Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000853.1 Hibiscus syriacus cultivar Beakdansim tig00001655_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: 42742
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1255 original size:13 final size:13
Alignment explanation
Indices: 1221--1255 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1211 GATTGTTTAA
1221 TTGATTGTAAAAG
1 TTGATTGTAAAAG
*
1234 GTGATTTGTAAAAG
1 TTGA-TTGTAAAAG
1248 TTGATTGT
1 TTGATTGT
1256 TTAATTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.26, T:0.43
Consensus pattern (13 bp):
TTGATTGTAAAAG
Found at i:1506 original size:19 final size:18
Alignment explanation
Indices: 1482--1538 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
1472 CGAATTAGCG
1482 TTGCGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
*
1501 TTGCGA-TTC-TCTCG--
1 TTGCGATTTCATTTCGCA
1515 -TGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
1532 TTGCGAT
1 TTGCGAT
1539 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 5 0.16
14 3 0.10
15 4 0.13
16 4 0.13
17 3 0.10
18 6 0.19
19 6 0.19
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:1537 original size:63 final size:63
Alignment explanation
Indices: 1411--1537 Score: 195
Period size: 63 Copynumber: 2.0 Consensus size: 63
1401 CGCGAAATTA
* *
1411 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCATTTTCATTTCGTATGCG
1 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCATTTTCATTTCGCATGCG
*
1474 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCG-TGCGA-TTTCATTTCGCATTGCG
1 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGC-ATTTTCATTTCGCA-TGCG
1537 A
1 A
1538 TAGTAATTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
62 14 0.24
63 45 0.76
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (63 bp):
AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCATTTTCATTTCGCATGCG
Found at i:1538 original size:31 final size:33
Alignment explanation
Indices: 1417--1538 Score: 164
Period size: 31 Copynumber: 3.8 Consensus size: 33
1407 ATTAAATTCG
*
1417 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* * **
1450 CGTTGC-ATTTTCATTTCGTA-TGCGAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1480 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1513 CG-TGCGA-TTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1539 AGTAATTTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
30 6 0.08
31 38 0.49
32 24 0.31
33 9 0.12
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:4018 original size:24 final size:24
Alignment explanation
Indices: 3984--4037 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
3974 TCTGAAACAC
*
3984 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
4008 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
4032 ATCAAA
1 ATCAAA
4038 TTTCGATACT
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:4787 original size:20 final size:20
Alignment explanation
Indices: 4762--4812 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
4752 TGTATTATCT
4762 CGTTGCGAAAGACAGAATCG
1 CGTTGCGAAAGACAGAATCG
*
4782 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGACAGAATCG
4802 CGTTGCGAAAG
1 CGTTGCGAAAG
4813 GCAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (20 bp):
CGTTGCGAAAGACAGAATCG
Found at i:5061 original size:19 final size:20
Alignment explanation
Indices: 5023--5072 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5013 ATTCATTTGA
*
5023 CTATCGCAATGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
5043 CTATCGCAACGTG-AAATGG
1 CTATCGCAACGCGAAAATGG
*
5062 CTATCACAACG
1 CTATCGCAACG
5073 ACAAAATCGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:5122 original size:14 final size:14
Alignment explanation
Indices: 5103--5156 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
5093 GAAAATCGCA
5103 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
5117 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
5134 CATTGCGATTCTCTCG
1 --TTGCGATTTTCTCG
5150 TTGCGAT
1 TTGCGAT
5157 AGTCAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:5122 original size:33 final size:33
