Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 113 of 136
Found at i:38213054 original size:2 final size:2
Alignment explanation
Indices: 38213049--38213075 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38213039 TGTGCATATA
38213049 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
38213076 ATTATGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38220276 original size:109 final size:109
Alignment explanation
Indices: 38220085--38220293 Score: 418
Period size: 109 Copynumber: 1.9 Consensus size: 109
38220075 ACTCAATTTT
38220085 ATTTATGTAAACTGTATTTTCTATGGGGTGAATCTAATTAACACCAAGCATTCACTACACCAAAA
1 ATTTATGTAAACTGTATTTTCTATGGGGTGAATCTAATTAACACCAAGCATTCACTACACCAAAA
38220150 CAGGCTTTTAGCGGCGCTTTTTTATGCCTTTAGCGCTTTTAAGC
66 CAGGCTTTTAGCGGCGCTTTTTTATGCCTTTAGCGCTTTTAAGC
38220194 ATTTATGTAAACTGTATTTTCTATGGGGTGAATCTAATTAACACCAAGCATTCACTACACCAAAA
1 ATTTATGTAAACTGTATTTTCTATGGGGTGAATCTAATTAACACCAAGCATTCACTACACCAAAA
38220259 CAGGCTTTTAGCGGCGCTTTTTTATGCCTTTAGCG
66 CAGGCTTTTAGCGGCGCTTTTTTATGCCTTTAGCG
38220294 GTGCTTTTAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 100 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (109 bp):
ATTTATGTAAACTGTATTTTCTATGGGGTGAATCTAATTAACACCAAGCATTCACTACACCAAAA
CAGGCTTTTAGCGGCGCTTTTTTATGCCTTTAGCGCTTTTAAGC
Found at i:38220492 original size:86 final size:86
Alignment explanation
Indices: 38220372--38220663 Score: 308
Period size: 86 Copynumber: 3.4 Consensus size: 86
38220362 ACGCCGCTAA
* * *
38220372 CTTTAGCGGCG-TTTATGTGAAAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTA-TA
1 CTTTAGCGGCGCTTTA-GT-CAAAAACGCCGCTAAAGATCGTGACCTTTAGCGGCGC-TTTAGCA
38220435 ACAAACGCCGCTAAAGAACATGAC
63 ACAAACGCCGCTAAAGAACATGAC
* * *
38220459 CTTTAGCGGCGCTTTTGTCACAAACGCCGCTAAAGATCGTGACCTTTAGCGGCACTTTAGCCAA-
1 CTTTAGCGGCGCTTTAGTCAAAAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAG-CAAC
* * * *
38220523 AAACGTCGCTAAAGATCGTGAT
65 AAACGCCGCTAAAGAACATGAC
* * * * *
38220545 CTTTAGCGGCGCTTTAGAT-ACAAACGTCGCTAAAGATCGTGAGCTTTAGCGACGCTTTAGCCAC
1 CTTTAGCGGCGCTTTAG-TCAAAAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCAAC
* * *
38220609 AAACGCCACTAAAGAATA-AAC
65 AAACGCCGCTAAAGAACATGAC
* *
38220630 CTTTAGTGACGCTTCTAG-CAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTT-TAGTCAAAAACGCCGCTAAA
38220664 AACATAAGCT
Statistics
Matches: 171, Mismatches: 27, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
85 32 0.19
86 120 0.70
87 16 0.09
88 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (86 bp):
CTTTAGCGGCGCTTTAGTCAAAAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGCAACA
AACGCCGCTAAAGAACATGAC
Found at i:38220603 original size:43 final size:43
Alignment explanation
Indices: 38220394--38220623 Score: 275
Period size: 43 Copynumber: 5.3 Consensus size: 43
38220384 TTATGTGAAA
* *
38220394 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTT-TATAAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGAT-AC
* * *
38220437 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTG-TCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGAT-AC
* ** *
38220480 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCACTTTAGCCAA
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGATAC
* *
38220523 AAACGTCGCTAAAGATCGTGATCTTTAGCGGCGCTTTAGATAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGATAC
* * * **
38220566 AAACGTCGCTAAAGATCGTGAGCTTTAGCGACGCTTTAGCCAC
1 AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGATAC
*
38220609 AAACGCCACTAAAGA
1 AAACGCCGCTAAAGA
38220624 ATAAACCTTT
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
43 164 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTTAGATAC
Found at i:38220676 original size:42 final size:42
Alignment explanation
Indices: 38220586--38220676 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
38220576 AAAGATCGTG
* *
38220586 AGCTTTAGCGACGCTTTAGCCACAAACGCCACTAAAGAATAA
1 AGCTTTAGCGACGCTTTAGCCAAAAACGCCACTAAAAAATAA
* * *
38220628 ACCTTTAGTGACGCTTCTAG-CAAAAACGCCGCTAAAAACAT-A
1 AGCTTTAGCGACGCTT-TAGCCAAAAACGCCACTAAAAA-ATAA
38220670 AGCTTTA
1 AGCTTTA
38220677 AAAAAATATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
42 36 0.88
43 5 0.12
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.22
Consensus pattern (42 bp):
AGCTTTAGCGACGCTTTAGCCAAAAACGCCACTAAAAAATAA
Found at i:38222494 original size:18 final size:18
Alignment explanation
Indices: 38222473--38222512 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38222463 AAAATAAAAT
38222473 AAAAGAATAAAAGCAATA
1 AAAAGAATAAAAGCAATA
** *
38222491 AAAAGCGTGAAAGCAATA
1 AAAAGAATAAAAGCAATA
38222509 AAAA
1 AAAA
38222513 AGACAGACAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.07, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAAGAATAAAAGCAATA
Found at i:38225722 original size:19 final size:19
Alignment explanation
Indices: 38225682--38225724 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
38225672 AATTTTAATT
*
38225682 AATATAAATAAACAAATTA
1 AATATAAATAAACAAATAA
*
38225701 AATAGTAAAT-AACAGATAA
1 AATA-TAAATAAACAAATAA
38225720 AATAT
1 AATAT
38225725 TTTTGCGGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 15 0.71
20 5 0.24
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
AATATAAATAAACAAATAA
Found at i:38225787 original size:41 final size:41
Alignment explanation
Indices: 38225729--38225840 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
38225719 AAATATTTTT
* * * * *
38225729 GCGGCGCTTTCTCAAAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGATCTAAGCATTA
38225770 GCGGCGCTTTTTAAAAAACGCCGCTAAAGATCTAAGCATTA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGATCTAAGCATTA
*
38225811 GCGGCGCTTTTTTAAAAACGCCGCTAAAGA
1 GCGGCGCTTTTTAAAAAACGCCGCTAAAGA
38225841 CCTGATAGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (41 bp):
GCGGCGCTTTTTAAAAAACGCCGCTAAAGATCTAAGCATTA
Found at i:38225981 original size:40 final size:39
Alignment explanation
Indices: 38225877--38226012 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
38225867 GGGCTTAGGT
* * *
38225877 TTTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCG-TTTT-CTAAAAGCGCCGCTAATGCTTGA
* *
38225917 TTTTTAGAGGCGCTTTCCTAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCG-TTTTCTAAAAGCGCCGCTAATGCTTGA
* * *
38225957 TCTTTAGCGGCGTTTTGTGTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTCT-AAAAGCGCCGCTAATGCTTGA
38225997 TTTTTAGCGGCGTTTT
1 TTTTTAGCGGCGTTTT
38226013 TTGTCCAAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 23 0.28
40 59 0.72
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTCTAAAAGCGCCGCTAATGCTTGA
Found at i:38232159 original size:17 final size:18
Alignment explanation
Indices: 38232139--38232172 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38232129 TCCTTTTTGT
*
38232139 ATTTTATTTCC-TTTTAA
1 ATTTTATCTCCATTTTAA
38232156 ATTTTATCTCCATTTTA
1 ATTTTATCTCCATTTTA
38232173 TTTCTGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTTTATCTCCATTTTAA
Found at i:38251227 original size:24 final size:24
Alignment explanation
Indices: 38251195--38251250 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
38251185 TACTAAAAGC
38251195 ACAGTGGATTGAACCTTGAAGATT
1 ACAGTGGATTGAACCTTGAAGATT
38251219 ACAGTGGATTGAACCTTGAAGATT
1 ACAGTGGATTGAACCTTGAAGATT
38251243 ACAGTGGA
1 ACAGTGGA
38251251 GGCAATCCGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (24 bp):
ACAGTGGATTGAACCTTGAAGATT
Found at i:38255782 original size:14 final size:14
Alignment explanation
Indices: 38255763--38255792 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38255753 TACACTATAT
38255763 AAACCTAAAATTAA
1 AAACCTAAAATTAA
38255777 AAACCTAAAATTAA
1 AAACCTAAAATTAA
38255791 AA
1 AA
38255793 GCCATCAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCTAAAATTAA
Found at i:38255904 original size:3 final size:3
Alignment explanation
Indices: 38255896--38255990 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
38255886 TTTAGTCCTC
* *
38255896 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * * * *
38255944 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
38255991 GCAATTTTTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:38261806 original size:22 final size:19
Alignment explanation
Indices: 38261779--38261824 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
38261769 TGGCGGCTAT
*
38261779 GAAGAAAAGAGAGGAAGAGGAA
1 GAAGAAAA-A-AGGAAGAAG-A
38261801 GAAGAAAAAAGGAAGAAGA
1 GAAGAAAAAAGGAAGAAGA
38261820 GAAGA
1 GAAGA
38261825 TAGGAGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 8 0.35
21 1 0.04
22 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (19 bp):
GAAGAAAAAAGGAAGAAGA
Found at i:38262569 original size:21 final size:21
Alignment explanation
Indices: 38262524--38262572 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38262514 GAAAGTGTTG
* *
38262524 ATACTTTTTAGAAAGATATCA
1 ATACTTGTTAGAAAGATAACA
* *
38262545 ATACTTGTTAGAAAGGTAACC
1 ATACTTGTTAGAAAGATAACA
38262566 ATACTTG
1 ATACTTG
38262573 CATAAGTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (21 bp):
ATACTTGTTAGAAAGATAACA
Found at i:38266464 original size:33 final size:33
Alignment explanation
Indices: 38266427--38266493 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
38266417 TTTTTTGGTG
38266427 TGAATTTTTTTACATAATTAAATATTTTTATTT
1 TGAATTTTTTTACATAATTAAATATTTTTATTT
**
38266460 TGAATTTTTTTAGTTAATTAAATATTTTTATTT
1 TGAATTTTTTTACATAATTAAATATTTTTATTT
38266493 T
1 T
38266494 TATTTATTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (33 bp):
TGAATTTTTTTACATAATTAAATATTTTTATTT
Found at i:38269977 original size:50 final size:50
Alignment explanation
Indices: 38269914--38270011 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
38269904 TCATTCGATA
38269914 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
38269964 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
1 CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGG
38270012 NNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (50 bp):
CACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTT
Found at i:38279134 original size:49 final size:50
Alignment explanation
Indices: 38279042--38279139 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 50
38279032 ATCTATTTAT
* * * * * *
38279042 AGGTTGAAAAAACTTTATTCTGATCAATGTCAAATAGATGAAGTGTAGTA
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
38279092 AGGTTG-AAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGT
38279140 TCTATATGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
49 36 0.86
50 6 0.14
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (50 bp):
AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAAAAGAAGTATAGTA
Found at i:38284773 original size:19 final size:19
Alignment explanation
Indices: 38284751--38284789 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
38284741 AATTGCATGG
38284751 TTAAAGTGATGGAAATGAA
1 TTAAAGTGATGGAAATGAA
38284770 TTAAAGTGATGGAAATGAA
1 TTAAAGTGATGGAAATGAA
38284789 T
1 T
38284790 GATTGTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.26, T:0.28
Consensus pattern (19 bp):
TTAAAGTGATGGAAATGAA
Found at i:38286843 original size:37 final size:37
Alignment explanation
Indices: 38286775--38286866 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 37
38286765 ATTAATGAAT
* * * *
38286775 GCATGATTAAGCATGCCACTGAGATTCTTAAACCGGAA
1 GCATGA-TAAGCATGCCACTAAAATTATTAAACCGAAA
* * *
38286813 GCATGATAAGCCTGCTACTAAAATTATTAAACTGAAA
1 GCATGATAAGCATGCCACTAAAATTATTAAACCGAAA
38286850 GCATGATAAGCATGCCA
1 GCATGATAAGCATGCCA
38286867 TTGATATTGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
37 39 0.87
38 6 0.13
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (37 bp):
GCATGATAAGCATGCCACTAAAATTATTAAACCGAAA
Found at i:38290648 original size:18 final size:17
Alignment explanation
Indices: 38290598--38290649 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
38290588 CAGCAACTTT
*
38290598 TTCTTCTTTAGCAAAAAC
1 TTCTTCTTT-GCAACAAC
*
38290616 TTCTGCTTTGACAACAAC
1 TTCTTCTTTG-CAACAAC
38290634 TTCTTCTTCTGCAACA
1 TTCTTCTT-TGCAACA
38290650 TCAATTTCCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 1 0.03
18 26 0.90
19 2 0.07
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (17 bp):
TTCTTCTTTGCAACAAC
Found at i:38304129 original size:17 final size:17
Alignment explanation
Indices: 38304107--38304148 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
38304097 TATAGCTCCG
38304107 ACAAGCTTCCAACCCGA
1 ACAAGCTTCCAACCCGA
38304124 ACAAGCTTCCAACCCGA
1 ACAAGCTTCCAACCCGA
38304141 ACAAGCTT
1 ACAAGCTT
38304149 TCGAATCACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.38, G:0.12, T:0.14
Consensus pattern (17 bp):
ACAAGCTTCCAACCCGA
Found at i:38304616 original size:25 final size:25
Alignment explanation
Indices: 38304587--38304654 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 25
38304577 TATTCTCTTA
*
38304587 CGAGCTGAATATCGGTAAGCTCATGT
1 CGAGCTGAATATCGGTAAGCTC-TCT
* *
38304613 -GAGCTGAATAACGATAAGCTCTCT
1 CGAGCTGAATATCGGTAAGCTCTCT
38304637 CGAGCTGAGA-ATCGGTAA
1 CGAGCTGA-ATATCGGTAA
38304655 CCCTAATGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
24 2 0.06
25 32 0.91
26 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (25 bp):
CGAGCTGAATATCGGTAAGCTCTCT
Found at i:38314519 original size:9 final size:9
Alignment explanation
Indices: 38314505--38314539 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
38314495 GATACTCTCA
38314505 TTCTTCTTG
1 TTCTTCTTG
38314514 TTCTTCTTG
1 TTCTTCTTG
*
38314523 TTCTTCTTC
1 TTCTTCTTG
38314532 TTCTTCTT
1 TTCTTCTT
38314540 CATATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.69
Consensus pattern (9 bp):
TTCTTCTTG
Found at i:38314520 original size:3 final size:3
Alignment explanation
Indices: 38314505--38314540 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
38314495 GATACTCTCA
* *
38314505 TTC TTC TTG TTC TTC TTG TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
38314541 ATATTTTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.28, G:0.06, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:38315583 original size:66 final size:66
Alignment explanation
Indices: 38315455--38315588 Score: 189
Period size: 66 Copynumber: 2.0 Consensus size: 66
38315445 GTGTCCTAGT
* * * * *
38315455 CCGTGTCCTTACTTATGTAACTCACTGAGTTGCCACACACGCCCGTGTGTCAAATCGCGTGTTAG
1 CCGTGTCCTCACTGATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCAAATCACGTGTTAG
38315520 G
66 G
* *
38315521 CCGTGTCCTCACTGATGTAACTCACTGAGTTGTCACACACGCCCATGTGCCAGAA-CATGTGTTA
1 CCGTGTCCTCACTGATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCA-AATCACGTGTTA
38315585 GG
65 GG
38315587 CC
1 CC
38315589 ATGTGCTAGG
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 58 0.97
67 2 0.03
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (66 bp):
CCGTGTCCTCACTGATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCAAATCACGTGTTAG
G
Found at i:38315605 original size:66 final size:66
Alignment explanation
Indices: 38315458--38315625 Score: 173
Period size: 66 Copynumber: 2.6 Consensus size: 66
38315448 TCCTAGTCCG
* * * * *
38315458 TGTCCTTACTTATGTAACTCACTGAGTTGCCACACACGCCCGTGTGTCAAATCGCGTGTTAGGCC
1 TGTCCTCACTCATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCAAATCACGTGTTAGGCC
*
38315523 G
66 A
* * *
38315524 TGTCCTCACTGATGTAACTCACTGAGTTGTCACACACGCCCATGTGCCAGAA-CATGTGTTAGGC
1 TGTCCTCACTCATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCA-AATCACGTGTTAGGC
38315588 CA
65 CA
* * *
38315590 TGTGCT-AGGTCATGTAAATCTA-TGAGTT-CCACACAC
1 TGTCCTCA-CTCATGTAACTC-ACTGAGTTGCCACACAC
38315626 TCTTGTGTGC
Statistics
Matches: 86, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
65 8 0.09
66 75 0.87
67 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (66 bp):
TGTCCTCACTCATGTAACTCACTGAGTTGCCACACACGCCCATGTGCCAAATCACGTGTTAGGCC
A
Found at i:38315968 original size:13 final size:13
Alignment explanation
Indices: 38315952--38315979 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38315942 AGTTTAATTA
38315952 ACTACCACACATG
1 ACTACCACACATG
38315965 ACTACCACACATG
1 ACTACCACACATG
38315978 AC
1 AC
38315980 CATTTGCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.39, G:0.07, T:0.14
Consensus pattern (13 bp):
ACTACCACACATG
Found at i:38322155 original size:20 final size:20
Alignment explanation
Indices: 38322130--38322169 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38322120 TTTAGTATAG
38322130 TTAAATCTGTTTGCCACTAA
1 TTAAATCTGTTTGCCACTAA
38322150 TTAAATCTGTTTGCCACTAA
1 TTAAATCTGTTTGCCACTAA
38322170 ACGTAACTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (20 bp):
TTAAATCTGTTTGCCACTAA
Found at i:38327033 original size:29 final size:27
Alignment explanation
Indices: 38326984--38327042 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
38326974 AATCTATCCT
*
38326984 TTTTATTTATTTATTTATTATTTAACTAA
1 TTTTATTTATTTAGTTATTATTT--CTAA
*
38327013 TTTTATTTATTCTCGTT-TTATTTCTAA
1 TTTTATTTATT-TAGTTATTATTTCTAA
38327040 TTT
1 TTT
38327043 GTGTTTCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.26
29 17 0.63
30 3 0.11
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTTATTTATTTAGTTATTATTTCTAA
Found at i:38331855 original size:88 final size:88
Alignment explanation
Indices: 38331706--38332208 Score: 443
Period size: 88 Copynumber: 5.7 Consensus size: 88
38331696 TTGAGTTGTT
* * *
38331706 ATTTAAGATCACAACCTTCAAACTTCAA-AGATTTTGAGAATCATAGAGTTAGTGATTTAAGATC
1 ATTTAAGATCACAACCTTCAAACTTCAAGA-ATTTTCAGAATCTTAGAGTTAGAGATTTAAGATC
38331770 ACGACTCCTCTTTAAGGTTTGCTG
65 ACGACTCCTCTTTAAGGTTTGCTG
** * * * *
38331794 ATTTAAGATTGCAACCTTCAAAATCCAAGAATATTT-AGAATATTAGAGTTAGAGGTTTAAGATC
1 ATTTAAGATCACAACCTTCAAACTTCAAGAAT-TTTCAGAATCTTAGAGTTAGAGATTTAAGATC
* * **
38331858 ACGAGTCCCCTTTAAGGTTTGCCA
65 ACGACTCCTCTTTAAGGTTTGCTG
* * * *
38331882 ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTTAGAATCTTAGACTTA-ACGATTTAAAATC
1 ATTTAAGATCACAACCTTCAAACTTCAAGAATTTTCAGAATCTTAGAGTTAGA-GATTTAAGATC
* * **
38331946 GCAACT-CTCCTTTAAGGTTCACTG
65 ACGACTCCT-CTTTAAGGTTTGCTG
* * * * *
38331970 ATTTAATATCGCAACCTTCAAACTTTAAGGATTTTCAGAATCTTAGCGTTAGCA-ATTTAAGAT-
1 ATTTAAGATCACAACCTTCAAACTTCAAGAATTTTCAGAATCTTAGAGTTAG-AGATTTAAGATC
* *
38332033 ATGGACT-TTCATTTAAGG-TT-CATCG
65 A-CGACTCCTC-TTTAAGGTTTGC-T-G
* * * * * * * *
38332058 ATTTAAAATCGCAACCTTCAAAATTCAAGGATTTTCAGAATCGTAGAGTTAGCGATTTAACATCG
1 ATTTAAGATCACAACCTTCAAACTTCAAGAATTTTCAGAATCTTAGAGTTAGAGATTTAAGATCA
* *
38332123 TGACTCC-CTTTTAAGGTTTGCCG
66 CGACTCCTC-TTTAAGGTTTGCTG
* * * *
38332146 ATTTAAGATCACAACCTTTCAAACTTCAA-AGATTTTTAGAATTTTAGTGTTAGCGATTTAAGA
1 ATTTAAGATCACAACC-TTCAAACTTCAAGA-ATTTTCAGAATCTTAGAGTTAGAGATTTAAGA
38332209 ATATCATTTC
Statistics
Matches: 335, Mismatches: 62, Indels: 35
0.78 0.14 0.08
Matches are distributed among these distances:
86 1 0.00
87 8 0.02
88 280 0.84
89 44 0.13
90 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (88 bp):
ATTTAAGATCACAACCTTCAAACTTCAAGAATTTTCAGAATCTTAGAGTTAGAGATTTAAGATCA
CGACTCCTCTTTAAGGTTTGCTG
Found at i:38332031 original size:176 final size:174
Alignment explanation
Indices: 38331706--38332213 Score: 534
Period size: 176 Copynumber: 2.9 Consensus size: 174
38331696 TTGAGTTGTT
* * * * *
38331706 ATTTAAGATCACAACCTTCAAACTTCAAAGATTTTGAGAATCATAGAGTTAGTGATTTAAGATCA
1 ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTCAGAATCATAGAGTTAGCGATTTAAAATCG
* * * *
38331771 CGACTCCTCTTTAAGGTTTGCTGATTTAAGATTGCAACCTTCAAAATCCAAGAATATTTAGAATA
66 CGACTCC-CTTTAAGGTTTGCTGATTTAAGATCGCAACCTTCAAACTTCAAGGAT-TTTAGAATA
* * * **
38331836 TTAGAGTTAG-AGGTTTAAGATCA-CGAGTCCCCTTTAAGGTTTGCCA
129 TTAGAGTTAGCA-ATTTAAGAT-ATCGACTCCCATTTAAGGTTCACCA
* * * *
38331882 ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTTAGAATCTTAGACTTAACGATTTAAAATCG
1 ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTCAGAATCATAGAGTTAGCGATTTAAAATCG
* ** * * *
38331947 CAACTCTCCTTTAAGGTTCACTGATTTAATATCGCAACCTTCAAACTTTAAGGATTTTCAGAATC
66 CGACTC-CCTTTAAGGTTTGCTGATTTAAGATCGCAACCTTCAAACTTCAAGGATTTT-AGAATA
* * ** * *
