Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 49 of 82
Found at i:17907513 original size:22 final size:22
Alignment explanation
Indices: 17907488--17907531 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17907478 TGCATTACTA
17907488 ATTTTTAAGCATTACATGATTG
1 ATTTTTAAGCATTACATGATTG
* * *
17907510 ATTTTTAGGTATTGCATGATTG
1 ATTTTTAAGCATTACATGATTG
17907532 GTTGATTTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.27, C:0.07, G:0.18, T:0.48
Consensus pattern (22 bp):
ATTTTTAAGCATTACATGATTG
Found at i:17907598 original size:22 final size:22
Alignment explanation
Indices: 17907542--17907598 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
17907532 GTTGATTTCA
* *
17907542 CATTGTTTGACTAGTTGATAGG
1 CATTGTGTGACTTGTTGATAGG
* **
17907564 CATTGCGTGACTTGTTTTTAGG
1 CATTGTGTGACTTGTTGATAGG
17907586 CATTGTGTGACTT
1 CATTGTGTGACTT
17907599 AGGTATCACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (22 bp):
CATTGTGTGACTTGTTGATAGG
Found at i:17908576 original size:33 final size:33
Alignment explanation
Indices: 17908508--17908577 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
17908498 ATCATATTAG
* * * *
17908508 CATGCCATGTCATCATTAATTATGATATATGAA
1 CATGCCATGTCATAATCAATTATGACATATCAA
*
17908541 CATGCCATGTCATAATCAATTATGACATTTCAA
1 CATGCCATGTCATAATCAATTATGACATATCAA
17908574 CATG
1 CATG
17908578 TCACATCAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (33 bp):
CATGCCATGTCATAATCAATTATGACATATCAA
Found at i:17909254 original size:15 final size:16
Alignment explanation
Indices: 17909227--17909260 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17909217 TAGATAAACT
17909227 TAACAACAAACAAAAA
1 TAACAACAAACAAAAA
*
17909243 TAACAA-AAACAATAA
1 TAACAACAAACAAAAA
17909258 TAA
1 TAA
17909261 AAATCTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.12
Consensus pattern (16 bp):
TAACAACAAACAAAAA
Found at i:17910064 original size:62 final size:65
Alignment explanation
Indices: 17909955--17910127 Score: 194
Period size: 62 Copynumber: 2.7 Consensus size: 65
17909945 AAAATTATAA
* * * * * * *
17909955 AAAAAATAAAAATATGTTA-AAACAATTTTAAAATTTTTGTAGTGGCGAAATTAT-AAAA-TTTC
1 AAAAAATAAAGACAAGTTATAAA-AATTTAAAAATTGTTGGAGGGGCGAAATTATAAAAATTTTC
17910017 T
65 T
* *
17910018 -AAAAGTAAAGACAAGTTATAAAAATTTAAAAATTGTTGGAGGGGCGAAATTATAAAAATTTTTT
1 AAAAAATAAAGACAAGTTATAAAAATTTAAAAATTGTTGGAGGGGCGAAATTATAAAAATTTTCT
* * *
17910082 AAAAAATACAGATAAATTATAAAAATTTAAAAATTGTTGG-GGGGCG
1 AAAAAATAAAGACAAGTTATAAAAATTTAAAAATTGTTGGAGGGGCG
17910128 GGGGGCCCCA
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
62 41 0.44
63 7 0.08
64 10 0.11
65 35 0.38
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (65 bp):
AAAAAATAAAGACAAGTTATAAAAATTTAAAAATTGTTGGAGGGGCGAAATTATAAAAATTTTCT
Found at i:17910113 original size:65 final size:62
Alignment explanation
Indices: 17909978--17910127 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 62
17909968 ATGTTAAAAC
* * * * * *
17909978 AATTTTAAAATTTTTGTAGTGGCGAAATTATAAAATTTCTAAAAGTAAAGACAAGTTATAAA
1 AATTTAAAAATTGTTGGAGGGGCGAAATTATAAAATTTCTAAAAATAAAGACAAATTATAAA
* * *
17910040 AATTTAAAAATTGTTGGAGGGGCGAAATTATAAAAATTTTTTAAAAAATACAGATAAATTATAAA
1 AATTTAAAAATTGTTGGAGGGGCGAAATTAT-AAAA-TTTCT-AAAAATAAAGACAAATTATAAA
17910105 AATTTAAAAATTGTTGG-GGGGCG
1 AATTTAAAAATTGTTGGAGGGGCG
17910128 GGGGGCCCCA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
62 27 0.36
63 4 0.05
64 10 0.13
65 35 0.46
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (62 bp):
AATTTAAAAATTGTTGGAGGGGCGAAATTATAAAATTTCTAAAAATAAAGACAAATTATAAA
Found at i:17917287 original size:43 final size:43
Alignment explanation
Indices: 17917226--17917311 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
17917216 ATTAAACCAC
* *
17917226 ACCAACAACATTTACAACTTTCCATTTTAAAGGGTATCCTAGG
1 ACCAACAACATTTACAACTTTCCATTTTAAAGGGCACCCTAGG
*
17917269 ACCAACAACATTTACAACTTTTCATTTTAAAGGGCACCCTAGG
1 ACCAACAACATTTACAACTTTCCATTTTAAAGGGCACCCTAGG
17917312 CAATCGAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (43 bp):
ACCAACAACATTTACAACTTTCCATTTTAAAGGGCACCCTAGG
Found at i:17923440 original size:35 final size:33
Alignment explanation
Indices: 17923400--17923468 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 33
17923390 GTTAGTTTGG
* * *
17923400 GTTTTGGTTGATCCCGGTAAAAATCATTGTGAAAA
1 GTTTTGGCTGAACCCGGT-AAAACCATTGT-AAAA
*
17923435 GTTTTGGCTGAACCTGGTAAAACCATTGTAAAA
1 GTTTTGGCTGAACCCGGTAAAACCATTGTAAAA
17923468 G
1 G
17923469 CTTGTGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 5 0.17
34 10 0.33
35 15 0.50
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (33 bp):
GTTTTGGCTGAACCCGGTAAAACCATTGTAAAA
Found at i:17930882 original size:17 final size:17
Alignment explanation
Indices: 17930849--17930883 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17930839 ACCCTAGGAG
17930849 GAGAAGAAAGAAAAAAA
1 GAGAAGAAAGAAAAAAA
17930866 GAGAA-AAAGAAAGAAAA
1 GAGAAGAAAGAAA-AAAA
17930883 G
1 G
17930884 CTTGGTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
GAGAAGAAAGAAAAAAA
Found at i:17932032 original size:29 final size:29
Alignment explanation
Indices: 17932000--17932089 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
17931990 GAGAGATGAA
17932000 TGGGATGTCCGGCTATGTGCACGATGTGG
1 TGGGATGTCCGGCTATGTGCACGATGTGG
* ** * * *
17932029 TGGGATG--C-GC-ATGAGCTGGGTGAGA
1 TGGGATGTCCGGCTATGTGCACGATGTGG
17932054 TGGGATGTCCGGCTATGTGCACGATGTGG
1 TGGGATGTCCGGCTATGTGCACGATGTGG
17932083 TGGGATG
1 TGGGATG
17932090 CACATGAACT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
25 16 0.36
26 2 0.04
27 2 0.04
28 2 0.04
29 23 0.51
ACGTcount: A:0.16, C:0.14, G:0.44, T:0.26
Consensus pattern (29 bp):
TGGGATGTCCGGCTATGTGCACGATGTGG
Found at i:17932057 original size:54 final size:54
Alignment explanation
Indices: 17931999--17932109 Score: 195
Period size: 54 Copynumber: 2.1 Consensus size: 54
17931989 AGAGAGATGA
* * *
17931999 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCGCATGAGCTGGGTGAG
1 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAACTAGGTGAG
17932053 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAACTAGGTGAG
1 ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAACTAGGTGAG
17932107 ATG
1 ATG
17932110 CACATAATGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.20, C:0.14, G:0.41, T:0.24
Consensus pattern (54 bp):
ATGGGATGTCCGGCTATGTGCACGATGTGGTGGGATGCACATGAACTAGGTGAG
Found at i:17932633 original size:19 final size:19
Alignment explanation
Indices: 17932609--17932665 Score: 114
Period size: 19 Copynumber: 3.0 Consensus size: 19
17932599 CCTTTTGACT
17932609 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17932628 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17932647 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
17932666 GTTAATAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:17937018 original size:39 final size:39
Alignment explanation
Indices: 17936970--17937053 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
17936960 TGTCTAAAGA
* *
17936970 TTTGGTGTTGACATTTGACTGTTATGCTGATAATTAATT
1 TTTGCTGTTGACATTGGACTGTTATGCTGATAATTAATT
*
17937009 TTTGCTGTTGACATTGGACTGTTATGTTGATAATTAATT
1 TTTGCTGTTGACATTGGACTGTTATGCTGATAATTAATT
17937048 TTTGCT
1 TTTGCT
17937054 ATGATATTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.50
Consensus pattern (39 bp):
TTTGCTGTTGACATTGGACTGTTATGCTGATAATTAATT
Found at i:17939664 original size:81 final size:81
Alignment explanation
Indices: 17939559--17939756 Score: 297
Period size: 81 Copynumber: 2.4 Consensus size: 81
17939549 TAAATTGGAT
* * * *
17939559 CAATTAAAAATTAGTTATTGGTCATCCAATTTGTCTTTAAATAAATCAAGGTAATTTAGAGATAA
1 CAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAA
*
17939624 TTTTCATATTTTTGAC
66 TATTCATATTTTTGAC
*
17939640 CAATCAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAA
1 CAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAA
17939705 TATTCATATTTTTGAC
66 TATTCATATTTTTGAC
* * * **
17939721 CAATTAAAATTTAATCATTGGTAATTTAATTTATCT
1 CAATTAAAATTTAGTTATTGGTCATCCAATTTATCT
17939757 ATAATAATTA
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 105 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (81 bp):
CAATTAAAATTTAGTTATTGGTCATCCAATTTATCTCTAAATAAATCAAGATAATTTAGAGATAA
TATTCATATTTTTGAC
Found at i:17940075 original size:18 final size:18
Alignment explanation
Indices: 17940029--17940086 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
17940019 ATTTTGATTC
*
17940029 ATTTGGAAGCATTC-AGAG
1 ATTTGGAGGCATTCGA-AG
* *
17940047 ATTGAGGAGGCATTTGAAG
1 ATT-TGGAGGCATTCGAAG
17940066 ATTTGGAGGCATTCGAAG
1 ATTTGGAGGCATTCGAAG
17940084 ATT
1 ATT
17940087 GATAGCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
18 19 0.58
19 13 0.39
20 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (18 bp):
ATTTGGAGGCATTCGAAG
Found at i:17940160 original size:23 final size:23
Alignment explanation
Indices: 17940133--17940208 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
17940123 CTAAAGTGAA
*
17940133 GATCAAGCAACAGCGAAGTTCGT
1 GATCAAGCAGCAGCGAAGTTCGT
*
17940156 GATCAAGCAGCAACGAAGTTCGT
1 GATCAAGCAGCAGCGAAGTTCGT
*
17940179 GATCAAGCAGCAGCAAAGTTCGT
1 GATCAAGCAGCAGCGAAGTTCGT
17940202 GATCAAG
1 GATCAAG
17940209 ATTAAGTCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (23 bp):
GATCAAGCAGCAGCGAAGTTCGT
Found at i:17940315 original size:51 final size:50
Alignment explanation
Indices: 17940194--17940316 Score: 176
Period size: 49 Copynumber: 2.5 Consensus size: 50
17940184 AGCAGCAGCA
* *
17940194 AAGTTCGTGATCAAGATTAAGTCGTCAAGACCCTTGAAGCGAAGATCAAG
1 AAGTTCGTGATCAAGATTAAGTCATAAAGACCCTTGAAGCGAAGATCAAG
* * *
17940244 -TGTTCGTGATCAAGATTAAGTCATAAAGATCCTTGAAGCGAATATCAAG
1 AAGTTCGTGATCAAGATTAAGTCATAAAGACCCTTGAAGCGAAGATCAAG
*
17940293 CAAGTTCGTGATCAAGACTAAGTC
1 -AAGTTCGTGATCAAGATTAAGTC
17940317 CAAGTTTGCG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
49 44 0.69
51 20 0.31
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (50 bp):
AAGTTCGTGATCAAGATTAAGTCATAAAGACCCTTGAAGCGAAGATCAAG
Found at i:17941906 original size:2 final size:2
Alignment explanation
Indices: 17941897--17941955 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
17941887 TTTATTCCCT
17941897 TA TA -A 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
17941938 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
