Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000298.1 Hibiscus syriacus cultivar Beakdansim tig00000549_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: 98314
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:6056 original size:14 final size:14
Alignment explanation
Indices: 6022--6067 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
6012 TGGATGAAAC
6022 AAATAAA-AAAATGA
1 AAATAAATAAAAT-A
*
6036 AATTAAATAAAATA
1 AAATAAATAAAATA
*
6050 AAATAAATGAAA-A
1 AAATAAATAAAATA
6063 AAATA
1 AAATA
6068 TATATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.21
14 17 0.61
15 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (14 bp):
AAATAAATAAAATA
Found at i:6166 original size:11 final size:11
Alignment explanation
Indices: 6150--6261 Score: 54
Period size: 12 Copynumber: 10.1 Consensus size: 11
6140 ACATAATGAA
6150 AATAAATAAAT
1 AATAAATAAAT
*
6161 AGTAAATAAAT
1 AATAAATAAAT
*
6172 AATAAAATAAAA
1 AAT-AAATAAAT
*
6184 AATATATAAAAT
1 AATAAAT-AAAT
* **
6196 ATAAAAATGTAT
1 A-ATAAATAAAT
6208 AATATAATAAAAT
1 AATA-AAT-AAAT
* *
6221 ACTAAAT-AGT
1 AATAAATAAAT
*
6231 AA-CAAT-AAT
1 AATAAATAAAT
6240 AATAAAT-AAT
1 AATAAATAAAT
6250 GAA-AAATAAAT
1 -AATAAATAAAT
6261 A
1 A
6262 TACATAATAT
Statistics
Matches: 75, Mismatches: 18, Indels: 17
0.68 0.16 0.15
Matches are distributed among these distances:
9 7 0.09
10 14 0.19
11 22 0.29
12 23 0.31
13 9 0.12
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:6173 original size:19 final size:16
Alignment explanation
Indices: 6148--6203 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
6138 AAACATAATG
6148 AAAATAAATAAATAGTAA
1 AAAATAAATAAA-A-TAA
6166 ATAAAT-AATAAAATAA
1 A-AAATAAATAAAATAA
*
6182 AAAATATATAAAATATA
1 AAAATAAATAAAATA-A
6199 AAAAT
1 AAAAT
6204 GTATAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 4 0.12
16 12 0.35
17 7 0.21
18 7 0.21
19 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATAAATAAAATAA
Found at i:6186 original size:15 final size:15
Alignment explanation
Indices: 6112--6245 Score: 63
Period size: 17 Copynumber: 7.8 Consensus size: 15
6102 TTTTTAAAAG
*
6112 AAAAATAATAAGAACA
1 AAAAATAATAA-AATA
6128 AAGAAACTAA-AAACATA
1 AA-AAA-TAATAAA-ATA
6145 ATGAAAATAAATAAATAGTA
1 A--AAAAT-AATAAA-A-TA
6165 AATAAATAATAAAATA
1 AA-AAATAATAAAATA
6181 AAAAATATATAAAATA
1 AAAAATA-ATAAAATA
* *
6197 TAAAAATGTATAATATA
1 -AAAAAT-AATAAAATA
*
6214 ATAAAATACTAAATAGTA
1 A-AAAATAATAAA-A-TA
6232 ACAATAATAATAAA
1 A-AA-AATAATAAA
6246 TAATGAAAAA
Statistics
Matches: 93, Mismatches: 9, Indels: 29
0.71 0.07 0.22
Matches are distributed among these distances:
15 5 0.05
16 19 0.20
17 29 0.31
18 20 0.22
19 17 0.18
20 3 0.03
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (15 bp):
AAAAATAATAAAATA
Found at i:6377 original size:17 final size:18
Alignment explanation
Indices: 6338--6377 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
6328 ACGTTAGGAA
*
6338 AATAT-AGTAAAAATAGT
1 AATATAAGTAAAAATAAT
6355 AA-ATAAGT-AAAATAAT
1 AATATAAGTAAAAATAAT
6371 AATATAA
1 AATATAA
6378 TATATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (18 bp):
AATATAAGTAAAAATAAT
Found at i:6419 original size:2 final size:2
Alignment explanation
Indices: 6372--6407 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6362 TAAAATAATA
6372 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6408 GGAAAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7746 original size:106 final size:106
Alignment explanation
Indices: 7527--7752 Score: 328
Period size: 106 Copynumber: 2.1 Consensus size: 106
7517 CAAGTAAGTA
* * *
7527 GCATTGT-TCCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTG
1 GCATTGTCT-CGAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTG
7591 TTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTT
65 TTTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTT
* * * * ** *
7633 GCGTTGTCTGGAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
1 GCATTGTCTCGAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGT
*
7698 TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTT
66 TTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTT
*
7739 GTATTGTCTCGAGT
1 GCATTGTCTCGAGT
7753 GTCACGATAT
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
106 104 0.99
107 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
GCATTGTCTCGAGTACAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGT
TTGTTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTT
Found at i:7776 original size:106 final size:105
Alignment explanation
Indices: 7537--7780 Score: 321
Period size: 106 Copynumber: 2.3 Consensus size: 105
7527 GCATTGTTCC
* * *
7537 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTACAATATCCTCCGT-GTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAA
*
7602 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
