Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003714.1 Hibiscus syriacus cultivar Beakdansim tig00007941_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: 47462
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:45 original size:3 final size:3
Alignment explanation
Indices: 37--76 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
27 GTTTTATATC
*
37 ATT ATT ATT ATT ACT ATT ACTT ATT A-T ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT A
77 CATTTGTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1203 original size:104 final size:102
Alignment explanation
Indices: 1088--1275 Score: 288
Period size: 104 Copynumber: 1.8 Consensus size: 102
1078 ATATATATAT
* * *
1088 ATATGCTTTAGTTTTATAATCGTATGTTGTTTTTCTGCATCCTATATTAC-TGTTTAACTTATAT
1 ATATGCTTTAGTTTTATAATCGTATGTTGTTTCTATGCATCCCATATTACATGTTTAA-TT-TAT
1152 ATATTATTAAATAGGTGTATTATATATATATAATATACGA
64 ATATTATT-AATAGGTGTATTATATATATATAATATACGA
*
1192 ATATGCTTTAGTTTTATAATCGTATGTTGTTTCTATGTATCCCATATTACATGTGTTTAATTTAT
1 ATATGCTTTAGTTTTATAATCGTATGTTGTTTCTATGCATCCCATATTACA--TGTTTAATTTAT
1257 ATATTATTAATAGGTGTAT
64 ATATTATTAATAGGTGTAT
1276 ATAATTTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
104 57 0.74
105 11 0.14
106 2 0.03
107 7 0.09
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.50
Consensus pattern (102 bp):
ATATGCTTTAGTTTTATAATCGTATGTTGTTTCTATGCATCCCATATTACATGTTTAATTTATAT
ATTATTAATAGGTGTATTATATATATATAATATACGA
Found at i:3155 original size:53 final size:54
Alignment explanation
Indices: 2998--3215 Score: 304
Period size: 53 Copynumber: 4.1 Consensus size: 54
2988 TTACCAAATA
* *
2998 GCACTAAGTGTGCATTTCACGGAATCCATCTTATGTGGATGAATAACTGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCG
* *
3051 GCACTAAGTGT--AATTCATGGAATTCATCCTATGTGGAT-AATAACTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCG
* * *
3102 GCACTAAGTGTGCATTTCACGAAATTCATCCTCTGTGAATGAATAA-TCG-TTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACT-GTTTCG
*
3155 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC-G
3210 GCACTA
1 GCACTA
3216 TTTTGTGCAA
Statistics
Matches: 144, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
50 12 0.08
51 34 0.24
53 82 0.57
54 9 0.06
55 7 0.05
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCG
Found at i:3253 original size:108 final size:104
Alignment explanation
Indices: 2998--3245 Score: 250
Period size: 104 Copynumber: 2.3 Consensus size: 104
2988 TTACCAAATA
** * * ** *
2998 GCACTAAGTGTGCATTTCACGGAATCCATCTTATGTGGATGAATAA-CTGTTTC-GCACTAAGTG
1 GCACTAAGTGTGCATAACACGAAATTCATAATATGTGAATGAATAATC-G-TTCGGCACTAAGTG
* *
3061 TAATTCATGGAATTCATCCTATGTGGATAATAACTGTTTCG
64 TAATTCACGGAATTCATCCTATGTGGATAATAACCGTTTCG
** ** *
3102 GCACTAAGTGTGCATTTCACGAAATTCATCCTCTGTGAATGAATAATCGTTCGGCACTAAGTGTG
1 GCACTAAGTGTGCATAACACGAAATTCATAATATGTGAATGAATAATCGTTCGGCACTAAGTGT-
*
3167 CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAG
65 -AATTCACGGAATTCATCCTATGTGGAT-AATAACCGTTTC-G
** *
3210 GCACTATTTTGTGCA-AACACGAAATTTATAATATGT
1 GCACTA-AGTGTGCATAACACGAAATTCATAATATGT
3246 TTATGAATTA
Statistics
Matches: 121, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
103 3 0.02
104 53 0.44
105 1 0.01
106 25 0.21
107 11 0.09
108 22 0.18
109 6 0.05
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.33
Consensus pattern (104 bp):
GCACTAAGTGTGCATAACACGAAATTCATAATATGTGAATGAATAATCGTTCGGCACTAAGTGTA
ATTCACGGAATTCATCCTATGTGGATAATAACCGTTTCG
Found at i:9166 original size:20 final size:20
Alignment explanation
Indices: 9121--9173 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
9111 TGATTGAATC
9121 AGTATCGATACCAAAGGGGGA
1 AGTATCGATACCAAA-GGGGA
*
9142 A-TATCGATACCGAA-GGGA
1 AGTATCGATACCAAAGGGGA
9160 ATGTATCGATACCA
1 A-GTATCGATACCA
9174 TTTTGAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 5 0.18
20 22 0.79
21 1 0.04
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (20 bp):
AGTATCGATACCAAAGGGGA
Found at i:9220 original size:19 final size:22
Alignment explanation
Indices: 9196--9266 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 22
9186 ATGCAAAATG
9196 GTATCGATACCATA-T-CAG-A
1 GTATCGATACCATAGTACAGCA
* * *
9215 GTATCGGTATCATAGTATAGCA
1 GTATCGATACCATAGTACAGCA
* *
9237 GTATCGATACCATGGTA-AG-G
1 GTATCGATACCATAGTACAGCA
9257 GTATCGATAC
1 GTATCGATAC
9267 TATGGAGTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 12 0.29
20 11 0.26
21 4 0.10
22 15 0.36
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATAGTACAGCA
Found at i:9905 original size:54 final size:54
Alignment explanation
Indices: 9591--9890 Score: 435
Period size: 54 Copynumber: 5.6 Consensus size: 54
9581 TTACCAAATA
* *
