Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_pilon, whole genome shotgun sequence
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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 43
Found at i:5284723 original size:3 final size:3
Alignment explanation
Indices: 5284715--5284780 Score: 98
Period size: 3 Copynumber: 22.3 Consensus size: 3
5284705 TATTTTTAAA
* * *
5284715 ATT ATT ATT ATT ATT TTT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5284763 ATT ATT A-T ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A
5284781 ATATATAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5284729 original size:21 final size:21
Alignment explanation
Indices: 5284704--5284768 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
5284694 TTTTTTCATT
5284704 TTATTTTTAAAATTATTATTA
1 TTATTTTTAAAATTATTATTA
5284725 TTATTTTT---ATTATTATTA
1 TTATTTTTAAAATTATTATTA
*
5284743 TTA-TTATAAATATTATTATTA
1 TTATTTTTAAA-ATTATTATTA
5284764 TTATT
1 TTATT
5284769 ATATTATTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 3 0.08
18 13 0.34
21 21 0.55
22 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATTTTTAAAATTATTATTA
Found at i:5289476 original size:84 final size:84
Alignment explanation
Indices: 5289331--5289484 Score: 195
Period size: 84 Copynumber: 1.8 Consensus size: 84
5289321 ATCTTTGCAG
* * * **
5289331 TTTTATTTTGCATTCGTACTTTTATGTTTTCTTTTACATTGCACAATTTGCATTCTTA-TTTTTA
1 TTTTATTTTGCATTCATACTTTTATGTTTTCTGTCACATTGCACAATTTGCATTCCCATTTTTTA
5289395 CATTTCCACATTATTTTCA
66 CATTTCCACATTATTTTCA
* ** *
5289414 TTTTCATTTTGCATTCATACTTTTATGTTTGT-TGTCATATTGTGCAGTTTGCATTCCCATTTTT
1 TTTT-ATTTTGCATTCATACTTTTATGTTT-TCTGTCACATTGCACAATTTGCATTCCCATTTTT
5289478 TACATTT
64 TACATTT
5289485 TCGCATTTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
83 4 0.07
84 43 0.73
85 12 0.20
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.56
Consensus pattern (84 bp):
TTTTATTTTGCATTCATACTTTTATGTTTTCTGTCACATTGCACAATTTGCATTCCCATTTTTTA
CATTTCCACATTATTTTCA
Found at i:5293612 original size:39 final size:40
Alignment explanation
Indices: 5293554--5293640 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 40
5293544 CAGATCCATG
* * * *
5293554 TGGGGCATTTTGAAGGCTCACATCAGTATGAA-AAAATGT
1 TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATGC
*
5293593 TGGGGCATTTTGAAAGCTCACATCAATAAGAAGCAAATGC
1 TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATGC
5293633 TGGGGCAT
1 TGGGGCAT
5293641 GCTAAAAGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.69
40 13 0.31
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.25
Consensus pattern (40 bp):
TGGGGCATTTTGAAAGCTCACATCAATAAGAAGAAAATGC
Found at i:5293649 original size:40 final size:39
Alignment explanation
Indices: 5293569--5293649 Score: 90
Period size: 40 Copynumber: 2.1 Consensus size: 39
5293559 CATTTTGAAG
* * * ** *
5293569 GCTCACATCAGTATGAAAAAATGTTGGGGCATTTTGAAA
1 GCTCACATCAATAAGAAAAAATGCTGGGGCATGCTAAAA
*
5293608 GCTCACATCAATAAGAAGCAAATGCTGGGGCATGCTAAAA
1 GCTCACATCAATAAGAA-AAAATGCTGGGGCATGCTAAAA
5293648 GC
1 GC
5293650 CCATTTCAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 15 0.44
40 19 0.56
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.22
Consensus pattern (39 bp):
GCTCACATCAATAAGAAAAAATGCTGGGGCATGCTAAAA
Found at i:5293750 original size:75 final size:75
Alignment explanation
Indices: 5293627--5294028 Score: 563
Period size: 75 Copynumber: 5.4 Consensus size: 75
5293617 AATAAGAAGC
* * * ** *
5293627 AAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATAGGAATGTTGACACGTTTTGAACAT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
5293692 TTGTATCAGA
66 TTGTATCAGA
* * *
5293702 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTTATGCATTTTGAATGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
*
5293767 TTGTATCAGC
66 TTGTATCAGA
* ** *
5293777 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATTAGAATCGGGAATGTTGATGTGTTTTGAACGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
*
5293842 TTGTATCAGC
66 TTGTATCAGA
* *
5293852 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGATGTGTTTTGAACGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
5293917 TTGTATCAGA
66 TTGTATCAGA
* * * * *
5293927 AAATGTTAGGGCATGCTGAAAGCCCGTTTTAATCAGAATCAGGAATGTTGATGCATTTTGAACGT
1 AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
5293992 TTGTATCA-A
66 TTGTATCAGA
** *
5294001 CAAATCCTGGGGCATGCTGAAGGCCCAT
1 -AAATGTTGGGGCATGCTGAAAGCCCAT
5294029 ATCATTTTAT
Statistics
Matches: 292, Mismatches: 34, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
74 1 0.00
75 291 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (75 bp):
AAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTGATGCGTTTTGAACGT
TTGTATCAGA
Found at i:5294015 original size:225 final size:225
Alignment explanation
Indices: 5293624--5294028 Score: 666
Period size: 225 Copynumber: 1.8 Consensus size: 225
5293614 ATCAATAAGA
5293624 AGCAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATAGGAATGTTGACACGTTTTGAA
1 AGCAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATAGGAATGTTGACACGTTTTGAA
* * *
5293689 CATTTGTATCAGAAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATTAGGAATGTTTAT
66 CATTTGTATCAGAAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGAT
* * **
5293754 GCATTTTGAATGTTTGTATCAGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATTAGAATCGG
131 GCATTTTGAACGTTTGTATCAACAAATCCTGGGGCATGCTGAAAGCCCATTTCAATTAGAATCGG
5293819 GAATGTTGATGTGTTTTGAACGTTTGTATC
196 GAATGTTGATGTGTTTTGAACGTTTGTATC
* * ***
5293849 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGTTGATGTGTTTTGAA
1 AGCAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATAGGAATGTTGACACGTTTTGAA
* * *
5293914 CGTTTGTATCAGAAAATGTTAGGGCATGCTGAAAGCCCGTTTTAATCAGAATCAGGAATGTTGAT
66 CATTTGTATCAGAAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGAT
*
5293979 GCATTTTGAACGTTTGTATCAACAAATCCTGGGGCATGCTGAAGGCCCAT
131 GCATTTTGAACGTTTGTATCAACAAATCCTGGGGCATGCTGAAAGCCCAT
5294029 ATCATTTTAT
Statistics
Matches: 164, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
225 164 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (225 bp):
AGCAAATGCTGGGGCATGCTAAAAGCCCATTTCAATCAGAAATAGGAATGTTGACACGTTTTGAA
CATTTGTATCAGAAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATGTTGAT
GCATTTTGAACGTTTGTATCAACAAATCCTGGGGCATGCTGAAAGCCCATTTCAATTAGAATCGG
GAATGTTGATGTGTTTTGAACGTTTGTATC
Found at i:5295361 original size:20 final size:22
Alignment explanation
Indices: 5295315--5295372 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
5295305 GACATCTACA
5295315 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
5295337 CTCTTCAAAGATGATATATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
5295359 CTTTTTAAAGATGA
1 CTCTTCAAAGATGA
5295373 AAACTTTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:5296141 original size:22 final size:21
Alignment explanation
Indices: 5296113--5296171 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
5296103 GGGTCATCTT
5296113 TAAGACCTACAGTGCAAGATGA
1 TAAGACCTACAGTGC-AGATGA
* * *
5296135 TAAGACCT-CAGGGC-CATCCA
1 TAAGACCTACAGTGCAGAT-GA
5296155 TAAGACCTACAGTGCAG
1 TAAGACCTACAGTGCAG
5296172 GATGTTTTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
19 2 0.07
20 9 0.31
21 10 0.34
22 8 0.28
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.17
Consensus pattern (21 bp):
TAAGACCTACAGTGCAGATGA
Found at i:5296237 original size:116 final size:116
Alignment explanation
Indices: 5296033--5296249 Score: 362
Period size: 116 Copynumber: 1.9 Consensus size: 116
5296023 CTATTTCCCA
* *
5296033 CATCCATAAAACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
1 CATCCATAAAACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAG
* *
5296098 CCTTCGGGTCATCTTTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
* * *
5296149 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAATCCTTCAGGAGTTTTTTGATATTTAAAG
1 CATCCATAAAACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAG
*
5296214 CCTCCGGGTCATCTGTAAGACCTACAGTGCAGGATG
66 CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATG
5296250 TTTTCAAAAA
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
116 93 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (116 bp):
CATCCATAAAACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAG
CCTCCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGC
Found at i:5296276 original size:74 final size:74
Alignment explanation
Indices: 5296155--5296327 Score: 285
Period size: 74 Copynumber: 2.3 Consensus size: 74
5296145 GGGCCATCCA
* *
5296155 TAAGACCTACAGTGCAGGATGTTTTCAAAAATCCTTCAGGAGTTTTTTGATATTTAAAGCCTCCG
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAGCCTCCG
5296220 GGTCATCTG
66 GGTCATCTG
5296229 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTC-GAGAGCTTTTTGATATTTAAAGCCTCC
1 TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAG-GAGCTTTTTGATATTTAAAGCCTCC
*
5296293 GTGTCATCTG
65 GGGTCATCTG
* *
5296303 TAAGACCTTCAATGCAGGATGTTTT
1 TAAGACCTACAGTGCAGGATGTTTT
5296328 TAAATGATTT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
73 1 0.01
74 92 0.99
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (74 bp):
TAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCAGGAGCTTTTTGATATTTAAAGCCTCCG
GGTCATCTG
Found at i:5296463 original size:89 final size:89
Alignment explanation
Indices: 5296288--5296854 Score: 933
Period size: 89 Copynumber: 6.4 Consensus size: 89
5296278 ATATTTAAAG
* * *
5296288 CCTCCGTGTCATCTGTAAGACCTTCAATGCAGGATGTTTTTAAAT--GATTTTAAGAAACTGATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
5296351 TTCAAAGGTTTCTTGATCTAAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
* *
5296375 CCTCCAGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAATTGATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
