Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3824
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 165587
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:9368 original size:47 final size:47
Alignment explanation
Indices: 9290--9972 Score: 1141
Period size: 47 Copynumber: 14.3 Consensus size: 47
9280 CCCTTCGGGA
* * * * * *
9290 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
9337 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9384 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9431 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9478 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9525 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
9574 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9623 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9670 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
9719 CTTATCACATATATATACACTTTCACATTCATCACATCAGCTATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9768 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
9815 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
9864 CTTATCATATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9911 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
9958 CTTATCACATATATA
1 CTTATCACATATATA
9973 TATCTACATA
Statistics
Matches: 606, Mismatches: 24, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
47 373 0.62
49 233 0.38
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:9566 original size:96 final size:94
Alignment explanation
Indices: 9290--9972 Score: 1141
Period size: 96 Copynumber: 7.2 Consensus size: 94
9280 CCCTTCGGGA
* * * * * * * *
9290 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
9355 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
9384 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
9449 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
9478 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
9543 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
*
9574 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9639 ACTTTCACATTCATCACATCGGCCATTAGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
9670 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
* *
9735 ACACTTTCACATTCATCACATCAGCTATTAGGC
62 ACACTTTCACATTCATCACATCGGCCATTAGGC
9768 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
* *
9833 ACTTTCACATTCATCACATTGGCCATTCGGC
64 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
9864 CTTATCATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
9929 TTTCACATTCATCACATCGGCCATTAGGC
66 TTTCACATTCATCACATCGGCCATTAGGC
9958 CTTATCACATATATA
1 CTTATCACATATATA
9973 TATCTACATA
Statistics
Matches: 562, Mismatches: 21, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
94 192 0.34
96 279 0.50
98 91 0.16
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (94 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGC
Found at i:9642 original size:145 final size:145
Alignment explanation
Indices: 9290--9974 Score: 1197
Period size: 145 Copynumber: 4.8 Consensus size: 145
9280 CCCTTCGGGA
* * * * * * *
9290 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9353 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
9416 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
9431 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9494 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
9559 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
*
9574 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9639 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
9704 CATCGGCCATTAGGC
131 CATCGGCCATTAGGC
* *
9719 CTTATCACATATATATACACTTTCACATTCATCACATCAGCTATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9784 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
* *
9849 CATTGGCCATTCGGC
131 CATCGGCCATTAGGC
*
9864 CTTAT--CATATATATACACTTTCACATTCATCACATCAGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
9927 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATA
9975 TCTACATATA
Statistics
Matches: 524, Mismatches: 14, Indels: 10
0.96 0.03 0.02
Matches are distributed among these distances:
140 1 0.00
141 92 0.18
143 152 0.29
145 279 0.53
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (145 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
CATCGGCCATTAGGC
Found at i:9983 original size:14 final size:14
