Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000137.1 Hibiscus syriacus cultivar Beakdansim tig00000250_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: 61647
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2139 original size:437 final size:434
Alignment explanation
Indices: 1311--2183 Score: 1570
Period size: 437 Copynumber: 2.0 Consensus size: 434
1301 ATATTTATAG
1311 GGAAATTGCTACATACTCTAGATACTCTCGCACTGTGACCCATAGGATTTATCACTATCATCCCA
1 GGAAATTGCTACATACTCTAGATACTCTCGCACTGTGACCCATAGGATTTATCACTATCATCCCA
*
1376 CTCACTATTGGTTTTAAATAAATTCCTCTAGCTCTAACCAACTTGGTACTAATGTATGAATATGT
66 CTCACTATTGGTTTTAAAGAAATTCCTCTAGCTCTAACCAACTTGGTACTAATGTATGAATATGT
1441 AGAACCAGGGTCAACTAAACAAATACAGGTTTATCGTAAAGAGGAAAATACATGTTATGATCATG
131 AGAACCAGGGTCAACTAAACAAATACAGGTTTATCGTAAAGAGGAAAATACATGTTATGATCATG
* * *
1506 GTCATCTCGATCCTCAGTGGTCTTAAGGTTGTAAATTCTAGTAACTCCTTAAGTCTTTTGCCTCG
196 GTAATCTCGATCCTCAGTGGTCTTAAGGTTGCAAATTCTAGTAACTCCTTAAGTCTCTTGCCTCG
* *
1571 GCATTGATTTTGTCTGTCCCCTGGACCTACCCCTTCTTCTGTTTCTATTTGAGGCTGCCACTAAT
261 GCATTGATTATGTCTGTCCCCTGGACCTACCCCTTCCTCTGTTTCTATTTGAGGCTGCCACTAAT
1636 CTTTCAGACTGTGCCAAATTATCACCATATTTCTTAGGGTAGTTCCGAGAAAATTGACCCATATC
326 CTTTCAGACTGTGCCAAATTATCACCATATTTCTTAGGGTAGTTCCGAGAAAATTGACCCATATC
1701 ACCACATAAAAAACATGCTCCCCTGAAAAATCTACAAACTCCTC
391 ACCACATAAAAAACATGCTCCCCTGAAAAATCTACAAACTCCTC
*
1745 GGAAATTGCTACATACTCTAGATACTCTCGCACTGTGACCCATAGGATTTATCACTATCATCCCG
1 GGAAATTGCTACATACTCTAGATACTCTCGCACTGTGACCCATAGGATTTATCACTATCATCCCA
1810 CTCACTATTGGTTTTAAAGAAATTCCTCTAGCTCTAACCAACTTGGTACTAATGTAT-ATATATG
66 CTCACTATTGGTTTTAAAGAAATTCCTCTAGCTCTAACCAACTTGGTACTAATGTATGA-ATATG
*
1874 TAGAACCAGGGTCAACTAAAACAAATACAGGTTTATCGTAAAGATGGAAAATACCTGTTATGATC
130 TAGAACCAGGGTCAACT-AAACAAATACAGGTTTATCGTAAAGA-GGAAAATACATGTTATGA--
1939 TCATGGTAATCTCGATCCTCAGTGGTCTTAAGGTTGCAAATTCTAG-AACTCCTTAAGTCTCTTG
191 TCATGGTAATCTCGATCCTCAGTGGTCTTAAGGTTGCAAATTCTAGTAACTCCTTAAGTCTCTTG
* *
2003 TCTCGGCATTGATTATGTCTGTCCCCTGGACCTACCCCTTCCTCTGTTTCTATTTGAGGCTGTCA
256 CCTCGGCATTGATTATGTCTGTCCCCTGGACCTACCCCTTCCTCTGTTTCTATTTGAGGCTGCCA
**
2068 CTAATCTTTCAGACTGTGCTGAATTATCACCATATTTCTTAGGGTAGTTCCGAGAAAATTGACCC
321 CTAATCTTTCAGACTGTGCCAAATTATCACCATATTTCTTAGGGTAGTTCCGAGAAAATTGACCC
*
2133 ATATCACCACATAAAAAACATGCTCCCCTGACAAATCTACAAACTCCTC
386 ATATCACCACATAAAAAACATGCTCCCCTGAAAAATCTACAAACTCCTC
2182 GG
1 GG
2184 TGTAATTTAC
Statistics
Matches: 421, Mismatches: 13, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
433 1 0.00
434 142 0.34
435 26 0.06
436 17 0.04
437 191 0.45
438 44 0.10
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (434 bp):
GGAAATTGCTACATACTCTAGATACTCTCGCACTGTGACCCATAGGATTTATCACTATCATCCCA
CTCACTATTGGTTTTAAAGAAATTCCTCTAGCTCTAACCAACTTGGTACTAATGTATGAATATGT
AGAACCAGGGTCAACTAAACAAATACAGGTTTATCGTAAAGAGGAAAATACATGTTATGATCATG
GTAATCTCGATCCTCAGTGGTCTTAAGGTTGCAAATTCTAGTAACTCCTTAAGTCTCTTGCCTCG
GCATTGATTATGTCTGTCCCCTGGACCTACCCCTTCCTCTGTTTCTATTTGAGGCTGCCACTAAT
CTTTCAGACTGTGCCAAATTATCACCATATTTCTTAGGGTAGTTCCGAGAAAATTGACCCATATC
