Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 127 of 284
Found at i:42422088 original size:28 final size:28
Alignment explanation
Indices: 42422007--42422092 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
42421997 GTGAGCATGA
**
42422007 ATATGAATGTGACAGGGCCTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
*
42422035 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* *
42422064 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
42422092 A
1 A
42422093 AATACAGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 27 0.53
29 24 0.47
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:42431340 original size:45 final size:43
Alignment explanation
Indices: 42431242--42431363 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 43
42431232 GTCATGGTCG
*
42431242 GTAAGCTCCTTCGAGCTGACCAGTAAGCTCAATTGAGCTAAAAC
1 GTAAGCT-CTTCGAGCTGAACAGTAAGCTCAATTGAGCTAAAAC
* * *
42431286 GATAGGCTCTATCGAGCTGAACGGTAAGCTCCAA-TGAGCTGAAAC
1 G-TAAGCTCT-TCGAGCTGAACAGTAAGCT-CAATTGAGCTAAAAC
* *
42431331 AGTAAGCTCTTACGAGCTAAATCAGTAGGCTCA
1 -GTAAGCTCTT-CGAGCTGAA-CAGTAAGCTCA
42431364 TACGAGCTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
44 4 0.06
45 49 0.77
46 11 0.17
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (43 bp):
GTAAGCTCTTCGAGCTGAACAGTAAGCTCAATTGAGCTAAAAC
Found at i:42431347 original size:23 final size:23
Alignment explanation
Indices: 42431242--42431372 Score: 78
Period size: 23 Copynumber: 5.8 Consensus size: 23
42431232 GTCATGGTCG
* * *
42431242 GTAAGCTCCTTCGAGCTG-ACCA
1 GTAAGCTCATACGAGCTGAAACA
* *
42431264 GTAAGCTCA-ATTGAGCTAAAAC-
1 GTAAGCTCATA-CGAGCTGAAACA
* *
42431286 GATAGGCTC-TATCGAGCTG-AACG
1 G-TAAGCTCATA-CGAGCTGAAACA
*
42431309 GTAAGCTCCA-ATGAGCTGAAACA
1 GTAAGCT-CATACGAGCTGAAACA
*
42431332 GTAAGCTCTTACGAGCT-AAATCA
1 GTAAGCTCATACGAGCTGAAA-CA
*
42431355 GTAGGCTCATACGAGCTG
1 GTAAGCTCATACGAGCTG
42431373 TGGTGAGTCC
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
22 32 0.39
23 51 0.61
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (23 bp):
GTAAGCTCATACGAGCTGAAACA
Found at i:42440337 original size:20 final size:20
Alignment explanation
Indices: 42440312--42440365 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
42440302 CACAGGAGCT
42440312 ACACGCCCGTGTGGTTTAGG
1 ACACGCCCGTGTGGTTTAGG
42440332 ACACGCCCGTGTGGTTTAGG
1 ACACGCCCGTGTGGTTTAGG
42440352 ACACGCCCGTGTGG
1 ACACGCCCGTGTGG
42440366 GCAGGCCGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.28, G:0.35, T:0.22
Consensus pattern (20 bp):
ACACGCCCGTGTGGTTTAGG
Found at i:42440924 original size:52 final size:52
Alignment explanation
Indices: 42440841--42440944 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
42440831 AACATGGCCA
* *
42440841 AATCATGTCATTTCATTATGCACACTCAACACATTTACAACACCATAACTTG
1 AATCATGTCATTTCATTATCCACACTCAACACATTCACAACACCATAACTTG
*
42440893 AATCTTGTCATTTCATTATCCACACTCAACACATTCACAACACCATAACTTG
1 AATCATGTCATTTCATTATCCACACTCAACACATTCACAACACCATAACTTG
42440945 TCAAACCAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.31
Consensus pattern (52 bp):
AATCATGTCATTTCATTATCCACACTCAACACATTCACAACACCATAACTTG
Found at i:42445500 original size:9 final size:9
Alignment explanation
Indices: 42445486--42445510 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
42445476 AGTTAGGGAC
42445486 TAAATTGAA
1 TAAATTGAA
42445495 TAAATTGAA
1 TAAATTGAA
42445504 TAAATTG
1 TAAATTG
42445511 TAAAACTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (9 bp):
TAAATTGAA
Found at i:42446672 original size:46 final size:46
Alignment explanation
Indices: 42446619--42446794 Score: 166
Period size: 46 Copynumber: 3.8 Consensus size: 46
42446609 TATTTGGGCA
* *
42446619 TCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42446665 TCCGAACTTGTTGAGTTGAGTCCGAG-T---TTGTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* *
42446710 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
42446758 -CTCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42446795 GCGAGTTACA
Statistics
Matches: 107, Mismatches: 11, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
42 6 0.06
43 5 0.05
45 3 0.03
46 57 0.53
47 24 0.22
48 2 0.02
50 4 0.04
51 6 0.06
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42446774 original size:93 final size:93
Alignment explanation
Indices: 42446615--42446785 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
42446605 GGGATATTTG
* * *
42446615 GGCATCCGAACTCATTGAGTTGAGTCTGAGTTCACTTATGGATGCGAATGTCCGAACTTGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
42446680 TTGAGTCCGAGTTTGTGAGATGTAACTA
66 TTGAGTCCGAGTTTGTGAGATGTAACTA
* * *
42446708 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CTCGAGCTCGTTGA
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC-CGAACTCGTTGA
42446772 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
42446786 CGCTTATGGG
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
92 1 0.01
93 70 0.99
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTTGTGAGATGTAACTA
Found at i:42448821 original size:42 final size:42
Alignment explanation
Indices: 42448713--42448867 Score: 151
Period size: 42 Copynumber: 3.7 Consensus size: 42
42448703 AGCTCGTACA
** *
42448713 ATGCCAATGTCCCAAACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCAAACGTGGTCTTACATGAAATCAAATA-CG
* *
42448756 ATGCC-ACTATCCTAGACAG-GGTCTTACATGAAATCAAATACG
1 ATGCCAAC-ATCCCAAAC-GTGGTCTTACATGAAATCAAATACG
*
42448798 ATGCCAACATCCCAAACGTGGTCTTACACAT-AACAT-AAGT-CG
1 ATGCCAACATCCCAAACGTGGTCTT--ACATGAA-ATCAAATACG
42448840 ATGCCAA-AGTCCCAAACGTGGTCTTACA
1 ATGCCAACA-TCCCAAACGTGGTCTTACA
42448868 CGATAACACA
Statistics
Matches: 96, Mismatches: 8, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
40 3 0.03
41 2 0.02
42 46 0.48
43 38 0.40
44 7 0.07
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (42 bp):
ATGCCAACATCCCAAACGTGGTCTTACATGAAATCAAATACG
Found at i:42463897 original size:27 final size:26
Alignment explanation
Indices: 42463841--42463900 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42463831 ATATGTATAT
* *
42463841 ATATCTGTTCTGGTGGCCTCGCCACT
1 ATATCTGTTCTGGTGACCTCGCCACA
* *
42463867 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTCGCCACA
42463894 ATATCTG
1 ATATCTG
42463901 GTAGCCTCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTCGCCACA
Found at i:42465578 original size:15 final size:15
Alignment explanation
Indices: 42465550--42465629 Score: 67
Period size: 15 Copynumber: 5.4 Consensus size: 15
42465540 GTAGCTTGGG
*
42465550 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
42465565 TCTT-TTTATTCTGGA
1 T-TTCTTTATTCTGGA
* *
42465580 TTTCTTTATTTTGGG
1 TTTCTTTATTCTGGA
* *
42465595 TTTCTCTA-TCTTAGA
1 TTTCTTTATTC-TGGA
*
42465610 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
42465624 TTTCTT
1 TTTCTT
42465630 GTTATCTTTG
Statistics
Matches: 51, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
14 10 0.20
15 37 0.73
16 4 0.08
ACGTcount: A:0.11, C:0.15, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42465618 original size:45 final size:44
Alignment explanation
Indices: 42465545--42465629 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 44
42465535 GTATCGTAGC
* *
42465545 TTGGGTTTCTTTATCCTGGATCTTTTTATTCTGGATTTCTTTATT
1 TTGGGTTTCTCTATCCTAGATCTTTTTATTC-GGATTTCTTTATT
* *
42465590 TTGGGTTTCTCTATCTTAGAT-TTCTTTATTCGGTTTTCTT
1 TTGGGTTTCTCTATCCTAGATCTT-TTTATTCGGATTTCTT
42465630 GTTATCTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
44 10 0.29
45 25 0.71
ACGTcount: A:0.11, C:0.14, G:0.15, T:0.60
Consensus pattern (44 bp):
TTGGGTTTCTCTATCCTAGATCTTTTTATTCGGATTTCTTTATT
Found at i:42468068 original size:46 final size:46
Alignment explanation
Indices: 42468015--42468187 Score: 172
Period size: 46 Copynumber: 3.7 Consensus size: 46
42468005 TTGGGCATCC
42468015 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCT
* * * * *
42468061 GAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCGTCT
* * * * *
42468108 GAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCT
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCT
* * *
42468154 GAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42468188 GCGGGTTACA
Statistics
Matches: 102, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 61 0.60
47 29 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCT
Found at i:42468167 original size:93 final size:93
Alignment explanation
Indices: 42468008--42468180 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
42467998 GGGATATTTG
* *
42468008 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCTGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAG
42468073 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
42468101 GGCATCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCTGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAG
*
42468166 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
42468181 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.30
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCTGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:42477947 original size:31 final size:30
Alignment explanation
Indices: 42477891--42477951 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
42477881 GATTCACGAC
* *
42477891 GACTACTACTGAGATCTCTTCCGATGTCCT
1 GACTACTACCGAGATCCCTTCCGATGTCCT
* *
42477921 NGACTGCTACCGAGATCCCTTTCGATGTCCT
1 -GACTACTACCGAGATCCCTTCCGATGTCCT
42477952 ACAATTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.31
Consensus pattern (30 bp):
GACTACTACCGAGATCCCTTCCGATGTCCT
Found at i:42484788 original size:248 final size:248
Alignment explanation
Indices: 42484350--42484844 Score: 963
Period size: 248 Copynumber: 2.0 Consensus size: 248
42484340 TCTAATACCA
42484350 CTAAATGTAACACCCCAAACCCGGCCTAGACGTTATGACCGGATCTAATGCGCCACATCGAAGCG
1 CTAAATGTAACACCCCAAACCCGGCCTAGACGTTATGACCGGATCTAATGCGCCACATCGAAGCG
42484415 TTCAAAACATTCCGTATTACTTAGTTGGAAAACTTAGTTGGTGTTGTAAAAGACACTTTTAAAAG
66 TTCAAAACATTCCGTATTACTTAGTTGGAAAACTTAGTTGGTGTTGTAAAAGACACTTTTAAAAG
42484480 TAGGTTAAAGTGAATGGAAGCTGTGCACCAGGTAGGAAACCAGGAAGAAGAGGAGGTGAGTCCGT
131 TAGGTTAAAGTGAATGGAAGCTGTGCACCAGGTAGGAAACCAGGAAGAAGAGGAGGTGAGTCCGT
* *
42484545 CGGACTGTTTAAGTACCAAGCTCCCTTCGGATCCAATCCTAGACATGCACACT
196 CGGACTGCTTAAGTACCAAGCTCCCTTCGAATCCAATCCTAGACATGCACACT
42484598 CTAAATGTAACACCCCAAACCCGGCCTAGACGTTATGACCGGATCTAATGCGCCACATCGAAGCG
1 CTAAATGTAACACCCCAAACCCGGCCTAGACGTTATGACCGGATCTAATGCGCCACATCGAAGCG
42484663 TTCAAAACATTCCGTATTACTTAGTTGGAAAACTTAGTTGGTGTTGTAAAAGACACTTTTAAAAG
66 TTCAAAACATTCCGTATTACTTAGTTGGAAAACTTAGTTGGTGTTGTAAAAGACACTTTTAAAAG
*
42484728 TAGGTTAAAGTGAATGGAAGCTGTGCACTAGGTAGGAAACCAGGAAGAAGAGGAGGTGAGTCCGT
131 TAGGTTAAAGTGAATGGAAGCTGTGCACCAGGTAGGAAACCAGGAAGAAGAGGAGGTGAGTCCGT
42484793 CGGACTGCTTAAGTACCAAGCTCCCTTCGAATCCAATCCTAGACATGCACAC
196 CGGACTGCTTAAGTACCAAGCTCCCTTCGAATCCAATCCTAGACATGCACAC
42484845 CGCCATTGCC
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
248 244 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (248 bp):
CTAAATGTAACACCCCAAACCCGGCCTAGACGTTATGACCGGATCTAATGCGCCACATCGAAGCG
TTCAAAACATTCCGTATTACTTAGTTGGAAAACTTAGTTGGTGTTGTAAAAGACACTTTTAAAAG
TAGGTTAAAGTGAATGGAAGCTGTGCACCAGGTAGGAAACCAGGAAGAAGAGGAGGTGAGTCCGT
CGGACTGCTTAAGTACCAAGCTCCCTTCGAATCCAATCCTAGACATGCACACT
Found at i:42495175 original size:46 final size:46
Alignment explanation
Indices: 42495069--42495369 Score: 336
Period size: 46 Copynumber: 6.5 Consensus size: 46
42495059 CATCATACCA
* * ** * * **
42495069 GAAATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCGCGAT-T
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
* * * *
42495114 CAAATGTGCAAGACCATGGTTGAAAAATACCATGGCAACATGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
* * *
42495160 GAAATGTGTAAGACCATGGTTGAAATATACTATGGCAACATGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
* *
42495206 GAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATAT
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
* * * *
42495252 GAAATAACTAAGACCATGGTTGAAAGATACAATGGCAACATGATAGG
