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCTTTCTGTGGTGAATGTGAAAGGAACA
1 TTCTCATTATGAACTCTTCTGGAAATATTAGTTCACCTCCTTCTGTGGTGAATGTGAAAGGAACA
292033 AGTTC
66 AGTTC
*
292038 TTTTCATTATGAACT
1 TTCTCATTATGAACT
292053 TTATCCTTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 79 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (70 bp):
TTCTCATTATGAACTCTTCTGGAAATATTAGTTCACCTCCTTCTGTGGTGAATGTGAAAGGAACA
AGTTC
Found at i:295109 original size:10 final size:10
Alignment explanation
Indices: 295094--295152 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
295084 TCTTTTTTAT
295094 TTTCTTCTTC
1 TTTCTTCTTC
295104 TTTCTTCTTC
1 TTTCTTCTTC
295114 TTTCTTCTTC
1 TTTCTTCTTC
*
295124 TTTTTTCTT-
1 TTTCTTCTTC
*
295133 TTT-TT-TTT
1 TTTCTTCTTC
295141 TTTCTTC-TC
1 TTTCTTCTTC
295150 TTT
1 TTT
295153 TTTTCTCTGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 2 0.05
8 5 0.11
9 9 0.20
10 28 0.64
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTCTTCTTC
Found at i:295113 original size:13 final size:13
Alignment explanation
Indices: 295095--295152 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
295085 CTTTTTTATT
295095 TTCTTC-TTCTTTC
1 TTCTTCTTTC-TTC
295108 TTCTTCTTTCTTC
1 TTCTTCTTTCTTC
*
295121 TTCTTTTTTCTT-
1 TTCTTCTTTCTTC
* *
295133 TT-TTTTTTTTTC
1 TTCTTCTTTCTTC
295145 TTC-TCTTT
1 TTCTTCTTT
295153 TTTTCTCTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 8 0.21
12 8 0.21
13 20 0.51
14 3 0.08
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTCTTTCTTC
Found at i:295153 original size:10 final size:9
Alignment explanation
Indices: 295093--295158 Score: 62
Period size: 10 Copynumber: 7.0 Consensus size: 9
295083 TTCTTTTTTA
295093 TTTTCTTCT
1 TTTTCTTCT
295102 TCTTTCTTCT
1 T-TTTCTTCT
295112 TCTTTCTTCT
1 T-TTTCTTCT
*
295122 TCTTTTTTCT
1 T-TTTCTTCT
*
295132 TTTT-TTTT
1 TTTTCTTCT
295140 TTTTCTTCT
1 TTTTCTTCT
*
295149 CTTTTTTTCT
1 -TTTTCTTCT
295159 CTGATAGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
8 7 0.14
9 7 0.14
10 36 0.72
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTTCT
Found at i:295153 original size:13 final size:13
Alignment explanation
Indices: 295077--295158 Score: 50
Period size: 13 Copynumber: 6.4 Consensus size: 13
295067 CTTGATTCAA
*
295077 TTTCTTTTCTTTT
1 TTTCTTCTCTTTT
295090 TTAT-TT-TCTTCTT
1 TT-TCTTCTCTT-TT
295103 CTTTCTTCT-TCTTT
1 -TTTCTTCTCT-TTT
*
295117 CTTCTTCT-TTTT
1 TTTCTTCTCTTTT
*
295129 TCTT-TT-TTTTTT
1 T-TTCTTCTCTTTT
295141 TTTCTTCTCTTTT
1 TTTCTTCTCTTTT
295154 TTTCT
1 TTTCT
295159 CTGATAGATG
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
11 3 0.05
12 16 0.29
13 27 0.48
14 8 0.14
15 2 0.04
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTCTTCTCTTTT
Found at i:295585 original size:7 final size:8
Alignment explanation
Indices: 295570--295596 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
295560 AATCAATCCC
295570 TCTTTTTT
1 TCTTTTTT
295578 TCTTTTTT
1 TCTTTTTT
295586 TCTTTTTT
1 TCTTTTTT
295594 TCT
1 TCT
295597 CTTCTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TCTTTTTT
Found at i:297678 original size:14 final size:14
Alignment explanation
Indices: 297660--297697 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
297650 GATGCGAATT
297660 CAAATGCAAAGATG
1 CAAATGCAAAGATG
* *
297674 TAAATACAAAGATG
1 CAAATGCAAAGATG
297688 CAAATGCAAA
1 CAAATGCAAA
297698 TGAAAAATGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (14 bp):
CAAATGCAAAGATG
Found at i:297683 original size:20 final size:20
Alignment explanation
Indices: 297641--297683 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
297631 ACAAACATAA
* *
297641 AAATACAAAGATGCGAATTC
1 AAATACAAAGATGCAAATAC
* *
297661 AAATGCAAAGATGTAAATAC
1 AAATACAAAGATGCAAATAC
297681 AAA
1 AAA
297684 GATGCAAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.14, T:0.19
Consensus pattern (20 bp):
AAATACAAAGATGCAAATAC
Found at i:299242 original size:23 final size:23
Alignment explanation
