Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002756.1 Hibiscus syriacus cultivar Beakdansim tig00005682_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: 44323
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1632 original size:15 final size:15
Alignment explanation
Indices: 1612--1641 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1602 TTAAAGTTAT
*
1612 GAAAAGTATATGAAA
1 GAAAAGAATATGAAA
1627 GAAAAGAATATGAAA
1 GAAAAGAATATGAAA
1642 ATGAAAATAA
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:0.63, C:0.00, G:0.20, T:0.17
Consensus pattern (15 bp):
GAAAAGAATATGAAA
Found at i:8753 original size:17 final size:17
Alignment explanation
Indices: 8729--8765 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
8719 TCTTTTGAAT
8729 TTCTT-TTTTT-TCTAA
1 TTCTTCTTTTTGTCTAA
*
8744 TTCTTCTTTTTGTCTTA
1 TTCTTCTTTTTGTCTAA
8761 TTCTT
1 TTCTT
8766 TTCTTTTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 5 0.26
17 9 0.47
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (17 bp):
TTCTTCTTTTTGTCTAA
Found at i:10338 original size:15 final size:16
Alignment explanation
Indices: 10318--10360 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
10308 AGTTATCTTC
10318 ATAATAACTATAGAT-
1 ATAATAACTATAGATG
10333 ATAATATA-TATAGATG
1 ATAATA-ACTATAGATG
*
10349 AAAATAACTATA
1 ATAATAACTATA
10361 TTAAAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.33
Consensus pattern (16 bp):
ATAATAACTATAGATG
Found at i:13268 original size:20 final size:21
Alignment explanation
Indices: 13231--13269 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13221 TAGGGTTTGA
13231 GTATCGATACTGGGATGAACG
1 GTATCGATACTGGGATGAACG
13252 GTATCGATACT-GGATGAA
1 GTATCGATACTGGGATGAA
13270 TTGAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (21 bp):
GTATCGATACTGGGATGAACG
Found at i:14907 original size:34 final size:34
Alignment explanation
Indices: 14869--14941 Score: 80
Period size: 34 Copynumber: 2.1 Consensus size: 34
14859 ACAAAAATCG
*
14869 AATAAA-AAAGAATTAATAATA-ATAATGATAAAA-T
1 AATAAATAAA-AATAAATAATATATAAT-A-AAAACT
*
14903 AATAAATGAAAATAAATAATATATAATAAAAACT
1 AATAAATAAAAATAAATAATATATAATAAAAACT
14937 AATAA
1 AATAA
14942 TATGTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 4 0.12
34 23 0.68
35 7 0.21
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.26
Consensus pattern (34 bp):
AATAAATAAAAATAAATAATATATAATAAAAACT
Found at i:14990 original size:23 final size:24
Alignment explanation
Indices: 14959--15009 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
14949 TCAAAAAGAA
* *
14959 AAAATTATATATTATATATG-TTT
1 AAAACTATATATTATACATGCTTT
14982 AAAACTATATATTATACATGCTTT
1 AAAACTATATATTATACATGCTTT
15006 AAAA
1 AAAA
15010 AAATGTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
AAAACTATATATTATACATGCTTT
Found at i:15049 original size:38 final size:37
Alignment explanation
Indices: 14983--15189 Score: 121
Period size: 38 Copynumber: 5.7 Consensus size: 37
14973 TATATGTTTA
* * * *
14983 AAACTATATATTATACATGCTTTAAAAAAATGTTTTC
1 AAACTATATAATATATATGTTTTCAAAAAATGTTTTC
* **
15020 GAAACTATATAATATATATATTTTCAAAAAAAAATTTTC
1 -AAACTATATAATATATATGTTTTC-AAAAAATGTTTTC
* *
15059 AAATCTATAT-A-ATATA---TTTCAAAAATTGTTTTTG
1 AAA-CTATATAATATATATGTTTTCAAAAAATG-TTTTC
* * * **
15093 AAATTATAT-AT-TATACGTTTTTAAAAATAAATTTTC
1 AAACTATATAATATATATGTTTTCAAAAA-ATGTTTTC
* **
15129 AACACTATATAATATATATGTCTTCAAAATTTGTTTTC
1 AA-ACTATATAATATATATGTTTTCAAAAAATGTTTTC
15167 AAA--ACTAT-A-ATATATGTTTTCAA
1 AAACTA-TATAATATATATGTTTTCAA
15190 TTTTTTTTAA
Statistics
Matches: 131, Mismatches: 26, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
33 15 0.11
34 24 0.18
35 2 0.02
36 17 0.13
37 12 0.09
38 32 0.24
39 29 0.22
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
AAACTATATAATATATATGTTTTCAAAAAATGTTTTC
Found at i:15137 original size:70 final size:72
Alignment explanation
Indices: 15007--15145 Score: 185
Period size: 70 Copynumber: 2.0 Consensus size: 72
14997 ACATGCTTTA
*
15007 AAAAAATGTTTTCGAAACTATATAATATATATATTTTCAAAAAAAAATTTTCAAATCTATATAAT
1 AAAAAATGTTTTCGAAACTATATAATATATACATTTTCAAAAAAAAATTTTCAAATCTATATAAT
15072 ATATTTC
66 ATATTTC
* * * * * *
15079 AAAAATTGTTTTTGAAATTATAT-AT-TATACGTTTTTAAAAATAAATTTTCAACA-CTATATAA