9591 GGCACTATGTGT-CAATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGC-ATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
* *
9645 GGCATTAAGTGTGCATTTCACGGAATTCATCTTATGTGGATGAATAA-TCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACT-GTTTC
* *
9699 GGCACTAAGTGTGCATTTCACAGAATTTATCCTATGTGTG-TGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTG-GATGAATAACTGTTTC
**
9753 GGCACTAAGTGTGCATTTCACTAAATTCATCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
*
9807 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
* ***
9861 GGCACTATGTGTGCAAAACACGGAATTCAT
1 GGCACTAAGTGTGCATTTCACGGAATTCAT
9891 AATATGTTTA
Statistics
Matches: 223, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
53 1 0.00
54 219 0.98
55 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTC
Found at i:9919 original size:54 final size:54
Alignment explanation
Indices: 9609--9929 Score: 241
Period size: 54 Copynumber: 5.9 Consensus size: 54
9599 GTGTCAATTT
** * * ***
9609 CACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATTAAGTGTGCATTT
1 CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
** * * ***
9663 CACGGAATTCATCTTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
* * ** * * ***
9717 CACAGAATTTATCCTATGTGTG-TGAATAACTGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATAATATGTG-GATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
** ** * * ***
9771 CACTAAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTGTGCATTT
1 CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
** * * *
9825 CACGGAATTCATTCTATGTGGATGAATAACTGTTTCGGCACTATGTGTGCAAAA
1 CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
** * *
9879 CACGGAATTCATAATATGTTTATGAATGACCGTGTGGGCACTACAG-GTGCA
1 CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTA-AGTGTGCA
9930 TTACAAAGAA
Statistics
Matches: 237, Mismatches: 27, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
53 1 0.00
54 234 0.99
55 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.33
Consensus pattern (54 bp):
CACGGAATTCATAATATGTGGATGAATAACCGTGTCGGCACTAAGTGTGCAAAA
Found at i:9919 original size:108 final size:108
Alignment explanation
Indices: 9591--9931 Score: 436
Period size: 108 Copynumber: 3.2 Consensus size: 108
9581 TTACCAAATA
* * *
9591 GGCACTATGTGT-CAATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATTAAGT
1 GGCACTAAGTGTGC-ATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGT
* *
9655 GTGCATTTCACGGAATTCATCTTATGTGGATGAATAATCGTTTC
65 GTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
* *
9699 GGCACTAAGTGTGCATTTCACAGAATTTATCCTATGTGTG-TGAATAACTGTTTCGGCACTAAGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTG-GATGAATAACTGTTTCGGCACTAAGT
** * *
9763 GTGCATTTCACTAAATTCATCCTATGTGGATGAATAACTGTTTC
65 GTGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
* *
9807 GGCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGGATGAATAACTGTTTCGGCACTATGTG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTG
*** * ** * * *
9872 TGCAAAACACGGAATTCATAATATGTTTATGAATGACCGTGTG
66 TGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
9915 GGCACTACAG-GTGCATT
1 GGCACTA-AGTGTGCATT
9932 ACAAAGAAAT
Statistics
Matches: 202, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
107 1 0.00
108 197 0.98
109 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (108 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTG
TGCATTTCACGGAATTCATCATATGTGGATGAATAACCGTTTC
Found at i:9921 original size:162 final size:162
Alignment explanation
Indices: 9591--9931 Score: 447
Period size: 162 Copynumber: 2.1 Consensus size: 162
9581 TTACCAAATA
* * *
9591 GGCACTATGTGT-CAATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCATTAAGT
1 GGCACTAAGTGTGC-ATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGT
***
9655 GTGCATTTCACGGAATTCATCTTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCATTTCAC
65 GTGCATTTCACGGAATTCATCTTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCAAAACAC
* ** * * *
9720 AGAATTTATCCTATGTGTGTGAATAACTGTTTC
130 AGAATTCATAATATGTGTATGAATAACCGTGTC
* *
9753 GGCACTAAGTGTGCATTTCACTAAATTCATCCTATGTGGATGAATAACTGTTTCGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTG
*
9818 TGCATTTCACGGAATTCAT-TCTATGTGGATGAATAA-CTGTTTCGGCACTATGTGTGCAAAACA
66 TGCATTTCACGGAATTCATCT-TATGTGGATGAATAATC-GTTTCGGCACTAAGTGTGCAAAACA
* * * *
9881 CGGAATTCATAATATGTTTATGAATGACCGTGTG
129 CAGAATTCATAATATGTGTATGAATAACCGTGTC
9915 GGCACTACAG-GTGCATT
1 GGCACTA-AGTGTGCATT
9932 ACAAAGAAAT
Statistics
Matches: 156, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
161 2 0.01
162 151 0.97
163 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (162 bp):
GGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTG
TGCATTTCACGGAATTCATCTTATGTGGATGAATAATCGTTTCGGCACTAAGTGTGCAAAACACA
GAATTCATAATATGTGTATGAATAACCGTGTC
Found at i:9998 original size:2 final size:2
Alignment explanation
Indices: 9991--10016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9981 AATAATAATG
9991 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
10017 TGATTTCATT
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
Found at i:11266 original size:23 final size:23
Alignment explanation
Indices: 11217--11294 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
11207 ATATATTTAA
11217 AATATGTATTTAATT-TTT-AAAT
1 AATAT-TATTTAATTATTTGAAAT
* *
11239 CATATTATTTATTTATTTGAAAT
1 AATATTATTTAATTATTTGAAAT
* *
11262 AATATTAATTACTTATTTGAAAT
1 AATATTATTTAATTATTTGAAAT
11285 AATATTATTT
1 AATATTATTT
11295 TTAAATTAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 8 0.17
22 7 0.15
23 33 0.69
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (23 bp):
AATATTATTTAATTATTTGAAAT
Found at i:11451 original size:22 final size:22
Alignment explanation
Indices: 11408--11451 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11398 AATAATACTA
* * *
11408 TTTTAAATAAATGATTAATTTT
1 TTTTAAAAAAATAAATAATTTT
11430 TTTTAAAAAAATAAAT-ATTTT
1 TTTTAAAAAAATAAATAATTTT
11451 T
1 T
11452 ATAATATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAAAAAATAAATAATTTT
Found at i:13663 original size:19 final size:19
Alignment explanation
Indices: 13639--13680 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
13629 CTTTAAGGGA
*
13639 GTATCGGGACACTACGGGT
1 GTATCGGGACACTACGAGT
13658 GTATCGGGACACTACGAGT
1 GTATCGGGACACTACGAGT
13677 GTAT
1 GTAT
13681 TGGTACCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (19 bp):
GTATCGGGACACTACGAGT
Found at i:18254 original size:21 final size:21
Alignment explanation
Indices: 18228--18282 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
18218 CAATTGGTCT
18228 TAGTGTATCGATACCTATTCA
1 TAGTGTATCGATACCTATTCA
*
18249 TAGTGTATCGGTACCTATTCA
1 TAGTGTATCGATACCTATTCA
*
18270 TAGTGTACCGATA
1 TAGTGTATCGATA
18283 TACCCTGTCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (21 bp):
TAGTGTATCGATACCTATTCA
Found at i:25687 original size:20 final size:20
Alignment explanation
Indices: 25633--25687 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
25623 TTAAATTCCA
*
25633 AAAGTGTCGATACTTATAAT
1 AAAGTATCGATACTTATAAT
*
25653 AAAGTATCAATACTTATAAT
1 AAAGTATCGATACTTATAAT
*
25673 AAAGTATCGACACTT
1 AAAGTATCGATACTT
25688 TCAACATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (20 bp):
AAAGTATCGATACTTATAAT
Found at i:25856 original size:202 final size:200
Alignment explanation
Indices: 25510--26228 Score: 888
Period size: 182 Copynumber: 3.8 Consensus size: 200
25500 TTTTTACTAC
* * * *
25510 CGGTTTTTTCATTTCGATACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGA-TGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* * *
25575 ATTTTTATAAAGTATCGACACTTTATTGGCGCTGTAACTTCTTTTCTTTTAAATTCCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
25640 CGATACTTATAATAAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGC
130 CGATACTTATAATAAAGTATCAATACTTATAATAAAGTATCGACACTTTC-ACATATCCGGTAGC
25705 TCTTTAT
194 TCTTTAT
* *
25712 CGGTTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCTATAC
1 CGGTTTTGTCATTTCGAGAT-GATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
25777 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
* * * *
25842 CGATACTTATAATAAAGTATC--GAC---------ACTAT---CA---T--CATATCTGGTAGCG
130 CGATACTTATAATAAAGTATCAATACTTATAATAAAGTATCGACACTTTCACATATCCGGTAGCT
*
25888 CTTTAC
195 CTTTAT
* ** *
25894 CTGTTTTGTCATTTATAGACTGATTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGA-TGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
25959 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTAC-AAAA--G
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATT-CTAAAAGTG
*
26021 T-G-T-C----------G-----ATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAG
129 TCGATACTTATAATAAAGTATCAATACTTATAATAAAGTATCGACACTTTC-ACATATCCGGTAG
*
26068 CTCTTTAC
193 CTCTTTAT
*
26076 CGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGA-TGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
26141 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGT
26206 CGATACTTATAATAAAGTATCAA
130 CGATACTTATAATAAAGTATCAA
26229 CACTATCAAC
Statistics
Matches: 443, Mismatches: 31, Indels: 86
0.79 0.06 0.15
Matches are distributed among these distances:
164 2 0.00
167 1 0.00
173 4 0.01
176 2 0.00
177 1 0.00
178 1 0.00
179 2 0.00
180 2 0.00
181 1 0.00
182 268 0.60
183 2 0.00
