Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001438.1 Hibiscus syriacus cultivar Beakdansim tig00002787_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: 163513
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:5643 original size:9 final size:9
Alignment explanation
Indices: 5629--5654 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5619 ATCAAAAATA
5629 TTATTATTT
1 TTATTATTT
5638 TTATTATTT
1 TTATTATTT
5647 TTATTATT
1 TTATTATT
5655 ATTAAACATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTATTATTT
Found at i:5926 original size:17 final size:18
Alignment explanation
Indices: 5889--5932 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
5879 TTATGGGATG
5889 AAAAAATAGTATTATTGT
1 AAAAAATAGTATTATTGT
5907 AAAAAAT-GTAATTATT-T
1 AAAAAATAGT-ATTATTGT
5924 AAAATAATA
1 AAAA-AATA
5933 TTTTACAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (18 bp):
AAAAAATAGTATTATTGT
Found at i:5965 original size:16 final size:17
Alignment explanation
Indices: 5946--5977 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5936 TACAACCATA
5946 ATATTAT-TTTTATATT
1 ATATTATATTTTATATT
5962 ATATTATATTTTATAT
1 ATATTATATTTTATAT
5978 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:16370 original size:14 final size:14
Alignment explanation
Indices: 16353--16379 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16343 ATAAATGAAC
16353 GAACATAAACAAAT
1 GAACATAAACAAAT
16367 GAACATAAACAAA
1 GAACATAAACAAA
16380 ACGGATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (14 bp):
GAACATAAACAAAT
Found at i:18569 original size:15 final size:15
Alignment explanation
Indices: 18551--18593 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
18541 GCCCCGCATC
*
18551 CATCCGCCCGCCCCA
1 CATCCTCCCGCCCCA
18566 CATCCTCCCGCCCCA
1 CATCCTCCCGCCCCA
18581 CATCCTCCCGCCC
1 CATCCTCCCGCCC
18594 AGTTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.67, G:0.09, T:0.12
Consensus pattern (15 bp):
CATCCTCCCGCCCCA
Found at i:18576 original size:19 final size:18
Alignment explanation
Indices: 18538--18593 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
18528 TGAGACATTA
*
18538 CCCGCCCCGCATCCATCCG
1 CCCGCCCCACATCC-TCCG
18557 CCCGCCCCACATCCT---
1 CCCGCCCCACATCCTCCG
18572 CCCGCCCCACATCCTCCCG
1 CCCGCCCCACATCCT-CCG
18591 CCC
1 CCC
18594 AGTTAAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 15 0.47
18 1 0.03
19 16 0.50
ACGTcount: A:0.11, C:0.68, G:0.11, T:0.11
Consensus pattern (18 bp):
CCCGCCCCACATCCTCCG
Found at i:20348 original size:10 final size:10
Alignment explanation
Indices: 20333--20368 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
20323 AATTTAGTTT
20333 GTTCGTATTC
1 GTTCGTATTC
20343 GTTCGTATTC
1 GTTCGTATTC
*
20353 GTTCATATTC
1 GTTCGTATTC
*
20363 ATTCGT
1 GTTCGT
20369 TAACATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (10 bp):
GTTCGTATTC
Found at i:20444 original size:20 final size:20
Alignment explanation
Indices: 20406--20444 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20396 GAATGCAAAC
* *
20406 GAACATAAACTAACGTAAAA
1 GAACATAAACAAACATAAAA
*
20426 GAACGTAAACAAACATAAA
1 GAACATAAACAAACATAAA
20445 CGAATGAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.13
Consensus pattern (20 bp):
GAACATAAACAAACATAAAA
Found at i:20616 original size:14 final size:14
Alignment explanation
Indices: 20597--20633 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20587 GAGATGGGCT
20597 GAATATAAATGAAC
1 GAATATAAATGAAC
*
20611 GAATATAAATGAAT
1 GAATATAAATGAAC
*
20625 GAACATAAA
1 GAATATAAA
20634 CGACCATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.59, C:0.05, G:0.14, T:0.22
Consensus pattern (14 bp):
GAATATAAATGAAC
Found at i:20635 original size:24 final size:24
Alignment explanation
Indices: 20608--20658 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
20598 AATATAAATG
* **
20608 AACGAATATAAATGAATGAACATA
1 AACGAACATAAATGAACAAACATA
*
20632 AACGACCATAAATGAACAAACATA
1 AACGAACATAAATGAACAAACATA
20656 AAC
1 AAC
20659 AAACGGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.59, C:0.16, G:0.10, T:0.16
Consensus pattern (24 bp):
AACGAACATAAATGAACAAACATA
Found at i:20657 original size:14 final size:14
Alignment explanation
Indices: 20601--20657 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
20591 TGGGCTGAAT
*
20601 ATAAATGAACGAAT
1 ATAAATGAACGAAC
*
20615 ATAAATGAATGAAC
1 ATAAATGAACGAAC
*
20629 AT--A--AACGACC
1 ATAAATGAACGAAC
*
20639 ATAAATGAACAAAC
1 ATAAATGAACGAAC
20653 ATAAA
1 ATAAA
20658 CAAACGGATT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
10 7 0.21
12 2 0.06
14 24 0.73
ACGTcount: A:0.60, C:0.12, G:0.11, T:0.18
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:28957 original size:18 final size:19
Alignment explanation
Indices: 28926--28967 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 19
28916 TTGAATTTAA
28926 AAAAATCAGAAAAAATTAC
1 AAAAATCAGAAAAAATTAC
28945 AAAAATCAG-AAAAATTAC
1 AAAAATCAGAAAAAATTAC
28963 AAAAA
1 AAAAA
28968 AAATTAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.71, C:0.10, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAATCAGAAAAAATTAC
Found at i:28968 original size:19 final size:20
Alignment explanation
Indices: 28925--28968 Score: 74
Period size: 19 Copynumber: 2.3 Consensus size: 20
28915 CTTGAATTTA
28925 AAAAAATCAGAAAAAATTAC
1 AAAAAATCAGAAAAAATTAC
28945 -AAAAATCAG-AAAAATTAC
1 AAAAAATCAGAAAAAATTAC
28963 AAAAAA
1 AAAAAA
28969 AATTAGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (20 bp):
AAAAAATCAGAAAAAATTAC
Found at i:29687 original size:43 final size:43
Alignment explanation
Indices: 29626--29800 Score: 260
Period size: 43 Copynumber: 4.1 Consensus size: 43
29616 TATAGCGGCA
* * * *
29626 CAATAGGTGTTGATATTTAGCGGCGTTTTTCCAATAAACGACG
1 CAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCG
*
29669 CAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCACAAACGCCG
1 CAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCG
*
29712 CAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCACAAACGCCG
1 CAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCG
* * * *
29755 TAATAGGTCTTGAGATTTAGCGGCGTTTTTCTCACAAACACCG
1 CAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCG
29798 CAA
1 CAA
29801 AAGATCTGGT
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 119 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
CAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCACAAACGCCG
Found at i:30030 original size:21 final size:21
Alignment explanation
Indices: 30004--30053 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
29994 TAAACTTGAC
**
30004 ATCCATAACAACAAATTTAAA
1 ATCCATAACAACAAAAATAAA
* *
30025 ATCCATAACAAGAAAAATGAA
1 ATCCATAACAACAAAAATAAA
30046 ATCCATAA
1 ATCCATAA
30054 TAATAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.58, C:0.18, G:0.04, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAAAATAAA
Found at i:30964 original size:36 final size:36
Alignment explanation
Indices: 30914--31002 Score: 144
Period size: 36 Copynumber: 2.5 Consensus size: 36
30904 CATAAGTGAG
* *
30914 GAATG-TAACTAAATTCCACTTGAACATCAGCAGTA
1 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
30949 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
1 GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
*
30985 GAATGTTGATTAAATTCC
1 GAATGTTAATTAAATTCC
31003 CAACCGTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
35 5 0.10
36 45 0.90
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (36 bp):
GAATGTTAATTAAATTCCACTTGAACAGCAGCAGTA
Found at i:35413 original size:23 final size:22
Alignment explanation
Indices: 35365--35413 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
35355 CCAGAATGTC
35365 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
35386 CAGGAGGGAACCGATCCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
35409 AAGGA
1 AAGGA
35414 AAATTGTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.33, G:0.29, T:0.06
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:36173 original size:30 final size:30
Alignment explanation
Indices: 36129--36222 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
36119 TTGAGATATA
36129 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
*
36160 TGGACAGTTACCGATGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
36190 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
36219 TGGA
1 TGGA
36223 TAGGTCCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.29
30 34 0.59
31 7 0.12
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:37429 original size:4 final size:4
Alignment explanation
Indices: 37422--37456 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
37412 AAAGAAACCC
*
37422 CTCA CTCA CTCA CTCA CTCA CTCA CTCG CTCA CTC
1 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTC
37457 TCTCTACTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.20, C:0.51, G:0.03, T:0.26
Consensus pattern (4 bp):
CTCA
Found at i:37946 original size:41 final size:41
Alignment explanation
Indices: 37852--38212 Score: 541
Period size: 41 Copynumber: 8.9 Consensus size: 41
37842 TTTAAAAAAC
*
37852 AAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTGTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
37890 AAACGCCACTAATGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
37931 AAACACCACTAATGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
37972 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A
* *
38014 CAAACGCCACAAAATTACGAGTCTATAGCGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
38056 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
*
38097 AAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
38138 AAACGCCACTAAAGT-CGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * * * *
38178 AAACGCTGCTAAAGTACTACTCTATCGTGGCGTTT
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT
38213 ACTCTTAAAA
Statistics
Matches: 296, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
38 20 0.07
40 53 0.18
41 185 0.62
42 2 0.01
43 36 0.12
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:38066 original size:125 final size:121
Alignment explanation
Indices: 37852--38212 Score: 521
Period size: 125 Copynumber: 3.0 Consensus size: 121
37842 TTTAAAAAAC
* *
37852 AAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTGTATAAAACGCCACTAATGTACGAGTCTAT
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAAAAAACGCCACAAAT-TACGAGTCTAT
* *
37915 AGCGGCGTTTGTATAAAAACACCACTAATGTACGAGTCTATAGCGGCGTTTGTATAA
65 AGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
37972 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAAACACAAACGCCACAAAATTACGAGTC
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGT-AA-A-AAACGCCAC-AAATTACGAGTC
38037 TATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
62 TATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
38097 AAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGT-CGAGTCTA
1 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTA-AAAAACGCCAC-AAATTACGAGTCTA
** * * * *
38161 TAGCGGCGTTTGTATAAAAACGCTGCTAAAGTACTACTCTATCGTGGCGTTT
64 TAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT
38213 ACTCTTAAAA
Statistics
Matches: 220, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
120 22 0.10
122 67 0.30
123 14 0.06
124 3 0.01
125 111 0.50
126 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (121 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAAAAAACGCCACAAATTACGAGTCTATA
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:38147 original size:166 final size:162
Alignment explanation
Indices: 37850--38174 Score: 560
Period size: 166 Copynumber: 2.0 Consensus size: 162
37840 GTTTTAAAAA
* *
37850 ACAAACGCCACTAAAGTACAAGTCTAGCGGCGTTTGTATAAAACGCCACTAATGTACGAGTCTAT
1 ACAAACGCCACAAAAGTACAAGTCTAGCGGCGTTTGTATAAAACGCCACTAAAGTACGAGTCTAT
