Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold1984.1
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: 321480
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1193 characters in sequence are not A, C, G, or T
Found at i:2757 original size:21 final size:21
Alignment explanation
Indices: 2731--2770 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2721 TTATTAAATG
2731 TGTCGTATTTATATCAAGGAT
1 TGTCGTATTTATATCAAGGAT
2752 TGTCGTATTTATATCAAGG
1 TGTCGTATTTATATCAAGG
2771 GTTTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (21 bp):
TGTCGTATTTATATCAAGGAT
Found at i:9302 original size:27 final size:27
Alignment explanation
Indices: 9264--9318 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
9254 CAAGTCAAGC
*
9264 TCTTCCAAAGATTCTGCTTGCTGCAAA
1 TCTTCCAAAGATTCTGCCTGCTGCAAA
*
9291 TCTTCCGAAGATTCTGCCTGCTGCAAA
1 TCTTCCAAAGATTCTGCCTGCTGCAAA
9318 T
1 T
9319 TCTCTGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (27 bp):
TCTTCCAAAGATTCTGCCTGCTGCAAA
Found at i:9790 original size:3 final size:3
Alignment explanation
Indices: 9782--9811 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9772 TTGTTTTCTA
9782 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9812 TTAAAACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:20371 original size:20 final size:20
Alignment explanation
Indices: 20346--20385 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
20336 TTAACGCAAT
20346 AGGGAAAAAACTATGGGAAC
1 AGGGAAAAAACTATGGGAAC
*
20366 AGGGAAAGAACTATGGGAAC
1 AGGGAAAAAACTATGGGAAC
20386 TGTTTTCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.33, T:0.10
Consensus pattern (20 bp):
AGGGAAAAAACTATGGGAAC
Found at i:21474 original size:16 final size:16
Alignment explanation
Indices: 21453--21487 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21443 TATAAAAGTT
21453 ATAAAAAATT-AAAACA
1 ATAAAAAATTCAAAA-A
21469 ATAAAAAATTCAAAAA
1 ATAAAAAATTCAAAAA
21485 ATA
1 ATA
21488 TATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (16 bp):
ATAAAAAATTCAAAAA
Found at i:21848 original size:12 final size:12
Alignment explanation
Indices: 21804--21854 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
21794 AACGAGTAAA
21804 ATATCTATTAAT
1 ATATCTATTAAT
*
21816 ATATATA-TATAT
1 ATATCTATTA-AT
* *
21828 ATAT-AATTAAA
1 ATATCTATTAAT
21839 ATATCTATTAAT
1 ATATCTATTAAT
21851 ATAT
1 ATAT
21855 ATAAATTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATCTATTAAT
Found at i:28466 original size:21 final size:21
Alignment explanation
Indices: 28440--28480 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28430 ATCTACTCAA
* *
28440 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
28461 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
28481 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:32529 original size:20 final size:21
Alignment explanation
Indices: 32504--32545 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
32494 GAAAATATAT
* *
32504 TTTCCATTCAA-TTTTCTATC
1 TTTCCAATCAAGTTTTCCATC
32524 TTTCCAATCAAGTTTTCCATC
1 TTTCCAATCAAGTTTTCCATC
32545 T
1 T
32546 CTTTAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTCCAATCAAGTTTTCCATC
Found at i:33144 original size:14 final size:15
Alignment explanation
Indices: 33118--33148 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
33108 TCCAGGTTCA
33118 TCAACACATTTTTCT
1 TCAACACATTTTTCT
33133 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
33147 TC
1 TC
33149 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:33583 original size:16 final size:16
Alignment explanation
Indices: 33562--33594 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33552 AAAAGTTATA
33562 AAAAAATT-AAAACAAT
1 AAAAAATTCAAAA-AAT
33578 AAAAAATTCAAAAAAT
1 AAAAAATTCAAAAAAT
33594 A
1 A
33595 TATAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAATTCAAAAAAT
Found at i:37694 original size:91 final size:90
Alignment explanation
Indices: 37535--37714 Score: 288
Period size: 91 Copynumber: 2.0 Consensus size: 90
37525 TAGAAACGCC
* *
37535 GCTATAGGTAGAGTATTAGCGGCGATTCCGAAAAAGCGCCGCAAAAATGTTAATCAGTACGCATC
1 GCTATAGGTAGAGTATTAGCGGCGATTCCAAAAAAGCGCCACAAAAATGTTAATCAGTACGCATC
37600 GTTTTACTTTAGCTTCTAGTCGAAA
66 GTTTTACTTTAGCTTCTAGTCGAAA
* * * **
37625 GCTATATGTGGAGTATTAGCGGCGCTTGTAAAAAAGCGCCACAAAAAATGTTAATCAGTACGCAT
1 GCTATAGGTAGAGTATTAGCGGCGATTCCAAAAAAGCGCCAC-AAAAATGTTAATCAGTACGCAT
37690 CGTTTTACTTTAGCTTCTAGTCGAA
65 CGTTTTACTTTAGCTTCTAGTCGAA
37715 CTATCGGCAC
Statistics
Matches: 82, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
90 35 0.43
91 47 0.57
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (90 bp):
GCTATAGGTAGAGTATTAGCGGCGATTCCAAAAAAGCGCCACAAAAATGTTAATCAGTACGCATC
GTTTTACTTTAGCTTCTAGTCGAAA
Found at i:41011 original size:87 final size:87
Alignment explanation
Indices: 40862--41032 Score: 265
Period size: 87 Copynumber: 2.0 Consensus size: 87
40852 TTTTTTCAGC
* *
40862 AGTGTTAATGCATTCATATTCTCGGCCAATTTGAAGCAGTTAATGGCTTTAAAGGAACCCGAA-C
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGAACCCGAATC
40926 CTGA-TAAATTGCATACTTCACGT
66 C--ACTAAATTGCATACTTCACGT
* * *
40949 AGTGTTAATGCATTGATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGCAGCCGAATC
1 AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGAACCCGAATC
41014 CACTAAATTGCATACTTCA
66 CACTAAATTGCATACTTCA
41033 AGTGAAGAAC
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
86 1 0.01
87 74 0.96
88 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (87 bp):
AGTGTTAATGCATTCATATTCTCAGCCAATTTGAAGCAGTTAATGGCTCTAAAGGAACCCGAATC
CACTAAATTGCATACTTCACGT
Found at i:43084 original size:14 final size:15
Alignment explanation
Indices: 43058--43088 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
43048 TCCAGGTTCA
43058 TCAACACATTTTTCT
1 TCAACACATTTTTCT
43073 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
43087 TC
1 TC
43089 CCATTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:50809 original size:14 final size:15
Alignment explanation
Indices: 50785--50813 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50775 CAGGTTCATT
50785 AACACATTTTTCTTC
1 AACACATTTTTCTTC
50800 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
50814 CCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:61354 original size:19 final size:18
Alignment explanation
Indices: 61306--61356 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
61296 AACTAAAAAA
61306 TAAAAAATTTA-AAATCT
1 TAAAAAATTTATAAATCT
*
61323 TATAAAATCTTATAGAAGT-T
1 TAAAAAAT-TTATA-AA-TCT
61343 TAAAAAATTTATAA
1 TAAAAAATTTATAA
61357 TTAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
17 7 0.25
18 4 0.14
19 6 0.21
20 10 0.36
21 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (18 bp):
TAAAAAATTTATAAATCT
Found at i:62378 original size:18 final size:17
Alignment explanation
Indices: 62346--62379 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
62336 CTGTTTGTGT
*
62346 TGCTTTTATATGTTATA
1 TGCTTTTAGATGTTATA
62363 TGCTTTTAAGATGTTAT
1 TGCTTTT-AGATGTTAT
62380 TTAAATCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGCTTTTAGATGTTATA
Found at i:63424 original size:30 final size:30
Alignment explanation
Indices: 63390--63524 Score: 148
Period size: 30 Copynumber: 4.4 Consensus size: 30
63380 CATAATTTAA
*
63390 TTTTAATT-TTTAGGTTATGTACATTCTATG
1 TTTT-ATTATTTATGTTATGTACATTCTATG
*
63420 TTTTATTATTTATGTTATGTACATACTATG
1 TTTTATTATTTATGTTATGTACATTCTATG
* * *
63450 TCTTATTATTTTATCATTTATGTTATTATT-TATG
1 TTTTATTA-TTTAT--GTTATG-TA-CATTCTATG
*
63484 TTTTATTATTTATGTTATGTTCATTCTATG
1 TTTTATTATTTATGTTATGTACATTCTATG
63514 TTTTATTATTT
1 TTTTATTATTT
63525 TATTTAATTT
Statistics
Matches: 88, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
29 6 0.07
30 47 0.53
31 10 0.11
33 10 0.11
34 13 0.15
35 2 0.02
ACGTcount: A:0.23, C:0.06, G:0.09, T:0.62
Consensus pattern (30 bp):
TTTTATTATTTATGTTATGTACATTCTATG
Found at i:63475 original size:12 final size:12
Alignment explanation
Indices: 63455--63501 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
63445 CTATGTCTTA
* *
63455 TTATTTTATCAT
1 TTATGTTATTAT
63467 TTATGTTATTAT
1 TTATGTTATTAT
63479 TTATGTTTTATTAT
1 TTATG--TTATTAT
63493 TTATGTTAT
1 TTATGTTAT
63502 GTTCATTCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 19 0.61
14 12 0.39
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (12 bp):
TTATGTTATTAT
Found at i:63487 original size:26 final size:29
Alignment explanation
Indices: 63458--63524 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 29
63448 TGTCTTATTA
*
63458 TTTTATCATTTATGTTA-TT-ATT-TATG
1 TTTTATTATTTATGTTAGTTCATTCTATG
63484 TTTTATTATTTATGTTATGTTCATTCTATG
1 TTTTATTATTTATGTTA-GTTCATTCTATG
63514 TTTTATTATTT
1 TTTTATTATTT
63525 TATTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 16 0.44
28 2 0.06
29 3 0.08
30 15 0.42
ACGTcount: A:0.21, C:0.04, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTTATTATTTATGTTAGTTCATTCTATG
Found at i:64191 original size:160 final size:159
Alignment explanation
Indices: 63690--64229 Score: 845
Period size: 157 Copynumber: 3.4 Consensus size: 159
63680 TAAAAAAATG
** * * * *
63690 AAAATAGTATATTTACTGAAAGTAATAAAATTCGAAAAAAAGAAAATTACGAACAAAGGGTCAAA
1 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
* * * * * * * *
63755 ATAAAGGTTTTTTACTAAA-TT-TATAATAAAACACACTAAAATAATATATTTTAGACATTATGT
66 ATAAGGGGTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACTTTATGT
63818 ACTAAAATAATATAAAATAATAAAATACA
131 ACTAAAATAATATAAAATAATAAAATACA
*
63847 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAATGGCCAAA
1 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
* *
63912 ATAAGGGGTTTTTACTAAATTTATATAAAAAAACAC-C-AAATTAATACATTTCTAATTTTATGT
66 ATAAGGGGTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACTTTATGT
63975 ACTAAAATAATATAAAATAATAAAATACA
131 ACTAAAATAATATAAAATAATAAAATACA
* * *
64004 AAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAACAAATGACCAAA
1 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
64069 ATAAGGGGTTTTTACTAAATTTATATTAAAAAAACACACTAAATTAATACATTTCAAACTTTATG
66 ATAAGGGGTTTTTACTAAATTTATA-TAAAAAAACACACTAAATTAATACATTTCAAACTTTATG
**
64134 TACTAAAATAATATAAAATAATAAAATATG
130 TACTAAAATAATATAAAATAATAAAATACA
64164 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
1 AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
64229 A
66 A
64230 AATCGGGAAA
Statistics
Matches: 352, Mismatches: 26, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
157 211 0.60
158 14 0.04
159 13 0.04
160 114 0.32
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.29
Consensus pattern (159 bp):
AAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAACAAAGGGCCAAA
ATAAGGGGTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAACTTTATGT
ACTAAAATAATATAAAATAATAAAATACA
Found at i:91473 original size:65 final size:65
Alignment explanation
Indices: 91369--91498 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
91359 ACTACTTAAC
91369 ATAATTGTCAGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT
1 ATAATTGTCAGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT
91434 ATAATTGTCAGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT
1 ATAATTGTCAGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT
91499 TCAATCCTAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (65 bp):
ATAATTGTCAGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT
Found at i:91512 original size:65 final size:65
Alignment explanation
Indices: 91378--91512 Score: 227
Period size: 65 Copynumber: 2.1 Consensus size: 65
91368 CATAATTGTC
** *
91378 AGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGTATAATTGTC
1 AGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGTATAATCCTA
91443 AGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGT-TCAATCCT
1 AGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGTAT-AATCCT
91507 A
65 A
91508 AGCAA
1 AGCAA
91513 TCCTATTTTC
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
64 1 0.02
65 65 0.98
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (65 bp):
AGCAACCTCTTGGCCTATTTACAAAAGCTTGGTTTTGTAGGTACGAGAGCTTGGGTATAATCCTA
Found at i:92789 original size:20 final size:20
Alignment explanation
Indices: 92748--92791 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
92738 TTTCTATTTC
*
92748 ATTAATTATATATTTATTTT
1 ATTAATTATATATTTATATT
*
92768 ATTAATTAGTGTATTTA-ATT
1 ATTAATTA-TATATTTATATT
92788 ATTA
1 ATTA
92792 TTTAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTAATTATATATTTATATT
Found at i:95512 original size:20 final size:20
Alignment explanation
Indices: 95471--95514 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
95461 TTTCTATTTC
*
95471 ATTAATTATATATTTATTTT
1 ATTAATTATATATTTATATT
*
95491 ATTAATTAGTGTATTTA-ATT
1 ATTAATTA-TATATTTATATT
95511 ATTA
1 ATTA
95515 TTTAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
ATTAATTATATATTTATATT
Found at i:96351 original size:3 final size:3
Alignment explanation
Indices: 96336--96372 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
96326 TAAATAATAA
96336 ATT A-T ATT AATT ATT ATT ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
96373 GAAATAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:96845 original size:17 final size:17
Alignment explanation
Indices: 96825--96858 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96815 AAAATAAAAG
96825 AAAGAAAAAAAGAAACA
1 AAAGAAAAAAAGAAACA
* *
96842 AAAGAAGAACAGAAACA
1 AAAGAAAAAAAGAAACA
96859 GAGAATGAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAGAAACA
Found at i:99912 original size:26 final size:26
Alignment explanation
Indices: 99882--99944 Score: 63
Period size: 32 Copynumber: 2.2 Consensus size: 26
99872 TAAGAAGGAC
99882 AGTTCTAAATGTATTAACATCTGTTA
1 AGTTCTAAATGTATTAACATCTGTTA
*
99908 AGTTCCCACACTAAATGTATTGACATCTGTTA
1 AGTT------CTAAATGTATTAACATCTGTTA
99940 AGTTC
1 AGTTC
99945 CTGCAGGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 12
0.70 0.02 0.28
Matches are distributed among these distances:
26 5 0.17
32 25 0.83
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (26 bp):
AGTTCTAAATGTATTAACATCTGTTA
Found at i:104211 original size:21 final size:21
Alignment explanation
Indices: 104179--104219 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
104169 GAACATTTGG
104179 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
104200 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
104220 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:115007 original size:14 final size:15
Alignment explanation
Indices: 114981--115011 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
114971 TCCGGGTTTA
114981 TCAACACATTTTTCT
1 TCAACACATTTTTCT
114996 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
115010 TC
1 TC
115012 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:117308 original size:20 final size:20
Alignment explanation
Indices: 117283--117455 Score: 60
Period size: 20 Copynumber: 8.4 Consensus size: 20
117273 GCCGGTGGAG
117283 AAGAAAGAAGGAGAAGAAAA
1 AAGAAAGAAGGAGAAGAAAA
*
117303 AAGAAAG-A-GA-AAGAAGGAG
1 AAGAAAGAAGGAGAAGAA--AA
*
117322 AAGAAAGAA--A-AAGAAAG
1 AAGAAAGAAGGAGAAGAAAA
*
117339 AA-AAGGAAAGGAGAAGAAAGGA
1 AAGAAAG-AAGGAGAAGAAA--A
* *
117361 AAGGAAAGGAGAAGAA-AGAAA
1 AA-GAAAGAAGGAGAAGA-AAA
**
117382 AAGAAAGAAAAAGAA-AGAAA
1 AAGAAAGAAGGAGAAGA-AAA
*
117402 AGGAAAGGAAAGGAGAAGAAGAA
1 AAGAAA-G-AAGGAGAAGAA-AA
* *
117425 GAAG-AAGAGGGAGGGAAGGAAA
1 -AAGAAAGAAGGA--GAAGAAAA
117447 AAGAAAGAA
1 AAGAAAGAA
117456 AAAAATAAGT
Statistics
Matches: 118, Mismatches: 15, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
16 3 0.03
17 11 0.09
18 2 0.02
19 16 0.14
20 35 0.30
21 11 0.09
22 17 0.14
23 18 0.15
24 5 0.04
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGAAAGAAGGAGAAGAAAA
Found at i:117341 original size:10 final size:10
Alignment explanation
Indices: 117300--117427 Score: 114
Period size: 10 Copynumber: 12.8 Consensus size: 10
117290 AAGGAGAAGA
117300 AAAAAGAAAG
1 AAAAAGAAAG
*
117310 AGAAAG-AAG
1 AAAAAGAAAG
* *
117319 GAGAAGAAAG
1 AAAAAGAAAG
117329 AAAAAGAAAG
1 AAAAAGAAAG
*
117339 AAAAGGAAAG
1 AAAAAGAAAG
* *
117349 GAGAAGAAAG
1 AAAAAGAAAG
* *
117359 GAAAGGAAAG
1 AAAAAGAAAG
* *
117369 GAGAAGAAAG
1 AAAAAGAAAG
117379 AAAAAGAAAG
1 AAAAAGAAAG
117389 AAAAAGAAAG
1 AAAAAGAAAG
*
117399 AAAAGGAAAG
1 AAAAAGAAAG
* *
117409 GAAAGGAGAAG
1 AAAAAGA-AAG
*
117420 AAGAAGAA
1 AAAAAGAA
117428 GAAGAGGGAG
Statistics
Matches: 95, Mismatches: 21, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
9 6 0.06
10 82 0.86
11 7 0.07
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:117381 original size:50 final size:49
Alignment explanation
Indices: 117283--117427 Score: 177
Period size: 50 Copynumber: 2.9 Consensus size: 49
117273 GCCGGTGGAG
** *
117283 AAGAAAGAAGGAGAAGAAAAAAGAAAGAGAAA-G-AAGGAGAAGAAAGAAA
1 AAGAAAGAAAAAGAA-AGAAAAGAAAG-GAAAGGAAAGGAGAAGAAAGAAA
* *
117332 AAGAAAGAAAAGGAAAGGAGAAGAAAGGAAAGGAAAGGAGAAGAAAGAAA
1 AAGAAAGAAAAAGAAA-GAAAAGAAAGGAAAGGAAAGGAGAAGAAAGAAA
*
117382 AAGAAAGAAAAAGAAAGAAAAGGAAAGGAAAGGAGAAGAAGAAGAA
1 AAGAAAGAAAAAGAAAGAAAA-GAAAGGAAAGGA-AAGGAGAAGAA
117428 GAAGAGGGAG
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
48 5 0.06
49 25 0.30
50 43 0.52
51 10 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (49 bp):
AAGAAAGAAAAAGAAAGAAAAGAAAGGAAAGGAAAGGAGAAGAAAGAAA
Found at i:117430 original size:40 final size:39
Alignment explanation
Indices: 117290--117430 Score: 121
Period size: 45 Copynumber: 3.5 Consensus size: 39
117280 GAGAAGAAAG
*
117290 AAGGAGAAG-AA-AAAAGAAAGAGAAAG-AAGGAGAA-GA
1 AAGGAGAAGAAAGAAAAGAAAAAGAAAGAAAGGA-AAGGA
* * * *
117326 AAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGGAAAGGA
1 AAGGAGAAGAAAGAAAAGAAAAAGA-AAGAAAGGAAAGGA
117366 AAGGAGAAGAAAGAAAAAGAAAGAAAAAGAAAGAAAAGGAAAGGA
1 AAGGAGAAGAAAG----A-AAAGAAAAAGAAAG-AAAGGAAAGGA
117411 AAGGAGAAG-AAGAAGAAGAA
1 AAGGAGAAGAAAGAA-AAGAA
117431 GAGGGAGGGA
Statistics
Matches: 84, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
36 7 0.08
37 2 0.02
38 9 0.11
39 6 0.07
40 24 0.29
44 7 0.08
45 29 0.35
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (39 bp):
AAGGAGAAGAAAGAAAAGAAAAAGAAAGAAAGGAAAGGA
Found at i:117430 original size:50 final size:51
Alignment explanation
Indices: 117314--117427 Score: 178
Period size: 50 Copynumber: 2.3 Consensus size: 51
117304 AGAAAGAGAA
* *
117314 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAGGAAAGGAGAAGAAAGGAAAGG
1 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAAGAAAGGAAAAGAAAGGAAAGG
117365 A-AAGGAGAAGAAAGAAAAAGAAAGAAAAAGAAA-GAAAAGGAAAGGAAAGG
1 AGAAGGAGAAGAAAGAAAAAGAAAGAAAAAGAAAGGAAAA-GAAAGGAAAGG
*
117415 AGAAGAAGAAGAA
1 AGAAGGAGAAGAA
117428 GAAGAGGGAG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
49 4 0.07
50 43 0.74
51 11 0.19
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (51 bp):
