Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 63 of 126
Found at i:12794480 original size:18 final size:18
Alignment explanation
Indices: 12794446--12794480 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12794436 TGCAGCGGTT
*
12794446 GTTCCTCTTGTTATTTTC
1 GTTCCTCTTGCTATTTTC
*
12794464 GTTCCTCTTGCTCTTTT
1 GTTCCTCTTGCTATTTT
12794481 GATCTATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.26, G:0.11, T:0.60
Consensus pattern (18 bp):
GTTCCTCTTGCTATTTTC
Found at i:12798249 original size:21 final size:21
Alignment explanation
Indices: 12798223--12798267 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
12798213 ATTGTGTTCG
12798223 GTAATCTTTCGATAACTTCAA
1 GTAATCTTTCGATAACTTCAA
12798244 GTAATCTTTCGATAACTTCAA
1 GTAATCTTTCGATAACTTCAA
12798265 GTA
1 GTA
12798268 TTTTCTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (21 bp):
GTAATCTTTCGATAACTTCAA
Found at i:12801594 original size:17 final size:17
Alignment explanation
Indices: 12801572--12801607 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12801562 ATTGTTTGAC
*
12801572 AATTTACTTTTTCATTT
1 AATTTAATTTTTCATTT
*
12801589 AATTTAATTTTTTATTT
1 AATTTAATTTTTCATTT
12801606 AA
1 AA
12801608 AATTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTAATTTTTCATTT
Found at i:12827350 original size:18 final size:20
Alignment explanation
Indices: 12827327--12827364 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
12827317 CAAAATTATT
12827327 ATTTT-CACCTTTTA-AAAG
1 ATTTTCCACCTTTTATAAAG
*
12827345 ATTTTCCAGCTTTTATAAAG
1 ATTTTCCACCTTTTATAAAG
12827365 CAACGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.45
Consensus pattern (20 bp):
ATTTTCCACCTTTTATAAAG
Found at i:12828105 original size:12 final size:12
Alignment explanation
Indices: 12828088--12828112 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12828078 AAGATAAAAC
12828088 GTCACTGTAGCA
1 GTCACTGTAGCA
12828100 GTCACTGTAGCA
1 GTCACTGTAGCA
12828112 G
1 G
12828113 AAAAAGACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (12 bp):
GTCACTGTAGCA
Found at i:12835900 original size:30 final size:30
Alignment explanation
Indices: 12835860--12835953 Score: 109
Period size: 30 Copynumber: 3.1 Consensus size: 30
12835850 CAAGAGTTTG
* *
12835860 TTTAGGTACAAATCAAAAGTTAAAAATTTA
1 TTTAGATACAAATTAAAAGTTAAAAATTTA
* * *
12835890 TTTAGATACAAATTAAAAATCAATAATTTA
1 TTTAGATACAAATTAAAAGTTAAAAATTTA
* *
12835920 TTT-GAGTGCAAATTAAAAGTTAAAAACTTA
1 TTTAGA-TACAAATTAAAAGTTAAAAATTTA
12835950 TTTA
1 TTTA
12835954 AATATAATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.04
30 50 0.96
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (30 bp):
TTTAGATACAAATTAAAAGTTAAAAATTTA
Found at i:12842184 original size:10 final size:10
Alignment explanation
Indices: 12842171--12842195 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12842161 TTTTAGGAAT
12842171 TTTTTTGAAA
1 TTTTTTGAAA
12842181 TTTTTTGAAA
1 TTTTTTGAAA
12842191 TTTTT
1 TTTTT
12842196 CGTCACCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (10 bp):
TTTTTTGAAA
Found at i:12844144 original size:15 final size:15
Alignment explanation
Indices: 12844120--12844165 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 15
12844110 CAATATTATT
12844120 AAATACAATAATACAA
1 AAATACAA-AATACAA
12844136 AAAT---AAATACAA
1 AAATACAAAATACAA
*
12844148 AAATATAAAATACAA
1 AAATACAAAATACAA
12844163 AAA
1 AAA
12844166 CAAAAAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 11 0.41
13 1 0.04
15 11 0.41
16 4 0.15
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATACAAAATACAA
Found at i:12844144 original size:20 final size:20
Alignment explanation
Indices: 12844119--12844171 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
12844109 ACAATATTAT
*
12844119 TAAATACAATAATACAAAAA
1 TAAATACAAAAATACAAAAA
*
12844139 TAAATACAAAAATATAAAATA
1 TAAATACAAAAATACAAAA-A
* *
12844160 CAAAAACAAAAA
1 TAAATACAAAAA
12844172 AAGGCTGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (20 bp):
TAAATACAAAAATACAAAAA
Found at i:12845361 original size:26 final size:28
Alignment explanation
Indices: 12845331--12845390 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
12845321 TGTTAATTTT
12845331 TAAAATA-AAACTTTAA-AAAAATAA-AA
1 TAAAATATAAA-TTTAATAAAAATAATAA
12845357 TAAAA-ATAAATTTAATAAAAATAATAA
1 TAAAATATAAATTTAATAAAAATAATAA
12845384 -AAAATAT
1 TAAAATAT
12845391 GAGAAAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
25 6 0.20
26 20 0.67
27 4 0.13
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (28 bp):
TAAAATATAAATTTAATAAAAATAATAA
Found at i:12845367 original size:15 final size:15
Alignment explanation
Indices: 12845345--12845385 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
12845335 ATAAAACTTT
12845345 AAAA-AAATAAAATA
1 AAAATAAATAAAATA
**
12845359 AAAATAAATTTAATA
1 AAAATAAATAAAATA
12845374 AAAAT-AATAAAA
1 AAAATAAATAAAA
12845386 AATATGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATAAATAAAATA
Found at i:12845387 original size:25 final size:26
Alignment explanation
Indices: 12845332--12845389 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
12845322 GTTAATTTTT
12845332 AAAATAAAACTTTAAAAAAATAAAATA
1 AAAAT-AAACTTTAAAAAAATAAAATA
*
12845359 AAAATAAA-TTTAATAAAAATAATA-A
1 AAAATAAACTTTAA-AAAAATAAAATA
12845384 AAAATA
1 AAAATA
12845390 TGAGAAAAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 12 0.41
26 12 0.41
27 5 0.17
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAAATAAACTTTAAAAAAATAAAATA
Found at i:12845856 original size:22 final size:23
Alignment explanation
Indices: 12845830--12845872 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12845820 TTCTCGAATA
12845830 AATTT-AAAAAAATAAAAAAAAT
1 AATTTCAAAAAAATAAAAAAAAT
* *
12845852 AATTTCTAATAAATAAAAAAA
1 AATTTCAAAAAAATAAAAAAA
12845873 TCAAGAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (23 bp):
AATTTCAAAAAAATAAAAAAAAT
Found at i:12847680 original size:13 final size:13
Alignment explanation
Indices: 12847611--12847686 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
12847601 ATATAAAATA
12847611 TATATTTTTTATT
1 TATATTTTTTATT
*
12847624 T-TATTAAGTTTATT
1 TATATT--TTTTATT
*
12847638 TATAATTTTTA-T
1 TATATTTTTTATT
* * * *
12847650 TAAAATTTTAAAT
1 TATATTTTTTATT
12847663 TATATTTTTTATT
1 TATATTTTTTATT
12847676 TATATTATTTT
1 TATATT-TTTT
12847687 TACATCGTAT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
12 14 0.29
13 21 0.43
14 11 0.22
15 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (13 bp):
TATATTTTTTATT
Found at i:12848330 original size:25 final size:25
Alignment explanation
Indices: 12848284--12848332 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
12848274 AAATTATTTA
* *
12848284 AATATATTAAAAATTATATTAAAAT
1 AATATATAAAAAATAATATTAAAAT
12848309 AATATATAAAAAATAA-ATTTAAAA
1 AATATATAAAAAATAATA-TTAAAA
12848333 AATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATATAAAAAATAATATTAAAAT
Found at i:12848334 original size:13 final size:14
Alignment explanation
Indices: 12848284--12848340 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
12848274 AAATTATTTA
*
12848284 AATATATTAAAAAT
1 AATATATAAAAAAT
*
12848298 --TATAT-TAAAAT
1 AATATATAAAAAAT
12848309 AATATATAAAAAAT
1 AATATATAAAAAAT
*
12848323 AA-ATTTAAAAAATT
1 AATATATAAAAAA-T
12848337 AATA
1 AATA
12848341 AACTGAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 14 0.40
14 10 0.29
15 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATATAAAAAAT
Found at i:12862072 original size:12 final size:12
Alignment explanation
Indices: 12862042--12862080 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
12862032 CATATTGAAC
12862042 TTTATT-AATTAA
1 TTTATTAAATT-A
*
12862054 TTAATTAAATTA
1 TTTATTAAATTA
12862066 TTTATTAAATTA
1 TTTATTAAATTA
12862078 TTT
1 TTT
12862081 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTATTAAATTA
Found at i:12865670 original size:20 final size:20
Alignment explanation
Indices: 12865645--12865697 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
12865635 ACAATATTAT
*
12865645 TAAATACAATAATATAAAAA
1 TAAATACAAAAATATAAAAA
12865665 TAAATACAAAAATATAAAATA
1 TAAATACAAAAATATAAAA-A
* *
12865686 CAAAAACAAAAA
1 TAAATACAAAAA
12865698 AAAGGTCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.19
Consensus pattern (20 bp):
TAAATACAAAAATATAAAAA
Found at i:12867540 original size:24 final size:24
