Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005946.1 Hibiscus syriacus cultivar Beakdansim tig00013960_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: 2465359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1103223 original size:19 final size:19
Alignment explanation
Indices: 1103201--1103265 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
1103191 GAAACCAAAA
*
1103201 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1103220 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1103234 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
1103253 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1103266 CTCTCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 10 0.27
16 2 0.05
17 3 0.08
19 22 0.59
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1103242 original size:14 final size:14
Alignment explanation
Indices: 1103223--1103279 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1103213 TTTCATTTCG
1103223 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1103237 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1103256 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1103270 CGTTGCGATT
1 CGTTGCGATT
1103280 TTCATTTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.25, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1103252 original size:33 final size:33
Alignment explanation
Indices: 1103206--1103287 Score: 155
Period size: 33 Copynumber: 2.5 Consensus size: 33
1103196 CAAAATCGCA
1103206 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1103239 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1103272 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1103288 AACCAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1105126 original size:91 final size:92
Alignment explanation
Indices: 1104946--1105218 Score: 500
Period size: 91 Copynumber: 3.0 Consensus size: 92
1104936 ATTGCTTAGT
*
1104946 AATTTATTCGGTTGCTGCCAA-TCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1105010 TCTTTGTTTTGTCTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTGGTTGAAAGTA
1105037 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1105102 TCTTTGTTTTGT-TTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTGGTTGAAAGTA
*
1105128 AATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1105193 TCTTTG-TTTGTCTTTGGTTG-AAGTA
66 TCTTTGTTTTGTCTTTGGTTGAAAGTA
1105218 A
1 A
1105219 TGCAATCCAT
Statistics
Matches: 178, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
90 11 0.06
91 112 0.63
92 55 0.31
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (92 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTGGTTGAAAGTA
Found at i:1105304 original size:19 final size:19
Alignment explanation
Indices: 1105264--1105391 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1105254 TAGTTTACTT
* *
1105264 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1105284 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1105303 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1105322 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
1105336 TCGCAACGCGAAACC-AAA
1 TCGCAACGCGAAACCAAAA
*
1105354 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1105368 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1105387 TCGCA
1 TCGCA
1105392 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 1 0.01
14 18 0.20
15 1 0.01
16 6 0.07
17 2 0.02
18 10 0.11
19 37 0.42
20 13 0.15
ACGTcount: A:0.45, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1105360 original size:32 final size:31
Alignment explanation
Indices: 1105300--1105391 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 31
1105290 CGCGAAACCA
**
1105300 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAA-CCAAATCGCAACGAC
1105332 AGAATCGCAACGCGAAACCAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAATCGCAACGAC
1105364 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACC-AAATCGCA
1105392 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.02
32 31 0.56
33 23 0.42
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (31 bp):
AAATCGCAACGCGAAACCAAATCGCAACGAC
Found at i:1105409 original size:19 final size:19
Alignment explanation
Indices: 1105387--1105520 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1105377 GAAACCAAAA
*
1105387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1105406 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
1105422 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1105439 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1105455 T--CGTTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
**
1105471 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1105490 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1105510 TCGTGTTGCGA
1 TCGCGTTGCGA
1105521 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
15 3 0.03
16 10 0.11
17 9 0.10
18 8 0.09
19 37 0.39
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1105428 original size:14 final size:14
Alignment explanation
Indices: 1105409--1105465 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1105399 TTTCATTTCG
1105409 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
1105423 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
1105440 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
1105456 CGTTGCGATT
1 CGTTGCGATT
1105466 TCATTTCGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:1105473 original size:32 final size:33
Alignment explanation
Indices: 1105392--1105483 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1105382 CAAAATCGCA
*
1105392 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
1105425 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
1105458 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1105484 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 19 0.34
33 37 0.66
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:1105492 original size:51 final size:47
Alignment explanation
Indices: 1105409--1105502 Score: 125
Period size: 51 Copynumber: 1.9 Consensus size: 47
1105399 TTTCATTTCG
1105409 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
1 CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
** *
1105456 CGTTGCGATTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATT
1 CGTTGCGA-TTC-TTT--CGTTGCGATTTTCATTTCGCATTGCGATT
1105503 TTAAGTTTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 8 0.20
48 3 0.08
49 3 0.08
51 26 0.65
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (47 bp):
CGTTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTCTGT
Found at i:1107428 original size:14 final size:14
Alignment explanation
Indices: 1107409--1107444 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1107399 ATTGTTTAAT
1107409 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1107423 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1107437 TGATTTGT
1 TGATTTGT
1107445 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1107564 original size:19 final size:19
Alignment explanation
Indices: 1107540--1107644 Score: 157
Period size: 19 Copynumber: 5.8 Consensus size: 19
1107530 GTGAAGGCAA
*
1107540 AAATGAATATCGCAATGCG
1 AAATGAAAATCGCAATGCG
1107559 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAATGCG
1107578 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAATGCG
*
1107595 --A-GAGAATCGCAATGCG
1 AAATGAAAATCGCAATGCG
1107611 AAATGAAAATCGCAATGCG
1 AAATGAAAATCGCAATGCG
1107630 AAATGAAAATCGCAA
1 AAATGAAAATCGCAA
1107645 CGAGAGAATC
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 62 0.79
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.15
Consensus pattern (19 bp):
AAATGAAAATCGCAATGCG
Found at i:1107682 original size:52 final size:52
Alignment explanation
Indices: 1107548--1107663 Score: 232
Period size: 52 Copynumber: 2.2 Consensus size: 52
1107538 AAAAATGAAT
1107548 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1107600 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1107652 ATCGCAATGCGA
1 ATCGCAATGCGA
1107664 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1107696 original size:33 final size:33
Alignment explanation
Indices: 1107659--1107866 Score: 214
Period size: 33 Copynumber: 6.2 Consensus size: 33
1107649 AGAATCGCAA
*
1107659 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
* *
1107692 TGCGATTTTCATTTCGGATTGCGATTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--T
* *
1107729 TGCGA--TTC-TCTCG--TTGCGATTTTCATTCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTC--TCG--T
1107761 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1107794 TGCGATTTTCATTTCCGCATTGTGATT-TCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1107827 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1107860 TGCGATT
1 TGCGATT
1107867 GTAATTTCCG
Statistics
Matches: 148, Mismatches: 12, Indels: 30
0.78 0.06 0.16
Matches are distributed among these distances:
30 1 0.01
31 2 0.01
32 29 0.20
33 64 0.43
34 22 0.15
35 14 0.09
37 16 0.11
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1107721 original size:18 final size:19
Alignment explanation
Indices: 1107653--1107852 Score: 158
Period size: 19 Copynumber: 11.7 Consensus size: 19
1107643 AACGAGAGAA
* *
1107653 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1107672 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1107688 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1107705 TCGGATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
1107723 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1107739 TCG--TTGCGATTTTCA-T
