Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 190 of 198
Found at i:58875906 original size:21 final size:20
Alignment explanation
Indices: 58875880--58875939 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 20
58875870 AATGTTACCA
*
58875880 TTATTATTATTATTATCATCT
1 TTATTATTATTATTAT-ATCG
58875901 TTATTATTATTATTAATATCG
1 TTATTATTATTATT-ATATCG
*
58875922 ATATTATTATTATTATAT
1 TTATTATTATTATTATAT
58875940 TTCCATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 4 0.11
21 30 0.83
22 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATTATTATTATTATATCG
Found at i:58875911 original size:294 final size:294
Alignment explanation
Indices: 58875320--58875899 Score: 1151
Period size: 294 Copynumber: 2.0 Consensus size: 294
58875310 AATTTGGTCC
58875320 TATTTTGTTGTTTTGTTTTATTTTGATTTAGCCCTAAGATTTTACTTTTGTTTCATTTTAGTCCA
1 TATTTTGTTGTTTTGTTTTATTTTGATTTAGCCCTAAGATTTTACTTTTGTTTCATTTTAGTCCA
58875385 TTGAGGCGCTGCGTTTTAGAACTTTGGGTTTATTTTCTGTTTCGGTCCTTCCCTTTTTACGCGCG
66 TTGAGGCGCTGCGTTTTAGAACTTTGGGTTTATTTTCTGTTTCGGTCCTTCCCTTTTTACGCGCG
*
58875450 CCGCAATTGGATCCTTTTCGTTTTCCTTTATTTCGGATTGGCCCTATATGTTTTATTTCATTTCG
131 CCGCAATTGGATCCTTTTCGTTTTCCTTTATTTCGGATTGGCCCTATATATTTTATTTCATTTCG
58875515 ATTTAATCCCTTTTTTAGCGTTTTTTATTATTTAGTCAATTTTTGTTAACTTTATTATTTTAATG
196 ATTTAATCCCTTTTTTAGCGTTTTTTATTATTTAGTCAATTTTTGTTAACTTTATTATTTTAATG
58875580 TTACCATTATTATTATTATTATCATCATCTTTAT
261 TTACCATTATTATTATTATTATCATCATCTTTAT
58875614 TATTTTGTTGTTTTGTTTTATTTTGATTTAGCCCTAAGATTTTACTTTTGTTTCATTTTAGTCCA
1 TATTTTGTTGTTTTGTTTTATTTTGATTTAGCCCTAAGATTTTACTTTTGTTTCATTTTAGTCCA
58875679 TTGAGGCGCTGCGTTTTAGAACTTTGGGTTTATTTTCTGTTTCGGTCCTTCCCTTTTTACGCGCG
66 TTGAGGCGCTGCGTTTTAGAACTTTGGGTTTATTTTCTGTTTCGGTCCTTCCCTTTTTACGCGCG
58875744 CCGCAATTGGATCCTTTTCGTTTTCCTTTATTTCGGATTGGCCCTATATATTTTATTTCATTTCG
131 CCGCAATTGGATCCTTTTCGTTTTCCTTTATTTCGGATTGGCCCTATATATTTTATTTCATTTCG
58875809 ATTTAATCCCTTTTTTAGCGTTTTTTATTATTTAGTCAATTTTTGTTAACTTTATTATTTTAATG
196 ATTTAATCCCTTTTTTAGCGTTTTTTATTATTTAGTCAATTTTTGTTAACTTTATTATTTTAATG
58875874 TTACCATTATTATTATTATTATCATC
261 TTACCATTATTATTATTATTATCATC
58875900 TTTATTATTA
Statistics
Matches: 285, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
294 285 1.00
ACGTcount: A:0.17, C:0.16, G:0.13, T:0.54
Consensus pattern (294 bp):
TATTTTGTTGTTTTGTTTTATTTTGATTTAGCCCTAAGATTTTACTTTTGTTTCATTTTAGTCCA
TTGAGGCGCTGCGTTTTAGAACTTTGGGTTTATTTTCTGTTTCGGTCCTTCCCTTTTTACGCGCG
CCGCAATTGGATCCTTTTCGTTTTCCTTTATTTCGGATTGGCCCTATATATTTTATTTCATTTCG
ATTTAATCCCTTTTTTAGCGTTTTTTATTATTTAGTCAATTTTTGTTAACTTTATTATTTTAATG
TTACCATTATTATTATTATTATCATCATCTTTAT
Found at i:58876076 original size:14 final size:14
Alignment explanation
Indices: 58876010--58876083 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
58876000 TATAAGTGCT
*
58876010 TATATATATATTTCA
1 TATATATTTATTT-A
58876025 TATA-ATTTATTTA
1 TATATATTTATTTA
* *
58876038 -ATATATATATATA
1 TATATATTTATTTA
*
58876051 TAT-TACTT-TTTA
1 TATATATTTATTTA
58876063 TATATATTTATTTA
1 TATATATTTATTTA
*
58876077 CATATAT
1 TATATAT
58876084 CTATGTACTC
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
12 9 0.19
13 15 0.32
14 19 0.40
15 4 0.09
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (14 bp):
TATATATTTATTTA
Found at i:58876579 original size:109 final size:109
Alignment explanation
Indices: 58876388--58876791 Score: 600
Period size: 110 Copynumber: 3.7 Consensus size: 109
58876378 TTTCTAATTG
* *
58876388 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
58876453 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
66 TGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
* *
58876497 AGGCAATGTTTTGCGTTTGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* *
58876562 TGTTCAACCAAATGGCTTAATATCCTTTTCAAAAATCTTAAAATA
66 TGTTTAACCAAATGGCTTAATATCCTTTT-AAAAATTTTAAAATA
* *
58876607 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACAAGCTCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
58876672 TGTTTAACCAAATAG-TTAAATATCCTTTCAAAAAATTTCAAAATA
66 TGTTTAACCAAATGGCTT-AATATCCTTT-TAAAAATTTTAAAATA
* * * * *
58876717 AGGCAATGTTTTGCGTTTGCAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
58876779 TGTTTAACCAAAT
66 TGTTTAACCAAAT
58876792 TGCCAAATAT
Statistics
Matches: 269, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
107 18 0.07
109 112 0.42
110 139 0.52
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (109 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
TGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATA
Found at i:58876767 original size:219 final size:217
Alignment explanation
Indices: 58876388--58876791 Score: 632
Period size: 219 Copynumber: 1.9 Consensus size: 217
58876378 TTTCTAATTG
* * *
58876388 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGTTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACAAGCCCTAAGGTGCTGGGTGTCGATTTTTCT
* * *
58876453 CGTTTAACCAAATGGCTTAATATCCTTTTAAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGAA
66 CGTTTAACCAAATAGCTTAATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAA
*
58876518 AATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTGTTCTTGTTCAACCAAATGGCTTAAT
131 AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGA-T-TTCTTGTTCAACCAAATGGCTTAAT
58876583 ATCCTTTTCAAAAATCTTAAAATA
194 ATCCTTTTCAAAAATCTTAAAATA
*
58876607 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACAAGCTCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACAAGCCCTAAGGTGCTGGGTGTCGATTTTTCT
*
58876672 TGTTTAACCAAATAG-TTAAATATCCTTTCAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTG
66 CGTTTAACCAAATAGCTT-AATATCCTTT-AAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTG
* * * * *
58876736 CAAATTCGAG-GAACGTACCCTAAGGTGCTGGGTTTCGATTTCTTGTTTAACCAAAT
129 AAAATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGTTCAACCAAAT
58876792 TGCCAAATAT
Statistics
Matches: 169, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
217 16 0.09
218 3 0.02
219 108 0.64
220 42 0.25
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (217 bp):
AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACAAGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTTAACCAAATAGCTTAATATCCTTTAAAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGAA
AATTCGAGAAAACATACCCTAAGGTGCTGGGTGTCGATTTCTTGTTCAACCAAATGGCTTAATAT
CCTTTTCAAAAATCTTAAAATA
Found at i:58878867 original size:46 final size:46
Alignment explanation
Indices: 58878683--58878947 Score: 431
Period size: 46 Copynumber: 6.0 Consensus size: 46
58878673 NNNNNNNNNN
58878683 AGTGTAGCTAAAGCTACCACTTATCAC-TTGTCAC-TGATCAGATA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
* *
58878727 AGTGTAGCT-AGGCTACAACTTATCACTTTGTCACTTGATCAGATA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
*
58878772 AGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTGATCAGAT-
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
58878816 A----AGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
*
58878858 AGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
58878904 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGA
58878948 AGTACTCAAA
Statistics
Matches: 207, Mismatches: 6, Indels: 14
0.91 0.03 0.06
Matches are distributed among these distances:
40 4 0.02
41 34 0.16
42 1 0.00
43 15 0.07
44 17 0.08
45 53 0.26
46 83 0.40
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (46 bp):
AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATA
Found at i:58878938 original size:92 final size:92
Alignment explanation
Indices: 58878683--58878947 Score: 431
Period size: 86 Copynumber: 3.0 Consensus size: 92
58878673 NNNNNNNNNN
* *
58878683 AGTGTAGCTAAAGCTACCACTTATCAC-TTGTCAC-TGATCAGATAAGTGTAGCT-AGGCTACAA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
58878745 CTTATCACTTTGTCACTTGATCAGATA
66 CTTATCACTTTGTCACTTGATCAGATA
*
58878772 AGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTGATCAGAT-A----AGCTAAAGCTACCA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
58878831 CTTATCACTTTGTCACTTGATCAGATA
66 CTTATCACTTTGTCACTTGATCAGATA
*
58878858 AGTGTAGCTAAAGCTACCACTCATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
1 AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
58878923 CTTATCACTTTGTCACTTGATCAGA
66 CTTATCACTTTGTCACTTGATCAGA
58878948 AGTACTCAAA
Statistics
Matches: 162, Mismatches: 5, Indels: 15
0.89 0.03 0.08
Matches are distributed among these distances:
85 4 0.02
86 43 0.27
87 33 0.20
88 17 0.10
89 17 0.10
90 9 0.06
92 39 0.24
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (92 bp):
AGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
CTTATCACTTTGTCACTTGATCAGATA
Found at i:58884430 original size:11 final size:11
Alignment explanation
Indices: 58884414--58884439 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58884404 TCTTTCTTTC
58884414 TTTCTCCCCTG
1 TTTCTCCCCTG
58884425 TTTCTCCCCTG
1 TTTCTCCCCTG
58884436 TTTC
1 TTTC
58884440 GTCTCTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.42, G:0.08, T:0.50
Consensus pattern (11 bp):
TTTCTCCCCTG
Found at i:58884465 original size:11 final size:11
Alignment explanation
Indices: 58884443--58884492 Score: 59
Period size: 10 Copynumber: 4.5 Consensus size: 11
58884433 CTGTTTCGTC
58884443 TCTTTCTCTGTT
1 TCTTT-TCTGTT
58884455 TCTTTTCTG-T
1 TCTTTTCTGTT
*
58884465 TCTTCTTTTGTT
1 TCTT-TTCTGTT
58884477 TCTTTT-TGTT
1 TCTTTTCTGTT
58884487 TCTTTT
1 TCTTTT
58884493 ATTTTACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 15 0.43
11 10 0.29
12 10 0.29
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.74
Consensus pattern (11 bp):
TCTTTTCTGTT
Found at i:58884468 original size:22 final size:23
Alignment explanation
