Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008323.1 Hibiscus syriacus cultivar Beakdansim tig00111027_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5101972
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 26
Found at i:3887514 original size:20 final size:20
Alignment explanation
Indices: 3887487--3887533 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3887477 TTCGGTAACG
3887487 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
3887506 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
3887527 TTTTACC
1 TTTTACC
3887534 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:3887577 original size:181 final size:182
Alignment explanation
Indices: 3887273--3887745 Score: 716
Period size: 181 Copynumber: 2.6 Consensus size: 182
3887263 CGTACTTACG
* *
3887273 AAAGTATCGACACTTTAAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
3887338 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
3887403 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * *
3887454 AAAGTATCGACACTTTTAATATATTCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
3887519 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
3887584 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * *
3887636 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
3887700 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
3887746 AATTTGGATC
Statistics
Matches: 263, Mismatches: 27, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
181 165 0.63
182 97 0.37
183 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:3888477 original size:228 final size:229
Alignment explanation
Indices: 3887811--3888526 Score: 1337
Period size: 230 Copynumber: 3.1 Consensus size: 229
3887801 ACCTACTTTT
*
3887811 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTTAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
*
3887876 ATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
*
3887941 ATATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
3888006 CAAATATAATAATAAATATGTTTTCAACAGTGAA
196 CAAATATAATAATAAATATGTTTTCAACAGTGAA
3888040 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
3888105 ATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
66 A-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAA
3888170 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
130 AAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAA
3888235 CCAAATATAATAATAAATATGTTTTCAACAGTGAA
195 CCAAATATAATAATAAATATGTTTTCAACAGTGAA
3888270 ATAAGTATGGACACTTTTATAAAAATGATATATAC-TTTTTGAAAGTTATGTAATTTATGTTTCA
1 ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
3888334 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
66 ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
*
3888399 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGATTTTAAATTTAACAATATTAAC
131 AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
* * *
3888464 TAAAGATAATAATAAATATATTTTC-ACAGTGAA
196 CAAATATAATAATAAATATGTTTTCAACAGTGAA
*
3888497 ATAAGTATGGACACTTTTATAAAAAGGATA
1 ATAAGTATGGACACTTTTATAAAAATGATA
3888527 GATAATTTAC
Statistics
Matches: 478, Mismatches: 8, Indels: 4
0.98 0.02 0.01
Matches are distributed among these distances:
227 37 0.08
228 150 0.31
229 95 0.20
230 196 0.41
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (229 bp):
ATAAGTATGGACACTTTTATAAAAATGATATATACTTTTTTGAAAGTTATGTAATTTATGTTTCA
ATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAA
AAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATATTAAC
CAAATATAATAATAAATATGTTTTCAACAGTGAA
Found at i:3890202 original size:16 final size:15
Alignment explanation
Indices: 3890174--3890215 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
3890164 CATAAAAATA
*
3890174 AAAGAAATGTGTCAT
1 AAAGAAATATGTCAT
3890189 AAAGAATATATGTCAT
1 AAAGAA-ATATGTCAT
3890205 AAAGATAATAT
1 AAAGA-AATAT
3890216 ATTAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 6 0.25
16 17 0.71
17 1 0.04
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (15 bp):
AAAGAAATATGTCAT
Found at i:3892594 original size:2 final size:2
Alignment explanation
Indices: 3892544--3892576 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3892534 ATTCAACCAT
3892544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3892577 GGTATTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3897757 original size:24 final size:24
Alignment explanation
Indices: 3897692--3897785 Score: 100
Period size: 24 Copynumber: 4.0 Consensus size: 24
3897682 CTAAACGAGC
* **
3897692 ATGTTCATGAACATATAAATGAGC
1 ATGTTCATGAACATATAACTGAAA
** *
3897716 AT-TAAACGAACATATAACTGAAA
1 ATGTTCATGAACATATAACTGAAA
*
3897739 ATGTTCATGAACATATAACCGAAA
1 ATGTTCATGAACATATAACTGAAA
**
3897763 ATGTTCATGATTATATAACTGAA
1 ATGTTCATGAACATATAACTGAA
3897786 CATATTAACA
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 17 0.30
24 39 0.70
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (24 bp):
ATGTTCATGAACATATAACTGAAA
Found at i:3899643 original size:2 final size:2
Alignment explanation
Indices: 3899636--3899660 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3899626 TTGAAAGGGG
3899636 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3899661 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3900782 original size:16 final size:16
Alignment explanation
Indices: 3900761--3900792 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3900751 TCTCATTCTC
*
3900761 TTTTTCTTTTTATTTA
1 TTTTTCTTTTAATTTA
3900777 TTTTTCTTTTAATTTA
1 TTTTTCTTTTAATTTA
3900793 GATCTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTCTTTTAATTTA
Found at i:3903218 original size:32 final size:33
Alignment explanation
Indices: 3903182--3903263 Score: 123
Period size: 32 Copynumber: 2.5 Consensus size: 33
3903172 AGCGTAAACT
3903182 AGCTATAACTATACCTAACTAATA-AAAAAAAA
1 AGCTATAACTATACCTAACTAATATAAAAAAAA
* *
3903214 AGCTATAACTATACCAAACTAATATATAAAAAA
1 AGCTATAACTATACCTAACTAATATAAAAAAAA
*
3903247 A-CTATAACTATGCCTAA
1 AGCTATAACTATACCTAA
3903264 AGCTTGTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 37 0.82
33 8 0.18
ACGTcount: A:0.55, C:0.17, G:0.04, T:0.24
Consensus pattern (33 bp):
AGCTATAACTATACCTAACTAATATAAAAAAAA
Found at i:3907821 original size:2 final size:2
Alignment explanation
Indices: 3907816--3907840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3907806 TGAAAGGGGG
3907816 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
3907841 CTTCGTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3916406 original size:17 final size:17
Alignment explanation
Indices: 3916386--3916418 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3916376 ATATTTATTT
*
3916386 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
3916403 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
3916419 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:3916456 original size:16 final size:17
Alignment explanation
Indices: 3916437--3916473 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3916427 TAAAATATTA
3916437 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
3916453 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
3916470 TTTT
1 TTTT
3916474 TTCATTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:3917491 original size:20 final size:20
Alignment explanation
Indices: 3917466--3917521 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3917456 ATCCTATTCC
3917466 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCTCA
*
3917486 CTGGTAATCTTACATTCTTA
1 CTGGTAATCTTACATTCTCA
*
3917506 CTGATAATCTTACATT
1 CTGGTAATCTTACATT
3917522 ATGTGAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (20 bp):
CTGGTAATCTTACATTCTCA
Found at i:3926533 original size:20 final size:20
Alignment explanation
Indices: 3926496--3926544 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
3926486 CTCAAAATCA
* * *
3926496 TTTTTCAAGATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
3926516 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
3926536 -ATTTCAAAA
1 TTTTTCAAAA
3926545 GAAAATCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:3930309 original size:31 final size:31
Alignment explanation
Indices: 3930266--3930328 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
3930256 ATTCTCAAGG
*
3930266 TATGACTCTCATTTTAAATTAGTCCCTAAAC
1 TATGACTCTCATTCTAAATTAGTCCCTAAAC
* *
3930297 TATGAC-CATCATTCTAAATTATTCCTTAAAC
1 TATGACTC-TCATTCTAAATTAGTCCCTAAAC
3930328 T
1 T
3930329 TTTAAACATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (31 bp):
TATGACTCTCATTCTAAATTAGTCCCTAAAC
Found at i:3940688 original size:2 final size:2
Alignment explanation
Indices: 3940681--3940709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3940671 CGTATTAATT
3940681 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3940710 TAAAATAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3954680 original size:28 final size:28
Alignment explanation
Indices: 3954625--3954680 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
3954615 CTATATTTAC
* * * *
3954625 ATTATGTCGTCGAGCTAGTACTTTAAAT
1 ATTATGTCGTCAAGCCAATACTTAAAAT
*
3954653 ATTATGTCGTCAAGCCAATGCTTAAAAT
1 ATTATGTCGTCAAGCCAATACTTAAAAT
3954681 CAACAATGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (28 bp):
ATTATGTCGTCAAGCCAATACTTAAAAT
Found at i:3960512 original size:37 final size:38
Alignment explanation
Indices: 3960466--3960574 Score: 168
Period size: 37 Copynumber: 2.9 Consensus size: 38
3960456 AACATAACGT
*
3960466 TAGAGTTTTACTAGGATTCAAACTCCGAAAAATAGT-A
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGTGA
*
3960503 TAGAATTTTACTAGGATTCAAACTCCTAAAAATA-TGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGTGA
* *
3960540 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAG
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAG
3960575 GATCCACAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.02
37 64 0.98
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (38 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGTGA
Found at i:3961210 original size:30 final size:31
Alignment explanation
Indices: 3961176--3961239 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
3961166 TATATATATA
3961176 TATATATATACTATTTTTA-TGTTTTTATT-T
1 TATATATATACTATTTTTACT-TTTTTATTAT
*
3961206 TATATATATATTATTTTTACTTTTTTATTAT
1 TATATATATACTATTTTTACTTTTTTATTAT
