Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005655.1 Hibiscus syriacus cultivar Beakdansim tig00013225_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: 194601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1292 original size:24 final size:24
Alignment explanation
Indices: 1260--1309 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1250 AGTTCAGATC
1260 TTTTCGAAACTAAACTACCAGTTT
1 TTTTCGAAACTAAACTACCAGTTT
*
1284 TTTTGGAAACTAAACTACCAGTTT
1 TTTTCGAAACTAAACTACCAGTTT
1308 TT
1 TT
1310 ATCATACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (24 bp):
TTTTCGAAACTAAACTACCAGTTT
Found at i:2111 original size:11 final size:11
Alignment explanation
Indices: 2095--2124 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2085 AGCCTACTAT
2095 CTTACCTCTCC
1 CTTACCTCTCC
2106 CTTACCTCTCC
1 CTTACCTCTCC
2117 CTTACCTC
1 CTTACCTC
2125 ATACATATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.53, G:0.00, T:0.37
Consensus pattern (11 bp):
CTTACCTCTCC
Found at i:2703 original size:21 final size:21
Alignment explanation
Indices: 2677--2716 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2667 TGCCACTGAA
*
2677 ACAAAAAACCCTTTTTTAAAT
1 ACAAAAAAACCTTTTTTAAAT
*
2698 ACAAAAAAACTTTTTTTAA
1 ACAAAAAAACCTTTTTTAA
2717 TGATTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (21 bp):
ACAAAAAAACCTTTTTTAAAT
Found at i:7599 original size:17 final size:19
Alignment explanation
Indices: 7567--7601 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
7557 TACTAAAGTG
7567 TAAAATTGTGTTTTAAACT
1 TAAAATTGTGTTTTAAACT
7586 TAAAATT-T-TTTTAAAC
1 TAAAATTGTGTTTTAAAC
7602 AATTTTTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (19 bp):
TAAAATTGTGTTTTAAACT
Found at i:12045 original size:41 final size:41
Alignment explanation
Indices: 11988--12070 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
11978 TGGAGTGTAT
11988 ATATATATATTAATTTTACACAAATAAATATTTTCCATAAA
1 ATATATATATTAATTTTACACAAATAAATATTTTCCATAAA
*
12029 ATATATATATTAATTTTATACAAATAAATATTTTCCATAAA
1 ATATATATATTAATTTTACACAAATAAATATTTTCCATAAA
12070 A
1 A
12071 CATTCACACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.42
Consensus pattern (41 bp):
ATATATATATTAATTTTACACAAATAAATATTTTCCATAAA
Found at i:15999 original size:21 final size:21
Alignment explanation
Indices: 15973--16064 Score: 118
Period size: 21 Copynumber: 4.4 Consensus size: 21
15963 TTGCATTTCG
15973 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
15994 CGTTGCGATAGTCTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
16015 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
16033 CGTGTTGCGATAGTCTACAGTGT
1 C--GTTGCGATAGTCTACAGTGT
16056 CGTTGCGAT
1 CGTTGCGAT
16065 TTTCCATTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
18 3 0.05
19 4 0.07
20 8 0.13
21 38 0.63
22 4 0.07
23 3 0.05
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:16041 original size:20 final size:20
Alignment explanation
Indices: 16016--16084 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
16006 CTACAGTGTC
16016 GTTGCGATTTTCCATTTCGT
1 GTTGCGATTTTCCATTTCGT
* * *
16036 GTTGCGATAGTCTACA-GT-GT
1 GTTGCGAT--TTTCCATTTCGT
*
16056 CGTTGCGATTTTCCATTTCGC
1 -GTTGCGATTTTCCATTTCGT
16077 GTTGCGAT
1 GTTGCGAT
16085 AGATGAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 4 0.11
20 19 0.51
21 10 0.27
22 4 0.11
ACGTcount: A:0.13, C:0.20, G:0.25, T:0.42
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGT
Found at i:16044 original size:41 final size:41
Alignment explanation
Indices: 15994--16086 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
15984 TCTACAGTGT
15994 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
*
16035 TGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
16076 CGTTGCGATAG
1 CGTTGCGATAG
16087 ATGAAAATCG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
Found at i:16101 original size:41 final size:41
Alignment explanation
Indices: 15994--16105 Score: 129
Period size: 41 Copynumber: 2.7 Consensus size: 41
15984 TCTACAGTGT
* * *
15994 CGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCGAAAATGTCGTTGCGATTTTCCATTTCG
* * * *
16035 TGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 CGTTGCGATAGTCGAAAATGTCGTTGCGATTTTCCATTTCG
16076 CGTTGCGATAGAT-GAAAATCG-CGTTGCGAT
1 CGTTGCGATAG-TCGAAAAT-GTCGTTGCGAT
16106 AGTGTACAGT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 62 0.97
42 2 0.03
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAAATGTCGTTGCGATTTTCCATTTCG
Found at i:16200 original size:41 final size:41
Alignment explanation
Indices: 16124--16278 Score: 215
Period size: 41 Copynumber: 3.8 Consensus size: 41
16114 GTCATTGCGA
*
16124 TCGTTGCGATTTTCCATTTCGCGTTGCTATAGTGTACAGTG
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTG
* * * *
16165 TCATTGCGATTTTCCATCTCGCATTGCGATCGTGTACAGTG
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTG
*
16206 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTG
1 TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTG
* *
16247 TCGTTACGATTTTCCAAATT--CGTTGCGATAGT
1 TCGTTGCGATTTTCC-ATTTCGCGTTGCGATAGT
16279 CTATAGTAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 12 0.12
41 86 0.85
42 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.23, T:0.39
Consensus pattern (41 bp):
TCGTTGCGATTTTCCATTTCGCGTTGCGATAGTGTACAGTG
Found at i:16211 original size:110 final size:103
Alignment explanation
Indices: 15970--16215 Score: 298
Period size: 110 Copynumber: 2.3 Consensus size: 103
15960 GCGTTGCATT
*
15970 TCGCGTTGCGATAGTCTACAGTGTCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
* * *
16035 TGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATT
66 CGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATC
* * *
16073 TCGCGTTGCGATAGATG-AAAATCG-CGTTGCGATAGTGTACAGTCATTGCGATCGTTGCGATTT
1 TCGCGTTGCGATAG-TGTACAGT-GTCGTTGCGATAGTCTACAG----T--G-TCGTTGCGATTT
* *
16136 TCCATTTCGCGTTGCTATAGTGTACAGTGTCATTGCGATTTTCCATC
57 TCCATTTCGCGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATC
* *
16183 TCGCATTGCGATCGTGTACAGTGTCGTTGCGAT
1 TCGCGTTGCGATAGTGTACAGTGTCGTTGCGAT
16216 TTTCCATTTC
Statistics
Matches: 119, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
103 34 0.29
104 2 0.02
107 1 0.01
109 4 0.03
110 78 0.66
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (103 bp):
TCGCGTTGCGATAGTGTACAGTGTCGTTGCGATAGTCTACAGTGTCGTTGCGATTTTCCATTTCG
CGTTGCGATAGTCTACAGTGTCATTGCGATTTTCCATC
Found at i:17106 original size:8 final size:8
Alignment explanation
Indices: 17093--17152 Score: 70
Period size: 8 Copynumber: 7.6 Consensus size: 8
17083 AACCCGACCC
17093 GACCCGTT
1 GACCCGTT
**
17101 GACCCGACC
1 GACCCG-TT
17110 GACCCGTT
1 GACCCGTT
*
17118 GACCTGTT
1 GACCCGTT
17126 GA-CCGTT
1 GACCCGTT
17133 GACCCGTT
1 GACCCGTT
17141 GA-CCGTT
1 GACCCGTT
17148 GACCC
1 GACCC
17153 TCATTGACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
7 13 0.30
8 24 0.56
9 6 0.14
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.22
Consensus pattern (8 bp):
GACCCGTT
Found at i:17113 original size:17 final size:18
Alignment explanation
Indices: 17084--17121 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
17074 GCCGGTCACA
17084 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
17102 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
17119 ACC
1 ACC
17122 TGTTGACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.18, C:0.50, G:0.21, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:17133 original size:15 final size:15
Alignment explanation
Indices: 17113--17152 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
17103 CCCGACCGAC
*
17113 CCGTTGACCTGTTGA
1 CCGTTGACCCGTTGA
17128 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
17143 CCGTTGACCC
1 CCGTTGACCC
17153 TCATTGACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.12, C:0.35, G:0.25, T:0.28
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:17135 original size:7 final size:7
Alignment explanation
Indices: 17113--17151 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
17103 CCCGACCGAC
17113 CCGTTGA
1 CCGTTGA
17120 CCTGTTGA
1 CC-GTTGA
17128 CCGTTGA
1 CCGTTGA
17135 CCCGTTGA
1 -CCGTTGA
17143 CCGTTGA
1 CCGTTGA
17150 CC
1 CC
17152 CTCATTGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.13, C:0.33, G:0.26, T:0.28
