Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 22
Found at i:3554552 original size:33 final size:32
Alignment explanation
Indices: 3554513--3554596 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 32
3554503 TCGCAACACG
*
3554513 GAAATGACTATCGCAACGAAAGAATCGCAATGC
1 GAAATGA-AATCGCAACGAAAGAATCGCAATGC
*
3554546 GAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATG-AAATCGCAACGAAAGAATCGCAATGC
3554579 GAAAATGAAATCGCAACG
1 G-AAATGAAATCGCAACG
3554597 CGAAACTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
33 41 0.87
34 6 0.13
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (32 bp):
GAAATGAAATCGCAACGAAAGAATCGCAATGC
Found at i:3554559 original size:19 final size:19
Alignment explanation
Indices: 3554535--3554601 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
3554525 GCAACGAAAG
3554535 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
3554554 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
3554568 AATCGCAATGCGAAAATG-A
1 AATCGCAATGCG-AAATGAA
*
3554587 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
3554602 CTAAATTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 3 0.08
19 20 0.51
20 1 0.03
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:3554611 original size:19 final size:19
Alignment explanation
Indices: 3554439--3554601 Score: 60
Period size: 20 Copynumber: 8.9 Consensus size: 19
3554429 TCGCAACGCG
* *
3554439 GAAATCGTAACGCGAATAT
1 GAAATCGCAACGCGAAAAT
* ** *
3554458 GACTATCGCAACATGGAAAT
1 GA-AATCGCAACGCGAAAAT
* *
3554478 GACTATCGCAACGCGAAATT
1 GA-AATCGCAACGCGAAAAT
* * * *
3554498 CACTATCGCAACACGGAAAT
1 GA-AATCGCAACGCGAAAAT
*
3554518 GACTATCGCAA--CG-AAA-
1 GA-AATCGCAACGCGAAAAT
*
3554534 G-AATCGCAATGCG-AAAT
1 GAAATCGCAACGCGAAAAT
*
3554551 GAAAATCGCAA--CG-AGA-
1 G-AAATCGCAACGCGAAAAT
*
3554567 G-AATCGCAATGCGAAAAT
1 GAAATCGCAACGCGAAAAT
3554585 GAAATCGCAACGCGAAA
1 GAAATCGCAACGCGAAA
3554602 CTAAATTCGC
Statistics
Matches: 114, Mismatches: 19, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
14 15 0.13
16 9 0.08
17 10 0.09
18 3 0.03
19 24 0.21
20 53 0.46
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (19 bp):
GAAATCGCAACGCGAAAAT
Found at i:3554636 original size:20 final size:19
Alignment explanation
Indices: 3554607--3554673 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
3554597 CGAAACTAAA
*
3554607 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
3554627 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
3554643 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
3554660 TTCGCATTGCGATT
1 TTCGCATTGCGATT
3554674 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 4 0.10
18 3 0.08
19 8 0.21
20 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:3554649 original size:34 final size:34
Alignment explanation
Indices: 3554611--3554706 Score: 149
Period size: 33 Copynumber: 2.9 Consensus size: 34
3554601 ACTAAATTCG
3554611 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
3554645 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
** * *
3554678 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
3554707 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 31 0.54
34 26 0.46
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:3554652 original size:14 final size:14
Alignment explanation
Indices: 3554633--3554686 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
3554623 CATTTTCGCA
3554633 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
3554647 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
3554664 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
3554680 TTGCGAT
1 TTGCGAT
3554687 AGTCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:3556338 original size:42 final size:42
Alignment explanation
Indices: 3556234--3556340 Score: 101
Period size: 42 Copynumber: 2.5 Consensus size: 42
3556224 ATAATGTTGG
* * * *
3556234 GAGGGACCTCTTCAACGATGACAATGGCCTCTTGAACGGTGT
1 GAGGGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGATGT
* ** * *
3556276 GAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG-
1 GAGGGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGAT-GT
3556318 G-GGAGGCCTCTTGAACGATGACA
1 GAGG-GGCCTCTTGAACGATGACA
3556341 GGTGAGTCGG
Statistics
Matches: 50, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
41 2 0.04
42 47 0.94
43 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (42 bp):
GAGGGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGATGT
Found at i:3556826 original size:20 final size:20
Alignment explanation
Indices: 3556803--3556889 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
3556793 GAAACTTAAA
*
3556803 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
3556823 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
3556843 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
**
3556863 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
3556883 ATCGCAA
1 ATCGCAA
3556890 CGAGAGAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:3556926 original size:19 final size:19
Alignment explanation
Indices: 3556906--3557002 Score: 60
Period size: 20 Copynumber: 5.3 Consensus size: 19
3556896 AATCGCAATG
*
3556906 CGATTTTCATTTCGCATTG
1 CGATTTTCATTTCGCATTA
3556925 CGA--TTC-TTTCG--TTA
1 CGATTTTCATTTCGCATTA
** * *
3556939 CGATAATCAAATTCGCATTG
1 CGATTTTC-ATTTCGCATTA
** *
3556959 CGATAGTCATTTTCGCGTTA
1 CGATTTTCA-TTTCGCATTA
*
3556979 CAATTTTCATTTCGCATTA
1 CGATTTTCATTTCGCATTA
3556998 CGATT
1 CGATT
3557003 CTCTCGTTGC
Statistics
Matches: 58, Mismatches: 13, Indels: 14
0.68 0.15 0.16
Matches are distributed among these distances:
14 5 0.09
16 7 0.12
17 3 0.05
18 4 0.07
19 17 0.29
20 22 0.38
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (19 bp):
CGATTTTCATTTCGCATTA
Found at i:3556973 original size:20 final size:20
Alignment explanation
Indices: 3556950--3557056 Score: 93
Period size: 20 Copynumber: 5.7 Consensus size: 20
3556940 GATAATCAAA
3556950 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
* * * **
3556970 TTCGCGTTACAATTTTCA-T
1 TTCGCATTGCGATAGTCATT
*
3556989 TTCGCATTACGAT--TC--T
1 TTCGCATTGCGATAGTCATT
*
3557005 CTCG--TTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
3557023 TTCGCGTTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
3557043 TTCGCATTGCGATA
1 TTCGCATTGCGATA
3557057 ATAAACTATT
Statistics
Matches: 70, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 2 0.03
18 4 0.06
19 12 0.17
20 40 0.57
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCATT
Found at i:3556990 original size:73 final size:73
Alignment explanation
Indices: 3556908--3557047 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 73
3556898 TCGCAATGCG
* *
3556908 ATTTTCATTTCGCATTGCGATTCTTTCGTTACGATAATCAAATTCGCATTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTACGATTCTCTCGTTACGATAATCAAATTCGCATTGCGATAGTCATTTTC
3556973 GCGTTACA
66 GCGTTACA
* * ** *
3556981 ATTTTCATTTCGCATTACGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGATAGTCATTTTC
1 ATTTTCATTTCGCATTACGATTCTCTCGTTACGATAATCAAATTCGCATTGCGATAGTCATTTTC
3557046 GC
66 GC
3557048 ATTGCGATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (73 bp):
ATTTTCATTTCGCATTACGATTCTCTCGTTACGATAATCAAATTCGCATTGCGATAGTCATTTTC
GCGTTACA
Found at i:3559011 original size:20 final size:20
Alignment explanation
Indices: 3558953--3559022 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
3558943 GAAACTTTAA
* **
3558953 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
3558973 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
3558993 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
3559013 ATCGCAACGC
1 ATCGCAACGC
3559023 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:3559061 original size:33 final size:33
Alignment explanation
Indices: 3558952--3559065 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
3558942 TGAAACTTTA
* *
3558952 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
3558990 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
3559026 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
3559059 AATCGCA
1 AATCGCA
3559066 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:3559452 original size:22 final size:22
Alignment explanation
Indices: 3559390--3559455 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
3559380 TGACCGTGAA
* *
3559390 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
3559412 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3559434 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
3559456 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:3559658 original size:20 final size:20
Alignment explanation
Indices: 3559633--3559684 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
3559623 GCTATGTAAA
3559633 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
3559653 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
3559673 TCGCATTGCGAT
1 TCGCATTGCGAT
3559685 TTACGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:3559694 original size:20 final size:20
Alignment explanation
Indices: 3559671--3559744 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
3559661 CGATAGTCAG
3559671 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
3559691 ATTCGCATTGCGATTTTTCAA
1 ATTCGCATTGCGA-TTTACGT
*
3559712 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
3559732 ATTTGCATTGCGA
1 ATTCGCATTGCGA
3559745 ATTAGGAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:3559726 original size:41 final size:40
Alignment explanation
Indices: 3559651--3559744 Score: 134
Period size: 41 Copynumber: 2.3 Consensus size: 40
3559641 CGATAGTCAG
*
3559651 ATTCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
** *
3559691 ATTCGCATTGCGATTTTTCAAATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGA-TAGTCAAATTCGCATTGCGATTTACGT
*
3559732 ATTTGCATTGCGA
1 ATTCGCATTGCGA
3559745 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 13 0.27
41 35 0.73
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (40 bp):
ATTCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
Found at i:3559767 original size:21 final size:21
Alignment explanation
Indices: 3559741--3559807 Score: 116
Period size: 21 Copynumber: 3.2 Consensus size: 21
3559731 TATTTGCATT
