Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold215
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: 2124891
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 7 of 16
Found at i:971150 original size:92 final size:91
Alignment explanation
Indices: 970981--971189 Score: 285
Period size: 92 Copynumber: 2.3 Consensus size: 91
970971 CTTTACCCAA
* * * * * * *
970981 CCACTAGATAGTATTGATGCACCATAAAGCCTGATTCCTTGGGGGCAATATATCCCGACCACTTA
1 CCACTAGATGGTATTGATGCATCACAAAGCCTGATTCCTTGGGGGCAAGATATCACAACCACTCA
971046 TTCCCAATCATATCCCTTTCTTTTAG
66 TTCCCAATCATATCCCTTTCTTTTAG
* * *
971072 CCACTAGATGGTATTAATGCATCACAAAGCTTGATTTCCTT-GGGGCGAGGATATCACAACCACT
1 CCACTAGATGGTATTGATGCATCACAAAGCCTGA-TTCCTTGGGGGC-AAGATATCACAACCACT
*
971136 CATTCCTAATCATATCCCTTTCTTTTAG
64 CATTCCCAATCATATCCCTTTCTTTTAG
*
971164 CCACTAGATGGTATTGATGGATCACA
1 CCACTAGATGGTATTGATGCATCACA
971190 TGACCACAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
91 34 0.33
92 69 0.67
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (91 bp):
CCACTAGATGGTATTGATGCATCACAAAGCCTGATTCCTTGGGGGCAAGATATCACAACCACTCA
TTCCCAATCATATCCCTTTCTTTTAG
Found at i:971972 original size:35 final size:35
Alignment explanation
Indices: 971925--972123 Score: 265
Period size: 35 Copynumber: 5.7 Consensus size: 35
971915 CTTTACCAAA
* *
971925 CAAACTCTTTTCATCATCGTTCAGCTGTATCTGGT
1 CAAACTCTTTCCATCATCGTTTAGCTGTATCTGGT
* * * *
971960 TAAACTCTTTTCATCATTGTTTGGCTGTATCTGGT
1 CAAACTCTTTCCATCATCGTTTAGCTGTATCTGGT
*
971995 CAAACTCTTTTCATCATCGTTT-GACTGTATCTGGT
1 CAAACTCTTTCCATCATCGTTTAG-CTGTATCTGGT
* *
972030 CAAACTCTTTCCATCATCGTTTAACTATATCTGGT
1 CAAACTCTTTCCATCATCGTTTAGCTGTATCTGGT
* *
972065 CAAACTCTTTCCATCATCGTTTTGACTATATCTGGT
1 CAAACTCTTTCCATCATCGTTTAG-CTGTATCTGGT
*
972101 CAAACTCTTTCCATCATTGTTTA
1 CAAACTCTTTCCATCATCGTTTA
972124 ACTATATTGG
Statistics
Matches: 148, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
34 1 0.01
35 115 0.78
36 32 0.22
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43
Consensus pattern (35 bp):
CAAACTCTTTCCATCATCGTTTAGCTGTATCTGGT
Found at i:972116 original size:71 final size:71
Alignment explanation
Indices: 971925--972130 Score: 308
Period size: 70 Copynumber: 2.9 Consensus size: 71
971915 CTTTACCAAA
** * * ** *
971925 CAAACTCTTTTCATCATCGTTCAG-CTGTATCTGGTTAAACTCTTTTCATCATTGTTTGGCTGTA
1 CAAACTCTTTTCATCATCGTTTTGACTGTATCTGGTCAAACTCTTTCCATCATTGTTTAACTATA
971989 TCTGGT
66 TCTGGT
*
971995 CAAACTCTTTTCATCATCG-TTTGACTGTATCTGGTCAAACTCTTTCCATCATCGTTTAACTATA
1 CAAACTCTTTTCATCATCGTTTTGACTGTATCTGGTCAAACTCTTTCCATCATTGTTTAACTATA
972059 TCTGGT
66 TCTGGT
* *
972065 CAAACTCTTTCCATCATCGTTTTGACTATATCTGGTCAAACTCTTTCCATCATTGTTTAACTATA
1 CAAACTCTTTTCATCATCGTTTTGACTGTATCTGGTCAAACTCTTTCCATCATTGTTTAACTATA
972130 T
66 T
972131 TGGCATTAAG
Statistics
Matches: 123, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
69 2 0.02
70 77 0.63
71 44 0.36
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (71 bp):
CAAACTCTTTTCATCATCGTTTTGACTGTATCTGGTCAAACTCTTTCCATCATTGTTTAACTATA
TCTGGT
Found at i:972267 original size:95 final size:95
Alignment explanation
Indices: 972096--972327 Score: 277
Period size: 95 Copynumber: 2.5 Consensus size: 95
972086 TTGACTATAT
* * * *
972096 CTGGTCAAACTCTTTC-CATCATTGTTTAACTATATTGGCATTAAGACTTGGTTAAACCTTTATT
1 CTGGTCAAACTCTTTCTCATCATTGTTTGACTGTATTGGCATTAAGACCTGGTCAAACCTTTATT
* *
972160 ACCGTTGCTTGACTCTATTGGCATTAGTAC
66 ACCGTTGCTTGACTATATTGGCATTAGGAC
* * * * *
972190 CTGGTCAAACTTTTTCTCATCATTGTTTGATTGTATTGGCGTTAGGACCTGGTCAAACCTTTCTT
1 CTGGTCAAACTCTTTCTCATCATTGTTTGACTGTATTGGCATTAAGACCTGGTCAAACCTTTATT
** ** **
972255 ATTGTTTTTTGACTATATTGGTGTTAGGAC
66 ACCGTTGCTTGACTATATTGGCATTAGGAC
** *
972285 CTGGTCAAACTCTTTCTCATTGTTGTTTGACTGTGTTGGCATT
1 CTGGTCAAACTCTTTCTCATCATTGTTTGACTGTATTGGCATT
972328 TTGACTATAT
Statistics
Matches: 114, Mismatches: 23, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
94 15 0.13
95 99 0.87
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (95 bp):
CTGGTCAAACTCTTTCTCATCATTGTTTGACTGTATTGGCATTAAGACCTGGTCAAACCTTTATT
ACCGTTGCTTGACTATATTGGCATTAGGAC
Found at i:972274 original size:47 final size:48
Alignment explanation
Indices: 972096--972327 Score: 227
Period size: 47 Copynumber: 4.9 Consensus size: 48
972086 TTGACTATAT
* * *
972096 CTGGTCAAACTCTTTC-CATCATTGTTTAACTATATTGGCATTAAGAC
1 CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATTAGGAC
* * * * * * * *
972143 TTGGTTAAAC-CTTTATTACCGTTGCTTGACTCTATTGGCATTAGTAC
1 CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATTAGGAC
* * * * *
972190 CTGGTCAAACTTTTTCTCATCATTGTTTGATTGTATTGGCGTTAGGAC
1 CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATTAGGAC
* * * **
972238 CTGGTCAAAC-CTTTCTTATTGTTTTTTGACTATATTGGTGTTAGGAC
1 CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATTAGGAC
* * *
972285 CTGGTCAAACTCTTTCTCATTGTTGTTTGACTGTGTTGGCATT
1 CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATT
972328 TTGACTATAT
Statistics
Matches: 145, Mismatches: 37, Indels: 5
0.78 0.20 0.03
Matches are distributed among these distances:
46 4 0.03
47 78 0.54
48 63 0.43
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (48 bp):
CTGGTCAAACTCTTTCTCATCGTTGTTTGACTATATTGGCATTAGGAC
Found at i:972412 original size:112 final size:112
Alignment explanation
Indices: 972223--972430 Score: 308
Period size: 112 Copynumber: 1.9 Consensus size: 112
972213 TGTTTGATTG
* * * * **
972223 TATTGGCGTTAGGACCTGGTCAAACCTTTCTTATTGTTTTTTGACTATATTGGTGTTAGGACCTG
1 TATTGGCGTTAGGACCTAGTCAAACCTTTCTCACTGTTGTTTGACTATATTGGCATTAGGACCTG
** *
972288 GTCAAACTCTTTCTCATTGTTGTTTGACTGTGTTGGCATTTTGACTA
66 GTCAAACTCTTTCTCATCATTGTTTAACTGTGTTGGCATTTTGACTA
* * *
972335 TATTGGTGTTAGGACCTAGTCAAACTTTTCTCACTGTTGTTTGGCTATATTGGCATTAGGACCTG
1 TATTGGCGTTAGGACCTAGTCAAACCTTTCTCACTGTTGTTTGACTATATTGGCATTAGGACCTG
972400 GTCAAACTCTTTCTCATCATTGTTTAACTGT
66 GTCAAACTCTTTCTCATCATTGTTTAACTGT
972431 ATTAACGTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.19, C:0.17, G:0.20, T:0.43
Consensus pattern (112 bp):
TATTGGCGTTAGGACCTAGTCAAACCTTTCTCACTGTTGTTTGACTATATTGGCATTAGGACCTG
GTCAAACTCTTTCTCATCATTGTTTAACTGTGTTGGCATTTTGACTA
Found at i:972442 original size:48 final size:47
Alignment explanation
Indices: 972342--972455 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 47
972332 CTATATTGGT
* * ** **
972342 GTTAGGACCTAGTCAAACTTTTCTCACTGTTGTTTGGCTATATTGGC
1 GTTAGGACCTGGTCAAACTTTTCTCACTATTGTTTAACTATATTAAC
* *
972389 ATTAGGACCTGGTCAAACTCTTTCTCA-TCATTGTTTAACTGTATTAAC
1 GTTAGGACCTGGTCAAACT-TTTCTCACT-ATTGTTTAACTATATTAAC
972437 GTTAGGACCTGGTCAAACT
1 GTTAGGACCTGGTCAAACT
972456 GTCTTCCTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
47 18 0.32
48 38 0.68
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (47 bp):
GTTAGGACCTGGTCAAACTTTTCTCACTATTGTTTAACTATATTAAC
Found at i:972742 original size:85 final size:84
Alignment explanation
Indices: 972651--972931 Score: 269
Period size: 85 Copynumber: 3.3 Consensus size: 84
972641 TTGGTCAACC
* * * *
972651 TGTCAGTTCAATC-CTGATCAAGCTTTTCGTCTTTTGTTTACCTATTGGCTTAATCTTGGGTAAA
1 TGTCAGTTCAATCTC-GATCAA-CTTTTCATCTTTTGTCTACCTGTCGGCTTAATCTTGGGTAAA
972715 TCCTCTTATCCTTTGTTGACT
64 TCCTCTTATCCTTTGTTGACT
* *** ** * * * *
972736 TGTCAGTTCAATC-CTGGTCAACTTCTTCATCTCCAGTCTATTTGTCAGCGTATTCTTGGCTAAA
1 TGTCAGTTCAATCTC-GATCAACTT-TTCATCTTTTGTCTACCTGTCGGCTTAATCTTGGGTAAA
* * *
972800 TCCTCTTAACATTTGTTGATT
64 TCCTCTTATCCTTTGTTGACT
* * * ** *
972821 TGTCAGTTCAATCTCGATCAACTCTTTCATCCTTTGTCTACCCGTCGGCTTACTCCCGAGTAAAT
1 TGTCAGTTCAATCTCGATCAACT-TTTCATCTTTTGTCTACCTGTCGGCTTAATCTTGGGTAAAT
*
972886 CCTTTTATCCTTTGTTGACT
65 CCTCTTATCCTTTGTTGACT
* *
972906 TATCAGTTTAATCTCGATCAACTTTT
1 TGTCAGTTCAATCTCGATCAACTTTT
972932 GTATCCCTTG
Statistics
Matches: 155, Mismatches: 38, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
84 6 0.04
85 147 0.95
86 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (84 bp):
TGTCAGTTCAATCTCGATCAACTTTTCATCTTTTGTCTACCTGTCGGCTTAATCTTGGGTAAATC
CTCTTATCCTTTGTTGACT
Found at i:972963 original size:85 final size:85
Alignment explanation
Indices: 972796--972963 Score: 194
Period size: 85 Copynumber: 2.0 Consensus size: 85
972786 TATTCTTGGC
* * *
972796 TAAATCCTCTTAACATTTGTTGATTTGTCAGTTCAATCTCGATCAACTCTTTCATCCTTTGTCTA
1 TAAATCCTCTTAACATTTGTTGACTTATCAGTTCAATCTCGATCAACTCTTTCATCCCTTGTCTA
* **
972861 CCCGTCGGCTTACTCCCGAG
66 CCCATCAACTTACTCCCGAG
* * * * * *
972881 TAAATCCTTTTATCCTTTGTTGACTTATCAGTTTAATCTCGATCAACT-TTTGTATCCCTTGTTT
1 TAAATCCTCTTAACATTTGTTGACTTATCAGTTCAATCTCGATCAACTCTTT-CATCCCTTGTCT
* *
972945 ACCCATCAATTTAGTCCCG
65 ACCCATCAACTTACTCCCG
972964 CTTAACCTCT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 3 0.04
85 65 0.96
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (85 bp):
TAAATCCTCTTAACATTTGTTGACTTATCAGTTCAATCTCGATCAACTCTTTCATCCCTTGTCTA
CCCATCAACTTACTCCCGAG
Found at i:974484 original size:166 final size:164
Alignment explanation
Indices: 973945--974582 Score: 611
Period size: 166 Copynumber: 3.9 Consensus size: 164
973935 CCTATTTCCA
* * * * *
973945 AAATACAGAGTTTTTTACTCCGTAAATGTTTTTC-GGGGCCATTTTTCTTGATTTTTAAATTTTA
1 AAATACGGAGTTTTCTACTCCGTAAAT-ATTTTCAGAGG--ATTTTTCTTGATTTTTAATTTTTA
*
974009 AAATTCATCAAATATTATTATTTAATTCATATTAAATCAGTTTCCAAAAATTCATTCATTTTCAT
