Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005461.1 Hibiscus syriacus cultivar Beakdansim tig00012504_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: 104619
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:285 original size:55 final size:53
Alignment explanation
Indices: 232--332 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
222 ATTTAAACAA
*
232 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGACAAAC
1 AAAGTTGAACAAGCTCTTCTCATTA-GAACTTCTTCTTCCTTCTTCAGACAAAC
*
285 AAGGTTGAACAAGCTCTTCTCATTAGAACTTCTTCTTCCTTCTTCAGA
1 AAAGTTGAACAAGCTCTTCTCATTAGAACTTCTTCTTCCTTCTTCAGA
333 TGAGTTCTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 9 0.20
53 36 0.80
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (53 bp):
AAAGTTGAACAAGCTCTTCTCATTAGAACTTCTTCTTCCTTCTTCAGACAAAC
Found at i:351 original size:166 final size:168
Alignment explanation
Indices: 69--447 Score: 631
Period size: 166 Copynumber: 2.2 Consensus size: 168
59 ACTCTTGATG
* *
69 AGTTCTTCTCATTATGAACTTTCTCTTCTTTCTTCAGATGATATCAAACAAAGGTTGAACAAGCT
1 AGTTCTTCTCATTATGAAC-TTCTTTTCCTTCTTC--A-G--ATCAAACAAAGGTTGAACAAGCT
134 CTTCTCATATGAATCTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTCATGAACTTTCTTTGGC
60 CTTCTCATATGAATCTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTCATGAACTTTCTTTGGC
199 CATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
125 CATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
243 AGTTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGA-CAAAC-AAGGTTGAACAAGCTCTTCTC
1 AGTTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATCAAACAAAGGTTGAACAAGCTCTTCTC
306 AT-TAGAA-CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTCATGAACTTTCTTTGGCCATG
66 ATAT-GAATCTTCTTCTTCCTTCTTCA-ATGAGTTCTTCTCATTCATGAACTTTCTTTGGCCATG
369 TTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
129 TTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
409 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
1 AGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGAT
448 GAGTTCTTCT
Statistics
Matches: 199, Mismatches: 2, Indels: 14
0.93 0.01 0.07
Matches are distributed among these distances:
165 19 0.10
166 127 0.64
167 18 0.09
168 1 0.01
170 1 0.01
171 1 0.01
173 13 0.07
174 19 0.10
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (168 bp):
AGTTCTTCTCATTATGAACTTCTTTTCCTTCTTCAGATCAAACAAAGGTTGAACAAGCTCTTCTC
ATATGAATCTTCTTCTTCCTTCTTCAATGAGTTCTTCTCATTCATGAACTTTCTTTGGCCATGTT
GATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
Found at i:828 original size:112 final size:113
Alignment explanation
Indices: 285--881 Score: 982
Period size: 113 Copynumber: 5.3 Consensus size: 113
275 TCAGACAAAC
*
285 AAGGTTGAACAAGCTCTTCTCATTA-GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT-
* ** * *
349 ATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAA
65 ATGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
*
398 AAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
463 TGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
*
511 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
576 TGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCAA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
624 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
689 TGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCAA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
737 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
801 TGAACTTTCTCTGGAAATGTTGATCCATTAAGTGATGAATTCAAGCAA
66 TGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
849 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC
882 CTCTGGTAAT
Statistics
Matches: 459, Mismatches: 24, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
112 109 0.24
113 312 0.68
114 38 0.08
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATGTTGATCCATCAAATGATGAATTCAAGCAA
Found at i:1548 original size:52 final size:52
