Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001547.1 Hibiscus syriacus cultivar Beakdansim tig00003041_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: 10425128
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 51
Found at i:1289218 original size:45 final size:43
Alignment explanation
Indices: 1289125--1289246 Score: 120
Period size: 45 Copynumber: 2.7 Consensus size: 43
1289115 AAAAGGAGAT
* *
1289125 AGAACAAAATAAAAAAGAAGAAGGAAAAAAGAAGAAAAATAAAAA
1 AGAA-AAAAGAAAAAAGAA-AAAGAAAAAAGAAGAAAAATAAAAA
* * **
1289170 AGAAGAAGGAAAAAGAAGAAAAAGAAAAAAGATAGAAAAAT-ATGA
1 AGAAAAAAG-AAAA-AAGAAAAAGAAAAAAGA-AGAAAAATAAAAA
*
1289215 AGAAAAAAGAAAAAAGCAAAAGAGAAAAAGAA
1 AGAAAAAAGAAAAAAGAAAAAGA-AAAAAGAA
1289247 AAAGGAGAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
43 10 0.16
44 13 0.20
45 28 0.44
46 13 0.20
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (43 bp):
AGAAAAAAGAAAAAAGAAAAAGAAAAAAGAAGAAAAATAAAAA
Found at i:1289235 original size:8 final size:7
Alignment explanation
Indices: 1289125--1289249 Score: 67
Period size: 7 Copynumber: 17.0 Consensus size: 7
1289115 AAAAGGAGAT
1289125 AGAACAAA
1 AGAA-AAA
*
1289133 ATAAAAA
1 AGAAAAA
*
1289140 AGAAGAA
1 AGAAAAA
*
1289147 GGAAAAA
1 AGAAAAA
1289154 AGAAGAAAA
1 AG-A-AAAA
*
1289163 ATAAAAA
1 AGAAAAA
*
1289170 AG-AAGA
1 AGAAAAA
*
1289176 AGGAAAA
1 AGAAAAA
1289183 AGAAGAAAA
1 AG-A-AAAA
1289192 AGAAAAA
1 AGAAAAA
1289199 AGATAGAAA
1 AGA-A-AAA
**
1289208 A-ATATGA
1 AGA-AAAA
1289215 AGAAAAA
1 AGAAAAA
1289222 AGAAAAA
1 AGAAAAA
*
1289229 AG-CAAA
1 AGAAAAA
1289235 AGAGAAAA
1 AGA-AAAA
1289243 AGAAAAA
1 AGAAAAA
1289250 GGAGAAAATA
Statistics
Matches: 90, Mismatches: 17, Indels: 21
0.70 0.13 0.16
Matches are distributed among these distances:
6 10 0.11
7 48 0.53
8 17 0.19
9 15 0.17
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (7 bp):
AGAAAAA
Found at i:1290612 original size:21 final size:21
Alignment explanation
Indices: 1290586--1290630 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1290576 GATTTCTGGG
* *
1290586 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1290607 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1290628 CAA
1 CAA
1290631 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1291106 original size:18 final size:20
Alignment explanation
Indices: 1291070--1291106 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1291060 GATATAAACC
*
1291070 ATATGATATAATAATAAATT
1 ATATGATATAATAAAAAATT
1291090 ATATGA-AT-ATAAAAAAT
1 ATATGATATAATAAAAAAT
1291107 AAGTTATGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 2 0.12
20 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
ATATGATATAATAAAAAATT
Found at i:1291113 original size:22 final size:20
Alignment explanation
Indices: 1291070--1291119 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
1291060 GATATAAACC
*
1291070 ATATGATATAATAATAAATT
1 ATATGATATAAAAATAAATT
*
1291090 ATATGAATATAAAAAATAAGTT
1 ATATG-ATAT-AAAAATAAATT
*
1291112 ATGTGATA
1 ATATGATA
1291120 AGATCTTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.20
21 7 0.28
22 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (20 bp):
ATATGATATAAAAATAAATT
Found at i:1292469 original size:103 final size:103
Alignment explanation
Indices: 1292140--1292461 Score: 572
Period size: 103 Copynumber: 3.1 Consensus size: 103
1292130 GTCGAGGGTC
*
1292140 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1292205 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1292243 TATGTGGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 TATGT-GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
*
1292308 CTTGATCCTTGGCATATGTATATGATTTTTAAGGAATGA
65 CTTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1292347 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTAAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1292412 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1292450 TATGTGGTCCTT
1 TATGTGGTCCTT
1292462 ATGGACATTA
Statistics
Matches: 210, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
103 109 0.52
104 101 0.48
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1294852 original size:2 final size:2
Alignment explanation
Indices: 1294840--1294871 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
1294830 AAGTGACATG
1294840 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