5296440 TTCAAAGGTTTCTTGATCTAAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
* * *
5296464 CCTTCGAGTCATCTGTAAGACCTCCAGTACAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
5296529 TTCAAAGGTTTCTTGATCTAAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
* * *
5296553 CCTCCAGGTCATCTATAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTAATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
5296618 TTCAAAGGTTTCTTGATCTAAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
*
5296642 CCTCCGGGTCATCTATAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
5296707 TTCAAAGGTTTCTTGATCTAAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
* * *
5296731 CCTTCGGGTCATCTGTAAGACCTCTAGTGCAGGAT-ATTTTAAATGAGATTTTAAGAAACTGATT
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
* *
5296795 TTCAAAGGTTTCTCGATCTTAAAT
66 TTCAAAGGTTTCTTGATCTAAAAT
* * *
5296819 CCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATG
1 CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATG
5296855 ATAAGACCTC
Statistics
Matches: 450, Mismatches: 27, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
87 41 0.09
88 82 0.18
89 327 0.73
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (89 bp):
CCTCCGGGTCATCTGTAAGACCTCCAGTGCAGGATGTTTTTAAATGAGATTTTAAGAAACTGATT
TTCAAAGGTTTCTTGATCTAAAAT
Found at i:5297009 original size:131 final size:130
Alignment explanation
Indices: 5296746--5297033 Score: 481
Period size: 131 Copynumber: 2.2 Consensus size: 130
5296736 GGGTCATCTG
*
5296746 TAAGACCTCTAGTGCAGGATATTTT-AAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTCG
1 TAAGACCTCTAGTGCA-GATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTCG
5296810 ATCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
65 ATCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
5296875 A
130 A
* * *
5296876 TAAGACCTCCAGTGCATGATGTTTTCAAATGAGATTTTAAGAAATTGATTTTCAAAGGTTTCTTG
1 TAAGACCTCTAGTGCA-GATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTCG
*
5296941 ATCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATTC
65 ATCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCC
5297006 A
130 A
*
5297007 TAATACCTCTAG-GCAGAATGTTTTCAA
1 TAAGACCTCTAGTGCAG-ATGTTTTCAA
5297034 CATTTGCATC
Statistics
Matches: 148, Mismatches: 8, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
129 1 0.01
130 35 0.24
131 112 0.76
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (130 bp):
TAAGACCTCTAGTGCAGATGTTTTCAAATGAGATTTTAAGAAACTGATTTTCAAAGGTTTCTCGA
TCTTAAATCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGATAAGACCTCAGGGCCATCCA
Found at i:5297173 original size:3 final size:3
Alignment explanation
Indices: 5297167--5297242 Score: 100
Period size: 3 Copynumber: 25.7 Consensus size: 3
5297157 TTTTTAAAAG
* *
5297167 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT AAA TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
5297214 TAT TAT TTT TAT TAT AAA TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5297243 ATATATAATT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:5297235 original size:26 final size:26
Alignment explanation
Indices: 5297185--5297261 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
5297175 TTATTATTAT
* * *
5297185 TATTATTATTATAAATATTATTAT-TA
1 TATTATTATTA-ATATATAATTATAAA
5297211 TATTATTATT--T-T-T-ATTATAAA
1 TATTATTATTAATATATAATTATAAA
5297232 TATTATTATTAATATATAATTATAAA
1 TATTATTATTAATATATAATTATAAA
5297258 TATT
1 TATT
5297262 TTTACAAACC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
20 5 0.12
21 12 0.28
22 1 0.02
23 1 0.02
24 1 0.02
25 1 0.02
26 22 0.51
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTATTATTAATATATAATTATAAA
Found at i:5297245 original size:12 final size:12
Alignment explanation
Indices: 5297167--5297261 Score: 99
Period size: 12 Copynumber: 8.1 Consensus size: 12
5297157 TTTTTAAAAG
*
5297167 TATTATTATTAT
1 TATTATTAATAT
*
5297179 TATTATTATTAT
1 TATTATTAATAT
*
5297191 TATTATAAATAT
1 TATTATTAATAT
5297203 TATTATT-ATAT
1 TATTATTAATAT
5297214 TATTATT--T-T
1 TATTATTAATAT
*
5297223 TATTATAAATAT
1 TATTATTAATAT
5297235 TATTATTAATAT
1 TATTATTAATAT
*
5297247 ATAATTATAAATAT
1 -T-ATTATTAATAT
5297261 T
1 T
5297262 TTTACAAACC
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.10
10 1 0.01
11 12 0.17
12 40 0.56
13 2 0.03
14 10 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATTATTAATAT
Found at i:5298396 original size:22 final size:22
Alignment explanation
Indices: 5298371--5298413 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5298361 GAATTATAGC
5298371 CTTTAGTCACTGATATTTTACA
1 CTTTAGTCACTGATATTTTACA
5298393 CTTTAGTCACTGATATTTTAC
1 CTTTAGTCACTGATATTTTAC
5298414 TTCTTTTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
CTTTAGTCACTGATATTTTACA
Found at i:5300258 original size:142 final size:142
Alignment explanation
Indices: 5300057--5300483 Score: 845
Period size: 142 Copynumber: 3.0 Consensus size: 142
5300047 GACTAGCCTA
5300057 GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
1 GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
5300122 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
66 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
5300187 AATAATTAATTT
131 AATAATTAATTT
5300199 GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
1 GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
5300264 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
66 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
5300329 AATAATTAATTT
131 AATAATTAATTT
*
5300341 GAGAGAAGAAAAGCTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
1 GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
5300406 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
66 TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
5300471 AATAATTAATTT
131 AATAATTAATTT
5300483 G
1 G
5300484 GCTTTATTTA
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
142 284 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (142 bp):
GAGAGAAGAAAAGTTGCAGAGAGATTCCCATAAGTGAGGGGTTTACATATAATCATCTTTAATGT
TAGTCTCAAACTTAGAGACATAATGATTGCTAGTAAGTTATCAGAACAAATAGATATTAACTATT
AATAATTAATTT
Found at i:5312765 original size:22 final size:22
Alignment explanation
Indices: 5312739--5312783 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5312729 AAATAGTGGA
*
5312739 AAATTTGA-AACTTATATTAAAT
1 AAATTGGATAACTTATA-TAAAT
*
5312761 AAATTGGATAATTTATATAAAT
1 AAATTGGATAACTTATATAAAT
5312783 A
1 A
5312784 TAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTGGATAACTTATATAAAT
Found at i:5320715 original size:18 final size:16
Alignment explanation
Indices: 5320683--5320727 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
5320673 TCAAAGTTAG
5320683 ATATTATTTTAAATAATT
1 ATATT-TTTTAAATAA-T
5320701 ATATTTTTTACAATAAT
1 ATATTTTTTA-AATAAT
5320718 ATTATTTTTT
1 A-TATTTTTT
5320728 CACTTGCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.28
18 18 0.72
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTTTTTAAATAAT
Found at i:5320850 original size:3 final size:3
Alignment explanation
Indices: 5320844--5320883 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5320834 ATAATAATAA
5320844 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 T
5320884 GTGTATATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:5322546 original size:72 final size:71
Alignment explanation
Indices: 5322430--5322570 Score: 221
Period size: 72 Copynumber: 2.0 Consensus size: 71
5322420 CCATGATTAT
* *
5322430 AGTTCAAGAGGGCAAAGTATAATTAACAATAAAAAATAGAAGGGACAAAATCAAAATAAACCAAA
1 AGTTCAAGAGGGAAAAGTATAATTAACAACAAAAAATAGAAGGGACAAAATCAAAATAAACCAAA
5322495 ATTTGA
66 ATTTGA
* *
5322501 AGTTCAAGGAGGGAAAAGTATACTTAACAACAAAATATA-AGAGGGACAAAATCAAAATAAACCA
1 AGTTCAA-GAGGGAAAAGTATAATTAACAACAAAAAATAGA-AGGGACAAAATCAAAATAAACCA
5322565 AAATTT
64 AAATTT
5322571 AAGGACCAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
71 8 0.12
72 56 0.88
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.18
Consensus pattern (71 bp):
AGTTCAAGAGGGAAAAGTATAATTAACAACAAAAAATAGAAGGGACAAAATCAAAATAAACCAAA
ATTTGA
Found at i:5350649 original size:20 final size:20
Alignment explanation
Indices: 5350624--5350661 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5350614 TTTAAAAGTG
5350624 ATGCATCGATGCACCAATCC
1 ATGCATCGATGCACCAATCC
5350644 ATGCATCGATGCACCAAT
1 ATGCATCGATGCACCAAT
5350662 TAATTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.21
Consensus pattern (20 bp):
ATGCATCGATGCACCAATCC
Found at i:5356579 original size:21 final size:21
Alignment explanation
Indices: 5356516--5356608 Score: 91
Period size: 23 Copynumber: 4.3 Consensus size: 21
5356506 GTGCTTAATA
*
5356516 CATCGATACACC-T-AACAGTG
1 CATCGATACACCTTGAA-TGTG
*
5356536 CATCGATGCATCCTTGAATGTG
1 CATCGATACA-CCTTGAATGTG
* *
5356558 CATCGATACACCATGAAGGTG
1 CATCGATACACCTTGAATGTG
*
5356579 CACCGATGCACACCTTGAATGTG
1 CATCGAT--ACACCTTGAATGTG
5356602 CATCGAT
1 CATCGAT
5356609 GCACAAGGCC
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.15
21 17 0.29
22 13 0.22
23 20 0.34
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
CATCGATACACCTTGAATGTG
Found at i:5356597 original size:23 final size:23
Alignment explanation
Indices: 5356533--5356613 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
5356523 ACACCTAACA
*
5356533 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* *
5356555 GTGCATCGAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
*
5356576 GTGCACCGATGCACACCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
5356599 GTGCATCGATGCACA
1 GTGCATCGATGCACA
5356614 AGGCCATGCA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
20 1 0.02
21 15 0.31
22 10 0.20
23 23 0.47
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:5356602 original size:44 final size:42
Alignment explanation