65 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
* ** *
7643 GAGTACAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTACAATATCCTCCG-TGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAA
* *
7708 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTCTCG
65 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCT-G
* *
7750 AGTGTCACGATATCCTCCGTG-G-AGTTGAAAT
1 -GAGT-ACAATATCCTCCGTGTGAAGTTGAAAT
7781 CGCATGTTGG
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
106 102 0.84
107 3 0.02
108 5 0.04
109 11 0.09
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTACAATATCCTCCGTGTGAAGTTGAAATTGGCTCTGAAACCGAGAAATTGTTTGTTGACAAC
CAACCGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTG
Found at i:7992 original size:36 final size:36
Alignment explanation
Indices: 7945--8020 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
7935 TGTTTGGAGA
* * *
7945 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
*
7981 GAAACTATCTCAAGCGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
8017 GAAA
1 GAAA
8021 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.21, T:0.22
Consensus pattern (36 bp):
GAAACTATCTCAAGCGAGACAAAATTCATTTCAAGG
Found at i:8181 original size:103 final size:103
Alignment explanation
Indices: 7920--8233 Score: 503
Period size: 103 Copynumber: 3.1 Consensus size: 103
7910 TTCGTTAAAT
* ** *
7920 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
7982 AAACTATCTCAAGCGAGATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGA-AAAATTCATTTCAAGGGAAA
8021 TGTTTTCAATGTTTAT-TTTCAAGAG-AACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
8084 AAACTATCTCAAGAGAGAAAAAATCATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAATTCATTTCAAGGGAAA
8122 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* * *
8187 AAACTATCTTAGGAGAGAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGAGAGAAAAATTCATTTCAAGGGAAA
8225 TGTTTTCAA
1 TGTTTTCAA
8234 GAGAAACTGT
Statistics
Matches: 198, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
99 22 0.11
100 7 0.04
101 53 0.27
102 35 0.18
103 81 0.41
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (103 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGAGAGAAAAATTCATTTCAAGGGAAA
Found at i:8387 original size:36 final size:36
Alignment explanation
Indices: 8347--8458 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
8337 CTTTCGAGTG
* *
8347 AAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
* ** * **
8383 AAAACAATCTTGAGTGA-A-AAATCTTCTTTCGAGA
1 AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
8417 AAAACAGTCTCAAGTGAGACAAAT-TATGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATCT-TGTTTTAAGA
8453 AAAACA
1 AAAACA
8459 AATTTGAGTG
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
34 27 0.46
35 3 0.05
36 29 0.49
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATCTTGTTTTAAGA
Found at i:8405 original size:34 final size:36
Alignment explanation
Indices: 8362--8471 Score: 120
Period size: 34 Copynumber: 3.1 Consensus size: 36
8352 GGTCTCAAGC
8362 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
1 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
* ** * **
8398 GA-A-AAATCTTCTTTCGAGAAAAACAGTCTCAAGT
1 GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
8432 GAGACAAAT-TATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGACAAATCT-TGTTTTAAGAAAAAC-AATCTTGAGT
8468 GAGA
1 GAGA
8472 TAATCATCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
34 27 0.47
35 3 0.05
36 26 0.45
37 2 0.03
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (36 bp):
GAGACAAATCTTGTTTTAAGAAAAACAATCTTGAGT
Found at i:8436 original size:70 final size:71
Alignment explanation
Indices: 8334--8469 Score: 206
Period size: 70 Copynumber: 1.9 Consensus size: 71
8324 AATGAAATGC
* *
8334 CTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCT-TGTTTTAAGAAAAAC-AATCTTGAG
1 CTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAT-TATGTTTTAAGAAAAACAAAT-TTGAG
8397 TGAAAAAT
64 TGAAAAAT
*
8405 CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAATTATGTTTTAAGAAAAACAAATTTGAGTG
1 CTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATTATGTTTTAAGAAAAACAAATTTGAGTG
8469 A
66 A
8470 GATAATCATC
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
69 1 0.02
70 45 0.75
71 14 0.23
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (71 bp):
CTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAATTATGTTTTAAGAAAAACAAATTTGAGTG
AAAAAT
Found at i:10098 original size:177 final size:180
Alignment explanation
Indices: 9597--10119 Score: 843
Period size: 182 Copynumber: 2.9 Consensus size: 180
9587 ATCAGGTATA
* * *
9597 ACTGAAGGGTTCATCTCATCAC--AGTCTTTGACCTAAC-AAA-AGTGGAGCAAAGACCGAATTG
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAGTGGAGCAAACACCGAATTG
** *
9658 CCAAG-GTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAGCCAGGGCTTTCGATTTT
