Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005688.1 Hibiscus syriacus cultivar Beakdansim tig00013308_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: 97347
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:304 original size:12 final size:12
Alignment explanation
Indices: 287--318 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
277 GTTGATGACT
287 TCCGTTTGGCCA
1 TCCGTTTGGCCA
299 TCCG-TTGGCCA
1 TCCGTTTGGCCA
310 TCCGTTTGG
1 TCCGTTTGG
319 GGAGTATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.06, C:0.31, G:0.28, T:0.34
Consensus pattern (12 bp):
TCCGTTTGGCCA
Found at i:9497 original size:22 final size:22
Alignment explanation
Indices: 9466--9511 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
9456 ATTTGTGTTT
9466 ATTTCAATTTCTCTAAAACACA
1 ATTTCAATTTCTCTAAAACACA
*
9488 ATTTCTATTTCTCTAAAACACA
1 ATTTCAATTTCTCTAAAACACA
9510 AT
1 AT
9512 CCTTTCTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTCAATTTCTCTAAAACACA
Found at i:15403 original size:31 final size:29
Alignment explanation
Indices: 15349--15415 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
15339 TCAGATTATA
15349 TAACTTTTTAAAATTACACTTTAGTC-CT
1 TAACTTTTTAAAATTACACTTTAGTCACT
* *
15377 TAAACTTTTCTAAAGTTTATACTTTAGTCACT
1 T-AACTTTT-TAAA-ATTACACTTTAGTCACT
15409 TAACTTT
1 TAACTTT
15416 CAAAATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 1 0.03
29 7 0.21
30 4 0.12
31 18 0.55
32 3 0.09
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.48
Consensus pattern (29 bp):
TAACTTTTTAAAATTACACTTTAGTCACT
Found at i:26755 original size:43 final size:43
Alignment explanation
Indices: 26707--26802 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 43
26697 GGGCTGTAAG
*
26707 AGTATCGATATTCAGGTTCATTG-TATCAAT-CTTACTTCACAAT
1 AGTATCGATATTCAGGTTCA-CGATATCAATAC-TACTTCACAAT
* * *
26750 AGTATCCG-TATTCGGGTTCACGATATCAATACTACTTCGCAGT
1 AGTAT-CGATATTCAGGTTCACGATATCAATACTACTTCACAAT
26793 AGTATCGATA
1 AGTATCGATA
26803 CTCTTAAGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
42 3 0.07
43 39 0.87
44 3 0.07
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (43 bp):
AGTATCGATATTCAGGTTCACGATATCAATACTACTTCACAAT
Found at i:27537 original size:41 final size:42
Alignment explanation
Indices: 27485--27567 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
27475 CGCAAATCAG
* *
27485 TTTCCAGATTCACAACGCGA-TTCTGACTATCGCATTGCGAT
1 TTTCCAAATTCACAACGCGATTTCTGACTATCGCAATGCGAT
***
27526 TTTCCAAATTCACGTTGCGATTTTCTGACTATCGCAATGCGA
1 TTTCCAAATTCACAACGCGA-TTTCTGACTATCGCAATGCGA
27568 ATATGTAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 16 0.46
43 19 0.54
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTCCAAATTCACAACGCGATTTCTGACTATCGCAATGCGAT
Found at i:27643 original size:20 final size:20
Alignment explanation
Indices: 27551--27685 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
27541 TGCGATTTTC
*
27551 TGACTATCGCAATGCGAATA
1 TGACTATCGCAATGCGATTA
* *
27571 TGTA-AATCGCAATGCGAGTA
1 TG-ACTATCGCAATGCGATTA
* *
27591 TGACTATCGCAACGCGAATA
1 TGACTATCGCAATGCGATTA
*
27611 TGTA-AATCGCAATGCGATTA
1 TG-ACTATCGCAATGCGATTA
*
27631 TGACTATCACAATGCGATTA
1 TGACTATCGCAATGCGATTA
* *
27651 TGACTATCGCAACGCGATTC
1 TGACTATCGCAATGCGATTA
* *
27671 TAACTGTCGCAATGC
1 TGACTATCGCAATGC
27686 TGAATTTCAA
Statistics
Matches: 95, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.02
20 91 0.96
21 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (20 bp):
TGACTATCGCAATGCGATTA
Found at i:27660 original size:40 final size:40
Alignment explanation
Indices: 27551--27690 Score: 174
Period size: 40 Copynumber: 3.5 Consensus size: 40
27541 TGCGATTTTC
*
27551 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTA
1 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
*
27591 TGACTATCGCAACGCGAATATGTAAATCGCAATGCGATTA
1 TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
* * * * *
27631 TGACTATCACAATGCGATTATG-ACTATCGCAACGCGATTC
1 TGACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTA
* *