184 2 0.00
185 2 0.00
186 1 0.00
187 1 0.00
188 2 0.00
191 4 0.01
197 1 0.00
200 2 0.00
202 142 0.32
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (200 bp):
CGGTTTTGTCATTTCGAGATGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGTC
GATACTTATAATAAAGTATCAATACTTATAATAAAGTATCGACACTTTCACATATCCGGTAGCTC
TTTAT
Found at i:25969 original size:182 final size:182
Alignment explanation
Indices: 25653--26345 Score: 1122
Period size: 182 Copynumber: 3.8 Consensus size: 182
25643 TACTTATAAT
* * * * * *
25653 AAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTATCGGTTT
1 AAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCGGTTT
* * * *
25718 TGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCTATACATTTTT
66 TGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
25783 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTA
131 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTA
* *
25835 AAAGTGTCGATACTTATAATAAAGTATCGACACTATCATCATATCTGGTAGCGCTTTACCTGTTT
1 AAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCGGTTT
* * *
25900 TGTCATTTATAGACTGATTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
25965 ATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTAC-A
131 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATT-CTA
* *
26017 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTACCGGTTT
1 AAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCGGTTT
*
26082 TGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
26147 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTA
131 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTA
* *
26199 AAAGTGTCGATACTTATAATAAAGTATCAACACTATCAACATAT-TCGGTAGCGCTTTACCTGTT
1 AAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCT-GGTAGCGCTTTACCGGTT
* *
26263 TTGTCATTTATAGACCGGTTTTGTCAT-TTTTTACCTGTTATATTGTTATGGATCGATACATTTT
65 TTGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTT
*
26327 TATAAAGTATCGACTCTTT
130 TATAAAGTATCGACACTTT
26346 CAATATATCC
Statistics
Matches: 474, Mismatches: 34, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
181 57 0.12
182 416 0.88
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (182 bp):
AAAGTGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCGGTTT
TGTCATTTAGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTA
Found at i:26201 original size:364 final size:363
Alignment explanation
Indices: 25653--26345 Score: 1244
Period size: 364 Copynumber: 1.9 Consensus size: 363
25643 TACTTATAAT
*
25653 AAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTATCGGTTT
1 AAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCGGTTT
* *
25718 TGTCATTTCGAGATCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCTATACATTTTT
66 TGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTT
*
25783 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCTAAAAGTGTCGATAC
131 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATAC
* *
25848 TTATAATAAAGTATCGACACTATCATCATA-TCTGGTAGCGCTTTACCTGTTTTGTCATTTATAG
196 TTATAATAAAGTATCAACACTATCAACATATTC-GGTAGCGCTTTACCTGTTTTGTCATTTATAG
*
25912 ACTGATTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
260 ACCGATTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
25977 CACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTACA
324 CACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTACA
* * *
26017 AAAGTGTCGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCTCTTTACCGGTTT
1 AAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCGGTTT
*
26082 TGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTT
26147 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATAC
131 ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATAC
26212 TTATAATAAAGTATCAACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGA
196 TTATAATAAAGTATCAACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGA
* *
26277 CCGGTTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACT
261 CCGATTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
26342 CTTT
326 CTTT
26346 CAATATATCC
Statistics
Matches: 315, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
363 56 0.18
364 257 0.82
365 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (363 bp):
AAAGTATCAATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACCGGTTT
TGTCATTTCGAGACCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATTTTT
ATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAGTGTCGATAC
TTATAATAAAGTATCAACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGA
CCGATTTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
CTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTACA
