Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000613.1 Hibiscus syriacus cultivar Beakdansim tig00001190_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: 61192
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Found at i:1730 original size:27 final size:27
Alignment explanation
Indices: 1700--1789 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
1690 CGTTGGGATC
*
1700 ACATTTTGCATATGCATTTGCATATTT
1 ACATTTTGCATATGCATTTACATATTT
*
1727 ACATTTTGCATATGCATTTACATCTTT
1 ACATTTTGCATATGCATTTACATATTT
** * *
1754 GTA-TTTGCATTTGCATTTA-A-ATTC
1 ACATTTTGCATATGCATTTACATATTT
1778 ACATCTTTGCAT
1 ACAT-TTTGCAT
1790 TTTTATGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
24 3 0.06
25 1 0.02
26 22 0.42
27 26 0.50
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.48
Consensus pattern (27 bp):
ACATTTTGCATATGCATTTACATATTT
Found at i:1762 original size:20 final size:19
Alignment explanation
Indices: 1723--1771 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
1713 GCATTTGCAT
1723 ATTTACATTTTGCATATGC
1 ATTTACATTTTGCATATGC
* *
1742 ATTTACATCTTTGTATTTGC
1 ATTTACAT-TTTGCATATGC
*
1762 ATTTGCATTT
1 ATTTACATTT
1772 AAATTCACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (19 bp):
ATTTACATTTTGCATATGC
Found at i:6972 original size:40 final size:40
Alignment explanation
Indices: 6917--7241 Score: 381
Period size: 40 Copynumber: 8.2 Consensus size: 40
6907 ATATGGAGAA
* * *
6917 TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGAT
1 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
6957 TTTATCTCATTCAAGATTGTTTTTCCTTTAAACAGAAGAT
1 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
6997 TTTATCTC-TGTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCAT-TCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
7037 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACATAAGAT
1 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
7077 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAAAT
1 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * *
7117 TTTATCTCGTTCAAGATTGTTTTTCCTTGAAATAAAATAT
1 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * ** * * *
7157 TTTATCTCGCTT-GAGA-TAATTTCCCTCGAAACAAAAGAT
1 TTTATCTC-ATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * * *
7196 TTTATCTCGCTT-GAGATAG-TTTCCCTCGAAACAGAAGAT
1 TTTATCTC-ATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
7235 TTTATCT
1 TTTATCT
7242 TGCTTGAGAT
Statistics
Matches: 256, Mismatches: 25, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
39 60 0.23
40 194 0.76
41 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (40 bp):
TTTATCTCATTCAAGATTGTTTTTCCTTGAAACAGAAGAT
Found at i:7131 original size:120 final size:120
Alignment explanation
Indices: 6917--7203 Score: 434
Period size: 120 Copynumber: 2.4 Consensus size: 120
6907 ATATGGAGAA
6917 TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGATTTTATCTCATTCAAGATTGTTTTTC
1 TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGATTTTATCTCATTCAAGATTGTTTTTC
* * *
6982 CTTTAAACAGAAGATTTTATCTCTGTCAAGATTGTTTTTCCTTGAAACAGAAGAT
66 CTTGAAACAGAAAATTTTATCTCTGTCAAGATTGTTTTTCCTTGAAACAAAAGAT
*
7037 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATCTCATTCAAGATTGTTTTTC
1 TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGATTTTATCTCATTCAAGATTGTTTTTC
* *
7102 CTTGAAACAGAAAATTTTATCTC-GTTCAAGATTGTTTTTCCTTGAAATAAAATAT
66 CTTGAAACAGAAAATTTTATCTCTG-TCAAGATTGTTTTTCCTTGAAACAAAAGAT
* ** * * * *
7157 TTTATCTCGCTTGAGA-TAATTTCCCTCGAAACAAAAGATTTTATCTC
1 TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGATTTTATCTC
7204 GCTTGAGATA
Statistics
Matches: 152, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
