Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008569.1 Hibiscus syriacus cultivar Beakdansim tig00111493_pilon, whole genome shotgun sequence
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: 1513883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1158635 original size:2 final size:2
Alignment explanation
Indices: 1158628--1158733 Score: 189
Period size: 2 Copynumber: 54.0 Consensus size: 2
1158618 CGAAATAATT
*
1158628 TA TA TA TA TG TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1158668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1158710 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
1158734 GTGTGTCTAC
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
1 2 0.02
2 98 0.98
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1159162 original size:105 final size:105
Alignment explanation
Indices: 1159010--1159574 Score: 1004
Period size: 105 Copynumber: 5.4 Consensus size: 105
1159000 GTATTGTTCC
1159010 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
1159075 CAGCGGTCCCTTCGTCATAAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1159115 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
* *
1159180 CAGCGGTCCTTTCATCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1159220 GAATCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1159285 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1159325 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1159390 CAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1159430 GAGTCTAATATCCTTCGTTGTGAAGTTGAAAATGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
1159495 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1159535 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1159575 GGTAAAACCT
Statistics
Matches: 437, Mismatches: 23, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 437 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1160414 original size:1 final size:1
Alignment explanation
Indices: 1160410--1160447 Score: 58
Period size: 1 Copynumber: 38.0 Consensus size: 1
1160400 CGTTTTTCTC
* *
1160410 TTTTTGTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1160448 CAACTTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.05, T:0.95
Consensus pattern (1 bp):
T
Found at i:1168789 original size:17 final size:16
Alignment explanation
Indices: 1168767--1168798 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1168757 TATGTACAAC
1168767 CAATGAATAAATAAATA
1 CAATGAATAAA-AAATA
1168784 CAATGAATAAAAAAT
1 CAATGAATAAAAAAT
1168799 GACCATCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (16 bp):
CAATGAATAAAAAATA
Found at i:1168918 original size:2 final size:2
Alignment explanation
Indices: 1168905--1168935 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1168895 CTATTAAAAG
*
1168905 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1168936 TAAAGTATAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1170330 original size:2 final size:2
Alignment explanation
Indices: 1170323--1170383 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
1170313 GAAAATAATT
*
1170323 TA TA TA TA TG TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1170364 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
1170384 AATAGTGTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1172413 original size:2 final size:2
Alignment explanation
Indices: 1172406--1172453 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1172396 TGATTTTAAC
1172406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1172448 TA TA TA
1 TA TA TA
1172454 CACACACCAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1182068 original size:10 final size:10
Alignment explanation
Indices: 1182054--1182139 Score: 56
Period size: 10 Copynumber: 8.8 Consensus size: 10
1182044 AGTTCGGTCT
1182054 AACCGGTTCA
1 AACCGGTTCA
* *
1182064 CACC-GATCA
1 AACCGGTTCA
*
1182073 AACCGGTTCG
1 AACCGGTTCA
*
1182083 AACCGG-TCGG
1 AACCGGTTC-A
1182093 AACCGGTT-A
1 AACCGGTTCA
1182102 AACCGG-TCAA
1 AACCGGTTC-A
*
1182112 AACCGGTTGAA
1 AACCGGTT-CA
*
1182123 AACC-GATCA
1 AACCGGTTCA
1182132 AACCGGTT
1 AACCGGTT
1182140 TTCCAGCAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 16
0.69 0.12 0.19
Matches are distributed among these distances:
8 1 0.02
9 20 0.34
10 30 0.52
11 7 0.12
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.16
Consensus pattern (10 bp):
AACCGGTTCA
Found at i:1182078 original size:19 final size:20
Alignment explanation
Indices: 1182054--1182139 Score: 79
Period size: 19 Copynumber: 4.4 Consensus size: 20
1182044 AGTTCGGTCT
*
1182054 AACCGGTTCACACCGATC-A
1 AACCGGTTCAAACCGATCAA
* * **
1182073 AACCGGTTCGAACCGGTCGG
1 AACCGGTTCAAACCGATCAA
*
1182093 AACCGGTT-AAACCGGTCAA
1 AACCGGTTCAAACCGATCAA
*
1182112 AACCGGTTGAAAACCGATC-A
1 AACCGGTT-CAAACCGATCAA
1182132 AACCGGTT
1 AACCGGTT
1182140 TTCCAGCAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 31 0.55
20 17 0.30
21 8 0.14
ACGTcount: A:0.31, C:0.29, G:0.23, T:0.16
Consensus pattern (20 bp):
AACCGGTTCAAACCGATCAA
Found at i:1182097 original size:29 final size:31
Alignment explanation
Indices: 1182065--1182139 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
1182055 ACCGGTTCAC
* *
1182065 ACCGATCAAACCGGTTC-GAACCGGTCG-GA
1 ACCGATCAAACCGGTTCAAAACCGGTCGAAA
* * *
1182094 ACCGGTTAAACCGG-TCAAAACCGGTTGAAA
1 ACCGATCAAACCGGTTCAAAACCGGTCGAAA
1182124 ACCGATCAAACCGGTT
1 ACCGATCAAACCGGTT
1182140 TTCCAGCAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 2 0.06
29 20 0.56
30 13 0.36
31 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (31 bp):
ACCGATCAAACCGGTTCAAAACCGGTCGAAA
Found at i:1187617 original size:18 final size:19
Alignment explanation
Indices: 1187578--1187621 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1187568 CAGTCTGACT
1187578 TGTTGACTTTGACCCAAAC
1 TGTTGACTTTGACCCAAAC
*
1187597 TGTTGACTTTGA-CCTAAC
1 TGTTGACTTTGACCCAAAC
1187615 TGTTGAC
1 TGTTGAC
1187622 CAAACCCGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTTGACTTTGACCCAAAC
Found at i:1187622 original size:31 final size:32
Alignment explanation
Indices: 1187583--1187653 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 32
1187573 TGACTTGTTG
* *
1187583 ACTTTGACCCAAA-CTGTTGACTTTGAC-CTA
1 ACTTTGACCCAAACCCGTTAACTTTGACTCTA
*
1187613 ACTGTTGA-CCAAACCCGTTAACTTTGACTTTA
1 ACT-TTGACCCAAACCCGTTAACTTTGACTCTA
1187645 ACTTTGACC
1 ACTTTGACC
1187654 AAGTTTTACT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
30 8 0.24
31 20 0.59
32 6 0.18
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.34
Consensus pattern (32 bp):
ACTTTGACCCAAACCCGTTAACTTTGACTCTA
Found at i:1195463 original size:16 final size:16
Alignment explanation
Indices: 1195413--1195463 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1195403 TATTTTTGCT
* *
1195413 ATTTTGATCCTTA-AA
1 ATTTTGGTCTTTATAA
* * *
1195428 ATTTTGGTTTTTCTAT
1 ATTTTGGTCTTTATAA
1195444 ATTTTGGTCTTTATAA
1 ATTTTGGTCTTTATAA
1195460 ATTT
1 ATTT
1195464 AAATACTTAT
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.24, C:0.08, G:0.10, T:0.59
Consensus pattern (16 bp):
ATTTTGGTCTTTATAA
Found at i:1196918 original size:18 final size:18
Alignment explanation
Indices: 1196891--1196925 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1196881 GCACTACATC
*
1196891 ATTCAAAAAAAGGTGTTG
1 ATTCAAAAAAACGTGTTG
*
1196909 ATTCATAAAAACGTGTT
1 ATTCAAAAAAACGTGTT
1196926 CGTTAAACAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (18 bp):
ATTCAAAAAAACGTGTTG
Found at i:1201664 original size:34 final size:34
Alignment explanation
Indices: 1201621--1201699 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
1201611 AGATTGGATT
*
1201621 TCAACTTCACAACGGAGGATATCTAATTCGAAGC
1 TCAACTTCACAACGGAGGATATCTAACTCGAAGC
1201655 TCAACTTCACAACGGAGGATATCTAACTCGAAGC
1 TCAACTTCACAACGGAGGATATCTAACTCGAAGC
1201689 TCAACTTCACA
1 TCAACTTCACA
1201700 GCGAATGAGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (34 bp):
TCAACTTCACAACGGAGGATATCTAACTCGAAGC
Found at i:1202045 original size:121 final size:121
Alignment explanation
Indices: 1201880--1202225 Score: 487
Period size: 121 Copynumber: 2.9 Consensus size: 121
1201870 TTACGCAAGA
* * * * * * *
1201880 TTGGATTTTAACTTCACAACGAATGATATTCAATTCAAAACTCAACTTCACAATGAAGGATCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
1201945 CCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACAAGCAGCAATACAACCC
66 CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCAAAAGCAGCAATACAACCC
1202001 TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* * * *
1202066 CCATGATTTCAACTTCACGACGAAGGATATCATGCCCAAAAGCAGCAATGCAACCC
66 CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCAAAAGCAGCAATACAACCC
* * * * * *
1202122 TTGGATTTCAACTTCAGGACAAAGGATATCCAACTCAAAGCTCAACTTCACGACGAATGAGCCAC
1 TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
* *
1202187 CCACGGTTTCAACTTCACAAAGAAGGATAAT-GTGCCCAA
66 CCACGATTTCAACTTCACGAAGAAGGAT-ATCGTGCCCAA