66 CCAAGTGTCCGAGC-ATGTCATAG-TTTGAACATAATCTATTCATAAGCCAGGGCTTTCGAGTTT
9721 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
129 CCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
9773 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGTGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAG-AGTGGAGCAAACACCGAATT
9838 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
65 GCCAAGTGTCCGAGCA-TGTCATAGTTTGAACATAATCTATTCAT-AAGCCAGGGCTTTCGAGTT
9903 T-CTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGA-GGACAAATC
128 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
9954 ACTGAA-GGTTCATCTCATCACAAAGTC-TTGGCCTGACAAAAGTAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAG-AGTGGAGCAAACACCGAATT
10017 GCCAAGTGTCCGAGCA-GTCATAGTTTGAACATAATCTATTCATAAGCCAGGGCTTTCGAGTTTC
65 GCCAAGTGTCCGAGCATGTCATAGTTTGAACATAATCTATTCATAAGCCAGGGCTTTCGAGTTTC
10081 CTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
130 CTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
10120 CGGATTTAAT
Statistics
Matches: 326, Mismatches: 11, Indels: 19
0.92 0.03 0.05
Matches are distributed among these distances:
176 41 0.13
177 66 0.20
178 13 0.04
179 53 0.16
180 20 0.06
181 40 0.12
182 73 0.22
183 20 0.06
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (180 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGAGTGGAGCAAACACCGAATTG
CCAAGTGTCCGAGCATGTCATAGTTTGAACATAATCTATTCATAAGCCAGGGCTTTCGAGTTTCC
TCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:13638 original size:19 final size:19
Alignment explanation
Indices: 13605--13641 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13595 TGCAGATTAT
13605 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
13624 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
13642 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:14939 original size:29 final size:27
Alignment explanation
Indices: 14903--14969 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 27
14893 ACAAAGAAAC
*
14903 TAAAATAATGAAATAATAAATAGTATAAA
1 TAAAATAATAAAATAA-AAATA-TATAAA
*
14932 TAAAATAATAAAATAAAAATATATATA
1 TAAAATAATAAAATAAAAATATATAAA
14959 -AAAAT-ATAAAA
1 TAAAATAATAAAA
14970 ATGTATGTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 6 0.17
26 5 0.14
27 5 0.14
28 5 0.14
29 15 0.42
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (27 bp):
TAAAATAATAAAATAAAAATATATAAA
Found at i:14954 original size:25 final size:26
Alignment explanation
Indices: 14903--14969 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
14893 ACAAAGAAAC
*
14903 TAAAATAATGAAATAATAAATAGTATAAA
1 TAAAATAAT--AA-AATAAATAATATAAA
*
14932 TAAAATAATAAAATAAA-AATATATA
1 TAAAATAATAAAATAAATAATATAAA
14957 TAAAA-ATATAAAA
1 TAAAATA-ATAAAA
14970 ATGTATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 1 0.03
25 17 0.49
26 6 0.17
27 2 0.06
29 9 0.26
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (26 bp):
TAAAATAATAAAATAAATAATATAAA
Found at i:15024 original size:26 final size:26
Alignment explanation
Indices: 14878--15071 Score: 67
Period size: 28 Copynumber: 7.6 Consensus size: 26
14868 AAAAAAAAGA
*
14878 AAAATAATAATAAGAACAA-AGAAAC-T
1 AAAATAATAATAA-AA-AATAGTAACAT
* *
14904 AAAATAATGAAATAATAAATAGTATAAAT
1 AAAATAAT--AATAAAAAATAGTA-ACAT
* *
14933 AAAATAATAAAATAAAAATA-T-ATAT
1 AAAATAATAATA-AAAAATAGTAACAT
**
14958 -AAA-AAT-AT-AAAAAT-GT-ATGT
1 AAAATAATAATAAAAAATAGTAACAT
*
14978 ATAAT-ATAATAAATACTAATAGTAACAT
1 AAAATAATAATAAA-A--AATAGTAACAT
*
15006 AAAATAATAATAAAAAATA--AATAT
1 AAAATAATAATAAAAAATAGTAACAT
* * *
15030 ATAATATTACT-AAAAATAGTAATCAT
1 AAAATAATAATAAAAAATAGTAA-CAT
15056 AGAAAT-ATAAATAAAA
1 A-AAATAAT-AATAAAA
15072 TGAAGTAATA
Statistics
Matches: 125, Mismatches: 20, Indels: 44
0.66 0.11 0.23
Matches are distributed among these distances:
20 10 0.08
21 4 0.03
22 3 0.02
23 12 0.10
24 16 0.13
25 5 0.04
26 21 0.17
27 15 0.12
28 22 0.18
29 17 0.14
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (26 bp):
AAAATAATAATAAAAAATAGTAACAT
Found at i:22089 original size:14 final size:14
Alignment explanation
Indices: 22078--22112 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
22068 AATATGTTTG
*
22078 TTCATTTATGTTCA
1 TTCATATATGTTCA
22092 TTCATATATGTTCA
1 TTCATATATGTTCA
*
22106 TTTATAT
1 TTCATAT
22113 TCATTCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (14 bp):
TTCATATATGTTCA
Found at i:22147 original size:24 final size:24
Alignment explanation
Indices: 22076--22148 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
22066 ATAATATGTT
*
22076 TGTTCATTTATGTTCATTCATATA
1 TGTTCATTTATGTTCATTCATTTA
* *
22100 TGTTCATTTATATTCATTCGTTTA
1 TGTTCATTTATGTTCATTCATTTA
* * *
22124 TGTTCGTTTATGTGCGTTCATTTA
1 TGTTCATTTATGTTCATTCATTTA
22148 T
1 T
22149 ATTTAGCTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (24 bp):
TGTTCATTTATGTTCATTCATTTA
Found at i:22426 original size:14 final size:14
