Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006519.1 Hibiscus syriacus cultivar Beakdansim tig00015884_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: 87583
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4399 original size:13 final size:14
Alignment explanation
Indices: 4376--4422 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4366 AATTAAACCA
4376 TAAACCATGAATCC
1 TAAACCATGAATCC
4390 TAAA-CATGAATCC
1 TAAACCATGAATCC
* * *
4403 TAAATCATAAACCC
1 TAAACCATGAATCC
4417 TAAACC
1 TAAACC
4423 CTAAACTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.47, C:0.28, G:0.04, T:0.21
Consensus pattern (14 bp):
TAAACCATGAATCC
Found at i:4426 original size:34 final size:34
Alignment explanation
Indices: 4369--4459 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 34
4359 GTGTATAAAT
* * * *
4369 TAAACCATAAACCATGAATCCTAAAC-ATGAATCC
1 TAAAACATAAACCATAAACCCTAAACTAT-AACCC
* *
4403 TAAATCATAAACCCTAAACCCTAAACTATAACCC
1 TAAAACATAAACCATAAACCCTAAACTATAACCC
* *
4437 TAAAACCTAAATCATAAACCCTA
1 TAAAACATAAACCATAAACCCTA
4460 TCATATAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 45 0.96
35 2 0.04
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (34 bp):
TAAAACATAAACCATAAACCCTAAACTATAACCC
Found at i:4427 original size:21 final size:21
Alignment explanation
Indices: 4401--4459 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
4391 AAACATGAAT
*
4401 CCTAAATCATAAACCCTAAAC
1 CCTAAATCATAAACCCTAAAA
4422 CCTAAA-C-TATAACCCTAAAA
1 CCTAAATCATA-AACCCTAAAA
4442 CCTAAATCATAAACCCTA
1 CCTAAATCATAAACCCTA
4460 TCATATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 2 0.06
20 16 0.47
21 14 0.41
22 2 0.06
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
CCTAAATCATAAACCCTAAAA
Found at i:4563 original size:14 final size:14
Alignment explanation
Indices: 4528--4564 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
4518 TAAAATTTTA
4528 TAATTATTAATAATG
1 TAATT-TTAATAATG
4543 T-ATTTTAATAATG
1 TAATTTTAATAATG
4556 TAATTTTAA
1 TAATTTTAA
4565 AAATCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 10 0.48
15 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (14 bp):
TAATTTTAATAATG
Found at i:6027 original size:61 final size:61
Alignment explanation
Indices: 5956--6096 Score: 180
Period size: 61 Copynumber: 2.4 Consensus size: 61
5946 AATCATGTGA
* * * * *
5956 CCATTCTGTAACTTTTAATAGTCGAGTAACTCAACAAAATGACTCTCTATAGCCGGGGGGT
1 CCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGGGAT
* * **
6017 CCATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAATAAGTCCCTATAGTTGGGGGAT
1 CCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGGGAT
6078 ---TTTTGTAACTTTTAATAGT
1 CCATTTTGTAACTTTTAATAGT
6097 TGGGAGATTC
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
58 19 0.27
61 52 0.73
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (61 bp):
CCATTTTGTAACTTTTAATAGTCGAATAACTCAACAAAATAACTCCCTATAGCCGGGGGAT
Found at i:9931 original size:51 final size:51
Alignment explanation
Indices: 9876--9983 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
9866 GGCTATATCG
* * * *
9876 ATATTTATTTATAAATTTGATATGAATATAAAATAATACCTAATTATATAA
1 ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
* *
9927 ATATTTATTTATAAATCTGTTATAAATATAAAATAATAACTAACTATATCA
1 ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
9978 ATATTT
1 ATATTT
9984 GAATCGTAAG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (51 bp):
ATATTTATTTATAAATCTGATATAAATATAAAATAATAACTAACTATATAA
Found at i:10923 original size:20 final size:19
Alignment explanation
Indices: 10900--10946 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
10890 CGATATACCA
10900 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
10920 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
10940 GGTAAAA
1 GGTAAAA
10947 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:11018 original size:162 final size:161
Alignment explanation
Indices: 10710--11034 Score: 465
Period size: 162 Copynumber: 2.0 Consensus size: 161
10700 ATCCAAATTA
* * **
10710 AAAATGTGTCGATCCAAAAACGATATAACAGGTAAACTATGACAAAACCGGTTGAAATGATAAAA
1 AAAATGTATCGATCCAAAAACGATATAACAGGTAAAATATGACAAAACCGGTCAAAATGATAAAA
* * * *
10775 CCGGTAAAGCGCTATCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTG
66 CCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTG
* *
10840 AATTTAAAATAGAAGCAGTTTTAAATCCTAT
131 AATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
* *
10871 AAAATGTATCGATCC-AAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAATGTATCGATCCAAAAACGATATAACAGGT-AAAATATGACAAAACCGGT--CAAAATGATA
* * *
10935 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
63 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
10999 GTGAATTTAAAAGAGAAGCAGTTTTAGAGCCTAT
128 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
11033 AA
1 AA
11035 TGTGTCGATA
Statistics
Matches: 145, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
160 16 0.11
161 31 0.21
162 51 0.35
163 47 0.32
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (161 bp):
AAAATGTATCGATCCAAAAACGATATAACAGGTAAAATATGACAAAACCGGTCAAAATGATAAAA
CCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTG
AATTTAAAAGAGAAGCAGTTTTAAAGCCTAT
Found at i:11103 original size:20 final size:19
Alignment explanation
Indices: 11080--11126 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
11070 CGATATAACA
11080 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
11100 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
11120 GGTAAAA
1 GGTAAAA
11127 TGATACCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:11128 original size:17 final size:19
Alignment explanation
Indices: 11089--11131 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
11079 AGGTAAAAAT
11089 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
11109 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
11126 ATGATA
1 ATGATA
11132 CCAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:13353 original size:21 final size:21
Alignment explanation
Indices: 13329--13393 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