1 TCGCATTGCGATTTTCATT
1107755 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1107774 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1107790 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1107807 TCCGCATTGTGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
1107824 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1107840 TCGCATTGCGATT
1 TCGCATTGCGATT
1107853 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 12, Indels: 46
0.72 0.06 0.23
Matches are distributed among these distances:
13 5 0.03
14 23 0.16
15 1 0.01
16 25 0.17
17 16 0.11
18 31 0.21
19 40 0.27
20 5 0.03
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1107732 original size:51 final size:52
Alignment explanation
Indices: 1107653--1107821 Score: 279
Period size: 51 Copynumber: 3.3 Consensus size: 52
1107643 AACGAGAGAA
* *
1107653 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1107705 TCGGATTGCGA-TTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCA-T
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1107755 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1107807 TCCGCATTGTGATTT
1 T-CGCATTGCGATTT
1107822 CATGTTGGGA
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
50 11 0.10
51 75 0.69
52 11 0.10
53 12 0.11
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1110118 original size:12 final size:12
Alignment explanation
Indices: 1110103--1110127 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1110093 TTCTTCGGGA
1110103 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1110115 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1110127 C
1 C
1110128 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:1110335 original size:24 final size:24
Alignment explanation
Indices: 1110300--1110347 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1110290 TCTGAAACAT
1110300 TATCAAAATCCGTG-TATTGACCAA
1 TATCAAAATCCG-GATATTGACCAA
*
1110324 TATCAAAGTCCGGATATTGACCAA
1 TATCAAAATCCGGATATTGACCAA
1110348 GACCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TATCAAAATCCGGATATTGACCAA
Found at i:1111061 original size:40 final size:40
Alignment explanation
Indices: 1111012--1111161 Score: 194
Period size: 40 Copynumber: 3.8 Consensus size: 40
1111002 AAATTTCAGT
* *
1111012 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
1111052 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * * **
1111092 GTTGCGATTTACGGATACGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACG-GATTATC
* *
1111132 GTTGCGATTTTCATATTCGCGTTGCGATTT
1 GTTGCGATTTACAGATTCGCGTTGCGATTT
1111162 TGGAAAATCG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 97 0.99
41 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:1111162 original size:20 final size:20
Alignment explanation
Indices: 1111012--1111161 Score: 158
Period size: 20 Copynumber: 7.5 Consensus size: 20
1111002 AAATTTCAGT
* * *
1111012 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1111032 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1111052 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1111072 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1111092 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1111112 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1111132 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1111152 GTTGCGATTT
1 GTTGCGATTT
1111162 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
20 111 0.99
21 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1112903 original size:17 final size:17
Alignment explanation
Indices: 1112881--1112914 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1112871 ATTGTACATG
1112881 TATGATAGCCATAGAAT
1 TATGATAGCCATAGAAT
*
1112898 TATGATAGCTATAGAAT
1 TATGATAGCCATAGAAT
1112915 CTTGTGAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (17 bp):
TATGATAGCCATAGAAT
Found at i:1113795 original size:18 final size:18
Alignment explanation
Indices: 1113772--1113820 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
1113762 AATATTTGTC
1113772 CCGAATGACCACTATATA
1 CCGAATGACCACTATATA
* *
1113790 CCGAATGACCACTATGTC
1 CCGAATGACCACTATATA
*
1113808 CCGAAGGACCACT
1 CCGAATGACCACT
1113821 GATAATCCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.33, C:0.33, G:0.16, T:0.18
Consensus pattern (18 bp):
CCGAATGACCACTATATA
Found at i:1117585 original size:21 final size:22
Alignment explanation
Indices: 1117561--1117619 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 22
1117551 TAATTATATA
1117561 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
*
1117582 TATATCAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
*
1117606 TATTATTGACTTAA
1 TA-TATTAACTTAA
1117620 TTTTAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 11 0.35
23 7 0.23
24 5 0.16
25 8 0.26
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:1119846 original size:3 final size:3
Alignment explanation
Indices: 1119835--1119864 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
1119825 AATTATTAAA
1119835 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AA
1119865 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1120250 original size:14 final size:14
Alignment explanation
Indices: 1120227--1120280 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1120217 GTAAGTTGGT
1120227 GTTTAAGGTTTAGG
1 GTTTAAGGTTTAGG
*
1120241 GTTTATGGTTTAGAG
1 GTTTAAGGTTTAG-G
* * *
1120256 GTATGAGG-TTATG
1 GTTTAAGGTTTAGG
1120269 GTTTAAGGTTTA
1 GTTTAAGGTTTA
1120281 TAATCTAGGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
13 7 0.23
14 18 0.58
15 6 0.19
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.44
Consensus pattern (14 bp):
GTTTAAGGTTTAGG
Found at i:1124824 original size:60 final size:59
Alignment explanation
Indices: 1124684--1124825 Score: 146
Period size: 60 Copynumber: 2.4 Consensus size: 59
1124674 TATGATAAAA
* * *
1124684 TATACAAATGGTCCCCAACTATATGGTGTTGTTTTGATGAGTCCCCTACATATTAAAAGT
1 TATA-AAATGGTCCTCGACTATATGGTGTTGTTTTGATGAGTCCCATACATATTAAAAGT
* * * *
1124744 TATAAGATGATTCC-CTGACTATA-GAGTGTTGTTTTGTTGAGTCTCATGAC-TATTAAAAGT
1 TATAAAATG-GTCCTC-GACTATATG-GTGTTGTTTTGATGAGTCCCAT-ACATATTAAAAGT
1124804 TATAAAATGGTCACTCGACTAT
1 TATAAAATGGTC-CTCGACTAT
1124826 TCATATGTTC
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
59 8 0.12
60 57 0.84
61 3 0.04
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (59 bp):
TATAAAATGGTCCTCGACTATATGGTGTTGTTTTGATGAGTCCCATACATATTAAAAGT
Found at i:1130012 original size:6 final size:6
Alignment explanation
Indices: 1130001--1130055 Score: 69
Period size: 6 Copynumber: 9.5 Consensus size: 6
1129991 GTTGTCTAGA
* *
1130001 GTGCGC GTGCGC GTGCGC GTGCGC GTGCGC GT--GT GTGTGC GTGCGC
1 GTGCGC GTGCGC GTGCGC GTGCGC GTGCGC GTGCGC GTGCGC GTGCGC
*
1130047 GCGCGC GTG
1 GTGCGC GTG
1130056 TGTGTGTCTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
4 3 0.07
6 39 0.93
ACGTcount: A:0.00, C:0.29, G:0.51, T:0.20
Consensus pattern (6 bp):
GTGCGC
Found at i:1130045 original size:22 final size:22
Alignment explanation
Indices: 1130017--1130061 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1130007 GTGCGCGTGC
*
1130017 GCGTGCGCGTGCGCGTGTGTGT
1 GCGTGCGCGCGCGCGTGTGTGT
1130039 GCGTGCGCGCGCGCGTGTGTGT
1 GCGTGCGCGCGCGCGTGTGTGT
1130061 G
1 G
1130062 TCTCTGTGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.51, T:0.24
Consensus pattern (22 bp):
GCGTGCGCGCGCGCGTGTGTGT
Found at i:1132014 original size:22 final size:22
Alignment explanation
Indices: 1131960--1132014 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1131950 GCTCACGAAC
*
1131960 GTGTTCATTTAATGTTCGTTTA
1 GTGTTCATTTAATATTCGTTTA
* * ** *
1131982 ATATTTGTTTAGTATTCGTTTA
1 GTGTTCATTTAATATTCGTTTA
1132004 GTGTTCATTTA
1 GTGTTCATTTA
1132015 TCGTTTGTTT
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.56
Consensus pattern (22 bp):
GTGTTCATTTAATATTCGTTTA
Found at i:1133485 original size:16 final size:16
Alignment explanation
Indices: 1133459--1133500 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1133449 CGAAATAAAA
1133459 AATAT-AATAATTCAT
1 AATATAAATAATTCAT
1133474 AATATAAATAATTCAT
1 AATATAAATAATTCAT
* *
1133490 TATATATATAA
1 AATATAAATAA
1133501 CTAACCGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATAAATAATTCAT
Found at i:1134037 original size:31 final size:29
Alignment explanation
Indices: 1134002--1134100 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 29
1133992 ATTTTTTGTC
1134002 AAATTTAATGGTAAAATTGATATTTTATCTA
1 AAATTTAA-GGTAAAA-TGATATTTTATCTA
* *
1134033 AAATTTAGGGGTTAAAATGATAATTTATCTA
1 AAATTTA-AGG-TAAAATGATATTTTATCTA
* * *
1134064 AAATTTAAGGTCTAACTAATATTTTATCTA
1 AAATTTAAGGT-AAAATGATATTTTATCTA
*
1134094 AAGTTTA
1 AAATTTA
1134101 GGGATAATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
29 1 0.02
30 22 0.39
31 29 0.51
32 5 0.09
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.42
Consensus pattern (29 bp):
AAATTTAAGGTAAAATGATATTTTATCTA
Found at i:1134092 original size:30 final size:31
Alignment explanation
Indices: 1134021--1134101 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
1134011 GGTAAAATTG
* *
1134021 ATATTTTATCTAAAATTTAGGGGTTAAAATG
1 ATATTTTATCTAAAATTTAGAGGTTAAAATA
* *
1134052 ATAATTTATCTAAAATTTA-AGGTCT-AACTA
1 ATATTTTATCTAAAATTTAGAGGT-TAAAATA
*
1134082 ATATTTTATCTAAAGTTTAG
1 ATATTTTATCTAAAATTTAG
1134102 GGATAATATT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
30 23 0.55
31 19 0.45
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (31 bp):
ATATTTTATCTAAAATTTAGAGGTTAAAATA
Found at i:1134813 original size:48 final size:49
