Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007015.1 Hibiscus syriacus cultivar Beakdansim tig00018116_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: 70201
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1813 original size:19 final size:19
Alignment explanation
Indices: 1789--1837 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1779 ATGACCAACA
* *
1789 AATTCGCAACGCGATCTCG
1 AATTCGCAACGCGAACTCC
*
1808 AATTCGCAATGCGAACTCC
1 AATTCGCAACGCGAACTCC
1827 AATTTCGCAAC
1 AA-TTCGCAAC
1838 TCAGTTTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (19 bp):
AATTCGCAACGCGAACTCC
Found at i:1977 original size:20 final size:20
Alignment explanation
Indices: 1904--1978 Score: 57
Period size: 20 Copynumber: 3.8 Consensus size: 20
1894 CAATACTGAA
* *
1904 TTTCAAATTCGCAACTAG-T
1 TTTCGAATTCGCAACTCGAT
*
1923 TTTCTGAATTCGCAACGCGAAT
1 TTTC-GAATTCGCAACTCG-AT
* *
1945 TTT-G-TTGTAGCAACTCGAT
1 TTTCGAAT-TCGCAACTCGAT
1964 TTTCGAATTCGCAAC
1 TTTCGAATTCGCAAC
1979 AGGTTTTAGT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
19 10 0.24
20 27 0.64
21 1 0.02
22 4 0.10
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (20 bp):
TTTCGAATTCGCAACTCGAT
Found at i:5074 original size:12 final size:12
Alignment explanation
Indices: 5057--5097 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
5047 AGCAAAAGGA
*
5057 AATCAAAATCGC
1 AATCAAAATCAC
*
5069 AATCAAAATCAA
1 AATCAAAATCAC
*
5081 AATCAAAATCCC
1 AATCAAAATCAC
5093 AATCA
1 AATCA
5098 CAACTGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:5078 original size:6 final size:6
Alignment explanation
Indices: 5056--5090 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5046 AAGCAAAAGG
* *
5056 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
5091 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:5360 original size:20 final size:20
Alignment explanation
Indices: 5333--5411 Score: 95
Period size: 20 Copynumber: 4.0 Consensus size: 20
5323 CAACGTGAAG
*
5333 TTGACTTTCGCGTTGCGAAT
1 TTGACTTTCACGTTGCGAAT
*
5353 TTGGCTTTCACGTTGCGAAT
1 TTGACTTTCACGTTGCGAAT
* **
5373 TTGACTATCACAATGCGAAT
1 TTGACTTTCACGTTGCGAAT
* *
5393 TTAACTTTCGCGTTGCGAA
1 TTGACTTTCACGTTGCGAA
5412 AGTGTACCTT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGACTTTCACGTTGCGAAT
Found at i:5571 original size:64 final size:64
Alignment explanation
Indices: 5470--5618 Score: 235
Period size: 64 Copynumber: 2.3 Consensus size: 64
5460 AATTTAAAAC
* *
5470 AACAAATAAACTTTTACAAATCAATTAAAGAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * *
5534 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
5598 AACAAATCAACTTTTACAAAT
1 AACAAATCAACTTTTACAAAT
5619 ACATCAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:6999 original size:21 final size:21
Alignment explanation
Indices: 6970--7082 Score: 102
Period size: 21 Copynumber: 5.4 Consensus size: 21
6960 GTGAATCGGG
* *
6970 CTCTCGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* **
6991 CTCTTGAACGATGAAAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
7012 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
**
7033 CTCTTGAA-GGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * * **
7054 CTTTTGAACGATAGGATAGGC
1 CTCTTGAACGGTGGGAGGGGC
7075 CTCTTGAA
1 CTCTTGAA
7083 TGATGACAGG
Statistics
Matches: 72, Mismatches: 18, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
20 2 0.03
