Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005619.1 Hibiscus syriacus cultivar Beakdansim tig00013067_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: 189028
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:909 original size:25 final size:27
Alignment explanation
Indices: 881--941 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
871 CAAGAGTCAT
881 CTCATGACTG-TT-ATTCACTCATATG
1 CTCATGACTGCTTCATTCACTCATATG
906 CTCATGA-TGCTTTCATTCACTCATATG
1 CTCATGACTGC-TTCATTCACTCATATG
*
933 CACATGACT
1 CTCATGACT
942 ACCATTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
24 2 0.06
25 7 0.23
26 2 0.06
27 19 0.61
28 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (27 bp):
CTCATGACTGCTTCATTCACTCATATG
Found at i:3109 original size:13 final size:12
Alignment explanation
Indices: 3091--3148 Score: 55
Period size: 13 Copynumber: 4.7 Consensus size: 12
3081 TATTATCCCC
3091 AGATAAAAACTAA
1 AGATAAAAA-TAA
3104 AGATAAAAATGAA
1 AGATAAAAAT-AA
*
3117 A-ATGAAAATTAA
1 AGAT-AAAAATAA
*
3129 AGATAAAGATAA
1 AGATAAAAATAA
*
3141 ATATAAAA
1 AGATAAAA
3149 GAGAAATAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 18 0.49
13 19 0.51
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (12 bp):
AGATAAAAATAA
Found at i:3141 original size:12 final size:13
Alignment explanation
Indices: 3091--3148 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
3081 TATTATCCCC
3091 AGATAAAAACTAA
1 AGATAAAAACTAA
3104 AGATAAAAA-TGAA
1 AGATAAAAACT-AA
* *
3117 A-ATGAAAATTAA
1 AGATAAAAACTAA
*
3129 AGATAAAGA-TAA
1 AGATAAAAACTAA
*
3141 ATATAAAA
1 AGATAAAA
3149 GAGAAATAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 19 0.51
13 18 0.49
ACGTcount: A:0.69, C:0.02, G:0.10, T:0.19
Consensus pattern (13 bp):
AGATAAAAACTAA
Found at i:9047 original size:23 final size:24
Alignment explanation
Indices: 9015--9060 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
9005 GTGGAAGCAA
*
9015 ATGGAGATGTAGTGG-AAAAATAT
1 ATGGAAATGTAGTGGCAAAAATAT
*
9038 ATGGAAATGTCGTGGCAAAAATA
1 ATGGAAATGTAGTGGCAAAAATA
9061 AAGTGTGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.43, C:0.04, G:0.28, T:0.24
Consensus pattern (24 bp):
ATGGAAATGTAGTGGCAAAAATAT
Found at i:13020 original size:43 final size:43
Alignment explanation
Indices: 12969--13190 Score: 180
Period size: 43 Copynumber: 5.2 Consensus size: 43
12959 TAAATTACCT
** *
12969 ACCTATTGCGGCGTTTATAAGAGAAACATCGCTAATTATCTGA
1 ACCTATTGCGGCGTTTATAAGAGAAACGCCGCTAAATATCTGA
* *
13012 ACCTATTGCGGCGTTTATAAGA-AACACGCCGTTAAATATCTAA
1 ACCTATTGCGGCGTTTATAAGAGAA-ACGCCGCTAAATATCTGA
* * * * * *
13055 ACCTATTGCGGTGTGTGTAAGAAAAACGCCGCTAAATGTATGA
1 ACCTATTGCGGCGTTTATAAGAGAAACGCCGCTAAATATCTGA
* * ** ** * *
13098 ACCTATTGCGGCGATTGTAAGAGAAGTGTTGCTAAATGTATGA
1 ACCTATTGCGGCGTTTATAAGAGAAACGCCGCTAAATATCTGA
* * * * * * *
13141 ACCTATTGAGGTGTTTGTAA-AAAAACACTGCT-AATGTCTGA
1 ACCTATTGCGGCGTTTATAAGAGAAACGCCGCTAAATATCTGA
13182 ACCTATTGC
1 ACCTATTGC
13191 AACGCTTTTT
Statistics
Matches: 147, Mismatches: 30, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
41 16 0.11
42 9 0.06
43 120 0.82
44 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (43 bp):
ACCTATTGCGGCGTTTATAAGAGAAACGCCGCTAAATATCTGA
Found at i:15411 original size:12 final size:12
Alignment explanation
Indices: 15394--15418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15384 AAGTAATTGT
15394 AAAATATGAAAA
1 AAAATATGAAAA
15406 AAAATATGAAAA
1 AAAATATGAAAA
15418 A
1 A
15419 TAAACTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATATGAAAA
Found at i:15472 original size:2 final size:2
Alignment explanation
Indices: 15465--15735 Score: 129
Period size: 2 Copynumber: 136.0 Consensus size: 2
15455 TTAAAACAAT
15465 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
15507 TA TA TA TA TA TA AA CTA TA TA -A TA -A TG TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
15547 AA CTA TA CA GTT TA TA TT TA TA CA CTA TA TA TA AA T- TA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
15589 TCA AA CTA TA TA TA T- TA TT TA TA -A TA TA AA CTA TA TA GTT TA
1 T-A TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
15631 T- TA TA GTT TA TA TA TA AA TA TA TA TCA -A CTA TA TA TA AA CTA
1 TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA -TA
* * * * *
15673 TA CA T- TT TA TA TT TA TA TA T- TA TG TA TA -A T- TA TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
15710 TA TA TA TA CTA TG TA TA AA T- TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA
15736 ATTTATTAAT
Statistics
Matches: 199, Mismatches: 43, Indels: 54
0.67 0.15 0.18
Matches are distributed among these distances:
1 14 0.07
2 172 0.86
3 13 0.07
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:15664 original size:65 final size:69
Alignment explanation
Indices: 15468--15667 Score: 191
Period size: 70 Copynumber: 2.9 Consensus size: 69
15458 AAACAATTAT
* * * * * * *
15468 ATATATATATATA-TATATA-TATATATATATATA-TATATATATATATATATAAACTATATAAT
1 ATATATATATAAACTATACAGTTTATATTTATACACTATATATAAATATATATCAACTATAT-AT
15530 AATGTA
65 -ATGTA
15536 ATATATATATAAACTATACAGTTTATATTTATACACTATATATAAATTATATATCAAACTATATA
1 ATATATATATAAACTATACAGTTTATATTTATACACTATATATAAA-TATATATC-AACTATATA
15601 TAT-T-
64 TATGTA
* * ***
15605 ATTTATAATATAAACTATATAG-TT-TA-TTATAGTTTATATATAAATATATATCAACTATATAT
1 ATATAT-ATATAAACTATACAGTTTATATTTATACACTATATATAAATATATATCAACTATATAT
15667 A
65 A
15668 AACTATACAT
Statistics
Matches: 114, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
65 11 0.10
66 8 0.07
67 15 0.13
68 14 0.12
69 12 0.11
70 26 0.23
71 11 0.10
72 9 0.08
73 8 0.07
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (69 bp):
ATATATATATAAACTATACAGTTTATATTTATACACTATATATAAATATATATCAACTATATATA
TGTA
Found at i:15829 original size:18 final size:18
Alignment explanation
Indices: 15712--15829 Score: 75
Period size: 18 Copynumber: 6.6 Consensus size: 18
15702 TTATAAATTA
* *
15712 TATATACTATGTATAAAT
1 TATATACTATATATAAAC
* *
15730 TATATA--ATTTATTAA-
1 TATATACTATATATAAAC