3559741 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
3559762 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
3559783 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3559804 GCGA
1 GCGA
3559808 TAGTCAGAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3562663 original size:40 final size:40
Alignment explanation
Indices: 3562608--3562689 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
3562598 AAGACATTTC
3562608 CTATGTTTTATTATTTTTCTGTTATTATTGGAATTGCAAT
1 CTATGTTTTATTATTTTTCTGTTATTATTGGAATTGCAAT
3562648 CTATGTTTTATTATTTTTCTGTTATTATTGGAATTGCAAT
1 CTATGTTTTATTATTTTTCTGTTATTATTGGAATTGCAAT
3562688 CT
1 CT
3562690 CTTGCATTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.22, C:0.09, G:0.12, T:0.57
Consensus pattern (40 bp):
CTATGTTTTATTATTTTTCTGTTATTATTGGAATTGCAAT
Found at i:3566109 original size:31 final size:31
Alignment explanation
Indices: 3566073--3566131 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3566063 AACTTAAAAG
* *
3566073 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
3566104 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
3566132 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3566181 original size:22 final size:22
Alignment explanation
Indices: 3566156--3566198 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566146 TAATAAATTA
*
3566156 TTTAAAATAAATTAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3566178 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3566199 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3566207 original size:22 final size:22
Alignment explanation
Indices: 3566158--3566206 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3566148 ATAAATTATT
* **
3566158 TAAAATAAATTAATCCATATTT
1 TAAAATAAATCAATCCATATAA
3566180 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3566203 TAAA
1 TAAA
3566207 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3566216 original size:32 final size:32
Alignment explanation
Indices: 3566178--3566880 Score: 542
Period size: 32 Copynumber: 24.7 Consensus size: 32
3566168 TAATCCATAT
3566178 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3566210 TTTAAAATAAATTAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
**
3566240 --T--AATAAATCAATCCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3566265 --T-AAATCAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566294 TTTAAAATAAATCAATACATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566326 TTTAAAATAAATCAATCCATA-T--T---TTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566352 --T--AATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566380 TTTAAAAT-AATCAAT---T-C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566401 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566433 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
**
3566463 --T--AATAAATCAATCCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566488 --T-AAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566517 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566549 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566581 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3566603 TTTAAAGTAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566635 TTTAAAATAAATCAATCCATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
* **
3566665 --T--AATAAATCAATTCATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566690 --T-AAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566719 TTTAAAATAGATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566751 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566773 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
3566805 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
3566827 TTTAAAGTAAATCAATCCATACTAATAAATTG
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
3566859 TTTAAAATAAATCAATCTATAC
1 TTTAAAATAAATCAATCCATAC
3566881 AACTACAATA
Statistics
Matches: 552, Mismatches: 41, Indels: 156
0.74 0.05 0.21
Matches are distributed among these distances:
21 8 0.01
22 67 0.12
23 8 0.01
24 4 0.01
25 19 0.03
26 106 0.19
27 17 0.03
28 19 0.03
29 4 0.01
30 8 0.01
31 24 0.04
32 268 0.49
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:3566291 original size:26 final size:26
Alignment explanation
Indices: 3566182--3566716 Score: 102
Period size: 26 Copynumber: 19.0 Consensus size: 26
3566172 CCATATTTTA
*
3566182 AAATAAATCAATCCATACTAATAAATTATTT
1 AAATAAATCAATCCATACAAAT-AA--A--T
* *
3566213 AAAATAAATTAATCCATACAACTACAAT
1 -AAATAAATCAATCCATACAAATA-AAT
***
3566241 -AATAAATCAATCCATA-TTTTAAAAT
1 AAATAAATCAATCCATACAAAT-AAAT
*
3566266 AAATCAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCCATACAAAT-AA--A--T
* *
3566297 AAAATAAATCAATACATACTAATAAATT
1 -AAATAAATCAATCCATACAAATAAA-T
** * * * * **
3566325 ATTTAAAATAAATCAATCCATAT-TTT
1 AAAT-AAATCAATCCATACAAATAAAT
*
3566351 ATAATAAATCAATCCATACTAATAAATT
1 A-AATAAATCAATCCATACAAATAAA-T
** * * * **
3566379 ATTTAAAAT-AATCAATTCATAT-TTT
1 AAAT-AAATCAATCCATACAAATAAAT
*
3566404 AAAATAAATCAATCCATACTAATAAATTATTT
1 -AAATAAATCAATCCATACAAAT-AA--A--T
*
3566436 AAAATAAATCAATCCATACAACTACAAT
1 -AAATAAATCAATCCATACAAATA-AAT
***
3566464 -AATAAATCAATCCATA-TTTTAAAAT
1 AAATAAATCAATCCATACAAAT-AAAT
3566489 AAATAAATCAATCCATACAAATAAATTATTT
1 AAATAAATCAATCCATACAAAT-AA--A--T
*
3566520 AAAATAAATCAATCCATACTAATAAATTATTT
1 -AAATAAATCAATCCATACAAAT-AA--A--T
* *
3566552 AAAATAAATCAATTCATACTAATAAATT
1 -AAATAAATCAATCCATACAAATAAA-T
** * * * **
3566580 ATTTAAAATAAATCAAT-C-TATATTTT
1 AAAT-AAATCAATCCATACAAATA-AAT
* *
3566606 AAAGTAAATCAATTCATACTAATAAATTATTT
1 AAA-TAAATCAATCCATACAAAT-AA--A--T
*
3566638 AAAATAAATCAATCCATACAACTACAAT
1 -AAATAAATCAATCCATACAAATA-AAT
* ***
3566666 -AATAAATCAATTCATA-TTTTAAAAT
1 AAATAAATCAATCCATACAAAT-AAAT
3566691 AAATAAATCAATCCATACAAATAAAT
1 AAATAAATCAATCCATACAAATAAAT
3566717 TATTTAAAAT
Statistics
Matches: 371, Mismatches: 86, Indels: 98
0.67 0.15 0.18
Matches are distributed among these distances:
25 17 0.05
26 139 0.37
27 27 0.07
28 36 0.10
29 5 0.01
30 3 0.01
31 9 0.02
32 132 0.36
33 3 0.01
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (26 bp):
AAATAAATCAATCCATACAAATAAAT
Found at i:3566356 original size:22 final size:22
Alignment explanation
Indices: 3566326--3566368 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566316 TAATAAATTA
3566326 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3566348 TTTATAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3566369 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3566405 original size:21 final size:22
Alignment explanation
Indices: 3566380--3566421 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566370 TAATAAATTA
*
3566380 TTTAAAAT-AATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
3566401 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3566422 CTAATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3566512 original size:18 final size:18
Alignment explanation
Indices: 3566489--3566546 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
3566479 ATTTTAAAAT
3566489 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
* *
3566507 AAATAAAT-TAT--TTA-
1 AAATAAATCAATCCATAC
3566521 AAATAAATCAATCCATAC
1 AAATAAATCAATCCATAC
*
3566539 TAATAAAT
1 AAATAAAT
3566547 TATTTAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 8 0.26
15 4 0.13
17 4 0.13
18 15 0.48
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAATCAATCCATAC
Found at i:3566524 original size:14 final size:14
Alignment explanation
Indices: 3566507--3566592 Score: 55
Period size: 14 Copynumber: 5.6 Consensus size: 14
3566497 CAATCCATAC
3566507 AAATAAATTATTTA
1 AAATAAATTATTTA
* *
3566521 AAATAAATCAATCCATA
1 AAATAAAT-TAT--TTA
*
3566538 CTAATAAATTATTTA
1 -AAATAAATTATTTA
*
3566553 AAATAAATCAATTCATA
1 AAATAAAT-TATT--TA
*
3566570 CTAATAAATTATTTA
1 -AAATAAATTATTTA
3566585 AAATAAAT
1 AAATAAAT
3566593 CAATCTATAT
Statistics
Matches: 54, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 22 0.41
15 9 0.17
17 9 0.17
18 14 0.26
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:3566561 original size:223 final size:224
Alignment explanation
Indices: 3566146--3566569 Score: 787
Period size: 223 Copynumber: 1.9 Consensus size: 224
3566136 ACAACTACAA
*
3566146 TAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
3566211 TTAAAATAAATTAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCA
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCA
3566276 ATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAA
131 ATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAA
3566341 TCCATATTTTATAATAAATCAATCCATAC
196 TCCATATTTTATAATAAATCAATCCATAC
*
3566370 TAATAAATTATTTAAAAT-AATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
3566434 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCA
66 TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCA
*
3566499 ATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAA
131 ATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAA
*
3566564 TTCATA
196 TCCATA
3566570 CTAATAAATT
Statistics
Matches: 194, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
223 176 0.91
224 18 0.09
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (224 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATCA
ATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAA
TCCATATTTTATAATAAATCAATCCATAC
Found at i:3566614 original size:54 final size:54
Alignment explanation
Indices: 3566464--3566879 Score: 395
Period size: 54 Copynumber: 7.3 Consensus size: 54
3566454 CAACTACAAT
* *
3566464 AATAAATCAATCCATATTTTAAAATAAATAAATCAATCCATACAAATAAATTATTTAA
1 AATAAATCAATCTATATTTT---A-AAATAAATCAATCCATACTAATAAATTATTTAA
*
3566522 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATC-A---AT-CT-AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
3566586 AATAAATCAATCTATATTTTAAAGTAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * ** * ** * **
3566640 AATAAATCAATCCATACAACTACAATAATAAATCAATTCATA-TTTTAAAATAAAT-A
1 AATAAATCAAT-C-TA-TATTTTAA-AATAAATCAATCCATACTAATAAATTATTTAA
* * * *
3566696 AATCAATCCATACAAATAAATTATTTAAAATAGATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAAT-C---TATA-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