Found at i:26450 original size:112 final size:112
Alignment explanation
Indices: 26217--26678 Score: 791
Period size: 112 Copynumber: 4.1 Consensus size: 112
26207 GATACTTATA
* * *
26217 ATAAAGTATCAACACTATCAACATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
26282 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
* * *
26328 ATAAAGTATCGACTCTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATCTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
26393 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
26440 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
26505 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
*
26552 ATAAAGTATCGACACTTTCAATATATGCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
26617 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATATAGTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
*
26664 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
26679 AAACCAACAA
Statistics
Matches: 334, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
111 66 0.20
112 268 0.80
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.45
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATTCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCAATACATTTTT
Found at i:26979 original size:21 final size:21
Alignment explanation
Indices: 26953--26996 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
26943 TAATATCATG
26953 TTATTATTGAAAGAAATTTAA
1 TTATTATTGAAAGAAATTTAA
26974 TTATTATTGAAAGAAATTTAA
1 TTATTATTGAAAGAAATTTAA
26995 TT
1 TT
26997 CAATAATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (21 bp):
TTATTATTGAAAGAAATTTAA
Found at i:27111 original size:7 final size:7
Alignment explanation
Indices: 27085--27494 Score: 209
Period size: 7 Copynumber: 57.7 Consensus size: 7
27075 TTCGTTCGGG
27085 ATTATTAT
1 ATTA-TAT
27093 ATTATAT
1 ATTATAT
*
27100 AATAT-T
1 ATTATAT
27106 ATATATAT
1 AT-TATAT
*
27114 TTTATAT
1 ATTATAT
27121 ATTAT-T
1 ATTATAT
27127 ATATAGTAT
1 AT-TA-TAT
27136 GAGTTATAT
1 -A-TTATAT
*
27145 AGTATAT
1 ATTATAT
27152 ATTATATT
1 ATTATA-T
27160 ATT-TAT
1 ATTATAT
*
27166 ATCATAT
1 ATTATAT
27173 ATTATAT
1 ATTATAT
*
27180 AGTATAT
1 ATTATAT
*
27187 A-TAGTGT
1 ATTA-TAT
27194 ATTATAGT
1 ATTATA-T
27202 ATATATAT
1 AT-TATAT
27210 ATTATAT
1 ATTATAT
*
27217 AGTATGAT
1 ATTAT-AT
27225 A-TATATT
1 ATTATA-T
27232 ATTATA-
1 ATTATAT
*
27238 A-TAGTTT
1 ATTA-TAT
*
27245 ATTATAA
1 ATTATAT
27252 AGTATATAT
1 A-T-TATAT
27261 ATTATAT
1 ATTATAT
* *
27268 AGTATGT
1 ATTATAT
27275 ATTATAT
1 ATTATAT
27282 A-TAT-T
1 ATTATAT
*
27287 ATAATAT
1 ATTATAT
27294 ATTATAT
1 ATTATAT
*
27301 ATTATTT
1 ATTATAT
27308 A-T-TAT
1 ATTATAT
27313 ATTA-AT
1 ATTATAT
27319 ATTATATT
1 ATTATA-T
27327 ATAGTATAT
1 AT--TATAT
27336 ATTATATT
1 ATTATA-T
*
27344 TTTATTAT
1 ATTA-TAT
27352 ATTATAT
1 ATTATAT
*
27359 ATTACA-
1 ATTATAT
27365 A-TATAT
1 ATTATAT
*
27371 ATAATAT
1 ATTATAT
*
27378 ATAATATT
1 ATTATA-T
27386 ATTTATAT
1 A-TTATAT
*
27394 ATT-TTT
1 ATTATAT
27400 ATTAT-T
1 ATTATAT
27406 ATTTATTAT
1 A-TTA-TAT
27415 ATTATAT
1 ATTATAT
27422 -TATATTAT
1 AT-TA-TAT
27430 ATTATA-
1 ATTATAT
27436 A-TATAT
1 ATTATAT
27442 ATTATAT
1 ATTATAT
27449 ATT-TAT
1 ATTATAT
27455 -TGTA-ATT
1 AT-TATA-T
27462 ATTATAT
1 ATTATAT
27469 -TTATAT
1 ATTATAT
* *
27475 TTTTTAT
1 ATTATAT
*
27482 ATTTATTT
1 A-TTATAT
27490 ATTAT
1 ATTAT
27495 TTTAGGTTCA
Statistics
Matches: 316, Mismatches: 35, Indels: 103
0.70 0.08 0.23
Matches are distributed among these distances:
5 15 0.05
6 49 0.16
7 157 0.50
8 62 0.20
9 25 0.08
10 7 0.02
11 1 0.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (7 bp):
ATTATAT
Found at i:27131 original size:23 final size:23
Alignment explanation
Indices: 27105--27484 Score: 130
Period size: 23 Copynumber: 16.8 Consensus size: 23
27095 TATATAATAT
27105 TATATATATTTTATATATTATTA
1 TATATATATTTTATATATTATTA
* *
27128 TATAGTATGA-GTTATATAGTA-TA
1 TATA-TAT-ATTTTATATATTATTA
27151 TAT-TATATTATTTATATCATATATTA
1 TATATATA-T-TTTATAT-AT-TATTA
* *
27177 TATAGTATA-TATAGTGTATTA-TA
1 TATA-TATATTTTA-TATATTATTA
* * *
27200 GTATATATATATTATATAGTATGA
1 -TATATATATTTTATATATTATTA
* *
27224 TATATAT-TATTATAATAGT-TTA
1 TATATATATTTTAT-ATATTATTA
* * *
27246 T-TATAAAGTATATATATTA-TA
1 TATATATATTTTATATATTATTA
* * *
27267 TAGTATGTATTATATATATTATAA
1 TA-TATATATTTTATATATTATTA
* *
27291 TATATTATATATTATTTATTA-TA
1 TATA-TATATTTTATATATTATTA
* *
27314 T-TA-ATATTATAT-TA-TAGTA
1 TATATATATTTTATATATTATTA
27333 TATATTATATTTT-TATTA-TATTA
1 TATA-TATATTTTATA-TATTATTA
*** *
27356 TATAT-TACAATATATA-TAATA
1 TATATATATTTTATATATTATTA
*
27377 TATA-ATATTATTTATATATTTTTA
1 TATATATA-T-TTTATATATTATTA
27401 T-TAT-TA-TTTAT-TA-TATTA
