Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007961.1 Hibiscus syriacus cultivar Beakdansim tig00110388_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: 2700559
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2617039 original size:25 final size:25
Alignment explanation
Indices: 2617004--2617051 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
2616994 GATATATAAA
* *
2617004 ATTTATCGTAAACCGTAGCAAAAAC
1 ATTTATCGTAAACCATAACAAAAAC
*
2617029 ATTTATTGTAAACCATAACAAAA
1 ATTTATCGTAAACCATAACAAAA
2617052 TTGACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (25 bp):
ATTTATCGTAAACCATAACAAAAAC
Found at i:2620462 original size:17 final size:18
Alignment explanation
Indices: 2620442--2620476 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2620432 AAAGTTAAAT
2620442 TAAAAAAATAA-AAATAA
1 TAAAAAAATAACAAATAA
*
2620459 TAAAGAAATAACAAATAA
1 TAAAAAAATAACAAATAA
2620477 AAGGGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
TAAAAAAATAACAAATAA
Found at i:2621776 original size:39 final size:38
Alignment explanation
Indices: 2621693--2621928 Score: 142
Period size: 39 Copynumber: 6.4 Consensus size: 38
2621683 ACATTTTCAA
*
2621693 ACTATATATTATATATATTTAAAAATGTTTTTCAAAAA-
1 ACTATATATTATATATTTTTAAAAATGTTTTT-AAAAAT
*
2621731 ACTATATATTATATACTTTTTAAAAATATTTTTAAAAAT
1 ACTATATATTATATA-TTTTTAAAAATGTTTTTAAAAAT
*
2621770 --TATATATTATATATATGTTTTCAAAATG-TTTTAAAAA-
1 ACTATATA-T-TATATAT-TTTTAAAAATGTTTTTAAAAAT
* * * * * * * * *
2621807 A-TAT-T-TT-TATATATATATATATATATATATATAT
1 ACTATATATTATATATTTTTAAAAATGTTTTTAAAAAT
* *
2621841 A-TATATA-TATATGTGTTTTCAAAATG-TTTT-AAAA-
1 ACTATATATTATATAT-TTTTAAAAATGTTTTTAAAAAT
* * *
2621875 ACTATATATTATATAAGTTTAAAAAATGTTTTTTTAAAA-
1 ACTATATATTATAT-ATTTTTAAAAATG-TTTTTAAAAAT
2621914 ACTATATATTATATA
1 ACTATATATTATATA
2621929 AGTTTTTATT
Statistics
Matches: 151, Mismatches: 29, Indels: 36
0.70 0.13 0.17
Matches are distributed among these distances:
32 5 0.03
33 10 0.07
34 6 0.04
35 11 0.07
36 20 0.13
37 12 0.08
38 39 0.26
39 48 0.32
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (38 bp):
ACTATATATTATATATTTTTAAAAATGTTTTTAAAAAT
Found at i:2621819 original size:2 final size:2
Alignment explanation
Indices: 2621814--2621852 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2621804 AAAATATTTT
2621814 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 T
2621853 GTGTTTTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2621987 original size:26 final size:26
Alignment explanation
Indices: 2621947--2622005 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
2621937 TTCAAAATGA
2621947 TTTC-AAAACTATATATTATATA-AGT
1 TTTCAAAAACTATATATTATATATA-T
*
2621972 TTTCAAAAATTATATATTATATATAT
1 TTTCAAAAACTATATATTATATATAT
2621998 TTTCAAAA
1 TTTCAAAA
2622006 TGTTTTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
25 4 0.13
26 26 0.84
27 1 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (26 bp):
TTTCAAAAACTATATATTATATATAT
Found at i:2621997 original size:37 final size:37
Alignment explanation
Indices: 2621970--2622077 Score: 134
Period size: 37 Copynumber: 3.0 Consensus size: 37
2621960 TATTATATAA
* *
2621970 GTTTTCAAAAATTATATATTATATATATTTTCAAAAT
1 GTTTTCAAAAACTATATAATATATATATTTTCAAAAT
*
2622007 GTTTTCAAAAACTATATAATATATACATTTTCAAAAAT
1 GTTTTCAAAAACTATATAATATATATATTTTC-AAAAT
*
2622045 CG-TTT--AAAACTATGTAATATATATA-TTTCAAAA
1 -GTTTTCAAAAACTATATAATATATATATTTTCAAAA
2622078 ATCATTTGCA
Statistics
Matches: 64, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
34 4 0.06
35 4 0.06
36 18 0.28
37 29 0.45
38 8 0.12
39 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (37 bp):
GTTTTCAAAAACTATATAATATATATATTTTCAAAAT
Found at i:2622091 original size:36 final size:35
Alignment explanation
Indices: 2621977--2622108 Score: 113
Period size: 36 Copynumber: 3.6 Consensus size: 35
2621967 TAAGTTTTCA
* * **
2621977 AAAATTATATATTATATATATTTTC-AAAATGTTTT
1 AAAACTATATAATATATATA-TTTCAAAAATCATTT
* *
2622012 CAAAAACTATATAATATATACATTTTCAAAAATCGTTT
1 --AAAACTATATAATATATATA-TTTCAAAAATCATTT
*
2622050 AAAACTATGTAATATATATATTTCAAAAATCATTT
