Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009634.1 Hibiscus syriacus cultivar Beakdansim tig00117034_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: 17174986
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 78
Found at i:1411830 original size:20 final size:20
Alignment explanation
Indices: 1411810--1411895 Score: 82
Period size: 20 Copynumber: 4.2 Consensus size: 20
1411800 AAATCGTAAT
*
1411810 GCGATACTGACTATCGCAAT
1 GCGATACTGACTATCGCAAC
* * **
1411830 GCGATAATAAAAAATCGCAAC
1 GCGATACT-GACTATCGCAAC
* * *
1411851 GAGATACTTACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
*
1411871 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
1411891 GCGAT
1 GCGAT
1411896 TTACATAGCG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 38 0.73
21 14 0.27
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1412157 original size:27 final size:27
Alignment explanation
Indices: 1412102--1412157 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1412092 ATCGCCGGCG
***
1412102 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCACAAAAAA
* *
1412129 AAATCCCTCACAATCATTCAGAAAAAA
1 AAATCCCTCACAACCATTCACAAAAAA
1412156 AA
1 AA
1412158 TCAACCTCCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.48, C:0.30, G:0.04, T:0.18
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCACAAAAAA
Found at i:1412467 original size:19 final size:19
Alignment explanation
Indices: 1412407--1412487 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
1412397 TTCGAGAATG
1412407 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
1412427 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
1412443 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1412460 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1412479 AAAATCGCA
1 AAAATCGCA
1412488 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1412534 original size:33 final size:33
Alignment explanation
Indices: 1412497--1412584 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
1412487 ATTGCGATTT
* *
1412497 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
1412530 TCATTTCGCGTTGCAATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1412563 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1412585 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1412586 original size:20 final size:19
Alignment explanation
Indices: 1412552--1412608 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
1412542 GCAATTCTCT
*
1412552 CGTTGCGATAGTCATTTCCG
1 CGTTGCGAT-TTCATTTCCG
*
1412572 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATT-TCATT-TCCG
1412592 CGTTGCGATTTCATTTC
1 CGTTGCGATTTCATTTC
1412609 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 1 0.03
19 5 0.16
20 25 0.78
21 1 0.03
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTCATTTCCG
Found at i:1416069 original size:14 final size:14
Alignment explanation
Indices: 1416050--1416081 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1416040 GTTTAATTGA
1416050 TTGTAAAAGGTGAT
1 TTGTAAAAGGTGAT
*
1416064 TTGTAAAAGTTGAT
1 TTGTAAAAGGTGAT
1416078 TTGT
1 TTGT
1416082 TTAATTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTGTAAAAGGTGAT
Found at i:1416306 original size:33 final size:32
Alignment explanation
Indices: 1416264--1416389 Score: 159
Period size: 33 Copynumber: 3.9 Consensus size: 32
1416254 ATTAAATTCG
1416264 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1416297 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
1416330 CGTTGCGA-TTGCATTTCGCATTGCGATCTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGAT-TC-CT
1416363 CGTTGCGATTTTCA-TTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1416390 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.02
31 1 0.01
32 16 0.20
33 55 0.68
34 4 0.05
35 3 0.04
ACGTcount: A:0.15, C:0.24, G:0.21, T:0.40
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1416382 original size:65 final size:66
Alignment explanation
Indices: 1416257--1416388 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
1416247 ACGCGAAATT
* *
1416257 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTGCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1416322 G
66 G
*
1416323 AAATTAGCGTTGCGA-TTGCATTTCGCATTGCGATCTCTCTCGTTGCGATTTTCA-TTCGCATTG
1 AAATTAGCGTTGCGATTTGCATTTCGCATTGCGAT-TCCCTCGTTGCGATTTTCATTTCGCATTG
1416386 CG
65 CG
1416388 A
1 A
1416389 TAGTAATTTC
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
65 30 0.48
66 32 0.52
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.39
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTGCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:1418659 original size:12 final size:12
Alignment explanation
Indices: 1418642--1418666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1418632 TTCTTCGGGA
1418642 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1418654 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1418666 C
1 C
1418667 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1419026 original size:20 final size:20
Alignment explanation
Indices: 1418998--1419075 Score: 129
Period size: 20 Copynumber: 3.9 Consensus size: 20
1418988 ATTCATTTGA
*
1418998 CTATTGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1419018 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1419038 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1419058 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1419076 CGCAATGCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1421099 original size:20 final size:19
Alignment explanation
Indices: 1421064--1421130 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1421054 CGAAACTTAA
1421064 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1421083 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1421103 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1421122 ATCGCAACG
1 ATCGCAACG
1421131 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1421138 original size:14 final size:14
Alignment explanation
Indices: 1421119--1421176 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1421109 ATGCGAAATG
1421119 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1421133 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1421149 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1421165 AAAATCGCAACG
1 AAAATCGCAACG
1421177 CGAAAACAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1421161 original size:32 final size:32
Alignment explanation
Indices: 1421103--1421191 Score: 142
Period size: 32 Copynumber: 2.8 Consensus size: 32
1421093 GGAAATGGCT
*
1421103 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1421136 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
**
1421168 ATCGCAACGCGAAAACAAATCGCA
1 ATCGCAACGCGAAATGAAATCGCA
1421192 TTGCGATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 38 0.72
33 15 0.28
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:1421182 original size:14 final size:15
Alignment explanation
Indices: 1421118--1421182 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 15
1421108 AATGCGAAAT
1421118 GAAAATCGCAACGAC
1 GAAAATCGCAACGAC
1421133 -AAAATCGCAACG-C
1 GAAAATCGCAACGAC
1421146 GAAATGAAATCGCAACGAC
1 G--A--AAATCGCAACGAC
1421165 -AAAATCGCAACG-C
1 GAAAATCGCAACGAC
1421178 GAAAA
1 GAAAA
1421183 CAAATCGCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.05
14 27 0.63
16 2 0.05
18 11 0.26
19 1 0.02
ACGTcount: A:0.49, C:0.25, G:0.18, T:0.08
Consensus pattern (15 bp):
GAAAATCGCAACGAC
Found at i:1421208 original size:18 final size:17
Alignment explanation
Indices: 1421187--1421278 Score: 74
Period size: 18 Copynumber: 5.6 Consensus size: 17
1421177 CGAAAACAAA
1421187 TCGCATTGCGATTTCATT
1 TCGC-TTGCGATTTCATT
*
1421205 TCGCGTTGCG-TTT--TG
1 TCGC-TTGCGATTTCATT
1421220 TCG-TTGCGATTTCA-T
1 TCGCTTGCGATTTCATT
*
1421235 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
1421251 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
1421267 TCGCATTGCGAT
1 TCGC-TTGCGAT
1421279 AGCCTTTCCG
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
13 5 0.08
14 12 0.20
15 7 0.12
16 7 0.12
17 12 0.20
18 16 0.27
ACGTcount: A:0.11, C:0.21, G:0.24, T:0.45
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:1421230 original size:31 final size:32
Alignment explanation
Indices: 1421192--1421278 Score: 151
Period size: 31 Copynumber: 2.8 Consensus size: 32
1421182 ACAAATCGCA
1421192 TTGCGATTTCATTTCGCGTTGCG-TTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1421223 TTGCGATTTCA-TTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
*
1421254 TTGCGATTTCATTTCGCATTGCGAT
1 TTGCGATTTCATTTCGCGTTGCGAT
1421279 AGCCTTTCCG
Statistics
Matches: 53, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
30 11 0.21
31 30 0.57
32 12 0.23
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
Found at i:1421257 original size:14 final size:14
Alignment explanation
Indices: 1421208--1421262 Score: 60
Period size: 14 Copynumber: 3.8 Consensus size: 14
1421198 TTTCATTTCG
1421208 CGTTGCG-TTTTGT
1 CGTTGCGATTTTGT
1421221 CGTTGCGATTTCAT-T
1 CGTTGCGATTT--TGT
1421236 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1421252 CGTTGCGATTT
1 CGTTGCGATTT