Alignment explanation
Indices: 5085--5155 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
5075 AAAATCGCAA
*
5085 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
** ** **
5118 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
5151 TGCGA
1 TGCGA
5156 TAGTCAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTCTCTCGT
Found at i:5286 original size:14 final size:14
Alignment explanation
Indices: 5269--5305 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
5259 ACATCATTAA
5269 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
5283 ACAAATCATCTTTT
1 ACAAATCAACATTT
5297 ACAAATCAA
1 ACAAATCAA
5306 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:7189 original size:20 final size:20
Alignment explanation
Indices: 7166--7219 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
7156 GAAACTTAAA
7166 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
7186 ATCGCAACGCTG-AAATGGCT
1 ATCGCAACGC-GAAAATGACT
* *
7206 ATCGTAATGCGAAA
1 ATCGCAACGCGAAA
7220 TAAAATCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:7286 original size:19 final size:18
Alignment explanation
Indices: 7236--7286 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
7226 CGCAACGACA
**
7236 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
7254 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
7273 AAATCGCATTGCGA
1 AAATCGCAATGCGA
7287 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:7317 original size:14 final size:14
Alignment explanation
Indices: 7298--7355 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
7288 TTTCATTTCG
7298 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
7312 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
7328 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
7344 CGTTGCGATTTT
1 CGTTGCGATTTT
7356 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:7328 original size:32 final size:33
Alignment explanation
Indices: 7281--7371 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
7271 ACAAATCGCA
*
7281 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
7314 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
7346 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
7372 AGCCATTTTC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:7407 original size:20 final size:20
Alignment explanation
Indices: 7358--7410 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
7348 GCGATTTTCA
*
7358 TTTCGCATTGCGATAGCCAT
1 TTTCGCGTTGCGATAGCCAT
*
7378 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGCCAT
*
7398 TTTCGTGTTGCGA
1 TTTCGCGTTGCGA
7411 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGCCAT
Found at i:7936 original size:18 final size:18
Alignment explanation
Indices: 7894--7936 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
7884 CGATCAGATG
* *
7894 ATGGCTCTGGGTGAGGTG
1 ATGGCTCTGGGCGAGGTA
*
7912 ATAGCTCTGGGCGAGGTA
1 ATGGCTCTGGGCGAGGTA
7930 ATGGCTC
1 ATGGCTC
7937 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.26
Consensus pattern (18 bp):
ATGGCTCTGGGCGAGGTA
Found at i:9280 original size:20 final size:20
Alignment explanation
Indices: 9255--9293 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9245 AATAGTTTCT
9255 GAAAATGAAAATCGCAACAA
1 GAAAATGAAAATCGCAACAA
**
9275 GAAAATGACTATCGCAACA
1 GAAAATGAAAATCGCAACA
9294 CGAATTTGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.15, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAA
Found at i:9303 original size:20 final size:20
Alignment explanation
Indices: 9265--9332 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
9255 GAAAATGAAA
* **
9265 ATCGCAACAAGAAAATGACT
1 ATCGCAACACGAATTTGACT
9285 ATCGCAACACGAATTTGACT
1 ATCGCAACACGAATTTGACT
*
9305 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAATTTGACT
9325 ATCGCAAC
1 ATCGCAAC
9333 GAGAGAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAACACGAATTTGACT
Found at i:9880 original size:17 final size:17
Alignment explanation
Indices: 9858--9912 Score: 83
Period size: 17 Copynumber: 3.1 Consensus size: 17
9848 GTTGCGATAG
9858 TAAGTATCGCATTGCGA
1 TAAGTATCGCATTGCGA
9875 TAAGTATCGCATTGCGA
