Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008716.1 Hibiscus syriacus cultivar Beakdansim tig00111769_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: 5677467
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 24
Found at i:3554784 original size:16 final size:16
Alignment explanation
Indices: 3554765--3554798 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3554755 TGAAAATATC
3554765 AGTTTATCAAAAAGAA
1 AGTTTATCAAAAAGAA
**
3554781 AGTTTATTGAAAAGAA
1 AGTTTATCAAAAAGAA
3554797 AG
1 AG
3554799 ATTAGTTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.18, T:0.26
Consensus pattern (16 bp):
AGTTTATCAAAAAGAA
Found at i:3555144 original size:20 final size:21
Alignment explanation
Indices: 3555119--3555170 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
3555109 TTTTACCAAT
*
3555119 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
3555139 TCGCAATGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
3555160 TCGCAATGCGA
1 TCGCAATGCGA
3555171 TAATGCGATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:3555197 original size:20 final size:20
Alignment explanation
Indices: 3555172--3555300 Score: 143
Period size: 20 Copynumber: 6.4 Consensus size: 20
3555162 GCAATGCGAT
3555172 AATGCGATACTGACTATCGC
1 AATGCGATACTGACTATCGC
3555192 AATGCGATACTGACTATCGC
1 AATGCGATACTGACTATCGC
*
3555212 AATGCGATACTTACTATCGC
1 AATGCGATACTGACTATCGC
* *
3555232 AATGCGATAAT-ACAAAATCGC
1 AATGCGATACTGAC--TATCGC
* * *
3555253 AACGAGATACTGACTTTCGC
1 AATGCGATACTGACTATCGC
* * *
3555273 AACGCGATTCTGACTTTCGC
1 AATGCGATACTGACTATCGC
*
3555293 AACGCGAT
1 AATGCGAT
3555301 TTACATAGCG
Statistics
Matches: 96, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 79 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
AATGCGATACTGACTATCGC
Found at i:3555273 original size:41 final size:40
Alignment explanation
Indices: 3555177--3555280 Score: 120
Period size: 41 Copynumber: 2.6 Consensus size: 40
3555167 GCGATAATGC
* * * *
3555177 GATACTGACTATCGCAATGCGATACTGACTATCGCAATGC
1 GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
*
3555217 GATACTTACTATCGCAATGCGATAAT-ACAAAATCGCAACGA
1 GATACTGACTATCGCAATGCGATAATGAC--AATCGCAACGA
* *
3555258 GATACTGACTTTCGCAACGCGAT
1 GATACTGACTATCGCAATGCGAT
3555281 TCTGACTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.04
40 24 0.44
41 28 0.52
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
GATACTGACTATCGCAATGCGATAATGACAATCGCAACGA
Found at i:3555515 original size:22 final size:22
Alignment explanation
Indices: 3555461--3555515 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
3555451 TCACTCTCTA
* *
3555461 CGGCGAAATCCGTCCCCATCTC
1 CGGCGAATTCCGTCCCCATCGC
** *
3555483 CGAAGATTTCCGTCCCCATCGC
1 CGGCGAATTCCGTCCCCATCGC
3555505 CGGCGAATTCC
1 CGGCGAATTCC
3555516 CTCACAATCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.18, C:0.42, G:0.20, T:0.20
Consensus pattern (22 bp):
CGGCGAATTCCGTCCCCATCGC
Found at i:3555852 original size:19 final size:19
Alignment explanation
Indices: 3555828--3555872 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3555818 GCAACGAGAG
*
3555828 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
3555847 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
3555866 AATCGCA
1 AATCGCA
3555873 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:3555971 original size:20 final size:19
Alignment explanation
Indices: 3555868--3555985 Score: 155
Period size: 19 Copynumber: 6.1 Consensus size: 19
3555858 GAAACCAAAA
*
3555868 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3555887 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
3555906 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
** *
3555925 TCGCGTTGCGATAGTCCTT
1 TCGCGTTGCGATTTTCATT
*
3555944 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
3555964 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
3555984 TC
1 TC
3555986 AACCAAAAGA
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
19 54 0.63
20 31 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:3558152 original size:21 final size:21
Alignment explanation
Indices: 3558128--3558194 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3558118 TCATTCCTCG
3558128 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3558149 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3558170 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3558191 AGAG
1 AGAG
3558195 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3558152 original size:42 final size:42
Alignment explanation
Indices: 3558076--3558194 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
3558066 GACTCGCCTG
* * * * * * *
3558076 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
3558118 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
3558160 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
3558195 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:3559581 original size:14 final size:14
Alignment explanation
Indices: 3559546--3559582 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3559536 GATTGTTTAA
*
3559546 TTGATTTATAAAAG
1 TTGATTTGTAAAAG
*
3559560 GTGATTTGTAAAAG
1 TTGATTTGTAAAAG
3559574 TTGATTTGT
1 TTGATTTGT
3559583 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:3559726 original size:14 final size:14
Alignment explanation
Indices: 3559704--3559768 Score: 58
Period size: 14 Copynumber: 4.3 Consensus size: 14
3559694 AATGCGAAAT
3559704 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
3559718 GATAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
3559736 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
* *
3559751 GAGAATCGCAACGC
1 GAAAATCGCAACGA
3559765 GAAA
1 GAAA
3559769 TTAAATTCGC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 10 0.24
ACGTcount: A:0.46, C:0.22, G:0.23, T:0.09
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:3559734 original size:33 final size:33
Alignment explanation
Indices: 3559689--3559778 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
3559679 AAAAAGTACT
* *
3559689 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
3559722 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
3559755 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAACGCGAAATGAAAATCGC
3559779 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:3559748 original size:19 final size:19
Alignment explanation
Indices: 3559689--3559749 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
3559679 AAAAAGTACT
*
3559689 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
3559708 ATCGCAA--CG--A-GATA
1 ATCGCAACGCGAAATGAAA
3559722 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
3559741 ATCGCAACG
1 ATCGCAACG
3559750 AGAGAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 10 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.54
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:3559820 original size:33 final size:33
Alignment explanation
Indices: 3559778--3559904 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
3559768 ATTAAATTCG
*
3559778 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
3559811 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AGT
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCACT
* * *
3559845 -GTTCCGGTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
3559877 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
3559905 AGTAATTTCC
Statistics
Matches: 81, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
31 3 0.04
32 1 0.01
33 73 0.90
34 1 0.01
35 3 0.04
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:3562195 original size:12 final size:12
Alignment explanation
Indices: 3562178--3562202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3562168 TCTTCGGGGA
3562178 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3562190 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3562202 C
1 C
3562203 AGGATTATGA
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:3562405 original size:23 final size:24
Alignment explanation
Indices: 3562372--3562424 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
3562362 CTGAAACATC
* *
3562372 ATCAAAATCCGTGTA-TGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
3562395 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
3562419 ATCAAA
1 ATCAAA
3562425 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:3563503 original size:20 final size:20
Alignment explanation
Indices: 3563478--3563535 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3563468 ATTCATTTGA
3563478 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
3563498 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
3563518 CTGTCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
3563536 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3563595 original size:19 final size:19
Alignment explanation
Indices: 3563554--3563621 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
