Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002927.1 Hibiscus syriacus cultivar Beakdansim tig00006049_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: 75287
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2495 original size:7 final size:7
Alignment explanation
Indices: 2483--2511 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
2473 TTGGGTCACT
2483 CAAATTC
1 CAAATTC
2490 CAAATTC
1 CAAATTC
2497 CAAATTC
1 CAAATTC
2504 CAAATTC
1 CAAATTC
2511 C
1 C
2512 TTTCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (7 bp):
CAAATTC
Found at i:4336 original size:29 final size:29
Alignment explanation
Indices: 4271--4336 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
4261 TAAAATTATC
*
4271 TTTT-TTTTTGTTTTAACTTATTAAATAT
1 TTTTATTTTTGTCTTAACTTATTAAATAT
* * *
4299 TTTTATTTTGGTCTTAATTTATT-AATTT
1 TTTTATTTTTGTCTTAACTTATTAAATAT
4327 TTTTATTTTT
1 TTTTATTTTT
4337 AATGTAAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (29 bp):
TTTTATTTTTGTCTTAACTTATTAAATAT
Found at i:4632 original size:30 final size:29
Alignment explanation
Indices: 4560--4682 Score: 140
Period size: 29 Copynumber: 4.1 Consensus size: 29
4550 AGATATTTTG
4560 ATATATTTTTAAAAGTTAAAATAATAATAAA
1 ATATATTTTT--AAGTTAAAATAATAATAAA
* *
4591 ATATATTTTTAATTTAAAATAAAAATAAA
1 ATATATTTTTAAGTTAAAATAATAATAAA
* * *
4620 ATATATTTTTTAAGTGAAGATAAGAATAAA
1 ATATA-TTTTTAAGTTAAAATAATAATAAA
* *
4650 AAATATTTTTATA-TTAAATTAATAATAAA
1 ATATATTTTTA-AGTTAAAATAATAATAAA
4679 ATAT
1 ATAT
4683 TTAAATATAT
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
29 43 0.55
30 25 0.32
31 10 0.13
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
ATATATTTTTAAGTTAAAATAATAATAAA
Found at i:4658 original size:59 final size:60
Alignment explanation
Indices: 4560--4682 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 60
4550 AGATATTTTG
* * *
4560 ATATATTTTTAAAAGTTAAAATAATAATAAAATATATTTTTA-ATTTAAAATAAAAATAAA
1 ATATATTTTTAAAAGTGAAAATAAGAATAAAAAATATTTTTATA-TTAAAATAAAAATAAA
* * * *
4620 ATATATTTTT-TAAGTGAAGATAAGAATAAAAAATATTTTTATATTAAATTAATAATAAA
1 ATATATTTTTAAAAGTGAAAATAAGAATAAAAAATATTTTTATATTAAAATAAAAATAAA
4679 ATAT
1 ATAT
4683 TTAAATATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 44 0.80
60 11 0.20
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (60 bp):
ATATATTTTTAAAAGTGAAAATAAGAATAAAAAATATTTTTATATTAAAATAAAAATAAA
Found at i:4683 original size:27 final size:27
Alignment explanation
Indices: 4644--4747 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 27
4634 TGAAGATAAG
4644 AATAA-AAAATATTTTTATATTAAATT
1 AATAATAAAATATTTTTATATTAAATT
* *
4670 AATAATAAAATATTTAAATATATTTCAAGTT
1 AATAATAAAATATTT--TTATA-TT-AAATT
4701 AATATATTTAAAAAATATTTTTATATTAAATT
1 AATA-A--T--AAAATATTTTTATATTAAATT
4733 AATAATAAAATATTT
1 AATAATAAAATATTT
4748 AAATATATTT
Statistics
Matches: 64, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
26 5 0.08
27 18 0.28
29 5 0.08
30 2 0.03
31 9 0.14
32 9 0.14
33 2 0.03
34 5 0.08
36 9 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (27 bp):
AATAATAAAATATTTTTATATTAAATT
Found at i:4717 original size:36 final size:36
Alignment explanation
Indices: 4676--4783 Score: 135
Period size: 36 Copynumber: 3.2 Consensus size: 36
4666 AATTAATAAT
4676 AAAATATTTAAATATATTTCAAGTTAATATATTTAA
1 AAAATATTTAAATATATTTCAAGTTAATATATTTAA
* *
4712 AAAATATTT--TTATA-TT-AAATTAATA-A--T--
1 AAAATATTTAAATATATTTCAAGTTAATATATTTAA
4739 AAAATATTTAAATATATTTCAAGTTAATATATTTAA
