Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 127 of 145
Found at i:42389534 original size:54 final size:52
Alignment explanation
Indices: 42389449--42389961 Score: 523
Period size: 54 Copynumber: 9.6 Consensus size: 52
42389439 TATGACCATT
*
42389449 TAGGGTAAAATGA-TCGAAATACCCGCATAGGGTAAAATGATCGCAATACCCCCA
1 TAGGGTAAAATGACT-GAAATACCC-CATAGGGTAAAATGA-CGAAATACCCCCA
* * *
42389503 CAAGGTAAAATGACTGAAATTCTCCCATAGGGT-AAATGACCGAAATACCCCCA
1 TAGGGTAAAATGACTGAAATAC-CCCATAGGGTAAAATGA-CGAAATACCCCCA
* * *
42389556 TAGGGTATAATGACTGAAATAACCTCATAGGGTAAAATGACAAAAATACCCCCA
1 TAGGGTAAAATGACTGAAAT-ACCCCATAGGGTAAAATGAC-GAAATACCCCCA
* * * *
42389610 TAGGGTAAAATAACCGAAATACCCCTTAGGGTAAAATGGCCGAAATATCCCCCA
1 TAGGGTAAAATGACTGAAATACCCCATAGGGTAAAAT-GACGAAATA-CCCCCA
* *
42389664 TAGGGTAAAATGACCGAAATACCCCCATAGAGTAAAATGATCGAAATACCCCCA
1 TAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGA-CGAAATACCCCCA
* * * *
42389718 TAGGGTAAAATGACTGAAATACTCCCACAAGGTAAAATGACTGAACTACTCCCA
1 TAGGGTAAAATGACTGAAATAC-CCCATAGGGTAAAATGAC-GAAATACCCCCA
* * * *
42389772 TAAGGT-AAATGA-TCGAAATACCCTTATAGGATAAAATGACTGAAATATCCCCA
1 TAGGGTAAAATGACT-GAAATACCC-CATAGGGTAAAATGAC-GAAATACCCCCA
** * * *
42389825 TAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATAATCAAAATACCTCCA
1 TAGGGTAAAATGACTGAAATACCCC-ATAGGGTAAAATGA-CGAAATACCCCCA
* * **
42389879 TAGGGTAAAATGACTAAAATATCCCCATAGGGTAAAATGACAGAAATTCCTTCA
1 TAGGGTAAAATGACTGAAATA-CCCCATAGGGTAAAATGAC-GAAATACCCCCA
**
42389933 TAGGGTAAAATGACTGTTATACCCC-TAGG
1 TAGGGTAAAATGACTGAAATACCCCATAGG
42389962 AGATGAAATG
Statistics
Matches: 387, Mismatches: 53, Indels: 40
0.81 0.11 0.08
Matches are distributed among these distances:
52 7 0.02
53 112 0.29
54 239 0.62
55 29 0.07
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (52 bp):
TAGGGTAAAATGACTGAAATACCCCATAGGGTAAAATGACGAAATACCCCCA
Found at i:42389826 original size:215 final size:215
Alignment explanation
Indices: 42389449--42389948 Score: 648
Period size: 215 Copynumber: 2.3 Consensus size: 215
42389439 TATGACCATT
* * * * *
42389449 TAGGGTAAAATGATCGAAATACCCGCATAGGGTAAAATGATCGCAATACCCCCACAAGGTAAAAT
1 TAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAAT
* * * *
42389514 GACTGAAATTCTCCCATAGGGTAAATGACCGAAATACCCCCATAGGGTATAATGACTGAAATAAC
66 GACTGAAATACTCCCACAAGGTAAATGACCGAAATACCCCCATAAGGTATAATGACTGAAATAAC
* *
42389579 CTCATAGGGTAAAATGACAAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCT-TAGGGTA
131 CTCATAGGATAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCTATAGGGTA
** *
42389643 AAATGGCCGAAATATCCCCCA
196 AAATAACCAAAATA-CCCCCA
*
42389664 TAGGGTAAAATGACCGAAATACCCCCATAGAGTAAAATGATCGAAATACCCCCATAGGGTAAAAT
1 TAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAAT
* * *
42389729 GACTGAAATACTCCCACAAGGTAAAATGACTGAACTACTCCCATAAGGTA-AATGA-TCGAAATA
66 GACTGAAATACTCCCACAAGGT-AAATGACCGAAATACCCCCATAAGGTATAATGACT-GAAATA
* * ** * *
42389792 CCCTTATAGGATAAAATGACTGAAATATCCCCATAGGGTAAAATGACCAAAATACCCCTATAGGG
129 ACCTCATAGGATAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCTATAGGG
* *
42389857 TAAAATAATCAAAATACCTCCA
194 TAAAATAACCAAAATACCCCCA
** * * **
42389879 TAGGGTAAAATGACTAAAATATCCCCATAGGGTAAAATGA-CAGAAATTCCTTCATAGGGTAAAA
1 TAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCATAGGGTAAAA
42389943 TGACTG
65 TGACTG
42389949 TTATACCCCT
Statistics
Matches: 248, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
214 2 0.01
215 206 0.83
216 40 0.16
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (215 bp):
TAGGGTAAAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAAT
GACTGAAATACTCCCACAAGGTAAATGACCGAAATACCCCCATAAGGTATAATGACTGAAATAAC
CTCATAGGATAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCTATAGGGTA
AAATAACCAAAATACCCCCA
Found at i:42389957 original size:242 final size:242
Alignment explanation
Indices: 42389449--42389945 Score: 728
Period size: 242 Copynumber: 2.1 Consensus size: 242
42389439 TATGACCATT
* *
42389449 TAGGGTAAAATGATCGAAATACCCGCATAGGGTAAAATGATCGCAATACCCCCACAAGGTAAAAT
1 TAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCACAAGGTAAAAT
* * * *
42389514 GACTGAAATTCTCCCATAGGGTAAATGACCGAAATACCCCCATAGGGTATAATGACTGAAATAAC
66 GACTGAAATACTCCCATAAGGTAAATGACCGAAATACCCCCATAGGATAAAATGACTGAAATAAC
* * *
42389579 CTCATAGGGTAAAATGACAAAAATACCCCCATAGGGTAAAATAACCGAAATACCCCTTAGGGTAA
131 CCCATAGGGTAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCATAGGGTAA
* * *
42389644 AATGGCCGAAATATCCCCCATAGGGTAAAATGACCGAAATACCCCCA
196 AATGACCAAAATATCCCCCATAGGGTAAAATGACAGAAATACCCCCA
* *
42389691 TAGAGTAAAATGATCGAAATACCCCCATAGGGTAAAATGA-CTGAAATACTCCCACAAGGTAAAA
1 TAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATC-GAAATACCCCCACAAGGTAAAA
* * ** *
42389755 TGACTGAACTACTCCCATAAGGTAAATGATCGAAATACCCTTATAGGATAAAATGACTGAAATAT
65 TGACTGAAATACTCCCATAAGGTAAATGACCGAAATACCCCCATAGGATAAAATGACTGAAATAA
* * *
42389820 CCCCATAGGGTAAAATGACCAAAATACCCCTATAGGGTAAAATAATCAAAATACCTCCATAGGGT
130 CCCCATAGGGTAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACC-CCATAGGGT
* * **
42389885 AAAATGACTAAAATAT-CCCCATAGGGTAAAATGACAGAAATTCCTTCA
194 AAAATGACCAAAATATCCCCCATAGGGTAAAATGACAGAAATACCCCCA
42389933 TAGGGTAAAATGA
1 TAGGGTAAAATGA
42389946 CTGTTATACC
Statistics
Matches: 226, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
241 1 0.00
242 204 0.90
243 21 0.09
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (242 bp):
TAGGGTAAAATGATCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCCACAAGGTAAAAT
GACTGAAATACTCCCATAAGGTAAATGACCGAAATACCCCCATAGGATAAAATGACTGAAATAAC
CCCATAGGGTAAAATGACAAAAATACCCCCATAGGGTAAAATAACCAAAATACCCCATAGGGTAA
AATGACCAAAATATCCCCCATAGGGTAAAATGACAGAAATACCCCCA
Found at i:42389974 original size:81 final size:80
Alignment explanation
Indices: 42389449--42389947 Score: 536
Period size: 81 Copynumber: 6.2 Consensus size: 80
42389439 TATGACCATT
* * * *
42389449 TAGGGTAAAATGA-TCGAAATACCCGCATAGGGTAAAATGA-TCGCAATACCCCCACAAGGTAAA
1 TAGGGTAAAATGACTCGAAATACCC-CATAGGGTAAAATGACT-GAAATATCCCCATAGGGTAAA
* *
42389512 ATGACTGAAATTCTCCCA
64 ATGACAGAAATAC-CCCA
* * *
42389530 TAGGGT-AAATGAC-CGAAATACCCCCATAGGGTATAATGACTGAAATAACCTCATAGGGTAAAA
1 TAGGGTAAAATGACTCGAAATA-CCCCATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAA
*
42389593 TGACAAAAATACCCCCA
65 TGACAGAAATA-CCCCA
* * * *
42389610 TAGGGTAAAATAAC-CGAAATACCCCTTAGGGTAAAATGGCCGAAATATCCCCCATAGGGTAAAA
1 TAGGGTAAAATGACTCGAAATACCCCATAGGGTAAAATGACTGAAATAT-CCCCATAGGGTAAAA
*
42389674 TGACCGAAATACCCCCA
65 TGACAGAAATA-CCCCA
*
42389691 TAGAGTAAAATGA-TCGAAATACCCCCATAGGGTAAAATGACTGAAATACTCCCACA-A-GGTAA
1 TAGGGTAAAATGACTCGAAATA-CCCCATAGGGTAAAATGACTGAAATA-TCCC-CATAGGGTAA
* *
42389753 AATGACTGAACTACTCCCA
63 AATGACAGAAATAC-CCCA
* * *
42389772 TAAGGT-AAATGA-TCGAAATACCCTTATAGGATAAAATGACTGAAATATCCCCATAGGGTAAAA
1 TAGGGTAAAATGACTCGAAATACCC-CATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAA
42389835 TGACCA-AAATACCCCTA
65 TGA-CAGAAATACCCC-A
* * *
42389852 TAGGGTAAAAT-AATCAAAATACCTCCATAGGGTAAAATGACTAAAATATCCCCATAGGGTAAAA
1 TAGGGTAAAATGACTCGAAATACC-CCATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAA
* *
42389916 TGACAGAAATTCCTTCA
65 TGACAGAAATACC-CCA
42389933 TAGGGTAAAATGACT
1 TAGGGTAAAATGACT
42389948 GTTATACCCC
Statistics
Matches: 357, Mismatches: 39, Indels: 43
0.81 0.09 0.10
Matches are distributed among these distances:
78 2 0.01
79 11 0.03
80 144 0.40
81 166 0.46
82 31 0.09
83 3 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (80 bp):
TAGGGTAAAATGACTCGAAATACCCCATAGGGTAAAATGACTGAAATATCCCCATAGGGTAAAAT
GACAGAAATACCCCA
Found at i:42417705 original size:30 final size:30
Alignment explanation
Indices: 42417669--42417734 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
42417659 TTTCAAAAGA
* * *
42417669 CACACGGGCGTGTTGCCAGGCCGTGTGTGT
1 CACACGGCCATGTTGCCAGGCCATGTGTGT
*
42417699 CACACGGCCATGTTGTCAGGCCATGTGTGT
1 CACACGGCCATGTTGCCAGGCCATGTGTGT
42417729 CACACG
1 CACACG
42417735 ACCGTGTGAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.15, C:0.29, G:0.33, T:0.23
Consensus pattern (30 bp):
CACACGGCCATGTTGCCAGGCCATGTGTGT
Found at i:42426252 original size:23 final size:23
Alignment explanation
Indices: 42426226--42426271 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42426216 GTCTCAGGGT
42426226 TAGGCACAATTCCTTAAAAAGAA
1 TAGGCACAATTCCTTAAAAAGAA
42426249 TAGGCACAATTCCTTAAAAAGAA
1 TAGGCACAATTCCTTAAAAAGAA
42426272 AATGACGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
TAGGCACAATTCCTTAAAAAGAA
Found at i:42426282 original size:24 final size:23
Alignment explanation
Indices: 42426230--42426282 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
42426220 CAGGGTTAGG
* *
42426230 CACAATTCCTTAAAAAGAATAGG
1 CACAATTCCTTAAAAAGAAAAGA
42426253 CACAATTCCTTAAAAAGAAAATGA
1 CACAATTCCTTAAAAAGAAAA-GA
*
42426277 CGCAAT
1 CACAAT
42426283 CTGGCAGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.49, C:0.19, G:0.11, T:0.21
Consensus pattern (23 bp):
CACAATTCCTTAAAAAGAAAAGA
Found at i:42427737 original size:24 final size:23
Alignment explanation
Indices: 42427710--42427760 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
42427700 CAATAATAAT
* *
42427710 ATGCAGAAAATTCTGCCAGTAAGA
1 ATGCAGAAAAGT-TGCCAGTAAAA
*
42427734 ATGCAGACAAGTTGCCAGTAAAA
1 ATGCAGAAAAGTTGCCAGTAAAA
42427757 ATGC
1 ATGC
42427761 GATAAATCGC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.20
Consensus pattern (23 bp):
ATGCAGAAAAGTTGCCAGTAAAA
Found at i:42434480 original size:167 final size:167
Alignment explanation
Indices: 42434199--42434535 Score: 467
Period size: 167 Copynumber: 2.0 Consensus size: 167
42434189 GAAAGCTGAA
* * * * *
42434199 CATCAAGTACCATCGGGTTTACTCCAATCGGTAATGATTTCAGAGTGGAAATGGGACAGCATCAC
1 CATCAAGTACCATCGGGTTTACTCCAACCGATAACGATTCCAGAATGGAAATGGGACAGCATCAC
* * * * *
42434264 GATGGATTTTGTGACAGGATTACCTCTGACTCCAAGGAAGAAGGATGCTATTTGGGTGATCGTTG
66 GATGGATTTTGTGACAGGATTACCTCTAACTCCAAAGAAGAAAGATGCTATTTGGGTAATCGTGG
* * *
42434329 ATAGATTGACAAAGTCGGCTCATTTTATACCGGTACG
131 ATAGATTGACAAAGTCAGCCCATTTTATACCGATACG
* * * * *
42434366 CATCAAGTGCCATCGGGTTTACTTCAACCGATAACGATTCCAGAATGGAAGTGGGACAGTATTAC
1 CATCAAGTACCATCGGGTTTACTCCAACCGATAACGATTCCAGAATGGAAATGGGACAGCATCAC
* * * *
42434431 GATGGATTTTGTGATAGGATTGCCTTTAACTCCAAAGAAGAAAGATGCTATTTGGGTAATTGTGG
66 GATGGATTTTGTGACAGGATTACCTCTAACTCCAAAGAAGAAAGATGCTATTTGGGTAATCGTGG
*
42434496 ATAGATTGACAAAGTCAGCCCATTTTATTCCGATACG
131 ATAGATTGACAAAGTCAGCCCATTTTATACCGATACG
42434533 CAT
1 CAT
42434536 TGATTATTCA
Statistics
Matches: 147, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
167 147 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (167 bp):
CATCAAGTACCATCGGGTTTACTCCAACCGATAACGATTCCAGAATGGAAATGGGACAGCATCAC
GATGGATTTTGTGACAGGATTACCTCTAACTCCAAAGAAGAAAGATGCTATTTGGGTAATCGTGG
ATAGATTGACAAAGTCAGCCCATTTTATACCGATACG
Found at i:42438008 original size:48 final size:49
Alignment explanation
Indices: 42437936--42438036 Score: 195
Period size: 48 Copynumber: 2.1 Consensus size: 49
42437926 TAATTGATGA
42437936 ATTATTTCCCTAAATCTATTGTCCATATAGTTTAGGATGTTATGAATGG
1 ATTATTTCCCTAAATCTATTGTCCATATAGTTTAGGATGTTATGAATGG
42437985 ATTATTTCCCT-AATCTATTGTCCATATAGTTTAGGATGTTATGAATGG