Consensus pattern (7 bp):
CCGTTGA
Found at i:18474 original size:18 final size:18
Alignment explanation
Indices: 18448--18483 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18438 TCGAAAGGAC
*
18448 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
18466 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
18484 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:19663 original size:23 final size:23
Alignment explanation
Indices: 19637--19710 Score: 87
Period size: 23 Copynumber: 3.2 Consensus size: 23
19627 AATTCTATTA
*
19637 TGATCCTGACCTGGATTCTGATC
1 TGATCATGACCTGGATTCTGATC
* *
19660 TGAT-ATTGACATTGATTCTGATC
1 TGATCA-TGACCTGGATTCTGATC
*
19683 TGATACATGACCTGGATTCTGATA
1 TGAT-CATGACCTGGATTCTGATC
19707 TGAT
1 TGAT
19711 ACTTGACTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 23 0.55
24 18 0.43
25 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (23 bp):
TGATCATGACCTGGATTCTGATC
Found at i:19700 original size:24 final size:24
Alignment explanation
Indices: 19643--19717 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
19633 ATTATGATCC
19643 TGACCTGGATTCTGATCTGATA-T
1 TGACCTGGATTCTGATCTGATACT
* * *
19666 TGACATTGATTCTGATCTGATACA
1 TGACCTGGATTCTGATCTGATACT
*
19690 TGACCTGGATTCTGATATGATACT
1 TGACCTGGATTCTGATCTGATACT
19714 TGAC
1 TGAC
19718 TTGAATTATG
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 20 0.45
24 24 0.55
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (24 bp):
TGACCTGGATTCTGATCTGATACT
Found at i:21092 original size:6 final size:6
Alignment explanation
Indices: 21083--21107 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21073 CCGTCTCGTC
21083 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
21108 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:21187 original size:21 final size:21
Alignment explanation
Indices: 21161--21229 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
21151 AGAAAATTAG
21161 CGCAACGACACTGTAAACTAT
1 CGCAACGACACTGTAAACTAT
* *
21182 CGCAACG-CGAAATGGAAA--AT
1 CGCAACGAC--ACTGTAAACTAT
* *
21202 CGTAACGACACTGTAGACTAT
1 CGCAACGACACTGTAAACTAT
21223 CGCAACG
1 CGCAACG
21230 CGAAAAGGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
19 5 0.14
20 9 0.25
21 16 0.44
22 6 0.17
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (21 bp):
CGCAACGACACTGTAAACTAT
Found at i:21208 original size:20 final size:20
Alignment explanation
Indices: 21180--21293 Score: 61
Period size: 20 Copynumber: 5.6 Consensus size: 20
21170 ACTGTAAACT
21180 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * **
21200 ATCGTAA--CGACACTGTAGACT
1 ATCGCAACGCGA-AATG--GAAA
*
21221 ATCGCAACGCGAAAAGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
21241 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
21262 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
*
21282 ATCGCAATGCGA
1 ATCGCAACGCGA
21294 TTTTCAACTA
Statistics
Matches: 65, Mismatches: 23, Indels: 12
0.65 0.23 0.12
Matches are distributed among these distances:
18 3 0.05
19 3 0.05
20 32 0.49
21 22 0.34
22 2 0.03
23 3 0.05
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:21270 original size:21 final size:21
Alignment explanation
Indices: 21241--21314 Score: 78
Period size: 21 Copynumber: 3.6 Consensus size: 21
21231 GAAAAGGAAA
*
21241 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
21262 ATCGCAACGCGAAATAGAA-A
1 ATCGCAACGCGATTTTCAACT
*
21282 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
21303 ATCGCAACGCGA
1 ATCGCAACGCGA
21315 ATTTGCGATA
Statistics
Matches: 39, Mismatches: 13, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:21294 original size:41 final size:41
Alignment explanation
Indices: 21176--21315 Score: 187
Period size: 41 Copynumber: 3.4 Consensus size: 41
21166 CGACACTGTA
* * *
21176 AACTATCGCAACGCGAAATGGAAAATCGTAACGAC-ACTGT-
1 AACTATCGCAACGCGAAATAGAAAATCGTAACG-CGATTTTC
21216 AGACTATCGCAACGCGAAA-AGGAAAATCGTAACGCGATTTTC
1 A-ACTATCGCAACGCGAAATA-GAAAATCGTAACGCGATTTTC
* *
21258 AACTATCGCAACGCGAAATAGAAAATCGCAATGCGATTTTC
1 AACTATCGCAACGCGAAATAGAAAATCGTAACGCGATTTTC
21299 AACTATCGCAACGCGAA
1 AACTATCGCAACGCGAA
21316 TTTGCGATAT
Statistics
Matches: 90, Mismatches: 5, Indels: 9
0.87 0.05 0.09
Matches are distributed among these distances:
40 2 0.02
41 86 0.96
42 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (41 bp):
AACTATCGCAACGCGAAATAGAAAATCGTAACGCGATTTTC
Found at i:21359 original size:19 final size:20
Alignment explanation
Indices: 21317--21362 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
21307 CAACGCGAAT
* * *
21317 TTGCGATATTGGATATCGCG
1 TTGCGATATTAGAGATCGCA
21337 TTGCGA-ATTAGAGATCGCA
1 TTGCGATATTAGAGATCGCA
21356 TTGCGAT
1 TTGCGAT
21363 TTTGTTGGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (20 bp):
TTGCGATATTAGAGATCGCA
Found at i:25686 original size:16 final size:16
Alignment explanation
Indices: 25665--25702 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
25655 TTAAAAATCT
25665 AAATATAAT-TTAATTA
1 AAATATAATATTAA-TA
*
25681 AAATATAATATTTATA
1 AAATATAATATTAATA
25697 AAATAT
1 AAATAT
25703 TAGTTTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATAATATTAATA
Found at i:30908 original size:16 final size:18
Alignment explanation
Indices: 30887--30920 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30877 AATTTTGAAG
30887 CAAATAA-A-TAAAATTA
1 CAAATAATAGTAAAATTA
30903 CAAATAATAGTAAAATTA
1 CAAATAATAGTAAAATTA
30921 AATATTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 1 0.06
18 8 0.50
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
CAAATAATAGTAAAATTA
Found at i:30947 original size:25 final size:24
Alignment explanation
Indices: 30890--30947 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
30880 TTTGAAGCAA
30890 ATAAATAAAATTACAAATAATAGT
1 ATAAATAAAATTACAAATAATAGT
30914 A-AAATTAAATATTA-AAAGT-ATAGGT
1 ATAAA-TAAA-ATTACAAA-TAATA-GT
30939 ATAAATAAA
1 ATAAATAAA
30948 CAACGTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
23 3 0.10
24 11 0.38
25 12 0.41
26 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (24 bp):
ATAAATAAAATTACAAATAATAGT
Found at i:31151 original size:18 final size:20
Alignment explanation
Indices: 31095--31153 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 20
31085 ATAATGATGC
*
31095 CTTTGTGGCACGTTTATCTCTGT
1 CTTTGTAGCACGTTT-T-TC-GT
31118 CTTTGTAGCACGTTTTTCGT
1 CTTTGTAGCACGTTTTTCGT
31138 CTTT-TAGC-CGTTTTTC
1 CTTTGTAGCACGTTTTTC
31154 CTATTTTATG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 8 0.23
19 4 0.11
20 6 0.17
21 2 0.06
22 1 0.03
23 14 0.40
ACGTcount: A:0.08, C:0.22, G:0.19, T:0.51
Consensus pattern (20 bp):
CTTTGTAGCACGTTTTTCGT
Found at i:31160 original size:18 final size:19
Alignment explanation
Indices: 31123--31161 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31113 TCTGTCTTTG
* *
31123 TAGCACGTTTTTCGTCTTT
1 TAGCACGTTTTTCCTATTT
31142 TAGC-CGTTTTTCCTATTT
1 TAGCACGTTTTTCCTATTT
31160 TA
1 TA
31162 TGTTTTCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.54
Consensus pattern (19 bp):
TAGCACGTTTTTCCTATTT
Found at i:35825 original size:2 final size:2
Alignment explanation
Indices: 35818--35857 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
35808 AAAGGACATC
35818 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35858 GATTGGGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36444 original size:16 final size:17
Alignment explanation
Indices: 36423--36465 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
36413 ATATAAAAAC
36423 AAATATTTAAATTTA-A
1 AAATATTTAAATTTATA
** *
36439 AAATATAAAAATTTATT
1 AAATATTTAAATTTATA
36456 AAATATTTAA
1 AAATATTTAA
36466 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTTAAATTTATA
Found at i:40703 original size:20 final size:21
Alignment explanation
Indices: 40669--40712 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
40659 TGGGGAATTT
40669 AGAATGAAGAGATGAAGAAGG
1 AGAATGAAGAGATGAAGAAGG
* *
40690 AGAA-GAAGATATGAAGAGGG
1 AGAATGAAGAGATGAAGAAGG
40710 AGA
1 AGA
40713 GGAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.39, T:0.09
Consensus pattern (21 bp):
AGAATGAAGAGATGAAGAAGG
Found at i:41424 original size:17 final size:17
Alignment explanation
Indices: 41404--41449 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
41394 TATAACTTCT
*
