Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008918.1 Hibiscus syriacus cultivar Beakdansim tig00112222_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: 50959
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:6466 original size:44 final size:45
Alignment explanation
Indices: 6405--6546 Score: 200
Period size: 44 Copynumber: 3.2 Consensus size: 45
6395 CTTTTTTGTT
* * * *
6405 GATTCCATCATACAAGGAGTTGGATTAGCATCACTC-TTTTGGTC
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
* *
6449 GATTCCATCACATAAGGAGTTGGATCAACATCAC-CATTTCGCTC
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
*
6493 GATTCCATCACATAAGGAGTTGGATTAACATCA-TCATTTTGCTT
1 GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
6537 GATTCCATCA
1 GATTCCATCA
6547 AAAAGGAAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.01
44 86 0.99
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
GATTCCATCACATAAGGAGTTGGATTAACATCACTCATTTTGCTC
Found at i:9653 original size:20 final size:20
Alignment explanation
Indices: 9628--9700 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
9618 AAAAAAAAAT
*
9628 TGGTCTTCATACCGAGGGAC
1 TGGTCTCCATACCGAGGGAC
***
9648 TGGTCTCCATACCGAAAAAC
1 TGGTCTCCATACCGAGGGAC
9668 TGGTCTCCATACC-AGAGGAC
1 TGGTCTCCATACCGAG-GGAC
*
9688 TGGTATCCATACC
1 TGGTCTCCATACC
9701 AAAGATTGAG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.02
20 43 0.98
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TGGTCTCCATACCGAGGGAC
Found at i:9666 original size:40 final size:39
Alignment explanation
Indices: 9622--9708 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 39
9612 CGTACCAAAA
* *
9622 AAAAATTGGTCTTCATACC-GAGGGACTGGTCTCCATACC
1 AAAAATTGGTCTCCATACCAGA-GGACTGGTATCCATACC
*
9661 GAAAAACTGGTCTCCATACCAGAGGACTGGTATCCATACC
1 -AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
*
9701 AAAGATTG
1 AAAAATTG
9709 AGTATACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 6 0.15
40 33 0.80
41 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (39 bp):
AAAAATTGGTCTCCATACCAGAGGACTGGTATCCATACC
Found at i:9719 original size:40 final size:41
Alignment explanation
Indices: 9635--9721 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 41
9625 AATTGGTCTT
* * *
9635 CATACC-GAGGGACTGGTCTCCATACCGAAAAACTGGTCTC
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
* *
9675 CATACCAGA-GGACTGGTATCCATACC-AAAGATTGAGTATA
1 CATACCAGAGGGACTGGTATCCATACCGAAAAACTG-GTATA
9715 CATACCA
1 CATACCA
9722 AAGGCTTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.15
40 32 0.80
41 2 0.05
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (41 bp):
CATACCAGAGGGACTGGTATCCATACCGAAAAACTGGTATA
Found at i:10452 original size:18 final size:20
Alignment explanation
Indices: 10429--10474 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
10419 TTTTTGGTGC
10429 CGATACTCAA-GG-GAGTAT
1 CGATACTCAAGGGAGAGTAT
10447 CGATAC-CAAGGGTAGAGTAT
1 CGATACTCAAGGG-AGAGTAT
10467 CGATACTC
1 CGATACTC
10475 CCCATAGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 8 0.33
20 12 0.50
21 1 0.04
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.22
Consensus pattern (20 bp):
CGATACTCAAGGGAGAGTAT
Found at i:10555 original size:19 final size:20
Alignment explanation
Indices: 10528--10572 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
10518 GCTAGTTTTT
* * *
10528 GTATTGATACTCAA-GGTGA
1 GTATCGATACCCAAGGGTCA
10547 GTATCGATACCCAAGGGTCA
1 GTATCGATACCCAAGGGTCA
10567 GTATCG
1 GTATCG
10573 TCACTGTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACCCAAGGGTCA
Found at i:11875 original size:30 final size:30
Alignment explanation
Indices: 11809--11936 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
11799 GTAAGCCACT
* *
11809 AAACTTTCTAGGTTTACGGAAAATGTCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
11839 -AACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
11868 AAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
11898 AAACTTTCTAGGTTTATGG-AAATGGCTCC
1 AAACTTTCTAGGTTTATGGAAAATGGCTCC
11927 AAACTTTCTA
1 AAACTTTCTA
11937 AATTTGTAAT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
29 47 0.49
30 48 0.51
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (30 bp):
AAACTTTCTAGGTTTATGGAAAATGGCTCC
Found at i:11921 original size:59 final size:59
Alignment explanation
Indices: 11809--11936 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
11799 GTAAGCCACT
*
11809 AAACTTTCTAGGTTTACGGAAAATGTCTCCAACTTTCTAGGTTTATGGAAAATGGCTCC
1 AAACTTTCTAGGTTTACGGAAAATGGCTCCAACTTTCTAGGTTTATGGAAAATGGCTCC
*
11868 AAACTTTCTAGGTTTATGGAAAATGGCTCCAAACTTTCTAGGTTTATGG-AAATGGCTCC
1 AAACTTTCTAGGTTTACGGAAAATGGCTCC-AACTTTCTAGGTTTATGGAAAATGGCTCC
11927 AAACTTTCTA
1 AAACTTTCTA
11937 AATTTGTAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 48 0.73
60 18 0.27
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (59 bp):
AAACTTTCTAGGTTTACGGAAAATGGCTCCAACTTTCTAGGTTTATGGAAAATGGCTCC
Found at i:13797 original size:47 final size:46
Alignment explanation
Indices: 13721--13852 Score: 166
Period size: 47 Copynumber: 2.9 Consensus size: 46
13711 AAAATAATAT
*
13721 AAAAT-CTCTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACC
1 AAAATACT-TTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC
* *
13767 AAAATA-TTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTATC
1 AAAATACTTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACC
*
13814 AATATACTTT-CCA-TTATT-CATAAGCTCGTAAGCTTATTT
1 AAAATACTTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