1 AAAACTATATAATATATATATTTCAAAAATCATTT
* *
2622085 GCAAACTCTAATATATATATATAT
1 -AAAACTAT-ATA-ATATATATAT
2622109 ATATATATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
35 14 0.17
36 24 0.30
37 24 0.30
38 18 0.22
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (35 bp):
AAAACTATATAATATATATATTTCAAAAATCATTT
Found at i:2622102 original size:2 final size:2
Alignment explanation
Indices: 2622095--2622119 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2622085 GCAAACTCTA
2622095 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 A
2622120 AGTAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2623059 original size:84 final size:84
Alignment explanation
Indices: 2622673--2623073 Score: 489
Period size: 82 Copynumber: 4.8 Consensus size: 84
2622663 GTGTCATCGT
* * * *
2622673 GCTGAATGGAATCGAACTCGATA-GTTTTTGTTGACAGAT--ACCTTTTCTCG-ATTTAGCTATG
1 GCTGAATGTAATCGAACTCGA-AGGTCTTTGTTGACAGATAGACC--TTCTCGCCTTGAGCTATG
* * * *
2622734 CTGTAATTTGACA-GCCCTTAA
63 CTGTAAATTGATATGCCTTTGA
* * * *
2622755 GCTGAATGGAATCGAACTCGAAGGTCTTCGTTGACAGATAGCCCTTCTCGCCTTGAGCTATCCTG
1 GCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTG
*
2622820 TAAATTGATGTGCCTTTGA
66 TAAATTGATATGCCTTTGA
* * *
2622839 GCTGAA--TAATCGAACTCGAAGGTC-TAGATTGATAGATAGCCCTTCTCGCCTTGAGCTATGCT
1 GCTGAATGTAATCGAACTCGAAGGTCTTTG-TTGACAGATAGACCTTCTCGCCTTGAGCTATGCT
*
2622901 GTAAATTTGATATGGCCTTTTA
65 GTAAA-TTGATAT-GCCTTTGA
* *
2622923 GCTGAATGTAATCGAACTCGAAGGTC-TTGCTGACAGATA-ACCCTTCTCGCCTTGAGTTATGCT
1 GCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGA-CCTTCTCGCCTTGAGCTATGCT
*
2622986 GTAAATTGATATGTCTTTGA
65 GTAAATTGATATGCCTTTGA
2623006 GCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTG
1 GCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTG
2623071 TAA
66 TAA
2623074 TAGGCTTGGG
Statistics
Matches: 280, Mismatches: 26, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
81 3 0.01
82 95 0.34
83 56 0.20
84 71 0.25
85 35 0.12
86 20 0.07
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (84 bp):
GCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAGACCTTCTCGCCTTGAGCTATGCTG
TAAATTGATATGCCTTTGA
Found at i:2624032 original size:2 final size:2
Alignment explanation
Indices: 2624019--2624055 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
2624009 CGTTTAAAAC
2624019 TA TA TA TCA TA TA TA T- TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2624056 ATAAAAAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 28 0.88
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2631930 original size:24 final size:25
Alignment explanation
Indices: 2631885--2631931 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2631875 TCACGAACAA
*
2631885 GCTCATTTGAAAAGTTCGTTTATTG
1 GCTCATTTGAAAAGTTCATTTATTG
*
2631910 GCTCATTT-ATAAGTTCATTTAT
1 GCTCATTTGAAAAGTTCATTTAT
2631932 CAAGTCAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (25 bp):
GCTCATTTGAAAAGTTCATTTATTG
Found at i:2632129 original size:23 final size:23
Alignment explanation
Indices: 2632097--2632169 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
2632087 TTATGAAATA
* *
2632097 TAAACCAACATGTTCACGGTCAC
1 TAAACGAACATGTTCACGGACAC
*
2632120 TAAACGAACATGTT-AGCAGACAC
1 TAAACGAACATGTTCA-CGGACAC
* * * *
2632143 TGAACGAATATGTTCACGAACGC
1 TAAACGAACATGTTCACGGACAC
2632166 TAAA
1 TAAA
2632170 TGAATTGAAC
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.21
Consensus pattern (23 bp):
TAAACGAACATGTTCACGGACAC
Found at i:2635100 original size:27 final size:26
Alignment explanation
Indices: 2635070--2635132 Score: 99
Period size: 27 Copynumber: 2.4 Consensus size: 26
2635060 TTTTCGTTCC
2635070 TAAAATTTTATATGTTTGCCCCCCTCT
1 TAAAATTTTATATGTTTG-CCCCCTCT
*
2635097 TAAAATTGTATATGTTTGCCCCCTCT
1 TAAAATTTTATATGTTTGCCCCCTCT
*
2635123 TAAATTTTTA
1 TAAAATTTTA
2635133 GAAATTCACC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.25, C:0.21, G:0.08, T:0.46
Consensus pattern (26 bp):
TAAAATTTTATATGTTTGCCCCCTCT
Found at i:2636404 original size:22 final size:22
Alignment explanation
