Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 21
Found at i:2332929 original size:19 final size:19
Alignment explanation
Indices: 2332891--2332929 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2332881 AAGAAAGAAG
*
2332891 AGAGACAGCCACAGAGAGC
1 AGAGACAGCCACAGACAGC
*
2332910 AGAGACAGCCACGGACAGC
1 AGAGACAGCCACAGACAGC
2332929 A
1 A
2332930 AGCAACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.28, G:0.31, T:0.00
Consensus pattern (19 bp):
AGAGACAGCCACAGACAGC
Found at i:2333971 original size:2 final size:2
Alignment explanation
Indices: 2333964--2333998 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2333954 TTATTATTTT
2333964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2333999 TTTGTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2337814 original size:21 final size:21
Alignment explanation
Indices: 2337697--2337814 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
2337687 ACGCGAAATA
**
2337697 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
2337717 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
2337737 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
2337758 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
2337779 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
2337800 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
2337815 ACACATAAAT
Statistics
Matches: 72, Mismatches: 22, Indels: 7
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.33
21 45 0.62
22 2 0.03
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:2337826 original size:20 final size:20
Alignment explanation
Indices: 2337801--2337954 Score: 87
Period size: 20 Copynumber: 7.7 Consensus size: 20
2337791 CGATTTTCCA
2337801 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTAAC-CAT
* *
2337821 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * **
2337841 AAATCGCAACGTGTATCTGT
1 AAATCGCAACGCGTAACCAT
****
2337861 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCAT
** * *
2337881 AAATCGCAATACGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
2337901 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCAT
* * *
2337921 AAATCACAACG-ATAATACAT
1 AAATCGCAACGCGTAA-CCAT
2337941 AAAATCGCAACGCG
1 -AAATCGCAACGCG
2337955 ATATTTAAAG
Statistics
Matches: 108, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
19 2 0.02
20 94 0.87
21 12 0.11
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTAACCAT
Found at i:2337850 original size:40 final size:40
Alignment explanation
Indices: 2337801--2337954 Score: 141
Period size: 40 Copynumber: 3.8 Consensus size: 40
2337791 CGATTTTCCA
2337801 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAAC-CATAAATCGCAACGCGTATCCGT
* * ** **
2337841 AAATCGCAACGTGTATCTGTAAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGT
** * * *
2337881 AAATCGCAATACGTATCCGTATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGT
* * *
2337921 AAATCACAACG-ATAATACATAAAATCGCAACGCG
1 AAATCGCAACGCGTAA-CCAT-AAATCGCAACGCG
2337955 ATATTTAAAG
Statistics
Matches: 90, Mismatches: 21, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
39 2 0.02
40 74 0.82
41 14 0.16
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTAACCATAAATCGCAACGCGTATCCGT
Found at i:2338377 original size:33 final size:33
Alignment explanation
Indices: 2338338--2338408 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2338328 TTCACTTAGA
*
2338338 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2338371 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2338404 TTTCA
1 TTTCA
2338409 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2338532 original size:20 final size:20
Alignment explanation
Indices: 2338488--2338597 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
2338478 TGCAGAAGAG
*
2338488 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
2338509 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
2338529 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
2338550 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
2338564 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
2338583 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
2338598 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:2338545 original size:41 final size:38
Alignment explanation
Indices: 2338481--2338597 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
2338471 TTCAATTTGC
* *
2338481 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2338519 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
2338560 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
2338593 AGAAT
1 AGAAT
2338598 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:2338567 original size:14 final size:14
Alignment explanation
Indices: 2338548--2338604 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2338538 GAGAAATGAA
2338548 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2338562 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
2338581 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2338595 AATCGCAACG
1 AATCGCAACG
2338605 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2338580 original size:33 final size:33
Alignment explanation
Indices: 2338540--2338620 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
2338530 CGCAACGAGA
2338540 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
2338573 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
2338606 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
2338621 TTGCGATTTC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:2338642 original size:18 final size:18
Alignment explanation
Indices: 2338616--2338711 Score: 91
Period size: 14 Copynumber: 5.7 Consensus size: 18
2338606 GAAACCAAAA
*
2338616 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2338634 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
2338648 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
2338666 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
2338680 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATT-TCATT
*
2338699 TCGTGTTGCGATT
1 TCGCGTTGCGATT
2338712 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
14 20 0.32
15 4 0.06
16 2 0.03
17 6 0.10
18 20 0.32
19 11 0.17
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:2338656 original size:14 final size:14
Alignment explanation
Indices: 2338637--2338725 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
2338627 TTTCATTTCG
2338637 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2338651 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
2338669 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2338683 CGTTGCGATTGTCATTT
1 CGTTGCGA-T-TC-TCT
2338700 CGTGTTGCGATTCTCT
1 C--GTTGCGATTCTCT
2338716 CGTTGCGATT
1 CGTTGCGATT
2338726 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.44
15 4 0.06
16 5 0.08
17 8 0.13
18 11 0.18
19 7 0.11
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2338707 original size:33 final size:32
Alignment explanation
Indices: 2338621--2338733 Score: 199
Period size: 32 Copynumber: 3.5 Consensus size: 32
2338611 CAAAATCGCA
2338621 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
2338653 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
*
2338685 TTGCGATTGTCATTTCGTGTTGCGATTCTCTCG
1 TTGCGATT-TCATTTCGCGTTGCGATTCTCTCG
2338718 TTGCGATTTTCATTTC
1 TTGCGA-TTTCATTTC
2338734 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
32 40 0.51
33 36 0.46
34 2 0.03
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2340589 original size:93 final size:93
Alignment explanation
Indices: 2340430--2340805 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
2340420 TAGATTGCTT
* * *
2340430 AGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACATTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2340495 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2340523 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2340588 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2340616 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2340681 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2340709 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2340774 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2340801 AGTAA
1 AGTAA
2340806 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 274 0.98
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2340893 original size:19 final size:19
Alignment explanation
Indices: 2340853--2340981 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2340843 TAGTTTACTT
* *
2340853 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2340873 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2340892 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
2340911 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
2340925 TCGCAACGCAAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2340944 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2340958 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2340977 TCGCA
1 TCGCA
2340982 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2340932 original size:33 final size:32
Alignment explanation
Indices: 2340889--2340981 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
2340879 CGCGAAACCA
**
2340889 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
2340921 AGAATCGCAACGCAAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2340954 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2340982 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2340979 original size:52 final size:52
Alignment explanation
Indices: 2340853--2340981 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
2340843 TAGTTTACTT
** *
2340853 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
* * *
2340905 T-G-AAAATCGCAACGACAGAATCGCAACGCAAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCAAAACCAAAATCGCAACG-CGAA-A
*
2340958 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
2340982 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 41 0.67
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
Found at i:2340999 original size:19 final size:19
Alignment explanation
Indices: 2340977--2341111 Score: 110
Period size: 19 Copynumber: 7.6 Consensus size: 19
2340967 GAAACCAAAA
*
2340977 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
