Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 163 of 171
Found at i:48412921 original size:59 final size:58
Alignment explanation
Indices: 48412826--48413033 Score: 211
Period size: 59 Copynumber: 3.5 Consensus size: 58
48412816 TTAAAAATCC
**
48412826 CATTTTGACCCCTCGAACTTCTCTAAAATTACATTTTAACCCTAAACTACTTTAAAATTA
1 CATTTTGA-CCCTTAAACTTCTCTAAAATTACATTTTAACCCTAAACT-CTTTAAAATTA
* * * * * *
48412886 CATTTTGACCCTTAAACTCCTCTAAAATTGCATTTTGACCTTAAAATTTTCTAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTACATTTTAACCCTAAACTCTT-TAAAATTA
* * * * * **
48412945 CATTTTAACCCTTAAACTTCTCCAAAATTACATTTTGACCCCCAAACTTCTCTAAAATCC
1 CATTTTGACCCTTAAACTTCTCTAAAATTACATTTT-AACCCTAAAC-TCTTTAAAATTA
* *
48413005 CATTTTGA-CCTTAAATTTCTCCAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
48413034 TGATTTTACC
Statistics
Matches: 122, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
58 2 0.02
59 92 0.75
60 26 0.21
61 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (58 bp):
CATTTTGACCCTTAAACTTCTCTAAAATTACATTTTAACCCTAAACTCTTTAAAATTA
Found at i:48413040 original size:30 final size:30
Alignment explanation
Indices: 48412826--48413033 Score: 233
Period size: 30 Copynumber: 7.0 Consensus size: 30
48412816 TTAAAAATCC
**
48412826 CATTTTGACCCCTCGAACTTCTCTAAAATTA
1 CATTTTGA-CCCTTAAACTTCTCTAAAATTA
* * *
48412857 CATTTTAACCC-TAAACTACTTTAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
* *
48412886 CATTTTGACCCTTAAACTCCTCTAAAATTG
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
* *
48412916 CATTTTGA-CCTTAAAATTTTCTAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
* *
48412945 CATTTTAACCCTTAAACTTCTCCAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
** **
48412975 CATTTTGACCCCCAAACTTCTCTAAAATCC
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
* *
48413005 CATTTTGA-CCTTAAATTTCTCCAAAATTA
1 CATTTTGACCCTTAAACTTCTCTAAAATTA
48413034 TGATTTTACC
Statistics
Matches: 146, Mismatches: 29, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
29 63 0.43
30 76 0.52
31 7 0.05
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
CATTTTGACCCTTAAACTTCTCTAAAATTA
Found at i:48413045 original size:89 final size:89
Alignment explanation
Indices: 48412819--48413033 Score: 281
Period size: 89 Copynumber: 2.4 Consensus size: 89
48412809 ATTTTCTTTA
** * **
48412819 AAAATCCCATTTTGACCCCTCGAACTTCTCTAAAATTACATTTTAACCC-TAAACTACTTTAAAA
1 AAAATCCCATTTTGA--CCTTAAATTTCTCTAAAATTACATTTTAACCCTTAAACTACTCCAAAA
**
48412883 TTACATTTTGACCCTTAAACTCCTCT
64 TTACATTTTGACCCCCAAACTCCTCT
** *
48412909 AAAATTGCATTTTGACCTTAAAATTT-TCTAAAATTACATTTTAACCCTTAAACTTCTCCAAAAT
1 AAAATCCCATTTTGACCTT-AAATTTCTCTAAAATTACATTTTAACCCTTAAACTACTCCAAAAT
*
48412973 TACATTTTGACCCCCAAACTTCTCT
65 TACATTTTGACCCCCAAACTCCTCT
*
48412998 AAAATCCCATTTTGACCTTAAATTTCTCCAAAATTA
1 AAAATCCCATTTTGACCTTAAATTTCTCTAAAATTA
48413034 TGATTTTACC
Statistics
Matches: 108, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
88 30 0.28
89 65 0.60
90 13 0.12
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (89 bp):
AAAATCCCATTTTGACCTTAAATTTCTCTAAAATTACATTTTAACCCTTAAACTACTCCAAAATT
ACATTTTGACCCCCAAACTCCTCT
Found at i:48413148 original size:59 final size:59
Alignment explanation
Indices: 48413055--48413176 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
48413045 TCGAATATCT
* ** * *
48413055 AAAAATTACCATATTACCCTCGAACATCTTAAAATTACAATTTTTCCCCTAAATGTCCA
1 AAAAATTACCATATTACCCCCGAACATCCAAAAATTACAATTTTACCCCCAAATGTCCA
* * * * *
48413114 AAAAATTATCATTTTGCCCCCGAACATCCAAAAATTACCATTTTACCCCCAAATTTCCA
1 AAAAATTACCATATTACCCCCGAACATCCAAAAATTACAATTTTACCCCCAAATGTCCA
48413173 AAAA
1 AAAA
48413177 TCACATTTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.40, C:0.27, G:0.03, T:0.30
Consensus pattern (59 bp):
AAAAATTACCATATTACCCCCGAACATCCAAAAATTACAATTTTACCCCCAAATGTCCA
Found at i:48413183 original size:28 final size:29
Alignment explanation
Indices: 48412929--48413228 Score: 117
Period size: 29 Copynumber: 10.2 Consensus size: 29
48412919 TTTGACCTTA
* * **
48412929 AAATTTTCTAAAATTA-CATTTTAACCCTT
1 AAATTTCCAAAAATTACCATTTT-ACCCCC
48412958 AAACTTCTCC-AAAATTA-CATTTTGACCCCC
1 AAA-TT-TCCAAAAATTACCATTTT-ACCCCC
* * * **
48412988 AAACTTCTCTAAAA-TCCCATTTTGA-CCTT
1 AAATTTC-CAAAAATTACCATTTT-ACCCCC
* ** *
48413017 AAATTTCTCCAAAATTATGATTTTACCCTC
1 AAATTTC-CAAAAATTACCATTTTACCCCC
* * * * *
48413047 GAATATCTAAAAATTACCATATTACCCTC
1 AAATTTCCAAAAATTACCATTTTACCCCC
* ** ** * * *
48413076 GAACATCTTAAAATTACAATTTTTCCCCT
1 AAATTTCCAAAAATTACCATTTTACCCCC
* * *
48413105 AAATGTCCAAAAAATTATCATTTTGCCCCC
1 AAATTTCC-AAAAATTACCATTTTACCCCC
* **
48413135 GAACATCCAAAAATTACCATTTTACCCCC
1 AAATTTCCAAAAATTACCATTTTACCCCC
* **
48413164 AAATTTCCAAAAATCA-CATTTTAATCCC
1 AAATTTCCAAAAATTACCATTTTACCCCC
* * *
48413192 AAATTTTCAAAAAAATTTCAATTTTGACCCCC
1 AAA-TTTC-CAAAAATTACCATTTT-ACCCCC
48413224 AAATT
1 AAATT
48413229 GCTCGAAAAT
Statistics
Matches: 205, Mismatches: 54, Indels: 22
0.73 0.19 0.08
Matches are distributed among these distances:
28 15 0.07
29 99 0.48
30 75 0.37
31 9 0.04
32 7 0.03
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATTTCCAAAAATTACCATTTTACCCCC
Found at i:48415008 original size:17 final size:17
Alignment explanation
Indices: 48414980--48415022 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
48414970 AAGAAAAAAT
48414980 AGTTACAAGAAGATGAAA
1 AGTTA-AAGAAGATGAAA
48414998 AGTTAAAGAAGATGAAA
1 AGTTAAAGAAGATGAAA
*
48415015 GGTTAAAG
1 AGTTAAAG
48415023 GTCAAGAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.26, T:0.19
Consensus pattern (17 bp):
AGTTAAAGAAGATGAAA
Found at i:48420475 original size:27 final size:27
Alignment explanation
Indices: 48420445--48420500 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
48420435 GAAATGGAGG
48420445 AGTTGAAATGTTTGAATTCTGACTTGT
1 AGTTGAAATGTTTGAATTCTGACTTGT
48420472 AGTTGAAATGTTTGAATTCTGACTTGT
1 AGTTGAAATGTTTGAATTCTGACTTGT
48420499 AG
1 AG
48420501 GAAGCATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (27 bp):
AGTTGAAATGTTTGAATTCTGACTTGT
Found at i:48422727 original size:29 final size:29
Alignment explanation
Indices: 48422660--48422715 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
48422650 TGCACATGCT
* * *
48422660 AGGGTTTCTCACACGGGCTTGCATATATA
1 AGGGGTTCTCACACAGGCTTGCACATATA
48422689 AGGGGTTCTCACACAGGCTTGCACATA
1 AGGGGTTCTCACACAGGCTTGCACATA
48422716 CAGTGGGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (29 bp):
AGGGGTTCTCACACAGGCTTGCACATATA
Found at i:48425258 original size:13 final size:14
Alignment explanation
Indices: 48425240--48425268 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
48425230 AAACCAGTGG
48425240 AAAATAGTTTT-TA
1 AAAATAGTTTTCTA
48425253 AAAATAGTTTTCTA
1 AAAATAGTTTTCTA
48425267 AA
1 AA
48425269 CCAAAACATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAATAGTTTTCTA
Found at i:48426216 original size:14 final size:15
Alignment explanation
Indices: 48426188--48426217 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48426178 ATAGGTTCAT
48426188 AAGTAGGGCTCGCAC
1 AAGTAGGGCTCGCAC
48426203 AAGTAGGG-TCGCAC
1 AAGTAGGGCTCGCAC
48426217 A
1 A
48426218 TGTATAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.30, C:0.23, G:0.33, T:0.13
Consensus pattern (15 bp):
AAGTAGGGCTCGCAC
Found at i:48426353 original size:23 final size:23
Alignment explanation
Indices: 48426310--48426354 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48426300 AAATCTACAA
* *
48426310 GGTTCGCATACTTTAGTATATAG
1 GGTTCGCATACTTCAATATATAG
48426333 GGTTCGCATA-TTCAATCATATA
1 GGTTCGCATACTTCAAT-ATATA
48426355 AGGTAAGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (23 bp):
GGTTCGCATACTTCAATATATAG
Found at i:48426721 original size:29 final size:29
Alignment explanation
Indices: 48426684--48426770 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
48426674 GGGGTTTTGT
* *
48426684 ACACAGGCTCGTACATACA-GGGGTTTCTC
1 ACACGGGCTCGCACATACATGGGG-TTCTC
* *
48426713 ACATGGGCTTGCACATACATGGGGTTCTC
1 ACACGGGCTCGCACATACATGGGGTTCTC
* * *
48426742 ACACGGGCTCACACATACAAGAGGTTCTC
1 ACACGGGCTCGCACATACATGGGGTTCTC
48426771 CTAGGGTTCA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (29 bp):
ACACGGGCTCGCACATACATGGGGTTCTC
Found at i:48430156 original size:27 final size:26
Alignment explanation
Indices: 48430096--48430158 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
48430086 TGATAAAATA
*
48430096 AATTATTTTTTTATAAAATTTATATT
1 AATTATTTTTTTATAAAATTAATATT
* *
48430122 ACTCTA-TTTTTTATTGAAATTAAGTATT
1 AAT-TATTTTTTTA-TAAAATTAA-TATT
48430150 AATTATTTT
1 AATTATTTT
48430159 ATTACCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
26 9 0.31
27 11 0.38
28 9 0.31
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (26 bp):
AATTATTTTTTTATAAAATTAATATT
Found at i:48431961 original size:29 final size:30
Alignment explanation
Indices: 48431929--48431995 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
48431919 AAAAAATGCG
*
48431929 ATTTTTGGATG-TTCG-GGGATAAAACGGTA
1 ATTTTTGGATGCTTCGTGGG-CAAAACGGTA
*
48431958 A-TTTTGGATGCTTCGTGGGCAAAATGGTA
1 ATTTTTGGATGCTTCGTGGGCAAAACGGTA
48431987 ATTTTTGGA
1 ATTTTTGGA
48431996 CACTTGGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 9 0.27
29 14 0.42
30 10 0.30
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.37
Consensus pattern (30 bp):
ATTTTTGGATGCTTCGTGGGCAAAACGGTA
Found at i:48432036 original size:29 final size:28
Alignment explanation
Indices: 48432004--48432225 Score: 207
Period size: 29 Copynumber: 7.7 Consensus size: 28
48431994 GACACTTGGA
*
48432004 GGTAAAAATGTAATTTTT-AAACGTACATG
1 GGTAAAAATGTAATTTTTGAAA-GTTCA-G
*
48432033 GGTAAAAAGGTAATTTTTGAAAGTTCAGG
1 GGTAAAAATGTAATTTTTGAAAGTTCA-G
* * * *
48432062 GGCAAAAATATGATTTTTGGAAGTTCGAG
1 GGTAAAAATGTAATTTTTGAAAGTTC-AG
48432091 GGTAAAAATGTAATTTTTTGAAAGTTC-G
1 GGTAAAAATGTAA-TTTTTGAAAGTTCAG
* *
48432119 AGGTAAAAATGTGATTTTTGAAAGTTTAG
1 -GGTAAAAATGTAATTTTTGAAAGTTCAG
* *
48432148 GGTAAAAAATGTAATTTTTGGAAATTTGAG
1 GGT-AAAAATGTAATTTTT-GAAAGTTCAG
* * *
48432178 GG-CAAAATGGTAATTTTTGAAAAGTTTAA
1 GGTAAAAAT-GTAATTTTTG-AAAGTTCAG
*
48432207 GGTCAAAATGTAATTTTTG
1 GGTAAAAATGTAATTTTTG
48432226 GACGATTCAG
Statistics
Matches: 162, Mismatches: 21, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
28 22 0.14
29 108 0.67
30 32 0.20
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.36
Consensus pattern (28 bp):
GGTAAAAATGTAATTTTTGAAAGTTCAG
Found at i:48432202 original size:87 final size:87
Alignment explanation
Indices: 48431985--48432225 Score: 249
Period size: 87 Copynumber: 2.8 Consensus size: 87
48431975 GGCAAAATGG
* * * * *
48431985 TAATTTTTGGACACTTGGA-GGTAAAAATGTAA-TTTTT-AAACGTACATGGGTAAAAAGGTAAT
1 TAATTTTTGGA-AATTCGAGGGTAAAAATGTAATTTTTTGAAA-GTTCA-AGGTAAAAATGTAAT
*
48432047 TTTTGAAAGTTCAGGGGCAAAAATA
63 TTTTGAAAGTTCAGGGGAAAAAATA
* * * *
48432072 TGATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTTGAAAGTTCGAGGTAAAAATGTGATTTT
1 TAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTGAAAGTTCAAGGTAAAAATGTAATTTT
* * *
48432137 TGAAAGTTTAGGGTAAAAAATG
66 TGAAAGTTCAGGGGAAAAAATA
* * * *
48432159 TAATTTTTGGAAATTTGAGGG-CAAAATGGTAA-TTTTTGAAAAGTTTAAGGTCAAAATGTAATT
1 TAATTTTTGGAAATTCGAGGGTAAAAAT-GTAATTTTTTG-AAAGTTCAAGGTAAAAATGTAATT
48432222 TTTG
64 TTTG
48432226 GACGATTCAG
Statistics
Matches: 129, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
86 16 0.12
87 102 0.79
88 8 0.06
89 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (87 bp):
TAATTTTTGGAAATTCGAGGGTAAAAATGTAATTTTTTGAAAGTTCAAGGTAAAAATGTAATTTT
TGAAAGTTCAGGGGAAAAAATA
Found at i:48432226 original size:58 final size:58
Alignment explanation
Indices: 48431978--48432227 Score: 199
Period size: 58 Copynumber: 4.3 Consensus size: 58
48431968 CTTCGTGGGC
* * * * ** *
48431978 AAAATGGTAATTTTTGGACACTTGGAGGTAAAAATGTAATTTTT-AAACGTACATGGGT-A