13319 AAGACAATCA
*
13329 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
13350 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
13371 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
13392 AG
1 AG
13394 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:14667 original size:4 final size:4
Alignment explanation
Indices: 14658--14682 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
14648 GCTAAGATTG
14658 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
14683 AAAGGACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:15279 original size:19 final size:19
Alignment explanation
Indices: 15257--15305 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
15247 AATGTAGGGT
15257 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
15276 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
15295 TAATTTTGTAT
1 TAATTTTGTAT
15306 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:15884 original size:201 final size:200
Alignment explanation
Indices: 15415--16747 Score: 1869
Period size: 200 Copynumber: 6.8 Consensus size: 200
15405 AATTTACAAT
* * * *
15415 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
15480 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
15545 ATGAGAGAATAGGCCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
15610 AATGA
196 AATGA
*
15615 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
15680 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
15745 ATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACAC-TTTTTTAGTTTGTGTCGATATTTTTGGTCCA
15810 GAATGA
195 GAATGA
* *
15816 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCTATATATAAAAAGTGTCGATTCCATAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
15881 CGAAACCCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
15946 ATGAGAGAATAGGTCTAAATAATGTGTTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
*
16011 AATAA
196 AATGA
* *
16016 ATGGCAAACA-GGTGCAACAGTAAAGTGT-GATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
16079 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGATTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
16144 ATGAGATAATAGGTCTAAATAATGTGTCGACATTTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACA-CTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
16209 GAATGA
195 GAATGA
* * *
16215 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCC---CAT--AAA-TATCGAAACCC--AAA-A
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCG-ATCCCATAAACA
* * * * * * * **** **
16271 --G-TA---TAATGTA-ATATGTAATTTTTCAA--TCT-AACCGGTACATATATACCGGT-T---
65 TCGAAACCCAAAAGTATA-ATGTAATATGT-AATTTTTCAATC--TA-ACCGGTACAAGTATACC
*
16322 ----TTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTG
125 GGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTG
*
16383 GTCCATAATGA
190 GTCCAGAATGA
*
16394 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
16459 CGAAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGT-TACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
16522 ATGAGATAATAGGTCTAAATAATGTGTCGACAC-TTTTT--TTAGTGTCGATATTTTTAGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
16584 AAT-A
196 AATGA
**
16588 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* *
16653 CGAAACCCATAAGTAT--TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
16716 ATGAGAGAATTGGTATATAAT-ATGTATCGACA
131 ATGAGAGAATAGGTCTA-AATAATGTGTCGACA
16748 TTGTTTAATG
Statistics
Matches: 1013, Mismatches: 81, Indels: 84
0.86 0.07 0.07
Matches are distributed among these distances:
179 70 0.07
180 33 0.03
182 2 0.00
184 7 0.01
185 7 0.01
186 6 0.01
187 18 0.02
188 8 0.01
189 1 0.00
190 2 0.00
191 10 0.01
192 16 0.02
193 39 0.04
194 111 0.11
195 37 0.04
196 7 0.01
197 4 0.00
198 160 0.16
199 61 0.06
200 216 0.21
201 198 0.20
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:16233 original size:399 final size:400
Alignment explanation
Indices: 15415--16747 Score: 2172
Period size: 378 Copynumber: 3.4 Consensus size: 400
15405 AATTTACAAT
* *
15415 ATGGAAAACAGGGTGCAACCATAAAGTGTCGATTCATATATAAAAAGTGTCGATCCCAAAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATT-ATATATAAAAAGTGTCGATCCCATAAACAT
* *
15480 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
* * *
15545 ATGAGAGAATAGGCCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
130 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
15610 AATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTA
195 AATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTA
15675 AACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
260 AACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
15740 GTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTG
325 GTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTG
15805 GTCCAGAATGA
390 GTCCAGAATGA
* *
15816 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCTATATATAAAAAGTGTCGATTCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGAT-TATATATAAAAAGTGTCGATCCCATAAACAT
*
15881 CGAAACCCAAAAGTATAATGTAATATATAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
*
15946 ATGAGAGAATAGGTCTAAATAATGTGTTGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
130 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
* *
16011 AATAAATGGCAAACA-GGTGCAACAGTAAAGTGT-GATCCATATATAAAAAGTGTCGATCCCGTA
195 AATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTA
16074 AACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
260 AACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCG
* *
16139 ATTTTATGAGATAATAGGTCTAAATAATGTGTCGACATTTTTTTTAGTTTGTGTCGATATTTTTG
325 GTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTG
16204 GTCCAGAATGA
390 GTCCAGAATGA
*
16215 ATGGCAAACAGGGTGCAA-C---------CG--------T--AAAGTGTCGATCCCATAAATATC
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATTATATATAAAAAGTGTCGATCCCATAAACATC
*
16260 GAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACATATATACCGGTTTTA
66 GAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTA
16325 TGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATA
131 TGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATA
16390 ATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAA
196 ATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAA
16455 ACATCGAAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGT-TACCGG
261 ACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG
*
16518 TTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTA----GTGTCGATATTTTTAG
326 TTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGG
16579 TCCAGAAT-A
391 TCCAGAATGA
* *
16588 ATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGAT-TATATATAAAAAGTGTCGATCCCATAAACAT
* * *
16653 CGAAACCCATAAGTAT--TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
65 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
* * *
16716 ATGAGAGAATTGGTATATAAT-ATGTATCGACA
130 ATGAGAGAATAGGTCTA-AATAATGTGTCGACA
16748 TTGTTTAATG
Statistics
Matches: 873, Mismatches: 34, Indels: 59
0.90 0.04 0.06
Matches are distributed among these distances:
373 19 0.02
374 23 0.03
378 210 0.24
379 62 0.07
380 44 0.05
383 2 0.00
389 2 0.00
392 70 0.08
393 3 0.00
394 36 0.04
398 1 0.00
399 187 0.21
400 17 0.02
401 196 0.22
402 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATTATATATAAAAAGTGTCGATCCCATAAACATC
GAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTA
TGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCATA
ATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAA
ACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG
TTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGTTTGTGTCGATATTTTTGG
TCCAGAATGA
Found at i:16634 original size:194 final size:198
Alignment explanation
Indices: 16237--16747 Score: 813
Period size: 194 Copynumber: 2.6 Consensus size: 198
16227 GTGCAACCGT
*
16237 AAAGTGTCGATCCCATAAATATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCC-AAAGTATAATGTAATATGTAATTTTTCAATCTAA
16302 CCGGTACATA-TATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGT
65 CCGGTACA-AGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTA-T
* * * **
16366 TTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCAT
128 TAGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCAT
16431 ATATAA
193 ATATAA
*
16437 AAAGTGTCGATCCCGTAAACATCGAAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
*
16502 CGGTACAAGT-TACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTT-T-TTAG
66 CGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTATTAG
16564 TGTCGATATTTTTAGTCCAGAAT-AATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATA
131 TGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATA
16628 TAA
196 TAA
*
16631 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTAT--TGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCA-AAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
16694 CCGGTACAAGTATACCGGTTTTATGAGAGAATTGGTATATAAT-ATGTATCGACA
65 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTGTCGACA
16748 TTGTTTAATG
Statistics
Matches: 293, Mismatches: 14, Indels: 14
0.91 0.04 0.04
Matches are distributed among these distances:
193 35 0.12
194 106 0.36
195 33 0.11
197 1 0.00
198 47 0.16
199 43 0.15
200 28 0.10
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (198 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAGTATAATGTAATATGTAATTTTTCAATCTAAC
CGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTATTAG
TGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATATA
TAA
Found at i:18745 original size:23 final size:23
Alignment explanation
Indices: 18719--18783 Score: 103
Period size: 23 Copynumber: 2.8 Consensus size: 23
18709 AAATATGATG
*
18719 TAATAGGTAGCGCTTATATAATA
1 TAATAGGTAGTGCTTATATAATA
* *
18742 TAATAGGTAGTGTTTATATAATG
1 TAATAGGTAGTGCTTATATAATA
18765 TAATAGGTAGTGCTTATAT
1 TAATAGGTAGTGCTTATAT
18784 TGTAAAGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.40
Consensus pattern (23 bp):
TAATAGGTAGTGCTTATATAATA
Found at i:18787 original size:21 final size:22
Alignment explanation
Indices: 18711--18788 Score: 95
Period size: 23 Copynumber: 3.5 Consensus size: 22
18701 ATAGGTAAAA
*
18711 ATATGATGTAATAGGTAGCGCTT
1 ATAT-ATGTAATAGGTAGTGCTT
* *
18734 ATATAATATAATAGGTAGTGTTT
1 ATAT-ATGTAATAGGTAGTGCTT
18757 ATATAATGTAATAGGTAGTGCTT
1 ATAT-ATGTAATAGGTAGTGCTT
18780 ATAT-TGTAA
1 ATATATGTAA
18789 AGTATATATC
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 5 0.10
23 44 0.90
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (22 bp):
ATATATGTAATAGGTAGTGCTT
Found at i:19131 original size:22 final size:22
Alignment explanation
Indices: 19087--19131 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19077 ATTACATAAC
*
19087 TTTACAAAAAGTATCGATCCTT
1 TTTACAAAAAGTATCGAACCTT
*
19109 TTTATAAAAAGTAT-GAACACTT
1 TTTACAAAAAGTATCGAAC-CTT
19131 T
1 T
19132 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTACAAAAAGTATCGAACCTT
Found at i:19182 original size:23 final size:23
Alignment explanation
Indices: 19150--19223 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
19140 TAGGTAAAAA
* *
19150 TATATGATGTAATAGGTAGCACT
1 TATATAATGTAATAGGTAGCGCT
*
19173 TATATAATGTAATAGGTAGCGTT
1 TATATAATGTAATAGGTAGCGCT
*
19196 TATATAATGTAATAGGTAGTGCT
1 TATATAATGTAATAGGTAGCGCT
19219 TATAT
1 TATAT
19224 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.35, C:0.05, G:0.20, T:0.39
Consensus pattern (23 bp):
TATATAATGTAATAGGTAGCGCT
Found at i:19327 original size:440 final size:433
Alignment explanation
Indices: 18454--19329 Score: 1529
Period size: 440 Copynumber: 2.0 Consensus size: 433
18444 ATATTATTAT
18454 TAAATTAAAAACAATAAACATATATTAATATTTATTATTATCTTTGGTTAATATTTTAAATTTAA
1 TAAATTAAAAACAATAAACATATATTAATATTTATTATTATCTTTGGTTAATATTTTAAATTTAA
* * *
18519 ATTCTAAATATTATTTTATAAAATATCAAAACAATTAAATAATTTTTTGTGCAAATGAAATTATT
66 ATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGAAAATAAAATTATT
*
18584 AAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAC
131 AAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAC
*
18649 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACAATTTCAATATAATAGGTAAAAATA