Indices: 5356516--5356608 Score: 125
Period size: 44 Copynumber: 2.2 Consensus size: 42
5356506 GTGCTTAATA
* *
5356516 CATCGATACACCTAACAGTGCATCGATGCATCCTTGAATGTG
1 CATCGATACACCTAACAGTGCACCGATGCAACCTTGAATGTG
*
5356558 CATCGATACACCATGAA-GGTGCACCGATGCACACCTTGAATGTG
1 CATCGATACACC-T-AACAGTGCACCGATGCA-ACCTTGAATGTG
5356602 CATCGAT
1 CATCGAT
5356609 GCACAAGGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
42 12 0.27
43 13 0.29
44 20 0.44
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (42 bp):
CATCGATACACCTAACAGTGCACCGATGCAACCTTGAATGTG
Found at i:5356629 original size:43 final size:42
Alignment explanation
Indices: 5356532--5356631 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
5356522 TACACCTAAC
* * *
5356532 AGTGCATCGATGCATCCTTGAATGTGCATCGATACACCATGA
1 AGTGCATCGATGCAACCTTGAATGTGCATCGATACACAAGGA
* * *
5356574 AGGTGCACCGATGCACACCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-ACCTTGAATGTGCATCGATACACAAGG-A
5356619 A-TGCATCGATGCA
1 AGTGCATCGATGCA
5356632 TCCGTCGGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.48
44 23 0.48
45 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAACCTTGAATGTGCATCGATACACAAGGA
Found at i:5364436 original size:16 final size:16
Alignment explanation
Indices: 5364397--5364428 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5364387 AGTTGATGTC
*
5364397 ATAAATATTGTTCCTT
1 ATAAACATTGTTCCTT
5364413 ATAAACATTGTTCCTT
1 ATAAACATTGTTCCTT
5364429 CAAAACATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
ATAAACATTGTTCCTT
Found at i:5370208 original size:17 final size:17
Alignment explanation
Indices: 5370169--5370201 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5370159 AGCTATTGAT
*
5370169 CAAT-AACAAGAAACAA
1 CAATCAACAAGAATCAA
5370185 CAATCAACAAGAATCAA
1 CAATCAACAAGAATCAA
5370202 GGATCAAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.64, C:0.21, G:0.06, T:0.09
Consensus pattern (17 bp):
CAATCAACAAGAATCAA
Found at i:5371412 original size:20 final size:20
Alignment explanation
Indices: 5371383--5371420 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5371373 TTTAAAAGTG
5371383 ATGCACCAATGCACCAATCC
1 ATGCACCAATGCACCAATCC
* *
5371403 ATGCATCAATGCATCAAT
1 ATGCACCAATGCACCAAT
5371421 GCACCAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.11, T:0.21
Consensus pattern (20 bp):
ATGCACCAATGCACCAATCC
Found at i:5371498 original size:45 final size:47
Alignment explanation
Indices: 5371443--5371537 Score: 124
Period size: 46 Copynumber: 2.1 Consensus size: 47
5371433 ATTTCAAACA
* * *
5371443 TCAAATGCATTTTATG-ATTCGATGCAC-ATACTATGCATCGATGCAC
1 TCAAATGCATTTGATGCA-TCGATGCACAAGACCATGCATCGATGCAC
*
5371489 TCAAA-GCATTTGATGCATCGATGCTCAAGACCATGCATCGATGCAC
1 TCAAATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
5371535 TCA
1 TCA
5371538 GGCTTTTTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
45 17 0.40
46 26 0.60
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (47 bp):
TCAAATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
Found at i:5375823 original size:21 final size:22
Alignment explanation
Indices: 5375790--5375857 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
5375780 AAAATGTTAG
5375790 TAAATA-AT-AATAATAATAAA
1 TAAATATATAAATAATAATAAA
* *
5375810 TAAATGT-TAAATAAAAATAAA
1 TAAATATATAAATAATAATAAA
*
5375831 -AAATATATATATATATATATAAA
1 TAAATATATAAATA-ATA-ATAAA
5375854 TAAA
1 TAAA
5375858 AATAAAAAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 11 0.30
21 16 0.43
22 2 0.05
23 5 0.14
24 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (22 bp):
TAAATATATAAATAATAATAAA
Found at i:5375905 original size:28 final size:28
Alignment explanation
Indices: 5375849--5375909 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
5375839 ATATATATAT
**
5375849 ATAAATAAAAATAAAAAGTCAAGGAAAAA
1 ATAAATAAAAATAAAAAG-CAACAAAAAA
5375878 ATAAATAAAAATTAAAAAG-AACAAAAAA
1 ATAAATAAAAA-TAAAAAGCAACAAAAAA
5375906 ATAA
1 ATAA
5375910 GTTAGAAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.38
29 11 0.38
30 7 0.24
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (28 bp):
ATAAATAAAAATAAAAAGCAACAAAAAA
Found at i:5375905 original size:29 final size:28
Alignment explanation
Indices: 5375849--5375906 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
5375839 ATATATATAT
*
5375849 ATAAATAAAAATAAAAAGTCAAGGAAAAA
1 ATAAATAAAAATAAAAAGACAA-GAAAAA
5375878 ATAAATAAAAATTAAAAAGAACAA-AAAAA
1 ATAAATAAAAA-TAAAAAG-ACAAGAAAAA
5375907 TAAGTTAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 16 0.62
30 7 0.27
31 3 0.12
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (28 bp):
ATAAATAAAAATAAAAAGACAAGAAAAA
Found at i:5377580 original size:35 final size:33
Alignment explanation
Indices: 5377529--5377623 Score: 124
Period size: 35 Copynumber: 2.9 Consensus size: 33
5377519 ATAGTTGAAC
*
5377529 TCAAAGG-TCTTTGTGTTTCAAGAGAAAC-ATTT
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAACGA-TT
*
5377561 TCATAGGTTCTTTTGGTGTTTCAAGAGAAACGATT
1 TCAAAGGTT-TTTT-GTGTTTCAAGAGAAACGATT
5377596 TCAAAGGTTTTTT-TGTTTCAAGAGAAAC
1 TCAAAGGTTTTTTGTGTTTCAAGAGAAAC
5377624 TATCTCCAGG
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
32 21 0.38
33 1 0.02
34 7 0.12
35 26 0.46
36 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (33 bp):
TCAAAGGTTTTTTGTGTTTCAAGAGAAACGATT
Found at i:5377668 original size:69 final size:65
Alignment explanation
Indices: 5377577--5377797 Score: 176
Period size: 65 Copynumber: 3.2 Consensus size: 65
5377567 GTTCTTTTGG
* ** * *
5377577 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTGTTTCAAGAGAAACTATCTCCAGGGAGGCAAA
1 TGTTTCAAGAGAAACGATTTCAAA-G-ATTGATGTTTCAAGAGAAACTATCT-CA-AGAGACAAA
*
5377642 ATTT
62 ACTT
* *
5377646 TGTTTCAAGAGAAAC-ATATTCAAAGATTGATGTTTCAAGAGAAATTGTCTCAAGAGACAAAACT
1 TGTTTCAAGAGAAACGAT-TTCAAAGATTGATGTTTCAAGAGAAACTATCTCAAGAGACAAAACT
5377710 T
65 T
* * * *
5377711 TGTTTCAAGGGAAACTG-TCTCAAGAGAGTTAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGCG
1 TGTTTCAAGAGAAAC-GATTTCAA-AGA-TT--GA--TGTTTCAAGAGAAACTATCTCAAGA--G
5377775 ACAAAACTT
57 ACAAAACTT
* *
5377784 AGTTTCAAAAGAAA
1 TGTTTCAAGAGAAA
5377798 ACTGTCTCAA
Statistics
Matches: 126, Mismatches: 15, Indels: 18
0.79 0.09 0.11
Matches are distributed among these distances:
65 28 0.22
66 6 0.05
67 22 0.17
68 3 0.02
69 22 0.17
71 24 0.19
73 21 0.17
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (65 bp):
TGTTTCAAGAGAAACGATTTCAAAGATTGATGTTTCAAGAGAAACTATCTCAAGAGACAAAACTT
Found at i:5377761 original size:36 final size:36
Alignment explanation
Indices: 5377676--5378171 Score: 405
Period size: 36 Copynumber: 14.1 Consensus size: 36
5377666 CAAAGATTGA
*
5377676 TGTTTCAAGAGAAATTGTCTC-A-AGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* **
5377711 TGTTTCAAGGGAAACTGTCTCAAGAGAGTTAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
5377747 TGTTTCAAGAGAAACTGTCTCAAGAGCGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
5377784 AGTTTCAAAAGAAAACTGTCTCAAGGGAGACGACATT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAATT
*
5377821 TGTTTCAAG-GAAAACATAT-TC-A-A-AG-----ATT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
5377849 TGTTTTCAA-AGGAAACTGTCTCAAGTGAGACAAAATT
1 TG-TTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* *
5377886 TGTTTCACGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
5377922 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
5377958 TGTTTCAAGAGAAGCTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
5377994 TAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 T-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
5378031 CGCTTCAAG-GAAAACATAT-TC-----A-A-ATATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
5378060 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATT
* * * * *
5378096 TATTTTAAGGGAAACTGCCTCAAGAGAGGC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
5378130 TGTTTAAAG-GAAAACTGACTCAAGAGAGACAAAACTT
1 TGTTTCAAGAG-AAACTGTCTCAAGAGAGACAAAA-TT
5378167 TGTTT
1 TGTTT
5378172 TGAGAAAATT
Statistics
Matches: 370, Mismatches: 55, Indels: 70
0.75 0.11 0.14
Matches are distributed among these distances:
28 9 0.02
29 27 0.07
30 4 0.01
31 1 0.00
32 2 0.01
33 3 0.01
34 29 0.08
35 22 0.06
36 180 0.49
37 74 0.20
38 19 0.05
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:5377828 original size:175 final size:172
Alignment explanation
Indices: 5377644--5377987 Score: 498
Period size: 175 Copynumber: 2.0 Consensus size: 172
5377634 GAGGCAAAAT
*
5377644 TTTGTTTCAA-GAGAAACATATTCAAAGA-TTGATGTTTC-AAGAGAAATTGTCTCAA-GAGACA
1 TTTGTTTCAAGGA-AAACATATTCAAAGATTTG-T-TTTCAAAG-GAAACTGTCTCAAGGAGACA
** *
5377705 AAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGTTAAAATTTGTTTCAAGAGAAACTGTCTCAA
62 AAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAA
* *
5377770 GAGCGACAAAACTTAGTTTCAAAAGAAAACTGTCTCAAGGGAGACGACA
126 GAGAGACAAAA-TTAGTTTCAAAAG-AAACTGTCTCAAGAGAGACGACA
5377819 TTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTTCAAAGGAAACTGTCTCAAGTGAGACAAAA
1 TTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTTCAAAGGAAACTGTCTCAAG-GAGACAAAA
*
5377884 TTTGTTTCACGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
65 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGA
* * *
5377949 GACAAAATTTGTTTCAAGAGAAGCTGTCTCAAGAGAGAC
130 GACAAAATTAGTTTCAAAAGAAACTGTCTCAAGAGAGAC
5377988 AAAATTTAGT
Statistics
Matches: 154, Mismatches: 10, Indels: 12
0.88 0.06 0.07
Matches are distributed among these distances:
173 17 0.11
174 27 0.18
175 96 0.62
176 14 0.09
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (172 bp):
TTTGTTTCAAGGAAAACATATTCAAAGATTTGTTTTCAAAGGAAACTGTCTCAAGGAGACAAAAT
TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAG
ACAAAATTAGTTTCAAAAGAAACTGTCTCAAGAGAGACGACA
Found at i:5377891 original size:65 final size:68
Alignment explanation
