Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008976.1 Hibiscus syriacus cultivar Beakdansim tig00112325_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: 52578
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1391 original size:19 final size:19
Alignment explanation
Indices: 1367--1414 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
1357 ATGTAGGGGA
1367 AATTTTGTATACGATTCAT
1 AATTTTGTATACGATTCAT
*
1386 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
1405 AATTTTGTAT
1 AATTTTGTAT
1415 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.10, T:0.52
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:4631 original size:200 final size:199
Alignment explanation
Indices: 4136--4853 Score: 840
Period size: 200 Copynumber: 3.6 Consensus size: 199
4126 GTAAACAGAT
* *
4136 GTGTCGATACATTTTATAAA-AGTATCGACCCCAAAAATATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACA-TTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAAT
* * * * * * *
4200 AGGTAAAATAACAATATAACCGGTATAAATATACTG-GTTAATTACAAAACATGTCAACATAATG
65 AGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAAC-GGTCAACATAATG
* * * * *
4264 TATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATACCCAACCAAGGTGCAT
129 TATCGACACTTTTTGAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTG--T
*
4329 GCATGCATAAA
191 --ACGCATAAA
* * * *
4340 GTGTCGATATATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
* *
4405 AGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAAGCGGCCAACATAATGT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAA-CGGTCAACATAATGT
* * *
4470 ATCGAAACTTTTTAAATTTGTGTCGATACTTGTTGTCCAGAATTAATGCCCAAACGAGGTGTACG
130 ATCGACACTTTTTGAATTTGTGTCGATACTT-TTGTCCAGAATGAATGCCCAAACGAGGTGTACG
4535 CATAAA
194 CATAAA
** *
4541 GTGTCGATACATTTA-AAATTTTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAGTA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
** * *
4605 GGTAAATTTACAATGTAATTGGTATAAATATACC-AGTTTTATGATAGAATA-GGTCAACATAAT
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGA-TTTAAT--TAGAAAACGGTCAACATAAT
* *
4668 GTATCGACACTTTTTTTGAATTTGTGTCGATACTTTTTTTCA-AAGTGAATGCCC-AACGAGGTG
128 GTATCGACAC--TTTTTGAATTTGTGTCGATACTTTTGTCCAGAA-TGAATGCCCAAACGAGGTG
*
4731 CACGCATAAA
190 TACGCATAAA
* * ** *
4741 GTGTCGATACATTTA-AAATTGTATTGATCCCAAAAACATTGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
** * * * *
4805 GGTAAATTTGTAATGTTACCGGTATAAATAAACCTATTTAGTTAGAAAA
66 GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAA
4854 TATGTAAATA
Statistics
Matches: 446, Mismatches: 58, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
198 6 0.01
199 1 0.00
200 209 0.47
201 36 0.08
202 28 0.06
203 9 0.02
204 81 0.18
205 75 0.17
206 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATAAATAGTATCGATCCCAAAAACATCAAAACCAATAATTATAATGTAATA
GGTAAATTTACAATGTAACCGGTATAAATATACCGATTTAATTAGAAAACGGTCAACATAATGTA
TCGACACTTTTTGAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCCAAACGAGGTGTACGCA
TAAA
Found at i:4887 original size:23 final size:23
Alignment explanation
Indices: 4861--4908 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4851 AAATATGTAA
*
4861 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
*
4884 ATATAAGCGCTACCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
4907 AT
1 AT
4909 TGTACTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:4965 original size:87 final size:87
Alignment explanation
Indices: 4861--5022 Score: 227
Period size: 87 Copynumber: 1.9 Consensus size: 87
4851 AAATATGTAA
* * * * *
4861 ATATAAGCGCTACCTATTATATTATATAAGCGCTACCTAATATGTTATTGTACTTAATAATA-TT
1 ATATAAGCGCTACCTATTACATTATATAAACACTACCTAATATATTATTATACTTAATAATATTT
4925 TCTAGTTAAATGCTTATTTTATT
66 TCT-GTTAAATGCTTATTTTATT
* * * *
4948 ATATAAGCGCTATCTATTACATTATATAAACATTACCTATTATATTATTATATTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACACTACCTAATATATTATTATACTTAATAATATTT
5013 TCTGTTAAAT
66 TCTGTTAAAT
5023 AATATAATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
87 60 0.92
88 5 0.08
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.46