196 TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACAATTTCAATATAATAGGTAAAAATA
* *
18714 TGATGTAATAGGTAGCGCTTATATAATATAATAGGTAGTGTTTATATAATGTAATAGGTAGTGCT
261 TGATGTAATAGGTAGCACTTATATAATATAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
* * *
18779 TATATTGTAAAGTATATATCCTTTTTATAAAAGTGTCCATACTTTTTTCATTGTGGAAAACATTA
326 TATATTGTAAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTA
18844 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
391 ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
*
18887 TAAATTAAAAATAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAAC--ATATATTA-ATATTTATTATTATCTTTGGTTAATATT-TTAAAT
18952 TTAAATTCTAAATATTATTTTATAAAATATCAAAAACAATCAAAT-ATTTTTTGTGAAAATAAAA
62 TTAAATTCTAAATATTATTTTATAAAATATC-AAAACAATCAAATAATTTTTTGTGAAAATAAAA
*
19016 TTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAAATTGAAACCTAAATTA
126 TTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTA
* *
19081 CATAACTTTACAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATATAATAGGTA
190 CATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACAATTTCAATATAATAGGT-
*
19146 AAAATATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAG
254 AAAA-ATATGATGTAATAGGTAGCACTTATATAATATAATAGGTAGCGTTTATATAATGTAATAG
*
19211 GTAGTGCTTATATTGTAAAGTATTTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGA
318 GTAGTGCTTATATTGTAAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGA
19276 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
383 AAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
19327 TAA
1 TAA
19330 TTATATATAT
Statistics
Matches: 419, Mismatches: 16, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
433 18 0.04
435 8 0.02
436 28 0.07
437 95 0.23
438 94 0.22
439 4 0.01
440 172 0.41
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (433 bp):
TAAATTAAAAACAATAAACATATATTAATATTTATTATTATCTTTGGTTAATATTTTAAATTTAA
ATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGAAAATAAAATTATT
AAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAAAAATTGAAACATAAATTACATAAC
TTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAACAATTTCAATATAATAGGTAAAAATA
TGATGTAATAGGTAGCACTTATATAATATAATAGGTAGCGTTTATATAATGTAATAGGTAGTGCT
TATATTGTAAAGTATATATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAACATTA
ATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAG
Found at i:19728 original size:23 final size:23
Alignment explanation
Indices: 19699--19746 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
19689 AAATAGGTCA
*
19699 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAATATATT
*
19722 ATATAAGCGCTACCTAATATGTT
1 ATATAAGCGCTACCTAATATATT
19745 AT
1 AT
19747 TGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATATATT
Found at i:21071 original size:22 final size:22
Alignment explanation
Indices: 21041--21091 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
21031 AAATTTTATG
*
21041 AATT-TAAATTTATT-TAAGAA
1 AATTATAAATTAATTATAAGAA
*
21061 AATATATAAATTAATTATAATAA
1 AAT-TATAAATTAATTATAAGAA
21084 AATTATAA
1 AATTATAA
21092 TAGAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.12
21 1 0.04
22 14 0.54
23 8 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AATTATAAATTAATTATAAGAA
Found at i:29991 original size:16 final size:16
Alignment explanation
Indices: 29967--30000 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29957 TATCGCCGAC
*
29967 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
29983 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
29999 CG
1 CG
30001 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:30833 original size:104 final size:98
Alignment explanation
Indices: 30712--30992 Score: 311
Period size: 104 Copynumber: 2.8 Consensus size: 98
30702 AAGGCCAAAA
* * *
30712 TTAGCGGATTTGGATTCAAATCTCATATATTTTATGATATTTAGCCAATTGGACTTGTGAATTAA
1 TTAGCGGATTTGGATTCAAATCTCATATCTTTTATGATATTTAGCCAATTTGACTTGTGAACTAA
30777 AGGTTTAATCCGGTTCATGTGATTACCTGAGATGATGAT
66 AGGTTTAATCCGGTTCAT-TG----CCTGAGATGAT-AT
* * * * * *
30816 TTAGCAGATTTGGATTCAATTCTCATATCTTTTATTATATTAAGCCGATTTGACTTGTGAACTGA
1 TTAGCGGATTTGGATTCAAATCTCATATCTTTTATGATATTTAGCCAATTTGACTTGTGAACTAA
*
30881 AGGTTTAATCCGG----TTGCCTGAGGTGATAT
66 AGGTTTAATCCGGTTCATTGCCTGAGATGATAT
* * * * *
30910 TGAGCGGATTCGGATTCAAATCCCATATCTTTTATGATACTTAG-CAGATTTGATTTGTGAACTA
1 TTAGCGGATTTGGATTCAAATCTCATATCTTTTATGATATTTAGCCA-ATTTGACTTGTGAACTA
* *
30974 AAGGTTTAGTCCAGTTCAT
65 AAGGTTTAATCCGGTTCAT
30993 ACGGTTACCT
Statistics
Matches: 149, Mismatches: 23, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
93 1 0.01
94 65 0.44
95 10 0.07
98 1 0.01
99 2 0.01
100 1 0.01
104 69 0.46
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (98 bp):
TTAGCGGATTTGGATTCAAATCTCATATCTTTTATGATATTTAGCCAATTTGACTTGTGAACTAA
AGGTTTAATCCGGTTCATTGCCTGAGATGATAT
Found at i:33027 original size:20 final size:20
Alignment explanation
Indices: 33002--33046 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
32992 TTATCCGGAA
*
33002 AAAAATCCGGTATGGGGTTT
1 AAAAATCCGGTATGAGGTTT
*
33022 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTATGAGGTTT
33042 AAAAA
1 AAAAA
33047 ATTGGATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTATGAGGTTT
Found at i:34076 original size:219 final size:219
Alignment explanation
Indices: 33382--34477 Score: 1729
Period size: 219 Copynumber: 5.0 Consensus size: 219
33372 AATAAGTTAA
* * *
33382 TTATGTAAAATAATAACTTTAATAATATTTGTTATC----AGGAAAAATCTACGTAGACTAAATG
1 TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
* *
33443 TTCAAAAAGAGTTGACATTTTAATGATTGCATATG-TTTTAAAATTTTATTTAATAAATAAGTGA
66 TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
* *
33507 CGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATACGAGGCATTTGCACCTTAAAAAA
131 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATAAGAGGCATTTGCACCTTAAAAAA
33572 ATTAACGTGACTCTTGAATTATTT
196 ATTAACGTGACTCTTGAATTATTT
*
33596 TTATGTAAAATAAGAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
1 TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
* * *
33661 TTCTAAAATATCTGACA-TTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