3563544 GAAATGAAAA
3563554 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3563570 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3563587 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
3563606 TCGCACTGTGATTTTC
1 TCGCATTGCGATTTTC
3563622 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 28 0.62
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3563757 original size:14 final size:14
Alignment explanation
Indices: 3563738--3563774 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3563728 CATCAATTAA
3563738 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3563752 ACAAATCATCTTTT
1 ACAAATCAACATTT
3563766 ACAAATCAA
1 ACAAATCAA
3563775 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3565654 original size:20 final size:19
Alignment explanation
Indices: 3565631--3565696 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
3565621 AACTTAAAAC
3565631 CGCAACGCGAAAATGACTAT
1 CGCAACGCG-AAATGACTAT
*
3565651 CGCAACGCGGAAATGGCTAT
1 CGCAACGC-GAAATGACTAT
* **
3565671 CGCAATGCGAAATGAAAAT
1 CGCAACGCGAAATGACTAT
3565690 CGCAACG
1 CGCAACG
3565697 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 14 0.36
20 24 0.62
21 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.14
Consensus pattern (19 bp):
CGCAACGCGAAATGACTAT
Found at i:3565691 original size:19 final size:18
Alignment explanation
Indices: 3565669--3565726 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 18
3565659 GGAAATGGCT
3565669 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
3565688 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
3565702 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
3565720 ATCGCAA
1 ATCGCAA
3565727 CGACAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 11
0.71 0.04 0.24
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 10 0.31
19 7 0.22
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:3565704 original size:14 final size:14
Alignment explanation
Indices: 3565685--3565741 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
3565675 ATGCGAAATG
3565685 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
3565699 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
3565715 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
3565731 AAAATCGCAAC
1 AAAATCGCAAC
3565742 TCGAAACACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.49, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3565727 original size:32 final size:33
Alignment explanation
Indices: 3565669--3565747 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
3565659 GGAAATGGCT
*
3565669 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
3565702 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
3565734 ATCGCAACTCGAAA
1 ATCGCAACGCGAAA
3565748 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:3565797 original size:14 final size:14
Alignment explanation
Indices: 3565778--3565833 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
3565768 TCATTTCGCT
3565778 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
3565792 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
3565808 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
3565824 TTGCGATTTT
1 TTGCGATTTT
3565834 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
14 19 0.53
16 8 0.22
18 9 0.25
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:3565840 original size:33 final size:33
Alignment explanation
Indices: 3565759--3565849 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3565749 ACAAATCGCA
*
3565759 TTGCGATTTTCATTTCGCTTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3565792 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
3565824 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
3565850 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:3565868 original size:20 final size:19
Alignment explanation
Indices: 3565834--3565888 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
3565824 TTGCGATTTT
*
3565834 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
3565853 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
3565873 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
3565889 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:3566391 original size:18 final size:18
Alignment explanation
Indices: 3566370--3566408 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3566360 CAGATGATGA
*
3566370 CTCTGGGTGAGGTGATAG
1 CTCTGGGCGAGGTGATAG
*
3566388 CTCTGGGCGAGGTGATGG
1 CTCTGGGCGAGGTGATAG
3566406 CTC
1 CTC
3566409 CCGAAGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.18, G:0.44, T:0.26
Consensus pattern (18 bp):
CTCTGGGCGAGGTGATAG
Found at i:3568040 original size:22 final size:22
Alignment explanation
Indices: 3568013--3568056 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3568003 GATGGAGATA
3568013 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3568035 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3568057 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3568270 original size:20 final size:20
Alignment explanation
Indices: 3568244--3568357 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
3568234 GATTATGTAT
3568244 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3568264 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3568284 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
3568304 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
3568325 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3568345 TATCGCATTGCGA
1 TATCGCGTTGCGA
3568358 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3568361 original size:41 final size:41
Alignment explanation
Indices: 3568224--3568359 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
3568214 CGTTTTGAAA
*
3568224 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
3568265 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * *
3568305 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
3568346 ATCGCATTGCGATT
1 ATCGCATTGCGATT
3568360 TTCCCAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 42 0.54
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:3568377 original size:41 final size:41
Alignment explanation
Indices: 3568224--3568379 Score: 109
Period size: 41 Copynumber: 3.8 Consensus size: 41
3568214 CGTTTTGAAA
* ** * * * *
3568224 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* *** * *
3568265 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
3568305 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
3568346 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
3568380 TTACTTATTC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.36
41 56 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:3578903 original size:2 final size:2
Alignment explanation
Indices: 3578896--3578924 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3578886 TTTTCAATTC
3578896 CT CT CT CT CT CT C- CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3578925 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3578912 original size:13 final size:13
Alignment explanation
Indices: 3578894--3578921 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3578884 ACTTTTCAAT
3578894 TCCTCTCTCTCTC
1 TCCTCTCTCTCTC
3578907 TCCTCTCTCTCTC
1 TCCTCTCTCTCTC
3578920 TC
1 TC
3578922 TCTATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (13 bp):
TCCTCTCTCTCTC
Found at i:3586026 original size:58 final size:59
Alignment explanation
Indices: 3585964--3586082 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 59
3585954 TAAAGTACGT
** *
3585964 AATGGT-CTCTCGACTATAGAATATTA-TTTATTAAGTCCCTCGACTATTAAAAGTTACA
1 AATGGTCCTC-CGACTATAGAATATTACTTTATTAAGTAACTCAACTATTAAAAGTTACA
* *
3586022 AATGGTCCTCCGACTATAGAATGTTACTTTGTTAAGTAACTCAACTATTAAAAGTTACA
1 AATGGTCCTCCGACTATAGAATATTACTTTATTAAGTAACTCAACTATTAAAAGTTACA
3586081 AA
1 AA
3586083 ATGGCCACAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
58 21 0.39
59 33 0.61
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (59 bp):
AATGGTCCTCCGACTATAGAATATTACTTTATTAAGTAACTCAACTATTAAAAGTTACA
Found at i:3586587 original size:16 final size:15
Alignment explanation
Indices: 3586566--3586600 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
3586556 TATAAAGTAG
3586566 TTATTAAATTAAATAA
1 TTATTAAATTAAAT-A
*
3586582 TTATTAAATTTAATA
1 TTATTAAATTAAATA
3586597 TTAT
1 TTAT
3586601 GATGTTGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATTAAATTAAATA
Found at i:3587557 original size:37 final size:37
Alignment explanation
Indices: 3587483--3587557 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
3587473 AAATATGAAG
* **
3587483 ACTTCACGAATGTATGACGTATTCAGGTAAATGAAAA
1 ACTTCACGAATGCATGACGTATTCAGACAAATGAAAA
* * *
3587520 ACTTCACGACTGCATGACGTCTTCAGACAAATTAAAA
1 ACTTCACGAATGCATGACGTATTCAGACAAATGAAAA
3587557 A
1 A
3587558 GCCATCAGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (37 bp):