27671 TAACTGTCGCAATGCTGAAT
1 TGACTATCGCAATGC-GAAT
27691 TTCAAATTCG
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 82 0.95
41 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (40 bp):
TGACTATCGCAATGCGAATATGTAAATCGCAATGCGATTA
Found at i:27681 original size:60 final size:61
Alignment explanation
Indices: 27548--27690 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 61
27538 CGTTGCGATT
* *
27548 TTCTGACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTATGACTATCGCAACGCGAA
1 TTCTAACTATCGCAATGCGAATATGTAAATCACAATGCGAGTATGACTATCGCAACGCGAA
* * * *
27609 TATGTAA--ATCGCAATGCGATTATG-ACTATCACAATGCGATTATGACTATCGCAACGCG-A
1 T-TCTAACTATCGCAATGCGAATATGTA-AATCACAATGCGAGTATGACTATCGCAACGCGAA
*
27668 TTCTAACTGTCGCAATGCTGAAT
1 TTCTAACTATCGCAATGC-GAAT
27691 TTCAAATTCG
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
58 4 0.06
59 3 0.04
60 54 0.79
61 4 0.06
62 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (61 bp):
TTCTAACTATCGCAATGCGAATATGTAAATCACAATGCGAGTATGACTATCGCAACGCGAA
Found at i:28533 original size:24 final size:24
Alignment explanation
Indices: 28501--28554 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
28491 GTATTCGAAA
28501 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
28525 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
28549 TTTGAT
1 TTTGAT
28555 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:30830 original size:18 final size:18
Alignment explanation
Indices: 30807--30841 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
30797 AGCAAAAGGC
*
30807 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
30825 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
30842 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:31044 original size:20 final size:20
Alignment explanation
Indices: 31019--31313 Score: 225
Period size: 20 Copynumber: 15.7 Consensus size: 20
31009 CACACTCATT
*
31019 TGACTATCGTAACGCGAATA
1 TGACTATCGCAACGCGAATA
*
31039 TGACTATCGCAACGAGAATA
1 TGACTATCGCAACGCGAATA
* * *
31059 TGACTATTGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* * *
31079 TGAATACCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
31096 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
31113 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
31130 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
*
31147 TGACTATCGCAACGCGAAAA
1 TGACTATCGCAACGCGAATA
31167 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
31187 TGACTATCGCAATGCGAATT
1 TGACTATCGCAACGCGAATA
* * *
31207 TAACTATCGCAACACGAATT
1 TGACTATCGCAACGCGAATA
*
31227 TGACTATCGCAA--CG-AGA
1 TGACTATCGCAACGCGAATA
*
31244 T-A--ATCGCAATGCGAA-A
1 TGACTATCGCAACGCGAATA
*
31260 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
31280 TGATTATCGCAACG-GTAATT
1 TGACTATCGCAACGCG-AATA
31300 TGACTATCGCAACG
1 TGACTATCGCAACG
31314 AGAAAATCAC
Statistics
Matches: 224, Mismatches: 31, Indels: 40
0.76 0.11 0.14
Matches are distributed among these distances:
14 22 0.10
15 2 0.01
16 7 0.03
17 11 0.05
18 4 0.02
19 15 0.07
20 163 0.73
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:31435 original size:36 final size:34
Alignment explanation
Indices: 31394--31473 Score: 114
Period size: 30 Copynumber: 2.4 Consensus size: 34
31384 TTACATTTCA
31394 ATCAATTAAACAAGCACAAATAAGAATTATTTACAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
31430 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
31460 ATCAATTAAACAAA
1 ATCAATTAAACAAA
31474 TCAACTCTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 28 0.70
32 2 0.05
34 3 0.08
36 7 0.17
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:31445 original size:30 final size:30
Alignment explanation
Indices: 31409--31474 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
31399 TTAAACAAGC
31409 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
31439 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
31469 ACAAAT
1 ACAAAT
31475 CAACTCTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:32925 original size:21 final size:18
