Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 285 of 295
Found at i:90369458 original size:16 final size:17
Alignment explanation
Indices: 90369434--90369476 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
90369424 ATTACATGTG
90369434 AAAATAATAAAATAAA-T
1 AAAA-AATAAAATAAATT
* *
90369451 AAACAATAAATTAAATT
1 AAAAAATAAAATAAATT
90369468 AAAAAATAA
1 AAAAAATAA
90369477 CTCTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAATAAAATAAATT
Found at i:90373918 original size:23 final size:23
Alignment explanation
Indices: 90373888--90373934 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
90373878 ATTCTACATA
90373888 AGCATGCCATAACACACTGCATG
1 AGCATGCCATAACACACTGCATG
90373911 AGCATGCCATAACACACTGCATG
1 AGCATGCCATAACACACTGCATG
90373934 A
1 A
90373935 TACTTAGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.30, G:0.17, T:0.17
Consensus pattern (23 bp):
AGCATGCCATAACACACTGCATG
Found at i:90375756 original size:11 final size:11
Alignment explanation
Indices: 90375740--90375781 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
90375730 AAAAATTTGA
90375740 AATAAAATAAT
1 AATAAAATAAT
90375751 AATAAAATAAT
1 AATAAAATAAT
* *
90375762 AA-AAACTGAT
1 AATAAAATAAT
90375772 AAATAAAATA
1 -AATAAAATA
90375782 TTGAGCTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 6 0.24
11 15 0.60
12 4 0.16
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:90380781 original size:16 final size:16
Alignment explanation
Indices: 90380760--90380813 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
90380750 TTTGGTTCGT
90380760 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
* * **
90380776 TGTAATAGTATAGAAT
1 TGTAATGGAATAGAGC
90380792 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
90380808 TGTAAT
1 TGTAAT
90380814 CAGTAATTCA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:90380847 original size:46 final size:43
Alignment explanation
Indices: 90380795--90380888 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 43
90380785 ATAGAATTGT
*
90380795 AATGGAATAGAGCTGTAATCAGTAATTCAATTG-TTTGGTTGAATGG
1 AATGGAATAGAACTGTAAT-AGT-ATTC--TTGATTTGGTTGAATGG
*
90380841 AATGGAATAGAACTGTAATGGTATTCTTGTATTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGG
90380885 AATG
1 AATG
90380889 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
42 3 0.07
44 21 0.48
45 2 0.05
46 18 0.41
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (43 bp):
AATGGAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGG
Found at i:90381930 original size:141 final size:142
Alignment explanation
Indices: 90381710--90381983 Score: 430
Period size: 141 Copynumber: 1.9 Consensus size: 142
90381700 TTTTATAGAC
* * **
90381710 CTATTATTAAAAATGGGTTTTAGTTTTAGTTTTTTGTTATCTTCTGGAAATTGATTGAGAGTTGA
1 CTATTATTAAAAATGAGTTTTAGTTTTAGATTTTTGTTATCTTCTGGAAATTGATCAAGAGTTGA
*
90381775 AATTGTTGAGAAATGAATTTTTATTC-TTTCTTGTTATATTCTAGAAATTGATAGAGAGTAGAAG
66 AAGTGTTGAGAAATGAATTTTTATTCTTTTCTTGTTATATTCTAGAAATTGAT--AGAGTAGAAG
90381839 AGAATTTTACAAAT
129 AGAATTTTACAAAT
90381853 CTATTATTAAGAAATGAGTTTTAGTTTTA-ATTTTT-TTATCTTCT-GAAATTGATCAAGAGTTG
1 CTATTATTAA-AAATGAGTTTTAGTTTTAGATTTTTGTTATCTTCTGGAAATTGATCAAGAGTTG
* *
90381915 AAAGTGTTGATAAATGAATTTTTATTCTTTTCTTGTTATGTTCTAGAAATTGATAGAGTAGAAGA
65 AAAGTGTTGAGAAATGAATTTTTATTCTTTTCTTGTTATATTCTAGAAATTGATAGAGTAGAAGA
90381980 GAAT
130 GAAT
90381984 GAGGAGTAAG
Statistics
Matches: 122, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
140 15 0.12
141 41 0.34
142 34 0.28
143 15 0.12
144 17 0.14
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (142 bp):
CTATTATTAAAAATGAGTTTTAGTTTTAGATTTTTGTTATCTTCTGGAAATTGATCAAGAGTTGA
AAGTGTTGAGAAATGAATTTTTATTCTTTTCTTGTTATATTCTAGAAATTGATAGAGTAGAAGAG
AATTTTACAAAT
Found at i:90383427 original size:9 final size:9
Alignment explanation
Indices: 90383383--90383504 Score: 59
Period size: 9 Copynumber: 12.8 Consensus size: 9
90383373 ATTATTATTA
90383383 TTATAAA-T
1 TTATAAATT
*
90383391 TTATAAGTT
1 TTATAAATT
*
90383400 TATATCAATT
1 T-TATAAATT
*
90383410 ATA-ATAATT
1 TTATA-AATT
90383419 TTATAAATT
1 TTATAAATT
* *
90383428 TTATGATTT
1 TTATAAATT
90383437 TTATAGAATT
1 TTATA-AATT
*
90383447 TTAATATATTT
1 TT-ATA-AATT
90383458 TTATAAAATT
1 TTAT-AAATT
*
90383468 TTAAAATATT
1 TTATAA-ATT
**
90383478 TTAGATATGTT
1 TT--ATAAATT
*
90383489 TTATAACTT
1 TTATAAATT
90383498 TTATAAA
1 TTATAAA
90383505 AAGAATTATA
Statistics
Matches: 84, Mismatches: 20, Indels: 19
0.68 0.16 0.15
Matches are distributed among these distances:
8 6 0.07
9 38 0.45
10 25 0.30
11 13 0.15
12 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (9 bp):
TTATAAATT
Found at i:90383459 original size:21 final size:20
Alignment explanation
Indices: 90383417--90383479 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
90383407 ATTATAATAA
*
90383417 TTTTATAAATTTT-AT-GAT
1 TTTTATAAATTTTAATATAT
90383435 TTTTATAGAATTTTAATATAT
1 TTTTATA-AATTTTAATATAT
*
90383456 TTTTATAAAATTTTAAAATAT
1 TTTTAT-AAATTTTAATATAT
90383477 TTT
1 TTT
90383480 AGATATGTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.18
19 6 0.15
20 2 0.05
21 23 0.59
22 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTATAAATTTTAATATAT
Found at i:90391562 original size:37 final size:37
Alignment explanation
Indices: 90391508--90391587 Score: 144
Period size: 37 Copynumber: 2.2 Consensus size: 37
90391498 CACAATCTCA
*
90391508 TCCA-TCTTCTCATATCATCTATTTTATGCAAATTGC
1 TCCACTCTTCTCATATCATATATTTTATGCAAATTGC
90391544 TCCACTCTTCTCATATCATATATTTTATGCAAATTGC
1 TCCACTCTTCTCATATCATATATTTTATGCAAATTGC
90391581 TCCACTC
1 TCCACTC
90391588 AGGACAAAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 4 0.10
37 38 0.90
ACGTcount: A:0.25, C:0.28, G:0.05, T:0.42
Consensus pattern (37 bp):
TCCACTCTTCTCATATCATATATTTTATGCAAATTGC
Found at i:90393304 original size:3 final size:3
Alignment explanation
Indices: 90393296--90393323 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
90393286 TTATGCTGTG
90393296 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
90393324 AGGAATGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:90395035 original size:4 final size:4
Alignment explanation
Indices: 90395028--90395082 Score: 83
Period size: 4 Copynumber: 13.8 Consensus size: 4
90395018 CATATATATA
* *
90395028 TATG TATG TATG TGTG TGTG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
90395076 TCTG TAT
1 TATG TAT
90395083 ATTGTGTGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:90396307 original size:18 final size:18
Alignment explanation
Indices: 90396284--90396338 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
90396274 TTCTTTTATC
*
90396284 AAATATATAAAAAATAAA
1 AAATATATATAAAATAAA
* *
90396302 AAATATGTATAAAATGAA
1 AAATATATATAAAATAAA
* *
90396320 AAATAAATATATAATAAA
1 AAATATATATAAAATAAA
90396338 A
1 A
90396339 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (18 bp):
AAATATATATAAAATAAA
Found at i:90396331 original size:24 final size:24
Alignment explanation
Indices: 90396293--90396339 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
90396283 CAAATATATA
*
90396293 AAAAATAAAAAATATGTATAAAATG
1 AAAAATAAAAAATAT-AATAAAATG
*
90396318 AAAAAT-AAATATATAATAAAAT
1 AAAAATAAAAAATATAATAAAAT
90396340 TCAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 7 0.35
25 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAAATAAAAAATATAATAAAATG
Found at i:90396349 original size:22 final size:21
Alignment explanation
Indices: 90396284--90396351 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
90396274 TTCTTTTATC
90396284 AAATATATAA-AAAA-T-AAA
1 AAATATATAATAAAATTAAAA
* *
90396302 AAATATGT-ATAAAATGAAAAA
1 AAATATATAATAAAAT-TAAAA
90396323 TAAATATATAATAAAATTCAAAA
1 -AAATATATAATAAAATT-AAAA
90396346 AAATAT
1 AAATAT
90396352 TATCTCAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
17 1 0.03
18 11 0.28
21 3 0.08
22 13 0.33
23 11 0.28
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.26
Consensus pattern (21 bp):
AAATATATAATAAAATTAAAA
Found at i:90396582 original size:19 final size:21
Alignment explanation
Indices: 90396553--90396595 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
90396543 TTAATTTTTT
*
90396553 AAAATTGATTAAAATTTGT-A
1 AAAATTGATTAAAAATTGTGA
90396573 AAAATT-ATTAAAAATTGTGA
1 AAAATTGATTAAAAATTGTGA
90396593 AAA
1 AAA
90396596 CTATAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (21 bp):
AAAATTGATTAAAAATTGTGA
Found at i:90397805 original size:24 final size:24
Alignment explanation
Indices: 90397777--90397828 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
90397767 TTTCTAAAAG
* *
90397777 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
*
90397801 ATTTAGCATTTATTAGCATAATTT
1 ATTTAGCATTTATTAGCATAATAT
90397825 ATTT
1 ATTT
90397829 GACCTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:90402754 original size:95 final size:95
Alignment explanation
Indices: 90402628--90402814 Score: 347
Period size: 95 Copynumber: 2.0 Consensus size: 95
90402618 CCCCTGTCTC
90402628 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
1 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
*
90402693 CATAACCTTGTAATTACATGAAATAGACAG
66 CATAACCCTGTAATTACATGAAATAGACAG
*
90402723 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAGAGTAATTTAT
1 GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
*
90402788 CATAACCCTGTAATTAGATGAAATAGA
66 CATAACCCTGTAATTACATGAAATAGA