119 27 0.18
120 125 0.82
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.43
Consensus pattern (120 bp):
TTTATCTCACTCAAGATTATTTTTCCTTGAAACATAAGATTTTATCTCATTCAAGATTGTTTTTC
CTTGAAACAGAAAATTTTATCTCTGTCAAGATTGTTTTTCCTTGAAACAAAAGAT
Found at i:7204 original size:39 final size:39
Alignment explanation
Indices: 7025--7269 Score: 208
Period size: 40 Copynumber: 6.2 Consensus size: 39
7015 GTTTTTCCTT
* * ** * * *
7025 GAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTT
1 GAAACAAAAGATTTTATCTCGCTTGAGATAG-TTTCCCTC
* * * * * *
7065 GAAACATAAGATTTTATCTC-ATTCAAGATTGTTTTTCCTT
1 GAAACAAAAGATTTTATCTCGCTT-GAGATAG-TTTCCCTC
* * * *
7105 GAAACAGAAA-ATTTTATCTCG-TTCAAGATTGTTTTTCCTT
1 GAAACA-AAAGATTTTATCTCGCTT-GAGATAG-TTTCCCTC
* * *
7145 GAAATAAAATATTTTATCTCGCTTGAGATAATTTCCCTC
1 GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
7184 GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
1 GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
* * *
7223 GAAACAGAAGATTTTATCTTGCTTGAGATAGTTTCTCTC
1 GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
7262 GAAACAAA
1 GAAACAAA
7270 TTTTGTCTCC
Statistics
Matches: 183, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
39 89 0.49
40 90 0.49
41 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (39 bp):
GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
Found at i:7284 original size:36 final size:38
Alignment explanation
Indices: 7025--7305 Score: 194
Period size: 40 Copynumber: 7.2 Consensus size: 38
7015 GTTTTTCCTT
* ** * * *
7025 GAAACAGAAGATTTTATCTCACTCAAGATTGTTTTTCCTT
1 GAAACA-AAGATTTTATCTCGCTTGAGATAG-TTTCCCTC
* * * * *
7065 GAAACATAAGATTTTATCTC-ATTCAAGATTGTTTTTCCTT
1 GAAACA-AAGATTTTATCTCGCTT-GAGATAG-TTTCCCTC
* * * * *
7105 GAAACAGAAAATTTTATCTCG-TTCAAGATTGTTTTTCCTT
1 GAAACA-AAGATTTTATCTCGCTT-GAGATAG-TTTCCCTC
* * *
7145 GAAATAAAATATTTTATCTCGCTTGAGATAATTTCCCTC
1 GAAA-CAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
7184 GAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
1 GAAAC-AAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
* *
7223 GAAACAGAAGATTTTATCTTGCTTGAGATAGTTTCTCTC
1 GAAACA-AAGATTTTATCTCGCTTGAGATAGTTTCCCTC
* * **
7262 GAAAC-AA-ATTTTGTCTCCCTTGAGACGGTTTCCCAT-
1 GAAACAAAGATTTTATCTCGCTTGAGATAGTTTCCC-TC
7298 GAAACAAA
1 GAAACAAA
7306 TTTTGTCTCC
Statistics
Matches: 210, Mismatches: 23, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
36 26 0.12
37 5 0.02
38 1 0.00
39 82 0.39
40 93 0.44
41 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (38 bp):
GAAACAAAGATTTTATCTCGCTTGAGATAGTTTCCCTC
Found at i:7318 original size:21 final size:21
Alignment explanation
Indices: 7292--7337 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
7282 TGAGACGGTT
7292 TCCCATGAAACAAATTTTGTC
1 TCCCATGAAACAAATTTTGTC
7313 TCCCATGAAACAAATTTTGTC
1 TCCCATGAAACAAATTTTGTC
7334 TCCC
1 TCCC
7338 TTGAGACAGT
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:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (21 bp):
TCCCATGAAACAAATTTTGTC
Found at i:7331 original size:57 final size:57
Alignment explanation
Indices: 7262--7382 Score: 197
Period size: 57 Copynumber: 2.1 Consensus size: 57
7252 AGTTTCTCTC
* *
7262 GAAACAAATTTTGTCTCCCTTGAGACGGTTTCCCATGAAACAAATTTTGTCTCCCAT
1 GAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACAAATTTTATCTCCCAT
* *
7319 GAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCCCTT
1 GAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACAAATTTTATCTCCCAT
*
7376 GAGACAA
1 GAAACAA
7383 TTTCACTTGA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (57 bp):
GAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCATGAAACAAATTTTATCTCCCAT