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATA-T
* * *
42495299 GAAATGAATAAGACCGTGGTTGAAAGATACCATGGCAACCTGATA-
1 GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
* *
42495344 GAAAATAAGTAAGACCATAGTTGAAA
1 G-AAATGAGTAAGACCATGGTTGAAA
42495370 AACACTATAG
Statistics
Matches: 219, Mismatches: 34, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
45 33 0.15
46 146 0.67
47 40 0.18
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.22
Consensus pattern (46 bp):
GAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGATAT
Found at i:42495183 original size:21 final size:21
Alignment explanation
Indices: 42495159--42495230 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 21
42495149 CAACATGATA
42495159 TGAAATGTGTAAGACCATGGT
1 TGAAATGTGTAAGACCATGGT
* * * * *
42495180 TGAAATATACTATGGCAACATGAT
1 TGAAATGT-GTA-AG-ACCATGGT
42495204 ATGAAATGTGTAAGACCATGGT
1 -TGAAATGTGTAAGACCATGGT
42495226 TGAAA
1 TGAAA
42495231 GATACCATGG
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 12 0.32
22 8 0.22
23 2 0.05
24 8 0.22
25 7 0.19
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.28
Consensus pattern (21 bp):
TGAAATGTGTAAGACCATGGT
Found at i:42500499 original size:20 final size:22
Alignment explanation
Indices: 42500460--42500501 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
42500450 CAATTTAAAT
*
42500460 AATAATAATGATGCAAAATGAA
1 AATAATAATGATGAAAAATGAA
42500482 AATAAT-ATGA-GAAAAATGAA
1 AATAATAATGATGAAAAATGAA
42500502 GATTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 4 0.21
22 6 0.32
ACGTcount: A:0.62, C:0.02, G:0.14, T:0.21
Consensus pattern (22 bp):
AATAATAATGATGAAAAATGAA
Found at i:42501321 original size:38 final size:38
Alignment explanation
Indices: 42501264--42501340 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
42501254 ACCTCTCCAT
*
42501264 TGAATGGTCATGGTGGTTCGAGGAGTTTATACTCTTCA
1 TGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTCA
42501302 TGAATGGTCATGG-GTGTTCGAGGAGTTTATACTCCTCA
1 TGAATGGTCATGGTG-GTTCGAGGAGTTTATACTCCTCA
42501340 T
1 T
42501341 TCTTGCTATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.36
Consensus pattern (38 bp):
TGAATGGTCATGGTGGTTCGAGGAGTTTATACTCCTCA
Found at i:42503010 original size:66 final size:66
Alignment explanation
Indices: 42502929--42503057 Score: 231
Period size: 66 Copynumber: 2.0 Consensus size: 66
42502919 GTGTCGCACA
* *
42502929 CATAGTGTCCATAATGATTCACGAATGTATATTGAGTCCGCACACTTAGTGCTACGTAATCAAAT
1 CATAGTGTCCATAATGATTCACGAATGTATATTGAGTCCGCACACTCAGTGCTACATAATCAAAT
42502994 C
66 C
*
42502995 CATAGTGTCCATAATGATTCACGAATGTATATTGAGTCCGCACACTCAGTGCTATATAATCAA
1 CATAGTGTCCATAATGATTCACGAATGTATATTGAGTCCGCACACTCAGTGCTACATAATCAA
42503058 CTCGCACACT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (66 bp):
CATAGTGTCCATAATGATTCACGAATGTATATTGAGTCCGCACACTCAGTGCTACATAATCAAAT
C
Found at i:42503063 original size:27 final size:27
Alignment explanation
Indices: 42503033--42503210 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42503023 ATATTGAGTC
* * * *
42503033 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42503060 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42503087 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42503115 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42503142 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42503169 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42503196 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42503211 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42503172 original size:82 final size:81
Alignment explanation
Indices: 42503054--42503209 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42503044 TGCTATATAA
* *
42503054 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42503119 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42503136 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42503200 CACTTAGTGC
65 CACTTAGTGC
42503210 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42511016 original size:90 final size:90
Alignment explanation
Indices: 42510863--42511041 Score: 349
Period size: 90 Copynumber: 2.0 Consensus size: 90
42510853 CTTTAGTTTA
42510863 CCAAATTACAGAAATGCCCTCGACTTGTAAAATTATGAAAGTACCCTCAATTTATAGAATTACTG
1 CCAAATTACAGAAATGCCCTCGACTTGTAAAATTATGAAAGTACCCTCAATTTATAGAATTACTG
42510928 TTTTACCATCGATTTATAGAATTAG
66 TTTTACCATCGATTTATAGAATTAG
*
42510953 CCAAATTCCAGAAATGCCCTCGACTTGTAAAATTATGAAAGTACCCTCAATTTATAGAATTACTG
1 CCAAATTACAGAAATGCCCTCGACTTGTAAAATTATGAAAGTACCCTCAATTTATAGAATTACTG
42511018 TTTTACCATCGATTTATAGAATTA
66 TTTTACCATCGATTTATAGAATTA
42511042 CCGTTTTACC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (90 bp):
CCAAATTACAGAAATGCCCTCGACTTGTAAAATTATGAAAGTACCCTCAATTTATAGAATTACTG
TTTTACCATCGATTTATAGAATTAG
Found at i:42511024 original size:27 final size:27
Alignment explanation
Indices: 42510994--42511223 Score: 325
Period size: 27 Copynumber: 8.5 Consensus size: 27
42510984 ATTATGAAAG
* *
42510994 TACCCTCAATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
42511021 TACCATCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
42511048 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
42511075 TACCCTCAATTTATAGAATTACAGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* *
42511102 TACCCTCGATTTATAGAATTATCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
42511129 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
**
42511156 TACCCTCGATTTATAGAATTATTGTTT
1 TACCCTCGATTTATAGAATTACCGTTT
* * *
42511183 TACCTTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTT
*
42511210 TACCTTCGATTTAT
1 TACCCTCGATTTAT
42511224 TATATTACTA
Statistics
Matches: 179, Mismatches: 24, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 179 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCGTTT
Found at i:42511231 original size:81 final size:81
Alignment explanation
Indices: 42510994--42511223 Score: 361
Period size: 81 Copynumber: 2.8 Consensus size: 81
42510984 ATTATGAAAG
*
42510994 TACCCTCAATTTATAGAATTACTGTTTTACCATCGATTTATAGAATTACCGTTTTACCCTCGATT
1 TACCCTCAATTTATAGAATTACTGTTTTACCATCGATTTATAGAATTACCATTTTACCCTCGATT
*
42511059 TACAGAATTACCATTT
66 TATAGAATTACCATTT
* * *
42511075 TACCCTCAATTTATAGAATTACAGTTTTACCCTCGATTTATAGAATTATCATTTTACCCTCGATT
1 TACCCTCAATTTATAGAATTACTGTTTTACCATCGATTTATAGAATTACCATTTTACCCTCGATT
*
42511140 TATAGAATTACCGTTT
66 TATAGAATTACCATTT
* * * * *
42511156 TACCCTCGATTTATAGAATTATTGTTTTACCTTCGATTTACAGAATTACCATTTTACCTTCGATT
1 TACCCTCAATTTATAGAATTACTGTTTTACCATCGATTTATAGAATTACCATTTTACCCTCGATT
42511221 TAT
66 TAT
42511224 TATATTACTA
Statistics
Matches: 136, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 136 1.00
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (81 bp):
TACCCTCAATTTATAGAATTACTGTTTTACCATCGATTTATAGAATTACCATTTTACCCTCGATT
TATAGAATTACCATTT
Found at i:42511308 original size:27 final size:27
Alignment explanation
Indices: 42511227--42511427 Score: 178
Period size: 27 Copynumber: 7.6 Consensus size: 27
42511217 GATTTATTAT
* ** **
42511227 ATTACTAAAATACCATTGGTTTACAAA
1 ATTACCAAAATACCCCTGGTTTGTAAA
* **
42511254 ATTACCAAAATA-CCCTCGATCAGT-AA
1 ATTACCAAAATACCCCT-GGTTTGTAAA
*
42511280 ATTACCAAAATAACCCTGGTTTGTAAA
1 ATTACCAAAATACCCCTGGTTTGTAAA
*
42511307 ATTACTAAAATACCCCTGGTTTGTAAA
1 ATTACCAAAATACCCCTGGTTTGTAAA
* *
42511334 ATTACCAAAATACCCCTGGCTTGCAAA
1 ATTACCAAAATACCCCTGGTTTGTAAA
* *
42511361 ATTACCAAAATACCCCTGATTTATAAA
1 ATTACCAAAATACCCCTGGTTTGTAAA
* * * *
42511388 A-TATCGAAATA-CTCTCGATTTGTAAA
1 ATTACCAAAATACCCCT-GGTTTGTAAA
*
42511414 A-TATCAAAATACCC
1 ATTACCAAAATACCC
42511428 ATGTAGGGTT
Statistics
Matches: 143, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
25 3 0.02
26 47 0.33
27 93 0.65
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
ATTACCAAAATACCCCTGGTTTGTAAA
Found at i:42511450 original size:27 final size:27
Alignment explanation
Indices: 42511420--42511745 Score: 355
Period size: 27 Copynumber: 12.0 Consensus size: 27
42511410 TAAAATATCA
* * *
42511420 AAATACCCATGTAGGGTTGAATTATCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
42511447 AAATAACCCTGTAGGGTATAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
*
42511474 AAATACCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
42511501 AAATAACCCTATAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
42511528 AAATACCCCTATAGGGTAAAATTATTGTCG
1 AAATACCCCTGTAGGGTAGAATTA---CCG
* *
42511558 AAATACCCTTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* *
42511585 AAATAACCCTATAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * **
42511612 AAATACCCCTATAGGGTAAAATTATTG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * *
42511639 AAATACCCCTGTAGGGCAAAATTACCA
1 AAATACCCCTGTAGGGTAGAATTACCG
** * *
42511666 AAATACCTTTGTAGGGTAGAAATACTG
1 AAATACCCCTGTAGGGTAGAATTACCG
42511693 AAATACCCCTGTAGGGTAGAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCG
* * * *
42511720 AGATACCCTTGTGGGGTAAAATTACC
1 AAATACCCCTGTAGGGTAGAATTACC
42511746 ATTTTGCCCC
Statistics
Matches: 249, Mismatches: 47, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
27 226 0.91
30 23 0.09
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
AAATACCCCTGTAGGGTAGAATTACCG
Found at i:42511581 original size:111 final size:108
Alignment explanation
Indices: 42511439--42511745 Score: 393
Period size: 111 Copynumber: 2.8 Consensus size: 108
42511429 TGTAGGGTTG
* * *
42511439 AATTATCGAAATAACCC-TGTAGGGTATAATTACCGAAATACCCCTGTAGGGTAGAATTACTGAA
1 AATTATCGAAAT-ACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAA
* *
42511503 ATAACCCTATAGGGTAGAATTACCGAAATACCCCTATAGGGTAA
65 ATAACCCTATAGGGTAAAATTACCGAAATACCCCTATAGGGCAA
* *
42511547 AATTATTGTCGAAATACCCTTGTAGGGTAGAATTACTGAAATAACCCTATAGGGTAGAATTACCG
1 AATTA---TCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCG
* ** *
42511612 AAATACCCCTATAGGGTAAAATTATTGAAATACCCCTGTAGGGCAA
63 AAATAACCCTATAGGGTAAAATTACCGAAATACCCCTATAGGGCAA
* * * * *
42511658 AATTACCAAAATACCTTTGTAGGGTAGAAATACTGAAATACCCCTGTAGGGTAGAATTACCGAGA
1 AATTATCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAA
* *
42511723 T-ACCCTTGTGGGGTAAAATTACC
66 TAACCC-TATAGGGTAAAATTACC
42511746 ATTTTGCCCC
Statistics
Matches: 171, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
107 3 0.02
108 72 0.42
110 4 0.02
111 92 0.54
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (108 bp):
AATTATCGAAATACCCTTGTAGGGTAGAATTACTGAAATACCCCTGTAGGGTAGAATTACCGAAA
TAACCCTATAGGGTAAAATTACCGAAATACCCCTATAGGGCAA
Found at i:42512024 original size:24 final size:25
Alignment explanation
Indices: 42511949--42512017 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 25
42511939 GGAAGTGCTC
** * *
42511949 AAAGGGCAATGCCCCAGTTTACCGA
1 AAAGGGCTTTGCCCCAGTTTATCAA
*
42511974 AAAGGGCTTTGCCCCGGTTTATCAA
1 AAAGGGCTTTGCCCCAGTTTATCAA
*
42511999 AAATGGCTTTGCCCCAGTT
1 AAAGGGCTTTGCCCCAGTT
42512018 ATTAAAAGAG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (25 bp):
AAAGGGCTTTGCCCCAGTTTATCAA
Found at i:42512030 original size:24 final size:24
Alignment explanation
Indices: 42511958--42512044 Score: 70
Period size: 25 Copynumber: 3.5 Consensus size: 24
42511948 CAAAGGGCAA
*
42511958 TGCCCCAGTTTACCGAAAAG-GGCTT
1 TGCCCCAG-TTATC-AAAAGAGGCTT
*
42511983 TGCCCCGGTTTATCAAAA-ATGGCTT
1 TGCCCCAG-TTATCAAAAGA-GGCTT
* *
42512008 TGCCCCAGTTATTAAAAGAGGCTA
1 TGCCCCAGTTATCAAAAGAGGCTT
*
42512032 GGCCACCAGTTAT
1 TGCC-CCAGTTAT
42512045 ATGATAAAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
24 19 0.37
25 33 0.63
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (24 bp):
TGCCCCAGTTATCAAAAGAGGCTT
Found at i:42512292 original size:31 final size:30
Alignment explanation
Indices: 42512238--42512347 Score: 122
Period size: 31 Copynumber: 3.8 Consensus size: 30
42512228 CGCTTACAGT
* * *
42512238 AAAGGCATCGG-CCAATGCTATGATTTATG
1 AAAGGCTTCGGCCCAGTGATATGATTTATG
42512267 AAACGGCTTCGGCCCAGTGATATGATTTATG
1 AAA-GGCTTCGGCCCAGTGATATGATTTATG
* *
42512298 AAAAG--TCGG-CCAATGATATGATTTATG
1 AAAGGCTTCGGCCCAGTGATATGATTTATG
42512325 AAAAGGCTTCGGCCCAGT-ATATG