Alignment explanation
Indices: 9960--10000 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
9950 CATTAGGCCT
9960 TATC-ACATATATA
1 TATCTACATATATA
*
9973 TATCTACATATACA
1 TATCTACATATATA
*
9987 TATCT-CATACATA
1 TATCTACATATATA
10000 T
1 T
10001 TTCACATTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (14 bp):
TATCTACATATATA
Found at i:10049 original size:48 final size:48
Alignment explanation
Indices: 9978--10194 Score: 326
Period size: 48 Copynumber: 4.5 Consensus size: 48
9968 ATATATATCT
* * * *
9978 ACATATACATATCTCATACATATTTCACATTCGCCATTCGACTTCACC
1 ACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACC
* *
10026 ACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACC
1 ACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACC
* * * *
10074 ACATATACATATCTCATACATATTTTACATTCGCCATTCGTCTTTACC
1 ACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACC
* *
10122 ACATATACATATCACACATATATTTCACATTAGCCATTCGGCTTTACC
1 ACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACC
10170 ACATATACATATCTCATATATATTT
1 ACATATACATATCTCATATATATTT
10195 ATCTTGTACA
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 149 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (48 bp):
ACATATACATATCTCATATATATTTCACATTAGCCATTCGGCTTTACC
Found at i:10088 original size:96 final size:96
Alignment explanation
Indices: 9978--10194 Score: 398
Period size: 96 Copynumber: 2.3 Consensus size: 96
9968 ATATATATCT
9978 ACATATACATATCTCATACATATTTCACATTCGCCATTCGACTTCACCACATATACATATCACAC
1 ACATATACATATCTCATACATATTTCACATTCGCCATTCGACTTCACCACATATACATATCACAC
10043 ATATATTTCACATTAGCCATTCGGCTTTACC
66 ATATATTTCACATTAGCCATTCGGCTTTACC
* * *
10074 ACATATACATATCTCATACATATTTTACATTCGCCATTCGTCTTTACCACATATACATATCACAC
1 ACATATACATATCTCATACATATTTCACATTCGCCATTCGACTTCACCACATATACATATCACAC
10139 ATATATTTCACATTAGCCATTCGGCTTTACC
66 ATATATTTCACATTAGCCATTCGGCTTTACC
*
10170 ACATATACATATCTCATATATATTT
1 ACATATACATATCTCATACATATTT
10195 ATCTTGTACA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 117 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (96 bp):
ACATATACATATCTCATACATATTTCACATTCGCCATTCGACTTCACCACATATACATATCACAC
ATATATTTCACATTAGCCATTCGGCTTTACC
Found at i:13075 original size:40 final size:40
Alignment explanation
Indices: 13030--13140 Score: 168
Period size: 40 Copynumber: 2.8 Consensus size: 40
13020 ATAACCACAA
* *
13030 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
13070 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
* *
13110 GCACAAATGCCTTCGGGTCTTAGCCCAGATA
1 GCACAAATGCCTTCGGGTCTTAACCCGGATA
13141 AAATCACTAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
Found at i:13158 original size:40 final size:40
Alignment explanation
Indices: 13074--13220 Score: 197
Period size: 40 Copynumber: 3.7 Consensus size: 40
13064 CAACTCGCAC
* * * * *
13074 AAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCAGATAAAATC-ACTAGCAT
*
13114 AAATGCCTTCGGGTCTTAGCCCAGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCAGATAAAATCACTAGCAT
* *
13154 AAATGCCTTCAGGACATAGCCCAGATAAAATCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCAGATAAAATCACTAGCAT
*
13194 AAATGCCTTCGGGACTTAGCCCGGATA
1 AAATGCCTTCGGGACTTAGCCCAGATA
13221 TCATTCAAAT
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 92 0.96
41 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.23
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCAGATAAAATCACTAGCAT
Found at i:13158 original size:80 final size:81
Alignment explanation
Indices: 13029--13220 Score: 210
Period size: 80 Copynumber: 2.4 Consensus size: 81
13019 TATAACCACA
* * * * * * * *
13029 AGCACAATTGCCTTCGGGTCTTAACCCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCAGGACATAG
* *
13093 CCCGGAT-ATATCAACT
66 CCCAGATAAAATC-ACT
* * * *
13109 CGCACAAATGCCTTCGGGTCTTAGCCCAGATAAAATC-ACTAGCATAAATGCCTTCAGGACATAG
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCAGGACATAG
13173 CCCAGATAAAATCACT
66 CCCAGATAAAATCACT
* *
13189 AGCATAAATGCCTTCGGGACTTAGCCCGGATA
1 AGCACAAATGCCTTCGGGTCTTAGCCCGGATA
13221 TCATTCAAAT
Statistics
Matches: 92, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
80 85 0.92
81 7 0.08
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (81 bp):
AGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAAGCAACTAGCACAAATGCCTTCAGGACATAG
CCCAGATAAAATCACT
Found at i:15470 original size:88 final size:87