Found at i:7365 original size:36 final size:36
Alignment explanation
Indices: 7313--7396 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 36
7303 AAATTTTGTC
* * *
7313 TCCCATGAAACAAATTTTGTCTCCCTTGAGACAGTT
1 TCCCTTGAAACAAATTTTATCTCCCTTGAGACAATT
7349 TCCCTTGAAACAAATTTTATCTCCCTTGAGACAATT
1 TCCCTTGAAACAAATTTTATCTCCCTTGAGACAATT
*
7385 TCACTTGAAACA
1 TCCCTTGAAACA
7397 GAAGATATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (36 bp):
TCCCTTGAAACAAATTTTATCTCCCTTGAGACAATT
Found at i:7417 original size:39 final size:36
Alignment explanation
Indices: 7318--7442 Score: 124
Period size: 36 Copynumber: 3.4 Consensus size: 36
7308 TTGTCTCCCA
* * * *
7318 TGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCT
1 TGAAACAAATATTATCTCCCTTGAGACAATTTCACT
*
7354 TGAAACAAATTTTATCTCCCTTGAGACAATTTCACT
1 TGAAACAAATATTATCTCCCTTGAGACAATTTCACT
* * * *
7390 TGAAACAGAAGATATTATCTCACTTGAGATAGTTTCGCT
1 TGAAAC--AA-ATATTATCTCCCTTGAGACAATTTCACT
*
7429 CGAAACACAATATT
1 TGAAACA-AATATT
7443 TTTAGAAACT
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
36 39 0.51
37 6 0.08
38 3 0.04
39 28 0.37
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (36 bp):
TGAAACAAATATTATCTCCCTTGAGACAATTTCACT
Found at i:7527 original size:43 final size:43
Alignment explanation
Indices: 7466--8060 Score: 675
Period size: 43 Copynumber: 13.6 Consensus size: 43
7456 CCTGATTTTC
* * *
7466 AGGGGTTTCTTGAAGAAAAGCTTGAGAGACCATCGTGTTATGC
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* *
7509 AGGGGTTTCTTGAGGAAAAGTTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGA-GACCATCGTGATATGT
* *
7552 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGAAAAGCTTGAGAGACCATCGTGATATGT
*
7595 AGGGGTTTCTTGATGATAAGCTTGA-AGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGA-GACCATCGTGATATGT
* * * *
7638 AGGGGTTCCTTGATGACAAGCTTGAAAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* *
7681 AGGGG-TTCTTTGATGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGAAAAGCTTGAGAGACCATCGTGATATGT
*
7724 ACGGGTTTCTTGATGAAAAGCTTGATG-GACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGA-GAGACCATCGTGATATGT
* * *
7767 AGGGGTTCCTTGATGACAAA-TTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGA-AAAGCTTGAGAGACCATCGTGATATGT
* *
7810 AGGGGTTTCTTGATGAAAAGCTTGGGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* * * *
7853 AGGGGTTCCTTGATGACAAGCTTGAGAAACCATCGTTATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* **
7896 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATAATGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
* *
7939 AGGGGTTCCTTGATGACAATTTGATGACAAACTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGA-AA----A-G-----CTTGAGAGACCATCGTGATATGT
* * *
7993 AAGGGTTTCTTGATGAAAAGCTTGAGGGACCATTGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
8036 AGGGG-TTCTTTGATGACAAA-CTTGA
1 AGGGGTTTC-TTGATGA-AAAGCTTGA
8061 TGATCACTTG
Statistics
Matches: 476, Mismatches: 51, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
42 14 0.03
43 406 0.85
44 17 0.04
48 2 0.00
49 2 0.00
53 2 0.00
54 33 0.07
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (43 bp):
AGGGGTTTCTTGATGAAAAGCTTGAGAGACCATCGTGATATGT
Found at i:7974 original size:54 final size:51
Alignment explanation
Indices: 7916--8110 Score: 174
Period size: 54 Copynumber: 3.9 Consensus size: 51
7906 TGATGAAAAG
*
7916 CTTGAGGGACCATAATGATATGTAGGGGTTCCTTGATGACAATTTGATGACAAA
1 CTTGAGGGACCATAGTGATATGTAGGGGTTCCTTGATGACAATTTGATG---AA
** * * *
7970 CTTGAGAAACCATCGTGATATGTAAGGGTTTCTTGATGA-AA----A-G--
1 CTTGAGGGACCATAGTGATATGTAGGGGTTCCTTGATGACAATTTGATGAA
* * *
