Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 76 of 82
Found at i:28450849 original size:45 final size:45
Alignment explanation
Indices: 28450789--28450879 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 45
28450779 AATATATTAA
* * *
28450789 TATTATTTCACTATAATAAATATTATAAAGCATATTACTTAATAT
1 TATTATTTCAATATAATAAATATGATAAAGAATATTACTTAATAT
* * * *
28450834 TATTATTTGAATATAATAAATGTGATAAAGAATATTATTTAGTAT
1 TATTATTTCAATATAATAAATATGATAAAGAATATTACTTAATAT
28450879 T
1 T
28450880 TTTTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (45 bp):
TATTATTTCAATATAATAAATATGATAAAGAATATTACTTAATAT
Found at i:28451033 original size:21 final size:21
Alignment explanation
Indices: 28450966--28451033 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
28450956 TTCTAATACA
* *
28450966 AAAATATTATTAAATTATAAT
1 AAAATATTATTTAATTATAGT
* * * *
28450987 AAAA-ATAATTTGTATTTTGGT
1 AAAATATTATTT-AATTATAGT
28451008 GAAAATATTATTTAATTATAGT
1 -AAAATATTATTTAATTATAGT
28451030 AAAA
1 AAAA
28451034 GTTATTTTGA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
20 5 0.15
21 13 0.38
22 10 0.29
23 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
AAAATATTATTTAATTATAGT
Found at i:28452344 original size:159 final size:158
Alignment explanation
Indices: 28452120--28452419 Score: 494
Period size: 159 Copynumber: 1.9 Consensus size: 158
28452110 AAAGTCTCAA
* * *
28452120 AAATATTTAAGAAAATTCAAATAAGTTCTTATTCTACTATTACGTTCAATCAAAGCCTTAATTTT
1 AAATATTCAAGAAAATTCAAAGAAGTTCTTATTCTACTATTACATTCAATCAAAGCCTTAATTTT
* * *
28452185 TATTTTGAGTGAAATAAGCTTTTATGATTAATAGGTGACTAATTACTATTAATCAAAATATCACT
66 TATTTTGAATCAAATAAG-TTTTATGATTAATAGGTGACTAATTACCATTAATCAAAATATCACT
28452250 TGTTATTTTTATACTCACGAAAGTTCTTG
130 TGTTATTTTTATACTCACGAAAGTTCTTG
*
28452279 AAATATTCAAGAAAATTCAAAGAAGTTCTTATTCTACTATTTCATTCAATCAAA-CCTTTAATTT
1 AAATATTCAAGAAAATTCAAAGAAGTTCTTATTCTACTATTACATTCAATCAAAGCC-TTAATTT
* *
28452343 TTATTTTGAATCAAATAAGTTTTATGATTAATGGGTGACTAATTACCATTAATCAAAATATCATT
65 TTATTTTGAATCAAATAAGTTTTATGATTAATAGGTGACTAATTACCATTAATCAAAATATCACT
28452408 TGTTATTTTTAT
130 TGTTATTTTTAT
28452420 GCTTACATGG
Statistics
Matches: 131, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
158 57 0.44
159 74 0.56
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (158 bp):
AAATATTCAAGAAAATTCAAAGAAGTTCTTATTCTACTATTACATTCAATCAAAGCCTTAATTTT
TATTTTGAATCAAATAAGTTTTATGATTAATAGGTGACTAATTACCATTAATCAAAATATCACTT
GTTATTTTTATACTCACGAAAGTTCTTG
Found at i:28453232 original size:2 final size:2
Alignment explanation
Indices: 28453225--28453270 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
28453215 ACATACATAC
28453225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28453267 AT AT
1 AT AT
28453271 TGTGGTACGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28458423 original size:180 final size:179
Alignment explanation
Indices: 28458120--28458479 Score: 711
Period size: 180 Copynumber: 2.0 Consensus size: 179
28458110 AAAATTACCA
28458120 ACAAATAATTATTTTATTTGTTGAAGATTTAAATATAATTAGCATCTATTAGGGGTATTAACTTT
1 ACAAATAATTATTTTATTTGTTGAAGATTTAAATATAATTAGCATCTATTAGGGGTATTAACTTT
28458185 GCCTCTATTGTATTAAGACAAAAAATAAAAGACATAATATTCAAAAAAGTCTAAAAAATATTTAA
66 GCCTCTATTGTATTAAGACAAAAAATAAAAGACATAATATTCAAAAAAGTCTAAAAAATATTTAA
28458250 GAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTT
131 GAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTT
28458299 ANCAAATAATTATTTTATTTGTTGAAGATTTAAATATAATTAGCATCTATTAGGGGTATTAACTT
1 A-CAAATAATTATTTTATTTGTTGAAGATTTAAATATAATTAGCATCTATTAGGGGTATTAACTT
28458364 TGCCTCTATTGTATTAAGACAAAAAATAAAAGACATAATATTCAAAAAAGTCTAAAAAATATTTA
65 TGCCTCTATTGTATTAAGACAAAAAATAAAAGACATAATATTCAAAAAAGTCTAAAAAATATTTA
28458429 AGAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTT
130 AGAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTT
28458479 A
1 A
28458480 ATTTTTATTT
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 1 0.01
180 179 0.99
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.39
Consensus pattern (179 bp):
ACAAATAATTATTTTATTTGTTGAAGATTTAAATATAATTAGCATCTATTAGGGGTATTAACTTT
GCCTCTATTGTATTAAGACAAAAAATAAAAGACATAATATTCAAAAAAGTCTAAAAAATATTTAA
GAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTT
Found at i:28458702 original size:159 final size:159
Alignment explanation
Indices: 28458430--28458727 Score: 447
Period size: 159 Copynumber: 1.9 Consensus size: 159
28458420 AAATATTTAA
** * * * *
28458430 GAAAATTTGAATAATTTCTTATTTTACTATTGTGTTCAATCAAACTCTTAATTTTTATTTTGAGT
1 GAAAATTCAAATAAGTTCTTATTCTACTATTGTATTCAATCAAACTCTTAATTTTCATTTTGAGT
* *
28458495 GAAATAAGCTTTTATAATTAATAGATGACTAATTACCATTAATTAAAATATCACTTGTTATTTTT
66 CAAATAAGCTTTTATAATTAATAGATGACTAATTACCATTAATCAAAATATCACTTGTTATTTTT
28458560 ATACTCACGAAAGTCCCTGAAATATTCGC
131 ATACTCACGAAAGTCCCTGAAATATTCGC
*
28458589 GAAAATTCAAATAAGTTCTTATTCTACTATT-TCATTTAATCAAAC-CTTTAATTTTCATTTTGA
1 GAAAATTCAAATAAGTTCTTATTCTACTATTGT-ATTCAATCAAACTC-TTAATTTTCATTTTGA
* * * *
28458652 GTCAAATAAGCTTTTATGATTAATGGGTGACTAATTACCATTAATCAAAATATCATTTGTTATTT
64 GTCAAATAAGCTTTTATAATTAATAGATGACTAATTACCATTAATCAAAATATCACTTGTTATTT
28458717 TTATACTCACG
129 TTATACTCACG
28458728 TGGTATTGAT
Statistics
Matches: 124, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
158 2 0.02
159 122 0.98
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (159 bp):
GAAAATTCAAATAAGTTCTTATTCTACTATTGTATTCAATCAAACTCTTAATTTTCATTTTGAGT
CAAATAAGCTTTTATAATTAATAGATGACTAATTACCATTAATCAAAATATCACTTGTTATTTTT
ATACTCACGAAAGTCCCTGAAATATTCGC
Found at i:28462452 original size:22 final size:20
Alignment explanation
Indices: 28462409--28462456 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
28462399 ATAATAAATA
* *
28462409 AATAAAAAATTTAAAATTAT
1 AATAAAAAAATTAAAATCAT
28462429 AATAAAACAAATTAAAATACAT
1 AATAAAA-AAATTAAAAT-CAT
28462451 AA-AAAA
1 AATAAAA
28462457 TAATAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.29
21 13 0.54
22 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAAAAAAATTAAAATCAT
Found at i:28462456 original size:21 final size:21
Alignment explanation
Indices: 28462401--28462483 Score: 53
Period size: 22 Copynumber: 3.8 Consensus size: 21
28462391 AAAGAAAAAT
28462401 AATAAATAAATAAAAAATTTAA
1 AATAAATAAA-AAAAAATTTAA
*
28462423 AATTATAAT-AAAACAAA-TTAA
1 AA-TA-AATAAAAAAAAATTTAA
* * *
28462444 AATACATAAAAAATAATAATAA
1 AATAAATAAAAAAAAAT-TTAA
*
28462466 TATAAAATTAAAAAAAAA
1 AAT-AAA-TAAAAAAAAA
28462484 ACCCACTACG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
19 2 0.04
20 8 0.17
21 6 0.13
22 12 0.26
23 6 0.13
24 12 0.26
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAATAAAAAAAAATTTAA
Found at i:28462467 original size:20 final size:18
Alignment explanation
Indices: 28462395--28462472 Score: 54
Period size: 18 Copynumber: 4.2 Consensus size: 18
28462385 CCTGAAAAAG
28462395 AAAAATAAT-AAATAAATA
1 AAAAATAATAAAAT-AATA
* *
28462413 AAAAAT-TTAAAATTATA
1 AAAAATAATAAAATAATA
*
28462430 ATAAAACAAATTAAAATACATA
1 A-AAAA-TAA-TAAAATA-ATA
28462452 AAAAATAATAATAAT-ATA
1 AAAAATAATAA-AATAATA
28462470 AAA
1 AAA
28462473 TTAAAAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 5 0.11
18 20 0.43
19 3 0.06
20 5 0.11
21 10 0.21
22 4 0.09
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATAATAAAATAATA
Found at i:28463383 original size:17 final size:16
Alignment explanation
Indices: 28463338--28463383 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
28463328 TTGTTTAGCT
28463338 AAAATAA-AAAT-ATA
1 AAAATAATAAATAATA
*
28463352 AAAATAAT-AAGAATA
1 AAAATAATAAATAATA
28463367 AAAATATATAAATAATA
1 AAAATA-ATAAATAATA
28463384 GCAATAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 9 0.35
15 9 0.35
16 2 0.08
17 6 0.23
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAATAATAAATAATA
Found at i:28463390 original size:23 final size:23
Alignment explanation
Indices: 28463340--28463383 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
28463330 GTTTAGCTAA
28463340 AATAAAAATATAAAAATAATAAG
1 AATAAAAATATAAAAATAATAAG
*
28463363 AATAAAAATATATAAATAATA
1 AATAAAAATATAAAAATAATA
28463384 GCAATAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (23 bp):
AATAAAAATATAAAAATAATAAG
Found at i:28463527 original size:23 final size:21
Alignment explanation
Indices: 28463501--28463563 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
28463491 ATATTTTAAA
*
28463501 AAAATAATAATAAATGAAAAAT
1 AAAA-AATAATAAATAAAAAAT
28463523 GAAAAAAATAATAAATAAAAAAT
1 --AAAAAATAATAAATAAAAAAT
28463546 AAAAAATAAATAATATAA
1 AAAAAAT-AATAA-ATAA
28463564 TTGGAATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 7 0.19
22 5 0.14
23 20 0.56
24 4 0.11
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (21 bp):
AAAAAATAATAAATAAAAAAT
Found at i:28463544 original size:14 final size:14
Alignment explanation
Indices: 28463501--28463560 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
28463491 ATATTTTAAA
*
