Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005369.1 Hibiscus syriacus cultivar Beakdansim tig00012204_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: 51948
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:335 original size:21 final size:20
Alignment explanation
Indices: 291--340 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
281 GAATGTGTTT
* * *
291 GATGTTGTATAGCCGTTGGG
1 GATGTTTTAGAGCCGTTAGG
311 GATGTTTTAGAGCCGTTTAGG
1 GATGTTTTAGAGCCG-TTAGG
332 GATGATTTT
1 GATG-TTTT
341 TTACTCAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.52
21 8 0.32
22 4 0.16
ACGTcount: A:0.18, C:0.08, G:0.34, T:0.40
Consensus pattern (20 bp):
GATGTTTTAGAGCCGTTAGG
Found at i:391 original size:21 final size:21
Alignment explanation
Indices: 365--439 Score: 150
Period size: 21 Copynumber: 3.6 Consensus size: 21
355 TGCCCATAAA
365 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGGTGCACTAT
386 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGGTGCACTAT
407 CATGGTGCATCGGTGCACTAT
1 CATGGTGCATCGGTGCACTAT
428 CATGGTGCATCG
1 CATGGTGCATCG
440 ATATCCCTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (21 bp):
CATGGTGCATCGGTGCACTAT
Found at i:394 original size:13 final size:13
Alignment explanation
Indices: 376--436 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
366 ATGGTGCATC
376 GGTGCACTATCAT
1 GGTGCACTATCAT
389 GGTG--C-ATC--
1 GGTGCACTATCAT
397 GGTGCACTATCAT
1 GGTGCACTATCAT
410 GGTG--C-ATC--
1 GGTGCACTATCAT
418 GGTGCACTATCAT
1 GGTGCACTATCAT
431 GGTGCA
1 GGTGCA
437 TCGATATCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 20
0.66 0.00 0.34
Matches are distributed among these distances:
8 8 0.21
10 8 0.21
11 8 0.21
13 14 0.37
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (13 bp):
GGTGCACTATCAT
Found at i:523 original size:20 final size:20
Alignment explanation
Indices: 495--546 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
485 GCAGCCTTCG
* **
495 GCATGGATGCACCTCAAGAT
1 GCATCGATGCACAGCAAGAT
*
515 GCATCGATGCACAGCAGGAT
1 GCATCGATGCACAGCAAGAT
535 GCATCGATGCAC
1 GCATCGATGCAC
547 TAAGTGCATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (20 bp):
GCATCGATGCACAGCAAGAT
Found at i:5833 original size:14 final size:14
Alignment explanation
Indices: 5814--5843 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5804 TTTATATTTT
*
5814 TTAAAATTACATTA
1 TTAAAAATACATTA
5828 TTAAAAATACATTA
1 TTAAAAATACATTA
5842 TT
1 TT
5844 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:5942 original size:7 final size:7
Alignment explanation
Indices: 5932--6089 Score: 64
Period size: 7 Copynumber: 22.7 Consensus size: 7
5922 AGGATTTATG
5932 GTTTAGT
1 GTTTAGT
*
5939 GTTTAGG
1 GTTTAGT
*
5946 GTTTAGG
1 GTTTAGT
*
5953 GTTTAGG
1 GTTTAGT
5960 GTTTA-T
1 GTTTAGT
5966 GGTTTA-T
1 -GTTTAGT
*
5973 AG-TTAGG
1 -GTTTAGT
5980 GTTTA-T
1 GTTTAGT
5986 GGTTTAGT
1 -GTTTAGT
*
5994 ATTTAGT
1 GTTTAGT
*
6001 GTTTAGG
1 GTTTAGT
*
6008 GATTA-T
1 GTTTAGT
6014 GGTTTAAG-
1 -GTTT-AGT
6022 GTTTA-T
1 GTTTAGT