3961237 TAT
1 TAT
3961240 TTTAATTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (31 bp):
TATATATATACTATTTTTACTTTTTTATTAT
Found at i:3961229 original size:23 final size:19
Alignment explanation
Indices: 3961197--3961295 Score: 67
Period size: 20 Copynumber: 5.0 Consensus size: 19
3961187 TATTTTTATG
3961197 TTTTTATTTTATATATATATTA
1 TTTTTATTTT-T-TAT-TATTA
3961219 TTTTTACTTTTTTATTATTA
1 TTTTTA-TTTTTTATTATTA
* * *
3961239 TTTTAATTATTTGTT-TTA
1 TTTTTATTTTTTATTATTA
* * * *
3961257 TTTATATATTTTTCTTCTTT
1 TTTTTAT-TTTTTATTATTA
3961277 TTTTATATTTTTTA-TATTA
1 TTTT-TATTTTTTATTATTA
3961296 CTTACTATTT
Statistics
Matches: 61, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
18 8 0.13
19 16 0.26
20 20 0.33
21 6 0.10
22 7 0.11
23 4 0.07
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTTTATTATTA
Found at i:3961256 original size:49 final size:48
Alignment explanation
Indices: 3961189--3961295 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 48
3961179 ATATATACTA
* *
3961189 TTTTTATGTT-TTTATTTTATATATATATTATTT-TTAC-TTTTTTATTAT
1 TTTTTATATTATTTGTTTTATATATATATT-TTTCTT-CTTTTTTTA-TAT
*
3961237 TATTTTA-ATTATTTGTTTTATTTATATATTTTTCTTCTTTTTTTATAT
1 T-TTTTATATTATTTGTTTTATATATATATTTTTCTTCTTTTTTTATAT
3961285 TTTTTATATTA
1 TTTTTATATTA
3961296 CTTACTATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
47 5 0.10
48 15 0.29
49 31 0.61
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (48 bp):
TTTTTATATTATTTGTTTTATATATATATTTTTCTTCTTTTTTTATAT
Found at i:3961280 original size:25 final size:24
Alignment explanation
Indices: 3961203--3961282 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
3961193 TATGTTTTTA
*
3961203 TTTTATATATATATTATTTTTAC-TT
1 TTTTATTTATATATT-TTTTT-CTTT
* *
3961228 TTTTA-TTAT-TATTTTAATTATTT
1 TTTTATTTATATATTTT-TTTCTTT
3961251 GTTTTATTTATATATTTTTCTTCTTT
1 -TTTTATTTATATATTTTT-TTCTTT
3961277 TTTTAT
1 TTTTAT
3961283 ATTTTTTATA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
22 2 0.05
23 8 0.18
24 8 0.18
25 15 0.34
26 11 0.25
ACGTcount: A:0.23, C:0.04, G:0.01, T:0.72
Consensus pattern (24 bp):
TTTTATTTATATATTTTTTTCTTT
Found at i:3961363 original size:26 final size:26
Alignment explanation
Indices: 3961330--3961379 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
3961320 TTATCTTATC
*
3961330 TTTTATTTAATTTGTTT-TTTCTTCA
1 TTTTATTTAATTTATTTATTTCTTCA
3961355 TTTTAATTTAATTTATTTATTTCTT
1 TTTT-ATTTAATTTATTTATTTCTT
3961380 ACCTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTATTTAATTTATTTATTTCTTCA
Found at i:3964109 original size:14 final size:13
Alignment explanation
Indices: 3964061--3964119 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 13
3964051 GAACAAAAAG
3964061 AAAAAAAAGAAGAA
1 AAAAAAAAG-AGAA
*
3964075 AAAAGCAAAGAGAA
1 AAAA-AAAAGAGAA
3964089 AATAAAAAAGAGAA
1 AA-AAAAAAGAGAA
3964103 ACAAAAATAA-AGAA
1 A-AAAAA-AAGAGAA
3964117 AAA
1 AAA
3964120 GTGAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.05
14 28 0.72
15 9 0.23
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:3965610 original size:116 final size:116
Alignment explanation
Indices: 3965406--3965615 Score: 325
Period size: 116 Copynumber: 1.8 Consensus size: 116
3965396 TCAAATGTCA
* *
3965406 ATTTCAACTTCACAGCGAAGGATATTCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCTAC
1 ATTTCAACTTCACAGCGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
*
3965471 GTTTTCAACTTCACGATAAAGGGAATCGTGCTCACCAGCAACATTCATTGG
66 GTTTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGCAACATTCATTGG
*
3965522 ATTTCAACTTCACGGCGAAGGATATCCAA-TTCAAGGCTCAACTTCACAACGAAGGGGCCATCCA
1 ATTTCAACTTCACAGCGAAGGATATCCAAGTT-AAGGCTCAACTTCACAACGAAGGGGCCATCCA
* * *
3965586 CAG-TTTCAACTTTACTACGAAGGGAATCGT
65 C-GTTTTCAACTTCACGACAAAGGGAATCGT
3965616 ACCCACAACA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
115 2 0.02
116 82 0.96
117 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (116 bp):
ATTTCAACTTCACAGCGAAGGATATCCAAGTTAAGGCTCAACTTCACAACGAAGGGGCCATCCAC
GTTTTCAACTTCACGACAAAGGGAATCGTGCTCACCAGCAACATTCATTGG
Found at i:3965740 original size:37 final size:35
Alignment explanation
Indices: 3965692--3965795 Score: 102
Period size: 36 Copynumber: 2.9 Consensus size: 35
3965682 AAACAAAGGG
*
3965692 TCTCGCTTGAGACTAATTTACCC-AAAACAAAATTTTA
1 TCTCTCTTGAGAC-AATTT-CCCTAAAAC-AAATTTTA
* * *
3965729 TCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTG
1 TCTCTCTTGAGACAATTTCCC-TAAAACAAATTTTA
* *
3965765 TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TCTCTCTTGAGACAATTTCCC-TAAAACAAA
3965796 ATCTTTGAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
35 3 0.05
36 42 0.69
37 16 0.26
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (35 bp):
TCTCTCTTGAGACAATTTCCCTAAAACAAATTTTA
Found at i:3965769 original size:36 final size:36
Alignment explanation
Indices: 3965716--3965795 Score: 142
Period size: 36 Copynumber: 2.2 Consensus size: 36
3965706 AATTTACCCA
3965716 AAACAAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
1 AAAC-AAATTTTATCTCTCTTGAGACAGTTTCCCTTG
*
3965753 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
1 AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
3965789 AAACAAA
1 AAACAAA
3965796 ATCTTTGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 38 0.90
37 4 0.10
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (36 bp):
AAACAAATTTTATCTCTCTTGAGACAGTTTCCCTTG
Found at i:3965907 original size:36 final size:36
Alignment explanation
Indices: 3965810--3965968 Score: 185
Period size: 37 Copynumber: 4.4 Consensus size: 36
3965800 TTGAATCTAT
* * * *
3965810 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGATAT
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * ** *
3965845 TTTCTTTTGGAACTAGGTTTTGTCTCTCTTGATACAA
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAA
3965882 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
* * *
3965918 TTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAAACAG
1 TTTCTCTTGAAACAAA-TTTTGTCTCTCTTGAGACAA
3965955 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
3965969 GTTTCTCTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
35 4 0.04
36 41 0.40
37 58 0.56
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:3965938 original size:73 final size:73
Alignment explanation
Indices: 3965810--3965968 Score: 212
Period size: 73 Copynumber: 2.2 Consensus size: 73
3965800 TTGAATCTAT
* * ** * * *
3965810 TTTC-CTTGAAACAAATTTCGTCTCCCTTGAGATATTTTCTTTTGGAACTAGGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
3965874 TGATACAA
66 TGAAACAA
* *
3965882 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
1 TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
*
3965947 TGAAACAG
66 TGAAACAA
3965955 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
3965969 GTTTCTCTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 4 0.05
73 71 0.95
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (73 bp):
TTTCTCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCCCTTGAAACAAAGTTTTGTCTCTCT
TGAAACAA
Found at i:3966125 original size:35 final size:34
Alignment explanation
Indices: 3966036--3966152 Score: 171
Period size: 34 Copynumber: 3.4 Consensus size: 34
3966026 CCTTGAGACA
* *
3966036 GTTTATCTTGAAACACGAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
3966070 GTTTCTCTTGAAACACAAAAAAATCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
*
3966104 GTTTCTCTTGAAACACAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTGAAACAC-AAAAAAACCTTTGAAATT
* *
3966139 ATTTCTCTTAAAAC
1 GTTTCTCTTGAAAC
3966153 CTAAGACCTT
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
34 47 0.63
35 28 0.37
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (34 bp):
GTTTCTCTTGAAACACAAAAAAACCTTTGAAATT
Found at i:3966838 original size:185 final size:185
Alignment explanation
Indices: 3966476--3966865 Score: 667
Period size: 185 Copynumber: 2.1 Consensus size: 185
3966466 ATAAAATTTT
*
3966476 AAATTTTAAATATATTATATATAACATATGAGCTCAGCCCAAACAATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACAATTTAAAACCCAATTAATAA
*
3966541 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
*
3966606 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTGAATTAAA
* *
3966661 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACTATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACAATTTAAAACCCAATTAATAA
*
3966726 TTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
3966790 TTATTTTATAATTATATATTATTTAAATTAATTATAAATTATTTTTTTGAATTATA
131 TTATTTTATAATTATATATTATTTAAATTAATTATAAATT-GTTTTTTGAATTAAA
* *
3966846 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
3966866 AATTAGAAAA
Statistics
Matches: 194, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
184 65 0.34
185 129 0.66
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGAGCTCAGCCCAAACAATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTTGAATTAAA
Found at i:3967603 original size:37 final size:37
Alignment explanation
Indices: 3967495--3967603 Score: 164
Period size: 37 Copynumber: 2.9 Consensus size: 37
3967485 AACATAACGT
* *
3967495 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGAA
1 TAGAGTTTTACTACGATTCAAACTCCTAAAAATATAA
3967532 TAGAGTTTTACTACGATTCAAACTCCTAAAAATATAA
1 TAGAGTTTTACTACGATTCAAACTCCTAAAAATATAA
* * * *
3967569 TAGAGTTCTACTATGATTTAAACTCTTAAAAATAT
1 TAGAGTTTTACTACGATTCAAACTCCTAAAAATAT
3967604 GATCCACAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (37 bp):
TAGAGTTTTACTACGATTCAAACTCCTAAAAATATAA
Found at i:3968124 original size:2 final size:2
Alignment explanation
Indices: 3968119--3968188 Score: 106
Period size: 2 Copynumber: 35.5 Consensus size: 2
3968109 TTTACTTTAG
* * *
3968119 TA TA TA TA TA TT TT TA GA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3968160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3968189 TTATGTTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3968286 original size:4 final size:4
Alignment explanation
Indices: 3968212--3968359 Score: 68
Period size: 4 Copynumber: 36.2 Consensus size: 4
3968202 TATTATCCGT
* * * * *
3968212 TTTA TTAA TTTA TATA TATA TTTA -CTA TTTT TTTA TGTT- TTTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TT-TA
* * * * * * *
3968260 TATA TATA TATA TATA TTATA TTTA TTTT TTTA TTTTT TTTA TTTA TTTGT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA -TTTA TTTA TTTA TTT-A
