Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007105.1 Hibiscus syriacus cultivar Beakdansim tig00018568_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: 286207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:138682 original size:2 final size:2
Alignment explanation
Indices: 138675--138724 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
138665 TTTAAATGTC
*
138675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
138717 TA T- TA TA T
1 TA TA TA TA T
138725 TGCTAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:139225 original size:31 final size:31
Alignment explanation
Indices: 139183--139245 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
139173 GTTGAAAATC
*
139183 GCGTTGTGATTTTCCATTTCGCGTTGCGATA
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATA
*
139214 GCGTTGCGATTTTTCATTTCGCGTTGCGATA
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATA
139245 G
1 G
139246 TTGAAAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.13, C:0.19, G:0.27, T:0.41
Consensus pattern (31 bp):
GCGTTGCGATTTTCCATTTCGCGTTGCGATA
Found at i:139239 original size:20 final size:20
Alignment explanation
Indices: 139214--139325 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
139204 CGTTGCGATA
*
139214 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTCCATTTC
* ** **
139234 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTCCATTTC
139255 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
* ** **
139275 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTCCATTTC
139296 GCGTTGCGATTTTCCATTTC
1 GCGTTGCGATTTTCCATTTC
139316 GCGTTGCGAT
1 GCGTTGCGAT
139326 AGTCTACAGT
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 40 0.57
21 30 0.43
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTTCCATTTC
Found at i:139258 original size:21 final size:21
Alignment explanation
Indices: 139232--139305 Score: 96
Period size: 21 Copynumber: 3.6 Consensus size: 21
139222 ATTTTTCATT
139232 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
139253 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
139273 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
139294 TCGCGTTGCGAT
1 TCGCGTTGCGAT
139306 TTTCCATTTC
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:139273 original size:41 final size:41
Alignment explanation
Indices: 139214--139328 Score: 221
Period size: 41 Copynumber: 2.8 Consensus size: 41
139204 CGTTGCGATA
*
139214 GCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
139255 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
139296 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGT
139329 CTACAGTTGT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
Found at i:139362 original size:82 final size:81
Alignment explanation
Indices: 139214--139365 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 81
139204 CGTTGCGATA
* *
139214 GCGTTGCGATTTTTCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGT
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTC-CGT
139279 TGCGATAGTTGAAAATC
65 TGCGATAGTTGAAAATC
* * *
139296 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCT-ACAGTTGTCGTTGCGATTTTCCAAATT-C
1 GCGTTGCGATTTTCCATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTTCC-AATTCC
139359 GTTGCGA
63 GTTGCGA
139366 AAATTCGTTG
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
82 44 0.71
83 15 0.24
84 3 0.05
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (81 bp):
GCGTTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCAATTCCGTT
GCGATAGTTGAAAATC
Found at i:139474 original size:5 final size:5
Alignment explanation
Indices: 139464--139491 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
139454 CGTATTACCA
139464 CGACC CGACC CGACC CGACC CGACC CGA
1 CGACC CGACC CGACC CGACC CGACC CGA
139492 GACGAGACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.57, G:0.21, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:139998 original size:6 final size:6
Alignment explanation
Indices: 139989--140015 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
139979 GTCGGTCTCA
139989 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
140016 AATACGTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:140143 original size:22 final size:22
Alignment explanation
Indices: 140114--140167 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
140104 AATTTAAAAA
140114 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
140136 ATTGCAACGACAATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
140158 ATCGCAACGA
1 ATCGCAACGA
140168 ATTTGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:140227 original size:20 final size:20
Alignment explanation
Indices: 140202--140257 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
140192 ACTATAGACT
140202 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
140222 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
140242 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
140258 CAACGAGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:146613 original size:11 final size:11
Alignment explanation
Indices: 146597--146625 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
146587 ATTCCAATAC
146597 TAGAGAGATTT
1 TAGAGAGATTT
146608 TAGAGAGATTT
1 TAGAGAGATTT
146619 TAGAGAG
1 TAGAGAG
146626 TTTCTTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (11 bp):
TAGAGAGATTT
Found at i:151289 original size:11 final size:11
Alignment explanation
Indices: 151273--151301 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
151263 CTTCCAATAC
151273 TAGAGAGATTT
1 TAGAGAGATTT
151284 TAGAGAGATTT
1 TAGAGAGATTT
151295 TAGAGAG
1 TAGAGAG
151302 TTTCTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (11 bp):
TAGAGAGATTT
Found at i:156051 original size:20 final size:20
Alignment explanation
Indices: 156028--156079 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
156018 AAATTTAGTG
156028 AGTAAAATAAA-AAAATTAAA
1 AGTAAAATAAACAAAA-TAAA
*
156048 AGTATAATAAACAAAATAAA
1 AGTAAAATAAACAAAATAAA
*
156068 AGAAAAAATAAA
1 AG-TAAAATAAA
156080 GTTAAGTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.17
Consensus pattern (20 bp):
AGTAAAATAAACAAAATAAA
Found at i:158557 original size:18 final size:18
Alignment explanation
Indices: 158500--158559 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
158490 TTTGAAGTGA
158500 ATAAA-AGAATTATATAG
1 ATAAACAGAATTATATAG
* * *
158517 ATCAAACTGAGATTATGTTG
1 AT-AAACAGA-ATTATATAG
*
158537 ATAATCAGAATTATATAG
1 ATAAACAGAATTATATAG
158555 ATAAA
1 ATAAA
158560 ATTGGTGATT
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
17 2 0.06
18 14 0.44
19 7 0.22
20 9 0.28
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (18 bp):
ATAAACAGAATTATATAG
Found at i:161708 original size:19 final size:20
Alignment explanation
Indices: 161675--161721 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
161665 TTTGCAGAGA
161675 AAACATCCTCCAAC-GCTAG
1 AAACATCCTCCAACGGCTAG
161694 AAATCATCC-CCAACGGCTAG
1 AAA-CATCCTCCAACGGCTAG
161714 AAACATCC
1 AAACATCC
161722 ACAAACTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.15
Consensus pattern (20 bp):
AAACATCCTCCAACGGCTAG
Found at i:163230 original size:19 final size:19
Alignment explanation
Indices: 163203--163239 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
163193 ATCTAATATC
* *
163203 ATTTTAAATATAATTAAAA
1 ATTTAAAATATAAATAAAA
163222 ATTTAAAATATAAATAAA
1 ATTTAAAATATAAATAAA
163240 TGAACCACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATTTAAAATATAAATAAAA
Found at i:167288 original size:51 final size:47
Alignment explanation
Indices: 167231--167352 Score: 138
Period size: 47 Copynumber: 2.5 Consensus size: 47
