Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 48 of 103
Found at i:18010493 original size:12 final size:12
Alignment explanation
Indices: 18010478--18010522 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
18010468 GGGTCTGTTG
*
18010478 TATGTATATATG
1 TATGTATATATA
18010490 TATGTATATATA
1 TATGTATATATA
*
18010502 TATATATATATA
1 TATGTATATATA
*
18010514 TATGAATAT
1 TATGTATAT
18010523 TTATGTGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (12 bp):
TATGTATATATA
Found at i:18010499 original size:2 final size:2
Alignment explanation
Indices: 18010482--18010516 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
18010472 CTGTTGTATG
* *
18010482 TA TA TA TG TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18010517 GAATATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18016336 original size:40 final size:37
Alignment explanation
Indices: 18016281--18016379 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 37
18016271 AGTTCATGTG
* *
18016281 CATCCCCCCACATCGTGCACAT-AGATGGAGTCATCGTGTT
1 CATCCCCCCACATCGTGCACATCAG-T---GCCATCGTGTA
*
18016321 CATCCCCCCACATCGTGAACAATCAGTGCCATCGTGTA
1 CATCCCCCCACATCGTGCAC-ATCAGTGCCATCGTGTA
*
18016359 CATCCCCCCACATCATGCACA
1 CATCCCCCCACATCGTGCACA
18016380 CAAGCACTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
37 1 0.02
38 27 0.52
40 19 0.37
41 3 0.06
42 2 0.04
ACGTcount: A:0.25, C:0.38, G:0.15, T:0.21
Consensus pattern (37 bp):
CATCCCCCCACATCGTGCACATCAGTGCCATCGTGTA
Found at i:18016372 original size:19 final size:19
Alignment explanation
Indices: 18016312--18016372 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
18016302 TAGATGGAGT
*
18016312 CATCGTGTTCATCCCCCCA
1 CATCGTGTACATCCCCCCA
* ****
18016331 CATCGTGAACAATCAGTGC-
1 CATCGTGTAC-ATCCCCCCA
18016350 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCCCA
18016369 CATC
1 CATC
18016373 ATGCACACAA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
18 4 0.14
19 21 0.72
20 4 0.14
ACGTcount: A:0.23, C:0.41, G:0.13, T:0.23
Consensus pattern (19 bp):
CATCGTGTACATCCCCCCA
Found at i:18022157 original size:26 final size:26
Alignment explanation
Indices: 18022128--18022177 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
18022118 AAAACATCCA
*
18022128 TTCAAAATTTTTATAAAAAATTTTTG
1 TTCAAAATTGTTATAAAAAATTTTTG
* *
18022154 TTCAAAATTGTTCTAAATAATTTT
1 TTCAAAATTGTTATAAAAAATTTT
18022178 GAAAACTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (26 bp):
TTCAAAATTGTTATAAAAAATTTTTG
Found at i:18030189 original size:12 final size:12
Alignment explanation
Indices: 18030162--18030212 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
18030152 AAAAGGGAGA
*
18030162 AAAGACAAGAAAG
1 AAAGAGAAG-AAG
18030175 AAAGAGAAGAAG
1 AAAGAGAAGAAG
* *
18030187 AAAGAGAATAGG
1 AAAGAGAAGAAG
18030199 AAAGAGAAGGAAG
1 AAAGAGAA-GAAG
18030212 A
1 A
18030213 GAGTGGGGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (12 bp):
AAAGAGAAGAAG
Found at i:18030406 original size:31 final size:31
Alignment explanation
Indices: 18030371--18030429 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
18030361 AAAAAAAAAA
*
18030371 AAAGAGTAGCGACAAAGGAGAAGAAGGAGAG
1 AAAGAGCAGCGACAAAGGAGAAGAAGGAGAG
*
18030402 AAAGAGCAGCGACAGAGGAGAAGAAGGA
1 AAAGAGCAGCGACAAAGGAGAAGAAGGA
18030430 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.51, C:0.08, G:0.39, T:0.02
Consensus pattern (31 bp):
AAAGAGCAGCGACAAAGGAGAAGAAGGAGAG
Found at i:18030495 original size:16 final size:17
Alignment explanation
Indices: 18030471--18030516 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
18030461 GATGCCAAAG
18030471 GAAAAGAAGAA-GAAGA
1 GAAAAGAAGAAGGAAGA
*
18030487 GAAAGGAAGAAGGAAGAA
1 GAAAAGAAGAAGGAAG-A
18030505 GAGAAAG-AGAAG
1 GA-AAAGAAGAAG
18030517 CACAGGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.40
17 4 0.16
18 8 0.32
19 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
GAAAAGAAGAAGGAAGA
Found at i:18030504 original size:20 final size:20
Alignment explanation
Indices: 18030474--18030516 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
18030464 GCCAAAGGAA
18030474 AAGAAGAAGAAGAGAAAG-G
1 AAGAAGAAGAAGAGAAAGAG
18030493 AAGAAGGAAGAAGAGAAAGAG
1 AAGAA-GAAGAAGAGAAAGAG
18030514 AAG
1 AAG
18030517 CACAGGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 5 0.23
20 13 0.59
21 4 0.18
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (20 bp):
AAGAAGAAGAAGAGAAAGAG
Found at i:18031264 original size:61 final size:60
Alignment explanation
Indices: 18031165--18031347 Score: 235
Period size: 60 Copynumber: 3.0 Consensus size: 60
18031155 ATATTTGATT
* * *
18031165 GTAAAA-GGGGACCTGAAGCTTCGATTTATATTAAGTGGCATAGGCAGTTCCCATGAGTAG
1 GTAAAAGGGGGACCTGAAGCCTCGATTTATATT-GGTGGCATAGGCAGTTCCCACGAGTAG
* * *
18031225 GTAAAAGGGGGACCTGAAGCCTCGATTTATATTGGGTGGCATAGGCAGATACCACGAGTAA
1 GTAAAAGGGGGACCTGAAGCCTCGATTTATATT-GGTGGCATAGGCAGTTCCCACGAGTAG
** * *
18031286 GT-AAAGGAAGACCTGAAGCCTCGATTTATATATGGTGGCGTGGGCAGTTCCCACGAGTAG
1 GTAAAAGGGGGACCTGAAGCCTCGATTTATAT-TGGTGGCATAGGCAGTTCCCACGAGTAG
18031346 GT
1 GT
18031348 GATGATGTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
60 57 0.53
61 50 0.47
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (60 bp):
GTAAAAGGGGGACCTGAAGCCTCGATTTATATTGGTGGCATAGGCAGTTCCCACGAGTAG
Found at i:18037407 original size:12 final size:13
Alignment explanation
Indices: 18037380--18037430 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 13
18037370 AAATGGGAGA
*
18037380 AAAGACAAGAAAG
1 AAAGAGAAGAAAG
18037393 AAAGAGAAG-AAG
1 AAAGAGAAGAAAG
*
18037405 AAAGAGAAG-AGG
1 AAAGAGAAGAAAG
*
18037417 AAAGAGAAGTAAG
1 AAAGAGAAGAAAG
18037430 A
1 A
18037431 GAGTGGGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 23 0.68
13 11 0.32
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (13 bp):
AAAGAGAAGAAAG
Found at i:18037576 original size:12 final size:12
Alignment explanation
Indices: 18037556--18037597 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
18037546 GAAGGAGAGG
*
18037556 GAAAAAAAAAGA
1 GAAAGAAAAAGA
18037568 GAAAGAAAAAGA
1 GAAAGAAAAAGA
18037580 -AGAAGAAAAAGA
1 GA-AAGAAAAAGA
18037592 GAAAGA
1 GAAAGA
18037598 GCAGCGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
GAAAGAAAAAGA
Found at i:18037618 original size:31 final size:31
Alignment explanation
Indices: 18037577--18037653 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
18037567 AGAAAGAAAA
*
18037577 AGAAGAAGAAA-AAGAGAAAGAGCAGCGATAG
1 AGAAGAAGAAAGAA-AGAAAGAGCAGCAATAG
* * *
18037608 AGGAGAAGAAAGTAAGAAGGAGCAGCAATAG
1 AGAAGAAGAAAGAAAGAAAGAGCAGCAATAG
18037639 AGAAGAAGAAAGAAA
1 AGAAGAAGAAAGAAA
18037654 AAAAAAGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 38 0.97
32 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.32, T:0.04
Consensus pattern (31 bp):
AGAAGAAGAAAGAAAGAAAGAGCAGCAATAG
Found at i:18037718 original size:20 final size:21
Alignment explanation
Indices: 18037686--18037734 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
18037676 ACGGTGCTAG
18037686 AAGAGAA-AGAGGAAGAAGAGA
1 AAGAGAAGA-AGGAAGAAGAGA
18037707 AAG-GAAGAAGGAAGAAGAGA
1 AAGAGAAGAAGGAAGAAGAGA
18037727 AAGAGAAG
1 AAGAGAAG
18037735 CGCCGGCTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (21 bp):
AAGAGAAGAAGGAAGAAGAGA
Found at i:18037879 original size:2 final size:2
Alignment explanation
Indices: 18037868--18037905 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
18037858 ACTTTGTCCC
18037868 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18037906 GTCATATTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18038490 original size:61 final size:60
Alignment explanation
Indices: 18038392--18038574 Score: 276
Period size: 61 Copynumber: 3.0 Consensus size: 60
18038382 ATATTTGATT
* * *
18038392 GTAAAGGGGGACTTGAAGCCCCGATTTATATTGGGTGGCATGAGCAGTTCTCACGAGTAG
1 GTAAAAGGGGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGTTCTCACGAGTAG
*
18038452 GTAAAAGGGAGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGATCTCACGAGTAG
1 GTAAAAGGG-GACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGTTCTCACGAGTAG
* * * * *
