Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168442.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_654, 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: 20543
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Found at i:330 original size:18 final size:18
Alignment explanation
Indices: 309--363 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
299 TTTGAACACG
309 TTTAAATAGTTATGACTA
1 TTTAAATAGTTATGACTA
* *
327 TTTAAACAATTAT--CTA
1 TTTAAATAGTTATGACTA
343 TTTCAAAT-GTTATGACTA
1 TTT-AAATAGTTATGACTA
361 TTT
1 TTT
364 GTTTTGTGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 17 0.57
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.47
Consensus pattern (18 bp):
TTTAAATAGTTATGACTA
Found at i:567 original size:180 final size:180
Alignment explanation
Indices: 12--1567 Score: 1036
Period size: 182 Copynumber: 8.5 Consensus size: 180
2 TTTTTTTGTA
* * * *
12 ATAAAACAATTGTTT-TAGTTAATATAA-ATTATTAAAAATAAAATAATACTAATTTATTAATAT
1 ATAAAACAATTGTTTCT-GTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATAT
* * * * * * * **
75 TT-AAAAATGAATGAGT-AAAGAATTAAAAAAATGAATTTGTTTA-CTGAAAAAGTTCAAATAGT
65 TTCAAAAATTAATAAGTAAAAG-ATT-TAAAAATAAATCTATTTATCAG-ACCAGTTCAAATAGT
* * * *
137 TATGACTATCTAAACAATTATCTATTTCAACA-CATTATGACTTTTTATTTTGTC
127 TATGACTATTTGAACAATTATCTATTTCAA-ATCATTATGACTTTTTGTTTGGTC
** * *
191 A-AAAAGCAATTGGATCTATTCATTGA-AAGCTTATTTCAAATAAAATAATA-TAAATTTATTAA
1 ATAAAA-CAATTGTTTCTGTTCA-T-ACAAGCTTATTTAAAATAAAATAATACT-AATTTATTAA
* * * * ** * *
253 TA-TTCAAAAAATTAATAAATAATA-ATTTAAACAATAAATTTATTTTTTTGAACACGTTTAAAT
62 TATTTC-AAAAATTAATAAGTAAAAGATTTAAA-AATAAATCTATTTATCAGACCA-GTTCAAAT
* * * * *
316 AGTTATGACTATTTAAACAATTATCTATTTCAAAT-GTTATGACTATTTGTTTTGTG
124 AGTTATGACTATTTGAACAATTATCTATTTCAAATCATTATGACTTTTTGTTTGGTC
* * * * *
372 ATAAATCACTTGTTTCTGTTCATACAAGCTTATTTAGAATAAAATAATATTAATTTATTAAAATT
1 ATAAAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATATT
* * ***
437 TC-AAAATTAATAAGTAAAAGA-TTAAAAAGAAATCTATTTACCAGGTGAGTTCAAATAGTTATG
66 TCAAAAATTAATAAGTAAAAGATTTAAAAATAAATCTATTTATCAGACCAGTTCAAATAGTTATG
* * *
500 ACTATTTGAACAAATATTTATTTCAAATCATTATGA-TCTTTTCTTTGGTC
131 ACTATTTGAACAATTATCTATTTCAAATCATTATGACT-TTTTGTTTGGTC
* * * * *
550 ATAATAAACAATTGTTTCTATTCATAAAAGTTTATTTGAAATAAAATAATATTAATTTATTAATA
1 AT-A-AAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATA
* ** * * * *
615 -TTCTAAAATTAATAAGTTGAAGATTTAAAAAATAAATCTATTTAGCAAACAAGTTCAAATAGTC
64 TTTCAAAAATTAATAAGTAAAAGATTT-AAAAATAAATCTATTTATCAGACCAGTTCAAATAGTT
* * * * * *
679 ATGTCCATTTGAACTATTATCTAATTTCAAATCGTTATGACATTTTGTTTTGTTGTAAA
128 ATGACTATTTGAACAATTATCT-ATTTCAAATCATTATGACTTTTTG-TTTG--GT--C
* ** *
738 ATAATACCAA-TGATTTACAATAATTGGTATTCATACAAAATTATTCAAAATAAAATAATACTAA
1 ATAA-AACAATTG-TTT-C------T-G--TTCATACAAGCTTATTTAAAATAAAATAATACTAA
* * * * * **
802 TTTATTATTATTTCAAAAATTAATAAG-----GATTTAAAAACAAATGTGTTTGTC-GAATTAGT
54 TTTATTAATATTTCAAAAATTAATAAGTAAAAGATTTAAAAATAAATCTATTTATCAG-ACCAGT
* * * * * * *
861 TCAAATAGTTAAGACTATTAG-ACAACTTATATGTTTCAACTCATTCTGACTTTTTGTTTAGTC
118 TCAAATAGTTATGACTATTTGAACAA-TTATCTATTTCAAATCATTATGACTTTTTGTTTGGTC
* * * * ** * * *
924 ATAAAATAATTGTTTCAGCTCATACATGCCAATTTGAAATATAATAATACTAATTTATTAACATT
1 ATAAAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATATT
* * * * * * * * *
989 TAAAAAATTAATAAGCAAGAA-ATTAAAAAGCACAAATCAATTTA-CTGAACAAGTTAAAATTGT
66 TCAAAAATTAATAAGTAA-AAGATTTAAAA--ATAAATCTATTTATCAG-ACCAGTTCAAATAGT
* * * **
1052 TATGACTATTTGAACAATTATTTATTTAAAATCATTATGACTTTTTATTTTATC
127 TATGACTATTTGAACAATTATCTATTTCAAATCATTATGACTTTTTGTTTGGTC
* * * * * * *
1106 ATAAAACAGTTGTTTCAGTGCATAAAAGCTTATTCAAAATAAAATAATA-TTACTTATTAATATT
1 ATAAAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATATT
* * * * * *
1170 TCAAAAATTGATAAGTTAGAGATTTAAAAAATAAAT-TAGTTTATCAAATCAGTTCAAATAATTA
66 TCAAAAATTAATAAGTAAAAGATTT-AAAAATAAATCTA-TTTATCAGACCAGTTCAAATAGTTA
** * * * * *
1234 CAACCATTTAAATAATTATCTATTTCAAATCATTATGAAC-ATTTGCTTGGTC
129 TGACTATTTGAACAATTATCTATTTCAAATCATTATG-ACTTTTTGTTTGGTC
* * * * * * * *
1286 ATAAACCAATTGTTTTTTTTTTTTATCATACAAGCCTATTCAAATTAAAATAAAACTAATTTACT
1 ATAAAACAATTG-----TTTCTGT-TCATACAAGCTTATTTAAAATAAAATAATACTAATTTATT
* ** * * *
1351 AATATTTCAAAAATTAATAAATAGGAGAGTTAAAAAATAAATCTGTTTA-CCGAACCAGTTCAAA
60 AATATTTCAAAAATTAATAAGTAAAAGA-TTTAAAAATAAATCTATTTATCAG-ACCAGTTCAAA
* * * *
1415 TAGTTATGACTATTTGAACAATTATATATTTCAAATTATTATAACCTTTTGTTAT-GTC
123 TAGTTATGACTATTTGAACAATTATCTATTTCAAATCATTATGACTTTTTGTT-TGGTC
