Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001700.1 Hibiscus syriacus cultivar Beakdansim tig00003398_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: 2632955
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 11
Found at i:470604 original size:165 final size:161
Alignment explanation
Indices: 470298--470606 Score: 381
Period size: 165 Copynumber: 1.9 Consensus size: 161
470288 TTTATGAAGA
* * * * *
470298 TCGAGTTCTATACTCTCTGATGGAATGGAGAGCGGACCCGTTTGTTGAAGATCGAGTTCTATACT
1 TCGAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGATCGAGTTCTATACT
* ** * * * * * * *
470363 CTCTGATGGAATAGAGGGCAGACCCGTTTGTTGAAGAGTGTTCGAGTTCTATACTCTCTGAAGGA
66 CCCTGAACGAATAGAGGGAACACACATTTGCTGAAGAGTATTCGAGTTCTATACTCCCTGAAGGA
470428 ATAGAGAGTGGACCCATTTGTTGAAGATTGT
131 ATAGAGAGTGGACCCATTTGTTGAAGATTGT
470459 TCGAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGATTGTTCGAG-TCTT
1 TCGAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGA----TCGAGTTC-T
*
470523 ATACTCCCTGAACGAATAG-GGAGAACACACATTTGCTGAAGATTATTCGAG-TCTTATACTCCC
61 ATACTCCCTGAACGAATAGAGG-GAACACACATTTGCTGAAGAGTATTCGAGTTC-TATACTCCC
*
470586 TGAAGGAATAGGGAGTGGACC
124 TGAAGGAATAGAGAGTGGACC
470607 AGTCATTCGA
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
161 46 0.37
164 6 0.05
165 72 0.58
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (161 bp):
TCGAGTTCTACACTCTCTGAAGGAATAGAGAGCGGACACGTTTATTGAAGATCGAGTTCTATACT
CCCTGAACGAATAGAGGGAACACACATTTGCTGAAGAGTATTCGAGTTCTATACTCCCTGAAGGA
ATAGAGAGTGGACCCATTTGTTGAAGATTGT
Found at i:471623 original size:8 final size:8
Alignment explanation
Indices: 471610--471638 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
471600 TGTGTAGCCG
471610 AGAGAGAT
1 AGAGAGAT
471618 AGAGAGAT
1 AGAGAGAT
471626 AGAGAG-T
1 AGAGAGAT
471633 AGAGAG
1 AGAGAG
471639 CTTGAGCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.41, T:0.10
Consensus pattern (8 bp):
AGAGAGAT
Found at i:475476 original size:28 final size:27
Alignment explanation
Indices: 475444--475524 Score: 67
Period size: 28 Copynumber: 3.0 Consensus size: 27
475434 AAATATAACA
475444 AATTATTATAAAATAAATTATTTTAAT
1 AATTATTATAAAATAAATTATTTTAAT
** * * *
475471 CAATTAAAATATAATAAATGATTAT-AT
1 -AATTATTATAAAATAAATTATTTTAAT
* *
475498 -ATATATTATTAAATATATTATTTTAAT
1 AAT-TATTATAAAATAAATTATTTTAAT
475525 TATTTACTAA
Statistics
Matches: 39, Mismatches: 12, Indels: 5
0.70 0.21 0.09
Matches are distributed among these distances:
25 2 0.05
26 14 0.36
27 4 0.10
28 19 0.49
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
AATTATTATAAAATAAATTATTTTAAT
Found at i:483834 original size:18 final size:18
Alignment explanation
Indices: 483813--483861 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
483803 GTTTGACCCG
*
483813 TTGACCCAACCCGATCTA
1 TTGACCCAACCCGATCCA
*
483831 TTGACCCAACCCGATCCG
1 TTGACCCAACCCGATCCA
*
483849 TTGACCCGACCCG
1 TTGACCCAACCCG
483862 TTGACCCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.43, G:0.16, T:0.18
Consensus pattern (18 bp):
TTGACCCAACCCGATCCA
Found at i:483855 original size:13 final size:12
Alignment explanation
Indices: 483839--483892 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 12
483829 TATTGACCCA
483839 ACCCGATCCGTTG
1 ACCCGA-CCGTTG
483852 ACCCGACCCGTTG
1 ACCCGA-CCGTTG
*
483865 ACCCAACACGTTG
1 ACCCGAC-CGTTG
*
483878 ACTCGACCGTTG
1 ACCCGACCGTTG
483890 ACC
1 ACC
483893 GTTTACCGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 8 0.23
13 27 0.77
ACGTcount: A:0.20, C:0.41, G:0.20, T:0.19
Consensus pattern (12 bp):
ACCCGACCGTTG
Found at i:484084 original size:58 final size:58
Alignment explanation
Indices: 483901--484092 Score: 158
Period size: 58 Copynumber: 3.3 Consensus size: 58
483891 CCGTTTACCG
* * * * * * **
483901 GGTGGTATTTTGGTAATTA-TTTTAAAATTGGTGACATATTGGGAATTAATTCGAAAAT
1 GGTGCTATTTTTGTAATTATTTTTAAAA-TGGTGATATTTTGGTAATTATTTTAAAAAT
* * * * * *
483959 GGTGCTATTTTTGTAATTTTTTTTAACAA--ATGCTATTTTCGTATTTTTTATTATAAAA-
1 GGTGCTATTTTTGTAATTATTTTTAA-AATGGTGATATTTTGGTAATTATT-TTA-AAAAT
* * * *
484017 AGTGATATTTTAGTAAATATTTTTAAAATGGTGATATTTTGGTAATTATTTTAAAAAT
1 GGTGCTATTTTTGTAATTATTTTTAAAATGGTGATATTTTGGTAATTATTTTAAAAAT
484075 GGTGCTATTTTTGTAATT
1 GGTGCTATTTTTGTAATT
484093 TTAAAAAAAT
Statistics
Matches: 99, Mismatches: 28, Indels: 14
0.70 0.20 0.10
Matches are distributed among these distances:
57 17 0.17
58 55 0.56
59 25 0.25
60 2 0.02
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (58 bp):
GGTGCTATTTTTGTAATTATTTTTAAAATGGTGATATTTTGGTAATTATTTTAAAAAT
Found at i:484091 original size:29 final size:29
Alignment explanation
Indices: 483901--484092 Score: 133
Period size: 29 Copynumber: 6.6 Consensus size: 29
483891 CCGTTTACCG
* *
483901 GGTGGTATTTTGGTAATTATTTTAAAATT
1 GGTGCTATTTTGGTAATTATTTTAAAAAT
* * * **
483930 GGTGAC-ATATTGGGAATTAATTCGAAAAT
1 GGTG-CTATTTTGGTAATTATTTTAAAAAT
* *
483959 GGTGCTATTTTTGTAATTTTTTTTAACAAA-
1 GGTGCTATTTTGGTAA-TTATTTTAA-AAAT
* * *
483989 --TGCTATTTTCGTATTTTTTATTATAAAA-
1 GGTGCTATTTTGGTAATTATT-TTA-AAAAT
* * * * *
484017 AGTGATATTTTAGTAAATATTTTTAAAAT
1 GGTGCTATTTTGGTAATTATTTTAAAAAT
*
484046 GGTGATATTTTGGTAATTATTTTAAAAAT
1 GGTGCTATTTTGGTAATTATTTTAAAAAT
*
484075 GGTGCTATTTTTGTAATT
1 GGTGCTATTTTGGTAATT
484093 TTAAAAAAAT
Statistics
Matches: 126, Mismatches: 28, Indels: 18
0.73 0.16 0.10
Matches are distributed among these distances:
27 5 0.04
28 23 0.18
29 76 0.60
30 19 0.15
31 3 0.02
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (29 bp):
GGTGCTATTTTGGTAATTATTTTAAAAAT
Found at i:484101 original size:29 final size:29
Alignment explanation
Indices: 484006--484102 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 29
483996 TTCGTATTTT
* *
484006 TTATTATAAAAA--GTGATATTTTAGTAA
1 TTATTAAAAAAATGGTGATATTTTGGTAA
* ***
484033 ATATTTTTAAAATGGTGATATTTTGGTAA
1 TTATTAAAAAAATGGTGATATTTTGGTAA
** * *
484062 TTATTTTAAAAATGGTGCTATTTTTGTAA
1 TTATTAAAAAAATGGTGATATTTTGGTAA
484091 TT-TTAAAAAAAT
1 TTATTAAAAAAAT
484103 ATATAAATGT
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 9 0.16
28 8 0.14
29 41 0.71
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.47
Consensus pattern (29 bp):
TTATTAAAAAAATGGTGATATTTTGGTAA
Found at i:485093 original size:42 final size:41
Alignment explanation
Indices: 485034--485194 Score: 223
Period size: 42 Copynumber: 3.8 Consensus size: 41
485024 GAAGTATTAT
*
485034 CAGGTCACTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
485076 CAGGTCCCTTTGCTGTGTGTGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTG-CAAGGTAAGCCTTACAGTTTAC
* * *
485118 CAAGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
485160 CAGGTCCCTTTGCAGTGTGCAAGGATAAACCTTAC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTAC
485195 TGTAACACCC
Statistics
Matches: 106, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
41 4 0.04
42 102 0.96
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.31
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:490657 original size:18 final size:18
Alignment explanation
Indices: 490636--490682 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
490626 CCGACTGAAA
*
490636 CTGTTTACCCGACCCGAC
1 CTGTTGACCCGACCCGAC
*
490654 CTGTTGACCCGACCTGAC
1 CTGTTGACCCGACCCGAC
*
490672 CCGTTGACCCG
1 CTGTTGACCCG
490683 TTGACCATTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.15, C:0.43, G:0.21, T:0.21
Consensus pattern (18 bp):
CTGTTGACCCGACCCGAC
Found at i:500224 original size:23 final size:20
Alignment explanation
Indices: 500170--500250 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
500160 TTTTGGTGTA
*
500170 GAGGGAATCGATACCCCCAT
1 GAGGGAATCGATTCCCCCAT
* *
500190 GAGGGAACCGATTCCCCCTTT
1 GAGGGAATCGATTCCCCC-AT
500211 GAAGAGGAATCGATTCCCCCA-
1 G-AG-GGAATCGATTCCCCCAT
* *
500232 CAGGGGAATCGATACCCCC
1 GA-GGGAATCGATTCCCCC
500251 TGGGGTTCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 31 0.62
21 3 0.06
22 2 0.04
23 14 0.28
ACGTcount: A:0.27, C:0.32, G:0.25, T:0.16
Consensus pattern (20 bp):
GAGGGAATCGATTCCCCCAT
Found at i:506964 original size:12 final size:13
Alignment explanation
Indices: 506939--506967 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
506929 GTTACAACCC
506939 GACCCGACCCGTT
1 GACCCGACCCGTT
506952 GACCCGA-CCGTT
1 GACCCGACCCGTT
506964 GACC
1 GACC
506968 GGGTGGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:507054 original size:29 final size:28
Alignment explanation
Indices: 507022--507159 Score: 127
Period size: 27 Copynumber: 4.9 Consensus size: 28
507012 AATTAATTCG
*
507022 AAAAGGGTGCTATTTTTGTAATTTTTTT
1 AAAAAGGTGCTATTTTTGTAATTTTTTT
* **
507050 AAAAA-ATGCTATTTTCATAATTTTTTT
1 AAAAAGGTGCTATTTTTGTAATTTTTTT
* * *
507077 ATAAA-GTGATATTTTTAGTAAATATTTTT
1 AAAAAGGTGCTATTTTT-GT-AATTTTTTT
* * * *
507106 AAAATGGTGATATTTTGGTAATTATTTT
1 AAAAAGGTGCTATTTTTGTAATTTTTTT
*
507134 AAAAATGGTGCTATATTTGTAATTTT
1 AAAAA-GGTGCTATTTTTGTAATTTT
507160 AAAAAAATAT
Statistics
Matches: 86, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
27 31 0.36
28 16 0.19
29 29 0.34
30 10 0.12
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (28 bp):
AAAAAGGTGCTATTTTTGTAATTTTTTT
Found at i:507116 original size:30 final size:29
Alignment explanation
Indices: 507082--507143 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
507072 TTTTTATAAA
*
507082 GTGATATTTTTAGTAAATATTTTTAAAATG
1 GTGATA-TTTTAGTAAATATTTTAAAAATG
* *
507112 GTGATATTTTGGTAATTATTTTAAAAATG
1 GTGATATTTTAGTAAATATTTTAAAAATG
507141 GTG
1 GTG
507144 CTATATTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (29 bp):
GTGATATTTTAGTAAATATTTTAAAAATG
Found at i:508218 original size:42 final size:41
Alignment explanation
Indices: 508113--508237 Score: 151
Period size: 42 Copynumber: 3.0 Consensus size: 41
508103 GAAGTATTAT
*
508113 CAGGTCCCTTTGCTGTGTGCGAAAGTAAGCCTTACAAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTAC-AGTTTAC
* * * *
508156 CATGTCCATTTGTTGTGTGCAATGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
508198 CAGGTCCCTTTGCTATGTGCAAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
508238 TCCTAGGCTC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 40 0.57
43 28 0.40
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:508261 original size:43 final size:42
Alignment explanation
Indices: 508113--508261 Score: 106
Period size: 43 Copynumber: 3.5 Consensus size: 42
508103 GAAGTATTAT
* * * * *
508113 CAGGTCCCTTTGCTGTGTGCGAA-AGTAAGCCTTACAAGTTTAC
1 CAGGTCCCTCTGCTATGTGC-AATGGTAAACCTTAC-AGTTTCC
* * * * * *