13853 GCATACTTAC
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
43 20 0.26
44 3 0.04
45 9 0.12
46 8 0.10
47 34 0.44
48 3 0.04
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.40
Consensus pattern (46 bp):
AAAATACTTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACC
Found at i:14741 original size:14 final size:14
Alignment explanation
Indices: 14722--14766 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
14712 AATTTTCATC
*
14722 TTTTTAAATTTATT
1 TTTTTAAATATATT
* * *
14736 TTTTTAAAAAAATA
1 TTTTTAAATATATT
14750 TTTTTAAATATATT
1 TTTTTAAATATATT
14764 TTT
1 TTT
14767 AGATATTTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAAATATATT
Found at i:15414 original size:21 final size:21
Alignment explanation
Indices: 15388--15645 Score: 232
Period size: 21 Copynumber: 12.4 Consensus size: 21
15378 TCGAAGTCCG
*
15388 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
*
15409 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
15430 CGTTGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* * *
15451 CGTTGCGA--TAGTCGAAGTCCA
1 CGTTGCGATTTATTCCAAGT--T
*
15472 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAGTT
*
15493 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
15512 CGCGTTGCAATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAGTT
* *
15535 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
15554 CGCGTTGCGATTTA-TCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
*
15576 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAGTT
* *
15595 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAGTT
*
15614 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAGTT
15637 CGTTGCGAT
1 CGTTGCGAT
15646 AGTCCAAAAT
Statistics
Matches: 198, Mismatches: 22, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.01
19 51 0.26
20 8 0.04
21 104 0.53
22 6 0.03
23 27 0.14
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAGTT
Found at i:15447 original size:42 final size:40
Alignment explanation
Indices: 15388--15603 Score: 281
Period size: 42 Copynumber: 5.2 Consensus size: 40
15378 TCGAAGTCCG
* *
15388 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTT
* * *
15430 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT--T
15472 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
* * *
15512 CGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
15554 CGCGTTGCGATTTA-TCCAAATTCGTTGCGATAGTCCAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
15595 CGTTGCGAT
1 CGTTGCGAT
15604 AGTCGAAGTT
Statistics
Matches: 156, Mismatches: 14, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 9 0.06
40 7 0.04
41 25 0.16
42 115 0.74
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT
Found at i:15518 original size:84 final size:82
Alignment explanation
Indices: 15377--15603 Score: 366
Period size: 84 Copynumber: 2.7 Consensus size: 82
15367 GTCCAAGTTC
* *
15377 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAATTCGTTGCGATTTA
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTTCGTTGCGATTTA
15442 TTCCAAGTTCGTTGCGATA
64 TTCCAAGTTCGTTGCGATA
* *
15461 GTCGAAGTCCACGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTA
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTT--CGTTGCGATTTA
15526 TTCCAAGTTCGTTGCGATA
64 TTCCAAGTTCGTTGCGATA
*
15545 GTCGAAGTTCGCGTTGCGATTTA-TCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGAT
1 GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGAT
15604 AGTCGAAGTT
Statistics
Matches: 134, Mismatches: 7, Indels: 7
0.91 0.05 0.05
Matches are distributed among these distances:
81 8 0.06
82 9 0.07
83 27 0.20
84 90 0.67
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (82 bp):
GTCGAAGTCCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATTTATT
CCAAGTTCGTTGCGATA
Found at i:15604 original size:60 final size:61
Alignment explanation
Indices: 15430--15652 Score: 249
Period size: 60 Copynumber: 3.6 Consensus size: 61
15420 ATTCCAAATT
* * * * * *
15430 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTCCACGTTGCGATTTATTCCAAATT--
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGT--TCGTTGCGA--TAGTCGAAGTTCG
* * * *
15493 CGTTGCGA--TAGTCCAAGTTCGCGTTGCAATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATT--CGTTGCGA--TAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
15556 CGTTGCGATTTA-TCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
15616 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
15653 AATCGCAACG
Statistics
Matches: 140, Mismatches: 11, Indels: 20
0.82 0.06 0.12
Matches are distributed among these distances:
60 43 0.31
61 42 0.30
62 7 0.05
63 31 0.22
64 7 0.05
65 10 0.07
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (61 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGTTGCGATAGTCGAAGTTCG
Found at i:15751 original size:6 final size:6
Alignment explanation
Indices: 15740--15774 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
15730 CACGTATTAT
15740 CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
15775 TACGAGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:16261 original size:5 final size:5
Alignment explanation
Indices: 16255--16363 Score: 132
Period size: 5 Copynumber: 21.0 Consensus size: 5
16245 GCCGTCCGTC
* *
16255 TCGTC TCGTC TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
1 TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG TCGTG
16305 TCGTG TCGTG T--TG TCGTG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGTG TCGTG TCGTG TCGTG TCGT-G TCGT-G TCGT-G TCGT-G TCGT-G