Indices: 2636376--2636428 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
2636366 TTTCATTTCG
2636376 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2636398 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
2636420 CGTTGCGAT
1 CGTTGCGAT
2636429 TTTCCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:2636958 original size:39 final size:39
Alignment explanation
Indices: 2636879--2636959 Score: 101
Period size: 40 Copynumber: 2.1 Consensus size: 39
2636869 ACTATTTAAG
* * * *
2636879 GCTCAATCCCACATAGTATTGGGAACAAGTGTTAGTAAT
1 GCTCAATCCCACATAGTATTGGAAACAACTATTAGGAAT
*
2636918 GCTCAAATCCCACATAGTATTGGAAAC-ACTATTGGGAAT
1 GCTC-AATCCCACATAGTATTGGAAACAACTATTAGGAAT
2636957 GCT
1 GCT
2636960 ATTTAAGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (39 bp):
GCTCAATCCCACATAGTATTGGAAACAACTATTAGGAAT
Found at i:2637199 original size:22 final size:22
Alignment explanation
Indices: 2637173--2637266 Score: 104
Period size: 22 Copynumber: 4.4 Consensus size: 22
2637163 AATTTGGAAA
*
2637173 ATCGCAACGACAATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
2637195 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
2637217 ATCGCAACG--AA-TTTTGAAA
1 ATCGCAACGACAACTGTAGACT
* *
2637236 ATCGTAACGATAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
2637258 ATCGCAACG
1 ATCGCAACG
2637267 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 12 0.21
20 2 0.03
21 2 0.03
22 42 0.72
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:2637438 original size:19 final size:19
Alignment explanation
Indices: 2637410--2637454 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2637400 ATTATCTGAG
*
2637410 ATTTTTTATCACTGACATT
1 ATTTTCTATCACTGACATT
* *
2637429 ATTTTCTATCATTGAGATT
1 ATTTTCTATCACTGACATT
2637448 ATTTTCT
1 ATTTTCT
2637455 CTTTACTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (19 bp):
ATTTTCTATCACTGACATT
Found at i:2638538 original size:18 final size:18
Alignment explanation
Indices: 2638515--2638551 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2638505 ATTTTTCCCT
2638515 TTTTATTTA-GAGTATTTA
1 TTTTATTTATGA-TATTTA
2638533 TTTTATTTATGATATTTA
1 TTTTATTTATGATATTTA
2638551 T
1 T
2638552 CATCCATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (18 bp):
TTTTATTTATGATATTTA
Found at i:2639249 original size:2 final size:2
Alignment explanation
Indices: 2639242--2639272 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2639232 ATATGAGATG
2639242 AT AT AT AT -T 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
2639273 TAGTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2643276 original size:3 final size:3
Alignment explanation
Indices: 2643268--2643365 Score: 151
Period size: 3 Copynumber: 32.7 Consensus size: 3
2643258 TTAATATATT
* *
2643268 TAA TAA TAA TAG TAA AAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2643316 TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2643364 TA
1 TA
2643366 TGGATAAAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2644663 original size:113 final size:113
Alignment explanation
Indices: 2643653--2644633 Score: 1685
Period size: 113 Copynumber: 8.7 Consensus size: 113
2643643 AGATAATATC
* * *
2643653 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTT
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2643717 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
2643766 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
2643831 TCATTATGAACCTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
2643879 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2643944 TCATTATGAACTTTCTCTGGTAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
2643992 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2644057 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
2644105 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2644170 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
*
2644218 AAACAAAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2644283 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
2644331 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