3566756 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* * *
3566810 AATAAATCAATCCATATTTTAAAGTAAATCAATCCATACTAATAAATTGTTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3566864 AATAAATCAATCTATA
1 AATAAATCAATCTATA
3566880 CAACTACAAT
Statistics
Matches: 303, Mismatches: 35, Indels: 44
0.79 0.09 0.12
Matches are distributed among these distances:
54 150 0.50
55 3 0.01
56 16 0.05
57 14 0.05
58 42 0.14
59 15 0.05
60 12 0.04
62 2 0.01
63 2 0.01
64 41 0.14
65 1 0.00
66 1 0.00
67 1 0.00
68 3 0.01
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.34
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:3566649 original size:202 final size:201
Alignment explanation
Indices: 3566298--3566771 Score: 790
Period size: 202 Copynumber: 2.4 Consensus size: 201
3566288 AAATTATTTA
* *
3566298 AAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATA-T--T---TTA--T--
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3566353 AATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATTCATATTTTAAAATAAATCAATC
66 AATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATTCATATTTTAAAATAAATCAATC
3566418 CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
131 CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
3566483 TAAAAT
196 TAAAAT
3566489 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* *
3566554 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAA-TCTATATTTTAAAGTAAATCAA
66 AATAAATCAATCCATACTAATAAATTATTTAAAAT-AATCAATTC-ATATTTTAAAATAAATCAA
* *
3566618 TTCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATAT
129 TCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATAT
3566683 TTTAAAAT
194 TTTAAAAT
*
3566691 AAATAAATCAATCCATACAAATAAATTATTTAAAATAGATCAATCCATACTAATAAATTATTTAA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
3566756 AATAAATCAATCCATA
66 AATAAATCAATCCATA
3566772 TTTTAAAATA
Statistics
Matches: 263, Mismatches: 8, Indels: 13
0.93 0.03 0.05
Matches are distributed among these distances:
191 47 0.18
192 1 0.00
194 1 0.00
197 3 0.01
199 1 0.00
201 36 0.14
202 174 0.66
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (201 bp):
AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
AATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATTCATATTTTAAAATAAATCAATC
CATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTT
TAAAAT
Found at i:3566777 original size:22 final size:22
Alignment explanation
Indices: 3566751--3566793 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566741 TAATAAATTA
3566751 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
3566773 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3566794 CTAATAAATT
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:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3566802 original size:22 final size:22
Alignment explanation
Indices: 3566753--3566801 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
3566743 ATAAATTATT
**
3566753 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
3566775 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
3566798 TAAA
1 TAAA
3566802 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:3566810 original size:224 final size:226
Alignment explanation
Indices: 3566489--3566950 Score: 720
Period size: 224 Copynumber: 2.0 Consensus size: 226
3566479 ATTTTAAAAT
3566489 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCC--AC-AAT-AATTATTTAA
* *
3566554 AATAAATCAATTCATACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAGTAAATCAAT
62 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAATCAAT
* *
3566619 TCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATATT
127 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
3566684 TTAAAATAAATAAATCAATCCATACAAATAAATTATTTA
192 TT---A-AAATAAATCAATCCATACAAATAAATTATTTA
* *
3566723 AAATAGATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-C-AT-A-T-TTTAAAATA
1 AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCACAATAATTATTTAAAATA
3566782 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAATCAATCCAT
66 AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAATCAATCCAT
* *
3566847 ACTAATAAATTGTTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAA
131 ACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAA
* *
3566912 AATAAATCAATTCATACTAATAAATTATTTA
196 AATAAATCAATCCATACAAATAAATTATTTA
3566943 AAATAAAT
1 AAATAAAT
3566951 TATTTTAAAA
Statistics
Matches: 217, Mismatches: 11, Indels: 14
0.90 0.05 0.06
Matches are distributed among these distances:
220 37 0.17
221 1 0.00
224 131 0.60
225 1 0.00
226 1 0.00
228 2 0.01
230 1 0.00
233 1 0.00
234 42 0.19
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (226 bp):
AAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCACAATAATTATTTAAAATA
AATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAGTAAATCAATCCAT
ACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAA
AATAAATCAATCCATACAAATAAATTATTTA
Found at i:3566831 original size:22 final size:22
Alignment explanation
Indices: 3566805--3566847 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3566795 TAATAAATTA
3566805 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
3566827 TTTAAAGTAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
3566848 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:3566915 original size:22 final size:22
Alignment explanation
Indices: 3566890--3566985 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
3566880 CAACTACAAT
3566890 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
* **
3566912 AATAAATCAATTCATACTAATAA
1 AATAAATCAATCCATA-TTTTAA
* ** * **
3566935 ATTATTTAAAATAAATTATTTTAA
1 AATAAAT-CAATCCA-TATTTTAA
*
3566959 AATAAATCAATCCATATTTTAT
1 AATAAATCAATCCATATTTTAA
3566981 AATAA
1 AATAA
3566986 TTTATTTTAT
Statistics
Matches: 53, Mismatches: 18, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
22 27 0.51
23 12 0.23
24 12 0.23
25 2 0.04
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:3566959 original size:15 final size:15
Alignment explanation
Indices: 3566930--3567032 Score: 100
Period size: 15 Copynumber: 6.5 Consensus size: 15
3566920 AATTCATACT
3566930 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
3566944 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
3566959 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
* *
3566981 AATAATTTATTTTAT
1 AATAAATTATTTTAA
*
3566996 AATAAATTATTTTAT
1 AATAAATTATTTTAA
3567011 AATAAATTATTTTAA
1 AATAAATTATTTTAA
3567026 AATAAAT
1 AATAAAT
3567033 AACCTTATTA
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
14 9 0.12
15 51 0.66
17 1 0.01
18 2 0.03
19 3 0.04
20 1 0.01
22 10 0.13
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:3566966 original size:47 final size:49
Alignment explanation
Indices: 3566904--3567017 Score: 142
Period size: 52 Copynumber: 2.3 Consensus size: 49
3566894 AATCAATCCA
* *
3566904 TATTTTAAAATAAATCAATTCATA-CTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAAAATAAAT
* *
3566951 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATA---TATAATAAATTATTTTAAAATAAAT
*
3567003 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
3567018 TATTTTAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
47 23 0.40
51 9 0.16
52 25 0.44
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (49 bp):
TATTTTAAAATAAATCAATCCATATATAATAAATTATTTTAAAATAAAT
Found at i:3566972 original size:69 final size:67
Alignment explanation
Indices: 3566890--3567032 Score: 207
Period size: 67 Copynumber: 2.1 Consensus size: 67
3566880 CAACTACAAT
3566890 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTA-TTTAAAATAAATTAT
1 AATAAATCAATCCATATTTTAAAAT-AATCAATT-ATA-TAATAAATTATTTTAAAATAAATTAT
3566954 TTTAA
63 TTTAA
* ** * *
3566959 AATAAATCAATCCATATTTTATAATAATTTATTTTATAATAAATTATTTTATAATAAATTATTTT
1 AATAAATCAATCCATATTTTAAAATAATCAATTATATAATAAATTATTTTAAAATAAATTATTTT
3567024 AA
66 AA
3567026 AATAAAT
1 AATAAAT
3567033 AACCTTATTA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
66 10 0.15
67 28 0.41
68 6 0.09
69 24 0.35
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATCAATCCATATTTTAAAATAATCAATTATATAATAAATTATTTTAAAATAAATTATTTT
AA
Found at i:3567017 original size:425 final size:422
Alignment explanation
Indices: 3566145--3566950 Score: 1400
Period size: 425 Copynumber: 1.9 Consensus size: 422
3566135 TACAACTACA
*
3566145 ATAATAAATTATTTAAAATAAATTAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
* *
3566210 TTTAAAATAAATTAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
66 TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATC
3566275 AATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCA
131 AATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCA
* *
3566340 ATCCATATTTTATAATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATTCATATTTTA
196 ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATCCATATTTTA
3566405 AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAA
261 AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAA
3566470 TCAATCCATATTTTAAAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCC
326 TCAATCCATATTTT--AATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCC
* *
3566535 ATACTAATAAATTATTTAAAATAAATCAATTCAT
389 AAAATAATAAATTATTTAAAATAAATCAATTCAT
* * *
3566569 ACTAATAAATTATTTAAAATAAATCAATCTATATTTTAAAGTAAATCAATTCATACTAATAAATT
1 A-TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT
*
3566634 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATTCATATTTTAAAATAAATAAAT
65 ATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAAT
* *
3566699 CAATCCATACAAATAAATTATTTAAAATAGATCAATCCATACTAATAAATTATTTAAAATAAATC
130 CAATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATC
3566764 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTT
195 AATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAAT-AATCAATCCATATTT
* * *
3566829 TAAAGTAAATCAATCCATACTAATAAATTGTTTAAAATAAATCAATCTATACAACTACAATAATA
259 TAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATA
* *
3566894 AATCAATCCATATTTT-A-AAATAAATCAATTCATACTAATAAATTATTTAAAATAAAT
324 AATCAATCCATATTTTAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAAT
3566951 TATTTTAAAA
Statistics
Matches: 364, Mismatches: 16, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
422 38 0.10
423 1 0.00
424 1 0.00
425 232 0.64
426 92 0.25
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (422 bp):
ATAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
TTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATAAATC
AATCCATACAAATAAATTATTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCA
ATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAATCAATCCATATTTTA
AAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAA
TCAATCCATATTTTAATAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCAA
AATAATAAATTATTTAAAATAAATCAATTCAT
Found at i:3567071 original size:18 final size:18
Alignment explanation
Indices: 3566987--3567080 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
3566977 TTATAATAAT
3566987 TTATTTT-AT-AAT-AAA
1 TTATTTTAATAAATAAAA
3567002 TTATTTT-AT-AAT-AAA
1 TTATTTTAATAAATAAAA
**
3567017 TTATTTTAAAATAAATAACC
1 TTATTTT--AATAAATAAAA
* **
3567037 TTA-TTAAATTATTTAAAA
1 TTATTTTAA-TAAATAAAA
*
3567055 TTATTTTAATAAATAAAT
1 TTATTTTAATAAATAAAA
3567073 TTATTTTA
1 TTATTTTA
3567081 TAATTGTTCT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
15 22 0.36
17 2 0.03
18 24 0.39
19 9 0.15
20 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTTTAATAAATAAAA
Found at i:3567851 original size:50 final size:50
Alignment explanation
Indices: 3567776--3567877 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
3567766 ACCAATGACA
*
3567776 ATTGTGAAAGTCTTTGTTTTCTTCTCCTCATGCTTGGGTCTGAAATTGGG
1 ATTGTGAAAGTCTTTGTTTTCTTCTCCTCATGCTTAGGTCTGAAATTGGG
3567826 ATTGTGAAAGTCTTTGTTTTCTTCTCCTCATGCTTAGGTCTGAAATTGGG
1 ATTGTGAAAGTCTTTGTTTTCTTCTCCTCATGCTTAGGTCTGAAATTGGG
3567876 AT
1 AT
3567878 CGACTGAGAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.18, C:0.16, G:0.23, T:0.44
Consensus pattern (50 bp):
ATTGTGAAAGTCTTTGTTTTCTTCTCCTCATGCTTAGGTCTGAAATTGGG
Found at i:3584194 original size:21 final size:21
Alignment explanation
Indices: 3584170--3584211 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3584160 AGTTTATTTT
*
3584170 TAAATTTTATTTTAATTATCG
1 TAAATTTTATTTCAATTATCG
*
3584191 TAAATTTTGTTTCAATTATCG
1 TAAATTTTATTTCAATTATCG
3584212 AACTTAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TAAATTTTATTTCAATTATCG
Found at i:3584258 original size:32 final size:32
Alignment explanation
Indices: 3584206--3584307 Score: 136
Period size: 32 Copynumber: 3.2 Consensus size: 32
3584196 TTTGTTTCAA
*
3584206 TTATCGAACTT-AAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAG-TTTTAAGTATTTGAAT
*
3584238 TTATCGAATTTGGAAGTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
* *
3584270 TTATCAAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGT-TTTAAGTATTTGAAT
3584302 TTATCG
1 TTATCG
3584308 TAAACTTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
32 46 0.74
33 16 0.26
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (32 bp):
TTATCGAACTTGGAAGTTTTAAGTATTTGAAT
Found at i:3584388 original size:17 final size:17
Alignment explanation
Indices: 3584368--3584401 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3584358 GTTTTTTTAT
3584368 AACCGATTTTTTAAAAA
1 AACCGATTTTTTAAAAA
3584385 AACCGATTTTTTAAAAA
1 AACCGATTTTTTAAAAA
3584402 CCGAAACCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (17 bp):
AACCGATTTTTTAAAAA
Found at i:3586626 original size:14 final size:14
Alignment explanation
Indices: 3586605--3586647 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
3586595 AAGCTTGTAG
3586605 CTGTAGAAAACAGA
1 CTGTAGAAAACAGA
3586619 -TAGTAGAAAACAGA
1 CT-GTAGAAAACAGA
3586633 CTGTAGAAAACAGA
1 CTGTAGAAAACAGA
3586647 C
1 C
3586648 AAGTCTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.51, C:0.14, G:0.21, T:0.14
Consensus pattern (14 bp):
CTGTAGAAAACAGA
Found at i:3588615 original size:36 final size:36
Alignment explanation
Indices: 3588565--3588669 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
3588555 TTACCTTCTG
* *
3588565 TTTCAGATGCAACAGGATCTGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
* *
3588601 TTTCAGAGGTAACAGGATCCGAATATGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
3588637 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTT
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTT
3588670 AGCGAATGCT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
Found at i:3600204 original size:26 final size:26
Alignment explanation
Indices: 3600156--3600206 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3600146 ATTATCTTAT
* * **
3600156 AATGTTGCTTGTGGAACTTAGCAAAA
1 AATGTTACTTGTCGAACCCAGCAAAA
3600182 AATGTTACTTGTCGAACCCAGCAAA
1 AATGTTACTTGTCGAACCCAGCAAA
3600207 TGCATTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (26 bp):
AATGTTACTTGTCGAACCCAGCAAAA
Found at i:3600328 original size:38 final size:40
Alignment explanation
Indices: 3600254--3600345 Score: 134
Period size: 38 Copynumber: 2.3 Consensus size: 40
3600244 ATGGCATTCC
*
3600254 GGGCCAAAATACATTTCCAGGTGAAGTAAAGGAGCTCTACTT
1 GGGCGAAAATACATTTCCAGGT--AGTAAAGGAGCTCTACTT
*
3600296 TGGCGAAAATACATTT-CAGGT-GTAAAGGAGCTCTACTT
1 GGGCGAAAATACATTTCCAGGTAGTAAAGGAGCTCTACTT
3600334 GGGCGAAAATAC
1 GGGCGAAAATAC
3600346 GTTTTCAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
38 28 0.60
41 5 0.11
42 14 0.30
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (40 bp):
GGGCGAAAATACATTTCCAGGTAGTAAAGGAGCTCTACTT
Found at i:3608083 original size:2 final size:2
Alignment explanation
Indices: 3608076--3608109 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3608066 CATGTAGCAA
*
3608076 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3608110 GTCATTATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3608443 original size:23 final size:23
Alignment explanation
Indices: 3608417--3608494 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
3608407 CACCACAGCT
3608417 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
3608440 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
3608463 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
3608486 TATAATAAT
1 CAT-ATAAT
3608495 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:3609361 original size:2 final size:2
Alignment explanation
Indices: 3609354--3609390 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3609344 ATACTGATAA
3609354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3609391 GACACCCGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3609436 original size:3 final size:3
Alignment explanation
Indices: 3609420--3609496 Score: 64
Period size: 3 Copynumber: 24.7 Consensus size: 3
3609410 GTCGAAAAAA
* * * *
3609420 TAT TAT TAAA TAT TAT TAT TAT TAT TAT TAA TAA TAT TAA TAT TAAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
* * *
3609467 TAT TAC TAA TAA TAT TAT TAT TAAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
3609497 CTATACCACA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
3 54 0.87
4 8 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:3609468 original size:25 final size:25
Alignment explanation
Indices: 3609420--3609496 Score: 115
Period size: 25 Copynumber: 3.2 Consensus size: 25
3609410 GTCGAAAAAA
3609420 TATTATT-A-AATATTATTATT-AT
1 TATTATTAATAATATTATTATTAAT
*
3609442 TATTATTAATAATATTAATATTAAT
1 TATTATTAATAATATTATTATTAAT
*
3609467 TATTACTAATAATATTATTATTAAT
1 TATTATTAATAATATTATTATTAAT
3609492 TATTA
1 TATTA
3609497 CTATACCACA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
22 7 0.14
23 1 0.02
24 11 0.22
25 30 0.61
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (25 bp):
TATTATTAATAATATTATTATTAAT
Found at i:3609497 original size:25 final size:25
Alignment explanation
Indices: 3609428--3609499 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
3609418 AATATTATTA
*
3609428 AATATTATTATT-ATTATTATTAAT
1 AATATTATTATTAATTATTACTAAT
*
3609452 AATATTAATATTAATTATTACTAAT
1 AATATTATTATTAATTATTACTAAT
3609477 AATATTATTATTAATTATTACTA
1 AATATTATTATTAATTATTACTA
3609500 TACCACAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 11 0.25
25 33 0.75
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
AATATTATTATTAATTATTACTAAT
Found at i:3610166 original size:145 final size:143
Alignment explanation
Indices: 3609821--3610168 Score: 373
Period size: 144 Copynumber: 2.4 Consensus size: 143
3609811 AGACCATCAA
*
3609821 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGGATCGGAGAAAATAAGCC
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGCC
* * * * * *
3609886 GAACGGGTTTTGGCCTCTTGCCTGCGATCGGGATCTTCGATTAACATTCTGAACAATTAAAGTTG
66 GAACGGGTTTTAGCCTCTTGCCGGCGATCGAGATCTTCGATCAACATTCTAAACAATAAAAGTTG
*
3609951 CGAGAGACCATCAC
131 CGAGAGA-CAACAC
* * * *
3609965 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGACGG-CAGATCAGAGAAAATAAGT
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGA-ATCGGAGAAAATAAGC
* * * * *
3610029 CGAACGGTTTTTAGCCTTTTTCCGGCGATCGAGATC-TCTGATCAATACTTC-AAACAGTGAAAA
65 CGAACGGGTTTTAGCCTCTTGCCGGCGATCGAGATCTTC-GATCAACA-TTCTAAACAAT-AAAA
*
3610092 GTTGTGTA-ATGTA-AACAC
127 GTTGCG-AGA-G-ACAACAC
* * * * * *
3610110 GAACAGCATACTGAAATTTCATGACGATCGGACGGTAGACGGTGGTGAATCGGAGAAAA
1 GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAA
3610169 CAAATCCAGA
Statistics
Matches: 169, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
143 2 0.01
144 99 0.59
145 64 0.38
146 3 0.02
147 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (143 bp):
GAACAACATACTGAAAATTCAGGACGATCAGACGGTGGACGGCGGTGAATCGGAGAAAATAAGCC
GAACGGGTTTTAGCCTCTTGCCGGCGATCGAGATCTTCGATCAACATTCTAAACAATAAAAGTTG
CGAGAGACAACAC
Found at i:3610850 original size:2 final size:2
Alignment explanation
Indices: 3610835--3610869 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3610825 TTTCGTACAT
*
3610835 TA TA TA T- TA AA 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
3610870 AAAGTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3613066 original size:55 final size:55
Alignment explanation
Indices: 3613002--3613143 Score: 205
Period size: 55 Copynumber: 2.6 Consensus size: 55
3612992 ACATTCAAGT
* * * *
3613002 GATTCATGAAGAAGGACGTCTGATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