90402815 TTATTATGTA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 89 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (95 bp):
GGGACATAAACTTGAAATACTACATTTGAGTTTGGATTTGAATCATAACTTTAAAAGTAATTTAT
CATAACCCTGTAATTACATGAAATAGACAG
Found at i:90407517 original size:21 final size:20
Alignment explanation
Indices: 90407492--90407540 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
90407482 AAAGAAATAC
*
90407492 CATAAAAATTTTAAAACTTTT
1 CATAAAAATTCTAAAA-TTTT
90407513 CAT-AAAATTCTAAAATTTT
1 CATAAAAATTCTAAAATTTT
90407532 CTATAAAAA
1 C-ATAAAAA
90407541 AAACCTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 13 0.52
21 7 0.28
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (20 bp):
CATAAAAATTCTAAAATTTT
Found at i:90410877 original size:63 final size:63
Alignment explanation
Indices: 90410806--90410933 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
90410796 TTGGGGCTAA
*
90410806 AGTAAGGAAATTTTGGTAAGGAAATGATTAAATTGAATTAAGAAAAGAGGAGAAAGGGACTAG
1 AGTAAGGAAATTTTGGTAAGGAAATAATTAAATTGAATTAAGAAAAGAGGAGAAAGGGACTAG
90410869 AGTAAGGAAATTTTGGTAAGGAAATAATTAAATTGAATTAAGAAAAGAGGAGAAAGGGACTAG
1 AGTAAGGAAATTTTGGTAAGGAAATAATTAAATTGAATTAAGAAAAGAGGAGAAAGGGACTAG
90410932 AG
1 AG
90410934 GTGGAAATTA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (63 bp):
AGTAAGGAAATTTTGGTAAGGAAATAATTAAATTGAATTAAGAAAAGAGGAGAAAGGGACTAG
Found at i:90411607 original size:25 final size:23
Alignment explanation
Indices: 90411578--90411641 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 23
90411568 CTATTTGGCA
*
90411578 TTTGTGGCGTATTCTGTATGTTGCC
1 TTTGTGGCGTATTCTGTA--TAGCC
* *
90411603 TTTGTGGCATACTCTG-ATAGCC
1 TTTGTGGCGTATTCTGTATAGCC
90411625 TTTGTGGCGTATTCTGT
1 TTTGTGGCGTATTCTGT
90411642 CTGGCCCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 18 0.55
24 1 0.03
25 14 0.42
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (23 bp):
TTTGTGGCGTATTCTGTATAGCC
Found at i:90411628 original size:22 final size:22
Alignment explanation
Indices: 90411600--90411665 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
90411590 TCTGTATGTT
90411600 GCCTTTGTGGCATACTCTGATA
1 GCCTTTGTGGCATACTCTGATA
* * * *
90411622 GCCTTTGTGGCGTATTCTGTCTG
1 GCCTTTGTGGCATACTCTG-ATA
* *
90411645 GCCCTTGTGGTATACTCTGAT
1 GCCTTTGTGGCATACTCTGAT
90411666 GAGTTTATAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.12, C:0.23, G:0.26, T:0.39
Consensus pattern (22 bp):
GCCTTTGTGGCATACTCTGATA
Found at i:90411631 original size:47 final size:45
Alignment explanation
Indices: 90411578--90411665 Score: 131
Period size: 45 Copynumber: 1.9 Consensus size: 45
90411568 CTATTTGGCA
*
90411578 TTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATAGCC
1 TTTGTGGCGTATTCTGTATG--GCCCTTGTGGCATACTCTGATAGCC
* *
90411625 TTTGTGGCGTATTCTGTCTGGCCCTTGTGGTATACTCTGAT
1 TTTGTGGCGTATTCTGTATGGCCCTTGTGGCATACTCTGAT
90411666 GAGTTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
45 19 0.50
47 19 0.50
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.43
Consensus pattern (45 bp):
TTTGTGGCGTATTCTGTATGGCCCTTGTGGCATACTCTGATAGCC
Found at i:90413796 original size:6 final size:6
Alignment explanation
Indices: 90413785--90413809 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
90413775 AATTGCATAG
90413785 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
90413810 AAAAAATTGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:90414003 original size:29 final size:29
Alignment explanation
Indices: 90413969--90414033 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
90413959 TAAATGAACT
90413969 TTAAATTT-TAAATTAAAAAAATAAAAAAA
1 TTAAATTTCTAAA-TAAAAAAATAAAAAAA
* * * *
90413998 TTAAATTTCTGAATATAAAAATATAAATA
1 TTAAATTTCTAAATAAAAAAATAAAAAAA
90414027 TTAAATT
1 TTAAATT
90414034 CCATACGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATTTCTAAATAAAAAAATAAAAAAA
Found at i:90422314 original size:148 final size:147
Alignment explanation
Indices: 90422116--90422525 Score: 523
Period size: 148 Copynumber: 2.8 Consensus size: 147
90422106 AAAACCTTAT
* *
90422116 TTCGAAATAGTT-AAAAAAATCAAAACTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTT
1 TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGAC--
* * *
90422180 AAAAAACATATTTTTTATTTTTCAAAATTTAAATTTTCTCC-TTTTTAAAAAAAAT-TATTTTTC
64 AAAAAAAAGA-TTTTTATTTTTCAAAATCTAAATTTTCTCCTTTTTTAAAAAAAATCTATTTTTC
* *
90422243 TTAAAGATTAACGATTTTAT
128 TTAAAGATTAAAGATTTTAC
* **
90422263 TTTGATGTAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACAA
1 TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACAA
* **
90422328 AAAAAAGATTTTTATTTTTCAAAATCTAAATTTTTTCCTTTTTTTTAAAAAATGCTATTTTTCTT
66 AAAAAAGATTTTTATTTTTCAAAATCTAAATTTTCTCCTTTTTTAAAAAAAAT-CTATTTTTCTT
*
90422393 AAAGATTAAAGCTTTTAC
130 AAAGATTAAAGATTTTAC
* * * *
90422411 TTCGAAATAGTTGAAAAAAATTAAAATTTTGTTTTAAAAATTTAAATTTTCCTTTAAAAT-A-AC
1 TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACAA
* *
90422474 AAAAAA-A--TTTATTTGTT-AAAATCTAAAATTTCTCTTTTTTTTAAAAAAAATC
66 AAAAAAGATTTTTATTT-TTCAAAATCTAAATTTTCTC-CTTTTTTAAAAAAAATC
90422526 AAAACTTTTC
Statistics
Matches: 231, Mismatches: 26, Indels: 16
0.85 0.10 0.06
Matches are distributed among these distances:
143 23 0.10
144 15 0.06
145 29 0.13
146 27 0.12
147 10 0.04
148 127 0.55
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (147 bp):
TTCGAAATAGTTGAAAAAAATTAAAACTTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACAA
AAAAAAGATTTTTATTTTTCAAAATCTAAATTTTCTCCTTTTTTAAAAAAAATCTATTTTTCTTA
AAGATTAAAGATTTTAC
Found at i:90422466 original size:20 final size:20
Alignment explanation
Indices: 90422426--90422469 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
90422416 AATAGTTGAA
**
90422426 AAAAATTAAAATTTTGTTTT
1 AAAAATTAAAATTTTCCTTT
*
90422446 AAAAATTTAAATTTTCCTTT
1 AAAAATTAAAATTTTCCTTT
90422466 AAAA
1 AAAA
90422470 TAACAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAAATTAAAATTTTCCTTT
Found at i:90422979 original size:34 final size:36
Alignment explanation
Indices: 90422929--90422999 Score: 101
Period size: 34 Copynumber: 2.0 Consensus size: 36
90422919 GGCCTTTGAC
* * *
90422929 AGGCTCAAAAAGGAAAGAA-GAAGAAA-AAAAGAAA
1 AGGCCCAAAAAAGAAAGAAGGAAAAAAGAAAAGAAA
90422963 AGGCCCAAAAAAGAAAGAAGGAAAAAAGAAAAGAAA
1 AGGCCCAAAAAAGAAAGAAGGAAAAAAGAAAAGAAA
90422999 A
1 A
90423000 ATAAAGGTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 17 0.53
35 6 0.19
36 9 0.28
ACGTcount: A:0.69, C:0.07, G:0.23, T:0.01
Consensus pattern (36 bp):
AGGCCCAAAAAAGAAAGAAGGAAAAAAGAAAAGAAA
Found at i:90422995 original size:16 final size:16
Alignment explanation
Indices: 90422946--90422997 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
90422936 AAAAGGAAAG
90422946 AAGAAGAAAAAAAGAA
1 AAGAAGAAAAAAAGAA
****
90422962 AAGGCCCAAAAAAG-A
1 AAGAAGAAAAAAAGAA
*
90422977 AAGAAGGAAAAAAGAA
1 AAGAAGAAAAAAAGAA
90422993 AAGAA
1 AAGAA
90422998 AAATAAAGGT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAAAAAGAA
Found at i:90428831 original size:18 final size:18
Alignment explanation
Indices: 90428808--90428862 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
90428798 TTATTTCTCG
90428808 TTATTTATATCTTTTTAT
1 TTATTTATATCTTTTTAT
* *
90428826 TTATTTATTTATTTTTAT
1 TTATTTATATCTTTTTAT
*
90428844 TCTAATTA-ATCTATTTTAT
1 T-TATTTATATCT-TTTTAT
90428863 GGTTAATCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATCTTTTTAT
Found at i:90436981 original size:10 final size:9
Alignment explanation
Indices: 90436968--90437001 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
90436958 ATTAATTTTG
90436968 ATTAAATTAA
1 ATTAAATT-A
90436978 ATTAAATTA
1 ATTAAATTA
*
90436987 ATCAAATTA
1 ATTAAATTA
90436996 ATTAAA
1 ATTAAA
90437002 ATAAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAAATTA
Found at i:90443733 original size:9 final size:9
Alignment explanation
Indices: 90443704--90443733 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
90443694 TAAATTTTAC
90443704 AATTCGAAT
1 AATTCGAAT
*
90443713 AACTCGAAT
1 AATTCGAAT
90443722 AATTCGAAT
1 AATTCGAAT
90443731 AAT
1 AAT
90443734 AAATTGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:90449829 original size:4 final size:4
Alignment explanation
Indices: 90449820--90449846 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
90449810 AGAGTAAGAT
90449820 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
90449847 TACTGATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:90455484 original size:47 final size:48
Alignment explanation
Indices: 90455432--90455537 Score: 117
Period size: 54 Copynumber: 2.1 Consensus size: 48
90455422 TGGTTGGACC
90455432 ATGGC-AACAAGTGATAAGC-GATATCCGTATAAGACCATAGCTAGGCT
1 ATGGCAAACAAGTGATAA-CTGATATCCGTATAAGACCATAGCTAGGCT
* *
90455479 ATGGCATCGAAAAACAAGTGATAACTGATTTCCGTATAAGACCATAGCTGGGCT
1 ATGG---C---AAACAAGTGATAACTGATATCCGTATAAGACCATAGCTAGGCT
90455533 ATGGC
1 ATGGC
90455538 TTTGGATTAA
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
47 4 0.08
50 1 0.02
51 1 0.02
53 1 0.02
54 42 0.86
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.23
Consensus pattern (48 bp):
ATGGCAAACAAGTGATAACTGATATCCGTATAAGACCATAGCTAGGCT
Found at i:90458562 original size:25 final size:25
Alignment explanation
Indices: 90458534--90458635 Score: 86
Period size: 25 Copynumber: 4.0 Consensus size: 25
90458524 TTACCTAAAT
90458534 AGCCTATGTGGCGTA-TTATTTGGAA
1 AGCCTATGTGGCG-AGTTATTTGGAA
*
90458559 AGCCT-TAGTGGAGAGGTTATTTGGGAA
1 AGCCTAT-GTGGCGA-GTTATTT-GGAA