18038513 GTAAAAGGGGACCTGAAGCCTCGATTTATATATGGTGGCATGGGCAGTTCCCATGAGTAG
1 GTAAAAGGGGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGTTCTCACGAGTAG
18038573 GT
1 GT
18038575 GATGATGTCT
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
60 55 0.49
61 57 0.51
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.25
Consensus pattern (60 bp):
GTAAAAGGGGACTTGAAGCCCCGATTTATATTTGGTGGCATGGGCAGTTCTCACGAGTAG
Found at i:18040613 original size:13 final size:13
Alignment explanation
Indices: 18040595--18040619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18040585 AGAGAAATTG
18040595 TGATTTTATAAAA
1 TGATTTTATAAAA
18040608 TGATTTTATAAA
1 TGATTTTATAAA
18040620 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:18047639 original size:20 final size:20
Alignment explanation
Indices: 18047611--18047667 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
18047601 TACATTGGTG
* *
18047611 CCATGTATCGATAGATTGCT
1 CCATCTATCAATAGATTGCT
18047631 CCATCTATCAATAGATTGTCT
1 CCATCTATCAATAGATTG-CT
* *
18047652 CGACCTATCAATAGAT
1 CCATCTATCAATAGAT
18047668 GAGAAGCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (20 bp):
CCATCTATCAATAGATTGCT
Found at i:18047661 original size:21 final size:20
Alignment explanation
Indices: 18047616--18047667 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
18047606 TGGTGCCATG
* *
18047616 TATCGATAGATTGCTCCATC
1 TATCAATAGATTGCTCCACC
*
18047636 TATCAATAGATTGTCTCGACC
1 TATCAATAGATTG-CTCCACC
18047657 TATCAATAGAT
1 TATCAATAGAT
18047668 GAGAAGCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (20 bp):
TATCAATAGATTGCTCCACC
Found at i:18054170 original size:5 final size:5
Alignment explanation
Indices: 18054160--18054184 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
18054150 CTGTATACAT
18054160 ATCAA ATCAA ATCAA ATCAA ATCAA
1 ATCAA ATCAA ATCAA ATCAA ATCAA
18054185 TGAGTGGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATCAA
Found at i:18054772 original size:32 final size:32
Alignment explanation
Indices: 18054735--18054803 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
18054725 TCTAAGTGCC
18054735 TTAATGATTCATAAATCATAATGTCATATCAT
1 TTAATGATTCATAAATCATAATGTCATATCAT
*
18054767 TTAATGATTCCTAAATCATAATGTCATATCAT
1 TTAATGATTCATAAATCATAATGTCATATCAT
18054799 TTAAT
1 TTAAT
18054804 TGGCCTCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (32 bp):
TTAATGATTCATAAATCATAATGTCATATCAT
Found at i:18057765 original size:54 final size:54
Alignment explanation
Indices: 18057700--18057818 Score: 166
Period size: 54 Copynumber: 2.2 Consensus size: 54
18057690 ATCTAAATGG
* * *
18057700 CTTGATCTTGATCACAAACTAGACTTGGGAACTTCACTCCAAGGGTCTGGGCAA
1 CTTGATCTTGATCACAAACTAAACTTGAGAACTTCACTCCAAGGGTCTAGGCAA
* ** * *
18057754 CTTGATCTTGATCACGAACTAAACTTGAGAACTTTGCTTCAAGGGTCTAGGCGA
1 CTTGATCTTGATCACAAACTAAACTTGAGAACTTCACTCCAAGGGTCTAGGCAA
18057808 CTTGATCTTGA
1 CTTGATCTTGA
18057819 GCACGTACCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (54 bp):
CTTGATCTTGATCACAAACTAAACTTGAGAACTTCACTCCAAGGGTCTAGGCAA
Found at i:18057841 original size:54 final size:54
Alignment explanation
Indices: 18057739--18057841 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 54
18057729 AACTTCACTC
* * * * *
18057739 CAAGGGTCTGGGCAACTTGATCTTGATCACGAACTAAACTTGAGAACTTTGCTT
1 CAAGGGTCTAGGCAACTTGATCTTGAGCACGAACCAAACTTAAAAACTTTGCTT
* *
18057793 CAAGGGTCTAGGCGACTTGATCTTGAGCACGTACCAAACTTAAAAACTT
1 CAAGGGTCTAGGCAACTTGATCTTGAGCACGAACCAAACTTAAAAACTT
18057842 CATCTTTAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (54 bp):
CAAGGGTCTAGGCAACTTGATCTTGAGCACGAACCAAACTTAAAAACTTTGCTT
Found at i:18064420 original size:17 final size:17
Alignment explanation
Indices: 18064390--18064433 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
18064380 TTTTATTAAT
* *
18064390 TATTTTTTACTTTTATA
1 TATTTTTAATTTTTATA
*
18064407 TTTTTTTAATTTTTATA
1 TATTTTTAATTTTTATA
18064424 TATTTTTAAT
1 TATTTTTAAT
18064434 ATAATTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TATTTTTAATTTTTATA
Found at i:18065613 original size:33 final size:32
Alignment explanation
Indices: 18065518--18065618 Score: 112
Period size: 33 Copynumber: 3.1 Consensus size: 32
18065508 CTGACAGATC
*
18065518 AAGTCCAAACACCAAAGTCCAAACAAATAACAA
1 AAGTCCAAACACCAAAGT-CAAACAAATATCAA
* *
18065551 AAGTCCAAACACCAATGTCAGAACGAATATCAA
1 AAGTCCAAACACCAAAGTCA-AACAAATATCAA
* * * *
18065584 GAGTCTAAAAACCAAAGTCGAAACAAATATAAA
1 AAGTCCAAACACCAAAGTC-AAACAAATATCAA
18065617 AA
1 AA
18065619 AACAAAAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
32 2 0.04
33 53 0.95
34 1 0.02
ACGTcount: A:0.55, C:0.22, G:0.10, T:0.13
Consensus pattern (32 bp):
AAGTCCAAACACCAAAGTCAAACAAATATCAA
Found at i:18073763 original size:21 final size:21
Alignment explanation
Indices: 18073725--18073773 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
18073715 AATCTTACCG
*
18073725 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTTGTTCCCTTGAA
18073746 TTTTTGCACTT-TTCCCTTGAA
1 TTTTT-CACTTGTTCCCTTGAA
18073767 TTTTTCA
1 TTTTTCA
18073774 ACCTAGGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 19 0.73
22 5 0.19
ACGTcount: A:0.14, C:0.20, G:0.08, T:0.57
Consensus pattern (21 bp):
TTTTTCACTTGTTCCCTTGAA
Found at i:18083912 original size:40 final size:38
Alignment explanation
Indices: 18083819--18083915 Score: 133
Period size: 38 Copynumber: 2.5 Consensus size: 38
18083809 ATAATCCCCG
*
18083819 TGTGCACGATGTGGGGGGACGCACACGATGGCACTGAT
1 TGTGCACGATGTGGGGGGACGCACACGATGGCACGGAT
*
18083857 TGTGCACGATGTGGGGGGACGCACACGATGGTGC-CGGCT
1 TGTGCACGATGTGGGGGGACGCACACGAT-G-GCACGGAT
*
18083896 ATGTGCACAATGTGGGGGGA
1 -TGTGCACGATGTGGGGGGA
18083916 TGTACATGAG
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 29 0.55
39 4 0.08
40 20 0.38
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.19
Consensus pattern (38 bp):
TGTGCACGATGTGGGGGGACGCACACGATGGCACGGAT
Found at i:18086228 original size:18 final size:17
Alignment explanation
Indices: 18086180--18086235 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
18086170 CAACCGACTG
18086180 CTTTCTCTCTTTCTTTCT
1 CTTTCT-TCTTTCTTTCT
18086198 -TTTCCTTCATTTCTTTCT
1 CTTT-CTTC-TTTCTTTCT
18086216 CCTTTCTTCTTTCTTT-T
1 -CTTTCTTCTTTCTTTCT
18086233 CTT
1 CTT
18086236 CTCAGCTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.09
17 6 0.18
18 18 0.53
19 4 0.12
20 3 0.09
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTCTTTCTTTCT
Found at i:18087023 original size:19 final size:18
Alignment explanation
Indices: 18087001--18087043 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
18086991 TTAATATTTT
18087001 AATATTATTTTATTCATAA
1 AATATTATTTTATTC-TAA
*
18087020 AATAATATTTTATTCTAA
1 AATATTATTTTATTCTAA
*
18087038 ATTATT
1 AATATT
18087044 TTTCTCACCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTATTTTATTCTAA
Found at i:18092896 original size:19 final size:19
Alignment explanation
Indices: 18092870--18092910 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
18092860 TTTGTTCTTC
18092870 ATTAATTA-T-TTAG-TTA
1 ATTAATTATTATTAGTTTA
18092886 ATTAATTATTATTAGTTTA
1 ATTAATTATTATTAGTTTA
18092905 ATTAAT
1 ATTAAT
18092911 CATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 1 0.05
18 4 0.18
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTAATTATTATTAGTTTA
Found at i:18093507 original size:21 final size:20
Alignment explanation
Indices: 18093465--18093507 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
18093455 AATATCAAAT
*
18093465 TTTTCCAGCACTTTTTCCTC
1 TTTTCCAGCACTTCTTCCTC
* *
18093485 TTTTCCAGTAGCTTCTTCTTC
1 TTTTCCAGCA-CTTCTTCCTC
18093506 TT
1 TT
18093508 CTTCTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.09, C:0.30, G:0.07, T:0.53
Consensus pattern (20 bp):
TTTTCCAGCACTTCTTCCTC
Found at i:18097478 original size:36 final size:37
Alignment explanation
Indices: 18097435--18097526 Score: 105
Period size: 36 Copynumber: 2.5 Consensus size: 37
18097425 GATATATGCC
* *
18097435 GTGTGGGAGTGCACATGACGATGATGGTG-AGGTGCA
1 GTGTGGGAGTGCACATGACGAGGATAGTGAAGGTGCA
* * * * *
18097471 GTGTGGGAGTGCACTTGATGAGGATATTGAAATGTGCG