28463501 AAAATAATAATAAAT
1 AAAA-AATAAAAAAT
*
28463516 GAAAAATGAAAAAAAT
1 AAAAAAT--AAAAAAT
*
28463532 AATAAATAAAAAAT
1 AAAAAATAAAAAAT
*
28463546 AAAAAATAAATAAT
1 AAAAAATAAAAAAT
28463560 A
1 A
28463561 TAATTGGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 23 0.62
15 3 0.08
16 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
AAAAAATAAAAAAT
Found at i:28463564 original size:30 final size:30
Alignment explanation
Indices: 28463498--28463552 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
28463488 TATATATTTT
* *
28463498 AAAAA-AAT-AATAATAAATGAAAAATGAA
1 AAAAATAATAAATAAAAAATAAAAAATGAA
28463526 AAAAATAATAAATAAAAAATAAAAAAT
1 AAAAATAATAAATAAAAAATAAAAAAT
28463553 AAATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 5 0.22
29 3 0.13
30 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (30 bp):
AAAAATAATAAATAAAAAATAAAAAATGAA
Found at i:28475686 original size:62 final size:62
Alignment explanation
Indices: 28475611--28475924 Score: 456
Period size: 62 Copynumber: 5.1 Consensus size: 62
28475601 CGTTAAAGAA
* * ** *
28475611 TTTAAATTGAACCTGTTATGAGATAGGTCGAGCCTAGATTAAGTCTAGGAACCTCAATTTTA
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
* * * * * *
28475673 TTTAAATCAAACCTGTTATGAGATGGGTCTAGCCTAGATTAAGTCTAGAAATCTCAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
*
28475735 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAA---T-
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
* *
28475793 TTTAAATCAAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
* *
28475855 TTTAAATCGAACCTGTTGTAAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTG
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
28475917 TTTAAATC
1 TTTAAATC
28475925 NNNNNNNNNN
Statistics
Matches: 227, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
58 54 0.24
59 1 0.00
61 1 0.00
62 171 0.75
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (62 bp):
TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAGGAATTTCAATTTTG
Found at i:28475862 original size:120 final size:120
Alignment explanation
Indices: 28475611--28475915 Score: 466
Period size: 120 Copynumber: 2.5 Consensus size: 120
28475601 CGTTAAAGAA
* * * **
28475611 TTTAAATTGAACCTGTTATGAGATAGGTCGAGCCTAGATTAAGTCTAGGAACCTCAATTTTATTT
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAA---T-TTT
* *
28475676 AAATCAAACCTGTTATGAGATGGGTCTAGCCTAGATTAAGTCTAGAAATCTCAATTTTG
62 AAATCAAACCTGTTATGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATCTCAATTTTG
28475735 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTAAAT
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTAAAT
* * * *
28475800 CAAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTTTAGGAATTTCAATTTTG
66 CAAACCTGTTATGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATCTCAATTTTG
*
28475855 TTTAAATCGAACCTGTTGTAAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTT
1 TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTT
28475916 GTTTAAATCN
Statistics
Matches: 169, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
120 116 0.69
121 1 0.01
124 52 0.31
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (120 bp):
TTTAAATCGAACCTGTTGTGAGATAGGTCGAGCCTAGATTAAGTCTAAGAATTTCAATTTTAAAT
CAAACCTGTTATGAGATAGGTCGAGCCTAGATTAAGTCTAGAAATCTCAATTTTG
Found at i:28477288 original size:13 final size:12
Alignment explanation
Indices: 28477270--28477321 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 12
28477260 GCAGTTAGCC
28477270 ACAAAACAGAAAA
1 ACAAAACA-AAAA
*
28477283 ACAAAAGAAAGAA
1 ACAAAACAAA-AA
28477296 ACAAAACAAAAATA
1 ACAAAAC-AAAA-A
28477310 ACAAAA-AAAAA
1 ACAAAACAAAAA
28477321 A
1 A
28477322 GGGGTGAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
11 2 0.06
12 6 0.18
13 16 0.47
14 10 0.29
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.02
Consensus pattern (12 bp):
ACAAAACAAAAA
Found at i:28481387 original size:2 final size:2
Alignment explanation
Indices: 28481370--28481409 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
28481360 GAAAGGATAC
* *
28481370 AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28481410 TTAAGGGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:28481725 original size:52 final size:52
Alignment explanation
Indices: 28481625--28481749 Score: 135
Period size: 52 Copynumber: 2.4 Consensus size: 52
28481615 TCTTGCTAAA
* * * ** *
28481625 AAGAAAAATCTTTAAGTA-TTTTGAGCATTTTAGAGTGGTTTTTAATACACG
1 AAGAAAAACCTTTAAGCATTTTTAAATATTTTAGAGTGATTTTTAATACACG
* * * *
28481676 AAGAAAAACTTTTAAGCATTTTTAAATATTTTGGAGTGATTTTTGATACATG
1 AAGAAAAACCTTTAAGCATTTTTAAATATTTTAGAGTGATTTTTAATACACG
* *
28481728 AAGACAAACCTTTGAGCATTTT
1 AAGAAAAACCTTTAAGCATTTT
28481750 GATCATTTTT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 15 0.25
52 45 0.75
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (52 bp):
AAGAAAAACCTTTAAGCATTTTTAAATATTTTAGAGTGATTTTTAATACACG
Found at i:28481890 original size:22 final size:22
Alignment explanation
Indices: 28481860--28481932 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
28481850 TTTTGGTGGA
28481860 TTTTAGGCATTGCATAA-TCAAT
1 TTTTAGGCATTGCATAACT-AAT
* *
28481882 TTTTGGGCATTGCGTAACTAAT
1 TTTTAGGCATTGCATAACTAAT
*
28481904 TTTTAGGCATTGCATTACTAAT
1 TTTTAGGCATTGCATAACTAAT
28481926 TTTTAGG
1 TTTTAGG
28481933 TATTATGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.18, T:0.44
Consensus pattern (22 bp):
TTTTAGGCATTGCATAACTAAT
Found at i:28485548 original size:21 final size:20
Alignment explanation
Indices: 28485522--28485571 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
28485512 AAGATCTAAC
* * *
28485522 TAATATTAAGTTTTTTTTTTT
1 TAATATTAAG-TTATATTTAT
28485543 TAATATTAAGTTATATTTAT
1 TAATATTAAGTTATATTTAT
28485563 TAATATTAA
1 TAATATTAA
28485572 TGATTTCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (20 bp):
TAATATTAAGTTATATTTAT
Found at i:28489129 original size:28 final size:28
Alignment explanation
Indices: 28489089--28489145 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
28489079 ATGTACGCAA
28489089 AAAGGCGTGCTTGTAATAAATGGTGATT
1 AAAGGCGTGCTTGTAATAAATGGTGATT
*
28489117 AAAGGCGTGCTTGTGATAAATGGTGATT
1 AAAGGCGTGCTTGTAATAAATGGTGATT
28489145 A
1 A
28489146 GATTGACAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAGGCGTGCTTGTAATAAATGGTGATT
Found at i:28489291 original size:162 final size:162
Alignment explanation
Indices: 28489117--28489475 Score: 567
Period size: 162 Copynumber: 2.2 Consensus size: 162
28489107 AATGGTGATT
* *
28489117 AAAGGCGTGCTTGTGATAAATGGTGATTAGATTGACAAGGCCAAGGTTGTTCCCTATTCTAATAG
1 AAAGGCGTGCTTGTGATAAATGGTGATTAAATTGACAAGGCAAAGGTTGTTCCCTATTCTAATAG
* *
28489182 AAAGAAAAAAAAAATCCAAGACATGATTGTGTGGGTAGCAAAAAATATTGGAGACATGTCTGATA
66 AAAGAAAAAAAAAATCCAAGACATGATTGTGTGGGTAGCAAAAAATATTGGAGACATGACTAATA
**
28489247 CCGA-ATTAAGGCAGTATTGCTTATGTAGGAAA
131 -CGAGATTAAGGCAGTATTGCTTACATAGGAAA
28489279 AAAGGCGTGCTTGTGATAAATGGTGATTAAATTGACAAGGCAAAGGTTGTTCCCTATTCTAATAG
1 AAAGGCGTGCTTGTGATAAATGGTGATTAAATTGACAAGGCAAAGGTTGTTCCCTATTCTAATAG
* * * *
28489344 AAAGATAAAAAATATCGAAGACATGATTGTGTGTGTAGCAAAAAATATTGGAGACATGACTAATA
66 AAAGAAAAAAAAAATCCAAGACATGATTGTGTGGGTAGCAAAAAATATTGGAGACATGACTAATA
* * *
28489409 CTAGATTAAGGTAGTATTGCTTACATAGGAAG
131 CGAGATTAAGGCAGTATTGCTTACATAGGAAA
* *
28489441 AAAGACGTGCTTGTGATAAATGGTGATCAAATTGA
1 AAAGGCGTGCTTGTGATAAATGGTGATTAAATTGA
28489476 GGTCAAAATA
Statistics
Matches: 181, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
161 2 0.01
162 179 0.99
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.28
Consensus pattern (162 bp):
AAAGGCGTGCTTGTGATAAATGGTGATTAAATTGACAAGGCAAAGGTTGTTCCCTATTCTAATAG
AAAGAAAAAAAAAATCCAAGACATGATTGTGTGGGTAGCAAAAAATATTGGAGACATGACTAATA
CGAGATTAAGGCAGTATTGCTTACATAGGAAA
Found at i:28491003 original size:15 final size:15
Alignment explanation
Indices: 28490980--28491021 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
28490970 TATATTACCA
28490980 AGAATATGATTGTTG
1 AGAATATGATTGTTG
*
28490995 AGTATATGATTGTTG
1 AGAATATGATTGTTG
*
28491010 AGAATGTGATTG
1 AGAATATGATTG
28491022 CTAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.29, T:0.40
Consensus pattern (15 bp):
AGAATATGATTGTTG
Found at i:28491262 original size:21 final size:21
Alignment explanation
Indices: 28491238--28491277 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28491228 ATTTTAAGCA
28491238 ATTAAAACAATAA-ATAATAAC
1 ATTAAAA-AATAATATAATAAC
28491259 ATTAAAAAATAATATAATA
1 ATTAAAAAATAATATAATA
28491278 TTTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTAAAAAATAATATAATAAC
Found at i:28494392 original size:21 final size:21
Alignment explanation
Indices: 28494353--28494392 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28494343 ATTTTAAGCA
*
28494353 ATTAAAACAATAAATAATAAC
1 ATTAAAACAATAAAGAATAAC
28494374 ATTAAAA-AATAAAAGAATA
1 ATTAAAACAAT-AAAGAATA
28494393 TTTTTATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (21 bp):