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACACTACCTAATATATTATTATACTTAATAATATTT
TCTGTTAAATGCTTATTTTATT
Found at i:5735 original size:15 final size:15
Alignment explanation
Indices: 5715--5747 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5705 ATTAATACGA
5715 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
*
5730 AAAAATTATAAAATT
1 AAAAATTATAAAAAT
5745 AAA
1 AAA
5748 TCTAATACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATTATAAAAAT
Found at i:5954 original size:20 final size:20
Alignment explanation
Indices: 5921--5976 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
5911 TCAAAGAATA
**
5921 TAAGATTATTAGTGGAAATG
1 TAAGATTACCAGTGGAAATG
*
5941 TAATATTACCAGTGGAAATG
1 TAAGATTACCAGTGGAAATG
5961 TAAGATTACCAG-GGAA
1 TAAGATTACCAGTGGAA
5977 TAAGATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (20 bp):
TAAGATTACCAGTGGAAATG
Found at i:6370 original size:21 final size:21
Alignment explanation
Indices: 6340--6566 Score: 134
Period size: 21 Copynumber: 11.0 Consensus size: 21
6330 GATTTACATA
*
6340 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
6361 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
6382 TTCGCGTTGCGA-A-TCTGGAAA
1 TTCGCGTTGCGATAGTC--CAAG
* ** * *
6403 CT-GATTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
6423 TTCGCGTTGCGATTTATTACAAA
1 TTCGCGTTGCGA--TAGTCCAAG
6446 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
6465 TT--CGTTGCGATAGTCAAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
6484 TTCGCATTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
6507 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
6526 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
6549 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
6567 AATCGCAACT
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
19 43 0.27
20 11 0.07
21 80 0.50
22 2 0.01
23 23 0.14
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:6497 original size:61 final size:62
Alignment explanation
Indices: 6408--6538 Score: 201
Period size: 61 Copynumber: 2.1 Consensus size: 62
6398 GGAAACTGAT
* * *
6408 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTT-CG
1 TTGCGATAGTCAAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCCG
* *
6469 TTGCGATAGTCAAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCAAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTC-CG
6532 TTGCGAT
1 TTGCGAT
6539 TTATTCCAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 54 0.86
63 9 0.14
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (62 bp):
TTGCGATAGTCAAAGTTCGCATTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCCG
Found at i:6505 original size:42 final size:42
Alignment explanation
Indices: 6459--6563 Score: 183
Period size: 42 Copynumber: 2.5 Consensus size: 42
6449 GTTGCGATAG
*
6459 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCATTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCAAAGTTCGCATTGCGATTTAT
* *
6501 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCAAAGTTCGCATTGCGATTTAT
6543 TCCAAATTCGTTGCGATAGTC
1 TCCAAATTCGTTGCGATAGTC
6564 CAAAATCGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCAAAGTTCGCATTGCGATTTAT
Found at i:6566 original size:61 final size:59
Alignment explanation
Indices: 6408--6567 Score: 146
Period size: 61 Copynumber: 2.6 Consensus size: 59
6398 GGAAACTGAT
* * * * *
6408 TTGCAATAGTCGAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCCAAGTTCG
1 TTGCGATAGTCAAAGTTCG-ATTGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAAGTTCG
* *
6469 TTGCGATAGTCAAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCAAAGTTCG-ATTGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAAGTT--CG
*
6532 TTGCGATTTATTCCAAA-TTCG-TTGCGA-TAGTCCAAA
1 TTGCGA--TAGT-CAAAGTTCGATTGCGATTAGTCCAAA
6568 ATCGCAACTA
Statistics
Matches: 87, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
61 62 0.71
63 14 0.16
65 7 0.08
66 4 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (59 bp):
TTGCGATAGTCAAAGTTCGATTGCGATTAGTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:6567 original size:19 final size:19
Alignment explanation
Indices: 6442--6567 Score: 119