1 ATTATTTCCCTAAATCTATTGTCCATATAGTTTAGGATGTTATGAATGG
42438033 ATTA
1 ATTA
42438037 ATCGTGTCTG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 41 0.79
49 11 0.21
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.44
Consensus pattern (49 bp):
ATTATTTCCCTAAATCTATTGTCCATATAGTTTAGGATGTTATGAATGG
Found at i:42439589 original size:3 final size:3
Alignment explanation
Indices: 42439581--42439676 Score: 147
Period size: 3 Copynumber: 30.7 Consensus size: 3
42439571 TGTGGAATGC
42439581 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
*
42439627 GGAAT GCAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 --AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
42439675 AA
1 AA
42439677 GATTTCGGTT
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
3 81 0.92
4 4 0.05
5 1 0.01
6 2 0.02
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42445419 original size:13 final size:14
Alignment explanation
Indices: 42445384--42445419 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
42445374 TTTCAAGAAG
42445384 ATTTTCTTTTAAAT
1 ATTTTCTTTTAAAT
42445398 ATTTTCTTTTAAA-
1 ATTTTCTTTTAAAT
*
42445411 ATTTACTTT
1 ATTTTCTTT
42445420 AATTTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTCTTTTAAAT
Found at i:42459470 original size:44 final size:43
Alignment explanation
Indices: 42459417--42460056 Score: 227
Period size: 44 Copynumber: 13.7 Consensus size: 43
42459407 AAGCCACAAG
42459417 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGCAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-AA
* * * * * * *
42459461 TCCTATCTCCCTGATATTACAGTGGAGCGGATTAAAATG-GAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAA-GCTAGAA
* * * *
42459505 TCTTATCTCTCTGA-AGTTACAACAGAGTAGATCGCATCAGATGGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TT---ACAGCG--GA--G---CAGATTGAAGCTAG-AA
42459559 TCTTATCTCCCT-AGGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGA-GATTACAGCGGAGCAGATTGAAGCTAG-AA
* * * * * *
42459603 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATG-GAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAA-GCTAGAA
* * * *
42459647 TCTTATCTCTCTGA-AGTTACAATAGAGTAGATCGCATCAGATGGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TTAC---AGCG--GA--G---CAGATTGAAGCTAG-AA
*
42459701 TCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-AA
* * * * * * * *
42459745 TCCTATCCCCCTGAGATTACAGTGGAACGGATTAAAATG-GAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAA-GCTAGAA
* * *
42459789 TCTTATCTCTCTGA-AGTTACAATAGAGTAGATCGCATCAGATGGAAGCTAGAAA
1 TCTTATCTCCCTGAGA-TTAC---AGCG--GA--G---CAGATTGAAGCTAG-AA
42459843 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAG-AA
* * * * * *
42459887 TCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATG-GAGGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAA-GCTAGAA
** * *
42459931 TCTTATCTCTTTGA-AGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAA
1 TCTTATCTCCCTGAGA-TTAC---AGCG--GA--G---CAGATTGAAGCTAG-AA
* *
42459985 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATCTAATAA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT-AGAA
* * *
42460029 TCCTATCTCACTGAGATTACAGTGGAGC
1 TCTTATCTCCCTGAGATTACAGCGGAGC
42460057 GAATTAAAAT
Statistics
Matches: 445, Mismatches: 84, Indels: 134
0.67 0.13 0.20
Matches are distributed among these distances:
43 4 0.01
44 260 0.58
45 18 0.04
46 4 0.01
47 17 0.04
49 16 0.04
51 17 0.04
52 4 0.01
53 17 0.04
54 84 0.19
55 4 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGAA
Found at i:42459663 original size:142 final size:142
Alignment explanation
Indices: 42459407--42460112 Score: 1216
Period size: 142 Copynumber: 5.0 Consensus size: 142
42459397 AAGTAGATTT
* * *
42459407 AAGCCACAAGTCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGCAATCCTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
* *
42459472 TGATATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAACAGAGTAGAT
66 TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
42459537 CGCATCAGATGG
131 CGCATCAGATGG
42459549 AAGCCAGAAATCTTATCTCCCT-AGGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
1 AAGCCAGAAATCTTATCTCCCTGA-GATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCC
42459613 CTGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGA
65 CTGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGA
42459678 TCGCATCAGATGG
130 TCGCATCAGATGG
* *
42459691 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAACAGATTGAAGCTAGTAATCCTATCCCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
*
42459756 TGAGATTACAGTGGAACGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
66 TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
42459821 CGCATCAGATGG
131 CGCATCAGATGG
*
42459833 AAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
* *
42459898 TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTTTGAAGTTACAGTAGAGTAGAT
66 TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
*
42459963 CGCATCAGATTG
131 CGCATCAGATGG
* * *
42459975 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATCTAATAATCCTATCTCAC
1 AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
* ** **
42460040 TGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGCAGAGTAGAT
66 TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
42460105 CGCATCAG
131 CGCATCAG
42460113 GTCTTATCTC
Statistics
Matches: 538, Mismatches: 24, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
141 1 0.00
142 536 1.00
143 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (142 bp):
AAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCC
TGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGAT
CGCATCAGATGG
Found at i:42460049 original size:98 final size:98
Alignment explanation
Indices: 42459870--42460051 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 98
42459860 TACAGCGGAG
* * * * * * *
42459870 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATGGAGGATCTT
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATGAAGAATCCT
**
42459935 ATCTCTTTGAAGTTACAGTAGAGTAGATCGCAT
66 ATCTCACTGAAGTTACAGTAGAGTAGATCGCAT
* * * *
42459968 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATT-GAATCTAATAATCC
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAAT-GAAGAATCC
42460032 TATCTCACTG-AGATTACAGT
65 TATCTCACTGAAG-TTACAGT
42460052 GGAGCGAATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
97 5 0.07
98 64 0.93
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (98 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATGAAGAATCCT
ATCTCACTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:42460080 original size:44 final size:44
Alignment explanation
Indices: 42459983--42460104 Score: 108
Period size: 44 Copynumber: 2.8 Consensus size: 44
42459973 TGAAGCCAGA
* **
42459983 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAATCTAAT
1 AATCTTATCTCACTGAGATTACAGCGGAGCAGATTGAAAATAAT
* *
42460027 AATCCTATCTCACTGAGATTACAGTGGAGC-GAATT-AAAATAA-
1 AATCTTATCTCACTGAGATTACAGCGGAGCAG-ATTGAAAATAAT
* * *
42460069 AGGATCTTATCTCTCTGA-AGTTACAGCAGAGTAGAT
1 A--ATCTTATCTCACTGAGA-TTACAGCGGAGCAGAT
42460105 CGCATCAGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
42 1 0.02
43 7 0.11
44 54 0.86
45 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCACTGAGATTACAGCGGAGCAGATTGAAAATAAT
Found at i:42463999 original size:69 final size:69
Alignment explanation
Indices: 42463917--42464052 Score: 218
Period size: 69 Copynumber: 2.0 Consensus size: 69
42463907 TTAATCTTTC
42463917 GTGGTACAAGGATCCAAAAGAGCTAATACATTATTATCCAAAGAAACAAAGTGATAATTAATGGA
1 GTGGTACAAGGATCCAAAAGAGCTAATACATTATTATCCAAAGAAACAAAGTGATAATTAATGGA
42463982 TTAT
66 TTAT
* * * * * *
42463986 GTGGTACAAGGATCTAGAAGAGCTGATACATTGTTATCTAGAGAAACAAAGTGATAATTAATGGA
1 GTGGTACAAGGATCCAAAAGAGCTAATACATTATTATCCAAAGAAACAAAGTGATAATTAATGGA
42464051 TT
66 TT
42464053 CTATTTTAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 61 1.00
ACGTcount: A:0.42, C:0.10, G:0.21, T:0.27
Consensus pattern (69 bp):
GTGGTACAAGGATCCAAAAGAGCTAATACATTATTATCCAAAGAAACAAAGTGATAATTAATGGA
TTAT
Found at i:42465733 original size:50 final size:50
Alignment explanation
Indices: 42465546--42465740 Score: 216
Period size: 50 Copynumber: 3.9 Consensus size: 50
42465536 TGATAATAAC
* ** * * *
42465546 GTGCCAAAGCCATGTCCCAGACATGGTCTTACATAGGATGTTTCTTGTAC-
1 GTGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CG
* * * * ** *
42465596 -TGCCAATGACATATCCCAGATATGGTCTTACATGGGAGTTCTCATATTG
1 GTGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* *
42465645 GTGCCAATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCG
1 GTGCCAAAGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATATCG
42465695 GTGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
1 GTGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT
42465741 NNNNNNNNNN
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
49 38 0.31
50 83 0.68
51 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
GTGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:42468252 original size:11 final size:12
Alignment explanation
Indices: 42468222--42468255 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
42468212 CGACCTGCCC
42468222 ATATTAATTTTT
1 ATATTAATTTTT
42468234 ATATTAATTTTT
1 ATATTAATTTTT
42468246 ATA-TAATTTT
1 ATATTAATTTT
42468256 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:42471734 original size:121 final size:122
Alignment explanation
Indices: 42471509--42471748 Score: 428
Period size: 121 Copynumber: 2.0 Consensus size: 122
42471499 AAATTGGATA
**
42471509 AATTTTATTCTTTGGTCCTCTAACTTGTTGATTTATTCTGGATAGGTCTGATAGCTTTGTTGGAT
1 AATTTTATTCTTTGGTCCTCTAACTTGTTGATTTATTCTGGATAGGTCTGATAGCTTTACTGGAT
*
42471574 TACAAAACCGTCCAAATTGGAGACCAAGTCAACCCAATATTCGACTACACATGACTG
66 TACAAAACAGTCCAAATTGGAGACCAAGTCAACCCAATATTCGACTACACATGACTG
42471631 AATTTTATTC-TTGGTCCTCTAACTTGTTGATTTATTCTGGATAGGTCTGATAGCTTTACTGGAT
1 AATTTTATTCTTTGGTCCTCTAACTTGTTGATTTATTCTGGATAGGTCTGATAGCTTTACTGGAT
* *
42471695 TACAAAATAGTCCAAATTGGAGACCAAGTCAACCCAATATTCGGCTACACATGA
66 TACAAAACAGTCCAAATTGGAGACCAAGTCAACCCAATATTCGACTACACATGA
42471749 TTGTCCATTT
Statistics
Matches: 113, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
121 103 0.91
122 10 0.09
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (122 bp):
AATTTTATTCTTTGGTCCTCTAACTTGTTGATTTATTCTGGATAGGTCTGATAGCTTTACTGGAT
TACAAAACAGTCCAAATTGGAGACCAAGTCAACCCAATATTCGACTACACATGACTG
Found at i:42472943 original size:25 final size:25
Alignment explanation
Indices: 42472909--42472958 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42472899 TAGGTAAATT
42472909 TCATCTAGATTAGAATTACATAGGG
1 TCATCTAGATTAGAATTACATAGGG
42472934 TCATCTAGATTAGAATTACATAGGG
1 TCATCTAGATTAGAATTACATAGGG
42472959 ATCAATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (25 bp):
TCATCTAGATTAGAATTACATAGGG
Found at i:42478082 original size:74 final size:75
Alignment explanation
Indices: 42477961--42478129 Score: 277
Period size: 74 Copynumber: 2.3 Consensus size: 75
42477951 ATTTTACAAA
* *
42477961 ATTAATAAGGGAATAATCTTATATCCTTTTGGAAAGAATATAATTCATTTTTCTAACTTT-CATT
1 ATTAATAAGGGAATAATCATATATCCTTTTGGAAAGAATATAATTCATTTTTCTAAATTTCCATT
*
42478025 TTCCTTCTCT