1 TAAGTATCGCATTGCGA
9892 TAGTCAGTATCGCATTGCGA
1 TA---AGTATCGCATTGCGA
9912 T
1 T
9913 TTTCCCAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 19 0.54
20 16 0.46
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (17 bp):
TAAGTATCGCATTGCGA
Found at i:9890 original size:37 final size:37
Alignment explanation
Indices: 9840--9912 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
9830 TGCGAAAGTC
* *
9840 AGTATCTCGTTGCGATAGTAAGTATCGCATTGCGATA
1 AGTATCGCATTGCGATAGTAAGTATCGCATTGCGATA
*
9877 AGTATCGCATTGCGATAGTCAGTATCGCATTGCGAT
1 AGTATCGCATTGCGATAGTAAGTATCGCATTGCGAT
9913 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (37 bp):
AGTATCGCATTGCGATAGTAAGTATCGCATTGCGATA
Found at i:9912 original size:20 final size:20
Alignment explanation
Indices: 9782--9912 Score: 135
Period size: 20 Copynumber: 6.7 Consensus size: 20
9772 CGCTTTGAAA
*
9782 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
9803 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
9823 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
9843 ATCTCGTTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
9863 ATCGCATTGCGATA---AGT
1 ATCGCATTGCGATAGTCAGT
9880 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
9900 ATCGCATTGCGAT
1 ATCGCATTGCGAT
9913 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
17 17 0.18
19 2 0.02
20 66 0.69
21 11 0.11
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:10023 original size:21 final size:21
Alignment explanation
Indices: 9983--10023 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9973 ACTGTAGACC
** *
9983 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATACAACT
10004 ATCGCAACGCGAAATACAAC
1 ATCGCAACGCGAAATACAAC
10024 GCGAATTTGC
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:0.37, C:0.32, G:0.15, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATACAACT
Found at i:10887 original size:26 final size:26
Alignment explanation
Indices: 10858--10943 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
10848 TTGACTGATA
10858 ATAATTATCTTATTTGAAAGCAGTAG
1 ATAATTATCTTATTTGAAAGCAGTAG
* *
10884 ATAATTATATTAATAT-ACAA-CTGATTGATA-
1 ATAATTATCTT-ATTTGA-AAGC--A--G-TAG
10914 ATAATTATCTTATTTGAAAGCAGTAG
1 ATAATTATCTTATTTGAAAGCAGTAG
10940 ATAA
1 ATAA
10944 CTCAAGTATG
Statistics
Matches: 46, Mismatches: 4, Indels: 20
0.66 0.06 0.29
Matches are distributed among these distances:
25 2 0.04
26 17 0.37
27 5 0.11
28 2 0.04
29 5 0.11
30 13 0.28
31 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (26 bp):
ATAATTATCTTATTTGAAAGCAGTAG
Found at i:10887 original size:29 final size:29
Alignment explanation
Indices: 10854--10943 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
10844 ACGATTGACT
10854 GATAATAATTATCTTATTTGAAAGCAGTA
1 GATAATAATTATCTTATTTGAAAGCAGTA
* * * * *
10883 GATAATTA-TAT-TAATAT-ACAA-CTGATT
1 GATAATAATTATCTTATTTGA-AAGCAG-TA
10910 GATAATAATTATCTTATTTGAAAGCAGTA
1 GATAATAATTATCTTATTTGAAAGCAGTA
10939 GATAA
1 GATAA
10944 CTCAAGTATG
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
26 3 0.07
27 14 0.31
28 6 0.13
29 19 0.42
30 3 0.07
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (29 bp):
GATAATAATTATCTTATTTGAAAGCAGTA
Found at i:10913 original size:56 final size:56
Alignment explanation
Indices: 10833--10943 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
10823 TTCTAGATTA
* *
10833 TATATTAATATACGATTGACTGATAATAATTATCTTATTTGAAAGCAGTAGATAAT
1 TATATTAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAGTAGATAAT
*
10889 TATATTAATATACAACTGATTGATAATAATTATCTTATTTGAAAGCAGTAGATAA
1 TATATTAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAGTAGATAA
10944 CTCAAGTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (56 bp):
TATATTAATATACAACTGACTGATAATAATTATCTTATTTGAAAGCAGTAGATAAT
Found at i:13790 original size:29 final size:29
Alignment explanation
Indices: 13755--13836 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
13745 AAACTAAATT
*
13755 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
13784 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
13813 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
