Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012630.1 Kokia drynarioides strain JFW-HI SEQ_127639, 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: 279347
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:584 original size:13 final size:13
Alignment explanation
Indices: 563--596 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
553 GTGAGCACTG
*
563 ATGTTAGTGCAAA
1 ATGTCAGTGCAAA
*
576 ATGTCAGTGCAAT
1 ATGTCAGTGCAAA
589 ATGTCAGT
1 ATGTCAGT
597 TCTGCACACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
ATGTCAGTGCAAA
Found at i:2982 original size:24 final size:24
Alignment explanation
Indices: 2938--2990 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2928 CAATTGCCGA
* *
2938 TGGTGGTAGGAGGATGTCGACACT
1 TGGTGGTAGGAAGATGTCGACAAT
*
2962 TGGTGGTGGGAAGAT-TGCGACAAT
1 TGGTGGTAGGAAGATGT-CGACAAT
2986 TGGTG
1 TGGTG
2991 TTTGGAGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.21, C:0.09, G:0.43, T:0.26
Consensus pattern (24 bp):
TGGTGGTAGGAAGATGTCGACAAT
Found at i:14361 original size:58 final size:59
Alignment explanation
Indices: 14291--14407 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 59
14281 GAAATAAAGA
*
14291 AATATTGCCTCGATTTTAAATATTTGTATTTTGGAGAAAAATT-TAAAATGACTTTAAT
1 AATATTGCCTCGATTTTAAATATTTGTATTTTGGAGAAAAATTAAAAAATGACTTTAAT
14349 AATATTGCCTCGATTTTAAATATTTGTATTTTGGAGAAAAATTAAAAAATGACTTTAAT
1 AATATTGCCTCGATTTTAAATATTTGTATTTTGGAGAAAAATTAAAAAATGACTTTAAT
14408 TAAAATATAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
58 43 0.75
59 14 0.25
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (59 bp):
AATATTGCCTCGATTTTAAATATTTGTATTTTGGAGAAAAATTAAAAAATGACTTTAAT
Found at i:14695 original size:29 final size:29
Alignment explanation
Indices: 14663--14872 Score: 172
Period size: 29 Copynumber: 7.2 Consensus size: 29
14653 AGTTTCGAAG
* * * *
14663 AGTTTAGGGTCAAAATGTAATTTTTAGAA
1 AGTTTAGGGTTAAAATATAATTTTAAAAA
* * * * ***
14692 AGTTAAAGGTTAAAATGTGATTTT-TGGA
1 AGTTTAGGGTTAAAATATAATTTTAAAAA
* * *
14720 AGTTCGAGGGTAAAAATATGATTTTAAAAA
1 AGTT-TAGGGTTAAAATATAATTTTAAAAA
*
14750 AATTTAGGGGTTAAAATATAATTTTAAAAA
1 AGTTTA-GGGTTAAAATATAATTTTAAAAA
* *
14780 AATTAAGGGTTAAAATATAATTTTAAAAA
1 AGTTTAGGGTTAAAATATAATTTTAAAAA
*
14809 AGTTTAGGGATCAAAATATAATTTT-AAAA
1 AGTTTAGGG-TTAAAATATAATTTTAAAAA
* ** *
14838 AGATCCGAGGTTAAAATGTAATTTTAAAAA
1 AGTTTAG-GGTTAAAATATAATTTTAAAAA
14868 AGTTT
1 AGTTT
14873 GTTATCAAAA
Statistics
Matches: 147, Mismatches: 28, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
28 6 0.04
29 88 0.60
30 53 0.36
ACGTcount: A:0.45, C:0.02, G:0.17, T:0.35
Consensus pattern (29 bp):
AGTTTAGGGTTAAAATATAATTTTAAAAA
Found at i:14789 original size:59 final size:59
Alignment explanation
Indices: 14726--14890 Score: 181
Period size: 59 Copynumber: 2.8 Consensus size: 59
14716 TGGAAGTTCG
* * *
14726 AGGGTAAAAATATGATTTTAAAAAAATTTAGGGGTTAAAATATAATTTTAAAAAAATTA
1 AGGGTAAAAATATAATTTTAAAAAAATTTAGGGATCAAAATATAATTTTAAAAAAATTA
* * * *
14785 AGGGTTAAAATATAATTTTAAAAAAGTTTAGGGATCAAAATATAATTTTAAAAAGA-TC
1 AGGGTAAAAATATAATTTTAAAAAAATTTAGGGATCAAAATATAATTTTAAAAAAATTA
* * * * ** *
14843 CGAGGTTAAAATGTAATTTTAAAAAAGTTT-GTTATCAAAATATGATTT
1 AG-GGTAAAAATATAATTTTAAAAAAATTTAGGGATCAAAATATAATTT
14891 CTAGAAAATT
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
58 17 0.18
59 76 0.82
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.35
Consensus pattern (59 bp):
AGGGTAAAAATATAATTTTAAAAAAATTTAGGGATCAAAATATAATTTTAAAAAAATTA
Found at i:14882 original size:29 final size:29
Alignment explanation
Indices: 14732--14890 Score: 106
Period size: 29 Copynumber: 5.4 Consensus size: 29
14722 TTCGAGGGTA
* * * * *
14732 AAAATATGATTTTAAAAAAATTTAGGGGTT
1 AAAATATAATTTTAAAAAAGTTT-GAGATC
* * * *
14762 AAAATATAATTTTAAAAAA-ATTAAGGGTT
1 AAAATATAATTTTAAAAAAGTTTGA-GATC
*
14791 AAAATATAATTTTAAAAAAGTTTAGGGATC
1 AAAATATAATTTTAAAAAAGTTT-GAGATC
** * *
14821 AAAATATAATTTT-AAAAAGATCCGAGGTT
1 AAAATATAATTTTAAAAAAG-TTTGAGATC
* **
14850 AAAATGTAATTTTAAAAAAGTTTGTTATC
1 AAAATATAATTTTAAAAAAGTTTGAGATC
*
14879 AAAATATGATTT
1 AAAATATAATTT
14891 CTAGAAAATT
Statistics
Matches: 101, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
29 59 0.58
30 42 0.42
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTAAAAAAGTTTGAGATC
Found at i:16229 original size:6 final size:6
Alignment explanation
Indices: 16218--16302 Score: 61
Period size: 6 Copynumber: 14.8 Consensus size: 6
16208 CCTTTTTTAA
* * * * *
16218 TTAAAT TTAAAT TTAAA- TTAAAT TTAAAC TCAAA- ATCAGT TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * * *
16264 TTAAA- ATAAAT TTAAAC TTAAA- ATAAAT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
16303 ATTAGGTTCA
Statistics
Matches: 59, Mismatches: 16, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
5 14 0.24
6 45 0.76
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:16238 original size:17 final size:17
Alignment explanation
Indices: 16219--16304 Score: 109
Period size: 17 Copynumber: 5.1 Consensus size: 17
16209 CTTTTTTAAT
*
16219 TAAATTTAAATTTAAAT
1 TAAATTTAAATTTAAAA
* *
16236 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
16253 TCAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
16270 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
16287 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
16304 T
1 T
16305 TAGGTTCAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:16261 original size:34 final size:34
Alignment explanation
Indices: 16219--16304 Score: 127
Period size: 34 Copynumber: 2.5 Consensus size: 34
16209 CTTTTTTAAT
*
16219 TAAATTTAAATTTAAATTAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAATAAATTTAAACTCAAAA
* * *
16253 TCAGTTTAAATTTAAAATAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAATAAATTTAAACTCAAAA
*
16287 TAAATTAAAATTTAAAAT
1 TAAATTTAAATTTAAAAT
16305 TAGGTTCAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATAAATTTAAACTCAAAA
Found at i:16971 original size:117 final size:114
Alignment explanation
Indices: 16783--17395 Score: 454
Period size: 117 Copynumber: 5.2 Consensus size: 114
16773 GATGGCTGCA
* * * * *
16783 ATCTGCCCTTGGCTTGGGGTAAAAGATTGGCTGATGGTGATTTGTCCCAGGCTCGGGGAAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGA-T--CGGATGGTGATTTGCCCCAGGCTCGGGGTAAGAGA
* * *
16848 TTGGATGGTTGTAATCTGCCCCAGGCTCGAGGTAAGAGATTGATTGATGGTG
63 TCGGATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGGTG
* * * *
16900 ATCTGCCCTAGGCTCGAGGTAAGAGATCGGATGGCTGCAATTTGCCCCAAGCTCAGGGTAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGG-TG--ATTTGCCCCAGGCTCGGGGTAAGAGA
* *
16965 TCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTG-TCTGATGGTG
63 TCGGATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGAT-TGATGGTG
* * * * * * * * *
17017 ATCTTCCCCAAGCTCGAGGTAAAAGATCGAATGGCTTCGATCTGCCCTAGGCTTGGGGCAAGAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGG--T-GATTTGCCCCAGGCTCGGGGTAAGAGA
* * * *
17082 TTGGTTAATGG-TG--ATCTGCCCTAGGCTCGGGGTAA-A-A-T-ATCGGATGGCTTCA
63 TCGG---ATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGAT-TGATGG--T-G
* * * * *** * * *
17134 ATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTGATCTGCTTTAGACTCGAGGTAAAAGA
1 ATCTGCCCTAGGCTCGGGGTAAAAGA-T--CGGATGGTGATTTGCCCCAGGCTCGGGGTAAGAGA
**
17199 TCGGATGGCTT-CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
63 TCGGATGG-TTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGGTG
** * *
17251 ATCTGCTTTAGGCTCGGGGTAAAAGATTGGCTGATGGTGATCTT-CCCCAGGCTCGGGGTAAAAG
1 ATCTGCCCTAGGCTCGGGGTAAAAGA-T--CGGATGGTGAT-TTGCCCCAGGCTCGGGGTAAGAG
* * * * * * * **
17315 ATCGAATGGCTCCAATTTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
62 ATCGGATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGGTG
*
17368 ATCTGTCCTAGGCTCGGGGTAAAAGATC
1 ATCTGCCCTAGGCTCGGGGTAAAAGATC
17396 AAATGACTGT
Statistics
Matches: 401, Mismatches: 69, Indels: 55
0.76 0.13 0.10
Matches are distributed among these distances:
114 19 0.05
115 3 0.01