AGAAGGAGAAGAAAGAAAAAGAAAGAAAAAGAAAGGAAAAGAAAGGAAAGG
Found at i:117813 original size:16 final size:18
Alignment explanation
Indices: 117782--117816 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
117772 ATAAAATCTG
117782 AAAATAATGTAAAATAAT
1 AAAATAATGTAAAATAAT
117800 AAAAT-ATG-AAAATAAT
1 AAAATAATGTAAAATAAT
117816 A
1 A
117817 TATTTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 3 0.18
18 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAATAATGTAAAATAAT
Found at i:117948 original size:157 final size:156
Alignment explanation
Indices: 117782--118348 Score: 808
Period size: 157 Copynumber: 3.7 Consensus size: 156
117772 ATAAAATCTG
117782 AAAATAATGTAAAATAATAAAA-TATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAG
1 AAAATAATGTAAAATAATAAAATTA-GAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAG
* * * *
117846 AAAAAAATACGACCAAAGGGCCGAAGTAAGGGTTATTTTTTGAAATTTATTTAAAAAATACAGTA
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTT-TTTTTTGAAATTTATTTAAAAAACACAATA
*
117911 AATTAATACATTTCAAACATAAAGTACT
129 AATTAATACATTTCAAACATAATGTACT
* * * *
117939 AAAATAATGTAAAATAATAAAATTAGAAAATAGTTTA-TTTT-TTAAAAGTAATAAAATCTGGAG
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAAT-TCGAG
* * * *
118002 AAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTACT-AAA-TT-TTAAAAAAACACAATT
65 AAAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT-TTGAAATTTATTTAAAAAACACAATA
*
118064 AATTAATACATTTCAAACATAATGTTCT
129 AATTAATACATTTCAAACATAATGTACT
*
118092 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAAA
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
* * * * *
118157 AAAAAATATGAACAAAGGGCCGAAGTAAGGGGTTTTTTTGTAAATTTATTTAAAAAAGACACTAA
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTG-AAATTTATTTAAAAAACACAATAA
*
118222 ATTAATACATTTCAAATATAATGTACT
130 ATTAATACATTTCAAACATAATGTACT
* *
118249 AAACTAATGTAAAATAATAAAATTAGAAAATAATAT-TTTTTATTGAAAGTAATAAAATTCGA-T
1 AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
* *
118312 AAAAAATATGAACAAATGGCCGAAATAAGGGTTTTTT
66 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTT
118349 ACTAAATTTG
Statistics
Matches: 366, Mismatches: 35, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
153 74 0.20
154 43 0.12
155 74 0.20
156 68 0.19
157 105 0.29
158 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (156 bp):
AAAATAATGTAAAATAATAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTGAAATTTATTTAAAAAACACAATAAA
TTAATACATTTCAAACATAATGTACT
Found at i:118138 original size:310 final size:309
Alignment explanation
Indices: 117782--118357 Score: 935
Period size: 310 Copynumber: 1.9 Consensus size: 309
117772 ATAAAATCTG
*
117782 AAAATAATGTAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAGA
1 AAAATAATGTAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAAA
* * * *
117847 AAAAAATACGACCAAAGGGCCGAAGTAAGGGTTATTTTTTG-AAATTTATTTAAAAAATACAGTA
66 AAAAAATACGAACAAAGGGCCGAAGTAAGGGGT-TTTTTTGTAAATTTATTTAAAAAAGACACTA
*
117911 AATTAATACATTTCAAACATAAAGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAGT-TT
130 AATTAATACATTTCAAACATAAAGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATT
*
117975 ATTTT-TTAAAAGTAATAAAATCTGGAGAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTT
195 -TTTTATTAAAAGTAATAAAAT-TCGA-AAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTT
118039 TACTAAATTTTAAAAAAACACAATTAATTAATACATTTCAAACATAATGTTCT
257 TACTAAATTTTAAAAAAACACAATTAATTAATACATTTCAAACATAATGTTCT
118092 AAAATAATGTAAAATAATAAAAT-TAGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAA
1 AAAATAATGTAAAATAATAAAATAT-GAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAA
*
118156 AAAAAAATATGAACAAAGGGCCGAAGTAAGGGGTTTTTTTGTAAATTTATTTAAAAAAGACACTA
65 AAAAAAATACGAACAAAGGGCCGAAGTAAGGGGTTTTTTTGTAAATTTATTTAAAAAAGACACTA
* * *
118221 AATTAATACATTTCAAATATAATGTACTAAACTAATGTAAAATAATAAAATTAGAAAATAATATT
130 AATTAATACATTTCAAACATAAAGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATT
* * * * *
118286 TTTTATTGAAAGTAATAAAATTCGATAAAAAATATGAACAAATGGCCGAAATAAGGGTTTTTTAC
195 TTTTATTAAAAGTAATAAAATTCGAAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTAC
118351 TAAATTT
260 TAAATTT
118358 GTTTTGAAGT
Statistics
Matches: 246, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
309 51 0.21
310 178 0.72
311 17 0.07
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.31
Consensus pattern (309 bp):
AAAATAATGTAAAATAATAAAATATGAAAATAATATATTTTTATTGAAAGTAATAAAATTCGAAA
AAAAAATACGAACAAAGGGCCGAAGTAAGGGGTTTTTTTGTAAATTTATTTAAAAAAGACACTAA
ATTAATACATTTCAAACATAAAGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATATTT
TTTATTAAAAGTAATAAAATTCGAAAAAAAATACGAACAAAGGGCCGAAATAAGAGTTTTTTACT
AAATTTTAAAAAAACACAATTAATTAATACATTTCAAACATAATGTTCT
Found at i:119685 original size:50 final size:49
Alignment explanation
Indices: 119624--119906 Score: 373
Period size: 50 Copynumber: 5.8 Consensus size: 49
119614 TGGCACTGAG
*
119624 GTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACTGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
*
119674 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCCGCACAGACAGAGGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* * * *
119724 GAG-TCAGTGCAAGACCATGTCTGGGACATGGCATCGGCTCA-A-GATGA
1 GTGCT-AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
*
119771 GTGAC-AGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACTGAGGA
1 GTG-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGAC-GAGGA
* *
119821 GTGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTC-GA-GATGA
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
* *
119867 GTGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCAC
1 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC
119907 CGATATGCGA
Statistics
Matches: 206, Mismatches: 19, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
46 31 0.15
47 48 0.23
48 3 0.01
49 11 0.05
50 113 0.55
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.20
Consensus pattern (49 bp):
GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACGAGGA
Found at i:119803 original size:97 final size:95
Alignment explanation
Indices: 119628--119906 Score: 398
Period size: 97 Copynumber: 2.9 Consensus size: 95
119618 ACTGAGGTGC
* *
119628 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACTGAGGAGTGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCA-A--GATGAGTGC-AGTGTAAGACCATG
*
119693 TCTGGGACATGGCATCCGCACAGACAGAGGAGAG
62 TCTGGGACATGGCATCGGCACAGACAGAGGAGAG
*
119727 TCAGTGCAAGACCATGTCTGGGACATGGCATCGGCTCAAGATGAGTGACAGTGTAAGACCATGTC
1 -CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAAGATGAGTG-CAGTGTAAGACCATGTC
* * *
119792 TGGGACATGGCATCGGCATAGACTGAGGAGTG
64 TGGGACATGGCATCGGCACAGACAGAGGAGAG
*
119824 CTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGAGATGAGTGCCAGTGTAAGACCATGTC
1 C-AGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAAGATGAGTG-CAGTGTAAGACCATGTC
*
119888 TAGGACATGGCATCGGCAC
64 TGGGACATGGCATCGGCAC
119907 CGATATGCGA
Statistics
Matches: 165, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
96 54 0.33
97 74 0.45
98 1 0.01
99 1 0.01
100 35 0.21
ACGTcount: A:0.27, C:0.21, G:0.32, T:0.20
Consensus pattern (95 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCTCAAGATGAGTGCAGTGTAAGACCATGTCTG
GGACATGGCATCGGCACAGACAGAGGAGAG
Found at i:119946 original size:48 final size:47
Alignment explanation
Indices: 119627--119948 Score: 288
Period size: 50 Copynumber: 6.7 Consensus size: 47
119617 CACTGAGGTG
* * *
119627 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGACTGAGGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCGA--GATGAGTC
* * * * **
119677 CTAGTGTAAGACCATGTCTGGGACATGGCATCCGCACAGACAGAGGAGAG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCG--AGATGAGTC
* * * * *
119727 TCAGTGCAAGACCATGTCTGGGACATGGCATCGGCTCAAGATGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCCGAGATGAGTC
* ** * *
119774 ACAGTGTAAGACCATGTCTGGGACATGGCATCGGCATAGACTGAGGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCGA--GATGAGTC
* * *
119824 CTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCTCGAGATGAGTG
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCCGAGATGAGTC
* * *
119870 CCAGTGTAAGACCATGTCTAGGACATGGCATCGGCACCGATATGCGATC
1 CCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CCGAGATGAG-TC
* *
119919 CCA-TGTAAGACCATATCTGGGATATGGCAT
1 CCAGTGTAAGACCATGTCTGGGACATGGCAT
119949 TGGTGTCCTA
Statistics
Matches: 234, Mismatches: 30, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
46 31 0.13
47 48 0.21
48 36 0.15
49 12 0.05
50 106 0.45
52 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.20
Consensus pattern (47 bp):
CCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCCGAGATGAGTC
Found at i:121906 original size:6 final size:6
Alignment explanation
Indices: 121895--121923 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
121885 GGATACAATT
121895 TAAGCA TAAGCA TAAGCA TAAGCA TAAGC
1 TAAGCA TAAGCA TAAGCA TAAGCA TAAGC
121924 TGAATTTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
TAAGCA
Found at i:124123 original size:36 final size:37
Alignment explanation
Indices: 124082--124165 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
124072 ACTAACACAA
** *
124082 TAACAATAATAA-TAGTTTTTTACTCAAAAT-ATTAC
1 TAACAATAATAATTAGGGTTTTACTCAAAATAATAAC
*
124117 TAAACAATAATAATTAGGGTTTTACTTAAAATAATAAC