17941956 AAAGATTCCG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17957613 original size:32 final size:33
Alignment explanation
Indices: 17957547--17957614 Score: 106
Period size: 31 Copynumber: 2.1 Consensus size: 33
17957537 AATTTTAACC
17957547 TTTATTAATTTTAAAAATTACTATTATATATTT
1 TTTATTAATTTTAAAAATTACTATTATATATTT
17957580 TTTATTAA-TTTAAAAA-TACTATTAT-TATCTT
1 TTTATTAATTTTAAAAATTACTATTATATAT-TT
17957611 TTTA
1 TTTA
17957615 GAAAAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 3 0.09
31 15 0.44
32 8 0.24
33 8 0.24
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (33 bp):
TTTATTAATTTTAAAAATTACTATTATATATTT
Found at i:17969758 original size:53 final size:53
Alignment explanation
Indices: 17969699--17969899 Score: 221
Period size: 53 Copynumber: 3.8 Consensus size: 53
17969689 TTAGACTTTG
* *
17969699 TCTTGATCACGAACTTCACTTAAGAACTTGATCACAAACTTCGCTGCTTGATA
1 TCTTGATCACGAACTTCACTTAATATCTTGATCACAAACTTCGCTGCTTGATA
* ** *
17969752 TCTTGATCACAAACTTCACTTAATATCTTGATCATGAACTTCGCTTCTTGATA
1 TCTTGATCACGAACTTCACTTAATATCTTGATCACAAACTTCGCTGCTTGATA
* * *
17969805 TCTTGATTATGAACTTCACTTGATATCTTGATCACAAACTTCGCT-C--GATA
1 TCTTGATCACGAACTTCACTTAATATCTTGATCACAAACTTCGCTGCTTGATA
* * * * * * *
17969855 TCTTTA-CTACAAACCTCGCTTGATATCTTAATCATAAACTTCGCT
1 TCTTGATC-ACGAACTTCACTTAATATCTTGATCACAAACTTCGCT
17969900 TGATATGTTG
Statistics
Matches: 127, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
50 40 0.31
52 1 0.01
53 86 0.68
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (53 bp):
TCTTGATCACGAACTTCACTTAATATCTTGATCACAAACTTCGCTGCTTGATA
Found at i:17969791 original size:25 final size:25
Alignment explanation
Indices: 17969699--17969936 Score: 154
Period size: 25 Copynumber: 9.2 Consensus size: 25
17969689 TTAGACTTTG
* *
17969699 TCTTGATCACGAACTTCACTTAAGA
1 TCTTGATCACGAACTTCACTTGATA
* * *
17969724 ACTTGATCACAAACTTCGCTGCTTGATA
1 TCTTGATCACGAACTT--C-ACTTGATA
* *
17969752 TCTTGATCACAAACTTCACTTAATA
1 TCTTGATCACGAACTTCACTTGATA
* *
17969777 TCTTGATCATGAACTTCGCTTCTTGATA
1 TCTTGATCACGAACTT--C-ACTTGATA
* *
17969805 TCTTGATTATGAACTTCACTTGATA
1 TCTTGATCACGAACTTCACTTGATA
* * *
17969830 TCTTGATCACAAACTTCGCTCGATA
1 TCTTGATCACGAACTTCACTTGATA
* * * *
17969855 TCTTTA-CTACAAACCTCGCTTGATA
1 TCTTGATC-ACGAACTTCACTTGATA
* ** *
17969880 TCTTAATCATAAACTTCGCTTGATA
1 TCTTGATCACGAACTTCACTTGATA
* * *
17969905 TGTTGATTACAAACTTTGCCACTTGATA
1 TCTTGATCACGAAC-TT--CACTTGATA
17969933 TCTT
1 TCTT
17969937 CACTTCCGAA
Statistics
Matches: 171, Mismatches: 31, Indels: 19
0.77 0.14 0.09
Matches are distributed among these distances:
24 1 0.01
25 111 0.65
26 5 0.03
27 2 0.01
28 52 0.30
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (25 bp):
TCTTGATCACGAACTTCACTTGATA
Found at i:17969879 original size:50 final size:50
Alignment explanation
Indices: 17969699--17969936 Score: 219
Period size: 53 Copynumber: 4.6 Consensus size: 50
17969689 TTAGACTTTG
* * * *
17969699 TCTTGATCACGAACTTCACTTAAGAACTTGATCACAAACTTCGCTGCTTGATA
1 TCTTGAT-ACAAACTTCACTTGATATCTTGATCACAAACTTCGCT-C-TGATA
* **
17969752 TCTTGATCACAAACTTCACTTAATATCTTGATCATGAACTTCGCTTCTTGATA
1 TCTTGAT-ACAAACTTCACTTGATATCTTGATCACAAACTTCGC-TC-TGATA
**
17969805 TCTTGATTATGAACTTCACTTGATATCTTGATCACAAACTTCGCTC-GATA
1 TCTTGA-TACAAACTTCACTTGATATCTTGATCACAAACTTCGCTCTGATA
* * * * *
17969855 TCTTTACTACAAACCTCGCTTGATATCTTAATCATAAACTTCGCT-TGATA
1 TCTTGA-TACAAACTTCACTTGATATCTTGATCACAAACTTCGCTCTGATA
*
17969905 TGTTGATTACAAACTTTGCCACTTGATATCTT
1 TCTTGA-TACAAAC-TT--CACTTGATATCTT
17969937 CACTTCCGAA
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
50 56 0.36
51 1 0.01
52 2 0.01
53 95 0.61
54 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (50 bp):
TCTTGATACAAACTTCACTTGATATCTTGATCACAAACTTCGCTCTGATA
Found at i:17969928 original size:103 final size:103
Alignment explanation
Indices: 17969699--17969936 Score: 259
Period size: 103 Copynumber: 2.3 Consensus size: 103
17969689 TTAGACTTTG
* * * * *
17969699 TCTTGATCACGAACTTCACTTAAGAACTTGATCACAAACTTCGCTGCTTGATATCTTGATCACAA
1 TCTTGATTACAAACTTCACTTGATATCTTGATCACAAACTTCGCTGC-TGATATCTTGATCACAA
* * *
17969764 ACTTCACTTAATATCTTGATCATGAACTTCGCTTCTTGATA
65 ACCTCACTTAATATCTTAATCATAAACTTCG--TCTTGATA
** *
17969805 TCTTGATTATGAACTTCACTTGATATCTTGATCACAAACTTCGCT-C-GATATCTTTA-CTACAA
1 TCTTGATTACAAACTTCACTTGATATCTTGATCACAAACTTCGCTGCTGATATCTTGATC-ACAA
* *
17969867 ACCTCGCTTGATATCTTAATCATAAACTTCG-CTTGATA
65 ACCTCACTTAATATCTTAATCATAAACTTCGTCTTGATA
*
17969905 TGTTGATTACAAACTTTGCCACTTGATATCTT
1 TCTTGATTACAAAC-TT--CACTTGATATCTT
17969937 CACTTCCGAA
Statistics
Matches: 114, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
100 18 0.16
101 2 0.02
102 1 0.01
103 52 0.46
105 1 0.01
106 40 0.35
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (103 bp):
TCTTGATTACAAACTTCACTTGATATCTTGATCACAAACTTCGCTGCTGATATCTTGATCACAAA
CCTCACTTAATATCTTAATCATAAACTTCGTCTTGATA
Found at i:17970803 original size:33 final size:33
Alignment explanation
Indices: 17970761--17970854 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
17970751 TTGTTGGTGC
*
17970761 AATGGGGTTTATATGGAGTTCAAGGAATGTATA
1 AATGGGGTTTATATGGAATTCAAGGAATGTATA
* *
17970794 AATGGGGTTTAGATGAAATTCAAGGAATGTATA
1 AATGGGGTTTATATGGAATTCAAGGAATGTATA
*
17970827 AATGGGGTCTATATGGAATTCAAGGAAT
1 AATGGGGTTTATATGGAATTCAAGGAAT
17970855 CGGCAAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.36, C:0.04, G:0.29, T:0.31
Consensus pattern (33 bp):
AATGGGGTTTATATGGAATTCAAGGAATGTATA
Found at i:17975532 original size:42 final size:42
Alignment explanation
Indices: 17975467--17975571 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
17975457 AGCTCATGTG
* *
17975467 CACTCCCCACTAC-CACATGGCTGGGTCATTATCGGCTTATGCA
1 CACT-CCCACT-CGCACATAGCTGGGTCATCATCGGCTTATGCA
*
17975510 CACTCCCACTCGCATATAGCTGGGTCATCATCGGCTTATGCA
1 CACTCCCACTCGCACATAGCTGGGTCATCATCGGCTTATGCA
* *
17975552 CACTTCTACTCGCACATAGC
1 CACTCCCACTCGCACATAGC
17975572 CGAGTCCACA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
41 1 0.02
42 50 0.91
43 4 0.07
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (42 bp):
CACTCCCACTCGCACATAGCTGGGTCATCATCGGCTTATGCA
Found at i:17977354 original size:72 final size:69
Alignment explanation
Indices: 17977261--17977410 Score: 228
Period size: 72 Copynumber: 2.1 Consensus size: 69
17977251 CATAACATAG
** * *
17977261 TTTTTTTTTTTTACCTTAACTTTTGCCTAAGTTGTCCTGTTAAGGATTTTCAACTTAGCATGCTT
1 TTTTTTTTTTTTACCTTAACTTTTGCCTAAGTCATCCTATTAAGGATTTTCAACTTAGCAAGCTT
17977326 TTTT
66 TTTT
*
17977330 TTTTTTTTCATTTTCACCTTAACTTTTGCTTAAGTCATCCTATTAAGGATTTTCAACTTAGCAAG
1 TTTTTTTT--TTTT-ACCTTAACTTTTGCCTAAGTCATCCTATTAAGGATTTTCAACTTAGCAAG
17977395 CTTTTTT
63 CTTTTTT
17977402 TTTTTTTTT
1 TTTTTTTTT
17977411 GTGGGCAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
69 8 0.11
70 1 0.01
71 4 0.05
72 60 0.82
ACGTcount: A:0.19, C:0.16, G:0.09, T:0.56
Consensus pattern (69 bp):
TTTTTTTTTTTTACCTTAACTTTTGCCTAAGTCATCCTATTAAGGATTTTCAACTTAGCAAGCTT
TTTT
Found at i:17985742 original size:140 final size:142
Alignment explanation
Indices: 17985480--17985750 Score: 422
Period size: 140 Copynumber: 1.9 Consensus size: 142
17985470 AAGTTTTCTC
* *
17985480 AATTAGTATCTGTCGTAACATGCGAGTCCGGAAACCCGATCGCTAGACGAGAGTGAAAACTCTAT
1 AATTAGTAGCTGTCGTAACATGCGAGTCCGGAAACCCGACCGCTAGACGAGAGTGAAAACTCTAT
* *
17985545 AACTAAGAGTCGCCACCAATCTTTTTTTCTAGGTGTGATTGGCCACCTATTGACTCGATTCTAAT
66 AACTAAGAGTCACCACCAATCTTTTTTACTAGGTGTGATTGGCCACCTATTGACTCGATTCTAAT
17985610 CTGCGGAGTCTT
131 CTGCGGAGTCTT
* * *
17985622 AATTAG-AGCTGTCGTAA-AGTGCGGGTCCGGGAACCCGACCGCTAGACGCGA-TGAAAACTCTA
1 AATTAGTAGCTGTCGTAACA-TGCGAGTCCGGAAACCCGACCGCTAGACGAGAGTGAAAACTCTA
* * *
17985684 TAACTAGGAGTCACCACCAATCTTTTTTACTAGGTGTGATTGGTCACCTATTGACTCGATTTTAA
65 TAACTAAGAGTCACCACCAATCTTTTTTACTAGGTGTGATTGGCCACCTATTGACTCGATTCTAA
17985749 TC
130 TC
17985751 GGCAAAGTCT
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
140 74 0.63
141 38 0.32
142 6 0.05
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.29
Consensus pattern (142 bp):
AATTAGTAGCTGTCGTAACATGCGAGTCCGGAAACCCGACCGCTAGACGAGAGTGAAAACTCTAT
AACTAAGAGTCACCACCAATCTTTTTTACTAGGTGTGATTGGCCACCTATTGACTCGATTCTAAT
CTGCGGAGTCTT
Found at i:17998480 original size:28 final size:28
Alignment explanation
Indices: 17998438--17998585 Score: 112
Period size: 28 Copynumber: 5.5 Consensus size: 28
17998428 TTCGGAAACT
* * *
17998438 TTGCTTGAGAACTTGATCACAAACTTCG
1 TTGCTTGATATCTTGATCACGAACTTCG
* *
17998466 TTGCTTGATATCTTGATCATGAACTTTG
1 TTGCTTGATATCTTGATCACGAACTTCG
*
17998494 CTT-CTTGATATCTTGATTACGAACTTC-
1 -TTGCTTGATATCTTGATCACGAACTTCG
* *
17998521 --GCTTGATATCTTGCTCATGAA--TC-
1 TTGCTTGATATCTTGATCACGAACTTCG
* * ** *
17998544 TCGCTTGATATCTTGCTCGTGAACTTCA
1 TTGCTTGATATCTTGATCACGAACTTCG
*
17998572 TCGCTTGATATCTT
1 TTGCTTGATATCTT
17998586 CAATTTAGAA
Statistics
Matches: 101, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
23 2 0.02
25 37 0.37
27 2 0.02
28 58 0.57
29 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (28 bp):
TTGCTTGATATCTTGATCACGAACTTCG
Found at i:17998531 original size:25 final size:25
Alignment explanation
Indices: 17998348--17998585 Score: 131
Period size: 25 Copynumber: 9.2 Consensus size: 25
17998338 TCGGACTTGG
* * *
17998348 TCTTGATCATGAACTTTGCTTGAGAA
1 TCTTGATCACGAACTTCGCTTGA-TA
* * *
17998374 T-TTGATCAAGAACTTCACTTGAGA
1 TCTTGATCACGAACTTCGCTTGATA
* * * *
17998398 ACTTGATCACGAGCTTTGTTTGATA
1 TCTTGATCACGAACTTCGCTTGATA
* * * *
17998423 TCTTGTTC-GGAAACTTTGCTTGAGA
1 TCTTGATCACG-AACTTCGCTTGATA
* *
17998448 ACTTGATCACAAACTTCGTTGCTTGATA
1 TCTTGATCACGAACTTC---GCTTGATA
* *
17998476 TCTTGATCATGAACTTTGCTTCTTGATA
1 TCTTGATCACGAAC-TT-C-GCTTGATA
*
17998504 TCTTGATTACGAACTTCGCTTGATA
1 TCTTGATCACGAACTTCGCTTGATA
* *
17998529 TCTTGCTCATGAA-TCTCGCTTGATA
1 TCTTGATCACGAACT-TCGCTTGATA
* **
17998554 TCTTGCTCGTGAACTTCATCGCTTGATA
1 TCTTGATCACGAAC-T--TCGCTTGATA
17998582 TCTT
1 TCTT
17998586 CAATTTAGAA
Statistics
Matches: 165, Mismatches: 35, Indels: 22
0.74 0.16 0.10
Matches are distributed among these distances:
24 3 0.02
25 102 0.62
26 2 0.01
27 3 0.02
28 52 0.32
29 2 0.01
30 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (25 bp):
TCTTGATCACGAACTTCGCTTGATA
Found at i:18000520 original size:19 final size:21
Alignment explanation
Indices: 18000481--18000522 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18000471 AATTACTTCA