*
37915 AGCGGCGTTTGTATAAAAACACCACTAATGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
66 AGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
37980 CTAAAGTACAAGTCTATAGCGGCGTTTGTAAAC
131 CTAAAGT-CAAGTCTATAGCGGCGTTTGTAAAC
* *
38013 ACAAACGCCACAAAATTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTC
1 ACAAACGCCACAAAAGTACAAGTC--TAGCGGCGTTTGTAT-AAAACGCCACTAAAGTACGAGTC
38078 TATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
63 TATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACG
*
38143 CCACTAAAGTCGAGTCTATAGCGGCGTTTGTA
128 CCACTAAAGTCAAGTCTATAGCGGCGTTTGTA
38175 TAAAAACGCT
Statistics
Matches: 153, Mismatches: 6, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
163 21 0.14
165 36 0.24
166 96 0.63
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (162 bp):
ACAAACGCCACAAAAGTACAAGTCTAGCGGCGTTTGTATAAAACGCCACTAAAGTACGAGTCTAT
AGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTCAAGTCTATAGCGGCGTTTGTAAAC
Found at i:39240 original size:2 final size:2
Alignment explanation
Indices: 39233--39267 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39223 ATTAATCCGA
39233 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
39268 ATACAGTAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39341 original size:2 final size:2
Alignment explanation
Indices: 39309--39421 Score: 57
Period size: 2 Copynumber: 59.5 Consensus size: 2
39299 ACTTATTTAG
*
39309 TA TA T- TA T- TA TA TT TA TA TA -A T- TA TA T- TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
39347 AA CA TA T- TA TA TGA CTA TA TA TT TA TA T- TA TA T- TG TA TA -A
1 TA TA TA TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
39387 TA TA TT TA TA T- TG TA TA GTA 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
39422 TATGTGGAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
1 10 0.12
2 69 0.80
3 6 0.07
4 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39395 original size:18 final size:18
Alignment explanation
Indices: 39370--39415 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
39360 ACTATATATT
39370 TATA-TTATATTGTATAA
1 TATATTTATATTGTATAA
*
39387 TATATTTATATTGTATAG
1 TATATTTATATTGTATAA
*
39405 TATATATATAT
1 TATATTTATAT
39416 ATATATTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (18 bp):
TATATTTATATTGTATAA
Found at i:39413 original size:39 final size:38
Alignment explanation
Indices: 39314--39420 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 38
39304 TTTAGTATAT
39314 TATTATATT-TATATA-ATTATATTATATAGTATAAACA
1 TATTATATTGTATATATA-TATATTATATAGTATAAACA
* * *
39351 TATTATA-TGACTATATATTTATATTATATTGTAT-AATA
1 TATTATATTG--TATATATATATATTATATAGTATAAACA
39389 TATTTATATTGTATAGTATATATATATATATA
1 TA-TTATATTGTATA-TATATATAT-TATATA
39421 TTATGTGGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
36 1 0.02
37 7 0.12
38 9 0.16
39 33 0.58
40 7 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (38 bp):
TATTATATTGTATATATATATATTATATAGTATAAACA
Found at i:40553 original size:25 final size:25
Alignment explanation
Indices: 40525--40625 Score: 91
Period size: 25 Copynumber: 4.0 Consensus size: 25
40515 GTATTCACGC
*
40525 ATATTATATATGATATTTATATTAT
1 ATATTATATATGATATATATATTAT
*
40550 ATATTATATA-GTATATGTATATGTATT
1 ATATTATATATG-ATATATATAT-TA-T
*
40577 ATATCATTATAT-ATATATATATTAT
1 ATATTA-TATATGATATATATATTAT
* * *
40602 TTATTATATGTTAT-TATATATTAT
1 ATATTATATATGATATATATATTAT
40626 TCTATTGTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
24 15 0.23
25 26 0.41
26 4 0.06
27 15 0.23
28 4 0.06
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (25 bp):
ATATTATATATGATATATATATTAT
Found at i:40620 original size:30 final size:28
Alignment explanation
Indices: 40525--40626 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 28
40515 GTATTCACGC
*
40525 ATATTATATAT-GATAT-TTA-TATTAT
1 ATATTATATATATATATATTATTATTAT
*
40550 ATATTATATAGTATATGTA-TATGTATTAT
1 ATATTATATA-TATATATATTAT-TATTAT
40579 ATCATTATATATATATATATTATTTATTAT
1 AT-ATTATATATATATATATTA-TTATTAT
*
40609 ATGTTAT-TATATAT-TATT
1 ATATTATATATATATATATT
40627 CTATTGTACA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
25 10 0.15
26 1 0.02
27 9 0.14
28 7 0.11
29 19 0.29
30 18 0.28
31 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (28 bp):
ATATTATATATATATATATTATTATTAT
Found at i:40624 original size:47 final size:45
Alignment explanation
Indices: 40538--40642 Score: 117
Period size: 47 Copynumber: 2.3 Consensus size: 45
40528 TTATATATGA
*
40538 TATT-TATAT-TATATATTATATAGTATATGTATATGTATTATATC
1 TATTATATATATATATATTATATAGTATATGTATATATATTAT-TC
* *
40582 -ATTATATATATATATATTATTTATTATATGTTATTATATATTATTC
1 TATTATATATATATATATTATATAGTATATG-TA-TATATATTATTC
* *
40628 TATTGTACATATATA
1 TATTATATATATATA
40643 CATTTATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
43 3 0.06
44 5 0.10
45 18 0.35
46 4 0.08
47 21 0.41
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (45 bp):
TATTATATATATATATATTATATAGTATATGTATATATATTATTC
Found at i:40641 original size:2 final size:2
Alignment explanation
Indices: 40525--40622 Score: 61
Period size: 2 Copynumber: 52.0 Consensus size: 2
40515 GTATTCACGC
*
40525 AT AT -T AT AT AT GAT AT TT AT AT -T AT AT AT -T AT AT AGT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
40566 GT AT AT GT AT -T AT AT CAT -T AT AT AT AT AT AT AT -T AT TT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40606 -T AT AT GT -T AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
40623 TATTCTATTG
Statistics
Matches: 75, Mismatches: 9, Indels: 24
0.69 0.08 0.22
Matches are distributed among these distances:
1 9 0.12
2 60 0.80
3 6 0.08
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (2 bp):
AT
Found at i:41841 original size:17 final size:17
Alignment explanation
Indices: 41821--41872 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
41811 TGATCTTGCA
41821 ATTTACAATTTTCTTTT
