Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 65 of 126
Found at i:19049339 original size:90 final size:90
Alignment explanation
Indices: 19049239--19049489 Score: 218
Period size: 90 Copynumber: 2.8 Consensus size: 90
19049229 TGGAACTGAA
* * * * *
19049239 TAAGTCCATAGATGAAAGAAACTATGGCATTA-TATCAAAAATGAGTAAGACCATAACTGAAAGA
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAAT-AAAAACGAGTAAGACCATAACTGAAAGA
* *
19049303 CGCTATGGCATAATGATTATAATGAG
65 CGCTATGACATAATGATTATAACGAG
* * * *** *
19049329 TAAGACCATAGCTAAAAGACATTATGGCATCACAATTGTAACGAGTAAGACCATAGCTGAAAGAC
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATAAAAACGAGTAAGACCATAACTGAAAGAC
* * *
19049394 GTTATGACATCATGATTGTAACGAG
66 GCTATGACATAATGATTATAACGAG
* * * *** * ***
19049419 TAAGGCCATAGCTAGAAGACGTTATGGCATCATAATTCTAACGAGTAAGACCATAGA-TGAAAGA
1 TAAGACCATAGATAAAAGAAACTATGGCATCACAATAAAAACGAGTAAGACCATA-ACTGAAAGA
*
19049483 TGCTATG
65 CGCTATG
19049490 GTATCATGAA
Statistics
Matches: 134, Mismatches: 25, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
90 132 0.99
91 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (90 bp):
TAAGACCATAGATAAAAGAAACTATGGCATCACAATAAAAACGAGTAAGACCATAACTGAAAGAC
GCTATGACATAATGATTATAACGAG
Found at i:19049490 original size:45 final size:45
Alignment explanation
Indices: 19049281--19049517 Score: 255
Period size: 45 Copynumber: 5.3 Consensus size: 45
19049271 TATCAAAAAT
* * * * * *
19049281 GAGTAAGACCATAACTGAAAGACGCTATGGCATAATGATTATAAT
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATAATTCTAAC
* * * *
19049326 GAGTAAGACCATAGCTAAAAGACATTATGGCATCACAATTGTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATAATTCTAAC
* * *
19049371 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGATTGTAAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATAATTCTAAC
*
19049416 GAGTAAGGCCATAGCT-AGAAGACGTTATGGCATCATAATTCTAAC
1 GAGTAAGACCATAGCTGA-AAGACGTTATGGCATCATAATTCTAAC
* * * *
19049461 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGAA-TC-AGAC
1 GAGTAAGACCATAGCTGAAAGACGTTATGGCATCAT-AATTCTA-AC
*
19049506 GAATAAGACCAT
1 GAGTAAGACCAT
19049518 GGTTGGAAGA
Statistics
Matches: 164, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
44 2 0.01
45 159 0.97
46 3 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (45 bp):
GAGTAAGACCATAGCTGAAAGACGTTATGGCATCATAATTCTAAC
Found at i:19049496 original size:90 final size:90
Alignment explanation
Indices: 19049281--19049498 Score: 303
Period size: 90 Copynumber: 2.4 Consensus size: 90
19049271 TATCAAAAAT
* *
19049281 GAGTAAGACCATA-ACTGAAAGACGCTATGGCATAATGATTATAATGAGTAAGACCATAGCTAAA
1 GAGTAAGACCATAGA-TGAAAGACGCTATGGCATCATGATTATAACGAGTAAGACCATAGCTAAA
*
19049345 AGACATTATGGCATCACAATTGTAAC
65 AGACATTATGGCATCACAATTCTAAC
* * * * * *
19049371 GAGTAAGACCATAGCTGAAAGACGTTATGACATCATGATTGTAACGAGTAAGGCCATAGCTAGAA
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGATTATAACGAGTAAGACCATAGCTAAAA
* *
19049436 GACGTTATGGCATCATAATTCTAAC
66 GACATTATGGCATCACAATTCTAAC
* *
19049461 GAGTAAGACCATAGATGAAAGATGCTATGGTATCATGA
1 GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGA
19049499 ATCAGACGAA
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
90 111 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (90 bp):
GAGTAAGACCATAGATGAAAGACGCTATGGCATCATGATTATAACGAGTAAGACCATAGCTAAAA
GACATTATGGCATCACAATTCTAAC
Found at i:19053028 original size:6 final size:6
Alignment explanation
Indices: 19053017--19053041 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19053007 CTCCTTCCTT
19053017 TCTTTC TCTTTC TCTTTC TCTTTC T
1 TCTTTC TCTTTC TCTTTC TCTTTC T
19053042 TATTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (6 bp):
TCTTTC
Found at i:19056250 original size:4 final size:4
Alignment explanation
Indices: 19056243--19056268 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19056233 AAATGCATGC
19056243 ATGA ATGA ATGA ATGA ATGA ATGA AT
1 ATGA ATGA ATGA ATGA ATGA ATGA AT
19056269 TGCCACAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATGA
Found at i:19061743 original size:39 final size:40
Alignment explanation
Indices: 19061698--19061882 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
19061688 GCTCCTCGTT
* * *
19061698 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
19061738 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
19061777 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
19061817 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
19061858 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
19061883 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:19061798 original size:40 final size:39
Alignment explanation
Indices: 19061665--19061882 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
19061655 AAATCACGTA
* * **
19061665 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
19061704 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
19061743 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
19061783 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
19061823 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
19061863 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
19061883 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:19069684 original size:40 final size:40
Alignment explanation
Indices: 19069584--19069755 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
19069574 GCTCCTCGTT
* * *
19069584 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
19069624 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
19069663 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
19069703 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
19069743 CAAATGCCTTCGG
1 CAAATGCCTTCGG
19069756 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.29
40 79 0.68
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:19069768 original size:80 final size:79
Alignment explanation
Indices: 19069584--19069808 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
19069574 GCTCCTCGTT
* * * * *
19069584 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
19069648 ATTTAACAACTCGCA
65 ATTTAACAACTCGCA
* * *
19069663 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
** *
19069728 AATTT-GTATCTCGCA
64 AATTTAACAACTCGCA
* * * * *
19069743 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
19069807 GA
63 GA
19069809 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 68 0.56
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAACAACTCGCA
Found at i:19069817 original size:41 final size:41
Alignment explanation
Indices: 19069740--19069817 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
19069730 TTTGTATCTC
* * *
19069740 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
19069781 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
19069818 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:19080375 original size:47 final size:46
Alignment explanation
Indices: 19080317--19080531 Score: 247
Period size: 45 Copynumber: 4.7 Consensus size: 46
19080307 TGAATCAAAG
* *
19080317 AAATAAGACCATAGTTGAAAGACACTATGGCAACACGACGGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGAC-GAAAAAT
* * *
19080364 GAATAAGACCATGGTTGAAAGACACTATAGCAACACA-ATGAAAAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACA-AGACGAAAAAT
* * ** * *
19080410 GAATAAGACCATGGTTGAAAGACATTATGGCATTAAGAAG-AGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAAAAAT
* * * *
19080455 AAATAAGACCATGGTTGAAAGACACCATGGCATCAAGAC-TAGAAT
1 AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAAAAAT
*
19080500 AAATAAGACCATGGTTGAAAGACACCATGGCA
1 AAATAAGACCATGGTTGAAAGACACTATGGCA
19080532 CACTTTGATC
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
45 76 0.51
46 40 0.27
47 33 0.22
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.18
Consensus pattern (46 bp):
AAATAAGACCATGGTTGAAAGACACTATGGCAACAAGACGAAAAAT
Found at i:19082325 original size:12 final size:12
Alignment explanation
Indices: 19082308--19082337 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19082298 TCAGGCAGTT
19082308 ACACGGCCTAGC
1 ACACGGCCTAGC
*
19082320 ACACGGCCTGGC
1 ACACGGCCTAGC
19082332 ACACGG
1 ACACGG
19082338 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:19090276 original size:3 final size:3
Alignment explanation
Indices: 19090268--19090300 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
19090258 AATTGAATTG
*
19090268 TTA TTA TTA TTA TTA TTC TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19090301 ATTTATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19094067 original size:18 final size:19
Alignment explanation
Indices: 19094029--19094075 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
19094019 TTGAGCTAAT
*
19094029 ATTCTTTTATTC-TTTACG
1 ATTCTTTCATTCTTTTACG
19094047 ATTCTTTCATTCTTTTA-G
1 ATTCTTTCATTCTTTTACG
19094065 ATT-TTTC-TTCT
1 ATTCTTTCATTCT
19094076 AAATCATTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 4 0.15
17 4 0.15
18 15 0.56
19 4 0.15
