Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004114.1 Hibiscus syriacus cultivar Beakdansim tig00009003_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: 1048340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:968532 original size:77 final size:77
Alignment explanation
Indices: 968434--968587 Score: 236
Period size: 77 Copynumber: 2.0 Consensus size: 77
968424 TTCGAGTATG
* *
968434 ATGGTTATCGATCGATATTGTTTAATGCATATGTAGCATTTTCGTATCAGTACCTTTGTGTACTT
1 ATGGTTACCGATCGATATTGTTTAATGCATACGTAGCATTTTCGTATCAGTACCTTTGTGTACTT
968499 TCAACACCATGT
66 TCAACACCATGT
* * * *
968511 ATGGTTACCGATTGATTTTGTTTATTGCATACGTTGCATTTTCGTATCAGTACCTTTGTGTACTT
1 ATGGTTACCGATCGATATTGTTTAATGCATACGTAGCATTTTCGTATCAGTACCTTTGTGTACTT
* *
968576 TCATCACTATGT
66 TCAACACCATGT
968588 GTGTATGCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (77 bp):
ATGGTTACCGATCGATATTGTTTAATGCATACGTAGCATTTTCGTATCAGTACCTTTGTGTACTT
TCAACACCATGT
Found at i:969200 original size:2 final size:2
Alignment explanation
Indices: 969187--969217 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
969177 AATGTTATGT
*
969187 TA TA TA TG 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 T
969218 TTGAAGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:972278 original size:53 final size:54
Alignment explanation
Indices: 972128--972332 Score: 313
Period size: 54 Copynumber: 3.8 Consensus size: 54
972118 ACGTAGTACT
* * *
972128 GATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTGTACACTTAGTGTC
1 GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTC
*
972182 GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTATTGTC
1 GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTC
* *
972236 GATACGGTCGTTCAT-AACATATTGTGAATTCTGTGGGTTGCACACTTAGTGCC
1 GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTC
* * * *
972289 GATACGGTGGTTCATAAGCATATTATGAATTCTATTGGTTGCAC
1 GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCAC
972333 TTGTAGTGCC
Statistics
Matches: 138, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
53 49 0.36
54 89 0.64
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (54 bp):
GATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTTGCACACTTAGTGTC
Found at i:972282 original size:107 final size:108
Alignment explanation
Indices: 972128--972332 Score: 322
Period size: 107 Copynumber: 1.9 Consensus size: 108
972118 ACGTAGTACT
* *
972128 GATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTGTACACTTAGTGTCGATACGGTCGT
1 GATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGT
*
972193 TCATAAACATATTATGAATTCTGTGGGTTGCACACTTATTGTC
66 TCATAAACATATTATGAATTCTATGGGTTGCACACTTATTGTC
* * * *
972236 GATACGGTCGTTCAT-AACATATTGTGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTGGT
1 GATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGT
* *
972300 TCATAAGCATATTATGAATTCTATTGGTTGCAC
66 TCATAAACATATTATGAATTCTATGGGTTGCAC
972333 TTGTAGTGCC
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
107 74 0.84
108 14 0.16
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (108 bp):
GATACAGTCGTTCATAAACATATTATGAATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGT
TCATAAACATATTATGAATTCTATGGGTTGCACACTTATTGTC
Found at i:972806 original size:18 final size:18
Alignment explanation
Indices: 972783--972829 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
972773 CCTTCCTCTT
972783 AGTATCGATACCCACATC
1 AGTATCGATACCCACATC
*
972801 AGTATCGATACCCATATC
1 AGTATCGATACCCACATC
972819 AGTATCGATAC
1 AGTATCGATAC
972830 TAATTGCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.34, C:0.28, G:0.13, T:0.26
Consensus pattern (18 bp):
AGTATCGATACCCACATC
Found at i:1002637 original size:77 final size:77
Alignment explanation
Indices: 1002545--1002692 Score: 235
Period size: 77 Copynumber: 1.9 Consensus size: 77
1002535 GATGGGTATC
* * *
1002545 GATCGATTTTGTTTAATGCATATGTTGCATTTTTGTATCTGTA-CATTTGTGTACTTTCGACACT
1 GATCAATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTATC-TTTGTGTACTTTCGACACT
1002609 ATGTGTGGTTATT
65 ATGTGTGGTTATT
* *
1002622 GATCAATTTTGTTTAATGCTTATGTTGCATTTTCGTATCAGTATCTTTGTGTACTTTCGGCACTA
1 GATCAATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTATCTTTGTGTACTTTCGACACTA
1002687 TGTGTG
66 TGTGTG
1002693 CATGCATGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
77 64 0.98
78 1 0.02
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.49
Consensus pattern (77 bp):
GATCAATTTTGTTTAATGCATATGTTGCATTTTCGTATCAGTATCTTTGTGTACTTTCGACACTA
TGTGTGGTTATT