Indices: 58884443--58884491 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
58884433 CTGTTTCGTC
58884443 TCTTTC-TCTGTTTCTTTTCTG-T
1 TCTTTCTTCTGTTTCTTTT-TGTT
*
58884465 TC-TTCTTTTGTTTCTTTTTGTT
1 TCTTTCTTCTGTTTCTTTTTGTT
58884487 TCTTT
1 TCTTT
58884492 TATTTTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 5 0.22
22 16 0.70
23 2 0.09
ACGTcount: A:0.00, C:0.18, G:0.08, T:0.73
Consensus pattern (23 bp):
TCTTTCTTCTGTTTCTTTTTGTT
Found at i:58884659 original size:18 final size:19
Alignment explanation
Indices: 58884636--58884671 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
58884626 ATTATTTATC
58884636 TAATAAATATCT-TTAAAA
1 TAATAAATATCTATTAAAA
58884654 TAATAAATATCTATTAAA
1 TAATAAATATCTATTAAA
58884672 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATAAATATCTATTAAAA
Found at i:58884680 original size:19 final size:18
Alignment explanation
Indices: 58884640--58884681 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
58884630 TTTATCTAAT
*
58884640 AAATATCTTTAAAATAAT
1 AAATATCTTTAAAATAAC
58884658 AAATATCTATT-AAATATAC
1 AAATATCT-TTAAAATA-AC
58884677 AAATA
1 AAATA
58884682 AAAATATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATCTTTAAAATAAC
Found at i:58888221 original size:4 final size:4
Alignment explanation
Indices: 58888212--58888248 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
58888202 TAATTGACAT
*
58888212 ATAA ATAA ATAA ATAA ATAA ATAC ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
58888249 CATCAAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:58888318 original size:8 final size:8
Alignment explanation
Indices: 58888307--58888334 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
58888297 AAATATAAAA
58888307 ATGTATAT
1 ATGTATAT
58888315 ATGTATAT
1 ATGTATAT
58888323 ATGTATAT
1 ATGTATAT
58888331 ATGT
1 ATGT
58888335 GCATAACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (8 bp):
ATGTATAT
Found at i:58888382 original size:3 final size:3
Alignment explanation
Indices: 58888374--58888409 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
58888364 ATAAATGAGT
58888374 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
58888410 TAATACTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:58889656 original size:14 final size:14
Alignment explanation
Indices: 58889637--58889663 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
58889627 ATTGGGTTGG
58889637 TTTGGGTTTTGGTA
1 TTTGGGTTTTGGTA
58889651 TTTGGGTTTTGGT
1 TTTGGGTTTTGGT
58889664 CCCCGAGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.00, G:0.37, T:0.59
Consensus pattern (14 bp):
TTTGGGTTTTGGTA
Found at i:58897456 original size:18 final size:18
Alignment explanation
Indices: 58897413--58897456 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
58897403 ACCAAATCCA
* *
58897413 AACCCAAGTATCCAACCC
1 AACCCAATTACCCAACCC
*
58897431 AACCCAATTACCCAACCG
1 AACCCAATTACCCAACCC
58897449 AACCCAAT
1 AACCCAAT
58897457 CATAAAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.41, C:0.43, G:0.05, T:0.11
Consensus pattern (18 bp):
AACCCAATTACCCAACCC
Found at i:58897636 original size:9 final size:9
Alignment explanation
Indices: 58897599--58897632 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
58897589 GTAGTGATTC
58897599 AATTCGGGT
1 AATTCGGGT
58897608 AATTCGGGT
1 AATTCGGGT
*
58897617 AATTCGGTT
1 AATTCGGGT
58897626 AATTCGG
1 AATTCGG
58897633 TTAACCGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.29, T:0.35
Consensus pattern (9 bp):
AATTCGGGT
Found at i:58902730 original size:37 final size:35
Alignment explanation
Indices: 58902663--58902739 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 35
58902653 CAATAGATAG
* * **
58902663 ATTCTGGTTTTGTTAAATCATAACTGTTTAAAAGTAT
1 ATTCTGATTTTGTTAAACCATAACCATTTAAAA--AT
*
58902700 ATTCTGATTTTGTTAAACCGTAACCATTTAAAAAT
1 ATTCTGATTTTGTTAAACCATAACCATTTAAAAAT
58902735 ATTCT
1 ATTCT
58902740 TTTTCCAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 7 0.20
37 28 0.80
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (35 bp):
ATTCTGATTTTGTTAAACCATAACCATTTAAAAAT
Found at i:58905417 original size:2 final size:2
Alignment explanation
Indices: 58905410--58905437 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
58905400 ACCAACATGC
58905410 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58905438 TCTTTTTCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58907345 original size:2 final size:2
Alignment explanation
Indices: 58907311--58907336 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58907301 AATGTAAAAG
58907311 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
58907337 GCATATATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58907382 original size:16 final size:16
Alignment explanation
Indices: 58907361--58907399 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
58907351 AATTATGGAG
*
58907361 ATATATGAAAGCATGT
1 ATATATAAAAGCATGT
*
58907377 ATATATAAAAGTATGT
1 ATATATAAAAGCATGT
58907393 ATATATA
1 ATATATA
58907400 TGTATACGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (16 bp):
ATATATAAAAGCATGT
Found at i:58907385 original size:34 final size:34
Alignment explanation
Indices: 58907337--58907401 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
58907327 ATATATATAT
*
58907337 GCATATATACATAAAATTATGGAGATATATGAAA
1 GCATATATACATAAAAGTATGGAGATATATGAAA
* * * *
58907371 GCATGTATATATAAAAGTATGTATATATATG
1 GCATATATACATAAAAGTATGGAGATATATG
58907402 TATACGTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (34 bp):
GCATATATACATAAAAGTATGGAGATATATGAAA
Found at i:58907921 original size:29 final size:28
Alignment explanation
Indices: 58907861--58907920 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
58907851 GATTTCGCGG
58907861 AAAATGGCCCATTCCGGTAAATAATAAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* *
58907889 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAA
58907917 AAAA
1 AAAA
58907921 AAAGGCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:58910476 original size:44 final size:44
Alignment explanation
Indices: 58910362--58910973 Score: 461
Period size: 45 Copynumber: 13.6 Consensus size: 44
58910352 TCATTCTAAC
* * ** **
58910362 CCACTGCAACTTC-AGGAATATAAGAATTGTAAGTTCAATCTATT
1 CCACTGCAACTTCAAGG-AGATAAGATTTGTATCTTCAATCTGCT
* * * *
58910406 CCGA-TACAACCTC-AGGAAGATGAGATTTGTATCTTTAATCTGCT
1 CC-ACTGCAACTTCAAGG-AGATAAGATTTGTATCTTCAATCTGCT
* *
58910450 CCGCTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCT
1 CCACTGCAACTTCAAGGAGATAAGATTT-GTATCTTCAATCTGCT
* * * *
58910495 CCACTGCAACTTGAGGGAGATAAGATTTATTATCTTCAATCTACT
1 CCACTGCAACTTCAAGGAGATAAGATTT-GTATCTTCAATCTGCT
* * * *
58910540 CCAATGCAACTTCAGGGAGATAAGATTTGTGACTTGCAGCTTTAATCTGTT
1 CCACTGCAACTTCAAGGAGATAAGATTTGT-A--T----CTTCAATCTGCT
* * * * *
58910591 CCACTACAACTCCAGGGAAATAAGATTTGCTATCTTCAATATGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTG-TATCTTCAATCTGCT
* *
58910636 CCACTGCAATTTCAGGGAGATAAGATTCAT-TATCTTCAATCTGCT
1 CCACTGCAACTTCAAGGAGATAAGATT--TGTATCTTCAATCTGCT
* * * *
58910681 CCACTGTAACTTC-AGAGATATAAGATTTATAGT-TTTAATCTGCT
1 CCACTGCAACTTCAAG-GAGATAAGATTTGTA-TCTTCAATCTGCT
* * * *
58910725 CCACTACAACTTCAGGGAGATAAGA-TT-TATGGTTCTAATCTACT
1 CCACTGCAACTTCAAGGAGATAAGATTTGTAT-CTTC-AATCTGCT
* * * * *
58910769 CCACTGCAACTTCAAGGAGATAAGATTTATGGT-TTTAATATGTT
1 CCACTGCAACTTCAAGGAGATAAGATTTGT-ATCTTCAATCTGCT
** * * *
58910813 ATACTACAACTTCAAAGAGATAAGATTTGCTATCTTCAATTTGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTG-TATCTTCAATCTGCT
* *
58910858 CCACTGCAAATTCAAGGAGATAAGATTTGCTATCTTCAATTTGCT
1 CCACTGCAACTTCAAGGAGATAAGATTTG-TATCTTCAATCTGCT
* * ** *
58910903 CCACCGTAACTTC-AGGAAGATAAGATTTGTGGCTTTAATCTGCT
1 CCACTGCAACTTCAAGG-AGATAAGATTTGTATCTTCAATCTGCT
* *
58910947 CCACTGCAACTTTAGGGAGATAAGATT
1 CCACTGCAACTTCAAGGAGATAAGATT
58910974 CGCCATGATG
Statistics
Matches: 458, Mismatches: 82, Indels: 56
0.77 0.14 0.09
Matches are distributed among these distances:
41 1 0.00
42 2 0.00
43 5 0.01
44 178 0.39
45 231 0.50
46 1 0.00
47 3 0.01
49 1 0.00
51 35 0.08
52 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (44 bp):
CCACTGCAACTTCAAGGAGATAAGATTTGTATCTTCAATCTGCT
Found at i:58910491 original size:45 final size:45
Alignment explanation
Indices: 58910435--58910973 Score: 466
Period size: 45 Copynumber: 11.9 Consensus size: 45
58910425 ATGAGATTTG
* *
58910435 TATCTTTAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTTAC
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * *
58910480 TATCTTCAATCTGCTCCACTGCAACTTGAGGGAGATAAGATTTAT
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * *
58910525 TATCTTCAATCTACTCCAATGCAACTTCAGGGAGATAAGATTTGTGAC
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT-T-AC
* * * * * * * *
58910573 TTGCAGCTTTAATCTGTTCCACTACAACTCCAGGGAAATAAGATTTGC
1 -T--ATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * * * *
58910621 TATCTTCAATATGCTCCACTGCAATTTCAGGGAGATAAGATTCAT
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* *
58910666 TATCTTCAATCTGCTCCACTGTAACTTC-AGAGATATAAGATTTA-
1 TATCTTCAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTAC
* * *
58910710 TAGT-TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTA-
1 TA-TCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
** *
58910754 T-GGTTCTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTA-
1 TATCTTC-AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * * * ** * * *
58910798 TGGT-TTTAATATGTTATACTACAACTTCAAAGAGATAAGATTTGC
1 T-ATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * *
58910843 TATCTTCAATTTGCTCCACTGCAAATTCAAGGAGATAAGATTTGC
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
* * * *
58910888 TATCTTCAATTTGCTCCACCGTAACTTC-AGGAAGATAAGATTT-G