*
6028 GGTTTAGA
1 -GTTTAGT
*
6036 GTTTAGA
1 GTTTAGT
**
6043 GTTTAAA
1 GTTTAGT
6050 GTTTAAG-
1 GTTT-AGT
6057 GTTTAG-
1 GTTTAGT
6063 GATTTAGT
1 G-TTTAGT
*
6071 GTTTAGG
1 GTTTAGT
*
6078 GTTTAGG
1 GTTTAGT
6085 GTTTA
1 GTTTA
6090 AGTTATGCAC
Statistics
Matches: 122, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
6 8 0.07
7 110 0.90
8 4 0.03
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (7 bp):
GTTTAGT
Found at i:5943 original size:14 final size:14
Alignment explanation
Indices: 5921--6089 Score: 139
Period size: 14 Copynumber: 12.1 Consensus size: 14
5911 AATTATGTGA
*
5921 TAGGATTTATGGTT
1 TAGGGTTTATGGTT
* *
5935 TAGTGTTTAGGGTT
1 TAGGGTTTATGGTT
*
5949 TAGGGTTTAGGGTT
1 TAGGGTTTATGGTT
* *
5963 TATGGTTTATAG-T
1 TAGGGTTTATGGTT
5976 TAGGGTTTATGGTT
1 TAGGGTTTATGGTT
**
5990 TAGTATTTA-GTGTT
1 TAGGGTTTATG-GTT
*
6004 TAGGGATTATGGTT
1 TAGGGTTTATGGTT
*
6018 TAAGGTTTATGGTT
1 TAGGGTTTATGGTT
*
6032 TAGAGTTTA-GAGTT
1 TAGGGTTTATG-GTT
** *
6046 TAAAGTTTAAGGTT
1 TAGGGTTTATGGTT
*
6060 TAGGATTTA-GTGTT
1 TAGGGTTTATG-GTT
*
6074 TAGGGTTTAGGGTT
1 TAGGGTTTATGGTT
6088 TA
1 TA
6090 AGTTATGCAC
Statistics
Matches: 125, Mismatches: 23, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
13 14 0.11
14 108 0.86
15 3 0.02
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (14 bp):
TAGGGTTTATGGTT
Found at i:5945 original size:21 final size:21
Alignment explanation
Indices: 5927--6089 Score: 136
Period size: 21 Copynumber: 7.8 Consensus size: 21
5917 GTGATAGGAT
* *
5927 TTATGGTTTAGTGTTTAGGGT
1 TTATGGTTTAGGGTTTATGGT
*
5948 TTAGGGTTTAGGGTTTATGGT
1 TTATGGTTTAGGGTTTATGGT
*
5969 TTATAG-TTAGGGTTTATGGT
1 TTATGGTTTAGGGTTTATGGT
* * * *
5989 TTA-GTATTTAGTGTTTAGGGA
1 TTATG-GTTTAGGGTTTATGGT
*
6010 TTATGGTTTAAGGTTTATGGT
1 TTATGGTTTAGGGTTTATGGT
* **
6031 TTA-GAGTTTAGAGTTTAAAGT
1 TTATG-GTTTAGGGTTTATGGT
* *
6052 TTAAGGTTTAGGATTTA-GTGT
1 TTATGGTTTAGGGTTTATG-GT
*
6073 TTAGGGTTTAGGGTTTA
1 TTATGGTTTAGGGTTTA
6090 AGTTATGCAC
Statistics
Matches: 112, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
20 18 0.16
21 92 0.82
22 2 0.02
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (21 bp):
TTATGGTTTAGGGTTTATGGT
Found at i:6018 original size:55 final size:55
Alignment explanation
Indices: 5921--6027 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
5911 AATTATGTGA
* * *
5921 TAGGATTTATGGTTTAGTGTTTAGGGTTTAGGGTTTAGGGTTTATGGTTTATAGT
1 TAGGATTTATGGTTTAGTATTTAGGGTTTAGGGATTAGGGTTTAAGGTTTATAGT
* * *
5976 TAGGGTTTATGGTTTAGTATTTAGTGTTTAGGGATTATGGTTTAAGGTTTAT
1 TAGGATTTATGGTTTAGTATTTAGGGTTTAGGGATTAGGGTTTAAGGTTTAT
6028 GGTTTAGAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.50
Consensus pattern (55 bp):
TAGGATTTATGGTTTAGTATTTAGGGTTTAGGGATTAGGGTTTAAGGTTTATAGT
Found at i:6229 original size:21 final size:21
Alignment explanation
Indices: 6194--6239 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6184 GTTAGATTAC
*
6194 ACCCTAAACCATAAATTCTAA
1 ACCCTAAACCATAAATCCTAA
*
6215 ACCCTAAA-CACTAAATCCTTA
1 ACCCTAAACCA-TAAATCCTAA
