Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 106 of 202
Found at i:32353189 original size:11 final size:11
Alignment explanation
Indices: 32353173--32353201 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
32353163 TTGTGATTTT
32353173 AAAAAAATTCA
1 AAAAAAATTCA
32353184 AAAAAAA-TCA
1 AAAAAAATTCA
32353194 AAAAAAAT
1 AAAAAAAT
32353202 GTGAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:32355179 original size:506 final size:505
Alignment explanation
Indices: 32354227--32355237 Score: 1968
Period size: 506 Copynumber: 2.0 Consensus size: 505
32354217 TCACCCGATC
32354227 TGATACGGGGTGGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGCTC
1 TGATACGGGGTGGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGCTC
32354292 TAAACGAACAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTAGAATTAAATC
66 TAAACGAACAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTAGAATTAAATC
32354357 CCCAAATTCAATTAAATGAACAGCAAGACACAAAGAACGAATGAATAGATGTTTTCGTAGTTCAA
131 CCCAAATTCAATTAAATGAACAGCAAGACACAAAGAACGAATGAATAGATGTTTTCGTAGTTCAA
*
32354422 GAAGACAAAATCGAACTCCAAGATCAATTCTCCACAAGCCGAATCTGTTCAAGAACACTAAACAG
196 GAAGACAAAATCGAACTCCAAGATCAATTCCCCACAAGCCGAATCTGTTCAAGAACACTAAACAG
32354487 CAACGAATTAAATCAATCAGATCTTTAATAGAAAATTAGGGATTTGGGCGACAAAAGAAAAGAAA
261 CAACGAATTAAATCAATCAGATCTTTAATAGAAAATTAGGGATTTGGGCGACAAAAGAAAAGAAA
*
32354552 GAAATTAATGAAATTGAATGAATTTGGAAGTAAAGAAAGAGTGCTAATCTGTCAATAACTTGAAT
326 GAAATTAATGAAATTGAACGAATTTGGAAGTAAAGAAAGAGTGCTAATCTGTCAATAACTTGAAT
32354617 CGACCAAGAATGCCCAAATTCCAGCAGCCTAATTTCACCCAACAAGAAGAAATAAAAAAAGAATG
391 CGACCAAGAATGCCCAAATTCCAGCAGCCTAATTTCACCCAACAAGAAGAAAT-AAAAAAGAATG
32354682 GCAAGAACCCTAAATTTTGGGGATTTTTGGATCGAATAGTTGCTGCCAATA
455 GCAAGAACCCTAAATTTTGGGGATTTTTGGATCGAATAGTTGCTGCCAATA
32354733 TGATACGGGGTGGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGCTC
1 TGATACGGGGTGGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGCTC
*
32354798 TAAACGAACAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTGGAATTAAATC
66 TAAACGAACAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTAGAATTAAATC
*
32354863 CCCAAATTCAATTAAATGATCAGCAAGACACAAAGAACGAATGAATAGATGTTTTCGTAGTTCAA
131 CCCAAATTCAATTAAATGAACAGCAAGACACAAAGAACGAATGAATAGATGTTTTCGTAGTTCAA
32354928 GAAGACAAAATCGAACTCCAAGATCAATTCCCCACAAGCCGAATCTGTTCAAGAACACTAAACAG
196 GAAGACAAAATCGAACTCCAAGATCAATTCCCCACAAGCCGAATCTGTTCAAGAACACTAAACAG
32354993 CAACGAATTAAATCAATCAGATCTTTAATAGAAAATTAGGGATTTGGGCGACAAAAGAAAAGAAA
261 CAACGAATTAAATCAATCAGATCTTTAATAGAAAATTAGGGATTTGGGCGACAAAAGAAAAGAAA
32355058 GAAATTAATGAAATTGAACGAATTTGGAAGTAAAGAAAGAGTGCTAATCTGTCAATAACTTGAAT
326 GAAATTAATGAAATTGAACGAATTTGGAAGTAAAGAAAGAGTGCTAATCTGTCAATAACTTGAAT
*
32355123 CGGCCAAGAATGCCCAAATTCCAGCAGCCTAATTTCACCCAACAAGAAGAAATAAAAAAGAATGG
391 CGACCAAGAATGCCCAAATTCCAGCAGCCTAATTTCACCCAACAAGAAGAAATAAAAAAGAATGG
32355188 CAAGAACCCTAAATTTTGGGGATTTTTGGATCGAATAGTTGCTGCCAATA
456 CAAGAACCCTAAATTTTGGGGATTTTTGGATCGAATAGTTGCTGCCAATA
32355238 AAAGGGATCG
Statistics
Matches: 500, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
505 62 0.12
506 438 0.88
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (505 bp):
TGATACGGGGTGGCGCGCGGACCAAGATCGAGTTGCCAAGTCACGAGAAACTCCTACGAAAGCTC
TAAACGAACAGATCTGAAATTAAAACAAAGAACAAGATTAAACTAATCAGATCTAGAATTAAATC
CCCAAATTCAATTAAATGAACAGCAAGACACAAAGAACGAATGAATAGATGTTTTCGTAGTTCAA
GAAGACAAAATCGAACTCCAAGATCAATTCCCCACAAGCCGAATCTGTTCAAGAACACTAAACAG
CAACGAATTAAATCAATCAGATCTTTAATAGAAAATTAGGGATTTGGGCGACAAAAGAAAAGAAA
GAAATTAATGAAATTGAACGAATTTGGAAGTAAAGAAAGAGTGCTAATCTGTCAATAACTTGAAT
CGACCAAGAATGCCCAAATTCCAGCAGCCTAATTTCACCCAACAAGAAGAAATAAAAAAGAATGG
CAAGAACCCTAAATTTTGGGGATTTTTGGATCGAATAGTTGCTGCCAATA
Found at i:32366805 original size:22 final size:22
Alignment explanation
Indices: 32366777--32366929 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
32366767 TTTATTGTTC
*
32366777 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
32366799 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
32366821 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
32366843 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
32366865 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
32366887 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
32366909 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
32366930 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:32369912 original size:22 final size:22
Alignment explanation
Indices: 32369879--32369932 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
32369869 TTTAAGTCGA
32369879 TTTAAT-TAGTTTATTACA-GCTT
1 TTTAATAT-GTTTATTACATG-TT
* *
32369901 TTTAATATGTTTGTTGCATGTT
1 TTTAATATGTTTATTACATGTT
32369923 TTTAATATGT
1 TTTAATATGT
32369933 CAAGTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 26 0.93
23 2 0.07
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTAATATGTTTATTACATGTT
Found at i:32370967 original size:22 final size:22
Alignment explanation
Indices: 32370939--32371002 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
32370929 CCTTTTTGAA
32370939 CCATTACCATTTCGTACCAAAT
1 CCATTACCATTTCGTACCAAAT
* **
32370961 CCATTACCATTTTGTGTCAAAT
1 CCATTACCATTTCGTACCAAAT
*
32370983 CCTTTACCATTTCGTACCAA
1 CCATTACCATTTCGTACCAA
32371003 TTCCCAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.28, C:0.30, G:0.06, T:0.36
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:32390739 original size:11 final size:11
Alignment explanation
Indices: 32390723--32390763 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
32390713 ACGAGATTGT
32390723 AAAAAAATCAA
1 AAAAAAATCAA
*
32390734 AAAAAATTCGAA
1 AAAAAAATC-AA
*
32390746 AAAAAATTCAA
1 AAAAAAATCAA
32390757 AAAAAAA
1 AAAAAAA
32390764 GTTTGTATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:32390763 original size:12 final size:11
Alignment explanation
Indices: 32390723--32390762 Score: 64
Period size: 12 Copynumber: 3.6 Consensus size: 11
32390713 ACGAGATTGT
32390723 AAAAAAA-TCA
1 AAAAAAATTCA
32390733 AAAAAAATTCGA
1 AAAAAAATTC-A
32390745 AAAAAAATTCA
1 AAAAAAATTCA
32390756 AAAAAAA
1 AAAAAAA
32390763 AGTTTGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 7 0.25
11 10 0.36
12 11 0.39
ACGTcount: A:0.78, C:0.07, G:0.03, T:0.12
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:32390829 original size:18 final size:19
Alignment explanation
Indices: 32390795--32390832 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
32390785 TTCTTTGTGT
*
32390795 ATTCAGTATTGAAAAAAAA
1 ATTCAGAATTGAAAAAAAA
32390814 ATTCAGAATT-AAAAAAAA
1 ATTCAGAATTGAAAAAAAA
32390832 A
1 A
32390833 AGTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATTCAGAATTGAAAAAAAA
Found at i:32390833 original size:19 final size:19
Alignment explanation
Indices: 32390795--32390833 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
32390785 TTCTTTGTGT
* *
32390795 ATTCAGTATTGAAAAAAAA
1 ATTCAGAATTAAAAAAAAA
32390814 ATTCAGAATTAAAAAAAAA
1 ATTCAGAATTAAAAAAAAA
32390833 A
1 A
32390834 GTAATTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (19 bp):
ATTCAGAATTAAAAAAAAA
Found at i:32392862 original size:14 final size:14
Alignment explanation
Indices: 32392843--32392897 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
32392833 TCTATTGAGC
32392843 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
32392857 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
* *
32392871 GAGTGAAATGAAAAA
1 GAG-AAAAAGAAAAA
*
32392886 GAAAGAAAAGAA
1 GAGA-AAAAGAA
32392898 TGATGAGAGC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:32404801 original size:17 final size:18
Alignment explanation
Indices: 32404778--32404839 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 18
32404768 AGATTGAGAA
32404778 TGAAAAAGAAATAGAGTT
1 TGAAAAAGAAATAGAGTT
*
32404796 TG-AAAAGAAATCGAG--
1 TGAAAAAGAAATAGAGTT
*
32404811 TGAAAAAGAAAAAGAGTT
1 TGAAAAAGAAATAGAGTT
*
32404829 TGCAAAAGAAA
1 TGAAAAAGAAA
32404840 CGAGTGAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
15 2 0.05
16 11 0.30
17 12 0.32
18 12 0.32