1 ATTTACAATTTTCTTTT
* *
41838 ATTT-CAATTGATCTCTT
1 ATTTACAATT-TTCTTTT
41855 ATTTACATCATTTTCTTT
1 ATTTACA--ATTTTCTTT
41873 AGTACTTCGT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 5 0.19
17 13 0.48
18 2 0.07
19 4 0.15
20 3 0.11
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTACAATTTTCTTTT
Found at i:42615 original size:5 final size:5
Alignment explanation
Indices: 42605--42630 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
42595 TATAAACTAG
42605 TAATA TAATA TAATA TAATA TAATA T
1 TAATA TAATA TAATA TAATA TAATA T
42631 TTCTATTTGA
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:43012 original size:20 final size:20
Alignment explanation
Indices: 42989--43055 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
42979 TTCGCAACGT
42989 GATTTTAACTATCGCATTGC
1 GATTTTAACTATCGCATTGC
* * *
43009 GATTTTCCAAAT-TCGCGTTGA
1 GATTTT--AACTATCGCATTGC
* **
43030 GATTTTGACTATCGCAGCGC
1 GATTTTAACTATCGCATTGC
43050 GATTTT
1 GATTTT
43056 CCAAATTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 17 0.49
21 13 0.37
22 3 0.09
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (20 bp):
GATTTTAACTATCGCATTGC
Found at i:43024 original size:41 final size:41
Alignment explanation
Indices: 42978--43062 Score: 107
Period size: 41 Copynumber: 2.1 Consensus size: 41
42968 CAGTTTCAAG
* **
42978 ATTCGCAACGTGATTTTAACTATCGCATTGCGATTTTCCAA
1 ATTCGCAACGAGATTTTAACTATCGCAGCGCGATTTTCCAA
*** *
43019 ATTCGCGTTGAGATTTTGACTATCGCAGCGCGATTTTCCAA
1 ATTCGCAACGAGATTTTAACTATCGCAGCGCGATTTTCCAA
43060 ATT
1 ATT
43063 TAAGTTAGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (41 bp):
ATTCGCAACGAGATTTTAACTATCGCAGCGCGATTTTCCAA
Found at i:43092 original size:19 final size:20
Alignment explanation
Indices: 43068--43108 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
43058 AAATTTAAGT
43068 TAGTCCAAATT-CGTTGCGA
1 TAGTCCAAATTACGTTGCGA
*
43087 TAGTCCAAGTTCACGTTGCGA
1 TAGTCCAAATT-ACGTTGCGA
43108 T
1 T
43109 TTCTTAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (20 bp):
TAGTCCAAATTACGTTGCGA
Found at i:43179 original size:6 final size:6
Alignment explanation
Indices: 43168--43194 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43158 GACACGTATT
43168 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
43195 CGGGACGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:43515 original size:19 final size:20
Alignment explanation
Indices: 43490--43580 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
43480 CTTATTTTGG
43490 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
43510 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
43530 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
*
43554 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
43573 ATTTTTCA
1 ATTTTTCA
43581 AAATCGCGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 30 0.50
20 7 0.12
21 4 0.07
23 6 0.10
24 3 0.05
25 10 0.17
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:43552 original size:44 final size:41
Alignment explanation
Indices: 43501--43582 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
43491 TTTTTCACTA
* *
43501 TCGCAACACTTTTTCACTATCGCAACAACACGTTTTTCAAACTC
1 TCGCAACACATTTTAACTATCGCAAC-ACA--TTTTTCAAACTC
43545 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
43583 ATCGCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 3 0.08
44 24 0.67
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAACTC
Found at i:45407 original size:8 final size:8
Alignment explanation
Indices: 45360--45438 Score: 58
Period size: 8 Copynumber: 9.9 Consensus size: 8
45350 TATTCTTTTG
45360 AATTTGTAT
1 AATTT-TAT
45369 AACTTTTAT
1 AA-TTTTAT
* *
45378 ACTTCTAT
1 AATTTTAT
*
45386 AATTTTAC
1 AATTTTAT
45394 AATTTTAT
1 AATTTTAT
*
45402 -AGTTT-T
1 AATTTTAT
45408 AATTATTAT
1 AATT-TTAT
45417 ATATTTT-T
1 A-ATTTTAT
45425 AATTTT-T
1 AATTTTAT
45432 AATTTTA
1 AATTTTA
45439 AAATGATGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
6 1 0.02
7 18 0.32
8 21 0.38
9 10 0.18
10 6 0.11
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (8 bp):
AATTTTAT
Found at i:45710 original size:51 final size:51
Alignment explanation
Indices: 45605--45715 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
45595 TCTTTGTAGA
** * **
45605 AAGGCGCGGTTCATGCACTGCGCCTTACGCTGATGTGGCACCACGTGGGTT
1 AAGGCGCGGCCCATGCACCGCGCCTTACGCTGACATGGCACCACGTGGGTT
* *
45656 AAGGCGCGGCCCATGCACCGCGCCTTATGCTGACATGGCGA-CATGCTGGG-T
1 AAGGCGCGGCCCATGCACCGCGCCTTACGCTGACATGGC-ACCACG-TGGGTT
45707 AAGGCGCGG
1 AAGGCGCGG
45716 TGCATGGGCC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
51 46 0.90
52 5 0.10
ACGTcount: A:0.17, C:0.29, G:0.35, T:0.19
Consensus pattern (51 bp):
AAGGCGCGGCCCATGCACCGCGCCTTACGCTGACATGGCACCACGTGGGTT
Found at i:49771 original size:13 final size:12
Alignment explanation
Indices: 49754--49806 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 12
49744 GTTAATAAAC
49754 AAAATTAACAAA
1 AAAATTAACAAA
49766 ATAAATTAAC-AA
1 A-AAATTAACAAA
*
49778 AAAATT--CAAC
1 AAAATTAACAAA
49788 AAAATTAACAAA
1 AAAATTAACAAA
49800 ATAAATT
1 A-AAATT
49807 TAGTATTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 5 0.15
12 8 0.24
13 13 0.38
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATTAACAAA
Found at i:52064 original size:29 final size:31
Alignment explanation
Indices: 52032--52105 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
52022 AAAAAATAAT
*
52032 ATAATTAAATAAAATATTAA-AGAA-ATTAA
1 ATAATTAAATAAAATATTAACAAAATATTAA
* *
52061 ATAATTACATAAAATACTAACAAAATATTAA
1 ATAATTAAATAAAATATTAACAAAATATTAA
52092 AT-A-T-AATAAAATAT
1 ATAATTAAATAAAATAT
52106 ACCTTAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
28 8 0.21
29 19 0.50
30 4 0.11
31 7 0.18
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (31 bp):
ATAATTAAATAAAATATTAACAAAATATTAA
Found at i:52104 original size:17 final size:18
Alignment explanation