1 TATATATATTTTATATATTATTA
* *
27419 TAT-TATATTATAT-TA-TAATA
1 TATATATATTTTATATATTATTA
*
27439 TATATTATATATTTATTGTAATTATTA
1 TATA-TATAT-TTTA-TAT-ATTATTA
* *
27466 TATTTATATTTTTTATATT
1 TATATATATTTTATATATT
27485 TATTTATTAT
Statistics
Matches: 267, Mismatches: 47, Indels: 86
0.67 0.12 0.22
Matches are distributed among these distances:
18 8 0.03
19 10 0.04
20 28 0.10
21 30 0.11
22 28 0.10
23 83 0.31
24 44 0.16
25 12 0.04
26 13 0.05
27 7 0.03
28 4 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (23 bp):
TATATATATTTTATATATTATTA
Found at i:27154 original size:49 final size:47
Alignment explanation
Indices: 27087--27451 Score: 234
Period size: 47 Copynumber: 7.8 Consensus size: 47
27077 CGTTCGGGAT
*
27087 TATTATATTA-TATAATATTATATATATTTTATATATTATTATATAGTA
1 TATTATA-TAGTAT-ATATTATATATATATTATATATTATTATATAGTA
27135 TGAGTTATATAGTATATATTATAT-TAT-TTATATCATATATTATATAGTA
1 T-A-TTATATAGTATATATTATATATATATTATAT-AT-TATTATATAGTA
* * *
27184 TA-TATAGT-GTATTATAGTATATATATATTATATAGTATGATATA-TA
1 TATTATA-TAGTA-TATATTATATATATATTATATATTATTATATAGTA
*
27230 TTATTATAATAGT-T-TATTATA-A-AGTA-TATATATTA-TATAGTA-TG
1 -TATTAT-ATAGTATATATTATATATA-TATTATATATTATTATA-TAGTA
* * *
27274 TATTATATA-TATTATAATATATTATATATTATTTATTA-TAT-TAATA
1 TATTATATAGTA-TATATTATA-TATATATTATATATTATTATATAGTA
* * *
27320 TTATAT-TATAGTATATATTATATTTTTATTATATTATATATTACAATA-TA
1 -TAT-TATATAGTATATATTATATATATATTATA-TAT-TATTA-TATAGTA
* * * * *
27370 TATAATATA-TA-ATATTATTTATATATT-TTTATTATTATTTATTA
1 TATTATATAGTATATATTATATATATATTATATATTATTATATAGTA
27414 TATTATATTA-TATTATATTATAATATATATTATATATT
1 TATTATA-TAGTA-TATATTAT-ATATATATTATATATT
27452 TATTGTAATT
Statistics
Matches: 254, Mismatches: 25, Indels: 75
0.72 0.07 0.21
Matches are distributed among these distances:
41 1 0.00
42 3 0.01
43 12 0.05
44 31 0.12
45 12 0.05
46 28 0.11
47 77 0.30
48 30 0.12
49 48 0.19
50 10 0.04
51 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (47 bp):
TATTATATAGTATATATTATATATATATTATATATTATTATATAGTA
Found at i:27228 original size:42 final size:39
Alignment explanation
Indices: 27087--27454 Score: 204
Period size: 40 Copynumber: 9.7 Consensus size: 39
27077 CGTTCGGGAT
27087 TATTATAT-TATATAATATTATATATATT-T--TATATAT-
1 TATTATATATATAT-ATA-TATATATATTATAGTATATATA
* *
27123 TATTATATAGTATGAGTTATATAGTATATATTATATTATTTATA
1 TATTATATA-TAT-A--TATATA-TATATATTATAGTATATATA
*
27167 TCA-TATATTATATAGTATATATAGTGTATTATAGTATATATA
1 T-ATTATA-TATATA-TATATATA-TATATTATAGTATATATA
*
27209 TATTATATAGTAT-GATATATAT-TATTATA--ATAGT-T-
1 TATTATATA-TATATATATATATATATTATAGTATA-TATA
* *
27244 TATTATAAAGTATATATAT-TATATAGTAT-GTATTATATA
1 TATTATATA-TATATATATATATATATTATAGTA-TATATA
* *
27283 TATTATA-ATATATTATATATTATTTATTATATTA-ATATTA
1 TATTATATATATA-TATATA-TATATATTATAGTATATA-TA
* * *
27323 TATTATAGTATATAT-TATATTTTTATTATATTATATAT-
1 TATTATA-TATATATATATATATATATTATAGTATATATA
**
27361 TACAATATATATA-ATATATA-ATATTAT--T-TATATA
1 TATTATATATATATATATATATATATTATAGTATATATA
* * *
27395 T-TTTTAT-TAT-TATTTAT-TATATTATATTATAT-TA
1 TATTATATATATATATATATATATATTATAGTATATATA
27429 TATTATA-ATATATAT-TATATAT-TTAT
1 TATTATATATATATATATATATATATTAT
27455 TGTAATTATT
Statistics
Matches: 268, Mismatches: 22, Indels: 85
0.71 0.06 0.23
Matches are distributed among these distances:
32 15 0.06
33 8 0.03
34 6 0.02
35 32 0.12
36 33 0.12
37 18 0.07
38 24 0.09
39 28 0.10
40 42 0.16
41 10 0.04
42 34 0.13
43 7 0.03
44 8 0.03
45 3 0.01
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.55
Consensus pattern (39 bp):
TATTATATATATATATATATATATATTATAGTATATATA
Found at i:27233 original size:72 final size:74
Alignment explanation
Indices: 27107--27342 Score: 217
Period size: 72 Copynumber: 3.2 Consensus size: 74
27097 TATAATATTA
* *
27107 TATATATTTTATATATTAT-TA-TATAGTATGAGTTATATAGTATATATTATATTATTTAT-ATC
1 TATATATATTATATAGTATGTATTATA-TAT-A-TTATATAGTATATA-TATATTATTTATAAT-
*
27169 A-TATATTATATAG
61 AGTATATTATAAAG
27182 TATATATAGTGTAT-TA-TA-GTA-TATATATATTATATAGTATGATATATATTA-TTATAATAG
1 TATATATA-T-TATATAGTATGTATTATATATATTATATAGTAT-ATATATATTATTTATAATAG
*
27242 TTTATTATAAAG
63 TATATTATAAAG
* *
27254 TATATATATTATATAGTATGTATTATATATATTATA-A-TATATTATATATTATTTATTATATTA
1 TATATATATTATATAGTATGTATTATATATATTATATAGTATA-TATATATTATTTATAATAGT-
*
27317 ATATTATATTA-
64 ATATTATA-AAG
27328 TAGTATATATTATAT
1 TA-TATATATTATAT
27343 TTTTATTATA
Statistics
Matches: 139, Mismatches: 7, Indels: 30
0.79 0.04 0.17
Matches are distributed among these distances:
70 3 0.02
71 9 0.06
72 52 0.37
73 16 0.12
74 25 0.18
75 28 0.20
76 3 0.02
77 3 0.02
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (74 bp):
TATATATATTATATAGTATGTATTATATATATTATATAGTATATATATATTATTTATAATAGTAT