1 GTGTGGGAGTGCACATGACGAGGATAGTG-AAGGTGCA
18097509 GTGTGGGAGTGCACATGA
1 GTGTGGGAGTGCACATGA
18097527 GCCAGGGGAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 24 0.52
38 22 0.48
ACGTcount: A:0.23, C:0.10, G:0.42, T:0.25
Consensus pattern (37 bp):
GTGTGGGAGTGCACATGACGAGGATAGTGAAGGTGCA
Found at i:18099038 original size:17 final size:18
Alignment explanation
Indices: 18099016--18099053 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
18099006 AAATTTTAAT
*
18099016 AAACTAAAATTAAAAC-A
1 AAACTAAAACTAAAACTA
18099033 AAACTAAAACTAAAACTA
1 AAACTAAAACTAAAACTA
18099051 AAA
1 AAA
18099054 ATATCAGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (18 bp):
AAACTAAAACTAAAACTA
Found at i:18099041 original size:6 final size:6
Alignment explanation
Indices: 18099016--18099053 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
18099006 AAATTTTAAT
*
18099016 AAACTA AAATTA AAAC-A AAACTA AAACTA AAACTA AAA
1 AAACTA AAACTA AAACTA AAACTA AAACTA AAACTA AAA
18099054 ATATCAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.71, C:0.13, G:0.00, T:0.16
Consensus pattern (6 bp):
AAACTA
Found at i:18101560 original size:38 final size:37
Alignment explanation
Indices: 18101518--18101619 Score: 127
Period size: 38 Copynumber: 2.7 Consensus size: 37
18101508 ATTGCCCTTA
* *
18101518 TGCACGATGTGGGGGGATGTACATGACGGCA-TTAGATG
1 TGCACGATGTGGGGGGATGCACATGACGCCAGTT--ATG
*
18101556 TGCACGATGTGGGGGGATGCACCGATGACTCCAGTTATG
1 TGCACGATGTGGGGGGATGCA-C-ATGACGCCAGTTATG
18101595 T-CACGATGTGGGGGGATGCACATGA
1 TGCACGATGTGGGGGGATGCACATGA
18101620 GCTGGGGAGG
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
36 4 0.07
37 1 0.02
38 39 0.67
39 5 0.09
40 7 0.12
41 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.23
Consensus pattern (37 bp):
TGCACGATGTGGGGGGATGCACATGACGCCAGTTATG
Found at i:18108349 original size:52 final size:51
Alignment explanation
Indices: 18108271--18108374 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 51
18108261 GCACATGACG
18108271 GTGATAGTGGTGTGCTATGTGAGTGCACACACTGATGATATATGCCATGTGC
1 GTGATAGTGGTGTGCTATGTGAGTGCACACACTGATGATATATG-CATGTGC
* *
18108323 GTGATAGTGGTGTGTTGTGTGAGTGCACACACTGATGATATATGCATGTGC
1 GTGATAGTGGTGTGCTATGTGAGTGCACACACTGATGATATATGCATGTGC
18108374 G
1 G
18108375 AGGGGGAGTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 8 0.16
52 42 0.84
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.32
Consensus pattern (51 bp):
GTGATAGTGGTGTGCTATGTGAGTGCACACACTGATGATATATGCATGTGC
Found at i:18115306 original size:20 final size:19
Alignment explanation
Indices: 18115272--18115311 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
18115262 GGTCTTAAAA
* *
18115272 TATAATTTTTTTAATTGGT
1 TATAATTTCTTTAATCGGT
18115291 TATAATTTCCTTTAATCGGT
1 TATAATTT-CTTTAATCGGT
18115311 T
1 T
18115312 TAAAGAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.25, C:0.07, G:0.10, T:0.57
Consensus pattern (19 bp):
TATAATTTCTTTAATCGGT
Found at i:18120633 original size:19 final size:19
Alignment explanation
Indices: 18120609--18120646 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
18120599 ACTTCTAAAC
18120609 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18120628 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
18120647 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:18121209 original size:60 final size:59
Alignment explanation
Indices: 18121076--18121238 Score: 179
Period size: 60 Copynumber: 2.7 Consensus size: 59
18121066 CTAGGAGCTA
* * *
18121076 CCCACGCCACCATATATAAATCGGGGCTTCA-GGT-CCCATTTACCTACTTGTGGGAACTG
1 CCCACGCCACCA-ATATAAATCGAGGCTT-ATGGTCCCCCTTTACCTACTAGTGGGAACTG
* * * *
18121135 CCCACACCACCCAATATAAATCAAGGCTTTTGGTCCCCCTTTACCTACTAGTGGGAATTG
1 CCCACGCCA-CCAATATAAATCGAGGCTTATGGTCCCCCTTTACCTACTAGTGGGAACTG
* *
18121195 CCCACGCCATCCAATATGAATCGAGACTTCAT-GTCCCCCTTTAC
1 CCCACGCCA-CCAATATAAATCGAGGCTT-ATGGTCCCCCTTTAC
18121239 AATCAAATAT
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 25 0.29
60 61 0.70
61 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (59 bp):
CCCACGCCACCAATATAAATCGAGGCTTATGGTCCCCCTTTACCTACTAGTGGGAACTG
Found at i:18122206 original size:15 final size:16
Alignment explanation
Indices: 18122186--18122219 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18122176 AGTTGCTCTC
18122186 TTTTTCTCTCTTTT-T
1 TTTTTCTCTCTTTTCT
*
18122201 TTTTTCTGTCTTTTCT
1 TTTTTCTCTCTTTTCT
18122217 TTT
1 TTT
18122220 ACTTTTGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTCTCTCTTTTCT
Found at i:18130543 original size:24 final size:24
Alignment explanation
Indices: 18130516--18130571 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
18130506 AGAAGACTGA
* *
18130516 AGAAGTAAGAAAAGATAAGAAAAG
1 AGAAGAAAGAAAAGAAAAGAAAAG
*
18130540 AGAAGAAAGAAAGGAAAAGAAAATG
1 AGAAGAAAGAAAAGAAAAGAAAA-G
18130565 A-AAGAAA
1 AGAAGAAA
18130572 ATTTGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (24 bp):
AGAAGAAAGAAAAGAAAAGAAAAG
Found at i:18130567 original size:6 final size:5
Alignment explanation
Indices: 18130522--18130572 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
18130512 CTGAAGAAGT
* * *
18130522 AAGAA AAGAT AAGAA AAGAG AAG-A AAGAA AGGAA AAGAA AATG-A AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA-GAA AAGAA
18130571 AA
1 AA
18130573 TTTGATTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.11
5 32 0.86
6 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (5 bp):
AAGAA
Found at i:18155305 original size:40 final size:39
Alignment explanation
Indices: 18155229--18155317 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
18155219 ATTGAATCTT
* * *
18155229 GCTGCAGCGAAATTTCTACCCAAAAACATAATGTTTCTC
1 GCTGCAGCGAAATTTCAACCCAAAAACATAAAGTTTCTA
18155268 GCTGCAGCGAAATTGT-AACCCAAAAA-ATAGAAAGTTTCTA
1 GCTGCAGCGAAATT-TCAACCCAAAAACAT--AAAGTTTCTA
*
18155308 ACTGCAGCGA
1 GCTGCAGCGA
18155318 GAAGCTACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
38 2 0.05
39 23 0.53
40 18 0.42
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (39 bp):
GCTGCAGCGAAATTTCAACCCAAAAACATAAAGTTTCTA
Found at i:18163896 original size:20 final size:18
Alignment explanation
Indices: 18163836--18163893 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 18
18163826 CAAAACCAAG
18163836 CTTTTTTCTTCCTTTCTC
1 CTTTTTTCTTCCTTTCTC
18163854 TCTTTTTTCTT--TTT-TC
1 -CTTTTTTCTTCCTTTCTC
18163870 CTTTCTTTCTTTCCTTTCTC
1 CTTT-TTTC-TTCCTTTCTC
18163890 CTTT
1 CTTT
18163894 CTTCCAACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.12
16 6 0.18
17 5 0.15
19 13 0.38
20 6 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTTCTTCCTTTCTC
Found at i:18185973 original size:43 final size:43
Alignment explanation
Indices: 18185926--18186020 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
18185916 GAGAGTAGAA
* **
18185926 AGTGCGCATAAGCCGAGGATAACCC-GATTATGTGCAAGTAGGG
1 AGTGCGCATAACCCGAGGATAACCCAG-CCATGTGCAAGTAGGG
* * * *
18185969 AGTGCTCATAACCCGATGATGACCCAGCCATGTGCGAGTAGGG
1 AGTGCGCATAACCCGAGGATAACCCAGCCATGTGCAAGTAGGG
18186012 AGTGCGCAT
1 AGTGCGCAT
18186021 GAGCTGGTGA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 42 0.98
44 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.32, T:0.19
Consensus pattern (43 bp):
AGTGCGCATAACCCGAGGATAACCCAGCCATGTGCAAGTAGGG
Found at i:18193826 original size:77 final size:77
Alignment explanation
Indices: 18193699--18193939 Score: 392
Period size: 77 Copynumber: 3.1 Consensus size: 77
18193689 AATGCCATAT
* *
18193699 ATTTTAATTTTGGGTGATTCATAAAAAATAGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
1 ATTTTAATTTTGGATGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
18193764 ATTAAGGATAGA
66 ATTAAGGATAGA
*
18193776 ATTTTAATTTTGGATGATTCATAAAGAATCGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
1 ATTTTAATTTTGGATGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
18193841 ATTAAGGATAGA
66 ATTAAGGATAGA
* * * **
18193853 ATTTTAATTTTGTATGATTCATAAAGAATAGAAAATTGTTTCCTACTTTAAAAGAAATTCGTAAA
1 ATTTTAATTTTGGATGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
* *
18193918 ATTAAGCATAGC
66 ATTAAGGATAGA