1 AAAAT-GTAATTTTTGGAAAGTTCGAGGGAAAAATGTAATTTTTGAAA-GTTTA-AGGTAA
* * * * * *
48432037 AAAAGGTAATTTTT-GAAAGTTC-AGGGGCAAAAATATGATTTTTGGAAGTTCGAGGGT-A
1 AAAATGTAATTTTTGGAAAGTTCGA-GGG-AAAAATGTAATTTTTGAAAGTT-TAAGGTAA
* * * *
48432095 AAAATGTAATTTTTTGAAAGTTCGAGGTAAAAATGTGATTTTTGAAAGTTTAGGGTAA
1 AAAATGTAATTTTTGGAAAGTTCGAGGGAAAAATGTAATTTTTGAAAGTTTAAGGTAA
* * *
48432153 AAAATGTAATTTTTGGAAA-TTTGAGGGCAAAATGGTAATTTTTGAAAAGTTTAAGGT-C
1 AAAATGTAATTTTTGGAAAGTTCGAGGGAAAAAT-GTAATTTTTG-AAAGTTTAAGGTAA
48432211 AAAATGTAATTTTTGGA
1 AAAATGTAATTTTTGGA
48432228 CGATTCAGGG
Statistics
Matches: 160, Mismatches: 22, Indels: 19
0.80 0.11 0.09
Matches are distributed among these distances:
56 1 0.01
57 23 0.14
58 107 0.67
59 28 0.17
60 1 0.01
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAAGTTCGAGGGAAAAATGTAATTTTTGAAAGTTTAAGGTAA
Found at i:48433820 original size:6 final size:6
Alignment explanation
Indices: 48433793--48433867 Score: 84
Period size: 6 Copynumber: 12.8 Consensus size: 6
48433783 ATCTTTATTT
* * *
48433793 ATTTAA ATTTAGA A-TT-A TTTTAA ATTTAA ATATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
48433840 ATTTAA ATTTAA ATTTAA A-ATAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
48433868 GTTTGAGCCT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 48 0.84
7 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:48433834 original size:18 final size:18
Alignment explanation
Indices: 48433793--48433867 Score: 93
Period size: 18 Copynumber: 4.3 Consensus size: 18
48433783 ATCTTTATTT
48433793 ATTTAAATTTAGAAT-T-A
1 ATTTAAATTTA-AATATAA
*
48433810 TTTTAAATTTAAATATAA
1 ATTTAAATTTAAATATAA
* *
48433828 ATTTAAACTTAAATTTAA
1 ATTTAAATTTAAATATAA
48433846 ATTTAAATTTAAA-ATAA
1 ATTTAAATTTAAATATAA
48433863 ATTTA
1 ATTTA
48433868 GTTTGAGCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
16 3 0.06
17 19 0.38
18 28 0.56
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTTAAATTTAAATATAA
Found at i:48434683 original size:30 final size:28
Alignment explanation
Indices: 48434652--48434854 Score: 183
Period size: 29 Copynumber: 7.0 Consensus size: 28
48434642 TCCCTAAACT
* *
48434652 TTCCAAAAATTACATTTTAACCCTCAAAC
1 TTCCAAAAATTACATTTTTACCC-CGAAC
* * *
48434681 TTTCTAAAAATTATATTTTAACCCCGAAC
1 -TTCCAAAAATTACATTTTTACCCCGAAC
* *
48434710 TTTCCAAAAATAACATTTTTGCTCCCGAAC
1 -TTCCAAAAATTACATTTTTAC-CCCGAAC
* *
48434740 TTCTATAAGA-TACATTTTTACCCTCGAAC
1 TTCCA-AAAATTACATTTTTACCC-CGAAC
* *
48434769 TTCCAAAAATCACATTTTTACTCCCGTAC
1 TTCCAAAAATTACATTTTTAC-CCCGAAC
*
48434798 TTCCAAAAATCACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCC-CGAAC
* * *
48434827 ATCTAAAAATTACCATTTTAACCCCGAA
1 TTCCAAAAATTA-CATTTTTACCCCGAA
48434855 TTTTTCCAAA
Statistics
Matches: 145, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.05
29 95 0.66
30 43 0.30
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.33
Consensus pattern (28 bp):
TTCCAAAAATTACATTTTTACCCCGAAC
Found at i:48434689 original size:29 final size:29
Alignment explanation
Indices: 48434620--48434875 Score: 172
Period size: 29 Copynumber: 8.8 Consensus size: 29
48434610 GAAGGTCTTT
*
48434620 GAACTTTCAAAAA-T-CATGTTTTTCCCT-
1 GAACTTTCAAAAATTACAT-TTTTACCCTC
* *
48434647 AAACTTTCCAAAAATTACATTTTAACCCTC
1 GAACTTT-CAAAAATTACATTTTTACCCTC
* * *
48434677 AAACTTTCTAAAAATTATATTTTAACCC-C
1 GAACTTTC-AAAAATTACATTTTTACCCTC
* *
48434706 GAACTTTCCAAAAATAACATTTTTGCTCC-C
1 GAACTTT-CAAAAATTACATTTTTAC-CCTC
*
48434736 GAAC-TTCTATAAGA-TACATTTTTACCCTC
1 GAACTTTC-A-AAAATTACATTTTTACCCTC
* *
48434765 GAACTTCCAAAAATCACATTTTTACTCC-C
1 GAACTTTCAAAAATTACATTTTTAC-CCTC
* * *
48434794 GTACTTCCAAAAATCACATTTTTACCCTC
1 GAACTTTCAAAAATTACATTTTTACCCTC
* *
48434823 GAAC-ATCTAAAAATTACCATTTTAACCC-C
1 GAACTTTC-AAAAATTA-CATTTTTACCCTC
* *
48434852 GAATTTTTCCAAAATTACTATTTT
1 GAA-CTTTCAAAAATTAC-ATTTT
48434876 GCTCCCAAGC
Statistics
Matches: 186, Mismatches: 24, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
27 6 0.03
28 15 0.08
29 98 0.53
30 65 0.35
31 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (29 bp):
GAACTTTCAAAAATTACATTTTTACCCTC
Found at i:48434776 original size:58 final size:58
Alignment explanation
Indices: 48434620--48434854 Score: 194
Period size: 58 Copynumber: 4.1 Consensus size: 58
48434610 GAAGGTCTTT
* ** * * *
48434620 GAACTTTCAAAAATCATGTTTTT-CCCT-AAACTTTCCAAAAATTACATTTTAAC-CCTC
1 GAACTTCCAAAAATCACATTTTTACCCTCGAAC-TTCCAAAAATAACATTTTTACTCC-C
* * * * * *
48434677 AAACTTTCTAAAAATTATATTTTAACCC-CGAACTTTCCAAAAATAACATTTTTGCTCCC
1 GAAC-TTCCAAAAATCACATTTTTACCCTCGAAC-TTCCAAAAATAACATTTTTACTCCC
* * *
48434736 GAACTTCTATAAGAT-ACATTTTTACCCTCGAACTTCCAAAAATCACATTTTTACTCCC
1 GAACTTCCA-AAAATCACATTTTTACCCTCGAACTTCCAAAAATAACATTTTTACTCCC
* * * * *
48434794 GTACTTCCAAAAATCACATTTTTACCCTCGAACATCTAAAAATTACCATTTTAAC-CCC
1 GAACTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAA-TAACATTTTTACTCCC
48434852 GAA
1 GAA
48434855 TTTTTCCAAA
Statistics
Matches: 145, Mismatches: 25, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
57 7 0.05
58 89 0.61
59 47 0.32
60 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (58 bp):
GAACTTCCAAAAATCACATTTTTACCCTCGAACTTCCAAAAATAACATTTTTACTCCC
Found at i:48434826 original size:87 final size:88
Alignment explanation
Indices: 48434662--48434850 Score: 215
Period size: 87 Copynumber: 2.1 Consensus size: 88
48434652 TTCCAAAAAT
* * *
48434662 TACATTTTAACCCTCAAACTTTCTAAAAATTATATTTTAACCCCGAACTTTCCAAAAATAACATT
1 TACATTTTAACCCTCAAACTTTCCAAAAATCACATTTTAACCCCGAACTTTCCAAAAATAACATT
* *
48434727 TTTGCTCCCGAACTTCTATAAGA
66 TTTACTCCCGAACATCTATAAGA
* * * * *
48434750 TACATTTTTACCCTCGAAC-TTCCAAAAATCACATTTTTACTCCCGTAC-TTCCAAAAATCACAT
1 TACATTTTAACCCTCAAACTTTCCAAAAATCACATTTTAAC-CCCGAACTTTCCAAAAATAACAT
*
48434813 TTTTAC-CCTCGAACATCTA-AAAA
65 TTTTACTCC-CGAACATCTATAAGA
48434836 TTACCATTTTAACCC
1 -TA-CATTTTAACCC
48434851 CGAATTTTTC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
86 5 0.06
87 47 0.55
88 33 0.39
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (88 bp):
TACATTTTAACCCTCAAACTTTCCAAAAATCACATTTTAACCCCGAACTTTCCAAAAATAACATT
TTTACTCCCGAACATCTATAAGA
Found at i:48434910 original size:146 final size:146
Alignment explanation
Indices: 48434652--48434932 Score: 324
Period size: 146 Copynumber: 1.9 Consensus size: 146
48434642 TCCCTAAACT
* * *
48434652 TTCCAAAAATTACATTTTAACCCTCAAACTTTCTAAAAATTATATTTTAACCCCGAACTTTCCAA
1 TTCCAAAAATCACATTTTAACCCTCAAACTATCTAAAAATTACATTTTAACCCCGAACTTTCCAA
* * * *
48434717 AAATAACATTTTTGCTCCCGAACTTCTATAAGATACATTTTTACCCTCGAACTT-CCAAAAATCA
66 AAATAACATTTTTGCTCCCGAACATCCATAAAATACATTTTTACCCTC-AAATTCCCAAAAATCA
48434781 CATTTTTACTCCCGTAC
130 CATTTTTACTCCCGTAC
* * *
48434798 TTCCAAAAATCACATTTTTACCCTCGAAC-ATCTAAAAATTACCATTTTAACCCCGAATTTTTCC
1 TTCCAAAAATCACATTTTAACCCTCAAACTATCTAAAAATTA-CATTTTAACCCCGAA-CTTTCC
* * *
48434862 -AAAATTAC-TATTTTGCTCCC-AAGCATCCA-AAAATTTCCA-TTTTGCCCTCAAATTCCCAAA
64 AAAAATAACAT-TTTTGCTCCCGAA-CATCCATAAAA--TACATTTTTACCCTCAAATTCCCAAA
*
48434922 AGTCACATTTT
125 AATCACATTTT
48434933 CAACTTCAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
145 21 0.18
146 85 0.75
147 8 0.07
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (146 bp):
TTCCAAAAATCACATTTTAACCCTCAAACTATCTAAAAATTACATTTTAACCCCGAACTTTCCAA
AAATAACATTTTTGCTCCCGAACATCCATAAAATACATTTTTACCCTCAAATTCCCAAAAATCAC
ATTTTTACTCCCGTAC
Found at i:48437169 original size:25 final size:25
Alignment explanation
Indices: 48437140--48437190 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
48437130 AATAAAGTCT
48437140 TATGTCTAATAAATCTCTTCCTAAG
1 TATGTCTAATAAATCTCTTCCTAAG
48437165 TATGTCTAATAAATCTCTTCCTAAG
1 TATGTCTAATAAATCTCTTCCTAAG
48437190 T
1 T
48437191 CTTCCACACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.41
Consensus pattern (25 bp):
TATGTCTAATAAATCTCTTCCTAAG
Found at i:48438155 original size:29 final size:29
Alignment explanation
Indices: 48438076--48438156 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 29
48438066 ATGATTACAG
* ** *
48438076 TTATCTGGTACTTTGTACTGGTGTTACAT
1 TTATCAGGTACTTTGTACCAGTGTTAAAT
* * **
48438105 TTATCAAGCACTTTGTGTCAGTGTTAAAT
1 TTATCAGGTACTTTGTACCAGTGTTAAAT
*
48438134 TTATCAGGTACTATGTACCAGTG
1 TTATCAGGTACTTTGTACCAGTG
48438157 GTGGATACCA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (29 bp):
TTATCAGGTACTTTGTACCAGTGTTAAAT
Found at i:48445090 original size:39 final size:40
Alignment explanation
Indices: 48445045--48445124 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
48445035 AAGAGAGTTA
**
48445045 AAAGAACC-TTGTTTTTAATAATATCAAGTGAAAAGAAAG
1 AAAGAACCTTTGTTTTTAATAATATCAAACGAAAAGAAAG
48445084 AAAGAACCTTTTGTTTTTAATAATATCAAACGAAAAGAAAG
1 AAAGAACC-TTTGTTTTTAATAATATCAAACGAAAAGAAAG
48445125 TTTCATTCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 8 0.22
41 29 0.78
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (40 bp):
AAAGAACCTTTGTTTTTAATAATATCAAACGAAAAGAAAG
Found at i:48445920 original size:29 final size:30
Alignment explanation
Indices: 48445888--48446139 Score: 253
Period size: 30 Copynumber: 8.4 Consensus size: 30
48445878 ATTTTACTTA
* *
48445888 AAAATTACATTTTGA-CCTCCAAAC-TTTCT
1 AAAATTACATTTTAACCCT-TAAACTTTTCT
* * * *
48445917 AAAATTGCATTTTGACCCTT-AATTTTTTT
1 AAAATTACATTTTAACCCTTAAACTTTTCT
* *
48445946 CAAAATTACATTTTAACCCTTAAATTTTTCC
1 -AAAATTACATTTTAACCCTTAAACTTTTCT
** *
48445977 AAAATTACATTTTAACCCCCAAAACTTTTCC
1 AAAATTACATTTTAA-CCCTTAAACTTTTCT
* **
48446008 AAATTTACATAATAACCCTCT-AACTTTTCT
1 AAAATTACATTTTAACCCT-TAAACTTTTCT
* * *
48446038 AAAATTAGATTTTAACCGTTAAACTTTTCA
1 AAAATTACATTTTAACCCTTAAACTTTTCT
* *
48446068 AAAATTATATTTTAACCCTTAAACTTTTTT
1 AAAATTACATTTTAACCCTTAAACTTTTCT
*
48446098 AAAATTACATTTTGACCC-TAAACTTTTCT
1 AAAATTACATTTTAACCCTTAAACTTTTCT
48446127 AAAATTACATTTT
1 AAAATTACATTTT
48446140 GAACTAAAAT
Statistics
Matches: 186, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
28 2 0.01
29 42 0.23
30 111 0.60
31 31 0.17
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTTAAACTTTTCT
Found at i:48446158 original size:28 final size:29
Alignment explanation
Indices: 48446098--48446167 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
48446088 AAACTTTTTT
* * * *
48446098 AAAATTACATTTTGACCCTAAACTTTTCT
1 AAAATTACATTTTGACACTAAAATTCTCA
48446127 AAAATTACATTTTGA-ACTAAAATTCTCA
1 AAAATTACATTTTGACACTAAAATTCTCA
48446155 AAAACTT-CATTTT
1 AAAA-TTACATTTT
48446168 TGACCCTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.53
29 17 0.47
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTGACACTAAAATTCTCA
Found at i:48450730 original size:2 final size:2
Alignment explanation
Indices: 48450723--48450790 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
48450713 AAATTTAAAC
48450723 AT AT AT AT 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 AT AT AT AT
48450765 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
48450791 GGGATTAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48450994 original size:30 final size:30
Alignment explanation
Indices: 48450940--48451100 Score: 184
Period size: 30 Copynumber: 5.4 Consensus size: 30
48450930 GAAATTTTGG
*
48450940 AAAGTTTG-GGGTCAAAATGTAATTTTCAA
1 AAAGTTTGAGGGTCAAAATGAAATTTTCAA
*
48450969 AAAGTTTGAGGGTTAAAATGAAATTTTCAA
1 AAAGTTTGAGGGTCAAAATGAAATTTTCAA
*
48450999 AAAGTTT-AGGGGTCAAAATGAAATTTT-AG
1 AAAGTTTGA-GGGTCAAAATGAAATTTTCAA
* * * *
48451028 AAAGTTTGAGAGTCAAAATGAATTTTTTAG
1 AAAGTTTGAGGGTCAAAATGAAATTTTCAA
* * **
48451058 AAAGTTTGAGGGCCAAAATAAAATTTTTGA
1 AAAGTTTGAGGGTCAAAATGAAATTTTCAA
*
48451088 AAAGTTTAAGGGT
1 AAAGTTTGAGGGT
48451101 TAAATTTTAA
Statistics
Matches: 114, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
29 33 0.29
30 81 0.71
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (30 bp):
AAAGTTTGAGGGTCAAAATGAAATTTTCAA
Found at i:48451046 original size:59 final size:58