2644396 TCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTC
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
*** * *
2644444 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * * *
2644509 TCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTC
66 TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
*** * *
2644557 AGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2644622 TCATTATGAACT
66 TCATTATGAACT
2644634 CTACCTTGCA
Statistics
Matches: 848, Mismatches: 19, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
113 786 0.93
114 62 0.07
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTT
Found at i:2645552 original size:83 final size:83
Alignment explanation
Indices: 2645394--2645872 Score: 725
Period size: 83 Copynumber: 5.8 Consensus size: 83
2645384 GTTCTGTAAT
* *
2645394 TTCTACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
*
2645459 TCCCACTTCAATGATTGA
66 TCCCACTTCAATGATTGG
* * *
2645477 TTATGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCAT
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACATATTCAT
* * *
2645540 CTTCCAAATTCAATGATTGG
64 TTTCCCACTTCAATGATTGG
* *
2645560 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG-ACACATTC-TTC
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATT-
* *
2645623 TTCCAAATTCAATGATTGG
65 TTCCCACTTCAATGATTGG
*
2645642 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
2645707 TCCCACTTCAATGATTGG
66 TCCCACTTCAATGATTGG
*
2645725 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
*
2645790 TCCCACTTCAATGATTGA
66 TCCCACTTCAATGATTGG
* *
2645808 TTATGTCC-AACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAACATATTCATT
1 TTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATT
2645872 T
65 T
2645873 GTTCTATTTA
Statistics
Matches: 368, Mismatches: 21, Indels: 14
0.91 0.05 0.03
Matches are distributed among these distances:
81 1 0.00
82 81 0.22
83 278 0.76
84 8 0.02
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (83 bp):
TTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
TCCCACTTCAATGATTGG
Found at i:2645849 original size:248 final size:247
Alignment explanation
Indices: 2645394--2645864 Score: 750
Period size: 248 Copynumber: 1.9 Consensus size: 247
2645384 GTTCTGTAAT
*
2645394 TTCTACCAAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
2645459 TCCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
66 TCCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* * * *
2645524 CTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAA
131 CTATTGACAAATTCATCTTCCAAATTCAATGATTGATTATGCCAAACCAGATCAGATAACTCAAA
2645589 GAACACTTCCAGAAGATGCTATGACACATTCTTCTTCCAAATTCAATGATTGG
196 GAACACTTCCAGAAGATGCTATGA-ACATTCTTCTTCCAAATTCAATGATTGG
* *
2645642 TTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
1 TTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
* * *
2645707 TCCCACTTCAATGATTGGTTCTG-CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
66 TCCCACTTCAATGATTGATTATGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
* * * *
2645771 GCTA-TGAACATATTCATTTTCCCACTTCAATGATTGATTATGTCC-AACCAGATCAGATAACTC
130 GCTATTG-ACAAATTCATCTTCCAAATTCAATGATTGATTATG-CCAAACCAGATCAGATAACTC
*
2645834 AAATAACACTTCCAGAAGATGCTATGAACAT
193 AAAGAACACTTCCAGAAGATGCTATGAACAT
2645865 ATTCATTTGT
Statistics
Matches: 205, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
247 8 0.04
248 195 0.95
249 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (247 bp):
TTCTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATATTCATTT
TCCCACTTCAATGATTGATTATGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTATTGACAAATTCATCTTCCAAATTCAATGATTGATTATGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAACATTCTTCTTCCAAATTCAATGATTGG
Found at i:2647029 original size:13 final size:12
Alignment explanation
Indices: 2647011--2647052 Score: 57
Period size: 14 Copynumber: 3.2 Consensus size: 12
2647001 ACCCCCTTTC
2647011 TTTTTCTTATTTT
1 TTTTTCTT-TTTT
2647024 TTTTTCTTCTTTTT
1 TTTTTC-T-TTTTT
2647038 TTTTTCTTTTTT
1 TTTTTCTTTTTT
2647050 TTT
1 TTT
2647053 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 8 0.30