Alignment explanation
Indices: 1470--2288 Score: 1346
Period size: 52 Copynumber: 15.7 Consensus size: 52
1460 CACTTCTTCG
* * *
1470 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1522 GATCAGATAACTCAAAGAACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCA
*
1577 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
1629 GATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1681 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1733 GATCAGATAACTC-AAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
1784 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1836 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1888 GATCAGATAACTCAAAGAACACTTCCAGAAGA-GCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1939 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
1991 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2043 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCA
*
2095 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2148 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2200 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
2252 GATTAGAT-ACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
2289 TGAGCACATA
Statistics
Matches: 734, Mismatches: 23, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
51 130 0.18
52 504 0.69
53 51 0.07
55 49 0.07
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:1816 original size:155 final size:156
Alignment explanation
Indices: 1470--2288 Score: 1380
Period size: 155 Copynumber: 5.2 Consensus size: 156
1460 CACTTCTTCG
* * * *
1470 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
*
1535 AAAGAACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
66 AAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
1600 TCCAGAAGATGCTATGTTCTGTCCAATCA
128 TCCAGAAGATGCTATGTTCTGTCCAATCA
* * *
1629 GATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATGTTATGATCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
*
1694 AAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCAGATCAGATAACTC-AAGAACACTTC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTTC
* *
1757 CAGAAGATGCTATGTTATGAT-CAACCA
130 CAGAAGATGCTATGTTCTG-TCCAATCA
1784 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
*
1849 AAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
1914 AGAAGA-GCTATGTTCTGTCCAATCA
131 AGAAGATGCTATGTTCTGTCCAATCA
1939 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
*
2004 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
* *
2069 AGAAGATGCTATGTTATGAT-CAACCA
131 AGAAGATGCTATGTTCTG-TCCAATCA
2095 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
*
2160 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
2225 CAGAAGATGCTATGTTCTGTCCAATCA
130 CAGAAGATGCTATGTTCTGTCCAATCA
*
2252 GATTAGAT-ACTCAAAGAACACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
2289 TGAGCACATA
Statistics
Matches: 627, Mismatches: 24, Indels: 22
0.93 0.04 0.03
Matches are distributed among these distances:
154 2 0.00
155 315 0.50
156 95 0.15
157 144 0.23
159 71 0.11
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (156 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
AGAAGATGCTATGTTCTGTCCAATCA
Found at i:1840 original size:207 final size:208
Alignment explanation
Indices: 1470--2288 Score: 1405
Period size: 207 Copynumber: 3.9 Consensus size: 208
1460 CACTTCTTCG
* * *
1470 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCCATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
*
1535 AAAGAACACTTCCAGAAGAAGATGCTATATTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
66 AAAGAACACTTCC---AGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
*
1600 TCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCT
128 TCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCT
1665 ATGTTATGATCAACCA
193 ATGTTATGATCAACCA
*