Alignment explanation
Indices: 32901--32945 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
32891 GAACGGTGGG
32901 AGGGGACTCTTGAGGGATGAT
1 AGGGGACTCTTGA---ATGAT
*
32922 AGGGGCCTCTTGAATGAT
1 AGGGGACTCTTGAATGAT
32940 AGGGGA
1 AGGGGA
32946 GGCCTCTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.22
Consensus pattern (18 bp):
AGGGGACTCTTGAATGAT
Found at i:33507 original size:20 final size:20
Alignment explanation
Indices: 33463--33539 Score: 100
Period size: 20 Copynumber: 3.8 Consensus size: 20
33453 TCGCAACACG
*
33463 AATGACTATCGCAACGCAAAA
1 AATGACTATCGCAACGC-GAA
*
33484 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
*
33504 AATGACTATCCCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
33524 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
33540 AGATAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
20 34 0.68
21 16 0.32
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:33607 original size:20 final size:20
Alignment explanation
Indices: 33582--33646 Score: 103
Period size: 20 Copynumber: 3.2 Consensus size: 20
33572 GTGATTCTTT
**
33582 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
33602 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
33622 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
33642 CGTTG
1 CGTTG
33647 TAAAAGTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:33820 original size:18 final size:18
Alignment explanation
Indices: 33797--33846 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
33787 TTTACTAAGC
33797 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
33815 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
33833 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
33847 TACGAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:35554 original size:20 final size:20
Alignment explanation
Indices: 35531--35637 Score: 92
Period size: 20 Copynumber: 5.5 Consensus size: 20
35521 TCTGAAACTT
*
35531 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
*
35551 AAAATCGCAATACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
35571 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
35591 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
35610 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
35629 AAAATCGCA
1 AAAATCGCA
35638 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
19 24 0.33
20 49 0.67
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:36041 original size:22 final size:22
Alignment explanation
Indices: 36014--36066 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
36004 GAGATAGACG
* *
36014 GATTTCGCCGGAGATGGGGACT
1 GATTTCGCCGGAGATAGGGACA
*
36036 GATTTCGTCGGAGATAGGGACA
1 GATTTCGCCGGAGATAGGGACA
*
36058 GATGTCGCC
1 GATTTCGCC
36067 TTAGAGAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.23
Consensus pattern (22 bp):
GATTTCGCCGGAGATAGGGACA
Found at i:36257 original size:20 final size:20
Alignment explanation
Indices: 36232--36427 Score: 128
Period size: 20 Copynumber: 9.7 Consensus size: 20
36222 GTGCTTTGAA
*
36232 AATCGCATTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
36252 AATCGCGTTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAG
*
36272 AATCGCATTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
36292 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
36312 ATTCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
36332 ACTCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* *
36352 ATTCGCATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
** * * *
36374 AATCGCAACGCGA-ATTTGGAA
1 AATCGCATTGCGATA-GT-CAG
*
36395 AATCGCAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
36415 AATCGCGTTGCGA
1 AATCGCATTGCGA
36428 ATCTGGAAAC
Statistics
Matches: 140, Mismatches: 27, Indels: 18
0.76 0.15 0.10
Matches are distributed among these distances:
19 2 0.01
20 107 0.76
21 18 0.13
22 13 0.09
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:36290 original size:40 final size:38
Alignment explanation