Indices: 5377709--5378171 Score: 331
Period size: 65 Copynumber: 6.6 Consensus size: 68
5377699 GAGACAAAAC
* ** *
5377709 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGTTAAAATTTGTTTCAA-GAGAAACTGTCTCAAGAG
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACTATCTCAAGA-
*
5377773 CGACAAAA
64 -G--AGAA
* * * * *
5377781 CTTAGTTTCAAAAGAAAACTGTCTCAAGGGAGACGACATTTGTTTCAAGGAAAACATAT-TC-A-
1 -TTTGTTTC-AAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAAC-TATCTCAAG
5377843 A-AG-A
63 AGAGAA
* * * *
5377847 TTTGTTTTCAAAGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCACGGGAAACTGTCTCAAGAG
1 TTTG-TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTATCTCAAGAG
5377912 AGACAAAA
65 AG----AA
* * *
5377920 TTTGTTTC-AAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAA-GAGAAGCTGTCTCAAGA
1 TTTGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACTATCTCAAGA
5377983 GAGACAAAA
64 GAG----AA
* * * * * *
5377992 TTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTCGCTTCAAGGAAAACATAT-TC-A-A
1 TTT-GTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAAC-TATCTCAAGA
* *
5378054 -ATAT
64 GAGAA
* * * **
5378058 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTATTTTAAGGGAAACTGCCTCAAGAGA
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTATCTCAAGAGA
5378123 GGCAA
66 -G-AA
*
5378128 TTTGTTT-AAAGGAAAACTGACTCAAGAGAGACAAAACTTTGTTT
1 TTTGTTTCAAAGG-AAACTGTCTCAAGAGAGACAAAA-TTTGTTT
5378172 TGAGAAAATT
Statistics
Matches: 314, Mismatches: 49, Indels: 56
0.75 0.12 0.13
Matches are distributed among these distances:
64 3 0.01
65 87 0.28
66 11 0.04
67 3 0.01
68 3 0.01
69 5 0.02
70 31 0.10
71 11 0.04
72 62 0.20
73 51 0.16
74 43 0.14
75 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (68 bp):
TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACTATCTCAAGAGA
GAA
Found at i:5377900 original size:139 final size:136
Alignment explanation
Indices: 5377709--5377966 Score: 372
Period size: 139 Copynumber: 1.9 Consensus size: 136
5377699 GAGACAAAAC
* ** *
5377709 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGTTAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGC
1 TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * *
5377774 GACAAAACTTAGTTTCAAAAGAAAACTGTCTCAAGGGAGACGACATTTGTTTCAAGGAAAACATA
66 GACAAAA-TTAGTTTCAAAAG-AAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATA
5377839 TTCAAAGA
129 TTCAAAGA
* * *
5377847 TTTGTTTTCAAAGGAAACTGTCTCAAGTGAGACAAAATTTGTTTCACGGGAAACTGTCTCAAGAG
1 TTTG-TTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAG
* *
5377912 AGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAG
65 AGACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAG
5377967 AGAAGCTGTC
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
137 30 0.28
138 15 0.14
139 61 0.58
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (136 bp):
TTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GACAAAATTAGTTTCAAAAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATT
CAAAGA
Found at i:5377931 original size:21 final size:21
Alignment explanation
Indices: 5377905--5377969 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
5377895 GGAAACTGTC
5377905 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
5377926 TC-A-AGAG---AAA-CTATC
1 TCAAGAGAGACAAAATTTGTT
5377941 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
5377962 TCAAGAGA
1 TCAAGAGA
5377970 AGCTGTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
15 4 0.12
16 4 0.12
17 4 0.12
19 4 0.12
20 4 0.12
21 12 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:5378054 original size:210 final size:210
Alignment explanation
Indices: 5377676--5378171 Score: 700
Period size: 210 Copynumber: 2.4 Consensus size: 210
5377666 CAAAGATTGA
* * *
5377676 TGTTTCAAGAGAAATTGTCTC-A-AGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAA-GGAAACTATCTCAAGAGAG
** * *
5377739 TTAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGCGACAAAACTTAGTTTCAAAAGAAAACTGTC
64 ACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAACTGTC
* * *
5377804 TCAAGGGAGACGACATTTGTTTCAAGGAAAACATATTCAAAGA-TTTGTTTTCAAAGGAAACTGT
129 TCAAGGGAGACGAAATTCGCTTCAAGGAAAACATATTCAAAGATTTTG-TTTCAAAGGAAACTGT
*
5377868 CTCAAGTGAGACAAAATT
193 CTCAAGAGAGACAAAATT
*
5377886 TGTTTCACGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAACTATCTCAAGAGAGA
* *
5377951 CAAAATTTGTTTCAAGAGAAGCTGTCTCAAGAGAGACAAAATTTAGTTCCAAAAG-AAACTGTCT
65 CAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAACTGTCT
*
5378015 CAAGGGAGACGAAATTCGCTTCAAGGAAAACATATTCAAATATTTTGTTTCAAAGGAAACTGTCT
130 CAAGGGAGACGAAATTCGCTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAAGGAAACTGTCT
5378080 CAAGAGAGACAAAATT
195 CAAGAGAGACAAAATT
* * * * *
5378096 TATTTTAAGGGAAACTGCCTCAAGAGAGGC--AATTTGTTTAAAGGAAAACTGA-CTCAAGAGAG
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGG-AAACT-ATCTCAAGAGAG
5378158 ACAAAACTTTGTTT
64 ACAAAA-TTTGTTT
5378172 TGAGAAAATT
Statistics
Matches: 258, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
207 1 0.00
208 33 0.13
209 8 0.03
210 124 0.48
211 82 0.32
212 10 0.04
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (210 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAACTATCTCAAGAGAGAC
AAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAACTGTCTC
AAGGGAGACGAAATTCGCTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAAGGAAACTGTCTC
AAGAGAGACAAAATT
Found at i:5378179 original size:36 final size:36
Alignment explanation
Indices: 5378058--5378172 Score: 128
Period size: 34 Copynumber: 3.2 Consensus size: 36
5378048 ATTCAAATAT
* *
5378058 TTTGTTTCAAAGG-AAACTGTCTCAAGAGAGACAAAA
1 TTTGTTT-TAAGGAAAACTGACTCAAGAGAGACAAAA
* * * *
5378094 TTTATTTTAAGGGAAACTGCCTCAAGAGAGGC--AA
1 TTTGTTTTAAGGAAAACTGACTCAAGAGAGACAAAA
*
5378128 TTTGTTTAAAGGAAAACTGACTCAAGAGAGACAAAA
1 TTTGTTTTAAGGAAAACTGACTCAAGAGAGACAAAA
5378164 CTTTGTTTT
1 -TTTGTTTT
5378173 GAGAAAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
34 29 0.45
35 4 0.06
36 25 0.38
37 7 0.11
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
TTTGTTTTAAGGAAAACTGACTCAAGAGAGACAAAA
Found at i:5379581 original size:95 final size:95
Alignment explanation
Indices: 5379392--5379652 Score: 301
Period size: 95 Copynumber: 2.7 Consensus size: 95
5379382 GGATAGCTGA
* * * * * * *
5379392 ATCCATAAAGCC-GGGGAGTTTAACAAATTTCTCTAGAGGGATAACTTAATATCATTGTATAG-A
1 ATCCATAAAGCCAGGGCA-TTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTA
*
5379455 TATTATAATCACCTTTATAAGGCTAGTTGAATATT
61 TATTATAATCACCTTTATAAGGCTAGCTGAATATT
*
5379490 ATCCATAAAGCCATGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
* *
5379555 TAATCACCTTTATCAGGCTAGCTGAATCTT
66 TAATCACCTTTATAAGGCTAGCTGAATATT
* * * * * *
5379585 ATCCATAAAGCCGGGGCGTTTAACCAGTTGTTCTAGAGGGATAGCTCAAGCTTTATTGTATATGT
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
5379650 ATA
65 ATA
5379653 TAATTATAAT
Statistics
Matches: 142, Mismatches: 18, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
94 4 0.03
95 91 0.64
96 6 0.04
97 2 0.01
98 36 0.25
99 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACCTTTATAAGGCTAGCTGAATATT
Found at i:5383611 original size:11 final size:11
Alignment explanation
Indices: 5383581--5383644 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
5383571 AGTAAATAAT
5383581 AATAATAAATA
1 AATAATAAATA
**
5383592 AATGTTAAATA
1 AATAATAAATA
*
5383603 AATAATAAACA
1 AATAATAAATA
*
5383614 AATAAAAAATCA
1 AATAATAAAT-A
* *
5383626 AAAAATATATA
1 AATAATAAATA
5383637 AA-AATAAA
1 AATAATAAA
5383645 AATAAAAAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
10 5 0.12
11 28 0.68
12 8 0.20
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (11 bp):
AATAATAAATA
Found at i:5383619 original size:8 final size:7
Alignment explanation
Indices: 5383598--5383680 Score: 53
Period size: 7 Copynumber: 11.0 Consensus size: 7
5383588 AATAAATGTT
5383598 AAATAAA
1 AAATAAA
*
5383605 TAATAAA
1 AAATAAA
5383612 CAAATAAA
1 -AAATAAA
5383620 AAATCAAA
1 AAAT-AAA
5383628 AAATATATA
1 AAATA-A-A
5383637 AAA-ATAA
1 AAATA-AA
5383644 AAATAAA
1 AAATAAA
*
5383651 AAGTCAAA
1 AAAT-AAA
5383659 GAAA-AAA
1 -AAATAAA
5383666 TAAATAAA
1 -AAATAAA
*
5383674 AATTAAA
1 AAATAAA
5383681 GAGAACAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
7 32 0.52
8 24 0.39
9 6 0.10
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (7 bp):
AAATAAA
Found at i:5397091 original size:21 final size:21
Alignment explanation
Indices: 5397065--5397118 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
5397055 GATATTGTGT
*
5397065 GTATATGACATACTCATTTCG
1 GTATATGACATACGCATTTCG
5397086 GTATATGACATACGCATTTCG
1 GTATATGACATACGCATTTCG
* *
5397107 GGAAATGACATA
1 GTATATGACATA
5397119 TACATTAGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (21 bp):
GTATATGACATACGCATTTCG
Found at i:5397124 original size:21 final size:20
Alignment explanation
Indices: 5397069--5397124 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
5397059 TTGTGTGTAT
* *
5397069 ATGACATACTCATTTCGGTAT
1 ATGACATA-TCATTTCGGGAA
*
5397090 ATGACATACGCATTTCGGGAA
1 ATGACATA-TCATTTCGGGAA
5397111 ATGACATATACATT
1 ATGACATAT-CATT
5397125 AGGAGTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (20 bp):
ATGACATATCATTTCGGGAA
Found at i:5399763 original size:25 final size:25
Alignment explanation
Indices: 5399735--5399807 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
5399725 CTTAATTCGT
5399735 AATAT-TTTATATATATTAACTTAAA
1 AATATATTT-TATATATTAACTTAAA
*
5399760 AATATATTTT-TATATTAACTTATTA
1 AATATATTTTATATATTAACTTA-AA
*
5399785 AATATGTTTTAT-TATTAACTTAA
1 AATATATTTTATATATTAACTTAA
5399808 TTTAAAAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 12 0.29
25 26 0.62
26 4 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (25 bp):
AATATATTTTATATATTAACTTAAA