63 AAATTCATCAAATA-TA-TATTTAATTCATATTAAATCAGTTTCAAAAAATTCATTCATTTTCA-
* * *** *
974074 TCA-TTTTGCA-TTTTTT-CTTTTTATTCTCACTATTTTTG
125 TGAGTTTTGAATTTTTTTCCTTGAAATTCT-ATTATTTTTG
* *
974112 AAATTCGGAGTTTTCTACTCCGTAAATATTTTTAGAGGGATTTTTCTT-AGTTTTTAATTTTTAA
1 AAATACGGAGTTTTCTACTCCGTAAATATTTTCAGA-GGATTTTTCTTGA-TTTTTAATTTTTAA
** *
974176 AATTCATCAAATAT-TA--TAATTCATATTAAATCAGTTTTTAAAAATTCATTCATTTTCAAGAG
64 AATTCATCAAATATATATTTAATTCATATTAAATCAGTTTCAAAAAATTCATTCATTTTCATGAG
*
974238 -TTT-CATTTTTTTCCTTGAAATTCTATTATTTTTG
129 TTTTGAATTTTTTTCCTTGAAATTCTATTATTTTTG
* ** *
974272 AAATATGGAGTTTTCTACTCCGTAAATATTTTTGGGACGATTTTTCTTGATTTTTAATTTTTAAA
1 AAATACGGAGTTTTCTACTCCGTAAATA-TTTTCAGAGGATTTTTCTTGATTTTTAATTTTTAAA
* * *
974337 ATTCATCAAATATCATCATTTAATTCATATTAAATTAGTTTTAAAAAATTCATTTATTTTCATGA
65 ATTCATCAAATAT-AT-ATTTAATTCATATTAAATCAGTTTCAAAAAATTCATTCATTTTCATGA
* * *
974402 GTTTTTAATTTTTTTCCTTGAAATT-TTTTGTTTTTG
128 GTTTTGAATTTTTTTCCTTGAAATTCTATTATTTTTG
* * * * * * **
974438 AACA-ACCGAGTTTTCTATTTCATAAATATTTTCAGAGGTTTTTTTCTCGATTTAAAATTTTTAA
1 AA-ATACGGAGTTTTCTACTCCGTAAATATTTTCAGAGG-ATTTTTCTTGATTTTTAATTTTTAA
* * * * * * *
974502 AATTCATCTAATATTAATATTAAACTC-TCATTAAATTAGTTTCAAGAAATTTAATTTA-TTTCA
64 AATTCATCAAATA-T-ATATTTAATTCAT-ATTAAATCAGTTTCAA-AAAATTCATTCATTTTCA
* *
974565 TAAATTTTGAATTTTTTT
125 TGAGTTTTGAATTTTTTT
974583 GTATACACTA
Statistics
Matches: 402, Mismatches: 49, Indels: 41
0.82 0.10 0.08
Matches are distributed among these distances:
159 2 0.00
160 83 0.21
161 55 0.14
162 1 0.00
163 3 0.01
165 52 0.13
166 147 0.37
167 57 0.14
168 2 0.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (164 bp):
AAATACGGAGTTTTCTACTCCGTAAATATTTTCAGAGGATTTTTCTTGATTTTTAATTTTTAAAA
TTCATCAAATATATATTTAATTCATATTAAATCAGTTTCAAAAAATTCATTCATTTTCATGAGTT
TTGAATTTTTTTCCTTGAAATTCTATTATTTTTG
Found at i:974909 original size:10 final size:11
Alignment explanation
Indices: 974889--974946 Score: 61
Period size: 11 Copynumber: 5.5 Consensus size: 11
974879 AAACTCAGCA
*
974889 AAAAAAGAGAG
1 AAAAAATAGAG
974900 AAAAAA-AGAGG
1 AAAAAATAGA-G
974911 AAAAAA-AGAG
1 AAAAAATAGAG
974921 AGAAAAATA-AG
1 A-AAAAATAGAG
974932 AAAAAATAG-G
1 AAAAAATAGAG
974942 AAAAA
1 AAAAA
974947 TAGTTTACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
10 18 0.42
11 24 0.56
12 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (11 bp):
AAAAAATAGAG
Found at i:974914 original size:23 final size:24
Alignment explanation
Indices: 974888--974932 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
974878 GAAACTCAGC
974888 AAAAAAAGAGAGAAAAA-AAGAGG
1 AAAAAAAGAGAGAAAAATAAGAGG
974911 AAAAAAAGAGAGAAAAATAAGA
1 AAAAAAAGAGAGAAAAATAAGA
974933 AAAAATAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (24 bp):
AAAAAAAGAGAGAAAAATAAGAGG
Found at i:974946 original size:11 final size:11
Alignment explanation
Indices: 974888--974932 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 11
974878 GAAACTCAGC
974888 AAAAAAAGAGAG
1 AAAAAAAGAG-G
974900 AAAAAAAGAGG
1 AAAAAAAGAGG
974911 AAAAAAAGAGAG
1 AAAAAAAGAG-G
974923 AAAAATAAGA
1 AAAAA-AAGA
974933 AAAAATAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.35
12 16 0.52
13 4 0.13
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
AAAAAAAGAGG
Found at i:976631 original size:155 final size:154
Alignment explanation
Indices: 976400--976919 Score: 446
Period size: 155 Copynumber: 3.4 Consensus size: 154
976390 TACATCAAAG
* * * * ** * * *
976400 GTATCCCCTA-AGAGCATTTTCGTAATTTCTCTAGAACTGAGTCTTAGGTCTTCACCGAGTCCAC
1 GTATCCCCTAGGGA-CATTTTCATAATTTTTCAAGAACCAACTCTTAGGTCATCACCAAGTCCAC
*
976464 TTTTATGCTGAAGGTGGGTATTTAGGGTAAGTTCATCCCATTTAAAATACTTTTTAAGTCCTTTA
65 TTTTATGTTGAAGGTGGGTATTTAGGGTAAGTTCATCCC-TTTAAAAT-CTTTTTAAGTCCTTTA
976529 GAGGTATTAGGTACTTTTACATTGAAA
128 GAGGTATTAGGTACTTTTACATTGAAA
* * * ** **
976556 GTATCCCCTAGGGACATTTTCATAATTTTTTAA-AACCAACTTTTAGGTCATCATCGGGTCTGCT
1 GTATCCCCTAGGGACATTTTCATAATTTTTCAAGAACCAACTCTTAGGTCATCACCAAGTCCACT
* * * * * *
976620 TTTAGGTTGAAGATGGATGTTTAGGGTAAGTTCAACCCTTCTAAAATCCTTTTTAAGTGCTTTA-
66 TTTATGTTGAAGGTGGGTATTTAGGGTAAGTTCATCCCTT-TAAAAT-CTTTTTAAGTCCTTTAG
* * * * **
976684 AGGGTATTAAGTGCTTCTACGTCCAAA
129 A-GGTATTAGGTACTTTTACATTGAAA
* * **
976711 GTATCCCCTAGGGAGATTTTCATAA-TTTCCAAGAACCAACTCTTAGGTTGTCACCAAGTCCACT
1 GTATCCCCTAGGGACATTTTCATAATTTTTCAAGAACCAACTCTTAGGTCATCACCAAGTCCACT
* * * * * * * *
976775 TTTATGTCGAAAGTGAGTATTTAGGATAGGTTCATCTCGTATATAATCTTTTTAAGTCCTTTAG-
66 TTTATGTTGAAGGTGGGTATTTAGGGTAAGTTCATC-CCTTTAAAATCTTTTTAAGTCCTTTAGA
*
976839 GGTTATCAGGATAC-TTT-CATGTCGAAA
130 GG-TATTAGG-TACTTTTACAT-T-GAAA
* * * * *
976866 GTATACACATAGGGACATTTTCATAATTTTT--AGAATCAAGTCATAGGTCATCAC
1 GTAT-CCCCTAGGGACATTTTCATAATTTTTCAAGAACCAACTCTTAGGTCATCAC
976920 TCTTACACCA
Statistics
Matches: 283, Mismatches: 69, Indels: 25
0.75 0.18 0.07
Matches are distributed among these distances:
153 4 0.01
154 30 0.11
155 199 0.70
156 45 0.16
157 5 0.02
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (154 bp):
GTATCCCCTAGGGACATTTTCATAATTTTTCAAGAACCAACTCTTAGGTCATCACCAAGTCCACT
TTTATGTTGAAGGTGGGTATTTAGGGTAAGTTCATCCCTTTAAAATCTTTTTAAGTCCTTTAGAG
GTATTAGGTACTTTTACATTGAAA
Found at i:982748 original size:3 final size:3
Alignment explanation
Indices: 982740--982790 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
982730 AGCAAAAAAG
982740 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
982788 TAA
1 TAA
982791 AACTTAGATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:984825 original size:21 final size:20
Alignment explanation
Indices: 984788--984834 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
984778 AATGGTCAGC
984788 TAAAAAAAGAGAGAAAAGAG
1 TAAAAAAAGAGAGAAAAGAG
* *
984808 ATAAAATAAGTAGA-AAAATAG
1 -TAAAAAAAG-AGAGAAAAGAG
984829 TAAAAA
1 TAAAAA
984835 CCAAACTAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.23
21 14 0.64
22 3 0.14
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (20 bp):
TAAAAAAAGAGAGAAAAGAG
Found at i:999088 original size:43 final size:43
Alignment explanation
Indices: 999040--999371 Score: 271
Period size: 43 Copynumber: 7.8 Consensus size: 43
999030 ACTTTTTTCC
*
999040 TTGTCTGCACGTCAGCTTAGACCCGAGAGACTTCCTTTATCTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTTCCTTTATCTT
* * * * *
999083 TTGTCTGCCAGTCA-CATAAACCCGGGAGACCAT-CTTTATCTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGA-CTTCCTTTATCTT
* * * *
999125 TTGTCTACCCATCAGCTTAGACCCGGGAGAC-CCCTTTTATCTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTTCC-TTTATCTT
* * * * * *
999168 TTGTCTACCCGTCGGCTTAGACCTGGGAGACCTCTTTTATCTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTTCCTTTATCTT
* * * * *
999211 TCGTCTGCCCGTCAG-TAAAAACCCGAGATACTTCATTTATCTT
1 TTGTCTGCCCGTCAGCT-TAGACCCGAGAGACTTCCTTTATCTT
** *
999254 TCATCTGCCCGTCAACTCT-GACCCGAGAGACTTCCTTTATCTT
1 TTGTCTGCCCGTCAGCT-TAGACCCGAGAGACTTCCTTTATCTT
* ** * * * * *
999297 TCGTCTG-GAGTCAGCTCAGACTCGGGAGACCTCTTTTATCTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTTCCTTTATCTT
* * *
999339 TTTTCTGCCCGTCAGTTTAGACCCGAAAGACTT
1 TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTT
999372 TCGTAGACTC
Statistics
Matches: 227, Mismatches: 53, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
42 66 0.29
43 159 0.70
44 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (43 bp):
TTGTCTGCCCGTCAGCTTAGACCCGAGAGACTTCCTTTATCTT
Found at i:999204 original size:85 final size:86
Alignment explanation
Indices: 999051--999225 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 86
999041 TGTCTGCACG
* *
999051 TCAGCTTAGACCCGAGAGACTTCCTTTATCTTTTGTCTGCCAGTCACATAAACCCGGGAGACCAT
1 TCAGCTTAGACCCGAGAGACTCCCTTTATCTTTTGTCTACCAGTCACATAAACCCGGGAGACCAT
*
999116 C-TTTATCTTTTGTCTACCCA
66 CTTTTATCTTTCGTCTACCCA
* * * * * *
999136 TCAGCTTAGACCCGGGAGAC-CCCTTTTATCTTTTGTCTACCCGTCGGCTTAGACCTGGGAGACC
1 TCAGCTTAGACCCGAGAGACTCCC-TTTATCTTTTGTCTACCAGTC-ACATAAACCCGGGAGACC
* *
999200 -TCTTTTATCTTTCGTCTGCCCG
64 ATCTTTTATCTTTCGTCTACCCA
999222 TCAG
1 TCAG
999226 TAAAAACCCG
Statistics
Matches: 76, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 40 0.53
86 34 0.45
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.33
Consensus pattern (86 bp):
TCAGCTTAGACCCGAGAGACTCCCTTTATCTTTTGTCTACCAGTCACATAAACCCGGGAGACCAT
CTTTTATCTTTCGTCTACCCA
Found at i:999421 original size:62 final size:62
Alignment explanation
Indices: 999314--999431 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
999304 GAGTCAGCTC
** * * *
999314 AGACTCGGGAGACCTCTTTTATCTTTTTTCTGCCCGTCAGTTTAGACCCGAAAGACTTTCGT
1 AGACTCGAAAGACCTCTTTTATCTTCTGTCTGCCCGTCAGCTTAGACCCGAAAGACTTTCGT
* *
999376 AGACTCGAAAGACCTCTTTTATCTTCTGTCTGCCTGTC-GACTTAGACCCGAGAGAC
1 AGACTCGAAAGACCTCTTTTATCTTCTGTCTGCCCGTCAG-CTTAGACCCGAAAGAC
999432 CTCCTTTATC
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 1 0.02
62 47 0.98
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.32
Consensus pattern (62 bp):
AGACTCGAAAGACCTCTTTTATCTTCTGTCTGCCCGTCAGCTTAGACCCGAAAGACTTTCGT
Found at i:999432 original size:43 final size:43
Alignment explanation
Indices: 999375--999537 Score: 170
Period size: 43 Copynumber: 3.8 Consensus size: 43
999365 AAGACTTTCG
* * *
999375 TAGACTCGAAAGACCTCTTTTATC-TTCTGTCTGCCTGTCGACT