21 69 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:7036 original size:42 final size:42
Alignment explanation
Indices: 6970--7088 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 42
6960 GTGAATCGGG
* *
6970 CTCTCGAACGGTGGGAGGGACCTCTTGAACGATGAAAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
* *
7012 CTCTTGAACGGTGGGAGGGGCCTCTTGAAGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
* * * ** *
7054 CTTTTGAACGATAGGATAGGCCTCTTGAATGATGA
1 CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGA
7089 CAGGTGCTTC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGCCTCTTGAACGATGAAAGGGGC
Found at i:7459 original size:21 final size:21
Alignment explanation
Indices: 7404--7478 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
7394 CTAAAGTAGA
*
7404 TACCTCACCACGTAAAGCACCA
1 TACCTCACCACGTAAAG-ACCC
** * *
7426 T-TGTCATCGCGTAAA-ACCTC
1 TACCTCACCACGTAAAGACC-C
*
7446 TACCTCACCACGTAAAGACCG
1 TACCTCACCACGTAAAGACCC
*
7467 TACCTCATCACG
1 TACCTCACCACG
7479 CCATGCACCA
Statistics
Matches: 39, Mismatches: 11, Indels: 7
0.68 0.19 0.12
Matches are distributed among these distances:
19 3 0.08
20 1 0.03
21 31 0.79
22 4 0.10
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (21 bp):
TACCTCACCACGTAAAGACCC
Found at i:9129 original size:20 final size:20
Alignment explanation
Indices: 9113--9196 Score: 150
Period size: 20 Copynumber: 4.2 Consensus size: 20
9103 CTTAAAATTA
9113 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
9133 CAACGCGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
*
9153 CAACACGAAAATGAAAATCG
1 CAACGCGAAAATGAAAATCG
*
9173 CAACGCGAAACTGAAAATCG
1 CAACGCGAAAATGAAAATCG
9193 CAAC
1 CAAC
9197 TTAAGTTTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.50, C:0.23, G:0.18, T:0.10
Consensus pattern (20 bp):
CAACGCGAAAATGAAAATCG
Found at i:9560 original size:22 final size:22
Alignment explanation
Indices: 9535--9589 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
9525 GGAGATAGAT
*
9535 AGATTTTGCCGAAGATGGGGAC
1 AGATTTCGCCGAAGATGGGGAC
* *
9557 AGATTTCGTCGGAGATGGGGAC
1 AGATTTCGCCGAAGATGGGGAC
* *
9579 GGATGTCGCCG
1 AGATTTCGCCG
9590 TAAAGAGTGA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.16, G:0.40, T:0.22
Consensus pattern (22 bp):
AGATTTCGCCGAAGATGGGGAC
Found at i:9787 original size:21 final size:21
Alignment explanation
Indices: 9761--9804 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9751 TATGTGTTGC
*
9761 GAATTTGGAAAATCGCAATGT
1 GAATTTGGAAAATCGCAACGT
9782 GAATTTGGAAAATCGCAACGT
1 GAATTTGGAAAATCGCAACGT
9803 GA
1 GA
9805 TTTACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (21 bp):
GAATTTGGAAAATCGCAACGT
Found at i:10945 original size:2 final size:2
Alignment explanation
Indices: 10938--10977 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
10928 AAAATATAAT
* *
10938 TA TA TA TA TA TA TA TA TA TA TA TA TA TG CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10978 GACAAGCCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:13201 original size:23 final size:24
Alignment explanation
Indices: 13174--13223 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
13164 CATCTAGGAA
* *
13174 TTTATTATTTTTTTC-TTTTTCTT
1 TTTATTACTTCTTTCATTTTTCTT
*
13197 TTTATTACTTCTTTCATTTTTTTT
1 TTTATTACTTCTTTCATTTTTCTT
13221 TTT
1 TTT
13224 GCATTTCTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTATTACTTCTTTCATTTTTCTT
Found at i:13914 original size:42 final size:40