66 TGCCTTCTCT
* *
42478035 ATTAAAAAGGGAATAATCATATATTCTTTTGGAAAGAATATAATTCATTTTTCTAAATTTCCATT
1 ATTAATAAGGGAATAATCATATATCCTTTTGGAAAGAATATAATTCATTTTTCTAAATTTCCATT
42478100 TGCCTTCTCT
66 TGCCTTCTCT
*
42478110 ATTAATAAGAGAATAATCAT
1 ATTAATAAGGGAATAATCAT
42478130 GGTTTTCCTT
Statistics
Matches: 87, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 56 0.64
75 31 0.36
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (75 bp):
ATTAATAAGGGAATAATCATATATCCTTTTGGAAAGAATATAATTCATTTTTCTAAATTTCCATT
TGCCTTCTCT
Found at i:42483746 original size:136 final size:136
Alignment explanation
Indices: 42483498--42483753 Score: 302
Period size: 136 Copynumber: 1.9 Consensus size: 136
42483488 GTTGGTCGAA
* * * * * *
42483498 ACTCACACGAGCTGTCGGTTGAAACGTAGCTACACGGTGTTGCTCTAAAAGTTGTTGAGTATCCG
1 ACTCACACAAGCTGTCGATTGAAACATAGCTACACGGTGTTGCTCTAAAAGCTATTGAGTATCCA
* * * * * *
42483563 TAACAAATGTCGAAACTCGGCCACCGGTAGGGCATCCAGGACTAGCACCCGAAACATGGCAACCT
66 CAACAAATGTCGAAACTCAGCCACCGGTAGGACATCCAAGACCAGCACCCAAAACATGGCAACCT
42483628 AGGTCT
131 AGGTCT
* *
42483634 ACTCACACAAGCTGTCGATCTG-AACATAGCTACATGGTGTTGCTCCT-AAAGCTATTGAGTATT
1 ACTCACACAAGCTGTCGAT-TGAAACATAGCTACACGGTGTTGCT-CTAAAAGCTATTGAGTATC
* * * *
42483697 CACAACAAATGTTGGAACTTAGCCACTGGTAGGACA-CTCAAGACCAGCACCCAAAAC
64 CACAACAAATGTCGAAACTCAGCCACCGGTAGGACATC-CAAGACCAGCACCCAAAAC
42483754 TTGGTAAACC
Statistics
Matches: 99, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
135 1 0.01
136 94 0.95
137 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (136 bp):
ACTCACACAAGCTGTCGATTGAAACATAGCTACACGGTGTTGCTCTAAAAGCTATTGAGTATCCA
CAACAAATGTCGAAACTCAGCCACCGGTAGGACATCCAAGACCAGCACCCAAAACATGGCAACCT
AGGTCT
Found at i:42490355 original size:46 final size:46
Alignment explanation
Indices: 42490287--42490376 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
42490277 TTTATTGCAA
* *
42490287 TAAGAGTTTTAGTTTTATTTATTTTCTTTACTATATCAGGTTTTAT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTACTATATCAGGTTTTAT
* *
42490333 TAAGAGTTTTAGTTTTACTTATTTTCTCTATTATATTAGGTTTT
1 TAAGAGTTTTAGTTTTACTTATTTTCTCTACTATATCAGGTTTT
42490377 TATTTCCTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (46 bp):
TAAGAGTTTTAGTTTTACTTATTTTCTCTACTATATCAGGTTTTAT
Found at i:42493105 original size:15 final size:16
Alignment explanation
Indices: 42493074--42493106 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42493064 GGCAAACATA
42493074 ATTTGAAATATAATAT
1 ATTTGAAATATAATAT
*
42493090 ATTTGTAATA-AATAT
1 ATTTGAAATATAATAT
42493105 AT
1 AT
42493107 GGTTATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
ATTTGAAATATAATAT
Found at i:42495574 original size:27 final size:27
Alignment explanation
Indices: 42495544--42495619 Score: 118
Period size: 27 Copynumber: 2.8 Consensus size: 27
42495534 AATGCTAATA
42495544 CGAGCACATA-AACGGGAAGCTCTCTTT
1 CGAGC-CATACAACGGGAAGCTCTCTTT
42495571 CGAGCCATACAACGGGAAGCTCTCTTT
1 CGAGCCATACAACGGGAAGCTCTCTTT
* *
42495598 CAAGCCATATAACGGGAAGCTC
1 CGAGCCATACAACGGGAAGCTC
42495620 ATGTGAGCCA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.09
27 42 0.91
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (27 bp):
CGAGCCATACAACGGGAAGCTCTCTTT
Found at i:42495634 original size:25 final size:27
Alignment explanation
Indices: 42495544--42495636 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
42495534 AATGCTAATA
*
42495544 CGAGCACATA-AACGGGAAGCTCTCTTT
1 CGAGC-CATATAACGGGAAGCTCTATTT
* *
42495571 CGAGCCATACAACGGGAAGCTCTCTTT
1 CGAGCCATATAACGGGAAGCTCTATTT
* *
42495598 CAAGCCATATAACGGGAAGCTC-ATGT
1 CGAGCCATATAACGGGAAGCTCTATTT
42495624 -GAGCCATATAACG
1 CGAGCCATATAACG
42495637 AAAAGCTCAT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
25 12 0.20
26 6 0.10
27 42 0.70
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (27 bp):
CGAGCCATATAACGGGAAGCTCTATTT
Found at i:42495700 original size:25 final size:25
Alignment explanation
Indices: 42495600--42495701 Score: 91
Period size: 25 Copynumber: 4.1 Consensus size: 25
42495590 CTCTCTTTCA
**
42495600 AGCCATATAACGGGAAGCTCATGTG
1 AGCCATATAACGGGAAGCTCATAAG
**
42495625 AGCCATATAACGAAAAGCTCATAAG
1 AGCCATATAACGGGAAGCTCATAAG
* ** *
42495650 AGCCATAT-TCTTGAAGCTC-TGGAG
1 AGCCATATAACGGGAAGCTCAT-AAG
* *
42495674 AGCCATATATCGGGATGCTCATAAG
1 AGCCATATAACGGGAAGCTCATAAG
42495699 AGC
1 AGC
42495702 TGTGGTGTGT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
23 1 0.02
24 17 0.28
25 42 0.69
26 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (25 bp):
AGCCATATAACGGGAAGCTCATAAG
Found at i:42503067 original size:25 final size:25
Alignment explanation
Indices: 42503014--42503080 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
42503004 CTCTTTCAAG
* ** *
42503014 CCATATAACGGGAAGCTTATGTGAG
1 CCATATAACGGGAAGCTCATAAGAA
*
42503039 CCATGTAACGGGAAGCTCATAAGAA
1 CCATATAACGGGAAGCTCATAAGAA
*
42503064 CCATAT-TCGGGAAGCTC
1 CCATATAACGGGAAGCTC
42503081 CGGGGAGCCA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
24 10 0.29
25 25 0.71
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (25 bp):
CCATATAACGGGAAGCTCATAAGAA
Found at i:42505971 original size:136 final size:136
Alignment explanation
Indices: 42505814--42506075 Score: 515
Period size: 136 Copynumber: 1.9 Consensus size: 136
42505804 TCACATTGTA
*
42505814 AGTTCTGCTCATAACCACAGAATCCCCTTTTTTTCTTTTTAATGAAATAAAATTTTAATTTTGGA
1 AGTTCTGCTCATAACCACAGAATCCCCTTTTTTTCTTTTTAATGAAATAAAAATTTAATTTTGGA
42505879 GGACTAGAAAAAACAATCAAGTGTCAAAAATAAGTTTTGGCAACTACTTAACAAACATGAACAGT
66 GGACTAGAAAAAACAATCAAGTGTCAAAAATAAGTTTTGGCAACTACTTAACAAACATGAACAGT
42505944 CACATT
131 CACATT
42505950 AGTTCTGCTCATAACCACAGAATCCCCTTTTTTTCTTTTTAATGAAATAAAAATTTAATTTTGGA
1 AGTTCTGCTCATAACCACAGAATCCCCTTTTTTTCTTTTTAATGAAATAAAAATTTAATTTTGGA
42506015 GGACTAGAAAAAACAATCAAGTGTCAAAAATAAGTTTTGGCAACTACTTAACAAACATGAA
66 GGACTAGAAAAAACAATCAAGTGTCAAAAATAAGTTTTGGCAACTACTTAACAAACATGAA
42506076 AATAAATTTA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 125 1.00
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (136 bp):
AGTTCTGCTCATAACCACAGAATCCCCTTTTTTTCTTTTTAATGAAATAAAAATTTAATTTTGGA
GGACTAGAAAAAACAATCAAGTGTCAAAAATAAGTTTTGGCAACTACTTAACAAACATGAACAGT
CACATT
Found at i:42513137 original size:21 final size:21
Alignment explanation
Indices: 42513111--42513161 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
42513101 CTACCTTTGA
42513111 TGTTGCGACACAGGGTTACTG
1 TGTTGCGACACAGGGTTACTG
* *
42513132 TGTTGCGACATAGGGTTATTG
1 TGTTGCGACACAGGGTTACTG
*
42513153 TGTTACGAC
1 TGTTGCGAC
42513162 GCAAGCTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.31, T:0.33
Consensus pattern (21 bp):
TGTTGCGACACAGGGTTACTG
Found at i:42517689 original size:28 final size:28
Alignment explanation
Indices: 42517632--42517693 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
42517622 TGAAAAAGCA
*
42517632 AAGACATGAATTTAATATGTAATATACT
1 AAGACATGAATTTAATATGTAACATACT
* *
42517660 AAGACATG-ATTTAAATATGTAGCATGCT
1 AAGACATGAATTT-AATATGTAACATACT
42517688 AAGACA
1 AAGACA
42517694 AAATAATGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (28 bp):
AAGACATGAATTTAATATGTAACATACT
Found at i:42519676 original size:24 final size:23
Alignment explanation
Indices: 42519624--42519677 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
42519614 AATTTTTTTC
*
42519624 ATTTTCATTTTCCTTTTCTTGTTC
1 ATTTTCATTTT-CTTTTCTTGTTA
*
42519648 TTTTTCATTATT-TTTCTCTTGTTA
1 ATTTTCATT-TTCTTT-TCTTGTTA
42519672 ATTTTC
1 ATTTTC
42519678 TCTCGACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 3 0.12
24 20 0.80
25 2 0.08
ACGTcount: A:0.11, C:0.17, G:0.04, T:0.69
Consensus pattern (23 bp):
ATTTTCATTTTCTTTTCTTGTTA
Found at i:42528054 original size:20 final size:20
Alignment explanation
Indices: 42528031--42528075 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
42528021 GAGCTTAAAC
* *
42528031 GAGCTGATTTAAGCTCAAAT
1 GAGCTAATTGAAGCTCAAAT
* *
42528051 GAGCTAATTGGAGCTGAAAT
1 GAGCTAATTGAAGCTCAAAT
42528071 GAGCT
1 GAGCT
42528076 TGTGGAGCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (20 bp):
GAGCTAATTGAAGCTCAAAT
Found at i:42535488 original size:27 final size:28
Alignment explanation
Indices: 42535445--42535860 Score: 375
Period size: 27 Copynumber: 15.4 Consensus size: 28
42535435 TGCATTTCGT
*
42535445 GGGT-AAATGACCAAAATACCCTCAG-A
1 GGGTAAAATGACCGAAATACCCTCAGAA
* *
42535471 GGGTAAAATGACCGAAATACCC-CCGTA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* *
42535498 GGGTAAAATGATCGAAATACCC-CCGAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* *
42535525 AGGTAAAATGACCGAAATACCC-CCGAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* *
42535552 GGCTAAAATGACTGAAATACCCCTC-GAA
1 GGGTAAAATGACCGAAATA-CCCTCAGAA
*
42535580 GGGTAAAATGATCGAAATACCCTC-GAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* * * *
42535607 AGATAAAATGACCGAAATACCC-CTGTA
1 GGGTAAAATGACCGAAATACCCTCAGAA
**
42535634 GGGTAAAATGACTAAAATACCCTCA-AA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* * *
42535661 AGGTAAAATGACCG-AATACCC-CCGGA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* *
42535687 GTGTAAAATGATCGAAATACCC-CTA-AA
1 GGGTAAAATGACCGAAATACCCTC-AGAA
** *
42535714 GGGTAAAATGGTCGAAATACCCT-TGAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
*
42535741 GGGTAAAATGACCAAAATACCCTC-GAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
* * * *
42535768 AGGTAAAATGGCTGAAATAACCTC-GAA
1 GGGTAAAATGACCGAAATACCCTCAGAA
*
42535795 GGGTAAAATGATCGAAATAGCCCT-A-AA
1 GGGTAAAATGACCGAAATA-CCCTCAGAA
* * *
42535822 GGGTAAAATGACTGAAATACCCCCA-TA
1 GGGTAAAATGACCGAAATACCCTCAGAA
42535849 GGGTAAAATGAC
1 GGGTAAAATGAC
42535861 TGTTATACCC
Statistics
Matches: 323, Mismatches: 52, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
25 1 0.00
26 29 0.09
27 266 0.82
28 26 0.08
29 1 0.00
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (28 bp):
GGGTAAAATGACCGAAATACCCTCAGAA
Found at i:42535516 original size:54 final size:54
Alignment explanation
Indices: 42535445--42535860 Score: 419
Period size: 54 Copynumber: 7.7 Consensus size: 54
42535435 TGCATTTCGT
* *
42535445 GGGT-AAATGACCAAAATACCCTC-AGAGGGTAAAATGACCGAAATACCCCCGTA
1 GGGTAAAATGACCGAAATACCCTCGA-AGGGTAAAATGACCGAAATACCCCCGAA
* * *
42535498 GGGTAAAATGATCGAAATACCCCCGAAAGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* * * *
42535552 GGCTAAAATGACTGAAATACCCCTCGAAGGGTAAAATGATCGAAATACCCTCGAA
1 GGGTAAAATGACCGAAATA-CCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* * * ** * *
42535607 AGATAAAATGACCGAAATACCC-CTGTAGGGTAAAATGACTAAAATACCCTCAAA
1 GGGTAAAATGACCGAAATACCCTC-GAAGGGTAAAATGACCGAAATACCCCCGAA
* * * * * **
42535661 AGGTAAAATGACCG-AATACCCCCGGAGTGTAAAATGATCGAAATACCCCTAAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
** * * *
42535714 GGGTAAAATGGTCGAAATACCCTTGAAGGGTAAAATGACCAAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* * * * * * **
42535768 AGGTAAAATGGCTGAAATAACCTCGAAGGGTAAAATGATCGAAATAGCCCTAAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* *
42535822 GGGTAAAATGACTGAAATACCC-CCATAGGGTAAAATGAC
1 GGGTAAAATGACCGAAATACCCTCGA-AGGGTAAAATGAC
42535861 TGTTATACCC
Statistics
Matches: 300, Mismatches: 56, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
53 48 0.16