116 7 0.02
117 347 0.87
118 6 0.01
119 4 0.01
120 15 0.04
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (114 bp):
ATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGTGATTTGCCCCAGGCTCGGGGTAAGAGATCG
GATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGATTGATGGTG
Found at i:17059 original size:156 final size:154
Alignment explanation
Indices: 16899--17256 Score: 432
Period size: 156 Copynumber: 2.3 Consensus size: 154
16889 GATTGATGGT
* * *
16899 GATCTGCCCTAGGCTCGAGGTAAGAGATCGG-ATGGCTGCAATTTGCCCCAAGCTCAGGGTAAGA
1 GATCTGCCCTAGGCTCGGGGTAAGAGATCGGTATGG-TG--ATCTGCCCCAAGCTCAGGGTAAAA
* * *
16963 GATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGTCTGATGGTGATCTTCCCCAA
63 GATCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTGATC-TCCCCAA
17028 G-CTCGAGGTAAAAGATCGAATGGCTTC
127 GACTCGAGGTAAAAGATCGAATGGCTTC
* * * * * * *
17055 GATCTGCCCTAGGCTTGGGGCAAGAGATTGGTTAATGGTGATCTGCCCTAGGCTCGGGGTAAAAT
1 GATCTGCCCTAGGCTCGGGGTAAGAGATCGG-T-ATGGTGATCTGCCCCAAGCTCAGGGTAAAAG
* * ***
17120 ATCGGATGGCTTCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTGATCTGCTTTAGA
64 ATCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTGATCTCCCCAAGA
*
17185 CTCGAGGTAAAAGATCGGATGGCTTC
129 CTCGAGGTAAAAGATCGAATGGCTTC
* * *
17211 AATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTGC
1 GATCTGCCCTAGGCTCGGGGTAAGAGATCGG-T-ATGGTGATCTGC
17257 TTTAGGCTCG
Statistics
Matches: 173, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
155 4 0.02
156 163 0.94
158 2 0.01
159 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (154 bp):
GATCTGCCCTAGGCTCGGGGTAAGAGATCGGTATGGTGATCTGCCCCAAGCTCAGGGTAAAAGAT
CGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTGATCTCCCCAAGACT
CGAGGTAAAAGATCGAATGGCTTC
Found at i:17263 original size:156 final size:156
Alignment explanation
Indices: 16950--17311 Score: 462
Period size: 156 Copynumber: 2.3 Consensus size: 156
16940 TTTGCCCCAA
* * * * *
16950 GCTCAGGGTAAGAGATCGGATGGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGTCTGATGG
1 GCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGG
* * * *
17015 TGATCTTCCCCAAGCTCGAGGTAAAAGATCGAATGGCTTCGATCTGCCCTAGGCTTGGGGCAAGA
66 TGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGCAAGA
*
17080 GATTGGTTAATGGTGATCTGCCCTAG
131 GATTGGCTAATGGTGATCTGCCCTAG
* *
17106 GCTCGGGGTAAAATATCGGATGGCTTCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGG
1 GCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGG
*** * *
17171 TGATCTG-CTTTAGACTCGAGGTAAAAGATCGGATGGCTTCAATCTGCCCCAGGCTCGGGGTAAG
66 TGATCTGCCCCAAG-CTCGAGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGCAAG
* **
17235 AGATTGGCTGATGGTGATCTGCTTTAG
130 AGATTGGCTAATGGTGATCTGCCCTAG
* *
17262 GCTCGGGGTAAAAGATTGGCTGATGG-TG--ATCTTCCCCAGGCTCGGGGTAA
1 GCTCGGGGTAAAAGA-T--CGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAA
17312 AAGATCGAAT
Statistics
Matches: 178, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
155 3 0.02
156 167 0.94
157 1 0.01
158 1 0.01
159 6 0.03
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (156 bp):
GCTCGGGGTAAAAGATCGGATGGCTGCAATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGG
TGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGCTTCAATCTGCCCCAGGCTCGGGGCAAGA
GATTGGCTAATGGTGATCTGCCCTAG
Found at i:17306 original size:39 final size:38
Alignment explanation
Indices: 16783--17394 Score: 331
Period size: 39 Copynumber: 15.7 Consensus size: 38
16773 GATGGCTGCA
** *
16783 ATCTGCCCTTGGCTTGGGGTAAAAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATT-GCTGATGGTG
* *
16822 ATTTGTCCCAGGCTCGGGG-AAAGAGATTG--GATGGTTG
1 ATCTGCCCCAGGCTCGGGGTAAA-AGATTGCTGATGG-TG
* * *
16859 TAATCTGCCCCAGGCTCGAGGTAAGAGATTGATTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAAAGATTG-CTGATGGTG
* * * *
16900 ATCTGCCCTAGGCTCGAGGTAAGAGA-T-CGGATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTGATGG-TG
* * * * *
16937 CAATTTGCCCCAAGCTCAGGGTAAGAGA-T-CGGATGGCTG
1 --ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTGATGG-TG
* *
16976 CAATCTGCCCTAGGCTCGGGGTAAGAGATTGTCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAAAGATTG-CTGATGGTG
* * *
17017 ATCTTCCCCAAGCTCGAGGTAAAAGA-T-C-GAATGGCTTCG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTG-ATGG--T-G
* * * * * *
17056 ATCTGCCCTAGGCTTGGGGCAAGAGATTGGTTAATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATT-GCTGATGGTG
* * * *
17095 ATCTGCCCTAGGCTCGGGGTAAAATA-T-CGGATGGCTTCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTGATGG--T-G
* *
17134 ATCTGCCCCAGGCTCGGGGTAAGAGACTGACTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTG-CTGATGGTG
*** * * * *
17173 ATCTGCTTTAGACTCGAGGTAAAAGA-T-CGGATGGCTTCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTGATGG--T-G
*
17212 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATT-GCTGATGGTG
***
17251 ATCTGCTTTAGGCTCGGGGTAAAAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATT-GCTGATGGTG
* *
17290 ATCTTCCCCAGGCTCGGGGTAAAAGA-T-C-GAATGGCTCCA
1 ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTG-ATGG-T--G
* * * * *
17329 ATTTACCCCAAGCTCGAGGTAAGAGATTGGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAAAGATT-GCTGATGGTG
* *
17368 ATCTGTCCTAGGCTCGGGGTAAAAGAT
1 ATCTGCCCCAGGCTCGGGGTAAAAGAT
17395 CAAATGACTG
Statistics
Matches: 444, Mismatches: 87, Indels: 84
0.72 0.14 0.14
Matches are distributed among these distances:
35 2 0.00
36 30 0.07
37 5 0.01
38 12 0.03
39 347 0.78
40 10 0.02
41 5 0.01
42 32 0.07
43 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (38 bp):
ATCTGCCCCAGGCTCGGGGTAAAAGATTGCTGATGGTG
Found at i:17424 original size:78 final size:78
Alignment explanation
Indices: 17268--17433 Score: 208
Period size: 78 Copynumber: 2.1 Consensus size: 78
17258 TTAGGCTCGG
* * * *
17268 GGTAAAAGATTGGCTGATGGTGATCTTCCCCAGGCTCGGGGTAAAAGATCGAATGGCTCCAATTT
1 GGTAAGAGATTGGCTGATGGTGATCTTCCCCAGGCTCGGGGTAAAAGATCAAATGACTCCAATCT
*
17333 ACCCCAAGCTCGA
66 ACCCCAAGATCGA
* ***
17346 GGTAAGAGATTGGCTGATGGTGATCTGT-CCTAGGCTCGGGGTAAAAGATCAAATGACTGTGATC
1 GGTAAGAGATTGGCTGATGGTGATCT-TCCCCAGGCTCGGGGTAAAAGATCAAATGACTCCAATC
* * *
17410 TGCCTCATGATCGA
65 TACCCCAAGATCGA
17424 GGTAAGAGAT
1 GGTAAGAGAT
17434 CGAAATCTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
78 74 0.99
79 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (78 bp):
GGTAAGAGATTGGCTGATGGTGATCTTCCCCAGGCTCGGGGTAAAAGATCAAATGACTCCAATCT
ACCCCAAGATCGA
Found at i:18704 original size:10 final size:10
Alignment explanation
Indices: 18691--18789 Score: 80
Period size: 10 Copynumber: 9.9 Consensus size: 10
18681 TTTCCTTTTC
*
18691 TTTTTCCTC-
1 TTTTTCTTCT
18700 TTTTT-TTCT
1 TTTTTCTTCT
*
18709 TTTTTTTTC-
1 TTTTTCTTCT
18718 TTTTTCTTCT
1 TTTTTCTTCT
18728 TTTTTCTT-T
1 TTTTTCTTCT
*
18737 CTTTTTCTTTT
1 -TTTTTCTTCT
*
18748 TTCTTTTTTCCT
1 TT-TTTCTT-CT
*
18760 TTTTACTTCT
1 TTTTTCTTCT
*
18770 TTTTTCTTTT
1 TTTTTCTTCT
18780 ATTTTTCTTC
1 -TTTTTCTTC
18790 ATCGATTCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
8 2 0.03
9 19 0.26
10 31 0.42
11 18 0.25
12 3 0.04
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCTTCT
Found at i:18708 original size:17 final size:17
Alignment explanation
Indices: 18686--18779 Score: 88
Period size: 18 Copynumber: 5.5 Consensus size: 17
18676 CGACCTTTCC
*
18686 TTTTCTTTTTCCTCTTT
1 TTTTCTTTTTTCTCTTT
*
18703 TTTTCTTTTTTTTTCTTT
1 TTTTC-TTTTTTCTCTTT
18721 TTCTTCTTTTTTCT-TTCT
1 TT-TTCTTTTTTCTCTT-T
18739 TTTTC-TTTTT-TCTTT
1 TTTTCTTTTTTCTCTTT
* *
18754 TTTCCTTTTTACT-TCTT
1 TTTTCTTTTTTCTCT-TT
18771 TTTTCTTTT
1 TTTTCTTTT
18780 ATTTTTCTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
15 6 0.09
16 12 0.19
17 21 0.33
18 22 0.34
19 3 0.05
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTTCTCTTT
Found at i:18710 original size:27 final size:26
Alignment explanation
Indices: 18680--18788 Score: 111
Period size: 25 Copynumber: 4.3 Consensus size: 26
18670 TCACCTCGAC
*
18680 CTTTCCTTTTCTTTTTCCTCTTTTTTT
1 CTTTCTTTTTCTTTTT-CTCTTTTTTT