1421263 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
13 7 0.19
14 14 0.39
15 2 0.06
16 2 0.06
17 11 0.31
ACGTcount: A:0.07, C:0.18, G:0.27, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1421315 original size:20 final size:19
Alignment explanation
Indices: 1421252--1421316 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
1421242 GCGATTTTGT
**
1421252 CGTTGCGATTTCATTT-CG
1 CGTTGCGATAGCATTTCCG
* *
1421270 CATTGCGATAGCCTTTCCG
1 CGTTGCGATAGCATTTCCG
*
1421289 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAG-CATTTCCG
*
1421309 TGTTGCGA
1 CGTTGCGA
1421317 AAGTAAACTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 12 0.32
19 12 0.32
20 13 0.35
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGCATTTCCG
Found at i:1421796 original size:18 final size:18
Alignment explanation
Indices: 1421748--1421813 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 18
1421738 TGTCGTTGTG
1421748 GAGGTGTATAGC-C-GGGT
1 GAGGTG-ATAGCTCTGGGT
* *
1421765 CGATGTGATGGCTCTGGGT
1 -GAGGTGATAGCTCTGGGT
*
1421784 GAGGTGATAGCTCT-GGC
1 GAGGTGATAGCTCTGGGT
*
1421801 GAGGTGATGGCTC
1 GAGGTGATAGCTC
1421814 CCGAAGTGGA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 18 0.45
18 18 0.45
19 4 0.10
ACGTcount: A:0.15, C:0.15, G:0.44, T:0.26
Consensus pattern (18 bp):
GAGGTGATAGCTCTGGGT
Found at i:1421806 original size:17 final size:18
Alignment explanation
Indices: 1421769--1421813 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
1421759 CCGGGTCGAT
*
1421769 GTGATGGCTCTGGGTGAG
1 GTGATGGCTCTGGGCGAG
*
1421787 GTGATAGCTCT-GGCGAG
1 GTGATGGCTCTGGGCGAG
1421804 GTGATGGCTC
1 GTGATGGCTC
1421814 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
GTGATGGCTCTGGGCGAG
Found at i:1423414 original size:21 final size:22
Alignment explanation
Indices: 1423390--1423432 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1423380 GATTTAGATA
1423390 GACGGA-TTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1423411 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1423433 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.19, C:0.16, G:0.47, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1423710 original size:20 final size:20
Alignment explanation
Indices: 1423616--1423710 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1423606 GATTATGTAT
*
1423616 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1423636 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
1423656 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
1423677 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1423697 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1423711 TTTCCAAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1423729 original size:41 final size:41
Alignment explanation
Indices: 1423638--1423771 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 41
1423628 AAAGTCAGTA
* * * ** *
1423638 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
* *
1423678 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
* ** *
1423720 TCGCGTTGCGAT-TTACTTATTCGCATTGCGA-TTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCAAAT
1423760 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1423772 TTACTTATTC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
40 23 0.30
41 52 0.68
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAAT
Found at i:1423743 original size:20 final size:20
Alignment explanation
Indices: 1423718--1423783 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
1423708 GATTTTCCAA
1423718 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1423738 ATTCGCATTGCGATTTCCCA
1 ATTCGCGTTGCGATTTACTT
1423758 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1423778 ATTCGC
1 ATTCGC
1423784 ATGCGAATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1423766 original size:40 final size:41
Alignment explanation
Indices: 1423699--1423789 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 41
1423689 ATAGTCAGTA
1423699 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
*
1423740 TCGCATTGCGA-TTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
1423780 TCGCA-TGCGA
1 TCGCATTGCGA
1423790 ATTGGGAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
39 5 0.10
40 33 0.67
41 11 0.22
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCAAATTCGCGTTGCGATTTACTTAT
Found at i:1424954 original size:5 final size:5
Alignment explanation
Indices: 1424944--1424997 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
1424934 GTCCGTCCGT
* *
1424944 CTCGG CTCGG CTCGG CACGG -TACGA CAT-GG CTCGG CTCGG CTCGG CTCGG
1 CTCGG CTCGG CTCGG CTCGG CT-CGG C-TCGG CTCGG CTCGG CTCGG CTCGG
1424994 CTCG
1 CTCG
1424998 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 1 0.02
5 39 0.95
7 1 0.02
ACGTcount: A:0.07, C:0.37, G:0.37, T:0.19
Consensus pattern (5 bp):
CTCGG
Found at i:1425303 original size:22 final size:22
Alignment explanation
Indices: 1425278--1425330 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
1425268 TCAGGAGTTA
** *
1425278 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
* *
1425300 CAGGGGTTACATGATATAATTT
1 CAGGAGTTACATGATATAATTC
1425322 CAGGAGTTA
1 CAGGAGTTA
1425331 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.38
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:1431126 original size:22 final size:22
Alignment explanation
Indices: 1431101--1431155 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
1431091 TCAGGAGTTA
* *
1431101 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1431123 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
1431145 CAGGAGTTATA
1 CAGGAGTTATA
1431156 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1434239 original size:23 final size:23
Alignment explanation
Indices: 1434209--1434283 Score: 136
Period size: 23 Copynumber: 3.3 Consensus size: 23
1434199 GTCGAGGGTT
1434209 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
1434232 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAC
1434255 CTATGTGGTCCTTCGGGACAAA-
1 CTATGTGGTCCTTCGGGACAAAC
1434277 -TATGTGG
1 CTATGTGG
1434284 CACTTCAGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.13
23 45 0.87
ACGTcount: A:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAC
Found at i:1436103 original size:48 final size:48
Alignment explanation
Indices: 1436047--1436139 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
1436037 TTGGCGGCGA
* *
1436047 TGGTGGCTTCACAATTGGAGGACTCGGGTATACGGGAGCCTTTGGAGC
1 TGGTGGCTTCACAAATGGAGGACTCGGGTAGACGGGAGCCTTTGGAGC
*
1436095 TGGTGGCTTCACAAATGGAGGACTCGGGTAGACGGGAGGCTTTGG
1 TGGTGGCTTCACAAATGGAGGACTCGGGTAGACGGGAGCCTTTGG
1436140 TGGCGTTGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.17, G:0.40, T:0.24
Consensus pattern (48 bp):
TGGTGGCTTCACAAATGGAGGACTCGGGTAGACGGGAGCCTTTGGAGC
Found at i:1438711 original size:3 final size:3
Alignment explanation
Indices: 1438696--1438760 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
1438686 AATTTTTTCA
* * *
1438696 TAT TAT ATAT TAT TA- TAT TA- AAA TAT TAT TAT TAT TAT TGT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1438740 ATAT ATAT TA- TAT TAT TAT TA
1 -TAT -TAT TAT TAT TAT TAT TA
1438761 AATAAAATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 5 0.10
3 37 0.71
4 10 0.19
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:1438739 original size:28 final size:25
Alignment explanation
Indices: 1438695--1438760 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 25
1438685 TAATTTTTTC
1438695 ATATTATATATTATTATATTAAAATATT
1 ATATTAT-TATTATTATA-T-AAATATT
* *
1438723 ATTATTATTATTGTTATATATATATT
1 A-TATTATTATTATTATATAAATATT
1438749 ATATTATTATTA
1 ATATTATTATTA
1438761 AATAAAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 10 0.29
26 7 0.21
27 1 0.03
28 10 0.29
29 6 0.18
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATATTATTATTATTATATAAATATT
Found at i:1438772 original size:3 final size:3
Alignment explanation
Indices: 1438761--1438808 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
1438751 ATTATTATTA
1438761 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1438808 A
1 A
1438809 CAAACCCACA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1440142 original size:21 final size:21
Alignment explanation
Indices: 1440091--1440143 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1440081 ATTATGACTA
1440091 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
* **
1440112 TCACGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
1440133 TCGCAATGCGA
1 TCGCAATGCGA
1440144 ATAAGTAAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:1440199 original size:20 final size:20
Alignment explanation
Indices: 1440174--1440246 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1440164 ATTGGGAAAT
*
1440174 TCGCAATGCGATACTGACTA
1 TCGCAACGCGATACTGACTA
* *
1440194 TCGCAACGCGATACTGTCTT
1 TCGCAACGCGATACTGACTA
*
1440214 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTA
*
1440234 TCGCAACGAGATA
1 TCGCAACGCGATA
1440247 ATACATAATC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTA
Found at i:1440461 original size:22 final size:22
Alignment explanation
Indices: 1440433--1440476 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1440423 CACTCTCTCA