* * * * *
3968311 TTTA TTTA TATA TTTT TTTC TTCTT TTTA TTTA TTT- TTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA
3968359 T
1 T
3968360 ATTACTTACT
Statistics
Matches: 111, Mismatches: 24, Indels: 18
0.73 0.16 0.12
Matches are distributed among these distances:
3 7 0.06
4 86 0.77
5 18 0.16
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:3968294 original size:17 final size:17
Alignment explanation
Indices: 3968274--3968359 Score: 70
Period size: 17 Copynumber: 5.2 Consensus size: 17
3968264 TATATATATA
* *
3968274 TATTATATTTATTTTTT
1 TATTTTATTTATTTATT
*
3968291 TATTTTTTTTATTTATT
1 TATTTTATTTATTTATT
* *
3968308 TGTTTTATTTATATATT
1 TATTTTATTTATTTATT
* *
3968325 T-TTTTCTTCTTTTTATT
1 TATTTTATT-TATTTATT
*
3968342 TA-TTT-TTTATTTTTT
1 TATTTTATTTATTTATT
3968357 TAT
1 TAT
3968360 ATTACTTACT
Statistics
Matches: 55, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
15 8 0.15
16 8 0.15
17 39 0.71
ACGTcount: A:0.17, C:0.02, G:0.01, T:0.79
Consensus pattern (17 bp):
TATTTTATTTATTTATT
Found at i:3968304 original size:21 final size:21
Alignment explanation
Indices: 3968279--3968359 Score: 76
Period size: 25 Copynumber: 3.7 Consensus size: 21
3968269 ATATATATTA
3968279 TATTTATTTTTTTATTTTTTT
1 TATTTATTTTTTTATTTTTTT
3968300 TATTTATTTGTTTTATTTATATATT
1 TATTTATTT-TTTTATTT-T-T-TT
* * *
3968325 TTTTTCTTCTTTTTA-TTTATT
1 TATTTATT-TTTTTATTTTTTT
3968346 T-TTTATTTTTTTAT
1 TATTTATTTTTTTAT
3968360 ATTACTTACT
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
19 6 0.12
20 5 0.10
21 12 0.24
22 8 0.16
23 2 0.04
24 3 0.06
25 13 0.26
26 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.01, T:0.80
Consensus pattern (21 bp):
TATTTATTTTTTTATTTTTTT
Found at i:3968362 original size:21 final size:20
Alignment explanation
Indices: 3968281--3968359 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 20
3968271 ATATATTATA
*
3968281 TTTATTTTTTTATTTTTTTT
1 TTTATTTTTTTATTTTATTT
3968301 ATTTATTTGTTTTATTTATATATT
1 -TTTATTT-TTTTATTT-TAT-TT
*
3968325 TTT-TTCTTCTTTTTATTTATTT
1 TTTATT-TT-TTTAT-TTTATTT
3968347 TTTATTTTTTTAT
1 TTTATTTTTTTAT
3968360 ATTACTTACT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
21 11 0.23
22 18 0.38
23 15 0.31
24 4 0.08
ACGTcount: A:0.15, C:0.03, G:0.01, T:0.81
Consensus pattern (20 bp):
TTTATTTTTTTATTTTATTT
Found at i:3968362 original size:38 final size:38
Alignment explanation
Indices: 3968274--3968353 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 38
3968264 TATATATATA
* *
3968274 TATTATATTTATTTTTTTATTTTTTTTATTTATTTGTTT
1 TATT-TATATATTTTTTTATTCTTTTTATTTATTTGTTT
*
3968313 TATTTATATATTTTTTTCTTCTTTTTATTTA-TT-TTT
1 TATTTATATATTTTTTTATTCTTTTTATTTATTTGTTT
3968349 TATTT
1 TATTT
3968354 TTTTATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 8 0.21
37 2 0.05
38 24 0.63
39 4 0.11
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.79
Consensus pattern (38 bp):
TATTTATATATTTTTTTATTCTTTTTATTTATTTGTTT
Found at i:3968436 original size:30 final size:30
Alignment explanation
Indices: 3968378--3968436 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
3968368 CTATTTTATC
* * *
3968378 TTTGTTTTCTTTATCTTTTATTTTATTTAA
1 TTTGTTTTCTTCATCTTTAATTTAATTTAA
3968408 TTTGTTTTTCTTCAT-TTTAATTTAATTTA
1 TTTG-TTTTCTTCATCTTTAATTTAATTTA
3968437 TTTATTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 16 0.64
31 9 0.36
ACGTcount: A:0.19, C:0.07, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTGTTTTCTTCATCTTTAATTTAATTTAA
Found at i:3970498 original size:27 final size:26
Alignment explanation
Indices: 3970443--3970512 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
3970433 AAAAGGTTAG
* **
3970443 ATAAAAAAATAAATAAATATTAAATA
1 ATAAAAAAATAAATAAAGAGGAAATA
3970469 ATAAAAAAATAAATCAAAGGAGGAAA-A
1 ATAAAAAAATAAAT-AAA-GAGGAAATA
*
3970496 ATAAATAAATAAATAAA
1 ATAAAAAAATAAATAAA
3970513 AAAGAATGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 17 0.45
27 17 0.45
28 4 0.11
ACGTcount: A:0.73, C:0.01, G:0.06, T:0.20
Consensus pattern (26 bp):
ATAAAAAAATAAATAAAGAGGAAATA
Found at i:3972047 original size:10 final size:10
Alignment explanation
Indices: 3972020--3972053 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
3972010 GAGCCTACAA
3972020 ATAATAATAAT
1 ATAATAA-AAT
3972031 AATAATAAAAT
1 -ATAATAAAAT
3972042 ATAATAAAAT
1 ATAATAAAAT
3972052 AT
1 AT
3972054 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 3 0.14
12 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:3972817 original size:36 final size:36
Alignment explanation
Indices: 3972747--3972835 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
3972737 GTTGTTTTTT
3972747 AAGAGAAACAATTTCAAAGG----TTTTTGTGTATC
1 AAGAGAAACAATTTCAAAGGTATTTTTTTGTGTATC
* * *
3972779 AAGAGAAGCATTTTCAAAGGTATTTTTTTGTGTTTC
1 AAGAGAAACAATTTCAAAGGTATTTTTTTGTGTATC
3972815 AAGAGAAACAATTTCAAAGGT
1 AAGAGAAACAATTTCAAAGGT
3972836 TTGTGTTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
32 18 0.38
36 30 0.62
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (36 bp):
AAGAGAAACAATTTCAAAGGTATTTTTTTGTGTATC
Found at i:3972900 original size:67 final size:65
Alignment explanation
Indices: 3972809--3972975 Score: 217
Period size: 67 Copynumber: 2.5 Consensus size: 65
3972799 TATTTTTTTG
* * * *
3972809 TGTTTCAAGAGAAACAATTTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTTAGGGGAGGCAAAAT
1 TGTTTCAAGAGAAACAA-TTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-
3972874 TT
64 TT
* * *
3972876 TGTTTCAAGAGAAACATATTCAAAGATTGGTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
1 TGTTTCAAGAGAAACA-ATTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
3972941 T
65 T
* *
3972942 TGTTTCAAGGGAAACAATCTCAAAGGTTTTTGTT
1 TGTTTCAAGAGAAACAAT-TCAAAGGTTTGTGTT
3972976 AACAGATAAC
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 2 0.02
66 29 0.33
67 55 0.63
68 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACAATTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:3973164 original size:84 final size:84
Alignment explanation
Indices: 3973055--3973757 Score: 680
Period size: 84 Copynumber: 8.5 Consensus size: 84
3973045 TTGGGGGTCT
* *
3973055 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
3973120 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * * * * * *
3973139 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGCCCTCGGAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG
**
3973204 TCGAACTCGGGGGTCTTTGG
65 TCGAACTCGAAGGTCTTTGG
* * * * * * ** *
3973224 -T---AGATATCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGTCTTCGAAGTTGAGTATAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAG
* **
3973285 TCGAACTTGGGGGTC----G
65 TCGAACTCGAAGGTCTTTGG
* * * * *
3973301 TTGGAAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTGCCTAGGAGCTGAACGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
3973366 CGAACTTGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* *
3973385 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
3973450 CGAACTCGAAGGTCTTTTGG
66 CGAACTCGAAGGTC-TTTGG
*** * * * * * * * * * * *
3973470 -TCATAGATAACTCTTCTAGCCTTGAA-TTATGTTGTAAATGATGTGCCCTCGAAGCTAAGTGCA
1 TTGGCAGATAACCCTTCTCGACTT-AAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTA
* * *
3973533 ATCAAACTCG-AGG-GTTT--
64 GTCGAACTCGAAGGTCTTTGG
* * * *
3973550 TTAGCAGATATCCCTTCTCGACTTTAGCTATGTTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
3973615 CGAACTCGAAGGTCTTTGG
66 CGAACTCGAAGGTCTTTGG
* * ** * *
3973634 TTGGCAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATAAGCCTTTGAGCTAAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
3973699 TGAACTCGAAGGTATTT-A
66 CGAACTCGAAGGTCTTTGG
* * *
3973717 TTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATG
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
3973758 TTGTCTTTAA
Statistics
Matches: 505, Mismatches: 95, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
77 1 0.00
78 1 0.00
80 44 0.09
81 135 0.27
82 6 0.01
83 36 0.07
84 222 0.44
85 60 0.12
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGG
Found at i:3973250 original size:165 final size:165
Alignment explanation
Indices: 3972978--3973757 Score: 739
Period size: 165 Copynumber: 4.7 Consensus size: 165
3972968 TTTTTGTTAA
* * * * * * * * *
3972978 CAGATAACCCTTATAGCCTTGAGTTATGCTGTAAATTATGTGCCCTCGGAGCTGAGTATAATCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
* * * *
3973043 ACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTGCCTTGGA
66 ACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
3973108 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
131 GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * *
3973143 CAGATAACCCTTCTCGACTTAAGTTATACTACAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
* * * * * *
3973208 ACTCGGGGGTCTTTGGTAGATATCCCTTCTCGACTTAAGCTATTCTGTAAATGATGTGTCTTCGA
66 ACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT-GG
* ** * * **
3973273 AGTTGAGTATAATCGAACTTGGGGGTC----GTTGG
130 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * * * * ** *
3973305 AAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATGATGTG-CCTAGGAGCTGAACGTAGTCGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
* * * * *
3973369 ACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
66 ACTCGAGGGTC--T--TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
**
3973434 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCA
127 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGG
* * * * * * * * * * * *
3973473 TAGATAACTCTTCTAGCCTTGAA-TTATGTTGTAAATGATGTGCCCTCGAAGCTAAGTGCAATCA
1 CAGATAACCCTTCTCGACTT-AAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCG
* * * *
3973537 AACTCGAGGGTTTTTAGCAGATATCCCTTCTCGACTTTAGCTATGTTGCAAATGATGTGCCTTGG
65 AACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGG
3973602 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
130 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
* * * ** * * * *
3973638 CAAATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATAAG-CCTTTGAGCTAAGCGTAGTTGA
1 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
* * * * * *
3973702 ACTCGAAGGTATTTATTGGCAGATAACCCTTCTAGCCTTAAGTTATGCTGCAAATG
66 ACTCG-AGG-GTCT-TTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATG
3973758 TTGTCTTTAA
Statistics