* * * * *
1473 ATAAAACAATTATTTCTATTCATACAAGTTTATTAAAAATAAAATAATACT-ATTGTAATAATA-
1 ATAAAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATT-TATTAATAT
* *
1536 TTCTAAAAATTAATAACTAAGAGATTTAAAAA
65 TTC-AAAAATTAATAAGTAAAAGATTTAAAAA
1568 ATTAAATAAA
Statistics
Matches: 1070, Mismatches: 230, Indels: 153
0.74 0.16 0.11
Matches are distributed among these distances:
175 50 0.05
177 41 0.04
178 33 0.03
179 37 0.03
180 203 0.19
181 170 0.16
182 210 0.20
183 26 0.02
184 5 0.00
185 10 0.01
186 39 0.04
187 114 0.11
188 9 0.01
190 3 0.00
191 22 0.02
192 39 0.04
193 5 0.00
194 1 0.00
197 38 0.04
198 15 0.01
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (180 bp):
ATAAAACAATTGTTTCTGTTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAATATT
TCAAAAATTAATAAGTAAAAGATTTAAAAATAAATCTATTTATCAGACCAGTTCAAATAGTTATG
ACTATTTGAACAATTATCTATTTCAAATCATTATGACTTTTTGTTTGGTC
Found at i:1551 original size:549 final size:547
Alignment explanation
Indices: 312--1551 Score: 1279
Period size: 549 Copynumber: 2.3 Consensus size: 547
302 GAACACGTTT
* * * *
312 AAATAGTTATGACTATTTAAACAATTATCTATTTCAAA-TGTTATGA-CTATTTGTTTTGTGATA
1 AAATAGTTATGACTATTTGAACAATTATATATTTCAAATTATTATGACCT-TTTG-TTTGTCATA
* * * * * *
375 AATCACTTGTTTCTGTTCATACAAGCTTATTTAGAATAAAATAATATTAATTTATTAAAATTTCA
64 AAACAATTGTTTCTATTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAAAATTTAA
* * *** *
440 AAATTAATAAGTAAAAGATTAAAAAGAAATCTATTTACCAGGTGAGTTCAAATAGTTATGACTAT
129 AAATTAATAAGCAAAAGATTAAAAAGAAATCAATTTACCAGACAAGTTAAAATAGTTATGACTAT
* * *
505 TTGAACAAATATTTATTTCAAATCATTATGATCTTTTCTTTGGTCATAATAAACAATTGTTTCTA
194 TTGAACAAATATTTATTTAAAATCATTATGATCTTTTATTTGATCATAATAAACAATTGTTTCTA
* * ** * *
570 TTCATAAAAGTTTATTTGAAATAAAATAATATTAATTTATTAATATTCTAAAATTAATAAGTTGA
259 TGCATAAAAGCTTATTCAAAATAAAATAATATTAACTTATTAATATTCAAAAATTAATAAGTTGA
* *** *
635 AGATTTAAAAAATAAATCTATTTAGCAAACAAGTTCAAATAGTCATGTCCATTTGAACTATTATC
324 AGATTTAAAAAATAAATCTATTTAGCAAACAAGTTCAAATAATCACAACCATTTGAAATATTATC
* *
700 TAATTTCAAATCGTTATGACATTTTGTTTTGTTGTAAAATAATACCAATGATTTACAATAATTGG
389 TAATTTCAAATCATTATGACATTTTGTCTTG-TGT-AAATAATACCAATGATTT--AATAATTGG
* * * *
765 TATTCATACAAAATTATTCAAAATAAAATAATACTAATTTATTATTATTTCAAAAATTAATAAGG
450 TATTCATACAAAACTATTCAAAATAAAATAAAACTAATTTACTAATATTTCAAAAATTAATAAGG
* * ** **
830 ATTTAAAAACAAATGTGTTTGTCGAATTAGTTC
515 ATTAAAAAACAAATCTGTTTACCGAACCAGTTC
* * * * * * *
863 AAATAGTTAAGACTATTAG-ACAACTTATATGTTTCAACTCATTCTGACTTTTTGTTTAGTCATA
1 AAATAGTTATGACTATTTGAACAA-TTATATATTTCAAATTATTATGACCTTTTGTTT-GTCATA
* * * ** * * *
927 AAATAATTGTTTC-AGCTCATACATGCCAATTTGAAATATAATAATACTAATTTATTAACATTTA
64 AAACAATTGTTTCTA-TTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAAAATTT-
* *
991 AAAAATTAATAAGCAAGAA-ATTAAAAAGCACAAATCAATTTA-CTGAACAAGTTAAAATTGTTA
127 AAAAATTAATAAGCAA-AAGATTAAAAAG---AAATCAATTTACCAG-ACAAGTTAAAATAGTTA
* * *
1054 TGACTATTTGAACAATTATTTATTTAAAATCATTATGA-CTTTTTATTTTATCAT-A-AAACAGT
187 TGACTATTTGAACAAATATTTATTTAAAATCATTATGATC-TTTTATTTGATCATAATAAACAAT
1116 TGTTTC-AGTGCATAAAAGCTTATTCAAAATAAAATAATATT-ACTTATTAATATTTCAAAAATT
251 TGTTTCTA-TGCATAAAAGCTTATTCAAAATAAAATAATATTAACTTATTAATA-TTCAAAAATT
* * *
1179 GATAAGTT-AGAGATTTAAAAAATAAAT-TAGTTTATCAAATC-AGTTCAAATAATTACAACCAT
314 AATAAGTTGA-AGATTTAAAAAATAAATCTA-TTTAGCAAA-CAAGTTCAAATAATCACAACCAT
*
1241 TT-AAATAATTATCT-ATTTCAAATCATTATGAACA-TTTG-CTTG-GT-CATAA-ACCAATTG-
376 TTGAAAT-ATTATCTAATTTCAAATCATTATG-ACATTTTGTCTTGTGTAAATAATACCAA-TGA
* ** ** ** *
1298 TTT-TTTTTTTTTA-TCATACAAGCCTATTCAAATTAAAATAAAACTAATTTACTAATATTTCAA
438 TTTAATAATTGGTATTCATACAAAACTATTCAAAATAAAATAAAACTAATTTACTAATATTTCAA
*
1361 AAATTAATAAATAGGAGAGTTAAAAAATAAATCTGTTTACCGAACCAGTTC
503 AAATTAAT--A-A-G-GA-TTAAAAAACAAATCTGTTTACCGAACCAGTTC
*
1412 AAATAGTTATGACTATTTGAACAATTATATATTTCAAATTATTATAACCTTTTGTTATGTCATAA
1 AAATAGTTATGACTATTTGAACAATTATATATTTCAAATTATTATGACCTTTTGTT-TGTCATAA
* * * * *
1477 AACAATTATTTCTATTCATACAAGTTTATTAAAAATAAAATAATACT-ATTGTAATAATATTCTA
65 AACAATTGTTTCTATTCATACAAGCTTATTTAAAATAAAATAATACTAATT-TATTAAAATT-TA
1541 AAAATTAATAA
128 AAAATTAATAA
1552 CTAAGAGATT
Statistics
Matches: 563, Mismatches: 95, Indels: 64
0.78 0.13 0.09
Matches are distributed among these distances:
543 51 0.09
544 5 0.01
545 1 0.00
546 1 0.00
547 9 0.02
548 11 0.02
549 130 0.23
550 13 0.02
551 30 0.05
552 66 0.12
553 60 0.11
554 112 0.20
555 5 0.01
556 69 0.12
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (547 bp):
AAATAGTTATGACTATTTGAACAATTATATATTTCAAATTATTATGACCTTTTGTTTGTCATAAA