54 204 0.68
55 48 0.16
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (54 bp):
GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
Found at i:42535803 original size:81 final size:81
Alignment explanation
Indices: 42535449--42535860 Score: 421
Period size: 81 Copynumber: 5.1 Consensus size: 81
42535439 TTTCGTGGGT
* * * * *
42535449 AAATGACCAAAATA-CCCTCAGAGGGTAAAAT-GACCGAAATACCCCCGTAGGGTAAAATGATCG
1 AAATGACCGAAATACCCCTGA-AGGGTAAAATGGA-CGAAATACCCTCGAAGGGTAAAATGACCG
42535512 AAATACCCCCGAAAGGTA
64 AAATACCCCCGAAAGGTA
* * *
42535530 AAATGACCGAAATACCCCCGAAGGCTAAAAT-GACTGAAATACCCCTCGAAGGGTAAAATGATCG
1 AAATGACCGAAATACCCCTGAAGGGTAAAATGGAC-GAAATA-CCCTCGAAGGGTAAAATGACCG
* *
42535594 AAATACCCTCGAAAGATA
64 AAATACCCCCGAAAGGTA
* * * *
42535612 AAATGACCGAAATACCCCTGTAGGGTAAAAT-GACTAAAATACCCTCAAAAGGTAAAATGACCG-
1 AAATGACCGAAATACCCCTGAAGGGTAAAATGGAC-GAAATACCCTCGAAGGGTAAAATGACCGA
*
42535675 AATACCCCCG-GAGTGTA
65 AATACCCCCGAAAG-GTA
* * * * *
42535692 AAATGATCGAAATACCCCTAAAGGGTAAAATGGTCGAAATACCCTTGAAGGGTAAAATGACCAAA
1 AAATGACCGAAATACCCCTGAAGGGTAAAATGGACGAAATACCCTCGAAGGGTAAAATGACCGAA
*
42535757 ATACCCTCGAAAGGTA
66 ATACCCCCGAAAGGTA
* * * * *
42535773 AAATGGCTGAAATA-ACCTCGAAGGGTAAAAT-GATCGAAATAGCCCT-AAAGGGTAAAATGACT
1 AAATGACCGAAATACCCCT-GAAGGGTAAAATGGA-CGAAATA-CCCTCGAAGGGTAAAATGACC
*
42535835 GAAATACCCCC-ATAGGGTA
63 GAAATACCCCCGA-AAGGTA
42535854 AAATGAC
1 AAATGAC
42535861 TGTTATACCC
Statistics
Matches: 279, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
79 2 0.01
80 68 0.24
81 126 0.45
82 83 0.30
ACGTcount: A:0.42, C:0.21, G:0.20, T:0.17
Consensus pattern (81 bp):
AAATGACCGAAATACCCCTGAAGGGTAAAATGGACGAAATACCCTCGAAGGGTAAAATGACCGAA
ATACCCCCGAAAGGTA
Found at i:42536244 original size:28 final size:28
Alignment explanation
Indices: 42536212--42536265 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
42536202 CACTGTACTG
42536212 GTTACTATATTGGGCTAAGGCCCACATT
1 GTTACTATATTGGGCTAAGGCCCACATT
* * *
42536240 GTTACTGTTTTGGGCTAAGGCTCACA
1 GTTACTATATTGGGCTAAGGCCCACA
42536266 CTGTACTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (28 bp):
GTTACTATATTGGGCTAAGGCCCACATT
Found at i:42536276 original size:33 final size:33
Alignment explanation
Indices: 42536202--42536296 Score: 92
Period size: 33 Copynumber: 3.0 Consensus size: 33
42536192 TGCATTGTTG
*
42536202 CACTGTACTGGTTACTATATTGGGCTAAGGC-C-
1 CACTGTACT-GTTACTGTATTGGGCTAAGGCTCA
* *
42536234 CAC---ATTGTTACTGTTTTGGGCTAAGGCTCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCTCA
* * *
42536264 CACTGTACTGTTACAGTATAGGGCTTAGGCTCA
1 CACTGTACTGTTACTGTATTGGGCTAAGGCTCA
42536297 GACTAATACT
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
28 19 0.38
29 3 0.06
30 3 0.06
32 3 0.06
33 22 0.44
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (33 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCTCA
Found at i:42536474 original size:6 final size:6
Alignment explanation
Indices: 42536459--42536487 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
42536449 TCACGCTTGC
42536459 TTTT-A TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
42536488 GTTGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:42539066 original size:30 final size:29
Alignment explanation
Indices: 42538990--42539067 Score: 81
Period size: 30 Copynumber: 2.7 Consensus size: 29
42538980 ATATGAGATG
* *
42538990 AAGTTTAATTTT-C-AAACTTTGGGGCAA
1 AAGTGTAATTTTGCTAAAGTTTGGGGCAA
*
42539017 AAGTGTAATTATG-TAAAAGTTTAGGGGCAA
1 AAGTGTAATTTTGCT-AAAGTTT-GGGGCAA
*
42539047 AATTGTAATTTTGCTAAAGTT
1 AAGTGTAATTTTGCTAAAGTT
42539068 AGAATCGAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
27 10 0.24
29 6 0.15
30 24 0.59
31 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.37
Consensus pattern (29 bp):
AAGTGTAATTTTGCTAAAGTTTGGGGCAA
Found at i:42539483 original size:50 final size:49
Alignment explanation
Indices: 42539405--42539641 Score: 226
Period size: 56 Copynumber: 4.9 Consensus size: 49
42539395 ATTTGGGTAA
* *
42539405 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-ATG
42539455 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA--ATG
42539511 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG---C-----
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAATG
** * *
42539552 --A-GTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-ATG
** *
42539599 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42539642 TGTTATGATC
Statistics
Matches: 157, Mismatches: 11, Indels: 37
0.77 0.05 0.18
Matches are distributed among these distances:
38 33 0.21
39 1 0.01
41 1 0.01
50 41 0.26
51 35 0.22
52 1 0.01
55 2 0.01
56 43 0.27
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (49 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAATG
Found at i:42539518 original size:56 final size:50
Alignment explanation
Indices: 42539405--42539641 Score: 228
Period size: 50 Copynumber: 4.8 Consensus size: 50
42539395 ATTTGGGTAA
* * *
42539405 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
42539455 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
42539511 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATT-G----G-C---
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** * * *
42539552 --A-GTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
42539599 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
42539642 TGTTATGATC
Statistics
Matches: 155, Mismatches: 13, Indels: 37
0.76 0.06 0.18
Matches are distributed among these distances:
38 31 0.20
39 2 0.01
44 1 0.01
46 1 0.01
50 41 0.26
51 35 0.23
55 3 0.02
56 41 0.26
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:42539640 original size:89 final size:92
Alignment explanation
Indices: 42539466--42539641 Score: 261
Period size: 89 Copynumber: 1.9 Consensus size: 92
42539456 GAGGTCCCAT
* **
42539466 GTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCC-T-AGATCATGAGACATCCCATGTAAGACCA
42539531 TGTCTGGGACATGGCATTGGCAGTCCCCC
64 TGTCTGGGACATGGCATTGGCAGTCCCCC
42539560 GTAAGACCATGTCTGGGACATGGCATGGGCA-CC-A-AT-ATGAGAACATCCCATGTAAGACCAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCCTAGATCATGAG-ACATCCCATGTAAGACCAT
*
42539621 GTCTGGGACATGGCTTTGGCA
65 GTCTGGGACATGGCATTGGCA
42539642 TGTTATGATC
Statistics
Matches: 77, Mismatches: 4, Indels: 7
0.88 0.05 0.08
Matches are distributed among these distances:
88 5 0.06
89 39 0.51
90 1 0.01
93 2 0.03
94 30 0.39
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (92 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCCTAGATCATGAGACATCCCATGTAAGACCATG
TCTGGGACATGGCATTGGCAGTCCCCC
Found at i:42541058 original size:20 final size:20
Alignment explanation
Indices: 42541001--42541132 Score: 88
Period size: 20 Copynumber: 6.6 Consensus size: 20
42540991 ATATGCTAAT
** *
42541001 AGAGGCACTAAAGTGCAAAT
1 AGAGGCACCGAAGTGCAAAC
* * *
42541021 AGAGGCA-CGATTGAGCAAGC
1 AGAGGCACCGA-AGTGCAAAC
*
42541041 AGAGGCACCGTAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
* *
42541061 AG-GGACACCGAAGTGTATAC
1 AGAGG-CACCGAAGTGCAAAC
*
42541081 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
* ** * *
42541101 AGAGACATTGAAGTGTATAC
1 AGAGGCACCGAAGTGCAAAC
*
42541121 ATAGGCACCGAA
1 AGAGGCACCGAA
42541133 CTACAAATCC
Statistics
Matches: 82, Mismatches: 26, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 3 0.04
20 75 0.91
21 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAC
Found at i:42541084 original size:40 final size:40
Alignment explanation
Indices: 42541040--42541132 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 40
42541030 ATTGAGCAAG
* *
42541040 CAGAGGCACCGTAGTGCAAACAGGGACACCGAAGTGTATA
1 CAGAGGCACCGAAGTGCAAACAGAGACACCGAAGTGTATA
* **
42541080 CAGAGGCACCAAAGTGCAAACAGAGACATTGAAGTGTATA
1 CAGAGGCACCGAAGTGCAAACAGAGACACCGAAGTGTATA
*
42541120 CATAGGCACCGAA
1 CAGAGGCACCGAA
42541133 CTACAAATCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.22, G:0.27, T:0.13
Consensus pattern (40 bp):
CAGAGGCACCGAAGTGCAAACAGAGACACCGAAGTGTATA
Found at i:42548638 original size:21 final size:22
Alignment explanation
Indices: 42548596--42548638 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
42548586 AAATTACATG
* *
42548596 AAATAATATAAATTATGTACAA
1 AAATAATATAAATTAAGCACAA
*
42548618 AAATAATGT-AATTAAGCACAA
1 AAATAATATAAATTAAGCACAA
42548639 TTTCACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (22 bp):
AAATAATATAAATTAAGCACAA
Found at i:42549392 original size:32 final size:32
Alignment explanation
Indices: 42549341--42549401 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
42549331 CATGTTCAAC
*
42549341 CTTTACTTTTCAGACTTTGAGCAAACTTTACT
1 CTTTACTTTTCAGAATTTGAGCAAACTTTACT
* * *
42549373 CTTTATTTTTGAGAATTTGAGCAATCTTT
1 CTTTACTTTTCAGAATTTGAGCAAACTTT
42549402 TATGTGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (32 bp):
CTTTACTTTTCAGAATTTGAGCAAACTTTACT
Found at i:42555105 original size:21 final size:22
Alignment explanation
Indices: 42555062--42555114 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
42555052 AATGTGTAAA
42555062 AAATAAAAATAAACATGAAAAT
1 AAATAAAAATAAACATGAAAAT
*
42555084 AAATAAAAATGAA-AT-AAGAAT
1 AAATAAAAATAAACATGAA-AAT
42555105 AAATAAAAAT
1 AAATAAAAAT
42555115 TATACAAGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 15 0.52
22 12 0.41
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (22 bp):
AAATAAAAATAAACATGAAAAT
Found at i:42555108 original size:10 final size:10
Alignment explanation
Indices: 42555062--42555114 Score: 61
Period size: 10 Copynumber: 5.0 Consensus size: 10
42555052 AATGTGTAAA
42555062 AAATAAAAAT
1 AAATAAAAAT
*
42555072 AAACATGAAAAT
1 -AA-ATAAAAAT
42555084 AAATAAAAAT
1 AAATAAAAAT
*
42555094 GAAATAAGAAT
1 -AAATAAAAAT
42555105 AAATAAAAAT
1 AAATAAAAAT
42555115 TATACAAGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 16 0.44
11 13 0.36
12 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.19
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:42555981 original size:140 final size:142
Alignment explanation
Indices: 42555796--42556065 Score: 379
Period size: 140 Copynumber: 1.9 Consensus size: 142
42555786 AAAAAACATA
* *
42555796 TTTTTATTTTTCAAAATCTAAACTTTTTCATTCTTTAAAAAAACACTATTTTTCTTAAAAATTAA
1 TTTTTATCTTTCAAAATCTAAACTTTCTCATTCTTTAAAAAAACACTATTTTTCTTAAAAATTAA
* * *
42555861 AGCTTTTATTTTTG-A-A-AAAAAAAATCAAATTTTTGTTTTAAAATTTTAAACTTTCCTTTCAA
66 AGCTTTTA-CTTTGAATAGAAAAAAAATCAAAATTTTGTTTTAAAAATTTAAACTTTCCTTTCAA
42555923 ATGACTACTTTTT
130 ATGACTACTTTTT
*
42555936 TTTTTATCTTTCAAAATCTAAACTTTCTC-TT-TTTAAAAAAAAACACTATTTTTCTTAAAGATT
1 TTTTTATCTTTCAAAATCTAAACTTTCTCATTCTTT--AAAAAAACACTATTTTTCTTAAAAATT
*
42555999 AAAGCTTTTACTTTGAAATAGTTGAAAAAAAATCAAAATTTTGTTTTAAAAATTTAAACTTTTCT
64 AAAGCTTTTACTTTG-AATA---GAAAAAAAATCAAAATTTTGTTTTAAAAATTTAAACTTTCCT
42556064 TT
125 TT
42556066 ATAATAACTA
Statistics
Matches: 114, Mismatches: 7, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
138 3 0.03
139 6 0.05
140 63 0.55
141 1 0.01
142 1 0.01
146 40 0.35
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (142 bp):
TTTTTATCTTTCAAAATCTAAACTTTCTCATTCTTTAAAAAAACACTATTTTTCTTAAAAATTAA
AGCTTTTACTTTGAATAGAAAAAAAATCAAAATTTTGTTTTAAAAATTTAAACTTTCCTTTCAAA
TGACTACTTTTT