ACTTCACGAATGCATGACGTATTCAGACAAATGAAAA
Found at i:3587889 original size:20 final size:20
Alignment explanation
Indices: 3587846--3587890 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
3587836 TTTTTGAATC
3587846 AAATTAA-TAGATATTATTT
1 AAATTAATTAGATATTATTT
3587865 --A-TAATTAGATATTATTT
1 AAATTAATTAGATATTATTT
3587882 AAATTAATT
1 AAATTAATT
3587891 GTAAATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.14
17 13 0.59
19 1 0.05
20 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AAATTAATTAGATATTATTT
Found at i:3592176 original size:2 final size:2
Alignment explanation
Indices: 3592169--3592221 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
3592159 TCATAATTTA
3592169 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
3592211 AT AT AT AT AT A
1 AT AT AT AT AT A
3592222 CACTCATAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3597625 original size:21 final size:21
Alignment explanation
Indices: 3597587--3597626 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3597577 TTTCATATAA
*
3597587 TTTATTTTTATCATATAAAGT
1 TTTATTTTCATCATATAAAGT
3597608 TTTATTTTACATCA-ATAAA
1 TTTATTTT-CATCATATAAA
3597627 ATTAATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTATTTTCATCATATAAAGT
Found at i:3597671 original size:6 final size:6
Alignment explanation
Indices: 3597660--3597728 Score: 138
Period size: 6 Copynumber: 11.5 Consensus size: 6
3597650 CAGCAAAATA
3597660 GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG
1 GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG GGAATG
3597708 GGAATG GGAATG GGAATG GGA
1 GGAATG GGAATG GGAATG GGA
3597729 TAGATAAGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.51, T:0.16
Consensus pattern (6 bp):
GGAATG
Found at i:3601167 original size:2 final size:2
Alignment explanation
Indices: 3601162--3601187 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3601152 GTTATATAAA
3601162 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
3601188 TTATTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3612263 original size:35 final size:35
Alignment explanation
Indices: 3612190--3612264 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
3612180 TGTCACGTCC
* **
3612190 AGTAAGGCACTGAGCACACAGCCGAGGAACTGGTA
1 AGTAAGGCACTAAGCACACAGCCGAGGAACTGCCA
*
3612225 AGTAAGGCCCTAAGCACACAGCCGAGGAACCT-CCA
1 AGTAAGGCACTAAGCACACAGCCGAGGAA-CTGCCA
3612260 AGTAA
1 AGTAA
3612265 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 33 0.94
36 2 0.06
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCACTAAGCACACAGCCGAGGAACTGCCA
Found at i:3612368 original size:24 final size:24
Alignment explanation
Indices: 3612341--3612431 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
3612331 CATAATTCAA
*
3612341 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
3612365 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
3612389 ATCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
3612412 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
3612432 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:3614949 original size:13 final size:13
Alignment explanation
Indices: 3614931--3614979 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 13
3614921 AACAGTCAAC
3614931 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3614944 GGTCAACAGGTCGGGTCG
1 GGTC-A-A---CGGGTCG
3614962 GGTCAACGGGTCG
1 GGTCAACGGGTCG
3614975 GGTCA
1 GGTCA
3614980 TGTTATGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 16 0.52
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 11 0.35
ACGTcount: A:0.16, C:0.22, G:0.45, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3614960 original size:18 final size:18
Alignment explanation
Indices: 3614937--3614978 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
3614927 CAACGGTCAA
3614937 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
3614955 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
3614973 CGGGTC
1 CGGGTC
3614979 ATGTTATGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:3617030 original size:35 final size:35
Alignment explanation
Indices: 3616957--3617031 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
3616947 CGTCACGTCC
* **
3616957 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGAAACCGCCA
* * *
3616992 AGTAAGGCCCTGATCACACAGCGGAGAAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGAAACCGCCA
3617027 AGTAA
1 AGTAA
3617032 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.28, G:0.27, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGAAACCGCCA
Found at i:3619659 original size:18 final size:18
Alignment explanation
Indices: 3619636--3619675 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3619626 AACGGTCAAC
3619636 GGGTCGGGTCAACGGGTT
1 GGGTCGGGTCAACGGGTT
3619654 GGGTCGGGTCAACGGGTT
1 GGGTCGGGTCAACGGGTT
3619672 GGGT
1 GGGT
3619676 AAATGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.15, G:0.53, T:0.23
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTT
Found at i:3619667 original size:31 final size:31
Alignment explanation
Indices: 3619629--3619689 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3619619 GCCGGTCAAC
* *
3619629 GGTCAACGGGTCGGGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
* *
3619660 GGTCAACGGGTTGGGTAAATGGGTCGGGTC
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTC
3619690 CGGTTATGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.15, C:0.16, G:0.48, T:0.21
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCG
Found at i:3619675 original size:13 final size:13
Alignment explanation
Indices: 3619629--3619658 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3619619 GCCGGTCAAC
3619629 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
3619642 GGTCAACGGGTTG
1 GGTCAACGGGTCG
3619655 GGTC
1 GGTC
3619659 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:3621941 original size:2 final size:2
Alignment explanation
Indices: 3621934--3621958 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3621924 TAAATTTCTG
3621934 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
3621959 GGATCGGATT
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:3623678 original size:2 final size:2
Alignment explanation
Indices: 3623671--3623708 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
3623661 GTATCATTGC
*
3623671 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3623709 TTACTTGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3625034 original size:20 final size:22
Alignment explanation
Indices: 3625009--3625049 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3624999 AGAGAGCATT
3625009 ATTT-AAATTT-TTTTAAAGAA
1 ATTTAAAATTTCTTTTAAAGAA
*
3625029 ATTTAAAATTTCTTTTGAAGA
1 ATTTAAAATTTCTTTTAAAGA
3625050 TTTGGATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTAAAATTTCTTTTAAAGAA
Found at i:3626259 original size:19 final size:18
Alignment explanation
Indices: 3626235--3626277 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3626225 AAAAAATACA
*
3626235 AATAAAAATTTATATCTAT
1 AATAAAAATATAT-TCTAT
* *
3626254 AATAAATATATATTTTAT
1 AATAAAAATATATTCTAT
3626272 AATAAA
1 AATAAA
3626278 TCAATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAAAAATATATTCTAT
Found at i:3626844 original size:96 final size:97
Alignment explanation
Indices: 3626714--3627024 Score: 313
Period size: 104 Copynumber: 3.1 Consensus size: 97
3626704 GGTCTAATTT
* * *
3626714 TGGAGGTTTCGATTAAAA-TCCTAATTATCGATGTAGGTAATCATTGTTACTTATGGGAAATC-A
1 TGGAGGTTTCGACTAAAAGT-CTAATTA-CTATGTAGGTAATCACTGTTACTTATGGGAAATCAA
* * *
3626777 -AATGTTTGAACGTTCGAATGACTTGGCGACCTG
64 CAATGCTTGAACGTTCGAAGGACTTGGCGACCTA
*
3626810 TGGAGGTTTCGACTAAAAGTCTAATTACATATGTAGGTCATCACTGTTACTTATGGGAAATCAAG
1 TGGAGGTTTCGACTAAAAGTCTAATTAC-TATGTAGGTAATCACTGTTACTTATGGGAAATC---
* *
3626875 GAAATCAATGCTTGAACGTTCGGAGGATTTGGCGACCTA
62 --AA-CAATGCTTGAACGTTCGAAGGACTTGGCGACCTA
* * *
3626914 TGGAGGTTTTGACTAAAAGCCTAATTACTGATGTAGGTAATCACTGTTACTTATAGGAAATTTAA
1 TGGAGGTTTCGACTAAAAGTCTAATTACT-ATGTAGGTAATCACTGTTACTTATGGGAAA--T--
* * * *
3626979 GAAACCAATGTTTGAACGTTTGGAGGACTTGGCGACCTA
61 -CAA-CAATGCTTGAACGTTCGAAGGACTTGGCGACCTA
3627018 TGGAGGT
1 TGGAGGT
3627025 CGCCCAGAGG
Statistics
Matches: 181, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
95 1 0.01
96 54 0.30
97 1 0.01
102 1 0.01
103 1 0.01
104 122 0.67
106 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (97 bp):
TGGAGGTTTCGACTAAAAGTCTAATTACTATGTAGGTAATCACTGTTACTTATGGGAAATCAACA
ATGCTTGAACGTTCGAAGGACTTGGCGACCTA
Found at i:3626962 original size:104 final size:105
Alignment explanation
Indices: 3626769--3627024 Score: 365
Period size: 104 Copynumber: 2.4 Consensus size: 105
3626759 GTTACTTATG
* * * *
3626769 GGAAATCAAATGTTTGAACGTTCGAATGACTTGGCGACCTGTGGAGGTTTCGACTAAAAGTCTAA
1 GGAAATC-AATGTTTGAACGTTCGGAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAA
* *
3626834 TTACATATGTAGGTCATCACTGTTACTTATGGGAAA-TCAA