Alignment explanation
Indices: 1134736--1134828 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 49
1134726 TGGCCACTAC
* *
1134736 ACTAAAGTTGTTTTTCAATTAAGACATTAATGTTGGCAAAATTGACCAA
1 ACTAAAGTTGTTTTTCAACTAAGACATTAATGTTAGCAAAATTGACCAA
* *
1134785 ACTAAAGTTG-TTTTCAACTAATACATTAATTTTAGCAAAATTGA
1 ACTAAAGTTGTTTTTCAACTAAGACATTAATGTTAGCAAAATTGA
1134829 TCAACCGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 30 0.75
49 10 0.25
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (49 bp):
ACTAAAGTTGTTTTTCAACTAAGACATTAATGTTAGCAAAATTGACCAA
Found at i:1142035 original size:29 final size:30
Alignment explanation
Indices: 1141996--1142063 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
1141986 CTATTTTTAT
*
1141996 CTTAGTACCTAGACTTTAGA-TTTTTAAAC
1 CTTAGTCCCTAGACTTTAGATTTTTTAAAC
* *
1142025 CTTAGTCCCTAGACTTTATATTTTTTACAC
1 CTTAGTCCCTAGACTTTAGATTTTTTAAAC
1142055 CTTAGTCCC
1 CTTAGTCCC
1142064 AATAGTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.25, C:0.24, G:0.09, T:0.43
Consensus pattern (30 bp):
CTTAGTCCCTAGACTTTAGATTTTTTAAAC
Found at i:1147872 original size:83 final size:83
Alignment explanation
Indices: 1147726--1148261 Score: 653
Period size: 83 Copynumber: 6.5 Consensus size: 83
1147716 ATGTAAATTA
* * * * *
1147726 TATGAAATGACAGAGATTCTCTAAATAATAATGGAAAATGTTTCCTCTGGAATGCGCATTTCATT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCGCCTTTCATT
1147791 TCGGATGGGATGGAACAC
66 TCGGATGGGATGGAACAC
* * *
1147809 TATGACATGACAGAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCACCGTTCATT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCGCCTTTCATT
* * * *
1147874 TTGGATAGAATTGAACAC
66 TCGGATGGGATGGAACAC
* ** * ** * * **
1147892 TATGATATGGTAGAGATTCTCTGAATAATAATAAAAAATGTTTCCCTTGGAATGTGTTTTTCATT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCGCCTTTCATT
* *
1147957 TCAGATGGGATTGAACAC
66 TCGGATGGGATGGAACAC
* * * * * *
1147975 TATGACATGACATATATTCTCTGAATAATAATGGAAAACGCTTCCCCTAGAATGCACCTTTCATT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCGCCTTTCATT
*
1148040 TCGGATTGGATGGAACAC
66 TCGGATGGGATGGAACAC
* * *
1148058 AATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGCTTT-CCCTGGAAAGCGTCTTTCAT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATG-TTTCCCCTGGAATGCGCCTTTCAT
*
1148122 TTCGGATGGGATGAAACAC
65 TTCGGATGGGATGGAACAC
* *
1148141 TATGACATGACAAAGATTCTCTGAATAATAATAGAAAATGCTTT-CCCTGGAATGCTCCTTTCAT
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATG-TTTCCCCTGGAATGCGCCTTTCAT
* *
1148205 TTCGGATGGGATGTAACTC
65 TTCGGATGGGATGGAACAC
* * * *
1148224 TATAACATGACAAAAATTCTCTAAATAATACTGGAAAA
1 TATGACATGACAAAGATTCTCTGAATAATAATGGAAAA
1148262 CACTATGACA
Statistics
Matches: 386, Mismatches: 66, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
83 384 0.99
84 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (83 bp):
TATGACATGACAAAGATTCTCTGAATAATAATGGAAAATGTTTCCCCTGGAATGCGCCTTTCATT
TCGGATGGGATGGAACAC
Found at i:1149286 original size:32 final size:32
Alignment explanation
Indices: 1149241--1149315 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
1149231 TCTTTCACAG
* *
1149241 ACCTTAAATAGTAAATAAAAGCATACACATAC
1 ACCTAAAACAGTAAATAAAAGCATACACATAC
1149273 ACCTAAAACAGTAAATAAAAGCATACACATAC
1 ACCTAAAACAGTAAATAAAAGCATACACATAC
1149305 ACCTAAAACAG
1 ACCTAAAACAG
1149316 ACTTTTCTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.55, C:0.21, G:0.07, T:0.17
Consensus pattern (32 bp):
ACCTAAAACAGTAAATAAAAGCATACACATAC
Found at i:1150164 original size:30 final size:30
Alignment explanation
Indices: 1150130--1150188 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
1150120 CTCGGCGTCA
* * *
1150130 TCCTCATCATCGTTCTCATCGTTATCATCG
1 TCCTCATCATCGTCCTCACCGTCATCATCG
* *
1150160 TCCTCCTTATCGTCCTCACCGTCATCATC
1 TCCTCATCATCGTCCTCACCGTCATCATC
1150189 ACTCTCAGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.15, C:0.39, G:0.08, T:0.37
Consensus pattern (30 bp):
TCCTCATCATCGTCCTCACCGTCATCATCG
Found at i:1151333 original size:2 final size:2
Alignment explanation
Indices: 1151326--1151355 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1151316 CACATATTTA
1151326 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
1151356 CATTCTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1152199 original size:19 final size:19
Alignment explanation
Indices: 1152161--1152238 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
1152151 CTATTTCAAA
*
1152161 AATATTTTAAATAA-ATTAT
1 AATAATTTAAATAATA-TAT
1152180 AATAATTTAAATAATATAT
1 AATAATTTAAATAATATAT
* * *
1152199 AATTGATTT-CATAATATTT
1 AA-TAATTTAAATAATATAT
* *
1152218 AAAAATTTTAAAAAATATAT
1 AATAA-TTTAAATAATATAT
1152238 A
1 A
1152239 GTTTTGTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
18 1 0.02
19 31 0.67
20 14 0.30
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (19 bp):
AATAATTTAAATAATATAT
Found at i:1152385 original size:18 final size:18
Alignment explanation
Indices: 1152362--1152396 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1152352 AGTTTACAAT
*
1152362 TAAATAATCAAATAAAAA
1 TAAATAATAAAATAAAAA
*
1152380 TAAATACTAAAATAAAA
1 TAAATAATAAAATAAAA
1152397 TAGTTAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAATAAAATAAAAA
Found at i:1154776 original size:2 final size:2
Alignment explanation
Indices: 1154769--1154802 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1154759 CACATATTTA
1154769 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
1154803 CATTCTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1155646 original size:19 final size:19
Alignment explanation
Indices: 1155608--1155675 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 19
1155598 CTATTTCAAA
*
1155608 AATATTTTAAATAA-ATTAT
1 AATAATTTAAATAATA-TAT
1155627 AATAATTTAAATAATATAT
1 AATAATTTAAATAATATAT
* * *
1155646 AATTGATTT-CATAATATTT
1 AA-TAATTTAAATAATATAT
*
1155665 AAAAATTTAAA
1 AATAATTTAAA
1155676 AAAATATAGT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 4 0.10
19 29 0.74
20 6 0.15
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (19 bp):
AATAATTTAAATAATATAT
Found at i:1155829 original size:18 final size:18
Alignment explanation
Indices: 1155806--1155840 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1155796 AGTTTACAAT
*
1155806 TAAATAATCAAATAAAAA
1 TAAATAATAAAATAAAAA
*
1155824 TAAATACTAAAATAAAA
1 TAAATAATAAAATAAAA
1155841 TAGTTAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAATAATAAAATAAAAA
Found at i:1157715 original size:33 final size:30
Alignment explanation
Indices: 1157673--1157739 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 30
1157663 TTTTTGACCC
1157673 AAATCAGTACATAAATTTGAGTTTTATTGGTTT
1 AAATCAGTAC-TAAATTTGA--TTTATTGGTTT
** *
1157706 AAATCAGTACTTGATTTGATTTCTTGGTTT
1 AAATCAGTACTAAATTTGATTTATTGGTTT
1157736 AAAT
1 AAAT
1157740 TAGTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 14 0.45
32 7 0.23
33 10 0.32
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (30 bp):
AAATCAGTACTAAATTTGATTTATTGGTTT
Found at i:1163789 original size:20 final size:18
Alignment explanation
Indices: 1163750--1163785 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1163740 TGAATGATCA
1163750 AAATAAAAATAAAATAAT
1 AAATAAAAATAAAATAAT
*
1163768 AAATAGAAAATTAAATAA
1 AAATA-AAAATAAAATAA
1163786 ATAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAATAAAAATAAAATAAT
Found at i:1164979 original size:24 final size:24
Alignment explanation
Indices: 1164948--1164999 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
1164938 AAGAAGTTGT
*
1164948 ATTAAAAATTTTAG-AGGAGCGAA
1 ATTAAAAACTTTAGCAGGAGCGAA
* *
1164971 ATTATAAAACTTTAGCAGGTGTGAA
1 ATTA-AAAACTTTAGCAGGAGCGAA
1164996 ATTA
1 ATTA
1165000 GAGTCTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.17
24 9 0.38
25 11 0.46
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (24 bp):
ATTAAAAACTTTAGCAGGAGCGAA
Found at i:1170817 original size:27 final size:26
Alignment explanation
Indices: 1170779--1170863 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 26
1170769 TTCAATTCAT
1170779 AATATTTTATATATATTAACTTAAAA
1 AATATTTTATATATATTAACTTAAAA
1170805 AATA-TTT-T-TATATTAACTTAATAA
1 AATATTTTATATATATTAACTTAA-AA
* *
1170829 ATATATTTTATTATTAAATTAA-TTTAAA
1 A-ATATTTTA-TA-TATATTAACTTAAAA
1170857 AATATTT
1 AATATTT
1170864 ATTTTTATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
23 13 0.26
24 4 0.08
25 6 0.12
26 7 0.14
27 6 0.12
28 4 0.08
29 3 0.06
30 7 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AATATTTTATATATATTAACTTAAAA
Found at i:1170834 original size:25 final size:23
Alignment explanation
Indices: 1170790--1170851 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 23
1170780 ATATTTTATA
1170790 TATATTAACTTAA-AAAATATTTT
1 TATATTAACTTAATAAAATA-TTT
1170813 TATATTAACTTAATAAATATATTT
1 TATATTAACTTAATAAA-ATATTT
*
1170837 TATTATTAAATTAAT
1 TA-TATTAACTTAAT
1170852 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 13 0.37
24 8 0.23
25 14 0.40
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTAACTTAATAAAATATTT
Found at i:1171089 original size:31 final size:32
Alignment explanation
Indices: 1171031--1171094 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
1171021 TAATCACATC
*
1171031 TTAATTAAATATAAAAGAATGTAACTAT-GTT
1 TTAATTAAATATAAAAGAAGGTAACTATAGTT
* *
1171062 TTAATTAAATA-ATAACGAAGGTGACTATAGTT
1 TTAATTAAATATA-AAAGAAGGTAACTATAGTT
1171094 T
1 T
1171095 ATATTTATTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 1 0.04
31 23 0.82
32 4 0.14
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (32 bp):