ACAATTGTTTCTATTCATACAAGCTTATTTAAAATAAAATAATACTAATTTATTAAAATTTAAAA
ATTAATAAGCAAAAGATTAAAAAGAAATCAATTTACCAGACAAGTTAAAATAGTTATGACTATTT
GAACAAATATTTATTTAAAATCATTATGATCTTTTATTTGATCATAATAAACAATTGTTTCTATG
CATAAAAGCTTATTCAAAATAAAATAATATTAACTTATTAATATTCAAAAATTAATAAGTTGAAG
ATTTAAAAAATAAATCTATTTAGCAAACAAGTTCAAATAATCACAACCATTTGAAATATTATCTA
ATTTCAAATCATTATGACATTTTGTCTTGTGTAAATAATACCAATGATTTAATAATTGGTATTCA
TACAAAACTATTCAAAATAAAATAAAACTAATTTACTAATATTTCAAAAATTAATAAGGATTAAA
AAACAAATCTGTTTACCGAACCAGTTC
Found at i:1794 original size:24 final size:24
Alignment explanation
Indices: 1743--1806 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1733 GATTTTTACT
*
1743 TAATTATTATTATA-T-ATTTATA
1 TAATTAATATTATATTAATTTATA
1765 TAATTAATATTATATTAATTTATA
1 TAATTAATATTATATTAATTTATA
1789 -ATATTAATAATTA-ATTAA
1 TA-ATTAAT-ATTATATTAA
1807 AAACCAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
22 13 0.35
23 2 0.05
24 18 0.49
25 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TAATTAATATTATATTAATTTATA
Found at i:1927 original size:18 final size:18
Alignment explanation
Indices: 1896--1964 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
1886 ATAATCTCTA
**
1896 TAATAATTCTTATAATAT
1 TAATAATTAATATAATAT
1914 TAATAATTAATATAAT-T
1 TAATAATTAATATAATAT
* *
1931 TATTCAATTAAACAATAATAT
1 TAAT-AATT-AA-TATAATAT
*
1952 TAATAATTTATAT
1 TAATAATTAATAT
1965 TCTTATTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
17 4 0.10
18 20 0.50
19 3 0.08
20 9 0.22
21 4 0.10
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATAATTAATATAATAT
Found at i:2050 original size:22 final size:22
Alignment explanation
Indices: 2021--2079 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 22
2011 ATAATAATTT
2021 TTAT-TATAATTAATAAGAACAA
1 TTATATATAATTAATAA-AACAA
*
2043 -TATATAT-ATATAATTAATACAA
1 TTATATATAAT-TAA-TAAAACAA
2065 TTATATATAA-TAATA
1 TTATATATAATTAATA
2080 TTTCATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
21 7 0.23
22 13 0.42
23 10 0.32
24 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (22 bp):
TTATATATAATTAATAAAACAA
Found at i:4040 original size:15 final size:15
Alignment explanation
Indices: 4012--4056 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
4002 TTTAATTTAT
* *
4012 TATATAATAAATTAA
1 TATATTATATATTAA
4027 TATATTATATATTAA
1 TATATTATATATTAA
*
4042 TATAATATATATTAA
1 TATATTATATATTAA
4057 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATTATATATTAA
Found at i:4047 original size:20 final size:20
Alignment explanation
Indices: 4003--4051 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3993 ATGATAGTTT
*
4003 TTAATTTATTATATAATAAA
1 TTAATATATTATATAATAAA
*
4023 TTAATATATTATAT-ATTAA
1 TTAATATATTATATAATAAA
4042 TATAATATAT
1 T-TAATATAT
4052 ATTAAAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTAATATATTATATAATAAA
Found at i:4146 original size:14 final size:14
Alignment explanation
Indices: 4116--4157 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
4106 AATAATAAAG
*
4116 TAATA-TTATTTTA
1 TAATATTTAATTTA
4129 -AATATTTAATTTA
1 TAATATTTAATTTA
4142 TAATATTTAAATTTA
1 TAATATTT-AATTTA
4157 T
1 T
4158 TTTATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 4 0.16
13 7 0.28
14 7 0.28
15 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATATTTAATTTA
Found at i:4156 original size:15 final size:15
Alignment explanation
Indices: 4125--4171 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
4115 GTAATATTAT
4125 TTTA-AATATTT-AA
1 TTTATAATATTTAAA
4138 TTTATAATATTTAAA
1 TTTATAATATTTAAA
** *
4153 TTTATTTTATATAAA
1 TTTATAATATTTAAA
4168 TTTA
1 TTTA
4172 AATTAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 18 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATAATATTTAAA
Found at i:4161 original size:20 final size:20
Alignment explanation
Indices: 4132--4185 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
4122 TATTTTAAAT
4132 ATTTAATTTATAATATTTAA
1 ATTTAATTTATAATATTTAA
* *
4152 ATTTATTTTATATAAATTTAA
1 ATTTAATTTATA-ATATTTAA
4173 A-TTAATTTATAAT
1 ATTTAATTTATAAT
4186 TATTATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 20 0.69
21 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTAATTTATAATATTTAA
Found at i:4186 original size:11 final size:11
Alignment explanation
Indices: 4134--4203 Score: 55
Period size: 10 Copynumber: 6.8 Consensus size: 11
4124 TTTTAAATAT
4134 TTAATTTATAA
1 TTAATTTATAA
4145 -T-ATTTA-AA
1 TTAATTTATAA
*
4153 TTTATTT-TATA
1 TTAATTTATA-A
*