1 AAAAAATGTTTTCGAAACTATATAATATATACATTTTCAAAAAAAAATTTTCAA-ATCTATATAA
15141 TATAT
65 TATAT
15146 ATGTCTTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
70 36 0.61
71 3 0.05
72 20 0.34
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (72 bp):
AAAAAATGTTTTCGAAACTATATAATATATACATTTTCAAAAAAAAATTTTCAAATCTATATAAT
ATATTTC
Found at i:15205 original size:31 final size:32
Alignment explanation
Indices: 15142--15219 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
15132 ACTATATAAT
*
15142 ATATATGTCTTCAAAATTTGTTTTCAAAACTATA
1 ATATATGTTTTC--AATTTGTTTTCAAAACTATA
*
15176 ATATATGTTTTCAATTT-TTTTTAAAACTATA
1 ATATATGTTTTCAATTTGTTTTCAAAACTATA
* *
15207 TTATACGTTTTCA
1 ATATATGTTTTCA
15220 TAAACATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.60
32 5 0.12
34 11 0.28
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (32 bp):
ATATATGTTTTCAATTTGTTTTCAAAACTATA
Found at i:15314 original size:72 final size:73
Alignment explanation
Indices: 15190--15357 Score: 175
Period size: 72 Copynumber: 2.3 Consensus size: 73
15180 ATGTTTTCAA
* * *
15190 TTTTTTTTAAAA-C-TATATTATACGTTTTCATAAACATTTTCAAAAAAAATATATTATACGTTT
1 TTTTTTTTAAAACCATATATTATACATTTTCA-AAACATTTTCAAAAAAAATATATAATACATTT
*
15253 TCAAAAATG
65 TCAAAAACG
* * * *
15262 TTTTTTTTAAAACCATATATTATTCATTTTC-AAA-TTTTTTAAAAAATTATATATAATACATTT
1 TTTTTTTTAAAACCATATATTATACATTTTCAAAACATTTTCAAAAAA-AATATATAATACATTT
*
15325 TCAAAACCG
65 TCAAAAACG
* *
15334 -CTTTTTAAAAACCTATATATTATA
1 TTTTTTTTAAAACC-ATATATTATA
15358 TGTGTTCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
71 21 0.26
72 44 0.55
73 1 0.01
74 14 0.17
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (73 bp):
TTTTTTTTAAAACCATATATTATACATTTTCAAAACATTTTCAAAAAAAATATATAATACATTTT
CAAAAACG
Found at i:30941 original size:12 final size:12
Alignment explanation
Indices: 30924--30951 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30914 CCTAAATACC
30924 TTTGTTTGAAAT
1 TTTGTTTGAAAT
30936 TTTGTTTGAAAT
1 TTTGTTTGAAAT
30948 TTTG
1 TTTG
30952 GCTTTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (12 bp):
TTTGTTTGAAAT
Found at i:30961 original size:21 final size:21
Alignment explanation
Indices: 30935--30984 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
30925 TTGTTTGAAA
30935 TTTTGTTTGAAATTTTGGCTT
1 TTTTGTTTGAAATTTTGGCTT
****
30956 TTTTGTTTTTTTTTTTGGCTT
1 TTTTGTTTGAAATTTTGGCTT
30977 TTTTGTTT
1 TTTTGTTT
30985 TTGTTTTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.04, G:0.16, T:0.74
Consensus pattern (21 bp):
TTTTGTTTGAAATTTTGGCTT
Found at i:30979 original size:15 final size:13
Alignment explanation
Indices: 30954--31000 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
30944 AAATTTTGGC
30954 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
*
30967 TTTTTGGCTTTTTT
1 TTTTTTG-TTTTTT
*
30981 GTTTTTGTTTTTAT
1 TTTTTTGTTTTT-T
30995 TTTTTT
1 TTTTTT
31001 AAAAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
13 11 0.39
14 17 0.61
ACGTcount: A:0.02, C:0.02, G:0.11, T:0.85
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:30985 original size:21 final size:21
Alignment explanation
Indices: 30947--30992 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
30937 TTGTTTGAAA
*
30947 TTTTGGCTTTTTTGTTTTTTT
1 TTTTGGCTTTTTTGTTTTTGT
30968 TTTTGGCTTTTTTGTTTTTGT
1 TTTTGGCTTTTTTGTTTTTGT
30989 TTTT
1 TTTT
30993 ATTTTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.00, C:0.04, G:0.15, T:0.80
Consensus pattern (21 bp):
TTTTGGCTTTTTTGTTTTTGT
Found at i:34158 original size:6 final size:6
Alignment explanation
Indices: 34140--34179 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
34130 ATAAAACATA
*
34140 ATAATT ATGATT ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAATT ATAATT ATAA
34180 GGAGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (6 bp):
ATAATT
Found at i:35652 original size:21 final size:21
Alignment explanation
Indices: 35623--35667 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35613 ATTCTGACAA
35623 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
35644 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
35665 TCG
1 TCG
35668 TAAAGCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:35991 original size:20 final size:20