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.16
Consensus pattern (18 bp):
TGAAAAAGAAATAGAGTT
Found at i:32404815 original size:33 final size:33
Alignment explanation
Indices: 32404778--32404852 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 33
32404768 AGATTGAGAA
*
32404778 TGAAAAAGAAATAGAGTTTG-AAAAGAAATCGAG
1 TGAAAAAGAAAAAGAGTTTGCAAAAGAAA-CGAG
32404811 TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
1 TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
32404844 TGAAGAAAG
1 TGAA-AAAG
32404853 TAATCAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 27 0.69
34 12 0.31
ACGTcount: A:0.56, C:0.04, G:0.25, T:0.15
Consensus pattern (33 bp):
TGAAAAAGAAAAAGAGTTTGCAAAAGAAACGAG
Found at i:32406488 original size:47 final size:47
Alignment explanation
Indices: 32406389--32406494 Score: 122
Period size: 47 Copynumber: 2.3 Consensus size: 47
32406379 CCTGAACTTC
* * * * * *
32406389 TTTAATGTGTCTTGAGTTTATTAATTGTGTTTTATTTAGTACAGCAA
1 TTTAATGTGTCTTAAGTCTATTAAATATGTTCTAATTAGTACAGCAA
* * **
32406436 ATTAATATGTCTTAAGTCTATTAAATATGTTCTAATTAGTACAGCTT
1 TTTAATGTGTCTTAAGTCTATTAAATATGTTCTAATTAGTACAGCAA
32406483 TTTAATGTGTCT
1 TTTAATGTGTCT
32406495 CTAGCTAATA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.49
Consensus pattern (47 bp):
TTTAATGTGTCTTAAGTCTATTAAATATGTTCTAATTAGTACAGCAA
Found at i:32411793 original size:111 final size:111
Alignment explanation
Indices: 32411599--32411820 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
32411589 TTCCAATGGA
*
32411599 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTCGACCCCTTCGTTGAGCCATTGCAATTTAT
1 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTCGACCCCTTCGTTGAGCCATTACAATTTAT
32411664 ATGGGCTCGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
66 ATGGGCTCGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
* *
32411710 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTTGACCCCTTCGTTGAGCCATTACCATTTAT
1 GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTCGACCCCTTCGTTGAGCCATTACAATTTAT
*
32411775 ATGGGCTTGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
66 ATGGGCTCGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
32411821 ATACGTGCTT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (111 bp):
GAATGTGATCATTGCTTGCTTGGTAACCTTTAATTCGACCCCTTCGTTGAGCCATTACAATTTAT
ATGGGCTCGGGTGCTTGATAGTCGGCAAGGCAAGTTTTTCCACCAT
Found at i:32415208 original size:33 final size:33
Alignment explanation
Indices: 32415171--32415266 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
32415161 TGAGTTAATG
32415171 CATGACTTAATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
*
32415204 CATGA---AATTT-A-CAT---AA-TTAAACTAA
1 CATGACTTAATTTAATGATGCAAACTT-AACTAA
32415229 CATGACTTAATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
32415262 CATGA
1 CATGA
32415267 AAGTTACATA
Statistics
Matches: 51, Mismatches: 2, Indels: 20
0.70 0.03 0.27
Matches are distributed among these distances:
24 2 0.04
25 13 0.25
28 7 0.14
29 2 0.04
30 7 0.14
33 18 0.35
34 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (33 bp):
CATGACTTAATTTAATGATGCAAACTTAACTAA
Found at i:32415354 original size:21 final size:22
Alignment explanation
Indices: 32415319--32415360 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
32415309 TAATGATGTG
*
32415319 CAAACTATGAAATAATTAAAACA
1 CAAACTA-GAAATAACTAAAACA
32415342 CAAACTA-AAATAACTAAAA
1 CAAACTAGAAATAACTAAAA
32415361 TAACTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.19
Consensus pattern (22 bp):
CAAACTAGAAATAACTAAAACA
Found at i:32415358 original size:9 final size:9
Alignment explanation
Indices: 32415344--32415369 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
32415334 TTAAAACACA
32415344 AACTAAAAT
1 AACTAAAAT
32415353 AACTAAAAT
1 AACTAAAAT
32415362 AACTAAAA
1 AACTAAAA
32415370 ATTAATGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:32418532 original size:14 final size:15
Alignment explanation
Indices: 32418507--32418535 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
32418497 TGAAAAGTGG
32418507 TCGAGTTGAATTGAA
1 TCGAGTTGAATTGAA
32418522 TCGAG-TGAATTGAA
1 TCGAGTTGAATTGAA
32418536 CCGACCAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (15 bp):
TCGAGTTGAATTGAA
Found at i:32422425 original size:58 final size:58
Alignment explanation
Indices: 32422335--32422452 Score: 220
Period size: 58 Copynumber: 2.0 Consensus size: 58
32422325 TCATCCGATT
32422335 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
1 TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
32422393 TAGCCTTATGCCTAGCTCACATAAGG-CTACAATCTCATTAGAGTGAATGGTCTTATCA
1 TAGCCTTATGCCTAGCTCACAT-AGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
32422451 TA
1 TA
32422453 CTCGATTTTA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
58 56 0.95
59 3 0.05
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (58 bp):
TAGCCTTATGCCTAGCTCACATAGGACTACAATCTCATTAGAGTGAATGGTCTTATCA
Found at i:32442601 original size:20 final size:20
Alignment explanation
Indices: 32442576--32442614 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
32442566 TTACTTCTTC
32442576 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
32442596 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
32442615 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:32447696 original size:92 final size:92
Alignment explanation
Indices: 32447586--32447789 Score: 320
Period size: 92 Copynumber: 2.2 Consensus size: 92
32447576 TAATGTGGAG
*
32447586 CATGCACCCGATTGTGCATGAATGTCGAGAGCTAGTTTTT-AGCTGGACATTCATGTATCTTCCA
1 CATGCACCCGATTGTGCATGAATGTCGAGAGCTA-TTTTTCAGCTGGACATACATGTATCTTCCA
* * *
32447650 GATTCAATGAAGCTACTTTAATGAAGAA
65 GATTCAACGAAGCTAATTTAAAGAAGAA
* * * *
32447678 CATGCACCCGATTTTGCATGAATGTTGGGAGCTATTTTTCAGCTGGACATAGATGTATCTTCCAG
1 CATGCACCCGATTGTGCATGAATGTCGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
32447743 ATTCAACGAAGCTAATTTAAAGAAGAA
66 ATTCAACGAAGCTAATTTAAAGAAGAA
32447770 CATGCACCCGATTGTGCATG
1 CATGCACCCGATTGTGCATG
32447790 TATTTTGAGA
Statistics
Matches: 102, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 5 0.05
92 97 0.95
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Consensus pattern (92 bp):
CATGCACCCGATTGTGCATGAATGTCGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
ATTCAACGAAGCTAATTTAAAGAAGAA
Found at i:32454335 original size:19 final size:18
Alignment explanation
Indices: 32454313--32454351 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
32454303 AGTTCAAGAG
32454313 AAAAAGAAAGAGAATAAAA
1 AAAAAGAAAGAGAA-AAAA
**
32454332 AAAAAGCGAGAGAAAAAA
1 AAAAAGAAAGAGAAAAAA
32454350 AA
1 AA
32454352 TGAGAGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAGAGAAAAAA
Found at i:32454337 original size:15 final size:16
Alignment explanation
Indices: 32454309--32454357 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
32454299 TGAGAGTTCA
*
32454309 AGAGAAAAAGAAAGAG
1 AGAGAAAAAAAAAGAG
* *
32454325 A-ATAAAAAAAAAGCG
1 AGAGAAAAAAAAAGAG
*
32454340 AGAGAAAAAAAATGAG
1 AGAGAAAAAAAAAGAG
32454356 AG
1 AG
32454358 TGACAAAAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.02, G:0.24, T:0.04
Consensus pattern (16 bp):
AGAGAAAAAAAAAGAG
Found at i:32458518 original size:46 final size:46
Alignment explanation
Indices: 32458446--32458544 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
32458436 TAACATTTCA
*
32458446 TACCAAATCGTATTACCATTTCGAACCAAATCACCTTACCAATTCG
1 TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
* *
32458492 TACCAAATCGTATTACCATTTTGAACCAAATCACATTACCATTTCG
1 TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
*
32458538 TAACAAA
1 TACCAAA
32458545 CCCAAAACTG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (46 bp):
TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
Found at i:32458544 original size:23 final size:23
Alignment explanation
Indices: 32458433--32458544 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 23
32458423 CTTTTTGAAC
* * * *
32458433 CATTAACATTTCATACCAAATCG
1 CATTACCATTTCGTAACAAATCA