167221 AATAGTAAGT
167231 AAAATAAATATAAAAAAATAAAAAGAAGAAGAAAAAACTATATAAATA-AA
1 AAAAT-AA-ATAAAAAAATAAAAA-AA-AAGAAAAAACTATATAAATATAA
* * * * * *
167281 ACAAATAAATAAAATAATAATAAAAAAGTAAAAATTATATATATATAT
1 A-AAATAAATAAAAAAATAAAAAAAAAGAAAAAACTATATAAATATAA
167329 AAAATAAATAAAAAAATAAAAAAA
1 AAAATAAATAAAAAAATAAAAAAA
167353 TAGTATATAT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
47 38 0.61
48 4 0.06
49 13 0.21
50 3 0.05
51 4 0.06
ACGTcount: A:0.75, C:0.02, G:0.03, T:0.20
Consensus pattern (47 bp):
AAAATAAATAAAAAAATAAAAAAAAAGAAAAAACTATATAAATATAA
Found at i:167338 original size:42 final size:41
Alignment explanation
Indices: 167285--167412 Score: 129
Period size: 41 Copynumber: 3.1 Consensus size: 41
167275 AATAAAACAA
167285 ATAAATAAAATAATAATAAAAAAGTAAAAATTATATATATATAT
1 ATAAAT-AAATAA-AATAAAAAA-TAAAAATTATATATATATAT
*
167329 A-AAATAAATAAAA-AAATAAA-AAAATAGTATATATATATAT
1 ATAAATAAATAAAATAAA-AAATAAAA-ATTATATATATATAT
* * * *
167369 ATAAATTAATAAAA-ATGATAATAAAAATAATATATATATAT
1 ATAAATAAATAAAATA-AAAAATAAAAATTATATATATATAT
167410 ATA
1 ATA
167413 TATATATATA
Statistics
Matches: 73, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
39 4 0.05
40 18 0.25
41 35 0.48
42 11 0.15
43 4 0.05
44 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.31
Consensus pattern (41 bp):
ATAAATAAATAAAATAAAAAATAAAAATTATATATATATAT
Found at i:167351 original size:7 final size:8
Alignment explanation
Indices: 167240--167354 Score: 54
Period size: 8 Copynumber: 13.4 Consensus size: 8
167230 TAAAATAAAT
167240 ATAAAAAA
1 ATAAAAAA
167248 ATAAAAAGA
1 ATAAAAA-A
*
167257 AGAAGAAAAA
1 A-TA-AAAAA
* *
167267 ACTATATAA
1 A-TAAAAAA
167276 ATAAAACAA
1 ATAAAA-AA
167285 ATAAATAAA
1 ATAAA-AAA
*
167294 AT--AATA
1 ATAAAAAA
167300 ATAAAAAA
1 ATAAAAAA
*
167308 GTAAAAATTA
1 ATAAAAA--A
* * *
167318 TATATATAT
1 -ATAAAAAA
167327 ATAAAATAA
1 ATAAAA-AA
167336 ATAAAAAA
1 ATAAAAAA
167344 ATAAAAAA
1 ATAAAAAA
167352 ATA
1 ATA
167355 GTATATATAT
Statistics
Matches: 79, Mismatches: 17, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
6 4 0.05
7 1 0.01
8 36 0.46
9 24 0.30
10 6 0.08
11 8 0.10
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (8 bp):
ATAAAAAA
Found at i:167361 original size:2 final size:2
Alignment explanation
Indices: 167356--167432 Score: 72
Period size: 2 Copynumber: 40.0 Consensus size: 2
167346 AAAAAAATAG
* * * * *
167356 TA TA TA TA TA TA TA TA AA T- TA -A TA AA AA TGA TA -A TA AA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
167396 TA -A 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
167433 ATCTAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
1 4 0.06
2 58 0.91
3 2 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (2 bp):
TA
Found at i:168647 original size:40 final size:35
Alignment explanation
Indices: 168592--168682 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 35
168582 CGAGGGTTTG
* *
168592 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTGTGTGTGT
1 GTGTTTCAAGAGAAACAATTTC-AAGGGTTTT-T-T-T-T
*
168632 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAGGGTTTTTTTT
168667 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
168683 TGTCTCAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
35 17 0.35
36 1 0.02
37 1 0.02
38 1 0.02
39 7 0.15
40 21 0.44
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACAATTTCAAGGGTTTTTTTT
Found at i:168717 original size:36 final size:36
Alignment explanation
Indices: 168668--168901 Score: 218
Period size: 36 Copynumber: 6.6 Consensus size: 36
168658 GTTTTTTTTG
168668 TGTTTCAAGAGAAACTGTCTCAAGA-AGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGA-GACAAAATT
* * *
168704 TGTTTCAAAAGAAACTGTTTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** * * *
168740 TAATTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
168777 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
168806 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
168842 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
*
168879 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
168902 AACTCGTTTT
Statistics
Matches: 164, Mismatches: 20, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
29 14 0.09
30 6 0.04
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 6 0.04
36 74 0.45
37 57 0.35
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:168902 original size:102 final size:102
Alignment explanation
Indices: 168702--168888 Score: 261
Period size: 102 Copynumber: 1.8 Consensus size: 102
168692 AAGGACAAAA
* *
168702 TTTGTTTCAAAAGAAACTGTTTCAAGAGAGACAAAACTTAATTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAATTCTAAAAGAAACTGTCTCAAGAG
168767 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * ** **
168804 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC-AAGGGAAACTGTCTCAAGAG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAATTCTAAAAGAAACTGTCTCAAGAG
168868 AGAC-AAGATTTTGTTTCAAGG
66 AGACGAA-A-TTTGTTTCAAGG
168889 GAAACTGTCT
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
100 2 0.03
101 22 0.30
102 50 0.68
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAATTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:169017 original size:37 final size:37
Alignment explanation
Indices: 168966--169038 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
168956 TCAAGGTTTA
* *
168966 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
*
169003 TGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACCATCTCAAGAGAGACAAAATT
169039 AATTTAAGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (37 bp):
TGTTTCAAGAGAAACCATCTCAAGAGAGACAAAATTT
Found at i:169060 original size:102 final size:102
Alignment explanation
Indices: 168939--169178 Score: 374
Period size: 102 Copynumber: 2.4 Consensus size: 102
168929 ATATTTTGTG
* *
168939 TTTCAAGGGAAACGTTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
169004 GTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGGAAACCACCCCAAGAGAGACAAAATTAA
*
169041 TTT-AAGAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TTTCAAG-GGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
* * * * *
169105 TGTTTTAAGGGAAACTACCCCAAGCGAGATAAAATTTA
65 TGTTTCAAGGGAAACCACCCCAAGAGAGACAAAATTAA
169143 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
169179 GGAGACAAAA
Statistics
Matches: 126, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
101 3 0.02
102 120 0.95
103 3 0.02
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACCACCCCAAGAGAGACAAAATTAA
Found at i:169202 original size:87 final size:87
Alignment explanation
Indices: 169087--169265 Score: 304
Period size: 87 Copynumber: 2.1 Consensus size: 87
169077 AGAAACTGTC
* * *
169087 TCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
169152 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * *
169174 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
169239 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
169261 TCAAG
1 TCAAG
169266 AGAAACTGTC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 86 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:169365 original size:189 final size:189
Alignment explanation
Indices: 168985--169370 Score: 501
Period size: 189 Copynumber: 2.0 Consensus size: 189
168975 AGAAACTATC
*
168985 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTAATTTAAGAGG
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTAATTTAAGAGG
* ** **
169050 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGG
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
* * * * * *
169115 GAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGGAAATGTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATGTT
* ** * *
169174 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAG-G
1 TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTAATTT-AAGAG
169238 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
65 GAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAA
** * * * *
169303 AGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACAG-ATTCAAATATTT-TGTT
130 AGAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGAAAA-AGTATTC-AATATTTATGTT
169363 TCAAGGGA
1 TCAAGGGA
169371 AACTTGGAAA
Statistics
Matches: 170, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
188 3 0.02
189 157 0.92
190 10 0.06
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTCGTTTCAAGGGAAACCATCTCAAGAGAGACAAAATTAATTTAAGAGG
AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAA
GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAAAGTATTCAATATTTATGTT
Found at i:169714 original size:106 final size:105
Alignment explanation
Indices: 169522--169843 Score: 428
Period size: 106 Copynumber: 3.0 Consensus size: 105
169512 TGTATTGTTC
* * * * * ** *
169522 CGAGTCCAATATCCTCCGCCGTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTAACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * *
169587 GCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCCGTCCCTTCG-TGTGAAGTTGAACTTGTGTTGTCT
* * * *
169628 CGAGTCCAATTTCATTTGTTGTGAAGTTAAAATTGGCTTTGAAATTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
169693 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCG-TGTGAAGTTGAACTTGTGTTGTCT
* * * *
169734 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAATTTTTTTGTTGACA
1 CGAGTCCAATATCATTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
169799 ACCAGCCGTCCCTTCGTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTGTGAAGTTGAACTTGTGTTGTCT
169839 CGAGT
1 CGAGT
169844 GGCACGATAT
Statistics
Matches: 189, Mismatches: 27, Indels: 1
0.87 0.12 0.00
Matches are distributed among these distances:
105 28 0.15
106 161 0.85
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (105 bp):
CGAGTCCAATATCATTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTGTGAAGTTGAACTTGTGTTGTCT
Found at i:170500 original size:32 final size:32
Alignment explanation
Indices: 170453--170526 Score: 114
Period size: 32 Copynumber: 2.3 Consensus size: 32
170443 AAATATTCGG
* *
170453 TGTTGAATCTCAAAAAATGGCCC-AACATTTGA
1 TGTTAAATCTAAAAAAAT-GCCCTAACATTTGA
170485 TGTTAAATCTAAAAAAATGCCCTAACATTTGA
1 TGTTAAATCTAAAAAAATGCCCTAACATTTGA
170517 TGTTAAATCT
1 TGTTAAATCT
170527 TCAAAGATGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 4 0.10
32 35 0.90
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (32 bp):
TGTTAAATCTAAAAAAATGCCCTAACATTTGA
Found at i:170537 original size:32 final size:31
Alignment explanation
Indices: 170465--170537 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
170455 TTGAATCTCA
**
170465 AAAAATGGCCCAACATTTGATGTTAAATCTAA
1 AAAAAT-GCCCAACATTTGATGTTAAATCTTC
170497 AAAAATGCCCTAACATTTGATGTTAAATCTTC
1 AAAAATGCCC-AACATTTGATGTTAAATCTTC
*
170529 AAAGATGCC
1 AAAAATGCC
170538 TTCATTGTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 4 0.11
32 33 0.89
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (31 bp):
AAAAATGCCCAACATTTGATGTTAAATCTTC
Found at i:171566 original size:69 final size:69
Alignment explanation
Indices: 171450--171587 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
171440 TGTCTCTCTC
*
171450 TTGATGCTCCATGATCTTCGAGTGGAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
171515 TCAT
66 TCAT
* * *
171519 TTGATGCTCTATGATCTTCGAGTGAAGTGGTTCAGTGATTC-GAAAATGATTGTGCTTGATCAAT
1 TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAG-AAATGATTGTGCTTGATCAAT
171583 CTCAT
65 CTCAT
171588 AGTTTGAATC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.37
Consensus pattern (69 bp):
TTGATGCTCCATGATCTTCGAGTGAAGTGATTCAGTAATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:171683 original size:14 final size:14
Alignment explanation
Indices: 171661--171697 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
171651 TTTTCTTCAA
*
171661 TTTTC-CTTTGTTT
1 TTTTCTCTTTGCTT
171674 TTTTCTCTTTGCTT
1 TTTTCTCTTTGCTT
171688 TTTTCTCTTT
1 TTTTCTCTTT
171698 TTGCTTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.00, C:0.19, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTCTCTTTGCTT
Found at i:171700 original size:16 final size:15
Alignment explanation
Indices: 171661--171704 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
171651 TTTTCTTCAA
171661 TTTTC-CTTTG-TTT
1 TTTTCTCTTTGCTTT
171674 TTTTCTCTTTGCTTT
1 TTTTCTCTTTGCTTT
*
171689 TTTCTCTTTTTGCTTT
1 TTT-TCTCTTTGCTTT
171705 GATTAAATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 5 0.19
14 5 0.19
15 6 0.22
16 11 0.41
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.75
Consensus pattern (15 bp):
TTTTCTCTTTGCTTT
Found at i:174948 original size:31 final size:29
Alignment explanation
Indices: 174855--174957 Score: 96
Period size: 30 Copynumber: 3.8 Consensus size: 29
174845 AAGAAAAAAC
*
174855 TATATAAATA-AAATAAATAAATAAAATA
1 TATATATATATAAATAAATAAATAAAATA
*
174883 -ATA-ATA-A-AAAGT-AA-AAATAATATA
1 TATATATATATAAA-TAAATAAATAAAATA
174907 TATATATATA-AAATAAATAAATAAAATA
1 TATATATATATAAATAAATAAATAAAATA
* *
174935 GTATATATCTATAAATTAATAAA
1 -TATATATATATAAATAAATAAA
174958 ATTGATAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
24 9 0.15
25 9 0.15
26 7 0.11
27 9 0.15
28 9 0.15
29 9 0.15
30 10 0.16
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (29 bp):
TATATATATATAAATAAATAAATAAAATA
Found at i:174980 original size:2 final size:2
Alignment explanation
Indices: 174973--175003 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
174963 TAATAAAATA
174973 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
175004 AAATCTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:184742 original size:21 final size:21
Alignment explanation
Indices: 184716--184768 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
184706 GAACGGCATC
184716 GGGGACGTTTCACCGACAGCT
1 GGGGACGTTTCACCGACAGCT
* ** *
184737 GGGGACGTTTTAGGGACGGCT
1 GGGGACGTTTCACCGACAGCT
184758 GGGGAC-TTTCA
1 GGGGACGTTTCA
184769 TATATGTCCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.23
Consensus pattern (21 bp):
GGGGACGTTTCACCGACAGCT
Found at i:188350 original size:26 final size:26
Alignment explanation
Indices: 188317--188374 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
188307 AAATCGGGTT
188317 TGCTGTTTATATTGAGTTGGTTTGGG
1 TGCTGTTTATATTGAGTTGGTTTGGG
188343 TGCTGTTTATATTGAGTTGGTTTGGG
1 TGCTGTTTATATTGAGTTGGTTTGGG
188369 TGCTGT
1 TGCTGT
188375 GTGTTTTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.10, C:0.05, G:0.34, T:0.50
Consensus pattern (26 bp):
TGCTGTTTATATTGAGTTGGTTTGGG
Found at i:191179 original size:16 final size:15
Alignment explanation
Indices: 191158--191198 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
191148 TACTACTCTT
191158 TTTATTATCTTTTTAC
1 TTTATTATCTTTTT-C
191174 TTTA-T-TCTATTTTC
1 TTTATTATCT-TTTTC
191188 TTTATTATCTT
1 TTTATTATCTT
191199 CTTTGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.36
15 7 0.32
16 7 0.32
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTATCTTTTTC
Found at i:202661 original size:105 final size:105
Alignment explanation
Indices: 202520--203223 Score: 1167
Period size: 105 Copynumber: 6.7 Consensus size: 105
202510 CAAGATAACA
* *
202520 CAAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAACAATTTTCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
202584 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACA
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