1 T-AACAATAATAATTAGGGTTTTACTCAAAATAATAAC
124155 TAACAATAATA
1 TAACAATAATA
124166 TAATGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 1 0.02
36 11 0.26
37 25 0.60
38 5 0.12
ACGTcount: A:0.50, C:0.10, G:0.05, T:0.36
Consensus pattern (37 bp):
TAACAATAATAATTAGGGTTTTACTCAAAATAATAAC
Found at i:124197 original size:23 final size:23
Alignment explanation
Indices: 124152--124198 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
124142 TTAAAATAAT
*
124152 AACTAACAATAATATAATGTAAA
1 AACTAACAATAATATAATCTAAA
*
124175 AACTAACAATTATACTAA-CTAAA
1 AACTAACAATAATA-TAATCTAAA
124198 A
1 A
124199 TAATAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 18 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.26
Consensus pattern (23 bp):
AACTAACAATAATATAATCTAAA
Found at i:124778 original size:35 final size:35
Alignment explanation
Indices: 124732--124802 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
124722 GAATAGTAAA
124732 CTCTATCAATACAATAAAAGCTTTCGTCTTAATAT
1 CTCTATCAATACAATAAAAGCTTTCGTCTTAATAT
124767 CTCTATCAATACAATAAAAGCTTTCGTCTTAATAT
1 CTCTATCAATACAATAAAAGCTTTCGTCTTAATAT
124802 C
1 C
124803 AATAGAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.37
Consensus pattern (35 bp):
CTCTATCAATACAATAAAAGCTTTCGTCTTAATAT
Found at i:128151 original size:40 final size:39
Alignment explanation
Indices: 128108--128242 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 39
128098 GCGTTTGGAT
128108 AAAAAACGCCGCTAAAAATCAATCATTAGCGGCGCTATTT-
1 AAAAAACGCCGCTAAAAATCAAT-ATTAGCGGCGCT-TTTC
* * * *
128148 AAAAAATGCCGCTAAAGATCGAGTATTAGTGGCGCTTTTC
1 AAAAAACGCCGCTAAAAATC-AATATTAGCGGCGCTTTTC
* *
128188 TAAAAACGCCACTAAAAAT-AGA-ATTAGCGGCG-TTTTCC
1 AAAAAACGCCGCTAAAAATCA-ATATTAGCGGCGCTTTT-C
*
128226 AAAAAGCGCCGCTAAAA
1 AAAAAACGCCGCTAAAA
128243 CTTAAACCTA
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
37 4 0.05
38 25 0.32
39 3 0.04
40 44 0.56
41 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCAATATTAGCGGCGCTTTTC
Found at i:128334 original size:41 final size:41
Alignment explanation
Indices: 128270--128423 Score: 236
Period size: 41 Copynumber: 3.8 Consensus size: 41
128260 TTTTTGGGGA
* *
128270 TTTAGCAGCGCTTTTGAAGAAGCGCCGCTAATGCTCTAGTC
1 TTTAGCGGCGCTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
* *
128311 TTTAACGGCGCTTTTGAAGAAGCGCCGCTAATACTCTGGTC
1 TTTAGCGGCGCTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
*
128352 TTTAGCGGTGCTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
1 TTTAGCGGCGCTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
* * *
128393 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAA
1 TTTAGCGGCGCTTTTGAAGAAGCGCCGCTAA
128424 AAACATTTTA
Statistics
Matches: 104, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 104 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (41 bp):
TTTAGCGGCGCTTTTGAAGAAGCGCCGCTAATGCTCTGGTC
Found at i:128726 original size:14 final size:14
Alignment explanation
Indices: 128709--128758 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
128699 AGGGTTTTTA
128709 GTTTAAGGAGTTGG
1 GTTTAAGGAGTTGG
* *
128723 GTTTAGGGA-TTATG
1 GTTTAAGGAGTT-GG
128737 GTTTAAGG-GTTGG
1 GTTTAAGGAGTTGG
128750 GATTTAAGG
1 G-TTTAAGG
128759 TTTAGGGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 4 0.14
14 25 0.86
ACGTcount: A:0.22, C:0.00, G:0.40, T:0.38
Consensus pattern (14 bp):
GTTTAAGGAGTTGG
Found at i:128740 original size:28 final size:27
Alignment explanation
Indices: 128695--128755 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
128685 TATCACTATA
* *
128695 GTTTAGGGTTTTTAGTTTAAGGAGTTGG
1 GTTTAGGGATTATAGTTTAAGG-GTTGG
*
128723 GTTTAGGGATTATGGTTTAAGGGTTGG
1 GTTTAGGGATTATAGTTTAAGGGTTGG
128750 GATTTA
1 G-TTTA
128756 AGGTTTAGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (27 bp):
GTTTAGGGATTATAGTTTAAGGGTTGG
Found at i:128762 original size:21 final size:22
Alignment explanation
Indices: 128725--128777 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
128715 GGAGTTGGGT
*
128725 TTAGGGA-TTATGGTTTAAGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
128746 TT-GGGATTTAAGGTTTAGGGG
1 TTAGGGATTTAAGGTTTAAGGG
*
128767 TTAGGGGTTTA
1 TTAGGGATTTA
128778 GGGGTTAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 16 0.59
22 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (22 bp):
TTAGGGATTTAAGGTTTAAGGG
Found at i:128777 original size:15 final size:15
Alignment explanation
Indices: 128757--128785 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
128747 TGGGATTTAA
128757 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
128772 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
128786 TCGACGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:129054 original size:15 final size:15
Alignment explanation
Indices: 129034--129062 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
129024 TGAGATTTAA
129034 GGTTTAGGGGTTAGG
1 GGTTTAGGGGTTAGG
129049 GGTTTAGGGGTTAG
1 GGTTTAGGGGTTAG
129063 ATGTTAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.34
Consensus pattern (15 bp):
GGTTTAGGGGTTAGG
Found at i:129060 original size:36 final size:36
Alignment explanation
Indices: 129013--129098 Score: 111
Period size: 36 Copynumber: 2.4 Consensus size: 36
129003 TAGTGATTAT
* *
129013 GGTTTAAGGGTTGAGAT-TTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGGTT-AGATGTTAAGGTTTAAGAGTTAGG
*
129049 GGTTTAGGGGTTAGATGTTAAGGTTTAAGAGTTAGG
1 GGTTTAAGGGTTAGATGTTAAGGTTTAAGAGTTAGG
* *
129085 GATTTAAGGTTTAG
1 GGTTTAAGGGTTAG
129099 GGATTCAGGG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 4 0.09
36 39 0.91
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.37
Consensus pattern (36 bp):
GGTTTAAGGGTTAGATGTTAAGGTTTAAGAGTTAGG
Found at i:130445 original size:17 final size:17
Alignment explanation
Indices: 130423--130465 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
130413 AATATATAAT
130423 ATTATAATGCAAAATTA
1 ATTATAATGCAAAATTA
130440 ATTATAATGCAAAATTA
1 ATTATAATGCAAAATTA
130457 ATATATAAT
1 AT-TATAAT
130466 ATTATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
ATTATAATGCAAAATTA
Found at i:132946 original size:37 final size:37
Alignment explanation
Indices: 132903--132982 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
132893 ATCTAAATCC
*
132903 AAATTCTCAAATTCATATTTCCAAACATAGCATTAGG
1 AAATTCTCAAATTCATATTTCCAAACATAACATTAGG
132940 AAATTCTCAAATTCATATTTCCAAACATAACATTAGG
1 AAATTCTCAAATTCATATTTCCAAACATAACATTAGG
132977 AAATTC
1 AAATTC
132983 ATATTTCTGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (37 bp):
AAATTCTCAAATTCATATTTCCAAACATAACATTAGG
Found at i:133516 original size:18 final size:18
Alignment explanation
Indices: 133493--133552 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
133483 TATGTATTCT
133493 AATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
* * **
133511 AATGTAA-AC-AATTTTCT
1 AATGTAATTCTAA-TATAG
*
133528 TATGTAATTCTAATATAG
1 AATGTAATTCTAATATAG
133546 AATGTAA
1 AATGTAA
133553 CTTGTTTTAT
Statistics
Matches: 29, Mismatches: 10, Indels: 6
0.64 0.22 0.13
Matches are distributed among these distances:
16 2 0.07
17 9 0.31
18 16 0.55
19 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (18 bp):
AATGTAATTCTAATATAG
Found at i:133789 original size:43 final size:43
Alignment explanation
Indices: 133728--133837 Score: 211
Period size: 43 Copynumber: 2.6 Consensus size: 43
133718 AAGTCATGTT
*
133728 TTTAGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
133771 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
133814 TTTAGCGGCGTTTGTGGGAAAAGC
1 TTTAGCGGCGTTTGTGGGAAAAGC
133838 ACCGATTGCG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTTGGTC
Found at i:133891 original size:43 final size:43
Alignment explanation
Indices: 133843--133949 Score: 187
Period size: 43 Copynumber: 2.5 Consensus size: 43
133833 AAAGCACCGA
*
133843 TTGCGAGAAAAGCGTCGCTAAAGGTTGTGGTCTTTAGCGGCGT
1 TTGCGAGAAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGT
133886 TTGCGAGAAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGT
1 TTGCGAGAAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGT
* *
133929 TTGTGGGAAAAGCGCCGCTAA
1 TTGCGAGAAAAGCGCCGCTAA
133950 TGTTAGCGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.22, C:0.18, G:0.35, T:0.25
Consensus pattern (43 bp):
TTGCGAGAAAAGCGCCGCTAAAGGTTGTGGTCTTTAGCGGCGT
Found at i:133925 original size:104 final size:104
Alignment explanation
Indices: 133745--133941 Score: 335
Period size: 104 Copynumber: 1.9 Consensus size: 104
133735 GCGTTTGTGG
* * *
133745 GAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCTT
1 GAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCTT
133810 GGTCTTTAGCGGCGTTTGTGGGAAAAGCACCGATTGCGA
66 GGTCTTTAGCGGCGTTTGTGGGAAAAGCACCGATTGCGA
133849 GAAAAGCGTCGCTAAAGGT-TGTGGTCTTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGT-T
1 GAAAAGCGTCGCTAAAGGTCT-TGGTCTTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCT
133912 GTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
65 -TGGTCTTTAGCGGCGTTTGTGGGAAAAGC
133942 GCCGCTAATG
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
103 2 0.02
104 86 0.98
ACGTcount: A:0.22, C:0.17, G:0.35, T:0.26
Consensus pattern (104 bp):
GAAAAGCGTCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGCGAGAAAAGCGCCGCTAAAGGTCTT
GGTCTTTAGCGGCGTTTGTGGGAAAAGCACCGATTGCGA
Found at i:134050 original size:22 final size:22
Alignment explanation