ATTATAAAG
Found at i:27483 original size:15 final size:16
Alignment explanation
Indices: 27281--27498 Score: 88
Period size: 18 Copynumber: 12.8 Consensus size: 16
27271 ATGTATTATA
**
27281 TATATTATAATATATT
1 TATATTATTTTATATT
27297 ATATATTATTTATTATATT
1 -TATATTA-TT-TTATATT
* * *
27316 AATATTATATTATA-G
1 TATATTATTTTATATT
27331 TATA-TA--TTATATT
1 TATATTATTTTATATT
* *
27344 TTTATTATATTATATAT
1 TATATTATTTTATAT-T
* * *
27361 TACAATATATATAATATAT
1 TA-TAT-TATTTTATAT-T
*
27380 AATATTATTTATATATT
1 TATATTATTT-TATATT
*
27397 TTTATTATTATTTATTATAT
1 TATATTA-T-TTTA-TAT-T
*
27417 TATATTATATTATATT
1 TATATTATTTTATATT
*
27433 ATAATATATATTATATATT
1 -T-ATAT-TATTTTATATT
27452 TAT-TGTAATTATTATATT
1 TATAT-T-ATT-TTATATT
27470 TATATT-TTTTATATT
1 TATATTATTTTATATT
27485 TATTTATTATTTTA
1 TA--TATTATTTTA
27499 GGTTCAAATT
Statistics
Matches: 155, Mismatches: 23, Indels: 45
0.70 0.10 0.20
Matches are distributed among these distances:
12 5 0.03
13 3 0.02
14 4 0.03
15 12 0.08
16 16 0.10
17 33 0.21
18 41 0.26
19 34 0.22
20 7 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
TATATTATTTTATATT
Found at i:27495 original size:20 final size:20
Alignment explanation
Indices: 27382--27497 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
27372 TAATATATAA
* *
27382 TATTA-TTTATATATTTTTAT
1 TATTATTTTTTATATTTAT-T
*
27402 TATTATTTATTATATTATATT
1 TATTATTTTTTATATT-TATT
* * *
27423 ATATTATATTATA-ATATATAT
1 -TATTATTTTTTATATTTAT-T
27444 TATATATTTATTGTAATTATTATATT
1 TAT-TATTT-TT-T-A-TATT-TATT
27470 TA-TATTTTTTATATTTATT
1 TATTATTTTTTATATTTATT
27489 TATTATTTT
1 TATTATTTT
27498 AGGTTCAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 24
0.69 0.09 0.22
Matches are distributed among these distances:
19 6 0.08
20 21 0.28
21 17 0.23
22 13 0.18
23 3 0.04
24 6 0.08
26 5 0.07
27 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.66
Consensus pattern (20 bp):
TATTATTTTTTATATTTATT
Found at i:36915 original size:65 final size:65
Alignment explanation
Indices: 36758--36941 Score: 207
Period size: 65 Copynumber: 2.8 Consensus size: 65
36748 ACCGTTAGAC
* * *
36758 CCTTAGTGCATCGGTGCACT--AAGAGTGCACCGATGCATCAAGTGCATTCGATG-TTTCAAAAT
1 CCTTAGTGCATCGGTGCA-TGGTA-AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
36820 AG
64 AG
* * *
36822 CCATAGTGCATCGATGCATGGCT-GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-
1 CCTTAGTGCATCGGTGCATGG-TAAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAAT
*
36885 AT
64 AG
* * *
36887 CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATGAATTGCATTCCATGTT
1 CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATCAAATGCATTCGATGTT
36942 CAATTTAATT
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 1 0.01
64 44 0.44
65 53 0.52
66 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (65 bp):
CCTTAGTGCATCGGTGCATGGTAAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAG
Found at i:36933 original size:129 final size:130
Alignment explanation
Indices: 36758--36991 Score: 296
Period size: 129 Copynumber: 1.8 Consensus size: 130
36748 ACCGTTAGAC
*
36758 CCTTAGTGCATCGGTGCACTAAGAGTGCACCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AG
1 CCTTAGTGCATCGGTGCACTAAGAGTGCACCGATGCATCAAGTGCATTCCATG-TTCAAAATAAG
*
36822 CCATAGTGCATCGATGCATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAA
65 CCATAGTGCATCGATGCATGGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAA
36886 T
130 T
* * * * **
36887 CCTTAGTGCATCGGTGCA-T-GGTAAGTGCATCGATGCATGAATTGCATTCCATGTTCAATTTAA
1 CCTTAGTGCATCGGTGCACTAAG--AGTGCACCGATGCATCAAGTGCATTCCATGTTCAAAATAA
** * * *
36950 TTCATGGTGCATCGATGCATGGATTAGTGCATCGGTGCATCA
64 GCCATAGTGCATCGATGCATGGACTAGTGCATCGATGCATCA
36992 CTCTGAAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 7 0.08
129 64 0.73
130 16 0.18
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (130 bp):
CCTTAGTGCATCGGTGCACTAAGAGTGCACCGATGCATCAAGTGCATTCCATGTTCAAAATAAGC
CATAGTGCATCGATGCATGGACTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAT
Found at i:36979 original size:65 final size:64
Alignment explanation
Indices: 36781--36991 Score: 219
Period size: 65 Copynumber: 3.3 Consensus size: 64
36771 GTGCACTAAG
* * * * *
36781 AGTGCACCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCATAGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATCAAATGCATTCCATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTT
* * * * *
36845 GGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTA
1 AGTGCATCGATGCATCAAATGCATTCCATG-TTTCATAAAATCCATAGTGCATCGATGCATGGTT
* * ** * *
36910 AGTGCATCGATGCATGAATTGCATTCCATG-TTCAATTTAATTCATGGTGCATCGATGCATGGAT