Found at i:1012022 original size:19 final size:20
Alignment explanation
Indices: 1011997--1012049 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1011987 TTTGGCCAGG
1011997 ATCATGTATTTTCATT-AAA
1 ATCATGTATTTTCATTAAAA
*
1012016 GTCATGTATTTTCATTAAAA
1 ATCATGTATTTTCATTAAAA
1012036 ATCATGTATTTTCA
1 ATCATGTATTTTCA
1012050 AAGGGATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (20 bp):
ATCATGTATTTTCATTAAAA
Found at i:1015872 original size:19 final size:20
Alignment explanation
Indices: 1015848--1015898 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1015838 TGGCCAAGAG
*
1015848 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
1015867 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
*
1015887 TATGTATTTTCA
1 CATGTATTTTCA
1015899 AAGGGATTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:1023165 original size:23 final size:23
Alignment explanation
Indices: 1023139--1023205 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1023129 GATGAGGTGA
1023139 AAACATCGTTGAGTTGGGTCTAC
1 AAACATCGTTGAGTTGGGTCTAC
* * *
1023162 AAACA-C-ATGA--T-CGT-GA-
1 AAACATCGTTGAGTTGGGTCTAC
1023178 AAACATCGTTGAGTTGGGTCTAC
1 AAACATCGTTGAGTTGGGTCTAC
1023201 AAACA
1 AAACA
1023206 CATGATCGTC
Statistics
Matches: 31, Mismatches: 6, Indels: 14
0.61 0.12 0.27
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
18 5 0.16
19 1 0.03
20 1 0.03
21 5 0.16
22 2 0.06
23 10 0.32
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (23 bp):
AAACATCGTTGAGTTGGGTCTAC
Found at i:1023189 original size:39 final size:39
Alignment explanation
Indices: 1023135--1023214 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
1023125 GATTGATGAG
1023135 GTGAAAACATCGTTGAGTTGGGTCTACAAACACATGATC
1 GTGAAAACATCGTTGAGTTGGGTCTACAAACACATGATC
1023174 GTGAAAACATCGTTGAGTTGGGTCTACAAACACATGATC
1 GTGAAAACATCGTTGAGTTGGGTCTACAAACACATGATC
1023213 GT
1 GT
1023215 CAGAGGATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (39 bp):
GTGAAAACATCGTTGAGTTGGGTCTACAAACACATGATC
Found at i:1023606 original size:23 final size:23
Alignment explanation
Indices: 1023580--1023627 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1023570 ATAAAGTACA
*
1023580 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
** *
1023603 ATAATGTAATAGGTAGTGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1023626 AT
1 AT
1023628 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1024061 original size:21 final size:21
Alignment explanation
Indices: 1024036--1024105 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
1024026 GATAGACACT
1024036 TTACAATATAACCACTACCTA
1 TTACAATATAACCACTACCTA
* *
1024057 TTACATTATAAACGA-TACCTA
1 TTACAATAT-AACCACTACCTA
* *
1024078 TTACATTATATAAGCGCTACCTA
1 TTACA--ATATAACCACTACCTA
1024101 TTACA
1 TTACA
1024106 TCATATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 19 0.49
22 6 0.15
23 14 0.36
ACGTcount: A:0.40, C:0.23, G:0.04, T:0.33
Consensus pattern (21 bp):
TTACAATATAACCACTACCTA
Found at i:1024098 original size:23 final size:22
Alignment explanation
Indices: 1024041--1024111 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
1024031 ACACTTTACA
*
1024041 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
*
1024064 ATA-AACGATACCTATTACATT
1 ATATAACGCTACCTATTACATT
*
1024085 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
1024108 ATAT
1 ATAT
1024112 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 21 0.50
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:1024311 original size:29 final size:30
Alignment explanation
Indices: 1024257--1024322 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
1024247 TCATTTGCAC
* *
1024257 AAAA-ATTATTTGATTTTTTGATATTTTAT
1 AAAATATTATTTGAATTTTTGATATTTAAT
1024286 AAAATATTATTTAGAATTTTT-A-ATTTAAT
1 AAAATATTATTT-GAATTTTTGATATTTAAT
1024315 AATAATAT
1 AA-AATAT
1024323 ATATCGTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.38
30 13 0.41
31 7 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (30 bp):
AAAATATTATTTGAATTTTTGATATTTAAT
Found at i:1024509 original size:22 final size:23
Alignment explanation
Indices: 1024478--1024539 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
1024468 ATATAACCAC
1024478 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1024501 TA-CTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1024523 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1024540 TTTACCTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1024533 original size:23 final size:23
Alignment explanation
Indices: 1024468--1024539 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