*
18707 CTTTTTTTTTCTTTTTCT-TCTTTTTT
1 CTTTCTTTTTCTTTTTCTCT-TTTTTT
*
18733 CTTTCTTTTTCTTTTT-TCTTTTTTC
1 CTTTCTTTTTCTTTTTCTCTTTTTTT
* *
18758 CTTT-TTACTTCTTTTT-TCTTTTATT
1 CTTTCTT-TTTCTTTTTCTCTTTTTTT
18783 -TTTCTT
1 CTTTCTT
18789 CATCGATTCT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
24 5 0.07
25 28 0.39
26 24 0.34
27 14 0.20
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (26 bp):
CTTTCTTTTTCTTTTTCTCTTTTTTT
Found at i:18713 original size:7 final size:7
Alignment explanation
Indices: 18686--18779 Score: 72
Period size: 7 Copynumber: 13.3 Consensus size: 7
18676 CGACCTTTCC
18686 TTTTCTT
1 TTTTCTT
*
18693 TTTCCTCT
1 TTTTCT-T
18701 TTTT-TT
1 TTTTCTT
*
18707 CTTT-TT
1 TTTTCTT
18713 TTTTC-T
1 TTTTCTT
18719 TTTTCTT
1 TTTTCTT
18726 CTTTT-TT
1 -TTTTCTT
*
18733 CTTTC-T
1 TTTTCTT
18739 TTTTCTT
1 TTTTCTT
18746 TTTTCTT
1 TTTTCTT
18753 TTTTCCTTT
1 TTTT-C-TT
18762 TTACTTCTT
1 TT--TTCTT
18771 TTTTCTT
1 TTTTCTT
18778 TT
1 TT
18780 ATTTTTCTTC
Statistics
Matches: 71, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 23 0.32
7 28 0.39
8 9 0.13
9 8 0.11
10 1 0.01
11 2 0.03
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:18769 original size:42 final size:40
Alignment explanation
Indices: 18698--18789 Score: 125
Period size: 42 Copynumber: 2.3 Consensus size: 40
18688 TTCTTTTTCC
18698 TCTTTTT-TTCTTTTTTTTTCTTTTTCTTCTTTTTTC-TT
1 TCTTTTTCTTCTTTTTTTTTCTTTTTCTTCTTTTTTCTTT
*
18736 TCTTTTTCTTTTTTCTTTTTTCCTTTTTACTTCTTTTTTCTTT
1 TCTTTTTCTTCTTT-TTTTTT-CTTTTT-CTTCTTTTTTCTTT
*
18779 TATTTTTCTTC
1 TCTTTTTCTTC
18790 ATCGATTCTG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
38 7 0.15
39 5 0.11
40 6 0.13
41 6 0.13
42 11 0.24
43 11 0.24
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (40 bp):
TCTTTTTCTTCTTTTTTTTTCTTTTTCTTCTTTTTTCTTT
Found at i:22785 original size:18 final size:19
Alignment explanation
Indices: 22749--22785 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22739 TATCTTCCAC
22749 TCTATCAAGAAATCTGTCT
1 TCTATCAAGAAATCTGTCT
*
22768 TCTATGAAGAAA-CTGTCT
1 TCTATCAAGAAATCTGTCT
22786 ATTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (19 bp):
TCTATCAAGAAATCTGTCT
Found at i:24299 original size:29 final size:28
Alignment explanation
Indices: 24267--24367 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 28
24257 AGTTTCGAAG
*
24267 AGTTTGGGGTCAAAATGTAATTTTTGGAA
1 AGTTTGGGGTAAAAATGTAATTTTTGG-A
* * * * *
24296 AGTTCGAGGTGAATATGTGATTTTTGGA
1 AGTTTGGGGTAAAAATGTAATTTTTGGA
* * **
24324 AGTTTAGGGGGTAAAAATGTGATTCTTATA
1 AGTTT--GGGGTAAAAATGTAATTTTTGGA
24354 AGTTTAGGGGTAAA
1 AGTTT-GGGGTAAA
24368 TATATGATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
28 5 0.09
29 30 0.53
30 22 0.39
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.37
Consensus pattern (28 bp):
AGTTTGGGGTAAAAATGTAATTTTTGGA
Found at i:24346 original size:30 final size:29
Alignment explanation
Indices: 24267--24400 Score: 94
Period size: 30 Copynumber: 4.6 Consensus size: 29
24257 AGTTTCGAAG
* *
24267 AGTTT-GGGGTCAAAATGTAATTTTTGGAA
1 AGTTTAGGGGTAAAAATGTGATTTTTGG-A
* * * *
24296 AG-TTCGAGGTGAATATGTGATTTTTGGA
1 AGTTTAGGGGTAAAAATGTGATTTTTGGA
* **
24324 AGTTTAGGGGGTAAAAATGTGATTCTTATA
1 AGTTTA-GGGGTAAAAATGTGATTTTTGGA
* *
24354 AGTTTAGGGGTAAATATATGA-TTTTGGAAA
1 AGTTTAGGGGTAAAAATGTGATTTTTGG--A
* *
24384 AGTTTAAGGGTCAAAAT
1 AGTTTAGGGGTAAAAAT
24401 ATAATTCGAG
Statistics
Matches: 81, Mismatches: 19, Indels: 9
0.74 0.17 0.08
Matches are distributed among these distances:
28 8 0.10
29 35 0.43
30 38 0.47
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (29 bp):
AGTTTAGGGGTAAAAATGTGATTTTTGGA
Found at i:24484 original size:59 final size:61
Alignment explanation
Indices: 24409--24557 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 61
24399 ATATAATTCG
* *
24409 AGGGTTAAAATGTAATTTTAGAAAAGTTTGGGA-ATCAAAATGTAATTTTAGAAAAATT-A
1 AGGGTTAAAATATAATTTTAGAAAAATTTGGGAGATCAAAATGTAATTTTAGAAAAATTGA
* * * *
24468 AGGGTTAAAATATAATTTTAGAAAAATTTAGGAGGTCAAAATGTAATTTTGGAAATATTGA
1 AGGGTTAAAATATAATTTTAGAAAAATTTGGGAGATCAAAATGTAATTTTAGAAAAATTGA
* *
24529 A-GGTCAAAATATAATTTTAAAAAAATTTG
1 AGGGTTAAAATATAATTTTAGAAAAATTTG
24558 TTGTCAAAAT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
59 30 0.38
60 47 0.59
61 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.17, T:0.34
Consensus pattern (61 bp):
AGGGTTAAAATATAATTTTAGAAAAATTTGGGAGATCAAAATGTAATTTTAGAAAAATTGA
Found at i:24563 original size:29 final size:29
Alignment explanation
Indices: 24415--24585 Score: 152
Period size: 29 Copynumber: 5.8 Consensus size: 29
24405 TTCGAGGGTT
* *
24415 AAAATGTAATTTTAGAAAAGTTTG-GGAATC
1 AAAATATAATTTTAGAAAAATTTGAGG--TC
* * *
24445 AAAATGTAATTTTAGAAAAA-TTAAGGGTT
1 AAAATATAATTTTAGAAAAATTTGA-GGTC
24474 AAAATATAATTTTAGAAAAATTTAGGAGGTC
1 AAAATATAATTTTAGAAAAATTT--GAGGTC
* * *
24505 AAAATGTAATTTTGGAAATA-TTGAAGGTC
1 AAAATATAATTTTAGAAAAATTTG-AGGTC
* **
24534 AAAATATAATTTTAAAAAAATTTGTTGTC
1 AAAATATAATTTTAGAAAAATTTGAGGTC
24563 AAAATATAATTTCT-GAAAAATTT
1 AAAATATAATTT-TAGAAAAATTT
24586 AGAGACCTCC
Statistics
Matches: 117, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.01
29 66 0.56
30 27 0.23
31 22 0.19
32 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.36
Consensus pattern (29 bp):
AAAATATAATTTTAGAAAAATTTGAGGTC
Found at i:25935 original size:17 final size:17
Alignment explanation
Indices: 25913--25998 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
25903 TTTTCCTAAT
25913 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
25930 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
* *
25947 TAAGTTTAAATTTTAAA
1 TAAATTTAAATTTAAAA
*
25964 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
25981 T-AATTTAAAATTTAAAA
1 TAAATTT-AAATTTAAAA
25998 T
1 T
25999 TTAAAATTTA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
16 5 0.09
17 53 0.91
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:25956 original size:34 final size:33
Alignment explanation
Indices: 25915--25998 Score: 132
Period size: 34 Copynumber: 2.5 Consensus size: 33
25905 TTCCTAATTA
25915 AATTTAAATTTAAAATAAATTTAAACTCAAAAT
1 AATTTAAATTTAAAATAAATTTAAACTCAAAAT
* *
25948 AAGTTTAAATTTTAAATAAATTTAAACTTAAAAT
1 AA-TTTAAATTTAAAATAAATTTAAACTCAAAAT
25982 AATTTAAAATTTAAAAT
1 AATTT-AAATTTAAAAT
25999 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.11
34 41 0.89
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (33 bp):
AATTTAAATTTAAAATAAATTTAAACTCAAAAT
Found at i:25964 original size:7 final size:7
Alignment explanation
Indices: 25965--26013 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
25955 AATTTTAAAT
25965 AAATTTA
1 AAATTTA
* *
25972 AACTTAA
1 AAATTTA
25979 AATAATTTA
1 AA-A-TTTA
25988 AAATTTA
1 AAATTTA
25995 AAATTTA
1 AAATTTA
26002 AAATTTA
1 AAATTTA
26009 AAATT
1 AAATT
26014 GAGTTCAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
7 30 0.83
8 1 0.03
9 5 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:37032 original size:17 final size:17
Alignment explanation
Indices: 36997--37038 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
36987 CTCTTTTGAC
*
36997 CTTTAACCTTCTATCTT
1 CTTTAACCTTCTATATT
37014 CTTTAACCTT-TCATATT
1 CTTTAACCTTCT-ATATT
37031 CTTGTAAC
1 CTT-TAAC
37039 TACTTTTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.77
18 4 0.18
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (17 bp):
CTTTAACCTTCTATATT
Found at i:37706 original size:17 final size:18
Alignment explanation
Indices: 37681--37714 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
37671 AATATTTTTA
*
37681 AAATTATTAA-AAATCAT
1 AAATAATTAACAAATCAT
37698 AAATAATTAACAAATCA
1 AAATAATTAACAAATCA
37715 AATTCTTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAATTAACAAATCAT
Found at i:37985 original size:10 final size:10
Alignment explanation
Indices: 37970--38047 Score: 56
Period size: 10 Copynumber: 7.7 Consensus size: 10
37960 ATTAGTAATT
37970 TTTTTAATAA
1 TTTTTAATAA
37980 TTTTTACA-AA
1 TTTTTA-ATAA