*
1440433 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1440455 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1440477 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1440762 original size:20 final size:20
Alignment explanation
Indices: 1440725--1440781 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 20
1440715 TATTCTCTCG
* **
1440725 TTGCGATAGTCAAATTCGCA
1 TTGCGATTGTCATTTTCGCA
**
1440745 TTGCGATTGTCATTTTCGTG
1 TTGCGATTGTCATTTTCGCA
*
1440765 TTGCGATTTTCATTTTC
1 TTGCGATTGTCATTTTC
1440782 AGAAACTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.18, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGATTGTCATTTTCGCA
Found at i:1442109 original size:17 final size:18
Alignment explanation
Indices: 1442072--1442118 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
1442062 TCCACTTCGG
*
1442072 GAGCCATCACTTCACCCA
1 GAGCCATCACCTCACCCA
*
1442090 GAGCTATCACCTCA-CCA
1 GAGCCATCACCTCACCCA
1442107 GAGCCATCACCT
1 GAGCCATCACCT
1442119 GATCGCCGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 14 0.54
18 12 0.46
ACGTcount: A:0.28, C:0.43, G:0.13, T:0.17
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1442749 original size:19 final size:19
Alignment explanation
Indices: 1442692--1442788 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
1442682 GGAATTGGCT
1442692 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* * *
1442711 ATCACAA--CG--A-CAAC
1 ATCGCAATGCGAAATGAAA
1442725 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1442744 ATCGCAAT--G--AT-AAA
1 ATCGCAATGCGAAATGAAA
*
1442758 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1442777 ATCGCAATGCGA
1 ATCGCAATGCGA
1442789 TTTGTGTTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
14 18 0.30
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 30 0.50
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1442780 original size:33 final size:33
Alignment explanation
Indices: 1442692--1442785 Score: 143
Period size: 33 Copynumber: 2.8 Consensus size: 33
1442682 GGAATTGGCT
* * *
1442692 ATCGCAATGCGAAATGAAAATCACAACGACAAC
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
1442725 ATCGCAATGCGAAATGAAAATCGCAATGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
*
1442758 ATCGCAACGCGAAATGAAAATCGCAATG
1 ATCGCAATGCGAAATGAAAATCGCAATG
1442786 CGATTTGTGT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.20, G:0.18, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAATGACAAA
Found at i:1442843 original size:19 final size:19
Alignment explanation
Indices: 1442816--1442860 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1442806 GATTTTGTCG
*
1442816 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1442835 TTGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCA
1442854 TTGCGAT
1 TTGCGAT
1442861 AGCCATTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1442875 original size:20 final size:19
Alignment explanation
Indices: 1442846--1442899 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1442836 TGCGATTTTT
1442846 ATTTCGCGTTGCGATAGCC
1 ATTTCGCGTTGCGATAGCC
*
1442865 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGCC
*
1442885 ATTTTTGCGTTGCGA
1 A-TTTCGCGTTGCGA
1442900 AAGTAAGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 4 0.13
20 24 0.77
21 3 0.10
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGCC
Found at i:1444916 original size:19 final size:19
Alignment explanation
Indices: 1444892--1444953 Score: 115
Period size: 19 Copynumber: 3.3 Consensus size: 19
1444882 GCAACGAGAG
1444892 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1444911 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1444930 AATCGCAATGCAAAATGAA
1 AATCGCAATGCGAAATGAA
1444949 AATCG
1 AATCG
1444954 TAACGAGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1445019 original size:20 final size:20
Alignment explanation
Indices: 1444994--1445069 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1444984 TCGTATTGCG
*
1444994 ATTTTCTCATTGCGATAGCC
1 ATTTTCGCATTGCGATAGCC
*
1445014 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCATTGCGATAGCC
*
1445034 ATTTTCGCATTGCGATAGTC
1 ATTTTCGCATTGCGATAGCC
*
1445054 ATTTTCGCGTTGCGAT
1 ATTTTCGCATTGCGAT
1445070 TTCCCCGTTG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCGCATTGCGATAGCC
Found at i:1445039 original size:40 final size:40
Alignment explanation
Indices: 1444994--1445069 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
1444984 TCGTATTGCG
*
1444994 ATTTTCTCATTGCGATAGCCATTTTCGCGTTGCGATAGCC
1 ATTTTCGCATTGCGATAGCCATTTTCGCGTTGCGATAGCC
*
1445034 ATTTTCGCATTGCGATAGTCATTTTCGCGTTGCGAT
1 ATTTTCGCATTGCGATAGCCATTTTCGCGTTGCGAT
1445070 TTCCCCGTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.39
Consensus pattern (40 bp):
ATTTTCGCATTGCGATAGCCATTTTCGCGTTGCGATAGCC
Found at i:1445754 original size:41 final size:41
Alignment explanation
Indices: 1445656--1445772 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 41
1445646 GAAAATCAGA
* * * ** *
1445656 ATCGCGTTGCGAAAGTCAGAATCGCTTTGCGA--AAGTCAGT
1 ATCGCGTTGCGAAAGTCAGTATCACATTGCGATTTTGT-ATT
*
1445696 ATCGCGTTGCGAAAGTCAGTATCACGTTGCGATTTTGTATT
1 ATCGCGTTGCGAAAGTCAGTATCACATTGCGATTTTGTATT
* *
1445737 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCGTTGCGAAAGTCAGTATCACATTGCGATTTT
1445773 CCAAATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
40 29 0.44
41 35 0.53
42 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (41 bp):
ATCGCGTTGCGAAAGTCAGTATCACATTGCGATTTTGTATT
Found at i:1445769 original size:20 final size:20
Alignment explanation
Indices: 1445615--1445768 Score: 148
Period size: 20 Copynumber: 7.7 Consensus size: 20
1445605 GATTCTGTAT
* * *
1445615 TATCTCGTTGAGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
1445635 AATCTCGTTGCGAAAATCAG
1 TATCGCGTTGCGAAAGTCAG
*
1445655 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
1445675 AATCGCTTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1445695 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1445715 TATCACGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1445736 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1445756 TATCGCATTGCGA
1 TATCGCGTTGCGA
1445769 TTTTCCAAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
19 3 0.03
20 96 0.84
21 13 0.11
22 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1445788 original size:41 final size:41
Alignment explanation
Indices: 1445695--1445790 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
1445685 CGAAAGTCAG
* * ** *
1445695 TATCGCGTTGCGAAAGTCAGTATCACGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTCAAA
*
1445736 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCACATTGCGATTTT-CAAA
*
1445778 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
1445791 TTACTTATTC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCACATTGCGATTTTCAAA
Found at i:1445802 original size:20 final size:21
Alignment explanation
Indices: 1445758--1445809 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1445748 ATAGTCAGTA
*
1445758 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1445779 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1445799 TCGCATTGCGA
1 TCGCATTGCGA
1445810 ATTGGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1445850 original size:21 final size:21
Alignment explanation
Indices: 1445799--1445850 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1445789 ATTTACTTAT
1445799 TCGCATTGCG-AATTGGAAAA
1 TCGCATTGCGAAATTGGAAAA
* **
1445819 TCACAACGCGAAATTGGAAAA
1 TCGCATTGCGAAATTGGAAAA
1445840 TCGCATTGCGA
1 TCGCATTGCGA
1445851 TAGTCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCATTGCGAAATTGGAAAA
Found at i:1446316 original size:2 final size:2
Alignment explanation
Indices: 1446261--1446299 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1446251 ATAAAAACAA
1446261 AT AT 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 AT AT A
1446300 GTTTTATTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1446326 original size:17 final size:17
Alignment explanation
Indices: 1446291--1446340 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1446281 ATATATATAT
*
1446291 ATATATATAGTTTTATTC
1 ATATATAT-TTTTTATTC
*
1446309 ATATATATTTTTTCTTC
1 ATATATATTTTTTATTC
*
1446326 ATTTATATTTCTTTA
1 ATATATATTT-TTTA
1446341 ATTTTAGTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (17 bp):
ATATATATTTTTTATTC
Found at i:1446411 original size:27 final size:29
Alignment explanation
Indices: 1446350--1446412 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 29
1446340 AATTTTAGTC
1446350 ATATTAATATATTTATTGATTACTTTTATA
1 ATATTAATATATTTATT-ATTACTTTTATA
*
1446380 A-ATTAATAATATTTA-T-TTATTTTTA-A
1 ATATTAAT-ATATTTATTATTACTTTTATA
1446406 ATATTAA
1 ATATTAA
1446413 GAAAGGGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 2 0.07
27 13 0.43
29 7 0.23
30 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
ATATTAATATATTTATTATTACTTTTATA
Found at i:1446565 original size:15 final size:17
Alignment explanation
Indices: 1446531--1446567 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
1446521 TTAGGAAAAT
1446531 TATTATATTCTTATTAA
1 TATTATATTCTTATTAA
*
1446548 TATT-TATTTTTA-TAA
1 TATTATATTCTTATTAA