18193930 ATTTTAATTT
1 ATTTTAATTT
18193940 GGAAAATTCA
Statistics
Matches: 153, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
77 153 1.00
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (77 bp):
ATTTTAATTTTGGATGATTCATAAAGAATAGGAAATTGTTTCCTACTTTAAAAGTAATTCCAAAA
ATTAAGGATAGA
Found at i:18201055 original size:36 final size:36
Alignment explanation
Indices: 18201007--18201107 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
18200997 ATGATATTGC
* * *
18201007 CTGTGCACGATGTAAGGGTACACACGATGGCATTAG
1 CTGTGCGCGATGTAGGGGTGCACACGATGGCATTAG
* *
18201043 TTGTGCGCGATGTAGGGGTGCACACGATGGTATTAG
1 CTGTGCGCGATGTAGGGGTGCACACGATGGCATTAG
* * *
18201079 CTATGCGCAATGTGGGGGTGCACACGATG
1 CTGTGCGCGATGTAGGGGTGCACACGATG
18201108 ACTCTGGCTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (36 bp):
CTGTGCGCGATGTAGGGGTGCACACGATGGCATTAG
Found at i:18211546 original size:27 final size:27
Alignment explanation
Indices: 18211495--18211546 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
18211485 ATATCTTGGT
*
18211495 GGTGGAAAATTACAATTTTGCCCCTAA
1 GGTGGAAAATTACAATTTTGACCCTAA
*
18211522 GGTGGTAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
18211547 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTAA
Found at i:18228282 original size:29 final size:29
Alignment explanation
Indices: 18228232--18228288 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
18228222 GGATATTTAA
*
18228232 TATATCTTGCTTAGCTACTGTGGATATTG
1 TATATCCTGCTTAGCTACTGTGGATATTG
* * *
18228261 TATATCCTGTTTATCTATTGTGGATATT
1 TATATCCTGCTTAGCTACTGTGGATATT
18228289 ATAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (29 bp):
TATATCCTGCTTAGCTACTGTGGATATTG
Found at i:18230673 original size:2 final size:2
Alignment explanation
Indices: 18230666--18230696 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18230656 TATGACATAG
18230666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18230697 CAACATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18242402 original size:36 final size:35
Alignment explanation
Indices: 18242357--18242429 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 35
18242347 CAACAACAAT
*
18242357 TCCTTTTCCATACCCATTTTTCAGAATTGAATTCA
1 TCCTCTTCCATACCCATTTTTCAGAATTGAATTCA
18242392 NTCCTCTTCCATACCCATTTTTCAGAATTGAATTCA
1 -TCCTCTTCCATACCCATTTTTCAGAATTGAATTCA
18242428 TC
1 TC
18242430 ATGATAACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 2 0.06
36 34 0.94
ACGTcount: A:0.25, C:0.27, G:0.05, T:0.41
Consensus pattern (35 bp):
TCCTCTTCCATACCCATTTTTCAGAATTGAATTCA
Found at i:18242749 original size:21 final size:22
Alignment explanation
Indices: 18242706--18242749 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18242696 TATTGGCCCA
* **
18242706 ATTTTTTTTTAATTTTTTGACC
1 ATTTTTTCTTAATTTTTCCACC
18242728 ATTTTTTCTTAA-TTTTCCACC
1 ATTTTTTCTTAATTTTTCCACC
18242749 A
1 A
18242750 CAAATATTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.20, C:0.16, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTTTTCTTAATTTTTCCACC
Found at i:18247989 original size:2 final size:2
Alignment explanation
Indices: 18247977--18248015 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
18247967 TATGACATAG
*
18247977 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18248016 GAACATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18248885 original size:20 final size:20
Alignment explanation
Indices: 18248838--18248893 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
18248828 GAAGAAGAAA
* *
18248838 AAGTTACTGGAAGCTTGAAG
1 AAGTTGCTGGAAACTTGAAG
*
18248858 AA-TCTGCTGGAAATTTGAAG
1 AAGT-TGCTGGAAACTTGAAG
*
18248878 AAGTTGCTAGAAACTT
1 AAGTTGCTGGAAACTT
18248894 AGATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (20 bp):
AAGTTGCTGGAAACTTGAAG
Found at i:18258760 original size:2 final size:2
Alignment explanation
Indices: 18258705--18258743 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18258695 NNNNCAAACC
18258705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18258744 GATAACACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18262151 original size:35 final size:33
Alignment explanation
Indices: 18262112--18262204 Score: 109
Period size: 32 Copynumber: 2.8 Consensus size: 33
18262102 TTTTGGATTT
18262112 TGGTTGATCCCGTGAAAAACCATTGTTGTAGGTTA
1 TGGTTGATCCCGTGAAAAACCATTGTTG--GGTTA
* ** *
18262147 TGGTTGAGCCTTTGAAAAACCACT-TTGGGTTA
1 TGGTTGATCCCGTGAAAAACCATTGTTGGGTTA
18262179 TGGTTGATCCCG-GTAAAAACCATTGT
1 TGGTTGATCCCGTG-AAAAACCATTGT
18262205 GAAAGGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
31 1 0.02
32 23 0.48
33 1 0.02
34 3 0.06
35 20 0.42
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (33 bp):
TGGTTGATCCCGTGAAAAACCATTGTTGGGTTA
Found at i:18264813 original size:13 final size:13
Alignment explanation
Indices: 18264795--18264820 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18264785 TTTTCCAGGA
18264795 ATTTTATAAAATC
1 ATTTTATAAAATC
18264808 ATTTTATAAAATC
1 ATTTTATAAAATC
18264821 GTAATTTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTATAAAATC
Found at i:18272075 original size:19 final size:19
Alignment explanation
Indices: 18272051--18272088 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
18272041 CCATTTAACT
*
18272051 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
18272070 TATTGGAGTATAATTTGAG
1 TATTGGAGTATAATTTGAG
18272089 GGTTTGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:18273488 original size:12 final size:13
Alignment explanation
Indices: 18273458--18273482 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18273448 AGAAAAATTG
18273458 TGATTTTATAAAA
1 TGATTTTATAAAA
18273471 TGATTTTATAAA
1 TGATTTTATAAA
18273483 TTATTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:18288044 original size:27 final size:27
Alignment explanation
Indices: 18288014--18288072 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
18288004 CTTGCAAGGC
*
18288014 TTGCTTCAAATTGACTTGGATGAATAA
1 TTGCTTCAAATTGACTTGGAAGAATAA
* * *
18288041 TTGCTTGAAATTGATTTGGAAGAATAC
1 TTGCTTCAAATTGACTTGGAAGAATAA
18288068 TTGCT
1 TTGCT
18288073 AAAAATGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
TTGCTTCAAATTGACTTGGAAGAATAA
Found at i:18288078 original size:27 final size:27
Alignment explanation
Indices: 18288021--18288078 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
18288011 GGCTTGCTTC
* **
18288021 AAATTGACTTGGATGAATAATTGCTTG
1 AAATTGACTTGGAAGAATAATTGCTAA
* *
18288048 AAATTGATTTGGAAGAATACTTGCTAA
1 AAATTGACTTGGAAGAATAATTGCTAA
18288075 AAAT
1 AAAT
18288079 GCTTAATGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (27 bp):
AAATTGACTTGGAAGAATAATTGCTAA
Found at i:18289955 original size:73 final size:74
Alignment explanation
Indices: 18289793--18289989 Score: 194
Period size: 73 Copynumber: 2.7 Consensus size: 74
18289783 GATGGCTGGT
* * * *
18289793 TCAAAA-ACAGAGA-AGACTTAATCGACCAAAAAGTAAGTTAGTTGACTAAGAGCCTATTGCCAA
1 TCAAAAGACAGAGACA-ACTTAATCGACTAAGAAGCAAGTTAGTCGACTAAGAGCCTATTGCCAA
18289856 AAATCTCGAC
65 AAATCTCGAC
* * * *
18289866 TTC--AAGATAGAAACAACTTAATCGACTAAGAAGGAAGTTAGTCGACTAAGAG-CTCATTGTCA
1 -TCAAAAGACAGAGACAACTTAATCGACTAAGAAGCAAGTTAGTCGACTAAGAGCCT-ATTGCCA
*
18289928 AAAAT-TGGGA-
64 AAAATCT-CGAC
* *
18289938 TCAAAAGACAGAGACAACTTAGTTGACTAAGAA-CACAGTTAGTCGACTAAGA
1 TCAAAAGACAGAGACAACTTAATCGACTAAGAAGCA-AGTTAGTCGACTAAGA
18289990 TCATTTTGCT
Statistics
Matches: 103, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
71 2 0.02
72 6 0.06
73 92 0.89
74 3 0.03
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (74 bp):
TCAAAAGACAGAGACAACTTAATCGACTAAGAAGCAAGTTAGTCGACTAAGAGCCTATTGCCAAA
AATCTCGAC
Found at i:18290458 original size:67 final size:62
Alignment explanation
Indices: 18290376--18290543 Score: 198
Period size: 61 Copynumber: 2.7 Consensus size: 62
18290366 AAAAGTTAGT
* * * *
18290376 TTTGGGTTTTCGTTGATCCCGTGAAAAACCATTGTTGTAGGTTGTGGTTGCGCTTTTGAAAAACC
1 TTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGAAAGTT-T-G-AGC-C-TTTGAAAAACC
18290441 AC
61 AC
* *
18290443 TTTGGGTTTTGGTTGAGCCCATGAAAAACCATTG-TGAAAGTTTGAGCCTTTGAAAAACCAC
