Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006847.1 Hibiscus syriacus cultivar Beakdansim tig00017408_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: 68995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1774 original size:57 final size:58
Alignment explanation
Indices: 1672--1781 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 58
1662 CCATGTTCTG
* *
1672 CAGCAAGATTTTTACATATGATCAATCCTCAACCACTGGATCTTCCTAGCTCATCCTC
1 CAGCAAGAATTTTACATATAATCAATCCTCAACCACTGGATCTTCCTAGCTCATCCTC
*
1730 CAGCAAGAATTTTACATATAATC-ATCTTCAACCACTGGATCTTCCTAGCTCA
1 CAGCAAGAATTTTACATATAATCAATCCTCAACCACTGGATCTTCCTAGCTCA
1782 GAGATTTAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 28 0.57
58 21 0.43
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.31
Consensus pattern (58 bp):
CAGCAAGAATTTTACATATAATCAATCCTCAACCACTGGATCTTCCTAGCTCATCCTC
Found at i:8083 original size:2 final size:2
Alignment explanation
Indices: 8076--8117 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
8066 TGTTAATAGA
8076 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
8118 TAATTAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8573 original size:14 final size:14
Alignment explanation
Indices: 8554--8580 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8544 TTATTTAGAT
8554 CATTTATATAAAAC
1 CATTTATATAAAAC
8568 CATTTATATAAAA
1 CATTTATATAAAA
8581 TCAAATTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (14 bp):
CATTTATATAAAAC
Found at i:11371 original size:23 final size:23
Alignment explanation
Indices: 11345--11392 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
11335 TCTTGATCAG
11345 TACCTTAAGGATGATTTTGAAAC
1 TACCTTAAGGATGATTTTGAAAC
11368 TACCTTAAGGATGATTTTGAAAC
1 TACCTTAAGGATGATTTTGAAAC
11391 TA
1 TA
11393 AGGAAATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (23 bp):
TACCTTAAGGATGATTTTGAAAC
Found at i:22490 original size:19 final size:20
Alignment explanation
Indices: 22466--22515 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
22456 GATAAATTTA
*
22466 TTAATAATTTTATAATC-TT
1 TTAATAATTTTATAAGCATT
*
22485 TTAATAAATTTAATAAGCATT
1 TTAAT-AATTTTATAAGCATT
22506 TT-ATAATTTT
1 TTAATAATTTT
22516 TTAAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 12 0.46
21 4 0.15
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (20 bp):
TTAATAATTTTATAAGCATT
Found at i:22492 original size:31 final size:31
Alignment explanation
Indices: 22452--22519 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
22442 ATTTATAGTA
* *
22452 TTTAGATAAATTTATTAATAATTTTATAATCT
1 TTTA-ATAAATTTAATAAGAATTTTATAATCT
* *
22484 TTTAATAAATTTAATAAGCATTTTATAATTT
1 TTTAATAAATTTAATAAGAATTTTATAATCT
22515 TTTAA
1 TTTAA
22520 ATTTCATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (31 bp):
TTTAATAAATTTAATAAGAATTTTATAATCT
Found at i:23271 original size:11 final size:10
Alignment explanation
Indices: 23248--23329 Score: 55
Period size: 11 Copynumber: 8.1 Consensus size: 10
23238 TAAAGTTTAA
*
23248 AAAT-TTATA
1 AAATATTATT
23257 AAATACTTATT
1 AAATA-TTATT
23268 AAAT-TTATT
1 AAATATTATT
23277 AAAATATTA-T
1 -AAATATTATT
*
23287 AAATTATTAAT
1 AAA-TATTATT
23298 AAAT-TTATCT
1 AAATATTAT-T
* *
23308 AAATACTATA
1 AAATATTATT
23318 AAATAATTATT
1 AAAT-ATTATT
23329 A
1 A
23330 TATTATCGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
9 15 0.26
10 20 0.34
11 23 0.40
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
AAATATTATT
Found at i:23280 original size:31 final size:30
Alignment explanation
Indices: 23244--23329 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
23234 TCAATAAAGT
23244 TTAAAAATTTATAAAATACTTATTAAATTTA
1 TTAAAAATTTATAAAATA-TTATTAAATTTA
* *
23275 TT-AAAATATTATAAATTATTAATAAATTTA
1 TTAAAAAT-TTATAAAATATTATTAAATTTA
* *
23305 TCTAAATA-CTATAAAATAATTATTA
1 T-TAAAAATTTATAAAAT-ATTATTA
23330 TATTATCGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
30 24 0.53
31 18 0.40
32 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (30 bp):
TTAAAAATTTATAAAATATTATTAAATTTA
Found at i:23281 original size:21 final size:19
Alignment explanation
Indices: 23248--23296 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