Alignment explanation
Indices: 13801--13914 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 40
13791 GCCCGAAGGT
* *
13801 CTTATGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGA
1 CTTATAGAT-GCCCGAATGACTTATCATCATGCTCGAAAGA
* *
13842 CTTATAGATGACCCGAATGATTTAAGCATCATGCTCGAAAGA
1 CTTATAGATG-CCCGAATGACTT-ATCATCATGCTCGAAAGA
* *
13884 CTTATTGATAGCCCGAAGGACTTACTCATCA
1 CTTATAGAT-GCCCGAATGACTTA-TCATCA
13915 AGAAACCCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 1 0.02
41 20 0.33
42 39 0.64
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (40 bp):
CTTATAGATGCCCGAATGACTTATCATCATGCTCGAAAGA
Found at i:14091 original size:57 final size:57
Alignment explanation
Indices: 13966--14092 Score: 157
Period size: 58 Copynumber: 2.2 Consensus size: 57
13956 GTTTATAGTT
* * * * *
13966 ATCATCAAGAAACTCCTAAAAATTAGGCTTAACTTCTTTTAAAAATTAAATGGGAGA
1 ATCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATAAATGGAAGA
* * *
14023 ATTCATCAAGAAACCCCTAAAAATCAGGCGTATCTTC-TTTAAAAAATCATTGGAAGTA
1 A-TCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATAAATGGAAG-A
14081 ATCATCAAGAAA
1 ATCATCAAGAAA
14093 GCTTTGAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
57 27 0.45
58 33 0.55
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (57 bp):
ATCATCAAGAAACCCCTAAAAATCAGGCGTAACTTCTTTTAAAAAATAAATGGAAGA
Found at i:14207 original size:55 final size:55
Alignment explanation
Indices: 14133--14329 Score: 231
Period size: 55 Copynumber: 3.6 Consensus size: 55
14123 GTTCATCATG
*
14133 TCAAGAAAGC-TCTAAAAATCAGGCTTAGTTTCTTTAAAAACTCATTTAACAATCA
1 TCAAGAAA-CTTCTAAAAATCAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* * * * *
14188 TCATGAAACTTCTAAAAATCCGACTTAGTTTCTTTGAAAACTCATTTAATAATCA
1 TCAAGAAACTTCTAAAAATCAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
* *
14243 TCAAGAAACTTCCAAAAATC-GGACTTAGCTTT-TTTCAAAACTCATTTAAAAAT-A
1 TCAAGAAACTTCTAAAAATCAGG-CTTAG-TTTCTTTAAAAACTCATTTAAAAATCA
** * *
14297 TCAAGAAACCCCTAAGAATTAGGCTTAGTTTCT
1 TCAAGAAACTTCTAAAAATCAGGCTTAGTTTCT
14330 AAAATTATTT
Statistics
Matches: 122, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
53 3 0.02
54 24 0.20
55 92 0.75
56 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (55 bp):
TCAAGAAACTTCTAAAAATCAGGCTTAGTTTCTTTAAAAACTCATTTAAAAATCA
Found at i:16066 original size:2 final size:2
Alignment explanation
Indices: 16059--16097 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16049 TCAGCTTTAT
16059 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
16098 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:20409 original size:6 final size:6
Alignment explanation
Indices: 20400--20465 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
20390 GTGTAAAGGT
* * *
20400 AAATGC AAATGTGA AAATGC AAATGC ATATGC AAATGTGA AAATGC AAATGC
1 AAATGC AAA--TGC AAATGC AAATGC AAATGC AAA--TGC AAATGC AAATGC
*
20452 ATATGC AAATGC AA
1 AAATGC AAATGC AA
20466 TGAAGGGATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
6 38 0.79
8 10 0.21
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
AAATGC
Found at i:20419 original size:14 final size:14
Alignment explanation
Indices: 20400--20450 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
20390 GTGTAAAGGT
20400 AAATGCAAATGTGA
1 AAATGCAAATGTGA
*
20414 AAATGCAAA--TGC
1 AAATGCAAATGTGA
*
20426 ATATGCAAATGTGA
1 AAATGCAAATGTGA
20440 AAATGCAAATG
1 AAATGCAAATG
