Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold53
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1214666
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.30
Warning! 104343 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:741238 original size:1 final size:1
Alignment explanation
Indices: 741232--741256 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
741222 GGAAGTAGAA
741232 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
741257 AACCATCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:743785 original size:2 final size:2
Alignment explanation
Indices: 743780--743814 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
743770 TGTGGAAAAT
743780 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
743815 GTTTTGAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:752081 original size:38 final size:38
Alignment explanation
Indices: 752039--752153 Score: 131
Period size: 46 Copynumber: 2.8 Consensus size: 38
752029 TCACAAGACC
752039 GAAGGCCAAGGACAACATTTTGAATTTTGCCCAAGGCT
1 GAAGGCCAAGGACAACATTTTGAATTTTGCCCAAGGCT
*
752077 GAAGGCCAAGGGTAACATTTTAAAATTTTGAATTTTGCCCAAGGCT
1 GAAGGCCAA-GG--AC-----AACATTTTGAATTTTGCCCAAGGCT
**
752123 GAAGGCCAAGGGGAACATTTTGAATTTTGCC
1 GAAGGCCAAGGACAACATTTTGAATTTTGCC
752154 GATCCAGTAG
Statistics
Matches: 65, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
38 26 0.40
39 2 0.03
41 2 0.03
45 2 0.03
46 33 0.51
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.27
Consensus pattern (38 bp):
GAAGGCCAAGGACAACATTTTGAATTTTGCCCAAGGCT
Found at i:752122 original size:46 final size:45
Alignment explanation
Indices: 752055--752151 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 45
752045 CAAGGACAAC
*
752055 ATTTTGAATTTTGCCCAAGGCTGAAGGCCAAGGGTAACATTTTAAA
1 ATTTTGAATTTTGCCCAAGGCTGAAGGCCAAGGGGAACATTTT-AA
*
752101 ATTTTGAATTTTGCCCAAGGCTGAAGGCCAAGGGGAACATTTTGA
1 ATTTTGAATTTTGCCCAAGGCTGAAGGCCAAGGGGAACATTTTAA
752146 ATTTTG
1 ATTTTG
752152 CCGATCCAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 7 0.14
46 42 0.86
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (45 bp):
ATTTTGAATTTTGCCCAAGGCTGAAGGCCAAGGGGAACATTTTAA
Found at i:758553 original size:14 final size:14
Alignment explanation
Indices: 758534--758566 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
758524 ACATCTTTTA
758534 TTTTTTAAATTCAT
1 TTTTTTAAATTCAT
758548 TTTTTTAAATTCAT
1 TTTTTTAAATTCAT
758562 TTTTT
1 TTTTT
758567 CTTTTGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTAAATTCAT
Found at i:766565 original size:2 final size:2
Alignment explanation
Indices: 766558--766598 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
766548 NNNNNNNNNN
*
766558 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
766599 CTCTCAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:768144 original size:53 final size:53
Alignment explanation
Indices: 768075--768217 Score: 243
Period size: 53 Copynumber: 2.7 Consensus size: 53
768065 GCAATAATAT
* *
768075 GCATACAATTTACACAGTCTATGTACAAGAATGGTGTAAAATTGGAATCATAC
1 GCATAGAATTCACACAGTCTATGTACAAGAATGGTGTAAAATTGGAATCATAC
768128 GCATA-ACATTCACACAGTCTATGTACAAGAATGGTGTAAAATTGGAATCATAC
1 GCATAGA-ATTCACACAGTCTATGTACAAGAATGGTGTAAAATTGGAATCATAC
*
768181 GCATAGAATTTACACAGTCTATGTACAAGAATGGTGT
1 GCATAGAATTCACACAGTCTATGTACAAGAATGGTGT
768218 GAAGGAAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
52 1 0.01
53 84 0.98
54 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (53 bp):
GCATAGAATTCACACAGTCTATGTACAAGAATGGTGTAAAATTGGAATCATAC
Found at i:775335 original size:18 final size:18
Alignment explanation
Indices: 775309--775359 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
775299 TTTATAAAAG
775309 TCCTGTAGGAATTATATT
1 TCCTGTAGGAATTATATT
* **
775327 TCCTATAGGAGAATGGTATT
1 TCCTGTA-G-GAATTATATT
775347 TCCTGTAGGAATT
1 TCCTGTAGGAATT
775360 TGATTCAGAC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 10 0.38
19 2 0.08
20 14 0.54
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (18 bp):
TCCTGTAGGAATTATATT
Found at i:777253 original size:82 final size:83
Alignment explanation
Indices: 777095--777258 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 83
777085 ATCTGGAACT
* *
777095 AGCATTATTCCCTTTCGACATTCAGGTTTGTAGCTGGTCTTGGAAGTTATTCCTCTTTTTACCCA
1 AGCATTATTCCCTTTCGACATTCAGATTTGTAGCTGGTCTTGGAAGTTATTCCTCTTTTTACACA
777160 AACAAGAATGTTTTCTAA
66 AACAAGAATGTTTTCTAA
* * * * **
777178 AGCATTATTCTCTTTTGACATTCAGATTTGTGGTTGGTCTT-GAAGTTATTCCTCTTTTTACATG
1 AGCATTATTCCCTTTCGACATTCAGATTTGTAGCTGGTCTTGGAAGTTATTCCTCTTTTTACACA
777242 AACAAGAATGTTTTCTA
66 AACAAGAATGTTTTCTA
777259 TGTGTACAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 37 0.51
83 36 0.49
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (83 bp):
AGCATTATTCCCTTTCGACATTCAGATTTGTAGCTGGTCTTGGAAGTTATTCCTCTTTTTACACA
AACAAGAATGTTTTCTAA
Found at i:778126 original size:12 final size:12
Alignment explanation
Indices: 778109--778134 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
778099 TTACTCAACC
778109 TTTCTTTAGAAT
1 TTTCTTTAGAAT
778121 TTTCTTTAGAAT
1 TTTCTTTAGAAT
778133 TT
1 TT
778135 ATACCCTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTTCTTTAGAAT
Found at i:780016 original size:119 final size:118
Alignment explanation
Indices: 779786--780016 Score: 275
Period size: 119 Copynumber: 1.9 Consensus size: 118
779776 TTGCAATAGC
* *
779786 AGCAAAATAATACAAAAATACACATCTTTTGCCTAATGTAACAAGTTGTTGAAATTGATCCCTTA
1 AGCAAAAAAATACAAAAATACACATCTTTTGCCTAATGTAACAAGTTGTTGAAATTGATCACTTA
* * * *
779851 CAAATTAACAATTTACCCTTTGAAGGTACAAATAGTACAGTTTTACTTGTGTA
66 CAAATCAACAATTTACCCTTTGAAGGAACAAATAGGACAGTGTTACTTGTGTA
* * * ** * * *
779904 AGCAAAAAAATTACAAAAATACACATCTTTTGCTTAATTTCACATTTTTTTGTAAA-TGGTCATT
1 AGCAAAAAAA-TACAAAAATACACATCTTTTGCCTAATGTAACAAGTTGTTG-AAATTGATCACT
* * **
779968 TGCAAATCAACAATTTACCCTTTGAAGGAATAAATAGGGTAGTGTTACT
64 TACAAATCAACAATTTACCCTTTGAAGGAACAAATAGGACAGTGTTACT
780017 AATGTAATCA
Statistics
Matches: 93, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
118 9 0.10
119 81 0.87
120 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (118 bp):
AGCAAAAAAATACAAAAATACACATCTTTTGCCTAATGTAACAAGTTGTTGAAATTGATCACTTA
CAAATCAACAATTTACCCTTTGAAGGAACAAATAGGACAGTGTTACTTGTGTA
Found at i:781093 original size:2 final size:2
Alignment explanation
Indices: 781086--781135 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
781076 TCAAATCCAG
781086 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
781128 CT CT CT CT
1 CT CT CT CT
781136 TTATGTACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:790175 original size:18 final size:18
Alignment explanation
Indices: 790152--790199 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 18
790142 AAAATGTCCG
*
790152 ATAGGAATTTTATTTCCT
1 ATAGGAATTGTATTTCCT
*
790170 ATAGGAGAATGGTATTTCCT
1 ATA-G-GAATTGTATTTCCT
*
790190 GTAGGAATTG
1 ATAGGAATTG
790200 ATTCAGACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
18 8 0.33
19 2 0.08
20 14 0.58
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (18 bp):
ATAGGAATTGTATTTCCT
Found at i:806084 original size:105 final size:105
Alignment explanation
Indices: 805902--806104 Score: 325
Period size: 105 Copynumber: 1.9 Consensus size: 105
805892 CCGTTGATAA
* *
805902 AGTTTAACCTTCAACATTGGCGTTTAAATTATTAGCAAAATACGAACAAAACATTCATAATTATT
1 AGTTTAACCTTCAACATCGGCGTTTAAATTATTAACAAAATACGAACAAAACATTCATAATTATT
* *
805967 TATGCCAATTATTGACAGCAAAATATTTTCATAAATAAAC
66 AATGCCAATTATTGACAACAAAATATTTTCATAAATAAAC
* * * **
806007 AGTTTTACCTTCAACATCGGCGTTTAAATTATTAACAAAATATGAACAAAACATTTATGGTTATT
1 AGTTTAACCTTCAACATCGGCGTTTAAATTATTAACAAAATACGAACAAAACATTCATAATTATT
806072 AATGCCAATTATTGACAACAAAATATTTTCATA
66 AATGCCAATTATTGACAACAAAATATTTTCATA
806105 TTATCACAGA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 89 1.00
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (105 bp):
AGTTTAACCTTCAACATCGGCGTTTAAATTATTAACAAAATACGAACAAAACATTCATAATTATT
AATGCCAATTATTGACAACAAAATATTTTCATAAATAAAC
Found at i:808619 original size:15 final size:15
Alignment explanation
Indices: 808595--808625 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
808585 TTATCAATCT
808595 TGTTGCGAAATTAAA
1 TGTTGCGAAATTAAA
*
808610 TGTTGTGAAATTAAA
1 TGTTGCGAAATTAAA
808625 T
1 T
808626 AAACAATTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (15 bp):
TGTTGCGAAATTAAA
Found at i:813868 original size:43 final size:43
Alignment explanation
Indices: 813819--813904 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
813809 AAATTTTATT
*
813819 CCGGTTAGAGATTTTCAAGGATGGATTTTGATAGAATAAAATC
1 CCGGTTAGAGATTTTCAAGGAAGGATTTTGATAGAATAAAATC
* *
813862 CCGGTTAGAGATTTTTAAGGAAGGATTTTGATAGAATTAAATC
1 CCGGTTAGAGATTTTCAAGGAAGGATTTTGATAGAATAAAATC
813905 AAAAGGACAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.34
Consensus pattern (43 bp):
CCGGTTAGAGATTTTCAAGGAAGGATTTTGATAGAATAAAATC
Found at i:823328 original size:98 final size:93
Alignment explanation
Indices: 823153--823345 Score: 260
Period size: 98 Copynumber: 2.0 Consensus size: 93
823143 GACCGGCATT
* * * *
823153 TATTTTTATTAAAAAAAATGTTTTCCTCTTAGAGAAGATCCATGATGTCTTCTTGATAGCTGACC
1 TATTTTTATAAAAAAAAATGCTTTCCTCTTAGAGAAGACCCATGATGTCTTCTTGATAGCTGAAC
*
823218 AAGCTTCCATCCGGGTCGTTATTAGCAA
66 AAGCTTCCATCCGGGCCGTTATTAGCAA
*
823246 TATTTTTATAAATAAAAAATGCTTTCCTCTTAGAGGAGACCCATGATTATTGTCTTCTTGATAGC
1 TATTTTTATAAA-AAAAAATGCTTTCCTCTTAGAGAAGACCCATG---A-TGTCTTCTTGATAGC
** *
823311 TGAACAAGCTTTTATCCGGGCCGTTGTTAGCAA
61 TGAACAAGCTTCCATCCGGGCCGTTATTAGCAA
823344 TA
1 TA
823346 CCCGCCCTGG
Statistics
Matches: 86, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
93 11 0.13
94 29 0.34
97 1 0.01
98 45 0.52
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.37
Consensus pattern (93 bp):
TATTTTTATAAAAAAAAATGCTTTCCTCTTAGAGAAGACCCATGATGTCTTCTTGATAGCTGAAC
AAGCTTCCATCCGGGCCGTTATTAGCAA
Found at i:831317 original size:32 final size:32
Alignment explanation
Indices: 831276--831404 Score: 249
Period size: 32 Copynumber: 4.0 Consensus size: 32
831266 TCACACATTG
831276 CTATCTTAGTGGCTGATATACATGTACGATAA
1 CTATCTTAGTGGCTGATATACATGTACGATAA
*
831308 CTATCTTAGTGGCTGATATGCATGTACGATAA
1 CTATCTTAGTGGCTGATATACATGTACGATAA
831340 CTATCTTAGTGGCTGATATACATGTACGATAA
1 CTATCTTAGTGGCTGATATACATGTACGATAA
831372 CTATCTTAGTGGCTGATATACATGTACGATAA
1 CTATCTTAGTGGCTGATATACATGTACGATAA
831404 C
1 C
831405 GTCTCGTCAT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 95 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (32 bp):
CTATCTTAGTGGCTGATATACATGTACGATAA
Found at i:832142 original size:30 final size:30
Alignment explanation
Indices: 832105--833457 Score: 1030
Period size: 30 Copynumber: 44.3 Consensus size: 30
832095 TAGACAATGC
*
832105 ATGAATGCTTACCTCACATACAGTCAGGCA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* ** ** * * *
832135 CTGAATGCTTACCTTGCATATTGTTAGGCT
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * *
832165 ATGAAGGATTACCTCACATACAGTCAGATA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * **
832195 ATGAATGCATACCTGACATAAAGTCACTCA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
832225 ATGCATGCTTACCTCACATACAGT-AGGACA
1 ATGAATGCTTACCTCACATACAGTCA-GACA
* * *
832255 ATGAATTCTAACCTCACATATAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
832285 ATGAATGCTTACCTCACATACGGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
832315 ATGAATG-TGTACCTCACACACAGTCAGACA
1 ATGAATGCT-TACCTCACATACAGTCAGACA
* * * *
832345 ATGAATGCTCACCTCACATACGGTCGGGCA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
832375 ATGAATGCTTACCTCACATACAGTCAAACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
832405 ATGAATGCTTACCTCACATACAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
832435 ATGAATGCTTACCTCACATACAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
832465 ATGAATGTTTACCTTACATACAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
832495 ATGAATGTTTACCTCACATACGGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
832525 CTGAATGCTTACCTCACATACGGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* ** * ** ** * * *
832555 CTGAATTTTTACATTGCATATTGTTAGGCT
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * *
832585 ATGAA-GGTTCACCTCCCATACAGTCAGATA
1 ATGAATGCTT-ACCTCACATACAGTCAGACA
* * *
832615 ATGAAT-CTTACCTCACATAAAGACAGA-T
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * *
832643 ATCAATGCTTTAGTTACCTTACATATTCACGT-AGTAATAAA
1 ATGAATGC-----TTACCTCACATA--CA-GTCAG----ACA
* * * * * *
832684 ATGAATGCTGAACT-TCATACATTCAGGCT
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * *
832713 ATGAATGCTGAACTAACATACAGTTAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
832743 ATGAATGCTGACCTCACATACAGTCAGAAA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * *
832773 AGGAATGCTTACCTCACATACAGTAAGAAA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
832803 ATGAATGCTCAGAGTGTACCTCACATACAGTTAGACA
1 ATGAATG--C----T-TACCTCACATACAGTCAGACA
* **
832840 ATGAATGCTTACCCCACATGGAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * **
832870 ATGAATGCTAACCTCGCA-AAAAACAGAC-
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * *
832898 ATCAATGCTTACCTTACATACAGTTAGATA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * *
832928 AGGAATGCTTACCTCACATACATTTAGATA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * *
832958 ATGTATGCTTTCCTAGCACATAGA-T-AGATA
1 ATGAATGCTTACCT--CACATACAGTCAGACA
* * *
832988 ATAAATGCTTACCAT-ACATACAGTTAGATA
1 ATGAATGCTTACC-TCACATACAGTCAGACA
*
833018 AGGAATGCTTACCTCACATACAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
833048 ATGTAA-GCTTACCTCACATACAGTCAGAAA
1 ATG-AATGCTTACCTCACATACAGTCAGACA
* * ** * *
833078 ATGAATGCTAAACTCTTATACAGTAAGAAA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* * * * *
833108 ACGAATACTTAACTCACATTA-AGTAAGATA
1 ATGAATGCTTACCTCACA-TACAGTCAGACA
* * *
833138 ATGAATGCTTTA-CTCACATACAGTTAAATA
1 ATGAATGC-TTACCTCACATACAGTCAGACA
*
833168 ATGAATGCTTTCCTCACATACAGTCACATACATTCAGACA
1 ATGAATGC--T--T-AC---C--TCACATACAGTCAGACA
* ** * * *
833208 GTGAATATTTAACTCACATACAGTTAGATA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
833238 ATGAATTCTTTA-CTCACATACAGTCAGACA
1 ATGAATGC-TTACCTCACATACAGTCAGACA
* * *
833268 AT-ATATGTTTACCCCACATACAGTCAGGCA
1 ATGA-ATGCTTACCTCACATACAGTCAGACA
* *
833298 ATTAAATGCTTATCTCACATACAGTCAGACA
1 A-TGAATGCTTACCTCACATACAGTCAGACA
* * * *
833329 ATGAATGCTTACCTCACATATAGTAAAACT
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
833359 ATGAATGCTTACCTCACATACAATAAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
833389 ATGAACGCTTACCTCACATACAGTCAGACA
1 ATGAATGCTTACCTCACATACAGTCAGACA
* *
833419 ATGAATGCTTACCTCACATACTGTCAGATA
1 ATGAATGCTTACCTCACATACAGTCAGACA
*
833449 ATAAATGCT
1 ATGAATGCT
833458 CGCCTACTCA
Statistics
Matches: 1058, Mismatches: 208, Indels: 114
0.77 0.15 0.08
Matches are distributed among these distances:
28 25 0.02
29 55 0.05
30 839 0.79
31 41 0.04
32 11 0.01
33 5 0.00
34 12 0.01
35 6 0.01
36 9 0.01
37 27 0.03
38 2 0.00
40 19 0.02
41 7 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (30 bp):
ATGAATGCTTACCTCACATACAGTCAGACA
Found at i:832873 original size:67 final size:67
Alignment explanation
Indices: 832753--832878 Score: 180
Period size: 67 Copynumber: 1.9 Consensus size: 67
832743 ATGAATGCTG
*
832753 ACCTCACATACAGTCAGAAAAGGAATGCTTACCTCACATACAGTAAGAAAATGAATGCTCAGAGT
1 ACCTCACATACAGTCAGAAAAGGAATGCTTACCCCACATACAGTAAGAAAATGAATGCTCAGAGT
832818 GT
66 GT
* * * ** * *
832820 ACCTCACATACAGTTAGACAATGAATGCTTACCCCACATGGAGTCAGACAATGAATGCT
1 ACCTCACATACAGTCAGAAAAGGAATGCTTACCCCACATACAGTAAGAAAATGAATGCT
832879 AACCTCGCAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 51 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (67 bp):
ACCTCACATACAGTCAGAAAAGGAATGCTTACCCCACATACAGTAAGAAAATGAATGCTCAGAGT
GT
Found at i:833286 original size:100 final size:100
Alignment explanation
Indices: 833110--833293 Score: 257
Period size: 100 Copynumber: 1.8 Consensus size: 100
833100 GTAAGAAAAC
* *
833110 GAATACTTAACTCACATTAAGTAAGATAATGAATGCTTTACTCACATACAGTTAAATAATGAATG
1 GAATACTTAACTCACATTAAGTAAGATAATGAATGCTTTACTCACATACAGTCAAACAATGAATG
*
833175 CTTTCCTCACATACAGTCACATACATTCAGACAGT
66 CTTTCCCCACATACAGTCACATACATTCAGACAGT
* * * *
833210 GAATATTTAACTCACA-TACAGTTAGATAATGAATTCTTTACTCACATACAGTCAGACAAT-ATA
1 GAATACTTAACTCACATTA-AGTAAGATAATGAATGCTTTACTCACATACAGTCAAACAATGA-A
833273 TG-TTTACCCCACATACAGTCA
64 TGCTTT-CCCCACATACAGTCA
833294 GGCAATTAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
99 6 0.08
100 68 0.92
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.30
Consensus pattern (100 bp):
GAATACTTAACTCACATTAAGTAAGATAATGAATGCTTTACTCACATACAGTCAAACAATGAATG
CTTTCCCCACATACAGTCACATACATTCAGACAGT
Found at i:850023 original size:21 final size:21
Alignment explanation
Indices: 849999--850303 Score: 366
Period size: 21 Copynumber: 14.6 Consensus size: 21
849989 AAAATAACAC
*
849999 CAGAAAGGAAGACAC-GAAGA
1 CAGAAAGTAAGACACGGAAGA
* *
850019 CCAGAAACTAAGACACGGATGA
1 -CAGAAAGTAAGACACGGAAGA
*
850041 CAGAAAGTAAGACACGAAAGA
1 CAGAAAGTAAGACACGGAAGA
850062 CAGAAAGTAAGACACGGAAGA
1 CAGAAAGTAAGACACGGAAGA
* *
850083 CAGAAAGTAAG--ACGAAAAA
1 CAGAAAGTAAGACACGGAAGA
*
850102 CAGAAAGTAAGACGCGGAAGA
1 CAGAAAGTAAGACACGGAAGA
* *
850123 CA-AGAAGTGAGACACGGAGGA
1 CAGA-AAGTAAGACACGGAAGA
* *
850144 CAGAAAGTAAGACACTGAAAA
1 CAGAAAGTAAGACACGGAAGA
*
850165 CAGAAAATAAGACACGGAAGA
1 CAGAAAGTAAGACACGGAAGA
* *
850186 CAGTAAGTAAGTCACGGAAGA
1 CAGAAAGTAAGACACGGAAGA
* * *
850207 CAGTAAGTAAGTCACAGAAGA
1 CAGAAAGTAAGACACGGAAGA
*
850228 CAGAATGTAAGACACGGAAGA
1 CAGAAAGTAAGACACGGAAGA
* *
850249 CAGAAAGTAAGGCACGGAAAA
1 CAGAAAGTAAGACACGGAAGA
*
850270 CAGAAAGTAAGACACAGAAGA
1 CAGAAAGTAAGACACGGAAGA
*
850291 CAGATAGTAAGAC
1 CAGAAAGTAAGAC
850304 TCCATGGCAA
Statistics
Matches: 242, Mismatches: 37, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.07
20 1 0.00
21 219 0.90
22 5 0.02
ACGTcount: A:0.51, C:0.15, G:0.27, T:0.07
Consensus pattern (21 bp):
CAGAAAGTAAGACACGGAAGA
Found at i:851573 original size:2 final size:2
Alignment explanation
Indices: 851566--851631 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
851556 TTACTATTGT
851566 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
851608 TC TAC -C TC TC TC TC TC TC TC TC TC
1 TC T-C TC TC TC TC TC TC TC TC TC TC
851632 CATATTGCCA
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 60 0.97
3 1 0.02
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:860907 original size:2 final size:2
Alignment explanation
Indices: 860900--860956 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
860890 TTCAAAGAAT
860900 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
860942 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
860957 GTGTTTCCCT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:863673 original size:25 final size:27
Alignment explanation
Indices: 863635--863696 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
863625 TGCGTCTCAG
*
863635 AAATCTAAA-AAAAA-GTTAACATATC
1 AAATATAAACAAAAAGGTTAACATATC
863660 AAATATAAACAAAAAGGTTAACATATC
1 AAATATAAACAAAAAGGTTAACATATC
863687 AAATATAAAC
1 AAATATAAAC
863697 TTATACAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 8 0.24
26 5 0.15
27 21 0.62
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (27 bp):
AAATATAAACAAAAAGGTTAACATATC
Found at i:865525 original size:21 final size:21
Alignment explanation
Indices: 865427--865533 Score: 115
Period size: 21 Copynumber: 5.1 Consensus size: 21
865417 GCAAGCAAAT
*
865427 CGTTTCGTGTAAACAGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* * *
865448 CATTTCGTGTAAATCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
* * * *
865469 CGTTTCGGGCAAAGCGTGCAG
1 CGTTTCGTGTAAACCGTTCAG
*
865490 CGTATCGTGTAAACCGTTCAG
1 CGTTTCGTGTAAACCGTTCAG
* *
865511 CGTTTCGTGTGAACCGTTTAG
1 CGTTTCGTGTAAACCGTTCAG
865532 CG
1 CG
865534 AGCATGTACC
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (21 bp):
CGTTTCGTGTAAACCGTTCAG
Found at i:868801 original size:8 final size:8
Alignment explanation
Indices: 868787--868820 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
868777 TGAAAAGTTT
868787 ACAGACGG
1 ACAGACGG
*
868795 ACGGACGG
1 ACAGACGG
868803 ACAGACGG
1 ACAGACGG
868811 ACA-ACGG
1 ACAGACGG
868818 ACA
1 ACA
868821 AAAGGTGATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.38, C:0.26, G:0.35, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:869522 original size:2 final size:2
Alignment explanation
Indices: 869515--869566 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
869505 GTATCTTTTC
869515 AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
869556 AG AG AG AG AG A
1 AG AG AG AG AG A
869567 TTTTACACCT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:870384 original size:36 final size:34
Alignment explanation
Indices: 870341--870598 Score: 136
Period size: 36 Copynumber: 7.4 Consensus size: 34
870331 ATTACATATA
*
870341 TTTCTGTAATGTTGTAACGATGTAAATTACATGCAT
1 TTTCTGTAATGTTGTAATGATGT--ATTACATGCAT
* *
870377 TTTCTGTAATGATGTAATGTTATGTATTACATGTAT
1 TTTCTGTAATGTTGTAATG--ATGTATTACATGCAT
* *
870413 TTTATGCAATGTTG---TGA-G--TTACATGCAT
1 TTTCTGTAATGTTGTAATGATGTATTACATGCAT
* *
870441 ATTCTGTAATGTTGTAATGATGTGAATTACATGTAT
1 TTTCTGTAATGTTGTAATGATGT--ATTACATGCAT
* * * * **
870477 TTTCTG-CATGATGCAATGACGTTAATTACATATACT
1 TTTCTGTAATGTTGTAATGATG-T-ATTACATGCA-T
* * * * **
870513 TTT-TGTAATGATATAATGTTGTGAGTTACGTTTAT
1 TTTCTGTAATGTTGTAATGATGT-A-TTACATGCAT
** * *
870548 TTTCTGTAATGACGTAATGTTGTGTATTACATGTAT
1 TTTCTGTAATGTTGTAATG--ATGTATTACATGCAT
870584 TTTCTGTAATGTTGT
1 TTTCTGTAATGTTGT
870599 TAGTTACATA
Statistics
Matches: 173, Mismatches: 32, Indels: 34
0.72 0.13 0.14
Matches are distributed among these distances:
28 20 0.12
30 1 0.01
31 4 0.02
32 1 0.01
33 2 0.01
35 29 0.17
36 108 0.62
37 1 0.01
38 7 0.04
ACGTcount: A:0.27, C:0.09, G:0.18, T:0.46
Consensus pattern (34 bp):
TTTCTGTAATGTTGTAATGATGTATTACATGCAT
Found at i:870596 original size:28 final size:28
Alignment explanation
Indices: 870561--870636 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 28
870551 CTGTAATGAC
* *
870561 GTAATGTTGTGTATTACATGTATTTTCT
1 GTAATGTTGTGTATTACATGTATATCCT
*
870589 GTAATGTTGT-TAGTTACATATATATCCT
1 GTAATGTTGTGTA-TTACATGTATATCCT
* * *
870617 GTAATGATGAGAATTACATG
1 GTAATGTTGTGTATTACATG
870637 GGTTGTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
27 2 0.05
28 36 0.92
29 1 0.03
ACGTcount: A:0.29, C:0.08, G:0.18, T:0.45
Consensus pattern (28 bp):
GTAATGTTGTGTATTACATGTATATCCT
Found at i:870701 original size:38 final size:40
Alignment explanation