66 TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
* *
33725 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAACTATACGAGGAGGCATTTGCACCATAAA
131 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATA--A-GAGGCATTTGCACCTTAAA
33790 AAAATTAACGTGACTCTTGAATTATTT
193 AAAATTAACGTGACTCTTGAATTATTT
* * * *
33817 TTATGCAAAATAAGAACTTTAATAATACTTATTATCATTTAGGAAAAATTTACGTAGACTATATG
1 TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
* * *
33882 TTCGAAAAGAGCTGGCATTTTAATGACTGTATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
66 TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
33947 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATAAGAGGCATTTGCACCTTAAAAAA
131 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATAAGAGGCATTTGCACCTTAAAAAA
34012 ATTAACGTGACTCTTGAATTATTT
196 ATTAACGTGACTCTTGAATTATTT
* *
34036 TCATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTGGACTATATG
1 TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
* *
34101 TTCGAAAAGATCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAATTGA
66 TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
* *
34166 TGTGATAAAAGGAATATAAACATATTTAGGTAAAAAGCTATACGAGGCATTTGCACCTTAAAAAA
131 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATAAGAGGCATTTGCACCTTAAAAAA
34231 ATTAACGTGACTCTTGAATTATTT
196 ATTAACGTGACTCTTGAATTATTT
*
34255 TTATGCAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
1 TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
* * * *
34320 TTTGAAAAGAGCTGGCATTTTAATGACTGTATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
66 TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
* * ** * * *
34385 TATGATAAAAGAAATATAAAAATATTTAGACAAAAAGATATACA-AGGTATTTGCACTTTTAAAA
131 TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATA-AGAGGCATTTGCAC-CTTAAAA
* *
34449 AAATCTAACTTGACTTTTGAATTATTT
194 AAAT-TAACGTGACTCTTGAATTATTT
34476 TT
1 TT
34478 GCACTCAATG
Statistics
Matches: 815, Mismatches: 55, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
214 34 0.04
217 17 0.02
218 106 0.13
219 419 0.51
220 11 0.01
221 142 0.17
222 86 0.11
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (219 bp):
TTATGTAAAATAAAAACTTTAATAATATTTATTATCATTTAGGAAAAATCTACGTAGACTATATG
TTCGAAAAGAGCTGACATTTTAATGATTGCATATGTTTTTAAAATTTTATTTAATAAATAAGTGA
TGTGATAAAAGAAATATAAACATATTTAGGTAAAAAGCTATAAGAGGCATTTGCACCTTAAAAAA
ATTAACGTGACTCTTGAATTATTT
Found at i:34746 original size:24 final size:23
Alignment explanation
Indices: 34713--34774 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
34703 AATTTTTTTA
* *
34713 TAAAAATAAAAATATTCTAAATT
1 TAAAAATAAAAATATTCAAAAAT
34736 TAAAAGATAAAAATATTCAAAAAT
1 TAAAA-ATAAAAATATTCAAAAAT
*
34760 TAAATATAATAAATA
1 TAAAAATAA-AAATA
34775 CTGTTGGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.26
24 25 0.74
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (23 bp):
TAAAAATAAAAATATTCAAAAAT
Found at i:35511 original size:65 final size:65
Alignment explanation
Indices: 35390--35523 Score: 180
Period size: 65 Copynumber: 2.1 Consensus size: 65
35380 ACCCATTTCA
* *
35390 AATGCATTTTGTGTACCGATGCACAAGCCATGCATCGATACACTATTGAATATTTTGAAACATCG
1 AATGCATTTTGTATACCGATGCACAAGCCATGCATCGATACACTACTGAATATTTTGAAACATCG
** * ** *
35455 AATGCATTTTGTATACCGATGCAC-AGACCATGCATCGATGTACTCCTGGCTCTTTTGAAACATC
1 AATGCATTTTGTATACCGATGCACAAG-CCATGCATCGATACACTACTGAATATTTTGAAACATC
35519 G
65 G
35520 AATG
1 AATG
35524 TAATTAGAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 2 0.03
65 58 0.97
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (65 bp):
AATGCATTTTGTATACCGATGCACAAGCCATGCATCGATACACTACTGAATATTTTGAAACATCG
Found at i:35537 original size:65 final size:66
Alignment explanation
Indices: 35402--35543 Score: 164
Period size: 65 Copynumber: 2.2 Consensus size: 66
35392 TGCATTTTGT
* * *
35402 GTACCGATGCACAAGCCATGCATCGATACACTATTGAATATTTTGAAACATCGAATGCATTTTGT
1 GTACCGATGCACAAGCCATGCATCGATACACTACTGAATATTTTGAAACATCGAATGCAATTAGT
35467 A
66 A
** * ** * *
35468 -TACCGATGCAC-AGACCATGCATCGATGTACTCCTGGCTCTTTTGAAACATCGAATGTAATTAG
1 GTACCGATGCACAAG-CCATGCATCGATACACTACTGAATATTTTGAAACATCGAATGCAATTAG
35531 -A
65 TA
35532 GTACCGATGCAC
1 GTACCGATGCAC
35544 TAAGTCTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
64 3 0.05
65 61 0.95
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (66 bp):
GTACCGATGCACAAGCCATGCATCGATACACTACTGAATATTTTGAAACATCGAATGCAATTAGT
A
Found at i:39271 original size:36 final size:36
Alignment explanation
Indices: 39219--39293 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
39209 TTCTAAACGC
39219 CCTAAGACATCATCGAGTCGTTCGAGTCAAAACCGA
1 CCTAAGACATCATCGAGTCGTTCGAGTCAAAACCGA
*
39255 CCTAGGACATCATCGAGTCGTTCGAGTCAAAACCGA
1 CCTAAGACATCATCGAGTCGTTCGAGTCAAAACCGA
39291 CCT
1 CCT
39294 CCTATTCCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (36 bp):
CCTAAGACATCATCGAGTCGTTCGAGTCAAAACCGA
Found at i:40851 original size:24 final size:24
Alignment explanation
Indices: 40819--40875 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
40809 ATTTAACAAA
40819 AAGGGGGAGAATAAGTGCTATAGT
1 AAGGGGGAGAATAAGTGCTATAGT
40843 AAGGGGGAGAATAAGTGCTATAGT
1 AAGGGGGAGAATAAGTGCTATAGT
40867 AAGGGGGAG
1 AAGGGGGAG
40876 TAATTTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.37, C:0.04, G:0.42, T:0.18
Consensus pattern (24 bp):
AAGGGGGAGAATAAGTGCTATAGT
Found at i:41328 original size:65 final size:65
Alignment explanation
Indices: 41252--41388 Score: 177
Period size: 65 Copynumber: 2.1 Consensus size: 65
41242 TACACTCATT
* * *
41252 TCGAATGCATTTTGTATACCGATGCACA-AGCCACGCATTGATGCACTCTTGAATATTTTGAACC
1 TCGAATGCATTTTGTATACCGATGCACAGA-CCACGCATCGATGCACTCCTGAATATTTTGAAAC
41316 A
65 A
* * * ** *
41317 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGTACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTATACCGATGCACAGACCACGCATCGATGCACTCCTGAATATTTTGAAACA
41382 TCGAATG
1 TCGAATG
41389 TAATTAGTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 61 0.98
66 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTATACCGATGCACAGACCACGCATCGATGCACTCCTGAATATTTTGAAACA