508156 CATGTCCATTTGTTGTGTGCAATGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTCTGCTATGTGCAATGGTAAACCTTACAGTTTCC
*
508198 CAGGTCCCTTTGCTATGTGCAA-GGATAAACCTTACAGTTTTCC
1 CAGGTCCCTCTGCTATGTGCAATGG-TAAACCTTACAG-TTTCC
* *
508241 TAGG-CTCCTCTGCTTTGTGCA
1 CAGGTC-CCTCTGCTATGTGCA
508262 CAGGTTAAGC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.02
42 38 0.43
43 49 0.55
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.34
Consensus pattern (42 bp):
CAGGTCCCTCTGCTATGTGCAATGGTAAACCTTACAGTTTCC
Found at i:508275 original size:43 final size:42
Alignment explanation
Indices: 508181--508275 Score: 95
Period size: 43 Copynumber: 2.2 Consensus size: 42
508171 TGTGCAATGG
*
508181 TAAGCCTTACAGTTTCCCAGGTCCCTTTGCTATGTGCAAGGAT
1 TAAG-CTTACAGTTTCCCAGGTCCCTCTGCTATGTGCAAGGAT
* * * *
508224 AAACCTTACAGTTTTCCTAGG-CTCCTCTGCTTTGTGCACAGG-T
1 TAAGCTTACAG-TTTCCCAGGTC-CCTCTGCTATGTGCA-AGGAT
508267 TAAGCTTAC
1 TAAGCTTAC
508276 TGGTGTATAG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
42 8 0.19
43 31 0.74
44 3 0.07
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (42 bp):
TAAGCTTACAGTTTCCCAGGTCCCTCTGCTATGTGCAAGGAT
Found at i:508828 original size:20 final size:20
Alignment explanation
Indices: 508781--508829 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
508771 GGATCAAACC
* *
508781 GAGTCAAACTGAATAGGTTT
1 GAGTCAACCTGAACAGGTTT
508801 GAGTCAACCTGAACAGGTTT
1 GAGTCAACCTGAACAGGTTT
508821 GAGTCAACC
1 GAGTCAACC
508830 CAAATCAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (20 bp):
GAGTCAACCTGAACAGGTTT
Found at i:508840 original size:20 final size:20
Alignment explanation
Indices: 508795--508842 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
508785 CAAACTGAAT
**
508795 AGGTTTGAGTCAACCTGAAC
1 AGGTTTGAGTCAACCCAAAC
508815 AGGTTTGAGTCAACCCAAATC
1 AGGTTTGAGTCAACCCAAA-C
508836 A-GTTTGA
1 AGGTTTGA
508843 ACCTTTGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (20 bp):
AGGTTTGAGTCAACCCAAAC
Found at i:510923 original size:39 final size:39
Alignment explanation
Indices: 510854--510971 Score: 116
Period size: 39 Copynumber: 3.0 Consensus size: 39
510844 TACAGCTAGT
* *
510854 GTAAGTCCTTATCT-CAGGCTCATTTTCTTTGTGCATAGG
1 GTAAGTCCTTAGCTACA-GCTCATTTGCTTTGTGCATAGG
* * *
510893 GTAAGTCCTTA-CTACAGACTCCTTTGCTTTGTGCACATG
1 GTAAGTCCTTAGCTACAG-CTCATTTGCTTTGTGCATAGG
* * *
510932 ATAAGTTCTTAGCATA-AGCTCATTTGCTTCGTGCATAGG
1 GTAAGTCCTTAGC-TACAGCTCATTTGCTTTGTGCATAGG
510971 G
1 G
510972 GAAAACCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
38 3 0.05
39 56 0.88
40 3 0.05
41 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (39 bp):
GTAAGTCCTTAGCTACAGCTCATTTGCTTTGTGCATAGG
Found at i:511035 original size:40 final size:40
Alignment explanation
Indices: 510949--511036 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
510939 CTTAGCATAA
* *
510949 GCTCA-TTTGCTTCGTGCATAGGGGAAAACCTTATCGCAT
1 GCTCATTTTGCATCATGCATAGGGGAAAACCTTATCGCAT
* * *
510988 GCCCATTTTGCATCATGCATAGGGGAAAACTTTA-CTGTAT
1 GCTCATTTTGCATCATGCATAGGGGAAAACCTTATC-GCAT
511028 GCTCATTTT
1 GCTCATTTT
511037 CTTTGTCCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 5 0.12
40 36 0.88
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (40 bp):
GCTCATTTTGCATCATGCATAGGGGAAAACCTTATCGCAT
Found at i:511206 original size:15 final size:17
Alignment explanation
Indices: 511169--511216 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 17
511159 TAGAGGGTAT
511169 TACTATTGTTTTAAAAA
1 TACTATTGTTTTAAAAA
*
511186 TA-TATT-TTTT-AAAC
1 TACTATTGTTTTAAAAA
511200 TACTATTGTTTTTAAAA
1 TACTATTG-TTTTAAAA
511217 GATTTGTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 4 0.15
17 6 0.23
18 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (17 bp):
TACTATTGTTTTAAAAA
Found at i:511213 original size:17 final size:17
Alignment explanation
Indices: 511169--511216 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
511159 TAGAGGGTAT
*
511169 TACTATTGTTTTAAAAA
1 TACTATTGTTTTTAAAA
*
511186 TA-TA-T-TTTTTAAAC
1 TACTATTGTTTTTAAAA
511200 TACTATTGTTTTTAAAA
1 TACTATTGTTTTTAAAA
511217 GATTTGTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
14 9 0.36
15 3 0.12
16 3 0.12
17 10 0.40
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (17 bp):
TACTATTGTTTTTAAAA
Found at i:511323 original size:15 final size:15
Alignment explanation
Indices: 511300--511338 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
511290 TGAATGTTTC
*
511300 CTTCGGACTGTAAGT
1 CTTCTGACTGTAAGT
511315 CTTCTGACTGTAAGT
1 CTTCTGACTGTAAGT
*
511330 ATTCTGACT
1 CTTCTGACT
511339 ATTACCTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (15 bp):
CTTCTGACTGTAAGT
Found at i:513012 original size:61 final size:63
Alignment explanation
Indices: 512922--513049 Score: 179
Period size: 68 Copynumber: 2.0 Consensus size: 63
512912 AACTAAAACC
512922 ACCTATTTATACAAAG-AAAAAAAAGAAA-AAAACCAAATGGTCAAAATTTTTAAAACCAACA
1 ACCTATTTATACAAAGAAAAAAAAAGAAATAAAACCAAATGGTCAAAATTTTTAAAACCAACA
* *
512983 ACCTATTTATACAAATAAAAAAAGAAAAAATAAATAAAACCAAATGGTCAAAATTTTTAAAACCA
1 ACCTATTTATAC----AAAGAAA-AAAAAAGAAATAAAACCAAATGGTCAAAATTTTTAAAACCA
513048 AC
61 AC
513050 TATTATACAG
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
61 12 0.21
65 3 0.05
66 2 0.03
67 9 0.16
68 32 0.55
ACGTcount: A:0.59, C:0.14, G:0.05, T:0.21
Consensus pattern (63 bp):
ACCTATTTATACAAAGAAAAAAAAAGAAATAAAACCAAATGGTCAAAATTTTTAAAACCAACA
Found at i:520830 original size:97 final size:96
Alignment explanation
Indices: 520665--520843 Score: 252
Period size: 97 Copynumber: 1.9 Consensus size: 96
520655 CTGTAACAGT
* * * *
520665 TATACCAAAATATTTTATTTGTTGTGACTCAATATATGCGAAAAAAGAATATTATTAGTATTCGT
1 TATACCAAAATATCTTATCTGTTATGACTCAATATATGCGAAAAAAGAATATTATCAGTATTCGT
520730 CCCAATTTTGGAAGTTATCCGCGAGTAAAAG
66 CCCAATTTTGGAAGTTATCCGCGAGTAAAAG
* * * * *
520761 TATACCAAAGTATCTTATCTGTTATGACTCAATCTGTG-TAAACAAGAGAATATTGTCAGTATTC
1 TATACCAAAATATCTTATCTGTTATGACTCAATATATGCGAAA-AA-AGAATATTATCAGTATTC
520825 GTCCCAATTTTGGAAGTTA
64 GTCCCAATTTTGGAAGTTA
520844 CCTTGCGAGT
Statistics
Matches: 72, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
95 3 0.04
96 34 0.47
97 35 0.49
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.36
Consensus pattern (96 bp):
TATACCAAAATATCTTATCTGTTATGACTCAATATATGCGAAAAAAGAATATTATCAGTATTCGT
CCCAATTTTGGAAGTTATCCGCGAGTAAAAG
Found at i:522333 original size:46 final size:46
Alignment explanation
Indices: 522283--522450 Score: 246
Period size: 46 Copynumber: 3.7 Consensus size: 46
522273 ACATTCATTT
* * * *
522283 ATGCATTTAAATTATGGCATCTTTTCATGCCTTCATGCATCTTTTC
1 ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
*
522329 ATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCCTTTC
1 ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
* *
522375 ATGCATTTTGATTATGGCATCCTTTCATGCCTTAATGCTTCCTTTC
1 ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
* * *
522421 ACGGATTTTGATTATGGCATCCTTTCATGC
1 ATGCATTTTAATTATGGCATCCTTTCATGC
522451 GTTTTGATTA
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (46 bp):
ATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCTTTC
Found at i:522370 original size:20 final size:20
Alignment explanation
Indices: 522299--522588 Score: 112
Period size: 26 Copynumber: 12.7 Consensus size: 20
522289 TTAAATTATG
* *
522299 GCATCTTTTCATGCCTTCAT
1 GCATCCTTTCATGCCTTAAT
* *
522319 GCATCTTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
522344 GGCATCCTTTTATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
522365 GCATCCTTTCATGCATTTTGATTAT
1 GCATCCTTTCATGC--CTT-A--AT
522390 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * **
522411 GCTTCCTTTCACGGATTTTGATTAT
1 GCATCCTTTCA-TG-CCTT-A--AT
*
522436 GGCATCCTTTCATGCGTTTTGATTAT
1 -GCATCCTTTCATGC--CTT-A--AT
*
522462 GGCATCTTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
522483 GCATCATTTCATGCATTTTGATTAT
1 GCATCCTTTCATGC--CTT-A--AT
522508 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
522529 GCATCCTTTCATGCATTTTGATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
522554 GACATCCTTTCATTCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
522575 GCATCCTTTCATGC
1 GCATCCTTTCATGC
522589 ATTTTGATTA
Statistics
Matches: 213, Mismatches: 25, Indels: 64
0.71 0.08 0.21
Matches are distributed among these distances:
20 76 0.36
21 12 0.06
22 10 0.05
23 9 0.04
24 10 0.05
25 12 0.06
26 84 0.39
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:522487 original size:46 final size:46
Alignment explanation
Indices: 522437--522601 Score: 285
Period size: 46 Copynumber: 3.6 Consensus size: 46
522427 TTTGATTATG
* *
522437 GCATCCTTTCATGCGTTTTGATTATGGCATCTTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAAT
*
522483 GCATCATTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAAT
* *
522529 GCATCCTTTCATGCATTTTGATTATGACATCCTTTCATTCCTTAAT
1 GCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAAT
522575 GCATCCTTTCATGCATTTTGATTATGG
1 GCATCCTTTCATGCATTTTGATTATGG
522602 ATTCGATTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 112 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAAT
Found at i:522487 original size:164 final size:164
Alignment explanation
Indices: 522293--522601 Score: 537
Period size: 164 Copynumber: 1.9 Consensus size: 164
522283 ATGCATTTAA
* * *
522293 ATTATGGCATCTTTTCATGCCTTCATGCATCTTTTCATGCATTTTAATTATGGCATCCTTTTATG
1 ATTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATG
* *
522358 CCTTAATGCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAATGCTTCCTTTCAC
66 CCTTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATGCCTTAATGCATCCTTTCAC
*
522423 GGATTTTGATTATGGCATCCTTTCATGCGTTTTG
131 GCATTTTGATTATGGCATCCTTTCATGCGTTTTG
*
522457 ATTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCATTTTGATTATGGCATCCTTTCATG
1 ATTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATG
* *
522522 CCTTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATTCCTTAATGCATCCTTTCAT
66 CCTTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATGCCTTAATGCATCCTTTCAC
522587 GCATTTTGATTATGG
131 GCATTTTGATTATGG
522602 ATTCGATTTA
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
164 136 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (164 bp):
ATTATGGCATCTTTTCATGCCTTAATGCATCATTTCATGCATTTTAATTATGGCATCCTTTCATG
CCTTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATGCCTTAATGCATCCTTTCAC
GCATTTTGATTATGGCATCCTTTCATGCGTTTTG
Found at i:522527 original size:118 final size:118
Alignment explanation
Indices: 522319--522566 Score: 408
Period size: 118 Copynumber: 2.1 Consensus size: 118