41404 ATAAATTAATAATTTTG
1 ATAAATTAATAATTTTA
* *
41421 ATAATTTAATTATTTTA
1 ATAAATTAATAATTTTA
41438 ATAAATTAATAA
1 ATAAATTAATAA
41450 GATAATAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (17 bp):
ATAAATTAATAATTTTA
Found at i:45363 original size:4 final size:4
Alignment explanation
Indices: 45333--45381 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
45323 GCACCTCTTT
* * * * *
45333 TATA TACA TACA TACA TACA TACA TATA TATA TATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
45381 T
1 T
45382 TCATTTAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (4 bp):
TATA
Found at i:48433 original size:3 final size:3
Alignment explanation
Indices: 48425--48569 Score: 218
Period size: 3 Copynumber: 47.7 Consensus size: 3
48415 GTAATATTTA
*
48425 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* *
48472 AAT AAT AAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
48520 AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48568 AA
1 AA
48570 ATTTAAATGA
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 122 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:48827 original size:76 final size:76
Alignment explanation
Indices: 48701--50173 Score: 2858
Period size: 76 Copynumber: 19.4 Consensus size: 76
48691 AAATGTTTTA
*
48701 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48766 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48777 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48842 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48853 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48918 AGGCTTTTTGG
66 AGGCTTTTTGG
*
48929 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
48994 AGGCTTTTTGG
66 AGGCTTTTTGG
49005 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49069 AGGCTTTTTGG
66 AGGCTTTTTGG
49080 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49145 AGGCTTTTTGG
66 AGGCTTTTTGG
49156 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49221 AGGCTTTTTGG
66 AGGCTTTTTGG
49232 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49297 AGGCTTTTTGG
66 AGGCTTTTTGG
49308 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49373 AGGCTTTTTGG
66 AGGCTTTTTGG
49384 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49449 AGGCTTTTTGG
66 AGGCTTTTTGG
49460 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49525 AGGCTTTTTGG
66 AGGCTTTTTGG
49536 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49601 AGGCTTTTTGG
66 AGGCTTTTTGG
*
49612 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49677 AGGCTTTTTGG
66 AGGCTTTTTGG
*
49688 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49753 AGGCTTTTTGG
66 AGGCTTTTTGG
*
49764 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49829 AGGCTTTTTGG
66 AGGCTTTTTGG
*
49840 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49905 AGGCTTTTTGG
66 AGGCTTTTTGG
*
49916 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
49981 AGGCTTTTTGG
66 AGGCTTTTTGG
49992 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
50057 AGGCTTTTTGG
66 AGGCTTTTTGG
50068 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
50133 AGGCTTTTTGG
66 AGGCTTTTTGG
50144 AAACATCATGCACTGAAGGACTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
50174 TGGGAAATAG
Statistics
Matches: 1381, Mismatches: 15, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 0.05
76 1306 0.95
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:51309 original size:54 final size:54
Alignment explanation
Indices: 51220--51429 Score: 296
Period size: 54 Copynumber: 3.9 Consensus size: 54
51210 ATAATCACTG
* * *
51220 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGTGACTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGACTTCTGCTCAGAT
* * * * ** *
51274 GTTCATAAAATATTTGACCACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGACTTCTGCTCAGAT
*
51328 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGT-AGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGA-CTTCTGCTCAGAT
*
51382 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGACTTCTGC
51430 CAAGATTTCT
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
54 136 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGACTTCTGCTCAGAT
Found at i:51359 original size:108 final size:108
Alignment explanation
Indices: 51220--51428 Score: 339
Period size: 108 Copynumber: 1.9 Consensus size: 108
51210 ATAATCACTG
* *
51220 GTTCGTAAAACATTTGACAATACATTCATCTTTTCCTGT-GACTTCTGCTCAGATGTTCATAAAA
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTAG-CTTCTGCTCAGATGTTCATAAAA
* * * *
51284 TATTTGACCACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
65 CATTTGACAACACATTCATCCTTTACTGTGGCTTCTGTTCAGAT
*
51328 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTAGCTTCTGCTCAGATGTTCGTAAAAC
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTAGCTTCTGCTCAGATGTTCATAAAAC
51393 ATTTGACAACACATTCATCCTTTACTGTGGCTTCTG
66 ATTTGACAACACATTCATCCTTTACTGTGGCTTCTG
51429 CCAAGATTTC
Statistics
Matches: 93, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 92 0.99
109 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (108 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTACTGTAGCTTCTGCTCAGATGTTCATAAAAC
ATTTGACAACACATTCATCCTTTACTGTGGCTTCTGTTCAGAT
Found at i:52465 original size:74 final size:75
Alignment explanation
Indices: 52293--52466 Score: 185
Period size: 75 Copynumber: 2.3 Consensus size: 75
52283 GATGTGGGCC
* * *
52293 TTCAGCATGCCCCAACAATTGCTGATACGATCATTCAAAAATGCATCAACAGTTCTGATTCTGAT
1 TTCAGCATGCCCCAATATTTGCTGATACAATCATTCAAAAAT-CATCAACAGTTCTGATTCTGAT
**
52358 TGAAATGGGTT
65 TGAAAAAGGTT
* * * *
52369 TTCAGCATGCCCCAGCAT-TTTGCTGATA-AAT-ATTCAGAATAT-TTCAACATTTTTGATTCTG
1 TTCAGCATGCCCCA--ATATTTGCTGATACAATCATTCA-AAAATCATCAACAGTTCTGATTCTG
*
52430 TTTGAAAAAAGGTT
63 ATTG-AAAAAGGTT
52444 TTCAGCATGCCCCAATATTTGCT
1 TTCAGCATGCCCCAATATTTGCT
52467 TCTTGTTAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
73 2 0.02
74 25 0.30
75 26 0.31
76 20 0.24
77 9 0.11
78 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (75 bp):
TTCAGCATGCCCCAATATTTGCTGATACAATCATTCAAAAATCATCAACAGTTCTGATTCTGATT
GAAAAAGGTT
Found at i:53809 original size:83 final size:83
Alignment explanation
Indices: 53669--53933 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
53659 TTTATTTCTA
* *
53669 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATTAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTG-CCAAACCAGATCAGATAACTCAA
53733 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
53752 CTATGAACAAATTCATCTTCTAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
53817 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
53835 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
53900 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
53918 CTATGAGCACATTCAT
1 CTATGAGCAAATTCAT
53934 TTGTTCCATT
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 2 0.01
83 172 0.99
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:62963 original size:3 final size:3
Alignment explanation
Indices: 62955--63100 Score: 211
Period size: 3 Copynumber: 47.7 Consensus size: 3
62945 GTAATATTTA
*
62955 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* *
63002 AAT AATT AAT TAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* **
63048 AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT AAT TTT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
63096 AAT AA
1 AAT AA
63101 ATTTAAATGA
Statistics
Matches: 128, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
3 119 0.93
4 9 0.07
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:68620 original size:21 final size:21
Alignment explanation
Indices: 68594--68635 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68584 GAATCATTGA
*
68594 GCCCTG-TGTGATCTTGTCTTT
1 GCCCTGTTGTAATCTT-TCTTT
68615 GCCCTGTTGTAATCTTTCTTT
1 GCCCTGTTGTAATCTTTCTTT
68636 CTTCCCCCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.07, C:0.24, G:0.19, T:0.50
Consensus pattern (21 bp):
GCCCTGTTGTAATCTTTCTTT
Found at i:76681 original size:17 final size:18
Alignment explanation
Indices: 76655--76690 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
76645 ATAATTTTCG
76655 TATTTAAATTTA-AATAT
1 TATTTAAATTTATAATAT
*
76672 TATTTGAATTTATAATAT
1 TATTTAAATTTATAATAT
76690 T
1 T