Found at i:43795 original size:325 final size:325
Alignment explanation
Indices: 43205--43858 Score: 1245
Period size: 325 Copynumber: 2.0 Consensus size: 325
43195 ATCTTTGGGA
*
43205 GAACATTTGCCTTAGAAATAGTAATCCAAATTTTCTTAGAGACCATATCCGTGCTGTTATGAAGC
1 GAACATTTGCCTTAGAAATAGTAATCCAAATTTTCTTAGAGACCATAACCGTGCTGTTATGAAGC
* *
43270 TTCAACCAATTATAACTTGACTTGGCCGAGTAGGAACCTGAGCTATGGTGGCGCCAGAGGATTTT
66 TTCAACCAATTATAACCTGACTTGGCCGAGTAGGAACCTGAGCTATGGTGGCACCAGAGGATTTT
43335 ATCCTCATAAGTGGGTACAATCAACGTATTCATAACCTTTTTTGCATTTTCCCTTGACAGCACCG
131 ATCCTCATAAGTGGGTACAATCAACGTATTCATAACCTTTTTTGCATTTTCCCTTGACAGCACCG
43400 AACAAACTTTATTCACATCCCATATGGGGCAGTCTGGAAGCATAAAATCTGCCACTTTAACAGGA
196 AACAAACTTTATTCACATCCCATATGGGGCAGTCTGGAAGCATAAAATCTGCCACTTTAACAGGA
*
43465 TCAACACTGTTATCCATGTAACTTTCATTCCACCGAAGAGGGCCTGAGTCCCCTTATCTGTCCAG
261 TCAACACTGTTATCCATGTAACTTTCATTCCACCGAAGAGGGCCTGAGTCCCCCTATCTGTCCAG
*
43530 GAACATTTTCCTTAGAAATAGTAATCCAAATTTTCTTAGAGACCATAACCGTGCTGTTATGAAGC
1 GAACATTTGCCTTAGAAATAGTAATCCAAATTTTCTTAGAGACCATAACCGTGCTGTTATGAAGC
43595 TTCAACCAATTATAACCTGACTTGGCCGAGTAGGAACCTGAGCTATGGTGGCACCAGAGGATTTT
66 TTCAACCAATTATAACCTGACTTGGCCGAGTAGGAACCTGAGCTATGGTGGCACCAGAGGATTTT
* *
43660 ATCCTCATAAGTGGGTACAATCACCGTATTCATAACCTTTTTTGTATTTTCCCTTGACAGCACCG
131 ATCCTCATAAGTGGGTACAATCAACGTATTCATAACCTTTTTTGCATTTTCCCTTGACAGCACCG
43725 AACAAACTTTATTCACATCCCATATGGGGCAGTCTGGAAGCATAAAATCTGCCACTTTAACAGGA
196 AACAAACTTTATTCACATCCCATATGGGGCAGTCTGGAAGCATAAAATCTGCCACTTTAACAGGA
43790 TCAACACTGTTATCCATGTAACTTTCATTCCACCGAAGAGGGCCTGAGTCCCCCTATCTGTCCAG
261 TCAACACTGTTATCCATGTAACTTTCATTCCACCGAAGAGGGCCTGAGTCCCCCTATCTGTCCAG
43855 GAAC
1 GAAC
43859 GCCCGAGTGG
Statistics
Matches: 322, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
325 322 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (325 bp):
GAACATTTGCCTTAGAAATAGTAATCCAAATTTTCTTAGAGACCATAACCGTGCTGTTATGAAGC
TTCAACCAATTATAACCTGACTTGGCCGAGTAGGAACCTGAGCTATGGTGGCACCAGAGGATTTT
ATCCTCATAAGTGGGTACAATCAACGTATTCATAACCTTTTTTGCATTTTCCCTTGACAGCACCG
AACAAACTTTATTCACATCCCATATGGGGCAGTCTGGAAGCATAAAATCTGCCACTTTAACAGGA
TCAACACTGTTATCCATGTAACTTTCATTCCACCGAAGAGGGCCTGAGTCCCCCTATCTGTCCAG
Found at i:46441 original size:20 final size:20
Alignment explanation
Indices: 46404--46452 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
46394 CTCTAAATCC
*
46404 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATTCCATTTTG
46424 TTTTTCAAAA-TCCAATTTTG
1 TTTTTCAAAATTCC-ATTTTG
*
46444 -CTTTCAAAA
1 TTTTTCAAAA
46453 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.31, C:0.14, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTTCAAAATTCCATTTTG
Found at i:48954 original size:21 final size:21
Alignment explanation
Indices: 48930--48970 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48920 CACCATCTGT
*
48930 CATCGTAGATCATCACATCAA
1 CATCGTAGACCATCACATCAA
*
48951 CATCGTAGACCGTCACATCA
1 CATCGTAGACCATCACATCA
48971 GTATCCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.32, G:0.12, T:0.22
Consensus pattern (21 bp):
CATCGTAGACCATCACATCAA
Found at i:59142 original size:3 final size:3
Alignment explanation
Indices: 59125--59162 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
59115 AAGCATTATG
59125 TAA TAA -AA TTAA TAA TAA TAA TAA TAA TAA TATA TAA T
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA T
59163 TATTGATAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 25 0.78
4 5 0.16
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:59214 original size:18 final size:18
Alignment explanation
Indices: 59159--59215 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
59149 TAATAATATA
59159 TAATTATTGATAAGTCAT
1 TAATTATTGATAAGTCAT
* ***
59177 TAAATT-TTAATAAAAGAT
1 T-AATTATTGATAAGTCAT
59195 TAATTATTGATAAGTCAT
1 TAATTATTGATAAGTCAT
59213 TAA
1 TAA
59216 ATTTTTTTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
17 4 0.14
18 21 0.72
19 4 0.14
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.42
Consensus pattern (18 bp):
TAATTATTGATAAGTCAT
Found at i:61323 original size:19 final size:19
Alignment explanation
Indices: 61299--61376 Score: 102
Period size: 19 Copynumber: 3.9 Consensus size: 19
61289 GATTGTCCAG
61299 GGGGTACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
61318 GGGGTACAGATTCCCCCTGCAA
1 GGGGTACAGATTCCCCC--C-A
*
61340 GGGGTACCGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
*
61359 GGGGGTACCGATTCCCCC
1 -GGGGTACAGATTCCCCC
61377 ATGTCTAACG
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
19 18 0.33
20 18 0.33
21 1 0.02
22 17 0.31
ACGTcount: A:0.18, C:0.37, G:0.28, T:0.17
Consensus pattern (19 bp):
GGGGTACAGATTCCCCCCA
Found at i:61377 original size:19 final size:20
Alignment explanation
Indices: 61295--61376 Score: 112
Period size: 20 Copynumber: 4.0 Consensus size: 20
61285 ATCAGATTGT
61295 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
61315 CCA-GGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
61334 CTGCAAGGGGTACCGATTCCCC
1 C--CAGGGGGTACAGATTCCCC
*
61356 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
61376 C
1 C
61377 ATGTCTAACG
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.30
20 22 0.39
21 2 0.04
22 16 0.28
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.16
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:62678 original size:19 final size:20
Alignment explanation
Indices: 62654--62701 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
62644 AACGATTTTC
*
62654 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
62673 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
62693 TTTTGAAAA
1 TTTTGAAAA
62702 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:64179 original size:21 final size:20
Alignment explanation
Indices: 64139--64240 Score: 159
Period size: 20 Copynumber: 5.0 Consensus size: 20
64129 ATTTGATTGT
64139 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
64159 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
* *
64179 CTAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
64199 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