522309 ATGCCTTCAT
* *
522319 GCATCTTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCATTTCATGCATTTT
* *
522384 GATTATGGCATCCTTTCATGCCTTAATGCTTCCTTTCACGGATTTTGATTATG
66 GATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCACGCATTTTGATTATG
* *
522437 GCATCCTTTCATGCGTTTTGATTATGGCAT-CTTTTCATGCCTTAATGCATCATTTCATGCATTT
1 GCATCCTTTCATGCATTTTAATTATGGCATCCTTTT-ATGCCTTAATGCATCATTTCATGCATTT
*
522501 TGATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATG
65 TGATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCACGCATTTTGATTATG
*
522555 ACATCCTTTCAT
1 GCATCCTTTCAT
522567 TCCTTAATGC
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
117 5 0.04
118 116 0.96
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (118 bp):
GCATCCTTTCATGCATTTTAATTATGGCATCCTTTTATGCCTTAATGCATCATTTCATGCATTTT
GATTATGGCATCCTTTCATGCCTTAATGCATCCTTTCACGCATTTTGATTATG
Found at i:526352 original size:33 final size:33
Alignment explanation
Indices: 526310--526382 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
526300 AGACTGAGAT
*
526310 TGTCTATTTTTCTGTAAAGTTATTGCAAAACTA
1 TGTCTATTTTTCTGTAAAGTTATTGAAAAACTA
* *
526343 TGTCTATTTTTCTGTGAAGTTGTTGAAAAACTA
1 TGTCTATTTTTCTGTAAAGTTATTGAAAAACTA
*
526376 TCTCTAT
1 TGTCTAT
526383 CAGTATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (33 bp):
TGTCTATTTTTCTGTAAAGTTATTGAAAAACTA
Found at i:528031 original size:46 final size:46
Alignment explanation
Indices: 527968--528256 Score: 380
Period size: 46 Copynumber: 6.4 Consensus size: 46
527958 TTTTCACACA
* *
527968 TTAATACATCCATTT-ATGCATTTTAATTATGGCATCCTTTCATACC
1 TTAATGCATCC-TTTCATGCATTTTAATTATGGCATCCTTTCATGCC
* * *
528014 TTGATGCATCATTTTATGCATTTTAATTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
* *
528060 TTAATGCATTCTTTCATGCATTTTTATTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
* * *
528106 TTAATGCATCCTTTCATGCATTTTGATTTTGGCATCCTTCCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
528152 TTAATGCATCC-TTC-T--ATTCCTT-A--AT-GCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATT--TTAATTATGGCATCCTTTCATGCC
* *
528192 TTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
528238 TTAATGCATCCTTTCATGC
1 TTAATGCATCCTTTCATGC
528257 CTTAATGCAT
Statistics
Matches: 216, Mismatches: 16, Indels: 22
0.85 0.06 0.09
Matches are distributed among these distances:
40 25 0.12
41 4 0.02
42 6 0.03
43 2 0.01
44 6 0.03
45 8 0.04
46 165 0.76
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.44
Consensus pattern (46 bp):
TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
Found at i:528058 original size:26 final size:25
Alignment explanation
Indices: 527974--528335 Score: 136
Period size: 20 Copynumber: 16.0 Consensus size: 25
527964 CACATTAATA
527974 CATCCATTT-ATGCATTTTAATTATGG
1 CATCC-TTTCATGCATTTT-ATTATGG
** *
528000 CATCCTTTCAT--A-CCT-TGAT-G
1 CATCCTTTCATGCATTTTATTATGG
* *
528020 CATCATTTTATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTT-ATTATGG
*
528046 CATCCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
*
528066 CATTCTTTCATGCATTTTTATTATGG
1 CATCCTTTCATGCA-TTTTATTATGG
*
528092 CATCCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
*
528112 CATCCTTTCATGCATTTTGATTTTGG
1 CATCCTTTCATGCATTTT-ATTATGG
* *
528138 CATCCTTCCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
528158 CATCC-TTC-T--ATTCCTTA--AT-G
1 CATCCTTTCATGCATT--TTATTATGG
*
528178 CATCCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
*
528198 CATCCTTTCATGCATTTTGATTATGA
1 CATCCTTTCATGCATTTT-ATTATGG
*
528224 CATCCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
*
528244 CATCCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
528264 CATCCTTTCATGCATTTTGATTATGG
1 CATCCTTTCATGCATTTT-ATTATGG
* *
528290 CATTCTTTCATGC--CTTA--AT-G
1 CATCCTTTCATGCATTTTATTATGG
*
528310 CATTCTTTCATGCATTTTGATTATGG
1 CATCCTTTCATGCATTTT-ATTATGG
528336 ATTATGTTTT
Statistics
Matches: 260, Mismatches: 31, Indels: 90
0.68 0.08 0.24
Matches are distributed among these distances:
18 1 0.00
19 2 0.01
20 120 0.46
21 15 0.06
22 10 0.04
23 16 0.06
24 9 0.03
25 15 0.06
26 72 0.28
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (25 bp):
CATCCTTTCATGCATTTTATTATGG
Found at i:528073 original size:20 final size:20
Alignment explanation
Indices: 528045--528322 Score: 234
Period size: 20 Copynumber: 12.7 Consensus size: 20
528035 TTTAATTATG
528045 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
528065 GCATTCTTTCATGCATTTTTATTAT
1 GCATCCTTTCATGC---CTTA--AT
528090 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
528111 GCATCCTTTCATGCATTTTGATTTT
1 GCATCCTTTCATGC--CTT-A--AT
*
528136 GGCATCCTTCCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
528157 GCATCC-TTCTATTCCTTAAT
1 GCATCCTTTC-ATGCCTTAAT
528177 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
528197 GCATCCTTTCATGCATTTTGATTAT
1 GCATCCTTTCATGC--CTT-A--AT
528222 GACATCCTTTCATGCCTTAAT
1 G-CATCCTTTCATGCCTTAAT
528243 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
528263 GCATCCTTTCATGCATTTTGATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
528288 GGCATTCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
528309 GCATTCTTTCATGC
1 GCATCCTTTCATGC
528323 ATTTTGATTA
Statistics
Matches: 215, Mismatches: 17, Indels: 52
0.76 0.06 0.18
Matches are distributed among these distances:
19 2 0.01
20 118 0.55
21 11 0.05
22 6 0.03
23 12 0.06
24 6 0.03
25 8 0.04
26 52 0.24
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:528115 original size:66 final size:66
Alignment explanation
Indices: 528045--528322 Score: 354
Period size: 66 Copynumber: 4.2 Consensus size: 66
528035 TTTAATTATG
* *
528045 GCATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTTTATTATGGCATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAA
528110 T
66 T
* * * *
528111 GCATCCTTTCATGCATTTTGATTTTGGCATCCTTCCATGC--CTT-A--AT-GCATCC-TTCTAT
1 GCATCCTTTCATGC--CTT-A--AT-GCATCCTTTCATGCATTTTGATTATGGCATCCTTTC-AT
*
528169 TCCTTAAT
59 GCCTTAAT
*
528177 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGACATCCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAA
528242 T
66 T
*
528243 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGGCATTCTTTCATGCCTTAA
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAA
528308 T
66 T
*
528309 GCATTCTTTCATGC
1 GCATCCTTTCATGC
528323 ATTTTGATTA
Statistics
Matches: 183, Mismatches: 15, Indels: 28
0.81 0.07 0.12
Matches are distributed among these distances:
60 13 0.07
61 1 0.01
62 2 0.01
63 2 0.01
64 2 0.01
65 5 0.03
66 134 0.73
67 5 0.03
68 2 0.01
69 2 0.01
70 2 0.01
71 1 0.01
72 12 0.07
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (66 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATGGCATCCTTTCATGCCTTAA
T
Found at i:528298 original size:46 final size:46
Alignment explanation
Indices: 528243--528335 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
528233 ATGCCTTAAT
528243 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATG
* *
528289 GCATTCTTTCATGCCTTAATGCATTCTTTCATGCATTTTGATTATG
1 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATG
528335 G
1 G
528336 ATTATGTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTGATTATG
Found at i:530275 original size:29 final size:28
Alignment explanation
Indices: 530224--530285 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
530214 ATTATGTTCA
*
530224 TTTTATTTTTATTCTATGTTTTTACTGTT
1 TTTTATTTTTATTATATGTTTTTACT-TT
*
530253 TTTTAGTTTTTATTATTTG-TTTTACTTT
1 TTTTA-TTTTTATTATATGTTTTTACTTT
530281 TTTTA
1 TTTTA
530286 ATTAAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 11 0.37
ACGTcount: A:0.15, C:0.05, G:0.06, T:0.74
Consensus pattern (28 bp):
TTTTATTTTTATTATATGTTTTTACTTT
Found at i:532252 original size:2 final size:2
Alignment explanation
Indices: 532245--532269 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
532235 TTATCCTTTC
532245 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
532270 CACACACATA
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:532596 original size:9 final size:9
Alignment explanation
Indices: 532584--532635 Score: 61
Period size: 9 Copynumber: 5.6 Consensus size: 9
532574 GAAAATTAAT
532584 AAAAAAAGA
1 AAAAAAAGA
532593 AAAAAAAGA
1 AAAAAAAGA
532602 AAAGAAAA-A
1 AAA-AAAAGA
532611 AATTAAAAAGA
1 AA--AAAAAGA
*
532622 AAACAAAGA
1 AAAAAAAGA
532631 AAAAA
1 AAAAA
532636 TAATAAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 25 0.68
10 8 0.22
11 4 0.11
ACGTcount: A:0.85, C:0.02, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:532606 original size:14 final size:14
Alignment explanation
Indices: 532587--532647 Score: 63
Period size: 14 Copynumber: 4.3 Consensus size: 14
532577 AATTAATAAA
532587 AAAAGAAAAAAAAG
1 AAAAGAAAAAAAAG
532601 AAAAGAAAAAAATTA-
1 AAAAGAAAAAAA--AG
*
532616 AAAAGAAAACAAAG
1 AAAAGAAAAAAAAG
*
532630 AAAA-AATAATAAAG
1 AAAAGAA-AAAAAAG
532644 AAAA
1 AAAA
532648 TCGATCAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 3 0.07
14 26 0.63
15 11 0.27
16 1 0.02
ACGTcount: A:0.82, C:0.02, G:0.10, T:0.07
Consensus pattern (14 bp):
AAAAGAAAAAAAAG
Found at i:532636 original size:23 final size:24
Alignment explanation
Indices: 532602--532647 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
532592 AAAAAAAAGA
532602 AAAGAAAAAAATTAA-AAAGAAAAC
1 AAAGAAAAAAA-TAATAAAGAAAAC
532626 AAAG-AAAAAATAATAAAGAAAA
1 AAAGAAAAAAATAATAAAGAAAA
532648 TCGATCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 14 0.67
24 4 0.19
ACGTcount: A:0.80, C:0.02, G:0.09, T:0.09
Consensus pattern (24 bp):
AAAGAAAAAAATAATAAAGAAAAC
Found at i:534630 original size:58 final size:57
Alignment explanation
Indices: 534537--534749 Score: 208
Period size: 58 Copynumber: 3.8 Consensus size: 57
534527 TTCAAATTTT
* ** * *
534537 TTTTTTAAAGAAACTAAGTTTGATTTTCA-GGGTTTCTTGATGATGATCTTCAATGAA
1 TTTTTAAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGAT-ATCTTCAATGAA
* *
534594 TTTTTAAAAGAAACTAAGCCTAATGTTTAGGGGTTTCTTGATG-T-T-TTCAAATGAG
1 TTTTTAAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATATCTTC-AATGAA
* * * * * *
534649 TTTTT---AGAAAGTAAGCTTAATTTTTAGGGCTTTGTTGATGATTATCTTAAAAGAA
1 TTTTTAAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGA-TATCTTCAATGAA
*
534704 TTTTTGAAAA-AAACTAAACCTAATTTTTAGGGGTTTCTTGATGATA
1 TTTTT-AAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATA
534750 ACTGAAAATG
Statistics
Matches: 126, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
52 30 0.24
54 4 0.03
55 21 0.17
56 2 0.02
57 26 0.21
58 42 0.33