* * *
90458586 A-CCTTTGTGGCGAGTTATCTGAAA
1 AGCCTATGTGGCGAGTTATTTGGAA
*
90458610 AGCTTATGTGGCGTA-TTATTTGGAA
1 AGCCTATGTGGCG-AGTTATTTGGAA
90458635 A
1 A
90458636 ACCTTAGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 14
0.74 0.10 0.17
Matches are distributed among these distances:
24 6 0.10
25 34 0.55
26 16 0.26
27 6 0.10
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.34
Consensus pattern (25 bp):
AGCCTATGTGGCGAGTTATTTGGAA
Found at i:90458590 original size:26 final size:25
Alignment explanation
Indices: 90458549--90458665 Score: 89
Period size: 26 Copynumber: 4.6 Consensus size: 25
90458539 ATGTGGCGTA
90458549 TTATTTGGAAAGCCTTAGTGGAGAGG
1 TTATTTGGAAAGCCTTAGTGGAGA-G
* *
90458575 TTATTTGGGAAA-CCTTTGTGGCGAG
1 TTATTT-GGAAAGCCTTAGTGGAGAG
* * *
90458600 TTATCTGAAAAG-CTTATGTGGCGTA-
1 TTATTTGGAAAGCCTTA-GTGGAG-AG
*
90458625 TTATTTGGAAAACCTTAGTAGTGAG-G
1 TTATTTGGAAAGCCTTAGT-G-GAGAG
*
90458651 TCATTTGGAAAGCCT
1 TTATTTGGAAAGCCT
90458666 GTAAAATGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
24 7 0.10
25 23 0.32
26 35 0.49
27 7 0.10
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (25 bp):
TTATTTGGAAAGCCTTAGTGGAGAG
Found at i:90458624 original size:76 final size:77
Alignment explanation
Indices: 90458498--90458665 Score: 218
Period size: 76 Copynumber: 2.2 Consensus size: 77
90458488 TTTATGACAA
* *
90458498 GTTATTT-GTAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAGC
1 GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAAC
*
90458562 CTTAGTGGAGAG
66 CTTAGTAGAGAG
* * * *
90458574 GTTATTTGGGAAA-CCTTTGTGGCGAGTTATCTGAAA-AGCTTATGTGGCGTATTATTTGGAAAA
1 GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCT-AAATAGCCTATGTGGCGTATTATTTGGAAAA
*
90458637 CCTTAGTAGTGAG
65 CCTTAGTAGAGAG
*
90458650 GTCATTT-GGAAAGCCT
1 GTTATTTGGGAAAGCCT
90458666 GTAAAATGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
75 5 0.06
76 68 0.85
77 7 0.09
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.35
Consensus pattern (77 bp):
GTTATTTGGGAAAGCCTTTGTAGCAAGTTACCTAAATAGCCTATGTGGCGTATTATTTGGAAAAC
CTTAGTAGAGAG
Found at i:90459763 original size:34 final size:34
Alignment explanation
Indices: 90459720--90459785 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
90459710 AATGCATAAT
*
90459720 TAAGTCTTTATTGTATTTTATTCCATATCACAAC
1 TAAGTCTTTATTGTATTTTATTCCACATCACAAC
90459754 TAAGTCTTTATTGTATTTTATTCCACATCACA
1 TAAGTCTTTATTGTATTTTATTCCACATCACA
90459786 TTATATGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (34 bp):
TAAGTCTTTATTGTATTTTATTCCACATCACAAC
Found at i:90470654 original size:30 final size:30
Alignment explanation
Indices: 90470620--90470682 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
90470610 ACTTAACAAG
90470620 CAAATGGCTCTAAAATAGA-AACAAAATTAA
1 CAAATGGCTCTAAAATA-ATAACAAAATTAA
* *
90470650 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGGCTCTAAAATAATAACAAAATTAA
90470680 CAA
1 CAA
90470683 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.57, C:0.13, G:0.06, T:0.24
Consensus pattern (30 bp):
CAAATGGCTCTAAAATAATAACAAAATTAA
Found at i:90479172 original size:26 final size:26
Alignment explanation
Indices: 90479143--90479192 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
90479133 CTCAGAAAAA
*
90479143 TTTTGATGATTTTACCCTTGGTAATT
1 TTTTGATGATTTTACCCTTAGTAATT
*
90479169 TTTTGATGATTTTGCCCTTAGTAA
1 TTTTGATGATTTTACCCTTAGTAA
90479193 AATTTCGAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.52
Consensus pattern (26 bp):
TTTTGATGATTTTACCCTTAGTAATT
Found at i:90479298 original size:6 final size:6
Alignment explanation
Indices: 90479287--90479323 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
90479277 TGCAAACGGA
* *
90479287 TCATTT TCATTT TCATTT TCATTT CCATTT CCATTT T
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT T
90479324 TGAAAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (6 bp):
TCATTT
Found at i:90483218 original size:12 final size:12
Alignment explanation
Indices: 90483201--90483225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90483191 GAGTAGCAAA
90483201 ACTGCCCTGAAT
1 ACTGCCCTGAAT
90483213 ACTGCCCTGAAT
1 ACTGCCCTGAAT
90483225 A
1 A
90483226 TTTGGATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.32, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCCCTGAAT
Found at i:90483432 original size:11 final size:11
Alignment explanation
Indices: 90483415--90483457 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
90483405 TAAATAAGAG
90483415 AAAATAAAATT
1 AAAATAAAATT
* *
90483426 TAAATAAAAATA
1 AAAAT-AAAATT
*
90483438 AAAATAAAAAT
1 AAAATAAAATT
90483449 AAAATAAAA
1 AAAATAAAA
90483458 GGACTCAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAAAATT
Found at i:90483436 original size:6 final size:6
Alignment explanation
Indices: 90483400--90483457 Score: 57
Period size: 6 Copynumber: 9.7 Consensus size: 6
90483390 ATAAGTCTTC
* **
90483400 AAAAAT AAATAAG AGAAAAT -AAAAT TTAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAA-AAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
90483449 -AAAAT AAAA
1 AAAAAT AAAA
90483458 GGACTCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
5 10 0.23
6 26 0.60
7 5 0.12
8 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:90489449 original size:30 final size:30
Alignment explanation
Indices: 90489408--90489464 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
90489398 ATGGCTATGA
*
90489408 CACACGGGCGTGTGGCCTACCCGTGTGTCT
1 CACACGAGCGTGTGGCCTACCCGTGTGTCT
*
90489438 CACACGAGCGTGTGGTCTACCCGTGTG
1 CACACGAGCGTGTGGCCTACCCGTGTG
90489465 GAAGTGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.32, G:0.33, T:0.23
Consensus pattern (30 bp):
CACACGAGCGTGTGGCCTACCCGTGTGTCT
Found at i:90497037 original size:7 final size:7
Alignment explanation
Indices: 90497029--90497059 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
90497019 AAGAGGGTCT
*
90497029 CTAGTCT
1 CTAGTCC
90497036 CTAGTCC
1 CTAGTCC
90497043 CTAGTCC
1 CTAGTCC
90497050 CTAGTCC
1 CTAGTCC
90497057 CTA
1 CTA
90497060 CCCTATTGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.39, G:0.13, T:0.32
Consensus pattern (7 bp):
CTAGTCC
Found at i:90499501 original size:45 final size:45
Alignment explanation
Indices: 90499452--90499670 Score: 330
Period size: 45 Copynumber: 4.9 Consensus size: 45
90499442 TCGGCCATGG
* * * *
90499452 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* *
90499497 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
90499542 TGCTTCCTCAAATTCTTCCATGAATTATGCACGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
*
90499587 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
* * * *
90499632 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
90499671 TCCACCTCTT
Statistics
Matches: 159, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 159 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
Found at i:90499605 original size:90 final size:90
Alignment explanation
Indices: 90499452--90499670 Score: 375
Period size: 90 Copynumber: 2.4 Consensus size: 90
90499442 TCGGCCATGG
* *
90499452 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAATGCTTCCTTAAATTCTTCCA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
90499517 TGAATTATGCATGATGTTGGTCAAA
66 TGAATTATGCATGATGTTGGTCAAA
* * * *
90499542 TGCTTCCTCAAATTCTTCCATGAATTATGCACGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
90499607 TGAATTATGCATGATGTTGGTCAAA
66 TGAATTATGCATGATGTTGGTCAAA
*
90499632 TGCTTCCTTAATTTGTTCCATAAATTATGCATGATGTTG
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTG
90499671 TCCACCTCTT
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 118 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (90 bp):
TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAATGCTTCCTCAAATTCTTCCA
TGAATTATGCATGATGTTGGTCAAA
Found at i:90505709 original size:45 final size:45
Alignment explanation
Indices: 90505660--90505923 Score: 411
Period size: 45 Copynumber: 5.9 Consensus size: 45
90505650 TCGGCCATGG
* * * * *
90505660 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
90505705 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
90505750 TGCTTCCTCAAATTCTTCCATGAATTATGCACGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
90505795 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
90505840 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
90505885 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
90505924 TCCACCTCTT
Statistics
Matches: 203, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 203 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:90511903 original size:30 final size:30
Alignment explanation
Indices: 90511859--90511925 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
90511849 TTAGCTTTTG
* *
90511859 CCACTACCAACTCCACTAGCCACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
* * *
90511889 CTACCACCTACTCCATTAGCTACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
90511919 CCACCAC
1 CCACCAC
90511926 TATTTGTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.46, G:0.06, T:0.22
Consensus pattern (30 bp):
CCACCACCTACTCCACTAGCCACACTTGCT
Found at i:90512497 original size:30 final size:30
Alignment explanation
Indices: 90512431--90512497 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
90512421 TAGGTACAAG
*
90512431 TGGTGGTGGAGCAAGTGTGGCTAATGGAGT
1 TGGTGGTAGAGCAAGTGTGGCTAATGGAGT