*
32458456 TATTACCATTTCG-AACCAAATCA
1 CATTACCATTTCGTAA-CAAATCA
* * * *
32458479 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTAACAAATCA
* *
32458502 TATTACCATTTTG-AACCAAATCA
1 CATTACCATTTCGTAA-CAAATCA
32458525 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTAACAAA
32458545 CCCAAAACTG
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 2 0.03
23 62 0.93
24 3 0.04
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTAACAAATCA
Found at i:32458836 original size:15 final size:17
Alignment explanation
Indices: 32458816--32458857 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
32458806 TGAAAAGAAG
32458816 TTAAAAAAAGTTT-G-A
1 TTAAAAAAAGTTTCGAA
32458831 TTAAAAAAAGTTTCGAA
1 TTAAAAAAAGTTTCGAA
32458848 TATAAAAAAA
1 T-TAAAAAAA
32458858 AGTGCTGTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
17 2 0.08
18 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.10, T:0.29
Consensus pattern (17 bp):
TTAAAAAAAGTTTCGAA
Found at i:32466700 original size:42 final size:43
Alignment explanation
Indices: 32466653--32466738 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 43
32466643 TTTCGAGGTG
* *
32466653 TGATTTCATGTAAGACCTTATCTAGGACATTGGCATCG-TATA
1 TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
* * * *
32466695 TGATTTCGTGTAAGACCCTGTCTGGGATAGTGGCATCGATATA
1 TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
32466738 T
1 T
32466739 TATAACATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (43 bp):
TGATTTCATGTAAGACCCTATCTAGGACAGTGGCATCGATATA
Found at i:32473418 original size:20 final size:20
Alignment explanation
Indices: 32473395--32473441 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32473385 GGGTTGAGGT
32473395 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
32473415 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
32473435 TGAGCTG
1 TGAGCTG
32473442 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:32486190 original size:92 final size:92
Alignment explanation
Indices: 32486080--32486293 Score: 322
Period size: 92 Copynumber: 2.3 Consensus size: 92
32486070 TAATGTGGAG
* *
32486080 CATGCACCCGATTGTGCATGAATGTTGAGAGCTAGTTTTT-AGCTGGACATTCATGTATCTTCCG
1 CATGCACCCGATTGTGCATGAATGTTGAGAGCTA-TTTTTCAGCTGGACATACATGTATCTTCCA
* * *
32486144 GATTCAATGAAGCTACTTTAATGAAGAA
65 GATTCAACGAAGCTAATTTAAAGAAGAA
* * *
32486172 CATGCACCCGATTTTGCATGAATGTTGGGAGCTATTTTTCAGCTGGACATAGATGTATCTTCCAG
1 CATGCACCCGATTGTGCATGAATGTTGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
32486237 ATTCAACGAAGCTAATTTAAAGAAGAA
66 ATTCAACGAAGCTAATTTAAAGAAGAA
* *
32486264 CATGCACCCGATTGTGCATGTATTTTGAGA
1 CATGCACCCGATTGTGCATGAATGTTGAGA
32486294 CCTGGTTGGT
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
91 5 0.05
92 104 0.95
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (92 bp):
CATGCACCCGATTGTGCATGAATGTTGAGAGCTATTTTTCAGCTGGACATACATGTATCTTCCAG
ATTCAACGAAGCTAATTTAAAGAAGAA
Found at i:32491436 original size:10 final size:10
Alignment explanation
Indices: 32491421--32491462 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
32491411 TTTGCAAGTT
32491421 TTGAGCTAAA
1 TTGAGCTAAA
* *
32491431 TTGAGCTGAT
1 TTGAGCTAAA
*
32491441 TTGAGCT-CA
1 TTGAGCTAAA
32491450 TTGAGCTAAA
1 TTGAGCTAAA
32491460 TTG
1 TTG
32491463 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:32497292 original size:20 final size:20
Alignment explanation
Indices: 32497267--32497313 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
32497257 AGCTCGTTTC
*
32497267 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
32497287 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
32497307 CAGCTCA
1 CAGCTCA
32497314 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:32501824 original size:46 final size:47
Alignment explanation
Indices: 32501752--32501857 Score: 169
Period size: 46 Copynumber: 2.3 Consensus size: 47
32501742 ATAAGTTAAG
* * *
32501752 TCATTTAATTTGTCTAATTTACTACAGCAATTTAAGTTGTCTTCAGT
1 TCATTTAATTTGTCTAAATTACTACAGCAATTTAAGTTGTCTTAAAT
*
32501799 T-ATTTAATTTGTCTAAATTATTACAGCAATTTAAGTTGTCTTAAAT
1 TCATTTAATTTGTCTAAATTACTACAGCAATTTAAGTTGTCTTAAAT
32501845 TCATTTAATTTGT
1 TCATTTAATTTGT
32501858 TTGTTTACAG
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
46 42 0.78
47 12 0.22
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (47 bp):
TCATTTAATTTGTCTAAATTACTACAGCAATTTAAGTTGTCTTAAAT
Found at i:32502223 original size:31 final size:31
Alignment explanation
Indices: 32502188--32502276 Score: 142
Period size: 31 Copynumber: 2.9 Consensus size: 31
32502178 CACCAAGTCC
* * *
32502188 CTTCATTGCTGATTGTTAACACCTAGAGGCT
1 CTTCATTGCTGATTGTTCACACCTAAAGACT
32502219 CTTCATTGCTGATTGTTCACACCTAAAGACT
1 CTTCATTGCTGATTGTTCACACCTAAAGACT
*
32502250 CTTCATTGCTGATTGTTCACACATAAA
1 CTTCATTGCTGATTGTTCACACCTAAA
32502277 ACTACCCAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.36
Consensus pattern (31 bp):
CTTCATTGCTGATTGTTCACACCTAAAGACT
Found at i:32505109 original size:21 final size:21
Alignment explanation
Indices: 32505084--32505126 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
32505074 AATTAAATTC
32505084 AGCTGGACACCTTAAAAACAT
1 AGCTGGACACCTTAAAAACAT
32505105 AGCTGGACACCTTAAAAACAT
1 AGCTGGACACCTTAAAAACAT
32505126 A
1 A
32505127 CATTAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.23, G:0.14, T:0.19
Consensus pattern (21 bp):
AGCTGGACACCTTAAAAACAT
Found at i:32505188 original size:41 final size:41
Alignment explanation
Indices: 32505142--32505249 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
32505132 AATTCGGCCA
* * *
32505142 AACATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
32505183 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
32505224 AACATGTAGTGGCAGCATTAAATTCG
1 AACATGTAGTGGCAGCATTAAATTCG
32505250 ACATATTAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:32513939 original size:10 final size:10
Alignment explanation
Indices: 32513924--32513985 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
32513914 TTTGAACCAT
*
32513924 TACCAATTCG
1 TACCAATTCA
*
32513934 TACCAAATACCA
1 TACC-AAT-TCA
*
32513946 TACCATTTCA
1 TACCAATTCA
32513956 TACCAATTCCA
1 TACCAATT-CA
* *
32513967 TACCATTTCG
1 TACCAATTCA
32513977 TACCAATTC
1 TACCAATTC
32513986 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:32513969 original size:21 final size:21
Alignment explanation
Indices: 32513924--32513986 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
32513914 TTTGAACCAT
* *
32513924 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
32513946 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
32513967 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
32513987 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:32514324 original size:26 final size:26
Alignment explanation
Indices: 32514309--32514358 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
32514299 AAAAAGTTCG
32514309 AAAAAAATT-GAAAAAAAACAAAAACA
1 AAAAAAATTCGAAAAAAAA-AAAAACA
*
32514335 AAAAAAATTCGAAAGAAAAAAAAA
1 AAAAAAATTCGAAAAAAAAAAAAA
32514359 TTGAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (26 bp):
AAAAAAATTCGAAAAAAAAAAAAACA
Found at i:32514354 original size:17 final size:16
Alignment explanation
Indices: 32514334--32514372 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
32514324 AAACAAAAAC
32514334 AAAAAAAATTCGAAAGA
1 AAAAAAAATT-GAAAGA
32514351 AAAAAAAATTGAAAGA
1 AAAAAAAATTGAAAGA
32514367 AAAAAA
1 AAAAAA
32514373 TTGTATACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAAAAATTGAAAGA
Found at i:32519144 original size:19 final size:19
Alignment explanation
Indices: 32519112--32519176 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
32519102 GAAGAAAAAG
*
32519112 AAAAGAAGACGAAAAT-AACA
1 AAAAGAA-AAGAAAATGAA-A
32519132 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAG-AAAATGAAA
*
32519152 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAA-TGAAA
32519171 AAAAGA
1 AAAAGA
32519177 GAATGAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 4 0.10
19 15 0.38
20 18 0.46
21 2 0.05