ATTAAAACAATAAAGAATAAC
Found at i:28494985 original size:25 final size:25
Alignment explanation
Indices: 28494924--28494993 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
28494914 ACGGATAGTA
* *
28494924 AGAAGAAGGA-AAAGAAAGCAATGTG
1 AGAAGAAGGAGAAA-AAGGCAAGGTG
* *
28494949 TGAA-AAAGAGAAAAAGGCAAGGTG
1 AGAAGAAGGAGAAAAAGGCAAGGTG
28494973 AGAAGAAGGAGAAAAAGGCAA
1 AGAAGAAGGAGAAAAAGGCAA
28494994 AAAGGAAGAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
24 16 0.43
25 21 0.57
ACGTcount: A:0.57, C:0.04, G:0.33, T:0.06
Consensus pattern (25 bp):
AGAAGAAGGAGAAAAAGGCAAGGTG
Found at i:28496032 original size:29 final size:29
Alignment explanation
Indices: 28495999--28496056 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
28495989 TCAGAAATAG
28495999 TGAGAAATAAAT-AAGAAGTTCTTCTCTCA
1 TGAGAAATAAATCAA-AAGTTCTTCTCTCA
* *
28496028 TGAGAAATAAATCAAAAGTTTTTTTCTCA
1 TGAGAAATAAATCAAAAGTTCTTCTCTCA
28496057 ATTCTCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (29 bp):
TGAGAAATAAATCAAAAGTTCTTCTCTCA
Found at i:28516060 original size:89 final size:90
Alignment explanation
Indices: 28515886--28516063 Score: 306
Period size: 89 Copynumber: 2.0 Consensus size: 90
28515876 TCACAAGGAA
*
28515886 ACCAAATTCCATTCCCCTTGGACAATTGACTTTCAAGTTTGCAGCCCCCTTCACCTGAATCTTGC
1 ACCAAATTCCATTCCCCTTGGACAATTGACTTTCAAGTTTGCAGACCCCTTCACCTGAATCTTGC
*
28515951 TTCAATGAACCTTAACGGGTCGAAC
66 TTCAATGAACCTTAAAGGGTCGAAC
*
28515976 ACCAAATTCCATTCCCCTTGGACAATTGACTTTCAAG-TTGTCA-ACCCCTTCAGCTGAATCTTG
1 ACCAAATTCCATTCCCCTTGGACAATTGACTTTCAAGTTTG-CAGACCCCTTCACCTGAATCTTG
28516039 CTTCAATGAACCTTAAAGGGTCGAA
65 CTTCAATGAACCTTAAAGGGTCGAA
28516064 TCAGTAGCGG
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
89 45 0.54
90 39 0.46
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (90 bp):
ACCAAATTCCATTCCCCTTGGACAATTGACTTTCAAGTTTGCAGACCCCTTCACCTGAATCTTGC
TTCAATGAACCTTAAAGGGTCGAAC
Found at i:28518623 original size:2 final size:2
Alignment explanation
Indices: 28518616--28518642 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28518606 AAAATTCAAG
28518616 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28518643 NCCTACCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28518668 original size:2 final size:2
Alignment explanation
Indices: 28518661--28518725 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
28518651 ACAATTCAAG
28518661 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
28518701 AT AT AT -T AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
28518726 TAAGACCAAA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28522552 original size:2 final size:2
Alignment explanation
Indices: 28522545--28522569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28522535 AAATTTCTCT
28522545 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 T
28522570 GAGAATTTCN
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28522596 original size:2 final size:2
Alignment explanation
Indices: 28522589--28522613 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28522579 NTTTACTTCT
28522589 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 T
28522614 GAGAATTTCA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28523115 original size:19 final size:18
Alignment explanation
Indices: 28523090--28523134 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
28523080 AAAATTTTAG
28523090 TATTTAT-TTAGATAAATA
1 TATTTATATTA-ATAAATA
*
28523108 TATGTTATATTAATAATTA
1 TAT-TTATATTAATAAATA
28523127 TATTTATA
1 TATTTATA
28523135 GATTCTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 13 0.54
20 3 0.12
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (18 bp):
TATTTATATTAATAAATA
Found at i:28526172 original size:12 final size:12
Alignment explanation
Indices: 28526155--28526183 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
28526145 AGAAAGCCTA
28526155 AGCATAGTTGTC
1 AGCATAGTTGTC
28526167 AGCATAGTTGTC
1 AGCATAGTTGTC
28526179 AGCAT
1 AGCAT
28526184 CGTCTTCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (12 bp):
AGCATAGTTGTC
Found at i:28528944 original size:40 final size:40
Alignment explanation
Indices: 28528899--28528979 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
28528889 GTGCAGCATA
28528899 TGCATATCTTTGGTAAGTACTTACTTACTTATGAACCATC
1 TGCATATCTTTGGTAAGTACTTACTTACTTATGAACCATC
28528939 TGCATATCTTTGGTAAGTACTTACTTACTTATGAACCATC
1 TGCATATCTTTGGTAAGTACTTACTTACTTATGAACCATC
28528979 T
1 T
28528980 ACACGGTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (40 bp):
TGCATATCTTTGGTAAGTACTTACTTACTTATGAACCATC
Found at i:28546856 original size:2 final size:2
Alignment explanation
Indices: 28546851--28546910 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
28546841 TTTTTTTGAA
* * * * * * *
28546851 AT AT AT AT AA AT AA AT AA AT -T TT AT AT AT CT AA AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28546892 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
28546911 ATTTTGTTTA
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28546890 original size:14 final size:14
Alignment explanation
Indices: 28546865--28546911 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
28546855 ATATAAATAA
28546865 ATAAATTTTATATAT
1 ATAAA-TTTATATAT
*
28546880 CTAAATTTATATAT
1 ATAAATTTATATAT
* *
28546894 ATATATATATATAT
1 ATAAATTTATATAT
28546908 ATAA
1 ATAA
28546912 TTTTGTTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 23 0.85
15 4 0.15
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
ATAAATTTATATAT
Found at i:28589179 original size:22 final size:23
Alignment explanation
Indices: 28589153--28589202 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
28589143 ATATTTTGTA
*
28589153 ATATAAAATGGTATGAATATA-T
1 ATATAAAATGGTATAAATATATT
* * *
28589175 ATATATAATTGTATAAATGTATT
1 ATATAAAATGGTATAAATATATT
28589198 ATATA
1 ATATA
28589203 TAATTATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (23 bp):
ATATAAAATGGTATAAATATATT
Found at i:28589358 original size:543 final size:536
Alignment explanation
Indices: 28588317--28589411 Score: 1985
Period size: 543 Copynumber: 2.0 Consensus size: 536
28588307 AACTAATTTT
**
28588317 TTATATATTTATATATATAGTCATATAAATAATATTTTTTATATATTAAAAAGAATTGATAGTAA
1 TTATATATACATATATATAGTCATATAAATAATATTTTTTATATATTAAAAAGAATTGATAGTAA
28588382 ACTTAATTAATAATATATTTAAAATATATTAACGTATTGTACATACGTATATAAATCATAATCAT
66 ACTTAATTAATAATATATTTAAAATATATTAACGTATTGTACATACGTATATAAATCATAATCAT
*
28588447 AGTAATTTAATATTAATAACTATATATATAAACCTATATTAATATGAAATTACAAATTATATATT
131 AGTAATTTAATATTAATAACTATATATATAAACATATATTAATATGAAATTACAAATTATATATT
*
28588512 TTAAATGATATAATTTATATGTTAATATTATAATATATGATAGTAAATATTTTACATATTAATAT
196 TTAAATGATATAAGTTATATGTTAATATTATAATATATGATAGTAAATATTTTACATATTAATAT
28588577 GTTATAATTATTATACCTTAGTAATATTTTGTAATATAAAATGGTATGAATATATACATATAATT
261 GTTATAATTATTATACCTTAGTAATATTTTGTAATATAAAATGGTATGAATATATACATATAATT
28588642 GTATAAATATATTATATATACATATACATAAGCATTACTATAATTTATAATAAACTTTATTTGTA
326 GTATAAATATATTATATATACATATACATAAGCATTACTATAATTTATAATAAACTTTATTTGTA
28588707 TGATTATATTTAATAACTTCATTTGTTATCACCTTAGATTTTATAATATATTGTTTATAATTAGT
391 TGATTATATTTAATAACTTCATTTGTTATCACCTTAGATTTTATAATATATTGTTTATAATTAGT
28588772 TATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTAAGTCATTAATTATATATC
456 TATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTAAGTCATTAATTATATATC
28588837 TATAATAAAGTCATATA
521 TATAATAAA-TCATATA
28588854 TTATATATACATATNATATAGTCATATAAATAATATTTTTTATATATTAAAAAGAATTGATAGTA
1 TTATATATACATAT-ATATAGTCATATAAATAATATTTTTTATATATTAAAAAGAATTGATAGTA
28588919 AACTTAATTAATAATATATTTAAAATATATTAACGTATTGTACATACGTATATAAATCATAATCA
65 AACTTAATTAATAATATATTTAAAATATATTAACGTATTGTACATACGTATATAAATCATAATCA
* * * *
28588984 TAGTAATTTAATATTAATTATATTTATTTATTTATAAATATGTATTAATATGAAATTACAAATTA
130 TAGTAATTTAATATTAA-TA-A-CTA--TATATATAAACATATATTAATATGAAATTACAAATTA
*
28589049 TATATTTTAAATGATATAAGTTATGTGTTAATATTATAATATATGATAGTAAATATTTTACATAT
190 TATATTTTAAATGATATAAGTTATATGTTAATATTATAATATATGATAGTAAATATTTTACATAT
*
28589114 TAATATGTTATAATTATTATACCTTAGTAATATTTTGTAATATAAAATGGTATGAATATATATAT
255 TAATATGTTATAATTATTATACCTTAGTAATATTTTGTAATATAAAATGGTATGAATATATACAT
* *
28589179 ATAATTGTATAAATGTATTATATATA-ATTATACATGAGCATTACTATAATTTATAATAAACTTT
320 ATAATTGTATAAATATATTATATATACA-TATACATAAGCATTACTATAATTTATAATAAACTTT
28589243 ATTTGTATGATTATATTTAATAACTTCATTTGTTATCACCTTAGATTTTATAATATATTGTTTAT
384 ATTTGTATGATTATATTTAATAACTTCATTTGTTATCACCTTAGATTTTATAATATATTGTTTAT
* *
28589308 AATTAGTTATTATTTATACAAATTTTGATATAAAACATTATAATATATAAGTTATGTCATTAATT
449 AATTAGTTATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTAAGTCATTAATT
28589373 ATATATCTATAATAAATCATATA
514 ATATATCTATAATAAATCATATA
28589396 TTATATATACATATAT
1 TTATATATACATATAT
28589412 TTAATTTATA
Statistics
Matches: 537, Mismatches: 14, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
537 12 0.02
538 132 0.25