Indices: 299213--299278 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
299203 CATATGAATT
*
299213 TGTCCCGAAGGACTACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
*
299236 TGTCCCGAATGACCACTATGAAA
1 TGTCCCGAAGGACCACTATGAAA
299259 TGTCCCGAAGGACCACTATG
1 TGTCCCGAAGGACCACTATG
299279 TCCCAAAGGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
TGTCCCGAAGGACCACTATGAAA
Found at i:299281 original size:18 final size:18
Alignment explanation
Indices: 299258--299293 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
299248 CCACTATGAA
*
299258 ATGTCCCGAAGGACCACT
1 ATGTCCCAAAGGACCACT
299276 ATGTCCCAAAGGACCACT
1 ATGTCCCAAAGGACCACT
299294 GATAATCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (18 bp):
ATGTCCCAAAGGACCACT
Found at i:306389 original size:29 final size:31
Alignment explanation
Indices: 306318--306390 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
306308 TGGCATAACA
*
306318 AAAATTTAAAAGACTAGAATAATAAAAATAT
1 AAAATTTAAAAGACCAGAATAATAAAAATAT
* *
306349 AAAATTT-GAAGACCA-AATAATACAAA-AT
1 AAAATTTAAAAGACCAGAATAATAAAAATAT
*
306377 GAAATTTAAAAGAC
1 AAAATTTAAAAGAC
306391 TAAAATGGCA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.22
29 15 0.42
30 6 0.17
31 7 0.19
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (31 bp):
AAAATTTAAAAGACCAGAATAATAAAAATAT
Found at i:307971 original size:3 final size:3
Alignment explanation
Indices: 307963--307997 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
307953 TGTAAATATA
307963 AAT AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
307998 CTTTAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:307976 original size:17 final size:17
Alignment explanation
Indices: 307963--307997 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
307953 TGTAAATATA
307963 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
307980 AATAATAATAATAATAAT
1 AATAATAATAA-AATAAT
307998 CTTTAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:319349 original size:17 final size:16
Alignment explanation
Indices: 319307--319349 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
319297 AGTAAAAGTG
319307 TAAAATATATTAAATAA
1 TAAAATA-ATTAAATAA
*
319324 TAAATATAATTATATAA
1 TAAA-ATAATTAAATAA
319341 TTAAAATAA
1 -TAAAATAA
319350 AAAAGAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAATAATTAAATAA
Found at i:322639 original size:105 final size:105
Alignment explanation
Indices: 322503--323195 Score: 1125
Period size: 105 Copynumber: 6.6 Consensus size: 105
322493 TTTGTCGGAT
* * * *
322503 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
322568 GGAATAGGCTCTTCTCATTATGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
322608 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
** *
322673 GGAACATACTCTTCTCATTACGAACCTTCTCCTTTAAGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
322713 GAGTTCTTCTCATTATGAACTCTTCTGAAAATATTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* *
322778 GGAAGATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
322818 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTGACCTCCTTCTGCGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
322883 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
322923 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
* * *
322988 TGAACAAGTTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
323028 GAGTTCTTTTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
*
323093 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAT
66 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* * *
323133 GAGTTATTCTCATTATGAACTCTTCTGGAAATGTTGGCTCACCTCCTTCTGTGGTGGATTTGA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGA
323196 TTGTTGTTAA
Statistics
Matches: 554, Mismatches: 34, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 554 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:324129 original size:8 final size:8
Alignment explanation
Indices: 324118--324185 Score: 90