Period size: 19 Copynumber: 6.2 Consensus size: 19
6432 CGATTTATTA
6442 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
*
6461 CAAGTTCGTTGCGATAGT-
1 CAAATTCGTTGCGATAGTC
*
6479 CAAAGTTCGCATTGCGATTTATTC
1 CAAA-TTCG--TTGCGA--TAGTC
6503 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
* * *
6522 GAAGTTCGCGTTGCGATTTATTC
1 CAAATT--CGTTGCGA--TAGTC
6545 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
6564 CAAA
1 CAAA
6568 ATCGCAACTA
Statistics
Matches: 87, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.03
19 37 0.43
21 28 0.32
23 15 0.17
24 4 0.05
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (19 bp):
CAAATTCGTTGCGATAGTC
Found at i:6666 original size:6 final size:6
Alignment explanation
Indices: 6655--6681 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6645 GACACGTATT
6655 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
6682 CGAGACGGAC
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:7495 original size:42 final size:41
Alignment explanation
Indices: 7436--7756 Score: 277
Period size: 42 Copynumber: 7.8 Consensus size: 41
7426 TGCGATTTTG
* *
7436 GACTACCGCAACGAACTTGGAATAAATCGCAACGCGAACTTT
1 GACTATCGCAACGAACTTGGAATAAATCGCAA-GCGAACTTC
* *
7478 GACTATCGCAACGAACTTGGAA-ACTATCGCAA-CGAACTTG
1 GACTATCGCAACGAACTTGGAATA-AATCGCAAGCGAACTTC
* * * * *
7518 GAATAAATCACAACGCGAACTTCGACT--ATCGCAA-CGAACTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAAGCGAACTTC
* * * * *
7560 GAATAAATCGCAACGCGAACTTCGACT--ATTGCAA-CGAACTTG
1 GACT--ATCGCAA--CGAACTTGGAATAAATCGCAAGCGAACTTC
* *
7602 GACTATCGCAACGAATTTGGGATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAA-GCGAACTTC
*
7644 GACTATCACAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAA-GCGAACTTC
7686 GACTATCGCAACGAACTTGGAATAAATTC-CAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAA-TCGCAA-GCGAACTTC
*
7728 GACTATCGCAACGAATTTGG-A-AAATCGCA
1 GACTATCGCAACGAACTTGGAATAAATCGCA
7757 TTGCGATAGT
Statistics
Matches: 245, Mismatches: 22, Indels: 26
0.84 0.08 0.09
Matches are distributed among these distances:
38 8 0.03
39 2 0.01
40 28 0.11
41 2 0.01
42 194 0.79
43 2 0.01
44 9 0.04
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (41 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAAGCGAACTTC
Found at i:7627 original size:61 final size:61
Alignment explanation
Indices: 7470--7664 Score: 234
Period size: 61 Copynumber: 3.2 Consensus size: 61
7460 AATCGCAACG
* * * *
7470 CGAACTTTGACTATCGCAACGAACTTGGAA-ACTATCGCAA--CGAACTTGGAATAAATCACAA
1 CGAACTTGGACTATCGCAACGAACTTGGAATA-AATCGCAACGCGAACTTCGACT--ATCACAA
* **
7531 CGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAA
1 --CGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAA
* * *
7594 CGAACTTGGACTATCGCAACGAATTTGGGATAAATCGCAATGCGAACTTCGACTATCACAA
1 CGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAA
7655 CGAACTTGGA
1 CGAACTTGGA
7665 ATAAATCGCA
Statistics
Matches: 117, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
61 65 0.56
63 41 0.35
64 1 0.01
65 10 0.09
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (61 bp):
CGAACTTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCACAA
Found at i:7669 original size:103 final size:103
Alignment explanation
Indices: 7444--7706 Score: 445
Period size: 103 Copynumber: 2.5 Consensus size: 103
7434 TGGACTACCG
*
7444 CAACGAACTTGGAATAAATCGCAACGCGAACTTTGACTATCGCAACGAACTTGGAAACTATCGCA
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGG--ACTATCGCA
*
7509 ACGAACTTGGAATAAATCACAACGCGAACTTCGACTATCG
64 ACGAACTTGGAATAAATCACAACGCGAACTTCGACTATCA
*
7549 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATTGCAACGAACTTGGACTATCGCAAC
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAAC
* * * *
7614 GAATTTGGGATAAATCGCAATGCGAACTTCGACTATCA
66 GAACTTGGAATAAATCACAACGCGAACTTCGACTATCA
7652 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
1 CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGA
7707 ATAAATTCCA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
103 98 0.65
105 52 0.35
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.21
Consensus pattern (103 bp):
CAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGACTATCGCAAC
GAACTTGGAATAAATCACAACGCGAACTTCGACTATCA
Found at i:7718 original size:21 final size:21
Alignment explanation
Indices: 7442--7712 Score: 199
Period size: 21 Copynumber: 13.0 Consensus size: 21
7432 TTTGGACTAC
7442 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
7463 CGCAACGCGAACTTTGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
*
7484 CGCAACGAACTTGGAA-ACTAT
1 CGCAACGAACTTGGAATA-AAT
7505 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* * *
7526 CACAACGCGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
7547 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
7568 CGCAACGCGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
* *
7589 TGCAACGAACTTGGACT--AT
1 CGCAACGAACTTGGAATAAAT
* *
7608 CGCAACGAATTTGGGATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
7629 CGCAATGCGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
*
7650 CACAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
* *
7671 CGCAACGCGAACTTCGACT--AT
1 CGCAA--CGAACTTGGAATAAAT
7692 CGCAACGAACTTGGAATAAAT
1 CGCAACGAACTTGGAATAAAT
7713 TCCAACGCGA
Statistics
Matches: 197, Mismatches: 31, Indels: 44
0.72 0.11 0.16
Matches are distributed among these distances:
19 65 0.33
21 83 0.42
22 1 0.01
23 48 0.24
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
CGCAACGAACTTGGAATAAAT
Found at i:7781 original size:21 final size:21
Alignment explanation
Indices: 7752--7804 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
7742 ATTTGGAAAA
*
7752 TCGCATTGCGATAGTCAAAGT
1 TCGCGTTGCGATAGTCAAAGT
* *
7773 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCAAAGT
7794 TCGCGTTGCGA
1 TCGCGTTGCGA
7805 ATTATCGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCAAAGT
Found at i:9164 original size:23 final size:25
Alignment explanation
Indices: 9111--9165 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
9101 TAAAAGGTCT
*
9111 AAAATTTTTAAAATAATTATAGAAA
1 AAAAATTTTAAAATAATTATAGAAA
*
9136 CAAAATTTT-AAAT-ATTATA-AAA
1 AAAAATTTTAAAATAATTATAGAAA
9158 AAGAAATT
1 AA-AAATT
9166 AAGGCACGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 11 0.42
24 4 0.15
25 7 0.27
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (25 bp):
AAAAATTTTAAAATAATTATAGAAA
Found at i:12272 original size:37 final size:37
Alignment explanation
Indices: 12224--12294 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
12214 TGTAGCCAAC
12224 ACACTATGGTTGATCCCTCTAGCTTAGCTCATGGTGA
1 ACACTATGGTTGATCCCTCTAGCTTAGCTCATGGTGA
*
12261 ACACTCTGGTTGATCCCTCTAGCTTAGCTCATGG
1 ACACTATGGTTGATCCCTCTAGCTTAGCTCATGG
12295 GATGAATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (37 bp):
ACACTATGGTTGATCCCTCTAGCTTAGCTCATGGTGA
Found at i:13782 original size:90 final size:91
Alignment explanation
Indices: 13605--13783 Score: 240
Period size: 90 Copynumber: 2.0 Consensus size: 91
13595 TATTAAAACG
* * *
13605 GATCAAAACTGATAGTTTAGGTACTAAACGCGTTAATTTTTTTAGTAACGGATACCAAAATGAAA
1 GATCAAAAATGATAGTTTAAGTACTAAACGCGTTAATTTTTTTAGCAACGGATACCAAAATGAAA
* *
13670 CAAAAATTAAACGTCGCGTATGATAT
66 CAAAAACTAAACGTCGCATATGATAT
* *
13696 GATCAAAAATGATAGTTTAAGTACTAAATGC-TATAA-TTTTTTAGCAAC-GAGTACTAAAATGA
1 GATCAAAAATGATAGTTTAAGTACTAAACGCGT-TAATTTTTTTAGCAACGGA-TACCAAAATGA
13758 AACAAAAACTAAACGTCAG-ATATGAT
64 AACAAAAACTAAACGTC-GCATATGAT
13784 TTAAAAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
89 2 0.03
90 44 0.56
91 32 0.41
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (91 bp):
GATCAAAAATGATAGTTTAAGTACTAAACGCGTTAATTTTTTTAGCAACGGATACCAAAATGAAA
CAAAAACTAAACGTCGCATATGATAT
Found at i:25149 original size:83 final size:82
Alignment explanation
Indices: 25023--25302 Score: 215
Period size: 85 Copynumber: 3.2 Consensus size: 82
25013 TTTACTAATT
* * *
25023 TATATATATATATATATTTACGTTATTATTATTATATGCGTATACTTTTTTTATTTGATTATTTT
1 TATATATGTATATATATTTAC--TATAATTATTATATACGTATACTTTTTTT-TTTGATTATTTT
25088 TGCTTAATGTTATATTTTAA
63 TGCTTAATGTTATATTTTAA
* * * * *
25108 TATATATGTATATACTGTTTTAC-A-AATTATTATATATGTATA-TATTATTTTTTAATTTAACT
1 TATATATGTATATA-T-ATTTACTATAATTATTATATACGTATACT-TTTTTTTTTGA-TT-ATT