38332012 TTAGCGTTAGCAATTTAAGATATGGACTTTCATTTAAGGTTCATCG
129 TTAGAGTTAGCAATTTAAGATATCGACTCCCATTTAAGGTTCACCA
* * * * *
38332058 ATTTAAAATCGCAACCTTCAAAATTCAAGGATTTTCAGAATCGTAGAGTTAGCGATTTAACATCG
1 ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTCAGAATCATAGAGTTAGCGATTTAAAATCG
* * * *
38332123 TGACTCCCTTTTAAGGTTTGCCGATTTAAGATCACAACCTTTCAAACTTCAAAGATTTTTAGAAT
66 CGACTCCC-TTTAAGGTTTGCTGATTTAAGATCGCAACC-TTCAAACTTCAAGGA-TTTTAGAAT
* * *
38332188 TTTAGTGTTAGCGATTTAAGAATATC
128 ATTAGAGTTAGCAATTTAAG-ATATC
38332214 ATTTCCCATA
Statistics
Matches: 274, Mismatches: 50, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
175 6 0.02
176 223 0.81
177 37 0.14
178 8 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (174 bp):
ATTTAAGATCACAACCTTCAAACTTCAAGGATTTTCAGAATCATAGAGTTAGCGATTTAAAATCG
CGACTCCCTTTAAGGTTTGCTGATTTAAGATCGCAACCTTCAAACTTCAAGGATTTTAGAATATT
AGAGTTAGCAATTTAAGATATCGACTCCCATTTAAGGTTCACCA
Found at i:38337642 original size:139 final size:140
Alignment explanation
Indices: 38337484--38337766 Score: 543
Period size: 139 Copynumber: 2.0 Consensus size: 140
38337474 ATCTCTATAT
38337484 TTTTATAATGTTATTTATTAGGTTAATATTTTATGATG-TAATTAATTAGTTCAAATAGTTAATA
1 TTTTATAATGTTATTTATTAGGTTAATATTTTATGATGTTAATTAATTA-TTCAAATAGTTAATA
38337548 TCATTCAATTAAAATATTCCTTAGTTATATAAAATTTGAAAGTAAAACTATAATTCTAAAATATA
65 TCATTCAATTAAAATATTCCTTAGTTATATAAAATTTGAAAGTAAAACTATAATTCTAAAATATA
38337613 AAAGAACT-AA
130 AAAGAACTAAA
38337623 TTTTATAATGTTATTTATTAGGTTAATATTTTATGATGTTAATTAATTATTCAAATAGTTAATAT
1 TTTTATAATGTTATTTATTAGGTTAATATTTTATGATGTTAATTAATTATTCAAATAGTTAATAT
38337688 CATTCAATTAAAATATTCCTTAGTTATATAAAATTTGAAAGTAAAACTATAATTCTAAAATATAA
66 CATTCAATTAAAATATTCCTTAGTTATATAAAATTTGAAAGTAAAACTATAATTCTAAAATATAA
38337753 AAGAACTAAA
131 AAGAACTAAA
38337763 TTTT
1 TTTT
38337767 TAAAAATAAA
Statistics
Matches: 142, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
139 126 0.89
140 16 0.11
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (140 bp):
TTTTATAATGTTATTTATTAGGTTAATATTTTATGATGTTAATTAATTATTCAAATAGTTAATAT
CATTCAATTAAAATATTCCTTAGTTATATAAAATTTGAAAGTAAAACTATAATTCTAAAATATAA
AAGAACTAAA
Found at i:38337793 original size:23 final size:24
Alignment explanation
Indices: 38337732--38337793 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
38337722 TTGAAAGTAA
*
38337732 AACTATAATTCT-AAAATATAAAAG
1 AACTA-AATTCTAAAAATAAAAAAG
*
38337756 AACTAAATTTTTAAAAATAAAAAAG
1 AACTAAA-TTCTAAAAATAAAAAAG
*
38337781 -ATTAAATTCTAAA
1 AACTAAATTCTAAA
38337794 TATATGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
23 8 0.25
24 13 0.41
25 11 0.34
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (24 bp):
AACTAAATTCTAAAAATAAAAAAG
Found at i:38340804 original size:25 final size:25
Alignment explanation
Indices: 38340775--38340838 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
38340765 CACACCACAG
* **
38340775 CTCGCATGAACTTCCTGTTATTCAA
1 CTCGCATGAGCTTCCCATTATTCAA
*
38340800 CTCGCACGAGCTTCCCATTATTCAA
1 CTCGCATGAGCTTCCCATTATTCAA
*
38340825 CTCACATGAGCTTC
1 CTCGCATGAGCTTC
38340839 TCTTTTACAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.31
Consensus pattern (25 bp):
CTCGCATGAGCTTCCCATTATTCAA
Found at i:38343875 original size:18 final size:18
Alignment explanation
Indices: 38343852--38343886 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38343842 CTTGAACTAA
*
38343852 ATAAATCATTTATAAAAC
1 ATAAATCATTAATAAAAC
*
38343870 ATAAATTATTAATAAAA
1 ATAAATCATTAATAAAA
38343887 AATCTTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATCATTAATAAAAC
Found at i:38345447 original size:25 final size:26
Alignment explanation
Indices: 38345418--38345486 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
38345408 AGCTGTAAAT
38345418 GGGAAGCTTC-T-TCGAGCTGAATAAC
1 GGGAAGCTTCATGT-GAGCTGAATAAC
*
38345443 GGGAAGC-TCATGTGAGTTGAATAAC
1 GGGAAGCTTCATGTGAGCTGAATAAC
*
38345468 GGGAAGC-TCATGCGAGCTG
1 GGGAAGCTTCATGTGAGCTG
38345487 TGGTGTGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
24 2 0.05
25 36 0.92
26 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.33, T:0.22
Consensus pattern (26 bp):
GGGAAGCTTCATGTGAGCTGAATAAC
Found at i:38354244 original size:17 final size:18
Alignment explanation
Indices: 38354217--38354251 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
38354207 GTAGGTTTGT
*
38354217 AAAAATAGAAATGGAAAC
1 AAAAATAGAAATGAAAAC
38354235 AAAAAT-GAAATGAAAAC
1 AAAAATAGAAATGAAAAC
38354252 TTGCAATCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.69, C:0.06, G:0.14, T:0.11
Consensus pattern (18 bp):
AAAAATAGAAATGAAAAC
Found at i:38355822 original size:28 final size:28
Alignment explanation
Indices: 38355782--38355916 Score: 107
Period size: 28 Copynumber: 4.9 Consensus size: 28
38355772 AAACACGATA
*
38355782 GAAAAGAATAGTCTTTGTGGCAAAATTT
1 GAAAAGAATAGTCTTTGTGGCAAAATCT
* *
38355810 GAAAAGAATAGTCTTTGTGG-AGAACTTT
1 GAAAAGAATAGTCTTTGTGGCA-AAATCT
* * * *
38355838 GAAAAAAATA-TCCTTTGAGGCGAACTCT
1 GAAAAGAATAGT-CTTTGTGGCAAAATCT
* * *
38355866 AAAAAGAATAGT-TGTTGTGACGAAATCT
1 GAAAAGAATAGTCT-TTGTGGCAAAATCT
* *
38355894 GAAAGGGAT-GTCTTTGTGGCAAA
1 GAAAAGAATAGTCTTTGTGGCAAA
38355917 CTCTAAATTG
Statistics
Matches: 86, Mismatches: 15, Indels: 13
0.75 0.13 0.11
Matches are distributed among these distances:
27 13 0.15
28 72 0.84
29 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (28 bp):
GAAAAGAATAGTCTTTGTGGCAAAATCT
Found at i:38356962 original size:13 final size:13
Alignment explanation
Indices: 38356927--38356983 Score: 55
Period size: 13 Copynumber: 4.3 Consensus size: 13
38356917 CTGACTCATT
*
38356927 TTTTGATTTAATTCA
1 TTTT-ATTT-ATTTA
38356942 TTTT-TTTATTT-
1 TTTTATTTATTTA
38356953 TTCTTATTTATTTA
1 TT-TTATTTATTTA
*
38356967 TTTTAGTTATTTA
1 TTTTATTTATTTA
38356980 TTTT
1 TTTT
38356984 TATCTCATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
11 2 0.05
12 5 0.14
13 24 0.65
14 2 0.05
15 4 0.11
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.74
Consensus pattern (13 bp):
TTTTATTTATTTA
Found at i:38356976 original size:17 final size:17
Alignment explanation
Indices: 38356941--38356982 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
38356931 GATTTAATTC
* *
38356941 ATTTTTTTATTTTTCTT
1 ATTTATTTATTTTACTT
*
38356958 ATTTATTTATTTTAGTT
1 ATTTATTTATTTTACTT
38356975 ATTTATTT
1 ATTTATTT
38356983 TTATCTCATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTTACTT
Found at i:38359399 original size:21 final size:22
Alignment explanation
Indices: 38359364--38359417 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
38359354 AAACATGGCC
*
38359364 GTGTGGCTA-TCCCACATG-CTA
1 GTGTGGCTACT-CCACACGCCTA
38359385 GTGTGGCTACTCCACACGCCTA
1 GTGTGGCTACTCCACACGCCTA
*
38359407 -TGTGTCTACTC
1 GTGTGGCTACTC
38359418 GTGTAGCTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.17, C:0.31, G:0.22, T:0.30
Consensus pattern (22 bp):
GTGTGGCTACTCCACACGCCTA
Found at i:38364363 original size:35 final size:35
Alignment explanation
Indices: 38364312--38364383 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
38364302 GGTGTTACAT
* * * *
38364312 ACCAAATGCTCATAAGAGCTAGTATCATCCAGCAC
1 ACCAAATGCTCATAAGAGCCAATACCATCCAACAC
*
38364347 ACCAGATGCTCATAAGAGCCAATACCATCCAACAC
1 ACCAAATGCTCATAAGAGCCAATACCATCCAACAC
38364382 AC
1 AC
38364384 TAGAAACACT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (35 bp):
ACCAAATGCTCATAAGAGCCAATACCATCCAACAC
Found at i:38365716 original size:20 final size:20
Alignment explanation
Indices: 38365691--38365729 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
38365681 AGCCCAAAAG
38365691 TTAGTGGATTTAATTATGTA
1 TTAGTGGATTTAATTATGTA
38365711 TTAGTGGATTTAATTATGT
1 TTAGTGGATTTAATTATGT
38365730 CACCACCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (20 bp):
TTAGTGGATTTAATTATGTA
Found at i:38368524 original size:23 final size:23
Alignment explanation
Indices: 38368493--38368543 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
38368483 ACCTACTTTC
* *
38368493 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
38368516 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
38368539 TTACA
1 TTACA
38368544 AAGGCATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:38369872 original size:18 final size:19
Alignment explanation
Indices: 38369833--38369872 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
38369823 ATGATAAAAT
*
38369833 ATTATATGAAATAACAATA
1 ATTATATGAAATAACAAGA
*
38369852 ATTATAT-AAATAATAAGA
1 ATTATATGAAATAACAAGA
38369870 ATT
1 ATT
38369873 TCAATTATCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
ATTATATGAAATAACAAGA
Found at i:38370369 original size:102 final size:98
Alignment explanation
Indices: 38370256--38370538 Score: 363
Period size: 102 Copynumber: 2.8 Consensus size: 98
38370246 TTTTTTTTAC
* *
38370256 TTTGGGACACTGATGGTCAGCATCAGTGTATTTTAAAATAAAA-TTGGGTG-TAGGCCATGTAAT
1 TTTGGAACACTGATGG-CAGCACCAGTGTA-TTTAAAA-AAAATTTGGGTGCT-GGCCATGTAAT
*
38370319 GGTCGGCACCAAGTACAATTTTGGCTCCCAATGCATTTT
62 GG-CGGCACCAAGTACAATTTCGGCTCCCAATGC-TTTT
*
38370358 TTTGGAACACTGATAGGCGGCACCAGTGTATTTAAAAAACAATTTGGGTGCTGGCCATGTAATGG
1 TTTGGAACACTGAT-GGCAGCACCAGTGTATTTAAAAAA-AATTTGGGTGCTGGCCATGTAATGG
*
38370423 CCTGCACCAAGTACAATTTCGGCTCCCAATGCTTTT
64 -CGGCACCAAGTACAATTTCGGCTCCCAATGCTTTT
** * *
38370459 TTTTTAACATTGATGGCAGGCACCAGTGTATTTAAAAAAAAATTTTGGTGCTGGCCATGTAATGG
1 TTTGGAACACTGATGGCA-GCACCAGTGTATTT-AAAAAAAATTTGGGTGCTGGCCATGTAATGG
38370524 CTGGCACCAAGTACA
64 C-GGCACCAAGTACA
38370539 TTTAATAAAA
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
100 6 0.04
101 74 0.46
102 79 0.49
103 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (98 bp):
TTTGGAACACTGATGGCAGCACCAGTGTATTTAAAAAAAATTTGGGTGCTGGCCATGTAATGGCG
GCACCAAGTACAATTTCGGCTCCCAATGCTTTT
Found at i:38370524 original size:101 final size:101
Alignment explanation
Indices: 38370256--38370538 Score: 378
Period size: 101 Copynumber: 2.8 Consensus size: 101
38370246 TTTTTTTTAC
* * *
38370256 TTTGGGACACTGATGGTCA-GCATCAGTGTATTTTAAAATAAAA-TTGGGTG-TAGGCCATGTAA
1 TTTGGAACACTGATGG-CAGGCACCAGTGTA-TTTAAAAAAAAATTTGGGTGCT-GGCCATGTAA
