Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004685.1 Hibiscus syriacus cultivar Beakdansim tig00010503_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: 136995
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5291 original size:21 final size:21
Alignment explanation
Indices: 5265--5327 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
5255 TTTTGGTGCA
*
5265 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
5286 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
5307 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
5328 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:5335 original size:21 final size:21
Alignment explanation
Indices: 5309--5348 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5299 CCCCCTTTGA
*
5309 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
5330 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
5349 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:10800 original size:175 final size:176
Alignment explanation
Indices: 10506--10986 Score: 788
Period size: 175 Copynumber: 2.7 Consensus size: 176
10496 TTAAAATTAC
10506 CGACACTTTTTTAAATGGTATCGACACA-TTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
10570 ATTATAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
10635 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCC-G-ATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGGAATGT
* *
10680 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
*
10745 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTT
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
10810 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
130 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCC---G-G--AATGT
*
10863 CGACACTTTTTAACAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTA-AATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
10928 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
65 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATA
10987 ATATGTTGAA
Statistics
Matches: 285, Mismatches: 12, Indels: 11
0.93 0.04 0.04
Matches are distributed among these distances:
174 26 0.09
175 135 0.47
180 1 0.00
183 120 0.42
184 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (176 bp):
CGACACTTTTTTAAATGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAATA
TTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTA
TATTACAAAATTATCTATTACATTATAAATATGGGTTCCGGAATGT
Found at i:12465 original size:3 final size:3
Alignment explanation
Indices: 12457--12537 Score: 72
Period size: 3 Copynumber: 27.0 Consensus size: 3
12447 ACTTGTTTGG
* * * **
12457 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GCC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * * * *
12505 AGC TTC ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
12538 GTCAGCTTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:12474 original size:12 final size:12
Alignment explanation
Indices: 12461--12549 Score: 88
Period size: 12 Copynumber: 7.4 Consensus size: 12
12451 GTTTGGATCA
* *
12461 TCATCTTCATCA
1 TCATCGTCATCT
* *
12473 TCATCATCATCA
1 TCATCGTCATCT
* *
12485 TCGTCATCATCT
1 TCATCGTCATCT
* *
12497 TCATCGCCAGCT
1 TCATCGTCATCT
*
12509 TCATCGTCATCA
1 TCATCGTCATCT
12521 TCATCGTCATCT
1 TCATCGTCATCT
*
12533 TCATCGTCAGCT
1 TCATCGTCATCT
12545 TCATC
1 TCATC
12550 TTCTGCGACC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:12480 original size:18 final size:18
Alignment explanation
Indices: 12461--12552 Score: 76
Period size: 18 Copynumber: 5.1 Consensus size: 18
12451 GTTTGGATCA
* *
12461 TCATCTTCATCATCATCA
1 TCATCATCATCATCATCT
*
12479 TCATCATCGTCATCATCT
1 TCATCATCATCATCATCT
** * * *
12497 TCATCGCCAGCTTCATCG
1 TCATCATCATCATCATCT
*
12515 TCATCATCATCGTCATCT
1 TCATCATCATCATCATCT
* * *
12533 TCATCGTCAGCTTCATCT
1 TCATCATCATCATCATCT
12551 TC
1 TC
12553 TGCGACCGCT
Statistics
Matches: 57, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (18 bp):
TCATCATCATCATCATCT
Found at i:12513 original size:36 final size:36
Alignment explanation
Indices: 12473--12549 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
12463 ATCTTCATCA
*
12473 TCATCATCATCATCGTCATCATCTTCATCGCCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
* * *
12509 TCATCGTCATCATCATCGTCATCTTCATCGTCAGCT
1 TCATCATCATCATCATCATCATCTTCATCGCCAGCT
12545 TCATC
1 TCATC
12550 TTCTGCGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.21, C:0.35, G:0.09, T:0.35
Consensus pattern (36 bp):
TCATCATCATCATCATCATCATCTTCATCGCCAGCT
Found at i:12552 original size:6 final size:6
Alignment explanation
Indices: 12461--12552 Score: 67
Period size: 6 Copynumber: 15.3 Consensus size: 6
12451 GTTTGGATCA
* * * * * * * *
12461 TCATCT TCATCA TCATCA TCATCA TCGTCA TCATCT TCATCG CCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * * *
12509 TCATCG TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
12553 TGCGACCGCT
Statistics
Matches: 68, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:14326 original size:178 final size:181
Alignment explanation
Indices: 14027--14950 Score: 1225
Period size: 199 Copynumber: 4.9 Consensus size: 181
14017 TATATTAGTG
* *
14027 TCGACAC-ATTA-T-TTATATATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTAAA
1 TCGACACAATTATTATTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAA
14089 AAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGA
66 AAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGA
14154 TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATA
131 TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATA
14205 TCGACAC-ATTA-T-TTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAA
1 TCGACACAATTATTATTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAA
14267 AAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGA
66 AAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGA
14332 TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATA
131 TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATA
14382 TCGACACAAACTATATTAGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTG
1 TCG--AC--AC-A-A-T--T------ATTA-TTATACATATTATCTCATAAAACCGGTATAATTG
14447 TA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
50 TACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGAC
14511 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAA
115 ACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAA
14576 TA
180 TA
14578 TCGACACAAACTATATTAGTGTCGACACATTATTTATACATATTATCTCATAAAACCGGTATAAT
1 TCG--AC--AC---A--A-T-T------ATTA-TTATACATATTATCTCATAAAACCGGTATAAT
*
14643 TATACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
48 TGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCG
*
14708 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAGA
113 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAA
14773 AATA
178 AATA
* * * *
14777 TCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTTTTCATAAAACCGGTAGACTT
1 TCGACAC-AA-T-TATTA-T-T--ATACA-TA--T-----TA--TCTCATAAAACCGGTATAATT
* * *
14842 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTG
49 GTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCG
14907 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
113 ACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTT
14951 GGCCATATTG
Statistics
Matches: 691, Mismatches: 17, Indels: 55
0.91 0.02 0.07
Matches are distributed among these distances:
177 12 0.02
178 166 0.24
179 2 0.00
181 2 0.00
184 1 0.00
185 6 0.01
186 1 0.00
187 1 0.00
188 4 0.01
189 2 0.00
191 4 0.01
193 2 0.00
194 1 0.00
195 121 0.18
196 58 0.08
197 2 0.00
198 111 0.16
199 195 0.28
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (181 bp):
TCGACACAATTATTATTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAA
AAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGA
TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATA
Found at i:14769 original size:199 final size:199
Alignment explanation
Indices: 14205--14950 Score: 1367
Period size: 199 Copynumber: 3.8 Consensus size: 199
14195 AAAAAAAATA
14205 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
1 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
14270 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
66 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
14335 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGG-AAAAAAATATCGACACAAACTATATT
131 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATT
14399 A--G
196 AGTG
14401 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTA-CGGTTAGATTGAAAAA
1 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
14465 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
66 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
14530 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATT
131 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATT
14595 AGTG
196 AGTG
*
14599 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTATACCGGTTAGATTGAAAAA
1 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
14664 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
66 TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
*
14729 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAGAAATATCGACACAAACTATATT
131 ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATT
14794 AGTG
196 AGTG
* * * *
14798 TCGACACATTATTTAGACATATT-TTTCATAAAACCGGTAGACTTGTACCGGTTAGATTGAAAAA
1 TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
* * *
14862 TTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATTGACACTTTTTATATATGGATC
66 TTACATATTACATTATACTTTTGG-GTTCGATGATTTTGGGATCGACACTTTTTATATATGGATC
14927 GACACTTTATGGGTGCACCCTGTT
130 GACACTTTATGGGTGCACCCTGTT
14951 GGCCATATTG
Statistics
Matches: 535, Mismatches: 10, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
195 119 0.22
196 75 0.14
198 109 0.20
199 232 0.43
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (199 bp):
TCGACACATTATTTATACATATTATCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAA
TTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCG
ACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATT
AGTG
Found at i:15115 original size:19 final size:19
Alignment explanation
Indices: 15069--15117 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
15059 TTATATTCAC
*
15069 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
15088 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
15107 ATACAAAATTA
1 ATACAAAATTA
15118 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:16948 original size:33 final size:33
Alignment explanation
Indices: 16911--16976 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
16901 CATCTTAATA
*
16911 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
16944 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
16977 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:17051 original size:21 final size:21
Alignment explanation
Indices: 17013--17074 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
17003 CTTATGCCTC
* * *
17013 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCTA
* *
17034 TCGAGTTTCTCTAT-GACTCGA
1 TCAAGTTTCTCT-TCGACTCTA
17055 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