Alignment explanation
Indices: 15286--15894 Score: 481
Period size: 88 Copynumber: 6.9 Consensus size: 87
15276 AATTCGTAAA
* * *** * **
15286 CCTTAACCCCCTAAGTAGTAGGGTAACAGG--TTGAATTACAGATCTTATCTCCCTAAATAGTAG
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
*
15349 CGGAGCAGATCGAAGACGGTGAG
66 CGGAGCAGATCGAAGACAGT-AG
* * * * * * * * *
15372 CCTTAACCCCTTAAGTAGTAAGGTAACAGGCCAAAAATTACAAATCTTATCACTCTAAGCAATAG
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
* ** *
15437 -GGAAACAGATCGAATTCACTAG
66 CGG-AGCAGATCGAAGACAGTAG
*
15459 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
*
15524 TGGAGCAGATCGAAGACAGTAAG
66 CGGAGCAGATCGAAGACAGT-AG
* *** * * *
15547 CTTTGACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATTATAGATCTCATCTCGCTAAGCAGCAG
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
*
15612 CGGAGCAGATCGAAGACAGTAA
66 CGGAGCAGATCGAAGACAGTAG
*** *
15634 CCTTTGACCCCCTAAGCAGTAGGGTAACAGG-CAGAAAATTACAGATCTTGCCTCCCTAAGCAAT
1 CC-TTGACCCCCTAAGCAGTAGGGTAACAGGCCA-AAAATTACAGATCTCATCTCCCTAAGCAGT
* * * * * *
15698 AGTGGAGTAGATCAAATACAGGAAAA
64 AGCGGAGCAGATCGAAGACA-G-TAG
* * ***** * * * *
15724 CCTTAACCCCCTAAGCAGTAGGGTAACACGTTGGGAATCACAGATCTTATCACCCTAAGAAGTAG
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
* *
15789 GGGAACAGATCGAAGAC-GATGAG
66 CGGAGCAGATCGAAGACAG-T-AG
* * * *** * * **
15812 CCTTAACCCCCTAAACAGTAGGGTAATAGGCTGGAAATTCACAGATTTTATCTCCCTGAAGTTGT
1 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATT-ACAGATCTCATCTCCCT-AAGCAGT
* *
15877 AGTGGAGCAGATTGAAGA
64 AGCGGAGCAGATCGAAGA
15895 TAGCGAATCT
Statistics
Matches: 425, Mismatches: 85, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
86 28 0.07
87 76 0.18
88 219 0.52
89 78 0.18
90 24 0.06
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (87 bp):
CCTTGACCCCCTAAGCAGTAGGGTAACAGGCCAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
CGGAGCAGATCGAAGACAGTAG
Found at i:15520 original size:44 final size:43
Alignment explanation
Indices: 15467--15608 Score: 117
Period size: 44 Copynumber: 3.2 Consensus size: 43
15457 AGCCTTGACC
15467 CCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTCATCT
1 CCCTAAGCAGTAGGGTAACAGGCTAAAAATTA-AGATCTCATCT
* * * * * * * * *
15511 CCCTAAGCAGTAGTGG-AGCAGATCGAAGACAGTAAGCTTTGA-CC
1 CCCTAAGCAGTAG-GGTAACAG-GCTAA-AAATTAAGATCTCATCT
* *
15555 CCCTAAGCAGTAGGGTAACAGGTTGAAAATTATAGATCTCATCT
1 CCCTAAGCAGTAGGGTAACAGGCTAAAAATTA-AGATCTCATCT
*
15599 CGCTAAGCAG
1 CCCTAAGCAG
15609 CAGCGGAGCA
Statistics
Matches: 71, Mismatches: 21, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
42 4 0.06
43 8 0.11
44 45 0.63
45 10 0.14
46 4 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGTAACAGGCTAAAAATTAAGATCTCATCT
Found at i:15586 original size:175 final size:173
Alignment explanation
Indices: 15286--15894 Score: 614
Period size: 175 Copynumber: 3.5 Consensus size: 173
15276 AATTCGTAAA
* ** **
15286 CCTTAACCCCCTAAGTAGTAGGGTAACAGG-T-TGAATTACAGATCTTATCTCCCTAAATAGTAG
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* * * * * * ***
15349 CGGAGCAGATCGAAGACGGTGAGCCTTAACCCCTTAAGTAGTAAGGTAACAGGCCAAAAATTACA
66 TGGAGCAGATCGAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATTACA
* * **
15414 AATCTTATCACTCTAAGCAATAGGGAAACAGATCGAATTCACTAG
131 GATCTTATCACCCTAAGCAATAGGG-AACAGATCGAAGACA-TAG
* *
15459 CCTTGACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTCATCTCCCTAAGCAGTAG
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* * *
15524 TGGAGCAGATCGAAGACAGTAAGCTTTGACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATTATA
66 TGGAGCAGATCGAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATTACA
* * * ** * *
15589 GATCTCATCTCGCTAAGCAGCAGCGGAGCAGATCGAAGACAGTAA
131 GATCTTATCACCCTAAGCAATAG-GGAACAGATCGAAGACA-TAG
* ** *
15634 CCTTTGACCCCCTAAGCAGTAGGGTAACAGGC-AGAAAATTACAGATCTTGCCTCCCTAAGCAAT
1 CC-TTAACCCCCTAAGCAGTAGGGTAACAGGCTA-AAAATTACAGATCTTATCTCCCTAAGCAGT
* * * * * * ** *
15698 AGTGGAGTAGATCAAATACAGGAAAACCTTAACCCCCTAAGCAGTAGGGTAACACGTTGGGAATC
64 AGTGGAGCAGATCGAAGACA-GTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATT
15763 ACAGATCTTATCACCCTAAG-AAGTAGGGGAACAGATCGAAGACGATGAG
128 ACAGATCTTATCACCCTAAGCAA-TA-GGGAACAGATCGAAGAC-AT-AG
* * ** * **
15812 CCTTAACCCCCTAAACAGTAGGGTAATAGGCTGGAAATTCACAGATTTTATCTCCCTGAAGTTGT
1 CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATT-ACAGATCTTATCTCCCT-AAGCAGT
*
15877 AGTGGAGCAGATTGAAGA