1 TAGACCCGAGAGACCTCCTTTATCTTTC-GTCTGCCTGTCGACT
* * *
999418 TAGACCCGAGAGACCTCCTTTATCTTTCGTCTTCCTATCGGCT
1 TAGACCCGAGAGACCTCCTTTATCTTTCGTCTGCCTGTCGACT
* * *
999461 TAGA-CCTAGGAGACTTCCTTTATCTTTCGTTTGCCTGTCGACT
1 TAGACCCGA-GAGACCTCCTTTATCTTTCGTCTGCCTGTCGACT
* * * *
999504 TAAACCCGAGA-AACTCCCTTATTTTTCGTCTGCC
1 TAGACCCGAGAGACCTCCTTTATCTTTCGTCTGCC
999538 CATTGGCTCT
Statistics
Matches: 98, Mismatches: 19, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 21 0.21
43 71 0.72
44 6 0.06
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.36
Consensus pattern (43 bp):
TAGACCCGAGAGACCTCCTTTATCTTTCGTCTGCCTGTCGACT
Found at i:999573 original size:86 final size:86
Alignment explanation
Indices: 999393--999562 Score: 204
Period size: 85 Copynumber: 2.0 Consensus size: 86
999383 AAAGACCTCT
* * * * * *
999393 TTTATC-TTCTGTCTGCCTGTCGACTTAGACCCGAGAGACCTCCTTTATCTTTCGTCTTCCTATC
1 TTTATCTTTC-GTTTGCCTGTCGACTTAAACCCGAGAGAACTCCCTTATCTTTCGTCTGCCCATC
*
999457 GGCTTAGACCTAGGAGACTTCC
65 GGCTTAGACCGAGGAGACTTCC
* *
999479 TTTATCTTTCGTTTGCCTGTCGACTTAAACCCGAGA-AACTCCCTTATTTTTCGTCTGCCCATTG
1 TTTATCTTTCGTTTGCCTGTCGACTTAAACCCGAGAGAACTCCCTTATCTTTCGTCTGCCCATCG
999543 GCTCT-GACCCGA-GAGACTTC
66 GCT-TAGA-CCGAGGAGACTTC
999563 TTCATCTCTT
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
85 35 0.49
86 34 0.47
87 3 0.04
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.36
Consensus pattern (86 bp):
TTTATCTTTCGTTTGCCTGTCGACTTAAACCCGAGAGAACTCCCTTATCTTTCGTCTGCCCATCG
GCTTAGACCGAGGAGACTTCC
Found at i:1000823 original size:163 final size:161
Alignment explanation
Indices: 1000600--1000897 Score: 390
Period size: 163 Copynumber: 1.8 Consensus size: 161
1000590 AATTACAGGA
* *
1000600 TTTTCTTCTCCGTAAATTTTTTCGAAAGGCTTTTTCATGGTTTTTAATTTTCAAAATTCATCAAA
1 TTTTCTACTCCGTAAATTTTTTCGAAAGGCTTTTTCA-GGTTTTCAATTTTCAAAATTCATCAAA
* * ** *
1000665 TATTATTATTTATTTCAT-ATAAAATCA-TTTCTCAAAA-ATTC-ATTCATTTTCATAAATTTTT
65 TATCACTATTTAACTCATAAT-AAATCAGGTT-T-AAAAGA-TCAATTCATTTTCATAAA-TTTT
1000726 GAATTTTTTCCTTCAAATTTTTTTTCGAAATACGGTG
125 GAATTTTTTCCTTCAAATTTTTTTTCGAAATACGGTG
** *
1000763 TTTTCTACTCCGTAAATTTTTTCGAGGGGACTTTTCTC-GGTTTTCAATTTTTAAAATTCATCAA
1 TTTTCTACTCCGTAAATTTTTTCGAAAGG-CTTTT-TCAGGTTTTCAATTTTCAAAATTCATCAA
*
1000827 ATATCACTATTTAACTCATAATAAATCAGGTTTAAAAGATCAATTCATTTTCATAAATTTTGAGT
64 ATATCACTATTTAACTCATAATAAATCAGGTTTAAAAGATCAATTCATTTTCATAAATTTTGAAT
1000892 TTTTTC
129 TTTTTC
1000898 TTTGAAATCC
Statistics
Matches: 118, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
162 19 0.16
163 88 0.75
164 9 0.08
165 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.08, T:0.48
Consensus pattern (161 bp):
TTTTCTACTCCGTAAATTTTTTCGAAAGGCTTTTTCAGGTTTTCAATTTTCAAAATTCATCAAAT
ATCACTATTTAACTCATAATAAATCAGGTTTAAAAGATCAATTCATTTTCATAAATTTTGAATTT
TTTCCTTCAAATTTTTTTTCGAAATACGGTG
Found at i:1000986 original size:167 final size:163
Alignment explanation
Indices: 1000645--1001161 Score: 367
Period size: 167 Copynumber: 3.1 Consensus size: 163
1000635 CATGGTTTTT
* * * ** *
1000645 AATTTTCAAAATTCATCAAATATTATTATTTATTTCATATAAAATCATTTCTCAAAAATTCATTC
1 AATTTTTAAAATTCATCAAATATCACTATTTAACTCATATAAAATCAGTTCTCAAAAATTCATTC
* * * *
1000710 ATTTTCATAAATTTTTGAATTTTTTCCTTCAAATTTTTTTTCGAAATACGGTGTTTTCTACTCCG
66 ATTTTCATAAATTTTTGAATTTTTTCCTTCAAATTTTTTTTCGAAAAACGGAGTTTTCTAATCCA
* **
1000775 TAAATTTTTTCGAGGGGACTTTTCTCGGTTTTC
131 TAAATATTTTCGAGGGGACTTTTCTCGGTTTAA
1000808 AATTTTTAAAATTCATCAAATATCACTATTTAACTCATA-ATAAATCAGGTT-T-AAAAGA-TCA
1 AATTTTTAAAATTCATCAAATATCACTATTTAACTCATATA-AAATCA-GTTCTCAAAA-ATTC-
* * * * **
1000869 ATTCATTTTCATAAA-TTTTGAGTTTTTTCTTTGAAATCCCCATTTTTTTTGAAAAATTGAGTTT
62 ATTCATTTTCATAAATTTTTGAATTTTTTCCTTCAAAT-----TTTTTTTCGAAAAACGGAGTTT
* *
1000933 TCTAATCCATAAATATTTTCGGGGGGA-TTTTCTTTGGTTTAA
122 TCTAATCCATAAATATTTTCGAGGGGACTTTTC-TCGGTTTAA
* ** ** * ** * * **
1000975 AATTTTTAAAATAT-ATCTAATAATTTC-ATGGAATTCCCATTAAATCAGTTTTGGAAAATTCAT
1 AATTTTTAAAAT-TCATCAAAT-ATCACTATTTAACTCATATAAAATCAGTTCTCAAAAATTCAT
** * * * *
1001038 TCATTTTCATTTATTTTT-AA-TTTTT--TTGAAATTTCTCTTTTTCCCAAAAAACCGAATTTTC
64 TCATTTTCATAAATTTTTGAATTTTTTCCTTCAAA-TT-T-TTTTT--CGAAAAACGGAGTTTTC
* * ** *
1001099 TATTCCATAAATATTTTCGA-GGGAATTTTCTTTAGTCTAA
124 TAATCCATAAATATTTTCGAGGGGACTTTTC-TCGGTTTAA
* *
1001139 AATTTTTAAAATGCATCTAATAT
1 AATTTTTAAAATTCATCAAATAT
1001162 TGTTATTGAA
Statistics
Matches: 286, Mismatches: 44, Indels: 48
0.76 0.12 0.13
Matches are distributed among these distances:
160 1 0.00
161 1 0.00
162 31 0.11
163 63 0.22
164 70 0.24
165 1 0.00
166 13 0.05
167 93 0.33
168 13 0.05
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (163 bp):
AATTTTTAAAATTCATCAAATATCACTATTTAACTCATATAAAATCAGTTCTCAAAAATTCATTC
ATTTTCATAAATTTTTGAATTTTTTCCTTCAAATTTTTTTTCGAAAAACGGAGTTTTCTAATCCA
TAAATATTTTCGAGGGGACTTTTCTCGGTTTAA
Found at i:1002830 original size:167 final size:167
Alignment explanation
Indices: 1002545--1002848 Score: 455
Period size: 167 Copynumber: 1.8 Consensus size: 167
1002535 TATTTCCATG
* * * * *
1002545 TTTATTTTTTTTAATCTTTTATATTCCTATGGGCATCCGTAGAGGTATGAAAGATTTCAAAAACG
1 TTTATTTTTTCTAATCTTCTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAAAAACA
* * *
1002610 TTTCATATCCTTTCAAGCTTCTATTAGGGTACGAAATGGTATTTTCGAAAATAAATAAAATTAAA
66 TTTCATATCCTTTCAAGCTTCCATTAGGGTACGAAATGGCATTTTCAAAAATAAATAAAATTAAA
1002675 TTAAATTGAACTGGTATTCTTGGGATAAATTCTAAGA
131 TTAAATTGAACTGGTATTCTTGGGATAAATTCTAAGA
* * *
1002712 TTTATTTTTTCTAATCTTCTATATTCCTATAGGTATCCGTAGGGGTATAAAATATTTCAAAAACA
1 TTTATTTTTTCTAATCTTCTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAAAAACA
** ** *
1002777 TTTTTTATCCTTTCGGGCTTCCATTAGGGTATGAAATGGCATTTTCAAAAATAAATAAAATTAAA
66 TTTCATATCCTTTCAAGCTTCCATTAGGGTACGAAATGGCATTTTCAAAAATAAATAAAATTAAA
*
1002842 TTGAATT
131 TTAAATT
1002849 AACACTTTCG
Statistics
Matches: 120, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
167 120 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (167 bp):
TTTATTTTTTCTAATCTTCTATATTCCTATAGGCATCCGTAGAGGTATAAAAGATTTCAAAAACA
TTTCATATCCTTTCAAGCTTCCATTAGGGTACGAAATGGCATTTTCAAAAATAAATAAAATTAAA
TTAAATTGAACTGGTATTCTTGGGATAAATTCTAAGA
Found at i:1005663 original size:27 final size:28
Alignment explanation
Indices: 1005596--1005671 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
1005586 TTATCAAAAG
* *
1005596 GAAGCCCACACTAGCTGGCACATGAATC
1 GAAGCCCACACTAGATGGCACATAAATC
* * *
1005624 GAAGCTCGCACTAGTTGGCACA-AAATC
1 GAAGCCCACACTAGATGGCACATAAATC
*
1005651 GAAGCCCATACTAGATGGCAC
1 GAAGCCCACACTAGATGGCAC
1005672 CTAAGTCTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (28 bp):
GAAGCCCACACTAGATGGCACATAAATC
Found at i:1005713 original size:26 final size:28
Alignment explanation
Indices: 1005652--1005716 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
1005642 CACAAAATCG
1005652 AAGCCCATACTAGATGGCACCTAAGTCTA
1 AAGCCCATACTAGATGGCA-CTAAGTCTA
* * *
1005681 AA-ACCATACTTGCTGGCA-TAAGT-TA
1 AAGCCCATACTAGATGGCACTAAGTCTA
1005706 AAGCCCATACT
1 AAGCCCATACT
1005717 CGCTAGCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 12 0.39
28 13 0.42
29 2 0.06
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.23
Consensus pattern (28 bp):
AAGCCCATACTAGATGGCACTAAGTCTA
Found at i:1005809 original size:27 final size:26
Alignment explanation
Indices: 1005777--1005855 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
1005767 ACCTGGCAGT
1005777 TAAGTCAAAGCCCACA-TTAG-TGGCA
1 TAAGTCAAAGCCCACACTT-GTTGGCA
*
1005802 TCCGAGTCAAAGCCCACACTTGTTGGCA
1 T--AAGTCAAAGCCCACACTTGTTGGCA
* *
1005830 TAAGTCAAAGCCCATATTTGTTGGCA
1 TAAGTCAAAGCCCACACTTGTTGGCA
1005856 CACAAGTCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.02
26 22 0.48
27 15 0.33
28 8 0.17
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (26 bp):
TAAGTCAAAGCCCACACTTGTTGGCA
Found at i:1005842 original size:26 final size:25
Alignment explanation
Indices: 1005750--1005855 Score: 88
Period size: 28 Copynumber: 4.0 Consensus size: 25
1005740 AAGTCCTATA
* **
1005750 AAGTCTAAGCCCACATTACCTGGCAGTT
1 AAGTCAAAGCCCACATT-GTTGGCA--T
1005778 AAGTCAAAGCCCACATTAG-TGGCAT
1 AAGTCAAAGCCCACATT-GTTGGCAT
*
1005803 CCGAGTCAAAGCCCACACTTGTTGGCAT
1 --AAGTCAAAGCCCACA-TTGTTGGCAT
*
1005831 AAGTCAAAGCCCATATTTGTTGGCA
1 AAGTCAAAGCCCACA-TTGTTGGCA
1005856 CACAAGTCTA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
25 1 0.01
26 22 0.32
27 20 0.29
28 25 0.37
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (25 bp):
AAGTCAAAGCCCACATTGTTGGCAT
Found at i:1006063 original size:28 final size:28
Alignment explanation
Indices: 1006013--1006303 Score: 159
Period size: 28 Copynumber: 10.5 Consensus size: 28
1006003 AAGTCCTATA
* * * *
1006013 AAGTCTAAGCCCACACTATTTGGCACTT
1 AAGTCAAAGCCCACATTAGTTGGCACAT
* * *
1006041 AAATCAAAGCCCACATTAGTTGGTATC-C
1 AAGTCAAAGCCCACATTAGTTGGCA-CAT
* * * *
1006069 GAGTCAAAGGCCATACTT-GCTGG--CAT
1 AAGTCAAAGCCCACA-TTAGTTGGCACAT
* * * *
1006095 ATGTCAAAGTCCACATTCGTTGGCACAC
1 AAGTCAAAGCCCACATTAGTTGGCACAT
* *
1006123 AAGTCTAAGCCCACATTCGTTGGCACAT
1 AAGTCAAAGCCCACATTAGTTGGCACAT
* *
1006151 AAGTCAATGCCCACATTCGTTGGCACAT
1 AAGTCAAAGCCCACATTAGTTGGCACAT
* * **
1006179 AAGTCAATGCCCACATTAGCTGGTGTC-T
1 AAGTCAAAGCCCACATTAGTTGG-CACAT
* * * *
1006207 AAGTCTAAGCTCATATTATTTGGCACCA-
1 AAGTCAAAGCCCACATTAGTTGGCA-CAT
* * * * **