2340996 TCGCGTTGTGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
*
2341012 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2341029 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2341045 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2341062 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2341081 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2341101 TCGTGTTGCGA
1 TCGCGTTGCGA
2341112 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 44 0.47
20 12 0.13
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2341028 original size:33 final size:33
Alignment explanation
Indices: 2340982--2341074 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
2340972 CAAAATCGCA
* *
2340982 TTGCGATTTTCATTTCGCGTTGTGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
* *
2341015 TTGTGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2341048 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2341075 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2343043 original size:14 final size:14
Alignment explanation
Indices: 2343024--2343059 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2343014 ATTGTTTAAT
2343024 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2343038 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2343052 TGATTTGT
1 TGATTTGT
2343060 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2343181 original size:19 final size:19
Alignment explanation
Indices: 2343165--2343262 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2343155 CAAAATGACT
2343165 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2343184 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2343203 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2343217 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2343236 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2343256 ATCGCAA
1 ATCGCAA
2343263 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2343294 original size:53 final size:53
Alignment explanation
Indices: 2343165--2343280 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
2343155 CAAAATGACT
2343165 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2343217 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2343270 ATCGCAATGCG
1 ATCGCAATGCG
2343281 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2343314 original size:14 final size:14
Alignment explanation
Indices: 2343295--2343349 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2343285 TAATTTCGCA
2343295 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
2343309 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
2343326 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
2343342 TTGCGATT
1 TTGCGATT
2343350 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:2343333 original size:19 final size:19
Alignment explanation
Indices: 2343309--2343505 Score: 202
Period size: 19 Copynumber: 11.4 Consensus size: 19
2343299 GATTCTCTCG
2343309 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2343328 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2343342 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2343361 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2343380 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2343394 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2343413 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2343432 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2343446 TTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2343465 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
2343479 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2343498 TTGCGATT
1 TTGCGATT
2343506 CTCTCGTTGC
Statistics
Matches: 149, Mismatches: 8, Indels: 42
0.75 0.04 0.21
Matches are distributed among these distances:
14 29 0.19
15 3 0.02
16 22 0.15
17 20 0.13
18 1 0.01
19 69 0.46
20 5 0.03
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2343387 original size:85 final size:86
Alignment explanation
Indices: 2343287--2343519 Score: 325
Period size: 85 Copynumber: 2.7 Consensus size: 86
2343277 TGCGTTTATA
*
2343287 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTG
2343352 C-ATT-TCGCATTGCGATTTTC
66 CGATTCTCGCATTGCGA-TTTC
* *
2343372 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCA-TT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATTT
* *
2343434 GCGATTCTCTCGTTGCGATTTC
65 GCGATTCTCGCATTGCGATTTC
* *
2343456 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
2343520 GTAATTTCCG
Statistics
Matches: 131, Mismatches: 9, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
83 9 0.07
84 13 0.10
85 99 0.76
86 3 0.02
87 7 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (86 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTG
CGATTCTCGCATTGCGATTTC
Found at i:2343505 original size:52 final size:52
Alignment explanation
Indices: 2343309--2343477 Score: 322
Period size: 52 Copynumber: 3.2 Consensus size: 52
2343299 GATTCTCTCG
2343309 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2343361 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
2343413 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
2343465 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2343478 GTTGGGATTT
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
51 8 0.07
52 108 0.93
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:2343527 original size:33 final size:33
Alignment explanation
Indices: 2343287--2343519 Score: 269
Period size: 33 Copynumber: 6.9 Consensus size: 33
2343277 TGCGTTTATA
2343287 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
2343320 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
2343353 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
2343393 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
2343424 ATTTCGCATTGCGATTCTCTCGTTGCGA-TTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
2343456 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
2343490 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
2343520 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 16, Indels: 30
0.79 0.07 0.14
Matches are distributed among these distances:
31 9 0.05
32 14 0.08
33 106 0.63
34 9 0.05
35 5 0.03
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.05
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:2346032 original size:24 final size:24
Alignment explanation
Indices: 2345998--2346044 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2345988 CTGAAACATC
2345998 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2346022 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2346045 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2346754 original size:20 final size:20
Alignment explanation
Indices: 2346726--2346955 Score: 230
Period size: 20 Copynumber: 11.5 Consensus size: 20
2346716 AAATTTCAGT
* * *
2346726 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2346746 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2346766 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2346786 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2346806 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
2346826 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
2346846 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
2346866 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2346886 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
2346906 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
**
2346926 GTTGCGATTTTA-ATATTCGC
1 GTTGCGA-TTTACGGATTCGC
2346946 GTTGCGATTT
1 GTTGCGATTT
2346956 TGGAAAATCG
Statistics
Matches: 183, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.02
20 175 0.96
21 5 0.03
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2346956 original size:20 final size:20
Alignment explanation
Indices: 2346922--2347019 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
2346912 ATTTATGTGT
*
2346922 TCGCGTTGCGATTTTAATAT
1 TCGCGTTGCGATTTTAATAA
2346942 TCGCGTTGCGATTTTGGAA-AA
1 TCGCGTTGCGATTTT--AATAA
** *
2346963 TCGCAATGCGAATTTGTACT-A
1 TCGCGTTGCG-ATTT-TAATAA
* *
2346984 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTT-AATAA
2347005 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
2347020 GGAAACTGAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.32
21 35 0.56
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTAATAA
Found at i:2346972 original size:21 final size:21
Alignment explanation
Indices: 2346942--2347059 Score: 82
Period size: 21 Copynumber: 5.7 Consensus size: 21
2346932 ATTTTAATAT
*
2346942 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
2346963 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
2346984 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
* *
2347005 TCGCGTTGCGATTTTGGAAAC
1 TCGCATTGCGATTTTGGAAAA
* **
2347026 T-G-ATTTGCGATTCTGG-GGA
1 TCGCA-TTGCGATTTTGGAAAA
2347045 TCGCATTGCGATTTT
1 TCGCATTGCGATTTT
2347060 TATTTCGCGT
Statistics
Matches: 72, Mismatches: 20, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
19 1 0.01
20 23 0.32
21 46 0.64
22 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:2347015 original size:42 final size:43
Alignment explanation
Indices: 2346922--2347020 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
2346912 ATTTATGTGT
* *
2346922 TCGCGTTGCG-ATTT-TAATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
** *
2346963 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAA-AA
*
2347005 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2347021 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 33 0.70
43 4 0.09
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTAATATTCGCATTGCGATTTTGCAAAA
Found at i:2348786 original size:4 final size:4
Alignment explanation
Indices: 2348777--2349163 Score: 774
Period size: 4 Copynumber: 96.8 Consensus size: 4
2348767 AGGTAAGGAA
2348777 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2348825 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2348873 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2348921 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2348969 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2349017 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2349065 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2349113 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2349161 TAT