Alignment explanation
Indices: 35672--35989 Score: 476
Period size: 20 Copynumber: 15.8 Consensus size: 20
35662 AATTCGTAAA
* *
35672 GCGAATACGTAAATCGCAAC
1 GCGAATACGTAAATCGCGAT
** * *
35692 GCGAATTTGGAAAATCGCAAT
1 GCGAA-TACGTAAATCGCGAT
*
35713 GCGATTACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35733 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35753 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35773 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35793 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35813 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35833 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
*
35853 GCGATTACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
*
35873 GCGATTACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
35893 GCGAATACGTAAATCGCGAT
1 GCGAATACGTAAATCGCGAT
* *
35913 GCGATTACGTAAATCGCAAT
1 GCGAATACGTAAATCGCGAT
* * *
35933 GCGATTACGTAAATCACAAT
1 GCGAATACGTAAATCGCGAT
*
35953 GCGAATACGTAAATCGCAAT
1 GCGAATACGTAAATCGCGAT
35973 GCGAAT-CTGTAAATCGC
1 GCGAATAC-GTAAATCGC
35990 AACGAGATTC
Statistics
Matches: 279, Mismatches: 17, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
19 1 0.00
20 263 0.94
21 15 0.05
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (20 bp):
GCGAATACGTAAATCGCGAT
Found at i:36001 original size:20 final size:20
Alignment explanation
Indices: 35961--36001 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
35951 ATGCGAATAC
* *
35961 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
35981 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
36001 G
1 G
36002 ACTATCGCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:36898 original size:24 final size:24
Alignment explanation
Indices: 36847--36900 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36837 GTATTCAAAA
*
36847 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
36871 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
36895 TTTGAT
1 TTTGAT
36901 GATTTTTCAG
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:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:39333 original size:20 final size:20
Alignment explanation
Indices: 39308--39396 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
39298 CAACGCGGAA
39308 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
39328 ATCGCAACACGGAAATAACT
1 ATCGCAACGCGGAAATGACT
* * *
39348 ATCACAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
39368 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
39388 ATTGCAACG
1 ATCGCAACG
39397 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 54 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:39423 original size:19 final size:19
Alignment explanation
Indices: 39401--39446 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39391 GCAACGAGAG
39401 AATCGCAATGCAAAATGAA
1 AATCGCAATGCAAAATGAA
* *
39420 AATCGCAATGCGAAATTAA
1 AATCGCAATGCAAAATGAA
39439 AATCGCAA
1 AATCGCAA
39447 CGAGTGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.50, C:0.17, G:0.15, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCAAAATGAA
Found at i:39447 original size:52 final size:53
Alignment explanation
Indices: 39391--39490 Score: 166
Period size: 53 Copynumber: 1.9 Consensus size: 53
39381 AATGACTATT
* *
39391 GCAACGAGAGAATCGCAATGC-AAAATGAAAATCGCAATGCGAAATTAAAATC
1 GCAACGAGAGAATCGCAATGCGAAAATGAAAATCACAACGCGAAATTAAAATC
*
39443 GCAACGAGTGAATCGCAATGCGAAAATGAAAATCACAACGCGAAATTA
1 GCAACGAGAGAATCGCAATGCGAAAATGAAAATCACAACGCGAAATTA
39491 GTTTCGCGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 20 0.45
53 24 0.55
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (53 bp):
GCAACGAGAGAATCGCAATGCGAAAATGAAAATCACAACGCGAAATTAAAATC
Found at i:39554 original size:33 final size:34
Alignment explanation
Indices: 39497--39589 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
39487 ATTAGTTTCG
39497 CGTTGCGATTTTCATTTTCGCATTGCGATTCA-CT
1 CGTTGCGATTTTCATTTTCGCATTGCGATT-ATCT
*
39531 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
** *
39564 CGTTGCGATAGTCATTTCCGCATTGC
1 CGTTGCGATTTTCATTTTCGCATTGC
39590 AATAGTCATT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
32 1 0.02
33 28 0.54
34 23 0.44
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