1006235 GAGTCAAAGCCCACACTAGCTGACACCC
1 AAGTCAAAGCCCACATTAGTTGGCACAT
* *
1006263 AGGTCTAAGCCCACACTT-GTTGG--CAT
1 AAGTCAAAGCCCACA-TTAGTTGGCACAT
1006289 AAGTCAAAGCCCACA
1 AAGTCAAAGCCCACA
1006304 CTCATTGGCA
Statistics
Matches: 197, Mismatches: 55, Indels: 24
0.71 0.20 0.09
Matches are distributed among these distances:
25 3 0.02
26 29 0.15
27 1 0.01
28 159 0.81
29 5 0.03
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (28 bp):
AAGTCAAAGCCCACATTAGTTGGCACAT
Found at i:1006538 original size:28 final size:28
Alignment explanation
Indices: 1006419--1006561 Score: 103
Period size: 28 Copynumber: 5.2 Consensus size: 28
1006409 ATGCTGGTGC
* * * *
1006419 AAGTCAAAGCCCACATTCATTAGCATAC
1 AAGTCAAAGCCCACATTCGTTGGCACAT
* * * * *
1006447 AAGTCTAAGCCCATATTCGCTAGCACGT
1 AAGTCAAAGCCCACATTCGTTGGCACAT
* * *
1006475 AAATCAAAGACCATACTT-GTTGG--CAT
1 AAGTCAAAGCCCACA-TTCGTTGGCACAT
* *
1006501 AATTCAAAGCCCACATTTGTTGGCACAT
1 AAGTCAAAGCCCACATTCGTTGGCACAT
* * *
1006529 AAGTCTAAGCCCACATTCGTAGGTACAT
1 AAGTCAAAGCCCACATTCGTTGGCACAT
1006557 AAGTC
1 AAGTC
1006562 CATGTCCACA
Statistics
Matches: 90, Mismatches: 21, Indels: 8
0.76 0.18 0.07
Matches are distributed among these distances:
25 2 0.02
26 19 0.21
28 67 0.74
29 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (28 bp):
AAGTCAAAGCCCACATTCGTTGGCACAT
Found at i:1006570 original size:28 final size:28
Alignment explanation
Indices: 1006498--1006573 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
1006488 TACTTGTTGG
* * * *
1006498 CATAATTCAAAGCCCACATTTGTTGGCA
1 CATAAGTCCAAGCCCACATTCGTAGGCA
* *
1006526 CATAAGTCTAAGCCCACATTCGTAGGTA
1 CATAAGTCCAAGCCCACATTCGTAGGCA
* *
1006554 CATAAGTCCATGTCCACATT
1 CATAAGTCCAAGCCCACATT
1006574 AACTGGCATC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (28 bp):
CATAAGTCCAAGCCCACATTCGTAGGCA
Found at i:1007157 original size:52 final size:51
Alignment explanation
Indices: 1007077--1007216 Score: 174
Period size: 52 Copynumber: 2.7 Consensus size: 51
1007067 TCTGAAAAGA
* * * *
1007077 AAATGTATTGATACATTTTCTATTGTATCGATACATTCT-GAGCTTTTGACCT
1 AAATGTATCGATAAATTTTC-ATTGTATCGATACATTCTAG-GCTTTTAACCC
* *
1007129 AAATGTATCGATATATTGTTCATTGTATCGATACATTCTAGGTTTTTAACCC
1 AAATGTATCGATAAATT-TTCATTGTATCGATACATTCTAGGCTTTTAACCC
*
1007181 AAATGTATCGATAAATTCTTCAATGTATCGATACAT
1 AAATGTATCGATAAATT-TTCATTGTATCGATACAT
1007217 GCAAGCAATT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 74 0.95
53 4 0.05
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (51 bp):
AAATGTATCGATAAATTTTCATTGTATCGATACATTCTAGGCTTTTAACCC
Found at i:1010491 original size:52 final size:52
Alignment explanation
Indices: 1010413--1010541 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1010403 CGAAATATGA
1010413 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
1010465 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1010517 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1010542 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:1010552 original size:52 final size:51
Alignment explanation
Indices: 1010413--1010561 Score: 237
Period size: 52 Copynumber: 2.9 Consensus size: 51
1010403 CGAAATATGA
1010413 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1010465 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1010517 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1010562 ATGTATCGAT
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
51 2 0.02
52 90 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1010568 original size:13 final size:13
Alignment explanation
Indices: 1010550--1010574 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010540 CAAAGATCAG
1010550 TGTATCGATACAA
1 TGTATCGATACAA
1010563 TGTATCGATACA
1 TGTATCGATACA
1010575 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1010650 original size:32 final size:33
Alignment explanation
Indices: 1010614--1010679 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1010604 AGTAGCTTAA
1010614 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1010646 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1010679 A
1 A
1010680 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1010653 original size:13 final size:13
Alignment explanation
Indices: 1010635--1010659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010625 ACAAAACTTA
1010635 TGTATCGATACAT
1 TGTATCGATACAT
1010648 TGTATCGATACA
1 TGTATCGATACA
1010660 ACACTTTATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1014339 original size:23 final size:23
Alignment explanation
Indices: 1014309--1014358 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1014299 GGAAAAAGCT
1014309 CACTGTCAACCACTCATCTAGCA
1 CACTGTCAACCACTCATCTAGCA
1014332 CACTGTCAACCACTCATCTAGCA
1 CACTGTCAACCACTCATCTAGCA
1014355 CACT
1 CACT
1014359 AAAGCTTCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.30, C:0.40, G:0.08, T:0.22
Consensus pattern (23 bp):
CACTGTCAACCACTCATCTAGCA
Found at i:1018130 original size:48 final size:49
Alignment explanation
Indices: 1018054--1018165 Score: 126
Period size: 48 Copynumber: 2.3 Consensus size: 49
1018044 ATTTGAATTA
*
1018054 AAAT-TTAATAATTAAAATATTTTATTTAA-ATTTAATTATAAAACAT-AT
1 AAATATTAATAATAAAAATATTTTATTTAATATTTAATT-TAAAA-ATAAT
* * *
1018102 AAATATTAAT-ATAAAAATAATTTT-TTTAATTTTTTATTTATAAATAAT
1 AAATATTAATAATAAAAAT-ATTTTATTTAATATTTAATTTAAAAATAAT
1018150 AAATATTAATAATAAA
1 AAATATTAATAATAAA
1018166 TCAAATTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
47 2 0.04
48 32 0.58
49 21 0.38
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (49 bp):
AAATATTAATAATAAAAATATTTTATTTAATATTTAATTTAAAAATAAT
Found at i:1019346 original size:22 final size:21
Alignment explanation
Indices: 1019317--1019366 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
1019307 TTAGTAGAGT
1019317 AAAAAAAAT-GAAAGAATGAAA
1 AAAAAAAATAGAAA-AATGAAA
*
1019338 AAAGAAAAATAGAAAAGTGAAA
1 AAA-AAAAATAGAAAAATGAAA
1019360 AAAAAAA
1 AAAAAAA
1019367 TATTTTTTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 7 0.27
22 15 0.58
23 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (21 bp):
AAAAAAAATAGAAAAATGAAA
Found at i:1019734 original size:16 final size:16
Alignment explanation
Indices: 1019700--1019751 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1019690 GAAAAAATAT
* *
1019700 ATTTTCTATCTTTC-C
1 ATTTTTTATCTTTCTA
*
1019715 ATTTTTTTTCTCTT-TA
1 ATTTTTTATCT-TTCTA
1019731 ATTTTTTATCTTTCTA
1 ATTTTTTATCTTTCTA
1019747 ATTTT
1 ATTTT
1019752 CCTTTTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTTTTTATCTTTCTA
Found at i:1021796 original size:15 final size:15
Alignment explanation
Indices: 1021764--1021812 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
1021754 TTCACTATAT
* *
1021764 TTAACATTTTATTCAA
1 TTAA-ATTTAATTTAA
1021780 TTAAATTTAATTTAA
1 TTAAATTTAATTTAA
1021795 TTAAATCTTAAGTTTAA
1 TTAAAT-TTAA-TTTAA
1021812 T
1 T
1021813 CCAATAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 15 0.52
16 8 0.28
17 6 0.21
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAAATTTAATTTAA
Found at i:1023794 original size:4 final size:4
Alignment explanation
Indices: 1023785--1023832 Score: 71
Period size: 4 Copynumber: 12.0 Consensus size: 4
1023775 TATCTATAGC
*
1023785 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAA- AAAT AAAA AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT
1023833 CTAAATCCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.82
5 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1024357 original size:2 final size:2
Alignment explanation
Indices: 1024350--1024390 Score: 73
Period size: 2 Copynumber: 20.0 Consensus size: 2
1024340 ACATGCACAA
1024350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
1024391 CAAAATCAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1028175 original size:25 final size:26
Alignment explanation
Indices: 1028141--1028213 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
1028131 CGATGTGAAA
*
1028141 TATCCTAATTTTTCAAAAATTG-TCG
1 TATCCTAATTTTTCAAAAATTGATAG
* * *
1028166 TATCCTAATTATACAAAAATTTGATAT
1 TATCCTAATTTTTCAAAAA-TTGATAG
* *
1028193 TGTCCTAAGTTTTCAAAAATT
1 TATCCTAATTTTTCAAAAATT
1028214 ATCATATCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 17 0.45
26 5 0.13
27 16 0.42
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (26 bp):
TATCCTAATTTTTCAAAAATTGATAG
Found at i:1030894 original size:16 final size:17
Alignment explanation
Indices: 1030865--1030897 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1030855 GTTAACATAA
*
1030865 TTTGTTAAGAGAAAAAT
1 TTTGGTAAGAGAAAAAT
1030882 TTTGGTAAG-GAAAAAT
1 TTTGGTAAGAGAAAAAT
1030898 GAGACAGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (17 bp):
TTTGGTAAGAGAAAAAT
Found at i:1031207 original size:28 final size:28
Alignment explanation
Indices: 1031172--1031229 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1031162 TTTGGGTAGA
1031172 AAAAGGGCATAAGAGCCTTACCCACACT
1 AAAAGGGCATAAGAGCCTTACCCACACT
*
1031200 AAAAGGGCATAAGAGCCTTACCTACACT
1 AAAAGGGCATAAGAGCCTTACCCACACT
1031228 AA
1 AA
1031230 CTTCCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (28 bp):
AAAAGGGCATAAGAGCCTTACCCACACT
Found at i:1036440 original size:15 final size:15
Alignment explanation