539 2 0.00
540 1 0.00
541 4 0.01
542 22 0.04
543 364 0.68
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.45
Consensus pattern (536 bp):
TTATATATACATATATATAGTCATATAAATAATATTTTTTATATATTAAAAAGAATTGATAGTAA
ACTTAATTAATAATATATTTAAAATATATTAACGTATTGTACATACGTATATAAATCATAATCAT
AGTAATTTAATATTAATAACTATATATATAAACATATATTAATATGAAATTACAAATTATATATT
TTAAATGATATAAGTTATATGTTAATATTATAATATATGATAGTAAATATTTTACATATTAATAT
GTTATAATTATTATACCTTAGTAATATTTTGTAATATAAAATGGTATGAATATATACATATAATT
GTATAAATATATTATATATACATATACATAAGCATTACTATAATTTATAATAAACTTTATTTGTA
TGATTATATTTAATAACTTCATTTGTTATCACCTTAGATTTTATAATATATTGTTTATAATTAGT
TATTATTTATACAAATTTTGATATAAAACATTATAACATATAAGTTAAGTCATTAATTATATATC
TATAATAAATCATATA
Found at i:28589443 original size:23 final size:21
Alignment explanation
Indices: 28589396--28589444 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
28589386 AAATCATATA
*
28589396 TTATATATACATATATTTAAT
1 TTATATATACATATATTTAAC
28589417 TTATATATAAGCAT-TATTATAAC
1 TTATATAT-A-CATATATT-TAAC
28589440 TTATA
1 TTATA
28589445 ATAGACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 8 0.33
22 5 0.21
23 11 0.46
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATATATACATATATTTAAC
Found at i:28589471 original size:131 final size:124
Alignment explanation
Indices: 28589336--28589590 Score: 316
Period size: 125 Copynumber: 2.0 Consensus size: 124
28589326 CAAATTTTGA
* * *
28589336 TATAAAACATTATAATATATAAGTTATGTCATTAATTATATATCTATAATA-AATCATA-TATTA
1 TATAAAACATTATAATAT-T-A-TT-TATAAATAATTATATA--TATAATAGAAT-ATATTA-TA
* * *
28589399 TATATACATATATTTAATTTATATATAAGCATTATTATAACTTATAATAGACTTTATTTATATGA
58 TATATACATATATTTAATTCA-ACATAAGCATTATTATAACTTATAATAAACTTTATTTATATGA
28589464 TTG
122 TTG
*
28589467 TATAAAACATTTTAATATTATTTATAAATAATTATATATATAATATGAATATATTATATATATAC
1 TATAAAACATTATAATATTATTTATAAATAATTATATATATAATA-GAATATATTATATATATAC
* * *
28589532 ATATATTTAATTCAACATAAGTATTATTGTAACTTATAATAAATTTTATTTATATGATT
65 ATATATTTAATTCAACATAAGCATTATTATAACTTATAATAAACTTTATTTATATGATT
28589591 ACAGTTATTA
Statistics
Matches: 111, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
125 47 0.42
126 25 0.23
127 18 0.16
128 2 0.02
129 1 0.01
130 1 0.01
131 17 0.15
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (124 bp):
TATAAAACATTATAATATTATTTATAAATAATTATATATATAATAGAATATATTATATATATACA
TATATTTAATTCAACATAAGCATTATTATAACTTATAATAAACTTTATTTATATGATTG
Found at i:28589525 original size:22 final size:22
Alignment explanation
Indices: 28589493--28589535 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28589483 ATTATTTATA
28589493 AATAATTATATATATA-ATATG
1 AATAATTATATATATACATATG
28589514 AATATATTATATATATACATAT
1 AATA-ATTATATATATACATAT
28589536 ATTTAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (22 bp):
AATAATTATATATATACATATG
Found at i:28589529 original size:17 final size:18
Alignment explanation
Indices: 28589499--28589538 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
28589489 TATAAATAAT
28589499 TATA-TATATAATATGA-A
1 TATATTATATAATAT-ACA
28589516 TATATTATAT-ATATACA
1 TATATTATATAATATACA
28589533 TATATT
1 TATATT
28589539 TAATTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 15 0.71
18 5 0.24
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
TATATTATATAATATACA
Found at i:28589644 original size:14 final size:16
Alignment explanation
Indices: 28589625--28589661 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
28589615 TACTTTAGTT
28589625 TTTATAA-TA-TATTA
1 TTTATAATTAGTATTA
28589639 TTTATAATTAGTTATTA
1 TTTATAATTAG-TATTA
28589656 TTTATA
1 TTTATA
28589662 CAAACTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
17 11 0.55
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATAATTAGTATTA
Found at i:28591574 original size:2 final size:2
Alignment explanation
Indices: 28591567--28591602 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28591557 ATTTTCCTAC
28591567 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
28591603 GTACTTTAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28599632 original size:105 final size:105
Alignment explanation
Indices: 28599496--28599712 Score: 274
Period size: 114 Copynumber: 2.0 Consensus size: 105
28599486 CTAATGTTAT
* *
28599496 GTGCAAGACCAAACCCTTATTGACCAGATAAACGGTTTAACACTATTG-GTTGTTGGAACTTAGA
1 GTGCAAGACCAAACCCTGATTGACCAGATAAACAG-TTAACACTATTGTGTTGTTGGAACTTAGA
*
28599560 TATAAACAAGGAACCTGAAAGAGTGACCTAGACAATGACAC
65 TATAAACAAGGAACCTGAAAAAGTGACCTAGACAATGACAC
* * * *
28599601 GTGCAAGACCTAACCCTGATTGACCAGATAAACAGTTAGCACTTTTGTTTTTTTCCATTTGTTGG
1 GTGCAAGACCAAACCCTGATTGACCAGATAAACAGTTAACACTATTG------T---GTTGTTGG
28599666 AACTTAGATATAAACAAGGAACCTGAAAAAGTGACCTAGACAATGAC
57 AACTTAGATATAAACAAGGAACCTGAAAAAGTGACCTAGACAATGAC
28599713 CATTACTACT
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
104 10 0.11
105 32 0.34
114 53 0.56
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (105 bp):
GTGCAAGACCAAACCCTGATTGACCAGATAAACAGTTAACACTATTGTGTTGTTGGAACTTAGAT
ATAAACAAGGAACCTGAAAAAGTGACCTAGACAATGACAC
Found at i:28599816 original size:29 final size:29
Alignment explanation
Indices: 28599774--28599832 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
28599764 TAAATCTTAT
28599774 CTACAGAACTACCTCAGAAGTCCTTGATA
1 CTACAGAACTACCTCAGAAGTCCTTGATA
28599803 CTACAGAACTACCTCAGAAGTCCTTGATA
1 CTACAGAACTACCTCAGAAGTCCTTGATA
28599832 C
1 C
28599833 ATAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.24
Consensus pattern (29 bp):
CTACAGAACTACCTCAGAAGTCCTTGATA
Found at i:28599950 original size:63 final size:64
Alignment explanation
Indices: 28599840--28599963 Score: 223
Period size: 63 Copynumber: 1.9 Consensus size: 64
28599830 TACATAAATT
28599840 AAAAATAGAGGTCAGATAACAATCCTTGTTTGAATCCTTCATCCAATCACCTCTAAGGACAAGCC
1 AAAAATAGAGGTCAGATAACAAT-CTTGTTTGAATCCTTCATCCAATCACCTCTAAGGACAAGCC
*
28599905 AAAAATAGAGGTCAGATAACAAT-TTGTTTGAATCCTTCATCCAATCATCTCTAAGGACA
1 AAAAATAGAGGTCAGATAACAATCTTGTTTGAATCCTTCATCCAATCACCTCTAAGGACA
28599964 TTATATAGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
63 35 0.60
65 23 0.40
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.27
Consensus pattern (64 bp):
AAAAATAGAGGTCAGATAACAATCTTGTTTGAATCCTTCATCCAATCACCTCTAAGGACAAGCC
Found at i:28604851 original size:2 final size:2
Alignment explanation
Indices: 28604844--28604868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28604834 ACCCCACAAT
28604844 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28604869 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28616741 original size:2 final size:2
Alignment explanation
Indices: 28616729--28616763 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28616719 TTCAAACAAT
* *
28616729 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28616764 CAAAGCTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:28625164 original size:15 final size:15
Alignment explanation
Indices: 28625117--28625399 Score: 68
Period size: 15 Copynumber: 19.5 Consensus size: 15
28625107 TATTTTATTT
28625117 TTTAAATATTAATAA
1 TTTAAATATTAATAA
*
28625132 TTT--ATA--ATTAA
1 TTTAAATATTAATAA
*
28625143 TTAAAATATTAATAA
1 TTTAAATATTAATAA
*
28625158 TTTAAATATCAAT-A
1 TTTAAATATTAATAA
*
28625172 TTT---TAAT-ATAA
1 TTTAAATATTAATAA
* * *
28625183 TTTAATTACTAATAT
1 TTTAAATATTAATAA
* *
28625198 TTTAATTAATAAT-A
1 TTTAAATATTAATAA
*
28625212 TTT---TATTTATAA
1 TTTAAATATTAATAA
* *
28625224 TTT-AATATTATTGTTA
1 TTTAAATATTA--ATAA
*
28625240 TTAAAATATTAATAA
1 TTTAAATATTAATAA
* * * *
28625255 TTTTAATTTTTATAT
1 TTTAAATATTAATAA
*
28625270 TCATTAAAAATTTAATATA
1 T--TTAAATA-TTAATA-A
*
28625289 TTAATAAT-TTAATAA
1 TTTA-AATATTAATAA
* * * *
28625304 ATAAAACATTAATAG
1 TTTAAATATTAATAA
28625319 TTTAAAATATTAAT-A
1 TTT-AAATATTAATAA
* *
28625334 TTTAATATTTTAATTA
1 TTTAA-ATATTAATAA
28625350 TATT-AATATTAATAA
1 T-TTAAATATTAATAA
*
28625365 TATTTAA-ATTATATAA
1 T-TTAAATATTA-ATAA
*
28625381 ---AAATATTAATAT
1 TTTAAATATTAATAA
28625393 TTTAAAT
1 TTTAAAT
28625400 TTTATAAATA
Statistics
Matches: 194, Mismatches: 43, Indels: 62
0.65 0.14 0.21
Matches are distributed among these distances:
10 2 0.01
11 17 0.09
12 9 0.05
13 10 0.05
14 18 0.09
15 87 0.45
16 28 0.14
17 15 0.08
18 7 0.04
19 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:28625187 original size:25 final size:25
Alignment explanation
Indices: 28625154--28625207 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
28625144 TAAAATATTA
28625154 ATAATTTAAATA-TCAATATTTTAAT
1 ATAATTTAAATACT-AATATTTTAAT
*
28625179 ATAATTTAATTACTAATATTTTAAT
1 ATAATTTAAATACTAATATTTTAAT
28625204 -TAAT
1 ATAAT
28625208 AATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 4 0.15
25 22 0.81
26 1 0.04
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
ATAATTTAAATACTAATATTTTAAT
Found at i:28625291 original size:16 final size:16
Alignment explanation
Indices: 28625272--28625355 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 16