1 TAT
2349164 TGATGGATGA
Statistics
Matches: 383, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 383 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:2351487 original size:54 final size:52
Alignment explanation
Indices: 2351370--2351563 Score: 173
Period size: 54 Copynumber: 3.8 Consensus size: 52
2351360 ATCAAATTTG
* * * *
2351370 AAAAACTTGGTTGATTTGCTTCCTC-T-TCATCATGTGAAGGTCAAA--TT-AA
1 AAAAACTTGGTTGATCTACTTTCTCATCTCTTCA--TGAAGGTCAAATCTTAAA
* * * * *
2351419 AAAAAGTTGGTTGATCTGCTTTCTCATCTCTTTATGAATGTTAAATCTTGAAAA
1 AAAAACTTGGTTGATCTACTTTCTCATCTCTTCATGAAGGTCAAATCTT--AAA
** * * *
2351473 AAAAACTTTTTTGATCTACTTCCTCATCTCTTCGTGAAGGTCAAATCTTTAA
1 AAAAACTTGGTTGATCTACTTTCTCATCTCTTCATGAAGGTCAAATCTTAAA
* *
2351525 AAAAACTTGGTTGATTTACTTTCTCATCTCTTCTTGAAG
1 AAAAACTTGGTTGATCTACTTTCTCATCTCTTCATGAAG
2351564 ATCCAATTAG
Statistics
Matches: 116, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
49 31 0.27
50 1 0.01
51 6 0.05
52 36 0.31
54 42 0.36
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (52 bp):
AAAAACTTGGTTGATCTACTTTCTCATCTCTTCATGAAGGTCAAATCTTAAA
Found at i:2351600 original size:49 final size:51
Alignment explanation
Indices: 2351483--2351619 Score: 152
Period size: 49 Copynumber: 2.7 Consensus size: 51
2351473 AAAAACTTTT
* * * **
2351483 TTGATCTACTTCCTCATCTCTTCGTGAAGGTCAAATCTTTAAAAAAACTTGG
1 TTGATTTACGTCCTCATCTCTTCGTGAAGATCAAATCTAGAAAAAAAC-TGG
* * * *
2351535 TTGATTTACTTTCTCATCTCTTCTTGAAGATCCAAT-TAGAAAAAAA-TGG
1 TTGATTTACGTCCTCATCTCTTCGTGAAGATCAAATCTAGAAAAAAACTGG
* *
2351584 TTGATTTGCGTCCTCATCTCTTCGTAAAGATCAAAT
1 TTGATTTACGTCCTCATCTCTTCGTGAAGATCAAAT
2351620 ATGAAAACCT
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
49 33 0.46
51 8 0.11
52 31 0.43
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (51 bp):
TTGATTTACGTCCTCATCTCTTCGTGAAGATCAAATCTAGAAAAAAACTGG
Found at i:2351626 original size:49 final size:49
Alignment explanation
Indices: 2351347--2351626 Score: 149
Period size: 49 Copynumber: 5.5 Consensus size: 49
2351337 TGCTTCCCCG
* * * *
2351347 TCTCTTTGTGAAGATCAAATTTG--AAAAACTTGGTTGATTTGCTTCCTCT
1 TCTCTTCGTGAAGATCAAA-TTGAAAAAAAC-TGGTTGATTTACGTCCTCA
* * * * * * *
2351396 TCATCAT-GTGAAGGTCAAATT-AAAAAAAGTTGGTTGATCTGCTTTCTCA
1 TC-TCTTCGTGAAGATCAAATTGAAAAAAA-CTGGTTGATTTACGTCCTCA
** * ** * *
2351445 TCTCTTTATGAATG-TTAAATCTTGAAAAAAAAACTTTTTTGATCTACTTCCTCA
1 TCTCTTCGTGAA-GATCAAA--TTG--AAAAAAAC-TGGTTGATTTACGTCCTCA
* * * *
2351499 TCTCTTCGTGAAGGTCAAATCTTTAAAAAAACTTGGTTGATTTACTTTCTCA
1 TCTCTTCGTGAAGATCAAA--TTGAAAAAAAC-TGGTTGATTTACGTCCTCA
* * *
2351551 TCTCTTCTTGAAGATCCAATTAGAAAAAAA-TGGTTGATTTGCGTCCTCA
1 TCTCTTCGTGAAGATCAAATT-GAAAAAAACTGGTTGATTTACGTCCTCA
*
2351600 TCTCTTCGTAAAGATCAAATATGAAAA
1 TCTCTTCGTGAAGATCAAAT-TGAAAA
2351627 CCTTGATGAT
Statistics
Matches: 184, Mismatches: 32, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
48 5 0.03
49 82 0.45
50 7 0.04
51 9 0.05
52 40 0.22
53 1 0.01
54 40 0.22
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (49 bp):
TCTCTTCGTGAAGATCAAATTGAAAAAAACTGGTTGATTTACGTCCTCA
Found at i:2351662 original size:48 final size:48
Alignment explanation
Indices: 2351598--2351703 Score: 140
Period size: 48 Copynumber: 2.2 Consensus size: 48
2351588 TTTGCGTCCT
* * * *
2351598 CATCTCTTCGTAAAGATCAAATATGAAAACCTTGATGATTTGCTGCAC
1 CATCTCTTTGTAAAGATCAAATATAAAAACCTTGATAATTTGATGCAC
* * * *
2351646 CATCTCTTTGTGAAGATCAAATCTAAAAACTTTGATAATTTGATTCAC
1 CATCTCTTTGTAAAGATCAAATATAAAAACCTTGATAATTTGATGCAC
2351694 CATCTCTTTG
1 CATCTCTTTG
2351704 CGAATATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (48 bp):
CATCTCTTTGTAAAGATCAAATATAAAAACCTTGATAATTTGATGCAC
Found at i:2351716 original size:48 final size:48
Alignment explanation
Indices: 2351623--2351727 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
2351613 ATCAAATATG
* * * * *
2351623 AAAACCTTGATGATTTGCTGCACCATCTCTTTGTGAAGATCAAATCTA
1 AAAACTTTGATAATTTGATGCACCATCTCTTTGCGAAGATAAAATCTA
* *
2351671 AAAACTTTGATAATTTGATTCACCATCTCTTTGCGAATATAAAATCTA
1 AAAACTTTGATAATTTGATGCACCATCTCTTTGCGAAGATAAAATCTA
*
2351719 GAAACTTTG
1 AAAACTTTG
2351728 CTGACATGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (48 bp):
AAAACTTTGATAATTTGATGCACCATCTCTTTGCGAAGATAAAATCTA
Found at i:2352852 original size:56 final size:56
Alignment explanation
Indices: 2352711--2353084 Score: 502
Period size: 56 Copynumber: 6.7 Consensus size: 56
2352701 AAATTCACCT
* * * * * *
2352711 ACTTATTATGAACTTCTTA-TGTTTGCACATATAGTTCCCATACGGAAATTCACAC
1 ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
* *
2352766 ACTTAGTATGAATTTCTTAG--TTTGCACACATAGTGCCCATACGGAAATTCATAC
1 ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
*
2352820 ACTTAGTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
1 ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
* *
2352876 ACTAATTATGAATTTCTTAGTTTTTGCACACATAGTACCCATACGGAAATTCATAA
1 ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
* * * * * *
2352932 ACTAATTATGAATTTCTTAACTTTTCGCACACAAAGTGCCCATATGGAAATTCATAC
1 ACTTATTATGAATTTCTT-AGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
* *
2352989 ACTTAGTATGAATTTCTTAGTTTTTACACACATAGTGCCCATACGGAAATTCATAA
1 ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
* * * *
2353045 ACTAATTATGAATTTATTAATTTTTTGCACACAAAGTGCC
1 ACTTATTATGAATTTCTT-AGTTTTTGCACACATAGTGCC
2353085 ATTTGATAAT
Statistics
Matches: 285, Mismatches: 29, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
54 51 0.18
55 17 0.06
56 151 0.53
57 66 0.23
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (56 bp):
ACTTATTATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA
Found at i:2352996 original size:169 final size:165
Alignment explanation
Indices: 2352715--2353077 Score: 555
Period size: 169 Copynumber: 2.2 Consensus size: 165
2352705 TCACCTACTT
* * * * * *
2352715 ATTATGAACTTCTTATGTTTGCACATATAGTTCCCATACGGAAATTCACACACTTAGTATGAATT
1 ATTATGAATTTCTTATTTTTGCACACATAGTACCCATACGGAAATTCACAAACTAAGTATGAATT
*
2352780 TCTTAGTTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTT
66 TCTTAGTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTT
*
2352845 GCACACATAGTGCCCATACGGAAATTCATAAACTA
131 ACACACATAGTGCCCATACGGAAATTCATAAACTA
* *
2352880 ATTATGAATTTCTTAGTTTTTGCACACATAGTACCCATACGGAAATTCATAAACTAATTATGAAT
1 ATTATGAATTTCTTA-TTTTTGCACACATAGTACCCATACGGAAATTCACAAACTAAGTATGAAT
* *
2352945 TTCTTAACTTTTCGCACACAAAGTGCCCATATGGAAATTCATACACTTAGTATGAATTTCTTAGT
65 TTCTT-A-GTTT-GCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
2353010 TTTTACACACATAGTGCCCATACGGAAATTCATAAACTA
127 TTTTACACACATAGTGCCCATACGGAAATTCATAAACTA
*
2353049 ATTATGAATTTATTAATTTTTTGCACACA
1 ATTATGAATTTCTT-A-TTTTTGCACACA
2353078 AAGTGCCATT
Statistics
Matches: 179, Mismatches: 14, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
165 14 0.08
166 47 0.26
167 1 0.01
168 3 0.02
169 101 0.56
170 13 0.07
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.36
Consensus pattern (165 bp):
ATTATGAATTTCTTATTTTTGCACACATAGTACCCATACGGAAATTCACAAACTAAGTATGAATT
TCTTAGTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGTTTTT
ACACACATAGTGCCCATACGGAAATTCATAAACTA
Found at i:2353011 original size:113 final size:113
Alignment explanation
Indices: 2352715--2353084 Score: 525
Period size: 113 Copynumber: 3.3 Consensus size: 113
2352705 TCACCTACTT
* * * * * *
2352715 ATTATGAACTTCTT-A-TGTTTGCACATATAGTTCCCATACGGAAATTCACACACTTAGTATGAA
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAA
* *
2352778 TTTCTTAG--TTTGCACACATAGTGCCCATACGGAAATTCATACACTT
66 TTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTA
* * * * * *
2352824 AGTATGAATTTCTT-AGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAATTATGAA
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAA
*
2352888 TTTCTTAGTTTTTGCACACATAGTACCCATACGGAAATTCATAAACTA
66 TTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTA
* *
2352936 ATTATGAATTTCTTAACTTTTCGCACACAAAGTGCCCATATGGAAATTCATACACTTAGTATGAA
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAA
*
2353001 TTTCTTAGTTTTTACACACATAGTGCCCATACGGAAATTCATAAACTA
66 TTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTA
* *
2353049 ATTATGAATTTATTAATTTTTTGCACACAAAGTGCC
1 ATTATGAATTTCTTAACTTTTTGCACACAAAGTGCC
2353085 ATTTGATAAT
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
109 13 0.06
110 49 0.21
112 48 0.21
113 122 0.53
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (113 bp):
ATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAGTATGAA
TTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTA
Found at i:2356329 original size:33 final size:33
Alignment explanation
Indices: 2356287--2356352 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2356277 TTCCTGTCTC
2356287 AGGTTACACAAGCACTGGGGCCTCCATTACTAT
1 AGGTTACACAAGCACTGGGGCCTCCATTACTAT
2356320 AGGTTACACAAGCACTGGGGCCTCCATTACTAT
1 AGGTTACACAAGCACTGGGGCCTCCATTACTAT
2356353 TATCTTTAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (33 bp):
AGGTTACACAAGCACTGGGGCCTCCATTACTAT
Found at i:2359886 original size:56 final size:56
Alignment explanation
Indices: 2359751--2360154 Score: 492
Period size: 56 Copynumber: 7.2 Consensus size: 56
2359741 ACCTACTTAT
* * * * *
2359751 TATGAACTTCTTA-TGTTTGCACATATAGTTCCCATACGGAAATTCA-AACACTTAG
1 TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAA-ACTAAG
* * * * *
2359806 TATGAATTTCTTAG--TTTGCACACATAGTTCCCATTCGGAAATTCATACATTTAG
1 TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
* * * *
2359860 TATTAATTTCTTAGTTTTTGCACACATAATGTCCATACGGAAATTCATAAACTAAT
1 TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
* *
2359916 TATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAT
1 TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
* * * * *
2359972 TATGAATATCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACACTTAG
1 TATGAATTTCTT-AGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
* * * *
2360029 TATGAATTTCTTAACTTTTTTCACACAAAGTGCCCATACGGAAATTCATAAACTAAT
1 TATGAATTTCTT-AGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
* * *
2360086 TATGAATTTCTTAGTTTTTGTACACATAGTGCCCATACAGAAATTCATAAACTAAT
1 TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
*
2360142 TATGAGTTTCTTA
1 TATGAATTTCTTA
2360155 ACATTCTACA
Statistics
Matches: 309, Mismatches: 35, Indels: 9
0.88 0.10 0.03
Matches are distributed among these distances:
54 47 0.15
55 13 0.04