Matches: 489, Mismatches: 109, Indels: 32
0.78 0.17 0.05
Matches are distributed among these distances:
161 26 0.05
162 40 0.08
163 1 0.00
164 47 0.10
165 258 0.53
166 24 0.05
167 35 0.07
168 33 0.07
169 25 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCCTCGGAGCTGAGTGTAATCGA
ACTCGAGGGTCTTTGGCAGATATCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
GCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
Found at i:3977772 original size:8 final size:8
Alignment explanation
Indices: 3977759--3977835 Score: 55
Period size: 8 Copynumber: 9.0 Consensus size: 8
3977749 AAAAGGTTAG
3977759 ATAAAAAA
1 ATAAAAAA
3977767 ATAAAAAA
1 ATAAAAAA
*
3977775 ATATTAAATA
1 ATA--AAAAA
3977785 ATAAAAAA
1 ATAAAAAA
3977793 ATAAATCAAA
1 ATAAA--AAA
** *
3977803 GGAGGAAAA
1 ATA-AAAAA
*
3977812 ATAAATAA
1 ATAAAAAA
*
3977820 ATAAATAA
1 ATAAAAAA
3977828 ATAAAAAA
1 ATAAAAAA
3977836 GAATGCAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
8 38 0.70
9 4 0.07
10 11 0.20
11 1 0.02
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.18
Consensus pattern (8 bp):
ATAAAAAA
Found at i:3979361 original size:10 final size:10
Alignment explanation
Indices: 3979334--3979367 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3979324 CAGCTGGGCC
*
3979334 TATAAAAAAA
1 TATAATAAAA
3979344 TAATAATAAAA
1 T-ATAATAAAA
3979355 TATAATAAAA
1 TATAATAAAA
3979365 TAT
1 TAT
3979368 TTTTTTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TATAATAAAA
Found at i:3980106 original size:32 final size:31
Alignment explanation
Indices: 3980027--3980166 Score: 135
Period size: 37 Copynumber: 4.4 Consensus size: 31
3980017 GTCTTTGGGT
*
3980027 TTCAAGAGAAACACTTTCAAAGGTTGTTT-T-
1 TTCAAGAGAAACAATTTCAAAGGTT-TTTGTG
*
3980057 TT-AAGAGAAACAATTTCAATGGTTTTTGTG
1 TTCAAGAGAAACAATTTCAAAGGTTTTTGTG
* *
3980087 TATCAAGAGAAGCATTTTCAAAGGGTTTTTTTTTGTG
1 T-TCAAGAGAAACAATTTCAAA-GG----TTTTTGTG
*
3980124 TTTCAAGAGAAACAATTTCAAAGGTTTATGT-
1 -TTCAAGAGAAACAATTTCAAAGGTTTTTGTG
3980155 TTCAAGAGAAAC
1 TTCAAGAGAAAC
3980167 TGTCTTAGGG
Statistics
Matches: 92, Mismatches: 8, Indels: 20
0.77 0.07 0.17
Matches are distributed among these distances:
28 3 0.03
29 21 0.23
30 15 0.16
31 1 0.01
32 21 0.23
33 2 0.02
36 2 0.02
37 26 0.28
38 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (31 bp):
TTCAAGAGAAACAATTTCAAAGGTTTTTGTG
Found at i:3980202 original size:67 final size:66
Alignment explanation
Indices: 3980122--3980288 Score: 203
Period size: 67 Copynumber: 2.5 Consensus size: 66
3980112 TTTTTTTTTG
* * *
3980122 TGTTTCAAGAGAAACAATTTCAAAGGTTTATGTTTCAAGAGAAACTGTCTTAGGGGAGACAAAAT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-
3980187 TT
65 TT
* * **
3980189 TGTTTCAAGAGAAAC-ATATTCAAA-GTTTGGTGTTTTAAGATTAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTT-ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
3980252 ATT
64 ATT
* * *
3980255 TGTTTCAAGGGAAACAATCTCAAAGGTTTTTGTT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTATGTT
3980289 AACAGATAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
66 31 0.36
67 55 0.64
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (66 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAT
T
Found at i:3980544 original size:164 final size:164
Alignment explanation
Indices: 3980273--3980674 Score: 563
Period size: 164 Copynumber: 2.5 Consensus size: 164
3980263 GGGAAACAAT
* * * *
3980273 CTCAAAGGTTTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATTATGTGCCCTC
1 CTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTC
* * *
3980338 GGAGCTGAGTATAATCGAACTTGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGGTATACTG
66 GGAGCTGAGTATAATCGAACTCGGGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
** ** *
3980403 CAAATGATGTGCCTTTGAGCTGAGTGTAATTGAA
131 CAAATGATGTGCCTAGGAGCTGAACGTAATCGAA
* *
3980437 CTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTC
1 CTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTC
* * *
3980502 GAAGCTGAGTATAATCGAACTCGGGGGTATTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTG
66 GGAGCTGAGTATAATCGAACTCGGGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
*
3980567 CAAATGATGTGCCTAGGAGCTGAACGTAGTCGAA
131 CAAATGATGTGCCTAGGAGCTGAACGTAATCGAA
* * * * * * *
3980601 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTT
1 CTCAAAGGTCTTT-GTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTT
3980666 -GGAGCTGAG
65 CGGAGCTGAG
3980675 CGTAGTCGGA
Statistics
Matches: 209, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
164 166 0.79
165 43 0.21
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (164 bp):
CTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTC
GGAGCTGAGTATAATCGAACTCGGGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTG
CAAATGATGTGCCTAGGAGCTGAACGTAATCGAA
Found at i:3980641 original size:84 final size:83
Alignment explanation
Indices: 3980277--3980904 Score: 509
Period size: 84 Copynumber: 7.6 Consensus size: 83
3980267 AACAATCTCA
* ** * * * * * *
3980277 AAGGTTTTTGTTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATTATGTGCCCTCGGAG
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAG
** *
3980342 CTGAGTATAATCGAACTTG
65 CTGAGCGTAATCGAACTCG
** * * * *
3980361 GGGGTC--T-TTGGCAGATAGCCCTTCTCGACTTAAGGTATACTGCAAATGATGTGCCTTTGAGC
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
* * *
3980423 TGAGTGTAATTGAACTCA
66 TGAGCGTAATCGAACTCG
* * * * * * * *
3980441 AAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTCGAAG
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAG
**
3980506 CTGAGTATAATCGAACTCG
65 CTGAGCGTAATCGAACTCG
** * * * * *
3980525 --GGGGTAT-TTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTAGGAGC
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
* *
3980587 TGAACGTAGTCGAACTCG
66 TGAGCGTAATCGAACTCG
*
3980605 AAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAG
1 AAGGTCTTT-GTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAG
* *
3980670 CTGAGCGTAGTCGGACTCG
65 CTGAGCGTAATCGAACTCG
* ** * * * * * * * * * *
3980689 AAGGTCTTTTGGTCACATATAACTCTTCTAGCCTTGATTTATGTTGTAAATGATGTGCCCTCGAA
1 AAGGTC-TTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGA
* *
3980754 GCTGAGTGCAATCGAACTCG
64 GCTGAGCGTAATCGAACTCG
* * * * * *
3980774 -AGG-GTTT-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGTCTTTGAGC
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
* * *
3980836 TAAGCGTAGTTGAACTCG
66 TGAGCGTAATCGAACTCG
* * * *
3980854 AAGGTATTTGTTGGCAGATAACCTTTCTAGCCTTAAGTTATGCTGCAAATG
1 AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
3980905 TTGTCTTTAA
Statistics
Matches: 420, Mismatches: 111, Indels: 27
0.75 0.20 0.05
Matches are distributed among these distances:
80 61 0.15
81 111 0.26
82 16 0.04
83 77 0.18
84 131 0.31
85 24 0.06
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
AAGGTCTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
TGAGCGTAATCGAACTCG
Found at i:3980769 original size:249 final size:247
Alignment explanation
Indices: 3980368--3980904 Score: 763
Period size: 249 Copynumber: 2.2 Consensus size: 247
3980358 TTGGGGGTCT
* * * * * *
3980368 TTGGCAGATAGCCCTTCTCGACTTAAGGTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
* *
3980433 TGAACTCAAAGGTCTTTATTGACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
66 CGAACTCAAAGGTCTTTATTCACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
* * * *
3980498 CTTCGAAGCTGAGTATAATCGAACTCGGGGGTATTTGGTAGATAGCCCTTCTCGACTTAAGCTAT
131 CCTCGAAGCTGAGTACAATCGAACTCGAGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
* *
3980563 GCTGCAAATGATGTGCCTAGGAGCTGAA-CGTAGTCGAACTCGAAGGTCTTTGG
196 GCTGCAAATGATATGCCTAGGAGCT-AAGCGTAGTCGAACTCGAAGGTATTT-G
*
3980616 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
* * * * *
3980681 CGGACTCGAAGGTCTTT-TGGTCACATATAACTCTTCTAGCCTTGATTTATGTTGTAAATGATGT
66 CGAACTCAAAGGTCTTTAT--TCACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
* *
3980745 GCCCTCGAAGCTGAGTGCAATCGAACTCGAGGGTTTTTGGCAGATAGCCCTTCTCGACTTAAGCT
129 GCCCTCGAAGCTGAGTACAATCGAACTCGAGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCT
* ** *
3980810 ATGCTGCAAATGATATGTCTTTGAGCTAAGCGTAGTTGAACTCGAAGGTATTTG
194 ATGCTGCAAATGATATGCCTAGGAGCTAAGCGTAGTCGAACTCGAAGGTATTTG
* * *
3980864 TTGGCAGATAACCTTTCTAGCCTTAAGTTATGCTGCAAATG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATG
3980905 TTGTCTTTAA
Statistics
Matches: 257, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
247 1 0.00
248 113 0.44
249 143 0.56
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (247 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
CGAACTCAAAGGTCTTTATTCACATATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGC
CCTCGAAGCTGAGTACAATCGAACTCGAGGGTATTTGGCAGATAGCCCTTCTCGACTTAAGCTAT
GCTGCAAATGATATGCCTAGGAGCTAAGCGTAGTCGAACTCGAAGGTATTTG
Found at i:3982816 original size:34 final size:34
Alignment explanation
Indices: 3982777--3982846 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
3982767 ACAAATTCAA
3982777 ACAGAATGCCTCAAATGATGAAATGATCTTCCTC
1 ACAGAATGCCTCAAATGATGAAATGATCTTCCTC
3982811 ACAGAATGCCTCAAATGATGAAATGATCTTCCTC
1 ACAGAATGCCTCAAATGATGAAATGATCTTCCTC
3982845 AC
1 AC
3982847 TTGGATGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (34 bp):
ACAGAATGCCTCAAATGATGAAATGATCTTCCTC
Found at i:3984792 original size:4 final size:4
Alignment explanation
Indices: 3984777--3984842 Score: 50
Period size: 4 Copynumber: 17.2 Consensus size: 4
3984767 AAAAGGTTAG
* * *
3984777 ATAA AAAA ATAA ATAA AT-A TTAA A-AA ATAA ATAA ATAA ATCAA A-AG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA
**
3984823 AGGA A-AA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA A
3984843 AAAGAATGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
3 9 0.18
4 37 0.76
5 3 0.06
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:3984821 original size:18 final size:17
Alignment explanation
Indices: 3984780--3984813 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3984770 AGGTTAGATA
3984780 AAAAAATAAATAAATATT
1 AAAAAATAAATAAATA-T
3984798 AAAAAATAAATAAATA
1 AAAAAATAAATAAATA
3984814 AATCAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATAAATAAATAT
Found at i:3986544 original size:37 final size:37
Alignment explanation
Indices: 3986465--3986548 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