Indices: 870616--870711 Score: 117
Period size: 40 Copynumber: 2.5 Consensus size: 40
870606 ATATATATCC
* * *
870616 TGTAATGATG-AGAATTACATGGGTTGTTTTTTTTGCATGA
1 TGTAATGATGTA-AATTACATGGGTTGTTTTCTGTGAATGA
* *
870656 TGCAATGATGTAAATTACATGGGTT-TTTTCTGT-AATGT
1 TGTAATGATGTAAATTACATGGGTTGTTTTCTGTGAATGA
870694 TGTAATGATGTAAATTAC
1 TGTAATGATGTAAATTAC
870712 GTATATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
38 20 0.41
39 6 0.12
40 22 0.45
41 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.22, T:0.44
Consensus pattern (40 bp):
TGTAATGATGTAAATTACATGGGTTGTTTTCTGTGAATGA
Found at i:872709 original size:2 final size:2
Alignment explanation
Indices: 872702--872769 Score: 118
Period size: 2 Copynumber: 34.0 Consensus size: 2
872692 CTTTGTCTTC
* *
872702 AG AG AG AG AG AG CG AG AG AG CG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
872744 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
872770 CACAACCCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.47, C:0.03, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:873797 original size:18 final size:18
Alignment explanation
Indices: 873774--873808 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
873764 TCTCTGGTAC
873774 TCTTTTTCAAAAGATTAT
1 TCTTTTTCAAAAGATTAT
873792 TCTTTTTCAAAAGATTA
1 TCTTTTTCAAAAGATTA
873809 GTCGAGAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.49
Consensus pattern (18 bp):
TCTTTTTCAAAAGATTAT
Found at i:877419 original size:2 final size:2
Alignment explanation
Indices: 877412--877453 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
877402 AACTAATCGA
877412 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
877454 TCTTAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:879017 original size:2 final size:2
Alignment explanation
Indices: 879010--879060 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
879000 AGATCAAACA
879010 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
879052 CT CT CT CT C
1 CT CT CT CT C
879061 AATAATAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:894781 original size:40 final size:40
Alignment explanation
Indices: 894705--895104 Score: 651
Period size: 40 Copynumber: 10.0 Consensus size: 40
894695 GATGCTGGGG
*
894705 AACAGGCTAAGGTGGTAGACT-ATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
*
894744 AACAGGCTGAGGTGGTAAACTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
*
894784 AACAAGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
*
894824 AACAGGCTGAGGTGGTAGACTCATC-TCAAACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTC-TACATCCTCATC
*
894864 AACAGGCTGAGGTGGTAGACTCATCTTCTACATTCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
894904 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
* *
894944 AACAGGCTGAGATGGTAGATTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
* * *
894984 AACAGACTTAGGTGGTAGACTCATCTTCTTCATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
* **
895024 AACAGCCTGAGGTGGTAGGTTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
*
895064 AACAGGCTAAGGTGGTAGACTCATCTTCTACATCCTCATC
1 AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
895104 A
1 A
895105 CTACACACAA
Statistics
Matches: 333, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
39 21 0.06
40 310 0.93
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (40 bp):
AACAGGCTGAGGTGGTAGACTCATCTTCTACATCCTCATC
Found at i:905517 original size:48 final size:47
Alignment explanation
Indices: 905446--905687 Score: 394
Period size: 48 Copynumber: 5.1 Consensus size: 47
905436 AAAGGTCATG
*
905446 TGCATGAAGCATTATACTTTTATACATCAATATGATATAATGCTTCA
1 TGCATGAAGCATAATACTTTTATACATCAATATGATATAATGCTTCA
*
905493 TGCATGAAGCAGTAATACTTTTATACATCAATATGATATATTGCTTCA
1 TGCATGAAGCA-TAATACTTTTATACATCAATATGATATAATGCTTCA
** *
905541 TGCATGAAGCATTAATACTTTTATACATCAATAAAATATAATGCTTCG
1 TGCATGAAGCA-TAATACTTTTATACATCAATATGATATAATGCTTCA
*
905589 TGCATGAAGCATTATACTTTTATACATCAATATGATATAATGCTTCA
1 TGCATGAAGCATAATACTTTTATACATCAATATGATATAATGCTTCA
*
905636 TGCATGAAGCATTAATACTTTTATACATCAATATGATATAAAGCTTCA
1 TGCATGAAGCA-TAATACTTTTATACATCAATATGATATAATGCTTCA
905684 TGCA
1 TGCA
905688 CATGGCCTTT
Statistics
Matches: 180, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
47 54 0.30
48 126 0.70
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (47 bp):
TGCATGAAGCATAATACTTTTATACATCAATATGATATAATGCTTCA
Found at i:905623 original size:95 final size:96
Alignment explanation
Indices: 905446--905687 Score: 416
Period size: 95 Copynumber: 2.5 Consensus size: 96
905436 AAAGGTCATG
905446 TGCATGAAGCATT-ATACTTTTATACATCAATATGATATAATGCTTCATGCATGAAGCAGTAATA
1 TGCATGAAGCATTAATACTTTTATACATCAATATGATATAATGCTTCATGCATGAAGCAGTAATA
*
905510 CTTTTATACATCAATATGATATATTGCTTCA
66 CTTTTATACATCAATATGATATAATGCTTCA
** * *
905541 TGCATGAAGCATTAATACTTTTATACATCAATAAAATATAATGCTTCGTGCATGAAGCA-TTATA
1 TGCATGAAGCATTAATACTTTTATACATCAATATGATATAATGCTTCATGCATGAAGCAGTAATA
905605 CTTTTATACATCAATATGATATAATGCTTCA
66 CTTTTATACATCAATATGATATAATGCTTCA
*
905636 TGCATGAAGCATTAATACTTTTATACATCAATATGATATAAAGCTTCATGCA
1 TGCATGAAGCATTAATACTTTTATACATCAATATGATATAATGCTTCATGCA
905688 CATGGCCTTT
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
95 95 0.69
96 42 0.31
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (96 bp):
TGCATGAAGCATTAATACTTTTATACATCAATATGATATAATGCTTCATGCATGAAGCAGTAATA
CTTTTATACATCAATATGATATAATGCTTCA
Found at i:905627 original size:23 final size:23
Alignment explanation
Indices: 905601--905675 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
905591 CATGAAGCAT
905601 TATACTTTTATACATCAATATGA
1 TATACTTTTATACATCAATATGA
* * * * * *
905624 TATAATGCTTCATGCATGAAGCATTA
1 TATACT--TTTATACATCAA-TATGA
905650 -ATACTTTTATACATCAATATGA
1 TATACTTTTATACATCAATATGA
905672 TATA
1 TATA
905676 AAGCTTCATG
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
22 3 0.08
23 17 0.47
25 13 0.36
26 3 0.08
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (23 bp):
TATACTTTTATACATCAATATGA
Found at i:909637 original size:2 final size:2
Alignment explanation
Indices: 909630--909660 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
909620 NNNNNNNNNN
909630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
909661 TATTTCGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:919914 original size:14 final size:14
Alignment explanation
Indices: 919895--919923 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
919885 TAGATATATG
919895 GTTTTTTTTTTTTT
1 GTTTTTTTTTTTTT
919909 GTTTTTTTTTTTTT
1 GTTTTTTTTTTTTT
919923 G
1 G
919924 GGGGGGGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (14 bp):
GTTTTTTTTTTTTT
Found at i:919915 original size:13 final size:13
Alignment explanation
Indices: 919897--919921 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
919887 GATATATGGT
919897 TTTTTTTTTTTTG
1 TTTTTTTTTTTTG
919910 TTTTTTTTTTTT
1 TTTTTTTTTTTT
919922 TGGGGGGGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.04, T:0.96
Consensus pattern (13 bp):
TTTTTTTTTTTTG
Found at i:924155 original size:18 final size:18
Alignment explanation
Indices: 924132--924166 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
924122 AAATCGTTAA
924132 TTAAAC-TTAAGTTTAAAC
1 TTAAACTTTAA-TTTAAAC
924150 TTAAACTTTAATTTAAA
1 TTAAACTTTAATTTAAA
924167 TATACGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (18 bp):
TTAAACTTTAATTTAAAC
Found at i:928933 original size:2 final size:2
Alignment explanation
Indices: 928926--928967 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
928916 ACGCCCGTTT
928926 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
928968 TTTTGCACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:932885 original size:23 final size:23
Alignment explanation
Indices: 932837--932885 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
932827 GATAAGCTAG
*
932837 CTTAATGTCTAGTTTTGTCAGTA
1 CTTAATGTCTAGTTTTGTCAGAA
932860 CTTAATGTC-AGTACTTTG-CAGAA
1 CTTAATGTCTAGT--TTTGTCAGAA
932883 CTT
1 CTT
932886 CTTCCACGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 3 0.13
23 16 0.70
24 4 0.17
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (23 bp):
CTTAATGTCTAGTTTTGTCAGAA
Found at i:933827 original size:2 final size:2
Alignment explanation
Indices: 933820--933873 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
933810 NNNNNNNNNN
933820 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
933862 CT CT CT CT CT CT
1 CT CT CT CT CT CT
933874 ATATATATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:933878 original size:2 final size:2
Alignment explanation
Indices: 933873--933906 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
933863 TCTCTCTCTC
933873 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
933907 CTTACATTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:936623 original size:16 final size:16
Alignment explanation
Indices: 936602--936632 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
936592 TATGTCTCTG
936602 TATTTACACATCAACA
1 TATTTACACATCAACA
*
936618 TATTTACACGTCAAC
1 TATTTACACATCAAC
936633 CCGGATTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (16 bp):
TATTTACACATCAACA
Found at i:947699 original size:9 final size:9
Alignment explanation
Indices: 947685--947713 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
947675 ATAATTATAA
947685 CATGTATTT
1 CATGTATTT
947694 CATGTATTT
1 CATGTATTT
947703 CATGTATTT
1 CATGTATTT
947712 CA
1 CA
947714 ATTATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (9 bp):
CATGTATTT
Found at i:950317 original size:2 final size:2
Alignment explanation
Indices: 950310--950341 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
950300 TAAGACAGGC
950310 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
950342 GTACCTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:969342 original size:2 final size:2
Alignment explanation
Indices: 969335--969401 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
969325 TTATATTTAG
969335 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
969377 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
969402 NTATATATAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:972203 original size:16 final size:15
Alignment explanation
Indices: 972173--972209 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
972163 CTCAAAAAGG
*
972173 AAAATAAAATTAAAA
1 AAAATAAAATAAAAA
972188 AAAATCAAAATAAAAA
1 AAAAT-AAAATAAAAA
972204 AAAATA
1 AAAATA
972210 TAGATTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAATAAAATAAAAA
Found at i:972997 original size:1 final size:1
Alignment explanation
Indices: 972991--973029 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
972981 GAATATTTCC
* **
972991 GGGGGGGGGGGGGGGCGGTNGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
973030 TCCGTTAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.92, T:0.03
Consensus pattern (1 bp):
G
Found at i:976078 original size:33 final size:30
Alignment explanation
Indices: 976049--976107 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
976039 AGGTGGAATG
*
976049 GGAATGATGGGAAATATGGGAGGAAGTGGA
1 GGAATGATGGGAAATATGGGAGGAGGTGGA
* * *
976079 GGCATGATGGGTAATATGGGGGGAGGTGG
1 GGAATGATGGGAAATATGGGAGGAGGTGG
976108 GGGAGGACCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.51, T:0.19