23238 TAAAGTTTAA
23248 AAATTTA-TAAAATACTTATT
1 AAATTTATTAAAATA-TTA-T
23268 AAATTTATTAAAATATTAT
1 AAATTTATTAAAATATTAT
23287 AAA-TTATTAA
1 AAATTTATTAA
23297 TAAATTTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 10 0.36
21 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTATTAAAATATTAT
Found at i:23300 original size:21 final size:21
Alignment explanation
Indices: 23248--23300 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
23238 TAAAGTTTAA
23248 AAATTT-ATAAAATACTTATT
1 AAATTTAATAAAATACTTATT
*
23268 AAATTTATTAAAATA-TTA-T
1 AAATTTAATAAAATACTTATT
23287 AAATTATTAATAAA
1 AAA-T-TTAATAAA
23301 TTTATCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 10 0.36
21 14 0.50
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATTTAATAAAATACTTATT
Found at i:23336 original size:30 final size:32
Alignment explanation
Indices: 23253--23329 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 32
23243 TTTAAAAATT
* *
23253 TATAAAATACTTATTAAATTTAT-TAAAATAT
1 TATAAAATAATTATTAAATTTATCTAAAATAC
* *
23284 TAT-AAATTATTAATAAATTTATCT-AAATAC
1 TATAAAATAATTATTAAATTTATCTAAAATAC
23314 TATAAAATAATTATTA
1 TATAAAATAATTATTA
23330 TATTATCGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
30 24 0.63
31 14 0.37
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (32 bp):
TATAAAATAATTATTAAATTTATCTAAAATAC
Found at i:23920 original size:13 final size:13
Alignment explanation
Indices: 23898--23959 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 13
23888 ACGTAAAAAT
*
23898 TAAATGAATATAA
1 TAAATAAATATAA
23911 TAAATAAATATAA
1 TAAATAAATATAA
23924 T-AAT-AATAATAA
1 TAAATAAAT-ATAA
23936 TTAATTATTAAATATAA
1 -TAA--A-TAAATATAA
23953 TAAATAA
1 TAAATAA
23960 TTAAAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
11 3 0.07
12 7 0.17
13 17 0.41
14 2 0.05
16 4 0.10
17 5 0.12
18 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TAAATAAATATAA
Found at i:23931 original size:24 final size:25
Alignment explanation
Indices: 23904--23995 Score: 77
Period size: 24 Copynumber: 3.6 Consensus size: 25
23894 AAATTAAATG
23904 AATATAATAA-ATAAATATAATAAT
1 AATATAATAATATAAATATAATAAT
23928 AATAATAATTAATTATTAAATATAATAAAT
1 AAT-ATAA-TAA-TA-TAAATATAAT-AAT
*
23958 AAT-TAA-AATATAAATA-ATATAGT
1 AATATAATAATATAAATATA-ATAAT
*
23981 AATATAGTAAT-TAAA
1 AATATAATAATATAAA
23996 ATAGATGTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
23 6 0.11
24 17 0.30
25 9 0.16
26 5 0.09
28 4 0.07
29 10 0.18
30 6 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (25 bp):
AATATAATAATATAAATATAATAAT
Found at i:24089 original size:11 final size:11
Alignment explanation
Indices: 24069--24106 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
24059 TAAAATATTA
24069 AATATAATAAAT
1 AATATAAT-AAT
24081 AAT-TAATAAT
1 AATATAATAAT
*
24091 AATATAATTAT
1 AATATAATAAT
24102 AATAT
1 AATAT
24107 TTTTGAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 6 0.25
11 15 0.62
12 3 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAATAAT
Found at i:24091 original size:14 final size:14
Alignment explanation
Indices: 24071--24105 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
24061 AAATATTAAA
24071 TATAATAA-ATAAT
1 TATAATAATATAAT
24084 TAATAATAATATAAT
1 T-ATAATAATATAAT
24099 TATAATA
1 TATAATA
24106 TTTTTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 1 0.05
14 13 0.65
15 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAATAATATAAT
Found at i:24303 original size:18 final size:18
Alignment explanation
Indices: 24277--24320 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
24267 AAATAGGACC
*
24277 CTCCGCTCCTATTCATCA
1 CTCCACTCCTATTCATCA
24295 CTCCACTCCTATTCATCA
1 CTCCACTCCTATTCATCA
*
24313 CTACACTC
1 CTCCACTC
24321 ATCCCTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.20, C:0.45, G:0.02, T:0.32
Consensus pattern (18 bp):
CTCCACTCCTATTCATCA
Found at i:26494 original size:22 final size:22
Alignment explanation
Indices: 26466--26519 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
26456 CCAAAATAAT
26466 AATAAAAATACTATTTTTATGC
1 AATAAAAATACTATTTTTATGC
26488 AATAAAAATACTATTTTTATGC
1 AATAAAAATACTATTTTTATGC
26510 AATAAAAATA