ACCACATAAAAAACATGCTCCCCTGAAAAATCTACAAACTCCTC
Found at i:3709 original size:127 final size:127
Alignment explanation
Indices: 3531--3849 Score: 385
Period size: 127 Copynumber: 2.5 Consensus size: 127
3521 CATCTTTAGG
* * * *
3531 AAGGATGATAAC-TCGGTTCCTACGTGATGAGGACGGCTGGTTATTTGGGTTGACACAGTTCCTA
1 AAGGGTGATAACAT-GGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTA
* * ** * * * *
3595 CATAATGAGGAAATCTGGTCGGGTGATGACACGGTTCCTACGCGATGAGGACG-CAT-TCCATCT
65 CATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGA-GTC-TGACCACCT
* * *
3658 AAGGGTGATAACATGGTTCCTACGTGATAAGGACGATTGGTTATCTGGGTTGACACAACTCCTAC
1 AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
* * *
3723 ATAATGAGGAGATCTGGTCAGTTGATAACACGACTCATACGTGATGAAGAGTTCTGACCACCT
66 ATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGAG-TCTGACCACCT
* * *
3786 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTAGTTATCT-GGTTGACACAATTCCTAC
1 AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
3850 GCTATAAGGA
Statistics
Matches: 164, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
126 1 0.01
127 115 0.70
128 48 0.29
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (127 bp):
AAGGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTATCTGGGTTGACACAATTCCTAC
ATAATGAGGAAATCTGGTCAGGTGATAACACGACTCATACGCGATGAAGAGTCTGACCACCT
Found at i:4099 original size:35 final size:34
Alignment explanation
Indices: 3990--4114 Score: 118
Period size: 35 Copynumber: 3.8 Consensus size: 34
3980 GACAAAATTC
* *
3990 GTTTCAAGGG-AATGACTCAAAGATG---GTTAT
1 GTTTCAAGGGAAACGACTCAAAGATGTTTGTTTT
* **
4020 GTTTCAAGAGAAACAGACTCAAAGA--TTTAATTT
1 GTTTCAAGGGAAAC-GACTCAAAGATGTTTGTTTT
*
4053 GTTTCATGGGAAACGATCTCAAAGATGTTTGTTTT
1 GTTTCAAGGGAAACGA-CTCAAAGATGTTTGTTTT
*
4088 GTTTCAAGGGAAACATACTCAAAGATG
1 GTTTCAAGGGAAAC-GACTCAAAGATG
4115 GGTGTTTCAC
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
30 9 0.12
31 2 0.03
32 12 0.16
33 22 0.29
35 29 0.39
36 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (34 bp):
GTTTCAAGGGAAACGACTCAAAGATGTTTGTTTT
Found at i:4300 original size:33 final size:34
Alignment explanation
Indices: 4225--4304 Score: 92
Period size: 33 Copynumber: 2.4 Consensus size: 34
4215 ATAAGATTTG
* ** *
4225 TTTCAAGAGAAAC-GATCTCAAAGATGGTTGTTG
1 TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
* *
4258 TTTCCAGTGAAACAGA-CTCAAAGATAATTTTTA
1 TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
4291 TTTCAAGTGAAACA
1 TTTCAAGTGAAACA
4305 ATTTCAGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (34 bp):
TTTCAAGTGAAACAGATCTCAAAGATAATTGTTA
Found at i:4665 original size:34 final size:34
Alignment explanation
Indices: 4622--4688 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
4612 AAAGGAAAAA
**
4622 TGTCTCAAGCGAGATGAAATTTGTTTTGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAT
*
4656 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAA
4689 AACACCATCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTGAGAAAT
Found at i:6072 original size:2 final size:2
Alignment explanation
Indices: 6065--6093 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6055 TCAGCTTTAT
6065 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 T
6094 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:9944 original size:16 final size:18
Alignment explanation
Indices: 9923--9960 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
9913 AAAGTCTTTT
9923 AAAAACA-ATTTTAAGA-
1 AAAAACATATTTTAAGAC
*
9939 AAAAACATTTTTTAAGAC
1 AAAAACATATTTTAAGAC
9957 AAAA
1 AAAA
9961 GCTAGTATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAACATATTTTAAGAC
Found at i:10233 original size:30 final size:29
Alignment explanation
Indices: 10198--10312 Score: 97
Period size: 30 Copynumber: 3.9 Consensus size: 29
10188 ATAAATCTTG
* * *
10198 AAAACATGAACTTAAAGGATTAAAATAACA
1 AAAACA-GAATTTAAAGGACTAAAATAGCA
* * *
10228 TAAACAGAAGTTAAGAGG-CTAAAATAGTA
1 AAAACAGAATTTAA-AGGACTAAAATAGCA
* *
10257 AAAACAGAAATTTAAAAGACCAAAATAGCA
1 AAAACAG-AATTTAAAGGACTAAAATAGCA
* *
10287 CAAACATGAATTTAAAGGATTAAAAT
1 AAAACA-GAATTTAAAGGACTAAAAT
10313 GGAAAAAATA
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
29 23 0.34
30 43 0.64
31 1 0.01
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (29 bp):
AAAACAGAATTTAAAGGACTAAAATAGCA
Found at i:10910 original size:21 final size:21
Alignment explanation
Indices: 10858--10903 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
10848 ACAAACAGAA
10858 AAGTAAAATTTAAGAAGTACC
1 AAGTAAAATTTAAGAAGTACC
10879 AAGTAAAATTTAAGAAGTACC
1 AAGTAAAATTTAAGAAGTACC
10900 AAGT
1 AAGT
10904 GGAATTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGTAAAATTTAAGAAGTACC
Found at i:11993 original size:128 final size:126
Alignment explanation
Indices: 11824--12193 Score: 431
Period size: 128 Copynumber: 2.9 Consensus size: 126
11814 CATCTTTAGG
* * *
11824 AAGGGTGATAACTCGATTCCTACGTGATGAGGATGACTGGTTATCTGGGTTGACACAGTTCCTAC
1 AAGGGTGATAACACGGTTCCTACGTGATGAGGAGGA-TGGTTATCTGGGTTGACACAGTTCCTAC
* *
11889 ATAATGAGGAAATCTGGTCGGGTGATGACACGGTTCCTACGCGATGAGGATGGT-AGACCATCT
65 ATAATGAGGAAATCTGGTCAGGTGATGACA-GGTTCCTACGTGATGAGGA-GGTCAGACCATCT
*
11952 AAGGGTGATAACACGGTTCCTACGTGATGAGGACGGATGGTTATCTGGGTTGACACAGCTCCTAC
1 AAGGGTGATAACACGGTTCCTACGTGATGAGGA-GGATGGTTATCTGGGTTGACACAGTTCCTAC
* * * * * * * *
12017 ATAATGAGGAGATCTGGTCAGTTGATGACATGTCTCATACGTGATGAAGAGTTCTGGCCATCT
65 ATAATGAGGAAATCTGGTCAGGTGATGACAGGT-TCCTACGTGATGAGGAGGTCAGACCATCT
* * * *
12080 AAAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTAGTTATCT-GGTTGACACGGTTCCTAC
1 AAGGGTGATAACACGGTTCCTACGTGATGAGGA-GGATGGTTATCTGGGTTGACACAGTTCCTAC
*** ***
12144 GCGATGAGGATGGCTGGTCAAGG-GATGACATGGTTCCTACGTGATGAGGA
65 ATAATGAGGAAATCTGGTC-AGGTGATGACA-GGTTCCTACGTGATGAGGA
12194 CGGCTGGCCA
Statistics
Matches: 207, Mismatches: 30, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
127 54 0.26
128 151 0.73
129 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (126 bp):
