Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 39 of 187
Found at i:12157336 original size:15 final size:15
Alignment explanation
Indices: 12157316--12157359 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
12157306 GGTCCTCCAC
12157316 TTAAAAATTATAAAA
1 TTAAAAATTATAAAA
* *
12157331 TTAAAAATTATTAAT
1 TTAAAAATTATAAAA
12157346 TATAAAAATTATAA
1 T-TAAAAATTATAA
12157360 TTTTGTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAAATTATAAAA
Found at i:12159830 original size:125 final size:125
Alignment explanation
Indices: 12159608--12159857 Score: 500
Period size: 125 Copynumber: 2.0 Consensus size: 125
12159598 AGTAGATTTC
12159608 TAGTGAATATAATTATTGAGATTAAGTACTGATATTGAACTGAATGAAATTAGAATGAATTGGTG
1 TAGTGAATATAATTATTGAGATTAAGTACTGATATTGAACTGAATGAAATTAGAATGAATTGGTG
12159673 ATTGATATGGATTTTATTGGAATTGGATTGAGAAAGTGGAAATTGATATGTGAGACTGAT
66 ATTGATATGGATTTTATTGGAATTGGATTGAGAAAGTGGAAATTGATATGTGAGACTGAT
12159733 TAGTGAATATAATTATTGAGATTAAGTACTGATATTGAACTGAATGAAATTAGAATGAATTGGTG
1 TAGTGAATATAATTATTGAGATTAAGTACTGATATTGAACTGAATGAAATTAGAATGAATTGGTG
12159798 ATTGATATGGATTTTATTGGAATTGGATTGAGAAAGTGGAAATTGATATGTGAGACTGAT
66 ATTGATATGGATTTTATTGGAATTGGATTGAGAAAGTGGAAATTGATATGTGAGACTGAT
12159858 ACTGAACTGA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 125 1.00
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (125 bp):
TAGTGAATATAATTATTGAGATTAAGTACTGATATTGAACTGAATGAAATTAGAATGAATTGGTG
ATTGATATGGATTTTATTGGAATTGGATTGAGAAAGTGGAAATTGATATGTGAGACTGAT
Found at i:12160235 original size:39 final size:39
Alignment explanation
Indices: 12160180--12160270 Score: 130
Period size: 39 Copynumber: 2.3 Consensus size: 39
12160170 TACTGTTACC
* * *
12160180 GTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAATATT
1 GTTACTGTTACTGATTCGA-CACTTTGTGTGTCGAATACT
*
12160219 GTTACTGTTACTGATTCGATACTTTGTGTGTCGAATACT
1 GTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACT
12160258 GTTACTGTTACTG
1 GTTACTGTTACTG
12160271 TTACCGTTAC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
39 46 0.98
40 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (39 bp):
GTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACT
Found at i:12160273 original size:51 final size:51
Alignment explanation
Indices: 12160218--12160334 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
12160208 TGTTGAATAT
* * *
12160218 TGTTACTGTTACTGATTCGATACTTTGTGTGTCGAATACTGTTACTGTTAC
1 TGTTACTGTTACTGATTCGACACTTTGTGTGTCGAACACTGTTACCGTTAC
* * *
12160269 TGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAACACTGTTACCGTTAC
1 TGTTACTGTTACTGATTCGACACTTTGTGTGTCGAACACTGTTACCGTTAC
*
12160320 TGATTAATGTTACTG
1 TG-TTACTGTTACTG
12160335 GTGTGTTTGG
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 47 0.84
52 9 0.16
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.41
Consensus pattern (51 bp):
TGTTACTGTTACTGATTCGACACTTTGTGTGTCGAACACTGTTACCGTTAC
Found at i:12160319 original size:90 final size:90
Alignment explanation
Indices: 12160155--12160324 Score: 250
Period size: 90 Copynumber: 1.9 Consensus size: 90
12160145 CAGGCACGTA
* * * * *
12160155 TGTGCCGACTACTGTTACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAATATTG
1 TGTGCCGAATACTGTTACTGTTACCGTTACCGTTACAGATTCAGCACTTTGTGTGTCGAACACTG
*
12160220 TTACTGTTACTGATTCGATACTTTG
66 TTACCGTTACTGATTCGATACTTTG
* * * *
12160245 TGTGTCGAATACTGTTACTGTTACTGTTACCGTTACCGATTCGGCACTTTGTGTGTCGAACACTG
1 TGTGCCGAATACTGTTACTGTTACCGTTACCGTTACAGATTCAGCACTTTGTGTGTCGAACACTG
12160310 TTACCGTTACTGATT
66 TTACCGTTACTGATT
12160325 AATGTTACTG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (90 bp):
TGTGCCGAATACTGTTACTGTTACCGTTACCGTTACAGATTCAGCACTTTGTGTGTCGAACACTG
TTACCGTTACTGATTCGATACTTTG
Found at i:12162866 original size:3 final size:3
Alignment explanation
Indices: 12162858--12163052 Score: 117
Period size: 3 Copynumber: 65.0 Consensus size: 3
12162848 TAGTATTACC
* * * ** * *
12162858 ATT ATT ATT ATT -TT GTT AAT ATT ACT ATT CCT CTT ATT -GT ATT TATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* **
12162905 ATT ACTT ATT ATT ATT ATT ATT ATT ATT ATC ATT ACC ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
12162951 ATA ATT AAT ATT AAT ATT AAT ATT GTT ATT ATT ACT ATT ACT ATT ACTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* * * * * ** *
12163000 -TT ATT ATT ACT AAT ATT TTT ATT TTT ATT TTT ACC ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12163047 ATT ATT
1 ATT ATT
12163053 TTTGAACTGT
Statistics
Matches: 142, Mismatches: 44, Indels: 12
0.72 0.22 0.06
Matches are distributed among these distances:
2 5 0.04
3 129 0.91
4 8 0.06
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12169650 original size:45 final size:44
Alignment explanation
Indices: 12169503--12170554 Score: 775
Period size: 44 Copynumber: 23.6 Consensus size: 44
12169493 AGATGGTGAA
* * * * * * * *
12169503 TCTTATCTACCTAAAGCTGCAGTGGACCAGATTAAAGCTAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAACAAG
* * ** * **
12169547 TCTTATCTTCCTAAAGTTGCAGTGGAGTGGATTGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
*
12169591 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAG
* * *
12169636 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAG
* * * ** *
12169681 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GAAACAAG
* * * * ** *
12169725 TCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
12169769 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAG
* * * * *
12169814 TCTTATC-CCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
* **
12169858 TCTTATGC-CCCTGAAGTTGTAGTGGAGCAGACTGAAGATGGCGAA-
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAG
* * ** * * * *
12169903 TCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAACAAG
* * * * **
12169947 TCCTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
*
12169991 TCTTATCTCCCTGAAGTTGCAGTGGGAGCAAACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTGAAGAAA-CAAG
* * *
12170037 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAG
* * * ** *
12170082 TCTTATCTTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCCAATAA-
1 TCTTATC-TCCCTGAAGTTGCAGTGGAGCAGACTGAA--GAAACAAG
* * * * ** *
12170128 TCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAAGTTACAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGAAACAAG
12170173 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAG
* * * * *
12170218 TCTTATC-CCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
* **
12170262 TCTTATGC-CCCTGAAGTTGTAGTGGAGCAGACTGAAGATGGCGAA-
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAG
* * ** * * * *
12170307 TCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAACAAG
* * * * **
12170351 TCCTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
12170395 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAG
* * * * *
12170440 TATTATC-CCTCTGAAGTTGTAGTGGGGCAGACTGAAGTAACCAG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
* * * ** *
12170484 CCTTATCTCCCTGAAATTGCAGTGGAGTAGGTTGAAGATACTAA-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAC-AAG
* * * *
12170528 TATTATCTCCTTGAGGTTGCAATGGAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAG
12170555 TAGATTGAGG
Statistics
Matches: 810, Mismatches: 163, Indels: 70
0.78 0.16 0.07
Matches are distributed among these distances:
43 13 0.02
44 388 0.48
45 339 0.42
46 69 0.09
47 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAG
Found at i:12169672 original size:89 final size:88
Alignment explanation
Indices: 12169503--12170554 Score: 813
Period size: 89 Copynumber: 11.8 Consensus size: 88
12169493 AGATGGTGAA
* * * * * * * * * *
12169503 TCTTATCTACCTAAAGCTGCAGTGGACCAGATTAAAGCTAATAA-TCTTATCTTCCTAAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAACAAGTCTTATCTCCCTGAAGTTGC
** * *
12169567 AGTGGAGTGGATTGAAGTTACAAG
65 AGTGGAGCAGACTGAAGTAACAAG
* *
12169591 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAGTCTTATCTCCCTGAAGTTGC
* *
12169656 AGTGGGGCAGACTGAAGATGACGAA-
65 AGTGGAGCAGACTGAAG-TAAC-AAG
* * * ** * * *
12169681 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCAATAA-TCCTATCTCCCTGAAGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-GAAACAAGTCTTATCTCCCTGAAGTTGC
* * * *
12169745 AGTGGAGCAGATTAAAGTTACAAA
65 AGTGGAGCAGACTGAAGTAACAAG
*
12169769 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATC-CCTCTAAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAGTCTTATCTCC-CTGAAGTTG
* * *
12169833 CAATGGGGCAGACTGAAGTAACTAG
64 CAGTGGAGCAGACTGAAGTAACAAG
* ** * *
12169858 TCTTATGC-CCCTGAAGTTGTAGTGGAGCAGACTGAAGATGGCGAA-TCTTATCTCCCTAAAATT
1 TCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAGTCTTATCTCCCTGAAGTT
** * * *
12169921 TTAGTGGAGCAGATTAAAGTCAATAA-
63 GCAGTGGAGCAGACTGAAGT-AACAAG
* * * * **
12169947 TCCTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAGTCTTATCTCCCTGAAGTTGCA
* *
12170012 GTGGGAGCAAACTGAAGAAAGCAAG
66 GT-GGAGCAGACTGAAGTAA-CAAG
* * *
12170037 TCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAA-TCTTATCTTCCCTGAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGA-AAC-AAGTCTTATC-TCCCTGAAGTT
* * * *
12170101 GCAGTAGAGCAGA-TTAAATCCCAATAA-
63 GCAGTGGAGCAGACTGAAGT---AACAAG
* * * * ** *
12170128 TCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAAGTTACAAATCTTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGAAACAAGTCTTATCTCCCTGAAGTTGC
*
12170193 AGTGGAGCAGACTGAAGAAAGCAAG
65 AGTGGAGCAGACTGAAGTAA-CAAG
* * * * *
12170218 TCTTATC-CCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGC-CCCTGAAGTTG
1 TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAGTCTTAT-CTCCCTGAAGTTG
* **
12170281 TAGTGGAGCAGACTGAAGATGGCGAA-
64 CAGTGGAGCAGACTGAAG-TAAC-AAG
* * ** * * * * * *
12170307 TCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAA-TCCTATCTCCCTGAAATTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG-AAACAAGTCTTATCTCCCTGAAGTTGC
* * *
12170371 AGTGGAGCAGATTAAAGTTACAAG
65 AGTGGAGCAGACTGAAGTAACAAG
*
12170395 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTATTATC-CCTCTGAAGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA-CAAGTCTTATCTCC-CTGAAGTTG
* * *
12170459 TAGTGGGGCAGACTGAAGTAACCAG
64 CAGTGGAGCAGACTGAAGTAACAAG
* * * ** * * * *
12170484 CCTTATCTCCCTGAAATTGCAGTGGAGTAGGTTGAAGATACTAA-TATTATCTCCTTGAGGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAC-AAGTCTTATCTCCCTGAAGTTGC
*
12170548 AATGGAG
65 AGTGGAG
12170555 TAGATTGAGG
Statistics
Matches: 759, Mismatches: 162, Indels: 86
0.75 0.16 0.09
Matches are distributed among these distances:
87 12 0.02
88 155 0.20
89 372 0.49
90 136 0.18
91 59 0.08
92 23 0.03
93 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAACAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGACTGAAGTAACAAG
Found at i:12169933 original size:222 final size:221
Alignment explanation
Indices: 12169501--12170554 Score: 1002
Period size: 222 Copynumber: 4.7 Consensus size: 221
12169491 GAAGATGGTG
* * * * * * * * *
12169501 AATCTTATCTACCTAAAGCTGCAGTGGACCAGATTAAAGCTA-ATAATCTTATCTTCCTAAAGTT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA-AGTCTTATCTCCCTGAAGTT
** * ** *
12169565 GCAGTGGAGTGGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGA-
65 GCAGTGGAGCAGACTGAAGAAACAAGTCTTATC-CCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
* * * *
12169629 AA-GCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTTATCTCCCT
129 AACG-AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCACGAATCCTATCTCCCT
* *
12169693 GAAGTTGCAGTAGAGCAGATTAAA-TC-CAA
192 GAAATTGCAGTGGAGCAGATTAAAGTCAC-A
* * *
12169722 TAATCCTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTTACAAATCTTATCTCCCTGAAGTT
1 -AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAGTCTTATCTCCCTGAAGTT
* * *
12169787 GCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCTCTAAAGTTGCAATGGGGCAGACTGAAG-
65 GCAGTGGAGCAGACTGAAGAAA-CAAGTCTTATCCC-CTGAAGTTGCAGTGGAGCAGACTGAAGA
* * * ** *
12169851 TAACTAGTCTTATGC-CCCTGAAGTTGTAGTGGAGCAGACTGAAGATGGCGAATCTTATCTCCCT
128 TAACGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCACGAATCCTATCTCCCT
* **
12169915 AAAATTTTAGTGGAGCAGATTAAAGTCA-A
192 GAAATTGCAGTGGAGCAGATTAAAGTCACA
* *
12169944 TAATCCTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTT
1 -AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAGTCTTATCTCCCTGAAGTT
* *
12170009 GCAGTGGGAGCAAACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAG
65 GCAGT-GGAGCAGACTGAAGAAA-CAAGTCTTAT-CCCCTGAAGTTGCAGTGGAGCAGACTGAAG