65 TTACATATGTAGGTAATCACTGTTACTTATAGGAAATTCAA
* * *
3626874 GGAAATCAATGCTTGAACGTTCGGAGGATTTGGCGACCTATGGAGGTTTTGACTAAAAGCCTAAT
1 GGAAATCAATGTTTGAACGTTCGGAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAAT
*
3626939 TAC-TGATGTAGGTAATCACTGTTACTTATAGGAAATTTAA
66 TACAT-ATGTAGGTAATCACTGTTACTTATAGGAAATTCAA
* *
3626979 -GAAACCAATGTTTGAACGTTTGGAGGACTTGGCGACCTATGGAGGT
1 GGAAATCAATGTTTGAACGTTCGGAGGACTTGGCGACCTATGGAGGT
3627025 CGCCCAGAGG
Statistics
Matches: 135, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
103 1 0.01
104 124 0.92
105 10 0.07
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (105 bp):
GGAAATCAATGTTTGAACGTTCGGAGGACTTGGCGACCTATGGAGGTTTCGACTAAAAGCCTAAT
TACATATGTAGGTAATCACTGTTACTTATAGGAAATTCAA
Found at i:3637642 original size:24 final size:23
Alignment explanation
Indices: 3637599--3637647 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
3637589 AATCTCAATA
*
3637599 TTTTTTAAATATGTTAATTTTAT
1 TTTTTTAAATATGTTAATTTAAT
*
3637622 TTTTTTTAATAAT-TTATATTTAAT
1 TTTTTTAAAT-ATGTTA-ATTTAAT
3637646 TT
1 TT
3637648 ATAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTAAATATGTTAATTTAAT
Found at i:3637864 original size:12 final size:13
Alignment explanation
Indices: 3637835--3637866 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
3637825 ATTTTTTCTA
3637835 AAAAATATTATTT
1 AAAAATATTATTT
*
3637848 AAAAATATTTTTT
1 AAAAATATTATTT
3637861 AAAAAT
1 AAAAAT
3637867 TCTAAACGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAATATTATTT
Found at i:3638637 original size:25 final size:24
Alignment explanation
Indices: 3638572--3638637 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
3638562 TAGAACTACA
3638572 TAAAATATTATTTTT-T-TCTATC
1 TAAAATATTATTTTTATATCTATC
* * * *
3638594 AAAAATATTAATATCATATGCTATC
1 TAAAATATTATTTTTATAT-CTATC
3638619 TAAAATATTATTTTTATAT
1 TAAAATATTATTTTTATAT
3638638 TAAAAATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
22 11 0.33
23 1 0.03
24 1 0.03
25 20 0.61
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (24 bp):
TAAAATATTATTTTTATATCTATC
Found at i:3645083 original size:31 final size:32
Alignment explanation
Indices: 3645025--3645086 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
3645015 AATGGGTATA
3645025 ATATGTGTTTAGTACATAAATTATTAATTTTG
1 ATATGTGTTTAGTACATAAATTATTAATTTTG
3645057 ATATGT-TTTAGTATC-TAAACTT-TTAATTTT
1 ATATGTGTTTAGTA-CATAAA-TTATTAATTTT
3645087 TTTCAAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (32 bp):
ATATGTGTTTAGTACATAAATTATTAATTTTG
Found at i:3647405 original size:24 final size:24
Alignment explanation
Indices: 3647348--3647407 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
3647338 TAGTCAGTAT
3647348 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* * *
3647372 CCGGACTTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
*
3647396 TCGAATTTTGAT
1 TCGAAATTTGAT
3647408 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:3651588 original size:21 final size:21
Alignment explanation
Indices: 3651506--3651594 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
3651496 ATGAATCGGG
** *
3651506 CTCTTGAACGATGGGAGGGAC
1 CTCTTGAACGATGAAAGGGGC
3651527 CTCTTGAACGATGACAA-GGGC
1 CTCTTGAACGATGA-AAGGGGC
*
3651548 CTCTTGAAC-AGTGAGAGGGGC
1 CTCTTGAACGA-TGAAAGGGGC
* *
3651569 CTATTGAACGATGAAAGGGGT
1 CTCTTGAACGATGAAAGGGGC
3651590 CTCTT
1 CTCTT
3651595 AAATGATAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.04
21 52 0.93
22 2 0.04
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAAAGGGGC
Found at i:3651594 original size:42 final size:42
Alignment explanation
Indices: 3651506--3651587 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
3651496 ATGAATCGGG
* *
3651506 CTCTTGAACGATGGGAGGGACCTCTTGAACGATGACAAGGGC
1 CTCTTGAACGATGAGAGGGACCTATTGAACGATGACAAGGGC
*
3651548 CTCTTGAAC-AGTGAGAGGGGCCTATTGAACGATGA-AAGGG
1 CTCTTGAACGA-TGAGAGGGACCTATTGAACGATGACAAGGG
3651588 GTCTCTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 6 0.17
42 30 0.83
ACGTcount: A:0.28, C:0.18, G:0.34, T:0.20
Consensus pattern (42 bp):
CTCTTGAACGATGAGAGGGACCTATTGAACGATGACAAGGGC
Found at i:3653341 original size:61 final size:61
Alignment explanation
Indices: 3653246--3653362 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
3653236 CTGAAGAAAT
* *
3653246 AAATGGGTCAACGTAGCATCTCCACCTGGATGTTGTACTTTCAGCCCTGGCCCGAATAACC
1 AAATGGGTCAACATAGCATCTCCACCTGGATGTTGTACTTTCAGCCATGGCCCGAATAACC
*
3653307 AAATGGGTCAACATAGCATCTCCACCTGGATGTTGTACTTTCATCCATGGCCCGAA
1 AAATGGGTCAACATAGCATCTCCACCTGGATGTTGTACTTTCAGCCATGGCCCGAA
3653363 GCAAGTATCC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (61 bp):
AAATGGGTCAACATAGCATCTCCACCTGGATGTTGTACTTTCAGCCATGGCCCGAATAACC
Found at i:3658756 original size:45 final size:45
Alignment explanation
Indices: 3658707--3658815 Score: 131
Period size: 39 Copynumber: 2.6 Consensus size: 45
3658697 TCAGAATTCA
*
3658707 TTTAGTAACCAACAGCAACAGCAGCAGCAGCAGCAGCATCCGTTG
1 TTTAGTAACCAACAGCAACAGCAGCAGCAGCAGCAGCATCCGCTG
**
3658752 TTTAGTAACCAACAGC--C--C--CAGCAGCCTCAGCATCCGCTG
1 TTTAGTAACCAACAGCAACAGCAGCAGCAGCAGCAGCATCCGCTG
* *
3658791 TTTACTAACCAACAACAACAGCAGC
1 TTTAGTAACCAACAGCAACAGCAGC
3658816 CACAGCAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
39 32 0.60
41 2 0.04
43 2 0.04
45 17 0.32
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (45 bp):
TTTAGTAACCAACAGCAACAGCAGCAGCAGCAGCAGCATCCGCTG
Found at i:3684513 original size:79 final size:80
Alignment explanation
Indices: 3684414--3684574 Score: 297
Period size: 80 Copynumber: 2.0 Consensus size: 80
3684404 GAAAAATCTT
*
3684414 GGGGTTTATGATTCCGAAGCAGCCC-AACCTAAAGTCTTCTGAAGAGTAAACTCGTGTGACTCAC
1 GGGGTTTATGATTCCGAAGCAGCCCAAACCTAAAGTCTGCTGAAGAGTAAACTCGTGTGACTCAC
3684478 CGAATTATTAAATGC
66 CGAATTATTAAATGC
*
3684493 GGGGTTTATGATTCCGAAGCAGCCCAAACCTCAAGTCTGCTGAAGAGTAAACTCGTGTGACTCAC
1 GGGGTTTATGATTCCGAAGCAGCCCAAACCTAAAGTCTGCTGAAGAGTAAACTCGTGTGACTCAC
3684558 CGAATTATTAAATGC
66 CGAATTATTAAATGC
3684573 GG
1 GG
3684575 CACCGCTTTA
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
79 25 0.32
80 54 0.68
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (80 bp):
GGGGTTTATGATTCCGAAGCAGCCCAAACCTAAAGTCTGCTGAAGAGTAAACTCGTGTGACTCAC
CGAATTATTAAATGC
Found at i:3692657 original size:13 final size:13
Alignment explanation
Indices: 3692639--3692669 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3692629 GTTATAAAAA
3692639 CATTACATTAAAC
1 CATTACATTAAAC
3692652 CATTACATTAAAC
1 CATTACATTAAAC
3692665 CATTA
1 CATTA
3692670 AACATTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (13 bp):
CATTACATTAAAC
Found at i:3692737 original size:34 final size:35
Alignment explanation
Indices: 3692662--3692802 Score: 185
Period size: 36 Copynumber: 3.9 Consensus size: 35
3692652 CATTACATTA
* *
3692662 AACCATTAAACATTACATTTATGAGATAAAAACAACA
1 AACCA-TAAACATTACATTTA-GAGATAGAAACAACG
*
3692699 AACCATAAACATTACATTTA-AGATAGAAATAACG
1 AACCATAAACATTACATTTAGAGATAGAAACAACG
3692733 AACCATAAACATTACATTTAGGAGATAGAAACAACG
1 AACCATAAACATTACATTTA-GAGATAGAAACAACG
* * *
3692769 AACCATACACATTACATTAAGAAGATAAAAACAA
1 AACCATAAACATTACATTTAG-AGATAGAAACAA
3692803 TAAACTATTC
Statistics
Matches: 94, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
34 31 0.33
35 1 0.01
36 57 0.61
37 5 0.05
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (35 bp):
AACCATAAACATTACATTTAGAGATAGAAACAACG
Found at i:3692816 original size:70 final size:70
Alignment explanation
Indices: 3692668--3692800 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 70
3692658 ATTAAACCAT
* *
3692668 TAAACATTACATTTATGAGATAAAAACAACAAACCATAAACATTACATTTAAGATAGAAATAACG
1 TAAACATTACATTTAGGAGATAAAAACAACAAACCATAAACATTACATTTAAGATAGAAAAAACG
*
3692733 AACCA
66 AAACA
* * *
3692738 TAAACATTACATTTAGGAGATAGAAACAACGAACCATACACATTACA-TTAAGA-AGATAAAAAC
1 TAAACATTACATTTAGGAGATAAAAACAACAAACCATAAACATTACATTTAAGATAGA-AAAAAC
3692801 AATAAACTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
68 3 0.05
69 11 0.19
70 43 0.75
ACGTcount: A:0.53, C:0.16, G:0.09, T:0.22
Consensus pattern (70 bp):
TAAACATTACATTTAGGAGATAAAAACAACAAACCATAAACATTACATTTAAGATAGAAAAAACG
AAACA
Found at i:3700086 original size:70 final size:70
Alignment explanation
Indices: 3699993--3700126 Score: 180
Period size: 70 Copynumber: 1.9 Consensus size: 70
3699983 GTTCAATATC
* *
3699993 TAAAAGTATCGATCATTATCGCATAAATATCAATATTTTAAATTTCGATATTTTTATCAACTTTT
1 TAAAAGTATCGATCATTACCGCATAAATATCAATATTTTAAATTTCGATA-TTTCATCAACTTTT
3700058 AACTTT
65 AACTTT
* * ** * *
3700064 TAAAA-TATCTATCATTACCGCATAAGTATTGATATTTTAACTTTTGATATTTCATCAACTTTT
1 TAAAAGTATCGATCATTACCGCATAAATATCAATATTTTAAATTTCGATATTTCATCAACTTTT
3700127 TCAATATTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
69 13 0.24
70 37 0.67
71 5 0.09
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (70 bp):
TAAAAGTATCGATCATTACCGCATAAATATCAATATTTTAAATTTCGATATTTCATCAACTTTTA
ACTTT
Found at i:3700300 original size:57 final size:58