*
18000481 AACTGATTACCATTGTTTCTT
1 AACTAATTACCATTGTTTCTT
18000502 AACTAATTACCA-T-TTTCTT
1 AACTAATTACCATTGTTTCTT
18000521 AA
1 AA
18000523 TTGAAGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (21 bp):
AACTAATTACCATTGTTTCTT
Found at i:18011635 original size:22 final size:22
Alignment explanation
Indices: 18011585--18011635 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
18011575 CAATATTCAC
18011585 AACTTTTCATATGACAAAACAA
1 AACTTTTCATATGACAAAACAA
* *
18011607 AATTTTTCATATGA-AAAGACAT
1 AACTTTTCATATGACAAA-ACAA
18011629 AACTTTT
1 AACTTTT
18011636 AATTTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 3 0.12
22 22 0.88
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (22 bp):
AACTTTTCATATGACAAAACAA
Found at i:18031390 original size:31 final size:31
Alignment explanation
Indices: 18031351--18031593 Score: 337
Period size: 31 Copynumber: 7.8 Consensus size: 31
18031341 CACGACATTG
*
18031351 GTTATATGCATGGTGTGTTACAACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
* * *
18031382 ATTATATGCATAGCGTGTTACAACATTTAAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
* * *
18031413 GTTATATGCATGGCATGTTACCACATTTTTC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
18031444 GTTATATGCATGGCATGTTATCAA-ATTTTAC
1 GTTATATGCATGGCGTGTTA-CAACATTTTAC
* *
18031475 GTTATATGCATAGCGTGTTACAACATTTTAT
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
18031506 GTTATTTGCATGGCGTGTTAGC-ACATTTTAC
1 GTTATATGCATGGCGTGTTA-CAACATTTTAC
*
18031537 GTTATATGCATGGCGTGTTACTACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
18031568 GTTATATGCATGGCGTGTAACAACAT
1 GTTATATGCATGGCGTGTTACAACAT
18031594 GACTGACAAA
Statistics
Matches: 187, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
30 4 0.02
31 180 0.96
32 3 0.02
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (31 bp):
GTTATATGCATGGCGTGTTACAACATTTTAC
Found at i:18036230 original size:31 final size:31
Alignment explanation
Indices: 18035982--18036245 Score: 341
Period size: 31 Copynumber: 8.5 Consensus size: 31
18035972 AATAAGAAAT
* *
18035982 AAATGTTGTGAAACGCCATGCATAACAAG-C
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
18036012 AAAATGTTGTGATACGCCATGCATAACAAGTA
1 -AAATGTTGTGACACGCCATGCATATCAAGTC
* * *
18036044 AAATGTTGTGACACACCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
18036075 AAATCTTGTGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* *
18036106 AAATATTGTGACACGCCAAGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
*
18036137 AAATGTTGTGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTC
**
18036168 AAACATTGTGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* **
18036199 AAATGTTGTCACACGCCATGCATATTGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTC
* *
18036230 AAATATTGTCACACGC
1 AAATGTTGTGACACGC
18036246 TAACGGTGAC
Statistics
Matches: 210, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
31 210 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTC
Found at i:18036905 original size:47 final size:46
Alignment explanation
Indices: 18036856--18037162 Score: 296
Period size: 47 Copynumber: 6.6 Consensus size: 46
18036846 AAACATGTCA
* * * *
18036856 TGTCACCAACTTTGAACTCTAGCTTGTCACAGCTTCACTCCATGGCA
1 TGTCACCAACTTTGAACTCT-GCGTGTCACAGATTCCCTCCATGGCG
* *
18036903 TGTCACCAACTTTGAACTCTGACGTGTAACAGATTCCCTCCATGGTG
1 TGTCACCAACTTTGAACTCTG-CGTGTCACAGATTCCCTCCATGGCG
* * * *
18036950 TCTCACAAACTCTGAACGT-TGGCGTGTCACAGATTCCCTCCATGCCG
1 TGTCACCAACTTTGAAC-TCT-GCGTGTCACAGATTCCCTCCATGGCG
* * * * * *
18036997 TGTCACCAACTCTAAACTCTGATGTGTCACAAATTCCCTCTATGGTG
1 TGTCACCAACTTTGAACTCTG-CGTGTCACAGATTCCCTCCATGGCG
* * * *
18037044 TCTCACCAACTTTGAACACTGACGTGTCACAAATTCCCACCATGGCAG
1 TGTCACCAACTTTGAACTCTG-CGTGTCACAGATTCCCTCCATGGC-G
* *
18037092 -GTCACCAACTTTTAACTCTAGCATGTCACAGATTCCCTCCATGGCG
1 TGTCACCAACTTTGAACTCT-GCGTGTCACAGATTCCCTCCATGGCG
* * *
18037138 TGCCACCAACTCTGAACGCTG-GTGT
1 TGTCACCAACTTTGAACTCTGCGTGT
18037163 GTCATAGCCG
Statistics
Matches: 213, Mismatches: 39, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
45 3 0.01
46 5 0.02
47 201 0.94
48 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (46 bp):
TGTCACCAACTTTGAACTCTGCGTGTCACAGATTCCCTCCATGGCG
Found at i:18037001 original size:94 final size:94
Alignment explanation
Indices: 18036858--18037166 Score: 336
Period size: 94 Copynumber: 3.3 Consensus size: 94
18036848 ACATGTCATG
* * * * * * * * *
18036858 TCACCAACTTTGAACTCTAGCTTGTCACAGCTTCACTCCATGGCATGTCACCAACTTTGAACTCT
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGCCGTGTCACCAACTTTAAACTCT
*
18036923 GACGTGTAACAGATTCCCTCCATGGTGTC
66 GACGTGTCACAGATTCCCTCCATGGTGTC
* * *
18036952 TCACAAACTCTGAACGTTGGCGTGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTAAACTCT
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGCCGTGTCACCAACTTTAAACTCT
* * *
18037017 GATGTGTCACAAATTCCCTCTATGGTGTC
66 GACGTGTCACAGATTCCCTCCATGGTGTC
* * * * * * *
18037046 TCACCAACTTTGAACACTGACGTGTCACAAATTCCCACCATGGCAG-GTCACCAACTTTTAACTC
1 TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCAT-GCCGTGTCACCAACTTTAAACTC
* *
18037110 T-AGCATGTCACAGATTCCCTCCATGGCGTGC
65 TGA-CGTGTCACAGATTCCCTCCATGGTGT-C
*
18037141 -CACCAACTCTGAACGCTGGTGTGTCA
1 TCACCAACTCTGAACGCTGGCGTGTCA
18037167 TAGCCGTGTC
Statistics
Matches: 177, Mismatches: 35, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
93 1 0.01
94 172 0.97
95 4 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (94 bp):
TCACCAACTCTGAACGCTGGCGTGTCACAGATTCCCTCCATGCCGTGTCACCAACTTTAAACTCT
GACGTGTCACAGATTCCCTCCATGGTGTC
Found at i:18037087 original size:141 final size:141
Alignment explanation
Indices: 18036905--18037166 Score: 348
Period size: 141 Copynumber: 1.9 Consensus size: 141
18036895 CCATGGCATG
* * * *
18036905 TCACCAACTTTGAACTCTGACGTGTAACAGATTCCCTCCATGG-TGTCTCACAAACTCTGAACGT
1 TCACCAACTTTGAACACTGACGTGTAACAAATTCCCACCATGGCAG-CTCACAAACTCTGAAC-T
* * * *
18036969 -TGGCGTGTCACAGATTCCCTCCATGCCGTGTCACCAACTCTAAACTCTGATGTGTCACAAATTC
64 CTAGCATGTCACAGATTCCCTCCATGCCGTGCCACCAACTCTAAACGCTGATGTGTCACAAATTC
18037033 CCTCTATGGTGTC
129 CCTCTATGGTGTC
* * * * *
18037046 TCACCAACTTTGAACACTGACGTGTCACAAATTCCCACCATGGCAGGTCACCAACTTTTAACTCT
1 TCACCAACTTTGAACACTGACGTGTAACAAATTCCCACCATGGCAGCTCACAAACTCTGAACTCT
* * *
18037111 AGCATGTCACAGATTCCCTCCATGGCGTGCCACCAACTCTGAACGCTGGTGTGTCA
66 AGCATGTCACAGATTCCCTCCATGCCGTGCCACCAACTCTAAACGCTGATGTGTCA
18037167 TAGCCGTGTC
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
140 1 0.01
141 101 0.98
142 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.27
Consensus pattern (141 bp):
TCACCAACTTTGAACACTGACGTGTAACAAATTCCCACCATGGCAGCTCACAAACTCTGAACTCT
AGCATGTCACAGATTCCCTCCATGCCGTGCCACCAACTCTAAACGCTGATGTGTCACAAATTCCC
TCTATGGTGTC
Found at i:18038850 original size:26 final size:25
Alignment explanation
Indices: 18038815--18038901 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 25
18038805 AATATTGATT
18038815 AAATTTTATTTATTTATCAACATCC
1 AAATTTTATTTATTTATCAACATCC
* ** **
18038840 AAATTCTTATTCAACTA--AACTATATT
1 AAATT-TTATTTATTTATCAAC-AT-CC
*
18038866 AAATTTTATTTATTTATCAACATCG
1 AAATTTTATTTATTTATCAACATCC
18038891 AAATTCTTATT
1 AAATT-TTATT
18038902 CAACTAAACT
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
24 3 0.07
25 20 0.43
26 20 0.43
27 3 0.07
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.47
Consensus pattern (25 bp):
AAATTTTATTTATTTATCAACATCC
Found at i:18038867 original size:51 final size:51
Alignment explanation
Indices: 18038812--18038913 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
18038802 TAAAATATTG
18038812 ATTAAATTTTATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
1 ATTAAATTTTATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
*
18038863 ATTAAATTTTATTTATTTATCAACATCGAAATTCTTATTCAACTAAACTAT
1 ATTAAATTTTATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
18038914 CTTTAATTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (51 bp):
ATTAAATTTTATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
Found at i:18038921 original size:26 final size:26
Alignment explanation
Indices: 18038840--18038921 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
18038830 ATCAACATCC
*
18038840 AAATTCTTATTCAACTAAACTATATT
1 AAATTCTTATTCAACTAAACTATCTT
* ** *
18038866 AAATT-TTATTTATTTATCAAC-ATC-G
1 AAATTCTTATTCAACTA--AACTATCTT
18038891 AAATTCTTATTCAACTAAACTATCTT
1 AAATTCTTATTCAACTAAACTATCTT
*
18038917 TAATT
1 AAATT
18038922 AATATTATTA
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
24 3 0.07
25 16 0.39
26 19 0.46
27 3 0.07
ACGTcount: A:0.39, C:0.15, G:0.01, T:0.45
Consensus pattern (26 bp):
AAATTCTTATTCAACTAAACTATCTT
Found at i:18038930 original size:51 final size:51
Alignment explanation
Indices: 18038812--18038927 Score: 178
Period size: 51 Copynumber: 2.3 Consensus size: 51
18038802 TAAAATATTG
*
18038812 ATTAAATTTTATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
1 ATTAAATTATATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
* *
18038863 ATTAAATTTTATTTATTTATCAACATCGAAATTCTTATTCAACTAAACTAT
1 ATTAAATTATATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
* *
18038914 CTTTAATTAATATT
1 ATTAAATT-ATATT
18038928 ATTATTTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 56 0.93
52 4 0.07
ACGTcount: A:0.39, C:0.14, G:0.01, T:0.47
Consensus pattern (51 bp):
ATTAAATTATATTTATTTATCAACATCCAAATTCTTATTCAACTAAACTAT
Found at i:18056389 original size:40 final size:38
Alignment explanation
Indices: 18056327--18056410 Score: 116
Period size: 40 Copynumber: 2.2 Consensus size: 38
18056317 TTTTATTAAA
18056327 AATAATTTTAAATTCAATAATATTATAAATAATAATAAT
1 AATAATTTTAAATTCAATAATATTAT-AATAATAATAAT
* *
18056366 GAATAATTTTAAATTTTAA-AATATTATAATAATATTAAT
1 -AATAATTTTAAA-TTCAATAATATTATAATAATAATAAT
18056405 AATAAT
1 AATAAT
18056411 AAATTAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
38 6 0.15
39 11 0.27
40 20 0.49
41 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (38 bp):
AATAATTTTAAATTCAATAATATTATAATAATAATAAT
Found at i:18056422 original size:14 final size:15
Alignment explanation
Indices: 18056391--18056444 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 15
18056381 TTAAAATATT
*
18056391 ATAATAATATTAATA
1 ATAATAATATTAAAA
18056406 ATAATAA-ATTAAAA
1 ATAATAATATTAAAA
* *
18056420 ATAATTATTTTAAAA
1 ATAATAATATTAAAA
*
18056435 A-ATTAATATT
1 ATAATAATATT