Indices: 134023--134066 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
134013 TAGTGGCGTT
*
134023 AAAAAGCGTCGCTAAAGGCCTA
1 AAAAAGCGTCGCTAAAAGCCTA
134045 AAAAAGCGTCGCTAAAAGCCTA
1 AAAAAGCGTCGCTAAAAGCCTA
134067 TTTTGGTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.14
Consensus pattern (22 bp):
AAAAAGCGTCGCTAAAAGCCTA
Found at i:136699 original size:15 final size:16
Alignment explanation
Indices: 136679--136716 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
136669 AAGATGGAGA
*
136679 TGAAAACCAA-AACCC
1 TGAAAACAAAGAACCC
136694 TGAAAACAAAGAACCC
1 TGAAAACAAAGAACCC
*
136710 TCAAAAC
1 TGAAAAC
136717 GTGAACACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.55, C:0.29, G:0.08, T:0.08
Consensus pattern (16 bp):
TGAAAACAAAGAACCC
Found at i:142200 original size:14 final size:15
Alignment explanation
Indices: 142174--142204 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
142164 TCCAGGTTCA
142174 TCAACACATTTTTCT
1 TCAACACATTTTTCT
142189 TCAACA-ATTTTTCT
1 TCAACACATTTTTCT
142203 TC
1 TC
142205 CCATTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (15 bp):
TCAACACATTTTTCT
Found at i:154447 original size:20 final size:21
Alignment explanation
Indices: 154422--154462 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
154412 GAAAATATAT
*
154422 TTTCCATTCAA-TTTTCCATC
1 TTTCCAGTCAAGTTTTCCATC
154442 TTTCCAGTCAAGTTTTCCATC
1 TTTCCAGTCAAGTTTTCCATC
154463 CCCTCAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.20, C:0.29, G:0.05, T:0.46
Consensus pattern (21 bp):
TTTCCAGTCAAGTTTTCCATC
Found at i:154645 original size:36 final size:36
Alignment explanation
Indices: 154605--154673 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
154595 TATATGTATA
* *
154605 TTTTCTTACCTTTTATTGTTGATGATCATACCTATG
1 TTTTCTTACCTTTTATTATCGATGATCATACCTATG
154641 TTTTCTTACCTTTTATTATCGATGATCATACCT
1 TTTTCTTACCTTTTATTATCGATGATCATACCT
154674 TCAATCACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.52
Consensus pattern (36 bp):
TTTTCTTACCTTTTATTATCGATGATCATACCTATG
Found at i:155118 original size:14 final size:15
Alignment explanation
Indices: 155093--155122 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
155083 CCAGGTTCAG
155093 CAACACATTTTTCTT
1 CAACACATTTTTCTT
155108 CAACA-ATTTTTCTT
1 CAACACATTTTTCTT
155122 C
1 C
155123 CCATTTCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
CAACACATTTTTCTT
Found at i:156168 original size:41 final size:41
Alignment explanation
Indices: 156111--156199 Score: 169
Period size: 41 Copynumber: 2.2 Consensus size: 41
156101 TGTCTCCGAT
156111 TAACTCTGGTTCATTCCTACAATGAAATAAAAAATTGTTTC
1 TAACTCTGGTTCATTCCTACAATGAAATAAAAAATTGTTTC
156152 TAACTCTGGTTCATTCCTACAATGAAATAAAAAATTGTTTC
1 TAACTCTGGTTCATTCCTACAATGAAATAAAAAATTGTTTC
*
156193 TATCTCT
1 TAACTCT
156200 CAGAGGCTCT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (41 bp):
TAACTCTGGTTCATTCCTACAATGAAATAAAAAATTGTTTC
Found at i:164240 original size:8 final size:8
Alignment explanation
Indices: 164229--164254 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
164219 ATTTATTTAT
164229 TTTTAAAA
1 TTTTAAAA
164237 TTTTAAAA
1 TTTTAAAA
164245 TTTTAAAA
1 TTTTAAAA
164253 TT
1 TT
164255 CAGATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:168600 original size:14 final size:15
Alignment explanation
Indices: 168576--168604 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
168566 CAGGTTCATT
168576 AACACATTTTTCTTC
1 AACACATTTTTCTTC
168591 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
168605 CCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:177544 original size:146 final size:146
Alignment explanation
Indices: 177341--177615 Score: 489
Period size: 146 Copynumber: 1.9 Consensus size: 146
177331 TTATACCTAT
*
177341 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGATTTTCAACTAAACGAGTTACGTGATTATCAA
1 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
177406 GTGAA-TTTTAAAAATAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAA
66 GTGAATTTTTAAAAA-AAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAA
177470 ATTTTTCAACTAAACGA
130 ATTTTTCAACTAAACGA
*
177487 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTTGACTTTCAACTAAACGAGTTACGTGATTATCAA
1 GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
* *
177552 GTGAATTTTTTTAAAAAAAATTAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAA
66 GTGAA-TTTTTAAAAAAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAA
177616 GGGTAACGAT
Statistics
Matches: 123, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
146 68 0.55
147 47 0.38
148 8 0.07
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (146 bp):
GTTTTTGGTTAAGCGAATCCTAGACGTTTTTCGACTTTCAACTAAACGAGTTACGTGATTATCAA
GTGAATTTTTAAAAAAAAAATAAAAATGTCACGCAAGAGAATTTAATAGAAAAATTTTAACAAAA
TTTTTCAACTAAACGA
Found at i:179305 original size:19 final size:18
Alignment explanation
Indices: 179257--179307 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
179247 AACTAAAAAA
*
179257 TAAAAAATTTA-AAATTT
1 TAAAAAATTTATAAAGTT
*
179274 TATAAAATCTTATAGAAGTT
1 TAAAAAAT-TTATA-AAGTT
179294 TAAAAAATTTATAA
1 TAAAAAATTTATAA
179308 TTAAAATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.25
18 4 0.14
19 6 0.21
20 11 0.39
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (18 bp):
TAAAAAATTTATAAAGTT
Found at i:181276 original size:16 final size:16
Alignment explanation
Indices: 181255--181305 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
181245 TTTTAATTTT
181255 TATGTTATGTACATTC
1 TATGTTATGTACATTC
*
181271 TATGTT-T-TATTATT-
1 TATGTTATGTA-CATTC
*
181285 TATGTTATGTACATAC
1 TATGTTATGTACATTC
181301 TATGT
1 TATGT
181306 CTTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (16 bp):
TATGTTATGTACATTC
Found at i:181279 original size:30 final size:29
Alignment explanation
Indices: 181245--181375 Score: 131
Period size: 30 Copynumber: 4.2 Consensus size: 29
181235 CATAATTTAA
181245 TTTTAATTTTTATGTTATGTACATTCTATG
1 TTTT-ATTTTTATGTTATGTACATTCTATG
*
181275 TTTTATTATTTATGTTATGTACATACTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
*
181305 TCTTATTATTTTATCAT-TTATGTTATTATT-TATG
1 --TT-TTATTTT-T-ATGTTATG-TA-CATTCTATG
*
181339 TTTTATTATTTATGTTATCTACATTCTATG
1 TTTTATT-TTTATGTTATGTACATTCTATG
181369 TTTTATT
1 TTTTATT
181376 ATTTTATTTA
Statistics
Matches: 85, Mismatches: 5, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
29 6 0.07
30 40 0.47
31 10 0.12
32 8 0.09
33 11 0.13
34 8 0.09
35 2 0.02
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.62
Consensus pattern (29 bp):
TTTTATTTTTATGTTATGTACATTCTATG
Found at i:181330 original size:12 final size:12
Alignment explanation
Indices: 181310--181357 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
181300 CTATGTCTTA
*
181310 TTATTTTATCAT
1 TTATGTTATCAT
*
181322 TTATGTTATTAT
1 TTATGTTATCAT
*
181334 TTATGTTTTATTAT
1 TTATG--TTATCAT
181348 TTATGTTATC
1 TTATGTTATC
181358 TACATTCTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 19 0.61
14 12 0.39
ACGTcount: A:0.23, C:0.04, G:0.06, T:0.67
Consensus pattern (12 bp):
TTATGTTATCAT
Found at i:181342 original size:26 final size:29
Alignment explanation
Indices: 181313--181379 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 29
181303 TGTCTTATTA
*
181313 TTTTATCATTTATGTTAT-T-ATT-TATG
1 TTTTATTATTTATGTTATCTAATTCTATG
181339 TTTTATTATTTATGTTATCTACATTCTATG
1 TTTTATTATTTATGTTATCTA-ATTCTATG
181369 TTTTATTATTT
1 TTTTATTATTT
181380 TATTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 17 0.47
27 1 0.03
29 3 0.08
30 15 0.42
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (29 bp):
TTTTATTATTTATGTTATCTAATTCTATG
Found at i:181350 original size:64 final size:67
Alignment explanation
Indices: 181253--181382 Score: 203
Period size: 64 Copynumber: 2.0 Consensus size: 67
181243 AATTTTAATT
*
181253 TTTATGTTATGTACATTCTATGTTTTATTATTTATGTTATGTACATACTATGTCTTATTATTTTA
1 TTTATGTTATGTA-ATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTA
181318 TCA
65 TCA
* *
181321 TTTATGTTAT-T-ATT-TATGTTTTATTATTTATGTTATCTACATTCTATGTTTTATTATTTTAT
1 TTTATGTTATGTAATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTAT
181383 TTAATTTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
64 45 0.76
65 3 0.05
67 1 0.02
68 10 0.17
ACGTcount: A:0.24, C:0.07, G:0.08, T:0.62
Consensus pattern (67 bp):
TTTATGTTATGTAATTCTATGTTTTATTATTTATGTTATCTACATACTATGTCTTATTATTTTAT
CA
Found at i:181851 original size:158 final size:157
Alignment explanation
Indices: 181533--182085 Score: 831
Period size: 158 Copynumber: 3.5 Consensus size: 157
181523 TACAAAAAGA
** * *
181533 AATAAAA-AATGAAAATAGTATATTTACTGAAAGTAATAAAATTCGAAAAAAAAAAGAAAATTAC
1 AATAAAATAA-GAAAATAGTATATTTTTTGAAAGTAATAAAATTCG---AAAATAAGAAAAATAC
* * * *
181597 GAACAAAGGGTCAAAATAAAGGTTTTTTACTAAATTTATA-AAAAAACACACAAAAATAATATAT
62 GAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACAAAATTAATACAT
*
181661 TTCAGACATTATGTACTAAAATAATATAAAAT
127 TTCA-ACTTTATGTACTAAAATAATATAAAAT
* *
181693 AATAAAATAATAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATACGAAC
1 AATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
* * *
181758 AAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAAACACCAAATTAATACATTTCT
66 AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACAAAATTAATACATTTC-
*
181823 AATTTTATGTACTAAAATAATATAAAAT
130 AACTTTATGTACTAAAATAATATAAAAT
*
181851 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