64 AGTGGAGCAGATCGAAGA
15895 TAGCGAATCT
Statistics
Matches: 355, Mismatches: 68, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
173 28 0.08
174 1 0.00
175 114 0.32
176 75 0.21
177 100 0.28
178 19 0.05
179 18 0.05
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (173 bp):
CCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAATTACAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGACAGTAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGTTGAAAATTACA
GATCTTATCACCCTAAGCAATAGGGAACAGATCGAAGACATAG
Found at i:15649 original size:44 final size:43
Alignment explanation
Indices: 15511--15657 Score: 136
Period size: 44 Copynumber: 3.3 Consensus size: 43
15501 GATCTCATCT
15511 CCCTAAGCAGTAGTGGAGCAGATCGAAGACAGTAAGCTTTGACC
1 CCCTAAGCAGTAG-GGAGCAGATCGAAGACAGTAAGCTTTGACC
* * * * * * * *
15555 CCCTAAGCAGTAGGGTAACAGGTTGAA-A-ATTATAGATCTCATCT
1 CCCTAAGCAGTAGGG-AGCAGATCGAAGACAGTA-AGCTTTGA-CC
* * *
15599 CGCTAAGCAGCAGCGGAGCAGATCGAAGACAGTAACCTTTGACC
1 CCCTAAGCAGTAG-GGAGCAGATCGAAGACAGTAAGCTTTGACC
15643 CCCTAAGCAGTAGGG
1 CCCTAAGCAGTAGGG
15658 TAACAGGCAG
Statistics
Matches: 76, Mismatches: 21, Indels: 13
0.69 0.19 0.12
Matches are distributed among these distances:
42 3 0.04
43 10 0.13
44 53 0.70
45 7 0.09
46 3 0.04
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (43 bp):
CCCTAAGCAGTAGGGAGCAGATCGAAGACAGTAAGCTTTGACC
Found at i:17303 original size:3 final size:3
Alignment explanation
Indices: 17295--17607 Score: 139
Period size: 3 Copynumber: 105.7 Consensus size: 3
17285 ATCATTTTAC
*** *
17295 TTA TTA TTA TTA TTA TTA TTA TTA TTA CCG TTA GTA TTA TT- TTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * *
17340 TTA CTA TTA TT- TT- TTA GTTA -TA TTA CTA TTA TTG TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
17382 TCA TTA TTA TTC TTA CTA TTA TTA TTA TTA CTA CTA CTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** **
17430 TTA ACA -TA TTA TTA TTA TTA TT- TTA CCA -TA TTA TTA TT- TCCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T--TA
* ** *
17473 TT- TT- TTA TATA TTA TTA TTG TTA TTA ACA TATA TTA TTA ATA TTAA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TT-A
* * * * * *
17519 TGTA CTA TTA TTT TCTA TTA TTA TTA TTA TTA CTA ATA TCA CTA TTA
1 T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * *
17566 TCA TT- TTT TTA TCA CCA TCA TTA TTT TTA TT- TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17608 TATTTATTCG
Statistics
Matches: 232, Mismatches: 58, Indels: 40
0.70 0.18 0.12
Matches are distributed among these distances:
2 23 0.10
3 191 0.82
4 16 0.07
5 2 0.01
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:19420 original size:3 final size:3
Alignment explanation
Indices: 19412--20052 Score: 254
Period size: 3 Copynumber: 215.0 Consensus size: 3
19402 TTCAAAATTT
* *
19412 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG CAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
19460 TAA T-A TAT TGA TAA TAA TAAA TAA TAA -AA GGAA TAA AAA TAA TAG
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA -TAA TAA TAA TAA TAA
* * * * * **
19505 TAC TAA TAA GAA TAT TAA CAA TAG TAA TAA TAA CGA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
19550 TAC TAA TATA TACA TGAA TAA TAA TAA TAA TAA TAA TACA TTAA TGA
1 TAA TAA TA-A TA-A T-AA TAA TAA TAA TAA TAA TAA TA-A -TAA TAA
* * * * *
19597 CAA TAA T-A TACGT TAA TAA TGA TAA TAA TAA TATG TAA -AA -AA GGGAA
1 TAA TAA TAA TA--A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA --TAA
* * * * * * * *
19644 TAA TTA TAG T-A TAG TAA GAA TAA TAA TAA GAA TAA TAG TAG TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
19691 TAAA TAA -AA GGTAA TAG TAA TAA AAA TAA AAA TAA AAA TAA TAG TAA
1 T-AA TAA TAA --TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * * *
19738 TAA TGA TAA TAA TAA TAG TAA TAA -AA CAGA GAA AAA AAA CAA -CA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
** * * * * * *
19782 TAA CGA TAA GAG CAA TAA TAA TAA TTA TTA TAA TAG TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
19829 -AT TAA TGA T-A TAA TAA T-A TAA TAA TAA TAA GCA -AA TAA GT-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
* ** * * *
19870 TGAA -AA GAA -AA T-A TAA CCA TAG TAA TAA TAG T-A TAG TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
19912 TAA TAG TAA GAA TAA TAA TGA TAA T-A TAA CAA TAA TAG TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ***
