Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 90 of 170
Found at i:28191734 original size:32 final size:32
Alignment explanation
Indices: 28191683--28191748 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
28191673 TTTTACAAAA
*
28191683 AATTTACAAACTTCTATCTCCCTAATTATTTT
1 AATTAACAAACTTCTATCTCCCTAATTATTTT
*
28191715 AATTAACAAACATTC-ATCTCTCTAATTATTTT
1 AATTAACAAAC-TTCTATCTCCCTAATTATTTT
28191747 AA
1 AA
28191749 AATAGCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 28 0.90
33 3 0.10
ACGTcount: A:0.36, C:0.20, G:0.00, T:0.44
Consensus pattern (32 bp):
AATTAACAAACTTCTATCTCCCTAATTATTTT
Found at i:28193365 original size:40 final size:40
Alignment explanation
Indices: 28193313--28193423 Score: 152
Period size: 40 Copynumber: 2.8 Consensus size: 40
28193303 TCAAAGTTAT
* * * *
28193313 CGAAGTATAAATAGGGGTACGTAAGTGCATTTAGGGGTAT
1 CGAAGTACAAATAGGGGCACGTATGTGCATTTAGGGGTAC
* *
28193353 CGCAA-TACAAATAGAGGCACATATGTGCATTTAGGGGTAC
1 CG-AAGTACAAATAGGGGCACGTATGTGCATTTAGGGGTAC
28193393 CGAAGTACAAATAGGGGCACGTATGTGCATT
1 CGAAGTACAAATAGGGGCACGTATGTGCATT
28193424 CATTCTATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 2 0.03
40 57 0.93
41 2 0.03
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (40 bp):
CGAAGTACAAATAGGGGCACGTATGTGCATTTAGGGGTAC
Found at i:28197168 original size:13 final size:12
Alignment explanation
Indices: 28197145--28197197 Score: 79
Period size: 13 Copynumber: 4.2 Consensus size: 12
28197135 GTATTACGAG
*
28197145 ATTGTAAAAAAA
1 ATTGAAAAAAAA
28197157 ATTCGAAAAAAAA
1 ATT-GAAAAAAAA
28197170 ATTGAAAAAAAA
1 ATTGAAAAAAAA
28197182 ATTAGAAAAAAAA
1 ATT-GAAAAAAAA
28197195 ATT
1 ATT
28197198 TAATTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
12 15 0.39
13 23 0.61
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:28197173 original size:25 final size:25
Alignment explanation
Indices: 28197145--28197197 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
28197135 GTATTACGAG
* *
28197145 ATTGTAAAAAAAATTCGAAAAAAAA
1 ATTGAAAAAAAAATTAGAAAAAAAA
28197170 ATTGAAAAAAAAATTAGAAAAAAAA
1 ATTGAAAAAAAAATTAGAAAAAAAA
28197195 ATT
1 ATT
28197198 TAATTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (25 bp):
ATTGAAAAAAAAATTAGAAAAAAAA
Found at i:28198312 original size:18 final size:17
Alignment explanation
Indices: 28198264--28198341 Score: 66
Period size: 18 Copynumber: 4.4 Consensus size: 17
28198254 TTGGGAATAA
*
28198264 AAATGAGTGTGAAAAAG
1 AAATGAGAGTGAAAAAG
* * *
28198281 AAAAGAAAACTGAAAAAG
1 AAATG-AGAGTGAAAAAG
*
28198299 AAAGTGAGATTGAAGAAAG
1 AAA-TGAGAGTGAA-AAAG
* *
28198318 AAACGAGAGTGCAAAAG
1 AAATGAGAGTGAAAAAG
28198335 AAATGAG
1 AAATGAG
28198342 TGATATGATA
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
17 14 0.30
18 25 0.53
19 8 0.17
ACGTcount: A:0.58, C:0.04, G:0.27, T:0.12
Consensus pattern (17 bp):
AAATGAGAGTGAAAAAG
Found at i:28205547 original size:29 final size:29
Alignment explanation
Indices: 28205514--28205586 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
28205504 ATGTATTAGT
*
28205514 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
28205543 TTAGGACATATTTAAAACACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
28205572 TTAGGACATATTTAA
1 TTAGGACATATTTAA
28205587 TAATATCTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:28210272 original size:29 final size:29
Alignment explanation
Indices: 28210239--28210311 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
28210229 ATGTATTAGT
*
28210239 TTAGGACATATTTAAAACACTTGAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
*
28210268 TTAGGAAATATTTAAAACACTTAAACTAA
1 TTAGGACATATTTAAAACACTTAAACTAA
28210297 TTAGGACATATTTAA
1 TTAGGACATATTTAA
28210312 TAATATCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACTTAAACTAA
Found at i:28211452 original size:20 final size:20
Alignment explanation
Indices: 28211427--28211488 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
28211417 GCAGTATAAA
28211427 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * * **
28211447 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTATGTGCATT
*
28211467 CAGGGGCACATATGTGCATT
1 CAGGGGCACGTATGTGCATT
28211487 CA
1 CA
28211489 TTCAATAATT
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCATT
Found at i:28211483 original size:40 final size:40
Alignment explanation
Indices: 28211379--28211488 Score: 159
Period size: 40 Copynumber: 2.8 Consensus size: 40
28211369 ATGGGTACTA
* *
28211379 AAGTATAAACAGGGGCATATATGTG-ATTAAGAGGTACCG
1 AAGTATAAACAGGGGCACATATGTGCATTCAGAGGTACCG
* * *
28211418 CAGTATAAACAGGGGCACGTATGTGCATTCAGGGGTACCG
1 AAGTATAAACAGGGGCACATATGTGCATTCAGAGGTACCG
*
28211458 AAGTACAAACAGGGGCACATATGTGCATTCA
1 AAGTATAAACAGGGGCACATATGTGCATTCA
28211489 TTCAATAATT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 22 0.35
40 40 0.65
ACGTcount: A:0.35, C:0.16, G:0.28, T:0.21
Consensus pattern (40 bp):
AAGTATAAACAGGGGCACATATGTGCATTCAGAGGTACCG
Found at i:28220581 original size:20 final size:20
Alignment explanation
Indices: 28220545--28220583 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
28220535 CACATAAACT
*
28220545 CATACCATAAAGGCATCAAA
1 CATACCATAAAGACATCAAA
28220565 CATACCA-AAAGTACATCAA
1 CATACCATAAAG-ACATCAA
28220584 CCAAAATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.26, G:0.08, T:0.15
Consensus pattern (20 bp):
CATACCATAAAGACATCAAA
Found at i:28225674 original size:12 final size:12
Alignment explanation
Indices: 28225642--28225676 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28225632 ACATTTACAG
28225642 AAGAAGAAGAAT
1 AAGAAGAAGAAT
*
28225654 AATAAGAAGAAT
1 AAGAAGAAGAAT
*
28225666 AAGATGAAGAA
1 AAGAAGAAGAA
28225677 GAACCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (12 bp):
AAGAAGAAGAAT
Found at i:28226320 original size:18 final size:18
Alignment explanation
Indices: 28226297--28226334 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28226287 TGATTGAGGT
28226297 GTCAAATGTGGCATATTC
1 GTCAAATGTGGCATATTC
28226315 GTCAAATGTGGCATATTC
1 GTCAAATGTGGCATATTC
28226333 GT
1 GT
28226335 TAGGCACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (18 bp):
GTCAAATGTGGCATATTC
Found at i:28244185 original size:17 final size:17
Alignment explanation
Indices: 28244160--28244194 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28244150 AGTATTTATA
28244160 TATTATATATACATATT
1 TATTATATATACATATT
* *
28244177 TATTTTATATATATATT
1 TATTATATATACATATT
28244194 T
1 T
28244195 TTTAGAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATATACATATT
Found at i:28249311 original size:40 final size:40
Alignment explanation
Indices: 28249228--28249341 Score: 124
Period size: 40 Copynumber: 2.9 Consensus size: 40
28249218 AAAATGCCAA
* * *
28249228 TAAAAATCGAGCATTAGCGGCGCTTTATGAAAATCGGCAC
1 TAAAAATCGAGCATTAGCGGCGTTTTTTGAAAAACGGCAC
* * *
28249268 TAAAGATCGAGCATTAGCGGCATTTTTTGAAAAAC-GCTGC
1 TAAAAATCGAGCATTAGCGGCGTTTTTTGAAAAACGGC-AC
* *
28249308 TAAAAAT-GAGCATTCGCGGTGTTTTTTAGAAAAA
1 TAAAAATCGAGCATTAGCGGCGTTTTTT-GAAAAA
28249342 TGCTAGAAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
39 19 0.31
40 43 0.69
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (40 bp):
TAAAAATCGAGCATTAGCGGCGTTTTTTGAAAAACGGCAC
Found at i:28249442 original size:41 final size:41
Alignment explanation
Indices: 28249385--28249571 Score: 185
Period size: 41 Copynumber: 4.6 Consensus size: 41
28249375 TTCTTACCTT
* ** *
28249385 TCGGGGTTTTGGCGGTGTTTTCAAAAAAGCGTCGCTAATGC
1 TCGGGGTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
* * *
28249426 TCGGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGC
1 TCGGGGTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
* ** ** * *
28249467 TTGGGGTTTTAATGGCATTTTTGAAAAAGCGTCGCTAATGT
1 TCGGGGTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
28249508 TCGGTGTTTTAGCAGTATTTTTTAAAAAGCGCCGCTAATGC
1 TCGGGGTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
* * *
28249549 TAGGGGTTTTAGAGGCGTTTTTG
1 TCGGGGTTTTAGCGGTGTTTTTG
28249572 TGCTGGGGGC
Statistics
Matches: 113, Mismatches: 33, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
41 113 1.00
ACGTcount: A:0.20, C:0.14, G:0.29, T:0.36
Consensus pattern (41 bp):
TCGGGGTTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:28249500 original size:82 final size:82
Alignment explanation
Indices: 28249408--28249559 Score: 223
Period size: 82 Copynumber: 1.9 Consensus size: 82
28249398 GGTGTTTTCA
* * * * *
28249408 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGCTTGGGG
1 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCAGTATTTTTGAAAAAGCGCCGCTAATGCTAGGGG
28249473 TTTTAATGGCATTTTTG
66 TTTTAATGGCATTTTTG
* * * *
28249490 AAAAAGCGTCGCTAATGTTCGGTGTTTTAGCAGTATTTTTTAAAAAGCGCCGCTAATGCTAGGGG
1 AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCAGTATTTTTGAAAAAGCGCCGCTAATGCTAGGGG
28249555 TTTTA
66 TTTTA
28249560 GAGGCGTTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 61 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (82 bp):
AAAAAGCGTCGCTAATGCTCGGGGCTTTAGCAGTATTTTTGAAAAAGCGCCGCTAATGCTAGGGG
TTTTAATGGCATTTTTG
Found at i:28249580 original size:26 final size:26
Alignment explanation
Indices: 28249546--28249596 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
28249536 GCGCCGCTAA
*
28249546 TGCTAGGGGTTTTAGAGGCGTTTTTG
1 TGCTAGGGGCTTTAGAGGCGTTTTTG
* * *
28249572 TGCTGGGGGCTTTAGCGGTGTTTTT
1 TGCTAGGGGCTTTAGAGGCGTTTTT
28249597 AAAAAGCGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.08, C:0.10, G:0.39, T:0.43
Consensus pattern (26 bp):
TGCTAGGGGCTTTAGAGGCGTTTTTG
Found at i:28249615 original size:189 final size:190
Alignment explanation
Indices: 28249387--28249760 Score: 453
Period size: 189 Copynumber: 2.0 Consensus size: 190
28249377 CTTACCTTTC
* * * **
28249387 GGGGTTTTGGCGGTGTTTTCAAAAAAGCGTCGCTAATGCTCGGGGCTTTAGCGGTGTTTTTGAAA
1 GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
* * * * * ** * * *
28249452 ATGCGCCTCTAATGCTTGGGGTTTTAATGGCATTTTTGAAAAAGCGTCGCTAATGTTCGGTGTTT
66 AAGCGCCGCTAATGCTCGGGGTTTTAACGACATTTTTGAAAAAGCACCACTAATGCTCGGGGTTT
* * * *
28249517 TAGCAGTATTTTTTAAAAAGCGCCGCTAATGCTAGGGGTTTTAGAGGCGTTTTTGTGCTG
131 TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCCTTTTTGTGCTG
* * * * *
28249577 GGGGCTTTAGCGGTGTTTT-TAAAAAGCGCCGCTAATGCTCGGTGTTTTAGTGGCATTTTTTAAA
1 GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
* * *
28249641 AAGCGCCGCTAATGCTCGGGGTTTTAGCGACATTTTTTAGAAAGCACCACTAATGCTCGGGGTTT
66 AAGCGCCGCTAATGCTCGGGGTTTTAACGACATTTTTGAAAAAGCACCACTAATGCTCGGGGTTT
* * * * *
28249706 TAGCGGCATTTTTTAGAAAGCTCCACTAATGCTCGGGGCTTTAGCGGCCTTTTTG
131 TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCCTTTTTG
28249761 GAAAAGCGCC
Statistics
Matches: 152, Mismatches: 32, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
189 135 0.89
190 17 0.11
ACGTcount: A:0.20, C:0.17, G:0.28, T:0.35