76691 TAAATCCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTAAATTTATAATAT
Found at i:82217 original size:15 final size:15
Alignment explanation
Indices: 82193--82226 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
82183 TTCAAAATAA
82193 AAAATAATTTAAATC
1 AAAATAATTTAAATC
* *
82208 AAAATGATTTATATC
1 AAAATAATTTAAATC
82223 AAAA
1 AAAA
82227 ATAACTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAATAATTTAAATC
Found at i:82750 original size:22 final size:21
Alignment explanation
Indices: 82725--82789 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
82715 TACTATTTTT
82725 AATTTATATATTTTCTTTATAA
1 AATTTATATATTTT-TTTATAA
*
82747 AATTTA-A-A----TTGATAA
1 AATTTATATATTTTTTTATAA
82762 AATTTATATAATTTTTTTATAA
1 AATTTATAT-ATTTTTTTATAA
82784 AATTTA
1 AATTTA
82790 AAAGATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
15 12 0.35
16 1 0.03
18 1 0.03
20 1 0.03
21 1 0.03
22 18 0.53
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
AATTTATATATTTTTTTATAA
Found at i:89318 original size:2 final size:2
Alignment explanation
Indices: 89311--89348 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
89301 TCTTTACTCA
89311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89349 GAATTCATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92495 original size:23 final size:23
Alignment explanation
Indices: 92469--92534 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
92459 ATAATTTTAA
*
92469 AAAATATATAAATTTTAAAAAAT
1 AAAATATATAAATTTTAAAAAAG
*
92492 AAAAT-TATATATTTTTAAAAAAG
1 AAAATATATA-AATTTTAAAAAAG
* * *
92515 AAAACACATAAATTTCAAAA
1 AAAATATATAAATTTTAAAA
92535 TAACCCCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 4 0.11
23 28 0.80
24 3 0.09
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
AAAATATATAAATTTTAAAAAAG
Found at i:92768 original size:12 final size:12
Alignment explanation
Indices: 92751--92782 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
92741 TGACGGCCAA
92751 ACGACGACAACT
1 ACGACGACAACT
92763 ACGACGACAACT
1 ACGACGACAACT
92775 ACGACGAC
1 ACGACGAC
92783 TTATAACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.34, G:0.19, T:0.06
Consensus pattern (12 bp):
ACGACGACAACT
Found at i:95255 original size:41 final size:41
Alignment explanation
Indices: 95197--95316 Score: 195
Period size: 41 Copynumber: 2.9 Consensus size: 41
95187 CTTGAATGGG
*
95197 AGAAACAGTATACATTGATGGTATATGATCTTAGCATTGCT
1 AGAAACAGTATATATTGATGGTATATGATCTTAGCATTGCT
*
95238 AGAAACAGTATATATTGATGGTATATGATCTTAGCACTGCT
1 AGAAACAGTATATATTGATGGTATATGATCTTAGCATTGCT
* * *
95279 AGAAACAGTATATATTGATGTTATATGATGTTAACATT
1 AGAAACAGTATATATTGATGGTATATGATCTTAGCATT
95317 TGGGACTCCA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (41 bp):
AGAAACAGTATATATTGATGGTATATGATCTTAGCATTGCT
Found at i:96680 original size:13 final size:12
Alignment explanation
Indices: 96662--96699 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
96652 CTTCATAAAT
96662 ATTTTTTAATTTA
1 ATTTTTTAA-TTA
96675 ATTTTTTAATTA
1 ATTTTTTAATTA
*
96687 A-TTTATAATTA
1 ATTTTTTAATTA
96698 AT
1 AT
96700 AATTTTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 4 0.17
13 9 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (12 bp):
ATTTTTTAATTA
Found at i:96726 original size:18 final size:16
Alignment explanation
Indices: 96687--96729 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
96677 TTTTTAATTA
96687 ATTTATAATTAATAAT
1 ATTTATAATTAATAAT
*
96703 -TTTATAAGTTCATATAT
1 ATTTATAA-TTAATA-AT
96720 ATTTATAATT
1 ATTTATAATT
96730 TATTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 7 0.30
16 5 0.22
17 4 0.17
18 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTTATAATTAATAAT
Found at i:96767 original size:18 final size:18
Alignment explanation
Indices: 96718--96769 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
96708 AAGTTCATAT
*
96718 ATATTT-ATAATTTATTTT
1 ATATTTAATAATTT-TTTA
* * *
96736 ATTTTTAGTCATTTTTTA
1 ATATTTAATAATTTTTTA
96754 ATATTTAATAATTTTT
1 ATATTTAATAATTTTT
96770 AGTTTTGTTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
ATATTTAATAATTTTTTA
Found at i:96780 original size:28 final size:29
Alignment explanation
Indices: 96736--96799 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
96726 AATTTATTTT
* *
96736 ATTTTTAGTCATTTTTTAATATTTAAT-A
1 ATTTTTAGTCATTTTTTAAGATTAAATAA
*
96764 ATTTTTAGT-TTTGTTTTAAGATTAAATAA
1 ATTTTTAGTCATT-TTTTAAGATTAAATAA
96793 ATTTTTA
1 ATTTTTA
96800 ACATAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 21 0.68
29 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (29 bp):
ATTTTTAGTCATTTTTTAAGATTAAATAA
Found at i:98377 original size:33 final size:33
Alignment explanation
Indices: 98340--98425 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
98330 GAATGGTGGA
*
98340 GGAGGAGGT-GAGGGTGGCGGAGG-AGGGGAAGGG
1 GGAGGAGGTGGA-GGTGGCGGAGGAAAGGG-AGGG
* * *
98373 GGAGGAGGCGGAGGTGGTGGAGGAAATGGAGGG
1 GGAGGAGGTGGAGGTGGCGGAGGAAAGGGAGGG
*
98406 GGAGGAGGTGGCGGTGGCGG
1 GGAGGAGGTGGAGGTGGCGG
98426 TGGGGCAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
33 39 0.89
34 5 0.11
ACGTcount: A:0.20, C:0.05, G:0.67, T:0.08
Consensus pattern (33 bp):
GGAGGAGGTGGAGGTGGCGGAGGAAAGGGAGGG
Found at i:98379 original size:18 final size:18
Alignment explanation
Indices: 98334--98380 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
98324 TGGCGGGAAT
*
98334 GGTGGAGGAGGAGGTGAG
1 GGTGGAGGAGGAGGGGAG
*
98352 GGTGGCGGAGGAGGGGAAG
1 GGTGGAGGAGGAGGGG-AG
98371 GG-GGAGGAGG
1 GGTGGAGGAGG
98381 CGGAGGTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.21, C:0.02, G:0.70, T:0.06
Consensus pattern (18 bp):
GGTGGAGGAGGAGGGGAG
Found at i:98394 original size:18 final size:16
Alignment explanation
Indices: 98334--98396 Score: 56
Period size: 18 Copynumber: 3.7 Consensus size: 16
98324 TGGCGGGAAT
*
98334 GGTGGAGGAGGAGGTGA
1 GGTGG-GGAGGAGGGGA
98351 GGGTGGCGGAGGAGGGGA
1 -GGTGG-GGAGGAGGGGA
*
98369 AG-GGGGAGGAGGCGGA
1 GGTGGGGAGGAGG-GGA
98385 GGTGGTGGAGGA
1 GGTGG-GGAGGA
98397 AATGGAGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 8 0.21
16 6 0.16
17 3 0.08
18 21 0.55
ACGTcount: A:0.21, C:0.03, G:0.68, T:0.08
Consensus pattern (16 bp):
GGTGGGGAGGAGGGGA
Found at i:100564 original size:16 final size:16
Alignment explanation
Indices: 100543--100576 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
100533 TTACTATTCA
*
100543 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
100559 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
100575 CG
1 CG
100577 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:101344 original size:15 final size:16
Alignment explanation
Indices: 101326--101358 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
101316 GTGGCAGATC
101326 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
101341 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
101357 AA
1 AA
101359 GAAAGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:118005 original size:29 final size:28
Alignment explanation
Indices: 117972--118031 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
117962 ATTTTGTTAA
*
117972 GTCATCCAACTATTAAAAGTTACAAAATG
1 GTCAT-CAACTATTAAAAGTTACAAAAAG
** *
118001 GTCATTGACTATTAAAAGTTATAAAAAG
1 GTCATCAACTATTAAAAGTTACAAAAAG
118029 GTC
1 GTC
118032 CCCGACTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (28 bp):
GTCATCAACTATTAAAAGTTACAAAAAG
Found at i:118038 original size:28 final size:28
Alignment explanation
Indices: 117980--118040 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
117970 AAGTCATCCA
* **
117980 ACTATTAAAAGTTACAAAATGGTCATTG
1 ACTATTAAAAGTTACAAAAAGGTCACCG
* *
118008 ACTATTAAAAGTTATAAAAAGGTCCCCG
1 ACTATTAAAAGTTACAAAAAGGTCACCG
118036 ACTAT
1 ACTAT
118041 GGGAAGTTGC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (28 bp):
ACTATTAAAAGTTACAAAAAGGTCACCG
Found at i:119426 original size:36 final size:37
Alignment explanation
Indices: 119381--119474 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 37
119371 AGTATATATG
* *
119381 TAATAATATAATTTTTGAAAATATTTTTTGAAA-CATA
1 TAAT-ATATAGTTTTAGAAAATATTTTTTGAAAGCATA
* * *
119418 TAATATATAGTTTTAGAAGATGTTTTTTGAAAGTATA
1 TAATATATAGTTTTAGAAAATATTTTTTGAAAGCATA
* *
119455 TAAGATATAGTTTTAAAAAA
1 TAATATATAGTTTTAGAAAA
119475 AATAGGTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 24 0.50