202625 CAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
202690 TTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAACG
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
202730 CAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTCCAGAGCCGA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
202795 TTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
202835 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
*
202900 ATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* * *
202941 CAAGTTCAACTTCACGACTAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGGGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCAGAGCCA
203006 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
*
203047 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAATAACTTCCCAATTTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
* *
203112 TTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACG
66 TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
* ** * *
203152 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGGACATTTTCCAAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
203217 ATTTCAA
65 ATTTCAA
203224 AGGATATTGG
Statistics
Matches: 562, Mismatches: 33, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
105 335 0.60
106 227 0.40
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
Found at i:203096 original size:317 final size:315
Alignment explanation
Indices: 202520--203223 Score: 1178
Period size: 317 Copynumber: 2.2 Consensus size: 315
202510 CAAGATAACA
*
202520 CAAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAACAATTTTCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCA
*
202584 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACGATGAAGGG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGG
* *
202649 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATAT
130 ACCGCTGGTTGTCAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
202714 TGGACTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
195 TGGACTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
* * *
202779 CCAATTCCAGAGCCGATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
260 CCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
202835 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAGCCA
* *
202900 ATTTCAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACT-AAGG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGA-TGAAGG
*
202964 GACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGGGCCAATTTCAACTTCACAGCGAAGGAT
129 GACCGCTGGTTGTCAA-AAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT
* *
203029 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAATAACT
193 ATTGGACTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACT
* *
203094 TCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACG
258 TCCCAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
203152 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGGACATTTTCCAAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCCCAATTTCAGAGCCA
203217 ATTTCAA
65 ATTTCAA
203224 AGGATATTGG
Statistics
Matches: 364, Mismatches: 21, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
315 37 0.10
316 99 0.27
317 228 0.63
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (315 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAATTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGATGAAGGGA
CCGCTGGTTGTCAAAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
GGACTCCAGACAACGCAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCC
CAATTCCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:203210 original size:211 final size:210
Alignment explanation
Indices: 202520--203223 Score: 1176
Period size: 211 Copynumber: 3.3 Consensus size: 210
202510 CAAGATAACA
* *
202520 CAAGTTCAACTTCACGACGAAGGGA-CGACTGGTTGTCAACAACAATTTTCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
202584 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACACAAGTTCAACTTCACGATGAAGGG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
202649 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGGATAT
130 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
202714 TGGACTCCAGACAACG
195 TGGACTCCAGACAACG
* * *
202730 CAAATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTCCAGAGCCGA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
202795 TTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGA
66 TTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGA
*
202860 CCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACATCGAAGGATAT
131 CCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
202925 TGGACTCCAGACAACG
195 TGGACTCCAGACAACG
* * *
202941 CAAGTTCAACTTCACGACTAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGGGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA-CAACAACTTCCCAATTTCAGAGCCA
*
203006 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
65 ATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
203071 ACCGCTGGTTGTCAACAATAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
130 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
203136 TGGACTCCAGATAACG
195 TGGACTCCAGACAACG
* ** * *
203152 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACGGACATTTTCCAAATTTCAAAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
203217 ATTTCAA
65 ATTTCAA
203224 AGGATATTGG
Statistics
Matches: 463, Mismatches: 27, Indels: 7
0.93 0.05 0.01
Matches are distributed among these distances:
210 135 0.29
211 227 0.49
212 101 0.22
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (210 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGA
CCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACG
Found at i:212569 original size:16 final size:17
Alignment explanation
Indices: 212548--212583 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
212538 TTACTATTCA
212548 TGTGAATAGTG-AATTT
1 TGTGAATAGTGAAATTT
212564 TGTGAATAGTGAAATTT
1 TGTGAATAGTGAAATTT
212581 TGT
1 TGT
212584 AGGCGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (17 bp):
TGTGAATAGTGAAATTT
Found at i:218172 original size:3 final size:3
Alignment explanation
Indices: 218164--218196 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
218154 ACTCATCTTT
218164 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
218197 ACTACTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:223172 original size:3 final size:3
Alignment explanation
Indices: 223164--223207 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
223154 TGAAGCATGC
*
223164 AAT AAT AAT AAT AA- AAGTT AAT AAT AAT AAT AAT AAC AAT AAT A
1 AAT AAT AAT AAT AAT AA--T AAT AAT AAT AAT AAT AAT AAT AAT A
223208 TTAACGGGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 2 0.06
3 32 0.89
5 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:227787 original size:43 final size:42
Alignment explanation
Indices: 227685--227798 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 42
227675 AGTGCTAGAA
* * * *
227685 CAAGAAATGATGAATGTTGGGGCACTTTTGAAGGTCCGTATCAT
1 CAAGAAAT-ATAAATGTTGGGGCA-TTTTGAAGGCCCATATAAT
* * * *
227729 CCATAAGTATTAATGTTGGGGCATTTTGAAGGCCCATATAAT
1 CAAGAAATATAAATGTTGGGGCATTTTGAAGGCCCATATAAT
*
227771 CAAGAAATAATAAATGTTGGGACATTTT
1 CAAGAAAT-ATAAATGTTGGGGCATTTT
227799 TTAAGGCCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
42 21 0.37
43 31 0.54
44 5 0.09
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (42 bp):
CAAGAAATATAAATGTTGGGGCATTTTGAAGGCCCATATAAT
Found at i:229088 original size:80 final size:79
Alignment explanation
Indices: 228935--229794 Score: 525
Period size: 80 Copynumber: 10.9 Consensus size: 79
228925 GAAGCTTCGA
* * * * * *