13 7 0.26
14 11 0.41
15 1 0.04
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:2647036 original size:10 final size:10
Alignment explanation
Indices: 2647007--2647055 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
2646997 CTTGACCCCC
2647007 TTTCTTTTTCT
1 TTTCTTTTT-T
2647018 TATT-TTTTTT
1 T-TTCTTTTTT
2647028 TCTTCTTTTTTT
1 T-TTC-TTTTTT
2647040 TTTCTTTTTT
1 TTTCTTTTTT
2647050 TTTCTT
1 TTTCTT
2647056 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 16 0.47
11 9 0.26
12 9 0.26
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:2647037 original size:14 final size:13
Alignment explanation
Indices: 2647011--2647052 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
2647001 ACCCCCTTTC
*
2647011 TTTTTCTTATTTT
1 TTTTTCTTTTTTT
2647024 TTTTTCTTCTTTTT
1 TTTTTCTT-TTTTT
2647038 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
2647051 TT
1 TT
2647053 CTTCAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 15 0.56
14 12 0.44
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Found at i:2659192 original size:27 final size:28
Alignment explanation
Indices: 2659154--2659208 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
2659144 GGATTTTCTC
2659154 TTTTTTTTTTCTATATCTCT-TCTCGTT
1 TTTTTTTTTTCTATATCTCTGTCTCGTT
* *
2659181 TTTTTTTTTTCTGTCTCTCTGTCTCGTT
1 TTTTTTTTTTCTATATCTCTGTCTCGTT
2659209 GTATATCTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.04, C:0.20, G:0.07, T:0.69
Consensus pattern (28 bp):
TTTTTTTTTTCTATATCTCTGTCTCGTT
Found at i:2659682 original size:3 final size:3
Alignment explanation
Indices: 2659664--2659754 Score: 109
Period size: 3 Copynumber: 31.7 Consensus size: 3
2659654 TTTAATATAT
* *
2659664 TAA TAA TAG TAA -AA TAA TAA TAA TAA GAA TAA T-A TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
2659709 TAA TAT TAA TAA TGA TAA TAA TAT TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2659755 TATGGATAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 8 0.11
3 66 0.89
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2662881 original size:55 final size:56
Alignment explanation
Indices: 2662781--2662889 Score: 202
Period size: 55 Copynumber: 1.9 Consensus size: 56
2662771 GTCGATACAA
2662781 AATACAATTATTTGCAATGCTACTAAAGCAAATGTTATCAAGTGGAATTTAGAAAAG
1 AATACAATTATTTGCAATGCTAC-AAAGCAAATGTTATCAAGTGGAATTTAGAAAAG
2662838 AATACAATTATTTGCAATGCTA-AAAGCAAATGTTATCAAGTGGAATTTAGAA
1 AATACAATTATTTGCAATGCTACAAAGCAAATGTTATCAAGTGGAATTTAGAA
2662890 TTTCCAGACC
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
55 30 0.58
57 22 0.42
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.30
Consensus pattern (56 bp):
AATACAATTATTTGCAATGCTACAAAGCAAATGTTATCAAGTGGAATTTAGAAAAG
Found at i:2668888 original size:4 final size:4
Alignment explanation
Indices: 2668881--2669043 Score: 308
Period size: 4 Copynumber: 40.8 Consensus size: 4
2668871 TAGCTATCTA
*
2668881 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TATG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
*
2668929 TCTG CCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
2668977 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
1 TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG TCTG
2669025 TCTG TCTG TCTG TCTG TCT
1 TCTG TCTG TCTG TCTG TCT
2669044 ATCTATCTAT
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 155 1.00
ACGTcount: A:0.01, C:0.25, G:0.25, T:0.50
Consensus pattern (4 bp):
TCTG
Found at i:2669072 original size:8 final size:8
Alignment explanation
Indices: 2669061--2669354 Score: 237
Period size: 8 Copynumber: 35.8 Consensus size: 8
2669051 TATCTATCTA
2669061 TCCATCCG
1 TCCATCCG
2669069 TCCATCCG
1 TCCATCCG
2669077 TCCATCCG
1 TCCATCCG
*
2669085 TCTATCCG
1 TCCATCCG
*
2669093 TCTATCCG
1 TCCATCCG
2669101 TCCATCCG
1 TCCATCCG
*
2669109 TCCATCCA
1 TCCATCCG
*
2669117 TCCGTCCG
1 TCCATCCG
2669125 TCCATCCG
1 TCCATCCG
*
2669133 TCTATCCATCGG
1 ----TCCATCCG
*
2669145 TCTATCCG
1 TCCATCCG
*
2669153 TCCGTCCG
1 TCCATCCG
*
2669161 TCTATCCG
1 TCCATCCG
*
2669169 TCCGTCCG
1 TCCATCCG
*
2669177 TCTATCCG