Alignment explanation
Indices: 12867495--12867540 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
12867485 AATAAAATAA
* *
12867495 AATAAAAATAAATTTAATAAAATT
1 AATAAAAATAAATTGAAAAAAATT
12867519 AATAAAAA-AAATATGAAAAAAA
1 AATAAAAATAAAT-TGAAAAAAA
12867541 AAAAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AATAAAAATAAATTGAAAAAAATT
Found at i:12869221 original size:40 final size:40
Alignment explanation
Indices: 12869176--12869258 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
12869166 TCCTCTAGAA
*
12869176 TTTTTAGTGGTTCATGAGTTAAACAAAATTGAATTTTCAT
1 TTTTTAGTGGTTCATGAGTTAAACAAAATTGAAATTTCAT
12869216 TTTTTAGTGGTTCATGAGTTAAACAAAATTGAAATTTCAT
1 TTTTTAGTGGTTCATGAGTTAAACAAAATTGAAATTTCAT
12869256 TTT
1 TTT
12869259 GTATGGTGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (40 bp):
TTTTTAGTGGTTCATGAGTTAAACAAAATTGAAATTTCAT
Found at i:12874190 original size:16 final size:17
Alignment explanation
Indices: 12874169--12874200 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12874159 AAATTAATCA
12874169 AAATATAAAA-AAATTC
1 AAATATAAAATAAATTC
12874185 AAATATAAAATAAATT
1 AAATATAAAATAAATT
12874201 ATTTTATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATAAAATAAATTC
Found at i:12881720 original size:17 final size:17
Alignment explanation
Indices: 12881698--12881733 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12881688 ATTGTTTGAC
*
12881698 AATTTACTTTTTCATTT
1 AATTTAATTTTTCATTT
*
12881715 AATTTAATTTTTTATTT
1 AATTTAATTTTTCATTT
12881732 AA
1 AA
12881734 AATTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTAATTTTTCATTT
Found at i:12883979 original size:29 final size:29
Alignment explanation
Indices: 12883935--12884037 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
12883925 TTAATTTATG
*
12883935 TAAAGAGTTTGTTTAGGTACAAATTAAAAT
1 TAAAGA-TTTATTTAGGTACAAATTAAAAT
* * *
12883965 TAAAAATTTATTTAGATATAAATTAAAAT
1 TAAAGATTTATTTAGGTACAAATTAAAAT
* * * *
12883994 CAATGATTTATTTAAGTGCAAATTAAAGAT
1 TAAAGATTTATTTAGGTACAAATTAAA-AT
*
12884024 TAAAGGTTTATTTA
1 TAAAGATTTATTTA
12884038 AATATAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 40 0.69
30 18 0.31
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.40
Consensus pattern (29 bp):
TAAAGATTTATTTAGGTACAAATTAAAAT
Found at i:12901810 original size:30 final size:29
Alignment explanation
Indices: 12901776--12901880 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
12901766 TTTATTATAT
*
12901776 TTAAATAAACCTTTAATCTTTAATTTGCAC
1 TTAAATAAACCTTTAAT-TTTAATTTGTAC
* * * *
12901806 TTAAATAAATCATTGATTTTTAATTTATA-
1 TTAAATAAA-CCTTTAATTTTAATTTGTAC
**
12901835 TCTAAATAAATTTTTAATTTTAATTTGTAC
1 T-TAAATAAACCTTTAATTTTAATTTGTAC
* *
12901865 CTAAACAAACTCTTTA
1 TTAAATAAAC-CTTTA
12901881 CATAAATTAA
Statistics
Matches: 57, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
29 22 0.39
30 30 0.53
31 5 0.09
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (29 bp):
TTAAATAAACCTTTAATTTTAATTTGTAC
Found at i:12901868 original size:29 final size:29
Alignment explanation
Indices: 12901777--12901869 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
12901767 TTATTATATT
** * *
12901777 TAAATAAACCTTTAATCTTTAATTTGCACT
1 TAAATAAATATTTAAT-TTTAATTTGTACC
* * * *
12901807 TAAATAAATCATTGATTTTTAATTTATATC
1 TAAATAAAT-ATTTAATTTTAATTTGTACC
*
12901837 TAAATAAATTTTTAATTTTAATTTGTACC
1 TAAATAAATATTTAATTTTAATTTGTACC
12901866 TAAA
1 TAAA
12901870 CAAACTCTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 19 0.39
30 26 0.53
31 4 0.08
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (29 bp):
TAAATAAATATTTAATTTTAATTTGTACC
Found at i:12903397 original size:108 final size:104
Alignment explanation
Indices: 12903212--12903419 Score: 292
Period size: 108 Copynumber: 2.0 Consensus size: 104
12903202 CAATGGTTCT
* *
12903212 ACATATATTCGGTCCTTAATTCTTCAAAGATTTGTGGAGAAGATGGATAGATTGCTGTGATATCT
1 ACATATATTCGGTCCTTAATTCTTCAAAGATTTGTGGAGAAGATAGATAGATTGCTGTAATATCT
12903277 TCATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGG
66 TCATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGG
* * * * *
12903316 ACATATATTCTGTCTTTATTTCTTCAAAAGATTTGTTGAGAAGATTATAGTTAGATTGCTGTAAT
1 ACATATATTCGGTCCTTAATTCTTC-AAAGATTTGTGGAGAAG---ATAGATAGATTGCTGTAAT
*
12903381 ATCTTCA-CTGCATGGCATAAGGTATCTTCAATGATTCTG
62 ATCTTCATC-GCATGGCATAAAGTATCTTCAATGATTCTG
12903420 ATGAGCTGAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
104 22 0.24
105 16 0.18
107 1 0.01
108 52 0.57
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.38
Consensus pattern (104 bp):
ACATATATTCGGTCCTTAATTCTTCAAAGATTTGTGGAGAAGATAGATAGATTGCTGTAATATCT
TCATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGG
Found at i:12903502 original size:12 final size:12
Alignment explanation
Indices: 12903485--12903523 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
12903475 AATTTTTTTA
12903485 AAATAATTTAAT
1 AAATAATTTAAT
12903497 AAATAATTTAAAT
1 AAATAATTT-AAT
12903510 AAATAA-TTAAT
1 AAATAATTTAAT
12903521 AAA
1 AAA
12903524 GTTCAATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 6 0.23
12 11 0.42
13 9 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAATAATTTAAT
Found at i:12906600 original size:87 final size:92
Alignment explanation
Indices: 12906468--12906645 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 92
12906458 AAGCCTGGGA
12906468 GATTTTTGTTGATTAAACTAAACATAACTCTTCCACTGTCCATAAAAATTATAGAATTGAACAAT
1 GATTTTTGTTGATTAAACTAAACATAACTCTTCCACTGTCCATAAAAATTATAGAATTGAACAAT
12906533 CTTTAATCAATTTATTCTTTGTTTGTG
66 CTTTAATCAATTTATTCTTTGTTTGTG
12906560 GATTTTTGTTGA-TAAAC-AAA-AT-ACTCTT-CACTGTCCATAAAAATTATAGAATTGAACAAT
1 GATTTTTGTTGATTAAACTAAACATAACTCTTCCACTGTCCATAAAAATTATAGAATTGAACAAT
12906620 CTTTAATCAATTTATTCTTTGTTTGT
66 CTTTAATCAATTTATTCTTTGTTTGT
12906646 ACAGGCTCAC
Statistics
Matches: 86, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
87 58 0.67
88 6 0.07
89 2 0.02
90 3 0.03
91 5 0.06
92 12 0.14
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (92 bp):
GATTTTTGTTGATTAAACTAAACATAACTCTTCCACTGTCCATAAAAATTATAGAATTGAACAAT
CTTTAATCAATTTATTCTTTGTTTGTG
Found at i:12911803 original size:17 final size:17
Alignment explanation
Indices: 12911769--12911800 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12911759 GAAATAAAAT
12911769 AATTTATTTTATATTTG
1 AATTTATTTTATATTTG
12911786 AATTT-TTTTATATTT
1 AATTTATTTTATATTT
12911801 TGATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
AATTTATTTTATATTTG
Found at i:12916460 original size:40 final size:40
Alignment explanation
Indices: 12916416--12916498 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
12916406 CACACCATAC
*
12916416 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
12916456 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
12916496 AAA
1 AAA
12916499 TTCTAGAGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (40 bp):
AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
Found at i:12917568 original size:20 final size:21
Alignment explanation
Indices: 12917530--12917570 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12917520 TATATATTAT
* *
12917530 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
12917551 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
12917571 AAATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:12924652 original size:102 final size:102
Alignment explanation
Indices: 12924483--12924684 Score: 273
Period size: 102 Copynumber: 2.0 Consensus size: 102
12924473 CAATGGTTCT
* * *
12924483 ACATATATTCGGTCCTTAATTCTTCGAAGATTTGTGGAGAAGATGGATAGATTGCTGCGATATCT
1 ACATATATTCGGTCCTTAATTCTTCCAAGATTTGTGGAGAAGAT-G-TAGATTGCTGCAAAATCT
12924548 TCA-TCGCATGGCATAAAGTATCTTCAATGATTCTGCTGG
64 TCACT-GCATGGCATAAAGTATCTTCAATGATTCTGCTGG
* * * * *
12924587 ACATATATTCTGTCTTTATTTCTTCACAAGATTTGTTGAGAAGAT-TAGATTGCTGTAAAATCTT
1 ACATATATTCGGTCCTTAATTCTTC-CAAGATTTGTGGAGAAGATGTAGATTGCTGCAAAATCTT
*
12924651 CACTGCATGGCATAAGGTATCTTCAATGATTCTG
65 CACTGCATGGCATAAAGTATCTTCAATGATTCTG
12924685 ATGAGCTGAA
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
102 47 0.54
103 1 0.01
104 22 0.25
105 17 0.20
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (102 bp):
ACATATATTCGGTCCTTAATTCTTCCAAGATTTGTGGAGAAGATGTAGATTGCTGCAAAATCTTC
ACTGCATGGCATAAAGTATCTTCAATGATTCTGCTGG
Found at i:12925538 original size:2 final size:2