Consensus pattern (190 bp):
GGGGCTTTAGCGGTGTTTTCAAAAAAGCGCCGCTAATGCTCGGGGCTTTAGCGGCATTTTTGAAA
AAGCGCCGCTAATGCTCGGGGTTTTAACGACATTTTTGAAAAAGCACCACTAATGCTCGGGGTTT
TAGCAGCATTTTTTAAAAAGCGCCACTAATGCTAGGGGCTTTAGAGGCCTTTTTGTGCTG
Found at i:28249631 original size:148 final size:149
Alignment explanation
Indices: 28249423--28249718 Score: 416
Period size: 148 Copynumber: 2.0 Consensus size: 149
28249413 GCGTCGCTAA
* * *
28249423 TGCTCGGGGCTTTAGCGGTGTTTTTGAAAATGCGCCTCTAATGCTTGGGGTTTTAATGGCATTTT
1 TGCTCGGGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAATGGCATTTT
* * * * * *
28249488 TGAAAAAGCGTCGCTAATGTTCGGTGTTTTAGC-AGTATTTTTTAAAAAGCGCCGCTAATGCTAG
66 TGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGA-CATTTTTTAAAAAGCACCACTAATGCTAG
*
28249552 GGGTTTTAGAGGCGTTTTTG
130 GGGTTTTAGAGGCATTTTTG
* * *
28249572 TGCTGGGGGCTTTAGCGGTGTTTTT-AAAAAGCGCCGCTAATGCTCGGTGTTTTAGTGGCATTTT
1 TGCTCGGGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAATGGCATTTT
* * *
28249636 TTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACATTTTTTAGAAAGCACCACTAATGCTCGG
66 TGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACATTTTTTAAAAAGCACCACTAATGCTAGG
*
28249701 GGTTTTAGCGGCATTTTT
131 GGTTTTAGAGGCATTTTT
28249719 TAGAAAGCTC
Statistics
Matches: 129, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
148 104 0.81
149 25 0.19
ACGTcount: A:0.20, C:0.16, G:0.28, T:0.36
Consensus pattern (149 bp):
TGCTCGGGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGTTTTAATGGCATTTT
TGAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACATTTTTTAAAAAGCACCACTAATGCTAGG
GGTTTTAGAGGCATTTTTG
Found at i:28249642 original size:41 final size:41
Alignment explanation
Indices: 28249592--28249816 Score: 288
Period size: 41 Copynumber: 5.5 Consensus size: 41
28249582 TTTAGCGGTG
* *
28249592 TTTTTAAAAAGCGCCGCTAATGCTCGGTGTTTTAGTGGCAT
1 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
*
28249633 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGACAT
1 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
* * *
28249674 TTTTTAGAAAGCACCACTAATGCTCGGGGTTTTAGCGGCAT
1 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
* * * * *
28249715 TTTTTAGAAAGCTCCACTAATGCTCGGGGCTTTAGCGGCCT
1 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
** * * * *
28249756 TTTTGGAAAAGCGCCGCTAATGCTAGGGGCTTTAGTGGCGT
1 TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
*
28249797 TTTTGAAAAAGCGCCGCTAA
1 TTTTTAAAAAGCGCCGCTAA
28249817 AAACATTTTA
Statistics
Matches: 165, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 165 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.32
Consensus pattern (41 bp):
TTTTTAAAAAGCGCCGCTAATGCTCGGGGTTTTAGCGGCAT
Found at i:28249677 original size:107 final size:108
Alignment explanation
Indices: 28249484--28249677 Score: 300
Period size: 107 Copynumber: 1.8 Consensus size: 108
28249474 TTTAATGGCA
* * *
28249484 TTTTTGAAAAAGCGTCGCTAATGTTCGGTGTTTTAGCAGTATTTTTTAAAAAGCGCCGCTAATGC
1 TTTTTGAAAAAGCGCCGCTAATGCTCGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGC
* *
28249549 TAGGGGTTTTAGAGGCGTTTTTGTGCTGGGGGCTTTAGCGGTG
66 TAGGGGTTTTAGAGACATTTTTGTGCTGGGGGCTTTAGCGGTG
**
28249592 TTTTT-AAAAAGCGCCGCTAATGCTCGGTGTTTTAGTGGCATTTTTTAAAAAGCGCCGCTAATGC
1 TTTTTGAAAAAGCGCCGCTAATGCTCGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGC
* *
28249656 TCGGGGTTTTAGCGACATTTTT
66 TAGGGGTTTTAGAGACATTTTT
28249678 TAGAAAGCAC
Statistics
Matches: 77, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
107 72 0.94
108 5 0.06
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.37
Consensus pattern (108 bp):
TTTTTGAAAAAGCGCCGCTAATGCTCGGTGTTTTAGCAGCATTTTTTAAAAAGCGCCGCTAATGC
TAGGGGTTTTAGAGACATTTTTGTGCTGGGGGCTTTAGCGGTG
Found at i:28250202 original size:15 final size:14
Alignment explanation
Indices: 28250164--28250198 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
28250154 ACTATTTTAA
28250164 GGTTTAGGGAGTAT
1 GGTTTAGGGAGTAT
*
28250178 GGATTTAGGGATTAT
1 GG-TTTAGGGAGTAT
28250193 GGTTTA
1 GGTTTA
28250199 AGGGTTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (14 bp):
GGTTTAGGGAGTAT
Found at i:28250473 original size:15 final size:15
Alignment explanation
Indices: 28250453--28250499 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
28250443 TATTTTAAGG
*
28250453 TTTAGGGAGTATGGA
1 TTTAGGGATTATGGA
*
28250468 TTTAGGGATTATAGA
1 TTTAGGGATTATGGA
28250483 -TTAGGGATTATGG-
1 TTTAGGGATTATGGA
28250496 TTTA
1 TTTA
28250500 AGTGTTAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.28, C:0.00, G:0.32, T:0.40
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:28250488 original size:14 final size:15
Alignment explanation
Indices: 28250453--28250493 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
28250443 TATTTTAAGG
* *
28250453 TTTAGGGAGTATGGA
1 TTTAGGGATTATAGA
28250468 TTTAGGGATTATAGA
1 TTTAGGGATTATAGA
28250483 -TTAGGGATTAT
1 TTTAGGGATTAT
28250494 GGTTTAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TTTAGGGATTATAGA
Found at i:28250527 original size:21 final size:22
Alignment explanation
Indices: 28250446--28250527 Score: 53
Period size: 21 Copynumber: 3.8 Consensus size: 22
28250436 GAGTTCATAT
*
28250446 TTTAAGGTTTAGGGAG-TATGGA
1 TTTAAGGTTTAGGG-GTTAGGGA
* * ** *
28250468 TTTAGGGATTATAGATTAGGGA
1 TTTAAGGTTTAGGGGTTAGGGA
* * *
28250490 -TTATGGTTTAAGTGTTA-GGA
1 TTTAAGGTTTAGGGGTTAGGGA
28250510 TTTAAGGTTTAGGGGTTA
1 TTTAAGGTTTAGGGGTTA
28250528 AGAGTTAGGG
Statistics
Matches: 43, Mismatches: 15, Indels: 5
0.68 0.24 0.08
Matches are distributed among these distances:
20 3 0.07
21 25 0.58
22 15 0.35
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.40
Consensus pattern (22 bp):
TTTAAGGTTTAGGGGTTAGGGA
Found at i:28250542 original size:21 final size:21
Alignment explanation
Indices: 28250518--28250558 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28250508 GATTTAAGGT
* *
28250518 TTAGGGGTTAAGAGTTAGGGG
1 TTAGAGGTTAAGAGCTAGGGG
28250539 TTAGAGGTTAAGAGCTAGGG
1 TTAGAGGTTAAGAGCTAGGG
28250559 ATTTAGTGTT
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:0.27, C:0.02, G:0.44, T:0.27
Consensus pattern (21 bp):
TTAGAGGTTAAGAGCTAGGGG
Found at i:28250899 original size:21 final size:21
Alignment explanation
Indices: 28250875--28250914 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28250865 TAGGGATTAT
*
28250875 GGTTTATGATTTAAGGGTTGG
1 GGTTTAAGATTTAAGGGTTGG
*
28250896 GGTTTAAGGTTTAAGGGTT
1 GGTTTAAGATTTAAGGGTT
28250915 AGAGATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGATTTAAGGGTTGG
Found at i:28259782 original size:15 final size:15
Alignment explanation
Indices: 28259762--28259812 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
28259752 ACTTTCATCA
28259762 TTCTTTTCATTCTTT
1 TTCTTTTCATTCTTT
*
28259777 TTCTTTTCACTCTTT
1 TTCTTTTCATTCTTT
*
28259792 TT-GTTTC-TCTCTTT
1 TTCTTTTCAT-TCTTT
28259806 TTCTTTT
1 TTCTTTT
28259813 TCTCGCTCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 11 0.37
15 19 0.63
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (15 bp):
TTCTTTTCATTCTTT
Found at i:28259798 original size:14 final size:15
Alignment explanation
Indices: 28259766--28259808 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
28259756 TCATCATTCT
* *
28259766 TTTCATTCTTTTTCT
1 TTTCACTCTTTTTCG
28259781 TTTCACTCTTTTT-G
1 TTTCACTCTTTTTCG
*
28259795 TTTCTCTCTTTTTC
1 TTTCACTCTTTTTC
28259809 TTTTTCTCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.05, C:0.23, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTCACTCTTTTTCG
Found at i:28259816 original size:14 final size:14
Alignment explanation
Indices: 28259772--28259816 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28259762 TTCTTTTCAT
*
28259772 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-TC
* *
28259787 TCTTTTTGTTTCTC
1 TCTTTTTCTTTTTC
28259801 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
28259815 TC
1 TC
28259817 GCTCGACAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:28261919 original size:14 final size:13
Alignment explanation
Indices: 28261900--28261935 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28261890 TGAACACAAA
28261900 AATTTTTTTTTTC
1 AATTTTTTTTTTC
28261913 GAA-TTTTTTTTTC
1 -AATTTTTTTTTTC
28261926 AATTTTTTTT
1 AATTTTTTTT
28261936 ACAATCTCGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.75
Consensus pattern (13 bp):
AATTTTTTTTTTC
Found at i:28261921 original size:13 final size:12
Alignment explanation
Indices: 28261903--28261940 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
28261893 ACACAAAAAT
28261903 TTTTTTTTTCGAA
1 TTTTTTTTTC-AA
28261916 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
28261928 TTTTTTTTACAA
1 TTTTTTTTTCAA
28261940 T
1 T
28261941 CTCGTAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.18, C:0.08, G:0.03, T:0.71
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:28276608 original size:50 final size:50
Alignment explanation
Indices: 28276502--28276613 Score: 125
Period size: 50 Copynumber: 2.2 Consensus size: 50
28276492 AAGAGGTCCC
* * * ** *
28276502 ATGTAAGACCATGTCTGGGACATGGCGTTGACACCGAGATGAGATGTCCC
1 ATGTAAGACCATGTCTGGGACATAGCATGGACACCGAGATGAGAACTCCA
** * * *
28276552 CCGTAAGACCATGTCTGGGACATAGCATGGGCACTGATATGAGAACTCCA
1 ATGTAAGACCATGTCTGGGACATAGCATGGACACCGAGATGAGAACTCCA
28276602 ATGTAAGACCAT
1 ATGTAAGACCAT
28276614 ATTTGGGATA
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.21
Consensus pattern (50 bp):
ATGTAAGACCATGTCTGGGACATAGCATGGACACCGAGATGAGAACTCCA
Found at i:28280611 original size:22 final size:22
Alignment explanation
Indices: 28280586--28280628 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28280576 AAGACCAATT
*
28280586 TTTCTCCTAAATTTTTATTTAG
1 TTTCTCCTAAATTTTAATTTAG
*
28280608 TTTCTCGTAAATTTTAATTTA
1 TTTCTCCTAAATTTTAATTTA
28280629 ACTATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTCTCCTAAATTTTAATTTAG
Found at i:28280681 original size:25 final size:24
Alignment explanation
Indices: 28280634--28280681 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
28280624 ATTTAACTAT
* *
28280634 TTAATTTTTAAATTTATTGAATTA
1 TTAATTTTTAAATTAATTAAATTA
*
28280658 TTAATATTTTATATTAATTAAATT
1 TTAAT-TTTTAAATTAATTAAATT
28280682 TTTGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATTTTTAAATTAATTAAATTA
Found at i:28283986 original size:18 final size:19
Alignment explanation
Indices: 28283958--28283994 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28283948 GAATTCACAT
*
28283958 CTTTCCTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTATCCA
28283977 CTTT-CTCTCTTCTATCCA
1 CTTTCCTCTCTTCTATCCA
28283995 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTATCCA
Found at i:28286395 original size:21 final size:21
Alignment explanation
Indices: 28286370--28286415 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