1681 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCAGATCAGATAACT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCAGATCAGATAACT
*
1745 C-AAGAACACTTCCAGAAGATGCTATGTTATGAT-CAACCAGATCAGATAACTCAAAGAACACTT
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTT
* *
1808 CCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
129 CCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
* *
1873 TGTTCTGTTCAACCA
194 TGTTATGATCAACCA
*
1888 GATCAGATAACTCAAAGAACACTTCCAGAAGA-GCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
*
1952 AAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCC
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
2017 AGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
131 AGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
2082 TTATGATCAACCA
196 TTATGATCAACCA
*
2095 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACT
*
2160 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTC
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTC
*
2225 CAGAAGATGCTATGTTCTGTCCAATCAGATTAGAT-ACTCAAAGAACACTTCCAGAAGATGCTAT
130 CAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
2289 TGAGCACATA
Statistics
Matches: 578, Mismatches: 23, Indels: 17
0.94 0.04 0.03
Matches are distributed among these distances:
205 1 0.00
206 29 0.05
207 305 0.53
208 45 0.08
209 126 0.22
210 12 0.02
211 59 0.10
212 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (208 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCC
AGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
TTATGATCAACCA
Found at i:3236 original size:1 final size:1
Alignment explanation
Indices: 3230--3334 Score: 66
Period size: 1 Copynumber: 105.0 Consensus size: 1
3220 CCTTGACCCC
* * * * ** * * * * * * *
3230 TTTTTTTTCTTTTTCTTTTTCTTCTTTTCCTTTCTTTTTTCTTTTCTTTCTTTCTCTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
3295 TTCTTTCTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3335 CTTCAAGCAT
Statistics
Matches: 74, Mismatches: 30, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:3243 original size:9 final size:9
Alignment explanation
Indices: 3230--3334 Score: 96
Period size: 9 Copynumber: 12.2 Consensus size: 9
3220 CCTTGACCCC
3230 TTTTTT-TT
1 TTTTTTCTT
*
3238 CTTTTTCTT
1 TTTTTTCTT
*
3247 TTTCTTCTT
1 TTTTTTCTT
*
3256 TTCCTTTC--
1 TT-TTTTCTT
3264 TTTTTTCTT
1 TTTTTTCTT
*
3273 TTCTTTCTT
1 TTTTTTCTT
* *
3282 TCTCTTCTT
1 TTTTTTCTT
3291 TTTTTTCTT
1 TTTTTTCTT
*
3300 TCTTTT-TT
1 TTTTTTCTT
3308 TTTTTT-TT
1 TTTTTTCTT
3316 TTTTTTCTT
1 TTTTTTCTT
3325 TTTTTT-TT
1 TTTTTTCTT
3333 TT
1 TT
3335 CTTCAAGCAT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
7 4 0.05
8 26 0.33
9 45 0.58
10 3 0.04
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:3263 original size:25 final size:23
Alignment explanation
Indices: 3230--3328 Score: 114
Period size: 25 Copynumber: 4.2 Consensus size: 23
3220 CCTTGACCCC
*
3230 TTTTT-TTTCTTTTTCTTTTTCT
1 TTTTTCTTTCTTTTTTTTTTTCT
*
3252 TCTTTTCCTTTCTTTTTTCTTTTCT
1 T-TTTT-CTTTCTTTTTTTTTTTCT
3277 TTCTTTCTCTTCTTTTTTTTCTTTCT
1 TT-TTTCT-TTCTTTTTTTT-TTTCT
3303 TTTTT-TTT-TTTTTTTTTTTCT
1 TTTTTCTTTCTTTTTTTTTTTCT
3324 TTTTT
1 TTTTT
3329 TTTTTTCTTC
Statistics
Matches: 68, Mismatches: 3, Indels: 13
0.81 0.04 0.15
Matches are distributed among these distances:
21 10 0.15
22 9 0.13
23 6 0.09
24 4 0.06
25 32 0.47
26 7 0.10
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (23 bp):
TTTTTCTTTCTTTTTTTTTTTCT
Found at i:3276 original size:22 final size:21
Alignment explanation
Indices: 3229--3333 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
3219 ACCTTGACCC
3229 CTTTT-TTTTCTTT-TTCTTTT
1 CTTTTCTTTTCTTTCTT-TTTT
*
3249 -TCTTCTTTTCCTTTCTTTTTT
1 CTTTTCTTTT-CTTTCTTTTTT
*
3270 CTTTTC-TTTCTTTC--TCTT
1 CTTTTCTTTTCTTTCTTTTTT
3288 CTTTT-TTTTCTTTCTTTTTT
1 CTTTTCTTTTCTTTCTTTTTT
* * *
3308 TTTTTTTTTTTTTTCTTTTTT
1 CTTTTCTTTTCTTTCTTTTTT
*
3329 TTTTT
1 CTTTT
3334 TCTTCAAGCA
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
18 16 0.23
