Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002168.1 Hibiscus syriacus cultivar Beakdansim tig00004424_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: 56004
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.34
Found at i:1277 original size:33 final size:32
Alignment explanation
Indices: 1233--1345 Score: 199
Period size: 33 Copynumber: 3.5 Consensus size: 32
1223 TCTTTTGGTT
1233 GAAATGAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAATCGCAACGAGAGAATCGCAACGC
*
1265 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-AATCGCAACGAGAGAATCGCAACGC
1298 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGA-AATCGCAACGAGAGAATCGCAACGC
1331 GAAATGAAATCGCAA
1 GAAATGAAATCGCAA
1346 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 14 0.18
33 64 0.82
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (32 bp):
GAAATGAAATCGCAACGAGAGAATCGCAACGC
Found at i:1278 original size:19 final size:18
Alignment explanation
Indices: 1236--1350 Score: 101
Period size: 14 Copynumber: 6.9 Consensus size: 18
1226 TTTGGTTGAA
1236 ATGAAATCGCAA--CGAG
1 ATGAAATCGCAACGCGAG
1252 A-G-AATCGCAACGCGAG
1 ATGAAATCGCAACGCGAG
1268 ATGACAATCGCAA--CGAG
1 ATGA-AATCGCAACGCGAG
*
1285 A-G-AATCGCAACGCGAA
1 ATGAAATCGCAACGCGAG
1301 ATGACAATCGCAA--CGAG
1 ATGA-AATCGCAACGCGAG
*
1318 A-G-AATCGCAACGCGAA
1 ATGAAATCGCAACGCGAG
*
1334 ATGAAATCGCAATGCGA
1 ATGAAATCGCAACGCGA
1351 TTTTGGTTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
14 24 0.30
15 1 0.01
16 16 0.20
17 12 0.15
18 12 0.15
19 16 0.20
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (18 bp):
ATGAAATCGCAACGCGAG
Found at i:1381 original size:14 final size:14
Alignment explanation
Indices: 1362--1418 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1352 TTTGGTTTCG
1362 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1376 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1395 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1409 CGTTGCGATT
1 CGTTGCGATT
1419 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1394 original size:33 final size:33
Alignment explanation
Indices: 1346--1426 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1336 GAAATCGCAA
**
1346 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1379 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1412 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
1427 TCTCGTTGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1429 original size:21 final size:21
Alignment explanation
Indices: 1403--1479 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
1393 CGCGTTGCGA
1403 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
1424 TTCTCTCGTTGGCGACAGTCA-
1 TTCTCTCGTT-GCGATTGTCAT
*
1445 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
1466 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1480 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.15
21 33 0.69
22 8 0.17
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:1466 original size:42 final size:41
Alignment explanation
Indices: 1402--1480 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
1392 TCGCGTTGCG
*
1402 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTT-GCGACAGTC
*
1444 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
1481 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 5 0.14
42 30 0.86
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:1622 original size:32 final size:33
Alignment explanation
Indices: 1557--1626 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
1547 AATACTAACT
* *
1557 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1590 TGAAAATCGCAACGACA-AATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1622 TGAAA
1 TGAAA
1627 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:2019 original size:39 final size:40
Alignment explanation
Indices: 1976--2057 Score: 96
Period size: 40 Copynumber: 2.1 Consensus size: 40
1966 TACGCGTAGC
*
1976 GATTATAATGGCGCTTTA-A-ATATCGCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGAT-TCGCGTTGCGATTTACG
** * *
2015 GATTATCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
2055 GAT
1 GAT
2058 CGCGTTGCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.39
40 20 0.56
41 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.38
Consensus pattern (40 bp):
GATTATAATGGCGATTTACAGATTCGCGTTGCGATTTACG
Found at i:2026 original size:20 final size:19
Alignment explanation
Indices: 2000--2167 Score: 160
Period size: 20 Copynumber: 8.6 Consensus size: 19
1990 TTTAAATATC