Indices: 1036420--1036453 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1036410 ACAGAAAAAG
1036420 GAAGTTTTGGAGAAT
1 GAAGTTTTGGAGAAT
1036435 GAAGTTTTGGAGAAT
1 GAAGTTTTGGAGAAT
1036450 GAAG
1 GAAG
1036454 ATATACCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (15 bp):
GAAGTTTTGGAGAAT
Found at i:1037007 original size:6 final size:6
Alignment explanation
Indices: 1036992--1037025 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1036982 AGTTGGATTT
* *
1036992 GAAATA GAAATG GAAATG GAAATG GAAAAG GAAA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAA
1037026 AGGGAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (6 bp):
GAAATG
Found at i:1037383 original size:21 final size:23
Alignment explanation
Indices: 1037353--1037427 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
1037343 ATATGTAAAA
1037353 AAATTATAAA-TT-TTAAAAATT
1 AAATTATAAATTTATTAAAAATT
* *
1037374 AAATTTTAAATTTATTAAATATT
1 AAATTATAAATTTATTAAAAATT
* * *
1037397 AAATAAGTATATATATTAATTAAATT
1 AAATTA-TAAATTTATTAA--AAATT
1037423 AAATT
1 AAATT
1037428 TTTTTTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
21 9 0.22
22 2 0.05
23 12 0.29
24 10 0.24
26 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (23 bp):
AAATTATAAATTTATTAAAAATT
Found at i:1037390 original size:16 final size:15
Alignment explanation
Indices: 1037359--1037402 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1037349 AAAAAAATTA
1037359 TAAATTTTAAA-AAT
1 TAAATTTTAAATAAT
*
1037373 TAAATTTTAAATTTAT
1 TAAATTTTAAA-TAAT
*
1037389 TAAATATTAAATAA
1 TAAATTTTAAATAA
1037403 GTATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 11 0.44
15 2 0.08
16 12 0.48
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTTTAAATAAT
Found at i:1039420 original size:19 final size:19
Alignment explanation
Indices: 1039396--1039441 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1039386 TTTACAAATA
1039396 TTTATTATAAAATACAACT
1 TTTATTATAAAATACAACT
* * *
1039415 TTTATTAT-CAATACTATT
1 TTTATTATAAAATACAACT
1039433 TTTATTATA
1 TTTATTATA
1039442 TTTCTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATTATAAAATACAACT
Found at i:1046672 original size:13 final size:13
Alignment explanation
Indices: 1046632--1046684 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1046622 CCGTTACAAG
1046632 CAATGTATCGATA
1 CAATGTATCGATA
1046645 CAA--T-TC-AT-
1 CAATGTATCGATA
1046653 C-ATGTATCGATA
1 CAATGTATCGATA
1046665 CAATGTATCGATA
1 CAATGTATCGATA
*
1046678 CATTGTA
1 CAATGTA
1046685 CCATGTATCG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 20 0.61
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1046672 original size:33 final size:33
Alignment explanation
Indices: 1046632--1046700 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1046622 CCGTTACAAG
*
1046632 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCACCATGTATCGATA
*
1046665 CAATGTATCGATACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGTATCGATA
1046698 CAA
1 CAA
1046701 ATAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 30 0.91
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGTATCGATA
Found at i:1047382 original size:18 final size:19
Alignment explanation
Indices: 1047359--1047415 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
1047349 CCCCTTAATC
*
1047359 AAAAAATTTCTCCGCTTTAAA
1 AAAAAATTTCTCCCCTTT--A
1047380 AAAAAATTTCTCCCCTTT-
1 AAAAAATTTCTCCCCTTTA
*
1047398 TAAAAATTTCTCCTCCTT
1 AAAAAATTTCTCC-CCTT
1047416 AATCAAGGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 12 0.36
19 4 0.12
21 17 0.52
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.39
Consensus pattern (19 bp):
AAAAAATTTCTCCCCTTTA
Found at i:1047385 original size:21 final size:21
Alignment explanation
Indices: 1047343--1047403 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
1047333 AGTTTTCATT
* *
1047343 TTTCTCCCCCTTAATCAAAAAA
1 TTTCTCCCCTTTAA-AAAAAAA
*
1047365 TTTCTCCGCTTTAAAAAAAAA
1 TTTCTCCCCTTTAAAAAAAAA
*
1047386 TTTCTCCCCTTTTAAAAA
1 TTTCTCCCCTTTAAAAAA
1047404 TTTCTCCTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 22 0.65
22 12 0.35
ACGTcount: A:0.36, C:0.26, G:0.02, T:0.36
Consensus pattern (21 bp):
TTTCTCCCCTTTAAAAAAAAA
Found at i:1047417 original size:17 final size:17
Alignment explanation
Indices: 1047381--1047415 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
1047371 CGCTTTAAAA
1047381 AAAAATTTCTCCCCTTTT
1 AAAAATTTCTCCCC-TTT
1047399 AAAAATTTCTCCTCCTT
1 AAAAATTTCTCC-CCTT
1047416 AATCAAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAAATTTCTCCCCTTT
Found at i:1047450 original size:22 final size:22
Alignment explanation
Indices: 1047343--1047450 Score: 95
Period size: 22 Copynumber: 5.1 Consensus size: 22
1047333 AGTTTTCATT
1047343 TTTCTCCCCC-TTAATCAAAAAA
1 TTTCTCCCCCTTTAATC-AAAAA
* **
1047365 TTTCT-CCGCTTTAAAAAAAAA
1 TTTCTCCCCCTTTAATCAAAAA
1047386 TTTCT-CCCCTTT--T-AAAAA
1 TTTCTCCCCCTTTAATCAAAAA
* **
1047404 TTTCTCCTCC-TTAATCAAGGCA
1 TTTCTCCCCCTTTAATCAA-AAA
1047426 TTTCTCCCCCTTTAATCAAAAA
1 TTTCTCCCCCTTTAATCAAAAA
1047448 TTT
1 TTT
1047451 ATTTATTTTC
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
18 12 0.18
19 3 0.04
20 1 0.01
21 21 0.31
22 23 0.34
23 8 0.12
ACGTcount: A:0.31, C:0.28, G:0.03, T:0.38
Consensus pattern (22 bp):
TTTCTCCCCCTTTAATCAAAAA
Found at i:1049333 original size:13 final size:13
Alignment explanation
Indices: 1049315--1049341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1049305 ATAGTACCAT
1049315 ATGTATCGATACA
1 ATGTATCGATACA
1049328 ATGTATCGATACA
1 ATGTATCGATACA
1049341 A
1 A
1049342 GGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1054765 original size:33 final size:33
Alignment explanation
Indices: 1054725--1054793 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1054715 TCGTTACAAG
*
1054725 CAATGTATCGATACAATT-CATCATGTATCGATA
1 CAATGTATCGATAC-ATTGCACCATGTATCGATA
* *
1054758 CAATGTATCGGTACATTGTACCATGTATCGATA
1 CAATGTATCGATACATTGCACCATGTATCGATA
1054791 CAA
1 CAA
1054794 ATAGTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACATTGCACCATGTATCGATA
Found at i:1054846 original size:19 final size:19
Alignment explanation
Indices: 1054822--1054889 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
1054812 CTGCCAATCT
1054822 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1054841 CATGTATCGATAC-----A
1 CATGTATCGATACAATGAA
1054855 -ATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1054873 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1054890 TATCGATACA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 12 0.28
14 1 0.02
18 1 0.02
19 29 0.67
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1054860 original size:13 final size:13
Alignment explanation
Indices: 1054842--1054900 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
1054832 TACAATGAAC
1054842 ATGTATCGATACA
1 ATGTATCGATACA
1054855 ATGTATCGATAC-
1 ATGTATCGATACA
1054867 A---AT-GA-AC-
1 ATGTATCGATACA
1054874 ATGTATCGATACA
1 ATGTATCGATACA
1054887 ATGTATCGATACA
1 ATGTATCGATACA
1054900 A
1 A
1054901 AGCATGATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 3 0.08
8 2 0.05
9 2 0.05
10 2 0.05
11 2 0.05
12 3 0.08
13 26 0.65
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1054864 original size:32 final size:32
Alignment explanation
Indices: 1054823--1054918 Score: 156
Period size: 32 Copynumber: 3.0 Consensus size: 32
1054813 TGCCAATCTC
1054823 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAATGAACATGTATCGATACA
1054855 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAATGAACATGTATCGATACA
* **
1054887 ATGTATCGATACAAAGCATGATGTATCGATAC
1 ATGTATCGATACAATG-AACATGTATCGATAC
1054919 GTCTGGGTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.78
33 13 0.22
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGTATCGATACAATGAACATGTATCGATACA
Found at i:1058675 original size:69 final size:69
Alignment explanation
Indices: 1058542--1058675 Score: 157
Period size: 69 Copynumber: 1.9 Consensus size: 69
1058532 TTTGTTGTTG
* * ** * *
1058542 AAAAATGGGGTTGGAGTATCCCCTTAGAGAAATGGGGTTGGAGTAGTCGTCGACAATGATATTTT
1 AAAAATGGGGTTGGAGTATCCCCTCAGAGAAATGGGGTCGGAGTAGTCCCCGACAAGGAAATTTT
1058607 AGGC
66 AGGC
*
1058611 AAAAATGGGGTTGGAGTATCCTCTCAGA-AGAATGGGGTCGGAGTA-TCCCCAGTA-AAGGAAAT
1 AAAAATGGGGTTGGAGTATCCCCTCAGAGA-AATGGGGTCGGAGTAGTCCCC-G-ACAAGGAAAT
1058673 TTT
63 TTT
1058676 GACATTTTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
68 4 0.07
69 50 0.91
70 1 0.02
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (69 bp):
AAAAATGGGGTTGGAGTATCCCCTCAGAGAAATGGGGTCGGAGTAGTCCCCGACAAGGAAATTTT
AGGC
Found at i:1063439 original size:3 final size:3
Alignment explanation
Indices: 1063431--1063486 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1063421 TTCCAAATCC
1063431 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1063479 TAT TAT TA
1 TAT TAT TA
1063487 ACTTTAAAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1064696 original size:13 final size:13
Alignment explanation
Indices: 1064678--1064703 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1064668 TACACAAAGT
1064678 ATGTATCGATACA
1 ATGTATCGATACA
1064691 ATGTATCGATACA
1 ATGTATCGATACA
1064704 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1064701 original size:32 final size:33