1 AATAAAAATA
26520 GTGATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (22 bp):
AATAAAAATACTATTTTTATGC
Found at i:41258 original size:2 final size:2
Alignment explanation
Indices: 41205--41241 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
41195 CCGCCCCGAT
*
41205 TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41242 TTTATATTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:47461 original size:37 final size:35
Alignment explanation
Indices: 47379--47490 Score: 104
Period size: 37 Copynumber: 3.2 Consensus size: 35
47369 TGAAAGTATT
**
47379 AAAATGGTTTTC-AAGTTTGGT-AATCAATTT-TAAA
1 AAAATGGTTTTCAAAGTTTGGTAAAT--ATTTGTTGA
* *
47413 AAAATGGTTTTCAAATTTTGGTAAATATTTCTTTGA
1 AAAATGGTTTTCAAAGTTTGGTAAATATTT-GTTGA
* * *
47449 AAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATATTTGTTGA
47485 AAAATG
1 AAAATG
47491 ATAATGAGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
34 16 0.25
35 9 0.14
36 19 0.29
37 21 0.32
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATATTTGTTGA
Found at i:52014 original size:21 final size:21
Alignment explanation
Indices: 51990--52050 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
51980 AACTTTGAAA
51990 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
52011 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
52025 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
52046 AAATG
1 AAATG
52051 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:52081 original size:37 final size:37
Alignment explanation
Indices: 51982--52100 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
51972 TGGTAACCAA
51982 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
52019 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
52054 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
52091 -GTTGAAAAAT
1 CTTTGAAAAAT
52101 GATAATGGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:59103 original size:28 final size:27
Alignment explanation
Indices: 59051--59117 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
59041 AACATTTTTT
** *
59051 TAATTTTCAAAAAATTGAAAATAAAAA
1 TAATTTTTTAAAAATTAAAAATAAAAA
59078 TAATTTTTTAAAAATTAAAAATTAAAAA
1 TAATTTTTTAAAAATTAAAAA-TAAAAA
59106 T-ATTTTTTAAAA
1 TAATTTTTTAAAA
59118 CCAAATTCGC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 29 0.81
28 7 0.19
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (27 bp):
TAATTTTTTAAAAATTAAAAATAAAAA
Found at i:60944 original size:31 final size:30
Alignment explanation
Indices: 60903--60996 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
60893 TTATAATAAA
*
60903 TAAT-AAATATAATTTATAATAATTTTATT-T
1 TAATAAAATATAA-TAATAATAATTTT-TTAT
*
60933 TAATAAAATATAATAATCATAATTTTTTAT
1 TAATAAAATATAATAATAATAATTTTTTAT
* * *
60963 TTATAAAAT-T-ATAGAT-ATAATATTTTAA
1 TAATAAAATATAATA-ATAATAATTTTTTAT
60991 TAATAA
1 TAATAA
60997 TATTGACATA
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
28 18 0.33
29 5 0.09
30 24 0.44
31 8 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
TAATAAAATATAATAATAATAATTTTTTAT
Found at i:60996 original size:14 final size:14
Alignment explanation
Indices: 60914--61000 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
60904 AATAAATATA
**
60914 ATTTATAATAATTTT
1 ATTT-TAATAATAAT
60929 ATTTTAATAA-AAT
1 ATTTTAATAATAAT
** *
60942 ATAATAATCATAAT
1 ATTTTAATAATAAT
* * * *
60956 TTTTTATTTATAAA
1 ATTTTAATAATAAT
*
60970 ATTATAGAT-ATAAT
1 ATTTTA-ATAATAAT
60984 ATTTTAATAATAAT
1 ATTTTAATAATAAT
60998 ATT
1 ATT
61001 GACATAATAA
Statistics
Matches: 53, Mismatches: 16, Indels: 7
0.70 0.21 0.09
Matches are distributed among these distances:
13 10 0.19
14 38 0.72
15 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (14 bp):
ATTTTAATAATAAT
Found at i:60996 original size:28 final size:28
Alignment explanation
Indices: 60928--60996 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
60918 ATAATAATTT
*
60928 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
60955 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
60983 TATTTTAATAATAA
1 TATTTTAATAATAA
60997 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:61449 original size:182 final size:182