18056445 TTTAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 18 0.56
15 14 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATATTAAAA
Found at i:18056427 original size:35 final size:36
Alignment explanation
Indices: 18056355--18056427 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 36
18056345 AATATTATAA
** *
18056355 ATAATAATAATGAATAATTTTAAATTTTAAAATATT
1 ATAATAATAATGAATAATAATAAATTTAAAAATATT
*
18056391 ATAATAAT-ATTAATAATAATAAA-TTAAAAATAATT
1 ATAATAATAATGAATAATAATAAATTTAAAAAT-ATT
18056426 AT
1 AT
18056428 TTTAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 7 0.22
35 17 0.53
36 8 0.25
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
ATAATAATAATGAATAATAATAAATTTAAAAATATT
Found at i:18056969 original size:15 final size:16
Alignment explanation
Indices: 18056949--18056983 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18056939 GACAATGTGG
18056949 TAAA-TTTATTAATTT
1 TAAATTTTATTAATTT
*
18056964 TAAATTTTATTATTTT
1 TAAATTTTATTAATTT
18056980 TAAA
1 TAAA
18056984 AAATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAAATTTTATTAATTT
Found at i:18057880 original size:11 final size:11
Alignment explanation
Indices: 18057860--18057893 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18057850 TGCACATGTA
*
18057860 TATTTGTTTTT
1 TATTTATTTTT
18057871 TATTTATTTTT
1 TATTTATTTTT
*
18057882 AATTTATTTTT
1 TATTTATTTTT
18057893 T
1 T
18057894 TTAAATAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:18057967 original size:25 final size:25
Alignment explanation
Indices: 18057935--18057983 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
18057925 TAAATAATTG
18057935 ATAATTTAAATATTAA-ATTTTATTT
1 ATAATTT-AATATTAATATTTTATTT
18057960 ATAATTTAATATTAATATTTTATT
1 ATAATTTAATATTAATATTTTATT
18057984 AAAAGTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATAATTTAATATTAATATTTTATTT
Found at i:18062782 original size:16 final size:16
Alignment explanation
Indices: 18062761--18062801 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
18062751 TTATTAATTA
*
18062761 TTTTTTACTTTTATAT
1 TTTTTTAATTTTATAT
18062777 TTTTTTAATTTTATAT
1 TTTTTTAATTTTATAT
*
18062793 ATTTTTAAT
1 TTTTTTAAT
18062802 ATAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTAATTTTATAT
Found at i:18064726 original size:43 final size:43
Alignment explanation
Indices: 18064653--18064779 Score: 173
Period size: 43 Copynumber: 3.0 Consensus size: 43
18064643 CAACTCTCCC
* * * * *
18064653 TCAGCTTATGTGCACTCCCACACAATACATAGCTGGGTCATCA
1 TCAGCTCATGTGCACTACTACACCACACATAGCTGGGTCATCA
* * *
18064696 TCAGCTCATGTGCACTACTACACCGCACATAGTTGGGACATCA
1 TCAGCTCATGTGCACTACTACACCACACATAGCTGGGTCATCA
*
18064739 TCAGCTCATGTGCACTACTATACCACACATAGCTGGGTCAT
1 TCAGCTCATGTGCACTACTACACCACACATAGCTGGGTCAT
18064780 AATTATCACA
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
TCAGCTCATGTGCACTACTACACCACACATAGCTGGGTCATCA
Found at i:18065959 original size:19 final size:20
Alignment explanation
Indices: 18065935--18065974 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
18065925 TGGCAAGGTG
18065935 AAATGGC-ATGGGAGCATGA
1 AAATGGCGATGGGAGCATGA
*
18065954 AAATGGCGTTGGGAGCATGA
1 AAATGGCGATGGGAGCATGA
18065974 A
1 A
18065975 GGTGGGGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.35, C:0.10, G:0.38, T:0.17
Consensus pattern (20 bp):
AAATGGCGATGGGAGCATGA
Found at i:18069451 original size:24 final size:24
Alignment explanation
Indices: 18069423--18069471 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
18069413 AGAATAGCAC
18069423 TATGTGC-TTTTTCTATAAGATCAT
1 TATGTGCTTTTTTC-ATAAGATCAT
18069447 TATGTGCTTTTTTCATAAGATCAT
1 TATGTGCTTTTTTCATAAGATCAT
18069471 T
1 T
18069472 TTTCTCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
TATGTGCTTTTTTCATAAGATCAT
Found at i:18070288 original size:2 final size:2
Alignment explanation
Indices: 18070281--18070310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18070271 ATTGCTTAAG
18070281 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
18070311 TTATCATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18071168 original size:20 final size:20
Alignment explanation
Indices: 18071143--18071195 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
18071133 AAGAAAAAGT
*
18071143 TGCTGGAAGCTTGAAGAATC
1 TGCTGGAAACTTGAAGAATC
*
18071163 TGCTGGAAATTTGAAGAAGT-
1 TGCTGGAAACTTGAAGAA-TC
*
18071183 TGCTAGAAACTTG
1 TGCTGGAAACTTG
18071196 GATCTTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (20 bp):
TGCTGGAAACTTGAAGAATC
Found at i:18076293 original size:22 final size:24
Alignment explanation
Indices: 18076268--18076311 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
18076258 GTCATCACTC
*
18076268 ATTCTTA-CAAC-CGTATTTCATA
1 ATTCTTATCAACAAGTATTTCATA
18076290 ATTCTTATCAACAAGTATTTCA
1 ATTCTTATCAACAAGTATTTCA
18076312 ATACTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 4 0.21
24 8 0.42
ACGTcount: A:0.34, C:0.20, G:0.05, T:0.41
Consensus pattern (24 bp):
ATTCTTATCAACAAGTATTTCATA
Found at i:18076425 original size:2 final size:2
Alignment explanation
Indices: 18076418--18076445 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18076408 ATTACTTAAG
18076418 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
18076446 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18090172 original size:22 final size:24
Alignment explanation
Indices: 18090141--18090209 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
18090131 TCACGACTTG
*
18090141 ATCTTAATCACGAAC-AC-TTGAT
1 ATCTTGATCACGAACTACGTTGAT
* *
18090163 ATCTTGATCATGAACTTCGTTTGAT
1 ATCTTGATCACGAACTACG-TTGAT
*
18090188 ATCTTGATCACGAACTTCGTTG
1 ATCTTGATCACGAACTACGTTG
18090210 CCGCTTGATC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.32
23 1 0.03
24 3 0.08
25 23 0.57
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (24 bp):
ATCTTGATCACGAACTACGTTGAT
Found at i:18090190 original size:25 final size:25
Alignment explanation
Indices: 18090158--18090231 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
18090148 TCACGAACAC
18090158 TTGATATCTTGATCATGAACTTCGT
1 TTGATATCTTGATCATGAACTTCGT
*
18090183 TTGATATCTTGATCACGAACTTCG-
1 TTGATATCTTGATCATGAACTTCGT
***
18090207 TTG-CCGCTTGATCATGAACTTCGT
1 TTGATATCTTGATCATGAACTTCGT
18090231 T
1 T
18090232 GCCATTTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 16 0.37
24 4 0.09
25 23 0.53
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.41
Consensus pattern (25 bp):
TTGATATCTTGATCATGAACTTCGT
Found at i:18090240 original size:23 final size:23
Alignment explanation
Indices: 18090166--18090242 Score: 91
Period size: 23 Copynumber: 3.3 Consensus size: 23
18090156 ACTTGATATC
**
18090166 TTGATCATGAACTTCGTTTGATAT
1 TTGATCATGAACTTCG-TTGCCAT
* **
18090190 CTTGATCACGAACTTCGTTGCCGC
1 -TTGATCATGAACTTCGTTGCCAT
18090214 TTGATCATGAACTTCGTTGCCAT
1 TTGATCATGAACTTCGTTGCCAT
18090237 TTGATC
1 TTGATC
18090243 TTCACTACGA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 26 0.59
24 3 0.07
25 15 0.34
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (23 bp):
TTGATCATGAACTTCGTTGCCAT
Found at i:18092136 original size:7 final size:7
Alignment explanation
Indices: 18092124--18092151 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
18092114 ACCTTGAGCC
18092124 TAGAAAG
1 TAGAAAG
18092131 TAGAAAG
1 TAGAAAG
18092138 TAGAAAG
1 TAGAAAG
18092145 TAGAAAG
1 TAGAAAG
18092152 GTGATGACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (7 bp):
TAGAAAG
Found at i:18096455 original size:21 final size:22
Alignment explanation
Indices: 18096420--18096461 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
18096410 TTTATAAAAT
*
18096420 TGCATTATCATATTTATTTATA
1 TGCATCATCATATTTATTTATA
*
18096442 TGCATCAT-ATATTTTTTTAT
1 TGCATCATCATATTTATTTAT
18096462 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.57
Consensus pattern (22 bp):
TGCATCATCATATTTATTTATA
Found at i:18096755 original size:30 final size:30
Alignment explanation
Indices: 18096714--18096784 Score: 115
Period size: 30 Copynumber: 2.4 Consensus size: 30
18096704 GCATGTAATC
* *
18096714 AAGTTCTTATATTTTTATTTTGAGTCAAAT
1 AAGTCCTTATATTTTTATTTTAAGTCAAAT
18096744 AAGTCCTTATATTTTTATTTTAAGTCAAAT
1 AAGTCCTTATATTTTTATTTTAAGTCAAAT
*
18096774 AAGTCTTTATA
1 AAGTCCTTATA
18096785 ATTAGTGATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.51
Consensus pattern (30 bp):
AAGTCCTTATATTTTTATTTTAAGTCAAAT
Found at i:18100974 original size:78 final size:78
Alignment explanation
Indices: 18100842--18101001 Score: 230
Period size: 78 Copynumber: 2.1 Consensus size: 78
18100832 GTAACATATG
* * *
18100842 ATGTTGCAGCAGCTATGACCAGAACAACGAAGCAAAATGACTACTGTGATTGAGGGACAAGCAAA
1 ATGTTGCAGCAACTATGACCAGAACAACGAAGCAAAATGACTACGGTGACTGAGGGACAAGCAAA
18100907 TCTAAAACACAAA
66 TCTAAAACACAAA
* * * * * *
18100920 ATGTTGCAGCAATTGTGACCAGTACAACGAAGCAAACTGAGTGCGGTGACTGAGGGACAAGCAAA
1 ATGTTGCAGCAACTATGACCAGAACAACGAAGCAAAATGACTACGGTGACTGAGGGACAAGCAAA
*
18100985 TCTAAAACACAAG
66 TCTAAAACACAAA
18100998 ATGT
1 ATGT
18101002 CTCTCTCAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (78 bp):
ATGTTGCAGCAACTATGACCAGAACAACGAAGCAAAATGACTACGGTGACTGAGGGACAAGCAAA
TCTAAAACACAAA
Found at i:18104206 original size:23 final size:23
Alignment explanation
Indices: 18104154--18104206 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
18104144 ATAAGAATTC
*
18104154 GTAACGCCACTCCATATATACTA
1 GTAACGCCACTCCACATATACTA
* * *
18104177 CTCACGCGACTCCACATCA-ACTA
1 GTAACGCCACTCCACAT-ATACTA
18104200 GTAACGC
1 GTAACGC
18104207 AATTCTATAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.32, C:0.36, G:0.11, T:0.21
Consensus pattern (23 bp):
GTAACGCCACTCCACATATACTA
Found at i:18104606 original size:92 final size:92
Alignment explanation
Indices: 18104479--18104769 Score: 438
Period size: 92 Copynumber: 3.2 Consensus size: 92
18104469 ATGTGGATTA
* * * * *
18104479 GTGATACGATTCCATATTAACTACCGACATAATTCAAAATTTAGTACTCACGTGACTCCATAACA
1 GTGACACGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
*
18104544 AATACTCCCGCAAATCAATATCAACTG
66 AATACTCTCGCAAATCAATATCAACTG
**
18104571 GTGATGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
1 GTGACACGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
* * *
18104636 AATACTTTCACGAATCAATATCAACTG
66 AATACTCTCGCAAATCAATATCAACTG
* * *
18104663 CTGACGCGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGTGTGACTCCATAACA
1 GTGACACGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
* *
18104728 AATACTCTTGCTAATCAATATCAACTG
66 AATACTCTCGCAAATCAATATCAACTG
18104755 GTGACACGATTCCAT
1 GTGACACGATTCCAT
18104770 TCCCACCATT
Statistics
Matches: 181, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 181 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.29
Consensus pattern (92 bp):
GTGACACGATTCCATATTAACTACCGACGTGATTCAACATTTAGTACTCGCGTGACTCCATAACA
AATACTCTCGCAAATCAATATCAACTG
Found at i:18105062 original size:29 final size:26
Alignment explanation
Indices: 18104998--18105075 Score: 138
Period size: 26 Copynumber: 3.0 Consensus size: 26
18104988 ATGAATGAAT
18104998 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGTAAATGATACA
18105024 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGTAAATGATACA
* *
18105050 ACAAAAAATAATATGGAAATGATACA
1 ACAAAGAATAATATGTAAATGATACA
18105076 GAATAATGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.22
Consensus pattern (26 bp):
ACAAAGAATAATATGTAAATGATACA
Found at i:18106755 original size:45 final size:45
Alignment explanation
Indices: 18106678--18106777 Score: 164
Period size: 45 Copynumber: 2.2 Consensus size: 45
18106668 GATATGCTCA
* * *
18106678 TGCAATGACTGCGTCTGCATCTGCATCACCCGCTGGATCTCCAAC
1 TGCATTGACTGCATCTGCATCTACATCACCCGCTGGATCTCCAAC
*
18106723 TGCATTGACTGCATCTGCATCTACATCGCCCGCTGGATCTCCAAC
1 TGCATTGACTGCATCTGCATCTACATCACCCGCTGGATCTCCAAC
18106768 TGCATTGACT
1 TGCATTGACT
18106778 ACTAGATCTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.20, C:0.34, G:0.19, T:0.27
Consensus pattern (45 bp):
TGCATTGACTGCATCTGCATCTACATCACCCGCTGGATCTCCAAC
Found at i:18108896 original size:23 final size:23
Alignment explanation
Indices: 18108841--18108901 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
18108831 TGAACAATAT
* *
18108841 TCACGCAATAACCTAGAAACCAG
1 TCACGCAATGACCTAAAAACCAG
18108864 TCACGCAATGACCTAAAAACCAG
1 TCACGCAATGACCTAAAAACCAG
* *
18108887 TCATGGAATGACCTA
1 TCACGCAATGACCTA
18108902 TCAATCAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.41, C:0.28, G:0.15, T:0.16
Consensus pattern (23 bp):
TCACGCAATGACCTAAAAACCAG
Found at i:18128257 original size:2 final size:2
Alignment explanation
Indices: 18128242--18128287 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
18128232 ATCCTACTTT
18128242 TA TA -A TA TA T- TA TA TA TA -A 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
18128281 TA TA TA T
1 TA TA TA T
18128288 TCATCTTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18143360 original size:4 final size:4
Alignment explanation
Indices: 18143346--18143378 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
18143336 GAAAAGTATT
18143346 GAAA TGAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA
18143379 TGATTTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
GAAA
Found at i:18146834 original size:46 final size:46
Alignment explanation
Indices: 18146767--18146861 Score: 172
Period size: 46 Copynumber: 2.1 Consensus size: 46
18146757 AGCACGAAGC
*
18146767 GGAGGAATAGAGAGAGAGGAGCGGCAGCTGGCACAAAAGGAAGAAA
1 GGAGGAATAGAGAGAGAGGAGCGGCAGCTGACACAAAAGGAAGAAA
*
18146813 GGAGGAATAGAGAGAGAGGAGCGGCAGCTGACGCAAAAGGAAGAAA
1 GGAGGAATAGAGAGAGAGGAGCGGCAGCTGACACAAAAGGAAGAAA
18146859 GGA
1 GGA
18146862 AAACTGAGCA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.11, G:0.42, T:0.04
Consensus pattern (46 bp):
GGAGGAATAGAGAGAGAGGAGCGGCAGCTGACACAAAAGGAAGAAA
Found at i:18147864 original size:13 final size:13
Alignment explanation
Indices: 18147846--18147871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18147836 AAATAAAGAG
18147846 TTACTTGATAAAA
1 TTACTTGATAAAA
18147859 TTACTTGATAAAA
1 TTACTTGATAAAA
18147872 ATAAATAATA
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:0.08, T:0.38
Consensus pattern (13 bp):
TTACTTGATAAAA
Found at i:18179257 original size:2 final size:2
Alignment explanation
Indices: 18179250--18179278 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18179240 TTTGCTAACA
18179250 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 A
18179279 ATTGTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18180479 original size:3 final size:3
Alignment explanation
Indices: 18180471--18180507 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
18180461 ATTATCTAAC
18180471 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
18180508 CAAATATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:18189072 original size:16 final size:17
Alignment explanation
Indices: 18189018--18189073 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 17
18189008 TTTTGTATTA
18189018 TTATTT-TAAATTAAATAT
1 TTATTTATAAA-T-AATAT
* *
18189036 TTTTTTATAAATAATAA
1 TTATTTATAAATAATAT
*
18189053 TTATTTA-AAATATTAT
1 TTATTTATAAATAATAT
18189069 TTATT
1 TTATT
18189074 ATTTAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 12 0.38
17 10 0.31
18 6 0.19
19 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATTTATAAATAATAT
Found at i:18194312 original size:14 final size:13
Alignment explanation
Indices: 18194293--18194331 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
18194283 TAAAAATGAC
18194293 AAATTTAAATTTAT
1 AAATTTAAATTT-T
18194307 AAATTTAATATTTT
1 AAATTTAA-ATTTT
*
18194321 AAATTAAAATT
1 AAATTTAAATT
18194332 AAAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:18194380 original size:33 final size:35
Alignment explanation
Indices: 18194310--18194387 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
18194300 AATTTATAAA
18194310 TTTAATATTTTAAATTAAAATTAAAAATATTAATAT
1 TTTAATATTTTAAATTAAAATT-AAAATATTAATAT
*
18194346 TTTCATATTTTAAATTATAAA-T-AAA-ATTAATAT
1 TTTAATATTTTAAATTA-AAATTAAAATATTAATAT
18194379 TTTAATATT
1 TTTAATATT
18194388 AATTTTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 16 0.41
34 3 0.08
36 17 0.44
37 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (35 bp):
TTTAATATTTTAAATTAAAATTAAAATATTAATAT
Found at i:18194400 original size:12 final size:13
Alignment explanation
Indices: 18194350--18194400 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
18194340 TAATATTTTC
18194350 ATATTTTAAATT-
1 ATATTTTAAATTA
** *
18194362 ATAAATAAAATTA
1 ATATTTTAAATTA
18194375 ATATTTTAATATTA
1 ATATTTTAA-ATTA
18194389 AT-TTTTAAATTA
1 ATATTTTAAATTA
18194401 TTAAGTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 13 0.42
13 12 0.39
14 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATTTTAAATTA
Found at i:18194527 original size:48 final size:51
Alignment explanation
Indices: 18194474--18194579 Score: 125
Period size: 48 Copynumber: 2.2 Consensus size: 51
18194464 AAAGGTTAAG
*
18194474 TTATTAATTATAT-ATTATAA-AATATTTTAAATT-TAAAATT-AATTA-AAA
1 TTATTAATTATATAATCATAATAATA-TTTAAATTGT-AAATTAAATTACAAA
* *
18194522 TTATTAA-TATTTAATCATAATAATATTTAAATTGTAAATTAAATTACCAA
1 TTATTAATTATATAATCATAATAATATTTAAATTGTAAATTAAATTACAAA
18194572 TTATTAAT
1 TTATTAAT
18194580 ATTTTCAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
47 4 0.08
48 26 0.53
49 10 0.20
50 9 0.18
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (51 bp):
TTATTAATTATATAATCATAATAATATTTAAATTGTAAATTAAATTACAAA
Found at i:18194728 original size:11 final size:11
Alignment explanation
Indices: 18194714--18194738 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18194704 TATTAATATT
18194714 TAAAAATAAAA
1 TAAAAATAAAA
18194725 TAAAAATAAAA
1 TAAAAATAAAA
18194736 TAA
1 TAA
18194739 TCATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:18219228 original size:17 final size:16
Alignment explanation
Indices: 18219208--18219242 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
18219198 CCAAACCTTC
18219208 TCTTCTCCTTCCTTCCT
1 TCTTCTCCTT-CTTCCT
18219225 TCTTCTCCTTCTTCCT
1 TCTTCTCCTTCTTCCT
18219241 TC
1 TC
18219243 CGACCTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (16 bp):
TCTTCTCCTTCTTCCT
Found at i:18219235 original size:9 final size:9
Alignment explanation
Indices: 18219208--18219289 Score: 54
Period size: 9 Copynumber: 9.8 Consensus size: 9
18219198 CCAAACCTTC
18219208 TCTTCTCCT
1 TCTTCTCCT
*
18219217 TCCT-TCCT
1 TCTTCTCCT
18219225 TCTTCTCCT
1 TCTTCTCCT
18219234 TC-T-TCCT
1 TCTTCTCCT
*
18219241 TC--CGACCT
1 TCTTC-TCCT
*
18219249 TTTTCTCCT
1 TCTTCTCCT
18219258 TCTTCTCAC-
1 TCTTCTC-CT
*
18219267 -CTT-GCCT
1 TCTTCTCCT
18219274 TCTTCTCCT
1 TCTTCTCCT
18219283 TCTTCTC
1 TCTTCTC
18219290 ACTGTCCGCA
Statistics
Matches: 56, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
6 1 0.02
7 7 0.12
8 18 0.32
9 28 0.50
10 2 0.04
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.51
Consensus pattern (9 bp):
TCTTCTCCT
Found at i:18219242 original size:24 final size:24
Alignment explanation
Indices: 18219204--18219287 Score: 93
Period size: 24 Copynumber: 3.5 Consensus size: 24
18219194 CCTCCCAAAC
18219204 CTTCT-CTTC-TCCTTCCTTCCTT
1 CTTCTCCTTCTTCCTTCCTTCCTT
**
18219226 CTTCTCCTTCTTCCTTCCGACCTT
1 CTTCTCCTTCTTCCTTCCTTCCTT
* *
18219250 TTTCTCCTTCTT-CTCACCTTGCCTT
1 CTTCTCCTTCTTCCT-TCCTT-CCTT
18219275 CTTCTCCTTCTTC
1 CTTCTCCTTCTTC
18219288 TCACTGTCCG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
22 5 0.10
23 6 0.12
24 24 0.48
25 15 0.30
ACGTcount: A:0.02, C:0.44, G:0.02, T:0.51
Consensus pattern (24 bp):
CTTCTCCTTCTTCCTTCCTTCCTT
Found at i:18225638 original size:19 final size:19
Alignment explanation
Indices: 18225600--18225659 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
18225590 ATTAAAAACT
*
18225600 AATAAATAATATCCAAATTAA
1 AATAAATAA-AT-AAAATTAA
18225621 AATAAATAAATAAAATTAA
1 AATAAATAAATAAAATTAA
* * *
18225640 AATAACTCAATAAAAATAA
1 AATAAATAAATAAAATTAA
18225659 A
1 A
18225660 CTAATTAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 24 0.69
20 2 0.06
21 9 0.26
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.25
Consensus pattern (19 bp):
AATAAATAAATAAAATTAA
Found at i:18235117 original size:2 final size:2
Alignment explanation
Indices: 18235110--18235213 Score: 144
Period size: 2 Copynumber: 53.5 Consensus size: 2
18235100 ATAAGAAAGC
18235110 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
* * *
18235152 TA T- TA CA TG GA -A T- TNA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
18235191 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
18235214 TACATGGAAT
Statistics
Matches: 92, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
1 4 0.04