* * * * * *
25170 ATTACTATTATCTTCTTTTTACTAA
61 TTTGCT-TAATGTTATATTT--TAA
* *
25195 TATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTCTTCTTTGAT
1 TATATATGTATATATATTTAC--TATAATTATTATATACGTATAC-----TTTTT-TT-TTTGAT
25260 TATTTTTGCTTAATGTTATATTTTAA
57 TATTTTTGCTTAATGTTATATTTTAA
25286 TATATATGTATATATAT
1 TATATATGTATATATAT
25303 ATATATATGT
Statistics
Matches: 147, Mismatches: 28, Indels: 34
0.70 0.13 0.16
Matches are distributed among these distances:
82 5 0.03
83 22 0.15
84 7 0.05
85 27 0.18
86 2 0.01
87 21 0.14
88 1 0.01
89 16 0.11
91 19 0.13
93 9 0.06
94 9 0.06
95 5 0.03
96 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.05, T:0.58
Consensus pattern (82 bp):
TATATATGTATATATATTTACTATAATTATTATATACGTATACTTTTTTTTTTGATTATTTTTGC
TTAATGTTATATTTTAA
Found at i:25201 original size:172 final size:173
Alignment explanation
Indices: 24951--25299 Score: 569
Period size: 172 Copynumber: 2.0 Consensus size: 173
24941 CTTTTTGTTG
* *
24951 TGTTTTACAATTTGCTATATATGTATATATTATTTTAATTTAACTATTACTATTATCTTCTTTTT
1 TGTTTTACAAATTACTATATATGTATATATTATTTTAATTTAACTATTACTATTATCTTCTTTTT
*
25016 ACTAATTTATATATATATATATATTTACGTTATTATTATTATATGCGTATAC-TTTTT-TTATTT
66 ACTAA-TTATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTCTTATTT
25079 GATTATTTTTGCTTAATGTTATATTTTAATATATATGTATATAC
130 GATTATTTTTGCTTAATGTTATATTTTAATATATATGTATATAC
*
25123 TGTTTTACAAATTATTATATATGTATATATTATTTTTTAATTTAACTATTACTATTATCTTCTTT
1 TGTTTTACAAATTACTATATATGTATATATTA--TTTTAATTTAACTATTACTATTATCTTCTTT
25188 TTACTAA-TATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTCT
64 TTACTAATTATATATATATATATATTTACGTTATTATTATTATATACGTATAC----TTTTTTCT
*
25252 TCTTTGATTATTTTTGCTTAATGTTATATTTTAATATATATGTATATA
125 TATTTGATTATTTTTGCTTAATGTTATATTTTAATATATATGTATATA
25300 TATATATATA
Statistics
Matches: 164, Mismatches: 5, Indels: 10
0.92 0.03 0.06
Matches are distributed among these distances:
172 73 0.45
174 38 0.23
177 5 0.03
178 48 0.29
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (173 bp):
TGTTTTACAAATTACTATATATGTATATATTATTTTAATTTAACTATTACTATTATCTTCTTTTT
ACTAATTATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTCTTATTTG
ATTATTTTTGCTTAATGTTATATTTTAATATATATGTATATAC
Found at i:25298 original size:10 final size:10
Alignment explanation
Indices: 25285--25317 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
25275 TTATATTTTA
25285 ATATATATGT
1 ATATATATGT
25295 ATATATA--T
1 ATATATATGT
25303 ATATATATGT
1 ATATATATGT
25313 ATATA
1 ATATA
25318 CTTATAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
ATATATATGT
Found at i:26478 original size:10 final size:10
Alignment explanation
Indices: 26463--26496 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
26453 TTCATTTACC
26463 ATTTATTTTT
1 ATTTATTTTT
26473 ATTTATTTTT
1 ATTTATTTTT
* *
26483 ATCTATTTCT
1 ATTTATTTTT
26493 ATTT
1 ATTT
26497 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:29210 original size:39 final size:39
Alignment explanation
Indices: 29139--29216 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
29129 CCCGGAATAT
* *
29139 TACCCGGGGACGCATCTGCTACTAAAGGGAAAGTAGCAC
1 TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
* * *
29178 TACCCGGGGACTCA-CTCGTTACCAAAGCGAAAGTTGCAC
1 TACCCGGGGACGCATCT-GCTACCAAAGCGAAAGTAGCAC
29217 CTGCTGCGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.17
Consensus pattern (39 bp):
TACCCGGGGACGCATCTGCTACCAAAGCGAAAGTAGCAC
Found at i:36930 original size:105 final size:105
Alignment explanation
Indices: 36748--37402 Score: 1045
Period size: 105 Copynumber: 6.4 Consensus size: 105
36738 AGGTTTTACC
*
36748 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
36813 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
36853 CAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
36918 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
36958 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
37023 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
37063 CAGAGCCAATTTCAACTT--C-AC-----A-ATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
37119 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* *