28625262 TTTTATATTC
28625272 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
28625288 ATTAATAATTTAATA-
1 ATTAAAAATTTAATAT
*
28625303 AATAAAACA-TTAATAGT
1 ATTAAAA-ATTTAATA-T
28625320 -TT-AAAATATTAATAT
1 ATTAAAAAT-TTAATAT
* *
28625335 -TTAATATTTTAATTAT
1 ATTAAAAATTTAA-TAT
28625351 ATTAA
1 ATTAA
28625356 TATTAATAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
14 1 0.02
15 21 0.39
16 28 0.52
17 4 0.07
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:28625292 original size:8 final size:8
Alignment explanation
Indices: 28625281--28625397 Score: 64
Period size: 8 Copynumber: 14.5 Consensus size: 8
28625271 CATTAAAAAT
28625281 TTAATATA
1 TTAATATA
28625289 TTAATA-A
1 TTAATATA
28625296 TTTAATA-A
1 -TTAATATA
* * *
28625304 ATAAAACA
1 TTAATATA
28625312 TTAATAGT-
1 TTAATA-TA
*
28625320 TTAAAATA
1 TTAATATA
28625328 TTAATAT-
1 TTAATATA
*
28625335 TTAATATT
1 TTAATATA
28625343 TTAATTATA
1 TTAA-TATA
28625352 TTAATATTA
1 TTAATA-TA
*
28625361 ATAATAT-
1 TTAATATA
28625368 TTAAATTATA
1 TT-AA-TATA
* *
28625378 TAAAAATA
1 TTAATATA
*
28625386 TTAATATT
1 TTAATATA
28625394 TTAA
1 TTAA
28625398 ATTTTATAAA
Statistics
Matches: 84, Mismatches: 15, Indels: 20
0.71 0.13 0.17
Matches are distributed among these distances:
7 14 0.17
8 50 0.60
9 19 0.23
10 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (8 bp):
TTAATATA
Found at i:28625338 original size:23 final size:22
Alignment explanation
Indices: 28625312--28625399 Score: 68
Period size: 25 Copynumber: 3.6 Consensus size: 22
28625302 AAATAAAACA
28625312 TTAATAGTTTAAAATATTAATAT
1 TTAATA-TTTAAAATATTAATAT
*
28625335 TTAATATTTTAATTATATTAATAT
1 TTAATA-TTTAA-AATATTAATAT
* *
28625359 TAATAATATTTAAATTATATAAAAAT
1 T--TAATATTTAAA--ATATTAATAT
*
28625385 ATTAATATTTTAAAT
1 -TTAATATTTAAAAT
28625400 TTTATAAATA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
23 13 0.25
24 11 0.21
25 15 0.28
26 13 0.25
27 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (22 bp):
TTAATATTTAAAATATTAATAT
Found at i:28625367 original size:39 final size:39
Alignment explanation
Indices: 28625202--28625368 Score: 102
Period size: 39 Copynumber: 4.3 Consensus size: 39
28625192 TAATATTTTA
* * **
28625202 ATTAATAATATT--TTATTT-ATAATTTAATATTATTGTT
1 ATTAATAATATTAATAATTTAATATTTTAATA-TATTAAT
*
28625239 ATTAA-AATATTAATAATTTTAAT-TTTT-ATATTCATTAAAA
1 ATTAATAATATTAATAA-TTTAATATTTTAATA-T-ATT-AAT
** * *
28625279 ATTTAAT-ATATTAATAATTTAATA-AATAAAACATTAAT
1 A-TTAATAATATTAATAATTTAATATTTTAATATATTAAT
28625317 AGTTTAA-AATATTAAT-ATTTAATATTTTAATTATATTAAT
1 A--TTAATAATATTAATAATTTAATATTTTAA-TATATTAAT
28625357 ATTAATAATATT
1 ATTAATAATATT
28625369 TAAATTATAT
Statistics
Matches: 101, Mismatches: 14, Indels: 28
0.71 0.10 0.20
Matches are distributed among these distances:
36 6 0.06
37 5 0.05
38 22 0.22
39 34 0.34
40 18 0.18
41 16 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (39 bp):
ATTAATAATATTAATAATTTAATATTTTAATATATTAAT
Found at i:28625369 original size:26 final size:25
Alignment explanation
Indices: 28625325--28625397 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
28625315 ATAGTTTAAA
28625325 ATATTAATATT-TAATATTTTAATT
1 ATATTAATATTATAATATTTTAATT
*
28625349 ATATTAATATTAATAATATTTAAATT
1 ATATTAATATT-ATAATATTTTAATT
* *
28625375 ATA-TAAAAATATTAATATTTTAA
1 ATATTAATATTA-TAATATTTTAA
28625398 ATTTTATAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 12 0.29
25 15 0.36
26 15 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTAATATTATAATATTTTAATT
Found at i:28625422 original size:26 final size:26
Alignment explanation
Indices: 28625286--28625407 Score: 91
Period size: 23 Copynumber: 5.0 Consensus size: 26
28625276 AAAATTTAAT
* *
28625286 ATATTAATAATTT-AA-TAAAT-AAA
1 ATATTAATATTTTAAATTATATAAAA
* * * *
28625309 ACATTAATAGTTTAAA--ATATTAAT
1 ATATTAATATTTTAAATTATATAAAA
*
28625333 AT-TTAATATTTT-AATTATAT--TA
1 ATATTAATATTTTAAATTATATAAAA
28625355 ATATTAATAATATTTAAATTATATAAAA
1 ATATTAAT-AT-TTTAAATTATATAAAA
*
28625383 ATATTAATATTTTAAATTTTATAAA
1 ATATTAATATTTTAAATTATATAAA
28625408 TAATTTATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
22 4 0.05
23 28 0.35
24 11 0.14
25 3 0.04
26 22 0.28
27 2 0.03
28 9 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATTAATATTTTAAATTATATAAAA
Found at i:28626035 original size:14 final size:16
Alignment explanation
Indices: 28626002--28626042 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
28625992 CTTTTAAGAG
28626002 AATAGCTATTACTAAGT
1 AATAGCTATTA-TAAGT
28626019 AATAGCTATT-T-AGT
1 AATAGCTATTATAAGT
28626033 AATAGCTATT
1 AATAGCTATT
28626043 CTTTGTGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 13 0.54
15 1 0.04
17 10 0.42
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (16 bp):
AATAGCTATTATAAGT
Found at i:28628089 original size:14 final size:14
Alignment explanation
Indices: 28628060--28628098 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28628050 ATTTAAAATC
28628060 AATAATTAT-A-AA
1 AATAATTATAACAA
28628072 AATAATTATAACAA
1 AATAATTATAACAA
*
28628086 AATAATAATAACA
1 AATAATTATAACA
28628099 TCAAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.38
13 1 0.04
14 14 0.58
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (14 bp):
AATAATTATAACAA
Found at i:28628761 original size:25 final size:25
Alignment explanation
Indices: 28628707--28628767 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
28628697 AATATATGCT
* *
28628707 TTATT-TAAT-TTAATTTTAAAATA
1 TTATTATAATATTAATATAAAAATA
28628730 -TATTTATAATATTAATATAAAAATA
1 TTA-TTATAATATTAATATAAAAATA
*
28628755 TTATTATATTATT
1 TTATTATAATATT
28628768 TGATAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 2 0.06
23 2 0.06
24 4 0.13
25 21 0.68
26 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTATTATAATATTAATATAAAAATA
Found at i:28635331 original size:25 final size:25
Alignment explanation
Indices: 28635272--28635332 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 25
28635262 ATGCATTTTT
28635272 ATTTAATTT-AAAATAAAAATATAAA
1 ATTT-ATTTAAAAATAAAAATATAAA
*
28635297 ACTTGA-TTAAAAATAAAAA-ATAACA
1 A-TTTATTTAAAAATAAAAATATAA-A
28635322 ATTTATTTAAA
1 ATTTATTTAAA
28635333 TTTTTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
24 9 0.30
25 19 0.63
26 2 0.07
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (25 bp):
ATTTATTTAAAAATAAAAATATAAA
Found at i:28635635 original size:11 final size:11
Alignment explanation
Indices: 28635619--28635678 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 11
28635609 TTTGAACCTT
28635619 TTTATTTTAAA
1 TTTATTTTAAA
*
28635630 TTTATTTTAAT
1 TTTATTTTAAA
**
28635641 TTTATCTATT-TT
1 TTTAT-T-TTAAA
28635653 TTTAATTTTAAA
1 TTT-ATTTTAAA
28635665 TTTATTTT-AA
1 TTTATTTTAAA
28635675 TTTA
1 TTTA
28635679 GTGAGAAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.15
11 22 0.54
12 9 0.22
13 4 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATTTTAAA
Found at i:28635637 original size:17 final size:17
Alignment explanation
Indices: 28635617--28635677 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
28635607 CATTTGAACC
*
28635617 TTTTTATTTTAAATTTA
1 TTTTAATTTTAAATTTA
*
28635634 TTTTAATTTTATCTATTT-
1 TTTTAATTTTA--AATTTA
28635652 TTTTAATTTTAAATTTA
1 TTTTAATTTTAAATTTA
28635669 TTTTAATTT
1 TTTTAATTT
28635678 AGTGAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.11
17 19 0.50
18 11 0.29
19 4 0.11
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTAATTTTAAATTTA
Found at i:28636977 original size:20 final size:20
Alignment explanation
Indices: 28636912--28636980 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 20
28636902 ATACTTTAAG
28636912 AATT-AAATGATCATCAATC
1 AATTAAAATGATCATCAATC
* **
28636931 AATATATAAATAAGAACATTTAT-
1 AAT-TA-AAAT--GATCATCAATC
28636954 AATTAAAATGATCATCAATC
1 AATTAAAATGATCATCAATC
28636974 AATTAAA
1 AATTAAA
28636981 TAGATATGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
19 10 0.26
20 8 0.21
21 4 0.11
22 6 0.16
23 3 0.08
24 7 0.18
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (20 bp):
AATTAAAATGATCATCAATC
Found at i:28637944 original size:13 final size:13
Alignment explanation
Indices: 28637918--28637960 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
28637908 TTCTTTCATT
28637918 TTAATTTTAAAATA
1 TTAA-TTTAAAATA
* *
28637932 TTTATTTATAATA
1 TTAATTTAAAATA
28637945 TTAATTTAAAATA
1 TTAATTTAAAATA
28637958 TTA
1 TTA
28637961 TTATATTCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 22 0.88
14 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAATTTAAAATA
Found at i:28645617 original size:17 final size:18
Alignment explanation
Indices: 28645588--28645626 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
28645578 AAATTAATAC
28645588 TTGA-TAAATTAATAATT
1 TTGATTAAATTAATAATT
*
28645605 TTGATTAAA-TAATATTT
1 TTGATTAAATTAATAATT
28645622 TTGAT
1 TTGAT
28645627 CGGTCTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (18 bp):