1202226 TGGATCGACT
Statistics
Matches: 201, Mismatches: 23, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
121 199 0.99
122 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (121 bp):
TTGGATTTCAACTTCACGACGAAGGATATTCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
CCACGATTTCAACTTCACGAAGAAGGATATCGTGCCCAAAAGCAGCAATACAACCC
Found at i:1203866 original size:16 final size:16
Alignment explanation
Indices: 1203830--1203880 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1203820 TATTTTTTCT
* *
1203830 ATTTTGATCCTTA-AA
1 ATTTTGGTCTTTATAA
* *
1203845 ATTTTGGTTTTTATAT
1 ATTTTGGTCTTTATAA
1203861 ATTTTGGTCTTTATAA
1 ATTTTGGTCTTTATAA
1203877 ATTT
1 ATTT
1203881 CAATACTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
15 10 0.34
16 19 0.66
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (16 bp):
ATTTTGGTCTTTATAA
Found at i:1204876 original size:20 final size:20
Alignment explanation
Indices: 1204853--1204903 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1204843 CACGGAATGT
*
1204853 AAGATTACTAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
1204873 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
1204893 AAGATTACCAG
1 AAGATTACCAG
1204904 GGAATAGGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:1204908 original size:18 final size:19
Alignment explanation
Indices: 1204853--1204909 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
1204843 CACGGAATGT
*
1204853 AAGATTACTAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1204873 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1204893 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1204910 GGATTACTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
18 7 0.19
20 29 0.81
ACGTcount: A:0.46, C:0.09, G:0.25, T:0.21
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1206276 original size:32 final size:32
Alignment explanation
Indices: 1206235--1206298 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1206225 TCGAATTACA
1206235 TAGTCCAACATCCAAACATAATTAAAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
*
1206267 TAGTCCAACATCCAAACATAATTAGAAAATGT
1 TAGTCCAACATCCAAACATAATTAAAAAATGT
1206299 CATGTTAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (32 bp):
TAGTCCAACATCCAAACATAATTAAAAAATGT
Found at i:1206514 original size:37 final size:37
Alignment explanation
Indices: 1206483--1206666 Score: 117
Period size: 37 Copynumber: 5.3 Consensus size: 37
1206473 ATAATATATT
** *
1206483 AGTGACCAAATAGGTAGTTTACCCTAAATAATAATCG
1 AGTGACCAAATAGGTAGTTTAAACTAAATAATAATCA
* * * *
1206520 AGTAACCAAA-A--CA---TAAATTAGATAATATAT-A
1 AGTGACCAAATAGGTAGTTTAAACTAAATAATA-ATCA
** *
1206551 AGTGACCAAATAGGTAGTTTACTCTAAATAATAATCT
1 AGTGACCAAATAGGTAGTTTAAACTAAATAATAATCA
* *
1206588 AGTGACCAAA-A--TA---TAAATTAGATAATATAT-A
1 AGTGACCAAATAGGTAGTTTAAACTAAATAATA-ATCA
** *
1206619 AGTGACCAAATAGGTAGTTTATCCTAAATAATAATCG
1 AGTGACCAAATAGGTAGTTTAAACTAAATAATAATCA
1206656 AGTGACCAAAT
1 AGTGACCAAAT
1206667 CATAAATTAG
Statistics
Matches: 107, Mismatches: 24, Indels: 32
0.66 0.15 0.20
Matches are distributed among these distances:
31 39 0.36
32 6 0.06
34 6 0.06
36 6 0.06
37 50 0.47
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.28
Consensus pattern (37 bp):
AGTGACCAAATAGGTAGTTTAAACTAAATAATAATCA
Found at i:1206559 original size:31 final size:31
Alignment explanation
Indices: 1206524--1206628 Score: 95
Period size: 31 Copynumber: 3.2 Consensus size: 31
1206514 TAATCGAGTA
*
1206524 ACCAAAACATAAATTAGATAATATATAAGTG
1 ACCAAAATATAAATTAGATAATATATAAGTG
* * * *
1206555 ACCAAATAGGTAGTTTACTCTAAATAATA-ATCTAGTG
1 ACCAAA-A--TA--TAAAT-TAGATAATATAT-AAGTG
1206592 ACCAAAATATAAATTAGATAATATATAAGTG
1 ACCAAAATATAAATTAGATAATATATAAGTG
1206623 ACCAAA
1 ACCAAA
1206629 TAGGTAGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
31 24 0.42
32 6 0.11
34 3 0.05
36 6 0.11
37 18 0.32
ACGTcount: A:0.50, C:0.11, G:0.10, T:0.28
Consensus pattern (31 bp):
ACCAAAATATAAATTAGATAATATATAAGTG
Found at i:1206567 original size:68 final size:68
Alignment explanation
Indices: 1206395--1206714 Score: 454
Period size: 68 Copynumber: 4.8 Consensus size: 68
1206385 ATAAAGTGCT
* *
1206395 CAAAACATAAATTAGATAATAGATAAGTGACCAAATAGGTAGTTTACCCTAAATAAAAAT--A-T
1 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
1206457 ATA-
66 A-AC
* * * *
1206460 -TAAA-TTATATTAGATAATATATTAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
1 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
1206523 AAC
66 AAC
* *
1206526 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACTCTAAATAATAATCTAGT
1 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
*
1206591 GAC
66 AAC
* *
1206594 CAAAATATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTATCCTAAATAATAATCGAGT
1 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
*
1206659 GAC
66 AAC
* * *
1206662 CAAATCATAAATTAGATAATATTTAAATGACCAAATAGGTAGTTTACCCTAAA
1 CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAA
1206715 AAAACCCTAA
Statistics
Matches: 227, Mismatches: 22, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
63 49 0.22
64 3 0.01
65 2 0.01
66 2 0.01
67 3 0.01
68 168 0.74
ACGTcount: A:0.47, C:0.11, G:0.12, T:0.30
Consensus pattern (68 bp):
CAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACCCTAAATAATAATCGAGT
AAC
Found at i:1209351 original size:11 final size:11
Alignment explanation
Indices: 1209335--1209371 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1209325 ATTTAAAAAG
1209335 TTTTAAACACA
1 TTTTAAACACA
1209346 TTTTAAACAC-
1 TTTTAAACACA
*
1209356 -TTTAAACATA
1 TTTTAAACACA
1209366 TTTTAA
1 TTTTAA
1209372 TTAACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (11 bp):
TTTTAAACACA
Found at i:1209442 original size:29 final size:29
Alignment explanation
Indices: 1209398--1209463 Score: 89
Period size: 30 Copynumber: 2.3 Consensus size: 29
1209388 AAAATATTAA
1209398 AAAAAATACTGAAAAA-TAGACCTCTAAT
1 AAAAAATACTGAAAAATTAGACCTCTAAT
* *
1209426 AAAAAATACTGAAAAAATTAGACTTGTAAT
1 AAAAAATACTG-AAAAATTAGACCTCTAAT
*
1209456 AACAAATA
1 AAAAAATA
1209464 AATATTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 11 0.33
29 5 0.15
30 17 0.52
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.23
Consensus pattern (29 bp):
AAAAAATACTGAAAAATTAGACCTCTAAT
Found at i:1212809 original size:158 final size:159
Alignment explanation
Indices: 1212554--1212898 Score: 545
Period size: 158 Copynumber: 2.2 Consensus size: 159
1212544 TGTGGTAAAT
* * *
1212554 GAGCATGTGGTTCAAATTTGGT--AAAAATGGACTTAAAATAAATCACAAATTGAAGGAATAAGG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAACGAACTTAAAATAAATCACAAATTGAAGAAATAAGG
* *
1212617 AGATTATGAAAATTTGAAGAACTAAATTGGAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGA
66 AGACTATGAAAATTTGAAGAACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGA
1212682 AAGTACACATGTATTCTACTATGGTTTAG
131 AAGTACACATGTATTCTACTATGGTTTAG
* * **
1212711 GAGCATGTGGCTCAAATTTGGTAAAAAAACGAACTTAAAA-AAATGATGAATTGAAGAAATAAGG
1 GAGCATGTGGTTCAAATTTGGTAAAAAAACGAACTTAAAATAAATCACAAATTGAAGAAATAAGG
* *
1212775 AGACTATGAATAA-TTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGATGAATTG
66 AGACTATGAA-AATTTGAAGAACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTG
1212839 AAAGTACACATGTATTCTACTATGGTTTAG
130 AAAGTACACATGTATTCTACTATGGTTTAG
1212869 GAGCATGTGGGTTCAAATTTGGTAAAAAAA
1 GAGCATGT-GGTTCAAATTTGGTAAAAAAA
1212899 TAGACTTAAA
Statistics
Matches: 172, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
157 21 0.12
158 115 0.67
159 36 0.21
ACGTcount: A:0.46, C:0.07, G:0.19, T:0.28
Consensus pattern (159 bp):
GAGCATGTGGTTCAAATTTGGTAAAAAAACGAACTTAAAATAAATCACAAATTGAAGAAATAAGG
AGACTATGAAAATTTGAAGAACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGA
AAGTACACATGTATTCTACTATGGTTTAG
Found at i:1212968 original size:158 final size:157
Alignment explanation
Indices: 1212554--1212937 Score: 425
Period size: 158 Copynumber: 2.4 Consensus size: 157
1212544 TGTGGTAAAT
* * * ** ** *
1212554 GAGCATGTGGTTCAAATTTGGT--AAAAATGGACTTAAAATAAATCACAAATTGAAGGAATAAGG
1 GAGCATGTGGCTCAAATTTGGTAAAAAAAAGAACTTAAAA-AAAGGAGGAATTGAAGAAATAAGG
* * * * * * *
1212617 AGATTATGAA-AATTTGAAGAACTAAATTGGAAAATAAAAAATTTGTTATCAAAAAGAGGAATTG
65 AAACTAGGAATAA-ATGAAGGAC-AAACTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTG
1212681 AAAGTACACATGTATTCTACTATGGTTTAG
128 AAAGTACACATGTATTCTACTATGGTTTAG
* * *
1212711 GAGCATGTGGCTCAAATTTGGTAAAAAAACGAACTTAAAAAAATGATGAATTGAAGAAATAAGGA
1 GAGCATGTGGCTCAAATTTGGTAAAAAAAAGAACTTAAAAAAAGGAGGAATTGAAGAAATAAGGA
* * * * *
1212776 GACTATGAATAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATCAAAAAGATGAATTGAA
66 AACTAGGAATAAATGAAGGAC-AAACTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAA
1212841 AGTACACATGTATTCTACTATGGTTTAG
130 AGTACACATGTATTCTACTATGGTTTAG
* ** *
1212869 GAGCATGTGGGTTCAAATTTGGTAAAAAAATAG-ACTTAAAATGGAGGAGGAATTGAAGAATTAA
1 GAGCATGT-GGCTCAAATTTGGTAAAAAAA-AGAACTTAAAA-AAAGGAGGAATTGAAGAAATAA