Alignment explanation
Indices: 12925531--12925561 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
12925521 AATATTTTCA
*
12925531 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12925562 AAACATAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12937773 original size:36 final size:39
Alignment explanation
Indices: 12937706--12937785 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 39
12937696 CACACCATAC
12937706 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTA
1 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTA
12937745 AAAATGAAA-TTCAA-TTTG-TTAACTCATGAACCACTA
1 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTA
12937781 AAAAT
1 AAAAT
12937786 TCCAGAGGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
36 23 0.56
37 4 0.10
38 5 0.12
39 9 0.22
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (39 bp):
AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTA
Found at i:12938852 original size:20 final size:21
Alignment explanation
Indices: 12938814--12938854 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12938804 TATATATTAT
* *
12938814 TTTAATATAATTTTTAATATA
1 TTTAATATAAATTTAAATATA
12938835 TTTAA-ATAAATTTAAATATA
1 TTTAATATAAATTTAAATATA
12938855 AAATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAATATAAATTTAAATATA
Found at i:12939461 original size:13 final size:13
Alignment explanation
Indices: 12939445--12939515 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
12939435 ATGTAAGAAT
12939445 AATATAAATAAAA
1 AATATAAATAAAA
**
12939458 AATAT-AATTTAA
1 AATATAAATAAAA
* *
12939470 AATTTTAATAAAA
1 AATATAAATAAAA
* *
12939483 ATTATAAATAAATTT
1 AATATAAATAAA--A
12939498 AATA-AAATAAAA
1 AATATAAATAAAA
12939510 AATATA
1 AATATA
12939516 TATTTTATAT
Statistics
Matches: 43, Mismatches: 11, Indels: 8
0.69 0.18 0.13
Matches are distributed among these distances:
12 13 0.30
13 20 0.47
14 7 0.16
15 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
AATATAAATAAAA
Found at i:12939512 original size:21 final size:22
Alignment explanation
Indices: 12939473--12939513 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
12939463 AATTTAAAAT
* *
12939473 TTTAATAAAAATTATAAATAAA
1 TTTAATAAAAATAAAAAATAAA
12939495 TTTAAT-AAAATAAAAAATA
1 TTTAATAAAAATAAAAAATA
12939514 TATATTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAATAAAAATAAAAAATAAA
Found at i:12942782 original size:20 final size:20
Alignment explanation
Indices: 12942759--12942844 Score: 73
Period size: 20 Copynumber: 4.0 Consensus size: 20
12942749 TTTGTTTTTG
*
12942759 TTTTTGTATTTTTATATTTA
1 TTTTTGTATTATTATATTTA
*
12942779 TTTTTGTATTATTGTATTTAA
1 TTTTTGTATTATTATATTT-A
* *
12942800 TAATATTGTTATCATCTTATATTTA
1 T--TTTTG-TAT--TATTATATTTA
*
12942825 TTTTTGTATTATTGTATTTA
1 TTTTTGTATTATTATATTTA
12942845 ATAATATTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
20 26 0.50
21 2 0.04
22 3 0.06
23 8 0.15
24 3 0.06
25 2 0.04
26 8 0.15
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTTTGTATTATTATATTTA
Found at i:12942826 original size:46 final size:46
Alignment explanation
Indices: 12942770--12942865 Score: 192
Period size: 46 Copynumber: 2.1 Consensus size: 46
12942760 TTTTGTATTT
12942770 TTATATTTATTTTTGTATTATTGTATTTAATAATATTGTTATCATC
1 TTATATTTATTTTTGTATTATTGTATTTAATAATATTGTTATCATC
12942816 TTATATTTATTTTTGTATTATTGTATTTAATAATATTGTTATCATC
1 TTATATTTATTTTTGTATTATTGTATTTAATAATATTGTTATCATC
12942862 TTAT
1 TTAT
12942866 TTATTATTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.61
Consensus pattern (46 bp):
TTATATTTATTTTTGTATTATTGTATTTAATAATATTGTTATCATC
Found at i:12945701 original size:18 final size:18
Alignment explanation
Indices: 12945678--12945724 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12945668 TTCCGGTTAC
*
12945678 ATTTTTTTTTAAATAATT
1 ATTTTTTATTAAATAATT
* *
12945696 ATTTTTTATTATATATTT
1 ATTTTTTATTAAATAATT
12945714 ATTTTTATATT
1 ATTTTT-TATT
12945725 TTAACCAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTATTAAATAATT
Found at i:12951339 original size:30 final size:29
Alignment explanation
Indices: 12951305--12951408 Score: 93
Period size: 29 Copynumber: 3.5 Consensus size: 29
12951295 TTTATTATAT
*
12951305 TTAAATAAACCTTTAATCTTTAATTTGCAC
1 TTAAATAAACCTTTAAT-TTTAATTTGTAC
* * * *
12951335 TTAAATAAATCATTGATTTTAATTTATA-
1 TTAAATAAACCTTTAATTTTAATTTGTAC
**
12951363 TCTAAATAAATTTTTAATTTTAATTTGTAC
1 T-TAAATAAACCTTTAATTTTAATTTGTAC
* *
12951393 CTAAACAAACTCTTTA
1 TTAAATAAAC-CTTTA
12951409 CATAAATTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
28 1 0.02
29 39 0.67
30 18 0.31
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.46
Consensus pattern (29 bp):
TTAAATAAACCTTTAATTTTAATTTGTAC
Found at i:12957272 original size:2 final size:2
Alignment explanation
Indices: 12957265--12957297 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12957255 TTTTCTATGT
12957265 TA TA TA TA 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 TA TA TA TA T
12957298 TGAAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12957470 original size:17 final size:17
Alignment explanation
Indices: 12957448--12957483 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12957438 ATTGTTTGAC
*
12957448 AATTTACTTTTTCATTT
1 AATTTAATTTTTCATTT
*
12957465 AATTTAATTTTTTATTT
1 AATTTAATTTTTCATTT
12957482 AA
1 AA
12957484 AATTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTAATTTTTCATTT
Found at i:12957994 original size:12 final size:12
Alignment explanation
Indices: 12957966--12958002 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
12957956 AATATTGAAC
12957966 TTTATT-AATTA
1 TTTATTAAATTA
12957977 -TTATTAAATTA
1 TTTATTAAATTA
12957988 TTTATTAAATTA
1 TTTATTAAATTA
12958000 TTT
1 TTT
12958003 TAAAAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.21
11 5 0.21
12 14 0.58
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTATTAAATTA
Found at i:12959647 original size:29 final size:29
Alignment explanation
Indices: 12959603--12959706 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
12959593 TTAATTTATG
*
12959603 TAAAGAGTTTGTTTAGGTACAAATTAAAAT
1 TAAAGA-TTTATTTAGGTACAAATTAAAAT
* * *
12959633 TAAAAATTTATTTAGATATAAATTAAAAAT
1 TAAAGATTTATTTAGGTACAAATT-AAAAT
* * * *
12959663 CAATGATTTATTTAAGTTCAAATTAAAGAT
1 TAAAGATTTATTTAGGTACAAATTAAA-AT
*
12959693 TAAAGGTTTATTTA
1 TAAAGATTTATTTA
12959707 AATATAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
29 18 0.31
30 40 0.69
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.40
Consensus pattern (29 bp):
TAAAGATTTATTTAGGTACAAATTAAAAT
Found at i:12965467 original size:100 final size:100
Alignment explanation
Indices: 12965363--12965562 Score: 391
Period size: 100 Copynumber: 2.0 Consensus size: 100
12965353 TGAGAGTTTG
12965363 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
1 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
12965428 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
66 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
*
12965463 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCATGTAAAAGATTGGAATATATATAGTTGA
1 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
12965528 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
66 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
12965563 TTTTTGTTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 99 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.43
Consensus pattern (100 bp):
ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
Found at i:12966532 original size:20 final size:20
Alignment explanation
Indices: 12966509--12966548 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12966499 AATCTAAAAT
*
12966509 AAAATTTATATTATTAAATAA
1 AAAATTAAT-TTATTAAATAA
12966530 AAAATTAATTTATTAAATA
1 AAAATTAATTTATTAAATA
12966549 TGTAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTAATTTATTAAATAA
Found at i:12979527 original size:31 final size:31
Alignment explanation
Indices: 12979489--12979549 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
12979479 AAATTGATTT
12979489 AAAAATAAATTTTAAAATTT-TAT-TTAAATTA
1 AAAAAT-AATTTT-AAATTTATATATTAAATTA
12979520 AAAAATAATTTTAAATTTATATATTAAATT
1 AAAAATAATTTTAAATTTATATATTAAATT
12979550 TAATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 6 0.21
30 9 0.32
31 13 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