6236 ACCC
1 ACCC
6240 GATTATGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (21 bp):
ACCCTAAACCATAAATCCTAA
Found at i:8617 original size:33 final size:33
Alignment explanation
Indices: 8557--8624 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
8547 AAAGATAATT
* * * *
8557 TTATAATTTGAGTCTTAAATATTTTTTTTATGA
1 TTATAATTTGAATATTAAATATCTTTTTAATGA
8590 TTATAATTTGAATATTAAAT-TACTTTTTAATGA
1 TTATAATTTGAATATTAAATAT-CTTTTTAATGA
8623 TT
1 TT
8625 TTATATACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.56
Consensus pattern (33 bp):
TTATAATTTGAATATTAAATATCTTTTTAATGA
Found at i:10622 original size:3 final size:3
Alignment explanation
Indices: 10614--10700 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
10604 GTTTAAGCCT
10614 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10662 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
10701 TCAAACACAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11686 original size:231 final size:231
Alignment explanation
Indices: 11436--11913 Score: 607
Period size: 231 Copynumber: 2.1 Consensus size: 231
11426 GCACTAGTAT
* *
11436 TTCGCGTTGAGGAGGTCTAGAATGTAGACGACATTATTCCTTCCTGTTGAGGACGTATAGTCGTA
1 TTCGCGTTGAGGAGGTCTAGAATATAGACGACATTATTCCTTCCTGTTGAGGACGTATAGTCATA
* * * * *
11501 TTTAGATAATTTTGCCTATAGAGACATCAATATTCCTTCATGTTGAAGAAGTCTAATTGTCTAGA
66 TTTAGATAATTGTGCCTACAGAGACAACAATATTCCTTCACGTTGAAGAAGTCTAATTGTCTAAA
* * * * *
11566 GATAATTTGA-TTTCATAAACGGCATTGCTCTTATGTGCTGAAGAGATCTAGTCGCTTTTGGGTG
131 GATAATTTGACTTTCA-AAACGACATCGCTCCTACGTGCTAAAGAGATCTAGTCGCTTTTGGGTG
* *
11630 ATTTACTCGATGTCAAATCTGATGATGACATTGCTTA
195 ATTTACTCGATGTCAAATCTCATGATGACATTGCTCA
** * * * * * *
11667 TTCGCGTTGAGGAGGTCTAGCCTATAGATGACATTGTTCCTTCGTGTTGAGGATGTCTTGTCATA
1 TTCGCGTTGAGGAGGTCTAGAATATAGACGACATTATTCCTTCCTGTTGAGGACGTATAGTCATA
* * * * * *
11732 TTTGGATAATTGTGCCTACAGAGACAACAATGTTCCTTCACGTTTAGGAAGTTTGATTGTCTAAA
66 TTTAGATAATTGTGCCTACAGAGACAACAATATTCCTTCACGTTGAAGAAGTCTAATTGTCTAAA
* * * *
11797 GTTAATTTGACTTTGAAAATGACATCGCTCCTACGTGCTAAAGAGATCTGGTCGCTTTTGGGTGA
131 GATAATTTGACTTTCAAAACGACATCGCTCCTACGTGCTAAAGAGATCTAGTCGCTTTTGGGTGA
* * *
11862 TTTTCTTGATGTCAAATCTCATGATGACATTGCTCC
196 TTTACTCGATGTCAAATCTCATGATGACATTGCTCA
* *
11898 TTCACGTTAAGGAGGT
1 TTCGCGTTGAGGAGGT
11914 ATAGTCATGA
Statistics
Matches: 209, Mismatches: 37, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
231 205 0.98
232 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.36
Consensus pattern (231 bp):
TTCGCGTTGAGGAGGTCTAGAATATAGACGACATTATTCCTTCCTGTTGAGGACGTATAGTCATA
TTTAGATAATTGTGCCTACAGAGACAACAATATTCCTTCACGTTGAAGAAGTCTAATTGTCTAAA
GATAATTTGACTTTCAAAACGACATCGCTCCTACGTGCTAAAGAGATCTAGTCGCTTTTGGGTGA
TTTACTCGATGTCAAATCTCATGATGACATTGCTCA
Found at i:12005 original size:24 final size:24
Alignment explanation
Indices: 11978--12033 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
11968 GTTTGAAAAA
11978 GTCATATGATATGATTCCATATGT
1 GTCATATGATATGATTCCATATGT
12002 GTCATATGATATGATTCCATATGT
1 GTCATATGATATGATTCCATATGT