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.06
Consensus pattern (19 bp):
AAAAGAAAAGAAAATGAAA
Found at i:32519146 original size:20 final size:20
Alignment explanation
Indices: 32519131--32519186 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
32519121 CGAAAATAAC
*
32519131 AAAAAGAAAAGAAAAATGAA
1 AAAAAGAAAAGAAAAATCAA
*
32519151 AAAAAG-AAAGAAAATTCAA
1 AAAAAGAAAAGAAAAATCAA
*
32519170 AAAAAGAGAATGAAAAA
1 AAAAAGA-AAAGAAAAA
32519187 AAAATGAGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.57
20 6 0.20
21 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAATCAA
Found at i:32519171 original size:37 final size:37
Alignment explanation
Indices: 32519092--32519190 Score: 98
Period size: 37 Copynumber: 2.6 Consensus size: 37
32519082 CCGTAAGAAT
* * *
32519092 ACAAAATGAAGAAGAAAAAGAAAAGAAGACGAAAATA
1 ACAAAAAGAAGAAGAAAAAGAAAAAAAGAAGAAAATA
32519129 ACAAAAAGAA-AAGAAAAATGAAAAAAAGAAAGAAAATTCA
1 ACAAAAAGAAGAAGAAAAA-GAAAAAAAG-AAGAAAA-T-A
32519169 A-AAAAAG-AGAATGAAAAA-AAAA
1 ACAAAAAGAAGAA-GAAAAAGAAAA
32519191 TGAGAAAAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
36 8 0.15
37 17 0.32
38 11 0.21
39 9 0.17
40 8 0.15
ACGTcount: A:0.75, C:0.04, G:0.15, T:0.06
Consensus pattern (37 bp):
ACAAAAAGAAGAAGAAAAAGAAAAAAAGAAGAAAATA
Found at i:32523490 original size:10 final size:10
Alignment explanation
Indices: 32523475--32523536 Score: 52
Period size: 10 Copynumber: 5.9 Consensus size: 10
32523465 TTTGAACCAT
*
32523475 TACCAATTCG
1 TACCAATTCA
*
32523485 TACCAAATACCA
1 TACC-AAT-TCA
*
32523497 TACCATTTCA
1 TACCAATTCA
32523507 TACCAATTCCA
1 TACCAATT-CA
* *
32523518 TACCATTTCG
1 TACCAATTCA
32523528 TACCAATTC
1 TACCAATTC
32523537 CCAAATACCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
10 22 0.54
11 14 0.34
12 5 0.12
ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31
Consensus pattern (10 bp):
TACCAATTCA
Found at i:32523520 original size:21 final size:21
Alignment explanation
Indices: 32523475--32523537 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
32523465 TTTGAACCAT
* *
32523475 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
*
32523497 TACCATTTCATACCAATTCCA
1 TACCATTTCGTACCAATTCCA
32523518 TACCATTTCGTACCAATTCC
1 TACCATTTCGTACCAATTCC
32523538 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 25 0.68
22 12 0.32
ACGTcount: A:0.33, C:0.33, G:0.03, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:32523557 original size:10 final size:10
Alignment explanation
Indices: 32523542--32523570 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
32523532 AATTCCCAAA
32523542 TACCAAAACG
1 TACCAAAACG
32523552 TACCAAAACG
1 TACCAAAACG
32523562 TACCAAAAC
1 TACCAAAAC
32523571 CAAATACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.31, G:0.07, T:0.10
Consensus pattern (10 bp):
TACCAAAACG
Found at i:32525383 original size:15 final size:16
Alignment explanation
Indices: 32525358--32525389 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
32525348 TATCTCACAC
32525358 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
32525374 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
32525389 T
1 T
32525390 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:32526389 original size:11 final size:11
Alignment explanation
Indices: 32526373--32526413 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
32526363 CTACAAACTT
32526373 TTTTTTTCGAA
1 TTTTTTTCGAA
*
32526384 TTTTTTTTCAAA
1 -TTTTTTTCGAA
*
32526396 TTTTTTTTGAA
1 TTTTTTTCGAA
32526407 TTTTTTT
1 TTTTTTT
32526414 ACAATCTCGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.73
Consensus pattern (11 bp):
TTTTTTTCGAA
Found at i:32526389 original size:12 final size:12
Alignment explanation
Indices: 32526372--32526413 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
32526362 ACTACAAACT
32526372 TTTTTTTTCGAA
1 TTTTTTTTCGAA
*
32526384 TTTTTTTTCAAA
1 TTTTTTTTCGAA
32526396 TTTTTTTT-GAA
1 TTTTTTTTCGAA
32526407 TTTTTTT
1 TTTTTTT
32526414 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:32528014 original size:41 final size:41
Alignment explanation
Indices: 32527969--32528073 Score: 165
Period size: 41 Copynumber: 2.6 Consensus size: 41
32527959 TCGGCCAAAC
* * *
32527969 ATGTAGTAGCAGCATTAAATTCGTCCAGGCATATTTATAAA
1 ATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTATAAA
* *
32528010 ATGTAGTGGCAGCATTAAATTAGTCCAGACACATTTATAAC
1 ATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTATAAA
32528051 ATGTAGTGGCAGCATTAAATTCG
1 ATGTAGTGGCAGCATTAAATTCG
32528074 ACATATTAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.30
Consensus pattern (41 bp):
ATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTATAAA
Found at i:32538322 original size:20 final size:19
Alignment explanation
Indices: 32538297--32538356 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
32538287 TCAAGTTCAT
32538297 TCAGCTCAATTTTAGCTCA
1 TCAGCTCAATTTTAGCTCA
* *
32538316 TCGAGCTCACTCTTAGCTCAA
1 TC-AGCTCAATTTTAGCTC-A
32538337 TCAGCTC-ATTTTAAGCTCA
1 TCAGCTCAATTTT-AGCTCA
32538356 T
1 T
32538357 TTGCGTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.21
20 24 0.71
21 3 0.09
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (19 bp):
TCAGCTCAATTTTAGCTCA
Found at i:32540627 original size:10 final size:10
Alignment explanation
Indices: 32540603--32540650 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
32540593 AGACCGTATA
32540603 CAATTTTTTT
1 CAATTTTTTT
32540613 C--TTTTTTT
1 CAATTTTTTT
32540621 CAATTTTTTT
1 CAATTTTTTT
**
32540631 TGATTTTTTT
1 CAATTTTTTT
*
32540641 CGATTTTTTT
1 CAATTTTTTT
32540651 TTCAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 8 0.24
10 25 0.76
ACGTcount: A:0.12, C:0.08, G:0.04, T:0.75
Consensus pattern (10 bp):
CAATTTTTTT
Found at i:32540631 original size:20 final size:20
Alignment explanation
Indices: 32540606--32540653 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
32540596 CCGTATACAA
32540606 TTTTTTTCTTTTTTTCAATT
1 TTTTTTTCTTTTTTTCAATT
** *
32540626 TTTTTTGATTTTTTTCGATT
1 TTTTTTTCTTTTTTTCAATT
32540646 TTTTTTTC
1 TTTTTTTC
32540654 AAATTTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.08, C:0.08, G:0.04, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTTTTTTCAATT
Found at i:32540650 original size:13 final size:12
Alignment explanation
Indices: 32540614--32540667 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 12
32540604 AATTTTTTTC
32540614 TTTTTTTCAA-T
1 TTTTTTTCAATT
*
32540625 TTTTTTT-GA--
1 TTTTTTTCAATT
*
32540634 TTTTTTTCGATT
1 TTTTTTTCAATT
32540646 TTTTTTTCAAATT
1 TTTTTTTC-AATT
32540659 TTTTTTTCA
1 TTTTTTTCA
32540668 CGAGTCTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
9 7 0.19
10 3 0.08
11 7 0.19
12 9 0.24
13 11 0.30
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:32542054 original size:20 final size:19
Alignment explanation
Indices: 32542018--32542078 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
32542008 TATAAACGCA
*
32542018 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
32542038 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
32542059 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
32542078 A
1 A
32542079 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:32545742 original size:21 final size:21
Alignment explanation
Indices: 32545713--32545796 Score: 91
Period size: 21 Copynumber: 4.0 Consensus size: 21
32545703 AATCTTGAAT
32545713 GAAACTGAGAGAAGAAA-AAAAA
1 GAAA-TGAGAGAA-AAAGAAAAA
32545735 GAAATGAGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
* * *
32545756 GAAATAAAAGAAAAAGAAAAT
1 GAAATGAGAGAAAAAGAAAAA
* *
32545777 GAGA-GTGAGAAAAAGAAAAA
1 GAAATGAGAGAAAAAGAAAAA
32545797 AGAATTTGAG
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.28
21 34 0.64
22 4 0.08
ACGTcount: A:0.70, C:0.01, G:0.23, T:0.06
Consensus pattern (21 bp):
GAAATGAGAGAAAAAGAAAAA
Found at i:32545764 original size:15 final size:14
Alignment explanation
Indices: 32545728--32545775 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
32545718 TGAGAGAAGA
*
32545728 AAAAAAAGAAATGAG