1 TTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGAAAGTTTGAGCCTTTGAAAAACCAC
*
18290504 TTTAGGTTTTGGTTGATCCCG-GTAAAAACCATTG-TGAAAG
1 TTTGGGTTTTGGTTGATCCCGTG-AAAAACCATTGTTGAAAG
18290544 GTTTTGGATA
Statistics
Matches: 91, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
60 1 0.01
61 48 0.53
62 1 0.01
63 2 0.02
64 1 0.01
65 1 0.01
66 6 0.07
67 31 0.34
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (62 bp):
TTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGAAAGTTTGAGCCTTTGAAAAACCAC
Found at i:18290468 original size:32 final size:32
Alignment explanation
Indices: 18290376--18290473 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 32
18290366 AAAAGTTAGT
* * * *
18290376 TTTGGGTTTTCGTTGATCCCGTGAAAAACCAT
1 TTTGGGTTTTGGTTGAGCCCATGAAAAACCAC
* * ***
18290408 TGTTGTAGGTTGTGGTTGCGCTTTTGAAAAACCAC
1 T-TTG--GGTTTTGGTTGAGCCCATGAAAAACCAC
18290443 TTTGGGTTTTGGTTGAGCCCATGAAAAACCA
1 TTTGGGTTTTGGTTGAGCCCATGAAAAACCA
18290474 TTGTGAAAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
32 23 0.46
33 3 0.06
34 3 0.06
35 21 0.42
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (32 bp):
TTTGGGTTTTGGTTGAGCCCATGAAAAACCAC
Found at i:18295776 original size:35 final size:33
Alignment explanation
Indices: 18295735--18295845 Score: 111
Period size: 35 Copynumber: 3.3 Consensus size: 33
18295725 AAACCCAAAG
*
18295735 TGGTTTTTCAAAGGCTCAACTACAACCTTTCACAA
1 TGGTTTTTCAAAGGCTCAACCACAACC--TCACAA
** *
18295770 TGGTTTTTCACGGGCTCAACCA-AAAC-CA-AA
1 TGGTTTTTCAAAGGCTCAACCACAACCTCACAA
*
18295800 GTGGTTTTTCAAAGACTCAACCACAACCTACAACAA
1 -TGGTTTTTCAAAGGCTCAACCACAACCT-C-ACAA
18295836 TGGTTTTTCA
1 TGGTTTTTCA
18295846 CGAGATCAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
30 2 0.03
31 21 0.34
32 3 0.05
34 4 0.06
35 30 0.48
36 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (33 bp):
TGGTTTTTCAAAGGCTCAACCACAACCTCACAA
Found at i:18295808 original size:31 final size:32
Alignment explanation
Indices: 18295766--18295862 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 32
18295756 ACAACCTTTC
18295766 ACAATGGTTTTTCACGGGCTCAACCAAAACCA
1 ACAATGGTTTTTCACGGGCTCAACCAAAACCA
* ** * *
18295798 A-AGTGGTTTTTCAAAGACTCAACCACAACCTACA
1 ACAATGGTTTTTCACGGGCTCAACCA-AAAC--CA
* *
18295832 ACAATGGTTTTTCACGAGATCAACCAAAACC
1 ACAATGGTTTTTCACGGGCTCAACCAAAACC
18295863 CAAAACTAAC
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
31 20 0.41
32 5 0.10
34 6 0.12
35 18 0.37
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (32 bp):
ACAATGGTTTTTCACGGGCTCAACCAAAACCA
Found at i:18295819 original size:66 final size:66
Alignment explanation
Indices: 18295691--18295862 Score: 222
Period size: 66 Copynumber: 2.6 Consensus size: 66
18295681 GCTTAGCCAA
** * * *
18295691 AACCTTTCACAATAATTTCT-ATCGGGATCAACTAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAA-CCAAAGTGGTTTTTCAAAGACTCAAC
*
18295755 TAC
64 CAC
*
18295758 AACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCAAAGTGGTTTTTCAAAGACTCAACCA
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCAAAGTGGTTTTTCAAAGACTCAACCA
18295823 C
66 C
* *
18295824 AACC-TACAACAATGGTTTTTCACGAGATCAACCAAAACC
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACC
18295863 CAAAACTAAC
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 60 0.65
67 30 0.32
68 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.26
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCAAAGTGGTTTTTCAAAGACTCAACCA
C
Found at i:18295855 original size:35 final size:32
Alignment explanation
Indices: 18295766--18295865 Score: 96
Period size: 35 Copynumber: 3.0 Consensus size: 32
18295756 ACAACCTTTC
* * *
18295766 ACAATGGTTTTTCACGGGCTCAACCAAAACCA
1 ACAATGGTTTTTCACGAGATCAACCAAACCCA
* *
18295798 A-AGTGGTTTTTCA-AAGACTCAACCACAACCTACA
1 ACAATGGTTTTTCACGAGA-TCAACCA-AACC--CA
18295832 ACAATGGTTTTTCACGAGATCAACCAAAACCCA
1 ACAATGGTTTTTCACGAGATCAACC-AAACCCA
18295865 A
1 A
18295866 AACTAACTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
30 1 0.02
31 18 0.33
32 4 0.07
33 3 0.06
34 3 0.06
35 21 0.39
36 4 0.07
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (32 bp):
ACAATGGTTTTTCACGAGATCAACCAAACCCA
Found at i:18296388 original size:73 final size:72
Alignment explanation
Indices: 18296254--18296447 Score: 200
Period size: 73 Copynumber: 2.7 Consensus size: 72
18296244 ACATAATGAT
* *
18296254 CTTAGTTGACTAACTGCGC-TCTTAGTCGACTAAGTTGTTTCTGTCTTTTGATCCTAGTTTCTAG
1 CTTAGTCGACTAACTTC-CTTCTTAGTCGACTAAGTTGTTTCTGTC-TTTGATCCTAGTTTCTAG
18296318 CAGT-GAGCA
64 CAGTAG-GCA
* * *
18296327 GTTAGTCGACTAACTTCCTTCTTAGTCGATTAAGTTGTTTCTGTC-TTGAAGTCC-AGATTTCTG
1 CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTTTCTGTCTTTG-A-TCCTAG-TTTCTA
*
18296390 GCAGTAGGCT
63 GCAGTAGGCA
** * *
18296400 CTTAGTCGACTAACTTAGTTCTTGGTCGACTAAGTCT-TCTCTGTCTTT
1 CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGT-TGTTTCTGTCTTT
18296448 CAATGCTCTT
Statistics
Matches: 102, Mismatches: 12, Indels: 13
0.80 0.09 0.10
Matches are distributed among these distances:
71 3 0.03
72 4 0.04
73 91 0.89
74 4 0.04
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.41
Consensus pattern (72 bp):
CTTAGTCGACTAACTTCCTTCTTAGTCGACTAAGTTGTTTCTGTCTTTGATCCTAGTTTCTAGCA
GTAGGCA
Found at i:18297694 original size:16 final size:16
Alignment explanation
Indices: 18297673--18297719 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
18297663 TTAGTTTCAG
18297673 TTTAATTTTAGTTGTC
1 TTTAATTTTAGTTGTC
*
18297689 TTTAATTTTCAG-TATC
1 TTTAATTTT-AGTTGTC
*
18297705 TTTAATTTTGGTTGT
1 TTTAATTTTAGTTGT
18297720 TTGAATAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 23 0.88
17 2 0.08
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (16 bp):
TTTAATTTTAGTTGTC
Found at i:18300579 original size:13 final size:13
Alignment explanation
Indices: 18300561--18300585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18300551 TTTCTAAAAA
18300561 TTTATAAAATCAT
1 TTTATAAAATCAT
18300574 TTTATAAAATCA
1 TTTATAAAATCA
18300586 CATTTATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:18311203 original size:19 final size:19
Alignment explanation
Indices: 18311179--18311215 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
18311169 CATTTGACTT
18311179 ATTGGAGTATGATTTGAGC
1 ATTGGAGTATGATTTGAGC
18311198 ATTGGAGTATGATTTGAG
1 ATTGGAGTATGATTTGAG
18311216 GTTGAGAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.32, T:0.38
Consensus pattern (19 bp):
ATTGGAGTATGATTTGAGC
Found at i:18311291 original size:28 final size:27
Alignment explanation
Indices: 18311259--18311311 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
18311249 TTCAGAGCAT
*
18311259 AGGGGTAAAATGGTAATTTTGCCACCCC
1 AGGGGCAAAATGGTAATTTT-CCACCCC
*
18311287 AGGGGCAAAATTGTAATTTTCCACC
1 AGGGGCAAAATGGTAATTTTCCACC
18311312 ACCAAGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (27 bp):
AGGGGCAAAATGGTAATTTTCCACCCC
Found at i:18314725 original size:43 final size:43
Alignment explanation
Indices: 18314636--18314758 Score: 124
Period size: 43 Copynumber: 2.9 Consensus size: 43
18314626 CACATCATCA
** * ** ***
18314636 TCATCACCAACTTATGCGCACTCCCTACTCACACATGGCTGGG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAAG
18314679 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAAG
1 TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAAG
* *
18314722 TCATC-CTC-GGCTTATGCGCACTCTCTACTCGTACATA
1 TCATCAC-CAGG-TTATGCGCACTCCCTACTCGCACATA
18314759 GTCGAGTCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.04
43 65 0.96
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.25
Consensus pattern (43 bp):
TCATCACCAGGTTATGCGCACTCCCTACTCGCACATAACCAAG
Found at i:18317252 original size:17 final size:17
Alignment explanation
Indices: 18317230--18317264 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18317220 AGTAAAATAT
18317230 GCACACACTAAGGGGGA
1 GCACACACTAAGGGGGA
*
18317247 GCACACACTTAGGGGGA
1 GCACACACTAAGGGGGA
18317264 G
1 G
18317265 GAAAACCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.23, G:0.37, T:0.09
Consensus pattern (17 bp):
GCACACACTAAGGGGGA