Alignment explanation
Indices: 3700231--3700347 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 58
3700221 ATTAACATAA
* * *
3700231 TAACATATCACAACCTA-TTTCTTTGTGAACCATGACATTCCTGGATGCAACCTATTT
1 TAACAGATCACAACCTACTTTCTTAGTGAACCATGACATTCCTGGACGCAACCTATTT
* * * * *
3700288 TAACAGATCACAATCTACTTTCTTAGTGAACCATTACATTCTTGGGCGTAACCTATTT
1 TAACAGATCACAACCTACTTTCTTAGTGAACCATGACATTCCTGGACGCAACCTATTT
3700346 TA
1 TA
3700348 TTAATAAGAA
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 15 0.29
58 36 0.71
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (58 bp):
TAACAGATCACAACCTACTTTCTTAGTGAACCATGACATTCCTGGACGCAACCTATTT
Found at i:3700691 original size:78 final size:78
Alignment explanation
Indices: 3700531--3700684 Score: 177
Period size: 78 Copynumber: 2.0 Consensus size: 78
3700521 AGGCGTAATA
* * * * * * * *
3700531 TATTTTATTATTAAAAATATTAAGATTCCATATTGCAACCTACTTTCTTAGTAAATCATTACATT
1 TATTTTATTAATAAAAATATTAAGATTACAGATCGCAACATACTTTCTTAATAAACCATGACATT
*
3700596 CTTGGACCCAACC
66 ATTGGACCCAACC
* *
3700609 TATTTTATTAATAAAAATATTGACG-TTACAGATCGCAACATA-TTTCTTAATGAACCATGACAT
1 TATTTTATTAATAAAAATATT-AAGATTACAGATCGCAACATACTTTCTTAATAAACCATGACAT
*
3700672 TATTGGACGCAAC
65 TATTGGACCCAAC
3700685 AGTATTTCTT
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
77 28 0.44
78 33 0.52
79 2 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (78 bp):
TATTTTATTAATAAAAATATTAAGATTACAGATCGCAACATACTTTCTTAATAAACCATGACATT
ATTGGACCCAACC
Found at i:3700701 original size:2 final size:2
Alignment explanation
Indices: 3700694--3700720 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3700684 CAGTATTTCT
3700694 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
3700721 CATAGCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3700769 original size:2 final size:2
Alignment explanation
Indices: 3700762--3700786 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3700752 TTTCGGTTCT
3700762 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
3700787 TCATAGCATT
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:3702641 original size:21 final size:20
Alignment explanation
Indices: 3702617--3702800 Score: 119
Period size: 21 Copynumber: 9.2 Consensus size: 20
3702607 CGTTGCGATT
3702617 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAA-GCGAAC
3702638 TTGGAAAATCGCAA-CGAAC
1 TTGGAAAATCGCAAGCGAAC
* ** * *
3702657 TTTGACTATCGTAA-CGAAT
1 TTGGAAAATCGCAAGCGAAC
3702676 TTGGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAA-GCGAAC
* **
3702697 TTCGACTATCGCAA-CGAA-
1 TTGGAAAATCGCAAGCGAAC
*
3702715 TTTGAAAATCGCAACGCGAAC
1 TTGGAAAATCGCAA-GCGAAC
* ** *
3702736 TTCGACTATCGCAACGTGAAC
1 TTGGAAAATCGCAA-GCGAAC
* ** *
3702757 TTCGATTATCGCAA-CGAAT
1 TTGGAAAATCGCAAGCGAAC
*
3702776 TTGAAAAATCGCAATGCGAA-
1 TTGGAAAATCGCAA-GCGAAC
3702796 TTGGA
1 TTGGA
3702801 CTATCGCAAA
Statistics
Matches: 128, Mismatches: 28, Indels: 15
0.75 0.16 0.09
Matches are distributed among these distances:
18 11 0.09
19 46 0.36
20 8 0.06
21 63 0.49
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGAAAATCGCAAGCGAAC
Found at i:3702733 original size:39 final size:40
Alignment explanation
Indices: 3702624--3702751 Score: 190
Period size: 39 Copynumber: 3.2 Consensus size: 40
3702614 ATTTTGGAAA
* *
3702624 ATCGCAACGCGAACTTGGAAAATCGCAA--CGAACTTTGACT
1 ATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
3702664 ATCGTAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
3702704 ATCGCAACGAATTT-GAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
3702743 ATCGCAACG
1 ATCGCAACG
3702752 TGAACTTCGA
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
38 18 0.22
39 34 0.41
40 30 0.37
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:3702757 original size:60 final size:60
Alignment explanation
Indices: 3702683--3702809 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
3702673 AATTTGGAAA
3702683 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTG-AAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACGCGAA-TTCGACT
* * * *
3702743 ATCGCAACGTGAACTTCGATTATCGCAACGAATTTGAAAAATCGCAATGCGAATTGGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACGCGAATTCGACT
3702803 ATCGCAA
1 ATCGCAA
3702810 AATCGCGTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
60 47 0.76
61 15 0.24
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (60 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGAAAAATCGCAACGCGAATTCGACT
Found at i:3720942 original size:121 final size:121
Alignment explanation
Indices: 3720728--3720972 Score: 427
Period size: 121 Copynumber: 2.0 Consensus size: 121
3720718 TCCATCCGAA
* *
3720728 ATTTTTCGCACCAACCCTGAAATCTAAATTTTCTTCAATTAATTACTTATTTTGCGGACTAATTC
1 ATTTTTCGAACCAACCCTAAAATCTAAATTTTCTTCAATTAATTACTTATTTTGCGGACTAATTC
3720793 CCTTCTGGTCCTTGTAACGATGTCCATGTAACACATTAAAAACCAATTTATTTCAT
66 CCTTCTGGTCCTTGTAACGATGTCCATGTAACACATTAAAAACCAATTTATTTCAT
* * *
3720849 ATTTTTCGAACCAACCCTAAAATCTAAGTTTTCTTCAATTAATTATTTATTTTGCGGATTAATTC
1 ATTTTTCGAACCAACCCTAAAATCTAAATTTTCTTCAATTAATTACTTATTTTGCGGACTAATTC
**
3720914 CCTTCTGGTCCTTGTAACGATGTCCATGTAACACATTCGAAACCAATTTATTTCAT
66 CCTTCTGGTCCTTGTAACGATGTCCATGTAACACATTAAAAACCAATTTATTTCAT
3720970 ATT
1 ATT
3720973 ACACATATAA
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 117 1.00
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (121 bp):
ATTTTTCGAACCAACCCTAAAATCTAAATTTTCTTCAATTAATTACTTATTTTGCGGACTAATTC
CCTTCTGGTCCTTGTAACGATGTCCATGTAACACATTAAAAACCAATTTATTTCAT
Found at i:3722065 original size:15 final size:15
Alignment explanation
Indices: 3722033--3722063 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3722023 TATTTTTAGA
3722033 TTATATAATTTTAAT
1 TTATATAATTTTAAT
3722048 TTATA-AATTTTAAT
1 TTATATAATTTTAAT
3722062 TT
1 TT
3722064 TAAGATATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATATAATTTTAAT
Found at i:3722108 original size:15 final size:15
Alignment explanation
Indices: 3722090--3722128 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3722080 AACCTTAAAG
*
3722090 TTTTAAATTTTATGT
1 TTTTAAATTTGATGT
* *
3722105 TTTTAAATGTGATTT
1 TTTTAAATTTGATGT
3722120 TTTTAAATT
1 TTTTAAATT
3722129 AATATAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (15 bp):
TTTTAAATTTGATGT
Found at i:3730745 original size:19 final size:19
Alignment explanation
Indices: 3730721--3730770 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3730711 AAAACGTTTT
3730721 TATGAATAGTATTATACTG
1 TATGAATAGTATTATACTG
*
3730740 TATGAATAGTATTATATTG
1 TATGAATAGTATTATACTG
*
3730759 TATGAACAGTAT
1 TATGAATAGTAT
3730771 CGTAAACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (19 bp):
TATGAATAGTATTATACTG
Found at i:3731522 original size:22 final size:22
Alignment explanation
Indices: 3731497--3731542 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3731487 GGCATATGAA
*
3731497 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
3731519 ATTTGTCCCGAAGGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
3731541 AT
1 AT
3731543 ACTGTATATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:3731861 original size:15 final size:16
Alignment explanation
Indices: 3731835--3731864 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3731825 TCATGACTTA
3731835 TTTCTCATTCTTATAT
1 TTTCTCATTCTTATAT
3731851 TTTCTCA-TCTTATA
1 TTTCTCATTCTTATA
3731865 ACTTATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTCTCATTCTTATAT
Found at i:3735557 original size:13 final size:13
Alignment explanation
Indices: 3735539--3735563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3735529 CCTAAAAAAA
3735539 TCAATAAAATAAT
1 TCAATAAAATAAT
3735552 TCAATAAAATAA
1 TCAATAAAATAA
3735564 ATATAATTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
TCAATAAAATAAT
Found at i:3740124 original size:16 final size:17
Alignment explanation
Indices: 3740094--3740131 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
3740084 AATAAATACT
3740094 AAATTTAGAAAAAAAAC
1 AAATTTAGAAAAAAAAC
3740111 AAATTTAG-AAAAAAAC
1 AAATTTAGAAAAAAAAC
3740127 AAATT
1 AAATT
3740132 ACAAAAGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATTTAGAAAAAAAAC
Found at i:3740137 original size:15 final size:16
Alignment explanation
Indices: 3740103--3740137 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3740093 TAAATTTAGA
*
3740103 AAAAAAACAAATTTAG
1 AAAAAAACAAATTTAC
3740119 AAAAAAACAAA-TTAC
1 AAAAAAACAAATTTAC
3740134 AAAA
1 AAAA
3740138 GGATTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAAAACAAATTTAC
Found at i:3741424 original size:2 final size:2
Alignment explanation
Indices: 3741419--3741443 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3741409 TTTAAAAAAC
3741419 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
3741444 CTTTTCAAAA
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:3741473 original size:53 final size:48
Alignment explanation
Indices: 3741379--3741483 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 48