Consensus pattern (30 bp):
GGAATGATGGGAAATATGGGAGGAGGTGGA
Found at i:984229 original size:12 final size:12
Alignment explanation
Indices: 984199--984239 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
984189 GCCCCCTGAT
984199 GGTGGAGGTGGTG
1 GGTGGAGGTGG-G
*
984212 GG-GGAGGAGGG
1 GGTGGAGGTGGG
984223 GGTGGAGGTGGG
1 GGTGGAGGTGGG
984235 GGTGG
1 GGTGG
984240 GACCATGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.12
12 20 0.80
13 2 0.08
ACGTcount: A:0.10, C:0.00, G:0.76, T:0.15
Consensus pattern (12 bp):
GGTGGAGGTGGG
Found at i:986159 original size:165 final size:164
Alignment explanation
Indices: 985872--986778 Score: 1109
Period size: 165 Copynumber: 5.5 Consensus size: 164
985862 AAAGAATCAT
* * *
985872 CTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACCCTATATATATTCCTTTGTTAAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTA--CTCTATATATTCCTATGTAAAA
* *
985934 CTTTGACCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATGATTTTCACAACTTTGAATCTAC
64 CTTCGACCCCCATTGTGGCCCCACCCTACCCCCGGGG-TCATGATTTTCACAACTTTGAATCTAC
* *
985999 ACTACCTGAGGAAGCTTTCACATAAGTTTCAGCTTTC
128 ACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
* * * * * *
986036 CTGACTGATTAGTTTCTAAGAAGAAGATTTTTAAATATTTACTCTGTTTATTCCTATGTAAAACA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * * * * *
986101 TCGACCTCCCATTGTGGCCCAAACCTACCCCCAGGGTTATGATTTTCACAAATTTGAATTTACAC
66 TCGACC-CCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACAC
986166 TACCTGAGGATGC-TTCTACACAAGTTTCAGCTTTC
130 TACCTGAGGATGCTTTC-ACACAAGTTTCAGCTTTC
* *
986201 CTGGCTAATTAGTTTCTGAGAAGAA-ATGTTTTAAAGATTTACTCTATATCA-TCATATGTTAAA
1 CTGGCTGATTAGTTTCTGAGAAGAAGAT-TTTTAAAGATTTACTCTATAT-ATTCCTATG-TAAA
* *
986264 A-TTCGACCCCCATTGTGGCCCCACCCTACCCCCAGGGGTTATTATTTTCACAACTTTGAATCTA
63 ACTTCGACCCCCATTGTGGCCCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTA
*
986328 CTA-TACCTGATGATGC-TTCAACACAAGTTTCAGCTTTGC
127 C-ACTACCTGAGGATGCTTTC-ACACAAGTTTCAGCTTT-C
* *
986367 C-GGCTGATTAGTTTCTGAGAAGAAGATTTTCAAAGATTTACTC--TATATTCCTTTGTTAAAA-
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATG-TAAAAC
*
986428 TTCGATCCCCCATTGTGGCCCCACCCTACCCCGGGGGTCATGATTTTCACAACTTTGAATCTACA
65 TTCGA-CCCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACA
* * *
986493 CTACCTGAGGATG-TTTCCATATAAGTGTCAGCTTTC
129 CTACCTGAGGATGCTTT-CACACAAGTTTCAGCTTTC
* * * *
986529 ATGGCCGATAAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGT---ACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
* * *
986591 TCAATCTCCCATTGTGG-CCCACCCTACCCCCGGGGGTCATGATTTTCACAAATTTGAATCTACA
66 TCGA-CCCCCATTGTGGCCCCACCCTACCCCC-GGGGTCATGATTTTCACAACTTTGAATCTACA
* * *
986655 TTACCTGATGATGCTTTCACACAAGTTTTAGCTTTC
129 CTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
* * *
986691 CTGGCTGATTAGTTTCT--G-AGAAGATTTTTAAAGATTTACTCTATATATTCATTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
*
986753 TCGACCCCCCATTGTGGCCCAACCCT
66 TCGA-CCCCCATTGTGGCCCCACCCT
986779 CAGGTGAGCT
Statistics
Matches: 645, Mismatches: 71, Indels: 55
0.84 0.09 0.07
Matches are distributed among these distances:
159 36 0.06
160 1 0.00
161 14 0.02
162 106 0.16
163 123 0.19
164 72 0.11
165 237 0.37
166 37 0.06
167 19 0.03
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (164 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACT
TCGACCCCCATTGTGGCCCCACCCTACCCCCGGGGTCATGATTTTCACAACTTTGAATCTACACT
ACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
Found at i:988185 original size:8 final size:8
Alignment explanation
Indices: 988174--988215 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
988164 TAAAAAGTTT
988174 ACAGACGG
1 ACAGACGG
*
988182 ACAGATGG
1 ACAGACGG
*
988190 ACGGACGG
1 ACAGACGG
988198 ACAGACGG
1 ACAGACGG
988206 AC-GACGG
1 ACAGACGG
988213 ACA
1 ACA
988216 AAAGGTGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.36, C:0.24, G:0.38, T:0.02
Consensus pattern (8 bp):
ACAGACGG
Found at i:988648 original size:165 final size:166
Alignment explanation
Indices: 988314--988907 Score: 684
Period size: 166 Copynumber: 3.6 Consensus size: 166
988304 CCCCGAGGGT
* * *
988314 CAACTTTGAATTTTCACTACCTGAGAATGCTT---C-CAAGTTTCAGCTTTCCTGGCATAATGGT
1 CAACTTTGAATCTACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCTAATGGT
* * * * *
988375 TTCTGAGAAGAAGATTTTAAAAAAATTTACGCTATATATTCCTATGTAAAAATTCACCACAACCC
66 TTCTGAGAAGAAGATTTT-TAAAGATTTACCCTATATATTCATATGTAAAAAGT-----CAA-CC
* * *
988440 CTCCCCATTGTTGCCCCACCCTACCCCCAAGGGTCATGATTTTCA
124 CT--CCATTGTGGCCCCACCCTACACACAAGGGTCATGATTTTCA
* * *
988485 CAACTTTGAATCTACACTACCTGAGGATGCTTCTACACAAGTTTCAGTTTTCCTGGCCTAATGGT
1 CAACTTTGAATCTACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCTAATGGT
* *
988550 TT-TGAGAAGGAGATTTTTAAAGATTTACCCTATATATTCATATGTAAAAAGTCAACCCTTCATT
66 TTCTGAGAAGAAGATTTTTAAAGATTTACCCTATATATTCATATGTAAAAAGTCAACCCTCCATT
988614 GTGGCCCCACCCTACACACAAGGGTCATGATTTTCA
131 GTGGCCCCACCCTACACACAAGGGTCATGATTTTCA
* * * * *
988650 CAACTTTGAATCTACACTACTTGAGAATGCTTCCAAACAAGTTTCAACTTTCCTGG-CTGATTGA
1 CAACTTTGAATCTACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCT-AATGG
* * * * * *
988714 TTTCTGAGAAGAAGGTTTTTAAAGATTTACTCTATATATTCTTATGTAAAAAGTCGACCCCCCAA
65 TTTCTGAGAAGAAGATTTTTAAAGATTTACCCTATATATTCATATGTAAAAAGTCAACCCTCCAT
* * *
988779 TGTGGCCCCACCCTACAAACGAGGGTCATGATTTTCT
130 TGTGGCCCCACCCTACACACAAGGGTCATGATTTTCA
* * * * * *
988816 CAACTTTGAATCCACACTACCT-AAAGATGCTTCCACAAAAGTTTCAGTTTTCCTGGCCTTATAG
1 CAACTTTGAATCTACACTACCTGAGA-ATGCTTCCACACAAGTTTCAGCTTTCCTGGCCTAATGG
988880 -TTCGTGAGAAGAAGATTTTTGAAA-ATTT
65 TTTC-TGAGAAGAAGATTTTT-AAAGATTT
988908 CTGGAAAATT
Statistics
Matches: 367, Mismatches: 46, Indels: 25
0.84 0.11 0.06
Matches are distributed among these distances:
164 2 0.01
165 98 0.27
166 153 0.42
167 9 0.02
168 3 0.01
171 29 0.08
173 30 0.08
174 15 0.04
175 28 0.08
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (166 bp):
CAACTTTGAATCTACACTACCTGAGAATGCTTCCACACAAGTTTCAGCTTTCCTGGCCTAATGGT
TTCTGAGAAGAAGATTTTTAAAGATTTACCCTATATATTCATATGTAAAAAGTCAACCCTCCATT
GTGGCCCCACCCTACACACAAGGGTCATGATTTTCA
Found at i:989042 original size:16 final size:15
Alignment explanation
Indices: 989016--989059 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
989006 GGATGGAAGG
*
989016 ACAGA-GACAGACAG
1 ACAGACGACAGACAC
*
989030 ACAGATGGACAGACAC
1 ACAGA-CGACAGACAC
989046 ACAGACGACAGACA
1 ACAGACGACAGACA
989060 AAATGTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 13 0.50
ACGTcount: A:0.48, C:0.25, G:0.25, T:0.02
Consensus pattern (15 bp):
ACAGACGACAGACAC
Found at i:995005 original size:16 final size:16
Alignment explanation
Indices: 994984--995031 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
994974 GGGGTATCAG
994984 GAGAAAACGTACCCAA
1 GAGAAAACGTACCCAA
*
995000 GAGAAAACGTACCCAG
1 GAGAAAACGTACCCAA
995016 GAGAAAACGTACCCAA
1 GAGAAAACGTACCCAA
995032 TCTCTAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.25, G:0.21, T:0.06
Consensus pattern (16 bp):
GAGAAAACGTACCCAA
Found at i:995077 original size:31 final size:31
Alignment explanation
Indices: 995039--995099 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
995029 CAATCTCTAG
**
995039 GGTACGTTTTCTCCTGGAGAAAACGTACCCA
1 GGTACGTTTTCTCCAAGAGAAAACGTACCCA
995070 GGTACGTTTTCTCCAAGAGAAAACGTACCC
1 GGTACGTTTTCTCCAAGAGAAAACGTACCC
995100 TATGAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (31 bp):
GGTACGTTTTCTCCAAGAGAAAACGTACCCA
Found at i:996035 original size:31 final size:31
Alignment explanation
Indices: 995997--996058 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
995987 TATTTTCATA
*
995997 GGGTACGTTTTCTCTTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
996028 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
1 GGGTACGTTTTCTCCTGGAGAAAACGTACCC
996059 TATAAATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (31 bp):
GGGTACGTTTTCTCCTGGAGAAAACGTACCC
Found at i:996085 original size:16 final size:16
Alignment explanation
Indices: 996066--996113 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
996056 CCCTATAAAT
996066 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
996082 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
996098 TGGGTACGTTTTCTCC
1 TGGGTACGTTTTCTCC
996114 AGCATTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.06, C:0.25, G:0.25, T:0.44
Consensus pattern (16 bp):
TGGGTACGTTTTCTCC
Found at i:1006247 original size:2 final size:2
Alignment explanation
Indices: 1006240--1006277 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1006230 TTTACTTTCA
1006240 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1006278 GTCACGAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1020253 original size:26 final size:25
Alignment explanation
Indices: 1020201--1020256 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
1020191 TAAATATAAT
*
1020201 AAAATGTAATTAAACATTTTACCATA
1 AAAATGTAATTAAACA-TTTACAATA
1020227 AAAATGATAATTAAACA-TTACAAATA
1 AAAATG-TAATTAAACATTTAC-AATA
1020253 AAAA
1 AAAA
1020257 ATAATAAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 4 0.15
26 13 0.48
27 10 0.37
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAATGTAATTAAACATTTACAATA
Found at i:1020256 original size:27 final size:27
Alignment explanation
Indices: 1020196--1020263 Score: 70
Period size: 27 Copynumber: 2.5 Consensus size: 27
1020186 ACAAATAAAT
*
1020196 ATAATAAAATG-TAATTAAACATTTTACC
1 ATAA-AAAATGATAATTAAACA-TTTACA
1020224 AT-AAAAATGATAATTAAACA-TTACAA
1 ATAAAAAATGATAATTAAACATTTAC-A
*
1020250 ATAAAAAATAATAA
1 ATAAAAAATGATAA
1020264 AGTAATGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 4 0.11
26 8 0.23
27 21 0.60
28 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.29
Consensus pattern (27 bp):
ATAAAAAATGATAATTAAACATTTACA
Found at i:1022144 original size:21 final size:21
Alignment explanation
Indices: 1022118--1022161 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1022108 CTTCATTTGC
*
1022118 AATAACAATATTAAGAACATA
1 AATAACAATAATAAGAACATA
1022139 AATAACAATAATAAGAACATA
1 AATAACAATAATAAGAACATA
1022160 AA
1 AA
1022162 CCACTCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.09, G:0.05, T:0.20
Consensus pattern (21 bp):
AATAACAATAATAAGAACATA
Found at i:1023602 original size:18 final size:18
Alignment explanation
Indices: 1023579--1023613 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1023569 GAAGACGAGG
1023579 AAGGTCAAGGAACACCTC
1 AAGGTCAAGGAACACCTC
1023597 AAGGTCAAGGAACACCT
1 AAGGTCAAGGAACACCT
1023614 GGAGGCGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (18 bp):
AAGGTCAAGGAACACCTC
Found at i:1023931 original size:14 final size:14
Alignment explanation
Indices: 1023912--1023938 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1023902 GGTGCCATTG
1023912 TGGAGTGAGCATCA
1 TGGAGTGAGCATCA
1023926 TGGAGTGAGCATC
1 TGGAGTGAGCATC
1023939 CTTTGCTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (14 bp):
TGGAGTGAGCATCA
Found at i:1024942 original size:21 final size:20
Alignment explanation
Indices: 1024917--1024978 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
1024907 GATAAACTAG
1024917 GTTTATCGACTGTTAACTATA
1 GTTTA-CGACTGTTAACTATA
* *
1024938 GTTTACGAATCGTAAACTATA
1 GTTTACGACT-GTTAACTATA
1024959 G-TTACCGAC-GTTAATCTATA
1 GTTTA-CGACTGTTAA-CTATA
1024979 TTTCACATCT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