Found at i:42556861 original size:42 final size:42
Alignment explanation
Indices: 42556763--42557014 Score: 294
Period size: 42 Copynumber: 6.1 Consensus size: 42
42556753 AGGTAAACTA
* * * * *
42556763 GAAAAGTAAACGGGCCTCCACACCTGGGTCTTTAAA--CTA-
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
*** * * *
42556802 GAAAAGTAAACAAACCTCCACACTTGGGTCTCTAAATGTAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
42556844 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * *
42556886 GAAAAGTGAATGGACCTCCGCACCTGGGACTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
42556928 GAAAAGTAAATGGACCTCCACACTTGAGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * *
42556970 GAAAAGTAAATGGAGCTCGACACCTGGGCCTCTAAATGTAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
42557012 GAA
1 GAA
42557015 TGTTTTCCTT
Statistics
Matches: 185, Mismatches: 25, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
39 31 0.17
41 1 0.01
42 153 0.83
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
Found at i:42565013 original size:4 final size:4
Alignment explanation
Indices: 42564990--42565031 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
42564980 TAAATAAACA
* * *
42564990 AATG AACG AATG AGTG AATG AATG GATG AATG AATG AATG AA
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AA
42565032 ATTAGGGCAC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (4 bp):
AATG
Found at i:42569281 original size:10 final size:10
Alignment explanation
Indices: 42569252--42569286 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
42569242 ACTAGACATG
42569252 AAAATAAATA
1 AAAATAAATA
42569262 AAAATGAAATA
1 AAAAT-AAATA
*
42569273 AGAATAAATA
1 AAAATAAATA
42569283 AAAA
1 AAAA
42569287 GTATACAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (10 bp):
AAAATAAATA
Found at i:42571703 original size:27 final size:27
Alignment explanation
Indices: 42571660--42571811 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
42571650 CACGACAGCT
42571660 AAGAATAGCCTTTGTGGCGAACTCTGA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
* * * *
42571687 TAGATTAGCCTTTGTGGTGAACACTGA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
* *
42571714 AAAAATAGCCTTGGTGGCGAACTCTGA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
* ** *
42571741 AAGAATAGCCTTTTTGGTAAACTCTAA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
** * * *
42571768 AAGAATAGTATTTGTTGCAAACTCTAA
1 AAGAATAGCCTTTGTGGCGAACTCTGA
*
42571795 AAGAATAGTCTTTGTGG
1 AAGAATAGCCTTTGTGG
42571812 TGTGTTTTAT
Statistics
Matches: 102, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGCGAACTCTGA
Found at i:42579433 original size:27 final size:27
Alignment explanation
Indices: 42579395--42579446 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
42579385 ATGGTGGGGG
42579395 TAAGGCAATATTAGCATGAAATTTATT
1 TAAGGCAATATTAGCATGAAATTTATT
* * *
42579422 TAAGGGAATATTTGCATGAATTTTA
1 TAAGGCAATATTAGCATGAAATTTA
42579447 ACTTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (27 bp):
TAAGGCAATATTAGCATGAAATTTATT
Found at i:42579576 original size:19 final size:20
Alignment explanation
Indices: 42579552--42579590 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
42579542 GCAAGCATGA
42579552 TTTTTAT-TTAATC-TAAGTT
1 TTTTTATGTT-ATCTTAAGTT
42579571 TTTTTATGTTATCTTAAGTT
1 TTTTTATGTTATCTTAAGTT
42579591 ATGAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTATGTTATCTTAAGTT
Found at i:42582510 original size:27 final size:27
Alignment explanation
Indices: 42582466--42582635 Score: 196
Period size: 27 Copynumber: 6.3 Consensus size: 27
42582456 CACGACAACT
* * * *
42582466 AAGAATAACCTTTCTGGTGAGCTCTAA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
*
42582493 AAGAATAGCATTTTTGGTGAACTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* * *
42582520 AATAATAGCGTTTTTGGTGAACTTTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* * *
42582547 AAGAATAGCCGTTGTGGCGAACTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
*
42582574 AAGAATAGCCTTTTTGGTGAACTTTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* * * *
42582601 AAGAATGGCCTTTATGGCGAATTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
42582628 AAGAATAG
1 AAGAATAG
42582636 TCTATGTGGT
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 119 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (27 bp):
AAGAATAGCCTTTTTGGTGAACTCTGA
Found at i:42583686 original size:22 final size:22
Alignment explanation
Indices: 42583637--42583686 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
42583627 CCATAAACCT
*
42583637 CATTTTTTTCATTTTTTTACAC
1 CATTTTTTTCATTTTTCTACAC
*
42583659 CATTTTTTTC-TTTTCTCTACTC
1 CATTTTTTTCATTTT-TCTACAC
42583681 C-TTTTT
1 CATTTTT
42583687 CGTTCATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (22 bp):
CATTTTTTTCATTTTTCTACAC
Found at i:42585181 original size:9 final size:9
Alignment explanation
Indices: 42585169--42585223 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
42585159 ATGACATGTG
42585169 TATATATTA
1 TATATATTA
42585178 TATATA-TA
1 TATATATTA
*
42585186 TATTATGTTA
1 TA-TATATTA
42585196 -ACT-TATTA
1 TA-TATATTA
42585204 TATATATTA
1 TATATATTA
*
42585213 TATATGTTA
1 TATATATTA
42585222 TA
1 TA
42585224 ATAATAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 9 0.24
9 27 0.71
10 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (9 bp):
TATATATTA
Found at i:42619923 original size:42 final size:41
Alignment explanation
Indices: 42619864--42620000 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 41
42619854 AATCATTGGT
*
42619864 GGTTGCTAGGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACC-TATTTTAAATGTGAAGGG
* * * * *
42619906 GGTTGCTAAGTGATGATTCC-CCGA--CT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCTATTTTAAATGTGAAGGG
*
42619939 GGTTGCTAAATGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACC-TATTTTAAATGTGAAGGG
42619981 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
42620001 CCCAAGGGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
33 20 0.27
34 2 0.03
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 1 0.01
41 2 0.03
42 39 0.53
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCTATTTTAAATGTGAAGGG
Found at i:42619953 original size:75 final size:75
Alignment explanation
Indices: 42619829--42620002 Score: 303
Period size: 75 Copynumber: 2.3 Consensus size: 75
42619819 ATTCCCCCAA
**
42619829 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAGGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATTTT
42619894 AAATGTGAAG
66 AAATGTGAAG
* * *
42619904 GGGGTTGCTAAGTGATGATTCCCCGACTCATTGGTGGTTGCTAAATGCTGATTCCACCGTATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATTTT
42619969 AAATGTGAAG
66 AAATGTGAAG
42619979 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
42620003 CAAGGGGTTG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATTTT
AAATGTGAAG
Found at i:42620015 original size:27 final size:27
Alignment explanation
Indices: 42619979--42620056 Score: 138
Period size: 27 Copynumber: 2.9 Consensus size: 27
42619969 AAATGTGAAG
42619979 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
* *
42620006 GGGGTTGCTAAGTGCTAATTTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
42620033 GGGGTTGCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
42620057 AACTCATTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.28
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:42627009 original size:348 final size:348
Alignment explanation
Indices: 42626540--42627235 Score: 1367
Period size: 348 Copynumber: 2.0 Consensus size: 348
42626530 AAGCGAAAAC
42626540 AGGTAAATTGGCATAATCGGTAAAAATAATTAATGTTTAAAACTGTGTGTTTAGAGTGAGATTTG
1 AGGTAAATTGGCATAATCGGTAAAAATAATTAATGTTTAAAACTGTGTGTTTAGAGTGAGATTTG
42626605 ATGTTGTCATAACAGGGGAAAATGTTCAGAATGTCATAAAACATAAGAATAAGAGATGAAATTTA
66 ATGTTGTCATAACAGGGGAAAATGTTCAGAATGTCATAAAACATAAGAATAAGAGATGAAATTTA
42626670 ATTTCCAAGCCTGGGGATAAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCA
131 ATTTCCAAGCCTGGGGATAAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCA
42626735 AAAAGTTGGGGGAGGACTATTTTAAAAAATGTGAACATTTAATGAGTTAAATTTGCTATTATAGA
196 AAAAGTTGGGGGAGGACTATTTTAAAAAATGTGAACATTTAATGAGTTAAATTTGCTATTATAGA
42626800 TCAAGAAAGATGAGAAGATAATCTCAAACGGGGAAAAGAGAAGGTCGTGAAGTAAATTGCAAAAT
261 TCAAGAAAGATGAGAAGATAATCTCAAACGGGGAAAAGAGAAGGTCGTGAAGTAAATTGCAAAAT
42626865 TACGATATTTTGCACCGAGGTAA
326 TACGATATTTTGCACCGAGGTAA
42626888 AGGTAAATTGGCATAATCGGTAAAAATAATTAATGTTTAAAACTGTGTG-TTAGAGTGAGAATTT
1 AGGTAAATTGGCATAATCGGTAAAAATAATTAATGTTTAAAACTGTGTGTTTAGAGTGAG-ATTT
42626952 GATGTTGTCATAACAGGGGAAAATGTTCAGAATGTCATAAAACATAAGAATAAGAGATGAAATTT
65 GATGTTGTCATAACAGGGGAAAATGTTCAGAATGTCATAAAACATAAGAATAAGAGATGAAATTT
*
42627017 AATTTCCAAGCTTGGGGATAAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTC
130 AATTTCCAAGCCTGGGGATAAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTC
42627082 AAAAAGTTGGGGGAGGACTATTTTAAAAAATGTGAACATTTAATGAGTTAAATTTGCTATTATAG
195 AAAAAGTTGGGGGAGGACTATTTTAAAAAATGTGAACATTTAATGAGTTAAATTTGCTATTATAG
42627147 ATCAAGAAAGATGAGAAGATAATCTCAAACGGGGAAAAGAGAAGGTCGTGAAGTAAATTGCAAAA
260 ATCAAGAAAGATGAGAAGATAATCTCAAACGGGGAAAAGAGAAGGTCGTGAAGTAAATTGCAAAA
42627212 TTACGATATTTTGCACCGAGGTAA
325 TTACGATATTTTGCACCGAGGTAA
42627236 GTAAGCATGT
Statistics
Matches: 346, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
347 10 0.03
348 336 0.97
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (348 bp):
AGGTAAATTGGCATAATCGGTAAAAATAATTAATGTTTAAAACTGTGTGTTTAGAGTGAGATTTG
ATGTTGTCATAACAGGGGAAAATGTTCAGAATGTCATAAAACATAAGAATAAGAGATGAAATTTA
ATTTCCAAGCCTGGGGATAAAAGTGTAAATATGCAAAAGTTTAGGGGCAAAATTGTAATTTTTCA
AAAAGTTGGGGGAGGACTATTTTAAAAAATGTGAACATTTAATGAGTTAAATTTGCTATTATAGA
TCAAGAAAGATGAGAAGATAATCTCAAACGGGGAAAAGAGAAGGTCGTGAAGTAAATTGCAAAAT
TACGATATTTTGCACCGAGGTAA
Found at i:42627571 original size:75 final size:75
Alignment explanation
Indices: 42627448--42627621 Score: 294
Period size: 75 Copynumber: 2.3 Consensus size: 75
42627438 ATTCCCCCAA
* *
42627448 GGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGTGGTAGCTAGGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTAGCTAAGTGCTGATTCCACCATATTTT
42627513 AAATGTGAAG
66 AAATGTGAAG
* * *
42627523 GGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTAGCTAAGTGCTGATTCCACCATATTTT
42627588 AAATGTGAAG
66 AAATGTGAAG
*
42627598 GGGGTTTCTAAGTGCTGATTCCCC
1 GGGGTTGCTAAGTGCTGATTCCCC
42627622 CAAGGGGTTC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 92 1.00
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.34
Consensus pattern (75 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTAGCTAAGTGCTGATTCCACCATATTTT
AAATGTGAAG
Found at i:42627629 original size:102 final size:102
Alignment explanation
Indices: 42627523--42627720 Score: 306
Period size: 102 Copynumber: 1.9 Consensus size: 102
42627513 AAATGTGAAG
* * * * *
42627523 GGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTCCTAAGTGCTGATTCCCAGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTT
* *
42627588 AAATGTGAAGGGGGTTTCTAAGTGCTGATTCCCCCAA
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