1 AGTGCATCGATGCATCAAATGCATTCCATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-T
36974 T
64 T
*
36975 AGTGCATCGGTGCATCA
1 AGTGCATCGATGCATCA
36992 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
63 3 0.02
64 49 0.40
65 67 0.55
66 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
AGTGCATCGATGCATCAAATGCATTCCATGTTTCATAAAATCCATAGTGCATCGATGCATGGTT
Found at i:39193 original size:25 final size:25
Alignment explanation
Indices: 39136--39193 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
39126 AACAACATAA
* * **
39136 TTAAATAAAAAATTTATTTCAGATTT
1 TTAAA-AAAAAAATTATTTCAAAAAT
*
39162 TTGAAAAAAAAATTATTTCAAAAAT
1 TTAAAAAAAAAATTATTTCAAAAAT
39187 TTAAAAA
1 TTAAAAA
39194 TTTATTTAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (25 bp):
TTAAAAAAAAAATTATTTCAAAAAT
Found at i:43395 original size:19 final size:20
Alignment explanation
Indices: 43366--43403 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
43356 AGAAATTTGT
43366 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
43386 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
43404 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:43456 original size:63 final size:63
Alignment explanation
Indices: 43371--43529 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 63
43361 TTTGTTGAAG
* * * * *
43371 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATATCGTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATACCCTCA
* ** ** *
43434 GTGCATCGATGTATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
*
43497 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGGAGTGCATCGATGCAT
43530 GCCTCCATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 78 0.95
64 4 0.05
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCATAAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATACCCTCA
Found at i:44839 original size:18 final size:18
Alignment explanation
Indices: 44816--44851 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44806 AGGAATGATA
44816 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
*
44834 TGTGGTCCTTTGGGACAT
1 TGTGGTCCTTCGGGACAT
44852 ATTGTATTCT
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:0.11, C:0.19, G:0.33, T:0.36
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:44965 original size:116 final size:119
Alignment explanation
Indices: 44728--45056 Score: 534
Period size: 117 Copynumber: 2.8 Consensus size: 119
44718 ATTGTCCTTC
44728 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGATCCCTAGC--
1 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACA-ATACTTGATCCCTAGCAT
44791 A--TATATGATTTCTTAAGGAATGATATGTGGTCCTTCGGGACATTGTGGTCCTTTG
65 ATGTATATGA-TTCTTAAGGAATGATATGTGGT-CTTCGGGACATTGTGGTCCTTTG
44846 GGACATAT-TGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACAATACTTGATCCCTAGCATA
1 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACAATACTTGATCCCTAGCATA
44910 TGTATATGATTCTTAAGGAATGATATGTGGTCTTC-GGAC-TTGTGGTCCTTTG
66 TGTATATGATTCTTAAGGAATGATATGTGGTCTTCGGGACATTGTGGTCCTTTG
* *
44962 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTTGATCCCTAGTAT
1 GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGAC-AATACTTGATCCCTAGCAT
45027 ATG--TATGATTCTTAAGGAATGATAT-TGGTC
65 ATGTATATGATTCTTAAGGAATGATATGTGGTC
45057 CTTATGGACA
Statistics
Matches: 203, Mismatches: 2, Indels: 15
0.92 0.01 0.07
Matches are distributed among these distances:
115 5 0.02
116 59 0.29
117 77 0.38
118 33 0.16
119 22 0.11
120 7 0.03
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (119 bp):
GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACAATACTTGATCCCTAGCATA
TGTATATGATTCTTAAGGAATGATATGTGGTCTTCGGGACATTGTGGTCCTTTG
Found at i:45133 original size:23 final size:21
Alignment explanation
Indices: 45073--45118 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
45063 GACATTATTA
45073 TATGGCACTACGGTGCAATTC
1 TATGGCACTACGGTGCAATTC
45094 TATGGCACTACGGTGCAATTC
1 TATGGCACTACGGTGCAATTC
45115 TATG
1 TATG
45119 TGGCACTTTG
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:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (21 bp):
TATGGCACTACGGTGCAATTC
Found at i:45141 original size:23 final size:23
Alignment explanation
Indices: 45066--45141 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 23
45056 CCTTATGGAC
*
45066 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
*
45090 ATTCTA--TGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* **
45111 ATTCTATGTGGCACTTTGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
45134 TTTATATG
1 ATTATATG
45142 AGCTGGTGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 21 0.47
23 21 0.47
24 3 0.07
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Done.