TTAATTAAATATAAAAGAAGGTAACTATAGTT
Found at i:1177143 original size:2 final size:2
Alignment explanation
Indices: 1177136--1177204 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1177126 GGGACCAAAT
1177136 TA TA TA TA TA TA TA 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
1177178 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1177205 GCATGTTTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1177403 original size:31 final size:31
Alignment explanation
Indices: 1177368--1177427 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1177358 AGGTCGCCAT
*
1177368 GCACGCCCAACGACCTATCA-GCACGCCCAGA
1 GCACGCCCAACGACCT-CCATGCACGCCCAGA
1177399 GCACGCCCAACGACCTCCATGCACGCCCA
1 GCACGCCCAACGACCTCCATGCACGCCCA
1177428 ACGACCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 2 0.07
31 25 0.93
ACGTcount: A:0.27, C:0.48, G:0.18, T:0.07
Consensus pattern (31 bp):
GCACGCCCAACGACCTCCATGCACGCCCAGA
Found at i:1177424 original size:20 final size:20
Alignment explanation
Indices: 1177399--1177447 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
1177389 CACGCCCAGA
1177399 GCACGCCCAACGACCTCCAT
1 GCACGCCCAACGACCTCCAT
1177419 GCACGCCCAACGACCTCCAT
1 GCACGCCCAACGACCTCCAT
1177439 GCACGCCCA
1 GCACGCCCA
1177448 GCTCGCCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.51, G:0.16, T:0.08
Consensus pattern (20 bp):
GCACGCCCAACGACCTCCAT
Found at i:1178115 original size:21 final size:21
Alignment explanation
Indices: 1178090--1178133 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1178080 AATTTAGTTA
1178090 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
1178111 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
1178132 AT
1 AT
1178134 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:1178147 original size:28 final size:28
Alignment explanation
Indices: 1178110--1178163 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1178100 TAGTATAAAT
*
1178110 TATTAGTTTGTTAGTTTAAGTTATATTA
1 TATTAATTTGTTAGTTTAAGTTATATTA
1178138 TATTAATTTGTTAGTTTAAGTTATAT
1 TATTAATTTGTTAGTTTAAGTTATAT
1178164 ATTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (28 bp):
TATTAATTTGTTAGTTTAAGTTATATTA
Found at i:1178376 original size:48 final size:49
Alignment explanation
Indices: 1178317--1178410 Score: 122
Period size: 51 Copynumber: 1.9 Consensus size: 49
1178307 AGTGCTTAAT
*
1178317 TAGTTTGTTAGTTT-GTTAT-TT-TAACTAAATTATATTATAATAAAGAAA
1 TAGTTTATTAGTTTAGTTATATTATAA-TAAATTATATTAT-ATAAAGAAA
*
1178365 TAGTTTATTAGTTTAAGTTATATTATAATATATTATATTATATAAA
1 TAGTTTATTAGTTT-AGTTATATTATAATAAATTATATTATATAAA
1178411 TTTAATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
48 13 0.32
50 10 0.25
51 14 0.35
52 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (49 bp):
TAGTTTATTAGTTTAGTTATATTATAATAAATTATATTATATAAAGAAA
Found at i:1181308 original size:60 final size:59
Alignment explanation
Indices: 1181236--1182181 Score: 1373
Period size: 60 Copynumber: 16.2 Consensus size: 59
1181226 TTTATAAGAT
* * * *
1181236 TTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATTATTTAATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAA--TGA
** *
1181297 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTAGGT-ATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATATTAATGA
*
1181355 TTTAGTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1181406 -TAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1181464 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1181524 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
* * *
1181584 TTTAGTAATGATCAGTAATATTGAAATTATTATTAAT-TTT--T-A-ATG--ATT--TGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1181635 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1181693 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1181753 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1181813 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
* *
1181873 TTTAATAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
* *
1181933 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
* *
1181993 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
* *
1182053 TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
*
1182111 TTAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1182169 TTTAGTAATGATT
1 -TTAGTAATGATT
1182182 TGATAGTAAT
Statistics
Matches: 835, Mismatches: 24, Indels: 54
0.91 0.03 0.06
Matches are distributed among these distances:
49 68 0.08
50 6 0.01
51 6 0.01
52 2 0.00
53 7 0.01
54 4 0.00
55 4 0.00
56 8 0.01
57 2 0.00
58 102 0.12
59 37 0.04
60 586 0.70
61 3 0.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
Found at i:1181458 original size:21 final size:20
Alignment explanation
Indices: 1181434--1181936 Score: 74
Period size: 21 Copynumber: 24.6 Consensus size: 20
1181424 ATGAAATTAT
1181434 TATTAATATTTAATGATTTGA
1 TATTAATATTTAAT-ATTTGA
* *
1181455 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181475 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1181493 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1181515 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181535 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
1181553 TTATTAATATTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1181575 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* *
1181595 TCAGTAATATTGAA-A-TT-A
1 T-ATTAATATTTAATATTTGA
*
1181613 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
*
1181635 TAGTAATGATTAGTAATAATGAAATT-A
1 TATTAAT-ATT--TAAT-AT----TTGA
*
1181662 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1181684 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181704 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1181722 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1181744 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181764 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1181782 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
* *
1181804 TATTAATGATTTAGTA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181824 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1181842 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
*
1181864 TATTAATGATTTAATA-ATGA
1 TATTAAT-ATTTAATATTTGA
* * *
1181884 TTAGTAATAATGAA-A-TT-A
1 -TATTAATATTTAATATTTGA
*
1181902 TTATTAATTTTTAATGATTTGA
1 -TATTAATATTTAAT-ATTTGA
1181924 TATTAATGATTTA
1 TATTAAT-ATTTA
1181937 GTAATGATTA
Statistics
Matches: 345, Mismatches: 84, Indels: 105
0.65 0.16 0.20
Matches are distributed among these distances:
18 77 0.22
19 15 0.04
20 52 0.15
21 126 0.37
22 52 0.15
24 6 0.02
25 6 0.02
27 3 0.01
28 8 0.02
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.48
Consensus pattern (20 bp):
TATTAATATTTAATATTTGA
Found at i:1181630 original size:229 final size:229
Alignment explanation
Indices: 1181233--1182181 Score: 1485
Period size: 229 Copynumber: 4.1 Consensus size: 229
1181223 GTATTTATAA
* * * *
1181233 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATTATTTAATAGTAAT--TTG
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATT-
**
1181296 ATAGTAATGATTAGTAATAATGAAATTATTATTAATTAGGT-ATGATTTGATAGTAATGATTTAG
65 -TAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTGATAGTAATGATTTAG
1181360 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
128 TAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAA
1181425 TGAAATTATTATTAATATTTAATGATTTGATATTAAT
193 TGAAATTATTATTAATATTTAATGATTTGATATTAAT
*
1181462 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
*
1181527 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGATTTAGTAA
66 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAA
* *
1181592 TGATCAGTAATATTGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGA
131 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGA
*
1181657 AATTATTATTAATTTTTAATGATTTGATATTAAT
196 AATTATTATTAATATTTAATGATTTGATATTAAT
*
1181691 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
* *
1181756 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGATTTAGTAA
66 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAA
1181821 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAATGATTTAATAATGATT
131 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG--A-T-A-G------TAATGATT
*
1181886 AGTAATAATGAAATTATTATTAATTTTTAATGATTTGATATTAAT
185 AGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1181931 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
*
1181996 AGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAA
66 AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAA
* *
1182060 TGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTTGATAGTAATGATTAGTAATGATTA
131 TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAG---T-A--A
*
1182124 GTAATAATAATTTATTATTAATATTTAATGATTTGATATTAAT
190 -TAATGA-AA-TTATTATTAATATTTAATGATTTGATATTAAT
1182167 GATTTAGTAATGATT
1 GATTTAGTAATGATT
1182182 TGATAGTAAT
Statistics
Matches: 677, Mismatches: 20, Indels: 39
0.92 0.03 0.05
Matches are distributed among these distances:
227 10 0.01
228 3 0.00
229 379 0.56
230 1 0.00
231 4 0.01
232 1 0.00
233 3 0.00
234 7 0.01
235 3 0.00
236 47 0.07
238 25 0.04
239 21 0.03
240 173 0.26
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.47
Consensus pattern (229 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
AGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTAA
TGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGA
AATTATTATTAATATTTAATGATTTGATATTAAT
Found at i:1181701 original size:25 final size:25
Alignment explanation