19958 CAA TAA -AA -AA TAA TAG TAA TGAA -AA TAA TAC TAA CGG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
*
20001 TAA TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA TAA TAAA TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA T-AA TAA
20047 TAA TAA
1 TAA TAA
20053 AGCAGCAAAT
Statistics
Matches: 470, Mismatches: 124, Indels: 88
0.69 0.18 0.13
Matches are distributed among these distances:
2 46 0.10
3 381 0.81
4 34 0.07
5 9 0.02
ACGTcount: A:0.60, C:0.03, G:0.08, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:19953 original size:17 final size:16
Alignment explanation
Indices: 19893--19963 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
19883 TAACCATAGT
*
19893 AATAATAGTATAGTAAT
1 AATAATAGTATA-TAAC
* *
19910 AATAATAGTA-AGAAT
1 AATAATAGTATATAAC
19925 AATAAT-GATAATATAAC
1 AATAATAG-T-ATATAAC
19942 AATAATAGTAATATAAC
1 AATAATAGT-ATATAAC
19959 AATAA
1 AATAA
19964 AAAATAATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
14 1 0.02
15 10 0.21
16 2 0.04
17 33 0.70
18 1 0.02
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (16 bp):
AATAATAGTATATAAC
Found at i:22303 original size:27 final size:27
Alignment explanation
Indices: 22273--22326 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
22263 TAAAACATTT
*
22273 CTTATAGAATTATAAAAAGCTTTTAAA
1 CTTATAGAATCATAAAAAGCTTTTAAA
22300 CTTATAGAATCATAAAAAGCTTTTAAA
1 CTTATAGAATCATAAAAAGCTTTTAAA
22327 ATATAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (27 bp):
CTTATAGAATCATAAAAAGCTTTTAAA
Found at i:31085 original size:5 final size:5
Alignment explanation
Indices: 31075--31248 Score: 323
Period size: 5 Copynumber: 34.6 Consensus size: 5
31065 TTTAGTATAT
31075 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
31125 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
31175 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTATA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TA-T-TA
31227 TATTA TATTA TATTA TA-TA TAT
1 TATTA TATTA TATTA TATTA TAT
31249 AAACTAAAGA
Statistics
Matches: 166, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
4 4 0.02
5 156 0.94
6 2 0.01
7 4 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:32360 original size:15 final size:15
Alignment explanation
Indices: 32340--32396 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
32330 CGATGAATTT
32340 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
32355 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
32370 ATTGAATTTATATTG
1 ATTGAATTTATATTG
32385 ATTGAA-TTATAT
1 ATTGAATTTATAT
32397 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:32796 original size:23 final size:23
Alignment explanation
Indices: 32766--32852 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
32756 GCTTTATCGA
* *
32766 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
32789 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
32810 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
32832 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
32853 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:37412 original size:5 final size:5
Alignment explanation
Indices: 37402--37483 Score: 125
Period size: 5 Copynumber: 16.6 Consensus size: 5
37392 TTTAGTATAT
37402 TATTA TATTA TA-TA TATTA TA-TA TA-TA TATATA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA TATTA
37450 TATTA TATTA TATTA TATTA TATTA TATATA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT-TA TAT
37484 ATAAACTAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 7
0.91 0.00 0.09
Matches are distributed among these distances:
4 12 0.16
5 51 0.70
6 10 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:38771 original size:15 final size:15
Alignment explanation
Indices: 38751--38807 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
38741 CGATGAATTT
38751 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
38766 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
38781 ATTGAATTTATATTG
1 ATTGAATTTATATTG
38796 ATTGAA-TTATAT
1 ATTGAATTTATAT
38808 AATATATATG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
14 6 0.16
15 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:39209 original size:23 final size:23
Alignment explanation
Indices: 39179--39265 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
39169 GCTTTATCGA
* *
