Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold26
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: 1656043
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.27
Warning! 334368 characters in sequence are not A, C, G, or T
File 2 of 8
Found at i:156098 original size:30 final size:30
Alignment explanation
Indices: 156062--156166 Score: 138
Period size: 30 Copynumber: 3.2 Consensus size: 30
156052 TTTTCTTTGG
156062 TGAGTGTGAGCGGTGGTGAGTAAAAATATT
1 TGAGTGTGAGCGGTGGTGAGTAAAAATATT
156092 TGAGTGTGAGCGGTGGTGAGTAAAAATATTTTCTTT
1 TGAGTGTGAGCGGTGGTGAGTAAAAATA------TT
156128 GGTGAGTGTGAGCGGTGGTGAGTAAAAATATT
1 --TGAGTGTGAGCGGTGGTGAGTAAAAATATT
156160 TGAGTGT
1 TGAGTGT
156167 TTATTTGAGT
Statistics
Matches: 67, Mismatches: 0, Indels: 16
0.81 0.00 0.19
Matches are distributed among these distances:
30 35 0.52
32 2 0.03
36 2 0.03
38 28 0.42
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (30 bp):
TGAGTGTGAGCGGTGGTGAGTAAAAATATT
Found at i:156118 original size:68 final size:67
Alignment explanation
Indices: 156040--156166 Score: 245
Period size: 68 Copynumber: 1.9 Consensus size: 67
156030 TGTGTGAGGT
156040 GTGAGTAAAATATTTTCTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATTTGAGTGTGAGCGG
1 GTGAGTAAAATATTTTCTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATTTGAGTGTGAGCGG
156105 TG
66 TG
156107 GTGAGTAAAAATATTTTCTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATTTGAGTGT
1 GTGAGT-AAAATATTTTCTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATTTGAGTGT
156167 TTATTTGAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 6 0.10
68 53 0.90
ACGTcount: A:0.27, C:0.04, G:0.34, T:0.35
Consensus pattern (67 bp):
GTGAGTAAAATATTTTCTTTGGTGAGTGTGAGCGGTGGTGAGTAAAAATATTTGAGTGTGAGCGG
TG
Found at i:160703 original size:22 final size:22
Alignment explanation
Indices: 160648--160703 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
160638 TTTTTGTTAA
*
160648 GTGTGTTAGGTAAACATATTAG
1 GTGTGTTAGGTGAACATATTAG
* **
160670 GTGTGTTGGGTGAGTATATTAG
1 GTGTGTTAGGTGAACATATTAG
160692 GTGTGTTAGGTG
1 GTGTGTTAGGTG
160704 GTGTGTTAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.39
Consensus pattern (22 bp):
GTGTGTTAGGTGAACATATTAG
Found at i:160721 original size:35 final size:34
Alignment explanation
Indices: 160669--160771 Score: 161
Period size: 34 Copynumber: 3.0 Consensus size: 34
160659 AAACATATTA
* *
160669 GGTGTGTTGGGTGAGTATATTAGGTGTGTTAGGT
1 GGTGTGTTAGGTAAGTATATTAGGTGTGTTAGGT
160703 GGTGTGTTAGGTAAAGTATATTAGGTGTGTTAGGT
1 GGTGTGTTAGGT-AAGTATATTAGGTGTGTTAGGT
* *
160738 GATGTGTTAGGTAAGCATATTAGGTGTGTTAGGT
1 GGTGTGTTAGGTAAGTATATTAGGTGTGTTAGGT
160772 AATGCGTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
34 32 0.50
35 32 0.50
ACGTcount: A:0.20, C:0.01, G:0.39, T:0.40
Consensus pattern (34 bp):
GGTGTGTTAGGTAAGTATATTAGGTGTGTTAGGT
Found at i:160781 original size:34 final size:34
Alignment explanation
Indices: 160671--160788 Score: 155
Period size: 34 Copynumber: 3.4 Consensus size: 34
160661 ACATATTAGG
* * * *
160671 TGTGTTGGGTGAGTATATTAGGTGTGTTAGGTGG
1 TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
*
160705 TGTGTTAGGTAAAGTATATTAGGTGTGTTAGGTGA
1 TGTGTTAGGT-AAGCATATTAGGTGTGTTAGGTGA
*
160740 TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTAA
1 TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
* *
160774 TGCGTTAGGTGAGCA
1 TGTGTTAGGTAAGCA
160789 AGATATTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
34 44 0.58
35 32 0.42
ACGTcount: A:0.22, C:0.03, G:0.37, T:0.38
Consensus pattern (34 bp):
TGTGTTAGGTAAGCATATTAGGTGTGTTAGGTGA
Found at i:164326 original size:21 final size:21
Alignment explanation
Indices: 164293--164342 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
164283 TTGGAAGTTG
*
164293 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
164315 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
164336 AAATAAA
1 AAATAAA
164343 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:166161 original size:15 final size:15
Alignment explanation
Indices: 166141--166170 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
166131 AAAAATGTCT
*
166141 AAAATGAGGAAGCTC
1 AAAATGAAGAAGCTC
166156 AAAATGAAGAAGCTC
1 AAAATGAAGAAGCTC
166171 CAAACGAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AAAATGAAGAAGCTC
Found at i:168269 original size:13 final size:13
Alignment explanation
Indices: 168251--168288 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
168241 CATTTTTCTT
168251 TGTATCGATACAA
1 TGTATCGATACAA
*
168264 TGTATCGATACAC
1 TGTATCGATACAA
168277 TGTATCGATACA
1 TGTATCGATACA
168289 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:168443 original size:20 final size:20
Alignment explanation
Indices: 168400--168445 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
168390 AAATCTTTTG
168400 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
168421 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
168441 CAAAA
1 CAAAA
168446 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:172690 original size:18 final size:19
Alignment explanation
Indices: 172667--172707 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
172657 ATTATGAGAT
* *
172667 AAATTAAGATATAA-TAAA
1 AAATTAAAAAATAATTAAA
172685 AAATTAAAAAATAATTAAA
1 AAATTAAAAAATAATTAAA
172704 AAAT
1 AAAT
172708 ATGACACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATTAAAAAATAATTAAA
Found at i:172800 original size:283 final size:280
Alignment explanation
Indices: 172260--172786 Score: 665
Period size: 283 Copynumber: 1.9 Consensus size: 280
172250 TTAATAAAAT
*
172260 AATTTTCTCTTAATTGAATAACTGTGATAAATTATTTAAATAATTTTTTATATTTTAATATCTTA
1 AATTTTCTCTTAATTGAATAACTGTGATAAATTATTTAAATAAATTTTTATATTTTAATATCTTA
** * * * * *
172325 GTAATCGAATTTGGAGTCAAATTTAAATTATTACGATAAATTATGCAAATTATGAGATGAATTAA
66 GTAATCGAATTTAAAGTAAAAATTAAATTATTACAACAAATTATGCAAATTATGAGATAAATTAA
* * * *
172390 AATATGATAAAAAAATTAAAAAAATAATTAAAACATAACATGAAAATGACAATAACATAAATATG
131 AATATAATAAAAAAATTAAAAAAATAATTAAAAAATAACATCAAAAT---AATAACATAAATATA
* * *
172455 ATTTTTAGTTTGTACGAAAATAAAGAAATAAATAAATTCTTAATACTTTAAAGCATACAAAAAAA
193 ATTTTTAGTTTGTACAAAAATAAAGAAATAAACAAATTCTTAATACTTTAAAACATACAAAAAAA
172520 TAACATAAAAACAAAATATGAAA
258 TAACATAAAAACAAAATATGAAA
* * *
172543 AATTTTCTCTTGATTGAATAATTTTGATAAATTATTTAAATAAATTTTTATATTTTAATA-CATT
1 AATTTTCTCTTAATTGAATAACTGTGATAAATTATTTAAATAAATTTTTATATTTTAATATC-TT
* * * * *
172607 AGATAATCTAATTTAAAGTAAAAATTGAATTATTATAACAATTTATGTAAATTATGAGATAAATT
65 AG-TAATCGAATTTAAAGTAAAAATTAAATTATTACAACAAATTATGCAAATTATGAGATAAATT
* *
172672 AAGATATAAT-AAAAAATT-AAAAAATAATTAAAAAATATGACA-CAAAAT-ATAATATAAATAT
129 AAAATATAATAAAAAAATTAAAAAAATAATTAAAAAATA--ACATCAAAATAATAACATAAATAT
* *
172733 AATTTTT-GATTTGT-CTAAAAATGAAA-AAATAAACAAATTTTTAGTACTTTAAAA
192 AATTTTTAG-TTTGTAC-AAAAAT-AAAGAAATAAACAAATTCTTAATACTTTAAAA
172787 TACACATACA
Statistics
Matches: 210, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
278 2 0.01
279 52 0.25
280 3 0.01
282 19 0.09
283 73 0.35
284 61 0.29
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.37
Consensus pattern (280 bp):
AATTTTCTCTTAATTGAATAACTGTGATAAATTATTTAAATAAATTTTTATATTTTAATATCTTA
GTAATCGAATTTAAAGTAAAAATTAAATTATTACAACAAATTATGCAAATTATGAGATAAATTAA
AATATAATAAAAAAATTAAAAAAATAATTAAAAAATAACATCAAAATAATAACATAAATATAATT
TTTAGTTTGTACAAAAATAAAGAAATAAACAAATTCTTAATACTTTAAAACATACAAAAAAATAA
CATAAAAACAAAATATGAAA
Found at i:172837 original size:14 final size:14
Alignment explanation
Indices: 172820--172872 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
172810 TTTTTTTTTA
172820 TTTTCTTTTCCCTT
1 TTTTCTTTTCCCTT
172834 TTTTC-TTTCCCTT
1 TTTTCTTTTCCCTT
*
172847 TATTT-TTTTCTCTAT
1 T-TTTCTTTTCCCT-T
172862 TTTTCTTTTCC
1 TTTTCTTTTCC
172873 TTTCTTTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 9 0.27
14 17 0.52
15 7 0.21
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCTTTTCCCTT
Found at i:172874 original size:28 final size:29
Alignment explanation
Indices: 172816--172875 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