37 24 0.50
ACGTcount: A:0.45, C:0.01, G:0.11, T:0.44
Consensus pattern (37 bp):
TAATATATAGTTTTAGAAAATATTTTTTGAAAGCATA
Found at i:119547 original size:91 final size:91
Alignment explanation
Indices: 119392--119566 Score: 221
Period size: 89 Copynumber: 1.9 Consensus size: 91
119382 AATAATATAA
* * * * * * **
119392 TTTTTGAAAATATTTTTTGAAACATATAATATATAGTTTTAGAAGATGTTTTTTGAAAGTATAT-
1 TTTTTGAAAATATGTTTTAAAAAATATAATATATAGTTTTAAAACACGTTTTTTGAAAACATATA
119456 A-AGATATAGTTTTAAAAAAAATAGG
66 ATAGATATAGTTTTAAAAAAAATAGG
119481 TTTTTGAAAATATGTTTTAAAAAATATATATTATATAGTTTTGAAAACACG-TTTTTGAAAACAT
1 TTTTTGAAAATATGTTTTAAAAAATATA-A-TATATAGTTTT-AAAACACGTTTTTTGAAAACAT
*
119545 ATAATATATATAGTTTTAAAAA
63 ATAATAGATATAGTTTTAAAAA
119567 CAAGTTTTGA
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
89 25 0.35
90 1 0.01
91 24 0.33
92 6 0.08
93 16 0.22
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (91 bp):
TTTTTGAAAATATGTTTTAAAAAATATAATATATAGTTTTAAAACACGTTTTTTGAAAACATATA
ATAGATATAGTTTTAAAAAAAATAGG
Found at i:119558 original size:39 final size:38
Alignment explanation
Indices: 119482--119584 Score: 129
Period size: 39 Copynumber: 2.7 Consensus size: 38
119472 AAAAATAGGT
* * *
119482 TTTTGAAAATATGTTTT-AAAAAATATATATTATATAG
1 TTTTGAAAACAAGTTTTGAAAACATATATATTATATAG
*
119519 TTTTGAAAACACGTTTTTGAAAACATATA-ATATATATAG
1 TTTTGAAAACAAG-TTTTGAAAACATATATAT-TATATAG
*
119558 TTTTAAAAACAAGTTTTGAAAACATAT
1 TTTTGAAAACAAGTTTTGAAAACATAT
119585 TTTGAATATA
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
37 11 0.19
38 20 0.34
39 27 0.47
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.41
Consensus pattern (38 bp):
TTTTGAAAACAAGTTTTGAAAACATATATATTATATAG
Found at i:119597 original size:2 final size:2
Alignment explanation
Indices: 119590--119624 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
119580 CATATTTTGA
119590 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119625 ATAGTTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:119686 original size:16 final size:15
Alignment explanation
Indices: 119662--119699 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
119652 CATATATAAT
119662 ATATAATTTTTTGAAA
1 ATATAA-TTTTTGAAA
*
119678 ATATTATTTTTGAAA
1 ATATAATTTTTGAAA
119693 ATATAAT
1 ATATAAT
119700 ATTATATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
ATATAATTTTTGAAA
Found at i:119725 original size:10 final size:10
Alignment explanation
Indices: 119698--119835 Score: 80
Period size: 10 Copynumber: 13.8 Consensus size: 10
119688 TGAAAATATA
*
119698 ATATTATATAG
1 ATATTAT-TAT
*
119709 ATTTTATTAT
1 ATATTATTAT
119719 ATATTA-TAT
1 ATATTATTAT
119728 -TA-TATTAT
1 ATATTATTAT
119736 ATAGTATATTA-
1 ATA-T-TATTAT
119747 ATATTATT-T
1 ATATTATTAT
119756 ATTATTATT-T
1 A-TATTATTAT
*
119766 GTA-T-TTAT
1 ATATTATTAT
119774 ATA-TATT-T
1 ATATTATTAT
119782 ATATATATTAT
1 ATAT-TATTAT
119793 ATATTATTATT
1 ATATTATTA-T
*
119804 ATTTATATTAT
1 ATAT-TATTAT
119815 ATATTTATTTATT
1 ATA-TTA-TTA-T
119828 ATATTATT
1 ATATTATT
119836 TTTTATTTTT
Statistics
Matches: 103, Mismatches: 7, Indels: 34
0.72 0.05 0.24
Matches are distributed among these distances:
7 4 0.04
8 14 0.14
9 14 0.14
10 25 0.24
11 25 0.24
12 17 0.17
13 4 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATATTATTAT
Found at i:119754 original size:26 final size:27
Alignment explanation
Indices: 119693--119834 Score: 86
Period size: 26 Copynumber: 5.3 Consensus size: 27
119683 ATTTTTGAAA
* *
119693 ATATAATATTATATAGATTTTATTATATATT
1 ATATTATATTATATAG--TATATTA-ATA-T
119724 ATATTATATTATATAGTATATTAATAT
1 ATATTATATTATATAGTATATTAATAT
*
119751 -TATT-TATTATTATTTGTAT-TT-ATAT
1 ATATTATATTA-TA-TAGTATATTAATAT
*
119776 ATATT-TATATATATTA-TATATTATTAT
1 ATATTATAT-TATA-TAGTATATTAATAT
* *
119803 -TATTTATATTATATA-TTTATTTAT-T
1 ATA-TTATATTATATAGTATATTAATAT
119828 ATATTAT
1 ATATTAT
119835 TTTTTATTTT
Statistics
Matches: 94, Mismatches: 8, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
25 17 0.18
26 33 0.35
27 17 0.18
28 6 0.06
29 6 0.06
31 15 0.16
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
ATATTATATTATATAGTATATTAATAT
Found at i:119762 original size:79 final size:82
Alignment explanation
Indices: 119679--119848 Score: 187
Period size: 79 Copynumber: 2.1 Consensus size: 82
119669 TTTTTGAAAA
119679 TATTATTTTTGAAAATATA-ATA-TTATATAGATT-T-TATTATATATTATATTATATTATATAG
1 TATTATTTTTGAAAATATATATATTTATATAGATTATATATTAT-TATTAT-TTATATTATATA-
119740 TATA-TTA-ATATTATTTAT
63 TATATTTATATATTATTTAT
* ** * *
119758 TATTA--TTTGTATTTATATATATTTATATATATTATATATTATTATTATTTATATTATATATTT
1 TATTATTTTTGAAAATATATATATTTATATAGATTATATATTATTATTATTTATATTATATATAT
*
119821 ATTTATTATATTATTTTT
66 ATTTA-TATATTATTTAT
119839 TATT-TTTTTG
1 TATTATTTTTG
119849 TCGAGATCCA
Statistics
Matches: 76, Mismatches: 6, Indels: 15
0.78 0.06 0.15
Matches are distributed among these distances:
77 9 0.12
78 6 0.08
79 30 0.39
80 7 0.09
81 20 0.26
82 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (82 bp):
TATTATTTTTGAAAATATATATATTTATATAGATTATATATTATTATTATTTATATTATATATAT
ATTTATATATTATTTAT
Found at i:119770 original size:16 final size:17
Alignment explanation
Indices: 119711--119823 Score: 83
Period size: 16 Copynumber: 6.4 Consensus size: 17
119701 TTATATAGAT
119711 TTTATTATATATTATATTA
1 TTTATTATATATT-TA-TA
119730 TATTATATAGTATATTAATATTA
1 T-TTAT-TA-TATATT--TA-TA
*
119753 TTTATTAT-TATTTGTA
1 TTTATTATATATTTATA
119769 TTTA-TATATATTTATA
1 TTTATTATATATTTATA
*
119785 TATATTATATA-TTAT-
1 TTTATTATATATTTATA
119800 TATTATT-TATATTATATA
1 T-TTATTATATATT-TATA
119818 TTTATT
1 TTTATT
119824 TATTATATTA
Statistics
Matches: 80, Mismatches: 4, Indels: 22
0.75 0.04 0.21
Matches are distributed among these distances:
15 8 0.10
16 25 0.31
17 15 0.19
18 1 0.01
19 5 0.06
20 5 0.06
21 4 0.05
22 10 0.12
23 7 0.09
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTATTATATATTTATA
Found at i:119774 original size:69 final size:69
Alignment explanation
Indices: 119701--119829 Score: 176
Period size: 67 Copynumber: 1.9 Consensus size: 69
119691 AAATATAATA
119701 TTATATAGATTTTATTATATATTATAT-TATATTA-TATAGTATATTA-ATA-TTATTTATTATT
1 TTATATAGA-TTTA-TATATATTATATAT-TATTATTAT-GTATATTATATATTTATTTATTATT
119762 ATTTGTAT
62 ATTTGTAT
* *
119770 TTATATATATTTATATATATTATATATTATTATTATTTATATTATATATTTATTTATTAT
1 TTATATAGATTTATATATATTATATATTATTATTATGTATATTATATATTTATTTATTAT
119830 ATTATTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
67 24 0.44
68 11 0.20
69 19 0.35
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (69 bp):
TTATATAGATTTATATATATTATATATTATTATTATGTATATTATATATTTATTTATTATTATTT
GTAT
Found at i:119779 original size:42 final size:40
Alignment explanation
Indices: 119693--119847 Score: 138
Period size: 42 Copynumber: 3.8 Consensus size: 40
119683 ATTTTTGAAA
* *
119693 ATATA-ATATTATATAGATTTTATTA-TATATTATATTATATT
1 ATATATATATTATAT-TA-TTTATTATTATTTTATATTATA-T
119734 ATATAGTATATTAATATTATTTATTATTATTTGTAT-TTATAT
1 ATATA-TATATT-ATATTATTTATTATTATTT-TATATTATAT
* *
119776 ATATTTATA-TATATTATATATTATTATTATTTATATTATAT
1 ATATATATATTATATTATTTATTATTA-T-TTTATATTATAT
* * * *
119817 ATTTATTTATTATATTATTTTTTATTTTTTT
1 ATATATATATTATATTATTTATTATTATTTT
119848 GTCGAGATCC
Statistics
Matches: 95, Mismatches: 10, Indels: 19
0.77 0.08 0.15
Matches are distributed among these distances:
39 15 0.16
40 8 0.08
41 24 0.25
42 26 0.27
43 15 0.16
44 7 0.07
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (40 bp):
ATATATATATTATATTATTTATTATTATTTTATATTATAT
Found at i:121016 original size:45 final size:45
Alignment explanation
Indices: 120907--121058 Score: 170
Period size: 45 Copynumber: 3.4 Consensus size: 45
120897 AATTTGATCC
* * * *
120907 TTTAACACTTTCTTCA--TTT-TTTTAATTTTATTTCTTATAATA
1 TTTAACATTTTCTTCATTTTTATTTTATTTTTATTTCTTTTAAAA
120949 TTTAACA-TTTCTTTCTATTTTTATTTTATTTTTATTTCTTTTAAAA
1 TTTAACATTTTC-TTC-ATTTTTATTTTATTTTTATTTCTTTTAAAA
* * * *
120995 ATTAATATTTTCTTCATTTTTA-TTTATTTTAAATTTCTTTTAAAT
1 TTTAACATTTTCTTCATTTTTATTTTATTTT-TATTTCTTTTAAAA
121040 TTTAACATTTTCTTCATTT
1 TTTAACATTTTCTTCATTT
121059 ATTTATTTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
41 4 0.04
42 10 0.11
43 1 0.01
44 8 0.09
45 39 0.41
46 28 0.30
47 4 0.04
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (45 bp):
TTTAACATTTTCTTCATTTTTATTTTATTTTTATTTCTTTTAAAA