Indices: 52072--52105 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52062 TAATTACATA
52072 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
52090 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
52106 ACCTTAAGTT
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:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:56258 original size:26 final size:24
Alignment explanation
Indices: 56194--56258 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
56184 ATCATTTTAA
*
56194 TTAAAATATTTATTATTAAAATAT
1 TTAAAATATATATTATTAAAATAT
*
56218 TTAAAATATAT-TTATTAATAT-T
1 TTAAAATATATATTATTAAAATAT
56240 TCTAACAATATAATATTAT
1 T-TAA-AATAT-ATATTAT
56259 ATTTTTTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
24 15 0.43
25 2 0.06
26 4 0.11
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAATATATATTATTAAAATAT
Found at i:56280 original size:14 final size:15
Alignment explanation
Indices: 56250--56288 Score: 71
Period size: 14 Copynumber: 2.7 Consensus size: 15
56240 TCTAACAATA
56250 TAATATTATATTTTT
1 TAATATTATATTTTT
56265 TAATATTATA-TTTT
1 TAATATTATATTTTT
56279 TAATATTATA
1 TAATATTATA
56289 ATAATATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAATATTATATTTTT
Found at i:56328 original size:23 final size:23
Alignment explanation
Indices: 56281--56331 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
56271 TATATTTTTA
*
56281 ATATTATAATAATATACTAAGTT
1 ATATTATAATAATATAATAAGTT
*
56304 ATATTGTAATAATATAATATA-TT
1 ATATTATAATAATATAATA-AGTT
56327 ATATT
1 ATATT
56332 TTTATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (23 bp):
ATATTATAATAATATAATAAGTT
Found at i:56448 original size:24 final size:24
Alignment explanation
Indices: 56396--56499 Score: 61
Period size: 24 Copynumber: 4.1 Consensus size: 24
56386 TTCATAGAAA
56396 AAATATTATTAAATTATTAATAAT
1 AAATATTATTAAATTATTAATAAT
* *
56420 GAATATTATT-TATATATTTAAT-AT
1 AAATATTATTAAAT-TA-TTAATAAT
* **
56444 AAATATAATAATTAAATAATTTTTAAT
1 AAATAT--T-ATTAAATTATTAATAAT
56471 AAATA-TATTTAAAATATATTAATTAAT
1 AAATATTA-TT-AAAT-TATTAA-TAAT
56498 AA
1 AA
56500 TTTTTAAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
23 3 0.05
24 21 0.36
25 9 0.15
26 7 0.12
27 17 0.29
28 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
AAATATTATTAAATTATTAATAAT
Found at i:56492 original size:23 final size:24
Alignment explanation
Indices: 56466--56512 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56456 TAAATAATTT
56466 TTAATAAAT-ATATTTAAAATATA
1 TTAATAAATAATATTTAAAATATA
* *
56489 TTAATTAATAATTTTTAAAATATA
1 TTAATAAATAATATTTAAAATATA
56513 ATATAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATAAATAATATTTAAAATATA
Found at i:57502 original size:18 final size:18
Alignment explanation
Indices: 57475--57520 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
57465 TTAATATTTA
*
57475 TATATCTTAATTTAAATT
1 TATATCTTAAATTAAATT
* *
57493 TATATGTTAAATTAATTT
1 TATATCTTAAATTAAATT
*
57511 TACATCTTAA
1 TATATCTTAA
57521 CTTTATATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (18 bp):
TATATCTTAAATTAAATT
Found at i:57558 original size:26 final size:27
Alignment explanation
Indices: 57514--57564 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
57504 TTAATTTTAC
*
57514 ATCTTAACTTTATATAATATTTTTTTT
1 ATCTTAACTTTATATAATATATTTTTT
57541 ATCTTAAC-TTAT-TAAATATATTTT
1 ATCTTAACTTTATAT-AATATATTTT
57565 ATTCTTCCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 13 0.59
27 8 0.36
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (27 bp):
ATCTTAACTTTATATAATATATTTTTT
Found at i:66300 original size:18 final size:18
Alignment explanation
Indices: 66277--66316 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
66267 AAGTCAAGTA
*
66277 ACCCGTTAGCCCGAACCG
1 ACCCGTTAACCCGAACCG
* *
66295 ACCCGTTAACCTGATCCG
1 ACCCGTTAACCCGAACCG
66313 ACCC
1 ACCC
66317 ATTGATCGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.45, G:0.17, T:0.15
Consensus pattern (18 bp):
ACCCGTTAACCCGAACCG
Found at i:68737 original size:24 final size:23
Alignment explanation
Indices: 68709--68815 Score: 90
Period size: 24 Copynumber: 4.5 Consensus size: 23
68699 ATATTTTATC
* *
68709 TGATTTCCGATTTGAATTCTGTTA
1 TGATTTCTGATCT-AATTCTGTTA
* * *
68733 TGATTTCTAATCTTAATTATGTTC
1 TGATTTCTGATC-TAATTCTGTTA
68757 TGATTTCTGATCTAGATTCTGTTA
1 TGATTTCTGATCTA-ATTCTGTTA
* *
68781 TGATATCTGATCTGAATTTTGCTT-
1 TGATTTCTGATCT-AATTCTG-TTA
*
68805 TGATTTTTGAT
1 TGATTTCTGAT
68816 ATCTCCATTT
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
23 2 0.03
24 61 0.91
25 4 0.06
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.52
Consensus pattern (23 bp):
TGATTTCTGATCTAATTCTGTTA
Found at i:68809 original size:48 final size:48
Alignment explanation
Indices: 68707--68815 Score: 123
Period size: 48 Copynumber: 2.3 Consensus size: 48
68697 GAATATTTTA
* * * *
68707 TCTGATTTCCGAT-TTGAATTCTGTTATGATTTCTAATCTTAATTATGT
1 TCTGATTTCTGATCTAG-ATTCTGTTATGATATCTAATCTGAATTATGT
* *
68755 TCTGATTTCTGATCTAGATTCTGTTATGATATCTGATCTGAATTTTGCT
1 TCTGATTTCTGATCTAGATTCTGTTATGATATCTAATCTGAATTATG-T
*
68804 T-TGATTTTTGAT
1 TCTGATTTCTGAT
68816 ATCTCCATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 48 0.92
49 4 0.08
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.52
Consensus pattern (48 bp):
TCTGATTTCTGATCTAGATTCTGTTATGATATCTAATCTGAATTATGT
Found at i:70979 original size:17 final size:17
Alignment explanation
Indices: 70957--70995 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
70947 ACTTTGATCA
* *
70957 AAAAGTTAAAATTTTTG
1 AAAAGTCAAAATTTTCG
70974 AAAAGTCAAAATTTTCG
1 AAAAGTCAAAATTTTCG
70991 AAAAG
1 AAAAG
70996 CCATATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.13, T:0.31
Consensus pattern (17 bp):
AAAAGTCAAAATTTTCG
Found at i:73253 original size:24 final size:24
Alignment explanation
Indices: 73211--73289 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
73201 TTTATCTAAT
* * *