Alignment explanation
Indices: 22409--22438 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22399 TTTACATCCG
22409 TTCATTTATGTTCA
1 TTCATTTATGTTCA
*
22423 TTCATTTGTGTTCA
1 TTCATTTATGTTCA
22437 TT
1 TT
22439 TATCATTTAA
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:0.17, C:0.13, G:0.10, T:0.60
Consensus pattern (14 bp):
TTCATTTATGTTCA
Found at i:22435 original size:24 final size:24
Alignment explanation
Indices: 22315--22441 Score: 96
Period size: 24 Copynumber: 5.4 Consensus size: 24
22305 AAAATATATT
*
22315 TTCATTTATGTTCATTTA-TTGTG
1 TTCATTTATGTTCGTTTATTTGTG
** * **
22338 TTTGTTTACGTTCGTTCGTTTGTG
1 TTCATTTATGTTCGTTTATTTGTG
* * * *
22362 TTCGTTAACGTTCGTTTATAT-TG
1 TTCATTTATGTTCGTTTATTTGTG
** **
22385 TTCATTTATGTTCGTTTACATCCG
1 TTCATTTATGTTCGTTTATTTGTG
* *
22409 TTCATTTATGTTCATTCATTTGTG
1 TTCATTTATGTTCGTTTATTTGTG
22433 TTCATTTAT
1 TTCATTTAT
22442 CATTTAAATG
Statistics
Matches: 80, Mismatches: 22, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
23 31 0.39
24 49 0.61
ACGTcount: A:0.15, C:0.13, G:0.15, T:0.57
Consensus pattern (24 bp):
TTCATTTATGTTCGTTTATTTGTG
Found at i:25388 original size:17 final size:18
Alignment explanation
Indices: 25371--25426 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
25361 TTGTTGAATT
25371 AAATTATTAATAATATTA
1 AAATTATTAATAATATTA
* *
25389 AAATT-TTATATATTTTTTA
1 AAATTATTA-ATA-ATATTA
25408 AAATTATTAATAATATTA
1 AAATTATTAATAATATTA
25426 A
1 A
25427 TATTTCTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 12 0.39
20 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTATTAATAATATTA
Found at i:25412 original size:37 final size:39
Alignment explanation
Indices: 25371--25450 Score: 137
Period size: 37 Copynumber: 2.1 Consensus size: 39
25361 TTGTTGAATT
25371 AAATTATTAATAATATTAAAATTT-TATATATTT-TTTA
1 AAATTATTAATAATATTAAAATTTCTATATATTTGTTTA
*
25408 AAATTATTAATAATATTAATATTTCTATATATTTGTTTA
1 AAATTATTAATAATATTAAAATTTCTATATATTTGTTTA
25447 AAAT
1 AAAT
25451 ACAATATAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 23 0.57
38 9 0.22
39 8 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (39 bp):
AAATTATTAATAATATTAAAATTTCTATATATTTGTTTA
Found at i:26359 original size:6 final size:6
Alignment explanation
Indices: 26348--26393 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
26338 AACATACATT
* * *
26348 AAGGAG AAGGAG AAGGAG AAGGGG AAGGGG AAGGGG AAGGGG AAGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGG
26394 TTTATAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:27451 original size:101 final size:101
Alignment explanation
Indices: 27276--27479 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
27266 TCATGCATCA
*
27276 ATTATTGATGTATTATTGCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
1 ATTATTGATGCATTATTGCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
27341 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
66 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
* *
27377 ATTATTGCTGCATTATTTCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
1 ATTATTGATGCATTATTGCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
27442 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
66 AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
27478 AT
1 AT
27480 ATGGGATTAA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (101 bp):
ATTATTGATGCATTATTGCAGATGTTGGAGGCCCGTGATTTCAACAATTATTGCCCAATTAATTG
AAGCAGTCGGGGCTTAATTTTTATATATAGGATATG
Found at i:27807 original size:42 final size:43
Alignment explanation
Indices: 27722--27808 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
27712 TTGATAGTTA
* ***
27722 TATATTAAAAAATAATTAATTAGTTTGTTTGTTAGTCGTTAGT
1 TATATTAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
*
27765 TATA-TAAAAAATATTTAATTAGTTTG-TAGTTAGTTAAATAGT
1 TATATTAAAAAATAATTAATTAGTTTGTTAGTTAG-TAAATAGT
27807 TA
1 TA
27809 AGTTATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 6 0.16
42 28 0.74
43 4 0.11
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (43 bp):
TATATTAAAAAATAATTAATTAGTTTGTTAGTTAGTAAATAGT
Found at i:29944 original size:31 final size:31
Alignment explanation
Indices: 29901--29959 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
29891 GACGGTGGAC
*
29901 TAGTGACTATTTTATTATAAATAGATAACAT
1 TAGTGACTATTTTATTACAAATAGATAACAT
* *
29932 TAGTGA-TAATTTTGTTACAAATTGATAA
1 TAGTGACT-ATTTTATTACAAATAGATAA
29960 TAGAAGATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 1 0.04
31 23 0.96
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (31 bp):
TAGTGACTATTTTATTACAAATAGATAACAT
Found at i:33336 original size:18 final size:18
Alignment explanation
Indices: 33313--33348 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33303 AACCATAACT
*
33313 TAAGATTTATACTTTAGG
1 TAAGATTTATACGTTAGG
33331 TAAGATTTATACGTTAGG
1 TAAGATTTATACGTTAGG