1 AAAATATTTAAATATATTTCAAGTTAATATATTTAA
4775 AAAATATTT
1 AAAATATTT
4784 TTAAGTGATG
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
27 9 0.15
29 5 0.08
30 2 0.03
31 9 0.15
32 9 0.15
33 2 0.03
34 5 0.08
36 18 0.31
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (36 bp):
AAAATATTTAAATATATTTCAAGTTAATATATTTAA
Found at i:4724 original size:63 final size:63
Alignment explanation
Indices: 4646--4786 Score: 282
Period size: 63 Copynumber: 2.2 Consensus size: 63
4636 AAGATAAGAA
4646 TAAAAAATATTTTTATATTAAATTAATAATAAAATATTTAAATATATTTCAAGTTAATATATT
1 TAAAAAATATTTTTATATTAAATTAATAATAAAATATTTAAATATATTTCAAGTTAATATATT
4709 TAAAAAATATTTTTATATTAAATTAATAATAAAATATTTAAATATATTTCAAGTTAATATATT
1 TAAAAAATATTTTTATATTAAATTAATAATAAAATATTTAAATATATTTCAAGTTAATATATT
4772 TAAAAAATATTTTTA
1 TAAAAAATATTTTTA
4787 AGTGATGAAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 78 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (63 bp):
TAAAAAATATTTTTATATTAAATTAATAATAAAATATTTAAATATATTTCAAGTTAATATATT
Found at i:4830 original size:2 final size:2
Alignment explanation
Indices: 4823--4852 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4813 TTTATATTAA
4823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4853 TTAATAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5868 original size:3 final size:3
Alignment explanation
Indices: 5860--5889 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5850 ATTCAAATGT
5860 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5890 ATCTAGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21384 original size:24 final size:23
Alignment explanation
Indices: 21352--21402 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
21342 AAACGAACGT
*
21352 TAAATGAACATATTCA-TGAACATA
1 TAAACGAACATATT-AGTGAACA-A
*
21376 TAAACGAACATGTTAGTGAACAA
1 TAAACGAACATATTAGTGAACAA
21399 TAAA
1 TAAA
21403 TAAATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (23 bp):
TAAACGAACATATTAGTGAACAA
Found at i:22140 original size:14 final size:15
Alignment explanation
Indices: 22121--22149 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
22111 AAAGGGACAG
22121 CCACTTT-CCACTTT
1 CCACTTTCCCACTTT
22135 CCACTTTCCCACTTT
1 CCACTTTCCCACTTT
22150 TCTTGTGGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.14, C:0.45, G:0.00, T:0.41
Consensus pattern (15 bp):
CCACTTTCCCACTTT
Found at i:25238 original size:22 final size:22
Alignment explanation
Indices: 25194--25238 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25184 TTTTTTGTTC
*
25194 AACCTAAAATATTATAATGTTT
1 AACCTAAAATATTATAATCTTT
*
25216 AACCTAAAA-AGTTATGATCTTT
1 AACCTAAAATA-TTATAATCTTT
25238 A
1 A
25239 TAACATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (22 bp):
AACCTAAAATATTATAATCTTT
Found at i:39490 original size:21 final size:21
Alignment explanation
Indices: 39460--39516 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
39450 GCGAATATGT
39460 AAATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
*
39481 AAATCTCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
*
39502 AAATCGCAATGCGAT
1 AAATCGCAACGCGAT
39517 TTTCAAAGCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.46, C:0.23, G:0.14, T:0.18
Consensus pattern (21 bp):
AAATCGCAACGCGATAATACA
Found at i:40158 original size:20 final size:20
Alignment explanation
Indices: 40133--40181 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40123 GCGATTATCT
40133 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