4164 TAAATTTA-AA
1 TTAATTTATAA
4174 TTAATTTATAA
1 TTAATTTATAA
4185 TT-ATTATATAA
1 TTAATT-TATAA
4196 -TAATTTAT
1 TTAATTTAT
4204 TACAAATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
8 2 0.04
9 6 0.12
10 21 0.44
11 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTAATTTATAA
Found at i:4535 original size:19 final size:19
Alignment explanation
Indices: 4508--4546 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4498 TAACCAAACC
*
4508 AGTTTAAATAATTATGACT
1 AGTTCAAATAATTATGACT
* *
4527 AGTTCAAATAGTTATTACT
1 AGTTCAAATAATTATGACT
4546 A
1 A
4547 TTTGAACAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (19 bp):
AGTTCAAATAATTATGACT
Found at i:7395 original size:13 final size:13
Alignment explanation
Indices: 7364--7397 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
7354 TAATATAATT
*
7364 AATTAATAATAAT
1 AATTAATAATAAC
*
7377 ATTTAATAATAAC
1 AATTAATAATAAC
7390 AATTAATA
1 AATTAATA
7398 TTAAATTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAATAATAAC
Found at i:7411 original size:26 final size:25
Alignment explanation
Indices: 7382--7430 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
7372 ATAATATTTA
7382 ATAAT-AACAATTAATATTAAATTAGT
1 ATAATCAA-AATTAATA-TAAATTAGT
*
7408 ATAATCAAATTTAATATAAATTA
1 ATAATCAAAATTAATATAAATTA
7431 TCATATGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 12 0.57
27 2 0.10
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
ATAATCAAAATTAATATAAATTAGT
Found at i:7828 original size:19 final size:20
Alignment explanation
Indices: 7772--7828 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 20
7762 AACTATAAAT
* *
7772 TATTTTATTAGTGTAACTAA
1 TATTATATTAGTATAACTAA
*
7792 TAATTATTATTATTTATAA-TAA
1 T-ATTA-TATTA-GTATAACTAA
7814 TATTATATTAGTATA
1 TATTATATTAGTATA
7829 TTATTGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.13
20 6 0.20
21 7 0.23
22 9 0.30
23 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (20 bp):
TATTATATTAGTATAACTAA
Found at i:8128 original size:12 final size:12
Alignment explanation
Indices: 8111--8135 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8101 TATTTCCTTC
8111 TATTATAATTAT
1 TATTATAATTAT
8123 TATTATAATTAT
1 TATTATAATTAT
8135 T
1 T
8136 GGATTGGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTATAATTAT
Found at i:8339 original size:19 final size:19
Alignment explanation
Indices: 8315--8358 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
8305 TATATAATTG
*
8315 TTATTTATAATAGTAAATA
1 TTATTTAAAATAGTAAATA
*
8334 TTATTTAAAATAGTTAATA
1 TTATTTAAAATAGTAAATA
*
8353 ATATTT
1 TTATTT
8359 TGAAAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
TTATTTAAAATAGTAAATA
Found at i:8465 original size:16 final size:16
Alignment explanation
Indices: 8444--8490 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
8434 ATTTATAAAT
8444 AATTAATTATTAATTA
1 AATTAATTATTAATTA
*
8460 AATTAAATTATATTATTA
1 AATT-AATTAT-TAATTA
8478 ATATTAATTATTA
1 A-ATTAATTATTA
8491 TATATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 12 0.46
19 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTAATTATTAATTA
Found at i:8497 original size:28 final size:29
Alignment explanation
Indices: 8445--8531 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 29
8435 TTTATAAATA
8445 ATTAATTATTAATTAAATTA-A-ATTA-TATT
1 ATTAA-TATTAATT--ATTATATATTATTATT
*
8474 ATTAATATTAATTATTATATATTATTATA
1 ATTAATATTAATTATTATATATTATTATT
8503 ATT-AT-TGTAA-TATTGATATATTATTATT
1 ATTAATAT-TAATTATT-ATATATTATTATT
8531 A
1 A
8532 CGATAATTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 30 0.59
29 11 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
ATTAATATTAATTATTATATATTATTATT
Found at i:8531 original size:34 final size:35
Alignment explanation
Indices: 8476--8556 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
8466 ATTATATTAT
**
8476 TAATATTAATTATTATATATTATTATAATT-ATTG
1 TAATATTAATTATTATATATTACGATAATTAATTG
* *
8510 TAATATTGATATATTAT-TATTACGATAATTAATTT
1 TAATATTAAT-TATTATATATTACGATAATTAATTG
*
8545 TAATATTCATTA
1 TAATATTAATTA
8557 ATTTTATAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 22 0.55
35 18 0.45
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (35 bp):
TAATATTAATTATTATATATTACGATAATTAATTG
Found at i:8601 original size:20 final size:21
Alignment explanation
Indices: 8567--8642 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
8557 ATTTTATAGT
* *
8567 ATAATAATGAAATATTAT-TA
1 ATAATAATTATATATTATATA
8587 ATAATAATTATATATTTACTATA