AAGGGTGATAACACGGTTCCTACGTGATGAGGAGGATGGTTATCTGGGTTGACACAGTTCCTACA
TAATGAGGAAATCTGGTCAGGTGATGACAGGTTCCTACGTGATGAGGAGGTCAGACCATCT
Found at i:12150 original size:41 final size:40
Alignment explanation
Indices: 12081--12198 Score: 137
Period size: 41 Copynumber: 2.9 Consensus size: 40
12071 TGGCCATCTA
* *
12081 AAGGTGATAACACGGTTCCTACGTGATGAGGATGGCTAGTT
1 AAGG-GATGACACGGTTCCTACGTGATGAGGATGGCTAGTC
** * * *
12122 ATCTGGTTGACACGGTTCCTACGCGATGAGGATGGCTGGTC
1 A-AGGGATGACACGGTTCCTACGTGATGAGGATGGCTAGTC
* *
12163 AAGGGATGACATGGTTCCTACGTGATGAGGACGGCT
1 AAGGGATGACACGGTTCCTACGTGATGAGGATGGCT
12199 GGCCATCTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
40 29 0.46
41 33 0.52
42 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.34, T:0.25
Consensus pattern (40 bp):
AAGGGATGACACGGTTCCTACGTGATGAGGATGGCTAGTC
Found at i:12184 original size:40 final size:41
Alignment explanation
Indices: 12090--12200 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 41
12080 AAAGGTGATA
* * ** *
12090 ACACGGTTCCTACGTGATGAGGATGGCTAGTTATCTGGTTG
1 ACACGGTTCCTACGTGATGAGGATGGCTGGTCATAGGGATG
*
12131 ACACGGTTCCTACGCGATGAGGATGGCTGGTCA-AGGGATG
1 ACACGGTTCCTACGTGATGAGGATGGCTGGTCATAGGGATG
* *
12171 ACATGGTTCCTACGTGATGAGGACGGCTGG
1 ACACGGTTCCTACGTGATGAGGATGGCTGG
12201 CCATCTTTAG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
40 31 0.51
41 30 0.49
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (41 bp):
ACACGGTTCCTACGTGATGAGGATGGCTGGTCATAGGGATG
Found at i:12393 original size:35 final size:34
Alignment explanation
Indices: 12309--12408 Score: 123
Period size: 35 Copynumber: 2.9 Consensus size: 34
12299 CTTAAAGATG
*
12309 GTTTTGTTTCAAGAGAAACAGACTCAAAGA--TTT
1 GTTTTGTTTCAAGGGAAACA-ACTCAAAGATGTTT
** *
12342 AATTCGTTTCAAGGGAAACAATCTCAAAGATGTTT
1 GTTTTGTTTCAAGGGAAACAA-CTCAAAGATGTTT
12377 GTTTTGTTTCAAGGGAAACAAACTCAAAGATG
1 GTTTTGTTTCAAGGGAAAC-AACTCAAAGATG
12409 GGTATGTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
32 1 0.02
33 24 0.43
35 29 0.52
36 2 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (34 bp):
GTTTTGTTTCAAGGGAAACAACTCAAAGATGTTT
Found at i:19793 original size:4 final size:4
Alignment explanation
Indices: 19784--19813 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
19774 TTTCCAGGTA
19784 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT
19814 CAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:21388 original size:19 final size:17
Alignment explanation
Indices: 21365--21425 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 17
21355 TAAATAAAAC
21365 AAGAAAAAATAGAAAATA
1 AAGAAAAAATA-AAAATA
**
21383 ACAGAAAACGTAAAAAATA
1 A-AGAAAAAAT-AAAAATA
*
21402 AAAAAAAAATAAAAATA
1 AAGAAAAAATAAAAATA
*
21419 AACAAAA
1 AAGAAAA
21426 TGAATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.37
18 7 0.20
19 14 0.40
20 1 0.03
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (17 bp):
AAGAAAAAATAAAAATA
Found at i:21503 original size:17 final size:15
Alignment explanation
Indices: 21481--21524 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