1 -AAAGGCTTCGGCCCAGTGATATG
42512348 TCGAGACTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
27 17 0.25
28 8 0.12
29 3 0.04
30 17 0.25
31 23 0.34
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (30 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATG
Found at i:42512316 original size:27 final size:28
Alignment explanation
Indices: 42512245--42512338 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 28
42512235 AGTAAAGGCA
* *
42512245 TCGGCCAATGCTATGATTTATGAAACGGC
1 TCGGCCAATGATATGATTTATGAAA-AGC
*
42512274 TTCGGCCCAGTGATATGATTTATGAAAAG-
1 -TCGG-CCAATGATATGATTTATGAAAAGC
42512303 TCGGCCAATGATATGATTTATGAAAAGGC
1 TCGGCCAATGATATGATTTATGAAAA-GC
42512332 TTCGGCC
1 -TCGGCC
42512339 CAGTATATGT
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.38
28 5 0.09
30 11 0.20
31 19 0.34
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (28 bp):
TCGGCCAATGATATGATTTATGAAAAGC
Found at i:42514678 original size:27 final size:27
Alignment explanation
Indices: 42514658--42514850 Score: 242
Period size: 27 Copynumber: 7.1 Consensus size: 27
42514648 ATTACCAAAG
* **
42514658 TACCTTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42514685 TACCTTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42514712 TACCCACGATTTATGGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42514739 TACCTTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42514766 TACCCTCGATTTATAGAATCACCCTTT
1 TACCCTCGATTTATAGAATTACCATTT
42514793 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42514820 TAGCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
42514847 TACC
1 TACC
42514851 TTCAAATGGG
Statistics
Matches: 144, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 144 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:42514722 original size:54 final size:54
Alignment explanation
Indices: 42514658--42514853 Score: 284
Period size: 54 Copynumber: 3.6 Consensus size: 54
42514648 ATTACCAAAG
* * * *
42514658 TACCTTCGATTTATAGAATTACTGTTTTACCTTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATTACCATTT
* * * *
42514712 TACCCACGATTTATGGAATTACCGTTTTACCTTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATTACCATTT
* * *
42514766 TACCCTCGATTTATAGAATCACCCTTTTACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATTACCATTT
*
42514820 TAGCCTCGATTTATAGAATTACCGTTTTACCTTC
1 TACCCTCGATTTATAGAATTACCGTTTTACCTTC
42514854 AAATGGGCCC
Statistics
Matches: 123, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 123 1.00
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (54 bp):
TACCCTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATTACCATTT
Found at i:42514759 original size:81 final size:81
Alignment explanation
Indices: 42514658--42515205 Score: 306
Period size: 81 Copynumber: 6.9 Consensus size: 81
42514648 ATTACCAAAG
* * * *
42514658 TACCTTCGATTTATAGAATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATT
1 TACCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGATT
* *
42514723 TATGGAATTACCGTTT
66 TATAGAATTACCATTT
* * * * *
42514739 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
1 TACCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGATT
42514804 TATAGAATTACCATTT
66 TATAGAATTACCATTT
* ** * ** **
42514820 TAGCC-TCGATTTATAGAATTACCGTTTTACCTTC-A--AAT-G-GGC-CCATTTGGCTGA-GAT
1 TA-CCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGAT
* * *
42514877 TGGGCTTTAAGGCTATT-CGTATTGT
65 T----TAT-A-G-AATTAC-CATT-T
* ** * * * *
42514902 TA---TCCATATT-TAGAA-TA-C--TTTAGTTTACCAAATTATAGAA--A------TGCCCTCG
1 TACCTTCGAT-TTATAGAATTACCGTTTTACCTT--CGATTTATAGAATCACCCTTTTACCCACG
***
42514951 ACTTGTA-AG-ATTACCAAAG
63 A-TT-TATAGAATTACCATTT
* * * *
42514970 TACCTTCGATTTATAGAATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATT
1 TACCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGATT
* *
42515035 TATGGAATTACCGTTT
66 TATAGAATTACCATTT
* * * * *
42515051 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
1 TACCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGATT
42515116 TATAGAATTACCATTT
66 TATAGAATTACCATTT
* * * * * *
42515132 TAGCC-TCGATTTATAGAATTACCGTTTTACCTTCAATTTACAGAATTACCGTTTTAGCCTCGAT
1 TA-CCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGAT
*
42515196 TTATAAAATT
65 TTATAGAATT
42515206 TCTAAAATAC
Statistics
Matches: 349, Mismatches: 77, Indels: 82
0.69 0.15 0.16
Matches are distributed among these distances:
68 2 0.01
69 4 0.01
70 3 0.01
71 10 0.03
72 3 0.01
73 9 0.03
74 5 0.01
75 21 0.06
76 3 0.01
77 5 0.01
78 7 0.02
79 12 0.03
80 10 0.03
81 248 0.71
82 7 0.02
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (81 bp):
TACCTTCGATTTATAGAATTACCGTTTTACCTTCGATTTATAGAATCACCCTTTTACCCACGATT
TATAGAATTACCATTT
Found at i:42514990 original size:27 final size:27
Alignment explanation
Indices: 42514970--42515205 Score: 296
Period size: 27 Copynumber: 8.7 Consensus size: 27
42514960 ATTACCAAAG
*
42514970 TACCTTCGATTTATAGAATTACTGTTT
1 TACCTTCGATTTATAGAATTACCGTTT
*
42514997 TACCTTTGATTTATAGAATTACCGTTT
1 TACCTTCGATTTATAGAATTACCGTTT
** *
42515024 TACCCACGATTTATGGAATTACCGTTT
1 TACCTTCGATTTATAGAATTACCGTTT
* * *
42515051 TACCTTCGATTTACAAAATTACCATTT
1 TACCTTCGATTTATAGAATTACCGTTT
* * *
42515078 TACCCTCGATTTATAGAATCACCCTTT
1 TACCTTCGATTTATAGAATTACCGTTT
* *
42515105 TACCCTCGATTTATAGAATTACCATTT
1 TACCTTCGATTTATAGAATTACCGTTT
42515132 TAGCC-TCGATTTATAGAATTACCGTTT
1 TA-CCTTCGATTTATAGAATTACCGTTT
* *
42515159 TACCTTCAATTTACAGAATTACCGTTT
1 TACCTTCGATTTATAGAATTACCGTTT
*
42515186 TAGCC-TCGATTTATAAAATT
1 TA-CCTTCGATTTATAGAATT
42515206 TCTAAAATAC
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.01
27 175 0.97
28 4 0.02
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (27 bp):
TACCTTCGATTTATAGAATTACCGTTT
Found at i:42515109 original size:312 final size:312
Alignment explanation
Indices: 42514544--42515167 Score: 1221
Period size: 312 Copynumber: 2.0 Consensus size: 312
42514534 ACACGAGCGT
* *
42514544 ATGGGCCCATTTGGCTGAGAATGGGCTTTAAGGCTATTCGTGTTGTTATCCCTATTTAGAATACT
1 ATGGGCCCATTTGGCTGAGAATGGGCTTTAAGGCTATTCGTATTGTTATCCATATTTAGAATACT
42514609 TTAGTTTACCAAATTATAGAAATGCCCTCGACTTGTAAGATTACCAAAGTACCTTCGATTTATAG
66 TTAGTTTACCAAATTATAGAAATGCCCTCGACTTGTAAGATTACCAAAGTACCTTCGATTTATAG
42514674 AATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATTTATGGAATTACCGTTT
131 AATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATTTATGGAATTACCGTTT
42514739 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
196 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
42514804 TATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAA
261 TATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAA
*
42514856 ATGGGCCCATTTGGCTGAGATTGGGCTTTAAGGCTATTCGTATTGTTATCCATATTTAGAATACT
1 ATGGGCCCATTTGGCTGAGAATGGGCTTTAAGGCTATTCGTATTGTTATCCATATTTAGAATACT
42514921 TTAGTTTACCAAATTATAGAAATGCCCTCGACTTGTAAGATTACCAAAGTACCTTCGATTTATAG
66 TTAGTTTACCAAATTATAGAAATGCCCTCGACTTGTAAGATTACCAAAGTACCTTCGATTTATAG
42514986 AATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATTTATGGAATTACCGTTT
131 AATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATTTATGGAATTACCGTTT
42515051 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
196 TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
42515116 TATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAA
261 TATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAA
42515168 TTTACAGAAT
Statistics
Matches: 309, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
312 309 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (312 bp):
ATGGGCCCATTTGGCTGAGAATGGGCTTTAAGGCTATTCGTATTGTTATCCATATTTAGAATACT
TTAGTTTACCAAATTATAGAAATGCCCTCGACTTGTAAGATTACCAAAGTACCTTCGATTTATAG
AATTACTGTTTTACCTTTGATTTATAGAATTACCGTTTTACCCACGATTTATGGAATTACCGTTT
TACCTTCGATTTACAAAATTACCATTTTACCCTCGATTTATAGAATCACCCTTTTACCCTCGATT
TATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAA
Found at i:42515233 original size:81 final size:81
Alignment explanation
Indices: 42514945--42515236 Score: 194
Period size: 81 Copynumber: 3.6 Consensus size: 81
42514935 TATAGAAATG
* * * * * * ** * **
42514945 CCCTCGACTTGTAAGATTACCAAAGTA-CCTTCGATTTATAGAATTACTGTTTTACCTTTGATTT
1 CCCTCGATTTATAAAATTACCAAAATAGCC-TCGATTTACAAAATTACCATTTTACCCTCAATTT
* * *
42515009 ATAGAATTACCGTTTTA
65 ACAGAATCACCCTTTTA
* ** **** *
42515026 CCCACGATTTATGGAATTACCGTTTTA-CCTTCGATTTACAAAATTACCATTTTACCCTCGATTT
1 CCCTCGATTTATAAAATTACCAAAATAGCC-TCGATTTACAAAATTACCATTTTACCCTCAATTT
*
42515090 ATAGAATCACCCTTTTA
65 ACAGAATCACCCTTTTA
* *** * * * *
42515107 CCCTCGATTTATAGAATTACCATTTTAGCCTCGATTTATAGAATTACCGTTTTACCTTCAATTTA
1 CCCTCGATTTATAAAATTACCAAAATAGCCTCGATTTACAAAATTACCATTTTACCCTCAATTTA
* *
42515172 CAGAATTACCGTTTTA
66 CAGAATCACCCTTTTA
* * * * *
42515188 GCCTCGATTTATAAAATTTCTAAAATA-CCATTGGTTTACAAAATTACCA
1 CCCTCGATTTATAAAATTACCAAAATAGCC-TCGATTTACAAAATTACCA
42515237 AAATACCCAC
Statistics
Matches: 168, Mismatches: 41, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
80 2 0.01
81 164 0.98
82 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (81 bp):
CCCTCGATTTATAAAATTACCAAAATAGCCTCGATTTACAAAATTACCATTTTACCCTCAATTTA
CAGAATCACCCTTTTA
Found at i:42515302 original size:27 final size:27
Alignment explanation
Indices: 42515199--42515480 Score: 172
Period size: 27 Copynumber: 10.7 Consensus size: 27
42515189 CCTCGATTTA
* * ** *
42515199 TAAAATTTCTAAAATACCATTGGTTTA
1 TAAAATTACCAAAATACCCCTGGTTTG
* * **
42515226 CAAAATTACCAAAATACCCAC-GATCAG
1 TAAAATTACCAAAATACCC-CTGGTTTG
42515253 T-AAATTACC-AAA-ACCCCTGGTTTG
1 TAAAATTACCAAAATACCCCTGGTTTG
*
42515277 TAAAATTACTAAAATACCCCTGGTTTG
1 TAAAATTACCAAAATACCCCTGGTTTG
* *
42515304 TAAAATTACCAAAATACCACTGGCTTG
1 TAAAATTACCAAAATACCCCTGGTTTG
* *
42515331 CAAAATTACCAAAATACCCCTGATTTG
1 TAAAATTACCAAAATACCCCTGGTTTG
* * ** *
42515358 TAAAATTATCGAAATA-CTATCGATTTG
1 TAAAATTACCAAAATACCCCT-GGTTTG
* * **
42515385 TAAAA-TATCGAAATACCCCT-GTAGGG
1 TAAAATTACCAAAATACCCCTGGT-TTG
* * *
42515411 TAGAATTACCAAAATA-CCCTGATTTA
1 TAAAATTACCAAAATACCCCTGGTTTG
* * * *
42515437 TAAAA-TATCGAAATA-CTCTCGATTTG
1 TAAAATTACCAAAATACCCCT-GGTTTG
*
42515463 TAAAA-TATCAAAATACCC
1 TAAAATTACCAAAATACCC
42515481 ATGTAGGGTT
Statistics
Matches: 198, Mismatches: 45, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
23 1 0.01
24 8 0.04
25 22 0.11
26 55 0.28
27 112 0.57
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (27 bp):
TAAAATTACCAAAATACCCCTGGTTTG
Found at i:42515346 original size:54 final size:54
Alignment explanation
Indices: 42515193--42515374 Score: 201
Period size: 54 Copynumber: 3.4 Consensus size: 54
42515183 TTTTAGCCTC
* * * * *
42515193 GATTTATAAAATTTCTAAAATACCATTGGTTTACAAAATTACCAAAATACCCAC-
1 GATTTGTAAAATTACCAAAATACCACTGGTTTGCAAAATTACCAAAATACCC-CT
** * * *
42515247 GATCAGT-AAATTACC-AAA-ACCCCTGGTTTGTAAAATTACTAAAATACCCCT
1 GATTTGTAAAATTACCAAAATACCACTGGTTTGCAAAATTACCAAAATACCCCT
* *
42515298 GGTTTGTAAAATTACCAAAATACCACTGGCTTGCAAAATTACCAAAATACCCCT
1 GATTTGTAAAATTACCAAAATACCACTGGTTTGCAAAATTACCAAAATACCCCT
* *
42515352 GATTTGTAAAATTATCGAAATAC
1 GATTTGTAAAATTACCAAAATAC
42515375 TATCGATTTG
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
50 1 0.01
51 30 0.29
52 11 0.11
53 9 0.09
54 53 0.51
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.29
Consensus pattern (54 bp):
GATTTGTAAAATTACCAAAATACCACTGGTTTGCAAAATTACCAAAATACCCCT
Found at i:42515390 original size:54 final size:54
Alignment explanation
Indices: 42515193--42515479 Score: 200
Period size: 54 Copynumber: 5.4 Consensus size: 54
42515183 TTTTAGCCTC
* * * * * **
42515193 GATTTATAAAATTTCTAAAATACCATTGGTTTACAAAATTACCAAAATACCCAC-
1 GATTTGTAAAATTACCAAAATACCACTGATTTGTAAAATTACCAAAATACCC-CT
** * * *
42515247 GATCAGT-AAATTACC-AAA-ACCCCTGGTTTGTAAAATTACTAAAATACCCCT
1 GATTTGTAAAATTACCAAAATACCACTGATTTGTAAAATTACCAAAATACCCCT
* ** *
42515298 GGTTTGTAAAATTACCAAAATACCACTGGCTTGCAAAATTACCAAAATACCCCT
1 GATTTGTAAAATTACCAAAATACCACTGATTTGTAAAATTACCAAAATACCCCT
* * * * *
42515352 GATTTGTAAAATTATCGAAATACTA-TCGATTTGTAAAA-TATCGAAATACCCCT
1 GATTTGTAAAATTACCAAAATACCACT-GATTTGTAAAATTACCAAAATACCCCT