39179 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
39202 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
39223 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
39245 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
39266 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:42365 original size:17 final size:17
Alignment explanation
Indices: 42343--42378 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42333 TCTCTATTTT
42343 TACACATAGAATAACTA
1 TACACATAGAATAACTA
42360 TACACATAGAATAACTA
1 TACACATAGAATAACTA
42377 TA
1 TA
42379 ACACTCCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (17 bp):
TACACATAGAATAACTA
Found at i:44759 original size:17 final size:18
Alignment explanation
Indices: 44731--44768 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
44721 ATAGAAGATA
*
44731 TTATTTAGTTTTATTTAT
1 TTATTTAGTTTTATTAAT
44749 TTATTTA-TTTTATTAAT
1 TTATTTAGTTTTATTAAT
44766 TTA
1 TTA
44769 GGTTAAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTATTTAGTTTTATTAAT
Found at i:53958 original size:19 final size:19
Alignment explanation
Indices: 53930--53968 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
53920 AGAGCGAAAG
53930 AAACGAG-AAACGGGCCAA
1 AAACGAGAAAACGGGCCAA
*
53948 AAACAGAGAAAATGGGCCAA
1 AAAC-GAGAAAACGGGCCAA
53968 A
1 A
53969 GTACGAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 3 0.17
20 11 0.61
ACGTcount: A:0.54, C:0.18, G:0.26, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAACGGGCCAA
Found at i:55415 original size:13 final size:13
Alignment explanation
Indices: 55397--55424 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55387 AGTTGTTTAT
55397 TAAACTAATTAAC
1 TAAACTAATTAAC
55410 TAAACTAATTAAC
1 TAAACTAATTAAC
55423 TA
1 TA
55425 TTGAAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:63828 original size:13 final size:13
Alignment explanation
Indices: 63810--63838 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
63800 GGTTGTTTAT
63810 TAAACTAATTAAC
1 TAAACTAATTAAC
63823 TAAACTAATTAAC
1 TAAACTAATTAAC
63836 TAA
1 TAA
63839 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:73519 original size:39 final size:39
Alignment explanation
Indices: 73460--73560 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
73450 ATCGTGATCT
** *
73460 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACG
73499 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACG
*
73538 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTAAAGC
73561 TCATCAGATC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTAAAGCACATAAGTGCTAAACG
Found at i:90332 original size:23 final size:22
Alignment explanation
Indices: 90302--90371 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 22
90292 AAAATAGAAG
90302 ATATTATTTTGTTTTATTTAGTTT
1 ATATTATTTT-TTTTATTTA-TTT
*
90326 -TATTATTTATTTTCATTTATTT
1 ATATTATTT-TTTTTATTTATTT
* *
90348 ATTTTGTTTTATTTTATTTATTT
1 ATATTATTTT-TTTTATTTATTT
90371 A
1 A
90372 GGTTAAGCTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 4 0.10
23 34 0.87
24 1 0.03
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.73
Consensus pattern (22 bp):
ATATTATTTTTTTTATTTATTT
Found at i:90347 original size:14 final size:13
Alignment explanation
Indices: 90314--90371 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
90304 ATTATTTTGT
90314 TTTATTTAGTTTTA
1 TTTATTTA-TTTTA
90328 -TTATTTATTTTCA
1 TTTATTTATTTT-A
90341 TTTATTTA-TTT-
1 TTTATTTATTTTA
*
90352 TGT-TTTATTTTA
1 TTTATTTATTTTA
90364 TTTATTTA
1 TTTATTTA
90372 GGTTAAGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 4 0.11
11 5 0.14
12 6 0.16
13 15 0.41
14 7 0.19
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:91637 original size:11 final size:11
Alignment explanation
Indices: 91623--91663 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
91613 TATTTTCTCC
91623 CTATTTTGCTA
1 CTATTTTGCTA
*
91634 CTATTTTACTA
1 CTATTTTGCTA
* *
91645 TTATGTTGCTA
1 CTATTTTGCTA
91656 CTATTTTG
1 CTATTTTG
91664 TTGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:91764 original size:30 final size:30
Alignment explanation
Indices: 91704--91764 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
91694 ATTTTATTGT
* * *
91704 TAATTTTTTTATTATTTTAAAGATATTTGC
1 TAATTTTGTTATTATTTTAAAGACACTTGC
* *
91734 TAATTTTGTTATTATTTTAGAGGCACTTGC
1 TAATTTTGTTATTATTTTAAAGACACTTGC
91764 T
1 T