ACGTcount: A:0.15, C:0.17, G:0.04, T:0.64
Consensus pattern (19 bp):
ATTCTTTCATTCTTTTACG
Found at i:19094862 original size:6 final size:6
Alignment explanation
Indices: 19094846--19094887 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
19094836 AGATTCAATG
* *
19094846 CAAAAA AAAAAA CAAAAA CAAAAG CAAAAA CAAAAA CAAAAA
1 CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA CAAAAA
19094888 AAGGGAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.00
Consensus pattern (6 bp):
CAAAAA
Found at i:19096811 original size:43 final size:44
Alignment explanation
Indices: 19096762--19096943 Score: 104
Period size: 44 Copynumber: 4.2 Consensus size: 44
19096752 CCTGAGGTTA
19096762 CAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCCTGGGCAG
1 CAGTGGAGTACATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
* * * * *
19096805 CAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAGGCAG
1 CAGTGGAGTACATTGAAGCCAGTACA-TTC-TATCTCCCTGGGCAG
* * ** *** * * * * * *
19096849 TAGTGGAGTAGATCAAAGATGGCAGATTTTACCTCCTTGAGGTTA-
1 CAGTGGAGTACATTGAAGCCAGTACATTCTATCTCCCTG-GG-CAG
* * *
19096894 TAGTGGAGTACATTGAAGCCAGTA-ATTCTATCTCCCTGGTCAA
1 CAGTGGAGTACATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
19096937 CAGTGGA
1 CAGTGGA
19096944 ATCAATCGAA
Statistics
Matches: 99, Mismatches: 32, Indels: 16
0.67 0.22 0.11
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 25 0.25
44 46 0.46
45 20 0.20
46 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
CAGTGGAGTACATTGAAGCCAGTACATTCTATCTCCCTGGGCAG
Found at i:19096875 original size:44 final size:44
Alignment explanation
Indices: 19096790--19096884 Score: 109
Period size: 44 Copynumber: 2.2 Consensus size: 44
19096780 CCAGTAATTC
* ** *
19096790 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTAGGCAGCAGTGGAATAGATCAAAGATGACAGATCT
* * * *
19096834 TATCTCCCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATTT
1 TATCTCCCTAGGCAGCAGTGGAATAGATCAAAGATGACAGATCT
*
19096878 TACCTCC
1 TATCTCC
19096885 TTGAGGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (44 bp):
TATCTCCCTAGGCAGCAGTGGAATAGATCAAAGATGACAGATCT
Found at i:19098812 original size:79 final size:78
Alignment explanation
Indices: 19098710--19098932 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 78
19098700 GCTCCTCGTT
* *
19098710 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
*
19098775 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
* *
19098790 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGA
*
19098854 ATTAGTATCTCGCA
65 ATTAGTAACTCGCA
* * * * *
19098868 CAAATGCCTTCGGATCTTAGTCCGGATATTGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGG-TATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCG
19098931 GA
63 GA
19098933 CATCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
78 45 0.36
79 60 0.48
80 20 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:19098827 original size:39 final size:40
Alignment explanation
Indices: 19098710--19098932 Score: 280
Period size: 39 Copynumber: 5.7 Consensus size: 40
19098700 GCTCCTCGTT
* *
19098710 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCA
* *
19098750 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
19098790 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
*
19098829 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
* * *
19098868 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAAC-TCGCA
19098909 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19098933 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 88 0.53
40 67 0.40
41 10 0.06
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCA
Found at i:19106731 original size:40 final size:40
Alignment explanation
Indices: 19106687--19106948 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
19106677 GCTCCTCGTT
* *
19106687 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
19106727 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
19106767 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
19106806 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
19106845 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
19106884 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
19106925 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19106949 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:19109801 original size:3 final size:3
Alignment explanation
Indices: 19109793--19109825 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
19109783 AATTGAATTG
*
19109793 TTA TTA TTA TTA TTA TTC TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
19109826 ATTTATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19111715 original size:16 final size:16
Alignment explanation
Indices: 19111682--19111711 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19111672 GATTTTCTGA
19111682 TTGTTTTTTCTTTTCT
1 TTGTTTTTTCTTTTCT
19111698 TTGTTTTTT-TTTTC
1 TTGTTTTTTCTTTTC
19111712 CTTTTTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (16 bp):
TTGTTTTTTCTTTTCT
Found at i:19119844 original size:31 final size:31
Alignment explanation
Indices: 19119809--19119872 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
19119799 TTTTAATCTC
19119809 AAAGTTAAAAACAATGGGAGCTAAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAGCAAAT
*
19119840 AAAGTTAAAAACAGTGGGAGCTAAAGCAAAT
1 AAAGTTAAAAACAATGGGAGCTAAAGCAAAT
19119871 AA
1 AA
19119873 TTCCTTTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.55, C:0.09, G:0.20, T:0.16
Consensus pattern (31 bp):
AAAGTTAAAAACAATGGGAGCTAAAGCAAAT
Found at i:19122076 original size:23 final size:23
Alignment explanation
Indices: 19122031--19122077 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
19122021 TCAGAGTAAT
**
19122031 TTAATCTCTATCAATTTTGAGAG
1 TTAATCTCTATCAATTTCAAGAG
19122054 TTAATCTCTATCAATTTCAAGAG
1 TTAATCTCTATCAATTTCAAGAG
19122077 T
1 T
19122078 GAGAAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (23 bp):
TTAATCTCTATCAATTTCAAGAG
Found at i:19122270 original size:51 final size:51
Alignment explanation
Indices: 19122168--19122286 Score: 141
Period size: 51 Copynumber: 2.3 Consensus size: 51
19122158 GCCCTCAAAG
* ** * *
19122168 TTTACATATTCTGCCAAATTGGTCTTGATTTAACAAATTTAGCCAATAACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
* * **
19122219 TTTACACATTTTATCAATTTGGTCCTGATTTAACATATTTAGCTTGA-AACA
1 TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGC-CAATAACA
19122270 TTTACACATTCTATCAA
1 TTTACACATTCTATCAA
19122287 CATTTACACA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 56 0.98
52 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTGGTCCTGATTTAACAAATTTAGCCAATAACA
Found at i:19129062 original size:9 final size:9
Alignment explanation
Indices: 19129048--19129073 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
19129038 ATTTTAACAA
19129048 ATAGAAAAC
1 ATAGAAAAC
19129057 ATAGAAAAC
1 ATAGAAAAC
19129066 ATAGAAAA
1 ATAGAAAA
19129074 ACTACTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.12
Consensus pattern (9 bp):
ATAGAAAAC
Found at i:19136323 original size:27 final size:27
Alignment explanation
Indices: 19136282--19136396 Score: 119
Period size: 27 Copynumber: 4.3 Consensus size: 27
19136272 ACATGTTAGA
* *
19136282 AAAAGAAAGCCTTTGTGCTGATCTATC
1 AAAAGAAAGCTTTTGTGCTGATCTATG
*
19136309 AAAAGAAAGCTTTTGTGGTGATCTATG
1 AAAAGAAAGCTTTTGTGCTGATCTATG
*
19136336 AAAAAAAAGCATTTATG-GCT-ATCTATG
1 AAAAGAAAGC-TTT-TGTGCTGATCTATG
* * *
19136363 AAAAGAAAGCCTTCGTGGC-AATCTATG
1 AAAAGAAAGCTTTTGT-GCTGATCTATG
19136390 AAAAGAA
1 AAAAGAA
19136397 TGCCTTTATG
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 65 0.87
28 5 0.07
29 2 0.03
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (27 bp):
AAAAGAAAGCTTTTGTGCTGATCTATG
Found at i:19136367 original size:54 final size:55
Alignment explanation
Indices: 19136280--19136407 Score: 152
Period size: 54 Copynumber: 2.3 Consensus size: 55
19136270 GAACATGTTA
* * * **
19136280 GAAAAAGAAAGCCTTTGT-GCTGATCTATCAAAAGAAAGCTTTTGTGGTGATCTAT
1 GAAAAA-AAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTCGTGGCAATCTAT
* *
19136335 GAAAAAAAAGCATTTATGGCT-ATCTATGAAAAGAAAGCCTTCGTGGCAATCTAT
1 GAAAAAAAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTCGTGGCAATCTAT
* *
19136389 GAAAAGAATGCCTTTATGG
1 GAAAAAAAAGCCTTTATGG
19136408 TGCACTCTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
54 53 0.85
55 9 0.15
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (55 bp):
GAAAAAAAAGCCTTTATGGCTGATCTATCAAAAGAAAGCCTTCGTGGCAATCTAT
Found at i:19140286 original size:40 final size:39
Alignment explanation
Indices: 19140227--19140349 Score: 165
Period size: 40 Copynumber: 3.1 Consensus size: 39
19140217 AGCTCGCATG
* *
19140227 GGGAGCTTTCACTAATACACAGCTTATCCGTAAGCTTACA
1 GGGAGC-TTCACTGATACACAGCTTATCCATAAGCTTACA
* *
19140267 GGAGAGCTTCGCTGATACACAGCTTATCCATAAGCTCACA
1 GG-GAGCTTCACTGATACACAGCTTATCCATAAGCTTACA
* *
19140307 TGGGAGTTTCACTGATACACAACTTATCCATAAGCTTACA
1 -GGGAGCTTCACTGATACACAGCTTATCCATAAGCTTACA
19140347 GGG