1024458 ACACTTTACA
* *
1024468 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1024491 ATATAAACGATA-CTATTACATT
1 ATATAAACGCTACCTATTACATT
* *
1024513 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1024536 ATAT
1 ATAT
1024540 TTTACCTATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 20 0.48
23 22 0.52
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:1024690 original size:427 final size:425
Alignment explanation
Indices: 1023694--1024738 Score: 1992
Period size: 425 Copynumber: 2.5 Consensus size: 425
1023684 TATTACATTA
1023694 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1023759 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
*
1023824 TTTGCACAAAAAATTATTTGATTATTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1023889 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
196 TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
1023954 TAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
261 TAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
1024019 ATAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATAAACGATACCTATTACAT
326 ATAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATAAACGATACCTATTACAT
1024084 TATATAAGCGCTACCTATTACATCATATTTTTACC
391 TATATAAGCGCTACCTATTACATCATATTTTTACC
1024119 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1024184 TTATGTTTCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
66 TTATGTTTCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTC
1024249 ATTTGCAC-AAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
130 ATTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTA
1024313 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATC
195 ATAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATC
1024378 TTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
260 TTAAAACTCACTC-AAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTT
1024443 TTATAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATATAAACGATA-CTAT
324 TTATAAAAA-GATAGACACTTTACAATATAACCACTACCTATTACA-T-TATAAACGATACCTAT
1024507 TACATTATATAAGCGCTACCTATTACATCATA-TTTTACC
386 TACATTATATAAGCGCTACCTATTACATCATATTTTTACC
*
1024546 TATTATATTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAAT
1 TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
1024611 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
66 TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
1024676 TTTGCACAAAAAATTATTTGA-TTTTTGATATTTTAT-AAATATTATTTAGAATTTTTAATTTAA
131 TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
1024739 CAACATTAAC
Statistics
Matches: 612, Mismatches: 2, Indels: 12
0.98 0.00 0.02
Matches are distributed among these distances:
425 236 0.39
426 197 0.32
427 131 0.21
428 37 0.06
429 11 0.02
ACGTcount: A:0.38, C:0.12, G:0.08, T:0.42
Consensus pattern (425 bp):
TATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAAT
TTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCA
TTTGCACAAAAAATTATTTGATTTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAA
TAATAATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAAAATCT
TAAAACTCACTCAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTT
ATAAAAAGATAGACACTTTACAATATAACCACTACCTATTACATTATAAACGATACCTATTACAT
TATATAAGCGCTACCTATTACATCATATTTTTACC
Found at i:1025012 original size:39 final size:39
Alignment explanation
Indices: 1024958--1025043 Score: 145
Period size: 39 Copynumber: 2.2 Consensus size: 39
1024948 CAAGTTGTAG
*
1024958 ATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGA
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
* *
1024997 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTGG
1 ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
1025036 ATTTTGAT
1 ATTTTGAT
1025044 GAGCATCGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGA
Found at i:1025323 original size:18 final size:18
Alignment explanation
Indices: 1025300--1025336 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1025290 CGAAATATAT
1025300 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1025318 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1025336 A
1 A
1025337 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1025791 original size:23 final size:23
Alignment explanation
Indices: 1025759--1025861 Score: 145
Period size: 23 Copynumber: 4.5 Consensus size: 23
1025749 GATAGATACT
*
1025759 TTACAATATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
* *
1025782 TTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTA
1025805 TTACATTATATAAACGATACCTA
1 TTACATTATATAAACGATACCTA
*
1025828 TTACATTATATAAGC-ACTACCTA
1 TTACATTATATAAACGA-TACCTA
*
1025851 TTACATCATAT
1 TTACATTATAT
1025862 GTTTACCTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
22 1 0.01
23 71 0.99
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (23 bp):
TTACATTATATAAACGATACCTA
Found at i:1025856 original size:46 final size:46
Alignment explanation
Indices: 1025759--1025861 Score: 179
Period size: 46 Copynumber: 2.2 Consensus size: 46
1025749 GATAGATACT
* *
1025759 TTACAATATATAAACGATACCTATTACATTATATAAGCGCTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
1025805 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
1 TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
*
1025851 TTACATCATAT
1 TTACATTATAT
1025862 GTTTACCTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (46 bp):
TTACATTATATAAACGATACCTATTACATTATATAAGCACTACCTA
Found at i:1028768 original size:183 final size:183
Alignment explanation
Indices: 1028460--1028942 Score: 896
Period size: 183 Copynumber: 2.6 Consensus size: 183
1028450 CGACACATTT
1028460 TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
1 TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
1028525 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
1028590 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
131 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
1028643 TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
1 TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
*
1028708 CAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
1028773 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
131 TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
*
1028826 TGGACAT-AAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
1 TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
* * * **
1028890 AAACCGGTATATTTATACCGGTTATATTGCAAATTTACCTATTTTATTATAAT
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
1028943 ATGTTGAAAG
Statistics
Matches: 292, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
182 104 0.36
183 188 0.64
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (183 bp):
TAGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATA
AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGA
TGTGTAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATA
Found at i:1030414 original size:3 final size:3
Alignment explanation
Indices: 1030406--1030480 Score: 69
Period size: 3 Copynumber: 25.0 Consensus size: 3
1030396 ACTTGTTTGG
* * ** * *
1030406 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC ATC TTC ATC GCC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1030454 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1030481 GTCAGCTTCA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.24, C:0.35, G:0.05, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1030423 original size:12 final size:12
Alignment explanation
Indices: 1030410--1030492 Score: 103
Period size: 12 Copynumber: 6.9 Consensus size: 12
1030400 GTTTGGATCA
*
1030410 TCATCTTCATCA
1 TCATCTTCATCG
* *
1030422 TCATCATCATCA
1 TCATCTTCATCG
1030434 TCATCTTCATCG
1 TCATCTTCATCG
* *
1030446 CCAGCTTCATCG
1 TCATCTTCATCG
*
1030458 TCATCATCATCG
1 TCATCTTCATCG
1030470 TCATCTTCATCG
1 TCATCTTCATCG
*
1030482 TCAGCTTCATC
1 TCATCTTCATC
1030493 TTCTGCGACC
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 61 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.36
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1030454 original size:36 final size:36
Alignment explanation
Indices: 1030414--1030492 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 36
1030404 GGATCATCAT
1030414 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
* * *
1030450 CTTCATCGTCATCATCATCGTCATCTTCATCGTCAG
1 CTTCATCATCATCATCATCATCATCTTCATCGCCAG
1030486 CTTCATC
1 CTTCATC
1030493 TTCTGCGACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.22, C:0.35, G:0.08, T:0.35
Consensus pattern (36 bp):
CTTCATCATCATCATCATCATCATCTTCATCGCCAG
Found at i:1030495 original size:6 final size:6
Alignment explanation
Indices: 1030410--1030495 Score: 73
Period size: 6 Copynumber: 14.3 Consensus size: 6
1030400 GTTTGGATCA
* * * * * * *
1030410 TCATCT TCATCA TCATCA TCATCA TCATCT TCATCG CCAGCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
* * * *
1030458 TCATCA TCATCG TCATCT TCATCG TCAGCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TC
1030496 TGCGACCGCT