91765 TGTTAAGTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (30 bp):
TAATTTTGTTATTATTTTAAAGACACTTGC
Found at i:94753 original size:52 final size:52
Alignment explanation
Indices: 94675--94780 Score: 178
Period size: 52 Copynumber: 2.0 Consensus size: 52
94665 ACTTTGAAGG
94675 ACAACATGTAACAGTTTTAGTAATGATTATATAAATGAATATGTCCAATAAA
1 ACAACATGTAACAGTTTTAGTAATGATTATATAAATGAATATGTCCAATAAA
* *
94727 ACAACATGTAGC-GATTTTAGTAATGATTATATAAATGAATATGTCCAGTAAA
1 ACAACATGTAACAG-TTTTAGTAATGATTATATAAATGAATATGTCCAATAAA
94779 AC
1 AC
94781 TTGAACATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
51 1 0.02
52 50 0.98
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (52 bp):
ACAACATGTAACAGTTTTAGTAATGATTATATAAATGAATATGTCCAATAAA
Found at i:103803 original size:30 final size:30
Alignment explanation
Indices: 103767--103826 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
103757 TATACAAAGA
103767 ATGAATGAATTTGGTAATTATTGTCTGTAT
1 ATGAATGAATTTGGTAATTATTGTCTGTAT
*
103797 ATGAATGAATTTGGTAATTATTTTCTGTAT
1 ATGAATGAATTTGGTAATTATTGTCTGTAT
103827 GGTATGATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.03, G:0.18, T:0.48
Consensus pattern (30 bp):
ATGAATGAATTTGGTAATTATTGTCTGTAT
Found at i:112065 original size:7 final size:7
Alignment explanation
Indices: 112053--112078 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
112043 TTTATTATTA
112053 TTTTTGG
1 TTTTTGG
112060 TTTTTGG
1 TTTTTGG
112067 TTTTTGG
1 TTTTTGG
112074 TTTTT
1 TTTTT
112079 TTGGGCCCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (7 bp):
TTTTTGG
Found at i:116186 original size:18 final size:19
Alignment explanation
Indices: 116159--116198 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
116149 TTGGACTTAG
* *
116159 AAGAAGGAAA-AAAATAAA
1 AAGAAAGAAACAAAAAAAA
116177 AAGAAAGAAACAAAAAAAA
1 AAGAAAGAAACAAAAAAAA
116196 AAG
1 AAG
116199 GAAAAGGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAGAAAGAAACAAAAAAAA
Found at i:121247 original size:23 final size:24
Alignment explanation
Indices: 121194--121249 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
121184 AAATTGTGAA
* *
121194 TTTAATTTTTTTACTTTAATTATC
1 TTTAACTTTTTGACTTTAATTATC
121218 TTT-ACTTTTTGA-TTTAATTAAT-
1 TTTAACTTTTTGACTTTAATT-ATC
121240 TTTAACTTTT
1 TTTAACTTTT
121250 AATATTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 10 0.36
23 15 0.54
24 3 0.11
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTAACTTTTTGACTTTAATTATC
Found at i:121256 original size:15 final size:14
Alignment explanation
Indices: 121237--121275 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
121227 TGATTTAATT
121237 AATTTTAACTTTTAA
1 AATTTTAA-TTTTAA
*
121252 TATTTTGAATTTTAA
1 AATTTT-AATTTTAA
121267 AATTTTAAT
1 AATTTTAAT
121276 ATTAGCCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 3 0.14
15 16 0.76
16 2 0.10
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
AATTTTAATTTTAA
Found at i:125472 original size:12 final size:12
Alignment explanation
Indices: 125455--125492 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
125445 ATTCCCCCAT
125455 AGATGTAAAACG
1 AGATGTAAAACG
*
125467 AGATGTAAAATG
1 AGATGTAAAACG
125479 AGATGTAAAACG
1 AGATGTAAAACG
125491 AG
1 AG
125493 GATTTTTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.05, G:0.26, T:0.18
Consensus pattern (12 bp):
AGATGTAAAACG
Found at i:128576 original size:13 final size:13
Alignment explanation
Indices: 128558--128583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
128548 GAATATTGCA
128558 TGAAAAATTTTAT
1 TGAAAAATTTTAT
128571 TGAAAAATTTTAT
1 TGAAAAATTTTAT
128584 CAATTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TGAAAAATTTTAT
Found at i:129775 original size:34 final size:33
Alignment explanation
Indices: 129737--129800 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
129727 GTATTGAAGG
* * *
129737 AAAGGTATACTTTGTGTATACCACTTGAAAAGAA
1 AAAGGTACACTATATGTATA-CACTTGAAAAGAA
*
129771 AAAGGTACACTATATGTGTACACTTGAAAA
1 AAAGGTACACTATATGTATACACTTGAAAA
129801 TGTTATATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 10 0.38
34 16 0.62
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (33 bp):
AAAGGTACACTATATGTATACACTTGAAAAGAA
Found at i:131984 original size:34 final size:34
Alignment explanation
Indices: 131945--132011 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
131935 AAAATGAGTG
131945 TGTTCGGTTAAGCCAATATGCTAGTGAATGGGTT