Alignment explanation
Indices: 48450940--48451094 Score: 184
Period size: 59 Copynumber: 2.6 Consensus size: 58
48450930 GAAATTTTGG
* * * *
48450940 AAAGTTTGGGGTCAAAATGTAATTTTCAAAAAGTTTGAGGGTTAAAATGAAATTTTCAA
1 AAAGTTTGGGGTCAAAATGAAATTTT-AGAAAGTTTGAGAGTCAAAATGAAATTTTCAA
* * *
48450999 AAAGTTTAGGGGTCAAAATGAAATTTTAGAAAGTTTGAGAGTCAAAATGAATTTTTTAG
1 AAAGTTT-GGGGTCAAAATGAAATTTTAGAAAGTTTGAGAGTCAAAATGAAATTTTCAA
* * *
48451058 AAAGTTTGAGGGCCAAAATAAAATTTTTGAAAAGTTT
1 AAAGTTTG-GGGTCAAAATGAAATTTTAG-AAAGTTT
48451095 AAGGGTTAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
58 1 0.01
59 57 0.69
60 25 0.30
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.34
Consensus pattern (58 bp):
AAAGTTTGGGGTCAAAATGAAATTTTAGAAAGTTTGAGAGTCAAAATGAAATTTTCAA
Found at i:48455800 original size:59 final size:58
Alignment explanation
Indices: 48455737--48455938 Score: 205
Period size: 59 Copynumber: 3.5 Consensus size: 58
48455727 CTTGGGCAGG
*
48455737 AAATGATAATTTTGGGAAAGTTCGGGGTCAAAAATAGAATTTTTAGACATTCGAGGGTA
1 AAATGATAATTTTTGGAAAGTTCGGGGT-AAAAATAGAATTTTTAGACATTCGAGGGTA
* * * * *
48455796 AAATGGTAATTTTTGGAAAGTTCAAGGTTAAAAACAGAA-TTTTATGACATCCG-GAGGTA
1 AAATGATAATTTTTGGAAAGTTC-GGGGTAAAAATAGAATTTTTA-GACATTCGAG-GGTA
** * * * *
48455855 AAATGATAA-TTTTGGAAAAATCGGGGTTAAAATGGATTTTTTGGA-AGTTCGAGGGTA
1 AAATGATAATTTTTGGAAAGTTCGGGGTAAAAATAGAATTTTTAGACA-TTCGAGGGTA
* *
48455912 AAATGATAATTTTTAGAAAGTTTGGGG
1 AAATGATAATTTTTGGAAAGTTCGGGG
48455939 GTTGAAATGT
Statistics
Matches: 115, Mismatches: 21, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
56 1 0.01
57 27 0.23
58 35 0.30
59 49 0.43
60 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.32
Consensus pattern (58 bp):
AAATGATAATTTTTGGAAAGTTCGGGGTAAAAATAGAATTTTTAGACATTCGAGGGTA
Found at i:48455885 original size:29 final size:28
Alignment explanation
Indices: 48455851--48455924 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
48455841 GACATCCGGA
48455851 GGTAAAATGATAATTTTGGAAAAATCG-G
1 GGTAAAATGATAATTTTGG-AAAATCGAG
* **
48455879 GGTTAAAATGGAT-TTTTTGGAAGTTCGAG
1 GG-TAAAAT-GATAATTTTGGAAAATCGAG
48455908 GGTAAAATGATAATTTT
1 GGTAAAATGATAATTTT
48455925 TAGAAAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
28 17 0.45
29 15 0.39
30 3 0.08
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
GGTAAAATGATAATTTTGGAAAATCGAG
Found at i:48455933 original size:30 final size:30
Alignment explanation
Indices: 48455737--48455993 Score: 146
Period size: 30 Copynumber: 8.7 Consensus size: 30
48455727 CTTGGGCAGG
*
48455737 AAATGATAATTTTGGGAAAGTTCG-GGGTCAA
1 AAATGATAATTTTTGGAAAGTTCGAGGGT--A
* * *
48455768 AAAT-AGAATTTTTAGACA-TTCGAGGGTA
1 AAATGATAATTTTTGGAAAGTTCGAGGGTA
* * *
48455796 AAATGGTAATTTTTGGAAAGTTCAAGGTTA
1 AAATGATAATTTTTGGAAAGTTCGAGGGTA
** * * *
48455826 AAAACAGAATTTTAT-GACA-TCCG-GAGGTA
1 AAATGATAATTTT-TGGAAAGTTCGAG-GGTA
**
48455855 AAATGATAA-TTTTGGAAAAATCG-GGGTTA
1 AAATGATAATTTTTGGAAAGTTCGAGGG-TA
48455884 AAATGGAT--TTTTTGG-AAGTTCGAGGGTA
1 AAAT-GATAATTTTTGGAAAGTTCGAGGGTA
* * * *
48455912 AAATGATAATTTTTAGAAAGTTTGGGGGTTG
1 AAATGATAATTTTTGGAAAGTTCGAGGG-TA
*
48455943 AAATG-TAATTTTTGGAGAGTTC-AGAGGTCA
1 AAATGATAATTTTTGGAAAGTTCGAG-GGT-A
* *
48455973 AAAT-ATGATTTTTGGATAGTT
1 AAATGATAATTTTTGGAAAGTT
48455994 TAGGGACCTT
Statistics
Matches: 171, Mismatches: 37, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
27 4 0.02
28 25 0.15
29 51 0.30
30 80 0.47
31 11 0.06
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (30 bp):
AAATGATAATTTTTGGAAAGTTCGAGGGTA
Found at i:48455994 original size:60 final size:59
Alignment explanation
Indices: 48455737--48455994 Score: 149
Period size: 59 Copynumber: 4.4 Consensus size: 59
48455727 CTTGGGCAGG
** * * * *
48455737 AAATGATAATTTTGGGAAAG-TTCGGGGTCAAAAATAGAATTTTTAGACA-TTCGAGGGTA
1 AAATGATAATTTTTAGAAAGTTTGGGGGT-TAAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * *** ** *
48455796 AAATGGTAATTTTTGGAAAG-TTCAAGGTTAAAAACAGAATTTTAT-GACA-TCCG-GAGGTA
1 AAATGATAATTTTTAGAAAGTTTGGGGGTT-AAAATGGAATTTT-TGGA-AGTTCGAG-GGTA
* ** * *
48455855 AAATGATAA-TTTTGGAAA-AATCGGGGTTAAAATGGATTTTTTGGAAGTTCGAGGGTA
1 AAATGATAATTTTTAGAAAGTTTGGGGGTTAAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
48455912 AAATGATAATTTTTAGAAAGTTTGGGGGTTGAAATGTAATTTTTGGAGAGTTC-AGAGGTCA
1 AAATGATAATTTTTAGAAAGTTTGGGGGTTAAAATGGAATTTTTGGA-AGTTCGAG-GGT-A
* * *
48455973 AAAT-ATGATTTTTGGATAGTTT
1 AAATGATAATTTTTAGAAAGTTT
48455995 AGGGACCTTC
Statistics
Matches: 162, Mismatches: 25, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
56 2 0.01
57 28 0.17
58 25 0.15
59 78 0.48
60 24 0.15
61 5 0.03
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (59 bp):
AAATGATAATTTTTAGAAAGTTTGGGGGTTAAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:48457061 original size:12 final size:12
Alignment explanation
Indices: 48457019--48457052 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
48457009 ATTTATTATT
*
48457019 ATTAATATTAAA
1 ATTATTATTAAA
48457031 ATTATTATTAAA
1 ATTATTATTAAA
48457043 ATTATTATTA
1 ATTATTATTA
48457053 CTATTATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATTATTAAA
Found at i:48457948 original size:17 final size:17
Alignment explanation
Indices: 48457921--48458001 Score: 99
Period size: 17 Copynumber: 4.8 Consensus size: 17
48457911 TAGATAAATT
* *
48457921 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
48457938 TAGATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
* **
48457955 TGAATTTAAACCTAAAA
1 TAAATTTAAATTTAAAA
48457972 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
48457989 TAAATTTAAATTT
1 TAAATTTAAATTT
48458002 TGTTGGGCCC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 52 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:48460797 original size:36 final size:36
Alignment explanation
Indices: 48460750--48460942 Score: 148
Period size: 36 Copynumber: 5.4 Consensus size: 36
48460740 AAATCTTGAC
* *
48460750 GGTTGCTTTAGACAAGGTCTATTCCAATGTTTCTAA
1 GGTTGCTTTAGACAAGGTCTATTCCAATCTTTTTAA
*
48460786 GGTTGCTTTAGAC--GG-GTATTCCAATCTTTTTTAAA
1 GGTTGCTTTAGACAAGGTCTATTCCAATC-TTTTT-AA
* *
48460821 GGTTGCATTAGACAAGGTCTATTCTAATCTTTTTAA
1 GGTTGCTTTAGACAAGGTCTATTCCAATCTTTTTAA
* * *
48460857 GGTTGCCTTAGACGA-GTCTA-TCTCAACCTTTTTTAAA
1 GGTTGCTTTAGACAAGGTCTATTC-CAATC-TTTTT-AA
* * * * *
48460894 AGCTACTTTAGACAAGATCTA-TCTCAACCTTTTTAA
1 GGTTGCTTTAGACAAGGTCTATTC-CAATCTTTTTAA
*
48460930 AGTTG-TCTTAGAC
1 GGTTGCT-TTAGAC
48460943 GGGTTTGTCT
Statistics
Matches: 129, Mismatches: 18, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
33 9 0.07
34 8 0.06
35 23 0.18
36 44 0.34
37 24 0.19
38 21 0.16
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (36 bp):
GGTTGCTTTAGACAAGGTCTATTCCAATCTTTTTAA
Found at i:48460868 original size:71 final size:73
Alignment explanation
Indices: 48460750--48460972 Score: 245
Period size: 73 Copynumber: 3.1 Consensus size: 73
48460740 AAATCTTGAC
* * * *
48460750 GGTTGCTTTAGACAAGGTCTATTCCAATGTTTCTAAGGTTGCTTTAGACGGGTAT-TC-CAATCT
1 GGTTGCTTTAGACAAGGTCTATTCTAATCTTTTTAAGGTTGCCTTAGACGGGTATATCTCAATCT
48460813 TTTTTAAA
66 TTTTTAAA
* * * *
48460821 GGTTGCATTAGACAAGGTCTATTCTAATCTTTTTAAGGTTGCCTTAGACGAGTCTATCTCAACCT
1 GGTTGCTTTAGACAAGGTCTATTCTAATCTTTTTAAGGTTGCCTTAGACGGGTATATCTCAATCT
48460886 TTTTTAAA
66 TTTTTAAA
* * * * * * * * * *
48460894 AGCTACTTTAGACAAGATCTA-TCTCAACCTTTTTAAAGTTGTCTTAGACGGGTTTGTCTCAATT
1 GGTTGCTTTAGACAAGGTCTATTCT-AATCTTTTTAAGGTTGCCTTAGACGGGTATATCTCAATC
48460958 TTTTTTAAA
65 TTTTTTAAA
*
48460967 GATTGC
1 GGTTGC
48460973 CTTAAATAAG
Statistics
Matches: 124, Mismatches: 25, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
71 48 0.39
72 5 0.04
73 71 0.57
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (73 bp):
GGTTGCTTTAGACAAGGTCTATTCTAATCTTTTTAAGGTTGCCTTAGACGGGTATATCTCAATCT
TTTTTAAA
Found at i:48464022 original size:5 final size:6
Alignment explanation
Indices: 48464007--48464031 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48463997 TTTATTTCTC
48464007 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
48464032 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:48478011 original size:17 final size:17
Alignment explanation
Indices: 48477978--48478011 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48477968 TCTAGGTTGA
**
48477978 ATAATTAAAATTTCTTT
1 ATAATTAAAATCACTTT
48477995 ATAATTAAAATCACTTT
1 ATAATTAAAATCACTTT
48478012 TACTCTAATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATTAAAATCACTTT
Found at i:48479215 original size:23 final size:23
Alignment explanation
Indices: 48479189--48479283 Score: 120
Period size: 23 Copynumber: 4.1 Consensus size: 23
48479179 ACTCGATCTA
*
48479189 TTAAACATAAATCACATTAATAT
1 TTAAGCATAAATCACATTAATAT
* *
48479212 TTAACCACAAATCACATTAATAT
1 TTAAGCATAAATCACATTAATAT
* *
48479235 TTAAGCATAAATTATC-TTAACAT
1 TTAAGCATAAATCA-CATTAATAT
*
48479258 TTAAGCATAAATCACAGTAATAT
1 TTAAGCATAAATCACATTAATAT
48479281 TTA
1 TTA
48479284 TTACATTTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
22 1 0.02
23 59 0.97
24 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (23 bp):
TTAAGCATAAATCACATTAATAT
Found at i:48479469 original size:66 final size:66
Alignment explanation
Indices: 48479361--48479563 Score: 255
Period size: 66 Copynumber: 3.1 Consensus size: 66
48479351 GATACACGGA
* * * *
48479361 TCTCCAAACACACCAAAAGACTCATAGATTCG-AACATATCCCAAAAGTGAAGCATATAGCTAAC
1 TCTCCAAACACACCAAAAGACTCATAGAAT-GAAACATGTCCCAAAAGTAAAGCATAAAGCTAAC
48479425 AC
65 AC
*
48479427 TCTCCAAACACACCAAAAGACTCATAGAATGAAACATGTCCCAACAGTAAAGCATAAAGCTAACA
1 TCTCCAAACACACCAAAAGACTCATAGAATGAAACATGTCCCAAAAGTAAAGCATAAAGCTAACA
48479492 C
66 C
** * ** * * * * *
48479493 TCTCCAAACATGCCAAAAGTCTCACGGAGTTAAACATGTCCTAAAAGTAAAGTATAAATCTAACA
1 TCTCCAAACACACCAAAAGACTCATAGAATGAAACATGTCCCAAAAGTAAAGCATAAAGCTAACA
48479558 C
66 C
48479559 TCTCC
1 TCTCC
48479564 TTATTTCCCC
Statistics
Matches: 120, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
65 1 0.01
66 119 0.99
ACGTcount: A:0.43, C:0.27, G:0.11, T:0.19
Consensus pattern (66 bp):
TCTCCAAACACACCAAAAGACTCATAGAATGAAACATGTCCCAAAAGTAAAGCATAAAGCTAACA
C
Found at i:48479864 original size:36 final size:36
Alignment explanation
Indices: 48479824--48479999 Score: 191
Period size: 36 Copynumber: 4.9 Consensus size: 36
48479814 TTCACTATCA
* *
48479824 CATGATATGAATAACATACCTACATATTTATTGTCT
1 CATGACATGAATAACATACCTACATATTTACTGTCT
* *
48479860 CATGACATGAATAACATA-CTCACATATTTACTCTCA
1 CATGACATGAATAACATACCT-ACATATTTACTGTCT
* *
48479896 CATGACATGAACT-ACGTA-CTCACATATTTATTGTCT
1 CATGACATGAA-TAACATACCT-ACATATTTACTGTCT
* *
48479932 CGTGACATGAATAATATATCC-ACATATTTACTGTCT
1 CATGACATGAATAACATA-CCTACATATTTACTGTCT
*
48479968 CATGGCATGAATAACATATCC-ACATATTTACT
1 CATGACATGAATAACATA-CCTACATATTTACT
48480000 TTCACAACAG
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
35 3 0.03
36 115 0.96
37 1 0.01
38 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (36 bp):
CATGACATGAATAACATACCTACATATTTACTGTCT
Found at i:48479928 original size:72 final size:72
Alignment explanation
Indices: 48479811--48479997 Score: 229
Period size: 72 Copynumber: 2.6 Consensus size: 72
48479801 TTAGCACAAT
* *
48479811 ATATTCACTATCACATGATATGAATAACATACCTACATATTTATTGTCTCATGACATGAATAACA
1 ATATTTACTATCACATGACATGAATAACATACCTACATATTTATTGTCTCATGACATGAATAACA
48479876 TA-CTCAC
66 TATC-CAC
* * *
48479883 ATATTTACTCTCACATGACATGAACT-ACGTA-CTCACATATTTATTGTCTCGTGACATGAATAA
1 ATATTTACTATCACATGACATGAA-TAACATACCT-ACATATTTATTGTCTCATGACATGAATAA
*
48479946 TATATCCAC
64 CATATCCAC
* * *
48479955 ATATTTACTGTCTCATGGCATGAATAACATATCC-ACATATTTA
1 ATATTTACTATCACATGACATGAATAACATA-CCTACATATTTA
48479998 CTTTCACAAC
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
71 3 0.03
72 93 0.94
73 2 0.02
74 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.35
Consensus pattern (72 bp):