3986455 TCTCATTATC
*
3986465 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACT
* * *
3986501 AATTTTCAAAGAAACATTTACCAAACTTTG-AAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACT
3986537 ATTTTTTCAAAG
1 A-TTTTTCAAAG
3986549 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 12 0.29
37 29 0.71
ACGTcount: A:0.44, C:0.19, G:0.05, T:0.32
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACT
Found at i:3991127 original size:21 final size:21
Alignment explanation
Indices: 3991103--3991163 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
3991093 TTCAAAGAAA
3991103 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
3991124 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
3991138 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
3991159 CATTT
1 CATTT
3991164 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:3991136 original size:35 final size:35
Alignment explanation
Indices: 3991055--3991164 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
3991045 CCATTTTCAT
* * *
3991055 TTTTC-AACAAACATCTACCAAACTTTGAAAAACTAA
1 TTTTCAAAGAAACATTTACCAAACTTTG-AAAAC-CA
3991091 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
3991126 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
3991161 TTTT
1 TTTT
3991165 TTCAAAGTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
35 40 0.57
36 10 0.14
37 20 0.29
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.31
Consensus pattern (35 bp):
TTTTCAAAGAAACATTTACCAAACTTTGAAAACCA
Found at i:3992234 original size:21 final size:21
Alignment explanation
Indices: 3992210--3992262 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3992200 TTCTAACTTA
3992210 AAACCCTAAACTGATAA-CCCT
1 AAACCCTAAACT-ATAATCCCT
* * **
3992231 AAACCATAACCTATAATCGTT
1 AAACCCTAAACTATAATCCCT
3992252 AAACCCTAAAC
1 AAACCCTAAAC
3992263 CTTAATATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.45, C:0.30, G:0.04, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACTATAATCCCT
Found at i:3994446 original size:90 final size:90
Alignment explanation
Indices: 3994281--3994446 Score: 212
Period size: 90 Copynumber: 1.8 Consensus size: 90
3994271 TTGCAGCAGA
* *
3994281 TTTTAACTAAATTGTTATATTCTTCAACCTAAAAAGTTATACAATTATTAATAATTTTGGCTACA
1 TTTTAACTAAAATGTTATATTCTTCAACCTAAAAAGTTACACAATTATTAATAATTTTGGCTACA
* *
3994346 ACCGATAATGTTAAATTGTGATGGG
66 ACAGAAAATGTTAAATTGTGATGGG
* * *
3994371 TTTTGAACTAAAATGTTATA-T-TTCTACTCTAAAAAGTTACATAATTGA-TAATAATTTTGGTT
1 TTTT-AACTAAAATGTTATATTCTTCAAC-CTAAAAAGTTACACAATT-ATTAATAATTTTGGCT
*
3994433 ACAATAGAAAATGT
63 ACAACAGAAAATGT
3994447 CTTAATGTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 5 0.08
90 45 0.69
91 15 0.23
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.40
Consensus pattern (90 bp):
TTTTAACTAAAATGTTATATTCTTCAACCTAAAAAGTTACACAATTATTAATAATTTTGGCTACA
ACAGAAAATGTTAAATTGTGATGGG
Found at i:3998723 original size:60 final size:60
Alignment explanation
Indices: 3998582--3998772 Score: 203
Period size: 60 Copynumber: 3.2 Consensus size: 60
3998572 ACATCACATG
* * * *
3998582 TCCTCAAATTATGATACTT-ATT-TCAAATTAGT-CACTAAACTCTTAAACATTTCAATTTCA
1 TCCTCAAACTATGATA-TTCATTCT-AAACTAGTCCAC-AAACTTTTGAACATTTCAATTTCA
* * * *
3998642 ACCTTAAACTATGACT-GTCATTCTAAAGTAGTCCACAAACTTTTGAACATTTCAATTTCA
1 TCCTCAAACTATGA-TATTCATTCTAAACTAGTCCACAAACTTTTGAACATTTCAATTTCA
* * *
3998702 TCCTCAAACTATGATATTCATTCTAAACTAGTCCCCAAAATTTTGAACATTTCATTTTCA
1 TCCTCAAACTATGATATTCATTCTAAACTAGTCCACAAACTTTTGAACATTTCAATTTCA
*
3998762 TCC-CCAACTAT
1 TCCTCAAACTAT
3998773 ACATATGTAC
Statistics
Matches: 111, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
59 9 0.08
60 97 0.87
61 5 0.05
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.37
Consensus pattern (60 bp):
TCCTCAAACTATGATATTCATTCTAAACTAGTCCACAAACTTTTGAACATTTCAATTTCA
Found at i:3998964 original size:60 final size:60
Alignment explanation
Indices: 3998891--3999007 Score: 153
Period size: 60 Copynumber: 1.9 Consensus size: 60
3998881 ATTTGGATAA
* * ** * * *
3998891 TTTGTGGATGAAATTGGAAGATTTAAATGTTTGAGGATTAATTTAAAATGAGGGTCACAG
1 TTTGGGGATGAAATTGGAAGATTCAAAAATTTAAAGATTAATTTAAAATGAGAGTCACAG
* *
3998951 TTTGGGGATGAAATTGGAATATTCAAAAATTTAAAGATTAATTTATAATGAGAGTCA
1 TTTGGGGATGAAATTGGAAGATTCAAAAATTTAAAGATTAATTTAAAATGAGAGTCA
3999008 TAATTTAAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.35
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAAGATTCAAAAATTTAAAGATTAATTTAAAATGAGAGTCACAG
Found at i:4002781 original size:60 final size:56
Alignment explanation
Indices: 4002621--4002793 Score: 283
Period size: 56 Copynumber: 3.0 Consensus size: 56
4002611 GAGAGTTGAT
*
4002621 AAAATGCTTGGCTAGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCTAGTGCC
1 AAAATGCTTGGCTAGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCAAGTGCC
4002677 AAAATGCTTGGCTAGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCAAGTGCC
1 AAAATGCTTGGCTAGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCAAGTGCC
* *
4002733 AAAATGCTTGGCGTGAGAGGCAATCGTGGAAGATACAGCTCATTTTATATTGCAAGTGCC
1 AAAATGCTTGGC-T---AGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCAAGTGCC
4002793 A
1 A
4002794 GGTTTCCTCA
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
56 67 0.61
57 1 0.01
60 42 0.38
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (56 bp):
AAAATGCTTGGCTAGGCAAACGTGGAAGATAGAGCTCATTTTATATTGCAAGTGCC
Found at i:4007964 original size:20 final size:20
Alignment explanation
Indices: 4007927--4007965 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4007917 AGATTGAGTG
* * *
4007927 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
4007947 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
4007966 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:4008147 original size:21 final size:21
Alignment explanation
Indices: 4008121--4008160 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4008111 CAGAACCCCA
*
4008121 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
4008142 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
4008161 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:4008189 original size:20 final size:21
Alignment explanation
Indices: 4008143--4008203 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
4008133 TTCCCCTGTG
4008143 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
4008166 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
4008186 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
4008204 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:4015021 original size:15 final size:15
Alignment explanation
Indices: 4014992--4015062 Score: 62
Period size: 15 Copynumber: 5.0 Consensus size: 15
4014982 GTGAAATTCT
*
4014992 AATTA-TTAAATAAA
1 AATTATTTATATAAA
4015006 AATTATTTATATAAA
1 AATTATTTATATAAA
*
4015021 AATTCA--TCTAT-AA
1 AATT-ATTTATATAAA
* *
4015034 TA-TATTTAAATAAA
1 AATTATTTATATAAA
4015048 AATTATTTATATAAA
1 AATTATTTATATAAA
4015063 TTTCATTGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.14
14 12 0.27
15 23 0.52
16 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:4015080 original size:41 final size:42
Alignment explanation
Indices: 4014997--4015080 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
4014987 ATTCTAATTA
4014997 TTAAATAAAAATTATTTATATAAAAATTCATCTATAATATAT
1 TTAAATAAAAATTATTTATATAAAAATTCATCTATAATATAT
*
4015039 TTAAATAAAAATTATTTATAT-AAATTTCAT-TGATAATATAT
1 TTAAATAAAAATTATTTATATAAAAATTCATCT-ATAATATAT
4015080 T
1 T
4015081 ATTTTATTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 1 0.03
41 18 0.45
42 21 0.52
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (42 bp):
TTAAATAAAAATTATTTATATAAAAATTCATCTATAATATAT
Found at i:4015241 original size:26 final size:26
Alignment explanation
Indices: 4015168--4015243 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
4015158 ATTAAAATTT
*
4015168 TACTTCAACATTTAATTAAATATTCAA
1 TACTTCAACATTTAATTAAAT-TTCAC
** *
4015195 TA-TT-AGGGATTT--TTAACTTTCAC
1 TACTTCA-ACATTTAATTAAATTTCAC
4015218 TACTTCAACATTTAATTAAATTTCAC
1 TACTTCAACATTTAATTAAATTTCAC
4015244 ATAATTTATC
Statistics
Matches: 37, Mismatches: 7, Indels: 11
0.67 0.13 0.20
Matches are distributed among these distances:
23 6 0.16
24 11 0.30
25 2 0.05
26 16 0.43
27 2 0.05
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.43
Consensus pattern (26 bp):
TACTTCAACATTTAATTAAATTTCAC
Found at i:4019006 original size:36 final size:35
Alignment explanation
Indices: 4018966--4019058 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 35
4018956 TTAAGCTCGC
4018966 GAGTTTTTGAGTCGAGTCGAGTCGAGCTCCATTTCA
1 GAGTTTTTGA-TCGAGTCGAGTCGAGCTCCATTTCA
*
4019002 GAG--TTT--TCGAGTTGAGTCGAGCTCCATTTCA
1 GAGTTTTTGATCGAGTCGAGTCGAGCTCCATTTCA
* * *
4019033 AAGTTTTCGATTCGAGTCAAGTCGAG
1 GAGTTTTTGA-TCGAGTCGAGTCGAG
4019059 ATCAACAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
31 26 0.55
33 2 0.04
34 3 0.06
36 16 0.34
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (35 bp):
GAGTTTTTGATCGAGTCGAGTCGAGCTCCATTTCA
Found at i:4019012 original size:31 final size:31
Alignment explanation
Indices: 4018977--4019050 Score: 121
Period size: 31 Copynumber: 2.4 Consensus size: 31
4018967 AGTTTTTGAG
*
4018977 TCGAGTCGAGTCGAGCTCCATTTCAGAGTTT
1 TCGAGTCGAGTCGAGCTCCATTTCAAAGTTT
*
4019008 TCGAGTTGAGTCGAGCTCCATTTCAAAGTTT
1 TCGAGTCGAGTCGAGCTCCATTTCAAAGTTT
*
4019039 TCGATTCGAGTC
1 TCGAGTCGAGTC
4019051 AAGTCGAGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (31 bp):
TCGAGTCGAGTCGAGCTCCATTTCAAAGTTT
Found at i:4019288 original size:43 final size:42
Alignment explanation
Indices: 4019241--4019520 Score: 248
Period size: 42 Copynumber: 6.6 Consensus size: 42
4019231 GTAAAGACCA
** * *
4019241 ATAGCGGCGTTTTTGGAACAAACATCGCAATAGGTCGATATCT
1 ATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTC-ATATCT
*
4019284 ATAGCAGC---TTTGGAACAAACGCCACAAAAGGTCGATATCT
1 ATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTC-ATATCT
* * * * * *
4019324 ATAGCGACGTTTTTAGAACAAGCGCCGCAAAAAGTCAGATCT
1 ATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTCATATCT
* * *
4019366 ATAGCGACATTTTTGGATAC-AA-GCTCACAAAAGGTCAGATCT
1 ATAGCGGCGTTTTTGGA-ACAAACGC-CACAAAAGGTCATATCT
* * * * *
4019408 ATAGCAGC-TTTTTGTAAAAAAACACCGCAAAAGGTCATATCT
1 ATAGCGGCGTTTTTG-GAACAAACGCCACAAAAGGTCATATCT
* * *