56 146 0.47
57 103 0.33
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (56 bp):
TATGAATTTCTTAGTTTTTGCACACATAGTGCCCATACGGAAATTCATAAACTAAG
Found at i:2360113 original size:170 final size:167
Alignment explanation
Indices: 2359729--2360175 Score: 569
Period size: 170 Copynumber: 2.7 Consensus size: 167
2359719 CCCACTACCA
*** * * * * *
2359729 ATACGGAAATTCACCTACTTATTATGAACTTCTTATGTTTGCACATATAGTTCCCATACGGAAAT
1 ATACGGAAATTCATAAACTAATTATGAATTTCTTATTTTTGCACACATAGTGCCCATACGGAAAT
* * * * * * *
2359794 TCA-AACACTTAGTATGAATTTCTT-A-GTTTGCACACATAGTTCCCATTCGGAAATTCATACAT
66 TCATAA-ACTAATTATGAATTTCTTAACTTTTGCACACAAAGTGCCCATACGGAAATTCATACAC
* * *
2359856 TTAGTATTAATTTCTTAGTTTTTGCACACATAATGTCC
130 TTAGTATGAATTTCTTACTTTTTGCACACATAATGCCC
2359894 ATACGGAAATTCATAAACTAATTATGAATTTCTTAATTTTTGCACACATAGTGCCCATACGGAAA
1 ATACGGAAATTCATAAACTAATTATGAATTTCTT-ATTTTTGCACACATAGTGCCCATACGGAAA
*
2359959 TTCATAAACTAATTATGAATATCTTAACTTTTTGCACACAAAGTGCCCATACGGAAATTCATACA
65 TTCATAAACTAATTATGAATTTCTTAAC-TTTTGCACACAAAGTGCCCATACGGAAATTCATACA
*
2360024 CTTAGTATGAATTTCTTAACTTTTTTCACACA-AAGTGCCC
129 CTTAGTATGAATTTCTT-ACTTTTTGCACACATAA-TGCCC
* *
2360064 ATACGGAAATTCATAAACTAATTATGAATTTCTTAGTTTTTGTACACATAGTGCCCATACAGAAA
1 ATACGGAAATTCATAAACTAATTATGAATTTCTTA-TTTTTGCACACATAGTGCCCATACGGAAA
* * * *
2360129 TTCATAAACTAATTATGAGTTTCTTAACATTCTACAAACAAAGTGCC
65 TTCATAAACTAATTATGAATTTCTTAAC-TTTTGCACACAAAGTGCC
2360176 ATTTAGTAAT
Statistics
Matches: 246, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
165 29 0.12
166 46 0.19
167 3 0.01
169 50 0.20
170 118 0.48
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.36
Consensus pattern (167 bp):
ATACGGAAATTCATAAACTAATTATGAATTTCTTATTTTTGCACACATAGTGCCCATACGGAAAT
TCATAAACTAATTATGAATTTCTTAACTTTTGCACACAAAGTGCCCATACGGAAATTCATACACT
TAGTATGAATTTCTTACTTTTTGCACACATAATGCCC
Found at i:2361870 original size:84 final size:83
Alignment explanation
Indices: 2361782--2361947 Score: 201
Period size: 83 Copynumber: 2.0 Consensus size: 83
2361772 AGAATTTTTT
* * * * * *
2361782 TTATTTAGATAAGTGAAAAGGGTTTTT-TGGTACGTATAT-GAAAACCATTTGAAGGAAAATAAA
1 TTATTCAGATAAGTGAAAAGAGTTTTTCT--CAAGTACATGGAAAA-CATTTGAAGGAAAAGAAA
2361845 TGAAAAAGAAAAACAAATATG
63 TGAAAAAGAAAAACAAATATG
* *
2361866 TTATTCATATAAGTGAAAAGAGTTTTTCTCAAGTACATGGAAAACATTTGAAGGAAAAGCAATGA
1 TTATTCAGATAAGTGAAAAGAGTTTTTCTCAAGTACATGGAAAACATTTGAAGGAAAAGAAATGA
* *
2361931 ACAATAAAAACAAATAT
66 AAAAGAAAAACAAATAT
2361948 TTGTCTAGAT
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
83 40 0.57
84 29 0.41
85 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (83 bp):
TTATTCAGATAAGTGAAAAGAGTTTTTCTCAAGTACATGGAAAACATTTGAAGGAAAAGAAATGA
AAAAGAAAAACAAATATG
Found at i:2363517 original size:47 final size:46
Alignment explanation
Indices: 2363455--2363623 Score: 229
Period size: 47 Copynumber: 3.7 Consensus size: 46
2363445 AAATCTATTG
*
2363455 CCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
1 CCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
2363500 CCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
1 CCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
* *
2363547 CCATTTAGATTCCATAAGCTCGTAAGCTTAATTTT-CCAATATACTTG
1 CCATTTA-ATTCCATAAGCTCGTAAGCTT-ATTTTACCAAAATACTTA
* * *
2363594 CCA-TT-ATTCCGTAATCTCATAAGCTTATTT
1 CCATTTAATTCCATAAGCTCGTAAGCTTATTT
2363624 GCATGGTTAC
Statistics
Matches: 114, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
43 4 0.04
44 18 0.16
45 6 0.05
46 3 0.03
47 78 0.68
48 5 0.04
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (46 bp):
CCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATACTTA
Found at i:2368055 original size:27 final size:27
Alignment explanation
Indices: 2368025--2368079 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
2368015 ATAACTTTTT
2368025 ACCCTTAAGTATCTCAAACACAATACG
1 ACCCTTAAGTATCTCAAACACAATACG
* *
2368052 ACCCTTAAGTATCTCGAGCACAATACG
1 ACCCTTAAGTATCTCAAACACAATACG
2368079 A
1 A
2368080 ATATAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.29, G:0.11, T:0.22
Consensus pattern (27 bp):
ACCCTTAAGTATCTCAAACACAATACG
Found at i:2370269 original size:22 final size:22
Alignment explanation
Indices: 2370239--2370292 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
2370229 AGATTTTTTA
*
2370239 TGAATAGTGATGAACAATACCG
1 TGAACAGTGATGAACAATACCG
*
2370261 TGAACAGTGATGAACAGTACCG
1 TGAACAGTGATGAACAATACCG
2370283 TGAACAGTGA
1 TGAACAGTGA
2370293 ACAGTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (22 bp):
TGAACAGTGATGAACAATACCG
Found at i:2370839 original size:47 final size:46
Alignment explanation
Indices: 2370785--2370943 Score: 225
Period size: 47 Copynumber: 3.5 Consensus size: 46
2370775 CCATATATCA
2370785 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTC
1 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTT-AATTC
2370832 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAGATTC
1 CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTA-ATTC
* *
2370879 CATAAGCTCGTAAGCTTAATTTT-CCAATATACTTGCCA-TT-ATTC
1 CATAAGCTCGTAAGCTT-ATTTTACCAAAATACTTACCATTTAATTC
* * *
2370923 CGTAAGTTCATAAGCTTATTT
1 CATAAGCTCGTAAGCTTATTT
2370944 GCATGGTTAC
Statistics
Matches: 105, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
43 4 0.04
44 18 0.17
46 3 0.03
47 75 0.71
48 5 0.05
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.38
Consensus pattern (46 bp):
CATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAATTC
Found at i:2377060 original size:30 final size:31
Alignment explanation
Indices: 2376998--2377065 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2376988 ATAAGATATG
2376998 AGCTATGTGATCTTATGAAAATATGAAAAGA
1 AGCTATGTGATCTTATGAAAATATGAAAAGA
* * *
2377029 AGCTATGTGA-CTATATGTATATGTG-AAAGA
1 AGCTATGTGATCT-TATGAAAATATGAAAAGA
2377059 AGCTATG
1 AGCTATG
2377066 AGCTTCTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (31 bp):
AGCTATGTGATCTTATGAAAATATGAAAAGA
Found at i:2382939 original size:2 final size:2
Alignment explanation
Indices: 2382934--2382965 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2382924 TCTAGAATTA
2382934 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
2382966 GATTTTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2390850 original size:213 final size:214
Alignment explanation
Indices: 2390483--2390909 Score: 847
Period size: 213 Copynumber: 2.0 Consensus size: 214
2390473 GTTCCATACC
2390483 TTCCGGACATCCAATGTCATTTAAAGTGTCTACAATAAAATTCCATTCCGAGCGATCGTAAGCTT
1 TTCCGGACATCCAATGTCATTTAAAGTGTCTACAATAAAATTCCATTCCGAGCGATCGTAAGCTT
2390548 TTTCAAGATCAATCTTAATTTCCATCCACCCCCTTTTCCTTTATTGTGTCGCATTGAGTTCACAA
66 TTTCAAGATCAATCTTAATTTCCATCCACCCCCTTTTCCTTTATTGTGTCGCATTGAGTTCACAA
2390613 CCTCCTATTCTATGATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAG-TCTCT
131 CCTCCTATTCTATGATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCT
2390677 GACTCCCAATCCAACATAA
196 GACTCCCAATCCAACATAA
2390696 TTCCGGACATCCAATGTCATTTAAAGTGTCTACAATAAAATTCCATTCCGAGCGATCGTAAGCTT
1 TTCCGGACATCCAATGTCATTTAAAGTGTCTACAATAAAATTCCATTCCGAGCGATCGTAAGCTT
2390761 TTTCAAGATCAATCTTAATTTCCATCCACCCCCTTTTCCTTTATTGTGTCGCATTGAGTTCACAA
66 TTTCAAGATCAATCTTAATTTCCATCCACCCCCTTTTCCTTTATTGTGTCGCATTGAGTTCACAA
2390826 CCTCCTATTCTATGATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCT
131 CCTCCTATTCTATGATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCT
2390891 GACTCCCAATCCAACATAA
196 GACTCCCAATCCAACATAA
2390910 AGATTTTAAG
Statistics
Matches: 213, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
213 189 0.89
214 24 0.11
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (214 bp):
TTCCGGACATCCAATGTCATTTAAAGTGTCTACAATAAAATTCCATTCCGAGCGATCGTAAGCTT
TTTCAAGATCAATCTTAATTTCCATCCACCCCCTTTTCCTTTATTGTGTCGCATTGAGTTCACAA
CCTCCTATTCTATGATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCT
GACTCCCAATCCAACATAA
Found at i:2391024 original size:106 final size:106
Alignment explanation
Indices: 2390839--2391051 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
2390829 CCTATTCTAT
2390839 GATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCTGACTCCCAATCCA
1 GATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCTGACTCCCAATCCA
2390904 ACATAAAGATTTTAAGACGATTTACAATCACATTCGTTATC
66 ACATAAAGATTTTAAGACGATTTACAATCACATTCGTTATC
2390945 GATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCTGACTCCCAATCCA
1 GATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCTGACTCCCAATCCA
2391010 ACATAAAGATTTTAAGACGATTTACAATCACATTCGTTATC
66 ACATAAAGATTTTAAGACGATTTACAATCACATTCGTTATC
2391051 G
1 G
2391052 TCTTATACAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.33
Consensus pattern (106 bp):
GATAACGTTATCTTCAATGCTTCTACCACGAACAAAATTAGTTTAGTTCTCTGACTCCCAATCCA
ACATAAAGATTTTAAGACGATTTACAATCACATTCGTTATC
Found at i:2401434 original size:31 final size:32
Alignment explanation
Indices: 2401361--2401436 Score: 82
Period size: 31 Copynumber: 2.4 Consensus size: 32
2401351 GAGCCTGAGA
* * *
2401361 GCCTACCCAAGAAATATTCTCGTGGCCACAGG
1 GCCTACTCAAGAAATAATCTCGGGGCCACAGG
* * * *
2401393 GACTATTCAAGAAA-AATCTTGGGGCCGCAGG
1 GCCTACTCAAGAAATAATCTCGGGGCCACAGG
2401424 GCCTACTCAAGAA
1 GCCTACTCAAGAA
2401437 TGGTCTCAGG
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (32 bp):
GCCTACTCAAGAAATAATCTCGGGGCCACAGG
Found at i:2405460 original size:13 final size:13
Alignment explanation
Indices: 2405444--2405471 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2405434 TGATATCAGC
2405444 AATGGTTGCGATT
1 AATGGTTGCGATT
2405457 AATGGTTGCGATT
1 AATGGTTGCGATT
2405470 AA
1 AA
2405472 GATAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (13 bp):
AATGGTTGCGATT
Found at i:2407037 original size:18 final size:18
Alignment explanation
Indices: 2407016--2407056 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
2407006 TACGATGTTT
2407016 CGTCTTTATTCCAATTTC
1 CGTCTTTATTCCAATTTC
*
2407034 CGTCTTTATTCCAATTTT
1 CGTCTTTATTCCAATTTC
2407052 CGTCT
1 CGTCT
2407057 GTGTCCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.27, G:0.07, T:0.51
Consensus pattern (18 bp):
CGTCTTTATTCCAATTTC
Found at i:2407499 original size:24 final size:24
Alignment explanation
Indices: 2407470--2407544 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
2407460 TAAGTCAATA
* *
2407470 GTCAGACCGATCAACGGTCAATGG
1 GTCAGACCGGTCAATGGTCAATGG
* *
2407494 GTCAGACCGGTCAATGGTCAACGA
1 GTCAGACCGGTCAATGGTCAATGG