* **
15745 TATAAACTATAGGTAAAC
1 TATATACTATATATAAAC
*
15763 TATATGAACTATATATAAAA
1 TATAT--ACTATATATAAAC
*
15783 AATTATA-TATATATAAAC
1 TA-TATACTATATATAAAC
*
15801 TATA-ATTTATATATAAAC
1 TATATA-CTATATATAAAC
15819 TATATACTATA
1 TATATACTATA
15830 GTTGATATTT
Statistics
Matches: 76, Mismatches: 15, Indels: 18
0.70 0.14 0.17
Matches are distributed among these distances:
15 5 0.07
16 8 0.11
17 7 0.09
18 40 0.53
19 2 0.03
20 11 0.14
21 3 0.04
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (18 bp):
TATATACTATATATAAAC
Found at i:15934 original size:9 final size:9
Alignment explanation
Indices: 15922--15951 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
15912 TATAGTTTAC
*
15922 ATATCAACT
1 ATATAAACT
15931 ATATAAACT
1 ATATAAACT
15940 ATATAAACT
1 ATATAAACT
15949 ATA
1 ATA
15952 GTTTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATAAACT
Found at i:15960 original size:18 final size:18
Alignment explanation
Indices: 15912--15967 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
15902 CTATATACTA
* *
15912 TATAGTTTACATATCAAC
1 TATAGTTTATATATAAAC
**
15930 TATA-TAAACTATATAAAC
1 TATAGTTTA-TATATAAAC
15948 TATAGTTTATATATAAAC
1 TATAGTTTATATATAAAC
15966 TA
1 TA
15968 ACACTATAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 2 0.07
18 26 0.87
19 2 0.07
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.39
Consensus pattern (18 bp):
TATAGTTTATATATAAAC
Found at i:16097 original size:31 final size:28
Alignment explanation
Indices: 16059--16173 Score: 77
Period size: 29 Copynumber: 3.8 Consensus size: 28
16049 ATATTAATGA
16059 ATAAACTATTTATATAGTATATACTACATAT
1 ATAAACTA--TATATAGTATATACTA-ATAT
* * * *
16090 ATAAACTATATATACTATATAGTTTACAT
1 ATAAACTATATATAGTATATA-CTAATAT
* * * *
16119 ATGAACTATATATTGTTTATTAATGAATTAT
1 ATAAACTATATATAGTATA-TACT-AA-TAT
16150 ATAAACTATTTATATAGTATATAC
1 ATAAACTA--TATATAGTATATAC
16174 GTTTATATTT
Statistics
Matches: 63, Mismatches: 15, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
29 31 0.49
30 4 0.06
31 17 0.27
32 2 0.03
33 9 0.14
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (28 bp):
ATAAACTATATATAGTATATACTAATAT
Found at i:16222 original size:27 final size:28
Alignment explanation
Indices: 16168--16227 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
16158 TTTATATAGT
*
16168 ATATACGTTTATATTTATATACTATATA
1 ATATACGTTTATATTTATATAATATATA
* *
16196 ATATA-GTTTATATTTATGTAATTTATA
1 ATATACGTTTATATTTATATAATATATA
*
16223 TTATA
1 ATATA
16228 TAAATTCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (28 bp):
ATATACGTTTATATTTATATAATATATA
Found at i:17506 original size:18 final size:18
Alignment explanation
Indices: 17485--17520 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17475 TAATATGCCA
*
17485 ACTATATACTATATACAT
1 ACTATATACTATACACAT
*
17503 ACTATATATTATACACAT
1 ACTATATACTATACACAT
17521 GCCCACATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
ACTATATACTATACACAT
Found at i:18066 original size:21 final size:18
Alignment explanation
Indices: 18026--18088 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
18016 ATAAGAGTCC
18026 TAATATAATAATCATAAT
1 TAATATAATAATCATAAT
*
18044 TAATATAATAAATCTATTTAT
1 TAATATAAT-AATC-A-TAAT
* *
18065 TAATTTAATTATCATAAT
1 TAATATAATAATCATAAT
18083 TAATAT
1 TAATAT
18089 TTTATTATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 17 0.46
19 5 0.14
20 4 0.11
21 11 0.30
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATAATAATCATAAT
Found at i:19485 original size:9 final size:9
Alignment explanation
Indices: 19441--19485 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
19431 CCGGTTCTTC
19441 CGACCGG-T
1 CGACCGGTT
19449 CGGACCGGTT
1 C-GACCGGTT
19459 CGACCGGTT
1 CGACCGGTT
*
19468 GGACCGGTT
1 CGACCGGTT
19477 CGACCGGTT
1 CGACCGGTT
19486 GAACCAGTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
8 1 0.03
9 30 0.91
10 2 0.06
ACGTcount: A:0.11, C:0.31, G:0.38, T:0.20
Consensus pattern (9 bp):
CGACCGGTT
Found at i:19485 original size:18 final size:18
Alignment explanation
Indices: 19441--19486 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
19431 CCGGTTCTTC
*
19441 CGACCGGTCGGACCGGTT
1 CGACCGGTTGGACCGGTT
19459 CGACCGGTTGGACCGGTT
1 CGACCGGTTGGACCGGTT
19477 CGACCGGTTG
1 CGACCGGTTG
19487 AACCAGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.11, C:0.30, G:0.39, T:0.20
Consensus pattern (18 bp):
CGACCGGTTGGACCGGTT
Found at i:22391 original size:25 final size:25
Alignment explanation
Indices: 22363--22413 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
22353 GGACTCGTAT
22363 TGAGTTTTGAGATTAATTGAGTGCA
1 TGAGTTTTGAGATTAATTGAGTGCA
22388 TGAGTTTTGAGATTAATTGAGTGCA
1 TGAGTTTTGAGATTAATTGAGTGCA
22413 T
1 T
22414 ACATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.27, T:0.41
Consensus pattern (25 bp):
TGAGTTTTGAGATTAATTGAGTGCA
Found at i:22774 original size:5 final size:5
Alignment explanation
Indices: 22764--22789 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
22754 TTAAGGTTTC
22764 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
22790 ATATATGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:24598 original size:53 final size:53
Alignment explanation
Indices: 24485--24588 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
24475 ATTAAATAGA
*
24485 ATCGATACTGATGAGGCAGTACTGATACTGTCAAAATAGAATGCTAAAATGAT
1 ATCGATACTGATGAGGCAGTACTGATACTGTCAAAACAGAATGCTAAAATGAT
*
24538 ATCGATACTTATGAGGCAGTACTGATACTGTCAAAACAGAATGCTAAAATG
1 ATCGATACTGATGAGGCAGTACTGATACTGTCAAAACAGAATGCTAAAATG
24589 GTACTGATAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.26
Consensus pattern (53 bp):
ATCGATACTGATGAGGCAGTACTGATACTGTCAAAACAGAATGCTAAAATGAT
Found at i:32203 original size:20 final size:20
Alignment explanation
Indices: 32178--32223 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
32168 TTGCATACAA
32178 TATCGGTACTGCCTTAACAG
1 TATCGGTACTGCCTTAACAG
*
32198 TATCGGTACTGCCTTATCAG
1 TATCGGTACTGCCTTAACAG
32218 TATCGG
1 TATCGG