12026 GTCATATG
1 GTCATATG
12034 TGATATGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (24 bp):
GTCATATGATATGATTCCATATGT
Found at i:12211 original size:31 final size:31
Alignment explanation
Indices: 12176--12234 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
12166 ATTGTCTACT
12176 TTGATGGCCTTGGTCCATGTACTATTTAACA
1 TTGATGGCCTTGGTCCATGTACTATTTAACA
* *
12207 TTGATGGCCTTGGTCCTTTTACTATTTA
1 TTGATGGCCTTGGTCCATGTACTATTTA
12235 GTGCTTAGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.44
Consensus pattern (31 bp):
TTGATGGCCTTGGTCCATGTACTATTTAACA
Found at i:12665 original size:25 final size:25
Alignment explanation
Indices: 12626--12761 Score: 120
Period size: 25 Copynumber: 5.4 Consensus size: 25
12616 TTGAAATTTT
*
12626 TTTGATG-AAGCAATTTTAAAGAATA
1 TTTGATGAAAG-AATTTTGAAGAATA
* *
12651 TTTGATGAAAGAATTTCGAAGAATG
1 TTTGATGAAAGAATTTTGAAGAATA
*
12676 TTTAATGAAAGAATTTTG-AGAA-A
1 TTTGATGAAAGAATTTTGAAGAATA
* *
12699 TGTTAGATGAAATAATTTTTGAAGAATG
1 T-TT-GATGAAAGAA-TTTTGAAGAATA
* *
12727 GTTGATGAAAGAATTTTG-AGAAATG
1 TTTGATGAAAGAATTTTGAAG-AATA
12752 TTTGAT-AAAG
1 TTTGATGAAAG
12762 TTTTTATTAA
Statistics
Matches: 92, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 12 0.13
25 56 0.61
26 17 0.18
27 6 0.07
ACGTcount: A:0.42, C:0.01, G:0.21, T:0.35
Consensus pattern (25 bp):
TTTGATGAAAGAATTTTGAAGAATA
Found at i:12740 original size:51 final size:50
Alignment explanation
Indices: 12654--12761 Score: 155
Period size: 51 Copynumber: 2.2 Consensus size: 50
12644 AAGAATATTT
*
12654 GATGAAAGAATTTCGAAGAATGTTTAATGAAAGAATTTTGAGAAATGTTA
1 GATGAAAGAATTTCGAAGAATGGTTAATGAAAGAATTTTGAGAAATGTTA
* * * *
12704 GATGAAATAATTTTTGAAGAATGGTTGATGAAAGAATTTTGAGAAATGTTT
1 GATGAAAGAA-TTTCGAAGAATGGTTAATGAAAGAATTTTGAGAAATGTTA
12755 GAT-AAAG
1 GATGAAAG
12762 TTTTTATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
50 12 0.24
51 39 0.76
ACGTcount: A:0.43, C:0.01, G:0.23, T:0.33
Consensus pattern (50 bp):
GATGAAAGAATTTCGAAGAATGGTTAATGAAAGAATTTTGAGAAATGTTA
Found at i:13452 original size:107 final size:107
Alignment explanation
Indices: 13255--13455 Score: 262
Period size: 107 Copynumber: 1.9 Consensus size: 107
13245 TAATTTAATA
* * *
13255 TGCCTTTATTCAGTTAGCTGAAGCAATCTATCCATAAAGCCATAGCTTTTAACCAATTACTTTAA
1 TGCCTTTATTCAGCTAGCTGAAGCAATATATACATAAAGCCATAGCTTTTAACCAATTACTTTAA
*
13320 AGGAACAGCTCAATTCTATTTTATATATACATATATATTATT
66 AGGAACAGCTCAATTCTATTGTATATATACATATATATTATT
** * *
13362 TGCCTTTATTTGGCTAGCTGAAAG-AATATATACATAAAGTCA-AGGCTTTTAACCAATTGCTTT
1 TGCCTTTATTCAGCTAGCTG-AAGCAATATATACATAAAGCCATA-GCTTTTAACCAATTACTTT
* * * *
13425 AGAGGAATAGCTCATTTTTATTGTATATATA
64 AAAGGAACAGCTCAATTCTATTGTATATATA
13456 TAATTAAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
106 1 0.01
107 76 0.95
108 3 0.04
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (107 bp):
TGCCTTTATTCAGCTAGCTGAAGCAATATATACATAAAGCCATAGCTTTTAACCAATTACTTTAA
AGGAACAGCTCAATTCTATTGTATATATACATATATATTATT
Found at i:16779 original size:66 final size:66