28286360 CAGTTGAAAC
28286370 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
28286391 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
28286412 CACA
1 CACA
28286416 TGATTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (21 bp):
CACACGAAAAGAATTATCCGA
Found at i:28289073 original size:17 final size:17
Alignment explanation
Indices: 28289051--28289098 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
28289041 AAAATAATAG
28289051 GGAAAAACTAT-AATTTT
1 GGAAAAA-TATGAATTTT
*
28289068 GGAAAAATGTGAATTTT
1 GGAAAAATATGAATTTT
28289085 GGACAAAAT-TGAAT
1 GGA-AAAATATGAAT
28289099 AGTACGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 21 0.75
18 5 0.18
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (17 bp):
GGAAAAATATGAATTTT
Found at i:28289092 original size:18 final size:16
Alignment explanation
Indices: 28289062--28289098 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
28289052 GAAAAACTAT
28289062 AATTTTGGAAAAATGTG
1 AATTTTGGAAAAAT-TG
28289079 AATTTTGGACAAAATTG
1 AATTTTGGA-AAAATTG
28289096 AAT
1 AAT
28289099 AGTACGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (16 bp):
AATTTTGGAAAAATTG
Found at i:28292045 original size:54 final size:55
Alignment explanation
Indices: 28291917--28292089 Score: 264
Period size: 54 Copynumber: 3.1 Consensus size: 55
28291907 ATGACAAATG
*
28291917 ATGGGCAAAACATGTCATGAAAC-TGTTGTGTTAATGGAA-AATAAAATAGAAGAGCGC
1 ATGGGCAAAA-ATGTCATGAAACATGTTGTGTTAATGGAAGAAT-AAA-AGAAGA-AGC
28291974 AT-GGCAAAAATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAA-AAGAAGC
1 ATGGGCAAAAATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAAGAAGAAGC
*
28292027 ATGGGCAAAAATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAAATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAAGAAGAAGC
28292082 ATGGGCAA
1 ATGGGCAA
28292090 TAAACTAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 10
0.91 0.01 0.08
Matches are distributed among these distances:
53 4 0.04
54 48 0.43
55 28 0.25
56 26 0.23
57 5 0.05
ACGTcount: A:0.45, C:0.09, G:0.24, T:0.23
Consensus pattern (55 bp):
ATGGGCAAAAATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAAGAAGAAGC
Found at i:28293425 original size:40 final size:40
Alignment explanation
Indices: 28293200--28293418 Score: 261
Period size: 40 Copynumber: 5.5 Consensus size: 40
28293190 AATGATGTCC
* * * *
28293200 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * *
28293240 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28293280 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCC-
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* *
28293318 GGTTAAGTCCTGAA-GCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
28293357 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
28293397 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
28293419 AACGAGTAGC
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 29 0.19
39 45 0.29
40 71 0.46
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:28297909 original size:20 final size:19
Alignment explanation
Indices: 28297872--28297910 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
28297862 GCATTCACAT
* *
28297872 CTTTCCTCTCTTCTTTCCA
1 CTTTCCTCTCTCCATTCCA
28297891 CTTTCTCTCTCTCCATTCCA
1 CTTTC-CTCTCTCCATTCCA
28297911 AAATTTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.49
Consensus pattern (19 bp):
CTTTCCTCTCTCCATTCCA
Found at i:28300269 original size:20 final size:20
Alignment explanation
Indices: 28300244--28300283 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28300234 TGAAACCACA
28300244 CGAAAAGAATTATCCGACAC
1 CGAAAAGAATTATCCGACAC
28300264 CGAAAAGAATTATCCGACAC
1 CGAAAAGAATTATCCGACAC
28300284 ATGATTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.15, T:0.15
Consensus pattern (20 bp):
CGAAAAGAATTATCCGACAC
Found at i:28302894 original size:17 final size:17
Alignment explanation
Indices: 28302872--28302919 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
28302862 TAAAATAAAG
28302872 GGAAAAACTAT-AATTTT
1 GGAAAAA-TATGAATTTT
*
28302889 GGAAAAATGTGAATTTT
1 GGAAAAATATGAATTTT
28302906 GGACAAAAT-TGAAT
1 GGA-AAAATATGAAT
28302920 AGTACGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 21 0.75
18 5 0.18
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (17 bp):
GGAAAAATATGAATTTT
Found at i:28302913 original size:18 final size:16
Alignment explanation
Indices: 28302883--28302919 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
28302873 GAAAAACTAT
28302883 AATTTTGGAAAAATGTG
1 AATTTTGGAAAAAT-TG
28302900 AATTTTGGACAAAATTG
1 AATTTTGGA-AAAATTG
28302917 AAT
1 AAT
28302920 AGTACGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (16 bp):
AATTTTGGAAAAATTG
Found at i:28308323 original size:22 final size:22
Alignment explanation
Indices: 28308298--28308340 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
28308288 AATACCAATT
*
28308298 TTTCTCCTAAATTTTTATTTAG
1 TTTCTCCTAAATTTTAATTTAG
*
28308320 TTTCTCGTAAATTTTAATTTA
1 TTTCTCCTAAATTTTAATTTA
28308341 ACTATTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTCTCCTAAATTTTAATTTAG
Found at i:28308393 original size:25 final size:24
Alignment explanation
Indices: 28308346--28308393 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
28308336 ATTTAACTAT
* *
28308346 TTAATTTTTAAATTTATTGAATTA
1 TTAATTTTTAAATTAATTAAATTA
*
28308370 TTAATATTTTATATTAATTAAATT
1 TTAAT-TTTTAAATTAATTAAATT
28308394 TTTGAGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTAATTTTTAAATTAATTAAATTA
Found at i:28311758 original size:18 final size:19
Alignment explanation
Indices: 28311730--28311766 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28311720 GAATTCACAT
*
28311730 CTTTCCTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTATCCA
28311749 CTTT-CTCTCTTCTATCCA
1 CTTTCCTCTCTTCTATCCA
28311767 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.08, C:0.41, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTATCCA
Found at i:28314168 original size:21 final size:21
Alignment explanation
Indices: 28314143--28314188 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
28314133 CAGTTGAAAC
28314143 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
28314164 CACACGAAAAGAATTATCCGA
1 CACACGAAAAGAATTATCCGA
28314185 CACA
1 CACA
28314189 TGATTTAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (21 bp):
CACACGAAAAGAATTATCCGA
Found at i:28316846 original size:17 final size:17
Alignment explanation
Indices: 28316824--28316871 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
28316814 AAAATAATAG
28316824 GGAAAAACTAT-AATTTT
1 GGAAAAA-TATGAATTTT
*
28316841 GGAAAAATGTGAATTTT
1 GGAAAAATATGAATTTT
28316858 GGACAAAAT-TGAAT
1 GGA-AAAATATGAAT
28316872 AGTACGTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 2 0.07
17 21 0.75
18 5 0.18
ACGTcount: A:0.46, C:0.04, G:0.19, T:0.31
Consensus pattern (17 bp):
GGAAAAATATGAATTTT
Found at i:28316865 original size:18 final size:16
Alignment explanation
Indices: 28316835--28316871 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
28316825 GAAAAACTAT
28316835 AATTTTGGAAAAATGTG
1 AATTTTGGAAAAAT-TG
28316852 AATTTTGGACAAAATTG
1 AATTTTGGA-AAAATTG
28316869 AAT
1 AAT
28316872 AGTACGTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (16 bp):
AATTTTGGAAAAATTG
Found at i:28318635 original size:33 final size:33
Alignment explanation
Indices: 28318567--28318636 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
28318557 CATAAAGATC
* *
28318567 TAAAATAAAATATTTGCAATATTTCAGTAATAA
1 TAAAATAAAATATTTGCAATATGTCAGAAATAA
*
28318600 TAAAATAAAATA-TTGTATATATGT-AGAAATAAA
1 TAAAATAAAATATTTGCA-ATATGTCAGAAAT-AA
28318633 TAAA
1 TAAA
28318637 CATGTAAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 9 0.28
33 23 0.72
ACGTcount: A:0.56, C:0.03, G:0.07, T:0.34
Consensus pattern (33 bp):
TAAAATAAAATATTTGCAATATGTCAGAAATAA
Found at i:28319862 original size:26 final size:26
Alignment explanation
Indices: 28319833--28319882 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28319823 CCACATTAGC
* *
28319833 TGGGCTAGGTTAATTGGGTTTTTGTT
1 TGGGCTAGGTTAAGTGGGTATTTGTT
28319859 TGGGCTAGGTTAAGTGGGTATTTG
1 TGGGCTAGGTTAAGTGGGTATTTG
28319883 GGATATGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.14, C:0.04, G:0.38, T:0.44
Consensus pattern (26 bp):
TGGGCTAGGTTAAGTGGGTATTTGTT
Found at i:28320336 original size:45 final size:44
Alignment explanation
Indices: 28320287--28320373 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
28320277 CGCCAGGAAA
* * *
28320287 ATAAGATTTGCTATTCTCAATCTGCCCCACTGTAACTTCAGGGCG
1 ATAAGAGTTG-TATTCTCAATCTGCCCCACTGCAACCTCAGGGCG
* * *
28320332 ATAAGAGTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGG
1 ATAAGAGTTGTATTCTCAATCTGCCCCACTGCAACCTCAGGG
28320374 AGACAAGACC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 27 0.75
45 9 0.25
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (44 bp):
ATAAGAGTTGTATTCTCAATCTGCCCCACTGCAACCTCAGGGCG
Found at i:28320483 original size:44 final size:44
Alignment explanation
Indices: 28320395--28321241 Score: 297
Period size: 44 Copynumber: 19.6 Consensus size: 44
28320385 GATGCGATTT
* * *
28320395 ACTGCAAATTC-AGAGAGATAAGATCTAT-TACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATCTGCTTCAATCCGCTCC
* * * *
28320439 ACTACAACTTCAAGGAGATAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * * ** * * *
28320483 ACTGCAACCTCAGGGAGATAAGATTTTCTTTTTCAGTCTGCCCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
** * * * * * ** *
28320527 ACTGTGACTTCAGGGGGATAAGACTTGTTTTC-TCTGTCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGA-TTATCTGCTTCAATCCGCTCC
* * * * * * *
28320571 ACTGCAACCTCAAGGAGATAAG---ACCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * *
28320612 ACTACAACTTC-AGAGAGATAAGATCTAT-TACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATCTGCTTCAATCCGCTCC
* * *
28320656 ACTACAACTTCAAGGAGA-AAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAA-GATTATCTGCTTCAATCCGCTCC
* * * * * * * * *
28320700 ACTGTAACCTCAGGGAGATAAG---ACCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * *
28320741 ACTGCAACTTC-AGAGTGATAAGATCTAT-TACTTTAATCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATCTGCTTCAATCCGCTCC
* * * * *
28320785 A---CAACTTTAGGGAGATAGGATTATCGGCTTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * * * *
28320826 ACTGCAACCTCAGGGAGATAAGATT-TACTTCTTCCATCTG-TCCC
1 ACTGCAACTTCAAGGAGATAAGATTAT-CTGCTTCAATCCGCT-CC
* * * * * * * *
28320870 ACTGCAACTTCAGGGGGATAAG---ACCTGATGCGATCCACTCT
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * *
28320911 ACTGCAACTTC-AGAGAGATAAGATCTAT-TACTTTAACCCGCTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATCTGCTTCAATCCGCTCC
* * * * * *
28320955 ACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * * *
28320999 ACTACAACCTCAAGGAGATAAGATTATTCAT-CTTCGATCTG-TCCC