172806 TAAATTTTTT
172816 TTTATTTTCTTTTCCCTTTTTTCTTTCCC
1 TTTATTTTCTTTTCCCTTTTTTCTTTCCC
* *
172845 TTTA-TTT-TTTTCTCTATTTTTCTTTTCC
1 TTTATTTTCTTTTCCCT-TTTTTCTTTCCC
172873 TTT
1 TTT
172876 CTTTCCCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 7 0.25
28 17 0.61
29 4 0.14
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTATTTTCTTTTCCCTTTTTTCTTTCCC
Found at i:175389 original size:21 final size:21
Alignment explanation
Indices: 175365--175408 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
175355 GTGTTTTGTT
175365 CATTTTCCTTCCAACAATTTG
1 CATTTTCCTTCCAACAATTTG
*
175386 CATTTTCCTTCCACCAATTTG
1 CATTTTCCTTCCAACAATTTG
175407 CA
1 CA
175409 AGAAAGGCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (21 bp):
CATTTTCCTTCCAACAATTTG
Found at i:179190 original size:52 final size:52
Alignment explanation
Indices: 179101--179229 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
179091 CGAAATATGA
* *
179101 AAATTTGCCTGCATGTATCGATACCTTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
* * *
179153 AAATTTGCCTGTATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
179205 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
179230 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTAGGC
Found at i:179242 original size:52 final size:51
Alignment explanation
Indices: 179101--179249 Score: 199
Period size: 52 Copynumber: 2.9 Consensus size: 51
179091 CGAAATATGA
*
179101 AAATTTGCCTGCATGTATCGATACCTTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATA-CATTCATAGTGTATCGATACATCTAGGC
* * * *
179153 AAATTTGCCTGTATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTCATAGTGTATCGATACATCTAGGC
***
179205 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTCAT-AGTGTATCGATACA
179250 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 3 0.04
52 82 0.96
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTCATAGTGTATCGATACATCTAGGC
Found at i:179256 original size:13 final size:13
Alignment explanation
Indices: 179238--179262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179228 CAAAGATCAG
179238 TGTATCGATACAA
1 TGTATCGATACAA
179251 TGTATCGATACA
1 TGTATCGATACA
179263 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:179325 original size:13 final size:13
Alignment explanation
Indices: 179307--179358 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
179297 AGCTTCGTAG
179307 CGATACATTGTAT
1 CGATACATTGTAT
179320 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
179339 CGATACATTGTAT
1 CGATACATTGTAT
179352 CGATACA
1 CGATACA
179359 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:185488 original size:13 final size:13
Alignment explanation
Indices: 185470--185497 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
185460 TTTTTTCATC
185470 ATTAATATTTATT
1 ATTAATATTTATT
185483 ATTAATATTTATT
1 ATTAATATTTATT
185496 AT
1 AT
185498 AATTGATCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
ATTAATATTTATT
Found at i:191012 original size:13 final size:13
Alignment explanation
Indices: 190991--191024 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
190981 TCCTCCGCAA
190991 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
191004 AAAACAAAAAAAC
1 AAAAAAAAAAAAC
191017 AACAAAAA
1 AA-AAAAA
191025 GGGTCCGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:191014 original size:16 final size:15
Alignment explanation
Indices: 190988--191024 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
190978 GCGTCCTCCG
190988 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
*
191003 CAAAACAAAAAAACAA
1 CAAAA-AAAAAAAAAA
191019 CAAAAA
1 CAAAAA
191025 GGGTCCGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:192502 original size:29 final size:30
Alignment explanation
Indices: 192456--192539 Score: 86
Period size: 28 Copynumber: 2.9 Consensus size: 30
192446 TCGCCCTTCA
* *
192456 AAAGCCCCCAAG-TCAGTGGCATCTTTTCC
1 AAAGCCCACAAGCTCAGTGGCAACTTTTCC
* *
192485 AAAGCCCACAAGCT-AGTGGCAAC-CTTCT
1 AAAGCCCACAAGCTCAGTGGCAACTTTTCC
* *
192513 AAAGTCCACAA-CTCAGTGGCACCTTTT
1 AAAGCCCACAAGCTCAGTGGCAACTTTT
192540 TTTTTTCTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
27 2 0.04
28 21 0.47
29 21 0.47
30 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.23
Consensus pattern (30 bp):
AAAGCCCACAAGCTCAGTGGCAACTTTTCC
Found at i:192530 original size:28 final size:27
Alignment explanation
Indices: 192450--192537 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 27
192440 TATTCCTCGC
* *
192450 CCTTCAAAAGCCCCCAAG-TCAGTGGCA
1 CCTTCTAAAGCCCACAAGCT-AGTGGCA
* *
192477 TCTTTTCCAAAGCCCACAAGCTAGTGGCAA
1 -C-CTTCTAAAGCCCACAAGCTAGTGGC-A
*
192507 CCTTCTAAAGTCCACAA-CTCAGTGGCA
1 CCTTCTAAAGCCCACAAGCT-AGTGGCA
192534 CCTT
1 CCTT
192538 TTTTTTTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
27 7 0.14
28 20 0.40
29 21 0.42
30 2 0.04
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (27 bp):
CCTTCTAAAGCCCACAAGCTAGTGGCA
Found at i:192624 original size:67 final size:70
Alignment explanation
Indices: 192507--192675 Score: 193
Period size: 68 Copynumber: 2.4 Consensus size: 70
192497 CTAGTGGCAA
* *
192507 CCTTCTAAAGTCCACAACTCAGTGGCACCTTTTTTTTTTCTTTTTAAAGCCCACAACTCAGTGGC
1 CCTTCT-AAGTCCACAACTCAGTGGCACC---TTTTCTTCCTTTTAAAGCCCACAACTCAGTGGC
192572 ACTC-TTTT
62 ACTCTTTTT
* *
192580 CCTTCTAAGTCCACAACTCTA-TGGCACC-TTTCTTCCTTTT-AAGCCCACAACTCCGTGGCATT
1 CCTTCTAAGTCCACAACTC-AGTGGCACCTTTTCTTCCTTTTAAAGCCCACAACTCAGTGGCACT
192642 CTTTTT
65 CTTTTT
* * **
192648 TCTTTTAAGTCCACAACTTGGTGGCACC
1 CCTTCTAAGTCCACAACTCAGTGGCACC
192676 CCTTTTAAAG
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
67 21 0.25
68 37 0.44
72 20 0.24
73 7 0.08
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (70 bp):
CCTTCTAAGTCCACAACTCAGTGGCACCTTTTCTTCCTTTTAAAGCCCACAACTCAGTGGCACTC
TTTTT
Found at i:192673 original size:34 final size:32
Alignment explanation
Indices: 192541--192665 Score: 117
Period size: 34 Copynumber: 3.7 Consensus size: 32
192531 GCACCTTTTT
*
192541 TTTTTCTTTTTAAAGCCCACAACTCAGTGGCA-C
1 TTTTTCCTTTT-AAGCCCACAACTC-GTGGCATC
* * * *
192574 TCTTTTCCTTCTAAGTCCACAACTCTATGGCACC
1 T-TTTTCCTTTTAAGCCCACAACTC-GTGGCATC
192608 TTTCTTCCTTTTAAGCCCACAACTCCGTGGCATTC
1 TTT-TTCCTTTTAAGCCCACAACT-CGTGGCA-TC
* *
192643 TTTTTTCTTTTAAGTCCACAACT
1 TTTTTCCTTTTAAGCCCACAACT
192666 TGGTGGCACC
Statistics
Matches: 76, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
33 20 0.26
34 51 0.67
35 5 0.07
ACGTcount: A:0.21, C:0.30, G:0.10, T:0.39
Consensus pattern (32 bp):
TTTTTCCTTTTAAGCCCACAACTCGTGGCATC
Found at i:193036 original size:51 final size:49
Alignment explanation
Indices: 192770--193051 Score: 238
Period size: 49 Copynumber: 5.8 Consensus size: 49
192760 CGTCTTCTTC
* * * * *
192770 TAAGTCCAATATCA-CTGGCCTTGAACCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGT-AGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
** * * *
192819 TAAAACTCAATATCGCTGGCCTTGAATCAGCATATT-G-A----CACCTT
1 TAAGTC-CAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * * * *
192863 GAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCACCCTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
*
192912 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCATCTTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
* * * **
192961 TAAGTCCAATAG-CGCTGGCCTTGAATCGGCATATTGGCACCTTTTCCGTCT
1 TAAGTCCAAT-GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACC-T-T
* * *
193012 TGAGTCCAATGTAGCTGGTCTTGAATCAGCACATTAGCAC
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
193052 AAGTCCAATA
Statistics
Matches: 190, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
43 26 0.14
44 9 0.05
45 1 0.01
48 1 0.01
49 91 0.48
50 29 0.15
51 33 0.17
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCTT
Found at i:193342 original size:154 final size:154
Alignment explanation
Indices: 193056--193350 Score: 527
Period size: 154 Copynumber: 1.9 Consensus size: 154
193046 TAGCACAAGT
193056 CCAATATCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTG
1 CCAATATCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTG
* * *
193121 AATCAGCACATTAACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCTTGAATTAGCGTA
66 AATCAGCACATTAACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAGCATA
193186 TTGGCATCTTTAACATCCTTAAGC
131 TTGGCATCTTTAACATCCTTAAGC
* *
193210 CCAATGTCGTTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTG
1 CCAATATCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTG
*
193275 AATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAGCATA
66 AATCAGCACATTAACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAGCATA
*
193340 TTGGTATCTTT
131 TTGGCATCTTT
193351 CTCACTTTTC
Statistics
Matches: 134, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
154 134 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (154 bp):
CCAATATCATTGGCCTTGTCTCAGCACATTGACATTCTTCTCCAAGTCTAATGCCGCTGACCGTG
AATCAGCACATTAACATCCTTTTTCTCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAGCATA
TTGGCATCTTTAACATCCTTAAGC
Found at i:194016 original size:19 final size:19
Alignment explanation
Indices: 193992--194057 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
193982 TGTCAACGAT
193992 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
194011 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
194025 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
194043 TTGTATCGATACATA
1 TTGTATCGATACATA
194058 CGAAGCTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:194029 original size:32 final size:32
Alignment explanation
Indices: 193993--194055 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
193983 GTCAACGATT
193993 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
194025 TGTATCGATACATAAGTGTTGTATCGATACA
1 TGTATCGATACATAAGTGTTGTATCGATACA
194056 TACGAAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:194030 original size:13 final size:13
Alignment explanation
Indices: 194012--194036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194002 ACATAAGTGT
194012 TGTATCGATACAA
1 TGTATCGATACAA
194025 TGTATCGATACA
1 TGTATCGATACA
194037 TAAGTGTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:194117 original size:13 final size:13
Alignment explanation
Indices: 194099--194123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194089 ATTACTCAAA
194099 TGTATCGATACAT
1 TGTATCGATACAT
194112 TGTATCGATACA
1 TGTATCGATACA
194124 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:194169 original size:52 final size:52
Alignment explanation
Indices: 194132--194257 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
194122 CACTGATCTT
*
194132 TGTATCGATATATGCAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
* *
194184 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATGCACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
194236 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
194258 ATTTTCATAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATGAAA
Found at i:199430 original size:8 final size:9
Alignment explanation
Indices: 199409--199434 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
199399 TTTCTTTATA
199409 AAAAATTTC
1 AAAAATTTC
199418 AAAAATTTC
1 AAAAATTTC
199427 AAAAATTT
1 AAAAATTT
199435 TATTTATCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (9 bp):
AAAAATTTC
Found at i:202259 original size:1 final size:1
Alignment explanation
Indices: 202255--202287 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
202245 TTTTTTTTTT
*
202255 GGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
202288 ATGGGAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.97, T:0.03
Consensus pattern (1 bp):
G
Found at i:202292 original size:13 final size:12
Alignment explanation
Indices: 202255--202292 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
202245 TTTTTTTTTT
202255 GGGGGGGGGG-G
1 GGGGGGGGGGTG
202266 GGGGGGGGGGTG
1 GGGGGGGGGGTG
202278 GGGGGGGGGGATG
1 GGGGGGGGGG-TG
202291 GG
1 GG
202293 AAGGGTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 10 0.40
12 11 0.44
13 4 0.16
ACGTcount: A:0.03, C:0.00, G:0.92, T:0.05
Consensus pattern (12 bp):
GGGGGGGGGGTG
Found at i:202298 original size:22 final size:22
Alignment explanation
Indices: 202254--202298 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
202244 GTTTTTTTTT
* **
202254 TGGGGGGGGGGGGGGGGGGGGG
1 TGGGGGGGGGGGAGGGGAAGGG
*
202276 TGGGGGGGGGGGATGGGAAGGG
1 TGGGGGGGGGGGAGGGGAAGGG
202298 T
1 T
202299 TGGAGTCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.84, T:0.09
Consensus pattern (22 bp):
TGGGGGGGGGGGAGGGGAAGGG
Found at i:541887 original size:2 final size:2
Alignment explanation
Indices: 541873--541915 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
541863 GATCCAAAGA
541873 AT AT AT A- AT -T AT 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 AT AT AT AT AT AT AT
541913 AT A
1 AT A
541916 ACCCATATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:542392 original size:15 final size:14
Alignment explanation
Indices: 542372--542410 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
542362 ATACAATCAA
542372 TTAATATTTAAATAT
1 TTAATATTTAAAT-T
*
542387 TTAATATTCAAATT
1 TTAATATTTAAATT
*
542401 TTAAAATTTA
1 TTAATATTTA
542411 TAGTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (14 bp):
TTAATATTTAAATT
Found at i:542638 original size:28 final size:31
Alignment explanation
Indices: 542584--542643 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
542574 GATTAGATTT
*
542584 AAAAATATAAATTATTATTTATAAATTAATA
1 AAAAATATAAAATATTATTTATAAATTAATA
*
542615 AAAAATTTAAAATATT-TTT-T-AATTAATA
1 AAAAATATAAAATATTATTTATAAATTAATA
542643 A
1 A
542644 TTATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 9 0.33
29 1 0.04
30 3 0.11
31 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
AAAAATATAAAATATTATTTATAAATTAATA
Found at i:543420 original size:14 final size:15
Alignment explanation
Indices: 543395--543424 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
543385 TTATTATCTC
543395 ATCAATATTTTTAAT
1 ATCAATATTTTTAAT
543410 ATCAATA-TTTTAAT
1 ATCAATATTTTTAAT
543424 A
1 A
543425 AAATTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCAATATTTTTAAT
Found at i:543580 original size:21 final size:21
Alignment explanation
Indices: 543554--543597 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
543544 TAATATTATT
543554 TAAATTAAAAAATATTA-ATAA
1 TAAATTAAAAAA-ATTACATAA
*
543575 TAAATTAAAATAATTACATAA
1 TAAATTAAAAAAATTACATAA
543596 TA
1 TA
543598 CTTATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAATTAAAAAAATTACATAA
Found at i:543913 original size:13 final size:13
Alignment explanation
Indices: 543895--543919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
543885 AAAAGAAAAA
543895 TATATTATATATC
1 TATATTATATATC
543908 TATATTATATAT
1 TATATTATATAT
543920 TAAAGCAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATTATATATC
Found at i:544480 original size:3 final size:3
Alignment explanation
Indices: 544464--544502 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
544454 TTCACTGCAG
* *
544464 CAA CAA CAG TAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
544503 GAACCAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.31, G:0.03, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:546285 original size:13 final size:15
Alignment explanation
Indices: 546267--546339 Score: 57
Period size: 14 Copynumber: 5.0 Consensus size: 15
546257 ATGAATAATT
546267 TATAAAA-AT-TAAA
1 TATAAAATATATAAA
546280 TATAAAATATATAAA
1 TATAAAATATATAAA
* *
546295 T-TAAATTAAATAAA
1 TATAAAATATATAAA
*
546309 -ATAATCATATA-AATA
1 TATAA-AATATATAA-A
546324 TTATAAAATATATAAA
1 -TATAAAATATATAAA
546340 ATTAAATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
13 7 0.15
14 18 0.39
15 9 0.20
16 6 0.13
17 6 0.13
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (15 bp):
TATAAAATATATAAA
Found at i:546290 original size:20 final size:19
Alignment explanation
Indices: 546267--546304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
546257 ATGAATAATT
546267 TATAAAAATTAAATATAAAA