32224 CACTACTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.33
Consensus pattern (20 bp):
TATCGGTACTGCCTTAACAG
Found at i:35717 original size:21 final size:21
Alignment explanation
Indices: 35688--35727 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
35678 ATTTTACACT
*
35688 GAGTGTACCGATACACCTAGA
1 GAGTATACCGATACACCTAGA
35709 GAGTATACCGATACACCTA
1 GAGTATACCGATACACCTA
35728 TGCTCCCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (21 bp):
GAGTATACCGATACACCTAGA
Found at i:43900 original size:21 final size:21
Alignment explanation
Indices: 43876--43915 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
43866 ATTTTACACT
43876 GAGTGTATTGATACACCTAGA
1 GAGTGTATTGATACACCTAGA
43897 GAGTGTATTGATACACCTA
1 GAGTGTATTGATACACCTA
43916 TGCTCCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.30
Consensus pattern (21 bp):
GAGTGTATTGATACACCTAGA
Found at i:48450 original size:15 final size:14
Alignment explanation
Indices: 48428--48478 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
48418 TTTCCATTTC
48428 CTTTTTTTCTTTAT
1 CTTTTTTTCTTTAT
*
48442 CTTTCTTTTGTTTAT
1 CTTT-TTTTCTTTAT
*
48457 CTTTTTTTTTCTTGAT
1 C--TTTTTTTCTTTAT
48473 CTTTTT
1 CTTTTT
48479 CTTCCTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 9 0.29
15 10 0.32
16 9 0.29
17 3 0.10
ACGTcount: A:0.06, C:0.14, G:0.04, T:0.76
Consensus pattern (14 bp):
CTTTTTTTCTTTAT
Found at i:48466 original size:16 final size:16
Alignment explanation
Indices: 48429--48478 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
48419 TTCCATTTCC
48429 TTTTTTTCTTTATC-T
1 TTTTTTTCTTTATCTT
* *
48444 TTCTTTTGTTTATCTT
1 TTTTTTTCTTTATCTT
*
48460 TTTTTTTCTTGATCTT
1 TTTTTTTCTTTATCTT
48476 TTT
1 TTT
48479 CTTCCTTCAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.78
Consensus pattern (16 bp):
TTTTTTTCTTTATCTT
Found at i:49059 original size:31 final size:35
Alignment explanation
Indices: 48994--49061 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
48984 AGTTTTTCAC
48994 CCGACCCGACCCGACCTGATAGATAATTTAAAAAAT
1 CCGACCCGACCCGACCTGATAGATAA-TTAAAAAAT
*
49030 CCGACCCGACCCGACTTGA-A-ATAA-TAAAAAAT
1 CCGACCCGACCCGACCTGATAGATAATTAAAAAAT
49062 TATTTTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 8 0.26
34 4 0.13
35 1 0.03
36 18 0.58
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.18
Consensus pattern (35 bp):
CCGACCCGACCCGACCTGATAGATAATTAAAAAAT
Found at i:50396 original size:23 final size:21
Alignment explanation
Indices: 50370--50412 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
50360 CGGATTCAAA
50370 ACCAAAAAGGTAGTATCGGTACC
1 ACCAAAAA-G-AGTATCGGTACC
**
50393 ACCACTAAGAGTATCGGTAC
1 ACCAAAAAGAGTATCGGTAC
50413 TACTATACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (21 bp):
ACCAAAAAGAGTATCGGTACC
Found at i:58323 original size:22 final size:22
Alignment explanation
Indices: 58295--58343 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
58285 GAAGTGATGA
58295 TGGAATTTGATGTTTTAAGACT
1 TGGAATTTGATGTTTTAAGACT
58317 TGGAATTTGATGTTTTAAGACT
1 TGGAATTTGATGTTTTAAGACT
58339 TGGAA
1 TGGAA
58344 ATGATGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (22 bp):
TGGAATTTGATGTTTTAAGACT
Found at i:58609 original size:2 final size:2
Alignment explanation
Indices: 58602--58630 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58592 ATCACTAGTT
58602 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58631 GATGTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59423 original size:20 final size:20
Alignment explanation
Indices: 59387--59424 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59377 ATCTTATTCC
**
59387 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
59407 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
59425 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:59487 original size:24 final size:24
Alignment explanation
Indices: 59450--59497 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
59440 CCTTAATGCA
*
59450 TATGGTGGATACAACCTTATGTAT
1 TATGGTGGACACAACCTTATGTAT
* *
59474 TATGGTGGGCACAACTTTATGTAT
1 TATGGTGGACACAACCTTATGTAT
59498 ATTAGCACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (24 bp):
TATGGTGGACACAACCTTATGTAT
Found at i:74494 original size:102 final size:102
Alignment explanation
Indices: 74338--74567 Score: 302
Period size: 102 Copynumber: 2.2 Consensus size: 102
74328 AAGAGAAGCT
* * * * *
74338 ATCTCAGGTGAGATAAGATTTTGTTTCGAGGAAAATAATTTCAAAATTTATGTTTCAATGGAAAA
1 ATCTCAAGTGAGATCA-ATTTTGTTTCAAGGAAAATAAATTCAAAATTTATGTTTCAAGGGAAAA
* * *
74403 TTATCTCAAGCGAGACGAAATTTGGTTT-TAGGAAAATA
65 CTATCTCAAGCGAGACAAAATTT-GTTTATAGGAAAACA
* * *
74441 ATCTCAAGTGAGATCAATTTTGTTTCAAGTG-GAATAAATTCAAAATTTGTGTTTCGAGGGAAAA
1 ATCTCAAGTGAGATCAATTTTGTTTCAAG-GAAAATAAATTCAAAATTTATGTTTCAAGGGAAAA
* *
74505 CTGTCTCAAGCGAGACAAAATTTGTTTATTGGAAAACA
65 CTATCTCAAGCGAGACAAAATTTGTTTATAGGAAAACA
74543 ATCTCAAGTGAGATCAATTTTGTTT
1 ATCTCAAGTGAGATCAATTTTGTTT
74568 AAAAAAATGT
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
101 4 0.04
102 93 0.83
103 15 0.13
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (102 bp):
ATCTCAAGTGAGATCAATTTTGTTTCAAGGAAAATAAATTCAAAATTTATGTTTCAAGGGAAAAC
TATCTCAAGCGAGACAAAATTTGTTTATAGGAAAACA
Found at i:74548 original size:36 final size:36
Alignment explanation
Indices: 74499--74568 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
74489 GTGTTTCGAG
**
74499 GGAAAACTGTCTCAAGCGAGA-CAAAATTTGTTTATT
1 GGAAAACAATCTCAAGCGAGATC-AAATTTGTTTATT
* *
74535 GGAAAACAATCTCAAGTGAGATCAATTTTGTTTA
1 GGAAAACAATCTCAAGCGAGATCAAATTTGTTTA
74569 AAAAAATGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 28 0.97
37 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (36 bp):
GGAAAACAATCTCAAGCGAGATCAAATTTGTTTATT
Found at i:79952 original size:15 final size:15
Alignment explanation
Indices: 79910--79954 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
79900 TCTTTTAAAG
*
79910 AATTTTAAGAAAAAT
1 AATTTTAAGACAAAT
79925 AATTTTAAGACAAAT
1 AATTTTAAGACAAAT
*
79940 AATTTTAACACAAAT