59 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (57 bp):
TTTTTAAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATATCTTCAATGAA
Found at i:534720 original size:110 final size:109
Alignment explanation
Indices: 534545--534805 Score: 299
Period size: 110 Copynumber: 2.3 Consensus size: 109
534535 TTTTTTTTAA
* * * *
534545 AGAAACTAAGTTTGATTTTCAGGGTTTCTTGATGATGATCTTCAATGAATTTTTAAAAGAAACTA
1 AGAAACTAAGCTTAATTTTCAGGGTTTCTTGATGATGATCTTAAAAGAATTTTTAAAAGAAACTA
*
534610 AGCCTAATGTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTT
66 AACCTAATGTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTT
* * * *
534654 AGAAAGTAAGCTTAATTTTTAGGGCTTTGTTGATGATTATCTTAAAAGAATTTTTGAAAA-AAAC
1 AGAAACTAAGCTTAATTTTCAGGG-TTTCTTGATGATGATCTTAAAAGAATTTTT-AAAAGAAAC
* * ** *
534718 TAAACCTAATTTTTAGGGGTTTCTTGATGATAACTGAAAATGAAAGATTTTA
64 TAAACCTAATGTTTAGGGGTTTCTTGATG-T--TTTCAAATG--AG-TTTTT
*
534770 AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 AGAAACTAAGCTTAATTTTC-AGGGTTTCTTGATGA
534806 GTAAGTCCTT
Statistics
Matches: 125, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
109 20 0.16
110 57 0.46
111 5 0.04
113 6 0.05
115 2 0.02
116 31 0.25
117 4 0.03
ACGTcount: A:0.33, C:0.08, G:0.19, T:0.39
Consensus pattern (109 bp):
AGAAACTAAGCTTAATTTTCAGGGTTTCTTGATGATGATCTTAAAAGAATTTTTAAAAGAAACTA
AACCTAATGTTTAGGGGTTTCTTGATGTTTTCAAATGAGTTTTT
Found at i:534776 original size:58 final size:55
Alignment explanation
Indices: 534539--534805 Score: 186
Period size: 58 Copynumber: 4.7 Consensus size: 55
534529 CAAATTTTTT
** * * * *
534539 TTTTAAAGAAACTAAGTTTGATTTTCA-GGGTTTCTTGATGATGATCTT-CAATGAAT
1 TTTT-AAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGAT-A-CTTAAAATGAAG
* * *
534595 TTTTAAAAGAAACTAAGCCTAATGTTTAGGGGTTTCTTGATG-T-TTTCAAATG-AG
1 TTTT--AAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATACTTAAAATGAAG
* * * * * *
534649 TTTTTAGAAAGTAAGCTTAATTTTTAGGGCTTTGTTGATGATTATCTTAAAA-GAAT
1 TTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGA-TA-CTTAAAATGAAG
* * *
534705 TTTTGAAAAAAACTAAACCTAATTTTTAGGGGTTTCTTGATGATAACTGAAAATGAAAG
1 TTTT--AAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGAT-ACTTAAAATG-AAG
* * * *
534764 ATTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 -TTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGA
534806 GTAAGTCCTT
Statistics
Matches: 165, Mismatches: 32, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
52 30 0.18
54 8 0.05
55 5 0.03
56 14 0.08
57 26 0.16
58 76 0.46
59 2 0.01
60 4 0.02
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.40
Consensus pattern (55 bp):
TTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATACTTAAAATGAAG
Found at i:535040 original size:39 final size:39
Alignment explanation
Indices: 534997--535084 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 39
534987 AGGGATCAAC
* * **
534997 ATCTCATTTGAA-ATGGTTTCACTCAAAACTGAAGATTTT
1 ATCTCACTTGAAGATAGTTTCACTCAAAACAAAAGA-TTT
* *
535036 ATCTCGCTT-AAGATAGTTTCACTCGAAACAAAAGATTT
1 ATCTCACTTGAAGATAGTTTCACTCAAAACAAAAGATTT
535074 ATCTCACTTGA
1 ATCTCACTTGA
535085 GATTTTGTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
38 13 0.32
39 27 0.68
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (39 bp):
ATCTCACTTGAAGATAGTTTCACTCAAAACAAAAGATTT
Found at i:535182 original size:59 final size:59
Alignment explanation
Indices: 535109--535228 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 59
535099 AAAACGAACA
*
535109 ACGCCCCACTAGAGGGGTTAACATTTC-CTTCACTCGATTCATGGCATTTCAAATCAGTG
1 ACGCCCCACCAGAGGGGTTAACATTTCTCTTC-CTCGATTCATGGCATTTCAAATCAGTG
** * * *
535168 ACGCCCCACCAGAGGGGTTAATTTTTCTTTTCCTTGATTCATGGCATTTTAAATCAGTG
1 ACGCCCCACCAGAGGGGTTAACATTTCTCTTCCTCGATTCATGGCATTTCAAATCAGTG
535227 AC
1 AC
535229 ACCTCACTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 51 0.94
60 3 0.06
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (59 bp):
ACGCCCCACCAGAGGGGTTAACATTTCTCTTCCTCGATTCATGGCATTTCAAATCAGTG
Found at i:535421 original size:211 final size:212
Alignment explanation
Indices: 535046--535448 Score: 576
Period size: 211 Copynumber: 1.9 Consensus size: 212
535036 ATCTCGCTTA
*
535046 AGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTTTGTTTTCTTAAAACGAACAAC
1 AGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTATGTTTTCTTAAAACGAACAAC
* *** * *
535111 GCCCCACTAGAGGGGTTAACATTTCCTTCACTCGATTCATGGCATTTCAAATCAGTGACGCCCCA
66 GCCCCACCAGAGGGGTTAACATTTCCTTCACTCGATTCACAACAGTTCAAATCAGTGACACCCCA
* * * * * ** * *
535176 CCAGAGGGGTTAATTTTTCTTTTCCTTGATTCATGGCATTTTAAATCAGTGACACCTCACTTGAG
131 CCAAAGGAGTAAACTTTTCCTTTCCTCAATTCATGGCATTCT-AATCAGCGACACCTCACTTGAG
535241 GGACAAACATATCAGTTG
195 GGACAAACATATCAGTTG
*
535259 AGATAGTTTCACTCGAAACAAAAGA-TTATCTCACTTGAGATTAT-TTTTCTTAAAATGAACAAC
1 AGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTATGTTTTCTTAAAACGAACAAC
* *
535322 GCCCCACCAGAGGGGTTAACATTTCCTTCACTTGATTCACAACAGTTCGAATCAGTGACACCCCA
66 GCCCCACCAGAGGGGTTAACATTTCCTTCACTCGATTCACAACAGTTCAAATCAGTGACACCCCA
* * **
535387 CCAAAGGAGTAAACTTTTCCTTTGCTCAATTCATGGTATTCTAATCAGCGATGCCTCACTTG
131 CCAAAGGAGTAAACTTTTCCTTTCCTCAATTCATGGCATTCTAATCAGCGACACCTCACTTG
535449 GGAGATCAGC
Statistics
Matches: 167, Mismatches: 23, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
210 17 0.10
211 107 0.64
212 18 0.11
213 25 0.15
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (212 bp):
AGATAGTTTCACTCGAAACAAAAGATTTATCTCACTTGAGATTATGTTTTCTTAAAACGAACAAC
GCCCCACCAGAGGGGTTAACATTTCCTTCACTCGATTCACAACAGTTCAAATCAGTGACACCCCA
CCAAAGGAGTAAACTTTTCCTTTCCTCAATTCATGGCATTCTAATCAGCGACACCTCACTTGAGG
GACAAACATATCAGTTG
Found at i:535508 original size:39 final size:39
Alignment explanation
Indices: 535459--535703 Score: 280
Period size: 39 Copynumber: 6.3 Consensus size: 39
535449 GGAGATCAGC
* *
535459 ATCTCGCTTGAGATGGTTTCACTCTAAACAGGAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCTAAACAGAAGATTTT
* * *
535498 ATCTAGCTTGAGATGGTTTCACT-TGAAATAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCT-AAACAGAAGA-TTTT
* * * *
535538 ATCTCGCTAGGGATAGTTTCAC-CTGACACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCT-AAACAGAAGATTTT
* *
535577 ATCTTGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCTAAACAGAAGATTTT
* *
535616 ATCTCGCTTAAGATAGTTTCACTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCTAAACAGAAGATTTT
* * * *
535655 ATCTCGCTTGAGATAATTTCACTCGAAATAAAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCTAAACAGAAGATTTT
*
535693 ATCTCACTTGA
1 ATCTCGCTTGA
535704 TATTTTTTAT
Statistics
Matches: 179, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
38 14 0.08
39 133 0.74
40 32 0.18
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCTAAACAGAAGATTTT
Found at i:535650 original size:22 final size:22
Alignment explanation
Indices: 535587--535651 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
535577 ATCTTGCTTG
535587 AGATAGTTTCACTCGAAACAGA
1 AGATAGTTTCACTCGAAACAGA
**
535609 AGAT--TTT-ATCTCG---CTTA
1 AGATAGTTTCA-CTCGAAACAGA
535626 AGATAGTTTCACTCGAAACAGA
1 AGATAGTTTCACTCGAAACAGA
535648 AGAT
1 AGAT
535652 TTTATCTCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 6 0.19
19 8 0.25
20 8 0.25
22 10 0.31
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (22 bp):
AGATAGTTTCACTCGAAACAGA
Found at i:536484 original size:64 final size:64
Alignment explanation
Indices: 536338--536496 Score: 198
Period size: 64 Copynumber: 2.5 Consensus size: 64
536328 GAATTAAATT
* * *
536338 GAACATTGAATGCATTTCATGCATCGATGCA-CACCATGCACCGATGCACTGAGGATTTTATAA
1 GAACATCGAATGCATTTGATGCATCGATGCACCACCATGCACCGATGCACTCAGGATTTTATAA
* * * * *
536401 GAACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGGTGCACTCTGGCTATTT-TG
1 GAACATCGAATGCATTTGATGCATCGATGCACCA-CCATGCACCGATGCACTCAGGAT-TTTATA
536465 A
64 A
*
536466 -AACATCGAATGCACTTGATGCATCGATGCAC
1 GAACATCGAATGCATTTGATGCATCGATGCAC
536497 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 29 0.35
64 32 0.38
65 20 0.24
66 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (64 bp):
GAACATCGAATGCATTTGATGCATCGATGCACCACCATGCACCGATGCACTCAGGATTTTATAA
Found at i:551467 original size:2 final size:2
Alignment explanation
Indices: 551460--551493 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
551450 ATGTAAAATC
551460 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
551494 CTTTTAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554876 original size:15 final size:15
Alignment explanation
Indices: 554856--554885 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
554846 TGTCAAAGTT
554856 AGTAGATCACGTGAA
1 AGTAGATCACGTGAA
554871 AGTAGATCACGTGAA
1 AGTAGATCACGTGAA
554886 CATATTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
AGTAGATCACGTGAA
Found at i:559379 original size:3 final size:3
Alignment explanation
Indices: 559371--559450 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
559361 AATATATATT
*
559371 TAA TAA TAA TAA TAA TGA 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
559419 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
559451 TGGGTAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:560052 original size:113 final size:114
Alignment explanation
Indices: 559771--560320 Score: 887
Period size: 113 Copynumber: 4.9 Consensus size: 114
559761 GATAGAATTA
* *
559771 TTGAACAAGTTCTTCTTATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
559835 ACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGCAAAAGG
66 ACTTTCTCTGGAAAAGATAATCCATCAA-ATGATGAATTCAGGCAAAAGG
559885 TTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * * *
559949 ACTTCCTCTGGAAAAGCTGATCCATCAAGTAATGAATTCAGGTAAAAGG
66 ACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGCAAAAGG
559998 TTGAACAAATTCTTCTCATTATGAACTTTC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* * * * *
560062 ACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 ACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGCAAAAGG
560111 TTGAACAAATTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
560175 ACTTTCTCTGGAAAAAATAATCCATCAAATGATGAATTCAGGCAAAAGG
66 ACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGCAAAAGG
560224 TTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
560288 ACCTTCTCTGGAAATG-TAAATCCATCAAATGAT
66 ACTTTCTCTGGAAAAGAT-AATCCATCAAATGAT
560321 AGATTTGAAT
Statistics
Matches: 407, Mismatches: 24, Indels: 11
0.92 0.05 0.02
Matches are distributed among these distances:
112 4 0.01
113 313 0.77
114 90 0.22
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
ACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGCAAAAGG
Found at i:561701 original size:83 final size:83
Alignment explanation
Indices: 561116--561699 Score: 1017
Period size: 83 Copynumber: 7.0 Consensus size: 83
561106 TTATTTCTAT
* * *
561116 TATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
*
561181 AACACTTCCAGAAGATAC
66 AACACTTCCAGAAGATGC
*
561199 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
*
561264 AACACTTCCAGAAGATGT
66 AACACTTCCAGAAGATGC
*
561282 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
561347 AACACTTCCAGAAGATGC
66 AACACTTCCAGAAGATGC
* *
561365 TATGAGCACATTCATCTTCTAAACTCAATGATTGGTTCTATCCAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
*
561430 AATACTTCCAGAAGATGC
66 AACACTTCCAGAAGATGC
*
561448 TATGAGCACATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
561513 AACACTTCCAGAAGATGC
66 AACACTTCCAGAAGATGC
* *
561531 TATGAACACATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
1 TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
561596 AACACTTCCAGAAGATGC
66 AACACTTCCAGAAGATGC
* *
561614 TATTG-GCAAATTCATCTTCTAAACTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 TA-TGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
561678 GAACACTTCCAGAAGATGC
65 GAACACTTCCAGAAGATGC
561697 TAT
1 TAT
561700 TGAGTCTCTT
Statistics
Matches: 482, Mismatches: 18, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
82 1 0.00
83 479 0.99
84 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
TATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGC
Found at i:573553 original size:17 final size:17
Alignment explanation
Indices: 573531--573565 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
573521 AAAATAAAAC
*
573531 ATATAAATATTATGAAA
1 ATATAAAAATTATGAAA
*
573548 ATATAAAAATTTTGAAA
1 ATATAAAAATTATGAAA
573565 A
1 A
573566 GAAACAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
ATATAAAAATTATGAAA
Found at i:574264 original size:13 final size:13
Alignment explanation
Indices: 574220--574266 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
574210 CTGTTCTTTG
*
574220 ATATTGAAAACTAA
1 ATATTTAAAA-TAA
574234 ATA-TTAAAATAA
1 ATATTTAAAATAA
*
574246 TTTATTTAAAATAA
1 -ATATTTAAAATAA
574260 ATATTTA
1 ATATTTA
574267 TTTATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 3 0.11
13 13 0.46
14 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (13 bp):
ATATTTAAAATAA
Found at i:575727 original size:14 final size:14
Alignment explanation
Indices: 575702--575747 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
575692 TGGGCCTGTA
575702 ATTAAT-TATTTAT
1 ATTAATATATTTAT
575715 ATTAATATATTTA-
1 ATTAATATATTTAT
*
575728 A-TAATATATTAAT
1 ATTAATATATTTAT
*
575741 AATAATA
1 ATTAATA
575748 ATAATAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAATATATTTAT
Found at i:575734 original size:12 final size:12
Alignment explanation
Indices: 575704--575744 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
575694 GGCCTGTAAT
575704 TAAT-TATTTATA
1 TAATATATTTA-A
575716 TTAATATATTTAA
1 -TAATATATTTAA
575729 TAATATA-TTAA
1 TAATATATTTAA
575740 TAATA
1 TAATA
575745 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 5 0.19
14 6 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TAATATATTTAA
Found at i:575743 original size:3 final size:3
Alignment explanation
Indices: 575726--575806 Score: 137
Period size: 3 Copynumber: 27.0 Consensus size: 3
575716 TTAATATATT
*
575726 TAA TAA T-A TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
575773 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
575807 GGGTAAAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 4
0.93 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:577321 original size:18 final size:18
Alignment explanation
Indices: 577295--577334 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
577285 GGAGGGTTTT
*
577295 TTAATCAAATTAAATGAA
1 TTAACCAAATTAAATGAA
*
577313 TTAACCAAATTAACTGAA
1 TTAACCAAATTAAATGAA
577331 TTAA
1 TTAA
577335 TCGAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (18 bp):
TTAACCAAATTAAATGAA
Found at i:577352 original size:2 final size:2
Alignment explanation
Indices: 577341--577381 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
577331 TTAATCGAAA
*
577341 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
577382 TACTTAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
AT
Found at i:577446 original size:7 final size:7
Alignment explanation
Indices: 577434--577458 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
577424 TAACCGAAAG
577434 TATTGAC
1 TATTGAC
577441 TATTGAC
1 TATTGAC
577448 TATTGAC
1 TATTGAC
577455 TATT
1 TATT
577459 TAATATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (7 bp):
TATTGAC
Found at i:578825 original size:44 final size:46
Alignment explanation
Indices: 578716--578832 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
578706 TATATTACAC
* *
578716 AAAAAAGGTTTGTTACAACAATAAGCACATGACAAAAAACATAGTA
1 AAAAAAAGTTAGTTACAACAATAAGCACATGACAAAAAACATAGTA
578762 AAAAAAAGTTAGTTACAACAATAAGCACATGACAAAAAA-ATAGT-
1 AAAAAAAGTTAGTTACAACAATAAGCACATGACAAAAAACATAGTA
578806 AAAAAAAGTTAGTTACAACAATAAGCA
1 AAAAAAAGTTAGTTACAACAATAAGCA
578833 AATTATAAGA
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
44 27 0.39
45 5 0.07
46 37 0.54
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.19
Consensus pattern (46 bp):
AAAAAAAGTTAGTTACAACAATAAGCACATGACAAAAAACATAGTA
Found at i:578984 original size:26 final size:25
Alignment explanation
Indices: 578951--578999 Score: 89
Period size: 26 Copynumber: 1.9 Consensus size: 25
578941 AAATATTTCG
578951 TTAATATTATTATTATTTTTATTAT
1 TTAATATTATTATTATTTTTATTAT
578976 TTAACTATTATTATTATTTTTATT
1 TTAA-TATTATTATTATTTTTATT
579000 TCTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTAATATTATTATTATTTTTATTAT
Found at i:585568 original size:13 final size:13
Alignment explanation
Indices: 585550--585592 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
585540 TTTTTTCATC
585550 TTTTAAAATTATT
1 TTTTAAAATTATT
585563 TTTTAAAATTA--
1 TTTTAAAATTATT
585574 TTTTAAAATGTATT
1 TTTTAAAAT-TATT
585588 TTTTA
1 TTTTA
585593 GGTATTCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 2 0.07
13 11 0.41
14 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TTTTAAAATTATT
Found at i:588258 original size:78 final size:78
Alignment explanation
Indices: 588160--588308 Score: 189
Period size: 77 Copynumber: 1.9 Consensus size: 78
588150 ATATAGTAAG
*
588160 TAAACATTAAAAGAATGTAATT-TTGATTACAA-CTCTTTTAAT-TGATATTTAATTTGAAATAA
1 TAAACATTAAAAGAATGTAATTCAT-ATTACAAGC-C-TTTAATGT-ATATTTAATTTGAAATAA
588222 TTAAATAAGATTTTCAA
62 TTAAATAAGATTTTCAA
* * * *
588239 TAAACATT-AAAGATTGTAATTCATATTATAAGCCTTTGATGTATATTTAATTTGAATTAATTAA
1 TAAACATTAAAAGAATGTAATTCATATTACAAGCCTTTAATGTATATTTAATTTGAAATAATTAA
588303 ATAAGA
66 ATAAGA
588309 AATTTATTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
77 32 0.52
78 20 0.32
79 10 0.16
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.42
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCATATTACAAGCCTTTAATGTATATTTAATTTGAAATAATTAA
ATAAGATTTTCAA
Found at i:588319 original size:20 final size:19
Alignment explanation
Indices: 588294--588333 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
588284 TTTAATTTGA
588294 ATTAATTAAATAAGAAATTT
1 ATTAATTAAA-AAGAAATTT
* *
588314 ATTAATTCAAAATAAATTT
1 ATTAATTAAAAAGAAATTT
588333 A
1 A
588334 AAAACCCTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
ATTAATTAAAAAGAAATTT
Found at i:591910 original size:19 final size:20
Alignment explanation
Indices: 591888--591932 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
591878 ATATATAAAA
* *
591888 AGAAGAAGAATAAAAA-GAG
1 AGAAAAAGAAAAAAAATGAG
591907 AGAAAAAGAAAAAAAATGAG
1 AGAAAAAGAAAAAAAATGAG
591927 A-AAAAA
1 AGAAAAA
591933 ATAAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAAAAAAAATGAG
Found at i:591919 original size:31 final size:31
Alignment explanation
Indices: 591821--591919 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
591811 ATATAAAGAT
* *
591821 AAAAAGGAGATAGAAGAAAAA-AGAG-AAAAG
1 AAAAAGAAGA-AGAATAAAAAGAGAGAAAAAG
* *
591851 AGAAAAGATAGAAAAATAAAAAG-GA-AAATATAT
1 A-AAAAGA-AGAAGAATAAAAAGAGAGAAA-A-AG
591884 AAAAAGAAGAAGAATAAAAAGAGAGAAAAAG
1 AAAAAGAAGAAGAATAAAAAGAGAGAAAAAG
591915 AAAAA
1 AAAAA
591920 AAATGAGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
30 1 0.02
31 36 0.65
32 13 0.24
33 5 0.09
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (31 bp):
AAAAAGAAGAAGAATAAAAAGAGAGAAAAAG
Found at i:591927 original size:18 final size:19
Alignment explanation
Indices: 591888--591937 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
591878 ATATATAAAA
*
591888 AGAAGAAGAATAAAAAGAG
1 AGAAAAAGAATAAAAAGAG
591907 AGAAAAAGAA-AAAAA-ATG
1 AGAAAAAGAATAAAAAGA-G
591925 AGAAAAA-AATAAA
1 AGAAAAAGAATAAA
591938 TCAAATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.11
18 16 0.57
19 9 0.32
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (19 bp):
AGAAAAAGAATAAAAAGAG
Found at i:593919 original size:42 final size:38
Alignment explanation
Indices: 593769--594127 Score: 403
Period size: 38 Copynumber: 9.2 Consensus size: 38
593759 CATAGAAACT
*
593769 TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
** * * * * *
593807 TTGATCTTTGTAATTTTTAACTTCATCGTGAAGAAAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
593845 TCAATATTTGTTATTCTTGACTCCCTCGTGAAGAGTAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
593883 TCAATATTTCAAGGTTATTCTTGACTTCCTCATGAAGAGAGG
1 TCAATCTTT----GTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
593925 TTAATCTTTGTTATTCTTAACTTCCTCGTTAAGAGAAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* * *
593963 TCGATCTTTGTTACTCTTGACTTCCTCGTGAAGAGATG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
594001 TCAATCTTTGTTATTCTTCACTTCCTCGTGAAGAGAAA
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
594039 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAG
1 TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
594077 TCAATCTTTTAATATTATTCTTGACTTCCTCGTGAAGAAAAG
1 TCAATC--TT--TGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
594119 TTAATCTTT
1 TCAATCTTT
594128 CGGTATTGTC
Statistics
Matches: 265, Mismatches: 48, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
38 198 0.75
40 4 0.02
42 63 0.24
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (38 bp):
TCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