73211 TTTC-GATTTGAATTTTGTTCTGA
1 TTTCTGATCTGAATTCTGTTTTGA
73234 TTTCTGATCT-AGATTCTGTTTTGA
1 TTTCTGATCTGA-ATTCTGTTTTGA
*
73258 TATCTGATCTGAATTCTGTTTTGA
1 TTTCTGATCTGAATTCTGTTTTGA
73282 TTTCTGAT
1 TTTCTGAT
73290 ATCTCTGTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.10
24 42 0.88
25 1 0.02
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.54
Consensus pattern (24 bp):
TTTCTGATCTGAATTCTGTTTTGA
Found at i:77648 original size:149 final size:148
Alignment explanation
Indices: 77379--77680 Score: 487
Period size: 149 Copynumber: 2.0 Consensus size: 148
77369 GAGTCGAGGG
* * * * * * *
77379 TCTACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
77444 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
77509 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* * *
77527 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
77592 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
77657 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
77676 TCTAC
1 TCTAC
77681 ACGGCACTTC
Statistics
Matches: 141, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 46 0.33
149 95 0.67
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:82420 original size:149 final size:148
Alignment explanation
Indices: 82151--82464 Score: 495
Period size: 149 Copynumber: 2.1 Consensus size: 148
82141 GAGTCGAGGG
* * * * * *
82151 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
82216 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
82281 ATGGCACTACGGTACAAT
131 ATGGCACTACGGTACAAT
* *
82299 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
82364 ACTTGATCCCTAGTATATGTATGTGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
82429 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTACAAT
82448 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
82465 TGCAATTATA
Statistics
Matches: 152, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
148 49 0.32
149 103 0.68
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTACAAT
Found at i:82465 original size:23 final size:23
Alignment explanation
Indices: 82432--82476 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
82422 ATTATTATAT
*
82432 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
82455 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
82477 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:82690 original size:21 final size:21
Alignment explanation
Indices: 82666--82726 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
82656 ATAAATAATT
*
82666 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
82687 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
82708 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
82727 GATATATGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:82732 original size:33 final size:33
Alignment explanation
Indices: 82668--82733 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
82658 AAATAATTTG
*
82668 ATGATAATGATAGAGATAATGATAATAATATAT
1 ATGATAATGATAGAGAAAATGATAATAATATAT
* * *
82701 ATGATAATGCTA-AGAAAATAGATGATGATATAT
1 ATGATAATGATAGAGAAAAT-GATAATAATATAT
82734 GTACATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.32
Consensus pattern (33 bp):
ATGATAATGATAGAGAAAATGATAATAATATAT
Found at i:84373 original size:16 final size:17
Alignment explanation
Indices: 84352--84383 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
84342 TACTATTAAT
84352 GTGAATAGT-AAATTTC
1 GTGAATAGTGAAATTTC
84368 GTGAATAGTGAAATTT
1 GTGAATAGTGAAATTT
84384 TGTCAGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (17 bp):
GTGAATAGTGAAATTTC
Found at i:89625 original size:18 final size:18
Alignment explanation
Indices: 89602--89637 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
89592 AGGGATCGAA
89602 ATATATTAAATTAACAAC
1 ATATATTAAATTAACAAC
89620 ATATATTAAATTAACAAC
1 ATATATTAAATTAACAAC
89638 GTAAGACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
ATATATTAAATTAACAAC
Found at i:91697 original size:6 final size:6
Alignment explanation
Indices: 91674--91715 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
91664 TACACAAATG
* *
91674 GTTGCA TTTGCT GTTTGCA GTTGCA GTTGCA GTTGCA -TTGCA
1 GTTGCA GTTGCA G-TTGCA GTTGCA GTTGCA GTTGCA GTTGCA
91716 TGCGTTCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
5 5 0.16
6 21 0.68
7 5 0.16
ACGTcount: A:0.14, C:0.17, G:0.29, T:0.40
Consensus pattern (6 bp):
GTTGCA
Found at i:91698 original size:19 final size:18
Alignment explanation
Indices: 91674--91716 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
91664 TACACAAATG
*
91674 GTTGCATTTGCTGTTTGCA
1 GTTGCATTTGCAG-TTGCA
*
91693 GTTGCAGTTGCAGTTGCA
1 GTTGCATTTGCAGTTGCA
91711 -TTGCAT
1 GTTGCAT
91717 GCGTTCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.14, C:0.16, G:0.28, T:0.42
Consensus pattern (18 bp):
GTTGCATTTGCAGTTGCA
Found at i:92351 original size:11 final size:11
Alignment explanation
Indices: 92335--92365 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
92325 TAAGACCGTA
92335 AGATGAGTGTT
1 AGATGAGTGTT
*
92346 AGATGAGTATT
1 AGATGAGTGTT
92357 AGATGAGTG
1 AGATGAGTG
92366 GAAATAGACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (11 bp):
AGATGAGTGTT
Found at i:92982 original size:6 final size:6
Alignment explanation
Indices: 92968--93177 Score: 240
Period size: 6 Copynumber: 33.7 Consensus size: 6
92958 AGAAAATGAG
* * * * *
92968 ATACAC ATACGC ATACAC ATACAC ATACAC ATACAC ATACGC ATACACGC
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC AT--ACGC
** *
93018 ATACGC ATACAT ATACACAC ATACGC ATACACGC ATACGC ATACGC ATACGC
1 ATACGC ATACGC AT--ACGC ATACGC AT--ACGC ATACGC ATACGC ATACGC
* * *
93070 ATACACGC ACACGC ATACGC ATACGC ATATGC ATACGC ATACGC ATACGT
1 AT--ACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
*
93120 ATACGC ATACGC ATACGC ATACAC ATACGC ATACGC ATACGC ATACGC
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
93168 ATACGC ATAC
1 ATACGC ATAC