* *
38370318 TGGTCGGCACCAAGTACAATTTTGGCTCCCAATGCATTTT
63 TGG-CTGCACCAAGTACAATTTCGGCTCCCAATGCATTTT
*
38370358 TTTGGAACACTGATAGGC-GGCACCAGTGTATTTAAAAAACAATTTGGGTGCTGGCCATGTAATG
1 TTTGGAACACTGAT-GGCAGGCACCAGTGTATTTAAAAAAAAATTTGGGTGCTGGCCATGTAATG
38370422 GCCTGCACCAAGTACAATTTCGGCTCCCAATGC-TTTT
65 G-CTGCACCAAGTACAATTTCGGCTCCCAATGCATTTT
** * *
38370459 TTTTTAACATTGATGGCAGGCACCAGTGTATTTAAAAAAAAATTTTGGTGCTGGCCATGTAATGG
1 TTTGGAACACTGATGGCAGGCACCAGTGTATTTAAAAAAAAATTTGGGTGCTGGCCATGTAATGG
38370524 CTGGCACCAAGTACA
66 CT-GCACCAAGTACA
38370539 TTTAATAAAA
Statistics
Matches: 163, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
100 5 0.03
101 82 0.50
102 73 0.45
103 3 0.02
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.30
Consensus pattern (101 bp):
TTTGGAACACTGATGGCAGGCACCAGTGTATTTAAAAAAAAATTTGGGTGCTGGCCATGTAATGG
CTGCACCAAGTACAATTTCGGCTCCCAATGCATTTT
Found at i:38370565 original size:51 final size:49
Alignment explanation
Indices: 38370470--38370642 Score: 150
Period size: 51 Copynumber: 3.4 Consensus size: 49
38370460 TTTTAACATT
* **
38370470 GATGGCAGGCACCAGTGTATTTAAAAAAAAATTTTGGTGCTGGCCATGTA
1 GATGGCTGGCACCAGTACATTTAAAAAAAAATTTTGGTGCTGGCCA-GTA
*
38370520 -ATGGCTGGCACCAAGTACATTTAATAAAAAAATTTTGGTGTTGGCCAGTA
1 GATGGCTGGCACC-AGTACATTTAA-AAAAAAATTTTGGTGCTGGCCAGTA
* * ** ** *
38370570 GATGGGTGGCACTAGTGTATTTGAAAAAAAAAATATTTATATGCTGGCTAGTA
1 GATGGCTGGCACCAGTACATTT--AAAAAAAAAT-TTT-GGTGCTGGCCAGTA
* *
38370623 GATGGCCGGCATCAAGTACA
1 GATGGCTGGCA-CCAGTACA
38370643 ATTTTTAGCT
Statistics
Matches: 98, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
49 11 0.11
50 19 0.19
51 39 0.40
52 5 0.05
53 19 0.19
54 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (49 bp):
GATGGCTGGCACCAGTACATTTAAAAAAAAATTTTGGTGCTGGCCAGTA
Found at i:38371603 original size:86 final size:87
Alignment explanation
Indices: 38371491--38371684 Score: 214
Period size: 91 Copynumber: 2.2 Consensus size: 87
38371481 CCTAGTATCG
* * * *
38371491 GCCAATGGATTCCCAAATTCAAAAAAATTTATTATTTTTAAAGCCTG-C-AT-CAGGCAATAATA
1 GCCATTGGGTTCCCAAACTCAAAAAAAATTA-T-TTTTTAAAGCCTGACAATACAGGCAATAATA
*
38371553 GGGCCAAAACACTAGGTAGTGCCA
64 GGGACAAAACACTAGGTAGTGCCA
* * * *
38371577 GTCATTGGGTTCCTAAACTCAAAAAAAATTATTTTTTAAAGCCTGATACAATCAACATGCAATCA
1 GCCATTGGGTTCCCAAACTCAAAAAAAATTATTTTTTAAAGCCTG--ACAAT--ACAGGCAATAA
* *
38371642 TGGGGACAAAACACTAGGTAGTGCCG
62 TAGGGACAAAACACTAGGTAGTGCCA
38371668 GCCATTGGGTTCCCAAA
1 GCCATTGGGTTCCCAAA
38371685 ACTTAAATCT
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
84 13 0.15
85 1 0.01
86 25 0.28
87 1 0.01
88 2 0.02
91 46 0.52
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.26
Consensus pattern (87 bp):
GCCATTGGGTTCCCAAACTCAAAAAAAATTATTTTTTAAAGCCTGACAATACAGGCAATAATAGG
GACAAAACACTAGGTAGTGCCA
Found at i:38373104 original size:21 final size:21
Alignment explanation
Indices: 38373078--38373131 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
38373068 TAGCGGTGGT
*
38373078 GGTGAGATTAGTTACTGTAGC
1 GGTGAGATTAGATACTGTAGC
*
38373099 GGTGAGATTAAATACTGTAGC
1 GGTGAGATTAGATACTGTAGC
38373120 GGTGAGATTAGA
1 GGTGAGATTAGA
38373132 AACAATGGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGC
Found at i:38373196 original size:29 final size:29
Alignment explanation
Indices: 38373151--38373285 Score: 153
Period size: 29 Copynumber: 4.6 Consensus size: 29
38373141 GGAGTGTGTG
* * *
38373151 TTTTTATTTCTAGAATACACCACATATAT
1 TTTTTATTTTTAAAATACACTACATATAT
* * *
38373180 TTTCTATTTTTAAAATATACTACATATTT
1 TTTTTATTTTTAAAATACACTACATATAT
* *
38373209 TTTTTATTTTTAAAATACAATACATGTATTT
1 TTTTTATTTTTAAAATACACTACA--TATAT
* *
38373240 TTTTTATTTTTAAAATCCATTACATATATT
1 TTTTTATTTTTAAAATACACTACATATA-T
38373270 TTTTTATTTTTAAAAT
1 TTTTTATTTTTAAAAT
38373286 TTTAAATACA
Statistics
Matches: 91, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
29 47 0.52
30 17 0.19
31 27 0.30
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTTTATTTTTAAAATACACTACATATAT
Found at i:38373328 original size:14 final size:15
Alignment explanation
Indices: 38373301--38373343 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
38373291 ATACAATGAA
* *
38373301 ATCCCATCTCCCATC
1 ATCCCCTCTTCCATC
38373316 -TCCCCTCTTCCATC
1 ATCCCCTCTTCCATC
38373330 ATTCCCCTCTTCCA
1 A-TCCCCTCTTCCA
38373344 CCGTTCCCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 12 0.50
16 12 0.50
ACGTcount: A:0.14, C:0.53, G:0.00, T:0.33
Consensus pattern (15 bp):
ATCCCCTCTTCCATC
Found at i:38373350 original size:16 final size:16
Alignment explanation
Indices: 38373311--38373351 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
38373301 ATCCCATCTC
38373311 CCATCTCCCCTCTTCCA
1 CCAT-TCCCCTCTTCCA
*
38373328 TCATTCCCCTCTTCCA
1 CCATTCCCCTCTTCCA
*
38373344 CCGTTCCC
1 CCATTCCC
38373352 TCCTCCCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.10, C:0.56, G:0.02, T:0.32
Consensus pattern (16 bp):
CCATTCCCCTCTTCCA
Found at i:38373462 original size:60 final size:59
Alignment explanation
Indices: 38373302--38373494 Score: 204
Period size: 59 Copynumber: 3.3 Consensus size: 59
38373292 TACAATGAAA
*
38373302 TCCCATCTCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCA-
1 TCCCATATCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCAT
* * * *
38373360 TCCCATGCAATACCCAT-TCCCAT-TTCC-T-ATTTCCC-ATTCCACCGTGCCCTCCTCCCATT
1 TCCCAT---AT-CCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCA-T
* *
38373419 TCCCAT-TCCCATCTCCCCTCTTCCATCGATTCCCCTCTTCCACCGTTCTCTCCTCTCAT
1 TCCCATATCCCATCTCCCCTCTTCCATC-ATTCCCCTCTTCCACCGTTCCCTCCTCCCAT
*
38373478 TCCCAT-TCCCATTTCCC
1 TCCCATATCCCATCTCCC
38373495 ATTCCCATTC
Statistics
Matches: 111, Mismatches: 12, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
54 5 0.05
55 6 0.05
56 4 0.04
57 21 0.19
58 12 0.11
59 30 0.27
60 22 0.20
61 6 0.05
62 5 0.05
ACGTcount: A:0.12, C:0.51, G:0.03, T:0.33
Consensus pattern (59 bp):
TCCCATATCCCATCTCCCCTCTTCCATCATTCCCCTCTTCCACCGTTCCCTCCTCCCAT
Found at i:38373486 original size:6 final size:6
Alignment explanation
Indices: 38373475--38373509 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
38373465 TCTCTCCTCT
38373475 CATTCC CATTCC CATTTCC CATTCC CATTCC CATT
1 CATTCC CATTCC CA-TTCC CATTCC CATTCC CATT
38373510 ATCAACAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.17, C:0.46, G:0.00, T:0.37
Consensus pattern (6 bp):
CATTCC
Found at i:38373495 original size:13 final size:12
Alignment explanation
Indices: 38373475--38373509 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
38373465 TCTCTCCTCT
38373475 CATTCCCATTCC
1 CATTCCCATTCC
38373487 CATTTCCCATTCC
1 CA-TTCCCATTCC
38373500 CATTCCCATT
1 CATTCCCATT
38373510 ATCAACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.17, C:0.46, G:0.00, T:0.37
Consensus pattern (12 bp):
CATTCCCATTCC
Found at i:38375310 original size:45 final size:45
Alignment explanation
Indices: 38375200--38375335 Score: 256
Period size: 45 Copynumber: 3.0 Consensus size: 45
38375190 CTTTCCTCTT
*
38375200 ATAGCCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
1 ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
38375245 A-AGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
1 ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
38375289 ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
1 ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
38375334 AT
1 AT
38375336 CAATCTCCTC
Statistics
Matches: 89, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
44 43 0.48
45 46 0.52
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.31
Consensus pattern (45 bp):
ATAGGCAAATGTATGAAGAACTTCTTATGAAATATATCATTCGAA
Found at i:38378677 original size:44 final size:45
Alignment explanation
Indices: 38378613--38378701 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 45
38378603 TGATAAAATA
38378613 TTATTAATATAAAATAAAAATAATTATAATTAT-TTTATATTATT
1 TTATTAATATAAAATAAAAATAATTATAATTATCTTTATATTATT
* * *
38378657 TTATTAATAGTAATAT-AAAATAATTTTAATTATCTTTATTTTATT
1 TTATTAATA-TAAAATAAAAATAATTATAATTATCTTTATATTATT
38378702 AATTATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
44 25 0.62
45 15 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (45 bp):
TTATTAATATAAAATAAAAATAATTATAATTATCTTTATATTATT
Found at i:38378705 original size:18 final size:19
Alignment explanation
Indices: 38378682--38378717 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
38378672 TAAAATAATT
38378682 TTAATTATCTTT-ATTTTA
1 TTAATTATCTTTCATTTTA
*
38378700 TTAATTATTTTTCATTTT
1 TTAATTATCTTTCATTTT
38378718 TAGTATTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTAATTATCTTTCATTTTA
Found at i:38381205 original size:12 final size:12
Alignment explanation
Indices: 38381188--38381212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38381178 GGGACAACAG
38381188 ACCCTCACTACA
1 ACCCTCACTACA
38381200 ACCCTCACTACA
1 ACCCTCACTACA
38381212 A
1 A
38381213 ATTAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (12 bp):
ACCCTCACTACA
Found at i:38381920 original size:44 final size:44
Alignment explanation
Indices: 38381865--38381953 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
38381855 AATTTATAGC
* * * *
38381865 TTCAGTTATGCTTCTTTTAACTCCTTGTAAAACCAGTTCGGTGT
1 TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
*
38381909 TTCAATTATGCTTCTCTCAACTCATTGTAAAACTAGTTCGGTGT
1 TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
38381953 T
1 T
38381954 GCTTATACCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.22, C:0.20, G:0.15, T:0.43
Consensus pattern (44 bp):
TTCAATTATGCTTCTCTCAACTCATTGTAAAACCAGTTCGGTGT
Found at i:38388271 original size:17 final size:17
Alignment explanation
Indices: 38388246--38388282 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
38388236 TCCAATTATC
*
38388246 TAAAAATATTAAAATTT
1 TAAAAATATTAAAATGT
*
38388263 TAAAGATATTAAAATGT
1 TAAAAATATTAAAATGT
38388280 TAA
1 TAA
38388283 TTTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TAAAAATATTAAAATGT
Found at i:38393756 original size:15 final size:15