2000 GCGTTGCGATTTACGGATTA
1 GCGTTGCGATTTACGGA-TA
* * *
2020 TCGTTGCGATTTACAGATTC
1 GCGTTGCGATTTACGGA-TA
* *
2040 TCGTTGCGATTTACGGATC
1 GCGTTGCGATTTACGGATA
*
2059 GCGTTGCGATATACGGATA
1 GCGTTGCGATTTACGGATA
* **
2078 CGCATTGCGA-TTACCCATA
1 -GCGTTGCGATTTACGGATA
2097 CGCGTTGCGATTTACGGATA
1 -GCGTTGCGATTTACGGATA
2117 -CGTTGCGATTTACGGATA
1 GCGTTGCGATTTACGGATA
* * *
2135 CGCGTTGCGATTTATGTGTTC
1 -GCGTTGCGATTTACG-GATA
2156 GCGTTGCGATTT
1 GCGTTGCGATTT
2168 TCATATTCGC
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
18 18 0.14
19 33 0.26
20 73 0.58
21 2 0.02
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.35
Consensus pattern (19 bp):
GCGTTGCGATTTACGGATA
Found at i:2086 original size:39 final size:39
Alignment explanation
Indices: 2003--2148 Score: 174
Period size: 39 Copynumber: 3.8 Consensus size: 39
1993 AAATATCGCG
* * * *
2003 TTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 TTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACGC
*
2042 GTTGCGATTTACGGAT-CGCGTTGCGATATACGGATACGC
1 -TTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
**
2081 ATTGCGA-TTACCCATACGCGTTGCGATTTACGGATACG-
1 -TTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
2119 TTGCGATTTACGGATACGCGTTGCGATTTA
1 TTGCGATTTACGGATACGCGTTGCGATTTA
2149 TGTGTTCGCG
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
37 6 0.07
38 27 0.29
39 45 0.49
40 14 0.15
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (39 bp):
TTGCGATTTACGGATACGCGTTGCGATTTACGGATACGC
Found at i:2176 original size:20 final size:20
Alignment explanation
Indices: 2154--2251 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
2144 ATTTATGTGT
*
2154 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAA
*
2174 TCGCGTTGCGATTTTCCAAAA
1 TCGCGTTGCGATTTT-CATAA
**
2195 TCGCAATGCGAATTTGT-ACT-A
1 TCGCGTTGCG-ATTT-TCA-TAA
*
2216 TCGCATTGCGATTTTCAATAA
1 TCGCGTTGCGATTTTC-ATAA
2237 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
2252 GGGAAACTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 13
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 20 0.31
21 38 0.59
22 4 0.06
23 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAA
Found at i:2247 original size:42 final size:43
Alignment explanation
Indices: 2154--2252 Score: 109
Period size: 42 Copynumber: 2.4 Consensus size: 43
2144 ATTTATGTGT
*
2154 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTCCAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCCAAAA
**
2195 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAATAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTCCAA-AA
*
2237 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
2253 GGAAACTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
41 11 0.23
42 34 0.71
43 3 0.06
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTCCAAAA
Found at i:2862 original size:51 final size:51
Alignment explanation
Indices: 2783--2901 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 51
2773 CACCCGTAGC
* * * * * *
2783 AGTA-AGCGCGCCTCCTGAATCGCCCTATATGCTGATTTGGCGCCACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCCCTATACGCTGACTGGGCGACACGTGG
* * **
2833 AGTATAGCGCGCCCCCTGTACCGCGCTATACGCTGACTGGGTTACACGTGG
1 AGTATAGCGCGCCCCCTGAACCGCCCTATACGCTGACTGGGCGACACGTGG
*
2884 AGTATAGCACGCCCCCTG
1 AGTATAGCGCGCCCCCTG
2902 CTCCGTGCTA
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
50 4 0.07
51 53 0.93
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (51 bp):
AGTATAGCGCGCCCCCTGAACCGCCCTATACGCTGACTGGGCGACACGTGG
Found at i:4500 original size:20 final size:20
Alignment explanation
Indices: 4475--4514 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4465 CAGAATGGGG
*
4475 GGAATCGGTACCCCTTCATA
1 GGAATCGATACCCCTTCATA
4495 GGAATCGATACCCCTTCATA
1 GGAATCGATACCCCTTCATA
4515 ATATCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (20 bp):
GGAATCGATACCCCTTCATA
Found at i:4628 original size:19 final size:19
Alignment explanation
Indices: 4604--4655 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
4594 CTCGGGGTAT
*
4604 TGTTCAAACAGTGATTTAC
1 TGTTCAAACAGTAATTTAC
*
4623 TGTTCAAATAGTAATTTAC
1 TGTTCAAACAGTAATTTAC
* *
4642 TATTCAAATAGTAA
1 TGTTCAAACAGTAA
4656 AATACTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
TGTTCAAACAGTAATTTAC
Found at i:4661 original size:19 final size:19
Alignment explanation
Indices: 4620--4666 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
4610 AACAGTGATT
* **
4620 TACTGTTCAAATAGTAATT
1 TACTATTCAAATAGTAAAA
4639 TACTATTCAAATAGTAAAA
1 TACTATTCAAATAGTAAAA
4658 TACTATTCA