Found at i:594101 original size:194 final size:194
Alignment explanation
Indices: 593772--594127 Score: 534
Period size: 194 Copynumber: 1.8 Consensus size: 194
593762 AGAAACTTCA
* ** *
593772 ATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTTGATCTTTGTAATTTTTAACTTCATCGTG
1 ATCTTTGTTACTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTAATTCTTAACTTCATCGTG
* *
593837 AAGAAAAGTCAATATTTGTTATTCTTGACTCCCTCGTGAAGAGTAGTCAATATTTCAAGGTTATT
66 AAGAAAAGTCAATATTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAAGATTATT
* *
593902 CTTGACTTCCTCATGAAGAGAGGTTAATCTTTGTTATTCTTAACTTCCTCGTTAAGAGAAGTCG
131 CTTGACTTCCTCATGAAGAAAAGTTAATCTTTGTTATTCTTAACTTCCTCGTTAAGAGAAGTCG
* * * * *
593966 ATCTTTGTTACTCTTGACTTCCTCGTGAAGAGATGTCAATCTTTGTTATTCTTCACTTCCTCGTG
1 ATCTTTGTTACTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTAATTCTTAACTTCATCGTG
* * * *
594031 AAGAGAAA-TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTTAATATTAT
66 AAGA-AAAGTCAATATTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAAGATTAT
*
594095 TCTTGACTTCCTCGTGAAGAAAAGTTAATCTTT
130 TCTTGACTTCCTCATGAAGAAAAGTTAATCTTT
594128 CGGTATTGTC
Statistics
Matches: 143, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
194 140 0.98
195 3 0.02
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (194 bp):
ATCTTTGTTACTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTAATTCTTAACTTCATCGTG
AAGAAAAGTCAATATTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAAGATTATT
CTTGACTTCCTCATGAAGAAAAGTTAATCTTTGTTATTCTTAACTTCCTCGTTAAGAGAAGTCG
Found at i:594170 original size:45 final size:43
Alignment explanation
Indices: 594049--594202 Score: 145
Period size: 42 Copynumber: 3.6 Consensus size: 43
594039 TCAATCTTTG
*
594049 TTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTT-TAATA
1 TTATTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCTAATA
* ** * *
594091 TTATTCTTGACTTCCTCGTGAAGAAAAGTT-AATCTTTCGGTATTG
1 TTATTCTTGACTCCCTCGTGAAGAGGA-TTCAATCTTTC--TAATA
* *
594136 TCT-TTCTTGACTCCCTTGTGAAGAGGATTCAATCTTTC-AATG
1 T-TATTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCTAATA
* * *
594178 TTATTCTCGACTTCCTCATGAAGAG
1 TTATTCTTGACTCCCTCGTGAAGAG
594203 AACTATGACT
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
41 1 0.01
42 53 0.59
43 1 0.01
44 2 0.02
45 32 0.36
46 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (43 bp):
TTATTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCTAATA
Found at i:594272 original size:42 final size:42
Alignment explanation
Indices: 594221--594483 Score: 193
Period size: 42 Copynumber: 6.4 Consensus size: 42
594211 CTCCCTCATA
* *
594221 AAGAAGAGTCAATCTTTCAATATTATTCTTGACTTCCTCGTG
1 AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
* *
594263 AAGAGGAGTCAATATTTCAATGTTATTATTGACTTCCTCGTG
1 AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
** ** ** *
594305 AAGAAAAGTTGAT-TTT---TGTTATTCTTGACTTTATTGTG
1 AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
* * * *
594343 AAGAGAAGTTAATC-TT---TGTTATTCTTGACTCCCTCGTT
1 AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
* * ** *
594381 AAGAGGAGTCAATATTTCAATGTTATTTTTGACTTTTTCATG
1 AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
** * * * *
594423 AAGAAAAGTCAGTCTTTCAGTGATTTCATTCTTTACTTTCTCGTG
1 AAGAGGAGTCAATCTTTCAATG--TT-ATTCTTGACTTCCTCGTG
*
594468 AAG-GGAGTCAACCTTT
1 AAGAGGAGTCAATCTTT
594484 ATTGTTGTCA
Statistics
Matches: 172, Mismatches: 41, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
38 59 0.34
39 2 0.01
41 3 0.02
42 80 0.47
44 11 0.06
45 17 0.10
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.41
Consensus pattern (42 bp):
AAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
Found at i:594334 original size:38 final size:38
Alignment explanation
Indices: 594243--594385 Score: 151
Period size: 38 Copynumber: 3.7 Consensus size: 38
594233 TCTTTCAATA
* *
594243 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATATTTCAATG
1 TTATTCTTGACTTCCTCGTGAAGAGAAGTTAAT-TTT---TG
* * *
594285 TTATTATTGACTTCCTCGTGAAGAAAAGTTGATTTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGAAGTTAATTTTTG
** * *
594323 TTATTCTTGACTTTATTGTGAAGAGAAGTTAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGAAGTTAATTTTTG
* *
594361 TTATTCTTGACTCCCTCGTTAAGAG
1 TTATTCTTGACTTCCTCGTGAAGAG
594386 GAGTCAATAT
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
38 53 0.63
41 3 0.04
42 28 0.33
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (38 bp):
TTATTCTTGACTTCCTCGTGAAGAGAAGTTAATTTTTG
Found at i:594506 original size:43 final size:45
Alignment explanation
Indices: 594409--594551 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 45
594399 AATGTTATTT
* * * *
594409 TTGACTTTTTCATGAAGAAAAGTCAGTC-TTTCAGTGATT-TCATTC
1 TTGAATTTCTCATGAAGAGAAGTCA-ACATTTCAGTG-TTGTCATTC
* * * * * *
594454 TTTACTTTCTCGTGAAG-GGAGTCAACCTTT-ATTGTTGTCATTC
1 TTGAATTTCTCATGAAGAGAAGTCAACATTTCAGTGTTGTCATTC
* * *
594497 TTGAATTTCTCATGAAGAGAAGTTAATATTTCAGTGTTGTGATTC
1 TTGAATTTCTCATGAAGAGAAGTCAACATTTCAGTGTTGTCATTC
594542 TTGAATTTCT
1 TTGAATTTCT
594552 TAGAAAGATG
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 2 0.03
43 24 0.31
44 17 0.22
45 35 0.45
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.44
Consensus pattern (45 bp):
TTGAATTTCTCATGAAGAGAAGTCAACATTTCAGTGTTGTCATTC
Found at i:594566 original size:45 final size:45
Alignment explanation
Indices: 594486--594585 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
594476 CAACCTTTAT
594486 TGTTGTCATTCTTGAATTTCTCATGAAGAGAAGTTAATATTTCAG
1 TGTTGTCATTCTTGAATTTCTCATGAAGAGAAGTTAATATTTCAG
* * * *
594531 TGTTGTGATTCTTGAATTTCTTA-GAA-AGATGAGTTAATCTTTTAG
1 TGTTGTCATTCTTGAATTTCTCATGAAGAGA--AGTTAATATTTCAG
*
594576 TGATGTCATT
1 TGTTGTCATT
594586 TTCAACTTGA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 3 0.06
44 3 0.06
45 41 0.87
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (45 bp):
TGTTGTCATTCTTGAATTTCTCATGAAGAGAAGTTAATATTTCAG
Found at i:595370 original size:134 final size:134
Alignment explanation
Indices: 595188--595809 Score: 652
Period size: 134 Copynumber: 4.6 Consensus size: 134
595178 TGATTTTGAA
* * * * ** *
595188 ATTTGGTCTTTCTGAAAAGAAGT-AAATCAAACCACATTC-GATTCAATATTTTCTGAAGATAAT
1 ATTTGGTCTTCCTGAAGAGAAGTGAAA-CAAATC-GATTCTGATTCAATATTCCCTGAAGATAAG
* * * * * * *
595251 TGGAGTAGATCAAA-TATTTCTCAAATATGATCTCCCCTAAAGAGTAGTGGAGCATATTTTTGTT
64 TGAAGTAGATCAAAGT-TTTCTCGAGTTTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTT
595315 CTTTTAG
128 CTTTTAG
*
595322 ATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGATTTTGATTCAATATTCCCTGAAGA-ACAGT
1 ATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGATTCTGATTCAATATTCCCTGAAGATA-AGT
* *
595386 GAAGTAGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTT-T
65 GAAGTAGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCT
595450 TTTCAG
130 TTT-AG
* ** * * ** **
595456 ATTTGGTCTTCCTGAAGAGTAGTGAAGTAAATCAATTCTGATTCAATCTTCTATGAAGAGCAGTG
1 ATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGATTCTGATTCAATATTCCCTGAAGATAAGTG
** * * * *
595521 AAGTCTATCAAAGTTTTCTCGAGTTTGATCTCCCTTAAAGAGTAGTGGAGCAGACTCTTATTGTT
66 AAGTAGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTT
595586 TTAG
131 TTAG
* * * * * *
595590 ATTTGGTCTTTCTGAAGAGAAATGAAGCAAATCGATTATGATTCAATCTTCCATGAAGAATAA-T
1 ATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGATTCTGATTCAATATTCCCTGAAG-ATAAGT
* * * * *
595654 GAAGTGGATCAAAGTTTTCTCGAGTTTGATCTTCCCTAAAGAGTAATGGAGCATATTATTCTTCT
65 GAAGTAGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCT
*
595719 TTCAG
130 TTTAG
* * * *
595724 ATTTGGTCTTCTTGAAGAGCAA-TGAAACAAATCGATTCCGATTCAATCTTCCCTGAATA-ACAG
1 ATTTGGTCTTCCTGAAGAG-AAGTGAAACAAATCGATTCTGATTCAATATTCCCTGAAGATA-AG
*
595787 TGGAA-TAAATCAAA-TTTTCTCGA
64 T-GAAGTAGATCAAAGTTTTCTCGA
595810 TCTGTTCTAC
Statistics
Matches: 415, Mismatches: 61, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
132 1 0.00
133 19 0.05
134 380 0.92
135 15 0.04
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (134 bp):
ATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGATTCTGATTCAATATTCCCTGAAGATAAGTG
AAGTAGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTCTT
TTAG
Found at i:595666 original size:268 final size:268
Alignment explanation
Indices: 595278--595774 Score: 733
Period size: 268 Copynumber: 1.9 Consensus size: 268
595268 TTCTCAAATA
* * * *
595278 TGATCTCCCCTAAAGAGTAGTGGAGCATATTTTTGTTCTTTTAGATTTGGTCTTCCTGAAGAGAA
1 TGATCTCCCCTAAAGAGTAGTGGAGCAGACTCTTATTCTTTTAGATTTGGTCTTCCTGAAGAGAA
* * * *
595343 GTGAAACAAATCGATTTTGATTCAATATTCCCTGAAGAACAGTGAAGTAGATCAAAGTTTTCTCG
66 ATGAAACAAATCGATTATGATTCAATATTCCATGAAGAACAATGAAGTAGATCAAAGTTTTCTCG
* * *
595408 AGTCTGATATCCCCTAAAGAGTAGTGGAGCAGATTCTTCTTTTTTCAGATTTGGTCTTCCTGAAG
131 AGTCTGATATCCCCTAAAGAGTAATGGAGCAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAG
* * ** *
595473 AGTAGTGAAGTAAATCAATTCTGATTCAATCTTCTATGAAGAGCAGTGAAGTCTATCAAAGTTTT
196 AGCAATGAAACAAATCAATTCCGATTCAATCTTCTATGAAGAGCAGTGAAGTCTATCAAAGTTTT
595538 CTCGAGTT
261 CTCGAGTT
* * *
595546 TGATCTCCCTTAAAGAGTAGTGGAGCAGACTCTTATTGTTTTAGATTTGGTCTTTCTGAAGAGAA
1 TGATCTCCCCTAAAGAGTAGTGGAGCAGACTCTTATTCTTTTAGATTTGGTCTTCCTGAAGAGAA
* * * *
595611 ATGAAGCAAATCGATTATGATTCAATCTTCCATGAAGAATAATGAAGTGGATCAAAGTTTTCTCG
66 ATGAAACAAATCGATTATGATTCAATATTCCATGAAGAACAATGAAGTAGATCAAAGTTTTCTCG
* * * * *
595676 AGTTTGATCTTCCCTAAAGAGTAATGGAGCATATTATTCTTCTTTCAGATTTGGTCTTCTTGAAG
131 AGTCTGATATCCCCTAAAGAGTAATGGAGCAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAG
*
595741 AGCAATGAAACAAATCGATTCCGATTCAATCTTC
196 AGCAATGAAACAAATCAATTCCGATTCAATCTTC
595775 CCTGAATAAC
Statistics
Matches: 200, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
268 200 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (268 bp):
TGATCTCCCCTAAAGAGTAGTGGAGCAGACTCTTATTCTTTTAGATTTGGTCTTCCTGAAGAGAA
ATGAAACAAATCGATTATGATTCAATATTCCATGAAGAACAATGAAGTAGATCAAAGTTTTCTCG
AGTCTGATATCCCCTAAAGAGTAATGGAGCAGATTATTCTTCTTTCAGATTTGGTCTTCCTGAAG
AGCAATGAAACAAATCAATTCCGATTCAATCTTCTATGAAGAGCAGTGAAGTCTATCAAAGTTTT
CTCGAGTT
Found at i:596002 original size:13 final size:13
Alignment explanation
Indices: 595984--596009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
595974 CCTATTTCTA
595984 TATTATTATTATT
1 TATTATTATTATT
595997 TATTATTATTATT
1 TATTATTATTATT
596010 ATTTTGTTTG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:596204 original size:19 final size:19
Alignment explanation
Indices: 596180--596225 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
