Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009230.1 Hibiscus syriacus cultivar Beakdansim tig00112836_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: 58983
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:2863 original size:22 final size:21
Alignment explanation
Indices: 2837--2898 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
2827 AGACAAGCTG
*
2837 TTAATATCAGGAGTTATTTGAT
1 TTAAT-TCAGGAGTTATATGAT
* *
2859 TTAATTCCAGGGGTTACATGAT
1 TTAATT-CAGGAGTTATATGAT
*
2881 ATAATTTCAGGAGTTATA
1 TTAA-TTCAGGAGTTATA
2899 ACAGCTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.40
Consensus pattern (21 bp):
TTAATTCAGGAGTTATATGAT
Found at i:8769 original size:22 final size:22
Alignment explanation
Indices: 8744--8785 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8734 ATGAGTTATT
* *
8744 TGATTTAATTCCAGGGGTTACA
1 TGATATAATTCCAGGAGTTACA
*
8766 TGATATAATTTCAGGAGTTA
1 TGATATAATTCCAGGAGTTA
8786 TAACAGCTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (22 bp):
TGATATAATTCCAGGAGTTACA
Found at i:17023 original size:16 final size:17
Alignment explanation
Indices: 16986--17023 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
16976 TGATAAAAAA
*
16986 TTAAACAAATTATTTGT
1 TTAAACAAATTATTTAT
17003 TTAAACAAATTA-TTAT
1 TTAAACAAATTATTTAT
17019 TTAAA
1 TTAAA
17024 TTAATTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAACAAATTATTTAT
Found at i:17763 original size:68 final size:67
Alignment explanation
Indices: 17642--17770 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 67
17632 TATTTGTTCA
* *
17642 TTCAAGTTTTGGTTTATTTTAATTTGACCCTCTTATTTCTTATTGTTAATTATACTTTACTCCTT
1 TTCAAGTTTTGGTTTATTTTAATTTGACCCTCTCATTTCTTATTATTAATTATA-TTT-CTCCTT
17707 GAAC
64 GAAC
* *
17711 TTCAAGTTTTGGTTT-TTTTATTTTGTCCCTCTCATTT-TCTATTATTAATTATATTTCTCC
1 TTCAAGTTTTGGTTTATTTTAATTTGACCCTCTCATTTCT-TATTATTAATTATATTTCTCC
17771 CCCTCAAATC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
66 4 0.07
67 4 0.07
68 32 0.58
69 15 0.27
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.57
Consensus pattern (67 bp):
TTCAAGTTTTGGTTTATTTTAATTTGACCCTCTCATTTCTTATTATTAATTATATTTCTCCTTGA
AC
Found at i:20449 original size:20 final size:20
Alignment explanation
Indices: 20424--20466 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
20414 GTGAACGGAC
20424 GGGGGTAGGTTGGTAATTAA
1 GGGGGTAGGTTGGTAATTAA
20444 GGGGGTAGGTTGGTAATTAA
1 GGGGGTAGGTTGGTAATTAA
20464 GGG
1 GGG
20467 TATAGCGCGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.00, G:0.49, T:0.28
Consensus pattern (20 bp):
GGGGGTAGGTTGGTAATTAA
Found at i:22915 original size:273 final size:271
Alignment explanation
Indices: 22431--22977 Score: 873
Period size: 273 Copynumber: 2.0 Consensus size: 271
22421 AAATCACTGG
* *
22431 CACTCCGATCTAAAGAAGCGTGAAAAGCGAAATCCTACAACATCTGATGTCAAAGATGACTCTAG
1 CACTCCGATCTAAAGAAGCGTGAAAAGCGAAATCCGACAACATCTGATGTCAAAGAAGACTCTAG
22496 TTGTCCAAGTGAAGCCACCCAGAAATCTGAAGGTGAAAGAGGAGCTGAAAGCATCCTTGTTGATA
66 TTGTCCAAGTGAAGCCACCCAGAAATCTGAAGGTGAAAGAGGAGCTGAAAGCATCCTTGTTGATA
* * *
22561 CTGCGGCCTACATGATATTGGAGAGTTCAACTTTGTCTCCAGCAACATCTTTAACTACTGAGTCG
131 CTCCGGCCTACATGATATTGGAGAGTTCAACTTTGTCTCCAGCAACATCTTCAACTACAGAGTCG
*
22626 TCCTCCTTTGTTGAAGATACTTG-TCCTCCTGCGGAAACATACCAAGCTCAAAGCAGTGGAGATT
196 TCCTCCTTTGTTGAAGATACTTGTTCCTCCGGCGGAAACATACCAAGCTCAAAGCAGTGGAGATT
*
22690 TTTGGAATAAT
261 TCTGGAATAAT
* *
22701 CACTCCGATCTAAAGAAGCGTGGAAAGCGAAATCCGACAATATCTGATCACGTCAAAGAAGACTC
1 CACTCCGATCTAAAGAAGCGTGAAAAGCGAAATCCGACAACATCTGAT---GTCAAAGAAGACTC
* ** *
22766 TAGTTGTCCAAGTGAAGCCACCCAGAATTCTGAAGGTGAAATTGGAGTTGAAAGCATCCTTGTTG
63 TAGTTGTCCAAGTGAAGCCACCCAGAAATCTGAAGGTGAAAGAGGAGCTGAAAGCATCCTTGTTG
* *
22831 ATACTCCGG-CTAACATGATCTTGGAGAGTTCAACTTTGTCTCCAGCGACATCTTCAACTACAGA
128 ATACTCCGGCCT-ACATGATATTGGAGAGTTCAACTTTGTCTCCAGCAACATCTTCAACTACAGA