1 TACTATTCA
4667 TAAAACATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (19 bp):
TACTATTCAAATAGTAAAA
Found at i:4762 original size:29 final size:31
Alignment explanation
Indices: 4730--4789 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4720 AAATTTTGAA
*
4730 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4759 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4790 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:7441 original size:111 final size:111
Alignment explanation
Indices: 7299--7631 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
7289 ATTACAAAAA
*
7299 TTAATTCTTAATATAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
7364 AATTAAAACGTTAAAATGTTAACGTATCAACAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
*
7410 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATCATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
7475 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAATGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
* *
7521 TTAATTCTTAATCTAATAACCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
7586 AATTAAAACGTTAAAATGTTACCGTATTAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
7632 ATGATTTCCA
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:7770 original size:12 final size:10
Alignment explanation
Indices: 7757--7797 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
7747 ATTAAAAAGA
*
7757 GAGAGTATTT
1 GAGAGAATTT
7767 GAGAGAAATTT
1 GAGAG-AATTT
7778 -AGAGAATTT
1 GAGAGAATTT
7787 GAGAGAATTT
1 GAGAGAATTT
7797 G
1 G
7798 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:12275 original size:21 final size:21
Alignment explanation
Indices: 12251--12292 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12241 TTGATAATGA
12251 ATTATGAATTATTTT-TTTAAT
1 ATTAT-AATTATTTTATTTAAT
*
12272 ATTATAATTTTTTTATTTAAT
1 ATTATAATTATTTTATTTAAT
12293 TAAAAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
ATTATAATTATTTTATTTAAT
Found at i:12965 original size:2 final size:2
Alignment explanation
Indices: 12958--12986 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12948 CAAGTGACTT
12958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12987 TACGCAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19591 original size:30 final size:28
Alignment explanation
Indices: 19555--19639 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 28
19545 GTTTGGTTAT
19555 TAAATTAGAATGAGAGTCATAATTTAGGAA
1 TAAATTAGAATGA-A-TCATAATTTAGGAA
* * * *
19585 TAAATTAAAATGAATAAAAAATTTAGGGA
1 TAAATTAGAATGAAT-CATAATTTAGGAA
19614 TAAATTTAGAATGAAATTCATAATTT
1 TAAA-TTAGAATG-AA-TCATAATTT
19640 GGGTACTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 1 0.02
29 15 0.34
30 19 0.43
31 8 0.18
32 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (28 bp):
TAAATTAGAATGAATCATAATTTAGGAA
Found at i:21326 original size:90 final size:90
Alignment explanation
Indices: 21173--21348 Score: 273
Period size: 90 Copynumber: 2.0 Consensus size: 90
21163 TAACACACCA
* * * **
21173 TTTTATAGTCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTTGAATTAATTAAATCTATAT
1 TTTTATAGTCAAGTTACCCTAATCATATAAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
* *
21238 TTAATTAATTGGAATTTAATAATCC
66 TTAATTAATTGAAATTAAATAATCC
21263 TTTTATA-TCCAAGTTACCCTAATCATATAAGGGATTTTATTATTTCAAATTAATTAAATCTATA
1 TTTTATAGT-CAAGTTACCCTAATCATATAAGGGATTTTATTATTTCAAATTAATTAAATCTATA
21327 TTTAATTAATTGAAATTAAATA
65 TTTAATTAATTGAAATTAAATA
21349 TTCGGGATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
89 1 0.01
90 77 0.99
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (90 bp):
TTTTATAGTCAAGTTACCCTAATCATATAAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAAATAATCC
Found at i:32745 original size:109 final size:111
Alignment explanation
Indices: 32557--32765 Score: 264
Period size: 109 Copynumber: 1.9 Consensus size: 111
32547 AATTATGAAA
* * *
32557 AATATATATATTAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTACCTTA
1 AATATATATATTAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCTTA
* *
32622 AGACAGCTCTTTTCTTCGATATTAAAAAATAAATAATTAAAACAAAT
66 AGACAGCTCCTTTCTT-AATATTAAAAAATAAATAATTAAAACAAAT
* * ***
32669 AATATATA-ATTTAT-AAA-ATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGTTTT
1 AATATATATATTAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTACCTT
* *
32731 AAGACTG-TCCTTTCTTAATATTGAAAAATAAATAA
65 AAGACAGCTCCTTTCTTAATATTAAAAAATAAATAA
32766 ATATTAAAAC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 17 0.20
109 34 0.40