33349 GTTTTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.19, T:0.42
Consensus pattern (18 bp):
TAAGATTTATACGTTAGG
Found at i:38472 original size:31 final size:31
Alignment explanation
Indices: 38416--38485 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
38406 CTTTTAAAAC
*
38416 TTGCAATAAAGTCCCTCAACTTTTAGTTCGT
1 TTGCAATAAAGTCCCTCAACATTTAGTTCGT
* *
38447 TTGTAATACAGTCCCAT-AACATTTAGTTCGT
1 TTGCAATAAAGTCCC-TCAACATTTAGTTCGT
38478 TTGCAATA
1 TTGCAATA
38486 TAGTATCTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (31 bp):
TTGCAATAAAGTCCCTCAACATTTAGTTCGT
Found at i:41744 original size:20 final size:20
Alignment explanation
Indices: 41696--41757 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
41686 AACTTAAATC
*
41696 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
41716 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
41734 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
41753 AAAAT
1 AAAAT
41758 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:41790 original size:14 final size:13
Alignment explanation
Indices: 41767--41856 Score: 57
Period size: 14 Copynumber: 6.9 Consensus size: 13
41757 TTAAATATCT
41767 ATAATATAATATTAA
1 ATAAT-TAATATT-A
41782 ATAATTAATAATT-
1 ATAATTAAT-ATTA
*
41795 -T-ATTTAT-TTA
1 ATAATTAATATTA
*
41805 AAAATTAATATTA
1 ATAATTAATATTA
41818 A-AATTAATATCT-
1 ATAATTAATAT-TA
41830 ATAATATAATATTAA
1 ATAAT-TAATATT-A
*
41845 AAAATTAATATT
1 ATAATTAATATT
41857 TAATTTATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
9 2 0.03
11 5 0.08
12 16 0.26
13 9 0.15
14 17 0.28
15 12 0.20
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAATTAATATTA
Found at i:41820 original size:64 final size:65
Alignment explanation
Indices: 41752--41908 Score: 236
Period size: 63 Copynumber: 2.5 Consensus size: 65
41742 TTATATGATA
41752 TAAAATTAAATATCTATAATATAATATTAAATAATTAATAATTT-ATTTATTT-AAAAATTAATA
1 TAAAATTAAATATCTATAATATAATATTAAATAATTAAT-ATTTAATTTATTTAAAAAATTAATA
41815 T
65 T
* *
41816 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAAAATTGATAT
1 TAAAATTAAATATCTATAATATAATATTAAATAATTAATATTTAATTTATTTAAAAAATTAATAT
*
41880 TAAAATTAAA-ATC-A-AATATAATATAAAAT
1 TAAAATTAAATATCTATAATATAATATTAAAT
41909 TAAATATAAA
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
62 17 0.20
63 39 0.45
64 28 0.33
65 2 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (65 bp):
TAAAATTAAATATCTATAATATAATATTAAATAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:41822 original size:12 final size:12
Alignment explanation
Indices: 41805--41911 Score: 69
Period size: 12 Copynumber: 8.7 Consensus size: 12
41795 TATTTATTTA
41805 AAAATTAATATT
1 AAAATTAATATT
41817 AAAATTAATATCT
1 AAAATTAATAT-T
*
41830 ATAATATAATATT
1 AAAAT-TAATATT
41843 AAAAAATTAATATT
1 --AAAATTAATATT
* *
41857 -TAATTTAT-TT
1 AAAATTAATATT
*
41867 AAAAAATTGATATT
1 --AAAATTAATATT
*
41881 AAAATTAA-AAT
1 AAAATTAATATT
*
41892 CAAATATAATA-T
1 AAAAT-TAATATT
41904 AAAATTAA
1 AAAATTAA
41912 ATATAAAACC
Statistics
Matches: 75, Mismatches: 10, Indels: 21
0.71 0.09 0.20
Matches are distributed among these distances:
10 2 0.03
11 15 0.20
12 26 0.35
13 13 0.17
14 15 0.20
15 4 0.05
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:41860 original size:26 final size:26
Alignment explanation
Indices: 41807--41888 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 26
41797 TTTATTTAAA
41807 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-TAT
41832 AATATAATATTAAAAAATTAATATT-T
1 AAT-TAATATTAAAAAATTAATATTAT
* * *
41858 AATTTAT-TTAAAAAATTGATATTAA
1 AATTAATATTAAAAAATTAATATTAT
41883 AATTAA
1 AATTAA
41889 AATCAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
24 15 0.31
25 11 0.22
26 11 0.22
27 1 0.02
28 11 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
AATTAATATTAAAAAATTAATATTAT
Found at i:42317 original size:19 final size:17
Alignment explanation
Indices: 42274--42317 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
42264 CATACACATA
*
42274 TAAAATATTTATGTTAT
1 TAAAATATGTATGTTAT
*
42291 TAATATATGTATGTTCACT
1 TAAAATATGTATGTT-A-T
42310 TAAAATAT
1 TAAAATAT
42318 TTTTAAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 13 0.59
18 1 0.05
19 8 0.36
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (17 bp):
TAAAATATGTATGTTAT
Found at i:44311 original size:63 final size:63
Alignment explanation
Indices: 44180--44335 Score: 159
Period size: 63 Copynumber: 2.5 Consensus size: 63
44170 AATTGTTCAA
* * * * * * * *
44180 GGTGTATCGATGCACATGAAGTGCATTGATGCACTCCTTTAAAATAAAACATTGAATGCCATC
1 GGTGTATCGATGCACAAGTAGTGCATCGATACACCCCCTTAAAATAAAACATCGAAGGCCATC
* * * ** *
44243 AGTGTATCGATGCACAAGTAGTGCATCGATACACCCCCTTAAAATGAATCATCGAAGGTGATT
1 GGTGTATCGATGCACAAGTAGTGCATCGATACACCCCCTTAAAATAAAACATCGAAGGCCATC
***
44306 GGTGTATCGATGCATGGGTAGTGCATCGAT
1 GGTGTATCGATGCACAAGTAGTGCATCGAT