** * * * * *
42515405 G-TAGGGTAGAATTACCAAAATACC-CTGATTTATAAAA-TATCGAAATA-CTCT
1 GAT-TTGTAAAATTACCAAAATACCACTGATTTGTAAAATTACCAAAATACCCCT
*
42515456 CGATTTGTAAAA-TATCAAAATACC
1 -GATTTGTAAAATTACCAAAATACC
42515480 CATGTAGGGT
Statistics
Matches: 186, Mismatches: 38, Indels: 21
0.76 0.16 0.09
Matches are distributed among these distances:
50 1 0.01
51 44 0.24
52 38 0.20
53 41 0.22
54 62 0.33
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (54 bp):
GATTTGTAAAATTACCAAAATACCACTGATTTGTAAAATTACCAAAATACCCCT
Found at i:42515400 original size:26 final size:26
Alignment explanation
Indices: 42515352--42515478 Score: 107
Period size: 26 Copynumber: 4.8 Consensus size: 26
42515342 AAATACCCCT
*
42515352 GATTTGTAAAATTATCGAAATACTATC
1 GATTTGTAAAA-TATCGAAATACTCTC
*
42515379 GATTTGTAAAATATCGAAATAC-CCC
1 GATTTGTAAAATATCGAAATACTCTC
** * * * *
42515404 TG-TAGGGTAGAATTACCAAAATACCCT-
1 -GAT-TTGTA-AAATATCGAAATACTCTC
*
42515431 GATTTATAAAATATCGAAATACTCTC
1 GATTTGTAAAATATCGAAATACTCTC
*
42515457 GATTTGTAAAATATCAAAATAC
1 GATTTGTAAAATATCGAAATAC
42515479 CCATGTAGGG
Statistics
Matches: 77, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
25 15 0.19
26 38 0.49
27 23 0.30
28 1 0.01
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (26 bp):
GATTTGTAAAATATCGAAATACTCTC
Found at i:42515465 original size:78 final size:79
Alignment explanation
Indices: 42515334--42515510 Score: 266
Period size: 78 Copynumber: 2.2 Consensus size: 79
42515324 TGGCTTGCAA
* *
42515334 AATTACCAAAATACCCCTGATTTGTAAAATTATCGAAATACTATCGATTTGTAAAATATCGAAAT
1 AATTACCAAAATA-CCCTGATTTATAAAATTATCGAAATACTATCGATTTGTAAAATATCAAAAT
*
42515399 ACCCCTGTAGGGTAG
65 ACCCATGTAGGGTAG
*
42515414 AATTACCAAAATACCCTGATTTATAAAA-TATCGAAATACTCTCGATTTGTAAAATATCAAAATA
1 AATTACCAAAATACCCTGATTTATAAAATTATCGAAATACTATCGATTTGTAAAATATCAAAATA
*
42515478 CCCATGTAGGGTTG
66 CCCATGTAGGGTAG
* *
42515492 AATTATCGAAATAACCCTG
1 AATTACCAAAAT-ACCCTG
42515511 TAGGGTATAA
Statistics
Matches: 89, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
78 56 0.63
79 20 0.22
80 13 0.15
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (79 bp):
AATTACCAAAATACCCTGATTTATAAAATTATCGAAATACTATCGATTTGTAAAATATCAAAATA
CCCATGTAGGGTAG
Found at i:42515644 original size:53 final size:53
Alignment explanation
Indices: 42515473--42515738 Score: 293
Period size: 53 Copynumber: 5.0 Consensus size: 53
42515463 TAAAATATCA
* * * * * *
42515473 AAATACCCATGTAGGGTTGAATTATCGAAATAACCCTGTAGGGTATAATTACCG
1 AAATACCCCTGTAGGGTAGAATTACCAAAAT-ACCCTGTAGGGTAAAATTACTG
* * ** *
42515527 AAATATCCCTGTAGGGTATAATTACTGAAATATCCCTGTAGGGTAGAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCAAAATA-CCCTGTAGGGTAAAATTACTG
* * *
42515581 AAATAACCCTGTAGGGTAGAATTACCAAAATACACTATAGGGTAAAATTACTG
1 AAATACCCCTGTAGGGTAGAATTACCAAAATACCCTGTAGGGTAAAATTACTG
*
42515634 AAATACCCCTGTAGGGTAGAATTACCAAAATACCCTTGTCGGGTAGAAA-TACTG
1 AAATACCCCTGTAGGGTAGAATTACCAAAATACCC-TGTAGGGTA-AAATTACTG
* * * * *
42515688 -AATACTCCTGTAGGGTATAATTACCGATATACCCTTGTGGGGTAAAATTAC
1 AAATACCCCTGTAGGGTAGAATTACCAAAATACCC-TGTAGGGTAAAATTAC
42515739 CATTTTGCCC
Statistics
Matches: 184, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
52 3 0.02
53 94 0.51
54 84 0.46
55 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (53 bp):
AAATACCCCTGTAGGGTAGAATTACCAAAATACCCTGTAGGGTAAAATTACTG
Found at i:42515739 original size:27 final size:26
Alignment explanation
Indices: 42515473--42515739 Score: 250
Period size: 27 Copynumber: 10.0 Consensus size: 26
42515463 TAAAATATCA
** *
42515473 AAATACCCATGTAGGGTTGAATTATCG
1 AAATACCC-TGTAGGGTAAAATTACCG
*
42515500 AAATAACCCTGTAGGGTATAATTACCG
1 AAAT-ACCCTGTAGGGTAAAATTACCG
* *
42515527 AAATATCCCTGTAGGGTATAATTACTG
1 AAATA-CCCTGTAGGGTAAAATTACCG
* *
42515554 AAATATCCCTGTAGGGTAGAATTACTG
1 AAATA-CCCTGTAGGGTAAAATTACCG
* *
42515581 AAATAACCCTGTAGGGTAGAATTACCA
1 AAAT-ACCCTGTAGGGTAAAATTACCG
* * *
42515608 AAATACACTATAGGGTAAAATTACTG
1 AAATACCCTGTAGGGTAAAATTACCG
* *
42515634 AAATACCCCTGTAGGGTAGAATTACCA
1 AAATA-CCCTGTAGGGTAAAATTACCG
* *
42515661 AAATACCCTTGTCGGGTAGAAA-TACTG
1 AAATACCC-TGTAGGGTA-AAATTACCG
*
42515688 -AATACTCCTGTAGGGTATAATTACCG
1 AAATAC-CCTGTAGGGTAAAATTACCG
* *
42515714 ATATACCCTTGTGGGGTAAAATTACC
1 AAATACCC-TGTAGGGTAAAATTACC
42515740 ATTTTGCCCC
Statistics
Matches: 203, Mismatches: 27, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.01
26 45 0.22
27 149 0.73
28 7 0.03
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (26 bp):
AAATACCCTGTAGGGTAAAATTACCG
Found at i:42515739 original size:80 final size:79
Alignment explanation
Indices: 42515473--42515740 Score: 288
Period size: 80 Copynumber: 3.3 Consensus size: 79
42515463 TAAAATATCA
* * * * * *
42515473 AAATACCCATGTAGGGTTGAATTATCGAAATAACCCTGTAGGGTATAATTACCGAAATATCCCTG
1 AAATACCC-TGTAGGGTAGAATTACCAAAATAACCCTGTAGGGTAGAAATACCAAAATA-CCCTG
42515538 TAGGGTATAATTACTG
64 TAGGGTATAATTACTG
** * * *
42515554 AAATATCCCTGTAGGGTAGAATTACTGAAATAACCCTGTAGGGTAGAATTACCAAAATACACTAT
1 AAATA-CCCTGTAGGGTAGAATTACCAAAATAACCCTGTAGGGTAGAAATACCAAAATACCCTGT
*
42515619 AGGGTAAAATTACTG
65 AGGGTATAATTACTG
* **
42515634 AAATACCCCTGTAGGGTAGAATTACCAAAAT-ACCCTTGTCGGGTAGAAATA-CTGAATACTCCT
1 AAATA-CCCTGTAGGGTAGAATTACCAAAATAACCC-TGTAGGGTAGAAATACCAAAATAC-CCT
*
42515697 GTAGGGTATAATTACCG
63 GTAGGGTATAATTACTG
* * *
42515714 ATATACCCTTGTGGGGTAAAATTACCA
1 AAATACCC-TGTAGGGTAGAATTACCA
42515741 TTTTGCCCCT
Statistics
Matches: 161, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
79 13 0.08
80 95 0.59
81 50 0.31
82 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (79 bp):
AAATACCCTGTAGGGTAGAATTACCAAAATAACCCTGTAGGGTAGAAATACCAAAATACCCTGTA
GGGTATAATTACTG
Found at i:42515963 original size:92 final size:92
Alignment explanation
Indices: 42515806--42515989 Score: 350
Period size: 92 Copynumber: 2.0 Consensus size: 92
42515796 TGGACTGTGT
* *
42515806 GGTTGACGGATTTGATTGTGAATATATGTTGGTGATATGAATGACTTGACTGTGATTGTTTGACT
1 GGTTGACGAATTTGATTGTGAATATATGTTGGTGACATGAATGACTTGACTGTGATTGTTTGACT
42515871 CAAATATGGGCATGACATTCTGTATAC
66 CAAATATGGGCATGACATTCTGTATAC
42515898 GGTTGACGAATTTGATTGTGAATATATGTTGGTGACATGAATGACTTGACTGTGATTGTTTGACT
1 GGTTGACGAATTTGATTGTGAATATATGTTGGTGACATGAATGACTTGACTGTGATTGTTTGACT
42515963 CAAATATGGGCATGACATTCTGTATAC
66 CAAATATGGGCATGACATTCTGTATAC
42515990 ATGACATGTT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.38
Consensus pattern (92 bp):
GGTTGACGAATTTGATTGTGAATATATGTTGGTGACATGAATGACTTGACTGTGATTGTTTGACT
CAAATATGGGCATGACATTCTGTATAC
Found at i:42515980 original size:45 final size:45
Alignment explanation
Indices: 42515842--42515980 Score: 112
Period size: 45 Copynumber: 3.0 Consensus size: 45
42515832 TGTTGGTGAT
42515842 ATGAATGACTTGACTGTGATTGTTTGACTCAAATATGGGCATGAC
1 ATGAATGACTTGACTGTGATTGTTTGACTCAAATATGGGCATGAC
* * * *
42515887 ATTCTGTAT-ACGGTTGAC-G-AATTTGATTG--TGAATATATGTTGG--TGAC
1 A---TGAATGAC--TTGACTGTGA-TTGTTTGACTCAA-ATATG--GGCATGAC
42515934 ATGAATGACTTGACTGTGATTGTTTGACTCAAATATGGGCATGAC
1 ATGAATGACTTGACTGTGATTGTTTGACTCAAATATGGGCATGAC
42515979 AT
1 AT
42515981 TCTGTATACA
Statistics
Matches: 70, Mismatches: 8, Indels: 32
0.64 0.07 0.29
Matches are distributed among these distances:
43 7 0.10
44 11 0.16
45 15 0.21
46 6 0.09
47 13 0.19
48 11 0.16
49 7 0.10
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (45 bp):
ATGAATGACTTGACTGTGATTGTTTGACTCAAATATGGGCATGAC
Found at i:42516062 original size:25 final size:25
Alignment explanation
Indices: 42516034--42516128 Score: 118
Period size: 25 Copynumber: 3.8 Consensus size: 25
42516024 AGGAAGTGCT
**
42516034 AAAAGGGCAATGCCCCAGTTTAACG
1 AAAAGGGCTTTGCCCCAGTTTAACG
* *
42516059 AAAAGGTCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTAACG
** *
42516084 AAAAGGGCTTTGCCCCAGTTTGTCA
1 AAAAGGGCTTTGCCCCAGTTTAACG
*
42516109 AAAAGCGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
42516129 ATTAAAAGAG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTAACG
Found at i:42518587 original size:27 final size:27
Alignment explanation
Indices: 42518567--42518830 Score: 332
Period size: 27 Copynumber: 9.8 Consensus size: 27
42518557 ATTACCAAAG
* **
42518567 TACCTTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
*
42518594 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42518621 AACCCTCGATTTAT-GGATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42518647 TACCTTCAATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
42518674 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
42518701 TACCCTCGATTTATAGAATTACCCTTT
1 TACCCTCGATTTATAGAATTACCATTT
42518728 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42518755 TATCCTCTATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * *
42518782 TACCTTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42518809 TAGCCTCGATTTATAAAATTAC
1 TACCCTCGATTTATAGAATTAC
42518831 TAAAATACCA
Statistics
Matches: 205, Mismatches: 31, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 20 0.10
27 185 0.90
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:42518848 original size:27 final size:27
Alignment explanation
Indices: 42518818--42518997 Score: 152
Period size: 27 Copynumber: 6.8 Consensus size: 27
42518808 TTAGCCTCGA
* **
42518818 TTTATAAAATTACTAAAATACCATTGG
1 TTTATAAAATTACCAAAATACCCCTGG
* *
42518845 TTTACAAAATTACCAAAATA-CCCTCG
1 TTTATAAAATTACCAAAATACCCCTGG
* * *
42518871 ATCAGT-AAATTACC-AAAT-CCCCTAG
1 TTTA-TAAAATTACCAAAATACCCCTGG
* *
42518896 TTTGTAAAATTACTAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCCTGG
*
42518923 TTTGTAAAATTACCAAAATACCCCTGG
1 TTTATAAAATTACCAAAATACCCCTGG
* ** * *
42518950 CTTGCAAAATTACCAAAATGCCCCTGA
1 TTTATAAAATTACCAAAATACCCCTGG
* * *
42518977 TTTGTAAAATTATCGAAATAC
1 TTTATAAAATTACCAAAATAC
42518998 TATCGATTTG
Statistics
Matches: 124, Mismatches: 24, Indels: 10
0.78 0.15 0.06
Matches are distributed among these distances:
24 1 0.01
25 17 0.14
26 17 0.14
27 89 0.72
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTATAAAATTACCAAAATACCCCTGG
Found at i:42519013 original size:54 final size:54
Alignment explanation
Indices: 42518850--42519028 Score: 147
Period size: 54 Copynumber: 3.4 Consensus size: 54
42518840 ATTGGTTTAC
** *
42518850 AAAATTACCAAAATA-CCCTCGATCAGT-AAATTACC-AAAT-CCCCT-AGTTTGT
1 AAAATTACCAAAATACCCCT-GATTTGTAAAATTACCAAAATACACCTGA-TTTGT
* * * ** *
42518901 AAAATTACTAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGCTTGC
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACACCTGATTTGT
* * * *
42518955 AAAATTACCAAAATGCCCCTGATTTGTAAAATTATCGAAATACTATC-GATTTGT
1 AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATAC-ACCTGATTTGT
* *
42519009 AAAA-TATCGAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
42519029 TAGGGTAGAA
Statistics
Matches: 102, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
51 18 0.18
52 12 0.12
53 17 0.17
54 54 0.53
55 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.28
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTGATTTGTAAAATTACCAAAATACACCTGATTTGT
Found at i:42519051 original size:27 final size:27
Alignment explanation
Indices: 42519016--42519285 Score: 308
Period size: 27 Copynumber: 10.0 Consensus size: 27
42519006 TGTAAAATAT
*
42519016 CGAAATACCCCTGTAGGGTAGAATTAT
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
42519043 CGAAATACCCCTGTAGGGTATAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
42519070 CGAAATATCCCTGTAGGGTATAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
*
42519097 CGAAATATCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * * *
42519124 TGAAATAACCCTATAGCGTGGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * *
42519151 CAAAATACCCCTATAGGGTAAAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
**
42519178 TAAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
42519205 CAAAATACCCTTGTCGGGTAGAAATAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* *
42519232 TG-AATACCCCTGTAGGGTATAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
* * * *
42519258 CGATATACCCTTGTGGGGTACAATTAC
1 CGAAATACCCCTGTAGGGTAGAATTAC