Alignment explanation
Indices: 38393736--38393765 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
38393726 AATTTCATGC
38393736 TTCAATCACCATGTT
1 TTCAATCACCATGTT
38393751 TTCAATCACCATGTT
1 TTCAATCACCATGTT
38393766 ATCACTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (15 bp):
TTCAATCACCATGTT
Found at i:38396167 original size:20 final size:21
Alignment explanation
Indices: 38396142--38396180 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
38396132 TATAAAATTA
*
38396142 ATTTTTCTAAA-AATATTTTT
1 ATTTTTCAAAATAATATTTTT
38396162 ATTTTTCAAAATAATATTT
1 ATTTTTCAAAATAATATTT
38396181 CCCAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTCAAAATAATATTTTT
Found at i:38401323 original size:21 final size:21
Alignment explanation
Indices: 38401289--38401343 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
38401279 TATTAAACAG
* *
38401289 CTAA-GGTTCGCATATAATTT
1 CTAAGGGTTCACATATAACTT
*
38401309 CTATGGGTTCACATATAACTT
1 CTAAGGGTTCACATATAACTT
*
38401330 CTAAGTGTTCACAT
1 CTAAGGGTTCACAT
38401344 TACAATTCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 3 0.10
21 26 0.90
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (21 bp):
CTAAGGGTTCACATATAACTT
Found at i:38401375 original size:23 final size:22
Alignment explanation
Indices: 38401349--38401393 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
38401339 CACATTACAA
* *
38401349 TTCCTATAGTGTTCGCATGTTAT
1 TTCCTATAG-GTTCACATATTAT
*
38401372 TTCCTCTAGGTTCACATATTAT
1 TTCCTATAGGTTCACATATTAT
38401394 ACTGTTCACG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (22 bp):
TTCCTATAGGTTCACATATTAT
Found at i:38401393 original size:22 final size:23
Alignment explanation
Indices: 38401294--38401393 Score: 59
Period size: 21 Copynumber: 4.6 Consensus size: 23
38401284 AACAGCTAAG
* * *
38401294 GTTCGCATATAATTT-CTAT-GG
1 GTTCACATATTATTTCCTATAGT
* *
38401315 GTTCACATATAACTT-CTA-AGT
1 GTTCACATATTATTTCCTATAGT
* *
38401336 GTTCACAT-TACAATTCCTATAGT
1 GTTCACATAT-TATTTCCTATAGT
* * *
38401359 GTTCGCATGTTATTTCCTCTAG-
1 GTTCACATATTATTTCCTATAGT
38401381 GTTCACATATTAT
1 GTTCACATATTAT
38401394 ACTGTTCACG
Statistics
Matches: 63, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.02
21 28 0.44
22 14 0.22
23 19 0.30
24 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (23 bp):
GTTCACATATTATTTCCTATAGT
Found at i:38401679 original size:19 final size:20
Alignment explanation
Indices: 38401641--38401679 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
38401631 TGGGTTTTGA
38401641 AGAAAAAATAGAGAATAAAT
1 AGAAAAAATAGAGAATAAAT
* *
38401661 AGAAAGAAT-GAGGATAAAT
1 AGAAAAAATAGAGAATAAAT
38401680 TCTATTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.15
Consensus pattern (20 bp):
AGAAAAAATAGAGAATAAAT
Found at i:38404705 original size:15 final size:15
Alignment explanation
Indices: 38404685--38404715 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38404675 ATCCAGGAAG
38404685 TTGGTCACATATAAT
1 TTGGTCACATATAAT
38404700 TTGGTCACATATAAT
1 TTGGTCACATATAAT
38404715 T
1 T
38404716 GGTAATGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTGGTCACATATAAT
Found at i:38413440 original size:26 final size:27
Alignment explanation
Indices: 38413411--38413461 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
38413401 CCACATTAGC
*
38413411 TGGGCTAGGTTAATTGGGT-TTTGGTT
1 TGGGCTAGGTTAAGTGGGTATTTGGTT
38413437 TGGGCTAGGTTAAGTGGGTATTTGG
1 TGGGCTAGGTTAAGTGGGTATTTGG
38413462 GATCTGTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.14, C:0.04, G:0.41, T:0.41
Consensus pattern (27 bp):
TGGGCTAGGTTAAGTGGGTATTTGGTT
Found at i:38418500 original size:2 final size:2
Alignment explanation
Indices: 38418493--38418535 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
38418483 TCATTTGCAG
38418493 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
38418535 G
1 G
38418536 CAATCCATGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:38421564 original size:48 final size:48
Alignment explanation
Indices: 38421494--38421590 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 48
38421484 TTCTTTGCTT
38421494 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
1 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
* * * *
38421542 AAAAACGCCTAAGTCGGCCTAACTTGCAATGATAAAGGATTCAACAGA
1 AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
38421590 A
1 A
38421591 TTCCCTTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.15
Consensus pattern (48 bp):
AAAAACGCCAAAGCCAGCCTAACTCGCAATGATAAAGGATTCAACAGA
Found at i:38421833 original size:36 final size:36
Alignment explanation
Indices: 38421793--38421863 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
38421783 ATCAAAGGCT
*
38421793 ACAATTAAAAGTTGTATACAATTAGAACTCTAAGAC
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
*
38421829 ACAATTAGAAGCTGTATACAATTAGAACTCTAAGA
1 ACAATTAAAAGCTGTATACAATTAGAACTCTAAGA
38421864 TTACATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.14, G:0.13, T:0.27
Consensus pattern (36 bp):
ACAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
Found at i:38421834 original size:19 final size:19
Alignment explanation
Indices: 38421810--38421863 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
38421800 AAAGTTGTAT
38421810 ACAATTAGAACTCTAAGAC
1 ACAATTAGAACTCTAAGAC
* *
38421829 ACAATTAGAA-GCT--GTAT
1 ACAATTAGAACTCTAAG-AC
38421846 ACAATTAGAACTCTAAGA
1 ACAATTAGAACTCTAAGA
38421864 TTACATAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
16 1 0.04
17 11 0.39
18 4 0.14
19 11 0.39
20 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (19 bp):
ACAATTAGAACTCTAAGAC
Found at i:38421851 original size:17 final size:17
Alignment explanation
Indices: 38421792--38421855 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
38421782 CATCAAAGGC
* *
38421792 TACAATTAAAAGTTGTA
1 TACAATTAGAAGCTGTA
*
38421809 TACAATTAGAA-CTCTAAGA
1 TACAATTAGAAGCTGT---A
*
38421828 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
38421845 TACAATTAGAA
1 TACAATTAGAA
38421856 CTCTAAGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
16 2 0.05
17 21 0.57
19 11 0.30
20 3 0.08
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:38424679 original size:17 final size:17
Alignment explanation
Indices: 38424657--38424720 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
38424647 CATCAAAGGC
*
38424657 TACAATTAAAAGCTGTA
1 TACAATTAGAAGCTGTA
*
38424674 TACAATTAGAA-CTCGAAGA
1 TACAATTAGAAGCT-G--TA
*
38424693 CACAATTAGAAGCTGTA
1 TACAATTAGAAGCTGTA
38424710 TACAATTAGAA
1 TACAATTAGAA
38424721 TTCTAAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
16 2 0.05
17 22 0.58
19 12 0.32
20 2 0.05
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (17 bp):
TACAATTAGAAGCTGTA
Found at i:38426071 original size:23 final size:23
Alignment explanation
Indices: 38426026--38426071 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38426016 TACTTAAATT
*
38426026 TATTTCAAATATATAAAATTATA
1 TATTTCAAATATATAAAACTATA
*
38426049 TATTT-AAATTTATAATAACTATA
1 TATTTCAAATATATAA-AACTATA
38426072 NNNNNNNNNN
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTTCAAATATATAAAACTATA
Found at i:38426600 original size:9 final size:9
Alignment explanation
Indices: 38426588--38426639 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
38426578 TTTTGTGAAC
38426588 TTTTTTTTA
1 TTTTTTTTA
*
38426597 TTTTTTTAA
1 TTTTTTTTA
*
38426606 TTTTGATTTA
1 TTTT-TTTTA
*
38426616 TATTTTTTA
1 TTTTTTTTA
* *
38426625 TTTTTATAA
1 TTTTTTTTA
38426634 TTTTTT
1 TTTTTT
38426640 ATTTATTTGT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:38426609 original size:15 final size:15
Alignment explanation
Indices: 38426591--38426643 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
38426581 TGTGAACTTT
*
38426591 TTTTTATTTTTTTAA
1 TTTTTATTTTTATAA
* *
38426606 TTTTGA--TTTATAT
1 TTTTTATTTTTATAA
38426619 TTTTTATTTTTATAA
1 TTTTTATTTTTATAA
38426634 TTTTTTATTT
1 -TTTTTATTT
38426644 ATTTGTTGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
13 10 0.33
15 11 0.37
16 9 0.30
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTATAA
Found at i:38434122 original size:63 final size:63
Alignment explanation
Indices: 38434055--38434181 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
38434045 AGTAAAAAAA
*
38434055 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTGTTTATATAGGAATTAGCCTGTAATTCC
1 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
38434118 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
1 AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
38434181 A
1 A
38434182 CTATAACTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (63 bp):
AAAAAAAAAGTCCTTCTCTATTAAGCTTTTATCCTATTTATATAGGAATTAGCCTGTAATTCC
Found at i:38435489 original size:24 final size:24
Alignment explanation
Indices: 38435444--38435489 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
38435434 AACAAAAATT
* * **
38435444 TAAATATTCCTAACAATTTAAACA
1 TAAAAATTCCAAACAAACTAAACA
38435468 TAAAAATTCCAAACAAACTAAA
1 TAAAAATTCCAAACAAACTAAA
38435490 ACTTCAATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (24 bp):
TAAAAATTCCAAACAAACTAAACA
Found at i:38437563 original size:41 final size:41
Alignment explanation
Indices: 38437478--38437635 Score: 183
Period size: 41 Copynumber: 3.8 Consensus size: 41
38437468 GTCTGACCTT
* * *
38437478 TCGGGGCTTTAGCGACATTTTTCGAAAAAGCGCCGCTAAAGC
1 TCGGGGATTTAGCGACGTTTTT-GAAAAAGCGCCGCTAATGC
* *
38437520 TCGGGGATATAGCGACGTTTTTGAAAAAGCGACGCTAATGC
1 TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
* * * *
38437561 TC-GGAACTTTAGCGGCGTTTTTGAAAAAGCGCCCCTAATTC
1 TCGGGGA-TTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
* * *
38437602 TCGGTGCTTTAGCGGCGTTTTTGAAAAAGCGCCG
1 TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCG
38437636 AAAAAATATT
Statistics
Matches: 99, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
40 3 0.03
41 76 0.77
42 20 0.20
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.27
Consensus pattern (41 bp):
TCGGGGATTTAGCGACGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:38441386 original size:43 final size:42
Alignment explanation
Indices: 38441272--38441452 Score: 186
Period size: 43 Copynumber: 4.3 Consensus size: 42
38441262 AAAAGTCATG
* * * *
38441272 TTTTTAGCGGCATTTGTGAAAAAGTGCCGCTAAAAGTTAT--
1 TTTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTTATGA
* *
38441312 TTTTATAGCGGCGTTTGTAATAGAAGCGCCGCTAAAGGTTATGA
1 TTTT-TAGCGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTTATGA
* * *
38441356 TTTTTAGCGACGTTTGTGGTAAAAGTGCCGCTAAAGGTCATGA
1 TTTTTAGCGGCGTTTGT-GTAAAAGCGCCGCTAAAGGTTATGA
* ***
38441399 TTTTTAGCGGCGTTTGTGTGAAAAGCGCTGCTAAAGACCATGA
1 TTTTTAGCGGCGTTTGTGT-AAAAGCGCCGCTAAAGGTTATGA
*
38441442 TCTTTAGCGGC
1 TTTTTAGCGGC
38441453 ATTTTTTCAC
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
40 4 0.03
41 12 0.10
42 20 0.17
43 78 0.66
44 4 0.03
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.33
Consensus pattern (42 bp):
TTTTTAGCGGCGTTTGTGTAAAAGCGCCGCTAAAGGTTATGA
Found at i:38443180 original size:595 final size:597
Alignment explanation
Indices: 38442038--38443231 Score: 2374
Period size: 595 Copynumber: 2.0 Consensus size: 597
38442028 ATTAATATAA
38442038 ATTTTTTAAATATAATATTATTTTTAGATAGTAATATGGTTTTGCCGATTGAGTTCTAACTCGAT
1 ATTTTTTAAATATAATATTATTTTTAGATAGTAATATGGTTTTGCCGATTGAGTTCTAACTCGAT
38442103 TGGCATGAACATTGTTGTCAATATAAGAGAACGTGGCATTATCCTCATGTTCATAGATTAGGGAT
66 TGGCATGAACATTGTTGTCAATATAAGAGAACGTGGCATTATCCTCATGTTCATAGATTAGGGAT
38442168 GAGTTATGACTAGTTATAGGTATTGTGTAAAAAAATAGATAAGATCTTGTAAGAAGATTATTAAA
131 GAGTTATGACTAGTTATAGGTATTGTGTAAAAAAATAGATAAGATCTTGTAAGAAGATTATTAAA
38442233 ATAATAATAACGCGGTTTTTTTTTGGGGATAAGTCAACTCTCCAATCCCATTGACAACTCATACA
196 ATAATAATAACGCGGTTTTTTTTTGGGGATAAGTCAACTCTCCAATCCCATTGACAACTCATACA
38442298 AACAGGAAACGTTTTTTTTAAACACATATAAATTTAATAAAAAAATAAGATAAGAAGAGTAGTAA
261 AACAGGAAACGTTTTTTTTAAACACATATAAATTTAATAAAAAAATAAGATAAGAAGAGTAGTAA
38442363 TAATGTATAATATTTGTAAAAATGATCCACAACCGTTGCTTTCGAAACAAAGAAATAGAGAAATA
326 TAATGTATAATATTTGTAAAAATGATCCACAACCGTTGCTTTCGAAACAAAGAAATAGAGAAATA
38442428 AGAAATTGAGGAGATAAGTTTGATTTGCCTTTTTTTGGTACATGTACCATTTGCTTTTGTTAGTT
391 AGAAATTGAGGAGATAAGTTTGATTTGCCTTTTTTTGGTACATGTACCATTTGCTTTTGTTAGTT
38442493 CAGTAAAAGATTCAGTTGGGAGATTATAGCCCACCACTTTGACCACGTCTTCAGAACTTTAAAAA
456 CAGTAAAAGATTCAGTTGGGAGATTATAGCCCACCACTTTGACCACGTCTTCAGAACTTTAAAAA
38442558 TAATATTATAATTATTCAATTATAGTAGAAAAAATAACGTAAAGGTTTACCAAGTAGGAGTTTCA
521 TAATATTATAATTATTCAATTATAGTAGAAAAAATAACGTAAAGGTTTACCAAGTAGGAGTTTCA
38442623 GAGTAATGTATT
586 GAGTAATGTATT
38442635 ATTTTTT-AA-ATAATATTATTTTTAGATAGTAATATGGTTTTGCCGATTGAGTTCTAACTCGAT
1 ATTTTTTAAATATAATATTATTTTTAGATAGTAATATGGTTTTGCCGATTGAGTTCTAACTCGAT
38442698 TGGCATGAACATTGTTGTCAATATAAGAGAACGTGGCATTATCCTCATGTTCATAGATTAGGGAT
66 TGGCATGAACATTGTTGTCAATATAAGAGAACGTGGCATTATCCTCATGTTCATAGATTAGGGAT
38442763 GAGTTATGACTAGTTATAGGTATTGTGTAAAAAAATAGATAAGATCTTGTAAGAAGATTATTAAA
131 GAGTTATGACTAGTTATAGGTATTGTGTAAAAAAATAGATAAGATCTTGTAAGAAGATTATTAAA
38442828 ATAATAATAACGCGGTTTTTTTTTGGGGATAAGTCAACTCTCCAATCCCATTGACAACTCATACA
196 ATAATAATAACGCGGTTTTTTTTTGGGGATAAGTCAACTCTCCAATCCCATTGACAACTCATACA
38442893 AACAGGAAACGTTTTTTTTAAACACATATAAATTTAATAAAAAAATAAGATAAGAAGAGTAGTAA
261 AACAGGAAACGTTTTTTTTAAACACATATAAATTTAATAAAAAAATAAGATAAGAAGAGTAGTAA
38442958 TAATGTATAATATTTGTAAAAATGATCCACAACCGTTGCTTTCGAAACAAAGAAATAGAGAAATA
326 TAATGTATAATATTTGTAAAAATGATCCACAACCGTTGCTTTCGAAACAAAGAAATAGAGAAATA
38443023 AGAAATTGAGGAGATAAGTTTGATTTGCCTTTTTTTGGTACATGTACCATTTGCTTTTGTTAGTT
391 AGAAATTGAGGAGATAAGTTTGATTTGCCTTTTTTTGGTACATGTACCATTTGCTTTTGTTAGTT
38443088 CAGTAAAAGATTCAGTTGGGAGATTATAGCCCACCACTTTGACCACGTCTTCAGAACTTTAAAAA
456 CAGTAAAAGATTCAGTTGGGAGATTATAGCCCACCACTTTGACCACGTCTTCAGAACTTTAAAAA
38443153 TAATATTATAATTATTCAATTATAGTAGAAAAAATAACGTAAAGGTTTACCAAGTAGGAGTTTCA
521 TAATATTATAATTATTCAATTATAGTAGAAAAAATAACGTAAAGGTTTACCAAGTAGGAGTTTCA
38443218 GAGTAATGTATT
586 GAGTAATGTATT
38443230 AT
1 AT
38443232 ACAATTAGGT
Statistics
Matches: 597, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
595 588 0.98
596 2 0.00
597 7 0.01
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (597 bp):
ATTTTTTAAATATAATATTATTTTTAGATAGTAATATGGTTTTGCCGATTGAGTTCTAACTCGAT
TGGCATGAACATTGTTGTCAATATAAGAGAACGTGGCATTATCCTCATGTTCATAGATTAGGGAT
GAGTTATGACTAGTTATAGGTATTGTGTAAAAAAATAGATAAGATCTTGTAAGAAGATTATTAAA
ATAATAATAACGCGGTTTTTTTTTGGGGATAAGTCAACTCTCCAATCCCATTGACAACTCATACA
AACAGGAAACGTTTTTTTTAAACACATATAAATTTAATAAAAAAATAAGATAAGAAGAGTAGTAA
TAATGTATAATATTTGTAAAAATGATCCACAACCGTTGCTTTCGAAACAAAGAAATAGAGAAATA
AGAAATTGAGGAGATAAGTTTGATTTGCCTTTTTTTGGTACATGTACCATTTGCTTTTGTTAGTT
CAGTAAAAGATTCAGTTGGGAGATTATAGCCCACCACTTTGACCACGTCTTCAGAACTTTAAAAA
TAATATTATAATTATTCAATTATAGTAGAAAAAATAACGTAAAGGTTTACCAAGTAGGAGTTTCA
GAGTAATGTATT
Found at i:38444718 original size:22 final size:23
Alignment explanation
Indices: 38444693--38444736 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
38444683 AAAATTTAAA
38444693 TAATATG-AAATAAAAATAACAT
1 TAATATGCAAATAAAAATAACAT
**
38444715 TAATATGCTTATAAAAATAACA
1 TAATATGCAAATAAAAATAACA
38444737 GAATCTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.30
Consensus pattern (23 bp):
TAATATGCAAATAAAAATAACAT
Found at i:38444976 original size:31 final size:32
Alignment explanation
Indices: 38444928--38445001 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
38444918 CCATCTAACG
* * * *
38444928 AAAAAATT-AATATCTTAAA-AAACATTAATT
1 AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
*
38444958 AAAAAATTAAAAAGCTTAAAGTAACATGAAAT
1 AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
38444990 AAAAAA-TAAAAA
1 AAAAAATTAAAAA
38445002 TATGAGTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 8 0.22
31 15 0.41
32 14 0.38
ACGTcount: A:0.66, C:0.05, G:0.04, T:0.24
Consensus pattern (32 bp):
AAAAAATTAAAAAGCTTAAAGAAACATGAAAT
Found at i:38445008 original size:140 final size:138
Alignment explanation
Indices: 38444767--38445116 Score: 375
Period size: 140 Copynumber: 2.5 Consensus size: 138
38444757 CATTCGTAAT
*
38444767 TATCTAACCATCTAACAAAATGAGTTAATATGTTAAAAATATTAATTAAAAATAAAAATAAAAAA
1 TATCTAACCATCTAACAAAA-GAGTTAATATGTTAAAAA-ATTAATT---AA-AAAATTAAAAAA
* * * *
38444832 CTTGAAGCAACATTAAATAAAAAATACAAATGTGAGT-AGTAAA-AGAATAAAACTCGAGACTCA
60 CTTAAAGCAACATGAAATAAAAAATAAAAATATGAGTAAG-AAAGA-AATAAAACTCGAGACTCA
* *
38444895 ATGTTGTAATTACAAC
123 AGGATGTAATTACAAC
* * * *
38444911 TATCTTACCATCTAACGAAAA-AATTAATATCTTAAAAAACATTAATTAAAAAATTAAAAAGCTT
1 TATCTAACCATCTAAC-AAAAGAGTTAATATGTT-AAAAA-ATTAATTAAAAAATTAAAAAACTT
* * *
38444975 AAAGTAACATGAAATAAAAAATAAAAATATGAGTAAGAGAGAAATTAAACTCGAGACTCAAGGAT
63 AAAGCAACATGAAATAAAAAATAAAAATATGAGTAAGAAAGAAATAAAACTCGAGACTCAAGGAT
*
38445040 GTAATTGCAAC
128 GTAATTACAAC
* * * *
38445051 TAAT-TAAACAATCTAACAAAAGAGCTAATATGTTAAAAAATTAATTAAAAATTTTAAAAATCTT
1 T-ATCT-AACCATCTAACAAAAGAGTTAATATGTTAAAAAATTAATTAAAAA-ATTAAAAAACTT
38445115 AA
63 AA
38445117 CATGAAATTA
Statistics
Matches: 175, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
139 12 0.07
140 97 0.55
141 25 0.14
143 10 0.06
144 27 0.15
145 4 0.02
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (138 bp):
TATCTAACCATCTAACAAAAGAGTTAATATGTTAAAAAATTAATTAAAAAATTAAAAAACTTAAA
GCAACATGAAATAAAAAATAAAAATATGAGTAAGAAAGAAATAAAACTCGAGACTCAAGGATGTA
ATTACAAC
Found at i:38446169 original size:23 final size:23
Alignment explanation
Indices: 38446143--38446189 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
38446133 TAAATTTTGA
*
38446143 ATTATTTAGTGATAATCTTTAGG
1 ATTATTTAGTGATAATATTTAGG
38446166 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
38446189 A
1 A
38446190 AAAATCTAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:38446186 original size:13 final size:13
Alignment explanation
Indices: 38446145--38446187 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
38446135 AATTTTGAAT
38446145 TATTTAGTGATAA
1 TATTTAGTGATAA
*
38446158 TCTTTAG-GAT--
1 TATTTAGTGATAA
38446168 TATTTAGTGATAA
1 TATTTAGTGATAA
38446181 TATTTAG
1 TATTTAG
38446188 GAAAAATCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:38452960 original size:721 final size:721
Alignment explanation
Indices: 38451578--38453019 Score: 2884
Period size: 721 Copynumber: 2.0 Consensus size: 721
38451568 CGTTAGCACC
38451578 GAAAAGTTCCAACAAAAGACCGAAGCGTATCTTCAGGAAATGGATCAGCAAATAAGTAAGTTAGC
1 GAAAAGTTCCAACAAAAGACCGAAGCGTATCTTCAGGAAATGGATCAGCAAATAAGTAAGTTAGC
38451643 ACTTACATTTAGTTGTTTGGAGAATAAGGAACTACCGTCTCAAACTGAGCCAAACCCACGTCAAA
66 ACTTACATTTAGTTGTTTGGAGAATAAGGAACTACCGTCTCAAACTGAGCCAAACCCACGTCAAA
38451708 ATACAATTGTTGTGACCATAAAGGATGCGTTAGGACTAGTGCTTGGCATAAGTTGTGACCACAAT
131 ATACAATTGTTGTGACCATAAAGGATGCGTTAGGACTAGTGCTTGGCATAAGTTGTGACCACAAT
38451773 GTTGAACAAGAAGAACAAAAGGCCAAACTAGTAGCTACCATAGAGCCGACACCACATAAACCATT
196 GTTGAACAAGAAGAACAAAAGGCCAAACTAGTAGCTACCATAGAGCCGACACCACATAAACCATT
38451838 TGTTGTACCTCCCCTATAGCCTGGAAGGCTCGCCCAAGTTAAAAAGGAACGAAAGAAAAAAATCC
261 TGTTGTACCTCCCCTATAGCCTGGAAGGCTCGCCCAAGTTAAAAAGGAACGAAAGAAAAAAATCC
38451903 TTGATATATTCTAAAAGGTAAAAATTAATATTACTTTACTTGATGCAATTAAGTAGGTTCCACGC
326 TTGATATATTCTAAAAGGTAAAAATTAATATTACTTTACTTGATGCAATTAAGTAGGTTCCACGC
38451968 TATGCAAAATTTCTGAAAGAACTGTGCACAAAAAAAATAAGCTCTAAGGAAACGAATGGGTAAAT
391 TATGCAAAATTTCTGAAAGAACTGTGCACAAAAAAAATAAGCTCTAAGGAAACGAATGGGTAAAT
38452033 ATGGGAGAAAACGTTTCTGCAATACTACAAAGGAAAATTTCACCTAAGTGTAAGGACCAATGTAT
456 ATGGGAGAAAACGTTTCTGCAATACTACAAAGGAAAATTTCACCTAAGTGTAAGGACCAATGTAT
38452098 GTTTTCTATATCCTGCAAAATAGATAATATTGACATAAAGAAAGCAATGTGTGATTTAGAAGTAT
521 GTTTTCTATATCCTGCAAAATAGATAATATTGACATAAAGAAAGCAATGTGTGATTTAGAAGTAT
38452163 CTATTAATGTAATGCCTTTATCTATTTTTAAATTTCTAAACTCGGGTCATTTGAAAGAAGCAGGT
586 CTATTAATGTAATGCCTTTATCTATTTTTAAATTTCTAAACTCGGGTCATTTGAAAGAAGCAGGT
38452228 GTGATTATTCAATTGGTAGATAGGTCTTGCGTATATCCAGAAGGGGTATTGGACGATGTCCTCGT
651 GTGATTATTCAATTGGTAGATAGGTCTTGCGTATATCCAGAAGGGGTATTGGACGATGTCCTCGT
38452293 ATAGGT
716 ATAGGT
38452299 GAAAAGTTCCAACAAAAGACCGAAGCGTATCTTCAGGAAATGGATCAGCAAATAAGTAAGTTAGC