1 AATTTTAAGACAAAT
79955 CTGGTCTGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (15 bp):
AATTTTAAGACAAAT
Found at i:82210 original size:3 final size:3
Alignment explanation
Indices: 82202--82250 Score: 62
Period size: 3 Copynumber: 15.3 Consensus size: 3
82192 CTATAAAAAT
*
82202 ATA ATA ATA ATA ATA ATA ATA ATAA ATAA ATA ATAA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA AT-A AT-A ATA AT-A ATA ATA ATA ATA
82250 A
1 A
82251 ACCTTGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 32 0.76
4 10 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:82216 original size:14 final size:14
Alignment explanation
Indices: 82194--82244 Score: 59
Period size: 14 Copynumber: 3.5 Consensus size: 14
82184 GTTGTAACCT
*
82194 ATAAAAATATAATA
1 ATAATAATATAATA
82208 ATAATAATAATAATA
1 ATAATAAT-ATAATA
82223 ATAAATAA-ATAATAA
1 AT-AATAATATAAT-A
82238 ATAATAA
1 ATAATAA
82245 AAATAAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 17 0.52
15 11 0.33
16 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATAATATAATA
Found at i:82251 original size:6 final size:6
Alignment explanation
Indices: 82194--82251 Score: 53
Period size: 6 Copynumber: 8.8 Consensus size: 6
82184 GTTGTAACCT
* *
82194 ATAAAA ATATAATA ATAATA ATAATA ATAATAA ATAAATA ATAAATA ATAAAA
1 ATAAAA ATA-AA-A ATAAAA ATAAAA ATAA-AA ATAAA-A ATAAA-A ATAAAA
82247 ATAAA
1 ATAAA
82252 CCTTGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
6 21 0.46
7 21 0.46
8 4 0.09
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
ATAAAA
Found at i:85203 original size:21 final size:22
Alignment explanation
Indices: 85167--85207 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
85157 GAGAAATTGT
85167 TTTTAAAATATAAAAAATGATG
1 TTTTAAAATATAAAAAATGATG
*
85189 TTTTAAAAT-TGAAAAATGA
1 TTTTAAAATATAAAAAATGA
85208 AAATAAACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (22 bp):
TTTTAAAATATAAAAAATGATG
Found at i:90606 original size:21 final size:21
Alignment explanation
Indices: 90564--90607 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
90554 ACTTCGGGAG
* *
90564 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
90585 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
90606 CT
1 CT
90608 CCTCCAGCTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:91830 original size:17 final size:19
Alignment explanation
Indices: 91802--91850 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
91792 TATTTTGAAA
91802 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
91820 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
91839 CACCGATGCACT
1 CATCGATGCACT
91851 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:93681 original size:14 final size:14
Alignment explanation
Indices: 93647--93689 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
93637 CCGAAATACA
93647 GAAATCAGATATCAG
1 GAAATCA-ATATCAG
93662 GAAATCAATATTCAG
1 GAAATCAATA-TCAG
93677 G-AATCAAGTATCA
1 GAAATCAA-TATCA
93690 TGTATCATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.47, C:0.14, G:0.16, T:0.23
Consensus pattern (14 bp):
GAAATCAATATCAG
Found at i:94470 original size:29 final size:30
Alignment explanation
Indices: 94434--94502 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
94424 TATTTTACAG
*
94434 AAATAGCACCCT-TTTTAAATGAATTACTA
1 AAATAGCACCCTATTTCAAATGAATTACTA
* * *
94463 AAATAGCA-TCTATTTCGAATTAATTACTA
1 AAATAGCACCCTATTTCAAATGAATTACTA
94492 AAATAGCACCC
1 AAATAGCACCC
94503 AGTCAACGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
28 2 0.06
29 30 0.91
30 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (30 bp):
AAATAGCACCCTATTTCAAATGAATTACTA
Found at i:100509 original size:14 final size:15
Alignment explanation
Indices: 100477--100517 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
100467 ACCTTCATAA
100477 AATATTGA-TTCCTC
1 AATATTGATTTCCTC
100491 AATATTGATTTCCT-
1 AATATTGATTTCCTC
*
100505 GATATCTGATTTC
1 AATAT-TGATTTC
100518 TGTATTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (15 bp):
AATATTGATTTCCTC
Found at i:106867 original size:29 final size:30
Alignment explanation
Indices: 106793--106861 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
106783 ACCGTTGACC
*
106793 GGGTGCTATTTTAGTAATTAATTCAAAATA
1 GGGTACTATTTTAGTAATTAATTCAAAATA
*
106823 -GGTACTATTTTAGTAATTAATTTAAAA-A
1 GGGTACTATTTTAGTAATTAATTCAAAATA
106851 GGGTACTATTT
1 GGGTACTATTT
106862 CTGTAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 1 0.03
29 35 0.97
ACGTcount: A:0.36, C:0.06, G:0.16, T:0.42
Consensus pattern (30 bp):
GGGTACTATTTTAGTAATTAATTCAAAATA
Found at i:108674 original size:29 final size:29
Alignment explanation
Indices: 108642--108709 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
108632 CATTTTACAG
*
108642 AAATAACACCTTTTTTAAATTAATTACTA
1 AAATAACACCTATTTTAAATTAATTACTA
*
108671 AAATAACACCTATTTTGAATTAATTACTA
1 AAATAACACCTATTTTAAATTAATTACTA
*
108700 AAATAGCACC
1 AAATAACACC
108710 CGATCAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (29 bp):
AAATAACACCTATTTTAAATTAATTACTA
Found at i:111988 original size:54 final size:54
Alignment explanation
Indices: 111919--112026 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
111909 CTGAGGTAAA
*
111919 ACCCTATAAAAATTTTCTAATACCAAGTTCAACCTTGGAGGTGAGGATCTCCAC
1 ACCCTATAAAAATTTTCTAATACCAAGTTCAACCATGGAGGTGAGGATCTCCAC
*
111973 ACCCTATAAAGATTTTCTAATACCAAGTTCAACCATGGAGGTGAGGATCTCCAC
1 ACCCTATAAAAATTTTCTAATACCAAGTTCAACCATGGAGGTGAGGATCTCCAC
112027 GAGAGTGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (54 bp):
ACCCTATAAAAATTTTCTAATACCAAGTTCAACCATGGAGGTGAGGATCTCCAC
Found at i:114158 original size:63 final size:63
Alignment explanation
Indices: 114055--114195 Score: 219
Period size: 63 Copynumber: 2.2 Consensus size: 63
114045 TTTCCAACTG
* ** *
114055 AGAGTATCGATACTGCTAAGGAAATTACCGATACTACCCCTATAGTATTGATACTCAAGGTAT
1 AGAGTATCGATTCTGCTAAGGAAAGCACCGATACTACCCCTATAATATTGATACTCAAGGTAT
* * *
114118 AGAGTATGGATTCTGCTAAGGAAAGCATCGATACTGCCCCTATAATATTGATACTCAAGGTAT