Alignment explanation
Indices: 1064660--1064723 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1064650 TAGCCAAACT
**
1064660 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1064692 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1064724 TTGGCCTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1066928 original size:21 final size:21
Alignment explanation
Indices: 1066895--1066944 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1066885 TTGCAAGTTG
*
1066895 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1066917 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1066938 AAATAAA
1 AAATAAA
1066945 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1068762 original size:15 final size:15
Alignment explanation
Indices: 1068742--1068772 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1068732 TAAAAATGTC
*
1068742 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1068757 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1068772 C
1 C
1068773 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1070863 original size:13 final size:13
Alignment explanation
Indices: 1070845--1070882 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1070835 CATTTTTCTT
1070845 TGTATCGATACAA
1 TGTATCGATACAA
*
1070858 TGTATCGATACAC
1 TGTATCGATACAA
1070871 TGTATCGATACA
1 TGTATCGATACA
1070883 GGGAGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1074499 original size:20 final size:19
Alignment explanation
Indices: 1074445--1074500 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1074435 AAAACCCTTA
*
1074445 AAAGTATCGATACACAGTTC
1 AAAGTATCGATACA-TGTTC
1074465 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
1074485 AATGTATCGATACATG
1 AAAGTATCGATACATG
1074501 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:1074588 original size:13 final size:13
Alignment explanation
Indices: 1074570--1074595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1074560 TACACAAAAT
1074570 ATGTATCGATACA
1 ATGTATCGATACA
1074583 ATGTATCGATACA
1 ATGTATCGATACA
1074596 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1074593 original size:32 final size:34
Alignment explanation
Indices: 1074552--1074616 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1074542 TAGCCAAACT
*
1074552 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1074584 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1074617 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1078685 original size:15 final size:15
Alignment explanation
Indices: 1078665--1078695 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1078655 TAAAAATGTC
*
1078665 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1078680 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1078695 C
1 C
1078696 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1080794 original size:13 final size:13
Alignment explanation
Indices: 1080776--1080813 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1080766 CATTTTTCTT
1080776 TGTATCGATACAA
1 TGTATCGATACAA
*
1080789 TGTATCGATACAC
1 TGTATCGATACAA
1080802 TGTATCGATACA
1 TGTATCGATACA
1080814 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1083388 original size:13 final size:13
Alignment explanation
Indices: 1083370--1083395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1083360 TACACAAAAT
1083370 ATGTATCGATACA
1 ATGTATCGATACA
1083383 ATGTATCGATACA
1 ATGTATCGATACA
1083396 CAAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1083393 original size:32 final size:34
Alignment explanation
Indices: 1083352--1083416 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
1083342 TAGCCAAACT
*
1083352 TGTATCGATACAC-AAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAAATTGTATCGATACAA
1083384 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAAATTGTATCGATACA
1083417 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 13 0.43
33 5 0.17
34 12 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (34 bp):
TGTATCGATACACAAAAAAATTGTATCGATACAA
Found at i:1084392 original size:50 final size:50
Alignment explanation
Indices: 1084317--1084498 Score: 197
Period size: 50 Copynumber: 3.8 Consensus size: 50
1084307 AAAGTCACAT
*
1084317 TTTTACCCAGATGTATCAATACATTTTTCAATGTATCGATACATTCTATC
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* * *
1084367 TTTTACCCAGATGTATCGATACATTTTTTAATATATCGATACA-TGTA--
1 TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* * *
1084414 ---T---GA-ATGTATCGATACATTCTTT-AATGTATCGATATATTCTGTC
1 TTTTACCCAGATGTATCGATACATT-TTTCAATGTATCGATACATTCTATC
*
1084457 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATTGATA
1 -TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATA
1084499 TATCTAGTTA
Statistics
Matches: 108, Mismatches: 11, Indels: 25
0.75 0.08 0.17
Matches are distributed among these distances:
40 27 0.25
41 6 0.06
44 1 0.01
47 1 0.01
49 3 0.03
50 44 0.41
51 26 0.24
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (50 bp):
TTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:1084394 original size:24 final size:24
Alignment explanation
Indices: 1084313--1084394 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
1084303 TGGAAAAGTC
*
1084313 ACATTTTTACCCAGATGTATCAAT
1 ACATTTTTACCCAGATGTATCGAT
1084337 ACATTTTT---CA-ATGTATCGAT
1 ACATTTTTACCCAGATGTATCGAT
1084357 ACATTCTATCTTTTACCCAGATGTATCGAT
1 --A--C-AT-TTTTACCCAGATGTATCGAT
1084387 ACATTTTT
1 ACATTTTT
1084395 TAATATATCG
Statistics
Matches: 47, Mismatches: 1, Indels: 20
0.69 0.01 0.29
Matches are distributed among these distances:
20 9 0.19
21 2 0.04
22 1 0.02
24 13 0.28
25 4 0.09
26 5 0.11
28 1 0.02
29 2 0.04
30 10 0.21
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.43
Consensus pattern (24 bp):
ACATTTTTACCCAGATGTATCGAT
Found at i:1084405 original size:20 final size:20
Alignment explanation
Indices: 1084377--1084447 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
1084367 TTTTACCCAG
1084377 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* * * *
1084397 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTTA
*
1084417 ATGTATCGATACATTCTTTA
1 ATGTATCGATACATTTTTTA
1084437 ATGTATCGATA
1 ATGTATCGATA
1084448 TATTCTGTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:1085397 original size:20 final size:22
Alignment explanation
Indices: 1085357--1085397 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1085347 TAGCCTTTGA
*
1085357 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1085379 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
1085398 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1089691 original size:24 final size:23
Alignment explanation
Indices: 1089659--1089722 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
1089649 TATATAAAAA
1089659 TTATTATTTTATATTTATTTATTC
1 TTATTATTTTATATTTATTTA-TC
* *
1089683 TTATTATTTAATAATT-TTTATC
1 TTATTATTTTATATTTATTTATC
*
1089705 TT-TTATTTTATTTTTATT
1 TTATTATTTTATATTTATT
1089723 ATTAAGTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 10 0.29
22 6 0.18
23 4 0.12
24 14 0.41
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (23 bp):
TTATTATTTTATATTTATTTATC
Found at i:1089724 original size:21 final size:22
Alignment explanation
Indices: 1089659--1089724 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 22
1089649 TATATAAAAA
1089659 TTATTATTTTATATTTATTTATTC
1 TTATTATTTTATATTTA-TTA-TC
*
1089683 TTATTATTTAATAATTT-TTATC
1 TTATTATTTTAT-ATTTATTATC
*
1089705 TT-TTATTTTATTTTTATTAT
1 TTATTATTTTATATTTATTAT
1089725 TAAGTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.08
21 12 0.32
22 4 0.11
23 3 0.08
24 11 0.30
25 4 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTATTTTATATTTATTATC
Found at i:1094686 original size:26 final size:27
Alignment explanation
Indices: 1094637--1094693 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1094627 ATAATTTAAA
1094637 AAAAAAATCAAATCACAATCTTAAATTT
1 AAAAAAATCAAATCACAA-CTTAAATTT
* *
1094665 AAAAAAATCAAATCAGAA-TTAATTTT
1 AAAAAAATCAAATCACAACTTAAATTT
1094691 AAA
1 AAA
1094694 TTTAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 10 0.37
28 17 0.63
ACGTcount: A:0.60, C:0.11, G:0.02, T:0.28
Consensus pattern (27 bp):
AAAAAAATCAAATCACAACTTAAATTT
Found at i:1096723 original size:103 final size:103
Alignment explanation
Indices: 1096532--1096803 Score: 280
Period size: 103 Copynumber: 2.6 Consensus size: 103
1096522 CTTTTAAAAT
* * *
1096532 TTTAAAATTAAGAAAAATATCTTATTT-AATCATGTAATTTTACTAATTTATTTAAATTTAAATT
1 TTTAAAATTAACAAAAA-ATTTTATTTAAAT-ATGTAATTTTATTAATTTATTTAAATTTAAATT
** * * * *
1096596 AATAAATATTTAAACTTATGGTCACGTGATATTAATTTAC
64 AATAAATATTTAAACAAATGGTCACATGATATTAAATAAA
* * *
1096636 TTTAAAATTAATAAAAAATTTTATTTAAATATGTAATTTTATTATTTTATTTAAATTTATATTAA
1 TTTAAAATTAACAAAAAATTTTATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATTAA
*
1096701 T-AATTTTTAAA-AAATGAAGTCACATGATATTAAATAAA
66 TAAATATTTAAACAAATG--GTCACATGATATTAAATAAA
* ***
1096739 ATTAAAATTAACAAACTTTTCCTATATATTTAAATATGTAATTTTTATTAATTTATTTAAATTTA
1 TTTAAAATTAACAAA-AAAT--T-T-TATTTAAATATGTAA-TTTTATTAATTTATTTAAATTTA
1096804 CATCAAACAA
Statistics
Matches: 141, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
101 3 0.02
102 9 0.06