21471 TTAATGGAGT
21481 AAAAAAATAAAAAGGTA
1 AAAAAAATAAAAA-G-A
21498 AAAAAAATTAAAAAGA
1 AAAAAAA-TAAAAAGA
21514 AATAAAAATAA
1 AA-AAAAATAA
21525 TGTGTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 13 0.52
18 6 0.24
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAATAAAAAGA
Found at i:21504 original size:18 final size:16
Alignment explanation
Indices: 21481--21524 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
21471 TTAATGGAGT
21481 AAAAAAATAAAAAGGTAA
1 AAAAAAATAAAAA-G-AA
*
21499 AAAAAATTAAAAAGAA
1 AAAAAAATAAAAAGAA
*
21515 ATAAAAATAA
1 AAAAAAATAA
21525 TGTGTACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 1 0.04
18 12 0.52
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAAAAGAA
Found at i:21649 original size:15 final size:13
Alignment explanation
Indices: 21621--21645 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21611 CATGATATTA
21621 AGAAAAAAATAAT
1 AGAAAAAAATAAT
21634 AGAAAAAAATAA
1 AGAAAAAAATAA
21646 AATAAAGTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:21649 original size:18 final size:18
Alignment explanation
Indices: 21626--21682 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
21616 TATTAAGAAA
21626 AAAATAATAGAAAAAAAT
1 AAAATAATAGAAAAAAAT
*
21644 AAAATAA-AG-TAAAAAT
1 AAAATAATAGAAAAAAAT
* * *
21660 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAAAAAAT
21679 AAAA
1 AAAA
21683 ACAAAAATAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 8 0.27
19 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAATAATAGAAAAAAAT
Found at i:21845 original size:25 final size:25
Alignment explanation
Indices: 21799--21847 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
21789 ATACATATAC
* *
21799 ATATATATATATATAATGATATAAG
1 ATATATATATATAAAATAATATAAG
21824 ATATATATA-ATTAAAATAATATAA
1 ATATATATATA-TAAAATAATATAA
21848 TATAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATATATATAAAATAATATAAG
Found at i:21850 original size:23 final size:25
Alignment explanation
Indices: 21793--21856 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
21783 ATACATATAC
* *
21793 ATATACATATATAT-ATATATAATG
1 ATATACATATATATAATATAAAATA
*
21817 ATATAAGATATATATAAT-TAAAATA
1 ATAT-ACATATATATAATATAAAATA
*
21842 ATATA-ATATAAATAA
1 ATATACATATATATAA
21857 AAAAAGGAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 9 0.26
24 5 0.15
25 18 0.53
26 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (25 bp):
ATATACATATATATAATATAAAATA
Found at i:33390 original size:302 final size:302
Alignment explanation
Indices: 32844--33447 Score: 1181
Period size: 302 Copynumber: 2.0 Consensus size: 302
32834 TTCTAAAACT
* *
32844 TATTTGAGATAACATATTTTACAAGCAAATTGAAGGAAGTTTGATGTATCTAACAACTATATATA
1 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTAATGTATCTAACAACTATATATA
32909 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
66 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
32974 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