AAAAATAATTTTAAATTTATATATTAAATTA
Found at i:12979595 original size:18 final size:18
Alignment explanation
Indices: 12979510--12979596 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 18
12979500 TTAAAATTTT
* * *
12979510 ATTTAAATTAAAAAATAA
1 ATTTAATTTAATAATTAA
*
12979528 TTTTAAATTT-ATATATTAA
1 ATTT-AATTTAATA-ATTAA
*
12979547 ATTTAATTTATATAATAAA
1 ATTTAATTTA-ATAATTAA
* **
12979566 AATTAA-AAAATAATTAA
1 ATTTAATTTAATAATTAA
12979583 ATTTAATTTAATAA
1 ATTTAATTTAATAA
12979597 AATTATATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
17 12 0.24
18 16 0.31
19 20 0.39
20 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTTAATTTAATAATTAA
Found at i:12987706 original size:4 final size:4
Alignment explanation
Indices: 12987699--12987725 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12987689 AATTAAAAAA
12987699 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
12987726 TTACTGTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:12988030 original size:30 final size:29
Alignment explanation
Indices: 12987996--12988099 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 29
12987986 TTTATTATAT
12987996 TTAAATAAACCTTTAATCTTTAATTTGAAC
1 TTAAATAAACCTTTAAT-TTTAATTTGAAC
* * *
12988026 TTAAATAAATCATTGATTTTTAATTT-ATA-
1 TTAAATAAA-CCTTTAATTTTAATTTGA-AC
* *
12988055 TCTAAATAAA-TTTTAATTTTAATTTGTAC
1 T-TAAATAAACCTTTAATTTTAATTTGAAC
* *
12988084 CTAAACAAACTCTTTA
1 TTAAATAAAC-CTTTA
12988100 CATAAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
28 20 0.35
29 2 0.04
30 30 0.53
31 5 0.09
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (29 bp):
TTAAATAAACCTTTAATTTTAATTTGAAC
Found at i:12989725 original size:13 final size:12
Alignment explanation
Indices: 12989700--12989738 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
12989690 AATTTTTTTA
12989700 AAATAATTTAAT
1 AAATAATTTAAT
12989712 AAATAATTTAAAT
1 AAATAATTT-AAT
*
12989725 AATTAA-TTAAT
1 AAATAATTTAAT
12989736 AAA
1 AAA
12989739 GTTCAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 5 0.21
12 11 0.46
13 8 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAATAATTTAAT
Found at i:12990242 original size:17 final size:17
Alignment explanation
Indices: 12990222--12990257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12990212 TTTATTAATT
*
12990222 TTAAATAAAAAATTAAA
1 TTAAATAAAAAAGTAAA
*
12990239 TTAAATGAAAAAGTAAA
1 TTAAATAAAAAAGTAAA
12990256 TT
1 TT
12990258 GTCAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAATAAAAAAGTAAA
Found at i:12990415 original size:2 final size:2
Alignment explanation
Indices: 12990408--12990440 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12990398 AATATTTTCA
12990408 AT 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 AT A
12990441 ACATAGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12992708 original size:29 final size:29
Alignment explanation
Indices: 12992638--12992704 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
12992628 TAAATTATTT
* *
12992638 ATTTATATATATAAATTATATATAAATAA
1 ATTTATATATATAAATTAAAAATAAATAA
*
12992667 ATTTATACATATAAATTAAAAAT-AA-AA
1 ATTTATATATATAAATTAAAAATAAATAA
12992694 A-TTATATATAT
1 ATTTATATATAT
12992705 TATATTTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 9 0.26
27 3 0.09
28 2 0.06
29 20 0.59
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
ATTTATATATATAAATTAAAAATAAATAA
Found at i:12992853 original size:43 final size:40
Alignment explanation
Indices: 12992763--12992910 Score: 114
Period size: 38 Copynumber: 3.8 Consensus size: 40
12992753 TTAAATATAA
* **
12992763 TTTT-ATTAAATTAAATTTAATTAT--TTTTTTAATTTTT
1 TTTTAATTAAATTAAATTTAATTATAAATTTAAAATTTTT
*
12992800 TATTAATTAAATTAAATTTAATATATAAATTTAAAATTTGTT
1 TTTTAATTAAATTAAATTTAAT-TATAAATTTAAAATTT-TT
*
12992842 TTTTAATTTAAA-TAAAATT--TTA-AAATTTAAAATTTTAT
1 TTTTAA-TTAAATTAAATTTAATTATAAATTTAAAATTTT-T
* * *
12992880 TTTAAATCAAATTTAAA-TAAATATATAAATT
1 TTTTAATTAAA-TTAAATTTAAT-TATAAATT
12992911 ATTAATACCA
Statistics
Matches: 89, Mismatches: 9, Indels: 21
0.75 0.08 0.18
Matches are distributed among these distances:
37 8 0.09
38 37 0.42
39 9 0.10
40 2 0.02
41 10 0.11
42 18 0.20
43 5 0.06
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (40 bp):
TTTTAATTAAATTAAATTTAATTATAAATTTAAAATTTTT
Found at i:12992886 original size:19 final size:19
Alignment explanation
Indices: 12992825--12992886 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
12992815 ATTTAATATA
12992825 TAAATTTAAAATTTGT-TTT
1 TAAATTTAAAATTT-TATTT
* ***
12992844 TTAATTT-AAATAAAATTT
1 TAAATTTAAAATTTTATTT
12992862 TAAAATTTAAAATTTTATTT
1 T-AAATTTAAAATTTTATTT
12992882 TAAAT
1 TAAAT
12992887 CAAATTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.25
19 15 0.47
20 9 0.28
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TAAATTTAAAATTTTATTT
Found at i:13001045 original size:14 final size:15
Alignment explanation
Indices: 13001021--13001063 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
13001011 CAGCTCAAAT
13001021 AAATATATATAATTA
1 AAATATATATAATTA
13001036 AAATAT-TATAATTGTA
1 AAATATATATAA-T-TA
13001052 TAAATATATATA
1 -AAATATATATA
13001064 TAAATTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.21
15 7 0.29
16 2 0.08
17 6 0.25
18 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (15 bp):
AAATATATATAATTA
Found at i:13006366 original size:16 final size:15
Alignment explanation
Indices: 13006334--13006362 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13006324 CGTTGTAAAC
13006334 TTATTTTTTTATCAT
1 TTATTTTTTTATCAT
13006349 TTATTTTTTTATCA
1 TTATTTTTTTATCA
13006363 ATTTTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (15 bp):
TTATTTTTTTATCAT
Found at i:13006892 original size:100 final size:100
Alignment explanation
Indices: 13006775--13006974 Score: 355
Period size: 100 Copynumber: 2.0 Consensus size: 100
13006765 AGTTTATAAA
13006775 AAAAAAAAAAATGTTAGAGATTTGAAAATGTGAGGCCAACTATATATATTCCAATCTTTTACATG
1 AAAAAAAAAAATGTTAGAGATTTGAAAATGTGAGGCCAACTATATATATTCCAATCTTTTACATG
*
13006840 AATTTTTTAAATAATAAAATCAAATTGAATCTCAT
66 AATTTTTTAAACAATAAAATCAAATTGAATCTCAT
** * *
13006875 AAAAAAAAATTTGTTAGAGATTTGAAAATGTGAGGTCAACTATATATATTCCAATCTTTTACTTG
1 AAAAAAAAAAATGTTAGAGATTTGAAAATGTGAGGCCAACTATATATATTCCAATCTTTTACATG
13006940 AATTTTTTAAACAATAAAATCAAATTGAATCTCAT
66 AATTTTTTAAACAATAAAATCAAATTGAATCTCAT
13006975 CAAACTCTCG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (100 bp):
AAAAAAAAAAATGTTAGAGATTTGAAAATGTGAGGCCAACTATATATATTCCAATCTTTTACATG
AATTTTTTAAACAATAAAATCAAATTGAATCTCAT
Found at i:13016833 original size:16 final size:16
Alignment explanation
Indices: 13016812--13016843 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13016802 GCATATCCTC
*
13016812 TTTTTATTTTTTATTT
1 TTTTTAATTTTTATTT
13016828 TTTTTAATTTTTATTT
1 TTTTTAATTTTTATTT
13016844 AAAAAAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTAATTTTTATTT
Found at i:13018627 original size:108 final size:105
Alignment explanation
Indices: 13018441--13018647 Score: 281
Period size: 108 Copynumber: 1.9 Consensus size: 105
13018431 TGGTTCTACA
* * *
13018441 ATATATTCGGTCCTTAATTTCTTCGAAGATTTGTGGAGAAGATGGATAGATTGCTATGATATCTT
1 ATATATTCGGTCCTTAATTTCTTCAAAGATTTGTGGAGAAGATAGATAGATTGCTATAATATCTT
13018506 CATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGGAC
66 CATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGGAC
* * * * *
13018546 ATATATTCTGT-CTTTATTTCTTCAAAAGATTTGTTGAGAAGATTATAGTTAGATTGCTGTAATA
1 ATATATTCGGTCCTTAATTTCTTC-AAAGATTTGTGGAGAAG---ATAGATAGATTGCTATAATA
* *
13018610 TCTTCATTGCATGGCATAAGGTATCTTCAATGATTCTG
62 TCTTCATCGCATGGCATAAAGTATCTTCAATGATTCTG
13018648 ATGAGCTGAA
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
104 11 0.12
105 25 0.28
108 52 0.59
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (105 bp):
ATATATTCGGTCCTTAATTTCTTCAAAGATTTGTGGAGAAGATAGATAGATTGCTATAATATCTT
CATCGCATGGCATAAAGTATCTTCAATGATTCTGCTGGAC
Found at i:13019313 original size:17 final size:17
Alignment explanation
Indices: 13019293--13019328 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13019283 TTTATTAATT
*
13019293 TTAAATAAAAAATTAAA
1 TTAAATAAAAAAGTAAA
*
13019310 TTAAATGAAAAAGTAAA
1 TTAAATAAAAAAGTAAA
13019327 TT
1 TT
13019329 TTCAAACAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
TTAAATAAAAAAGTAAA