Indices: 36232--36427 Score: 176
Period size: 40 Copynumber: 4.9 Consensus size: 38
36222 GTGCTTTGAA
* * *
36232 AATCGCATTGCGACAGTCAGAATCGCGTTGCGATAGTTAG
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGAT--TTAC
*
36272 AATCGCATTGCGATAGTCATAATCGCATTGCGATTTAC
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTAC
* * *
36310 ATATTCGCGTTGCGATAGTCATACTCGCATTGCGATTTAC
1 A-A-TCGCATTGCGATAGTCAGAATCGCATTGCGATTTAC
* ** *
36350 ATATTCGCATTGCGATAGTCGGAAAATCGCAACGCGAATTTGGAA
1 A-A-TCGCATTGCGATAGTC--AGAATCGCATTGCG-ATTT--AC
* *
36395 AATCGCAATGCGATAGTCAGAATCGCGTTGCGA
1 AATCGCATTGCGATAGTCAGAATCGCATTGCGA
36428 ATCTGGAAAC
Statistics
Matches: 132, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
38 4 0.03
39 1 0.01
40 85 0.64
41 10 0.08
42 10 0.08
43 19 0.14
44 1 0.01
45 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (38 bp):
AATCGCATTGCGATAGTCAGAATCGCATTGCGATTTAC
Found at i:37884 original size:14 final size:13
Alignment explanation
Indices: 37865--37896 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
37855 CTCCATATTT
37865 TTCTTGTTCTTCTC
1 TTCTTGTTCTTC-C
37879 TTCTTGTTCTTCC
1 TTCTTGTTCTTCC
37892 TTCTT
1 TTCTT
37897 CTTTTGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.00, C:0.28, G:0.06, T:0.66
Consensus pattern (13 bp):
TTCTTGTTCTTCC
Found at i:46415 original size:21 final size:21
Alignment explanation
Indices: 46375--46415 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
46365 TTTCTCTGCT
* *
46375 TTGATGCCATGGATGTTCGTC
1 TTGATGCCATGGAGGATCGTC
*
46396 TTGATGCCTTGGAGGATCGT
1 TTGATGCCATGGAGGATCGT
46416 TTTCATGATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.37
Consensus pattern (21 bp):
TTGATGCCATGGAGGATCGTC
Found at i:46996 original size:2 final size:2
Alignment explanation
Indices: 46989--47027 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46979 ACATAAATGA
46989 AT AT 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 AT AT A
47028 AATTAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48285 original size:17 final size:18
Alignment explanation
Indices: 48263--48304 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
48253 CAATTAAAAC
48263 TATAATAAAAATATA-AT
1 TATAATAAAAATATATAT
*
48280 TATAAT-AAAATATATTT
1 TATAATAAAAATATATAT
48297 TATAATAA
1 TATAATAA
48305 TGCATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 8 0.36
17 13 0.59
18 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATAATAAAAATATATAT
Found at i:58612 original size:24 final size:24
Alignment explanation
Indices: 58576--58644 Score: 102
Period size: 24 Copynumber: 2.9 Consensus size: 24
58566 AGTAAGGGTA
*
58576 TGCAAATATACTTGTCGTGGCGAG
1 TGCAAATAAACTTGTCGTGGCGAG
*
58600 TGCAAATAAACTTGTCGTGGTGAG
1 TGCAAATAAACTTGTCGTGGCGAG
* *
58624 TGCAAATTAACATGTCGTGGC
1 TGCAAATAAACTTGTCGTGGC
58645 ATTTTTGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (24 bp):
TGCAAATAAACTTGTCGTGGCGAG
Found at i:59365 original size:31 final size:31
Alignment explanation
Indices: 59305--59366 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
59295 AAGTATATTA
**
59305 CTTAGTGTTCAAGAGAAACTAAGTTAAGATC
1 CTTAGTGTTCAAGAGAAACTAAGAGAAGATC
59336 CTTAGTGTTCGAA-AGAAACTAAGAGAAGATC
1 CTTAGTGTTC-AAGAGAAACTAAGAGAAGATC
59367 AATATGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (31 bp):
CTTAGTGTTCAAGAGAAACTAAGAGAAGATC
Found at i:67989 original size:13 final size:13
Alignment explanation
Indices: 67971--67995 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
67961 TGGTCCTTTT
67971 GTTTCTTCCATTA
1 GTTTCTTCCATTA
67984 GTTTCTTCCATT
1 GTTTCTTCCATT
67996 GGTGCCATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
GTTTCTTCCATTA
Found at i:72142 original size:55 final size:56
Alignment explanation
Indices: 72058--72164 Score: 207
Period size: 55 Copynumber: 1.9 Consensus size: 56
72048 GGCTCAAGTC
72058 CACACCAAAACAACTATGCATTGACCCAAAACACATAAATAGCT-CCTTAGTTCAT
1 CACACCAAAACAACTATGCATTGACCCAAAACACATAAATAGCTCCCTTAGTTCAT
72113 CACACCAAAACAACTATGCATTGACCCAAAACACATAAATAGCTCCCTTAGT