1 AATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
* * * * *
181916 AAATGACCAAAATGAGGGGTTTTTACTAAATTTATATAAAAAACACACTAAATTAATACATTTCA
66 AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACAAAATTAATACATTTC-
181981 AACTTTATGTACTAAAATAATATAAAAT
130 AACTTTATGTACTAAAATAATATAAAAT
*
182009 AATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
1 AATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
182074 AAAGGGCCAAAA
66 AAAGGGCCAAAA
182086 AATCGGGAAA
Statistics
Matches: 363, Mismatches: 27, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
157 51 0.14
158 271 0.75
159 1 0.00
160 38 0.10
161 2 0.01
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (157 bp):
AATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGAAAATAAGAAAAATACGAAC
AAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACAAAATTAATACATTTCA
ACTTTATGTACTAAAATAATATAAAAT
Found at i:184306 original size:18 final size:18
Alignment explanation
Indices: 184279--184329 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
184269 AGTGTTCAAA
184279 AAGATAATCCACTCCTAC
1 AAGATAATCCACTCCTAC
* *
184297 AAGGTAATCCATTCCTAC
1 AAGATAATCCACTCCTAC
*
184315 AAGATAATCAACTCC
1 AAGATAATCCACTCC
184330 ATTGATTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (18 bp):
AAGATAATCCACTCCTAC
Found at i:188037 original size:20 final size:20
Alignment explanation
Indices: 188012--188061 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
188002 TGGCTTAAAA
188012 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
188032 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
188049 GTGGTAGTGGATT
1 TTGGTAGTGGATT
188062 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:193800 original size:14 final size:15
Alignment explanation
Indices: 193776--193804 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
193766 CAGGTTCATT
193776 AACACATTTTTCTTC
1 AACACATTTTTCTTC
193791 AACA-ATTTTTCTTC
1 AACACATTTTTCTTC
193805 CCATTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (15 bp):
AACACATTTTTCTTC
Found at i:195973 original size:18 final size:18
Alignment explanation
Indices: 195950--195990 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
195940 TTCTACAATG
195950 GATAACAGCTCTGGAGAT
1 GATAACAGCTCTGGAGAT
195968 GATAACAGCTCTGGAGAT
1 GATAACAGCTCTGGAGAT
195986 GATAA
1 GATAA
195991 ACTTACCCTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (18 bp):
GATAACAGCTCTGGAGAT
Found at i:196101 original size:27 final size:25
Alignment explanation
Indices: 196054--196109 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 25
196044 TAAAAATATA
196054 ATTTTATAATCTTAATATTTAAAAT
1 ATTTTATAATCTTAATATTTAAAAT
*
196079 ATTTTATAACTTTATAATATTTAAAAT
1 ATTTTATAA-TCT-TAATATTTAAAAT
196106 ATTT
1 ATTT
196110 AAAGGATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 9 0.32
26 2 0.07
27 17 0.61
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTATAATCTTAATATTTAAAAT
Found at i:196216 original size:18 final size:18
Alignment explanation
Indices: 196195--196230 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
196185 AAATCTTAAA
196195 AAGTTTAAATGAAAAACT
1 AAGTTTAAATGAAAAACT
196213 AAGTTTAAATGAAAAACT
1 AAGTTTAAATGAAAAACT
196231 TTTCAGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
AAGTTTAAATGAAAAACT
Found at i:200173 original size:28 final size:28
Alignment explanation
Indices: 200141--200195 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
200131 AATTAATTTT
200141 TAATAT-TTTTTGAATTTTTAAAAAATTA
1 TAATATATTTTT-AATTTTTAAAAAATTA
* *
200169 TAATATATTTTTTATTTTTATAAAATT
1 TAATATATTTTTAATTTTTAAAAAATT
200196 TTTAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
TAATATATTTTTAATTTTTAAAAAATTA
Found at i:200196 original size:39 final size:39
Alignment explanation
Indices: 200153--200241 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
200143 ATATTTTTTG
* *
200153 AATTTTTAAAAAAT-TATAATATATTTTTTATTTTTAT-AA
1 AATTTTTAAAAAATCT-TAATA-ACTTTCTATTTTTATGAA
* * *
200192 AATTTTTAAATAATCTTAATAACTTTCTATTTTTTTGGA
1 AATTTTTAAAAAATCTTAATAACTTTCTATTTTTATGAA
200231 AATTTTTAAAA
1 AATTTTTAAAA
200242 TTAATTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
38 12 0.29
39 29 0.69
40 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.54
Consensus pattern (39 bp):
AATTTTTAAAAAATCTTAATAACTTTCTATTTTTATGAA
Found at i:209130 original size:29 final size:28
Alignment explanation
Indices: 209059--209130 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
209049 ATAATTAATT
209059 AATTTTTAAT-ATTTTTGAATTTTTAAA
1 AATTTTTAATAATTTTTGAATTTTTAAA
* *
209086 AATTTATAATATATTTTT-TATTTTTACAA
1 AATTTTTAATA-ATTTTTGAATTTTTA-AA
209115 AATTTTTAAATAATTT
1 AATTTTT-AATAATTT
209131 CAATAACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 9 0.24
28 7 0.18
29 18 0.47
30 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (28 bp):
AATTTTTAATAATTTTTGAATTTTTAAA
Found at i:211261 original size:24 final size:25
Alignment explanation
Indices: 211234--211284 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
211224 TTGAGTTCGA
211234 ATTTTA-TATTTTT-TAAATATTATT
1 ATTTTATTATTTTTGT-AATATTATT
*
211258 A-TTTATTATTTTTGTAATTTTATT
1 ATTTTATTATTTTTGTAATATTATT
211282 ATT
1 ATT
211285 AATTAGAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
23 4 0.17
24 17 0.74
25 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
ATTTTATTATTTTTGTAATATTATT
Found at i:211289 original size:24 final size:24
Alignment explanation
Indices: 211240--211289 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
211230 TCGAATTTTA
*
211240 TATTTTTTAAATATTATTATTTAT
1 TATTTTTTAAATATTATTATTAAT
*
211264 TATTTTTGT-AATTTTATTATTAAT
1 TATTTTT-TAAATATTATTATTAAT
211288 TA
1 TA
211290 GAATTATAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTTTAAATATTATTATTAAT
Found at i:216790 original size:18 final size:17
Alignment explanation
Indices: 216757--216795 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
216747 TTGTATAAAT
216757 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
216775 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
216792 TGTG
1 TGTG
216796 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:217048 original size:23 final size:23
Alignment explanation
Indices: 217021--217118 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
217011 AGTGTTATTG
*
217021 ATCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
217044 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
217067 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
217089 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
217112 ATCAGTG
1 ATCAGTG
217119 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:217087 original size:45 final size:45
Alignment explanation
Indices: 217023--217111 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
217013 TGTTATTGAT
* *
217023 CAGTGGTAACTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
*
217068 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
217112 ATCAGTGTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.20, C:0.22, G:0.26, T:0.31
Consensus pattern (45 bp):
CAGTGGTAACTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:220495 original size:45 final size:45
Alignment explanation
Indices: 220431--220519 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
220421 GGATGGGACA
220431 TTGAGATTGTGTATTGATTATCGTCAACTTAACAAAGTGACAGTG
1 TTGAGATTGTGTATTGATTATCGTCAACTTAACAAAGTGACAGTG
*
220476 TTGAGATTGTGTATTGATTATCGTCAACTTAATAAAGTGACAGT
1 TTGAGATTGTGTATTGATTATCGTCAACTTAACAAAGTGACAGT
220520 AAAGAATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.37
Consensus pattern (45 bp):
TTGAGATTGTGTATTGATTATCGTCAACTTAACAAAGTGACAGTG
Found at i:221148 original size:93 final size:93
Alignment explanation
Indices: 220979--221159 Score: 317
Period size: 93 Copynumber: 1.9 Consensus size: 93
220969 AGATATCGGC
* *
220979 AATAATTGAGTGGAAGCCTCCAAGAAATGTATCTGAAGTTAGGAGTTTTCTGGGCTTAGCCGGAT
1 AATAATTGAATGGAAACCTCCAAGAAATGTATCTGAAGTTAGGAGTTTTCTGGGCTTAGCCGGAT
* *
221044 ATTATCGTCGATTTGTAGAAGGTTTTAT
66 ATTACCGTCGATTCGTAGAAGGTTTTAT
*
221072 AATAGTTGAATGGAAACCTCCAAGAAATGTATCTGAAGTTAGGAGTTTTCTGGGCTTAGCCGGAT
1 AATAATTGAATGGAAACCTCCAAGAAATGTATCTGAAGTTAGGAGTTTTCTGGGCTTAGCCGGAT
221137 ATTACCGTCGATTCGTAGAAGGT
66 ATTACCGTCGATTCGTAGAAGGT
221160 AATTGGGAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 83 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (93 bp):
AATAATTGAATGGAAACCTCCAAGAAATGTATCTGAAGTTAGGAGTTTTCTGGGCTTAGCCGGAT
ATTACCGTCGATTCGTAGAAGGTTTTAT
Found at i:222977 original size:18 final size:17
Alignment explanation
Indices: 222944--222982 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
222934 TTGTATAAAT
222944 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
222962 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
222979 TGTG
1 TGTG
222983 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:223235 original size:23 final size:23
Alignment explanation
Indices: 223208--223305 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
223198 AGTGTTATTG
223208 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
223231 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
223254 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
223276 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
223299 ATCAGTG
1 ATCAGTG
223306 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:223274 original size:45 final size:45