ATATTTACTATCACATGACATGAATAACATACCTACATATTTATTGTCTCATGACATGAATAACA
TATCCAC
Found at i:48489088 original size:23 final size:23
Alignment explanation
Indices: 48489062--48489182 Score: 147
Period size: 23 Copynumber: 5.2 Consensus size: 23
48489052 ACACTAGCAC
48489062 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
48489085 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
48489108 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
48489133 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
* *
48489156 GCTCTCTAATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
48489179 GCTC
1 GCTC
48489183 AGTACTTTGT
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 61 0.72
24 1 0.01
25 16 0.19
26 3 0.04
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:48489168 original size:46 final size:49
Alignment explanation
Indices: 48489062--48489182 Score: 160
Period size: 48 Copynumber: 2.6 Consensus size: 49
48489052 ACACTAGCAC
* * *
48489062 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCT
1 GCTCTCTAATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT
* *
48489111 -CTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCAC-T-TCGTG-T
1 GCTCTCTAATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT
*
48489156 GCTCTCTAATTAGCACTTTGTGTGCTC
1 GCTCTCTAATTAGCACTGTGTGTGCTC
48489183 AGTACTTTGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
45 1 0.02
46 28 0.44
47 1 0.02
48 34 0.53
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (49 bp):
GCTCTCTAATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCTCGTGCT
Found at i:48489211 original size:39 final size:39
Alignment explanation
Indices: 48489147--48489221 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
48489137 TCCGATTAGC
*
48489147 ACTTCGTGTGCTCTCTAATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTAATTAGCACTTTGTGTGCTCAGT
* **
48489186 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTAATTAGCACTTTGTGTGCTC
48489222 TCTGTTGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTAATTAGCACTTTGTGTGCTCAGT
Found at i:48489216 original size:23 final size:23
Alignment explanation
Indices: 48489181--48489274 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
48489171 CTTTGTGTGC
*
48489181 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
48489204 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
48489227 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
48489252 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
48489274 T
1 T
48489275 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:48495565 original size:17 final size:17
Alignment explanation
Indices: 48495543--48495596 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
48495533 TAATTAATTT
*
48495543 TTTAAAATATAAAAAAA
1 TTTAAAATATAAAAATA
48495560 TTTAAAA-ATAAAAATTA
1 TTTAAAATATAAAAA-TA
*
48495577 TTGAAAATATAAAAATA
1 TTTAAAATATAAAAATA
48495594 TTT
1 TTT
48495597 TTTAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.22
17 18 0.56
18 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
TTTAAAATATAAAAATA
Found at i:48495612 original size:20 final size:21
Alignment explanation
Indices: 48495566--48495612 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
48495556 AAAATTTAAA
*
48495566 AATAAAAATTATTGAAAATAT
1 AATAAATATTATTGAAAATAT
* *
48495587 AA-AAATATTTTTTAAAAT-T
1 AATAAATATTATTGAAAATAT
48495606 AATAAAT
1 AATAAAT
48495613 TATTGACATG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 17 0.77
21 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AATAAATATTATTGAAAATAT
Found at i:48499469 original size:39 final size:39
Alignment explanation
Indices: 48499423--48499610 Score: 155
Period size: 39 Copynumber: 4.8 Consensus size: 39
48499413 ATAATTTAGT
* * * *
48499423 AGTGTTTATAGTGTCACTACTAATTTAGTATAGTATTAC
1 AGTGTTTACAGTGTCACTACCAATTCAGTATAGCATTAC
* * *
48499462 -GATGTTTACAGTGTCACTGCCAGTTCAGTATAGCATTGC
1 AG-TGTTTACAGTGTCACTACCAATTCAGTATAGCATTAC
* * *
48499501 AGTGTTTACAGTGTCACTACCATTTCAGTAT-GCCACTGC
1 AGTGTTTACAGTGTCACTACCAATTCAGTATAG-CATTAC
* * * * ***
48499540 TGTGTTTACAGTGTCATTGCCAGTTCAGTATAGCATCGT
1 AGTGTTTACAGTGTCACTACCAATTCAGTATAGCATTAC
* * * *
48499579 AGTGTTTATAGTGTCACTGCTAGTTCAGTATA
1 AGTGTTTACAGTGTCACTACCAATTCAGTATA
48499611 CTTCCGATGT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
38 2 0.02
39 120 0.97
40 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (39 bp):
AGTGTTTACAGTGTCACTACCAATTCAGTATAGCATTAC
Found at i:48499514 original size:78 final size:79
Alignment explanation
Indices: 48499423--48499610 Score: 231
Period size: 78 Copynumber: 2.4 Consensus size: 79
48499413 ATAATTTAGT
* *
48499423 AGTGTTTATAGTGTCACTACTAATTTAGTATAG-TATTAC-GATGTTTACAGTGTCACTGCCAGT
1 AGTGTTTATAGTGTCACTACTAATTTAGTATAGCCACTACTG-TGTTTACAGTGTCACTGCCAGT
*
48499486 TCAGTATAGCATTGC
65 TCAGTATAGCATCGC
* * * *
48499501 AGTGTTTACAGTGTCACTAC-CATTTCAGTAT-GCCACTGCTGTGTTTACAGTGTCATTGCCAGT
1 AGTGTTTATAGTGTCACTACTAATTT-AGTATAGCCACTACTGTGTTTACAGTGTCACTGCCAGT
*
48499564 TCAGTATAGCATCGT
65 TCAGTATAGCATCGC
* * *
48499579 AGTGTTTATAGTGTCACTGCTAGTTCAGTATA
1 AGTGTTTATAGTGTCACTACTAATTTAGTATA
48499611 CTTCCGATGT
Statistics
Matches: 92, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
77 5 0.05
78 84 0.91
79 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (79 bp):
AGTGTTTATAGTGTCACTACTAATTTAGTATAGCCACTACTGTGTTTACAGTGTCACTGCCAGTT
CAGTATAGCATCGC
Found at i:48506249 original size:39 final size:39
Alignment explanation
Indices: 48506206--48506370 Score: 154
Period size: 39 Copynumber: 4.2 Consensus size: 39
48506196 TCACTACTGC
* *
48506206 TTTAGTATAGTATTGC-GATGTTTACAGTGTCACCGTCAG
1 TTTAGTATAGCATTGCAG-TGTTTACAGTGTCACCGCCAG
* * *
48506245 TTTAGTATAGCATTGTAGTGTTTATAGTGTCACTGCCAG
1 TTTAGTATAGCATTGCAGTGTTTACAGTGTCACCGCCAG
* * *
48506284 TTTGGTAT-GCCATTGCAGTGTTTACAGTGTCACTGCTAG
1 TTTAGTATAG-CATTGCAGTGTTTACAGTGTCACCGCCAG
* * * * * * *
48506323 TTCAATATAGCATCGTAGTGTTTATAGTGTCACTGCTAG
1 TTTAGTATAGCATTGCAGTGTTTACAGTGTCACCGCCAG
*
48506362 TTCAGTATA
1 TTTAGTATA
48506371 CTTACGATGT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.01
39 104 0.97
40 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.39
Consensus pattern (39 bp):
TTTAGTATAGCATTGCAGTGTTTACAGTGTCACCGCCAG
Found at i:48507680 original size:194 final size:191
Alignment explanation
Indices: 48507290--48507682 Score: 678
Period size: 194 Copynumber: 2.0 Consensus size: 191
48507280 ACTTAGCAGT
*
48507290 AATAAAAAACAGACAACTCCCCGATGGTATTTCTAATCACTTGAGCAAAACAATTTCTCCAATTT
1 AATAAAAAACAGACAACTCCCCGATGGTATTTCTAATCACTCGAGCAAAACAATTTCTCCAATTT
* *
48507355 AGACACAATCCATCGCATTAAAATGAAAAAAGAGGAAAAAAATGAAAAAGAAGAAGACGAAGGGC
66 AGACACAATCCACCGCATTAAAACGAAAAAAGAGGAAAAAAATGAAAAAGAAGAAGACGAAGGGC
48507420 ATTCTTCAACCTTTAAAATAAACTATTTAAGTGCATAACTTCCATTTAACGAAGAGGAGAA
131 ATTCTTCAACCTTTAAAATAAACTATTTAAGTGCATAACTTCCATTTAACGAAGAGGAGAA
*
48507481 AATAAAAAATAGACAACTCCCCGATGGTATTTCTAATCACTCGAGCAAAACAATTTCTCCAATTT
1 AATAAAAAACAGACAACTCCCCGATGGTATTTCTAATCACTCGAGCAAAACAATTTCTCCAATTT
* * *
48507546 AGACATAATCCACCTCATTAAAACGCAAAAAGAGGAAAAATAAAATGAAAAAGAAGAAGACGAAG
66 AGACACAATCCACCGCATTAAAACGAAAAAAGAGG--AAA-AAAATGAAAAAGAAGAAGACGAAG
* *
48507611 GGCGTTCTTCAACCTTTAAAATAAACTATTTAAGTGCATAACTTCTATTTAACGAAGAGGAGAA
128 GGCATTCTTCAACCTTTAAAATAAACTATTTAAGTGCATAACTTCCATTTAACGAAGAGGAGAA
48507675 AATAAAAA
1 AATAAAAA
48507683 TATATACTTC
Statistics
Matches: 190, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
191 93 0.49
193 3 0.02
194 94 0.49
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.23
Consensus pattern (191 bp):
AATAAAAAACAGACAACTCCCCGATGGTATTTCTAATCACTCGAGCAAAACAATTTCTCCAATTT
AGACACAATCCACCGCATTAAAACGAAAAAAGAGGAAAAAAATGAAAAAGAAGAAGACGAAGGGC
ATTCTTCAACCTTTAAAATAAACTATTTAAGTGCATAACTTCCATTTAACGAAGAGGAGAA
Found at i:48517172 original size:26 final size:27
Alignment explanation
Indices: 48517119--48517173 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
48517109 TGTTTTTTGA
* *
48517119 TAAAATTTAAATTATTGAATTTTTTAT
1 TAAAATTTAAATTATTAAATTTTCTAT
48517146 TAAAA-TTAAA-TATTAAATATTTCTAT
1 TAAAATTTAAATTATTAAAT-TTTCTAT
48517172 TA
1 TA
48517174 CCAAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.28
26 13 0.52
27 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (27 bp):
TAAAATTTAAATTATTAAATTTTCTAT
Found at i:48519441 original size:21 final size:21
Alignment explanation
Indices: 48519403--48519444 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48519393 GAGCTTTGAA
**
48519403 TTTTGTTCTCCATGATGCTTC
1 TTTTGTTCTCCAACATGCTTC
*
48519424 TTTTGTTCTCGAACATGCTTC
1 TTTTGTTCTCCAACATGCTTC
48519445 CCAACTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.24, G:0.14, T:0.50
Consensus pattern (21 bp):
TTTTGTTCTCCAACATGCTTC
Found at i:48521891 original size:16 final size:18
Alignment explanation
Indices: 48521859--48521892 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48521849 TTTTTATTAC
48521859 GATCAATCGTGAAATTTT
1 GATCAATCGTGAAATTTT
48521877 GATCAATC-T-AAATTTT
1 GATCAATCGTGAAATTTT
48521893 TAAATTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (18 bp):
GATCAATCGTGAAATTTT
Found at i:48522192 original size:19 final size:20
Alignment explanation
Indices: 48522165--48522202 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
48522155 TACCAAAAAA
*
48522165 TAAATTTTTAACT-TTTGAT
1 TAAACTTTTAACTATTTGAT
*
48522184 TAAACTTTTTACTATTTGA
1 TAAACTTTTAACTATTTGA
48522203 AACTTCGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (20 bp):
TAAACTTTTAACTATTTGAT
Found at i:48525653 original size:29 final size:29
Alignment explanation
Indices: 48525596--48525841 Score: 184
Period size: 30 Copynumber: 8.5 Consensus size: 29
48525586 ACTCTTCTTG
* *
48525596 AATTACATTTTAACCTCTGAACTTCTCCAA
1 AATTACATTTTAA-CTCTAAACTTTTCCAA
* *
48525626 AATTGCATTTTAACTTTAAACTTTTCCAA
1 AATTACATTTTAACTCTAAACTTTTCCAA
*
48525655 AATTACATTTTAACCCTAAAC-TTTCCAA
1 AATTACATTTTAACTCTAAACTTTTCCAA
* * * *
48525683 AATTACATTTTGATCCCTCAAC-TTTCTTAA
1 AATTACATTTT-AACTCTAAACTTTTC-CAA
* *
48525713 AATTACATTTTGACCTCTAAATTTTTCC--
1 AATTACATTTT-AACTCTAAACTTTTCCAA
* **
48525741 --TTACATTTTAACCTCTAAACTTTTTCGT
1 AATTACATTTTAA-CTCTAAACTTTTCCAA
* * * *
48525769 AATCACATTTTAACCCCTACAC-TTTCCCA
1 AATTACATTTTAA-CTCTAAACTTTTCCAA
* *
48525798 AATTATCATTTTGAC-CTTAAATTTTTCCAA
1 AATTA-CATTTTAACTC-TAAACTTTTCCAA
48525828 AATTACATTTTAAC
1 AATTACATTTTAAC
48525842 CCCAAAATTC
Statistics
Matches: 175, Mismatches: 30, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.01
26 21 0.12
28 19 0.11
29 63 0.36
30 67 0.38
31 4 0.02
ACGTcount: A:0.33, C:0.23, G:0.02, T:0.42
Consensus pattern (29 bp):
AATTACATTTTAACTCTAAACTTTTCCAA
Found at i:48525794 original size:86 final size:83
Alignment explanation
Indices: 48525600--48525843 Score: 215
Period size: 86 Copynumber: 2.8 Consensus size: 83
48525590 TTCTTGAATT
* * * * * *
48525600 ACATTTTAACCTCTGAACTTCTCCAAAATT-GCATTTTAACTTTAAACTTTTCCAAAATTACATT
1 ACATTTTAACCCCTCAACTT-TCCAAAATTATCATTTTGACCTTAAATTTTTCC----TTACATT
*
48525664 TTAACCCTAAACTTTCCAAAATT
61 TTAACCCTAAACTTTCCAAAATC
* * *
48525687 ACATTTTGATCCCTCAACTTTCTTAAAATTA-CATTTTGACCTCTAAATTTTTCCTTACATTTTA
1 ACATTTTAACCCCTCAACTTTC-CAAAATTATCATTTTGACCT-TAAATTTTTCCTTACATTTTA
* **
48525751 ACCTCTAAACTTTTTCGTAATC
64 ACC-CTAAAC-TTTCCAAAATC
*
48525773 ACATTTTAACCCCT-ACACTTTCCCAAATTATCATTTTGACCTTAAATTTTTCCAAAATTACATT
1 ACATTTTAACCCCTCA-ACTTTCCAAAATTATCATTTTGACCTTAAATTTTTCC----TTACATT
48525837 TTAACCC
61 TTAACCC
48525844 CAAAATTCTA
Statistics
Matches: 130, Mismatches: 16, Indels: 21
0.78 0.10 0.13
Matches are distributed among these distances:
84 13 0.10
85 24 0.18
86 38 0.29
87 31 0.24
88 11 0.08
89 13 0.10
ACGTcount: A:0.32, C:0.24, G:0.02, T:0.41
Consensus pattern (83 bp):