1 ACTGCAACTTCAAGGAGATAAGATTA-TC-TGCTTCAATCCGCT-CC
* * * * *
28321044 ACTGCAACTTCAGGGGGATAAG---ACCTGCTTACTCAGTCTGCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGC-T--TCAATCCGCTCC
* * * * * * *
28321088 GCTGCAACCTCAGGGAGATAAGACCTA-ATG---CGATCCACTCC
1 ACTGCAACTTCAAGGAGATAAGA-TTATCTGCTTCAATCCGCTCC
* * * * *
28321129 ACTTCAACTTC-AGAGAGATAAGATATAT-TACTTTAACCCACTCC
1 ACTGCAACTTCAAG-GAGATAAGAT-TATCTGCTTCAATCCGCTCC
* * * * **
28321173 ACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTTCTCC
1 ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
* * *
28321217 ACTACAACCTCAGGGAGATAAGATT
1 ACTGCAACTTCAAGGAGATAAGATT
28321242 TACTATCTTC
Statistics
Matches: 584, Mismatches: 165, Indels: 108
0.68 0.19 0.13
Matches are distributed among these distances:
40 10 0.02
41 132 0.23
42 4 0.01
43 16 0.03
44 372 0.64
45 47 0.08
47 2 0.00
48 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
ACTGCAACTTCAAGGAGATAAGATTATCTGCTTCAATCCGCTCC
Found at i:28320695 original size:217 final size:213
Alignment explanation
Indices: 28320255--28320722 Score: 706
Period size: 217 Copynumber: 2.2 Consensus size: 213
28320245 TGCTGTTGTA
* * * * *
28320255 GCTTCAATCTGTTCCACTAC-ACCGCCAGGAAAATAAGATTTGCTATTCTCAATCTGCCCCACTG
1 GCTTCAATCTGCTCCACTGCAACC-TCAGGGAGATAAGATTTGCTATTCTCAATCTGCCCCACTG
* *
28320319 TAACTTCAGGGCGATAAGAGTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAGGGAGACAAGACC
65 TAACTTCAGGGCGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACC
*
28320384 TGATGCGATTTACTGCAAATTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTT
130 TGATGCGATTTACTACAAATTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTT
*
28320449 CAAGGAGATAGGATTATCG
195 CAAGGAGAAAGGATTATCG
* * *
28320468 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTTCT-TTTTCAGTCTGCCCCACTGT
1 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTATTCTCAATCTGCCCCACTGT
* * * *
28320532 GACTTCAGGGGGATAAGACTTGTTTTCTCTGTCTGCTCCACTGCAACCTCAAGGAGATAAGACCT
66 AACTTCAGGGCGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACCT
*
28320597 GATGCGATCCACTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACA
131 GATGCGAT----T-TACTACAAATTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACA
28320662 ACTTCAAGGAGAAAGGATTATCG
191 ACTTCAAGGAGAAAGGATTATCG
*
28320685 GCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGA
1 GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGA
28320723 CCTGATGCGA
Statistics
Matches: 231, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
212 85 0.37
213 34 0.15
214 3 0.01
216 1 0.00
217 108 0.47
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (213 bp):
GCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCTATTCTCAATCTGCCCCACTGT
AACTTCAGGGCGATAAGACTTGTTTTCTCAGTCTGCTCCACTGCAACCTCAAGGAGACAAGACCT
GATGCGATTTACTACAAATTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACTACAACTTC
AAGGAGAAAGGATTATCG
Found at i:28320698 original size:129 final size:129
Alignment explanation
Indices: 28320563--28321239 Score: 541
Period size: 129 Copynumber: 5.2 Consensus size: 129
28320553 GTTTTCTCTG
*
28320563 TCTGCTCCACTGCAACCTCAAGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
*
28320628 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAAGGAGAAAGGATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* * *
28320692 TCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGT
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
* *
28320757 GATAAGATCTATTACTTTAATCCGCT-C-C-ACAACTTTAGGGAGATAGGATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* * * * * *
28320818 TCTGCTCCACTGCAACCTCAGGGAGATAAGA-TTTACTTC-TTCCATCTGTCCCACTGCAACTTC
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGA-TGCGATCCA-C--T-CTACTACAACTTC
* * * * * * * * * *
28320881 AGGGGGATAAGACCTGA-TGC---GATCCACTCTACTGCAACTTCAGAGAGATAA-GATCTAT-T
61 AGAGAGATAAGATCT-ATTACTTTAATCCGCTCCACTACAACTTCAGGGAGA-AAGGAT-TATCG
* *
28320940 ACTTTAA
123 GCTTCAA
* * * * * * * * *
28320947 CCCGCTCCACTACAACTTCAGGGAGATAGGA--TTAT-CGGCCTCAATCTGCTCCACTACAACCT
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGC-G-ATCCA-CT-CT--ACTACAACTT
** * * *
28321009 CA-AGGAGATAAGAT-TATTCATCTTCGATCTG-TCCCACTGCAACTTCAGGGGGATAA-G---A
60 CAGA-GAGATAAGATCTATT-A-CTTTAATCCGCT-CCACTACAACTTCAGGGAGA-AAGGATTA
* * *
28321067 CCTGCTTACTCAG
120 TCGGC-T--TCAA
* * * *
28321080 TCTGCTCCGCTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTTCAACTTCAGAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
* * * *
28321145 GATAAGATATATTACTTTAACCCACTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAA
66 GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
* *
28321209 TCTTCTCCACTACAACCTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACCTCAGGGAGATAAGA
28321240 TTTACTATCT
Statistics
Matches: 433, Mismatches: 77, Indels: 76
0.74 0.13 0.13
Matches are distributed among these distances:
125 6 0.01
126 70 0.16
127 5 0.01
128 9 0.02
129 238 0.55
130 30 0.07
131 7 0.02
132 6 0.01
133 54 0.12
134 3 0.01
135 4 0.01
136 1 0.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.26
Consensus pattern (129 bp):
TCTGCTCCACTGCAACCTCAGGGAGATAAGACCTGATGCGATCCACTCTACTACAACTTCAGAGA
GATAAGATCTATTACTTTAATCCGCTCCACTACAACTTCAGGGAGAAAGGATTATCGGCTTCAA
Found at i:28320832 original size:85 final size:86
Alignment explanation
Indices: 28320741--28321026 Score: 255
Period size: 85 Copynumber: 3.3 Consensus size: 86
28320731 GATCCACTCT
* *
28320741 ACTGCAACTTCAGAGTGATAAGATCTATTACTTTAATCCGCT-CCACAACTTTAGGGAGATAGGA
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCCACAACTTCAGGGAGATAGGA
28320805 TTATCGGCTTCAATCTGCTCC
66 TTATCGGCTTCAATCTGCTCC
* * * ** * *
28320826 ACTGCAACCTCAGGGAGATAAGATTTACTT-CTTCCATCTG-TCCCACTGCAACTTCAGGGGGAT
1 ACTGCAACTTCAGAGAGATAAGATCTA-TTACTTTAATCCGCTCCCA---CAACTTCAGGGAGAT
* * * * * * ** *
28320889 A--A-GACCTGATGCGATCCACTCT
62 AGGATTATCGGCTTCAATCTGCTCC
*
28320911 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCC-C-ACAACTTCAGGGAGATAG
*
28320976 GATTATCGGCCTCAATCTGCTCC
64 GATTATCGGCTTCAATCTGCTCC
* *
28320999 ACTACAACCTCA-AGGAGATAAGAT-TATT
1 ACTGCAACTTCAGA-GAGATAAGATCTATT
28321027 CATCTTCGAT
Statistics
Matches: 150, Mismatches: 38, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
84 3 0.02
85 89 0.59
86 6 0.04
87 7 0.05
88 45 0.30
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (86 bp):
ACTGCAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCCACAACTTCAGGGAGATAGGA
TTATCGGCTTCAATCTGCTCC
Found at i:28321084 original size:89 final size:88
Alignment explanation
Indices: 28320817--28321110 Score: 244
Period size: 89 Copynumber: 3.4 Consensus size: 88
28320807 ATCGGCTTCA
* * * *
28320817 ATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TACTTCTTCCATCTGTCCCACTGCAACTTC
1 ATCTGCTCCACTGCAACCTCAAGGAGATAAGATTATTCATCTTCAATCTGTCCCACTGCAACTTC
* *
28320881 AGGGGGATAAGACCTG-ATGC-G
66 AGGGGGATAAGACCTGCATACTC
** * * * * * *
28320902 ATCCACTCTACTGCAACTTC-AGAGAGATAAGATCTATT-A-CTTTAACCCG-CTCCACTACAAC
1 ATCTGCTCCACTGCAACCTCAAG-GAGATAAGAT-TATTCATCTTCAATCTGTC-CCACTGCAAC
* * * * ***
28320963 TTCAGGGAGATAGGA-TTATCGGCCTC
63 TTCAGGGGGATAAGACCT-GCATACTC
* *
28320989 AATCTGCTCCACTACAACCTCAAGGAGATAAGATTATTCATCTTCGATCTGTCCCACTGCAACTT
1 -ATCTGCTCCACTGCAACCTCAAGGAGATAAGATTATTCATCTTCAATCTGTCCCACTGCAACTT
*
28321054 CAGGGGGATAAGACCTGCTTACTC
65 CAGGGGGATAAGACCTGCATACTC
* *
28321078 AGTCTGCTCCGCTGCAACCTCAGGGAGATAAGA
1 A-TCTGCTCCACTGCAACCTCAAGGAGATAAGA
28321111 CCTAATGCGA
Statistics
Matches: 155, Mismatches: 40, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
84 3 0.02
85 54 0.35
86 2 0.01
87 5 0.03
88 27 0.17
89 62 0.40
90 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (88 bp):
ATCTGCTCCACTGCAACCTCAAGGAGATAAGATTATTCATCTTCAATCTGTCCCACTGCAACTTC
AGGGGGATAAGACCTGCATACTC
Found at i:28321121 original size:218 final size:218
Alignment explanation
Indices: 28320871--28321289 Score: 714
Period size: 218 Copynumber: 1.9 Consensus size: 218
28320861 ATCTGTCCCA
* * * * *
28320871 CTGCAACTTCAGGGGGATAAGACCTGATGCGATCCACTCTACTGCAACTTCAGAGAGATAAGATC
1 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATA
*
28320936 TATTACTTTAACCCGCTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
66 TATTACTTTAACCCACTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
*
28321001 TACAACCTCAAGGAGATAAGA-TTATTCATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAA
131 TACAACCTCAAGGAGATAAGATTTACT-ATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAA
28321065 GACCTGCTTACTCAGTCTGCTCCG
195 GACCTGCTTACTCAGTCTGCTCCG
*
28321089 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTTCAACTTCAGAGAGATAAGATA
1 CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATA
* *
28321154 TATTACTTTAACCCACTCCACTACAACTTCAGGGAGATAGGATTATCGGCTTCAATCTTCTCCAC
66 TATTACTTTAACCCACTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
* *
28321219 TACAACCTCAGGGAGATAAGATTTACTATCTTCGATCTGTCCCACTGTAACTTCAGGGGGATAAG
131 TACAACCTCAAGGAGATAAGATTTACTATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAAG
28321284 ACCTGC
196 ACCTGC
28321290 AATTTCCCAA
Statistics
Matches: 188, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
218 184 0.98
219 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (218 bp):
CTGCAACCTCAGGGAGATAAGACCTAATGCGATCCACTCCACTGCAACTTCAGAGAGATAAGATA
TATTACTTTAACCCACTCCACTACAACTTCAGGGAGATAGGATTATCGGCCTCAATCTGCTCCAC
TACAACCTCAAGGAGATAAGATTTACTATCTTCGATCTGTCCCACTGCAACTTCAGGGGGATAAG
ACCTGCTTACTCAGTCTGCTCCG
Found at i:28321441 original size:129 final size:129
Alignment explanation
Indices: 28321281--28321722 Score: 731
Period size: 129 Copynumber: 3.4 Consensus size: 129
28321271 TCAGGGGGAT
* * *
28321281 AAGACCTGCAATTTCCCAACCTATTCCACTGCTAACCAGGGATATAGGACTTGTGGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
*
28321346 GCTTCCTTACACTTGAAGATAAGATTCGCCATCTTCGATCTGCTCCGCTACTGCTTAGGGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGAC
*
28321410 AAGATCTGTAATTTCCTAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
* * * *
28321475 ACTTCCTTACACTTGAAGATAAGATTCACCGTCTTCGACCTGCTCCGCTACTGCTTAGAGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGAC
* * *
28321539 AAGATCTGTAATTTCCCAACATGTTCCACTGCTGACCAGGGATGTAGGACTTGTGGCTTAAATCT
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
* ** * *
28321604 GCTTCCTTACACTTGAAGATAAGATTTGTTGTCTTCGATTTGCTCTGCTACTGCTTAGGGAGAC
66 GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGAC
28321668 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTG
1 AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTG
28321723 ATTTCACCGA
Statistics
Matches: 288, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 288 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (129 bp):
AAGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCT
GCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGAC
Found at i:28322988 original size:8 final size:8
Alignment explanation
Indices: 28322977--28323033 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
28322967 CATTTTTACT
28322977 TTTTCATA
1 TTTTCATA
28322985 TTTTCATA
1 TTTTCATA
28322993 TTTTCATA
1 TTTTCATA
28323001 TTTTC--A
1 TTTTCATA
*
28323007 TTTTCATTT
1 TTTTCA-TA
28323016 TTTTCAT-
1 TTTTCATA
28323023 TTTTCAT-
1 TTTTCATA
28323030 TTTT
1 TTTT
28323034 TTTACTCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
6 6 0.13
7 11 0.24
8 22 0.49
9 6 0.13
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTCATA
Found at i:28323018 original size:22 final size:22
Alignment explanation
Indices: 28322984--28323032 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
28322974 ACTTTTTCAT
28322984 ATTTTCA-TATTTTCATATTTTC
1 ATTTTCATTATTTTCAT-TTTTC
*
28323006 ATTTTCATTTTTTTCATTTTTC
1 ATTTTCATTATTTTCATTTTTC
28323028 ATTTT
1 ATTTT
28323033 TTTTACTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTTTCATTATTTTCATTTTTC
Found at i:28323035 original size:16 final size:15
Alignment explanation
Indices: 28322976--28323033 Score: 75
Period size: 16 Copynumber: 3.9 Consensus size: 15
28322966 TCATTTTTAC
28322976 TTTTTCATATTTTCA
1 TTTTTCATATTTTCA
28322991 TATTTTCATATTTTCA
1 T-TTTTCATATTTTCA
*
28323007 -TTTTCATTTTTTTCA
1 TTTTTCA-TATTTTCA
28323022 TTTTTCAT-TTTT
1 TTTTTCATATTTT
28323034 TTTACTCAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.26
15 9 0.23
16 20 0.51
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTCATATTTTCA
Found at i:28323928 original size:8 final size:8
Alignment explanation
Indices: 28323887--28323911 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
28323877 TCTCCTTTTC
28323887 TTTTTCCT
1 TTTTTCCT
28323895 TTTTTCCT
1 TTTTTCCT
28323903 TTTTTCCT
1 TTTTTCCT
28323911 T
1 T
28323912 CTCTCTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCCT
Found at i:28335077 original size:55 final size:56
Alignment explanation
Indices: 28334991--28335095 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 56
28334981 GAGCTATTTT
* * *
28334991 GAGAGTTACACAGCCTGGCACACTCATGTGTG-ACATGGCCGTGTGACCCTACCCA
1 GAGAGTTACACAGCCTGGCACACTAATGTGTGTACACGGCCATGTGACCCTACCCA
* *
28335046 GAGAGTTACACATG-CTGGGACAC-AATCGTGTGTCCACGGCCATGTGACCC
1 GAGAGTTACACA-GCCTGGCACACTAAT-GTGTGTACACGGCCATGTGACCC
28335096 CTGTTGTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
54 2 0.05
55 25 0.60
56 15 0.36
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.20
Consensus pattern (56 bp):
GAGAGTTACACAGCCTGGCACACTAATGTGTGTACACGGCCATGTGACCCTACCCA
Found at i:28339745 original size:50 final size:50
Alignment explanation
Indices: 28339563--28339749 Score: 259
Period size: 50 Copynumber: 3.8 Consensus size: 50
28339553 CACATCTCTA
* ** * * ** *
28339563 GCCGATGCC-TATCCCAGACATGGTCTTACACTTACTCTTCTTTGTCCGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGT
* *
28339612 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACTCCCCGGTCTGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGT
28339662 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGT
* *
28339712 GCCAATGCCATGTCCTAGACATGGTCTTACACTGGCAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCAC
28339750 ACTTACTGTT
Statistics
Matches: 124, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
49 9 0.07
50 115 0.93
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.27
Consensus pattern (50 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACTCCTCGGTCTGT
Found at i:28339833 original size:44 final size:44
Alignment explanation
Indices: 28339770--28339864 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
28339760 ATGGTCCAAC
* *
28339770 CATGGTCTTTTCCGTCAATTCTTTCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
*
28339814 CATGGACTTTTTCGTCAATTCTTCCTTAATTGCCATGTTATAAA
1 CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
28339858 CATGGAC
1 CATGGAC
28339865 CTTGAGATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (44 bp):
CATGGACTTTTCCGTCAATTCTTCCTTAATTGCCATGTTATAAA
Found at i:28348145 original size:260 final size:259
Alignment explanation
Indices: 28347703--28348221 Score: 821
Period size: 260 Copynumber: 2.0 Consensus size: 259
28347693 AAGTTCTTGA
* *
28347703 AAGTTCTTCAATGTAGAATTGAACCCAAAAATATATAATTCAAACGAGGATATTTGGAAACTTCT
1 AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAA--TCT
* *
28347768 TGAAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTATCATCTTCATCGAT
64 TGAAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTATCATCTTCATCAAC
* * *
28347833 GAATAAAGGTCAAACACTGTTTTCGGTTATGCTTTGTTAATAGTATTTATAATTTTTTTTTACTT
129 GAATAAAGGCCAAACACTGTTTTCGGTTATCCTTTGTGAATAGTATTTATAA--TTTTTTTACTT
28347898 AAGTTCTTGAATGTATAACTAATATTAAACTAATGTTTAG-AAGTGAAGTTTTAGTGCTGAAACA
192 AAGTTCTTGAATGTATAACTAATATTAAACTAATGTTT-GCAAGTGAAGTTTTAGTGCTGAAACA
28347962 TCTC
256 TCTC
* * *
28347966 AAGTTCTTCAATGTAGAACTGAACCCAGATATATATAATTCAAACGAGGAAATTTGGAAA-GTTG
1 AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAATCTTG
28348030 AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTA-CAATCTTCATCAACG
66 AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTATC-ATCTTCATCAACG
* * *
28348094 AATAAAGGCCGAACACCT-TTTTTGGTTATCCTTTGTGAGTAGTATTTATAATTTTTTTACTTAA
130 AATAAAGGCCAAACA-CTGTTTTCGGTTATCCTTTGTGAATAGTATTTATAATTTTTTTACTTAA
*
28348158 GTTCTTGGATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATC
194 GTTCTTGAATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATC
28348222 ATAAATGGCA
Statistics
Matches: 239, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
257 1 0.00
258 74 0.31
259 1 0.00
260 105 0.44
261 2 0.01
263 56 0.23
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.38
Consensus pattern (259 bp):
AAGTTCTTCAATGTAGAACTGAACCCAAAAATATATAATTCAAACGAGGAAATTTGGAAATCTTG
AAAGTTATTTGTAAAAATTTTGAAATTATAGGAATTATAGTGAAATCTATCATCTTCATCAACGA
ATAAAGGCCAAACACTGTTTTCGGTTATCCTTTGTGAATAGTATTTATAATTTTTTTACTTAAGT
TCTTGAATGTATAACTAATATTAAACTAATGTTTGCAAGTGAAGTTTTAGTGCTGAAACATCTC
Found at i:28351159 original size:11 final size:11
Alignment explanation
Indices: 28351143--28351190 Score: 78
Period size: 11 Copynumber: 4.4 Consensus size: 11
28351133 AATAAAGAAT
*
28351143 GATGCTTGATG
1 GATGCTTGAAG
28351154 GATGCTTGAAG
1 GATGCTTGAAG
28351165 GATGCTTGAAG
1 GATGCTTGAAG
*
28351176 GATGCTTGAGG
1 GATGCTTGAAG
28351187 GATG
1 GATG
28351191 ATGAATGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.29
Consensus pattern (11 bp):
GATGCTTGAAG
Found at i:28356738 original size:43 final size:41
Alignment explanation
Indices: 28356595--28356834 Score: 225
Period size: 41 Copynumber: 5.7 Consensus size: 41
28356585 TCTTTGAATG
* * * *
28356595 TAAGG-GGTTACTAAGTGCAGATTCCCCGAATCATTGATCAA
1 TAAGGTGGTTGCTAAGTGCTGATTCCCCGTATCATTGAT-TA
* *
28356636 AAAGG-GGTTGCTATGTGCTGATTCCCCGTATCATTGATTA
1 TAAGGTGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * *
28356676 TAAGGTGGTTGCTAAGTGCTGATTCCACTGTATCCTTGATTG
1 TAAGGTGGTTGCTAAGTGCTGATTCC-CCGTATCATTGATTA
* *
28356718 TGAAAGG-GGTTGCTATGTGCTGATTCCCCGTATCATTTATTA
1 T--AAGGTGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
* * * **
28356760 TAAGGTGGTTGCTAAGTGGTGATTCCACCGGGATCCTTTGAACA
1 TAAGGTGGTTGCTAAGTGCTGATTCC-CC-GTAT-CATTGATTA
* *
28356804 TGAGGTGGTTGCTAAGTGGTGATTCCACCGT
1 TAAGGTGGTTGCTAAGTGCTGATTCC-CCGT
28356835 GTAACGGTTA
Statistics
Matches: 166, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
40 9 0.05
41 70 0.42
42 27 0.16
43 23 0.14
44 37 0.22
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (41 bp):
TAAGGTGGTTGCTAAGTGCTGATTCCCCGTATCATTGATTA
Found at i:28360784 original size:41 final size:40
Alignment explanation
Indices: 28360739--28361392 Score: 276
Period size: 41 Copynumber: 15.6 Consensus size: 40
28360729 CTTTGAATGT
* *
28360739 AAGGGGTTGCTAAGTGCAGATTCCCTGAATCATTGATCAAA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGAT-AAA
* * * *
28360780 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * **
28360820 AAGGTGGTTGCTAAGTGCTGATTCCATC-ATATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGA-ATCATTGA-T-AAA
* * * * *
28360864 AAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * ** * **
28360904 AAGGTGGTTTCTAAGTGCTAATT-CCAAATTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCCCCGA--ATCATTGA-T-AAA
* * * * * *
28360948 AAGGGATTGCTACGTGGTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * * *
28360988 AAGGTGGTTGCTAAGTGTTGATTCCACTGTATCCTAAATTG-T-GA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAAT-C---ATTGATAAA
* * * * *
28361032 AAGGGGTTGCTATGTGCTAATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * * * **
28361072 AAGGTGGTTGCTAAGTGTTGATTCCATCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCATTGA-T-AAA
* * * * *
28361116 AAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * * * **
28361156 AAGGTGGTTGCTAAGTGTTGATTCCATCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCATTGA-T-AAA
* * * *
28361200 AAGGGGTTGCTACA-TGTTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTA-AGTGCTGATTCCCCGAATCATTGATAAA
* * * **
28361240 ATGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGA
1 AAGG-GGTTGCTAAGTGCTGATTCC-CCGAATCATTGA-T-AAA
* * * * *
28361284 AAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTAT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
* * * * *
28361324 AAGGTGGTAGCTAAGTGGTGATTCCACCGGGATCCTTTGA-ACAT
1 AAGG-GGTTGCTAAGTGCTGATTCC-CC-GAAT-CATTGATA-AA
*
28361368 GAGGTGGTTGCTAAGTGCTGATTCC
1 AAGG-GGTTGCTAAGTGCTGATTCC
28361393 ACCGTGTAAC
Statistics
Matches: 477, Mismatches: 97, Indels: 75
0.73 0.15 0.12
Matches are distributed among these distances:
38 4 0.01
39 1 0.00
40 36 0.08
41 159 0.33
42 100 0.21
43 112 0.23
44 60 0.13
45 1 0.00
46 4 0.01
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.36
Consensus pattern (40 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGATAAA
Found at i:28360882 original size:84 final size:84
Alignment explanation
Indices: 28360779--28361349 Score: 901
Period size: 84 Copynumber: 6.8 Consensus size: 84
28360769 CATTGATCAA
28360779 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
28360844 CATCATATCCTTGATTGTG
66 CATCGTATCCTTGATTGTG
* * *
28360863 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTTATTATAAGGTGGTTTCTAAGTGCTAATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
***
28360928 CAAATTATCCTTGATTGTG
66 CATCGTATCCTTGATTGTG
* * * *
28360947 AAAGGGATTGCTACGTGGTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
**
28361012 CA-CTGTATCCTAAATTGTG
66 CATC-GTATCCTTGATTGTG
* *
28361031 AAAGGGGTTGCTATGTGCTAATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28361096 CATCGTATCCTTGATTGTG
66 CATCGTATCCTTGATTGTG
* *
28361115 AAAGGGGTTGCTATGTGCTGATTCCCTGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28361180 CATCGTATCCTTGATTGTG