16353 TCGTGG TCGTG
1 TCGT-G TCGTG
16364 GTAATACGTG
Statistics
Matches: 100, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
3 3 0.03
5 62 0.62
6 35 0.35
ACGTcount: A:0.00, C:0.20, G:0.41, T:0.39
Consensus pattern (5 bp):
TCGTG
Found at i:16563 original size:21 final size:21
Alignment explanation
Indices: 16537--16579 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
16527 TTGCGATAAC
16537 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCATT
16558 GCGAACTTCGACTATCGCATT
1 GCGAACTTCGACTATCGCATT
16579 G
1 G
16580 TGATTTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (21 bp):
GCGAACTTCGACTATCGCATT
Found at i:16617 original size:21 final size:21
Alignment explanation
Indices: 16591--16645 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
16581 GATTTACATA
16591 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
16612 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
16633 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
16646 TCTGGAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:22397 original size:42 final size:42
Alignment explanation
Indices: 22350--22468 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
22340 TTCCCCGAAA
* * *
22350 TCCCGTGTTTGTTTTATGCAATTCGTTTTCCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
*
22392 TCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTT
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
*
22434 TCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAA
1 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
22469 TGTAATTCAT
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.46
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTT
Found at i:22662 original size:23 final size:22
Alignment explanation
Indices: 22626--22702 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
22616 CATTTTCATC
22626 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT--AATATTT
22650 AAAATA-TATTTATTAATATTT
1 AAAATATTATTTATTAATATTT
* *
22671 AAAATAATATAATATT-ATATTT
1 AAAATATTAT-TTATTAATATTT
**
22693 TTAATATTAT
1 AAAATATTAT
22703 ATAAAATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
21 13 0.28
22 16 0.34
23 12 0.26
24 6 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATTATTTATTAATATTT
Found at i:22669 original size:21 final size:23
Alignment explanation
Indices: 22626--22676 Score: 79
Period size: 21 Copynumber: 2.3 Consensus size: 23
22616 CATTTTCATC
22626 AAAATATTATTTATTAAAATATTT
1 AAAATATTATTTATT-AAATATTT
22650 AAAATA-TATTTATT-AATATTT
1 AAAATATTATTTATTAAATATTT
22671 AAAATA
1 AAAATA
22677 ATATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 13 0.48
23 8 0.30
24 6 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATTATTTATTAAATATTT
Found at i:22698 original size:22 final size:24
Alignment explanation
Indices: 22628--22705 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 24
22618 TTTTCATCAA
* * *
22628 AATATTATTTATTAAAATATTTAA-
1 AATA-TATATATTAATATTTTTAAT
* **
22652 AATATATTTATTAATATTTAAAAT
1 AATATATATATTAATATTTTTAAT
22676 AATATA-ATATT-ATATTTTTAAT
1 AATATATATATTAATATTTTTAAT
*
22698 ATTATATA
1 AATATATA
22706 AAATAATCAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
22 14 0.32
23 20 0.45
24 10 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATATATATATTAATATTTTTAAT
Found at i:22706 original size:24 final size:23
Alignment explanation
Indices: 22643--22692 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
22633 TATTTATTAA
*
22643 AATATTTAAAAT-ATAT-TTATT
1 AATATTTAAAATAATATAATATT
22664 AATATTTAAAATAATATAATATT
1 AATATTTAAAATAATATAATATT
22687 -ATATTT
1 AATATTT
22693 TTAATATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 10 0.38
23 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTAAAATAATATAATATT
Found at i:23038 original size:20 final size:20
Alignment explanation
Indices: 23013--23281 Score: 294
Period size: 20 Copynumber: 13.4 Consensus size: 20
23003 GATTTTCCAT
* ** *
23013 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
23033 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
23053 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23073 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
23093 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
23113 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
23133 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23153 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
23173 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
23193 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
23213 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
23233 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
23253 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
23273 AATCACAAC
1 AATCGCAAC
23282 ACTGAAATTT
Statistics
Matches: 213, Mismatches: 28, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
19 3 0.01
20 207 0.97
21 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:23992 original size:24 final size:24
Alignment explanation
Indices: 23953--23999 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
23943 AAATTTGGTC
23953 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
23977 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
24000 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:24191 original size:12 final size:12
Alignment explanation
Indices: 24174--24198 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24164 ATATAATCCT