40153 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
40173 TGTTGCGAT
1 CGTTGCGAT
40182 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:40211 original size:20 final size:20
Alignment explanation
Indices: 40149--40204 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
40139 GATAGTCAAA
* **
40149 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
40169 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
40189 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
40205 ATGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:41559 original size:18 final size:18
Alignment explanation
Indices: 41538--41586 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
41528 CTCCACTTCG
41538 AGAGCCATCACCTCACCC
1 AGAGCCATCACCTCACCC
*
41556 AGAGCCATCACCTCATCC
1 AGAGCCATCACCTCACCC
41574 AGAGCCATCACCT
1 AGAGCCATCACCT
41587 GATCGACCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.45, G:0.12, T:0.14
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:41666 original size:33 final size:34
Alignment explanation
Indices: 41629--41704 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 34
41619 GAATTTGACT
* * *
41629 ATCGCAACGGGATAATTGCAATGC-GAAATAAAA
1 ATCGCAACGGGAAAATAGCAATGCAAAAATAAAA
* *
41662 ATCGCAACGTGAAAATAGCAATGCAAAAATGAAA
1 ATCGCAACGGGAAAATAGCAATGCAAAAATAAAA
41696 ATCGCAACG
1 ATCGCAACG
41705 CAAATTTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 21 0.57
34 16 0.43
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (34 bp):
ATCGCAACGGGAAAATAGCAATGCAAAAATAAAA
Found at i:41694 original size:20 final size:20
Alignment explanation
Indices: 41671--41708 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41661 AATCGCAACG
*
41671 TGAAAATAGCAATGCAAAAA
1 TGAAAATAGCAACGCAAAAA
*
41691 TGAAAATCGCAACGCAAA
1 TGAAAATAGCAACGCAAA
41709 TTTAGTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.16, G:0.16, T:0.13
Consensus pattern (20 bp):
TGAAAATAGCAACGCAAAAA
Found at i:42340 original size:21 final size:21
Alignment explanation
Indices: 42291--42345 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
42281 ACTCATCTAT
*
42291 CATCATTCAAGAGGCCTCTTTC
1 CATCGTTCAAGAGGCCTC-TTC
42313 CATCGTTCAAGAGGCCTC-TC
1 CATCGTTCAAGAGGCCTCTTC
42333 CTATCGTTCAAGA
1 C-ATCGTTCAAGA
42346 AGCCCCTATC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 3 0.10
21 11 0.35
22 17 0.55
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCTCTTC
Found at i:43990 original size:20 final size:20
Alignment explanation
Indices: 43967--44025 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
43957 ACGCTAAACT
43967 CAAAATCGCAATGCGAAAGC
1 CAAAATCGCAATGCGAAAGC
*
43987 CAAAATCGTAATGCGAAAGC
1 CAAAATCGCAATGCGAAAGC
* *
44007 CAAAACCGCAACGCGAAAG
1 CAAAATCGCAATGCGAAAG
44026 TCAATTCGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.46, C:0.25, G:0.20, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGC
Found at i:44110 original size:20 final size:20
Alignment explanation
Indices: 44082--44150 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
44072 GCAATTTTCT
* * *
44082 CGTTACGATTGTCAAATTCC
1 CGTTGCGATAGTCAAATTCA
*
44102 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCA
*
44122 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCA
44142 CGTTGCGAT
1 CGTTGCGAT
44151 TTTTGCGTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCA
Found at i:44153 original size:74 final size:74
Alignment explanation
Indices: 44048--44192 Score: 193