42519285 C
1 C
42519286 ATTTTGCCCC
Statistics
Matches: 209, Mismatches: 33, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
26 21 0.10
27 188 0.90
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (27 bp):
CGAAATACCCCTGTAGGGTAGAATTAC
Found at i:42519516 original size:25 final size:25
Alignment explanation
Indices: 42519488--42519582 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
42519478 AGGAAGTGCT
**
42519488 AAAAGGGCAATGCCCCAGTTTAACG
1 AAAAGGGCTTTGCCCCAGTTTAACG
*
42519513 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTAACG
* *
42519538 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTAACG
42519563 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
42519583 ATTAAAAGAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 65 1.00
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.23
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTAACG
Found at i:42520825 original size:75 final size:75
Alignment explanation
Indices: 42520702--42520851 Score: 264
Period size: 75 Copynumber: 2.0 Consensus size: 75
42520692 TCTAACTCTG
42520702 TTTACTGTTATAGATTGAAATGATATATTGAGAAACCACTATAGATAGTAGCACAATACTGGAAC
1 TTTACTGTTATAGATTGAAATGATATATTGAGAAACCACTATAGATAGTAGCACAATACTGGAAC
42520767 TCTCTAGTTA
66 TCTCTAGTTA
* * * *
42520777 TTTACTGTTATAGATTGGAATGCTATATTGAGAAACTACTATAGATAGTAGCACAATACTGGAAT
1 TTTACTGTTATAGATTGAAATGATATATTGAGAAACCACTATAGATAGTAGCACAATACTGGAAC
42520842 TCTCTAGTTA
66 TCTCTAGTTA
42520852 GAGAAACTGT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.35
Consensus pattern (75 bp):
TTTACTGTTATAGATTGAAATGATATATTGAGAAACCACTATAGATAGTAGCACAATACTGGAAC
TCTCTAGTTA
Found at i:42522366 original size:27 final size:27
Alignment explanation
Indices: 42522100--42522364 Score: 341
Period size: 27 Copynumber: 9.8 Consensus size: 27
42522090 ATTACCAAAG
**
42522100 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
*
42522127 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42522154 TACCCTTGATTTATAAAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * *
42522181 TACCCTCAATTTACAGAATTATCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42522208 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
42522235 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42522262 TACTCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42522289 TATCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* * * *
42522316 TACCTTCAATTTACAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
42522343 TACCCTCAATTTATAAAATTAC
1 TACCCTCGATTTATAGAATTAC
42522365 TAAAATACCA
Statistics
Matches: 209, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 209 1.00
ACGTcount: A:0.30, C:0.20, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:42522373 original size:27 final size:27
Alignment explanation
Indices: 42522343--42522506 Score: 118
Period size: 27 Copynumber: 6.1 Consensus size: 27
42522333 ATTACTATTT
* *
42522343 TACCCTCAATTTATAAAATTACTAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * * *
42522370 TACCATTGGTTTACAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
*
42522397 TACCCTCGA-TCAGT-AAATTACCAAAA
1 TACCCTCGATTTA-TAAAATTACCAAAA
* * *
42522423 TAACCCT-GGTTTGTAAAATTACTAAAA
1 T-ACCCTCGATTTATAAAATTACCAAAA
* ** *
42522450 TACCCTTGGGTTGTAAAATTACCAAAA
1 TACCCTCGATTTATAAAATTACCAAAA
* * * * *
42522477 TACCCTTGATTTGTGAAATTATCGAAA
1 TACCCTCGATTTATAAAATTACCAAAA
42522504 TAC
1 TAC
42522507 TATCGATATG
Statistics
Matches: 110, Mismatches: 22, Indels: 10
0.77 0.15 0.07
Matches are distributed among these distances:
26 22 0.20
27 88 0.80
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTATAAAATTACCAAAA
Found at i:42522596 original size:54 final size:54
Alignment explanation
Indices: 42522529--42522713 Score: 253
Period size: 54 Copynumber: 3.4 Consensus size: 54
42522519 AAATATCGAA
*
42522529 ATACCCCTGTAGGGTAGAATTACTGAAATAACCCTATAGGGTAGAATTACCGAG
1 ATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAG
* * * *
42522583 ATACCCCTATAGGGTAAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAA
1 ATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAG
* * * *
42522637 ATACCCTTGTAGGGTAGAAATACTAAAATACCCCTGTAGGGTAGAATTACCGAG
1 ATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAG
* * * *
42522691 ATAACCTTGTGGGGTAAAATTAC
1 ATACCCCTGTAGGGTAGAATTAC
42522714 CATTTTGCCC
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 114 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (54 bp):
ATACCCCTGTAGGGTAGAATTACTGAAATACCCCTATAGGGTAGAATTACCGAG
Found at i:42522706 original size:81 final size:81
Alignment explanation
Indices: 42522516--42522715 Score: 206
Period size: 81 Copynumber: 2.5 Consensus size: 81
42522506 CTATCGATAT
* * * ** *
42522516 GTAAAA-TATCGAAATACCCCTGTAGGGTAGAATTACTGAAATAACCCTATAGGGTAGAATTACC
1 GTAAAATTACCGAAATAACCCTATAGGGTAGAATTACCAAAATAACCCTATAGGGTAGAAATACC
* *
42522580 GAGATACCCCTATAGG
66 AAAATACCCCTATAGG
* * *
42522596 GTAAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAAT-ACCCTTGTAGGGTAGAAATAC
1 GTAAAATTACCGAAATAACCCTATAGGGTAGAATTACCAAAATAACCC-TATAGGGTAGAAATAC
* *
42522660 TAAAATACCCCTGTAGG
65 CAAAATACCCCTATAGG
* * * * * *
42522677 GTAGAATTACCGAGATAACCTTGTGGGGTAAAATTACCA
1 GTAAAATTACCGAAATAACCCTATAGGGTAGAATTACCA
42522716 TTTTGCCCCT
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
80 10 0.10
81 89 0.90
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (81 bp):
GTAAAATTACCGAAATAACCCTATAGGGTAGAATTACCAAAATAACCCTATAGGGTAGAAATACC
AAAATACCCCTATAGG
Found at i:42522714 original size:27 final size:27
Alignment explanation
Indices: 42522525--42522689 Score: 213
Period size: 27 Copynumber: 6.1 Consensus size: 27
42522515 TGTAAAATAT
*
42522525 CGAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTATAGGGTAGAATTAC
* *
42522552 TGAAATAACCCTATAGGGTAGAATTAC
1 CGAAATACCCCTATAGGGTAGAATTAC
* *
42522579 CGAGATACCCCTATAGGGTAAAATTAC
1 CGAAATACCCCTATAGGGTAGAATTAC
*
42522606 TGAAATACCCCTATAGGGTAGAATTAC
1 CGAAATACCCCTATAGGGTAGAATTAC
* * * *
42522633 CAAAATACCCTTGTAGGGTAGAAATAC
1 CGAAATACCCCTATAGGGTAGAATTAC
** *
42522660 TAAAATACCCCTGTAGGGTAGAATTAC
1 CGAAATACCCCTATAGGGTAGAATTAC
42522687 CGA
1 CGA
42522690 GATAACCTTG
Statistics
Matches: 118, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 118 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (27 bp):
CGAAATACCCCTATAGGGTAGAATTAC
Found at i:42522955 original size:25 final size:25
Alignment explanation
Indices: 42522917--42522987 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
42522907 AGGAAGTGCT
** *
42522917 AAAAGGGCAATGCCCTAGTTTAACGA
1 AAAAGGGCTTTGCCCCAGTTT-ACGA
**
42522943 AAAA-GGCTTTGCCCCAGTTTATTA
1 AAAAGGGCTTTGCCCCAGTTTACGA
42522967 AAAAGGGCTTTGCCCCAGTTT
1 AAAAGGGCTTTGCCCCAGTTT
42522988 TTAAAAGAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 6 0.15
25 29 0.74
26 4 0.10
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACGA
Found at i:42522991 original size:24 final size:24
Alignment explanation
Indices: 42522942--42522999 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 24
42522932 TAGTTTAACG
42522942 AAAAAGGCTTTGCCCCAGTTTATT
1 AAAAAGGCTTTGCCCCAGTTTATT
42522966 AAAAAGGGCTTTGCCCCAGTTT-TT
1 AAAAA-GGCTTTGCCCCAGTTTATT
42522990 AAAAGAGGCT
1 AAAA-AGGCT
42523000 AGGCTTCTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAAGGCTTTGCCCCAGTTTATT
Found at i:42523241 original size:30 final size:30
Alignment explanation
Indices: 42523207--42523288 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 30
42523197 CGCTTACAGT
*
42523207 AAAGGCATCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGTGATATGATTTATGA
42523237 AAAGGCTTCGGCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCAGTGATATGATTTATGA
42523267 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGG-CCAGTGATATG
42523289 TCGAGACTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 45 0.90
31 5 0.10
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (30 bp):
AAAGGCTTCGGCCAGTGATATGATTTATGA
Found at i:42538343 original size:6 final size:6
Alignment explanation
Indices: 42538334--42538426 Score: 82
Period size: 6 Copynumber: 15.2 Consensus size: 6
42538324 AATAAAATTG
* *
42538334 AAATAA AAATAA AAAGAA AAATAA AAATAA AAATAA AAATAA ATTAA-AT
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA A--AATAA
* * * *
42538383 AAATTA AATTAA ATAA-ATA AAATAA AAATAA GAATAA GAATAA A
1 AAATAA AAATAA A-AATA-A AAATAA AAATAA AAATAA AAATAA A
42538427 TAAAAAAAGG
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
5 2 0.03
6 61 0.86
7 6 0.08
8 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:42538359 original size:5 final size:5
Alignment explanation
Indices: 42538351--42538431 Score: 53
Period size: 5 Copynumber: 15.8 Consensus size: 5
42538341 AATAAAAAGA
* * *
42538351 AAAAT AAAAAT AAAAAT AAAA- ATAAAT TAAAT -AAAT TAAAT TAAAT
1 AAAAT -AAAAT -AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
42538397 -AAAT AAAAT AAAAAT AAGAAT AAGAAT -AAAT AAAA
1 AAAAT AAAAT -AAAAT AA-AAT AA-AAT AAAAT AAAA
42538432 AAAGGAGGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 15
0.81 0.01 0.18
Matches are distributed among these distances:
4 12 0.18
5 30 0.45
6 25 0.37
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:42538384 original size:9 final size:9
Alignment explanation
Indices: 42538370--42538408 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
42538360 ATAAAAATAA
42538370 AAATAAATT
1 AAATAAATT
42538379 AAATAAATT
1 AAATAAATT
42538388 AAATTAAA-T
1 AAA-TAAATT
*
42538397 AAATAAAAT
1 AAATAAATT
42538406 AAA
1 AAA
42538409 AATAAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.14
9 20 0.71
10 4 0.14
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAATAAATT
Found at i:42538392 original size:14 final size:14
Alignment explanation
Indices: 42538373--42538405 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
42538363 AAAATAAAAA
42538373 TAAATTAAATAAAT
1 TAAATTAAATAAAT
42538387 TAAATTAAATAAAT
1 TAAATTAAATAAAT
*
42538401 AAAAT
1 TAAAT
42538406 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTAAATAAAT
Found at i:42545740 original size:26 final size:26
Alignment explanation
Indices: 42545711--42545770 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 26
42545701 TCCCTTTGAA
* * *
42545711 TCATTCGATATTTTGCACACTAAGTG
1 TCATTCAATATCTCGCACACTAAGTG
42545737 TCATTCTCAATATCTCGCACACTAAGTG
1 TCA-T-TCAATATCTCGCACACTAAGTG
*
42545765 CCATTC
1 TCATTC
42545771 TCAATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.18
27 2 0.07
28 21 0.75
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.35
Consensus pattern (26 bp):
TCATTCAATATCTCGCACACTAAGTG
Found at i:42545786 original size:28 final size:28
Alignment explanation
Indices: 42545718--42545796 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
42545708 GAATCATTCG
*
42545718 ATATTTTGCACACTAAGTGTCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* *
42545746 ATATCTCGCACACTAAGTGCCATTCTCA
1 ATATTTTGCACACTAAGTGCCATTCTCA
* * *
42545774 ATATTTTGTACACTGAGTACCAT
1 ATATTTTGCACACTAAGTGCCAT
42545797 ATGTGATTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.35
Consensus pattern (28 bp):
ATATTTTGCACACTAAGTGCCATTCTCA
Found at i:42551735 original size:9 final size:10
Alignment explanation
Indices: 42551696--42551728 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42551686 AACTTAATAA
42551696 AAGA-AAAAT
1 AAGATAAAAT
*
42551705 AAAATAAAAT
1 AAGATAAAAT
42551715 AAGATAAAAT
1 AAGATAAAAT
42551725 AAGA
1 AAGA
42551729 CAAATAATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 3 0.14
10 18 0.86
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (10 bp):
AAGATAAAAT
Found at i:42560332 original size:41 final size:40
Alignment explanation
Indices: 42560205--42560349 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
42560195 CTCGCACAAG
** * * * *
42560205 GCCTTCGGTTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
42560245 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
42560285 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