37159 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * *
37224 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTC-CAATCT
66 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
* *
37263 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* *
37328 ACGAAGGGACCGCTGCTTGTCAAC-AA-AATT-TC-A-TT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
** * * *
37363 CAGATTCAATTTCAACTCCACAACGAAGGACATCGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
37403 GAAACAACAC
Statistics
Matches: 522, Mismatches: 17, Indels: 27
0.92 0.03 0.05
Matches are distributed among these distances:
96 92 0.18
97 1 0.00
98 1 0.00
99 2 0.00
100 36 0.07
101 1 0.00
102 6 0.01
103 1 0.00
104 98 0.19
105 284 0.54
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:37156 original size:306 final size:304
Alignment explanation
Indices: 36779--37359 Score: 1038
Period size: 306 Copynumber: 1.9 Consensus size: 304
36769 AACGAAGGAT
36779 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATT
1 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATT
* *
36844 TCTCAATTTCAGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCCAGACAACGTAAGTTC
66 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * *
36909 AACTTCACGACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTTCAGAGCCAATTTCAA
131 AACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTC-CAATCTCAGAGCCAATTTCAA
*
36973 CTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTG
194 CTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTG
* *
37038 GTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
259 CTTGTCAAC-AAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
37085 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATT
1 ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATT
*
37150 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTC
66 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
37215 AACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCAATTTCAACT
131 AACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCAATTTCAACT
*
37280 TCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCT
196 TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCT
37345 TGTCAACAAAATTTC
261 TGTCAACAAAATTTC
37360 ATTCAGATTC
Statistics
Matches: 264, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
304 7 0.03
305 94 0.36
306 163 0.62
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (304 bp):
ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACATT
TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGAGCCAATTTCAACT
TCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCT
TGTCAACAAAATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
Found at i:37189 original size:201 final size:205
Alignment explanation
Indices: 36748--37402 Score: 990
Period size: 201 Copynumber: 3.2 Consensus size: 205
36738 AGGTTTTACC
*
36748 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
36813 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACGACG
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTT----AC-
*
36878 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
126 AACGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACG
36943 AACATTTCTCAATTT
191 AACATTTCTCAATTT
36958 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
37023 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTT-C-AC-A
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTACAACGA
37085 -ATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACAT
131 TATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACAT
37149 TTCTCAATTT
196 TTCTCAATTT
* *
37159 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * *
37224 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTC-CAATCTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTT-ACAAC
* * *
37287 GAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC
129 ----GATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
37352 -AA-AATT-TC-A-TT
190 GAACATTTCTCAATTT
** * * *
37363 CAGATTCAATTTCAACTCCACAACGAAGGACATCGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
37403 GAAACAACAC
Statistics