Alignment explanation
Indices: 16654--16782 Score: 188
Period size: 66 Copynumber: 2.0 Consensus size: 66
16644 AGTATGAAGA
* *
16654 CTCTAGCAGGTTCAGTCGATGCTGATAATTCCTTGTATAGGTTCAGCACCAACTGGTAATTCCTA
1 CTCTAGCAGGTTCAGTCGATGCTGATAATTCCTTGTATAGGTTCAACACCAACTAGTAATTCCTA
16719 T
66 T
* * * *
16720 CTCTGGCAGGTTCAGTCGTTTCTGGTAATTCCTTGTATAGGTTCAACA-CACACTAGTAATTCC
1 CTCTAGCAGGTTCAGTCGATGCTGATAATTCCTTGTATAGGTTCAACACCA-ACTAGTAATTCC
16783 GTATGGACCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 2 0.04
66 54 0.96
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (66 bp):
CTCTAGCAGGTTCAGTCGATGCTGATAATTCCTTGTATAGGTTCAACACCAACTAGTAATTCCTA
T
Found at i:17393 original size:18 final size:17
Alignment explanation
Indices: 17366--17399 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
17356 TATAAGTTTG
*
17366 GAATTTGTTTTATTTAT
1 GAATTTGTTTAATTTAT
17383 GAATATTGTTTAATTTA
1 GAAT-TTGTTTAATTTA
17400 CTTTTGTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (17 bp):
GAATTTGTTTAATTTAT
Found at i:21773 original size:23 final size:21
Alignment explanation
Indices: 21730--21784 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 21
21720 TCTTTATTTT
21730 TTAAAATAAAATTATTCTAAA
1 TTAAAATAAAATTATTCTAAA
21751 TTAAGAATATAAATATATT-TAAAAA
1 TTAA-AATA-AAAT-TATTCT--AAA
21776 TTAAAATAA
1 TTAAAATAA
21785 TTAAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 6 0.21
24 8 0.28
25 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TTAAAATAAAATTATTCTAAA
Found at i:21790 original size:16 final size:18
Alignment explanation
Indices: 21749--21827 Score: 53
Period size: 15 Copynumber: 4.6 Consensus size: 18
21739 AATTATTCTA
*
21749 AATTAAGAATATAAATAT
1 AATTAAAAATATAAATAT
*
21767 ATTTAAAAAT-TAAA-AT
1 AATTAAAAATATAAATAT
*
21783 AATT-AAAATAATAATACTAA
1 AATTAAAAAT-ATAA-A-TAT
*
21803 AAATAAAAAT-TAAAT-T
1 AATTAAAAATATAAATAT
21819 -ATTAAAAAT
1 AATTAAAAAT
21828 TTTGAATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
15 13 0.27
16 5 0.10
17 8 0.17
18 10 0.21
19 3 0.06
20 4 0.08
21 5 0.10
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (18 bp):
AATTAAAAATATAAATAT
Found at i:21856 original size:21 final size:22
Alignment explanation
Indices: 21818--21858 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21808 AAAATTAAAT
**
21818 TATTAAAAATTTTGAATATTCA
1 TATTAAAAATACTGAATATTCA
21840 TATTAAAAATACT-AATATT
1 TATTAAAAATACTGAATATT
21859 ATTATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
TATTAAAAATACTGAATATTCA
Found at i:22069 original size:25 final size:26
Alignment explanation
Indices: 22036--22084 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
22026 ACAAAATTAA
* *
22036 ATTAGTCGATACTTACAAT-TTTTGG
1 ATTAATCGAAACTTACAATATTTTGG
*
22061 ATTAATCGAAACTTATAATATTTT
1 ATTAATCGAAACTTACAATATTTT
22085 CTAATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (26 bp):
ATTAATCGAAACTTACAATATTTTGG
Found at i:22288 original size:13 final size:13
Alignment explanation
Indices: 22272--22296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22262 ATGATATGCA