Found at i:121121 original size:17 final size:18
Alignment explanation
Indices: 121096--121129 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
121086 CTTTATTATT
*
121096 CTTTCTTTTTA-TCTTAA
1 CTTTATTTTTATTCTTAA
121113 CTTTATTTTTATTCTTA
1 CTTTATTTTTATTCTTA
121130 TTTCTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTATTTTTATTCTTAA
Found at i:129079 original size:2 final size:2
Alignment explanation
Indices: 129072--129101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
129062 TATTCAACCA
129072 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
129102 AACCCTCCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:132497 original size:13 final size:14
Alignment explanation
Indices: 132468--132509 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
132458 ACTTATAGTT
132468 TATATTTTAATTAA
1 TATATTTTAATTAA
132482 TATATTTTAA-TAA
1 TATATTTTAATTAA
*
132495 TATA-TGTAATTAA
1 TATATTTTAATTAA
132508 TA
1 TA
132510 CACTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 12 0.46
14 10 0.38
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (14 bp):
TATATTTTAATTAA
Found at i:132752 original size:159 final size:155
Alignment explanation
Indices: 132462--132776 Score: 569
Period size: 159 Copynumber: 2.0 Consensus size: 155
132452 TTTATCACTT
132462 ATAGTTTATATTTTAATTAATATATTTTAATAATATATGTAATTAATACACTTTTTTATAAATCA
1 ATAGTTTATA-TTTAATTAATATATTTTAATAATATATGTAATTAATACACTTTTTTATAAATCA
132527 GTATATTCTATATTATATAAATTATAATTAATGTTATAATTAATATCTTTATACATATATAATTA
65 GTATATTCTATATTATATAAATTATAATTAATGTTATAATTAATATCTTTATACATATATAATTA
132592 ATTTCTATGGTAATTTAATTTAACAA
130 ATTTCTATGGTAATTTAATTTAACAA
132618 ATAGTTTATA-TTAATTAATATATTTTAATAATATATGTAATTAATACACTTTTTTTATAAATCA
1 ATAGTTTATATTTAATTAATATATTTTAATAATATATGTAATTAATACAC-TTTTTTATAAATCA
132682 GTATATTCTATATTATTATAAAATTCTATAATTAATGTTATAATTAATATCTTTATACATATATA
65 GTATATTCTATATTA-TAT-AAA-T-TATAATTAATGTTATAATTAATATCTTTATACATATATA
132747 ATTAATTTCTATGGTAATTTAATTTAACAA
126 ATTAATTTCTATGGTAATTTAATTTAACAA
132777 TAATATAATA
Statistics
Matches: 154, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
154 39 0.25
155 29 0.19
156 13 0.08
157 3 0.02
158 1 0.01
159 69 0.45
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (155 bp):
ATAGTTTATATTTAATTAATATATTTTAATAATATATGTAATTAATACACTTTTTTATAAATCAG
TATATTCTATATTATATAAATTATAATTAATGTTATAATTAATATCTTTATACATATATAATTAA
TTTCTATGGTAATTTAATTTAACAA
Found at i:135393 original size:27 final size:25
Alignment explanation
Indices: 135339--135393 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
135329 TATTTAAGAT
* *
135339 TATATATAATAAAAATAATATATTA
1 TATATATAATAAAAATAATAGATAA
135364 TATATATAATAAAGAATTAATAGATAA
1 TATATATAATAAA-AA-TAATAGATAA
135391 TAT
1 TAT
135394 TGACGAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 13 0.50
26 2 0.08
27 11 0.42
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (25 bp):
TATATATAATAAAAATAATAGATAA
Found at i:135598 original size:13 final size:13
Alignment explanation
Indices: 135566--135599 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
135556 TATCTATAGT
*
135566 ATTTATTTTGCAT
1 ATTTATTTTGCAG
*
135579 ATCTATTTTGCAG
1 ATTTATTTTGCAG
135592 ATTTATTT
1 ATTTATTT
135600 AATAAGTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (13 bp):
ATTTATTTTGCAG
Found at i:143160 original size:2 final size:2
Alignment explanation
Indices: 143150--143215 Score: 56
Period size: 2 Copynumber: 36.0 Consensus size: 2
143140 AAAAAATAAA
*
143150 AT AT A- AT AT AT AT AT AT AT A- AT -T AT AT AT AA ACT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
143189 AT -T AA AT -T AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
143216 TATGTTTAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
1 7 0.13
2 44 0.85
3 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:143199 original size:13 final size:12
Alignment explanation
Indices: 143158--143217 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 12
143148 AAATATAATA
143158 TATATATATATAAT
1 TATATAT-TA-AAT
*
143172 TATATA-TAAAC
1 TATATATTAAAT
143183 TATATTATTAAAT
1 TATA-TATTAAAT
143196 TATATA-TATAAT
1 TATATATTA-AAT
143208 ATATATATTA
1 -TATATATTA
143218 TGTTTAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 8 0.21
12 9 0.23
13 14 0.36
14 8 0.21
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (12 bp):
TATATATTAAAT
Found at i:143201 original size:24 final size:25
Alignment explanation
Indices: 143150--143217 Score: 95
Period size: 24 Copynumber: 2.7 Consensus size: 25
143140 AAAAAATAAA
143150 ATATAATATATATATATATAATTATAT
1 ATATAATATATATAT-TA-AATTATAT
143177 ATA-AACTATAT-TATTAAATTATAT
1 ATATAA-TATATATATTAAATTATAT
143201 ATATAATATATATATTA
1 ATATAATATATATATTA
143218 TGTTTAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 16 0.42
25 9 0.24
26 5 0.13
27 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (25 bp):
ATATAATATATATATTAAATTATAT
Found at i:143661 original size:2 final size:2
Alignment explanation
Indices: 143654--143876 Score: 232
Period size: 2 Copynumber: 115.0 Consensus size: 2
143644 CTTTCAATTT
* * *
143654 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TA AA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * * *
143697 TA TA TG TA TA TA TA TA -A AA TA TA GTA T- TA TA AA TG TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * *
143737 T- TA TA TA TG TA TA TA TA TG TA TA TA TA TA TA -A GTA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
143778 -A T- TA TA TA TA TA TA TA TA TA TA T- TA TG TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
143816 TA TA TA TA TA TA TA TA TC TA TA TA TA TA TA TA TC TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
143858 TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA
143877 GAAACACTAA
Statistics
Matches: 183, Mismatches: 25, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
1 10 0.05
2 169 0.92
3 4 0.02
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:144056 original size:19 final size:19
Alignment explanation
Indices: 144009--144073 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
143999 CTTATAGTAC
* * *
144009 ATATATGTATAAACCATGT
1 ATATATATATAAACTATAT
*
144028 AGAGTATATATAAACTATAT
1 ATA-TATATATAAACTATAT
* *
144048 ATATATATATAACCTGTAT
1 ATATATATATAAACTATAT
144067 ATATATA
1 ATATATA
144074 AACAATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 23 0.61
20 15 0.39
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (19 bp):
ATATATATATAAACTATAT
Found at i:144541 original size:20 final size:21
Alignment explanation
Indices: 144502--144560 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
144492 AAATAATTTT
* * *
144502 ATATAATATGTATGTATAAACC
1 ATAT-ATATATATATATAAACA
*
144524 ATGTATAT-TATATATAAACA
1 ATATATATATATATATAAACA
144544 ATATATATATATATATA
1 ATATATATATATATATA
144561 TAAACTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 17 0.53
21 12 0.38
22 3 0.09
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
ATATATATATATATATAAACA
Found at i:144562 original size:23 final size:22
Alignment explanation
Indices: 144527--144571 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
144517 ATAAACCATG
144527 TATATTATATATAAACAATATA
1 TATATTATATATAAACAATATA
*
144549 TATATATATATATAAACTATATA
1 TATAT-TATATATAAACAATATA
144572 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
TATATTATATATAAACAATATA
Found at i:145110 original size:11 final size:11
Alignment explanation
Indices: 145086--145139 Score: 63
Period size: 11 Copynumber: 4.9 Consensus size: 11
145076 CGATACCCTA
*
145086 CTACAGTGCTG
1 CTACAGTACTG
*
145097 CTATAGTACTG
1 CTACAGTACTG
* *
145108 CTATAGTATTG
1 CTACAGTACTG
145119 CTACAGTACTG
1 CTACAGTACTG
*
145130 GTACAGTACT
1 CTACAGTACT
145140 TCCGTAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (11 bp):
CTACAGTACTG
Found at i:145858 original size:24 final size:24
Alignment explanation
Indices: 145831--145896 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
145821 AGCTCGTATA
145831 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* *
145855 AATTTGCACCGAAGTGCCGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
*
145879 AA-ATGCACCGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
145897 TATAAGATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 13 0.35