110 20 0.24
111 5 0.06
112 8 0.10
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.37
Consensus pattern (111 bp):
AATATATATATTAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTACCTTA
AGACAGCTCCTTTCTTAATATTAAAAAATAAATAATTAAAACAAAT
Found at i:34305 original size:3 final size:3
Alignment explanation
Indices: 34297--34349 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
34287 ATTATTTATT
* *
34297 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
34341 TAA TAA TAA
1 TAA TAA TAA
34350 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:34321 original size:19 final size:18
Alignment explanation
Indices: 34297--34352 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
34287 ATTATTTATT
34297 TAATAATAATAATATAATA
1 TAATAATAATAATA-AATA
* *
34316 TAATAATAATATTAAAACA
1 TAATAATAATAAT-AAATA
*
34335 AAATAATAATAATAAATA
1 TAATAATAATAATAAATA
34353 AAACAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 4 0.13
19 26 0.84
20 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATAATAATAAATA
Found at i:34325 original size:22 final size:22
Alignment explanation
Indices: 34297--34359 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
34287 ATTATTTATT
* * *
34297 TAATAATAATAATATAATATAA
1 TAATAATAATAAAACAAAATAA
*
34319 TAATAATATTAAAACAAAATAA
1 TAATAATAATAAAACAAAATAA
34341 TAATAATAAATAAAACAAA
1 TAATAAT-AATAAAACAAA
34360 TGAAATAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 25 0.71
23 10 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
TAATAATAATAAAACAAAATAA
Found at i:35031 original size:113 final size:111
Alignment explanation
Indices: 34701--35260 Score: 734
Period size: 113 Copynumber: 5.0 Consensus size: 111
34691 GAGTTATGCA
** *
34701 AAAAGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATTA
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
** * * *
34766 TGAA-TTTTCTCTGGAAAAGTTGATCCATCGAGTGACGAATTCAAAC
66 TGAACTTGAC-CTGGAAATGTTGATCCATCGAATGATGAATTCAAAC
*
34812 AAAAAGTTGAACAAATTCTTCTCATCATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCTC
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT---GAGTTCTTCTC
* *
34874 ATTATGAACTCT-ACCTGGCAATGTTGATCCATCAAATGATGAATTCAAAC
62 ATTATGAACT-TGACCTGGAAATGTTGATCCATCGAATGATGAATTCAAAC
*
34924 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCAT
1 AAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCAT
* * **
34989 TATGAACTTGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGTG
64 TATGAACTTGACCTGGAAATGTTGATCCATCGAATGATGAATTCAA-AC
* *
35038 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-TTCTTCAGATGAGTTCTTCTCATT
* * *
35103 ATGAACTTGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGC
65 ATGAACTTGACCTGGAAATGTTGATCCATCGAATGATGAATTCAAAC
*
35150 GAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 -AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCAT
* * * * *
35215 TATGAACTCGACCTGGAAATGTTAATACATTGAATGATGGATTCAA
64 TATGAACTTGACCTGGAAATGTTGATCCATCGAATGATGAATTCAA
35261 CTTTGCTAAA
Statistics
Matches: 404, Mismatches: 30, Indels: 27
0.88 0.07 0.06
Matches are distributed among these distances:
109 16 0.04
110 1 0.00
111 4 0.01
112 101 0.25
113 259 0.64
114 7 0.02
115 6 0.01
116 10 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (111 bp):
AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTGACCTGGAAATGTTGATCCATCGAATGATGAATTCAAAC
Found at i:35672 original size:22 final size:22
Alignment explanation
Indices: 35647--35701 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
35637 GATAAAGCTT
* *
35647 TCATATTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
35669 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
35691 TCATCTTTGAA
1 TCATCTTTGAA
35702 GAGTGTAGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:42460 original size:16 final size:15
Alignment explanation
Indices: 42439--42484 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
42429 AAAAAATGTA
42439 ATATAAATGCGAAAAT
1 ATATAAATGC-AAAAT
42455 ATATAAATGCCAAAA-
1 ATATAAATG-CAAAAT
*
42470 ATAAAAATGCAAAAT
1 ATATAAATGCAAAAT
42485 GTGCAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 13 0.48
17 1 0.04
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.22
Consensus pattern (15 bp):
ATATAAATGCAAAAT
Found at i:45724 original size:3 final size:3
Alignment explanation
Indices: 45716--45745 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
45706 TTTATGGCTA
*
45716 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
45746 TAAAAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Done.