1 TGTTCGGTTAAGCCAATATGCTAGTGAATGGGTT
131979 TGTTCGGTTAAGCCAATATGCTAGTGAATGGGT
1 TGTTCGGTTAAGCCAATATGCTAGTGAATGGGT
132012 CTAAACAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.30, T:0.34
Consensus pattern (34 bp):
TGTTCGGTTAAGCCAATATGCTAGTGAATGGGTT
Found at i:146169 original size:18 final size:17
Alignment explanation
Indices: 146123--146160 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
146113 TATAACGGGC
146123 CACCA-TGTAGGCCCACA
1 CACCAGTGT-GGCCCACA
146140 CACCAGTGTGGCCCACA
1 CACCAGTGTGGCCCACA
146157 CACC
1 CACC
146161 CAGATTGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.26, C:0.45, G:0.18, T:0.11
Consensus pattern (17 bp):
CACCAGTGTGGCCCACA
Found at i:153798 original size:56 final size:56
Alignment explanation
Indices: 153712--153831 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
153702 ACAAGGGATG
153712 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
153768 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
153824 ATGGGCAA
1 ATGGGCAA
153832 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:155045 original size:40 final size:40
Alignment explanation
Indices: 154961--155146 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
154951 TCGAATGATG
* * * *
154961 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
155001 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
155041 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
155081 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
155122 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
155147 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.01
40 118 0.91
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:155153 original size:80 final size:79
Alignment explanation
Indices: 155014--155179 Score: 219
Period size: 80 Copynumber: 2.1 Consensus size: 79
155004 GGACTAAGAT
* **
155014 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGAACGAG-TAGCT
*
155078 AAATCCGGGTTAAGTC
65 AAATCC-GGTTAAATC
* *
155094 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCT
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCT
* *
155158 ATATCCGGTTAAATT
65 AAATCCGGTTAAATC
155173 CCGAAGG
1 CCGAAGG
155180 TACGTGATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGTCCCGAAGGCATTTGAACGAGTAGCTA
AATCCGGTTAAATC
Found at i:161688 original size:56 final size:56
Alignment explanation
Indices: 161602--161721 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
161592 ACAAGGGATG
161602 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
161658 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
161714 ATGGGCAA
1 ATGGGCAA
161722 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:162993 original size:78 final size:79
Alignment explanation
Indices: 162845--163025 Score: 224
Period size: 78 Copynumber: 2.3 Consensus size: 79
162835 TCGAATGATG
* * *
162845 TCCGGGCTAAGTCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTG
1 TCCGGGCTAAGCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
162910 TGCGAGATACTA-A
66 TGCGAGATACTATA
* * * **
162923 TTCCGGGCTAAGCCCGAAGGCATTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 -TCCGGGCTAAGCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCATT
*
162986 TGTGCGAGTTACTATA
64 TGTGCGAGATACTATA
*
163002 TCCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATT
163026 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
77 1 0.01
78 50 0.56
79 38 0.43
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGCTAAGCCCGAAGGCATTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTTG
TGCGAGATACTATA
Found at i:163034 original size:40 final size:40
Alignment explanation
Indices: 162845--163046 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
162835 TCGAATGATG
* * *
162845 TCCGGGCTAAGT-CCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATA
* *
162884 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-A
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA
*
162923 TTCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
*
162962 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
* **
163002 TCCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATA
163042 TCCGG
1 TCCGG
163047 TTAAATTCCG
Statistics
Matches: 142, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
38 24 0.17
39 33 0.23
40 78 0.55
41 7 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA
Done.