** *
90512461 AAGTGGTAGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTAGAGCAAGTGTGGCTAATGGAGT
90512491 TGGTGGT
1 TGGTGGT
90512498 GACAAAGGCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.21, C:0.06, G:0.46, T:0.27
Consensus pattern (30 bp):
TGGTGGTAGAGCAAGTGTGGCTAATGGAGT
Found at i:90513532 original size:90 final size:88
Alignment explanation
Indices: 90513379--90513733 Score: 376
Period size: 91 Copynumber: 3.9 Consensus size: 88
90513369 AATAAAAATC
* **
90513379 AATTGAAAATACCTCAGCGTATGAT-CTGAAGCTCAACTCACCTCTCGCAATATGAATTGATTTT
1 AATTGAAAATACCTCAGCG--TG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTT
* *
90513443 TTTGACAAACATAAATTGAAAAAAAAGA
63 TTTGAAAAACA-AAATTG-AAAAACAGA
* * * * *
90513471 AATTGAAAATATCTCAGCGTGTCCTGAGGCTGAACTCACCTCTCGCAATATGAGTTAATTTTTTG
1 AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT
90513536 GAAAAACAAAATTTGAAAAACAGA
66 GAAAAACAAAA-TTGAAAAACAGA
* ** * *
90513560 ATTTGAAAATACCTCAGCGTGTGAGTCAAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTT
1 AATTGAAAATACCTCAGCGTGT-CCT-GAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTT
*
90513625 TT-AAAACACAGAAATTGAAGAACAGA
64 TTGAAAA-ACA-AAATTGAAAAACAGA
* * * *
90513651 AATGGAAAACACCTCAGC--GTCTTGAGGTTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT
1 AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGA-TTTTTT
* *
90513714 TTAAAGACAGAAATTGAAAA
65 TGAAAAACA-AAATTGAAAA
90513734 TACCTCAACA
Statistics
Matches: 226, Mismatches: 29, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
87 30 0.13
88 21 0.09
89 37 0.16
90 54 0.24
91 63 0.28
92 21 0.09
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (88 bp):
AATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGCTGATTTTTTT
GAAAAACAAAATTGAAAAACAGA
Found at i:90513568 original size:13 final size:14
Alignment explanation
Indices: 90513536--90513568 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
90513526 TAATTTTTTG
90513536 GAAAAACAAAATTT
1 GAAAAACAAAATTT
*
90513550 GAAAAACAGAATTT
1 GAAAAACAAAATTT
90513564 GAAAA
1 GAAAA
90513569 TACCTCAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.64, C:0.06, G:0.12, T:0.18
Consensus pattern (14 bp):
GAAAAACAAAATTT
Found at i:90513600 original size:181 final size:177
Alignment explanation
Indices: 90513381--90513712 Score: 443
Period size: 181 Copynumber: 1.8 Consensus size: 177
90513371 TAAAAATCAA
* *
90513381 TTGAAAATACCTCAGCGTATGATCTGAAGCTCAACTCACCTCTCGCAATATGAATTGATTTTTTT
1 TTGAAAATACCTCAGCGTATGATC-GAAGCTCAACTCACCACTCGCAATATGAACTGATTTTTTT
* * * * * *
90513446 GACAA-ACATAAATTGAAAAAAAAGAAATTGAAAATATCTCAGCGTGTCCTGAGGCTGAACTCAC
65 -AAAACACAGAAATTG-AAAAAAAGAAATGGAAAACACCTCAGC--GTCCTGAGGCTCAACTCAC
*
90513510 CTCTCGCAATATGAGTTAATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
126 CTCTCGCAATATGAGCTAATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
* *
90513562 TTGAAAATACCTCAGCGTGTGAGTC-AAGGCTCAACTCACCACTCGCAATATGAGCTGATTTTTT
1 TTGAAAATACCTCAGCGTATGA-TCGAA-GCTCAACTCACCACTCGCAATATGAACTGATTTTTT
* * * *
90513626 TAAAACACAGAAATTGAAGAACAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTCACCTC
64 TAAAACACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTC
*
90513691 TCGCAATATGAGCTGATTTTTT
129 TCGCAATATGAGCTAATTTTTT
90513713 TTTAAAGACA
Statistics
Matches: 132, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
178 39 0.30
180 27 0.20
181 64 0.48
182 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (177 bp):
TTGAAAATACCTCAGCGTATGATCGAAGCTCAACTCACCACTCGCAATATGAACTGATTTTTTTA
AAACACAGAAATTGAAAAAAAGAAATGGAAAACACCTCAGCGTCCTGAGGCTCAACTCACCTCTC
GCAATATGAGCTAATTTTTTGGAAAAACAAAATTTGAAAAACAGAAT
Found at i:90513917 original size:75 final size:74
Alignment explanation
Indices: 90513639--90514181 Score: 722
Period size: 73 Copynumber: 7.4 Consensus size: 74
90513629 AACACAGAAA
* * * * *
90513639 TTGAAGAACAGAAATGGAAAACACCTC-A-GCGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
90513702 GCTGATTTTTT
66 GTTGA--TTTT
* * *
90513713 TTTAAAGACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90513778 GTTGA-TTT
66 GTTGATTTT
** * * * * *
90513786 TTGACGAACAAAAATTGAAATTACCTC-A-GCGTCTTGAGGTTCAACTCACCTATCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90513849 GTTGATTTTT
66 GTTGA-TTTT
*
90513859 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
90513924 GCTGATTTTT
66 GTTGA-TTTT
* * *
90513934 TTTAAAGACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90513999 GTTGA-TTT
66 GTTGATTTT
* * * * * *
90514007 TTGACAAACAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTATCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90514072 GTTGATTTT
66 GTTGATTTT
* *
90514081 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAGCTTACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
90514146 GTTGA-TTT
66 GTTGATTTT
* *
90514154 TTGAAAAGCATAAATTGAAAATACCTCA
1 TTGAAAAACAGAAATTGAAAATACCTCA
90514182 GTGATAAACA
Statistics
Matches: 412, Mismatches: 50, Indels: 15
0.86 0.10 0.03
Matches are distributed among these distances:
71 36 0.09
72 1 0.00
73 143 0.35
74 88 0.21
75 108 0.26
76 36 0.09
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (74 bp):
TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTT
Found at i:90514182 original size:147 final size:146
Alignment explanation
Indices: 90513639--90514181 Score: 716
Period size: 147 Copynumber: 3.7 Consensus size: 146
90513629 AACACAGAAA
* * * * *
90513639 TTGAAGAACAGAAATGGAAAACACCTCAGCGTCTTGAGGTTCAACTCACCTCTCGCAATATGAGC
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
** *
90513704 TGATTTTTTTTTAAAGACAGAAATTGAAAATACCTCAACATGTCTTGAGGCTCAACTCACCTCTC
66 TGA-TTTTTTGAAAAG-CAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTC
90513769 GCAATATGAGTTGA-TTT
129 GCAATATGAGTTGATTTT
** * * * *
90513786 TTGACGAACAAAAATTGAAATTACCTCAGCGTCTTGAGGTTCAACTCACCTATCGCAATATGAGT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
* *
90513851 TGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGTTCAACTCACCTCTCG
66 TGA-TTTTTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCG
*
90513916 CAATATGAGCTGATTTTT
130 CAATATGAGTTGA-TTTT
* * *
90513934 TTTAAAGACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
* * * * *
90513999 GTTGA-TTTTTGACAAA-CAAAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTAT
64 GTTGATTTTTTGA-AAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCT
90514062 CGCAATATGAGTTGATTTT
128 CGCAATATGAGTTGATTTT
* * *
90514081 TTGAAAAACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAGCTTACCTCTCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTC-A-GCGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
*
90514146 GTTGA-TTTTTGAAAAGCATAAATTGAAAATACCTCA
64 GTTGATTTTTTGAAAAGCAGAAATTGAAAATACCTCA
90514182 GTGATAAACA
Statistics
Matches: 354, Mismatches: 36, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
146 62 0.18
147 165 0.47
148 86 0.24
149 4 0.01
150 37 0.10
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (146 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTTTGAAAAGCAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGC
AATATGAGTTGATTTT
Found at i:90514455 original size:16 final size:15
Alignment explanation
Indices: 90514430--90514477 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
90514420 CTATTTTAAG
90514430 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
90514445 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
90514462 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
90514477 T
1 T
90514478 ATTCTTAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:90515406 original size:19 final size:19
Alignment explanation
Indices: 90515359--90515398 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
90515349 TATTTTGTTA
90515359 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
90515378 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
90515397 TT
1 TT
90515399 ACTTTTTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:90519482 original size:16 final size:15
Alignment explanation
Indices: 90519457--90519504 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
90519447 CTATTTTAAG
90519457 TTTATTTTAATTTTA
1 TTTATTTTAATTTTA
90519472 TTTATTTTTAATTATTA
1 TTTA-TTTTAATT-TTA
90519489 -TTATTTTAGATTTTA
1 TTTATTTTA-ATTTTA
90519504 T
1 T
90519505 ATTCTTAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.41
16 14 0.48
17 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTATTTTAATTTTA
Found at i:90520396 original size:18 final size:19
Alignment explanation
Indices: 90520373--90520436 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 19
90520363 TTCCTTTAAA
*
90520373 TTATTTTGT-TATTTATTT
1 TTATTTTATCTATTTATTT
*
90520391 TTATTTTATCTTTTTATTT
1 TTATTTTATCTATTTATTT
*
90520410 TTATTTCATCT-TTTACTTT
1 TTATTTTATCTATTTA-TTT
90520429 TTACTTTT
1 TTA-TTTT
90520437 TACGTTTTCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 12 0.31
19 24 0.62
20 3 0.08
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (19 bp):
TTATTTTATCTATTTATTT
Found at i:90520408 original size:19 final size:18
Alignment explanation
Indices: 90520384--90520436 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
90520374 TATTTTGTTA
90520384 TTTATTTTTATTTTATCTT
1 TTTATTTTTATTTTATC-T
*
90520403 TTTATTTTTATTTCATCT
1 TTTATTTTTATTTTATCT
90520421 TTTACTTTTTACTTTT
1 TTTA-TTTTTA-TTTT
90520437 TACGTTTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 22 0.73
20 3 0.10