1 TCCATCCG
*
2669185 TCCGTCTATCCA
1 T-C--C-ATCCG
*
2669197 TCCGTCCG
1 TCCATCCG
2669205 TCCATCCG
1 TCCATCCG
*
2669213 TCCGTCCG
1 TCCATCCG
* **
2669221 TCCGTCTA
1 TCCATCCG
2669229 TCCATCCG
1 TCCATCCG
*
2669237 TCCATCCA
1 TCCATCCG
*
2669245 TCCGTCCG
1 TCCATCCG
2669253 TCCATCCG
1 TCCATCCG
* *
2669261 TCCGTCCA
1 TCCATCCG
*
2669269 CCCATCCG
1 TCCATCCG
**
2669277 TCCATCTA
1 TCCATCCG
*
2669285 TCCATCCA
1 TCCATCCG
*
2669293 TCCATCCA
1 TCCATCCG
*
2669301 TCCATCCA
1 TCCATCCG
*
2669309 TCCATCCA
1 TCCATCCG
*
2669317 TCCATCCA
1 TCCATCCG
*
2669325 TCCATCCA
1 TCCATCCG
*
2669333 TCCATCCA
1 TCCATCCG
*
2669341 TCCATCCA
1 TCCATCCG
2669349 TCCATC
1 TCCATC
2669355 TATCTATAGT
Statistics
Matches: 237, Mismatches: 41, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
8 222 0.94
9 2 0.01
11 1 0.00
12 12 0.05
ACGTcount: A:0.15, C:0.47, G:0.11, T:0.28
Consensus pattern (8 bp):
TCCATCCG
Found at i:2669075 original size:12 final size:12
Alignment explanation
Indices: 2669061--2669354 Score: 245
Period size: 12 Copynumber: 24.8 Consensus size: 12
2669051 TATCTATCTA
* *
2669061 TCCATCCGTCCA
1 TCCATCCATCCG
*
2669073 TCCGTCCATCCG
1 TCCATCCATCCG
* * **
2669085 TCTATCCGTCTA
1 TCCATCCATCCG
*
2669097 TCCGTCCATCCG
1 TCCATCCATCCG
2669109 TCCATCCATCCG
1 TCCATCCATCCG
*
2669121 TCCGTCCATCCG
1 TCCATCCATCCG
* *
2669133 TCTATCCATCGG
1 TCCATCCATCCG
* *
2669145 TCTATCCGTCCG
1 TCCATCCATCCG
* *
2669157 TCCGTCTATCCG
1 TCCATCCATCCG
*
2669169 ----TCCGTCCG
1 TCCATCCATCCG
* *
2669177 TCTATCCGTCCG
1 TCCATCCATCCG
*
2669189 TCTATCCATCCG
1 TCCATCCATCCG
*
2669201 TCCGTCCATCCG
1 TCCATCCATCCG
* *
2669213 TCCGTCCGTCCG
1 TCCATCCATCCG
*
2669225 TCTATCCATCCG
1 TCCATCCATCCG
2669237 TCCATCCATCCG
1 TCCATCCATCCG
*
2669249 TCCGTCCATCCG
1 TCCATCCATCCG
* * *
2669261 TCCGTCCACCCA
1 TCCATCCATCCG
* **
2669273 TCCGTCCATCTA
1 TCCATCCATCCG
*
2669285 TCCATCCATCCA
1 TCCATCCATCCG
*
2669297 TCCATCCATCCA
1 TCCATCCATCCG
*
2669309 TCCATCCATCCA
1 TCCATCCATCCG
*
2669321 TCCATCCATCCA
1 TCCATCCATCCG
*
2669333 TCCATCCATCCA
1 TCCATCCATCCG
2669345 TCCATCCATC
1 TCCATCCATC
2669355 TATCTATAGT
Statistics
Matches: 237, Mismatches: 41, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
8 6 0.03
12 231 0.97
ACGTcount: A:0.15, C:0.47, G:0.11, T:0.28
Consensus pattern (12 bp):
TCCATCCATCCG
Found at i:2672721 original size:22 final size:22
Alignment explanation
Indices: 2672693--2672747 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2672683 TTGAGTATAA
*
2672693 TGCTTTGGATTCATCAGCTTTC
1 TGCTTTGAATTCATCAGCTTTC
2672715 TGCTTTGAATTCATCAGCTTTC
1 TGCTTTGAATTCATCAGCTTTC
2672737 TGCTTTGAATT
1 TGCTTTGAATT
2672748 GTGTAATGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (22 bp):
TGCTTTGAATTCATCAGCTTTC
Found at i:2673247 original size:8 final size:7
Alignment explanation
Indices: 2673234--2673293 Score: 60
Period size: 6 Copynumber: 9.1 Consensus size: 7
2673224 GTGATGGATG
2673234 AATTTTT
1 AATTTTT
2673241 AAATTTTT
1 -AATTTTT
2673249 AA-TTTT
1 AATTTTT
2673255 AA-TTTT
1 AATTTTT
2673261 AA-TTTT
1 AATTTTT
2673267 AA-TTTT
1 AATTTTT
2673273 AA-TTTT
1 AATTTTT
2673279 AA-TTTT
1 AATTTTT
2673285 AATCTTTT
1 AAT-TTTT
2673293 A
1 A
2673294 TCTAAATCCG
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
6 36 0.72
7 2 0.04
8 12 0.24
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (7 bp):
AATTTTT
Found at i:2673256 original size:6 final size:6
Alignment explanation
Indices: 2673245--2673287 Score: 86
Period size: 6 Copynumber: 7.2 Consensus size: 6
2673235 ATTTTTAAAT
2673245 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA T
2673288 CTTTTATCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:2685053 original size:17 final size:18
Alignment explanation
Indices: 2685031--2685072 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2685021 AACCAAAAAA
*
2685031 AAATAAAATG-ATAATGC
1 AAATAAAATGAATAAAGC
2685048 AAAT-AAATGAATAAAGC
1 AAATAAAATGAATAAAGC
2685065 AAATAAAA
1 AAATAAAA
2685073 GGAAGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 14 0.64
18 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (18 bp):