17075 TGATTGTCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.40
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:19320 original size:17 final size:18
Alignment explanation
Indices: 19298--19340 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
19288 ATATATCCGG
19298 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
19315 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
19335 TATCAT
1 TATCAT
19341 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:19358 original size:20 final size:19
Alignment explanation
Indices: 19303--19349 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
19293 TCCGGTATCA
19303 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
19322 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
19343 TTTTACC
1 TTTTACC
19350 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:19506 original size:20 final size:20
Alignment explanation
Indices: 19483--19528 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
19473 TCCGGTAACG
*
19483 TTTTACCGGTTTTATCATTT
1 TTTTACCGGTTTTATCATAT
19503 TTTTACCGGTTTTATCATAT
1 TTTTACCGGTTTTATCATAT
19523 TTTTAC
1 TTTTAC
19529 ATGGTATATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.09, T:0.59
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:19694 original size:182 final size:180
Alignment explanation
Indices: 19270--19741 Score: 685
Period size: 182 Copynumber: 2.6 Consensus size: 180
19260 CGTACTTACG
* * *
19270 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTT-ATACCGGTTT
* * *
19335 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
19399 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
19450 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTTATACCGGTTT
* * *
19515 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
19580 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
19632 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCTATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TATACCGGTTT
* * *
19697 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
19742 AATTTGGATC
Statistics
Matches: 261, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
180 91 0.35
181 75 0.29
182 95 0.36
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:19743 original size:181 final size:179
Alignment explanation
Indices: 19270--19743 Score: 678
Period size: 180 Copynumber: 2.6 Consensus size: 179
19260 CGTACTTACG
* * *
19270 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTT-ATACCGGTTT
* ** *
19335 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAAGTATCGACACATTATA
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATA
* *
19400 GGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
130 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
19450 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTTTACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTTATACCGGTTT
* * *
19515 TATCATATTTTTACATGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACA-TTTTTAAAAGTATCGACACATTAT
** *
19580 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * *
19632 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTGACCGGTTTTATCATTTCTATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TATACCGGTTT
* * *
19697 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAA
65 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAA
19744 TTTGGATCGA
Statistics
Matches: 262, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
180 91 0.35
181 81 0.31
182 90 0.34
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (179 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTATACCGGTTTT
ATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTAAAAGTATCGACACATTATAG
GAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:25601 original size:2 final size:2
Alignment explanation
Indices: 25594--25631 Score: 67
Period size: 2 Copynumber: 18.5 Consensus size: 2
25584 ACATTTGTTC
25594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
25632 GATGCAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34866 original size:3 final size:3
Alignment explanation
Indices: 34860--34906 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
34850 TTTATTGTTG
* **
34860 TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA CTA TTA AAA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
34905 TT
1 TT
34907 GTTACAAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:34902 original size:21 final size:21
Alignment explanation
Indices: 34860--34911 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
34850 TTTATTGTTG
* ** *
34860 TTATTATTATTATTTTATTTA
1 TTATTATTACTATTAAAATTA
34881 TTATTATTACTATTAAAATTA
1 TTATTATTACTATTAAAATTA
*
34902 TTATTGTTAC
1 TTATTATTAC
34912 AAACAGACCC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTATTACTATTAAAATTA
Found at i:36352 original size:16 final size:16
Alignment explanation
Indices: 36331--36361 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36321 TTTTACTTTC
*
36331 ATATATTTATGATTAT
1 ATATATTTATCATTAT
36347 ATATATTTATCATTA
1 ATATATTTATCATTA
36362 GTATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATCATTAT
Found at i:36615 original size:17 final size:16
Alignment explanation
Indices: 36583--36617 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
36573 CCATTTTTTG
36583 ATATTTTTAAATAAAA
1 ATATTTTTAAATAAAA
36599 ATATTTTTAAATAAAA
1 ATATTTTTAAATAAAA
36615 ATA
1 ATA
36618 AATATTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTTTTAAATAAAA
Found at i:36796 original size:11 final size:13
Alignment explanation
Indices: 36759--36798 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