1 GGG
19140350 GAAATTTTCC
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 3 0.04
40 64 0.88
41 6 0.08
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (39 bp):
GGGAGCTTCACTGATACACAGCTTATCCATAAGCTTACA
Found at i:19140365 original size:40 final size:39
Alignment explanation
Indices: 19140240--19140365 Score: 103
Period size: 40 Copynumber: 3.2 Consensus size: 39
19140230 AGCTTTCACT
* * **
19140240 AATACACAGCTTATCCGTAAGCTTACAGGAG-AGCTTCGC
1 AATACACAGCTTATCCATAAGCTTACAGGGGAATTTTC-C
* * * *
19140279 TGATACACAGCTTATCCATAAGCTCACATGGG-AGTTTCAC
1 -AATACACAGCTTATCCATAAGCTTACAGGGGAATTTTC-C
* *
19140319 TGATACACAACTTATCCATAAGCTTACAGGGGAAATTTTCC
1 -AATACACAGCTTATCCATAAGCTTACAGGGG-AATTTTCC
19140360 AATACA
1 AATACA
19140366 AAACGTATAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
40 66 0.92
41 1 0.01
42 5 0.07
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (39 bp):
AATACACAGCTTATCCATAAGCTTACAGGGGAATTTTCC
Found at i:19145994 original size:50 final size:50
Alignment explanation
Indices: 19145881--19146026 Score: 132
Period size: 50 Copynumber: 2.9 Consensus size: 50
19145871 TTTATTGTAC
* * * * * **
19145881 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAAAAATGGTCTTACAGGGGACCTCTCATATCGG
* * * * * * *
19145931 TGCCCATGCCATGTTCTAGACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAAAATGGTCTTACAGG-GGACCTCTCATATCGG
* *
19145981 TGCCAACGTCATGTCCCAAAAATGGTCTTACATGGGACCTCTCATA
1 TGCCAACGCCATGTCCCAAAAATGGTCTTACAGGGGACCTCTCATA
19146027 ACCTTAATGA
Statistics
Matches: 76, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
49 1 0.01
50 74 0.97
51 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAAAATGGTCTTACAGGGGACCTCTCATATCGG
Found at i:19146050 original size:56 final size:54
Alignment explanation
Indices: 19145981--19146089 Score: 155
Period size: 56 Copynumber: 2.0 Consensus size: 54
19145971 CTCATCTCGG
*
19145981 TGCCAACGTCATGTCCCAAAAATGGTCTTACATGGGACCTCTCATAACCTTAATGA
1 TGCCAACGCCATGTCCCAAAAATGGTCTTACATGGGA--TCTCATAACCTTAATGA
* * **
19146037 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGATCTCATTCCCTTAATG
1 TGCCAACGCCATGTCCCAAAAATGGTCTTACATGGGATCTCATAACCTTAATG
19146090 CCATGACATT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 14 0.29
56 34 0.71
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (54 bp):
TGCCAACGCCATGTCCCAAAAATGGTCTTACATGGGATCTCATAACCTTAATGA
Found at i:19152323 original size:79 final size:82
Alignment explanation
Indices: 19152212--19152396 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
19152202 GCTACTCGTT
* *
19152212 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
19152275 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
19152292 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
19152355 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
19152372 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
19152397 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:19152396 original size:40 final size:40
Alignment explanation
Indices: 19152193--19152396 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
19152183 CGGAATTTAA
** *
19152193 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19152233 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
19152273 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
19152312 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
19152352 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
19152392 CCGGA
1 CCGGA
19152397 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:19162257 original size:27 final size:27
Alignment explanation
Indices: 19162226--19162277 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19162216 ACAAGTGAGG
19162226 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
19162253 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
19162278 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:19167727 original size:45 final size:43
Alignment explanation
Indices: 19167575--19167923 Score: 192
Period size: 44 Copynumber: 8.0 Consensus size: 43
19167565 ACTCGATGTG
* * * *
19167575 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACTTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-CTCACTTCA
* * * * *
19167620 ATCCGCTCCACTACAACTTCAGGGAGATAGGATTTTCGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTC-ACTTCA
* * *
19167664 ATCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGTCATCTTCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCA-CTTCA
* * *
19167709 ATCTGCCCCACTGCAACTTCAGTTGG-GATAAGACCTGCTTACTT-A
1 ATCTGCTCCACTGCAACTTCAG--GGAGATAAGA--TTCTCACTTCA
* * * * * * * *
19167754 GTCTGCTCCACTGTAACTTTAGGGAAATAAGACT-TGACGT-G
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
** * * * * *
19167795 ATCCACTCTACTGCAACTTCAGAGAGATAAGATCCATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTC-TCACTTCA
* * * * *
19167839 ATTCT-CTCCACTACAACTTCAGGGAGATAGGATTATTGACTCCA
1 A-TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-CTCACTTCA
* *
19167883 ATCTACTCCACTGTAA-TATCAGGGAGATAAGATT-T-ACTTCA
1 ATCTGCTCCACTGCAACT-TCAGGGAGATAAGATTCTCACTTCA
19167924 CTGACCTGTT
Statistics
Matches: 230, Mismatches: 59, Indels: 34
0.71 0.18 0.11
Matches are distributed among these distances:
41 33 0.14
42 1 0.00
43 11 0.05
44 96 0.42
45 74 0.32
46 10 0.04
47 4 0.02
48 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (43 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCTCACTTCA
Found at i:19182126 original size:5 final size:5
Alignment explanation
Indices: 19182112--19182145 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
19182102 ATATAATGCT
*
19182112 ATATC TTATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
19182146 ATTAATAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (5 bp):
ATATC
Found at i:19182990 original size:16 final size:17
Alignment explanation
Indices: 19182952--19182990 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19182942 AAAAAATTAT
*
19182952 AAATAAAATATTCAAAA
1 AAATAAAACATTCAAAA
*
19182969 ATATAAAACATT-AAAA
1 AAATAAAACATTCAAAA
19182985 AAATAA
1 AAATAA
19182991 TCAATCAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAATAAAACATTCAAAA
Found at i:19183205 original size:4 final size:4
Alignment explanation
Indices: 19183196--19183229 Score: 59
Period size: 4 Copynumber: 8.2 Consensus size: 4
19183186 TGTAAAACAA
19183196 CATT CATT CATT CATT CATT CATT CATCT CATT C
1 CATT CATT CATT CATT CATT CATT CAT-T CATT C
19183230 CTTGTTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (4 bp):
CATT
Found at i:19185396 original size:22 final size:23
Alignment explanation
Indices: 19185360--19185402 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
19185350 TATGTATTCA
19185360 TAATAGTTATATATTATATTACT
1 TAATAGTTATATATTATATTACT
* *
19185383 TAATAG-TATGTATTCTATTA
1 TAATAGTTATATATTATATTA
19185403 TTCTATTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (23 bp):
TAATAGTTATATATTATATTACT
Found at i:19185740 original size:11 final size:11
Alignment explanation
Indices: 19185726--19185751 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19185716 AGAATTATCA
19185726 TTTATTTATAT
1 TTTATTTATAT
19185737 TTTATTTATAT
1 TTTATTTATAT
19185748 TTTA
1 TTTA
19185752 AGTAATAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTATAT
Found at i:19185918 original size:16 final size:16
Alignment explanation
Indices: 19185894--19185938 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
19185884 TGGGCTCGAG
**
19185894 CTTTCTTGGGCTTGAAT
1 CTTT-TTGGGCTCCAAT
19185911 CTTTTTGGGCTCCAAT
1 CTTTTTGGGCTCCAAT
*
19185927 TTTTTTGGGCTC
1 CTTTTTGGGCTC
19185939 AAAATTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 21 0.84
17 4 0.16
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.49
Consensus pattern (16 bp):
CTTTTTGGGCTCCAAT
Found at i:19187501 original size:19 final size:19
Alignment explanation
Indices: 19187474--19187510 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19187464 AAGTATACTA
*
19187474 TTTTGGTATTTTTTTAATT
1 TTTTGGTATTATTTTAATT
*
19187493 TTTTTGTATTATTTTAAT
1 TTTTGGTATTATTTTAAT
19187511 AAAAAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (19 bp):
TTTTGGTATTATTTTAATT
Found at i:19187585 original size:17 final size:17
Alignment explanation
Indices: 19187563--19187595 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19187553 AATAAAAAGC
19187563 TATAAAATTTTTAATAT
1 TATAAAATTTTTAATAT
*
19187580 TATAAACTTTTTAATA
1 TATAAAATTTTTAATA
19187596 AAAACTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAAATTTTTAATAT
Found at i:19188032 original size:11 final size:11
Alignment explanation
Indices: 19188013--19188082 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 11
19188003 TATCGAAACC
*
19188013 ATAACAACAAA
1 ATAATAACAAA
* *
19188024 ATAAAAACAAT
1 ATAATAACAAA
*
19188035 ATAATAATAAA
1 ATAATAACAAA
19188046 ATAATAACAAA
1 ATAATAACAAA
* * **
19188057 ACAACAATGAA
1 ATAATAACAAA
19188068 ATAATAACAAA
1 ATAATAACAAA
19188079 ATAA
1 ATAA