*
37990 TTTTAAAT-A
1 TTTTTAATAA
*
37999 TTGTTTTATAA
1 TT-TTTAATAA
38010 TTTTTAATAA
1 TTTTTAATAA
*
38020 CTTTTTTTATAA
1 --TTTTTAATAA
38032 -TTTTAA-AA
1 TTTTTAATAA
38040 TATTTTAA
1 T-TTTTAA
38048 ACAAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
8 2 0.04
9 9 0.17
10 30 0.56
11 4 0.07
12 9 0.17
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:38138 original size:21 final size:21
Alignment explanation
Indices: 38087--38146 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
38077 TTTGAAATTT
*
38087 TAATTTTTTTA-ATAATTTAAA
1 TAATTTTTTTACA-ATTTTAAA
*
38108 T-ATATTTTTTACGATTTTAAA
1 TAAT-TTTTTTACAATTTTAAA
38129 TAATTTTTTTACAATTTT
1 TAATTTTTTTACAATTTT
38147 TGTGTTTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTTTTTACAATTTTAAA
Found at i:38576 original size:22 final size:22
Alignment explanation
Indices: 38551--38597 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
38541 TATATAGTAC
38551 TTGA-ATTTAACCTTTTTTTAAT
1 TTGATATTTAA-CTTTTTTTAAT
*
38573 TTGATATTTAATTTTTTTTAAT
1 TTGATATTTAACTTTTTTTAAT
38595 TTG
1 TTG
38598 GTACTCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (22 bp):
TTGATATTTAACTTTTTTTAAT
Found at i:38651 original size:32 final size:31
Alignment explanation
Indices: 38584--38672 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 31
38574 TGATATTTAA
*
38584 TTTTTTTTAATTTGGTACTCAAACTTAACAC
1 TTTTTTTTAATTTGGTACTTAAACTTAACAC
*
38615 TTTTTTTTAATTTGGTACTTAAACTTGACAC
1 TTTTTTTTAATTTGGTACTTAAACTTAACAC
*
38646 TTTTTTTTCAAGTTGGTACTTAAACTT
1 TTTTTTTT-AATTTGGTACTTAAACTT
38673 TTTGGGATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 37 0.69
32 17 0.31
ACGTcount: A:0.26, C:0.13, G:0.09, T:0.52
Consensus pattern (31 bp):
TTTTTTTTAATTTGGTACTTAAACTTAACAC
Found at i:39320 original size:18 final size:18
Alignment explanation
Indices: 39281--39323 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
39271 TTTTGGTTAA
*
39281 AATTAAATTAATCGATTG
1 AATTAATTTAATCGATTG
*
39299 AATTAATTTAATTCGGTT-
1 AATTAATTTAA-TCGATTG
39317 AATTAAT
1 AATTAAT
39324 CGATCAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (18 bp):
AATTAATTTAATCGATTG
Found at i:40572 original size:17 final size:17
Alignment explanation
Indices: 40552--40613 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
40542 GGAAGATAGA
40552 AGGTTAAAGGTCAAGGG
1 AGGTTAAAGGTCAAGGG
40569 AGGTT-AAGG--AAGATGG
1 AGGTTAAAGGTCAAG--GG
*
40585 AAGGTTAAAAGTCAAGGG
1 -AGGTTAAAGGTCAAGGG
40603 AGGTTAAAGGT
1 AGGTTAAAGGT
40614 TGAACATCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
14 3 0.08
16 6 0.16
17 20 0.54
18 5 0.14
20 3 0.08
ACGTcount: A:0.39, C:0.03, G:0.39, T:0.19
Consensus pattern (17 bp):
AGGTTAAAGGTCAAGGG
Found at i:40580 original size:34 final size:34
Alignment explanation
Indices: 40537--40609 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
40527 AATATGAAAA
*
40537 GTTAAGGAAGATAGAAGGTTAAAGGTCAAGGGAG
1 GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
*
40571 GTTAAGGAAGATGGAAGGTTAAAAGTCAAGGGAG
1 GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
40605 GTTAA
1 GTTAA
40610 AGGTTGAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.41, C:0.03, G:0.37, T:0.19
Consensus pattern (34 bp):
GTTAAGGAAGATAGAAGGTTAAAAGTCAAGGGAG
Found at i:50437 original size:33 final size:34
Alignment explanation
Indices: 50374--50447 Score: 114
Period size: 33 Copynumber: 2.2 Consensus size: 34
50364 AGACTATGAA
* *
50374 AGGTTAAGGAAGATAGAAGGTTAAAGGTCAAAGG
1 AGGTTAAGGAAGATAGAAAGTTAAAAGTCAAAGG
*
50408 AGGTTAAGGAAGAT-GAAAGTTAAAAGTCAAGGG
1 AGGTTAAGGAAGATAGAAAGTTAAAAGTCAAAGG
50441 AGGTTAA
1 AGGTTAA
50448 AGGTTGAACA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.45, C:0.03, G:0.34, T:0.19
Consensus pattern (34 bp):
AGGTTAAGGAAGATAGAAAGTTAAAAGTCAAAGG
Found at i:51507 original size:23 final size:24
Alignment explanation
Indices: 51476--51520 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
51466 TAAATCAGAA
51476 AAATATCTC-T-AGAGATTTTTTC
1 AAATATCTCTTCAGAGATTTTTTC
51498 AAATAATCTCTTCAGAGATTTTT
1 AAAT-ATCTCTTCAGAGATTTTT
51521 CAATTCAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 1 0.05
25 10 0.50
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (24 bp):
AAATATCTCTTCAGAGATTTTTTC
Found at i:51772 original size:17 final size:17
Alignment explanation
Indices: 51719--51778 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
51709 TAATCACTTT
*
51719 AATATTAAATT-AATAA
1 AATATTAAATTAAATTA
51735 AATATT--ATTAAGA-TA
1 AATATTAAATTAA-ATTA
*
51750 AGTATTAAATTAAATTA
1 AATATTAAATTAAATTA
51767 AATATTAAATTA
1 AATATTAAATTA
51779 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
14 3 0.08
15 7 0.19
16 8 0.22
17 18 0.50
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
AATATTAAATTAAATTA
Found at i:63139 original size:15 final size:15
Alignment explanation
Indices: 63119--63156 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
63109 ATTATTTTTA
63119 ATAAAATATATATGC
1 ATAAAATATATATGC
*
63134 AT-AAA-ATATATGT
1 ATAAAATATATATGC
63147 ATAAAATATA
1 ATAAAATATA
63157 CAATTTGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 9 0.45
14 6 0.30
15 5 0.25
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (15 bp):
ATAAAATATATATGC
Found at i:69537 original size:51 final size:51
Alignment explanation
Indices: 69477--69589 Score: 154
Period size: 51 Copynumber: 2.2 Consensus size: 51
69467 CGCTTCATTG
* * * *
69477 TATCGATAGAAATCTGAGGGTTTCATTTGGTATCGGTAGAACCTATTACAA
1 TATCGATAGAAATCTGAAGGTTTCATTTAGTATCGGTAAAACCCATTACAA
* * *
69528 TATCGATAGAAATCTGAAGGTTTCATTTAGTATTGGTAAAACCCATTAGAG
1 TATCGATAGAAATCTGAAGGTTTCATTTAGTATCGGTAAAACCCATTACAA
*
69579 TATCGGTAGAA
1 TATCGATAGAA
69590 GTGTAGGGGA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (51 bp):
TATCGATAGAAATCTGAAGGTTTCATTTAGTATCGGTAAAACCCATTACAA
Found at i:80747 original size:26 final size:26
Alignment explanation
Indices: 80717--80824 Score: 135
Period size: 26 Copynumber: 4.2 Consensus size: 26
80707 CCCCAGCATG
* *
80717 ATTTTGTTGATTTTACCCCTAGTAAA
1 ATTTTGATGATTTTACCCCTGGTAAA
*
80743 ATTTTGATGATTTTACCCTTGGTAAA
1 ATTTTGATGATTTTACCCCTGGTAAA
* *
80769 ATTTTGACGATTTTACTCCTGGTAAA
1 ATTTTGATGATTTTACCCCTGGTAAA
** * *
80795 ATTTTGACCATTTTTCCCATGGTAAA
1 ATTTTGATGATTTTACCCCTGGTAAA
80821 ATTT
1 ATTT
80825 CAAGAAAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (26 bp):
ATTTTGATGATTTTACCCCTGGTAAA
Found at i:97962 original size:18 final size:19
Alignment explanation
Indices: 97935--97982 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
97925 CATTTTCTTT
*
97935 TTCCTTTTCTTCTCTTC-C
1 TTCCTCTTCTTCTCTTCTC
*
97953 TTCCTCTTC-TCTTTTCTC
1 TTCCTCTTCTTCTCTTCTC
*
97971 TTCCTCCTCTTC
1 TTCCTCTTCTTC
97983 AACACTCCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.24
18 17 0.68
19 2 0.08
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (19 bp):
TTCCTCTTCTTCTCTTCTC
Found at i:121674 original size:7 final size:7
Alignment explanation
Indices: 121627--121695 Score: 77
Period size: 7 Copynumber: 10.0 Consensus size: 7
121617 CAAAACCAAC
121627 CCGTTGA
1 CCGTTGA
*
121634 CCATTGA
1 CCGTTGA
121641 CCGTTGA
1 CCGTTGA
*
121648 -CGTTGG
1 CCGTTGA
*
121654 CTGTTGA
1 CCGTTGA
*
121661 CCATTGA
1 CCGTTGA
*
121668 CAGTTGA
1 CCGTTGA
*
121675 TCGTTGA
1 CCGTTGA
121682 CCGTTGA
1 CCGTTGA
121689 CCGTTGA
1 CCGTTGA
121696 TGTTGATTAT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
6 5 0.10
7 44 0.90
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (7 bp):
CCGTTGA
Found at i:121680 original size:21 final size:20
Alignment explanation
Indices: 121637--121719 Score: 71
Period size: 20 Copynumber: 4.1 Consensus size: 20
121627 CCGTTGACCA
* *
121637 TTGACCGTTGACGTTG-GCTG
1 TTGACCATTGACGTTGATC-G
121657 TTGACCATTGACAGTTGATCG
1 TTGACCATTGAC-GTTGATCG
*
121678 TTGACCGTTGACCGTTGAT-G
1 TTGACCATTGA-CGTTGATCG
** *
121698 TTGATTATTGACTTTGATCG
1 TTGACCATTGACGTTGATCG
121718 TT
1 TT
121720 AATGTTGACT
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.12