Period size: 74 Copynumber: 2.0 Consensus size: 74
44038 GCGATTTTCG
* * *
44048 CGTTGCGATAGTCTAATACGCTTTGCAATTTTCT-CGTTACGATTGTCAAATTCCCGTTGCGATA
1 CGTTGCGATAGTCAAATACGCGTTGCAATTTT-TGCGTTACGATAGTCAAATTCCCGTTGCGATA
44112 ATCAAATTCA
65 ATCAAATTCA
* * ** * *
44122 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGTGATAGTCAAATTCGCGTTGCGATAT
1 CGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTACGATAGTCAAATTCCCGTTGCGATAA
44187 TCAAAT
66 TCAAAT
44193 GAATGTGTAA
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 1 0.02
74 60 0.98
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATACGCGTTGCAATTTTTGCGTTACGATAGTCAAATTCCCGTTGCGATAA
TCAAATTCA
Found at i:44180 original size:20 final size:20
Alignment explanation
Indices: 44155--44192 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44145 TGCGATTTTT
*
44155 GCGTTGTGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
*
44175 GCGTTGCGATATTCAAAT
1 GCGTTGCGATAGTCAAAT
44193 GAATGTGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:44386 original size:18 final size:18
Alignment explanation
Indices: 44363--44397 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44353 AAGCTGGTTG
*
44363 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
44381 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
44398 GCCTTTTGCT
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:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:46679 original size:24 final size:24
Alignment explanation
Indices: 46645--46698 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
46635 CTGAAACATC
*
46645 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAA
* *
46669 ATCAAAGTCCGGGTATTGACCAAA
1 ATCAAAATCCGAGTATTGACCAAA
46693 ATCAAA
1 ATCAAA
46699 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAA
Found at i:47374 original size:17 final size:17
Alignment explanation
Indices: 47352--47386 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
47342 CGGATGGGGA
47352 AAGATGTCGTTGGATAT
1 AAGATGTCGTTGGATAT
47369 AAGATGTCGTTGGATAT
1 AAGATGTCGTTGGATAT
47386 A
1 A
47387 GGAACGGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (17 bp):
AAGATGTCGTTGGATAT
Found at i:47562 original size:20 final size:20
Alignment explanation
Indices: 47536--47583 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
47526 GAAATTCAGT
47536 GTTGCGATAGCCAGAATCGC
1 GTTGCGATAGCCAGAATCGC
* * *
47556 TTTGCGATAGTCAGAATTGC
1 GTTGCGATAGCCAGAATCGC
47576 GTTGCGAT
1 GTTGCGAT
47584 TTACATATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (20 bp):
GTTGCGATAGCCAGAATCGC
Found at i:47816 original size:2 final size:2
Alignment explanation
Indices: 47809--47866 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
47799 ATTTTATCGA
47809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47851 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
47867 GTGTTGAGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48074 original size:30 final size:30
Alignment explanation
Indices: 48033--48090 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
48023 AGTGACAACC
* *
48033 ATAGGTCTCCAGGAGCACATGGCGACCTCT
1 ATAGGTCTCCAGGAGCACACGACGACCTCT
*
48063 ATAGGTTTCCAGGAGCACACGACGACCT
1 ATAGGTCTCCAGGAGCACACGACGACCT
48091 ATGGAGCACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.19
Consensus pattern (30 bp):
ATAGGTCTCCAGGAGCACACGACGACCTCT
Found at i:48164 original size:38 final size:38
Alignment explanation