* * * **
12170074 ATGACGAATCTTATCTTCCCTGAAGTTGCAGTAGAGCAGA-TTAA-ATCCCAATAATCCTATCTC
127 ATAACGAATCTTATC-TCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT--CACGAATCCTATCTC
* * *
12170137 CCTGAAGTTGTAGTGGAGCAGATTAAAAGTTACA
189 CCTGAAATTGCAGTGGAGCAGATT-AAAGTCACA
* * * * *
12170171 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCTTATC-CCTCTAAAGT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CAAGTCTTATCTCC-CTGAAGT
* * * * *
12170235 TGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTGTAGTGGAGCAGACTGAAGA
64 TGCAGTGGAGCAGACTGAAGAAACAAGTCTTAT-CCCCTGAAGTTGCAGTGGAGCAGACTGAAGA
** * * ** * * **
12170300 TGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAG-TCAATAATCCTATCTCCCTG
128 TAACGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCACGAATCCTATCTCCCTG
*
12170364 AAATTGCAGTGGAGCAGATTAAAGTTACA
193 AAATTGCAGTGGAGCAGATTAAAGTCACA
* * * * * *
12170393 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTATTATC-CCTCTGAAGT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CAAGTCTTATCTCC-CTGAAGT
* * * * * * * **
12170457 TGTAGTGGGGCAGACTGAAGTAACCAGCCTTATCTCCCTGAAATTGCAGTGGAGTAGGTTGAAGA
64 TGCAGTGGAGCAGACTGAAGAAACAAGTCTTATC-CCCTGAAGTTGCAGTGGAGCAGACTGAAGA
* * * * *
12170522 T-ACTAATATTATCTCCTTGAGGTTGCAATGGAG
128 TAACGAATCTTATCTCCCTGAAGTTGCAGTGGAG
12170555 TAGATTGAGG
Statistics
Matches: 715, Mismatches: 95, Indels: 45
0.84 0.11 0.05
Matches are distributed among these distances:
221 23 0.03
222 336 0.47
223 133 0.19
224 35 0.05
225 107 0.15
226 58 0.08
227 23 0.03
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (221 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAGTCTTATCTCCCTGAAGTTG
CAGTGGAGCAGACTGAAGAAACAAGTCTTATCCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAA
CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATCACGAATCCTATCTCCCTGAAA
TTGCAGTGGAGCAGATTAAAGTCACA
Found at i:12170607 original size:404 final size:399
Alignment explanation
Indices: 12169491--12170506 Score: 1741
Period size: 404 Copynumber: 2.5 Consensus size: 399
12169481 ATGGATTGAA
* * ** ** * *
12169491 GAAGATGGTGAATCTTATCTACCTAAAGCTGCAGTGGACCAGATTAAAG-CTAATAATCTTATCT
1 GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTC-AATAATCCTATCT
* ** * *
12169555 TCCT-AAAGTTGCAGTGGAGTGGATTGAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGC
65 CCCTGAAA-TTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
12169619 AGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCT
129 AGACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCT
12169684 TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCAATAATCCTATCTCCCTGAAGTTGTAGTG
194 TATCTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCAATAAT-CTATCTCCCTGAAGTTGTAGTG
12169749 GAGCAGATTAAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
258 GAGCAGATTAAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAG
12169814 TCTTATCCCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTGTA
323 TCTTATCCCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTGTA
12169879 GTGGAGCAGACT
388 GTGGAGCAGACT
12169891 GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAATCCTATCTC
1 GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAATCCTATCTC
12169956 CCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGGAGCA
66 CCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGT-GGAGCA
*
12170021 AACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTT
130 GACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTT
12170086 ATCTTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCCAATAATCCTATCTCCCTGAAGTTGTAGT
195 ATC-TCCCTGAAGTTGCAGTAGAGCAGATTAAAT-CCAATAAT-CTATCTCCCTGAAGTTGTAGT
12170151 GGAGCAGATTAAAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
257 GGAGCAGATT-AAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCA
12170216 AGTCTTATCCCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTG
321 AGTCTTATCCCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTG
12170281 TAGTGGAGCAGACT
386 TAGTGGAGCAGACT
12170295 GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAATCCTATCTC
1 GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAATCCTATCTC
12170360 CCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
66 CCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* * * * * **
12170425 ACTGAAGAAAGCAAGTATTATCCCTCTGAAGTTGTAGTGGGGCAGACTGAAG-TAACCAGCCTTA
131 ACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTTA
*
12170489 TCTCCCTGAAATTGCAGT
196 TCTCCCTGAAGTTGCAGT
12170507 GGAGTAGGTT
Statistics
Matches: 587, Mismatches: 23, Indels: 11
0.95 0.04 0.02
Matches are distributed among these distances:
400 104 0.18
401 92 0.16
402 40 0.07
403 95 0.16
404 256 0.44
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (399 bp):
GAAGATGGCGAATCTTATCTCCCTAAAATTTTAGTGGAGCAGATTAAAGTCAATAATCCTATCTC
CCTGAAATTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
ACTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTTA
TCTCCCTGAAGTTGCAGTAGAGCAGATTAAATCCAATAATCTATCTCCCTGAAGTTGTAGTGGAG
CAGATTAAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGCAAGTCT
TATCCCTCTAAAGTTGCAATGGGGCAGACTGAAGTAACTAGTCTTATGCCCCTGAAGTTGTAGTG
GAGCAGACT
Found at i:12170719 original size:23 final size:23
Alignment explanation
Indices: 12170693--12170741 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
12170683 TACAGTGGAA
*
12170693 TGGATCAAAGCAACAGGACACAG
1 TGGATCAAAGCAACAAGACACAG
** *
12170716 TGGATTGAAGCAACAAGACGCAG
1 TGGATCAAAGCAACAAGACACAG
12170739 TGG
1 TGG
12170742 GCTGGAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.31, T:0.12
Consensus pattern (23 bp):
TGGATCAAAGCAACAAGACACAG
Found at i:12172067 original size:6 final size:6
Alignment explanation
Indices: 12172052--12172142 Score: 60
Period size: 6 Copynumber: 15.3 Consensus size: 6
12172042 CTTATTGTAT
* * * *
12172052 TTATTA TTATTG TTATTA TTACTA TTACTA TTACTT- TTATTA TTACTA
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTA-TTA TTATTA TTATTA
* * * * ** *
12172100 ATATTT TTATTT TTATTT TTACCA CTATTA TTATTA TT-TTA TT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
12172143 TTTAAACTGT
Statistics
Matches: 67, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
5 7 0.10
6 59 0.88
7 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.01, T:0.64
Consensus pattern (6 bp):
TTATTA
Found at i:12172113 original size:24 final size:24
Alignment explanation
Indices: 12172053--12172142 Score: 92
Period size: 24 Copynumber: 3.8 Consensus size: 24
12172043 TTATTGTATT
* *
12172053 TATTATTATTGTTATTATTACTAT
1 TATTATTATTTTTATTATTACTAA
* *
12172077 TACTATTACTTTTATTATTACTAA
1 TATTATTATTTTTATTATTACTAA
* * * *
12172101 TATTTTTATTTTTATTTTTACCAC
1 TATTATTATTTTTATTATTACTAA
*
12172125 TATTATTATTATT-TTATT
1 TATTATTATTTTTATTATT
12172143 TTTAAACTGT
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
23 4 0.08
24 49 0.92
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (24 bp):
TATTATTATTTTTATTATTACTAA
Found at i:12172275 original size:12 final size:12
Alignment explanation
Indices: 12172258--12172316 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
12172248 AATTAGTTTG
*
12172258 TTTATTTTTTAT
1 TTTATTATTTAT
12172270 TTTATTATTTAT
1 TTTATTATTTAT
*
12172282 CTTATTATTTAT
1 TTTATTATTTAT
12172294 TCTTATTATTCCT-T
1 T-TTATTATT--TAT
12172308 TTTATTATT
1 TTTATTATT
12172317 GGTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
12 22 0.54
13 16 0.39
14 2 0.05
15 1 0.02
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTATTATTTAT
Found at i:12173081 original size:46 final size:44
Alignment explanation
Indices: 12172986--12173347 Score: 362
Period size: 46 Copynumber: 8.6 Consensus size: 44
12172976 TACGTATGAT
* *
12172986 CACTTATCAC-TTGTCAC-TGATTAGATAAATGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-GCTAC
*
12173029 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
* *
12173075 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAA
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
12173121 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
12173157 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
12173193 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
*
12173239 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
12173275 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* *
12173321 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
12173348 AGTACTCAAA
Statistics
Matches: 284, Mismatches: 12, Indels: 43
0.84 0.04 0.13
Matches are distributed among these distances:
36 93 0.33
38 5 0.02
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 11 0.04
44 11 0.04
45 17 0.06
46 134 0.47
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:12173162 original size:36 final size:36
Alignment explanation
Indices: 12173121--12173311 Score: 247
Period size: 36 Copynumber: 5.0 Consensus size: 36
12173111 CTAAGGCTAA
*
12173121 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12173157 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12173193 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
12173235 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
12173275 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12173311 C
1 C
12173312 TAAAGCTACC
Statistics
Matches: 139, Mismatches: 6, Indels: 20
0.84 0.04 0.12
Matches are distributed among these distances:
36 100 0.72
38 3 0.02
40 3 0.02
42 3 0.02
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:12173243 original size:82 final size:82
Alignment explanation
Indices: 12173029--12173347 Score: 397
Period size: 82 Copynumber: 3.9 Consensus size: 82
12173019 GCTAGGCTAC
* * *
12173029 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTCTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
12173094 TGATCAGATAAGTGTAGCTAAGG
66 TGATCAGATAA--GTA--T-A-G
* *
12173117 CTAACACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG----CACTTATCACTTTTT
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTAT
12173172 CACTTGATCAGATAAGTATAG
62 CACTTGATCAGATAAGTATAG
* *
12173193 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
*
12173258 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
*
12173275 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
12173340 TGATCAGA
66 TGATCAGA
12173348 AGTACTCAAA
Statistics
Matches: 209, Mismatches: 8, Indels: 30
0.85 0.03 0.12
Matches are distributed among these distances:
72 29 0.14
74 3 0.01
76 2 0.01
77 1 0.00
78 3 0.01
80 3 0.01
82 134 0.64
86 1 0.00
88 1 0.00
90 3 0.01
92 29 0.14
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TGATCAGATAAGTATAG
Found at i:12173283 original size:118 final size:118
Alignment explanation
Indices: 12173075--12173311 Score: 420
Period size: 118 Copynumber: 2.0 Consensus size: 118
12173065 CTAAGGCTAC
*
12173075 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAGGCTAACACTTATCACTTTGTCACT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
12173140 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
* * *
12173193 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
* *
12173258 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
12173311 C
1 C
12173312 TAAAGCTACC
Statistics
Matches: 113, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 113 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (118 bp):
CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAACACTTATCACTTTGTCACT
TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:12176408 original size:88 final size:88
Alignment explanation
Indices: 12176259--12176486 Score: 348
Period size: 88 Copynumber: 2.6 Consensus size: 88
12176249 TAATTAATAA
* * * *
12176259 TTAAAGATAACAGATCTTGCCTTCCTGGATAGACAGCGAAGCAGATCGAAGACTCCAGCCTTGCG
1 TTAAAGATAACAAATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
**
12176324 TCCATTGGTTGCAGTGGAGTAGG
66 TCCATCAGTTGCAGTGGAGTAGG
*
12176347 TTAAAGATAACAAATCTTGCCTTCCTACATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
1 TTAAAGATAACAAATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
*
12176412 TCCATCAGTTGGAGTGGAGTAGG
66 TCCATCAGTTGCAGTGGAGTAGG
* * * *
12176435 TTGAAGATAGCAAATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGA
1 TTAAAGATAACAAATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGA
12176487 TTACAAGTCT
Statistics
Matches: 127, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 127 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (88 bp):