19188083 CAACGAAACA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 45 1.00
ACGTcount: A:0.71, C:0.10, G:0.01, T:0.17
Consensus pattern (11 bp):
ATAATAACAAA
Found at i:19188071 original size:30 final size:30
Alignment explanation
Indices: 19188029--19188085 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
19188019 ACAAAATAAA
19188029 AACAATATAATAATAA-AATAATAACAAAAC
1 AACAATATAATAATAACAA-AATAACAAAAC
19188059 AACAATGA-AATAATAACAAAATAACAA
1 AACAAT-ATAATAATAACAAAATAACAA
19188086 CGAAACAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.18
Consensus pattern (30 bp):
AACAATATAATAATAACAAAATAACAAAAC
Found at i:19188090 original size:22 final size:22
Alignment explanation
Indices: 19188013--19188086 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 22
19188003 TATCGAAACC
* *
19188013 ATAACAACAAAATAAAAACAAT
1 ATAACAACAAAATAATAACAAA
* *
19188035 ATAATAATAAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
* **
19188057 ACAACAATGAAATAATAACAAA
1 ATAACAACAAAATAATAACAAA
19188079 ATAACAAC
1 ATAACAAC
19188087 GAAACAGTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.70, C:0.12, G:0.01, T:0.16
Consensus pattern (22 bp):
ATAACAACAAAATAATAACAAA
Found at i:19188233 original size:14 final size:14
Alignment explanation
Indices: 19188214--19188246 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19188204 AACTAATTAA
*
19188214 CTTTTCGAGTATAC
1 CTTTTCGAGTACAC
19188228 CTTTTCGAGTACAC
1 CTTTTCGAGTACAC
19188242 CTTTT
1 CTTTT
19188247 GGATCTGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.12, T:0.45
Consensus pattern (14 bp):
CTTTTCGAGTACAC
Found at i:19188550 original size:35 final size:31
Alignment explanation
Indices: 19188470--19188538 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
19188460 TTCCTTCGCA
* *
19188470 CAAACAGCATGACAGAAACTAACAAAGCAAG
1 CAAACAGCACGACAGAAACCAACAAAGCAAG
19188501 CAAACAGCACGACAGAAACCAACAAAGCAAG
1 CAAACAGCACGACAGAAACCAACAAAGCAAG
19188532 CAAACAG
1 CAAACAG
19188539 GCAACTGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.55, C:0.26, G:0.16, T:0.03
Consensus pattern (31 bp):
CAAACAGCACGACAGAAACCAACAAAGCAAG
Found at i:19201886 original size:61 final size:58
Alignment explanation
Indices: 19201814--19201946 Score: 178
Period size: 61 Copynumber: 2.2 Consensus size: 58
19201804 TCCAAAAATA
* * *
19201814 ATATTATTTTAATAGTTTTAATATTAAATTAAAT-TAAATATTTATCTTGTATATAAGTATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCT-AATATTTATCTTG-ATA-AA-TATT
* *
19201875 CTATTAATTTAATAGATTTAATATAAAATTTAATCTAATATTTATCTTGATAAATATT
1 ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
19201933 ATATTAATTTAATA
1 ATATTAATTTAATA
19201947 TTAAAGTGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
58 17 0.26
59 2 0.03
60 3 0.05
61 42 0.65
62 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (58 bp):
ATATTAATTTAATAGATTTAATATAAAATTAAATCTAATATTTATCTTGATAAATATT
Found at i:19202384 original size:25 final size:26
Alignment explanation
Indices: 19202343--19202394 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
19202333 AAAAAATTAA
* *
19202343 CTTTGGTTTTCTTAAA-CTTATTTTC
1 CTTTGGTTTTCTCAAACCTGATTTTC
19202368 CTTTGTGTTTT-TCAAACCTGATTTTC
1 CTTTG-GTTTTCTCAAACCTGATTTTC
19202394 C
1 C
19202395 AACAGCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (26 bp):
CTTTGGTTTTCTCAAACCTGATTTTC
Found at i:19215450 original size:22 final size:22
Alignment explanation
Indices: 19215425--19215469 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
19215415 AAATTATTAA
* *
19215425 TATATTGAATTTTAATTAATTT
1 TATAATGAATTTTAATAAATTT
*
19215447 TATAATGAATTTTCATAAATTT
1 TATAATGAATTTTAATAAATTT
19215469 T
1 T
19215470 GATTTATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (22 bp):
TATAATGAATTTTAATAAATTT
Found at i:19218606 original size:45 final size:45
Alignment explanation
Indices: 19218555--19218642 Score: 122
Period size: 45 Copynumber: 2.0 Consensus size: 45
19218545 TGTGAACCGA
* * *
19218555 ACATCATAAATTAGTAAGGTGGTTGCTATGTGCTGATTCCACCAG
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
** *
19218600 ACATCATTGATTAATAAGGTGGTTACTGTGTGCTGAATCCACC
1 ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCACC
19218643 GAGTATCTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (45 bp):
ACATCATAAATTAATAAGGTGGTTACTATGTGCTGAATCCACCAG
Found at i:19233196 original size:40 final size:41
Alignment explanation
Indices: 19233100--19233204 Score: 126
Period size: 40 Copynumber: 2.6 Consensus size: 41
19233090 TGAATGATGT
*
19233100 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
* * * *
19233140 CCGGACTAAGAT-CCGAAGGCATTTGTGC-GAGTTACTATAA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCTAAGTGACCATAA
*
19233180 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
19233205 AACGAGTAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
39 1 0.02
40 46 0.84
41 8 0.15
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (41 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCATAA
Found at i:19240223 original size:51 final size:50
Alignment explanation
Indices: 19240153--19240350 Score: 200
Period size: 51 Copynumber: 3.9 Consensus size: 50
19240143 ATCAATGATG
* * * *
19240153 TTCGGTTCACATAGTAGCCTGCACATAGTAATACACATGTGACCATTACCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCA
* * * * *
19240204 TTCGATACACGCAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCA
* * * * * * * * *
19240255 TCCGGTAGACATAGTACCCTGCACATAGTACTATAGATGCGACC-TATCA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA
19240304 TTCCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TT-CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
19240351 CATTTTTAAT
Statistics
Matches: 113, Mismatches: 31, Indels: 6
0.75 0.21 0.04
Matches are distributed among these distances:
49 3 0.03
50 36 0.32
51 72 0.64
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (50 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATACCA
Found at i:19240331 original size:101 final size:101
Alignment explanation
Indices: 19240161--19240346 Score: 275
Period size: 101 Copynumber: 1.8 Consensus size: 101
19240151 TGTTCGGTTC
* *
19240161 ACATAGTAGCCTGCACATAGTAATACACATGTGACCATTACCATTCGATACACGCAGTAGCCTGC
1 ACATAGTACCCTGCACATAGTAATACACATGCGACCA-TACCATTCGATACACGCAGTAGCCTGC
19240226 ACATAGTACTACACACGTGATCGAAACTATCCGGTAG
65 ACATAGTACTACACACGTGATCGAAACTATCCGGTAG
* * * * * *
19240263 ACATAGTACCCTGCACATAGTACTATAGATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGC
1 ACATAGTACCCTGCACATAGTAATACACATGCGACCATACCATT-CGATACACGCAGTAGCCTGC
19240327 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
19240347 CCATCATTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 6 0.08
101 38 0.51
102 31 0.41
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (101 bp):
ACATAGTACCCTGCACATAGTAATACACATGCGACCATACCATTCGATACACGCAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAACTATCCGGTAG
Found at i:19242490 original size:24 final size:26
Alignment explanation
Indices: 19242448--19242500 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
19242438 TTCTCCTAAA
*
19242448 TTTCAAATTTATTGCATTATTTAAT-T
1 TTTCAAATTTATTGAATTA-TTAATAT
19242474 TTTC-AATTTATT-AATTATTAATAT
1 TTTCAAATTTATTGAATTATTAATAT
19242498 TTT
1 TTT
19242501 ATGAAAATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 5 0.20
24 8 0.32
25 8 0.32
26 4 0.16
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAATAT
Found at i:19242499 original size:25 final size:26
Alignment explanation
Indices: 19242448--19242500 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
19242438 TTCTCCTAAA
* *
19242448 TTTCAAATTTATTGCATTATTTAATT
1 TTTCAAATTTATTGAATTATTAAATT
19242474 TTTC-AATTTATT-AATTATTAATATT
1 TTTCAAATTTATTGAATTATTAA-ATT
19242499 TT
1 TT
19242501 ATGAAAATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.29
25 13 0.54
26 4 0.17
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTCAAATTTATTGAATTATTAAATT
Found at i:19245932 original size:17 final size:17
Alignment explanation
Indices: 19245897--19245930 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
19245887 CTTCACTTAT
19245897 TCATTTCAACACACCTC
1 TCATTTCAACACACCTC
19245914 TCATTTC--CACACCTC
1 TCATTTCAACACACCTC
19245929 TC
1 TC
19245931 TCTCTCTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (17 bp):
TCATTTCAACACACCTC
Found at i:19247941 original size:28 final size:27
Alignment explanation
Indices: 19247900--19247964 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 27
19247890 AATACGAAAG
* *
19247900 AAAAGAAATTATATATTAAA-ATAAATTT
1 AAAATAAATAATATA-TAAATA-AAATTT
19247928 AAAATAAATAATATATAAATGAAAATTT
1 AAAATAAATAATATATAAAT-AAAATTT
*
19247956 GAAATAAAT
1 AAAATAAAT
19247965 TGAAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 4 0.12
28 27 0.84
29 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAATAAATAATATATAAATAAAATTT
Found at i:19248317 original size:3 final size:3
Alignment explanation
Indices: 19248309--19248368 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