24 24 0.65
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.21
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:147445 original size:137 final size:145
Alignment explanation
Indices: 147235--147519 Score: 489
Period size: 140 Copynumber: 2.0 Consensus size: 145
147225 CAAAATTTCA
147235 CTTCAAAACCCATTTTCTTTAATCTGTCATAACTCCTTTATCTTTTGAATTTAAGATAACTTAAG
1 CTTCAAAACCCATTTTCTTTAATCTGTCATAACTCCTTTATCTTTTGAATTTAAGATAACTTAAG
147300 CTTCATTAAGCTTAG-T-T-ATCTAATGATCAAAACCCAACCTTTAATTCAATAAATAATCAAC-
66 CTTCATTAAGCTTAGTTATCATCTAATGATCAAAACCCAACCTTTAATTCAATAAATAATCAACA
147361 AAATC-AAAACTCAC
131 AAATCAAAAACTCAC
*
147375 CTTCAAAACCCA-TTTC-TTAATC-GTCATAACTCCTTTTTC-TTTGAATTTAAGATAACTTAAG
1 CTTCAAAACCCATTTTCTTTAATCTGTCATAACTCCTTTATCTTTTGAATTTAAGATAACTTAAG
147436 CTTTCATTAAGCTTAGTTATCATCTAATGATCAAAACCCAACCTTTAATTCAATAAATAATCAAC
66 C-TTCATTAAGCTTAGTTATCATCTAATGATCAAAACCCAACCTTTAATTCAATAAATAATCAAC
147501 AAAATCAAAAACTCAC
130 AAAATCAAAAACTCAC
147517 CTT
1 CTT
147520 TGCCTAGCTT
Statistics
Matches: 138, Mismatches: 1, Indels: 10
0.93 0.01 0.07
Matches are distributed among these distances:
136 23 0.17
137 30 0.22
138 7 0.05
139 5 0.04
140 56 0.41
141 5 0.04
142 12 0.09
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (145 bp):
CTTCAAAACCCATTTTCTTTAATCTGTCATAACTCCTTTATCTTTTGAATTTAAGATAACTTAAG
CTTCATTAAGCTTAGTTATCATCTAATGATCAAAACCCAACCTTTAATTCAATAAATAATCAACA
AAATCAAAAACTCAC
Found at i:148094 original size:21 final size:21
Alignment explanation
Indices: 148070--148120 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
148060 TAGTTTATAG
**
148070 AAACCCTAAACTTTAAACCAT
1 AAACCCTAAACCCTAAACCAT
* *
148091 AAACACTAACCCCTAAACCAT
1 AAACCCTAAACCCTAAACCAT
148112 AAACCCTAA
1 AAACCCTAA
148121 TATAAATGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACCAT
Found at i:148118 original size:14 final size:14
Alignment explanation
Indices: 148070--148120 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
148060 TAGTTTATAG
**
148070 AAACCCTAAACTTT
1 AAACCCTAAACCAT
*
148084 AAACCATAAA-CACT
1 AAACCCTAAACCA-T
*
148098 AACCCCTAAACCAT
1 AAACCCTAAACCAT
148112 AAACCCTAA
1 AAACCCTAA
148121 TATAAATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 27 0.93
15 2 0.07
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:148466 original size:9 final size:9
Alignment explanation
Indices: 148443--148483 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
148433 TGCATGTATG
*
148443 GTATATATA
1 GTATATAAA
148452 -TATATAAA
1 GTATATAAA
*
148460 CTATATAAA
1 GTATATAAA
148469 GTA-ATAAA
1 GTATATAAA
148477 GTATATA
1 GTATATA
148484 GTTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.54
9 13 0.46
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (9 bp):
GTATATAAA
Found at i:148522 original size:7 final size:7
Alignment explanation
Indices: 148492--148569 Score: 50
Period size: 7 Copynumber: 11.3 Consensus size: 7
148482 TAGTTTATAA
148492 AAACCCT
1 AAACCCT
*
148499 AAGCCCT
1 AAACCCT
*
148506 AAGCCCT
1 AAACCCT
148513 AAACCCT
1 AAACCCT
***
148520 AAAATAT
1 AAACCCT
**
148527 AAACTTT
1 AAACCCT
*
148534 AAACCAT
1 AAACCCT
* *
148541 ACACACT
1 AAACCCT
148548 -AACCCT
1 AAACCCT
*
148554 AAACCAT
1 AAACCCT
148561 AAACCCT
1 AAACCCT
148568 AA
1 AA
148570 TATAAATAGA
Statistics
Matches: 54, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
6 4 0.07
7 50 0.93
ACGTcount: A:0.46, C:0.33, G:0.03, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:148967 original size:19 final size:19
Alignment explanation
Indices: 148918--148999 Score: 94
Period size: 19 Copynumber: 4.2 Consensus size: 19
148908 ATTTTATATA
* *
148918 ATATATATGTATAAACCAT
1 ATATATATATATAAACTAT
*
148937 GTATAGTATATATAAACTAT
1 ATATA-TATATATAAACTAT
148957 ATATATATATATATATTA-TAT
1 ATATATATATATA-A--ACTAT
148978 ATATATATATATAAACTAT
1 ATATATATATATAAACTAT
148997 ATA
1 ATA
149000 AGTAAATTAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.02
19 18 0.33
20 18 0.33
21 16 0.30
22 1 0.02
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (19 bp):
ATATATATATATAAACTAT
Found at i:148999 original size:2 final size:2
Alignment explanation
Indices: 148938--148990 Score: 72
Period size: 2 Copynumber: 26.0 Consensus size: 2
148928 ATAAACCATG
*
148938 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA T- TA TA TA TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
148981 TA TA TA TA TA
1 TA TA TA TA TA
148991 AACTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
1 1 0.02
2 42 0.91
3 3 0.07
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:149095 original size:21 final size:21
Alignment explanation
Indices: 149071--149121 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
149061 TAGTTTATAG
**
149071 AAACCCTAAACTTTAAACCAT
1 AAACCCTAAACCCTAAACCAT
* *
149092 AAACACTAACCCCTAAACCAT
1 AAACCCTAAACCCTAAACCAT
149113 AAACCCTAA
1 AAACCCTAA
149122 TATAAATGGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACCAT
Found at i:149119 original size:14 final size:14
Alignment explanation
Indices: 149071--149121 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
149061 TAGTTTATAG
**
149071 AAACCCTAAACTTT
1 AAACCCTAAACCAT
*
149085 AAACCATAAA-CACT
1 AAACCCTAAACCA-T
*
149099 AACCCCTAAACCAT
1 AAACCCTAAACCAT
149113 AAACCCTAA
1 AAACCCTAA
149122 TATAAATGGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 27 0.93
15 2 0.07
ACGTcount: A:0.49, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACCAT
Found at i:149507 original size:2 final size:2
Alignment explanation
Indices: 149452--149498 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
149442 GCATGTATGG
149452 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
149493 TA TA TA
1 TA TA TA
149499 AACTATATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:149954 original size:13 final size:13
Alignment explanation
Indices: 149922--149948 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
149912 TAATTTACAT
149922 TTAAATAATTTTA
1 TTAAATAATTTTA
149935 TTAAATAATTTTA
1 TTAAATAATTTTA
149948 T
1 T
149949 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:149984 original size:20 final size:20
Alignment explanation
Indices: 149952--150003 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
149942 ATTTTATATA
*
149952 ATAT-GTATCTATAAACCAT
1 ATATAGTATATATAAACCAT
* *
149971 GTATAGTATATATAAACTAT
1 ATATAGTATATATAAACCAT
149991 ATATA-TATATATA
1 ATATAGTATATATA
150004 TATATATACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (20 bp):
ATATAGTATATATAAACCAT
Found at i:150036 original size:2 final size:2
Alignment explanation
Indices: 149972--150018 Score: 58
Period size: 2 Copynumber: 22.0 Consensus size: 2
149962 ATAAACCATG
*
149972 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA TA TA TA TA CTA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA
150015 TA TA
1 TA TA
150019 AAGTAAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 35 0.88
3 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:150550 original size:7 final size:7
Alignment explanation
Indices: 150540--150601 Score: 65
Period size: 7 Copynumber: 8.9 Consensus size: 7
150530 ATAGATACCT
150540 TAAACCA
1 TAAACCA
*
150547 TAAACCT
1 TAAACCA
*
150554 TAAATCA
1 TAAACCA
150561 TAAACTC-
1 TAAAC-CA
150568 TAAACCA
1 TAAACCA
150575 TAAACCA
1 TAAACCA
150582 TAAA-CA
1 TAAACCA
*
150588 CTAAACTA
1 -TAAACCA
150596 TAAACC
1 TAAACC
150602 CTAATATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 3 0.07
7 40 0.89
8 2 0.04
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:150571 original size:21 final size:21
Alignment explanation
Indices: 150547--150601 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
150537 CCTTAAACCA
* * *
150547 TAAACCTTAAATCATAAACTC
1 TAAACCATAAACCATAAACAC
150568 TAAACCATAAACCATAAACAC
1 TAAACCATAAACCATAAACAC
*
150589 TAAACTATAAACC
1 TAAACCATAAACC
150602 CTAATATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (21 bp):
TAAACCATAAACCATAAACAC
Found at i:150883 original size:13 final size:13
Alignment explanation
Indices: 150851--150877 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
150841 TAATTTACAT
150851 TTAAATAATTTTA
1 TTAAATAATTTTA
150864 TTAAATAATTTTA
1 TTAAATAATTTTA
150877 T
1 T
150878 ATAATAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:151091 original size:32 final size:32