AAATAAAATGAATAAAGC
Found at i:2685104 original size:13 final size:13
Alignment explanation
Indices: 2685086--2685111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2685076 AGATAAAAAG
2685086 ATAAAAATAGAAA
1 ATAAAAATAGAAA
2685099 ATAAAAATAGAAA
1 ATAAAAATAGAAA
2685112 GAAAGTAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
ATAAAAATAGAAA
Found at i:2685138 original size:32 final size:34
Alignment explanation
Indices: 2685102--2685173 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 34
2685092 ATAGAAAATA
* *
2685102 AAAATAGAAAGAAAGTAGATA-AATA-A-ATAAGT
1 AAAATAGAAAAAAAGT-GAAAGAATATATATAAGT
*
2685134 AAAATATAAAAAAAGTGAAAGAATATATATAAGT
1 AAAATAGAAAAAAAGTGAAAGAATATATATAAGT
2685168 AAAATA
1 AAAATA
2685174 ATAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.09
32 18 0.53
33 1 0.03
34 12 0.35
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (34 bp):
AAAATAGAAAAAAAGTGAAAGAATATATATAAGT
Found at i:2685272 original size:2 final size:2
Alignment explanation
Indices: 2685259--2685325 Score: 79
Period size: 2 Copynumber: 34.5 Consensus size: 2
2685249 AAAATAGGAA
*
2685259 AT AT AA AT AT AT AT AT AT AT AT AT A- AT A- AT ACT A- AT GAT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT -AT AT
2685299 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
2685326 ATTAATAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
1 4 0.07
2 49 0.86
3 4 0.07
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:2693774 original size:43 final size:42
Alignment explanation
Indices: 2693726--2693949 Score: 216
Period size: 43 Copynumber: 5.2 Consensus size: 42
2693716 AAGGAAATTA
*
2693726 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATATGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* * * *
2693769 GCGGCGTTTATTCCAAAAAAATGCAGCTATAGATATGACTTTTT
1 GCGGCGTTTGTTCC--AAAAACGCCGCTATAGATATGACCTTTT
* * *
2693813 GCGGTGTTTGTTCCAAAAACG-CTCTATAGATATCAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* ** * * * *
2693855 GTGGTATTTGTTCCAAAAACACCGCTATAAATATCAACATTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* * * *
2693898 GCGGCGTTTGTTCCAAAAATGTCGCTATAGATCTTGACCTATT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT-ATGACCTTTT
2693941 GCGGCGTTT
1 GCGGCGTTT
2693950 TTGGTTCTCA
Statistics
Matches: 147, Mismatches: 29, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
41 10 0.07
42 32 0.22
43 67 0.46
44 38 0.26
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:2699712 original size:20 final size:20
Alignment explanation
Indices: 2699687--2699779 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
2699677 TTTTCCCAAT
2699687 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
2699707 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
2699727 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
2699748 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
2699769 TCGCAATGCGA
1 TCGCAATGCGA
2699780 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:2699729 original size:41 final size:41
Alignment explanation
Indices: 2699684--2699779 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
2699674 CGATTTTCCC
2699684 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
2699725 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
2699766 AAATCGCAATGCGA
1 AATTCGCAATGCGA
2699780 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:2699733 original size:21 final size:20
Alignment explanation
Indices: 2699687--2699779 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2699677 TTTTCCCAAT
*
2699687 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
2699707 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
2699727 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
2699748 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
2699769 TCGCAATGCGA
1 TCGCAATGCGA
2699780 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:2699793 original size:20 final size:20
Alignment explanation
Indices: 2699768--2699861 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2699758 AATTGGGAAA
*