1 AGAGTATCGATTCTGCTAAGGAAAGCACCGATACTACCCCTATAATATTGATACTCAAGGTAT
114181 AGAGTATCGATTCTG
1 AGAGTATCGATTCTG
114196 GGCCATATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (63 bp):
AGAGTATCGATTCTGCTAAGGAAAGCACCGATACTACCCCTATAATATTGATACTCAAGGTAT
Found at i:114582 original size:63 final size:63
Alignment explanation
Indices: 114479--114619 Score: 228
Period size: 63 Copynumber: 2.2 Consensus size: 63
114469 TTTCCAACTG
* * *
114479 AGAGTATCGATACTGCTAAGGAAATTACCGATACTACCCCTATAGTATTGATACTCAAGGTAT
1 AGAGTATCGATTCTGCTAAGGAAAGTACCGATAATACCCCTATAGTATTGATACTCAAGGTAT
* * *
114542 AGAGTATGGATTCTGCTAAGGAAAGTATCGATAATGCCCCTATAGTATTGATACTCAAGGTAT
1 AGAGTATCGATTCTGCTAAGGAAAGTACCGATAATACCCCTATAGTATTGATACTCAAGGTAT
114605 AGAGTATCGATTCTG
1 AGAGTATCGATTCTG
114620 GGCCATATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (63 bp):
AGAGTATCGATTCTGCTAAGGAAAGTACCGATAATACCCCTATAGTATTGATACTCAAGGTAT
Found at i:114745 original size:424 final size:424
Alignment explanation
Indices: 113957--114808 Score: 1650
Period size: 424 Copynumber: 2.0 Consensus size: 424
113947 TAACACATTT
113957 GAGATGATTTCTGGGTGTTTCCCGGTCTTAAAAAAATATTTATGAGTTTGAATATCGATACTAGA
1 GAGATGATTTCTGGGTGTTTCCCGGTCTTAAAAAAATATTTATGAGTTTGAATATCGATACTAGA
114022 TGAATTGGGATAAAAAATAGGAATTTCCAACTGAGAGTATCGATACTGCTAAGGAAATTACCGAT
66 TGAATTGGGATAAAAAATAGGAATTTCCAACTGAGAGTATCGATACTGCTAAGGAAATTACCGAT
*
114087 ACTACCCCTATAGTATTGATACTCAAGGTATAGAGTATGGATTCTGCTAAGGAAAGCATCGATAC
131 ACTACCCCTATAGTATTGATACTCAAGGTATAGAGTATGGATTCTGCTAAGGAAAGCATCGATAA
114152 TGCCCCTATAATATTGATACTCAAGGTATAGAGTATCGATTCTGGGCCATATTTTCAACAACAGA
196 TGCCCCTATAATATTGATACTCAAGGTATAGAGTATCGATTCTGGGCCATATTTTCAACAACAGA
*
114217 AGCCATTTTTGGTATTGATACTCATTGGGGTATCGATACTTGACCTTAGAGTATCAATACTACAA
261 AGCCATTTTTGGTATTGATACTCATTAGGGTATCGATACTTGACCTTAGAGTATCAATACTACAA
114282 GTGGAGTATCGATACTACTCACTTTAGATGGTTAGATTTAAAATATTGAAGGCTCGTAAGAGCTA
326 GTGGAGTATCGATACTACTCACTTTAGATGGTTAGATTTAAAATATTGAAGGCTCGTAAGAGCTA
114347 AGAATGGTCTGTAATGATAGAACTTAGTCTGTAG
391 AGAATGGTCTGTAATGATAGAACTTAGTCTGTAG
*
114381 GAGATGATTTCTGGGTGTTTCCCGGTCTTAAAAAAATATTTATGAGTTTGAATATCTATACTAGA
1 GAGATGATTTCTGGGTGTTTCCCGGTCTTAAAAAAATATTTATGAGTTTGAATATCGATACTAGA
114446 TGAATTGGGATAAAAAATAGGAATTTCCAACTGAGAGTATCGATACTGCTAAGGAAATTACCGAT
66 TGAATTGGGATAAAAAATAGGAATTTCCAACTGAGAGTATCGATACTGCTAAGGAAATTACCGAT
*
114511 ACTACCCCTATAGTATTGATACTCAAGGTATAGAGTATGGATTCTGCTAAGGAAAGTATCGATAA
131 ACTACCCCTATAGTATTGATACTCAAGGTATAGAGTATGGATTCTGCTAAGGAAAGCATCGATAA
*
114576 TGCCCCTATAGTATTGATACTCAAGGTATAGAGTATCGATTCTGGGCCATATTTTCAACAACAGA
196 TGCCCCTATAATATTGATACTCAAGGTATAGAGTATCGATTCTGGGCCATATTTTCAACAACAGA
114641 AGCCATTTTTGGTATTGATACTCATTAGGGTATCGATACTTGACCTTAGAGTATCAATACTACAA
261 AGCCATTTTTGGTATTGATACTCATTAGGGTATCGATACTTGACCTTAGAGTATCAATACTACAA
114706 GTGGAGTATCGATACTACTCACTTTAGATGGTTAGATTTAAAATATTGAAGGCTCGTAAGAGCTA
326 GTGGAGTATCGATACTACTCACTTTAGATGGTTAGATTTAAAATATTGAAGGCTCGTAAGAGCTA
*
114771 AGAATGGTCTGTAATGATAGAACTTAGTCTGTGG
391 AGAATGGTCTGTAATGATAGAACTTAGTCTGTAG
114805 GAGA
1 GAGA
114809 CGTAAATGGC
Statistics
Matches: 422, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
424 422 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (424 bp):
GAGATGATTTCTGGGTGTTTCCCGGTCTTAAAAAAATATTTATGAGTTTGAATATCGATACTAGA
TGAATTGGGATAAAAAATAGGAATTTCCAACTGAGAGTATCGATACTGCTAAGGAAATTACCGAT
ACTACCCCTATAGTATTGATACTCAAGGTATAGAGTATGGATTCTGCTAAGGAAAGCATCGATAA
TGCCCCTATAATATTGATACTCAAGGTATAGAGTATCGATTCTGGGCCATATTTTCAACAACAGA
AGCCATTTTTGGTATTGATACTCATTAGGGTATCGATACTTGACCTTAGAGTATCAATACTACAA
GTGGAGTATCGATACTACTCACTTTAGATGGTTAGATTTAAAATATTGAAGGCTCGTAAGAGCTA
AGAATGGTCTGTAATGATAGAACTTAGTCTGTAG
Found at i:116132 original size:45 final size:45
Alignment explanation
Indices: 116067--116289 Score: 338
Period size: 45 Copynumber: 5.0 Consensus size: 45
116057 TCTCTTATAT
* **
116067 CATCCTTTCATACTGATAATGCACCCATATGCATTTCAATTATGG
1 CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
* * *
116112 TATCCTTTCATGCCTATAATGCACCCATATGCATTTCAATTATGA
1 CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
* *
116157 CATCCTTTCATGCAAATAATGCACCCATATGCATTTTAATTATGG
1 CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
* * *
116202 CATCCTTTTATGCCAATAATGCAACCATATGCATTTTAATTATGG
1 CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
*
116247 CATCCTTTCATGTCAATAATGCACCCATATGCATTTCAATTAT
1 CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTAT
116290 TCATTCATTT
Statistics
Matches: 161, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 161 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (45 bp):
CATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATGG
Found at i:116189 original size:90 final size:89
Alignment explanation
Indices: 116021--116289 Score: 344
Period size: 90 Copynumber: 3.0 Consensus size: 89
116011 TCATTAATAA
* * * ** * *
116021 CATCCATTCATGCTTATAATGC-GCCATTATGCATTTTCTCTTAT-ATCATCCTTTCATACTGAT
1 CATCCTTTCATGCCTATAATGCAACCA-TATGCA-TTTCAATTATGA-CATCCTTTCATGC-AAT
116084 AATGCACCCATATGCATTTCAATTATGG
62 AATGCACCCATATGCATTTCAATTATGG
* *
116112 TATCCTTTCATGCCTATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATGCAAATAAT
1 CATCCTTTCATGCCTATAATGCAACCATATGCATTTCAATTATGACATCCTTTCATGC-AATAAT
*
116177 GCACCCATATGCATTTTAATTATGG
65 GCACCCATATGCATTTCAATTATGG
* * * *
116202 CATCCTTTTATGCCAATAATGCAACCATATGCATTTTAATTATGGCATCCTTTCATGTCAATAAT
1 CATCCTTTCATGCCTATAATGCAACCATATGCATTTCAATTATGACATCCTTTCATG-CAATAAT
116267 GCACCCATATGCATTTCAATTAT
65 GCACCCATATGCATTTCAATTAT
116290 TCATTCATTT
Statistics
Matches: 158, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
90 128 0.81
91 27 0.17
92 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (89 bp):
CATCCTTTCATGCCTATAATGCAACCATATGCATTTCAATTATGACATCCTTTCATGCAATAATG
CACCCATATGCATTTCAATTATGG
Found at i:117390 original size:3 final size:3
Alignment explanation
Indices: 117382--117412 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
117372 CCACGTGAAA
117382 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