Period size: 8 Copynumber: 9.0 Consensus size: 8
324108 TTCTTTTTTC
324118 TTTTCATT
1 TTTTCATT
324126 TTTTCATT
1 TTTTCATT
*
324134 TTTTTATT
1 TTTTCATT
324142 TTTT-ATT
1 TTTTCATT
324149 TTTT-ATT
1 TTTTCATT
324156 TTTT-A-T
1 TTTTCATT
*
324162 TTTTCACT
1 TTTTCATT
324170 TTTTCATT
1 TTTTCATT
324178 TTTTCATT
1 TTTTCATT
324186 CATTCTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
6 5 0.09
7 16 0.29
8 35 0.62
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCATT
Found at i:324135 original size:14 final size:15
Alignment explanation
Indices: 324105--324185 Score: 82
Period size: 14 Copynumber: 5.6 Consensus size: 15
324095 CGAACCCTCC
324105 TTTTTC-TTTTTTC-
1 TTTTTCATTTTTTCA
324118 -TTTTCATTTTTTCA
1 TTTTTCATTTTTTCA
*
324132 TTTTTTTATTTTTT-A
1 -TTTTTCATTTTTTCA
*
324147 TTTTTTATTTTTT-A
1 TTTTTCATTTTTTCA
*
324161 TTTTTCACTTTTTCA
1 TTTTTCATTTTTTCA
324176 TTTTTTCATT
1 -TTTTTCATT
324186 CATTCTTTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 9
0.82 0.06 0.13
Matches are distributed among these distances:
12 5 0.09
13 7 0.12
14 25 0.43
15 2 0.03
16 19 0.33
ACGTcount: A:0.11, C:0.10, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTCATTTTTTCA
Found at i:324151 original size:36 final size:36
Alignment explanation
Indices: 324105--324181 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
324095 CGAACCCTCC
* * * *
324105 TTTTTCTTTTTTCTTTTCAT-TTTTTCATTTTTTTAT
1 TTTTTATTTTTTATTTT-ATATTTTTCACTTTTTCAT
*
324141 TTTTTATTTTTTATTTTTTATTTTTCACTTTTTCAT
1 TTTTTATTTTTTATTTTATATTTTTCACTTTTTCAT
324177 TTTTT
1 TTTTT
324182 CATTCATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.10, C:0.09, G:0.00, T:0.81
Consensus pattern (36 bp):
TTTTTATTTTTTATTTTATATTTTTCACTTTTTCAT
Found at i:324195 original size:44 final size:43
Alignment explanation
Indices: 324105--324196 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 43
324095 CGAACCCTCC
* * * **
324105 TTTTTCTTTTTTCTTTTCATTTTTTCATTTTTTTATTTTTTAT
1 TTTTTATTTTTTCTTTTCACTTTTTCATTTTTTCATTCATTAT
* *
324148 TTTTTATTTTTTATTTTTCACTTTTTCATTTTTTCATTCATTCT
1 TTTTTATTTTTT-CTTTTCACTTTTTCATTTTTTCATTCATTAT
324192 TTTTT
1 TTTTT
324197 TTTCAAGCAT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 11 0.27
44 30 0.73
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (43 bp):
TTTTTATTTTTTCTTTTCACTTTTTCATTTTTTCATTCATTAT
Found at i:355104 original size:16 final size:16
Alignment explanation
Indices: 355074--355107 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 16
355064 AAGATATATT
355074 AAAATAAAATAAATAA
1 AAAATAAAATAAATAA
355090 AAAATGAAAATAATATAA
1 AAAAT-AAAATAA-ATAA
355108 TAATACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (16 bp):
AAAATAAAATAAATAA
Found at i:355831 original size:64 final size:64
Alignment explanation
Indices: 355762--355905 Score: 168
Period size: 64 Copynumber: 2.2 Consensus size: 64
355752 TCAAATTCCT
*
355762 TAAAAAAAGCTAAAACA-TCTTAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC
1 TAAAAAAAGATAAAACATTC-TAAATCCTAATTAAAACAC-TAAAACCTATTTAAACTAAAATAC
355825 C
64 C
* * * * * *
355826 TAAAAAATA-ATATAATATTCTAAATCTTAATTATAATACTAAAACCTATTTAAACTTAAATACC
1 TAAAAAA-AGATAAAACATTCTAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACC
355890 TAAAACAAAGATAAAA
1 TAAAA-AAAGATAAAA
355906 TATAAAAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
63 5 0.07
64 52 0.78
65 10 0.15
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (64 bp):
TAAAAAAAGATAAAACATTCTAAATCCTAATTAAAACACTAAAACCTATTTAAACTAAAATACC
Found at i:357359 original size:21 final size:21
Alignment explanation
Indices: 357333--357387 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
357323 TTTTACACTG
357333 AGTGTATCGATACCCTTTGAT
1 AGTGTATCGATACCCTTTGAT
*
357354 AGTGTACCGATACCCTTTGAT
1 AGTGTATCGATACCCTTTGAT
357375 AGTGT-TCCGATAC
1 AGTGTAT-CGATAC
357388 ACTTAGTCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (21 bp):
AGTGTATCGATACCCTTTGAT
Done.