3741369 TTCAAAGATC
* **
3741379 ATATATATTATATATGTTTTCAAAAATCATTTTAAAAAACTATATATAT
1 ATATATATTATATATCTTTTCAAAAAAAATTTTAAAAAACTATAT-TAT
*
3741428 ATATATATATATATATCTTTTCAAAATAAAATGTTTTCAAAAACTATATTAT
1 ATATATAT-TATATATCTTTTCAAAA-AAAA--TTTTAAAAAACTATATTAT
3741480 ATAT
1 ATAT
3741484 GTTTTCAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
49 8 0.17
50 16 0.33
51 2 0.04
52 7 0.15
53 15 0.31
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.45
Consensus pattern (48 bp):
ATATATATTATATATCTTTTCAAAAAAAATTTTAAAAAACTATATTAT
Found at i:3741509 original size:39 final size:38
Alignment explanation
Indices: 3741431--3741569 Score: 158
Period size: 39 Copynumber: 3.6 Consensus size: 38
3741421 TATATATATA
*
3741431 TATATATATATATCTTTTCAAAATAAAATGTTTTCAAAAAC
1 TATAT-TATATATGTTTTCAAAA-AAAA-GTTTTCAAAAAC
* *
3741472 TATATTATATATGTTTTCAAAAAAACAATTTTAAAAAAC
1 TATATTATATATGTTTTCAAAAAAA-AGTTTTCAAAAAC
* *
3741511 TATA-TATTATATGTTTTCAAAAATATGTTTTCAAAAAC
1 TATATTA-TATATGTTTTCAAAAAAAAGTTTTCAAAAAC
*
3741549 TATACTATATA--TTTTCAAAAA
1 TATATTATATATGTTTTCAAAAA
3741570 CTATATATTA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
36 10 0.11
38 20 0.23
39 36 0.41
40 17 0.19
41 5 0.06
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.42
Consensus pattern (38 bp):
TATATTATATATGTTTTCAAAAAAAAGTTTTCAAAAAC
Found at i:3741538 original size:14 final size:14
Alignment explanation
Indices: 3741519--3741547 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3741509 ACTATATATT
3741519 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
3741533 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
3741547 A
1 A
3741548 CTATACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:3741587 original size:24 final size:22
Alignment explanation
Indices: 3741533--3741582 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
3741523 GTTTTCAAAA
*
3741533 ATATGTTTTCAAAAACTATACT
1 ATATATTTTCAAAAACTATACT
3741555 ATATATTTTCAAAAACTATA-T
1 ATATATTTTCAAAAACTATACT
3741576 ATTATAT
1 A-TATAT
3741583 ATTTTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATATTTTCAAAAACTATACT
Found at i:3741607 original size:2 final size:2
Alignment explanation
Indices: 3741600--3741640 Score: 57
Period size: 2 Copynumber: 20.0 Consensus size: 2
3741590 AAATTATTAT
3741600 TA TA TA TA TA TA TA TA TA TA TA T- TA TCA TA TA TA CTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA
3741641 ATGTAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 1 0.03
2 31 0.86
3 4 0.11
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3745849 original size:9 final size:8
Alignment explanation
Indices: 3745835--3746184 Score: 104
Period size: 8 Copynumber: 40.6 Consensus size: 8
3745825 GTGTTAGATA
3745835 AAAAAAAGT
1 AAAAAAA-T
3745844 AAAAAAAT
1 AAAAAAAT
3745852 AAAGAAAAT
1 AAA-AAAAT
3745861 --AAAAAT
1 AAAAAAAT
3745867 AAAATAAATT
1 AAAA-AAA-T
*
3745877 AAATAAAT
1 AAAAAAAT
*
3745885 AAATAAAT
1 AAAAAAAT
*
3745893 AAATAAAT
1 AAAAAAAT
3745901 AAATAAAAT
1 AAA-AAAAT
3745910 ---AAAAT
1 AAAAAAAT
*
3745915 AAAGAAGAT
1 AAA-AAAAT
3745924 AAAATAAGAT
1 AAAA-AA-AT
**
3745934 AAAGAACGT
1 AAA-AAAAT
**
3745943 AAAAGGAT
1 AAAAAAAT
3745951 AAAGAAAACAT
1 -AA-AAAA-AT
* *
3745962 AAAGAGAT
1 AAAAAAAT
3745970 AAAGTAAAGAT
1 AAA--AAA-AT
**
3745981 -AAAAGGT
1 AAAAAAAT
3745988 AAATAAAAT
1 AAA-AAAAT
*
3745997 AAAGATAAAG
1 AAA-A-AAAT
3746007 AAAAAAA-
1 AAAAAAAT
3746014 ATAAAAAAT
1 A-AAAAAAT
3746023 -AAAAAAT
1 AAAAAAAT
3746030 AAAATAAAT
1 AAAA-AAAT
*
3746039 AAATAAAT
1 AAAAAAAT
*
3746047 AAATAATAGT
1 AAA-AA-AAT
3746057 AAAAATAAT
1 AAAAA-AAT
*
3746066 ATATATATAAT
1 A-A-A-AAAAT
*
3746077 AAATAAAT
1 AAAAAAAT
*
3746085 AAATAAAT
1 AAAAAAAT
* *
3746093 AGAAACAAG
1 A-AAAAAAT
*
3746102 AAAATAAT
1 AAAAAAAT
*
3746110 AAAATAAT
1 AAAAAAAT
3746118 AAAATAAAT
1 AAAA-AAAT
3746127 ACAAAGAAAAT
1 --AAA-AAAAT
*
3746138 AAAATAAT
1 AAAAAAAT
3746146 AAAAATAAT
1 AAAAA-AAT
** *
3746155 AAAAGTAG
1 AAAAAAAT
3746163 AAAAAAAT
1 AAAAAAAT
*
3746171 AATAGAAAT
1 AA-AAAAAT
3746180 AAAAA
1 AAAAA
3746185 TTATAGGGGA
Statistics
Matches: 259, Mismatches: 44, Indels: 77
0.68 0.12 0.20
Matches are distributed among these distances:
5 5 0.02
6 5 0.02
7 10 0.04
8 104 0.40
9 86 0.33
10 30 0.12
11 17 0.07
12 2 0.01
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3745883 original size:4 final size:4
Alignment explanation
Indices: 3745863--3746093 Score: 107
Period size: 4 Copynumber: 54.2 Consensus size: 4
3745853 AAGAAAATAA
3745863 AAAT AAAAT AAATT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAAAT
1 AAAT -AAAT AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT
* * * * * *
3745915 AAAG AAGAT AAAAT AAGAT AAAG AACGT AAA- AGGAT AAAG AAA- ACAT
1 AAAT AA-AT -AAAT AA-AT AAAT AA-AT AAAT A-AAT AAAT AAAT AAAT
* * ** * *
3745962 AAAG AGAT AAAGT AAAGAT AAA- AGGT AAAT AAAAT AAAGAT AAAGA AAAA
1 AAAT AAAT AAA-T -AA-AT AAAT AAAT AAAT -AAAT -AA-AT AAA-T AAAT
3746012 AAAT AAA- AAAT AAA- AAAT AAAAT AAAT AAAT AAAT AAAT -AAT AGTAA-
1 AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT AAAT A--AAT
*
3746059 AAAT AATAT ATAT ATAAT AAAT AAAT AAAT AAAT A
1 AAAT AA-AT AAAT A-AAT AAAT AAAT AAAT AAAT A
3746094 GAAACAAGAA
Statistics
Matches: 178, Mismatches: 23, Indels: 51
0.71 0.09 0.20
Matches are distributed among these distances:
3 15 0.08
4 100 0.56
5 53 0.30
6 9 0.05
7 1 0.01
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:3745905 original size:38 final size:37
Alignment explanation
Indices: 3745833--3746157 Score: 151
Period size: 38 Copynumber: 8.6 Consensus size: 37
3745823 ACGTGTTAGA
* *
3745833 TAAAAAAAAGTAAAA-AAATAAAGAAAATAAA-AATAAAA
1 TAAAATAAA-TAAAATAAATAAA-TAAATAAATAA-AAAA
*
3745871 TAAATTAAAT-AAATAAATAAATAAATAAATAAATAAAA
1 TAAAATAAATAAAATAAATAAATAAATAAAT-AA-AAAA
* * * * *
3745909 TAAAATAAAGAAGATAAAATAAGATAAAGAACGTAAAAGGA
1 TAAAATAAATAAAAT-AAATAA-ATAAATAA-ATAAAA-AA
* * * **
3745950 TAAAGA-AAACATAAAGAGATAAAGTAAAGATAAA-AGGTAAA
1 TAAA-ATAAATA-AAATAAATAAA-T-AA-ATAAATA-AAAAA
*
3745991 TAAAATAAAGATAAAGA-AAAAAAATAAA-AAATAAAAAA
1 TAAAAT-AA-ATAAA-ATAAATAAATAAATAAATAAAAAA
*
3746029 TAAAATAAAT-AAATAAATAAAT-AAT-AGT-AAAAA
1 TAAAATAAATAAAATAAATAAATAAATAAATAAAAAA
* * *
3746062 TAATATATATATAATAAATAAATAAATAAATAGAAACAA
1 TAAAATAAATAAAATAAATAAATAAATAAATA-AAA-AA
* *
3746101 GAAAAT-AATAAAAT-AATAAAATAAATACAA-AGAAAA
1 TAAAATAAATAAAATAAAT-AAATAAATA-AATAAAAAA
3746137 TAAAAT-AATAAAA-ATAATAAA
1 TAAAATAAATAAAATA-AATAAA
3746158 AGTAGAAAAA
Statistics
Matches: 221, Mismatches: 35, Indels: 64
0.69 0.11 0.20
Matches are distributed among these distances:
33 13 0.06
34 16 0.07
35 12 0.05
36 31 0.14
37 18 0.08
38 53 0.24
39 13 0.06
40 12 0.05
41 31 0.14
42 16 0.07
43 6 0.03
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (37 bp):
TAAAATAAATAAAATAAATAAATAAATAAATAAAAAA
Found at i:3745946 original size:19 final size:19
Alignment explanation
Indices: 3745830--3745939 Score: 74
Period size: 18 Copynumber: 6.1 Consensus size: 19
3745820 GAAACGTGTT
3745830 AGATAAAA-AAAAGTAAA-A
1 AGATAAAATAAAA-TAAAGA
* *
3745848 AAAT-AAAGAAAAT-AA-A
1 AGATAAAATAAAATAAAGA
* *
3745864 A-ATAAAATAAATTAAATA
1 AGATAAAATAAAATAAAGA
* *
3745882 A-ATAAATAAATAAATAAATA
1 AGATAAA-ATA-AAATAAAGA
3745902 A-ATAAAATAAAATAAAGA
1 AGATAAAATAAAATAAAGA
*
3745920 AGATAAAATAAGATAAAGA
1 AGATAAAATAAAATAAAGA
3745939 A
1 A
3745940 CGTAAAAGGA
Statistics
Matches: 77, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
15 2 0.03
16 11 0.14
17 6 0.08
18 23 0.30
19 21 0.27
20 14 0.18
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.18
Consensus pattern (19 bp):
AGATAAAATAAAATAAAGA
Found at i:3746016 original size:19 final size:19
Alignment explanation
Indices: 3745839--3746037 Score: 61
Period size: 19 Copynumber: 9.8 Consensus size: 19
3745829 TAGATAAAAA
*
3745839 AAAGTAAAAAAATAAAGA-
1 AAAGAAAAAAAATAAAGAT
* *
3745857 AAATAAAAATAAAATAAA-TT
1 AAA-GAAAA-AAAATAAAGAT
*
3745877 AAATAAATAAATAA-ATAA-AT
1 AAAGAAA-AAA-AATA-AAGAT
* *
3745897 AAATAAATAAAATAAA-AT
1 AAAGAAAAAAAATAAAGAT
*
3745915 AAAGAAGATAAAAT-AAGAT
1 AAAGAA-AAAAAATAAAGAT
* *
3745934 AAAGAACGTAAAAGGATAAAGAA
1 AAAGAA---AAAA-AATAAAGAT
*
3745957 AACATAAAGAGATAAAGTAAAGAT
1 AA-AGAAA-A-A-AAA-TAAAGAT
*
3745981 AAAAGGTAAATAAAATAAAGAT
1 -AAA-G-AAAAAAAATAAAGAT
*
3746003 AAAGAAAAAAAATAAAAAAT
1 AAAGAAAAAAAAT-AAAGAT
*
3746023 AAA-AAATAAAATAAA
1 AAAGAAAAAAAATAAA
3746038 TAAATAAATA
Statistics
Matches: 140, Mismatches: 19, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
18 19 0.14
19 43 0.31
20 33 0.24
21 7 0.05
22 10 0.07
23 11 0.08
24 12 0.09
25 2 0.01
26 3 0.02
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.17
Consensus pattern (19 bp):
AAAGAAAAAAAATAAAGAT
Found at i:3746054 original size:19 final size:19
Alignment explanation
Indices: 3745863--3746093 Score: 90
Period size: 19 Copynumber: 11.7 Consensus size: 19
3745853 AAGAAAATAA
3745863 AAATAAAATAAAT--TAAAT