Indices: 1181624--1181705 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 25
1181614 TATTAATTTT
*
1181624 TAATGATTTGATAGTAATGA-TTAG
1 TAATGATTTGATATTAATGATTTAG
* *** * * *
1181648 TAATAATGAAATTATTATTAATTT-T
1 TAATGATTTGA-TATTAATGATTTAG
1181673 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATATTAATGATTTAG
1181698 TAATGATT
1 TAATGATT
1181706 AGTAATAATG
Statistics
Matches: 40, Mismatches: 15, Indels: 5
0.67 0.25 0.08
Matches are distributed among these distances:
24 17 0.43
25 21 0.52
26 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (25 bp):
TAATGATTTGATATTAATGATTTAG
Found at i:1182057 original size:10 final size:10
Alignment explanation
Indices: 1182044--1182128 Score: 58
Period size: 10 Copynumber: 8.7 Consensus size: 10
1182034 AATGATTTGA
1182044 TAGTAATGAT
1 TAGTAATGAT
1182054 TAGTAATGAT
1 TAGTAATGAT
1182064 TAGTAAT-A-
1 TAGTAATGAT
*
1182072 -A-TAATTTAT
1 TAGTAA-TGAT
*
1182081 TATTAAT-AT
1 TAGTAATGAT
1182090 T--TAATGATTT
1 TAGTAATGA--T
1182100 GATAGTAATGAT
1 --TAGTAATGAT
1182112 TAGTAATGAT
1 TAGTAATGAT
1182122 TAGTAAT
1 TAGTAAT
1182129 AATAATTTAT
Statistics
Matches: 63, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
6 3 0.05
7 6 0.10
8 2 0.03
9 4 0.06
10 37 0.59
11 3 0.05
12 2 0.03
14 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:1182165 original size:14 final size:14
Alignment explanation
Indices: 1182149--1182196 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
1182139 TATTAATATT
*
1182149 TAATGATTTGATAT
1 TAATGATTTGATAG
1182163 TAATGA-TT--TAG
1 TAATGATTTGATAG
1182174 TAATGATTTGATAG
1 TAATGATTTGATAG
1182188 TAATGATTT
1 TAATGATTT
1182197 ACGACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 8 0.27
12 2 0.07
13 2 0.07
14 18 0.60
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:1182178 original size:25 final size:25
Alignment explanation
Indices: 1182149--1182197 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1182139 TATTAATATT
*
1182149 TAATGATTTGATATTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
1182174 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
1182198 CGACTTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:1184541 original size:30 final size:30
Alignment explanation
Indices: 1184507--1184610 Score: 115
Period size: 30 Copynumber: 3.4 Consensus size: 30
1184497 TCCCTTAAAC
*
1184507 AACTAATAAACTATTCTTTAATATAACGTT-
1 AACTAATAAACTATTCTTTAATATAA-ATTA
1184537 AACTAATAAACTATTCTTTAATATAAATTA
1 AACTAATAAACTATTCTTTAATATAAATTA
*
1184567 AACTAATAAA-TGATT-TTTAATTATAATTTA
1 AACTAATAAACT-ATTCTTTAA-TATAAATTA
* *
1184597 CTACTAAAAAACTA
1 -AACTAATAAACTA
1184611 ATTAACTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
29 8 0.12
30 47 0.72
31 9 0.14
32 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (30 bp):
AACTAATAAACTATTCTTTAATATAAATTA
Found at i:1184835 original size:21 final size:21
Alignment explanation
Indices: 1184788--1184827 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1184778 TTTATATATG
*
1184788 ATATAACTTAAACTAACAATA
1 ATATTACTTAAACTAACAATA
1184809 ATATTACTTAAACTAACAA
1 ATATTACTTAAACTAACAA
1184828 ACTAATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (21 bp):
ATATTACTTAAACTAACAATA
Found at i:1184908 original size:18 final size:18
Alignment explanation
Indices: 1184855--1184909 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1184845 TTGTTTTACC
*
1184855 CTAATTTATAATAATAAA
1 CTAATTTATAACAATAAA
1184873 CTAA--T-TAAC--T-AA
1 CTAATTTATAACAATAAA
1184885 -TAATTTATAACAATAAA
1 CTAATTTATAACAATAAA
1184902 CTAATTTA
1 CTAATTTA
1184910 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 3 0.10
12 2 0.07
13 2 0.07
14 4 0.14
15 3 0.10
16 2 0.07
17 2 0.07
18 11 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAATTTATAACAATAAA
Found at i:1184968 original size:35 final size:37
Alignment explanation
Indices: 1184929--1185000 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 37
1184919 TCTTTTATAT
1184929 AACTT-AA-ACTAATAAACT-ATTTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTTTTA-TATAATAA
1184964 AACTTAAACTACTAATAAACTAATTTTTTATATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATATAATA
1185001 TAAATTCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.15
36 2 0.06
38 18 0.55
39 8 0.24
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTAAACACTAATAAACTAATTTTTTATATAATAA
Found at i:1185082 original size:28 final size:27
Alignment explanation
Indices: 1185036--1185088 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
1185026 TAACTATTTA
1185036 ACTAACTACAAACTAATTAAATATTAG
1 ACTAACTACAAACTAATTAAATATTAG
*
1185063 ACTAACTAACAAACTAATTAATTATT
1 ACTAACT-ACAAACTAATTAAATATT
1185089 TTTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.32
Consensus pattern (27 bp):
ACTAACTACAAACTAATTAAATATTAG
Found at i:1185204 original size:9 final size:9
Alignment explanation
Indices: 1185172--1185209 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1185162 CTAACAAACT
1185172 AATAATTTAA
1 AATAA-TTAA
1185182 AATAA-TAA
1 AATAATTAA
*
1185190 ACTAATTAA
1 AATAATTAA
1185199 AATAATTAA
1 AATAATTAA
1185208 AA
1 AA
1185210 AAAACTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:1185409 original size:12 final size:11
Alignment explanation
Indices: 1185379--1185413 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1185369 CGTTCATGGA
1185379 CTGCAATAATG
1 CTGCAATAATG
*
1185390 CAGCAATAAGTG
1 CTGCAATAA-TG
1185402 CTGCAATAATG
1 CTGCAATAATG
1185413 C
1 C
1185414 AGTTGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (11 bp):
CTGCAATAATG
Found at i:1185557 original size:29 final size:28
Alignment explanation
Indices: 1185510--1185593 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
1185500 AAAGGCATAG
*
1185510 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGCTGGGATCCC-TGGCGACCTACAAT
1185539 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGCTGGGAT-CCCTGGCGACCTACAAT
1185568 GTCGCTGGGATTCCCTGGCGACCTAC
1 GTCGCTGGGA-TCCCTGGCGACCTAC
1185594 CCACGTTGCA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
29 48 0.92
30 4 0.08
ACGTcount: A:0.15, C:0.31, G:0.30, T:0.24
Consensus pattern (28 bp):
GTCGCTGGGATCCCTGGCGACCTACAAT
Found at i:1185680 original size:21 final size:21
Alignment explanation
Indices: 1185618--1185680 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
1185608 TGCACGGCCA
1185618 TGCAGAGACTCCAACCTCG-CC
1 TGCAGAGACTCC-ACCTCGCCC
* * *
1185639 --CAGACACATGCCACGTTGCCC
1 TGCAGAGAC-T-CCACCTCGCCC
1185660 TGCAGAGACTCCACCTCGCCC
1 TGCAGAGACTCCACCTCGCCC
1185681 AGGGCCATGT
Statistics
Matches: 31, Mismatches: 6, Indels: 10
0.66 0.13 0.21
Matches are distributed among these distances:
19 6 0.19
20 5 0.16
21 13 0.42
22 1 0.03
23 6 0.19
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.14
Consensus pattern (21 bp):
TGCAGAGACTCCACCTCGCCC
Found at i:1185768 original size:33 final size:33
Alignment explanation
Indices: 1185726--1185791 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1185716 AAGCATGGAC
1185726 TGCATGGTGACCTTTGGCGAGCTGGGAGTGCAT
1 TGCATGGTGACCTTTGGCGAGCTGGGAGTGCAT
*
1185759 TGCATGGTGACCTTTGGCGAGCTGGGCGTGCAT
1 TGCATGGTGACCTTTGGCGAGCTGGGAGTGCAT
1185792 GGAGGTCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.14, C:0.20, G:0.39, T:0.27
Consensus pattern (33 bp):
TGCATGGTGACCTTTGGCGAGCTGGGAGTGCAT
Found at i:1185818 original size:31 final size:31
Alignment explanation
Indices: 1185780--1185840 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1185770 CTTTGGCGAG
*
1185780 CTGGGCGTGCATGG-AGGTCGTTGGGCGTGCT
1 CTGGGCGTGC-TGGTAGGTCGCTGGGCGTGCT
1185811 CTGGGCGTGCTGGTAGGTCGCTGGGCGTGC
1 CTGGGCGTGCTGGTAGGTCGCTGGGCGTGC
1185841 ATGGCGACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.05, C:0.21, G:0.49, T:0.25
Consensus pattern (31 bp):
CTGGGCGTGCTGGTAGGTCGCTGGGCGTGCT
Found at i:1185858 original size:29 final size:29
Alignment explanation
Indices: 1185825--1185882 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1185815 GCGTGCTGGT
1185825 AGGTCGCTGGGCGTGCATGGCGACCTACC
1 AGGTCGCTGGGCGTGCATGGCGACCTACC
1185854 AGGTCGCTGGGCGTGCATGGCGACCTACC
1 AGGTCGCTGGGCGTGCATGGCGACCTACC
1185883 CCCAGGACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.31, G:0.38, T:0.17
Consensus pattern (29 bp):
AGGTCGCTGGGCGTGCATGGCGACCTACC
Found at i:1195579 original size:35 final size:36
Alignment explanation
Indices: 1195516--1195584 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
1195506 TTATAAGATT
* *
1195516 TATATTTTTGTTTAAATTTTTGTATATGTTATCTTA
1 TATATTCTCGTTTAAATTTTTGTATATGTTATCTTA
1195552 TATATTCTCGTTTAAA-TTTTGTATATGTTATCT
1 TATATTCTCGTTTAAATTTTTGTATATGTTATCT
1195585 CACTGAATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 17 0.55
36 14 0.45
ACGTcount: A:0.25, C:0.06, G:0.09, T:0.61
Consensus pattern (36 bp):
TATATTCTCGTTTAAATTTTTGTATATGTTATCTTA
Found at i:1195707 original size:38 final size:38
Alignment explanation
Indices: 1195665--1195779 Score: 212
Period size: 38 Copynumber: 3.0 Consensus size: 38
1195655 GCTATTAGAC
1195665 TTTTAACGGATTATTGACATGATACACTGAATATATAT
1 TTTTAACGGATTATTGACATGATACACTGAATATATAT
*
1195703 TTTTAACGGATTATTGACATGATACACTGAATGTATAT
1 TTTTAACGGATTATTGACATGATACACTGAATATATAT
*
1195741 TTTTAACGGATTATTGACATGAAACACTGAATATATAT
1 TTTTAACGGATTATTGACATGATACACTGAATATATAT
1195779 T
1 T
1195780 AAAAAGGGTA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 74 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (38 bp):
TTTTAACGGATTATTGACATGATACACTGAATATATAT
Found at i:1198944 original size:21 final size:21
Alignment explanation