20451 CATATGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 10 0.32
14 21 0.68
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.22
Consensus pattern (14 bp):
AAATGCAAATGTGA
Found at i:20438 original size:26 final size:26
Alignment explanation
Indices: 20402--20462 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
20392 GTAAAGGTAA
20402 ATGCAAATGTGAAAATGCAAATGCAT
1 ATGCAAATGTGAAAATGCAAATGCAT
20428 ATGCAAATGTGAAAATGCAAATGCAT
1 ATGCAAATGTGAAAATGCAAATGCAT
20454 ATGCAAATG
1 ATGCAAATG
20463 CAATGAAGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (26 bp):
ATGCAAATGTGAAAATGCAAATGCAT
Found at i:24042 original size:60 final size:61
Alignment explanation
Indices: 23969--24134 Score: 191
Period size: 59 Copynumber: 2.8 Consensus size: 61
23959 TGCATCATAT
* * *
23969 ATTCTTAAACTATGACTCTCATTCTAAATT-GACCTCTAAACTTTTGAATATTATAATTTC
1 ATTCTTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
* * * *
24029 ATTCTCAAACTATGA-TATTCATTTTAAATTAGTCCT-TAAAC-TTTAAACATTCTAATTTC
1 ATTCTTAAACTATGACT-CTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
* *
24088 A-TCATTAAACTATGACCCTCATTCTAAATTGGTCC-CTAAACTTTTAA
1 ATTC-TTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAA
24135 CTTTTTTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
58 2 0.02
59 47 0.53
60 35 0.40
61 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (61 bp):
ATTCTTAAACTATGACTCTCATTCTAAATTAGTCCTCTAAACTTTTAAACATTATAATTTC
Found at i:26395 original size:11 final size:11
Alignment explanation
Indices: 26379--26404 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
26369 ATAATTTTAA
26379 AAAAAATCTTT
1 AAAAAATCTTT
26390 AAAAAATCTTT
1 AAAAAATCTTT
26401 AAAA
1 AAAA
26405 TATTATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAAAATCTTT
Found at i:30446 original size:31 final size:33
Alignment explanation
Indices: 30406--30500 Score: 88
Period size: 32 Copynumber: 3.0 Consensus size: 33
30396 TCGACTATCG
* *
30406 GGTCGGGTCAA-ATTTGATCGGTCGATTTTTGA
1 GGTCAGGTCAATATTAGATCGGTCGATTTTTGA
** * * *
30438 -GTCAGGTCAATATCGGATCGATTGA-TTTTCA
1 GGTCAGGTCAATATTAGATCGGTCGATTTTTGA
* *
30469 GGTCGGGTCAATATTAGATCGGTCAATTTTTG
1 GGTCAGGTCAATATTAGATCGGTCGATTTTTG
30501 TGTCGAGTCA
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
31 14 0.30
32 29 0.62
33 4 0.09
ACGTcount: A:0.22, C:0.14, G:0.27, T:0.37
Consensus pattern (33 bp):
GGTCAGGTCAATATTAGATCGGTCGATTTTTGA
Found at i:30489 original size:32 final size:31
Alignment explanation
Indices: 30406--30513 Score: 83
Period size: 32 Copynumber: 3.4 Consensus size: 31
30396 TCGACTATCG
* * *
30406 GGTCGGGTCAA-ATTTGATCGGTCGATTTTT
1 GGTCGGGTCAATATTAGATCGATCGATTTTA
* ** *
30436 GAGTCAGGTCAATATCGGATCGATTGATTTTCA
1 G-GTCGGGTCAATATTAGATCGATCGATTTT-A
* * *
30469 GGTCGGGTCAATATTAGATCGGTCAATTTTT
1 GGTCGGGTCAATATTAGATCGATCGATTTTA
*
30500 GTGTCGAGTCAATA
1 G-GTCGGGTCAATA
30514 ATGAATTGAA
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
30 1 0.02
31 10 0.17
32 48 0.80
33 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.27, T:0.36
Consensus pattern (31 bp):
GGTCGGGTCAATATTAGATCGATCGATTTTA
Found at i:30933 original size:16 final size:16
Alignment explanation
Indices: 30896--30927 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
30886 ATTATATTTG
30896 AATAAATATTTATATA
1 AATAAATATTTATATA
30912 AATAAAT-TTTATATA
1 AATAAATATTTATATA
30927 A
1 A