*
1212933 TGAAA
63 GGAAA
1212938 TCAGGGACTA
Statistics
Matches: 201, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
157 21 0.10
158 115 0.57
159 44 0.22
160 21 0.10
ACGTcount: A:0.46, C:0.07, G:0.20, T:0.27
Consensus pattern (157 bp):
GAGCATGTGGCTCAAATTTGGTAAAAAAAAGAACTTAAAAAAAGGAGGAATTGAAGAAATAAGGA
AACTAGGAATAAATGAAGGACAAACTGAAAAATAAAAAATTTGTTATCAAAAAGAGGAATTGAAA
GTACACATGTATTCTACTATGGTTTAG
Found at i:1213773 original size:2 final size:2
Alignment explanation
Indices: 1213766--1213795 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1213756 ATGTAATTAA
1213766 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1213796 TTAAGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1213804 original size:2 final size:2
Alignment explanation
Indices: 1213799--1213833 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1213789 TATATATTTA
1213799 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1213834 ATTAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1214961 original size:41 final size:43
Alignment explanation
Indices: 1214876--1214970 Score: 127
Period size: 43 Copynumber: 2.2 Consensus size: 43
1214866 TAATGTGACA
* *
1214876 ATATATATTATTAAATCATTTGAAGCGATGCATCAAGATATAT
1 ATATATATTATTAAATAATTTGAAGCGACGCATCAAGATATAT
* * * **
1214919 ATATATATTGTTGAATAATTTGAAGCGACGTATCAATTTATAT
1 ATATATATTATTAAATAATTTGAAGCGACGCATCAAGATATAT
1214962 ATATATATT
1 ATATATATT
1214971 TTGATAAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (43 bp):
ATATATATTATTAAATAATTTGAAGCGACGCATCAAGATATAT
Found at i:1214993 original size:2 final size:2
Alignment explanation
Indices: 1214986--1215019 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1214976 AAGATTAATA
1214986 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1215020 TATTGAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1217032 original size:27 final size:27
Alignment explanation
Indices: 1216992--1217056 Score: 112
Period size: 27 Copynumber: 2.3 Consensus size: 27
1216982 AATCTTCTTT
1216992 TAAAATTTTAAAAATTCATCTCCTACCA
1 TAAAA-TTTAAAAATTCATCTCCTACCA
1217020 TAAAATTTAAAAATTCATCTCCTACCA
1 TAAAATTTAAAAATTCATCTCCTACCA
1217047 TAAAAATTTA
1 T-AAAATTTA
1217057 TGTCCATCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 23 0.64
28 13 0.36
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.35
Consensus pattern (27 bp):
TAAAATTTAAAAATTCATCTCCTACCA
Found at i:1218370 original size:22 final size:22
Alignment explanation
Indices: 1218340--1218393 Score: 99
Period size: 22 Copynumber: 2.4 Consensus size: 22
1218330 CAAATAAAAA
1218340 AATTATATTTATATTTCAAACCT
1 AATT-TATTTATATTTCAAACCT
1218363 AATTTATTTATATTTCAAACCT
1 AATTTATTTATATTTCAAACCT
1218385 AATTTATTT
1 AATTTATTT
1218394 TTCACTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 27 0.87
23 4 0.13
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTATTTATATTTCAAACCT
Found at i:1224665 original size:21 final size:21
Alignment explanation
Indices: 1224639--1224686 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1224629 TCTTGCGAAT
* *
1224639 TAATGTAACAATTACTTAATA
1 TAATGTAACAACTACTTAAAA
*
1224660 TAATGTAACCACTACTTAAAA
1 TAATGTAACAACTACTTAAAA
1224681 TAATGT
1 TAATGT
1224687 TTGAATTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.06, T:0.35
Consensus pattern (21 bp):
TAATGTAACAACTACTTAAAA
Found at i:1226680 original size:31 final size:29
Alignment explanation
Indices: 1226616--1226694 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 29
1226606 AGTAGGTCCC
* *
1226616 TAATAATAAATATTAAAAAATTGAATTCA
1 TAATAATAAATATTAAAAAATTAAATACA
*
1226645 TAATAATAAATATTGAGAAAAATTAAATACT
1 TAATAATAAATATT-A-AAAAATTAAATACA
*
1226676 TAATAAAAAATATTAAAAA
1 TAATAATAAATATTAAAAA
1226695 TCCCTATAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 18 0.41
30 2 0.05
31 24 0.55
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.32
Consensus pattern (29 bp):
TAATAATAAATATTAAAAAATTAAATACA
Found at i:1228526 original size:273 final size:272
Alignment explanation
Indices: 1228029--1228575 Score: 875
Period size: 273 Copynumber: 2.0 Consensus size: 272
1228019 GCAACAAAGG
*
1228029 GATTATTCCAGAAATCTCCACTGCTTTGAGCTTGGTATGTTTCCGCCGGAGGAAGACAAGTATCT
1 GATTATTCCAAAAATCTCCACTGCTTTGAGCTTGGTATGTTTCCGCC-GAGGAAGACAAGTATCT
* *
1228094 TCAACAAAGGAGGAAAACTCTGTAGTTGAAGATGTCGCTGGAGACAAAGTTGAACTCTCCAAGAT
65 TCAACAAAGGAGGAAAACTCAGTAGTTAAAGATGTCGCTGGAGACAAAGTTGAACTCTCCAAGAT
*
1228159 CATGTTAGCCGGAGTATCAACAAGGATGCTTTCAACTCCAATTTCACCTTCAGAATTCTGGGTGG
130 CATGTTAGCCGCAGTATCAACAAGGATGCTTTCAACTCCAATTTCACCTTCAGAATTCTGGGTGG
* *
1228224 CTTCACTTGGACAACTAGAGTCTTCTTTGACGTGATCAGATATTGTCGGATTTCGCTTTCCACGC
195 CTTCACTTGGACAACTAGAGTCATCTTTGAC---ATCAGATATTGTAGGATTTCGCTTTCCACGC
1228289 TTCTTTAGATCGGAGT
257 TTCTTTAGATCGGAGT
*
1228305 GATTATTCCAAAAATCTCCACTGCTTTGAGCTTGGTATGTTTCCG-C-AGGAGGACAAGTATCTT
1 GATTATTCCAAAAATCTCCACTGCTTTGAGCTTGGTATGTTTCCGCCGAGGAAGACAAGTATCTT
** * *
1228368 CAACAAAGGAGGACGACTCAGTAGTTAAAGATGTTGCTGGAGACAAAGTTGAACTCTCCAATATC
66 CAACAAAGGAGGAAAACTCAGTAGTTAAAGATGTCGCTGGAGACAAAGTTGAACTCTCCAAGATC
* ** *
1228433 ATG-TAGGCCGCAGTATCAACAAGGATGCTTTCAGCTCCTCTTTCACCTTCAGATTTCTGGGTGG
131 ATGTTA-GCCGCAGTATCAACAAGGATGCTTTCAACTCCAATTTCACCTTCAGAATTCTGGGTGG
* *
1228497 CTTCACTTGGACAACTAGAGTCATCTTTGACATCAGATGTTGTAGGATTTCGCTTTTCACGCTTC
195 CTTCACTTGGACAACTAGAGTCATCTTTGACATCAGATATTGTAGGATTTCGCTTTCCACGCTTC
1228562 TTTAGATCGGAGT
260 TTTAGATCGGAGT
1228575 G
1 G
1228576 CCAGTGATTT
Statistics
Matches: 253, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
270 45 0.18
272 2 0.01
273 161 0.64
275 1 0.00
276 44 0.17
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (272 bp):
GATTATTCCAAAAATCTCCACTGCTTTGAGCTTGGTATGTTTCCGCCGAGGAAGACAAGTATCTT
CAACAAAGGAGGAAAACTCAGTAGTTAAAGATGTCGCTGGAGACAAAGTTGAACTCTCCAAGATC
ATGTTAGCCGCAGTATCAACAAGGATGCTTTCAACTCCAATTTCACCTTCAGAATTCTGGGTGGC
TTCACTTGGACAACTAGAGTCATCTTTGACATCAGATATTGTAGGATTTCGCTTTCCACGCTTCT
TTAGATCGGAGT
Found at i:1230564 original size:20 final size:20
Alignment explanation
Indices: 1230539--1230581 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
1230529 CCGCGCTATA
1230539 CCCTTAATTACCAACCTACC
1 CCCTTAATTACCAACCTACC
1230559 CCCTTAATTACCAACCTACC
1 CCCTTAATTACCAACCTACC
1230579 CCC
1 CCC
1230582 GTCCGTTCAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (20 bp):
CCCTTAATTACCAACCTACC
Found at i:1233355 original size:69 final size:68
Alignment explanation
Indices: 1233235--1233365 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 68
1233225 GATTTGAGGG
* *
1233235 GGAGAAATATAATTAATAATAGAAAAATGAGAGGGACAAAATAAAAAAAACCAAAACTTGAAGTT
1 GGAGAAATATAATTAACAATAGAAAAATAAGAGGGACAAAATAAAAAAAACCAAAACTTGAAGTT
1233300 CAA
66 CAA
* * * *
1233303 GGAGTAAAGTATAATTAACAATA-AGAAATAAGAGGGTCAAATTAAAATAAACCAAAACTTGAA
1 GGAG-AAA-TATAATTAACAATAGAAAAATAAGAGGGACAAAATAAAAAAAACCAAAACTTGAA
1233366 TGAACAAATA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
68 4 0.07
69 38 0.69
70 13 0.24
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.19
Consensus pattern (68 bp):
GGAGAAATATAATTAACAATAGAAAAATAAGAGGGACAAAATAAAAAAAACCAAAACTTGAAGTT
CAA
Found at i:1233698 original size:16 final size:17
Alignment explanation
Indices: 1233664--1233698 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1233654 TTTTTTGGAT
*
1233664 AACAAATTATTTGTTTA
1 AACAAATTATTTATTTA
1233681 AACAAATTA-TTATTTA
1 AACAAATTATTTATTTA
1233697 AA
1 AA
1233699 TTAATTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (17 bp):
AACAAATTATTTATTTA
Found at i:1242251 original size:22 final size:22
Alignment explanation
Indices: 1242221--1242262 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1242211 TCAGCTGTTA
* *
1242221 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
*
1242243 TAACCCCTGGAATTAAATCA
1 TAACCCCTGAAATTAAATCA
1242263 AATAACTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:1242268 original size:22 final size:22
Alignment explanation
Indices: 1242220--1242268 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1242210 TTCAGCTGTT
* * *
1242220 ATAACTCCTGAAATTATATCAT
1 ATAACCCCTGAAATTAAATCAA
* *
1242242 GTAACCCCTGGAATTAAATCAA
1 ATAACCCCTGAAATTAAATCAA
1242264 ATAAC
1 ATAAC
1242269 TCATGTAACT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (22 bp):
ATAACCCCTGAAATTAAATCAA
Found at i:1248140 original size:22 final size:22
Alignment explanation
Indices: 1248110--1248169 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
1248100 TCAGCTGTTA
* *
1248110 TAACTCCTGAAATTATATCATG
1 TAACCCCTGAAATTAAATCATG
* **
1248132 TAACCCCTGGAATTAAATCAAA
1 TAACCCCTGAAATTAAATCATG
* *
1248154 TAACTCCTGATATTAA
1 TAACCCCTGAAATTAA
1248170 CAGCTTGTCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCCCTGAAATTAAATCATG
Found at i:1256733 original size:29 final size:29
Alignment explanation
Indices: 1256688--1256745 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1256678 GTGTTGGCCG