20 23 0.44
21 21 0.40
22 2 0.04
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.40
Consensus pattern (20 bp):
TTGACCATTGACGTTGATCG
Found at i:121682 original size:41 final size:40
Alignment explanation
Indices: 121628--121719 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 40
121618 AAAACCAACC
* * *
121628 CGTTGACCATTGACCGTTGA-CGTTGGCTGTTGACCATTGA
1 CGTTGATCGTTGACCGTTGACCGTT-GATGTTGACCATTGA
**
121668 CAGTTGATCGTTGACCGTTGACCGTTGATGTTGATTATTGA
1 C-GTTGATCGTTGACCGTTGACCGTTGATGTTGACCATTGA
*
121709 CTTTGATCGTT
1 CGTTGATCGTT
121720 AATGTTGACT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
40 10 0.23
41 30 0.68
42 4 0.09
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (40 bp):
CGTTGATCGTTGACCGTTGACCGTTGATGTTGACCATTGA
Found at i:121724 original size:26 final size:26
Alignment explanation
Indices: 121685--121738 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
121675 TCGTTGACCG
* *
121685 TTGACCGTTGATGTTGATTATTGACT
1 TTGACCGTTAATGTTGACTATTGACT
*
121711 TTGATCGTTAATGTTGACTATTGACT
1 TTGACCGTTAATGTTGACTATTGACT
121737 TT
1 TT
121739 TTTCGAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.11, G:0.20, T:0.48
Consensus pattern (26 bp):
TTGACCGTTAATGTTGACTATTGACT
Found at i:124135 original size:26 final size:26
Alignment explanation
Indices: 124106--124160 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
124096 TGAGAATTAC
124106 AGAGCAAAGAAAGTGAGCTAGTAGAT
1 AGAGCAAAGAAAGTGAGCTAGTAGAT
124132 AGAGCAAAGAAAGTGAGCTAGTAGAT
1 AGAGCAAAGAAAGTGAGCTAGTAGAT
124158 AGA
1 AGA
124161 TGTGTAATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.31, T:0.15
Consensus pattern (26 bp):
AGAGCAAAGAAAGTGAGCTAGTAGAT
Found at i:124501 original size:18 final size:17
Alignment explanation
Indices: 124459--124501 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
124449 GTTTTAAGTT
*
124459 TATAATATTTTATATTA
1 TATAATTTTTTATATTA
* *
124476 TGTTATTTTTATATATTA
1 TATAATTTTT-TATATTA
124494 TATAATTT
1 TATAATTT
124502 AAAAAACATA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TATAATTTTTTATATTA
Found at i:125301 original size:8 final size:8
Alignment explanation
Indices: 125287--125316 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
125277 TGGATTAAGA
125287 CTAAAATT
1 CTAAAATT
*
125295 TTAAAATT
1 CTAAAATT
125303 CTAAAATT
1 CTAAAATT
125311 CTAAAA
1 CTAAAA
125317 GTATAAGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (8 bp):
CTAAAATT
Found at i:126242 original size:56 final size:56
Alignment explanation
Indices: 126180--126292 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
126170 CTCTTGAGTA
126180 AGTAAAAGGGTTAGAAATTTATTAAGTACTTGAGATTTACGAATGCCCCCTCGGGC
1 AGTAAAAGGGTTAGAAATTTATTAAGTACTTGAGATTTACGAATGCCCCCTCGGGC
126236 AGTAAAAGGGTTAGAAATTTATTAAGTACTTGAGATTTACGAATGCCCCCTCGGGC
1 AGTAAAAGGGTTAGAAATTTATTAAGTACTTGAGATTTACGAATGCCCCCTCGGGC
126292 A
1 A
126293 AAGTCCTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (56 bp):
AGTAAAAGGGTTAGAAATTTATTAAGTACTTGAGATTTACGAATGCCCCCTCGGGC
Found at i:131078 original size:9 final size:9
Alignment explanation
Indices: 131064--131099 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
131054 ACACCAAAAA
131064 ACCTTCATC
1 ACCTTCATC
131073 ACCTTCATC
1 ACCTTCATC
**
131082 TTCTTCATC
1 ACCTTCATC
131091 ACCTTCATC
1 ACCTTCATC
131100 TTCTTCTTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (9 bp):
ACCTTCATC
Found at i:131114 original size:18 final size:18
Alignment explanation
Indices: 131066--131105 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
131056 ACCAAAAAAC
131066 CTTCATCACCTTCATCTT
1 CTTCATCACCTTCATCTT
131084 CTTCATCACCTTCATCTT
1 CTTCATCACCTTCATCTT
131102 CTTC
1 CTTC
131106 TTCATCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.40, G:0.00, T:0.45
Consensus pattern (18 bp):
CTTCATCACCTTCATCTT
Found at i:131830 original size:23 final size:23
Alignment explanation
Indices: 131802--132163 Score: 490
Period size: 23 Copynumber: 15.7 Consensus size: 23
131792 TTCTTATGTC
131802 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
131825 TGTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
131848 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
131871 TGTGCTTAAGTATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
131894 TATACTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
131917 TTTGCTCAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
131940 TATGCTTAAATATTATTGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
131963 TATGCTTAAATTTTAATATGATT
1 TATGCTTAAATATTAATGTGATT
* *
131986 TATGCTTAAATATTTATGTTATT
1 TATGCTTAAATATTAATGTGATT
132009 TATGCTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
132032 TATGCTTAAATATTAATATGGTT
1 TATGCTTAAATATTAATGTGATT
* * * *
132055 TGTACTCAAATATTAATGTGGTT
1 TATGCTTAAATATTAATGTGATT
*
132078 TATGGTTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
* *
132101 TTTGCTTAAATATTAATATGATT
1 TATGCTTAAATATTAATGTGATT
*
132124 TATGATTAAATATTAATGTGATT
1 TATGCTTAAATATTAATGTGATT
*
132147 TGTGCTTAAATAATTAA
1 TATGCTTAAAT-ATTAA
132164 GATGTGATAT
Statistics
Matches: 291, Mismatches: 47, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
23 286 0.98
24 5 0.02
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (23 bp):
TATGCTTAAATATTAATGTGATT
Found at i:136969 original size:25 final size:24
Alignment explanation
Indices: 136941--136988 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
136931 ATTAAAAATA
136941 CTAAAAACATT-AAAATAAATATTTC
1 CTAAAAA-ATTAAAAATAAA-ATTTC
*
136966 CTAATAAATTAAAAATAAAATTT
1 CTAAAAAATTAAAAATAAAATTT
136989 AAAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (24 bp):
CTAAAAAATTAAAAATAAAATTTC
Found at i:137484 original size:29 final size:28
Alignment explanation
Indices: 137452--137546 Score: 70
Period size: 28 Copynumber: 3.4 Consensus size: 28
137442 ATATTTTTTA
137452 TAAAATTTTAAATATATAAATAT-AAATTC
1 TAAAATTTTAAA-ATA-AAATATAAAATTC
** * *
137481 TAAAAAGTTAAAATAATATATAAAATTG
1 TAAAATTTTAAAATAAAATATAAAATTC
* *
137509 GAAAATTTT-AAA-AAAATTTAAAAATTC
1 TAAAATTTTAAAATAAAATAT-AAAATTC
*
137536 TTTAAATTTTA
1 -TAAAATTTTA
137547 GAATTGAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
26 5 0.10
27 14 0.28
28 21 0.42
29 10 0.20
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (28 bp):
TAAAATTTTAAAATAAAATATAAAATTC
Found at i:137519 original size:28 final size:28
Alignment explanation
Indices: 137453--137535 Score: 71
Period size: 28 Copynumber: 3.0 Consensus size: 28
137443 TATTTTTTAT
* *
137453 AAAATTTT-AAATATATAAATATAAATTCT
1 AAAATTTTAAAATA-ATATATA-AAATTCG
** *
137482 AAAAAGTTAAAATAATATATAAAATTGG
1 AAAATTTTAAAATAATATATAAAATTCG
* *
137510 AAAATTTTAAAAAAATTTA-AAAATTC
1 AAAATTTTAAAATAATATATAAAATTC
137536 TTTAAATTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 6 0.14
28 20 0.47
29 12 0.28
30 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAATTTTAAAATAATATATAAAATTCG
Found at i:142148 original size:18 final size:17
Alignment explanation
Indices: 142105--142155 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
142095 CAGTATAAAA
*
142105 TAAATATAA-AAACAATT
1 TAAATTTAATAAA-AATT
142122 TAAATTTAATAATAAATT
1 TAAATTTAATAA-AAATT
142140 GTAAA-TTAATAAAAAT
1 -TAAATTTAATAAAAAT
142156 AAATGAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 12 0.40
18 13 0.43
19 5 0.17
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (17 bp):
TAAATTTAATAAAAATT
Found at i:151483 original size:17 final size:17
Alignment explanation
Indices: 151461--151501 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
151451 ACATATATGG
151461 AAATGCAATGACAATAA
1 AAATGCAATGACAATAA
*
151478 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
151495 TAATGCA
1 AAATGCA
151502 GGAATAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:153737 original size:13 final size:14
Alignment explanation
Indices: 153719--153748 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
153709 GTCAACACAA