ACATTTTAACCCCTCAACTTTCCAAAATTATCATTTTGACCTTAAATTTTTCCTTACATTTTAAC
CCTAAACTTTCCAAAATC
Found at i:48525830 original size:115 final size:112
Alignment explanation
Indices: 48525631--48525838 Score: 267
Period size: 114 Copynumber: 1.8 Consensus size: 112
48525621 TCCAAAATTG
* *
48525631 CATTTTAACTTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
1 CATTTTAACTCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
*
48525696 TCCCTCAACTTTCTTAAAATTACATTTTGACCTCTAAATTTTTCCTTA
66 -CCCTCAAATTTCTTAAAATTACATTTTGACCTCTAAATTTTTCCTTA
* ** * *
48525744 CATTTTAACCTCTAAACTTTTTCGTAATCACATTTTAACCCCTACACTTTCCCAAATTATCATTT
1 CATTTTAA-CTCTAAACTTTTCCAAAATCACATTTTAA-CCCTAAACTTTCCAAAATTA-CATTT
*
48525809 TGA-CCTTAAATTT-TTCCAAAATTACATTTT
63 TGACCCTCAAATTTCTT--AAAATTACATTTT
48525839 AACCCCAAAA
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
113 10 0.12
114 32 0.40
115 31 0.38
116 8 0.10
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (112 bp):
CATTTTAACTCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
CCCTCAAATTTCTTAAAATTACATTTTGACCTCTAAATTTTTCCTTA
Found at i:48525850 original size:115 final size:112
Alignment explanation
Indices: 48525631--48525850 Score: 264
Period size: 115 Copynumber: 1.9 Consensus size: 112
48525621 TCCAAAATTG
* *
48525631 CATTTTAACTTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
1 CATTTTAACTCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
* * * *
48525696 TCCCTCAACTTTCTTAAAATTACATTTTGACCTCTAAATTTTTCCTTA
66 -CCCTCAAATTTCTTAAAATTACATTTTAACCCCAAAATTTTTCCTTA
* ** * *
48525744 CATTTTAACCTCTAAACTTTTTCGTAATCACATTTTAACCCCTACACTTTCCCAAATTATCATTT
1 CATTTTAA-CTCTAAACTTTTCCAAAATCACATTTTAA-CCCTAAACTTTCCAAAATTA-CATTT
*
48525809 TGA-CCTTAAATTT-TTCCAAAATTACATTTTAACCCCAAAATT
63 TGACCCTCAAATTTCTT--AAAATTACATTTTAACCCCAAAATT
48525851 CTAAAAAAAT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
113 10 0.11
114 32 0.36
115 40 0.44
116 8 0.09
ACGTcount: A:0.33, C:0.24, G:0.02, T:0.42
Consensus pattern (112 bp):
CATTTTAACTCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTCCAAAATTACATTTTGA
CCCTCAAATTTCTTAAAATTACATTTTAACCCCAAAATTTTTCCTTA
Found at i:48531986 original size:16 final size:16
Alignment explanation
Indices: 48531962--48531998 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
48531952 AATAGTTTTT
*
48531962 AAATATATATGGTTTG
1 AAATATATATGCTTTG
*
48531978 AAATTTATATGCTTTG
1 AAATATATATGCTTTG
48531994 AAATA
1 AAATA
48531999 AAATTAGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (16 bp):
AAATATATATGCTTTG
Found at i:48534433 original size:15 final size:16
Alignment explanation
Indices: 48534413--48534442 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
48534403 GAACAATTAC
48534413 CATTAATTAT-TAAAA
1 CATTAATTATATAAAA
48534428 CATTAATTATATAAA
1 CATTAATTATATAAA
48534443 TAAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (16 bp):
CATTAATTATATAAAA
Found at i:48536863 original size:5 final size:5
Alignment explanation
Indices: 48536855--48536920 Score: 62
Period size: 5 Copynumber: 12.8 Consensus size: 5
48536845 TAAATTTGAT
* * * *
48536855 TAAAA TAAAA -ATAAT TAAAA TCAAAA TAGTAG TAAAA TAAAC TAAAA
1 TAAAA TAAAA TA-AAA TAAAA T-AAAA TA-AAA TAAAA TAAAA TAAAA
48536902 TAAAA TAAAA TAAAA TAAA
1 TAAAA TAAAA TAAAA TAAA
48536921 TCGGTGTGAC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
4 1 0.02
5 39 0.80
6 9 0.18
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:48538602 original size:44 final size:46
Alignment explanation
Indices: 48538547--48538657 Score: 136
Period size: 49 Copynumber: 2.3 Consensus size: 46
48538537 TGATAAACTT
* *
48538547 TTTATTTTATTTTATTGAT-AATTTCAAGAGTATTCATCTAATT-A
1 TTTATTTTATTTTATTGATAAATTTCAAGAATATTCACCTAATTGA
*
48538591 TTTATTTTATTTTATTCATTGATAAATTTCAAGAATATTCACCTAATTGT
1 TTTATTTTA--TT-TT-ATTGATAAATTTCAAGAATATTCACCTAATTGA
48538641 TTTATTTTTATTTTATT
1 TTTA-TTTTATTTTATT
48538658 TCGGTCACTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
44 9 0.16
46 2 0.04
47 5 0.09
48 8 0.14
49 24 0.42
50 4 0.07
51 5 0.09
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (46 bp):
TTTATTTTATTTTATTGATAAATTTCAAGAATATTCACCTAATTGA
Found at i:48548913 original size:29 final size:29
Alignment explanation
Indices: 48548816--48549037 Score: 209
Period size: 30 Copynumber: 7.4 Consensus size: 29
48548806 TAAAAAAACC
* *
48548816 CATTTTGACCCTCGAACTTCTCCAAAATTA
1 CATTTTAACCC-CAAACTTCTCCAAAATTA
*
48548846 CATTTTAACCCTCAAACTTTTCCATAAATTA
1 CATTTTAACCC-CAAACTTCTCCA-AAATTA
** * *
48548877 CATTTTAACCTTAAACTTTTCTAAAATTA
1 CATTTTAACCCCAAACTTCTCCAAAATTA
*
48548906 CATTTTAACCCCTAAACTTTTCCAAAATTA
1 CATTTTAACCCC-AAACTTCTCCAAAATTA
* *
48548936 CATTTTGACACCCAAACTTCTCTAAAATCT-
1 CATTTTAAC-CCCAAACTTCTCCAAAAT-TA
48548966 CATTTTAACCCCAAACTTCTCCAAAATTAA
1 CATTTTAACCCCAAACTTCTCCAAAATT-A
* *
48548996 GATTTT-ACCCTCGAA-TATC-CCAAAATTA
1 CATTTTAACCC-CAAACT-TCTCCAAAATTA
*
48549024 CCATTTTACCCCCA
1 -CATTTTAACCCCA
48549038 TATATCTAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 21
0.80 0.09 0.10
Matches are distributed among these distances:
28 2 0.01
29 52 0.32
30 89 0.55
31 20 0.12
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
CATTTTAACCCCAAACTTCTCCAAAATTA
Found at i:48549001 original size:60 final size:60
Alignment explanation
Indices: 48548816--48548994 Score: 242
Period size: 60 Copynumber: 3.0 Consensus size: 60
48548806 TAAAAAAACC
* *
48548816 CATTTTGAC-CCTCGAACTTCTCCAAAATTACATTTTAACCCTCAAACTTTTCCATAAATTA
1 CATTTTGACACCTCAAACTTCTCTAAAATTACATTTTAACCC-CAAACTTTTCCA-AAATTA
* *
48548877 CATTTT-A-ACCTTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTA
1 CATTTTGACACCTCAAACTTCTCTAAAATTACATTTTAACCCC-AAACTTTTCCAAAATTA
*
48548936 CATTTTGACACC-CAAACTTCTCTAAAATCT-CATTTTAACCCCAAACTTCTCCAAAATTA
1 CATTTTGACACCTCAAACTTCTCTAAAAT-TACATTTTAACCCCAAACTTTTCCAAAATTA
48548995 AGATTTTACC
Statistics
Matches: 106, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
59 29 0.27
60 67 0.63
61 10 0.09
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (60 bp):
CATTTTGACACCTCAAACTTCTCTAAAATTACATTTTAACCCCAAACTTTTCCAAAATTA
Found at i:48549042 original size:29 final size:28
Alignment explanation
Indices: 48548985--48549067 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 28
48548975 CCCAAACTTC
** *
48548985 TCCAAAATTAAGATTTTACCCTCGAATA
1 TCCAAAATTACCATTTTACCCTCCAATA
48549013 TCCCAAAATTACCATTTTACCC-CCATATA
1 T-CCAAAATTACCATTTTACCCTCCA-ATA
*
48549042 TCTAAAAGTTACCATTTTA-CCTCCAA
1 TCCAAAA-TTACCATTTTACCCTCCAA
48549068 ATTTCCTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
28 11 0.23
29 36 0.77
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCTCCAATA
Found at i:48552200 original size:9 final size:9
Alignment explanation
Indices: 48552186--48552217 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
48552176 ACAAAGTTGA
48552186 AGAAGACTT
1 AGAAGACTT
48552195 AGAAGACTT
1 AGAAGACTT
48552204 AGAAGACTT
1 AGAAGACTT
48552213 -GAAGA
1 AGAAGA
48552218 AGGTTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.47, C:0.09, G:0.25, T:0.19
Consensus pattern (9 bp):
AGAAGACTT
Found at i:48560383 original size:36 final size:36
Alignment explanation
Indices: 48560332--48560402 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
48560322 AAAAATGGCA
*
48560332 TCGTTTTGAGGGCTGAGTTTCAGACCCAAAACAACG
1 TCGTTTTGAGAGCTGAGTTTCAGACCCAAAACAACG
*
48560368 TCGTTTTGAGAGCTGAGTTTCATACCCAAAACAAC
1 TCGTTTTGAGAGCTGAGTTTCAGACCCAAAACAAC
48560403 ATCATTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (36 bp):
TCGTTTTGAGAGCTGAGTTTCAGACCCAAAACAACG
Found at i:48561031 original size:30 final size:30
Alignment explanation
Indices: 48560829--48561024 Score: 245
Period size: 30 Copynumber: 6.6 Consensus size: 30
48560819 ATTTTGACCT
*
48560829 TAAACTTCTCCAAAATTACATTTTGACCCC
1 TAAACTTCTCCAAAATTACATTTTAACCCC
*
48560859 T-AACTTCTCTAAAATTACATTTTAACCCC
1 TAAACTTCTCCAAAATTACATTTTAACCCC
*
48560888 TAAACTTCTACAAAATTACATTTTAACCCC
1 TAAACTTCTCCAAAATTACATTTTAACCCC
* *
48560918 TAAA-TGTCTCTAAAAATACATTTTAACCCC
1 TAAACT-TCTCCAAAATTACATTTTAACCCC
* * *
48560948 TAAACATCTCCAAAATTATATTTTAACCCT
1 TAAACTTCTCCAAAATTACATTTTAACCCC
* * **
48560978 TAAAGTTCACCAAAATCCCATTTTAACCCC
1 TAAACTTCTCCAAAATTACATTTTAACCCC
*
48561008 -AAACTTCTCTAAAATTA
1 TAAACTTCTCCAAAATTA
48561025 TGATTTTGCC
Statistics
Matches: 139, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
29 40 0.29
30 99 0.71
ACGTcount: A:0.38, C:0.27, G:0.02, T:0.34
Consensus pattern (30 bp):
TAAACTTCTCCAAAATTACATTTTAACCCC
Found at i:48561051 original size:28 final size:28
Alignment explanation
Indices: 48561018--48561094 Score: 82
Period size: 30 Copynumber: 2.7 Consensus size: 28
48561008 AAACTTCTCT
*
48561018 AAAATTATGATTTTGCCCCGAACATCCA
1 AAAATTATCATTTTGCCCCGAACATCCA
* * * *
48561046 AAAATTACCATTTTTGCCCTTGAATATCTA
1 AAAATTATCA-TTTTGCCC-CGAACATCCA
*
48561076 AAAATTATCATTTTACCCC
1 AAAATTATCATTTTGCCCC
48561095 TAAGTTTCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 8 0.21
29 15 0.38
30 16 0.41
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.35
Consensus pattern (28 bp):
AAAATTATCATTTTGCCCCGAACATCCA
Found at i:48561147 original size:30 final size:30
Alignment explanation
Indices: 48561113--48561189 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
48561103 CAAAAATGAC
*
48561113 ATTTTCGA-CCTCAAATTTTCCAAAAGTTCA
1 ATTTT-GACCCTCAAATTTTCAAAAAGTTCA
* * *
48561143 ATTTTAATCC-CAAAGTTTTCAAAAATTTCA
1 ATTTTGACCCTCAAA-TTTTCAAAAAGTTCA
48561173 ATTTTGACCCTCAAATT
1 ATTTTGACCCTCAAATT
48561190 CCTCAAAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.13
30 30 0.77
31 4 0.10
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (30 bp):
ATTTTGACCCTCAAATTTTCAAAAAGTTCA
Found at i:48561948 original size:320 final size:322
Alignment explanation
Indices: 48561364--48561948 Score: 677
Period size: 321 Copynumber: 1.8 Consensus size: 322
48561354 TTTAAAATCG
* * *
48561364 AGGCAATATCATTTTCGTGTGGAAATCTCAAAAAATCATGCCCTAACATGTTGGGTGTGATTTTT
1 AGGCAATATCATTTTCGTGTGAAAATCTCAAAAAACCATGCCCTAACATGCTGGGTGTGATTTTT
* * * * *
48561429 CATATAATCTGCATAATCAAATATCCTCTTCCAAACTTTTCAAATGCCCTTTAATTTCGAGATTC
66 CATATAATCTGCATAATCAAATATCCTCTTCAAAACTTTTAAAATACCCTTCAATTTCGAAATTC
* * *
48561494 CGAGAACATCGTGCCCTAACATGTTGGACACAACTTCAATTCTCTGAGAAATTCAAAACATATAG
131 CGAGAACATCGTGCCATAACATGTTGGACACAACTTCAATTCTCCGAGAAATTCAAAACATAGAG
* * * * * * *
48561559 GCATTCTTCTTCAAATCTAATTTTTGAAAATCACGAGAAATAAGTTATGTGTCCGAGGATATTAT
196 ACATTCTTCTTCAAATATAATTTTTGAAAATCACGAGAAATAAGTTATGAGTACAAAGATATCAT
48561624 TTTAAGCTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAATAAAAACA
261 TTTAAGCTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAATAAAAACA
* **
48561686 AGGCAATATCCTTTT-GTGTGAAAA-CTTCGAAAAAACCATGCCCTAATGTGCTGGGTGT-A-TT
1 AGGCAATATCATTTTCGTGTGAAAATC-TC-AAAAAACCATGCCCTAACATGCTGGGTGTGATTT
* * * * * * *
48561747 TTCGTATAAT-TCGCGTGATCGAATATCCTCTTCAAAATTTTTTAAAATATCCTTCAATTTTGAA
64 TTCATATAATCT-GCATAATCAAATATCCTCTTCAAAA-CTTTTAAAATACCCTTCAATTTCGAA
* * * *
48561811 ATTCCGAGAACATCGTGCCATAACGTGTTGGACACGACTTCAATTCTCCGATAAATTCGAAAC-T
127 ATTCCGAGAACATCGTGCCATAACATGTTGGACACAACTTCAATTCTCCGAGAAATTCAAAACAT
* * * * * * *
48561875 CACGA-ACGTTTTTC-TCAAATATGATTTTTGAAAATTATGCGAAGAT-ATTTATGAGTACAAAG
192 -A-GAGACATTCTTCTTCAAATATAATTTTTGAAAATCACGAGAA-ATAAGTTATGAGTACAAAG
48561937 ATCA-CATTTTAA
254 AT-ATCATTTTAA
48561949 ATTTCGTTCG
Statistics
Matches: 216, Mismatches: 39, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
319 1 0.00
320 78 0.36
321 97 0.45
322 40 0.19
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (322 bp):
AGGCAATATCATTTTCGTGTGAAAATCTCAAAAAACCATGCCCTAACATGCTGGGTGTGATTTTT
CATATAATCTGCATAATCAAATATCCTCTTCAAAACTTTTAAAATACCCTTCAATTTCGAAATTC
CGAGAACATCGTGCCATAACATGTTGGACACAACTTCAATTCTCCGAGAAATTCAAAACATAGAG