*
1256688 TAGGTCGCCATGCCTTCCGGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
* *
1256717 TAGGTCGCCATGTCTTCCCGGCGAGCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
1256746 AAGAGATAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.14, C:0.36, G:0.28, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:1256833 original size:20 final size:20
Alignment explanation
Indices: 1256804--1256855 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1256794 CCATCCGACC
*
1256804 GAGGCTATCCGAGAGCATCT
1 GAGGCCATCCGAGAGCATCT
1256824 GAGGCCATCCGAGAGCATCT
1 GAGGCCATCCGAGAGCATCT
1256844 GAGGCCATCCGA
1 GAGGCCATCCGA
1256856 ACGAGCTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.31, T:0.15
Consensus pattern (20 bp):
GAGGCCATCCGAGAGCATCT
Found at i:1256950 original size:29 final size:29
Alignment explanation
Indices: 1256887--1256950 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
1256877 GAGCGAGGGT
*
1256887 AGGTCACCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1256916 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1256945 AGGTCG
1 AGGTCG
1256951 AGGGCATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.22, C:0.30, G:0.34, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1256962 original size:24 final size:26
Alignment explanation
Indices: 1256894--1256966 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 26
1256884 GGTAGGTCAC
*
1256894 CCGGAGTGCATGGCGACCTACAAGGT
1 CCGGAGGGCATGGCGACCTACAAGGT
*
1256920 CGCCCGGAGTGCATGGCGACCTACAAGGT
1 ---CCGGAGGGCATGGCGACCTACAAGGT
1256949 -C-GAGGGCATGGCGACCTA
1 CCGGAGGGCATGGCGACCTA
1256967 TGTGTTGGGA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
24 16 0.37
25 1 0.02
29 26 0.60
ACGTcount: A:0.22, C:0.29, G:0.36, T:0.14
Consensus pattern (26 bp):
CCGGAGGGCATGGCGACCTACAAGGT
Found at i:1257067 original size:29 final size:29
Alignment explanation
Indices: 1257025--1257168 Score: 218
Period size: 29 Copynumber: 5.0 Consensus size: 29
1257015 GAGCAAGGGT
*
1257025 AGGTCGCCCGGAGTGCATGGCGATCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
1257054 AGGTCGCCCAGAGTGTATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
1257083 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
1257112 AGGCCGCCCGAAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
1257141 AGGTCGCCCGGAAG-GCATGACGACCTAC
1 AGGTCGCCCGG-AGTGCATGGCGACCTAC
1257169 GGCCAACACT
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
29 102 0.98
30 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:1261035 original size:21 final size:21
Alignment explanation
Indices: 1261007--1261082 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
1260997 TTTAGAATAA
*
1261007 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
1261028 ATCACAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
1261047 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
1261070 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1261083 TATGTAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 10 0.22
21 24 0.53
23 11 0.24
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:1261047 original size:42 final size:42
Alignment explanation
Indices: 1260980--1261072 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
1260970 GAGCTATGTC
* *
1260980 TCGACTATCGCAACGAATTTAGAATAAATCGCAACGCGAACT
1 TCGACTATCACAACGAACTTAGAATAAATCGCAACGCGAACT
*
1261022 TCGACTATCACAACGAACTTGGAATAAATCGCAACGCGAACT
1 TCGACTATCACAACGAACTTAGAATAAATCGCAACGCGAACT
*
1261064 TGGACTATC
1 TCGACTATC
1261073 GCAATGCGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (42 bp):
TCGACTATCACAACGAACTTAGAATAAATCGCAACGCGAACT
Found at i:1261062 original size:23 final size:23
Alignment explanation
Indices: 1261001--1261067 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 23
1260991 AACGAATTTA
*
1261001 GAATAAATCGCAACGCGAACTTC
1 GAATAAATCGCAACGCGAACTTG
* *
1261024 GACT--ATCACAA--CGAACTTG
1 GAATAAATCGCAACGCGAACTTG
1261043 GAATAAATCGCAACGCGAACTTG
1 GAATAAATCGCAACGCGAACTTG
1261066 GA
1 GA
1261068 CTATCGCAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
19 10 0.29
21 12 0.34
23 13 0.37
ACGTcount: A:0.39, C:0.24, G:0.19, T:0.18
Consensus pattern (23 bp):
GAATAAATCGCAACGCGAACTTG
Found at i:1262263 original size:17 final size:17
Alignment explanation
Indices: 1262237--1262283 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 17
1262227 CAAAGTTGTT
*
1262237 AAAAATTAAAAAGTA-AG
1 AAAAAATAAAAA-TAGAG
1262254 AAAAAATAAAAATATGAG
1 AAAAAATAAAAATA-GAG
1262272 AACAAAATAAAA
1 AA-AAAATAAAA
1262284 TAAAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 2 0.08
17 11 0.42
18 4 0.15
19 9 0.35
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (17 bp):
AAAAAATAAAAATAGAG
Found at i:1272996 original size:17 final size:19
Alignment explanation
Indices: 1272957--1273001 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1272947 CTTTTTCATT
1272957 TCATAATCAATATTTCAAC
1 TCATAATCAATATTTCAAC
1272976 TCATAATCAAT-TTTCAA-
1 TCATAATCAATATTTCAAC
*
1272993 TCATTATCA
1 TCATAATCA
1273002 TAAAAATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 8 0.32
18 6 0.24
19 11 0.44
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (19 bp):
TCATAATCAATATTTCAAC
Found at i:1279024 original size:14 final size:14
Alignment explanation
Indices: 1279005--1279049 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
1278995 TGATAAGTTG
1279005 GTTTTAATGTATAT
1 GTTTTAATGTATAT
*
1279019 GTTTTAATGTGTAT
1 GTTTTAATGTATAT
1279033 GTTTTAATGTATAT
1 GTTTTAATGTATAT
1279047 GTT
1 GTT
1279050 AAGGATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:1279196 original size:34 final size:34
Alignment explanation
Indices: 1279157--1279229 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1279147 TTAAGTTTAA
*
1279157 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAACTTCGAATACCATAATTTGTAT
* * *
1279191 TTTAATTTTAAACTTCGAGTACTATAATTTGTAT
1 TTTAATGTTAAACTTCGAATACCATAATTTGTAT
*
1279225 ATTAA
1 TTTAA
1279230 AAACAATTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (34 bp):
TTTAATGTTAAACTTCGAATACCATAATTTGTAT
Found at i:1279763 original size:21 final size:20
Alignment explanation
Indices: 1279739--1279809 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 20
1279729 GGTGTCATAA
*
1279739 AACCCTGCGGGCTAGTCATGT
1 AACCCTGCGGGCTAG-AATGT
*
1279760 AA-CCTGACGGGCTAAGAATAT
1 AACCCTG-CGGGCT-AGAATGT
*
1279781 AACCCTGAGGGCTAGGAATGT
1 AACCCTGCGGGCTA-GAATGT
1279802 AACCCTGC
1 AACCCTGC
1279810 AGAGATGGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 5 0.12
21 30 0.73
22 6 0.15
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (20 bp):
AACCCTGCGGGCTAGAATGT
Found at i:1281354 original size:30 final size:30
Alignment explanation
Indices: 1281275--1281368 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
1281265 TAATTAGTAC
* *
1281275 AAAAATAATAATTA-ATAA--ATTTAAATA
1 AAAAATAATATTTATATAATTATTTTAATA
* * *
1281302 AATAATAAT-TATATAAATATTATTTTAATA
1 AAAAATAATATTTATATA-ATTATTTTAATA
* *
1281332 AAAAATAATATTTATATAATTATATTACTA
1 AAAAATAATATTTATATAATTATTTTAATA
*
1281362 TAAAATA
1 AAAAATA
1281369 TAAAAACTAT
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
26 2 0.04
27 10 0.20
28 1 0.02
30 32 0.63
31 6 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAAATAATATTTATATAATTATTTTAATA
Found at i:1289147 original size:190 final size:189
Alignment explanation
Indices: 1288825--1289287 Score: 525
Period size: 190 Copynumber: 2.4 Consensus size: 189
1288815 AACTAATTTT
* * * * *
1288825 AAAAACATATGCGGCGTTTCTTGCCAAAACGCCACTAATGTACGAATAATTTGCGGCGTTTGTTA
1 AAAAACATCTACGGCATTTTTTGACAAAACGCCACTAATGTACGAATAATTTGCGGCGTTTGTTA
* * * * * ** *
1288890 CTAAAACGTCGCTATATGTGAACCATATTGCGACGTTTTTGTCAAAATGCCGGTAAAGTACTAAT
66 CCAAAACGCCACTATATGTGAACCATATTACGACATTTTTGTCAAAACACCGCTAAAGTACTAAT
1288955 TTGTTACGGCGTTTATTAAAGAA-CGCCCCTATATGTCTAAAGATAATGACGTTTAAATA
131 TTGTTACGGCGTTTATTAAA-AAGCGCCCCTATATGTCTAAAGATAATGACGTTTAAATA
* * **
1289014 AAAAACATCTATGGCATTTTTTGTCAAAACGCCACTAATGATTTGAATAATTTGCGGCGTTTGTT
1 AAAAACATCTACGGCATTTTTTGACAAAACGCCACTAATG-TACGAATAATTTGCGGCGTTTGTT
* * * * **
1289079 ACCAAAACGCCACTATATGTGAACCCTCTTATGGCATTTTTGTCAAAACACCGCTGTAGTACTAA
65 ACCAAAACGCCACTATATGTGAACCATATTACGACATTTTTGTCAAAACACCGCTAAAGTACTAA
** *** * *
1289144 TTTGTTGTGGCGTTTATTAAAAAGCGTTGCTATATGTCTAAAGTTAATGGCGTTTAAATA
130 TTTGTTACGGCGTTTATTAAAAAGCGCCCCTATATGTCTAAAGATAATGACGTTTAAATA
* * * ** * * *
1289204 AAAAACATTTGCGGCATTTTTTGACAAAACGCCACAAAAATACTAATTATTTGTGGCGTTTGTGT
1 AAAAACATCTACGGCATTTTTTGACAAAACGCCACTAATGTACGAATAATTTGCGGCGTTTGT-T
* *
1289269 -CAAAAACGCCGCTATATGT
65 ACCAAAACGCCACTATATGT
1289288 CTAAATTTAG
Statistics
Matches: 228, Mismatches: 43, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
189 71 0.31
190 157 0.69
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (189 bp):
AAAAACATCTACGGCATTTTTTGACAAAACGCCACTAATGTACGAATAATTTGCGGCGTTTGTTA