4019450 ATAGCGGCGTTTTGTTGAAACAAACGCCACAAAAGGTCAGATTT
1 ATAGCGGCG-TTT-TTGGAACAAACGCCACAAAAGGTCATATCT
4019494 ATAGCGGCGTTTTTGGATACAAACGCC
1 ATAGCGGCGTTTTTGGA-ACAAACGCC
4019521 GCTAATTACC
Statistics
Matches: 194, Mismatches: 31, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
40 34 0.18
41 9 0.05
42 71 0.37
43 43 0.22
44 34 0.18
45 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
ATAGCGGCGTTTTTGGAACAAACGCCACAAAAGGTCATATCT
Found at i:4023649 original size:64 final size:63
Alignment explanation
Indices: 4023563--4023772 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 63
4023553 TGCACTAAGA
* * * *
4023563 GTGCATCGATGCGTCAAGTGCATTCGATGATTCAAAATAGCCAGAGTGCGTCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGATTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* * **
4023627 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-ATTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
4023691 T
63 G
* * **
4023692 GTGCATCGATGCATGAAATACATTCGAT-ATTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGATTCAAAATA-TCCA-GAGTGCATCGATGCATGG--
4023755 TG
62 TG
*
4023757 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
4023773 CTTTGAAAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 46 0.39
65 62 0.53
66 4 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGATTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:4026451 original size:21 final size:19
Alignment explanation
Indices: 4026421--4026487 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 19
4026411 CGTGCATTGG
4026421 TGCACCTTCATGGTGTATCGA
1 TGCA-CTTCA-GGTGTATCGA
* *
4026442 TGCACATTCAAGGATGCATCCA
1 TGCAC-TTC-AGG-TGTATCGA
*
4026464 TGCACTGTTAGGTGTATCGA
1 TGCACT-TCAGGTGTATCGA
4026484 TGCA
1 TGCA
4026488 TTAAGCACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 11 0.30
21 13 0.35
22 13 0.35
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (19 bp):
TGCACTTCAGGTGTATCGA
Found at i:4032232 original size:64 final size:62
Alignment explanation
Indices: 4032164--4032373 Score: 217
Period size: 65 Copynumber: 3.3 Consensus size: 62
4032154 TGCACTAAGA
* * *
4032164 GTGCATCGATGCATCAAGTGAATTCGATGATTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTCAAAATATCCAGAGTGCATCGATGCATGG-TG
** *
4032228 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGAATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG--TTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
4032292 T
62 G
* **
4032293 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTATTCCATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAAAATA-TCCA-GAGTGCATCGATGCATGG--T
4032357 G
62 G
*
4032358 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
4032374 CTTTGAAAAT
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 46 0.38
65 65 0.54
66 4 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (62 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:4033191 original size:41 final size:41
Alignment explanation
Indices: 4033146--4033252 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 41
4033136 ACCATATTGA
* * * *
4033146 GGCGTTTGTATAAAAACGTCGCTAAATTATTATTCTGTTGC
1 GGCGTTTGTATAAAAACGCCACTAAAATACTATTCTGTTGC
*
4033187 GGCGTTTGTATAAAAACGCCACTAAAATACTATTCTTTTGC
1 GGCGTTTGTATAAAAACGCCACTAAAATACTATTCTGTTGC
*
4033228 GGTGTTTGT-TGAAAAAACGCCACTA
1 GGCGTTTGTAT--AAAAACGCCACTA
4033253 TAGATTAACC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 1 0.02
41 44 0.76
42 13 0.22
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (41 bp):
GGCGTTTGTATAAAAACGCCACTAAAATACTATTCTGTTGC
Found at i:4033468 original size:83 final size:81
Alignment explanation
Indices: 4033270--4033469 Score: 240
Period size: 83 Copynumber: 2.5 Consensus size: 81
4033260 ACCATATTGC
* * * * *
4033270 AAAAACACCGCTAAAGTACTA-TTTTTCACGGTGTTTATTGAGAAACGCCACTATGGATGAACCT
1 AAAAACGCCGCTAAAGTACTACTTTGTCACGGCGTTTATTGAGAAACGCCACTATAGATGAACCA
4033334 ATTGAGGCGTTTGTAT
66 ATTGAGGCGTTTGTAT
* * ** * *
4033350 AAAAATGCCGCTAAAGTACTACTCTGTTGCAGCGTTTGTTGAAGAAACGCCACTATAGATGAACC
1 AAAAACGCCGCTAAAGTACTACTTTGTCACGGCGTTTATTG-AGAAACGCCACTATAGATGAA-C
** *
4033415 CAATTTTGGCGTTTTTAT
64 CAATTGAGGCGTTTGTAT
*
4033433 ATAAACGCCGCTAAAGTACTACTTTGTCACGGCGTTT
1 AAAAACGCCGCTAAAGTACTACTTTGTCACGGCGTTT
4033470 TGTATAAAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
80 19 0.20
81 12 0.12
82 20 0.21
83 46 0.47
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGTACTACTTTGTCACGGCGTTTATTGAGAAACGCCACTATAGATGAACCA
ATTGAGGCGTTTGTAT
Found at i:4051998 original size:54 final size:54
Alignment explanation
Indices: 4051930--4052246 Score: 463
Period size: 54 Copynumber: 5.9 Consensus size: 54
4051920 TTAACAAATA
* * *
4051930 GGCACTAAGTGTGCAATTCATGGAATTCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
4051984 GGTACTAAGGGTGCATTTCACGGAATTCATCCTATATGGGTGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
4052038 GACACTAAGTGTGCATTTCACGAAATTCATCATATGTGGGTGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
4052092 GGCACTAAGTGTGTATTTCACGGAATTCATCTTATGTGGGTGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
4052146 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATAAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
4052200 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA
4052247 TCATTTTGAC
Statistics
Matches: 234, Mismatches: 29, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 234 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:4052121 original size:108 final size:108
Alignment explanation
Indices: 4051932--4052283 Score: 490
Period size: 108 Copynumber: 3.3 Consensus size: 108
4051922 AACAAATAGG
* * * *
4051932 CACTAAGTGTGCAATTCATGGAATTCATCCTATGTGGATGAATAACCGTTTTGGTACTAAGGGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTG
*
4051997 CATTTCACGGAATTCATCCTATATGGGTGAATAACCATTTCGA
66 CATTTCACGGAATTCATCCTATGTGGGTGAATAACCATTTCGA
* * *
4052040 CACTAAGTGTGCATTTCACGAAATTCATCATATGTGGGTGAATAACCGTTTTGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTG
* * * *
4052105 TATTTCACGGAATTCATCTTATGTGGGTGAATAACCGTTTCGG
66 CATTTCACGGAATTCATCCTATGTGGGTGAATAACCATTTCGA
* * * *
4052148 CACTAAGTGTGCATTTCAC-AGAATTCATCCTATGTGGATAAATAACCATTTCGGCACTAAGTGT
1 CACTAAGTGTGCAATTCACGA-AATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGT
* * *
4052212 GCATTTCACGGAATTCATCCTATGTGGATGAATAATCATTTTGA
65 GCATTTCACGGAATTCATCCTATGTGGGTGAATAACCATTTCGA
* **
4052256 CACTATGTGTGCAAAGCACGAAATTCAT
1 CACTAAGTGTGCAATTCACGAAATTCAT
4052284 AATTTATTTA
Statistics
Matches: 214, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.00
108 212 0.99
109 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (108 bp):
CACTAAGTGTGCAATTCACGAAATTCATCCTATGTGGATGAATAACCGTTTTGGCACTAAGTGTG
CATTTCACGGAATTCATCCTATGTGGGTGAATAACCATTTCGA
Found at i:4052197 original size:162 final size:162
Alignment explanation
Indices: 4051930--4052283 Score: 501
Period size: 162 Copynumber: 2.2 Consensus size: 162
4051920 TTAACAAATA
* * *
4051930 GGCACTAAGTGTGCAATTCATGGAATTCATCCTATGTGGATGAATAACCGTTTTGGTACTAAGGG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGGG
* * *
4051995 TGCATTTCACGGAATTCATCCTATATGGGTGAATAACCATTTCGACACTAAGTGTGCATTTCACG
66 TGCATTTCACAGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACG
* *
4052060 AAATTCATCATATGTGGGTGAATAACCGTTTT
131 AAATTCATCATATGTGGATGAATAACCATTTT
* * * * *
4052092 GGCACTAAGTGTGTATTTCACGGAATTCATCTTATGTGGGTGAATAACCGTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGGG
* *
4052157 TGCATTTCACAGAATTCATCCTATGTGGATAAATAACCATTTCGGCACTAAGTGTGCATTTCACG
66 TGCATTTCACAGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACG
* * *
4052222 GAATTCATCCTATGTGGATGAATAATCATTTT
131 AAATTCATCATATGTGGATGAATAACCATTTT
* * ** *
4052254 GACACTATGTGTGCAAAGCACGAAATTCAT
1 GGCACTAAGTGTGCAATTCACGGAATTCAT
4052284 AATTTATTTA
Statistics
Matches: 167, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
162 167 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (162 bp):
GGCACTAAGTGTGCAATTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGGG
TGCATTTCACAGAATTCATCCTATATGGATAAATAACCATTTCGACACTAAGTGTGCATTTCACG
AAATTCATCATATGTGGATGAATAACCATTTT
Found at i:4052281 original size:54 final size:54
Alignment explanation
Indices: 4051930--4052283 Score: 431
Period size: 54 Copynumber: 6.6 Consensus size: 54
4051920 TTAACAAATA
* * * * *
4051930 GGCACTAAGTGTGCAATTCATGGAATTCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
* * * * *
4051984 GGTACTAAGGGTGCATTTCACGGAATTCATCCTATATGGGTGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
* * * * *
4052038 GACACTAAGTGTGCATTTCACGAAATTCATCATATGTGGGTGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
* * * * *
4052092 GGCACTAAGTGTGTATTTCACGGAATTCATCTTATGTGGGTGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
*
4052146 GGCACTAAGTGTGCATTTCAC-AGAATTCATCCTATGTGGATAAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGA-AATTCATCCTATGTGGATGAATAACCATTTC
* * *
4052200 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAATCATTTT
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
* * ***
4052254 GACACTATGTGTGCAAAGCACGAAATTCAT
1 GGCACTAAGTGTGCATTTCACGAAATTCAT
4052284 AATTTATTTA
Statistics
Matches: 261, Mismatches: 37, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
54 261 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTC
Found at i:4055139 original size:24 final size:24
Alignment explanation
Indices: 4055110--4055159 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4055100 TGGTGGTTGA
*
4055110 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
4055134 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
4055158 TT
1 TT
4055160 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:4055666 original size:18 final size:17
Alignment explanation
Indices: 4055634--4055668 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
4055624 CACGTGAGGA
4055634 TTATTTTCTTCTTATTT
1 TTATTTTCTTCTTATTT
*
4055651 TTATTTATCTTTTTATTT
1 TTATTT-TCTTCTTATTT
4055669 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (17 bp):
TTATTTTCTTCTTATTT
Found at i:4065195 original size:24 final size:24
Alignment explanation
Indices: 4065166--4065215 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4065156 TGGTGGTTGA
*
4065166 TTTAATGGT-TGTTTAAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