TTAAAGATAACAAATCTTGCCTTCCTGCATAGACAGCGAAGCAGATCGAAGACCCCAGCCTTGCC
TCCATCAGTTGCAGTGGAGTAGG
Found at i:12176688 original size:44 final size:44
Alignment explanation
Indices: 12176625--12176874 Score: 145
Period size: 44 Copynumber: 5.5 Consensus size: 44
12176615 CCAGTAATCC
12176625 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
* * * * *
12176669 TATCTCTCTGA-AGTTACAGTAGAGTAGATCGCATTAGATTAAAGCCAAAAATCT
1 TATCTCCCTGAGA-TTACAGT-G-G-AG--CGGATTAAAATAAAG-----GATCT
* * ** * *
12176723 TATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTACTA--ATCC
1 TATCTCCCTGAGATTACAGTGGAGCGGATT-AAAATA-AAGGATCT
* *
12176767 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATTT
1 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
* * ** * * *
12176811 TATCTCTCTGA-AGTTACAGTAGAGTAGA-TCACAT-CAGG-TCT
1 TATCTCCCTGAGA-TTACAGTGGAGCGGATTAAAATAAAGGATCT
12176852 TATCTCCCTGAGATTACAGTGGA
1 TATCTCCCTGAGATTACAGTGGA
12176875 ATAGACCGAA
Statistics
Matches: 156, Mismatches: 32, Indels: 39
0.69 0.14 0.17
Matches are distributed among these distances:
41 21 0.13
42 4 0.03
43 10 0.06
44 72 0.46
45 1 0.01
46 1 0.01
47 2 0.01
49 16 0.10
50 3 0.02
51 3 0.02
52 1 0.01
53 1 0.01
54 20 0.13
55 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCT
Found at i:12176784 original size:98 final size:97
Alignment explanation
Indices: 12176605--12176786 Score: 215
Period size: 98 Copynumber: 1.9 Consensus size: 97
12176595 TATAAGGAAG
* ** * * *
12176605 TAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTT
1 TAGATTAAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAA-GATCCT
*
12176670 ATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
65 ATCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
* ** *
12176703 TAGATTAAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTACTA-ATCC
1 TAGATTAAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATT-AAAATA-AAGATCC
12176767 TATCTCCCTG-AGATTACAGT
64 TATCTCCCTGAAG-TTACAGT
12176787 GGAGCGGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
97 2 0.03
98 63 0.90
99 4 0.06
100 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (97 bp):
TAGATTAAAGCCAAAAATCCTATCTCCCTGAGATTACAGCGGAGCAGATTAAAATAAAGATCCTA
TCTCCCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:12177082 original size:50 final size:50
Alignment explanation
Indices: 12176924--12177238 Score: 197
Period size: 50 Copynumber: 6.3 Consensus size: 50
12176914 GCAGTGGAAC
*
12176924 AGATTAAAGCCACAACAGCGAATCATGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *** *
12176974 AGATTAAAGCTACAACAGCAAATCTTAC-TCCCCAGGCGA-TGCAGCGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCC-GAC-ATTGCAGTTAAAA
* * *
12177024 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * ** * ** **
12177074 AGACTAAAGCCATAGCGGTGAGTGTTACTTTCCTGGAGA-TGCAGTGGAGC
1 AGATTAAAGCCACAACAGCGAATCTTGC-TTCCCCGACATTGCAGTTAAAA
* * * * * * *
12177124 TGATTAAAGCCACAA-TGTCGTATCCTACTTCCTCGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACAG-CGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * *
12177174 AGATTAAAGCTACAGCAGCGAATCTTACTTTCCCAACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* *
12177224 GGATTAAAGTCACAA
1 AGATTAAAGCCACAA
12177239 TGACGAATCT
Statistics
Matches: 193, Mismatches: 64, Indels: 16
0.71 0.23 0.06
Matches are distributed among these distances:
49 15 0.08
50 164 0.85
51 14 0.07
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:12177203 original size:100 final size:100
Alignment explanation
Indices: 12176913--12177206 Score: 333
Period size: 100 Copynumber: 2.9 Consensus size: 100
12176903 TCCCAAACGG
*
12176913 TGCAGTGGAACAGATTAAAGCCACAACAG-CGAATCATGCTTCCCCGACATTGCAGTTAAAAAGA
1 TGCAGTGGAACAGATTAAAGCCACAA-TGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGA
* * ** *
12176977 TTAAAGCTACAACAGCAAATCTTACTCCCCAGGCGA
65 TTAAAGCTACAGCAGCGAATCTTACTTTCCAGGAGA
* *
12177013 TGCAGCGGAACAGATTAAAGCCAC-ATCGGT-GAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
1 TGCAGTGGAACAGATTAAAGCCACAAT--GTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAG
* * * * * * * *
12177076 ACTAAAGCCATAGCGGTGAGTGTTACTTTCCTGGAGA
64 ATTAAAGCTACAGCAGCGAATCTTACTTTCCAGGAGA
* * * * * * *
12177113 TGCAGTGGAGCTGATTAAAGCCACAATGTCGTATCCTACTTCCTCGACATTGCGGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACAATGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGAT
12177178 TAAAGCTACAGCAGCGAATCTTACTTTCC
66 TAAAGCTACAGCAGCGAATCTTACTTTCC
12177207 CAACATTGCA
Statistics
Matches: 158, Mismatches: 31, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
99 3 0.02
100 153 0.97
101 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAAAGCCACAATGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCTACAGCAGCGAATCTTACTTTCCAGGAGA
Found at i:12177217 original size:100 final size:99
Alignment explanation
Indices: 12176913--12177247 Score: 311
Period size: 100 Copynumber: 3.4 Consensus size: 99
12176903 TCCCAAACGG
*
12176913 TGCAGTGGAACAGATTAAAGCCACAACAG-CGAATCATGCTTCCCCGACATTGCAGTTAAAAAGA
1 TGCAGTGGAACAGATTAAAGCCACAA-TGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGA
* * * *
12176977 TTAAAGCTACAACAGCAAATCTTAC-TCCCCAGGCGA
65 TTAAAGCTACAGCAGCGAATCTTACTTTCCCA-AC-A
* *
12177013 TGCAGCGGAACAGATTAAAGCCAC-ATCGGT-GAATCTTGCTTCCCCGACATTGCAGTTAAAAAG
1 TGCAGTGGAACAGATTAAAGCCACAAT--GTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAG
* * * * * * * ** *
12177076 ACTAAAGCCATAGCGGTGAGTGTTACTTTCCTGGAGA
64 ATTAAAGCTACAGCAGCGAATCTTACTTTCC-CAACA
* * * * * * *
12177113 TGCAGTGGAGCTGATTAAAGCCACAATGTCGTATCCTACTTCCTCGACATTGCGGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACAATGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGAT
12177178 TAAAGCTACAGCAGCGAATCTTACTTTCCCAACA
66 TAAAGCTACAGCAGCGAATCTTACTTTCCCAACA
* * * *
12177212 TTGCAGT-TAAAAGGATTAAAGTCACAATGACGAATC
1 -TGCAGTGGAACA-GATTAAAGCCACAATGTCGAATC
12177248 TCACTCTCTC
Statistics
Matches: 184, Mismatches: 42, Indels: 18
0.75 0.17 0.07
Matches are distributed among these distances:
99 6 0.03
100 173 0.94
101 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (99 bp):
TGCAGTGGAACAGATTAAAGCCACAATGTCGAATCATGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCTACAGCAGCGAATCTTACTTTCCCAACA
Found at i:12185355 original size:36 final size:32
Alignment explanation
Indices: 12185295--12185361 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 32
12185285 TTCATACCTA
*
12185295 AAAAATAATTATAAAAAATGAATATTGATATT
1 AAAAATAATTATAAAAAATGAATATGGATATT
12185327 AAAAATAAATATATAAAAAATTGCAATATGGATAT
1 AAAAAT-AAT-TATAAAAAA-TG-AATATGGATAT
12185362 CATAAATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 6 0.20
33 3 0.10
34 9 0.30
35 2 0.07
36 10 0.33
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.31
Consensus pattern (32 bp):
AAAAATAATTATAAAAAATGAATATGGATATT
Found at i:12185665 original size:16 final size:16
Alignment explanation
Indices: 12185644--12185682 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
12185634 ATATATATAC
*
12185644 TTTTTTGAATTTTTTA
1 TTTTTTGAATATTTTA
12185660 TTTTTTGAATATTTTA
1 TTTTTTGAATATTTTA
12185676 TTATTTT
1 TT-TTTT
12185683 AAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (16 bp):
TTTTTTGAATATTTTA
Found at i:12189336 original size:17 final size:17
Alignment explanation
Indices: 12189314--12189347 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12189304 GCGCAAGGCA
*
12189314 TGGCGCGCGTGGAGGAG
1 TGGCGCACGTGGAGGAG
*
12189331 TGGCGCATGTGGAGGAG
1 TGGCGCACGTGGAGGAG
12189348 GCTGGCTCCG
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:0.15, C:0.15, G:0.56, T:0.15
Consensus pattern (17 bp):
TGGCGCACGTGGAGGAG
Found at i:12190080 original size:132 final size:131
Alignment explanation
Indices: 12189959--12191474 Score: 2292
Period size: 132 Copynumber: 11.5 Consensus size: 131
12189949 AAATAGGGTA
*
12189959 ACTGGCTTCAATGTACTCCACTGTAAACACAGGGAGGTAAAATTCACTATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCAC-ATCTTTGATCTGCTCCA
* * * * *
12190024 CCACTGCTTAGAGAAACAAGATCTGAAATATTCAATCTATTCCACTGCTGCCCAGGG-AGATAGA
65 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAG-TAGA
12190088 ATT
129 ATT
**
12190091 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAACCCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCA-CATCTTTGATCTGCTCCA
* * *
12190156 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCCATTTCGCTGCTGCCAAGGGAAGTAGAA
65 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
12190221 TT
130 TT
* * *
12190223 ATTGGCTTCAATATACTCCACTGTAACCTCAGGGAGGTAAAATCTGC-CATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-T-CACATCTTTGATCTGCTCC
*
12190287 ACTACTGCTTAGGGAGGA-AAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGAGAAGTAG
64 ACTACTGCTTAGGGA-GACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAG
12190351 AATT
128 AATT
* *
12190355 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATTTTTTATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCA-CATCTTTGATCTGCTCCA
* * *
12190420 CTACTGCTTGGGGAGACAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCAGGGAAGTAGAA
65 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
12190485 TT
130 TT
* * * *
12190487 ATTGGCTTCAATGTACTCCACTGCAACCTCAAGGAGGTAAAATCTGC-CATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-T-CACATCTTTGATCTGCTCC
*
12190551 ACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
64 ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
12190616 ATT
129 ATT
*
12190619 ATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC-CATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-T-CACATCTTTGATCTGCTCC
* *
12190683 ACTACTGTTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
64 ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
12190748 ATT
129 ATT
* * *
12190751 ACTGGCCTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCTGC-CATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-T-CACATCTTTGATCTGCTCC
* *
12190815 ACTACTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGCAGA
64 ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
12190880 ATT
129 ATT
12190883 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCA-CATCTTTGATCTGCTCCA
* * * *
12190948 CTACTGCTTGGGGAGACAAGATCTGAAATCTTTAATCTATTCCACTGCTACCCAGGGAAGTAGAA
65 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
12191013 TT
130 TT
*
12191015 ATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGC-CATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAAT-T-CACATCTTTGATCTGCTCC
* * * *
12191079 ACTACTGCTTAGGGAGGCAAGATCTGAAATCTTTAATCTATTCCGCTGCTGCCTAGGTAAGTAGA
64 ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
12191144 ATT
129 ATT
*
12191147 ATTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAA-TCTACCATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-A-CATCTTTGATCTGCTCC
* *
12191211 ACTATTGCTTAGGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
64 ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGA
12191276 ATT
129 ATT
* * * * *
12191279 ACTGGCCTCAATGTACTCCACTGTAACCTCAAGGAGGTAAAATCCGCTATCTTTGATCTGCTCCA
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCAC-ATCTTTGATCTGCTCCA
* * * *
12191344 CTACTGCTTAGGGAGACAAGATCTAAAATCTTCAATCTATTCCACTGCTGACCAGGGAAGTAGGA
65 CTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAA
12191409 TT
130 TT
* *
12191411 ACTGGCTTCAATGTACTCCACTGCAACCTCAGGGAGGTAAAATTCAACATCTTTGATCTGCTCC
1 ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTC-ACATCTTTGATCTGCTCC
12191475 GCTCTCTATC
Statistics
Matches: 1278, Mismatches: 86, Indels: 40
0.91 0.06 0.03
Matches are distributed among these distances:
129 1 0.00
130 3 0.00
131 5 0.00
132 1257 0.98
133 9 0.01
134 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (131 bp):
ACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACATCTTTGATCTGCTCCAC
TACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGGAAGTAGAAT
T
Found at i:12190609 original size:44 final size:44
Alignment explanation
Indices: 12190430--12191269 Score: 149
Period size: 44 Copynumber: 19.1 Consensus size: 44
12190420 CTACTGCTTG
* * *
12190430 GGGAGACAAGATCTGAAATCTTTAATCTATTCCACTGCTGCCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * * **
12190474 GGGAAG-TAGAAT-T--ATTGGCTTCAATGTACTCCACTGCAACCTCA
1 GGGAGGCAAG-ATCTGAAAT--CTTCAATCTACTCCACTGCTGCC-CA
* * * ** ** * * **
12190518 AGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* *
12190562 GGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * * *
12190606 GGGAAG-TAGAAT-T--ATTGGCTTCAATGTACTCCACTG-TAACCACA
1 GGGAGGCAAG-ATCTGAAAT--CTTCAATCTACTCCACTGCT-GCC-CA
* * ** ** * * ***
12190650 GGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGTTTA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* *
12190694 GGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * * * *
12190738 GGGAAG-TAGAATTACTG---GCCTCAATGTACTCCACTG-TAACCTCA
1 GGGAGGCAAG-A-T-CTGAAATCTTCAATCTACTCCACTGCT-GCC-CA
* * * ** ** * * **
12190782 AGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* *
12190826 GGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * *
12190870 GGGAAGC-AGAATTACTG---GCTTCAATGTACTCCACTG-TAACCACA
1 GGGAGGCAAG-A-T-CTGAAATCTTCAATCTACTCCACTGCT-GCC-CA
* * * * ** * * ***
12190914 GGGAGGTAAAAT-TCACCATCTTTGATCTGCTCCACTACTGCTTG
1 GGGAGGCAAGATCTGA-AATCTTCAATCTACTCCACTGCTGCCCA
* * * *
12190958 GGGAGACAAGATCTGAAATCTTTAATCTATTCCACTGCTACCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * * *
12191002 GGGAAG-TAGAAT-T--ATTGGCTTCAATGTACTCCACTG-TAACCACA
1 GGGAGGCAAG-ATCTGAAAT--CTTCAATCTACTCCACTGCT-GCC-CA
* * ** ** * * **
12191046 GGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * *
12191090 GGGAGGCAAGATCTGAAATCTTTAATCTATTCCGCTGCTGCCTA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
* * * * * *
12191134 GGTAAG-TAGAAT-T--ATTGGCTTCAATGTACTCCACTG-TAACCACA
1 GGGAGGCAAG-ATCTGAAAT--CTTCAATCTACTCCACTGCT-GCC-CA
* * * ** * ** **
12191178 GGGAGGTAAAATCT-ACCATCTTTGATCTGCTCCACTATTGCTTA
1 GGGAGGCAAGATCTGA-AATCTTCAATCTACTCCACTGCTGCCCA
* *
12191222 GGGAGGCAAGATCTGAAATCTTCAATCTATTCCGCTGCTGCCCA
1 GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
12191266 GGGA
1 GGGA
12191270 AGTAGAATTA
Statistics
Matches: 530, Mismatches: 205, Indels: 122
0.62 0.24 0.14
Matches are distributed among these distances:
41 9 0.02
42 8 0.02
43 120 0.23
44 280 0.53
45 98 0.18
46 11 0.02
47 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (44 bp):
GGGAGGCAAGATCTGAAATCTTCAATCTACTCCACTGCTGCCCA
Found at i:12193803 original size:18 final size:18
Alignment explanation
Indices: 12193781--12193819 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
12193771 AATTTGACAG
*
12193781 AAAAAATCTGAAAGAATGA
1 AAAAAATGT-AAAGAATGA
12193800 AAAAAATGTAAAGAATGA
1 AAAAAATGTAAAGAATGA
12193818 AA
1 AA
12193820 GAACATTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.67, C:0.03, G:0.15, T:0.15
Consensus pattern (18 bp):
AAAAAATGTAAAGAATGA
Found at i:12195795 original size:13 final size:13
Alignment explanation
Indices: 12195777--12195803 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12195767 TGGTTCAATT
12195777 CTTCACTAGAAAA
1 CTTCACTAGAAAA
12195790 CTTCACTAGAAAA
1 CTTCACTAGAAAA
12195803 C
1 C
12195804 AAATCTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.22
Consensus pattern (13 bp):
CTTCACTAGAAAA
Found at i:12199067 original size:63 final size:63
Alignment explanation
Indices: 12198968--12199096 Score: 231
Period size: 63 Copynumber: 2.0 Consensus size: 63
12198958 CAACCTGATT
*
12198968 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATATGCCTCATTCTCGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATACGCCTCATTCTCGATGTGATAAGAA
* *
12199031 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCTTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATACGCCTCATTCTCGATGTGATAAGAA
12199094 TAT
1 TAT
12199097 CTCCATGTGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (63 bp):
TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATACGCCTCATTCTCGATGTGATAAGAA
Found at i:12199981 original size:63 final size:61
Alignment explanation
Indices: 12199908--12200028 Score: 163
Period size: 61 Copynumber: 2.0 Consensus size: 61
12199898 TTATGTTATG
* *
12199908 ATTTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATGTTACTAAATTATATATTTTC
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAA-AATATGACTAAATTATATATTTTC
** *
12199971 ATTTTTATTAAATTATATTTGGTAATAATTATATTAAAATATGACTAAATTATTTATT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGACTAAATTATATATT
12200029 ATTAAATTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 18 0.35
62 18 0.35
63 12 0.23
64 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.52
Consensus pattern (61 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGACTAAATTATATATTTTC
Found at i:12200234 original size:16 final size:16
Alignment explanation
Indices: 12200213--12200284 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
12200203 TGAATTACTG
*
12200213 ATTATAGCTCTATTCC
1 ATTACAGCTCTATTCC
* * *
12200229 ATTATAGTTTTATTCC
1 ATTACAGCTCTATTCC
*
12200245 ATTACAACTCTATTCC
1 ATTACAGCTCTATTCC
12200261 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
12200277 ATTACAGC
1 ATTACAGC
12200285 GAACTAAACG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:12206023 original size:11 final size:11
Alignment explanation
Indices: 12205995--12206028 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
12205985 AATCTTTTTA
* *
12205995 TTTATTCTCGT
1 TTTATTTTCTT
12206006 TTTATTTTCTT
1 TTTATTTTCTT
12206017 TTTATTTTCTT
1 TTTATTTTCTT
12206028 T
1 T
12206029 ACACCATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTATTTTCTT
Found at i:12208764 original size:16 final size:16
Alignment explanation
Indices: 12208735--12208768 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12208725 AGCCAATACT
*
12208735 TTGGGCGTACTCTTTC
1 TTGGGCGTAATCTTTC
*
12208751 TTGGGTGTAATCTTTC
1 TTGGGCGTAATCTTTC
12208767 TT
1 TT
12208769 TACTTGAAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.18, G:0.24, T:0.50
Consensus pattern (16 bp):
TTGGGCGTAATCTTTC
Found at i:12211855 original size:253 final size:253
Alignment explanation
Indices: 12211322--12212273 Score: 1644
Period size: 253 Copynumber: 3.8 Consensus size: 253
12211312 TTAATTTTGC
*
12211322 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACTTTTGAAGGGAAAAAGGAAAGAAAGTTGTA
1 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
12211387 GAAAGATATTCTATTCTTTAAAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGG
66 GAAAGATATTCTATTCTTT-AAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGG
* * *
12211452 GCTTTATATTTAGGTGTAAAGATAAAATCAGCCTCTAATGTTTAATCATTTTTTTCATTTTGGCC
130 ACTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCATTTTTTTCATTTTGGCC
12211517 CTCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
195 CTCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
12211576 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
1 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
12211641 GAAAGATATTCTATTCTTTAAAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGG
66 GAAAGATATTCTATTCTTT-AAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGG
12211706 ACTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCA-TTTTTTCATTTTGGCC
130 ACTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCATTTTTTTCATTTTGGCC
*
12211770 CCCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
195 CTCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
12211829 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
1 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
*
12211894 GAAAGATATTCTATTCTTTAAAAAAAGTATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGGA
66 GAAAGATATTCTATTCTTTAAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGGA
12211959 CTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCATTTTTTTTCATTTTGGCC
131 CTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCA-TTTTTTTCATTTTGGCC
*
12212024 CTCATC-TTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
195 CTCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
* *
12212082 CAAGGTTTTCCATCATTGGGGAATTAAGAATACACATTTGAAGGGAAAAAAGAAAGAAAGTTGTA
1 CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
** * ***
12212147 GAAAGATATTCTATTCTTTAAAAAAGGTATCGGAGTTTTTTT-GAAAATTTTTTTAACAATTGGG
66 GAAAGATATTCTATTCTTTAAAAAAAATATCAGAGTTTTTTTAGAAAA-AAATTTAACAATTGGG
* * * * * *
12212211 CCTTTATATTTAGGCATGAAGATAAATTTAGCCCCTAATGTTTAAACA--TTTTTCATTTTGGCC
130 ACTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCATTTTTTTCATTTTGGCC
12212274 ATTATTTTTT
Statistics
Matches: 674, Mismatches: 21, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
250 15 0.02
252 97 0.14
253 368 0.55
254 194 0.29
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (253 bp):
CAAGGTTTTCCATCATTAGGGAATTAAGAATACACATTTGAAGGGAAAAAGGAAAGAAAGTTGTA
GAAAGATATTCTATTCTTTAAAAAAAATATCAGAGTTTTTTTAGAAAAAAATTTAACAATTGGGA
CTTTATATTTAGGTATAAAGATAAAATCAGCCCCTAATGTTTAATCATTTTTTTCATTTTGGCCC
TCAACTTTTAAAATTTACGAAAAATTTGATTGAAATGCTAAATTTTTAACGACATTGG
Found at i:12222178 original size:23 final size:23
Alignment explanation
Indices: 12222143--12222187 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12222133 AAAATGACCC
12222143 AAATTGCACAATCTCAAACATTT
1 AAATTGCACAATCTCAAACATTT
**
12222166 AAATTGCTTAATCTCAAACATT
1 AAATTGCACAATCTCAAACATT
12222188 CAAAACATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.42, C:0.20, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATTGCACAATCTCAAACATTT
Found at i:12226460 original size:20 final size:19
Alignment explanation
Indices: 12226418--12226463 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
12226408 TTCCAGCTCT
*
12226418 TTTTTTTCTTTTTCAAACT
1 TTTTTTTCTTTTTCAAACA
**
12226437 TTTTTTTCTTTTTTCATTCA
1 TTTTTTTC-TTTTTCAAACA
12226457 TTTTTTT
1 TTTTTTT
12226464 ACTAACACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTCTTTTTCAAACA
Found at i:12226931 original size:27 final size:27
Alignment explanation
Indices: 12226863--12226934 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
12226853 GGTGGAGGGC
* * *
12226863 CTGCCACAGGAGACACCAAAGGTGCCT
1 CTGCCACAGGAGGCACCAAAGGTACCA
* * * *
12226890 GTGGCAGAGGTGGCACCAAAGGTACCA
1 CTGCCACAGGAGGCACCAAAGGTACCA
*
12226917 CTGCCACAGGCGGCACCA
1 CTGCCACAGGAGGCACCA
12226935 CTGCACCATT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.32, G:0.31, T:0.10
Consensus pattern (27 bp):
CTGCCACAGGAGGCACCAAAGGTACCA
Found at i:12227461 original size:76 final size:77
Alignment explanation
Indices: 12227256--12227479 Score: 213
Period size: 76 Copynumber: 2.9 Consensus size: 77
12227246 GTTTAATTAT
* *
12227256 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAATTAATATTATTATTATGGTTAGTTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGT-AAAAA--AATATTATTA-T-T-GTTAGTTAT
** * *
12227321 TAGGATTAGTAAAAATCG
60 TATTATTAGTAAAAACCC
* **** * *
12227339 TAATTATTATT-TTAGTTAGTATGATTGTTAGTTTTTACAT-TATATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAATAT-TATTATTGTTAGTTATTATTA
12227402 TTAGT-AAAACCC
65 TTAGTAAAAACCC
* * *
12227414 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTA-TTATTATTAT
1 TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAATATTATTATTGTTAGTTATTATTAT
12227478 TA
66 TA
12227480 TTATTATTAT
Statistics
Matches: 115, Mismatches: 23, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
75 27 0.23
76 47 0.41
77 2 0.02
78 2 0.02
79 7 0.06
81 1 0.01
82 19 0.17
83 10 0.09
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (77 bp):
TAATTATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAATATTATTATTGTTAGTTATTATTAT
TAGTAAAAACCC
Found at i:12227462 original size:3 final size:3
Alignment explanation
Indices: 12227454--12227496 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12227444 AGTAAAAAAC
12227454 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12227497 GTGTTAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12231050 original size:12 final size:12
Alignment explanation
Indices: 12231035--12231066 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
12231025 CTCGGGATTT
12231035 GGCTCGAGCTCC
1 GGCTCGAGCTCC
12231047 GGCTCGAGCTCC
1 GGCTCGAGCTCC
*
12231059 GGTTCGAG
1 GGCTCGAG
12231067 ATTAGGATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.34, G:0.38, T:0.19
Consensus pattern (12 bp):
GGCTCGAGCTCC
Found at i:12234835 original size:159 final size:160
Alignment explanation
Indices: 12234288--12235182 Score: 1353
Period size: 159 Copynumber: 5.6 Consensus size: 160
12234278 ACTTCAAAAC
* *
12234288 AAATTTAGTAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
12234353 ACTTT-AAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
* * *
12234417 AATGCATTGATTTAGTGTGTTTTTTTAAAT
131 AATGTATTAATTTAGTGTGTGTTTTTAAAT
* *
12234447 AAATTTAGTAAAAAACCCTTATTTTGGCCCCTTTT-TTCATATTTTTCTTTTTTCCCAGATTTTA