Found at i:13026878 original size:17 final size:17
Alignment explanation
Indices: 13026844--13026875 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13026834 GAAATAAAAT
13026844 AATTTATTTTATATTTG
1 AATTTATTTTATATTTG
13026861 AATTT-TTTTATATTT
1 AATTTATTTTATATTT
13026876 TGATTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (17 bp):
AATTTATTTTATATTTG
Found at i:13031796 original size:40 final size:40
Alignment explanation
Indices: 13031752--13031834 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
13031742 CACACCATAC
*
13031752 AAAATGAAATTTCAATTTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
13031792 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
1 AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
13031832 AAA
1 AAA
13031835 TTCTAGAGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (40 bp):
AAAATGAAAATTCAATTTTGTTTAACTCATGAACCACTAA
Found at i:13032867 original size:14 final size:14
Alignment explanation
Indices: 13032834--13032870 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
13032824 TAGTTTAGTT
13032834 TATTAATTTTTTAAA
1 TATT-ATTTTTTAAA
13032849 T-TTATTTTTTAAA
1 TATTATTTTTTAAA
13032862 TATTATTTT
1 TATTATTTT
13032871 AATATAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 9 0.43
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTTTTTAAA
Found at i:13032906 original size:20 final size:22
Alignment explanation
Indices: 13032856--13032908 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
13032846 AAATTTATTT
*
13032856 TTTAAATATTATTTTAATATAAT
1 TTTAAATA-TATTTTAATATAAA
*
13032879 TTTTAATATA-TTTAA-ATAAA
1 TTTAAATATATTTTAATATAAA
13032899 TTTAAATATA
1 TTTAAATATA
13032909 AAATAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 13 0.48
21 5 0.19
22 2 0.07
23 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTAAATATATTTTAATATAAA
Found at i:13033529 original size:24 final size:22
Alignment explanation
Indices: 13033502--13033554 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 22
13033492 GAATAATATA
*
13033502 AATAAAAAATATAATTTAAATTTT
1 AATAAAAAATATAA-ATAAA-TTT
*
13033526 AATAAAAATTATAAATAAATTT
1 AATAAAAAATATAAATAAATTT
13033548 AATAAAA
1 AATAAAA
13033555 TAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 10 0.37
23 4 0.15
24 13 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAAATATAAATAAATTT
Found at i:13033548 original size:22 final size:24
Alignment explanation
Indices: 13033502--13033571 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 24
13033492 GAATAATATA
*
13033502 AATAAAAAATATAATTTAAATTTT
1 AATAAAAAATATAATATAAATTTT
*
13033526 AATAAAAATTATAA-ATAAA-TTT
1 AATAAAAAATATAATATAAATTTT
*
13033548 AATAAAATAA-A-AATATATATTTT
1 AATAAAA-AATATAATATAAATTTT
13033571 A
1 A
13033572 TATTTTTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 2 0.05
22 15 0.38
23 9 0.23
24 13 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
AATAAAAAATATAATATAAATTTT
Found at i:13038326 original size:2 final size:2
Alignment explanation
Indices: 13038314--13038344 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13038304 TTCTATGTTT
*
13038314 TA TA TA CA 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 TA TA TA T
13038345 TGAAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13038517 original size:17 final size:17
Alignment explanation
Indices: 13038495--13038530 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13038485 ATTGTTTGAC
*
13038495 AATTTACTTTTTCATTT
1 AATTTAATTTTTCATTT
*
13038512 AATTTAATTTTTTATTT
1 AATTTAATTTTTCATTT
13038529 AA
1 AA
13038531 AATTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTAATTTTTCATTT
Found at i:13040746 original size:29 final size:30
Alignment explanation
Indices: 13040704--13040805 Score: 93
Period size: 30 Copynumber: 3.4 Consensus size: 30
13040694 AATTTATGTA
*
13040704 AAGAGTTTGTTTAGGTACAAATTAAAATTAC
1 AAGA-TTTATTTAGGTACAAATTAAAATTAC
* * *
13040735 AA-ATTTATTTAGATATAAATTAAAAAT-C
1 AAGATTTATTTAGGTACAAATTAAAATTAC
* *
13040763 AATGATTTATTTAAGTGCAAATTAAAGATTA-
1 AA-GATTTATTTAGGTACAAATTAAA-ATTAC
*
13040794 AAGGTTTATTTA
1 AAGATTTATTTA
13040806 AATATAATAA
Statistics
Matches: 57, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.05
29 20 0.35
30 28 0.49
31 6 0.11
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (30 bp):
AAGATTTATTTAGGTACAAATTAAAATTAC
Found at i:13046662 original size:100 final size:100
Alignment explanation
Indices: 13046463--13046661 Score: 382
Period size: 99 Copynumber: 2.0 Consensus size: 100
13046453 TGAGAGTTTG
13046463 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
1 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
13046528 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
66 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
*
13046563 ATGAGATTCAATTTGATTTTATTG-TTAAAAAATTCATGTAAAAGATTGGAATATATATAGTTGA
1 ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
13046627 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
66 CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
13046662 TTGTTTTATA
Statistics
Matches: 98, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
99 74 0.76
100 24 0.24
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (100 bp):
ATGAGATTCAATTTGATTTTATTGTTTAAAAAATTCAAGTAAAAGATTGGAATATATATAGTTGA
CCTCACATTTTCAAATCTCTAACAAATTTTTTTTT
Found at i:13059021 original size:20 final size:20
Alignment explanation
Indices: 13058996--13059036 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
13058986 GATTCAAGAA
13058996 GACTTTAGTCTTCTGCAGGG
1 GACTTTAGTCTTCTGCAGGG
13059016 GACTTTAGTCTTCTGCAGGG
1 GACTTTAGTCTTCTGCAGGG
13059036 G
1 G
13059037 GAAACAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.20, G:0.32, T:0.34
Consensus pattern (20 bp):
GACTTTAGTCTTCTGCAGGG
Found at i:13065417 original size:27 final size:25
Alignment explanation
Indices: 13065362--13065426 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 25
13065352 TATATAAAAA
* *
13065362 ATAAATTATATAT-AATTTTTATTT
1 ATAATTTATATATAAATTTTTATAT
*
13065386 TTAATTTATATATAAATTTATTTATAT
1 ATAATTTATATATAAA-TT-TTTATAT
*
13065413 ATAATTTACATATA
1 ATAATTTATATATA
13065427 TATAAAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 11 0.33
25 2 0.06
26 2 0.06
27 18 0.55
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
ATAATTTATATATAAATTTTTATAT
Found at i:13065420 original size:15 final size:15
Alignment explanation
Indices: 13065389--13065431 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
13065379 TTTATTTTTA
13065389 ATTTATATATAAATTT
1 ATTTATATAT-AATTT
13065405 ATTTATATATAATTT
1 ATTTATATATAATTT
**
13065420 ACATATATATAA
1 ATTTATATATAA
13065432 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTTATATATAATTT
Found at i:13065452 original size:23 final size:24
Alignment explanation
Indices: 13065415--13065477 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 24
13065405 ATTTATATAT
13065415 AATTTACATATATATAAAAATAAAA
1 AATTTA-ATATATATAAAAATAAAA
**
13065440 AATTT-ATATATATGTAAATAAAA
1 AATTTAATATATATAAAAATAAAA
*
13065463 ATTTTAATATATATA
1 AATTTAATATATATA
13065478 TATGTGTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
23 20 0.61
24 8 0.24
25 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
AATTTAATATATATAAAAATAAAA
Found at i:13070574 original size:20 final size:22
Alignment explanation
Indices: 13070539--13070581 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13070529 ATAACGAAAT
*
13070539 TTTTTATTATATTAATTT-TAA
1 TTTTTATTATAATAATTTCTAA
13070560 TTTTTATT-TAATAATTTCTAA
1 TTTTTATTATAATAATTTCTAA
13070581 T
1 T
13070582 AACAAATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTATTATAATAATTTCTAA
Found at i:13072651 original size:4 final size:4
Alignment explanation
Indices: 13072644--13072686 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
13072634 TCTCTCTCTC
* * *
13072644 TCTA TCTA TCTA TCTA TCTA TTTA TCTA TCTA TATA TATA TCT
1 TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCTA TCT
13072687 TTCTTTTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (4 bp):
TCTA
Found at i:13074372 original size:20 final size:21
Alignment explanation
Indices: 13074336--13074393 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
13074326 AAATAATTTA
*
13074336 ATTTAATTTA-ATGAAATT-AT
1 ATTTAATATATAT-AAATTAAT
13074356 ATTTAATATATATAAATTAAT