1 AAAAAAAGAAA-AAG
*
32545743 AGAAAAAGAAAAAG
1 AAAAAAAGAAAAAG
32545757 AAATAAAAGAAAAAG
1 AAA-AAAAGAAAAAG
32545772 AAAA
1 AAAA
32545776 TGAGAGTGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (14 bp):
AAAAAAAGAAAAAG
Found at i:32545885 original size:12 final size:12
Alignment explanation
Indices: 32545868--32545907 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
32545858 AGTGAAAAGC
32545868 AAAAAGAGATTG
1 AAAAAGAGATTG
*
32545880 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
32545892 AAAGAGAGCTTG
1 AAAAAGAGATTG
32545904 AAAA
1 AAAA
32545908 GAAATCGAGT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.60, C:0.03, G:0.23, T:0.15
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:32548753 original size:29 final size:29
Alignment explanation
Indices: 32548716--32548788 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
32548706 TTAGATATTA
* *
32548716 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
32548745 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
32548774 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
32548789 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:32550002 original size:17 final size:18
Alignment explanation
Indices: 32549961--32549999 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
32549951 ATTTGAAAAT
*
32549961 AAAATCGAAAAAAATAAA
1 AAAATTGAAAAAAATAAA
*
32549979 AAAATTGAAAAAAAGAAA
1 AAAATTGAAAAAAATAAA
32549997 AAA
1 AAA
32550000 TTGTATACGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.03, G:0.08, T:0.10
Consensus pattern (18 bp):
AAAATTGAAAAAAATAAA
Found at i:32551991 original size:15 final size:15
Alignment explanation
Indices: 32551966--32552012 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
32551956 AGAAAAGAAT
32551966 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
32551982 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
32551997 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
32552012 A
1 A
32552013 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:32552059 original size:12 final size:12
Alignment explanation
Indices: 32552042--32552117 Score: 50
Period size: 12 Copynumber: 6.3 Consensus size: 12
32552032 AGTGAAAAGC
32552042 AAAAAGAGATTG
1 AAAAAGAGATTG
*
32552054 AAAAAGAAATTG
1 AAAAAGAGATTG
*
32552066 --AAAGAGA-AG
1 AAAAAGAGATTG
*
32552075 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
32552090 AAAAAGAAATTG
1 AAAAAGAGATTG
* *
32552102 AAAGAGAGCTTG
1 AAAAAGAGATTG
32552114 AAAA
1 AAAA
32552118 GAAATCGAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 25 0.52
13 5 0.10
15 7 0.15
ACGTcount: A:0.62, C:0.01, G:0.25, T:0.12
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:32552083 original size:15 final size:15
Alignment explanation
Indices: 32552065--32552098 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
32552055 AAAAGAAATT
32552065 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
32552080 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
32552095 GAAA
1 GAAA
32552099 TTGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:32555487 original size:20 final size:20
Alignment explanation
Indices: 32555462--32555508 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
32555452 AGCTCGTTTC
* *
32555462 CAGCTCATTTGAGCTCAAGT
1 CAGCTCATTCGAGATCAAGT
*
32555482 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
32555502 CAGCTCA
1 CAGCTCA
32555509 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:32557119 original size:22 final size:22
Alignment explanation
Indices: 32557091--32557243 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
32557081 TTTATTGTTC
*
32557091 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
32557113 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
32557135 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
32557157 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
32557179 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
32557201 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
32557223 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
32557244 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:32562988 original size:52 final size:52
Alignment explanation
Indices: 32562929--32563027 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
32562919 TGCACATATA
* *
32562929 TGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTGTT
1 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGTT
32562981 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
32563028 CGTTTCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (52 bp):
TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGTT
Found at i:32564420 original size:20 final size:20
Alignment explanation
Indices: 32564397--32564443 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
32564387 GGGTTAAAAT
*
32564397 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
32564417 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
32564437 TGAGCTG
1 TGAGCTG
32564444 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:32565865 original size:59 final size:63
Alignment explanation
Indices: 32565802--32565943 Score: 166
Period size: 70 Copynumber: 2.2 Consensus size: 63
32565792 ATTTAAAGGG
* *
32565802 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTA
*
32565861 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTA
32565926 ATGTA
59 ATGTA
32565931 AAGCATAGACATG
1 AAGCATAGACATG
32565944 TATTTAAGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 50 0.72
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTA
Found at i:32565906 original size:70 final size:70
Alignment explanation
Indices: 32565823--32565959 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
32565813 TGAATTAAAT
*
32565823 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
32565888 TTCAA
66 TTCAA
* *
32565893 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
32565958 TT
66 TT
32565960 GGGCATGCAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAAATTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:32567600 original size:29 final size:29
Alignment explanation
Indices: 32567563--32567635 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
32567553 TTAGATATTA
* *
32567563 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
32567592 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
32567621 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
32567636 ACTAATACAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.47
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:32568866 original size:24 final size:23
Alignment explanation
Indices: 32568812--32568867 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
32568802 GTTTAATTAA
**
32568812 GAAATGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGAATTGGTAC
***
32568835 GTTTTGGTATTTGGGAATTGGTAC
1 GAAATGGTATTT-GGAATTGGTAC
32568859 GAAATGGTA
1 GAAATGGTA
32568868 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGAATTGGTAC
Found at i:32570711 original size:18 final size:18
Alignment explanation
Indices: 32570655--32570711 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
32570645 AGTGCGAGCG
32570655 AGAAAAAGAAATCGAAGAAAA
1 AGAAAAAGAAATC--A-AAAA
* **
32570676 AGAAAAAGAGATTGAAAA
1 AGAAAAAGAAATCAAAAA
32570694 AGAAAAAGAAATCAAAAA
1 AGAAAAAGAAATCAAAAA
32570712 GGAGAGTGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 19 0.63
21 11 0.37
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AGAAAAAGAAATCAAAAA
Found at i:32573507 original size:52 final size:52
Alignment explanation
Indices: 32573448--32573546 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
32573438 TGCACATATA
* * *
32573448 TGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTGTT
1 TGAGCTTCAACCGAGCTAGAAATAAGATCTTAAGCTGCTGTCCATTATTGTT
32573500 TGAGCTTCAACCGAGCTAGAAATAAGATCTTAAGCTGCTGTCCATTA
1 TGAGCTTCAACCGAGCTAGAAATAAGATCTTAAGCTGCTGTCCATTA
32573547 CGTTTCCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.31
Consensus pattern (52 bp):