30928 TTTAAAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATATTTATATA
Found at i:32484 original size:15 final size:15
Alignment explanation
Indices: 32440--32484 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
32430 CTAGGTGGGC
* *
32440 GGATGTGGGGCGGGC
1 GGATGCGGGGCGGGT
* *
32455 AGATACGGGGCGGGT
1 GGATGCGGGGCGGGT
32470 GGATGCGGGGCGGGT
1 GGATGCGGGGCGGGT
32485 AATGTCTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.11, C:0.13, G:0.62, T:0.13
Consensus pattern (15 bp):
GGATGCGGGGCGGGT
Found at i:33635 original size:17 final size:15
Alignment explanation
Indices: 33598--33636 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
33588 AAATTCTAAA
*
33598 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
33613 TATTTATATAAAAACT
1 TATTTATATAAAAA-T
33629 CTATTTAT
1 -TATTTAT
33637 TTTTTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 1 0.05
17 7 0.33
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:33640 original size:63 final size:63
Alignment explanation
Indices: 33567--33697 Score: 244
Period size: 63 Copynumber: 2.1 Consensus size: 63
33557 CTTTGTTCTA
* *
33567 TATTTGTTTTTTTAACAAGTGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAACTC
1 TATTTATTTTTTTAACAAATGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAACTC
33630 TATTTATTTTTTTAACAAATGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAACTC
1 TATTTATTTTTTTAACAAATGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAACTC
33693 TATTT
1 TATTT
33698 GTTGATAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (63 bp):
TATTTATTTTTTTAACAAATGAAATTCTAAATATTTAAATAAAAATTATTTATATAAAAACTC
Found at i:44184 original size:60 final size:60
Alignment explanation
Indices: 44073--44185 Score: 165
Period size: 60 Copynumber: 1.9 Consensus size: 60
44063 TATATCATAC
* *
44073 TACTTTGTTGAGTCCTCCAACTATTAAAAGTTACAAAATAATCCCTCGACTATAGGGTGT
1 TACTTTGTTAAGTCCTCCAACTATTAAAAGTTACAAAATAATCACTCGACTATAGGGTGT
* * *
44133 TACTTTGTTAAGTCC-CTCGACTATTAAAAGTTACAAAATAGTCACTTGACTAT
1 TACTTTGTTAAGTCCTC-CAACTATTAAAAGTTACAAAATAATCACTCGACTAT
44186 TCATTATATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
59 1 0.02
60 46 0.98
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (60 bp):
TACTTTGTTAAGTCCTCCAACTATTAAAAGTTACAAAATAATCACTCGACTATAGGGTGT
Found at i:50873 original size:2 final size:2
Alignment explanation
Indices: 50866--50898 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
50856 AAAATAAAAT
50866 TA TA 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 TA TA T
50899 TAAAAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53403 original size:23 final size:24
Alignment explanation
Indices: 53377--53422 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
53367 CCGAAAGACA
53377 ACAT-AGGTTTGTCCCAAAGGACC
1 ACATAAGGTTTGTCCCAAAGGACC
* *
53400 ACATAAGTTTTGTCTCAAAGGAC
1 ACATAAGGTTTGTCCCAAAGGAC
53423 TGTTCGCTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (24 bp):
ACATAAGGTTTGTCCCAAAGGACC
Found at i:54807 original size:30 final size:30
Alignment explanation
Indices: 54771--54828 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
54761 TGAAGCCTGA
*
54771 CAGGATCAACAGCAGTAGGGCGTGGTCCAG
1 CAGGATCAACAGCAGCAGGGCGTGGTCCAG
*
54801 CAGGATCAGCAGCAGCAGGGCGTGGTCC
1 CAGGATCAACAGCAGCAGGGCGTGGTCC
54829 CCTCTTTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.26, G:0.38, T:0.12
Consensus pattern (30 bp):
CAGGATCAACAGCAGCAGGGCGTGGTCCAG
Done.