Indices: 48108--48185 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
48098 ACTTGGCGAC
**
48108 CTATAGAGCTGCAACAGCGAGGGAAGAGGGAAGAGTTG
1 CTATAGAGCTGCAACAGCGAGGGAAGAGAAAAGAGTTG
*
48146 CTATGGAGCTGCAACAGCGAGGGAAGAGAAAAGAGTTG
1 CTATAGAGCTGCAACAGCGAGGGAAGAGAAAAGAGTTG
48184 CT
1 CT
48186 GCAACATTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.37, T:0.14
Consensus pattern (38 bp):
CTATAGAGCTGCAACAGCGAGGGAAGAGAAAAGAGTTG
Found at i:55362 original size:7 final size:7
Alignment explanation
Indices: 55350--55377 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
55340 TGGCTCCACC
55350 GCTCCAG
1 GCTCCAG
55357 GCTCCAG
1 GCTCCAG
55364 GCTCCAG
1 GCTCCAG
55371 GCTCCAG
1 GCTCCAG
55378 CCAACTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (7 bp):
GCTCCAG
Found at i:64887 original size:24 final size:26
Alignment explanation
Indices: 64832--64887 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
64822 CTCGAACTCA
* *
64832 AAAAAATTTAGAAGTTCGATTGAAGC
1 AAAAAATTTAGAAGATCAATTGAAGC
**
64858 CTAAAATTT-G-AGATCAATTGAAGC
1 AAAAAATTTAGAAGATCAATTGAAGC
64882 AAAAAA
1 AAAAAA
64888 ATAATTCGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
24 16 0.67
25 1 0.04
26 7 0.29
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (26 bp):
AAAAAATTTAGAAGATCAATTGAAGC
Found at i:66440 original size:25 final size:25
Alignment explanation
Indices: 66412--66493 Score: 66
Period size: 25 Copynumber: 3.3 Consensus size: 25
66402 AATGTATGAG
66412 ATGCTAACTTATCTTCCCAAAAGCA
1 ATGCTAACTTATCTTCCCAAAAGCA
* *
66437 ATGCTAA--TATACAT-CCACAAAGAA
1 ATGCTAACTTAT-CTTCCCA-AAAGCA
*
66461 AT-AT-ACATGTATCTTCCCAAAAGCA
1 ATGCTAAC-T-TATCTTCCCAAAAGCA
66486 ATGCTAAC
1 ATGCTAAC
66494 ATATTTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
22 1 0.02
23 7 0.17
24 9 0.21
25 16 0.38
26 7 0.17
27 2 0.05
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (25 bp):
ATGCTAACTTATCTTCCCAAAAGCA
Found at i:71984 original size:16 final size:15
Alignment explanation
Indices: 71945--71985 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
71935 GAATCTGGGT
71945 AAAAGATTTTAGAAA
1 AAAAGATTTTAGAAA
71960 AAAAGATTTTAGAAA
1 AAAAGATTTTAGAAA
*
71975 AAAAGAATTTA
1 AAAAGATTTTA
71986 TAGTGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (15 bp):
AAAAGATTTTAGAAA
Found at i:72573 original size:22 final size:21
Alignment explanation
Indices: 72548--72590 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
72538 TATTTTACTA
*
72548 TATTATAATAAATGTTTATTAT
1 TATTATAATAAAT-TGTATTAT
* *
72570 TATTTTATTAAATTGTATTAT
1 TATTATAATAAATTGTATTAT
72591 GTTATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (21 bp):
TATTATAATAAATTGTATTAT
Found at i:74212 original size:19 final size:19
Alignment explanation
Indices: 74188--74228 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
74178 ATCTTGCATG
*
74188 GGGGGTATCGGTACCCTCT
1 GGGGGTATCGATACCCTCT
74207 GGGGGTATCGATACCCTCT
1 GGGGGTATCGATACCCTCT
74226 GGG
1 GGG
74229 CAATCTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.12, C:0.24, G:0.39, T:0.24
Consensus pattern (19 bp):
GGGGGTATCGATACCCTCT
Found at i:74891 original size:14 final size:15
Alignment explanation
Indices: 74859--74891 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
74849 TTAACAATTC
74859 AAAGTTCTAAATCTG
1 AAAGTTCTAAATCTG
74874 -AAGTTCTAAATC-G
1 AAAGTTCTAAATCTG
74887 AAAGT
1 AAAGT
74892 AGGCAAGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (15 bp):
AAAGTTCTAAATCTG
Done.