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTATTTTTATTTTATCT
Found at i:90531129 original size:22 final size:23
Alignment explanation
Indices: 90531081--90531129 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
90531071 ATATTACATA
**
90531081 TGTATAAAAAATAAAAATTATTT
1 TGTATAAAAAATAAAAATTATAG
90531104 TGTA-AAAAAATATAAAA-TATAG
1 TGTATAAAAAATA-AAAATTATAG
90531126 TGTA
1 TGTA
90531130 GCATTTAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (23 bp):
TGTATAAAAAATAAAAATTATAG
Found at i:90554223 original size:33 final size:33
Alignment explanation
Indices: 90554179--90554242 Score: 103
Period size: 33 Copynumber: 1.9 Consensus size: 33
90554169 TTTTGTTTGA
90554179 TTAAATCAAGATT-AAAAAAGAGGTTAGGGTTAG
1 TTAAATCAAGATTAAAAAAAG-GGTTAGGGTTAG
*
90554212 TTAAATTAAGATTAAAAAAAGGGTTAGGGTT
1 TTAAATCAAGATTAAAAAAAGGGTTAGGGTT
90554243 TTCTGATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.30
Consensus pattern (33 bp):
TTAAATCAAGATTAAAAAAAGGGTTAGGGTTAG
Found at i:90558840 original size:13 final size:13
Alignment explanation
Indices: 90558822--90558885 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
90558812 AGTTTGGCAA
90558822 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
90558835 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* * *
90558848 TGCTATGGAAAAA
1 TGCTTTTGAAAAG
* *
90558861 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
90558874 TGCTTTTGAAAA
1 TGCTTTTGAAAA
90558886 TTTTGGTTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:90559106 original size:24 final size:24
Alignment explanation
Indices: 90559071--90559124 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
90559061 TATTTTAATA
*
90559071 TATAAA-ATATAAATTTTAAATATT
1 TATAAACA-ATAAATATTAAATATT
* *
90559095 TTTAAACAATAAATATTAATTATT
1 TATAAACAATAAATATTAAATATT
90559119 TATAAA
1 TATAAA
90559125 ATTTAATTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (24 bp):
TATAAACAATAAATATTAAATATT
Found at i:90559713 original size:27 final size:27
Alignment explanation
Indices: 90559683--90559755 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
90559673 TTTCTCAAGT
*
90559683 TGGTACCTAAACTTTTTTTTTGTCTTG
1 TGGTACCTAAACTATTTTTTTGTCTTG
90559710 TGGTACCTAAACTATTTTTTTGTCTTG
1 TGGTACCTAAACTATTTTTTTGTCTTG
90559737 TGGTACCTAAACTATTTTT
1 TGGTACCTAAACTATTTTT
90559756 CCATTACCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.52
Consensus pattern (27 bp):
TGGTACCTAAACTATTTTTTTGTCTTG
Found at i:90560891 original size:17 final size:18
Alignment explanation
Indices: 90560860--90560893 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
90560850 ATATCATGTA
90560860 TTTTATTTTCATTTTCAC
1 TTTTATTTTCATTTTCAC
*
90560878 TTTT-TTTTCCTTTTCA
1 TTTTATTTTCATTTTCA
90560894 AAGAATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTATTTTCATTTTCAC
Found at i:90567975 original size:20 final size:21
Alignment explanation
Indices: 90567947--90567986 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
90567937 GCTATAAATC
*
90567947 CTTATAATTT-TTTTTGTAAA
1 CTTAAAATTTATTTTTGTAAA
90567967 CTTAAAATTTAGTTTTTGTA
1 CTTAAAATTTA-TTTTTGTA
90567987 TTTTGTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
CTTAAAATTTATTTTTGTAAA
Found at i:90576828 original size:34 final size:36
Alignment explanation
Indices: 90576757--90576829 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
90576747 ATAGTATGAT
* *
90576757 TTGAAATTTTCTAAATAATGTATTACAAATTTTTTTC
1 TTGAAATTTTCTAAACAA-GTATTACAAATTTATTTC
*
90576794 TTGAAATTTTCTAAACAA-TA-TACAACTTTATTTC
1 TTGAAATTTTCTAAACAAGTATTACAAATTTATTTC
90576828 TT
1 TT
90576830 ATTGAAACTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 14 0.42
35 2 0.06
37 17 0.52
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (36 bp):
TTGAAATTTTCTAAACAAGTATTACAAATTTATTTC
Found at i:90582614 original size:23 final size:23
Alignment explanation
Indices: 90582569--90582617 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
90582559 GCTCCAATAT
* *
90582569 TAACAACAATGACGATAATAGAA
1 TAACAACAATAACAATAATAGAA
90582592 TAACAACAATAACAAATAA-AGAA
1 TAACAACAATAAC-AATAATAGAA
90582615 TAA
1 TAA
90582618 TAATGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.16
Consensus pattern (23 bp):
TAACAACAATAACAATAATAGAA
Found at i:90583420 original size:18 final size:19
Alignment explanation
Indices: 90583392--90583428 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
90583382 AAAAAAAATG
*
90583392 AAATAAAATAAGATAAAAC
1 AAATAAAATAAGAGAAAAC
90583411 AAAT-AAATAAGAGAAAAC
1 AAATAAAATAAGAGAAAAC
90583429 GAAGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (19 bp):
AAATAAAATAAGAGAAAAC
Found at i:90583647 original size:21 final size:21
Alignment explanation
Indices: 90583608--90583647 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90583598 CAAGTGGGCA
**
90583608 TGGGCGGTGGTGGCAGGTGCT
1 TGGGCGGTGGCAGCAGGTGCT
*
90583629 TGGGCGGTGGCAGCTGGTG
1 TGGGCGGTGGCAGCAGGTG
90583648 TCAGACGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.57, T:0.23
Consensus pattern (21 bp):
TGGGCGGTGGCAGCAGGTGCT
Found at i:90584214 original size:44 final size:44
Alignment explanation
Indices: 90584095--90585128 Score: 844
Period size: 44 Copynumber: 23.5 Consensus size: 44
90584085 CGCCATCGTC
* * * * *
90584095 GATCTGCTTTCTTCGATCTTCTTCACCACCAGTATGGGAAAACAA
1 GATCTGCTATCTTCGATCTACTTCA-CACCAATATAGGAAGACAA
* * * * * *
90584140 AATCTGC-ATCGTCGGTCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* *
90584183 GATCTGATATCTTCGATCTACTTCACGCC-A-AT--GAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* *
90584223 GATCTGCTTTCTTCGATCTACTTCACCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCA-CACCAATATAGGAAGACAA
* * *
90584268 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * *
90584313 GATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAAATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * * *
90584356 GATCTGATGTCTTTGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * * ** *
90584400 GATCTGCTTTCTTCGATCTACTTCACGCTAATGCATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * *
90584444 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* *
90584489 GATCTGCTTTCTTCGATCTACTTCACCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCA-CACCAATATAGGAAGACAA
* * * * * * *
90584534 GATCTGC-GTCGTCGATCCACTTC-CAATCATTATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * * * *
90584577 GACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACTA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * * *
90584621 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * * * *
90584666 GATCTGC-GTCGTCGATCCACTTC-CAATCATTATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * * * *
90584709 GACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * * *
90584753 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
90584798 GATCTGC-ATCTTGGATCCACTTC-CTATCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * *
90584841 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * *
90584885 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
90584930 GATCTG-TATCTTGGATCCACTTC-CTATCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* * * *
90584973 GACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
* * * *
90585017 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-ACACCAATATAGGAAGACAA
* * * * *
90585062 GATCTGC-GTCGTCGATCCACTTC-CTACCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCAC-ACCAATATAGGAAGACAA
* *
90585105 GATCAGCTATTTTCGATCTACTTC
1 GATCTGCTATCTTCGATCTACTTC
90585129 TTGCCCCGGG
Statistics
Matches: 780, Mismatches: 177, Indels: 65
0.76 0.17 0.06
Matches are distributed among these distances:
40 29 0.04
41 3 0.00
42 10 0.01
43 137 0.18
44 382 0.49
45 219 0.28
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
GATCTGCTATCTTCGATCTACTTCACACCAATATAGGAAGACAA
Found at i:90584650 original size:132 final size:132
Alignment explanation
Indices: 90584095--90585128 Score: 1274
Period size: 132 Copynumber: 7.8 Consensus size: 132
90584085 CGCCATCGTC
* * * * * *
90584095 GATCTGCTTTCTTCGATCTTCTTCACCACCAGTATGGGAAAACAAAATCTGCATCGTCGGTCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
* * *
90584160 TTCCTACCAATATAGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCC---A-ATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
90584221 AA
131 AA
* * * *
90584223 GATCTGCTTTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCTTTCTTCGATCTA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCA
* * * * * * * * * *
90584288 CTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAA
65 CTTC-CTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAA
* * *
90584351 AATAG
128 GACAA
* * * * * *** * * *
90584356 GATCTGATGTCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTA
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATCGTCGATCCA
** ** * * * * * * * ***
90584420 CTTCACGCT-AATGCATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAA
65 CTTC-CTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAA
90584484 GACAA
128 GACAA
* *
90584489 GATCTGCTTTCTTCGATCTACTTCACCACCAATATGGGAAGACAAGATCTGCGTCGTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
* * * *
90584554 TTCCAATCATTATAGGAAGATAGGACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
*
90584619 TA
131 AA
* *
90584621 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCGTCGTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