1 GAAAAGTTCCAACAAAAGACCGAAGCGTATCTTCAGGAAATGGATCAGCAAATAAGTAAGTTAGC
38452364 ACTTACATTTAGTTGTTTGGAGAATAAGGAACTACCGTCTCAAACTGAGCCAAACCCACGTCAAA
66 ACTTACATTTAGTTGTTTGGAGAATAAGGAACTACCGTCTCAAACTGAGCCAAACCCACGTCAAA
38452429 ATACAATTGTTGTGACCATAAAGGATGCGTTAGGACTAGTGCTTGGCATAAGTTGTGACCACAAT
131 ATACAATTGTTGTGACCATAAAGGATGCGTTAGGACTAGTGCTTGGCATAAGTTGTGACCACAAT
38452494 GTTGAACAAGAAGAACAAAAGGCCAAACTAGTAGCTACCATAGAGCCGACACCACATAAACCATT
196 GTTGAACAAGAAGAACAAAAGGCCAAACTAGTAGCTACCATAGAGCCGACACCACATAAACCATT
38452559 TGTTGTACCTCCCCTATAGCCTGGAAGGCTCGCCCAAGTTAAAAAGGAACGAAAGAAAAAAATCC
261 TGTTGTACCTCCCCTATAGCCTGGAAGGCTCGCCCAAGTTAAAAAGGAACGAAAGAAAAAAATCC
38452624 TTGATATATTCTAAAAGGTAAAAATTAATATTACTTTACTTGATGCAATTAAGTAGGTTCCACGC
326 TTGATATATTCTAAAAGGTAAAAATTAATATTACTTTACTTGATGCAATTAAGTAGGTTCCACGC
38452689 TATGCAAAATTTCTGAAAGAACTGTGCACAAAAAAAATAAGCTCTAAGGAAACGAATGGGTAAAT
391 TATGCAAAATTTCTGAAAGAACTGTGCACAAAAAAAATAAGCTCTAAGGAAACGAATGGGTAAAT
38452754 ATGGGAGAAAACGTTTCTGCAATACTACAAAGGAAAATTTCACCTAAGTGTAAGGACCAATGTAT
456 ATGGGAGAAAACGTTTCTGCAATACTACAAAGGAAAATTTCACCTAAGTGTAAGGACCAATGTAT
38452819 GTTTTCTATATCCTGCAAAATAGATAATATTGACATAAAGAAAGCAATGTGTGATTTAGAAGTAT
521 GTTTTCTATATCCTGCAAAATAGATAATATTGACATAAAGAAAGCAATGTGTGATTTAGAAGTAT
38452884 CTATTAATGTAATGCCTTTATCTATTTTTAAATTTCTAAACTCGGGTCATTTGAAAGAAGCAGGT
586 CTATTAATGTAATGCCTTTATCTATTTTTAAATTTCTAAACTCGGGTCATTTGAAAGAAGCAGGT
38452949 GTGATTATTCAATTGGTAGATAGGTCTTGCGTATATCCAGAAGGGGTATTGGACGATGTCCTCGT
651 GTGATTATTCAATTGGTAGATAGGTCTTGCGTATATCCAGAAGGGGTATTGGACGATGTCCTCGT
38453014 ATAGGT
716 ATAGGT
38453020 AAATGAACTA
Statistics
Matches: 721, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
721 721 1.00
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (721 bp):
GAAAAGTTCCAACAAAAGACCGAAGCGTATCTTCAGGAAATGGATCAGCAAATAAGTAAGTTAGC
ACTTACATTTAGTTGTTTGGAGAATAAGGAACTACCGTCTCAAACTGAGCCAAACCCACGTCAAA
ATACAATTGTTGTGACCATAAAGGATGCGTTAGGACTAGTGCTTGGCATAAGTTGTGACCACAAT
GTTGAACAAGAAGAACAAAAGGCCAAACTAGTAGCTACCATAGAGCCGACACCACATAAACCATT
TGTTGTACCTCCCCTATAGCCTGGAAGGCTCGCCCAAGTTAAAAAGGAACGAAAGAAAAAAATCC
TTGATATATTCTAAAAGGTAAAAATTAATATTACTTTACTTGATGCAATTAAGTAGGTTCCACGC
TATGCAAAATTTCTGAAAGAACTGTGCACAAAAAAAATAAGCTCTAAGGAAACGAATGGGTAAAT
ATGGGAGAAAACGTTTCTGCAATACTACAAAGGAAAATTTCACCTAAGTGTAAGGACCAATGTAT
GTTTTCTATATCCTGCAAAATAGATAATATTGACATAAAGAAAGCAATGTGTGATTTAGAAGTAT
CTATTAATGTAATGCCTTTATCTATTTTTAAATTTCTAAACTCGGGTCATTTGAAAGAAGCAGGT
GTGATTATTCAATTGGTAGATAGGTCTTGCGTATATCCAGAAGGGGTATTGGACGATGTCCTCGT
ATAGGT
Found at i:38455336 original size:13 final size:13
Alignment explanation
Indices: 38455318--38455373 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
38455308 AAATTTGAAT
38455318 TATTTAGTGATAA
1 TATTTAGTGATAA
*
38455331 TATTTAGTGATCA
1 TATTTAGTGATAA
38455344 TATTTAG-GAT--
1 TATTTAGTGATAA
38455354 TATTTAGTGATAA
1 TATTTAGTGATAA
38455367 TATTTAG
1 TATTTAG
38455374 AAAAAATCTA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 7 0.18
11 3 0.08
12 3 0.08
13 26 0.67
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:38456580 original size:21 final size:22
Alignment explanation
Indices: 38456556--38456596 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38456546 TAATAACTGA
*
38456556 ATATTTTA-TATAATTTTTTTC
1 ATATTTTATTAGAATTTTTTTC
38456577 ATATTTTATTAGAATTTTTT
1 ATATTTTATTAGAATTTTTT
38456597 AAGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTTTATTAGAATTTTTTTC
Found at i:38456697 original size:19 final size:19
Alignment explanation
Indices: 38456675--38456733 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
38456665 TATTAAAATT
38456675 TTTATTAAGTTTTATAATA
1 TTTATTAAGTTTTATAATA
* * *
38456694 TTTATAAATTTTTATGAT-
1 TTTATTAAGTTTTATAATA
38456712 TCTT-TTAAGTTTTTATAA-A
1 T-TTATTAAG-TTTTATAATA
38456731 TTT
1 TTT
38456734 TGTAATTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 6 0.19
19 25 0.81
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATTAAGTTTTATAATA
Found at i:38456707 original size:10 final size:10
Alignment explanation
Indices: 38456654--38456790 Score: 71
Period size: 10 Copynumber: 14.5 Consensus size: 10
38456644 TTTATTGCTT
38456654 TTTTTAT-AA
1 TTTTTATAAA
38456663 TTTATTA-AAA
1 TTT-TTATAAA
*
38456673 TTTTTATTAA
1 TTTTTATAAA
*
38456683 GTTTTAT-AA
1 TTTTTATAAA
*
38456692 TATTTATAAA
1 TTTTTATAAA
*
38456702 TTTTTAT-GA
1 TTTTTATAAA
*
38456711 TTCTTT-TAAG
1 TT-TTTATAAA
38456721 TTTTTATAAA
1 TTTTTATAAA
*
38456731 -TTTTGT-AA
1 TTTTTATAAA
* *
38456739 --TTTCTAAG
1 TTTTTATAAA
*
38456747 TTTATATAAA
1 TTTTTATAAA
38456757 TTTTTAGT--A
1 TTTTTA-TAAA
38456766 TTTTTATAAA
1 TTTTTATAAA
* *
38456776 TTTTAATAAC
1 TTTTTATAAA
38456786 TTTTT
1 TTTTT
38456791 TATTATAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 25
0.69 0.14 0.18
Matches are distributed among these distances:
7 4 0.04
8 4 0.04
9 32 0.33
10 55 0.57
11 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (10 bp):
TTTTTATAAA
Found at i:38457513 original size:27 final size:27
Alignment explanation
Indices: 38457475--38457529 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
38457465 TCTAGTATTG
38457475 TATAAAAAAGAACATATATGATAAGAA
1 TATAAAAAAGAACATATATGATAAGAA
38457502 TATAAAAAAGAACATATATGATAAGAA
1 TATAAAAAAGAACATATATGATAAGAA
38457529 T
1 T
38457530 CTATAGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.24
Consensus pattern (27 bp):
TATAAAAAAGAACATATATGATAAGAA
Found at i:38462670 original size:9 final size:9
Alignment explanation
Indices: 38462653--38462689 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38462643 TGAGTTTTTG
38462653 AATTCGAAT
1 AATTCGAAT
*
38462662 AACTCGAAT
1 AATTCGAAT
38462671 AATTCGAAT
1 AATTCGAAT
38462680 AATTCGAAT
1 AATTCGAAT
38462689 A
1 A
38462690 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38463421 original size:5 final size:5
Alignment explanation
Indices: 38463411--38463437 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
38463401 TTCAAAAATT
38463411 TTCGA TTCGA TTCGA TTCGA TTCGA TT
1 TTCGA TTCGA TTCGA TTCGA TTCGA TT
38463438 GAATGCTCAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (5 bp):
TTCGA
Found at i:38468537 original size:61 final size:61
Alignment explanation
Indices: 38468442--38468563 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
38468432 CTAGCCAATT
38468442 TTTCATTTTACGCGATTAAGTCATTTTTCTTTAATCGATCACTCAAACGACAAAATTAAAA
1 TTTCATTTTACGCGATTAAGTCATTTTTCTTTAATCGATCACTCAAACGACAAAATTAAAA
*
38468503 TTTCATTTTACGCGATTAAGTCCTTTTTCTTTAATCGATCACTCAAACGACAAAATTAAAA
1 TTTCATTTTACGCGATTAAGTCATTTTTCTTTAATCGATCACTCAAACGACAAAATTAAAA
38468564 CACGAAAATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (61 bp):
TTTCATTTTACGCGATTAAGTCATTTTTCTTTAATCGATCACTCAAACGACAAAATTAAAA
Found at i:38473793 original size:13 final size:13
Alignment explanation
Indices: 38473775--38473802 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
38473765 TGTGATTAAT
38473775 TAGCTTAAAACCA
1 TAGCTTAAAACCA
38473788 TAGCTTAAAACCA
1 TAGCTTAAAACCA
38473801 TA
1 TA
38473803 TGTTTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (13 bp):
TAGCTTAAAACCA
Found at i:38474954 original size:27 final size:27
Alignment explanation
Indices: 38474898--38474962 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
38474888 TGGCAAACAA
** *
38474898 GTGTATGCCATTAGGTCTGGCGAGTAG
1 GTGTATGCCAGCAGGTCTGGCAAGTAG
38474925 GTGTATGCCAGCAGGTCTGGCAAGCT-G
1 GTGTATGCCAGCAGGTCTGGCAAG-TAG
*
38474952 GTGTTTGCCAG
1 GTGTATGCCAG
38474963 TGGATTTGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (27 bp):
GTGTATGCCAGCAGGTCTGGCAAGTAG
Found at i:38478172 original size:17 final size:17
Alignment explanation
Indices: 38478150--38478268 Score: 77
Period size: 17 Copynumber: 6.8 Consensus size: 17
38478140 ATTTTCTTAT
38478150 AAAATATTAAAAAATTA
1 AAAATATTAAAAAATTA
*
38478167 AAAATA--AAAAAGTATA
1 AAAATATTAAAAAAT-TA
*
38478183 AAAAGTATT-AAATATTA
1 AAAA-TATTAAAAAATTA
*
38478200 AAAATATTAAAATTGATATA
1 AAAATATTAAAA--AAT-TA
*
38478220 AAATTA-TAAAAATTATTA
1 AAAATATTAAAAA--ATTA
*
38478238 AAAATGA-TAAAAACTTA
1 AAAAT-ATTAAAAAATTA
38478255 AAAATATTAGAAAA
1 AAAATATTA-AAAA
38478269 NNNNNNNNNN
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
15 6 0.07
16 11 0.14
17 27 0.33
18 14 0.17
19 16 0.20
20 7 0.09
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (17 bp):
AAAATATTAAAAAATTA
Found at i:38478184 original size:16 final size:16
Alignment explanation
Indices: 38478159--38478258 Score: 53
Period size: 19 Copynumber: 5.8 Consensus size: 16
38478149 TAAAATATTA
38478159 AAAAATT-AAAAATA-
1 AAAAATTAAAAAATAT
*
38478173 AAAAAGTATAAAAAGTATT
1 AAAAA-T-TAAAAAATA-T
*
38478192 AAATATT-AAAAATAT
1 AAAAATTAAAAAATAT
*
38478207 TAAAATTGATATAAAATTAT
1 AAAAATT-A-A-AAAA-TAT
38478227 AAAAATTATTAAAAATGAT
1 AAAAATTA--AAAAAT-AT
38478246 AAAAACTTAAAAA
1 AAAAA-TTAAAAA
38478259 TATTAGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
14 5 0.07
15 7 0.10
16 7 0.10
17 7 0.10
18 7 0.10
19 20 0.30
20 14 0.21
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAAAATAT
Found at i:38478185 original size:9 final size:8
Alignment explanation
Indices: 38478150--38478261 Score: 61
Period size: 9 Copynumber: 12.9 Consensus size: 8
38478140 ATTTTCTTAT
38478150 AAAATATTA
1 AAAATA-TA
38478159 AAAA-ATTA
1 AAAATA-TA
38478167 AAAATA-A
1 AAAATATA
38478174 AAAAGTATA
1 AAAA-TATA
38478183 AAAAGTAT-
1 AAAA-TATA
*
38478191 TAAATATTA
1 AAAATA-TA
38478200 AAAATATTA
1 AAAATA-TA
38478209 AAATTGATATA
1 AAA---ATATA
*
38478220 AAATTATA
1 AAAATATA
38478228 AAAATTATTA
1 AAAA-TA-TA
38478238 AAAATGATA
1 AAAAT-ATA
38478247 AAAACT-TA
1 AAAA-TATA
38478255 AAAATAT
1 AAAATAT
38478262 TAGAAAANNN
Statistics
Matches: 86, Mismatches: 4, Indels: 27
0.74 0.03 0.23
Matches are distributed among these distances:
7 8 0.09
8 28 0.33
9 34 0.40
10 8 0.09
11 5 0.06
12 3 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (8 bp):
AAAATATA
Found at i:38478202 original size:26 final size:25
Alignment explanation
Indices: 38478150--38478211 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