1 AAATTTAGTAAAAAACCCTTATTTTGG--CCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTA
* * *
12234511 TTATTTTCAAAAAATATACTATTTTTGTATTTTATTATTTTATATTATTTTAGTACATTACGTTT
64 TTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTT
* *
12234576 GAAATGTATTCATTTAGTGTGTTTTTTTAAAT
129 GAAATGTATTAATTTAGTGTGTGTTTTTAAAT
12234608 AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
12234673 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
66 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
*
12234738 AATGTATTAATTTAGT-T-TGTTTTTATAT
131 AATGTATTAATTTAGTGTGTGTTTTTAAAT
*
12234766 AAATTTAGTAAAAAAACCCTTATTTTGGCCTTTTGTTCCTATTTTTCTTTTTTCCCGGATTTTAT
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTAT
12234831 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTG
65 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTG
*
12234896 AAATGTATTAATTTAGT-T-TGTTTTTATAT
130 AAATGTATTAATTTAGTGTGTGTTTTTAAAT
* * *
12234925 AAATTTAGTAAAAAAACCCTTATTTTGGCC-CTTGTTCTTATTTTTCTTTTTTTCCCGAATTTTA
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTC-TTTTTTCCCGGATTTTA
* * *
12234989 TTACTTTC-AAAAATATACTATTTTTGTATTTTATTTTTTTATATTATTTTACTACATTATGTTT
64 TTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTT
* *
12235053 GAAATATATTAATTTAGTGTGTGTTTTTAAAA
129 GAAATGTATTAATTTAGTGTGTGTTTTTAAAT
* * * * **
12235085 AAAATTAGTAAAAAATCATTATTTTGGCCCTTTGTTCGTAATTTTT-TTATTTT--CAAATTTTA
1 AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGT-ATTTTTCTT-TTTTCCCGGATTTTA
* ** *
12235147 TTTCTTTCAGTAAATATACTATTTTCGTTTTTTATT
64 TTACTTTCAAAAAATATACTATTTTCGTATTTTATT
12235183 TCTTTTCGTA
Statistics
Matches: 686, Mismatches: 38, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
158 117 0.17
159 279 0.41
160 167 0.24
161 123 0.18
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (160 bp):
AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
AATGTATTAATTTAGTGTGTGTTTTTAAAT
Found at i:12234878 original size:319 final size:317
Alignment explanation
Indices: 12234288--12235182 Score: 1356
Period size: 319 Copynumber: 2.8 Consensus size: 317
12234278 ACTTCAAAAC
*
12234288 AAATTTAGTAAAAAACTCTTATTTTGGCCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGG-CCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
12234353 ACTTT-AAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
65 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
* * *
12234417 AATGCATTGATTTAGTGTGTTTTTTTAAATAAATTTAGTAAAAAACCCTTATTTTGGCCCCTTTT
130 AATGTATTAATTTAGTGTGTGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTTGG--CCTTTT
* *
12234482 -TTCATATTTTTCTTTTTTCCCAGATTTTATTATTTTCAAAAAATATACTATTTTTGTATTTTAT
193 GTTCATATTTTTCTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTAT
* *
12234546 TATTTTATATTATTTTAGTACATTACGTTTGAAATGTATTCATTTAGTGTGTTTTTTTAAAT
258 TATTTTATATTATTTTAGTACATTACGTTTGAAATGTATTAATTTAGT-T-TGTTTTTAAAT
12234608 AAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
1 AAATTTAGTAAAAAACCCTTATTTTGGCC-TTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATT
12234673 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
65 ACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGA
*
12234738 AATGTATTAATTTAGT-T-TGTTTTTATATAAATTTAGTAAAAAAACCCTTATTTTGGCCTTTTG
130 AATGTATTAATTTAGTGTGTGTTTTTAAATAAATTTAGT-AAAAAACCCTTATTTTGGCCTTTTG
* *
12234801 TTCCTATTTTTCTTTTTTCCCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
194 TTCATATTTTTCTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
* *
12234866 ATTTTATATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTTTGTTTTTATAT
259 ATTTTATATTATTTTAGTACATTACGTTTGAAATGTATTAATTTAGTTTGTTTTTAAAT
* * *
12234925 AAATTTAGTAAAAAAACCCTTATTTTGGCCCTTGTTCTTATTTTTCTTTTTTTCCCGAATTTTAT
1 AAATTTAGT-AAAAAACCCTTATTTTGGCCTTTGTTCGTATTTTTC-TTTTTTCCCGGATTTTAT
* * *
12234990 TACTTTC-AAAAATATACTATTTTTGTATTTTATTTTTTTATATTATTTTACTACATTATGTTTG
64 TACTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTG
* * * * * *
12235054 AAATATATTAATTTAGTGTGTGTTTTTAAAAAAAATTAGTAAAAAATCATTATTTTGGCCCTTTG
129 AAATGTATTAATTTAGTGTGTGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTTGGCCTTTTG
* * * ** *
12235119 TTCGTAATTTTT-TTATTTT--CAAATTTTATTTCTTTCAGTAAATATACTATTTTCGTTTTTTA
194 TTCAT-ATTTTTCTT-TTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTA
12235181 TT
257 TT
12235183 TCTTTTCGTA
Statistics
Matches: 532, Mismatches: 33, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
317 141 0.27
318 80 0.15
319 153 0.29
320 85 0.16
321 73 0.14
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (317 bp):
AAATTTAGTAAAAAACCCTTATTTTGGCCTTTGTTCGTATTTTTCTTTTTTCCCGGATTTTATTA
CTTTCAAAAAATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATTATGTTTGAA
ATGTATTAATTTAGTGTGTGTTTTTAAATAAATTTAGTAAAAAACCCTTATTTTGGCCTTTTGTT
CATATTTTTCTTTTTTCCCAGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTAT
TTTATATTATTTTAGTACATTACGTTTGAAATGTATTAATTTAGTTTGTTTTTAAAT
Found at i:12235190 original size:17 final size:17
Alignment explanation
Indices: 12235168--12235200 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12235158 AAATATACTA
*
12235168 TTTTCGTTTTTTATTTC
1 TTTTCGTATTTTATTTC
12235185 TTTTCGTATTTTATTT
1 TTTTCGTATTTTATTT
12235201 TTTCATAAAC
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:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCGTATTTTATTTC
Found at i:12235231 original size:16 final size:16
Alignment explanation
Indices: 12235185--12235234 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
12235175 TTTTTATTTC
12235185 TTTTC-GTATTTTATT
1 TTTTCAGTATTTTATT
***
12235200 TTTTCA-TAAACATATT
1 TTTTCAGT-ATTTTATT
12235216 TTTTCAGTATTTTATT
1 TTTTCAGTATTTTATT
12235232 TTT
1 TTT
12235235 AATGTTATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 6 0.23
16 19 0.73
17 1 0.04
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (16 bp):
TTTTCAGTATTTTATT
Found at i:12235346 original size:67 final size:70
Alignment explanation
Indices: 12235267--12235406 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 70
12235257 ACTCATTACA
* * * * **
12235267 ACATGCTAAATAAATTTCATAAAAAATATAT-CTAATTAACAT-A-GAATGTACATAACATGAGT
1 ACATGCTAAATAAATCTCATAAAAAATATATGCTAAATAAAATAATAAAACTACATAACATGAGT
12235329 TTTTT
66 TTTTT
*
12235334 ACATGCTAAATAAATCTCATAAAAAATATATGCTAAATAAAATAATAAAACTACATAACATTAGT
1 ACATGCTAAATAAATCTCATAAAAAATATATGCTAAATAAAATAATAAAACTACATAACATGAGT
12235399 TTTTT
66 TTTTT
12235404 ACA
1 ACA
12235407 CAAATAATAC
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
67 30 0.48
68 9 0.14
69 1 0.02
70 23 0.37
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (70 bp):
ACATGCTAAATAAATCTCATAAAAAATATATGCTAAATAAAATAATAAAACTACATAACATGAGT
TTTTT
Found at i:12235523 original size:20 final size:20
Alignment explanation
Indices: 12235483--12235571 Score: 94
Period size: 20 Copynumber: 4.5 Consensus size: 20
12235473 TTTTCCCGTG
* *
12235483 TCTTCTCC-TTCTTTTTC-T
1 TCTTCTCCTTTCCTTTCCTT
12235501 TCTTCTCCTTTCCTTTCCTT
1 TCTTCTCCTTTCCTTTCCTT
*
12235521 TCTTCTCCTTTCCTTTTCTT
1 TCTTCTCCTTTCCTTTCCTT
* *
12235541 TCTTTTTTCTTT-CTTCTCCTT
1 TC-TTCTCCTTTCCTT-TCCTT
12235562 TCTTCTCCTT
1 TCTTCTCCTT
12235572 CAGCCGAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
18 8 0.14
19 7 0.12
20 31 0.53
21 13 0.22
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (20 bp):
TCTTCTCCTTTCCTTTCCTT
Found at i:12235547 original size:10 final size:10
Alignment explanation
Indices: 12235491--12235571 Score: 67
Period size: 10 Copynumber: 8.1 Consensus size: 10
12235481 TGTCTTCTCC
*
12235491 TTCTTTTTC-
1 TTCTTTTCCT
*
12235500 TTCTTCTCCT
1 TTCTTTTCCT
*
12235510 TTCCTTTCCT
1 TTCTTTTCCT
*
12235520 TTCTTCTCCT
1 TTCTTTTCCT
12235530 TTCCTTTT-CT
1 TT-CTTTTCCT
*
12235540 TTCTTTTTTCT
1 TTC-TTTTCCT
*
12235551 TTCTTCTCCT
1 TTCTTTTCCT
*
12235561 TTCTTCTCCT
1 TTCTTTTCCT
12235571 T
1 T
12235572 CAGCCGAATG
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
9 8 0.14
10 42 0.71
11 9 0.15
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTTTCCT
Found at i:12235835 original size:28 final size:30
Alignment explanation
Indices: 12235784--12235840 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 30
12235774 TTTTTTAAAT
*
12235784 TTTTTAGTATTATTTCAGTGAAAA-AACCC
1 TTTTTAGTATTATTTCAGTAAAAATAACCC
**
12235813 TTTTTA-TATTATTTTTGTAAAAATAACC
1 TTTTTAGTATTATTTCAGTAAAAATAACC
12235841 TCATTTCACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTTTAGTATTATTTCAGTAAAAATAACCC
Found at i:12248794 original size:28 final size:27
Alignment explanation
Indices: 12248761--12248859 Score: 119
Period size: 28 Copynumber: 3.6 Consensus size: 27
12248751 TAATGAGATT
*
12248761 AGCACTAAGTGTGCGAGTTTAATTGAA
1 AGCACTAAGTGTGCGAGTATAATTGAA
*
12248788 ATGCACTAAGTGTGCGAGTATAATGGTAA
1 A-GCACTAAGTGTGCGAGTATAATTG-AA
* *
12248817 AGCACTAAGTGTGCGAGTGTGATT-ATTA
1 AGCACTAAGTGTGCGAGTATAATTGA--A
12248845 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
12248860 TACTTATTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 1 0.02
28 58 0.92
29 3 0.05
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTATAATTGAA
Found at i:12261004 original size:3 final size:3
Alignment explanation
Indices: 12260996--12261059 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
12260986 TTTCCAGCTG
12260996 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12261044 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
12261060 CGAGCCTCTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12261471 original size:24 final size:24
Alignment explanation
Indices: 12261444--12261510 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
12261434 TGTTGACAAG
12261444 AAATAATAATATATAAATTTT-AAA
1 AAATAATAATA-ATAAATTTTCAAA
*
12261468 AAATTATAA-AA-AATATTTTCAAA
1 AAATAATAATAATAA-ATTTTCAAA
*
12261491 AAAAATATAATAATAAATTT
1 AAATA-ATAATAATAAATTT
12261511 AAATTTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 2 0.06
22 6 0.17
23 7 0.20
24 12 0.34
25 6 0.17
26 2 0.06
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAATAATAATAAATTTTCAAA
Found at i:12261501 original size:48 final size:47
Alignment explanation
Indices: 12261402--12261510 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 47
12261392 AAATATTTTC
* * * *
12261402 AATAATAAT-AATTTTAATAAATATAAAAATATTGTTGACAAGAAAT
1 AATAATAATAAATTTTAAAAAATATAAAAATATTGTTCAAAAAAAAT
12261448 AATAATATATAAATTTTAAAAAATTATAAAAAATATT-TTCAAAAAAAAT
1 AATAATA-ATAAATTTTAAAAAA-TAT-AAAAATATTGTTCAAAAAAAAT
12261497 -ATAATAATAAATTT
1 AATAATAATAAATTT
12261511 AAATTTAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
46 7 0.13
47 10 0.18
48 17 0.31
49 12 0.22
50 9 0.16
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (47 bp):
AATAATAATAAATTTTAAAAAATATAAAAATATTGTTCAAAAAAAAT
Found at i:12262259 original size:6 final size:6
Alignment explanation
Indices: 12262250--12262287 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
12262240 TATATTTATA
*
12262250 AATATT AATATT AATATT AATA-T AAAATT AATATT AAT
1 AATATT AATATT AATATT AATATT AATATT AATATT AAT
12262288 TATTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATATT
Found at i:12262417 original size:24 final size:23
Alignment explanation
Indices: 12262349--12262417 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 23
12262339 TAATATAAAA
*
12262349 TTAAAT-TTTATTATTATAATTT
1 TTAAATATTTATTATTATTATTT
12262371 TTAAATATTTATT-TATATGTATTT
1 TTAAATATTTATTAT-TAT-TATTT
12262395 TTAAATATTTATATATTATTATT
1 TTAAATATTTAT-TATTATTATT
12262418 CTTATCAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
22 7 0.17
23 9 0.22
24 20 0.49
25 4 0.10
26 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (23 bp):
TTAAATATTTATTATTATTATTT
Found at i:12264917 original size:16 final size:18
Alignment explanation
Indices: 12264896--12264928 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
12264886 TAATTTTTAA
12264896 AAAAATA-T-AATACATC
1 AAAAATACTAAATACATC
12264912 AAAAATACTAAATACAT
1 AAAAATACTAAATACAT
12264929 TAAAGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATACTAAATACATC
Found at i:12268119 original size:31 final size:30
Alignment explanation
Indices: 12268061--12268121 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
12268051 AATAGCTCAA
12268061 TGACTTAAATAAAAATTCTAAATAGTTTAG
1 TGACTTAAATAAAAATTCTAAATAGTTTAG
* * *
12268091 TGACTTAAATGAAAACTTTTGAATAGTTTAG
1 TGACTTAAAT-AAAAATTCTAAATAGTTTAG
12268122 CGACCATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.37
31 17 0.63