1446563 TATTA
1 TATTA
1446568 AAGAAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.39
16 7 0.39
17 4 0.22
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATATTCTTATTAA
Found at i:1455585 original size:75 final size:74
Alignment explanation
Indices: 1455480--1455710 Score: 219
Period size: 75 Copynumber: 3.1 Consensus size: 74
1455470 GAAGCAAATT
* * *
1455480 CTGAAAGCCCATTTCAATC-ATAATCAGGAATATTGACGCATTTTGAATGTTCACGTCA-A-CAA
1 CTGAAAGCCCATTTCAATCAAAAAT-TGGAATATTGACGCATTTTGAACG-TC-CGT-ATAGCAA
*
1455542 ATGCTGGGGCATG
62 ATACTGGGGCATG
* * *
1455555 CTGAAAGCACATTTCAATCAAAAATTGGAATATTGGCGCATTTTGAACGTCTGTATTAGCAAATA
1 CTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCCGTA-TAGCAAATA
1455620 CTGGGGCATG
65 CTGGGGCATG
* * * *
1455630 CTGAAAGCCCATTTCAAT-AAGAAATTGGAATA---A--CACTTTGAACGTTCATATCAGTAAAT
1 CTGAAAGCCCATTTCAATCAA-AAATTGGAATATTGACGCATTTTGAACGTCCGTAT-AGCAAAT
*
1455689 GCTGGGGCATG
64 ACTGGGGCATG
*
1455700 CTGAAGGCCCA
1 CTGAAAGCCCA
1455711 CATCATTATG
Statistics
Matches: 134, Mismatches: 16, Indels: 17
0.80 0.10 0.10
Matches are distributed among these distances:
69 1 0.01
70 39 0.29
72 1 0.01
73 2 0.01
74 5 0.04
75 82 0.61
76 4 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (74 bp):
CTGAAAGCCCATTTCAATCAAAAATTGGAATATTGACGCATTTTGAACGTCCGTATAGCAAATAC
TGGGGCATG
Found at i:1457750 original size:45 final size:45
Alignment explanation
Indices: 1457696--1457794 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
1457686 GGAAGCTTTT
* * * *
1457696 TGATATTTTTAAAGCCT-TCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCT-GGGTCATCCGTAAGACCTACAGTGCA
1457741 TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
1 TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
1457786 TGATGTTTT
1 TGATGTTTT
1457795 CAAAAAGCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 48 0.98
46 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (45 bp):
TGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGACCTACAGTGCA
Found at i:1457812 original size:121 final size:121
Alignment explanation
Indices: 1457598--1458039 Score: 692
Period size: 121 Copynumber: 3.7 Consensus size: 121
1457588 CTATTTCCCA
* * **
1457598 CATCTGTAAGCCATTCAGTGCATGATATTTTTAAAGCCTCTGGGTCATCCGTAAGTCCTACAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAACCCTACAGTG
*
1457663 CATAATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
66 CATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
1457719 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAGA-CCTACAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAA-ACCCTACAGT
* * *
1457783 GCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATATTTTTAAAGCCTCCAGGT
65 GCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
* *
1457840 CATCTGTAATCCCTTCAGTGCATGATGTTTTTAAAGCCT-TCGGGTCATCTGTAAACCCTACAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCT-GGGTCATCCGTAAACCCTACAGT
*
1457904 GCAGGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCC-TCGGGT
65 GCATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
* * * ** *
1457960 TATTTGTAAACCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCTATAAACCCTTCAGTG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAACCCTACAGTG
1458025 CATGATGTTTTCAAA
66 CATGATGTTTTCAAA
1458040 GCCTTTGGGT
Statistics
Matches: 298, Mismatches: 19, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
120 78 0.26
121 220 0.74
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (121 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTGGGTCATCCGTAAACCCTACAGTG
CATGATGTTTTCAAAAAGCCTTCGGAAGCTTTTTGATATTTTTAAAGCCTTCGGGT
Found at i:1457873 original size:45 final size:45
Alignment explanation
Indices: 1457817--1457915 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
1457807 AGAAGCTTTT
* * *
1457817 TGATATTTTTAAAGCCTCCAGGTCATCTGTAATCCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
* *
1457862 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAACCCTACAGTGCA
1 TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
*
1457907 GGATGTTTT
1 TGATGTTTT
1457916 CAAAAAGCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (45 bp):
TGATGTTTTTAAAGCCTCCAGGTCATCTGTAAACCCTACAGTGCA
Found at i:1458023 original size:45 final size:45
Alignment explanation
Indices: 1457938--1458080 Score: 216
Period size: 45 Copynumber: 3.2 Consensus size: 45
1457928 GGAAGCTTTT
* * *
1457938 TGATATTTTTAAAGCCTC-GGGTTATTTGTAAACCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
*
1457982 TGATGTTTTTAAAGCCTCTGGGTCATCTATAAACCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
* * *
1458027 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTTAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
1458072 TGATGTTTT
1 TGATGTTTT
1458081 CAAATACCTC
Statistics
Matches: 90, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
44 17 0.19
45 73 0.81
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (45 bp):
TGATGTTTTTAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
Found at i:1458167 original size:165 final size:162
Alignment explanation
Indices: 1457696--1458196 Score: 449
Period size: 165 Copynumber: 3.0 Consensus size: 162
1457686 GGAAGCTTTT
* * *
1457696 TGATATTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTTAAAGCCTCTG
1 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTC-G
* * * * *
1457761 GGTCATCCGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCAGAAGCTTTTTGATATTTT
65 GGCCATCCATAAGACCTAAAGTGCAGGATGTTTTCAAAAAGCCTTC-GGAGCTTTTTGATA--TT
** *
1457826 TAAAGCCTCCAGGTCATCTGTAATCCCTTCAGTGCA
127 TAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
* * *
1457862 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAACCCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CC-T
** ** **** *** * * * * **
1457927 CGGAAGCTTTTTGAT-ATTTTTAAAGCCT-C-GG--GTTATTTGTAAACCCTTCAGTGCATGATG
63 CGG--GC-CATCCATAAGACCTAAAG--TGCAGGATGTT-TTCAAAAAGCCTTCGGAGCTTTTTG
* *
1457987 -TTTTTAAAGCCTCTGGGTCATCTATAAACCCTTCAGTGCA
122 ATATTTAAAGCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
* *
1458027 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAATACCTCA
1 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA-ACCTC-
*
1458092 GGGCCATCCATAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTT
64 GGGCCATCCATAAGACCTAAAGTGCAGGATGTTTTCAAAAAGCCTTC-GGAGCTTTTTGATATTT
* *
1458157 AAAACCTCTGGGTCATCTGTAAGA-CCTACAGTGCA
128 AAAGCCTCTGGGTCATCTGTAA-ACCCTTCAGTGCA
*
1458192 AGATG
1 TGATG
1458197 ATAAGACCTC
Statistics
Matches: 255, Mismatches: 61, Indels: 39
0.72 0.17 0.11
Matches are distributed among these distances:
160 1 0.00
161 4 0.02
162 9 0.04
163 12 0.05
164 16 0.06
165 123 0.48
166 51 0.20
167 4 0.02
168 12 0.05
169 12 0.05
170 7 0.03
171 3 0.01
172 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (162 bp):
TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTCGG
GCCATCCATAAGACCTAAAGTGCAGGATGTTTTCAAAAAGCCTTCGGAGCTTTTTGATATTTAAA
GCCTCTGGGTCATCTGTAAACCCTTCAGTGCA
Found at i:1458372 original size:3 final size:3
Alignment explanation
Indices: 1458364--1458413 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
1458354 AATTTTTTCA
*
1458364 TAT TAT TAT TAT TAT TGT TAT TAT TA- TAT ATAT TA- TAT ATAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT
1458409 TAT TA
1 TAT TA
1458414 AACGAAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1458466 original size:22 final size:22
Alignment explanation
Indices: 1458439--1458480 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1458429 TAATAATACA
1458439 AACCCACAGCCCA-TTTACAAAG
1 AACCCA-AGCCCAGTTTACAAAG
*
1458461 AACCCATGCCCAGTTTACAA
1 AACCCAAGCCCAGTTTACAA
1458481 GCCCAACCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.36, G:0.10, T:0.17
Consensus pattern (22 bp):
AACCCAAGCCCAGTTTACAAAG
Found at i:1459717 original size:20 final size:20
Alignment explanation
Indices: 1459694--1459733 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1459684 TATATATATA
1459694 TATAGTTTTATTCATATTAT
1 TATAGTTTTATTCATATTAT
* * *
1459714 TATATTTTTCTTCATTTTAT
1 TATAGTTTTATTCATATTAT
1459734 ATTTCTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (20 bp):
TATAGTTTTATTCATATTAT
Found at i:1459774 original size:30 final size:30
Alignment explanation
Indices: 1459740--1459798 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
1459730 TTATATTTCT
1459740 TTAATTTTCAT-ATTAAT-ATATATTATTTGA
1 TTAATTTT-ATAATTAATAATAT-TTATTTGA
1459770 TTAATTTTATAAATTAATAATATTTATTT
1 TTAATTTTAT-AATTAATAATATTTATTT
1459799 ATTTTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 2 0.08
30 8 0.31
31 12 0.46
32 4 0.15
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (30 bp):
TTAATTTTATAATTAATAATATTTATTTGA
Found at i:1460058 original size:2 final size:2
Alignment explanation
Indices: 1460051--1460082 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1460041 ACAAAAACCC
*
1460051 TA TA TA TA TA TA AA 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
1460083 ACTTTTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1461427 original size:55 final size:57
Alignment explanation
Indices: 1461355--1461474 Score: 183
Period size: 56 Copynumber: 2.2 Consensus size: 57
1461345 ATGAGCAAAG