42627625 GGGGTTCCTAAGTGCTGTTTCCCAGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTCCTAAGTGCTGATTCCCAGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTT
*
42627690 AAATGTGAAAGGGGTTGCTAAGTGTTGATTC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTC
42627721 TCCGAATCAC
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 86 1.00
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (102 bp):
GGGGTTCCTAAGTGCTGATTCCCAGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:42627737 original size:177 final size:177
Alignment explanation
Indices: 42627418--42627756 Score: 518
Period size: 177 Copynumber: 1.9 Consensus size: 177
42627408 ATTGAATATA
* *
42627418 AAGGGAGTTGCTAAGTTCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCTCGAATCATTGGT
1 AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCTCGAATCATTGGT
* * * *
42627483 GGTAGCTAGGTGCTGATTCCACCATATTTTAAATGTGAAGGGGGTTGCTAAGTGTTGATTCCCCG
66 GGTAGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
* * *
42627548 ACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTG
131 AATCACTGGTGGTTGCTAAGTGCTGAATCCACCATATTTTAAATGTG
* * * *
42627595 AAGGGGGTTTCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGTTTCC-CAGACTCATTGG
1 AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCTC-GAATCATTGG
* * *
42627659 TGGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCTCC
65 TGGTAGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCC
42627724 GAATCACTGGTGGTTGCTAAGTGCTGAATCCAC
130 GAATCACTGGTGGTTGCTAAGTGCTGAATCCAC
42627757 TGATAACGGA
Statistics
Matches: 145, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
176 1 0.01
177 144 0.99
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (177 bp):
AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCTCGAATCATTGGT
GGTAGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
AATCACTGGTGGTTGCTAAGTGCTGAATCCACCATATTTTAAATGTG
Found at i:42630694 original size:4 final size:4
Alignment explanation
Indices: 42630682--42630712 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
42630672 TAAAATTAGT
42630682 TAAA T-AA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
42630713 AAGGATAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:42637968 original size:31 final size:31
Alignment explanation
Indices: 42637930--42638151 Score: 390
Period size: 31 Copynumber: 7.1 Consensus size: 31
42637920 NNNNNNNNNN
*
42637930 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42637961 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
42637993 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42638024 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
42638056 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42638087 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
42638119 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
42638150 AA
1 AA
42638152 ATTATCTAAG
Statistics
Matches: 183, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
31 93 0.51
32 90 0.49
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:42638029 original size:63 final size:63
Alignment explanation
Indices: 42637930--42638148 Score: 438
Period size: 63 Copynumber: 3.5 Consensus size: 63
42637920 NNNNNNNNNN
42637930 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
42637993 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
42638056 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
42638119 AAGAGTAATTGAATCCTAATAAAACTCTTT
1 AAGAGTAATTGAATCCTAATAAAACTCTTT
42638149 AAAATTATCT
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 156 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (63 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTCAAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:42639087 original size:20 final size:19
Alignment explanation
Indices: 42639049--42639105 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 19
42639039 CTACAAAGTT
*
42639049 AAAATTAAAGAAGTATTCA
1 AAAATTAAACAAGTATTCA
*
42639068 AAAATTAATACAAGTTTTCA
1 AAAATTAA-ACAAGTATTCA
*
42639088 AAAA-TAAA-AAATATTCA
1 AAAATTAAACAAGTATTCA
42639105 A
1 A
42639106 TCATCCCCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.24
18 1 0.03
19 11 0.33
20 13 0.39
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAATTAAACAAGTATTCA
Found at i:42648726 original size:18 final size:19
Alignment explanation
Indices: 42648694--42648729 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
42648684 TTCAATCCAC
42648694 CATTTCATGTTCCATTTCA
1 CATTTCATGTTCCATTTCA
42648713 CATTTCAT-TTCCATTTC
1 CATTTCATGTTCCATTTC
42648730 TCAACATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.19, C:0.28, G:0.03, T:0.50
Consensus pattern (19 bp):
CATTTCATGTTCCATTTCA
Found at i:42654492 original size:87 final size:88
Alignment explanation
Indices: 42654340--42654539 Score: 264
Period size: 87 Copynumber: 2.3 Consensus size: 88
42654330 ACATAAAAAA
* *
42654340 AAAAAAAGCAATTAAGCCCCTCCTTTTTTGTTTGCACTCAATTGAGCACTTCAACTTTTAAAATG
1 AAAAAAAGCAATTAAGCCCCTGC--TTTTGTTTGCACTCAATTGAGCACTTCAACTTTCAAAATG
*
42654405 CATC-AAAAAGGCCCTCAAAATTCTTC
64 CATCAAAAAAAG-CCTCAAAATT-TTC
* * * *
42654431 AAAAAAAGCAATTAAGTCCCTGCTTTT-TTT-CACTCAATTGGGTACTTGAACTTTCAAAATGCA
1 AAAAAAAGCAATTAAGCCCCTGCTTTTGTTTGCACTCAATTGAGCACTTCAACTTTCAAAATGCA
42654494 TCAAAAAAAGCCTCAAAATTTTC
66 TCAAAAAAAGCCTCAAAATTTTC
*
42654517 -AAAACAGCAATTAAGCCCCTGCT
1 AAAAAAAGCAATTAAGCCCCTGCT
42654540 CTTATTAAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
85 21 0.21
86 3 0.03
87 41 0.41
88 9 0.09
89 4 0.04
91 21 0.21
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (88 bp):
AAAAAAAGCAATTAAGCCCCTGCTTTTGTTTGCACTCAATTGAGCACTTCAACTTTCAAAATGCA
TCAAAAAAAGCCTCAAAATTTTC
Found at i:42654793 original size:11 final size:10
Alignment explanation
Indices: 42654767--42654828 Score: 67
Period size: 9 Copynumber: 6.5 Consensus size: 10
42654757 NNNNNNNNNA
**
42654767 TTTTATAAAA
1 TTTTATAATT
42654777 TTTTATAATT
1 TTTTATAATT
*
42654787 TTTT-TATTT
1 TTTTATAATT
*
42654796 TTTTACAATT
1 TTTTATAATT
42654806 TTTT-TAATT
1 TTTTATAATT
42654815 TTTT-TAATT
1 TTTTATAATT
42654824 TTTTA
1 TTTTA
42654829 ATATTTTAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
9 25 0.57
10 19 0.43
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATAATT
Found at i:42654797 original size:9 final size:9
Alignment explanation
Indices: 42654777--42654827 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
42654767 TTTTATAAAA
*
42654777 TTTTATAAT
1 TTTTTTAAT
42654786 TTTTTT-AT
1 TTTTTTAAT
42654794 TTTTTTACAAT
1 TTTTTT--AAT
42654805 TTTTTTAAT
1 TTTTTTAAT
42654814 TTTTTTAAT
1 TTTTTTAAT
42654823 TTTTT
1 TTTTT
42654828 AATATTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
8 8 0.21
9 22 0.58
11 8 0.21
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:42654799 original size:19 final size:19
Alignment explanation
Indices: 42654777--42654836 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
42654767 TTTTATAAAA
*
42654777 TTTTATAATTTTTTTATTT
1 TTTTATAATTTTTTTAATT
*
42654796 TTTTACAATTTTTTTAATT
1 TTTTATAATTTTTTTAATT
*
42654815 TTTT-TAA-TTTTTTAATA
1 TTTTATAATTTTTTTAATT
42654832 TTTTA
1 TTTTA
42654837 ATATTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 13 0.36
18 2 0.06
19 21 0.58
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTATAATTTTTTTAATT
Found at i:42654829 original size:8 final size:8
Alignment explanation
Indices: 42654775--42654838 Score: 56
Period size: 8 Copynumber: 7.4 Consensus size: 8
42654765 NATTTTATAA
*
42654775 AATTTTAT
1 AATTTTTT
42654783 AATTTTTTT
1 AA-TTTTTT
*
42654792 ATTTTTTT
1 AATTTTTT
42654800 ACAATTTTTTT
1 --AA-TTTTTT
42654811 AATTTTTTT
1 AA-TTTTTT
42654820 AATTTTTT
1 AATTTTTT
*
42654828 AATATTTT
1 AATTTTTT
42654836 AAT
1 AAT
42654839 ATTAAAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
8 24 0.50
9 17 0.35
10 1 0.02
11 6 0.12
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
AATTTTTT
Found at i:42654835 original size:9 final size:9
Alignment explanation
Indices: 42654766--42654841 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
42654756 NNNNNNNNNN
*
42654766 ATTTTATAAA
1 ATTTT-TAAT
42654776 ATTTTATAAT
1 ATTTT-TAAT
*
42654786 -TTTTTTAT
1 ATTTTTAAT
*
42654794 TTTTTTACAAT
1 ATTTTT--AAT
*
42654805 TTTTTTAAT
1 ATTTTTAAT
*
42654814 TTTTTTAAT
1 ATTTTTAAT
42654823 -TTTTTAAT
1 ATTTTTAAT
42654831 A-TTTTAAT
1 ATTTTTAAT
42654839 ATT
1 ATT
42654842 AAAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
8 19 0.33
9 22 0.38
10 9 0.16
11 8 0.14
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:42659335 original size:24 final size:25
Alignment explanation
Indices: 42659284--42659341 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
42659274 TGCCTTCTCA
* * *
42659284 AGCTTCCCGTTATATGGTTCTTGCG
1 AGCTTCCCGTTATATAGCTCTTGAG
*
42659309 AGCTTCCCGTTA-ATAGCTCTTTAG
1 AGCTTCCCGTTATATAGCTCTTGAG
*
42659333 AGCATCCCG
1 AGCTTCCCG
42659342 ATTGATTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (25 bp):
AGCTTCCCGTTATATAGCTCTTGAG
Found at i:42666766 original size:21 final size:23
Alignment explanation
Indices: 42666716--42666760 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
42666706 TTAATGCGCC
* *
42666716 AATTATATTACTTTTTTTAGATA
1 AATTATATTACTTTTTTAAAATA
42666739 AATTATATTAC-TTTTTAAAATA
1 AATTATATTACTTTTTTAAAATA
42666761 TATATAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTATATTACTTTTTTAAAATA
Found at i:42666815 original size:12 final size:13
Alignment explanation
Indices: 42666798--42666826 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42666788 TATCATGAGT
42666798 TTTAAAAAA-ATA
1 TTTAAAAAACATA
42666810 TTTAAAAAACATA
1 TTTAAAAAACATA
42666823 TTTA
1 TTTA
42666827 GTCGGTACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAAAACATA
Found at i:42666959 original size:16 final size:18
Alignment explanation
Indices: 42666926--42666960 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
42666916 TTAAAATCTT
42666926 TATATACAAAGTTAAAAA
1 TATATACAAAGTTAAAAA
*
42666944 TATATA-AATGTTAAAAA
1 TATATACAAAGTTAAAAA
42666961 GTAAATATGA
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:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
TATATACAAAGTTAAAAA
Found at i:42667714 original size:30 final size:30
Alignment explanation
Indices: 42667680--42667740 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
42667670 GATTGGGGAT
* *
42667680 TGGGAGGGAGTAAAAGCTTTGGGGGAAAAG
1 TGGGAAGGAGTAAAAGCTTTGAGGGAAAAG
*
42667710 TGGGAAGGAGTAAAAGTTTTGAGGGAAAAG
1 TGGGAAGGAGTAAAAGCTTTGAGGGAAAAG
42667740 T
1 T
42667741 AAAAAGATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.02, G:0.43, T:0.20
Consensus pattern (30 bp):
TGGGAAGGAGTAAAAGCTTTGAGGGAAAAG
Found at i:42667895 original size:9 final size:9
Alignment explanation
Indices: 42667878--42667908 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
42667868 TCGAGTTGAT
42667878 TCGAATAAC
1 TCGAATAAC
*
42667887 TCGATTAAC
1 TCGAATAAC
42667896 TCGAATAAC
1 TCGAATAAC
42667905 TCGA
1 TCGA
42667909 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:42668966 original size:2 final size:2
Alignment explanation
Indices: 42668959--42668983 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42668949 ATACTTAAAA