38478140 ATTTTCTTAT
38478150 AAAATATTAAAAA--ATTAAAAATAA
1 AAAATA-TAAAAAGTATTAAAAATAA
* *
38478174 AAAAGTATAAAAAGTATTAAATATTA
1 AAAA-TATAAAAAGTATTAAAAATAA
*
38478200 AAAATATTAAAA
1 AAAATATAAAAA
38478212 TTGATATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 10 0.31
25 9 0.28
26 13 0.41
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.27
Consensus pattern (25 bp):
AAAATATAAAAAGTATTAAAAATAA
Found at i:38478239 original size:29 final size:26
Alignment explanation
Indices: 38478197--38478268 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 26
38478187 GTATTAAATA
* *
38478197 TTAAAAATATTAAAATTGATATAAAAT
1 TTAAAAATATTAAAAATGATA-AAAAC
38478224 TATAAAAATTATTAAAAATGATAAAAAC
1 T-TAAAAA-TATTAAAAATGATAAAAAC
38478252 TTAAAAATATTAGAAAA
1 TTAAAAATATTA-AAAA
38478269 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
26 5 0.12
27 11 0.28
28 11 0.28
29 13 0.32
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (26 bp):
TTAAAAATATTAAAAATGATAAAAAC
Found at i:38478392 original size:21 final size:21
Alignment explanation
Indices: 38478368--38478412 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
38478358 AAAATCTAAT
38478368 AAAT-TATTTATAAAATTTATA
1 AAATATATTTA-AAAATTTATA
*
38478389 AAATATATTTAAAATTTTATA
1 AAATATATTTAAAAATTTATA
38478410 AAA
1 AAA
38478413 ACCTGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AAATATATTTAAAAATTTATA
Found at i:38481672 original size:26 final size:26
Alignment explanation
Indices: 38481620--38481673 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
38481610 TCGAACCGAG
** *
38481620 TAAGATGGAATTAGAATTGAATTGAA
1 TAAGATGGAATTAGAATCAAATCGAA
*
38481646 TAAGATGGAATTCGAATCAAATCGAA
1 TAAGATGGAATTAGAATCAAATCGAA
38481672 TA
1 TA
38481674 TATTTGTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (26 bp):
TAAGATGGAATTAGAATCAAATCGAA
Found at i:38486001 original size:27 final size:29
Alignment explanation
Indices: 38485953--38486016 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
38485943 TAAAAATGTA
*
38485953 TTAAAAATATTTTTA-TAATTTTT-AATT
1 TTAAAAATATTTCTATTAATTTTTGAATT
*
38485980 TTAAAAATAATTTCTATT-TTTTTTGAATT
1 TTAAAAAT-ATTTCTATTAATTTTTGAATT
*
38486009 TTTAAAAT
1 TTAAAAAT
38486017 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 8 0.26
28 11 0.35
29 12 0.39
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
TTAAAAATATTTCTATTAATTTTTGAATT
Found at i:38486002 original size:28 final size:28
Alignment explanation
Indices: 38485953--38486016 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
38485943 TAAAAATGTA
*
38485953 TTAAAAATATTTTTATAATTTTT-AATT
1 TTAAAAATATTTCTATAATTTTTGAATT
**
38485980 TTAAAAATAATTTCTATTTTTTTTGAATT
1 TTAAAAAT-ATTTCTATAATTTTTGAATT
*
38486009 TTTAAAAT
1 TTAAAAAT
38486017 TTCAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 8 0.26
28 12 0.39
29 11 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTAAAAATATTTCTATAATTTTTGAATT
Found at i:38486189 original size:3 final size:3
Alignment explanation
Indices: 38486181--38486211 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38486171 TTAAATTGAC
38486181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38486212 AAAGTTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38487579 original size:14 final size:14
Alignment explanation
Indices: 38487560--38487588 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38487550 ATAGAAACAC
38487560 TCAAAAACCCAATA
1 TCAAAAACCCAATA
38487574 TCAAAAACCCAATA
1 TCAAAAACCCAATA
38487588 T
1 T
38487589 ATGTATCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (14 bp):
TCAAAAACCCAATA
Found at i:38491408 original size:102 final size:102
Alignment explanation
Indices: 38491284--38491486 Score: 388
Period size: 102 Copynumber: 2.0 Consensus size: 102
38491274 GAGATTGACA
*
38491284 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACATGAATGATCTCAATGGC
1 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
*
38491349 AATCTAAATGATCACATTGAGAATCTTCACATGGGCT
66 AATCTAAATGATCACATTGAGAATCCTCACATGGGCT
38491386 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
1 GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
38491451 AATCTAAATGATCACATTGAGAATCCTCACATGGGC
66 AATCTAAATGATCACATTGAGAATCCTCACATGGGC
38491487 CGTGTGGTGG
Statistics
Matches: 99, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.43, C:0.13, G:0.21, T:0.22
Consensus pattern (102 bp):
GAACTTTACAGAGAAAGAGAAAAGAATTGAGAAAAATGGTTAGAAACAGGAATGATCTCAATGGC
AATCTAAATGATCACATTGAGAATCCTCACATGGGCT
Found at i:38493971 original size:12 final size:12
Alignment explanation
Indices: 38493954--38493981 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38493944 GACCTATCAG
38493954 TTTTGATGAACA
1 TTTTGATGAACA
38493966 TTTTGATGAACA
1 TTTTGATGAACA
38493978 TTTT
1 TTTT
38493982 TTGGTAGCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (12 bp):
TTTTGATGAACA
Found at i:38506948 original size:27 final size:27
Alignment explanation
Indices: 38506918--38506979 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
38506908 ACCTAAATCC
38506918 AAATGTAAAAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
* *
38506945 AAATGGAAAACCCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGTTTCATTA
38506972 AAATGTAA
1 AAATGTAA
38506980 TACCTACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (27 bp):
AAATGTAAAAACCTTATGGTTTCATTA
Found at i:38507921 original size:27 final size:27
Alignment explanation
Indices: 38507865--38507922 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
38507855 AGGTCAAAAC
* * *
38507865 TTTATTTTAAAAATTTAAAATTTTTAT
1 TTTATTTTAAAAATCTAAAATCTCTAT
* *
38507892 TTTATTTTTAAAAATCTAAACTCTCTTT
1 TTTA-TTTTAAAAATCTAAAATCTCTAT
38507920 TTT
1 TTT
38507923 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATTTTAAAAATCTAAAATCTCTAT
Found at i:38508222 original size:148 final size:149
Alignment explanation
Indices: 38507890--38508229 Score: 424
Period size: 148 Copynumber: 2.3 Consensus size: 149
38507880 TAAAATTTTT
*
38507890 ATTTTATTTTT-AAAAATCTAAAC--TCTC-TTTTTTTAAAAAAAAAGTCACTATTTTTCTTAAA
1 ATTTT-TTTTTGAAAAATCTAAACTTTCTCATTTTTTT---TAAAAAGTCACTATTTTTCTTAAA
* * * * *
38507951 AGTTAAAGCTTTATTTCGAAATGGTTGAACAAGATCAAAACGTTGTTGTAAAAAATTTAAACTTT
62 AATCAAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTT
38508016 TCCTTTAAAATGACTAAAAAAAG
127 TCCTTTAAAATGACTAAAAAAAG
*
38508039 ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTTAAAA-TCACTATTTTTCTTAAAAATC
1 ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTAAAAAGTCACTATTTTTCTTAAAAATC
* * * *
38508103 AAAACTTTATTTCGAAATTGTTGAAAAAGATTAAAACTTTGTT-TTAAAAATTTAAAATTTTCCT
66 AAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTTTCCT
* * *
38508167 TTAATATGACTAAAAACAT
131 TTAAAATGACTAAAAAAAG
* * *
38508186 ATTTTTATTTT-AAAACTTTAAACTTTCTCTTTTTTTTTTAAAAA
1 ATTTTT-TTTTGAAAAATCTAAACTTTCTC-ATTTTTTTTAAAAA
38508230 AAAGATCAAA
Statistics
Matches: 167, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
147 57 0.34
148 78 0.47
149 21 0.13
151 4 0.02
152 7 0.04
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.44
Consensus pattern (149 bp):
ATTTTTTTTTGAAAAATCTAAACTTTCTCATTTTTTTTAAAAAGTCACTATTTTTCTTAAAAATC
AAAACTTTATTTCGAAATGGTTGAAAAAGATCAAAACGTTGTTGTAAAAAATTTAAAATTTTCCT
TTAAAATGACTAAAAAAAG
Found at i:38508553 original size:39 final size:39
Alignment explanation
Indices: 38508498--38508699 Score: 273
Period size: 39 Copynumber: 5.2 Consensus size: 39
38508488 TAGTAGATAA
*
38508498 CTGTTGTACTTCGGTACCCCTGACCGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* *
38508537 CTGTTGTACTTTGGTACCCCTGATTGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * *
38508576 TTGTTGTACTTCGGTACCCCTGATCAG-ACTTACGTTCCC
1 CTGTTGTACTTCGGTACCCCTGA-CTGCACTTACGTGCCC
38508615 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
1 CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
* * * * *
38508654 CTGTTGTACTTCAGTA-CCCTTATTTGCACTCATGTGCCC
1 CTGTTGTACTTCGGTACCCCTGA-CTGCACTTACGTGCCC
38508693 CTGTTGT
1 CTGTTGT
38508700 TCGGTACGCC
Statistics
Matches: 144, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
38 7 0.05
39 136 0.94
40 1 0.01
ACGTcount: A:0.13, C:0.33, G:0.19, T:0.35
Consensus pattern (39 bp):
CTGTTGTACTTCGGTACCCCTGACTGCACTTACGTGCCC
Found at i:38508606 original size:20 final size:20
Alignment explanation
Indices: 38508503--38508637 Score: 68
Period size: 19 Copynumber: 6.9 Consensus size: 20
38508493 GATAACTGTT
**
38508503 GTACTTCGGTACCCCTGACC
1 GTACTTCGGTACCCCTGATA
* * *
38508523 GCACTTAC-GTGCCCCTG-TT
1 GTACTT-CGGTACCCCTGATA
* *
38508542 GTACTTTGGTACCCCTGATT
1 GTACTTCGGTACCCCTGATA
* * * *
38508562 GCACTTAC-GTGCCCTTG-TT
1 GTACTT-CGGTACCCCTGATA
38508581 GTACTTCGGTACCCCTGATCA
1 GTACTTCGGTACCCCTGAT-A
* *
38508602 G-ACTTAC-GTTCCCCTG-TT
1 GTACTT-CGGTACCCCTGATA
38508620 GTACTTCGGTACCCCTGA
1 GTACTTCGGTACCCCTGA
38508638 CTGCACTTAC
Statistics
Matches: 86, Mismatches: 18, Indels: 22
0.68 0.14 0.17
Matches are distributed among these distances:
18 3 0.03
19 40 0.47
20 40 0.47
21 3 0.03
ACGTcount: A:0.14, C:0.33, G:0.20, T:0.33
Consensus pattern (20 bp):
GTACTTCGGTACCCCTGATA
Found at i:38508654 original size:20 final size:20
Alignment explanation
Indices: 38508511--38508656 Score: 97
Period size: 20 Copynumber: 7.5 Consensus size: 20
38508501 TTGTACTTCG
**
38508511 GTACCCCTGACCGCACTTAC
1 GTACCCCTGATTGCACTTAC
* * **
38508531 GTGCCCCTG-TTGTACTTTG
1 GTACCCCTGATTGCACTTAC
38508550 GTACCCCTGATTGCACTTAC
1 GTACCCCTGATTGCACTTAC
* * *
38508570 GTGCCCTTG-TTGTACTT-C
1 GTACCCCTGATTGCACTTAC
*
38508588 GGTACCCCTGATCAG-ACTTAC
1 -GTACCCCTGAT-TGCACTTAC
* *
38508609 GTTCCCCTG-TTGTACTT-C
1 GTACCCCTGATTGCACTTAC
*
38508627 GGTACCCCTGACTGCACTTAC
1 -GTACCCCTGATTGCACTTAC
*
38508648 GTGCCCCTG
1 GTACCCCTG
38508657 TTGTACTTCA
Statistics
Matches: 95, Mismatches: 22, Indels: 18
0.70 0.16 0.13
Matches are distributed among these distances:
18 3 0.03
19 40 0.42
20 49 0.52
21 3 0.03
ACGTcount: A:0.14, C:0.35, G:0.20, T:0.32
Consensus pattern (20 bp):
GTACCCCTGATTGCACTTAC
Done.