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.38
Consensus pattern (30 bp):
TGACTTAAATAAAAATTCTAAATAGTTTAG
Found at i:12270563 original size:23 final size:22
Alignment explanation
Indices: 12270531--12270592 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
12270521 CCCGACCCAT
*
12270531 TTTTTGATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
12270555 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
12270577 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
12270593 TTGTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:12270605 original size:16 final size:16
Alignment explanation
Indices: 12270566--12270607 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
12270556 TTTTATTAAA
*
12270566 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
12270582 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
12270598 ATTAAAATTA
1 ATTAAAATTA
12270608 TATCAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:12270722 original size:110 final size:111
Alignment explanation
Indices: 12270602--12270805 Score: 356
Period size: 111 Copynumber: 1.8 Consensus size: 111
12270592 ATTGTTATTA
* * * *
12270602 AAATTATATCAAATTA-TATTTTTTTCACCAGTCAAAACATTTTTTAAAATCTAACATTTTGTTA
1 AAATTATATCAAATTATTAATTGTTACACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTA
*
12270666 GTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATC
66 GTAAAATTATTAATTATTAATTGTATTAATTGTTAGTAAAATTATC
12270712 AAATTATATCAAATTATTAATTGTTACACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTA
1 AAATTATATCAAATTATTAATTGTTACACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTA
12270777 GTAAAATTATTAATTATTAATTGTATTAA
66 GTAAAATTATTAATTATTAATTGTATTAA
12270806 GGGCAATTTA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 16 0.18
111 72 0.82
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (111 bp):
AAATTATATCAAATTATTAATTGTTACACCAGTCAAAACATTTTGTAAAATCTAACATTTTGTTA
GTAAAATTATTAATTATTAATTGTATTAATTGTTAGTAAAATTATC
Found at i:12270865 original size:30 final size:29
Alignment explanation
Indices: 12270825--12270890 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
12270815 ACTAAAAAAA
*
12270825 GCCG-TTTTTTTCAAAATTTACCGAAATGG
1 GCCGATTTTTTT-AAAATTTACCGAAATAG
** *
12270854 GCCGATTTTTTTATTATTTACCGGAATAG
1 GCCGATTTTTTTAAAATTTACCGAAATAG
12270883 GCC-ATTTT
1 GCCGATTTT
12270891 CCGCGAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.16
29 20 0.62
30 7 0.22
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (29 bp):
GCCGATTTTTTTAAAATTTACCGAAATAG
Found at i:12271992 original size:13 final size:13
Alignment explanation
Indices: 12271974--12271999 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12271964 TTAATTTAAC
12271974 ATTGCGGTCAAAA
1 ATTGCGGTCAAAA
12271987 ATTGCGGTCAAAA
1 ATTGCGGTCAAAA
12272000 GTTAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (13 bp):
ATTGCGGTCAAAA
Found at i:12277297 original size:13 final size:14
Alignment explanation
Indices: 12277279--12277309 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
12277269 CGGGGAAGTC
12277279 AAAACTAAAAC-TA
1 AAAACTAAAACATA
12277292 AAAACTAAAACATA
1 AAAACTAAAACATA
12277306 AAAA
1 AAAA
12277310 ATATATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.74, C:0.13, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAACTAAAACATA
Found at i:12277355 original size:15 final size:15
Alignment explanation
Indices: 12277319--12277360 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
12277309 AATATATATT
12277319 TTAAACATAAAAAAC
1 TTAAACATAAAAAAC
12277334 TTAAAACATAAAAAAC
1 TT-AAACATAAAAAAC
12277350 TTAAAC-TAAAA
1 TTAAACATAAAA
12277361 CTAAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
TTAAACATAAAAAAC
Found at i:12277368 original size:19 final size:21
Alignment explanation
Indices: 12277330--12277376 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
12277320 TAAACATAAA
12277330 AAACTTAAAACATAAAAAACTT
1 AAAC-TAAAACATAAAAAACTT
12277352 AAACTAAAAC-T-AAAAACTT
1 AAACTAAAACATAAAAAACTT
12277371 AAACTA
1 AAACTA
12277377 GTATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.56
20 1 0.04
21 6 0.24
22 4 0.16
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACTAAAACATAAAAAACTT
Found at i:12287446 original size:18 final size:18
Alignment explanation
Indices: 12287419--12287457 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12287409 CTCCGCCTGC
*
12287419 TTGCTCGACTTAACGGGA
1 TTGCTCGACTTAACAGGA
*
12287437 TTGCTTGACTTAACAGGA
1 TTGCTCGACTTAACAGGA
12287455 TTG
1 TTG
12287458 AAAAAGTTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (18 bp):
TTGCTCGACTTAACAGGA
Found at i:12295138 original size:11 final size:12
Alignment explanation
Indices: 12295108--12295140 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12295098 TTATTAAATA
*
12295108 TATATTTTTACT
1 TATATTTTTAAT
12295120 TATATTTTTAAT
1 TATATTTTTAAT
12295132 TAT-TTTTTA
1 TATATTTTTA
12295141 TGTCTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (12 bp):
TATATTTTTAAT
Found at i:12302696 original size:15 final size:15
Alignment explanation
Indices: 12302676--12302713 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
12302666 CTTGACTTTC
12302676 ATTGTTATTATTATT
1 ATTGTTATTATTATT
*
12302691 ATTGTTATTATTGTT
1 ATTGTTATTATTATT
*
12302706 ATTTTTAT
1 ATTGTTAT
12302714 GATTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (15 bp):
ATTGTTATTATTATT
Found at i:12302860 original size:12 final size:12
Alignment explanation
Indices: 12302845--12302870 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12302835 ATTATTTACG
12302845 TATTTATTTTTT
1 TATTTATTTTTT
12302857 TATTTATTTTTT
1 TATTTATTTTTT
12302869 TA
1 TA
12302871 AGTTGGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TATTTATTTTTT
Found at i:12306485 original size:4 final size:4
Alignment explanation
Indices: 12306478--12306546 Score: 63
Period size: 4 Copynumber: 17.0 Consensus size: 4
12306468 TTTCTCCTTC
*
12306478 CTTT CTTT CCTT -TTT CTTTT CTTT CTTT CTTT C-TT -TTT CTTT CTGTTT
1 CTTT CTTT CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CTTT CTTT C--TTT
*
12306526 CATTT CTAT CTTT CTTT CTTT
1 C-TTT CTTT CTTT CTTT CTTT
12306547 TTATTTATTC
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
3 6 0.11
4 36 0.67
5 8 0.15
6 4 0.07
ACGTcount: A:0.03, C:0.23, G:0.01, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:12306538 original size:33 final size:34
Alignment explanation
Indices: 12306479--12306548 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
12306469 TTCTCCTTCC
* * *
12306479 TTTCTTTCCTTTTTCTTTTCTTTCTTTCTTTCTT
1 TTTCTTTCCTGTTTCATTTCTATCTTTCTTTCTT
12306513 TTTCTTT-CTGTTTCATTTCTATCTTTCTTTCTT
1 TTTCTTTCCTGTTTCATTTCTATCTTTCTTTCTT
12306546 TTT
1 TTT
12306549 ATTTATTCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.03, C:0.21, G:0.01, T:0.74
Consensus pattern (34 bp):
TTTCTTTCCTGTTTCATTTCTATCTTTCTTTCTT
Found at i:12308237 original size:31 final size:32
Alignment explanation
Indices: 12308196--12308255 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
12308186 AAACACCAAA
* *
12308196 TAAAATAAGAAATTAAAGAA-AACGAAAACAC
1 TAAAAGAAGAAATTAAAGAACAAAGAAAACAC
*
12308227 TAAAAGAAGAAATTTAAGAACAAAGAAAA
1 TAAAAGAAGAAATTAAAGAACAAAGAAAA
12308256 AATAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.68, C:0.07, G:0.12, T:0.13
Consensus pattern (32 bp):
TAAAAGAAGAAATTAAAGAACAAAGAAAACAC
Found at i:12308517 original size:25 final size:24
Alignment explanation
Indices: 12308484--12308534 Score: 93
Period size: 25 Copynumber: 2.1 Consensus size: 24
12308474 AAATCACAAG
12308484 AAAAAAATTTTGCACAAAGAAACT
1 AAAAAAATTTTGCACAAAGAAACT
12308508 AAAAATAATTTTGCACAAAGAAACT
1 AAAAA-AATTTTGCACAAAGAAACT
12308533 AA
1 AA
12308535 CTTCCAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 5 0.19
25 21 0.81
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.22
Consensus pattern (24 bp):
AAAAAAATTTTGCACAAAGAAACT
Found at i:12313503 original size:22 final size:22
Alignment explanation
Indices: 12313478--12313520 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12313468 TATCCAAACA
12313478 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
12313500 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
12313521 ACTAGAGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:12327633 original size:2 final size:2
Alignment explanation
Indices: 12327626--12327664 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12327616 CCTATAATGT
12327626 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
12327665 ATCATATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12328682 original size:17 final size:18
Alignment explanation
Indices: 12328653--12328699 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
12328643 AAATAAATAA
* *
12328653 ATAAAATGA-ATAAAATT
1 ATAAAAAGATATAAAAAT
12328670 ATAAAAA-ATATAAAAAT
1 ATAAAAAGATATAAAAAT
12328687 ATAAAAAGATATA
1 ATAAAAAGATATA
12328700 TAAGTATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 1 0.04
17 20 0.77
18 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (18 bp):
ATAAAAAGATATAAAAAT
Found at i:12328928 original size:3 final size:3
Alignment explanation
Indices: 12328825--12328908 Score: 87
Period size: 3 Copynumber: 28.0 Consensus size: 3
12328815 AATGGAAATG
* * * *
12328825 TAA TGA TAA TAA TAG TAA TAT TAA TAA TAA TAC TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * *
12328873 TAA TGA TGA TGA TGA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12328909 CCTAATTAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12330709 original size:21 final size:21
Alignment explanation
Indices: 12330679--12330722 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
12330669 GATTCGCTGC
* *
12330679 CTTCAGCTTTAATCTGTTCCA
1 CTTCAACTTTAATCTATTCCA
12330700 CTTCAACTTTAATCTATTCCA
1 CTTCAACTTTAATCTATTCCA
12330721 CT
1 CT
12330723 ACAATGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.05, T:0.43
Consensus pattern (21 bp):
CTTCAACTTTAATCTATTCCA
Found at i:12331000 original size:132 final size:132
Alignment explanation
Indices: 12330762--12331007 Score: 280
Period size: 132 Copynumber: 1.9 Consensus size: 132
12330752 ATTGATCTGT
* * **
12330762 TCCACTACTGCTTAGAGAAACAGGATCTACAATCTTTATCCTACTCCACTGTTGCTCAGGGAGAT
1 TCCACTACTGCTTAGAGAAACAGGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAT
* * * ** *
12330827 AGGACTGGGGGCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTTTAATCT
66 AGGACTGAGGGCTTAAATCTACTTCCCTACCACATCAGGAAGACAAGATTCACCATCTTTAATCT
12330892 AC
131 AC
* * *
12330894 TCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTTCACTACTGCTCAGGGAGAT
1 TCCACTACTGCTTAGAGAAACAGGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAT
* ** ** * *
12330959 AAGG-CTGATGTTTTTTATCTACTTCGCTGCCA-ATACAGGAAGACAAGAT
66 -AGGACTGAGGGCTTAAATCTACTTCCCTACCACAT-CAGGAAGACAAGAT
12331008 CTGCTACTTT
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
131 1 0.01
132 88 0.96
133 3 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
TCCACTACTGCTTAGAGAAACAGGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAT
AGGACTGAGGGCTTAAATCTACTTCCCTACCACATCAGGAAGACAAGATTCACCATCTTTAATCT
AC
Found at i:12331114 original size:88 final size:88
Alignment explanation
Indices: 12331019--12331244 Score: 310
Period size: 88 Copynumber: 2.6 Consensus size: 88
12331009 TGCTACTTTC
* *
12331019 TTCGATCTACTTCGCTGCCAATACAAGAAAACGAGA-CATGCTATTTTCAACCTACTCCACTGCT
1 TTCGATCTACTTCGCTGCCAATACAAGAAAACAAGATC-TGCTATCTTCAACCTACTCCACTGCT
* * * *
12331083 GCTCAGGAAGATAAGGTTTGTGTT
65 GCTCAAGAAGACAAGGCTAGTGTT
* * *
12331107 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTG
1 TTCGATCTACTTCGCTGCCAATACAAGAAAACAAGATCTGCTATCTTCAACCTACTCCACTGCTG
* *
12331172 CTCAAGAAGACGAGGCTAGTTTT
66 CTCAAGAAGACAAGGCTAGTGTT
* * *
12331195 TTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAA
1 TTCGATCTACTTCGCTGCCAATACAAGAAAACAAGATCTGCTATCTTCAA
12331245 TTTACTTCGT
Statistics
Matches: 124, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
88 123 0.99
89 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (88 bp):
TTCGATCTACTTCGCTGCCAATACAAGAAAACAAGATCTGCTATCTTCAACCTACTCCACTGCTG
CTCAAGAAGACAAGGCTAGTGTT
Found at i:12331172 original size:136 final size:133
Alignment explanation
Indices: 12330928--12331305 Score: 392
Period size: 136 Copynumber: 2.8 Consensus size: 133
12330918 ATCTACAATC
* * **
12330928 TTCAACCTACTTCACTACTGCTCAGGGAGATAAGG-CTGATGTTTTTTATCTACTTCGCTGCCAA