* * * *
90584686 TTCCAATCATTATAGGAAGATAGGACCTGTTATCTTTGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
90584751 AA
131 AA
* * *
90584753 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTGGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
90584818 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
90584883 AA
131 AA
* * *
90584885 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGTATCTTGGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
90584950 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
90585015 AA
131 AA
* *
90585017 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCGTCGTCGATCCAC
1 GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
* * * *
90585082 TTCCTACCAATATAGGAAGATAGGATCAGCTATTTTCGATCTACTTC
66 TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTC
90585129 TTGCCCCGGG
Statistics
Matches: 803, Mismatches: 91, Indels: 20
0.88 0.10 0.02
Matches are distributed among these distances:
128 49 0.06
129 29 0.04
130 22 0.03
131 18 0.02
132 558 0.69
133 104 0.13
134 23 0.03
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (132 bp):
GATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCGTCGATCCAC
TTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGAC
AA
Found at i:90585262 original size:46 final size:46
Alignment explanation
Indices: 90585212--90585405 Score: 166
Period size: 46 Copynumber: 4.3 Consensus size: 46
90585202 ATCTGCTTTG
90585212 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
* ** * * * * *
90585258 CTGCCAAATACAGGGAGATAGAGTTAT-C-AGCTTCAATGTACTCCA
1 CTGCCAAATACAGGAAGGCA-AGATCTGCAATCTTCAATCTATTCCA
*** * * * * * * *
90585303 CTG--TGGT-CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CG
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCT-ATTCCA
90585346 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
1 CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
90585392 CTGCCAAATACAGG
1 CTGCCAAATACAGG
90585406 GAGATAGAGT
Statistics
Matches: 109, Mismatches: 31, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
41 3 0.03
42 10 0.09
43 13 0.12
44 1 0.01
45 20 0.18
46 58 0.53
47 4 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (46 bp):
CTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
Found at i:90585376 original size:134 final size:134
Alignment explanation
Indices: 90585136--90585473 Score: 613
Period size: 134 Copynumber: 2.5 Consensus size: 134
90585126 TTCTTGCCCC
** *
90585136 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCTGCCATCTTC
1 GGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
*
90585201 GATCTGCTTTGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
90585266 TACA
131 TACA
*
90585270 GGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTGGTCAGGGAGGTAAAATCTGCCATCTTC
1 GGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
90585335 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
90585400 TACA
131 TACA
* *
90585404 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
90585469 GATCT
66 GATCT
90585474 TCAATCTATT
Statistics
Matches: 196, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 196 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (134 bp):
GGGAGATAGAGTTATCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACA
Found at i:90585480 original size:95 final size:95
Alignment explanation
Indices: 90585375--90585663 Score: 551
Period size: 95 Copynumber: 3.0 Consensus size: 95
90585365 AAGATCTGCA
90585375 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
90585440 TAGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TGGTCAGGGAGGTAAAATCTGCCATCTTTG
90585470 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
90585535 TGGTCAGGGAGGTAAAATCTGCCATCTTTG
66 TGGTCAGGGAGGTAAAATCTGCCATCTTTG
*
90585565 ATCTTCAATCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
90585630 TGGTCAGGGAGGTAAAATCTGCCATCTTCG
66 TGGTCAGGGAGGTAAAATCTGCCATCTTTG
90585660 ATCT
1 ATCT
90585664 GCTTCGCTGC
Statistics
Matches: 191, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 191 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (95 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TGGTCAGGGAGGTAAAATCTGCCATCTTTG
Found at i:90585723 original size:134 final size:134
Alignment explanation
Indices: 90585565--90585840 Score: 509
Period size: 134 Copynumber: 2.1 Consensus size: 134
90585555 GCCATCTTTG
*
90585565 ATCTTCAATCTATTCTACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
90585630 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
90585695 TGCA-
131 TG-AT
90585699 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
1 ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
*
90585764 TTGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
66 TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
90585829 TGAT
131 TGAT
90585833 ATCTTCAA
1 ATCTTCAA
90585841 CCAGCTCTGC
Statistics
Matches: 138, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
133 1 0.01
134 137 0.99
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (134 bp):
ATCTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGTTATCGGCTTCAATGTACTCCACTG
TGGTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATC
TGAT
Found at i:90585934 original size:86 final size:86
Alignment explanation
Indices: 90585788--90586137 Score: 556
Period size: 86 Copynumber: 4.1 Consensus size: 86
90585778 AAATCTGCCA
* * * *
90585788 TCTTCGATCTGCTTCGCTGCCAAATACAGGAAAGCAAGATCTGATATCTTCAACCAGCTCTGCTA
1 TCTTCGATCTGCTTCGCTGTC-AATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTA
90585853 CAAACGAGAGAGGCAAGGTTTG
65 CAAACGAGAGAGGCAAGGTTTG
* *
90585875 TCTTCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
90585940 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
*
90585961 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCAGCTCTACTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
*
90586026 AAACGAGAGTGGCAAGGTTTG
66 AAACGAGAGAGGCAAGGTTTG
* * *
90586047 TCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATAACTTCAACCAGCTCTGCTAC
1 TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
* * *
90586112 GACCGAGAGAGGCAAGGTTTA
66 AAACGAGAGAGGCAAGGTTTG
90586133 TCTTC
1 TCTTC
90586138 AATTTTTACT
Statistics
Matches: 247, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
86 227 0.92
87 20 0.08
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (86 bp):
TCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGATATCTTCAACCAGCTCTACTAC
AAACGAGAGAGGCAAGGTTTG
Found at i:90585997 original size:42 final size:42
Alignment explanation
Indices: 90585863--90586083 Score: 107
Period size: 42 Copynumber: 5.2 Consensus size: 42
90585853 CAAACGAGAG
* *
90585863 AGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAGTGCAGGA
1 AGGCAAGGTTTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
* * * * * * *
90585905 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGACCTGCTTC-GCTGTCAATGCAG-GA
* *
90585948 GTGGCAAGGTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
* * * * * * *
90585991 AGGCAAGATCTGCTATCTTCAACCAGC-TCTACT-ACAA-AC-GAGA
1 AGGCAAGGT-T--TGTCTTCGACCTGCTTC-GCTGTCAATGCAG-GA
*
90586034 GTGGCAAGGTTTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
1 -AGGCAAGGTTTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
90586077 AGGCAAG
1 AGGCAAG
90586084 ATCTGATAAC
Statistics
Matches: 123, Mismatches: 36, Indels: 40
0.62 0.18 0.20
Matches are distributed among these distances:
41 25 0.20
42 33 0.27
43 16 0.13
44 25 0.20
45 24 0.20
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.26
Consensus pattern (42 bp):
AGGCAAGGTTTGTCTTCGACCTGCTTCGCTGTCAATGCAGGA
Found at i:90590274 original size:19 final size:20
Alignment explanation
Indices: 90590250--90590293 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
90590240 CGTGAAAGTC
* *
90590250 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGAAATG
90590269 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
90590289 -AATGC
1 TAATGC
90590294 CAAAAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:90592838 original size:23 final size:23
Alignment explanation
Indices: 90592793--90592841 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
90592783 GCTCCAATAT
* *
90592793 TAACAACAATGACGATAATAGAA
1 TAACAACAATAACAATAATAGAA
90592816 TAACAACAATAACAAATAA-AGAA
1 TAACAACAATAAC-AATAATAGAA
90592839 TAA
1 TAA
90592842 TAATGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.63, C:0.12, G:0.08, T:0.16
Consensus pattern (23 bp):
TAACAACAATAACAATAATAGAA
Found at i:90593872 original size:21 final size:21
Alignment explanation
Indices: 90593833--90593872 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
90593823 CAAGTGGGCA
**
90593833 TGGGCGGTGGTGGCAGGTGCT
1 TGGGCGGTGGCAGCAGGTGCT
*
90593854 TGGGCGGTGGCAGCTGGTG
1 TGGGCGGTGGCAGCAGGTG
90593873 TCAGACGCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.15, G:0.57, T:0.23
Consensus pattern (21 bp):
TGGGCGGTGGCAGCAGGTGCT
Found at i:90594466 original size:18 final size:18
Alignment explanation
Indices: 90594394--90594466 Score: 78
Period size: 19 Copynumber: 4.1 Consensus size: 18
90594384 TTTTAGAAAA
*
90594394 TTTTTA-AAATTTTAACT
1 TTTTTATAAATTTTAAAT
* *
90594411 TTTTTATATATTTTTAGAT
1 TTTTTATA-AATTTTAAAT
90594430 TTTTT-TAAATTTTATAAT
1 TTTTTATAAATTTTA-AAT
*
90594448 TTTTTATAAATTATAAAT
1 TTTTTATAAATTTTAAAT
90594466 T
1 T