* *
1461355 TGTACA-TTTGTTGTATGTTACT-AAATGTGTATGGAGTTAATATATTTATA-TTGA
1 TGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTTGA
* *
1461409 TGTATATTTTGTTGTATGTTACTAAAATGTATCTGGAGTTAATATATGTATATTTGA
1 TGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTTGA
1461466 TGTACATTT
1 TGTACATTT
1461475 GATTTTAATT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
54 5 0.09
55 16 0.28
56 25 0.43
57 12 0.21
ACGTcount: A:0.29, C:0.04, G:0.17, T:0.49
Consensus pattern (57 bp):
TGTACATTTTGTTGTATGTTACTAAAATGTATATGGAGTTAATATATGTATATTTGA
Found at i:1476751 original size:55 final size:56
Alignment explanation
Indices: 1476690--1477090 Score: 320
Period size: 55 Copynumber: 7.3 Consensus size: 56
1476680 GATAAATGGC
* * * * *
1476690 ACTTGAAAAATCTTCAAAT-GATAAGTCCGCTCCTTATTTC-TTCAGGGAGTATAAA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTA-TCCGTTCAGGGAGTATAAA
*
1476745 ACTTGAACAATCTTC-AATAAACAAGTCCGCTCCCTATCCGTTCAGGGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTATCCGTTCAGGGAGTATAAA
* * ** * ** *
1476800 ACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCC-TTCAAAGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTA-TCCGTTCAGGGAGTATAAA
* * * ** * *
1476855 ACTCGAATAATCTTCATA-AAATGAGTCTGCTCCCTATCCGTTCAGGGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTATCCGTTCAGGGAGTATAAA
* * ** * * *
1476910 ACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCC-TTCAGAGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTA-TCCGTTCAGGGAGTATAAA
* ** * ** *
1476965 ACTCGAACAATCTTC-AATAAACGGGTCCGCTCTCTATTCC-TTCAAAGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTA-TCCGTTCAGGGAGTATAAA
* * * *
1477020 ACTCGAACAATCTTC-AACAAACAGGTCCGCTCCCTATCCGTTCAGGGAGTATAGA
1 ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTATCCGTTCAGGGAGTATAAA
* *
1477075 ACTCGAATAATCTTCA
1 ACTTGAACAATCTTCA
1477091 TAAAACGAGT
Statistics
Matches: 303, Mismatches: 34, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
54 12 0.04
55 284 0.94
56 7 0.02
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (56 bp):
ACTTGAACAATCTTCAAATAAACAAGTCCGCTCCCTATCCGTTCAGGGAGTATAAA
Found at i:1476891 original size:110 final size:110
Alignment explanation
Indices: 1476714--1477100 Score: 525
Period size: 110 Copynumber: 3.5 Consensus size: 110
1476704 CAAATGATAA
* * * * *
1476714 GTCCGCTC-CTTATTTCTTCAGGGAGTATAAAACTTGAACAATCTTCA-ATAAACAAGTCCGCTC
1 GTCCGCTCTC-TATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGAGTCCGCTC
1476777 CCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
64 CCTATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
* * * *
1476824 GTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCGAATAATCTTCATAAAATGAGTCTGCTCCC
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCC
1476889 TATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
66 TATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
* *
1476934 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ATAAACGGGTCCGCTCT
1 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGAGTCCGCTCC
** *
1476998 CTATTCC-TTCAAAGAGTATAGAACTCGAACAATCTTCA-ACAAACAG
65 CTA-TCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGG
* * *
1477044 GTCCGCTCCCTA-TCCGTTCAGGGAGTATAGAACTCGAATAATCTTCATAAAACGAGT
1 GTCCGCTCTCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGT
1477101 TTGCTTCACC
Statistics
Matches: 248, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
109 5 0.02
110 237 0.96
111 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (110 bp):
GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCC
TATCCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGG
Found at i:1476970 original size:165 final size:165
Alignment explanation
Indices: 1476730--1477100 Score: 572
Period size: 165 Copynumber: 2.2 Consensus size: 165
1476720 TCCTTATTTC
* * * *
1476730 TTCAGGGAGTATAAAACTTGAACAATCTTCA-ATAAACAAGTCCGCTCCCTATCCGTTCAGGGAG
1 TTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGAGTCCGCTCCCTATCCGTTCAGAGAG
1476794 TATAGAACTCGAACAATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACT
65 TATAGAACTCGAACAATCTTCAAT-AAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACT
* * *
1476858 CGAATAATCTTCATA-AAA-TGAGTCTGCTCCCTATCCG
129 CGAACAATCTTCA-ACAAACAG-GTCCGCTCCCTATCCG
* *
1476895 TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCC-TTCAGAGAG
1 TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTA-TCCGTTCAGAGAG
1476959 TATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTC
65 TATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTC
1477024 GAACAATCTTCAACAAACAGGTCCGCTCCCTATCCG
130 GAACAATCTTCAACAAACAGGTCCGCTCCCTATCCG
*
1477060 TTCAGGGAGTATAGAACTCGAATAATCTTCATAAAACGAGT
1 TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGAGT
1477101 TTGCTTCACC
Statistics
Matches: 190, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
164 1 0.01
165 182 0.96
166 7 0.04
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (165 bp):
TTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGAGTCCGCTCCCTATCCGTTCAGAGAGT
ATAGAACTCGAACAATCTTCAATAAACGGGTCCGCTCTCTATTCCTTCAAAGAGTATAGAACTCG
AACAATCTTCAACAAACAGGTCCGCTCCCTATCCG
Found at i:1478344 original size:45 final size:45
Alignment explanation
Indices: 1478277--1478362 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
1478267 CAAACTCAAC
*
1478277 TCAAGTCGCCCTTTGCGAGTTTTCAACTTGAGA-CCTCCTTTGGTT
1 TCAAGACGCCCTTTGCGAGTTTTCAACTTGA-ACCCTCCTTTGGTT
* * *
1478322 TCAAGACGCCCTTTTCGGGTTTTCATCTTGAACCCTCCTTT
1 TCAAGACGCCCTTTGCGAGTTTTCAACTTGAACCCTCCTTT
1478363 TATTTCTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 1 0.03
45 35 0.97
ACGTcount: A:0.15, C:0.29, G:0.17, T:0.38
Consensus pattern (45 bp):
TCAAGACGCCCTTTGCGAGTTTTCAACTTGAACCCTCCTTTGGTT
Found at i:1478448 original size:7 final size:7
Alignment explanation
Indices: 1478379--1478430 Score: 104
Period size: 7 Copynumber: 7.4 Consensus size: 7
1478369 TTTTTTTTTC
1478379 TTTCATT
1 TTTCATT
1478386 TTTCATT
1 TTTCATT
1478393 TTTCATT
1 TTTCATT
1478400 TTTCATT
1 TTTCATT
1478407 TTTCATT
1 TTTCATT
1478414 TTTCATT
1 TTTCATT
1478421 TTTCATT
1 TTTCATT
1478428 TTT
1 TTT
1478431 TTTCATTTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTCATT
Found at i:1478450 original size:21 final size:21
Alignment explanation
Indices: 1478379--1478448 Score: 104
Period size: 21 Copynumber: 3.1 Consensus size: 21
1478369 TTTTTTTTTC
1478379 TTTCATTTTTCATTTTTCATT
1 TTTCATTTTTCATTTTTCATT
1478400 TTTCATTTTTCATTTTTCATT
1 TTTCATTTTTCATTTTTCATT
1478421 TTTCATTTTTTTTCATTTTTTCATT
1 TTTCA---TTTTTCA-TTTTTCATT
1478446 TTT
1 TTT
1478449 TTATTATTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
21 26 0.58
24 7 0.16
25 12 0.27
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTCATTTTTCATTTTTCATT
Found at i:1478467 original size:18 final size:17
Alignment explanation
Indices: 1478384--1478502 Score: 103
Period size: 14 Copynumber: 7.4 Consensus size: 17
1478374 TTTTCTTTCA
1478384 TTTTTCATTTTTCA---
1 TTTTTCATTTTTCATTT
1478398 TTTTTCATTTTTCA---
1 TTTTTCATTTTTCATTT
1478412 TTTTTCATTTTTCATTT
1 TTTTTCATTTTTCATTT
1478429 TTTTTCATTTTTTCATTT
1 TTTTTCA-TTTTTCATTT
* *
1478447 TTTTATTATTTTTC--CT
1 TTTT-TCATTTTTCATTT
* *
1478463 TTTTT-ATTTCTCCTTT
1 TTTTTCATTTTTCATTT
*
1478479 TTTTTCTTTTTTCATTT
1 TTTTTCATTTTTCATTT
*
1478496 CTTTTCA
1 TTTTTCA
1478503 GGAGAAATAT
Statistics
Matches: 88, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
14 34 0.39
15 1 0.01
16 11 0.12
17 20 0.23
18 20 0.23
19 2 0.02
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATTTTTCATTT
Found at i:1478471 original size:14 final size:14
Alignment explanation
Indices: 1478365--1478481 Score: 88
Period size: 14 Copynumber: 8.8 Consensus size: 14
1478355 CCTCCTTTTA
*
1478365 TTTC-TTTTTTTTT
1 TTTCATTTTTTATT
*
1478378 CTTTCATTTTTCATT
1 -TTTCATTTTTTATT
*
1478393 TTTCATTTTTCATT
1 TTTCATTTTTTATT
*
1478407 TTTCATTTTTCATT
1 TTTCATTTTTTATT
1478421 TTTCA---TTT-TT
1 TTTCATTTTTTATT
1478431 TTTCATTTTTTCA-T
1 TTTCATTTTTT-ATT
*
1478445 TTT--TTTATTATT
1 TTTCATTTTTTATT
*
1478457 TTTCCTTTTTTATT
1 TTTCATTTTTTATT
* *
1478471 TCTCCTTTTTT
1 TTTCATTTTTT
1478482 TTCTTTTTTC
Statistics
Matches: 88, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
10 7 0.08
11 3 0.03
12 9 0.10
13 3 0.03
14 59 0.67
15 7 0.08
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCATTTTTTATT
Found at i:1478496 original size:24 final size:24
Alignment explanation
Indices: 1478384--1478497 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 24
1478374 TTTTCTTTCA
* *
1478384 TTTTTCATTTTTCATTTTTCA---
1 TTTTTCTTTTTTCATTTCTCATTT
* *
1478405 TTTTTCATTTTTCATTTTTCATTT
1 TTTTTCTTTTTTCATTTCTCATTT
* *
1478429 TTTTTCATTTTTTCATTTTTTTATTAT
1 TTTTTC-TTTTTTCA-TTTCTCATT-T
* *
1478456 TTTTCCTTTTTT-ATTTCTCCTTT
1 TTTTTCTTTTTTCATTTCTCATTT
1478479 TTTTTCTTTTTTCATTTCT
1 TTTTTCTTTTTTCATTTCT
1478498 TTTCAGGAGA
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
21 21 0.27
23 12 0.15
24 18 0.23
25 8 0.10
26 14 0.18
27 6 0.08
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTCTTTTTTCATTTCTCATTT
Found at i:1488169 original size:45 final size:45
Alignment explanation
Indices: 1488054--1488188 Score: 220
Period size: 45 Copynumber: 3.0 Consensus size: 45