Found at i:18319419 original size:17 final size:17
Alignment explanation
Indices: 18319397--18319429 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
18319387 AGATATGACG
18319397 TAATTACGTAAAAATTT
1 TAATTACGTAAAAATTT
*
18319414 TAATTATGTAAAAATT
1 TAATTACGTAAAAATT
18319430 CTTTAGTACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TAATTACGTAAAAATTT
Found at i:18322715 original size:21 final size:21
Alignment explanation
Indices: 18322691--18322736 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
18322681 GGTGTTCTTT
**
18322691 TGTTTCC-CCCTCAATTTTTTC
1 TGTTTCCTCCCT-AATTGCTTC
18322712 TG-TTCCTCCCTAATTGCTTC
1 TGTTTCCTCCCTAATTGCTTC
18322732 TGTTT
1 TGTTT
18322737 ATTTCTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.09, C:0.30, G:0.09, T:0.52
Consensus pattern (21 bp):
TGTTTCCTCCCTAATTGCTTC
Found at i:18327417 original size:14 final size:17
Alignment explanation
Indices: 18327398--18327438 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 17
18327388 TATTTTTATT
18327398 ATAATTATT-AA-AGA-
1 ATAATTATTCAAGAGAC
18327412 ATAATT-TTCAAGAGAC
1 ATAATTATTCAAGAGAC
18327428 ATAATTATTCA
1 ATAATTATTCA
18327439 CATGAAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 2 0.09
14 8 0.35
15 3 0.13
16 6 0.26
17 4 0.17
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (17 bp):
ATAATTATTCAAGAGAC
Found at i:18332789 original size:20 final size:20
Alignment explanation
Indices: 18332764--18332802 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18332754 CAAATATCAT
*
18332764 TTTTTCTAGCAGCTTCTTCA
1 TTTTTCCAGCAGCTTCTTCA
*
18332784 TTTTTCCAGTAGCTTCTTC
1 TTTTTCCAGCAGCTTCTTC
18332803 TTCTTCTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.26, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTTCCAGCAGCTTCTTCA
Found at i:18333535 original size:2 final size:2
Alignment explanation
Indices: 18333528--18333572 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18333518 GTTATGTATG
18333528 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18333570 TA T
1 TA T
18333573 TTATGCAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:18344933 original size:73 final size:72
Alignment explanation
Indices: 18344772--18344933 Score: 184
Period size: 73 Copynumber: 2.2 Consensus size: 72
18344762 GACAGAGAAG
* * * * *
18344772 ACTTAGTCGACCAAGAAGTAAGTTAGTCGACTAAGAGCTTATTGCCAAAAATCTGGACTTCAAGA
1 ACTTAGTCGACTAAGAAGGAAGTTAGTCGACCAAGAGCTCATTGCCAAAAATCGGGAC-TCAAGA
*
18344837 CAGAAACA
65 CAAAAACA
* * *
18344845 ACTTAATCAATTAAGAAGGAAGTTAGTCGACCAAGAGCTCATTGCCAACAAAT-GGGA-TCAGAA
1 ACTTAGTCGACTAAGAAGGAAGTTAGTCGACCAAGAGCTCATTGCCAA-AAATCGGGACTC--AA
18344908 GACAAAAACA
63 GACAAAAACA
*
18344918 ACTTAGTCGGCTAAGA
1 ACTTAGTCGACTAAGA
18344934 GCACAGTTAG
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
71 2 0.03
73 67 0.92
74 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (72 bp):
ACTTAGTCGACTAAGAAGGAAGTTAGTCGACCAAGAGCTCATTGCCAAAAATCGGGACTCAAGAC
AAAAACA
Found at i:18346335 original size:34 final size:35
Alignment explanation
Indices: 18346220--18346338 Score: 116
Period size: 35 Copynumber: 3.4 Consensus size: 35
18346210 AAGCTATTTG
* * *
18346220 TGAGGGTTGTGCTTGCT-TCCATGGAAAGGCATTTA
1 TGAGGGTTGTGCTTGCTCT-CGTGAAAAGGCATTAA
* * * ** **
18346255 TAAGGATTGTACTTGCTCTCGTGAAAACTCATTGT
1 TGAGGGTTGTGCTTGCTCTCGTGAAAAGGCATTAA
*
18346290 TGAGGGGTGTGCTTGCTCTCGTGAAAAGGCA-TAA
1 TGAGGGTTGTGCTTGCTCTCGTGAAAAGGCATTAA
18346324 TGAGGGTTGTGCTTG
1 TGAGGGTTGTGCTTG
18346339 AATATGTTAA
Statistics
Matches: 65, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
34 15 0.23
35 49 0.75
36 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (35 bp):
TGAGGGTTGTGCTTGCTCTCGTGAAAAGGCATTAA
Found at i:18350516 original size:38 final size:39
Alignment explanation
Indices: 18350428--18350523 Score: 106
Period size: 38 Copynumber: 2.5 Consensus size: 39
18350418 TTATATGCAT
* * *
18350428 TCCCCCACATCGTGCACATAGCTAGAGTCATCGTGTGCA
1 TCCCCCACATCGTGCACATAGCTAGAGCCATCATGTACA
* *
18350467 TCCCCCCACATCGTGCACA-ATC-AGTGCCATCATGTACA
1 T-CCCCCACATCGTGCACATAGCTAGAGCCATCATGTACA
*
18350505 TCCCCCTACATCATGCACA
1 TCCCCC-ACATCGTGCACA
18350524 CGGGCACTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 5 0.10
38 24 0.49
39 3 0.06
40 17 0.35
ACGTcount: A:0.25, C:0.39, G:0.15, T:0.22
Consensus pattern (39 bp):
TCCCCCACATCGTGCACATAGCTAGAGCCATCATGTACA
Found at i:18353068 original size:2 final size:2
Alignment explanation
Indices: 18353061--18353085 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18353051 ACAGCTCATC
18353061 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18353086 CTGTGAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18353742 original size:2 final size:2
Alignment explanation
Indices: 18353735--18353840 Score: 203
Period size: 2 Copynumber: 52.5 Consensus size: 2
18353725 TAGCTGGATT
18353735 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18353777 AG AG AG AG AG NAG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
18353820 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
18353841 CTTTCCATAA
Statistics
Matches: 103, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 101 0.98
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:18354614 original size:35 final size:36
Alignment explanation
Indices: 18354548--18354630 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
18354538 TATGAGTGCA
*
18354548 CACATTGATGATATATGCCATGTGCGATGTGGGAGTG
1 CACA-TGATGATATACGCCATGTGCGATGTGGGAGTG
* *
18354585 CACATGATGATAT-CGCCTTGTGCGGTGTGGGAGTG
1 CACATGATGATATACGCCATGTGCGATGTGGGAGTG
* *
18354620 CATAGGATGAT
1 CACATGATGAT
18354631 TCTAGCTATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 28 0.68
36 9 0.22
37 4 0.10
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (36 bp):
CACATGATGATATACGCCATGTGCGATGTGGGAGTG
Found at i:18355969 original size:4 final size:4
Alignment explanation
Indices: 18355960--18356021 Score: 51
Period size: 4 Copynumber: 15.5 Consensus size: 4
18355950 CGTGCCTTAC
*
18355960 TTCT TTCT TTCT CTCTCT TT-T TT-T TTCT TTCCT TTCCT TTC- TCCT
1 TTCT TTCT TTCT -T-TCT TTCT TTCT TTCT TT-CT TT-CT TTCT TTCT
18356005 TTCT TTCT TTC- TTCT TT
1 TTCT TTCT TTCT TTCT TT
18356022 TCTTCCTTGG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
3 11 0.22
4 25 0.50
5 11 0.22
6 3 0.06
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTCT
Found at i:18356023 original size:16 final size:15
Alignment explanation
Indices: 18355960--18356025 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
18355950 CGTGCCTTAC
18355960 TTCTTTCTTTCTC-T
1 TTCTTTCTTTCTCTT
* * *
18355974 CTCTTTTTTTTTCTT
1 TTCTTTCTTTCTCTT
* *
18355989 TCCTTTCCTTTCTCCT
1 TTCTTT-CTTTCTCTT
18356005 TTCTTTCTTTCTTCTT
1 TTCTTTCTTTC-TCTT
18356021 TTCTT
1 TTCTT
18356026 CCTTGGCTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
14 10 0.26
15 10 0.26
16 19 0.49
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (15 bp):
TTCTTTCTTTCTCTT
Found at i:18358893 original size:37 final size:37
Alignment explanation
Indices: 18358840--18358958 Score: 181
Period size: 37 Copynumber: 3.2 Consensus size: 37
18358830 TAATGTTGTG
18358840 TGATGATGTTGAAGTGTGCGAGTAGAGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGAGAGTGCACACA
*
18358877 TGATGAT-TAT-AGAGTGTGCGAGTAGATAGTGCACACA
1 TGATGATGT-TGA-AGTGTGCGAGTAGAGAGTGCACACA
18358914 TGATGATGTTGAAGTGTGCGAGTACG-GAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTA-GAGAGTGCACACA
18358951 TGATGATG
1 TGATGATG
18358959 ATATTGAATT
Statistics
Matches: 75, Mismatches: 2, Indels: 10
0.86 0.02 0.11
Matches are distributed among these distances:
36 2 0.03
37 70 0.93
38 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGAGAGTGCACACA
Found at i:18359027 original size:2 final size:2
Alignment explanation
Indices: 18359022--18359060 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
18359012 TATATATATA
18359022 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
18359061 TATAGAAAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:18365464 original size:24 final size:24
Alignment explanation