1 TATAAAAATTAAAT-TAAAA
*
546287 TATATAAATTAAATTAAA
1 TATAAAAATTAAATTAAA
546305 TAAAATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TATAAAAATTAAATTAAAA
Found at i:546293 original size:9 final size:9
Alignment explanation
Indices: 546279--546341 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
546269 TAAAAATTAA
546279 ATATAAAAT
1 ATATAAAAT
*
546288 ATATAAATT
1 ATATAAAAT
* *
546297 AAATTAAAT
1 ATATAAAAT
546306 A-A-AATAAT
1 ATATAA-AAT
546314 CATAT-AAAT
1 -ATATAAAAT
546323 ATTATAAAAT
1 A-TATAAAAT
546333 ATATAAAAT
1 ATATAAAAT
546342 TAAATTAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
7 1 0.02
8 5 0.12
9 30 0.70
10 7 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
ATATAAAAT
Found at i:546326 original size:29 final size:25
Alignment explanation
Indices: 546272--546351 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
546262 TAATTTATAA
*
546272 AAATTAAATATAAAATATATAAATT
1 AAATTAAATAAAAAATATATAAATT
546297 AAATTAAATAAAATAATCATATAAA-T
1 AAATTAAATAAAA-AAT-ATATAAATT
*
546323 --ATT--ATAAAATATATA-AAATT
1 AAATTAAATAAAAAATATATAAATT
546343 AAATTAAAT
1 AAATTAAAT
546352 TTTATATTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
19 3 0.07
20 4 0.09
21 2 0.04
22 9 0.20
24 5 0.11
25 12 0.26
26 4 0.09
27 7 0.15
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATTAAATAAAAAATATATAAATT
Found at i:554197 original size:21 final size:21
Alignment explanation
Indices: 554172--554212 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
554162 GATAGTTAAA
554172 AATTT-TATTTTGAATCTCAAG
1 AATTTATATTTT-AATCTCAAG
*
554193 AATTTATATTTTAATTTCAA
1 AATTTATATTTTAATCTCAA
554213 TCCCCGACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
AATTTATATTTTAATCTCAAG
Found at i:555775 original size:17 final size:18
Alignment explanation
Indices: 555753--555795 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
555743 TATGTTGGGG
* *
555753 ATTTTAATTTTTTTATA-
1 ATTTTAATTTTATTAAAT
555770 ATTTTAATTTTATTAAAT
1 ATTTTAATTTTATTAAAT
555788 ATTTTAAT
1 ATTTTAAT
555796 ATATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTAATTTTATTAAAT
Found at i:555807 original size:18 final size:19
Alignment explanation
Indices: 555765--555827 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
555755 TTTAATTTTT
*
555765 TTATA-ATTTTAAT-TTTA
1 TTATATATTTTAATATATA
*
555782 TTAAATATTTTAATATATA
1 TTATATATTTTAATATATA
* *
555801 TT-TATATATTAAAATA-A
1 TTATATATTTTAATATATA
555818 TTATATATTT
1 TTATATATTT
555828 AATTTAATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
17 7 0.19
18 25 0.68
19 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTATATATTTTAATATATA
Found at i:557103 original size:2 final size:2
Alignment explanation
Indices: 557096--557132 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
557086 GATGATTTTA
* *
557096 AT AT AT AT AT AT AT AT AT AT AT AA AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
557133 CACACTGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:557798 original size:13 final size:13
Alignment explanation
Indices: 557782--557829 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
557772 ATTACACAAA
557782 TATATTAAAATTT
1 TATATTAAAATTT
*
557795 TATAATATAAATTAT
1 TATATTA-AAATT-T
557810 TAATATATAAAATTT
1 T-ATAT-TAAAATTT
557825 TATAT
1 TATAT
557830 AAATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
13 6 0.21
14 9 0.31
15 4 0.14
16 8 0.28
17 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATTAAAATTT
Found at i:557855 original size:29 final size:26
Alignment explanation
Indices: 557783--557857 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 26
557773 TTACACAAAT
*
557783 ATATTAAAATTTTATAATATAAATTATTA
1 ATATTAAAA-TTT-T-ATATAAATTATAA
557812 ATATATAAAATTTTATATAAATATATAAA
1 ATAT-TAAAATTTTATATAAAT-TAT-AA
557841 ATATTAAAATATTTATA
1 ATATTAAAAT-TTTATA
557858 ATATAAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 8 0.20
28 10 0.24
29 18 0.44
30 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATTAAAATTTTATATAAATTATAA
Found at i:557880 original size:11 final size:11
Alignment explanation
Indices: 557795--557891 Score: 57
Period size: 11 Copynumber: 9.4 Consensus size: 11
557785 ATTAAAATTT
557795 TATAATATAAA
1 TATAATATAAA
557806 T-T-AT-T-AA
1 TATAATATAAA
557813 TAT-ATA-AAA
1 TATAATATAAA
* *
557822 TTTTATATAAA
1 TATAATATAAA
557833 TAT-ATA-AAA
1 TATAATATAAA
* **
557842 TATTAAAATATT
1 TA-TAATATAAA
557854 TATAATATAAA
1 TATAATATAAA
* *
557865 AATAATATAAT
1 TATAATATAAA
557876 TATAATTATAAA
1 TATAA-TATAAA
557888 TATA
1 TATA
557892 TGAATTATTA
Statistics
Matches: 65, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
7 3 0.05
8 4 0.06
9 11 0.17
10 8 0.12
11 27 0.42
12 12 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TATAATATAAA
Found at i:557897 original size:21 final size:22
Alignment explanation
Indices: 557796--557899 Score: 65
Period size: 21 Copynumber: 4.6 Consensus size: 22
557786 TTAAAATTTT
557796 ATAATATAAATTATTAATATATAAA
1 ATAATAT-AATTA-TAATATA-AAA
*
557821 ATTTTATATAA--AT-ATATAAAA
1 A--TAATATAATTATAATATAAAA
* *
557842 TATTAAAATATTTATAATATAAAA
1 -A-TAATATAATTATAATATAAAA
*
557866 ATAATATAATTATAAT-TATAA
1 ATAATATAATTATAATATAAAA
557887 AT-ATATGAATTAT
1 ATAATAT-AATTAT
557900 TATGATGATT
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
20 4 0.06
21 21 0.32
22 19 0.29
23 4 0.06
24 9 0.14
25 1 0.02
26 2 0.03
27 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (22 bp):
ATAATATAATTATAATATAAAA
Found at i:559118 original size:19 final size:18
Alignment explanation
Indices: 559093--559160 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
559083 AATTCAACGA
559093 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
559111 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
559127 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
559143 TATTGTATCGATACATAA
1 T-TTGTATCGATACATAA
559161 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
18 1 0.02
19 27 0.63
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:559131 original size:32 final size:32
Alignment explanation
Indices: 559095--559157 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
559085 TTCAACGATT
*
559095 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
559127 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
559158 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:559132 original size:13 final size:13
Alignment explanation
Indices: 559114--559138 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559104 ACATAAGTGT
559114 TGTATCGATACAA
1 TGTATCGATACAA
559127 TGTATCGATACA
1 TGTATCGATACA
559139 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:559204 original size:20 final size:20
Alignment explanation
Indices: 559179--559233 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
559169 TGCCAAGGAA
559179 ATGTATCGATACATTAT-TT
1 ATGTATCGATACATTATCTT
*
559198 CATGTATCGATACATGAATCTT
1 -ATGTATCGATACAT-TATCTT
559220 -TGTATCGATACATT
1 ATGTATCGATACATT
559234 TGGGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 27 0.87
21 2 0.06
22 2 0.06
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTATCTT
Found at i:561640 original size:52 final size:51
Alignment explanation
Indices: 561578--561751 Score: 179
Period size: 52 Copynumber: 3.3 Consensus size: 51
561568 CAATTCTCCG
* * *
561578 CAATCGGGGATATTCCATCTCTGATTTTATTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCATCTCCGATTTTATT-CTAAAACACCAATTTTTCCA
* * **
561630 CAATCGGGGATACTCCAATC-CCGGTTTTATTTTCAAAACACCAATTTTTCTT
1 CAATCGGGGATACTCC-ATCTCCGATTTTATTCT-AAAACACCAATTTTTCCA
* * * * *
561682 TAATCAGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACCAATTTTTTCA
1 CAATCGGGGATACTCCATCTCCGATTTTA-TT-CTAAAACACCAATTTTTCCA
*
561735 CAATCGAGGATACTCCA
1 CAATCGGGGATACTCCA
561752 ACCTTGTTAT
Statistics
Matches: 98, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
51 3 0.03
52 61 0.62
53 34 0.35
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (51 bp):
CAATCGGGGATACTCCATCTCCGATTTTATTCTAAAACACCAATTTTTCCA
Found at i:561788 original size:28 final size:29