90594467 ATAAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
17 12 0.26
18 14 0.30
19 20 0.43
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (18 bp):
TTTTTATAAATTTTAAAT
Found at i:90596753 original size:14 final size:15
Alignment explanation
Indices: 90596721--90596755 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
90596711 CATTCCTCAA
90596721 CAGAATCAGATCATAT
1 CAGAATCAGAT-ATAT
90596737 CAGAATCAGAT-TAT
1 CAGAATCAGATATAT
90596751 CAGAA
1 CAGAA
90596756 ATATACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.42
16 11 0.58
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (15 bp):
CAGAATCAGATATAT
Found at i:90602593 original size:20 final size:20
Alignment explanation
Indices: 90602568--90602617 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
90602558 TGGCTTAAAA
90602568 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
90602588 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
90602605 GTGGTAGTGGATT
1 TTGGTAGTGGATT
90602618 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:90607231 original size:20 final size:20
Alignment explanation
Indices: 90607206--90607255 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
90607196 TGGCTTAAAA
90607206 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
90607226 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
90607243 GTGGTAGTGGATT
1 TTGGTAGTGGATT
90607256 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:90611375 original size:17 final size:18
Alignment explanation
Indices: 90611345--90611378 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90611335 ACTGTTATTA
*
90611345 TTATTTTTTCTTTCTTTT
1 TTATTTTATCTTTCTTTT
90611363 TTATTTTAT-TTTCTTT
1 TTATTTTATCTTTCTTT
90611379 CTTTTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.82
Consensus pattern (18 bp):
TTATTTTATCTTTCTTTT
Found at i:90611388 original size:26 final size:24
Alignment explanation
Indices: 90611339--90611383 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
90611329 AAGGTTACTG
90611339 TTATTATTATTTTTTCTTTCTTTT
1 TTATTATTATTTTTTCTTTCTTTT
90611363 TTATT-TTA--TTTTCTTTCTTTT
1 TTATTATTATTTTTTCTTTCTTTT
90611384 CTTTTCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.62
23 3 0.14
24 5 0.24
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (24 bp):
TTATTATTATTTTTTCTTTCTTTT
Found at i:90612182 original size:17 final size:18
Alignment explanation
Indices: 90612162--90612202 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
90612152 TATTTAGTTA
90612162 TTTATTTTAAAG-ATGAT
1 TTTATTTTAAAGTATGAT
*
90612179 TTTA-TTTAATGTATGAT
1 TTTATTTTAAAGTATGAT
90612196 TTTATTT
1 TTTATTT
90612203 AATGTATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.29
17 13 0.62
18 2 0.10
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (18 bp):
TTTATTTTAAAGTATGAT
Found at i:90612203 original size:17 final size:17
Alignment explanation
Indices: 90612174--90612209 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
90612164 TATTTTAAAG
90612174 ATGATTTTATTTAATGT
1 ATGATTTTATTTAATGT
90612191 ATGATTTTATTTAATGT
1 ATGATTTTATTTAATGT
90612208 AT
1 AT
90612210 TGTTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
ATGATTTTATTTAATGT
Found at i:90612420 original size:12 final size:12
Alignment explanation
Indices: 90612403--90612430 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
90612393 TTTAGATTTA
90612403 TTATTATTATTG
1 TTATTATTATTG
90612415 TTATTATTATTG
1 TTATTATTATTG
90612427 TTAT
1 TTAT
90612431 CGTTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (12 bp):
TTATTATTATTG
Found at i:90614284 original size:31 final size:32
Alignment explanation
Indices: 90614249--90614311 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
90614239 AAATTAATAT
90614249 AAACTTAT-AACAATCATAAAAAA-ATAATAAA
1 AAACTTATAAAC-ATCATAAAAAATATAATAAA
* *
90614280 AAACTTATAAACATTATAAAAAATCTAATAAA
1 AAACTTATAAACATCATAAAAAATATAATAAA
90614312 TTTTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (32 bp):
AAACTTATAAACATCATAAAAAATATAATAAA
Found at i:90614289 original size:11 final size:10
Alignment explanation
Indices: 90614267--90614415 Score: 58
Period size: 10 Copynumber: 15.0 Consensus size: 10
90614257 AACAATCATA
*
90614267 AAAAAATAAT
1 AAAAAATTAT
90614277 AAAAAACTTAT
1 AAAAAA-TTAT
*
90614288 -AAACATTAT
1 AAAAAATTAT
*
90614297 AAAAAA-TCT
1 AAAAAATTAT
* *
90614306 AATAAATTTT
1 AAAAAATTAT
*
90614316 AATAAATTAT
1 AAAAAATTAT
** *
90614326 -AAATCTTTT
1 AAAAAATTAT
90614335 ATAAAAATTAAT
1 A-AAAAATT-AT
*
90614347 GAAAATATT-T
1 -AAAAAATTAT
*
90614357 AAAATATTAT
1 AAAAAATTAT
**
90614367 AAAAACGTAT
1 AAAAAATTAT
* *
90614377 -ACAAATTCTT
1 AAAAAATT-AT
*
90614387 AAAAACTTAT
1 AAAAAATTAT
*
90614397 -AAAAATCAT
1 AAAAAATTAT
90614406 AAAAAATTAT
1 AAAAAATTAT
90614416 TAAGAACATT
Statistics
Matches: 100, Mismatches: 28, Indels: 22
0.67 0.19 0.15
Matches are distributed among these distances:
9 35 0.35
10 44 0.44
11 13 0.13
12 7 0.07
13 1 0.01
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:90614408 original size:19 final size:20
Alignment explanation
Indices: 90614365--90614415 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
90614355 TTAAAATATT
* *
90614365 ATAAAAACGTATACAAATTC
1 ATAAAAACTTATACAAAATC
*
90614385 TTAAAAACTTATA-AAAATC
1 ATAAAAACTTATACAAAATC
*
90614404 ATAAAAAATTAT
1 ATAAAAACTTAT
90614416 TAAGAACATT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
ATAAAAACTTATACAAAATC
Found at i:90614429 original size:19 final size:20
Alignment explanation
Indices: 90614366--90614429 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
90614356 TAAAATATTA
* *
90614366 TAAAAACGTATACAAATTC-T
1 TAAAAACTTATA-AAAATCAT
90614386 TAAAAACTTATAAAAATCA-
1 TAAAAACTTATAAAAATCAT
* *
90614405 TAAAAAATTATTAAGAA-CAT
1 TAAAAACTTA-TAAAAATCAT
90614425 TAAAA
1 TAAAA
90614430 TCGATACAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.28
Consensus pattern (20 bp):
TAAAAACTTATAAAAATCAT
Found at i:90614986 original size:11 final size:10
Alignment explanation
Indices: 90614952--90615027 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 10
90614942 ATAGTTCATG
90614952 TTTTTATGAT-
1 TTTTTAT-ATA
90614962 TTTTTA-ATA
1 TTTTTATATA
*
90614971 -ATTTATATCA
1 TTTTTATAT-A
*
90614981 TTTTTATTTTA
1 TTTTTA-TATA
90614992 TTTTTATAT-
1 TTTTTATATA
90615001 TTTTTA-ATA
1 TTTTTATATA
90615010 TTTTT-TATGA
1 TTTTTATAT-A
90615020 TTTTTATA
1 TTTTTATA
90615028 AGTTTTTAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
8 8 0.15
9 15 0.28
10 15 0.28
11 13 0.25
12 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (10 bp):
TTTTTATATA
Found at i:90615002 original size:19 final size:21
Alignment explanation
Indices: 90614952--90615028 Score: 81
Period size: 20 Copynumber: 3.9 Consensus size: 21
90614942 ATAGTTCATG
*
90614952 TTTTTATGATTTTT-TAATAA
1 TTTTTATGATTTTTATAATAT
* * **
90614972 TTTATATCATTTTTATTTTA-
1 TTTTTATGATTTTTATAATAT
90614992 TTTTTAT-ATTTTT-TAATAT
1 TTTTTATGATTTTTATAATAT
90615011 TTTTTATGATTTTTATAA
1 TTTTTATGATTTTTATAA
90615029 GTTTTTAAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
18 3 0.07
19 13 0.28
20 24 0.52
21 6 0.13
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (21 bp):
TTTTTATGATTTTTATAATAT
Found at i:90615033 original size:20 final size:20
Alignment explanation
Indices: 90614992--90615056 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
90614982 TTTTATTTTA
*
90614992 TTTTTAT-ATTTTT-TAATAT
1 TTTTTATGATTTTTATAA-GT
90615011 TTTTTATGATTTTTATAAG-
1 TTTTTATGATTTTTATAAGT
* * *
90615030 TTTTTAAGAAGTTTTATAGGT
1 TTTTTATG-ATTTTTATAAGT
90615051 TTTTTA
1 TTTTTA
90615057 ATAAAATTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 14 0.37
20 15 0.39
21 9 0.24
ACGTcount: A:0.26, C:0.00, G:0.09, T:0.65
Consensus pattern (20 bp):
TTTTTATGATTTTTATAAGT
Found at i:90615110 original size:10 final size:9
Alignment explanation
Indices: 90615074--90615146 Score: 53
Period size: 10 Copynumber: 8.0 Consensus size: 9
90615064 TGTAAATATG
90615074 TTTTTATTAA
1 TTTTTA-TAA
* *
90615084 TTTTAAAAA
1 TTTTTATAA
90615093 TTGTTTATAA
1 TT-TTTATAA
*
90615103 --TTTATTA
1 TTTTTATAA
90615110 TTTTTATAA
1 TTTTTATAA
*
90615119 -TATTATAA
1 TTTTTATAA
90615127 GTTTTTATTAA
1 -TTTTTA-TAA
90615138 TTTTTATAA
1 TTTTTATAA
90615147 GTTTATATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
7 6 0.12
8 7 0.14
9 13 0.27
10 20 0.41
11 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:90615152 original size:28 final size:28
Alignment explanation
Indices: 90615073--90615153 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 28
90615063 TTGTAAATAT
* *
90615073 GTTTTTATTAATTTTAAAAATTGTTTATAA
1 GTTTTTATTAATTTTTATAA--GTTTATAA
90615103 ---TTTATT-ATTTTTATAA-TATTATAA
1 GTTTTTATTAATTTTTATAAGT-TTATAA
90615127 GTTTTTATTAATTTTTATAAGTTTATA
1 GTTTTTATTAATTTTTATAAGTTTATA
90615154 TCAAATTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
23 1 0.02
24 6 0.14
26 8 0.19
27 12 0.28
28 15 0.35
29 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
GTTTTTATTAATTTTTATAAGTTTATAA
Found at i:90617876 original size:31 final size:30
Alignment explanation
Indices: 90617797--90617883 Score: 102
Period size: 31 Copynumber: 2.8 Consensus size: 30
90617787 TTACTAAATC
* *
90617797 AACTTTGATTTGATGCAATTATACACATGA
1 AACTTTGATTTGATTCAATTATATACATGA
* * *
90617827 AACTTTAATTATGATTCAAATATATACTTGA
1 AACTTTGATT-TGATTCAATTATATACATGA
*
90617858 AACTTTGATATTGGTTCAATTATATA