1 ATTTAATATATATAAATTAAT
* *
13074377 ATTAAAAATTATATAAA
1 ATTTAATA-TATATAAA
13074394 AAATAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 10 0.31
22 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTTAATATATATAAATTAAT
Found at i:13074377 original size:14 final size:14
Alignment explanation
Indices: 13074358--13074407 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
13074348 GAAATTATAT
*
13074358 TTAATATATATAAA
1 TTAATATATAAAAA
13074372 TTAATAT-TAAAAA
1 TTAATATATAAAAA
13074385 TT-ATATA-AAAAA
1 TTAATATATAAAAA
*
13074397 TAAATTATATA
1 TTAA-TATATA
13074408 TAATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
12 10 0.33
13 8 0.27
14 11 0.37
15 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAATATATAAAAA
Found at i:13074443 original size:16 final size:16
Alignment explanation
Indices: 13074422--13074452 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13074412 TTTTATTTTT
13074422 AATTTATATATATATG
1 AATTTATATATATATG
*
13074438 AATTTATTTATATAT
1 AATTTATATATATAT
13074453 AAATAAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTATATATATATG
Found at i:13074451 original size:22 final size:22
Alignment explanation
Indices: 13074418--13074485 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
13074408 TAATTTTTAT
*
13074418 TTTTAATTTATATATATATGAA
1 TTTTAATATATATATATATGAA
* * **
13074440 -TTTATTTATATATAAATAAAAA
1 TTTTA-ATATATATATATATGAA
13074462 TTTTAATATATATATATATGAA
1 TTTTAATATATATATATATGAA
13074484 TT
1 TT
13074486 CGAATCAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 4 0.11
22 27 0.77
23 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TTTTAATATATATATATATGAA
Found at i:13074898 original size:17 final size:17
Alignment explanation
Indices: 13074876--13074911 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13074866 ATTGTTTGAC
*
13074876 AATTTACTTTTTCATTT
1 AATTTAATTTTTCATTT
*
13074893 AATTTAATTTTTTATTT
1 AATTTAATTTTTCATTT
13074910 AA
1 AA
13074912 AATTAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTTAATTTTTCATTT
Found at i:13085588 original size:22 final size:22
Alignment explanation
Indices: 13085563--13085634 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
13085553 TATTTAATAA
13085563 TAAATAAGATGATAACAATTAT
1 TAAATAAGATGATAACAATTAT
**
13085585 TAAATAA-AT-AT-ACAAAAAT
1 TAAATAAGATGATAACAATTAT
*
13085604 AAATATAAGATGATAACAATATTAT
1 TAA-ATAAGATGATAAC-A-ATTAT
13085629 TAAATA
1 TAAATA
13085635 CAATAATACA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 8 0.21
20 6 0.16
21 4 0.11
22 9 0.24
23 2 0.05
24 4 0.11
25 5 0.13
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
TAAATAAGATGATAACAATTAT
Found at i:13085618 original size:42 final size:46
Alignment explanation
Indices: 13085566--13085657 Score: 156
Period size: 46 Copynumber: 2.1 Consensus size: 46
13085556 TTAATAATAA
13085566 ATAAGATGATAAC-A-ATTATTAAATA-AAT-ATACAAAAATAAAT
1 ATAAGATGATAACAATATTATTAAATACAATAATACAAAAATAAAT
13085608 ATAAGATGATAACAATATTATTAAATACAATAATACAAAAATAAAT
1 ATAAGATGATAACAATATTATTAAATACAATAATACAAAAATAAAT
13085654 ATAA
1 ATAA
13085658 AATACAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
42 13 0.28
43 1 0.02
44 11 0.24
45 3 0.07
46 18 0.39
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.28
Consensus pattern (46 bp):
ATAAGATGATAACAATATTATTAAATACAATAATACAAAAATAAAT
Found at i:13085668 original size:20 final size:20
Alignment explanation
Indices: 13085629--13085667 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
13085619 ACAATATTAT
13085629 TAAATACAATAATACAAAAA
1 TAAATACAATAATACAAAAA
*
13085649 TAAATATAA-AATACAAAAA
1 TAAATACAATAATACAAAAA
13085668 AAAACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAATACAATAATACAAAAA
Found at i:13085678 original size:19 final size:19
Alignment explanation
Indices: 13085639--13085678 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
13085629 TAAATACAAT
* * *
13085639 AATACAAAAATAAATATAA
1 AATACAAAAAAAAACAAAA
13085658 AATACAAAAAAAAACAAAA
1 AATACAAAAAAAAACAAAA
13085677 AA
1 AA
13085679 AAAAGTCGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (19 bp):
AATACAAAAAAAAACAAAA
Found at i:13086811 original size:20 final size:19
Alignment explanation
Indices: 13086771--13086834 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
13086761 TGTTAATTTT
13086771 TAAAATAAAACTTAAA-AAAA
1 TAAAATAAAA--TAAATAAAA
13086791 TAAAATAAAATAAATATAAA
1 TAAAATAAAATAAATA-AAA
** *
13086811 TTTAATAAAATTAATAAAA
1 TAAAATAAAATAAATAAAA
13086830 -AAAAT
1 TAAAAT
13086835 GAGGAAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 26 0.70
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAATAAAATAAATAAAA
Found at i:13089091 original size:21 final size:22
Alignment explanation
Indices: 13089062--13089107 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
13089052 AAAATATAAA
* *
13089062 AAATATATTTTTTA-TTTTATT
1 AAATATATTTATAATTTTTATT
*
13089083 AAATTTATTTATAATTTTTATT
1 AAATATATTTATAATTTTTATT
13089105 AAA
1 AAA
13089108 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATATTTATAATTTTTATT
Found at i:13089134 original size:13 final size:13
Alignment explanation
Indices: 13089065--13089135 Score: 56
Period size: 13 Copynumber: 5.5 Consensus size: 13
13089055 ATATAAAAAA
13089065 TATATTTTTTATT
1 TATATTTTTTATT
*
13089078 T-TATTAAATTTATT
1 TATATT--TTTTATT
*
13089092 TATAATTTTTA-T
1 TATATTTTTTATT
* * * *
13089104 TAAAATTTTAAAT
1 TATATTTTTTATT
13089117 TATATTTTTTATT
1 TATATTTTTTATT
13089130 TATATT
1 TATATT
13089136 ATTCTTACAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
12 14 0.31
13 21 0.47
14 7 0.16
15 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATATTTTTTATT
Found at i:13089752 original size:20 final size:21
Alignment explanation
Indices: 13089727--13089781 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 21
13089717 AAAATTATTT
* *
13089727 TATATTTAAATTTAT-TTAAA
1 TATATTAAAAATTATATTAAA
13089747 TATATTAAAAATTATATTAAAA
1 TATATTAAAAATTATATT-AAA
13089769 TAATATATAAAAA
1 T-ATAT-TAAAAA
13089782 ATAAATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 13 0.45
21 2 0.07
22 4 0.14
23 4 0.14
24 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATTAAAAATTATATTAAA
Found at i:13089784 original size:11 final size:12
Alignment explanation
Indices: 13089744--13089796 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
13089734 AAATTTATTT
13089744 AAATATATTAAA
1 AAATATATTAAA
*
13089756 AATTATATTAAA
1 AAATATATTAAA
13089768 ATAATATA-TAAA
1 A-AATATATTAAA
*
13089780 AAATAAATTTAAA
1 AAATATA-TTAAA
13089793 AAAT
1 AAAT
13089797 TAATAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 5 0.14
12 17 0.49
13 13 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AAATATATTAAA
Found at i:13089791 original size:25 final size:25
Alignment explanation
Indices: 13089745--13089793 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
13089735 AATTTATTTA
* *
13089745 AATATATTAAAAATTATATTAAAAT
1 AATATATAAAAAATAATATTAAAAT
13089770 AATATATAAAAAATAA-ATTTAAAA
1 AATATATAAAAAATAATA-TTAAAA
13089794 AATTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATATATAAAAAATAATATTAAAAT
Found at i:13089795 original size:13 final size:14
Alignment explanation
Indices: 13089745--13089801 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
13089735 AATTTATTTA
*
13089745 AATATATTAAAAAT
1 AATATATAAAAAAT
*
13089759 --TATAT-TAAAAT
1 AATATATAAAAAAT
13089770 AATATATAAAAAAT
1 AATATATAAAAAAT
*
13089784 AA-ATTTAAAAAATT
1 AATATATAAAAAA-T
13089798 AATA
1 AATA
13089802 AACTAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
11 5 0.14
12 5 0.14
13 14 0.40
14 10 0.29
15 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATATAAAAAAT
Found at i:13091327 original size:30 final size:30
Alignment explanation
Indices: 13091271--13091327 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
13091261 ACAAATATAA
* **
13091271 ATATATAATTTTTTTAATTTTATTAAATTT
1 ATATATAATTTTATTAAAATTATTAAATTT
13091301 ATATATAATTATTATTAAAATT-TTAAA
1 ATATATAATT-TTATTAAAATTATTAAA
13091328 CTTTTATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 15 0.65
31 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATATAATTTTATTAAAATTATTAAATTT
Found at i:13093243 original size:2 final size:2
Alignment explanation
Indices: 13093236--13093268 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13093226 CTGTGGCATG