1 AAAT-AAATAAATAATAAAT
3745881 AAATAAATAAATAAATAAAT
1 AAATAAATAAAT-AATAAAT
*
3745901 AAATAAAATAAAATAAAGAAGAT
1 AAAT-AAAT-AAAT-AATAA-AT
*
3745924 AAAATAAGATAAAGAACGTAAA-
1 -AAATAA-ATAAATAA--TAAAT
* * *
3745946 AGGATAAAGAAA-ACATAAAG
1 A-AATAAATAAATA-ATAAAT
* *
3745966 AGATAAAGTAAA-GATAAA-
1 AAATAAA-TAAATAATAAAT
** *
3745984 AGGTAAATAAAATAA-AGAT
1 AAATAAAT-AAATAATAAAT
*
3746003 AAAGAAA-AAA-AATAAA-
1 AAATAAATAAATAATAAAT
3746019 AAATAAA-AAATAAAATAAAT
1 AAATAAATAAAT--AATAAAT
3746039 AAATAAATAAATAATAGTAA-
1 AAATAAATAAATAATA--AAT
3746059 AAATAATATATATATAATAAAT
1 AAATAA-ATA-A-ATAATAAAT
3746081 AAATAAATAAATA
1 AAATAAATAAATA
3746094 GAAACAAGAA
Statistics
Matches: 169, Mismatches: 15, Indels: 57
0.70 0.06 0.24
Matches are distributed among these distances:
16 11 0.07
17 14 0.08
18 15 0.09
19 33 0.20
20 28 0.17
21 24 0.14
22 22 0.13
23 14 0.08
24 8 0.05
ACGTcount: A:0.71, C:0.01, G:0.07, T:0.20
Consensus pattern (19 bp):
AAATAAATAAATAATAAAT
Found at i:3746203 original size:6 final size:5
Alignment explanation
Indices: 3745847--3746172 Score: 73
Period size: 5 Copynumber: 67.4 Consensus size: 5
3745837 AAAAAGTAAA
* *
3745847 AAAAT -AAAG AAAAT AAAAAT AAAAT -AAAT TAAAT -AAAT -AAAT -AAAT
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * *
3745893 -AAAT -AAAT -AAAT AAAAT AAAAT -AAAG AAGAT AAAAT AAGAT -AAAG
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
** * * * * * *
3745938 AACGT AAAAGG ATAAAG AAAAC ATAAA- GAGAT AAAGT AAAGAT AAAAGGT
1 AAAAT AAAA-T A-AAAT AAAAT A-AAAT AAAAT AAAAT AAA-AT AAAA--T
*
3745988 -AAAT AAAAT AAAGAT -AAAG AAAA- AAAAT AAAA- AATAA- AAAAT AAAAT
1 AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT
* * * *
3746035 -AAAT -AAAT -AAAT -AAAT AATAGT AAAA- ATAAT ATATAT ATAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT A-AAAT AAAAT AAAAT
*
3746081 -AAAT -AAAT -AAAT AGAAAC AAGAA- AATAAT AAAAT --AAT AAAAT
1 AAAAT AAAAT AAAAT A-AAAT AA-AAT AA-AAT AAAAT AAAAT AAAAT
* *
3746123 -AAAT ACAAAG AAAAT AAAAT AATAAA AATAAT AAAAGT AGAAA- AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AA-AAT AA-AAT AAAA-T A-AAAT AAAAT
3746171 AA
1 AA
3746173 TAGAAATAAA
Statistics
Matches: 249, Mismatches: 37, Indels: 70
0.70 0.10 0.20
Matches are distributed among these distances:
3 3 0.01
4 89 0.36
5 100 0.40
6 50 0.20
7 7 0.03
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:3749256 original size:20 final size:20
Alignment explanation
Indices: 3749231--3749270 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3749221 GTATTGGAAT
3749231 TTGTTCCTTTCAAGTTAAAA
1 TTGTTCCTTTCAAGTTAAAA
*
3749251 TTGTTCCTTTCGAGTTAAAA
1 TTGTTCCTTTCAAGTTAAAA
3749271 CTGCTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (20 bp):
TTGTTCCTTTCAAGTTAAAA
Found at i:3749786 original size:63 final size:63
Alignment explanation
Indices: 3749680--3749833 Score: 254
Period size: 63 Copynumber: 2.4 Consensus size: 63
3749670 CATAACAAGT
3749680 TACTCTTTGTAGGTATTGACCACTGAGAATCTATCTACCGTATCACTTACGTGTTTGTGGTGG
1 TACTCTTTGTAGGTATTGACCACTGAGAATCTATCTACCGTATCACTTACGTGTTTGTGGTGG
* * *** *
3749743 TACTCTTTGTAGGCATTGACCACTGAGAATCTGTCTGTTGTATCACTTAGGTGTTTGTGGTGG
1 TACTCTTTGTAGGTATTGACCACTGAGAATCTATCTACCGTATCACTTACGTGTTTGTGGTGG
3749806 TACTCTTTGTAGGTATTGACCACTGAGA
1 TACTCTTTGTAGGTATTGACCACTGAGA
3749834 TAGGTGTTTG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (63 bp):
TACTCTTTGTAGGTATTGACCACTGAGAATCTATCTACCGTATCACTTACGTGTTTGTGGTGG
Found at i:3755935 original size:22 final size:22
Alignment explanation
Indices: 3755910--3755963 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
3755900 ACCTTGAATG
* *
3755910 CTGAACGGTTCAACATTCAGCA
1 CTGAATGGTTCAACATTCAACA
3755932 CTGAATGGTTCAACATTCAACA
1 CTGAATGGTTCAACATTCAACA
3755954 CTGAATGGTT
1 CTGAATGGTT
3755964 TCATTCAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (22 bp):
CTGAATGGTTCAACATTCAACA
Found at i:3755970 original size:20 final size:21
Alignment explanation
Indices: 3755910--3755973 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
3755900 ACCTTGAATG
* *
3755910 CTGAACGGTTCAACATTCAGCA
1 CTGAATGGTT-AACATTCAACA
3755932 CTGAATGGTTCAACATTCAACA
1 CTGAATGGTT-AACATTCAACA
*
3755954 CTGAATGGTT-TCATTCAACA
1 CTGAATGGTTAACATTCAACA
3755974 GTAAACAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
20 9 0.23
22 30 0.77
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (21 bp):
CTGAATGGTTAACATTCAACA
Found at i:3757731 original size:24 final size:25
Alignment explanation
Indices: 3757678--3757731 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
3757668 TTTTTAAAAG
* *
3757678 TTTAATTTAATAGTTATCTAACATT
1 TTTAATTTAATAATTATATAACATT
*
3757703 ATTAATTT-ATAATTATAATAA-ATT
1 TTTAATTTAATAATTAT-ATAACATT
3757727 TTTAA
1 TTTAA
3757732 GAAAAATGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAATTTAATAATTATATAACATT
Found at i:3763234 original size:45 final size:44
Alignment explanation
Indices: 3763088--3763238 Score: 180
Period size: 45 Copynumber: 3.4 Consensus size: 44
3763078 AGGATTACTT
* *
3763088 GGTTGTGGAAATTAAAATCAAATGATTAGTTCTTTTCAATTATTG
1 GGTTGTGAAAATTAAAATCAAAAGATTAGTTC-TTTCAATTATTG
* *
3763133 GGTTCTGAAAATTAGAATCAAAAGATTAGTTGCTTTCAATTATTG
1 GGTTGTGAAAATTAAAATCAAAAGATTAGTT-CTTTCAATTATTG
* * *
3763178 GATTGTGAAAATTAAAATAAAAAGATTAGTTCATTGT-GATTATTG
1 GGTTGTGAAAATTAAAATCAAAAGATTAGTTC-TT-TCAATTATTG
3763223 GGTTG-GTAAAATTAAA
1 GGTTGTG-AAAATTAAA
3763239 GGATTAATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
44 2 0.02
45 88 0.96
46 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (44 bp):
GGTTGTGAAAATTAAAATCAAAAGATTAGTTCTTTCAATTATTG
Found at i:3763516 original size:18 final size:18
Alignment explanation
Indices: 3763493--3763539 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
3763483 AAAAAGAAAT
*
3763493 AGGAGAAGGAGAATAAGA
1 AGGAGAAGGAGAAGAAGA
* *
3763511 AGGAGAAGAAGCAGAAGA
1 AGGAGAAGGAGAAGAAGA
*
3763529 AGGAGGAGGAG
1 AGGAGAAGGAG
3763540 GTAATTGTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02
Consensus pattern (18 bp):
AGGAGAAGGAGAAGAAGA
Found at i:3766938 original size:15 final size:16
Alignment explanation
Indices: 3766918--3766951 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3766908 TGAGACCTTA
3766918 CCCGCCCC-ACATCCG
1 CCCGCCCCTACATCCG
3766933 CCCGCCCCTACATCCG
1 CCCGCCCCTACATCCG
3766949 CCC
1 CCC
3766952 ACCCACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.12, C:0.68, G:0.12, T:0.09
Consensus pattern (16 bp):
CCCGCCCCTACATCCG
Found at i:3778349 original size:20 final size:20
Alignment explanation
Indices: 3778326--3778373 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
3778316 AAGAATAGGA
3778326 GAAGAAAGAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
*
3778346 GAAGAAATAAGAGAAAAGAG
1 GAAGAAAGAAGAGAAAAGAG
*
3778366 AAAGAAAG
1 GAAGAAAG
3778374 GAGAAGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (20 bp):
GAAGAAAGAAGAGAAAAGAG
Found at i:3778370 original size:13 final size:14
Alignment explanation
Indices: 3778324--3778386 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 14
3778314 AAAAGAATAG
3778324 GAGAAGAA-AG-AA
1 GAGAAGAAGAGAAA
*
3778336 GAGAA-AAGAGGAA
1 GAGAAGAAGAGAAA
*
3778349 GA-AATAAGAGAAA
1 GAGAAGAAGAGAAA
3778362 -AG-AGAA-AGAAA
1 GAGAAGAAGAGAAA
3778373 GGAGAAGAAGAGAA
1 -GAGAAGAAGAGAA
3778387 TATCGGTTCG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
11 7 0.17
12 13 0.32
13 13 0.32
14 4 0.10
15 4 0.10
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (14 bp):
GAGAAGAAGAGAAA
Found at i:3779735 original size:918 final size:918
Alignment explanation
Indices: 3778339--3780070 Score: 2952
Period size: 918 Copynumber: 1.9 Consensus size: 918
3778329 GAAAGAAGAG
* **
3778339 AAAAGAGGAAGAAATAAGAGAAAAGAGAAAGAAAGGAGAAGAAGAGAATATCGGTTCGTGCTACA
1 AAAAGAGGAAGAAAGAAGAGAAAAGAGAAAGAAAGGAGAAGAAGAGAATAAAGGTTCGTGCTACA
* *
3778404 TTCTTCGACAAATTTATATGAAATTAGTTTAATAGTTTGTTAATTTTTTGAAAGAACGAAGGTGA
66 TTATTCGACAAACTTATATGAAATTAGTTTAATAGTTTGTTAATTTTTTGAAAGAACGAAGGTGA
3778469 ACTAAGCTTGAAGAAATTTTATTTAAGGTATTTTATAATTATTTTTATAAATATTTGTTAATGTT
131 ACTAAGCTTGAAGAAATTTTATTTAAGGTATTTTATAATTATTTTTATAAATATTTGTTAATGTT
*
3778534 ACGATAGTTGTTATGTTTATTTTTATATTGTTGCTATATATATTATATTTTATCTATTATAAATA
196 ACGATAGTTGTTATGTTTATTTTTATATTGTTGCTATATATATTATATTTTATCTATTACAAATA
* *
3778599 CAAATTTTGATGTTGTAGAGAAAATGAGCAACAACTTTTTCACGATTGTCCACTATAATGTATAT
261 CAAATTTTGATGTTGTAGAGAAAATGAGCAACAACTTTTTCACGATTGTCCACTACAATGTACAT
**
3778664 ATTATGGAAAATGAGGTCGGAGTTGTTTTCCAGCCTGAAAGACCTATAAATATGATGTTCAAAAG
326 ATTATGGAAAATGAGGTCAAAGTTGTTTTCCAGCCTGAAAGACCTATAAATATGATGTTCAAAAG
* *
3778729 GGACATCACATTTATAGAAATGAAGCAGATGATAGAAAGAAAAATCTGAGCTGCAATTGATGGTT
391 GGACATCACATTTATAGAAATGAAGCAGAGGACAGAAAGAAAAATCTGAGCTGCAATTGATGGTT
* * *
3778794 TGAAGTACATGTTCATGGTATGTCCCAATCCAGTTAGATATGTTGCAATACTAGTTGAAGAAGAA
456 TGAAGTACAGGTTCATAGTATGTCCCAATCCAGTTAGATATGTTGCAATACCAGTTGAAGAAGAA
*