Alignment explanation
Indices: 61076--61498 Score: 686
Period size: 182 Copynumber: 2.3 Consensus size: 182
61066 ATTAACCAAT
* * * **
61076 ATATTTTTACCTGTTATATTTTTATAGATCGATATATTTTTATAAAGTATCGACACTTTATTGGC
1 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTACC
* * *
61141 GCTATAACTTATTTTCTTTTAAATTCTAAAAGTGTCGATACTTATAATAAAGTATCGACACTTTC
66 GCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGAAACTTATAATAAAGTATCGACACTATC
* *
61206 AACATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCGGTTTTGTC
131 AACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
61258 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATATAC
1 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTAT-TAC
61323 CGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGAAACTTATAATAAAGTATCGACACTAT
65 CGCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGAAACTTATAATAAAGTATCGACACTAT
* ** * *
61388 CAACATATCTGGTAGCGCTTTACTTGTTTTGTCATTTATAGATCGGTTTTGTC
130 CAACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
*
61441 AT-TTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGTCACTTT
1 ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
61499 CAAGATATCC
Statistics
Matches: 224, Mismatches: 16, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
182 113 0.50
183 111 0.50
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
ATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATTACC
GCTATAACTTATTCTCTTTTAAATTCTAAAAGTGTCGAAACTTATAATAAAGTATCGACACTATC
AACATATCCGGTAGCGCTTTACCGGTTTTGTCATTTAGAGACCGGTTTTGTC
Found at i:61609 original size:112 final size:112
Alignment explanation
Indices: 61370--61871 Score: 853
Period size: 112 Copynumber: 4.5 Consensus size: 112
61360 GAAACTTATA
* * * * *
61370 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACTTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
61435 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
61481 ATAAAGTATCGTCACTTTCAAGATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
61546 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
61593 ATAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCTGTTTTGTCATATATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
61658 TTTGTCATTTTTTTACCTGTTATTTTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
** * * *
61705 ATAAAGTATCGACACTTTCAATATATCTAGTAGAGTTTTACATGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
61770 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
61817 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTT
61872 TTTTTACCTG
Statistics
Matches: 364, Mismatches: 26, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
111 65 0.18
112 299 0.82
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:61759 original size:224 final size:222
Alignment explanation
Indices: 61370--62032 Score: 970
Period size: 224 Copynumber: 3.0 Consensus size: 222
61360 GAAACTTATA
* * * *
61370 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACTTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCA-TTATAGA-CGGT
*
61435 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGTCACTTT
64 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
* * * *
61499 CAAGATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGTTTTGTCATTTTTTTACCT
129 CAATATATCCGGTAGAGCTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
61564 GTTATATTGTTATGGATCGATACATTTTT
194 GTTATATTGTTATGGATCGATACATTTTT
*
61593 ATAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCTGTTTTGTCATATATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCAT-TATAGA-CGGT
*
61658 TTTGTCATTTTTTTACCTGTTATTTTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
64 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTT
** *
61723 CAATATATCTAGTAGAGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
129 CAATATATCCGGTAGAGCTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCT
61788 GTTATATTGTTATGGATCGATACATTTTT
194 GTTATATTGTTATGGATCGATACATTTTT
61817 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTC-------A------
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTATAGACGGTTT
61869 --T--TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