Found at i:39594 original size:20 final size:20
Alignment explanation
Indices: 39566--39616 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
39556 GATTATCTCG
39566 TTGCGATAGTCATTTCCGCA
1 TTGCGATAGTCATTTCCGCA
* *
39586 TTGCAATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCA
39606 TTGCGATAGTC
1 TTGCGATAGTC
39617 TGTTTTGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCA
Found at i:41574 original size:20 final size:20
Alignment explanation
Indices: 41549--41590 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
41539 TGAACTTAAA
41549 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
41569 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
41589 AT
1 AT
41591 GCGAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:41655 original size:67 final size:68
Alignment explanation
Indices: 41546--41676 Score: 187
Period size: 67 Copynumber: 1.9 Consensus size: 68
41536 TACTGAACTT
41546 AAAATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATGCGAAATGA-A-AATCGCAA
1 AAAATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTAT-CGAAATGAGAGAATCGCAA
41609 CAAC
65 CAAC
* * * *
41613 AAAATCGTAACGCGAAAATGACTATCGCAATGC-AAATTTGACTATCGCAATGAGAGAATCGCAA
1 AAAATCGCAACGCGAAAATGACTATCGCAACGCGAAA-ATGACTATCGAAATGAGAGAATCGCAA
41677 TGCGATTTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
66 10 0.18
67 39 0.68
68 8 0.14
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (68 bp):
AAAATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGAAATGAGAGAATCGCAAC
AAC
Found at i:41738 original size:20 final size:20
Alignment explanation
Indices: 41713--41791 Score: 113
Period size: 20 Copynumber: 4.0 Consensus size: 20
41703 CTTTCGTTGC
**
41713 GATAGTCAAATTCACATTGT
1 GATAGTCATTTTCACATTGT
* *
41733 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCACATTGT
*
41753 GATAGTCATTTTCGCATTGT
1 GATAGTCATTTTCACATTGT
41773 GATAGTCATTTTCACATTG
1 GATAGTCATTTTCACATTG
41792 CAATTCTCTC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (20 bp):
GATAGTCATTTTCACATTGT
Found at i:41757 original size:40 final size:40
Alignment explanation
Indices: 41709--41792 Score: 132
Period size: 40 Copynumber: 2.1 Consensus size: 40
41699 GATTCTTTCG
*
41709 TTGCGATAGTCAAATTCACATTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCACATTGTGATAGTCATTTTCACA
** *
41749 TTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCACA
1 TTGCGATAGTCAAATTCACATTGTGATAGTCATTTTCACA
41789 TTGC
1 TTGC
41793 AATTCTCTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (40 bp):
TTGCGATAGTCAAATTCACATTGTGATAGTCATTTTCACA
Found at i:41827 original size:20 final size:20
Alignment explanation
Indices: 41801--41852 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
41791 GCAATTCTCT
41801 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
41821 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
41841 CATTGCGATAGT
1 CGTTGCGATAGT
41853 AAACTATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:42245 original size:6 final size:6
Alignment explanation
Indices: 42234--42262 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42224 ACTCATCCCA
42234 TGGAGG TGGAGG TGGAGG TGGAGG TGGAG
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAG
42263 AATAGGGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.66, T:0.17
Consensus pattern (6 bp):
TGGAGG
Found at i:43765 original size:20 final size:20
Alignment explanation
Indices: 43720--43787 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
43710 GAAACTTTAA
**
43720 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
*
43740 AGCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
43760 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
43780 ATCGCAAC
1 ATCGCAAC
43788 GCAAGAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.18, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:43858 original size:20 final size:20
Alignment explanation
Indices: 43833--43879 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
43823 GATTCTCTCG
43833 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
43853 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
43873 TTGCGAT
1 TTGCGAT
43880 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Done.