24174 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24186 GAAGAAGAAAAA
1 GAAGAAGAAAAA
24198 G
1 G
24199 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:26518 original size:19 final size:19
Alignment explanation
Indices: 26496--26802 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
26486 CGGAAAATAC
*
26496 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
26515 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
26529 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
26549 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
26563 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26582 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
26601 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
26615 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26634 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
26653 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
26667 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
26686 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
26705 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26724 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26743 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
26757 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26776 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
26795 AATCGCAA
1 AATCGCAA
26803 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 5 0.02
19 151 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:26611 original size:52 final size:53
Alignment explanation
Indices: 26524--26802 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
26514 AAATCCCAAC
*
26524 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
26577 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
26629 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
26681 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
26738 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
26790 ATGAAAATCGCAA
1 ATGAAAATCGCAA
26803 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:26647 original size:71 final size:71
Alignment explanation
Indices: 26563--26802 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
26553 GCAACGAGAG
*
26563 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
26628 AATGAA
66 AATGAA
* * *
26634 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
26694 TACGAAATGAA
61 TGCGAAATGAA
26705 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
26770 AATGAA
66 AATGAA
26776 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
26803 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:26748 original size:142 final size:137
Alignment explanation
Indices: 26496--26834 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
26486 CGGAAAATAC
* * * *
26496 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
26559 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
26624 GCGAAATGAA
128 GCGAAATGAA
26634 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
26699 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
26764 ATGCGAAATGAA
126 ATGCGAAATGAA
26776 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
26835 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:26940 original size:19 final size:19
Alignment explanation
Indices: 26831--26932 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
26821 AAATTATAAA
26831 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
26850 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
26870 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
26886 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
26903 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
26922 CGCATTGCGAT
1 CGCATTGCGAT
26933 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:27058 original size:14 final size:14
Alignment explanation
Indices: 27039--27075 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
27029 CATCAATTAC
27039 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
27053 ACAAATCATCTTTT
1 ACAAATCAACTTTT
27067 ACAAATCAA
1 ACAAATCAA
27076 TTAAACAATC
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:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:27087 original size:12 final size:12
Alignment explanation
Indices: 27070--27142 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
27060 ATCTTTTACA
27070 AATCAATTAAAC
1 AATCAATTAAAC
*
27082 AATCAA--AAATTG
1 AATCAATTAAA--C
**
27094 AATCAACTTTTAC
1 AATCAA-TTAAAC
27107 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
27120 AATCAA-AAAAC
1 AATCAATTAAAC
27131 AATCAATTAAAC
1 AATCAATTAAAC
27143 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:27104 original size:38 final size:38
Alignment explanation
Indices: 27056--27128 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
27046 AACTTTTACA
*
27056 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
27094 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
27129 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:29016 original size:14 final size:14
Alignment explanation
Indices: 28997--29053 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
28987 GCGAAATGAA
*
28997 AATCGCAACGACAG
1 AATCGCAACGAAAG
29011 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
29028 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
29044 AATCGCAACG
1 AATCGCAACG
29054 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:29024 original size:33 final size:33