131 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
*
33039 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAT
196 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
33104 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
261 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
33146 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTAATGTATCTAACAACTATATATA
1 TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTAATGTATCTAACAACTATATATA
33211 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
66 AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
33276 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
131 TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
33341 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
196 GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
33406 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
261 AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
33448 ATCTACTCAA
Statistics
Matches: 299, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
302 299 1.00
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (302 bp):
TATTTGAGATAACATACTTTACAAGCAAATTGAAGGAAGTTTAATGTATCTAACAACTATATATA
AGACTTGTTATTATGATGTTATAAGTCTCATTATTTAGGTACATGAAATGCCCAAGAGAGAGACA
TCTTCTAGCTATCAAGAGAATGTTTTAATACTTGTAAAGAGCCATTGAATAGTAAGGGTGAACAT
GATTAAACACAATATAATATTGGAGAAAGAAAACTTGATATCTAACCCCCTCGATATCTATTTAC
AGGGATAAATATTTGATTACAAAGGAAATTTATAAAGTATAA
Found at i:33782 original size:122 final size:124
Alignment explanation
Indices: 33560--33937 Score: 367
Period size: 110 Copynumber: 3.2 Consensus size: 124
33550 ATGTCAAACA
* * * * *
33560 CCACAAAATGGTAACATTAGTGACGGTTTTTCTAAAAATGTCGCTATAGACTCATCTTTTACGGC
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCTAAAAACGCCGCTATAAACTCATCTTTTACGGC
* * * *
33625 ATTTTTAAAATAAATGCCGCAATAAATTAGTGCATTAGTGGTATTTTT-AATACAAATG
66 ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
* * * * *
33683 CCATAAAATGGTAATATTAGCGA-AGTTTTT-TAAAAAACGCCGTTATAAACTCGTCTTTTGCGG
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCT-AAAAACGCCGCTATAAACTCATCTTTTACGG
* * *
33746 TATTTTTAAAACAAATACCTCAATAAATCAGTGCATTAGTGGCGTTTTTAAATACAAATG
65 CATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
* * * * *
33806 TCACAAAATGGTAACATTAGTGGCA--TTTTCT--ATA----GC-AT----T-ATCTTTTGCGGC
1 CCACAAAATGGTAACATTAGCGACAGTTTTTCTAAAAACGCCGCTATAAACTCATCTTTTACGGC
* ** * * * *
33857 TTTTTTAAAACAAGCACCGCAATAAATCAGTGCATTAGTGGCGTTTTTAGATTCAAACG
66 ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
33916 CCACAAAATGGTAACATTAGCG
1 CCACAAAATGGTAACATTAGCG
33938 GTGTTTTTAT
Statistics
Matches: 216, Mismatches: 35, Indels: 21
0.79 0.13 0.08
Matches are distributed among these distances:
110 82 0.38
111 1 0.00
115 2 0.01
116 1 0.00
120 2 0.01
121 1 0.00
122 77 0.36
123 49 0.23
124 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (124 bp):
CCACAAAATGGTAACATTAGCGACAGTTTTTCTAAAAACGCCGCTATAAACTCATCTTTTACGGC
ATTTTTAAAACAAATACCGCAATAAATCAGTGCATTAGTGGCATTTTTAAATACAAATG