42560326 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
42560350 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:42568473 original size:40 final size:40
Alignment explanation
Indices: 42568418--42568494 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
42568408 GACACCCAAA
42568418 GAGGAATCCACCTAGATTTCACTTGTTATCTGACTCTAAG
1 GAGGAATCCACCTAGATTTCACTTGTTATCTGACTCTAAG
* *
42568458 GAGGAATCCATCTAGATTTCACTTGTTATTTGACTCT
1 GAGGAATCCACCTAGATTTCACTTGTTATCTGACTCT
42568495 GAATCAGACG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (40 bp):
GAGGAATCCACCTAGATTTCACTTGTTATCTGACTCTAAG
Found at i:42571289 original size:5 final size:5
Alignment explanation
Indices: 42571279--42571377 Score: 76
Period size: 6 Copynumber: 18.2 Consensus size: 5
42571269 TATGTCTTTC
*
42571279 AAAAT AAAAT AATAAT AAAATT GAAAT GAAAAT AAAAAT CAAAAAT AAAAAT
1 AAAAT AAAAT AA-AAT AAAA-T AAAAT -AAAAT -AAAAT --AAAAT -AAAAT
*
42571331 AAAAAT AAAAT -AAAG AAAAT AAAAAT AAGAAT -AAAT AAAAT AAAAT
1 -AAAAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT
42571377 A
1 A
42571378 GGAGGATTCA
Statistics
Matches: 81, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
4 6 0.07
5 31 0.38
6 38 0.47
7 6 0.07
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:42571311 original size:6 final size:6
Alignment explanation
Indices: 42571279--42571365 Score: 79
Period size: 6 Copynumber: 14.3 Consensus size: 6
42571269 TATGTCTTTC
* * * *
42571279 AAAAT- AAAATA ATAAT- AAAATT GAAATG AAAATA AAAATCA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA
* *
42571326 AAAATA AAAATA AAATAAA GAAAATA AAAATA AGAATA AA
1 AAAATA AAAATA AAA-ATA -AAAATA AAAATA AAAATA AA
42571366 TAAAATAAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
5 9 0.13
6 45 0.67
7 10 0.15
8 3 0.04
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:42571317 original size:12 final size:11
Alignment explanation
Indices: 42571279--42571375 Score: 78
Period size: 11 Copynumber: 8.8 Consensus size: 11
42571269 TATGTCTTTC
42571279 AAAAT-AAAAT
1 AAAATAAAAAT
*
42571289 AATAATAAAATT
1 AA-AATAAAAAT
* *
42571301 GAAATGAAAAT
1 AAAATAAAAAT
42571312 AAAAATCAAAAAT
1 -AAAAT-AAAAAT
42571325 AAAAATAAAAAT
1 -AAAATAAAAAT
*
42571337 AAAAT--AAAG
1 AAAATAAAAAT
42571346 AAAATAAAAAT
1 AAAATAAAAAT
42571357 AAGAAT--AAAT
1 AA-AATAAAAAT
42571367 AAAATAAAA
1 AAAATAAAA
42571376 TAGGAGGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
9 11 0.16
10 8 0.11
11 22 0.31
12 18 0.26
13 11 0.16
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:42571356 original size:26 final size:25
Alignment explanation
Indices: 42571320--42571369 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
42571310 ATAAAAATCA
42571320 AAAATAAAAATAAAAATAAAATAAAG
1 AAAATAAAAATAAAAAT-AAATAAAG
*
42571346 AAAATAAAAATAAGAATAAATAAA
1 AAAATAAAAATAAAAATAAATAAA
42571370 ATAAAATAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (25 bp):
AAAATAAAAATAAAAATAAATAAAG
Found at i:42571368 original size:10 final size:9
Alignment explanation
Indices: 42571320--42571374 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
42571310 ATAAAAATCA
42571320 AAAATAAA-
1 AAAATAAAT
42571328 AATAA-AAAT
1 AA-AATAAAT
*
42571337 AAAATAAAG
1 AAAATAAAT
42571346 AAAATAAAAAT
1 AAAAT--AAAT
42571357 AAGAATAAAT
1 AA-AATAAAT
42571367 AAAATAAA
1 AAAATAAA
42571375 ATAGGAGGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
8 7 0.18
9 18 0.46
10 6 0.15
11 5 0.13
12 3 0.08
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (9 bp):
AAAATAAAT
Found at i:42579458 original size:28 final size:28
Alignment explanation
Indices: 42579427--42579484 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
42579417 ACTTATGGAT
42579427 TATTTTGAGATATTATTGATAGGGATTA
1 TATTTTGAGATATTATTGATAGGGATTA
42579455 TATTTTGAGATATTATTGATAGGGATTA
1 TATTTTGAGATATTATTGATAGGGATTA
42579483 TA
1 TA
42579485 AATTGAGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.47
Consensus pattern (28 bp):
TATTTTGAGATATTATTGATAGGGATTA
Found at i:42579490 original size:28 final size:28
Alignment explanation
Indices: 42579431--42579492 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
42579421 ATGGATTATT
**
42579431 TTGAGATATTATTGATAGGGATTATATT
1 TTGAGATATTATTGATAGGGATTATAAA
42579459 TTGAGATATTATTGATAGGGATTATAAA
1 TTGAGATATTATTGATAGGGATTATAAA
42579487 TTGAGA
1 TTGAGA
42579493 AGAATTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (28 bp):
TTGAGATATTATTGATAGGGATTATAAA
Found at i:42586720 original size:25 final size:25
Alignment explanation
Indices: 42586686--42586735 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
42586676 GGCAGGGGAG
42586686 CCTGAAATCACTCTGACTCTGTCTC
1 CCTGAAATCACTCTGACTCTGTCTC
42586711 CCTGAAATCACTCTGACTCTGTCTC
1 CCTGAAATCACTCTGACTCTGTCTC
42586736 ACAAAAGTTC
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:0.20, C:0.36, G:0.12, T:0.32
Consensus pattern (25 bp):
CCTGAAATCACTCTGACTCTGTCTC
Found at i:42588743 original size:27 final size:27
Alignment explanation
Indices: 42588699--42588865 Score: 126
Period size: 27 Copynumber: 6.3 Consensus size: 27
42588689 CTTGACAAAT
* *
42588699 CTTCCACAT-A-ACAGTCCTGGTGGAC
1 CTTCCACATAAGATAGTCCTGATGGAC
* * *
42588724 CTTCCATATAGGATAGTCCTAATGGAC
1 CTTCCACATAAGATAGTCCTGATGGAC
*
42588751 CTTTCACATAAGATAGTCCT-A-GCGAAC
1 CTTCCACATAAGATAGTCCTGATG-G-AC
* *
42588778 CTTCCACATAATATAGTCTTGATGGAC
1 CTTCCACATAAGATAGTCCTGATGGAC
* * **
42588805 CCTCCACATATGATAGTATTGATGGAC
1 CTTCCACATAAGATAGTCCTGATGGAC
* * * * **
42588832 CTTCCATACATGATAGTCCTAACAGAC
1 CTTCCACATAAGATAGTCCTGATGGAC
42588859 CTTCCAC
1 CTTCCAC
42588866 TTATATGGTA
Statistics
Matches: 112, Mismatches: 24, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
25 9 0.08
26 2 0.02
27 98 0.88
28 2 0.02
29 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.28
Consensus pattern (27 bp):
CTTCCACATAAGATAGTCCTGATGGAC
Found at i:42590730 original size:47 final size:47
Alignment explanation
Indices: 42590486--42590752 Score: 207
Period size: 46 Copynumber: 5.8 Consensus size: 47
42590476 AGGGTATAAT
* *
42590486 GCCGATGCCATGTTCCAGACATGGTCTTACACT-GTCTTTCATAT-TAA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAG-CTCTCATATGT-A
* * * *
42590533 GTCGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCATGCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGTA
* * *
42590579 GCCGATG-CATGTCCCAGACAT-GTCTTAGACTGGCT-TACATCTCG-A
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT-CATAT-GTA
* ** * **
42590624 GGTCGATG-CATGTCCCAGAC-TTATCTTACACTAGCTCTCATCTCAA
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATGTA
* * *
42590670 TGCTGATGTCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTG
1 -GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATGTA
*
42590719 GCCGATG-CATGTCCTAGACAT-GTCTTACACTAGC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC
42590753 ATACAAATAA
Statistics
Matches: 180, Mismatches: 27, Indels: 27
0.77 0.12 0.12
Matches are distributed among these distances:
44 9 0.05
45 21 0.12
46 66 0.37
47 58 0.32
48 25 0.14
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATGTA
Found at i:42595685 original size:13 final size:13
Alignment explanation
Indices: 42595663--42595695 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
42595653 AAGGGTTTGT
42595663 TTAT-TAAACTAA
1 TTATCTAAACTAA
42595675 TTATCTAAACTAA
1 TTATCTAAACTAA
*
42595688 TTAACTAA
1 TTATCTAA
42595696 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:42598468 original size:19 final size:19
Alignment explanation
Indices: 42598430--42598468 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42598420 GAACAAGTTA
**
42598430 AATATTTATCTTAATGTTC
1 AATATTTATCTTAAAATTC
42598449 AATATTTATCTTAAAATTC
1 AATATTTATCTTAAAATTC
42598468 A
1 A
42598469 GAAAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (19 bp):
AATATTTATCTTAAAATTC
Found at i:42600651 original size:10 final size:10
Alignment explanation
Indices: 42600634--42600670 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
42600624 AACTTAATAA
42600634 AAGA-AAAAT
1 AAGATAAAAT
*
42600643 AAAATAAAAT
1 AAGATAAAAT
42600653 AAGATAAAAT
1 AAGATAAAAT
42600663 AAGATAAA
1 AAGATAAA
42600671 TAATTGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 3 0.12
10 22 0.88
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (10 bp):
AAGATAAAAT
Found at i:42600659 original size:15 final size:14
Alignment explanation
Indices: 42600639--42600673 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
42600629 AATAAAAGAA
42600639 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
42600653 AAGATAAAATAAGAT
1 AA-ATAAAATAAAAT
42600668 AAATAA
1 AAATAA
42600674 TTGAATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:42606775 original size:30 final size:30
Alignment explanation
Indices: 42606741--42606797 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
42606731 TTCTCGAGCC
42606741 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
42606771 TAGGGGTAAAATTGTAATTTTGCAAAA
1 TAGGGGCAAAAGTGTAAATATGCAAAA
42606798 TTTTGAGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:42631267 original size:25 final size:25
Alignment explanation
Indices: 42631238--42631285 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
42631228 TTATAATATG
** *
42631238 AAAATAACTGTTTTGCCCCTAGGTA
1 AAAATAACCATTTTACCCCTAGGTA
*
42631263 AAAATGACCATTTTACCCCTAGG
1 AAAATAACCATTTTACCCCTAGG
42631286 GTTTAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (25 bp):
AAAATAACCATTTTACCCCTAGGTA
Found at i:42631463 original size:26 final size:25
Alignment explanation
Indices: 42631418--42631489 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
42631408 GAGGAAGTGC
* *
42631418 AAAAGGGC-TATGCCCCAGTTTACCG
1 AAAAGGGCTTTTG-CCCAGTTTACCA
**
42631443 AAAAGGGCTTTTGCCCTAGTTTATTA
1 AAAAGGGCTTTTGCCC-AGTTTACCA
42631469 AAAAGGGCTTTTGGCCCAGTT
1 AAAAGGGCTTTT-GCCCAGTT
42631490 ACTAAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.28
26 25 0.62
27 4 0.10
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCAGTTTACCA
Found at i:42631471 original size:25 final size:25
Alignment explanation
Indices: 42631443--42631496 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
42631433 CAGTTTACCG
*
42631443 AAAAGGGCTTTT-GCCCTAGTTTATTA
1 AAAAGGGCTTTTGGCCC-AG-TTACTA
42631469 AAAAGGGCTTTTGGCCCAGTTACTA
1 AAAAGGGCTTTTGGCCCAGTTACTA
42631494 AAA
1 AAA
42631497 GAGGCTAGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (25 bp):
AAAAGGGCTTTTGGCCCAGTTACTA
Found at i:42631502 original size:25 final size:26
Alignment explanation
Indices: 42631428--42631502 Score: 68
Period size: 26 Copynumber: 2.9 Consensus size: 26
42631418 AAAAGGGCTA
* *
42631428 TGCCCCAGTTTACCGAAAAG-GGCTTT
1 TGCCCTAGTTTA-CTAAAAGAGGCTTT
*
42631454 TGCCCTAGTTTATTAAAA-AGGGCTTT
1 TGCCCTAGTTTACTAAAAGA-GGCTTT
42631480 TGGCCC-AG-TTACTAAAAGAGGCT
1 T-GCCCTAGTTTACTAAAAGAGGCT
42631503 AGGCCTCCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
25 16 0.39
26 21 0.51
27 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (26 bp):
TGCCCTAGTTTACTAAAAGAGGCTTT
Found at i:42631748 original size:31 final size:31
Alignment explanation
Indices: 42631705--42631806 Score: 152
Period size: 31 Copynumber: 3.3 Consensus size: 31
42631695 CATATTGTTA
* *
42631705 CAGTAATATGAATAATGAAAAGGCTTTGGCC
1 CAGTGATATGAATAATGAAAAGGCTTCGGCC
*
42631736 CAGTGATATGAATAATGAAAAGGCTTCAGCC
1 CAGTGATATGAATAATGAAAAGGCTTCGGCC
* *
42631767 TAGTGATATGAATAATGTAAAGGCTTCGGCC
1 CAGTGATATGAATAATGAAAAGGCTTCGGCC
42631798 CAGT-ATATG
1 CAGTGATATG
42631807 GTGAGATTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
30 5 0.08
31 59 0.92
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (31 bp):
CAGTGATATGAATAATGAAAAGGCTTCGGCC
Found at i:42644348 original size:40 final size:40
Alignment explanation
Indices: 42644304--42644527 Score: 308
Period size: 40 Copynumber: 5.6 Consensus size: 40
42644294 AAGTGAATAT
* * * * **
42644304 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
42644344 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