36749 TGTTTAATAA
36759 AATATA-TATATT
1 AATATATTATATT
*
36771 AATATATTATCTT
1 AATATATTATATT
36784 AA-A-ATTATATT
1 AATATATTATATT
36795 AATA
1 AATA
36799 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:37321 original size:26 final size:26
Alignment explanation
Indices: 37270--37326 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
37260 TAATTCTTTC
37270 TTTTCAAAATTTTATATATACTTATTA
1 TTTTCAAAATTTTATATATAC-TATTA
* *
37297 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAAT-TTTATATATACTATTA
37323 TTTT
1 TTTT
37327 ATTTTCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 9 0.33
27 9 0.33
28 9 0.33
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (26 bp):
TTTTCAAAATTTTATATATACTATTA
Found at i:38839 original size:8 final size:7
Alignment explanation
Indices: 38815--38856 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
38805 TTTTCATACA
38815 TGCA-TT
1 TGCATTT
38821 TGCATTT
1 TGCATTT
38828 TGCATCTT
1 TGCAT-TT
38836 TGCATTT
1 TGCATTT
* *
38843 TTCATTG
1 TGCATTT
38850 TGCATTT
1 TGCATTT
38857 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:38839 original size:15 final size:14
Alignment explanation
Indices: 38815--38856 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
38805 TTTTCATACA
38815 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
38828 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
38843 TTCATTGTGCATTT
1 TGCATTTTGCATTT
38857 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:38952 original size:27 final size:27
Alignment explanation
Indices: 38916--38975 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
38906 CATTCACATA
38916 TTTACATTTGCATTTACATTTGCATTT
1 TTTACATTTGCATTTACATTTGCATTT
* * *
38943 TTTACGTTTGTATTTACATTTTCA-TT
1 TTTACATTTGCATTTACATTTGCATTT
38969 TTTACAT
1 TTTACAT
38976 AATTACATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.13, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTACATTTGCATTTACATTTGCATTT
Found at i:38969 original size:12 final size:12
Alignment explanation
Indices: 38915--38942 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
38905 ACATTCACAT
38915 ATTTACATTTGC
1 ATTTACATTTGC
38927 ATTTACATTTGC
1 ATTTACATTTGC
38939 ATTT
1 ATTT
38943 TTTACGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.54
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:39862 original size:108 final size:108
Alignment explanation
Indices: 39668--39883 Score: 414
Period size: 108 Copynumber: 2.0 Consensus size: 108
39658 CCTGGGCTAA
*
39668 GTACCCACCCAACATTAGAGGAGTAATGATGCATAAACAAGTGGAAGTGTTATCTACCACTATAG
1 GTACACACCCAACATTAGAGGAGTAATGATGCATAAACAAGTGGAAGTGTTATCTACCACTATAG
39733 TACTTTCTATTTTCAGCATCTTGTTTGAACTTGTTTTTTGTTT
66 TACTTTCTATTTTCAGCATCTTGTTTGAACTTGTTTTTTGTTT
*
39776 GTACACACCCAACATTAGAGGAGTAATGATGCATAAACAAGTGGAAGTGTTATCTACCACTGTAG
1 GTACACACCCAACATTAGAGGAGTAATGATGCATAAACAAGTGGAAGTGTTATCTACCACTATAG
39841 TACTTTCTATTTTCAGCATCTTGTTTGAACTTGTTTTTTGTTT
66 TACTTTCTATTTTCAGCATCTTGTTTGAACTTGTTTTTTGTTT
39884 CTTTTCTCCG
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (108 bp):
GTACACACCCAACATTAGAGGAGTAATGATGCATAAACAAGTGGAAGTGTTATCTACCACTATAG
TACTTTCTATTTTCAGCATCTTGTTTGAACTTGTTTTTTGTTT
Found at i:40850 original size:7 final size:7
Alignment explanation
Indices: 40838--40898 Score: 70
Period size: 7 Copynumber: 8.6 Consensus size: 7
40828 TATACTCATA
40838 AAAAAAG
1 AAAAAAG
40845 AAAAAAG
1 AAAAAAG
*
40852 AAAAAGG
1 AAAAAAG
40859 AAAAAATG
1 AAAAAA-G
40867 AGAAAAAG
1 A-AAAAAG
*
40875 AAAAAGG
1 AAAAAAG
*
40882 AAAAAGG
1 AAAAAAG
40889 AAAAAA-
1 AAAAAAG
40895 AAAA
1 AAAA
40899 GGAAAATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 4 0.08
7 35 0.73
8 4 0.08
9 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:40855 original size:6 final size:6
Alignment explanation
Indices: 40839--40904 Score: 55
Period size: 6 Copynumber: 10.8 Consensus size: 6
40829 ATACTCATAA
* **
40839 AAAAAG AAAAAAG AAAAAG GAAAA- AATGAG AAAAAG AAAAAGG AAAAAGG
1 AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA-G
*
40889 AAAAA- AAAAAG GAAAA
1 AAAAAG AAAAAG AAAAA
40905 TTGAATCAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
5 7 0.14
6 23 0.47
7 19 0.39
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:43263 original size:114 final size:114
Alignment explanation
Indices: 43063--43290 Score: 420
Period size: 114 Copynumber: 2.0 Consensus size: 114
43053 GTGCCACGTT
*
43063 CTCATAGTAGAAATAATGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* *
43128 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATAAATTTG
43177 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
43242 GTTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATAAATTTG
66 GTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATAAATTTG
43291 ATGATAGTCT
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATAAATTTG
Found at i:44569 original size:75 final size:75
Alignment explanation
Indices: 44302--44631 Score: 372
Period size: 76 Copynumber: 4.4 Consensus size: 75
44292 ATTAACAAGA
* * *
44302 AGCAAATGTTGGGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATGTTGATGTATCCTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
* *
44367 TATTTATATC
66 CATTCATATC
* * * * * *
44377 AGCAAAATGCTGGGGCATGCTGAAAACCCCTTTCAATCAGAATGAGGAATATTGATGTATCCTAA
1 AGC-AAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
** *
44442 ATGTTTATATC
65 ACATTCATATC
* * * **
44453 AGTAAAATGTTGGGGCATGCTGAAAGCCCCTTTTAATCAGAATGAAGAATGTTGATGTATTTTGA
1 AG-CAAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGA
* *
44518 ACGTTCGTATC
65 ACATTCATATC