8013 CTTGAGGGACCATTGTGATATGTAGGGGTTCTTTGATGACAAACTTGATGATCA
1 CTTGAGGGACCATAGTGATATGTAGGGGTTCCTTGATGAC-AATTTGATGA--A
*
8067 CTTGAGGGACCA-ACGTGATATGTAGGGGTTCCTTGGTGACAATT
1 CTTGAGGGACCATA-GTGATATGTAGGGGTTCCTTGATGACAATT
8111 AAGAAACTGA
Statistics
Matches: 113, Mismatches: 16, Indels: 25
0.73 0.10 0.16
Matches are distributed among these distances:
43 33 0.29
45 2 0.02
48 1 0.01
49 2 0.02
50 1 0.01
53 5 0.04
54 69 0.61
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (51 bp):
CTTGAGGGACCATAGTGATATGTAGGGGTTCCTTGATGACAATTTGATGAA
Found at i:8032 original size:97 final size:98
Alignment explanation
Indices: 7861--8101 Score: 353
Period size: 97 Copynumber: 2.5 Consensus size: 98
7851 GTAGGGGTTC
* *
7861 CTTGATGACAAGCTTGAGAAACCATCGTTATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
1 CTTGATGACAAACTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
7926 CATAATGATATGTAGGGGTTCCTTGATGAC-AA
66 CATAATGATATGTAGGGGTTCCTTGATGACAAA
* *
7958 TTTGATGACAAACTTGAGAAACCATCGTGATATGTAAGGGTTTCTTGATGAAAAGCTTGAGGGAC
1 CTTGATGACAAACTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
** *
8023 CATTGTGATATGTAGGGGTTCTTTGATGACAAA
66 CATAATGATATGTAGGGGTTCCTTGATGACAAA
** * *
8056 CTTGATGATC--ACTTGAGGGACCAACGTGATATGTAGGGGTTCCTTG
1 CTTGATGA-CAAACTTGAGAAACCATCGTGATATGTAGGGGTTTCTTG
8102 GTGACAATTA
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
97 119 0.92
98 9 0.07
99 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (98 bp):
CTTGATGACAAACTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCTTGAGGGAC
CATAATGATATGTAGGGGTTCCTTGATGACAAA
Found at i:8266 original size:90 final size:91
Alignment explanation
Indices: 8110--8343 Score: 355
Period size: 91 Copynumber: 2.6 Consensus size: 91
8100 TGGTGACAAT
* * *
8110 TAAGAAACTGAGCCTTTGGGGGTTTCTTGATTTTTTAAGTCATTCGGGCCATCCATAAGACCTTC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TTTTTAAGTCCTTCGGGCCATCCATAAGACATTC
*
8175 AGTGC-AGAATGTTTTCAAATGAGA-TC
65 AGTGCAAG-ATGTTTTCAAATAAGATTC
8201 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACATTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACATTCA
*
8266 GTGCAAGATGTTTTCAAATAAGATTT
66 GTGCAAGATGTTTTCAAATAAGATTC
* * * *
8292 TAAGAAACTAAGTCTTCGGGGGTTTCTTGATTTTTAAATCCTTCGGGTCATC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATC
8344 TGTAAGCCTT
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
90 52 0.39
91 80 0.61
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (91 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACATTCA
GTGCAAGATGTTTTCAAATAAGATTC
Found at i:8828 original size:91 final size:91
Alignment explanation
Indices: 8716--8885 Score: 288
Period size: 91 Copynumber: 1.9 Consensus size: 91
8706 GTGGATCAAC
* *
8716 ATTTTCAATGGAGAGTTCATAATGAGAAGAACTCA-CTCAAAGAGGAAGAAGAAGTTCATAATGA
1 ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATC-CAAAGAGGAAGAAGAAGTTCATAATGA
*
8780 GAATAACTTGTTCAACCTTGCATCAGT
65 GAAGAACTTGTTCAACCTTGCATCAGT
*
8807 ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAG
1 ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAG
8872 AAGAACTTGTTCAA
66 AAGAACTTGTTCAA
8886 TCCAATGCAT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
91 73 0.99
92 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (91 bp):
ATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGCATCAGT
Found at i:9060 original size:15 final size:15
Alignment explanation
Indices: 9040--9086 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
9030 CTTAAAAAAA
9040 TATTATAGA-TATTAT
1 TATTATA-ATTATTAT
9055 TATTATAATTATTAT
1 TATTATAATTATTAT
9070 TATTAATAATT-TTAT
1 TATT-ATAATTATTAT
9085 TA
1 TA
9087 CATATGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.03