1 TTCAACCTACTTCACTGCTGCTCAGGAAGATAAGGTCTGATGTTTTCAATCTACTTCGCTGCCAA
* * *
12330992 TACAGGAAGACAAGATCTGCTA-CTTTCT-TCGA-TCTACTTCGCTGCCAATACAAGAAAACGAG
66 TACAGGAAGACAAGATCTGCTATC-TTCTACCTACTCCAC-T-GCTGCC--T-CAAGAAAACGAG
12331054 AC-ATGCTATT
125 ACTA-G-TATT
* * *
12331064 TTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGTTTG-TGTTTTCGATCTACTTCGCTGCCAA
1 TTCAACCTACTTCACTGCTGCTCAGGAAGATAAGGTCTGATGTTTTCAATCTACTTCGCTGCCAA
* *
12331128 TACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTG-CTCAAGAAGACGAGGCTAGT
66 TACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTGCCTCAAGAAAACGAGACTAGT
*
12331192 TTT
131 ATT
* * *** * * * * * * *
12331195 TTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCAATTTACTTCGTTGCCA
1 TTCAACCTACTTCACTGCTGCT-CAGGAAGATAAGGTCTGATGTTTTCAATCTACTTCGCTGCCA
*
12331260 ATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGC
65 ATACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTGC
12331306 TCAGGGAGAT
Statistics
Matches: 207, Mismatches: 27, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
131 19 0.09
132 27 0.13
133 65 0.31
135 1 0.00
136 85 0.41
137 6 0.03
138 4 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.30
Consensus pattern (133 bp):
TTCAACCTACTTCACTGCTGCTCAGGAAGATAAGGTCTGATGTTTTCAATCTACTTCGCTGCCAA
TACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTGCCTCAAGAAAACGAGACTAGT
ATT
Found at i:12331252 original size:45 final size:45
Alignment explanation
Indices: 12330975--12331295 Score: 249
Period size: 45 Copynumber: 7.2 Consensus size: 45
12330965 GATGTTTTTT
*
12330975 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTACTTTCTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTA---TCTTCA
* * * *
12331023 ATCTACTTCGCTGCCAATACAAGAAAACGAGA-CATGCTATTTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTTCA
* * * *** * * * * * *
12331068 ACCTACTCCACTGCTGCT-CAGGAAGATAAGGTTTG-TGTTTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
*
12331111 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCT
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* * * *** * * * * * *
12331156 ACCTACTCCACTGCTGCT-CAAGAAGACGAG-GCTAG-TTTTTTCG
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCT-GCTATCTTCA
*
12331199 ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
* *
12331244 ATTTACTTCGTTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
1 ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
*
12331289 ACCTACT
1 ATCTACT
12331296 CCACTGCTGC
Statistics
Matches: 206, Mismatches: 59, Indels: 19
0.73 0.21 0.07
Matches are distributed among these distances:
43 38 0.18
44 46 0.22
45 87 0.42
47 1 0.00
48 34 0.17
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
Found at i:12331281 original size:133 final size:133
Alignment explanation
Indices: 12331114--12331375 Score: 407
Period size: 133 Copynumber: 2.0 Consensus size: 133
12331104 GTTTTCGATC
*
12331114 TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCTACCTACTCCACTGCTGCTCAAGA
1 TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAAGA
* * * * *
12331179 AGACGAGGCTAGTTTTTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTCA
66 AGACAAGGCTAGTGTTTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTACAATCTTCA
12331244 ATT
131 ATT
* * *
12331247 TACTTCGTTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAGGG
1 TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAAGA
* * * *
12331312 AGATAAGGTTTGTGTTTTCGATCTACTTCACTATCAATACAGGAAGACAAGATCTACAATCTTC
66 AGACAAGGCTAGTGTTTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTACAATCTTC
12331376 TTCAATCCAT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
133 116 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (133 bp):
TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCAACCTACTCCACTGCTGCTCAAGA
AGACAAGGCTAGTGTTTTCGATCTACTTCACTACCAATACAGGAAGACAAGATCTACAATCTTCA
ATT
Found at i:12331321 original size:221 final size:222
Alignment explanation
Indices: 12330911--12331376 Score: 661
Period size: 221 Copynumber: 2.1 Consensus size: 222
12330901 CTGCTTAGGG
* * * * * *
12330911 AGACAGGATCTACAATCTTCAACCTACTTCACTACTGCTCAGGGAGATAAGGCTGATGTTTTTTA
1 AGACAAGATCTACAATCTTCTACCTACTCCACTACTGCTCAAGAAGACAAGGCTGATGTTTTTTA
* *
12330976 TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTACTTTCTTCGATCTACTTCGCTGCCAAT
66 TCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTA--TTCTTCAATCTACTTCGCTGCCAAT
* *
12331041 ACAAGAAAACGAGACATGCTATTTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGTTTGTGT
129 ACAAGAAAACAAGACATGCTATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGTTTGTGT
* *
12331106 TTTCGATCTACTTCGCTGCCAATACAGGA
194 TTTCGATCTACTTCACTACCAATACAGGA
* * * *
12331135 AGACAAGATCTGCTATCTTCTACCTACTCCACTGCTGCTCAAGAAGACGAGGCT-A-GTTTTTTC
1 AGACAAGATCTACAATCTTCTACCTACTCCACTACTGCTCAAGAAGACAAGGCTGATGTTTTTT-
* *
12331198 GATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTA-TCTTCAATTTACTTCGTTGCCAAT
65 -ATCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTCTTCAATCTACTTCGCTGCCAAT
* * *
12331262 ACAGGAAGACAAGATC-TGCTATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTTTGTG
129 ACAAGAAAACAAGA-CATGCTATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGTTTGTG
*
12331326 TTTTCGATCTACTTCACTATCAATACAGGA
193 TTTTCGATCTACTTCACTACCAATACAGGA
12331356 AGACAAGATCTACAATCTTCT
1 AGACAAGATCTACAATCTTCT
12331377 TCAATCCATT
Statistics
Matches: 215, Mismatches: 24, Indels: 9
0.87 0.10 0.04
Matches are distributed among these distances:
221 124 0.58
222 8 0.04
223 1 0.00
224 82 0.38
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (222 bp):
AGACAAGATCTACAATCTTCTACCTACTCCACTACTGCTCAAGAAGACAAGGCTGATGTTTTTTA
TCTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATTCTTCAATCTACTTCGCTGCCAATAC
AAGAAAACAAGACATGCTATCTTCAACCTACTCCACTGCTGCTCAGGAAGATAAGGTTTGTGTTT
TCGATCTACTTCACTACCAATACAGGA
Found at i:12343704 original size:3 final size:3
Alignment explanation
Indices: 12343603--12343684 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
12343593 AATGGAAATG
* * * * *
12343603 TAA TGA TAA TAA CAG TAA TAT TAA TAA TATA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* *
12343649 TAA TAA TAA TGA TAA TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12343685 CCTAATTAGT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 61 0.95
4 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12346107 original size:22 final size:21
Alignment explanation
Indices: 12346090--12346130 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
12346080 AGAATAAGGA
12346090 GAAAACAACAAGAAAATAACAT
1 GAAAACAACAA-AAAATAACAT
*
12346112 TAAAACAACAAAAAATAAC
1 GAAAACAACAAAAAATAAC
12346131 GGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.10
Consensus pattern (21 bp):
GAAAACAACAAAAAATAACAT
Found at i:12346591 original size:17 final size:17
Alignment explanation
Indices: 12346554--12346610 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
12346544 ACAATTATTT
* *
12346554 AATTTTAAAAAATTCAT
1 AATTTTAAAAAATTAAA
*
12346571 AATTTTATAAAATTAAA
1 AATTTTAAAAAATTAAA
*
12346588 AATTATTTAAAAAGTATAAA
1 AA-T-TTTAAAAAAT-TAAA
12346608 AAT
1 AAT
12346611 ATTTTTTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 16 0.50
18 1 0.03
19 9 0.28
20 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AATTTTAAAAAATTAAA
Found at i:12351440 original size:20 final size:20
Alignment explanation
Indices: 12351408--12351446 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12351398 ATTTAATGGT
12351408 TATATTTAAATATT-TAAAA
1 TATATTTAAATATTCTAAAA
*
12351427 TATAGTTTATATATTCTAAA
1 TATA-TTTAAATATTCTAAA
12351447 TAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATTTAAATATTCTAAAA
Found at i:12353932 original size:21 final size:20
Alignment explanation
Indices: 12353888--12353941 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
12353878 GAAATTAATC
**
12353888 ATTT-TATATTTTTAAATTT
1 ATTTATATATTTTTAAAAAT
12353907 A-TTATATAATTTTTAAAAAT
1 ATTTATAT-ATTTTTAAAAAT
*
12353927 ATTTATGTATTTTTA
1 ATTTATATATTTTTA
12353942 TATATTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 4 0.14
20 18 0.62
21 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTATATATTTTTAAAAAT
Found at i:12363514 original size:24 final size:24
Alignment explanation
Indices: 12363487--12363534 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
12363477 TTCAATTCAA
*
12363487 AAGTTGAGAGATGATGGATGAGAT
1 AAGTGGAGAGATGATGGATGAGAT
12363511 AAGTGGAGAGATGATGGATGAGAT
1 AAGTGGAGAGATGATGGATGAGAT
12363535 GAATTGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.23
Consensus pattern (24 bp):
AAGTGGAGAGATGATGGATGAGAT
Found at i:12363533 original size:12 final size:12
Alignment explanation
Indices: 12363494--12363536 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
12363484 CAAAAGTTGA
12363494 GAGATGATGGAT
1 GAGATGATGGAT
*
12363506 GAGATAAGTGGA-
1 GAGATGA-TGGAT
12363518 GAGATGATGGAT
1 GAGATGATGGAT
12363530 GAGATGA
1 GAGATGA
12363537 ATTGTTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.42, T:0.21
Consensus pattern (12 bp):
GAGATGATGGAT
Found at i:12365813 original size:18 final size:18
Alignment explanation
Indices: 12365764--12365814 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
12365754 AGCTCTCAGT
12365764 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* *** *
12365782 CAGTAAGCTACCTTCATC
1 CATTCTTCTCCCTTCATC
12365800 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
12365815 CTTCATTCCT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.41, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:12368826 original size:32 final size:32
Alignment explanation
Indices: 12368786--12368872 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
12368776 ACTTTTCCGA
*
12368786 AAAATATTTTCAGGAAATC-TGCCAAACAACAG
1 AAAATATTTTCAGCAAATCAT-CCAAACAACAG
* *
12368818 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCA-AATCATCCAAACAACAG
*
12368851 AAAATATTTTCTAGTAAATCAT
1 AAAATATTTTC-AGCAAATCAT
12368873 TTTTCCAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
32 12 0.27
33 31 0.69
34 2 0.04
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACAACAG
Found at i:12368892 original size:14 final size:15
Alignment explanation
Indices: 12368847--12368904 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
12368837 CATCCAAACA
12368847 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
* *
12368861 CTAGTAAATCATTTTT
1 CCAGAAAATCA-TTTT
12368877 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
*
12368891 CCGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
12368905 ACTGTCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 19 0.51
15 11 0.30
16 7 0.19
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:12374066 original size:45 final size:45
Alignment explanation
Indices: 12373976--12374100 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
12373966 AGAATTGTAA
* * ** * * *
12373976 CCTGAACCAGAAGGGAAAGGTACAACCGGTAATGAAACAGCAGAT
1 CCTGAACCAGAAGGCAAAGATACAGTCAGTGATGAAACAACAGAT
* *
12374021 CCTGAACCAGAAGGCAAAGATACAGTCAGTGATGGAACAATAGAT
1 CCTGAACCAGAAGGCAAAGATACAGTCAGTGATGAAACAACAGAT
*
12374066 CCTGAATCAGAAGGCAAAGATACAGTCAGTGATGA
1 CCTGAACCAGAAGGCAAAGATACAGTCAGTGATGA
12374101 GACGGAGGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (45 bp):
CCTGAACCAGAAGGCAAAGATACAGTCAGTGATGAAACAACAGAT
Found at i:12378788 original size:23 final size:25
Alignment explanation
Indices: 12378743--12378788 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
12378733 TTGATCTATT
*
12378743 TTTTACTTTTGTATATATCATTTTA
1 TTTTACTTTTGTATATATAATTTTA
12378768 TTTTAC-TTT-TATATATAATTT
1 TTTTACTTTTGTATATATAATTT
12378789 ATATCACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 3 0.15
25 6 0.30
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTACTTTTGTATATATAATTTTA
Found at i:12388264 original size:18 final size:19
Alignment explanation
Indices: 12388230--12388270 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
12388220 TATTAGGATA
12388230 ATTAA-TATTAATATAATT
1 ATTAAGTATTAATATAATT
*
12388248 ATTAAGTATT-ATTTAATT
1 ATTAAGTATTAATATAATT
12388266 -TTAAG
1 ATTAAG
12388271 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 12 0.57
19 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTAAGTATTAATATAATT
Found at i:12395796 original size:10 final size:9
Alignment explanation
Indices: 12395771--12395812 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