19248299 AACTAATATA
* * * * * *
19248309 AAT AAT AAT ACT AAT AGT TAT AAT AAC ATT AAT AAT AAT AAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19248357 AAT GAA- AAT AAT
1 AAT -AAT AAT AAT
19248369 TGAGTAATTA
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19248346 original size:15 final size:15
Alignment explanation
Indices: 19248309--19248359 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
19248299 AACTAATATA
19248309 AATAATAAT-ACTAAT
1 AATAATAATAAC-AAT
* * *
19248324 AGTTATAATAACATT
1 AATAATAATAACAAT
19248339 AATAATAATAACAAT
1 AATAATAATAACAAT
19248354 AATAAT
1 AATAAT
19248360 GAAAATAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATAATAACAAT
Found at i:19252424 original size:23 final size:23
Alignment explanation
Indices: 19252398--19252441 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
19252388 CCTCATCCGC
19252398 TACACACCAACTCCGACCATCTT
1 TACACACCAACTCCGACCATCTT
19252421 TACACACCAACTCCGACCATC
1 TACACACCAACTCCGACCATC
19252442 CCAACACGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.45, G:0.05, T:0.18
Consensus pattern (23 bp):
TACACACCAACTCCGACCATCTT
Found at i:19252448 original size:23 final size:23
Alignment explanation
Indices: 19252399--19252448 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
19252389 CTCATCCGCT
***
19252399 ACACACCAACTCCGACCATCTTT
1 ACACACCAACTCCGACCATCCCA
19252422 ACACACCAACTCCGACCATCCCA
1 ACACACCAACTCCGACCATCCCA
19252445 ACAC
1 ACAC
19252449 GCCATGTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.48, G:0.04, T:0.14
Consensus pattern (23 bp):
ACACACCAACTCCGACCATCCCA
Found at i:19257907 original size:85 final size:94
Alignment explanation
Indices: 19257735--19257916 Score: 231
Period size: 85 Copynumber: 2.0 Consensus size: 94
19257725 TTACGAGGGT
* * *
19257735 AAAGAGCCCTCAAAATTTTTCAATAAAAAAGTAATTGAGCGTTTGCTTTTTTTTTTGCATTCAAT
1 AAAGAGCCCTCAAAATTTTTCAATAAAAAAGCAATTGAGAGTTTGCTTTTTTTTTTGCACTCAAT
* *
19257800 TGGGTACTTGAACTTTCAAAATGCATAAA
66 TAGGTACTTGAACTTCCAAAATGCATAAA
19257829 AAAGA-CCCTCAAAATTTTTC-A-AAAAAAGCAATT-A-AG-TT-C-TTTTTTTTT-CACTCAAT
1 AAAGAGCCCTCAAAATTTTTCAATAAAAAAGCAATTGAGAGTTTGCTTTTTTTTTTGCACTCAAT
*
19257885 TAGGTGCTTGAA-TTGCCAAAATGCATAAA
66 TAGGTACTTGAACTT-CCAAAATGCATAAA
19257914 AAA
1 AAA
19257917 CTTGTAACAC
Statistics
Matches: 81, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
84 2 0.02
85 33 0.41
86 9 0.11
87 1 0.01
88 2 0.02
89 1 0.01
90 1 0.01
91 11 0.14
92 1 0.01
93 15 0.19
94 5 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (94 bp):
AAAGAGCCCTCAAAATTTTTCAATAAAAAAGCAATTGAGAGTTTGCTTTTTTTTTTGCACTCAAT
TAGGTACTTGAACTTCCAAAATGCATAAA
Found at i:19259376 original size:50 final size:53
Alignment explanation
Indices: 19259281--19259423 Score: 141
Period size: 50 Copynumber: 2.7 Consensus size: 53
19259271 TTTCTTGTAC
* * * * * *
19259281 TGCCAATGTCATATCTCAGATATGGTCTTACATGGGAGTTCTCAT-A-TC-GG
1 TGCCAATGACATGTCCCAGACATGGTCTTACATGGGACTTCTCATAACTCAGA
* *
19259331 TGCCCATGACATGTCCTAGACATGGTCTTACATGGGACCTT-TCATAATCTCAATGA
1 TGCCAATGACATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATAA-CTC-A-GA
*
19259387 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGACATGTCCCAGACATGGTCTTACATGGGA
19259424 TCTCTTTACC
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
50 35 0.47
51 3 0.04
53 2 0.03
56 35 0.47
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (53 bp):
TGCCAATGACATGTCCCAGACATGGTCTTACATGGGACTTCTCATAACTCAGA
Found at i:19266415 original size:41 final size:41
Alignment explanation
Indices: 19266359--19266442 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
19266349 TGGGAGACCT
* *
19266359 ATCATCTCGTTGCCAACGCCATGTCCCAGACAT-AGTCTTAC
1 ATCATCTCGGTGCCAACACCATGTCCCAGACATGA-TCTTAC
* *
19266400 ATCATCTTGGTGCCAACACCATGTTCCAGACATGATCTTAC
1 ATCATCTCGGTGCCAACACCATGTCCCAGACATGATCTTAC
19266441 AT
1 AT
19266443 GGGACCTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 37 0.97
42 1 0.03
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (41 bp):
ATCATCTCGGTGCCAACACCATGTCCCAGACATGATCTTAC
Found at i:19267547 original size:20 final size:20
Alignment explanation
Indices: 19267516--19267566 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
19267506 TAAAACTTGT
19267516 AAAAA-TAT-AAAAAAATTA
1 AAAAATTATAAAAAAAATTA
** **
19267534 AAATTTTATAAAAATCATTA
1 AAAAATTATAAAAAAAATTA
19267554 AAAAATTATAAAA
1 AAAAATTATAAAA
19267567 TGCATCAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 19 0.76
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTATAAAAAAAATTA
Found at i:19267576 original size:20 final size:20
Alignment explanation
Indices: 19267539--19267577 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19267529 AATTAAAATT
*
19267539 TTATAAAAATCATTAAAAAA
1 TTATAAAAATCATCAAAAAA
19267559 TTAT-AAAATGCATCAAAAA
1 TTATAAAAAT-CATCAAAAA
19267578 GGCTCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.28
Consensus pattern (20 bp):
TTATAAAAATCATCAAAAAA
Found at i:19267793 original size:12 final size:10
Alignment explanation
Indices: 19267760--19267785 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19267750 TTTTACAAAT
19267760 TTTATATTTC
1 TTTATATTTC
19267770 TTTATATTTC
1 TTTATATTTC
19267780 TTTATA
1 TTTATA
19267786 ATTTTCTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTATATTTC
Found at i:19269986 original size:16 final size:16
Alignment explanation
Indices: 19269962--19269995 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19269952 TAAGTGCAAA
19269962 AAAAATTATAAATTAT
1 AAAAATTATAAATTAT
*
19269978 AAAATTTATAAATTAT
1 AAAAATTATAAATTAT
19269994 AA
1 AA
19269996 TATATAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAAATTATAAATTAT
Found at i:19284694 original size:17 final size:17
Alignment explanation
Indices: 19284668--19284701 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19284658 TGACCTAAGG
*
19284668 GGTTCGATACATTAACT
1 GGTTCAATACATTAACT
*
19284685 GGTTCAATACCTTAACT
1 GGTTCAATACATTAACT
19284702 ACAAATTCAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (17 bp):
GGTTCAATACATTAACT
Found at i:19290594 original size:32 final size:33
Alignment explanation
Indices: 19290549--19290612 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
19290539 ACTAAAGAAT
* * *
19290549 CTAAACATATAATT-AAAACTTGAGATTTAAAC
1 CTAAAAATATAATTAAAAACTTAAAATTTAAAC
*
19290581 CTAAAAATCTAATTAAAAACTTAAAATTTAAA
1 CTAAAAATATAATTAAAAACTTAAAATTTAAA
19290613 ATAAAACCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.31
Consensus pattern (33 bp):
CTAAAAATATAATTAAAAACTTAAAATTTAAAC
Found at i:19291790 original size:14 final size:15
Alignment explanation
Indices: 19291771--19291799 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19291761 TTAAGCTTAT
19291771 ATAAAAATA-TATAC
1 ATAAAAATAGTATAC
19291785 ATAAAAATAGTATAC
1 ATAAAAATAGTATAC
19291800 GATAGATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.07, G:0.03, T:0.28
Consensus pattern (15 bp):
ATAAAAATAGTATAC
Found at i:19291846 original size:24 final size:23
Alignment explanation
Indices: 19291819--19291947 Score: 117
Period size: 24 Copynumber: 5.7 Consensus size: 23
19291809 AAATAATGAT
* *
19291819 ATGATAAGTTTAAAATTATAGTA
1 ATGATAAATTTAAAATAATAGTA
* *
19291842 CATGATAAATTTCAAATTATGATGT-
1 -ATGATAAATTTAAAATAAT-A-GTA
*
19291867 ATGATAAATTT-AAATAATATTA
1 ATGATAAATTTAAAATAATAGTA
19291889 ATGAT-AATTT-AAATAATAGT-
1 ATGATAAATTTAAAATAATAGTA
*
19291909 AT-ATTAAATATTAAAATAATACTA
1 ATGA-TAAAT-TTAAAATAATAGTA
19291933 ATGATAAATTTAAAA
1 ATGATAAATTTAAAA
19291948 CAATGTTAAG
Statistics
Matches: 90, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 18 0.20
22 8 0.09
23 21 0.23
24 35 0.39
25 2 0.02
26 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATAGTA
Found at i:19304990 original size:150 final size:150
Alignment explanation
Indices: 19304719--19305006 Score: 549
Period size: 150 Copynumber: 1.9 Consensus size: 150
19304709 TTGTAAGTTG
*
19304719 TTGTTTTTGCATTTTGAAATGTTTCATTGTGCATGCATTGAAGACAATGCATCCCTTAGGGTTGG
1 TTGTTTTTGCATTTTGAAATGTTTCATTGTGCATGCATCGAAGACAATGCATCCCTTAGGGTTGG
*
19304784 GGGTGTGTTGTGTTGTAAATATAGTATGCAATAGTTATATGTTTTAATATTCATGCATTTTGTCA
66 GGGTGTGTTGTGCTGTAAATATAGTATGCAATAGTTATATGTTTTAATATTCATGCATTTTGTCA
19304849 TTCATTTTGCCATTAGATAC
131 TTCATTTTGCCATTAGATAC
*
19304869 TTGTTTTTGCATTTTGAAATGTTTCATTGTTCATGCATCGAAGACAATGCATCCCTTAGGGTTGG
1 TTGTTTTTGCATTTTGAAATGTTTCATTGTGCATGCATCGAAGACAATGCATCCCTTAGGGTTGG
19304934 GGGTGTGTTGTGCTGTAAATATAGTATGCAATAGTTATATGTTTTAATATTCATGCATTTTGTCA
66 GGGTGTGTTGTGCTGTAAATATAGTATGCAATAGTTATATGTTTTAATATTCATGCATTTTGTCA
19304999 TTCATTTT
131 TTCATTTT
19305007 TTCATTACAT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 135 1.00
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (150 bp):
TTGTTTTTGCATTTTGAAATGTTTCATTGTGCATGCATCGAAGACAATGCATCCCTTAGGGTTGG
GGGTGTGTTGTGCTGTAAATATAGTATGCAATAGTTATATGTTTTAATATTCATGCATTTTGTCA
TTCATTTTGCCATTAGATAC
Found at i:19308630 original size:41 final size:41