CCAAAACGCCACTATATGTGAACCATATTACGACATTTTTGTCAAAACACCGCTAAAGTACTAAT
TTGTTACGGCGTTTATTAAAAAGCGCCCCTATATGTCTAAAGATAATGACGTTTAAATA
Found at i:1290886 original size:13 final size:13
Alignment explanation
Indices: 1290868--1290900 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1290858 AAATAAACGC
1290868 CACTATTGATTAA
1 CACTATTGATTAA
1290881 CACTATTGATTAA
1 CACTATTGATTAA
1290894 CACTATT
1 CACTATT
1290901 ATGGCGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (13 bp):
CACTATTGATTAA
Found at i:1291978 original size:18 final size:17
Alignment explanation
Indices: 1291955--1292009 Score: 62
Period size: 17 Copynumber: 3.3 Consensus size: 17
1291945 TAAAGCACTT
1291955 TTTAAATATATAAAATAA
1 TTTAAA-ATATAAAATAA
1291973 TTT-AAATATAAAATAAA
1 TTTAAAATATAAAAT-AA
*
1291990 TATAAAATA-AAAA-AA
1 TTTAAAATATAAAATAA
1292005 TTTAA
1 TTTAA
1292010 TAAAAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
15 6 0.18
16 9 0.27
17 10 0.30
18 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTTAAAATATAAAATAA
Found at i:1291983 original size:16 final size:16
Alignment explanation
Indices: 1291962--1292009 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
1291952 CTTTTTAAAT
1291962 ATATAAAATAATTTAA
1 ATATAAAATAATTTAA
*
1291978 ATATAAAATAAATATAA
1 ATATAAAAT-AATTTAA
*
1291995 A-ATAAAAAAATTTAA
1 ATATAAAATAATTTAA
1292010 TAAAAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATATAAAATAATTTAA
Found at i:1291989 original size:11 final size:11
Alignment explanation
Indices: 1291975--1292000 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1291965 TAAAATAATT
1291975 TAAATATAAAA
1 TAAATATAAAA
1291986 TAAATATAAAA
1 TAAATATAAAA
1291997 TAAA
1 TAAA
1292001 AAAATTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAATATAAAA
Found at i:1292140 original size:27 final size:27
Alignment explanation
Indices: 1292099--1292162 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
1292089 ATAAATCGTA
* *
1292099 ATTGAGTTATAATAATTTTAATTTATG
1 ATTGAGTTATAATAATATCAATTTATG
* *
1292126 ATTGAGTTATGATAATATCAATTTGTG
1 ATTGAGTTATAATAATATCAATTTATG
1292153 ATTGAGTTAT
1 ATTGAGTTAT
1292163 CATTGTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.34, C:0.02, G:0.16, T:0.48
Consensus pattern (27 bp):
ATTGAGTTATAATAATATCAATTTATG
Found at i:1293860 original size:134 final size:132
Alignment explanation
Indices: 1293677--1294121 Score: 570
Period size: 134 Copynumber: 3.3 Consensus size: 132
1293667 GTAAATCGAA
* * * ** *
1293677 CTCGTTTCAATCTTCCTTGAAGAACAGTGGAATGAATCAATGTCCCCATATATGATTTTCCCTC-
1 CTCGATTCAATCTTCCCTG-AGGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
*
1293741 AGAAAGAAGCAGAATAGATCATTCTCTTTCAAGATTTGATATTCCTTGAGTAACAGTGGAACAAG
65 AG-AAGAAGCAGAATAGATC-TTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
*
1293806 TCTAC
128 TCTGC
* *
1293811 CTCGATTCAATCTTCCCTGAGTGACAGTAGAATGAATCAACATCTCCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAG-GACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * * * * *
1293876 AGAAGAAGCATAATAGACCCCTCTCTTTCAAGATTTGATATCCCCTGAGTAATATTGGAACAAGT
65 AGAAGAAGCAGAATAGA-TCTTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
1293941 CTGC
129 CTGC
* * *
1293945 CTCAATTCAATCTTCCCTTAGAGACAATGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAG-GACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCA
* * *
1294010 AGAAGAAAC-GAAATAGATCTATCTTTTTCAAGATTTGATATTCCCTGAGTAACAGTGAAACAAG
65 AGAAGAAGCAG-AATAGATCT-TCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAG
1294074 TCTGC
128 TCTGC
* * *
1294079 CTCGATTCAATCTTCCCTGAAGAATAGTGGAATGAGTCAACAT
1 CTCGATTCAATCTTCCCTG-AGGACAGTGGAATGAATCAACAT
1294122 TTCTCGATCT
Statistics
Matches: 268, Mismatches: 37, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
133 3 0.01
134 260 0.97
135 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.30
Consensus pattern (132 bp):
CTCGATTCAATCTTCCCTGAGGACAGTGGAATGAATCAACATCCCCATATCTGATTTTCCCTCAA
GAAGAAGCAGAATAGATCTTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
GC
Found at i:1294338 original size:18 final size:19
Alignment explanation
Indices: 1294315--1294355 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
1294305 TTTTTAATAT
1294315 TATTATCATTATTATTT-A
1 TATTATCATTATTATTTAA
*
1294333 TATTATTATTATTATTTAA
1 TATTATCATTATTATTTAA
1294352 TATT
1 TATT
1294356 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTATCATTATTATTTAA
Found at i:1298410 original size:23 final size:22
Alignment explanation
Indices: 1298363--1298418 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
1298353 TCCCATTGTA
* *
1298363 AAAAAAGATATTAAGTTAAAGT
1 AAAAAAGATATTAAATTAAAAT
1298385 AAAAAAGA-ATTAAATATCAAAAT
1 AAAAAAGATATTAAAT-T-AAAAT
*
1298408 AAAAAGGATAT
1 AAAAAAGATAT
1298419 AATTTAGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 11 0.39
24 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.11, T:0.23
Consensus pattern (22 bp):
AAAAAAGATATTAAATTAAAAT
Found at i:1299058 original size:17 final size:17
Alignment explanation
Indices: 1299027--1299059 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1299017 CTCTACACAT
1299027 AATATATTTATTATTAA
1 AATATATTTATTATTAA
1299044 AATAT-TTTATATATTA
1 AATATATTTAT-TATTA
1299060 TACATAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATATTTATTATTAA
Found at i:1309777 original size:23 final size:23
Alignment explanation
Indices: 1309759--1309819 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
1309749 CTCGTATAAA
1309759 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1309782 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1309805 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1309820 TATAAAATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1311446 original size:19 final size:19
Alignment explanation
Indices: 1311422--1311474 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1311412 TCTTGAGAGG
1311422 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
*
1311441 ATGCATTGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
1311460 ATGCATCGATGCACT
1 ATGCATCGATGCACT
1311475 AATTGCATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:1314896 original size:83 final size:83
Alignment explanation
Indices: 1314745--1314908 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 83
1314735 GTGTATATCT
* * * *
1314745 GTTTAATACTTTAAATTTAAATGATCTTATTATCTATTTAAATTTAGATATTAAAAGATATATGG
1 GTTTAATACTTTAAATTTAAATAATATTATTATATATTTAAATTTAGATATTAAAAGATATATAG
* *
1314810 TTGGAGTAAATCTCTCAG
66 TTGGAGAAAAGCTCTCAG
* * *
1314828 GTTTAATATTTTAAATTTTAAA-AATATTATTATATGTTTAAATTTAGATATTAAAAG-TGATTT
1 GTTTAATACTTTAAA-TTTAAATAATATTATTATATATTTAAATTTAGATATTAAAAGAT-ATAT
1314891 AGTTGGAGAAAAGCTCTC
64 AGTTGGAGAAAAGCTCTC
1314909 TTGAAATTCC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 1 0.01
83 63 0.90
84 6 0.09
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.44
Consensus pattern (83 bp):
GTTTAATACTTTAAATTTAAATAATATTATTATATATTTAAATTTAGATATTAAAAGATATATAG
TTGGAGAAAAGCTCTCAG
Found at i:1316316 original size:23 final size:23
Alignment explanation
Indices: 1316284--1316351 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
1316274 AATAATTAGG
1316284 GGAA-TATCTTCTGCAATTTATTA
1 GGAATTATCTT-TGCAATTTATTA
**
1316307 GG-ATTATCTTTTGTGATTT-TTA
1 GGAATTATC-TTTGCAATTTATTA
*
1316329 GGAATTATCTTTGCAAATTATTA
1 GGAATTATCTTTGCAATTTATTA
1316352 CGAGATGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
22 13 0.36
23 21 0.58
24 2 0.06
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (23 bp):
GGAATTATCTTTGCAATTTATTA
Found at i:1316333 original size:45 final size:46
Alignment explanation
Indices: 1316284--1316376 Score: 113
Period size: 46 Copynumber: 2.0 Consensus size: 46
1316274 AATAATTAGG
*
1316284 GGAA-TATCTTCTGCAATTTATTA-G-GATTATCTTTT-GTGATTTTTA
1 GGAATTATCTT-TGCAAATTATTACGAGA-TATCTTTTAG-GATTTTTA
*
1316329 GGAATTATCTTTGCAAATTATTACGAGATGTCTTTTAGGATTTTTA
1 GGAATTATCTTTGCAAATTATTACGAGATATCTTTTAGGATTTTTA
1316375 GG
1 GG
1316377 GTTTTTAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
45 15 0.36
46 24 0.57
47 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (46 bp):
GGAATTATCTTTGCAAATTATTACGAGATATCTTTTAGGATTTTTA
Found at i:1316507 original size:29 final size:27
Alignment explanation
Indices: 1316463--1316523 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
1316453 TTGTTATTCT
*
1316463 TTTTTTCTATTATAAAGGTTTTACTTTTC
1 TTTTTTCTATTATAAA-GTTTTA-TTTTA
*
1316492 TTTTTTCTTATT-TAAATTTTTATTTTA
1 TTTTTTC-TATTATAAAGTTTTATTTTA
1316519 TTTTT
1 TTTTT
1316524 CTTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.31
28 5 0.17
29 11 0.38
30 4 0.14
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (27 bp):
TTTTTTCTATTATAAAGTTTTATTTTA
Found at i:1320236 original size:30 final size:30
Alignment explanation
Indices: 1320164--1320242 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
1320154 ATTTTTGAAT
* * *
1320164 TTTTCTTCGTTTATTTTGATTTTTAATTTC