93178 CAACCCGTAC
Statistics
Matches: 181, Mismatches: 15, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
6 159 0.88
8 22 0.12
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (6 bp):
ATACGC
Found at i:93979 original size:18 final size:18
Alignment explanation
Indices: 93956--93996 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
93946 GATTTCTATT
93956 AAAATGTGCTTCAGTATA
1 AAAATGTGCTTCAGTATA
*
93974 AAAATGTGCTTCATTATA
1 AAAATGTGCTTCAGTATA
93992 AAAAT
1 AAAAT
93997 TCAAGTAAAA
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:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (18 bp):
AAAATGTGCTTCAGTATA
Found at i:94846 original size:31 final size:31
Alignment explanation
Indices: 94808--94903 Score: 102
Period size: 31 Copynumber: 3.1 Consensus size: 31
94798 GAACCTCGAC
* * * *
94808 AACTGTCCATAGGTCCCGAAGAACCTATGTA
1 AACTGTCCATATGTCCCAAAGAACATAAGTA
* * ** *
94839 AACTGTCCACATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAAGTA
*
94870 AATTGTCCATATGTCCCAAAGAACATAAGTA
1 AACTGTCCATATGTCCCAAAGAACATAAGTA
94901 AAC
1 AAC
94904 CCTCGACTCT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAAGTA
Found at i:95816 original size:20 final size:20
Alignment explanation
Indices: 95793--95851 Score: 109
Period size: 20 Copynumber: 3.0 Consensus size: 20
95783 ACATCCCTAA
95793 CTGGGGTATAGATACCCTGT
1 CTGGGGTATAGATACCCTGT
*
95813 CTGGGGTATAGATACACTGT
1 CTGGGGTATAGATACCCTGT
95833 CTGGGGTATAGATACCCTG
1 CTGGGGTATAGATACCCTG
95852 ATAATATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.29
Consensus pattern (20 bp):
CTGGGGTATAGATACCCTGT
Found at i:97041 original size:12 final size:12
Alignment explanation
Indices: 97012--97042 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
97002 CGGTTTTTTT
*
97012 ACCGGATAAAAA
1 ACCGGTTAAAAA
97024 ACCGGTTAAAAA
1 ACCGGTTAAAAA
97036 ACCGGTT
1 ACCGGTT
97043 TTTATCCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.16
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:97172 original size:17 final size:18
Alignment explanation
Indices: 97152--97185 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
97142 GTTTTTTTAT
97152 AACC-GGTTTTTTAAAAA
1 AACCAGGTTTTTTAAAAA
*
97169 AACCAGTTTTTTTAAAA
1 AACCAGGTTTTTTAAAA
97186 CTGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCAGGTTTTTTAAAAA
Found at i:97410 original size:27 final size:27
Alignment explanation
Indices: 97369--97422 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
97359 AGAGACTTTA
97369 ATTTAACACGGCTATTAAAAACAACCT
1 ATTTAACACGGCTATTAAAAACAACCT
* *
97396 ATTTAATACGTCTATTAAAAACAACCT
1 ATTTAACACGGCTATTAAAAACAACCT
97423 TCAAGTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.20, G:0.06, T:0.30
Consensus pattern (27 bp):
ATTTAACACGGCTATTAAAAACAACCT
Found at i:97892 original size:2 final size:2
Alignment explanation
Indices: 97887--97917 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
97877 AATACAAGGT
97887 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 T
97918 TCATTCTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:111825 original size:64 final size:63
Alignment explanation
Indices: 111712--111856 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 63
111702 GAGCACTAAG
* * * *
111712 GATGCATCGATGCATAAAATGCATTCGATGTTTAAAAAATAGCCTGGTGCATCGATGCATGGA-
1 GATGCATCGGTGCATGAAATGCATTCGATGTTCAAAAAATA-CATGGTGCATCGATGCATGGAC
* *
111775 GAGTGCATCGGTGCATGAAATGTATTCGATGTTCAATTAAAT-CATAGGTGCATCGATGCATGGA
1 GA-TGCATCGGTGCATGAAATGCATTCGATGTTCAA-AAAATACAT-GGTGCATCGATGCATGGA
111839 C
63 C
111840 TGATGCATCGGTGCATG
1 -GATGCATCGGTGCATG
111857 CCTTTGAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
63 4 0.06
64 47 0.66
65 18 0.25
66 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (63 bp):
GATGCATCGGTGCATGAAATGCATTCGATGTTCAAAAAATACATGGTGCATCGATGCATGGAC
Found at i:119105 original size:2 final size:2
Alignment explanation
Indices: 119098--119167 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
119088 TATGAGTAAG
119098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119140 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
119168 CAGAATTGGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:120177 original size:15 final size:15
Alignment explanation
Indices: 120159--120193 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
120149 CGAGGGTATT
120159 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
120174 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
120189 GTAGT
1 GTAGT
120194 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:120804 original size:2 final size:2
Alignment explanation
Indices: 120797--120833 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
120787 ATTTTAAACG
120797 TA 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 TA T
120834 GTAAATGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124923 original size:21 final size:21
Alignment explanation
Indices: 124892--124976 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
124882 TAATCAAAAG
* *
124892 GTTATGACCTTTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
* *
124913 TTTAAGACCTTTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
*
124934 GTTAAGATCATTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
124955 GTTAAGACCATTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
124976 G
1 G
124977 ATTTGTTGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.34, C:0.08, G:0.24, T:0.34
Consensus pattern (21 bp):
GTTAAGACCATTTGATGAAGA
Found at i:126620 original size:29 final size:30
Alignment explanation
Indices: 126580--126678 Score: 87
Period size: 30 Copynumber: 3.2 Consensus size: 30
126570 TAAGCCACAA
126580 TTAAATATAATTAAAATAAAAGAGTAAAAT
1 TTAAATATAATTAAAATAAAAGAGTAAAAT
* *
126610 TTAAATA-AATTTAAAGA-ACACAAAATGATTAAA-
1 TTAAATATAA-TTAAA-ATA-A-AAGA-G-TAAAAT
* *
126643 TTAAATATAATTAAAATATAAGTGTAAAAT