117413 GTAGAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:117804 original size:32 final size:32
Alignment explanation
Indices: 117738--117812 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
117728 TCAGTGTAGA
* *
117738 ATTTAGATAATGCACAACAGAGTCAGTGTTGC
1 ATTTAGATAATGCACAACAGAGTCAGTATCGC
** * *
117770 ATTTAGATAATGCACAGGAGTGTTAGTATCGC
1 ATTTAGATAATGCACAACAGAGTCAGTATCGC
*
117802 ATTTATATAAT
1 ATTTAGATAAT
117813 ACGTAACAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (32 bp):
ATTTAGATAATGCACAACAGAGTCAGTATCGC
Found at i:118165 original size:22 final size:22
Alignment explanation
Indices: 118137--118188 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
118127 ACTTCATGCA
*
118137 TATCTTTCAGAGTATTGTATTG
1 TATCTTTAAGAGTATTGTATTG
118159 TATCTTTAAGAGTATTGTATTG
1 TATCTTTAAGAGTATTGTATTG
118181 TATCTTTA
1 TATCTTTA
118189 GTGGGCATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (22 bp):
TATCTTTAAGAGTATTGTATTG
Found at i:118729 original size:20 final size:20
Alignment explanation
Indices: 118707--118782 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
118697 ATGTGTTACT
118707 AAAATTAAATTGATTTTTATA
1 AAAATTAAATTGATTTTTA-A
*
118728 AACAATTTAATT--TTTTATAAA
1 AA-AATTAAATTGATTTT-T-AA
*
118749 AAAATTAAATTGATTTCTAA
1 AAAATTAAATTGATTTTTAA
*
118769 AAAAATAAATTGAT
1 AAAATTAAATTGAT
118783 AGGTGTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
20 27 0.59
21 7 0.15
22 12 0.26
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (20 bp):
AAAATTAAATTGATTTTTAA
Found at i:118756 original size:19 final size:19
Alignment explanation
Indices: 118720--118779 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
118710 ATTAAATTGA
* *
118720 TTTTTATAAACAATTTAAT
1 TTTTTATAAAAAAATTAAT
118739 TTTTTATAAAAAAATTAAAT
1 TTTTTATAAAAAAATT-AAT
* * *
118759 TGATTTCTAAAAAAATAAAT
1 T-TTTTATAAAAAAATTAAT
118779 T
1 T
118780 GATAGGTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 14 0.41
20 8 0.24
21 12 0.35
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTTTATAAAAAAATTAAT
Found at i:119475 original size:3 final size:3
Alignment explanation
Indices: 119467--119503 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
119457 TGATATTTAT
119467 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
119504 AGTTTAAATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:120963 original size:18 final size:18
Alignment explanation
Indices: 120936--120993 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
120926 AGATGAGAGC
120936 TTTT-TTATTTCATTTTA
1 TTTTCTTATTTCATTTTA
*
120953 TTTTCTTATTT-ACTTTA
1 TTTTCTTATTTCATTTTA
*
120970 TTTTTCTTA-TTCATCCTTA
1 -TTTTCTTATTTCAT-TTTA
120989 TTTTC
1 TTTTC
120994 CCTCTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 11 0.32
18 20 0.59
19 3 0.09
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTCTTATTTCATTTTA
Found at i:120969 original size:17 final size:19
Alignment explanation
Indices: 120936--120980 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
120926 AGATGAGAGC
*
120936 TTTT-TTATTTCATTTTA-
1 TTTTCTTATTTCACTTTAT
120953 TTTTCTTATTT-ACTTTAT
1 TTTTCTTATTTCACTTTAT
120971 TTTTCTTATT
1 TTTTCTTATT
120981 CATCCTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTTATTTCACTTTAT
Found at i:131286 original size:54 final size:55
Alignment explanation
Indices: 131190--131295 Score: 124
Period size: 54 Copynumber: 1.9 Consensus size: 55
131180 CGAAATGAAA
* * *
131190 ATTCACAAACTCATTATAAATTCCATGGATTGCACACATAGTG-CCAAAATGGTT
1 ATTCACAAACACATTATAAATACAATGGATTGCACACATAGTGTCCAAAATGGTT
* * * ** *
131244 ATTCATAAACACATTATGAATACAATGGGTTGCACATTTAGTGTCGAAAATG
1 ATTCACAAACACATTATAAATACAATGGATTGCACACATAGTGTCCAAAATG
131296 CACCGTTATG
Statistics
Matches: 42, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
54 35 0.83
55 7 0.17
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (55 bp):
ATTCACAAACACATTATAAATACAATGGATTGCACACATAGTGTCCAAAATGGTT
Found at i:135582 original size:32 final size:32
Alignment explanation
Indices: 135471--135583 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 32
135461 GATTGTATGT
*
135471 TGCATAGTAGTGTCAGTGTTGCATTCAAATAA
1 TGCACAGTAGTGTCAGTGTTGCATTCAAATAA
* * *
135503 TGCAAAATAGAGTCAGTGTTGCATTCAAATAA
1 TGCACAGTAGTGTCAGTGTTGCATTCAAATAA
* * *
135535 TGTACAGTAGGGTCAGTGTTGCATTCAGATAA
1 TGCACAGTAGTGTCAGTGTTGCATTCAAATAA
* *
135567 TACACAGGAGTGTCAGT
1 TGCACAGTAGTGTCAGT
135584 ATTGTAGTAA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (32 bp):
TGCACAGTAGTGTCAGTGTTGCATTCAAATAA
Found at i:139110 original size:68 final size:68
Alignment explanation
Indices: 138985--139588 Score: 870
Period size: 68 Copynumber: 8.9 Consensus size: 68
138975 GGCGTAGGTA
* * * *
138985 TGCATTTAAAAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTTCCTTTGAGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
139050 ATG
66 ATG
* ** *
139053 TGTATTTGTTAGGAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
139118 ATG
66 ATG
* *
139121 TGCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGGGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
*
139186 CTG
66 ATG
* * *
139189 TGCATTTGACAGAAAGGTGTTAATTATGCCAGTTAGATGAAAGACTACA-TGCCTTTGAGGACTA
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTA-AGTGCCTTTGAGGCCTA
139253 GATG
65 GATG
* * * * *
139257 TGCTTTTGACAAAAAGGTGTCAATTATGCCATTTAGATGAAATGCTAAGTGCCTTTAAGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
*
139322 CTG
66 ATG
* *
139325 TGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTATGAGGCCTA-
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
139389 ACTG
66 A-TG
* * *
139393 TGCATTTGACAGAAAGATGTCAATTATGCCAGTTAAATGAAAGGCTAAGTGTCTTTGAGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
*
139458 TTG
66 ATG
* * * **
139461 TGCATTTGATAGAAAGGTGTCAATTATGACAGTTAGATGAAAGACTAAGTGATTTTGAGGCCTAG
1 TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
*
139526 CTG
66 ATG
*
139529 TGCATTTGACAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