Alignment explanation
Indices: 28978--29070 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
28968 GCGAAACCAA
*
28978 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
29011 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
29044 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
29071 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:29035 original size:19 final size:19
Alignment explanation
Indices: 28941--29075 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
28931 TAGTTTACTT
* *
28941 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
28961 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
28980 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
28999 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
29013 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
29032 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
29046 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
29065 TCGCAATGCGA
1 TCGCAACGCGA
29076 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:29093 original size:19 final size:19
Alignment explanation
Indices: 29071--29199 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
29061 AAAATCGCAA
29071 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
29090 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
29104 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
29123 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
29137 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
29156 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
29175 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
29195 TGCGA
1 TGCGA
29200 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:29113 original size:33 final size:33
Alignment explanation
Indices: 29071--29162 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
29061 AAAATCGCAA
29071 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
29104 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
29137 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
29163 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:29402 original size:93 final size:93
Alignment explanation
Indices: 29243--29622 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
29233 TTGAATGGAT
29243 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29308 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
29336 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29401 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
29429 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29493 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
29521 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29586 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
29614 AAATTTACT
1 AAATTTACT
29623 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:29556 original size:185 final size:186
Alignment explanation
Indices: 29243--29622 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
29233 TTGAATGGAT
29243 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29308 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
29373 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
29429 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
29493 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
29558 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
29614 AAATTTACT
1 AAATTTACT
29623 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:31343 original size:14 final size:14
Alignment explanation
Indices: 31324--31413 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
31314 TTGAAATGAA
31324 AATCGCAACGAGAG
1 AATCGCAACGAGAG
31338 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
31355 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
31371 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
31390 AATCGCAACGAGAG
1 AATCGCAACGAGAG
31404 AATCGCAACG
1 AATCGCAACG
31414 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31361 original size:33 final size:33
Alignment explanation
Indices: 31316--31430 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
31306 TCTTTTGGTT
31316 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
31349 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31382 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
31415 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
31431 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:31362 original size:19 final size:18
Alignment explanation
Indices: 31323--31435 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
31313 GTTGAAATGA
31323 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
31338 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
31355 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
31371 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
31388 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
31404 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
31421 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
31436 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:31466 original size:14 final size:14
Alignment explanation
Indices: 31447--31501 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
31437 TTTGGTTTCG
31447 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
31461 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
31480 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
31494 CGTTGCGA