Alignment explanation
Indices: 561737--561813 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
561727 TTTTTTCACA
* ** * *
561737 ATCGAGGATACTCCAACCTTGTTA-TTTC
1 ATCGGGGATACTCCAACCCCGTTACCTCC
561765 ATCGGGGATACTCCAACCCCGTTACCTCC
1 ATCGGGGATACTCCAACCCCGTTACCTCC
*
561794 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
561814 ACTTTATTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 39 0.93
29 3 0.07
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCGTTACCTCC
Found at i:567105 original size:13 final size:13
Alignment explanation
Indices: 567087--567113 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
567077 CTCTTTAATG
567087 TTTTAACTTTTAA
1 TTTTAACTTTTAA
567100 TTTTAACTTTTAA
1 TTTTAACTTTTAA
567113 T
1 T
567114 CATGTATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTAACTTTTAA
Found at i:568617 original size:11 final size:11
Alignment explanation
Indices: 568601--568625 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
568591 AGTTATGAGC
568601 TAAAAAGAAAA
1 TAAAAAGAAAA
568612 TAAAAAGAAAA
1 TAAAAAGAAAA
568623 TAA
1 TAA
568626 GAATATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (11 bp):
TAAAAAGAAAA
Found at i:571810 original size:35 final size:35
Alignment explanation
Indices: 571771--571842 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
571761 AAAGTACCAA
571771 GTTTATAATGCAAAAACAAAGCATATCAATGTAAG
1 GTTTATAATGCAAAAACAAAGCATATCAATGTAAG
* *
571806 GTTTATAATGTAAGAACAAAGCATATCAATGTAAG
1 GTTTATAATGCAAAAACAAAGCATATCAATGTAAG
571841 GT
1 GT
571843 ATCACTGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.28
Consensus pattern (35 bp):
GTTTATAATGCAAAAACAAAGCATATCAATGTAAG
Found at i:571898 original size:19 final size:19
Alignment explanation
Indices: 571874--571911 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
571864 GAAGAATGAA
571874 AGATTCAACTTCAGAAGAT
1 AGATTCAACTTCAGAAGAT
571893 AGATTCAACTTCAGAAGAT
1 AGATTCAACTTCAGAAGAT
571912 TGTGATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
AGATTCAACTTCAGAAGAT
Found at i:573426 original size:4 final size:4
Alignment explanation
Indices: 573417--573443 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
573407 CTTTATACCA
573417 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
573444 CAAGGAAGCG
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:574372 original size:17 final size:16
Alignment explanation
Indices: 574350--574388 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
574340 ATAATTTTAT
574350 TTTTTAATATCTTTAAA
1 TTTTTAATAT-TTTAAA
*
574367 TTTTTATTATTTTAAA
1 TTTTTAATATTTTAAA
574383 TATTTT
1 T-TTTT
574389 CTTCTAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTAATATTTTAAA
Found at i:575437 original size:24 final size:25
Alignment explanation
Indices: 575409--575476 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 25
575399 TTAATTTTAT
*
575409 TTTTTATTTATAATTTTAATTTA-AG
1 TTTTT-TTTATAATTTTAATTGATAG
*
575434 TTTTTTTTATTATTTCTTAATTGATAG
1 TTTTTTTTA-TAATT-TTAATTGATAG
*
575461 TTTTTTTTATCATTTT
1 TTTTTTTTATAATTTT
575477 TTAATTGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 4 0.11
25 11 0.31
26 10 0.28
27 11 0.31
ACGTcount: A:0.24, C:0.03, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTTTTATAATTTTAATTGATAG
Found at i:575446 original size:27 final size:27
Alignment explanation
Indices: 575424--575484 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
575414 ATTTATAATT
*
575424 TTAATTTA-AGTTTTTTTTATTATTTC
1 TTAATTGATAGTTTTTTTTATTATTTC
* *
575450 TTAATTGATAGTTTTTTTTATCATTTT
1 TTAATTGATAGTTTTTTTTATTATTTC
575477 TTAATTGA
1 TTAATTGA
575485 ATTGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.66
Consensus pattern (27 bp):
TTAATTGATAGTTTTTTTTATTATTTC
Found at i:577561 original size:13 final size:13
Alignment explanation
Indices: 577543--577571 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
577533 TTAGACCCTG
577543 ATTTTGTTTTTAT
1 ATTTTGTTTTTAT
577556 ATTTTGTTTTTAT
1 ATTTTGTTTTTAT
577569 ATT
1 ATT
577572 ATATATTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (13 bp):
ATTTTGTTTTTAT
Found at i:582575 original size:20 final size:21
Alignment explanation
Indices: 582537--582575 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
582527 TTTAAATATA
* *
582537 AATATAAATAATTTTATTTTT
1 AATATAAATAATATAATTTTT
582558 AATA-AAATAATATAATTT
1 AATATAAATAATATAATTT
582576 GACTCATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATATAAATAATATAATTTTT
Found at i:582636 original size:24 final size:24
Alignment explanation
Indices: 582609--582654 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
582599 TATATGCTAT
582609 TAAT-ATATTAAATATAAATTTTTA
1 TAATAATATTAAAT-TAAATTTTTA
* *
582633 TAATAATCTTAAATTTAATTTT
1 TAATAATATTAAATTAAATTTT
582655 GTTTTTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TAATAATATTAAATTAAATTTTTA
Found at i:582720 original size:22 final size:24
Alignment explanation
Indices: 582695--582746 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
582685 ACAAATAATA
*
582695 AAATAAAAAAC-TCAA-ATTTATT
1 AAATAAAAAACTTAAAGATTTATT
*
582717 AAATATAAAACTTTAAAGATTTATT
1 AAATAAAAAAC-TTAAAGATTTATT
582742 AAATA
1 AAATA
582747 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
24 3 0.12
25 12 0.48
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAAAAACTTAAAGATTTATT
Found at i:582941 original size:18 final size:19
Alignment explanation
Indices: 582918--582957 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
582908 TTTTTAATGA
* *
582918 ATTAAATGATATTATTT-T
1 ATTAAATAAAATTATTTAT
582936 ATTAAATAAAATTATTTAT
1 ATTAAATAAAATTATTTAT
582955 ATT
1 ATT
582958 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
ATTAAATAAAATTATTTAT
Found at i:583022 original size:28 final size:28
Alignment explanation
Indices: 582990--583046 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
582980 GACATGATAC
582990 AACTAATACATTTAAATAAAATTAACTT
1 AACTAATACATTTAAATAAAATTAACTT
*
583018 AACTAATACATTTAAATAAAATTTACTT
1 AACTAATACATTTAAATAAAATTAACTT
583046 A
1 A
583047 GACAAGATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (28 bp):
AACTAATACATTTAAATAAAATTAACTT
Found at i:583972 original size:12 final size:12
Alignment explanation
Indices: 583955--583991 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
583945 AATTTAATTA
583955 AAATATAAAAAT
1 AAATATAAAAAT
583967 AAATATAAAAAAT
1 AAATAT-AAAAAT
583980 AAATATAAAAAT
1 AAATATAAAAAT
583992 GATTATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATATAAAAAT
Found at i:583977 original size:13 final size:13
Alignment explanation
Indices: 583955--583990 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
583945 AATTTAATTA
583955 AAATAT-AAAAAT
1 AAATATAAAAAAT
583967 AAATATAAAAAAT
1 AAATATAAAAAAT
583980 AAATATAAAAA
1 AAATATAAAAA
583991 TGATTATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATATAAAAAAT
Found at i:593728 original size:17 final size:18
Alignment explanation
Indices: 593706--593774 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 18
593696 AAGAGTGGTG
593706 AAGGAAAAAG-GAAGAAA
1 AAGGAAAAAGAGAAGAAA
* *
593723 AAGGAAGAAGATAAGAAA
1 AAGGAAAAAGAGAAGAAA
*
593741 AAGAAAAAAATAGAGAAAGAAAA
1 AAG--GAAAA-AGAG-AAG-AAA
593764 AAGGAAAAAGA
1 AAGGAAAAAGA
593775 ATGGATAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 9 0.22
18 9 0.22
20 6 0.15
21 7 0.17
22 3 0.08
23 6 0.15
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (18 bp):
AAGGAAAAAGAGAAGAAA
Found at i:593757 original size:18 final size:18
Alignment explanation
Indices: 593717--593758 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
593707 AGGAAAAAGG
* *
593717 AAGAAAAAGGAAGAAGAT
1 AAGAAAAAGGAAAAAAAT
593735 AAGAAAAA-GAAAAAAAT
1 AAGAAAAAGGAAAAAAAT
593752 AGAGAAA
1 A-AGAAA
593759 GAAAAAAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (18 bp):
AAGAAAAAGGAAAAAAAT
Found at i:594270 original size:33 final size:35
Alignment explanation
Indices: 594208--594273 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 35
594198 TCGATGATAG
* *