Found at i:34026 original size:232 final size:231
Alignment explanation
Indices: 33613--34035 Score: 544
Period size: 232 Copynumber: 1.8 Consensus size: 231
33603 CTATAGACTC
* ** * *
33613 ATCTTTTACGGCATTTTTAAAATAAATGCCGCAATAAATTAGTGCATTAGTGGTATTTTTAATAC
1 ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTAATAC
* * *
33678 AAATGCCATAAAATGGTAATATTAGCGAAGTTTTTTAAAAAACGCCGTTATAAACTCGTCTTTTG
66 AAACGCCACAAAATGGTAACATTAGCG-AGTTTTTTAAAAAACGCCGTTATAAACTCGTCTTTTG
* * * *
33743 CGGTATTTTTAAAACAAATACCTCAATAAATCAGTGCATTAGTGGCGTTTTTAAATACAAATGTC
130 CGGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAATGTC
33808 ACAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
195 ACAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
* * * * *
33845 ATCTTTTGCGGCTTTTTTAAAACAAGCACCGCAATAAATCAGTGCATTAGTGGCGTTTTTAGATT
1 ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTA-ATA
* * ** *
33910 CAAACGCCACAAAATGGTAACATTAGCG-GTGTTTTTATATAAACGTCGTTATTGACTTGTCTTT
65 CAAACGCCACAAAATGGTAACATTAGCGAGT-TTTTTA-AAAAACGCCGTTATAAACTCGTCTTT
* * ** **
33974 TGTGGTGTTTTT-AAACAAACGTCGCAATAGGTCAGTGAATTAGTGACGTTTTTAAATACAAA
128 TGCGGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAA
34036 CGCCGCAAGT
Statistics
Matches: 160, Mismatches: 28, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
231 2 0.01
232 100 0.62
233 58 0.36
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (231 bp):
ATCTTTTACGGCATTTTTAAAACAAACACCGCAATAAATCAGTGCATTAGTGGCATTTTTAATAC
AAACGCCACAAAATGGTAACATTAGCGAGTTTTTTAAAAAACGCCGTTATAAACTCGTCTTTTGC
GGTATTTTTAAAACAAACACCGCAATAAATCAGTGAATTAGTGACGTTTTTAAATACAAATGTCA
CAAAATGGTAACATTAGTGGCATTTTCTATAGCATT
Found at i:35653 original size:51 final size:51
Alignment explanation
Indices: 35577--35675 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
35567 TTAAAAGTTG
* *
35577 ATGTTTCTTATCTGTCCTAAAAATGGGTGGAAGAGACTACATTTTATGTTT
1 ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATGTTT
35628 ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATG
1 ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATG
35676 AAGATAAATA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.39
Consensus pattern (51 bp):
ATGTTTCTTATATGTCATAAAAATGGGTGGAAGAGACTACATTTTATGTTT
Found at i:37022 original size:2 final size:2
Alignment explanation
Indices: 37015--37058 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
37005 ACATAAATGC
37015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37057 AT
1 AT
37059 TTACACTTGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39110 original size:4 final size:4
Alignment explanation
Indices: 39101--39125 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
39091 CTAGTAAATG
39101 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
39126 ACAAGGTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:43105 original size:6 final size:6
Alignment explanation
Indices: 43093--43130 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
43083 TCTATGAATG