* *
2407518 GTTAGATCGGTCAATGGTCAATGG
1 GTCAGACCGGTCAATGGTCAATGG
2407542 GTC
1 GTC
2407545 GAGTCGGGTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (24 bp):
GTCAGACCGGTCAATGGTCAATGG
Found at i:2417345 original size:22 final size:22
Alignment explanation
Indices: 2417320--2417367 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
2417310 AATCATACCA
* *
2417320 AAAACATCTTAATTACATCAAG
1 AAAACATCATAATCACATCAAG
* *
2417342 AAAACCTCATAATCACTTCAAG
1 AAAACATCATAATCACATCAAG
2417364 AAAA
1 AAAA
2417368 TTATTTCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.52, C:0.21, G:0.04, T:0.23
Consensus pattern (22 bp):
AAAACATCATAATCACATCAAG
Found at i:2417530 original size:3 final size:3
Alignment explanation
Indices: 2417522--2417549 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2417512 AAAGGATGAA
2417522 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
2417550 TCAACAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2427747 original size:30 final size:30
Alignment explanation
Indices: 2427699--2427757 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2427689 TTTGATCCCT
*
2427699 AAACTTTTCAAAGATTATACCTTGGTCACC
1 AAACTTTTCAAAGATTATAACTTGGTCACC
* *
2427729 AAACTTTATCAAA-TTTATAATTTGGTCAC
1 AAACTTT-TCAAAGATTATAACTTGGTCAC
2427758 TAAATATATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTTCAAAGATTATAACTTGGTCACC
Found at i:2431407 original size:33 final size:34
Alignment explanation
Indices: 2431339--2431408 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
2431329 TAAGTGTGTT
* *
2431339 GTTCATTAAAGTATGCATTGCACTTAATATGCTA
1 GTTCATTAAAGCATGCATTACACTTAATATGCTA
* *
2431373 GTTCATTAAAGCATGCATTACA-TTAATCTTCTA
1 GTTCATTAAAGCATGCATTACACTTAATATGCTA
2431406 GTT
1 GTT
2431409 AAGTTTGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.38
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (34 bp):
GTTCATTAAAGCATGCATTACACTTAATATGCTA
Found at i:2431509 original size:17 final size:17
Alignment explanation
Indices: 2431489--2431541 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
2431479 TTAATAAGGT
*
2431489 TAGTTCACTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
2431506 TAGTTCATTCATTAAAC
1 TAGTTCATTAATCAAAC
*
2431523 TAGTGCATTAATCAAAC
1 TAGTTCATTAATCAAAC
2431540 TA
1 TA
2431542 CATCTAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.34
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:2441767 original size:27 final size:28
Alignment explanation
Indices: 2441708--2441769 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
2441698 TTACTTATAT
2441708 CAATTTCCTTCTTACAACATTCGCAGGG
1 CAATTTCCTTCTTACAACATTCGCAGGG
* *
2441736 TAATTTCCTTCTT-CAACATT-GCCATGG
1 CAATTTCCTTCTTACAACATTCG-CAGGG
2441763 CAATTTC
1 CAATTTC
2441770 AGCGTTTCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 17 0.57
28 12 0.40
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.37
Consensus pattern (28 bp):
CAATTTCCTTCTTACAACATTCGCAGGG
Found at i:2444284 original size:2 final size:2
Alignment explanation
Indices: 2444277--2444302 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2444267 ACTGGTCAAT
2444277 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
2444303 CTAAAAGCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2444787 original size:3 final size:3
Alignment explanation
Indices: 2444772--2444836 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
2444762 TGTCTCGATT
* * * * *
2444772 TTA TTA TTT TTA TTA TTA TAA TAA TTA TTA TTA TAA TAA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2444819 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
2444837 AATAATCTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2446499 original size:118 final size:117
Alignment explanation
Indices: 2446259--2446506 Score: 266
Period size: 118 Copynumber: 2.1 Consensus size: 117
2446249 TTTCTAATAT
* * *
2446259 TTATTTATTTTTTAATATTAAAGAAAAGGGTTGTCTTAAAGCAACTAGATGTCATTTTCTGATAA
1 TTATTTATTTATTAATATTAAAGAAAAGGGATGTCTTAAAACAACTAGATGTCATTTTCTGATAA
* ***** * * * * *
2446324 TTTTAAATAAAAAATACTATATTTTAGTTTTATTATTATATTGTTATTAATAT
66 TTTTAAATAAAAAATACCATATTTTAAAACCATAAGTACATTGATATT-ATAC
* * *
2446377 TTATTTATTTATTAATATTAAAGAAAGGGGATGTCTTAAAATAACTAGATGTCATTTTCTGATAT
1 TTATTTATTTATTAATATTAAAGAAAAGGGATGTCTTAAAACAACTAGATGTCATTTTCTGATAA
* *
2446442 TTTTAAATAAATAAATACCCTATTTATAAAACCCTAAGTACATAT-ATATT-TAC
66 TTTTAAATAAA-AAATACCATATTT-TAAAACCATAAGTACAT-TGATATTATAC
2446495 TTATTTACTTTA
1 TTATTTA-TTTA
2446507 GTTTTATAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
118 79 0.74
119 15 0.14
120 12 0.11
121 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (117 bp):
TTATTTATTTATTAATATTAAAGAAAAGGGATGTCTTAAAACAACTAGATGTCATTTTCTGATAA
TTTTAAATAAAAAATACCATATTTTAAAACCATAAGTACATTGATATTATAC
Found at i:2447744 original size:28 final size:28
Alignment explanation
Indices: 2447701--2447755 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2447691 TTTAATTTTT
* *
2447701 ATTTTATTTTTATCTATTTTGTATATAC
1 ATTTTATTTTGATCTAATTTGTATATAC
* *
2447729 ATTTTATTTTGCTCTAATTTGTTTATA
1 ATTTTATTTTGATCTAATTTGTATATA
2447756 TTGATTTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.64
Consensus pattern (28 bp):
ATTTTATTTTGATCTAATTTGTATATAC
Found at i:2449451 original size:6 final size:7
Alignment explanation
Indices: 2449410--2449450 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
2449400 TTTTCAAACA
2449410 TGCA-TT
1 TGCATTT
2449416 TGCATTT
1 TGCATTT
2449423 TGCATCTT
1 TGCAT-TT
2449431 TGCATTT
1 TGCATTT
2449438 T-CATTT
1 TGCATTT
2449444 TGCATTT
1 TGCATTT
2449451 GTACTTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.31
7 15 0.47
8 7 0.22
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.56
Consensus pattern (7 bp):
TGCATTT
Found at i:2451976 original size:12 final size:11
Alignment explanation
Indices: 2451959--2452003 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
2451949 CTCATTCATC
2451959 AAAAAAAAAAGG
1 AAAAAAAAAA-G
*
2451971 AAAAAAGAAAG
1 AAAAAAAAAAG
2451982 AAAAAAAGAAAG
1 AAAAAAA-AAAG
2451994 AAGAAAAAAA
1 AA-AAAAAAA
2452004 TGAATCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 7 0.24
12 17 0.59
13 5 0.17
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:2451987 original size:19 final size:18
Alignment explanation
Indices: 2451959--2452003 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
2451949 CTCATTCATC
2451959 AAAAAAAAAAGGAAAAAAG
1 AAAAAAAAAA-GAAAAAAG
*
2451978 AAAGAAAAAAAGAAAGAAG
1 AAA-AAAAAAAGAAAAAAG
2451997 AAAAAAA
1 AAAAAAA
2452004 TGAATCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 13 0.54
20 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAG
Found at i:2451995 original size:16 final size:15
Alignment explanation
Indices: 2451974--2452003 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
2451964 AAAAAGGAAA
2451974 AAAGAAAGAAAAAAAG
1 AAAG-AAGAAAAAAAG
2451990 AAAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
2452004 TGAATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAAAAAAG
Found at i:2453494 original size:118 final size:118
Alignment explanation
Indices: 2453286--2453509 Score: 378
Period size: 118 Copynumber: 1.9 Consensus size: 118
2453276 CCAGAAATAG
* *
2453286 AATATTGAGGCATCTCAAAAGCCCATTTCAGACAGAAATGATCCATGTGTGGCATTTTGAAGGCC
1 AATATTGAGGCATCTCAAAAGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGACC
2453351 CACGACAGTATGAATATTTAGGCATTTCTGAAAGCTCATATTAGCAAGAAGCA
66 CACGACAGTATGAATATTTAGGCATTTCTGAAAGCTCATATTAGCAAGAAGCA
*
2453404 AATATTTG-GGCATCTCGAAAGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGAC
1 AATA-TTGAGGCATCTCAAAAGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGAC
* * *
2453468 CCACGTCAGTATGAATATTTGGGCATTTTTGAAAGCTCATAT
65 CCACGACAGTATGAATATTTAGGCATTTCTGAAAGCTCATAT
2453510 CACCATGAAG
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
118 96 0.97
119 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (118 bp):
AATATTGAGGCATCTCAAAAGCCCATTTCAGACAGAAATGATCCATGTGGGGCATTTTGAAGACC
CACGACAGTATGAATATTTAGGCATTTCTGAAAGCTCATATTAGCAAGAAGCA
Found at i:2454380 original size:22 final size:22
Alignment explanation
Indices: 2454352--2454408 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
2454342 ACATCTACAT
*
2454352 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
2454374 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
* *
2454396 TTTTCAAATATGA
1 TCTTCAAAGATGA
2454409 AAGCTTTACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:2455168 original size:42 final size:42
Alignment explanation
Indices: 2455063--2455484 Score: 481
Period size: 42 Copynumber: 9.9 Consensus size: 42
2455053 ATTTTGTAAG
* * * *
2455063 TCCTCCGGGCCATCCATAAGACCTCCAGTGCAGGATGTTTAAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATG-TT-AAA
**
2455107 TCCTTCGGGTCATCTATAAGACCTTTAGTGCAAGATGTTAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
*
2455149 T-CTTACGGGTCAT-TCATAAGACCTCCAGTGCAGGATGTTTAAAA
1 TCCTT-CGGGTCATCT-ATAAGACCTCCAGTGCAAGATG-TT-AAA
*
2455193 TCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
* * * * * *
2455235 TCC-TCTTGTTCATCCATAAGACCTCCAGTGTAGGATATTTAAAA
1 TCCTTC-GGGTCATCTATAAGACCTCCAGTGCAAGAT-GTT-AAA
* *
2455279 TCCTTCGGGTCATCTGTAAGACCTCCAGTACAAGATGTTAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
*
2455321 TCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
* *
2455363 TCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATGTTTAAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATG-TT-AAA
* * *
2455407 TCATTCAGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAA
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
* * * * *
2455449 TCCTTCGTGCCATCCATAACACCTTCAGTGCAAGAT
1 TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGAT
2455485 ATTTTCAAAT
Statistics
Matches: 323, Mismatches: 43, Indels: 26
0.82 0.11 0.07
Matches are distributed among these distances:
41 6 0.02
42 170 0.53
43 14 0.04
44 127 0.39
45 6 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (42 bp):
TCCTTCGGGTCATCTATAAGACCTCCAGTGCAAGATGTTAAA
Found at i:2455223 original size:86 final size:85
Alignment explanation
Indices: 2455068--2455484 Score: 495
Period size: 86 Copynumber: 4.9 Consensus size: 85
2455058 GTAAGTCCTC
* * **
2455068 CGGGCCATCCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTTT
1 CGGGTCATTCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTCC
2455133 AGTGCAAGATGTTAAATCTT
66 AGTGCAAGATGTTAAATCTT
*
2455153 ACGGGTCATTCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTGTAAGACCTC
1 -CGGGTCATTCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTC
*
2455218 CAGTGCAAGATGTTAAATCCT
65 CAGTGCAAGATGTTAAATCTT
* * * * * *
2455239 CTTGTTCATCCATAAGACCTCCAGTGTAGGATATTTAAAATCCTTCGGGTCATCTGTAAGACCTC
1 C-GGGTCATTCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTC
*
2455304 CAGTACAAGATGTTAAATCCTT
65 CAGTGCAAGATGTTAAAT-CTT
* * *
2455326 CGGGTCA-TCTGTAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATCCATAAGACCTC
1 CGGGTCATTC-ATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTC
*
2455388 CAGTGCAGGATGTTTAAAATCATT
65 CAGTGCAAGATG-TT-AAATC-TT
* * * * * * * *
2455412 CAGGTCA-TCTGTAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGTGCCATCCATAACACCTT
1 CGGGTCATTC-ATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTC
2455474 CAGTGCAAGAT
65 CAGTGCAAGAT
2455485 ATTTTCAAAT
Statistics
Matches: 295, Mismatches: 30, Indels: 12
0.88 0.09 0.04
Matches are distributed among these distances:
84 36 0.12
85 7 0.02
86 249 0.84
87 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (85 bp):
CGGGTCATTCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTCC
AGTGCAAGATGTTAAATCTT
Found at i:2455349 original size:128 final size:127
Alignment explanation
Indices: 2455079--2455484 Score: 523
Period size: 128 Copynumber: 3.2 Consensus size: 127
2455069 GGGCCATCCA
* * ** * *
2455079 TAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCATCTATAAGACCTTTAGTGCAAGATG
1 TAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATT
* *
2455144 TT-AAAT-CTTACGGGTCAT-TCATAAGACCTCCAGTGCAGGATGTTTAAAATCCTTCGGGTCAT
64 TTAAAATCCTT-CGGGTCATCT-GTAAGACCTCCAGTGCAAGATG-TT-AAATCCTTCGGGTCAT
2455206 CTG
125 CTG
* * *
2455209 TAAGACCTCCAGTGCAAGATGTTAAATCC-TCTTGTTCATCCATAAGACCTCCAGTGTAGGATAT
1 TAAGACCTCCAGTGCAAGATGTTAAATCCTTC-GGGTCATCCATAAGACCTCCAGTGCAGGAT-T
*
2455273 TTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTACAAGATGTTAAATCCTTCGGGTCATCTG
64 TTAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCTG
2455337 TAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATGTT
1 TAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGAT-TT
* * * * **
2455402 TAAAATCATTCAGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGTGCCATCCA
65 TAAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCTG
* *
2455465 TAACACCTTCAGTGCAAGAT
1 TAAGACCTCCAGTGCAAGAT
2455485 ATTTTCAAAT
Statistics
Matches: 245, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
127 2 0.01
128 180 0.73
129 8 0.03
130 51 0.21
131 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (127 bp):
TAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCCATAAGACCTCCAGTGCAGGATTTT
AAAATCCTTCGGGTCATCTGTAAGACCTCCAGTGCAAGATGTTAAATCCTTCGGGTCATCTG
Found at i:2455810 original size:3 final size:3
Alignment explanation
Indices: 2455795--2455853 Score: 75
Period size: 3 Copynumber: 20.0 Consensus size: 3
2455785 TGTTTCAATT
* * * *
2455795 TTA TTA TTT TTA TTA TTA TAA TAA TTA TTA TTA TAA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2455842 TTA TTA TTA TTA
1 TTA TTA TTA TTA
2455854 AATAATTTTA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2457256 original size:54 final size:54
Alignment explanation
Indices: 2457153--2457257 Score: 126
Period size: 54 Copynumber: 1.9 Consensus size: 54
2457143 TTGGTCATAA
* * *
2457153 TTTAATTATAATTTTATTATTTTCCTTTAAATTTTAATATGTTTAAATTAATAC
1 TTTAATTATAATTTTATTATTTTCCTATAAATTATAATATATTTAAATTAATAC
*
2457207 TTTAATTATTATTTTATTATTTTACACATATAAA-TAT-ATATATTT-AATTAA
1 TTTAATTATAATTTTATTATTTT-C-C-TATAAATTATAATATATTTAAATTAA
2457258 ATTTCTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
54 28 0.64
55 8 0.18
56 3 0.07
57 5 0.11
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (54 bp):
TTTAATTATAATTTTATTATTTTCCTATAAATTATAATATATTTAAATTAATAC
Found at i:2460580 original size:23 final size:23
Alignment explanation
Indices: 2460546--2460600 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
2460536 TATTATAGGT
*
2460546 ATTACTGGTGGCAATGTCCAAGA
1 ATTACTGCTGGCAATGTCCAAGA
*
2460569 ATTACTGCTGGCAATGTTCAAGA
1 ATTACTGCTGGCAATGTCCAAGA
*
2460592 ATTATTGCT
1 ATTACTGCT
2460601 TTGTCCTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTACTGCTGGCAATGTCCAAGA
Found at i:2465644 original size:55 final size:55
Alignment explanation
Indices: 2465572--2466042 Score: 513
Period size: 55 Copynumber: 8.6 Consensus size: 55
2465562 TGGACAAGTG
* * * * * *
2465572 ATAATGAGTTTGTGAATTATCGTATTGGCAATATGTATACAAATCCC-TGTAATTC
1 ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAA-CCCACGTAATTC
* * *
2465627 ATAACGAGTTTATGAATTACCGTATTGGCACTATGTGTGCAAACCCACGTAATTC
1 ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAACCCACGTAATTC
* * *
2465682 ATAATGATTTTGTGAATTA-CAGTATCAGCACTATGTGTGCAAACCCACGTAATTC
1 ATAATGAGTTTATGAATTATC-GTATCGGCACTATGTGTGCAAACCCACGTAATTC
* ** ** *
2465737 ATAATGTGTTTACAAATTA-CTGTATCATCCCTATGTGTGCAAACCCACGTAATTC
1 ATAATGAGTTTATGAATTATC-GTATCGGCACTATGTGTGCAAACCCACGTAATTC
* *
2465792 ATAATGAGTTTATGAATTATCGTA-CTGGCACTATATGTGCAAATCCACGTAATTC
1 ATAATGAGTTTATGAATTATCGTATC-GGCACTATGTGTGCAAACCCACGTAATTC
* * * * * * * *
2465847 ATAATGAGTCTATGAATTATCGTATCGACGCTATGTATGTAAATCCACATGATTC
1 ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAACCCACGTAATTC
* * *
2465902 ATAAAGAATTTATGAATTACCGTATCGGCACTATGTGTGCAAACCCACGTAATTC
1 ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAACCCACGTAATTC
* * * ** *
2465957 ATAATGAATTTATGAATTACCATATTAGTACTATGTGTGC-AACCCACAG-AATTC
1 ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAACCCAC-GTAATTC
*
2466011 ATAATGAGTTTATGAATTATCATATCGGCACT
1 ATAATGAGTTTATGAATTATCGTATCGGCACT
2466043 TAGGTGCAAC
Statistics
Matches: 353, Mismatches: 57, Indels: 13
0.83 0.13 0.03
Matches are distributed among these distances:
54 44 0.12
55 307 0.87
56 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (55 bp):
ATAATGAGTTTATGAATTATCGTATCGGCACTATGTGTGCAAACCCACGTAATTC
Found at i:2465743 original size:26 final size:26
Alignment explanation
Indices: 2465714--2465797 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 26
2465704 TATCAGCACT
2465714 ATGTGTGCAAACCCACGTAATTCATA
1 ATGTGTGCAAACCCACGTAATTCATA
* ** * *
2465740 ATGTGTTTACAAA-TTACTGTATCATCCCT-
1 ATGTG--TGCAAACCCAC-GTA--ATTCATA
2465769 ATGTGTGCAAACCCACGTAATTCATA
1 ATGTGTGCAAACCCACGTAATTCATA
2465795 ATG
1 ATG
2465798 AGTTTATGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 14
0.63 0.15 0.22
Matches are distributed among these distances:
25 4 0.10
26 8 0.20
27 10 0.24
28 10 0.24
29 5 0.12
30 4 0.10
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (26 bp):
ATGTGTGCAAACCCACGTAATTCATA
Found at i:2469579 original size:42 final size:43
Alignment explanation
Indices: 2469504--2469584 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
2469494 TAAATTGACA
*
2469504 TTTAAATTAATGGAATTAAATAAAGATCTAATTGAATTGAATT
1 TTTAAATTAATGGAATTAAATAAAGATCAAATTGAATTGAATT
* * **
2469547 TTTAAATTAATTGAATTATAT-TGGATCAAATTGAATTG
1 TTTAAATTAATGGAATTAAATAAAGATCAAATTGAATTG
2469585 CCTAAGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 14 0.42
43 19 0.58
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (43 bp):
TTTAAATTAATGGAATTAAATAAAGATCAAATTGAATTGAATT
Found at i:2471057 original size:16 final size:16
Alignment explanation
Indices: 2471010--2471059 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2471000 TTATGTTAAG
2471010 TTATTT-TTTATTCATAT
1 TTATTTGTTTATT--TAT
* *
2471027 TTA-TGGTTCATTTAT
1 TTATTTGTTTATTTAT
2471042 TTATTTGTTTATTTAT
1 TTATTTGTTTATTTAT
2471058 TT
1 TT
2471060 TGGGTATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 6 0.22
16 13 0.48
17 8 0.30
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (16 bp):
TTATTTGTTTATTTAT
Found at i:2473418 original size:20 final size:21
Alignment explanation
Indices: 2473389--2473429 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2473379 AAGTTCATCA
2473389 TTTTCAAGTTCTT-TTTCAATT
1 TTTTCAAGTT-TTGTTTCAATT
2473410 TTTTC-AGTTTTGTTTCAATT
1 TTTTCAAGTTTTGTTTCAATT
2473430 AGTTATTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 12 0.63
21 5 0.26
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTCAAGTTTTGTTTCAATT
Found at i:2478522 original size:34 final size:33
Alignment explanation
Indices: 2478475--2478544 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 33
2478465 TTTTGTTAAT
* * *
2478475 TTGTTCTTACTAACGTACTAACTTTTTACTTTTA
1 TTGTTATTACTAACGTACTAACATTTTA-TATTA
* *
2478509 TTGTTATTCCTAACTTACTAACATTTTATATTA
1 TTGTTATTACTAACGTACTAACATTTTATATTA
2478542 TTG
1 TTG
2478545 CACAAACTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
33 7 0.23
34 24 0.77
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.53
Consensus pattern (33 bp):
TTGTTATTACTAACGTACTAACATTTTATATTA
Found at i:2478652 original size:17 final size:17
Alignment explanation
Indices: 2478593--2478644 Score: 104
Period size: 17 Copynumber: 3.1 Consensus size: 17
2478583 CAACAACCTT
2478593 GTGGTGACCAGCCTTGG
1 GTGGTGACCAGCCTTGG
2478610 GTGGTGACCAGCCTTGG
1 GTGGTGACCAGCCTTGG
2478627 GTGGTGACCAGCCTTGG
1 GTGGTGACCAGCCTTGG
2478644 G
1 G
2478645 GGATGACCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (17 bp):
GTGGTGACCAGCCTTGG
Found at i:2479291 original size:5 final size:5
Alignment explanation
Indices: 2479281--2479331 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
2479271 ATTTTTTTAC
* * * *
2479281 TATTT TATTT TATTT TATCT TGTTC TATTTT TATTT TATTT T-TAT TATTT
1 TATTT TATTT TATTT TATTT TATTT TA-TTT TATTT TATTT TATTT TATTT
2479331 T
1 T
2479332 TATCTTTGAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
4 3 0.08
5 29 0.81
6 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:2479296 original size:21 final size:23
Alignment explanation
Indices: 2479270--2479323 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
2479260 CTTCGTTTTA
2479270 TATTTTTT-TACTA-TTTTATTT
1 TATTTTTTGTACTATTTTTATTT
*
2479291 TATTTTATCTTGTTCTATTTTTATTT
1 TA-TTT-T-TTGTACTATTTTTATTT
2479317 TATTTTT
1 TATTTTT
2479324 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 2 0.07
22 3 0.11
23 2 0.07
24 3 0.11
25 7 0.26
26 10 0.37
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (23 bp):
TATTTTTTGTACTATTTTTATTT
Found at i:2483088 original size:7 final size:7