Indices: 18365437--18365485 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
18365427 CGTGCCTTAC
*
18365437 TTCTTTCTCTCATT-TTTTTTTTCT
1 TTCTTTCTCTC-TTCCTTTTTTTCT
*
18365461 TTCTTTCTTTCTTCCTTTTTTTCT
1 TTCTTTCTCTCTTCCTTTTTTTCT
18365485 T
1 T
18365486 CCTTGGCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTTTCTCTCTTCCTTTTTTTCT
Found at i:18365486 original size:12 final size:12
Alignment explanation
Indices: 18365452--18365489 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
18365442 TCTCTCATTT
*
18365452 TTTTTTTCTTTC
1 TTTTTTTCTTCC
*
18365464 TTTCTTTCTTCC
1 TTTTTTTCTTCC
18365476 TTTTTTTCTTCC
1 TTTTTTTCTTCC
18365488 TT
1 TT
18365490 GGCTTCCTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTTTCTTCC
Found at i:18366424 original size:18 final size:19
Alignment explanation
Indices: 18366385--18366424 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
18366375 GTAATATTTT
18366385 AATATTATTTTATTCATAA
1 AATATTATTTTATTCATAA
18366404 AATATTATTTTATTC-TAA
1 AATATTATTTTATTCATAA
18366422 AAT
1 AAT
18366425 TCTCCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
AATATTATTTTATTCATAA
Found at i:18372368 original size:15 final size:15
Alignment explanation
Indices: 18372348--18372376 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18372338 TCAAGCCTAA
18372348 CAACCTTGAGTGATC
1 CAACCTTGAGTGATC
18372363 CAACCTTGAGTGAT
1 CAACCTTGAGTGAT
18372377 ACAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (15 bp):
CAACCTTGAGTGATC
Found at i:18373403 original size:18 final size:18
Alignment explanation
Indices: 18373380--18373418 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18373370 CAAGTGGAAA
18373380 ATTTTA-GAATAAAATAAT
1 ATTTTATGAAT-AAATAAT
*
18373398 ATTTTATTAATAAATAAT
1 ATTTTATGAATAAATAAT
18373416 ATT
1 ATT
18373419 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTTATGAATAAATAAT
Found at i:18375080 original size:42 final size:42
Alignment explanation
Indices: 18375020--18375145 Score: 182
Period size: 42 Copynumber: 3.0 Consensus size: 42
18375010 TGTGATAATT
*
18375020 ATGACCCAACTATGTGCGGTGTAGAAGTGCACATGAGCTGATG
1 ATGACCCAGC-ATGTGCGGTGTAGAAGTGCACATGAGCTGATG
18375063 ATGACCCAGCATGTGCGGTGTA-AGAGTGCACATGAGCTGATG
1 ATGACCCAGCATGTGCGGTGTAGA-AGTGCACATGAGCTGATG
* * *
18375105 ATGACCCAGCCATGTGCGGTGTGGGAGTGCACATAAGCTGA
1 ATGACCCAG-CATGTGCGGTGTAGAAGTGCACATGAGCTGA
18375146 GAGAGAGTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
41 1 0.01
42 39 0.51
43 36 0.47
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (42 bp):
ATGACCCAGCATGTGCGGTGTAGAAGTGCACATGAGCTGATG
Found at i:18380207 original size:33 final size:33
Alignment explanation
Indices: 18380165--18380232 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
18380155 TTTCATAAAG
18380165 CAAGCTTGAAACCATTTTTCATATCACAAAGTT
1 CAAGCTTGAAACCATTTTTCATATCACAAAGTT
*
18380198 CAAGCTTGAAACCATTTTTCTTATCACAAAGTT
1 CAAGCTTGAAACCATTTTTCATATCACAAAGTT
18380231 CA
1 CA
18380233 TCAAAATACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (33 bp):
CAAGCTTGAAACCATTTTTCATATCACAAAGTT
Found at i:18386004 original size:2 final size:2
Alignment explanation
Indices: 18385997--18386037 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
18385987 CTGAATATTA
*
18385997 TC TC TC TC TC TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
18386038 TAACTCATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:18390336 original size:38 final size:40
Alignment explanation
Indices: 18390293--18390398 Score: 117
Period size: 38 Copynumber: 2.7 Consensus size: 40
18390283 ATAGTGCCCG
* *
18390293 TGTGCACGATGTGGGGGGATGTACATGATGGC-ACTAAT-
1 TGTGCACGATGTGGGGGGATGCACATGATGGCGACGAATA
* * * * **
18390331 TGTGCACGATGTAGAGGGATACACATGATGGCGTCGGGTA
1 TGTGCACGATGTGGGGGGATGCACATGATGGCGACGAATA
*
18390371 TGTGCACGATGTGGGCGGATGCACATGA
1 TGTGCACGATGTGGGGGGATGCACATGA
18390399 GCCGGGTGTG
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 28 0.52
39 2 0.04
40 24 0.44
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGCACATGATGGCGACGAATA
Found at i:18413974 original size:72 final size:73
Alignment explanation
Indices: 18413810--18413997 Score: 252
Period size: 72 Copynumber: 2.6 Consensus size: 73
18413800 CAAAGAGCTC
* * ***
18413810 TTAGTCGACTAACTTTCTTTTTGGTCGACTAAGTTGGTTCTATCTTTTGGTCACAGATTCTAGCA
1 TTAGTCGACTAACTTACATTTTGGTCGACTAAGTTGGTTCTATCTTGAAGTCACAGATTCTAGCA
*
18413875 GAGAGTAT
66 GAGAGCAT
* * * * *
18413883 TTAGTCGACTAACTCACATTTTGGTCGACTAAGTTGGTTCTGTCTTGAAGT-ATAGATTTTGGCA
1 TTAGTCGACTAACTTACATTTTGGTCGACTAAGTTGGTTCTATCTTGAAGTCACAGATTCTAGCA
18413947 GAGAGCAT
66 GAGAGCAT
* *
18413955 TTAGTCAACTAACTTACATTTTGGTCGACTAAGTCGGTTCTAT
1 TTAGTCGACTAACTTACATTTTGGTCGACTAAGTTGGTTCTAT
18413998 TTCTCAATAT
Statistics
Matches: 100, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 56 0.56
73 44 0.44
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (73 bp):
TTAGTCGACTAACTTACATTTTGGTCGACTAAGTTGGTTCTATCTTGAAGTCACAGATTCTAGCA
GAGAGCAT
Found at i:18422940 original size:21 final size:22
Alignment explanation
Indices: 18422915--18422955 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18422905 CCTAGGTGGA
*
18422915 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18422936 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18422956 AAAAAAAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18422956 original size:20 final size:21
Alignment explanation
Indices: 18422915--18422959 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18422905 CCTAGGTGGA
*
18422915 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
18422936 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
18422956 AAAA
1 AAAA
18422960 AAAGGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:18422960 original size:21 final size:20
Alignment explanation
Indices: 18422913--18422960 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
18422903 ACCCTAGGTG
*
18422913 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
18422933 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
18422955 GAAAAA
1 GAAAAA
18422961 AAGGTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:18425205 original size:22 final size:22
Alignment explanation
Indices: 18425177--18425220 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
18425167 TTCGATTGGT
18425177 ATCAGAGC-TTTTGGTTTTAAAG
1 ATCAGAGCTTTTTGG-TTTAAAG
18425199 ATCAGAGCTTTTTGGTTTAAAG
1 ATCAGAGCTTTTTGGTTTAAAG
18425221 TTGTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (22 bp):
ATCAGAGCTTTTTGGTTTAAAG
Found at i:18429988 original size:21 final size:22
Alignment explanation
Indices: 18429962--18430002 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18429952 CCTAGGTGAA
*
18429962 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
18429983 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
18430003 AAAAAAAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:18430003 original size:20 final size:21
Alignment explanation
Indices: 18429962--18430006 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
18429952 CCTAGGTGAA
*
18429962 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
18429983 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
18430003 AAAA
1 AAAA
18430007 AAAACGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:18430007 original size:21 final size:21
Alignment explanation
Indices: 18429961--18430008 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
18429951 CCCTAGGTGA
*
18429961 AAAAATTCAAGGGAAAAGTGT
1 AAAAATTCAAGGAAAAAGTGT
* *
18429982 GAAAATTCAAGGAAACAAGTGA
1 AAAAATTCAAGGAAA-AAGTGT
18430004 AAAAA
1 AAAAA
18430009 AACGTAAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (21 bp):
AAAAATTCAAGGAAAAAGTGT
Found at i:18436503 original size:2 final size:2
Alignment explanation
Indices: 18436455--18436490 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18436445 NNNNNNNNNG
18436455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18436491 CGTATGAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18443495 original size:2 final size:2
Alignment explanation