Indices: 1198905--1198944 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1198895 TTATATTTTA
* *
1198905 ATGATGATACGATATTATCTT
1 ATGATGAAACGATAATATCTT
*
1198926 ATGATGAAACGTTAATATC
1 ATGATGAAACGATAATATC
1198945 ACTATTAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (21 bp):
ATGATGAAACGATAATATCTT
Found at i:1201781 original size:23 final size:23
Alignment explanation
Indices: 1201755--1201800 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1201745 AAAAAAAAAT
*
1201755 CACAAAGACATAAATAAATGTGC
1 CACAAAGACATAAATAAACGTGC
*
1201778 CACAAAGACATATATAAACGTGC
1 CACAAAGACATAAATAAACGTGC
1201801 AACACATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (23 bp):
CACAAAGACATAAATAAACGTGC
Found at i:1202029 original size:30 final size:30
Alignment explanation
Indices: 1201994--1202069 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
1201984 GCGGGGTAAA
*
1201994 TTTTTATATTTTTATTATAGTTTAAGTTAT
1 TTTTTATATTTATATTATAGTTTAAGTTAT
1202024 TTTTTATATTTATATTATAGTTTAAGTTGAT
1 TTTTTATATTTATATTATAGTTTAAGTT-AT
* * *
1202055 ATTATATATATATAT
1 TTTTTATATTTATAT
1202070 ATAATATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 27 0.66
31 14 0.34
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.62
Consensus pattern (30 bp):
TTTTTATATTTATATTATAGTTTAAGTTAT
Found at i:1202041 original size:18 final size:19
Alignment explanation
Indices: 1201996--1202041 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1201986 GGGGTAAATT
1201996 TTTATATT-TTTATTATAG
1 TTTATATTATTTATTATAG
*
1202014 TTTA-AGTTATTTTTTATA-
1 TTTATA-TTATTTATTATAG
1202032 TTTATATTAT
1 TTTATATTAT
1202042 AGTTTAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 9 0.38
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTATATTATTTATTATAG
Found at i:1203331 original size:7 final size:7
Alignment explanation
Indices: 1203319--1203343 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1203309 TTTCAATTGT
1203319 AATTTTA
1 AATTTTA
1203326 AATTTTA
1 AATTTTA
1203333 AATTTTA
1 AATTTTA
1203340 AATT
1 AATT
1203344 AATCAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:1206197 original size:190 final size:190
Alignment explanation
Indices: 1205655--1206570 Score: 1398
Period size: 188 Copynumber: 4.8 Consensus size: 190
1205645 CATTCGAGTC
* *
1205655 CGATGCATGTACGAACATGATTATGAGAAAATATATGTTGGACGGATATTGCATCCTACACTCAC
1 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
1205720 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
66 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
*
1205785 CTGCATTTTGTTTTGTGCCTGTTGTGATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
131 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* *
1205845 CGATGCATATACAAACATGATTATGAGAAAATATATGTTGGACGGATATTGCATCCTACAGTCAG
1 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACA--C--
* * *
1205910 TCACACATGAATTTGAGTAACATAGGTTTCGGACTCTCCTTTTACTGTTCCATGTTTCTGTACTG
62 TCACACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTG
*
1205975 GAACCTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTATGTT
127 GAACCTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
1206039 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
1 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
* *
1206104 ACATGAATCCGAGTAACATAGGTTTTGGACTCTCCTTTCACTGTTCTATGTTTCTGTACTGGAAC
66 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
* * *
1206169 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGCGGATGTTGTTTCGTTTAGTGTACGTT
131 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* * * * *
1206229 CGATGCATATATGAACATGATTACGAG--AACATATGTTGGACGGATATCACATCCTACACACAC
1 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
*
1206292 ACATGAATCCGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
66 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
* * * *
1206357 CTGCATTTTGTTTTGTGCCTGTTCTGATCCTAGTGGATGTTGTTTCGTTCGATGTATGTT
131 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* * * * *
1206417 CGACGCATATATGAACATGATTATGTG--AACATATGTTGGACGGATATCGCATCCGACACT--C
1 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
* * * **
1206478 ACATGAATCTGAGTAATGA-ATG-TTTGTTAAACTCCTTTTACTGTTCTATGTTTCTGTACTGGA
66 ACATGAATCTGAGTAA-CATAGGTTTTG-GACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGA
* *
1206541 ACCTGCATTCTGTTTTGTGCCTATTGTAAT
129 ACCTGCATTTTGTTTTGTGCCTGTTGTAAT
1206571 TTCTCATTCA
Statistics
Matches: 673, Mismatches: 47, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
185 4 0.01
186 77 0.11
187 1 0.00
188 204 0.30
190 203 0.30
192 2 0.00
194 182 0.27
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (190 bp):
CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
Found at i:1206352 original size:188 final size:189
Alignment explanation
Indices: 1205655--1206570 Score: 1367
Period size: 190 Copynumber: 4.8 Consensus size: 189
1205645 CATTCGAGTC
* * *
1205655 CGATGCATGTACGAACATGATTATGAGAAAATATATGTTGGACGGATATTGCATCCTACACTCAC
1 CGATGCATATACGAACATGATTATGAG-AAATATATGTTGGACGGATATCGCATCCTACACACAC
1205720 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
65 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
*
1205785 CTGCATTTTGTTTTGTGCCTGTTGTGATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
130 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* *
1205845 CGATGCATATACAAACATGATTATGAGAAAATATATGTTGGACGGATATTGCATCCTACAGTCAG
1 CGATGCATATACGAACATGATTATGAG-AAATATATGTTGGACGGATATCGCATCCTACA--CA-
* * *
1205910 TCACACATGAATTTGAGTAACATAGGTTTCGGACTCTCCTTTTACTGTTCCATGTTTCTGTACTG
62 -CACACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTG
*
1205975 GAACCTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTATGTT
126 GAACCTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
*
1206039 CGATGCATATACGAACATGATTATGAGAAAATATATGTTGGACGGATATCGCATCCTACACTCAC
1 CGATGCATATACGAACATGATTATGAG-AAATATATGTTGGACGGATATCGCATCCTACACACAC
* *
1206104 ACATGAATCCGAGTAACATAGGTTTTGGACTCTCCTTTCACTGTTCTATGTTTCTGTACTGGAAC
65 ACATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAAC
* * *
1206169 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGCGGATGTTGTTTCGTTTAGTGTACGTT
130 CTGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* * * *
1206229 CGATGCATATATGAACATGATTACGAG-AACATATGTTGGACGGATATCACATCCTACACACACA
1 CGATGCATATACGAACATGATTATGAGAAATATATGTTGGACGGATATCGCATCCTACACACACA
*
1206293 CATGAATCCGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAACC
66 CATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAACC
* * * *
1206358 TGCATTTTGTTTTGTGCCTGTTCTGATCCTAGTGGATGTTGTTTCGTTCGATGTATGTT
131 TGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
* * * * * *
1206417 CGACGCATATATGAACATGATTATGTG-AACATATGTTGGACGGATATCGCATCC--GACACTCA
1 CGATGCATATACGAACATGATTATGAGAAATATATGTTGGACGGATATCGCATCCTACACACACA
* * * **
1206479 CATGAATCTGAGTAATGA-ATG-TTTGTTAAACTCCTTTTACTGTTCTATGTTTCTGTACTGGAA
66 CATGAATCTGAGTAA-CATAGGTTTTG-GACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAA
* *
1206542 CCTGCATTCTGTTTTGTGCCTATTGTAAT
129 CCTGCATTTTGTTTTGTGCCTGTTGTAAT
1206571 TTCTCATTCA
Statistics
Matches: 671, Mismatches: 49, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
185 4 0.01
186 81 0.12
187 1 0.00
188 200 0.30
190 202 0.30
192 2 0.00
194 181 0.27
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (189 bp):
CGATGCATATACGAACATGATTATGAGAAATATATGTTGGACGGATATCGCATCCTACACACACA
CATGAATCTGAGTAACATAGGTTTTGGACTCTCCTTTTACTGTTCTATGTTTCTGTACTGGAACC
TGCATTTTGTTTTGTGCCTGTTGTAATCCTAGTGGATGTTGTTTCGTTCAATGTACGTT
Found at i:1207110 original size:10 final size:10
Alignment explanation
Indices: 1207079--1207134 Score: 57
Period size: 10 Copynumber: 6.0 Consensus size: 10
1207069 AAATTCTTAT
1207079 ATTAATATTA
1 ATTAATATTA
* *
1207089 AAT-ATATAA
1 ATTAATATTA
1207098 ATTAATATTA
1 ATTAATATTA
*
1207108 ATTATTATTA
1 ATTAATATTA
1207118 A-TAAT-TTA
1 ATTAATATTA
1207126 A-TAATATTA
1 ATTAATATTA
1207135 TATTTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
8 8 0.21
9 13 0.34
10 17 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTAATATTA
Found at i:1207136 original size:57 final size:54
Alignment explanation
Indices: 1207075--1207205 Score: 126
Period size: 52 Copynumber: 2.4 Consensus size: 54
1207065 TACTAAATTC
* * *
1207075 TTATATTAATATTAAATATATAAATTAATATTAATTATTATTAATAATTTAATAATA
1 TTATATTAATATTAAATATATAAA-TAATATTAACTA-CATTAATAAATT-ATAATA
* * * *
1207132 TTATATTTATA-AAAATA-ATAGATAATATTAACTACATTAATAAATTATTATA
1 TTATATTAATATTAAATATATAAATAATATTAACTACATTAATAAATTATAATA
*
1207184 -TATTATTAA-ATTAAACATATAA
1 TTA-TATTAATATTAAATATATAA
1207206 TATCATATGC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
51 3 0.05
52 14 0.23
53 13 0.22
54 11 0.18
55 4 0.07
56 5 0.08
57 10 0.17
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (54 bp):
TTATATTAATATTAAATATATAAATAATATTAACTACATTAATAAATTATAATA
Found at i:1207265 original size:24 final size:24
Alignment explanation
Indices: 1207238--1207308 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
1207228 TCTGAGTTCA
1207238 TATTAATATTTAAAAATATAATAT
1 TATTAATATTTAAAAATATAATAT
* * *
1207262 TATTAA-AATTATATATAT-ATA-
1 TATTAATATTTAAAAATATAATAT
*
1207283 TATTAAATATTTTAATAAT-TAATAT
1 TATT-AATA-TTTAAAAATATAATAT
1207308 T
1 T
1207309 TTTTTAGGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
21 4 0.11
22 5 0.14
23 11 0.31
24 14 0.40
25 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTAATATTTAAAAATATAATAT
Found at i:1207306 original size:15 final size:15
Alignment explanation
Indices: 1207239--1207310 Score: 53
Period size: 15 Copynumber: 4.7 Consensus size: 15