Found at i:5399768 original size:27 final size:26
Alignment explanation
Indices: 5399736--5399818 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 26
5399726 TTAATTCGTA
5399736 ATATTTTATATATATTAACTTAAAAAT
1 ATATTTTAT-TATATTAACTTAAAAAT
*
5399763 ATA-TTT-TTATATTAACTTATTAAAT
1 ATATTTTATTATATTAACTTA-AAAAT
* *
5399788 ATGTTTTATTATTAACTTAATTTAAAAAT
1 ATATTTTATTA-T-A-TTAACTTAAAAAT
5399817 AT
1 AT
5399819 TTTATTTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
24 12 0.26
25 7 0.15
26 6 0.13
27 6 0.13
28 1 0.02
29 7 0.15
30 7 0.15
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (26 bp):
ATATTTTATTATATTAACTTAAAAAT
Found at i:5399821 original size:27 final size:26
Alignment explanation
Indices: 5399748--5399824 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 26
5399738 ATTTTATATA
*
5399748 TATTAACTTAA--AAATATATTTT-T
1 TATTAACTTAATTAAAAATATTTTAT
* *
5399771 ATATTAACTT-ATTAAATATGTTTTAT
1 -TATTAACTTAATTAAAAATATTTTAT
5399797 TATTAACTTAATTTAAAAATATTTTAT
1 TATTAACTTAA-TTAAAAATATTTTAT
5399824 T
1 T
5399825 TTCATTTATA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
23 1 0.02
24 9 0.20
25 19 0.42
26 2 0.04
27 14 0.31
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.53
Consensus pattern (26 bp):
TATTAACTTAATTAAAAATATTTTAT
Found at i:5400034 original size:31 final size:31
Alignment explanation
Indices: 5399964--5400038 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
5399954 TAAACCGTGA
* *
5399964 TGACCACATCTTAATTAAATAAAAATGAAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
5399995 TGACCATATCTTAATTAAATAAAAACGAAAG
1 TGACCATATCTTAATTAAATAAAAACGAAAG
**
5400026 TGGTCATATCTTA
1 TGACCATATCTTA
5400039 TATTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (31 bp):
TGACCATATCTTAATTAAATAAAAACGAAAG
Found at i:5403751 original size:31 final size:31
Alignment explanation
Indices: 5403713--5403867 Score: 274
Period size: 31 Copynumber: 5.0 Consensus size: 31
5403703 CAATTACCTT
* *
5403713 TTTGACTAATGGTTAAAGTCTTGTACTATTG
1 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
*
5403744 TTTGACTAATAGTTAAAGTTTTGTACTCTTG
1 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
5403775 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
1 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
5403806 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
1 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
*
5403837 TTTGACTAATTGTTAAAGTTTTGTACTCTTG
1 TTTGACTAATGGTTAAAGTTTTGTACTCTTG
5403868 CTATAAAAGT
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 119 1.00
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (31 bp):
TTTGACTAATGGTTAAAGTTTTGTACTCTTG
Found at i:5404284 original size:3 final size:3
Alignment explanation
Indices: 5404262--5404306 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
5404252 TGTCCGAATT
* *
5404262 TTA TTT TTA TTAA CTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5404307 ATTGTATTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
4 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5406921 original size:21 final size:18
Alignment explanation
Indices: 5406882--5406916 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5406872 AATATAGTCA
5406882 TAATTATTTTTTAAAAAT
1 TAATTATTTTTTAAAAAT
5406900 TAATTATTTTTTAAAAA
1 TAATTATTTTTTAAAAA
5406917 AAATTGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTATTTTTTAAAAAT
Found at i:5420213 original size:17 final size:17
Alignment explanation
Indices: 5420188--5420232 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
5420178 ACCGTTGGAA
*
5420188 CACTTAGTGCATCGGTG
1 CACTAAGTGCATCGGTG
5420205 CACTAAGTGTGCATCGGTG
1 CACTAA--GTGCATCGGTG
*
5420224 TACTAAGTG
1 CACTAAGTG
5420233 TGCATCAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 8 0.33
19 16 0.67
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (17 bp):
CACTAAGTGCATCGGTG
Found at i:5420218 original size:19 final size:19
Alignment explanation
Indices: 5420194--5420238 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
5420184 GGAACACTTA
5420194 GTGCATCGGTGCACTAAGT
1 GTGCATCGGTGCACTAAGT
*
5420213 GTGCATCGGTGTACTAAGT
1 GTGCATCGGTGCACTAAGT
5420232 GTGCATC
1 GTGCATC
5420239 AATGCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (19 bp):
GTGCATCGGTGCACTAAGT
Found at i:5420317 original size:64 final size:65
Alignment explanation
Indices: 5420229--5420391 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
5420219 CGGTGTACTA
* * * *
5420229 AGTGTGCATCAATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCTAAGTTCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * * * * *
5420293 TGTGTGCATTGATGCATAAAATGCAATCGATGTTTTCATTAAAACTTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * *
5420358 AGAGTGCATCGATGCATAAACTGCATTTGATGTT
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTT
5420392 CAATTTATTC
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 34 0.41
65 48 0.59
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.33
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
Found at i:5423054 original size:23 final size:23
Alignment explanation
Indices: 5423024--5423111 Score: 67
Period size: 23 Copynumber: 3.8 Consensus size: 23
5423014 GCATGGCTTT
5423024 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTCAAGGA
* *
5423047 GTGCATCGGTGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAAGGA
* *
5423069 -TGTATCGATGCACATACAAAGG-
1 GTGCATCGATGCACATTC-AAGGA
*
5423091 GATACATCGATGCACTATTCA
1 G-TGCATCGATGCAC-ATTCA
5423112 GTGCATCGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
20 1 0.02
21 12 0.24
22 3 0.06
23 17 0.35
24 13 0.27
25 3 0.06
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.26
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAAGGA
Found at i:5423120 original size:44 final size:43
Alignment explanation
Indices: 5423023--5423124 Score: 109
Period size: 44 Copynumber: 2.3 Consensus size: 43
5423013 TGCATGGCTT
* * * *
5423023 TGTGCATCGATGCACATTCAAGGAGTGCATCGGTGCATCTTCA
1 TGTGCATCGATGCACATACAAGGAGTACATCGATGCATATTCA
*
5423066 TGATGTATCGATGCACATACAAAGG-GATACATCGATGCACTATTCA
1 TG-TGCATCGATGCACATAC-AAGGAG-TACATCGATGCA-TATTCA
5423112 -GTGCATCGATGCA
1 TGTGCATCGATGCA
5423125 TTAAGCACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
43 2 0.04
44 27 0.55
45 15 0.31
46 5 0.10
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (43 bp):
TGTGCATCGATGCACATACAAGGAGTACATCGATGCATATTCA
Found at i:5423629 original size:20 final size:20
Alignment explanation
Indices: 5423604--5423643 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5423594 TCATCCATAA
5423604 AACTTGTGCACAACAACTAC
1 AACTTGTGCACAACAACTAC
5423624 AACTTGTGCACAACAACTAC
1 AACTTGTGCACAACAACTAC
5423644 TAGCTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (20 bp):
AACTTGTGCACAACAACTAC
Found at i:5428834 original size:64 final size:65
Alignment explanation
Indices: 5428748--5428928 Score: 231
Period size: 65 Copynumber: 2.8 Consensus size: 65
5428738 TGGAACACTT
* * * *
5428748 AGTGCATCGGTGCACT-AAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCT
1 AGTGCATCGATGCA-TGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCT
5428811 A
65 A
* * * * * *
5428812 AGTTCATCGATGCATGGTGTGTGCATAGATGCATAAAATGCAATCGATGTTTTCATTAAAACCTG
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
* *
5428877 AGTGCATCGATGCATGGAGAGTGCATCGATGCATAAACTGCATTCGATGTTT
1 AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTT
5428929 AATTTATTTA
Statistics
Matches: 99, Mismatches: 16, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
63 1 0.01
64 47 0.47
65 51 0.52
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
AGTGCATCGATGCATGGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTA
Found at i:5430944 original size:16 final size:17
Alignment explanation
Indices: 5430906--5430946 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5430896 GAGTAGTTAA
* *
5430906 AATTATTTTATATTTTT
1 AATTATTTAATATTATT
5430923 AA-TATTTAATA-TATT
1 AATTATTTAATATTATT
5430938 AATTATTTA
1 AATTATTTA
5430947 TAATTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTATTTAATATTATT
Found at i:5432145 original size:23 final size:23
Alignment explanation
Indices: 5432113--5432169 Score: 96
Period size: 23 Copynumber: 2.4 Consensus size: 23
5432103 GATTTTCCTT
*
5432113 CTTTGGTTTTCTTTCAGCATTGTA
1 CTTT-GTTTTCTTTCAGCATTGCA
5432137 CTTTGTTTTCTTTCAGCATTGCA
1 CTTTGTTTTCTTTCAGCATTGCA
5432160 CTTTGTTTTC
1 CTTTGTTTTC
5432170 CTTCTGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.11, C:0.19, G:0.14, T:0.56
Consensus pattern (23 bp):
CTTTGTTTTCTTTCAGCATTGCA
Found at i:5438743 original size:34 final size:32
Alignment explanation
Indices: 5438681--5438750 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5438671 CCTTACAAAC
* *
5438681 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
5438713 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
5438747 TCCC
1 TCCC
5438751 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:5439059 original size:21 final size:21
Alignment explanation
Indices: 5439033--5439074 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5439023 CCAGAATGGG
*
5439033 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5439054 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5439075 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5439320 original size:30 final size:31
Alignment explanation
Indices: 5439273--5439363 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
5439263 AAATTTTGAA
5439273 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5439302 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5439333 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5439364 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:5439580 original size:24 final size:24
Alignment explanation