103 70 0.50
104 20 0.14
106 1 0.01
107 1 0.01
108 15 0.11
109 22 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (103 bp):
TTTAAAATTAACAAAAAATTTTATTTAAATATGTAATTTTATTAATTTATTTAAATTTAAATTAA
TAAATATTTAAACAAATGGTCACATGATATTAAATAAA
Found at i:1101637 original size:33 final size:32
Alignment explanation
Indices: 1101580--1101643 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 32
1101570 TTTATTGTTT
1101580 AATTTATTTTATTTATATAAATTTAAGTATTTA
1 AATTTATTTTATTTATAT-AATTTAAGTATTTA
*
1101613 AATTTAATATTTATTTATAT-ATTTAATTATT
1 AATTT-AT-TTTATTTATATAATTTAAGTATT
1101644 ATTTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 15 0.54
34 2 0.07
35 11 0.39
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (32 bp):
AATTTATTTTATTTATATAATTTAAGTATTTA
Found at i:1101638 original size:19 final size:18
Alignment explanation
Indices: 1101607--1101664 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 18
1101597 TAAATTTAAG
1101607 TATTTAA-ATTTAATATT
1 TATTTAATATTTAATATT
1101624 TATTTATATATTTAAT-TAT
1 TATTTA-ATATTTAATAT-T
1101643 TATTTAAT-TTT-ATATTT
1 TATTTAATATTTAATA-TT
1101660 TATTT
1 TATTT
1101665 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.06
17 15 0.42
18 5 0.14
19 14 0.39
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTAATATTTAATATT
Found at i:1101652 original size:35 final size:33
Alignment explanation
Indices: 1101561--1101664 Score: 95
Period size: 35 Copynumber: 2.9 Consensus size: 33
1101551 ATTACATTAA
1101561 ATATTTAAATTTATTGTTTAATTTAT-TTTATTTAT
1 ATATTT-AA-TTATT-TTTAATTTATATTTATTTAT
* *
1101596 ATAAATTTAAGTA-TTTAAATTTAATATTTATTTAT
1 AT--ATTTAATTATTTTTAATTT-ATATTTATTTAT
1101631 ATATTTAATTATTATTTAATTTTATATTTTATTT
1 ATATTTAATTATT-TTTAA-TTTATA-TTTATTT
1101665 TTTAAAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
33 15 0.26
34 4 0.07
35 22 0.39
36 12 0.21
37 4 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (33 bp):
ATATTTAATTATTTTTAATTTATATTTATTTAT
Found at i:1101656 original size:23 final size:25
Alignment explanation
Indices: 1101607--1101659 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
1101597 TAAATTTAAG
*
1101607 TATTTAAATTTAATATTT-ATTTATA
1 TATTTAAATTTATTATTTAATTT-TA
1101632 TATTT-AA-TTATTATTTAATTTTA
1 TATTTAAATTTATTATTTAATTTTA
1101655 TATTT
1 TATTT
1101660 TATTTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 15 0.58
24 6 0.23
25 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTTAAATTTATTATTTAATTTTA
Found at i:1101665 original size:12 final size:12
Alignment explanation
Indices: 1101561--1101665 Score: 62
Period size: 12 Copynumber: 9.0 Consensus size: 12
1101551 ATTACATTAA
*
1101561 ATATTTAAATTT
1 ATATTTAATTTT
*
1101573 ATTGTTTAA-TTT
1 A-TATTTAATTTT
1101585 AT-TTT-A-TTT
1 ATATTTAATTTT
* *
1101594 ATA-TAAATTTA
1 ATATTTAATTTT
*
1101605 AGTATTTAAATTTA
1 A-TATTT-AATTTT
1101619 ATATTT-ATTTAT
1 ATATTTAATTT-T
*
1101631 ATATTTAATTAT
1 ATATTTAATTTT
1101643 -TATTTAATTTT
1 ATATTTAATTTT
*
1101654 ATATTTTATTTT
1 ATATTTAATTTT
1101666 TTAAAATAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
9 7 0.09
10 4 0.05
11 18 0.24
12 24 0.32
13 15 0.20
14 7 0.09
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:1102584 original size:2 final size:2
Alignment explanation
Indices: 1102577--1102606 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1102567 CTTTGTCATT
1102577 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1102607 GCACACTTTC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1102983 original size:17 final size:17
Alignment explanation
Indices: 1102944--1102985 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1102934 GTTATTATGA
*
1102944 AATTTTAATTTTTAATT
1 AATTTTTATTTTTAATT
**
1102961 TTTTTTTATTTTTAATT
1 AATTTTTATTTTTAATT
1102978 AATTTTTA
1 AATTTTTA
1102986 ATATTTTTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
AATTTTTATTTTTAATT
Found at i:1103148 original size:16 final size:19
Alignment explanation
Indices: 1103110--1103150 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 19
1103100 TTTTAATAAT
1103110 TATTTATTTGATATTTAAA
1 TATTTATTTGATATTTAAA
1103129 -ATTT-TTT-ATA-TTAAA
1 TATTTATTTGATATTTAAA
1103144 TATTTAT
1 TATTTAT
1103151 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
15 5 0.25
16 7 0.35
17 4 0.20
18 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTTATTTGATATTTAAA
Found at i:1103408 original size:6 final size:7
Alignment explanation
Indices: 1103387--1103411 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1103377 TGACTATTTT
1103387 AAATAAA
1 AAATAAA
1103394 AAATAAA
1 AAATAAA
1103401 AAATAAA
1 AAATAAA
1103408 AAAT
1 AAAT
1103412 GCTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:1103724 original size:60 final size:60
Alignment explanation
Indices: 1103614--1103732 Score: 161
Period size: 60 Copynumber: 2.0 Consensus size: 60
1103604 ATATAAAGTT
* * *
1103614 AATTTTTAAAATCAATTTAATTATATCAAATATATAAATATATATTAAAAATATCTTTAA
1 AATTTTTAAAATCAATTTAATTATATCAAATATATAAATATACATAAAAAATATATTTAA
* *
1103674 AATTCTTTAAAATCAATTTAATTATAT-TAATATATAAA-ATGCATGAAAAAATATATTTA
1 AATT-TTTAAAATCAATTTAATTATATCAAATATATAAATATACAT-AAAAAATATATTTA
1103733 TAGCCATTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
59 4 0.08
60 26 0.50
61 22 0.42
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (60 bp):
AATTTTTAAAATCAATTTAATTATATCAAATATATAAATATACATAAAAAATATATTTAA
Found at i:1106340 original size:21 final size:20
Alignment explanation
Indices: 1106311--1106353 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1106301 GACTAGTGTG
* *
1106311 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1106332 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1106352 GG
1 GG
1106354 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1106803 original size:13 final size:13
Alignment explanation
Indices: 1106785--1106822 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1106775 ATAATCCCCC
1106785 TGTATCGATACAG
1 TGTATCGATACAG
*
1106798 TGTATCGATACAT
1 TGTATCGATACAG
1106811 TGTATCGATACA
1 TGTATCGATACA
1106823 AAGAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1108924 original size:15 final size:15
Alignment explanation
Indices: 1108904--1108934 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1108894 ATTTCGTTTG
*
1108904 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1108919 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1108934 G
1 G
1108935 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1110766 original size:21 final size:21
Alignment explanation
Indices: 1110737--1110781 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1110727 AAATTTTTAT
*
1110737 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1110757 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1110779 TTT
1 TTT
1110782 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1114584 original size:9 final size:9
Alignment explanation
Indices: 1114570--1114600 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1114560 CATCAAGGAC
1114570 GATGAAGAT
1 GATGAAGAT
1114579 GATGAAGAT
1 GATGAAGAT
*
1114588 GATGATGAT
1 GATGAAGAT
1114597 GATG
1 GATG
1114601 GTGACTCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGAAGAT
Found at i:1119141 original size:13 final size:13
Alignment explanation
Indices: 1119123--1119159 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1119113 ACAGCATTCT
1119123 TTGTATCGATACA
1 TTGTATCGATACA
1119136 TTGTATCGATACA
1 TTGTATCGATACA
*
1119149 CTGTATCGATA
1 TTGTATCGATA
1119160 TAGGGGGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1119337 original size:22 final size:21
Alignment explanation
Indices: 1119294--1119335 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
1119284 AAAATTCTTG
1119294 TTTTTCACTTCAAAATACATCA
1 TTTTTCAC-TCAAAATACATCA
1119316 TTTTTCA-TCAAAAT-CATCA
1 TTTTTCACTCAAAATACATCA
1119335 T
1 T
1119336 CAAAAACAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 7 0.35
22 7 0.35
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTTTCACTCAAAATACATCA
Found at i:1121718 original size:13 final size:13
Alignment explanation
Indices: 1121700--1121724 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1121690 ACACACAGTA
1121700 TGTATCGATACAT
1 TGTATCGATACAT
1121713 TGTATCGATACA
1 TGTATCGATACA
1121725 CCATAAAATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1121721 original size:32 final size:33
Alignment explanation
Indices: 1121680--1121747 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1121670 GTAGCTAAAC
**
1121680 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
1121712 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
1121745 TTG
1 TTG
1121748 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:1123630 original size:32 final size:30
Alignment explanation
Indices: 1123594--1123652 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
1123584 GAAATCAAAT
1123594 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
1123626 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
1123653 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:1123968 original size:32 final size:33
Alignment explanation
Indices: 1123912--1123975 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1123902 TACAAGCCAA
*