1 TTTTCTTAGTTTTTTTTTATTTTTAATTTC
1320194 TTTTCTTAGTTTTTTTTTATTTTTAATTTC
1 TTTTCTTAGTTTTTTTTTATTTTTAATTTC
1320224 TTTTCTTAGTTTTTATTTT
1 TTTTCTTAGTTTTT-TTTT
1320243 TGGCGTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 41 0.91
31 4 0.09
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.75
Consensus pattern (30 bp):
TTTTCTTAGTTTTTTTTTATTTTTAATTTC
Found at i:1320673 original size:14 final size:14
Alignment explanation
Indices: 1320654--1320680 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1320644 TCGGTTCCCC
1320654 TTCTTTTATTTTTT
1 TTCTTTTATTTTTT
1320668 TTCTTTTATTTTT
1 TTCTTTTATTTTT
1320681 CCAAACCACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (14 bp):
TTCTTTTATTTTTT
Found at i:1322454 original size:21 final size:23
Alignment explanation
Indices: 1322410--1322487 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
1322400 GATTAGGGTA
1322410 ATTATCTTTTGCAATTTATTAGG
1 ATTATCTTTTGCAATTTATTAGG
**
1322433 ATTATCTTTTGTGA-TT-TTAGG
1 ATTATCTTTTGCAATTTATTAGG
*
1322454 AATTA-CATTTGCAATTTATTAGG
1 -ATTATCTTTTGCAATTTATTAGG
1322477 AGTTATCTTTT
1 A-TTATCTTTT
1322488 AGGATTTTTA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 11 0.25
22 9 0.20
23 20 0.45
24 4 0.09
ACGTcount: A:0.26, C:0.08, G:0.14, T:0.53
Consensus pattern (23 bp):
ATTATCTTTTGCAATTTATTAGG
Found at i:1327627 original size:13 final size:13
Alignment explanation
Indices: 1327609--1327643 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1327599 AATATACTTA
1327609 GAAAATCTTTTTG
1 GAAAATCTTTTTG
1327622 GAAAATCTTTTTG
1 GAAAATCTTTTTG
1327635 GAAAATCTT
1 GAAAATCTT
1327644 AAAATTCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (13 bp):
GAAAATCTTTTTG
Found at i:1334882 original size:13 final size:13
Alignment explanation
Indices: 1334864--1334888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1334854 TCGAATATAC
1334864 TTGGAAAATCTTT
1 TTGGAAAATCTTT
1334877 TTGGAAAATCTT
1 TTGGAAAATCTT
1334889 AAAATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TTGGAAAATCTTT
Found at i:1337898 original size:20 final size:21
Alignment explanation
Indices: 1337873--1337924 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1337863 TTTTCCCAAT
*
1337873 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1337893 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1337914 TCGCAATGCGA
1 TCGCAATGCGA
1337925 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1337938 original size:20 final size:20
Alignment explanation
Indices: 1337913--1338047 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
1337903 AATTGGGAAA
1337913 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
1337933 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
1337953 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
1337974 ATCGTAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1337994 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1338014 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1338034 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1338048 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1337957 original size:61 final size:61
Alignment explanation
Indices: 1337910--1338041 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
1337900 GCGAATTGGG
* * * *
1337910 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
1337971 AAAATCGTAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1338032 ATAATCGCAA
1 AAAATCGCAA
1338042 TGCGATTTTC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1338243 original size:22 final size:22
Alignment explanation
Indices: 1338215--1338258 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1338205 CACTCTCTCA
*
1338215 CCCATCTCCTACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1338237 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1338259 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.45, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1338551 original size:20 final size:20
Alignment explanation
Indices: 1338512--1338570 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1338502 GCGATTATCT
**
1338512 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1338532 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
1338552 TGTTGTGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1338571 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1339915 original size:18 final size:18
Alignment explanation
Indices: 1339889--1339933 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1339879 TCCACTTTGG
*
1339889 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1339907 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1339925 GAGCCATCA
1 GAGCCATCA
1339934 TCTGATCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1340440 original size:20 final size:20
Alignment explanation
Indices: 1340415--1340455 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1340405 TAGTTTACTT
1340415 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1340435 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1340455 T
1 T
1340456 TGCGATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1340479 original size:19 final size:19
Alignment explanation
Indices: 1340455--1340565 Score: 64
Period size: 19 Copynumber: 6.4 Consensus size: 19
1340445 GAAATGGCTA
1340455 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
1340474 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
*
1340488 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
*
1340506 TTGCGA-TTT--TGT--CG
1 TTGCGATTTTCATTTCGCG
* *
1340520 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCG
***
1340539 TTGCGATAGCCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
1340559 TTGCGAT
1 TTGCGAT
1340566 AGTCATTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.25
15 3 0.04
16 6 0.09
17 2 0.03
18 13 0.19
19 18 0.26
20 10 0.14
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1340491 original size:14 final size:14
Alignment explanation
Indices: 1340472--1340529 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1340462 TTTCATTTCG
1340472 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1340486 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1340502 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1340518 CGTTGCAATTTT
1 CGTTGCGATTTT
1340530 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1340502 original size:32 final size:33
Alignment explanation
Indices: 1340455--1340545 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1340445 GAAATGGCTA
*
1340455 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1340488 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1340520 TTGCAATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1340546 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1340564 original size:20 final size:19
Alignment explanation
Indices: 1340530--1340573 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1340520 TTGCAATTTT
1340530 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
* *
1340549 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCATTGCGATAGC
1340569 CATTT
1 CATTT
1340574 TTTGTTGCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:1342449 original size:14 final size:14
Alignment explanation
Indices: 1342430--1342465 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1342420 ATTGTTTAAT
1342430 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1342444 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1342458 TGATTTGT
1 TGATTTGT
1342466 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1342573 original size:20 final size:20
Alignment explanation
Indices: 1342548--1342586 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1342538 ATGTTGAAGG
1342548 CAAAACAGACTATCGCAACA
1 CAAAACAGACTATCGCAACA
*
1342568 CAAAACTGACTATCGCAAC
1 CAAAACAGACTATCGCAAC
1342587 GAGAGAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.13
Consensus pattern (20 bp):
CAAAACAGACTATCGCAACA
Found at i:1342616 original size:19 final size:19
Alignment explanation
Indices: 1342592--1342634 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1342582 GCAACGAGAG
1342592 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342611 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1342630 AATCG
1 AATCG
1342635 TAACGAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1342644 original size:19 final size:19
Alignment explanation
Indices: 1342592--1342644 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1342582 GCAACGAGAG
* *
1342592 AATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAATGAA
* *
1342611 AATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAATGAA
*
1342630 AATCGTAACGAGAAA
1 AATCGCAACGAGAAA
1342645 ATCGCAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAACGAGAAATGAA
Found at i:1342706 original size:19 final size:20
Alignment explanation