Alignment explanation
Indices: 2483047--2483100 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
2483037 CAAAGCAAAG
2483047 AGAAGAA
1 AGAAGAA
2483054 AGAA-AA
1 AGAAGAA
2483060 A-AAGCAA
1 AGAAG-AA
2483067 AGAA-AA
1 AGAAGAA
2483073 AG-A-AA
1 AGAAGAA
2483078 AGAAGAA
1 AGAAGAA
2483085 AGAAGAA
1 AGAAGAA
2483092 AGAGAGAA
1 AGA-AGAA
2483100 A
1 A
2483101 AAAAAAGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
5 7 0.17
6 8 0.20
7 19 0.46
8 7 0.17
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:2483106 original size:33 final size:31
Alignment explanation
Indices: 2483047--2483115 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
2483037 CAAAGCAAAG
*
2483047 AGAAGAAAGAAAAAAAGCAAAGAAAAAGAAA
1 AGAAGAAAGAAAAAAAGCAAAAAAAAAGAAA
*
2483078 AGAAGAAAGAAGAAAGAGAG-AAAAAAAAAGACA
1 AGAAGAAAGAA-AAA-A-AGCAAAAAAAAAGAAA
2483111 AGAAG
1 AGAAG
2483116 CACATGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 11 0.33
32 3 0.09
33 17 0.52
34 2 0.06
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (31 bp):
AGAAGAAAGAAAAAAAGCAAAAAAAAAGAAA
Found at i:2486373 original size:103 final size:103
Alignment explanation
Indices: 2486170--2486400 Score: 277
Period size: 103 Copynumber: 2.3 Consensus size: 103
2486160 GCCAAATTTT
** * *
2486170 GAAATTGTTTCACTTGAAACAAAATTGATTTCGCTTGAGATAGTTTTCCTAAAAACTAATTTCGT
1 GAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAGTTTTCCTAAAAACAAATTTCGT
* *
2486235 ATTGTTTGAGACAATTTTCCCTAAAAACACAAAAATGG
66 ATCGATTGAGACAATTTTCCCTAAAAACACAAAAATGG
* * * *
2486273 GAAATTGTTTCACTTGAAACAAAATTGATAACATTTGAGATTGTTTTTCTTAAAAACAAATTTCT
1 GAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAG-TTTTCCTAAAAACAAATTTCG
* * ** ** **
2486338 TCTCGATTGAGACAGTTTTCCCTTTAAATGC-AAAATTT
65 TATCGATTGAGACAATTTTCCCTAAAAACACAAAAATGG
2486376 GAAA-TGTTTCACTTGAAACAAAATT
1 GAAATTGTTTCACTTGAAACAAAATT
2486401 TTATCTCACC
Statistics
Matches: 109, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
102 21 0.19
103 47 0.43
104 41 0.38
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (103 bp):
GAAATTGTTTCACTTGAAACAAAATTGATAACACTTGAGATAGTTTTCCTAAAAACAAATTTCGT
ATCGATTGAGACAATTTTCCCTAAAAACACAAAAATGG
Found at i:2495039 original size:189 final size:190
Alignment explanation
Indices: 2494719--2495097 Score: 751
Period size: 189 Copynumber: 2.0 Consensus size: 190
2494709 ATTTAAACAC
2494719 AAACTTGAATAACTCGACTCAATTCGGAAAAAAAAATTGAGTTTAAAAATAGGATTTGTTAACTC
1 AAACTTGAATAACTCGACTCAATTCGGAAAAAAAAATTGAGTTTAAAAATAGGATTTGTTAACTC
2494784 GAATAACTCAAAATCTTTTGACTTTACTCAAGTTGAATGGTCAAACTTACCAAGGCAATGAGCTT
66 GAATAACTCAAAATCTTTTGACTTTACTCAAGTTGAATGGTCAAACTTACCAAGGCAATGAGCTT
2494849 ATGCAGGTCTATAGATGTACAACACAATTAAAACAAGGTCTCTTCAG-CCCAACAATGAG
131 ATGCAGGTCTATAGATGTACAACACAATTAAAACAAGGTCTCTTCAGCCCCAACAATGAG
2494908 AAACTTGAATAACTCGACTCAATTCGGAAAAAAAAATTGAGTTTAAAAATAGGATTTGTTAACTC
1 AAACTTGAATAACTCGACTCAATTCGGAAAAAAAAATTGAGTTTAAAAATAGGATTTGTTAACTC
2494973 GAATAACTCAAAATCTTTTGACTTTACTCAAGTTGAATGGTCAAACTTACCAAGGCAATGAGCTT
66 GAATAACTCAAAATCTTTTGACTTTACTCAAGTTGAATGGTCAAACTTACCAAGGCAATGAGCTT
2495038 ATGCAGGTCTATAGATGTACAACACAATTAAAACAAGGTCTCTTCAGCCCCAACAATGAG
131 ATGCAGGTCTATAGATGTACAACACAATTAAAACAAGGTCTCTTCAGCCCCAACAATGAG
2495098 CTTATGCACT
Statistics
Matches: 189, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
189 177 0.94
190 12 0.06
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (190 bp):
AAACTTGAATAACTCGACTCAATTCGGAAAAAAAAATTGAGTTTAAAAATAGGATTTGTTAACTC
GAATAACTCAAAATCTTTTGACTTTACTCAAGTTGAATGGTCAAACTTACCAAGGCAATGAGCTT
ATGCAGGTCTATAGATGTACAACACAATTAAAACAAGGTCTCTTCAGCCCCAACAATGAG
Found at i:2496236 original size:54 final size:54
Alignment explanation
Indices: 2496157--2496473 Score: 422
Period size: 54 Copynumber: 6.1 Consensus size: 54
2496147 ACTCATAGTA
* * * *
2496157 CCAATACGGATATTCATAAAGTTATTATGAATTTCTTAAGTTGCACACACATTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
* * *
2496211 CCAAAACAAAAATTCATAAACTTATTATG----------GTTGCACACATAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
*
2496255 CCGATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
*
2496309 CCAATAAGGAAAA-TCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
1 CCAAT-ACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
* * *
2496363 CCAATACGGAAATTCATAAACTTATTATGAATTTATTAAGTTGCACACACAGTT
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
* *
2496417 CCAATACGAAAATTCATAAACTTGTTATGAATTTCTTAAGTTGTACACACAGTG
1 CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
2496471 CCA
1 CCA
2496474 TTCGGTAAAT
Statistics
Matches: 229, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
44 39 0.17
53 5 0.02
54 179 0.78
55 6 0.03
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (54 bp):
CCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTG
Found at i:2496267 original size:44 final size:44
Alignment explanation
Indices: 2496196--2496283 Score: 131
Period size: 44 Copynumber: 2.0 Consensus size: 44
2496186 AATTTCTTAA
*
2496196 GTTGCACACACATTGCCAAAACAAAAATTCATAAACTTATTATG
1 GTTGCACACACAGTGCCAAAACAAAAATTCATAAACTTATTATG
* * * *
2496240 GTTGCACACATAGTGCCGATACGAAAATTCATAAACTTATTATG
1 GTTGCACACACAGTGCCAAAACAAAAATTCATAAACTTATTATG
2496284 AATTTCTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.28
Consensus pattern (44 bp):
GTTGCACACACAGTGCCAAAACAAAAATTCATAAACTTATTATG
Found at i:2496849 original size:21 final size:21
Alignment explanation
Indices: 2496824--2496864 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2496814 TATTAATCAA
2496824 TACTTACAACAGTATCGATAC
1 TACTTACAACAGTATCGATAC
* *
2496845 TACTTGCATCAGTATCGATA
1 TACTTACAACAGTATCGATA
2496865 TTGTTCATCG
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:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (21 bp):
TACTTACAACAGTATCGATAC
Found at i:2503571 original size:54 final size:54
Alignment explanation
Indices: 2503342--2503572 Score: 275
Period size: 54 Copynumber: 4.3 Consensus size: 54
2503332 ATTCTATGGT
* * * * * * ***
2503342 TTGCACACGCATTGCCAATACGGTAATTCACAAACTCATTATGAATTACGTGGGG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAAG
* ** * *
2503397 TTGCAAACATGGTACCAATACGGAAATTCATAAACTTATTAT-AATTTTTTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAA-TTTCTTAAG
* *
2503451 TTGCACACATAGTGCCAATACGGAAATTCAGAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
*
2503505 TTGCACACACAGTGCCAATATGGAAATTCATAAACTTATTATGAATTTCTTAAG
1 TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
*
2503559 TTGCACAAACAGTG
1 TTGCACACACAGTG
2503573 TCATTCAATA
Statistics
Matches: 151, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
54 114 0.75
55 37 0.25
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (54 bp):
TTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAG
Found at i:2504028 original size:18 final size:19
Alignment explanation
Indices: 2503989--2504036 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
2503979 GGAATCCATG
*
2503989 GTATCGATACCATCATATTA
1 GTATCGATACCA-CATAGTA
2504009 GTATCGATACC-CATAGTA
1 GTATCGATACCACATAGTA
*
2504027 GTATTGATAC
1 GTATCGATAC
2504037 TACTTGCAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (19 bp):
GTATCGATACCACATAGTA
Found at i:2504139 original size:20 final size:20
Alignment explanation
Indices: 2504089--2504139 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2504079 TATAAACCTG
2504089 TAGTATCGATATTGTTATTC
1 TAGTATCGATATTGTTATTC
* * *
2504109 CAGTATAGATATTGTTCTTC
1 TAGTATCGATATTGTTATTC
*
2504129 TAGTACCGATA
1 TAGTATCGATA
2504140 CCCTTATCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (20 bp):
TAGTATCGATATTGTTATTC
Found at i:2510042 original size:60 final size:60
Alignment explanation
Indices: 2509963--2510086 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
2509953 ATGATTATTA
* * * *
2509963 TTTTAAATATTTTAATTTCATC-CTTATACTATAAC-TATCATTTTAAATT-AGTCCTCAAAC
1 TTTTAAATATTTCAATTTCATCGC-CAAACTAAAACAT-TCATTTTAAATTGA-TCCTCAAAC
*
2510023 TTTTAAATATTTCACTTTCATCGCCAAACTAAAACATTCATTTTAAATTGATCCTCAAAC
1 TTTTAAATATTTCAATTTCATCGCCAAACTAAAACATTCATTTTAAATTGATCCTCAAAC
2510083 TTTT
1 TTTT
2510087 TGAACATTCT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
60 53 0.95
61 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (60 bp):
TTTTAAATATTTCAATTTCATCGCCAAACTAAAACATTCATTTTAAATTGATCCTCAAAC
Found at i:2510110 original size:60 final size:60
Alignment explanation
Indices: 2510000--2510113 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
2509990 ACTATAACTA
* *
2510000 TCATTTTAAATTAGTCCTCAAACTTTTAAATATTTCACTTTCATCGCCAAACTAAAACAT
1 TCATTTTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCGCCAAACTAAAACAT
* *
2510060 TCATTTTAAATT-GATCCTCAAACTTTTTGAACA-TTCTAATTTTATC-CCAAACTA
1 TCATTTTAAATTAG-TCCTCAAAC-TTTTAAACATTTC-AATTTCATCGCCAAACTA
2510114 TATGTATATA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
59 1 0.02
60 32 0.68
61 14 0.30
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (60 bp):
TCATTTTAAATTAGTCCTCAAACTTTTAAACATTTCAATTTCATCGCCAAACTAAAACAT
Found at i:2510364 original size:59 final size:59
Alignment explanation
Indices: 2510261--2510426 Score: 174
Period size: 59 Copynumber: 2.8 Consensus size: 59
2510251 ATTTGGATGA
** **
2510261 AATTGGGCATGAAATTAGAATATTCAAAAGTTTGGGGACCAATTTAGAA-AGAGGATTAT
1 AATTGGGCATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATA-AGGATTAT
* *
2510320 AATTAGGG-ATGAAATTAGAATGTTCAAAAGTTTAAGGATTAATTTAGAATAAGGGTTAT
1 AATT-GGGCATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATAAGGATTAT
* * * * * *
2510379 AGTTTGGGTATTAAATTAAAATATTCAAAAAATTTAAGGATTAGTTTA
1 A-ATTGGGCATGAAATTAGAATATTC-AAAAGTTTAAGGATTAATTTA
2510427 AAATGAGACT
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 51 0.57
60 20 0.22
61 19 0.21
ACGTcount: A:0.42, C:0.04, G:0.20, T:0.34
Consensus pattern (59 bp):
AATTGGGCATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATAAGGATTAT
Found at i:2510440 original size:61 final size:60
Alignment explanation
Indices: 2510331--2510447 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 60
2510321 ATTAGGGATG
* * * * **
2510331 AAATTAGAATGTTCAAAAGTTTAAGGATTAATTTAGAATAAGGGTTATAGTTTGGGTATT
1 AAATTAAAATATTCAAAAATTTAAGGATTAATTTAAAATAAGACTTATAGTTTGGGTATT
* *
2510391 AAATTAAAATATTCAAAAAATTTAAGGATTAGTTTAAAATGAGACTTATAGTTTGGG
1 AAATTAAAATATTC-AAAAATTTAAGGATTAATTTAAAATAAGACTTATAGTTTGGG