1 TGCATTTGAC-AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAG
139589 TAAAATACTA
Statistics
Matches: 474, Mismatches: 57, Indels: 9
0.88 0.11 0.02
Matches are distributed among these distances:
67 1 0.00
68 428 0.90
69 45 0.09
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (68 bp):
TGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAG
ATG
Found at i:139615 original size:10 final size:10
Alignment explanation
Indices: 139600--139629 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
139590 AAAATACTAG
139600 ATGTATAAAA
1 ATGTATAAAA
139610 ATGTATAAAA
1 ATGTATAAAA
*
139620 TTGTATAAAA
1 ATGTATAAAA
139630 GGCATGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (10 bp):
ATGTATAAAA
Found at i:139976 original size:45 final size:45
Alignment explanation
Indices: 139608--139971 Score: 536
Period size: 45 Copynumber: 8.1 Consensus size: 45
139598 AGATGTATAA
* * *
139608 AAATGTATAAAATTGTATAAAAGGCATGAAAGAATGCCATAAATG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
* *
139653 AAATGTATAATAGTGTATAAAAGGCATGGAAGGATGCCATAATTG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
* * *
139698 AAATGTATAATAGTGTATATAAGGCATGAAATGATGACATAAATG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
* *
139743 AAATGTATAATAGAGTATAAAAGGCATGAAAGGATGCCATAATTG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
*
139788 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGTCATAAATG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
*
139833 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGTCATAAATG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
139878 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATG-CATAAATG
1 AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
* * ** *
139922 AAAT-TCAT-ATAAGTGCATTATTGGCATGAAAGGATGCCATAATTG
1 AAATGT-ATAAT-AGTGTATAAAAGGCATGAAAGGATGCCATAAATG
139967 AAATG
1 AAATG
139972 CATATGGGTA
Statistics
Matches: 292, Mismatches: 23, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
43 3 0.01
44 35 0.12
45 254 0.87
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (45 bp):
AAATGTATAATAGTGTATAAAAGGCATGAAAGGATGCCATAAATG
Found at i:140007 original size:45 final size:45
Alignment explanation
Indices: 139900--140021 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
139890 GTGTATAAAA
** * *
139900 GGCATGAAAGGATG-CATAAATGAAATTCATATAAGTGCATTATT
1 GGCATGAAACAATGCCATAAATGAAATGCATATAAGTACATTATT
** * **
139944 GGCATGAAAGGATGCCATAATTGAAATGCATATGGGTACATTATT
1 GGCATGAAACAATGCCATAAATGAAATGCATATAAGTACATTATT
*
139989 GGCATGAAACAATTCCATAAATGAAAATGCATA
1 GGCATGAAACAATGCCATAAATG-AAATGCATA
140022 ATGGTGCATT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
44 14 0.21
45 44 0.66
46 9 0.13
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (45 bp):
GGCATGAAACAATGCCATAAATGAAATGCATATAAGTACATTATT
Found at i:146560 original size:16 final size:15
Alignment explanation
Indices: 146535--146568 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
146525 CTGCAATTTC
*
146535 TTAATATAATTAGTA
1 TTAATATAATTAATA
146550 TTAATTATAATTAATA
1 TTAA-TATAATTAATA
146566 TTA
1 TTA
146569 TGATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
TTAATATAATTAATA
Found at i:154237 original size:21 final size:21
Alignment explanation
Indices: 154211--154255 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
154201 CTTCGACCAT
154211 AAAATCTATCACGATCTGCAC
1 AAAATCTATCACGATCTGCAC
*
154232 AAAATCTATCACGATCTGTAC
1 AAAATCTATCACGATCTGCAC
154253 AAA
1 AAA
154256 GTCACAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (21 bp):
AAAATCTATCACGATCTGCAC
Found at i:154739 original size:37 final size:37
Alignment explanation
Indices: 154637--154741 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
154627 CCTTTTCGTC
* *
154637 CTACTAGGATTCAAATTCCTAAAAAAAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
154674 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
154711 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
154742 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:155918 original size:17 final size:18
Alignment explanation
Indices: 155896--155929 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
155886 ACCTTACTAA
155896 CTCTTTCATTT-TTTCCT
1 CTCTTTCATTTATTTCCT
*
155913 CTCTTTTATTTATTTCC
1 CTCTTTCATTTATTTCC
155930 ATCATCTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.09, C:0.26, G:0.00, T:0.65
Consensus pattern (18 bp):
CTCTTTCATTTATTTCCT
Found at i:159173 original size:16 final size:14
Alignment explanation
Indices: 159154--159200 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
159144 GGCAAAAATA
159154 AAAAAAGAAAAGAAGC
1 AAAAAAG-AAAGAA-C
159170 AAAAAAG-AAGAA-
1 AAAAAAGAAAGAAC
159182 AAAAAAGAAAGAAC
1 AAAAAAGAAAGAAC
159196 AAAAA
1 AAAAA
159201 TAAAAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 10 0.34
16 7 0.24
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAGAAC
Found at i:159208 original size:16 final size:16
Alignment explanation
Indices: 159146--159210 Score: 62
Period size: 16 Copynumber: 4.0 Consensus size: 16
159136 ACAAAAAGGG
159146 CAAAAATAAAAAAAGAA
1 CAAAAAT-AAAAAAGAA
**
159163 -AAGAAGCAAAAAAGAA
1 CAA-AAATAAAAAAGAA
*
159179 GAAAAA-AAAGAAAGAA
1 CAAAAATAAA-AAAGAA
159195 CAAAAATAAAAAAGAA
1 CAAAAATAAAAAAGAA
159211 AAGGGGACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 3 0.08
16 30 0.75
17 7 0.17
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (16 bp):
CAAAAATAAAAAAGAA
Found at i:159212 original size:27 final size:28
Alignment explanation
Indices: 159148--159213 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 28
159138 AAAAAGGGCA
159148 AAAATAAAAAAAGAAAAGAAGCAAAAAAG
1 AAAA-AAAAAAAGAAAAGAAGCAAAAAAG
* *
159177 AAGAAAAAAAAG-AAAGAA-C-AAAAAT
1 AAAAAAAAAAAGAAAAGAAGCAAAAAAG
*
159202 AAAAAAGAAAAG
1 AAAAAAAAAAAG
159214 GGGACAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 15 0.45
26 1 0.03
27 6 0.18
28 8 0.24
29 3 0.09