1 ATAATAATTATATA-TTA-TATA
*
8610 ATAAT-ATTATATGTT-TATA
1 ATAATAATTATATATTATATA
*
8629 ATTATAATTA-ATAT
1 ATAATAATTATATAT
8643 CATCAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.23
20 16 0.34
21 5 0.11
22 8 0.17
23 7 0.15
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (21 bp):
ATAATAATTATATATTATATA
Found at i:8833 original size:19 final size:19
Alignment explanation
Indices: 8794--8833 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8784 ATTTTATATT
* *
8794 TTGTATATAAATATTTGAA
1 TTGTATATAAATAATTAAA
*
8813 TTGTATATAATTAATTAAA
1 TTGTATATAAATAATTAAA
8832 TT
1 TT
8834 AATTAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (19 bp):
TTGTATATAAATAATTAAA
Found at i:8965 original size:16 final size:18
Alignment explanation
Indices: 8930--8966 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
8920 TCGTAGCAAT
8930 TATTTAATTAAATAACTA
1 TATTTAATTAAATAACTA
*
8948 TATTT-ATT-AATAAGTA
1 TATTTAATTAAATAACTA
8964 TAT
1 TAT
8967 AATTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (18 bp):
TATTTAATTAAATAACTA
Found at i:8986 original size:9 final size:11
Alignment explanation
Indices: 8962--9036 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
8952 TATTAATAAG
8962 TATATAATTAA
1 TATATAATTAA
8973 TATAT-ATTAAA
1 TATATAATT-AA
8984 TATTATGAATTAA
1 TA-TAT-AATTAA
8997 T-TATAATTAA
1 TATATAATTAA
*
9007 -ATATGTATTAA
1 TATAT-AATTAA
9018 -AT-TAATTAAA
1 TATATAATT-AA
*
9028 TAAATAATT
1 TATATAATT
9037 TGAATAATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
9 3 0.06
10 15 0.29
11 20 0.38
12 8 0.15
13 3 0.06
14 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (11 bp):
TATATAATTAA
Found at i:9005 original size:24 final size:24
Alignment explanation
Indices: 8967--9045 Score: 78
Period size: 24 Copynumber: 3.3 Consensus size: 24
8957 ATAAGTATAT
8967 AATTAA-TATATATTAAATATTATG
1 AATTAATTATA-ATTAAATATTATG
*
8991 AATTAATTATAATTAAATATGTATTA
1 AATTAATTATAATTAAATAT-TA-TG
9017 AATTAATTA-AA-TAAATAATT-TG
1 AATTAATTATAATTAAAT-ATTATG
9039 AA-TAATT
1 AATTAATT
9046 TATTAGTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
24 21 0.43
25 10 0.20
26 10 0.20
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
AATTAATTATAATTAAATATTATG
Found at i:9401 original size:25 final size:25
Alignment explanation
Indices: 9354--9401 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
9344 AAATAGAATT
*
9354 TATTTGAAATAATTTAAACATATAA
1 TATTTGAAATAATTTAAAAATATAA
*
9379 TATTTTAAAT-ATTTATAAAATAT
1 TATTTGAAATAATTTA-AAAATAT
9402 CATAGGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TATTTGAAATAATTTAAAAATATAA
Found at i:10377 original size:20 final size:20
Alignment explanation
Indices: 10348--10407 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
10338 AATTAACTAA
10348 ATTAATTATTCTATTATAAT
1 ATTAATTATTCTATTATAAT
*
10368 ATTAAGTATTACTTATTAT--T
1 ATTAATTATT-C-TATTATAAT
*
10388 CTTAATTATT-TATTATAAT
1 ATTAATTATTCTATTATAAT
10407 A
1 A
10408 CTATTGTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
17 6 0.19
19 1 0.03
20 18 0.56
21 1 0.03
22 6 0.19
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
ATTAATTATTCTATTATAAT
Found at i:12384 original size:180 final size:181
Alignment explanation
Indices: 12154--12575 Score: 442
Period size: 180 Copynumber: 2.3 Consensus size: 181
12144 TAGATTTAAT
* * ** *
12154 TTTTTTGAAATCTCATT-TTTATTAATATTTTGAATGTTGCTAAATTAGTATTAATTTATTCTAA
1 TTTTTT-AAATCTC-TTAGTTATTAAT-TTTTGAATATTATTAAATTAGTATTAATTTATTCCAA
* * * * *
12218 ATAACCTTTTATGAACTAAAATAATTATTTTATAACCAAATAAAATA-TTAGAATGATTTGAAAT
63 ATAACCTTGTACGAAC-AAAATAATTATTTTATAACAAAAGAAAA-AGTCAGAATGATTTGAAAT
* * * *
12282 AGATAATTATTC-TAATAG-TCTTAACCATTTGAACTGATTCGA-TAAACAAATTTA
126 AGATAATCATTCAT-ATAGTTCTTAACCATTTCAACTGATTCAAGCAAACAAATTTA
* *
12336 TTTTTTAAATCTCTTAGTTATTAATTTTTGAATATTATTAAATTAGTATTATTTTAATCCAAATA
1 TTTTTTAAATCTCTTAGTTATTAATTTTTGAATATTATTAAATTAGTATTAATTTATTCCAAATA
* * *
12401 AGCTTGTACGAACAAAATAATTATTTTATGACAAAAGAAAAAGGTCATAATGATTTGAAATAGAT
66 ACCTTGTACGAACAAAATAATTATTTTATAACAAAAGAAAAA-GTCAGAATGATTTGAAATAGAT
* * * * ** *
12466 AATCATTCATATAGTTTTTAACTATTTCAATTGGTTCAAGCAATTAGATTTA
130 AATCATTCATATAGTTCTTAACCATTTCAACTGATTCAAGCAAACAAATTTA
* * ** * *
12518 TTTTTT-AATTTTTTAGTTATTAAGTTTCAGAATATTATTAAATTAGTTTTAGTTTATT
1 TTTTTTAAATCTCTTAGTTATTAA-TTTTTGAATATTATTAAATTAGTATTAATTTATT
12576 TCGAATAAAA
Statistics
Matches: 200, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
178 1 0.00
179 25 0.12
180 76 0.38
181 49 0.25