153719 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
153732 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
153746 TCA
1 TCA
153749 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:156284 original size:18 final size:19
Alignment explanation
Indices: 156249--156287 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
156239 AATAAATATA
156249 AATACAATTTAAATTTAAT
1 AATACAATTTAAATTTAAT
156268 AATA-AATTGTAAA-TTAAT
1 AATACAATT-TAAATTTAAT
156286 AA
1 AA
156288 AAACAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (19 bp):
AATACAATTTAAATTTAAT
Found at i:157368 original size:16 final size:16
Alignment explanation
Indices: 157340--157377 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
157330 TCAAGTTAAC
157340 AAAAGATAAATAAAGG
1 AAAAGATAAATAAAGG
157356 AATAAGA-AAATAAAGG
1 AA-AAGATAAATAAAGG
157372 AAAAGA
1 AAAAGA
157378 GAATGCTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 13 0.62
17 4 0.19
ACGTcount: A:0.71, C:0.00, G:0.18, T:0.11
Consensus pattern (16 bp):
AAAAGATAAATAAAGG
Found at i:174130 original size:18 final size:18
Alignment explanation
Indices: 174107--174146 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
174097 GATAAATCTA
*
174107 AAAATATAAATATAAAT-T
1 AAAATACAAAT-TAAATAT
174125 AAAATACAAATTAAATAT
1 AAAATACAAATTAAATAT
174143 AAAA
1 AAAA
174147 AATATCCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATACAAATTAAATAT
Found at i:176152 original size:36 final size:36
Alignment explanation
Indices: 176108--176215 Score: 207
Period size: 36 Copynumber: 3.0 Consensus size: 36
176098 CCAACTCTTG
*
176108 GATGTCTAATTTCCTTGCTCTTCCTGTAGGATCTAA
1 GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
176144 GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
1 GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
176180 GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
1 GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
176216 CTCCATATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.42
Consensus pattern (36 bp):
GATGTCTAATTTCCTTGCTCTTCCTGTGGGATCTAA
Found at i:182186 original size:14 final size:14
Alignment explanation
Indices: 182169--182198 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
182159 TTTAAACTGT
182169 AAAAGATAAATATA
1 AAAAGATAAATATA
182183 AAAAGATAAATATA
1 AAAAGATAAATATA
182197 AA
1 AA
182199 TTAAATACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AAAAGATAAATATA
Found at i:182205 original size:11 final size:11
Alignment explanation
Indices: 182189--182220 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
182179 TATAAAAAGA
182189 TAAATATAAAT
1 TAAATATAAAT
*
182200 TAAATACAAAT
1 TAAATATAAAT
182211 TAAATATAAA
1 TAAATATAAA
182221 CAATATCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATATAAAT
Found at i:183020 original size:82 final size:82
Alignment explanation
Indices: 182879--183198 Score: 403
Period size: 82 Copynumber: 3.9 Consensus size: 82
182869 CGTATAGTTC
* * ** *
182879 CATCAATTCATGGCACCTAGTGCCTAGC-AGATAAATTGCAATAAGTGAGCCCAACTCTAGTTAG
1 CATCAATTCTTGGCACCCAGTGCCTAGCGA-ATAAACCGCAATAAGTGAGCCCAACTCTAGTTGG
182943 ATTAACCAACAATAAATT
65 ATTAACCAACAATAAATT
* * * * * *
182961 CGTTAATTCTTGGCACCCAGTGCCTAGTGGATAAACCGTAATAAGTGAGCCTAACTCTAGTTGGA
1 CATCAATTCTTGGCACCCAGTGCCTAGCGAATAAACCGCAATAAGTGAGCCCAACTCTAGTTGGA
183026 TTAACCAACAATAAATT
66 TTAACCAACAATAAATT
* * * * * *
183043 CAACAATTCCTT-GCACCTAGTGCCTAGCGAAT-AACTTGTAATAAGTGACCCCAGCTCTAGTTG
1 CATCAATT-CTTGGCACCCAGTGCCTAGCGAATAAAC-CGCAATAAGTGAGCCCAACTCTAGTTG
*
183106 GATTAATCAACAATAAATT
64 GATTAACCAACAATAAATT
* * *
183125 CATCATTTCCTGGCACCCAATGCCTAGCGAATAAACCGCAATAAGTGAGCCCAACTCTAGTTGGA
1 CATCAATTCTTGGCACCCAGTGCCTAGCGAATAAACCGCAATAAGTGAGCCCAACTCTAGTTGGA
183190 TTAACCAAC
66 TTAACCAAC
183199 GGGTTTGAAC
Statistics
Matches: 201, Mismatches: 32, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
81 5 0.02
82 190 0.95
83 6 0.03
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (82 bp):
CATCAATTCTTGGCACCCAGTGCCTAGCGAATAAACCGCAATAAGTGAGCCCAACTCTAGTTGGA
TTAACCAACAATAAATT
Found at i:183090 original size:164 final size:164
Alignment explanation
Indices: 182882--183198 Score: 465
Period size: 164 Copynumber: 1.9 Consensus size: 164
182872 ATAGTTCCAT
*
182882 CAATTCATGGCACCTAGTGCCTAGCAGATAAATTGCAATAAGTGAGCCCAACTCTAGTTAGATTA
1 CAATTCATGGCACCTAGTGCCTAGCAGATAAATTGCAATAAGTGACCCCAACTCTAGTTAGATTA
* * * * * * *
182947 ACCAACAATAAATTCGTTAATTCTTGGCACCCAGTGCCTAGTGGATAAACCGTAATAAGTGAGCC
66 ACCAACAATAAATTCATCAATTCCTGGCACCCAATGCCTAGCGAATAAACCGCAATAAGTGAGCC
*
183012 TAACTCTAGTTGGATTAACCAACAATAAATTCAA
131 CAACTCTAGTTGGATTAACCAACAATAAATTCAA
* * * * * *
183046 CAATTCCTTGCACCTAGTGCCTAGC-GAATAACTTGTAATAAGTGACCCCAGCTCTAGTTGGATT
1 CAATTCATGGCACCTAGTGCCTAGCAG-ATAAATTGCAATAAGTGACCCCAACTCTAGTTAGATT
* *
183110 AATCAACAATAAATTCATCATTTCCTGGCACCCAATGCCTAGCGAATAAACCGCAATAAGTGAGC
65 AACCAACAATAAATTCATCAATTCCTGGCACCCAATGCCTAGCGAATAAACCGCAATAAGTGAGC
183175 CCAACTCTAGTTGGATTAACCAAC
130 CCAACTCTAGTTGGATTAACCAAC
183199 GGGTTTGAAC
Statistics
Matches: 135, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
163 1 0.01
164 134 0.99
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (164 bp):
CAATTCATGGCACCTAGTGCCTAGCAGATAAATTGCAATAAGTGACCCCAACTCTAGTTAGATTA
ACCAACAATAAATTCATCAATTCCTGGCACCCAATGCCTAGCGAATAAACCGCAATAAGTGAGCC
CAACTCTAGTTGGATTAACCAACAATAAATTCAA
Found at i:190387 original size:82 final size:82
Alignment explanation
Indices: 190248--190483 Score: 310
Period size: 82 Copynumber: 2.9 Consensus size: 82
190238 GCATAGTTCC
* * * *
190248 GTCAATTCATGGCACCCAGTGCCTAGCGAATAAATCGCAATAAGTGTGTCCAGCTCTAGTCGGAT
1 GTCAATTCCTGGCACCCAGTGCCTAGCGAATAAATCGCAATAAGTGAGCCCAACTCTAGTCGGAT
*
190313 TAAGCAACAATAAATTT
66 TAACCAACAATAAATTT
* * * *
190330 GTCAATTCCTGGCATCTAGTGCCTAGCGAATAAATCACAATAAGTGAGCCCAACTCTAGTTGGAT
1 GTCAATTCCTGGCACCCAGTGCCTAGCGAATAAATCGCAATAAGTGAGCCCAACTCTAGTCGGAT
190395 TAACCAACAATAAATTT
66 TAACCAACAATAAATTT
* * * * ** * **
190412 GTCAATTCCTAGCACCCAATGCCTACCGGATAAGCCGTAATAAGTGAGCCCAACTCTAGTTAGAT
1 GTCAATTCCTGGCACCCAGTGCCTAGCGAATAAATCGCAATAAGTGAGCCCAACTCTAGTCGGAT
190477 TAACCAA
66 TAACCAA
190484 TGGTTTTGTG
Statistics
Matches: 134, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 134 1.00
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (82 bp):
GTCAATTCCTGGCACCCAGTGCCTAGCGAATAAATCGCAATAAGTGAGCCCAACTCTAGTCGGAT
TAACCAACAATAAATTT
Found at i:192178 original size:40 final size:41
Alignment explanation
Indices: 192122--192206 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
192112 CTTTTTCAGT
* * * *
192122 TATCCAACTAGTGTTGGGCACAC-TTTAATCTTCATTGGTA
1 TATCCAACAAGAGTTGGGCACACATTTAATATTCATCGGTA
* *
192162 TATCCAACAAGAGTTGGGCTCACATTTAATATTCATCGGTT
1 TATCCAACAAGAGTTGGGCACACATTTAATATTCATCGGTA
192203 TATC
1 TATC
192207 AGACTAGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
40 20 0.53
41 18 0.47
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (41 bp):
TATCCAACAAGAGTTGGGCACACATTTAATATTCATCGGTA
Found at i:192219 original size:41 final size:40
Alignment explanation
Indices: 192122--192221 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 40
192112 CTTTTTCAGT
* *
192122 TATCCAACTAGTGTTGGGCACACTTTAATCTTCATTGGTA
1 TATCCAACTAGTGTTGGGCACACTTTAATATTCATCGGTA
* * * *
192162 TATCCAACAAGAGTTGGGCTCACATTTAATATTCATCGGTT
1 TATCCAACTAGTGTTGGGCACAC-TTTAATATTCATCGGTA
192203 TAT-CAGACTAGTGTTGGGC
1 TATCCA-ACTAGTGTTGGGC
192222 GTAACCTTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
40 22 0.44
41 28 0.56
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (40 bp):
TATCCAACTAGTGTTGGGCACACTTTAATATTCATCGGTA
Found at i:197022 original size:7 final size:7
Alignment explanation
Indices: 197004--197051 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
196994 TAGCAATATT
197004 TCTTTT-
1 TCTTTTC
197010 TCTTTTC
1 TCTTTTC
197017 TCTTTTC
1 TCTTTTC
197024 TCTTTTC
1 TCTTTTC
197031 TCTTTT-
1 TCTTTTC
197037 TCTTTTC
1 TCTTTTC