22272 TATATATTATGTG
1 TATATATTATGTG
22285 TATATATTATGT
1 TATATATTATGT
22297 ATAATATATC
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:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TATATATTATGTG
Found at i:22587 original size:19 final size:19
Alignment explanation
Indices: 22556--22593 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
22546 TAAACTTTTT
*
22556 TAAAAAATCAATTTGGCCC
1 TAAAAAATCAATTTAGCCC
22575 TAAAAAA-CTAATTTAGCCC
1 TAAAAAATC-AATTTAGCCC
22594 ATTTGTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
TAAAAAATCAATTTAGCCC
Found at i:23007 original size:18 final size:19
Alignment explanation
Indices: 22984--23019 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22974 TGACATAGTT
22984 TTAAATCTATA-CAAAAAA
1 TTAAATCTATACCAAAAAA
*
23002 TTAAATTTATACCAAAAA
1 TTAAATCTATACCAAAAA
23020 GATATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAATCTATACCAAAAAA
Found at i:26645 original size:15 final size:15
Alignment explanation
Indices: 26625--26655 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26615 TCGAAATATG
26625 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
26640 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
26655 A
1 A
26656 TCTCCCCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAATGTTTTCAACA
Found at i:28498 original size:20 final size:21
Alignment explanation
Indices: 28452--28512 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
28442 TTCCCCTGTG
*
28452 GGGGGAATCAGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
28475 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
28495 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
28513 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:33951 original size:22 final size:22
Alignment explanation
Indices: 33895--33954 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
33885 AAACCATTCA
* *
33895 GGGGGAATTGGTACCCCCTTGG
1 GGGGGAATCGGTTCCCCCTTGG
33917 GGGGGAATCGGTTCCCCCTTGG
1 GGGGGAATCGGTTCCCCCTTGG
33939 GGGGGAATCGGTTCCC
1 GGGGGAATCGGTTCCC
33955 TCTGAGCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.12, C:0.25, G:0.42, T:0.22
Consensus pattern (22 bp):
GGGGGAATCGGTTCCCCCTTGG
Found at i:34206 original size:15 final size:15
Alignment explanation
Indices: 34186--34217 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
34176 TCGAAATATC
34186 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
34201 AAAATGTTTTCAACA
1 AAAATGTTTTCAACA
34216 AA
1 AA
34218 TCACCATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (15 bp):
AAAATGTTTTCAACA
Found at i:35728 original size:20 final size:21
Alignment explanation
Indices: 35703--35741 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35693 TCTCTTTATC
*
35703 TCCTTCT-TCCCTTTATTTCT
1 TCCTTCTCTCCCTCTATTTCT
35723 TCCTTCTCTCCCTCTATTT
1 TCCTTCTCTCCCTCTATTT
35742 TCTCTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.56
Consensus pattern (21 bp):
TCCTTCTCTCCCTCTATTTCT
Done.