1207229 CTGAGTTCAT
*
1207239 ATTAATA-TTTAAAA
1 ATTAATATTTTAATA
1207253 ATATAATATTATTAA-A
1 AT-TAATATT-TTAATA
*
1207269 ATT-ATA-TATATATA
1 ATTAATATTTTA-ATA
1207283 TATTAAATATTTTAATA
1 -ATT-AATATTTTAATA
1207300 ATTAATATTTT
1 ATTAATATTTT
1207311 TTTAGGGTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 17
0.71 0.03 0.26
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 6 0.13
15 17 0.36
16 7 0.15
17 10 0.21
18 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTAATATTTTAATA
Found at i:1210895 original size:23 final size:23
Alignment explanation
Indices: 1210869--1210929 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1210859 CTCATATAAA
*
1210869 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1210892 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1210915 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1210930 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1211116 original size:103 final size:103
Alignment explanation
Indices: 1210945--1211265 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
1210935 TAATGTCCAT
1210945 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
1211010 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
1211048 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
1211113 GACTTCACACAAGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
1211151 AAGGACCACATATCATTTCTTAAGAATCATATACATATATTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
1211216 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
**
1211254 AAAAACCACATA
1 AAGGACCACATA
1211266 GACCCTCGAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1212202 original size:2 final size:2
Alignment explanation
Indices: 1212195--1212219 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1212185 ATATTTCATT
1212195 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1212220 CAAAGATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1214097 original size:30 final size:30
Alignment explanation
Indices: 1214063--1214120 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
1214053 TTTTCCTCTC
1214063 TAATGATATTTTAAAAGTTTCAATTTAAGT
1 TAATGATATTTTAAAAGTTTCAATTTAAGT
1214093 TAATGATATTTTAAAAGTTTCAATTTAA
1 TAATGATATTTTAAAAGTTTCAATTTAA
1214121 ATTCTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (30 bp):
TAATGATATTTTAAAAGTTTCAATTTAAGT
Found at i:1222456 original size:32 final size:32
Alignment explanation
Indices: 1222417--1222492 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
1222407 TCAAAACATA
*
1222417 ATATTATATTGACACGCTTTAAAAATTGATCG
1 ATATTATATTGACACGATTTAAAAATTGATCG
* **
1222449 ATCTTATATTGATTCGATTTAAAAATTGATCG
1 ATATTATATTGACACGATTTAAAAATTGATCG
*
1222481 ATATGATATTGA
1 ATATTATATTGA
1222493 TCCCGACCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (32 bp):
ATATTATATTGACACGATTTAAAAATTGATCG
Found at i:1222481 original size:16 final size:16
Alignment explanation
Indices: 1222434--1222482 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1222424 ATTGACACGC
1222434 TTTAAAAATTGATCGA
1 TTTAAAAATTGATCGA
*
1222450 TCTT--ATATTGATTCGA
1 T-TTAAAAATTGA-TCGA
1222466 TTTAAAAATTGATCGA
1 TTTAAAAATTGATCGA
1222482 T
1 T
1222483 ATGATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
15 8 0.30
16 11 0.41
17 8 0.30
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (16 bp):
TTTAAAAATTGATCGA
Found at i:1227173 original size:17 final size:17
Alignment explanation
Indices: 1227151--1227189 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1227141 TGAATCAAAT
1227151 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1227168 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1227185 -AATTA
1 TAATTA
1227190 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1230093 original size:23 final size:23
Alignment explanation
Indices: 1230067--1230115 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1230057 TTACGAGCAT
1230067 GTTCGTTTAACGTTAGCGAACAC
1 GTTCGTTTAACGTTAGCGAACAC
1230090 GTTCGTTTAACGTTAGCGAACAC
1 GTTCGTTTAACGTTAGCGAACAC
1230113 GTT
1 GTT
1230116 TGGTAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
GTTCGTTTAACGTTAGCGAACAC
Found at i:1233875 original size:3 final size:3
Alignment explanation
Indices: 1233867--1233974 Score: 216
Period size: 3 Copynumber: 36.0 Consensus size: 3
1233857 TTTATTAATG
1233867 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1233915 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1233963 GAA GAA GAA GAA
1 GAA GAA GAA GAA
1233975 AGGAGAGAAT
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1244537 original size:14 final size:14
Alignment explanation
Indices: 1244518--1244545 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1244508 TTAGTCGATC
1244518 ATTGTTATATTTTA
1 ATTGTTATATTTTA
1244532 ATTGTTATATTTTA
1 ATTGTTATATTTTA
1244546 GTTATGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
ATTGTTATATTTTA
Found at i:1244741 original size:2 final size:2
Alignment explanation
Indices: 1244734--1244762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1244724 TTTTAATCTT
1244734 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1244763 TGGTACTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1260671 original size:20 final size:20
Alignment explanation
Indices: 1260642--1260680 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260632 AGAGCTCATA
*
1260642 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1260662 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1260681 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1262920 original size:4 final size:4
Alignment explanation
Indices: 1262892--1263103 Score: 106
Period size: 4 Copynumber: 51.0 Consensus size: 4
1262882 TTTATTTTAA
* * * ** *
1262892 ATTT TTTT ATTG ATTT ATTT GTTT ATTT ATTT -TAG ATTT ATTT GTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
* * * * * *
1262939 GTTT ATTT ATTT GTTT GTTT ATTT ATTT ATTC ATTT CGAATTT ATGT ATTC
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT ATTT ATTT
* ** * * **
1262990 ATTT ATTT -TTA ATTT ATTT ATTT -TGG GTTT ATTT ATTT ATTCA ACTCAA
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T A-T-TT
* *
1263039 ATTT ATTT ATTT ATTT ATTTT GAATT ATTT ATTT ATTT AGTT ATTT CAAATTT
1 ATTT ATTT ATTT ATTT A-TTT -ATTT ATTT ATTT ATTT ATTT ATTT ---ATTT
*
1263092 ATTT TTTT ATTT
1 ATTT ATTT ATTT
1263104 TGAAATTATT
Statistics
Matches: 157, Mismatches: 37, Indels: 28
0.71 0.17 0.13
Matches are distributed among these distances:
3 4 0.03
4 134 0.85
5 7 0.04
6 4 0.03
7 8 0.05
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.67
Consensus pattern (4 bp):
ATTT
Found at i:1263030 original size:23 final size:22
Alignment explanation
Indices: 1262877--1263012 Score: 77
Period size: 23 Copynumber: 6.2 Consensus size: 22
1262867 TACAACATCA
* * *
1262877 ATTTTTTTATTTTAAATTTTTTT
1 ATTTATTTATTTT-GATTTATTT
*
1262900 ATTGATTTA-TTTG-TTTATTT
1 ATTTATTTATTTTGATTTATTT
*
1262920 ATTTTAGATTTA-TTTG-TTTGTTT
1 A-TTT--ATTTATTTTGATTTATTT
*
1262943 ATTTATTT-GTTTG-TTTATTT
1 ATTTATTTATTTTGATTTATTT
* * *
1262963 ATTTATTCATTTCGAATTTATGT
1 ATTTATTTATTTTG-ATTTATTT
* *
1262986 ATTCATTTATTTTTAATTTATTT
1 ATTTATTTA-TTTTGATTTATTT
1263009 ATTT
1 ATTT
1263013 TGGGTTTATT
Statistics
Matches: 88, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
20 28 0.32
21 5 0.06
22 6 0.07
23 46 0.52
24 3 0.03
ACGTcount: A:0.21, C:0.02, G:0.07, T:0.70
Consensus pattern (22 bp):
ATTTATTTATTTTGATTTATTT
Found at i:1263032 original size:61 final size:62
Alignment explanation
Indices: 1262940--1263072 Score: 180
Period size: 61 Copynumber: 2.2 Consensus size: 62
1262930 TATTTGTTTG
** ** * *
1262940 TTTATTTATTTGTTTGTTTATTTATTTATTCATTTCGAATTTATGTATTCATTTATTTTTAA
1 TTTATTTATTTGTGGGTTTATTTATTTATTCAACTCAAATTTATGTATTCATTTATTTTGAA
* *
1263002 TTTATTTATTT-TGGGTTTATTTATTTATTCAACTCAAATTTATTTATTTATTTATTTTGAA
1 TTTATTTATTTGTGGGTTTATTTATTTATTCAACTCAAATTTATGTATTCATTTATTTTGAA
1263063 -TTATTTATTT
1 TTTATTTATTT
1263073 ATTTAGTTAT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 10 0.16
61 42 0.67
62 11 0.17
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (62 bp):
TTTATTTATTTGTGGGTTTATTTATTTATTCAACTCAAATTTATGTATTCATTTATTTTGAA
Found at i:1263071 original size:49 final size:46
Alignment explanation
Indices: 1263017--1263122 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 46
1263007 TTATTTTGGG
1263017 TTTATTTATTTA-TTCAACTCAAATTTATTTATTTATTTATTTTG-AATTA
1 TTTATTTATTTAGTT-AACTCAAATTTA--T-TTT-TTTATTTTGAAATTA
**
1263066 TTTATTTATTTAGTTATTTCAAATTTATTTTTTTATTTTGAAATTA
1 TTTATTTATTTAGTTAACTCAAATTTATTTTTTTATTTTGAAATTA
*
1263112 TTTATTAATTT
1 TTTATTTATTT
1263123 GAAGGGATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
45 9 0.17
46 18 0.35
47 1 0.02
49 22 0.42
50 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (46 bp):
TTTATTTATTTAGTTAACTCAAATTTATTTTTTTATTTTGAAATTA
Found at i:1263075 original size:26 final size:27
Alignment explanation
Indices: 1263039--1263103 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
1263029 TTCAACTCAA
* **
1263039 ATTTATTTATTTATTTATTTTGAA-TT
1 ATTTATTTATTTAGTTATTTCAAATTT
1263065 ATTTATTTATTTAGTTATTTCAAATTT
1 ATTTATTTATTTAGTTATTTCAAATTT
*
1263092 ATTTTTTTATTT
1 ATTTATTTATTT
1263104 TGAAATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (27 bp):
ATTTATTTATTTAGTTATTTCAAATTT
Found at i:1263095 original size:23 final size:22
Alignment explanation
Indices: 1263017--1263117 Score: 82
Period size: 23 Copynumber: 4.5 Consensus size: 22
1263007 TTATTTTGGG
**
1263017 TTTATTTATTTATTCAACTCAAA
1 TTTATTTATTTATT-ATTTCAAA