2 88 0.96
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18235232 original size:59 final size:59
Alignment explanation
Indices: 18235109--18235233 Score: 223
Period size: 59 Copynumber: 2.1 Consensus size: 59
18235099 AATAAGAAAG
*
18235109 CTATATATATATATATATATATATATATATATATATATATATATATTACATGGAATTNA
1 CTATATATATATATATATATATATATATATATATATATATATATATTACATGGAATTCA
* *
18235168 ATATATATATATATATATATATATATATATATATATATATATATATTACATGGAATTCT
1 CTATATATATATATATATATATATATATATATATATATATATATATTACATGGAATTCA
18235227 CTATATA
1 CTATATA
18235234 ATTTACAAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (59 bp):
CTATATATATATATATATATATATATATATATATATATATATATATTACATGGAATTCA
Found at i:18236660 original size:2 final size:2
Alignment explanation
Indices: 18236653--18236687 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
18236643 AGGATTTTAA
18236653 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 A
18236688 AATCAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18237132 original size:3 final size:3
Alignment explanation
Indices: 18237124--18237187 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
18237114 ATGCATAACG
18237124 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18237172 ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA A
18237188 ATGTATAAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18237435 original size:27 final size:27
Alignment explanation
Indices: 18237397--18237448 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
18237387 TTCAATGCAA
*
18237397 AAGCACCTGAGGTCCTTCCAAGCGCAG
1 AAGCACCCGAGGTCCTTCCAAGCGCAG
18237424 AAGCACCCGAGGTCCTTCCAAGCGC
1 AAGCACCCGAGGTCCTTCCAAGCGC
18237449 GAAAGTGCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.37, G:0.25, T:0.13
Consensus pattern (27 bp):
AAGCACCCGAGGTCCTTCCAAGCGCAG
Found at i:18253762 original size:53 final size:54
Alignment explanation
Indices: 18253680--18253789 Score: 141
Period size: 53 Copynumber: 2.0 Consensus size: 54
18253670 GTCATGGTTG
* * *
18253680 TTCCTGGCATGTAGTGGGTTAACTAGTTTTTTGGGTTGTTAGCGTGT-CGGCTA
1 TTCCTGGCATGTAGTGGATAAACTAGTTTTTTGGGTTGTTAGCATGTACGGCTA
* * * *
18253733 TTCCTGGCGTGTTGTGGATAAACTGGTTTTTTGGGTTTTTAGCATGTCACGGCTA
1 TTCCTGGCATGTAGTGGATAAACTAGTTTTTTGGGTTGTTAGCATGT-ACGGCTA
18253788 TT
1 TT
18253790 AGTGTAACGA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 40 0.83
55 8 0.17
ACGTcount: A:0.14, C:0.14, G:0.30, T:0.43
Consensus pattern (54 bp):
TTCCTGGCATGTAGTGGATAAACTAGTTTTTTGGGTTGTTAGCATGTACGGCTA
Found at i:18253856 original size:31 final size:31
Alignment explanation
Indices: 18253818--18253895 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
18253808 TTACAATGAT
*
18253818 TGGCGTGTCACGACATTTGAC-TTGATATGCA
1 TGGCGTGTCACAACATTTGACATT-ATATGCA
* *
18253849 TGGCGTGTTACAACATTTTACATTATATGCA
1 TGGCGTGTCACAACATTTGACATTATATGCA
*
18253880 TGGCGTGTAACAACAT
1 TGGCGTGTCACAACAT
18253896 GACTGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 40 0.95
32 2 0.05
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (31 bp):
TGGCGTGTCACAACATTTGACATTATATGCA
Found at i:18256416 original size:63 final size:63
Alignment explanation
Indices: 18256349--18256504 Score: 242
Period size: 63 Copynumber: 2.5 Consensus size: 63
18256339 TGATGTAACT
* *
18256349 GTGCATGTGCGGAGTGGGTAGTGCATATGCCGGTTGAATGACGATGTTGTGACAAC-TACAACC
1 GTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTGTGAC-ACTTACAACC
* *
18256412 GTGCATATGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTGTGACACTTACAACT
1 GTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTGTGACACTTACAACC
* *
18256475 GTGCATGTGCAGAGTGGGCAGTGCACATGC
1 GTGCATGTGCGGAGTGGGCAGTGCATATGC
18256505 AGGTAATGAT
Statistics
Matches: 85, Mismatches: 7, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
62 2 0.02
63 83 0.98
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTGTGACACTTACAACC
Found at i:18260514 original size:16 final size:15
Alignment explanation
Indices: 18260495--18260549 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 15
18260485 AAAATTCTTC
18260495 GTATAAAATTAATTGT
1 GTATAAAA-TAATTGT
*
18260511 GTATAGGAAAAAAATTGT
1 GTAT---AAAATAATTGT
18260529 GTATAAAATATATTGT
1 GTATAAAATA-ATTGT
18260545 GTATA
1 GTATA
18260550 CAAAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 5 0.15
16 14 0.42
18 10 0.30
19 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.38
Consensus pattern (15 bp):
GTATAAAATAATTGT
Found at i:18260533 original size:34 final size:32
Alignment explanation
Indices: 18260481--18260625 Score: 119
Period size: 33 Copynumber: 4.2 Consensus size: 32
18260471 TATACAAAAG
* *
18260481 AAAAAAAATTCTTCGTATAAAATTAATTGTGTATAG
1 AAAAAAAATT-AT-GTATAAAATTAA-T-TGTATAA
* * *
18260517 GAAAAAAATTGTGTATAAAATATATTGTGTATACA
1 AAAAAAAATTATGTATAAAAT-TAAT-TGTATA-A
* * *
18260552 AAAAGAATTAATTTTGTATACAATGAATTGTATAA
1 AAAA-AA--AATTATGTATAAAATTAATTGTATAA
18260587 AATAAAAAATTATGTATAAAATTAATTGTATAA
1 AA-AAAAAATTATGTATAAAATTAATTGTATAA
18260620 AAAAAA
1 AAAAAA
18260626 TTCTGTATAC
Statistics
Matches: 91, Mismatches: 12, Indels: 16
0.76 0.10 0.13
Matches are distributed among these distances:
32 4 0.04
33 25 0.27
34 17 0.19
35 11 0.12
36 19 0.21
37 2 0.02
38 13 0.14
ACGTcount: A:0.52, C:0.03, G:0.10, T:0.34
Consensus pattern (32 bp):
AAAAAAAATTATGTATAAAATTAATTGTATAA
Found at i:18260604 original size:33 final size:30
Alignment explanation
Indices: 18260561--18260637 Score: 91
Period size: 33 Copynumber: 2.5 Consensus size: 30
18260551 AAAAAGAATT
*
18260561 AATTTTGTATACAATGAATTGTATAAAATAAAA
1 AATTATGTATACAATGAATTGTAT--AA-AAAA
* *
18260594 AATTATGTATAAAATTAATTGTATAAAAAA
1 AATTATGTATACAATGAATTGTATAAAAAA
*
18260624 AATTCTGTATACAA
1 AATTATGTATACAA
18260638 AAAAAAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 16 0.41
31 2 0.05
33 21 0.54
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTATGTATACAATGAATTGTATAAAAAA
Found at i:18260632 original size:16 final size:15
Alignment explanation
Indices: 18260590--18260642 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 15
18260580 TGTATAAAAT
18260590 AAAAAATTATGTATAA
1 AAAAAATT-TGTATAA
**
18260606 AATTAA-TTGTATAA
1 AAAAAATTTGTATAA
18260620 AAAAAATTCTGTATACA
1 AAAAAATT-TGTATA-A
18260637 AAAAAA
1 AAAAAA
18260643 AAATGTATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.37
15 2 0.07
16 10 0.33
17 7 0.23
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (15 bp):
AAAAAATTTGTATAA
Found at i:18262210 original size:31 final size:31
Alignment explanation
Indices: 18262175--18262503 Score: 272
Period size: 31 Copynumber: 10.6 Consensus size: 31
18262165 TACCACAAAC
* *
18262175 CATAACAAGTAAAATGTTGTGACACGCCATG
1 CATAACAAGCAAAATGTTCTGACACGCCATG
*
18262206 CATAATAAGCAAAATGTTCT-ACCACGCCATG
1 CATAACAAGCAAAATGTTCTGA-CACGCCATG
** * * *
18262237 CATAACAAGTTAAACGTTGTGATACGCCATG
1 CATAACAAGCAAAATGTTCTGACACGCCATG
* *
18262268 CA-ACACAAGCAAAATGTTCTGATATGCCATG
1 CATA-ACAAGCAAAATGTTCTGACACGCCATG
*
18262299 CA-ACACAAGCAAAATGTTCTGATACGCCATG
1 CATA-ACAAGCAAAATGTTCTGACACGCCATG
* * *
18262330 CA-ACACAAGCAAAATGTTTTAACACACCATG
1 CATA-ACAAGCAAAATGTTCTGACACGCCATG
* * * * *
18262361 GATACCCTA-CAAAATGTTCTGACACGTCGTG
1 CATA-ACAAGCAAAATGTTCTGACACGCCATG
** *
18262392 CATAACCACCCAAAATGTTCTGACACGCCATA
1 CATAA-CAAGCAAAATGTTCTGACACGCCATG
** * *
18262424 CATAACAAGTTAAACGTTGTGACACGCCATG
1 CATAACAAGCAAAATGTTCTGACACGCCATG
* * * * * *
18262455 TATAACAAGTAAATTGTTTTGACAAGCCATA
1 CATAACAAGCAAAATGTTCTGACACGCCATG
*
18262486 CATAACAAGTAAAATGTT
1 CATAACAAGCAAAATGTT
18262504 GTCACAAGCT
Statistics
Matches: 242, Mismatches: 50, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
30 2 0.01
31 211 0.87
32 29 0.12
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (31 bp):
CATAACAAGCAAAATGTTCTGACACGCCATG
Found at i:18262278 original size:62 final size:62
Alignment explanation
Indices: 18262175--18262505 Score: 303
Period size: 62 Copynumber: 5.3 Consensus size: 62
18262165 TACCACAAAC
*
18262175 CATAACAAGTAAAATGTTGTGACACGCCATGCATAATAAGCAAAATGTTCT-ACCACGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGCAAAATGTTCTGA-CACGCCATG
* * * * *
18262237 CATAACAAGTTAAACGTTGTGATACGCCATGCA-ACACAAGCAAAATGTTCTGATATGCCATG
1 CATAACAAGTAAAATGTTGTGACACGCCATGCATA-ACAAGCAAAATGTTCTGACACGCCATG
* * * * * *
18262299 CA-ACACAAGCAAAATGTTCTGATACGCCATGCA-ACACAAGCAAAATGTTTTAACACACCATG
1 CATA-ACAAGTAAAATGTTGTGACACGCCATGCATA-ACAAGCAAAATGTTCTGACACGCCATG
* * * * * * * ** *
18262361 GATACCCTA-CAAAATGTTCTGACACGTCGTGCATAACCACCCAAAATGTTCTGACACGCCATA
1 CATA-ACAAGTAAAATGTTGTGACACGCCATGCATAA-CAAGCAAAATGTTCTGACACGCCATG
* * * * * * * *
18262424 CATAACAAGTTAAACGTTGTGACACGCCATGTATAACAAGTAAATTGTTTTGACAAGCCATA
1 CATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGCAAAATGTTCTGACACGCCATG
18262486 CATAACAAGTAAAATGTTGT
1 CATAACAAGTAAAATGTTGT
18262506 CACAAGCTAA
Statistics
Matches: 217, Mismatches: 45, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
61 2 0.01
62 166 0.76
63 49 0.23
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (62 bp):
CATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGCAAAATGTTCTGACACGCCATG
Found at i:18262338 original size:93 final size:94
Alignment explanation
Indices: 18262175--18262503 Score: 321
Period size: 93 Copynumber: 3.5 Consensus size: 94
18262165 TACCACAAAC
* * *
18262175 CATA-ACAAGTAAAATGTTGTGACACGCCATGCATAATAAGCAAAATGTTCT-ACCACGCCATGC
1 CATACACAAGCAAAATGTTCTGACACGCCATGCATAACAAGCAAAATGTTCTGA-CACGCCATGC
*
18262238 ATAACAAGTTAAACGTTGTGATACGCCATG
65 ATAACAAGTTAAACGTTGTGACACGCCATG
* * *
18262268 CA-ACACAAGCAAAATGTTCTGATATGCCATGCA-ACACAAGCAAAATGTTCTGATACGCCATGC
1 CATACACAAGCAAAATGTTCTGACACGCCATGCATA-ACAAGCAAAATGTTCTGACACGCCATGC
** * * * *
18262331 A-ACACAAGCAAAATGTTTTAACACACCATG
65 ATA-ACAAGTTAAACGTTGTGACACGCCATG
* * * * * ** *
18262361 GATACCCTA-CAAAATGTTCTGACACGTCGTGCATAACCACCCAAAATGTTCTGACACGCCATAC
1 CATACACAAGCAAAATGTTCTGACACGCCATGCATAA-CAAGCAAAATGTTCTGACACGCCATGC
18262425 ATAACAAGTTAAACGTTGTGACACGCCATG
65 ATAACAAGTTAAACGTTGTGACACGCCATG
* * * * * * *
18262455 TATA-ACAAGTAAATTGTTTTGACAAGCCATACATAACAAGTAAAATGTT
1 CATACACAAGCAAAATGTTCTGACACGCCATGCATAACAAGCAAAATGTT
18262504 GTCACAAGCT
Statistics
Matches: 184, Mismatches: 43, Indels: 18
0.75 0.18 0.07
Matches are distributed among these distances:
92 3 0.02
93 106 0.58
94 74 0.40