* *
3613057 GATTCATGAAGATGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGACC
1 GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
*
3613112 GATCCATGAAGAAAGG-CATCCGATGAATGAAG
1 GATTCATGAAG-AAGGACATCCGATGAATGAAG
3613144 TTTGAAGTTG
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
55 75 0.96
56 3 0.04
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (55 bp):
GATTCATGAAGAAGGACATCCGATGAATGAAGAAATCTGAAACTGATTGAAGAAC
Found at i:3616559 original size:49 final size:49
Alignment explanation
Indices: 3616499--3616602 Score: 124
Period size: 49 Copynumber: 2.1 Consensus size: 49
3616489 AAAGAGAAAA
* *
3616499 AAAAAACAGAGC-CAAA-AAAAAGAGAAAAGAACAAAGAAATTAAAGCAAAG
1 AAAAAACAGAGCACAAAGAAAAAGA-AAAAGAA-AAAGAAA-AAAAACAAAG
*
3616549 AAAAAA-AGAGCAACAAAGAACAAGAAAAAGAAAAAGAAAAAAAACAAAG
1 AAAAAACAGAGC-ACAAAGAAAAAGAAAAAGAAAAAGAAAAAAAACAAAG
3616598 AAAAA
1 AAAAA
3616603 GGGACGATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
49 18 0.38
50 13 0.27
51 11 0.23
52 6 0.12
ACGTcount: A:0.75, C:0.09, G:0.14, T:0.02
Consensus pattern (49 bp):
AAAAAACAGAGCACAAAGAAAAAGAAAAAGAAAAAGAAAAAAAACAAAG
Found at i:3616567 original size:18 final size:17
Alignment explanation
Indices: 3616523--3616592 Score: 58
Period size: 18 Copynumber: 4.2 Consensus size: 17
3616513 AAAAAAAGAG
*
3616523 AAAAGAACAAAG-AAAT
1 AAAAGAACAAAGAAAAA
*
3616539 TAAAG--CAAAGAAAAA
1 AAAAGAACAAAGAAAAA
*
3616554 AAGAGCAACAAAGAACAAGA
1 AAAAG-AACAAAGAA-AA-A
3616574 AAAAGAA-AAAGAAAAA
1 AAAAGAACAAAGAAAAA
3616590 AAA
1 AAA
3616593 CAAAGAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
14 5 0.12
15 6 0.14
16 8 0.19
17 2 0.05
18 13 0.30
19 4 0.09
20 5 0.12
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.03
Consensus pattern (17 bp):
AAAAGAACAAAGAAAAA
Found at i:3616579 original size:6 final size:6
Alignment explanation
Indices: 3616563--3616603 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
3616553 AAAGAGCAAC
* *
3616563 AAAGAA CAAGAA AAAGAA AAAGAA AAAAAA CAAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA AAAG
3616604 GGACGATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:3617673 original size:32 final size:32
Alignment explanation
Indices: 3617637--3617710 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
3617627 GCATCGTTAA
* *
3617637 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
***
3617669 AGATTCAACATTGAATATTGGGGCATATATGG
1 AGATTCAACAACAAATATTGGGGCATATATGG
*
3617701 GGATTCAACA
1 AGATTCAACA
3617711 TCCTGATGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (32 bp):
AGATTCAACAACAAATATTGGGGCATATATGG
Found at i:3618035 original size:43 final size:43
Alignment explanation
Indices: 3617986--3618109 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
3617976 ACGAAGGCGC
**
3617986 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * *
3618029 GATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
3618072 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
3618110 ACACAAGCAG
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.30, C:0.31, G:0.19, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:3618412 original size:43 final size:43
Alignment explanation
Indices: 3618321--3618444 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
3618311 ACGAAGGCAC
* * **
3618321 CATCCACGATATCAACTCCACGACGGAGGATATCATACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * *
3618364 GATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * * *
3618407 CATCCACGGTTTCAACTTCACGACGAAGGAAATCGTAC
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC
3618445 ACACAAGCAG
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:3618481 original size:335 final size:335
Alignment explanation
Indices: 3617871--3618991 Score: 1909
Period size: 335 Copynumber: 3.3 Consensus size: 335
3617861 TGCAGCTTTT
*
3617871 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
* *
3617936 TTCACGATGAAGGATATTCAAGTCAAGGCTCAACTTCATGACGAAGGCGCCATCCACGATTTCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
3618001 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
3618066 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
*
3618131 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGACGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
*
3618196 TTTCAGTTTC
326 TTCCAGTTTC
* *
3618206 AGAGCCAATTTTAACTTCGCGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
* * * * *
3618271 TTCACGACGAAGGATATTCAAGTTAAGGCTCAATTTCATGACGAAGGCACCATCCACGATATCAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
*
3618336 CTCCACGACGGAGGATATCATACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
*
3618401 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTTATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
*
3618466 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCATTAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
3618531 TTCCAGTTTC
326 TTCCAGTTTC
* * *
3618541 AGAGCCAATTTTAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAAGCTTGGATTTCAAC
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
* *
3618606 TTCACGACGAAGGATATTCAAGTCAAGGCTCAATTTCACGACGAAGGCGCCATCCACGATTTAAA
66 TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
3618671 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
131 CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
* * * *
3618736 CCCACACATCCACGATTTCAACTTCACGACGAAGGGAATCGTACACACAAGCAGTATCCATCTCT
196 CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
* *
3618801 AGATTGGATTTCAACTTCACGACGAATGATATCCAACTCGAAGAAGGAGTGTCTGTCAATAAACT
261 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
3618866 TTCCAGTTTC
326 TTCCAGTTTC
* * * *
3618876 AGAGTCAATTTCAACTTCACGTCGAAGGATATTGGCCTCGAAACAACACAACTTAACTTGGATTT
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACAC-A---AGCTTGGATTT
* * *
3618941 CAACTTCACGACGAAGGATATCCAATTCAAGGTTCAACTTCACGACGAAGG
62 CAACTTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGG
3618992 GAATCGTACC
Statistics
Matches: 742, Mismatches: 40, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
335 684 0.92
336 1 0.00
339 57 0.08
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (335 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACAACACAAGCTTGGATTTCAAC
TTCACGACGAAGGATATTCAAGTCAAGGCTCAACTTCACGACGAAGGCGCCATCCACGATTTCAA
CTCCACGACGGAGGATATCGTACCAATGGATCCACGATTTCAACTCCACGACGGAGGATATCGTG
CCCACACATCCACGGTTTCAACTTCACGACGAAGGAAATCGTACACACAAGCAGCATTCATCTCT
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGAAGGAGTGTCTGTCAATAAACT
TTCCAGTTTC
Found at i:3618718 original size:43 final size:43
Alignment explanation
Indices: 3618656--3618779 Score: 160
Period size: 43 Copynumber: 2.9 Consensus size: 43
3618646 ACGAAGGCGC
* **
3618656 CATCCACGATTTAAACTCCACGACGGAGGATATCGTACCAATG
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* * *
3618699 GATCCACGATTTCAACTCCACGACGGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
* *
3618742 CATCCACGATTTCAACTTCACGACGAAGGGA-ATCGTAC
1 CATCCACGATTTCAACTCCACGACGGA-GGATATCGTAC
3618780 ACACAAGCAG
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
43 67 0.96
44 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACA
Found at i:3619122 original size:36 final size:36
Alignment explanation
Indices: 3619082--3619160 Score: 113
Period size: 36 Copynumber: 2.2 Consensus size: 36
3619072 AATGAGCCAT
* *
3619082 CCTTGAAACAAATTTTGTCTCTCATGAGACAGTTTC
1 CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
**
3619118 CCTTGAAACAAATTTTATCTCTTTTGAGACAATTTC
1 CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
*
3619154 TCTTGAA
1 CCTTGAA
3619161 GCATCATTTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.39
Consensus pattern (36 bp):
CCTTGAAACAAATTTTATCTCTCATGAGACAATTTC
Found at i:3619453 original size:3 final size:3
Alignment explanation
Indices: 3619437--3619519 Score: 67
Period size: 3 Copynumber: 26.7 Consensus size: 3
3619427 GTCGAAAAAA
* * * * *
3619437 TAT TAT TAAA TAT TAT TAT TAC TAT TAT TAT TAA TAA TAA TAT TAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
3619483 TAT TAAT TAT TAC TAA TAA TAT TAT TAT TAAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TA
3619520 CTATACCACA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
3 60 0.88
4 8 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (3 bp):
TAT
Found at i:3619467 original size:15 final size:15
Alignment explanation
Indices: 3619447--3619514 Score: 77
Period size: 15 Copynumber: 4.7 Consensus size: 15
3619437 TATTATTAAA
* *
3619447 TATTATTATTACTAT
1 TATTATTAATAATAT
*
3619462 TATTATTAATAATAA
1 TATTATTAATAATAT
*
3619477 TATTATT-ATTA-AT
1 TATTATTAATAATAT
*
3619490 TATTACTAATAATAT
1 TATTATTAATAATAT
3619505 TATTATTAAT
1 TATTATTAAT
3619515 TATTACTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
13 7 0.16
14 6 0.14
15 30 0.70
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTATTAATAATAT
Found at i:3619469 original size:25 final size:25
Alignment explanation
Indices: 3619437--3619524 Score: 90
Period size: 28 Copynumber: 3.4 Consensus size: 25
3619427 GTCGAAAAAA
3619437 TATTATTA-AATATTATTATTACTAT
1 TATTATTATAATATTATTATTA-TAT
*
3619462 TATTATTAATAATAATATTATTATTAAT
1 TATTATT-ATAATATTATTATTA-T-AT
*
3619490 TATTACTAATAATATTATTATTA-AT
1 TATTA-TTATAATATTATTATTATAT
*
3619515 TATTACTATA
1 TATTATTATA
3619525 CCACAAAACA
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
24 3 0.06
25 14 0.26
26 1 0.02
27 13 0.25
28 21 0.40
29 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTATTATAATATTATTATTATAT
Found at i:3619492 original size:40 final size:40
Alignment explanation
Indices: 3619435--3619514 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
3619425 AGGTCGAAAA
* * *
3619435 AATATTATTAAATATTATTATTACTATTATTATTAATAAT
1 AATATTATTAAATATTATTACTAATAATATTATTAATAAT
* *
3619475 AATATTATT-ATTAATTATTACTAATAATATTATTATTAAT
1 AATATTATTAAAT-ATTATTACTAATAATATTATTAATAAT
3619515 TATTACTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (40 bp):
AATATTATTAAATATTATTACTAATAATATTATTAATAAT
Found at i:3620059 original size:145 final size:145
Alignment explanation
Indices: 3619791--3620099 Score: 440
Period size: 145 Copynumber: 2.1 Consensus size: 145
3619781 TCTCGTCGTT