Indices: 18443483--18443521 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
18443473 GTTGTTTGTC
18443483 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18443522 GTAAGTTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18445340 original size:19 final size:19
Alignment explanation
Indices: 18445312--18445350 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
18445302 AGGTTTGGTG
*
18445312 AGAAACCCTCGGCCAGTTA
1 AGAAACCCTCAGCCAGTTA
* *
18445331 AGAAATCCTCAGCTAGTTA
1 AGAAACCCTCAGCCAGTTA
18445350 A
1 A
18445351 TAATTTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
AGAAACCCTCAGCCAGTTA
Found at i:18446887 original size:91 final size:90
Alignment explanation
Indices: 18446723--18446902 Score: 315
Period size: 91 Copynumber: 2.0 Consensus size: 90
18446713 ATTTCAAATC
* *
18446723 AAAAACAATCAAAAAGTAATTTCTACTACACAGGGGTATTTTGATCATTTTATCCAAAATTTTCG
1 AAAAACAATCAAAAAGTAATTTCTACTACACAAGGGTATTTTGATCATTTTACCCAAAATTTTCG
*
18446788 AACTTTGGCAAAAATATGATATACG
66 AACCTTGGCAAAAATATGATATACG
*
18446813 ANAAAACAATCAAAAAGTAATTTCTACTACACAAGGGTATTTTGATCATTTTACCCAAAATTTTT
1 A-AAAACAATCAAAAAGTAATTTCTACTACACAAGGGTATTTTGATCATTTTACCCAAAATTTTC
18446878 GAACCTTGGCAAAAATATGATATAC
65 GAACCTTGGCAAAAATATGATATAC
18446903 AAGTAATAAG
Statistics
Matches: 85, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
90 1 0.01
91 84 0.99
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (90 bp):
AAAAACAATCAAAAAGTAATTTCTACTACACAAGGGTATTTTGATCATTTTACCCAAAATTTTCG
AACCTTGGCAAAAATATGATATACG
Found at i:18451150 original size:2 final size:2
Alignment explanation
Indices: 18451143--18451174 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18451133 AATCATCTCC
18451143 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18451175 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18459528 original size:35 final size:35
Alignment explanation
Indices: 18459489--18459732 Score: 181
Period size: 35 Copynumber: 7.2 Consensus size: 35
18459479 CTAGGCTTAG
* *
18459489 CCAAAACCTTTCACAATGGTTTTT-ACCGGGATCAA
1 CCAAAACCTTTCACAATGGTTTTTCA-AGGGCTCAA
* * * *
18459524 CCAAAACC---CAAAATGGTTTTTCAAAGGTTTAA
1 CCAAAACCTTTCACAATGGTTTTTCAAGGGCTCAA
* * * *
18459556 CCACAACCTTTCACAACGATTTTTCACGGGCTCAA
1 CCAAAACCTTTCACAATGGTTTTTCAAGGGCTCAA
* *
18459591 CCAAAACC---CA-AAGTGGTTTTTCAAAGGCTTAA
1 CCAAAACCTTTCACAA-TGGTTTTTCAAGGGCTCAA
* *
18459623 CCACAACCTTTCACAATGGTTTTTCATGGGCTCAA
1 CCAAAACCTTTCACAATGGTTTTTCAAGGGCTCAA
*
18459658 CCAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCAAGGGCTCAA
* * * * *
18459690 CCACAACC-TACAACAATGGTTTTTCACGAGATCAA
1 CCAAAACCTTTC-ACAATGGTTTTTCAAGGGCTCAA
18459725 CCAAAACC
1 CCAAAACC
18459733 CAACAACTAA
Statistics
Matches: 163, Mismatches: 32, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
31 4 0.02
32 73 0.45
33 1 0.01
34 1 0.01
35 80 0.49
36 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.25
Consensus pattern (35 bp):
CCAAAACCTTTCACAATGGTTTTTCAAGGGCTCAA
Found at i:18459579 original size:67 final size:67
Alignment explanation
Indices: 18459481--18459735 Score: 370
Period size: 67 Copynumber: 3.8 Consensus size: 67
18459471 GGCTTTTACT
* * *
18459481 AGGCTTAGCCAAAACCTTTCACAATGGTTTTT-ACCGGGATCAACCAAAACCCAAAATGGTTTTT
1 AGGCTTAACCACAACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTT
18459545 CAA
65 CAA
* * * *
18459548 AGGTTTAACCACAACCTTTCACAACGATTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
18459613 AA
66 AA
* *
18459615 AGGCTTAACCACAACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
18459680 AA
66 AA
* * *
18459682 AGGCTCAACCACAACC-TACAACAATGGTTTTTCACGAGATCAACCAAAACCCAA
1 AGGCTTAACCACAACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
18459736 CAACTAACTT
Statistics
Matches: 170, Mismatches: 16, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
66 2 0.01
67 167 0.98
68 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (67 bp):
AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
AA
Found at i:18462668 original size:27 final size:27
Alignment explanation
Indices: 18462612--18462668 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
18462602 TTTAACAAGT
* * *
18462612 ATTCTTCCAAATCATTTTCAAGCTGAC
1 ATTCATCCAAATCATTTTAAAGCTAAC
*
18462639 ATTCATCCAAGTCATTTTAAAG-TAAGC
1 ATTCATCCAAATCATTTTAAAGCTAA-C
18462666 ATT
1 ATT
18462669 GCAAGATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (27 bp):
ATTCATCCAAATCATTTTAAAGCTAAC
Found at i:18466060 original size:39 final size:39
Alignment explanation
Indices: 18466017--18466097 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
18466007 TTTATAAGGT
18466017 AAACATTTTTTAATT-GAACAAGTGTATGAATAATAACTA
1 AAACATTTTTTAATTAG-ACAAGTGTATGAATAATAACTA
18466056 AAACATTTTTTAATTAGACAAGTGTATGAATAATAACTA
1 AAACATTTTTTAATTAGACAAGTGTATGAATAATAACTA
18466095 AAA
1 AAA
18466098 AATGTGCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.35
Consensus pattern (39 bp):
AAACATTTTTTAATTAGACAAGTGTATGAATAATAACTA
Found at i:18467296 original size:35 final size:35
Alignment explanation
Indices: 18467257--18467432 Score: 127
Period size: 35 Copynumber: 5.2 Consensus size: 35
18467247 TAGGCTTAGT
18467257 CAAAACCTTTCACAATGGTTTTTGC-TAGGATCAAC
1 CAAAACCTTTCACAATGGTTTTT-CATAGGATCAAC
* * * * *
18467292 CAAAACC---CAAAATGATTTTTCAAAGGTTTAAC
1 CAAAACCTTTCACAATGGTTTTTCATAGGATCAAC
* * *
18467324 CACAACCTTTCACAATGGTTTTTCATGGGCTCAAC
1 CAAAACCTTTCACAATGGTTTTTCATAGGATCAAC
* * *
18467359 CAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAAT
1 CAAAACCTTTCACAA-TGGTTTTTCATAGGATCAAC
* * **
18467391 CACAACC-TACAACAATGGTTTTTCACGGGATCAAC
1 CAAAACCTTTC-ACAATGGTTTTTCATAGGATCAAC
18467426 CAAAACC
1 CAAAACC
18467433 CAACAACTAA
Statistics
Matches: 110, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
31 3 0.03
32 49 0.45
34 1 0.01
35 55 0.50
36 2 0.02
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (35 bp):
CAAAACCTTTCACAATGGTTTTTCATAGGATCAAC
Found at i:18467325 original size:32 final size:32
Alignment explanation
Indices: 18467270--18467435 Score: 127
Period size: 32 Copynumber: 5.0 Consensus size: 32
18467260 AACCTTTCAC
* *
18467270 AATGGTTTTTGC-TAGGATCAACCAAAACCCAA
1 AATGGTTTTT-CAAAGGCTCAACCAAAACCCAA
* * * * *
18467302 AATGATTTTTCAAAGGTTTAACCACAACCTTTCAC
1 AATGGTTTTTCAAAGGCTCAACCAAAACC---CAA
**
18467337 AATGGTTTTTCATGGGCTCAACCAAAACCCAA
1 AATGGTTTTTCAAAGGCTCAACCAAAACCCAA
* * *
18467369 AGTGGTTTTTCAAAGGCTCAATCACAACCTACAA
1 AATGGTTTTTCAAAGGCTCAACCAAAACC--CAA
** *
18467403 CAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 -AATGGTTTTTCAAAGGCTCAACCAAAACCCAA
18467436 CAACTAACTT
Statistics
Matches: 103, Mismatches: 24, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
31 1 0.01
32 48 0.47
33 3 0.03
34 3 0.03
35 48 0.47
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (32 bp):
AATGGTTTTTCAAAGGCTCAACCAAAACCCAA
Found at i:18467344 original size:67 final size:66
Alignment explanation
Indices: 18467260--18467435 Score: 221
Period size: 67 Copynumber: 2.6 Consensus size: 66
18467250 GCTTAGTCAA
* *
18467260 AACCTTTCACAATGGTTTTTGCTAGGATCAACCAAAACCCAAAATGATTTTTCAAAGGTTTAACC
1 AACCTTTCACAATGGTTTTT-CTAGGATCAACCAAAACCCAAAATGATTTTTCAAAGGCTCAACC
18467325 AC
65 AC
* * * * *
18467327 AACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAATC
1 AACCTTTCACAATGGTTTTTC-TAGGATCAACCAAAACCCAAAATGATTTTTCAAAGGCTCAACC
18467392 AC
65 AC
*
18467394 AACC-TACAACAATGGTTTTTC-ACGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCTA--GGATCAACCAAAACCCAA
18467436 CAACTAACTT
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
66 3 0.03
67 92 0.97
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (66 bp):
AACCTTTCACAATGGTTTTTCTAGGATCAACCAAAACCCAAAATGATTTTTCAAAGGCTCAACCA
C
Found at i:18470883 original size:9 final size:10
Alignment explanation
Indices: 18470862--18470890 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
18470852 CTAAGGTAGT
18470862 TTTTATGAAA
1 TTTTATGAAA
18470872 TTTTAT-AAA
1 TTTTATGAAA
18470881 TTTTATGAAA
1 TTTTATGAAA
18470891 AATGGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (10 bp):
TTTTATGAAA
Done.