3778859 GATGATATTGGAACCATGATTGGATTACATGAGTCAACAAATATTTCAGTTATTGAGTTATTTGT
521 GATAATATTGGAACCATGATTGGATTACATGAGTCAACAAATATTTCAGTTATTGAGTTATTTGT
* *
3778924 TGATGTGCGTAACATATCTGATGTTCCT-GATCATCAAGAAATGTGGCTGGAAATTCATCTGAAA
586 TGATGTGCGTAACATATCTGATGCTCCTGGATCATCAAGAAATGTGGCTGAAAATTCATCTGAAA
* * *
3778988 TGGCTTTCGGAAGTGAATTTGAGAACCTGACATACAGATCGATAAACAATTTTATGGCACTATTG
651 TAGCTTTCAGAAGTGAATTTGAGAACCTGACATACAGATAGATAAACAATTTTATGGCACTATTG
* *
3779053 GAAAGTGGAAATGAAGTC-GTAGGAACATCCGCACTAGCAGAGTACAAGGAGAGAAACATATATA
716 GAAAGTGGAAATGAAGTCGGT-GGAACATCCACACTAGAAGAGTACAAGGAGAGAAACATATATA
3779117 ACTCGAAATTGACTGTTGATGTTGATGTTGAAAATCGACGAGGACGGATGGTTGGGGGTTGTGGT
780 ACTCGAAATTGACTGTTGATGTTGATGTTGAAAATCGACGAGGACGGATGGTTGGGGGTTGTGGT
3779182 TGGAGGATTGGGGTTGGTTTTTAAATATAAATATGAGGTGTAGGGAGGGAGAGGATTACACCGGG
845 TGGAGGATTGGGGTTGGTTTTTAAATATAAATATGAGGTGTAGGGAGGGAGAGGATTACACCGGG
3779247 AATGAAAAA
910 AATGAAAAA
* *
3779256 AAAAGAGGAGAAGAAAGAAGAG-AAA-AGATAGAAAGGAGAATAAGAGAATAAAGGTTCGTGCTA
1 AAAAGA-G-GAAGAAAGAAGAGAAAAGAGAAAGAAAGGAGAAGAAGAGAATAAAGGTTCGTGCTA
* *
3779319 CATTATTCGACAAACTTATATGAAATTAGTTTAATAGTTTGTTAATTTTTTTGGAAGAATGAAGG
64 CATTATTCGACAAACTTATATGAAATTAGTTTAATAGTTTGTTAA-TTTTTTGAAAGAACGAAGG
*
3779384 TGAACTAAGTTTGAAGAAATTTTATTTAAGGTATTTTATAATTATTTTTATAAATATTTGTTAAT
128 TGAACTAAGCTTGAAGAAATTTTATTTAAGGTATTTTATAATTATTTTTATAAATATTTGTTAAT
*
3779449 GTTACGATTGTTGTTATGTTTATTTTTATATTGTTGCTATATATATTATATTTTATCTATTACAA
193 GTTACGATAGTTGTTATGTTTATTTTTATATTGTTGCTATATATATTATATTTTATCTATTACAA
3779514 ATACAAATTTTGATGTTGTAGAGAAAATGAGCAACAACCTTTTT-ACGATTGTCCACTACAATGT
258 ATACAAATTTTGATGTTGTAGAGAAAATGAGCAACAA-CTTTTTCACGATTGTCCACTACAATGT
* *
3779578 ACATATTATGGAAAATGAGGTCAAAGTTGTTTTTCAGTCTGAAAGACCTATAAATATGATGTTCA
322 ACATATTATGGAAAATGAGGTCAAAGTTGTTTTCCAGCCTGAAAGACCTATAAATATGATGTTCA
* *
3779643 AAAGGGACATCACATTTGTAGAAATGAAGCAGAGGACAGAAAGAAAAATTTGAGCTGCAATTGAT
387 AAAGGGACATCACATTTATAGAAATGAAGCAGAGGACAGAAAGAAAAATCTGAGCTGCAATTGAT
* *
3779708 GGTTTGAAGTACAGGTTCATAGTATGTCCCAATTCAGTTAGATATGTTGCAGTACCAGTTGAAGA
452 GGTTTGAAGTACAGGTTCATAGTATGTCCCAATCCAGTTAGATATGTTGCAATACCAGTTGAAGA
* * *
3779773 ATATGATAATATTGTAACCATGATTGGATTACATGAGTCAACAAATATTTCAGTTATTGAGTTAT
517 AGAAGATAATATTGGAACCATGATTGGATTACATGAGTCAACAAATATTTCAGTTATTGAGTTAT
* *
3779838 TTGTTGATGTGCGTAACATATTTGATGCTCCTGGGTCATCAAGAAATGTGGCTGAAAATTCATCT
582 TTGTTGATGTGCGTAACATATCTGATGCTCCTGGATCATCAAGAAATGTGGCTGAAAATTCATCT
* * * * *
3779903 GAAATAGCTTTCAGAAGTGAGTTTGAGGACTTGATATATAGATAGATAAACAATTTTATGGCACT
647 GAAATAGCTTTCAGAAGTGAATTTGAGAACCTGACATACAGATAGATAAACAATTTTATGGCACT
* *
3779968 ATTGGAAAGTGGAAATGAAGTCGGTGGAACATCTACACTAGAAGAGTACGAGGAGAGAAACATAT
712 ATTGGAAAGTGGAAATGAAGTCGGTGGAACATCCACACTAGAAGAGTACAAGGAGAGAAACATAT
*
3780033 ATAACTCGGAATTGACTGTTGATGTTGATGTTGAAAAT
777 ATAACTCGAAATTGACTGTTGATGTTGATGTTGAAAAT
3780071 TGATGGGGAG
Statistics
Matches: 761, Mismatches: 48, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
917 83 0.11
918 476 0.63
919 200 0.26
920 2 0.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (918 bp):
AAAAGAGGAAGAAAGAAGAGAAAAGAGAAAGAAAGGAGAAGAAGAGAATAAAGGTTCGTGCTACA
TTATTCGACAAACTTATATGAAATTAGTTTAATAGTTTGTTAATTTTTTGAAAGAACGAAGGTGA
ACTAAGCTTGAAGAAATTTTATTTAAGGTATTTTATAATTATTTTTATAAATATTTGTTAATGTT
ACGATAGTTGTTATGTTTATTTTTATATTGTTGCTATATATATTATATTTTATCTATTACAAATA
CAAATTTTGATGTTGTAGAGAAAATGAGCAACAACTTTTTCACGATTGTCCACTACAATGTACAT
ATTATGGAAAATGAGGTCAAAGTTGTTTTCCAGCCTGAAAGACCTATAAATATGATGTTCAAAAG
GGACATCACATTTATAGAAATGAAGCAGAGGACAGAAAGAAAAATCTGAGCTGCAATTGATGGTT
TGAAGTACAGGTTCATAGTATGTCCCAATCCAGTTAGATATGTTGCAATACCAGTTGAAGAAGAA
GATAATATTGGAACCATGATTGGATTACATGAGTCAACAAATATTTCAGTTATTGAGTTATTTGT
TGATGTGCGTAACATATCTGATGCTCCTGGATCATCAAGAAATGTGGCTGAAAATTCATCTGAAA
TAGCTTTCAGAAGTGAATTTGAGAACCTGACATACAGATAGATAAACAATTTTATGGCACTATTG
GAAAGTGGAAATGAAGTCGGTGGAACATCCACACTAGAAGAGTACAAGGAGAGAAACATATATAA
CTCGAAATTGACTGTTGATGTTGATGTTGAAAATCGACGAGGACGGATGGTTGGGGGTTGTGGTT
GGAGGATTGGGGTTGGTTTTTAAATATAAATATGAGGTGTAGGGAGGGAGAGGATTACACCGGGA
ATGAAAAA
Found at i:3781136 original size:20 final size:20
Alignment explanation
Indices: 3781103--3781141 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3781093 CTTCTTCTCC
* *
3781103 TTTCTTTCTATTTTTTCTTA
1 TTTCTTCCTATTTTCTCTTA
*
3781123 TTTCTTCCTCTTTTCTCTT
1 TTTCTTCCTATTTTCTCTT
3781142 TTTTTTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCTTCCTATTTTCTCTTA
Found at i:3781579 original size:29 final size:29
Alignment explanation
Indices: 3781547--3781608 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
3781537 TTATTTCACA
* *
3781547 AAATAA-TTTGTCGACTGCATTATTCGAG
1 AAATAATTTTGTCCACTACATTATTCGAG
*
3781575 TAAATAATTTTTTCCACTACATTATTCGAG
1 -AAATAATTTTGTCCACTACATTATTCGAG
3781605 AAAT
1 AAAT
3781609 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (29 bp):
AAATAATTTTGTCCACTACATTATTCGAG
Found at i:3782656 original size:15 final size:15
Alignment explanation
Indices: 3782636--3782669 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3782626 TTTAGCTGGG
3782636 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
*
3782651 CGGGCGGATGCGGGG
1 CGGGCGGATGCGGGA
3782666 CGGG
1 CGGG
3782670 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.09, C:0.21, G:0.65, T:0.06
Consensus pattern (15 bp):
CGGGCGGATGCGGGA
Found at i:3785476 original size:34 final size:37
Alignment explanation
Indices: 3785429--3785500 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 37
3785419 TATTAAACAT
3785429 TTTTATAATTTTAA-TTTTGTAAA-AAAA-ATATAAA
1 TTTTATAATTTTAATTTTTGTAAAGAAAATATATAAA
*
3785463 TTTTATGAA-TTTAATTTTTTTAAAGAAAATATATAAA
1 TTTTAT-AATTTTAATTTTTGTAAAGAAAATATATAAA
3785500 T
1 T
3785501 ATTTTTTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 11 0.33
35 10 0.30
36 4 0.12
37 8 0.24
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTATAATTTTAATTTTTGTAAAGAAAATATATAAA
Found at i:3787824 original size:17 final size:17
Alignment explanation
Indices: 3787785--3787824 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3787775 AAATGATCAA
*
3787785 ATTAAATTAATATTAAT
1 ATTAAATTAATATGAAT
3787802 ATTAAATTAATA-GAAT
1 ATTAAATTAATATGAAT
3787818 ATATAAA
1 AT-TAAA
3787825 CAATAAAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATTAAATTAATATGAAT
Found at i:3788089 original size:15 final size:15
Alignment explanation
Indices: 3788071--3788126 Score: 55
Period size: 15 Copynumber: 3.8 Consensus size: 15
3788061 ATTTAATCTA
3788071 AAATTTTAAATTCAT
1 AAATTTTAAATTCAT
*
3788086 AAATTGATAAA-TCAT
1 AAATT-TTAAATTCAT
*
3788101 ACATTTTAAAATT--T
1 AAATTTT-AAATTCAT
3788115 AAATTTTAAATT
1 AAATTTTAAATT
3788127 TTAAAAATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 5 0.15
14 8 0.24
15 16 0.47
16 5 0.15
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (15 bp):
AAATTTTAAATTCAT
Found at i:3800808 original size:2 final size:2
Alignment explanation
Indices: 3800801--3800851 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
3800791 TCGGGCCGGG
* * * *
3800801 TA TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3800841 TA TA TA TA TA T
1 TA TA TA TA TA T
3800852 TTTTTGATCG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3801393 original size:13 final size:13
Alignment explanation
Indices: 3801375--3801399 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3801365 GGGTATAGGG
3801375 CCGGGTAATCGGA
1 CCGGGTAATCGGA
3801388 CCGGGTAATCGG
1 CCGGGTAATCGG
3801400 GGCAGAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.24, G:0.40, T:0.16
Consensus pattern (13 bp):
CCGGGTAATCGGA
Found at i:3801946 original size:44 final size:44
Alignment explanation
Indices: 3801875--3801964 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
3801865 TATCTCAAAG
* *
3801875 GAACTAAAATTGAAGTTTAGATCTTTTCTCATTTAATATACATT
1 GAACTAAAATTGAAGTTCAGATATTTTCTCATTTAATATACATT
3801919 GAACTAAAATTGAAGTTCAGATATTTTCTCATTTAATATACATT
1 GAACTAAAATTGAAGTTCAGATATTTTCTCATTTAATATACATT
3801963 GA
1 GA
3801965 TTTTTTTAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (44 bp):
GAACTAAAATTGAAGTTCAGATATTTTCTCATTTAATATACATT
Found at i:3807576 original size:20 final size:20
Alignment explanation
Indices: 3807553--3807599 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
3807543 CAAATTCGTG
*
3807553 TTGCGATTTTTCATTTCGCA
1 TTGCGATTTTCCATTTCGCA
*
3807573 TTGCGATTTTCCATTTCGCG
1 TTGCGATTTTCCATTTCGCA
3807593 TTGCGAT
1 TTGCGAT
3807600 AGTCTACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.19, T:0.47
Consensus pattern (20 bp):
TTGCGATTTTCCATTTCGCA
Found at i:3807619 original size:22 final size:22
Alignment explanation
Indices: 3807592--3807634 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3807582 TCCATTTCGC
3807592 GTTGCGATAGTCTACAGTTGTT
1 GTTGCGATAGTCTACAGTTGTT
3807614 GTTGCGATAGTCTACAGTTGT
1 GTTGCGATAGTCTACAGTTGT
3807635 CAAAATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.28, T:0.40
Consensus pattern (22 bp):
GTTGCGATAGTCTACAGTTGTT
Done.