44336 GTACATGTTA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (63 bp):
GGTGTATCGATGCACAAGTAGTGCATCGATACACCCCCTTAAAATAAAACATCGAAGGCCATC
Found at i:45707 original size:31 final size:31
Alignment explanation
Indices: 45620--45756 Score: 104
Period size: 31 Copynumber: 4.4 Consensus size: 31
45610 AGTCGAGGGT
*
45620 TTACCTATGTTCTACGGAAC-ATATGGACAG
1 TTACCTATGTTCTAAGGAACTATATGGACAG
* *** *
45650 AATTATCTATG-TCTTTTGAGAC-ATATGGATAG
1 --TTACCTATGTTCTAAGGA-ACTATATGGACAG
45682 TATACCTATGTTCTAAGGAA-TATATGGACAG
1 T-TACCTATGTTCTAAGGAACTATATGGACAG
* **
45713 TTTACCTAGGTTCTTTGGAACT-TATGGACAG
1 -TTACCTATGTTCTAAGGAACTATATGGACAG
*
45744 TTACCGATGTTCT
1 TTACCTATGTTCT
45757 TTATGACCTC
Statistics
Matches: 84, Mismatches: 15, Indels: 14
0.74 0.13 0.12
Matches are distributed among these distances:
30 12 0.14
31 46 0.55
32 26 0.31
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTAAGGAACTATATGGACAG
Found at i:45728 original size:63 final size:61
Alignment explanation
Indices: 45620--45756 Score: 159
Period size: 63 Copynumber: 2.2 Consensus size: 61
45610 AGTCGAGGGT
* * * * *
45620 TTACCTATGTTCTACGGAACATATGGACAGAATTATCTATGTCTTTTGAGACATATGGATAG
1 TTACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTGGA-ACATATGGACAG
* * *
45682 TATACCTATGTTCTAAGGAATATATGGACAG-TTTACCTAGGTTCTTTGGAACTTATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGG-TCTTTGGAACATATGGACAG
*
45744 TTACCGATGTTCT
1 TTACCTATGTTCT
45757 TTATGACCTC
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
61 11 0.17
62 19 0.30
63 34 0.53
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (61 bp):
TTACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTGGAACATATGGACAG
Found at i:45959 original size:13 final size:14
Alignment explanation
Indices: 45941--45973 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
45931 TTTGAAATGA
45941 TATATGTGATATG-
1 TATATGTGATATGT
*
45954 TATATGTGATTTGT
1 TATATGTGATATGT
45968 TATATG
1 TATATG
45974 GAATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (14 bp):
TATATGTGATATGT
Found at i:59062 original size:25 final size:25
Alignment explanation
Indices: 59015--59062 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
59005 ATTTATTATT
*
59015 TGTAATATAATTTAATATGAGATGA
1 TGTAATATAATTTAAGATGAGATGA
* * *
59040 TGTATTATATTTTAAGATTAGAT
1 TGTAATATAATTTAAGATGAGAT
59063 TTATTATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (25 bp):
TGTAATATAATTTAAGATGAGATGA
Found at i:60543 original size:24 final size:24
Alignment explanation
Indices: 60501--60564 Score: 105
Period size: 24 Copynumber: 2.7 Consensus size: 24
60491 GTGTGACCTT
60501 TAGTTGAAAG-AAATAACACTC-C
1 TAGTTGAAAGAAAATAACACTCTC
60523 ATAGTTGAAAGAAAATAACACTCTC
1 -TAGTTGAAAGAAAATAACACTCTC
60548 TAGTTGAAAGAAAATAA
1 TAGTTGAAAGAAAATAA
60565 ATCCACCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
23 10 0.26
24 28 0.72
25 1 0.03
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (24 bp):
TAGTTGAAAGAAAATAACACTCTC
Found at i:60807 original size:28 final size:28
Alignment explanation
Indices: 60753--60821 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 28
60743 TTAAAATACC
60753 TTTTATTTTTATTTTTAACTTATTAAATAAA
1 TTTTATTTTTA---TTAACTTATTAAATAAA
* *
60784 TTTTGTTTTTATTAACTTATTAAATATA
1 TTTTATTTTTATTAACTTATTAAATAAA
60812 TTTTATTTTT
1 TTTTATTTTT
60822 TATTTTAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 25 0.71
31 10 0.29
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (28 bp):
TTTTATTTTTATTAACTTATTAAATAAA
Found at i:60900 original size:31 final size:31
Alignment explanation
Indices: 60732--60907 Score: 93
Period size: 31 Copynumber: 5.8 Consensus size: 31
60722 ATGTTTTATA
* ** *
60732 TATCTTAA-ATTTTAAAATACCTTTTATTTT
1 TATCTTAACTTTTTAAAATATATTTTATTCT
* * * *
60762 TATTTTTAACTTATT-AAATAAATTTTGTT-T
1 TA-TCTTAACTTTTTAAAATATATTTTATTCT
* * *
60792 T-TATTAACTTATT-AAATATATTTTATTTTT
1 TATCTTAACTTTTTAAAATATATTTTA-TTCT
* * *
60822 TATTTTAA--TGTAAAAATATAAATTTTA-TCTT
1 TATCTTAACTTTTTAAAATAT--ATTTTATTC-T
* *
60853 TATCTTCAC--TTCAAAATATATTTTATTCT
1 TATCTTAACTTTTTAAAATATATTTTATTCT
60882 TATCTTAACTTTTTAAAATATATTTT
1 TATCTTAACTTTTTAAAATATATTTT
60908 TAAATGCATT
Statistics
Matches: 114, Mismatches: 19, Indels: 25
0.72 0.12 0.16
Matches are distributed among these distances:
28 21 0.18
29 19 0.17
30 15 0.13
31 50 0.44
32 9 0.08
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (31 bp):
TATCTTAACTTTTTAAAATATATTTTATTCT
Found at i:61186 original size:30 final size:29
Alignment explanation
Indices: 60753--61188 Score: 139
Period size: 30 Copynumber: 14.7 Consensus size: 29
60743 TTAAAATACC
* ** *
60753 TTTTATTTTTATTTTTAACTTATTAAATAAA
1 TTTTA-TTTTA-TCTTAACTTAAAAAATATA
* * **
60784 TTTTGTTTT-TATTAACTTATTAAATATA
1 TTTTATTTTATCTTAACTTAAAAAATATA
* *
60812 TTTTATTTTTTATTTTAA-TGTAAAAATATAAA
1 TTTTA--TTTTATCTTAACT-TAAAAA-ATATA
* *
60844 TTTTATCTTTATCTTCACTT-CAAAATATA