197044 T-TTTTC
1 TCTTTTC
197050 TC
1 TC
197052 ATTCAACATT
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
6 18 0.46
7 21 0.54
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (7 bp):
TCTTTTC
Found at i:197064 original size:27 final size:27
Alignment explanation
Indices: 197005--197056 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
196995 AGCAATATTT
* *
197005 CTTTTTCTTTTCTCTTTTCTCTTTTCT
1 CTTTTTCTTTTCTCTTTTCTCTATTCA
197032 CTTTTTCTTTTCT-TTTTCTC-ATTCA
1 CTTTTTCTTTTCTCTTTTCTCTATTCA
197057 ACATTTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 7 0.30
27 13 0.57
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (27 bp):
CTTTTTCTTTTCTCTTTTCTCTATTCA
Found at i:198699 original size:69 final size:68
Alignment explanation
Indices: 198587--198723 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 68
198577 GATAGTCCAT
198587 ATCTTCTAATATGCTGCCCATACAAAAATTTCGCAGGTCGATGCGATCAATAATTACTTCCATGG
1 ATCTTCTAATATGCTGCCCATACAAAAATTTCGCAGGTCGATGCGATCAATAATTACTTCCATGG
198652 TAG
66 TAG
*
198655 NATCTTCTAATATGCTGCCCATACAAAAATTTCGCAGGTTGATGCGATCAATAATTACTTCCATG
1 -ATCTTCTAATATGCTGCCCATACAAAAATTTCGCAGGTCGATGCGATCAATAATTACTTCCATG
198720 GTAG
65 GTAG
198724 CCAGCCTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (68 bp):
ATCTTCTAATATGCTGCCCATACAAAAATTTCGCAGGTCGATGCGATCAATAATTACTTCCATGG
TAG
Found at i:210979 original size:16 final size:16
Alignment explanation
Indices: 210958--210988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
210948 ATAATGTTAA
210958 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
210974 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
210989 GGATCCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:213642 original size:21 final size:21
Alignment explanation
Indices: 213603--213653 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
213593 TAAATACAGA
* **
213603 CTTCTACCGATACTTGTGACAG
1 CTTCTACCAATACAAGTGA-AG
213625 -TTCTACCAATACAAGTGAAG
1 CTTCTACCAATACAAGTGAAG
213645 CTTCTACCA
1 CTTCTACCA
213654 GAATAAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (21 bp):
CTTCTACCAATACAAGTGAAG
Found at i:216641 original size:24 final size:24
Alignment explanation
Indices: 216609--216658 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
216599 CATCTGTTTG
216609 CACGTCATATGTAGTGCTAAAATT
1 CACGTCATATGTAGTGCTAAAATT
216633 CACGTCATATGTAGTGCTAAAATT
1 CACGTCATATGTAGTGCTAAAATT
216657 CA
1 CA
216659 ACCTGGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (24 bp):
CACGTCATATGTAGTGCTAAAATT
Found at i:221073 original size:19 final size:20
Alignment explanation
Indices: 221049--221089 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
221039 AGTTCTACCG
* *
221049 AAACAAGTATG-CAAAATTC
1 AAACAAGCATGCCAAAACTC
221068 AAACAAGCATGCCAAAACTC
1 AAACAAGCATGCCAAAACTC
221088 AA
1 AA
221090 GTTTATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.22, G:0.10, T:0.15
Consensus pattern (20 bp):
AAACAAGCATGCCAAAACTC
Found at i:224897 original size:21 final size:21
Alignment explanation
Indices: 224873--224914 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
224863 AAAAGTCAAG
224873 AGGTTTTAGAAAATAAGGTAT
1 AGGTTTTAGAAAATAAGGTAT
224894 AGGTTTTAGAAAATAAGGTAT
1 AGGTTTTAGAAAATAAGGTAT
224915 CGGGACCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.24, T:0.33
Consensus pattern (21 bp):
AGGTTTTAGAAAATAAGGTAT
Found at i:226570 original size:25 final size:25
Alignment explanation
Indices: 226516--226657 Score: 101
Period size: 25 Copynumber: 5.6 Consensus size: 25
226506 TTTACTGAAG
* *
226516 ACTGGCTCGTAAGAGCGATATTCTG
1 ACTGGCTCGTAAGAGCAATATTCTC
* * * *
226541 TCTGGTTTGTAAGAGCAATATTTTC
1 ACTGGCTCGTAAGAGCAATATTCTC
*
226566 ACTGGCTCGTAAGAGTAATATTCT-
1 ACTGGCTCGTAAGAGCAATATTCTC
* ** * *
226590 ATCTAGCTCGTAAGAGTGATGTTCTG
1 A-CTGGCTCGTAAGAGCAATATTCTC
* *
226616 AATGGCTCGTAAGAGCGATACTT-T-
1 ACTGGCTCGTAAGAGCAATA-TTCTC
226640 ATCTAGGCTCGTAAGAGC
1 A-CT-GGCTCGTAAGAGC
226658 TAAACTCTGT
Statistics
Matches: 93, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
24 2 0.02
25 75 0.81
26 16 0.17
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (25 bp):
ACTGGCTCGTAAGAGCAATATTCTC
Found at i:226577 original size:50 final size:50
Alignment explanation
Indices: 226516--226657 Score: 151
Period size: 50 Copynumber: 2.8 Consensus size: 50
226506 TTTACTGAAG
* * * * *
226516 ACTGGCTCGTAAGAGCGATATTCTGTCTGGTTTGTAAGAGCAATATTTTC
1 ACTGGCTCGTAAGAGCGATATTCTATCTAGCTCGTAAGAGCAATATTCTC
** ** * *
226566 ACTGGCTCGTAAGAGTAATATTCTATCTAGCTCGTAAGAGTGATGTTCTG
1 ACTGGCTCGTAAGAGCGATATTCTATCTAGCTCGTAAGAGCAATATTCTC
*
226616 AATGGCTCGTAAGAGCGATACTT-TATCTAGGCTCGTAAGAGC
1 ACTGGCTCGTAAGAGCGATA-TTCTATCTA-GCTCGTAAGAGC
226658 TAAACTCTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
50 62 0.83
51 13 0.17
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (50 bp):
ACTGGCTCGTAAGAGCGATATTCTATCTAGCTCGTAAGAGCAATATTCTC
Found at i:226674 original size:26 final size:26
Alignment explanation
Indices: 226619--226687 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 26
226609 TGTTCTGAAT
* * *
226619 GGCTCGTAAGAGCGATACTTTATCTA
1 GGCTCGTAAGAGCTAAACTCTATCTA
* *
226645 GGCTCGTAAGAGCTAAACTCTGTCTG
1 GGCTCGTAAGAGCTAAACTCTATCTA
*
226671 GGCTCGTATGAGCTAAA
1 GGCTCGTAAGAGCTAAA
226688 TTTTTGGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (26 bp):
GGCTCGTAAGAGCTAAACTCTATCTA
Found at i:235158 original size:20 final size:20
Alignment explanation
Indices: 235135--235179 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
235125 AATTAAGAGC
235135 TATTT-TTTAATTTAATGTAT
1 TATTTATTT-ATTTAATGTAT
* *
235155 TATTTATTTATTTATTTTAT
1 TATTTATTTATTTAATGTAT
235175 TATTT
1 TATTT
235180 CCACATGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTTATTTATTTAATGTAT
Found at i:237610 original size:25 final size:25
Alignment explanation
Indices: 237582--237639 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
237572 CCATAAGGGA
237582 ATCATACAGATTATGCCACAAAGGC
1 ATCATACAGATTATGCCACAAAGGC
** *
237607 ATCATACAGATTATGCCATGAAGGT
1 ATCATACAGATTATGCCACAAAGGC
237632 ATCATACA
1 ATCATACA
237640 TAATCATGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (25 bp):
ATCATACAGATTATGCCACAAAGGC
Found at i:238780 original size:30 final size:29
Alignment explanation
Indices: 238746--238804 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
238736 GGAAAAGGAC
* * *
238746 TTAATGTGTAAATTTATTAAATTTTATGAT
1 TTAATGGGAAAATTGATT-AATTTTATGAT
*
238776 TTAATGGGAAAATTGATTTATTTTATGAT
1 TTAATGGGAAAATTGATTAATTTTATGAT
238805 AGATCAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.51
Consensus pattern (29 bp):
TTAATGGGAAAATTGATTAATTTTATGAT
Found at i:248730 original size:43 final size:42
Alignment explanation
Indices: 248676--248790 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
248666 TACTTGATGT
* * * *
248676 TTAAATGGAAGACTAATGTCTCGGGTTGAGCATGAGAATTTA
1 TTAAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAAATTA
* ** * *
248718 TATAAAAGGAAGACTCATGACTCGAAAATGGGCATGAGAAATTG
1 T-TAAAAGGAAGACTCATGTCTCG-GGATGAGCATGAGAAATTA
248762 TT-AAAGGAAGACTCATGTCTCGGGATGAG
1 TTAAAAGGAAGACTCATGTCTCGGGATGAG
248791 AATAAGATTA
Statistics
Matches: 58, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
41 4 0.07
42 20 0.34
43 20 0.34
44 14 0.24
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (42 bp):
TTAAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAAATTA
Found at i:248844 original size:81 final size:85
Alignment explanation
Indices: 248676--248837 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 85
248666 TACTTGATGT
* * * * *
248676 TTAAATGGAAGACTAATGTCTCGGGTTGAGCATGAGAATTTATATAAAAGGAAGACTCATGACTC
1 TTAAATGGAAGACTAATGTCTCGGGATGAGAATAAGAATTTATAT-AAAGAAAGACTCACGACTC
**
248741 GAAAATGGGCATGAGAAATTG
65 GAAAATAAGCATGAGAAATTG
*
248762 TTAAA-GGAAGACTCATGTCTCGGGATGAGAATAAG-A-TTATACT-AAGAAAGACTCACGACTC
1 TTAAATGGAAGACTAATGTCTCGGGATGAGAATAAGAATTTATA-TAAAGAAAGACTCACGACTC