15 23 0.77
16 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
TATTATAATTATTAT
Found at i:11127 original size:28 final size:30
Alignment explanation
Indices: 11096--11167 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 30
11086 TTTTAGACAT
*
11096 TTAAATGTATGTTT-TGCTA-TTTAATCCC
1 TTAAATCTATGTTTGTGCTATTTTAATCCC
* * *
11124 TTAAATCTTTGTTTGTTCTATTTTAATCCT
1 TTAAATCTATGTTTGTGCTATTTTAATCCC
11154 TTAAATTCT-TGTTT
1 TTAAA-TCTATGTTT
11168 TTTGCTGGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 12 0.32
29 4 0.11
30 18 0.49
31 3 0.08
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.57
Consensus pattern (30 bp):
TTAAATCTATGTTTGTGCTATTTTAATCCC
Found at i:20414 original size:37 final size:38
Alignment explanation
Indices: 20359--20455 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 38
20349 GTTGTCTCTT
* * * *
20359 TTGAGATAGTTT-TGCTTGAAACA-CAAGTTTGCCTTCC
1 TTGAGATTGTTTCT-CTTGAAACACCAAATTTACCTCCC
*
20396 TTGAGATTGTTTCTCTTGAAACACCAAATTTATCTCCC
1 TTGAGATTGTTTCTCTTGAAACACCAAATTTACCTCCC
* *
20434 TTAAGATTGTTTCACTTGAAAC
1 TTGAGATTGTTTCTCTTGAAAC
20456 TATTTTTCTT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 20 0.39
38 31 0.61
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (38 bp):
TTGAGATTGTTTCTCTTGAAACACCAAATTTACCTCCC
Found at i:21576 original size:16 final size:15
Alignment explanation
Indices: 21555--21588 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
21545 TAAGTAAATC
*
21555 TTTGGTAAGATGTAGA
1 TTTGGTAAAATGTA-A
21571 TTTGGTAAAATGTAA
1 TTTGGTAAAATGTAA
21586 TTT
1 TTT
21589 TAGGTATCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (15 bp):
TTTGGTAAAATGTAA
Found at i:22837 original size:29 final size:29
Alignment explanation
Indices: 22803--22864 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
22793 AACGAAAGAA
* *
22803 ACCAAATCTTATGTTTTCTGAATCCAATG
1 ACCAAATCTTATATTTTATGAATCCAATG
22832 ACCAAATCTTATATTTTATGAATCCAATG
1 ACCAAATCTTATATTTTATGAATCCAATG
22861 ACCA
1 ACCA
22865 TAAGTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.35
Consensus pattern (29 bp):
ACCAAATCTTATATTTTATGAATCCAATG
Found at i:27668 original size:2 final size:2
Alignment explanation
Indices: 27661--27702 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
27651 TCAATCTACA
27661 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
27703 TTACGAAATA
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:30669 original size:20 final size:22
Alignment explanation
Indices: 30640--30680 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
30630 TTTCTCAATT
30640 TCTCACC-TTT-CTCTCTCTTC
1 TCTCACCTTTTCCTCTCTCTTC
*
30660 TCTCATCTTTTCCTCTCTCTT
1 TCTCACCTTTTCCTCTCTCTT
30681 TTTATCTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 3 0.17
22 9 0.50
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (22 bp):
TCTCACCTTTTCCTCTCTCTTC
Found at i:31463 original size:21 final size:21
Alignment explanation
Indices: 31434--31475 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31424 GAATATAAAG
* * *
31434 GTTACGACCTTTTGATTAAGA
1 GTTAAGACCATTTGATGAAGA
31455 GTTAAGACCATTTGATGAAGA
1 GTTAAGACCATTTGATGAAGA
31476 TATTTATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (21 bp):
GTTAAGACCATTTGATGAAGA
Found at i:33681 original size:62 final size:62
Alignment explanation
Indices: 33580--33704 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
33570 TCTAGTTTTA
*
33580 GTTTGCAAACTACAAAAGGAGTACTTCTTCATGGTCCACATGGAACGGGAAAGACTTCTTTG
1 GTTTGCAAACTACAAAAGGAGTACTTCTTCATGGACCACATGGAACGGGAAAGACTTCTTTG
33642 GTTTGCAAACTACAAAAGGAGTACTTCTTCATGGACCACATGGAACGGGAAAGACTTCTTTG