21 18 0.53
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (20 bp):
GTTTACGACTGTTAACTATA
Found at i:1025022 original size:39 final size:40
Alignment explanation
Indices: 1024951--1025041 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 40
1024941 TACGAATCGT
* *
1024951 AAACTATAGTTACCGACGTTAATCTATATTTCACATCTGC
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGC
* *
1024991 AAACTATAGTTAACG-CGATAATCTATGTTTCACATCTGT
1 AAACTATAGTTAACGACGATAATCTATATTTCACATCTGC
*
1025030 GAACTATAGTTA
1 AAACTATAGTTA
1025042 CCACTGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 32 0.70
40 14 0.30
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (40 bp):
AAACTATAGTTAACGACGATAATCTATATTTCACATCTGC
Found at i:1025611 original size:40 final size:40
Alignment explanation
Indices: 1025499--1025618 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 40
1025489 ATTTAAAAGA
* * * * *
1025499 CATAAACTATAATTCACGATCCTATACTATAGTTT-TAAGA
1 CATAAACTATAATTCACGTTCGTAAACTATAGTTTAT-CGT
* * * *
1025539 GATAAACTATAATTTACGTTTGTTAA-TCATAGTTTATCGT
1 CATAAACTATAATTCACGTTCGTAAACT-ATAGTTTATCGT
*
1025579 CCTAAACTATAATTCACGTTCGTAAACTATAGTTTA-CGT
1 CATAAACTATAATTCACGTTCGTAAACTATAGTTTATCGT
1025618 C
1 C
1025619 TGTTAAACAT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
39 5 0.08
40 56 0.89
41 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (40 bp):
CATAAACTATAATTCACGTTCGTAAACTATAGTTTATCGT
Found at i:1025617 original size:20 final size:19
Alignment explanation
Indices: 1025567--1025634 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 19
1025557 TTTGTTAATC
*
1025567 ATAGTTTATCGTCCTAAACT
1 ATAGTTTA-CGTCGTAAACT
* *
1025587 ATAATTCACGTTCGTAAACT
1 ATAGTTTACG-TCGTAAACT
1025607 ATAGTTTACGTCTGTTAAAC-
1 ATAGTTTACGTC-G-TAAACT
1025627 ATAGTTTA
1 ATAGTTTA
1025635 TGAGTATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
19 4 0.10
20 31 0.77
21 5 0.12
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (19 bp):
ATAGTTTACGTCGTAAACT
Found at i:1027409 original size:20 final size:20
Alignment explanation
Indices: 1027344--1027409 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
1027334 ATGTAGTTTC
* *
1027344 ACAATTTGTTAAACTATAATAA
1 ACAA-TTGTT-AATTATAATTA
* * * * *
1027366 ACAACTCTTACTTATAGTTT
1 ACAATTGTTAATTATAATTA
1027386 ACAATTGTTAATTATAATTA
1 ACAATTGTTAATTATAATTA
1027406 ACAA
1 ACAA
1027410 ATGTGAATCT
Statistics
Matches: 32, Mismatches: 12, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.78
21 3 0.09
22 4 0.12
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (20 bp):
ACAATTGTTAATTATAATTA
Found at i:1027491 original size:20 final size:20
Alignment explanation
Indices: 1027466--1027504 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1027456 CAGATAGATA
1027466 AACTAT-GATTATCATTCGTT
1 AACTATAGATTA-CATTCGTT
*
1027486 AACTATAGTTTACATTCGT
1 AACTATAGATTACATTCGT
1027505 GAAATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (20 bp):
AACTATAGATTACATTCGTT
Found at i:1027512 original size:20 final size:20
Alignment explanation
Indices: 1027478--1027578 Score: 71
Period size: 21 Copynumber: 4.9 Consensus size: 20
1027468 CTATGATTAT
*
1027478 CATTCGTTAACTATAGTTTA
1 CATTCGTTAAATATAGTTTA
*
1027498 CATTCGTGAAATATAGTTTCA
1 CATTCGTTAAATATAGTTT-A
* * *
1027519 CAGAT-GTAAAATATAGTTAA
1 CA-TTCGTTAAATATAGTTTA
* *
1027539 CGAATCGTTAACTATAGTTTA
1 C-ATTCGTTAAATATAGTTTA
*
1027560 GGATTCG-TAAACTATAGTT
1 -CATTCGTTAAA-TATAGTT
1027579 AACAGCTGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 24 0.38
21 39 0.61
22 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (20 bp):
CATTCGTTAAATATAGTTTA
Found at i:1031858 original size:168 final size:167
Alignment explanation
Indices: 1031608--1032097 Score: 734
Period size: 168 Copynumber: 2.9 Consensus size: 167
1031598 CATGTGAGGA
* * *
1031608 AAAAACTGAATGCATGGTTATGATGTCCATGA-ACCCTTCTACCAAAATTGTGAAATTCAT-AGC
1 AAAAACTAAATGCATGATTATGATGTCCATGAGGCCCTT-TACCAAAATTGTGAAATTCATGA-C
* *
1031671 CTCTGGTTCAGGGGTTCAGGCTCTAGAGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAA
64 CTCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAA
*
1031736 TGTAAGAAAATCTTCTTCTCTACTACCATTTATATTTGTT
129 TCTAAGAAAAT-TTCTTCTCTACTACCATTTATATTTGTT
*
1031776 AAAAACTAAATGCATGATTATGATGTCCATGAGGTCCTTTACCAAAATTGTGAAATTCATGACCT
1 AAAAACTAAATGCATGATTATGATGTCCATGAGGCCCTTTACCAAAATTGTGAAATTCATGACCT
* * * * *
1031841 CTGGGTCAGGCGTTCAGGCTCTAGGGTGGGGCCAATATTGCCATATAGTTAAGATGTATGAAATC
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
* *
1031906 TTAGAAAATTGTCTTCTCTACTCCCATTTATATTTGTT
131 TAAGAAAATT-TCTTCTCTACTACCATTTATATTTGTT
* * *
1031944 AAAAACTAAATGCATGACTATGATGTCCATGAGGCCCTGTACCAAAATTGTGAAATTCATGACCC
1 AAAAACTAAATGCATGATTATGATGTCCATGAGGCCCTTTACCAAAATTGTGAAATTCATGACCT
1032009 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAAAATGTATTAAA
66 CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGT--AAAAATGTATTAAA
1032074 TCTTAA-AAAATGTTCTTCTCTACT
129 TC-TAAGAAAAT-TTCTTCTCTACT
1032098 CCCACACGTG
Statistics
Matches: 291, Mismatches: 24, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
167 1 0.00
168 253 0.87
169 5 0.02
170 29 0.10
171 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (167 bp):
AAAAACTAAATGCATGATTATGATGTCCATGAGGCCCTTTACCAAAATTGTGAAATTCATGACCT
CTGGGTCAGGGGTTCAGGCTCTAGGGTGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATC
TAAGAAAATTTCTTCTCTACTACCATTTATATTTGTT
Found at i:1032118 original size:168 final size:167
Alignment explanation
Indices: 1031573--1032170 Score: 685
Period size: 168 Copynumber: 3.6 Consensus size: 167
1031563 CCAAATATTC
* * *
1031573 AAAAATCTTCTTCTCTACTTCCACA-CATGTGAGG-AAAAAACTGAATGCATGGTTATGATGTCC
1 AAAAATCTTCTTCTCTAC-TCC-CATCATATG-GGTAAAAAACTAAATGCATGATTATGATGTCC
* * *
1031636 ATGA-ACCCTTCTACCAAAATTGTGAAATTCAT-AGCCTCTGGTTCAGGGGTTCAGGCTCTAGAG
63 ATGAGGCCC-TCTACCAAAATTGTGAAATTCATGA-CCTCTGGGTCAGGGGTTCAGGCTCTAGGG
*
1031699 TGGGGCCAATATGGCCATATAGTAAAAATGTATTAAAT-GTA
126 TGGGGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* * ** *
1031740 AGAAAATCTTCTTCTCTACTACCATTTATATTTGTTAAAAACTAAATGCATGATTATGATGTCCA
1 A-AAAATCTTCTTCTCTACTCCCA-TCATATGGGTAAAAAACTAAATGCATGATTATGATGTCCA
* * *
1031805 TGAGGTCCTTTACCAAAATTGTGAAATTCATGACCTCTGGGTCAGGCGTTCAGGCTCTAGGGTGG
64 TGAGGCCCTCTACCAAAATTGTGAAATTCATGACCTCTGGGTCAGGGGTTCAGGCTCTAGGGTGG
* * * *
1031870 GGCCAATATTGCCATATAGTTAAGATGTATGAAATCTTA
129 GGCCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
* * ** * *
1031909 GAAAAT-TGTCTTCTCTACTCCCATTTATATTTGTTAAAAACTAAATGCATGACTATGATGTCCA
1 AAAAATCT-TCTTCTCTACTCCCA-TCATATGGGTAAAAAACTAAATGCATGATTATGATGTCCA
* *
1031973 TGAGGCCCTGTACCAAAATTGTGAAATTCATGACCCCTGGGTCAGGGGTTCAGGCTCTAGGGTGG
64 TGAGGCCCTCTACCAAAATTGTGAAATTCATGACCTCTGGGTCAGGGGTTCAGGCTCTAGGGTGG
1032038 GGCCAATATGGCCATATAGTAAAAAAATGTATTAAATCTTA
129 GGCCAATATGGCCATATAGT--AAAAATGTATTAAATCTTA
* ** * * ** *
1032079 AAAAATGTTCTTCTCTACTCCCA-CACGTGGGCAAAAAACTGAATAAATGGTTATGATGTCC-T-
1 AAAAATCTTCTTCTCTACTCCCATCATATGGGTAAAAAACTAAATGCATGATTATGATGTCCATG
**
1032141 -CTCTCCTCTACCAAAATTGTGAAATTCATG
66 AGGC-CCTCTACCAAAATTGTGAAATTCATG
1032171 CTCAGGGGTT
Statistics
Matches: 373, Mismatches: 46, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
165 1 0.00
166 27 0.07
167 6 0.02
168 297 0.80
169 5 0.01
170 36 0.10
171 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (167 bp):
AAAAATCTTCTTCTCTACTCCCATCATATGGGTAAAAAACTAAATGCATGATTATGATGTCCATG
AGGCCCTCTACCAAAATTGTGAAATTCATGACCTCTGGGTCAGGGGTTCAGGCTCTAGGGTGGGG
CCAATATGGCCATATAGTAAAAATGTATTAAATCTTA
Found at i:1032284 original size:336 final size:332
Alignment explanation
Indices: 1031573--1032286 Score: 705
Period size: 336 Copynumber: 2.1 Consensus size: 332
1031563 CCAAATATTC
* * ** * **
1031573 AAAAATCTTCTTCTCTACTTCCACACATGTG-AGGAAAAAACTGAATGCATGGTTATGATGTCCA
1 AAAAATTTTCTTCTCTA-TTCCACACATATGTA-TTAAAAACTAAATGCATGACTATGATGTCCA
* *
1031637 TGAACCCTTCTACCAAAATTGTGAAATTCATAGCCTCTGGTTCAGGGGTTCAGGCTCTAGAGTGG
64 TGAACCCTTCTACCAAAATTGTGAAATTCATAGCCCCTGGGTCAGGGGTTCAGGCTCTAGAGTGG
*
1031702 GGCCAATATGGCCATATAGTAAAAATGTATTAAATGTAAGAAAATCTTCTTCTCTACTACCATTT
129 GGCCAATATGGCCATATAGTAAAAATGTATTAAATGTAAGAAAATCTTCTTCTCTACTACCA-TC
* ** ** ** * *
1031767 ATATTTGTTAAAAACTAAATGCATGATTATGATGTCCATGAGGTCCTTTACCAAAATTGTGAAAT
193 ACATGGGCAAAAAACTAAATAAATGATTATGATGTCCATGAGCTCCTCTACCAAAATTGTGAAAT
* * * * * *
1031832 TCATGACCTCTGGGTCAGGCGTTCAGGCTCTAGGGTGGGGCCAATATTGCCATATAGTTAAGATG
258 TCATGA-CTCGGGGTCAGGCGATCAGGCTCGAGGGGGGGGCCAATATGGCAATATAGTTAAGATG
*
1031897 TATGAAATCTT
322 CATGAAATCTT
* * * * *
1031908 AGAAAATTGTCTTCTCTACTCC-CATTTATATTTGTTAAAAACTAAATGCATGACTATGATGTCC
1 A-AAAATTTTCTTCTCTATTCCACA--CATATGTATTAAAAACTAAATGCATGACTATGATGTCC
* * *
1031972 ATGAGGCCC-TGTACCAAAATTGTGAAATTCAT-GACCCCTGGGTCAGGGGTTCAGGCTCTAGGG
63 ATGA-ACCCTTCTACCAAAATTGTGAAATTCATAG-CCCCTGGGTCAGGGGTTCAGGCTCTAGAG
* * *
1032035 TGGGGCCAATATGGCCATATAGTAAAAAAATGTATTAAATCTTAA-AAAATGTTCTTCTCTACTC
126 TGGGGCCAATATGGCCATATAGT--AAAAATGTATTAAAT-GTAAGAAAATCTTCTTCTCTACTA
* * * **
1032099 CCA-CACGTGGGCAAAAAACTGAATAAATGGTTATGATGTCC-T-CTCTCCTCTACCAAAATTGT
188 CCATCACATGGGCAAAAAACTAAATAAATGATTATGATGTCCATGAGCTCCTCTACCAAAATTGT
* * * * *
1032161 GAAATTCATG-CTCAGGGGTTCAGGAC-ATGAGGTTGGGGGGGGGGGGGGCAATATGGCAATATA
253 GAAATTCATGACTC-GGGG-TCAGG-CGATCAGGCT--CGAGGGGGGGGCCAATATGGCAATATA
* *
1032224 GTGTTA-ATGCAT-ATAATGTTT
313 GT-TAAGATGCATGA-AAT-CTT
*
1032245 AAAAATTTTCTTCTCTATTCTCACACATCTGTATTAAAAACT
1 AAAAATTTTCTTCTCTATTC-CACACATATGTATTAAAAACT
1032287 GACATATAAT
Statistics
Matches: 305, Mismatches: 55, Indels: 37
0.77 0.14 0.09
Matches are distributed among these distances:
332 3 0.01
333 3 0.01
334 38 0.12
335 8 0.03
336 204 0.67
337 9 0.03
338 37 0.12
339 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (332 bp):
AAAAATTTTCTTCTCTATTCCACACATATGTATTAAAAACTAAATGCATGACTATGATGTCCATG
AACCCTTCTACCAAAATTGTGAAATTCATAGCCCCTGGGTCAGGGGTTCAGGCTCTAGAGTGGGG
CCAATATGGCCATATAGTAAAAATGTATTAAATGTAAGAAAATCTTCTTCTCTACTACCATCACA
TGGGCAAAAAACTAAATAAATGATTATGATGTCCATGAGCTCCTCTACCAAAATTGTGAAATTCA
TGACTCGGGGTCAGGCGATCAGGCTCGAGGGGGGGGCCAATATGGCAATATAGTTAAGATGCATG
AAATCTT
Found at i:1036545 original size:2 final size:2
Alignment explanation
Indices: 1036538--1036566 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1036528 AATATCCGCT
1036538 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1036567 TATCTATAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1036708 original size:2 final size:2
Alignment explanation
Indices: 1036701--1036763 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
1036691 TAAGCAGCTC
1036701 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1036743 CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT C
1036764 GTTTATAGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1038643 original size:2 final size:2
Alignment explanation
Indices: 1038636--1038680 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1038626 AACGTGTGCA
1038636 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1038678 TG T
1 TG T
1038681 ATATATATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1039736 original size:10 final size:10
Alignment explanation
Indices: 1039723--1039786 Score: 65
Period size: 10 Copynumber: 6.4 Consensus size: 10
1039713 GGGTGGATTT