596170 AAGCATGTTG
596180 TCGTCGCCGGTAGAGCTCC
1 TCGTCGCCGGTAGAGCTCC
*
596199 TCGTCGTCGGTAGAGCTCC
1 TCGTCGCCGGTAGAGCTCC
*
596218 TCATCGCC
1 TCGTCGCC
596226 CATCATCAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.37, G:0.28, T:0.24
Consensus pattern (19 bp):
TCGTCGCCGGTAGAGCTCC
Found at i:596650 original size:2 final size:2
Alignment explanation
Indices: 596643--596678 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
596633 TTTTCATTCG
* *
596643 AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
596679 TATTCTTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:596907 original size:21 final size:22
Alignment explanation
Indices: 596859--596910 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
596849 ATCTAACATA
596859 GGACAGCGGTGATCGGAGCCCT
1 GGACAGCGGTGATCGGAGCCCT
596881 GGACAGCGGTGAAT-GGAGCCC-
1 GGACAGCGGTG-ATCGGAGCCCT
596902 GGACAGCGG
1 GGACAGCGG
596911 CACGATGGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.31
22 18 0.62
23 2 0.07
ACGTcount: A:0.21, C:0.25, G:0.44, T:0.10
Consensus pattern (22 bp):
GGACAGCGGTGATCGGAGCCCT
Found at i:597019 original size:25 final size:25
Alignment explanation
Indices: 596966--597019 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
596956 AAAAATCTTA
* *
596966 AAAAAATAAAAATGAATTATTTAAT
1 AAAAAAGAAAAATGAATTATTTAAG
596991 AAAAAAGAAAATATG-A-TATTTATAG
1 AAAAAAGAAAA-ATGAATTATTTA-AG
597016 AAAA
1 AAAA
597020 CTTTAGGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 16 0.64
26 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (25 bp):
AAAAAAGAAAAATGAATTATTTAAG
Found at i:604237 original size:2 final size:2
Alignment explanation
Indices: 604230--604271 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
604220 TAAATTTCAA
604230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
604271 A
1 A
604272 ACTAAATCGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:608373 original size:21 final size:21
Alignment explanation
Indices: 608347--608386 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
608337 GAGTGAAGAA
*
608347 AAGAGAAATGCAAACAACTAT
1 AAGAGAAATGAAAACAACTAT
608368 AAGAGAAATGAAAACAACT
1 AAGAGAAATGAAAACAACT
608387 GAAATATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.15, T:0.12
Consensus pattern (21 bp):
AAGAGAAATGAAAACAACTAT
Found at i:610421 original size:20 final size:20
Alignment explanation
Indices: 610385--610422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
610375 ATCCTATTCC
**
610385 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
610405 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
610423 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:615682 original size:3 final size:3
Alignment explanation
Indices: 615674--615725 Score: 58
Period size: 3 Copynumber: 18.7 Consensus size: 3
615664 AGAAAGAAAA
* *
615674 AAG AAG AAG AAG AA- AAA AAG AAG AA- AA- AAT AAG AAG AAG AAG AA-
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
615718 AAG AAG AA
1 AAG AAG AA
615726 AAAATAAGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:615710 original size:30 final size:27
Alignment explanation
Indices: 615662--615735 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
615652 TATTTTACCT
* *
615662 AAAGAAAGAAAAAAGAAGAAGAAGAAAA
1 AAAG-AAGAAAAAATAAGAAGAAGAAGA
615690 AAAGAAGAAAAAATAAGAAGAAGAAGA
1 AAAGAAGAAAAAATAAGAAGAAGAAGA
615717 AAAGAAGAAAAAATAAGAA
1 AAAGAAGAAAAAATAAGAA
615736 AAATAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
27 40 0.91
28 4 0.09
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (27 bp):
AAAGAAGAAAAAATAAGAAGAAGAAGA
Found at i:615737 original size:8 final size:8
Alignment explanation
Indices: 615666--615727 Score: 63
Period size: 8 Copynumber: 7.4 Consensus size: 8
615656 TTACCTAAAG
615666 AAAGAA-A
1 AAAGAAGA
615673 AAAGAAGA
1 AAAGAAGA
*
615681 AGAAGAAAA
1 A-AAGAAGA
615690 AAAGAAGAAA
1 AAAGAAG--A
*
615700 AAATAAGA
1 AAAGAAGA
615708 AGAAGAAGA
1 A-AAGAAGA
615717 AAAGAAGA
1 AAAGAAGA
615725 AAA
1 AAA
615728 AATAAGAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.13
8 19 0.41
9 14 0.30
10 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (8 bp):
AAAGAAGA
Found at i:615776 original size:24 final size:25
Alignment explanation
Indices: 615662--615776 Score: 83
Period size: 27 Copynumber: 4.5 Consensus size: 25
615652 TATTTTACCT
615662 AAAGAAAGAAAAAAGAAGAAGAAGAAAA
1 AAAGAAA-AAAAAA-AAGAAGAAG-AAA
*
615690 AAAGAAGAAAAAATAAGAAGAAGAAGA
1 AAAGAA-AAAAAAAAAGAAGAAGAA-A
* * * *
615717 AAAGAAGAAAAAATAAGAAAAATAAT
1 AAAGAA-AAAAAAAAAGAAGAAGAAA
* * *
615743 AATG--ATAAAAAAAGAA-AAGGAA
1 AAAGAAAAAAAAAAAGAAGAAGAAA
615765 AAAGAAAAAAAA
1 AAAGAAAAAAAA
615777 TAAATAAAGG
Statistics
Matches: 71, Mismatches: 12, Indels: 12
0.75 0.13 0.13
Matches are distributed among these distances:
22 6 0.08
23 10 0.14
24 5 0.07
26 5 0.07
27 33 0.46
28 11 0.15
29 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.05
Consensus pattern (25 bp):
AAAGAAAAAAAAAAAGAAGAAGAAA
Found at i:617117 original size:19 final size:19
Alignment explanation
Indices: 617095--617136 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
617085 TAAATTTCTT
*
617095 TAAAAGATTTGGTTTTCCG
1 TAAAAGATTTGGTTTTCCC
617114 TAAAAGATTTGGTTTTCCC
1 TAAAAGATTTGGTTTTCCC
617133 TAAA
1 TAAA
617137 GAGTAGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (19 bp):
TAAAAGATTTGGTTTTCCC
Found at i:617368 original size:133 final size:132
Alignment explanation
Indices: 617179--617509 Score: 414
Period size: 133 Copynumber: 2.5 Consensus size: 132
617169 TTGGTCTAGT
* * * * *
617179 TGAATACCAATGAAGTAAATCAAGTTTGA-TTAACTCTTCCTTGAAGAGCAATGAAGTGGATCAA
1 TGAATA-CAGTGAAGCAAATCAAGTTCGATTTAA-TCTTCCTTAAAGAGCAACGAAGTGGATCAA
* * * * * * * * *
617243 AGTTTTTCAAGTCTGATCTCCCCTAAATAGTAGTGGAGTAGATCCTCGTTCTTTTAGATTTG-TT
64 AGTTGTTCAAGTCTAATATCCCCTAAAGAGTAGTGGAGAAGATACTCCTTCTTTCAGAATTGATT
617307 ATTCC
129 -TTCC
* * *
617312 TGAATAGCAGTGAAGCAAATCAAGTTCGATTTAATCTTCCCTAAAGAGTAGCGAAGTGGATCAAA
1 TGAATA-CAGTGAAGCAAATCAAGTTCGATTTAATCTTCCTTAAAGAGCAACGAAGTGGATCAAA
*
617377 GTTGTTCAAGTCTAATATCCCTTAAAGAGTAGTGGAGAAGATACTCCTTCTTTCAGAATTGATTT
65 GTTGTTCAAGTCTAATATCCCCTAAAGAGTAGTGGAGAAGATACTCCTTCTTTCAGAATTGATTT
617442 TCC
130 TCC
* * *
617445 TGAAGACAAGTGAAGCAAATCAAGTTCGATTCAATCTTCCTTAAAGAGCAACGAAGTGAATCAAA
1 TGAATAC-AGTGAAGCAAATCAAGTTCGATTTAATCTTCCTTAAAGAGCAACGAAGTGGATCAAA
617510 TTCTTTTCGA
Statistics
Matches: 170, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
132 1 0.01
133 163 0.96
134 6 0.04
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (132 bp):
TGAATACAGTGAAGCAAATCAAGTTCGATTTAATCTTCCTTAAAGAGCAACGAAGTGGATCAAAG
TTGTTCAAGTCTAATATCCCCTAAAGAGTAGTGGAGAAGATACTCCTTCTTTCAGAATTGATTTT
CC
Found at i:619484 original size:21 final size:21
Alignment explanation
Indices: 619460--619500 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
619450 TTTACATATT
*
619460 CGTTTAA-TTTCCTATTATTTG
1 CGTTTAAGCTTCCTA-TATTTG
619481 CGTTTAAGCTTCCTATATTT
1 CGTTTAAGCTTCCTATATTT
619501 ATGGTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (21 bp):
CGTTTAAGCTTCCTATATTTG
Found at i:624905 original size:31 final size:30
Alignment explanation
Indices: 624784--624905 Score: 73
Period size: 31 Copynumber: 3.8 Consensus size: 30
624774 TTAGGTCCAT
* *
624784 AAGGAATTACCAGTCGGCGCTGAACCTATAT
1 AAGGAATTACCAG-CAGCGCTGAACCTATAC
* * * *
624815 AAGGAATTACCAACAGTGACTGAACCTGCCAGAG
1 AAGGAATTACCAGCAGCG-CTGAACCT---ATAC
* ** * *
624849 ATAGGAATTACTAGTTGATGTTGAACCTATAC
1 A-AGGAATTACCAGCAG-CGCTGAACCTATAC
624881 AAGGAATTACCAGCAGCGACTGAAC
1 AAGGAATTACCAGCAGCG-CTGAAC
624906 TTGTCAAATT
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
30 4 0.06
31 37 0.55
32 3 0.04
34 3 0.04
35 18 0.27
36 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.21
Consensus pattern (30 bp):
AAGGAATTACCAGCAGCGCTGAACCTATAC
Found at i:625001 original size:12 final size:12
Alignment explanation
Indices: 624980--625014 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
624970 TAGAGATATT
624980 AGAAATCAGAGC
1 AGAAATCAGAGC
* *
624992 AGATATCAGAAC
1 AGAAATCAGAGC
625004 AGAAATCAGAG
1 AGAAATCAGAG
625015 AAAACATTCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.23, T:0.11
Consensus pattern (12 bp):
AGAAATCAGAGC
Found at i:630736 original size:18 final size:18
Alignment explanation
Indices: 630708--630760 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
630698 CATATGAATT
630708 TATCCCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
* *
630726 TGTCTCGAAGGACCACTA
1 TATCCCGAAGGACCACTA
630744 TATCCCGAAGGACCACT
1 TATCCCGAAGGACCACT
630761 CTTTAAGAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TATCCCGAAGGACCACTA
Found at i:631720 original size:21 final size:19
Alignment explanation
Indices: 631688--631726 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
631678 TGGTATCGGT
631688 ACCCTTGGTATCGATACTA
1 ACCCTTGGTATCGATACTA
631707 ACCCTCTGAGTATCGATACT
1 ACCCT-TG-GTATCGATACT
631727 CCTTGATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (19 bp):
ACCCTTGGTATCGATACTA
Found at i:634389 original size:10 final size:10
Alignment explanation
Indices: 634376--634432 Score: 78
Period size: 10 Copynumber: 5.7 Consensus size: 10
634366 CCACATGCAA
634376 CTAAATGCTT
1 CTAAATGCTT
*
634386 CTAAATGCAT
1 CTAAATGCTT
634396 CTAAATGCTT
1 CTAAATGCTT
*
634406 CTAAATGCAT
1 CTAAATGCTT
* *
634416 CTAAATGGTC
1 CTAAATGCTT
634426 CTAAATG
1 CTAAATG
634433 AGCTATTAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.33
Consensus pattern (10 bp):
CTAAATGCTT
Found at i:634393 original size:20 final size:20
Alignment explanation
Indices: 634370--634432 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
634360 ATTCCACCAC
*
634370 ATGCAACTAAATGCTTCTAA
1 ATGCATCTAAATGCTTCTAA
634390 ATGCATCTAAATGCTTCTAA
1 ATGCATCTAAATGCTTCTAA
* *
634410 ATGCATCTAAATGGTCCTAA
1 ATGCATCTAAATGCTTCTAA
634430 ATG
1 ATG
634433 AGCTATTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.32
Consensus pattern (20 bp):
ATGCATCTAAATGCTTCTAA
Found at i:635226 original size:19 final size:19
Alignment explanation
Indices: 635202--635250 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
635192 GTCCAAACCA
*
635202 GTCTGAACCGGTTTGACCG
1 GTCTGAACCGGGTTGACCG
635221 GTCTGAACCGGGTTGACCG
1 GTCTGAACCGGGTTGACCG
* *
635240 ATCTGACCCGG
1 GTCTGAACCGG
635251 CCCGACCCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (19 bp):
GTCTGAACCGGGTTGACCG
Found at i:635294 original size:19 final size:18
Alignment explanation