*
1263040 TTTATTTATTTATTTATTTTGAATTA
1 TTTATTTATTTA-TTA-TTTCAA--A
1263066 TTTATTTATTTAGTTATTTCAAA
1 TTTATTTATTTA-TTATTTCAAA
* *
1263089 TTTATTTTTTTA-T-TTTGAAA
1 TTTATTTATTTATTATTTCAAA
1263109 -TTATTTATT
1 TTTATTTATT
1263118 AATTTGAAGG
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
19 8 0.12
20 6 0.09
21 1 0.02
23 25 0.38
24 5 0.08
25 5 0.08
26 16 0.24
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (22 bp):
TTTATTTATTTATTATTTCAAA
Found at i:1266883 original size:14 final size:14
Alignment explanation
Indices: 1266854--1266912 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1266844 TCAATTTTAG
* *
1266854 TAATTATTTTATTT
1 TAATTATTTAAATT
* *
1266868 TAATCATTAAAATT
1 TAATTATTTAAATT
*
1266882 T-ATTTTTTAAATT
1 TAATTATTTAAATT
1266895 TAATTATTTAAATT
1 TAATTATTTAAATT
1266909 TAAT
1 TAAT
1266913 GTCATGTTTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
13 10 0.28
14 26 0.72
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTATTTAAATT
Found at i:1269907 original size:29 final size:29
Alignment explanation
Indices: 1269866--1269974 Score: 123
Period size: 29 Copynumber: 3.7 Consensus size: 29
1269856 GAGGAGCAGG
1269866 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
1269895 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
* * *
1269924 --GACCTACAAGGTCGCCGACCTACAAGGTCGCC
1 AGGA-GTGC-A--T-GGCGACCTACAAGGTCGCC
*
1269956 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
1269975 TGCTGGGAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
27 2 0.03
28 2 0.03
29 38 0.57
30 1 0.01
31 1 0.01
32 19 0.28
33 2 0.03
34 2 0.03
ACGTcount: A:0.24, C:0.30, G:0.32, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:1269928 original size:16 final size:16
Alignment explanation
Indices: 1269907--1269955 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
1269897 GAGTGCATGG
1269907 CGACCTACAAGGTCGC
1 CGACCTACAAGGTCGC
1269923 CGACCTACAAGGTCGC
1 CGACCTACAAGGTCGC
1269939 CGACCTACAAGGTCGC
1 CGACCTACAAGGTCGC
1269955 C
1 C
1269956 CGGAGTGCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.24, C:0.39, G:0.24, T:0.12
Consensus pattern (16 bp):
CGACCTACAAGGTCGC
Found at i:1272523 original size:13 final size:15
Alignment explanation
Indices: 1272505--1272537 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1272495 ATAATGTTTT
1272505 CAAAATAAG-TA-AC
1 CAAAATAAGATAGAC
1272518 CAAAATAAGATAGAC
1 CAAAATAAGATAGAC
1272533 CAAAA
1 CAAAA
1272538 ACAAAAGGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.64, C:0.15, G:0.09, T:0.12
Consensus pattern (15 bp):
CAAAATAAGATAGAC
Found at i:1272877 original size:28 final size:28
Alignment explanation
Indices: 1272823--1272877 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
1272813 CTATCATTGT
* * **
1272823 TTTCAAGAACTGGCTCGATGATTTAATG
1 TTTCAAGAACTAGCTCGATAACATAATG
*
1272851 TTTCAAGCACTAGCTCGATAACATAAT
1 TTTCAAGAACTAGCTCGATAACATAAT
1272878 ATAAATGAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (28 bp):
TTTCAAGAACTAGCTCGATAACATAATG
Found at i:1273139 original size:28 final size:29
Alignment explanation
Indices: 1273083--1273139 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
1273073 ATTCGGGGAC
** *
1273083 CATTTTATAACTTTTAATAGTTAATAGAT
1 CATTTTATAACTTTTAATAGGCAAGAGAT
1273112 CATTTTATAAC-TTTAATAGGCAAGAGAT
1 CATTTTATAACTTTTAATAGGCAAGAGAT
1273140 TCAACAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.42
Consensus pattern (29 bp):
CATTTTATAACTTTTAATAGGCAAGAGAT
Found at i:1277779 original size:16 final size:17
Alignment explanation
Indices: 1277754--1277803 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
1277744 TATTATAGTT
1277754 TATA-TATATAAATATA
1 TATATTATATAAATATA
*
1277770 TAT-TTATATAAAGATA
1 TATATTATATAAATATA
* *
1277786 TATATTGTCTAAATATA
1 TATATTATATAAATATA
1277803 T
1 T
1277804 TTCAATAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (17 bp):
TATATTATATAAATATA
Found at i:1277779 original size:18 final size:18
Alignment explanation
Indices: 1277756--1277791 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1277746 TTATAGTTTA
1277756 TATATATAA-ATATATATT
1 TATATA-AAGATATATATT
1277774 TATATAAAGATATATATT
1 TATATAAAGATATATATT
1277792 GTCTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TATATAAAGATATATATT
Found at i:1284069 original size:162 final size:162
Alignment explanation
Indices: 1283869--1284180 Score: 414
Period size: 162 Copynumber: 1.9 Consensus size: 162
1283859 ATAATGGAAC
* *
1283869 ATGCGCCTTTCATTTCGGATGTGATGAAACACTATGACATGACAAAGATTCTCTGAATAATAAT-
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAAAGATTCTCTGAATAATAATA
* * * * * *
1283933 GAAAA-ATGTTTCCCCTGA-AATGCGCCTTTTATTTCTGATGGGATGGAACACTATGACATGACA
66 GAAAACA--CTT-CCCTGAGAATACACCTTTCATTTCGGATGGGATGAAACACTATGACATGACA
* * *
1283996 TATATTCTCTAAATAATAATGGAGTTTCCCTTGGA
128 GAGATTATCTAAATAATAATGGAGTTTCCCTTGGA
* * *
1284031 ATGCACCTTTCATTTCGGATGGGATGAAACATTATGACATGACAGAGATTCTTTGAATAATAATA
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAAAGATTCTCTGAATAATAATA
* * *
1284096 GAAAACACTTCCCTTAGAATACACCTTTCATTTCGGATGGGATGAAACACTATGATATGGCAGAG
66 GAAAACACTTCCCTGAGAATACACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAG
*
1284161 ATTATCTGAATAATAATGGA
131 ATTATCTAAATAATAATGGA
1284181 AAACACTATG
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
161 5 0.04
162 118 0.91
163 5 0.04
164 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.31
Consensus pattern (162 bp):
ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAAAGATTCTCTGAATAATAATA
GAAAACACTTCCCTGAGAATACACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAG
ATTATCTAAATAATAATGGAGTTTCCCTTGGA
Found at i:1284184 original size:83 final size:82
Alignment explanation
Indices: 1283869--1284187 Score: 367
Period size: 83 Copynumber: 3.9 Consensus size: 82
1283859 ATAATGGAAC
* * *
1283869 ATGCGCCTTTCATTTCGGATGTGATGAAACACTATGACATGACAAAGATTCTCTGAATAATAATG
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
* *** *
1283934 AAAAATGTTTCCCCTGAA
66 GAAAACACTTCCCTTG-A
* * * * * * *
1283952 ATGCGCCTTTTATTTCTGATGGGATGGAACACTATGACATGACATATATTCTCTAAATAATAATG
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
**
1284017 G---A-GTTTCCCTTGGA
66 GAAAACACTTCCCTT-GA
* * *
1284031 ATGCACCTTTCATTTCGGATGGGATGAAACATTATGACATGACAGAGATTCTTTGAATAATAATA
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
1284096 GAAAACACTTCCCTTAGA
66 GAAAACACTTCCCTT-GA
* * * *
1284114 ATACACCTTTCATTTCGGATGGGATGAAACACTATGATATGGCAGAGATTATCTGAATAATAATG
1 ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
1284179 GAAAACACT
66 GAAAACACT
1284188 ATGATATGAC
Statistics
Matches: 202, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
79 65 0.32
80 2 0.01
82 1 0.00
83 134 0.66
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (82 bp):
ATGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
GAAAACACTTCCCTTGA
Found at i:1287104 original size:2 final size:2
Alignment explanation
Indices: 1287097--1287138 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1287087 CACCTATTTA
1287097 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
1287139 GTCATTTTAT
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:1288185 original size:19 final size:19
Alignment explanation
Indices: 1288158--1288211 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1288148 AAACAAGTTT
*
1288158 AAAATTAAATAATCAAATA-
1 AAAAATAAATAAT-AAATAC
*
1288177 AAAAATAAAAAATAAATAC
1 AAAAATAAATAATAAATAC
*
1288196 TAAAATAAAATAATAA
1 AAAAAT-AAATAATAA
1288212 TAAAATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 5 0.17
19 16 0.55
20 8 0.28
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATAAATAATAAATAC
Found at i:1288220 original size:8 final size:8
Alignment explanation
Indices: 1288173--1288263 Score: 57
Period size: 8 Copynumber: 11.8 Consensus size: 8
1288163 TAAATAATCA
1288173 AATAAAA-
1 AATAAAAT
1288180 AATAAAA-
1 AATAAAAT
1288187 AAT-AAAT
1 AATAAAAT
*
1288194 ACTAAAAT
1 AATAAAAT
1288202 AA-AATAAT
1 AATAA-AAT
1288210 AATAAAAT
1 AATAAAAT
* *
1288218 AATTAATT
1 AATAAAAT
* *
1288226 ACTTAAAT
1 AATAAAAT
1288234 AATAAAA-
1 AATAAAAT
* **
1288241 ATTTTAAT
1 AATAAAAT
1288249 GAATAAAAT
1 -AATAAAAT
1288258 AATAAA
1 AATAAA
1288264 TTTATAAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
6 3 0.05
7 18 0.28
8 36 0.56
9 7 0.11
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (8 bp):
AATAAAAT
Found at i:1288247 original size:24 final size:25
Alignment explanation
Indices: 1288173--1288263 Score: 69
Period size: 24 Copynumber: 3.6 Consensus size: 25
1288163 TAAATAATCA
* * *
1288173 AATAAAA-AATAAAAAATAAATACTAA
1 AATAAAATAAT-AAAAATAATTAAT-G
*
1288199 AATAAAATAATAATAAAATAATTAATT
1 AATAAAATAAT-A-AAAATAATTAATG
* * *
1288226 ACTTAAATAATAAAAAT-TTTAATG
1 AATAAAATAATAAAAATAATTAATG
1288250 AATAAAATAATAAA
1 AATAAAATAATAAA
1288264 TTTATAAAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
24 17 0.31
25 5 0.09
26 8 0.15
27 14 0.26
28 10 0.19
ACGTcount: A:0.68, C:0.02, G:0.01, T:0.29
Consensus pattern (25 bp):
AATAAAATAATAAAAATAATTAATG
Found at i:1293912 original size:31 final size:31
Alignment explanation
Indices: 1293877--1293948 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1293867 CGAAAAACAT
* * *
1293877 GTTTTGGTCACTTATGTCATTATTTTATTAA
1 GTTTTGGTCACTAACGTCATCATTTTATTAA
* * * *
1293908 GTTTTGATTACTAACGTTATCGTTTTATTAA
1 GTTTTGGTCACTAACGTCATCATTTTATTAA
1293939 GTTTTGGTCA
1 GTTTTGGTCA
1293949 TTTGGTCGTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (31 bp):
GTTTTGGTCACTAACGTCATCATTTTATTAA
Done.