Alignment explanation
Indices: 19308568--19308714 Score: 231
Period size: 41 Copynumber: 3.6 Consensus size: 41
19308558 CATTGAATGT
* * *
19308568 AAGGGCTTGCTAGGTGCAGATTCCTCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
* *
19308609 AAGGGGTTACTAAGTGTAGATTCCCCGAATCATTGATCGAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
* *
19308650 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCACTGATCAAA
1 AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
19308691 AAGGGGTTGCTAAGTGCAGATTCC
1 AAGGGGTTGCTAAGTGCAGATTCC
19308715 TCAAGGGGTT
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 97 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
AAGGGGTTGCTAAGTGCAGATTCCCCGAATCATTGATCGAA
Found at i:19308725 original size:26 final size:25
Alignment explanation
Indices: 19308691--19308784 Score: 152
Period size: 26 Copynumber: 3.6 Consensus size: 25
19308681 ACTGATCAAA
19308691 AAGGGGTTGCTAAGTGCAGATTCCTC
1 AAGGGGTTGCTAAGTGCAGATTCC-C
19308717 AAGGGGTTGCTAAGTGCAGATTCCCC
1 AAGGGGTTGCTAAGTGCAGATT-CCC
*
19308743 GAGGGGTTGCTAAGTGCAGATTCCC
1 AAGGGGTTGCTAAGTGCAGATTCCC
19308768 TAAGGGGTTGCTAAGTG
1 -AAGGGGTTGCTAAGTG
19308785 TTAATGTAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
25 3 0.05
26 59 0.92
27 2 0.03
ACGTcount: A:0.22, C:0.18, G:0.34, T:0.26
Consensus pattern (25 bp):
AAGGGGTTGCTAAGTGCAGATTCCC
Found at i:19310159 original size:27 final size:27
Alignment explanation
Indices: 19310129--19310306 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
19310119 ATATTGAGTC
* * * *
19310129 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
19310156 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19310183 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
19310211 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
19310238 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
19310265 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
19310292 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
19310307 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:19310268 original size:82 final size:81
Alignment explanation
Indices: 19310150--19310305 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
19310140 TGCTATATAA
* *
19310150 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
19310215 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
19310232 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
19310296 CACTTAGTGC
65 CACTTAGTGC
19310306 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19311942 original size:14 final size:14
Alignment explanation
Indices: 19311923--19311954 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
19311913 ATTTTCACAC
19311923 ATTCATGATTACAT
1 ATTCATGATTACAT
19311937 ATTCATGATTACAT
1 ATTCATGATTACAT
19311951 ATTC
1 ATTC
19311955 TTACATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.06, T:0.44
Consensus pattern (14 bp):
ATTCATGATTACAT
Found at i:19317528 original size:30 final size:30
Alignment explanation
Indices: 19317492--19317549 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
19317482 CTTGAGGTTT
19317492 GTCCAAACAAAAATGGATGCATTTAAGTTC
1 GTCCAAACAAAAATGGATGCATTTAAGTTC
19317522 GTCCAAACAAAAATGGATGCATTTAAGT
1 GTCCAAACAAAAATGGATGCATTTAAGT
19317550 GATTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (30 bp):
GTCCAAACAAAAATGGATGCATTTAAGTTC
Found at i:19318599 original size:11 final size:11
Alignment explanation
Indices: 19318583--19318608 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19318573 TATTCAATAA
19318583 CATAAACGAAT
1 CATAAACGAAT
19318594 CATAAACGAAT
1 CATAAACGAAT
19318605 CATA
1 CATA
19318609 TACATACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.19, G:0.08, T:0.19
Consensus pattern (11 bp):
CATAAACGAAT
Found at i:19329023 original size:10 final size:10
Alignment explanation
Indices: 19329008--19329037 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
19328998 ATTATTAAGT
19329008 TAAAGTAAAA
1 TAAAGTAAAA
19329018 TAAAGTAAAA
1 TAAAGTAAAA
19329028 TAAAGTAAAA
1 TAAAGTAAAA
19329038 AGATGGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (10 bp):
TAAAGTAAAA
Found at i:19333338 original size:29 final size:29
Alignment explanation
Indices: 19333308--19333489 Score: 108
Period size: 29 Copynumber: 6.3 Consensus size: 29
19333298 GTAACCGTCT
19333308 CTTTTCATATTCGATGATCGAAACCA-CC
1 CTTTTCATATTCGATGATCGAAACCATCC
* * * *
19333336 TCTTTTCATAATCGA-CAGTCGAAGCTATCC
1 -CTTTTCATATTCGATGA-TCGAAACCATCC
* **
19333366 CTTTTCATATTCGATGGTCGTCACCATCC
1 CTTTTCATATTCGATGATCGAAACCATCC
* ** *
19333395 CTTTTCATAGTT-GATGGTCGTCACCATAC
1 CTTTTCATA-TTCGATGATCGAAACCATCC
* * *
19333424 CTTTTCATAATCGAT-AGTC-AAAGCTATCA
1 CTTTTCATATTCGATGA-TCGAAA-CCATCC
* * *
19333453 CTTTTCATATTCAAT-AGCTG-AAGCATCC
1 CTTTTCATATTCGATGATC-GAAACCATCC
19333481 CTTTTCATA
1 CTTTTCATA
19333490 ATTGATGCTG
Statistics
Matches: 119, Mismatches: 25, Indels: 19
0.73 0.15 0.12
Matches are distributed among these distances:
28 16 0.13
29 99 0.83
30 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (29 bp):
CTTTTCATATTCGATGATCGAAACCATCC
Found at i:19333511 original size:28 final size:29
Alignment explanation
Indices: 19333420--19333516 Score: 96
Period size: 28 Copynumber: 3.4 Consensus size: 29
19333410 GGTCGTCACC
* *
19333420 ATACCTTTTCATAATCGATAG-TCAAAGCT
1 ATACCTTTTCATAATTGATAGCT-GAAGCT
*
19333449 AT-CACTTTTCAT-ATTCAATAGCTGAAGC-
1 ATAC-CTTTTCATAATT-GATAGCTGAAGCT
*
19333477 ATCCCTTTTCATAATTGAT-GCTGAAGCT
1 ATACCTTTTCATAATTGATAGCTGAAGCT
19333505 ATACCTTTTCAT
1 ATACCTTTTCAT
19333517 TGGTCGATGA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
27 8 0.14
28 26 0.46
29 22 0.39
30 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (29 bp):
ATACCTTTTCATAATTGATAGCTGAAGCT
Found at i:19337669 original size:21 final size:23
Alignment explanation
Indices: 19337627--19337671 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
19337617 CACTGCTCCA
19337627 TGTCTAAAGTCTACTACCAGTATC
1 TGTCTAAAGTCTACTA-CAGTATC
19337651 TGTCTAAAGTCTAC-A-AGTATC
1 TGTCTAAAGTCTACTACAGTATC
19337672 GGTCCAACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
23 1 0.05
24 14 0.67
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.33
Consensus pattern (23 bp):
TGTCTAAAGTCTACTACAGTATC
Found at i:19338244 original size:43 final size:43
Alignment explanation
Indices: 19338161--19338285 Score: 162
Period size: 43 Copynumber: 2.9 Consensus size: 43
19338151 TAAATCCAAC
* *
19338161 AACCCAAGATTATCTTATCCTC-TTTTAAATTTTTTTTTCAAT
1 AACCCAAGATTATCTTATCCTCTTTTTAAATTCTTTTTTCAAA
* *
19338203 AACCCAAGATTATCTTCTCCTCTTTTTAGATTCTTTTTTCAAA
1 AACCCAAGATTATCTTATCCTCTTTTTAAATTCTTTTTTCAAA
* * ** *
19338246 AATCCAAGATTATCTTTTTTTCTTTTTAAATTCCTTTTTC
1 AACCCAAGATTATCTTATCCTCTTTTTAAATTCTTTTTTC
19338286 TAGGATAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 21 0.29
43 51 0.71
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (43 bp):
AACCCAAGATTATCTTATCCTCTTTTTAAATTCTTTTTTCAAA
Found at i:19338898 original size:18 final size:19
Alignment explanation
Indices: 19338875--19338913 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
19338865 AATTTGAAAT
*
19338875 AAAACA-GAAAATTTTGGA
1 AAAACATGAAAATTTGGGA
19338893 AAAACATGAAAATTTGGGA
1 AAAACATGAAAATTTGGGA
19338912 AA
1 AA
19338914 CAAGGGTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.56, C:0.05, G:0.18, T:0.21
Consensus pattern (19 bp):
AAAACATGAAAATTTGGGA
Found at i:19339332 original size:10 final size:11
Alignment explanation
Indices: 19339307--19339331 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19339297 AAAACACTTT
19339307 AAAACATACAA
1 AAAACATACAA
19339318 AAAACATACAA
1 AAAACATACAA
19339329 AAA
1 AAA
19339332 CCAACCAACT
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:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (11 bp):
AAAACATACAA
Found at i:19342776 original size:39 final size:39
Alignment explanation
Indices: 19342722--19342975 Score: 235
Period size: 39 Copynumber: 6.5 Consensus size: 39
19342712 TATAATTGTA
** * *
19342722 CCCTGATCGTGCATACGTGCCCCTTTTGTACTTCAATAC
1 CCCTGATCGCACATACGTGCCCCTATTGTACTTCAGTAC
* * *
19342761 CCTTGATCGCACATACGTGCCCCTGTTGTACTTC-GGAC
1 CCCTGATCGCACATACGTGCCCCTATTGTACTTCAGTAC
* * * * *
19342799 CCCTAATCGTACATACATTCCCCTATTGTACTTCAATAC
1 CCCTGATCGCACATACGTGCCCCTATTGTACTTCAGTAC
* * * * *
19342838 TCTTGATCAG-ACTTACATGCCCCTATTGTACTTCGGTAC
1 CCCTGATC-GCACATACGTGCCCCTATTGTACTTCAGTAC
*
19342877 CCCTGATCGCACTTACGTGCCCCTATTGTACTT-AGGTAC
1 CCCTGATCGCACATACGTGCCCCTATTGTACTTCA-GTAC
* * * * *
19342916 CCCTGATTGCACTTATGTGCCCCTATTGTGCTTCGGTAC
1 CCCTGATCGCACATACGTGCCCCTATTGTACTTCAGTAC
* * *
19342955 CCCTGATAGCACTTTCGTGCC
1 CCCTGATCGCACATACGTGCC
19342976 ATGATTACGT
Statistics
Matches: 178, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
38 31 0.17
39 146 0.82
40 1 0.01
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.33
Consensus pattern (39 bp):
CCCTGATCGCACATACGTGCCCCTATTGTACTTCAGTAC
Found at i:19342879 original size:19 final size:19