* * * *
3619791 GATCGGAATCTCCGATCACCATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATA
1 GATCGGGATCTACGATCAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
* * ** *
3619856 CTGAAAATTCAGGACGATCACACGGTGGACGGCGGTGGATCGGAGAAAATAAGCCGAACGGTTTT
66 CTGAAAATTCAAGACGATCACACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTT
* *
3619921 TGGCCTCTTGCCTGC
131 TAGCCTCTTGCCGGC
* * *
3619936 GATCGGGATCTACGATTAACATTCTGAACGGTCAAAAGTTGCGCGAGACCATCACGAACAACATA
1 GATCGGGATCTACGATCAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
* *
3620001 CTGAAAATTCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGTCGAACGGTTTT
66 CTGAAAATTCAAGACGATCACACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTT
*
3620066 TAGCCTTTTGCCGGC
131 TAGCCTCTTGCCGGC
*
3620081 GATCAGGATC-ACCGATCAA
1 GATCGGGATCTA-CGATCAA
3620100 TACTTCAAAC
Statistics
Matches: 144, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
144 1 0.01
145 143 0.99
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (145 bp):
GATCGGGATCTACGATCAACATTCCGAACGGTCAAAAGTTGCGCAAGACCATCACGAACAACATA
CTGAAAATTCAAGACGATCACACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTT
TAGCCTCTTGCCGGC
Found at i:3620140 original size:145 final size:144
Alignment explanation
Indices: 3619798--3620325 Score: 377
Period size: 145 Copynumber: 3.6 Consensus size: 144
3619788 GTTGATCGGA
* * ** * * *
3619798 ATCTCCGATCACCATTCCGAACGGTCAAAAGTTGTGCAAGACCATCACGAACAACATACTGAAAA
1 ATCTACGATCAACATTCTAAACAGTCAAAAGTTGCGCAAGA-CAACACGAACAACATACTGAAAA
* * * ** * *
3619863 TTCAGGACGATCACACGGTGGACGGCGGTGGATCGGAGAAAATAAGCCGAACGGTTTTTGGCCTC
65 TTCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTTTAGCCTC
* *
3619928 TTGCCTGCGATCGGG
130 TTGCCGGCGATCAGG
* * * * *
3619943 ATCTACGATTAACATTCTGAACGGTCAAAAGTTGCGCGAGACCATCACGAACAACATACTGAAAA
1 ATCTACGATCAACATTCTAAACAGTCAAAAGTTGCGCAAGA-CAACACGAACAACATACTGAAAA
* *
3620008 TTCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGTCGAACGGTTTTTAGCCTT
65 TTCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTTTAGCCTC
3620073 TTGCCGGCGATCAGG
130 TTGCCGGCGATCAGG
* * * * * *
3620088 ATC-ACCGATCAATACTTC-AAACAGTGAAAAGTTGTGTAATGTA-AACATGAACAGCATACTGA
1 ATCTA-CGATCAACA-TTCTAAACAGTCAAAAGTTGCGCAA-G-ACAACACGAACAACATACTGA
* * * * * ** * * * * * *
3620150 AATTTTATGACGATCGGACGGTAGACGGTGG-TGAATCGGAGAAAACAAATCC-AGACGATATTT
62 AAATTCAAGACGATCAGACGGTGGACGACGGCAG-ATCAGAGAAAA-TAAGCCGA-ACGGTTTTT
* * *
3620213 GGCCTCTCGCCGGTGATC-GG
124 AGCCTCTTGCCGGCGATCAGG
* * * ** * * * *
3620233 AACCTCCGATCAATATTCCGAACGGTCAAAAGTTGCGCGATGTCAACACGAACATCATACTGAAA
1 -ATCTACGATCAACATTCTAAACAGTCAAAAGTTGCGC-AAGACAACACGAACAACATACTGAAA
* * *
3620298 TTTC-AGAACAATCGGACGGTGGCACGAC
64 ATTCAAG-ACGATCAGACGGTGG-ACGAC
3620326 AACGCAGTAA
Statistics
Matches: 306, Mismatches: 63, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
144 2 0.01
145 210 0.69
146 89 0.29
147 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (144 bp):
ATCTACGATCAACATTCTAAACAGTCAAAAGTTGCGCAAGACAACACGAACAACATACTGAAAAT
TCAAGACGATCAGACGGTGGACGACGGCAGATCAGAGAAAATAAGCCGAACGGTTTTTAGCCTCT
TGCCGGCGATCAGG
Found at i:3625947 original size:23 final size:23
Alignment explanation
Indices: 3625921--3625998 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
3625911 CACCACAGCT
3625921 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
3625944 CATATAATTGCACCGGAGTACCG
1 CATATAATTGCACCGAAGTGCCA
* *
3625967 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
3625990 TATAATAAT
1 CAT-ATAAT
3625999 GTCCATAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:3626212 original size:103 final size:103
Alignment explanation
Indices: 3626017--3626318 Score: 547
Period size: 103 Copynumber: 3.0 Consensus size: 103
3626007 GGACCACATA
* * *
3626017 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA-ACTTCACACATGTTC
1 TCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
3626081 CAAAGAATACATATATGTCCCGAAGGACCACATATCAT
66 CAAAGAATACATATATGTCCCGAAGGACCACATATCAT
3626119 TCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
1 TCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
3626184 CAAAGAATACATATATGTCCCGAAGGACCACATATCAT
66 CAAAGAATACATATATGTCCCGAAGGACCACATATCAT
*
3626222 TACTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
1 TCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
3626287 CAAAGAATAC--ATATGTCCCGAAGGACCACATA
66 CAAAGAATACATATATGTCCCGAAGGACCACATA
3626319 GACCCTCGAC
Statistics
Matches: 195, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
101 22 0.11
102 46 0.24
103 127 0.65
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
TCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTC
CAAAGAATACATATATGTCCCGAAGGACCACATATCAT
Found at i:3630718 original size:23 final size:23
Alignment explanation
Indices: 3630692--3630760 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
3630682 CACCACATCT
*
3630692 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
3630715 CGTAGAATTACACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
* *
3630738 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
3630761 TATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:3634625 original size:22 final size:22
Alignment explanation
Indices: 3634599--3634644 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3634589 AATGAAGAAA
3634599 TTTTATGGTAACCTCGTTGATT
1 TTTTATGGTAACCTCGTTGATT
3634621 TTTTATGGTAACCTCGTTGATT
1 TTTTATGGTAACCTCGTTGATT
3634643 TT
1 TT
3634645 GGAAGAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.13, G:0.17, T:0.52
Consensus pattern (22 bp):
TTTTATGGTAACCTCGTTGATT
Found at i:3637929 original size:15 final size:15
Alignment explanation
Indices: 3637898--3637938 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3637888 TTTGATTTAA
*
3637898 TTATTTCAAGTTTGTT
1 TTATTT-AAGTTAGTT
*
3637914 TTTTTTAAGTTAGTT
1 TTATTTAAGTTAGTT
3637929 TTATTTAAGT
1 TTATTTAAGT
3637939 CTATTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.63
Consensus pattern (15 bp):
TTATTTAAGTTAGTT
Found at i:3640844 original size:32 final size:31
Alignment explanation
Indices: 3640808--3640894 Score: 95
Period size: 34 Copynumber: 2.7 Consensus size: 31
3640798 TTGCAAATTG
3640808 TTTTTGAAAATCAATATAATATAGTTAAAACA
1 TTTTTGAAAAT-AATATAATATAGTTAAAACA
* * *
3640840 TTTTTGAAAATATGTATATTATATATTTAAAATA
1 TTTTTGAAAATA---ATATAATATAGTTAAAACA
*
3640874 -TTTTGAAAATTATATAATATA
1 TTTTTGAAAATAATATAATATA
3640895 TAGTTTTGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
30 9 0.19
31 1 0.02
32 11 0.23
33 10 0.21
34 16 0.34
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (31 bp):
TTTTTGAAAATAATATAATATAGTTAAAACA
Found at i:3640870 original size:34 final size:32
Alignment explanation
Indices: 3640809--3641048 Score: 109
Period size: 33 Copynumber: 7.2 Consensus size: 32
3640799 TGCAAATTGT
* *
3640809 TTTTGAAAATCA-ATATAATATAGTTAAAACA
1 TTTTGAAAATTATATATTATATAGTTAAAACA
* * *
3640840 TTTTTGAAAATATGTATATTATATATTTAAAATA
1 -TTTTGAAAAT-TATATATTATATAGTTAAAACA
* *
3640874 TTTTGAAAATTATATAATATATAGTTTTGAAAACG
1 TTTTGAAAATTATATATTATATAG--TT-AAAACA
* * *
3640909 TTTT-AAAA-TATATAATATATACTTTTGAAAACG
1 TTTTGAAAATTATATATTATATA--GTT-AAAACA
* **
3640942 TTATGAAACATT-TATA-TA-ATTTTTAAAACCA
1 TTTTGAAA-ATTATATATTATATAGTTAAAA-CA
**
3640973 -TTTGAAAACTTATATAAGATATAGTTGTAAAA-A
1 TTTTGAAAA-TTATATATTATATAG-T-TAAAACA
* * *
3641006 TAATTTTAAAGTTTATATAATATATAGTTAAAAACA
1 T--TTTGAAA-ATTATATATTATATAGTT-AAAACA
3641042 TTTTGAA
1 TTTTGAA
3641049 TCAATAATAT
Statistics
Matches: 163, Mismatches: 22, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
29 1 0.01
30 12 0.07
31 8 0.05
32 22 0.13
33 40 0.25
34 34 0.21
35 23 0.14
36 23 0.14
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (32 bp):
TTTTGAAAATTATATATTATATAGTTAAAACA
Found at i:3640922 original size:33 final size:35
Alignment explanation
Indices: 3640841--3640961 Score: 126
Period size: 33 Copynumber: 3.5 Consensus size: 35
3640831 GTTAAAACAT
* * **
3640841 TTTTGAAAATATGTATATTATATA--TTT-AAAATA
1 TTTTGAAAAT-TATATAATATATACTTTTGAAAACG
*
3640874 TTTTGAAAATTATATAATATATAGTTTTGAAAACG
1 TTTTGAAAATTATATAATATATACTTTTGAAAACG
3640909 TTTT-AAAA-TATATAATATATACTTTTGAAAACG
1 TTTTGAAAATTATATAATATATACTTTTGAAAACG
*
3640942 TTATGAAACATTTATATAAT
1 TTTTGAAA-A-TTATATAAT
3640962 TTTTAAAACC
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
32 11 0.15
33 37 0.49
34 10 0.13
35 9 0.12
37 8 0.11
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (35 bp):
TTTTGAAAATTATATAATATATACTTTTGAAAACG
Found at i:3641068 original size:28 final size:31
Alignment explanation
Indices: 3641022--3641098 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 31
3641012 TAAAGTTTAT
* ** *
3641022 ATAATATATAGTTAAAAAC-ATTTTGAATCA
1 ATAACATATAGTTTTAAACGATTTTGAAACA
* *
3641052 AT-A-ATATAGTTTTAAACGTTTTTGAAACT
1 ATAACATATAGTTTTAAACGATTTTGAAACA
3641081 ATAACATATAGTTTTAAA
1 ATAACATATAGTTTTAAA
3641099 ACGTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 12 0.31
29 11 0.28
30 3 0.08
31 13 0.33
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (31 bp):
ATAACATATAGTTTTAAACGATTTTGAAACA
Found at i:3641122 original size:32 final size:29
Alignment explanation
Indices: 3641042--3641106 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 29
3641032 GTTAAAAACA
* *
3641042 TTTTGAATCAATAATATAGTTTTAAACGT
1 TTTTGAAACTATAATATAGTTTTAAACGT
3641071 TTTTGAAACTATAACATATAGTTTTAAAACGT
1 TTTTGAAACTAT-A-ATATAGTTTT-AAACGT
3641103 TTTT
1 TTTT
3641107 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 10 0.32
30 1 0.03
31 10 0.32
32 10 0.32
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTGAAACTATAATATAGTTTTAAACGT
Found at i:3641215 original size:13 final size:13
Alignment explanation
Indices: 3641197--3641221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3641187 ATTCTTTTTT
3641197 TATTTATTATTTA
1 TATTTATTATTTA
3641210 TATTTATTATTT
1 TATTTATTATTT
3641222 GTTTTGTTTT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTATTATTTA
Found at i:3642028 original size:62 final size:62
Alignment explanation
Indices: 3641931--3642054 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
3641921 AAGGAGAGTG
3641931 TTCTGGGCTTGTTTAGACTTTCCGGCCACCGCCGGTGGTAGCCGGAGGCGGCGGTGGAAGGC