1294872 AAGGAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1294905 original size:16 final size:15
Alignment explanation
Indices: 1294884--1294913 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1294874 GGAAAAGGTA
1294884 ATTGAAAAGCTAAAGG
1 ATTGAAAAG-TAAAGG
1294900 ATTGAAAAGTAAAG
1 ATTGAAAAGTAAAG
1294914 TTCTGATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (15 bp):
ATTGAAAAGTAAAGG
Found at i:1295474 original size:21 final size:21
Alignment explanation
Indices: 1295448--1295492 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1295438 GATTTCTGGG
* *
1295448 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1295469 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1295490 CAA
1 CAA
1295493 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1297201 original size:98 final size:99
Alignment explanation
Indices: 1297083--1297383 Score: 514
Period size: 98 Copynumber: 3.0 Consensus size: 99
1297073 AGGGTCTATG
1297083 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1297148 TCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TCCTTGGCATATGTATATGATTCTTAAGGAATGA
1297182 TGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1 TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
1297246 TCCTTGGCATATGTATATGATTCTTAAGGAATGATA
66 TCCTTGGCATATGTATATGATTCTTAAGGAATG--A
* *
1297282 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACATATACTT
1 --TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* * *
1297347 GATCCCTAGTATATGTATATGATTCTTAAGGAATGA
64 GATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1297383 T
1 T
1297384 ATGTGGTCCT
Statistics
Matches: 192, Mismatches: 5, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
98 88 0.46
99 10 0.05
100 1 0.01
101 1 0.01
102 9 0.05
103 83 0.43
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.37
Consensus pattern (99 bp):
TGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGA
TCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1297402 original size:103 final size:103
Alignment explanation
Indices: 1297079--1297394 Score: 552
Period size: 103 Copynumber: 3.1 Consensus size: 103
1297069 GTCGAGGGTC
1297079 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1297144 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATG-
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1297181 -A--TGGTCCTTC-GGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1297242 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* *
1297280 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1297345 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1297383 TATGTGGTCCTT
1 TATGTGGTCCTT
1297395 ATGGACATTA
Statistics
Matches: 204, Mismatches: 5, Indels: 9
0.94 0.02 0.04
Matches are distributed among these distances:
98 88 0.43
99 9 0.04
100 1 0.00
101 1 0.00
102 9 0.04
103 96 0.47
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1297478 original size:23 final size:23
Alignment explanation
Indices: 1297401--1297478 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
1297391 CCTTATGGAC
*
1297401 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * * *
1297425 ATTCTACGCGGCACTGCGGTGTA
1 ATTATATGTGGCACTACGGTGCA
* *
1297448 ATTGTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
1297471 TTTATATG
1 ATTATATG
1297479 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 13, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
23 38 0.93
24 3 0.07
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:1300657 original size:21 final size:21
Alignment explanation
Indices: 1300631--1300675 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1300621 GATTTCTGGG
*
1300631 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
1300652 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1300673 CAA
1 CAA
1300676 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1302356 original size:103 final size:103
Alignment explanation
Indices: 1302178--1302492 Score: 534
Period size: 103 Copynumber: 3.1 Consensus size: 103
1302168 GTCGAGGGTC
*
1302178 TATGTGGTCCTTCGGGACATATATGTATTC-TTGGAACATGTGTGAAGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1302242 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1302280 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1302345 TTGATCCTTGGCATATGTATATTATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