4065190 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
4065214 TT
1 TT
4065216 GGTTCATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:4065722 original size:17 final size:16
Alignment explanation
Indices: 4065691--4065724 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4065681 CACGTGAGGA
4065691 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
4065707 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
4065724 T
1 T
4065725 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:4069994 original size:54 final size:53
Alignment explanation
Indices: 4069805--4069981 Score: 264
Period size: 54 Copynumber: 3.3 Consensus size: 53
4069795 TTACCAAATA
* *
4069805 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGTTGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGG-TGAATAACCGTTTC
* *
4069859 GGCACTAAGTGTGCATTTCATGGAATTTATCCTATCTAGGTGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGT-GGTGAATAACCGTTTC
* *
4069913 GACACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGG-TGAATAACCGTTTC
*
4069967 GGCACTATGTGTGCA
1 GGCACTAAGTGTGCA
4069982 AAGCACAAAA
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
53 2 0.02
54 107 0.96
55 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (53 bp):
GGCACTAAGTGTGCATTTCATGGAATTCATCCTATGTGGTGAATAACCGTTTC
Found at i:4077201 original size:31 final size:31
Alignment explanation
Indices: 4077163--4077223 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
4077153 CTTTATCATG
*
4077163 TCTTTCTTATTATGTTGATTTGAGATACAAA
1 TCTTTCTTAATATGTTGATTTGAGATACAAA
4077194 TCTTTCTTAATATGTTGATTTGAGATACAA
1 TCTTTCTTAATATGTTGATTTGAGATACAA
4077224 GGTTTATAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.48
Consensus pattern (31 bp):
TCTTTCTTAATATGTTGATTTGAGATACAAA
Found at i:4077607 original size:23 final size:23
Alignment explanation
Indices: 4077581--4077625 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4077571 TGTTTTCACC
*
4077581 CCTAAACTTTTATAAGTTTATCT
1 CCTAAAATTTTATAAGTTTATCT
*
4077604 CCTAAAATTTTATAATTTTATC
1 CCTAAAATTTTATAAGTTTATC
4077626 AACTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (23 bp):
CCTAAAATTTTATAAGTTTATCT
Found at i:4077631 original size:23 final size:23
Alignment explanation
Indices: 4077582--4077631 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4077572 GTTTTCACCC
* **
4077582 CTAAACTTTTATAAGTTTATCTC
1 CTAAAATTTTATAAGTTTATCAA
*
4077605 CTAAAATTTTATAATTTTATCAA
1 CTAAAATTTTATAAGTTTATCAA
4077628 CTAA
1 CTAA
4077632 TATAAAATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (23 bp):
CTAAAATTTTATAAGTTTATCAA
Found at i:4082803 original size:14 final size:14
Alignment explanation
Indices: 4082781--4082827 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
4082771 TACAAAGAAA
*
4082781 AATTAATATAGTTT
1 AATTTATATAGTTT
4082795 AATTTATATA----
1 AATTTATATAGTTT
4082805 AA-TTATATAGTTT
1 AATTTATATAGTTT
4082818 AATTTATATA
1 AATTTATATA
4082828 AAAAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:4082814 original size:23 final size:24
Alignment explanation
Indices: 4082780--4082829 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
4082770 ATACAAAGAA
4082780 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
4082804 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
4082827 AAA
1 AAA
4082830 AAAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:4083540 original size:14 final size:14
Alignment explanation
Indices: 4083521--4083563 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
4083511 TTGGCACTTA
4083521 TTCTTTCAAATTGC
1 TTCTTTCAAATTGC
4083535 TTCTTTCAAATTGC
1 TTCTTTCAAATTGC
4083549 TTCTTTCAAATTGC
1 TTCTTTCAAATTGC
4083563 T
1 T
4083564 CTAACATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.21, C:0.21, G:0.07, T:0.51
Consensus pattern (14 bp):
TTCTTTCAAATTGC
Found at i:4085217 original size:97 final size:98
Alignment explanation
Indices: 4085101--4085298 Score: 272
Period size: 97 Copynumber: 2.0 Consensus size: 98
4085091 TGGAGCGATG
* **
4085101 GGTTATTTGGAGAGAGGGAAACAATTAATAGCAGAAGAAAAAGAAAAATACGAGGGAAATGACAA
1 GGTTATTTGGAGAGAGGGAAACAATTAAGAGCAGAAGAAAAAGAAAAATACGAGAAAAATGACAA
*
4085166 -GGTTTGATTATTTGGCGCCACCACCTTATATA
66 TAGTTTGATTATTTGGCGCCACCACCTTATATA
* * *
4085198 GGTTGTTTGGAGAGAGGGAAACAATTAAGAGCAGAAGAAAAATAAAAATAGGAGAAAAATGACAA
1 GGTTATTTGGAGAGAGGGAAACAATTAAGAGCAGAAGAAAAAGAAAAATACGAGAAAAATGACAA
* * *
4085263 TTCTAGTTTGGTTATTTGGTGCCACCGCCTTATATA
66 ---TAGTTTGATTATTTGGCGCCACCACCTTATATA
4085299 ATTTATATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
97 59 0.68
101 28 0.32
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (98 bp):
GGTTATTTGGAGAGAGGGAAACAATTAAGAGCAGAAGAAAAAGAAAAATACGAGAAAAATGACAA
TAGTTTGATTATTTGGCGCCACCACCTTATATA
Found at i:4085349 original size:28 final size:29
Alignment explanation
Indices: 4085313--4085439 Score: 136
Period size: 28 Copynumber: 4.4 Consensus size: 29
4085303 ATATTAATAA
4085313 AGTATTTATAATTAATATTAAAATAATTAT
1 AGTA-TTATAATTAATATTAAAATAATTAT
*
4085343 A-TATTATAATTAATATAAAAATAATTAT
1 AGTATTATAATTAATATTAAAATAATTAT
**
4085371 A-TATTATAATTAATATTAATTTAATTAAT
1 AGTATTATAATTAATATTAAAATAATT-AT
* * * *
4085400 ATTAATATTAATTTATATTAATATAA-TAT
1 AGTATTA-TAATTAATATTAAAATAATTAT
4085429 AGT-TTATAATT
1 AGTATTATAATT
4085440 TGTAATTAAT
Statistics
Matches: 85, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.06
28 49 0.58
29 9 0.11
30 6 0.07
31 16 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
AGTATTATAATTAATATTAAAATAATTAT
Found at i:4085388 original size:6 final size:6
Alignment explanation
Indices: 4085366--4085428 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
4085356 TATAAAAATA
4085366 ATTATAT ATT-AT AATTAAT ATTAAT -TT-A- ATTAAT ATTAAT ATTAAT
1 ATTA-AT ATTAAT -ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT
4085412 -TT-AT ATTAAT A-TAAT AT
1 ATTAAT ATTAAT ATTAAT AT
4085429 AGTTTATAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
4 5 0.10
5 14 0.29
6 24 0.50
7 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:4085426 original size:21 final size:21
Alignment explanation
Indices: 4085297--4085436 Score: 94
Period size: 21 Copynumber: 6.4 Consensus size: 21
4085287 CCGCCTTATA
4085297 TAATTTATATTAATA-AAGTATTT
1 TAATTTATATTAATATAA-TA--T
* *
4085320 ATAATTAATATTAAAAT-A-AT
1 -TAATTTATATTAATATAATAT
* *
4085340 TATATATTATAATTAATATAAAAA
1 TA-AT-TTAT-ATTAATATAATAT
4085364 TAATTATATATT-ATAATTAATAT
1 TAATT-TATATTAAT-A-TAATAT
4085387 TAATTTA-ATTAATATTAATAT
1 TAATTTATATTAATA-TAATAT
4085408 TAATTTATATTAATATAATA-
1 TAATTTATATTAATATAATAT
*
4085428 TAGTTTATA
1 TAATTTATA
4085437 ATTTGTAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.02
20 11 0.11
21 28 0.29
22 24 0.25
23 15 0.15
24 17 0.18
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (21 bp):
TAATTTATATTAATATAATAT
Found at i:4085481 original size:31 final size:30
Alignment explanation
Indices: 4085443--4085627 Score: 153
Period size: 31 Copynumber: 5.8 Consensus size: 30
4085433 TATAATTTGT
*
4085443 AATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAAACTATAGT-TATAA
4085474 AATTAATATTAATATAAACTATATGTTAT-A
1 AATTAATATTAATATAAACTATA-GTTATAA
*
4085504 AATTATATAGTATAATTTATAAACTATAGTTAATAT
1 AATTA-ATA-T-TAA--TATAAACTATAGTT-ATAA
*
4085540 AATTAATATTAATAT--AGTATAGTTTATAA
1 AATTAATATTAATATAAACTATAG-TTATAA
*
4085569 ACTATATACTATATTAATATAAATTATAGTTA-AGA
1 A--AT-TA--ATATTAATATAAACTATAGTTATA-A
*
4085604 TAATTAACATTAATATAAACTATA
1 -AATTAATATTAATATAAACTATA
4085628 TAGTACATTA
Statistics
Matches: 129, Mismatches: 7, Indels: 36
0.75 0.04 0.21
Matches are distributed among these distances:
29 10 0.08
30 8 0.06
31 49 0.38
32 5 0.04
33 8 0.06
34 17 0.13
35 20 0.16
36 12 0.09
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (30 bp):
AATTAATATTAATATAAACTATAGTTATAA
Found at i:4085483 original size:65 final size:63
Alignment explanation
Indices: 4085409--4085621 Score: 193
Period size: 65 Copynumber: 3.3 Consensus size: 63
4085399 TATTAATATT
* * *
4085409 AATTTATATTAATATAATATAGTTTATAATTTGTAATTAATATTAATATAAAATATAGTCTATAA
1 AATTAATATTAATATAATATAGTTTATAAATTATAA-TAATATTAATATAAAATATAGT-TATAA
* *
4085474 AATTAATATTAATATAAACTATA-TGTTATAAATTAT-ATAGTA-TAATTTATAAACTATAGTTA
1 AATTAATATTAATAT-AA-TATAGT-TTATAAATTATAATAATATTAA--TATAAAATATAGTT-
*
4085536 ATAT
60 ATAA
* * *
4085540 AATTAATATTAATATAGTATAGTTTATAAACTAT-ATACTATATTAATATAAATTATAGTTA-AG
1 AATTAATATTAATATAATATAGTTTATAAATTATAATA--ATATTAATATAAAATATAGTTATA-
4085603 A
63 A
*
4085604 TAATTAACATTAATATAA
1 -AATTAATATTAATATAA
4085622 ACTATATAGT
Statistics
Matches: 123, Mismatches: 13, Indels: 24
0.77 0.08 0.15
Matches are distributed among these distances:
63 1 0.01
64 21 0.17
65 49 0.40
66 36 0.29
67 16 0.13
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.44
Consensus pattern (63 bp):
AATTAATATTAATATAATATAGTTTATAAATTATAATAATATTAATATAAAATATAGTTATAA
Found at i:4085495 original size:24 final size:25
Alignment explanation
Indices: 4085450--4085496 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
4085440 TGTAATTAAT
**
4085450 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
4085475 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
4085497 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:4085557 original size:43 final size:40
Alignment explanation
Indices: 4085508--4085598 Score: 119
Period size: 43 Copynumber: 2.2 Consensus size: 40
4085498 GTTATAAATT
*
4085508 ATATAGTATAATTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAATTTATAAACTATA--TAATAT-ATTAATATAA
* *
4085551 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAATTTATAAACTATATAATATATTAATATAA
4085591 ATTATAGT
1 A-TATAGT
4085599 TAAGATAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.23
41 11 0.25
43 23 0.52
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (40 bp):
ATATAGTATAATTTATAAACTATATAATATATTAATATAA
Found at i:4085561 original size:29 final size:29
Alignment explanation
Indices: 4085528--4085620 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
4085518 ATTTATAAAC
4085528 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
4085557 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
4085593 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
4085621 AACTATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:4085635 original size:22 final size:22