228935 CTTGACTCCGTCGTGAAGATGAGTCAATATTTCAATGTTATTCTTGATTTCCTCATGGAA-AGAA
1 CTTGACTCCCTCTTAAAGA-GAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGT-GAAGAGAA
* *
228999 TTCAATCTTTGTTATT
64 GTCAATATTTGTTATT
* * * *
229015 TTTGAATCCCTCTTAAAGTAGAGTCAATATTTCAATATTATTCTTGACTTCCTCGTGAAGAGAAG
1 CTTGACTCCCTCTTAAAG-AGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
229080 TCAATCTTTGTTATT
65 TCAATATTTGTTATT
* * * * * *
229095 CTTAACTCCCTCGTGAACATGAGTCAATCTTTCAATGTTATTCTTGACTTTCTGGTGAAGAGAAG
1 CTTGACTCCCTCTTAAAGA-GAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
229160 TTAATATTTGTTATT
65 TCAATATTTGTTATT
* **
229175 CTTGACTCCCTCATT-AAGAGGAGTCAATCTTTCAATGTTATTCTTGACCTCCTCGTTTAGAGAA
1 CTTGACTCCCTC-TTAAAGA-GAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAA
*
229239 TTCAATATTTGTTATT
64 GTCAATATTTGTTATT
** *
229255 CTTGACTTTCT-TCTAAAGAGAAGTTAATC-TT---TGTTATTCTTGACTTCCTCGT-AACGAGA
1 CTTGACTCCCTCT-TAAAGAG-AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAA-GAGA
** *
229314 AGTTGATATTTTTTATT
63 AGTCAATATTTGTTATT
* * * * *
229331 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTC----TTATTCTTGACTTCCTCATTAAGAGAAG
1 CTTGACTCCCTCTTAAAGAG-AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAG
*
229392 TCAATCTTTGTTATT
65 TCAATATTTGTTATT
* * * * * * * * * * *
229407 CTTTACTTCCTCGTGAAGATAAGTTAATCTTT---T-TTATTCCTAACTCCCTCGCGAAGAGGAG
1 CTTGACTCCCTCTTAAAGA-GAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
229468 TCAATCTTTGTTTTT
65 TCAATATTTGTTATT
* * * * * * *
229483 CTTGACTTCCTCGTAAAGAGAATTCAATC-TT---TGTTGTTCTTGACTCCCTCATGAATATG-A
1 CTTGACTCCCTCTTAAAGAG-AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGA-GAA
*
229543 GTCAATCTTTCTTTGTTATT
64 GTCAA----TATTTGTTATT
* * * * * * *
229563 CTTGACTTCCTCATGAAGAGAAGTCAATC-GT---TGTTATTCCTGAC-TCTCTC-TCCAAGAGG
1 CTTGACTCCCTCTTAAAGAG-AGTCAATCTTTCAATGTTATTCTTGACTTC-CTCGT-GAAGAGA
*
229622 AGTCAATCTTTCAATGTTATT
63 AGTCAAT-ATT---TGTTATT
* * * * * *
229643 ATTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTATTGACTTCCTCGTGAAGAGAAT
1 CTTGACTCCCTCTTAAAGAG-AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAG
* *
229708 TCAATCTTTGTCATT
65 TCAATATTTGTTATT
** ** * * * * *
229723 CTTGACTTTCTAGTGAAGAGAAGTCAATATTTCAATATTGTCATTCTTGACTTTCTCATGAA-AG
1 CTTGACTCCCTCTTAAAGAG-AGTCAATCTTTC-A-A-TGTTATTCTTGACTTCCTCGTGAAGAG
229787 AAGTCAAT
62 AAGTCAAT
229795 CTCTCAATAC
Statistics
Matches: 641, Mismatches: 102, Indels: 72
0.79 0.13 0.09
Matches are distributed among these distances:
75 4 0.01
76 207 0.32
77 7 0.01
78 1 0.00
79 11 0.02
80 347 0.54
81 4 0.01
82 10 0.02
83 22 0.03
84 25 0.04
85 3 0.00
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (79 bp):
CTTGACTCCCTCTTAAAGAGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAAGT
CAATATTTGTTATT
Found at i:229107 original size:38 final size:38
Alignment explanation
Indices: 228970--229750 Score: 651
Period size: 38 Copynumber: 19.9 Consensus size: 38
228960 AATATTTCAA
* * *
228970 TGTTATTCTTGATTTCCTCATGGAA-AGAATTCAATCTT
1 TGTTATTCTTGACTTCCTCGT-GAAGAGAAGTCAATCTT
* * * * * *
229008 TGTTATTTTTGAATCCCTCTTAAAGTAG-AGTCAATATTT
1 TGTTATTCTTGACTTCCTCGTGAAG-AGAAGTCAAT-CTT
*
229047 CAATATTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229088 TGTTATTCTTAACTCCCTCGTGAACATG-AGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATC-TT
* * * *
229127 CAATGTTATTCTTGACTTTCTGGTGAAGAGAAGTTAATATT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
229168 TGTTATTCTTGACTCCCTCATTAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* ** * *
229207 CAATGTTATTCTTGACCTCCTCGTTTAGAGAATTCAATATT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229248 TGTTATTCTTGACTTTCTTC-TAAAGAGAAGTTAATCTT
1 TGTTATTCTTGAC-TTCCTCGTGAAGAGAAGTCAATCTT
** *
229286 TGTTATTCTTGACTTCCTCGT-AACGAGAAGTTGATATT
1 TGTTATTCTTGACTTCCTCGTGAA-GAGAAGTCAATCTT
*
229324 TTTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229362 TCTTATTCTTGACTTCCTCATTAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229400 TGTTATTCTTTACTTCCTCGTGAAGATAAGTTAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * * * *
229438 TTTTATTCCTAACTCCCTCGCGAAGAGGAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229476 TGTTTTTCTTGACTTCCTCGTAAAGAGAATTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
229514 TGTTGTTCTTGACTCCCTCATGAATATG-AGTCAATCTTTCTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAA----TCTT
* *
229556 TGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCGT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229594 TGTTATTCCTGAC-TCTCTC-TCCAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTC-CTCGT-GAAGAGAAGTCAATC-TT
*
229633 CAATGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCTTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* *
229675 CAATGTTATTATTGACTTCCTCGTGAAGAGAATTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
229716 TGTCATTCTTGACTTTCTAGTGAAGAGAAGTCAAT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAAT
229751 ATTTCAATAT
Statistics
Matches: 604, Mismatches: 104, Indels: 70
0.78 0.13 0.09
Matches are distributed among these distances:
37 12 0.02
38 377 0.62
39 17 0.03
41 12 0.02
42 183 0.30
43 3 0.00
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.41
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
Found at i:229210 original size:160 final size:157
Alignment explanation
Indices: 228935--229750 Score: 686
Period size: 160 Copynumber: 5.2 Consensus size: 157
228925 GAAGCTTCGA
* *
228935 CTTGAC-TCCGTCGTGAAGATG-AGTCAATATTTCAATGTTATTCTTGA-TTTCCTCATGGAA-A
1 CTTGACTTCC-TCGTGAAGA-GAAGTCAATCTTT---TGTTATTCTTGACTTT-CTCGT-GAAGA
* * * * * * * *
228996 GAA-TTCAATCTTTGTTATTTTTGAATCCCTCTTAAAGTAG-AGTCAATATTTCAATATTATTCT
59 GAAGTT-AATATTTGTTATTCTTGACTTCCTCGTGAAG-AGAAGTCAATCTTTCAATGTTATTCT
229059 TGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
122 TGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
229095 CTTAACTCCCTCGTGAACATG-AGTCAATCTTTCAATGTTATTCTTGACTTTCTGGTGAAGAGAA
1 CTTGACTTCCTCGTGAAGA-GAAGTCAATCTTT---TGTTATTCTTGACTTTCTCGTGAAGAGAA
* * * * *
229159 GTTAATATTTGTTATTCTTGACTCCCTCATTAAGAGGAGTCAATCTTTCAATGTTATTCTTGACC
62 GTTAATATTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACT
** * *
229224 TCCTCGTTTAGAGAATTCAATATTTGTTATT
127 TCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * *
229255 CTTGACTTTCTTC-TAAAGAGAAGTTAATC-TTTGTTATTCTTGACTTCCTCGT-AACGAGAAGT
1 CTTGAC-TTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTTCTCGTGAA-GAGAAGT
* *
229317 TGATATTTTTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTC----TTATTCTTGACTTC
64 TAATATTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTTC
* *
229378 CTCATTAAGAGAAGTCAATCTTTGTTATT
129 CTCGTGAAGAGAAGTCAATCTTTGTTATT
* * * * * ** * * *
229407 CTTTACTTCCTCGTGAAGATAAGTTAATCTTTT-TTATTCCTAACTCCCTCGCGAAGAGGAGTCA
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTTCTCGTGAAGAGAAGTTA
* * * * * *
229471 ATCTTTGTTTTTCTTGACTTCCTCGTAAAGAGAATTCAATC-TT---TGTTGTTCTTGACTCCCT
66 ATATTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTTCCT
* *
229532 CATGAATATG-AGTCAATCTTTCTTTGTTATT
131 CGTGAAGA-GAAGTCAA----TCTTTGTTATT
* * * * * * *
229563 CTTGACTTCCTCATGAAGAGAAGTCAATC-GTTGTTATTCCTGACTCTCTC-TCCAAGAGGAGTC
1 CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTTCTCGT-GAAGAGAAGTT
* * *
229626 AATCTTTCAATGTTATTATTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTATTGAC
65 AAT-ATT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGAC
* *
229691 TTCCTCGTGAAGAGAATTCAATCTTTGTCATT
126 TTCCTCGTGAAGAGAAGTCAATCTTTGTTATT
* *
229723 CTTGACTTTCTAGTGAAGAGAAGTCAAT
1 CTTGACTTCCTCGTGAAGAGAAGTCAAT
229751 ATTTCAATAT
Statistics
Matches: 546, Mismatches: 81, Indels: 58