* * ** **
44529 AGCAATTGATGGGGCATGCTGAAAGCCTATTTCAATCAGAATCAAGAATGTTGATGTATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
*
44594 CATTCGTATC
66 CATTCATATC
* *
44604 AGCAATTGTTGGGGCATGCTGAAGGCCC
1 AGCAAATGTTGGGGCATGCTGAAAGCCC
44632 ATATCATCCT
Statistics
Matches: 224, Mismatches: 29, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
75 93 0.42
76 131 0.58
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCCTTTCAATCAGAATCAAGAATGTTGATGTATCCTGAA
CATTCATATC
Found at i:45938 original size:22 final size:22
Alignment explanation
Indices: 45912--45991 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
45902 TACATCTACA
45912 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
*
45934 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAGATTCT
* * *
45956 CTTTTTAAAGATAATAGATTCT
1 CTCTTCAAAGATGATAGATTCT
* *
45978 CTTTTCGAAGATGA
1 CTCTTCAAAGATGA
45992 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (22 bp):
CTCTTCAAAGATGATAGATTCT
Found at i:46914 original size:113 final size:113
Alignment explanation
Indices: 46353--46901 Score: 886
Period size: 113 Copynumber: 4.9 Consensus size: 113
46343 ATCCATCGCA
*
46353 ATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
*
46417 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTA
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* *
46466 ATGGATCAACATTTCCAGA-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAG
1 ATGGATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
46530 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
65 TTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * *
46579 ATAGATCAGCTTTCCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
46644 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
* * *
46692 ATGAATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAAT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
** * * ** * *
46757 TCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCACTCG
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
46805 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
1 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
**
46870 TCATAATGAGAAGAGCTTGTTTGACCTTTTGC
66 TCATAATGAGAAGAGCTTGTTCAACCTTTTGC
46902 ATGACTTTAT
Statistics
Matches: 407, Mismatches: 28, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
113 405 1.00
114 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (113 bp):
ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
TCATAATGAGAAGAGCTTGTTCAACCTTTTGCTCAAATCCATCACTTG
Found at i:47253 original size:3 final size:3
Alignment explanation
Indices: 47239--47298 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
47229 TTACCCATTT
* *
47239 TTA TTG TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
47284 AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
47299 CAAACAGACC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:48803 original size:2 final size:2
Alignment explanation
Indices: 48796--48842 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48786 ATTTATGTCA
48796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48838 AT AT A
1 AT AT A
48843 AATAATATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49213 original size:11 final size:13
Alignment explanation
Indices: 49176--49215 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
49166 TGTTTAATAA
49176 AATATA-TATATT
1 AATATATTATATT
*
49188 AATATATTATCTT
1 AATATATTATATT
49201 AA-A-ATTATATT
1 AATATATTATATT
49212 AATA
1 AATA
49216 AACTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:52983 original size:23 final size:23
Alignment explanation
Indices: 52957--53013 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
52947 TAAAAATGTG
52957 ATGTAATAGGTAGCACTTATATA
1 ATGTAATAGGTAGCACTTATATA
** *
52980 ATGTAATTTGTAGCGCTTATATA
1 ATGTAATAGGTAGCACTTATATA
**
53003 ATAAAATAGGT
1 ATGTAATAGGT
53014 TAATTACTGG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (23 bp):
ATGTAATAGGTAGCACTTATATA
Found at i:53063 original size:87 final size:87
Alignment explanation
Indices: 52963--53280 Score: 564
Period size: 87 Copynumber: 3.7 Consensus size: 87
52953 TGTGATGTAA
* **
52963 TAGGTAGCACTTATATAATGTAATTTGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
53028 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* *
53050 TAGGTACCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGAAAAC
1 TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
53115 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
53137 TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
1 TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
53202 ATTATCAAGCACAATAACATAT
66 ATTATCAAGCACAATAACATAT
* * *
53224 TAGGTAGCGCTTATATAACGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
1 TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTA
53281 TTTAATTTGT
Statistics
Matches: 221, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 221 1.00
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (87 bp):
TAGGTACCACTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAATTACTGGAAAC
ATTATCAAGCACAATAACATAT
Found at i:53067 original size:23 final size:23
Alignment explanation
Indices: 53041--53100 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
53031 ATCAAGCACA
*
53041 ATAACATATTAGGTACCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
** *
53064 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCGCTTAT
* *
53087 ATAATAAAATAGGT
1 ATAACATAATAGGT
53101 TAATTACTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTACCGCTTAT
Found at i:53154 original size:23 final size:23