*
64220 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
64240 C
1 C
64241 TGTCTAACGA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
20 56 0.76
21 18 0.24
ACGTcount: A:0.19, C:0.37, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:66955 original size:2 final size:2
Alignment explanation
Indices: 66948--66972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66938 TAGATTCTCC
66948 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
66973 CTTCTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71765 original size:54 final size:54
Alignment explanation
Indices: 71675--72279 Score: 601
Period size: 54 Copynumber: 11.2 Consensus size: 54
71665 GGGAAGGAAA
* ** *
71675 AGAAGATTGTTCGAGTTC-TACTCCCTGAAACAAGAGGGAGATAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* *
71728 AGAAGATCGTTCGAGTTCTTACTCCCTGAAGCAAGAGGTAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
71782 AGAACATCGTTCAAGTT-TCTACTCCCTGAAGCAAGAGGGAGTGAACTCGTAGGC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * *
71836 ATAAGATTATTCGAGTTCCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
71890 AGAAGATTGTTTGAGTTCTTATTCCCTAAAGAAAGAGGGAGCGAACCCGTAAGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
71944 AGAAGATTGTTTGAGTTCCTACTCCTTGAACCAAGAGGAAGCGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* ** * * * * * *
71998 AGAAGATTGTTCGAGTTCCTACAACCTAAAGAAAGAAGGAGC-AATCCGTTGGT
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* ** * *
72051 AGAATATCATTCGAGTTC-TACTCCCTGAATCAAGAGGGAGCAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * *
72104 AGAAGATTGTTCGAGTTATACACTCCTTGAAGCAAGAGAGAGCGAACCCGTTGAC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * * ***
72159 ATAAGATTATTCGAGTTCTATACTCCCTAAAGAAAAAGGGAGCGAACCCGTTCAC
1 AGAAGATTGTTCGAGTTCT-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
* * * * *
72214 AGAAGA-TGTTTGAGTTTCATACTCCCTGAAGAAAGAGGGATCGAACCCGCTAGTC
1 AGAAGATTGTTCGAG-TTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGGC
*
72269 -GAATATTGTTC
1 AGAAGATTGTTC
72280 AAAGAAGAGG
Statistics
Matches: 451, Mismatches: 92, Indels: 16
0.81 0.16 0.03
Matches are distributed among these distances:
52 17 0.04
53 63 0.14
54 284 0.63
55 87 0.19
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (54 bp):
AGAAGATTGTTCGAGTTCTTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGC
Found at i:72470 original size:20 final size:19
Alignment explanation
Indices: 72434--72475 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
72424 GATTAAAATA
72434 TATATATTATAAATATTAAT
1 TATATATTATAAATATT-AT
* *
72454 TATATATTATTATTATTAT
1 TATATATTATAAATATTAT
72473 TAT
1 TAT
72476 TAATTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTATAAATATTAT
Found at i:77633 original size:26 final size:26
Alignment explanation
Indices: 77604--77655 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
77594 CAAGTTCCGA
77604 ATCTCAGAATGTCCGGACTCGGCATT
1 ATCTCAGAATGTCCGGACTCGGCATT
77630 ATCTCAGAATGTCCGGACTCGGCATT
1 ATCTCAGAATGTCCGGACTCGGCATT
77656 CTTGATTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (26 bp):
ATCTCAGAATGTCCGGACTCGGCATT
Found at i:81381 original size:31 final size:31
Alignment explanation
Indices: 81343--81415 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
81333 TCAACGTTGT
81343 TTTGTTGAGT-ATTCTGACTATAAGGCGATGC
1 TTTGTTGAGTCATTC-GACTATAAGGCGATGC
* *
81374 TTTGTTGAGTCATTCGACTATAAGGTGTTGC
1 TTTGTTGAGTCATTCGACTATAAGGCGATGC
81405 TTTGTTGAGTC
1 TTTGTTGAGTC
81416 CCCGACTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
31 35 0.90
32 4 0.10
ACGTcount: A:0.19, C:0.12, G:0.26, T:0.42
Consensus pattern (31 bp):
TTTGTTGAGTCATTCGACTATAAGGCGATGC
Found at i:81424 original size:30 final size:31
Alignment explanation
Indices: 81358--81424 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
81348 TGAGTATTCT
**
81358 GACTATAAGGCGATGCTTTGTTGAGTCATTC
1 GACTATAAGGCGATGCTTTGTTGAGTCACCC
* *
81389 GACTATAAGGTGTTGCTTTGTTGAGTC-CCC
1 GACTATAAGGCGATGCTTTGTTGAGTCACCC
81419 GACTAT
1 GACTAT
81425 TAAAGTTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (31 bp):
GACTATAAGGCGATGCTTTGTTGAGTCACCC
Found at i:84083 original size:18 final size:18
Alignment explanation
Indices: 84060--84117 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 18
84050 GTGGTGGTGG
84060 TGGTGGTGGAGATGGAGA
1 TGGTGGTGGAGATGGAGA
*
84078 TGGTGGTGGAGATGTAGA
1 TGGTGGTGGAGATGGAGA
*
84096 ---TGATGGAGATGGAGA
1 TGGTGGTGGAGATGGAGA
*
84111 TGTTGGT
1 TGGTGGT
84118 AGTGATGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.39
18 20 0.61
ACGTcount: A:0.22, C:0.00, G:0.50, T:0.28
Consensus pattern (18 bp):
TGGTGGTGGAGATGGAGA
Found at i:84100 original size:21 final size:19
Alignment explanation
Indices: 84060--84113 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
84050 GTGGTGGTGG
84060 TGGTGGTGGAGATG-GAGA
1 TGGTGGTGGAGATGTGAGA
84078 TGGTGGTGGAGATGTAGATGA
1 TGGTGGTGGAGATGT-GA-GA
* *
84099 TGGAGATGGAGATGT
1 TGGTGGTGGAGATGT
84114 TGGTAGTGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 14 0.45
20 2 0.06
21 15 0.48
ACGTcount: A:0.24, C:0.00, G:0.50, T:0.26
Consensus pattern (19 bp):
TGGTGGTGGAGATGTGAGA
Found at i:84105 original size:9 final size:9
Alignment explanation
Indices: 84070--84164 Score: 53
Period size: 9 Copynumber: 11.2 Consensus size: 9
84060 TGGTGGTGGA
84070 GATGGAGAT
1 GATGGAGAT
* *
84079 GGTGGTGGA-
1 GATGG-AGAT
*
84088 GATGTAGAT
1 GATGGAGAT
84097 GAT-G-GA-
1 GATGGAGAT
84103 GATGGAGAT
1 GATGGAGAT
*
84112 GTTGGTAG-T
1 GATGG-AGAT
*
84121 GATGTAGAT
1 GATGGAGAT
84130 GATGGAGAT
1 GATGGAGAT
*
84139 GGT-G-G-T
1 GATGGAGAT
*
84145 GATGTAGAT
1 GATGGAGAT
84154 GATGGAGAT
1 GATGGAGAT
84163 GA
1 GA
84165 AAATGGTTGT
Statistics
Matches: 62, Mismatches: 14, Indels: 20
0.65 0.15 0.21
Matches are distributed among these distances:
6 6 0.10
7 4 0.06
8 8 0.13
9 40 0.65
10 4 0.06
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (9 bp):
GATGGAGAT
Found at i:84105 original size:33 final size:33
Alignment explanation
Indices: 84066--84248 Score: 217
Period size: 33 Copynumber: 5.9 Consensus size: 33