1 TTCTGGGCTTGTTTAGACTTTCCGGCCACCGCCGGTGGTAGCCGGAGGCGGCGGTGGAAGGC
3641993 TTCTGGGCTTGTTTAGACTTTCCGGCCACCGCCGGTGGTAGCCGGAGGCGGCGGTGGAAGGC
1 TTCTGGGCTTGTTTAGACTTTCCGGCCACCGCCGGTGGTAGCCGGAGGCGGCGGTGGAAGGC
3642055 GGAGTGGCTA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.11, C:0.26, G:0.40, T:0.23
Consensus pattern (62 bp):
TTCTGGGCTTGTTTAGACTTTCCGGCCACCGCCGGTGGTAGCCGGAGGCGGCGGTGGAAGGC
Found at i:3643894 original size:92 final size:92
Alignment explanation
Indices: 3643737--3643917 Score: 299
Period size: 92 Copynumber: 2.0 Consensus size: 92
3643727 CATAGTAACA
* *
3643737 CCCGTTAATATTGAGTGATCGATTTATTACAAATCGATAACGTTAGCGACTAATTTGTTACTTTT
1 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
* * *
3643802 AAAACTTTAATAGGAAAAACAAAATTG
66 AAAACTTCAATAAGAAAAAAAAAATTG
* *
3643829 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGTGACCAATTTGTTGCTTTT
1 CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
3643894 AAAACTTCAATAAGAAAAAAAAAA
66 AAAACTTCAATAAGAAAAAAAAAA
3643918 CTTACTCAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
92 82 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (92 bp):
CCCGTTAATATTGAGTGACCGATTTATTACAAATCGATAACGTTAGCGACCAATTTGTTACTTTT
AAAACTTCAATAAGAAAAAAAAAATTG
Found at i:3645942 original size:28 final size:28
Alignment explanation
Indices: 3645902--3645964 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
3645892 CCAACCTCAA
3645902 GTTCCATTAGATGAAAGTGATCTGCTTT
1 GTTCCATTAGATGAAAGTGATCTGCTTT
3645930 GTTCCATTAGATGAAAGTGATCTGCTTT
1 GTTCCATTAGATGAAAGTGATCTGCTTT
3645958 GTTCCAT
1 GTTCCAT
3645965 CTCCAAATCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.40
Consensus pattern (28 bp):
GTTCCATTAGATGAAAGTGATCTGCTTT
Found at i:3647264 original size:31 final size:31
Alignment explanation
Indices: 3647226--3647284 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3647216 TGTTAACACA
*
3647226 AGACATCTAAAGTGGTAACGTTTGTAATGTC
1 AGACATCTAAAGTGGTAACGTTTATAATGTC
3647257 AGACATCTAAAGTGGTAACGTTTATAAT
1 AGACATCTAAAGTGGTAACGTTTATAAT
3647285 TTAGGCATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (31 bp):
AGACATCTAAAGTGGTAACGTTTATAATGTC
Found at i:3648755 original size:19 final size:19
Alignment explanation
Indices: 3648733--3648769 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3648723 AACATTAAAA
3648733 AATAATAATATT-TTTTTTC
1 AATAAT-ATATTGTTTTTTC
3648752 AATAATATATTGTTTTTT
1 AATAATATATTGTTTTTT
3648770 GGAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
AATAATATATTGTTTTTTC
Found at i:3650922 original size:220 final size:212
Alignment explanation
Indices: 3650492--3650923 Score: 760
Period size: 220 Copynumber: 2.0 Consensus size: 212
3650482 TGGTTCCTTG
3650492 CAGTGTTAAATATGATCCTGAAGCCATGACTAAACTTCACATGTATGACAAAGTCTCCCCTGTGA
1 CAGTGTTAAATATGATCCTGAAGCCATGACTAAACTTCACATGTATGACAAAGTCTCCCCTGTGA
3650557 ATGCCCCTCGGGGATAGACAATTCACAGATAAGGGAACATGAGGGATCTCTTTACTTATGAGATT
66 ATGCCCCTCGGGGATAGACAATTCACAGATAAGGGAACATGAGGGATCTCTTTACTTATGAGATT
3650622 GAATTCGTTTAAAAGTATAGATGGCCATCTCGGTGGGATGCTTATTTGAAGATGGAAGGTGCACG
131 GAATTCGTTTAAAAGTATAGATGGCCATCTCGGTGGGATGCTTATTTGAAGATGGAAGGTGCACG
3650687 TGTGCACTGGTTCTCAA
196 TGTGCACTGGTTCTCAA
3650704 CAGTGTTAAATATGATCCTGAAGCCATGACT-AACTTCACATGTATGACAAAGTCTCCCCTGTGA
1 CAGTGTTAAATATGATCCTGAAGCCATGACTAAACTTCACATGTATGACAAAGTCTCCCCTGTGA
3650768 ACTGCCCCTCGGGGATAGACAATTCACAGATAATAAGGGAACATGAGAGGATCTCTTTTACTTAT
66 A-TGCCCCTCGGGGATAGACAATTCACAG---ATAAGGGAACATGAG-GGATCTC-TTTACTTAT
3650833 GAGATTGAATTCG-TTAAAAGTGATATTAGATGGCCATCTCGGTGGGATGCTTATTTGAAGATGG
125 GAGATTGAATTCGTTTAAAA--G-TA-TAGATGGCCATCTCGGTGGGATGCTTATTTGAAGATGG
3650897 AAGGTGCACGTGTGCACTGGTTCTCAA
186 AAGGTGCACGTGTGCACTGGTTCTCAA
3650924 TTCTAAACTC
Statistics
Matches: 210, Mismatches: 0, Indels: 12
0.95 0.00 0.05
Matches are distributed among these distances:
211 34 0.16
212 58 0.28
215 15 0.07
216 13 0.06
217 22 0.10
218 1 0.00
219 2 0.01
220 65 0.31
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (212 bp):
CAGTGTTAAATATGATCCTGAAGCCATGACTAAACTTCACATGTATGACAAAGTCTCCCCTGTGA
ATGCCCCTCGGGGATAGACAATTCACAGATAAGGGAACATGAGGGATCTCTTTACTTATGAGATT
GAATTCGTTTAAAAGTATAGATGGCCATCTCGGTGGGATGCTTATTTGAAGATGGAAGGTGCACG
TGTGCACTGGTTCTCAA
Found at i:3652991 original size:31 final size:31
Alignment explanation
Indices: 3652924--3652983 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
3652914 CAATTTAAGG
*
3652924 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3652955 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
3652984 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:3653187 original size:20 final size:20
Alignment explanation
Indices: 3653162--3653201 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3653152 TATTGAATAT
*
3653162 TATGAAGGGGTATCGATTCC
1 TATGAAGGGGTACCGATTCC
3653182 TATGAAGGGGTACCGATTCC
1 TATGAAGGGGTACCGATTCC
3653202 CCCCATTCTG
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:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TATGAAGGGGTACCGATTCC
Found at i:3653522 original size:31 final size:30
Alignment explanation
Indices: 3653487--3653544 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
3653477 AAGGGGAAAT
*
3653487 GTTCTAGCTTAGCCCGGTAAAAGCTAGGAAG
1 GTTCTAGCTTAGCCCGG-AAAAACTAGGAAG
*
3653518 GTTCTAGTTTAGCCCGGAAAAACTAGG
1 GTTCTAGCTTAGCCCGGAAAAACTAGG
3653545 GAGTTGTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (30 bp):
GTTCTAGCTTAGCCCGGAAAAACTAGGAAG
Found at i:3655189 original size:20 final size:21
Alignment explanation
Indices: 3655164--3655209 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
3655154 ATAATCGAGA
3655164 AATCATTTTGCAACTTTTAG-
1 AATCATTTTGCAACTTTTAGT
3655184 AATCATTTTGCAACTTTTAGT
1 AATCATTTTGCAACTTTTAGT
3655205 AATCA
1 AATCA
3655210 ACGAACTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (21 bp):
AATCATTTTGCAACTTTTAGT
Found at i:3665533 original size:149 final size:150
Alignment explanation
Indices: 3665254--3665545 Score: 380
Period size: 149 Copynumber: 2.0 Consensus size: 150
3665244 GGTCCAAAAA
* *
3665254 GGATAGGAATTTATCTTGATTAAGAAGTCGACTTATCAACCACACCAAATTGTCCCCATAAACTG
1 GGATAGGAATTTATCTTGATTAAGAAGTCCACTTATCAACCACACCAAAGTGTCCCCATAAACTG
* *
3665319 GAACAAACAGAAAAACAACGGGCATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGGAAAA
66 GAACAAACAGAAAAACAACGGACATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGAAAAA
*
3665384 GGGAA-GCAAAATCATCCTG
131 GAGAATGCAAAATCATCCTG
*
3665403 GGATAGGAATTTATCTTGA-TAAGAAG-CACACTTATCAACCATACCAAAGTGTGCCCC-TAAAC
1 GGATAGGAATTTATCTTGATTAAGAAGTC-CACTTATCAACCACACCAAAGTGT-CCCCATAAAC
* * * * * * *
3665465 TGGAAGAAGCAGAAACAAGAACTGACGTTTG-TGGCATTCTCAGAACAGTAACAT-AAAGAGATG
64 TGGAACAAACAGAAA-AACAACGGACATTTGCGGGC-TTCTCAGAACAGTAACATAAAAG-GAAG
3665528 AAAAAGAGAATGCAAAAT
126 AAAAAGAGAATGCAAAAT
3665546 TCAATTTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
147 1 0.01
148 53 0.43
149 63 0.51
150 7 0.06
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.20
Consensus pattern (150 bp):
GGATAGGAATTTATCTTGATTAAGAAGTCCACTTATCAACCACACCAAAGTGTCCCCATAAACTG
GAACAAACAGAAAAACAACGGACATTTGCGGGCTTCTCAGAACAGTAACATAAAAGGAAGAAAAA
GAGAATGCAAAATCATCCTG
Found at i:3677172 original size:20 final size:20
Alignment explanation
Indices: 3677135--3677177 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3677125 AATCCACCAC
3677135 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
3677155 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
3677175 ATG
1 ATG
3677178 GGCCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:3679814 original size:21 final size:21
Alignment explanation
Indices: 3679785--3679825 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3679775 AAGGGAGAAG
*
3679785 AAAATGATAGAAAGTAAAAGT
1 AAAAAGATAGAAAGTAAAAGT
*
3679806 AAAAAGATAGAAAGTGAAAG
1 AAAAAGATAGAAAGTAAAAG
3679826 GTGAAAACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.15
Consensus pattern (21 bp):
AAAAAGATAGAAAGTAAAAGT
Found at i:3687554 original size:20 final size:20
Alignment explanation
Indices: 3687517--3687559 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3687507 AATCCACCAC
3687517 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGCTTCTAA
* * *
3687537 ATGCATCTATATGGTTCTAA
1 ATGCAACTAAATGCTTCTAA
3687557 ATG
1 ATG
3687560 GGCCTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGCTTCTAA
Found at i:3693014 original size:27 final size:28
Alignment explanation
Indices: 3692957--3693014 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3692947 TTACGTGCAC
3692957 AAAAAATCCGAATATCTGATTTTGGGTAA
1 AAAAAATCCGAATATCTGATTTTGGG-AA
*
3692986 AAAATATCCGAA-ATC-GAATTTT-GGAA
1 AAAAAATCCGAATATCTG-ATTTTGGGAA
3693012 AAA
1 AAA
3693015 CCGGTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 3 0.11
28 8 0.30
29 11 0.41
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (28 bp):
AAAAAATCCGAATATCTGATTTTGGGAA
Found at i:3693213 original size:40 final size:40
Alignment explanation
Indices: 3693130--3693209 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
3693120 TCAAACCGGA
*
3693130 TAAAAAACTGATTTTTTATCCGAAAAAAATCTGGTTTTTT
1 TAAAAAACTGATTTTTTATCCGAAAAAAATCCGGTTTTTT
*
3693170 TAAAAAACTGGA-TTTTTATCCG-AAAAAATCCGTTTTTTT
1 TAAAAAACT-GATTTTTTATCCGAAAAAAATCCGGTTTTTT
3693209 T
1 T
3693210 TAAACTGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
39 16 0.43
40 19 0.51
41 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.42
Consensus pattern (40 bp):
TAAAAAACTGATTTTTTATCCGAAAAAAATCCGGTTTTTT
Found at i:3696413 original size:26 final size:26
Alignment explanation
Indices: 3696384--3696433 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3696374 GTTTTGAAAA
*
3696384 AAAATTAAAAGTTTAGGTACTAAATC
1 AAAATTAAAAGTTAAGGTACTAAATC
* *
3696410 AAAATTGATAGTTAAGGTACTAAA
1 AAAATTAAAAGTTAAGGTACTAAA
3696434 AGAATTAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.14, T:0.30
Consensus pattern (26 bp):
AAAATTAAAAGTTAAGGTACTAAATC
Found at i:3698151 original size:2 final size:2
Alignment explanation
Indices: 3698144--3698186 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3698134 AGTGGTTATC
3698144 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
3698186 A