2510448 GACATATGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
60 12 0.25
61 36 0.75
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.37
Consensus pattern (60 bp):
AAATTAAAATATTCAAAAATTTAAGGATTAATTTAAAATAAGACTTATAGTTTGGGTATT
Found at i:2512769 original size:25 final size:25
Alignment explanation
Indices: 2512741--2512788 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2512731 TAACATTAGA
*
2512741 TACCTTTGAATTGAAGTGTTGATTG
1 TACCTCTGAATTGAAGTGTTGATTG
2512766 TACCTCTGAATTGAAGTGTTGAT
1 TACCTCTGAATTGAAGTGTTGAT
2512789 AGATGGCGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (25 bp):
TACCTCTGAATTGAAGTGTTGATTG
Found at i:2526356 original size:28 final size:28
Alignment explanation
Indices: 2526323--2526390 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
2526313 GTTGTTTCAT
*
2526323 AACCCTGAGATCTACTGGTGAACCATTC
1 AACCCTGAGATCTACTAGTGAACCATTC
*
2526351 GACCCTGAGATCTACTAGTGAACCATTC
1 AACCCTGAGATCTACTAGTGAACCATTC
2526379 AACCCTGAGATC
1 AACCCTGAGATC
2526391 GAACAGTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (28 bp):
AACCCTGAGATCTACTAGTGAACCATTC
Found at i:2533193 original size:23 final size:23
Alignment explanation
Indices: 2533167--2533239 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
2533157 CAACTCGTAT
*
2533167 AAATGCACCGAAGTACCGCATAG
1 AAATGCACCGAAGTACCACATAG
* * * *
2533190 AAATGCACTGTAGTGCCACGTAG
1 AAATGCACCGAAGTACCACATAG
* * *
2533213 AATTGCACCGAAGTGCCATATA-
1 AAATGCACCGAAGTACCACATAG
2533235 AAATG
1 AAATG
2533240 TCCCTAAGGA
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
22 4 0.10
23 35 0.90
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTACCACATAG
Found at i:2534806 original size:20 final size:22
Alignment explanation
Indices: 2534781--2534838 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
2534771 TTCCCCTTGA
2534781 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
2534801 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
2534824 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
2534839 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:2534913 original size:64 final size:64
Alignment explanation
Indices: 2534826--2534987 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 64
2534816 TCTTTAACAT
* * * *
2534826 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
** * * ** * *
2534890 GTGCATCGATGTGC-TCCTTATGCATCGATGCACTAATTGCATTTGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
2534954 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATACACA
2534988 CTGAACAATT
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
63 2 0.03
64 67 0.86
65 9 0.12
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:2540982 original size:39 final size:40
Alignment explanation
Indices: 2540928--2541007 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
2540918 TGAGTGTTTT
2540928 ACAACGGTTAATCAAGGAGATTTGGTTCGAGGA-TGCCTA
1 ACAACGGTTAATCAAGGAGATTTGGTTCGAGGACTGCCTA
2540967 ACAAC-GTTAATTCAAGGAGATTTGGTTCGAGGACTGCCTA
1 ACAACGGTTAA-TCAAGGAGATTTGGTTCGAGGACTGCCTA
2541007 A
1 A
2541008 ACTAAAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
38 5 0.13
39 27 0.69
40 7 0.18
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (40 bp):
ACAACGGTTAATCAAGGAGATTTGGTTCGAGGACTGCCTA
Found at i:2543754 original size:23 final size:23
Alignment explanation
Indices: 2543726--2543810 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 23
2543716 TTGGTGCTGA
*
2543726 GGGAATCGATACCCCCCTTGCAG
1 GGGAATCGATACCCCCCTTGAAG
* * *
2543749 GGGAATTGATTCCCCCTTTGAAG
1 GGGAATCGATACCCCCCTTGAAG
* * *
2543772 GGGAACCGAT-TCCCCC-TGTAG
1 GGGAATCGATACCCCCCTTGAAG
2543793 GGGAATCGATACCCCCCT
1 GGGAATCGATACCCCCCT
2543811 GGGGTTCTAT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 13 0.27
22 9 0.18
23 27 0.55
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAATCGATACCCCCCTTGAAG
Found at i:2545414 original size:18 final size:18
Alignment explanation
Indices: 2545379--2545417 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
2545369 AGAGCAACAC
*
2545379 GAGGAACAAGCACCTCCA
1 GAGGAACAACCACCTCCA
* *
2545397 GAGGAACAACCTCGTCCA
1 GAGGAACAACCACCTCCA
2545415 GAG
1 GAG
2545418 TATCAAATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.31, G:0.26, T:0.08
Consensus pattern (18 bp):
GAGGAACAACCACCTCCA
Found at i:2548458 original size:22 final size:23
Alignment explanation
Indices: 2548433--2548486 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
2548423 CTTAATTCAA
*
2548433 TTTCATATA-TTCATTATAACCT
1 TTTCATATAGCTCATTATAACCT
* * *
2548455 TTTCATATAGCTCCTTATATCTT
1 TTTCATATAGCTCATTATAACCT
2548478 TTTCATATA
1 TTTCATATA
2548487 ACTTATCTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.28, C:0.19, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTCATATAGCTCATTATAACCT
Found at i:2549318 original size:20 final size:20
Alignment explanation
Indices: 2549293--2549330 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2549283 TTCCCCTTGA
2549293 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
2549313 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
2549331 TTAACATATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:2549429 original size:64 final size:64
Alignment explanation
Indices: 2549339--2549499 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
2549329 CTTTAACATA
* * *
2549339 TGCATTGATGCACTACC-CATGCATCGATACACAAATCATC-TTCGATGTTTTCATTTTAAAGGG
1 TGCATCGATGCACT-CCTTATGCATCGATACACAAAT-ATCATTCGATGTTTCCATTTTAAAGGG
2549402 G
64 G
* * * * * *
2549403 TGCATCGATGTACTCCTTATGCATCGATGCACTAATTTCATTCGATGTTTCCATTTTTAATGGG
1 TGCATCGATGCACTCCTTATGCATCGATACACAAATATCATTCGATGTTTCCATTTTAAAGGGG
* *
2549467 TGCATCGATGCACTTCTTGTGCATCGATACACA
1 TGCATCGATGCACTCCTTATGCATCGATACACA
2549500 CTGAACAATA
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
63 4 0.05
64 77 0.95
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (64 bp):
TGCATCGATGCACTCCTTATGCATCGATACACAAATATCATTCGATGTTTCCATTTTAAAGGGG
Found at i:2561313 original size:236 final size:225
Alignment explanation
Indices: 2560885--2561346 Score: 611
Period size: 236 Copynumber: 2.0 Consensus size: 225
2560875 CTACTGACAA
* * * *
2560885 ATTATACGTGAGAAGTTAAACTACGACTACACTGACTTCGACAAGGTAGAAGTTTAGTTGAAGAC
1 ATTATACGCGAGAAGTTAAACTACGAATACACTGACTTCGACAAAGTAGAAGTTCAGTTGAAGAC
* *
2560950 TACTACAAGGAGATGCAATCCTTACTCATAACCGAAAAAGAAGTGGTCACCATATCAATATTCAT
66 TACTACAAGGAGATGCAATCCTTACTCATAACCGAAAAAGAAGAGGTCACCATATCAAGATTCAT
* * *
2561015 CGTCGGATTAAACTCAAATATCATTAATCTTCTTGATCTCCATGGGTATGAAAACCTTGAAGATG
131 CGTCGGATTAAACTCAAACATCATTAATCTTCTTGATCTCCATGGGTACGAAAACCTTGAAGATA
*
2561080 CTCTAAAGAAAACAATGACAATAGAAGCAC
196 CACTAAAGAAAACAATGACAATAGAAGCAC
* * *
2561110 ATTATATGCGAGAAGTTAAATTATGAATACACTGACTTCGACAAAGTAGAAGTTCAGTTGAAGAC
1 ATTATACGCGAGAAGTTAAACTACGAATACACTGACTTCGACAAAGTAGAAGTTCAGTTGAAGAC
* * *
2561175 TACTACATGGAGATGCAATCCTTACTTAATAGGGTAACATAACCGAAAAAGAAGAGGTCACCGTG
66 TACTACAAGGAGATGCAATCCTTAC---------T--CATAACCGAAAAAGAAGAGGTCACCATA
* * *
2561240 TCAAGATTCATCGTCGGATTAAACTCAAACATCACTT-ATCTTTTTTATTTCCATGGGTACGAAA
120 TCAAGATTCATCGTCGGATTAAACTCAAACATCA-TTAATCTTCTTGATCTCCATGGGTACGAAA
* * *
2561304 ACCTTGAAGATACACTAAAGAAAATAATGATAATCGAAGCAC
184 ACCTTGAAGATACACTAAAGAAAACAATGACAATAGAAGCAC
2561346 A
1 A
2561347 AATCCAAATG
Statistics
Matches: 203, Mismatches: 22, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
225 82 0.40
234 1 0.00
236 118 0.58
237 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (225 bp):
ATTATACGCGAGAAGTTAAACTACGAATACACTGACTTCGACAAAGTAGAAGTTCAGTTGAAGAC
TACTACAAGGAGATGCAATCCTTACTCATAACCGAAAAAGAAGAGGTCACCATATCAAGATTCAT
CGTCGGATTAAACTCAAACATCATTAATCTTCTTGATCTCCATGGGTACGAAAACCTTGAAGATA
CACTAAAGAAAACAATGACAATAGAAGCAC
Found at i:2574529 original size:23 final size:24
Alignment explanation
Indices: 2574503--2574550 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2574493 AGTAGTTCGA
*
2574503 AAAAAAAAAGAAAAAA-AGATGTT
1 AAAAAAAAACAAAAAAGAGATGTT
*
2574526 AAAAAAAGACAAAAAAGGAGATGTT
1 AAAAAAAAACAAAAAA-GAGATGTT
2574551 GTTCGAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
25 7 0.33
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (24 bp):
AAAAAAAAACAAAAAAGAGATGTT
Found at i:2574584 original size:11 final size:11
Alignment explanation
Indices: 2574570--2574599 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2574560 AAAAGAGAAA
*
2574570 AAAAGAAATGG
1 AAAACAAATGG
2574581 AAAACAAATGG
1 AAAACAAATGG
2574592 AAAACAAA
1 AAAACAAA
2574600 ACAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (11 bp):
AAAACAAATGG
Found at i:2576123 original size:19 final size:18
Alignment explanation
Indices: 2576087--2576123 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2576077 CTGTGCTTAT
*
2576087 TTTTCAAAATCAAAATAG
1 TTTTCAAAATAAAAATAG
2576105 TTTTCAAAATAAAAGATAG
1 TTTTCAAAATAAAA-ATAG
2576124 ACTTTGGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.32
Consensus pattern (18 bp):
TTTTCAAAATAAAAATAG
Found at i:2576554 original size:21 final size:21
Alignment explanation
Indices: 2576514--2576573 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
2576504 TATTTTCAAC
2576514 TTTAAAATCTTTTCT-TTATTTTA
1 TTTAAAATCTTTT-TATTA--TTA
*
2576537 TTTTAAATCATTTTTATTATTA
1 TTTAAAATC-TTTTTATTATTA
2576559 TTTAAAATCTTTTTA
1 TTTAAAATCTTTTTA
2576574 CCAAAACCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 6 0.18
22 11 0.33
23 9 0.27
24 7 0.21
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTAAAATCTTTTTATTATTA
Found at i:2578537 original size:3 final size:3
Alignment explanation
Indices: 2578522--2578617 Score: 156
Period size: 3 Copynumber: 31.7 Consensus size: 3
2578512 TTTTTATCCA
* *
2578522 TAT TAT TAA TAT TAT TAT TAT TATT TAT TAT TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
*
2578568 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2578616 TA
1 TA
2578618 AATATATATT
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
3 83 0.97
4 3 0.03
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:2578629 original size:11 final size:11
Alignment explanation
Indices: 2578613--2578644 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
2578603 TTATTATTAT
2578613 TATTAAATATA
1 TATTAAATATA
2578624 TATTAAATATA
1 TATTAAATATA
2578635 TATATAAATA
1 TAT-TAAATA
2578645 ATTAATTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Done.