1 GTTTGCAAACTACAAAAGGAGTACTTCTTCATGGACCACATGGAACGGGAAAGACTTCTTTG
33704 G
1 G
33705 CTTGGCTATG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (62 bp):
GTTTGCAAACTACAAAAGGAGTACTTCTTCATGGACCACATGGAACGGGAAAGACTTCTTTG
Found at i:35027 original size:54 final size:54
Alignment explanation
Indices: 34959--35394 Score: 601
Period size: 54 Copynumber: 8.1 Consensus size: 54
34949 CTATGTGTTC
* * * *
34959 TATCGGCACTAAGTGTGCAATCCACATAATTCATAATGTGTTTATGAAGGATCG
1 TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
35013 TATCAGCACTAAGTGTGCAATCCAC-GAAATTCATAATGTGTTTATGAACGACCG
1 TATCAGCACTAAGTGTGCAATCCACAG-AATTCATAATGTGTTTATGAACGACCG
* * *
35067 TATCAACACCAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACCG
1 TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
* * **
35121 TATC-GACACTAAGTGTACAA-CACACAAAATTCATAATGTGTTTATGAACGAGTG
1 TATCAG-CACTAAGTGTGCAATC-CACAGAATTCATAATGTGTTTATGAACGACCG
*
35175 TATCAGCACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACCG
1 TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
* *
35229 TATC-GACACTAAGTGTACAATCCACAGGATTCATAATGTGTTTATGAACGACCG
1 TATCAG-CACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
* *
35283 TATCGGCACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACCG
1 TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
* * * ** * *
35337 TATCAACACTAAGTATGCAACCCACAGAATTCATAAAATGTTTATGAATGACTG
1 TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
35391 TATC
1 TATC
35395 GACAATAATG
Statistics
Matches: 341, Mismatches: 33, Indels: 16
0.87 0.08 0.04
Matches are distributed among these distances:
53 2 0.01
54 335 0.98
55 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (54 bp):
TATCAGCACTAAGTGTGCAATCCACAGAATTCATAATGTGTTTATGAACGACCG
Found at i:41935 original size:54 final size:54
Alignment explanation
Indices: 41872--42372 Score: 637
Period size: 54 Copynumber: 9.3 Consensus size: 54
41862 GTGTACTATT
* * *
41872 GACACTAAGTGTGCAATCCATGGAATTCATAATGTGTTTGTGAATGACTGTATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * * * * *
41926 GACACTAAGTGTGTAATCTAAGAAATTTATAATGTGTTTATGAACGACTGTATG
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * *
41980 GACAATAAGTGTGCAATCCACGAAATTCATAATGTGTTTGTGAACGACTGTATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * * * *
42034 GGCACTAAGTGTGCAGTCCATGGAATTCATAATGTATTTATGAACGACTATATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * * * *
42088 GACACTAAGTGTGCAACCCACAGAATTCATAATGTGTTAACGAACGACCGTATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
** **
42142 GACACTAAGTGTGCAATCCATAGAATTCATAATGTGTTTATGAACGACAATATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * *
42196 GGCACTAAGTGTGCAATCCAC-GAGATTCATAATGTATTTATGAACGACCGTATC
1 GACACTAAGTGTGCAATCCACGGA-ATTCATAATGTGTTTATGAACGACTGTATC
* *
42250 GGCACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACCGTATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
* * * * *
42304 GACACAAAGTGTGTAACCCACAGAATTCATAATATGTTTATGAACGA-TCGTATC
1 GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACT-GTATC
*
42358 GACACTATGTGTGCA
1 GACACTAAGTGTGCA
42373 CCTCAAAGAA
Statistics
Matches: 389, Mismatches: 55, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
53 2 0.01
54 385 0.99
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (54 bp):
GACACTAAGTGTGCAATCCACGGAATTCATAATGTGTTTATGAACGACTGTATC
Found at i:43632 original size:36 final size:36
Alignment explanation
Indices: 43585--43657 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
43575 TTTACCTCCT
43585 CCTCTCTAATAATAGGAGGATCATCCTATATTGGGC
1 CCTCTCTAATAATAGGAGGATCATCCTATATTGGGC
43621 CCTCTCTAATAATAGGAGGATCATCCTATATTGGGC