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTAC
** * * *
58910932 TGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATT
1 TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
58910974 CGCCATGATG
Statistics
Matches: 401, Mismatches: 76, Indels: 35
0.78 0.15 0.07
Matches are distributed among these distances:
43 2 0.00
44 136 0.34
45 222 0.55
46 2 0.00
47 2 0.00
48 2 0.00
49 2 0.00
50 2 0.00
51 31 0.08
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (45 bp):
TATCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTAC
Found at i:58910616 original size:141 final size:134
Alignment explanation
Indices: 58910362--58910973 Score: 507
Period size: 134 Copynumber: 4.5 Consensus size: 134
58910352 TCATTCTAAC
* * * * ** * * * *
58910362 CCACTGCAACTTCAGGAATATAAGAATT-GTAAGTTCAATCTATTCCGATACAACCTCAG-GAAG
1 CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAG-AG
* * * * * *
58910425 ATGAGATTTGTATCTTTAATCTGCTCCGCTGCAACTTCAAGGAGATAAGATTTACTATCTTCAAT
65 ATAAGATTTATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTATCTTCAAT
58910490 CTGCT
130 CTGCT
* *
58910495 CCACTGCAACTTGAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAGAGA
* * * *
58910560 TAAGATTTGTGACTTGCAGCTTTAATCTGTTCCACTACAACTCCAGGGAAATAAGATTTGCTATC
66 TAAGA-TT-T-A--T--AGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTATC
*
58910625 TTCAATATGCT
124 TTCAATCTGCT
* * * * * *
58910636 CCACTGCAATTTCAGGGAGATAAGATTCATTATCTTCAATCTGCTCCACTGTAACTTCAGAGATA
1 CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAGAGA
* **
58910701 TAAGATTTATAGTTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTA-T-GGTTCTAAT
66 TAAGATTTATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTATCTTC-AAT
*
58910764 CTACT
130 CTGCT
* ** * * ** ** * * *
58910769 CCACTGCAACTTCAAGGAGATAAGATTTATGGT-TTTAATATGTTATACTACAACTTCAAAGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAGAGA
* * * * * * * *
58910833 TAAGATTTGCTATCTTCAATTTGCTCCACTGCAAATTCAAGGAGATAAGATTTGCTATCTTCAAT
66 TAAGATTT-ATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTATCTTCAAT
*
58910898 TTGCT
130 CTGCT
* * * * ** * * * * *
58910903 CCACCGTAACTTCAGGAAGATAAGATTT-GTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAGAGA
58910967 TAAGATT
66 TAAGATT
58910974 CGCCATGATG
Statistics
Matches: 384, Mismatches: 81, Indels: 27
0.78 0.16 0.05
Matches are distributed among these distances:
132 33 0.09
133 96 0.25
134 130 0.34
135 6 0.02
136 2 0.01
138 1 0.00
139 2 0.01
140 2 0.01
141 112 0.29
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (134 bp):
CCACTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGAGAGA
TAAGATTTATAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACTATCTTCAATC
TGCT
Found at i:58910625 original size:96 final size:90
Alignment explanation
Indices: 58910362--58910973 Score: 374
Period size: 89 Copynumber: 6.8 Consensus size: 90
58910352 TCATTCTAAC
* * * **
58910362 CCACTGCAACTTCAGGAATATAAGAATTGTA--AG-TTCAATCTATTCCGA-TACAAC-CTCA-G
1 CCACTGCAACTTCAGGGAGATAAG-ATTTTACTAGCTTCAATCTGCTCC-ACTACAACTC-CAGG
* *
58910421 GAAGATGAGATTTGTATCTTTAATCTGCT
63 GAA-ATAAGATTTGTATCTTCAATCTGCT
* * * * ** *
58910450 CCGCTGCAACTTCAAGGAGATAAGA-TTTACTATCTTCAATCTGCTCCACTGCAACTTGAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTCAATCTGCTCCACTACAACTCCAGGGAA
* *
58910514 ATAAGATTTATTATCTTCAATCTACT
66 ATAAGATTT-GTATCTTCAATCTGCT
* * *
58910540 CCAATGCAACTTCAGGGAGATAAGATTTGTGACTTGCAGCTTTAATCTGTTCCACTACAACTCCA
1 CCACTGCAACTTCAGGGAGATAAGATTT-T-AC-T--AGCTTCAATCTGCTCCACTACAACTCCA
*
58910605 GGGAAATAAGATTTGCTATCTTCAATATGCT
61 GGGAAATAAGATTTG-TATCTTCAATCTGCT
* * * * ** * * *
58910636 CCACTGCAATTTCAGGGAGATAAGA-TTCATTATCTTCAATCTGCTCCACTGTAACTTCAGAGAT
1 CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTCAATCTGCTCCACTACAACTCCAGGGAA
* *
58910700 ATAAGATTTATAGT-TTTAATCTGCT
66 ATAAGATTTGTA-TCTTCAATCTGCT
* * * * * *
58910725 CCACTACAACTTCAGGGAGATAAGA-TTTA-T-GGTTCTAATCTACTCCACTGCAACTTCAAGGA
1 CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTC-AATCTGCTCCACTACAACTCCAGGGA
* * * * * *
58910787 GATAAGATTTATGGT-TTTAATATGTT
65 AATAAGATTTGT-ATCTTCAATCTGCT
** * ** * * * * * * * *
58910813 ATACTACAACTTCAAAGAGATAAGA-TTTGCTATCTTCAATTTGCTCCACTGCAAATTCAAGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTCAATCTGCTCCACTACAACTCCAGGGAA
*
58910877 ATAAGATTTGCTATCTTCAATTTGCT
66 ATAAGATTTG-TATCTTCAATCTGCT
* * * * * * * ** *
58910903 CCACCGTAACTTCAGGAAGATAAGA-TTT-GTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTCAATCTGCTCCACTACAACTCCAGGGAA
58910966 ATAAGATT
66 ATAAGATT
58910974 CGCCATGATG
Statistics
Matches: 415, Mismatches: 88, Indels: 41
0.76 0.16 0.08
Matches are distributed among these distances:
86 3 0.01
87 4 0.01
88 90 0.22
89 132 0.32
90 105 0.25
91 2 0.00
92 2 0.00
93 3 0.01
94 1 0.00
95 2 0.00
96 71 0.17
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (90 bp):
CCACTGCAACTTCAGGGAGATAAGATTTTACTAGCTTCAATCTGCTCCACTACAACTCCAGGGAA
ATAAGATTTGTATCTTCAATCTGCT
Found at i:58910860 original size:222 final size:228
Alignment explanation
Indices: 58910435--58910973 Score: 668
Period size: 222 Copynumber: 2.4 Consensus size: 228
58910425 ATGAGATTTG
* * * *
58910435 TATCTTTAATCTGCTCCGCTGCAACTTCA-AGGAGATAAGATTTACTA-TCTTCAATCTGCTCCA
1 TATCTTCAATCTGCTCCACTGTAACTTCAGA-GAGATAAGATTTA-TAGT-TTTAATCTGCTCCA
* *
58910498 CTGCAACTTGAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAGGGAGATAA
63 CTGCAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAAGGAGATAA
* * **
58910563 GATTTGTGACTTGCAGCTTTAATCTGTTCCACTACAACTCCAGGGAAATAAGATTTGCTATCTTC
128 GATTTGTGAC-TG-AGCTTTAATATGTTACACTACAACTCCAAAGAAATAAGATTTGCTATCTTC
* * *
58910628 AATATGCTCCACTGCAATTTCAGGGAGATAAGATTCAT
191 AATATGCTCCACTGCAAATTCAAGGAGATAAGATTCAC
* *
58910666 TATCTTCAATCTGCTCCACTGTAACTTCAGAGATATAAGATTTATAGTTTTAATCTGCTCCACTA
1 TATCTTCAATCTGCTCCACTGTAACTTCAGAGAGATAAGATTTATAGTTTTAATCTGCTCCACTG
*
58910731 CAACTTCAGGGAGATAAGATTTATGGT-TC-T-AATCTACTCCACTGCAACTTCAAGGAGATAAG
66 CAACTTCAGGGAGATAAGATTTAT--TATCTTCAATCTACTCCAATGCAACTTCAAGGAGATAAG
* * * *
58910793 A-TT-T-A-TG-GTTTTAATATGTTATACTACAACTTCAAAGAGATAAGATTTGCTATCTTCAAT
129 ATTTGTGACTGAGCTTTAATATGTTACACTACAACTCCAAAGAAATAAGATTTGCTATCTTCAAT
* **
58910853 TTGCTCCACTGCAAATTCAAGGAGATAAGATTTGC
194 ATGCTCCACTGCAAATTCAAGGAGATAAGATTCAC
* * * * *
58910888 TATCTTCAATTTGCTCCACCGTAACTTCAG-GAAGATAAGATTTGTGGCTTTAATCTGCTCCACT
1 TATCTTCAATCTGCTCCACTGTAACTTCAGAG-AGATAAGATTTATAGTTTTAATCTGCTCCACT
*
58910952 GCAACTTTAGGGAGATAAGATT
65 GCAACTTCAGGGAGATAAGATT
58910974 CGCCATGATG
Statistics
Matches: 272, Mismatches: 31, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
221 1 0.00
222 150 0.55
224 2 0.01
226 1 0.00
227 1 0.00
228 2 0.01
229 31 0.11
230 41 0.15
231 41 0.15
232 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (228 bp):
TATCTTCAATCTGCTCCACTGTAACTTCAGAGAGATAAGATTTATAGTTTTAATCTGCTCCACTG
CAACTTCAGGGAGATAAGATTTATTATCTTCAATCTACTCCAATGCAACTTCAAGGAGATAAGAT
TTGTGACTGAGCTTTAATATGTTACACTACAACTCCAAAGAAATAAGATTTGCTATCTTCAATAT
GCTCCACTGCAAATTCAAGGAGATAAGATTCAC
Found at i:58911619 original size:15 final size:15
Alignment explanation
Indices: 58911594--58911628 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
58911584 GACTCTATTT
*
58911594 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
58911608 TAATTAATATTAAGA
1 TAATTAATATTAAGA
58911623 TAATTA
1 TAATTA
58911629 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:58920526 original size:152 final size:152
Alignment explanation
Indices: 58920250--58920555 Score: 603
Period size: 152 Copynumber: 2.0 Consensus size: 152
58920240 TTTTTTTATG
58920250 TCCTTCACCCTGTTATGGTCAAACCGACTTTTAAGAAGTCAACAATAGATGGCGGTGGCAAGATT
1 TCCTTCACCCTGTTATGGTCAAACCGACTTTTAAGAAGTCAACAATAGATGGCGGTGGCAAGATT
58920315 GGTCTACAAGTTTCCAAGTTTCTTCATGTTTGAAAGTATAAACAAATTGATGAGGTGAGGTCGAC
66 GGTCTACAAGTTTCCAAGTTTCTTCATGTTTGAAAGTATAAACAAATTGATGAGGTGAGGTCGAC
58920380 CTCGGACTCTTAATGGAAGGAA
131 CTCGGACTCTTAATGGAAGGAA
*
58920402 TCCTTCACCCTGTTATGGTCAACCCGACTTTTAAGAAGTCAACAATAGATGGCGGTGGCAAGATT
1 TCCTTCACCCTGTTATGGTCAAACCGACTTTTAAGAAGTCAACAATAGATGGCGGTGGCAAGATT
58920467 GGTCTACAAGTTTCCAAGTTTCTTCATGTTTGAAAGTATAAACAAATTGATGAGGTGAGGTCGAC
66 GGTCTACAAGTTTCCAAGTTTCTTCATGTTTGAAAGTATAAACAAATTGATGAGGTGAGGTCGAC
58920532 CTCGGACTCTTAATGGAAGGAA
131 CTCGGACTCTTAATGGAAGGAA
58920554 TC
1 TC
58920556 ATTTCACAGT
Statistics
Matches: 153, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 153 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (152 bp):
TCCTTCACCCTGTTATGGTCAAACCGACTTTTAAGAAGTCAACAATAGATGGCGGTGGCAAGATT
GGTCTACAAGTTTCCAAGTTTCTTCATGTTTGAAAGTATAAACAAATTGATGAGGTGAGGTCGAC
CTCGGACTCTTAATGGAAGGAA
Found at i:58922237 original size:27 final size:26
Alignment explanation
Indices: 58922211--58922278 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
58922201 ATTGAAATAT
*
58922211 TAACTTAGAAAAAAATAATTTATATA
1 TAACTTAGAAAAAAATAATTTAGATA
* *
58922237 TCACTTATAACAAAAA-AATTTAGATA
1 TAACTTAGAA-AAAAATAATTTAGATA
*
58922263 CTAACTT-GAATAAAAT
1 -TAACTTAGAAAAAAAT
58922279 GATATAACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
25 4 0.12
26 19 0.58
27 10 0.30
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (26 bp):
TAACTTAGAAAAAAATAATTTAGATA
Found at i:58929692 original size:20 final size:20
Alignment explanation
Indices: 58929667--58929715 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
58929657 ACAGTCACGA
58929667 AACACCATCTTCAGAGTCTC
1 AACACCATCTTCAGAGTCTC
*
58929687 AACACCAGCTTCAGAGTCTC
1 AACACCATCTTCAGAGTCTC
58929707 AACACCATC
1 AACACCATC
58929716 GATACATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.20
Consensus pattern (20 bp):
AACACCATCTTCAGAGTCTC