0.80 0.12 0.08
Matches are distributed among these distances:
151 7 0.01
152 140 0.26
153 6 0.01
155 4 0.01
156 131 0.24
157 2 0.00
159 8 0.01
160 208 0.38
161 13 0.02
163 1 0.00
164 26 0.05
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (157 bp):
CTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTTCTCGTGAAGAGAAGTTA
ATATTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTCAATGTTATTCTTGACTTCCT
CGTGAAGAGAAGTCAATCTTTGTTATT
Found at i:229772 original size:45 final size:45
Alignment explanation
Indices: 229715--230592 Score: 713
Period size: 45 Copynumber: 19.5 Consensus size: 45
229705 AATTCAATCT
* * * * * *
229715 TTGTCATTCTTGACTTTCTAGTGAAGAGAAGTCAATATTTCAATA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * *
229760 TTGTCATTCTTGACTTTCTCATGAA-AGAAGTCAATCTCTCAATA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
229804 CTGTCATTCTTGACTTTCTCGGGAAGAGGAGTCATTATTTCAGTG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * *
229849 TTGTC-TTCATTGACTTTCTCGTGAAGAGGATTCAATCTCTTAATG
1 TTGTCATTC-TTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
*
229894 TTG-CACTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTG
1 TTGTCA-TTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * *
229939 TTGGC-TTCCTTGATTTTCTCATGAAGATGAGTCAATCTTTTAGTG
1 TTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
229984 TTTTCATTCTTGACTTTCTC-TCAAAGAGGAGTCAGTC-TTTCGATA
1 TTGTCATTCTTGACTTTCTCGT-GAAGAGGAGTCAATCTTTTAG-TG
** * *
230029 TTGTTTTTCTTGACTTTCTCGCGAAGAAGAGTCAATCTTTTAGTG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* *** ** *
230074 TTGTCCTTCTTGACTTTCTCACAAAGAGGAGTCAATCTTTCGGTA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* ** * *
230119 TTGT-TTTCCTTGACTTTCTTATAAAGAAGAGTCAATCTTTTAGTG
1 TTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * *
230164 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAGTCTTTTGGTA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
230209 TTGT-TTTCCTTTACTTTCTCGAGAAGAGAAGTCAATCTTTTAATG
1 TTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * *
230254 TTGTCCTTCTTGACTTTATCGCGAAGAGAAGTCAATCTTTTGGTA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * *
230299 TTGT-TTTCCTTGACTTTCTCGTGAAGAGGTGTCAATATTTTAGTG
1 TTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * *** ** *
230344 TTATTC-TTGTTGAATTTTTCTCACAAAGAGGAGTCAATCTTTCGGTA
1 TT-GTCATTCTTG-A-CTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * *
230391 TTAT-TTTCCTTGACTTTCTCGTAAAGAGGAGTCAATCTTTTAGTG
1 TTGTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * ** *
230436 TTGTCCTTTTTGACGTTCCCGCGAAGAGGAGTTAATCTTTCGGTA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* *
230481 TTGGT--TTCCTTGACTTTCTCATGAAGAGGAGTCAATATTTTAGTG
1 TT-GTCATT-CTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
* *
230526 TTGTCCTTCTTGACTTTCTC-TCGAAGAGAAGTCAATCTTTTAGTG
1 TTGTCATTCTTGACTTTCTCGT-GAAGAGGAGTCAATCTTTTAGTG
*
230571 TTGTCATTTTTTGACTTTCTCG
1 TTGTCA-TTCTTGACTTTCTCG
230593 CGGAAAAGAG
Statistics
Matches: 667, Mismatches: 136, Indels: 58
0.77 0.16 0.07
Matches are distributed among these distances:
44 61 0.09
45 537 0.81
46 41 0.06
47 28 0.04
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTG
Found at i:229920 original size:90 final size:90
Alignment explanation
Indices: 229715--230565 Score: 934
Period size: 90 Copynumber: 9.4 Consensus size: 90
229705 AATTCAATCT
* * * * * ** *
229715 TTGTCATTCTTGACTTTCTAGTGAAGAGAAGTCAATATTTCAATATTGTCATT-CTTGACTTTCT
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGT-TTTCCTTGACTTTCT
* * * * * *
229779 CATGAA-AGAAGTCAATCTCTCAATA
65 CGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * * * *
229804 CTGTCATTCTTGACTTTCTCGGGAAGAGGAGTCATTATTTCAGTGTTGTCTTCATTGACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* * *
229869 GTGAAGAGGATTCAATCTCTTAATG
66 GTGAAGAGGAGTCAATCTTTTAGTG
** * ** *
229894 TTG-CACTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTTAGTGTTGGCTTCCTTGATTTTCT
1 TTGTC-CTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCT
* *
229958 CATGAAGATGAGTCAATCTTTTAGTG
65 CGTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * *
229984 TTTTCATTCTTGACTTTCTCTCAAAGAGGAGTCAGTCTTTCGATATTGTTTTTCTTGACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* *
230049 GCGAAGAAGAGTCAATCTTTTAGTG
66 GTGAAGAGGAGTCAATCTTTTAGTG
* * *
230074 TTGTCCTTCTTGACTTTCTCACAAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTT
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* * *
230139 ATAAAGAAGAGTCAATCTTTTAGTG
66 GTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
230164 TTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAGTCTTTTGGTATTGTTTTCCTTTACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* * *
230229 GAGAAGAGAAGTCAATCTTTTAATG
66 GTGAAGAGGAGTCAATCTTTTAGTG
* * *
230254 TTGTCCTTCTTGACTTTATCGCGAAGAGAAGTCAATCTTTTGGTATTGTTTTCCTTGACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* *
230319 GTGAAGAGGTGTCAATATTTTAGTG
66 GTGAAGAGGAGTCAATCTTTTAGTG
* * * * * * *
230344 TTATTCTTGTTGAATTTTTCTCACAAAGAGGAGTCAATCTTTCGGTATTATTTTCCTTGACTTTC
1 TTGTCCTTCTTG-A-CTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTC
*
230409 TCGTAAAGAGGAGTCAATCTTTTAGTG
64 TCGTGAAGAGGAGTCAATCTTTTAGTG
* * * * *
230436 TTGTCCTTTTTGACGTTCCCGCGAAGAGGAGTTAATCTTTCGGTATTGGTTTCCTTGACTTTCTC
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
* *
230501 ATGAAGAGGAGTCAATATTTTAGTG
66 GTGAAGAGGAGTCAATCTTTTAGTG
* *
230526 TTGTCCTTCTTGACTTTCTCTCGAAGAGAAGTCAATCTTT
1 TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTT
230566 TAGTGTTGTC
Statistics
Matches: 644, Mismatches: 112, Indels: 11
0.84 0.15 0.01
Matches are distributed among these distances:
88 2 0.00
89 58 0.09
90 505 0.78
91 3 0.00
92 76 0.12
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (90 bp):
TTGTCCTTCTTGACTTTCTCGCGAAGAGGAGTCAATCTTTCGGTATTGTTTTCCTTGACTTTCTC
GTGAAGAGGAGTCAATCTTTTAGTG
Found at i:231448 original size:133 final size:133
Alignment explanation
Indices: 230977--231431 Score: 669
Period size: 133 Copynumber: 3.4 Consensus size: 133
230967 AATGTTTAAT
* * * *
230977 TTTCAGATTCAGTCTTCCTAAATAGCAGTGAAGCAAATTGATTCTGATTCAATCTTCCCTTAATA
1 TTTCAGATTCAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* * * *
231042 GCAATGAAGTGAATCAAGTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGAGA-ATATTCTT
66 ACAGTGAAATGAATCAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGA-ACATATTCTT
231106 CTTC
130 CTTC
* * * * *
231110 TTTCAGATTCGGTCTTTCTTAAGAACAGTGAAGAAAATCGATTCTGATTCAATCTTCCCTGAAGA
1 TTTCAGATTCAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* * *
231175 ACAGTGAAATGAATCAAGTTTTCTCGATTCTGATCTCCCCTAAAGAGTAGTGGAGCAAATTCTTC
66 ACAGTGAAATGAATCAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATTCTTC
231240 TTC
131 TTC
* * *
231243 TTTCAGATTCAGTCTTCCTAAAGAGAAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGA
1 TTTCAGATTCAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
* *
231308 ACAGTGAAATGAATAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATTATTC
66 ACAGTGAAATGAATCAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATTCTTC
231373 TTC
131 TTC
* * * *
231376 TTTCAGATTTAGTCTTCATGAAGAGCACTGAAGCAAATCGATTCTGATTCAATCTT
1 TTTCAGATTCAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTT
231432 ACTTGAATAG
Statistics
Matches: 285, Mismatches: 36, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
133 285 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (133 bp):
TTTCAGATTCAGTCTTCCTAAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGA
ACAGTGAAATGAATCAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATTCTTC
TTC