1 TTTTAT-TTTATCTTAACTTAAAAAATATA
**
60873 TTTTATTCTTATCTTAACTTTTTAAAATATA
1 TTTTATT-TTATCTTAAC-TTAAAAAATATA
**
60904 -TTT-TTAAATGCATTAACTTAAAAAATAT-
1 TTTTATTTTAT-C-TTAACTTAAAAAATATA
** * *
60932 TTAAACATTTTAATTTTAATTTTAATATAAA-A-A
1 TT--TTATTTT-ATCTTAA-CTTAA-A-AAATATA
* * *
60965 TATT-TTTTATATTCACTT--AAAATATA
1 TTTTATTTTATCTTAACTTAAAAAATATA
* *
60991 TTTTATTCTTATTTTAAATTTAAAAATATATA
1 TTTTATT-TTATCTT-AACTTAAAAA-ATATA
* * * * *
61023 TTTTATAATTATCATAGATTTTAAAAATATC
1 TTTTAT-TTTATCTTA-ACTTAAAAAATATA
* ***
61054 TTTTATTTGTGTCTTAACTTGTCAAATATA
1 TTTTATTT-TATCTTAACTTAAAAAATATA
* * * *
61084 --TT-TTTTATTTTAA-TATAAAACACATG
1 TTTTATTTTATCTTAACT-TAAAAAATATA
* *
61110 TTTTAATTTTATCTTCACTT-AAAAGTATA
1 TTTT-ATTTTATCTTAACTTAAAAAATATA
* *
61139 TTTTGTTCTTATTTTAACTTAAAAAATATA
1 TTTTATT-TTATCTTAACTTAAAAAATATA
61169 TTTTATTCTTATCTTAACTT
1 TTTTATT-TTATCTTAACTT
61189 TTCTAAAAAT
Statistics
Matches: 298, Mismatches: 67, Indels: 81
0.67 0.15 0.18
Matches are distributed among these distances:
24 3 0.01
25 3 0.01
26 15 0.05
27 5 0.02
28 38 0.13
29 59 0.20
30 73 0.24
31 54 0.18
32 40 0.13
33 5 0.02
34 3 0.01
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (29 bp):
TTTTATTTTATCTTAACTTAAAAAATATA
Found at i:61316 original size:31 final size:29
Alignment explanation
Indices: 61278--61375 Score: 133
Period size: 29 Copynumber: 3.3 Consensus size: 29
61268 ATTTTTGAAA
*
61278 AAAATATATTTTTAAAATTTAAGTTAATAAT
1 AAAATATATTTTT--AATTTAAGTTAAGAAT
**
61309 AAAATATATTTTTAATTTAAAATAAGAAT
1 AAAATATATTTTTAATTTAAGTTAAGAAT
*
61338 AAAATATATTTTTAAGTTAAGTTAAGAAT
1 AAAATATATTTTTAATTTAAGTTAAGAAT
*
61367 AATATATAT
1 AAAATATAT
61376 ATATATATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 47 0.78
31 13 0.22
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
AAAATATATTTTTAATTTAAGTTAAGAAT
Found at i:61326 original size:29 final size:29
Alignment explanation
Indices: 61278--61404 Score: 128
Period size: 29 Copynumber: 4.2 Consensus size: 29
61268 ATTTTTGAAA
** *
61278 AAAATATATTTTTAAAATTTAAGTTAATAAT
1 AAAATATATTTTT--AATTTAAAATAAGAAT
61309 AAAATATATTTTTAATTTAAAATAAGAAT
1 AAAATATATTTTTAATTTAAAATAAGAAT
* **
61338 AAAATATATTTTTAAGTTAAGTTAAGAAT
1 AAAATATATTTTTAATTTAAAATAAGAAT
* * * *
61367 AATATATATATATATATATTAAAATAATAAT
1 AAAATATATTTTTA-AT-TTAAAATAAGAAT
61398 AAAATAT
1 AAAATAT
61405 TTAAATATAT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 50 0.62
30 1 0.01
31 29 0.36
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (29 bp):
AAAATATATTTTTAATTTAAAATAAGAAT
Found at i:61350 original size:60 final size:60
Alignment explanation
Indices: 61278--61404 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 60
61268 ATTTTTGAAA
* * * *
61278 AAAATATATTTTTAAAATTTAAGTTAATAATAAAATATATTTTTA-AT-TTAAAATAAGAAT
1 AAAATATATTTTT--AAGTTAAGTTAAGAATAAAATATATATATATATATTAAAATAAGAAT
* *
61338 AAAATATATTTTTAAGTTAAGTTAAGAATAATATATATATATATATATTAAAATAATAAT
1 AAAATATATTTTTAAGTTAAGTTAAGAATAAAATATATATATATATATTAAAATAAGAAT
61398 AAAATAT
1 AAAATAT
61405 TTAAATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
58 25 0.42
59 2 0.03
60 32 0.54
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (60 bp):
AAAATATATTTTTAAGTTAAGTTAAGAATAAAATATATATATATATATTAAAATAAGAAT
Found at i:61507 original size:29 final size:31
Alignment explanation
Indices: 61452--61524 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
61442 ATAAAGATAA
61452 AATATATATTTTTAATTTAAAATAAAATATAT
1 AATATATATTTTTAA-TTAAAATAAAATATAT
* *
61484 ATTATATATTTTTAA-T-AAGTAAAATATAT
1 AATATATATTTTTAATTAAAATAAAATATAT
*
61513 AAAATATATTTT
1 AATATATATTTT
61525 CTTGAACCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 22 0.59
30 1 0.03
32 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (31 bp):
AATATATATTTTTAATTAAAATAAAATATAT
Found at i:61555 original size:2 final size:2
Alignment explanation
Indices: 61550--61581 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
61540 AAAAAAGATA
61550 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
61582 TTCACTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62420 original size:21 final size:21
Alignment explanation
Indices: 62394--62465 Score: 101
Period size: 21 Copynumber: 3.4 Consensus size: 21
62384 TTTCAGTAAG
* *
62394 AGTATCCATACTTCTGGGGAA
1 AGTATCGATACTTCTGGGAAA
62415 AGTATCGATACTTCT-GGAAA
1 AGTATCGATACTTCTGGGAAA
*
62435 ACGTATCGATACTTCTGGTAAA
1 A-GTATCGATACTTCTGGGAAA
62457 AGTATCGAT
1 AGTATCGAT
62466 TCTCAAGGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 5 0.11
21 36 0.78
22 5 0.11
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTTCTGGGAAA
Found at i:64328 original size:30 final size:30
Alignment explanation
Indices: 64286--64363 Score: 138
Period size: 30 Copynumber: 2.6 Consensus size: 30
64276 AAGGTGTTAC
*
64286 AAAAAGTAAAATATATTTAATAAGTTAAGAT
1 AAAAA-TAAAATATATTTAATAAGTTAAAAT