42644384 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
42644424 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
42644464 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * *
42644503 AACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
42644528 TGAACGAGGA
Statistics
Matches: 171, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 35 0.20
40 136 0.80
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:42644402 original size:80 final size:80
Alignment explanation
Indices: 42644265--42644527 Score: 318
Period size: 80 Copynumber: 3.3 Consensus size: 80
42644255 TTGAATGCTG
* * * * *
42644265 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAG-TGAATATATCCGGATTAAGAT-CCGAAGGCC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCC
*
42644327 TTTGTGCGAGATACTAAA
63 TTTGTGCGAGTTACTAAA
* * *
42644345 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
**
42644410 GTGCGAGTTGTTAAA
66 GTGCGAGTTACTAAA
* * *
42644425 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGG-CATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
*
42644489 GTGTGAGTTACTAAA
66 GTGCGAGTTACTAAA
* *
42644504 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42644528 TGAACGAGGA
Statistics
Matches: 159, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
79 35 0.22
80 116 0.73
81 8 0.05
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTAAGTCCCGAAGGCCTTT
GTGCGAGTTACTAAA
Found at i:42644479 original size:120 final size:120
Alignment explanation
Indices: 42644265--42644527 Score: 318
Period size: 120 Copynumber: 2.2 Consensus size: 120
42644255 TTGAATGCTG
* * *
42644265 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGATTAAGATCCGAAGGCCTT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
* **
42644329 TGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
66 CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
* * * *
42644385 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTG-TTAAATCCGGGTTAAG-TCCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAG-TGAATAAATCCGGATTAAGAT-CCGAAGGCA
* ** * *
42644447 TTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
64 TTCGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
42644504 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42644528 TGAACGAGGA
Statistics
Matches: 122, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
119 34 0.28
120 80 0.66
121 8 0.07
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGATTAAGATCCGAAGGCATT
CGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:42646703 original size:43 final size:43
Alignment explanation
Indices: 42646649--42646804 Score: 129
Period size: 43 Copynumber: 3.6 Consensus size: 43
42646639 AAATCATACA
*
42646649 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGATGTGGTCTTACACGTAATCAAATATCG
* * * *
42646692 ATGCCATTGTCCCAGACAG-GGTCTTACACGAAATCAGATAT-G
1 ATGCCAATGTCCCAGA-TGTGGTCTTACACGTAATCAAATATCG
* ** * *** *
42646734 ATGTCGTTGCCCCAGGCATGGTCTTACACGTAAATCAGAA-GTCG
1 ATGCCAATGTCCCAGATGTGGTCTTACACGT-AATCA-AATATCG
* *
42646778 ATGCCAACGTACCAGATGTGGTCTTAC
1 ATGCCAATGTCCCAGATGTGGTCTTAC
42646805 TCAAAAACAC
Statistics
Matches: 85, Mismatches: 23, Indels: 9
0.73 0.20 0.08
Matches are distributed among these distances:
42 24 0.28
43 40 0.47
44 21 0.25
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGATGTGGTCTTACACGTAATCAAATATCG
Found at i:42646761 original size:42 final size:43
Alignment explanation
Indices: 42646649--42646783 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 43
42646639 AAATCATACA
* * ** * * *
42646649 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATCG
1 ATGCCATTGCCCCAGACATGGTCTTACACGAAATCAGATATCG
* *
42646692 ATGCCATTGTCCCAGACAGGGTCTTACACGAAATCAGATAT-G
1 ATGCCATTGCCCCAGACATGGTCTTACACGAAATCAGATATCG
* * *
42646734 ATGTCGTTGCCCCAGGCATGGTCTTACACGTAAATCAGA-AGTCG
1 ATGCCATTGCCCCAGACATGGTCTTACACG-AAATCAGATA-TCG
42646778 ATGCCA
1 ATGCCA
42646784 ACGTACCAGA
Statistics
Matches: 75, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 27 0.36
43 43 0.57
44 5 0.07
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (43 bp):
ATGCCATTGCCCCAGACATGGTCTTACACGAAATCAGATATCG
Found at i:42659031 original size:130 final size:131
Alignment explanation
Indices: 42658746--42659113 Score: 397
Period size: 130 Copynumber: 2.8 Consensus size: 131
42658736 GGCGGGATTT
*
42658746 GATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAA
1 GATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGATCAAAA
* * * *
42658811 TAAGCGAATATCCCTTCAAAATTTCACTCATGTCTTCTAAAAATCCTTTAAAACGAAGGTGATGT
66 TAA-CGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAAATCCTTCAAAACGAAGGTAATAT
42658876 TC
130 TC
* * *
42658878 GATATTTGGCAATTCGCGAAATCGTGCCCTAAGGTGTTGGGTTGCAATTTCTTGTTTGATCAAAA
1 GATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGATCAAAA
* * *** * * * *
42658943 TAA-TAAGGTCCCTTTTGAATTTCACTTATGTTTTCTAAAAA-CTCTTCAACACTAAGGTAATAT
66 TAACGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAAATC-CTTCAAAACGAAGGTAATAT
42659006 TC
130 TC
* * * * *
42659008 GATGTTTGGCAATTCAG-GGAATCGTGCCCTATCGTGCTGGGTTGCGATTTC-CTATTTG-TCCA
1 GATATTTGGCAATTC-GCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTC-GTTTGAT-CA
* * * *
42659070 AAATGATCGAAGATTCCTTTAGAATTTCACTCATG-CTCTCTAAA
63 AAAT-AACGAAGATCCCTTCAAAATTTCACTCATGTCT-TCTAAA
42659114 TTCTAAAATA
Statistics
Matches: 197, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
129 2 0.01
130 100 0.51
131 3 0.02
132 92 0.47
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.35
Consensus pattern (131 bp):
GATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGATCAAAA
TAACGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAAATCCTTCAAAACGAAGGTAATATT
C
Found at i:42660332 original size:40 final size:40
Alignment explanation
Indices: 42660272--42660348 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
42660262 CGATGTTTTG
* *
42660272 CAGGCGAATGATGGGATATGTCCACAATGACGAATTAATA
1 CAGGCGAATGACGGGATATGTCCACAATGACCAATTAATA
* *
42660312 CAGGTGAATGACGGGATATGTCCATAATGACCAATTA
1 CAGGCGAATGACGGGATATGTCCACAATGACCAATTA
42660349 TTAATTCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (40 bp):
CAGGCGAATGACGGGATATGTCCACAATGACCAATTAATA
Found at i:42660460 original size:31 final size:31
Alignment explanation
Indices: 42660422--42660484 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
42660412 CGCGCTAAAG
42660422 TTAACTCATGGAAGGACCTGGCTTAAGCCTT
1 TTAACTCATGGAAGGACCTGGCTTAAGCCTT
*
42660453 TTAACTCATGTAAGGACCTGGCTTAAGCCTT
1 TTAACTCATGGAAGGACCTGGCTTAAGCCTT
42660484 T
1 T
42660485 ATGAAGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (31 bp):
TTAACTCATGGAAGGACCTGGCTTAAGCCTT
Found at i:42671211 original size:132 final size:129
Alignment explanation
Indices: 42670978--42671359 Score: 401
Period size: 132 Copynumber: 2.9 Consensus size: 129
42670968 TTTAAAATTT
*
42670978 CTTTAAAACAAAAGTGAGATTT-GATATTTGGCAATTCGCGGAATCGTGCCCTAACGTGCTGGGT
1 CTTTAAAAC-AAAG-GAGATTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGT
* * *
42671042 TGCAATTTCTCGTTTGCTCAAAATAAGCGAATATCCCTTCAAAATTTCACTCATGTCTTCTAAAA
64 TGCAATTTCTTGTTTG-TCAAAATAATCGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAA
42671107 ATC
128 A-C
* * *
42671110 CTTTAAAACAAAGGCGATGTTCGATATTTGGCAATTCGCGAAATCGTGCCCTAATGTGTTGGGTT
1 CTTTAAAACAAAGGAGAT-TTCGATATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGTT
* *** * *
42671175 GCAATTTCTTGTTTGATCAAAATAATCGAAGGTCCCTTTTGAATTTCACTTATGTTTTCTAAAAA
65 GCAATTTCTTGTTTG-TCAAAATAATCGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAAA
42671240 C
129 C
* * * * * *
42671241 TTTTCAAAACGAAGGTA-ATATTCGATGTTTGGCAATTCGGGGAATCGTTCCCT-ATCGTCCTGG
1 CTTT-AAAACAAAGG-AGAT-TTCGATATTTGGCAATTCGCGGAATCGTGCCCTAAT-GTGCTGG
* * * * * * * *
42671304 GTTGCGATTTCCTATTTGTCCAAAATGATCGAAGATTCCTTTAGAACTTCACTCAT
62 GTTGCAATTTCTTGTTTGT-CAAAATAATCGAAGATCCCTTCAAAATTTCACTCAT
42671360 ACTCTCTAAA
Statistics
Matches: 211, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
130 4 0.02
131 13 0.06
132 194 0.92
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (129 bp):
CTTTAAAACAAAGGAGATTTCGATATTTGGCAATTCGCGGAATCGTGCCCTAATGTGCTGGGTTG
CAATTTCTTGTTTGTCAAAATAATCGAAGATCCCTTCAAAATTTCACTCATGTCTTCTAAAAAC
Found at i:42673244 original size:15 final size:15
Alignment explanation
Indices: 42673224--42673269 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
42673214 ATTATGATAT
42673224 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
42673239 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
*
42673254 AT-TATCTTAGATTTC
1 -TGTATCTTGGATTTC
42673269 T
1 T
42673270 TTGTCCTGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (15 bp):
TGTATCTTGGATTTC
Found at i:42682832 original size:43 final size:43
Alignment explanation
Indices: 42682784--42682953 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
42682774 ATAGGATTTC
*
42682784 CGATATGTG-TTCTCGTGTAAGACCATGTCTAGGACGTTGGCAT
1 CGATATGTGATT-TCGTGTAAGACCATGTCTGGGACGTTGGCAT
* *
42682827 CGATATGTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
1 CGATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGCAT
* * * *
42682870 CG-TATTTGA-TTCGTGTAAGACCCTATCTGGGATAG-TGGCAT
1 CGATATGTGATTTCGTGTAAGACCATGTCTGGGA-CGTTGGCAT
* * * * *
42682911 TGATATGTGATTGCATGTAAGACCACGTTTGGGACGTTGGCAT
1 CGATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGCAT
42682954 TGTACGATAT
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
41 27 0.26
42 13 0.12
43 62 0.60
44 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (43 bp):
CGATATGTGATTTCGTGTAAGACCATGTCTGGGACGTTGGCAT
Found at i:42687141 original size:25 final size:25
Alignment explanation
Indices: 42687113--42687191 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
42687103 CTAATGGCCG
42687113 ATGTGATGAATGTGAAAGTGCATAT
1 ATGTGATGAATGTGAAAGTGCATAT
* * * **
42687138 ATGTGAT-AAGGCTTAATG-GC--CG
1 ATGTGATGAATG-TGAAAGTGCATAT
*
42687160 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGCATAT
42687185 ATGTGAT
1 ATGTGAT
42687192 AAAGCCTTAT
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 11 0.29
23 4 0.11
24 5 0.13
25 18 0.47
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGCATAT
Found at i:42687155 original size:47 final size:47
Alignment explanation
Indices: 42687097--42687478 Score: 602
Period size: 47 Copynumber: 8.1 Consensus size: 47
42687087 TTAAATGAGT
*
42687097 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
42687144 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * **
42687191 TAAAGCCTTATAGTTGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
42687240 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42687287 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42687334 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42687381 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
42687428 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
42687475 TAAG
1 TAAG
42687479 TCCCGAAGGG
Statistics
Matches: 308, Mismatches: 25, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
47 267 0.87
49 41 0.13
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:42687355 original size:143 final size:141
Alignment explanation
Indices: 42687097--42687478 Score: 602
Period size: 143 Copynumber: 2.7 Consensus size: 141
42687087 TTAAATGAGT
* *
42687097 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGATAAGGCTTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* * **
42687162 GTGATGAATGTGAAAGTGTATATATGTGATAAAGCCTTATAGTTGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
42687227 TATATATATGTGA
131 --TATATATGTGA
*
42687240 TAAGGCTTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
*
42687305 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
42687370 TATATATGTGA
131 TATATATGTGA
* * * * * *
42687381 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAAC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
* *
42687446 GTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 GTGATGAATGTGAAAGTGTATATATGTGATAAG