Found at i:231498 original size:41 final size:41
Alignment explanation
Indices: 231394--231490 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
231384 TTAGTCTTCA
* * *
231394 TGAAGAGCACTGAAGCAAATCGATTCTGATTCAATCTTACT
1 TGAAGAGCACTGAAGCAAATCAATTCTGATTAAATCTTACC
* * *
231435 TGAATAGCAGTGAAGCAAATCAATTCTGATTAAATCTTCCC
1 TGAAGAGCACTGAAGCAAATCAATTCTGATTAAATCTTACC
*
231476 TGAAGAGCATTGAAG
1 TGAAGAGCACTGAAG
231491 TAGATCAAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
TGAAGAGCACTGAAGCAAATCAATTCTGATTAAATCTTACC
Found at i:231624 original size:175 final size:173
Alignment explanation
Indices: 231249--231624 Score: 515
Period size: 175 Copynumber: 2.2 Consensus size: 173
231239 CTTCTTTCAG
* *
231249 ATTCAGTCTTCCTAAAGAGAAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAACAGTG
1 ATTCAATCTTCCTAATGAGAAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAACAGTG
* *
231314 AAATGAATAAAGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAACATATTATTCTTCTTT
66 AAATGAATAAAGTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGAACAGATTATTCTTCTTT
* * **
231379 CAGATTTAGTCTTCATGAAGAGCACTGAAGCAAATCGATTCTG
131 CAGATGTAGTATTCATGAAGAGCACTGAAGCAAATCGATTCCA
* * * *
231422 ATTCAATCTTACTTGAAT-AGCAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAGCAT
1 ATTCAATCTT-CCT-AATGAGAAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAACAG
* *
231486 TGAAGT-AGATCAAAGTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGAGA-AGATTCTTCT
64 TGAAATGA-AT-AAAGTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGA-ACAGATTATTCT
* * * *
231549 TCTTTCAGATGTGGTATTCTTGAAGTGCAGTGAAGCAAATCGATTCCA
126 TCTTTCAGATGTAGTATTCATGAAGAGCACTGAAGCAAATCGATTCCA
231597 ATTCAATCTTCCCTAATGAGAAGTGAAG
1 ATTCAATCTT-CCTAATGAGAAGTGAAG
231625 TGGATCAAAG
Statistics
Matches: 176, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
173 10 0.06
174 55 0.31
175 110 0.62
176 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (173 bp):
ATTCAATCTTCCTAATGAGAAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAACAGTG
AAATGAATAAAGTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGAACAGATTATTCTTCTTT
CAGATGTAGTATTCATGAAGAGCACTGAAGCAAATCGATTCCA
Found at i:231679 original size:134 final size:134
Alignment explanation
Indices: 231435--232130 Score: 952
Period size: 134 Copynumber: 5.2 Consensus size: 134
231425 CAATCTTACT
* * * * * *
231435 TGAATAGCAGTGAAGCAAATCAATTCTGATTAAATCTTCCCTGAAGAGCATTGAAGTAGATCAAA
1 TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAA
* * * * *
231500 GTTTTCTCGAGTCTAATCTCCCCTAAAGAGTAGTGGAGAAGATTCTTCTTCTTTCAGATGTGGTA
66 GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTC
*
231565 TTCT
131 TTCC
* **
231569 TGAAGTGCAGTGAAGCAAATCGATTCCAATTCAATCTTCCCT-AATGAGAAGTGAAGTGGATCAA
1 TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAA-GAGAAGTGAAGTGGATCAA
231633 AGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATA---TTCTTCTTTCAGATTTGGT
65 AGTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGT
231695 CTTCC
130 CTTCC
* * * * * * *
231700 TGAAGAGTAGTGAAGCAAATCGATTTTGATTCGATATTCCCTAAAGAGAAATGAAGTGAATC-AA
1 TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAA
* * * * * *
231764 GTTTTATCGAGTTTGATCTTCCCTAAAGAGTAGTGAAGCATATTCTTTTTCTTTCAGATTTGGTA
66 GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTC
231829 TTCC
131 TTCC
* *
231833 TGAAGAGCAGTGAAGCAAATCGATTCTAATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATCAAA
1 TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAA
* * * *
231898 GTTTTCTCGAGTCCGATCTTCCCTAAAGAGTAATGGAACATATTCTTCTTCTTCTTTCAGATTTG
66 GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATA---TTCTTCTTCTTTCAGATTTG
231963 GTCTTCC
128 GTCTTCC
* * *
231970 TGAAGAGCAGTGAAGCAAATCGATTATGATTCAATCTTCCCTGAAGAGCAGTAAAGTGGATCAAA
1 TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAA
* *
232035 GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTTTTCTTCTTCCAGATTTGGTC
66 GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTC
232100 TTCC
131 TTCC
*
232104 TTGAAGAGCATTGAAGCAAATCGATTC
1 -TGAAGAGCAGTGAAGCAAATCGATTC
232131 ACTTGAATCA
Statistics
Matches: 493, Mismatches: 59, Indels: 19
0.86 0.10 0.03
Matches are distributed among these distances:
130 40 0.08
131 71 0.14
132 2 0.00
133 77 0.16
134 155 0.31
135 24 0.05
137 124 0.25
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (134 bp):
TGAAGAGCAGTGAAGCAAATCGATTCTGATTCAATCTTCCCTGAAGAGAAGTGAAGTGGATCAAA
GTTTTCTCGAGTCTGATCTCCCCTAAAGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTC
TTCC
Found at i:231801 original size:46 final size:43
Alignment explanation
Indices: 231602--231801 Score: 115
Period size: 46 Copynumber: 4.5 Consensus size: 43
231592 TTCCAATTCA
* * * *
231602 ATCTTCCCTAATGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTG
1 ATCTTCCCTAAAGAGTAGTGAAGTGAATC---GTTTT-TCGAGTTTG
* * *
231649 ATCTCCCCTAAAGAGTAGTGGAGCAT-ATTC-TTCTTTC-AGATTTG
1 ATCTTCCCTAAAGAGTAGTGAAG--TGAATCGTT-TTTCGAG-TTTG
* * ** * *
231693 GTCTT-CCTGAAGAGTAGTGAAGCAAATCGATTTT-GA-TTCG
1 ATCTTCCCTAAAGAGTAGTGAAGTGAATCGTTTTTCGAGTTTG
* * *
231733 ATATTCCCTAAAGAGAAATGAAGTGAATCAAGTTTTATCGAGTTTG
1 ATCTTCCCTAAAGAGTAGTGAAGTGAATC--GTTTT-TCGAGTTTG
231779 ATCTTCCCTAAAGAGTAGTGAAG
1 ATCTTCCCTAAAGAGTAGTGAAG
231802 CATATTCTTT
Statistics
Matches: 113, Mismatches: 27, Indels: 27
0.68 0.16 0.16
Matches are distributed among these distances:
40 6 0.05
41 18 0.16
42 7 0.06
43 22 0.19
44 11 0.10
45 4 0.04
46 23 0.20
47 19 0.17
48 2 0.02
49 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (43 bp):
ATCTTCCCTAAAGAGTAGTGAAGTGAATCGTTTTTCGAGTTTG
Found at i:232328 original size:3 final size:3
Alignment explanation
Indices: 232320--232349 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
232310 GGCCTGTCTT
232320 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
232350 ACTACTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:246834 original size:27 final size:27
Alignment explanation
Indices: 246796--246854 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
246786 AGTAATAGAA
*
246796 TCCACCTCTGGCTTATGTATTCATTGG
1 TCCACCTCTGGCTTATGTATTCATCGG
246823 TCCACCTCTGGCTTATGTATTCATCGG
1 TCCACCTCTGGCTTATGTATTCATCGG
246850 TCCAC
1 TCCAC
246855 ATACATCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.15, C:0.31, G:0.17, T:0.37
Consensus pattern (27 bp):
TCCACCTCTGGCTTATGTATTCATCGG
Found at i:250168 original size:77 final size:79
Alignment explanation
Indices: 250081--250227 Score: 194
Period size: 77 Copynumber: 1.9 Consensus size: 79
250071 TTAATAAATT
**
250081 TCTTATTTAATTAATTC-AAATTAAATAT-ACATT-AAAGACTTATAATCTGAATTACAATCTTT
1 TCTTATTTAATT-ATTCTAAATTAAATATCA-ATTAAAAGACTTATAATCAAAATTACAATCTTT
250143 -AATGTTTATTTAAAA
64 CAATGTTTATTTAAAA
* * * *
250158 TCTTATTTAATTATTCTGAATTAAATATCAATTAAAAGAGTTGTAATCAAAATTACATTCTTTCA
1 TCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTTCA
250223 ATGTT
66 ATGTT
250228 ACTTACTATA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
76 4 0.07
77 25 0.42
78 25 0.42
79 6 0.10
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (79 bp):
TCTTATTTAATTATTCTAAATTAAATATCAATTAAAAGACTTATAATCAAAATTACAATCTTTCA
ATGTTTATTTAAAA
Found at i:259097 original size:43 final size:43
Alignment explanation
Indices: 259071--259197 Score: 227
Period size: 43 Copynumber: 3.0 Consensus size: 43
259061 ATTAGAAATG
* *
259071 CCTCTATAAAAACTGACCTGTTGTGGCGTTAGTATAAAAAACA
1 CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
259114 CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
1 CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
*
259157 CCTCTATAGAACCTGACCTGTTGTGGCGTTTGTATAAAAAA
1 CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAA
259198 TAATGCTATA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 81 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (43 bp):
CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
Found at i:259207 original size:43 final size:43
Alignment explanation
Indices: 259071--259239 Score: 223
Period size: 43 Copynumber: 3.9 Consensus size: 43
259061 ATTAGAAATG
*
259071 CCTCTATAAAAACTGACCTGTTGTGGCGTTAGTATAAAAAACA
1 CCTCTATAAAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
*
259114 CCTCTATAGAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
1 CCTCTATAAAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
* * *
259157 CCTCTATAGAACCTGACCTGTTGTGGCGTTTGTATAAAAAATA
1 CCTCTATAAAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
* * * * * *
259200 -ATGCTATAAAACCTAACTTGTTGTGACATTTGTATAAAAA
1 CCT-CTATAAAACCTGACCTGTTGTGGCGTTAGTATAAAAA
259240 TGCCGCTATA
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
42 1 0.01
43 114 0.99
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (43 bp):
CCTCTATAAAACCTGACCTGTTGTGGCGTTAGTATAAAAAACA
Found at i:266307 original size:20 final size:20
Alignment explanation
Indices: 266274--266312 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
266264 TTTTTATATT
* *
266274 AAGATCAAATTACGTTTTAA
1 AAGATAAAAATACGTTTTAA
266294 AAGATAAAAATACGTTTTA
1 AAGATAAAAATACGTTTTA
266313 TGCTACTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (20 bp):
AAGATAAAAATACGTTTTAA
Found at i:270171 original size:43 final size:43
Alignment explanation
Indices: 270120--270327 Score: 188
Period size: 43 Copynumber: 4.8 Consensus size: 43
270110 CGTTTGTTGC
* * *
270120 AAACGCCGCAAAAGGTATAGATATTTAGCGGCGTTTGGCAGAA
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAGAA
* *
270163 AAACGCCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAGAA
* * ** ** *
270206 AAACGCCGCAATAGGTGTTGATTTTTACCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAGAA
* * * *
270249 AAACGCCGCAGA-AGATGTTGATATTTGGCGGCGTTTTCGTC-G-C
1 AAACGCCGCA-ATAGGTGTTGATATTTAGCGGCG-TTT-GGCAGAA
* * * *
270292 AAACGCCGCAATATGTCTTGAGATTTCGCGGCGTTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
270328 TTATCACAAA
Statistics
Matches: 138, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
42 4 0.03
43 128 0.93
44 4 0.03
45 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGGCAGAA
Found at i:270253 original size:86 final size:86
Alignment explanation
Indices: 270163--270343 Score: 208
Period size: 86 Copynumber: 2.1 Consensus size: 86
270153 TTTGGCAGAA
* *
270163 AAACGCCGCA-ATAGGTGTTGATATTTAGCGGC-ATTT-GGCAGACAAACGCCGCAATAGGTGTT
1 AAACGCCGCAGA-AGATGTTGATATTTAGCGGCGATTTCGGC-G-CAAACGCCGCAATAGGTCTT
** *
270225 GATTTTTAC-CGGCGTTTTTCCCAC
63 GAGATTT-CGCGGCGTTTTTACCAC
* * * *
270249 AAACGCCGCAGAAGATGTTGATATTTGGCGGCGTTTTCGTCGCAAACGCCGCAATATGTCTTGAG
1 AAACGCCGCAGAAGATGTTGATATTTAGCGGCGATTTCGGCGCAAACGCCGCAATAGGTCTTGAG
*
270314 ATTTCGCGGCGTTTTTATCAC
66 ATTTCGCGGCGTTTTTACCAC
270335 AAACGCCGC
1 AAACGCCGC
270344 TAAATGTATG
Statistics
Matches: 81, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
85 1 0.01
86 73 0.90
87 5 0.06
88 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (86 bp):
AAACGCCGCAGAAGATGTTGATATTTAGCGGCGATTTCGGCGCAAACGCCGCAATAGGTCTTGAG
ATTTCGCGGCGTTTTTACCAC
Found at i:270736 original size:21 final size:21
Alignment explanation
Indices: 270712--270782 Score: 115
Period size: 21 Copynumber: 3.4 Consensus size: 21
270702 GATATATTAT
*
270712 TTCTCTCTGTGCTGTCGCTGC
1 TTCTCTCTGTGCTGCCGCTGC
270733 TTCTCTCTGTGCTGCCGCTGC
1 TTCTCTCTGTGCTGCCGCTGC
* *
270754 CTCTCTCTGTGCTGCCACTGC
1 TTCTCTCTGTGCTGCCGCTGC
270775 TTCTCTCT
1 TTCTCTCT
270783 CTGTTTCCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.01, C:0.38, G:0.20, T:0.41
Consensus pattern (21 bp):
TTCTCTCTGTGCTGCCGCTGC
Found at i:270796 original size:21 final size:21
Alignment explanation
Indices: 270772--270838 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
270762 GTGCTGCCAC
* *
270772 TGCTTCTCTCTCTGTTTCCGT
1 TGCTGCTCTCTCTGCTTCCGT
** * *
270793 TGCTGCTCTAGCTGCTTCTGC
1 TGCTGCTCTCTCTGCTTCCGT
*
270814 TGCTGCTCTCTCTGCTTCCCT
1 TGCTGCTCTCTCTGCTTCCGT
270835 TGCT
1 TGCT
270839 TCATTTTCCG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.01, C:0.36, G:0.18, T:0.45
Consensus pattern (21 bp):
TGCTGCTCTCTCTGCTTCCGT
Found at i:280461 original size:83 final size:80
Alignment explanation
Indices: 280334--280542 Score: 251
Period size: 82 Copynumber: 2.5 Consensus size: 80
280324 TAGTACATGT
* * * *
280334 TTTTGTGGCGTTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGCGGCGTTTGTAGGA-AAAT
1 TTTTGCGGCGTTTTTAGAAAA-CGCCACTATAAAC-AACTATATTGCGGCGTTTATA-GACAAA-
*
280397 CGCCGCTAAATTATTACTC
62 CGCCGCTAAATTACTACTC
* *
280416 TTTTGCGGCGTTTTTAGCATAAACGCCACTATAAACAACTCTATTGCGGCGTTTATATACAAACG
1 TTTTGCGGCGTTTTTAG-A-AAACGCCACTATAAACAACTATATTGCGGCGTTTATAGACAAACG
280481 CCGCTAAATTACTACTC
64 CCGCTAAATTACTACTC
* *
280498 TATTGCGGTGTTTTTTTAGAAAACGCCACTATAAACAACTATATT
1 TTTTGCGGCG--TTTTTAGAAAACGCCACTATAAACAACTATATT
280543 CTGGCATTTG
Statistics
Matches: 111, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
82 69 0.62
83 32 0.29
84 10 0.09
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (80 bp):
TTTTGCGGCGTTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTATAGACAAACGCC
GCTAAATTACTACTC
Found at i:280464 original size:41 final size:39
Alignment explanation
Indices: 280340--280542 Score: 142
Period size: 41 Copynumber: 4.9 Consensus size: 39
280330 ATGTTTTTGT
* * *
280340 GGCGTTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGC
1 GGCGTTTTTAGAAAA-CGCCACTATAAAC-AACTCTATTGC
* * ** *
280380 GGCGTTTGTAGGAAAATCGCCGCTA-AATTATTACTCTTTTGC
1 GGCGTTTTTA-GAAAA-CGCCACTATAA--ACAACTCTATTGC
280422 GGCGTTTTTAGCATAAACGCCACTATAAACAACTCTATTGC
1 GGCGTTTTTAG-A-AAACGCCACTATAAACAACTCTATTGC
* * * *
280463 GGCGTTTATATACAAACGCCGCTA-AATTACTACTCTATTGC
1 GGCGTTTTTAGA-AAACGCCACTATAA--ACAACTCTATTGC
* *
280504 GGTGTTTTTTTAGAAAACGCCACTATAAACAACTATATT
1 GGCG--TTTTTAGAAAACGCCACTATAAACAACTCTATT
280543 CTGGCATTTG
Statistics
Matches: 126, Mismatches: 25, Indels: 23
0.72 0.14 0.13
Matches are distributed among these distances:
39 2 0.02
40 21 0.17
41 57 0.45
42 33 0.26
43 13 0.10
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (39 bp):
GGCGTTTTTAGAAAACGCCACTATAAACAACTCTATTGC
Found at i:280604 original size:83 final size:82
Alignment explanation
Indices: 280436--280607 Score: 193
Period size: 83 Copynumber: 2.1 Consensus size: 82
280426 TTTTTAGCAT
* * * * *
280436 AAACGCCACTATAAACAACTCTATTGCGGCGTTTATATACAAACGCCGCTAAATTACTACTCTAT
1 AAACGCCACTATAAACAACTATATTGCGGCATTTAGATACAAACGCCGCTAAATTACCACCCTAT
* ** * * *
280501 TGCGGTGTTTTTTTAGA
66 TGCAGCATTTGTTGAAA
* * *
280518 AAACGCCACTATAAACAACTATATT-CTGGCATTTGAGCTATAAACGCCGCTAACTTACCACCCT
1 AAACGCCACTATAAACAACTATATTGC-GGCATTT-AGATACAAACGCCGCTAAATTACCACCCT
280582 ATTGCAGCATTTGTTGAAA
64 ATTGCAGCATTTGTTGAAA
280601 AAACGCC
1 AAACGCC
280608 GCTAAAGTTT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
81 1 0.01
82 30 0.41
83 43 0.58
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (82 bp):
AAACGCCACTATAAACAACTATATTGCGGCATTTAGATACAAACGCCGCTAAATTACCACCCTAT
TGCAGCATTTGTTGAAA
Found at i:282005 original size:12 final size:14
Alignment explanation
Indices: 281981--282013 Score: 52
Period size: 12 Copynumber: 2.5 Consensus size: 14
281971 ACTTGATTAG
281981 AGAAAGAGAAAGAA
1 AGAAAGAGAAAGAA
281995 A-AAAG-GAAAGAA
1 AGAAAGAGAAAGAA
282007 AGAAAGA
1 AGAAAGA
282014 AACTTGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
12 8 0.47
13 8 0.47
14 1 0.06
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AGAAAGAGAAAGAA
Done.