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (6 bp):
TCATCT
Found at i:1032290 original size:197 final size:197
Alignment explanation
Indices: 1031955--1032851 Score: 1656
Period size: 197 Copynumber: 4.6 Consensus size: 197
1031945 TTTAAATTAG
*
1031955 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032020 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1032085 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAA-
1032149 AAA
195 AAA
1032152 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
*
1032217 ATTGTACCAGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1032282 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1032347 AA
196 AA
*
1032349 AATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032414 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
1032478 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1032540 AA
196 AA
1032542 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032607 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1032672 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTTGAAAA
131 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTC-TGGAAA
1032737 AAA
195 AAA
1032740 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-G-ATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032803 ATTGTACCGGTTAGATTG-AAAATTACATATT---TTATA-TTTTGGGTTCGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGAT
1032852 TTTTTTATAT
Statistics
Matches: 688, Mismatches: 6, Indels: 18
0.97 0.01 0.03
Matches are distributed among these distances:
191 13 0.02
192 5 0.01
193 127 0.18
194 61 0.09
195 21 0.03
196 81 0.12
197 284 0.41
198 96 0.14
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (197 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AA
Found at i:1032679 original size:390 final size:393
Alignment explanation
Indices: 1031955--1033004 Score: 1823
Period size: 390 Copynumber: 2.7 Consensus size: 393
1031945 TTTAAATTAG
*
1031955 TATCGACACAAACTCTATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032020 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGA-TTTGGGAT
1032085 CGACACTTTTTATATATGGATCGACACTTTAT-GGTGCACCCTGTTTTCCATTCATTCTGGAAAT
130 CGACAC-TTTT-TATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAT
1032149 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
193 AAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGT
*
1032214 ATAATTGTACCAGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
258 ATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGG
1032279 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
323 GATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGA
1032344 AAAAAA
388 AAAAAA
1032350 -ATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032414 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
1032479 GACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCT-GAAA-AAA
131 GACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAA
1032542 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
196 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032607 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
261 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
*
1032672 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTTGAAAA
326 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
1032737 AAA
391 AAA
1032740 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACC-G-ATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032803 ATTGTACCGGTTAGATTG-AAAATTACATATT---TTATA-TTTTGGGTTC---GATTT----T-
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
*
1032855 -----TTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAA
131 GACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAA
* *
1032915 TATCGACAAAAACTATATTA---TCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
196 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
1032977 ATTGTACCGGTTAGATTG-AAAATTACAT
261 ATTGTACCGGTTAGATTGAAAAATTACAT
1033005 CCTTTTGGCC
Statistics
Matches: 645, Mismatches: 6, Indels: 34
0.94 0.01 0.05
Matches are distributed among these distances:
369 10 0.02
370 59 0.09
371 50 0.08
372 4 0.01
373 22 0.03
377 1 0.00
381 5 0.01
384 10 0.02
385 5 0.01
388 13 0.02
389 21 0.03
390 200 0.31
391 82 0.13
392 30 0.05
393 14 0.02
394 119 0.18
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (393 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTGGGATC
GACACTTTTTATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAATAAA
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCACATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
AAA
Found at i:1033151 original size:18 final size:18
Alignment explanation
Indices: 1033128--1033172 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1033118 TTATATTCAC
1033128 ATACAAAATATAAATCGT
1 ATACAAAATATAAATCGT
* *
1033146 ATACAAATTATAAATCTT
1 ATACAAAATATAAATCGT
1033164 ATACAAAAT
1 ATACAAAAT
1033173 TAACCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (18 bp):
ATACAAAATATAAATCGT
Found at i:1035099 original size:21 final size:21
Alignment explanation
Indices: 1035059--1035123 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1035049 CCCCTTATGC
* *
1035059 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
1035080 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
1035101 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
1035122 CT
1 CT
1035124 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:1037337 original size:21 final size:22
Alignment explanation
Indices: 1037313--1037353 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
1037303 GGTATCATTT
1037313 TACCGGTTTTATCAT-TTTTGA
1 TACCGGTTTTATCATATTTTGA
1037334 TACCGGTTTTATCATATTTT
1 TACCGGTTTTATCATATTTT
1037354 TACCTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.54
Consensus pattern (22 bp):
TACCGGTTTTATCATATTTTGA
Found at i:1037366 original size:20 final size:19
Alignment explanation
Indices: 1037310--1037357 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 19
1037300 TCCGGTATCA
1037310 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
1037329 TTTGATACCGGTTTTATCATAT
1 TTT--TACCGGTTTTATCAT-T
1037351 TTTTACC
1 TTTTACC
1037358 TGTTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.12
20 4 0.15
21 15 0.58
22 4 0.15
ACGTcount: A:0.19, C:0.17, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1037987 original size:228 final size:226
Alignment explanation
Indices: 1037586--1038027 Score: 785
Period size: 228 Copynumber: 1.9 Consensus size: 226
1037576 TTAAAACTGC
1037586 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
* **
1037651 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTAAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
1037716 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
1037781 GTATGGACACTTTTATAAAATGATATATACTT
195 GTATGGACACTTTTATAAAATGATATATACTT
*
1037813 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
1037878 ATTAATTAAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
65 ATTAATTAAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTA
* *
1037943 TTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAA
130 TTTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAA
1038008 GTATGGACACTTTTATAAAA
195 GTATGGACACTTTTATAAAA
1038028 AGGATAGATA
Statistics
Matches: 205, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
227 36 0.18
228 169 0.82
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (226 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTAAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAATGATATATACTT
Found at i:1038711 original size:6 final size:6
Alignment explanation
Indices: 1038700--1038727 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1038690 ATAATATAAA
1038700 ATATTT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
1038728 GATATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:1042674 original size:2 final size:2
Alignment explanation
Indices: 1042667--1042707 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1042657 GACACTAAAT
1042667 TA TA TA TA TA TA TA TA TA 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 TA TA TA T
1042708 GCATATTAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1042924 original size:2 final size:2
Alignment explanation
Indices: 1042917--1042952 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1042907 ATCCTAACTC
1042917 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
1042953 TCAATTGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1044251 original size:38 final size:38
Alignment explanation
Indices: 1044208--1044281 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
1044198 TATAAGTTTC
* *
1044208 TTTTGTATTCTTCTTCTCTCGACATTAGTGAGTTTTTT
1 TTTTGTATTCTTATTCTCTCGACATTAGTGAATTTTTT
* * *
1044246 TTTTGTATTTTTATTTTCTTGACATTAGTGAATTTT
1 TTTTGTATTCTTATTCTCTCGACATTAGTGAATTTT
1044282 CTCATTTTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.16, C:0.11, G:0.12, T:0.61
Consensus pattern (38 bp):
TTTTGTATTCTTATTCTCTCGACATTAGTGAATTTTTT
Done.