42687479 TCCCGAAGGG
Statistics
Matches: 222, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
141 100 0.45
143 122 0.55
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (141 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGAT
GTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
TATATATGTGA
Found at i:42694372 original size:57 final size:58
Alignment explanation
Indices: 42694311--42694421 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 58
42694301 AAATCCACAT
* *
42694311 ACCTGTATCTAGCCCATTAGGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATAGCCCATTAGGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
42694368 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGTCCGTTAGGCCCA
1 ACCTGTATATAGCCCATTAGGCCCAAATCACATTCATATGGCCCATTAGGCCCA
42694422 GTCACATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 22 0.47
58 25 0.53
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (58 bp):
ACCTGTATATAGCCCATTAGGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:42694377 original size:29 final size:29
Alignment explanation
Indices: 42694322--42694421 Score: 132
Period size: 29 Copynumber: 3.5 Consensus size: 29
42694312 CCTGTATCTA
*
42694322 GCCCATTAGGCCC-AATCATAT-TCATATG
1 GCCCATTAGGCCCAAATCACATGT-ATATG
*
42694350 GCCCATTAGGCCCAAATCACCTGTATATG
1 GCCCATTAGGCCCAAATCACATGTATATG
*
42694379 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATGTATATG
* *
42694408 GTCCGTTAGGCCCA
1 GCCCATTAGGCCCA
42694422 GTCACATAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
28 13 0.20
29 50 0.78
30 1 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATGTATATG
Found at i:42696931 original size:42 final size:42
Alignment explanation
Indices: 42696828--42697131 Score: 371
Period size: 42 Copynumber: 7.3 Consensus size: 42
42696818 AAAAGAACCA
* *
42696828 TTCATTGCATTTAGAGTCCCAGGTGTGGAGGCCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
42696869 TTGATTGCATTTATAAGCCTAGGTGTGGAGGTCCATTTACATT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTAC-TT
* *
42696912 TT-ATTGCATTTAGAGGCCTAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
42696953 TTCATTACATTTAAAGGCCCAGGTGTGGAGGTCCATTCT-CTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATT-TACTT
* * * * *
42696995 TTTATTGCATTTAGAGGCCTAGGTGTGAAAGTCCATTCACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
42697037 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTGCTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
42697079 TTCATTGAATTTAAAGGCCCAGGTGTGGAGATCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
42697121 TTCATTACATT
1 TTCATTGCATT
42697132 GTATATAAAG
Statistics
Matches: 222, Mismatches: 36, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
41 38 0.17
42 180 0.81
43 4 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:42698250 original size:146 final size:148
Alignment explanation
Indices: 42697869--42698488 Score: 691
Period size: 144 Copynumber: 4.2 Consensus size: 148
42697859 TATATTTAAA
* *
42697869 AAAGTTTAGATTTTAAAAAATAAAAA-CTATTTTTTTAATCATTTT-AAGGAAAATTTTAAAA-T
1 AAAGTTTAGATTTTAAAAAATAAAAATCT-TTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAATT
* *
42697931 TTTAAAACAAAGTTTTGATTTTTTTTCAACTA-TTCCAAATAAAAGCTTTGATCTTTAAGAAAAA
65 TTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAAA
42697995 TAGTGGTTTTTTTTAAAAAAATAAAAAAGAG
130 TAGT-G-TTTTTTT-------T---AAAGAG
* * *
42698026 AAAGTTTAGATTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAAG-AAAGTTT-AAATTT
1 AAAGTTTAGATTTTAAAAAATAAAAATCTTTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAATTT
* *
42698089 TTAAAACAAAGTTTTGA-TTTTTTT-AACTATCTCAAAATAAAAGCTTTAATCTTTAAGAAAAAT
66 TTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAAAT
42698152 AGTGTTTTTTTTAAAGAG
131 AGTGTTTTTTTTAAAGAG
42698170 AAAGTTTAGATTTTAAAAAATAAAAATCTGCTTTTTTTAGTCATTTTAAAGG-AAAGTTT-AAAT
1 AAAGTTTAGATTTTAAAAAATAAAAATCT--TTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAAT
* *
42698233 CTTTAAAACAAAATTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAA
64 TTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAA
*
42698298 ATAGT-TTTTTTTAAAAGAG
129 ATAGTGTTTTTTTTAAAGAG
* * * * * * *
42698317 AAAGTTTAGATTTT-TAAAATAAAAATATATTTATTATTCATTTTAAAGGAAAAGTTTGAATTTT
1 AAAGTTTAGATTTTAAAAAATAAAAATCTTTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAATTT
* * ** * * *
42698381 TTAAAACAAATTTTTTA-GCTTTTTCAACTATTTCGAAAT-AAAGTTTTAATTTTTAATAAAAAT
66 TTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAAAT
* * *
42698444 AATG-ATTTTTTAAAG-C
131 AGTGTTTTTTTTAAAGAG
* *
42698460 AAACTTT-GATTTTGCAAAAA-AAAAATCTT
1 AAAGTTTAGATTTT-AAAAAATAAAAATCTT
42698489 GCCACCATAC
Statistics
Matches: 412, Mismatches: 38, Indels: 40
0.84 0.08 0.08
Matches are distributed among these distances:
142 6 0.01
143 13 0.03
144 89 0.22
145 27 0.07
146 77 0.19
147 35 0.08
148 40 0.10
154 7 0.02
155 6 0.01
156 43 0.10
157 64 0.16
158 5 0.01
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (148 bp):
AAAGTTTAGATTTTAAAAAATAAAAATCTTTTTTTTAGTCATTTTAAAGGAAAAGTTTAAAATTT
TTAAAACAAAGTTTTGATTTTTTTTCAACTATTTCGAAATAAAAGCTTTAATCTTTAAGAAAAAT
AGTGTTTTTTTTAAAGAG
Found at i:42702689 original size:30 final size:30
Alignment explanation
Indices: 42702622--42702690 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
42702612 GTTGTCCCAA
* * *
42702622 CCCTTTTCATAGCTCGATAGCCAAAGCTAT
1 CCCTTTTTACAGCTCGATAGCAAAAGCTAT
42702652 CCCTTTTTACAGCTCGATAGCAAAAGCTAT
1 CCCTTTTTACAGCTCGATAGCAAAAGCTAT
42702682 CCCTTTTTA
1 CCCTTTTTA
42702691 TTATTTGATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.33
Consensus pattern (30 bp):
CCCTTTTTACAGCTCGATAGCAAAAGCTAT
Found at i:42702716 original size:29 final size:30
Alignment explanation
Indices: 42702680--42702758 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 30
42702670 AGCAAAAGCT
42702680 ATCCCTTTTTATTATTTGATGGTCATCACC
1 ATCCCTTTTTATTATTTGATGGTCATCACC
* * *
42702710 AT-CCTTTTTCATT-GTTGTTGGTCGTCACC
1 ATCCCTTTTT-ATTATTTGATGGTCATCACC
* *
42702739 ATCCCTTTTCATAATTTGAT
1 ATCCCTTTTTATTATTTGAT
42702759 AGCCGAAGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
29 24 0.62
30 15 0.38
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (30 bp):
ATCCCTTTTTATTATTTGATGGTCATCACC
Found at i:42702833 original size:30 final size:29
Alignment explanation
Indices: 42702799--42702865 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
42702789 ATCCGAAGCT
* *
42702799 ATCCCTTTTCATTGTTTGATGGTCATCACC
1 ATCCCTTTTCATT-ATTGATGGTCATAACC
*
42702829 ATCCCTTTTCATTATTGATGGTCGTAACC
1 ATCCCTTTTCATTATTGATGGTCATAACC
42702858 ATCCCTTT
1 ATCCCTTT
42702866 CCTAATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 21 0.62
30 13 0.38
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.43
Consensus pattern (29 bp):
ATCCCTTTTCATTATTGATGGTCATAACC
Found at i:42702838 original size:119 final size:119
Alignment explanation
Indices: 42702622--42702879 Score: 349
Period size: 119 Copynumber: 2.2 Consensus size: 119
42702612 GTTGTCCCAA
** * *
42702622 CCCTTTTCATAGCTCGATAGCCAAAGCTATCCCTTTTTACAGCTCGATAGCAAAAGCTATCCCTT
1 CCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTTACAACTCGATAGCAAAAGCTATCCCTT
* * * * *
42702687 TTTATTATTTGATGGTCATCACCATCCTTTTTCATTGTTGTTGGTCGTCACCAT
66 TTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
* * * **
42702741 CCCTTTTCATAATTTGATAGCCGAAGCTAT-CCTTTTTCACAATTCGATATCCGAAGCTATCCCT
1 CCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTT-ACAACTCGATAGCAAAAGCTATCCCT
*
42702805 TTTCATTGTTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
65 TTTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
*
42702860 CCC-TTTCCTAATTTGATAGC
1 CCCTTTTCATAATTTGATAGC
42702880 TAAGGTTATA
Statistics
Matches: 122, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
118 23 0.19
119 99 0.81
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.39
Consensus pattern (119 bp):
CCCTTTTCATAATTTGATAGCCAAAGCTATCCCTTTTTACAACTCGATAGCAAAAGCTATCCCTT
TTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
Found at i:42702858 original size:29 final size:29
Alignment explanation
Indices: 42702680--42702865 Score: 117
Period size: 30 Copynumber: 6.3 Consensus size: 29
42702670 AGCAAAAGCT
* * *
42702680 ATCCCTTTTTATTATTTGATGGTCATCACC
1 ATCCCTTTTCATTA-TTGATGGTCGTAACC
* * * *
42702710 ATCCTTTTTCATTGTTGTTGGTCGTCACC
1 ATCCCTTTTCATTATTGATGGTCGTAACC
* * * *
42702739 ATCCCTTTTCATAATTTGATAGCCG-AAGCT
1 ATCCCTTTTCATTA-TTGATGGTCGTAA-CC
* ** * *
42702769 ATCCTTTTTCACAATTCGAT-ATCCG-AAGCT
1 ATCCCTTTTCATTATT-GATGGT-CGTAA-CC
* * *
42702799 ATCCCTTTTCATTGTTTGATGGTCATCACC
1 ATCCCTTTTCATT-ATTGATGGTCGTAACC
42702829 ATCCCTTTTCATTATTGATGGTCGTAACC
1 ATCCCTTTTCATTATTGATGGTCGTAACC
42702858 ATCCCTTT
1 ATCCCTTT
42702866 CCTAATTTGA
Statistics
Matches: 121, Mismatches: 28, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
29 48 0.40
30 69 0.57
31 4 0.03
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (29 bp):
ATCCCTTTTCATTATTGATGGTCGTAACC
Found at i:42702875 original size:29 final size:28
Alignment explanation
Indices: 42702813--42702876 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
42702803 CTTTTCATTG
* * *
42702813 TTTGATGGTCATCACCATCCCTTTTCAT
1 TTTGATGGTCATAACCATCCCTTTCCAA
*
42702841 TATTGATGGTCGTAACCATCCCTTTCCTAA
1 T-TTGATGGTCATAACCATCCCTTTCC-AA
42702871 TTTGAT
1 TTTGAT
42702877 AGCTAAGGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 27 0.90
30 2 0.07
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (28 bp):
TTTGATGGTCATAACCATCCCTTTCCAA
Found at i:42702914 original size:119 final size:119
Alignment explanation
Indices: 42702622--42702931 Score: 345
Period size: 119 Copynumber: 2.6 Consensus size: 119
42702612 GTTGTCCCAA
** * * * * * ** **
42702622 CCCTTTTCATAGCTCGATAGCCAAAGCTATCCCTTTTTACAGCTCGATAGCAAAAGCTATCCCTT
1 CCCTTTTCATAATTTGATAGCCGAAGCTATACATTTTCACAATTCGATAGCCGAAGCTATCCCTT
* * * * *
42702687 TTTATTATTTGATGGTCATCACCATCCTTTTTCATTGTTGTTGGTCGTCACCAT
66 TTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
* * *
42702741 CCCTTTTCATAATTTGATAGCCGAAGCTATCCTTTTTCACAATTCGATATCCGAAGCTATCCCTT
1 CCCTTTTCATAATTTGATAGCCGAAGCTATACATTTTCACAATTCGATAGCCGAAGCTATCCCTT
*
42702806 TTCATTGTTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
66 TTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
* * * * * *
42702860 CCC-TTTCCTAATTTGATAG-CTAAGGTTATACATTTTCATTACTTTGATAGCCGAAGCTATCCC
1 CCCTTTTCATAATTTGATAGCCGAA-GCTATACATTTTCA-CAATTCGATAGCCGAAGCTATCCC
*
42702923 ATTTCATTA
64 TTTTCATTA
42702932 GCCGGTGATC
Statistics
Matches: 161, Mismatches: 28, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
117 3 0.02
118 26 0.16
119 132 0.82
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (119 bp):
CCCTTTTCATAATTTGATAGCCGAAGCTATACATTTTCACAATTCGATAGCCGAAGCTATCCCTT
TTCATTATTTGATGGTCATCACCATCCCTTTTCATTATTGATGGTCGTAACCAT
Found at i:42705565 original size:34 final size:33
Alignment explanation
Indices: 42705514--42705584 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 33
42705504 AATATCTGAA
42705514 CAGTCTGGGCTTAAGCCCA-TATCAGTGGCAGTAT
1 CAGTCTGGGCTTAAGCCCATTA-CAGT-GCAGTAT
*
42705548 CAGTGTGGGCCTT-AGCCCATTACAGTGCAGTAT
1 CAGTCTGGG-CTTAAGCCCATTACAGTGCAGTAT
42705581 CAGT
1 CAGT
42705585 AATGCACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
33 11 0.32
34 18 0.53
35 5 0.15
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.27
Consensus pattern (33 bp):
CAGTCTGGGCTTAAGCCCATTACAGTGCAGTAT
Found at i:42707506 original size:19 final size:19
Alignment explanation
Indices: 42707484--42707541 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
42707474 AATTTATGTA
42707484 ATATAATGTTATTTATATG
1 ATATAATGTTATTTATATG
* *
42707503 ATATGATG--A-TTATTATC
1 ATATAATGTTATTTA-TATG
42707520 AT-TAATGTTATTTATATG
1 ATATAATGTTATTTATATG
42707538 ATAT
1 ATAT
42707542 GAAGATTGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 6 0.20
19 11 0.37
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
ATATAATGTTATTTATATG
Done.