TGAGCTTCAACCGAGCTAGAAATAAGATCTTAAGCTGCTGTCCATTATTGTT
Found at i:32581582 original size:15 final size:15
Alignment explanation
Indices: 32581557--32581603 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
32581547 AGAAAAGAAT
32581557 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
32581573 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
32581588 AAA-AATATGAAAATG
1 AAAGAA-ATGAAAATG
32581603 A
1 A
32581604 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:32585761 original size:27 final size:26
Alignment explanation
Indices: 32585705--32585763 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
32585695 AAAAAATTCG
* *
32585705 AAAAAAAAAGAAAAAAAGAAGTGAGC
1 AAAAAAAAAGAAAAAAAGAAGAGAGA
*
32585731 AAAAAAAAAGAGTAAAAAGAAGA-AGA
1 AAAAAAAAAGA-AAAAAAGAAGAGAGA
32585757 AAAAAAA
1 AAAAAAA
32585764 GAAGTGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 20 0.69
27 9 0.31
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAAGAAGAGAGA
Found at i:32589295 original size:20 final size:20
Alignment explanation
Indices: 32589270--32589316 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
32589260 AGCTCATTTC
*
32589270 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
32589290 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
32589310 CAGCTCA
1 CAGCTCA
32589317 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:32589319 original size:10 final size:10
Alignment explanation
Indices: 32589260--32589319 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
32589250 AGCTCTGTTT
*
32589260 AGCTCATTTCC
1 AGCTCAATT-C
* *
32589271 AGCTCACTTG
1 AGCTCAATTC
*
32589281 AGCTCAAGTC
1 AGCTCAATTC
32589291 AGCTC-ATTC
1 AGCTCAATTC
*
32589300 GAGATCAATTC
1 -AGCTCAATTC
32589311 AGCTCAATT
1 AGCTCAATT
32589320 TTAACCCAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 3 0.08
10 24 0.62
11 12 0.31
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:32602534 original size:11 final size:11
Alignment explanation
Indices: 32602511--32602549 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
32602501 ACGAGATTGT
32602511 AAAAAAA-TCA
1 AAAAAAATTCA
* *
32602521 AAAAAATTTGA
1 AAAAAAATTCA
32602532 AAAAAAATTCA
1 AAAAAAATTCA
32602543 AAAAAAA
1 AAAAAAA
32602550 AGTTTGTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.77, C:0.05, G:0.03, T:0.15
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:32602617 original size:17 final size:17
Alignment explanation
Indices: 32602583--32602617 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
32602573 TCCTTTGTGT
* *
32602583 ATTCAGTATTGAAAAAA
1 ATTCAGAATTAAAAAAA
32602600 ATTCAGAATTAAAAAAA
1 ATTCAGAATTAAAAAAA
32602617 A
1 A
32602618 AGTGATTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.26
Consensus pattern (17 bp):
ATTCAGAATTAAAAAAA
Found at i:32606373 original size:15 final size:14
Alignment explanation
Indices: 32606336--32606386 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
32606326 CTATGAGCGA
32606336 GAAAAG-AAAAGAG
1 GAAAAGAAAAAGAG
* *
32606349 AAAAACAAAAAGAG
1 GAAAAGAAAAAGAG
*
32606363 TGAAAAGAAAAAGAAA
1 -GAAAAGAAAAAG-AG
32606379 GAAAAGAA
1 GAAAAGAA
32606387 TGATGAGAGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 18 0.60
16 1 0.03
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAAAAGAAAAAGAG
Found at i:32611096 original size:52 final size:52
Alignment explanation
Indices: 32611037--32611135 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
32611027 TGCACATATA
* *
32611037 TGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTGTT
1 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGTT
32611089 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
32611136 CGTTTCCTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (52 bp):
TGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTGTT
Found at i:32611661 original size:13 final size:13
Alignment explanation
Indices: 32611640--32611674 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
32611630 ATAAGTTGCT
* *
32611640 GTTAGTTAAATTA
1 GTTAATTAAATAA
32611653 GTTAATTAAATAA
1 GTTAATTAAATAA
32611666 GTTAATTAA
1 GTTAATTAA
32611675 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:32614879 original size:11 final size:11
Alignment explanation
Indices: 32614863--32614887 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
32614853 CTCCAAAGCT
32614863 AGGAATCTTCA
1 AGGAATCTTCA
32614874 AGGAATCTTCA
1 AGGAATCTTCA
32614885 AGG
1 AGG
32614888 GACGTTCTAG
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (11 bp):
AGGAATCTTCA
Found at i:32616377 original size:23 final size:23
Alignment explanation
Indices: 32616346--32616456 Score: 132
Period size: 23 Copynumber: 4.8 Consensus size: 23
32616336 TTTTTGAACC
* *
32616346 ATTAACATTTCGTACCAAATCGT
1 ATTACCATTTCGTACCAAATCAT
* *
32616369 ATTACCATTTCGAACCAAATCAC
1 ATTACCATTTCGTACCAAATCAT
* * *
32616392 CTTACCAATTCGTACCAAATCGT
1 ATTACCATTTCGTACCAAATCAT
* *
32616415 ATTACCATTTTGAACCAAATCAT
1 ATTACCATTTCGTACCAAATCAT
*
32616438 ATTACCATTTCGTAACAAA
1 ATTACCATTTCGTACCAAA
32616457 CCCAAAACTG
Statistics
Matches: 71, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.37, C:0.25, G:0.06, T:0.32
Consensus pattern (23 bp):
ATTACCATTTCGTACCAAATCAT
Found at i:32616421 original size:46 final size:46
Alignment explanation
Indices: 32616345--32616456 Score: 161
Period size: 46 Copynumber: 2.4 Consensus size: 46
32616335 TTTTTTGAAC
* *
32616345 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
32616391 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* * *
32616437 TATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
32616457 CCCAAAACTG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:32620747 original size:23 final size:23
Alignment explanation
Indices: 32620715--32620818 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
32620705 TTTTTTGAAC
* * *
32620715 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGAACCAAATCA
*
32620738 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGAACCAAATCA
* * * *
32620761 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGAACCAAATCA
* *
32620784 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGAACCAAATCA
32620807 CATTACCATTTC
1 CATTACCATTTC
32620819 ATAACAAACC
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.32
Consensus pattern (23 bp):
CATTACCATTTCGAACCAAATCA
Found at i:32620791 original size:46 final size:46
Alignment explanation
Indices: 32620715--32620814 Score: 164
Period size: 46 Copynumber: 2.2 Consensus size: 46
32620705 TTTTTTGAAC
* *
32620715 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
32620761 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
32620807 CATTACCA
1 CATTACCA
32620815 TTTCATAACA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:32626059 original size:41 final size:41
Alignment explanation
Indices: 32626002--32626109 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
32625992 TTTAATATGT
* *
32626002 CGAATTTAATGCTGCCACTACATGTTATAAATGTGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
32626043 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
32626084 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
32626110 TGGCTGAATT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 64 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Found at i:32627822 original size:14 final size:15
Alignment explanation
Indices: 32627789--32627828 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
32627779 ACACAAACAA
32627789 TTTTTTTAAATCACG
1 TTTTTTTAAATCACG
* *
32627804 ATTTTTTAAATCACT
1 TTTTTTTAAATCACG
32627819 TTTTTTTAAA
1 TTTTTTTAAA
32627829 AAAATTCGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTTTTAAATCACG
Found at i:32632173 original size:23 final size:23
Alignment explanation
Indices: 32632138--32632249 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
32632128 CGGTTCTGGG
* * *
32632138 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACAAAATGGTAATGCGA
* *
32632161 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