594208 AATTTTTTAACAAATTATTAGTTTCCTAAAAATCA
1 AATTATTTAACAAATTATTAGTTTACTAAAAATCA
*
594243 AATTATTTAA-AAATT-TTTGTTTACTAAAAAT
1 AATTATTTAACAAATTATTAGTTTACTAAAAAT
594274 ATTTAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 14 0.50
34 5 0.18
35 9 0.32
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
AATTATTTAACAAATTATTAGTTTACTAAAAATCA
Found at i:596069 original size:2 final size:2
Alignment explanation
Indices: 596062--596094 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
596052 GTTAGATTTG
596062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
596095 TTAGATAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:596294 original size:18 final size:18
Alignment explanation
Indices: 596236--596306 Score: 52
Period size: 18 Copynumber: 3.9 Consensus size: 18
596226 TCTGATGTGA
*
596236 ATTTCTATTTTATTATTT
1 ATTTCTATTTTGTTATTT
* *** **
596254 ATTTTTAGCGTGATTATGA
1 ATTTCTATTTTG-TTATTT
596273 ATTTCTATTTTGTTATTT
1 ATTTCTATTTTGTTATTT
* *
596291 ATTTTTATTATGTTAT
1 ATTTCTATTTTGTTAT
596307 AATAAAATTT
Statistics
Matches: 37, Mismatches: 15, Indels: 2
0.69 0.28 0.04
Matches are distributed among these distances:
18 25 0.68
19 12 0.32
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (18 bp):
ATTTCTATTTTGTTATTT
Found at i:597251 original size:14 final size:14
Alignment explanation
Indices: 597232--597261 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
597222 TTAAATTATT
597232 ATTTAATAATAAAA
1 ATTTAATAATAAAA
*
597246 ATTTAATTATAAAA
1 ATTTAATAATAAAA
597260 AT
1 AT
597262 ATATAAAATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATTTAATAATAAAA
Found at i:598614 original size:2 final size:2
Alignment explanation
Indices: 598607--598654 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
598597 GAACCCTCCC
*
598607 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
598649 CT CT CT
1 CT CT CT
598655 ATATATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:598659 original size:2 final size:2
Alignment explanation
Indices: 598654--598679 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
598644 TCTCTCTCTC
598654 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
598680 AAAGACAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:599073 original size:118 final size:115
Alignment explanation
Indices: 598938--599172 Score: 303
Period size: 114 Copynumber: 2.0 Consensus size: 115
598928 ATCAAAAGAT
* *
598938 TATTATTTATAAATGTTAGTGATGAAAATATATTATTTTTTAAAATTAAATGATCAAAACTAAAA
1 TATTATTTATAAATGTTAGTGAT-AAAA-ATATTATATTTCAAAATTAAATGATCAAAACT--AA
* *
599003 ACT-TTCCAAAAAAAGCAATTTACTCAATTAATATGA-TTGTGATTAATTTGTTA
62 A-TGATCCAAAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
* * * *
599056 TATTATTTGTAAATGTTAGTGATCAAAATATTATATTTCAAAGTTACATGATCAAAACTAAATGA
1 TATTATTTATAAATGTTAGTGATAAAAATATTATATTTCAAAATTAAATGATCAAAACTAAATGA
** * *
599121 TCCCCAAAAAGTAATTTACTCGATTAATATGATTTGTGATGAATTTGTTA
66 TCCAAAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
599171 TA
1 TA
599173 GATTACAAGT
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
113 1 0.01
114 31 0.30
115 18 0.17
116 28 0.27
117 3 0.03
118 22 0.21
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (115 bp):
TATTATTTATAAATGTTAGTGATAAAAATATTATATTTCAAAATTAAATGATCAAAACTAAATGA
TCCAAAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
Found at i:599128 original size:116 final size:117
Alignment explanation
Indices: 598938--599172 Score: 307
Period size: 116 Copynumber: 2.0 Consensus size: 117
598928 ATCAAAAGAT
* *
598938 TATTATTTATAAATGTTAGTGATGAAAATATATTATTTTTTAAAATTAAATGATCAAAACTAAAA
1 TATTATTTATAAATGTTAGTGATGAAAATATATTATATTTCAAAATTAAATGATCAAAACTAAAA
** *
599003 ACTTTCCAAAAAAAGCAATTTACTCAATTAATATGA-TTGTGATTAATTTGTTA
66 AC--TCCCCAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
* * * *
599056 TATTATTTGTAAATGTTAGTGAT-CAAA-ATATTATATTTCAAAGTTACATGATCAAAACTAAAT
1 TATTATTTATAAATGTTAGTGATGAAAATATATTATATTTCAAAATTAAATGATCAAAACTAAA-
* * *
599119 GA-TCCCCAAAAAGTAATTTACTCGATTAATATGATTTGTGATGAATTTGTTA
65 AACTCCCCAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
599171 TA
1 TA
599173 GATTACAAGT
Statistics
Matches: 103, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
114 28 0.27
115 18 0.17
116 31 0.30
117 4 0.04
118 22 0.21
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (117 bp):
TATTATTTATAAATGTTAGTGATGAAAATATATTATATTTCAAAATTAAATGATCAAAACTAAAA
ACTCCCCAAAAAGCAATTTACTCAATTAATATGATTTGTGATGAATTTGTTA
Found at i:607400 original size:52 final size:52
Alignment explanation
Indices: 607315--607439 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
607305 ATATGAAAAG
* * *
607315 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
607367 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
607419 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
607440 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:607452 original size:52 final size:51
Alignment explanation
Indices: 607315--607460 Score: 204
Period size: 52 Copynumber: 2.8 Consensus size: 51
607305 ATATGAAAAG
* *
607315 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
607367 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
607419 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACAT
607461 TTGAGTAATG
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:607474 original size:21 final size:21
Alignment explanation
Indices: 607448--607501 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
607438 CAAAGATCAG
607448 TGTATCGATACATTTGAGTAA
1 TGTATCGATACATTTGAGTAA
607469 TGTATCGATACATTTGAGTAA
1 TGTATCGATACATTTGAGTAA
607490 TGTATCGATACA
1 TGTATCGATACA
607502 ATGTATCGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
TGTATCGATACATTTGAGTAA
Found at i:607506 original size:13 final size:13
Alignment explanation
Indices: 607488--607514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
607478 ACATTTGAGT
607488 AATGTATCGATAC
1 AATGTATCGATAC
607501 AATGTATCGATAC
1 AATGTATCGATAC
607514 A
1 A
607515 TTTGAGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:607510 original size:34 final size:34
Alignment explanation
Indices: 607467--607535 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
607457 ACATTTGAGT
607467 AATGTATCGATACATTTGAGTAATGTATCGATAC
1 AATGTATCGATACATTTGAGTAATGTATCGATAC
607501 AATGTATCGATACATTTGAGTAATGTATCGATAC
1 AATGTATCGATACATTTGAGTAATGTATCGATAC
607535 A
1 A
607536 TTTTTTGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (34 bp):
AATGTATCGATACATTTGAGTAATGTATCGATAC
Found at i:607592 original size:33 final size:33
Alignment explanation
Indices: 607555--607621 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
607545 AGTAGCTTAA
607555 ATTGTATCGATACAAA-AAAATATGTATCGATAC
1 ATTGTATCGATA-AAACAAAATATGTATCGATAC
***
607588 ATTGTATCGATAAAACACTTTATGTATCGATAC
1 ATTGTATCGATAAAACAAAATATGTATCGATAC
607621 A
1 A
607622 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATAAAACAAAATATGTATCGATAC
Found at i:612079 original size:13 final size:14
Alignment explanation
Indices: 612061--612098 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
612051 ATCGCACGCT
612061 TTTTTTTTTTAAA-
1 TTTTTTTTTTAAAG
*
612074 TTTTTTTTCTAAAG
1 TTTTTTTTTTAAAG
*
612088 TTTTTATTTTA
1 TTTTTTTTTTA
612099 TTTTATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTTTTTTTTAAAG
Found at i:612171 original size:27 final size:25
Alignment explanation
Indices: 612141--612213 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 25
612131 TTTGGTTTTA
*
612141 ATTTTAATTTCTGTTTTTTAATTATAT
1 ATTTTAATTTCTGTTTTCTAA--ATAT
**
612168 ATTTTTAATTTTCAATTTTCTAAATAT
1 A-TTTTAA-TTTCTGTTTTCTAAATAT
*
612195 ATTTTAAATTTTTGTTTTC
1 ATTTT-AATTTCTGTTTTC
612214 CTAATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
26 12 0.32
27 8 0.22
28 6 0.16
29 11 0.30
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.64
Consensus pattern (25 bp):
ATTTTAATTTCTGTTTTCTAAATAT
Found at i:612764 original size:203 final size:203
Alignment explanation
Indices: 612415--613399 Score: 1602