Indices: 5439522--5439595 Score: 130
Period size: 24 Copynumber: 3.0 Consensus size: 24
5439512 AAGCTCCCCC
5439522 TTTTTCATTAAGAAATTGAATTTT
1 TTTTTCATTAAGAAATTGAATTTT
5439546 TTTATTCATTAAGAAATTGAATTTT
1 TTT-TTCATTAAGAAATTGAATTTT
*
5439571 TTTTTTATTAAGAAATTGAATTTT
1 TTTTTCATTAAGAAATTGAATTTT
5439595 T
1 T
5439596 CAAACCAAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 24 0.50
25 24 0.50
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTTTCATTAAGAAATTGAATTTT
Found at i:5442273 original size:34 final size:32
Alignment explanation
Indices: 5442211--5442280 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
5442201 CCTTACAAAC
* *
5442211 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
5442243 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
5442277 TCCC
1 TCCC
5442281 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:5442589 original size:21 final size:21
Alignment explanation
Indices: 5442563--5442604 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5442553 CCAGAATGGG
*
5442563 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5442584 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
5442605 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:5442776 original size:19 final size:19
Alignment explanation
Indices: 5442710--5442765 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
5442700 GAGCCTCGGG
*
5442710 TTACTGTTCAAATAGTGAT
1 TTACTGTTCAAATAGTAAT
5442729 TTACTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAT
5442748 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAATAGTAA
5442766 ATTGCTATTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:5442888 original size:30 final size:31
Alignment explanation
Indices: 5442841--5442931 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
5442831 AAATTTTGAA
5442841 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5442870 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5442901 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
5442932 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:5449429 original size:35 final size:36
Alignment explanation
Indices: 5449383--5449463 Score: 128
Period size: 35 Copynumber: 2.3 Consensus size: 36
5449373 AACATAGTCA
5449383 TCAATTACATTCTAAACCCCAAAATCC-AAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAAATACT
* *
5449418 TCAATTACATTCTAAACCTCAAATTCCAAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAAATACT
*
5449454 TCAATCACAT
1 TCAATTACAT
5449464 GCCCAACCCC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 25 0.60
36 17 0.40
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.28
Consensus pattern (36 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAAATACT
Found at i:5449477 original size:36 final size:35
Alignment explanation
Indices: 5449396--5449479 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 35
5449386 ATTACATTCT
* * * *
5449396 AAACCCCAAAATCCAAAATACTTCAATTACATTCT
1 AAACCCCAAATTCCAAAATACTTCAATCACATGCC
*
5449431 AAACCTCAAATTCCAAAAATACTTCAATCACATGCC
1 AAACCCCAAATTCC-AAAATACTTCAATCACATGCC
*
5449467 CAACCCCAAATTC
1 AAACCCCAAATTC
5449480 ATAATCCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 12 0.29
36 29 0.71
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (35 bp):
AAACCCCAAATTCCAAAATACTTCAATCACATGCC
Found at i:5450450 original size:36 final size:34
Alignment explanation
Indices: 5450409--5450505 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 34
5450399 AATGGATTAT
* * *
5450409 GAATTTTGGGTTGGTCATGTAATTTAAGTATTTTTG
1 GAATTTTGGGTTAG-AATGTAATTGAAGTA-TTTTG
* *
5450445 GAATTTTAGGTTTAGAATGTAATTGAATTATTTTG
1 GAATTTT-GGGTTAGAATGTAATTGAAGTATTTTG
*
5450480 GAATTTGGGGTTTAGAATGTAATTGA
1 GAATTTTGGG-TTAGAATGTAATTGA
5450506 TGACCGTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
34 2 0.04
35 26 0.50
36 19 0.37
37 5 0.10
ACGTcount: A:0.28, C:0.01, G:0.25, T:0.46
Consensus pattern (34 bp):
GAATTTTGGGTTAGAATGTAATTGAAGTATTTTG
Found at i:5450492 original size:35 final size:36
Alignment explanation
Indices: 5450425--5450505 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
5450415 TGGGTTGGTC
* *
5450425 ATGTAATTTAAGTATTTTTGGAATTTTAGGTTTAGA
1 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
* *
5450461 ATGTAATTGAATTA-TTTTGGAATTTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
5450496 ATGTAATTGA
1 ATGTAATTGA
5450506 TGACCGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 29 0.71
36 12 0.29
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (36 bp):
ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTAGA
Found at i:5474412 original size:21 final size:21
Alignment explanation
Indices: 5474373--5474413 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
5474363 AATTGAATTT
5474373 ATTCAAAGTTTTCATCAAAATA
1 ATTCAAAG-TTTCATCAAAATA
5474395 ATTCAAAG-TTCAATCAAAA
1 ATTCAAAGTTTC-ATCAAAA
5474414 CCTTAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.32
Consensus pattern (21 bp):
ATTCAAAGTTTCATCAAAATA
Found at i:5482578 original size:84 final size:84
Alignment explanation
Indices: 5482437--5482609 Score: 294
Period size: 84 Copynumber: 2.1 Consensus size: 84
5482427 TCCAAAATTT
5482437 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAA
5482502 AAATGATTTAGAACTTTCA
66 AAATGATTTAGAACTTTCA
* **
5482521 AAAGTTGAAAATGATTTTCTTTTGAAA-ACAAAAATGGTCTTTAAAAATTAAAATGAAATTTTAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGA-AAAAATGGGCTTTAAAAAACAAAATGAAATTTTAA
*
5482585 AATATGATTTAGAACTTTCA
65 AAAATGATTTAGAACTTTCA
5482605 AAAGT
1 AAAGT
5482610 AAGATGTGAA
Statistics
Matches: 84, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
83 1 0.01
84 83 0.99
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.34
Consensus pattern (84 bp):
AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAA
AAATGATTTAGAACTTTCA
Found at i:5483882 original size:19 final size:19
Alignment explanation
Indices: 5483858--5483894 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5483848 TAGTTTCCCT
*
5483858 AATAGTTTTGATACTTTCC
1 AATAGTTTTGAAACTTTCC
5483877 AATAGTTTTGAAACTTTC
1 AATAGTTTTGAAACTTTC
5483895 ATTAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (19 bp):
AATAGTTTTGAAACTTTCC
Found at i:5486449 original size:21 final size:21
Alignment explanation
Indices: 5486425--5486497 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
5486415 AACTTTCGAA
* *
5486425 GATAGTTTCTCGAAAAGTTTT
1 GATACTTTCCCGAAAAGTTTT
5486446 GATACTTTCCCGAAAAGTTTT
1 GATACTTTCCCGAAAAGTTTT
* * *
5486467 TATACTTTCCCGAAACGTTTC
1 GATACTTTCCCGAAAAGTTTT
5486488 GATACTTTCC
1 GATACTTTCC
5486498 AATAGTTTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (21 bp):
GATACTTTCCCGAAAAGTTTT
Found at i:5487853 original size:84 final size:84
Alignment explanation
Indices: 5487736--5487908 Score: 276
Period size: 84 Copynumber: 2.1 Consensus size: 84
5487726 TTCAAAATTT
** *
5487736 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATCAAATTTTAAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGAATTCAAAAAACAAAATCAAATTTTAAA
5487801 AAATGATTTAGAACTTTCA
66 AAATGATTTAGAACTTTCA
* *
5487820 AAAGTTGAAAATGATTTTCTTTTGAAA-ACAAAAATGGAATTCAAAAATCAAAATGAAATTTTAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGA-AAAAATGGAATTCAAAAAACAAAATCAAATTTTAA
*
5487884 AATATGATTTAGAACTTTCA
65 AAAATGATTTAGAACTTTCA
5487904 AAAGT
1 AAAGT
5487909 ATGATGTGAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 1 0.01
84 81 0.99
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.32
Consensus pattern (84 bp):
AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGAATTCAAAAAACAAAATCAAATTTTAAA
AAATGATTTAGAACTTTCA
Found at i:5487928 original size:22 final size:21
Alignment explanation
Indices: 5487874--5487928 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5487864 AAATCAAAAT
*
5487874 GAAATTTTAAAATATGATTTA
1 GAAATTTTAAAATATGATTGA
* *
5487895 GAACTTTCAAAAGTATGATGTGA
1 GAAATTTTAAAA-TATGAT-TGA
5487918 -AAATTTTAAAA
1 GAAATTTTAAAA
5487929 AAGAATGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 10 0.37
22 15 0.56
23 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
GAAATTTTAAAATATGATTGA
Found at i:5489189 original size:19 final size:20
Alignment explanation
Indices: 5489139--5489190 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
5489129 TAAAAGGCCT
*
5489139 ATTTTTACCAAAAGTTTCCAA
1 ATTTTT-CCAAGAGTTTCCAA
* * *
5489160 ACTTCTACAAGAGTTT-CAA
1 ATTTTTCCAAGAGTTTCCAA
5489179 ATTTTTCCAAGA
1 ATTTTTCCAAGA
5489191 CAGTTTCCCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (20 bp):
ATTTTTCCAAGAGTTTCCAA
Found at i:5490313 original size:17 final size:16
Alignment explanation
Indices: 5490293--5490329 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5490283 AATCCATGGA
5490293 AACAAGAAAGAAGAACC
1 AACAA-AAAGAAGAACC
5490310 AAC--AAAGAAGAACC
1 AACAAAAAGAAGAACC
5490324 AACAAA
1 AACAAA
5490330 TGTTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.78
16 1 0.06
17 3 0.17
ACGTcount: A:0.68, C:0.19, G:0.14, T:0.00
Consensus pattern (16 bp):
AACAAAAAGAAGAACC
Found at i:5490318 original size:14 final size:14
Alignment explanation
Indices: 5490299--5490329 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5490289 TGGAAACAAG
5490299 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5490313 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5490327 AAA
1 AAA
5490330 TGTTGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.19, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAAGAACCAAC
Found at i:5491312 original size:19 final size:20
Alignment explanation
Indices: 5491262--5491313 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
5491252 TAAAAGGCCT
*
5491262 ATTTTTACCAAAAGTTTCCAA
1 ATTTTT-CCAAGAGTTTCCAA
* * *
5491283 ACTTCTACAAGAGTTT-CAA
1 ATTTTTCCAAGAGTTTCCAA
5491302 ATTTTTCCAAGA