Alignment explanation
Indices: 53128--53187 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
53118 ATCAAGCACA
*
53128 ATAACATATTAGGTACCACTTAT
1 ATAACATAATAGGTACCACTTAT
** * *
53151 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTACCACTTAT
* *
53174 ATAATAAAATAGGT
1 ATAACATAATAGGT
53188 TAATTACTGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTACCACTTAT
Found at i:53241 original size:23 final size:23
Alignment explanation
Indices: 53215--53274 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
53205 ATCAAGCACA
*
53215 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
53238 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
* *
53261 ATAATAAAATAGGT
1 ATAACATAATAGGT
53275 TAATTATTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:53546 original size:24 final size:24
Alignment explanation
Indices: 53519--53570 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
53509 AACATCAAAT
53519 ACAATAA-AACAATATTATTTATTA
1 ACAATAATAACAATATTATTT-TTA
*
53543 ACAA-AATAATAATATTATTTTTA
1 ACAATAATAACAATATTATTTTTA
53566 A-AATA
1 ACAATA
53571 TTAGAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 7 0.28
24 16 0.64
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (24 bp):
ACAATAATAACAATATTATTTTTA
Found at i:53598 original size:14 final size:14
Alignment explanation
Indices: 53579--53623 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
53569 TATTAGAATA
*
53579 ATTTATTTAATATT
1 ATTTATTAAATATT
53593 ATTTATGTAAATATT
1 ATTTAT-TAAATATT
53608 A-TTATTAAAATATT
1 ATTTATT-AAATATT
53622 AT
1 AT
53624 ATCTATAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 1 0.04
14 18 0.67
15 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:53637 original size:28 final size:29
Alignment explanation
Indices: 53602--53680 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 29
53592 TATTTATGTA
* *
53602 AATA-TTATTATTAAAATATTAT-ATCTAT
1 AATATTTATTAATAAAAAATTATGAT-TAT
*
53630 AAT-TTTATAAATAAAAAATTATGATTAT
1 AATATTTATTAATAAAAAATTATGATTAT
*
53658 TATATTTATTAA-AATAAAATTAT
1 AATATTTATTAATAA-AAAATTAT
53681 TATAAATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 25 0.60
29 17 0.40
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
AATATTTATTAATAAAAAATTATGATTAT
Found at i:53646 original size:29 final size:31
Alignment explanation
Indices: 53614--53684 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 31
53604 TATTATTATT
53614 AAAATATTATATCTATAAT-TTTA-T-AAATA
1 AAAATATTATAT-TATAATATTTATTAAAATA
*
53643 AAAA-ATTATGATTATTATATTTATTAAAATA
1 AAAATATTAT-ATTATAATATTTATTAAAATA
*
53674 AAATTATTATA
1 AAAATATTATA
53685 AATTATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
28 10 0.29
29 10 0.29
30 1 0.03
31 9 0.26
32 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
AAAATATTATATTATAATATTTATTAAAATA
Found at i:54945 original size:199 final size:198
Alignment explanation
Indices: 54550--55217 Score: 927
Period size: 198 Copynumber: 3.4 Consensus size: 198
54540 CACATATGTT
* * * *
54550 ACATCGAAACCGATAATTATAATGTAATAGATAAATTTATAATGTAAC-CAGTATAAATATACCG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGT-ACTCGGTAGAAATATACCG
* * ***
54614 GTTTTATGAGAGAATAGGTCTACATAATGTATCGACACAAATTTAA-AAAGTGTCGATACATTTT
65 GTTTTATGAGAAAATAGGTCTACATAATGTATCGACAC-ATTTTAAGTTTGTGTCGATAC-TTTT
* * * *
54678 GTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTATCGATACACTTATTAAAAGT-TCGAT
128 TTCCAGAATGAATGCC-AACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGAT
54742 CCCAAAA
192 CCCAAAA
* * * *
54749 ACATCGAAACCAATAATTATAATGTAGTATGTAAATTTACAATGTACTCGGTAGAAATATATCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATACCGG
54814 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
66 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
* * * *
54879 CAGAATGAATGTCCAACGAGATACACACATAAAGTGTCGATACATTTATTAAAAGTATCTATCCC
131 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCC
54944 AAAA
195 AAAA
* * * *
54948 A-ATCCAAACTGATAATTACAATGTAATAGGTAAATTTACAATGTACCCGGTAGAAATATACCGG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATACCGG
* * *
55012 TTTTATGAGAAAATAGGTTTACATAATGTATCGACACGTTTTAAGTTTGTGTTGATACTTTTTTC
66 TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
*
55077 CAGAATGAATGCCCAACGAGGTGCACGCATAAAGTGTCGATACATTTA--AAATTGTATCGATCC
131 CAGAATGAATG-CCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAA-AGTATCGATCC
55140 CAAAA
194 CAAAA
* *
55145 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTTA-TCGGTATAAATATACTG
1 ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATG-TACTCGGTAGAAATATACCG
*
55209 ATTTTATGA
65 GTTTTATGA
55218 TAGAATATGT
Statistics
Matches: 417, Mismatches: 45, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
196 3 0.01
197 15 0.04
198 283 0.68
199 116 0.28
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (198 bp):
ACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATGTACTCGGTAGAAATATACCGG
TTTTATGAGAAAATAGGTCTACATAATGTATCGACACATTTTAAGTTTGTGTCGATACTTTTTTC
CAGAATGAATGCCAACGAGGTGCACGCATAAAGTGTCGATACATTTATTAAAAGTATCGATCCCA
AAA
Found at i:55277 original size:23 final size:23
Alignment explanation
Indices: 55221--55277 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
55211 TTTATGATAG
* *
55221 AATATGTCAATATAAGCGCTACCT
1 AATATGT-TATATAAGCACTACCT
* **
55245 ATTACATTATATAAGCACTACCT
1 AATATGTTATATAAGCACTACCT
55268 AATATGTTAT
1 AATATGTTAT
55278 TGTACTTGAT
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.35
Consensus pattern (23 bp):
AATATGTTATATAAGCACTACCT
Found at i:62293 original size:37 final size:36
Alignment explanation
Indices: 62235--62353 Score: 179