Found at i:58930110 original size:20 final size:20
Alignment explanation
Indices: 58930085--58930127 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
58930075 GCTAACGGAC
*
58930085 TTACAACGGTTTTGACCATA
1 TTACAACGGCTTTGACCATA
*
58930105 TTACAACGGCTTTGACTATA
1 TTACAACGGCTTTGACCATA
58930125 TTA
1 TTA
58930128 ACTCTAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (20 bp):
TTACAACGGCTTTGACCATA
Found at i:58933251 original size:20 final size:20
Alignment explanation
Indices: 58933226--58933268 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
58933216 GCTAACGGAC
*
58933226 TTACAACGGTTTTGACCATA
1 TTACAACGGCTTTGACCATA
*
58933246 TTACAACGGCTTTGACTATA
1 TTACAACGGCTTTGACCATA
58933266 TTA
1 TTA
58933269 ACTCTAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (20 bp):
TTACAACGGCTTTGACCATA
Found at i:58938868 original size:25 final size:25
Alignment explanation
Indices: 58938840--58938906 Score: 98
Period size: 25 Copynumber: 2.7 Consensus size: 25
58938830 TTACCGATTC
*
58938840 CAGCTCTTATGAGCTTACTGATACT
1 CAGCTCGTATGAGCTTACTGATACT
*
58938865 CAGCTCGTATGAGCTTACTGATATT
1 CAGCTCGTATGAGCTTACTGATACT
* *
58938890 CAGCTCGGAGGAGCTTA
1 CAGCTCGTATGAGCTTA
58938907 TCGTTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACTGATACT
Found at i:58949247 original size:44 final size:44
Alignment explanation
Indices: 58949197--58949286 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
58949187 CTAATATATA
58949197 TTTTATCTCCTATATAGCTCAGAATATTATTTGTTTTCCTATTT
1 TTTTATCTCCTATATAGCTCAGAATATTATTTGTTTTCCTATTT
*
58949241 TTTTATCTCCTATATAGCTCAGAATCTTATTTGTTTTCCTATTT
1 TTTTATCTCCTATATAGCTCAGAATATTATTTGTTTTCCTATTT
58949285 TT
1 TT
58949287 CGTTAGTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.56
Consensus pattern (44 bp):
TTTTATCTCCTATATAGCTCAGAATATTATTTGTTTTCCTATTT
Found at i:58953533 original size:39 final size:39
Alignment explanation
Indices: 58953479--58953557 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
58953469 GCCAAACATC
58953479 ATTAAAATTACATCTTCTTACATTCTTAAACGCGAGGAA
1 ATTAAAATTACATCTTCTTACATTCTTAAACGCGAGGAA
*
58953518 ATTAAAATTACATCTTCTTACATTCTTAAAGGCGAGGAA
1 ATTAAAATTACATCTTCTTACATTCTTAAACGCGAGGAA
58953557 A
1 A
58953558 ATTGTCCCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.33
Consensus pattern (39 bp):
ATTAAAATTACATCTTCTTACATTCTTAAACGCGAGGAA
Found at i:58960415 original size:18 final size:17
Alignment explanation
Indices: 58960392--58960459 Score: 59
Period size: 18 Copynumber: 3.9 Consensus size: 17
58960382 TTATTTTTTT
58960392 AAAATCATATAATATAAC
1 AAAAT-ATATAATATAAC
*
58960410 AAAATCATATAAT-TAAT
1 AAAAT-ATATAATATAAC
* *
58960427 AATTATATATAATAAAAAC
1 AA-AATATATAAT-ATAAC
58960446 AAAATAT-TAATATA
1 AAAATATATAATATA
58960460 TTTAATAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
16 2 0.05
17 16 0.39
18 19 0.46
19 4 0.10
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATATAATATAAC
Found at i:58964377 original size:13 final size:13
Alignment explanation
Indices: 58964359--58964384 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58964349 CCACCTTCTC
58964359 TCCCTACAGTCTT
1 TCCCTACAGTCTT
58964372 TCCCTACAGTCTT
1 TCCCTACAGTCTT
58964385 CTACACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.38, G:0.08, T:0.38
Consensus pattern (13 bp):
TCCCTACAGTCTT
Found at i:58964580 original size:23 final size:24
Alignment explanation
Indices: 58964535--58964580 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
58964525 CTTCGTGGGA
* *
58964535 TTTTTGTGTTCTTTGTTGGGTTTC
1 TTTTTGTGTTCTTTCTTGAGTTTC
*
58964559 TTTTTTTGTT-TTTCTTGAGTTT
1 TTTTTGTGTTCTTTCTTGAGTTT
58964581 TAAGACTCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.02, C:0.07, G:0.20, T:0.72
Consensus pattern (24 bp):
TTTTTGTGTTCTTTCTTGAGTTTC
Found at i:58965357 original size:6 final size:6
Alignment explanation
Indices: 58965338--58965367 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
58965328 ACCTTCAATT
*
58965338 TGTATA TGTTTA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA
58965368 AAAGAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (6 bp):
TGTATA
Found at i:58970502 original size:41 final size:41
Alignment explanation
Indices: 58970457--58970537 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
58970447 CAAACTGTGT
* * * *
58970457 AACAATGGTTAAA-AAGAAAAACCATTTATACACAGTCCCGG
1 AACAATAG-TAAACAAGAAAAACCATGTACAAACAGTCCCGG
58970498 AACAATAGTAAACAAGAAAAACCATGTACAAACAGTCCCG
1 AACAATAGTAAACAAGAAAAACCATGTACAAACAGTCCCG
58970538 AACTCTCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 4 0.11
41 31 0.89
ACGTcount: A:0.49, C:0.21, G:0.14, T:0.16
Consensus pattern (41 bp):
AACAATAGTAAACAAGAAAAACCATGTACAAACAGTCCCGG
Found at i:58984369 original size:14 final size:14
Alignment explanation
Indices: 58984346--58984378 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58984336 TTATGAATTC
58984346 TATTTATTTTTAAT
1 TATTTATTTTTAAT
*
58984360 TATTTGTTTTTAAT
1 TATTTATTTTTAAT
58984374 T-TTTA
1 TATTTA
58984379 AATCCACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTATTTTTAAT
Found at i:58985202 original size:30 final size:29
Alignment explanation
Indices: 58985159--58985233 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
58985149 TAATCCCAAT
*
58985159 TAGTTAGGAGACTAAATTTTAAAAAAA-TAA
1 TAGTTAGGTGACTAAA--TTAAAAAAATTAA
* *
58985189 TAGTTGGGTGACTAAATTAAAAAAATTGA
1 TAGTTAGGTGACTAAATTAAAAAAATTAA
*
58985218 TAATTAGGTGACTAAA
1 TAGTTAGGTGACTAAA
58985234 AAAAGAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 9 0.23
29 16 0.41
30 14 0.36
ACGTcount: A:0.48, C:0.04, G:0.17, T:0.31
Consensus pattern (29 bp):
TAGTTAGGTGACTAAATTAAAAAAATTAA
Found at i:58985802 original size:40 final size:39
Alignment explanation
Indices: 58985748--58985905 Score: 195
Period size: 40 Copynumber: 4.2 Consensus size: 39
58985738 AAATATATTT
* * *
58985748 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
*
58985787 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 A-TTTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTAA
58985828 ATTTTTTTAATTTTAAAATATTTTTAAAATAC----T--
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
*
58985861 -TTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAA
1 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
*
58985899 AATTTTT
1 ATTTTTT
58985906 AAAATAAAAA
Statistics
Matches: 104, Mismatches: 6, Indels: 18
0.81 0.05 0.14
Matches are distributed among these distances:
32 30 0.29
35 1 0.01
36 1 0.01
39 6 0.06
40 59 0.57
41 7 0.07
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTAA
Found at i:58985803 original size:17 final size:17
Alignment explanation
Indices: 58985781--58985886 Score: 54
Period size: 17 Copynumber: 6.0 Consensus size: 17
58985771 TTTACATACT
* *
58985781 TTTTAAATTTTTTTTAA
1 TTTTAAAATATTTTTAA
58985798 TTTTAAAATATTTTTAAAATA
1 TTTTAAAATATTTTT---A-A
** *
58985819 CTTTTTTTAATTTTTTTAA
1 --TTTTAAAATATTTTTAA
58985838 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
** ** *
58985855 -AAT-ACTTTTTTTTAA
1 TTTTAAAATATTTTTAA
58985870 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
58985887 AATATTTTTT
Statistics
Matches: 63, Mismatches: 18, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
15 9 0.14
16 2 0.03
17 36 0.57
19 1 0.02
20 2 0.03
21 1 0.02
23 12 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:58985812 original size:11 final size:11
Alignment explanation
Indices: 58985798--58985911 Score: 91
Period size: 11 Copynumber: 10.9 Consensus size: 11
58985788 TTTTTTTTAA
58985798 TTTTAAAATAT
1 TTTTAAAATAT
58985809 TTTTAAAATACT
1 TTTTAAAATA-T
**
58985821 TTTTTTAAT-T
1 TTTTAAAATAT
*
58985831 TTTT----TAA
1 TTTTAAAATAT
58985838 TTTTAAAATAT
1 TTTTAAAATAT
58985849 TTTTAAAATACT
1 TTTTAAAATA-T
** *
58985861 TTTT--TTTAA
1 TTTTAAAATAT
58985870 TTTTAAAATAT
1 TTTTAAAATAT
58985881 TTTTAAAATAT
1 TTTTAAAATAT
*
58985892 TTTTTAAA-AT
1 TTTTAAAATAT
58985902 TTTTAAAATA
1 TTTTAAAATA
58985912 AAAATGGGCC
Statistics
Matches: 81, Mismatches: 12, Indels: 20
0.72 0.11 0.18
Matches are distributed among these distances:
6 1 0.01
7 4 0.05
9 4 0.05
10 16 0.20
11 43 0.53
12 13 0.16
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:58985870 original size:32 final size:31
Alignment explanation
Indices: 58985829--58985911 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 31
58985819 CTTTTTTTAA
58985829 TTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTTAATTTTAAAATATTTTTAAAATA-T
58985861 TTTTTTTAATTTTAAAATATTTTTAAAATAT
1 TTTTTTTAATTTTAAAATATTTTTAAAATAT
**
58985892 TTTTTAAAATTTTTAAAATA
1 TTTTTTTAA-TTTTAAAATA
58985912 AAAATGGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 8 0.17
32 40 0.83
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATAT
Found at i:58985893 original size:21 final size:22
Alignment explanation
Indices: 58985758--58985911 Score: 91
Period size: 21 Copynumber: 7.5 Consensus size: 22
58985748 ATTTTTTAAA
* *
58985758 TTTTAAAATATTTTTTACATACT
1 TTTTAAAATATTTTTAAAATA-T
* *
58985781 TTTT-AAAT-TTTTT---TTAA
1 TTTTAAAATATTTTTAAAATAT
58985798 TTTTAAAATATTTTTAAAATACT
1 TTTTAAAATATTTTTAAAATA-T
** *
58985821 TTTTTTAAT-TTTTT----TAA
1 TTTTAAAATATTTTTAAAATAT
58985838 TTTTAAAATATTTTTAAAATACT
1 TTTTAAAATATTTTTAAAATA-T
** *
58985861 TTTT--TTTAATTTTAAAATAT
1 TTTTAAAATATTTTTAAAATAT
*
58985881 TTTTAAAATATTTTTTAAA-AT
1 TTTTAAAATATTTTTAAAATAT
58985902 TTTTAAAATA
1 TTTTAAAATA
58985912 AAAATGGGCC
Statistics
Matches: 100, Mismatches: 17, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
17 11 0.11
18 13 0.13
19 5 0.05
20 5 0.05
21 29 0.29
22 22 0.22
23 15 0.15
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAAATATTTTTAAAATAT
Found at i:58995399 original size:7 final size:7
Alignment explanation
Indices: 58995387--58995411 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
58995377 TTTATTCAGA
58995387 AATCGCT
1 AATCGCT
58995394 AATCGCT
1 AATCGCT
58995401 AATCGCT
1 AATCGCT
58995408 AATC
1 AATC
58995412 ACATTTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (7 bp):
AATCGCT
Found at i:58997154 original size:15 final size:15
Alignment explanation
Indices: 58997119--58997164 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
58997109 TTTCGACGAG
58997119 TTATTTTAAATAATT
1 TTATTTTAAATAATT
58997134 TT-TTTTAAA-AATAT
1 TTATTTTAAATAAT-T
* *
58997148 TTATTTTTAATGATT
1 TTATTTTAAATAATT
58997163 TT
1 TT
58997165 TAAATGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 10 0.38
15 11 0.42
16 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTTTAAATAATT
Found at i:58997866 original size:5 final size:5
Alignment explanation
Indices: 58997856--58997885 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
58997846 CCATTAAGTC
58997856 ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA
58997886 TTACAAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:58999315 original size:41 final size:39
Alignment explanation
Indices: 58999193--58999328 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
58999183 ACCAGTTTGG
* * * *
58999193 CACCCAGTGCCTCATTGGATAAATCGAAGTAATAATTTGA
1 CACCCAGTGCCTCA-TCGATTAATCGAAGTAGTAAATTGA
* * * *
58999233 CACCCAGTGTCTCATCGGTTAAAACGAAGT-G--AATTGC
1 CACCCAGTGCCTCATCGATT-AATCGAAGTAGTAAATTGA
*
58999270 CACCCAGCGCCTCATCGTATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCG-ATTAAT-CGAAGTAGTAAATTGA
*
58999311 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
58999329 CTCAAAGTCG
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
39 4 0.05
40 22 0.29
41 20 0.27
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGATTAATCGAAGTAGTAAATTGA
Found at i:59005368 original size:40 final size:39
Alignment explanation
Indices: 59005308--59005444 Score: 125
Period size: 40 Copynumber: 3.5 Consensus size: 39
59005298 AACACACCAG
*
59005308 TTTGGCACCCAGTGCCTCATCGAATAATTCGAAGTAATAA
1 TTTGACACCCAGTGCCTCATCGAATAATTCGAAGT-ATAA
* ** ** * *
59005348 TTTGACACCCAGTGTCTCATCGGTTAAAACAAAGT-GAA
1 TTTGACACCCAGTGCCTCATCGAATAATTCGAAGTATAA
* *
59005386 -TTGGCACCCCGTGCCTCATCGAATTAATTCGAAGTAGTAA
1 TTTGACACCCAGTGCCTCATCGAA-TAATTCGAAGTA-TAA
* *
59005426 ATTGACACCCAGTGTCTCA
1 TTTGACACCCAGTGCCTCA
59005445 GCGACTCAAA
Statistics
Matches: 73, Mismatches: 20, Indels: 7
0.73 0.20 0.07
Matches are distributed among these distances:
37 18 0.25
38 10 0.14
40 30 0.41
41 15 0.21
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
TTTGACACCCAGTGCCTCATCGAATAATTCGAAGTATAA
Found at i:59005612 original size:17 final size:16
Alignment explanation
Indices: 59005583--59005629 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
59005573 TCAAATGATC
*
59005583 AATATATATTCAATAT
1 AATATAAATTCAATAT
59005599 -ATATACCAATTCAAT-T
1 AATATA--AATTCAATAT
59005615 AATATAAATTCAATA
1 AATATAAATTCAATA
59005630 AATTTATCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
15 13 0.50
16 1 0.04
17 12 0.46
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (16 bp):
AATATAAATTCAATAT
Found at i:59006533 original size:25 final size:28
Alignment explanation
Indices: 59006489--59006539 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
59006479 TCCTTCTTTT
*
59006489 CTTTCTTTCCTCTCTATTTTGTTTCTAC
1 CTTTCTTTCCTCTCTATTTTCTTTCTAC
59006517 CTTTCTTT-CTCT-T-TTTTCTTTCT
1 CTTTCTTTCCTCTCTATTTTCTTTCT
59006540 TTATTTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 1 0.05
27 4 0.18
28 8 0.36
ACGTcount: A:0.04, C:0.27, G:0.02, T:0.67
Consensus pattern (28 bp):
CTTTCTTTCCTCTCTATTTTCTTTCTAC
Found at i:59009480 original size:17 final size:16
Alignment explanation
Indices: 59009458--59009528 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 16
59009448 AACAAGTAAT
59009458 TTAAAAATTATAAACAA
1 TTAAAAATTATAAA-AA
* *
59009475 TTAAAAATAACATAAAAT
1 TTAAAAAT--TATAAAAA
59009493 TTCCAAAAATTATTAAAAA
1 TT--AAAAATTA-TAAAAA
*
59009512 TTAAAAATTAAAAAAA
1 TTAAAAATTATAAAAA
59009528 T
1 T
59009529 AGTATAACGT
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
16 6 0.14
17 16 0.36
18 4 0.09
19 12 0.27
20 6 0.14
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAATTATAAAAA
Found at i:59010814 original size:84 final size:81
Alignment explanation
Indices: 59010651--59010879 Score: 246
Period size: 84 Copynumber: 2.7 Consensus size: 81
59010641 CAAGCAAGGG
* *
59010651 ACTTGGT-CCCTTGGTTTGGTAAATATTCCTCTTTTAGTCCTCTAAATTTATAAACTTGTCATTA
1 ACTTGGTCCCCTTGGTTTGGTAAA-ATTCCTC-TTTAGTCCTCTAAATTTGT-AACTTGTCACT-
*
59010715 AATTAAATGGTAAAAATAAA
62 AATTAAATGGGAAAAATAAA
* *
59010735 ATTTGGTCCCCTTGATTTGGTAAAATTCCTCATTTAGGTCCTCTAAATTTGTAATCTTGTCAGCT
1 ACTTGGTCCCCTTGGTTTGGTAAAATTCCTC-TTTA-GTCCTCTAAATTTGTAA-CTTGTCA-CT
**
59010800 -ATTAAATGGGAAAAATGTA
62 AATTAAATGGGAAAAATAAA
* ** * *
59010819 CCTTGAACCCATTGGTTTGGTAAAATTCCTCTTGTAGTCCTCCAAATTTGTGAACTTGTCA
1 ACTTGGTCCCCTTGGTTTGGTAAAATTCCTCTT-TAGTCCTCTAAATTTGT-AACTTGTCA
59010880 TATAAGTACT
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
83 23 0.19
84 64 0.52
85 36 0.29
86 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (81 bp):
ACTTGGTCCCCTTGGTTTGGTAAAATTCCTCTTTAGTCCTCTAAATTTGTAACTTGTCACTAATT
AAATGGGAAAAATAAA
Found at i:59012217 original size:15 final size:13
Alignment explanation
Indices: 59012178--59012222 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
59012168 TGTGGCGAGC
59012178 ATAAATTTTAAAAA
1 ATAAA-TTTAAAAA
*
59012192 ATATATTTAAAAA
1 ATAAATTTAAAAA
59012205 ATAAATTAATAAAAA
1 ATAAATT--TAAAAA
59012220 ATA
1 ATA
59012223 GTATAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 14 0.52
14 4 0.15
15 9 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATAAATTTAAAAA
Found at i:59037399 original size:21 final size:21
Alignment explanation
Indices: 59037375--59037416 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
59037365 TTGTTAGTGA
59037375 ATAGAAGATGAAACTGGAAAT
1 ATAGAAGATGAAACTGGAAAT
59037396 ATAGAAGATGAAACTGGAAAT
1 ATAGAAGATGAAACTGGAAAT
59037417 TGTTGCAATT
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:0.52, C:0.05, G:0.24, T:0.19
Consensus pattern (21 bp):
ATAGAAGATGAAACTGGAAAT
Found at i:59040223 original size:22 final size:22
Alignment explanation
Indices: 59040198--59040240 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59040188 TTATTTTTTC
59040198 TTAAAATAGTAAAATTAAACCA
1 TTAAAATAGTAAAATTAAACCA
* *
59040220 TTAAAATATTAAAATTCAACC
1 TTAAAATAGTAAAATTAAACC
59040241 CACCAGTCCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.30
Consensus pattern (22 bp):
TTAAAATAGTAAAATTAAACCA
Found at i:59040428 original size:12 final size:13
Alignment explanation
Indices: 59040400--59040438 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
59040390 AAAATTTAGC
59040400 TATTATTTAAAATAA
1 TATTATTT-AAA-AA
59040415 TATT-TTTAAAAA
1 TATTATTTAAAAA
59040427 TATTATTTAAAA
1 TATTATTTAAAA
59040439 TGAGTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.26
13 10 0.43
14 3 0.13
15 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATTATTTAAAAA
Found at i:59041543 original size:24 final size:26
Alignment explanation
Indices: 59041498--59041545 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
59041488 TGGAGGTTAT
*
59041498 AGATAAATTTTTTTGAGTTTCAATTG
1 AGATAAATTTTGTTGAGTTTCAATTG
*
59041524 AGATATATTTTGTT-AG-TTCAAT
1 AGATAAATTTTGTTGAGTTTCAAT
59041546 GATTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 2 0.10
26 12 0.60
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (26 bp):
AGATAAATTTTGTTGAGTTTCAATTG
Found at i:59044578 original size:101 final size:101
Alignment explanation
Indices: 59044449--59044658 Score: 411
Period size: 101 Copynumber: 2.1 Consensus size: 101
59044439 TAGTTCTATG
*
59044449 TTAGCATAATTAATGGATGAGGTTGTTCTGAATAACTTTTGAATATGATAGTAAAGTTTTGAGCT
1 TTAGTATAATTAATGGATGAGGTTGTTCTGAATAACTTTTGAATATGATAGTAAAGTTTTGAGCT
59044514 CAGAAGGTTATATAATGACATGTAATTATAAGGTAA
66 CAGAAGGTTATATAATGACATGTAATTATAAGGTAA
59044550 TTAGTATAATTAATGGATGAGGTTGTTCTGAATAACTTTTGAATATGATAGTAAAGTTTTGAGCT
1 TTAGTATAATTAATGGATGAGGTTGTTCTGAATAACTTTTGAATATGATAGTAAAGTTTTGAGCT
59044615 CAGAAGGTTATATAATGACATGTAATTATAAGGTAA
66 CAGAAGGTTATATAATGACATGTAATTATAAGGTAA
59044651 TTAGTATA
1 TTAGTATA
59044659 TATATATATA
Statistics
Matches: 108, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 108 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.38
Consensus pattern (101 bp):
TTAGTATAATTAATGGATGAGGTTGTTCTGAATAACTTTTGAATATGATAGTAAAGTTTTGAGCT
CAGAAGGTTATATAATGACATGTAATTATAAGGTAA
Found at i:59051016 original size:40 final size:40
Alignment explanation
Indices: 59050895--59051025 Score: 117
Period size: 40 Copynumber: 3.3 Consensus size: 40
59050885 GACTTCGAGT
* * * *
59050895 CGATGAGACACTGGGTGTAAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATT-ATC
* * * * * *
59050936 TGATGAGGCATTGGGTGCCAA--T-TTACTTC-AGTTTAGC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGA-ATTATC
59050973 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
*
59051013 CGATGAGGCACTG
1 CGATGAGACACTG
59051026 AGTGCCAAAC
Statistics
Matches: 68, Mismatches: 17, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
37 18 0.26
38 8 0.12
39 2 0.03
40 23 0.34
41 17 0.25
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTATTACTTCGAATTATC
Found at i:59053022 original size:26 final size:26
Alignment explanation
Indices: 59052993--59053050 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
59052983 ATAAGAGTCA
* * *