66 CATCGTATCCTTGATTGTG
** * *
28361199 AAAGGGGTTGCTACATGTTGATTCCCCGTATCATTGATTATATGGTGGTTGCTAAGTGCTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
*
28361264 CACCGTATCCTTGATTGTG
66 CATCGTATCCTTGATTGTG
* * *
28361283 AAAGGGGTTGCTATGTGTTGATTCCCCGTATCATTGATTATAAGGTGGTAGCTAAGTGGTGATTC
1 AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
28361348 CA
66 CA
28361350 CCGGGATCCT
Statistics
Matches: 448, Mismatches: 37, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
84 447 1.00
85 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (84 bp):
AAAGGGGTTGCTATGTGCTGATTCCCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
CATCGTATCCTTGATTGTG
Found at i:28361390 original size:44 final size:42
Alignment explanation
Indices: 28360784--28361397 Score: 511
Period size: 42 Copynumber: 14.6 Consensus size: 42
28360774 ATCAAAAAGG
* * *
28360784 GGTTGCTATGTGCTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * *
28360825 GGTTGCTAAGTGCTGATTCCATCATATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * *
28360868 GGTTGCTATGTGCTGATTCC-CCGTATCATTTATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * *** *
28360909 GGTTTCTAAGTGCTAATTCCAAATTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * * *
28360952 GATTGCTACGTGGTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * ** *
28360993 GGTTGCTAAGTGTTGATTCCACTGTATCCTAAATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * *
28361036 GGTTGCTATGTGCTAATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * *
28361077 GGTTGCTAAGTGTTGATTCCATCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * *
28361120 GGTTGCTATGTGCTGATTCC-CTGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * *
28361161 GGTTGCTAAGTGTTGATTCCATCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* *
28361204 GGTTGCTACA-TGTTGATTCC-CCGTATCATTGATTAT-ATGGT
1 GGTTGCTA-AGTGCTGATTCCACCGTATCCTTGATTATGA-GGT
*
28361245 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATG--AGGT
* * * *
28361288 GGTTGCTATGTGTTGATTCC-CCGTATCATTGATTATAAGGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
* * * **
28361329 GGTAGCTAAGTGGTGATTCCACCGGGATCCTTTGAACATGAGGT
1 GGTTGCTAAGTGCTGATTCCACC-GTATCC-TTGATTATGAGGT
28361373 GGTTGCTAAGTGCTGATTCCACCGT
1 GGTTGCTAAGTGCTGATTCCACCGT
28361398 GTAACGGTTA
Statistics
Matches: 447, Mismatches: 95, Indels: 60
0.74 0.16 0.10
Matches are distributed among these distances:
39 1 0.00
40 18 0.04
41 122 0.27
42 146 0.33
43 110 0.25
44 49 0.11
45 1 0.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAGGT
Found at i:28369689 original size:30 final size:32
Alignment explanation
Indices: 28369648--28369707 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
28369638 GTCACTGTAC
*
28369648 TGGGCTTAGGCCCACTTG-TTCTGTATTGGTT
1 TGGGCTTAGGCCCAATTGATTCTGTATTGGTT
*
28369679 TGGGC-TAGGCCCAATTGATTCTGTTTTGG
1 TGGGCTTAGGCCCAATTGATTCTGTATTGG
28369708 ATGCGACCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.12, C:0.18, G:0.30, T:0.40
Consensus pattern (32 bp):
TGGGCTTAGGCCCAATTGATTCTGTATTGGTT
Found at i:28373417 original size:13 final size:13
Alignment explanation
Indices: 28373399--28373434 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
28373389 GGCTTATCGG
28373399 TAATGTTTTTTAC
1 TAATGTTTTTTAC
28373412 TAATGTTTTTTAC
1 TAATGTTTTTTAC
*
28373425 TAAGGTTTTT
1 TAATGTTTTT
28373435 AGAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.22, C:0.06, G:0.11, T:0.61
Consensus pattern (13 bp):
TAATGTTTTTTAC
Found at i:28377374 original size:66 final size:66
Alignment explanation
Indices: 28377268--28377410 Score: 171
Period size: 66 Copynumber: 2.2 Consensus size: 66
28377258 GACTTACCTC
* * * * * * *
28377268 GTGTTTACTGTCCCGATGTACTTTCTTTGTTCCGTGTTTACCCTCTCGGTGGACTATCTCTATTT
1 GTGTTTACTGTCCCAATGAAATTTCTTTGTTCCATGTTTACCCTCCCGATGGACTATCTCTATTC
28377333 T
66 T
* ** *
28377334 GTGTTTATTGTCCCAATGAAATTT-TTCTGTTCCATGTTTACTGTCCCGATGTACTATCTCTATT
1 GTGTTTACTGTCCCAATGAAATTTCTT-TGTTCCATGTTTACCCTCCCGATGGACTATCTCTATT
28377398 CT
65 CT
28377400 GTGTTTACTGT
1 GTGTTTACTGT
28377411 TCCGATAGAC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 2 0.03
66 62 0.97
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.48
Consensus pattern (66 bp):
GTGTTTACTGTCCCAATGAAATTTCTTTGTTCCATGTTTACCCTCCCGATGGACTATCTCTATTC
T
Found at i:28377405 original size:33 final size:33
Alignment explanation
Indices: 28377267--28377416 Score: 120
Period size: 33 Copynumber: 4.5 Consensus size: 33
28377257 TGACTTACCT
* * *
28377267 CGTGTTTACTGTCCCGATGTACTTTCTTTGTTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
** * * * *
28377300 CGTGTTTACCCTCTCGGTGGACTATCTCTATTT
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
* * * * * * * *
28377333 TGTGTTTATTGTCCCAATGAAATTTTTCTGTTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
*
28377366 CATGTTTACTGTCCCGATGTACTATCTCTATTC
1 CGTGTTTACTGTCCCGATGTACTATCTCTATTC
* *
28377399 TGTGTTTACTGTTCCGAT
1 CGTGTTTACTGTCCCGAT
28377417 AGACTTTCTC
Statistics
Matches: 83, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
33 83 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.47
Consensus pattern (33 bp):
CGTGTTTACTGTCCCGATGTACTATCTCTATTC
Found at i:28380107 original size:20 final size:19
Alignment explanation
Indices: 28380082--28380186 Score: 86
Period size: 20 Copynumber: 5.3 Consensus size: 19
28380072 TACTTCGATA
28380082 CCCCTGATTGCACATACGTG
1 CCCCTGATTGCAC-TACGTG
* * * *
28380102 CCCCTGTTTGTACTTCGGTA
1 CCCCTGATTGCACTAC-GTG
*
28380122 CCCCTGACTGCACTTACGTG
1 CCCCTGATTGCAC-TACGTG
* * *
28380142 CCCCTG-TTGTACTTCGGTA
1 CCCCTGATTGCACTAC-GTG
28380161 CCCCTGATTGCACATACGTG
1 CCCCTGATTGCAC-TACGTG
28380181 CCCCTG
1 CCCCTG
28380187 TTTGTACTTC
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.03
19 14 0.22
20 44 0.69
21 4 0.06
ACGTcount: A:0.14, C:0.36, G:0.20, T:0.30
Consensus pattern (19 bp):
CCCCTGATTGCACTACGTG
Found at i:28380182 original size:79 final size:79
Alignment explanation
Indices: 28380047--28380460 Score: 605
Period size: 79 Copynumber: 5.2 Consensus size: 79
28380037 AATTATTGTA
* * *
28380047 TGAATGCACTTACGTGCCTCTATTATACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTG
1 TGAATGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTG
28380112 TACTTCGGTACCCC
66 TACTTCGGTACCCC
* *
28380126 TGACTGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTG
1 TGAATGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTG
28380191 TACTTCGGTACCCC
66 TACTTCGGTACCCC
* * * * *
28380205 TAAATACACTTACATG-CCCTAGTTGTACTTCGATACCCCTGATTGCACATACATGCCCTTGTTT
1 TGAATGCACTTACGTGCCCCT-GTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTT
* *
28380269 GTAGTTTGGTACCCC
65 GTACTTCGGTACCCC
* * *
28380284 TGAATGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTACCTCTGTTGG
1 TGAATGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTG
*
28380349 TACTTCAGTACCCC
66 TACTTCGGTACCCC
* * ** *
28380363 TGGATGCACTTACGTGCCCCTATTTGTACTTCGATACCCCTGATTGCACATTTGTTCCCCTGTTT
1 TGAATGCACTTACGTGCCCCT-GTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTT
*
28380428 GTACTTTGGTACCCC
65 GTACTTCGGTACCCC
28380443 TGAATGCACTTACGTGCC
1 TGAATGCACTTACGTGCC
28380461 ACTATTTATA
Statistics
Matches: 297, Mismatches: 35, Indels: 5
0.88 0.10 0.01
Matches are distributed among these distances:
78 4 0.01
79 222 0.75
80 71 0.24
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (79 bp):
TGAATGCACTTACGTGCCCCTGTTGTACTTCGATACCCCTGATTGCACATACGTGCCCCTGTTTG
TACTTCGGTACCCC
Found at i:28380453 original size:20 final size:19
Alignment explanation
Indices: 28380277--28380453 Score: 65
Period size: 20 Copynumber: 8.9 Consensus size: 19
28380267 TTGTAGTTTG
* *
28380277 GTACCCCTGAATGCACTTAC
1 GTACCCCTGATTGCACTT-T
* * *
28380297 GTGCCCCTG-TTGTACTTC
1 GTACCCCTGATTGCACTTT
**
28380315 GATACCCCTGATTGCACATAC
1 G-TACCCCTGATTGCAC-TTT
* * *
28380336 GTACCTCTG-TTGGTACTTCA
1 GTACCCCTGATT-GCACTT-T
*
28380356 GTACCCCTGGA-TGCACTTAC
1 GTACCCCT-GATTGCACTT-T
* * *
28380376 GTGCCCCT-ATTTGTACTTC
1 GTACCCCTGA-TTGCACTTT
28380395 GATACCCCTGATTGCACATTT
1 G-TACCCCTGATTGCAC-TTT
* * *
28380416 GTTCCCCTGTTTGTACTTT
1 GTACCCCTGATTGCACTTT
*
28380435 GGTACCCCTGAATGCACTT
1 -GTACCCCTGATTGCACTT
28380454 ACGTGCCACT
Statistics
Matches: 118, Mismatches: 26, Indels: 26
0.69 0.15 0.15
Matches are distributed among these distances:
18 3 0.03
19 21 0.18
20 85 0.72
21 9 0.08
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.34
Consensus pattern (19 bp):
GTACCCCTGATTGCACTTT
Found at i:28380478 original size:40 final size:40
Alignment explanation
Indices: 28380047--28380487 Score: 473
Period size: 40 Copynumber: 11.1 Consensus size: 40
28380037 AATTATTGTA
* * * *
28380047 TGAATGCACTTACGTGCCTCT-ATTATACTTCGATACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
28380086 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
*
28380126 TGACTGCACTTACGTGCCCCTG-TTGTACTTCGGTACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
28380165 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
28380205 TAAATACACTTACATG-CCCTAG-TTGTACTTCGATACCCC
1 TGAATGCACTTACGTGCCCCT-GTTTGTACTTCGGTACCCC
* * * * * *
28380244 TGATTGCACATACATGCCCTTGTTTGTAGTTTGGTACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
*
28380284 TGAATGCACTTACGTGCCCCTG-TTGTACTTCGATACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * * *
28380323 TGATTGCACATACGTACCTCTGTTGGTACTTCAGTACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
28380363 TGGATGCACTTACGTGCCCCTATTTGTACTTCGATACCCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
28380403 TGATTGCACATT-TGTTCCCCTGTTTGTACTTTGGTACCCC
1 TGAATGCAC-TTACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
28380443 TGAATGCACTTACGTGCCACTATTTATAC-TCTGGTAACCC
1 TGAATGCACTTACGTGCCCCTGTTTGTACTTC-GGTACCCC
28380483 TGAAT
1 TGAAT
28380488 CAAATAGAAT
Statistics
Matches: 331, Mismatches: 62, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
39 123 0.37
40 206 0.62
41 2 0.01
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (40 bp):
TGAATGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:28385390 original size:50 final size:50
Alignment explanation
Indices: 28385262--28385456 Score: 160
Period size: 50 Copynumber: 3.9 Consensus size: 50
28385252 GATAATAACA
* * ** * * *
28385262 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAT-CGG
** ** * **
28385311 TGCCAATACCACATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * * ** *
28385361 TGCCCATGCCATGTCCCAGACATAGTCTTACGGGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* * *
28385411 TGCCAACGCCATGTTCCAGGCATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATA
28385457 ACCTCAATAA
Statistics
Matches: 113, Mismatches: 31, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
48 1 0.01
49 36 0.32
50 76 0.67