TTGATTAAATTAATAATT
Found at i:28649837 original size:20 final size:18
Alignment explanation
Indices: 28649804--28649840 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
28649794 GGAGAGTAGG
28649804 AAAATTTATTAATTAATT
1 AAAATTTATTAATTAATT
28649822 AAAATATTATTTAATTAAT
1 AAAAT-TTA-TTAATTAAT
28649841 AAATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 3 0.18
20 9 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATTTATTAATTAATT
Found at i:28649846 original size:16 final size:16
Alignment explanation
Indices: 28649810--28649852 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
28649800 TAGGAAAATT
28649810 TATTAATTAATTAAAA
1 TATTAATTAATTAAAA
*
28649826 TATTATTTAATTAATAA
1 TATTAATTAATTAA-AA
28649843 -ATTAA-TAATT
1 TATTAATTAATT
28649853 TATTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATTAATTAATTAAAA
Found at i:28649853 original size:20 final size:20
Alignment explanation
Indices: 28649812--28649890 Score: 55
Period size: 19 Copynumber: 4.2 Consensus size: 20
28649802 GGAAAATTTA
*
28649812 TTAATTAATTAAAATATTAT
1 TTAATTAATTAAAATATAAT
*
28649832 TTAATTAA-TAAATTAATAAT
1 TTAATTAATTAAAAT-ATAAT
**
28649852 TT-ATT-ATT-TTATAT-A-
1 TTAATTAATTAAAATATAAT
*
28649867 TTAATTAATAAAAAT-TAAT
1 TTAATTAATTAAAATATAAT
28649886 TTAAT
1 TTAAT
28649891 AAGATATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 15
0.66 0.12 0.22
Matches are distributed among these distances:
15 2 0.05
16 4 0.09
17 5 0.11
18 5 0.11
19 14 0.32
20 14 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATTAATTAAAATATAAT
Found at i:28649872 original size:27 final size:26
Alignment explanation
Indices: 28649809--28649890 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 26
28649799 GTAGGAAAAT
28649809 TTATTAATTAATTAAAATATTATTTAA
1 TTATTAATTAA-TAAAATATTATTTAA
* ** *
28649836 TTAATAAATTAATAATTTATTATTTTA
1 TT-ATTAATTAATAAAATATTATTTAA
28649863 TATATTAATTAATAAAA-ATTAATTTAA
1 T-TATTAATTAATAAAATATT-ATTTAA
28649890 T
1 T
28649891 AAGATATTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 3 0.07
27 32 0.73
28 9 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTATTAATTAATAAAATATTATTTAA
Found at i:28650334 original size:21 final size:21
Alignment explanation
Indices: 28650287--28650336 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
28650277 TCGTGTATAT
*
28650287 ATATAATTTTAATGTATAAAG
1 ATATTATTTTAATGTATAAAG
* * * *
28650308 AAATTATTTTGATGTATGAGG
1 ATATTATTTTAATGTATAAAG
28650329 ATATTATT
1 ATATTATT
28650337 AATTTATATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (21 bp):
ATATTATTTTAATGTATAAAG
Found at i:28650453 original size:17 final size:18
Alignment explanation
Indices: 28650433--28650470 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
28650423 TAAATCAATA
28650433 TTAATTAAAATTATT-AT
1 TTAATTAAAATTATTAAT
28650450 TTAATTAAAATTATTAAT
1 TTAATTAAAATTATTAAT
28650468 TTA
1 TTA
28650471 TCGAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTAAAATTATTAAT
Found at i:28664935 original size:60 final size:60
Alignment explanation
Indices: 28664830--28664955 Score: 182
Period size: 60 Copynumber: 2.1 Consensus size: 60
28664820 AAAGAAAAAT
* * *
28664830 TTTTAAGTATTTTGAGCATTTTTGAGTAATTTTTGATACACGAAAAAAAACTTTTGAACA
1 TTTTGAGTATTTTAAGCATTTTTGAGTAATTTTTGATACACGAAAAAAAACCTTTGAACA
* * *
28664890 TTTTGAGTATTTTAAGTA-TTTTGAAGTAATTTTTGATATATGAAAAAAAACCTTTGAACA
1 TTTTGAGTATTTTAAGCATTTTTG-AGTAATTTTTGATACACGAAAAAAAACCTTTGAACA
28664950 TTTTGA
1 TTTTGA
28664956 ACATTCTTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 5 0.08
60 54 0.92
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (60 bp):
TTTTGAGTATTTTAAGCATTTTTGAGTAATTTTTGATACACGAAAAAAAACCTTTGAACA
Found at i:28665112 original size:44 final size:44
Alignment explanation
Indices: 28665062--28665152 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
28665052 AGTTTTTGTG
* * * * *
28665062 GTTTTTAAATATTATGTAA-TCGGTTTTTGGATATTATGTGACTA
1 GTTTTTAAATATTACGTAACT-GATTTTTAGATATTACGTAACTA
*
28665106 GTTTTTAAGTATTACGTAACTGATTTTTAGATATTACGTAACTA
1 GTTTTTAAATATTACGTAACTGATTTTTAGATATTACGTAACTA
28665150 GTT
1 GTT
28665153 GATATGACAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.48
Consensus pattern (44 bp):
GTTTTTAAATATTACGTAACTGATTTTTAGATATTACGTAACTA
Found at i:28665132 original size:22 final size:22
Alignment explanation
Indices: 28665063--28665148 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
28665053 GTTTTTGTGG
* * *
28665063 TTTTTAAATATTATGTAA-TCGG
1 TTTTTAGATATTACGTAACT-GA
* * *
28665085 TTTTTGGATATTATGTGACT-A
1 TTTTTAGATATTACGTAACTGA
28665106 GTTTTTA-AGTATTACGTAACTGA
1 -TTTTTAGA-TATTACGTAACTGA
28665129 TTTTTAGATATTACGTAACT
1 TTTTTAGATATTACGTAACT
28665149 AGTTGATATG
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
21 1 0.02
22 48 0.92
23 3 0.06
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (22 bp):
TTTTTAGATATTACGTAACTGA
Found at i:28668886 original size:23 final size:23
Alignment explanation
Indices: 28668769--28668886 Score: 75
Period size: 22 Copynumber: 5.2 Consensus size: 23
28668759 ATAATATTAA
28668769 ATATTATTTAATTATAATAAAAG
1 ATATTATTTAATTATAATAAAAG
* * * *
28668792 GT-TTAATTATCTTCA-AATACAAG
1 ATATTATTTA-ATT-ATAATAAAAG
* *
28668815 ATATTATTAAATTATGATAAAA-
1 ATATTATTTAATTATAATAAAAG
* * * *
28668837 ATA-TATTTGTATTTTGATGAAA-
1 ATATTATTT-AATTATAATAAAAG
28668859 ATATTATTTAATTATAATAAAAG
1 ATATTATTTAATTATAATAAAAG
*
28668882 GTATT
1 ATATT
28668887 TTAATTTTAT
Statistics
Matches: 69, Mismatches: 19, Indels: 14
0.68 0.19 0.14
Matches are distributed among these distances:
21 4 0.06
22 32 0.46
23 27 0.39
24 6 0.09
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (23 bp):
ATATTATTTAATTATAATAAAAG
Found at i:28696059 original size:2 final size:2
Alignment explanation
Indices: 28696052--28696149 Score: 105
Period size: 2 Copynumber: 51.0 Consensus size: 2
28696042 AAGACTTCAA
* *
28696052 AG AG AG AG A- AG A- AG AA AG AG AG AA AG -G AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* * * * *
28696090 AG AG AG AG AG AG AG AG AG AG AG AG AG TG TG TG TG TG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28696132 AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG
28696150 GACTGTTTGA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
1 4 0.05
2 82 0.95
ACGTcount: A:0.48, C:0.00, G:0.47, T:0.05
Consensus pattern (2 bp):
AG
Found at i:28703172 original size:3 final size:3
Alignment explanation
Indices: 28703166--28703195 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28703156 GAAGGAGGAT
*
28703166 AAG AAG ACG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
28703196 CGAAGATCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:28714843 original size:15 final size:16
Alignment explanation
Indices: 28714823--28714859 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
28714813 ATGCGATAAT
28714823 ATATAATAATTT-TTA
1 ATATAATAATTTGTTA
28714838 ATATAA-AATTTGTTA
1 ATATAATAATTTGTTA
*
28714853 ATTTAAT
1 ATATAAT
28714860 TTATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
ATATAATAATTTGTTA
Found at i:28731837 original size:17 final size:18
Alignment explanation
Indices: 28731817--28731850 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28731807 ATTTAAAAAA
28731817 GAAATAAA-AATAAAATT
1 GAAATAAACAATAAAATT
28731834 GAAATAAACAATAAAAT
1 GAAATAAACAATAAAAT
28731851 AAGCTTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.21
Consensus pattern (18 bp):
GAAATAAACAATAAAATT
Found at i:28734205 original size:17 final size:17
Alignment explanation
Indices: 28734183--28734215 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28734173 TCGGCACCAC
28734183 AAAACAAAAAAAATAAA
1 AAAACAAAAAAAATAAA
*
28734200 AAAACAAAGAAAATAA
1 AAAACAAAAAAAATAA
28734216 TAGCAGCCCT
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:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAACAAAAAAAATAAA
Found at i:28734310 original size:12 final size:12
Alignment explanation
Indices: 28734272--28734310 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28734262 CCCAGAAGGG
*
28734272 AACCACAAAACAA
1 AACCA-AAAAAAA
*
28734285 AACCAAGAAAAA
1 AACCAAAAAAAA
28734297 AACCAAAAAAAA
1 AACCAAAAAAAA
28734309 AA
1 AA
28734311 AACCTCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.77, C:0.21, G:0.03, T:0.00
Consensus pattern (12 bp):
AACCAAAAAAAA
Found at i:28759336 original size:3 final size:3
Alignment explanation
Indices: 28759330--28759360 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
28759320 GTGTGTCCGT
28759330 GAG GAG GAG GAG GAG GAG GAGG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GA-G GAG GAG GAG
28759361 ATATGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:28759343 original size:39 final size:36
Alignment explanation
Indices: 28759269--28759340 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
28759259 TTCCCTTTTT
28759269 TTTTAAAAAAAATTGGTGTGTCCGTGAGGAGGAGGA