1488044 CCCATGCTTG
*
1488054 TTATTCACAAAAATAAATCCTAACCGCATGATATCTA-ATTGCATGC
1 TTATTCA-AAAAATAAA-CCTAACCGCATGATATCTAGTTTGCATGC
1488100 TTATTC-AAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
*
1488144 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
1488189 ATTTACTCGA
Statistics
Matches: 85, Mismatches: 2, Indels: 5
0.92 0.02 0.05
Matches are distributed among these distances:
43 19 0.22
44 23 0.27
45 37 0.44
46 6 0.07
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (45 bp):
TTATTCAAAAAATAAACCTAACCGCATGATATCTAGTTTGCATGC
Found at i:1492583 original size:5 final size:5
Alignment explanation
Indices: 1492575--1492612 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1492565 ATTTTACATA
1492575 TCATT TCATT TCATT TCATT TCATT TCATT TCATT TCA
1 TCATT TCATT TCATT TCATT TCATT TCATT TCATT TCA
1492613 GAAGCCTAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (5 bp):
TCATT
Found at i:1495327 original size:35 final size:35
Alignment explanation
Indices: 1495259--1495327 Score: 131
Period size: 34 Copynumber: 2.0 Consensus size: 35
1495249 CAGTAAAACC
1495259 AGAATTGGAATTATTTTACAAAAGAGTAGAAAAAA
1 AGAATTGGAATTATTTTACAAAAGAGTAGAAAAAA
1495294 AGAA-TGGAATTATTTTACAAAAGAGTAGAAAAAA
1 AGAATTGGAATTATTTTACAAAAGAGTAGAAAAAA
1495328 CACCATGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 30 0.88
35 4 0.12
ACGTcount: A:0.55, C:0.03, G:0.17, T:0.25
Consensus pattern (35 bp):
AGAATTGGAATTATTTTACAAAAGAGTAGAAAAAA
Found at i:1502791 original size:18 final size:18
Alignment explanation
Indices: 1502768--1502838 Score: 79
Period size: 18 Copynumber: 3.8 Consensus size: 18
1502758 TGAATATTTG
*
1502768 TCCCGAATGACCACTATA
1 TCCCGAAGGACCACTATA
*
1502786 TCCCGAAGGACCACTAATTG
1 TCCCGAAGGACCACT-A-TA
* * *
1502806 TTCCAAAGAACCACTATA
1 TCCCGAAGGACCACTATA
1502824 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
1502839 GATAATCCCT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
18 27 0.64
19 2 0.05
20 13 0.31
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATA
Found at i:1503363 original size:64 final size:64
Alignment explanation
Indices: 1503236--1503361 Score: 155
Period size: 64 Copynumber: 2.0 Consensus size: 64
1503226 GCATCCCTTG
* * * *
1503236 ACAGTTGCATCGATGCACTACCTATACATCGGTGCACAAATCTCATTCGATGTTTATATTTTAA
1 ACAGGTGCATCGATGCACTACCTATACATCGATGCACAAATCGCATTCGATGTTCATATTTTAA
* ** *
1503300 ACAGGTGCATCGATGCACT-CCTTATGCATCGATGCATTAATGGCATTCGATGTTCATTATTT
1 ACAGGTGCATCGATGCACTACC-TATACATCGATGCACAAATCGCATTCGATGTTCA-TATTT
1503362 AAGAGTGCAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
63 2 0.04
64 45 0.87
65 5 0.10
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (64 bp):
ACAGGTGCATCGATGCACTACCTATACATCGATGCACAAATCGCATTCGATGTTCATATTTTAA
Found at i:1509456 original size:18 final size:18
Alignment explanation
Indices: 1509433--1509505 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
1509423 ACTGAATATT
1509433 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1509451 TGTCCCAAAGGACCACTAA
1 TGTCCCGAAGGACCACT-A
* *
1509470 CTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
1509489 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1509506 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
18 31 0.66
19 2 0.04
20 14 0.30
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1511246 original size:31 final size:31
Alignment explanation
Indices: 1511211--1511277 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1511201 TTTTGACCAG
*
1511211 ATTCAATGATCAAATTGA-TATTTTATCTAAA
1 ATTCAAGGATCAAATT-ACTATTTTATCTAAA
* *
1511242 ATTCAAGGATGAAATTACTATTTTATCTAAC
1 ATTCAAGGATCAAATTACTATTTTATCTAAA
1511273 ATTCA
1 ATTCA
1511278 GGGTCAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (31 bp):
ATTCAAGGATCAAATTACTATTTTATCTAAA
Found at i:1517241 original size:671 final size:671
Alignment explanation
Indices: 1515955--1517263 Score: 2282
Period size: 671 Copynumber: 2.0 Consensus size: 671
1515945 AATTGGCAAA
*
1515955 AATTTGTTTAGGGAGTAAGGAGAATAAAAGATAGGAAACTTTGCACAACGATTTATAATGGTTCG
1 AATTTGTTTAGGGAGTAAGGAGAATAAAAGATAGGAAACTTTGCACAACAATTTATAATGGTTCG
1516020 ACTTCTCAACTAAGTCTACCTCCACTACCTTAGCTCCTCACTAAGAATTTTCTAACAAATTCACT
66 ACTTCTCAACTAAGTCTACCTCCACTACCTTAGCTCCTCACTAAGAATTTTCTAACAAATTCACT
1516085 AATTTGTTCTTTCTTTTTCAAGGACAAAGAGATAACATTTACAAAACTCCCTAGCTTTTAACAGG
131 AATTTGTTCTTTCTTTTTCAAGGACAAAGAGATAACATTTACAAAACTCCCTAGCTTTTAACAGG
* *
1516150 TTCATCTAGAATAAAAACCCCTTTACAAAAGGTAAAAAGAAGTAAACAAAGAAACCTCTTAAAGG
196 TTCAGCTAGAACAAAAACCCCTTTACAAAAGGTAAAAAGAAGTAAACAAAGAAACCTCTTAAAGG
* * *
1516215 TACGTGTTTACAAATTTAAAGCTTATAAGAACAAAATATTTACAAGAGAATAGGAATAAAGAGTG
261 TACGTGTTTACAAATTTAAAGATCATAAGAACAAAATATTTACAAAAGAATAGGAATAAAGAGTG
* *
1516280 AAAAGCTCTTCTCTTGTGTTTGATTGCTTAGAAATGTGTTCTAACCCTTCTTTAAGTGTCTTGAA
326 AAAAGCTCTTCTCTTGTGTTTGATTGCTTAGAAAGGTGTTCTAACCCTTCTTCAAGTGTCTTGAA
*
1516345 CTTGTATTTATATGTTGGAATGAGCTTGTGGCCGTTTCTAGCCGTTGGGAGTGATTTGGAGTCAT
391 CTTGTATTTATATGTTGGAATGAGCTTGTGGCCGTTTCTAGCCATTGGGAGTGATTTGGAGTCAT
* * * *
1516410 TGGGAATGTTTTTCTCTGTAAAATAAAATTTCCCAGTACAGAGGGTATCAGTACTCCTATAGGGA
456 TGGGAATGTTTTTCTCTGCAAAATAAAACTGCCCAGTACAGAGGGTATCAATACTCCTATAGGGA
1516475 GTATCGGTACTACCTTTTTTAATTTTAAATAAAAATAGTCATTACTAGCTGTTGGGCATGACGAT
521 GTATCGGTACTACCTTTTTTAATTTTAAATAAAAATAGTCATTACTAGCTGTTGGGCATGACGAT
* *
1516540 ATCGATACTAAGCCTATGGTATCGATACTATTATGTAAAGTAGTATCAGTACCCCTTTGGGTATC
586 ATCGATACTAAGCCTACGGTATCAATACTATTATGTAAAGTAGTATCAGTACCCCTTTGGGTATC
1516605 GGTACCATTTTTGCATTCTAG
651 GGTACCATTTTTGCATTCTAG
* * * *
1516626 AATTTGTTTAAGGG-GTAAGGAGAATAAAATATAGGAAACTTTGCATAATAATTTATAGTGGTTC
1 AATTTGTTT-AGGGAGTAAGGAGAATAAAAGATAGGAAACTTTGCACAACAATTTATAATGGTTC
*
1516690 GACTTCTCAACTAAGTCTACCTCCACTACCTTAGCTCCTCACTAAGGATTTTCTAACAAATTCAC
65 GACTTCTCAACTAAGTCTACCTCCACTACCTTAGCTCCTCACTAAGAATTTTCTAACAAATTCAC
* * *
1516755 TAATTTGTTCTTTCTTTTT-AATGACAAAGAGATAACCTTTACAAAACTCTCTAGCTTTTAACAG
130 TAATTTGTTCTTTCTTTTTCAAGGACAAAGAGATAACATTTACAAAACTCCCTAGCTTTTAACAG
*
1516819 GTTCAGCTAGAACCAAAACCCCTTTACAAAAGGTAAAAAGAAGTAAACAAAGAAACCTCTTAAAG
195 GTTCAGCTAGAACAAAAACCCCTTTACAAAAGGTAAAAAGAAGTAAACAAAGAAACCTCTTAAAG
**
1516884 GTATTTGTTTACAAATTTAAAGATCATAAGAACAAAATATTTACAAAAGAATAGGAATAAAGAGT
260 GTACGTGTTTACAAATTTAAAGATCATAAGAACAAAATATTTACAAAAGAATAGGAATAAAGAGT
*
1516949 GAAAAAGCTCTTCTCTTGTGTTTGATTGCTTGGAAAGGTGTTCTAACCCTTCTTCAAGTGTCTTG
325 G-AAAAGCTCTTCTCTTGTGTTTGATTGCTTAGAAAGGTGTTCTAACCCTTCTTCAAGTGTCTTG
* *
1517014 AACTTGTATTTATATGTTGGAATGAGCTTGTGGTCGTTTTTAGCCATTGGG-GTGATTTGGAGTC
389 AACTTGTATTTATATGTTGGAATGAGCTTGTGGCCGTTTCTAGCCATTGGGAGTGATTTGGAGTC
*
1517078 ATTGGGGATGTTTTTCTCTGCAAAATAAAACTGCCCAGTACAGAGGGTATCAATACTCCTATAGG
454 ATTGGGAATGTTTTTCTCTGCAAAATAAAACTGCCCAGTACAGAGGGTATCAATACTCCTATAGG
* *
1517143 GAGTATCGGTACTACCTTTTTTTATTTTAAAATAAAACTAGTCATTACTAGCTGTTGGGCATGAC
519 GAGTATCGGTACTACCTTTTTTAATTTT-AAATAAAAATAGTCATTACTAGCTGTTGGGCATGAC
1517208 GATATCGATACTAAGCCTACGGTATCAATACTATTATGTAAAGTAGTATCAGTACC
583 GATATCGATACTAAGCCTACGGTATCAATACTATTATGTAAAGTAGTATCAGTACC
1517264 ATTTTTGCAT
Statistics
Matches: 603, Mismatches: 32, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
670 265 0.44
671 334 0.55
672 4 0.01
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Consensus pattern (671 bp):
AATTTGTTTAGGGAGTAAGGAGAATAAAAGATAGGAAACTTTGCACAACAATTTATAATGGTTCG
ACTTCTCAACTAAGTCTACCTCCACTACCTTAGCTCCTCACTAAGAATTTTCTAACAAATTCACT
AATTTGTTCTTTCTTTTTCAAGGACAAAGAGATAACATTTACAAAACTCCCTAGCTTTTAACAGG
TTCAGCTAGAACAAAAACCCCTTTACAAAAGGTAAAAAGAAGTAAACAAAGAAACCTCTTAAAGG
TACGTGTTTACAAATTTAAAGATCATAAGAACAAAATATTTACAAAAGAATAGGAATAAAGAGTG
AAAAGCTCTTCTCTTGTGTTTGATTGCTTAGAAAGGTGTTCTAACCCTTCTTCAAGTGTCTTGAA
CTTGTATTTATATGTTGGAATGAGCTTGTGGCCGTTTCTAGCCATTGGGAGTGATTTGGAGTCAT
TGGGAATGTTTTTCTCTGCAAAATAAAACTGCCCAGTACAGAGGGTATCAATACTCCTATAGGGA
GTATCGGTACTACCTTTTTTAATTTTAAATAAAAATAGTCATTACTAGCTGTTGGGCATGACGAT
ATCGATACTAAGCCTACGGTATCAATACTATTATGTAAAGTAGTATCAGTACCCCTTTGGGTATC
GGTACCATTTTTGCATTCTAG
Found at i:1519625 original size:17 final size:17
Alignment explanation
Indices: 1519583--1519625 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1519573 TTATCTTAGT
* *
1519583 TTCCTTCACTTCATCGG
1 TTCCTTCATTTCATCAG
1519600 TTCCTTCATTTCATCAG
1 TTCCTTCATTTCATCAG
1519617 TTCCTTCAT
1 TTCCTTCAT
1519626 GAGTGACTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.07, T:0.47
Consensus pattern (17 bp):
TTCCTTCATTTCATCAG
Found at i:1528260 original size:22 final size:22
Alignment explanation
Indices: 1528225--1528269 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
1528215 CATAATTATT
1528225 TAAAAAATTAAAT-AAAAATAA
1 TAAAAAATTAAATAAAAAATAA
*
1528246 TAAAAATATTTAATAAAAAATAA
1 TAAAAA-ATTAAATAAAAAATAA
1528269 T
1 T
1528270 TTTTTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATTAAATAAAAAATAA
Found at i:1531940 original size:2 final size:2
Alignment explanation
Indices: 1531933--1531974 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1531923 AGAATGAAGA
1531933 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1531975 GATTATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1540634 original size:21 final size:21
Alignment explanation