64317 AAAAATAAAATATATTTAATAAGTTAAAAT
1 AAAAATAAAATATATTTAATAAGTTAAAAT
64347 AAAAATAAAATATATTT
1 AAAAATAAAATATATTT
64364 TTAAAATTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 41 0.89
31 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
AAAAATAAAATATATTTAATAAGTTAAAAT
Found at i:67574 original size:37 final size:36
Alignment explanation
Indices: 67500--67574 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
67490 CAAATCGTAA
*
67500 AATATTTATATATTTTCTTTAAAAAATTAAATTTAT
1 AATATTTATATATTTTCTTTAAAAAATTAAATATAT
* *
67536 AATATTTATATAATTTTTTTTACAAAATTTAAA-ATAT
1 AATATTTATAT-ATTTTCTTTA-AAAAATTAAATATAT
67573 AA
1 AA
67575 AAAAAGTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 11 0.32
37 14 0.41
38 9 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (36 bp):
AATATTTATATATTTTCTTTAAAAAATTAAATATAT
Found at i:72426 original size:21 final size:21
Alignment explanation
Indices: 72401--72445 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
72391 AGTTTTAGTC
*
72401 CAAATTGACCCAAGTAAAATT
1 CAAATTGACCCAAATAAAATT
72422 CAAATTGACCCAAATAAAATT
1 CAAATTGACCCAAATAAAATT
72443 CAA
1 CAA
72446 GCACTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.51, C:0.20, G:0.07, T:0.22
Consensus pattern (21 bp):
CAAATTGACCCAAATAAAATT
Found at i:72685 original size:22 final size:22
Alignment explanation
Indices: 72655--72707 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
72645 AAAAAATCGA
72655 GACTTAAACCTCTCATTTTATT
1 GACTTAAACCTCTCATTTTATT
*
72677 GGCTTAAACCTCTCATTTTATT
1 GACTTAAACCTCTCATTTTATT
72699 GACTTAAAC
1 GACTTAAAC
72708 AATTCTCGAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.42
Consensus pattern (22 bp):
GACTTAAACCTCTCATTTTATT
Found at i:74337 original size:17 final size:17
Alignment explanation
Indices: 74302--74344 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
74292 ATTAAAGGAG
* *
74302 CTAGTTTGATTAATGAA
1 CTAGTTTAATTAATAAA
*
74319 CTAGTTTAATTATTAAA
1 CTAGTTTAATTAATAAA
74336 CTAGCTTTA
1 CTAG-TTTA
74345 TTGAACGAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
CTAGTTTAATTAATAAA
Found at i:78313 original size:29 final size:24
Alignment explanation
Indices: 78258--78306 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
78248 AGTAGATAGT
78258 TTTTTATTTTATTTTATGAATTTG
1 TTTTTATTTTATTTTATGAATTTG
78282 TTTTTATTTTATTTTATGAATTTG
1 TTTTTATTTTATTTTATGAATTTG
78306 T
1 T
78307 ACGGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATTTTATGAATTTG
Found at i:80600 original size:16 final size:16
Alignment explanation
Indices: 80579--80609 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
80569 ATAGTGCTAC
80579 AGTGTACCGATGCACT
1 AGTGTACCGATGCACT
80595 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
80610 AAAAACATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.23
Consensus pattern (16 bp):
AGTGTACCGATGCACT
Found at i:80654 original size:21 final size:21
Alignment explanation
Indices: 80630--80669 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
80620 AATATAAATT
* * *
80630 GTGTATCGGTGCATTGCTATA
1 GTGTACCGATGCACTGCTATA
80651 GTGTACCGATGCACTGCTA
1 GTGTACCGATGCACTGCTA
80670 CAGTAACTTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.33
Consensus pattern (21 bp):
GTGTACCGATGCACTGCTATA
Found at i:81247 original size:24 final size:23
Alignment explanation
Indices: 81202--81266 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
81192 AGCTCGTATA
*
81202 AATTGCACCGAAG-GACCGCGTAG
1 AATTGCACCGAAGTG-CCACGTAG
81225 CAATTGCACCGAAGTGCCACGTAG
1 -AATTGCACCGAAGTGCCACGTAG
* *
81249 AAATGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
81267 TACAAGATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 16 0.43
24 20 0.54
25 1 0.03
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:88699 original size:15 final size:15
Alignment explanation
Indices: 88679--88713 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
88669 TCGGAGTCCA
88679 AGTTGGGATGATCCT
1 AGTTGGGATGATCCT
88694 AGTTGGGATGATCCT
1 AGTTGGGATGATCCT
88709 AGTTG
1 AGTTG
88714 ATCCCTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (15 bp):
AGTTGGGATGATCCT
Found at i:97190 original size:20 final size:20
Alignment explanation
Indices: 97167--97206 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
97157 ATTCCACCAC
*
97167 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
97187 ATGCATCTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
97207 TGGGCTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:97628 original size:17 final size:19
Alignment explanation
Indices: 97598--97634 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
97588 ATTTATTCAA
*
97598 ATAATCATATATAAATAAT
1 ATAATCATATATAAAAAAT
97617 ATAAT-ATA-ATAAAAAAT
1 ATAATCATATATAAAAAAT
97634 A
1 A
97635 GTTTTACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATCATATATAAAAAAT
Done.