Alignment explanation
Indices: 151072--151174 Score: 181
Period size: 32 Copynumber: 3.2 Consensus size: 32
151062 CGGATCATTT
151072 ACAGGTCAGGTTGAAAACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAAACAAGTCAGGTTGAAA
*
151104 ACATGTCAGGTTGAAAACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAAACAAGTCAGGTTGAAA
151136 ACAGGTCAGGTTGAAAAC-AGATCAGGTTGAAA
1 ACAGGTCAGGTTGAAAACAAG-TCAGGTTGAAA
151168 ACAGGTC
1 ACAGGTC
151175 GGGTAATACC
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 2 0.03
32 66 0.97
ACGTcount: A:0.40, C:0.14, G:0.27, T:0.19
Consensus pattern (32 bp):
ACAGGTCAGGTTGAAAACAAGTCAGGTTGAAA
Found at i:151097 original size:16 final size:16
Alignment explanation
Indices: 151076--151170 Score: 156
Period size: 16 Copynumber: 5.9 Consensus size: 16
151066 TCATTTACAG
151076 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
*
151092 GTCAGGTTGAAAACAT
1 GTCAGGTTGAAAACAA
151108 GTCAGGTTGAAAACAA
1 GTCAGGTTGAAAACAA
*
151124 GTCAGGTTGAAAACAG
1 GTCAGGTTGAAAACAA
151140 GTCAGGTTGAAAAC-A
1 GTCAGGTTGAAAACAA
151155 GATCAGGTTGAAAACA
1 G-TCAGGTTGAAAACA
151171 GGTCGGGTAA
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
15 1 0.01
16 72 0.99
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (16 bp):
GTCAGGTTGAAAACAA
Found at i:154948 original size:6 final size:6
Alignment explanation
Indices: 154928--154967 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
154918 ATATCAGACA
*
154928 AAAGAG ACA-AG AAAGAG AAAGAG AAAGAG AAAGAAG AAAG
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG AAAG-AG AAAG
154968 TATCTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:155972 original size:13 final size:13
Alignment explanation
Indices: 155954--155979 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155944 ATTATGTATT
155954 TTGTTTTTTTTTC
1 TTGTTTTTTTTTC
155967 TTGTTTTTTTTTC
1 TTGTTTTTTTTTC
155980 AATTTTGAAT
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:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (13 bp):
TTGTTTTTTTTTC
Found at i:156628 original size:2 final size:2
Alignment explanation
Indices: 156621--156656 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
156611 TATATTTTCA
156621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
156657 GAGTTAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157322 original size:60 final size:60
Alignment explanation
Indices: 157241--157366 Score: 134
Period size: 60 Copynumber: 2.1 Consensus size: 60
157231 TTTGGGGATC
* * *
157241 AATTTAGAAATAGGGTAATAGTTT-ATGGATGAAA-TTAGAATGTTCAAAAGTAT-AAGTATT
1 AATTTAGAAATAGAGTAATAGTTTGA-AGAT-AAAGTTAGAATATTCAAAAGTATAAAG-ATT
* * *
157301 AATTTAG-AATGAGAGTCATAGTTTGAAGATAAAGTTGGAATATTCAAAAGTTTAAAGATT
1 AATTTAGAAAT-AGAGTAATAGTTTGAAGATAAAGTTAGAATATTCAAAAGTATAAAGATT
157361 AATTTA
1 AATTTA
157367 AAACGTGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
59 6 0.11
60 46 0.82
61 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.35
Consensus pattern (60 bp):
AATTTAGAAATAGAGTAATAGTTTGAAGATAAAGTTAGAATATTCAAAAGTATAAAGATT
Found at i:167213 original size:14 final size:15
Alignment explanation
Indices: 167194--167223 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
167184 ACTGAAATTC
167194 AAATTTT-ATTTTTT
1 AAATTTTAATTTTTT
167208 AAATTTTAATTTTTT
1 AAATTTTAATTTTTT
167223 A
1 A
167224 TTAGTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AAATTTTAATTTTTT
Found at i:170415 original size:30 final size:29
Alignment explanation
Indices: 170381--170439 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
170371 ATCTTAATGG
170381 AAAAT-GATAATTTTGGAACCTTTTAATAGT
1 AAAATAGATAATTTT-GAA-CTTTTAATAGT
* *
170411 AAAATAGCTAATTTTTAACTTTTAATAGT
1 AAAATAGATAATTTTGAACTTTTAATAGT
170440 CGAAAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 7 0.27
31 8 0.31
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (29 bp):
AAAATAGATAATTTTGAACTTTTAATAGT
Found at i:171422 original size:58 final size:61
Alignment explanation
Indices: 171315--171428 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 61
171305 AGTGTCTAAA
* *
171315 TTTTATTTATTTCAAAATTATACCTGATATTTATTTTTTGCTTCATTTTAGTATCTAAGTTT
1 TTTTATTTATTTCAAAAGTATACCTAATATTTATTTTTT-CTTCATTTTAGTATCTAAGTTT
171377 TTTTATTTATTTCAAAAGTATACCTAATATTTA-TTTTT-TT-ATTTTAGTATCT
1 TTTTATTTATTTCAAAAGTATACCTAATATTTATTTTTTCTTCATTTTAGTATCT
171429 CGTTGTTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
58 12 0.24
59 2 0.04
61 5 0.10
62 31 0.62
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (61 bp):
TTTTATTTATTTCAAAAGTATACCTAATATTTATTTTTTCTTCATTTTAGTATCTAAGTTT
Found at i:173136 original size:16 final size:16
Alignment explanation
Indices: 173085--173127 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
173075 TGGTATTACA
173085 TGACTTGTTATCAAAC
1 TGACTTGTTATCAAAC
173101 TGACTTGTTATCAAAC
1 TGACTTGTTATCAAAC
173117 TGACTTGTTAT
1 TGACTTGTTAT
173128 GAACCTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (16 bp):
TGACTTGTTATCAAAC
Found at i:173796 original size:19 final size:20
Alignment explanation
Indices: 173760--173803 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
173750 AGTATATACA
*
173760 ATATACCATATACCATTTTC
1 ATATACCATATACCATTTAC
*
173780 ATATTCCATAT-CCATTTAC
1 ATATACCATATACCATTTAC
173799 ATATA
1 ATATA
173804 TTATCCATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.36, C:0.23, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATACCATATACCATTTAC
Found at i:174209 original size:13 final size:12
Alignment explanation
Indices: 174181--174235 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 12
174171 TTTTACCACT
174181 TATAT-TATTATA
1 TATATATATT-TA
174193 TATATATACTTTA
1 TATATATA-TTTA
174206 TATATATA-TTA
1 TATATATATTTA
174217 TATACTTATATTT-
1 TATA--TATATTTA
174230 TATATA
1 TATATA
174236 CTTTTATAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
11 9 0.24
12 5 0.13
13 20 0.53
14 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (12 bp):
TATATATATTTA
Found at i:174211 original size:17 final size:17
Alignment explanation
Indices: 174189--174243 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
174179 CTTATATTAT
174189 TATATATATATACTTTA
1 TATATATATATACTTTA
174206 TATATATATTATA-TACTTA
1 TATATATA-TATACT--TTA
*
174225 TAT-TTTATATACTTT-
1 TATATATATATACTTTA
174240 TATA
1 TATA
174244 ATGATTATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 11
0.73 0.02 0.25
Matches are distributed among these distances:
15 3 0.09
16 2 0.06
17 13 0.41
18 8 0.25
19 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (17 bp):
TATATATATATACTTTA
Found at i:174219 original size:26 final size:25
Alignment explanation
Indices: 174181--174243 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
174171 TTTTACCACT
174181 TATATTATTATATA-TATATACTTTA
1 TATATTATTATATACT-TATACTTTA
*
174206 TATATATATTATATACTTATATTTTA
1 TATAT-TATTATATACTTATACTTTA
174232 TATACTT-TTATA
1 TATA-TTATTATA
174244 ATGATTATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 10 0.29
26 22 0.65
27 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATTATTATATACTTATACTTTA
Found at i:174226 original size:15 final size:15
Alignment explanation
Indices: 174178--174243 Score: 61
Period size: 15 Copynumber: 4.6 Consensus size: 15
174168 ATTTTTTACC
174178 ACTTATATTATTATAT
1 ACTTATA-TATTATAT
174194 A--TATATACTT-TAT
1 ACTTATATA-TTATAT
174207 A--TATATATTATAT
1 ACTTATATATTATAT
*
174220 ACTTATATTTTATAT
1 ACTTATATATTATAT
*
174235 ACTTTTATA
1 ACTTATATA
174244 ATGATTATAC
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
12 2 0.05
13 16 0.37
14 6 0.14
15 18 0.42
16 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
ACTTATATATTATAT
Found at i:179026 original size:2 final size:2
Alignment explanation
Indices: 179019--179052 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
179009 AACCATGAGC
179019 AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
179053 GCAATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:182057 original size:2 final size:2
Alignment explanation
Indices: 182050--182076 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
182040 ACATACATAC
182050 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
182077 GCTAATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.