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:28390987 original size:50 final size:50
Alignment explanation
Indices: 28390881--28391121 Score: 250
Period size: 50 Copynumber: 4.7 Consensus size: 50
28390871 GGGAGTGAGA
* **
28390881 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGAACATGGCATTGGC---ACCGA-G--ATGAGAGG
* *
28390937 TCCCATGTAAGACCATGCCTGGAACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATGAGAGG
* * * * *
28390987 TCCCATGGAAGACCATATTTGGGACATCGCATTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATGAGAGG
* * * **
28391037 TCCCCCT-TAAGACCATGTCTGGAACATGGCATGGGCACCGATATGAGAAC
1 T-CCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATGAGAGG
* * *
28391087 TCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGAACATGGCATTGG
28391122 TAGTACAGAA
Statistics
Matches: 156, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
49 4 0.03
50 111 0.71
51 4 0.03
52 1 0.01
53 3 0.02
56 33 0.21
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGAACATGGCATTGGCACCGAGATGAGAGG
Found at i:28404830 original size:15 final size:15
Alignment explanation
Indices: 28404810--28404864 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
28404800 ACTCTCAACA
*
28404810 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
28404825 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
28404840 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
28404854 TTCTTTT-TCTC
1 TTCTTTTCTCTC
28404865 GCTCGATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:28405977 original size:12 final size:12
Alignment explanation
Indices: 28405960--28405984 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28405950 TTTCGCATGA
28405960 CAGCCTTCATTT
1 CAGCCTTCATTT
28405972 CAGCCTTCATTT
1 CAGCCTTCATTT
28405984 C
1 C
28405985 GCATGACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CAGCCTTCATTT
Found at i:28416331 original size:20 final size:20
Alignment explanation
Indices: 28416303--28416348 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
28416293 GCTGATAGAA
*
28416303 AGCTAAATTGAGCTCGAATG
1 AGCTAAATTGAGCTCAAATG
*
28416323 AGCTGAATTGAGCTCAAATG
1 AGCTAAATTGAGCTCAAATG
28416343 AGCTAA
1 AGCTAA
28416349 TCGAAGCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (20 bp):
AGCTAAATTGAGCTCAAATG
Found at i:28416356 original size:20 final size:19
Alignment explanation
Indices: 28416312--28416368 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
28416302 AAGCTAAATT
* *
28416312 GAGCTCGAATGAGCTGAATT
1 GAGCTCAAATGAGCT-AATC
28416332 GAGCTCAAATGAGCTAATC
1 GAGCTCAAATGAGCTAATC
* *
28416351 GAAGCTGAAACGAGCTAA
1 G-AGCTCAAATGAGCTAA
28416369 AGGAGCTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (19 bp):
GAGCTCAAATGAGCTAATC
Found at i:28417990 original size:24 final size:24
Alignment explanation
Indices: 28417954--28418001 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
28417944 CATTTCATAC
*
28417954 CAAATCCCGTACCATTTCGTACCA
1 CAAATCCCATACCATTTCGTACCA
*
28417978 CAAATCTCATACCATTTCGTACCA
1 CAAATCCCATACCATTTCGTACCA
28418002 ATACCCAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.27
Consensus pattern (24 bp):
CAAATCCCATACCATTTCGTACCA
Found at i:28419703 original size:22 final size:24
Alignment explanation
Indices: 28419666--28419709 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
28419656 TGTTTGGAAC
28419666 GATTTCAAGAATCAAGAAAATCAA
1 GATTTCAAGAATCAAGAAAATCAA
*
28419690 GATTTC-A-AATCAAGGAAATC
1 GATTTCAAGAATCAAGAAAATC
28419710 GTGGTCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 1 0.05
24 6 0.32
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.23
Consensus pattern (24 bp):
GATTTCAAGAATCAAGAAAATCAA
Found at i:28426413 original size:18 final size:18
Alignment explanation
Indices: 28426392--28426430 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
28426382 AAAGGAAGAT
28426392 AGAAAAAGA-AATTGAAAA
1 AGAAAAAGAGAA-TGAAAA
28426410 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
28426428 AGA
1 AGA
28426431 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.08
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:28426460 original size:33 final size:33
Alignment explanation
Indices: 28426420--28426487 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
28426410 AGAAAAAGAG
28426420 AATGAAAAAGAGCAAAAAGAGATTGAGAGTGAA
1 AATGAAAAAGAGCAAAAAGAGATTGAGAGTGAA
28426453 AATGAAAAAGAGCAAAAAGAGATTGAGAGTGAA
1 AATGAAAAAGAGCAAAAAGAGATTGAGAGTGAA
28426486 AA
1 AA
28426488 GGAATGTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.59, C:0.03, G:0.26, T:0.12
Consensus pattern (33 bp):
AATGAAAAAGAGCAAAAAGAGATTGAGAGTGAA
Found at i:28428266 original size:33 final size:34
Alignment explanation
Indices: 28428229--28428300 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
28428219 GAGTTAGTTT
28428229 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
* *
28428262 ATTAATTTTAGTTCAGCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
28428296 ATTAA
1 ATTAA
28428301 TTTGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 30 0.83
34 6 0.17
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.40
Consensus pattern (34 bp):
ATTAAATTTAGTTCAGCTCAAATAAGTGTTAGTA
Found at i:28435428 original size:20 final size:20
Alignment explanation
Indices: 28435388--28435428 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28435378 GTAATGAAAG
*
28435388 AAAGAAAAAAAGAAATCAAA
1 AAAGAAAAAAAGAAATAAAA
* *
28435408 AAAGAAAAAGAGAATTAAAA
1 AAAGAAAAAAAGAAATAAAA
28435428 A
1 A
28435429 GTGCAAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.07
Consensus pattern (20 bp):
AAAGAAAAAAAGAAATAAAA
Found at i:28445458 original size:25 final size:25
Alignment explanation
Indices: 28445430--28445477 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
28445420 CAACTTCTAA
28445430 AGAAAA-CTCAAGAGAGAATTCTTGG
1 AGAAAAGCTCAAG-GAGAATTCTTGG
28445455 AGAAAAGCTCAAGGAGAATTCTT
1 AGAAAAGCTCAAGGAGAATTCTT
28445478 CACTTAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (25 bp):
AGAAAAGCTCAAGGAGAATTCTTGG
Found at i:28448318 original size:17 final size:18
Alignment explanation
Indices: 28448279--28448318 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
28448269 AGAGACTTTG
*
28448279 GAAAAAGAAAATGAGTTA
1 GAAAAAGAAAATGAGTGA
28448297 GAAAAAG-AAATGAGTG-
1 GAAAAAGAAAATGAGTGA
28448313 GAAAAA
1 GAAAAA
28448319 TGAGAGAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (18 bp):
GAAAAAGAAAATGAGTGA
Found at i:28452268 original size:6 final size:6
Alignment explanation
Indices: 28452257--28452305 Score: 64
Period size: 6 Copynumber: 8.0 Consensus size: 6
28452247 CTTTATTTTA
*
28452257 TTTTCT TTTTCT TTTTCACT CTTT-T TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTT--CT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
28452306 ACAGTCTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 4 0.11
6 29 0.76
8 5 0.13
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:28452518 original size:18 final size:16
Alignment explanation
Indices: 28452480--28452518 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
28452470 ATGCATATTA
*
28452480 CTTGTACAGATTGTAG
1 CTTGTACAGATTGGAG
28452496 CTTGTACAGATTCGGATG
1 CTTGTACAGATT-GGA-G
28452514 CTTGT
1 CTTGT
28452519 TCGTGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (16 bp):
CTTGTACAGATTGGAG
Found at i:28453987 original size:20 final size:20
Alignment explanation
Indices: 28453939--28453987 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
28453929 TTTAACTTAG
28453939 TTCAGCTCACTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
* * *
28453959 GTCAACTCATTCGAGCTCAA
1 TTCAGCTCACTCGAGCTCAA
28453979 TTCAGCTCA
1 TTCAGCTCA
28453988 ATCTTAACCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (20 bp):
TTCAGCTCACTCGAGCTCAA
Found at i:28454110 original size:23 final size:25
Alignment explanation
Indices: 28454054--28454111 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
28454044 AATAAACCAT
28454054 TTAATTTGTTTTTAGTTAAAGTTAAA
1 TTAATTTGTTTTTA-TTAAAGTTAAA
*
28454080 TT-AGTTGTTTATT-TT-AAGTT-AA
1 TTAATTTGTTT-TTATTAAAGTTAAA
28454102 TTAATTTGTT
1 TTAATTTGTT
28454112 AAAATCTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.14
23 11 0.39
24 2 0.07
25 7 0.25
26 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (25 bp):
TTAATTTGTTTTTATTAAAGTTAAA
Found at i:28457488 original size:233 final size:233
Alignment explanation
Indices: 28457074--28457539 Score: 896
Period size: 233 Copynumber: 2.0 Consensus size: 233
28457064 AAGATTTCAC
28457074 AACTCCATTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
1 AACTCCATTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
*
28457139 TGGCTTCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
66 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
*
28457204 AGAACTCAAAGAGAATTTTCACTCAAAGTAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
131 AGAACTCAAAGAGAATTTTCACTCAAAGCAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
28457269 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
196 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
*
28457307 AACTCCCTTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
1 AACTCCATTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
*
28457372 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAGAAAATTCTTGA
66 TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
28457437 AGAACTCAAAGAGAATTTTCACTCAAAGCAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
131 AGAACTCAAAGAGAATTTTCACTCAAAGCAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
28457502 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
196 ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
28457540 CTATTTTCTA
Statistics
Matches: 229, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
233 229 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (233 bp):
AACTCCATTCAAACGGCTCTAATCTCCCCTCCAATGAAGAACAATGGCAAGAAGAAGGCTTAAGA
TGGCTCCCACAATCAAAGAGATTGTTAAAACTACTTCCAAAGAAAACTCAAGAAAAAATTCTTGA
AGAACTCAAAGAGAATTTTCACTCAAAGCAAATCTGAAATTTTCAATGTAATTATAATGTGTTCA
ATAAGGTGGCCGGCCATGCCTATTAATAGGCCTTCTAT
Found at i:28459585 original size:22 final size:24
Alignment explanation
Indices: 28459551--28459594 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 24
28459541 CTTGGACCAA
28459551 GATTTCCAAGA-T-TTGAAATCTT
1 GATTTCCAAGATTCTTGAAATCTT
* *
28459573 GATTTTCATGATTCTTGAAATC
1 GATTTCCAAGATTCTTGAAATC
28459595 GCTCCAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.50
23 1 0.06
24 8 0.44
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (24 bp):
GATTTCCAAGATTCTTGAAATCTT
Found at i:28473362 original size:23 final size:23
Alignment explanation
Indices: 28473329--28473429 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 23
28473319 AAACACTTGT
28473329 TTTTTCATTTTCACACTCTTTTTC