ACATTCTTCTTCAAATATAATTTTTGAAAATCACGAGAAATAAGTTATGAGTACAAAGATATCAT
TTTAAGCTTAATTCAAAATTTCAAGTTCTCAAAAAATATACAAATAATTTTAAATAAAAACA
Found at i:48563004 original size:8 final size:8
Alignment explanation
Indices: 48562991--48563021 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
48562981 CTAGAAAATC
48562991 ATCCCTCA
1 ATCCCTCA
48562999 ATCCCTCA
1 ATCCCTCA
48563007 ATCCCTC-
1 ATCCCTCA
48563014 ATCCCTCA
1 ATCCCTCA
48563022 TTGTATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.23, C:0.52, G:0.00, T:0.26
Consensus pattern (8 bp):
ATCCCTCA
Found at i:48563012 original size:16 final size:15
Alignment explanation
Indices: 48562991--48563021 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
48562981 CTAGAAAATC
48562991 ATCCCTCAATCCCTCA
1 ATCCCTC-ATCCCTCA
48563007 ATCCCTCATCCCTCA
1 ATCCCTCATCCCTCA
48563022 TTGTATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.23, C:0.52, G:0.00, T:0.26
Consensus pattern (15 bp):
ATCCCTCATCCCTCA
Found at i:48566853 original size:18 final size:18
Alignment explanation
Indices: 48566794--48566888 Score: 62
Period size: 19 Copynumber: 5.5 Consensus size: 18
48566784 CAACCCATTG
48566794 TTTTT-TTTATTA-ATTTA
1 TTTTTATTT-TTATATTTA
* *
48566811 TTTTGATTATTTATATTTC
1 TTTTTATT-TTTATATTTA
* *
48566830 TATTTATTTTTATCTTTA
1 TTTTTATTTTTATATTTA
48566848 TTTTTA-TTTTA-A---A
1 TTTTTATTTTTATATTTA
48566861 TTTTTATTTATTA-ATATTA
1 TTTTTATTT-TTATAT-TTA
48566880 TTTTTATTT
1 TTTTTATTT
48566889 CTTTTTCAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
13 7 0.11
14 2 0.03
15 4 0.07
17 9 0.15
18 18 0.30
19 21 0.34
ACGTcount: A:0.24, C:0.02, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTTTATTTTTATATTTA
Found at i:48566886 original size:6 final size:6
Alignment explanation
Indices: 48566797--48566888 Score: 67
Period size: 6 Copynumber: 14.5 Consensus size: 6
48566787 CCCATTGTTT
* * * * *
48566797 TTTTTA TTAATTTA TTTTGA TTATTTA TATTTC TATTTA TTTTTA TCTTTA
1 TTTTTA TT--TTTA TTTTTA TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * *
48566848 TTTTTA TTTTAAA TTTTTA TTTATTA ATATTA TTTTTA TTT
1 TTTTTA TTTT-TA TTTTTA TTT-TTA TTTTTA TTTTTA TTT
48566889 CTTTTTCAGA
Statistics
Matches: 67, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
6 48 0.72
7 13 0.19
8 6 0.09
ACGTcount: A:0.25, C:0.02, G:0.01, T:0.72
Consensus pattern (6 bp):
TTTTTA
Found at i:48572267 original size:20 final size:20
Alignment explanation
Indices: 48572242--48572283 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
48572232 CGAAAGCTCC
48572242 AAAATAGCTAATATATTAAT
1 AAAATAGCTAATATATTAAT
48572262 AAAATAGCTAATATATTAAT
1 AAAATAGCTAATATATTAAT
48572282 AA
1 AA
48572284 CTTGTGATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AAAATAGCTAATATATTAAT
Found at i:48583173 original size:22 final size:21
Alignment explanation
Indices: 48583137--48583178 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
48583127 TATGCTTGGA
48583137 AGGAATTCAACTTGGTAGATAT
1 AGGAATTCAACTTGGT-GATAT
* *
48583159 AGGAATTCCATTTGGTGATA
1 AGGAATTCAACTTGGTGATA
48583179 ATCACAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AGGAATTCAACTTGGTGATAT
Found at i:48594478 original size:27 final size:25
Alignment explanation
Indices: 48594439--48594502 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
48594429 CAAATAAATT
* *
48594439 ATTTTTTGA-TAAAATTTAAATTATTGA
1 ATTTTTT-ATTAAAA-TTAAA-TACTAA
48594466 ATTTTTTATTAAAATTAAATACTAA
1 ATTTTTTATTAAAATTAAATACTAA
48594491 ATATTTTTATTA
1 AT-TTTTTATTA
48594503 CTAAAAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
25 6 0.18
26 15 0.45
27 12 0.36
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (25 bp):
ATTTTTTATTAAAATTAAATACTAA
Found at i:48595072 original size:23 final size:24
Alignment explanation
Indices: 48595042--48595113 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 24
48595032 TTATAAAAAT
*
48595042 ATTCAAAAAATA-AAAAATTTAAA
1 ATTCAAAAAATATAAAAATATAAA
48595065 ATTCAAAAAATATAAAAATATAAAA
1 ATTCAAAAAATATAAAAATAT-AAA
* *
48595090 AATCATAAAATTAATAAAAATATA
1 ATTCA-AAAAAT-ATAAAAATATA
48595114 GCACGAAGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 12 0.29
24 7 0.17
25 7 0.17
26 6 0.14
27 10 0.24
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.26
Consensus pattern (24 bp):
ATTCAAAAAATATAAAAATATAAA
Found at i:48595082 original size:17 final size:16
Alignment explanation
Indices: 48595036--48595113 Score: 61
Period size: 17 Copynumber: 4.6 Consensus size: 16
48595026 TAAATTTTAT
*
48595036 AAAAATATTCAAAAAATA
1 AAAAATA-T-AAAAATTA
*
48595054 AAAAAT-TTAAAATTCA
1 AAAAATATAAAAATT-A
48595070 AAAAATATAAAAATATA
1 AAAAATATAAAAAT-TA
48595087 AAAAATCAT-AAAATTAA
1 AAAAAT-ATAAAAATT-A
48595104 TAAAAATATA
1 -AAAAATATA
48595114 GCACGAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
15 5 0.10
16 9 0.18
17 21 0.42
18 15 0.30
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATATAAAAATTA
Found at i:48595097 original size:18 final size:18
Alignment explanation
Indices: 48595036--48595113 Score: 60
Period size: 18 Copynumber: 4.5 Consensus size: 18
48595026 TAAATTTTAT
*
48595036 AAAAATATTCAAAA-AATA
1 AAAAATA-TAAAAATAATA
*
48595054 AAAAAT-TTAAAAT--TCA
1 AAAAATATAAAAATAAT-A
48595070 AAAAATATAAAAAT-ATA
1 AAAAATATAAAAATAATA
*
48595087 AAAAATCATAAAATTAAT-
1 AAAAAT-ATAAAAATAATA
48595105 AAAAATATA
1 AAAAATATA
48595114 GCACGAAGTA
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
15 1 0.02
16 12 0.24
17 16 0.31
18 20 0.39
19 2 0.04
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATATAAAAATAATA
Found at i:48595099 original size:9 final size:8
Alignment explanation
Indices: 48595033--48595113 Score: 58
Period size: 8 Copynumber: 9.5 Consensus size: 8
48595023 ATTTAAATTT
48595033 TATAAAAA
1 TATAAAAA
48595041 TATTCAAAAA
1 TA-T-AAAAA
48595051 -ATAAAAAA
1 TAT-AAAAA
* *
48595059 TTTAAAAT
1 TATAAAAA
48595067 TCA-AAAAA
1 T-ATAAAAA
48595075 TATAAAAA
1 TATAAAAA
48595083 TATAAAAAA
1 TAT-AAAAA
*
48595092 TCATAAAAT
1 T-ATAAAAA
48595101 TAATAAAAA
1 T-ATAAAAA
48595110 TATA
1 TATA
48595114 GCACGAAGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
7 1 0.02
8 29 0.50
9 21 0.36
10 7 0.12
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (8 bp):
TATAAAAA
Found at i:48599705 original size:44 final size:44
Alignment explanation
Indices: 48599642--48599729 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
48599632 AACAAATAGT
* *
48599642 GGAAATGATCACAGACACAGATTTGAGAATATGGAAGCAAAAAA
1 GGAAATGATCACAAACACAGATTTGAGAATATGAAAGCAAAAAA
* * *
48599686 GGAAATGATGAGAAACACAGATTTGAGAATTTGAAAGCAAAAAA
1 GGAAATGATCACAAACACAGATTTGAGAATATGAAAGCAAAAAA
48599730 CAAGTAGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.17
Consensus pattern (44 bp):
GGAAATGATCACAAACACAGATTTGAGAATATGAAAGCAAAAAA
Found at i:48600953 original size:43 final size:42
Alignment explanation
Indices: 48600890--48601203 Score: 369
Period size: 43 Copynumber: 7.3 Consensus size: 42
48600880 TTATGAGGAA
*
48600890 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTCACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CCAC
*
48600933 AAACGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTCCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTT-CCCAC
* * * *
48600976 AAACACCG-TCAAAGAACATGGTCTTTAGTGGCGCTTTTACAAC
1 AAACGCCGCT-AAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
* * * *
48601019 AAATGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTCGCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
* * * * *
48601062 AAACGCCGCTAAAGAACATGGTATTTAGCGACACTTTTCTCAT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
* * * *
48601105 AAATGCTGCTAAAGAACATGGTCTTTAGCGACGCTTTTACCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCAC
*
48601148 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTCCCTAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCC-AC
48601191 AAACGCCGCTAAA
1 AAACGCCGCTAAA
48601204 ATTAACAGAT
Statistics
Matches: 237, Mismatches: 29, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
42 6 0.03
43 226 0.95
44 5 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCAC
Found at i:48601124 original size:129 final size:128
Alignment explanation
Indices: 48600890--48601203 Score: 414
Period size: 129 Copynumber: 2.4 Consensus size: 128
48600880 TTATGAGGAA
*
48600890 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTCACCACAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTC-CCACAAACGCCGCTAAAGAACATGGT
* * * * * *
48600955 CTTTAGTGGCGCTTTCCCCACAAACACCGTCAAAGAACATGGTCTTTAGTGGCGCTTTTACAAC
65 ATTTAGCGACACTTTCCCCACAAACACCGTCAAAGAACATGGTCTTTAGCGACGCTTTTACAAC
* * * *
48601019 AAATGCCGCTAAAGAACATGGTCTTTAGTGGCGCTTTTCGCATAAACGCCGCTAAAGAACATGGT
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCCCACAAACGCCGCTAAAGAACATGGT
* * * ** * *
48601084 ATTTAGCGACACTTTTCTCATAAATGCTG-CTAAAGAACATGGTCTTTAGCGACGCTTTTACCAC
65 ATTTAGCGACACTTTCCCCACAAACACCGTC-AAAGAACATGGTCTTTAGCGACGCTTTTACAAC
*
48601148 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTCCCTACAAACGCCGCTAAA
1 AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCC-ACAAACGCCGCTAAA
48601204 ATTAACAGAT
Statistics
Matches: 159, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
128 6 0.04
129 149 0.94
130 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (128 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGAACATGGTA
TTTAGCGACACTTTCCCCACAAACACCGTCAAAGAACATGGTCTTTAGCGACGCTTTTACAAC
Found at i:48607067 original size:32 final size:32
Alignment explanation
Indices: 48607030--48607094 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
48607020 ATTTAAGTTT
48607030 AAAATATATATTAGTGACAACATTTTACTTAA
1 AAAATATATATTAGTGACAACATTTTACTTAA
48607062 AAAATATATATTAGTGACAACATTTTACTTAA
1 AAAATATATATTAGTGACAACATTTTACTTAA
48607094 A
1 A
48607095 TATTTGGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.37
Consensus pattern (32 bp):
AAAATATATATTAGTGACAACATTTTACTTAA
Found at i:48607184 original size:8 final size:8
Alignment explanation
Indices: 48607167--48607292 Score: 62
Period size: 8 Copynumber: 15.5 Consensus size: 8
48607157 TTATAATTAA
48607167 AAATAATT
1 AAATAATT
*
48607175 AAATATTT
1 AAATAATT
*
48607183 AATTAA--
1 AAATAATT
*
48607189 ATATAATT
1 AAATAATT
*
48607197 AAACAATT
1 AAATAATT
48607205 AAAT-ATT
1 AAATAATT
**
48607212 TTA-AATT
1 AAATAATT
48607219 AAATAATT
1 AAATAATT
48607227 AAATATAATT
1 -AA-ATAATT
**
48607237 ATTTAATT
1 AAATAATT
*
48607245 AAATATTTT
1 AAATA-ATT
*
48607254 AAATTAAAT
1 AAA-TAATT
**
48607263 ATTTAATT
1 AAATAATT
48607271 AAACATAATT
1 -AA-ATAATT
48607281 AAATAATT
1 AAATAATT
48607289 AAAT
1 AAAT
48607293 CTTTTAAATT
Statistics
Matches: 84, Mismatches: 24, Indels: 20
0.66 0.19 0.16
Matches are distributed among these distances:
6 4 0.05
7 8 0.10
8 46 0.55
9 13 0.15
10 13 0.15
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (8 bp):
AAATAATT
Found at i:48607205 original size:40 final size:40
Alignment explanation
Indices: 48607159--48607291 Score: 133
Period size: 40 Copynumber: 3.2 Consensus size: 40
48607149 GGTTGTTTTT
48607159 ATAATTAAAAATAATTAAATATTTAATTAAATATAATTAA
1 ATAATTAAAAATAATTAAATATTTAATTAAATATAATTAA
* * * ** *
48607199 ACAATTAAATAT-TTTAAATTAAATAATTAAATATAATTAT
1 ATAATTAAAAATAATTAAA-TATTTAATTAAATATAATTAA
* * *
48607239 TTAATTAAATATTTTAAATTAAATATTTAATTAAACATAATTAA
1 ATAATTAAA-A--AT-AATTAAATATTTAATTAAATATAATTAA
48607283 ATAATTAAA
1 ATAATTAAA
48607292 TCTTTTAAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
39 5 0.07
40 35 0.49
43 1 0.01
44 25 0.35
45 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (40 bp):
ATAATTAAAAATAATTAAATATTTAATTAAATATAATTAA
Found at i:48607206 original size:22 final size:22
Alignment explanation
Indices: 48607160--48607206 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
48607150 GTTGTTTTTA
* *