Alignment explanation
Indices: 223210--223298 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
223200 TGTTATTGAT
* *
223210 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
223255 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
223299 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:229880 original size:15 final size:16
Alignment explanation
Indices: 229860--229891 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
229850 TTTAAATATA
229860 TAATAAAA-ATAAAAT
1 TAATAAAACATAAAAT
229875 TAATAAAACATAAAAT
1 TAATAAAACATAAAAT
229891 T
1 T
229892 TTATCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
TAATAAAACATAAAAT
Found at i:238932 original size:153 final size:153
Alignment explanation
Indices: 238654--238956 Score: 597
Period size: 153 Copynumber: 2.0 Consensus size: 153
238644 TACAGAAGGG
238654 AGGCCGGACTTTTCCAACTATGGCCTTATTTATTGCTAATAAGATAATGCAAAAAATGGGCTATG
1 AGGCCGGACTTTTCCAACTATGGCCTTATTTATTGCTAATAAGATAATGCAAAAAATGGGCTATG
238719 ACTTGGAAAATCCTGTCGGACTAAAAAATGGGAAGGGGCTTGACGAAGGCACAAAAGAATACATT
66 ACTTGGAAAATCCTGTCGGACTAAAAAATGGGAAGGGGCTTGACGAAGGCACAAAAGAATACATT
238784 AAAAGAAGGGGAGGCTATCCGCT
131 AAAAGAAGGGGAGGCTATCCGCT
238807 AGGCCGGACTTTTCCAACTATGGCCTTATTTATTGCTAATAAGATAATGCAAAAAATGGGCTATG
1 AGGCCGGACTTTTCCAACTATGGCCTTATTTATTGCTAATAAGATAATGCAAAAAATGGGCTATG
238872 ACTTGGAAAATCCTGTCGGACTAAAAAATGGGAAGGGGCTTGACGAAGGCACAAAAGAATACATT
66 ACTTGGAAAATCCTGTCGGACTAAAAAATGGGAAGGGGCTTGACGAAGGCACAAAAGAATACATT
*
238937 AAAAGATGGGGAGGCTATCC
131 AAAAGAAGGGGAGGCTATCC
238957 TCCGACGTAC
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 149 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (153 bp):
AGGCCGGACTTTTCCAACTATGGCCTTATTTATTGCTAATAAGATAATGCAAAAAATGGGCTATG
ACTTGGAAAATCCTGTCGGACTAAAAAATGGGAAGGGGCTTGACGAAGGCACAAAAGAATACATT
AAAAGAAGGGGAGGCTATCCGCT
Found at i:249439 original size:19 final size:18
Alignment explanation
Indices: 249415--249453 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
249405 TTCTAACATA
249415 TATCTACCTAAATAAGATT
1 TATCTACCTAAATAA-ATT
249434 TATCTACCTAAATAAATT
1 TATCTACCTAAATAAATT
249452 TA
1 TA
249454 AAATATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
TATCTACCTAAATAAATT
Found at i:251292 original size:6 final size:6
Alignment explanation
Indices: 251281--251348 Score: 127
Period size: 6 Copynumber: 11.3 Consensus size: 6
251271 ATTATTAATA
*
251281 TTCTTT TCCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
251329 TTCTTT TTCTTT TTCTTT TT
1 TTCTTT TTCTTT TTCTTT TT
251349 GCTTAAGAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:251544 original size:111 final size:111
Alignment explanation
Indices: 251344--251760 Score: 708
Period size: 111 Copynumber: 3.7 Consensus size: 111
251334 TTTCTTTTTC
* ** *
251344 TTTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAAAGAGACAACAGCCAAGCACCCCACCCT
1 TTTTT-CTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCC
* *
251409 GGTTACTCAGCCTAACATACTCCTAATTTATTATATTTAAATATATA
65 GGTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
*
251456 TTTTTCTTAAGAATATATTGAACTTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
*
251521 GTTACTCAACCCAACATACTCCTAATTTGTTATATTTAAATATATA
66 GTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
* *
251567 TTTTTCTTAAGAATATATTGAACTTTTTGACGCGAAGAGAGATGATAGCCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
251632 GTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
66 GTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
* *
251678 TTTTTCTTAAGAATATATTGAACCTTTTGACGCAAAGAGAGATGACAGTCAAGCACCCCACCCCG
1 TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
*
251743 GTTACTCAGCCCAACATA
66 GTTACTCAACCCAACATA
251761 TTCTTAAAAA
Statistics
Matches: 290, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
111 285 0.98
112 5 0.02
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (111 bp):
TTTTTCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCACCCCG
GTTACTCAACCCAACATACTCCTAATTTATTATATTTAAATATATA
Found at i:256413 original size:6 final size:6
Alignment explanation
Indices: 256402--256430 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
256392 ATAATGGTAG
256402 CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
1 CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
256431 TTCAACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (6 bp):
CAGTAA
Found at i:256461 original size:45 final size:45
Alignment explanation
Indices: 256410--256514 Score: 167
Period size: 45 Copynumber: 2.3 Consensus size: 45
256400 AGCAGTAACA
*
256410 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCTGAATCT-
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAAT-TG
* *
256455 GTAACAGTAACGGTAACAGTATTCGACACACAAAGTGCCGAATTG
1 GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATTG
256500 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
256515 GTCGGCACAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 1 0.02
45 54 0.98
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATTG
Found at i:257495 original size:16 final size:17
Alignment explanation
Indices: 257470--257501 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
257460 TAAACCCTAA
257470 TTTTTCCTTTCTTTCTC
1 TTTTTCCTTTCTTTCTC
257487 TTTTT-CTTTCTTTCT
1 TTTTTCCTTTCTTTCT
257502 TTCTCCCCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCCTTTCTTTCTC
Found at i:259818 original size:17 final size:17
Alignment explanation
Indices: 259796--259829 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
259786 GTTTTTAAGG
259796 TCTGTACTAATAAAAGC
1 TCTGTACTAATAAAAGC
259813 TCTGTACTAATAAAAGC
1 TCTGTACTAATAAAAGC
259830 ATGGCAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
TCTGTACTAATAAAAGC
Found at i:262700 original size:153 final size:153
Alignment explanation
Indices: 262449--262747 Score: 465
Period size: 153 Copynumber: 2.0 Consensus size: 153
262439 TTTAAGCTCC
*
262449 TTGCAATTTGACAATCGAAGGGTTTTAAGCTTGGAAAGTGTAGTAAGAGCTGAAGGAATGCCAAT
1 TTGCAATTTGACAATCGAAGGGTTTTAAGCTTGGAAAGTGTAGGAAGAGCTGAAGGAATGCCAAT
* * *
262514 GAAATTGTTACCACTAAGATCAAGTAATATCAAAGAGGATAGACCATAAATATCACTT-GGAATA
66 GAAATTGTTACCACTAAGATCAAGTAATATCAAAGAGGATAAACAAGAAATATCA-TTAGGAATA
*
262578 TCTGCTTCACAAAGATTGCGAACA
130 TCTCCTTCACAAAGATTGCGAACA
* *
262602 TTGCAATTTGACAATCGAAGGGTTTTAAGCTTGGAAGGTGTAGGAAGAGCTGGAGGAATGCCAAT
1 TTGCAATTTGACAATCGAAGGGTTTTAAGCTTGGAAAGTGTAGGAAGAGCTGAAGGAATGCCAAT
** * *
262667 GAAATTGTTACCACTAAGATCAAGTTTTTTCAAAGAGGATAAACAAGAAATATCATTAGGAATGT
66 GAAATTGTTACCACTAAGATCAAGTAATATCAAAGAGGATAAACAAGAAATATCATTAGGAATAT
* *
262732 CTCCTTCCCGAAGATT
131 CTCCTTCACAAAGATT
262748 CCTATCCCTT
Statistics
Matches: 132, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
152 2 0.02
153 130 0.98
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (153 bp):
TTGCAATTTGACAATCGAAGGGTTTTAAGCTTGGAAAGTGTAGGAAGAGCTGAAGGAATGCCAAT
GAAATTGTTACCACTAAGATCAAGTAATATCAAAGAGGATAAACAAGAAATATCATTAGGAATAT
CTCCTTCACAAAGATTGCGAACA
Found at i:279625 original size:17 final size:18
Alignment explanation
Indices: 279592--279625 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
279582 AAAATTTTAA
279592 TAAAATATATAATAGTAG
1 TAAAATATATAATAGTAG
*
279610 TAAAATTTAT-ATAGTA
1 TAAAATATATAATAGTA
279626 AATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (18 bp):
TAAAATATATAATAGTAG
Found at i:279631 original size:18 final size:18
Alignment explanation
Indices: 279589--279635 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
279579 TTTAAAATTT
279589 TAATAAAATATATAATAG
1 TAATAAAATATATAATAG
* *
279607 TAGTAAAATTTAT-ATAG
1 TAATAAAATATATAATAG
279624 TAA-ATAAATATA
1 TAATA-AAATATA
279636 ATTATGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 12 0.50
18 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (18 bp):
TAATAAAATATATAATAG
Found at i:285211 original size:14 final size:13
Alignment explanation
Indices: 285192--285225 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
285182 AAAGAAAAAA
285192 GAGAGAGAGAGAGT
1 GAGAGAGAGAGA-T
285206 GAGAGAGAGAGAT
1 GAGAGAGAGAGAT
285219 G-GAGAGA
1 GAGAGAGA
285226 ATATGTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 2 0.10
14 12 0.60
ACGTcount: A:0.44, C:0.00, G:0.50, T:0.06
Consensus pattern (13 bp):
GAGAGAGAGAGAT
Found at i:303093 original size:15 final size:15
Alignment explanation
Indices: 303067--303099 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
303057 TTTGATGATT
303067 TTGGGCTATTGGGCTG
1 TTGGGCTATTGGG-TG
303083 TTGGG-TATTGGGTG
1 TTGGGCTATTGGGTG
303097 TTG
1 TTG
303100 TAATTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.06, C:0.06, G:0.45, T:0.42
Consensus pattern (15 bp):
TTGGGCTATTGGGTG
Found at i:303513 original size:87 final size:87
Alignment explanation
Indices: 303356--303691 Score: 293
Period size: 87 Copynumber: 3.8 Consensus size: 87
303346 CACTTCAACT
* * * * * * *
303356 TGCTCCGCTGTAATCTTAGGGAGATAAGACCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
1 TGCTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATCTGCTCCACTGTAACCTCAGAG
*
303421 GGATAAGATCTGCAATTCTTCGGTC
63 AGATAAGATCTGCAATTCTTCGGTC
* * * * *
303446 TACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTGCTCCACTGTAACCTCAGAGAGA
** **
303511 TAAGATCCT-TTATT-TT-AATC
66 TAAGAT-CTGCAATTCTTCGGTC
* * * * * * * *
303531 CGCTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCGATCTGCTCCGCTGTAACCTCAGGG