182 49 0.25
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (181 bp):
TTTTTTAAATCTCTTAGTTATTAATTTTTGAATATTATTAAATTAGTATTAATTTATTCCAAATA
ACCTTGTACGAACAAAATAATTATTTTATAACAAAAGAAAAAGTCAGAATGATTTGAAATAGATA
ATCATTCATATAGTTCTTAACCATTTCAACTGATTCAAGCAAACAAATTTA
Found at i:12937 original size:18 final size:19
Alignment explanation
Indices: 12914--12954 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
12904 AAACAAGTAA
*
12914 TAATTTATA-TATTTAAAT
1 TAATTTATATTAGTTAAAT
12932 TAATTTATATTAGTTAAAT
1 TAATTTATATTAGTTAAAT
12951 TAAT
1 TAAT
12955 ATAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTTATATTAGTTAAAT
Found at i:13165 original size:23 final size:22
Alignment explanation
Indices: 13114--13178 Score: 53
Period size: 23 Copynumber: 2.9 Consensus size: 22
13104 AAATTACTAG
*
13114 TTATTTT-AATACTATAAATATAT
1 TTATTTTAAATA-T-TAAATCTAT
*
13137 TAATTTTAAATATTAAATCTAAT
1 TTATTTTAAATATTAAATCT-AT
*
13160 TTA-TTTATATAATTAAATC
1 TTATTTTAAAT-ATTAAATC
13179 AAATAGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 12 0.34
23 19 0.54
24 4 0.11
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTTAAATATTAAATCTAT
Found at i:13322 original size:22 final size:21
Alignment explanation
Indices: 13294--13339 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
13284 AATTAATCTA
13294 TATAATTAATAATTAAAAATAT
1 TATAATTAATAATTAAAAA-AT
* **
13316 TATAATTTATTTTTAAAAAAT
1 TATAATTAATAATTAAAAAAT
13337 TAT
1 TAT
13340 TTTAATATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TATAATTAATAATTAAAAAAT
Found at i:13609 original size:18 final size:18
Alignment explanation
Indices: 13571--13609 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
13561 ATTCAGTTAT
*
13571 TAATATTTATAATTAATA
1 TAATATTTAAAATTAATA
13589 TAATATTTAAATATTAA-A
1 TAATATTTAAA-ATTAATA
13607 TAA
1 TAA
13610 ACTATTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATTTAAAATTAATA
Found at i:14732 original size:43 final size:43
Alignment explanation
Indices: 14667--14775 Score: 129
Period size: 43 Copynumber: 2.6 Consensus size: 43
14657 TTAAATTATA
*
14667 TTAATA-TA-AATTATTAAATAAATACATTTTGTATTAAAATATTT
1 TTAATATTAGAATT-TTAATTAAAT--ATTTTGTATTAAAATATTT
*
14711 TT-A-ATTAGAATTTGT-ATTAAATTTTTTGTATTAAAATATTT
1 TTAATATTAGAATTT-TAATTAAATATTTTGTATTAAAATATTT
14752 TTAATATTAGAATTTTAATTAAAT
1 TTAATATTAGAATTTTAATTAAAT
14776 TTATTAATAC
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
41 20 0.35
42 3 0.05
43 27 0.47
44 7 0.12
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (43 bp):
TTAATATTAGAATTTTAATTAAATATTTTGTATTAAAATATTT
Found at i:14738 original size:41 final size:43
Alignment explanation
Indices: 14693--14777 Score: 140
Period size: 41 Copynumber: 2.0 Consensus size: 43
14683 AATAAATACA
14693 TTTTGTATTAAAATATTTTT-A-ATTAGAATTTGT-ATTAAATT
1 TTTTGTATTAAAATATTTTTAATATTAGAATTT-TAATTAAATT
14734 TTTTGTATTAAAATATTTTTAATATTAGAATTTTAATTAAATT
1 TTTTGTATTAAAATATTTTTAATATTAGAATTTTAATTAAATT
14777 T
1 T
14778 ATTAATACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
41 20 0.49
42 2 0.05
43 19 0.46
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (43 bp):
TTTTGTATTAAAATATTTTTAATATTAGAATTTTAATTAAATT
Found at i:15151 original size:18 final size:18
Alignment explanation
Indices: 15125--15170 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
15115 ATTGTTATTA
15125 TTAAGATAATAAAATAATG
1 TTAAGATAAT-AAATAATG
15144 TTAA-ATAATAAATAA--
1 TTAAGATAATAAATAATG
15159 TTAAGATAATAA
1 TTAAGATAATAA
15171 TATAGTTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 4 0.15
16 7 0.27
17 6 0.23
18 5 0.19
19 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
TTAAGATAATAAATAATG
Found at i:15476 original size:22 final size:22
Alignment explanation
Indices: 15450--15495 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
15440 TTATAATATT
*
15450 TATTATAATAATAATAATTTAA
1 TATTATAATAATAATAATTAAA
* *
15472 TATTATTATAATAATTATTAAA
1 TATTATAATAATAATAATTAAA
15494 TA
1 TA
15496 ATAATTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTATAATAATAATAATTAAA
Found at i:15482 original size:19 final size:19
Alignment explanation
Indices: 15435--15487 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
15425 ATTTAAATAT
* *
15435 TATTTTTATAAT-ATTTAT
1 TATTATTATAATAATTTAA
* *
15453 TATAATAATAATAATTTAA
1 TATTATTATAATAATTTAA
15472 TATTATTATAATAATT
1 TATTATTATAATAATT
15488 ATTAAATAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTATTATAATAATTTAA
Found at i:15486 original size:14 final size:14