Alignment explanation
Indices: 19342857--19342958 Score: 89
Period size: 19 Copynumber: 5.3 Consensus size: 19
19342847 GACTTACATG
19342857 CCCCTATTGTACTTCGGTA
1 CCCCTATTGTACTTCGGTA
* * *
19342876 CCCCTGATCGCACTTAC-GTG
1 CCCCT-ATTGTACTT-CGGTA
*
19342896 CCCCTATTGTACTTAGGTA
1 CCCCTATTGTACTTCGGTA
* ** *
19342915 CCCCTGATTGCACTTATGTG
1 CCCCT-ATTGTACTTCGGTA
*
19342935 CCCCTATTGTGCTTCGGTA
1 CCCCTATTGTACTTCGGTA
19342954 CCCCT
1 CCCCT
19342959 GATAGCACTT
Statistics
Matches: 64, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
19 33 0.52
20 30 0.47
21 1 0.02
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (19 bp):
CCCCTATTGTACTTCGGTA
Found at i:19342899 original size:20 final size:20
Alignment explanation
Indices: 19342848--19342975 Score: 86
Period size: 20 Copynumber: 6.5 Consensus size: 20
19342838 TCTTGATCAG
* *
19342848 ACTTACATGCCCCT-ATTGT
1 ACTTACGTGCCCCTGATTGC
* *
19342867 ACTT-CGGTACCCCTGATCGC
1 ACTTAC-GTGCCCCTGATTGC
*
19342887 ACTTACGTGCCCCT-ATTGT
1 ACTTACGTGCCCCTGATTGC
* *
19342906 ACTTAGGTACCCCTGATTGC
1 ACTTACGTGCCCCTGATTGC
* *
19342926 ACTTATGTGCCCCT-ATTGT
1 ACTTACGTGCCCCTGATTGC
* * *
19342945 GCTT-CGGTACCCCTGATAGC
1 ACTTAC-GTGCCCCTGATTGC
*
19342965 ACTTTCGTGCC
1 ACTTACGTGCC
19342976 ATGATTACGT
Statistics
Matches: 82, Mismatches: 20, Indels: 13
0.71 0.17 0.11
Matches are distributed among these distances:
18 1 0.01
19 39 0.48
20 40 0.49
21 2 0.02
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (20 bp):
ACTTACGTGCCCCTGATTGC
Found at i:19342930 original size:78 final size:78
Alignment explanation
Indices: 19342735--19342975 Score: 281
Period size: 78 Copynumber: 3.1 Consensus size: 78
19342725 TGATCGTGCA
* * * *
19342735 TACGTGCCCCTTTTGTACTTCAATACCCTTGATCGCACATACGTGCCCCTGTTGTACTTCGG-AC
1 TACGTGCCCCTATTGTACTTCAATACCCTTGATAGCACTTACGTGCCCCTATTGTACTTCGGTAC
* * *
19342799 CCCTAATCGTACA
66 CCCTGATCGCACT
* * * *
19342812 TACATTCCCCTATTGTACTTCAATACTCTTGATCAG-ACTTACATGCCCCTATTGTACTTCGGTA
1 TACGTGCCCCTATTGTACTTCAATACCCTTGAT-AGCACTTACGTGCCCCTATTGTACTTCGGTA
19342876 CCCCTGATCGCACT
65 CCCCTGATCGCACT
* * * * *
19342890 TACGTGCCCCTATTGTACTT-AGGTACCCCTGATTGCACTTATGTGCCCCTATTGTGCTTCGGTA
1 TACGTGCCCCTATTGTACTTCA-ATACCCTTGATAGCACTTACGTGCCCCTATTGTACTTCGGTA
*
19342954 CCCCTGATAGCACT
65 CCCCTGATCGCACT
*
19342968 TTCGTGCC
1 TACGTGCC
19342976 ATGATTACGT
Statistics
Matches: 138, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
77 54 0.39
78 84 0.61
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (78 bp):
TACGTGCCCCTATTGTACTTCAATACCCTTGATAGCACTTACGTGCCCCTATTGTACTTCGGTAC
CCCTGATCGCACT
Found at i:19346925 original size:23 final size:23
Alignment explanation
Indices: 19346893--19346962 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
19346883 TATAATATAT
*
19346893 GCTTTGATATGCTATATGACATG
1 GCTTTGATATGATATATGACATG
19346916 G-TCTTGATATGATATATGACATG
1 GCT-TTGATATGATATATGACATG
* * *
19346939 GCTTTGATAAGTTATATGATATG
1 GCTTTGATATGATATATGACATG
19346962 G
1 G
19346963 AAAGTTTCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.95
24 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTTTGATATGATATATGACATG
Found at i:19354989 original size:3 final size:3
Alignment explanation
Indices: 19354981--19355038 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
19354971 ATTTGTAAAA
* * * * *
19354981 AAT AAT AAT AAT AAT AAT AAT ATTT AAT AAT AGT AAT AGT AGT GAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
*
19355027 GAT AAT AAT AAT
1 AAT AAT AAT AAT
19355039 TTGGGCCTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 44 0.96
4 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:19367805 original size:23 final size:23
Alignment explanation
Indices: 19367761--19367805 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
19367751 TATGCTATTT
*
19367761 GACATGGTTCTGATATGATATAC
1 GACATGGTTCTGATAAGATATAC
*
19367784 GACATGGCTT-TGATAAGTTATA
1 GACATGG-TTCTGATAAGATATA
19367806 GGATATGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (23 bp):
GACATGGTTCTGATAAGATATAC
Found at i:19375704 original size:50 final size:50
Alignment explanation
Indices: 19375631--19375823 Score: 162
Period size: 50 Copynumber: 3.9 Consensus size: 50
19375621 ACATTAGGGG
* * *
19375631 GATGAG-ACT-CCATGTAAGACCATGTCTGGGATATGGCGTTGGCATCAA
1 GATGAGAACTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCAA
** * * * * *
19375679 GATGAGAGGTCCCCCGTAAGACCATGTCTGCGACATGGCATGGGCACCGA
1 GATGAGAACTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCAA
* * * * **
19375729 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACA
1 GATGAGAACTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCA-A
* * *
19375780 G--GA-AACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GATGAGAAC-TCCCACGTAAGACCATGTCTGGGATATGGCATTGGCA
19375824 TGTTATTATC
Statistics
Matches: 113, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
48 9 0.08
49 36 0.32
50 67 0.59
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
GATGAGAACTCCCACGTAAGACCATGTCTGGGATATGGCATTGGCACCAA
Found at i:19376051 original size:20 final size:20
Alignment explanation
Indices: 19376026--19376074 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
19376016 TGAGTTATTT
19376026 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
19376046 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
19376066 AAG-AAGCAA
1 AAGTAAGCAA
19376075 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:19385498 original size:21 final size:22
Alignment explanation
Indices: 19385472--19385519 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
19385462 AATAATAAAA
19385472 ATAATTTA-ATCATATTTTAAT
1 ATAATTTATATCATATTTTAAT
*
19385493 ATAA-TTATTTCATATTTTAAT
1 ATAATTTATATCATATTTTAAT
19385514 ATAATT
1 ATAATT
19385520 ATTTTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 20 0.83
22 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATTTATATCATATTTTAAT
Found at i:19385520 original size:21 final size:21
Alignment explanation
Indices: 19385481--19385523 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19385471 AATAATTTAA
19385481 TCATATTTTAATATAATTATT
1 TCATATTTTAATATAATTATT
19385502 TCATATTTTAATATAATTATT
1 TCATATTTTAATATAATTATT
19385523 T
1 T
19385524 TAATATCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATATTTTAATATAATTATT
Found at i:19390278 original size:32 final size:32
Alignment explanation
Indices: 19390237--19390311 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
19390227 TGCATGTGTG
*
19390237 TAACTCTTCATCTTCAAGTATCTTCACATTTC
1 TAACTCTTCATCTTCAAGTATCTTAACATTTC
*
19390269 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
1 TAACTCTTCATCTTCAAGTATCTTAACATTTC
*
19390301 TAACTTTTCAT
1 TAACTCTTCAT
19390312 AATTTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.25, C:0.27, G:0.03, T:0.45
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTATCTTAACATTTC
Found at i:19394712 original size:16 final size:16
Alignment explanation
Indices: 19394691--19394743 Score: 58
Period size: 16 Copynumber: 3.3 Consensus size: 16
19394681 ATGTGTGTAA
19394691 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
19394707 CTCTTCA-CATTTCTAA--
1 CTCTTCATC--TTC-AAGT
19394723 CTCTTCATCTTCAAGT
1 CTCTTCATCTTCAAGT
19394739 CTCTT
1 CTCTT
19394744 AACATTTCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 19 0.61
17 4 0.13
18 2 0.06
ACGTcount: A:0.19, C:0.32, G:0.04, T:0.45
Consensus pattern (16 bp):
CTCTTCATCTTCAAGT
Found at i:19394729 original size:32 final size:32
Alignment explanation
Indices: 19394688--19394762 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
19394678 TGCATGTGTG
*
19394688 TAACTCTTCATCTTCAAGTCTCTTCACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
19394720 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
1 TAACTCTTCATCTTCAAGTCTCTTAACATTTC
19394752 TAACTCTTCAT
1 TAACTCTTCAT
19394763 AATTTATTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (32 bp):
TAACTCTTCATCTTCAAGTCTCTTAACATTTC
Found at i:19397034 original size:24 final size:25
Alignment explanation
Indices: 19396981--19397044 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 25
19396971 CATAAAAATA
* *
19396981 AAAATATATAATTTAGTAAAATTCT
1 AAAATATATATTTTAATAAAATTCT
* *
19397006 -TAATATATATTTTAATATAATT-T
1 AAAATATATATTTTAATAAAATTCT
*
19397029 AAAATAAAATATTTTA
1 AAAAT-ATATATTTTA
19397045 TTTTAAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 21 0.68
25 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATATATATTTTAATAAAATTCT
Found at i:19397039 original size:29 final size:29
Alignment explanation
Indices: 19397007--19397063 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
19396997 TAAAATTCTT
19397007 AATA-TATATTTTAATATAATTTAAAATAA
1 AATATTATATTTTAA-ATAATTTAAAATAA
* * *
19397036 AATATTTTATTTTAAATTATTTCAAATA
1 AATATTATATTTTAAATAATTTAAAATA
19397064 TATTATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
AATATTATATTTTAAATAATTTAAAATAA
Found at i:19397075 original size:30 final size:30