**
22895 GTTTTCCTCCTTTGTTGAAGATACTTGTCTTCCTCCGGCGGAAACATACCAAGCTCAAAGCAGTG
192 GTCGTCCTCCTTTGTTGAAGATACTTG--TTCCTCCGGCGGAAACATACCAAGCTCAAAGCAGTG
22960 GAGATTTCTGGAATAAT
255 GAGATTTCTGGAATAAT
22977 C
1 C
22978 CCTTTGTTGC
Statistics
Matches: 253, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
270 45 0.18
272 2 0.01
273 155 0.61
276 51 0.20
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (271 bp):
CACTCCGATCTAAAGAAGCGTGAAAAGCGAAATCCGACAACATCTGATGTCAAAGAAGACTCTAG
TTGTCCAAGTGAAGCCACCCAGAAATCTGAAGGTGAAAGAGGAGCTGAAAGCATCCTTGTTGATA
CTCCGGCCTACATGATATTGGAGAGTTCAACTTTGTCTCCAGCAACATCTTCAACTACAGAGTCG
TCCTCCTTTGTTGAAGATACTTGTTCCTCCGGCGGAAACATACCAAGCTCAAAGCAGTGGAGATT
TCTGGAATAAT
Found at i:26375 original size:21 final size:21
Alignment explanation
Indices: 26333--26375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26323 CTTAATTCAA
* *
26333 ACATTATTTTAAGTAGTGGTT
1 ACATTATATTAAGTAATGGTT
*
26354 ACATTATATTAAGTAATTGTT
1 ACATTATATTAAGTAATGGTT
26375 A
1 A
26376 TATATTAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (21 bp):
ACATTATATTAAGTAATGGTT
Found at i:32665 original size:22 final size:22
Alignment explanation
Indices: 32640--32695 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
32630 TATTAGAGTG
32640 ATAAATAAATTAGGTTTGAAAT
1 ATAAATAAATTAGGTTTGAAAT
32662 ATAAATAAATTAGGTTTGAAAT
1 ATAAATAAATTAGGTTTGAAAT
32684 ATAAATATAATT
1 ATAAATA-AATT
32696 TTTGTAGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 29 0.88
23 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (22 bp):
ATAAATAAATTAGGTTTGAAAT
Found at i:45977 original size:15 final size:16
Alignment explanation
Indices: 45959--46042 Score: 75
Period size: 15 Copynumber: 5.2 Consensus size: 16
45949 AAAAGGGAAC
45959 AAAT-AAAAAGATGAA
1 AAATAAAAAAGATGAA
*
45974 AAATGAAAAA-ATGAA
1 AAATAAAAAAGATGAA
** *
45989 AAGGAAAAAAAATGAA
1 AAATAAAAAAGATGAA
46005 AAATGAAAAAAGAAATGAAA
1 AAAT-AAAAAAG--ATG-AA
46025 AAATAAAAAAGA-GAA
1 AAATAAAAAAGATGAA
46040 AAA
1 AAA
46043 GGAGGGTTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 21 0.37
16 13 0.23
17 7 0.12
19 10 0.18
20 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (16 bp):
AAATAAAAAAGATGAA
Found at i:45981 original size:7 final size:7
Alignment explanation
Indices: 45959--46019 Score: 50
Period size: 7 Copynumber: 8.1 Consensus size: 7
45949 AAAAGGGAAC
*
45959 AAATAAA
1 AAATGAA
45966 AAGATGAA
1 AA-ATGAA
45974 AAATGAAA
1 AAATG-AA
45982 AAATGAA
1 AAATGAA
**
45989 AAGGAAAAA
1 AA--ATGAA
45998 AAATGAA
1 AAATGAA
46005 AAATGAA
1 AAATGAA
*
46012 AAAAGAA
1 AAATGAA
46019 A
1 A
46020 TGAAAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
7 26 0.59
8 13 0.30
9 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAATGAA
Found at i:45983 original size:8 final size:8
Alignment explanation
Indices: 45959--46034 Score: 55
Period size: 8 Copynumber: 10.4 Consensus size: 8
45949 AAAAGGGAAC
45959 AAAT-AAA
1 AAATGAAA
45966 AAGATG-AA
1 AA-ATGAAA
45974 AAATGAAA
1 AAATGAAA
45982 AAATGAAA
1 AAATGAAA
45990 AGGAA--AAA
1 A--AATGAAA
45998 AAATG-AA
1 AAATGAAA
46005 AAATGAAA
1 AAATGAAA
46013 AAA-G---
1 AAATGAAA
46017 AAATGAAA
1 AAATGAAA
46025 AAAT-AAA
1 AAATGAAA
46032 AAA
1 AAA
46035 GAGAAAAAGG
Statistics
Matches: 57, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
4 3 0.05
5 1 0.02
6 2 0.04
7 19 0.33
8 30 0.53
10 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (8 bp):
AAATGAAA
Found at i:46020 original size:19 final size:19
Alignment explanation
Indices: 45993--46036 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
45983 AATGAAAAGG
45993 AAAAA-AAATG-AAAAATGA
1 AAAAAGAAATGAAAAAAT-A
46011 AAAAAGAAATGAAAAAATA
1 AAAAAGAAATGAAAAAATA
46030 AAAAAGA
1 AAAAAGA
46037 GAAAAAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.21
19 13 0.54