1 TTTTAAAAAAAATTGGTGTGTCCGTGAGGAGGAGGA
28759305 NTTTTAAAAAAAA-TGGTGTGTCCGTGAGGAGGAGGA
1 -TTTTAAAAAAAATTGGTGTGTCCGTGAGGAGGAGGA
28759341 GGAGGAGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.26
Consensus pattern (36 bp):
TTTTAAAAAAAATTGGTGTGTCCGTGAGGAGGAGGA
Found at i:28762154 original size:40 final size:40
Alignment explanation
Indices: 28762109--28762250 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
28762099 GATCTTAAAC
* **
28762109 CATAAACTTAAATAACTAAAAATAAATATCCATACAACGA
1 CATAAACTTAAATAACTAAAAATAAATATCCAAACAAAAA
* * * * * *
28762149 TATAAACTTGAATAACTATATATAAATATCCAAATAATAA
1 CATAAACTTAAATAACTAAAAATAAATATCCAAACAAAAA
* * *
28762189 CATAAACTTAAATAACTAAACACAAAGATCCAAACAAAAAA
1 CATAAACTTAAATAACTAAAAATAAATATCCAAAC-AAAAA
*
28762230 CATAAACTTAAATAACCAAAA
1 CATAAACTTAAATAACTAAAA
28762251 TTATAATTTT
Statistics
Matches: 83, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
40 60 0.72
41 23 0.28
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (40 bp):
CATAAACTTAAATAACTAAAAATAAATATCCAAACAAAAA
Found at i:28764159 original size:27 final size:27
Alignment explanation
Indices: 28764103--28764159 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
28764093 TTAACTGATC
* * *
28764103 AATTATTAAGATTTCAAATTAATTATA
1 AATTATTAAGATTTAAAATAAAATATA
*
28764130 AATTATTAATATTTTAAAATAAAATA-A
1 AATTATTAAGA-TTTAAAATAAAATATA
28764157 AAT
1 AAT
28764160 AAAAATAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTATTAAGATTTAAAATAAAATATA
Found at i:28764255 original size:15 final size:15
Alignment explanation
Indices: 28764237--28764278 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
28764227 TAAATTATAA
28764237 TTAATTATTAATATT
1 TTAATTATTAATATT
28764252 TTAATTA--AAT-TT
1 TTAATTATTAATATT
*
28764264 TAAATTATTAATATT
1 TTAATTATTAATATT
28764279 AAAAAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 3 0.13
15 9 0.39
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAATTATTAATATT
Found at i:28764295 original size:12 final size:12
Alignment explanation
Indices: 28764278--28764324 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
28764268 TTATTAATAT
28764278 TAAAAAATATAA
1 TAAAAAATATAA
*
28764290 TAAAAATAAATAA
1 TAAAAA-ATATAA
*
28764303 TTAAATAA-ATAA
1 -TAAAAAATATAA
28764315 TAAAAAATAT
1 TAAAAAATAT
28764325 TTTTATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.21
12 12 0.41
13 6 0.21
14 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAAAATATAA
Found at i:28766892 original size:39 final size:39
Alignment explanation
Indices: 28766849--28766940 Score: 112
Period size: 39 Copynumber: 2.4 Consensus size: 39
28766839 TTCAATTGAT
* *
28766849 TTAATGGATGGTAGTAAGCAAAGGATTGGTTGAGTCAAC
1 TTAATGGATGGTAGCAAGCAAAGGAGTGGTTGAGTCAAC
* * * * *
28766888 TTAATGGATGGCAACGAGGAAAGGAGTGGTTGAGTCCAC
1 TTAATGGATGGTAGCAAGCAAAGGAGTGGTTGAGTCAAC
*
28766927 TTAATGGATTGTAG
1 TTAATGGATGGTAG
28766941 AGCCTTCACG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.32, C:0.09, G:0.33, T:0.27
Consensus pattern (39 bp):
TTAATGGATGGTAGCAAGCAAAGGAGTGGTTGAGTCAAC
Found at i:28780672 original size:18 final size:18
Alignment explanation
Indices: 28780615--28780666 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
28780605 AGTTCTACAA
28780615 ATAATTTATAAGTAACAC
1 ATAATTTATAAGTAACAC
28780633 ATAATTTATAAGTAACAC
1 ATAATTTATAAGTAACAC
*
28780651 ATAATTTATAAATAAC
1 ATAATTTATAAGTAAC
28780667 TTATAAACTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.35
Consensus pattern (18 bp):
ATAATTTATAAGTAACAC
Found at i:28780728 original size:17 final size:16
Alignment explanation
Indices: 28780706--28780754 Score: 71
Period size: 16 Copynumber: 3.0 Consensus size: 16
28780696 AATTATTNAC
28780706 AAAATAAAAAATAAAAT
1 AAAATAAAAAA-AAAAT
*
28780723 AAAATAAAAAAAAAAA
1 AAAATAAAAAAAAAAT
*
28780739 AAAAAAAAAAAAAAAT
1 AAAATAAAAAAAAAAT
28780755 TTTAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 18 0.62
17 11 0.38
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAATAAAAAAAAAAT
Found at i:28780732 original size:1 final size:1
Alignment explanation
Indices: 28780706--28780753 Score: 60
Period size: 1 Copynumber: 48.0 Consensus size: 1
28780696 AATTATTNAC
* * * *
28780706 AAAATAAAAAATAAAATAAAATAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28780754 TTTTAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (1 bp):
A
Found at i:28781545 original size:21 final size:21
Alignment explanation
Indices: 28781511--28781550 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28781501 CTTATATATA
*
28781511 TTTTAAAATATTAATACTTAG
1 TTTTAAAATATTAAAACTTAG
* *
28781532 TTTTAAATTTTTAAAACTT
1 TTTTAAAATATTAAAACTT
28781551 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTTAAAATATTAAAACTTAG
Found at i:28783207 original size:291 final size:291
Alignment explanation
Indices: 28782671--28783246 Score: 861
Period size: 291 Copynumber: 2.0 Consensus size: 291
28782661 TATCCAGAAG
* * *
28782671 GTTCCAGAAAAGCAGGAAATTGAGGCCAAAAAAGGGAGAGGCCGCCTCCGGGGGAGGAAAAAGAA
1 GTTCCAGAAAACCAGGAAATTGAGGCAAAAAAAGGGAGAGGCCGCATCCGGGGGAGGAAAAAGAA
* * *
28782736 TCAGCAGGAAGAAAATTTAGATGAAAAAGAAACAAACTTGATCGAAAAAGATGGAACTATTCACA
66 TCAGCAGGAAGAAAATTTAGAGGAAAAAGAAACAAACTTGATAGAAAAAGATGGAACTATTAACA
** * * *
28782801 TAAAAGATGGAGTGGATGAAGAGGAGGAGTCGAGTTCGTTGCAAAACAAGGATATTAATGCAAGA
131 TAAAAGATAAAGTGGATGAAGAGGAGGAGCCAAGTTCGATGCAAAACAAGGATATTAATGCAAGA
* * *
28782866 AAAGATGAGGAGAAAGTGGAGGATTCGAAGAATGGGGTTAAGGAGAGTTGTGAT-GAAGGGATAG
196 AAAGATGAAGAGAAAGTGGAAGATTCGAAGAATGAGGTTAAGGAGAGTTGTGATGGAAGGG-TAG
*
28782930 ATGTGAATTTGGAGAAGATGACATTAAGGAGA
260 AGGTGAATTTGGAGAAGATGACATTAAGGAGA
* * *
28782962 GTTCCGGAAAACCAGGAAATTGAGGTAAAAAAAGGGAGAGGCTGCAAT-CGGGGGAGGAAAAAGA
1 GTTCCAGAAAACCAGGAAATTGAGGCAAAAAAAGGGAGAGGCCGC-ATCCGGGGGAGGAAAAAGA
* *
28783026 ATCAGCAGGAAGAGAAA-TTAGAGGAAAAAGAAGCAAACTTGATAGAAAAAGATGGAATTATTAA
65 ATCAGCAGGAAGA-AAATTTAGAGGAAAAAGAAACAAACTTGATAGAAAAAGATGGAACTATTAA
* * * *
28783090 CATAAAAGATAAAGTGGATGAGGAGGAGGAGCCAAGTTCGATGCCAAACGAGGATATTAATGTAA
129 CATAAAAGATAAAGTGGATGAAGAGGAGGAGCCAAGTTCGATGCAAAACAAGGATATTAATGCAA
* *
28783155 GAAAAGATGAAGAGAAAGTGGAAGATTTGAAGAATGAGGTTAAGGAGAGTTGTGATGGAAGGGTG
194 GAAAAGATGAAGAGAAAGTGGAAGATTCGAAGAATGAGGTTAAGGAGAGTTGTGATGGAAGGGTA
*
28783220 GAGGTGGATTTGGAGAAGATGACATTA
259 GAGGTGAATTTGGAGAAGATGACATTA
28783247 GGGGAGTGGT
Statistics
Matches: 255, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
291 245 0.96
292 10 0.04
ACGTcount: A:0.43, C:0.08, G:0.32, T:0.17
Consensus pattern (291 bp):
GTTCCAGAAAACCAGGAAATTGAGGCAAAAAAAGGGAGAGGCCGCATCCGGGGGAGGAAAAAGAA
TCAGCAGGAAGAAAATTTAGAGGAAAAAGAAACAAACTTGATAGAAAAAGATGGAACTATTAACA
TAAAAGATAAAGTGGATGAAGAGGAGGAGCCAAGTTCGATGCAAAACAAGGATATTAATGCAAGA
AAAGATGAAGAGAAAGTGGAAGATTCGAAGAATGAGGTTAAGGAGAGTTGTGATGGAAGGGTAGA
GGTGAATTTGGAGAAGATGACATTAAGGAGA
Found at i:28790214 original size:33 final size:33
Alignment explanation
Indices: 28790177--28790245 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
28790167 ATTAAATTAG
* *
28790177 TATATTACATCGTTATTAATTATGATATGTAAA
1 TATATTACATCATCATTAATTATGATATGTAAA
* *
28790210 TATATTACATTATCATTAATTATGATATGTTAA
1 TATATTACATCATCATTAATTATGATATGTAAA
28790243 TAT
1 TAT
28790246 GCCACGTCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (33 bp):
TATATTACATCATCATTAATTATGATATGTAAA
Found at i:28790841 original size:2 final size:2
Alignment explanation
Indices: 28790834--28790883 Score: 56
Period size: 2 Copynumber: 27.0 Consensus size: 2
28790824 TAAATGTATG
28790834 TA TA TA TA -A TA TA T- TA CT- TA T- TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
28790872 TA TA TA TA TA TA
1 TA TA TA TA TA TA
28790884 GATGAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
1 5 0.12
2 36 0.86
3 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28790870 original size:13 final size:13
Alignment explanation
Indices: 28790834--28790880 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
28790824 TAAATGTATG
*
28790834 TATATATAATATA
1 TATATATATTATA
28790847 T-TACT-TATTATA
1 TATA-TATATTATA
28790859 TATATATATTATA
1 TATATATATTATA
28790872 TATATATAT
1 TATATATAT
28790881 ATAGATGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATATTATA
Found at i:28790948 original size:26 final size:26
Alignment explanation
Indices: 28790918--28790967 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
28790908 ATATTATAAC
28790918 GTTTTATATCAAAGTTTGTATAAAAT
1 GTTTTATATCAAAGTTTGTATAAAAT
*
28790944 GTTTTATATCAAATTTTGTATAAA
1 GTTTTATATCAAAGTTTGTATAAA
28790968 TAATATGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (26 bp):
GTTTTATATCAAAGTTTGTATAAAAT
Found at i:28790957 original size:14 final size:14
Alignment explanation
Indices: 28790918--28790957 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
28790908 ATATTATAAC
28790918 GTTTTATATCAAA-
1 GTTTTATATCAAAT
28790931 GTTTGTATA--AAAT
1 GTTT-TATATCAAAT