59052993 TAATTAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACAAAGAACCTT
* *
59053019 TAATCAGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAACCTT
59053045 TAATCA
1 TAATCA
59053051 AGAGCTTCGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAACCTT
Found at i:59055001 original size:16 final size:15
Alignment explanation
Indices: 59054980--59055032 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
59054970 AGAGTAGAAA
59054980 GAAAATTGGAAGAATG
1 GAAAATT-GAAGAATG
** *
59054996 GAAAATTGAATGGGTA
1 GAAAATTGAA-GAATG
59055012 GAAAATTAGAAGAATG
1 GAAAATT-GAAGAATG
59055028 GAAAA
1 GAAAA
59055033 CATTAATTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.53, C:0.00, G:0.28, T:0.19
Consensus pattern (15 bp):
GAAAATTGAAGAATG
Found at i:59057425 original size:44 final size:44
Alignment explanation
Indices: 59057336--59057425 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
59057326 GTTAGAATAA
* * * * * *
59057336 AATAGAAGTTGTGATAGTTGTAGATTTAAAAATAATTATATTTT
1 AATAGAAGTTGTGATAATTGCACACTTAAAAATAATTAAAATTT
*
59057380 AATAGAATTTGTGATAATTGCACACTTAAAAATAATTAAAATTT
1 AATAGAAGTTGTGATAATTGCACACTTAAAAATAATTAAAATTT
59057424 AA
1 AA
59057426 ATTACAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (44 bp):
AATAGAAGTTGTGATAATTGCACACTTAAAAATAATTAAAATTT
Found at i:59058080 original size:6 final size:6
Alignment explanation
Indices: 59058069--59058093 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
59058059 CCCCGTTCTC
59058069 CCATTA CCATTA CCATTA CCATTA C
1 CCATTA CCATTA CCATTA CCATTA C
59058094 AACCTTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (6 bp):
CCATTA
Found at i:59065265 original size:44 final size:44
Alignment explanation
Indices: 59065215--59065305 Score: 130
Period size: 44 Copynumber: 2.1 Consensus size: 44
59065205 ATTGAAGTAA
* *
59065215 AATAGAAATTGTGGTAA-CTATACATTTAAAAATAATTATAATTT
1 AATAGAAATTGTGGTAATC-ACACATTTAAAAATAATTATAACTT
* *
59065259 AATAGAAGTTGTGGTAATCACACGTTTAAAAATAATTATAACTT
1 AATAGAAATTGTGGTAATCACACATTTAAAAATAATTATAACTT
59065303 AAT
1 AAT
59065306 TTACAATTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 41 0.98
45 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.36
Consensus pattern (44 bp):
AATAGAAATTGTGGTAATCACACATTTAAAAATAATTATAACTT
Found at i:59075785 original size:5 final size:5
Alignment explanation
Indices: 59075775--59075802 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59075765 TTACTTAGCC
59075775 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
59075803 CAAAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:59075948 original size:8 final size:8
Alignment explanation
Indices: 59075935--59075961 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
59075925 ACAGAGGGCG
59075935 TTTTTTCT
1 TTTTTTCT
59075943 TTTTTTCT
1 TTTTTTCT
59075951 TTTTTTCT
1 TTTTTTCT
59075959 TTT
1 TTT
59075962 ACTCAATTTT
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:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTCT
Found at i:59076692 original size:2 final size:2
Alignment explanation
Indices: 59076685--59076719 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59076675 TATACGCATT
*
59076685 TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59076720 TATTATTCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59076768 original size:20 final size:22
Alignment explanation
Indices: 59076743--59076790 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 22
59076733 AATTTTTTTA
59076743 ATACATACATATT-CTA-AA-AT
1 ATACATACAT-TTCCTATAATAT
*
59076763 ATACATTCATTTCCTATAATAT
1 ATACATACATTTCCTATAATAT
59076785 ATACAT
1 ATACAT
59076791 TTTTCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 2 0.08
20 12 0.50
21 2 0.08
22 8 0.33
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (22 bp):
ATACATACATTTCCTATAATAT
Found at i:59093174 original size:19 final size:22
Alignment explanation
Indices: 59093132--59093174 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 22
59093122 ACTCGATAGC
*
59093132 AAATACAAAAGTTGTTAATTTA
1 AAATACAAAAGTTGTTAATATA
59093154 AAAT-CAAAA-TT-TTAATATA
1 AAATACAAAAGTTGTTAATATA
59093173 AA
1 AA
59093175 TAGATTAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 5 0.25
22 4 0.20
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (22 bp):
AAATACAAAAGTTGTTAATATA
Found at i:59094070 original size:18 final size:18
Alignment explanation
Indices: 59094047--59094099 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
59094037 ACTTATTAAG
59094047 GGTGGCCGCCATGGTGGT
1 GGTGGCCGCCATGGTGGT
* *
59094065 GGTGGCCACCATGGCGGT
1 GGTGGCCGCCATGGTGGT
*
59094083 GATGGCCGCCATGGTGG
1 GGTGGCCGCCATGGTGG
59094100 GGCTTAGGCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.09, C:0.25, G:0.47, T:0.19
Consensus pattern (18 bp):
GGTGGCCGCCATGGTGGT
Found at i:59094121 original size:6 final size:6
Alignment explanation
Indices: 59094112--59094137 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
59094102 CTTAGGCTTA
59094112 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
59094138 TGTTTGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:59095009 original size:17 final size:17
Alignment explanation
Indices: 59094983--59095020 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
59094973 TATTATATAC
59094983 TTTT-AAATTTTAATTA
1 TTTTAAAATTTTAATTA
*
59094999 TTTTAAAATTTTATTTA
1 TTTTAAAATTTTAATTA
59095016 TTTTA
1 TTTTA
59095021 TAAAAAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAAAATTTTAATTA
Found at i:59095393 original size:18 final size:20
Alignment explanation
Indices: 59095372--59095417 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
59095362 TTTTTAAAAA
*
59095372 ATTATAAATTTGTAAAATATT
1 ATTA-AAATTTATAAAATATT
59095393 ATTAAAATTTATAAAA-A-T
1 ATTAAAATTTATAAAATATT
59095411 ATTAAAA
1 ATTAAAA
59095418 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 1 0.04
20 11 0.46
21 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTAAAATTTATAAAATATT
Found at i:59095409 original size:21 final size:21
Alignment explanation
Indices: 59095372--59095414 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
59095362 TTTTTAAAAA
*
59095372 ATTATAAATTTGTAAAATATT
1 ATTATAAATTTATAAAATATT
59095393 ATTA-AAATTTATAAAAATATT
1 ATTATAAATTTAT-AAAATATT
59095414 A
1 A
59095415 AAAAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTATAAATTTATAAAATATT
Found at i:59095420 original size:21 final size:21
Alignment explanation
Indices: 59095377--59095430 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
59095367 AAAAAATTAT
* **
59095377 AAATTTGT-AAAATATTATTA
1 AAATTTATAAAAATATTAAAA
59095397 AAATTTATAAAAATATTAAAA
1 AAATTTATAAAAATATTAAAA
*
59095418 AAA-TTAAAAAAAT
1 AAATTTATAAAAAT
59095431 CAAAAATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATTTATAAAAATATTAAAA
Found at i:59095632 original size:10 final size:10
Alignment explanation
Indices: 59095617--59095682 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
59095607 CAACTTAAAC
*
59095617 TTTTTAATGA
1 TTTTTAATAA
59095627 TTTTTAATAA
1 TTTTTAATAA
**
59095637 -TTTT-ATTG
1 TTTTTAATAA
*
59095645 TTTTGAATAA
1 TTTTTAATAA
59095655 TATTTTAATAA
1 T-TTTTAATAA
*
59095666 ATTTTAATAA
1 TTTTTAATAA
59095676 TATTTTA
1 T-TTTTA
59095683 CTTATTTATA
Statistics
Matches: 43, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
8 2 0.05
9 7 0.16
10 21 0.49
11 13 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:59095680 original size:11 final size:11
Alignment explanation
Indices: 59095645--59095682 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
59095635 AATTTTATTG
59095645 TTTTGAATAATA
1 TTTT-AATAATA
59095657 TTTTAATAA-A
1 TTTTAATAATA
59095667 TTTTAATAATA
1 TTTTAATAATA
59095678 TTTTA
1 TTTTA
59095683 CTTATTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.40
11 11 0.44
12 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TTTTAATAATA
Found at i:59097273 original size:18 final size:18
Alignment explanation
Indices: 59097248--59097288 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59097238 TAGATGTGAT
* *
59097248 TTTA-ATTCTTTTATATA
1 TTTATATTCTTTCATAAA
59097265 TTTATATTCTTTCATAAA
1 TTTATATTCTTTCATAAA
59097283 TTTATA
1 TTTATA
59097289 ATTTTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTATATTCTTTCATAAA
Found at i:59097824 original size:27 final size:27
Alignment explanation
Indices: 59097764--59097828 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
59097754 AAATTAGAAA
* *
59097764 ATAAAAA-ATAAAGAAAAATGACTTGC
1 ATAAAAATAAAAAAAAAAATGACTTGC
* *
59097790 CTAGAAATAAAAAAAAAAACTGAC-TGC
1 ATAAAAATAAAAAAAAAAA-TGACTTGC
59097817 ATAAAAATAAAA
1 ATAAAAATAAAA
59097829 CATGTAAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 5 0.16
27 22 0.71
28 4 0.13
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (27 bp):
ATAAAAATAAAAAAAAAAATGACTTGC
Found at i:59100197 original size:36 final size:36
Alignment explanation
Indices: 59100151--59100259 Score: 200
Period size: 36 Copynumber: 3.0 Consensus size: 36
59100141 GGTAGCATTA
*
59100151 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
59100187 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
59100223 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
59100259 G
1 G
59100260 GTAGCCTTAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:59100207 original size:21 final size:20
Alignment explanation
Indices: 59100179--59100244 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
59100169 AGTGAAAAAG
59100179 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
* **
59100199 TGATCAAGTG--A-A--AAAG
1 TGAT-AAGTGCTATACTTATC
59100215 TGATAAGTGCTATACTTATC
1 TGATAAGTGCTATACTTATC
59100235 TGATCAAGTG
1 TGAT-AAGTG