19 3 0.04
20 16 0.23
21 30 0.42
22 6 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
CTTTTCTTTTCTTTCTTTTTT
Found at i:3329 original size:13 final size:13
Alignment explanation
Indices: 3231--3337 Score: 110
Period size: 13 Copynumber: 8.2 Consensus size: 13
3221 CTTGACCCCT
3231 TTTTTTTCTTTTTC
1 TTTTTTT-TTTTTC
*
3245 TTTTTCTTCTTTTC
1 TTTTT-TTTTTTTC
* *
3259 -CTTTCTTTTTTC
1 TTTTTTTTTTTTC
* *
3271 TTTTCTTTCTTTC
1 TTTTTTTTTTTTC
*
3284 TCTTCTTTTTTTTC
1 T-TTTTTTTTTTTC
*
3298 TTTCTTTTTTTT-
1 TTTTTTTTTTTTC
3310 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
3323 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
3336 TT
1 TT
3338 CAAGCATAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
12 17 0.22
13 38 0.49
14 20 0.26
15 2 0.03
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTTTC
Found at i:3330 original size:25 final size:25
Alignment explanation
Indices: 3232--3337 Score: 115
Period size: 27 Copynumber: 4.1 Consensus size: 25
3222 TTGACCCCTT
*
3232 TTTTTTCTTTTTCTTTTTCTTCTTTTC
1 TTTTTT-TTTTTCTTTTT-TTTTTTTC
* * *
3259 CTTTCTTTTTTCTTTTCTTTCTTTCTC
1 TTTTTTTTTTTCTTTT-TTT-TTTTTC
*
3286 TTCTTTTTTTTCTTTCTTTTTTTTT-
1 TTTTTTTTTTTCTTT-TTTTTTTTTC
3311 TTTTTTTTTTTCTTTTTTTTTTTTC
1 TTTTTTTTTTTCTTTTTTTTTTTTC
3336 TT
1 TT
3338 CAAGCATAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
24 9 0.14
25 16 0.24
26 16 0.24
27 24 0.36
28 1 0.02
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTTTTTTTCTTTTTTTTTTTTC
Found at i:14698 original size:19 final size:19
Alignment explanation
Indices: 14663--14712 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 19
14653 ATAATTCTAT
14663 TAAAATAATATTTAAAAACA-A
1 TAAAATAA-A-TT-AAAACATA
14684 TAAAATAAATTAAAACATA
1 TAAAATAAATTAAAACATA
14703 TAAAATAAAT
1 TAAAATAAAT
14713 GACTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.21
19 13 0.46
20 1 0.04
21 8 0.29
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAATAAATTAAAACATA
Found at i:15563 original size:29 final size:28
Alignment explanation
Indices: 15521--15578 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
15511 TCGTTGGTAG
* *
15521 TTTGTTTGTTTTCTTTTCTCTGTTTTTTT
1 TTTGTTTGTTTTC-TGTCTCTGTCTTTTT
15550 TTTGTTCTG-TTTCTGTCTCTGTCTTTTT
1 TTTGTT-TGTTTTCTGTCTCTGTCTTTTT
15578 T
1 T
15579 CTGTCTCGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 14 0.54
29 10 0.38
30 2 0.08
ACGTcount: A:0.00, C:0.14, G:0.12, T:0.74
Consensus pattern (28 bp):
TTTGTTTGTTTTCTGTCTCTGTCTTTTT
Found at i:15956 original size:3 final size:3
Alignment explanation
Indices: 15948--16080 Score: 203
Period size: 3 Copynumber: 43.7 Consensus size: 3
15938 TTATTTATTA
*
15948 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
15995 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
16043 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
16081 AATGGATAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 112 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:22355 original size:2 final size:2
Alignment explanation
Indices: 22350--22397 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
22340 CTTGAGGGCA
22350 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
22392 AT AT AT
1 AT AT AT
22398 CTGCTGCTAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33577 original size:7 final size:7
Alignment explanation
Indices: 33565--33590 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
33555 CGTTGTTGCT
33565 GAAATTA
1 GAAATTA
33572 GAAATTA
1 GAAATTA
33579 GAAATTA
1 GAAATTA
33586 GAAAT
1 GAAAT
33591 CAGAGGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.15, T:0.27
Consensus pattern (7 bp):
GAAATTA
Found at i:44911 original size:26 final size:26
Alignment explanation
Indices: 44888--44952 Score: 103
Period size: 26 Copynumber: 2.5 Consensus size: 26
44878 CATATATTCG
*
44888 GGTCGGGTCGGGTGAAACTTTATTTT
1 GGTCGGGTCGGGTGAAACATTATTTT
* *
44914 GGTCGGGTCAGATGAAACATTATTTT