Period size: 203 Copynumber: 4.9 Consensus size: 203
612405 ATTGTATTTA
* * * **
612415 CATAATTTATAATAATACTTAAATTTGAAAATTTTTG-AAAAAGTTACAAATGATCAATTTTTAA
1 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAA-TTTCCA
* * * *
612479 AAAATTTCTACGTATCG-AAAATTCTTAGGAGTCTAACACAAATGGTGAAAACTAGCCTTAAGGT
65 AAAATTTCTAGGTAT-GAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTAAGGT
* *
612543 TTTCCGGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTATATTTACAT
129 TTTCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACAT
*
612608 AATTTGTTTC
194 AATTTGTCTC
612618 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
1 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
612683 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTAAGGTTT
66 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTAAGGTTT
*
612748 TCCGGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATAA
131 TCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATAA
612813 TTTGTCTC
196 TTTGTCTC
*
612821 CATAATTTATGATAATACTTAAATTTGAAAATTTTCTAAAAAAGTTACCAATGATCAATTTCCAA
1 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
* *
612886 AAATTTCTAAGTATGAAAAATTTTTAGGAGTTTAACACAAATGGCGGAAACTAAG-CTTAAGGTT
66 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACT-AGCCTTAAGGTT
612950 TTCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATA
130 TTCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATA
613015 ATTTGTCTC
195 ATTTGTCTC
*
613024 CATAATTTATGAAAATACTTAAATTTGAAAATTTTCG-AAAAAGTTACCAATGATCAATTTCCAA
1 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
613088 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTTAAGGTT
66 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCC-TTAAGGTT
* * * * * *
613153 TTTCAGTAGCTAAAGTTTTTGATTTAAATTTTTGAAAATTTTAAGAATTTTATTGTATTTACATA
130 TTCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATA
*
613218 ATTTGTTTC
195 ATTTGTCTC
**
613227 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAA-TTACCAATGATCAATTTTTAA
1 CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
* * * *
613291 AAATTTCTAGATATGGAAAATTTTTAGGAGTCTAACACAAATGACGGAAACTAGCCTCAAGGTTT
66 AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTAAGGTTT
* * *
613356 TTCAGTAGTCAAAGTTTTCGATTTTAATTTTTGTAGATATTAAG
131 TCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAG
613400 TTCACCTAAT
Statistics
Matches: 736, Mismatches: 40, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
201 2 0.00
202 124 0.17
203 584 0.79
204 26 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (203 bp):
CATAATTTATGATAATACTTAAATTTGAAAATTTTCGAAAAAAGTTACCAATGATCAATTTCCAA
AAATTTCTAGGTATGAAAAATTTTTAGGAGTCTAACACAAATGGCGGAAACTAGCCTTAAGGTTT
TCCAGTAGCCAAAGTTTTCGATTTTAATTTTTGTAAATATTAAGAATTTTATTGTATTTACATAA
TTTGTCTC
Found at i:616179 original size:2 final size:2
Alignment explanation
Indices: 616174--616208 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
616164 ATACACTATA
616174 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
616209 ATATATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:617969 original size:21 final size:21
Alignment explanation
Indices: 617945--617984 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
617935 TGAATATTTT
* *
617945 TATAATTACGTTGATGGAACA
1 TATAATTACCTTAATGGAACA
617966 TATAATTACCTTAATGGAA
1 TATAATTACCTTAATGGAA
617985 GCATCATACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (21 bp):
TATAATTACCTTAATGGAACA
Found at i:618641 original size:15 final size:15
Alignment explanation
Indices: 618600--618653 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
618590 TCAATAATTT
618600 ATTATAATTAATTATA
1 ATTATAATT-ATTATA
* * *
618616 ATAATATTTATTATG
1 ATTATAATTATTATA
618631 ATTATAATTATTATA
1 ATTATAATTATTATA
*
618646 AATATAAT
1 ATTATAAT
618654 CTGATAAAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 24 0.77
16 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTATAATTATTATA
Found at i:623783 original size:13 final size:12
Alignment explanation
Indices: 623761--623830 Score: 59
Period size: 13 Copynumber: 5.3 Consensus size: 12
623751 ACCTTCACTG
623761 TTTCAAATTGAA
1 TTTCAAATTGAA
*
623773 TTTCAAAATTGACTG
1 TTTC-AAATTGA--A
623788 TTTCAAATTGAA
1 TTTCAAATTGAA
*
623800 TTTCAAAATTGACTG
1 TTTC-AAATTGA--A
*
623815 TTTCAAATTGAT
1 TTTCAAATTGAA
623827 TTTC
1 TTTC
623831 CTACCAGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 12 0.25
13 14 0.29
14 14 0.29
15 8 0.17
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.44
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:623795 original size:27 final size:27
Alignment explanation
Indices: 623757--623830 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
623747 TGCAACCTTC
623757 ACTGTTTCAAATTGAATTTCAAAATTG
1 ACTGTTTCAAATTGAATTTCAAAATTG
623784 ACTGTTTCAAATTGAATTTCAAAATTG
1 ACTGTTTCAAATTGAATTTCAAAATTG
*
623811 ACTGTTTCAAATTGATTTTC
1 ACTGTTTCAAATTGAATTTC
623831 CTACCAGCTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (27 bp):
ACTGTTTCAAATTGAATTTCAAAATTG
Found at i:623797 original size:14 final size:14
Alignment explanation
Indices: 623757--623825 Score: 74
Period size: 14 Copynumber: 5.1 Consensus size: 14
623747 TGCAACCTTC
623757 ACTGTTTCAAATTG
1 ACTGTTTCAAATTG
*
623771 A--ATTTCAAAATTG
1 ACTGTTTC-AAATTG
623784 ACTGTTTCAAATTG
1 ACTGTTTCAAATTG
*
623798 A--ATTTCAAAATTG
1 ACTGTTTC-AAATTG
623811 ACTGTTTCAAATTG
1 ACTGTTTCAAATTG
623825 A
1 A
623826 TTTTCCTACC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
12 8 0.18
13 14 0.31
14 15 0.33
15 8 0.18
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (14 bp):
ACTGTTTCAAATTG
Found at i:628507 original size:15 final size:15
Alignment explanation
Indices: 628487--628536 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
628477 TTCAAATTGA
628487 ATTTCAAAATTGGCT
1 ATTTCAAAATTGGCT
**
628502 ATTTC-AAATT--AA
1 ATTTCAAAATTGGCT
628514 ATTTCAAAATTGGCT
1 ATTTCAAAATTGGCT
*
628529 GTTTCAAA
1 ATTTCAAA
628537 TTGATTTTCC
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 5 0.19
15 12 0.44
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (15 bp):
ATTTCAAAATTGGCT
Found at i:628545 original size:27 final size:27
Alignment explanation
Indices: 628474--628545 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
628464 CAACCTTCAT
628474 TATTTCAAATTGAATTTCAAAATTGGC
1 TATTTCAAATTGAATTTCAAAATTGGC
*
628501 TATTTCAAATTAAATTTCAAAATTGGC
1 TATTTCAAATTGAATTTCAAAATTGGC
* *
628528 TGTTTCAAATTGATTTTC
1 TATTTCAAATTGAATTTC
628546 CTACCAGCTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (27 bp):
TATTTCAAATTGAATTTCAAAATTGGC
Found at i:629702 original size:2 final size:2
Alignment explanation
Indices: 629686--629737 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
629676 AAAATTATTG
*
629686 TA TA T- TA TA TA -A TA TA TG TA T- TA -A T- TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
629722 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
629738 GTTGTAATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
1 6 0.14
2 36 0.86
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:629730 original size:35 final size:34
Alignment explanation
Indices: 629686--629762 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 34
629676 AAAATTATTG
*
629686 TATAT-TATATA-ATATATGTAT-TAATTATATAATA
1 TATATATATATATATATA-GT-TGTAATAATATAA-A
629720 TATATATATATATATATAGTTGTAATAATATAAA
1 TATATATATATATATATAGTTGTAATAATATAAA
629754 T-TATATATA
1 TATATATATA
629763 GACCATGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
33 8 0.21
34 8 0.21
35 18 0.46
36 5 0.13
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (34 bp):
TATATATATATATATATAGTTGTAATAATATAAA
Found at i:632994 original size:16 final size:17
Alignment explanation
Indices: 632975--633015 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
632965 TTTATATTTT
632975 AATTATTTTGA-GTTTG
1 AATTATTTTGAGGTTTG
*
632991 AATT-TTTTTAGGTTTG
1 AATTATTTTGAGGTTTG
633007 AACTTATTT
1 AA-TTATTT
633016 GAATTCGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 11 0.52
17 2 0.10