1123912 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
*
1123945 TGTATTGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
1123976 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:1124519 original size:9 final size:9
Alignment explanation
Indices: 1124505--1124538 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
1124495 AACCATCAAG
1124505 GATGATGAA
1 GATGATGAA
1124514 GATGATGAA
1 GATGATGAA
*
1124523 GATGATGAT
1 GATGATGAA
1124532 GATGATG
1 GATGATG
1124539 GTGACTCAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (9 bp):
GATGATGAA
Found at i:1124520 original size:3 final size:3
Alignment explanation
Indices: 1124505--1124538 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1124495 AACCATCAAG
* *
1124505 GAT GAT GAA GAT GAT GAA GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1124539 GTGACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:1128368 original size:33 final size:33
Alignment explanation
Indices: 1128331--1128397 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1128321 TTCAACGATT
1128331 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1128364 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1128397 T
1 T
1128398 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1128369 original size:13 final size:13
Alignment explanation
Indices: 1128351--1128375 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1128341 CATAAAATGT
1128351 TGTATCGATACAA
1 TGTATCGATACAA
1128364 TGTATCGATACA
1 TGTATCGATACA
1128376 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1128456 original size:13 final size:13
Alignment explanation
Indices: 1128438--1128462 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1128428 ATTACTCAAA
1128438 TGTATCGATACAT
1 TGTATCGATACAT
1128451 TGTATCGATACA
1 TGTATCGATACA
1128463 CTGATCTTTG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1128564 original size:52 final size:52
Alignment explanation
Indices: 1128471--1128594 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 52
1128461 CACTGATCTT
* *
1128471 TGTATCGATACATGCAGGC-AATTTGCCGAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1128522 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1128574 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
1128595 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
51 19 0.28
52 49 0.72
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1132714 original size:13 final size:13
Alignment explanation
Indices: 1132696--1132721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1132686 ACAGCATTCT
1132696 TTGTATCGATACA
1 TTGTATCGATACA
1132709 TTGTATCGATACA
1 TTGTATCGATACA
1132722 GGGGGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1133189 original size:20 final size:21
Alignment explanation
Indices: 1133164--1133206 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
1133154 GCAGCACCCA
*
1133164 CCAGGTCACGACC-GGCAGCC
1 CCAGGTCACAACCAGGCAGCC
*
1133184 CCAGGTCGCAACCAGGCAGCC
1 CCAGGTCACAACCAGGCAGCC
1133205 CC
1 CC
1133207 CACACTAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.21, C:0.47, G:0.28, T:0.05
Consensus pattern (21 bp):
CCAGGTCACAACCAGGCAGCC
Found at i:1135284 original size:13 final size:13
Alignment explanation
Indices: 1135266--1135290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1135256 ACACACAGTA
1135266 TGTATCGATACAT
1 TGTATCGATACAT
1135279 TGTATCGATACA
1 TGTATCGATACA
1135291 CCATAAAATG
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1135287 original size:32 final size:33
Alignment explanation
Indices: 1135246--1135313 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1135236 GTAGCTAAAC
**
1135246 TTGTATCGATACA-CACAGTATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
*
1135278 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCACAAAATGTATCGATACA
1135311 TTG
1 TTG
1135314 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCACAAAATGTATCGATACA
Found at i:1136455 original size:463 final size:463
Alignment explanation
Indices: 1135590--1136980 Score: 2647
Period size: 463 Copynumber: 3.0 Consensus size: 463
1135580 GCTTTTGTTC
* * *
1135590 TTATTGTTATTATTTTCAAAGCTCTTTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
1 TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
*
1135655 CTAATTAGAGGCAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
66 CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
*
1135720 GAAAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
131 GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
1135785 GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
196 GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
1135850 AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
261 AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
1135915 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
326 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
1135980 AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCACCCCCTCTTGGTTCACTACTTCATA
391 AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCACCCCCTCTTGGTTCACTACTTCATA
1136045 AGCTTTCA
456 AGCTTTCA
1136053 TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
1 TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
1136118 CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
66 CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
1136183 GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
131 GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
1136248 GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
196 GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
1136313 AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
261 AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
1136378 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
326 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
1136443 AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCACCCCCTCTTGGTTCACTACTTCATA
391 AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCACCCCCTCTTGGTTCACTACTTCATA
1136508 AGCTTTCA
456 AGCTTTCA
1136516 TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
1 TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
1136581 CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
66 CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
1136646 GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
131 GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
*
1136711 GTAAAAGATACGAGTTGTAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
196 GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
* *
1136776 GGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGCCGTTTTTGGACCGAACCTC
261 AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
1136841 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
326 TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
* * * *
1136906 AATTTGTTCAAAACCCGAAAATTCGAAAAGAATCAATTCACCCCCCCTCTTGGTTCATTACTTCC
391 AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCA--CCCCCTCTTGGTTCACTACTTCA
*
1136971 TAAACTTTCA
454 TAAGCTTTCA
1136981 ATGTTTGATG
Statistics
Matches: 913, Mismatches: 13, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
463 883 0.97
465 30 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (463 bp):
TTATTGTTATTATTTTTAAAGCACATTGTATTTGATTTCGAGCTTAAATTCCCACAAACACCAGC
CTAATTAGAGGTAAACTTTGTTTGTAGAAAAATCTTTGTTTTCATAAGGTTGTATTAAACCTTGA
GAGAGAATCTCTTTGGAACTTGTGGTATAGTTCGCAAAGAGATTGTACGGTTGGTATCTAAGCCC
GTAAAAGATACGAGTTATAAGGTTATACCTTTGCCTTAAAGGTAATCAATTCGGTTAGTGAATTG
AGTAATCACTCGACAAGGAAGTGTCGAGGAGAGAGGACGTAGGTGTCGTTTTTGGACCGAACCTC
TATAAATATTTTGTGTCAAGTTTTCCTTCCCTAATCTCTTTTTCATTTCGAATTGTTTTGTTCCA
AATTTGTTCAAAACCCAAAAATTCGAAAAGAACCAATTCACCCCCTCTTGGTTCACTACTTCATA
AGCTTTCA
Found at i:1138555 original size:11 final size:12
Alignment explanation
Indices: 1138529--1138553 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1138519 AATTTATTTA
1138529 TTAAAAATTATT
1 TTAAAAATTATT
1138541 TTAAAAATTATT
1 TTAAAAATTATT
1138553 T
1 T
1138554 AATTATTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAAAAATTATT
Found at i:1139615 original size:16 final size:16
Alignment explanation
Indices: 1139593--1139700 Score: 96
Period size: 16 Copynumber: 6.8 Consensus size: 16
1139583 TCGATTGATC
1139593 CGAACCCGAAATGAC-
1 CGAACCCGAAATGACT
* *
1139608 CTGAACCCG-AATCAACC
1 C-GAACCCGAAAT-GACT
*
1139625 CGAACTCGAAATGACT
1 CGAACCCGAAATGACT
* *
1139641 CAAACTCGAAATGACT
1 CGAACCCGAAATGACT
*
1139657 CGAATCCGAAATGACT
1 CGAACCCGAAATGACT
*
1139673 CGAACTCGAAATGAC-
1 CGAACCCGAAATGACT
*
1139688 CTGAACCTGAAAT
1 C-GAACCCGAAAT
1139701 AACTTAACTC
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
15 5 0.07
16 67 0.88
17 4 0.05
ACGTcount: A:0.39, C:0.29, G:0.17, T:0.16
Consensus pattern (16 bp):
CGAACCCGAAATGACT
Found at i:1145432 original size:12 final size:12
Alignment explanation
Indices: 1145415--1145457 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
1145405 AATTTTTTTA
1145415 ATTTTAAAAAAT
1 ATTTTAAAAAAT
1145427 ATTTTAAAAAAT
1 ATTTTAAAAAAT
*
1145439 ATTTTTTAAAATAT
1 A--TTTTAAAAAAT
1145453 ATTTT
1 ATTTT
1145458 TTTACGTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
ATTTTAAAAAAT
Done.