1 CCTCTCTAATAATAGGAGGATCATCCTATATTGGGC
43657 C
1 C
43658 AGATTTAACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (36 bp):
CCTCTCTAATAATAGGAGGATCATCCTATATTGGGC
Found at i:44974 original size:49 final size:52
Alignment explanation
Indices: 44919--45043 Score: 143
Period size: 49 Copynumber: 2.4 Consensus size: 52
44909 TGGACTTCTA
* **
44919 TTAGTTTTACTAAATTCT-C-TATGTTCAACAGAAG-T-ATT-TATTTCGGGTT
1 TTAGTTTTATTAAATT-TACGT-TGTTCAACAGAAGTTGATTCTATTTCAAGTT
*
44968 TTAGTTTTATTAAATTTACGTTGTTCAAGAGAAGTTGATTCTATTTCAAGTT
1 TTAGTTTTATTAAATTTACGTTGTTCAACAGAAGTTGATTCTATTTCAAGTT
45020 TTAGTTTTATTAAATCTTGACGTT
1 TTAGTTTTATTAAAT-TT-ACGTT
45044 TAATAAAGTC
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
48 1 0.02
49 28 0.43
50 2 0.03
51 3 0.05
52 24 0.37
53 2 0.03
54 5 0.08
ACGTcount: A:0.27, C:0.10, G:0.14, T:0.49
Consensus pattern (52 bp):
TTAGTTTTATTAAATTTACGTTGTTCAACAGAAGTTGATTCTATTTCAAGTT
Found at i:45351 original size:35 final size:35
Alignment explanation
Indices: 45302--45369 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
45292 AAAAAATAAA
*
45302 TTTATTCATCAAGTGACATGACTTATTATAACAAG
1 TTTATTCATCAAGTGACATGACCTATTATAACAAG
*
45337 TTTATTCATTAAGTGACATGACCTATTATAACA
1 TTTATTCATCAAGTGACATGACCTATTATAACA
45370 TCAATTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (35 bp):
TTTATTCATCAAGTGACATGACCTATTATAACAAG
Found at i:51836 original size:40 final size:40
Alignment explanation
Indices: 51779--51874 Score: 140
Period size: 40 Copynumber: 2.4 Consensus size: 40
51769 ATTTGACACT
* *
51779 TTAATATTATGGGTTGTTTATGGATTTTATT-GTTTTAGAC
1 TTAATATTATGGTTTGTTTATGGATTTT-TTGGTTCTAGAC
*
51819 TTAATATTATGGTTTGTTTATGGATTTTTTGGTTCTAGAG
1 TTAATATTATGGTTTGTTTATGGATTTTTTGGTTCTAGAC
*
51859 TTAATATTGTGGTTTG
1 TTAATATTATGGTTTG
51875 AATCTTGAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
39 2 0.04
40 49 0.96
ACGTcount: A:0.21, C:0.02, G:0.22, T:0.55
Consensus pattern (40 bp):
TTAATATTATGGTTTGTTTATGGATTTTTTGGTTCTAGAC
Found at i:51898 original size:75 final size:74
Alignment explanation
Indices: 51819--52035 Score: 296
Period size: 75 Copynumber: 2.9 Consensus size: 74
51809 TGTTTTAGAC
* * *
51819 TTAATATTATGGTTTGTTTATGGATTTT-TTGGTTCTAGAGTTAATATTGTGGTTTGAATCTTGA
1 TTAATATTATGGTTTGTTTATGGATTTTATT-GTTCTAAACTTAATATTGTGGTTTGAGTCTTGA
51883 GATTTGACATT
65 GATTTGACA-T
* * * *
51894 TTAATATTATGATTTGTTTATGGATTTTATTGTTATAAACTTAATATTGTAGTTAGAGTCTTGAG
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTCTAAACTTAATATTGTGGTTTGAGTCTTGAG
51959 ATTTGACAT
66 ATTTGACAT
* * * *
51968 TT--TATTGTGGTTTGTTTATGAATTTTATTGTTCTAAACTTAATATTGTGTTTTGAGTCTTGAA
1 TTAATATTATGGTTTGTTTATGGATTTTATTGTTCTAAACTTAATATTGTGGTTTGAGTCTTGAG
52031 ATTTG
66 ATTTG
52036 TTTATGGTTT
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
72 58 0.46
74 3 0.02
75 63 0.50
76 2 0.02
ACGTcount: A:0.25, C:0.04, G:0.18, T:0.53
Consensus pattern (74 bp):
TTAATATTATGGTTTGTTTATGGATTTTATTGTTCTAAACTTAATATTGTGGTTTGAGTCTTGAG
ATTTGACAT
Found at i:55734 original size:37 final size:37
Alignment explanation
Indices: 55691--56150 Score: 591
Period size: 37 Copynumber: 12.4 Consensus size: 37
55681 GTATAAAATA
* * *
55691 ATTTTGAATATATATATAATATAGAGTTTTTAAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
55728 ATTTTGAATATATATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAA-A-ATATATATAATATATAGTTTTTGAAAAC
55767 ATTTTG-AAA-A-A-AT-ATATATAGTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
55799 ATTTTG-AAA-ATATAT-ATATA-A-TTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
55831 ATTTTGAAAACATATATATAATATATAATTTTTGAAAAC
1 ATTTTG-AAA-ATATATATAATATATAGTTTTTGAAAAC
*
55870 ATTTTGAAAATATATATAGTATATAGTTTTTGAAAAC