1 ATTTTTCCAAGA
5491314 CAGTTTCCCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (20 bp):
ATTTTTCCAAGAGTTTCCAA
Found at i:5492426 original size:17 final size:16
Alignment explanation
Indices: 5492406--5492442 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5492396 AATCCATGGA
5492406 AACAAGAAAGAAGAACC
1 AACAA-AAAGAAGAACC
5492423 AAC--AAAGAAGAACC
1 AACAAAAAGAAGAACC
5492437 AACAAA
1 AACAAA
5492443 TGTTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.78
16 1 0.06
17 3 0.17
ACGTcount: A:0.68, C:0.19, G:0.14, T:0.00
Consensus pattern (16 bp):
AACAAAAAGAAGAACC
Found at i:5492431 original size:14 final size:14
Alignment explanation
Indices: 5492412--5492442 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5492402 TGGAAACAAG
5492412 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5492426 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5492440 AAA
1 AAA
5492443 TGTTGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.19, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAAGAACCAAC
Found at i:5494793 original size:83 final size:84
Alignment explanation
Indices: 5494650--5494821 Score: 267
Period size: 83 Copynumber: 2.1 Consensus size: 84
5494640 TCCAAAATTT
*
5494650 AAAGTTGAAAATGATTTTATTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAA
1 AAAGTTGAAAATGATTTTATTTTGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAA-TTTAAA
5494715 AA-ATGATTTAGAACATTCA
65 AATATGATTTAGAACATTCA
* **
5494734 AAAGTTGAAAATGATTTTATTTTGAAAG-CAAAATGGACTTTAAAAATTAAAATGAAATTTAAAA
1 AAAGTTGAAAATGATTTTATTTTGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAATTTAAAA
* *
5494798 ATATGATTTAGAACTTTCG
66 ATATGATTTAGAACATTCA
5494817 AAAGT
1 AAAGT
5494822 AAGATATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
82 8 0.10
83 45 0.56
84 28 0.35
ACGTcount: A:0.49, C:0.05, G:0.13, T:0.33
Consensus pattern (84 bp):
AAAGTTGAAAATGATTTTATTTTGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAATTTAAAA
ATATGATTTAGAACATTCA
Found at i:5495373 original size:26 final size:28
Alignment explanation
Indices: 5495344--5495398 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 28
5495334 TAGTTCACCA
*
5495344 TAATGATTTTG-GTTAA-AATTTTG-TTT
1 TAATG-TTTTGTGTTACAAATTTTGATTT
*
5495370 TAATGTTTTGTTTTACAAATTTTGATTT
1 TAATGTTTTGTGTTACAAATTTTGATTT
5495398 T
1 T
5495399 TGACCTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 7 0.29
28 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (28 bp):
TAATGTTTTGTGTTACAAATTTTGATTT
Found at i:5497444 original size:19 final size:19
Alignment explanation
Indices: 5497417--5497460 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5497407 TTTTCTTTTG
*
5497417 AAAACAAAAATCG-AATTTA
1 AAAATAAAAAT-GAAATTTA
*
5497436 AAAATAAAAATGAAATTTT
1 AAAATAAAAATGAAATTTA
5497455 AAAATA
1 AAAATA
5497461 TGATTTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (19 bp):
AAAATAAAAATGAAATTTA
Found at i:5497464 original size:84 final size:83
Alignment explanation
Indices: 5497310--5497481 Score: 274
Period size: 84 Copynumber: 2.1 Consensus size: 83
5497300 TCCAAAATTT
* **
5497310 AAAGTTGAAAATGATTTTCTTTTGAAAAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAAAAAAATCGAATTTAAAAAACAAAATGAAATTTTAAAA
5497375 AATGATTTAGAACTTTCA
66 AATGATTTAGAACTTTCA
*
5497393 AAAGTTGAAATTGATTTTCTTTTGAAAACAAAAATCGAATTTAAAAATA-AAAATGAAATTTTAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAA-AAAAATCGAATTTAAAAA-ACAAAATGAAATTTTAA
*
5497457 AATATGATTTAGAACTTTCA
64 AAAATGATTTAGAACTTTCA
5497477 AAAGT
1 AAAGT
5497482 ATGATGTGAA
Statistics
Matches: 82, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
83 27 0.33
84 54 0.66
85 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.34
Consensus pattern (83 bp):
AAAGTTGAAAATGATTTTCTTTTGAAAAAAAAATCGAATTTAAAAAACAAAATGAAATTTTAAAA
AATGATTTAGAACTTTCA
Found at i:5497501 original size:22 final size:21
Alignment explanation
Indices: 5497447--5497501 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
5497437 AAATAAAAAT
*
5497447 GAAATTTTAAAATATGATTTA
1 GAAATTTTAAAATATGATTGA
* *
5497468 GAACTTTCAAAAGTATGATGTGA
1 GAAATTTTAAAA-TATGAT-TGA
5497491 -AAATTTTAAAA
1 GAAATTTTAAAA
5497502 AAGAATGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 10 0.37
22 15 0.56
23 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (21 bp):
GAAATTTTAAAATATGATTGA
Found at i:5498762 original size:19 final size:20
Alignment explanation
Indices: 5498712--5498763 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
5498702 TAAAAGGCCT
*
5498712 ATTTTTACCAAAAGTTTCCAA
1 ATTTTT-CCAAGAGTTTCCAA
* * *
5498733 ACTTCTACAAGAGTTT-CAA
1 ATTTTTCCAAGAGTTTCCAA
5498752 ATTTTTCCAAGA
1 ATTTTTCCAAGA
5498764 TAGTTTCCCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (20 bp):
ATTTTTCCAAGAGTTTCCAA
Found at i:5501725 original size:84 final size:84
Alignment explanation
Indices: 5501584--5501756 Score: 274
Period size: 84 Copynumber: 2.1 Consensus size: 84
5501574 TCCAAAATTT
* * *
5501584 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATGGGCTTTAAAAAACAAAATGAAATTTTAAA
1 AAAGTTGAAAATGATTTTATTTCGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAATTTTAAA
5501649 AAATGATTTAGAACATTCA
66 AAATGATTTAGAACATTCA
* **
5501668 AAAGTTGAAAATGATTTTATTTCGAAAGCAAAAATGGACTTTAAAAATTAAAATGAAATTTTAAA
1 AAAGTTGAAAATGATTTTATTTCGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAATTTTAAA
* *
5501733 ATATGATTTAGAACTTTCA
66 AAATGATTTAGAACATTCA
5501752 AAAGT
1 AAAGT
5501757 AAGATGTGAA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (84 bp):
AAAGTTGAAAATGATTTTATTTCGAAAGAAAAAATGGACTTTAAAAAACAAAATGAAATTTTAAA
AAATGATTTAGAACATTCA
Found at i:5502309 original size:26 final size:28
Alignment explanation
Indices: 5502280--5502334 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 28
5502270 TAGTTCACCA
*
5502280 TAATGATTTTG-GTTAA-AATTTTG-TTT
1 TAATG-TTTTGTGTTACAAATTTTGATTT
*
5502306 TAATGTTTTGTTTTACAAATTTTGATTT
1 TAATGTTTTGTGTTACAAATTTTGATTT
5502334 T
1 T
5502335 TGACCTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 7 0.29
28 4 0.17
ACGTcount: A:0.25, C:0.02, G:0.13, T:0.60
Consensus pattern (28 bp):
TAATGTTTTGTGTTACAAATTTTGATTT
Found at i:5504385 original size:83 final size:84
Alignment explanation
Indices: 5504246--5504417 Score: 269
Period size: 83 Copynumber: 2.1 Consensus size: 84
5504236 TCCAAAATTT
*
5504246 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATAGGCTTTAAAAAACAAAATG-AAATTTAAA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATAGGATTTAAAAAACAAAATGAAAATTTAAA
5504310 AAATGATTTAGAACTTTCA
66 AAATGATTTAGAACTTTCA
* *
5504329 AAAGTTGAAAATGATTTTCTTTTGAAA-ACAAAAAT-GGAATTTAAATATCAAAATGAAAATTTA
1 AAAGTTGAAAATGATTTTCTTTTGAAAGA-AAAAATAGG-ATTTAAAAAACAAAATGAAAATTTA
*
5504392 AAATATGATTTAGAACTTTCA
64 AAAAATGATTTAGAACTTTCA
5504413 AAAGT
1 AAAGT
5504418 ATGATGTGAA
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
82 3 0.04
83 47 0.57
84 32 0.39
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.33
Consensus pattern (84 bp):
AAAGTTGAAAATGATTTTCTTTTGAAAGAAAAAATAGGATTTAAAAAACAAAATGAAAATTTAAA
AAATGATTTAGAACTTTCA
Found at i:5504437 original size:22 final size:20
Alignment explanation
Indices: 5504382--5504437 Score: 51
Period size: 22 Copynumber: 2.7 Consensus size: 20
5504372 AATATCAAAA
5504382 TGAAAA-TTTAAAATATGAT
1 TGAAAATTTTAAAATATGAT
* * *
5504401 TTAGAACTTTCAAAAGTATGAT
1 TGA-AAATTTTAAAA-TATGAT
5504423 GTGAAAATTTTAAAA
1 -TGAAAATTTTAAAA
5504438 AATAATGCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 6 0.22
22 15 0.56
23 2 0.07
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (20 bp):
TGAAAATTTTAAAATATGAT
Found at i:5505698 original size:19 final size:20
Alignment explanation
Indices: 5505648--5505699 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
5505638 TAAAAGGCCT
*
5505648 ATTTTTACCAAAAGTTTCCAA
1 ATTTTT-CCAAGAGTTTCCAA
* * *
5505669 ACTTCTACAAGAGTTT-CAA
1 ATTTTTCCAAGAGTTTCCAA
5505688 ATTTTTCCAAGA
1 ATTTTTCCAAGA
5505700 CAGTTTCCCG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
19 12 0.50
20 8 0.33
21 4 0.17
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.37
Consensus pattern (20 bp):
ATTTTTCCAAGAGTTTCCAA
Found at i:5506823 original size:9 final size:9
Alignment explanation
Indices: 5506811--5506868 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
5506801 AGTCGGGTCG
*
5506811 GGTCAGACC
1 GGTCAAACC
*
5506820 GGTCAAATC
1 GGTCAAACC
*
5506829 GGTTCAGACC
1 GG-TCAAACC
5506839 GGTCAAACC
1 GGTCAAACC
5506848 GGTTCGAAACC
1 GG-TC-AAACC
5506859 GGTCCAAACC
1 GGT-CAAACC
5506869 AATCAGAACC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
9 17 0.43
10 15 0.38
11 8 0.20
ACGTcount: A:0.28, C:0.31, G:0.26, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:5506830 original size:19 final size:19
Alignment explanation
Indices: 5506808--5506845 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5506798 GTCAGTCGGG
5506808 TCGGGTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
*
5506827 TCGGTTCAGACCGGTCAAA
1 TCGGGTCAGACCGGTCAAA
5506846 CCGGTTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (19 bp):
TCGGGTCAGACCGGTCAAA
Found at i:5506850 original size:19 final size:19
Alignment explanation
Indices: 5506813--5506868 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 19
5506803 TCGGGTCGGG
*
5506813 TCAGACCGGTCAAATCGGT
1 TCAGACCGGTCAAACCGGT
5506832 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
5506851 TCGAAACCGGTCCAAACC
1 TC-AGACCGGT-CAAACC
5506869 AATCAGAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 20 0.61
20 7 0.21
21 6 0.18
ACGTcount: A:0.29, C:0.32, G:0.23, T:0.16
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:5506911 original size:21 final size:21
Alignment explanation
Indices: 5506864--5506921 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