*
1039723 TGGTGGATCG
1 TGGTGGAACG
*
1039733 TGGTGGAGCG
1 TGGTGGAACG
* *
1039743 TGGTGGATCC
1 TGGTGGAACG
*
1039753 TGGTGGAACA
1 TGGTGGAACG
*
1039763 TGGTGGAAAG
1 TGGTGGAACG
*
1039773 TGGTGGAGCG
1 TGGTGGAACG
1039783 TGGT
1 TGGT
1039787 AGAAAGATGT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 45 1.00
ACGTcount: A:0.16, C:0.09, G:0.50, T:0.25
Consensus pattern (10 bp):
TGGTGGAACG
Found at i:1039739 original size:20 final size:20
Alignment explanation
Indices: 1039723--1039786 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
1039713 GGGTGGATTT
*
1039723 TGGTGGATCGTGGTGGAGCG
1 TGGTGGATCCTGGTGGAGCG
* *
1039743 TGGTGGATCCTGGTGGAACA
1 TGGTGGATCCTGGTGGAGCG
***
1039763 TGGTGGAAAGTGGTGGAGCG
1 TGGTGGATCCTGGTGGAGCG
1039783 TGGT
1 TGGT
1039787 AGAAAGATGT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.09, G:0.50, T:0.25
Consensus pattern (20 bp):
TGGTGGATCCTGGTGGAGCG
Found at i:1039748 original size:30 final size:30
Alignment explanation
Indices: 1039723--1039779 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1039713 GGGTGGATTT
* * **
1039723 TGGTGGATCGTGGTGGAGCGTGGTGGATCC
1 TGGTGGAACATGGTGGAAAGTGGTGGATCC
1039753 TGGTGGAACATGGTGGAAAGTGGTGGA
1 TGGTGGAACATGGTGGAAAGTGGTGGA
1039780 GCGTGGTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.18, C:0.09, G:0.49, T:0.25
Consensus pattern (30 bp):
TGGTGGAACATGGTGGAAAGTGGTGGATCC
Found at i:1042605 original size:89 final size:89
Alignment explanation
Indices: 1042454--1042744 Score: 512
Period size: 89 Copynumber: 3.3 Consensus size: 89
1042444 CGTAGTAGAA
* *
1042454 CCGTGAATATGTGACTGGGGCGTTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
1 CCGTGAATGTGTGACTGGGGCATTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
1042519 CCGTAGTAGAACCGTGGAGTTGAT
66 CCGTAGTAGAACCGTGGAGTTGAT
1042543 CCGTGAATGTGTGACTGGGGCATTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
1 CCGTGAATGTGTGACTGGGGCATTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
*
1042608 CCGTAGTAGAACC-TAGGAGTAGAT
66 CCGTAGTAGAACCGT-GGAGTTGAT
* * *
1042632 CTGTGAATGTGTGACTGGGGCATTAGCGATTATTTGATTTTGCGGTGTCAACCGTGGAAAATATT
1 CCGTGAATGTGTGACTGGGGCATTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
1042697 CCGTAGTAGAACCGTGGAGTTGAT
66 CCGTAGTAGAACCGTGGAGTTGAT
1042721 CCGTGAATGTGTGACTGGGGCATT
1 CCGTGAATGTGTGACTGGGGCATT
1042745 TCCCACTTTT
Statistics
Matches: 192, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
88 1 0.01
89 190 0.99
90 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.31
Consensus pattern (89 bp):
CCGTGAATGTGTGACTGGGGCATTAACGATTATTTGATTTTCCGGTGTCAACCGTGGAAAATATT
CCGTAGTAGAACCGTGGAGTTGAT
Found at i:1043405 original size:21 final size:22
Alignment explanation
Indices: 1043366--1043407 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1043356 GAGGTCGTTG
**
1043366 AACCACAATGAACCGCAATGAT
1 AACCACAATGAACAACAATGAT
1043388 AACC-CAATGAACAACAATGA
1 AACCACAATGAACAACAATGA
1043408 ACTTATATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.50, C:0.26, G:0.12, T:0.12
Consensus pattern (22 bp):
AACCACAATGAACAACAATGAT
Found at i:1046188 original size:2 final size:2
Alignment explanation
Indices: 1046181--1046227 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1046171 AATTTAACAC
1046181 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1046223 AG AG A
1 AG AG A
1046228 TATCCCCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1047989 original size:35 final size:35
Alignment explanation
Indices: 1047895--1047989 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
1047885 TAACCCCCTT
* *
1047895 CCCCACAGTAACGCAC-TTCTACGCATATACCGTTG
1 CCCCACAATCACGCACTTTC-ACGCATATACCGTTG
* * * *
1047930 CCCCACAATCACGCATTTTGACGCATATACCTTTT
1 CCCCACAATCACGCACTTTCACGCATATACCGTTG
*
1047965 CCCCGCAATCACGCACTTTCACGCA
1 CCCCACAATCACGCACTTTCACGCA
1047990 CTTTTCGTTG
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 48 0.96
36 2 0.04
ACGTcount: A:0.25, C:0.39, G:0.12, T:0.24
Consensus pattern (35 bp):
CCCCACAATCACGCACTTTCACGCATATACCGTTG
Found at i:1057814 original size:161 final size:160
Alignment explanation
Indices: 1057486--1057906 Score: 680
Period size: 161 Copynumber: 2.6 Consensus size: 160
1057476 ATAACTTTGT
*
1057486 TCGATCTTACCCAATATCAAACTTGACCTAGATATTATCATGATATAAACCTGTATACCAAATTT
1 TCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATG--ATAAACCTGTATACCAAATTT
* * * *
1057551 CATTTCAATATGTTCATCCTCTGAGAAGAAAATGAGGGAAACTGTAAATAACTGGAATTTTTCTA
64 CATTCCAATATGTTCATCCTCTGCGAAGAAAATGAGAGAAACTGTAAATAACTGGAATTTGTCTA
* *
1057616 TGTCCAAGGGCCATAACTCTATTGAAAATTGC
129 CGTCCAAGGGCCATAACTCTATTGAAAATAGC
* * *
1057648 TCGATCGTACCCTATATCGAACTTGACCTAGATATTATCATGATAAACCTGTAAACCAAATTTCA
1 TCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCA
*
1057713 TTCCAATATGTTCATCCTCTGCGAAGAAAATGAGCAGAAATTGTAAATAACTGGAATTTGTCTAC
66 TTCCAATATGTTCATCCTCTGCGAAGAAAATGAG-AGAAACTGTAAATAACTGGAATTTGTCTAC
1057778 GTCCAAGGGCCATAACTCTATTGAAAATAGC
130 GTCCAAGGGCCATAACTCTATTGAAAATAGC
* * *
1057809 TCGATCGTACCCAAAATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACTAAATTTAA
1 TCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCA
*
1057874 TTCCAATATGTTCATCCTCTGCAAAGAAAATGA
66 TTCCAATATGTTCATCCTCTGCGAAGAAAATGA
1057907 ATGGAAACTG
Statistics
Matches: 240, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
160 54 0.22
161 147 0.61
162 39 0.16
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (160 bp):
TCGATCGTACCCAATATCAAACTTGACCTAGATATTATCATGATAAACCTGTATACCAAATTTCA
TTCCAATATGTTCATCCTCTGCGAAGAAAATGAGAGAAACTGTAAATAACTGGAATTTGTCTACG
TCCAAGGGCCATAACTCTATTGAAAATAGC
Found at i:1065359 original size:14 final size:14
Alignment explanation
Indices: 1065340--1065368 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1065330 TACAGAGATA
1065340 TCGGGGTTTAAAAG
1 TCGGGGTTTAAAAG
1065354 TCGGGGTTTAAAAG
1 TCGGGGTTTAAAAG
1065368 T
1 T
1065369 TGATTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.07, G:0.34, T:0.31
Consensus pattern (14 bp):
TCGGGGTTTAAAAG
Found at i:1071905 original size:12 final size:11
Alignment explanation
Indices: 1071884--1071908 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1071874 ACAGCCATGG
1071884 GATTAAAAAAA
1 GATTAAAAAAA
1071895 GATTAAAAAAA
1 GATTAAAAAAA
1071906 GAT
1 GAT
1071909 GGACGCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (11 bp):
GATTAAAAAAA
Found at i:1073641 original size:31 final size:32
Alignment explanation
Indices: 1073544--1073664 Score: 165
Period size: 32 Copynumber: 3.8 Consensus size: 32
1073534 AGCTACAAAT
* *
1073544 ATTTCATCGGTCTGAGGTTGTTTTTGAGGCGG
1 ATTTCCTCGGTCTGATGTTGTTTTTGAGGCGG
*
1073576 ATTTCCTCGGCCTGATGTTGTTTTTGAGGCGG
1 ATTTCCTCGGTCTGATGTTGTTTTTGAGGCGG
* *
1073608 ATTTCCTCGGTCTGATGTT-TTTTTTAGGTGG
1 ATTTCCTCGGTCTGATGTTGTTTTTGAGGCGG
*
1073639 ATTTCAC-CGGTCTGGTGTTGTTTTTG
1 ATTTC-CTCGGTCTGATGTTGTTTTTG
1073665 GAGATGTCCT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 26 0.33
32 53 0.67
ACGTcount: A:0.10, C:0.15, G:0.30, T:0.45
Consensus pattern (32 bp):
ATTTCCTCGGTCTGATGTTGTTTTTGAGGCGG
Found at i:1073660 original size:63 final size:64
Alignment explanation
Indices: 1073544--1073664 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 64
1073534 AGCTACAAAT
1073544 ATTTCATCGGTCTGAGGTTGTTTTTGAGGCGGATTTCCTCGGCCTGATGTTGTTTTTGAGGCGG
1 ATTTCATCGGTCTGAGGTTGTTTTTGAGGCGGATTTCCTCGGCCTGATGTTGTTTTTGAGGCGG
* * * * * *
1073608 ATTTCCTCGGTCTGATGTT-TTTTTTAGGTGGATTTCAC-CGGTCTGGTGTTGTTTTTG
1 ATTTCATCGGTCTGAGGTTGTTTTTGAGGCGGATTTC-CTCGGCCTGATGTTGTTTTTG
1073665 GAGATGTCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 32 0.64
64 18 0.36
ACGTcount: A:0.10, C:0.15, G:0.30, T:0.45
Consensus pattern (64 bp):
ATTTCATCGGTCTGAGGTTGTTTTTGAGGCGGATTTCCTCGGCCTGATGTTGTTTTTGAGGCGG
Found at i:1088745 original size:24 final size:25
Alignment explanation
Indices: 1088555--1089741 Score: 1774
Period size: 25 Copynumber: 48.0 Consensus size: 25
1088545 CTTAGCTTAA
1088555 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
**
1088580 ACCATTCCCCCGTGGAAAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088605 ACCATTCCCCCCGTGGATTAATCCTG
1 ACCATT-CCCCCGTGGATTAATCCTG
**
1088631 ACCATTTTCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088656 ACCATTCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088681 ACCATTCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088706 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088731 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088755 ACCATTCCCCCCGTGGATTAATCCTG
1 ACCATT-CCCCCGTGGATTAATCCTG
*
1088781 ACCATTCCCCCGTGTATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088806 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088831 ACCATTCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088856 ACTATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088881 ACCATTCCCCCGTGTATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1088906 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088931 ACCATTCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1088956 ACTATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
** *
1088981 ACCATTCCCCCGTGGATTTGTACTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089006 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
**
1089030 AAAATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089054 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* *
1089078 ACCATTCCCCCGTGGATAAATCATG
1 ACCATTCCCCCGTGGATTAATCCTG
1089103 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089128 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089152 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089176 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089200 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1089225 ACCATTCCCCCGTAGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
**
1089250 ACCA-TCCCCCGTTCATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089274 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089298 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089322 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1089346 ACCATTCCCCCGTCGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* *
1089371 ACCATTTCCCCGTAGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* **
1089396 ACCATTCCCCCCTTCATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
**
1089421 ACCATTCCCCC-TTCATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089445 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089469 ACCATT-CCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* * *
1089493 ACCATTCTCCCGTGGATAAATCATG
1 ACCATTCCCCCGTGGATTAATCCTG
* * * * *
1089518 ACCAATCTCCCGTGGATAAATTCTT
1 ACCATTCCCCCGTGGATTAATCCTG
* *
1089543 ACCATTTCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* * * *
1089568 ACCAATCCCCCATGGATAAATCATG
1 ACCATTCCCCCGTGGATTAATCCTG
1089593 ACCATTCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* * *
1089618 AACATCCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1089643 ACCATTCCCCCGTGGATAAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* *
1089668 ACCATT-CCCCGTGGATAAACCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
* *
1089692 ACCATTCCCCCGTGGATAAATACTG
1 ACCATTCCCCCGTGGATTAATCCTG
*
1089717 ACCATCCCCCCGTGGATTAATCCTG