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
55907 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAT
1 ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
*
55944 ATTTTGGAAACATATATATAATATATAGTTTTTTGAAAAT
1 ATTTT-GAAA-ATATATATAATATATAG-TTTTTGAAAAC
* *
55984 ATTTTGAATATATATAT-ATAATATAGTTTTTAAAAAC
1 ATTTTGAAAATATATATAAT-ATATAGTTTTTGAAAAC
56021 ATTTTGAAAAAAGTATATATAATATATAGTTTTTGAAAAC
1 ATTTTG--AAAA-TATATATAATATATAGTTTTTGAAAAC
*
56061 ATTTTGAAAATATATATAAATATATAATTTTTGAAAAC
1 ATTTTGAAAATATATAT-AATATATAGTTTTTGAAAAC
* *
56099 ATTTTGAAAGCATATATATAATATAAAGTTTTTGAAAAT
1 ATTTTGAAA--ATATATATAATATATAGTTTTTGAAAAC
56138 ATTTTGAAAATAT
1 ATTTTGAAAATAT
56151 GTCATATAAT
Statistics
Matches: 381, Mismatches: 20, Indels: 44
0.86 0.04 0.10
Matches are distributed among these distances:
32 44 0.12
33 4 0.01
34 10 0.03
35 2 0.01
36 7 0.02
37 108 0.28
38 55 0.14
39 96 0.25
40 53 0.14
41 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
Found at i:55771 original size:11 final size:11
Alignment explanation
Indices: 55757--55840 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
55747 AATATATAGT
55757 TTTTGAAAATA
1 TTTTGAAAATA
*
55768 TTTTGAAAAAA
1 TTTTGAAAATA
* * *
55779 TATAT-ATAGT-
1 T-TTTGAAAATA
*
55789 TTTTGAAAACA
1 TTTTGAAAATA
55800 TTTTGAAAATA
1 TTTTGAAAATA
* *
55811 TATAT-ATAAT-
1 T-TTTGAAAATA
55821 TTTTGAAAATA
1 TTTTGAAAATA
55832 TTTTGAAAA
1 TTTTGAAAA
55841 CATATATATA
Statistics
Matches: 53, Mismatches: 14, Indels: 12
0.67 0.18 0.15
Matches are distributed among these distances:
9 4 0.08
10 8 0.15
11 37 0.70
12 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAATA
Found at i:55789 original size:32 final size:32
Alignment explanation
Indices: 55748--55850 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
55738 TATATATATA
55748 ATATATAGTTTTTGAAAATATTTTGAAAAAAT
1 ATATATAGTTTTTGAAAATATTTTGAAAAAAT
* *
55780 ATATATAGTTTTTGAAAACATTTTGAAAATAT
1 ATATATAGTTTTTGAAAATATTTTGAAAAAAT
* *
55812 ATATATAATTTTTGAAAATATTTTGAAAACAT
1 ATATATAGTTTTTGAAAATATTTTGAAAAAAT
55844 ATATATA
1 ATATATA
55851 ATATATAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 66 1.00
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.44
Consensus pattern (32 bp):
ATATATAGTTTTTGAAAATATTTTGAAAAAAT
Found at i:56230 original size:14 final size:13
Alignment explanation
Indices: 56201--56258 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
56191 ATTATAATAT
56201 TTTATTATATGTTA
1 TTTATTATAT-TTA
56215 TTTATTATATTCTA
1 TTTATTATATT-TA
56229 -TTATT-TATTATA
1 TTTATTATATT-TA
56241 TTCTA-T-TATTTA
1 TT-TATTATATTTA
56253 TTTATT
1 TTTATT
56259 TTCTTTCTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
11 2 0.05
12 11 0.28
13 12 0.31
14 14 0.36
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTATTATATTTA
Found at i:56232 original size:17 final size:17
Alignment explanation
Indices: 56212--56258 Score: 87
Period size: 17 Copynumber: 2.8 Consensus size: 17
56202 TTATTATATG
56212 TTATTTATTATATTCTA
1 TTATTTATTATATTCTA
56229 TTATTTATTATATTCTA
1 TTATTTATTATATTCTA
56246 TTATTTATT-TATT
1 TTATTTATTATATT
56259 TTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 4 0.13
17 26 0.87
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTTATTATATTCTA
Found at i:56239 original size:24 final size:24
Alignment explanation
Indices: 56192--56239 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
56182 ATATTATATA
* *
56192 TTATAATATTTTATTATATGTTAT
1 TTATAATATTCTATTATATATTAT
* *
56216 TTATTATATTCTATTATTTATTAT
1 TTATAATATTCTATTATATATTAT
56240 ATTCTATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
TTATAATATTCTATTATATATTAT
Done.