59100245 ACAAAGTGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 13
0.63 0.12 0.25
Matches are distributed among these distances:
15 5 0.15
16 5 0.15
17 1 0.03
18 2 0.06
19 1 0.03
20 9 0.27
21 10 0.30
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (20 bp):
TGATAAGTGCTATACTTATC
Found at i:59100218 original size:82 final size:84
Alignment explanation
Indices: 59100115--59100348 Score: 244
Period size: 82 Copynumber: 2.8 Consensus size: 84
59100105 TTTGAGTACT
*
59100115 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCATTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC--TAGCTACACTTATCTGATCAAGTGAAAAAGT
59100180 GATAAGTG-C-TA-T-ACTTA
64 GATAAGTGCCTTACTAACTTA
*
59100197 TCTGATCAAGTGAAAAAGTGATAA---GT-GCTA--T--ACTTATCTGATCAAGTGACAAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
59100254 TAAGTGGTAGCCTTAGCTACACTTA
66 TAA---GT-GCCTTA-CTA-ACTTA
* * *
59100279 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AG-GGACAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTAGCTACACTTATCTGATCAAGTGAAAAAGTG
59100342 ATAAGTG
65 ATAAGTG
59100349 ATCATATGTA
Statistics
Matches: 127, Mismatches: 6, Indels: 35
0.76 0.04 0.21
Matches are distributed among these distances:
72 28 0.22
74 1 0.01
75 2 0.02
76 3 0.02
77 1 0.01
78 4 0.03
79 2 0.02
80 1 0.01
82 51 0.40
85 3 0.02
86 3 0.02
87 3 0.02
89 11 0.09
90 2 0.02
91 12 0.09
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (84 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTAGCTACACTTATCTGATCAAGTGAAAAAGTGA
TAAGTGCCTTACTAACTTA
Found at i:59100331 original size:45 final size:46
Alignment explanation
Indices: 59100223--59100348 Score: 213
Period size: 46 Copynumber: 2.8 Consensus size: 46
59100213 AGTGATAAGT
*
59100223 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
59100269 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCC-TA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
*
59100314 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
59100349 ATCATATGTA
Statistics
Matches: 78, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
43 12 0.15
44 5 0.06
45 19 0.24
46 42 0.54
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTA
Found at i:59103356 original size:13 final size:13
Alignment explanation
Indices: 59103323--59103365 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
59103313 AGCTTGATTG
*
59103323 AAAACTTGATTAA
1 AAAACTTGATGAA
59103336 AAACACTTGATGAA
1 AAA-ACTTGATGAA
59103350 AAAACTTGATGAA
1 AAAACTTGATGAA
59103363 AAA
1 AAA
59103366 GTGAACATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
13 16 0.57
14 12 0.43
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (13 bp):
AAAACTTGATGAA
Found at i:59106692 original size:171 final size:171
Alignment explanation
Indices: 59106497--59106845 Score: 698
Period size: 171 Copynumber: 2.0 Consensus size: 171
59106487 TCCAACTGTA
59106497 AAAGAAGTTATTTGTTGTTCTTGTTGTTGGCTATTTTTATTTATTTATTTTGGGTGTTTTCGATT
1 AAAGAAGTTATTTGTTGTTCTTGTTGTTGGCTATTTTTATTTATTTATTTTGGGTGTTTTCGATT
59106562 TGTTTTTGAAGTGACATTAATAGGAGAAAACTAGGTGTAAGTCAAGATGATACTAGAAGGTCAAT
66 TGTTTTTGAAGTGACATTAATAGGAGAAAACTAGGTGTAAGTCAAGATGATACTAGAAGGTCAAT
59106627 ATTAGTTTCTTAGTGTAAGAAAGTGAAGTATTGATGAAAGC
131 ATTAGTTTCTTAGTGTAAGAAAGTGAAGTATTGATGAAAGC
59106668 AAAGAAGTTATTTGTTGTTCTTGTTGTTGGCTATTTTTATTTATTTATTTTGGGTGTTTTCGATT
1 AAAGAAGTTATTTGTTGTTCTTGTTGTTGGCTATTTTTATTTATTTATTTTGGGTGTTTTCGATT
59106733 TGTTTTTGAAGTGACATTAATAGGAGAAAACTAGGTGTAAGTCAAGATGATACTAGAAGGTCAAT
66 TGTTTTTGAAGTGACATTAATAGGAGAAAACTAGGTGTAAGTCAAGATGATACTAGAAGGTCAAT
59106798 ATTAGTTTCTTAGTGTAAGAAAGTGAAGTATTGATGAAAGC
131 ATTAGTTTCTTAGTGTAAGAAAGTGAAGTATTGATGAAAGC
59106839 AAAGAAG
1 AAAGAAG
59106846 GGAGGGTTTG
Statistics
Matches: 178, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
171 178 1.00
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.41
Consensus pattern (171 bp):
AAAGAAGTTATTTGTTGTTCTTGTTGTTGGCTATTTTTATTTATTTATTTTGGGTGTTTTCGATT
TGTTTTTGAAGTGACATTAATAGGAGAAAACTAGGTGTAAGTCAAGATGATACTAGAAGGTCAAT
ATTAGTTTCTTAGTGTAAGAAAGTGAAGTATTGATGAAAGC
Found at i:59108666 original size:2 final size:2
Alignment explanation
Indices: 59108659--59108685 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59108649 GCTTATATTT
59108659 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 T
59108686 TTGTAGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59109127 original size:16 final size:16
Alignment explanation
Indices: 59109106--59109164 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
59109096 TAGTTCAACA
59109106 ATTTAAAATTAAAAAT
1 ATTTAAAATTAAAAAT
*
59109122 ATTT--AACTAAAAAT
1 ATTTAAAATTAAAAAT
* *
59109136 -TAATAAAAATAAAAAT
1 AT-TTAAAATTAAAAAT
*
59109152 ATTAAAAATTAAA
1 ATTTAAAATTAAA
59109165 TTTAATATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
13 1 0.03
14 10 0.30
16 21 0.64
17 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTTAAAATTAAAAAT
Found at i:59119390 original size:83 final size:83
Alignment explanation
Indices: 59119301--59119467 Score: 271
Period size: 83 Copynumber: 2.0 Consensus size: 83
59119291 AAGTTACATT
*
59119301 AGTTTTGATTATTTTAGGTTTTAGTTGTTTCGAGTTTAACTCACCTCAAACTATGATAATTATGG
1 AGTTTTGATTATTTTAGGTTTTAATTGTTTCGAGTTTAACTCACCTCAAACTATGATAATTATGG
*
59119366 TTTACCATGTGTCCTTTG
66 TTTACCATGGGTCCTTTG
* * * * *
59119384 AGTTTTGATTATTTTAGGTTTTAATTGTTTTGAGTTTAACTCACTTCGAACTATGCTAGTTATGG
1 AGTTTTGATTATTTTAGGTTTTAATTGTTTCGAGTTTAACTCACCTCAAACTATGATAATTATGG
59119449 TTTACCATGGGTCCTTTG
66 TTTACCATGGGTCCTTTG
59119467 A
1 A
59119468 ATTCGAGCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (83 bp):
AGTTTTGATTATTTTAGGTTTTAATTGTTTCGAGTTTAACTCACCTCAAACTATGATAATTATGG
TTTACCATGGGTCCTTTG
Found at i:59119736 original size:14 final size:14
Alignment explanation
Indices: 59119717--59119746 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59119707 AAGGTGTAAT
59119717 AAAAAATAAAAATA
1 AAAAAATAAAAATA
*
59119731 AAAAAATATAAATA
1 AAAAAATAAAAATA
59119745 AA
1 AA
59119747 TCTATTATAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAAAATAAAAATA
Found at i:59120185 original size:16 final size:16
Alignment explanation
Indices: 59120145--59120185 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
59120135 TAATTTATTA
59120145 AATAAAAT-TTATCTT
1 AATAAAATATTATCTT
* *
59120160 AAT-TAATATTATTTT
1 AATAAAATATTATCTT
59120175 AATAAAATATT
1 AATAAAATATT
59120186 TAAATTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.14
15 12 0.57
16 6 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:59120410 original size:17 final size:19
Alignment explanation
Indices: 59120371--59120415 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
59120361 AAATTAATTA
59120371 ATAAATTAATTGAACTTGT
1 ATAAATTAATTGAACTTGT
*
59120390 -TAAATTTA-TGAACTT-T
1 ATAAATTAATTGAACTTGT
59120406 ATAAA-TAATT
1 ATAAATTAATT
59120416 ATGTGAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 7 0.32
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (19 bp):
ATAAATTAATTGAACTTGT
Found at i:59120528 original size:28 final size:27
Alignment explanation
Indices: 59120470--59120531 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
59120460 TTGTTGATTT
* *
59120470 AATTCTCACTTTTTTCTCTGCTAACAT
1 AATTCTCACTTTTTTATCTGCTAACAA
*
59120497 AATTCTCACTTTCTTTATTTGCTATA-AA
1 AATTCTCACTTT-TTTATCTGCTA-ACAA
59120525 AATTCTC
1 AATTCTC
59120532 GATATGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 12 0.40
28 17 0.57
29 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (27 bp):
AATTCTCACTTTTTTATCTGCTAACAA
Found at i:59126762 original size:2 final size:2
Alignment explanation
Indices: 59126755--59126782 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
59126745 AATTCTGTAG
59126755 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59126783 TACAAATTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59128211 original size:10 final size:11
Alignment explanation
Indices: 59128197--59128238 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
59128187 TTCTATTATT
59128197 TTAATATTAAA
1 TTAATATTAAA
*
59128208 -TAATTTTAAAA
1 TTAATATT-AAA
59128219 TTAA-ATTAAA
1 TTAATATTAAA
59128229 TTAATATTAA
1 TTAATATTAA
59128239 TGATTCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 13 0.50
11 10 0.38
12 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:59128215 original size:16 final size:17
Alignment explanation
Indices: 59128194--59128238 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
59128184 TTTTTCTATT
59128194 ATTTTAATATTAAA-TA
1 ATTTTAATATTAAATTA
*
59128210 ATTTTAAAATTAAATTA
1 ATTTTAATATTAAATTA
*
59128227 A-ATTAATATTAA
1 ATTTTAATATTAA
59128239 TGATTCTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTAATATTAAATTA
Found at i:59128291 original size:16 final size:14
Alignment explanation
Indices: 59128254--59128300 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
59128244 CTAAATTAAT
59128254 TAAATA-TTTCTAA
1 TAAATATTTTCTAA
59128267 -AAATATTTTCTAA
1 TAAATATTTTCTAA
*
59128280 TAAATAATTTTTTGAA
1 TAAAT-ATTTTCT-AA
59128296 TAAAT
1 TAAAT
59128301 TCATTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 7 0.24
14 4 0.14
15 6 0.21
16 7 0.24
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (14 bp):
TAAATATTTTCTAA
Found at i:59130682 original size:21 final size:21
Alignment explanation
Indices: 59130638--59130675 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59130628 TAATTTGTAA
59130638 TAAATTATTAATAATATTATT
1 TAAATTATTAATAATATTATT
59130659 TAAATTA-TAAT-ATATTA
1 TAAATTATTAATAATATTA
59130676 ATATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATTATTAATAATATTATT
Found at i:59133504 original size:20 final size:22
Alignment explanation