Period size: 35 Copynumber: 3.3 Consensus size: 36
62225 TCCCATTATC
* *
62235 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTG-AAAACT
*
62271 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
62307 A-TTTTCAAAGAAACATTTACCAAACTTTGAAAACT
1 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
62342 ATTTTTTCAAAG
1 A-TTTTTCAAAG
62354 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
35 34 0.45
36 13 0.17
37 29 0.38
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACT
Found at i:62309 original size:21 final size:21
Alignment explanation
Indices: 62285--62345 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
62275 TTCAAAGAAA
62285 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
62306 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
62320 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
62341 TATTT
1 CATTT
62346 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 5 0.17
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 9 0.30
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:66895 original size:37 final size:36
Alignment explanation
Indices: 66836--66949 Score: 142
Period size: 35 Copynumber: 3.2 Consensus size: 36
66826 ATCCCATTAT
* *
66836 CATTTTTC-AACAAACATCTACCAAACTTTAAAAAAT
1 CATTTTTCAAACAAACATTTACCAAACTTT-AAAAAC
* *
66872 TATTTTTCAAATAAACATTTACCAAACTTTAAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTAAAAAC
* * *
66908 CA-TTTTCAAAGAAACATTTATCAAACTTTGAAAAC
1 CATTTTTCAAACAAACATTTACCAAACTTTAAAAAC
66943 CATTTTT
1 CATTTTT
66950 TTTTAAAATT
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.47
36 17 0.25
37 19 0.28
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (36 bp):
CATTTTTCAAACAAACATTTACCAAACTTTAAAAAC
Found at i:72996 original size:36 final size:36
Alignment explanation
Indices: 72949--73021 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
72939 GAACCTTGGA
* *
72949 AATGATAATTAGATAAAAGGGATCATATTTGAGATT
1 AATGATAATTAGATAAAAGGGACCATATTTAAGATT
** *
72985 AATGATAATTAGATGTAATGGACCATATTTAAGATT
1 AATGATAATTAGATAAAAGGGACCATATTTAAGATT
73021 A
1 A
73022 GATTTAGACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (36 bp):
AATGATAATTAGATAAAAGGGACCATATTTAAGATT
Found at i:77169 original size:125 final size:125
Alignment explanation
Indices: 77009--77383 Score: 714
Period size: 125 Copynumber: 3.0 Consensus size: 125
76999 TTTAGATAAA
77009 ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
1 ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
*
77074 TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATGTTATTAATGATCATCTAT
66 TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
* *
77134 ATGTCATACGTAAAACTTTTTAATGTTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
1 ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
77199 TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
66 TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
77259 ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
1 ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
*
77324 TGTATTTATAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
66 TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
77384 TTAAAATTTT
Statistics
Matches: 244, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 244 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (125 bp):
ATATCATACGTAAAACTTTTTAATGCTTTAATGAGATTGTGATATTGTAGTTCACTATTAATTTA
TGTATTTTTAAATAATCACATTGAATTAAGTATATAGTCATATTATTAATGATCATCTAT
Found at i:106150 original size:21 final size:22
Alignment explanation
Indices: 106100--106153 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
106090 ATTAAATGGT
*
106100 AATAAACAAAATTATCAAAATA
1 AATAAACAAAATAATCAAAATA
*
106122 AATTAACAAAA-AATCCAAAA-A
1 AATAAACAAAATAAT-CAAAATA
106143 AATAAACAAAA
1 AATAAACAAAA
106154 CAAATTTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (22 bp):
AATAAACAAAATAATCAAAATA
Found at i:117737 original size:2 final size:2
Alignment explanation
Indices: 117730--117764 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
117720 TGGTTTTCCT
*
117730 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
117765 CATTTGATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:120036 original size:19 final size:19
Alignment explanation
Indices: 120012--120064 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
120002 ATAAGACCTA
120012 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
120031 GTGCATCGGTACACTTGGG
1 GTGCATCGGTACACTTGGG
120050 GTGCATCGGTACACT
1 GTGCATCGGTACACT
120065 AATTACATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.17, C:0.23, G:0.34, T:0.26
Consensus pattern (19 bp):
GTGCATCGGTACACTTGGG
Found at i:120145 original size:65 final size:65
Alignment explanation
Indices: 120070--120206 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
120060 ACACTAATTA
* * * *
120070 CATTCAATGTTTCAA-AAGAGTCAAGAGTGCATCGATGCATGGCCTGTGCATCAATACATAAAAT
1 CATTCGATGTTTCAATAA-AATCAAGAGTGCATCGATGCATGGCCTGTACATCAATACACAAAAT
120134 G
65 G
* ** **
120135 CATTCGATGTTTCAATAAAATCATGAGTGCATCGATGCATGGTTTGTACATCGGTACACAAAATG
1 CATTCGATGTTTCAATAAAATCAAGAGTGCATCGATGCATGGCCTGTACATCAATACACAAAATG
120200 CATTCGA
1 CATTCGA
120207 AATAGGGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 60 0.97
66 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (65 bp):
CATTCGATGTTTCAATAAAATCAAGAGTGCATCGATGCATGGCCTGTACATCAATACACAAAATG
Found at i:121695 original size:42 final size:42
Alignment explanation
Indices: 121635--121778 Score: 225
Period size: 42 Copynumber: 3.4 Consensus size: 42
121625 CTGGTTAAAC
*