2699768 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
2699788 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
2699809 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
2699829 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
2699849 TTCGCAACGCGAT
1 ATCGCAACGCGAT
2699862 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2699842 original size:41 final size:41
Alignment explanation
Indices: 2699765--2699842 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
2699755 GCGAATTGGG
* * **
2699765 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
2699806 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
2699843 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:2700343 original size:19 final size:19
Alignment explanation
Indices: 2700300--2700365 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
2700290 CGAGAATGAG
* *
2700300 AATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATAAA
*
2700320 TATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
**
2700339 AATCGCAAACGCGAAACCAA
1 AATCGC-AACGCGAAATAAA
2700359 AATCGCA
1 AATCGCA
2700366 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:2700443 original size:19 final size:19
Alignment explanation
Indices: 2700361--2700432 Score: 117
Period size: 20 Copynumber: 3.7 Consensus size: 19
2700351 GAAACCAAAA
*
2700361 TCGCATTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
2700381 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2700400 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
2700420 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2700433 GTCTGGTCGC
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2700443 original size:39 final size:40
Alignment explanation
Indices: 2700366--2700443 Score: 115
Period size: 39 Copynumber: 2.0 Consensus size: 40
2700356 CAAAATCGCA
* *
2700366 TTGCGATTTTCATTTTCGCGTTGCGATTTTCATTTCGCGG
1 TTGCGATTTTCATTTTCGCGTTGCGATTGTCATGTCGCGG
2700406 TTGCGATTTTCA-TTTCGCGTTGCGATTGTC-TGGTCGCG
1 TTGCGATTTTCATTTTCGCGTTGCGATTGTCAT-GTCGCG
2700444 ATAGTCCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 1 0.03
39 22 0.63
40 12 0.34
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.45
Consensus pattern (40 bp):
TTGCGATTTTCATTTTCGCGTTGCGATTGTCATGTCGCGG
Found at i:2700463 original size:33 final size:33
Alignment explanation
Indices: 2700415--2700498 Score: 116
Period size: 33 Copynumber: 2.5 Consensus size: 33
2700405 GTTGCGATTT
* *
2700415 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
2700448 TCCATTTCGCG-TGCGATTCTCTCGTTGCGATAG
1 T-CATTTCGCGTTGCGATTCTCTCGTCGCGATAG
2700481 TCATTTCCGCGTTGCGAT
1 TCATTT-CGCGTTGCGAT
2700499 CTCATATCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.11
33 25 0.56
34 15 0.33
ACGTcount: A:0.12, C:0.25, G:0.26, T:0.37
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:2700510 original size:38 final size:33
Alignment explanation
Indices: 2700405--2700525 Score: 102
Period size: 33 Copynumber: 3.5 Consensus size: 33
2700395 TCATTTCGCG
** * *
2700405 GTTGCGATTTTCATTT-CGCGTTGCGATTGTCTG
1 GTTGCGATAGTCATTTCCGCG-TGCGATTCTCTC
*
2700438 GTCGCGATAGTCCATTT-CGCGTGCGATTCTCTC
1 GTTGCGATAGT-CATTTCCGCGTGCGATTCTCTC
2700471 GTTGCGATAGTCATTTCCGCGTTGCGATCTCATATCTC
1 GTTGCGATAGTCATTTCCGCG-TGCGAT-TC---TCTC
**
2700509 GTTGCGATTTTCATTTC
1 GTTGCGATAGTCATTTC
2700526 AACCAGAAAG
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
32 5 0.07
33 32 0.44
34 15 0.21
35 2 0.03
38 19 0.26
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.40
Consensus pattern (33 bp):
GTTGCGATAGTCATTTCCGCGTGCGATTCTCTC
Found at i:2700513 original size:18 final size:19
Alignment explanation
Indices: 2700467--2700516 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2700457 CGTGCGATTC
* *
2700467 TCTCGTTGCGATAGTCATT
1 TCTCGTTGCGATACTCATA
*
2700486 TCCGCGTTGCGAT-CTCATA
1 T-CTCGTTGCGATACTCATA
2700505 TCTCGTTGCGAT
1 TCTCGTTGCGAT
2700517 TTTCATTTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.38
19 6 0.23
20 10 0.38
ACGTcount: A:0.14, C:0.26, G:0.22, T:0.38
Consensus pattern (19 bp):
TCTCGTTGCGATACTCATA
Done.