Indices: 59133479--59133539 Score: 63
Period size: 23 Copynumber: 2.8 Consensus size: 22
59133469 ATCAGTATAT
59133479 GACACAT-AAGTGCCTGAA-AC
1 GACACATAAAGTGCCTGAATAC
* * *
59133499 GACACATGAGGTGCCTAAAATAC
1 GACACATAAAGTGCCT-GAATAC
*
59133522 AACACATAAAGTGCCTGA
1 GACACATAAAGTGCCTGA
59133540 TCGGCAAAGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
20 7 0.22
21 7 0.22
22 3 0.09
23 15 0.47
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (22 bp):
GACACATAAAGTGCCTGAATAC
Found at i:59134526 original size:24 final size:24
Alignment explanation
Indices: 59134498--59134543 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
59134488 TTCTTTTATG
59134498 TATTAGT-TAATAATAATAATATAT
1 TATTAGTATAATAA-AATAATATAT
*
59134522 TATTATTATAATAAAATAATAT
1 TATTAGTATAATAAAATAATAT
59134544 TTAATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
TATTAGTATAATAAAATAATATAT
Found at i:59134689 original size:6 final size:6
Alignment explanation
Indices: 59134678--59134707 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59134668 CCATAATATA
59134678 ATAATT ATAATT ATAATT ATAATT ATAATT
1 ATAATT ATAATT ATAATT ATAATT ATAATT
59134708 TATCAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:59135323 original size:2 final size:2
Alignment explanation
Indices: 59135312--59135346 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
59135302 TTGATGAATC
59135312 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59135347 ATGAAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:59135717 original size:6 final size:6
Alignment explanation
Indices: 59135706--59135732 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
59135696 GAAAAAAAAT
59135706 AATGAA AATGAA AATGAA AATGAA AAT
1 AATGAA AATGAA AATGAA AATGAA AAT
59135733 CAATTGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
AATGAA
Found at i:59136394 original size:21 final size:21
Alignment explanation
Indices: 59136370--59136410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
59136360 TCATCGTTTA
59136370 GTCTCGAGACATCT-AGAATAT
1 GTCTCGAGACA-CTAAGAATAT
*
59136391 GTCTTGAGACACTAAGAATA
1 GTCTCGAGACACTAAGAATA
59136411 AAAATAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (21 bp):
GTCTCGAGACACTAAGAATAT
Found at i:59138475 original size:24 final size:24
Alignment explanation
Indices: 59138448--59138502 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
59138438 AAATAGCCTA
* *
59138448 TAACGGGTAGCTCCAAAGAGTAAT
1 TAACGGGTAACTCCAAAGAGCAAT
* *
59138472 TAACGGGTAACTCCGAAGAGCACT
1 TAACGGGTAACTCCAAAGAGCAAT
59138496 TAACGGG
1 TAACGGG
59138503 AAGCACCGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (24 bp):
TAACGGGTAACTCCAAAGAGCAAT
Found at i:59138609 original size:26 final size:26
Alignment explanation
Indices: 59138550--59138603 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
59138540 GAACTAATGA
*
59138550 GAAGCTCACAAAGAGCCTTTAATCGG
1 GAAGCTCACAAAGAGCCTATAATCGG
*
59138576 GAAGCTCACGAAGAGCCATATAA-CGG
1 GAAGCTCACAAAGAGCC-TATAATCGG
59138602 GA
1 GA
59138604 CACTCATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (26 bp):
GAAGCTCACAAAGAGCCTATAATCGG
Found at i:59141106 original size:2 final size:2
Alignment explanation
Indices: 59141099--59141125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59141089 CTTAATAATA
59141099 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
59141126 ATTTCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59142495 original size:8 final size:8
Alignment explanation
Indices: 59142482--59142529 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
59142472 TTACTCTTCG
59142482 TTTTTTTC
1 TTTTTTTC
59142490 TTTTTTTC
1 TTTTTTTC
*
59142498 TTTTATTTA
1 TTTT-TTTC
* *
59142507 TTTGTTTG
1 TTTTTTTC
*
59142515 TTTTATTC
1 TTTTTTTC
59142523 TTTTTTT
1 TTTTTTT
59142530 TCCTTTCTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
8 26 0.81
9 6 0.19
ACGTcount: A:0.06, C:0.06, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:59143893 original size:15 final size:16
Alignment explanation
Indices: 59143862--59143894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
59143852 ATATCCTTTT
*
59143862 AAATTTCAAACACATA
1 AAATTTCAAACAAATA
59143878 AAATTTCAAA-AAATA
1 AAATTTCAAACAAATA
59143893 AA
1 AA
59143895 GGCAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATTTCAAACAAATA
Found at i:59146929 original size:10 final size:10
Alignment explanation
Indices: 59146914--59146986 Score: 69
Period size: 10 Copynumber: 7.2 Consensus size: 10
59146904 CAGTGGGGGC
*
59146914 AAAAAAGTAA
1 AAAAAAGCAA
*
59146924 AAAAAAGTAA
1 AAAAAAGCAA
59146934 AAAAACGAGCAA
1 AAAAA--AGCAA
59146946 ATAAAAAGCAA
1 A-AAAAAGCAA
59146957 AAAAAA-CAA
1 AAAAAAGCAA
*
59146966 AAAAAACCAA
1 AAAAAAGCAA
*
59146976 ATAAAAG-AA
1 AAAAAAGCAA
59146985 AA
1 AA
59146987 TACCTCTACC
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
9 12 0.22
10 28 0.51
11 6 0.11
12 5 0.09
13 4 0.07
ACGTcount: A:0.78, C:0.08, G:0.08, T:0.05
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:59146976 original size:19 final size:19
Alignment explanation
Indices: 59146943--59146986 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
59146933 AAAAAACGAG
*
59146943 CAAATAAAAAGCAAAAAAAA
1 CAAA-AAAAACCAAAAAAAA
*
59146963 CAAAAAAAACCAAATAAAA
1 CAAAAAAAACCAAAAAAAA
*
59146982 GAAAA
1 CAAAA
59146987 TACCTCTACC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.80, C:0.11, G:0.05, T:0.05
Consensus pattern (19 bp):
CAAAAAAAACCAAAAAAAA
Found at i:59148752 original size:46 final size:46
Alignment explanation
Indices: 59148696--59148893 Score: 124
Period size: 46 Copynumber: 4.3 Consensus size: 46
59148686 TAACTCTATC
59148696 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCT
1 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCT
* * * * * * * * *
59148742 TTCTTGTATTTGGCAG-CGAAGCAGATCGAA-AATGACAGATTTTACC
1 TCCCTGTATTTGGCAGTGGAA-TAGATTGAAGATTG-CAGATCTTGCT
* * * * * ** *
59148788 TCCTTGTGA-CT-ACAGTGGAGTACATTGAAG-CCG-ATAACTCTAT-C-
1 TCCCTGT-ATTTGGCAGTGGAATAGATTGAAGATTGCA-GA-TCT-TGCT
59148832 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCT
1 TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCT
*
59148878 TTCCTGTATTTGGCAG
1 TCCCTGTATTTGGCAG
59148894 CGAAGCAAAT
Statistics
Matches: 108, Mismatches: 30, Indels: 28
0.65 0.18 0.17
Matches are distributed among these distances:
43 2 0.02
44 9 0.08
45 39 0.36
46 56 0.52
47 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (46 bp):
TCCCTGTATTTGGCAGTGGAATAGATTGAAGATTGCAGATCTTGCT
Found at i:59148855 original size:136 final size:135
Alignment explanation
Indices: 59148587--59148999 Score: 675
Period size: 136 Copynumber: 3.1 Consensus size: 135
59148577 GCAGAGCTGG
** * *
59148587 TTGAAGATTATAGATCTTGCCTTCCTGTATTTGGCAGCGAAGCAGATCGAAGATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAAATGGCAGATTTTA
* * * *
59148652 CCTCC-CTAACTACAGAGGAGTACATTGAAGCTGATAACTCTATCTCCCTGTATTTGGCAGTGGA
66 CCTCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
59148716 ATAGA
131 ATAGA
* *
59148721 TTGAAGATTGCAGATCTTGCTTTCTTGTATTTGGCAGCGAAGCAGATCGAAAATGACAGATTTTA
1 TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAAATGGCAGATTTTA
59148786 CCTCCTTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGG
66 CCTCC-TGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGG
59148851 AATAGA
130 AATAGA
*
59148857 TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAAATCGAAAATGGCAGATTTTA
1 TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAAATGGCAGATTTTA
* *
59148922 CCTCCCTGTGACTACGGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTAG
66 CCT-CCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGG
59148987 AATAGA
130 AATAGA
*
59148993 GTGAAGA
1 TTGAAGA
59149000 AAACCAGATC
Statistics
Matches: 260, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
134 64 0.25
136 194 0.75
137 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (135 bp):
TTGAAGATTGCAGATCTTGCTTTCCTGTATTTGGCAGCGAAGCAGATCGAAAATGGCAGATTTTA
CCTCCTGTGACTACAGTGGAGTACATTGAAGCCGATAACTCTATCTCCCTGTATTTGGCAGTGGA
ATAGA
Found at i:59149106 original size:82 final size:82
Alignment explanation
Indices: 59149004--59149574 Score: 971
Period size: 82 Copynumber: 7.0 Consensus size: 82
59148994 TGAAGAAAAC
*
59149004 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
*
59149069 CGGAGCGGACAAAACCA
66 CGGAGCAGACAAAACCA
59149086 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
*
59149151 CGGAGCGGACAAAACCA
66 CGGAGCAGACAAAACCA
*
59149168 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCGTCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
*
59149233 CGGAGAAGACAAAACCA
66 CGGAGCAGACAAAACCA
*
59149250 CAGATCTTATCTCCCTAAGCAATAGTGGAGCGGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
*
59149315 CGGAGCGGACAAAACCA
66 CGGAGCAGACAAAACCA
* *
59149332 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTACCTCCCTAAGCAATAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
* *
59149397 TGGAGCAGACAGAACCA
66 CGGAGCAGACAAAACCA
* * *
59149414 CAGATCTTATCTCCTTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGTAATAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
* *
59149479 TGGAGCAGACAGAACCA
66 CGGAGCAGACAAAACCA
* *
59149496 CGGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTATTATCTCCCTAAGCAGTAG
1 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
*
59149561 TGGAGCAGACAAAA
66 CGGAGCAGACAAAA
59149575 AAAAAACCAA
Statistics
Matches: 466, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 466 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (82 bp):
CAGATCTTATCTCCCTAAGCAATAGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAG
CGGAGCAGACAAAACCA
Done.