1 ACCATTCCCCCGTGGATTAATCCTG
1089742 GTAGGCAGTT
Statistics
Matches: 1071, Mismatches: 81, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
23 4 0.00
24 336 0.31
25 684 0.64
26 47 0.04
ACGTcount: A:0.22, C:0.35, G:0.15, T:0.28
Consensus pattern (25 bp):
ACCATTCCCCCGTGGATTAATCCTG
Found at i:1090136 original size:2 final size:2
Alignment explanation
Indices: 1090124--1090160 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
1090114 TTCATACAAT
1090124 GA GA TGA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA -GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1090161 TTGCATGACA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1094565 original size:2 final size:2
Alignment explanation
Indices: 1094558--1094622 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1094548 NNNNNNNNNN
1094558 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1094600 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1094623 GATGGATTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1097587 original size:47 final size:47
Alignment explanation
Indices: 1097518--1097702 Score: 334
Period size: 47 Copynumber: 3.9 Consensus size: 47
1097508 CACAGACATG
*
1097518 TACAACGTTAACGTGAGTGAAATCTATATTTGTTCAATCTCACCACA
1 TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACCACA
*
1097565 TACAACGTTAATGTGAGTGAAATCTATACTTGTTCAATCTCACCACA
1 TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACCACA
* *
1097612 TACAACGTTAATGTGAGTGAAATCTATATTTGTTCAATCTCACCACA
1 TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACCACA
1097659 TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACC
1 TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACC
1097703 TCACATCCTT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 133 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (47 bp):
TACAACGTTAACGTGAGTGAAATCTATACTTGTTCAATCTCACCACA
Found at i:1099618 original size:2 final size:2
Alignment explanation
Indices: 1099611--1099648 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1099601 CTGGCGTAAG
1099611 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1099649 AACTGGTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1100360 original size:4 final size:4
Alignment explanation
Indices: 1100345--1100392 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
1100335 ATTGATAAAN
* * * *
1100345 CTGT CCGT CTGT CTGT CTGT CCGT CTGT CCGT CTGT CCGT CTGT CTGT
1 CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
1100393 AGACGCAACT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (4 bp):
CTGT
Found at i:1100362 original size:8 final size:8
Alignment explanation
Indices: 1100345--1100389 Score: 81
Period size: 8 Copynumber: 5.6 Consensus size: 8
1100335 ATTGATAAAN
1100345 CTGTCCGT
1 CTGTCCGT
*
1100353 CTGTCTGT
1 CTGTCCGT
1100361 CTGTCCGT
1 CTGTCCGT
1100369 CTGTCCGT
1 CTGTCCGT
1100377 CTGTCCGT
1 CTGTCCGT
1100385 CTGTC
1 CTGTC
1100390 TGTAGACGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.00, C:0.36, G:0.24, T:0.40
Consensus pattern (8 bp):
CTGTCCGT
Found at i:1103550 original size:29 final size:29
Alignment explanation
Indices: 1103508--1103779 Score: 436
Period size: 29 Copynumber: 9.4 Consensus size: 29
1103498 TCTGCAGCTA
1103508 CTGTATGTATACAGTAATTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103537 CTGTATGTATACAGTAGTTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
* * *
1103566 CTGTATATATACAGTGATATTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103595 CTGTATGTATACAGTGATTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
1103624 CTGTATGTATACAGTAATTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103653 CTGTATGTATACAGTGATTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103682 CTGTATGTATACAGTAGTTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103711 CTGTATGTATACAGTAGTTTTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
* * *
1103740 CTGTATATAAACAGTAATATTGTTTTTAC
1 CTGTATGTATACAGTAATTTTGTTTTTAC
*
1103769 CTGTATTTATA
1 CTGTATGTATA
1103780 TAGTTTTCCC
Statistics
Matches: 226, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 226 1.00
ACGTcount: A:0.24, C:0.10, G:0.15, T:0.51
Consensus pattern (29 bp):
CTGTATGTATACAGTAATTTTGTTTTTAC
Found at i:1108505 original size:25 final size:25
Alignment explanation
Indices: 1106184--1108489 Score: 2814
Period size: 25 Copynumber: 91.8 Consensus size: 25
1106174 GACCAACAGA
1106184 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1106209 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
*
1106234 GTTGTCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
1106259 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1106284 GTTATCATGTAGGTATATATACGGG
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1106309 GTTGTTATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
*
1106334 GTTATCATGTAGGTATATATACGGG
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1106359 GTTATCATATATGTATATGTAAGGA
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1106384 TTTTTCATGTATGTATATGTACTGG
1 GTTATCATGTAGGTATATGTACGGG
*
1106409 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106434 GTTTTTATGTAGGTATATGAACGGG
1 GTTATCATGTAGGTATATGTACGGG
* *
1106459 GTTAACATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1106484 GTTTTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
1106509 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* *
1106534 GTTATCATATAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
1106559 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106584 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1106609 GTTGTTATGTAGGTATATGTATGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1106634 GTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1106659 GTTATCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1106684 GTTGTTATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106709 TTTATCATGTAGGTATATATACGGA
1 GTTATCATGTAGGTATATGTACGGG
* **
1106734 GTTATCATGTTGGTATATGTACGTA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106759 GTTGTTAAGTAGGTATATGTTA-GGG
1 GTTATCATGTAGGTATATG-TACGGG
* * **
1106784 CTTATCATGTAGTTATATGTACGTA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106809 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1106834 GTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
1106859 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1106884 GTTATATCATGTAGATATATGTACGGG
1 G-T-TATCATGTAGGTATATGTACGGG
**
1106911 GTTATCATGTAGGTATATGTACGTA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106936 GTTGTTATGTAGGTATATGTAAGGG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106961 CTTATCATGTAGTTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1106986 GTTGTGATGTTGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
1107011 GTTATCATGTAGGTATATGTACGGAG
1 GTTATCATGTAGGTATATGTACGG-G
* *
1107037 TTATATCATGTAGGTATATGTATGGG
1 GT-TATCATGTAGGTATATGTACGGG
* * *
1107063 GTTATCATGTAGGTTTATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1107088 GTTACCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107113 CTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1107138 GTTATC-----GGTATATGTATGGG
1 GTTATCATGTAGGTATATGTACGGG
1107158 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1107183 GTTATCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
*
1107208 GTTATCATGTAGGTATATGTATGGG
1 GTTATCATGTAGGTATATGTACGGG
1107233 GTTATCATGTAGGTATATGTACGGAG
1 GTTATCATGTAGGTATATGTACGG-G
*
1107259 GTGT-TACA--TAGGTATATGTACGGA
1 GT-TAT-CATGTAGGTATATGTACGGG
* *
1107283 GTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1107308 GTTATCATGTAGGTATGTGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* **
1107333 GTTATCATGTAGGCATATGTATTGG
1 GTTATCATGTAGGTATATGTACGGG
*
1107358 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* ** * *
1107383 GTTTTCATGTATATATATGCACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1107408 GTTGTTATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107433 TTTATCATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1107458 GTTATAATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1107483 GTTGTTATGTAGGTTTATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107508 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107533 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107558 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1107583 GTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* *
1107608 GTTATCACGTAGGTATATGTACGGAA
1 GTTATCATGTAGGTATATGTACGG-G
* * *
1107634 G-TGTGATTTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
1107658 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
*
1107684 GTTATCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
*
1107709 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1107734 GTTGTTATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1107759 GTTATCATTTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1107785 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
*
1107811 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1107836 GTTTTTATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1107861 ATTCTCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
1107886 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1107912 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1107938 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1107964 GTTATCATGTAGGTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* * * *
1107989 GTTTTTATGTAGGTATATGTACAGA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1108014 ATTCTCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
1108039 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1108065 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1108091 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
**
1108117 GTTATCATGTAGGTATATGTACGTA
1 GTTATCATGTAGGTATATGTACGGG
* * *
1108142 GTTTTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1108167 GTTCTCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
1108192 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
1108218 GTTATCATGTAGGTATATGTACGGGG
1 GTTATCATGTAGGTATATGTAC-GGG
*
1108244 GTTATCATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * * * *
1108269 GTTGTTATGTAGATTTATGTAAGGG
1 GTTATCATGTAGGTATATGTACGGG
*
1108294 GTTATCATGTAGTTATATGTACGGG
1 GTTATCATGTAGGTATATGTACGGG
* *
1108319 GTTATCATGTAGTTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1108344 GTTGTTATGTAGGTATATGTACGTG
1 GTTATCATGTAGGTATATGTACGGG
* * *
1108369 GTTGTTATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
*
1108394 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
*
1108419 GTTATCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
* *
1108444 GTTGTCATGTAGGTATATGTACGGA
1 GTTATCATGTAGGTATATGTACGGG
*
1108469 GTTATCCTGTAGGTATATGTA
1 GTTATCATGTAGGTATATGTA
1108490 TAAAGTTATT
Statistics
Matches: 1996, Mismatches: 261, Indels: 48
0.87 0.11 0.02
Matches are distributed among these distances:
20 19 0.01
23 2 0.00
24 6 0.00
25 1632 0.82
26 290 0.15
27 47 0.02
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.39
Consensus pattern (25 bp):
GTTATCATGTAGGTATATGTACGGG
Found at i:1109144 original size:22 final size:22