Indices: 1540610--1540649 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1540600 ACCGGTTTTG
**
1540610 CCGGTTTTCAGTCGGTTCACC
1 CCGGTTTTCAACCGGTTCACC
1540631 CCGGTTTTCAACCGGTTCA
1 CCGGTTTTCAACCGGTTCA
1540650 TTGTTATACC
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:0.12, C:0.33, G:0.23, T:0.33
Consensus pattern (21 bp):
CCGGTTTTCAACCGGTTCACC
Found at i:1543627 original size:3 final size:3
Alignment explanation
Indices: 1543619--1543647 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1543609 GAATAGGGTT
1543619 TTG TTG TTG TTG TTG TTG TTG TTG -TG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1543648 GTATAAGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:1545044 original size:20 final size:20
Alignment explanation
Indices: 1545016--1545060 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1545006 ATTTAATTTC
*
1545016 TAAAGTTATAAAATTATTAT
1 TAAATTTATAAAATTATTAT
**
1545036 TAAATTTATTGAATTATTAT
1 TAAATTTATAAAATTATTAT
*
1545056 AAAAT
1 TAAAT
1545061 AATTATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
TAAATTTATAAAATTATTAT
Found at i:1546684 original size:65 final size:65
Alignment explanation
Indices: 1546614--1546761 Score: 169
Period size: 65 Copynumber: 2.3 Consensus size: 65
1546604 TACACTAGGG
* * *
1546614 GTGCATCGGTACACT-AATTATATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGT
1 GTGCATCGGTACACTAAAATATATTCGATGTATCAATAA-AGCCAAGAGTGCATCGATGCATGGT
1546677 CT
65 -T
* * ** *
1546679 GTGCATCGGTATA-TAAAATGTATTCGATGTATCAATAAATTCAAGAGTGCATTGATGCATGGTT
1 GTGCATCGGTACACTAAAATATATTCGATGTATCAATAAAGCCAAGAGTGCATCGATGCATGGTT
*
1546743 GTGCATCCGTACAC-AAAAT
1 GTGCATCGGTACACTAAAAT
1546762 GCATTCGAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
64 18 0.26
65 50 0.71
66 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGGTACACTAAAATATATTCGATGTATCAATAAAGCCAAGAGTGCATCGATGCATGGTT
Found at i:1555361 original size:65 final size:64
Alignment explanation
Indices: 1555284--1555419 Score: 202
Period size: 65 Copynumber: 2.1 Consensus size: 64
1555274 ACACTAATTA
* *
1555284 CATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTCTGTGCATCAGTACATAAAAT
1 CATTCGATGTTTCAATAA-AGCCAAGAGTGCATCGATGCATGGT-TGTGCATCAGTACACAAAAT
1555348 G
64 G
** *
1555349 CATTCGATGTTTCAATAAATTCAAGAGTGCATCGATGCATGGTTGTGCATCGGTACACAAAATG
1 CATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTTGTGCATCAGTACACAAAATG
1555413 CATTCGA
1 CATTCGA
1555420 AATAGGGTGT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
64 26 0.40
65 37 0.57
66 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAGCCAAGAGTGCATCGATGCATGGTTGTGCATCAGTACACAAAATG
Found at i:1556749 original size:68 final size:69
Alignment explanation
Indices: 1556646--1556776 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 69
1556636 TTTTAACATT
* * * *
1556646 TCCGGTAAAAATACCCAACGATAACAAAACCGGTAGCGCCTAATAATGTTTCTGGTCATTTTTAT
1 TCCGGTAAAAATACCCAACAATAAAAAAACCGGTAGCGCCTAATAATGTTTATGGTAATTTTTAT
1556711 CAAA
66 CAAA
* * *
1556715 TCCGGT-AAAATGCCCAATAATAAAAAAATCGGTAGCGCCTAATAATGTTTATGGTAATTTTT
1 TCCGGTAAAAATACCCAACAATAAAAAAACCGGTAGCGCCTAATAATGTTTATGGTAATTTTT
1556777 TTATCGATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
68 49 0.89
69 6 0.11
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (69 bp):
TCCGGTAAAAATACCCAACAATAAAAAAACCGGTAGCGCCTAATAATGTTTATGGTAATTTTTAT
CAAA
Found at i:1558030 original size:21 final size:20
Alignment explanation
Indices: 1557992--1558030 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1557982 TAAAAGGAAA
* *
1557992 AAAAAACTTAAAACATATCC
1 AAAAAACTGAAAAAATATCC
1558012 AAAAAACTGAACAAAATAT
1 AAAAAACTGAA-AAAATAT
1558031 ATGTACGAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.64, C:0.15, G:0.03, T:0.18
Consensus pattern (20 bp):
AAAAAACTGAAAAAATATCC
Found at i:1559185 original size:12 final size:12
Alignment explanation
Indices: 1559164--1559193 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1559154 TTAATAAAAT
*
1559164 AAAAAGTATATA
1 AAAAATTATATA
1559176 AAAAATTATATA
1 AAAAATTATATA
1559188 AAAAAT
1 AAAAAT
1559194 GATAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (12 bp):
AAAAATTATATA
Found at i:1570980 original size:21 final size:21
Alignment explanation
Indices: 1570938--1570980 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1570928 TTTCTGGGTT
* * *
1570938 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1570959 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1570980 A
1 A
1570981 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1571041 original size:66 final size:67
Alignment explanation
Indices: 1570938--1571096 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 67
1570928 TTTCTGGGTT
* * *
1570938 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
1571001 CTAG
64 CTAG
* * *
1571005 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
1571070 TG
66 AG
*
1571072 AGGGGAATCGATACCCCCAGGGGGG
1 AGGGGAATCGGTACCCCCAGGGGGG
1571097 GGAACTGATT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
65 2 0.02
66 22 0.27
67 58 0.71
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.18
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:1571440 original size:29 final size:29
Alignment explanation
Indices: 1571406--1571477 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
1571396 CATATTATGA
**
1571406 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1571435 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
1571464 TACTTGACATGAAT
1 TACATGACATGAAT
1571478 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:1571831 original size:23 final size:22
Alignment explanation
Indices: 1571771--1571838 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
1571761 TTATGGACAT
1571771 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1571793 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1571815 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
1571838 A
1 A
1571839 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1577897 original size:21 final size:21
Alignment explanation
Indices: 1577855--1577897 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1577845 TTTCTGGGTT
* * *
1577855 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1577876 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1577897 A
1 A
1577898 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1577958 original size:66 final size:67
Alignment explanation
Indices: 1577855--1578027 Score: 224
Period size: 67 Copynumber: 2.6 Consensus size: 67
1577845 TTTCTGGGTT
* * *
1577855 AGGGGAATCGGTACCCATTCA-AGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATG
1 AGGGGAATCGGTACCC--CCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATG
1577918 CTAG
64 CTAG
* * *
1577922 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGCT
1 AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
*
1577987 TG
66 AG
* *
1577989 AGGGGAATCGATACCCCCAGGGGGGGAACCGATTCCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGGAACCGATACCCCC
1578028 ATGAGAAAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 2 0.02
66 22 0.23
67 52 0.55
68 18 0.19
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (67 bp):
AGGGGAATCGGTACCCCCAGGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCT
AG
Found at i:1578389 original size:27 final size:27
Alignment explanation
Indices: 1578318--1578396 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 27
1578308 GATTACATTC
1578318 CATATTATG-A-TACATGACATGAATT
1 CATATTATGTATTACATGACATGAATT
**
1578343 TGTATTAAATGTATTACATGACATGAATT
1 CATATT--ATGTATTACATGACATGAATT
1578372 CATATTATGTATTACATGACATGAA
1 CATATTATGTATTACATGACATGAA
1578397 AATGCAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 4 0.09
27 22 0.48
28 1 0.02
29 19 0.41
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (27 bp):
CATATTATGTATTACATGACATGAATT
Found at i:1578765 original size:22 final size:22
Alignment explanation
Indices: 1578691--1578757 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
1578681 TTATGGACAT
1578691 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1578713 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1578735 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
1578757 A
1 A
1578758 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:1581305 original size:16 final size:17
Alignment explanation
Indices: 1581275--1581307 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1581265 CTCTAAATTT
1581275 TTAAAAAAAGAGAAAAA
1 TTAAAAAAAGAGAAAAA
1581292 TTAAAAAAAG-GAAAAA
1 TTAAAAAAAGAGAAAAA
1581308 CAGTTGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
TTAAAAAAAGAGAAAAA
Found at i:1585596 original size:33 final size:33
Alignment explanation
Indices: 1585559--1585623 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1585549 AAGTCAGCTT
1585559 ATCATTACAACATTGACAACACTTTTCACCCTC
1 ATCATTACAACATTGACAACACTTTTCACCCTC
*
1585592 ATCATTACAACATTGACTACACTTTTCACCCT
1 ATCATTACAACATTGACAACACTTTTCACCCT
1585624 TGTCCTACGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (33 bp):
ATCATTACAACATTGACAACACTTTTCACCCTC
Found at i:1589556 original size:28 final size:28
Alignment explanation
Indices: 1589524--1589584 Score: 122