Alignment explanation
Indices: 15430--15498 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 14
15420 CTTAGATTTA
* *
15430 AATATTATTTTTAT
1 AATATTATTATAAT
15444 AATATTTATTATAAT
1 AATA-TTATTATAAT
* *
15459 AATA--ATAAT-TT
1 AATATTATTATAAT
15470 AATATTATTATAAT
1 AATATTATTATAAT
15484 -A-ATTATTA-AAT
1 AATATTATTATAAT
15495 AATA
1 AATA
15499 ATTTAAAATA
Statistics
Matches: 43, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
11 8 0.19
12 12 0.28
13 6 0.14
14 5 0.12
15 12 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATTATTATAAT
Found at i:15497 original size:25 final size:26
Alignment explanation
Indices: 15441--15503 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
15431 ATATTATTTT
15441 TATAATATTTATTATAATAATAATAA
1 TATAATATTTATTATAATAATAATAA
* *
15467 TTTAATA-TTATTATAATAATTATTAA
1 TATAATATTTATTATAATAA-TAATAA
15493 -ATAATAATTTA
1 TATAAT-ATTTA
15504 AAATATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
25 16 0.52
26 12 0.39
27 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATAATATTTATTATAATAATAATAA
Found at i:16049 original size:16 final size:16
Alignment explanation
Indices: 16019--16114 Score: 63
Period size: 16 Copynumber: 5.8 Consensus size: 16
16009 ATCTATTATA
*
16019 TATTTAATAAATATAAT
1 TATTT-ATAATTATAAT
16036 TATTTATAATTATAAAT
1 TATTTATAATTAT-AAT
*
16053 AATTATATAATTAT-AT
1 TATT-TATAATTATAAT
* *
16069 AATTTAT-TTTATAAAT
1 TATTTATAATTAT-AAT
**
16085 ATAAGTATAATATATAA-
1 -TATTTATAAT-TATAAT
16102 TATTTATAATTAT
1 TATTTATAATTAT
16115 TTACTAATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
14 4 0.06
15 6 0.10
16 23 0.37
17 15 0.24
18 12 0.19
19 3 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (16 bp):
TATTTATAATTATAAT
Found at i:16056 original size:20 final size:20
Alignment explanation
Indices: 16031--16132 Score: 72
Period size: 20 Copynumber: 5.2 Consensus size: 20
16021 TTTAATAAAT
16031 ATAATTATTTATAATTATAA
1 ATAATTATTTATAATTATAA
16051 ATAATTA--TATAATTAT--
1 ATAATTATTTATAATTATAA
*
16067 ATAATTTATTTTATAAATATAA
1 ATAA-TTA-TTTATAATTATAA
* * * **
16089 GT-ATAATATATAA-TATTT
1 ATAATTATTTATAATTATAA
*
16107 ATAATTATTTACTAATTATTA
1 ATAATTATTTA-TAATTATAA
16128 ATAAT
1 ATAAT
16133 AATAATATAA
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
16 4 0.06
17 3 0.05
18 13 0.21
19 12 0.19
20 20 0.32
21 10 0.16
22 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (20 bp):
ATAATTATTTATAATTATAA
Found at i:16122 original size:11 final size:10
Alignment explanation
Indices: 16030--16132 Score: 60
Period size: 10 Copynumber: 10.6 Consensus size: 10
16020 ATTTAATAAA
16030 TATAATTATT
1 TATAATTATT
*
16040 TATAATTATA
1 TATAATTATT
*
16050 AATAATTA--
1 TATAATTATT
16058 TATAATTA--
1 TATAATTATT
16066 TATAATTTATTT
1 TATAA-TTA-TT
**
16078 TATAAATATAAG
1 TAT-AAT-TATT
16090 TATAA-TA--
1 TATAATTATT
16097 TATAA-TATT
1 TATAATTATT
16106 TATAATTATT
1 TATAATTATT
16116 TACTAATTATT
1 TA-TAATTATT
*
16127 AATAAT
1 TATAAT
16133 AATAATATAA
Statistics
Matches: 77, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
7 7 0.09
8 12 0.16
9 10 0.13
10 26 0.34
11 11 0.14
12 7 0.09
13 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (10 bp):
TATAATTATT
Found at i:16148 original size:36 final size:35
Alignment explanation
Indices: 16031--16148 Score: 114
Period size: 39 Copynumber: 3.2 Consensus size: 35
16021 TTTAATAAAT
16031 ATAATTATTTATAATTATAAATAATTATATAAT-TA
1 ATAATTATTTATAATTATAAATAA-TATATAATATA
* *
16066 TATAATTTATTTTATAAATATAAGTATAATATATAATATTT
1 -ATAA-TTA-TTTATAATTATAA--ATAATATATAATA-TA
*
16107 ATAATTATTTACTAATTATTAATAATA-ATAATATA
1 ATAATTATTTA-TAATTATAAATAATATATAATATA
16142 ACTAATT
1 A-TAATT
16149 GAAATTATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
35 2 0.03
36 15 0.22
37 9 0.13
38 16 0.23
39 18 0.26
40 8 0.12
41 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (35 bp):
ATAATTATTTATAATTATAAATAATATATAATATA
Found at i:16182 original size:77 final size:76
Alignment explanation
Indices: 16030--16185 Score: 183
Period size: 77 Copynumber: 2.0 Consensus size: 76
16020 ATTTAATAAA
* **
16030 TATAATTATTTATAATTATAAATAATTATATAATTATATAATTTATTTTATAAATATAAGTATAA
1 TATAATTATTTATAATTATAAATAATTATATAATTATATAATTGAAATTATAAATATAAGTATAA
16095 TATATAATATT
66 TATATAATATT
* * * *
16106 TATAATTATTTACTAATTATTAATAA-TA-ATAA-TATAACTAATTGAAATTATATTATTTAATT
1 TATAATTATTTA-TAATTATAAATAATTATATAATTAT-A-TAATTGAAATTATA-AATATAAGT
*
16168 ATAATATATTATATT
62 ATAATATATAATATT
16183 TAT
1 TAT