1 CGTTGCGA
31502 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:31664 original size:33 final size:33
Alignment explanation
Indices: 31622--31692 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
31612 AATACTAACT
31622 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
31655 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
31688 TGAAA
1 TGAAA
31693 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:31925 original size:22 final size:22
Alignment explanation
Indices: 31873--31927 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
31863 TGGTTGTGAG
**
31873 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
31895 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
31917 GGATTTCTTCG
1 GGATTTCTTCG
31928 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:32098 original size:20 final size:20
Alignment explanation
Indices: 32073--32266 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
32063 CTTTAAATAT
32073 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32093 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
32115 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32134 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
32154 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
32174 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
32194 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
32214 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
32234 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
32254 CGCGTTGCGATTT
1 CGCGTTGCGATTT
32267 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:32260 original size:60 final size:60
Alignment explanation
Indices: 32073--32266 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
32063 CTTTAAATAT
**
32073 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
32134 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
32194 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
32254 CGCGTTGCGATTT
1 CGCGTTGCGATTT
32267 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:32283 original size:21 final size:20
Alignment explanation
Indices: 32259--32335 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
32249 ATATTCGCGT
32259 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
32280 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
32300 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
32322 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
32336 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:32346 original size:20 final size:20
Alignment explanation
Indices: 32321--32372 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
32311 AAGAATCGCG
*
32321 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
32341 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
32361 TTGCGATTCTGG
1 TTGCGATTCTGG
32373 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:32913 original size:15 final size:15
Alignment explanation
Indices: 32890--32929 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
32880 TATTTTCCAG
*
32890 AATTTAAATTTTAAT
1 AATTCAAATTTTAAT
*
32905 AATTCAAATTTTAGT
1 AATTCAAATTTTAAT
32920 AATTCAAATT
1 AATTCAAATT
32930 GCATAAATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTCAAATTTTAAT
Found at i:47455 original size:33 final size:34
Alignment explanation
Indices: 47418--47497 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
47408 ATATATTATA
*
47418 AAAAAATAGAAAAAGA-AAATGAAAACGAAAGAGA-
1 AAAAAATAGAAAAAGAGAAA-GAAAA-GAAATAGAG
*
47452 AAAAAAT-GAAAATGAGAAAGAAAAGAAATAGAG
1 AAAAAATAGAAAAAGAGAAAGAAAAGAAATAGAG
47485 AAAAAATGAGAAA
1 AAAAAAT-AGAAA
47498 TGAAAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 7 0.17
33 19 0.47
34 10 0.25
35 4 0.10
ACGTcount: A:0.72, C:0.01, G:0.19, T:0.07
Consensus pattern (34 bp):
AAAAAATAGAAAAAGAGAAAGAAAAGAAATAGAG
Found at i:47457 original size:21 final size:21
Alignment explanation
Indices: 47425--47480 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
47415 ATAAAAAAAT
*
47425 AGAAA-AAGAAAATGAAAACG
1 AGAAAGAAAAAAATGAAAACG
*
47445 A-AAGAGAAAAAAATGAAAATG
1 AGAA-AGAAAAAAATGAAAACG
47466 AGAAAGAAAAGAAAT
1 AGAAAGAAAA-AAAT
47481 AGAGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 2 0.07
21 20 0.67
22 6 0.20
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.07
Consensus pattern (21 bp):
AGAAAGAAAAAAATGAAAACG
Found at i:47457 original size:27 final size:26
Alignment explanation
Indices: 47427--47503 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 26
47417 AAAAAAATAG
47427 AAAAAGAAAATGA-AAACGAAAGAGAAA
1 AAAAAGAAAATGAGAAA-GAAA-AGAAA
*
47454 AAAATGAAAATGAGAAAGAAAAGAAA
1 AAAAAGAAAATGAGAAAGAAAAGAAA
*
47480 TAGAGAA-AAAATGAGAAATGAAAA
1 -A-AAAAGAAAATGAGAAA-GAAAA
47504 AAATATGCGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
26 5 0.12
27 28 0.65
28 10 0.23
ACGTcount: A:0.71, C:0.01, G:0.19, T:0.08
Consensus pattern (26 bp):
AAAAAGAAAATGAGAAAGAAAAGAAA
Found at i:47470 original size:17 final size:17
Alignment explanation
Indices: 47448--47506 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
47438 GAAAACGAAA
47448 GAGAAAAAAATGAAAAT
1 GAGAAAAAAATGAAAAT
47465 GAGAAAGAAAA-G-AAAT
1 GAGAAA-AAAATGAAAAT
47481 -AGAGAAAAAATGAGAAAT
1 GAGA-AAAAAATGA-AAAT
47499 GA-AAAAAA
1 GAGAAAAAA
47507 TATGCGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 7 0.19
16 7 0.19
17 12 0.33
18 9 0.25
19 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.08
Consensus pattern (17 bp):
GAGAAAAAAATGAAAAT
Done.