95 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (94 bp):
CATACACAAGCAAAATGTTCTGACACGCCATGCATAACAAGCAAAATGTTCTGACACGCCATGCA
TAACAAGTTAAACGTTGTGACACGCCATG
Found at i:18265049 original size:31 final size:31
Alignment explanation
Indices: 18264665--18265045 Score: 462
Period size: 31 Copynumber: 12.3 Consensus size: 31
18264655 AATAAGAAAT
* * *
18264665 AAATGTTGTGAAACGCCATGCATAACAAGCA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* *
18264696 AAATGTTGTGACACGCCATGCATAGCAAGCA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
*
18264727 AAATGTTGTGACACACCATGTC-TAAT-AAGTA
1 AAATGTTGTGACACGCCATG-CAT-ATCAAGTA
* *
18264758 AAATATTGTGACACACCATGCATGAT-AAGTA
1 AAATGTTGTGACACGCCATGCAT-ATCAAGTA
*
18264789 AAATGTTGTGACACGCCATGCATATCAAGCA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * *
18264820 AAATGTTGTGACATGCAATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
*
18264851 AAATGTTGTGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * *
18264882 AAATCTTGTAACACGCCATGCATATCGAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
18264913 AAATGTTGTGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCATATCAAGTA
*
18264944 AAATGTTGTGACACGCCATGCATATCAAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * * *
18264975 AAATGTTGTCAAACGCCATGCATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTA
* * * * * * *
18265006 GAATGTTATCACACACCATACATATCGAGTC
1 AAATGTTGTGACACGCCATGCATATCAAGTA
18265037 AAATGTTGT
1 AAATGTTGT
18265046 CACATGCTAA
Statistics
Matches: 312, Mismatches: 34, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
30 3 0.01
31 307 0.98
32 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATATCAAGTA
Found at i:18265560 original size:29 final size:29
Alignment explanation
Indices: 18265513--18265570 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
18265503 TGTCAACCAT
18265513 TCAAGAAATGCCGTATCACACACTCTAAA
1 TCAAGAAATGCCGTATCACACACTCTAAA
* * *
18265542 TCAAGCAATGCTGTGTCACACACTCTAAA
1 TCAAGAAATGCCGTATCACACACTCTAAA
18265571 CCATGGCGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (29 bp):
TCAAGAAATGCCGTATCACACACTCTAAA
Found at i:18265700 original size:47 final size:47
Alignment explanation
Indices: 18265618--18265999 Score: 353
Period size: 47 Copynumber: 8.1 Consensus size: 47
18265608 ACACTCTAAA
* * * *
18265618 CATGGTGTGTCACCAACTCTGAACTCT-AGCTTGTCACAGCTTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGA-CGTGTCACAGATTCCCTC
* *
18265665 CATGGCGTGTCACCAACTCTGAACTATGACGTGTCACAGATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * * * *
18265712 CATGCCATCTCACCAACTCTGAACGCTTG-CGTGTCACAAATTCCTTT
1 CATGGCGTCTCACCAACTCTGAACTC-TGACGTGTCACAGATTCCCTC
* * *
18265759 CATGCCGTCTCACTAACTCTGAA-TGCTGGCGTGTCACAGATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACT-CTGACGTGTCACAGATTCCCTC
* * *
18265806 CAT-GCAGTCTTACCAACTCTGAACTCTGGCGTATCACAGATTCCCTC
1 CATGGC-GTCTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * * * * *
18265853 CATGCCATGTCACAAACTCTGAACGCTGGCGTGTCACAGATTCCCTT
1 CATGGCGTCTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
* * * *
18265900 CATGTCGTGTCACCAATTTTGAACTCT-AGCGTGTCACAGATTCCCTC
1 CATGGCGTCTCACCAACTCTGAACTCTGA-CGTGTCACAGATTCCCTC
* * * * * *
18265947 CATGGCATCTCACCAA-TTTTAAATGCTGGCGTGTCACAGATTCCCAC
1 CATGGCGTCTCACCAACTCTGAACT-CTGACGTGTCACAGATTCCCTC
18265994 CATGGC
1 CATGGC
18266000 ATGCCACAGA
Statistics
Matches: 280, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
46 9 0.03
47 266 0.95
48 5 0.02
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.28
Consensus pattern (47 bp):
CATGGCGTCTCACCAACTCTGAACTCTGACGTGTCACAGATTCCCTC
Found at i:18265700 original size:94 final size:94
Alignment explanation
Indices: 18265618--18265997 Score: 406
Period size: 94 Copynumber: 4.0 Consensus size: 94
18265608 ACACTCTAAA
* * * * * * *
18265618 CATGGTGTGTCACCAACTCTGAACTCTAGCTTGTCACAGCTTCCCTCCATGGCGTGTCACCAACT
1 CATGCTGTCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGCCATCTCACCAACT
* *
18265683 CTGAACTATGACGTGTCACAGATTCCCTC
66 CTGAACTCTGGCGTGTCACAGATTCCCTC
** * * * * * * *
18265712 CATGCCATCTCACCAACTCTGAACGCTTGCGTGTCACAAATTCCTTTCATGCCGTCTCACTAACT
1 CATGCTGTCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGCCATCTCACCAACT
18265777 CTGAA-TGCTGGCGTGTCACAGATTCCCTC
66 CTGAACT-CTGGCGTGTCACAGATTCCCTC
* * * * * *
18265806 CATGCAGTCTTACCAACTCTGAACTCTGGCGTATCACAGATTCCCTCCATGCCATGTCACAAACT
1 CATGCTGTCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGCCATCTCACCAACT
* *
18265871 CTGAACGCTGGCGTGTCACAGATTCCCTT
66 CTGAACTCTGGCGTGTCACAGATTCCCTC
* * * *
18265900 CATG-TCGTGTCACCAATTTTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCATCTCACCAA-
1 CATGCT-GTCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGCCATCTCACCAAC
* * * *
18265963 TTTTAAATGCTGGCGTGTCACAGATTCCCAC
65 TCTGAACT-CTGGCGTGTCACAGATTCCCTC
18265994 CATG
1 CATG
18265998 GCATGCCACA
Statistics
Matches: 236, Mismatches: 46, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
93 5 0.02
94 231 0.98
ACGTcount: A:0.22, C:0.32, G:0.17, T:0.28
Consensus pattern (94 bp):
CATGCTGTCTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGCCATCTCACCAACT
CTGAACTCTGGCGTGTCACAGATTCCCTC
Found at i:18265976 original size:141 final size:141
Alignment explanation
Indices: 18265624--18266007 Score: 495
Period size: 141 Copynumber: 2.7 Consensus size: 141
18265614 TAAACATGGT
* * * *
18265624 GTGTCACCAACTCTGAACTCTAGCTTGTCACAGCTTCCCTCCATGGCGTGTCACCAACTCTGAAC
1 GTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCATCTCACCAACTCTGAAC
* * * * *
18265689 TATGACGTGTCACAGATTCCCTCCATGCCATCTCACCAACTCTGAACGCTTGCGTGTCACAAATT
66 TCTGGCGTGTCACAGATTCCCTCCATGCCATGTCACAAACTCTGAACGCTGGCGTGTCACAAATT
*
18265754 CCTTTCATGCC
131 CCCTTCATGCC
* * * *
18265765 GTCTCACTAACTCTGAA-TGCTGGCGTGTCACAGATTCCCTCCAT-GCAGTCTTACCAACTCTGA
1 GTGTCACCAACTCTGAACT-CTAGCGTGTCACAGATTCCCTCCATGGCA-TCTCACCAACTCTGA
* *
18265828 ACTCTGGCGTATCACAGATTCCCTCCATGCCATGTCACAAACTCTGAACGCTGGCGTGTCACAGA
64 ACTCTGGCGTGTCACAGATTCCCTCCATGCCATGTCACAAACTCTGAACGCTGGCGTGTCACAAA
*
18265893 TTCCCTTCATGTC
129 TTCCCTTCATGCC
* * * * *
18265906 GTGTCACCAATTTTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCATCTCACCAA-TTTTAAA
1 GTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCATCTCACCAACTCTGAAC
* * *
18265970 TGCTGGCGTGTCACAGATTCCCACCATGGCATGCCACA
66 T-CTGGCGTGTCACAGATTCCCTCCATGCCATGTCACA
18266008 GATTCCCTTC
Statistics
Matches: 208, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
140 8 0.04
141 196 0.94
142 4 0.02
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.28
Consensus pattern (141 bp):
GTGTCACCAACTCTGAACTCTAGCGTGTCACAGATTCCCTCCATGGCATCTCACCAACTCTGAAC
TCTGGCGTGTCACAGATTCCCTCCATGCCATGTCACAAACTCTGAACGCTGGCGTGTCACAAATT
CCCTTCATGCC
Found at i:18268318 original size:13 final size:13
Alignment explanation
Indices: 18268300--18268351 Score: 79
Period size: 13 Copynumber: 4.0 Consensus size: 13
18268290 AAATTACAAA
18268300 TATATATATATAT
1 TATATATATATAT
18268313 TATATATATATA-
1 TATATATATATAT
*
18268325 TATATAATATATAA
1 TATAT-ATATATAT
18268339 TATATATATATAT
1 TATATATATATAT
18268352 ATTGGCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 5 0.14
13 26 0.72
14 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATATATATAT
Found at i:18268370 original size:2 final size:2
Alignment explanation
Indices: 18268299--18268353 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
18268289 AAAATTACAA
18268299 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT A- AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18268338 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
18268354 TGGCATATNT
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 47 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18268409 original size:17 final size:15
Alignment explanation
Indices: 18268299--18268402 Score: 85
Period size: 15 Copynumber: 7.0 Consensus size: 15
18268289 AAAATTACAA
18268299 ATATATATATATATT
1 ATATATATATATATT
18268314 ATATATATATATA-T
1 ATATATATATATATT
18268328 ATA-ATATATA-A-T
1 ATATATATATATATT
18268340 ATATATATATATATT
1 ATATATATATATATT
*
18268355 GGCATATNTA-ATATATT
1 ---ATATATATATATATT
* * *
18268372 GATTTTTATAGTGTA-T
1 -ATATATATA-TATATT
18268388 ATATATATATATATT
1 ATATATATATATATT
18268403 GCATATAGAT
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
12 5 0.07
13 14 0.19
14 8 0.11
15 27 0.38
16 2 0.03
17 10 0.14
18 6 0.08
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.50
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:18274570 original size:26 final size:26
Alignment explanation
Indices: 18274520--18274572 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
18274510 CTTATTGGCT
18274520 CTTCTTTCCTTAACTTCAATAAAAAA
1 CTTCTTTCCTTAACTTCAATAAAAAA
* *
18274546 CTTCGTTTTCTTAATTTCAATAAAAAA
1 CTTC-TTTCCTTAACTTCAATAAAAAA
18274573 AAGCCTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (26 bp):
CTTCTTTCCTTAACTTCAATAAAAAA
Found at i:18274605 original size:695 final size:685
Alignment explanation
Indices: 18273286--18274662 Score: 2116
Period size: 695 Copynumber: 2.0 Consensus size: 685
18273276 TATTGCAGTG
*
18273286 GCGACCCCTAACTCAAAGAAAGTACTGGCACTTAATAAAAGAAAATCATTGCATAGTTAAATATA
1 GCGACCCCTAACTCAAAGAAAGTACTAGCACTTAATAAAAGAAAATCATTGCATAGTTAAATATA
* * * * * *
18273351 TAACTAATTAAGCTATATACAGGGCTGGCTTTAGCAAGGGTTTTAGATCCCCAATTTTCATTGGC
66 TAACTAATTAAGCTATATACAAGGCTGGATTTACCAAGGGCTTTAGATCCCAAATTTTCATAGGC
*
18273416 CCCATAATTTTATAATAATAATATAATTAATTATAGTAAAAAATACAAAAATTAAGTTAATTTAT
131 CCCATAATTTTATAATAATAATATAACTAATTATAGTAAAAAATACAAAAATTAAGTTAATTTAT
* *
18273481 TAAAATATCTAGTTAGTCTCTCATGCTTAATAAATATCTATTTTCACTTTCCTTATTAATTCCCA
196 TAAAATATCTAGCTAGTCTCTCATGCTTAATAAATATCTATTTTCACTATCCTTATTAATTCCCA
*
18273546 ACTATTTACCTCATTTCCTATTACAAATATATAAAAGTCAAAATAATTAAAAAATGAGATATTCT
261 ACTATTTACCTCATTTCCTATTAAAAATATATAAAAGTCAAAATAATTAAAAAATGAGATATTCT
* *
18273611 CTCACTTTCCTAATTATGTGCCTAATAAATCTCAATTTTTTATCACTTTTCAATTCCCACAATGC
326 CTCACTTTCCTAATTATGTGCCTAATAAATCTCAATCTTTTATCACTTCTCAATTCCCACAATGC
*
18273676 TATTAATTCTCAATAATTTCTTCTATTCCCAATCAACTAAGGATAATATATATTTAATGATCTCT
391 TATTAATTCTCAATAATTTCTTCTATTCCCAATCAACCAAGGATAATATATATTTAATGATCTCT
* * * * *
18273741 AACCGTAATTTTTTTCCTATATATAAAATCAATTGTTTGATTGAATTTATAAGGTCCACTTTTGA
456 AACCATAATTTTTTTCCTATACATAAAATCAATTGTTTGATTAAATTTATAAGATCCACTTATGA