12395761 TAAAGCATAA
12395771 AAAATATAA-
1 AAAATA-AAT
12395780 AAAATAAAT
1 AAAATAAAT
12395789 AAATATAAAT
1 AAA-ATAAAT
12395799 CAAAATAAAT
1 -AAAATAAAT
12395809 AAAA
1 AAAA
12395813 AAGAAAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.07
9 13 0.43
10 12 0.40
11 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:12395813 original size:10 final size:10
Alignment explanation
Indices: 12395770--12395813 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
12395760 CTAAAGCATA
*
12395770 AAAAATATA-
1 AAAAATAAAT
12395779 AAAAATAAAT
1 AAAAATAAAT
*
12395789 AAATATAAAT
1 AAAAATAAAT
*
12395799 CAAAATAAAT
1 AAAAATAAAT
12395809 AAAAA
1 AAAAA
12395814 AGAAAAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.20
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:12396434 original size:18 final size:17
Alignment explanation
Indices: 12396413--12396454 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
12396403 AATATTAATA
12396413 TAATTATTAAGGA-TTATT
1 TAATT-TTAA-GATTTATT
12396431 TAATTTTAAGATTTTATT
1 TAATTTTAAGA-TTTATT
12396449 TAATTT
1 TAATTT
12396455 ATCTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 4 0.18
18 16 0.73
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (17 bp):
TAATTTTAAGATTTATT
Found at i:12396474 original size:20 final size:20
Alignment explanation
Indices: 12396441--12396500 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
12396431 TAATTTTAAG
12396441 ATTT-TATTTAATTTATCTTT
1 ATTTATATTT-ATTTATCTTT
*
12396461 ATTTATATTTATTTATCTTC
1 ATTTATATTTATTTATCTTT
* * *
12396481 AATTAAATGTATTTATCTTT
1 ATTTATATTTATTTATCTTT
12396501 TGGGAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 29 0.85
21 5 0.15
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (20 bp):
ATTTATATTTATTTATCTTT
Found at i:12398342 original size:16 final size:18
Alignment explanation
Indices: 12398309--12398342 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12398299 TGTTAATAGA
12398309 ATGAATTTAGTGTTAATT
1 ATGAATTTAGTGTTAATT
12398327 ATGAATTT-GT-TTAATT
1 ATGAATTTAGTGTTAATT
12398343 GTGTGTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
ATGAATTTAGTGTTAATT
Found at i:12403661 original size:21 final size:22
Alignment explanation
Indices: 12403607--12403666 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
12403597 ATGAGTTTAA
*
12403607 CACTTCAG-TGCTCTATGCTTAG
1 CACTT-AGATGCTCTTTGCTTAG
*
12403629 CACTTAGATGCTCTTTGTTTAG
1 CACTTAGATGCTCTTTGCTTAG
*
12403651 CA-TTCGATGCTCTTTG
1 CACTTAGATGCTCTTTG
12403667 GTGCTGTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.44
22 19 0.56
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (22 bp):
CACTTAGATGCTCTTTGCTTAG
Found at i:12404315 original size:17 final size:17
Alignment explanation
Indices: 12404293--12404384 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 17
12404283 CTTATCAAGA
12404293 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
12404310 TAAATATTAAGA-T-AAT
1 TAAATATTAA-ATTAAAT
*
12404326 TAATTTATTAAATT-AAT
1 TAA-ATATTAAATTAAAT
* * *
12404343 AAAATACT--ATCAAGA-
1 TAAATATTAAATTAA-AT
12404358 TAAATATTAAATTAAAT
1 TAAATATTAAATTAAAT
*
12404375 TTAATATTAA
1 TAAATATTAA
12404385 TTTTAGAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
14 2 0.03
15 7 0.12
16 12 0.21
17 36 0.62
18 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:12404555 original size:18 final size:18
Alignment explanation
Indices: 12404528--12404564 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12404518 TTTGTGGTAA
* *
12404528 AAAAATTGTGTTAATTTT
1 AAAAAGTGTGCTAATTTT
12404546 AAAAAGTGTGCTAATTTT
1 AAAAAGTGTGCTAATTTT
12404564 A
1 A
12404565 TTGATGAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.43
Consensus pattern (18 bp):
AAAAAGTGTGCTAATTTT
Found at i:12404999 original size:15 final size:15
Alignment explanation
Indices: 12404972--12405010 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
12404962 GGCGCCGAAA
*
12404972 GCCGAGAAAAAGCCC
1 GCCGAGAAGAAGCCC
* *
12404987 GCTGAGAAGAAGCCT
1 GCCGAGAAGAAGCCC
12405002 GCCGAGAAG
1 GCCGAGAAG
12405011 CCAACGGAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.36, C:0.26, G:0.33, T:0.05
Consensus pattern (15 bp):
GCCGAGAAGAAGCCC
Found at i:12411838 original size:14 final size:13
Alignment explanation
Indices: 12411806--12411841 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
12411796 TTTTATTATG
*
12411806 TTTAAATTTGATA
1 TTTAATTTTGATA
12411819 TTTAATTTTGATA
1 TTTAATTTTGATA
12411832 TTTTAATTTT
1 -TTTAATTTT
12411842 TAATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (13 bp):
TTTAATTTTGATA
Found at i:12423145 original size:21 final size:21
Alignment explanation
Indices: 12423119--12423173 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
12423109 TAGTGAAATA
12423119 ATGTCTCGAGACTTGAT-CCTT
1 ATGTCTCGAGACTTG-TGCCTT
* *
12423140 ATGTCTCGAGATTTTGTGTCTT
1 ATGTCTCGAGA-CTTGTGCCTT
12423162 ATGTCTCGAGAC
1 ATGTCTCGAGAC
12423174 ATGTATCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (21 bp):
ATGTCTCGAGACTTGTGCCTT
Found at i:12425877 original size:57 final size:57
Alignment explanation
Indices: 12425762--12425909 Score: 192
Period size: 57 Copynumber: 2.6 Consensus size: 57
12425752 CGGACTATCT
* * * *
12425762 TTGATGTCATACCGTCTTTTAGCTATAGTCTTACTCATTCTACTGTCAAATCATTAC
1 TTGATGCCATAACATCTTTTAGCTATGGTCTTACTCATTCTACTGTCAAATCATTAC
* * * *
12425819 TTGTTGCCATAAC-TTTTTTCATCTATGGTCTTATTCATTCTA-TCGTCAAATCATTAC
1 TTGATGCCATAACATCTTTT-AGCTATGGTCTTACTCATTCTACT-GTCAAATCATTAC
12425876 TTGATGCCATAACATCTTTTAGCTATGGTCTTAC
1 TTGATGCCATAACATCTTTTAGCTATGGTCTTAC
12425910 ATAATATAAC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
56 6 0.08
57 66 0.86
58 5 0.06
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (57 bp):
TTGATGCCATAACATCTTTTAGCTATGGTCTTACTCATTCTACTGTCAAATCATTAC
Found at i:12427948 original size:17 final size:17
Alignment explanation
Indices: 12427926--12427959 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12427916 TGTACCTAGA
*
12427926 TATATATGTACACATTT
1 TATATATATACACATTT
*
12427943 TATATATATACATATTT
1 TATATATATACACATTT
12427960 ATTTATCCTT
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:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (17 bp):
TATATATATACACATTT
Found at i:12427987 original size:12 final size:12
Alignment explanation
Indices: 12427970--12428009 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
12427960 ATTTATCCTT
12427970 TATATTTTAAAA
1 TATATTTTAAAA
* *
12427982 TATATTTTTATA
1 TATATTTTAAAA
12427994 TATATTTTATAAA
1 TATATTTTA-AAA
12428007 TAT
1 TAT
12428010 TTTGTAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
12 18 0.78
13 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TATATTTTAAAA
Found at i:12427994 original size:10 final size:11
Alignment explanation
Indices: 12427970--12428012 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
12427960 ATTTATCCTT
*
12427970 TATATTTTAAAA
1 TATATTTT-ATA
12427982 TATATTTTTATA
1 TATA-TTTTATA
12427994 TATATTTTATA
1 TATATTTTATA
*
12428005 AATATTTT
1 TATATTTT
12428013 GTAATTCACG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 14 0.50
12 10 0.36
13 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATATTTTATA
Found at i:12428247 original size:4 final size:4
Alignment explanation
Indices: 12428198--12428229 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
12428188 TTTTTTATAC
12428198 TTTA GTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
12428230 GCTATGATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:12428600 original size:112 final size:109
Alignment explanation
Indices: 12428412--12428693 Score: 404
Period size: 112 Copynumber: 2.6 Consensus size: 109
12428402 TTTCAAATTG
12428412 AGGCAATATTTTGCGTTTGGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
1 AGGCAATATTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTC
* **
12428477 TCGTTCGACCAAATAGCTAAATATCCTTTTAAAAACTTTTCAAAAATA
65 TCGTTCAACCAAATAGCTAAATATCCTTCCAAAAA--TTTCAAAAA-A
*
12428525 AGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
12428590 CGTTCAACCAAATAGCTAAATATCCTTCCAAAAATTTCAAAAAA
66 CGTTCAACCAAATAGCTAAATATCCTTCCAAAAATTTCAAAAAA
* * * * * * * * *
12428634 AGGCAATATTTTGCATTCGAAAATTCAAG-GAACGTGCCCTAATGTACTGGGTTTCGATTT
1 AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTT
12428694 CCCGATTGAC
Statistics
Matches: 155, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
108 26 0.17
109 25 0.16
110 9 0.06
112 78 0.50
113 17 0.11
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (109 bp):
AGGCAATATTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTCCAAAAATTTCAAAAAA
Found at i:12444060 original size:19 final size:19
Alignment explanation
Indices: 12444036--12444075 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
12444026 TAAAAGCAAC
12444036 ACAACATCAACCCAAATAA
1 ACAACATCAACCCAAATAA
* **
12444055 ACAACATGATTCCAAATAA
1 ACAACATCAACCCAAATAA
12444074 AC
1 AC
12444076 TACAAAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.28, G:0.03, T:0.15
Consensus pattern (19 bp):
ACAACATCAACCCAAATAA
Found at i:12446897 original size:91 final size:89
Alignment explanation
Indices: 12446715--12447112 Score: 546
Period size: 91 Copynumber: 4.4 Consensus size: 89
12446705 AAAATTAATT
* * * * *
12446715 AATTAATATAATATTACAACAGCATAAATTAAACAAAAAAAGTATATTGAACTACATTTTAAACT
1 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAGTATGTTAAACTACAGTTTAAACT
*
12446780 TTAAATTTAGTTAATTGAAGCCTA
66 TTAAAGTTAGTTAATTGAAGCCTA
* *
12446804 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAGCTATC-GTTTAA
1 AATTAATATAATAGTACAATAGCATAAATTAAAC--AAAAAAAGTATGTTAAACTA-CAGTTTAA
*
12446868 ACTTTAAAGTTAGTTAATTGAAGCATA
63 ACTTTAAAGTTAGTTAATTGAAGCCTA
**
12446895 AATTAATATAATAGTACAAGTACAACAGCATAAATTAAACAAAAAATTTATGTTAAACTACAGTT
1 AATTAATATAATAGTACAA-T-----AGCATAAATTAAACAAAAAAAGTATGTTAAACTACAGTT
*
12446960 TAAACTTTAAAGTTAGTTAATTGAAACCTA
60 TAAACTTTAAAGTTAGTTAATTGAAGCCTA
* *
12446990 AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAACCACAGTTTAAA
1 AATTAATATAATAGTACAATAGCATAAATTAAAC--AAAAAAAGTATGTTAAACTACAGTTTAAA
*
12447055 CTTTAAAGTTAGATAATTGAAGCCTA
64 CTTTAAAGTTAGTTAATTGAAGCCTA
*
12447081 AATTAATATAATAGTACAACAGCATAAATTAA
1 AATTAATATAATAGTACAATAGCATAAATTAA
12447113 TTAATTGAAG
Statistics
Matches: 275, Mismatches: 22, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
89 46 0.17
91 145 0.53
92 2 0.01
94 2 0.01
95 66 0.24
97 14 0.05
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (89 bp):
AATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAGTATGTTAAACTACAGTTTAAACT
TTAAAGTTAGTTAATTGAAGCCTA
Found at i:12447054 original size:186 final size:186
Alignment explanation
Indices: 12446729--12447099 Score: 627
Period size: 186 Copynumber: 2.0 Consensus size: 186
12446719 AATATAATAT
* * *
12446729 TACAACAGCATAAATTAAACAAAAAAAGTATATTGAACTACATTTTAAACTTTAAATTTAGTTAA
1 TACAACAGCATAAATTAAACAAAAAAAGTATATTAAACTACAGTTTAAACTTTAAAGTTAGTTAA
* * *
12446794 TTGAAGCCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAGCT
66 TTGAAACCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAACC
*
12446859 ATCGTTTAAACTTTAAAGTTAGTTAATTGAAGCATAAATTAATATAATAGTACAAG
131 ATCGTTTAAACTTTAAAGTTAGATAATTGAAGCATAAATTAATATAATAGTACAAG
** *
12446915 TACAACAGCATAAATTAAACAAAAAATTTATGTTAAACTACAGTTTAAACTTTAAAGTTAGTTAA
1 TACAACAGCATAAATTAAACAAAAAAAGTATATTAAACTACAGTTTAAACTTTAAAGTTAGTTAA
12446980 TTGAAACCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAACC
66 TTGAAACCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAACC
*
12447045 A-CAGTTTAAACTTTAAAGTTAGATAATTGAAGCCTAAATTAATATAATAGTACAA
131 ATC-GTTTAAACTTTAAAGTTAGATAATTGAAGCATAAATTAATATAATAGTACAA
12447100 CAGCATAAAT
Statistics
Matches: 173, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 1 0.01
186 172 0.99
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (186 bp):
TACAACAGCATAAATTAAACAAAAAAAGTATATTAAACTACAGTTTAAACTTTAAAGTTAGTTAA
TTGAAACCTAAATTAATATAATAGTACAATAGCATAAATTAAACAAAAAAAAAGTCTGTTAAACC
ATCGTTTAAACTTTAAAGTTAGATAATTGAAGCATAAATTAATATAATAGTACAAG
Found at i:12447275 original size:7 final size:7
Alignment explanation
Indices: 12447263--12447289 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12447253 TAAGGTCTGG
12447263 TATTTAA
1 TATTTAA
12447270 TATTTAA
1 TATTTAA
12447277 TATTTAA
1 TATTTAA
12447284 TATTTA
1 TATTTA
12447290 TTTATAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TATTTAA
Done.