48607160 TAATTAAAAATAATTAAATATT
1 TAATTAAAAATAATTAAACAAT
*
48607182 TAATTAAATATAATTAAACAAT
1 TAATTAAAAATAATTAAACAAT
48607204 TAA
1 TAA
48607207 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TAATTAAAAATAATTAAACAAT
Found at i:48607221 original size:44 final size:44
Alignment explanation
Indices: 48607171--48607390 Score: 227
Period size: 44 Copynumber: 5.0 Consensus size: 44
48607161 AATTAAAAAT
*
48607171 AATTAAATATTTAATTAAATATAATTAAACAATTAAATATTTTA
1 AATTAAATATTTAATTAAATATAATTAAATAATTAAATATTTTA
**
48607215 AATT-AA-A--TAATTAAATATAATTATTTAATTAAATATTTTA
1 AATTAAATATTTAATTAAATATAATTAAATAATTAAATATTTTA
* *
48607255 AATTAAATATTTAATTAAACATAATTAAATAATTAAATCTTTTA
1 AATTAAATATTTAATTAAATATAATTAAATAATTAAATATTTTA
* * **
48607299 AATTAAATATTTAATTAACTGATACTGTTTATAATTAAATA-TTT-
1 AATTAAATATTTAATTAAAT-ATAAT-TAAATAATTAAATATTTTA
**
48607343 AATTAAACATAATTAAATAATTAAATATAATTATTTAATTAAATATTT
1 AATT-AA-AT-ATT---TAATTAAATATAATTAAATAATTAAATATTT
48607391 ATTCATCAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 21
0.79 0.09 0.11
Matches are distributed among these distances:
40 34 0.23
41 2 0.01
42 2 0.01
43 2 0.01
44 55 0.38
45 9 0.06
46 13 0.09
47 3 0.02
48 12 0.08
49 6 0.04
50 8 0.05
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (44 bp):
AATTAAATATTTAATTAAATATAATTAAATAATTAAATATTTTA
Found at i:48607242 original size:22 final size:22
Alignment explanation
Indices: 48607170--48607292 Score: 82
Period size: 22 Copynumber: 5.8 Consensus size: 22
48607160 TAATTAAAAA
* *
48607170 TAATTAAATATTTAATTA-AAT
1 TAATTAAATAATTAAATATAAT
* *
48607191 ATAATTAAACAATTAAATAT-TT
1 -TAATTAAATAATTAAATATAAT
48607213 TAAATTAAATAATTAAATATAAT
1 T-AATTAAATAATTAAATATAAT
*
48607236 T-ATT---TAATTAAATAT-TT
1 TAATTAAATAATTAAATATAAT
* * *
48607253 TAAATTAAATATTTAATTA-AACA
1 T-AATTAAATAATTAAATATAA-T
48607276 TAATTAAATAATTAAAT
1 TAATTAAATAATTAAAT
48607293 CTTTTAAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
17 2 0.03
18 11 0.14
19 3 0.04
21 4 0.05
22 55 0.71
23 3 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATTAAATAATTAAATATAAT
Found at i:48607243 original size:18 final size:18
Alignment explanation
Indices: 48607159--48607388 Score: 81
Period size: 18 Copynumber: 11.7 Consensus size: 18
48607149 GGTTGTTTTT
*
48607159 ATAATTAAAAATAATTAAA
1 ATAATTAAATATAATT-AA
48607178 TATTTAATTAAATATAATTAA
1 -A--TAATTAAATATAATTAA
*
48607199 ACAATTAAATATTTTAAATTAA
1 ATAATTAAATA---T-AATTAA
*
48607221 ATAATTAAATATAATTAT
1 ATAATTAAATATAATTAA
*
48607239 TTAATTAAATATTTTAAATTAAA
1 ATAATTAAATA---T-AATT-AA
*
48607262 TATTTAATTAAACATAATTAA
1 -A--TAATTAAATATAATTAA
* *
48607283 ATAATTAAATCT--TT-T
1 ATAATTAAATATAATTAA
48607298 A-AATTAAATATTTAATTAA
1 ATAATTAAATA--TAATTAA
* * ***
48607317 CTGATACTGTTTATAATTAAA
1 AT-A-ATTAAATATAATT-AA
*
48607338 TATTTAATTAAACATAATTAA
1 -A--TAATTAAATATAATTAA
*
48607359 ATAATTAAATATAATTAT
1 ATAATTAAATATAATTAA
*
48607377 TTAATTAAATAT
1 ATAATTAAATAT
48607389 TTATTCATCA
Statistics
Matches: 157, Mismatches: 27, Indels: 54
0.66 0.11 0.23
Matches are distributed among these distances:
14 8 0.05
15 1 0.01
16 3 0.02
18 61 0.39
19 1 0.01
20 9 0.06
21 11 0.07
22 50 0.32
23 3 0.02
24 1 0.01
26 9 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (18 bp):
ATAATTAAATATAATTAA
Found at i:48611182 original size:21 final size:21
Alignment explanation
Indices: 48611158--48611290 Score: 94
Period size: 21 Copynumber: 6.4 Consensus size: 21
48611148 TGATCGAAAC
*
48611158 ATACAAAGGCACCGAAGTGCA
1 ATACAAGGGCACCGAAGTGCA
*
48611179 ATACAGGGGCACC-AGAGTGCA
1 ATACAAGGGCACCGA-AGTGCA
* *
48611200 ATA-AAGGGCATCGGAGTGCA
1 ATACAAGGGCACCGAAGTGCA
* * *
48611220 ATACAGGGGAACC-ATAATGCA
1 ATACAAGGGCACCGA-AGTGCA
* * *
48611241 ATACAGGGGCATCGAATTGCA
1 ATACAAGGGCACCGAAGTGCA
* * *
48611262 ATACAGGGGCATC-AGAGTGTA
1 ATACAAGGGCACCGA-AGTGCA
48611283 ATACAAGG
1 ATACAAGG
48611291 TTTATCCATT
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
20 18 0.20
21 71 0.79
22 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (21 bp):
ATACAAGGGCACCGAAGTGCA
Found at i:48611216 original size:20 final size:20
Alignment explanation
Indices: 48611173--48611227 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
48611163 AAGGCACCGA
*
48611173 AGTGCAATACAGGGGCACCAG
1 AGTGCAATA-AAGGGCACCAG
* *
48611194 AGTGCAATAAAGGGCATCGG
1 AGTGCAATAAAGGGCACCAG
*
48611214 AGTGCAATACAGGG
1 AGTGCAATAAAGGG
48611228 GAACCATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 21 0.70
21 9 0.30
ACGTcount: A:0.35, C:0.18, G:0.35, T:0.13
Consensus pattern (20 bp):
AGTGCAATAAAGGGCACCAG
Found at i:48611218 original size:41 final size:42
Alignment explanation
Indices: 48611158--48611290 Score: 169
Period size: 42 Copynumber: 3.2 Consensus size: 42
48611148 TGATCGAAAC
* *
48611158 ATACAAAGGCACCGAAGTGCAATACAGGGGCACCAGAGTGCA
1 ATACAAGGGCATCGAAGTGCAATACAGGGGCACCAGAGTGCA
* * * *
48611200 ATA-AAGGGCATCGGAGTGCAATACAGGGGAACCATAATGCA
1 ATACAAGGGCATCGAAGTGCAATACAGGGGCACCAGAGTGCA
* * * *
48611241 ATACAGGGGCATCGAATTGCAATACAGGGGCATCAGAGTGTA
1 ATACAAGGGCATCGAAGTGCAATACAGGGGCACCAGAGTGCA
48611283 ATACAAGG
1 ATACAAGG
48611291 TTTATCCATT
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
41 35 0.47
42 40 0.53
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (42 bp):
ATACAAGGGCATCGAAGTGCAATACAGGGGCACCAGAGTGCA
Found at i:48613479 original size:15 final size:15
Alignment explanation
Indices: 48613459--48613507 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
48613449 GGTAGGATAT
48613459 GATATGATATGATCC
1 GATATGATATGATCC
* **
48613474 GATATGGTATGATTT
1 GATATGATATGATCC
48613489 GATATGATATGATCC
1 GATATGATATGATCC
48613504 GATA
1 GATA
48613508 CATCATGATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (15 bp):
GATATGATATGATCC
Found at i:48613492 original size:30 final size:30
Alignment explanation
Indices: 48613449--48613507 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
48613439 AAAGTATGGG
48613449 GGTAGGATATGATATGATATGATCCGATAT
1 GGTAGGATATGATATGATATGATCCGATAT
* *
48613479 GGTATGATTTGATATGATATGATCCGATA
1 GGTAGGATATGATATGATATGATCCGATA
48613508 CATCATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.25, T:0.36
Consensus pattern (30 bp):
GGTAGGATATGATATGATATGATCCGATAT
Found at i:48613520 original size:5 final size:5
Alignment explanation
Indices: 48613454--48613501 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
48613444 ATGGGGGTAG
** * *
48613454 GATAT GATAT GATAT GATCC GATAT GGTAT GATTT GATAT GATAT GAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GAT
48613502 CCGATACATC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.33, C:0.04, G:0.23, T:0.40
Consensus pattern (5 bp):
GATAT
Found at i:48613528 original size:30 final size:30
Alignment explanation
Indices: 48613454--48613529 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
48613444 ATGGGGGTAG
**
48613454 GATATGATATGATATGATCCGATATGGTAT
1 GATATGATATGATATGATCCGATATCATAT
*
48613484 GATTTGATATGATATGATCCGATA-CATCAT
1 GATATGATATGATATGATCCGATATCAT-AT
* *
48613514 GATATGAGAAGATATG
1 GATATGATATGATATG
48613530 TTTTGGTATG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 1 0.03
30 38 0.97
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (30 bp):
GATATGATATGATATGATCCGATATCATAT
Found at i:48614540 original size:26 final size:26
Alignment explanation
Indices: 48614511--48614561 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
48614501 AAATAAACAA
48614511 TTAATAAAATCAATTGGTCAAATCAG
1 TTAATAAAATCAATTGGTCAAATCAG
* * *
48614537 TTAATAGAATTAGTTGGTCAAATCA
1 TTAATAAAATCAATTGGTCAAATCA
48614562 ACCACTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (26 bp):
TTAATAAAATCAATTGGTCAAATCAG
Found at i:48621482 original size:29 final size:29
Alignment explanation
Indices: 48621449--48621516 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
48621439 CATGTCATAA
48621449 CAGAAACAAAACAATGCTGCAACAAGCAG
1 CAGAAACAAAACAATGCTGCAACAAGCAG
48621478 CAGAAACAAAACAATGCTGCAACAAGCAG
1 CAGAAACAAAACAATGCTGCAACAAGCAG
48621507 CAGAAACAAA
1 CAGAAACAAA
48621517 CCCAAAACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.54, C:0.24, G:0.16, T:0.06
Consensus pattern (29 bp):
CAGAAACAAAACAATGCTGCAACAAGCAG
Found at i:48624390 original size:22 final size:23
Alignment explanation
Indices: 48624354--48624413 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
48624344 CCCACTAGTA
48624354 CTGCTGTTGCCCACCA-GCTTCAAC
1 CTGCT-TTG-CCACCACGCTTCAAC
*
48624378 TTGCTTTGCCACCACTGGCTTCAAC
1 CTGCTTTGCCACCAC--GCTTCAAC
48624403 CTGCTTTGCCA
1 CTGCTTTGCCA
48624414 TCATCGCCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.19
23 3 0.10
24 4 0.13
25 18 0.58
ACGTcount: A:0.15, C:0.38, G:0.17, T:0.30
Consensus pattern (23 bp):
CTGCTTTGCCACCACGCTTCAAC
Found at i:48626060 original size:30 final size:30
Alignment explanation
Indices: 48626014--48626456 Score: 321
Period size: 30 Copynumber: 15.1 Consensus size: 30
48626004 AAAAATTATA
*
48626014 TTTTACCCCT-AAACTTTCAAAAATTCCAT
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
*
48626043 TTTTAACCCTAAAACTTTCAAAAATTACAT
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
* *
48626073 TTTTACCCCTAAAACTTCCAAAAATTCCA-
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
*
48626102 -TTTAACCCCAAAAC-TTCTAAAAATTCCA-
1 TTTTAACCCTAAAACTTTC-AAAAATTCCAT
*
48626130 -TTTGACCCTAAAACTTTCAAAAATT--AT
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
* * *
48626157 ATTTT-ACCCTCAAACTTCCAAAAAATCCAT
1 -TTTTAACCCTAAAACTTTCAAAAATTCCAT
* *
48626187 TTTTAACCCCAAAA-TTTCTAAAAATTACAT
1 TTTTAACCCTAAAACTTTC-AAAAATTCCAT
** *** *
48626217 TTTTCCCCCCCGAA-TTTCCAAAAATTCCAC
1 TTTTAACCCTAAAACTTT-CAAAAATTCCAT
* * * **
48626247 TTTTGA-CCTCGAAAC-TTCTAAAAACTATAT
1 TTTTAACCCT-AAAACTTTC-AAAAATTCCAT
* *
48626277 TTTTACCCCCAAAACTTTCAAAAATTCCA-
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
* * * * *
48626306 TTTTGACCCCAAAACTTCCAAAAATTACAA
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
* * *
48626336 TTTT-ACCCTTAAACTTCCAAAAATTCTAT
1 TTTTAACCCTAAAACTTTCAAAAATTCCAT
*
48626365 TTTTAACCCTAAAA-TTTCCAAAAATTACAT
1 TTTTAACCCTAAAACTTT-CAAAAATTCCAT
**
48626395 TTTT-ACCCTCGAA-TTTCCAAAAATTCCA-
1 TTTTAACCCTAAAACTTT-CAAAAATTCCAT
* * * *
48626423 TTTTAACCTTGAAACTGTAAAAAATTACCAT
1 TTTTAACCCTAAAACTTTCAAAAATT-CCAT
48626454 TTT
1 TTT
48626457 ACCCCAAATT
Statistics
Matches: 330, Mismatches: 61, Indels: 44
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.00
27 2 0.01
28 63 0.19
29 110 0.33
30 145 0.44
31 9 0.03
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
TTTTAACCCTAAAACTTTCAAAAATTCCAT
Found at i:48626455 original size:59 final size:60
Alignment explanation
Indices: 48625995--48626474 Score: 367
Period size: 59 Copynumber: 8.2 Consensus size: 60
48625985 GAAAGTCTCT
* * *
48625995 AAATTATCCAAAAATT--ATATTTT-ACCCCTAAACTTT-CAAAAATTCCATTTTTAACCCTA
1 AAATT-TCCAAAAATTCCAT-TTTTAACCCCAAAACTTTCCAAAAATTACATTTTT-ACCCTC
* * *
48626054 AAACTTT-CAAAAATTACATTTTT-ACCCCTAAAAC-TTCCAAAAATTCCA-TTTAACCC-C
1 AAA-TTTCCAAAAATTCCATTTTTAACCCC-AAAACTTTCCAAAAATTACATTTTTACCCTC
* * * * *
48626111 AAAACTTCTAAAAATTCCA--TTTGACCCTAAAACTTT-CAAAAATTATA-TTTTACCCTC
1 -AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTTACCCTC
* * * * *
48626168 AAACTTCCAAAAAATCCATTTTTAACCCCAAAA-TTTCTAAAAATTACATTTTTCCCCCCC
1 AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTT-ACCCTC
* * * * * * * * *
48626228 GAATTTCCAAAAATTCCACTTTTGACCTCGAAAC-TTCTAAAAACTATATTTTTACCCCC
1 AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTTACCCTC
* * *
48626287 AAAACTTT-CAAAAATTCCA-TTTTGACCCCAAAAC-TTCCAAAAATTACAATTTTACCCTT
1 -AAA-TTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTTACCCTC
* * *
48626346 AAACTTCCAAAAATTCTATTTTTAACCCTAAAA-TTTCCAAAAATTACATTTTTACCCTC
1 AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTTACCCTC
* *** * *
48626405 GAATTTCCAAAAATTCCA-TTTTAACCTTGAAACTGT-AAAAAATTACCA-TTTTACCC-C
1 AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTA-CATTTTTACCCTC
48626462 AAATTATCCAAAA
1 AAATT-TCCAAAA
48626475 TTTTGTTTTT
Statistics
Matches: 346, Mismatches: 51, Indels: 49
0.78 0.11 0.11
Matches are distributed among these distances:
56 40 0.12
57 19 0.05
58 92 0.27
59 113 0.33
60 79 0.23
61 3 0.01
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.34
Consensus pattern (60 bp):
AAATTTCCAAAAATTCCATTTTTAACCCCAAAACTTTCCAAAAATTACATTTTTACCCTC
Found at i:48626535 original size:30 final size:30
Alignment explanation
Indices: 48626001--48626537 Score: 165
Period size: 30 Copynumber: 18.4 Consensus size: 30
48625991 CTCTAAATTA
* * *
48626001 TCCAAAAATTA-TATTTTACCCCTAAACTT
1 TCCAAAAATTACCATTTTAACCCTGAACTT
*
48626030 T-CAAAAATT-CCATTTTTAACCCTAAAACTT
1 TCCAAAAATTACCA-TTTTAACCCT-GAACTT
* *
48626060 T-CAAAAATTA-CATTTTTACCCCTAAAAC-T
1 TCCAAAAATTACCA-TTTTAACCCT-GAACTT
**
48626089 TCCAAAAATT-CCA-TTTAACCCCAAAAC-T
1 TCCAAAAATTACCATTTTAA-CCCTGAACTT
* * *
48626117 TCTAAAAATT-CCA-TTTGACCCTAAAACTT
1 TCCAAAAATTACCATTTTAACCCT-GAACTT
* *
48626146 T-CAAAAATTA-TATTTT-ACCCTCAAAC-T
1 TCCAAAAATTACCATTTTAACCCT-GAACTT
* ** *
48626173 TCCAAAAAAT-CCATTTTTAACCCCAAAATT
1 TCCAAAAATTACCA-TTTTAACCCTGAACTT
* ** *
48626203 TCTAAAAATTA-CATTTTTCCCCCCCGAA-TT
1 TCCAAAAATTACCA-TTTT-AACCCTGAACTT
*
48626233 TCCAAAAATT-CCACTTTTGA-CCTCGAAAC-T
1 TCCAAAAATTACCA-TTTTAACCCT-G-AACTT
* * * * **
48626263 TCTAAAAACTA-TATTTTTACCCCCAAAACTT
1 TCCAAAAATTACCA-TTTTA-ACCCTGAACTT
* **
48626294 T-CAAAAATT-CCATTTTGACCCCAAAAC-T
1 TCCAAAAATTACCATTTT-AACCCTGAACTT
* *
48626322 TCCAAAAATTACAATTTT-ACCCTTAAAC-T
1 TCCAAAAATTACCATTTTAACCC-TGAACTT
* * *
48626351 TCCAAAAATT-CTATTTTTAACCCTAAAATT
1 TCCAAAAATTACCA-TTTTAACCCTGAACTT
*
48626381 TCCAAAAATTA-CATTTTTACCCTCGAA-TT
1 TCCAAAAATTACCATTTTAACCCT-GAACTT
* *
48626410 TCCAAAAATT-CCATTTTAACCTTGAAACTG
1 TCCAAAAATTACCATTTTAACCCTG-AACTT
* * *
48626440 T-AAAAAATTACCATTTT-ACCC-CAAATT
1 TCCAAAAATTACCATTTTAACCCTGAACTT
**** * **
48626467 ATCC-AAAATTTTGTTTTTGATCCC-GATTTT
1 -TCCAAAAATTACCATTTT-AACCCTGAACTT
*
48626497 TCTAAAAATTACCATTTTAACCCTGAACTT
1 TCCAAAAATTACCATTTTAACCCTGAACTT
*
48626527 TCCCAAAATTA
1 TCCAAAAATTA
48626538 TCGTTTGCAA
Statistics
Matches: 391, Mismatches: 71, Indels: 91
0.71 0.13 0.16
Matches are distributed among these distances:
27 8 0.02
28 84 0.21
29 121 0.31
30 168 0.43
31 8 0.02
32 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
TCCAAAAATTACCATTTTAACCCTGAACTT
Found at i:48634811 original size:22 final size:21
Alignment explanation
Indices: 48634758--48634831 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
48634748 ATTAATTTTT
*
48634758 TTTAAAAAATT-ATTAAAAT-
1 TTTAAAAAATTAATAAAAATA
**
48634777 TTTAGTAAA-TAATAAATAATA
1 TTTAAAAAATTAATAAA-AATA
*
48634798 TTTAAAAAATTAATAAAAACCA
1 TTTAAAAAATTAATAAAAA-TA
48634820 TTT-AAAAATTAA
1 TTTAAAAAATTAA
48634832 AGTCCAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
18 1 0.02
19 11 0.25
20 3 0.07
21 18 0.41
22 11 0.25
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.36
Consensus pattern (21 bp):
TTTAAAAAATTAATAAAAATA
Found at i:48635774 original size:22 final size:21
Alignment explanation
Indices: 48635738--48635779 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
48635728 GATGTTTGGA
48635738 AGGAATTCAACTTGGTAGATAT
1 AGGAATTCAACTTGGT-GATAT
* *
48635760 AGGAATTCCATTTGGTGATA
1 AGGAATTCAACTTGGTGATA
48635780 ATCACAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AGGAATTCAACTTGGTGATAT
Found at i:48644061 original size:517 final size:517
Alignment explanation
Indices: 48643088--48644191 Score: 1851
Period size: 517 Copynumber: 2.1 Consensus size: 517
48643078 TAGGTTTCTT
* * *
48643088 TACCTCAGC-AATTTCTTCTTCTTGGGCAAAACCAATTACTTGCTCTA-GTCCATCGCAG-TCTT
1 TACCTCA-CTAATTTCTTCTTCTTGGGTAAAACCAATGACGTGCTCTAGGT-CATCGCAGTTC-T
*
48643150 CTATGTAGAGTTCTTCTATATTCAACATACTTTGAGCAACACGAATTGAGAACATTGTTTTCAAT
63 CTATGGAGAGTTCTTCTATATTCAACATACTTTGAGCAACACGAATTGAGAACATTGTTTTCAAT
*
48643215 TTATTGCATTTCGAAATATAAACCCTCTTTAGACTTTGGAGGATTGCAATTGCACGATGTGATGG
128 TTATTGCATTTCGAAATATAAACCCTCTTTAGACTTTGGAGGATTGCAATTGCACGATGGGATGG
*
48643280 CTCTACTTTTTCCATGTTGAAGACTTGAACAAGTTCAGGACAGTTTCCTATGTCAAGATGTTCCA
193 CTCTACTTTTTCCATGTTGAAGACTTCAACAAGTTCAGGACAGTTTCCTATGTCAAGATGTTCCA
* *
48643345 AGAATTGTAGCCATTTTGGATACACATATTTCAAGCTTCTGCAATCTTTGATCTCAAGAGTTTTC
258 AGAATTGAAGCCATTTTGGATACACATATTTCAAGCTTCTGCAATCTTTGATCTCAAGAATTTTC
48643410 AGCTTGGGCCAGCAAGAAAGAGGATAACCATTCTGCATATTTCAAACACACATCATAGTGAGATA
323 AGCTTGGGCCAGCAAGAAAGAGGATAACCATTCTGCATATTTCAAACACACATCATAGTGAGATA
* **
48643475 TGTATTTTTAACTTCTTTTCTTTTAATATTACCAAAAAAAAAAAGCGTCTTTCTCGGCCCAAAAA
388 TGTATTTTTAACTTCTTTTCTTTTAATATTACAAAAAAAAAAAAGCGTCTTTCTCAACCCAAAAA
* *
48643540 AACTGAAAGCATAAAGCCAAGAACATTTAAGAACATTAAAAAGAAAAAGGGGAAGAACAAGTACA
453 AACTGAAAGCATAAAGCCAAAAACAGTTAAGAACATTAAAAAGAAAAAGGGGAAGAACAAGTACA
*
48643605 TACCTCACTAATTCCTTCTTCTTGGGTAAAACCAATGACGTGCTCTAGGTCATCGCAGTTCTCTA
1 TACCTCACTAATTTCTTCTTCTTGGGTAAAACCAATGACGTGCTCTAGGTCATCGCAGTTCTCTA
* *
48643670 TGCGA-AGTTCTTCTATATTCAACATACTTTGAGCAACGCGAGTTGAGAACATTGTTTTCAATTT
66 TG-GAGAGTTCTTCTATATTCAACATACTTTGAGCAACACGAATTGAGAACATTGTTTTCAATTT
* * ** *
48643734 ATTGCATTTTGAAATATGAACTTTCTTTAGACTTTGGAGGCTTGCAATTGCACGATGGGATGGCT
130 ATTGCATTTCGAAATATAAACCCTCTTTAGACTTTGGAGGATTGCAATTGCACGATGGGATGGCT
*
48643799 CTACTTTTTCCATGTTGAAGACTTCAACAAGTTCAGGACAGTTTCTTAT-TACAAGATGTTCCAA
195 CTACTTTTTCCATGTTGAAGACTTCAACAAGTTCAGGACAGTTTCCTATGT-CAAGATGTTCCAA
48643863 GAATTGAAGCCATTTTGGATACACATATTTCAAGCTTCTGCAATCTTTGATCTCAAGAATTTTCA
259 GAATTGAAGCCATTTTGGATACACATATTTCAAGCTTCTGCAATCTTTGATCTCAAGAATTTTCA
*
48643928 GCTTGGGCCAGCAAGAAAGAGGATAATCATTCTGCATATTTCAAACACACATCATAGTGAGATAT
324 GCTTGGGCCAGCAAGAAAGAGGATAACCATTCTGCATATTTCAAACACACATCATAGTGAGATAT
48643993 GTATTTTTAACTTCTTTTCTTTTAATATTACAAAAAAAAAAAAGC-TCCTTTCTCAACCCAAAAA
389 GTATTTTTAACTTCTTTTCTTTTAATATTACAAAAAAAAAAAAGCGT-CTTTCTCAACCCAAAAA
* *
48644057 AACTGAAAGCATAAAGCCAAAAATAGTTAAGAACATTAAAAAGGAAAAGGGGAAGAACAAGTACA
453 AACTGAAAGCATAAAGCCAAAAACAGTTAAGAACATTAAAAAGAAAAAGGGGAAGAACAAGTACA
*
48644122 TACCTCACTAATTTCTTCTTCTTGGGTAAAACCAATGACGTGCAGTTCTAGGTCATTGCAGTTCT
1 TACCTCACTAATTTCTTCTTCTTGGGTAAAACCAATGACGTGC---TCTAGGTCATCGCAGTTCT
48644187 CTATG
63 CTATG
48644192 TAAAGGCTTT
Statistics
Matches: 551, Mismatches: 27, Indels: 15
0.93 0.05 0.03
Matches are distributed among these distances:
516 3 0.01
517 520 0.94
518 5 0.01
520 23 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (517 bp):
TACCTCACTAATTTCTTCTTCTTGGGTAAAACCAATGACGTGCTCTAGGTCATCGCAGTTCTCTA
TGGAGAGTTCTTCTATATTCAACATACTTTGAGCAACACGAATTGAGAACATTGTTTTCAATTTA
TTGCATTTCGAAATATAAACCCTCTTTAGACTTTGGAGGATTGCAATTGCACGATGGGATGGCTC
TACTTTTTCCATGTTGAAGACTTCAACAAGTTCAGGACAGTTTCCTATGTCAAGATGTTCCAAGA
ATTGAAGCCATTTTGGATACACATATTTCAAGCTTCTGCAATCTTTGATCTCAAGAATTTTCAGC
TTGGGCCAGCAAGAAAGAGGATAACCATTCTGCATATTTCAAACACACATCATAGTGAGATATGT
ATTTTTAACTTCTTTTCTTTTAATATTACAAAAAAAAAAAAGCGTCTTTCTCAACCCAAAAAAAC
TGAAAGCATAAAGCCAAAAACAGTTAAGAACATTAAAAAGAAAAAGGGGAAGAACAAGTACA
Found at i:48646595 original size:27 final size:27
Alignment explanation
Indices: 48646564--48646618 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
48646554 AACTTTATAA
48646564 ATTTAAA-AATATTTAGTT-TTTAATTAT
1 ATTTAAATAA-ATTTA-TTATTTAATTAT
*
48646591 ATTTAAATAAATTTATTATTTATTTAT
1 ATTTAAATAAATTTATTATTTAATTAT
48646618 A
1 A
48646619 AGTCTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 21 0.84
28 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (27 bp):
ATTTAAATAAATTTATTATTTAATTAT
Found at i:48646739 original size:37 final size:37
Alignment explanation
Indices: 48646689--48646838 Score: 282
Period size: 37 Copynumber: 4.1 Consensus size: 37
48646679 AGTATATCAA
* *
48646689 ATATTATTTCATATATATGCCTTATTTAAAAATATTT
1 ATATTATTTCATATATATACCCTATTTAAAAATATTT
48646726 ATATTATTTCATATATATACCCTATTTAAAAATATTT
1 ATATTATTTCATATATATACCCTATTTAAAAATATTT
48646763 ATATTATTTCATATATATACCCTATTTAAAAATATTT
1 ATATTATTTCATATATATACCCTATTTAAAAATATTT
48646800 ATATTATTTCATATATATACCCTATTTAAAAATATTT
1 ATATTATTTCATATATATACCCTATTTAAAAATATTT
48646837 AT
1 AT
48646839 TCAATCTTTT
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 111 1.00
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (37 bp):
ATATTATTTCATATATATACCCTATTTAAAAATATTT
Found at i:48647063 original size:25 final size:26
Alignment explanation
Indices: 48647035--48647087 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
48647025 TTTAAATTGA
*
48647035 TAAAA-TAAATTATTGAATA-TTTTAT
1 TAAAATTAAA-TATTAAATATTTTTAT
48647060 TAAAATTAAATATTAAATATTTTTAT
1 TAAAATTAAATATTAAATATTTTTAT
48647086 TA
1 TA
48647088 CGAAAAAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAAATTAAATATTAAATATTTTTAT
Found at i:48652207 original size:21 final size:21
Alignment explanation
Indices: 48652170--48652296 Score: 55
Period size: 21 Copynumber: 5.9 Consensus size: 21
48652160 AAAACGACTA
* *
48652170 AAAAATAATATTC-AAACAAC
1 AAAAATAACAATCAAAACAAC
**
48652190 AAAAATAACAATCAAAACTGC
1 AAAAATAACAATCAAAACAAC
** * *
48652211 AGCAA-AACGATATTAAAAACAAT
1 AAAAATAAC-A-A-TCAAAACAAC
* *
48652234 AAAAATAGCAA-CAAAAACAAT
1 AAAAATAACAATC-AAAACAAC
*
48652255 AAAAATAACAA-CAAAAAAAAGTC
1 AAAAATAACAATC-AAAACAA--C
*
48652278 AAAAACAACAATCAAAACA
1 AAAAATAACAATCAAAACA
48652297 GTAAAAAAAA
Statistics
Matches: 79, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
20 14 0.18
21 35 0.44
22 2 0.03
23 25 0.32
24 3 0.04
ACGTcount: A:0.68, C:0.16, G:0.04, T:0.13
Consensus pattern (21 bp):
AAAAATAACAATCAAAACAAC
Found at i:48652249 original size:20 final size:20
Alignment explanation
Indices: 48652226--48652336 Score: 82
Period size: 21 Copynumber: 5.3 Consensus size: 20
48652216 AACGATATTA
*
48652226 AAAACAATAAAAATAGCAAC
1 AAAACAATAAAAATAACAAC
48652246 AAAAACAATAAAAATAACAAC
1 -AAAACAATAAAAATAACAAC
* *
48652267 AAAAAAAAGTCAAAAACAACAATC
1 -AAAACAA-T-AAAAATAACAA-C
* *
48652291 AAAACAGTAAAAAAAAGC-AC
1 AAAACAATAAAAATAA-CAAC
* * *
48652311 AAAACAGTAAAAA-ATCACC
1 AAAACAATAAAAATAACAAC
48652330 AAAACAA
1 AAAACAA
48652337 CAATATAATT
Statistics
Matches: 76, Mismatches: 9, Indels: 12
0.78 0.09 0.12
Matches are distributed among these distances:
18 1 0.01
19 8 0.11
20 14 0.18
21 34 0.45
22 3 0.04
23 15 0.20
24 1 0.01
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (20 bp):
AAAACAATAAAAATAACAAC
Found at i:48653865 original size:148 final size:149
Alignment explanation
Indices: 48653577--48653865 Score: 370
Period size: 149 Copynumber: 1.9 Consensus size: 149
48653567 TGAGAATATG
* * * ** * *
48653577 GAAGCAAAAACAATGGATTTGAAAGCAGGTTTTTTTTTGTATTTTTTCTTGATTGAGACAATACA
1 GAAGAAAAAACAATGGATTTCAAAGCAGGTTTTATTTTGTATTTTCCCTTAATTGACACAATACA
* * *
48653642 AGAAAATGTGAAAACTGAAAAACAATTAGCGGAAATGATCACAAACACAGATCTGAGGATTGGAA
66 AGAAAATGTGAAAACTGAAAAACAAATAGCGGAAACGATCACAAACACAGATCTGAGAATTGGAA
*
48653707 AGCATAAAACAATTTGGAT
131 AGCAGAAAACAATTTGGAT
*
48653726 GAAGAAAAAACAATGGATTTCAAAGCAGGTTCTTGCATTTT-T-TTTTCCCTTAATTGACAGAAT
1 GAAGAAAAAACAATGGATTTCAAAGCAGGTT-TT--ATTTTGTATTTTCCCTTAATTGACACAAT
** * * *
48653789 ACAAGAAAATGTGAAAA-TGAAAAACAAATATTGG-AACGATCAGAAACACAGATTTGAGAATTT
63 ACAAGAAAATGTGAAAACTGAAAAACAAATAGCGGAAACGATCACAAACACAGATCTGAGAATTG
48653852 GAAAGCAGAAAACA
128 GAAAGCAGAAAACA
48653866 CTTAGTAGTT
Statistics
Matches: 120, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
148 37 0.31
149 43 0.36
150 35 0.29
151 1 0.01
152 4 0.03
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.26
Consensus pattern (149 bp):
GAAGAAAAAACAATGGATTTCAAAGCAGGTTTTATTTTGTATTTTCCCTTAATTGACACAATACA
AGAAAATGTGAAAACTGAAAAACAAATAGCGGAAACGATCACAAACACAGATCTGAGAATTGGAA
AGCAGAAAACAATTTGGAT
Done.