248823 -AAAATAAGCATGAGA
65 GAAAATAAGCATGAGA
248838 TTTTGTTCTA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
81 13 0.19
82 16 0.24
83 5 0.07
84 2 0.03
85 26 0.39
86 5 0.07
ACGTcount: A:0.41, C:0.12, G:0.23, T:0.23
Consensus pattern (85 bp):
TTAAATGGAAGACTAATGTCTCGGGATGAGAATAAGAATTTATATAAAGAAAGACTCACGACTCG
AAAATAAGCATGAGAAATTG
Found at i:251005 original size:13 final size:13
Alignment explanation
Indices: 250989--251050 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
250979 TTATTATTGC
* *
250989 TTTTTAAAAGTGT
1 TTTTGAAAAGTGA
* *
251002 TTTTAAAAAGTGC
1 TTTTGAAAAGTGA
*
251015 TTTGGAAAAGTGA
1 TTTTGAAAAGTGA
251028 TTTTGAAAAGT-A
1 TTTTGAAAAGTGA
*
251040 CTTTGAAAAGT
1 TTTTGAAAAGT
251051 TTGGTTTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
12 11 0.26
13 31 0.74
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.40
Consensus pattern (13 bp):
TTTTGAAAAGTGA
Found at i:251023 original size:26 final size:25
Alignment explanation
Indices: 250994--251050 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
250984 ATTGCTTTTT
* *
250994 AAAAGTGTTTTTAAAAAGTGCTTTGG
1 AAAAGTGATTTTAAAAAGTACTTT-G
*
251020 AAAAGTGATTTTGAAAAGTACTTTG
1 AAAAGTGATTTTAAAAAGTACTTTG
251045 AAAAGT
1 AAAAGT
251051 TTGGTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (25 bp):
AAAAGTGATTTTAAAAAGTACTTTG
Found at i:251425 original size:21 final size:21
Alignment explanation
Indices: 251401--251440 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
251391 TTGAAAAGCC
251401 AAAAATTTCCTTCAAAAGTAA
1 AAAAATTTCCTTCAAAAGTAA
251422 AAAAATTTCCTTCAAAAGT
1 AAAAATTTCCTTCAAAAGT
251441 TGCTTGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATTTCCTTCAAAAGTAA
Found at i:251477 original size:17 final size:18
Alignment explanation
Indices: 251455--251496 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
251445 TGTTTAGCAT
251455 TGCTTTTGAT-TCAAAAG
1 TGCTTTTGATGTCAAAAG
*
251472 TGCTTTTTATGTCAAAAG
1 TGCTTTTGATGTCAAAAG
251490 TGCTTTT
1 TGCTTTT
251497 AAAAAGCACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.48
Consensus pattern (18 bp):
TGCTTTTGATGTCAAAAG
Found at i:252197 original size:201 final size:200
Alignment explanation
Indices: 251830--252231 Score: 572
Period size: 201 Copynumber: 2.0 Consensus size: 200
251820 CTTGGGTGAG
*
251830 AATTTGGCTTTCCATAGTGATATCCATTTTTCCTTATTTTCAAAAGGTTGAGTCTTCACACTTCA
1 AATTTGGCTTTCCATAATGATATCCATTTTTCCTTATTTTCAAAAGGTTGAGTCTTCACACTTCA
* * * *
251895 TGTTGCCACATCGTATGCATTGACCATGGAAAAGTTTTCACCATTCTTATGTTTCTAGCATAAAA
66 TGTTGCCACATCATATGCATTGACCATGGAAAAGTCTCCACCATTCATATGTTTCTAGCATAAAA
* * * * * **
251960 CATCTCTATTTTCTTCGTTAAAAGAGATTGGAATGCTGACTGTGACATTATAAATTTCTTT-ATG
131 CATCTCTATTTGCTTCATTAAAAGAAATTAGAATGCTAACTACG-CATTAT-AATTTCTTTAATG
252024 GATTTGT
194 GATTTGT
* * * *
252031 AATTTTGCTTTCCATAATGATCTCCATTTTTCCTTGTTTTCAAAAGGTTGAGTCTTCACACTTCT
1 AATTTGGCTTTCCATAATGATATCCATTTTTCCTTATTTTCAAAAGGTTGAGTCTTCACACTTCA
* * * *
252096 TTTTTCCACATCATATGCATTGACCATGGAAATGTCTCCATCATTCATATGTTTCTAGCATAAAA
66 TGTTGCCACATCATATGCATTGACCATGGAAAAGTCTCCACCATTCATATGTTTCTAGCATAAAA
* * *
252161 CATCTCTATTTGCTTCATTGAAAGAAATTAGAATGCTAAGTACGCATTATAATTTTTTTAATGGA
131 CATCTCTATTTGCTTCATTAAAAGAAATTAGAATGCTAACTACGCATTATAATTTCTTTAATGGA
252226 TTTGT
196 TTTGT
252231 A
1 A
252232 TAACACCTTG
Statistics
Matches: 177, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
199 8 0.05
200 17 0.10
201 152 0.86
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (200 bp):
AATTTGGCTTTCCATAATGATATCCATTTTTCCTTATTTTCAAAAGGTTGAGTCTTCACACTTCA
TGTTGCCACATCATATGCATTGACCATGGAAAAGTCTCCACCATTCATATGTTTCTAGCATAAAA
CATCTCTATTTGCTTCATTAAAAGAAATTAGAATGCTAACTACGCATTATAATTTCTTTAATGGA
TTTGT
Found at i:255532 original size:28 final size:27
Alignment explanation
Indices: 255464--255532 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 27
255454 TGTTACATTT
*
255464 ATATAGATCGATTATTTAACTAGTAGACA
1 ATATA-AT-GATTATTTAACTAGTACACA
*
255493 A-AGTAAAAGATTATTTAACTAGATACACA
1 ATA-T-AATGATTATTTAACTAG-TACACA
255522 ATATAATGATT
1 ATATAATGATT
255533 TTTCCTTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
28 21 0.64
29 10 0.30
30 2 0.06
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (27 bp):
ATATAATGATTATTTAACTAGTACACA
Found at i:257522 original size:3 final size:3
Alignment explanation
Indices: 257514--257544 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
257504 AGCCTAAACC
257514 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
257545 TAAGCATCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:271089 original size:71 final size:71
Alignment explanation
Indices: 270973--271157 Score: 226
Period size: 71 Copynumber: 2.6 Consensus size: 71
270963 GTCCGATGGC
* * * * * * ** *
270973 TGAGATCCTACATTTCTTGTGGATTCTCTACAGCATCGTAAGTCACTGTAAAGTGAAACTGGTTC
1 TGAGATCCTACATTTGTTGCGAATTCTCTACAGCATTGTGAGTCACTATAAAGTGAAAAAGGTCC
*
271038 AATGCT
66 AATGAT
*
271044 TGAGATCCTACATTTGATGCGAATTCTCTACAGCATTGTGAGTCACTATAAAGTGAAAAAGGTCC
1 TGAGATCCTACATTTGTTGCGAATTCTCTACAGCATTGTGAGTCACTATAAAGTGAAAAAGGTCC
*
271109 GATGAT
66 AATGAT
* * **
271115 TGAGATACTGCATTTGTTGCGAATTCTCTATGGCATTGTGAGT
1 TGAGATCCTACATTTGTTGCGAATTCTCTACAGCATTGTGAGT
271158 TATTAAATGT
Statistics
Matches: 97, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 97 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.34
Consensus pattern (71 bp):
TGAGATCCTACATTTGTTGCGAATTCTCTACAGCATTGTGAGTCACTATAAAGTGAAAAAGGTCC
AATGAT
Found at i:271299 original size:114 final size:114
Alignment explanation
Indices: 271099--271421 Score: 470
Period size: 114 Copynumber: 2.8 Consensus size: 114
271089 CTATAAAGTG
* * * *
271099 AAAAAGGTCCGATGATTGAGATACTGCATTTGTTGCGAATTCTCTATGGCATTGTGAGTTATTAA
1 AAAAAGGTTCGATGACTGAGATACTGCATTTGTTACGAATTCTCTATGGCATCGTGAGTTATTAA
* *
271164 ATGTGAAATGAATTCGAGTATGGATTATAGGGCCTAAGATGGCCAAGAT
66 ATGTGAAATGAATTCGAGTATGGATTACAGGGCCTAAGATAGCCAAGAT
*
271213 AAAAAGGTTCGATGACTGAGATCCTGCATTTGTTACGAATTCTCTATGGCATCGTGAGTTATTAA
1 AAAAAGGTTCGATGACTGAGATACTGCATTTGTTACGAATTCTCTATGGCATCGTGAGTTATTAA
* *
271278 ATGTGAAATGAATTCGAGTATGAATTACAGGGCCTAAGATAGCTAAGAT
66 ATGTGAAATGAATTCGAGTATGGATTACAGGGCCTAAGATAGCCAAGAT
* * * *
271327 AAAAAGG-TCTGATGACTAAGATTCTGCATTTGTTACGGATTCTCTATGGCATCATGAGTTATTA
1 AAAAAGGTTC-GATGACTGAGATACTGCATTTGTTACGAATTCTCTATGGCATCGTGAGTTATTA
* *
271391 AATGT-AAGATGAATCCGAGAATGGATATACA
65 AATGTGAA-ATGAATTCGAGTATGGAT-TACA
271422 ATTGGTTTGG
Statistics
Matches: 190, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
113 4 0.02
114 182 0.96
115 4 0.02
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (114 bp):
AAAAAGGTTCGATGACTGAGATACTGCATTTGTTACGAATTCTCTATGGCATCGTGAGTTATTAA
ATGTGAAATGAATTCGAGTATGGATTACAGGGCCTAAGATAGCCAAGAT
Found at i:274061 original size:29 final size:30
Alignment explanation
Indices: 274015--274073 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
274005 GAATTGGATC
* *
274015 AAATCAAAATTTTATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
274045 AAATCAAAA-TTCATGTATACAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
274074 TTAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.65
30 9 0.35
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:276897 original size:4 final size:4
Alignment explanation
Indices: 276888--276912 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
276878 ACTTCCATAA
276888 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
276913 ATTTACTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:277485 original size:28 final size:29
Alignment explanation
Indices: 277422--277489 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 29
277412 TTTAATAATT
* *
277422 TATATTTTTATAATTTTTAAAAGATTAAA
1 TATAATTTTATAATTGTTAAAAGATTAAA
* *
277451 T-TAAATTTTATAA-TGTTAAAAGGTTAAG
1 TAT-AATTTTATAATTGTTAAAAGATTAAA
277479 TATAATTTTAT
1 TATAATTTTAT
277490 TTTTACTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (29 bp):
TATAATTTTATAATTGTTAAAAGATTAAA
Done.