1 GGTCGGGTCGGGTGAAACATTATTTT
44940 GGTCGGGTCGGGT
1 GGTCGGGTCGGGT
44953 CAGTTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.17, C:0.12, G:0.37, T:0.34
Consensus pattern (26 bp):
GGTCGGGTCGGGTGAAACATTATTTT
Found at i:48955 original size:7 final size:7
Alignment explanation
Indices: 48943--48969 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48933 CATGTTCTCC
48943 AAAATTG
1 AAAATTG
48950 AAAATTG
1 AAAATTG
48957 AAAATTG
1 AAAATTG
48964 AAAATT
1 AAAATT
48970 CCCAAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (7 bp):
AAAATTG
Found at i:52689 original size:2 final size:2
Alignment explanation
Indices: 52682--52724 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
52672 AATCTGGATT
52682 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52724 T
1 T
52725 GCTGTAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53139 original size:13 final size:14
Alignment explanation
Indices: 53121--53149 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
53111 AACAGAAAAA
53121 GTTGTTTTAAA-TT
1 GTTGTTTTAAAGTT
53134 GTTGTTTTAAAGTT
1 GTTGTTTTAAAGTT
53148 GT
1 GT
53150 AGATCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (14 bp):
GTTGTTTTAAAGTT
Found at i:55177 original size:21 final size:21
Alignment explanation
Indices: 55153--55199 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
55143 ATCGAAAATA
*
55153 TTATTATTT-ATACCGGTTTTG
1 TTATTATTTCA-ACCGATTTTG
*
55174 TTATTTTTTCAACCGATTTTG
1 TTATTATTTCAACCGATTTTG
55195 TTATT
1 TTATT
55200 GTTGGACTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.60
Consensus pattern (21 bp):
TTATTATTTCAACCGATTTTG
Found at i:57438 original size:27 final size:26
Alignment explanation
Indices: 57397--57450 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
57387 CTCTATTTAT
*
57397 ATTATGTTATTGAGCAAATGATTGAAA
1 ATTATGTTATCGAGCAAAT-ATTGAAA
* *
57424 ATTATGTTGTCGAGCAAATATTTAAA
1 ATTATGTTATCGAGCAAATATTGAAA
57450 A
1 A
57451 GTAACAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (26 bp):
ATTATGTTATCGAGCAAATATTGAAA
Found at i:58497 original size:30 final size:30
Alignment explanation
Indices: 58461--58548 Score: 149
Period size: 30 Copynumber: 2.9 Consensus size: 30
58451 CAAGAACCGA
58461 CAACTCAAGGAGGAGACACGGAAACAACGG
1 CAACTCAAGGAGGAGACACGGAAACAACGG
58491 CAACTCAAGGAGGAGACACGGAAACAACGG
1 CAACTCAAGGAGGAGACACGGAAACAACGG
** *
58521 CAACTCAAGGAGGCTACACGGGAACAAC
1 CAACTCAAGGAGGAGACACGGAAACAAC
58549 AACGACGACG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.42, C:0.25, G:0.28, T:0.05
Consensus pattern (30 bp):
CAACTCAAGGAGGAGACACGGAAACAACGG
Found at i:59741 original size:3 final size:3
Alignment explanation
Indices: 59733--59773 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
59723 CACCAGTTGC
59733 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
59774 GAGTAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:71358 original size:16 final size:17
Alignment explanation
Indices: 71337--71377 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
71327 GTTGGAACCT
*
71337 TAGTGCATCGGTGCA-C
1 TAGTGCATCGATGCATC
71353 TAGTGCATCGATGCATC
1 TAGTGCATCGATGCATC
*
71370 AAGTGCAT
1 TAGTGCAT
71378 TCAATGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (17 bp):
TAGTGCATCGATGCATC
Found at i:71430 original size:64 final size:65
Alignment explanation
Indices: 71355--71513 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 65
71345 CGGTGCACTA
*
71355 GTGCATCGATGCATCAAGTGCATTCAATGTT-TTA-AAATAACC-CGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATCAAATGCATTCAATGTTCTTATAAA-AACCTC-AGTGCATCGATGCATGGT
71417 TG
64 TG
* * *
71419 GTGCATCGATGCATCAAATGCATTCGATGTTCTTATAAAATCCTCAGTGCATCGGTGCATGG-T-
1 GTGCATCGATGCATCAAATGCATTCAATGTTCTTATAAAAACCTCAGTGCATCGATGCATGGTTG
* * ** *
71482 GTACATCGATGTATGGAATGCATTCGATGTTC
1 GTGCATCGATGCATCAAATGCATTCAATGTTC
71514 AATTTAATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 28 0.33