20 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAAAGAAATGAAAAAATA
Found at i:47159 original size:136 final size:136
Alignment explanation
Indices: 46913--47262 Score: 558
Period size: 136 Copynumber: 2.6 Consensus size: 136
46903 GGTGAACCAG
*
46913 CATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
46978 AGAAGAGCTTGTTCGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
47043 GATCAG
131 GATCAA
*
47049 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* *
47114 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
47179 GATCAA
131 GATCAA
* ** ** *
47185 CATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAAC-GAGGAAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
*
47249 AGAAGAACTTGTTC
66 AGAAGAGCTTGTTC
47263 AACTTCGCAT
Statistics
Matches: 198, Mismatches: 16, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
135 34 0.17
136 164 0.83
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTCGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:47602 original size:331 final size:332
Alignment explanation
Indices: 47178--47919 Score: 1059
Period size: 331 Copynumber: 2.2 Consensus size: 332
47168 CTCGCTTGAG
* * *
47178 GGATCAACATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCAAACGAG-GAAGAAGAAGTT
1 GGATCAACATTTCCA-TGAAGAGTTCATAATGAGAAGAACTCATC-CATGAGAG-AGAAGAAGTT
*
47242 CATAATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAGAAGA
63 CATAATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGA
*
47307 ACTCGTCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTC
128 ACTCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTC
* * * * *
47372 ATGACATTTCGAATTAGTGACACCTAGCTTGAGGGATTGATATTTTC-A-GAAGAGTTCATAATG
193 ACGACATTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATG
* * * *
47435 AGAAGAACTCATCCTAAAGGAGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAGTCCATCAC
258 AGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCAC
47500 AGAAAGAGAT
323 AGAAAGAGAT
* *
47510 GGATCAACATTTCCAATGGAGAGTTCATAATAAGAAGAACTCATCCATGAGAGAGAAGAAGTTCA
1 GGATCAACATTTCC-ATGAAGAGTTCATAATGAGAAGAACTCATCCATGAGAGAGAAGAAGTTCA
* *
47575 TAATGAGAAGAACTTGTTCAACTTCGCATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAAC
65 TAATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAAC
* * * * *
47640 TCATCCGATAGAGGGAGAAGAAGTTCATAATGAGAAGAGTTTTTTTGACCTATCACTTGATTCAC
130 TCATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCAC
** *
47705 GACATTTCGAATCAGTGATGCCTCGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATGAG
195 GACATTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATGAG
*
47770 AAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATTCACCACAG
260 AAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAG
** *
47835 ATGGAGGT
325 AAAGAGAT
* * * *
47843 GAACCAACATTTCC-TGAAGAGTTCATAATGAGAAGAACTCGTCC-T-A-A-AGGAGAAGTTCAT
1 GGATCAACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCCATGAGAGAGAAGAAGTTCAT
* * *
47903 GAGGAGAAGAATTTGTT
66 AATGAGAAGAACTTGTT
47920 TAATCTAACG
Statistics
Matches: 367, Mismatches: 39, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
327 26 0.07
328 1 0.00
329 1 0.00
330 1 0.00
331 201 0.55
332 42 0.11
333 95 0.26
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (332 bp):
GGATCAACATTTCCATGAAGAGTTCATAATGAGAAGAACTCATCCATGAGAGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTCGCATCAACATTTTCAATGGAGAGCTCATAATGAAAAGAACT
CATCCGAAAGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACG
ACATTTCGAATCAGTGACACCTAGCTTGAGGGATCGACATTTCCAATGAAGAGTTCATAATGAGA
AGAACTCATCATAAAGGAGAAAGTTCATAATGAGAAGAACTTATTCCTTTCAAATCCACCACAGA
AAGAGAT
Found at i:47627 original size:90 final size:92
Alignment explanation
Indices: 47512--47677 Score: 275
Period size: 90 Copynumber: 1.8 Consensus size: 92
47502 AAAGAGATGG