Indices: 1342682--1342731 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1342672 GTGATTTTGT
1342682 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGCCATTTTCG
1342701 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
1342721 CGTTGCGATAG
1 CGTTGCGATAG
1342732 TCAAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:1343746 original size:24 final size:24
Alignment explanation
Indices: 1343719--1343772 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1343709 GTATTCGAAA
*
1343719 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATATTGGTCAATACCCAGAC
* *
1343743 TTTGATATTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
1343767 TTTGAT
1 TTTGAT
1343773 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:1343964 original size:12 final size:12
Alignment explanation
Indices: 1343947--1343971 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1343937 ATATAATCCT
1343947 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1343959 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1343971 G
1 G
1343972 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1346285 original size:19 final size:19
Alignment explanation
Indices: 1346263--1346346 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1346253 GGAAATTACT
1346263 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1346282 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1346301 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1346315 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1346334 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1346347 TTTAATTTCG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
14 8 0.15
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.74
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1346357 original size:19 final size:19
Alignment explanation
Indices: 1346311--1346358 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1346301 ATCGCAACGC
*
1346311 TAATTTCGCAATGCGAAAT
1 TAATTTCGCAACGCGAAAT
* ** *
1346330 GAAAATCGCAACGCGAATT
1 TAATTTCGCAACGCGAAAT
1346349 TAATTTCGCA
1 TAATTTCGCA
1346359 TTGCGATTCT
Statistics
Matches: 21, Mismatches: 8, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (19 bp):
TAATTTCGCAACGCGAAAT
Found at i:1346364 original size:19 final size:19
Alignment explanation
Indices: 1346342--1346416 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
1346332 AAATCGCAAC
*
1346342 GCGAATTTAATTTCGCATT
1 GCGAATTTCATTTCGCATT
*
1346361 GCG-A-TTC-TCTCG--TT
1 GCGAATTTCATTTCGCATT
* *
1346375 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCATT
*
1346394 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCATT
1346413 GCGA
1 GCGA
1346417 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 5 0.11
16 7 0.15
17 6 0.13
18 1 0.02
19 27 0.59
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCATT
Found at i:1346364 original size:38 final size:33
Alignment explanation
Indices: 1346283--1346349 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
1346273 GAAATGAAAA
1346283 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
*
1346316 TCGCAATGCGAAATGAAAATCGCAACGCGAATT
1 TCGCAATGCGAAATGAAAATCGCAACGCTAATT
1346349 T
1 T
1346350 AATTTCGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGCTAATT
Found at i:1346417 original size:19 final size:19
Alignment explanation
Indices: 1346373--1346417 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1346363 GATTCTCTCG
*
1346373 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1346392 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1346411 TTGCGAT
1 TTGCGAT
1346418 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1347976 original size:42 final size:41
Alignment explanation
Indices: 1347917--1348122 Score: 164
Period size: 42 Copynumber: 4.9 Consensus size: 41
1347907 GTGAATCAGG
* *
1347917 CTCTTGAATGGTGGGAGGGACCTCTTCAATGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1347959 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
1348001 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * *
1348043 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1348085 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1348123 GCGAGTCGGG
Statistics
Matches: 126, Mismatches: 30, Indels: 16
0.73 0.17 0.09
Matches are distributed among these distances:
41 9 0.07
42 106 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1348058 original size:84 final size:84
Alignment explanation
Indices: 1347947--1348122 Score: 343
Period size: 84 Copynumber: 2.1 Consensus size: 84
1347937 CCTCTTCAAT
*
1347947 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1348012 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1348031 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1348096 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1348115 GATGACAG
1 GATGACAG
1348123 GCGAGTCGGG
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 91 1.00
ACGTcount: A:0.23, C:0.17, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1348517 original size:91 final size:90
Alignment explanation
Indices: 1348339--1348525 Score: 295
Period size: 91 Copynumber: 2.0 Consensus size: 90
1348329 ATGTTTCAAA
*
1348339 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
*
1348404 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAACAACCGAATAAATTT
1348432 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
1348496 CAGTATTGGCAACAACCGAATAAATTT
64 CAGAATTGGCAACAACCGAATAAATTT
1348523 ACT
1 ACT
1348526 AAGCAATCTA
Statistics
Matches: 89, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.46
93 21 0.24
95 27 0.30
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAACAACCGAATAAATTT
Found at i:1348728 original size:63 final size:63
Alignment explanation
Indices: 1348669--1348806 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 63
1348659 CTTAGAGCGG
* * *
1348669 CAACCTCAC-CACATAAAGTAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACACAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * * *** *
1348732 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACACAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
1348795 CGATCTCCTCAC
1 CAACCTCCTCAC
1348807 GCAAGGCATT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
62 1 0.02
63 64 0.98
ACGTcount: A:0.27, C:0.38, G:0.16, T:0.20
Consensus pattern (63 bp):
CAACCTCCTCACACAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:1348807 original size:63 final size:63
Alignment explanation
Indices: 1348692--1348822 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
1348682 TAAAGTAGAC
1348692 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1348755 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1348818 ACCTC
1 ACCTC
1348823 ATCACGTAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:1350327 original size:19 final size:19
Alignment explanation
Indices: 1350274--1350423 Score: 184
Period size: 19 Copynumber: 8.1 Consensus size: 19
1350264 TCTTTTGGTT
*
1350274 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1350293 GATAATCAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1350313 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
1350330 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
1350346 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1350365 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1350384 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1350403 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1350422 GA
1 GA
1350424 TTTTGGTTTC
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 8 0.07
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 83 0.73
20 16 0.14
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1350441 original size:19 final size:19
Alignment explanation
Indices: 1350419--1350463 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1350409 AAAATCGCAA
*
1350419 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
1350438 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
1350457 TGCGATT
1 TGCGATT
1350464 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:1351082 original size:20 final size:20
Alignment explanation
Indices: 1351057--1351110 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1351047 GATTTTGTAT
1351057 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1351077 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1351097 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1351111 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1351926 original size:19 final size:18
Alignment explanation
Indices: 1351902--1351944 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
1351892 TTCTAAAAAA
1351902 TAAAATAT-TAAAAATCATT
1 TAAAATATATAAAAAT-A-T
1351921 TAAAATATATAAAAATAT
1 TAAAATATATAAAAATAT
1351939 TAAAAT
1 TAAAAT
1351945 TGTAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.30
19 9 0.39
20 7 0.30
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATATATAAAAATAT
Found at i:1351935 original size:10 final size:9
Alignment explanation
Indices: 1351903--1351943 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
1351893 TCTAAAAAAT
1351903 AAAATATTA
1 AAAATATTA
*
1351912 AAAATCATTT
1 AAAAT-ATTA
1351922 AAAATATATA
1 AAAATAT-TA
1351932 AAAATATTA
1 AAAATATTA
1351941 AAA
1 AAA
1351944 TTGTAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATATTA
Found at i:1353271 original size:2 final size:2
Alignment explanation
Indices: 1353223--1353258 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1353213 TCTTACCCAA
1353223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1353259 ATCCATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1354218 original size:33 final size:33
Alignment explanation
Indices: 1354171--1354246 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1354161 CACATGCAAC
*
1354171 AAAGTTTCATTAGTTGATCCGCATATTTGACAT
1 AAAGGTTCATTAGTTGATCCGCATATTTGACAT
1354204 AAAGGTTCATTAGTTGATCCGCATATTTGACAT
1 AAAGGTTCATTAGTTGATCCGCATATTTGACAT
*
1354237 AAAGGATCAT
1 AAAGGTTCAT
1354247 CGGTAAGGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (33 bp):
AAAGGTTCATTAGTTGATCCGCATATTTGACAT
Found at i:1368270 original size:20 final size:20
Alignment explanation
Indices: 1368245--1368348 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 20
1368235 TTTAAACAGA
1368245 ATAAATGAACGAATATAAAT
1 ATAAATGAACGAATATAAAT
** *
1368265 ATAAATGAACGGTTGTAAAT
1 ATAAATGAACGAATATAAAT
* *
1368285 A-AATATAAACGAATATAATAA
1 ATAA-ATGAACGAATATAA-AT
*
1368306 ATGAATGTAAACGAATATAAAT
1 ATAAATG--AACGAATATAAAT
*
1368328 GA-ACAT-AAGCGAATATAAAT
1 -ATAAATGAA-CGAATATAAAT
1368348 A
1 A
1368349 AATAAAATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
19 5 0.08
20 39 0.61
21 4 0.06
22 4 0.06
23 12 0.19
ACGTcount: A:0.57, C:0.06, G:0.12, T:0.25
Consensus pattern (20 bp):
ATAAATGAACGAATATAAAT
Found at i:1368299 original size:10 final size:10
Alignment explanation
Indices: 1368286--1368346 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1368276 GTTGTAAATA
1368286 AATATAAACG
1 AATATAAACG
*
1368296 AATATAATAAATG
1 -A-AT-ATAAACG
*
1368309 AATGTAAACG
1 AATATAAACG
*
1368319 AATATAAATG
1 AATATAAACG
* *
1368329 AACATAAGCG
1 AATATAAACG
1368339 AATATAAA
1 AATATAAA
1368347 TAAATAAAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
10 26 0.68
11 3 0.08
12 3 0.08
13 6 0.16
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (10 bp):
AATATAAACG
Found at i:1368316 original size:23 final size:23
Alignment explanation
Indices: 1368280--1368360 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
1368270 TGAACGGTTG
1368280 TAAATAAATATAAACGAATATAA
1 TAAATAAATATAAACGAATATAA
* *
1368303 TAAATGAATGTAAACG-A-AT-A
1 TAAATAAATATAAACGAATATAA
* * *
1368323 TAAATGAACATAAGCGAATATAAA
1 TAAATAAATATAAACGAATAT-AA
1368347 TAAATAAA-ATAAAC
1 TAAATAAATATAAAC
1368361 TAACATAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
20 14 0.30
21 3 0.06
22 3 0.06
23 19 0.40
24 8 0.17
ACGTcount: A:0.62, C:0.06, G:0.09, T:0.23
Consensus pattern (23 bp):
TAAATAAATATAAACGAATATAA
Found at i:1368360 original size:43 final size:43
Alignment explanation
Indices: 1368280--1368379 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
1368270 TGAACGGTTG
* * ** *
1368280 TAAATAAATATAAACGAATATAATAAATGAATGTAAACGAATA
1 TAAATGAACATAAACGAATATAATAAATGAAAATAAACGAACA
* *
1368323 TAAATGAACATAAGCGAATATAAATAAAT-AAAATAAACTAACA
1 TAAATGAACATAAACGAATAT-AATAAATGAAAATAAACGAACA
1368366 TAAATGAACATAAA
1 TAAATGAACATAAA
1368380 TCACAACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 41 0.85
44 7 0.15
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (43 bp):
TAAATGAACATAAACGAATATAATAAATGAAAATAAACGAACA
Found at i:1368440 original size:18 final size:18
Alignment explanation
Indices: 1368417--1368453 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1368407 CATTAGTATA
1368417 AATTTTAATTTAATAGTT
1 AATTTTAATTTAATAGTT
* *
1368435 AATTTTTATTTAATTGTT
1 AATTTTAATTTAATAGTT
1368453 A
1 A
1368454 TGGGTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
AATTTTAATTTAATAGTT
Found at i:1369032 original size:3 final size:3
Alignment explanation
Indices: 1369024--1369966 Score: 1048
Period size: 3 Copynumber: 320.0 Consensus size: 3
1369014 TGGTAATGGC
1369024 TCT TCT TCT TCT TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
1369071 TCT TCT TCT TCT TCT TCT TCT TCT TCT CCT TCT TC- TCT T-T TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1369117 TCT TCTT TCT TCT TCT TC- TCT TCT TCT TCT TC- TCT TCT TCTT TCT
1 TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
1369162 TCT TCT TCT TCT TCCT TCT TCT TCT TCT CTCT TC- TCT TC- TCT TC-
1 TCT TCT TCT TCT T-CT TCT TCT TCT TCT -TCT TCT TCT TCT TCT TCT
*
1369206 TCT TCT TCT CTCT TCT TCT TCT TCT TC- TCC TCT CTCT TC- TCT TCT
1 TCT TCT TCT -TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT TCT
* *
1369251 CCT CTCT TCT TCT TCTT TCT TC- TCT TCT CCT TCT TCT CTCT TCT TCT
1 TCT -TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT
1369298 TCT TCT TC- TCT TCT TC- TCT TCT TCT TC- TCT TCT TC- TCT TCTT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
*
1369340 TCT TCT TCTT TCT TCT TCT CCT TCT TCT TCT TCT TCT TC- TCT TC-
1 TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * *
1369384 TCT TCT TCT T-T CCT TCT CCT TCT TCT TCT TCT TCT TCT TCT CCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
1369431 CCT TCT TC- TCT TCT TC- TCT TCT TCT TCT CCT T-T TCT T-T TC- TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
1369474 TCT TCTT TCT CCT TCT TCTT TCT TCT TCT TCT TCT TCT CCT TC- TCT
1 TCT TC-T TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1369520 TCT CCT TC- TCT TCT CCT TC- TCT TCT CCT TCT CCT TC- TCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * * *
1369565 TCT CCT TCT CCT TCT CCT TCT CCT TC- TCT TCT CCT CTCT TCT CCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TCT
* * *
1369610 TCT CCT T-T TCT TCT CCT TCT TCT TCT CCT TCT TCT TCT TC- TCAT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T
*
1369654 TCT TCTT TCAT TCT TCT TCT T-T TC- TCT TCT TCT TCT TCT CCT TCT
1 TCT TC-T TC-T TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
1369699 TCT TC- TCT TCT T-T CCTT TCT TC- TCT TCT TCT TC- TCTT TCT TCT
1 TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TC-T TCT TCT
*
1369742 CTCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT CCT TCT TCT
1 -TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * * *
1369787 TCT CCT TCT TCT TCT CCT TCT CCT TCT TCT CCT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* * * *
1369835 CCT TCT CCT TCT TCT T-A TCAT TCT CCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT TCT TCT TCT
*
1369880 TCCT TCT TCT TCT TCCT TCT TCT TCT CCT TCT TCT TCT TCT TCT TCT
1 T-CT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1369927 TCT TCT TC- TCT TCT TCT TC- TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1369967 CCATCTTCAT
Statistics
Matches: 800, Mismatches: 78, Indels: 124
0.80 0.08 0.12
Matches are distributed among these distances:
2 77 0.10
3 660 0.82
4 63 0.08
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:1371239 original size:31 final size:31
Alignment explanation
Indices: 1371203--1371261 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1371193 AACATAAAAG
* *
1371203 AGTTTTGCAATACTGATATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
1371234 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
1371262 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1371355 original size:54 final size:52
Alignment explanation
Indices: 1371276--1371596 Score: 152
Period size: 54 Copynumber: 6.0 Consensus size: 52
1371266 ACAACTACAA
* *
1371276 TAATAAATTATT-AAGTAAATTAATTTATATTTTAAAATAAATCAATCAATAT
1 TAATAAATTATTAAAATAAATCAATTTATATTTTAAAATAAATCAATC-ATAT
* **
1371328 TAATAAATTATTTAAAATAAATCAATTTATACAACTACAATAATAAATCAATCTATAT
1 TAATAAATTA-TTAAAATAAATCAATTTAT---ATTTTAA-AATAAATCAATC-ATAT
* * *
1371386 T-TTAAA--A-T-AAATCAATCTATGTTAATAAATTATTTAAAATAAATCAATTCATAT
1 TAATAAATTATTAAAATAAATCAAT-TT-AT--A-T-TTTAAAATAAATCAA-TCATAT
* * * *
1371440 T-TTAAA--A-T-AAATTAATCCATACTAATAAATTATTTAAAATAAATCAATC-TA-
1 TAATAAATTATTAAAATAAAT-CA-A-T-TTATA-T-TTTAAAATAAATCAATCATAT
* * ** *
1371491 T-A-CAATTA-AAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTAA-AATAAATCAATTTATATTTTAAAATAAATCAA-TCATAT
*
1371542 TAATAAATTATTTAAAATAAATTAATTTATATTTTAAAATAAATCAATTCATAT
1 TAATAAATTA-TTAAAATAAATCAATTTATATTTTAAAATAAATCAA-TCATAT
1371596 T
1 T
1371597 TTAAAATAAA
Statistics
Matches: 213, Mismatches: 31, Indels: 48
0.73 0.11 0.16
Matches are distributed among these distances:
48 15 0.07
49 3 0.01
50 6 0.03
51 3 0.01
52 25 0.12
53 17 0.08
54 106 0.50
55 9 0.04
56 2 0.01
57 10 0.05
58 17 0.08
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (52 bp):
TAATAAATTATTAAAATAAATCAATTTATATTTTAAAATAAATCAATCATAT
Done.