* *
43093 TATGTA CATGTA CATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TA
43131 AAAAGATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (6 bp):
TATGTA
Found at i:47678 original size:27 final size:27
Alignment explanation
Indices: 47640--47703 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
47630 AATGACTCTG
*
47640 AATCATTCAAAATGTAC-TCATGTGTTA
1 AATCATTCAAAATATACTTC-TGTGTTA
*
47667 AATCATTCAAAATATACTTCTGTGTTG
1 AATCATTCAAAATATACTTCTGTGTTA
47694 AATCATTCAA
1 AATCATTCAA
47704 TATTGTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (27 bp):
AATCATTCAAAATATACTTCTGTGTTA
Found at i:49040 original size:30 final size:30
Alignment explanation
Indices: 49006--49078 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
48996 ATACATGAAT
49006 TTTAGATAAAATA-CTATTTTGATCC-TAAAC
1 TTTAGATAAAATATC-ATTTTGA-CCTTAAAC
* *
49036 TTTAGATGAAATATCATTTTGACCTTTTAAC
1 TTTAGATAAAATATCATTTTGACC-TTAAAC
49067 TTTAGATAAAAT
1 TTTAGATAAAAT
49079 GTCAAATTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 2 0.05
30 19 0.51
31 16 0.43
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (30 bp):
TTTAGATAAAATATCATTTTGACCTTAAAC
Found at i:50372 original size:60 final size:59
Alignment explanation
Indices: 50231--50373 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 59
50221 AAGGGTATAG
* *
50231 TACACAAATGGTCCCTTGACTATAGGGTCTTACTTTGTTGAGCCCTCTGACTATTAAAAGT
1 TACA-AAATGGTCCC-TGACTATAGGGACTTACTTTGTTGAGCACTCTGACTATTAAAAGT
* * * *
50292 TACAAAATGATCCTCCGACTATA-GGACGTTGCTTTGTTGAGTCATTC-GACTATTAAAAGT
1 TACAAAATGGTCC-CTGACTATAGGGAC-TTACTTTGTTGAG-CACTCTGACTATTAAAAGT
50352 TACAAAATGGTCACCTGACTAT
1 TACAAAATGGTC-CCTGACTAT
50374 TCATATATTC
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
59 3 0.04
60 58 0.83
61 9 0.13
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (59 bp):
TACAAAATGGTCCCTGACTATAGGGACTTACTTTGTTGAGCACTCTGACTATTAAAAGT
Found at i:60163 original size:115 final size:113
Alignment explanation
Indices: 59956--60187 Score: 387
Period size: 115 Copynumber: 2.0 Consensus size: 113
59946 GACATTATCA
*
59956 GTTTCAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTGGTTTGATTATCTTTCAGGACATG
1 GTTTCAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTGGTTTGATTATCTTTCAGGACACG
*
60021 ACGGTTTTAAAATTAGTGAAATTAGCTTCAATCCTCTATTT-TTTATG
66 ACGGTTATAAAATTAGTGAAATTAGCTTCAATCCTCTATTTATTTATG
60068 GTTTCAAAATTAAATGAAATTAAGTCTTGTCCTTAACTTTTTTTGGTTTGATTATCTTTCAGGAC
1 GTTTC-AAATTAAATGAAATTAAGTCTTGTCCTTAA--TTTTTTGGTTTGATTATCTTTCAGGAC
*
60133 ACGACGGTTAT-AAATTAGTGAAATTAAGCTTCAATCTTCTATTTATTTATG
63 ACGACGGTTATAAAATTAGTGAAATT-AGCTTCAATCCTCTATTTATTTATG
60184 GTTT
1 GTTT
60188 AATTACCTTT
Statistics
Matches: 112, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
112 5 0.04
113 30 0.27
114 14 0.12
115 53 0.47
116 10 0.09
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (113 bp):
GTTTCAAATTAAATGAAATTAAGTCTTGTCCTTAATTTTTTGGTTTGATTATCTTTCAGGACACG
ACGGTTATAAAATTAGTGAAATTAGCTTCAATCCTCTATTTATTTATG
Done.