5506854 AAACCGGTCC
* *
5506864 AAACCAATCAGAACCAGTTGA
1 AAACCGATCAGAACCGGTTGA
5506885 AAACCGATCAGAACCGGTTGA
1 AAACCGATCAGAACCGGTTGA
*
5506906 AAACCGGTCA-AACCGG
1 AAACCGATCAGAACCGG
5506922 ATTCCAGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.41, C:0.26, G:0.21, T:0.12
Consensus pattern (21 bp):
AAACCGATCAGAACCGGTTGA
Found at i:5515660 original size:17 final size:16
Alignment explanation
Indices: 5515640--5515676 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
5515630 AATCCATGGA
5515640 AACAAGAAAGAAGAACC
1 AACAA-AAAGAAGAACC
5515657 AAC--AAAGAAGAACC
1 AACAAAAAGAAGAACC
5515671 AACAAA
1 AACAAA
5515677 TGTTGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 14 0.78
16 1 0.06
17 3 0.17
ACGTcount: A:0.68, C:0.19, G:0.14, T:0.00
Consensus pattern (16 bp):
AACAAAAAGAAGAACC
Found at i:5515665 original size:14 final size:14
Alignment explanation
Indices: 5515646--5515676 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5515636 TGGAAACAAG
5515646 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5515660 AAAGAAGAACCAAC
1 AAAGAAGAACCAAC
5515674 AAA
1 AAA
5515677 TGTTGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.19, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAGAAGAACCAAC
Found at i:5519239 original size:26 final size:27
Alignment explanation
Indices: 5519210--5519263 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
5519200 TAGTTCACCA
5519210 TAATGATTTTG-GTTA-AAATTTGGATT
1 TAATG-TTTTGTGTTACAAATTTGGATT
* *
5519236 TAATGTTTTGTTTTACAAATTTTGATT
1 TAATGTTTTGTGTTACAAATTTGGATT
5519263 T
1 T
5519264 TTGACCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.21
26 8 0.33
27 11 0.46
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (27 bp):
TAATGTTTTGTGTTACAAATTTGGATT
Found at i:5521345 original size:83 final size:81
Alignment explanation
Indices: 5521192--5521360 Score: 243
Period size: 83 Copynumber: 2.1 Consensus size: 81
5521182 TCCAAAATTT
* *
5521192 AAAGTTGAAAATGATTTTCTTTTAAAAGAAAAAAATGGGCTTTAAAAAAATGACATTTTAAAAAA
1 AAAGTTGAAAATGATTTTCTTTTAAAAGAAAAAAATGGACTTTAAAAAAATGAAATTTTAAAAAA
5521257 TGATTTAGAACTTTCA
66 TGATTTAGAACTTTCA
* *
5521273 AAAGTTGAAAATG-TTTTCTTTTGAAAG-CAAAAATGGACTTTAAAAATCAAAATGAAATTTTAA
1 AAAGTTGAAAATGATTTTCTTTTAAAAGAAAAAAATGGACTTT--AAA--AAAATGAAATTTTAA
*
5521336 AATATGATTTAGAACTTTCA
62 AAAATGATTTAGAACTTTCA
5521356 AAAGT
1 AAAGT
5521361 AAGATGTGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
79 12 0.15
80 13 0.16
81 16 0.20
83 38 0.48
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (81 bp):
AAAGTTGAAAATGATTTTCTTTTAAAAGAAAAAAATGGACTTTAAAAAAATGAAATTTTAAAAAA
TGATTTAGAACTTTCA
Found at i:5528127 original size:23 final size:23
Alignment explanation
Indices: 5528101--5528151 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5528091 GGTATGATTC
** *
5528101 CCCCTACCTAGGGGGAATCAGTT
1 CCCCTACAAAGGGCGAATCAGTT
* *
5528124 CCCCTTCAAAGGGCGAATCGGTT
1 CCCCTACAAAGGGCGAATCAGTT
5528147 CCCCT
1 CCCCT
5528152 TCAAGTGGTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.22
Consensus pattern (23 bp):
CCCCTACAAAGGGCGAATCAGTT
Found at i:5528152 original size:23 final size:23
Alignment explanation
Indices: 5528110--5528155 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5528100 CCCCCTACCT
*
5528110 AGGGGGAATCAGTTCCCCTTCAA
1 AGGGCGAATCAGTTCCCCTTCAA
*
5528133 AGGGCGAATCGGTTCCCCTTCAA
1 AGGGCGAATCAGTTCCCCTTCAA
5528156 GTGGTATCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.26, T:0.22
Consensus pattern (23 bp):
AGGGCGAATCAGTTCCCCTTCAA
Found at i:5543093 original size:16 final size:17
Alignment explanation
Indices: 5543072--5543105 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5543062 ATCTCTTAAA
*
5543072 TTTTGATTGA-TGAATG
1 TTTTGAGTGATTGAATG
5543088 TTTTGAGTGATTGAATG
1 TTTTGAGTGATTGAATG
5543105 T
1 T
5543106 CTGGTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (17 bp):
TTTTGAGTGATTGAATG
Found at i:5547025 original size:8 final size:8
Alignment explanation
Indices: 5547014--5547046 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
5547004 AGCCGACAAG
5547014 GCTAGAAA
1 GCTAGAAA
*
5547022 GCTAGCAA
1 GCTAGAAA
5547030 GCTAGAAA
1 GCTAGAAA
5547038 GCTAGAAA
1 GCTAGAAA
5547046 G
1 G
5547047 AATGAACTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.12
Consensus pattern (8 bp):
GCTAGAAA
Found at i:5554067 original size:16 final size:16
Alignment explanation
Indices: 5554046--5554076 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5554036 AAAATTGTTA
5554046 ACTTTTATTTTGACCG
1 ACTTTTATTTTGACCG
5554062 ACTTTTATTTTGACC
1 ACTTTTATTTTGACC
5554077 AAAAATTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.52
Consensus pattern (16 bp):
ACTTTTATTTTGACCG
Found at i:5556481 original size:24 final size:24
Alignment explanation
Indices: 5556365--5556479 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
5556355 TCTATTTGAT
5556365 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
5556389 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
5556413 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
5556437 TTCTGATC-GAATACTTGACCTGGA
1 TTCTGATCTG-ATACTTGACATGGA
* * *
5556461 TTTTGATATGAAACTTGAC
1 TTCTGATCTGATACTTGAC
5556480 CTAGATTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
23 2 0.02
24 78 0.95
25 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:5556715 original size:2 final size:2
Alignment explanation
Indices: 5556710--5556746 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5556700 TATATATATA
5556710 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
5556747 TTTAAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:5559670 original size:2 final size:2
Alignment explanation
Indices: 5559665--5559691 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5559655 TATATTTTTA
5559665 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5559692 AACAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5561093 original size:59 final size:60
Alignment explanation
Indices: 5560959--5561122 Score: 165
Period size: 59 Copynumber: 2.8 Consensus size: 60
5560949 ATTTGGGAAT
* ** * * *
5560959 GAAT-TTCAAAAGTTTGAGGCCCACTTTAGAATGAGACTCATGGTTTGTGGATGAAACTA
1 GAATATTCAAAAGTTTAAGTACCAATTTAGAATGAGACTCATAGTTTGAGGATGAAACTA
* * * * *
5561018 GAATGTTCAAAAGTTTAAAG-ACTAATTTAGAATGAGATTCGTAGTTTGAGG-TGAAATTA
1 GAATATTCAAAAGTTT-AAGTACCAATTTAGAATGAGACTCATAGTTTGAGGATGAAACTA
* * *
5561077 GAATATTCAAATGTTTAAGTACCAATTTAAAATGAGAGT-ATAGTTT
1 GAATATTCAAAAGTTTAAGTACCAATTTAGAATGAGACTCATAGTTT
5561123 AGGGACATAT
Statistics
Matches: 87, Mismatches: 15, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
58 9 0.10
59 41 0.47
60 35 0.40
61 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (60 bp):
GAATATTCAAAAGTTTAAGTACCAATTTAGAATGAGACTCATAGTTTGAGGATGAAACTA
Found at i:5571387 original size:64 final size:65
Alignment explanation
Indices: 5571265--5571418 Score: 197
Period size: 64 Copynumber: 2.4 Consensus size: 65
5571255 ACTCCATTTC
** *
5571265 GAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTG-AACATT
1 GAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATG
**
5571329 GAATGCATTTTGTGTACCGATGCACATA-CCATGCATCGATGCACTCCAGGCTCA-TTTGAAACA
1 GAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCCAGAAT-ATTTTGAAACA
5571392 TG
64 TG
* * *
5571394 GAATGTAATTAGTGTACCGATGCAC
1 GAATGCATTTTGTGTACCGATGCAC
5571419 CCCTAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 50 0.63
65 29 0.37
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (65 bp):
GAATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATG
Found at i:5571511 original size:21 final size:21
Alignment explanation
Indices: 5571485--5571529 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
5571475 CTAGTGTACA
*
5571485 GATGCACCTTGGTTATGCATC
1 GATGCACCTTGGCTATGCATC
5571506 GATGCACCTTGGCTATGCATC
1 GATGCACCTTGGCTATGCATC
5571527 GAT
1 GAT
5571530 ACACACATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (21 bp):
GATGCACCTTGGCTATGCATC
Found at i:5572785 original size:169 final size:168
Alignment explanation
Indices: 5572506--5572840 Score: 643
Period size: 169 Copynumber: 2.0 Consensus size: 168
5572496 GCATCGAGAC
5572506 TTACCGCCATCACCAATGGGTTCACCAGTCTTTTCCTCGTAAAACCCAACCCATGGGTTATCACA
1 TTACCGCCATCACCAATGGGTTCACCAGTCTTTTCCTCGTAAAACCCAACCCATGGGTTATCACA
*
5572571 CTGTCGTCGTTTTCACCGGAGGTCGTGGGTAAGTTTCGGGTTTATAGTTTGGTTAAATTTTTTTT
66 CTGTCATCGTTTTCACCGGAGGTCGTGGGTAAGTTTCGGGTTTATAGTTTGGTTAAA-TTTTTTT
5572636 TTCGGTTTTGGTTGATGTTTTAGTTTAAATGTTAGTCGA
130 TTCGGTTTTGGTTGATGTTTTAGTTTAAATGTTAGTCGA
5572675 TTACCGCCATCACCAATGGGTTCACCAGTCTTTTCCTCGTAAAACCCAACCCATGGGTTATCACA
1 TTACCGCCATCACCAATGGGTTCACCAGTCTTTTCCTCGTAAAACCCAACCCATGGGTTATCACA
5572740 CTGTCATCGTTTTCACCGGAGGTCGTGGGTAAGTTTCGGGTTTATAGTTTGGTTAAATTTTTTTT
66 CTGTCATCGTTTTCACCGGAGGTCGTGGGTAAGTTTCGGGTTTATAGTTTGGTTAAATTTTTTTT
*
5572805 TCGGTTTTGGTTGATGTTTTGGTTTAAATGTTAGTC
131 TCGGTTTTGGTTGATGTTTTAGTTTAAATGTTAGTC
5572841 TATTTTGGTG
Statistics
Matches: 164, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
168 43 0.26
169 121 0.74
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (168 bp):
TTACCGCCATCACCAATGGGTTCACCAGTCTTTTCCTCGTAAAACCCAACCCATGGGTTATCACA
CTGTCATCGTTTTCACCGGAGGTCGTGGGTAAGTTTCGGGTTTATAGTTTGGTTAAATTTTTTTT
TCGGTTTTGGTTGATGTTTTAGTTTAAATGTTAGTCGA
Found at i:5582694 original size:18 final size:17
Alignment explanation
Indices: 5582671--5582721 Score: 75
Period size: 18 Copynumber: 2.9 Consensus size: 17
5582661 AATCAAAGGG
5582671 AAAAAATAAAATAACATA
1 AAAAAATAAAATAA-ATA
5582689 AAAAAATAAAATAAATA
1 AAAAAATAAAATAAATA
*
5582706 AAAGTAATAAAATAAA
1 AAA-AAATAAAATAAA
5582722 AACATAATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 6 0.19
18 25 0.81
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (17 bp):
AAAAAATAAAATAAATA
Done.