16186 TAATATACAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
74 3 0.04
75 5 0.07
76 25 0.37
77 35 0.51
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (76 bp):
TATAATTATTTATAATTATAAATAATTATATAATTATATAATTGAAATTATAAATATAAGTATAA
TATATAATATT
Found at i:16535 original size:17 final size:17
Alignment explanation
Indices: 16515--16564 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
16505 TAATATATTA
16515 ATTATAATATTATAAGT
1 ATTATAATATTATAAGT
*
16532 ATTATAATATTTTATAATT
1 ATTATAATA--TTATAAGT
*
16551 AAT-TAATATTATAA
1 ATTATAATATTATAA
16565 AATTAATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 9 0.31
18 5 0.17
19 9 0.31
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTATAATATTATAAGT
Found at i:16707 original size:27 final size:27
Alignment explanation
Indices: 16643--16725 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
16633 TTTCAACAAT
*
16643 TATTA-ATTAATCAAATAGTAAAATAA
1 TATTATATTATTCAAATAGTAAAATAA
16669 TATTATATTATTCAAATA-TATAAATATA
1 TATTATATTATTCAAATAGTA-AAATA-A
* *
16697 TATTATA-TATT--ATTTGTAAAATAA
1 TATTATATTATTCAAATAGTAAAATAA
16721 TATTA
1 TATTA
16726 AATATTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
24 6 0.12
25 7 0.14
26 9 0.18
27 20 0.40
28 8 0.16
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATATTATTCAAATAGTAAAATAA
Found at i:18086 original size:23 final size:23
Alignment explanation
Indices: 18060--18129 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 23
18050 TACATATAAA
18060 ATTATTTTTATTAAGATAAATAT
1 ATTATTTTTATTAAGATAAATAT
*
18083 ATTA----TAATAAG-TATAATACT
1 ATTATTTTTATTAAGATA-AATA-T
*
18103 ATTATTTTTATGAAGAT-AATAT
1 ATTATTTTTATTAAGATAAATAT
18125 ATTAT
1 ATTAT
18130 AATTATAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 15
0.67 0.05 0.27
Matches are distributed among these distances:
18 2 0.05
19 10 0.27
20 5 0.14
22 6 0.16
23 8 0.22
24 5 0.14
25 1 0.03
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (23 bp):
ATTATTTTTATTAAGATAAATAT
Found at i:18098 original size:40 final size:41
Alignment explanation
Indices: 18045--18132 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 41
18035 TCAATATTTA
*
18045 TATAATACATATAA-A-ATTATTTTTATTAAGATAAATATAT
1 TATAATACATATAATACATTATTTTTATGAAGAT-AATATAT
18085 TATAATA-AGTATAATACTATTATTTTTATGAAGATAATATAT
1 TATAATACA-TATAATAC-ATTATTTTTATGAAGATAATATAT
18127 TATAAT
1 TATAAT
18133 TATAATATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
39 1 0.02
40 12 0.28
41 1 0.02
42 13 0.30
43 16 0.37
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (41 bp):
TATAATACATATAATACATTATTTTTATGAAGATAATATAT
Found at i:19227 original size:19 final size:20
Alignment explanation
Indices: 19180--19227 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
19170 ATTAATAAAA
*
19180 ATTTATAATAAATTTATAATT
1 ATTTA-AATAAATATATAATT
*
19201 ATAT-AATAAATAT-TAATT
1 ATTTAAATAAATATATAATT
19219 ATTTAAATA
1 ATTTAAATA
19228 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
21 3 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATAAATATATAATT
Found at i:19598 original size:17 final size:18
Alignment explanation
Indices: 19578--19621 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
19568 TTAATTTAGT
19578 ATATTAATTAA-ATAAAA
1 ATATTAATTAATATAAAA
* *
19595 ATATTTATTAATATAATA
1 ATATTAATTAATATAAAA
19613 A-ATTAATTA
1 ATATTAATTA
19622 TTAGTAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATTAATTAATATAAAA
Found at i:20072 original size:26 final size:29
Alignment explanation
Indices: 20021--20085 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 29
20011 ATATTCATTA
*
20021 ATTAATAATTAATTAAATAATGAATATTTT
1 ATTAATAATTAATTAAATAA-GAATATTTC
20051 ATTAATAATT-ATTAAAT-A-AATATTTC
1 ATTAATAATTAATTAAATAAGAATATTTC
*
20077 ATTATTAAT
1 ATTAATAAT
20086 ATTTCTATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 15 0.45
28 1 0.03
29 7 0.21
30 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (29 bp):
ATTAATAATTAATTAAATAAGAATATTTC
Found at i:20206 original size:21 final size:21
Alignment explanation
Indices: 20147--20209 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
20137 TAATATGAAA
* *
20147 TATT-ATTATTTAATATTATTT
1 TATTAATTATTTAAAATTA-AT
**
20168 TATTAATTA-AAAATAATTAAT
1 TATTAATTATTTAA-AATTAAT
20189 TATTAATTATTTAAAATTAAT
1 TATTAATTATTTAAAATTAAT
20210 ATTTTAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 23 0.70
22 10 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTAATTATTTAAAATTAAT
Done.