13093236 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
13093269 GTTGAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:13096746 original size:16 final size:17
Alignment explanation
Indices: 13096725--13096756 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
13096715 AAATTAATCA
13096725 AAATATAAAA-AAATTC
1 AAATATAAAATAAATTC
13096741 AAATATAAAATAAATT
1 AAATATAAAATAAATT
13096757 ATTTTATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATATAAAATAAATTC
Found at i:13104498 original size:27 final size:26
Alignment explanation
Indices: 13104443--13104498 Score: 60
Period size: 26 Copynumber: 2.1 Consensus size: 26
13104433 TTTGTTATAC
* *
13104443 AATTTTATAAAAAAATACTTAAATTT
1 AATTTTATAAAAAAATAATTAAATGT
*
13104469 AATTTTTTAAAAAAATATATTGAAA-GT
1 AATTTTATAAAAAAATA-ATT-AAATGT
13104496 AAT
1 AAT
13104499 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 16 0.64
27 6 0.24
28 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (26 bp):
AATTTTATAAAAAAATAATTAAATGT
Found at i:13104930 original size:13 final size:12
Alignment explanation
Indices: 13104890--13104928 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
13104880 CATATTGAAC
13104890 TTTATT-AATTA
1 TTTATTAAATTA
13104901 TTTATTTAAATTA
1 TTTA-TTAAATTA
13104914 TTTATTAAATTA
1 TTTATTAAATTA
13104926 TTT
1 TTT
13104929 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.15
12 13 0.50
13 9 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTATTAAATTA
Found at i:13106577 original size:29 final size:29
Alignment explanation
Indices: 13106533--13106636 Score: 100
Period size: 30 Copynumber: 3.5 Consensus size: 29
13106523 TTAATTTATG
*
13106533 TAAAGAGTTTGTTTAGGTACAAATTAAAAT
1 TAAAGA-TTTATTTAGGTACAAATTAAAAT
* * *
13106563 TAAAAATTTATTTAGATATAAATTAAAAAT
1 TAAAGATTTATTTAGGTACAAATT-AAAAT
* * * *
13106593 CAATGATTTATTTAAGTGCAAATTAAAGAT
1 TAAAGATTTATTTAGGTACAAATTAAA-AT
*
13106623 TAAAGGTTTATTTA
1 TAAAGATTTATTTA
13106637 AATATAATAA
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
29 18 0.31
30 40 0.69
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (29 bp):
TAAAGATTTATTTAGGTACAAATTAAAAT
Found at i:13112742 original size:15 final size:16
Alignment explanation
Indices: 13112716--13112745 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
13112706 TTTAATTAAA
13112716 AAATTGATAAAAAAAT
1 AAATTGATAAAAAAAT
13112732 AAATT-ATAAAAAAA
1 AAATTGATAAAAAAA
13112746 AATATAGGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATTGATAAAAAAAT
Found at i:13127832 original size:2 final size:2
Alignment explanation
Indices: 13127827--13127852 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13127817 AAAAATGTGC
13127827 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13127853 GAACAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13128832 original size:15 final size:16
Alignment explanation
Indices: 13128793--13128835 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 16
13128783 ATATATATAT
13128793 ATATATTAAAAATTAAA
1 ATATA-TAAAAATTAAA
13128810 ATTATATAAAAA-TAAA
1 A-TATATAAAAATTAAA
13128826 ATATATAAAA
1 ATATATAAAA
13128836 TTTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.36
16 5 0.20
17 7 0.28
18 4 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATATAAAAATTAAA
Found at i:13128885 original size:15 final size:15
Alignment explanation
Indices: 13128851--13128903 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
13128841 ATTTTTAATT
*
13128851 TTTATATATATGTGAA
1 TTTATATATATAT-AA
*
13128867 TTTATTTATATATAA
1 TTTATATATATATAA
*
13128882 TTTATATATAAATAA
1 TTTATATATATATAA
*
13128897 TATATAT
1 TTTATAT
13128904 TTATTTTAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (15 bp):
TTTATATATATATAA
Found at i:13128886 original size:11 final size:11
Alignment explanation
Indices: 13128870--13128907 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
13128860 ATGTGAATTT
13128870 ATTTATATATA
1 ATTTATATATA
13128881 ATTTATATATA
1 ATTTATATATA
* *
13128892 AATAATATAT-
1 ATTTATATATA
13128902 ATTTAT
1 ATTTAT
13128908 TTTAAGTCGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
10 4 0.17
11 19 0.83
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTTATATATA
Found at i:13141107 original size:62 final size:62
Alignment explanation
Indices: 13140985--13141133 Score: 153
Period size: 62 Copynumber: 2.4 Consensus size: 62
13140975 TTTAGGATTA
*
13140985 TTGACAAAAATAACTTGAATAATCTACTTGTCATAAATTGAAGGAAATTATTCAATGTGTTT
1 TTGACAAAAATAACTTGAATAATCTACTTGTCATAAATTGAAGGAAATTATTCAAAGTGTTT
* * * *
13141047 TTGACTAAAAA-AATCTTGAATAAT-TAC-T-TCATAAAAATTGAATGAGATTGTTGAAAGTGTT
1 TTGAC-AAAAATAA-CTTGAATAATCTACTTGTCAT--AAATTGAAGGAAATTATTCAAAGTGTT
13141108 T
62 T
* * *
13141109 TTAATCAGAAATACCTTGAATAATC
1 TTGA-CAAAAATAACTTGAATAATC
13141134 ATATTCAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
60 4 0.06
61 1 0.01
62 50 0.69
63 17 0.24
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (62 bp):
TTGACAAAAATAACTTGAATAATCTACTTGTCATAAATTGAAGGAAATTATTCAAAGTGTTT
Found at i:13142178 original size:6 final size:6
Alignment explanation
Indices: 13142167--13142200 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
13142157 AAAAATAGTT
13142167 AATTAA AATTAA AATTAA AATTTATA AATTAA AA
1 AATTAA AATTAA AATTAA AA-TTA-A AATTAA AA
13142201 CATTTTGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.65
7 6 0.23
8 3 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
AATTAA
Found at i:13142184 original size:12 final size:14
Alignment explanation
Indices: 13142167--13142200 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
13142157 AAAAATAGTT
13142167 AATTAAAA-TTA-A
1 AATTAAAATTTATA
13142179 AATTAAAATTTATA
1 AATTAAAATTTATA
13142193 AATTAAAA
1 AATTAAAA
13142201 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 3 0.15
14 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATTAAAATTTATA
Found at i:13145337 original size:21 final size:23
Alignment explanation
Indices: 13145313--13145362 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 23
13145303 CTTTTTCTTC
*
13145313 AAAATTTCAATTAAA-AATAAA-
1 AAAATTTCAATAAAACAATAAAT
13145334 AAAA-TT-AATAAAACAATAAAT
1 AAAATTTCAATAAAACAATAAAT
13145355 AAAATTTC
1 AAAATTTC
13145363 TAAAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 8 0.33
22 2 0.08
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAATTTCAATAAAACAATAAAT
Found at i:13145654 original size:29 final size:30
Alignment explanation
Indices: 13145621--13145678 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
13145611 CAATTCCCAA
13145621 TAAAT-GAAAAAATCAAGA-AATTTTTTTTT
1 TAAATAGAAAAAAT-AAGACAATTTTTTTTT
* *
13145650 TAAATATAAAAAATAAGACTATTTTTTTT
1 TAAATAGAAAAAATAAGACAATTTTTTTT
13145679 ATCTAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (30 bp):
TAAATAGAAAAAATAAGACAATTTTTTTTT
Found at i:13151517 original size:23 final size:23
Alignment explanation
Indices: 13151490--13151538 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
13151480 TTCGTATTTC
*
13151490 TTTTATTATTTTT-GCTTTCTATT
1 TTTTATT-TTTTTAGCATTCTATT
*
13151513 TTTTATTTTTTTATCATTCTATT
1 TTTTATTTTTTTAGCATTCTATT
13151536 TTT
1 TTT
13151539 ATGTGCCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTTATTTTTTTAGCATTCTATT
Found at i:13155883 original size:50 final size:49
Alignment explanation
Indices: 13155829--13155938 Score: 121
Period size: 49 Copynumber: 2.2 Consensus size: 49
13155819 TTTCAAGAAC
* * * *
13155829 AGATAAGAATTTAAAAAGTTGTTGAACATCTGCTGAGATGTGCTTTTTCA
1 AGATAAG-ATTTAAAAAGTTCTTGAACATCTGCTGAAAAGAGCTTTTTCA
** * * *
13155879 AGATAAGATTTTTAAAGTTCTTGAGCCTTTGCTGAAAAGAGCTTTTTCA
1 AGATAAGATTTAAAAAGTTCTTGAACATCTGCTGAAAAGAGCTTTTTCA
*
13155928 AGATGAGATTT
1 AGATAAGATTT
13155939 TTTTAAAGTT
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
49 43 0.86
50 7 0.14
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (49 bp):
AGATAAGATTTAAAAAGTTCTTGAACATCTGCTGAAAAGAGCTTTTTCA
Found at i:13155912 original size:49 final size:48
Alignment explanation
Indices: 13155843--13156551 Score: 267
Period size: 47 Copynumber: 15.3 Consensus size: 48
13155833 AAGAATTTAA
* * * * *
13155843 AAAGTTGTTGAACATCTGCTGAGATGTGCTTTTTCAAGATAAGATTTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGAT-AGATTTTT
* * *