47512 ATCAACATTTCCAATGGAGAGTTCATAAT-AAGAAGAACTCATCC-AT-GAGAGAGAAGAAGTTC
1 ATCAACATTTCCAATGGAGAGTTCATAATGAA-AAGAACTCATCCGATAGAGAGAGAAGAAGTTC
47574 ATAATGAGAAGAACTTGTTCAACTTCGC
65 ATAATGAGAAGAACTTGTTCAACTTCGC
* * *
47602 ATCAATATTTTCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGAGAGAAGAAGTTCA
47667 TAATGAGAAGA
66 TAATGAGAAGA
47678 GTTTTTTTGA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
90 39 0.56
91 4 0.06
92 27 0.39
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (92 bp):
ATCAACATTTCCAATGGAGAGTTCATAATGAAAAGAACTCATCCGATAGAGAGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACTTCGC
Found at i:48063 original size:14 final size:14
Alignment explanation
Indices: 48046--48078 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
48036 GTTAAAAAAA
48046 TATTATTAAATTAT
1 TATTATTAAATTAT
48060 TATTATTAAATTAT
1 TATTATTAAATTAT
48074 TATTA
1 TATTA
48079 ATTTTAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTATTAAATTAT
Found at i:51667 original size:34 final size:35
Alignment explanation
Indices: 51629--51701 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
51619 AAGATGTACA
* *
51629 TAAATTTTATGGTAGGATATGAA-TTTTAAATTTT
1 TAAATTTTATGGTAGGAGATGAATTTTTAAAATTT
51663 TAAATTTTATGGTAGGAGATGAATTTTTAAAATTT
1 TAAATTTTATGGTAGGAGATGAATTTTTAAAATTT
51698 TAAA
1 TAAA
51702 AGAAGATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 22 0.61
35 14 0.39
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (35 bp):
TAAATTTTATGGTAGGAGATGAATTTTTAAAATTT
Found at i:53663 original size:2 final size:2
Alignment explanation
Indices: 53651--53709 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
53641 AAATCATTCA
53651 AT AT A- 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
53692 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
53710 TATTAATCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53774 original size:2 final size:2
Alignment explanation
Indices: 53767--53796 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
53757 TTATTCAACA
53767 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
53797 CTTGATGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54873 original size:2 final size:2
Alignment explanation
Indices: 54868--54915 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
54858 TATATTTAAT
* *
54868 TC TC TC TC TC TC -C TC TC CC TC TC CC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
54909 TC TC TC T
1 TC TC TC T
54916 TAAATATATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:56079 original size:157 final size:159
Alignment explanation
Indices: 55773--56115 Score: 530
Period size: 158 Copynumber: 2.2 Consensus size: 159
55763 TTCCTCCTCC
* * *
55773 ATTTTAAGTCTATGTTTTTACAAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
55838 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
66 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
* * *
55903 AGTCTCCTTATTTCTTCAATTCATCATTT
131 AATATCCTTATTCCTTCAATTCATCATTT
* * *
55932 -TTTTAAGTTCGTTTTTTTACCAAATTTGAGCCACATGCTCCTAAACCATAGTAGAATACATGTG
1 ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
* *
55996 TACTTTCAATTC-TCTTTTTGGTAACAAATTTTTTATTTTTCAATTTAGTTCTTCAAATT-TTCA
66 TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTC-AATTATTCA
** *
56059 TAATATCCTTATTCCTTCAATTTGTGATTT
130 TAATATCCTTATTCCTTCAATTCATCATTT
56089 ATTTTAAGTCCATTTTTTTACCAAATT
1 ATTTTAAGTCCATTTTTTTACCAAATT
56116 GTTTTATTTA
Statistics
Matches: 166, Mismatches: 16, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
157 68 0.41
158 98 0.59
ACGTcount: A:0.28, C:0.17, G:0.08, T:0.47
Consensus pattern (159 bp):
ATTTTAAGTCCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATAGTAGAATACATGTG
TACTTTCAATTCATCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCCTTCAATTATTCAT
AATATCCTTATTCCTTCAATTCATCATTT
Done.