13837 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:15147 original size:15 final size:15
Alignment explanation
Indices: 15124--15153 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
15114 ACGAGGCTGG
15124 AATTACAACAATAAC
1 AATTACAACAATAAC
*
15139 AATTCCAACAATAAC
1 AATTACAACAATAAC
15154 TATGAGAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTACAACAATAAC
Found at i:18549 original size:29 final size:29
Alignment explanation
Indices: 18514--18595 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
18504 AAACTAAATT
*
18514 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
18543 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
18572 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
18596 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:21737 original size:36 final size:36
Alignment explanation
Indices: 21696--21774 Score: 97
Period size: 36 Copynumber: 2.2 Consensus size: 36
21686 ATTCTATTTT
* *
21696 ATCATT-AAAAATATATTATAATTGAATTATGATATC
1 ATCATTGAAAAATACATT-TAATTGAATTATAATATC
** *
21732 ATCATTGTTATATACATTTAATTGAATTATAATATC
1 ATCATTGAAAAATACATTTAATTGAATTATAATATC
21768 ATCATTG
1 ATCATTG
21775 TTATATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 30 0.81
37 7 0.19
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (36 bp):
ATCATTGAAAAATACATTTAATTGAATTATAATATC
Found at i:21738 original size:19 final size:18
Alignment explanation
Indices: 21706--21782 Score: 56
Period size: 19 Copynumber: 4.3 Consensus size: 18
21696 ATCATTAAAA
* *
21706 ATATATTATAATTGAATT
1 ATATATCATCATTGAATT
21724 ATGATATCATCATTG--TT
1 AT-ATATCATCATTGAATT
*
21741 ATATA-CATTTAATTGAATT
1 ATATATCA--TCATTGAATT
21760 ATAATATCATCATTG--TT
1 AT-ATATCATCATTGAATT
21777 ATATAT
1 ATATAT
21783 ATTTTATGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 16
0.71 0.06 0.24
Matches are distributed among these distances:
15 2 0.04
16 7 0.15
17 13 0.27
18 2 0.04
19 19 0.40
20 3 0.06
21 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (18 bp):
ATATATCATCATTGAATT
Found at i:21775 original size:36 final size:36
Alignment explanation
Indices: 21714--21786 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
21704 AAATATATTA
*
21714 TAATTGAATTATGATATCATCATTGTTATATACATT
1 TAATTGAATTATAATATCATCATTGTTATATACATT
*
21750 TAATTGAATTATAATATCATCATTGTTATATATATT
1 TAATTGAATTATAATATCATCATTGTTATATACATT
21786 T
1 T
21787 TATGATAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (36 bp):
TAATTGAATTATAATATCATCATTGTTATATACATT
Found at i:21795 original size:31 final size:34
Alignment explanation
Indices: 21727--21797 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 34
21717 TTGAATTATG
*
21727 ATATCATCATTGTTATATACATTTAATTGAATTATA
1 ATATCATCATTGTTATATACATTT-ATT-AATGATA
*
21763 ATATCATCATTGTTATATATA-TT-TT-ATGATA
1 ATATCATCATTGTTATATACATTTATTAATGATA
21794 ATAT
1 ATAT
21798 TGATTGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 9 0.27
33 2 0.06
35 2 0.06
36 20 0.61
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (34 bp):
ATATCATCATTGTTATATACATTTATTAATGATA
Found at i:22948 original size:28 final size:27
Alignment explanation
Indices: 22917--22975 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
22907 TGATTTGGAC
* * *
22917 TCACTGTTTTGCGTTCATTTTTATTTAA
1 TCACTGATTTACGTT-ATTTTTAATTAA
*
22945 TCACTGATTTACGTTTTTTTTAATTAA
1 TCACTGATTTACGTTATTTTTAATTAA
22972 -CACT
1 TCACT
22976 AACATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 10 0.37
28 13 0.48
ACGTcount: A:0.22, C:0.15, G:0.08, T:0.54
Consensus pattern (27 bp):
TCACTGATTTACGTTATTTTTAATTAA
Found at i:25268 original size:23 final size:23
Alignment explanation
Indices: 25242--25286 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
25232 TATGACAGCT
*
25242 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
25265 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
25287 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:28381 original size:21 final size:22
Alignment explanation
Indices: 28357--28397 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28347 GATTTGTGCT