1 TTTTTC-TTTTCACACTCTTTTTC
**
28473353 TTTTTCTTTTGTCACTCTTTTT-
1 TTTTTCTTTTCACACTCTTTTTC
* * * *
28473375 TTTATCACTCTCATCATTC-TTTTC
1 TTTTTC-TTTTCA-CACTCTTTTTC
** *
28473399 TTTCTTCTTTTTTCACTCTTTTTG
1 TTT-TTCTTTTCACACTCTTTTTC
28473423 TTTTTCT
1 TTTTTCT
28473430 CTTTTTCTCT
Statistics
Matches: 57, Mismatches: 15, Indels: 11
0.69 0.18 0.13
Matches are distributed among these distances:
22 5 0.09
23 28 0.49
24 22 0.39
25 2 0.04
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTTCTTTTCACACTCTTTTTC
Found at i:28484250 original size:40 final size:40
Alignment explanation
Indices: 28484167--28484429 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
28484157 TTGAATGCTG
* * * * * *
28484167 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
28484207 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
28484247 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
28484287 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
28484327 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28484367 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
28484406 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28484430 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:28484449 original size:79 final size:80
Alignment explanation
Indices: 28484206--28484464 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
28484196 AAGTGAATAT
* * * * * * *
28484206 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
28484270 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
28484286 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
28484351 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
28484366 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
28484430 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
28484445 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
28484465 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:28488735 original size:27 final size:27
Alignment explanation
Indices: 28488693--28488901 Score: 271
Period size: 27 Copynumber: 7.8 Consensus size: 27
28488683 TCGTAATCTG
* *
28488693 CCACAAAGGCATTTCTTTCATGGTTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
*
28488720 CCACAAAGGAAATTCTTTCATGATATGC-
1 CCACAAAGGCAATTCTTTCATGAT-T-CA
**
28488748 CC-CAAAGGCAATTCTTTCATGATTTG
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
28488774 CCACAAAGACATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
28488801 CCACAAAGGCAATTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
*
28488828 CCACAAAGGCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
28488855 CTACAAA-GCATTTCTTTCATGATTCA
1 CCACAAAGGCAATTCTTTCATGATTCA
* *
28488881 CCATAGAGGCAATTCTTTCAT
1 CCACAAAGGCAATTCTTTCAT
28488902 CACGTGTTGA
Statistics
Matches: 160, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
26 26 0.16
27 130 0.81
28 3 0.02
29 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (27 bp):
CCACAAAGGCAATTCTTTCATGATTCA
Found at i:28488792 original size:81 final size:80
Alignment explanation
Indices: 28488691--28488901 Score: 300
Period size: 81 Copynumber: 2.6 Consensus size: 80
28488681 CTTCGTAATC
* *
28488691 TGCCACAAAGGCATTTCTTTCATGGTTCACCACAAAGGAAATTCTTTCATGATATGC-CC-CAAA
1 TGCCACAAA-GCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGAT-T-CACCACAAA
28488754 GGCAATTCTTTCATGATT
63 GGCAATTCTTTCATGATT
28488772 TGCCACAAAGACATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGG
1 TGCCACAAAG-CATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGG
*
28488837 CATTTCTTTCATGATT
65 CAATTCTTTCATGATT
** * * *
28488853 CACTACAAAGCATTTCTTTCATGATTCACCATAGAGGCAATTCTTTCAT
1 TGCCACAAAGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCAT
28488902 CACGTGTTGA
Statistics
Matches: 119, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
79 1 0.01
80 41 0.34
81 77 0.65
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (80 bp):
TGCCACAAAGCATTTCTTTCATGATTCACCACAAAGGCAATTCTTTCATGATTCACCACAAAGGC
AATTCTTTCATGATT
Found at i:28500418 original size:18 final size:18
Alignment explanation
Indices: 28500395--28500437 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28500385 ATCATGCATG
28500395 TAAAATCTGA-AGTAAATT
1 TAAAAT-TGACAGTAAATT
*
28500413 TAAAATTTACAGTAAATT
1 TAAAATTGACAGTAAATT
28500431 TAAAATT
1 TAAAATT
28500438 TACAACGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 21 0.91
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (18 bp):
TAAAATTGACAGTAAATT
Found at i:28500438 original size:18 final size:18
Alignment explanation
Indices: 28500405--28500441 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28500395 TAAAATCTGA
28500405 AGTAAATTTAAAATTTAC
1 AGTAAATTTAAAATTTAC
28500423 AGTAAATTTAAAATTTAC
1 AGTAAATTTAAAATTTAC
28500441 A
1 A
28500442 ACGTATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AGTAAATTTAAAATTTAC
Found at i:28501458 original size:73 final size:73
Alignment explanation
Indices: 28501367--28501512 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
28501357 TAACAGCCAA
*
28501367 CTCCACATACAAATGGGATCCCAAATTGCTTACCAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
28501432 GCTAAGAG
66 GCTAAGAG
28501440 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
1 CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
28501505 GCTAAGAG
66 GCTAAGAG
28501513 GATTAGAACT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.19
Consensus pattern (73 bp):
CTCCACATACAAATGGGATCCCAAATTGCTTACAAATTGCATAACATCAAAGCAGGTCCAAGCAA
GCTAAGAG
Found at i:28508754 original size:66 final size:66
Alignment explanation
Indices: 28508643--28508774 Score: 219
Period size: 66 Copynumber: 2.0 Consensus size: 66
28508633 GCAGACTTGA
*
28508643 TTGATTTAAATTTAAAACAGTGGAAGGAGGAAGTAATTACTAGACTCTTTAGAAACAAAGAGGCA
1 TTGATTTAAATTTAAAACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
28508708 G
66 G
* * * *
28508709 TTGATTTAAATTTAAGACAGTGGAATGAGGAAGTAATTACCAGACTCTTTAGTAATAAAGAGGCA
1 TTGATTTAAATTTAAAACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
28508774 G
66 G
28508775 AGGTGATCCT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (66 bp):
TTGATTTAAATTTAAAACAGTGGAAGGAGGAAGTAATTACCAGACTCTTTAGAAACAAAGAGGCA
G
Found at i:28511014 original size:16 final size:16
Alignment explanation
Indices: 28510948--28511014 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
28510938 GGTTCACTGG
*
28510948 AATGAAATAGAGTTAT
1 AATGAAATAGAGCTAT
* * *
28510964 AATGGAATAGATCTGT
1 AATGAAATAGAGCTAT
* *
28510980 AATGAAATAAAACTAT
1 AATGAAATAGAGCTAT
* *
28510996 AATGGAATAGAGCTGT
1 AATGAAATAGAGCTAT
28511012 AAT
1 AAT
28511015 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.48, C:0.04, G:0.19, T:0.28
Consensus pattern (16 bp):
AATGAAATAGAGCTAT
Found at i:28511051 original size:46 final size:44
Alignment explanation
Indices: 28510995--28511084 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 44
28510985 AATAAAACTA
* *
28510995 TAATGGAATAGAGCTGTAATCAGTAATTCAATT-T-TTTGGTTGAATG
1 TAATGAAATAGAACTGTAAT-AGT-ATTC--TTGTGTTTGGTTGAATG
28511041 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
1 TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
28511085 GAATAGATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
42 2 0.05
43 1 0.03
44 16 0.40
45 3 0.08
46 18 0.45
ACGTcount: A:0.32, C:0.06, G:0.22, T:0.40
Consensus pattern (44 bp):
TAATGAAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATG
Found at i:28511269 original size:61 final size:58
Alignment explanation
Indices: 28511174--28511310 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 58
28511164 TTGTTATTAA
* *
28511174 ATTTTAATA-ACATTATTATTAAATATAAGTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAAGTTAATAAAAAT---AATAAATAATTTAATAAC
* *
28511235 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAAGTTAATAAAAATAATAAATAATTTAATAAC
28511293 ATTCTTAATATAATTATT
1 ATT-TTAATATAATTATT
28511311 TTTATATTAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
58 18 0.26
59 14 0.20
61 37 0.53
62 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAAGTTAATAAAAATAATAAATAATTTAATAAC
Found at i:28511333 original size:59 final size:58
Alignment explanation
Indices: 28511174--28511348 Score: 183
Period size: 61 Copynumber: 2.9 Consensus size: 58
28511164 TTGTTATTAA
* * *
28511174 ATTTTAATA-ACATTATTATTAAATATAAGTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAAATTAATAAAAAT---AATAAATAATTTAATAAC
* *
28511235 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAAATTAATAAAAATAATAAATAATTTAATAAC
* * * *
28511293 ATTCTTAATATAATTATTTTTATAT-TAAATTATATTAAAATATTTAAAATAATTTA
1 ATT-TTAATATAATTATTATTAAATATAAATTA-ATAAAAATA-AT-AAATAATTTA
28511349 TTTACTACCT
Statistics
Matches: 99, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
58 24 0.24
59 27 0.27
60 1 0.01
61 46 0.46
62 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (58 bp):
ATTTTAATATAATTATTATTAAATATAAATTAATAAAAATAATAAATAATTTAATAAC
Found at i:28517844 original size:15 final size:16
Alignment explanation
Indices: 28517815--28517844 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28517805 CAAACATGCT
28517815 TTAACACATTATCAAA
1 TTAACACATTATCAAA
28517831 TTAACACA-TATCAA
1 TTAACACATTATCAA
28517845 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:28518042 original size:17 final size:17
Alignment explanation
Indices: 28518020--28518061 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
28518010 AGATCTTCAA
28518020 CGAGCTTCCAACCCAAT
1 CGAGCTTCCAACCCAAT
*
28518037 CGAGCTTCCAACCTAAT
1 CGAGCTTCCAACCCAAT
28518054 CGAGCTTC
1 CGAGCTTC
28518062 TGATAATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.21
Consensus pattern (17 bp):
CGAGCTTCCAACCCAAT
Found at i:28521478 original size:14 final size:14
Alignment explanation
Indices: 28521459--28521486 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28521449 TAAAGTTATA
28521459 TTTAATAATTCATT
1 TTTAATAATTCATT
28521473 TTTAATAATTCATT
1 TTTAATAATTCATT
28521487 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:28521958 original size:19 final size:19
Alignment explanation
Indices: 28521936--28521973 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28521926 TTAATCATCC
28521936 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
28521955 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
28521974 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:28525619 original size:25 final size:25
Alignment explanation
Indices: 28525572--28525622 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
28525562 AAATCACATC
* *
28525572 AACGTGCTACAAAGAGTAGACTATA
1 AACGTGCTACAAAAAGCAGACTATA
*
28525597 AACGTGCTACAAAAAGCATACTATA
1 AACGTGCTACAAAAAGCAGACTATA
28525622 A
1 A
28525623 TTTTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.18, G:0.16, T:0.20
Consensus pattern (25 bp):
AACGTGCTACAAAAAGCAGACTATA
Done.