Period size: 28 Copynumber: 2.2 Consensus size: 28
1589514 AAAGCCGTAG
1589524 GTGATGGGTAATTTTAACAAAAATAGAT
1 GTGATGGGTAATTTTAACAAAAATAGAT
1589552 GTGATGGGTAATTTTAACAAAAATAGAT
1 GTGATGGGTAATTTTAACAAAAATAGAT
1589580 GTGAT
1 GTGAT
1589585 TTGGATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.33
Consensus pattern (28 bp):
GTGATGGGTAATTTTAACAAAAATAGAT
Found at i:1600341 original size:21 final size:21
Alignment explanation
Indices: 1600315--1600359 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1600305 GATTTCTGGG
* *
1600315 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1600336 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1600357 CAA
1 CAA
1600360 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1601997 original size:22 final size:22
Alignment explanation
Indices: 1601969--1602022 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
1601959 TCCTTATGGA
1601969 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1601991 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
1602013 CAATTCTACG
1 CAATTCTACG
1602023 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:1608037 original size:6 final size:6
Alignment explanation
Indices: 1608026--1608051 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1608016 ATTCGGATAT
1608026 GCTTTA GCTTTA GCTTTA GCTTTA GC
1 GCTTTA GCTTTA GCTTTA GCTTTA GC
1608052 ACCTAGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.19, T:0.46
Consensus pattern (6 bp):
GCTTTA
Found at i:1617119 original size:2 final size:2
Alignment explanation
Indices: 1617112--1617140 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1617102 ATTTTTCTCA
1617112 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 A
1617141 CTTTTTCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1623553 original size:2 final size:2
Alignment explanation
Indices: 1623546--1623589 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
1623536 AAGTTATGAG
1623546 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1623586 AT AT
1 AT AT
1623590 GATAACAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1623592 original size:194 final size:192
Alignment explanation
Indices: 1623375--1623752 Score: 729
Period size: 194 Copynumber: 2.0 Consensus size: 192
1623365 GATCTAGGTG
1623375 AATATATATATATATATATATGATAACAATGTATAAGTTATATGAATTAGATCTATGTGAACTGG
1 AATATATATATATATATATATGATAACAATGTATAAGTTATATGAATTAGATCTATGTGAACTGG
*
1623440 TATAATTGATTTATGTGATTAAATGAAATTAGAGATAAGCTGAGTATAATGGACCTATATGATAA
66 TATAATTGATTTATGTGATTAAATGAAATTAGAGATAAGCTGAGTATAATGAACCTATATGATAA
1623505 TATGAGAATGTTATAGGAACTAGGTGATAATAAGTTATGAGATATATATATATATATATATAT
131 TATGAGAATGTTATAGGAACTAGGTGATAATAAGTTATGAGA-ATATATATATATATATATAT
1623568 AATATATATTATATATATATATGATAACAATGTATAAGTTATATGAATTAGATCTATGTGAACTG
1 AATATATA-TATATATATATATGATAACAATGTATAAGTTATATGAATTAGATCTATGTGAACTG
1623633 GTATAATTGATTTATGTGATTAAATGAAATTAGAGATAAGCTGAGTATAATGAACCTATATGATA
65 GTATAATTGATTTATGTGATTAAATGAAATTAGAGATAAGCTGAGTATAATGAACCTATATGATA
1623698 ATATGAGAATGTTATAGGAACTAGGTGATAATAAGTTATGAGAATATATATATAT
130 ATATGAGAATGTTATAGGAACTAGGTGATAATAAGTTATGAGAATATATATATAT
1623753 TCTTATGTGA
Statistics
Matches: 183, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
193 20 0.11
194 163 0.89
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.37
Consensus pattern (192 bp):
AATATATATATATATATATATGATAACAATGTATAAGTTATATGAATTAGATCTATGTGAACTGG
TATAATTGATTTATGTGATTAAATGAAATTAGAGATAAGCTGAGTATAATGAACCTATATGATAA
TATGAGAATGTTATAGGAACTAGGTGATAATAAGTTATGAGAATATATATATATATATATAT
Found at i:1623603 original size:28 final size:28
Alignment explanation
Indices: 1623549--1623603 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1623539 TTATGAGATA
*
1623549 TATATATATATATATATATAATATATAT
1 TATATATATATATATATACAATATATAT
*
1623577 TATATATATATATGATA-ACAATGTATA
1 TATATATATATAT-ATATACAATATATA
1623604 AGTTATATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.88
29 3 0.12
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (28 bp):
TATATATATATATATATACAATATATAT
Found at i:1629585 original size:31 final size:31
Alignment explanation
Indices: 1629542--1629611 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
1629532 TATCATTGAC
* * * *
1629542 CTGAACCCGAGTTGGACATGGAAATTGTGGAT
1 CTGAA-CCGAGTTGAACACGAAAATTATGGAT
*
1629574 CTGAACCGAGTTGAACCCGAAAATTATGGAT
1 CTGAACCGAGTTGAACACGAAAATTATGGAT
1629605 CTGAACC
1 CTGAACC
1629612 AAACTTACAC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 28 0.85
32 5 0.15
ACGTcount: A:0.31, C:0.20, G:0.26, T:0.23
Consensus pattern (31 bp):
CTGAACCGAGTTGAACACGAAAATTATGGAT
Found at i:1631242 original size:31 final size:31
Alignment explanation
Indices: 1631172--1631235 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
1631162 TTACATCGAA
*
1631172 GACCATATTGCAAACGGACTAAATGTTGAGG
1 GACCATATTGCAAACAGACTAAATGTTGAGG
* *
1631203 GACCATATTGTAAACAGACTAAATGTTGGGG
1 GACCATATTGCAAACAGACTAAATGTTGAGG
1631234 GA
1 GA
1631236 TTATATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (31 bp):
GACCATATTGCAAACAGACTAAATGTTGAGG
Found at i:1632554 original size:30 final size:31
Alignment explanation
Indices: 1632518--1632576 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
1632508 CTTTTGCAAC
1632518 TTGCAATATAATCCCCCAAC-TTTAGTCCGT
1 TTGCAATATAATCCCCCAACATTTAGTCCGT
* **
1632548 TTGCAATATGATCCTTCAACATTTAGTCC
1 TTGCAATATAATCCCCCAACATTTAGTCC
1632577 ATTTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TTGCAATATAATCCCCCAACATTTAGTCCGT
Found at i:1633578 original size:183 final size:181
Alignment explanation
Indices: 1633328--1633699 Score: 608
Period size: 183 Copynumber: 2.0 Consensus size: 181
1633318 ATTAAATTTT
* *
1633328 AAATATTATATATATTATATATAACATATGGCTTAAGTCCAAACCATTTAAAACTCAATTAATAA
1 AAATATTATATATATTATATATAACATATGGCTTAAGCCCAAACCATTTAAAACCCAATTAATAA
1633393 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAATTTCATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTT-ATATAAAATTT
*
1633457 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTT-AATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTAT-AA-T-TTTTTTGAATTAAA
1633511 AAATATTATATATATTATATATAACATATGGAC-TAAGCCCAAACCATTTAAAACCCAA-TATAT
1 AAATATTATATATATTATATATAACATATGG-CTTAAGCCCAAACCATTTAAAACCCAATTA-AT
* *
1633574 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAAT
64 AATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAATTTATATAAAAT
1633639 TTTTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTGAATTAAA
128 TTTTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTGAATTAAA
1633693 AAATATT
1 AAATATT
1633700 TAATTTTTGT
Statistics
Matches: 179, Mismatches: 5, Indels: 11
0.92 0.03 0.06
Matches are distributed among these distances:
181 6 0.03
182 17 0.09
183 105 0.59
184 44 0.25
185 7 0.04
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (181 bp):
AAATATTATATATATTATATATAACATATGGCTTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATTTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTGAATTAAA
Found at i:1634579 original size:2 final size:2
Alignment explanation
Indices: 1634572--1634630 Score: 100
Period size: 2 Copynumber: 29.5 Consensus size: 2
1634562 TGTATGTATG
* *
1634572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1634614 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1634631 GTATTTATAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1634778 original size:36 final size:36
Alignment explanation
Indices: 1634736--1634826 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 36
1634726 TGATAATGAT
*
1634736 ATGCATGTATGTATATATGTATGATATTGATAATTG
1 ATGCATGTATGTATATATGTACGATATTGATAATTG
1634772 ATGCATGTATGTATATATGTACGATATTGATAATTG
1 ATGCATGTATGTATATATGTACGATATTGATAATTG
*
1634808 ATGCATGTATGTACATATG
1 ATGCATGTATGTATATATG
1634827 ATAAACATGC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (36 bp):
ATGCATGTATGTATATATGTACGATATTGATAATTG
Found at i:1634925 original size:21 final size:20
Alignment explanation
Indices: 1634901--1634987 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
1634891 GTACATGTTC
1634901 TATATGTATACATACATACTT
1 TATAT-TATACATACATACTT
*
1634922 TATA-TATACACACTTATACTT
1 TATATTATACATAC--ATACTT
* * *
1634943 TATATTATATATATACACTT
1 TATATTATACATACATACTT
* *
1634963 TATATTATTATATATATACTT
1 TATATTA-TACATACATACTT
1634984 TATA
1 TATA
1634988 CTTTATACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
19 8 0.14
20 12 0.21
21 30 0.54
22 6 0.11
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.48
Consensus pattern (20 bp):
TATATTATACATACATACTT
Found at i:1634989 original size:7 final size:7
Alignment explanation
Indices: 1634935--1635007 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
1634925 ATATACACAC
1634935 TTATACT
1 TTATACT
1634942 TTATA-T
1 TTATACT
1634948 TATATA-T
1 T-TATACT
* *
1634955 ATACACT
1 TTATACT
*
1634962 TTATATT
1 TTATACT
1634969 ATTATA-T
1 -TTATACT
*
1634976 ATATACT
1 TTATACT
1634983 TTATACT
1 TTATACT
1634990 TTATAC-
1 TTATACT
1634996 TTATACT
1 TTATACT
*
1635003 ATATA
1 TTATA
1635008 AGTATATATA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
6 15 0.28
7 33 0.62
8 5 0.09
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (7 bp):
TTATACT
Done.