Matches: 418, Mismatches: 17, Indels: 26
0.91 0.04 0.06
Matches are distributed among these distances:
200 26 0.06
201 164 0.39
202 2 0.00
203 3 0.01
204 36 0.09
205 2 0.00
206 2 0.00
207 3 0.01
208 3 0.01
209 55 0.13
210 122 0.29
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (205 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTTCAGAGCCAATTTCAACTTACAACGA
TATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGAACAT
TTCTCAATTT
Found at i:39133 original size:85 final size:85
Alignment explanation
Indices: 39044--39299 Score: 237
Period size: 83 Copynumber: 3.1 Consensus size: 85
39034 TATGTATATA
39044 TTTTTAATTTAACTATTACTATTATCTTCTTTTTACTAATTTATATATATATATATATTTACGTT
1 TTTTTAATTTAACTATTACTATTATCTTC-TTTTACTAATTTATATATATATATATATTTACGTT
39109 ATTATTAT-TATGCGTATACT
65 ATTATTATATATGCGTATACT
* * * * * * * * *
39129 TTTTTTATTTGATTATT--T-TT-GCTTAATGTTA-TATTTTAATATATGTATATACTGTTTTAC
1 TTTTTAATTTAACTATTACTATTATCTT-CTTTTACTAATTT-ATATATATATATA-T-ATTTAC
** ** *
39189 -AAATTATTATATATGTATATATT
62 GTTATTATTATATATGCGTATACT
39212 ATTTTTAATTTAACTATTACTATTATCTTCTTTTACT-A---ATATATATATATATATTTACGTT
1 -TTTTTAATTTAACTATTACTATTATCTTCTTTTACTAATTTATATATATATATATATTTACGTT
*
39273 ATTATTATTATATACGTATACT
65 ATTATTA-TATATGCGTATACT
39295 TTTTT
1 TTTTT
39300 TTTTCTTTGA
Statistics
Matches: 129, Mismatches: 29, Indels: 29
0.69 0.16 0.16
Matches are distributed among these distances:
80 5 0.04
81 24 0.19
82 24 0.19
83 37 0.29
84 14 0.11
85 14 0.11
86 1 0.01
87 6 0.05
88 4 0.03
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.57
Consensus pattern (85 bp):
TTTTTAATTTAACTATTACTATTATCTTCTTTTACTAATTTATATATATATATATATTTACGTTA
TTATTATATATGCGTATACT
Found at i:39260 original size:166 final size:167
Alignment explanation
Indices: 39015--39349 Score: 495
Period size: 169 Copynumber: 2.0 Consensus size: 167
39005 CTTTTTGTTG
* *
39015 TGTTTTACAATTTGCTATATATGTATATATTTTTAATTTAACTATTACTATTATCTTCTTTTTAC
1 TGTTTTACAAATTACTATATATGTATATATTTTTAATTTAACTATTACTATTATCTTCTTTTTAC
*
39080 TAATTTATATATATATATATATTTACGTTATTATTA-T-TATGCGTATAC-TTTTTTTATTTGAT
66 T-A--TATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTATTTGAT
39142 TATTTTTGCTTAATGTTATATTTT-A-ATATATGTATATAC
128 TA-TTTTGCTTAATGTTATATTTTAATATATATGTATATAC
*
39181 TGTTTTACAAATTATTATATATGTATATATTATTTTTAATTTAACTATTACTATTATCTTC-TTT
1 TGTTTTACAAATTACTATATATG--TATA-TATTTTTAATTTAACTATTACTATTATCTTCTTTT
*
39245 TACTA-ATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTCTTTG
63 TACTATATATATATATATATATTTACGTTATTATTATTATATACGTATAC--TTTTTTTTATTTG
39309 ATTATTTTGCTTAATGTTATATTTTAATATATATGTATATA
126 ATTATTTTGCTTAATGTTATATTTTAATATATATGTATATA
39350 TATATATATA
Statistics
Matches: 154, Mismatches: 5, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
164 30 0.19
165 1 0.01
166 30 0.19
167 1 0.01
168 32 0.21
169 47 0.31
170 13 0.08
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.57
Consensus pattern (167 bp):
TGTTTTACAAATTACTATATATGTATATATTTTTAATTTAACTATTACTATTATCTTCTTTTTAC
TATATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTATTTGATTAT
TTTGCTTAATGTTATATTTTAATATATATGTATATAC
Found at i:39337 original size:85 final size:85
Alignment explanation
Indices: 39086--39350 Score: 241
Period size: 85 Copynumber: 3.2 Consensus size: 85
39076 TTACTAATTT
*
39086 ATATATATATATATATTTACGTTATTATTA-T-TATGCGTATAC---TTTTTTTATTTGATTATT
1 ATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTATTTGATTA-T
39146 TTTGCTTAATGTTATATTTTA
65 TTTGCTTAATGTTATATTTTA
* * * * * * * *
39167 ATATATGTATATACTGTTTTAC---A-AATTATTATATATGTATA-TATTATTTTTAATTTAACT
1 ATATATATATATA-T-ATTTACGTTATTATTATTATATACGTATACT-TTTTTTTTTATTTGATT
* * * *
39227 A--TTACTATTATCTTCT-TTTACTA
63 ATTTTGCT-TAATGTTATATTT--TA
*
39250 ATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTCTTTGATTATT
1 ATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTATTTGATTATT
39315 TTGCTTAATGTTATATTTTA
66 TTGCTTAATGTTATATTTTA
*
39335 ATATATATGTATATAT
1 ATATATATATATATAT
39351 ATATATATAT
Statistics
Matches: 138, Mismatches: 27, Indels: 34
0.69 0.14 0.17
Matches are distributed among these distances:
79 4 0.03
80 2 0.01