66 TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
*
61930 ATATATCCGGTAGCA-CTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTA
131 ATATATCCGGTAG-AGCTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTG
* * *
61994 TTATATTGTTATGGATC-AAATTATTTTA
195 TTATATTGTTATGGATCGATA-CATTTTT
62022 ATAAAGTATCG
1 ATAAAGTATCG
62033 GCACAAACCG
Statistics
Matches: 412, Mismatches: 24, Indels: 26
0.89 0.05 0.06
Matches are distributed among these distances:
204 2 0.00
205 150 0.36
206 1 0.00
207 1 0.00
216 1 0.00
222 1 0.00
223 64 0.16
224 192 0.47
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (222 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTATAGACGGTTT
TGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTCA
ATATATCCGGTAGAGCTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGT
TATATTGTTATGGATCGATACATTTTT
Found at i:61885 original size:93 final size:93
Alignment explanation
Indices: 61768--61964 Score: 369
Period size: 93 Copynumber: 2.1 Consensus size: 93
61758 TTATAGACCG
61768 GTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
* *
61832 TTTCAATATATCCGGTAGCGCTTTACCT
66 TTTCAATATATCCGGTAGCACTTTACAT
61860 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
61925 TTTCAATATATCCGGTAGCACTTTACAT
66 TTTCAATATATCCGGTAGCACTTTACAT
61953 GTTTTGTCATTT
1 GTTTTGTCATTT
61965 ATAGACCGGT
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 9 0.09
93 93 0.91
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (93 bp):
GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
TTTCAATATATCCGGTAGCACTTTACAT
Found at i:61901 original size:205 final size:204
Alignment explanation
Indices: 61656--62032 Score: 641
Period size: 205 Copynumber: 1.8 Consensus size: 204
61646 ATATAGACCG
*
61656 GTTTTGTCATTTTTTTACCTGTTATTTTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
1 GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
61721 TTCAATATATCTAGTAG-AGTTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
66 TTCAATATATCCAGTAGCA-CTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
* * *
61785 CCTGTTATATTGTTATGGATC-GATACATTTTTATAAAGTATCGACACTTTCAATATATCCGGTA
130 CCTATTATATTGTTATGGATCAAAT-CATTTTAATAAAGTATCGACACTTTCAATATATCCGGTA
61849 GCGCTTTACCT
194 GCGCTTTACCT
61860 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
*
61925 TTTCAATATATCCGGTAGCACTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
65 TTTCAATATATCCAGTAGCACTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTA
*
61990 CCTATTATATTGTTATGGATCAAATTATTTTAATAAAGTATCG
130 CCTATTATATTGTTATGGATCAAATCATTTTAATAAAGTATCG
62033 GCACAAACCG
Statistics
Matches: 162, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
204 9 0.06
205 150 0.93
206 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (204 bp):
GTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTCAATATATCCAGTAGCACTTTACATGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTAC
CTATTATATTGTTATGGATCAAATCATTTTAATAAAGTATCGACACTTTCAATATATCCGGTAGC
GCTTTACCT
Found at i:67315 original size:21 final size:21
Alignment explanation
Indices: 67289--67342 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
67279 GCGTTGCATT
67289 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
67310 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
67331 TCGCGTTGCGAT
1 TCGCGTTGCGAT
67343 TTTTCAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:67410 original size:22 final size:22
Alignment explanation
Indices: 67381--67434 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
67371 TTTTCCAAAT
67381 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
*
67403 TTGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATAGTCTACAGTTG
67425 TCGTTGCGAT
1 TCGTTGCGAT
67435 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.39
Consensus pattern (22 bp):
TCGTTGCGATAGTCTACAGTTG
Found at i:68843 original size:2 final size:2
Alignment explanation
Indices: 68836--68861 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68826 AAATTCCTCA
68836 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
68862 TCAACACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.