1 CACACCAAAACAACTATGCATTGACCCAAAACACATAAATAGCTCCCTTAGT
72165 CCATTTAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 44 0.86
56 7 0.14
ACGTcount: A:0.42, C:0.30, G:0.07, T:0.21
Consensus pattern (56 bp):
CACACCAAAACAACTATGCATTGACCCAAAACACATAAATAGCTCCCTTAGTTCAT
Found at i:77193 original size:16 final size:17
Alignment explanation
Indices: 77172--77226 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 17
77162 TAAATAAAGG
77172 TATATATGAAAT-TAAA
1 TATATATGAAATATAAA
*
77188 TATATAAGAAATATAAA
1 TATATATGAAATATAAA
77205 TATA-AT--AATATAAA
1 TATATATGAAATATAAA
77219 TATATATG
1 TATATATG
77227 TATATATATC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.35
15 2 0.06
16 12 0.35
17 8 0.24
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.36
Consensus pattern (17 bp):
TATATATGAAATATAAA
Found at i:79832 original size:27 final size:26
Alignment explanation
Indices: 79802--79863 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
79792 TAGATCTAAG
79802 AAATATTCAAATTTAATATTTT-AATTA
1 AAATATT-AAA-TTAATATTTTAAATTA
79829 AAATAATATAAATTAATATTTTAAATTA
1 AAAT-AT-TAAATTAATATTTTAAATTA
79857 AAATATT
1 AAATATT
79864 TACTTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 14 0.44
29 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATATTAAATTAATATTTTAAATTA
Found at i:79862 original size:15 final size:15
Alignment explanation
Indices: 79816--79864 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 15
79806 ATTCAAATTT
79816 AATATTTT-AATTAA
1 AATATTTTAAATTAA
* *
79830 AATAATATAAATT--
1 AATATTTTAAATTAA
79843 AATATTTTAAATTAA
1 AATATTTTAAATTAA
79858 AATATTT
1 AATATTT
79865 ACTTTTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 11 0.39
14 6 0.21
15 11 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAAATTAA
Found at i:79905 original size:26 final size:26
Alignment explanation
Indices: 79873--79924 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
79863 TTACTTTTAA
79873 AATAAGAAAGAATTAAAATACCCTTT
1 AATAAGAAAGAATTAAAATACCCTTT
* *
79899 AATAAGAAATAATTAAAATATCCTTT
1 AATAAGAAAGAATTAAAATACCCTTT
79925 TAGTAATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.31
Consensus pattern (26 bp):
AATAAGAAAGAATTAAAATACCCTTT
Found at i:80432 original size:20 final size:20
Alignment explanation
Indices: 80394--80432 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
80384 TTTAAGTTGT
*
80394 AAAACTTGACTCGACTTAAA
1 AAAACTTGACTCGAATTAAA
* *
80414 AAAATTTGACTTGAATTAA
1 AAAACTTGACTCGAATTAA
80433 TTTCGAGTTA
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:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (20 bp):
AAAACTTGACTCGAATTAAA
Found at i:83651 original size:13 final size:13
Alignment explanation
Indices: 83633--83675 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
83623 ACTTTTTCGA
83633 TCAAAGTCAACGG
1 TCAAAGTCAACGG
* *
83646 TCAAAGGCAACAG
1 TCAAAGTCAACGG
*
83659 TTAAAGTCAACGG
1 TCAAAGTCAACGG
83672 TCAA
1 TCAA
83676 CAGGGGTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.16
Consensus pattern (13 bp):
TCAAAGTCAACGG
Found at i:86548 original size:33 final size:33
Alignment explanation
Indices: 86483--86546 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
86473 GATTTCTAAT
*
86483 TTATAGACTGCTCTTTCGTCCAAATATTTTTTA
1 TTATAGACTGCTCTCTCGTCCAAATATTTTTTA
86516 TTATAGACTG-T-TCTCGTACCAAATATTTTTT
1 TTATAGACTGCTCTCTCGT-CCAAATATTTTTT
86547 TAATTGTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 5 0.17
32 14 0.48
33 10 0.34
ACGTcount: A:0.25, C:0.17, G:0.09, T:0.48
Consensus pattern (33 bp):
TTATAGACTGCTCTCTCGTCCAAATATTTTTTA
Found at i:89733 original size:21 final size:21
Alignment explanation
Indices: 89709--89748 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
89699 AATAGCGCCC
89709 AATAGCACCAGCGACGACCGT
1 AATAGCACCAGCGACGACCGT
* *
89730 AATAGCGCCCGCGACGACC
1 AATAGCACCAGCGACGACC
89749 ACAATCACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.38, G:0.25, T:0.07
Consensus pattern (21 bp):
AATAGCACCAGCGACGACCGT
Done.