42668959 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
42668984 CTAACCACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42669910 original size:199 final size:199
Alignment explanation
Indices: 42669570--42670166 Score: 1079
Period size: 199 Copynumber: 3.0 Consensus size: 199
42669560 CTAATTATCA
*
42669570 ACAAGAAAAAACTTGAAAAAGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
1 ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
* *
42669635 TCCATATTAAGGCTTTTCTAGGGACAAAGGACAGGAAAAGAGTGAGAATGGAAAATTTGTTAATC
66 TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
*
42669700 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTCGCTTAAGCATTAGATTGACAAATTTTTA
131 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
42669765 ATCC
196 ATCC
42669769 ACAAGAAAAAACTTGAAAAGGGCA-CCCTAAAAGAGATTATGTTCACCGACACATTATCTTACAA
1 ACAAGAAAAAACTTGAAAAGGGCATCCC-AAAAGAGATTATGTTCACCGACACATTATCTTACAA
42669833 TTCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAAT
65 TTCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAAT
42669898 CAAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTT
130 CAAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTT
42669963 AATCC
195 AATCC
* *
42669968 ACAAGAAAAAACTTGGAAAGGGCATCCCAAAAGAGATTATGTTCACTGACACATTATCTTACAAT
1 ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
* * * * *
42670033 TCCATATTAAGGCTTTTCTATGTACAAAGGATAGGAAAAGAATGAGGATGGGAAATTTGTTAACC
66 TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
42670098 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
131 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
42670163 ATCC
196 ATCC
42670167 TCCCCTTTTT
Statistics
Matches: 385, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
198 3 0.01
199 379 0.98
200 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (199 bp):
ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
ATCC
Found at i:42676404 original size:9 final size:9
Alignment explanation
Indices: 42676386--42676431 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
42676376 CACTTAAATC
42676386 CAACTCTCT
1 CAACTCTCT
*
42676395 CAATTCTCT
1 CAACTCTCT
*
42676404 CAACTCTTT
1 CAACTCTCT
* *
42676413 CAATTCTTT
1 CAACTCTCT
42676422 CAACTCTCT
1 CAACTCTCT
42676431 C
1 C
42676432 TAGTTTTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (9 bp):
CAACTCTCT
Found at i:42676409 original size:18 final size:18
Alignment explanation
Indices: 42676386--42676431 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
42676376 CACTTAAATC
42676386 CAACTCTCTCAATTCTCT
1 CAACTCTCTCAATTCTCT
* *
42676404 CAACTCTTTCAATTCTTT
1 CAACTCTCTCAATTCTCT
42676422 CAACTCTCTC
1 CAACTCTCTC
42676432 TAGTTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:42676674 original size:10 final size:10
Alignment explanation
Indices: 42676643--42676668 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
42676633 AGTTTTTAAA
42676643 ATTTTAAATT
1 ATTTTAAATT
42676653 ATTTTAAATT
1 ATTTTAAATT
42676663 ATTTTA
1 ATTTTA
42676669 TTTTATCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:42681372 original size:12 final size:12
Alignment explanation
Indices: 42681357--42681389 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
42681347 TGTTGTCATT
42681357 AATGCCAACATC
1 AATGCCAACATC
*
42681369 AATGCCCACATC
1 AATGCCAACATC
42681381 AATGCCAAC
1 AATGCCAAC
42681390 GTATCCAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.36, G:0.09, T:0.15
Consensus pattern (12 bp):
AATGCCAACATC
Found at i:42681596 original size:6 final size:6
Alignment explanation
Indices: 42681585--42681631 Score: 67
Period size: 6 Copynumber: 7.8 Consensus size: 6
42681575 ACTGGGGTGG
* * *
42681585 AGATGA AGATGA AGATGA AGATGA AGATGA GGGTGG AGATGA AGATG
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGATG
42681632 GCTATGAGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.40, T:0.17
Consensus pattern (6 bp):
AGATGA
Found at i:42681602 original size:36 final size:36
Alignment explanation
Indices: 42681561--42681631 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
42681551 AAGGCAATGG
42681561 AGATGAAGACGAAAACTG-GGGTGGAGATGAAGATGA
1 AGATGAAGACGAAAA-TGAGGGTGGAGATGAAGATGA
* *
42681597 AGATGAAGATGAAGATGAGGGTGGAGATGAAGATG
1 AGATGAAGACGAAAATGAGGGTGGAGATGAAGATG
42681632 GCTATGAGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.41, C:0.03, G:0.41, T:0.15
Consensus pattern (36 bp):
AGATGAAGACGAAAATGAGGGTGGAGATGAAGATGA
Found at i:42682735 original size:8 final size:8
Alignment explanation
Indices: 42682722--42682746 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42682712 TTATCAGCTC
42682722 TTATTATT
1 TTATTATT
42682730 TTATTATT
1 TTATTATT
42682738 TTATTATT
1 TTATTATT
42682746 T
1 T
42682747 GAAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:42682988 original size:27 final size:25
Alignment explanation
Indices: 42682958--42683008 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
42682948 TTGTTTTAAC
42682958 TTAATAAATTT-TCTTTGAGTTTTTCTT
1 TTAA-AAATTTCTC-TTGA-TTTTTCTT
*
42682985 TTAAGAATTTCTCTTGATTTTTCT
1 TTAAAAATTTCTCTTGATTTTTCT
42683009 CTTGCCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.61
Consensus pattern (25 bp):
TTAAAAATTTCTCTTGATTTTTCTT
Found at i:42690061 original size:21 final size:21
Alignment explanation
Indices: 42690037--42690087 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
42690027 AGAAGCTCGT
* *
42690037 AAGAGCTGAATAGAAGCACAA
1 AAGAGCTGAACAAAAGCACAA
* *
42690058 AAGAGCTAAACAAAAGCTCAA
1 AAGAGCTGAACAAAAGCACAA
42690079 AAGAGCTGA
1 AAGAGCTGA
42690088 TCCACCCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.10
Consensus pattern (21 bp):
AAGAGCTGAACAAAAGCACAA
Found at i:42692633 original size:14 final size:14
Alignment explanation
Indices: 42692590--42692634 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
42692580 AATTAACTAC
42692590 ACATTAGTCTTAAT
1 ACATTAGTCTTAAT
*
42692604 GCATTATTGTTCTTAAT
1 ACATTA--G-TCTTAAT
42692621 ACATTAGTCTTAAT
1 ACATTAGTCTTAAT
42692635 GTATTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 1 0.04
17 12 0.46
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (14 bp):
ACATTAGTCTTAAT
Found at i:42695904 original size:20 final size:20
Alignment explanation
Indices: 42695876--42695915 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42695866 CATATAATCA
*
42695876 CTATATCACACTACTTTTAC
1 CTATATCACACTAATTTTAC
* *
42695896 CTATTTCACTCTAATTTTAC
1 CTATATCACACTAATTTTAC
42695916 AAAACCTCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (20 bp):
CTATATCACACTAATTTTAC
Found at i:42697693 original size:18 final size:18
Alignment explanation
Indices: 42697672--42697715 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
42697662 AAAATATATT
42697672 AAATCAATGTTTTCAAGA
1 AAATCAATGTTTTCAAGA
*
42697690 AAATCAGTGTTTTCAAGA
1 AAATCAATGTTTTCAAGA
42697708 AAATCAAT
1 AAATCAAT
42697716 TTCATAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (18 bp):
AAATCAATGTTTTCAAGA
Found at i:42706240 original size:50 final size:50
Alignment explanation
Indices: 42706135--42706314 Score: 171
Period size: 50 Copynumber: 3.5 Consensus size: 50
42706125 GGGGATGATA
* * **
42706135 TCCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTATTGACGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCA---A---TATGAGAGG
* * *
42706191 TCCCATGTAAGACCATGTCTGGGACATGGCCTTGGTACCAATATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAGG
** * * **
42706241 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAGG
* *
42706291 TCCCATGTAAGCCCATATCTGGGA
1 TCCCATGTAAGACCATGTCTGGGA
42706315 TATGACATTG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
50 69 0.66
53 1 0.01
56 35 0.33
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAATATGAGAGG
Found at i:42706602 original size:20 final size:20
Alignment explanation
Indices: 42706577--42706626 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
42706567 ATGAGTTATT
42706577 TAAGTAAGCAAGTAAGTAAA
1 TAAGTAAGCAAGTAAGTAAA
42706597 TAAGTAAG-AGAGTAAGTAAA
1 TAAGTAAGCA-AGTAAGTAAA
*
42706617 GAAG-AAGCAA
1 TAAGTAAGCAA
42706627 AGACCATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.56, C:0.04, G:0.24, T:0.16
Consensus pattern (20 bp):
TAAGTAAGCAAGTAAGTAAA
Found at i:42711481 original size:11 final size:11
Alignment explanation
Indices: 42711465--42711490 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42711455 TCCAACGCCC
42711465 GAATAGAAGAT
1 GAATAGAAGAT
42711476 GAATAGAAGAT
1 GAATAGAAGAT
42711487 GAAT
1 GAAT
42711491 TCTCCTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (11 bp):
GAATAGAAGAT
Found at i:42711649 original size:16 final size:17
Alignment explanation
Indices: 42711628--42711662 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42711618 AAATATTAAG
42711628 AAATAAA-AACAAACAA
1 AAATAAACAACAAACAA
*
42711644 AAATAAACATCAAACAA
1 AAATAAACAACAAACAA
42711661 AA
1 AA
42711663 GCCGTTCCCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAAACAACAAACAA
Found at i:42714341 original size:46 final size:45
Alignment explanation
Indices: 42714228--42714480 Score: 301
Period size: 46 Copynumber: 5.5 Consensus size: 45
42714218 TGATGTCATG
* * * * * *
42714228 GTGTCTTTCAACCATGTTCTTATTCATTCTCGACTTGGTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTTCGTCATGTTGCCATA
* ** ** * *
42714273 GTGTCTTTCAACCATGACCTTATTCATTTTTCGTTGTGTTTCCATT
1 GTGTCTTTCAACTATGGTCTTATTCA-TTTTCGTCATGTTGCCATA
*
42714319 GTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTT-CGTCATGTTGCCATA
*
42714365 GTGTCTTTCAACTATGGTGC-TATTCATTTTCTGTCATGATGCCATA
1 GTGTCTTTCAACTATGGT-CTTATTCATTTTC-GTCATGTTGCCATA
* *
42714411 GTTTCTTTCAACTATGGTCATATTCATTTTCTGTCATGTTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTTC-GTCATGTTGCCATA
42714457 GTGTCTTTCAACTATGGTCTTATT
1 GTGTCTTTCAACTATGGTCTTATT
42714481 TGTTTGATTC
Statistics
Matches: 180, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
45 30 0.17
46 149 0.83
47 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (45 bp):
GTGTCTTTCAACTATGGTCTTATTCATTTTCGTCATGTTGCCATA
Found at i:42714389 original size:92 final size:93
Alignment explanation
Indices: 42714217--42714523 Score: 311
Period size: 92 Copynumber: 3.4 Consensus size: 93
42714207 AAATGATCGG
* * * * * * * *
42714217 ATGATGTCATGGTGTCTTTCAACCATGTTCTTATTCATTCTCGA-CTTGGTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
* * *
42714281 CAACCAT-GACCTTATTCATTTT-TCGTT
66 CAACTATGGTCCTTATTCATTTTCT-GTC
* * * *
42714308 GTGTTTCCATTGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
*
42714373 CAACTATGGTGC-TATTCATTTTCTGTC
66 CAACTATGGTCCTTATTCATTTTCTGTC
* * **
42714400 ATGATGCCATAGTTTCTTTCAACTATGGTCATATTCATTTTCTGTCATGTTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
** **
42714465 CAACTATGGT-CTTATTTGTTTGAT-TC
66 CAACTATGGTCCTTATTCATTTTCTGTC
* * * *
42714491 GTGATGCCATAGCGTCTTTCAGCTATGATCTTA
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTA
42714524 CTCGATAGAA
Statistics
Matches: 179, Mismatches: 33, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
91 65 0.36
92 111 0.62
93 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.45
Consensus pattern (93 bp):
ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
CAACTATGGTCCTTATTCATTTTCTGTC
Found at i:42714666 original size:45 final size:45
Alignment explanation
Indices: 42714314--42714666 Score: 134
Period size: 45 Copynumber: 7.8 Consensus size: 45
42714304 CGTTGTGTTT
* * * *
42714314 CCATTGTGTCTTTCAACTATGGTCTTATTCATTTTCCA-TCAT-GTTG
1 CCATAGTGTCTTTAAACTATGGTCTTAATCA-TTTCTAGT-ATAG-TG
* *
42714360 CCATAGTGTCTTTCAACTATGGTGC-TATTCATTTTCT-GTCAT-GATG
1 CCATAGTGTCTTTAAACTATGGT-CTTAATCA-TTTCTAGT-ATAG-TG
* * * *
42714406 CCATAGTTTCTTTCAACTATGGTCATATTCATTTTCT-GTCAT-GTTG
1 CCATAGTGTCTTTAAACTATGGTCTTAATCA-TTTCTAGT-ATAG-TG
* * ** * * *
42714452 CCATAGTGTCTTTCAACTATGGTCTTATTTGTTT-GATTCGT-GATG
1 CCATAGTGTCTTTAAACTATGGTCTTAATCATTTCTAGT-ATAG-TG
* * * * * *** *
42714497 CCATAGCGTCTTTCAGCTATGATCTTACTCGATAGAATCGT-TA-TG
1 CCATAGTGTCTTTAAACTATGGTCTTAATC-AT-TTCTAGTATAGTG
* ** * * * *
42714542 TCATAACGTCTTTTAGCCATGGTCTTACTCATTTCTAGTATAGTG
1 CCATAGTGTCTTTAAACTATGGTCTTAATCATTTCTAGTATAGTG
* * * * * * *
42714587 CCATAGTGTCTTTCATCTCTGGTGTTATTTATTTCTGGTATAGTG
1 CCATAGTGTCTTTAAACTATGGTCTTAATCATTTCTAGTATAGTG
*
42714632 CCATAGTGTCTTTAAACTATGGTCTAAATCATTTC
1 CCATAGTGTCTTTAAACTATGGTCTTAATCATTTC
42714667 CTTCAAGCCA
Statistics
Matches: 246, Mismatches: 51, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
43 3 0.01
44 4 0.02
45 126 0.51
46 111 0.45
47 1 0.00
48 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.16, T:0.44
Consensus pattern (45 bp):
CCATAGTGTCTTTAAACTATGGTCTTAATCATTTCTAGTATAGTG
Found at i:42716329 original size:15 final size:14
Alignment explanation
Indices: 42716300--42716333 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
42716290 AATTAAGTTG
*
42716300 ATAAAGAAAATAAA
1 ATAAACAAAATAAA
42716314 ATAAACAAACATAAA
1 ATAAACAAA-ATAAA
42716329 ATAAA
1 ATAAA
42716334 ATAAAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (14 bp):
ATAAACAAAATAAA
Found at i:42718555 original size:27 final size:27
Alignment explanation
Indices: 42718525--42718581 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
42718515 TGTCTACAAG
42718525 CTTCAAGGATGGTACCCAATATATTTT
1 CTTCAAGGATGGTACCCAATATATTTT
42718552 CTTCAAGGATGGTACCCAATATATTTT
1 CTTCAAGGATGGTACCCAATATATTTT
42718579 CTT
1 CTT
42718582 ACTCTCTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (27 bp):
CTTCAAGGATGGTACCCAATATATTTT
Found at i:42730813 original size:16 final size:16
Alignment explanation
Indices: 42730792--42730822 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42730782 GATAATTATG
42730792 GTGAAATGATATGCGT
1 GTGAAATGATATGCGT
42730808 GTGAAATGATATGCG
1 GTGAAATGATATGCG
42730823 AATGTGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (16 bp):
GTGAAATGATATGCGT
Found at i:42733175 original size:28 final size:28
Alignment explanation
Indices: 42733121--42733216 Score: 113
Period size: 28 Copynumber: 3.4 Consensus size: 28
42733111 GAGCCCTATA
* *
42733121 CAATAACAGT-ACAGTGTAGGCCTTAGCC
1 CAAT-ACAGTAACAATGTGGGCCTTAGCC
* * *
42733149 CAAAATAGTAACAATGTGGGCTTTAGCC
1 CAATACAGTAACAATGTGGGCCTTAGCC
* *
42733177 CAATACAGTAATAGTGTGGGCCTTAGCC
1 CAATACAGTAACAATGTGGGCCTTAGCC
42733205 CAATACAGTAAC
1 CAATACAGTAAC
42733217 CAGTACAGTG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 4 0.07
28 52 0.93
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (28 bp):
CAATACAGTAACAATGTGGGCCTTAGCC
Found at i:42733356 original size:26 final size:26
Alignment explanation
Indices: 42733324--42733397 Score: 121
Period size: 26 Copynumber: 2.8 Consensus size: 26
42733314 ACACACCAAT
42733324 ATCGCAGCAAAGCTGCCAGTAATAGA
1 ATCGCAGCAAAGCTGCCAGTAATAGA
*
42733350 ATTGCAGCAAAGCTGCCAGTAATAGA
1 ATCGCAGCAAAGCTGCCAGTAATAGA
* *
42733376 ATCGCAACGAAGCTGCCAGTAA
1 ATCGCAGCAAAGCTGCCAGTAA
42733398 CAGTATATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
ATCGCAGCAAAGCTGCCAGTAATAGA
Found at i:42733616 original size:27 final size:27
Alignment explanation
Indices: 42733586--42733645 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
42733576 CATCTCCTAG
*
42733586 GGGTATAACAGTTATTTTACCCTATGA
1 GGGTATAACAGTCATTTTACCCTATGA
** * *
42733613 GGGTATTTCAGTCATTTTACCCTTTGG
1 GGGTATAACAGTCATTTTACCCTATGA
42733640 GGGTAT
1 GGGTAT
42733646 TCGATCAGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.23, T:0.40
Consensus pattern (27 bp):
GGGTATAACAGTCATTTTACCCTATGA
Found at i:42733646 original size:27 final size:26
Alignment explanation
Indices: 42733599--42733844 Score: 253
Period size: 27 Copynumber: 9.2 Consensus size: 26
42733589 TATAACAGTT
* *
42733599 ATTTTACCCTATGAGGGTATTTCAGTC
1 ATTTTACCCTTTGGGGGTATTTC-GTC
42733626 ATTTTACCCTTTGGGGGTA-TTCGATC
1 ATTTTACCCTTTGGGGGTATTTCG-TC
* * *
42733652 AGTTTACCCTCTAGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCG-TC
* *
42733679 ATTTTACCCTTCGGGGGTACTTCGGTC
1 ATTTTACCCTTTGGGGGTATTTC-GTC
42733706 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCG-TC
*
42733733 ATTTTACCCTTCGGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCG-TC
* * *
42733760 ATTTTAACCTGTGAGGGTATTTCGGTC
1 ATTTTACCCTTTGGGGGTATTTC-GTC
* *
42733787 ATTTTA-CCTTCTAGGGGTATTTCGGTG
1 ATTTTACCCTT-TGGGGGTATTTC-GTC
* *
42733814 ATTTTACCCTCTAGGGGTATTTCAGTC
1 ATTTTACCCTTTGGGGGTATTTC-GTC
42733841 ATTT
1 ATTT
42733845 GCCCACGAAT
Statistics
Matches: 188, Mismatches: 24, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
25 1 0.01
26 25 0.13
27 157 0.84
28 5 0.03
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTTTGGGGGTATTTCGTC
Found at i:42733730 original size:54 final size:54
Alignment explanation
Indices: 42733599--42733844 Score: 293
Period size: 54 Copynumber: 4.6 Consensus size: 54
42733589 TATAACAGTT
* * *
42733599 ATTTTACCCTATGAGGGTATTTC-AGTCATTTTACCCTTTGGGGGTA-TTCGATC
1 ATTTTACCCTCTGGGGGTATTTCGA-TCATTTTACCCTTCGGGGGTATTTCGATC
* * * *
42733652 AGTTTACCCTCTAGGGGTATTTCGATCATTTTACCCTTCGGGGGTACTTCGGTC
1 ATTTTACCCTCTGGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGATC
*
42733706 ATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGATC
1 ATTTTACCCTCTGGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGATC
* * * * * * *
42733760 ATTTTAACCTGTGAGGGTATTTCGGTCATTTTA-CCTTCTAGGGGTATTTCGGTG
1 ATTTTACCCTCTGGGGGTATTTCGATCATTTTACCCTTC-GGGGGTATTTCGATC
*
42733814 ATTTTACCCTCTAGGGGTATTTC-AGTCATTT
1 ATTTTACCCTCTGGGGGTATTTCGA-TCATTT
42733845 GCCCACGAAT
Statistics
Matches: 166, Mismatches: 23, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
53 44 0.27
54 122 0.73
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (54 bp):
ATTTTACCCTCTGGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTCGATC
Found at i:42733778 original size:81 final size:80
Alignment explanation
Indices: 42733599--42733844 Score: 329
Period size: 81 Copynumber: 3.0 Consensus size: 80
42733589 TATAACAGTT
* *
42733599 ATTTTACCCTATGAGGGTATTTCAGTCATTTTACCCTTTGGGGGTA-TTCGATCAGTTTACCCTC
1 ATTTTACCCT-TGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTC
42733663 TAGGGGTATTTCGATC
65 TAGGGGTATTTCGATC
* *
42733679 ATTTTACCCTTCGGGGGTACTTCGGTCATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCT-
1 ATTTTACCCTT-GAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTC
*
42733743 TCGGGGGTATTTCGATC
65 T-AGGGGTATTTCGATC
* * * *
42733760 ATTTTAACCTGTGAGGGTATTTCGGTCATTTTA-CCTTCTAGGGGTATTTCGGTGATTTTACCCT
1 ATTTTACCCT-TGAGGGTATTTCGGTCATTTTACCCTT-TGGGGGTATTTCGATCATTTTACCCT
42733824 CTAGGGGTATTTC-AGTC
64 CTAGGGGTATTTCGA-TC
42733841 ATTT
1 ATTT
42733845 GCCCACGAAT
Statistics
Matches: 147, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
79 1 0.01
80 47 0.32
81 97 0.66
82 2 0.01
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (80 bp):
ATTTTACCCTTGAGGGTATTTCGGTCATTTTACCCTTTGGGGGTATTTCGATCATTTTACCCTCT
AGGGGTATTTCGATC
Found at i:42744558 original size:45 final size:45
Alignment explanation
Indices: 42744494--42744588 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
42744484 TAACAGATAC
* * *
42744494 TCGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGT
42744539 TCGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGT
42744584 TCGGT
1 TCGGT
42744589 TCACATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (45 bp):
TCGGTGGAATCAGCACATAGCAACCACCTAACTAATCAATGATGT
Found at i:42744659 original size:51 final size:50
Alignment explanation
Indices: 42744597--42744771 Score: 190
Period size: 51 Copynumber: 3.5 Consensus size: 50
42744587 GTTCACATAT
* *
42744597 TAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACACGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCA-TACCATCCGGTACACGTAG
* * * * * * *
42744648 TAGCCTACACATAGTACTACACACGTGATCGAAACTATCCGGTACGCATAG
1 TAGCCTGCACATAGTACTACACATGTGA-CCATACCATCCGGTACACGTAG
* * * *
42744699 AAGCCTGCATATAGTACTACACATGCGACC-TATCATTCCGGTACACGTAG
1 TAGCCTGCACATAGTACTACACATGTGACCATACCA-TCCGGTACACGTAG
*
42744749 TAGCCTGCACATAGGACTACACA
1 TAGCCTGCACATAGTACTACACA
42744772 AACGTGATCC
Statistics
Matches: 99, Mismatches: 23, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
49 2 0.02
50 33 0.33
51 62 0.63
52 2 0.02
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.22
Consensus pattern (50 bp):
TAGCCTGCACATAGTACTACACATGTGACCATACCATCCGGTACACGTAG
Found at i:42746079 original size:19 final size:20
Alignment explanation
Indices: 42746055--42746092 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
42746045 TGAGCTGATT
42746055 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
42746074 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
42746093 ATTCAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:42748221 original size:18 final size:18
Alignment explanation
Indices: 42748200--42748238 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42748190 TCTTTTTATT
42748200 TTTCAAATTT-TTTCTCAA
1 TTTC-AATTTCTTTCTCAA
*
42748218 TTTCAATTTCTTTTTCAA
1 TTTCAATTTCTTTCTCAA
42748236 TTT
1 TTT
42748239 TCTTTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCAATTTCTTTCTCAA
Found at i:42748242 original size:13 final size:12
Alignment explanation
Indices: 42748218--42748297 Score: 61
Period size: 12 Copynumber: 6.4 Consensus size: 12
42748208 TTTTTCTCAA
42748218 TTTCAATTTCTT
1 TTTCAATTTCTT
42748230 TTTCAATTTTCTTT
1 TTTCAA-TTTC-TT
*
42748244 TCTTCGATTTCTT
1 T-TTCAATTTCTT
* **
42748257 TTTCTATCACTT
1 TTTCAATTTCTT
**
42748269 TTTTTATTTCTT
1 TTTCAATTTCTT
**
42748281 TTTCTTTTTCTT
1 TTTCAATTTCTT
42748293 TTTCA
1 TTTCA
42748298 CATGCTGTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
12 37 0.67
13 7 0.13
14 7 0.13
15 4 0.07
ACGTcount: A:0.11, C:0.17, G:0.01, T:0.70
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:42748294 original size:5 final size:6
Alignment explanation
Indices: 42748224--42748296 Score: 51
Period size: 6 Copynumber: 11.7 Consensus size: 6
42748214 TCAATTTCAA
* * **
42748224 TTTCTT TTTCAAT TTTC-T TTTCTT CGATTTCTT TTTCTA TCACTT TTT-TT
1 TTTCTT TTTC-TT TTTCTT TTTCTT ---TTTCTT TTTCTT TTTCTT TTTCTT
42748274 ATTTCTT TTTCTT TTTCTT TTTC
1 -TTTCTT TTTCTT TTTCTT TTTC
42748297 ACATGCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
5 7 0.13
6 33 0.62
7 7 0.13
9 6 0.11
ACGTcount: A:0.08, C:0.18, G:0.01, T:0.73
Consensus pattern (6 bp):
TTTCTT
Done.