1 AACTTTGAT-TTGATTCAATTATATA
90617884 TAATTAAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
30 9 0.19
31 37 0.79
32 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (30 bp):
AACTTTGATTTGATTCAATTATATACATGA
Found at i:90622929 original size:9 final size:9
Alignment explanation
Indices: 90622915--90622939 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
90622905 TAATTTAAAT
90622915 TTTTAAAAA
1 TTTTAAAAA
90622924 TTTTAAAAA
1 TTTTAAAAA
90622933 TTTTAAA
1 TTTTAAA
90622940 TGGCTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:90623046 original size:31 final size:30
Alignment explanation
Indices: 90623008--90623097 Score: 108
Period size: 31 Copynumber: 2.9 Consensus size: 30
90622998 GATACCCTCG
* *
90623008 TATATATATAATTAAATCAAAATCAAAATT
1 TATATATATAATTGAATCAAAATAAAAATT
*
90623038 CTATATATATATTTGAATCAAAATAAAAATT
1 -TATATATATAATTGAATCAAAATAAAAATT
* *
90623069 TAATAAATATGATTGAATCAAAACTAAAA
1 T-ATATATATAATTGAATCAAAA-TAAAA
90623098 TACATTTATC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 1 0.02
31 45 0.88
32 5 0.10
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (30 bp):
TATATATATAATTGAATCAAAATAAAAATT
Found at i:90632052 original size:5 final size:5
Alignment explanation
Indices: 90632032--90632109 Score: 79
Period size: 5 Copynumber: 15.8 Consensus size: 5
90632022 GTAGTGGATG
* * * *
90632032 ATGAT AGGAC ATGAT ATGAT ATGAT ATGAT ATGTT TTGAT -TCGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT ATGAT AT-GAT ATGAT
* *
90632082 ATGAT ACGA- ATGAT ATGAT AAGAT ATGA
1 ATGAT ATGAT ATGAT ATGAT ATGAT ATGA
90632110 GTTAGCTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
4 4 0.07
5 54 0.92
6 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (5 bp):
ATGAT
Found at i:90632366 original size:15 final size:15
Alignment explanation
Indices: 90632325--90632367 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
90632315 GTTTCACACT
* *
90632325 TTTTTGGATTTTGTA
1 TTTTTGGACTTTATA
*
90632340 TGTTTCGGACTTTATA
1 T-TTTTGGACTTTATA
90632356 TTTTTGGACTTT
1 TTTTTGGACTTT
90632368 TAAGGAACTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.14, C:0.07, G:0.19, T:0.60
Consensus pattern (15 bp):
TTTTTGGACTTTATA
Found at i:90635447 original size:26 final size:27
Alignment explanation
Indices: 90635414--90635469 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
90635404 TAAAAAAATT
90635414 AATAAATTTAACCCTTAATATTTA-AA
1 AATAAATTTAACCCTTAATATTTACAA
**
90635440 AATAAATTTAACTTTTAATATTTACAA
1 AATAAATTTAACCCTTAATATTTACAA
90635467 AAT
1 AAT
90635470 CCGCTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (27 bp):
AATAAATTTAACCCTTAATATTTACAA
Found at i:90643373 original size:14 final size:14
Alignment explanation
Indices: 90643354--90643380 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
90643344 AAAAACTGAT
90643354 TTGTCATTCTCATG
1 TTGTCATTCTCATG
90643368 TTGTCATTCTCAT
1 TTGTCATTCTCAT
90643381 AATTTAGTAC
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:0.15, C:0.22, G:0.11, T:0.52
Consensus pattern (14 bp):
TTGTCATTCTCATG
Found at i:90649454 original size:18 final size:18
Alignment explanation
Indices: 90649433--90649474 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
90649423 GAAATATTTA
*
90649433 TTTTAATGT-TTTTAGTAT
1 TTTTAATGTATTATA-TAT
*
90649451 TTTTGATGTATTATATAT
1 TTTTAATGTATTATATAT
90649469 TTTTAA
1 TTTTAA
90649475 AATTTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
TTTTAATGTATTATATAT
Found at i:90649974 original size:17 final size:18
Alignment explanation
Indices: 90649930--90650000 Score: 60
Period size: 17 Copynumber: 4.1 Consensus size: 18
90649920 ATAATTTTTT
* *
90649930 TAAATTATAAAAAAAAT-
1 TAAAATATAAAAAATATA
* *
90649947 TAGAATTTAAAAAATATA
1 TAAAATATAAAAAATATA
90649965 TAAAA-ATAAAAAAT-T-
1 TAAAATATAAAAAATATA
*
90649980 TAAAATTTACAAAAATATA
1 TAAAATATA-AAAAATATA
90649999 TA
1 TA
90650001 TTAAAATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.12
16 3 0.07
17 27 0.64
18 5 0.12
19 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (18 bp):
TAAAATATAAAAAATATA
Found at i:90649998 original size:32 final size:32
Alignment explanation
Indices: 90649939--90650037 Score: 89
Period size: 33 Copynumber: 3.2 Consensus size: 32
90649929 TTAAATTATA
* * *
90649939 AAAAAAATTAGAATTTAAAAAATATATAAAAAT
1 AAAAAATTTAAAATTTACAAAA-ATATAAAAAT
*
90649972 AAAAAATTTAAAATTTACAAAAATAT--ATAT
1 AAAAAATTTAAAATTTACAAAAATATAAAAAT
* * *
90650002 -TAAAATTATTAAATTTTCAAAAA-ATAAAAAT
1 AAAAAATT-TAAAATTTACAAAAATATAAAAAT
90650033 AAAAA
1 AAAAA
90650038 GTTATATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
29 8 0.15
30 16 0.30
31 3 0.06
32 7 0.13
33 19 0.36
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (32 bp):
AAAAAATTTAAAATTTACAAAAATATAAAAAT
Found at i:90650530 original size:21 final size:21
Alignment explanation
Indices: 90650504--90650566 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
90650494 ATAATTTGTT
90650504 ATATTTTCATAATTTTATATA
1 ATATTTTCATAATTTTATATA
* * * *
90650525 ATATTTTTATATTTTTTTACA
1 ATATTTTCATAATTTTATATA
* * *
90650546 TTTTTTTCAAAATTTTATATA
1 ATATTTTCATAATTTTATATA
90650567 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTTCATAATTTTATATA
Found at i:90651934 original size:29 final size:29
Alignment explanation
Indices: 90651902--90651958 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
90651892 AGTAGCGTCC
* *
90651902 CCTACTTTTTAGATTTTACAGTTTTGTCT
1 CCTACTTTATAAATTTTACAGTTTTGTCT
*
90651931 CCTACTTTATAAATTTTATAGTTTTGTC
1 CCTACTTTATAAATTTTACAGTTTTGTC
90651959 CAAATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (29 bp):
CCTACTTTATAAATTTTACAGTTTTGTCT
Found at i:90654854 original size:15 final size:15
Alignment explanation
Indices: 90654821--90654852 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
90654811 CGATACTCCC
90654821 ATATTACTTTTCTTT
1 ATATTACTTTTCTTT
90654836 ATATTA-TTTT-TTT
1 ATATTACTTTTCTTT
90654849 ATAT
1 ATAT
90654853 ATATAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATTACTTTTCTTT
Found at i:90662728 original size:18 final size:17
Alignment explanation
Indices: 90662705--90662742 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
90662695 ACATAATTCT
90662705 AATTTA-TTAATATATCAA
1 AATTTATTTAA-ATAT-AA
90662723 AATTTATTTAAATATAA
1 AATTTATTTAAATATAA
90662740 AAT
1 AAT
90662743 AGTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTATTTAAATATAA
Found at i:90663365 original size:19 final size:19
Alignment explanation
Indices: 90663307--90663366 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
90663297 AAAATTCTAA
*
90663307 TTTTAA-AATTTGTATAACTT
1 TTTTAATAATTT-T-TAAATT
* *
90663327 TTTTTAT-ATTTTTATGATT
1 TTTTAATAATTTTTA-AATT
90663346 TTTTAATAATTTTTAAATT
1 TTTTAATAATTTTTAAATT
90663365 TT
1 TT
90663367 AAAAAGGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
18 2 0.06
19 14 0.44
20 16 0.50
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAATAATTTTTAAATT
Found at i:90674965 original size:23 final size:22
Alignment explanation
Indices: 90674916--90674957 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
90674906 AACATCAATG
*
90674916 AAATAAATTCTAAAATCTAAAAA
1 AAATAAATTATAAAA-CTAAAAA
90674939 AAATAAATTATAAAA-TAAA
1 AAATAAATTATAAAACTAAA
90674958 CTAAAAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
23 14 0.78
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (22 bp):
AAATAAATTATAAAACTAAAAA
Found at i:90677164 original size:29 final size:30
Alignment explanation
Indices: 90677114--90677181 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
90677104 TGGCCCAAGA
* * *
90677114 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTAAAGGACTAATAGT
*
90677144 GTAAATATGAAAAGTTAAAGGACTAATAGT
1 GTAAATATCAAAAGTTAAAGGACTAATAGT
*
90677174 GAAAATAT
1 GTAAATAT
90677182 TTTAAGGGTG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.50, C:0.04, G:0.18, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTAAAGGACTAATAGT
Found at i:90679658 original size:46 final size:46
Alignment explanation
Indices: 90679606--90679821 Score: 290
Period size: 46 Copynumber: 4.7 Consensus size: 46
90679596 AGTGTGCTCT
**
90679606 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
** *
90679652 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
90679698 GTGATATAAAATGAATAAGACCATGGTTGAAAGATAACATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* *
90679744 GTGATATGAAATGAATAAGACCATGGTTGAAAGATATCATGGCAAC
1 CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
* * * *
90679790 ATGACA-GAAAATGAATAATACCATAGTTGAAA
1 CTGATATG-AAATGAATAAGACCATGGTTGAAA
90679822 AACACTATGG
Statistics
Matches: 156, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 155 0.99
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:90680140 original size:16 final size:17
Alignment explanation
Indices: 90680119--90680151 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
90680109 ATGATGGAGC
90680119 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
90680135 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
90680152 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:90681609 original size:3 final size:3
Alignment explanation
Indices: 90681601--90681625 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
90681591 GATTTAAGAA
90681601 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
90681626 TTTTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Done.