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCT-GA--TGCGATCTGCTCCACTGTAACCTCAGAG
*
303595 AGACAAGATCTGCAATTCTTCGGTC
63 AGATAAGATCTGCAATTCTTCGGTC
* * * * * *
303620 TGTTCCACTGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGA
1 TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTGCTCCACTGTAACCTCAGAGAGA
303685 TAAGATC
66 TAAGATC
303692 CTTTGATCCG
Statistics
Matches: 188, Mismatches: 50, Indels: 19
0.73 0.19 0.07
Matches are distributed among these distances:
84 1 0.01
85 27 0.14
86 4 0.02
87 97 0.52
88 6 0.03
89 28 0.15
90 25 0.13
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (87 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTGCTCCACTGTAACCTCAGAGAGA
TAAGATCTGCAATTCTTCGGTC
Found at i:303555 original size:44 final size:44
Alignment explanation
Indices: 303357--303648 Score: 134
Period size: 46 Copynumber: 6.6 Consensus size: 44
303347 ACTTCAACTT
* * * ** *
303357 GCTCCGCTGTAATCTT-AGGGAGATAAGACCTCTGGCTTCAATCT
1 GCTCCACTGTAA-CTTCAGGGAGATAAGATCTATATCTTCAATCC
* * ** *
303401 GCTCCACTGTAACCTCAGGGGGATAAGATCTGCA-ATTCTTCGGTCT
1 GCTCCACTGTAACTTCAGGGAGATAAGATCT--ATA-TCTTCAATCC
* * * * * * * *
303447 ACTCCACTGTAACCTCAGAGAGATAAGACCT-GA--TGCGATCT
1 GCTCCACTGTAACTTCAGGGAGATAAGATCTATATCTTCAATCC
* * * * *
303488 ACTCTACTGTAACTTCAGAGAGATAAGATCCTTTAT-TTTAATCC
1 GCTCCACTGTAACTTCAGGGAGATAAGAT-CTATATCTTCAATCC
* * *
303532 GCTCCACTGTAACTTCAGGGAGATAGGAT-TATATCTTCGATCT
1 GCTCCACTGTAACTTCAGGGAGATAAGATCTATATCTTCAATCC
* * * ** *
303575 GCTCCGCTGTAACCTCAGGGAGACAAGATCTGCA-ATTCTTCGGTCT
1 GCTCCACTGTAACTTCAGGGAGATAAGATCT--ATA-TCTTCAATCC
*
303621 GTTCCACTGTAA-TCTCAGGGAGATAAGA
1 GCTCCACTGTAACT-TCAGGGAGATAAGA
303649 CCTGATGTGA
Statistics
Matches: 194, Mismatches: 40, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
41 32 0.16
42 6 0.03
43 33 0.17
44 55 0.28
45 1 0.01
46 67 0.35
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTCCACTGTAACTTCAGGGAGATAAGATCTATATCTTCAATCC
Found at i:303685 original size:41 final size:41
Alignment explanation
Indices: 303397--303689 Score: 158
Period size: 46 Copynumber: 6.8 Consensus size: 41
303387 TCTGGCTTCA
* * * *
303397 ATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TT-G
* * * **
303443 GTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATGCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTGATTTG
* * * *
303484 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGA-CC-TGA-TTTG
* * * * *
303528 ATCCGCTCCACTGTAACTTCAGGGAGATAGGA-TTATATCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCT-GAT-TT-G
* * * * *
303571 ATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTGCAATTCTTCG
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTG--A-T-TT-G
* * * *
303617 GTCTGTTCCACTGTAA-TCTCAGGGAGATAAGACCTGATGTG
1 ATCTGCTCCACTGTAACT-TCAGAGAGATAAGACCTGATTTG
* *
303658 ATCTTCTCTACTGTAACTTCAGAGAGATAAGA
1 ATCTGCTCCACTGTAACTTCAGAGAGATAAGA
303690 TCCTTTGATC
Statistics
Matches: 195, Mismatches: 40, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
41 58 0.30
42 8 0.04
43 31 0.16
44 31 0.16
45 1 0.01
46 66 0.34
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (41 bp):
ATCTGCTCCACTGTAACTTCAGAGAGATAAGACCTGATTTG
Found at i:303687 original size:174 final size:170
Alignment explanation
Indices: 303392--303775 Score: 565
Period size: 174 Copynumber: 2.2 Consensus size: 170
303382 AGACCTCTGG
* * *
303392 CTTCAATCTGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
303457 AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCC---
*
303522 ATTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATTA-TAT
128 --TTTAATCCGCTCCACTGTAATC-TCAAGGAGATAGGATTACTAT
* **
303566 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGACAAGATCTGCAATTCTTCGGTCTGTTCCACTGT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
* * * *
303631 AATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTTT
66 AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
* *
303696 GATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTAT
131 AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAT
* *
303736 CTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCT
303776 CTGGCTTCAA
Statistics
Matches: 192, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
169 34 0.18
170 41 0.21
174 117 0.61
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (170 bp):
CTTCGATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTACTCCACTGT
AACCTCAGAGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
AATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAT
Found at i:303789 original size:44 final size:43
Alignment explanation
Indices: 303356--303794 Score: 249
Period size: 44 Copynumber: 10.2 Consensus size: 43
303346 CACTTCAACT
* * * *
303356 TGCTCCGCTGTAATCTTAGGGAGATAAGACCTCTGGCTTCAATC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCTCT-GCTTCGATC
* * * *
303400 TGCTCCACTGTAACCTCAGGGGGATAAGATCTGCAATTCTTCGGTC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCT-C--TGCTTCGATC
* * * * *
303446 TACTCCACTGTAACCTCAGAGAGATAAGA-C-CTGATGCGATC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGCTTCGATC
* * * * ** **
303487 TACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATC
1 TGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTGCTTCGATC
* * * *
303531 CGCTCCACTGTAA-CTTCAGGGAGATAGGAT-TATATCTTCGATC
1 TGCTCCACTGTAATC-TCAGGGAGATAAGATCTCT-GCTTCGATC
* * * * *
303574 TGCTCCGCTGTAACCTCAGGGAGACAAGATCTGCAATTCTTCGGTC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCT-C--TGCTTCGATC
* *
303620 TGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGATGT-GATC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGCT-TCGATC
* * *
303661 TTCTCTACTGTAA-CTTCAGAGAGATAAGATC-CT--TT-GATC
1 TGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGCTTCGATC
* * * * * *
303700 CGCTCCATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCT-CT-GCTTCGATC
* *
303744 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAATCTCAGGGAGATAAGATCTCT-GCTTCGATC
303788 TGCTCCA
1 TGCTCCA
303795 ATGCAACCGA
Statistics
Matches: 305, Mismatches: 66, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
39 26 0.09
40 6 0.02
41 60 0.20
42 6 0.02
43 34 0.11
44 102 0.33
45 4 0.01
46 65 0.21
47 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (43 bp):
TGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGCTTCGATC
Found at i:303839 original size:86 final size:85
Alignment explanation
Indices: 303735--303946 Score: 232
Period size: 86 Copynumber: 2.5 Consensus size: 85
303725 AGGATTACTA
* * * *
303735 TCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCT-GCTCCAATG
1 TCTTTGATCTGCTTCGCTGTAAT-GCAGGAAGACAAGATCTACT-GCTTCAA-CTAGCTCCAATG
303798 CAACCGATGGAGGCAAGGCTTTG
63 CAACCGATGGAGGCAAGGCTTTG
* * * *
303821 TCTTTGATCTGCTTCGCTGTTAATGCAGGAAGGCAAGATCTACTTCTTTAACTAGCTCCACTGCA
1 TCTTTGATCTGCTTCGCTG-TAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCA
* *
303886 ATCGATGGATGCAAGGCTTTG
65 ACCGATGGAGGCAAGGCTTTG
* * *
303907 T-TTTCGATCTGCTTCGCTGTCAATGTAGAAAGGCAAGATC
1 TCTTT-GATCTGCTTCGCTGT-AATGCAGGAAGACAAGATC
303947 CTTTGTCTTC
Statistics
Matches: 109, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
85 6 0.06
86 97 0.89
87 6 0.06
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (85 bp):
TCTTTGATCTGCTTCGCTGTAATGCAGGAAGACAAGATCTACTGCTTCAACTAGCTCCAATGCAA
CCGATGGAGGCAAGGCTTTG
Found at i:305210 original size:1 final size:1
Alignment explanation
Indices: 305204--306000 Score: 1594
Period size: 1 Copynumber: 797.0 Consensus size: 1
305194 CTCTCCAAAG
305204 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305269 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305334 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305399 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305464 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305529 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305594 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305659 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305724 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305789 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305854 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305919 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
305984 TTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTT
306001 AGGAAGCAAA
Statistics
Matches: 796, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 796 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:313463 original size:60 final size:60
Alignment explanation
Indices: 313395--313514 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
313385 AAGCCAAGCT
313395 AATTCTCGGCCCCTGTCCGACTCTGACTCATACTTCAAACTTAATAGATCAGCCTGAACC
1 AATTCTCGGCCCCTGTCCGACTCTGACTCATACTTCAAACTTAATAGATCAGCCTGAACC
* *
313455 AATTCTCGGCCCCTGTCCGACTCTGATTCATACTTCAAACTTAATAGATCAGCTTGAACC
1 AATTCTCGGCCCCTGTCCGACTCTGACTCATACTTCAAACTTAATAGATCAGCCTGAACC
313515 GCTAGAGTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (60 bp):
AATTCTCGGCCCCTGTCCGACTCTGACTCATACTTCAAACTTAATAGATCAGCCTGAACC
Found at i:316967 original size:3 final size:3
Alignment explanation
Indices: 316959--316989 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
316949 NNNNNNNNNN
316959 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
316990 AGTTAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.