1 TTAAATATAATTAAAATAAAAGAGTAAAAT
126673 TTAAAT
1 TTAAAT
126679 TTAAGAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
29 6 0.11
30 20 0.37
31 4 0.07
32 4 0.07
33 14 0.26
34 6 0.11
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (30 bp):
TTAAATATAATTAAAATAAAAGAGTAAAAT
Found at i:126923 original size:101 final size:103
Alignment explanation
Indices: 126791--126990 Score: 325
Period size: 102 Copynumber: 2.0 Consensus size: 103
126781 AATTAATATC
* *
126791 CCTTTAATATTATATTTTTAAAAATTATATAAAGAAATAAAA-AATTAGAGTGGGACACGA-CCA
1 CCTTTAAAATTATATTTTTAAAAATTATATAAAGAAATAAAATAATTAGAGTAGGACACGACCCA
*
126854 CCTACAAAACTCTTTAAACTTTTAAGAGAAAAGAAAACT
66 CC-ACAAAACTCTTTAAAATTTTAAGAGAAAAGAAAACT
126893 CCTTTAAAATTATA-TTTTAAAAATTATATAAAGAAATAAAATAATTAGAGTAGGACACGACCCA
1 CCTTTAAAATTATATTTTTAAAAATTATATAAAGAAATAAAATAATTAGAGTAGGACACGACCCA
* *
126957 CCACAAAACTCTTTAAAATTTTAAGGGATAAGAA
66 CCACAAAACTCTTTAAAATTTTAAGAGAAAAGAA
126991 GGCTCCAGTA
Statistics
Matches: 91, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
101 27 0.30
102 59 0.65
103 5 0.05
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.29
Consensus pattern (103 bp):
CCTTTAAAATTATATTTTTAAAAATTATATAAAGAAATAAAATAATTAGAGTAGGACACGACCCA
CCACAAAACTCTTTAAAATTTTAAGAGAAAAGAAAACT
Found at i:128189 original size:2 final size:2
Alignment explanation
Indices: 128182--128224 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
128172 TTCAAACAAT
128182 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
128224 T
1 T
128225 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:129022 original size:3 final size:3
Alignment explanation
Indices: 129014--129040 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
129004 GGACAGAGTC
129014 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
129041 TCAGTGTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:129628 original size:3 final size:3
Alignment explanation
Indices: 129622--129661 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
129612 GATGGTTTTT
129622 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
129662 GTTTTAACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:132190 original size:4 final size:4
Alignment explanation
Indices: 132181--132232 Score: 54
Period size: 4 Copynumber: 12.8 Consensus size: 4
132171 TAGTCCCTGT
*
132181 TTTA TTTA TTTTA TTT- TATTA TTTA TTTA TTT- TTATT TTTA TTTA TTTA
1 TTTA TTTA -TTTA TTTA T-TTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA
132230 TTT
1 TTT
132233 TACTGTTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
3 3 0.07
4 32 0.76
5 7 0.17
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:132211 original size:16 final size:16
Alignment explanation
Indices: 132182--132228 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
132172 AGTCCCTGTT
132182 TTATTTATTTTATTTTA
1 TTATTTA-TTTATTTTA
132199 TTATTTATTTATTTTTA
1 TTATTTATTTA-TTTTA
132216 TT-TTTATTTATTT
1 TTATTTATTTATTT
132229 ATTTTACTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.10
16 12 0.41
17 14 0.48
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTATTTATTTATTTTA
Found at i:132224 original size:20 final size:22
Alignment explanation
Indices: 132181--132233 Score: 85
Period size: 20 Copynumber: 2.5 Consensus size: 22
132171 TAGTCCCTGT
132181 TTTATTTA-TTTTATTTTATTA
1 TTTATTTATTTTTATTTTATTA
132202 TTTATTTATTTTTA-TTT-TTA
1 TTTATTTATTTTTATTTTATTA
132222 TTTATTTATTTT
1 TTTATTTATTTT
132234 ACTGTTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.48
21 11 0.35
22 5 0.16
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTATTTATTTTTATTTTATTA
Found at i:133030 original size:184 final size:183
Alignment explanation
Indices: 132724--133086 Score: 676
Period size: 184 Copynumber: 2.0 Consensus size: 183
132714 AATATCGAAC
132724 CTATTCCGCTATTATTTCGTTATTTTAATTAAAAAACATGTTTTATTTAAAAAAATCAGTTCTTC
1 CTATTCCGCTATTATTTCGTTATTTTAATTAAAAAACATGTTTTATTTAAAAAAATCAGTTCTTC
132789 GAAAAAATTCACGATCGTGATATCCGCAATGACCGCAATAGCATCCGTTATATACGCAAACCGTG
66 GAAAAAATTCACGATCGTGATATCCGCAATGACCGCAATAGCATCCGTTATATACGCAAACCGTG
132854 ATAAACGC-GACGACCGAAATATGACTAC-AACGCTATTTAAACTCTGAACCT
131 ATAAACGCAGACGACCGAAATATGACTACAAACGCTATTTAAACTCTGAACCT
132905 CTATTCCGCTATTATTTCGTTATTTTAATTAAAAAACATGTTTTTATTTTAAAAAAATCAGTTTC
1 CTATTCCGCTATTATTTCGTTATTTTAATTAAAAAACATG-TTTTA-TTTAAAAAAATCAG-TTC
132970 TTCGAAAAAATTCACGATCGTGATATCCGCAATGACCGCAATAGCATCCGTTATATACGCAAACC
63 TTCGAAAAAATTCACGATCGTGATATCCGCAATGACCGCAATAGCATCCGTTATATACGCAAACC
133035 GTGATAAACGCGAGACGACCGAAATATGACTACAAACGCTATTTAAACTCTG
128 GTGATAAACGC-AGACGACCGAAATATGACTACAAACGCTATTTAAACTCTG
133087 CTCATGCCAC
Statistics
Matches: 176, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
181 40 0.23
182 5 0.03
183 14 0.08
184 79 0.45
186 20 0.11
187 18 0.10
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (183 bp):
CTATTCCGCTATTATTTCGTTATTTTAATTAAAAAACATGTTTTATTTAAAAAAATCAGTTCTTC
GAAAAAATTCACGATCGTGATATCCGCAATGACCGCAATAGCATCCGTTATATACGCAAACCGTG
ATAAACGCAGACGACCGAAATATGACTACAAACGCTATTTAAACTCTGAACCT
Found at i:145195 original size:20 final size:20
Alignment explanation
Indices: 145187--145225 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
145177 TATTAGAGGC
145187 TTGGTATCAATATCAGATGG
1 TTGGTATCAATATCAGATGG
*
145207 TTGGTATCGATATCAGATG
1 TTGGTATCAATATCAGATG
145226 AACTAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.26, T:0.36
Consensus pattern (20 bp):
TTGGTATCAATATCAGATGG
Found at i:150747 original size:34 final size:34
Alignment explanation
Indices: 150708--150775 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
150698 TCAGTGGGTA
150708 ATGTGCATGTGGTTCTTACCGTATCAGTGATGAT
1 ATGTGCATGTGGTTCTTACCGTATCAGTGATGAT
150742 ATGTGCATGTGGTTCTTACCGTATCAGTGATGAT
1 ATGTGCATGTGGTTCTTACCGTATCAGTGATGAT
150776 TTGAACATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (34 bp):
ATGTGCATGTGGTTCTTACCGTATCAGTGATGAT
Done.