1 A
3698187 ATGTTTCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3700578 original size:32 final size:31
Alignment explanation
Indices: 3700530--3700645 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 31
3700520 GGTTGGCTTA
*
3700530 AACCGAAAATCAACCGATCCGATATTGACCC
1 AACCCAAAATCAACCGATCCGATATTGACCC
* *
3700561 AACCCAAAATCTAACCGATCCGGTATTAACCC
1 AACCCAAAATC-AACCGATCCGATATTGACCC
* * *
3700593 GACCCAAAAATCAACCGACCCGATATTGATCCG
1 AACCC-AAAATCAACCGATCCGATATTGA-CCC
*
3700626 AACCGGAAAA-CAACCGATCC
1 AACC-CAAAATCAACCGATCC
3700646 AATAATCACC
Statistics
Matches: 70, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
31 10 0.14
32 45 0.64
33 15 0.21
ACGTcount: A:0.39, C:0.34, G:0.13, T:0.15
Consensus pattern (31 bp):
AACCCAAAATCAACCGATCCGATATTGACCC
Found at i:3700657 original size:64 final size:64
Alignment explanation
Indices: 3700535--3700660 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 64
3700525 GCTTAAACCG
* ** *
3700535 AAAATCAACCGATCCGATATTGACCCAACCCAAAATCTAACCGATCCGGTATTAACCCGACCCA
1 AAAATCAACCGACCCGATATTGACCCAACCCAAAATCTAACCGATCCAATAATAACCCGACCCA
* * *
3700599 AAAATCAACCGACCCGATATTGATCCGAACCGGAAAA-C-AACCGATCCAATAATCACCCGACC
1 AAAATCAACCGACCCGATATTGA-CCCAACC-CAAAATCTAACCGATCCAATAATAACCCGACC
3700661 TGATCCGATT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 42 0.79
65 7 0.13
66 4 0.08
ACGTcount: A:0.39, C:0.34, G:0.12, T:0.15
Consensus pattern (64 bp):
AAAATCAACCGACCCGATATTGACCCAACCCAAAATCTAACCGATCCAATAATAACCCGACCCA
Found at i:3703622 original size:18 final size:18
Alignment explanation
Indices: 3703599--3703635 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3703589 AACGAATTTT
3703599 GAGGAAGTGGTGGAACAC
1 GAGGAAGTGGTGGAACAC
* *
3703617 GAGGAAGTGTTGGACCAC
1 GAGGAAGTGGTGGAACAC
3703635 G
1 G
3703636 CGGAGAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.43, T:0.14
Consensus pattern (18 bp):
GAGGAAGTGGTGGAACAC
Found at i:3713020 original size:126 final size:127
Alignment explanation
Indices: 3712795--3713178 Score: 709
Period size: 126 Copynumber: 3.0 Consensus size: 127
3712785 AAAAGAAACA
*
3712795 GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAG-ATTTTTTT
1 GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAGCTTTTTTTT
3712859 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
66 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
* * *
3712921 GAAAGTAGCATCGATGCAGGATGAGTTAACC-AAAGCAACGATCCATACAAGTGAGCTTTTTTTT
1 GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAGCTTTTTTTT
3712985 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
66 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
3713047 GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAGCTTTTTTTT
1 GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAGCTTTTTTTT
3713112 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
66 ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
*
3713174 CAAAG
1 GAAAG
3713179 AGGGGGCGAT
Statistics
Matches: 248, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
125 22 0.09
126 129 0.52
127 97 0.39
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (127 bp):
GAAAGTAGCATCAATGCAGGATGAGTTAACCAAAAGCAATGATCCAAACAAGTGAGCTTTTTTTT
ACTATGTTTGATCACAATGATCAGAACCGACTAAATCAAGTAAACGGAGCAGTCACGGCATG
Found at i:3730833 original size:184 final size:184
Alignment explanation
Indices: 3730512--3730899 Score: 627
Period size: 184 Copynumber: 2.1 Consensus size: 184
3730502 ATTAAATTTT
* *
3730512 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTTAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
3730577 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
3730642 CTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTT-AATTAAA
131 CTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
* * *
3730696 AAATATTTTATATATTATATATAACATATGGGCTAAGTCCAAACCATTTAAAATCCAATTAATAA
1 AAATATTTAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
* * * * *
3730761 TTTAAGATCTAATAATTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
3730826 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
131 CTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
* *
3730880 AAAAATTTAAT-TTTTATATA
1 AAATATTTAATATATTATATA
3730900 AATTATAAAA
Statistics
Matches: 188, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
183 14 0.07
184 174 0.93
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (184 bp):
AAATATTTAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
CTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTGAATTAAA
Found at i:3733617 original size:2 final size:2
Alignment explanation
Indices: 3733612--3733649 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3733602 GTGTGTGTGC
3733612 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
3733650 CTTTGGCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3736524 original size:23 final size:23
Alignment explanation
Indices: 3736494--3736555 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 23
3736484 TCTTCTTTTT
*
3736494 GGTATAACCGATATCATTCAGGC
1 GGTATAACCGATATCATTCACGC
3736517 GGTATAACCGACCATATATCATTCACGC
1 GGTATAACCG-----ATATCATTCACGC
3736545 GGTATAACCGA
1 GGTATAACCGA
3736556 CCATATATCA
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
23 11 0.33
28 22 0.67
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (23 bp):
GGTATAACCGATATCATTCACGC
Found at i:3736546 original size:28 final size:28
Alignment explanation
Indices: 3736504--3736565 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
3736494 GGTATAACCG
*
3736504 ATATCATTCAGGCGGTATAACCGACCAT
1 ATATCATTCACGCGGTATAACCGACCAT
3736532 ATATCATTCACGCGGTATAACCGACCAT
1 ATATCATTCACGCGGTATAACCGACCAT
3736560 ATATCA
1 ATATCA
3736566 ATCAGGCGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (28 bp):
ATATCATTCACGCGGTATAACCGACCAT
Found at i:3736583 original size:28 final size:28
Alignment explanation
Indices: 3736522--3736590 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 28
3736512 CAGGCGGTAT
* ** *
3736522 AACCGACCATATATCATTCACGCGGTAT
1 AACCGACCATATATCAATCACGCGACAG
*
3736550 AACCGACCATATATCAATCAGGCGACAG
1 AACCGACCATATATCAATCACGCGACAG
*
3736578 AGCCGACCATATA
1 AACCGACCATATA
3736591 ATAAAACTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.19
Consensus pattern (28 bp):
AACCGACCATATATCAATCACGCGACAG
Found at i:3736999 original size:2 final size:2
Alignment explanation
Indices: 3736992--3737030 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
3736982 CATATTATTC
3736992 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3737031 CATACTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3748240 original size:21 final size:21
Alignment explanation
Indices: 3748214--3748253 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3748204 CCCCCTTTGA
*
3748214 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3748235 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3748254 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3752890 original size:2 final size:2
Alignment explanation
Indices: 3752883--3752924 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3752873 CAAACTATCC
3752883 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
3752925 CTTTCCAGTC
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:3755299 original size:23 final size:22
Alignment explanation
Indices: 3755273--3755317 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3755263 CCGAGTGGCA
*
3755273 TATGAAATTTGTCCCGAATGACC
1 TATG-AATTTATCCCGAATGACC
*
3755296 TATGTATTTATCCCGAATGACC
1 TATGAATTTATCCCGAATGACC
3755318 ACTGTATATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (22 bp):
TATGAATTTATCCCGAATGACC
Found at i:3755309 original size:22 final size:22
Alignment explanation
Indices: 3755279--3755339 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
3755269 GGCATATGAA
3755279 ATTTGTCCCGAATGACCTA-TGT
1 ATTTGTCCCGAATGACC-ACTGT
*
3755301 ATTTATCCCGAATGACCACTGT
1 ATTTGTCCCGAATGACCACTGT
* *
3755323 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAATGACC
3755340 GCGTAGACCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCACTGT
Found at i:3756005 original size:20 final size:20
Alignment explanation
Indices: 3755951--3755994 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3755941 TTTTCTTTAG
3755951 GGGGAATCGATACCCCCCAT
1 GGGGAATCGATACCCCCCAT
3755971 GGGGAATCGATACCCCCCAT
1 GGGGAATCGATACCCCCCAT
3755991 GGGG
1 GGGG
3755995 TATCTGTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (20 bp):
GGGGAATCGATACCCCCCAT
Found at i:3759055 original size:2 final size:2
Alignment explanation
Indices: 3759048--3759111 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3759038 AAAAGTATGC
3759048 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
3759090 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3759112 TATTTATTCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3760748 original size:45 final size:48
Alignment explanation
Indices: 3760681--3760778 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 48
3760671 TTATTTTCGT
**
3760681 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCGGTTAGG-TTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAATTAGGTTTTA
* *
3760728 TTTTTCGAA-CAA-GCATGCGAATTAGATATCATGCAATTAGGTTTTA
1 TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAATTAGGTTTTA
3760774 TTTTT
1 TTTTT
3760779 TGTGAATAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
45 26 0.57
46 11 0.24
47 9 0.20
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (48 bp):
TTTTTCGAATAAATGCATGCGAACTAGATATCATGCAATTAGGTTTTA
Found at i:3770465 original size:25 final size:23
Alignment explanation
Indices: 3770434--3770515 Score: 71
Period size: 22 Copynumber: 3.6 Consensus size: 23
3770424 AAGAAAGAAG
3770434 AAATGAAAAAAAAAGAAAAAAATA
1 AAATGAAAAAAAAAGAAAAAAA-A
* *
3770458 ATAATGAAAAATGAAA-AAATAAAA
1 A-AATGAAAAA-AAAAGAAAAAAAA
* *
3770482 AAA-GAAGAAAAAAGAAAAAGAA
1 AAATGAAAAAAAAAGAAAAAAAA
*
3770504 AAA-GAAATAAAA
1 AAATGAAAAAAAA
3770516 GGAGGGTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
21 3 0.06
22 21 0.45
23 2 0.04
24 3 0.06
25 15 0.32
26 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (23 bp):
AAATGAAAAAAAAAGAAAAAAAA
Done.