28790944 GTTTTATATCAAAT
1 GTTTTATATCAAAT
28790958 TTTGTATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 7 0.30
13 8 0.35
14 8 0.35
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (14 bp):
GTTTTATATCAAAT
Found at i:28793965 original size:2 final size:2
Alignment explanation
Indices: 28793958--28793995 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28793948 GTACATTGAC
28793958 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28793996 CTATTTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28794992 original size:8 final size:8
Alignment explanation
Indices: 28794963--28795003 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
28794953 CATGTTCTTG
*
28794963 TATATATA
1 TATATGTA
*
28794971 TATATATA
1 TATATGTA
28794979 TATATGTA
1 TATATGTA
28794987 TATATGTA
1 TATATGTA
*
28794995 TGTATGTA
1 TATATGTA
28795003 T
1 T
28795004 TTTCTGCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (8 bp):
TATATGTA
Found at i:28794996 original size:12 final size:12
Alignment explanation
Indices: 28794963--28794999 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
28794953 CATGTTCTTG
*
28794963 TATATATATATA
1 TATATATATGTA
28794975 TATATATATGTA
1 TATATATATGTA
*
28794987 TATATGTATGTA
1 TATATATATGTA
28794999 T
1 T
28795000 GTATTTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (12 bp):
TATATATATGTA
Found at i:28798362 original size:22 final size:21
Alignment explanation
Indices: 28798337--28798411 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
28798327 TATCATCTAC
28798337 CACAAACCAGCAGTAAATCAAT
1 CACAAACCAGCAG-AAATCAAT
**
28798359 CACAAACCAGCAAGAAATCTCT
1 CACAAACCAGC-AGAAATCAAT
** * *
28798381 CACAAAATAGCACCAAATCATT
1 CACAAACCAGCA-GAAATCAAT
28798403 CACAAACCA
1 CACAAACCA
28798412 ATAGCTAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 1 0.02
22 39 0.93
23 2 0.05
ACGTcount: A:0.49, C:0.31, G:0.07, T:0.13
Consensus pattern (21 bp):
CACAAACCAGCAGAAATCAAT
Found at i:28798652 original size:30 final size:30
Alignment explanation
Indices: 28798616--28798677 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
28798606 TCTGTTTCAA
*
28798616 AGTTGTTTCTTCTGCCTACTACCTTACTTG
1 AGTTGTTTCTTCTGCCTACAACCTTACTTG
* * *
28798646 AGTTGTTTTTTCTGTCTACAATCTTACTTG
1 AGTTGTTTCTTCTGCCTACAACCTTACTTG
28798676 AG
1 AG
28798678 CAGGTTGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.16, C:0.21, G:0.15, T:0.48
Consensus pattern (30 bp):
AGTTGTTTCTTCTGCCTACAACCTTACTTG
Found at i:28799793 original size:27 final size:27
Alignment explanation
Indices: 28799693--28799791 Score: 144
Period size: 27 Copynumber: 3.7 Consensus size: 27
28799683 GCCTGCGAGA
* *
28799693 AGAGAGAAAGTGGAGAGGCCAGCGAGA
1 AGAGAGAAAGTGGAGAGGCCAGCGGGT
*
28799720 AGAGAGAAAGTGGAGAGGCCAACGGGT
1 AGAGAGAAAGTGGAGAGGCCAGCGGGT
* *
28799747 AGAGAGAAGGTGGAGAGGTCAGCGGGT
1 AGAGAGAAAGTGGAGAGGCCAGCGGGT
*
28799774 AGAGAGAAGGTGGAGAGG
1 AGAGAGAAAGTGGAGAGG
28799792 TCGACGACTA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.36, C:0.08, G:0.48, T:0.07
Consensus pattern (27 bp):
AGAGAGAAAGTGGAGAGGCCAGCGGGT
Found at i:28799803 original size:27 final size:27
Alignment explanation
Indices: 28799687--28799807 Score: 136
Period size: 27 Copynumber: 4.5 Consensus size: 27
28799677 GTGGTGGCCT
* *
28799687 GCGAGAAGAGAGAAAGTGGAGAGGCCA
1 GCGAGTAGAGAGAAAGTGGAGAGGTCA
* *
28799714 GCGAGAAGAGAGAAAGTGGAGAGGCCA
1 GCGAGTAGAGAGAAAGTGGAGAGGTCA
* * *
28799741 ACGGGTAGAGAGAAGGTGGAGAGGTCA
1 GCGAGTAGAGAGAAAGTGGAGAGGTCA
* *
28799768 GCGGGTAGAGAGAAGGTGGAGAGGTC-
1 GCGAGTAGAGAGAAAGTGGAGAGGTCA
*
28799794 GACGACTAGAGAGA
1 G-CGAGTAGAGAGA
28799808 GAAAATGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
26 1 0.01
27 84 0.99
ACGTcount: A:0.36, C:0.10, G:0.46, T:0.07
Consensus pattern (27 bp):
GCGAGTAGAGAGAAAGTGGAGAGGTCA
Found at i:28800237 original size:3 final size:3
Alignment explanation
Indices: 28800224--28800255 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
28800214 TAATATTACA
28800224 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28800256 TCATAATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:28800296 original size:9 final size:9
Alignment explanation
Indices: 28800280--28800316 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28800270 TATATATTTT
28800280 AAAAAAATA
1 AAAAAAATA
*
28800289 AGAAAAATA
1 AAAAAAATA
28800298 AAAAAAATA
1 AAAAAAATA
28800307 AAAAAAATA
1 AAAAAAATA
28800316 A
1 A
28800317 TAAATAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (9 bp):
AAAAAAATA
Found at i:28805663 original size:22 final size:22
Alignment explanation
Indices: 28805638--28805695 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
28805628 AACCAGTAGT
* *
28805638 AAATCAATCAC-AAATAAGCAAG
1 AAATCACTCACAAAAT-AGCAAC
* *
28805660 AAATCTCTCACAAAATAGCACC
1 AAATCACTCACAAAATAGCAAC
28805682 AAATCACTCACAAA
1 AAATCACTCACAAA
28805696 CCAATAGCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.53, C:0.26, G:0.05, T:0.16
Consensus pattern (22 bp):
AAATCACTCACAAAATAGCAAC
Found at i:28817780 original size:6 final size:6
Alignment explanation
Indices: 28817769--28817806 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
28817759 CCCTTGTCTG
* *
28817769 AACCTT AACCTT AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA
28817807 TTTCTCTTCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (6 bp):
AACCCT
Found at i:28822147 original size:2 final size:2
Alignment explanation
Indices: 28822140--28822187 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28822130 ATGTTTTGTG
28822140 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
28822182 TA TA TA
1 TA TA TA
28822188 NGTTATAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28822200 original size:99 final size:93
Alignment explanation
Indices: 28822077--28822277 Score: 235
Period size: 99 Copynumber: 2.1 Consensus size: 93
28822067 GTAAATATCC
28822077 TACATAT-TAATATGTTATAATTATTACACCTTAATAAT-ATTCAATAATATAAAATGTTTTGTG
1 TACATATAT-ATA-GTTATAATTATTACACCTTAATAATGATTC-ATAATATAAAATG--TTGTG
* *
28822140 TATATATATATATATATATATATATATATATATATA
61 AATATATATATA-AT-TATATAAATATAT-TATATA
* * * * *
28822176 TATATATATATANGTTATAATTATTACACTTTAGTAATGTTTCGTAATATAAAATGTTGTGAATA
1 TACATATATATA-GTTATAATTATTACACCTTAATAATGATTCATAATATAAAATGTTGTGAATA
*
28822241 TATATATAATTGTATAAATATATTATATA
65 TATATATAATTATATAAATATATTATATA
28822270 TACATATA
1 TACATATA
28822278 ATTAATTTAT
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
94 13 0.14
95 11 0.12
96 2 0.02
97 16 0.18
99 44 0.49
100 4 0.04
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (93 bp):
TACATATATATAGTTATAATTATTACACCTTAATAATGATTCATAATATAAAATGTTGTGAATAT
ATATATAATTATATAAATATATTATATA
Found at i:28822290 original size:17 final size:16
Alignment explanation
Indices: 28822240--28822292 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
28822230 TGTTGTGAAT
*
28822240 ATATATATAATTGTATAA
1 ATATAT-TAATT-TATAC
*
28822258 ATATATT-ATATATAC
1 ATATATTAATTTATAC
28822273 ATATAATTAATTTATAC
1 ATAT-ATTAATTTATAC
28822290 ATA
1 ATA
28822293 AATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 8 0.27
16 5 0.17
17 11 0.37
18 6 0.20
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (16 bp):
ATATATTAATTTATAC
Found at i:28839033 original size:6 final size:6
Alignment explanation
Indices: 28839022--28839048 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28839012 AAAGCTAGTG
28839022 TTGGAA TTGGAA TTGGAA TTGGAA TTG
1 TTGGAA TTGGAA TTGGAA TTGGAA TTG
28839049 CTGTTGCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (6 bp):
TTGGAA
Found at i:28840736 original size:2 final size:2
Alignment explanation
Indices: 28840729--28840755 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28840719 TGGATGTGCC
28840729 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
28840756 GTAATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28855847 original size:17 final size:17
Alignment explanation
Indices: 28855825--28855865 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
28855815 CGAAATAAGT
28855825 TTTAAAGATAATATCTA
1 TTTAAAGATAATATCTA
28855842 TTTAAAGATAATATCTA
1 TTTAAAGATAATATCTA
*
28855859 TTGAAAG
1 TTTAAAG
28855866 GCTCGCCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (17 bp):
TTTAAAGATAATATCTA
Found at i:28866996 original size:2 final size:2
Alignment explanation
Indices: 28866991--28867025 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
28866981 CACTAGTGTG
*
28866991 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28867026 CNNNNNNNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:28867099 original size:2 final size:2
Alignment explanation
Indices: 28867061--28867091 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
28867051 NNNNNNNNNN
*
28867061 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28867092 CCATATATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.