28357 GCAAAGTG-AGCAATAATTCAC
1 GCAAAGTGAAGCAATAATTCAC
28378 GCAAAGTGAAGCAATAATTC
1 GCAAAGTGAAGCAATAATTC
28398 GGGTGGACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.20
Consensus pattern (22 bp):
GCAAAGTGAAGCAATAATTCAC
Found at i:28562 original size:26 final size:26
Alignment explanation
Indices: 28526--28577 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
28516 TCGGTTGTAA
* *
28526 GAAGAAGAAAGAAGGGTGAAGGAAAG
1 GAAGAAAAAAGAAAGGTGAAGGAAAG
28552 GAAGAAAAAAGAAAGGTGAAGGAAAG
1 GAAGAAAAAAGAAAGGTGAAGGAAAG
28578 AAAGGTAACC
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:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (26 bp):
GAAGAAAAAAGAAAGGTGAAGGAAAG
Found at i:29550 original size:18 final size:18
Alignment explanation
Indices: 29527--29562 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29517 GGTAAAACCA
29527 GAGTGTAAAGGGTGGCGT
1 GAGTGTAAAGGGTGGCGT
29545 GAGTGTAAAGGGTGGCGT
1 GAGTGTAAAGGGTGGCGT
29563 CTCAAGTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.50, T:0.22
Consensus pattern (18 bp):
GAGTGTAAAGGGTGGCGT
Found at i:31294 original size:21 final size:23
Alignment explanation
Indices: 31241--31298 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
31231 TAAATTTTAT
31241 TTAAATA-TATT--TAATCATTA
1 TTAAATAGTATTAGTAATCATTA
*
31261 TTAAATTATTATTAGTAATCATTA
1 TTAAA-TAGTATTAGTAATCATTA
31285 TT-AA-AGTATTAGTA
1 TTAAATAGTATTAGTA
31299 TCAAATCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 5 0.15
21 11 0.33
22 4 0.12
23 2 0.06
24 11 0.33
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (23 bp):
TTAAATAGTATTAGTAATCATTA
Found at i:31295 original size:27 final size:27
Alignment explanation
Indices: 31252--31500 Score: 293
Period size: 27 Copynumber: 9.3 Consensus size: 27
31242 TAAATATATT
*
31252 TAATCATTATTA-AA-TT-ATTATTAG
1 TAATCATTATTATAATTTCATTATTAC
* *
31276 TAATCATTATTA-AA-GT-ATTAGTATC
1 TAATCATTATTATAATTTCATTATTA-C
*
31301 AAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
*
31328 TAATCATTACTA-AA--TCATTAATATA-
1 TAATCATTATTATAATTTCATT-AT-TAC
* *
31353 AAATCATTATTATAATTTCATTAATAC
1 TAATCATTATTATAATTTCATTATTAC
31380 TAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
31407 TAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
31434 TAATCATTATTATAATTTCATTATTAGTATC
1 TAATCATTATTATAATTTCATTA-T--TA-C
*
31465 AAATCATTATTATAATTTCATTATTAC
1 TAATCATTATTATAATTTCATTATTAC
31492 TAATCATTA
1 TAATCATTA
31501 CTAAATCAAC
Statistics
Matches: 196, Mismatches: 15, Indels: 25
0.83 0.06 0.11
Matches are distributed among these distances:
24 26 0.13
25 23 0.12
26 10 0.05
27 97 0.49
28 14 0.07
30 3 0.02
31 23 0.12
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.48
Consensus pattern (27 bp):
TAATCATTATTATAATTTCATTATTAC
Found at i:31321 original size:14 final size:14
Alignment explanation
Indices: 31304--31495 Score: 172
Period size: 14 Copynumber: 13.9 Consensus size: 14
31294 TAGTATCAAA
31304 TCATTATTATAATT
1 TCATTATTATAATT
31318 TCATTATTACTAA--
1 TCATTATTA-TAATT
*
31331 TCATTACTA-AA--
1 TCATTATTATAATT
* **
31342 TCATTAATATAAAA
1 TCATTATTATAATT
31356 TCATTATTATAATT
1 TCATTATTATAATT
*
31370 TCATTAATACTAA--
1 TCATTATTA-TAATT
31383 TCATTATTATAATT
1 TCATTATTATAATT
31397 TCATTATTACTAA--
1 TCATTATTA-TAATT
31410 TCATTATTATAATT
1 TCATTATTATAATT
31424 TCATTATTACTAA--
1 TCATTATTA-TAATT
31437 TCATTATTATAATT
1 TCATTATTATAATT
**
31451 TCATTATTAGTATCAAA
1 TCATTATTA-TA--ATT
31468 TCATTATTATAATT
1 TCATTATTATAATT
31482 TCATTATTACTAAT
1 TCATTATTA-TAAT
31496 CATTACTAAA
Statistics
Matches: 150, Mismatches: 11, Indels: 33
0.77 0.06 0.17
Matches are distributed among these distances:
11 10 0.07
12 11 0.07
13 34 0.23
14 65 0.43
15 18 0.12
16 2 0.01
17 10 0.07
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.49
Consensus pattern (14 bp):
TCATTATTATAATT
Found at i:33844 original size:28 final size:31
Alignment explanation
Indices: 33784--33849 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
33774 TCATATAATA
33784 TAATATCATATATAACTTAAACTAACAAACAAAC
1 TAATATCATATATAACTTAAACT---AAACAAAC
33818 TAATAT-A-ATATAACTTAAACT-AACAAAC