* * * *
32632184 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACAAAATGGTAATGCGA
* *
32632207 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
* *
32632230 TTTGGTACGAAATGTTAATG
1 TTTGGTACAAAATGGTAATG
32632250 GTTCAAAAAG
Statistics
Matches: 68, Mismatches: 21, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 68 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (23 bp):
TTTGGTACAAAATGGTAATGCGA
Found at i:32632200 original size:46 final size:46
Alignment explanation
Indices: 32632138--32632249 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
32632128 CGGTTCTGGG
*
32632138 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* *
32632184 TTTGGTACGAATTGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
32632230 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
32632250 GTTCAAAAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:32634829 original size:12 final size:12
Alignment explanation
Indices: 32634812--32634838 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
32634802 GTCGTCAAGC
32634812 CAAGGTGAGTAT
1 CAAGGTGAGTAT
32634824 CAAGGTGAGTAT
1 CAAGGTGAGTAT
32634836 CAA
1 CAA
32634839 ATTGAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.11, G:0.30, T:0.22
Consensus pattern (12 bp):
CAAGGTGAGTAT
Found at i:32646444 original size:22 final size:22
Alignment explanation
Indices: 32646392--32646456 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
32646382 TATTTGGGAA
* * *
32646392 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
32646414 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
32646436 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
32646457 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:32651563 original size:12 final size:12
Alignment explanation
Indices: 32651546--32651588 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
32651536 AATACAAACT
32651546 TTTTTTTTGAAA
1 TTTTTTTTGAAA
*
32651558 TTTTTTTTCGAAT
1 TTTTTTTT-GAAA
32651571 TTTTTTTTG--A
1 TTTTTTTTGAAA
32651581 TTTTTTTT
1 TTTTTTTT
32651589 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 8 0.29
12 9 0.32
13 11 0.39
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTTGAAA
Found at i:32651563 original size:13 final size:12
Alignment explanation
Indices: 32651545--32651588 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
32651535 GAATACAAAC
32651545 TTTTTTTTTGAAA
1 TTTTTTTTTG-AA
*
32651558 TTTTTTTTCGAA
1 TTTTTTTTTGAA
32651570 TTTTTTTTTG-A
1 TTTTTTTTTGAA
32651581 TTTTTTTT
1 TTTTTTTT
32651589 ACAATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 9 0.31
12 11 0.38
13 9 0.31
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:32654921 original size:22 final size:22
Alignment explanation
Indices: 32654862--32654921 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
32654852 CCATTTCCAT
* *
32654862 TTTCGTACCAAATCCATTACCA
1 TTTCATACCAAATCCCTTACCA
** *
32654884 TTTCATTTCAAATCCCTTACCG
1 TTTCATACCAAATCCCTTACCA
*
32654906 TTTCATACCAATTCCC
1 TTTCATACCAAATCCC
32654922 AAATACCAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (22 bp):
TTTCATACCAAATCCCTTACCA
Found at i:32658476 original size:12 final size:12
Alignment explanation
Indices: 32658433--32658476 Score: 63
Period size: 11 Copynumber: 3.7 Consensus size: 12
32658423 TAGTTTCTCG
*
32658433 AAAAAAAACTCGA
1 AAAAAAAATTC-A
32658446 AAAAAAAATTC-
1 AAAAAAAATTCA
32658457 AAAAAAAATTCA
1 AAAAAAAATTCA
32658469 AAAAAAAA
1 AAAAAAAA
32658477 ACTAGTTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.38
12 8 0.28
13 10 0.34
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:32658541 original size:15 final size:14
Alignment explanation
Indices: 32658515--32658557 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
32658505 GGATATCAAG
32658515 TTGTGAAAAAAAAA
1 TTGTGAAAAAAAAA
*
32658529 TTTTTGAAGAAAAAAA
1 -TTGTGAA-AAAAAAA
32658545 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
32658558 CGAGAGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 6 0.24
15 12 0.48
16 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (14 bp):
TTGTGAAAAAAAAA
Found at i:32660601 original size:20 final size:20
Alignment explanation
Indices: 32660578--32660631 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
32660568 AGTTTTTCCC
*
32660578 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
32660598 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
32660618 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
32660632 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:32660613 original size:30 final size:30
Alignment explanation
Indices: 32660578--32660651 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
32660568 AGTTTTTCCC
32660578 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
32660608 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
32660638 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
32660652 TGGATTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:32660641 original size:20 final size:20
Alignment explanation
Indices: 32660578--32660642 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
32660568 AGTTTTTCCC
* * * *
32660578 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
32660598 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
32660617 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
32660638 AGCTC
1 AGCTC
32660643 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:32667292 original size:22 final size:22
Alignment explanation
Indices: 32667255--32667319 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
32667245 CCTTTTTGAA
*
32667255 CCATTTCCATTTTCGTACCAAAT
1 CCATTACCA-TTTCGTACCAAAT
* **
32667278 CTATTACCATTTCGTTTCAAAT
1 CCATTACCATTTCGTACCAAAT
* * *
32667300 CCCTTACCGTTTCATACCAA
1 CCATTACCATTTCGTACCAA
32667320 TTCCCAAATA
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
22 25 0.78
23 7 0.22
ACGTcount: A:0.26, C:0.31, G:0.05, T:0.38
Consensus pattern (22 bp):
CCATTACCATTTCGTACCAAAT
Found at i:32667943 original size:13 final size:13
Alignment explanation
Indices: 32667922--32667956 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
32667912 ATAAGTTGCT
* *
32667922 GTTAGTTAAATTA
1 GTTAATTAAATAA
32667935 GTTAATTAAATAA
1 GTTAATTAAATAA
32667948 GTTAATTAA
1 GTTAATTAA
32667957 TTTGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (13 bp):
GTTAATTAAATAA
Found at i:32668939 original size:15 final size:15
Alignment explanation
Indices: 32668919--32668961 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
32668909 TAGTTTAATG
32668919 ATTTTTATTTTTTTT
1 ATTTTTATTTTTTTT
*
32668934 ATTTTTA-TTTATTT
1 ATTTTTATTTTTTTT
32668948 ATTTCTTAGTTTTT
1 ATTT-TTA-TTTTT
32668962 AAGTTAGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.43
15 10 0.43
17 3 0.13
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTTTTTT
Found at i:32674457 original size:10 final size:11
Alignment explanation
Indices: 32674442--32674470 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
32674432 CAACTCAAAT
32674442 TTTTTTTTGA-
1 TTTTTTTTGAC
32674452 TTTTTTTTGAC
1 TTTTTTTTGAC
32674463 TTTTTTTT
1 TTTTTTTT
32674471 ACGTTACGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:32676023 original size:20 final size:19
Alignment explanation
Indices: 32676000--32676064 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
32675990 AAGCTCAAAC
32676000 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
32676020 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
32676040 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
32676060 GAGCT
1 GAGCT
32676065 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:32695030 original size:22 final size:22
Alignment explanation
Indices: 32694978--32695042 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
32694968 TATTTGGGAA
* * *
32694978 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
32695000 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
32695022 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