13155892 AAAGTTCTTGAGCCTTTGCTGAAAAGAGCTTTTTCAAGATGAGATTTTTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGAT-AGA--TTTTT
* *
13155943 AAAGTTGTTGAG-CTTCTGCTAAGAGGAGCTTGTTT-AAG--AGAATTTT
1 AAAGTTGTTGAGCCTT-TGCTGAGAGGAGCTT-TTTCAAGATAGATTTTT
* * *
13155989 AAAGTTGTTGAGCCTCTGCTTAGAGGGGC-TTTTCAAGA-AG---TTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * *
13156032 AAAGTTATTGAG-CTTCTGCTGATAGGAGC-TTTCCAAGAT-G----TT
1 AAAGTTGTTGAGCCTT-TGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* ** * * * *
13156074 AAAGCTCTGCTTAGAGGAACTTTTTTTAAGATGAG-ATTTT--A-A-AG-TTGTT
1 AAAG-T-TG-TT-GA-G--CCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * *
13156123 -AAGCCT-CT--G---TTG-AGAGA--AGCTTTTTCAAGATGAGATTTTTTT
1 AAAG-TTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGAT-AGA--TTTTT
* * *
13156165 AAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTGTTCAAGA-A-AATTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * * *
13156211 AAAGTTGTTGATCCTCTGCTTAGATGAGC-TTTTCAAGA-AG---TTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* *** * * *
13156254 AAAGTTATTGAGCCTCCACTTAGAAGAG-TTTTTCAAGATAAATTTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * * *
13156301 AAAGTTGTTGAG-CTTCTACTTAGATGAGCTTTTTCAAGA-A-TTTTTT
1 AAAGTTGTTGAGCCTT-TGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * * * * * * *
13156347 AAAAGTTATTAAGCCTATACTAAGATGAGCATTTTCAAGAT-GAATTTT
1 -AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
* * * * *
13156395 AAAATTGTTAAGCTTTTGCTGAAAGGAGCATTTTCAAGAT-GAATTTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAG-ATTTTT
* * * *
13156443 AAAGTTGTTGAGCCTCTGCTTAGAGAAACTTTTTCAA-A-A-ATTTTTT
1 AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGA-TTTTT
* * * *
13156489 AAAAGTTGTTGAACCTCTGCTGAGAGGAG-TATTTTTAAGAT-GAATTTT
1 -AAAGTTGTTGAGCCTTTGCTGAGAGGAGCT-TTTTCAAGATAGATTTTT
13156537 AAAGTTGTTGAGCCT
1 AAAGTTGTTGAGCCT
13156552 CTAATTAGAG
Statistics
Matches: 509, Mismatches: 90, Indels: 124
0.70 0.12 0.17
Matches are distributed among these distances:
33 2 0.00
34 4 0.01
35 3 0.01
36 3 0.01
37 1 0.00
39 2 0.00
41 1 0.00
42 13 0.03
43 73 0.14
44 5 0.01
45 18 0.04
46 76 0.15
47 139 0.27
48 64 0.13
49 54 0.11
50 5 0.01
51 43 0.08
52 3 0.01
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (48 bp):
AAAGTTGTTGAGCCTTTGCTGAGAGGAGCTTTTTCAAGATAGATTTTT
Found at i:13156322 original size:47 final size:47
Alignment explanation
Indices: 13156110--13156553 Score: 315
Period size: 47 Copynumber: 9.4 Consensus size: 47
13156100 TAAGATGAGA
* *
13156110 TTTTAAAGTTGTTAAGCCTCTG-TT-GAGAGAAGCTTTTTCAAGATGAGATTT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGA-AG-AGCTTTTTCAAGA--A-A-AT
* * *
13156161 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTGTTCAAGAAAA-
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGAAAAT
* *
13156207 TTTTAAAGTTGTTGATCCTCTGCTTAGATGAGC-TTTTCAAG--AA-
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGAAAAT
* * **
13156250 GTTTAAAGTTATTGAGCCTCCACTTAGAAGAG-TTTTTCAAGATAAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGA-AAAT
* * * *
13156297 TTTTAAAGTTGTTGAGCTTCTACTTAGATGAGCTTTTTCAAG-AATT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGAAAAT
* * * * * * * *
13156343 TTTTAAAAGTTATTAAGCCTATACTAAGATGAGCATTTTCAAGATGAA-
1 TTTT-AAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGA-AAAT
* * * * * * *
13156391 TTTTAAAATTGTTAAGCTTTTGCTGA-AAGGAGCATTTTCAAGATGAAT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAA-GAGCTTTTTCAAGA-AAAT
* *
13156439 TTTTAAAGTTGTTGAGCCTCTGCTTAG-AGAAACTTTTTCAA-AAATT
1 TTTTAAAGTTGTTGAGCCTCTGCTTAGAAG-AGCTTTTTCAAGAAAAT
* * * * *
13156485 TTTTAAAAGTTGTTGAACCTCTGCTGAGAGGAG-TATTTTTAAGATGAA-
1 TTTT-AAAGTTGTTGAGCCTCTGCTTAGAAGAGCT-TTTTCAAGA-AAAT
13156533 TTTTAAAGTTGTTGAGCCTCT
1 TTTTAAAGTTGTTGAGCCTCT
13156554 AATTAGAGAA
Statistics
Matches: 320, Mismatches: 53, Indels: 44
0.77 0.13 0.11
Matches are distributed among these distances:
43 36 0.11
45 7 0.02
46 47 0.15
47 139 0.43
48 51 0.16
49 3 0.01
51 33 0.10
52 2 0.01
53 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (47 bp):
TTTTAAAGTTGTTGAGCCTCTGCTTAGAAGAGCTTTTTCAAGAAAAT
Found at i:13156449 original size:142 final size:140
Alignment explanation
Indices: 13156096--13156553 Score: 471
Period size: 142 Copynumber: 3.2 Consensus size: 140
13156086 AGAGGAACTT
* * * *
13156096 TTTTTAAGATGAGATTTTAAAGTTGTTAAGCCTCTGTTGAGAGAAGCTTTTTCAAGATGAGATTT
1 TTTTCAAGATGA-ATTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAGATGA-A--T
* * ** *
13156161 TTTTAAAGTTGTTGAGCCTCTGCTGAGAGGAGCTTGTTCAAGAAAATTTT-AAAGTTGTTGATCC
62 TTTTAAAGTTGTTGAGCCTCTGCTTAGA-GAGCTTTTTCAAGAATTTTTTAAAAGTTGTT-AACC
*
13156225 TCTGCTTAGATGAGC-
125 TCTGCTAAGATGAGCA
* * * ** * *
13156240 TTTTC-A-A-GAAGTTTAAAGTTATTGAGCCTCCACTTAGAA-GAG-TTTTTCAAGATAAATTTT
1 TTTTCAAGATGAATTTTAAAGTTGTTAAGCCTCTGCTGA-AAGGAGCTTTTTCAAGATGAATTTT
* * * *
13156300 TAAAGTTGTTGAGCTTCTACTTAGATGAGCTTTTTCAAGAATTTTTTAAAAGTTATTAAGCCTAT
65 TAAAGTTGTTGAGCCTCTGCTTAGA-GAGCTTTTTCAAGAATTTTTTAAAAGTTGTTAA-CCTCT
*
13156365 ACTAAGATGAGCA
128 GCTAAGATGAGCA
* * * *
13156378 TTTTCAAGATGAATTTTAAAATTGTTAAGCTTTTGCTGAAAGGAGCATTTTCAAGATGAATTTTT
1 TTTTCAAGATGAATTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAGATGAATTTTT
* *
13156443 AAAGTTGTTGAGCCTCTGCTTAGAGAAACTTTTTCAAAAATTTTTTAAAAGTTGTTGAACCTCTG
66 AAAGTTGTTGAGCCTCTGCTTAGAG-AGCTTTTTCAAGAATTTTTTAAAAGTTGTT-AACCTCTG
* * *
13156508 CTGAGAGGAGTA
129 CTAAGATGAGCA
* *
13156520 TTTTTAAGATGAATTTTAAAGTTGTTGAGCCTCT
1 TTTTCAAGATGAATTTTAAAGTTGTTAAGCCTCT
13156554 AATTAGAGAA
Statistics
Matches: 254, Mismatches: 49, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
136 45 0.18
137 22 0.09
138 6 0.02
139 13 0.05
140 25 0.10
141 27 0.11
142 109 0.43
143 3 0.01
144 4 0.02
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (140 bp):
TTTTCAAGATGAATTTTAAAGTTGTTAAGCCTCTGCTGAAAGGAGCTTTTTCAAGATGAATTTTT
AAAGTTGTTGAGCCTCTGCTTAGAGAGCTTTTTCAAGAATTTTTTAAAAGTTGTTAACCTCTGCT
AAGATGAGCA
Found at i:13161535 original size:31 final size:28
Alignment explanation
Indices: 13161477--13161546 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 28
13161467 TATTAATTTA
*
13161477 TTATTTAATTTTTTAAAAAAATTAAAAT
1 TTATTTAATTTTTTAAAAAAATAAAAAT
13161505 TTATTT-ATTTATCTTAAAAATTAATAAAAAT
1 TTATTTAATTT-T-TTAAAAA--AATAAAAAT
13161536 TCATATTTAAT
1 T--TATTTAAT
13161547 CATTAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
27 4 0.12
28 7 0.21
29 7 0.21
31 9 0.26
33 5 0.15
34 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (28 bp):
TTATTTAATTTTTTAAAAAAATAAAAAT
Found at i:13163873 original size:80 final size:80
Alignment explanation
Indices: 13163771--13163931 Score: 241
Period size: 80 Copynumber: 2.0 Consensus size: 80
13163761 AAAAGTGGGC
* * * *
13163771 AAAATCGAAAATTTTGATATGATATAATGTTTAAGCAAATCATTTTCTTACACGAACAGATGCTA
1 AAAATAGAAAATGTTGATATGATATAATGTTTAAACAAATCACTTTCTTACACGAACAGATGCTA
13163836 TAAAAAATTAAATGA
66 TAAAAAATTAAATGA
* * * * *
13163851 AAAATAGAAAATGTTGATATGATATAATGTTTAAATAACTCGCTTTCTTACATGAATAGATGCTA
1 AAAATAGAAAATGTTGATATGATATAATGTTTAAACAAATCACTTTCTTACACGAACAGATGCTA
13163916 TAAAAAATTAAATGA
66 TAAAAAATTAAATGA
13163931 A
1 A
13163932 TTATCTTATG
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (80 bp):
AAAATAGAAAATGTTGATATGATATAATGTTTAAACAAATCACTTTCTTACACGAACAGATGCTA
TAAAAAATTAAATGA
Found at i:13164740 original size:29 final size:29
Alignment explanation
Indices: 13164708--13164784 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 29
13164698 TTTAAAGGTT
13164708 AATAAAAATTTATATTTAATTATTAATAA
1 AATAAAAATTTATATTTAATTATTAATAA
* *
13164737 AAT---AATAT-TATTTAATTTATTGATAA
1 AATAAAAATTTATATTTAA-TTATTAATAA
*
13164763 TATATAAAATTTATATATTAAT
1 AATA-AAAATTTATAT-TTAAT
13164785 AATATATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
25 7 0.19
26 15 0.41
29 3 0.08
30 4 0.11
31 4 0.11
32 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (29 bp):
AATAAAAATTTATATTTAATTATTAATAA
Found at i:13167276 original size:20 final size:19
Alignment explanation
Indices: 13167251--13167288 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
13167241 TTTTATGGTT
13167251 TTAATTTAATTTTATTTTTC
1 TTAA-TTAATTTTATTTTTC
*
13167271 TTAATTATTTTTATTTTT
1 TTAATTAATTTTATTTTT
13167289 TCAGTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (19 bp):
TTAATTAATTTTATTTTTC
Done.