1 TAATATCATATATAACTTAAACTAAACAAAC
33846 TAAT
1 TAAT
33850 GATTTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 11 0.34
32 14 0.44
33 1 0.03
34 6 0.19
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.29
Consensus pattern (31 bp):
TAATATCATATATAACTTAAACTAAACAAAC
Found at i:33915 original size:25 final size:27
Alignment explanation
Indices: 33877--33927 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
33867 TTTTACCCGG
33877 TCTCTTCTTATCCCTTTC-TTCTTCTT
1 TCTCTTCTTATCCCTTTCTTTCTTCTT
*
33903 TCTC-TCTTCTCCCTTTCTTTCTTCT
1 TCTCTTCTTATCCCTTTCTTTCTTCT
33928 CCCTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (27 bp):
TCTCTTCTTATCCCTTTCTTTCTTCTT
Found at i:33920 original size:15 final size:15
Alignment explanation
Indices: 33890--33941 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
33880 CTTCTTATCC
*
33890 CTTTCTTCT-TCTTT
1 CTTTCTTCTCCCTTT
*
33904 CTCTCTTCTCCCTTT
1 CTTTCTTCTCCCTTT
33919 CTTTCTTCTCCCTTT
1 CTTTCTTCTCCCTTT
33934 CTTTCTTC
1 CTTTCTTC
33942 ATAACCGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 8 0.24
15 26 0.76
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
CTTTCTTCTCCCTTT
Found at i:34495 original size:30 final size:31
Alignment explanation
Indices: 34425--34496 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
34415 CACTATAAGG
*
34425 TCGCCCCGACTGCATGGCGACCTACAAGGGCT
1 TCGCCCCGACTGCATGGCGACCTACAA-GGAT
*
34457 TCGCCCCGACTGCATGGCGACCTTCAA-GAT
1 TCGCCCCGACTGCATGGCGACCTACAAGGAT
*
34487 TTGCCCCGAC
1 TCGCCCCGAC
34497 AGTATGGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 11 0.30
32 26 0.70
ACGTcount: A:0.18, C:0.39, G:0.25, T:0.18
Consensus pattern (31 bp):
TCGCCCCGACTGCATGGCGACCTACAAGGAT
Found at i:36097 original size:31 final size:31
Alignment explanation
Indices: 36062--36124 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
36052 ACGAATTCGA
36062 GATGTCCAAGCATGGAAGCAACGTGCAATGG
1 GATGTCCAAGCATGGAAGCAACGTGCAATGG
36093 GATGTCCAAGCATGGAAGCAACGTGCAATGG
1 GATGTCCAAGCATGGAAGCAACGTGCAATGG
36124 G
1 G
36125 GTTTCAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.33, T:0.16
Consensus pattern (31 bp):
GATGTCCAAGCATGGAAGCAACGTGCAATGG
Found at i:37709 original size:21 final size:21
Alignment explanation
Indices: 37685--37724 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37675 ATGTTTAATG
37685 AAAAAGATA-CTAATTGTTAAC
1 AAAAAGATATC-AATTGTTAAC
*
37706 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
37725 CCAAGTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:39299 original size:15 final size:15
Alignment explanation
Indices: 39281--39315 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39271 GTTTTTCTCC
*
39281 TCTTCCTTTTCTTCA
1 TCTTCCCTTTCTTCA
39296 TCTTCCCTTTCTTCA
1 TCTTCCCTTTCTTCA
39311 TCTTC
1 TCTTC
39316 ATTCACCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.37, G:0.00, T:0.57
Consensus pattern (15 bp):
TCTTCCCTTTCTTCA
Found at i:40352 original size:34 final size:33
Alignment explanation
Indices: 40291--40361 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
40281 CCTTTACAAC
*
40291 TCCCTAGTTTTTCACGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACACGGGATAAACTAGAACCTT
* * *
40324 TCCCTAGCTTTTACACGGGCTTAGCTAGAACCTT
1 TCCCTAG-TTTTACACGGGATAAACTAGAACCTT
40358 TCCC
1 TCCC
40362 CTTTACAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (33 bp):
TCCCTAGTTTTACACGGGATAAACTAGAACCTT
Found at i:40598 original size:20 final size:22
Alignment explanation
Indices: 40573--40612 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40563 AGTCGTATAT
40573 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
40593 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
40613 TATACAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:41626 original size:15 final size:16
Alignment explanation
Indices: 41601--41634 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41591 AATATTCTAA
41601 ACTGAGTAGTATCGAT
1 ACTGAGTAGTATCGAT
*
41617 ACTG-GTAGTATCGGT
1 ACTGAGTAGTATCGAT
41632 ACT
1 ACT
41635 ACCCAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (16 bp):
ACTGAGTAGTATCGAT
Done.