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAAAGAAAAGAAGCAAAAAAG
Found at i:159892 original size:22 final size:22
Alignment explanation
Indices: 159818--159894 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
159808 GCTACCCCAT
*
159818 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
159840 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
159862 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
159884 CAAACCTTTGA
1 CAAACCTTTGA
159895 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:160923 original size:106 final size:106
Alignment explanation
Indices: 160720--162198 Score: 2129
Period size: 106 Copynumber: 14.0 Consensus size: 106
160710 ATATCGTGCC
* * * * * * * *
160720 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGCCAAC-AACAATTTTCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
160784 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
160825 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
160890 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
160931 ACTCCAGATAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
160996 AATTTCAGAGCCAATTTCAACTTAACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
161037 ACTCTAGACAACGCAATTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * **
161102 AATTTCAGAGCCAATTTCAACTTCACAACAAATTATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
161143 ACTCCAGACAACGCAAGTTCAACTTGACGACAAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
161208 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
161249 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACTGCTGGTTGACAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
161314 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
161355 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
161420 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
161461 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
161526 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
161567 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
161632 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
161673 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
161738 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
161779 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTCTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
161844 AATTTCAGAGCCAATTTCAACTACACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
161885 ACTCAAGACAACTCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
161950 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATCTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
161991 AC-CCAATACAACAG-AAGCTCAACTTCACGATGAAAAGG-CGGCTGATTGTCAAC-AA-AA-TT
1 ACTCC-AGACAAC-GCAAGTTCAACTTCACGACG-AAGGGACCGCTGGTTGTCAACAAACAACTT
* * *
162050 -TC-A-TTCAGAGTCAATTTTAACTTCACAGCGAAGG-TATTGG
63 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * * *
162090 ACTCAAGACAACACAAGTTCAACTTCACAACAAAGGGACGGCTTGTTATCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
162155 GGTTCCAGAGCCAATTTCAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
162196 ACT
1 ACT
162199 TGGAACAATG
Statistics
Matches: 1242, Mismatches: 116, Indels: 31
0.89 0.08 0.02
Matches are distributed among these distances:
98 4 0.00
99 39 0.03
100 32 0.03
101 3 0.00
102 3 0.00
103 3 0.00
104 4 0.00
105 74 0.06
106 1076 0.87
107 4 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:162987 original size:37 final size:37
Alignment explanation
Indices: 162930--163034 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
162920 CCTTTTCGTC
*
162930 CTACTAGGATTCAAATTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
162967 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
163004 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
163035 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:165440 original size:20 final size:20
Alignment explanation
Indices: 165415--165454 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
165405 TTTTTCCATG
165415 ATCCCTTAAATTCAATCACA
1 ATCCCTTAAATTCAATCACA
*
165435 ATCCCTTGAATTCAATCACA
1 ATCCCTTAAATTCAATCACA
165455 CAAGTCCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.30
Consensus pattern (20 bp):
ATCCCTTAAATTCAATCACA
Found at i:184659 original size:22 final size:22
Alignment explanation
Indices: 184632--184674 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
184622 TCCATTTCAG
184632 CATCAACA-CCATCAAAATCTTC
1 CATCAA-AGCCATCAAAATCTTC
*
184654 CATCAAAGCCATCAACATCTT
1 CATCAAAGCCATCAAAATCTT
184675 TATAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.40, C:0.35, G:0.02, T:0.23
Consensus pattern (22 bp):
CATCAAAGCCATCAAAATCTTC
Found at i:185975 original size:30 final size:29
Alignment explanation
Indices: 185882--186032 Score: 119
Period size: 30 Copynumber: 5.2 Consensus size: 29
185872 ATGTCTCATA
* * *
185882 CAGAATCAGGATGCGGAACGAAGCCCCATA
1 CAGAATCAGGAAG-GGAACGAAGTCCCATG
* * * *
185912 TAGAATCA--TA-GGAACGAAATCTCATG
1 CAGAATCAGGAAGGGAACGAAGTCCCATG
* **
185938 GAGAATCAGGACAATGAACGAAGTCCCATG
1 CAGAATCAGGA-AGGGAACGAAGTCCCATG
* * * *
185968 CATAATCAAGATAGGGAACGAATTCCCATA
1 CAGAATCAGGA-AGGGAACGAAGTCCCATG
*
185998 CAGAATTAGGAAGGGAACGAAGTCCCATG
1 CAGAATCAGGAAGGGAACGAAGTCCCATG
186027 CAGAAT
1 CAGAAT
186033 AAAAATACAT
Statistics
Matches: 92, Mismatches: 25, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
26 19 0.21
29 23 0.25
30 50 0.54
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (29 bp):
CAGAATCAGGAAGGGAACGAAGTCCCATG
Found at i:186023 original size:29 final size:30
Alignment explanation
Indices: 185953--186032 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
185943 TCAGGACAAT
*
185953 GAACGAAGTCCCATGCATAATCAAGATAGG
1 GAACGAAGTCCCATGCAGAATCAAGATAGG
* * * *
185983 GAACGAATTCCCATACAGAATTAGGA-AGG
1 GAACGAAGTCCCATGCAGAATCAAGATAGG
186012 GAACGAAGTCCCATGCAGAAT
1 GAACGAAGTCCCATGCAGAAT
186033 AAAAATACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (30 bp):
GAACGAAGTCCCATGCAGAATCAAGATAGG
Done.