64 30 0.36
65 22 0.26
66 4 0.05
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCAATGTTCTTATAAAAACCTCAGTGCATCGATGCATGGTTG
Found at i:74041 original size:11 final size:11
Alignment explanation
Indices: 74025--74077 Score: 60
Period size: 10 Copynumber: 5.0 Consensus size: 11
74015 TTTATAAGAG
74025 AGGAGAGATGC
1 AGGAGAGATGC
74036 AGGAGATG-TG-
1 AGGAGA-GATGC
74046 AGGAGAGATGC
1 AGGAGAGATGC
74057 AGGAGATG-TG-
1 AGGAGA-GATGC
74067 AGGAGAGATGC
1 AGGAGAGATGC
74078 GGTATTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
9 2 0.06
10 16 0.44
11 16 0.44
12 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.47, T:0.13
Consensus pattern (11 bp):
AGGAGAGATGC
Found at i:74050 original size:21 final size:21
Alignment explanation
Indices: 74024--74077 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
74014 ATTTATAAGA
74024 GAGGAGAGATGCAGGAGATGT
1 GAGGAGAGATGCAGGAGATGT
74045 GAGGAGAGATGCAGGAGATGT
1 GAGGAGAGATGCAGGAGATGT
74066 GAGGAGAGATGC
1 GAGGAGAGATGC
74078 GGTATTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.48, T:0.13
Consensus pattern (21 bp):
GAGGAGAGATGCAGGAGATGT
Found at i:76221 original size:29 final size:30
Alignment explanation
Indices: 76181--76260 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
76171 ATAATTAATT
*
76181 TATTAA-ATTAAATTAAAATCAGGA-TTAAG
1 TATTAAGATTAAATTAAAAT-AAGATTTAAG
* *
76210 T-TTAAGATTAAATTAATATAATATTTAAG
1 TATTAAGATTAAATTAAAATAAGATTTAAG
76239 TATTAATGATTAAATGTAAAAT
1 TATTAA-GATTAAAT-TAAAAT
76261 TTTATCTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 6 0.14
29 19 0.45
30 4 0.10
31 8 0.19
32 5 0.12
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (30 bp):
TATTAAGATTAAATTAAAATAAGATTTAAG
Found at i:76332 original size:22 final size:20
Alignment explanation
Indices: 76295--76338 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
76285 TAAGTATATA
*
76295 AAATTAAAAAATAAATGATT
1 AAATTAAAAAATAAATAATT
76315 AAATTAAAATGAATAAATAATT
1 AAATTAAAA--AATAAATAATT
76337 AA
1 AA
76339 GTTGTCAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
22 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AAATTAAAAAATAAATAATT
Found at i:78723 original size:2 final size:2
Alignment explanation
Indices: 78716--78743 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
78706 AATTTAAAGT
78716 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
78744 AATTCTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:85693 original size:4 final size:4
Alignment explanation
Indices: 85684--85709 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
85674 AAGCAAAATT
85684 GAAA GAAA GAAA GAAA GAAA GAAA GA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA
85710 CAAAGAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:87756 original size:13 final size:15
Alignment explanation
Indices: 87718--87747 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
87708 AATTTGAGGA
87718 TACAAAGCATGGAAT
1 TACAAAGCATGGAAT
87733 TACAAAGCATGGAAT
1 TACAAAGCATGGAAT
87748 ATAAGCATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
TACAAAGCATGGAAT
Found at i:96676 original size:16 final size:16
Alignment explanation
Indices: 96643--96676 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
96633 TTTTTTAAAT
**
96643 ATGTTCCCCTTCCTTA
1 ATGTTCCCCTTCAATA
96659 ATGTTCCCCTTCAATA
1 ATGTTCCCCTTCAATA
96675 AT
1 AT
96677 TAAAGGTTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.41
Consensus pattern (16 bp):
ATGTTCCCCTTCAATA
Found at i:100565 original size:21 final size:21
Alignment explanation
Indices: 100541--100587 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
100531 CTTTTCATTG
**
100541 AGGGAACGATCATTTTGGTGA
1 AGGGAACGATCATTGAGGTGA
* *
100562 AGGGATCGATCCTTGAGGTGA
1 AGGGAACGATCATTGAGGTGA
100583 AGGGA
1 AGGGA
100588 TTAATCAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.38, T:0.23
Consensus pattern (21 bp):
AGGGAACGATCATTGAGGTGA
Done.