32695043 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:32697379 original size:20 final size:20
Alignment explanation
Indices: 32697356--32697402 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
32697346 GGGTTGAGGT
32697356 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
32697376 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
32697396 TGAGCTG
1 TGAGCTG
32697403 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:32700468 original size:19 final size:17
Alignment explanation
Indices: 32700431--32700497 Score: 57
Period size: 19 Copynumber: 3.8 Consensus size: 17
32700421 TATGGGAAAG
*
32700431 AAAAGAATGAAAAAGAA
1 AAAAGAAAGAAAAAGAA
* *
32700448 AGAAG--AGAAAATGTAA
1 AAAAGAAAGAAAAAG-AA
32700464 AAAAGAAAGTAAAAAGAA
1 AAAAGAAAG-AAAAAGAA
32700482 AACAAGAAAAGAAAAA
1 AA-AAG-AAAGAAAAA
32700498 CAAGAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
15 6 0.15
16 6 0.15
17 4 0.10
18 6 0.15
19 13 0.33
20 4 0.10
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (17 bp):
AAAAGAAAGAAAAAGAA
Found at i:32700490 original size:33 final size:32
Alignment explanation
Indices: 32700426--32700504 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 32
32700416 GAGTATATGG
*
32700426 GAAAGAAAAGAATGAAAAAGAAAGAAGAGAAAA
1 GAAA-AAAAGAAAGAAAAAGAAAGAAGAGAAAA
*
32700459 TGTAAAAAAGAAAGTAAAAAGAAA-ACA-AGAAAA
1 -GAAAAAAAGAAAG-AAAAAGAAAGA-AGAGAAAA
32700492 GAAAAACAAGAAA
1 GAAAAA-AAGAAA
32700505 ATATGAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 5 0.13
33 21 0.54
34 13 0.33
ACGTcount: A:0.73, C:0.03, G:0.19, T:0.05
Consensus pattern (32 bp):
GAAAAAAAGAAAGAAAAAGAAAGAAGAGAAAA
Found at i:32700491 original size:13 final size:14
Alignment explanation
Indices: 32700475--32700505 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
32700465 AAAGAAAGTA
32700475 AAAAG-AAAACAAG
1 AAAAGAAAAACAAG
32700488 AAAAGAAAAACAAG
1 AAAAGAAAAACAAG
32700502 AAAA
1 AAAA
32700506 TATGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAACAAG
Found at i:32701902 original size:15 final size:15
Alignment explanation
Indices: 32701882--32701914 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
32701872 GGTGAGATTT
32701882 ATTCTG-CTTGTGAGA
1 ATTCTGCCTT-TGAGA
32701897 ATTCTGCCTTTGAGA
1 ATTCTGCCTTTGAGA
32701912 ATT
1 ATT
32701915 TCTATAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (15 bp):
ATTCTGCCTTTGAGA
Found at i:32711884 original size:20 final size:20
Alignment explanation
Indices: 32711847--32711884 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
32711837 TTTCAACTCC
*
32711847 AATCAGCTCATTTGAGCTTA
1 AATCAGCTCATTTAAGCTTA
*
32711867 AATCAGCTCGTTTAAGCT
1 AATCAGCTCATTTAAGCT
32711885 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (20 bp):
AATCAGCTCATTTAAGCTTA
Found at i:32740322 original size:27 final size:27
Alignment explanation
Indices: 32740292--32740438 Score: 99
Period size: 27 Copynumber: 5.5 Consensus size: 27
32740282 TCAAGCTCTC
*
32740292 TTTCAATTTCTTTT-TTCGCTTTTTCTT
1 TTTCAATTTCTTTTCTTC-CATTTTCTT
* *
32740319 TTTCAATTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTC-TTC-CATTTTCTT
32740348 TTTCAATTTTCTTTTCTT-CATTTTCTT
1 TTTCAA-TTTCTTTTCTTCCATTTTCTT
* * *
32740375 TTTC--TCTCACTTT-TTCGA-TTTCTT
1 TTTCAATTTC-TTTTCTTCCATTTTCTT
** * * *
32740399 TTTCTTTTTGTTTTCTTTCAATTTCTT
1 TTTCAATTTCTTTTCTTCCATTTTCTT
*
32740426 TTTCAATCTCTTT
1 TTTCAATTTCTTT
32740439 CTCCTTTTCT
Statistics
Matches: 93, Mismatches: 18, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
24 15 0.16
25 7 0.08
26 5 0.05
27 40 0.43
29 18 0.19
30 8 0.09
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (27 bp):
TTTCAATTTCTTTTCTTCCATTTTCTT
Found at i:32740333 original size:17 final size:18
Alignment explanation
Indices: 32740310--32740352 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
32740300 TCTTTTTTCG
* *
32740310 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
32740328 -TTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
32740345 CTTTTTCA
1 CTTTTTCA
32740353 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.14, C:0.19, G:0.00, T:0.67
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:32740362 original size:12 final size:12
Alignment explanation
Indices: 32740313--32740438 Score: 59
Period size: 12 Copynumber: 10.6 Consensus size: 12
32740303 TTTTTCGCTT
32740313 TTTCTTTTTCAA
1 TTTCTTTTTCAA
32740325 TTT-TTTTTC-A
1 TTTCTTTTTCAA
32740335 -TTC----TCAA
1 TTTCTTTTTCAA
32740342 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
32740354 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
32740369 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
32740381 TCACTTTTTCGA
1 TTTCTTTTTCAA
**
32740393 TTTCTTTTTCTTT
1 TTTCTTTTTC-AA
*
32740406 TTGTTTTCTTTCAA
1 TT-TCTT-TTTCAA
32740420 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
32740432 TCTCTTT
1 TTTCTTT
32740439 CTCCTTTTCT
Statistics
Matches: 85, Mismatches: 16, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
6 2 0.02
7 1 0.01
8 3 0.04
9 2 0.02
10 1 0.01
11 6 0.07
12 38 0.45
13 12 0.14
14 12 0.14
15 8 0.09
ACGTcount: A:0.11, C:0.19, G:0.02, T:0.68
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:32740448 original size:51 final size:51
Alignment explanation
Indices: 32740335--32740448 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
32740325 TTTTTTTTCA
* * **
32740335 TTCTCAATTTCTTTTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACT
1 TTCTCCATTTCTTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACT
* * * * *
32740386 TTTTCGATTTCTTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATCTCT
1 TTCTCCATTTCTTTTTCAATTTTCTTTTC-TTCAATTTCTTTTTCAATCACT
*
32740437 TTCTCCTTTTCT
1 TTCTCCATTTCT
32740449 CGCTCAATGG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 9 0.18
51 42 0.82
ACGTcount: A:0.10, C:0.22, G:0.02, T:0.67
Consensus pattern (51 bp):
TTCTCCATTTCTTTTTCAATTTTCTTTTCTTCAATTTCTTTTTCAATCACT
Found at i:32744343 original size:23 final size:23
Alignment explanation
Indices: 32744316--32744427 Score: 134
Period size: 23 Copynumber: 4.9 Consensus size: 23
32744306 CTCTTTGAAC
*
32744316 CATTACCATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
32744339 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
32744362 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
32744385 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
32744408 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
32744428 CCCAAAACCG
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:32744385 original size:46 final size:46
Alignment explanation
Indices: 32744316--32744427 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
32744306 CTCTTTGAAC
32744316 CATTACCATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* * *
32744362 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
*
32744408 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
32744428 CCCAAAACCG
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.36, C:0.28, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:32749817 original size:18 final size:18
Alignment explanation
Indices: 32749796--32749837 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
32749786 TAAGAACTTG
* *
32749796 AAAACATAAAATTCGTTA
1 AAAACATAAAAATCATTA
32749814 AAAACATAAAAATCATTA
1 AAAACATAAAAATCATTA
32749832 AAAACA
1 AAAACA
32749838 GGATTGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAACATAAAAATCATTA
Found at i:32750688 original size:41 final size:41
Alignment explanation
Indices: 32750630--32750737 Score: 189
Period size: 41 Copynumber: 2.6 Consensus size: 41
32750620 TTTAATATGT
*
32750630 CGAATTTAATGCTGCCACTACATGTTATAAATATGTCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
32750671 TGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
1 CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
*
32750712 CGAATTTAATGCTGCTACTACATGTT
1 CGAATTTAATGCTGCCACTACATGTT
32750738 TGGCCGAATT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
CGAATTTAATGCTGCCACTACATGTTATAAATATGCCTGGA
Done.