Indices: 635251--635294 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
635241 TCTGACCCGG
635251 CCCGA-CCCGTTGACCGA
1 CCCGACCCCGTTGACCGA
**
635268 CCTAACCCCGTTGATCCGA
1 CCCGACCCCGTTGA-CCGA
635287 CCCGACCC
1 CCCGACCC
635295 AGTGACATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 3 0.14
18 8 0.38
19 10 0.48
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.14
Consensus pattern (18 bp):
CCCGACCCCGTTGACCGA
Found at i:635445 original size:28 final size:29
Alignment explanation
Indices: 635296--635439 Score: 200
Period size: 29 Copynumber: 5.0 Consensus size: 29
635286 ACCCGACCCA
* * *
635296 GTGACATTCTAGGAATTTTTATTGAAAAAT
1 GTGACATTCTGGGAATTTTT-GTGAAAAAG
* *
635326 GTGAGATTCTGGAAATTTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
*
635355 GTGTCATTCTGGGAA-TTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
* *
635383 GTGACATTATGGGAATTTTTGTGGAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAG
635412 GTGACATTCTGGGAATTTTTGTGAAAAA
1 GTGACATTCTGGGAATTTTTGTGAAAAA
635440 ATGACAAGTT
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 26 0.26
29 57 0.57
30 17 0.17
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAATTTTTGTGAAAAAG
Found at i:635445 original size:57 final size:58
Alignment explanation
Indices: 635296--635439 Score: 200
Period size: 57 Copynumber: 2.5 Consensus size: 58
635286 ACCCGACCCA
* * * * *
635296 GTGACATTCTAGGAATTTTTATTGAAAAATGTGAGATTCTGGAAATTTTTGTGAAAAAG
1 GTGACATTCTGGGAATTTTT-GTGAAAAAGGTGACATTATGGAAATTTTTGTGAAAAAG
* * *
635355 GTGTCATTCTGGGAA-TTTTGTGAAAAAGGTGACATTATGGGAATTTTTGTGGAAAAG
1 GTGACATTCTGGGAATTTTTGTGAAAAAGGTGACATTATGGAAATTTTTGTGAAAAAG
635412 GTGACATTCTGGGAATTTTTGTGAAAAA
1 GTGACATTCTGGGAATTTTTGTGAAAAA
635440 ATGACAAGTT
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
57 46 0.61
58 16 0.21
59 13 0.17
ACGTcount: A:0.33, C:0.06, G:0.26, T:0.36
Consensus pattern (58 bp):
GTGACATTCTGGGAATTTTTGTGAAAAAGGTGACATTATGGAAATTTTTGTGAAAAAG
Found at i:635453 original size:57 final size:57
Alignment explanation
Indices: 635339--635456 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 57
635329 AGATTCTGGA
* * *
635339 AATTTTTGTGAAAAAGGTGTCATTCTGGGAATTTTGTGAAAAAGGTGACATTATGGG
1 AATTTTTGTGAAAAAGGTGACATTCTGGGAATTTTGTGAAAAAGATGACAGTATGGG
*
635396 AATTTTTGTGGAAAAGGTGACATTCTGGGAATTTTTGTGAAAAA-ATGACAAGT-TGGG
1 AATTTTTGTGAAAAAGGTGACATTCTGGGAA-TTTTGTGAAAAAGATGAC-AGTATGGG
635453 AATT
1 AATT
635457 ATTTTTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
57 41 0.75
58 14 0.25
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (57 bp):
AATTTTTGTGAAAAAGGTGACATTCTGGGAATTTTGTGAAAAAGATGACAGTATGGG
Found at i:635474 original size:57 final size:57
Alignment explanation
Indices: 635295--635476 Score: 156
Period size: 57 Copynumber: 3.2 Consensus size: 57
635285 GACCCGACCC
* * * * * *
635295 AGTGACATTCTAGGAATTTTTATTGAAAAATG-TGAGATTCTGGAAATTTTTGTGAAAAA
1 AGTGACATTCTGGGAA-TTTT-GTGAAAAA-GATGACAGTATGGGAATTTTTGTGAAAAA
* * * * *
635354 GGTGTCATTCTGGGAATTTTGTGAAAAAGGTGACATTATGGGAATTTTTGTGGAAAA
1 AGTGACATTCTGGGAATTTTGTGAAAAAGATGACAGTATGGGAATTTTTGTGAAAAA
* *
635411 GGTGACATTCTGGGAATTTTTGTGAAAAA-ATGACAAGT-TGGGAATTATTT-TTAAAAA
1 AGTGACATTCTGGGAA-TTTTGTGAAAAAGATGAC-AGTATGGGAATT-TTTGTGAAAAA
*
635468 ATTGACATT
1 AGTGACATT
635477 TTGGAAATGT
Statistics
Matches: 104, Mismatches: 15, Indels: 10
0.81 0.12 0.08
Matches are distributed among these distances:
56 1 0.01
57 69 0.66
58 21 0.20
59 13 0.12
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.36
Consensus pattern (57 bp):
AGTGACATTCTGGGAATTTTGTGAAAAAGATGACAGTATGGGAATTTTTGTGAAAAA
Found at i:635480 original size:29 final size:28
Alignment explanation
Indices: 635297--635489 Score: 129
Period size: 29 Copynumber: 6.7 Consensus size: 28
635287 CCCGACCCAG
* * * *
635297 TGACATTCTAGGAATTTTTATTGAAAAATG
1 TGACATTTTGGGAATTTTT-GTGAAAAA-A
* * * *
635327 TGAGATTCTGGAAATTTTTGTGAAAAAGG
1 TGACATTTTGGGAATTTTTGTGAAAAA-A
* * *
635356 TGTCATTCTGGGAA-TTTTGTGAAAAAGG
1 TGACATTTTGGGAATTTTTGTGAAAAA-A
* **
635384 TGACATTATGGGAATTTTTGTGGAAAAGG
1 TGACATTTTGGGAATTTTTGT-GAAAAAA
*
635413 TGACATTCTGGGAATTTTTGTGAAAAAA
1 TGACATTTTGGGAATTTTTGTGAAAAAA
** *
635441 TGACAAGTTGGGAATTATTT-TTAAAAAA
1 TGACATTTTGGGAATT-TTTGTGAAAAAA
* *
635469 TTGACATTTTGGAAATGTTTG
1 -TGACATTTTGGGAATTTTTG
635490 AATGTGGACT
Statistics
Matches: 136, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
28 54 0.40
29 61 0.45
30 21 0.15
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (28 bp):
TGACATTTTGGGAATTTTTGTGAAAAAA
Found at i:636544 original size:28 final size:28
Alignment explanation
Indices: 636511--636571 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
636501 AGGATAACTC
* *
636511 TTTTATGGGATTTACTGCAGTATAATTT
1 TTTTATGAGATTTACTGCACTATAATTT
*
636539 TTTTATGAGATTTACTGGACTATAATTT
1 TTTTATGAGATTTACTGCACTATAATTT
*
636567 GTTTA
1 TTTTA
636572 GTGTACCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (28 bp):
TTTTATGAGATTTACTGCACTATAATTT
Found at i:642810 original size:29 final size:28
Alignment explanation
Indices: 642762--642979 Score: 203
Period size: 29 Copynumber: 7.7 Consensus size: 28
642752 GACCCGAACC
* *
642762 AGTGACATTTTGGGAATTTTTGTGAAAA
1 AGTGACATTCTGAGAATTTTTGTGAAAA
642790 AGATGACATTCT-AGAATTTTTTGTGAAAA
1 AG-TGACATTCTGAGAA-TTTTTGTGAAAA
* * *
642819 TGGTGACATTTTGGGAATTTTTGTGAAAA
1 -AGTGACATTCTGAGAATTTTTGTGAAAA
642848 ATGTGACATTCTGAGAATTTTTGTG-AAA
1 A-GTGACATTCTGAGAATTTTTGTGAAAA
*
642876 AGTGACATTCTGGGAATTTTTGTGGAAAA
1 AGTGACATTCTGAGAATTTTTGT-GAAAA
* ** *
642905 GGTGACATTAGGGGAATTTTTGTGAAAA
1 AGTGACATTCTGAGAATTTTTGTGAAAA
* *
642933 ACTGACAATT-TGGGAATTATTT-T-AAAA
1 AGTGAC-ATTCTGAGAATT-TTTGTGAAAA
* * *
642960 ATTGACATTTTGGGAATTTT
1 AGTGACATTCTGAGAATTTT
642980 CGAATGTGGA
Statistics
Matches: 164, Mismatches: 16, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
26 5 0.03
27 38 0.23
28 27 0.16
29 90 0.55
30 4 0.02
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (28 bp):
AGTGACATTCTGAGAATTTTTGTGAAAA
Found at i:642910 original size:56 final size:56
Alignment explanation
Indices: 642762--642979 Score: 255
Period size: 58 Copynumber: 3.9 Consensus size: 56
642752 GACCCGAACC
*
642762 AGTGACATTTTGGGAATTTTTGTGAAAAAGATGACATTCT-AGAATTTTTTGTGAAA
1 AGTGACATTTTGGGAATTTTTGTGAAAAAGGTGACATTCTGAGAA-TTTTTGTGAAA
*
642818 ATGGTGACATTTTGGGAATTTTTGTGAAAAATGTGACATTCTGAGAATTTTTGTGAAA
1 A--GTGACATTTTGGGAATTTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTGAAA
* * ** *
642876 AGTGACATTCTGGGAATTTTTGTGGAAAAGGTGACATTAGGGGAATTTTTGTGAAAA
1 AGTGACATTTTGGGAATTTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTG-AAA
* * * * *
642933 ACTGACAATTTGGGAATTATTT-T-AAAAA-TTGACATTTTGGGAATTTT
1 AGTGACATTTTGGGAATT-TTTGTGAAAAAGGTGACATTCTGAGAATTTT
642980 CGAATGTGGA
Statistics
Matches: 142, Mismatches: 15, Indels: 11
0.85 0.09 0.07
Matches are distributed among these distances:
55 16 0.11
56 51 0.36
57 19 0.13
58 52 0.37
59 4 0.03
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (56 bp):
AGTGACATTTTGGGAATTTTTGTGAAAAAGGTGACATTCTGAGAATTTTTGTGAAA
Found at i:644057 original size:27 final size:27
Alignment explanation
Indices: 644002--644062 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
643992 AGGATAACTC
* *
644002 TTTTTATGGGATTTACTGCAGTATAAT
1 TTTTTATGAGATTTACTGCACTATAAT
* *
644029 TTTTTATGAGATTTACTGGACTATGAT
1 TTTTTATGAGATTTACTGCACTATAAT
644056 TTGTTTA
1 TT-TTTA
644063 GTGTAACTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.51
Consensus pattern (27 bp):
TTTTTATGAGATTTACTGCACTATAAT
Found at i:654691 original size:10 final size:10
Alignment explanation
Indices: 654678--654714 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
654668 CCACATGCAA
654678 CTAAATGCTT
1 CTAAATGCTT
*
654688 CTAAATGCAT
1 CTAAATGCTT
*
654698 CTAAATGGTT
1 CTAAATGCTT
654708 CTAAATG
1 CTAAATG
654715 AGGTATTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (10 bp):
CTAAATGCTT
Found at i:654695 original size:20 final size:20
Alignment explanation
Indices: 654672--654714 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
654662 ATTCCACCAC
654672 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* *
654692 ATGCATCTAAATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
654712 ATG
1 ATG
654715 AGGTATTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:655376 original size:18 final size:18
Alignment explanation
Indices: 655346--655380 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
655336 TTAACATTAC
655346 TTGCACAAACCTTATTCT
1 TTGCACAAACCTTATTCT
655364 TTGCA-AAATCCTTATTC
1 TTGCACAAA-CCTTATTC
655381 AAATCACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.40
Consensus pattern (18 bp):
TTGCACAAACCTTATTCT
Found at i:659669 original size:13 final size:13
Alignment explanation
Indices: 659653--659677 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
659643 AGCTAAAATT
659653 ATAAATTATATTC
1 ATAAATTATATTC
659666 ATAAATTATATT
1 ATAAATTATATT
659678 TTAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATTATATTC
Found at i:661942 original size:10 final size:10
Alignment explanation
Indices: 661899--661933 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
661889 GATGGATATT
*
661899 ATTGGTCTGA
1 ATTGGTCAGA
661909 ATTGGTCAGA
1 ATTGGTCAGA
*
661919 ATTGGTCAAA
1 ATTGGTCAGA
661929 ATTGG
1 ATTGG
661934 CCTGAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.34
Consensus pattern (10 bp):
ATTGGTCAGA
Found at i:668856 original size:21 final size:22
Alignment explanation
Indices: 668832--668912 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 22
668822 TTGGTGCAGA
*
668832 GGGAATCGATTCCCCCCATGA-
1 GGGAACCGATTCCCCCCATGAG
** *
668853 GGGAACCGATTCCCCCTTTGAAT
1 GGGAACCGATTCCCCCCATG-AG
* *
668876 GGCAACCGATTCCCCCCA-CAG
1 GGGAACCGATTCCCCCCATGAG
* *
668897 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
668913 ATGGGGTTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
21 31 0.66
22 1 0.02
23 15 0.32
ACGTcount: A:0.23, C:0.37, G:0.22, T:0.17
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:677954 original size:24 final size:24
Alignment explanation
Indices: 677927--677986 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
677917 ATCGGCTGGC
* *
677927 TGGTGAACCTCTTCACTGACGGGT
1 TGGTGAACATCTTCACTGACAGGT
** * *
677951 TGGTGGGCATCTTCATTGGCAGGT
1 TGGTGAACATCTTCACTGACAGGT
677975 TGGTGAACATCT
1 TGGTGAACATCT
677987 CCAGATGCAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.32
Consensus pattern (24 bp):
TGGTGAACATCTTCACTGACAGGT
Done.