18 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (17 bp):
AATTATTTTGAGGTTTG
Found at i:633085 original size:16 final size:16
Alignment explanation
Indices: 633066--633117 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
633056 GCTTATTTAG
633066 GTTCGAACCTTTTCAA
1 GTTCGAACCTTTTCAA
* **
633082 GTTCGAGCCTTTTTGA
1 GTTCGAACCTTTTCAA
633098 GTTCGAACCTTTTCAA
1 GTTCGAACCTTTTCAA
633114 GTTC
1 GTTC
633118 AAGCTTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (16 bp):
GTTCGAACCTTTTCAA
Found at i:633086 original size:32 final size:31
Alignment explanation
Indices: 633050--633133 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 31
633040 TCTTTTTTAG
633050 GTTCGAGCTTATTT-AGGTTCGAACCTTTTCAA
1 GTTCGAGCTT-TTTGA-GTTCGAACCTTTTCAA
633082 GTTCGAGCCTTTTTGAGTTCGAACCTTTTCAA
1 GTTCGAG-CTTTTTGAGTTCGAACCTTTTCAA
*
633114 GTTCAAGCTTTTTCGAGTTC
1 GTTCGAGCTTTTT-GAGTTC
633134 AAGTTCGAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
31 6 0.12
32 38 0.79
33 4 0.08
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.42
Consensus pattern (31 bp):
GTTCGAGCTTTTTGAGTTCGAACCTTTTCAA
Found at i:633126 original size:16 final size:16
Alignment explanation
Indices: 633075--633136 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
633065 GGTTCGAACC
*
633075 TTTTCAAGTTCGAGCCT
1 TTTTCAAGTTCAAG-CT
* *
633092 TTTT-GAGTTCGAA-CC
1 TTTTCAAGTTC-AAGCT
633107 TTTTCAAGTTCAAGCT
1 TTTTCAAGTTCAAGCT
*
633123 TTTTCGAGTTCAAG
1 TTTTCAAGTTCAAG
633137 TTCGAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
15 7 0.19
16 24 0.67
17 5 0.14
ACGTcount: A:0.21, C:0.19, G:0.18, T:0.42
Consensus pattern (16 bp):
TTTTCAAGTTCAAGCT
Found at i:633347 original size:18 final size:18
Alignment explanation
Indices: 633299--633357 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
633289 TTATTAATAT
633299 ATTTATT-TATTAAAATCTA
1 ATTTATTATA-TAAAAT-TA
633318 TATTTA-TATATAAAATTA
1 -ATTTATTATATAAAATTA
633336 ATTTATTATATAAAATTA
1 ATTTATTATATAAAATTA
633354 ATTT
1 ATTT
633358 TTAAATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.14
18 18 0.49
19 7 0.19
20 7 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATTATATAAAATTA
Found at i:633381 original size:15 final size:14
Alignment explanation
Indices: 633269--633381 Score: 59
Period size: 16 Copynumber: 7.2 Consensus size: 14
633259 TTTTAGGTAA
633269 ATTT-TTATTATAAT
1 ATTTATTATTA-AAT
633283 ATGTTATTATTAATAT
1 AT-TTATTATTAA-AT
633299 ATTTATTTATTAAAATCTAT
1 ATTTA-TTATT--AA---AT
*
633319 ATTTATATATAAAATT
1 ATTTAT-TATTAAA-T
633335 AATTTATTATATAAA-
1 -ATTTATTAT-TAAAT
* *
633350 ATTAATTTTTAAAT
1 ATTTATTATTAAAT
633364 ATTTATTATTACAAT
1 ATTTATTATTA-AAT
633379 ATT
1 ATT
633382 ATATATTGTC
Statistics
Matches: 79, Mismatches: 6, Indels: 27
0.71 0.05 0.24
Matches are distributed among these distances:
13 4 0.05
14 18 0.23
15 13 0.16
16 19 0.24
17 9 0.11
18 4 0.05
19 1 0.01
20 11 0.14
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (14 bp):
ATTTATTATTAAAT
Found at i:634326 original size:22 final size:22
Alignment explanation
Indices: 634273--634316 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
634263 TAAAGCTCAT
*
634273 GATATAATTTACTTTTTAATAA
1 GATATAATTTACTTTCTAATAA
*
634295 GATATAATTTACTTTCTGATAA
1 GATATAATTTACTTTCTAATAA
634317 ATTATTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (22 bp):
GATATAATTTACTTTCTAATAA
Found at i:647567 original size:1 final size:1
Alignment explanation
Indices: 647561--647651 Score: 74
Period size: 1 Copynumber: 91.0 Consensus size: 1
647551 AAATCTTCAC
* * ** * * * **
647561 TTTTTTTTTGTTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTCCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
647626 TTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
647652 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:647610 original size:33 final size:33
Alignment explanation
Indices: 647560--647650 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
647550 CAAATCTTCA
*
647560 CTTTTTTTT-TGTT-TTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
647591 CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
647624 CTTTTTTTTGTTTTGTTTTTTTCTTTT
1 CTTTTTTTTGTTTTGTTTTTTT-TTTT
647651 TCCAATTGCC
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 9 0.16
32 3 0.05
33 40 0.71
34 4 0.07
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.86
Consensus pattern (33 bp):
CTTTTTTTTGTTTTGTTTTTTTTTTTCTTTTTC
Found at i:657553 original size:17 final size:18
Alignment explanation
Indices: 657526--657560 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
657516 ATTTAGATTG
657526 AAATAAAAATACTAATTA
1 AAATAAAAATACTAATTA
*
657544 AAAT-AAAATATTAATTA
1 AAATAAAAATACTAATTA
657561 GACTCATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAAATACTAATTA
Found at i:660165 original size:11 final size:11
Alignment explanation
Indices: 660151--660175 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
660141 TAATAAAATG
660151 ATTAAACTCAA
1 ATTAAACTCAA
660162 ATTAAACTCAA
1 ATTAAACTCAA
660173 ATT
1 ATT
660176 CTCGGTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAAACTCAA
Found at i:660228 original size:28 final size:27
Alignment explanation
Indices: 660188--660280 Score: 93
Period size: 28 Copynumber: 3.3 Consensus size: 27
660178 CGGTAGATAA
*
660188 TATCTCATAAATAATACTTACTGAATAT
1 TATCTCATGAATAATACTTACT-AATAT
*
660216 TATCTCATGAATATTACTTTACATACA-A-
1 TATCTCATGAATAATAC-TTAC-TA-ATAT
660244 TATCTCAT-AAGTAATACTTACTAAATAT
1 TATCTCATGAA-TAATACTTACT-AATAT
660272 TATCTCATG
1 TATCTCATG
660281 TATATTACCC
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
26 2 0.04
27 8 0.15
28 36 0.67
29 6 0.11
30 2 0.04
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (27 bp):
TATCTCATGAATAATACTTACTAATAT
Found at i:660302 original size:56 final size:56
Alignment explanation
Indices: 660184--660303 Score: 177
Period size: 56 Copynumber: 2.1 Consensus size: 56
660174 TTCTCGGTAG
* ** *
660184 ATAATATCTCATAAATAATACTTACTGAATATTATCTCATGAATATTACTTTACAT
1 ATAATATCTCATAAATAATACTTACTAAATATTATCTCATGAATATTACCCTACAA
* * *
660240 ACAATATCTCATAAGTAATACTTACTAAATATTATCTCATGTATATTACCCTACAA
1 ATAATATCTCATAAATAATACTTACTAAATATTATCTCATGAATATTACCCTACAA
660296 ATAATATC
1 ATAATATC
660304 CCACAGATGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (56 bp):
ATAATATCTCATAAATAATACTTACTAAATATTATCTCATGAATATTACCCTACAA
Found at i:662276 original size:226 final size:224
Alignment explanation
Indices: 661880--662298 Score: 561
Period size: 226 Copynumber: 1.9 Consensus size: 224
661870 TCGTCATATG
* * * * *
661880 CTCAATCGGTTGGCACGCGTGTGTGGAAATGGGTGTGGTCGTGCCGAAAGGTTAGGCTTGCACTT
1 CTCAATCGGTTGGCACGCGTGTGTGGAAACGGGTATGGTCATGCCGAAAGGTTAGGCTTCCACCT
* * * **
661945 GCGATGATGCTGCCAATGACTCCAGGACTAAGTTCCCTAATTCGAGTAGAGGGTCTTTGTTATGG
66 GAGATGATGCTGCCAATGACTCCAGGACCAAGTTCCCTAATTCGAGTAAAGGGTCCCTGTTATGG
* * * *
662010 CACACGCAAAAGCTGCAGGTGTGGGCTTGGCCTAGCCATGCCCTTTAAGTAAGGGTAGTCTCGTA
131 CACACGCAAAAGCTGCAAGTGTGAGCTTGGCCTAGCCATGCCCTTTAAGCAAGGGCAGTCTCGTA
662075 GCCCTTGCATTGGCAATGGTAGGTTCGTC
196 GCCCTTGCATTGGCAATGGTAGGTTCGTC
* * *
662104 CTCAATCGGTTGGCACGCGTGTGTAGGGAACGAGGTATGGTCATGTCGGAAGGTTAGGCTTCCAC
1 CTCAATCGGTTGGCACGCGTGTGT-GGAAACG-GGTATGGTCATGCCGAAAGGTTAGGCTTCCAC
** *
662169 CTGTAG-TGATGCTGCCAATGACTTTAGGACCAAGTTCCCTAATTCGAGTAAAGGGTCCCTGTTG
64 CTG-AGATGATGCTGCCAATGACTCCAGGACCAAGTTCCCTAATTCGAGTAAAGGGTCCCTGTTA
* * * * * * *
662233 TGGCGCACGTAGAAGTTGCAAGTGTGAGCTTGGGCTGGCCATGCCCTTTGAGCAAGGGCAGTCTC
128 TGGCACACGCAAAAGCTGCAAGTGTGAGCTTGGCCTAGCCATGCCCTTTAAGCAAGGGCAGTCTC
662298 G
193 G
662299 CGACCCTATG
Statistics
Matches: 165, Mismatches: 27, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
224 24 0.15
225 5 0.03
226 135 0.82
227 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.32, T:0.26
Consensus pattern (224 bp):
CTCAATCGGTTGGCACGCGTGTGTGGAAACGGGTATGGTCATGCCGAAAGGTTAGGCTTCCACCT
GAGATGATGCTGCCAATGACTCCAGGACCAAGTTCCCTAATTCGAGTAAAGGGTCCCTGTTATGG
CACACGCAAAAGCTGCAAGTGTGAGCTTGGCCTAGCCATGCCCTTTAAGCAAGGGCAGTCTCGTA
GCCCTTGCATTGGCAATGGTAGGTTCGTC
Done.