81 32 0.23
82 8 0.06
83 19 0.14
84 13 0.09
85 46 0.33
86 7 0.05
87 7 0.05
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (85 bp):
ATATATATATATATATTTACGTTATTATTATTATATACGTATACTTTTTTTTTTATTTGATTATT
TTGCTTAATGTTATATTTTA
Found at i:39348 original size:10 final size:10
Alignment explanation
Indices: 39335--39367 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
39325 TTATATTTTA
39335 ATATATATGT
1 ATATATATGT
39345 ATATATA--T
1 ATATATATGT
39353 ATATATATGT
1 ATATATATGT
39363 ATATA
1 ATATA
39368 CTTATAAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
8 8 0.38
10 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (10 bp):
ATATATATGT
Found at i:41883 original size:60 final size:59
Alignment explanation
Indices: 41790--41945 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 59
41780 GTATATGCGT
* *
41790 ATAGTTTGGGATGAAATTGGAATGTTCAGAAAGTTTG-GAGACTAATTTAGAATGA-AGGTC
1 ATAGTTTGGGATGAAATTGAAATGTTTA-AAAGTTTGAGA-ACTAATTTAGAATGATA-GTC
*
41850 ATAGTTTGGGGTTGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
* * *
41910 ATGGTTTAGGAATGAAATTGAAATATTTAAAAGTTT
1 ATAGTTT-GGGATGAAATTGAAATGTTTAAAAGTTT
41946 AGGGATCAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
60 64 0.75
61 21 0.25
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATGTTTAAAAGTTTGAGAACTAATTTAGAATGATAGTC
Found at i:42617 original size:60 final size:61
Alignment explanation
Indices: 42492--42634 Score: 182
Period size: 60 Copynumber: 2.4 Consensus size: 61
42482 TTATAGTACG
* * * * * *
42492 TTTGTTGAGTCTCTC-ACTTATTAAAAGTTACAAAAATGGTCCCTCATTTATAGGATGTGGC
1 TTTGTGGAGTCCCTCGAC-TATTAAAAGTTACAAAAATGGTCACTCAATTATAAGATGTGAC
* *
42553 TTTGTGGAGTCCCTTGACTATTAAAAGTTAC-AAAATGGTCACTCAATTATAAGATGTTAC
1 TTTGTGGAGTCCCTCGACTATTAAAAGTTACAAAAATGGTCACTCAATTATAAGATGTGAC
*
42613 TTTGTTGAGTCCCTCGACTATT
1 TTTGTGGAGTCCCTCGACTATT
42635 TAGTATGTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
60 44 0.62
61 25 0.35
62 2 0.03
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (61 bp):
TTTGTGGAGTCCCTCGACTATTAAAAGTTACAAAAATGGTCACTCAATTATAAGATGTGAC
Found at i:42874 original size:18 final size:18
Alignment explanation
Indices: 42851--42889 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
42841 TCATTTCATA
*
42851 ACTTTTAACACTCAGGGG
1 ACTTTTAACACTCAGGAG
*
42869 ACTTTTAATACTCAGGAG
1 ACTTTTAACACTCAGGAG
42887 ACT
1 ACT
42890 CAACAAAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (18 bp):
ACTTTTAACACTCAGGAG
Found at i:42998 original size:3 final size:3
Alignment explanation
Indices: 42984--43055 Score: 126
Period size: 3 Copynumber: 23.7 Consensus size: 3
42974 AACTTTACCC
*
42984 TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43032 TAA TAAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TA
43056 TCCACAAGGT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:46384 original size:17 final size:17
Alignment explanation
Indices: 46344--46382 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
46334 TTAATATTTT
46344 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
*
46361 GTATTTAATTTCTTTAA
1 GTATTTAATTTATTTAA
46378 -TATTT
1 GTATTT
46383 TACTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:48612 original size:14 final size:14
Alignment explanation
Indices: 48558--48605 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
48548 TATTTAGTAC
*
48558 TTTTTATTGT-AGT
1 TTTTTATTGTAATT
* *
48571 TGTTTATTG-AACT
1 TTTTTATTGTAATT
48584 TTTTTATTGTAATT
1 TTTTTATTGTAATT
48598 TTTTTATT
1 TTTTTATT
48606 TATATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.19, C:0.02, G:0.10, T:0.69
Consensus pattern (14 bp):
TTTTTATTGTAATT
Found at i:48665 original size:32 final size:33
Alignment explanation
Indices: 48629--48692 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
48619 TACTTAATTC
48629 GTTAATATGGTGGA-TTTATT-TTAATTTATTTT
1 GTTAATATGGTGGACTTT-TTGTTAATTTATTTT
* *
48661 GTTAATTTGTTGGACTTTTTGTTAATTTATTT
1 GTTAATATGGTGGACTTTTTGTTAATTTATTT
48693 GCTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.22, C:0.02, G:0.16, T:0.61
Consensus pattern (33 bp):
GTTAATATGGTGGACTTTTTGTTAATTTATTTT
Done.