121635 CTTCTAATAATCCGATTGGAAATTCCAATGATTCACCTAATG
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATG
* *
121677 CTTCTAATAATCCTATTGGAAATTTCAATGATTCACCTAATA
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATG
121719 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATG
1 CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATG
*
121761 ATTCGGTTAATAATCCTA
1 CTTC---TAATAATCCTA
121779 AAGTGTGGGA
Statistics
Matches: 93, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 82 0.88
45 11 0.12
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (42 bp):
CTTCTAATAATCCTATTGGAAATTCCAATGATTCACCTAATG
Found at i:123078 original size:17 final size:17
Alignment explanation
Indices: 123030--123084 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
123020 AAACTTATTA
*
123030 ATATATAGGGACTAAAT
1 ATATATAAGGACTAAAT
*
123047 ATATAATTAA--CCTAAAT
1 ATAT-A-TAAGGACTAAAT
123064 ATATATAAGGACTAAAT
1 ATATATAAGGACTAAAT
123081 -TATA
1 ATATA
123085 AATATACAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
15 3 0.10
16 5 0.16
17 20 0.65
18 1 0.03
19 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (17 bp):
ATATATAAGGACTAAAT
Found at i:124121 original size:21 final size:22
Alignment explanation
Indices: 124097--124139 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
124087 TTGCTGAATT
*
124097 AGGCCTATGTGCC-TTGTAATC
1 AGGCCTACGTGCCTTTGTAATC
*
124118 AGGCCTGCGTGCCTTTGTAATC
1 AGGCCTACGTGCCTTTGTAATC
124140 GGGCTCCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (22 bp):
AGGCCTACGTGCCTTTGTAATC
Found at i:124664 original size:94 final size:95
Alignment explanation
Indices: 124522--124693 Score: 226
Period size: 94 Copynumber: 1.8 Consensus size: 95
124512 CATCTGGATA
* * *
124522 ACTTGAATAGAATCTATTTCATTACTCTTCCGTGAAGTTCAAATTCAAACTTGGA-TCAC-TCAA
1 ACTTGAATAGAATCTATTTCACTACTCCTCCGTGAAGTTCAAATTCAAACTTGAATTCACTTCAA
124585 CTACTCTTCCGTGAAGTTTAAAAATGATTG
66 CTACTCTTCCGTGAAGTTTAAAAATGATTG
* * *
124615 ACTTGACA-AGAATCTAATTTCACTACTCCTCCGTGAA-TATCAGATTCAAAGTTGAATTCGCTT
1 ACTTGA-ATAGAATCT-ATTTCACTACTCCTCCGTGAAGT-TCAAATTCAAACTTGAATTCACTT
*
124678 CCACTACTCTTCCGTG
63 CAACTACTCTTCCGTG
124694 GAGGTTACAT
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
93 14 0.21
94 34 0.51
95 3 0.04
96 16 0.24
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (95 bp):
ACTTGAATAGAATCTATTTCACTACTCCTCCGTGAAGTTCAAATTCAAACTTGAATTCACTTCAA
CTACTCTTCCGTGAAGTTTAAAAATGATTG
Found at i:124987 original size:20 final size:20
Alignment explanation
Indices: 124938--124987 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
124928 TAGATGACAC
* *
124938 AAAGAATTTACAAATTACCT
1 AAAGGATTTAAAAATTACCT
*
124958 AAAGGCTTTAAAAATTACCT
1 AAAGGATTTAAAAATTACCT
**
124978 GGAGGATTTA
1 AAAGGATTTA
124988 TTAATGACCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGGATTTAAAAATTACCT
Found at i:132022 original size:19 final size:20
Alignment explanation
Indices: 131979--132022 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
131969 ATTATCCTAT
131979 TATTAT-AATTAATATTAAC
1 TATTATAAATTAATATTAAC
131998 TA-TATAAATTAA-ATTATA-
1 TATTATAAATTAATATTA-AC
132016 TATTATA
1 TATTATA
132023 TATAATAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TATTATAAATTAATATTAAC
Found at i:132024 original size:23 final size:25
Alignment explanation
Indices: 131980--132027 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
131970 TTATCCTATT
131980 ATTATAATTAATATTAACTATATAA
1 ATTATAATTAATATTAACTATATAA
132005 ATTA-AATTATATATT-A-TATATAA
1 ATTATAATTA-ATATTAACTATATAA
132028 TAAACCTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.32
24 6 0.27
25 9 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTATAATTAATATTAACTATATAA
Found at i:132890 original size:21 final size:22
Alignment explanation
Indices: 132866--132912 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
132856 TTGCTGAATT
*
132866 GGGCCTATGTGCC-TTGTAATC
1 GGGCCTACGTGCCTTTGTAATC
*
132887 GGGCCTGCGTGCCTTTGTAATC
1 GGGCCTACGTGCCTTTGTAATC
132909 GGGC
1 GGGC
132913 TCCCAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.11, C:0.26, G:0.34, T:0.30
Consensus pattern (22 bp):
GGGCCTACGTGCCTTTGTAATC
Found at i:135272 original size:58 final size:60
Alignment explanation
Indices: 135200--135335 Score: 138
Period size: 58 Copynumber: 2.3 Consensus size: 60
135190 TAAGCTAGGG
* * * * *
135200 TAAAA-TACACAAATGGTCC-CCTGACTATAGGATA-TTGTTTTCTTGAGT-CTTTGACTAT
1 TAAAATTACA-AAATGGTCCTCCTAACTATAGGA-AGTTATCTTCTTGAGTCCCTCGACTAT
* * *
135258 TAAAATTACAAAAT-GACCTCCTAACTATATGAAGTTATCTTGTTGAGTCCCTCGACTAT
1 TAAAATTACAAAATGGTCCTCCTAACTATAGGAAGTTATCTTCTTGAGTCCCTCGACTAT
135317 TAAAAGTTACAAAATGGTC
1 TAAAA-TTACAAAATGGTC
135336 ACCGACTGTT
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
57 4 0.06
58 31 0.49
59 17 0.27
60 9 0.14
61 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (60 bp):
TAAAATTACAAAATGGTCCTCCTAACTATAGGAAGTTATCTTCTTGAGTCCCTCGACTAT
Found at i:136452 original size:56 final size:56
Alignment explanation
Indices: 136389--136504 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 56
136379 AAATTAATTC
*
136389 TTATTATAACGTATGGTT-TATATCATAATATATTATTAAAATGATGTACTG-AAATA
1 TTATTATAACGTAT-GTTATATATCATAA-ATACTATTAAAATGATGTACTGAAAATA
** **
136445 TTATTATAATTTATGTTATATATTGTAAATACTATTAAAATGATGTACTGAAAATA
1 TTATTATAACGTATGTTATATATCATAAATACTATTAAAATGATGTACTGAAAATA
136501 TTAT
1 TTAT
136505 GGATAATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
55 24 0.45
56 29 0.55
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.45
Consensus pattern (56 bp):
TTATTATAACGTATGTTATATATCATAAATACTATTAAAATGATGTACTGAAAATA
Done.