Alignment explanation
Indices: 1109119--1109245 Score: 254
Period size: 22 Copynumber: 5.8 Consensus size: 22
1109109 ATTTCTGTAT
1109119 TTACACTTACCGATATAATTGG
1 TTACACTTACCGATATAATTGG
1109141 TTACACTTACCGATATAATTGG
1 TTACACTTACCGATATAATTGG
1109163 TTACACTTACCGATATAATTGG
1 TTACACTTACCGATATAATTGG
1109185 TTACACTTACCGATATAATTGG
1 TTACACTTACCGATATAATTGG
1109207 TTACACTTACCGATATAATTGG
1 TTACACTTACCGATATAATTGG
1109229 TTACACTTACCGATATA
1 TTACACTTACCGATATA
1109246 CACTTACCGA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (22 bp):
TTACACTTACCGATATAATTGG
Found at i:1109249 original size:14 final size:14
Alignment explanation
Indices: 1109230--1109259 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1109220 TATAATTGGT
1109230 TACACTTACCGATA
1 TACACTTACCGATA
1109244 TACACTTACCGATA
1 TACACTTACCGATA
1109258 TA
1 TA
1109260 ATTGGTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (14 bp):
TACACTTACCGATA
Found at i:1115774 original size:2 final size:2
Alignment explanation
Indices: 1115767--1115874 Score: 180
Period size: 2 Copynumber: 54.0 Consensus size: 2
1115757 ATTTCACCCG
* * * *
1115767 TC TC TC TC TC TC TC TC TC TC TC TC TC CC CC TC TC TA TC TC CC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1115809 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1115851 TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
1115875 CAAAGTAAGT
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.01, C:0.52, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1131753 original size:32 final size:33
Alignment explanation
Indices: 1131684--1131763 Score: 144
Period size: 32 Copynumber: 2.5 Consensus size: 33
1131674 GGCCTCCCCA
1131684 TTAGGGCATTAGACACCATAGTTGGGGCGCCCG
1 TTAGGGCATTAGACACCATAGTTGGGGCGCCCG
*
1131717 TTAGGGCATTAGACACCATAGTT-GGGTGCCCG
1 TTAGGGCATTAGACACCATAGTTGGGGCGCCCG
1131749 TTAGGGCATTAGACA
1 TTAGGGCATTAGACA
1131764 GGTTGGGACC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 23 0.50
33 23 0.50
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (33 bp):
TTAGGGCATTAGACACCATAGTTGGGGCGCCCG
Found at i:1131826 original size:19 final size:19
Alignment explanation
Indices: 1131779--1131832 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
1131769 GGACCACTCT
1131779 CCCAATTGGGATATAATAG
1 CCCAATTGGGATATAATAG
***
1131798 CCGGTTTGGGATATAATAG
1 CCCAATTGGGATATAATAG
*
1131817 CCCAAATGGGATATAA
1 CCCAATTGGGATATAA
1131833 ATTTTAAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (19 bp):
CCCAATTGGGATATAATAG
Found at i:1133041 original size:19 final size:19
Alignment explanation
Indices: 1133017--1133069 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
1133007 ACTTAAAATG
1133017 TATATCCCATTTGGGCTAT
1 TATATCCCATTTGGGCTAT
***
1133036 TATATCCCAAACGGGCTAT
1 TATATCCCATTTGGGCTAT
1133055 TATATCCCATTTGGG
1 TATATCCCATTTGGG
1133070 AGAGTGATCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (19 bp):
TATATCCCATTTGGGCTAT
Found at i:1138186 original size:2 final size:2
Alignment explanation
Indices: 1138179--1138203 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1138169 ATTCAATACT
1138179 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1138204 TACAATCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1138470 original size:27 final size:27
Alignment explanation
Indices: 1138431--1138536 Score: 185
Period size: 27 Copynumber: 3.9 Consensus size: 27
1138421 ACAGTGATTG
*
1138431 ATTGATCCGTGCATTATTTCCATGCTT
1 ATTGATCCATGCATTATTTCCATGCTT
1138458 ATTGATCCATGCATTATTTCCATGCTT
1 ATTGATCCATGCATTATTTCCATGCTT
*
1138485 ATTGATCCGTGCATTATTTCCATGCTT
1 ATTGATCCATGCATTATTTCCATGCTT
*
1138512 ATTGACCCATGCATTATTTCCATGC
1 ATTGATCCATGCATTATTTCCATGC
1138537 GTCAGCGAAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (27 bp):
ATTGATCCATGCATTATTTCCATGCTT
Found at i:1143610 original size:80 final size:80
Alignment explanation
Indices: 1143477--1143980 Score: 735
Period size: 80 Copynumber: 6.3 Consensus size: 80
1143467 AGCTGATTTT
* *
1143477 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACAGTTTCA
1 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCCA
1143542 TTGTTCAGTAACTTC
66 TTGTTCAGTAACTTC
1143557 TTGCTGCGTAATTATACACGGTC-TTCTGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCC
1 TTGCTGCGTAATTATACACGGTCTTTC-GTGCTCAGTAACTCAATGTGTCAATATACACGGTTCC
1143621 ATTGTTCAGTAACTTC
65 ATTGTTCAGTAACTTC
1143637 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCCA
1 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCCA
*
1143702 TTGTTCTGTAACTTC
66 TTGTTCAGTAACTTC
* * * *
1143717 TTGCTGCGTAATTATACACGGTC-TTCTGTGTTCAGTAACTTAATGTGTCAATATACACAGTTTC
1 TTGCTGCGTAATTATACACGGTCTTTC-GTGCTCAGTAACTCAATGTGTCAATATACACGGTTCC
1143781 ATTGTTCAGTAACTTC
65 ATTGTTCAGTAACTTC
* *
1143797 TTGCTGCGTAATTCTACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATACACACGGTCTCC
1 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGT-TCC
**
1143862 CGTGTTCAGTAACTTC
65 ATTGTTCAGTAACTTC
* * * * * * * ** * **
1143878 TTGCTGCGTAATTATACACGGCCCTCCATGTTCAATAACTTAATGTGTCAATATA-TTGTTTTTA
1 TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCCA
1143942 TTGTTCAGTAACTTC
66 TTGTTCAGTAACTTC
* *
1143957 TTGCTGTGTAATTATGCACGGTCT
1 TTGCTGCGTAATTATACACGGTCT
1143981 CCCGTGTTCA
Statistics
Matches: 383, Mismatches: 36, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
79 41 0.11
80 274 0.72
81 68 0.18
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (80 bp):
TTGCTGCGTAATTATACACGGTCTTTCGTGCTCAGTAACTCAATGTGTCAATATACACGGTTCCA
TTGTTCAGTAACTTC
Found at i:1144230 original size:16 final size:16
Alignment explanation
Indices: 1144208--1144245 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1144198 TGACGGACAT
*
1144208 CTGTGTACTGTAGTAC
1 CTGTGTACTATAGTAC
*
1144224 TTGTGTACTATAGTAC
1 CTGTGTACTATAGTAC
1144240 CTGTGT
1 CTGTGT
1144246 TTGAGTACCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (16 bp):
CTGTGTACTATAGTAC
Found at i:1145427 original size:2 final size:2
Alignment explanation
Indices: 1145420--1145459 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1145410 CTAAAATCAA
1145420 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1145460 GGGGCTTACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1150105 original size:29 final size:29
Alignment explanation
Indices: 1150071--1150193 Score: 246
Period size: 29 Copynumber: 4.2 Consensus size: 29
1150061 GTATTACATG
1150071 TAAACAAACTGTGTGTATATCTACATATA
1 TAAACAAACTGTGTGTATATCTACATATA
1150100 TAAACAAACTGTGTGTATATCTACATATA
1 TAAACAAACTGTGTGTATATCTACATATA
1150129 TAAACAAACTGTGTGTATATCTACATATA
1 TAAACAAACTGTGTGTATATCTACATATA
1150158 TAAACAAACTGTGTGTATATCTACATATA
1 TAAACAAACTGTGTGTATATCTACATATA
1150187 TAAACAA
1 TAAACAA
1150194 NNNNNNNNNN
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 94 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (29 bp):
TAAACAAACTGTGTGTATATCTACATATA
Found at i:1151710 original size:219 final size:220
Alignment explanation
Indices: 1151327--1151772 Score: 777
Period size: 219 Copynumber: 2.0 Consensus size: 220
1151317 TACAAGGTCA
* *
1151327 CAAAGTCCCATAACTCCAACAAAAAGTATCGACCAATACTGATTTTCGAACTTAACCAAGGTAAT
1 CAAAGTCCCAGAACTCAAACAAAAAGTATCGACCAATACTGATTTTCGAACTTAACCAAGGTAAT
* * *
1151392 AGTGGTATGAACATTTGTTATAAATTTATTGAAAATCCGTCAAAATTTGTACGCATGAGAGCGCT
66 AGTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTACGCATGAGAGCGCT
* *
1151457 TACAAAAAAGTGTGATAAATCCGTCAATATTTGTAGGCATGAGAGCGCTTATAAGGTCAATTTTT
131 TACAAAAAAGTGTGATAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTT
1151522 GGATAAACC-AGTCATTATTGTGGT
196 GGATAAACCAAGTCATTATTGTGGT
* *
1151546 CAAAGTCCCAGAACTCAAACAAAAAGTATCGACCAATGCTGATTTTCGAACTTGACCAAGGTAAT
1 CAAAGTCCCAGAACTCAAACAAAAAGTATCGACCAATACTGATTTTCGAACTTAACCAAGGTAAT
*
1151611 AGTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTTAAAATTTGTACGCATGAGAGCGCT
66 AGTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTACGCATGAGAGCGCT
1151676 TACAAAAAAGTGTGATAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTT
131 TACAAAAAAGTGTGATAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTT
*
1151741 TGATAAACCAGAGTCATTATTGTGGT
196 GGATAAACCA-AGTCATTATTGTGGT
1151767 CAAAGT
1 CAAAGT
1151773 ATTAGTGTTA
Statistics
Matches: 214, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
219 193 0.90
221 21 0.10
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (220 bp):
CAAAGTCCCAGAACTCAAACAAAAAGTATCGACCAATACTGATTTTCGAACTTAACCAAGGTAAT
AGTGGTATAAACATTTGGTATAAATTTAATGAAAATCCGTCAAAATTTGTACGCATGAGAGCGCT
TACAAAAAAGTGTGATAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTT
GGATAAACCAAGTCATTATTGTGGT
Found at i:1152104 original size:165 final size:162
Alignment explanation
Indices: 1151832--1152156 Score: 526
Period size: 165 Copynumber: 2.0 Consensus size: 162
1151822 TTGTAGGCAA
1151832 GAGAGCGCGTACAAGGTCACAAAGTCCCATAACTCCAACAAAAAGTATCAACCAATGCTGATTTT
1 GAGAGCGCGTACAAGGTCACAAAGTCCCATAACTCCAACAAAAAGTATCAACCAATGCTGATTTT
* * * * *
1151897 CGAATTTGACCATGGTAATAGTGGTATAAACATTTGGTATAAATATTAAAATGAAAATCCGTTAA
66 CAAACTTGACCATGGTAATAGTGATATAAACATTTGGTATAAAT-CT--AATGAAAATCCGTCAA
1151962 AATTTGTAGGCATGAGAGCGCTTACAAAAAAGTAT
128 AATTTGTAGGCATGAGAGCGCTTACAAAAAAGTAT
* *
1151997 GAGAGCGCTTACAAGGTCACAAAGTCCCATAACTCCAACAAAACGTATCAACCAATGCTGATTTT
1 GAGAGCGCGTACAAGGTCACAAAGTCCCATAACTCCAACAAAAAGTATCAACCAATGCTGATTTT
1152062 CAAACTTGACCGA-GGTAATAGTGATATAAACATTTGGTATAAATCTAATGAAAATCCGTCAAAA
66 CAAACTTGACC-ATGGTAATAGTGATATAAACATTTGGTATAAATCTAATGAAAATCCGTCAAAA
* *
1152126 TTTGTAGGCGTGAGATCGCTTACAAAAAAGT
130 TTTGTAGGCATGAGAGCGCTTACAAAAAAGT
1152157 GTGACAGACG
Statistics
Matches: 150, Mismatches: 9, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
162 46 0.31
164 1 0.01
165 102 0.68
166 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (162 bp):
GAGAGCGCGTACAAGGTCACAAAGTCCCATAACTCCAACAAAAAGTATCAACCAATGCTGATTTT
CAAACTTGACCATGGTAATAGTGATATAAACATTTGGTATAAATCTAATGAAAATCCGTCAAAAT
TTGTAGGCATGAGAGCGCTTACAAAAAAGTAT
Found at i:1153512 original size:17 final size:17
Alignment explanation
Indices: 1153490--1153522 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1153480 TCTATAACAA
1153490 TCGGCAATAATGGGTAG
1 TCGGCAATAATGGGTAG
1153507 TCGGCAATAATGGGTA
1 TCGGCAATAATGGGTA
1153523 CATATGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.24
Consensus pattern (17 bp):
TCGGCAATAATGGGTAG
Found at i:1159809 original size:21 final size:23
Alignment explanation
Indices: 1159756--1159802 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1159746 AAATAAGGTA
1159756 TCTGTGACATTATTTTTTCTCAT
1 TCTGTGACATTATTTTTTCTCAT
1159779 TCTGTGACATTATTTTTTCTCAT
1 TCTGTGACATTATTTTTTCTCAT
1159802 T
1 T
1159803 GATACATACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.09, T:0.57
Consensus pattern (23 bp):
TCTGTGACATTATTTTTTCTCAT
Found at i:1166955 original size:21 final size:21
Alignment explanation
Indices: 1166929--1166987 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
1166919 GTAAAACGTA
*
1166929 TGCAACGAATGCAAGAGTTCG
1 TGCAACGAATGCGAGAGTTCG
*
1166950 TGCAACGTAA-GCGAGGGTTCG
1 TGCAACG-AATGCGAGAGTTCG
* *
1166971 TCCAACGTATGCGAGAG
1 TGCAACGAATGCGAGAG
1166988 CTCGCGCGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.29, C:0.20, G:0.32, T:0.19
Consensus pattern (21 bp):
TGCAACGAATGCGAGAGTTCG
Done.