Alignment explanation
Indices: 19397013--19397072 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
19397003 TCTTAATATA
19397013 TATTTTAATATAATTTAAAATAAAATATTT
1 TATTTTAATATAATTTAAAATAAAATATTT
* * * *
19397043 TATTTTAA-ATTATTTCAAATATATTATTT
1 TATTTTAATATAATTTAAAATAAAATATTT
19397072 T
1 T
19397073 TATATTTTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TATTTTAATATAATTTAAAATAAAATATTT
Found at i:19400552 original size:50 final size:50
Alignment explanation
Indices: 19400485--19400719 Score: 263
Period size: 50 Copynumber: 4.6 Consensus size: 50
19400475 CAATGTCATA
* ** ** * * * *
19400485 TCCCAGATATGGTCTTACATGAAAGTTCTCATATAGGTGCCCATGCTATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
* ** *
19400535 TCCTAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
*
19400585 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
* *
19400635 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCT--A-GGTGCCAACGCCATG
*
19400691 TCCCAGACATGGTCTTACATGGGATCTCT
1 TCCCAGACATGGTCTTACATGGGACCTCT
19400720 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 21, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
50 113 0.72
53 4 0.03
56 41 0.26
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTAGGTGCCAACGCCATG
Found at i:19400683 original size:56 final size:54
Alignment explanation
Indices: 19400532--19400898 Score: 326
Period size: 50 Copynumber: 6.6 Consensus size: 54
19400522 TGCCCATGCT
* ** *
19400532 ATGTCCTAGACATGGTCTTACGGGGGACCTCTC--ATCT--TGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCTCATGATGCCAACGCC
*
19400582 ATGTCCCAGACATGGTCTTACATGGGACCTCTC--ATCTC--GGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCTCATGATGCCAACGCC
*
19400632 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCA-AATCTC-ATGATGCCAACGCC
*
19400688 ATGTCCCAGACATGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAACGTCGGTG
1 ATGTCCCAGACATGGTCTTACATGGGA-C-C--T-CTCAAA--TC-T--CA--TG-A------TG
19400753 CCAACGCC
47 CCAACGCC
** *
19400761 ATGTCTGAGACATGGTCTTACATGGGACCTCTC--ATCTC--GGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCTCATGATGCCAACGCC
*
19400811 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCA-AATCTC-ATGATGCCAACGCC
* *
19400867 ATGCCCCAGACATGGTCTTACATGGGATCTCT
1 ATGTCCCAGACATGGTCTTACATGGGACCTCT
19400899 TTACCCAAAT
Statistics
Matches: 268, Mismatches: 17, Indels: 58
0.78 0.05 0.17
Matches are distributed among these distances:
50 120 0.45
53 10 0.04
56 77 0.29
57 2 0.01
58 1 0.00
60 3 0.01
61 4 0.01
62 2 0.01
63 2 0.01
64 3 0.01
65 1 0.00
66 3 0.01
67 1 0.00
68 2 0.01
69 1 0.00
71 1 0.00
72 1 0.00
73 34 0.13
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.26
Consensus pattern (54 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCAAATCTCATGATGCCAACGCC
Found at i:19400877 original size:179 final size:179
Alignment explanation
Indices: 19400570--19400923 Score: 681
Period size: 179 Copynumber: 2.0 Consensus size: 179
19400560 CTCTCATCTT
19400570 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
*
19400635 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGACA
66 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGCCCCAGACA
19400700 TGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAACGTC
131 TGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAACGTC
**
19400749 GGTGCCAACGCCATGTCTGAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
19400814 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGCCCCAGACA
66 TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGCCCCAGACA
19400879 TGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAA
131 TGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAA
19400924 TCCAATACAT
Statistics
Matches: 172, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
179 172 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.26
Consensus pattern (179 bp):
GGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATG
TCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGCCCCAGACA
TGGTCTTACATGGGATCTCTTTACCCAAATGTCATGACATTTGAACGTC
Found at i:19403045 original size:24 final size:26
Alignment explanation
Indices: 19402995--19403043 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
19402985 TTGTTAAGAC
*
19402995 TCTTATAAAAGAAACCTAAGAGAAAT
1 TCTTATAAAAGAAACCAAAGAGAAAT
19403021 TCTTA-AAAA-AAACTCAAAGAGAA
1 TCTTATAAAAGAAAC-CAAAGAGAA
19403044 TTTATAAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 12 0.57
26 5 0.24
ACGTcount: A:0.57, C:0.12, G:0.10, T:0.20
Consensus pattern (26 bp):
TCTTATAAAAGAAACCAAAGAGAAAT
Found at i:19403051 original size:24 final size:24
Alignment explanation
Indices: 19402997--19403051 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
19402987 GTTAAGACTC
* *
19402997 TTATAAAAGAAACCTAAGAGAAAT
1 TTATAAAAAAAACCAAAGAGAAAT
19403021 TCT-TAAAAAAAACTCAAAGAG-AAT
1 T-TATAAAAAAAAC-CAAAGAGAAAT
19403045 TTATAAA
1 TTATAAA
19403052 CTCAAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 1 0.04
24 18 0.69
25 7 0.27
ACGTcount: A:0.58, C:0.09, G:0.09, T:0.24
Consensus pattern (24 bp):
TTATAAAAAAAACCAAAGAGAAAT
Found at i:19407145 original size:20 final size:20
Alignment explanation
Indices: 19407110--19407163 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
19407100 AAAGAAAAGA
19407110 AAACTC-AAAGAGAATTTAT
1 AAACTCAAAAGAGAATTTAT
*
19407129 AAACTCAAAAAAGAATTTAT
1 AAACTCAAAAGAGAATTTAT
19407149 AAACTCAAAAGAGAA
1 AAACTCAAAAGAGAA
19407164 GTTGAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.20
Consensus pattern (20 bp):
AAACTCAAAAGAGAATTTAT
Found at i:19435043 original size:8 final size:8
Alignment explanation
Indices: 19435030--19435059 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
19435020 CATAACTGAA
*
19435030 AATAAAAG
1 AATAAAAC
19435038 AATAAAAC
1 AATAAAAC
19435046 AATAAAAC
1 AATAAAAC
19435054 AATAAA
1 AATAAA
19435060 TTCCACATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.77, C:0.07, G:0.03, T:0.13
Consensus pattern (8 bp):
AATAAAAC
Found at i:19435582 original size:23 final size:24
Alignment explanation
Indices: 19435546--19435594 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
19435536 CCCGACCCGA
*
19435546 TTTATATATTAAATATA-TATTTT
1 TTTATATATTAAATATACTACTTT
19435569 TTTAT-TATTAAAATATACTACTTT
1 TTTATATATT-AAATATACTACTTT
19435593 TT
1 TT
19435595 GTTTAATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTATATATTAAATATACTACTTT
Found at i:19435593 original size:22 final size:23
Alignment explanation
Indices: 19435546--19435593 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
19435536 CCCGACCCGA
**
19435546 TTTATATATTAAATATATATTTT
1 TTTATATATTAAATATATATACT
19435569 TTTAT-TATTAAA-ATATACTACT
1 TTTATATATTAAATATATA-TACT
19435591 TTT
1 TTT
19435594 TGTTTAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 5 0.23
22 12 0.55
23 5 0.23
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATATATTAAATATATATACT
Found at i:19440103 original size:19 final size:20
Alignment explanation
Indices: 19440067--19440105 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
19440057 CACCATTTGA
*
19440067 TGTTACTCGAAATTAATGAT
1 TGTTACTCGAAATGAATGAT
19440087 TGTTACTCG-AATGAATGAT
1 TGTTACTCGAAATGAATGAT
19440106 AATGGCTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
TGTTACTCGAAATGAATGAT
Found at i:19444361 original size:50 final size:50
Alignment explanation
Indices: 19444307--19444447 Score: 178
Period size: 50 Copynumber: 2.8 Consensus size: 50
19444297 TATTGAAGTT
19444307 ATGAGAGGCCTCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGCCTCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * * *
19444357 ATGAGAGGTCC-CCCGTTAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGG-CCTCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * * *
19444407 ATGAGA-ACTCTCATGTAAGACCATATCTGGGATATGGCATT
1 ATGAGAGGC-CTCACGTAAGACCATGTCTGGGACATGGCATT
19444448 TGTAGTACAT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 73 0.95
51 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
ATGAGAGGCCTCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:19446134 original size:24 final size:24
Alignment explanation
Indices: 19446102--19446152 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
19446092 TGATGTAGAA
*
19446102 AGTAATGAAAGGCTCGTTACAGTT
1 AGTAATGAAAGGCTCGTTACAATT
*
19446126 AGTAGTGAAAGGCTCGTTACAATT
1 AGTAATGAAAGGCTCGTTACAATT
19446150 AGT
1 AGT
19446153 TAGGGAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (24 bp):
AGTAATGAAAGGCTCGTTACAATT
Found at i:19451998 original size:29 final size:29
Alignment explanation
Indices: 19451956--19452013 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
19451946 ACCATGTCTA
*
19451956 GGACACGGCATTTGCCCCGAGATGAGAGG
1 GGACACGGCATTTGCACCGAGATGAGAGG
* *
19451985 GGACATGGCGTTTGCACCGAGATGAGAGG
1 GGACACGGCATTTGCACCGAGATGAGAGG
19452014 TCCCCCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.21, G:0.40, T:0.16
Consensus pattern (29 bp):
GGACACGGCATTTGCACCGAGATGAGAGG
Done.