84056 GTGGTGGTGG
* * *
84066 TGGAGATGGAGATGGTGGTGGAGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
* *
84099 TGGAGATGGAGATGTTGGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
84132 T---G--G-AGATGGT-G--GTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
* *
84156 TGGAGATGAAAATGGTTGTAGTGATGTAGATGA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
84189 TGGAGATGAAGATGGTGGTAGTGATGTAGA-GA
1 TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
*
84221 TGGAGATGAAGATGGTTGTAGTGA-GTAG
1 TGGAGATGAAGATGGTGGTAGTGATGTAG
84249 TTGAATAGAT
Statistics
Matches: 133, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
24 14 0.11
26 1 0.01
27 7 0.05
28 1 0.01
29 1 0.01
30 7 0.05
31 5 0.04
32 25 0.19
33 72 0.54
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.28
Consensus pattern (33 bp):
TGGAGATGAAGATGGTGGTAGTGATGTAGATGA
Found at i:84141 original size:24 final size:24
Alignment explanation
Indices: 84114--84163 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
84104 ATGGAGATGT
84114 TGGTAGTGATGTAGATGATGGAGA
1 TGGTAGTGATGTAGATGATGGAGA
*
84138 TGGTGGTGATGTAGATGATGGAGA
1 TGGTAGTGATGTAGATGATGGAGA
84162 TG
1 TG
84164 AAAATGGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.44, T:0.30
Consensus pattern (24 bp):
TGGTAGTGATGTAGATGATGGAGA
Found at i:84157 original size:57 final size:58
Alignment explanation
Indices: 84070--84248 Score: 204
Period size: 57 Copynumber: 3.0 Consensus size: 58
84060 TGGTGGTGGA
* *
84070 GATGGAGATGGTGGTGGAGATGTAGATGATGGAGATGGAGAT-GTTGGTAGTGATGTAGAT
1 GATGGAGATGGTGGT-G-GATGTAGATGATGGAGATGAAAATGGTT-GTAGTGATGTAGAT
84130 GATGGAGATGGTGGT-GATGTAGATGATGGAGATGAAAATGGTTGTAGTGATGTAGAT
1 GATGGAGATGGTGGTGGATGTAGATGATGGAGATGAAAATGGTTGTAGTGATGTAGAT
*
84187 GATGGAGATGAAGATGGTGGTAGTGATGTAGA-GATGGAGATGAAGATGGTTGTAGTGA-GTAG
1 GAT---G--G-AGATGGTGGT-G-GATGTAGATGATGGAGATGAAAATGGTTGTAGTGATGTAG
84249 TTGAATAGAT
Statistics
Matches: 106, Mismatches: 3, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
57 39 0.37
58 3 0.03
60 16 0.15
62 1 0.01
63 10 0.09
64 4 0.04
65 25 0.24
66 8 0.08
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.28
Consensus pattern (58 bp):
GATGGAGATGGTGGTGGATGTAGATGATGGAGATGAAAATGGTTGTAGTGATGTAGAT
Found at i:85226 original size:35 final size:36
Alignment explanation
Indices: 85186--85262 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 36
85176 TGAGCATCAG
85186 TAAAAGCATCATATTACCTAAACCCATTAGAGTA-A
1 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
85221 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
1 TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
85257 TAAAAG
1 TAAAAG
85263 AAGGGCTCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 34 0.83
36 7 0.17
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (36 bp):
TAAAAGCATCATATTACCTAAACCCATTAGAGTACA
Found at i:85260 original size:18 final size:18
Alignment explanation
Indices: 85204--85260 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
85194 TCATATTACC
85204 TAAACCCATTAGAGTA-A
1 TAAACCCATTAGAGTACA
** * * * *
85221 TAAAAGCATCATATTACC
1 TAAACCCATTAGAGTACA
85239 TAAACCCATTAGAGTACA
1 TAAACCCATTAGAGTACA
85257 TAAA
1 TAAA
85261 AGAAGGGCTC
Statistics
Matches: 27, Mismatches: 12, Indels: 1
0.68 0.30 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (18 bp):
TAAACCCATTAGAGTACA
Found at i:85572 original size:15 final size:15
Alignment explanation
Indices: 85538--85654 Score: 100
Period size: 15 Copynumber: 8.1 Consensus size: 15
85528 CAGCACTATC
85538 AATACAAGCAG-ATT
1 AATACAAGCAGAATT
* *
85552 ATTACGAGCAGAATT
1 AATACAAGCAGAATT
**
85567 AATACGTGCAGAATT
1 AATACAAGCAGAATT
* *
85582 ATTACAAGCATAATT
1 AATACAAGCAGAATT
* **
85597 AGTATGAGCAGAATT
1 AATACAAGCAGAATT
*
85612 ATTAC-A--AGAATT
1 AATACAAGCAGAATT
85624 AATACAAGCAGAATT
1 AATACAAGCAGAATT
85639 -ATCACAAGCAGAATT
1 AAT-ACAAGCAGAATT
85654 A
1 A
85655 TCACAAGAAT
Statistics
Matches: 82, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.12
13 1 0.01
14 12 0.15
15 59 0.72
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (15 bp):
AATACAAGCAGAATT
Found at i:85623 original size:12 final size:14
Alignment explanation
Indices: 85575--85669 Score: 63
Period size: 15 Copynumber: 6.8 Consensus size: 14
85565 TTAATACGTG
85575 CAGAATTATTACAA
1 CAGAATTATTACAA
* * * *
85589 GCATAATTAGTATGAG
1 -CAGAATTATTA-CAA
85605 CAGAATTATTAC-A
1 CAGAATTATTACAA
*
85618 -AGAATTAATACAA
1 CAGAATTATTACAA
*
85631 GCAGAATTATCACAA
1 -CAGAATTATTACAA
*
85646 GCAGAATTATCAC-A
1 -CAGAATTATTACAA
85660 -AGAATTATTA
1 CAGAATTATTA
85670 ATATGCAGAC
Statistics
Matches: 64, Mismatches: 12, Indels: 11
0.74 0.14 0.13
Matches are distributed among these distances:
12 19 0.30
13 1 0.02
14 1 0.02
15 42 0.66
16 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (14 bp):
CAGAATTATTACAA
Found at i:85630 original size:42 final size:42
Alignment explanation
Indices: 85576--85666 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
85566 TAATACGTGC
* * ** *
85576 AGAATTATTACAAGCATAATTAGT-ATGAGCAGAATTATTACA
1 AGAATTAATACAAGCAGAATTA-TCACAAGCAGAATTATCACA
85618 AGAATTAATACAAGCAGAATTATCACAAGCAGAATTATCACA
1 AGAATTAATACAAGCAGAATTATCACAAGCAGAATTATCACA
85660 AGAATTA
1 AGAATTA
85667 TTAATATGCA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.26
Consensus pattern (42 bp):
AGAATTAATACAAGCAGAATTATCACAAGCAGAATTATCACA
Found at i:85661 original size:30 final size:30
Alignment explanation
Indices: 85538--85654 Score: 134
Period size: 30 Copynumber: 4.0 Consensus size: 30
85528 CAGCACTATC
*
85538 AATACAAGCAG-ATTATTACGAGCAGAATT
1 AATACAAGCAGAATTATTACAAGCAGAATT
** *
85567 AATACGTGCAGAATTATTACAAGCATAATT
1 AATACAAGCAGAATTATTACAAGCAGAATT
* **
85597 AGTATGAGCAGAATTATTAC-A--AGAATT
1 AATACAAGCAGAATTATTACAAGCAGAATT
*
85624 AATACAAGCAGAATTATCACAAGCAGAATT
1 AATACAAGCAGAATTATTACAAGCAGAATT
85654 A
1 A
85655 TCACAAGAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
27 21 0.29
28 1 0.01
29 10 0.14
30 40 0.56
ACGTcount: A:0.46, C:0.13, G:0.15, T:0.26
Consensus pattern (30 bp):
AATACAAGCAGAATTATTACAAGCAGAATT
Done.