* * *
18273806 ATTGTTTCCTCATTGGCTCTTTTTTCCTTAACTTCAATAAAAAGCTTCATTTTCTTAATTTCAAT
521 ATTCTTTCCTCATTGGCTCTTCTTTCCTTAACTTCAATAAAAAACTTCATTTTCTTAATTTCAAT
* *
18273871 AAAAAAAATGCCTCATTTGAATATTTAGCTTTAGGCTTATGAAGTTATTGAACCGTTGTTAGCTA
586 AAAAAAAATGCCTCATTTCAATATTTAGCTTTAGGCTTATGAAGTTATTGAAACGTTGTTAGCTA
18273936 TATATCTCATTATAATACAAGGTAAGATACCTTTC
651 TATATCTCATTATAATACAAGGTAAGATACCTTTC
* * *
18273971 GCGACCCTTAACTCAAAGAAAGTACTAGCATTTAATAAAAGAAAATCATTGCATAGTTACATATA
1 GCGACCCCTAACTCAAAGAAAGTACTAGCACTTAATAAAAGAAAATCATTGCATAGTTAAATATA
*
18274036 TAACTAATTAAGCTATATACAAGGC-GGATTTACCAAGGGCTTTAGATCTCAAATTTTCATAGGC
66 TAACTAATTAAGCTATATACAAGGCTGGATTTACCAAGGGCTTTAGATCCCAAATTTTCATAGGC
18274100 CCCATAATTTTATAATAATAATATAACTAATTATAGTAAAAATATACAAAAATTAAGTTAATTTA
131 CCCATAATTTTATAATAATAATATAACTAATTATAGTAAAAA-ATACAAAAATTAAGTTAATTTA
* * * *
18274165 TTTATATATCTAGCTATTCTCTTATGCTTAATAAATATCTATTTTCTCTTACTACCACATCCTTA
195 TTAAAATATCTAGCTAGTCTCTCATGCTTAATAAATATCTA-TTT-TC--ACT-----ATCCTTA
* * * *
18274230 TTAATTCTCAACTATTTACCTCATTTTCTATTAAAAATATATAAAGGAT-AAAATAATTAATGAA
251 TTAATTCCCAACTATTTACCTCATTTCCTATTAAAAATATATAAAAG-TCAAAATAATTAA-AAA
** * * *
18274294 ATGAGATATTCTCTGGCTTTTCTAATTATGTGTCTAATAAATCTTAATCTTTTATCACTTCTCAA
314 ATGAGATATTCTCTCACTTTCCTAATTATGTGCCTAATAAATCTCAATCTTTTATCACTTCTCAA
18274359 TTCCCACAATGCTATTAATTCTCAATAATTTCTTCTATTCCCAATCAACCAAGGATAATATATAT
379 TTCCCACAATGCTATTAATTCTCAATAATTTCTTCTATTCCCAATCAACCAAGGATAATATATAT
* * **
18274424 TTATTGATCTTTAACCATAATTTTTTTCCTATACATAAAA-CTAATTGTTTTTTTCAAATTT-TA
444 TTAATGATCTCTAACCATAATTTTTTTCCTATACATAAAATC-AATTGTTTGATT-AAATTTATA
* ** * *
18274487 ATATCTTCTTATGAATTTCTTTCCTTATTGGCTCTTCTTTCCTTAACTTCAATAAAAAACTTCGT
507 AGATCCACTTATGAA-TTCTTTCCTCATTGGCTCTTCTTTCCTTAACTTCAATAAAAAACTTCAT
18274552 TTTCTTAATTTCAATAAAAAAAA-GCCTCATTTCAATATTTAGCTTTAGGCTTATGAAGTTATTG
571 TTTCTTAATTTCAATAAAAAAAATGCCTCATTTCAATATTTAGCTTTAGGCTTATGAAGTTATTG
* *
18274616 AAACGTTGTTGGTTATATATCTCATTATAATACAAGGTAAGATACCT
636 AAACGTTGTTAGCTATATATCTCATTATAATACAAGGTAAGATACCT
18274663 CTCTCTAAGA
Statistics
Matches: 625, Mismatches: 52, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
684 74 0.12
685 143 0.23
686 3 0.00
687 2 0.00
689 3 0.00
694 61 0.10
695 267 0.43
696 72 0.12
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (685 bp):
GCGACCCCTAACTCAAAGAAAGTACTAGCACTTAATAAAAGAAAATCATTGCATAGTTAAATATA
TAACTAATTAAGCTATATACAAGGCTGGATTTACCAAGGGCTTTAGATCCCAAATTTTCATAGGC
CCCATAATTTTATAATAATAATATAACTAATTATAGTAAAAAATACAAAAATTAAGTTAATTTAT
TAAAATATCTAGCTAGTCTCTCATGCTTAATAAATATCTATTTTCACTATCCTTATTAATTCCCA
ACTATTTACCTCATTTCCTATTAAAAATATATAAAAGTCAAAATAATTAAAAAATGAGATATTCT
CTCACTTTCCTAATTATGTGCCTAATAAATCTCAATCTTTTATCACTTCTCAATTCCCACAATGC
TATTAATTCTCAATAATTTCTTCTATTCCCAATCAACCAAGGATAATATATATTTAATGATCTCT
AACCATAATTTTTTTCCTATACATAAAATCAATTGTTTGATTAAATTTATAAGATCCACTTATGA
ATTCTTTCCTCATTGGCTCTTCTTTCCTTAACTTCAATAAAAAACTTCATTTTCTTAATTTCAAT
AAAAAAAATGCCTCATTTCAATATTTAGCTTTAGGCTTATGAAGTTATTGAAACGTTGTTAGCTA
TATATCTCATTATAATACAAGGTAAGATACCTTTC
Found at i:18286648 original size:18 final size:18
Alignment explanation
Indices: 18286623--18286661 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
18286613 ACGTGACTCT
* *
18286623 TTTTTTTTTCTTT-TTTA
1 TTTTATTTTATTTATTTA
18286640 TTTTATTTTATTTATTTA
1 TTTTATTTTATTTATTTA
18286658 TTTT
1 TTTT
18286662 TATTCTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTTTATTTATTTA
Found at i:18288051 original size:75 final size:75
Alignment explanation
Indices: 18287928--18288079 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
18287918 CCTTGTTCTT
18287928 GAGGTCTAACACCTTTTGAGAGGATCCAAATGGCTTTTCAAAAATCCATAGTTGCTGAGAGATAA
1 GAGGTCTAACACCTTTTGAGAGGATCCAAATGGCTTTTCAAAAATCCATAGTTGCTGAGAGATAA
18287993 TCAACAAACA
66 TCAACAAACA
18288003 GAGGTCTAACACCTTTTGAGAGGATCCAAATGGCTTTTCAAAAATCCATAGTTGCTGAGAGATAA
1 GAGGTCTAACACCTTTTGAGAGGATCCAAATGGCTTTTCAAAAATCCATAGTTGCTGAGAGATAA
18288068 TCAACAAACA
66 TCAACAAACA
18288078 GA
1 GA
18288080 CCACCTCTGT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (75 bp):
GAGGTCTAACACCTTTTGAGAGGATCCAAATGGCTTTTCAAAAATCCATAGTTGCTGAGAGATAA
TCAACAAACA
Found at i:18288691 original size:3 final size:3
Alignment explanation
Indices: 18288683--18288739 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
18288673 TTAAAACTCA
*
18288683 AAG AAG AAG AAG AAG AAG AAG AAG AAG -AT AAG AAGG AAG CAA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG -AAG AAG
*
18288728 AA- AAG AAA AAG A
1 AAG AAG AAG AAG A
18288740 GCATTGCATT
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
2 5 0.11
3 35 0.78
4 5 0.11
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:18308983 original size:3 final size:3
Alignment explanation
Indices: 18308975--18309017 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
18308965 AAAATCAAAA
* * *
18308975 AAT AAT AAT GAT AGT AAA AAT AAT AA- AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18309018 AAGTAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:18308993 original size:26 final size:25
Alignment explanation
Indices: 18308964--18309030 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
18308954 TTTAATATTA
* *
18308964 AAAAATCAAAAAATAATAATGATAGT
1 AAAAAT-AAAAAATAATAATAATAAT
18308990 AAAAATAATAAAATAATAATAATAAT
1 AAAAATAA-AAAATAATAATAATAAT
*
18309016 AAAAGTAAAAAATAA
1 AAAAATAAAAAATAA
18309031 ATGAAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.24
26 28 0.76
ACGTcount: A:0.72, C:0.01, G:0.04, T:0.22
Consensus pattern (25 bp):
AAAAATAAAAAATAATAATAATAAT
Found at i:18309032 original size:29 final size:27
Alignment explanation
Indices: 18308956--18309031 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 27
18308946 TACTTATATT
*
18308956 TAATATTAAAAAATCAAAA-AATAATAA
1 TAATAGTAAAAAAT-AAAATAATAATAA
*
18308983 TGATAGTAAAAATAATAAAATAATAATAA
1 TAATAGT-AAAA-AATAAAATAATAATAA
18309012 TAATAAAAGTAAAAAATAAA
1 TAAT---AGTAAAAAATAAA
18309032 TGAAATGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
27 5 0.12
28 8 0.20
29 14 0.35
30 6 0.15
31 4 0.10
32 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (27 bp):
TAATAGTAAAAAATAAAATAATAATAA
Found at i:18324503 original size:138 final size:138
Alignment explanation
Indices: 18324255--18324664 Score: 624
Period size: 138 Copynumber: 3.0 Consensus size: 138
18324245 GTTACGACAG
* ** *
18324255 TCTATCTATATACTTACTAGGTTTTTACTTAACTCTTTTGATTAGGTGCAATGTTGACTTCATTC
1 TCTATCTATATACTAACTAGGTTTTCCCTTAACTCTTTTGATTTGGTGCAATGTTGACTTCATTC
* * * * *
18324320 TCTACCTATAGATACATCCTCCCTACCTCAGTCACAACAGACACCAAGCTTCTCATCTCCTCATT
66 TCTGCCTATAGATATATCCTCCCTCCCTCAGCCACAACACACACCAAGCTTCTCATCTCCTCATT
18324385 TTTCAACA
131 TTTCAACA
* * *
18324393 TCTATCTATATACTAACTAGATTTTCCCTTAACTCCTTTGATTTGGTGCAATGTTTACTTCATTC
1 TCTATCTATATACTAACTAGGTTTTCCCTTAACTCTTTTGATTTGGTGCAATGTTGACTTCATTC
* *
18324458 TCTGCCTATAGATATATCCTCCCTCCCTCAGCCACAACATACACCAAGCTTCTCATTTCCTCATT
66 TCTGCCTATAGATATATCCTCCCTCCCTCAGCCACAACACACACCAAGCTTCTCATCTCCTCATT
*
18324523 TTTCAACG
131 TTTCAACA
* *
18324531 TCTATCTATATACTAACTAGGTTTTCCCTTAACTCTTTTGATTTTGTGCAACGTTGACTTCATTC
1 TCTATCTATATACTAACTAGGTTTTCCCTTAACTCTTTTGATTTGGTGCAATGTTGACTTCATTC
* * *
18324596 TCTGCCTATAGATATATCCTCCTTACCGT-AGCCACAACACACACCAAGCTTCTCATCTCGTCAT
66 TCTGCCTATAGATATATCCTCCCT-CCCTCAGCCACAACACACACCAAGCTTCTCATCTCCTCAT
18324660 TTTTC
130 TTTTC
18324665 TGACCAGGTT
Statistics
Matches: 247, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
138 244 0.99
139 3 0.01
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (138 bp):
TCTATCTATATACTAACTAGGTTTTCCCTTAACTCTTTTGATTTGGTGCAATGTTGACTTCATTC
TCTGCCTATAGATATATCCTCCCTCCCTCAGCCACAACACACACCAAGCTTCTCATCTCCTCATT
TTTCAACA
Found at i:18330542 original size:21 final size:20
Alignment explanation
Indices: 18330513--18330567 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
18330503 TATTATAATA
* *
18330513 AAAAATATTTTTATCATTTT
1 AAAATTATTTTTATAATTTT
* * *
18330533 ATTATTTATTTTTTTAATTTT
1 A-AAATTATTTTTATAATTTT
18330554 AAAATTATTTTTAT
1 AAAATTATTTTTAT
18330568 TAACCAAACT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
AAAATTATTTTTATAATTTT
Found at i:18331329 original size:30 final size:30
Alignment explanation
Indices: 18331290--18331359 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
18331280 AATCAAATTA
*
18331290 CGACACCCTTGTTTTGACAAAGCGGTCGTT
1 CGACCCCCTTGTTTTGACAAAGCGGTCGTT
18331320 CGACCCCCTTGTTTTGACAAAGCGGTCGTT
1 CGACCCCCTTGTTTTGACAAAGCGGTCGTT
18331350 CGACCCCCTT
1 CGACCCCCTT
18331360 CGGATGGGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.17, C:0.33, G:0.21, T:0.29
Consensus pattern (30 bp):
CGACCCCCTTGTTTTGACAAAGCGGTCGTT
Found at i:18332978 original size:20 final size:20
Alignment explanation
Indices: 18332942--18332980 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
18332932 TTTTCCCATC
*
18332942 TTTTTTTTTTCTTTTTCTTT
1 TTTTTTTTTTCTATTTCTTT
*
18332962 TTTTTTTTTTGTATTTCTT
1 TTTTTTTTTTCTATTTCTT
18332981 CTTTGATGAA
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:0.03, C:0.08, G:0.03, T:0.87
Consensus pattern (20 bp):
TTTTTTTTTTCTATTTCTTT
Found at i:18339243 original size:19 final size:19
Alignment explanation
Indices: 18339211--18339249 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18339201 TCCCAAGAAC
18339211 AAAGAGAGAAAAAAAATAA
1 AAAGAGAGAAAAAAAATAA
18339230 AAAGA-AGAAGAAAAAATAA
1 AAAGAGAGAA-AAAAAATAA
18339249 A
1 A
18339250 CATAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAGAGAGAAAAAAAATAA
Found at i:18348338 original size:2 final size:2
Alignment explanation
Indices: 18348331--18348366 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18348321 NNNNNNNNNN
18348331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18348367 GGAGGAGAAA
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):
AT
Found at i:18351160 original size:31 final size:31
Alignment explanation
Indices: 18351125--18351195 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
18351115 ATGATGAAGG
18351125 GAAGGGTTGCATTAATTGTACTAGCTAGCTC
1 GAAGGGTTGCATTAATTGTACTAGCTAGCTC
18351156 GAAGGGTTGCATTAATTGTACTAGCTAGCTC
1 GAAGGGTTGCATTAATTGTACTAGCTAGCTC
18351187 GAAGGGTTG
1 GAAGGGTTG
18351196 TTTCTCTCTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.31
Consensus pattern (31 bp):
GAAGGGTTGCATTAATTGTACTAGCTAGCTC
Done.