Alignment explanation
Indices: 4085610--4085712 Score: 88
Period size: 22 Copynumber: 4.8 Consensus size: 22
4085600 AAGATAATTA
4085610 ACATTAATATAAACTATATAGT
1 ACATTAATATAAACTATATAGT
4085632 ACATTAATATAAAC--TATAGT
1 ACATTAATATAAACTATATAGT
** * * *
4085652 TTATAAATTATATACTATA-GGT
1 ACATTAA-TATAAACTATATAGT
* *
4085674 -TATAAAGTATAAACTATATAGT
1 ACATTAA-TATAAACTATATAGT
*
4085696 ACACTAATATAAACTAT
1 ACATTAATATAAACTAT
4085713 TGTTTATAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
20 10 0.15
21 22 0.34
22 28 0.43
23 5 0.08
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (22 bp):
ACATTAATATAAACTATATAGT
Found at i:4085727 original size:21 final size:20
Alignment explanation
Indices: 4085637--4085729 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 20
4085627 ATAGTACATT
4085637 AATATAAACTATAGTTTATA
1 AATATAAACTATAGTTTATA
* *
4085657 AATTATATACTATAGGTTATA
1 AA-TATAAACTATAGTTTATA
* *
4085678 AAGTATAAACTATA-TAGTACA
1 AA-TATAAACTATAGT-TTATA
*
4085699 CTAATATAAACTATTGTTTATA
1 --AATATAAACTATAGTTTATA
4085721 AACTATAAA
1 AA-TATAAA
4085730 TTACATATAT
Statistics
Matches: 57, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
20 4 0.07
21 37 0.65
22 13 0.23
23 3 0.05
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (20 bp):
AATATAAACTATAGTTTATA
Found at i:4085790 original size:15 final size:16
Alignment explanation
Indices: 4085766--4085806 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
4085756 AAATAGATAC
4085766 ATATACTATAGGTTAT
1 ATATACTATAGGTTAT
*
4085782 ATATA-TATAGTTTAT
1 ATATACTATAGGTTAT
*
4085797 ATATAGTATA
1 ATATACTATA
4085807 CATAGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.46
Consensus pattern (16 bp):
ATATACTATAGGTTAT
Found at i:4085806 original size:20 final size:19
Alignment explanation
Indices: 4085779--4085817 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
4085769 TACTATAGGT
*
4085779 TATATATATATAGTTTATA
1 TATATATACATAGTTTATA
4085798 TATAGTATACATAGTTTATA
1 TATA-TATACATAGTTTATA
4085818 CTTACATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (19 bp):
TATATATACATAGTTTATA
Found at i:4085928 original size:21 final size:20
Alignment explanation
Indices: 4085904--4085947 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
4085894 ATGCATAATG
*
4085904 TTTAGGTTTTAGGGTTTATTA
1 TTTAGGATTTAGGGTTTA-TA
*
4085925 TTTATGATTTAGGGTTTATA
1 TTTAGGATTTAGGGTTTATA
4085945 TTT
1 TTT
4085948 TAATGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.59
Consensus pattern (20 bp):
TTTAGGATTTAGGGTTTATA
Found at i:4085949 original size:35 final size:35
Alignment explanation
Indices: 4085910--4085978 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
4085900 AATGTTTAGG
* *
4085910 TTTTAGGGTTTATTATTTATGATTTAGGGTTTATA
1 TTTTAAGGTTTATGATTTATGATTTAGGGTTTATA
*
4085945 TTTTAATGTTTATGATTTATGATTTAGGGTTTAT
1 TTTTAAGGTTTATGATTTATGATTTAGGGTTTAT
4085979 GCATATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.23, C:0.00, G:0.19, T:0.58
Consensus pattern (35 bp):
TTTTAAGGTTTATGATTTATGATTTAGGGTTTATA
Found at i:4085956 original size:21 final size:21
Alignment explanation
Indices: 4085911--4085978 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
4085901 ATGTTTAGGT
4085911 TTTAGGGTTTATTATTTATGA
1 TTTAGGGTTTATTATTTATGA
4085932 TTTAGGGTTTA-TATTT-T-A
1 TTTAGGGTTTATTATTTATGA
* *
4085950 ---A-TGTTTATGATTTATGA
1 TTTAGGGTTTATTATTTATGA
4085967 TTTAGGGTTTAT
1 TTTAGGGTTTAT
4085979 GCATATTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
14 5 0.14
15 5 0.14
16 1 0.03
17 1 0.03
18 1 0.03
19 1 0.03
20 6 0.16
21 17 0.46
ACGTcount: A:0.24, C:0.00, G:0.19, T:0.57
Consensus pattern (21 bp):
TTTAGGGTTTATTATTTATGA
Found at i:4086374 original size:2 final size:2
Alignment explanation
Indices: 4086367--4086504 Score: 107
Period size: 2 Copynumber: 72.0 Consensus size: 2
4086357 ATAGTGTTTC
4086367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
4086409 TC TA TA GA T- TA CT- TA TA T- TA GT- TA -A CA TA CA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
4086448 CTA TA T- TA -A TA TA -A TT TA TA AA CTA TA TA T- TT TA TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
4086487 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
4086505 ATTAAATGTA
Statistics
Matches: 110, Mismatches: 12, Indels: 28
0.73 0.08 0.19
Matches are distributed among these distances:
1 10 0.09
2 95 0.86
3 5 0.05
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:4086765 original size:17 final size:18
Alignment explanation
Indices: 4086717--4086767 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
4086707 TTTCTATTCT
*
4086717 CTCTAAATTTCCCAATTTTC
1 CTCTAAA-TTCTCAA-TTTC
4086737 CTCTAAATTCTCAATTTC
1 CTCTAAATTCTCAATTTC
*
4086755 C-CTATATTCTCAA
1 CTCTAAATTCTCAA
4086768 AATTTCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 11 0.38
18 5 0.17
19 6 0.21
20 7 0.24
ACGTcount: A:0.27, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
CTCTAAATTCTCAATTTC
Found at i:4086774 original size:27 final size:27
Alignment explanation
Indices: 4086722--4086777 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
4086712 ATTCTCTCTA
* *
4086722 AATTTCCCAATTTTCCTCTAAATTCTC
1 AATTTCCCAATATTCCTCAAAATTCTC
*
4086749 AATTTCCCTATATT-CTCAAAATTTCTC
1 AATTTCCCAATATTCCTCAAAA-TTCTC
4086776 AA
1 AA
4086778 CTAAATTCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (27 bp):
AATTTCCCAATATTCCTCAAAATTCTC
Found at i:4086881 original size:15 final size:13
Alignment explanation
Indices: 4086861--4087017 Score: 68
Period size: 12 Copynumber: 12.5 Consensus size: 13
4086851 ATTTTGAATA
4086861 ATATATAGTTTAT
1 ATATATAGTTTAT
4086874 ACATATATAGTTTAT
1 --ATATATAGTTTAT
*
4086889 ATATATAGTTCACAT
1 ATATATAGTT--TAT
* * *
4086904 AAACATA-ATT-T
1 ATATATAGTTTAT
*
4086915 ATATATAGCTTAT
1 ATATATAGTTTAT
4086928 A-ATA-A--TTAT
1 ATATATAGTTTAT
* *
4086937 ATAGTTTA-TAATAT
1 ATA-TATAGT-TTAT
*
4086951 AAATATAGTTTAT
1 ATATATAGTTTAT
*
4086964 ATATA-AATTTAT
1 ATATATAGTTTAT
*
4086976 AT-TATA-TGTAT
1 ATATATAGTTTAT
*
4086987 ATATATA-TATAT
1 ATATATAGTTTAT
*
4086999 ATATATA-TATAT
1 ATATATAGTTTAT
4087011 ATATATA
1 ATATATA
4087018 TTTTTTTCAA
Statistics
Matches: 113, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
9 5 0.04
10 1 0.01
11 16 0.14
12 42 0.37
13 22 0.19
14 7 0.06
15 20 0.18
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.47
Consensus pattern (13 bp):
ATATATAGTTTAT
Found at i:4086956 original size:18 final size:18
Alignment explanation
Indices: 4086917--4086971 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
4086907 CATAATTTAT
* *
4086917 ATATAGCTTATAATA-ATT
1 ATATAGTTTATAATATA-A
4086935 ATATAGTTTATAATATAA
1 ATATAGTTTATAATATAA
4086953 ATATAGTTTAT-ATATAA
1 ATATAGTTTATAATATAA
4086970 AT
1 AT
4086972 TTATATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 8 0.24
18 25 0.74
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (18 bp):
ATATAGTTTATAATATAA
Found at i:4086968 original size:2 final size:2
Alignment explanation
Indices: 4086943--4087018 Score: 84
Period size: 2 Copynumber: 38.5 Consensus size: 2
4086933 TTATATAGTT
* * * * *
4086943 TA TA -A TA TA AA TA TA GTT TA TA TA TA AA TT TA TA T- TA TA TG
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
4086984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4087019 TTTTTTCAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4090148 original size:30 final size:31
Alignment explanation
Indices: 4090109--4090173 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
4090099 AATTGATTTT
* * * *
4090109 TTATTATTAAAATTTTTAAAA-GTTATAAAG
1 TTATCATTAAAAGTTTTAAAATATTATAAAA
4090139 TTATCATTAAAAGTTTTAAAATATTATAAAA
1 TTATCATTAAAAGTTTTAAAATATTATAAAA
4090170 TTAT
1 TTAT
4090174 TAAAGGAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (31 bp):
TTATCATTAAAAGTTTTAAAATATTATAAAA
Found at i:4090233 original size:18 final size:18
Alignment explanation
Indices: 4090210--4090248 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4090200 CTTAAAAAAA
4090210 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
* *
4090228 TTTAAACTTTTTATATAT
1 TTTAAAATTATTATATAT
4090246 TTT
1 TTT
4090249 TGTTGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:4105563 original size:30 final size:30
Alignment explanation
Indices: 4105521--4105591 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
4105511 TGATATTTAC
* *
4105521 ATATCACTTCATCAAAGTGATGATATGATA
1 ATATCACATCATCAAAGTGATGATACGATA
* *
4105551 ATGTCACATCATCAAAGTGGTGATACGATA
1 ATATCACATCATCAAAGTGATGATACGATA
*
4105581 ATATCATATCA
1 ATATCACATCA
4105592 ATAATATATT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (30 bp):
ATATCACATCATCAAAGTGATGATACGATA
Found at i:4106760 original size:16 final size:15
Alignment explanation
Indices: 4106718--4106774 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
4106708 TTATTATATT
4106718 TTTAATATTTT-GTA
1 TTTAATATTTTAGTA
*
4106732 TTTAATTTATTTAAGTA
1 TTTAA--TATTTTAGTA
*
4106749 TTTAATATTTTACTTA
1 TTTAATATTTTA-GTA
4106765 TTTAAT-TTTT
1 TTTAATATTTT
4106775 TTGCAGCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 5 0.14
15 10 0.28
16 13 0.36
17 8 0.22
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTAATATTTTAGTA
Found at i:4106775 original size:16 final size:16
Alignment explanation
Indices: 4106729--4106775 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
4106719 TTAATATTTT
4106729 GTATTTAATTTATTTAA
1 GTATTTAATTT-TTTAA
* *
4106746 GTATTTAATATTTTAC
1 GTATTTAATTTTTTAA
*
4106762 TTATTTAATTTTTT
1 GTATTTAATTTTTT
4106776 TGCAGCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 16 0.62
17 10 0.38
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (16 bp):
GTATTTAATTTTTTAA
Found at i:4109079 original size:35 final size:33
Alignment explanation
Indices: 4109040--4109124 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
4109030 GTATTTCAGT
*
4109040 TAATTTTGTT-TATTATCATTTAATATCAATTATTG
1 TAATTTTGTTATATTACCATTTAATA-C--TTATTG
*
4109075 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATACTTATTG
* *
4109110 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
4109125 TAAAATTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 2 0.05
38 12 0.29
ACGTcount: A:0.28, C:0.07, G:0.09, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATACTTATTG
Done.