1302383 TATGTAGTCCTTCGGGACATATATGTATTCTTTGGAACA--TGTGAAGTCTGGTGAGAC-CATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
1302445 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATG-
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
1302482 -ATGTGGTCCTT
1 TATGTGGTCCTT
1302493 ATGGACATTA
Statistics
Matches: 204, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
98 10 0.05
100 38 0.19
101 18 0.09
102 30 0.15
103 108 0.53
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:1302541 original size:23 final size:23
Alignment explanation
Indices: 1302509--1302567 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
1302499 ATTATTATAT
1302509 GCACTACGGTGCAATTCTACGCG
1 GCACTACGGTGCAATTCTACGCG
* * * *
1302532 GCACTGCGGTGCAATTGTATGGG
1 GCACTACGGTGCAATTCTACGCG
*
1302555 GCACTTCGGTGCA
1 GCACTACGGTGCA
1302568 TTTATATGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (23 bp):
GCACTACGGTGCAATTCTACGCG
Found at i:1302575 original size:23 final size:23
Alignment explanation
Indices: 1302509--1302575 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1302499 ATTATTATAT
* * * *
1302509 GCACTACGGTGCAATTCTACGCG
1 GCACTGCGGTGCAATTATATGGG
*
1302532 GCACTGCGGTGCAATTGTATGGG
1 GCACTGCGGTGCAATTATATGGG
* *
1302555 GCACTTCGGTGCATTTATATG
1 GCACTGCGGTGCAATTATATG
1302576 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.28
Consensus pattern (23 bp):
GCACTGCGGTGCAATTATATGGG
Found at i:1306484 original size:134 final size:134
Alignment explanation
Indices: 1306075--1307049 Score: 1146
Period size: 134 Copynumber: 7.3 Consensus size: 134
1306065 ACCAGTCTCA
* * * * *
1306075 ATTCAATCTTCCCTTAGTAATAGTGGAATGAATTAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *** * * * * *
1306140 TAAGCGGAAAATATCCCCCTC-TTTAAGATTTGATATTCCCTAAATAACAGCGGAACGAGTCTAC
66 GAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTAC
1306204 CTCG
131 CTCG
* ** * * *
1306208 ATTCAATATTCCCTGGGGAACAATGGAATGAATCAACGTCCCCAGATCTAATTTTTCCTCAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * * * *
1306273 GAAGCGGAACGTATCACTTTTTTTTTCAAATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTT
66 GAAGCAGAACATATCA-TTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTA
*
1306338 CCCCG
130 CCTCG
* **
1306343 ATTCAATCTTCCCCT-TGGAACAGTGGAATGAATCAAATTCCCCCAGATCTGA-TTTCCCTCAAG
1 ATTCAATCTT-CCCTAAGGAACAGTGGAATGAATCAACGT-CCCCAGATCTGATTTTCCCTCAAG
1306406 AAGAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
64 AAGAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
1306471 ACCTCG
129 ACCTCG
* *
1306477 ATTCAATCTTTCCTAAGGAACAGTGGAATGAAACAACGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *
1306542 GACGCAGAACATATC-TCTCTCTTTTAAGATTTGATATTCTCTGAGTAACAATGGAACAAGTCTA
66 GAAGCAGAACATATCAT-TCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTA
1306606 CCTCG
130 CCTCG
* * *
1306611 ATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTTAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * * * *
1306676 GAAGTAGAATAAAT-ATT-TCTTTTAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGTCTGC
66 GAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTAC
1306739 CTCG
131 CTCG
* * * * *
1306743 ACTCAATATTTCCTGAGGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *
1306808 GAAGCAGAACATATC--CCTCTATTTCAAGATTTGATATTCCCTGAGTAACAATGGAATAAGCCT
66 GAAGCAGAACATATCATTCTCT-TTTC-AGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
* *
1306871 GCCTCA
129 ACCTCG
* * *
1306877 ATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *
1306942 GAAGC-GAAAAAGATCCA-TCTC-TTTCAAGATTTGATATTCCCCGAGTGACAGTGGAACAAGTC
66 GAAGCAG-AACATAT-CATTCTCTTTTC-AGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
*
1307004 TACCTTG
128 TACCTCG
* * **
1307011 ATTCAATCTTCTCTGAA-GAACAGAGGAATGGGTCAACGT
1 ATTCAATCTTCCCT-AAGGAACAGTGGAATGAATCAACGT
1307050 TTCTAGATCT
Statistics
Matches: 722, Mismatches: 104, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
132 117 0.16
133 88 0.12
134 403 0.56
135 96 0.13
136 18 0.02
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (134 bp):
ATTCAATCTTCCCTAAGGAACAGTGGAATGAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTAC
CTCG
Found at i:1306807 original size:266 final size:264
Alignment explanation
Indices: 1306075--1307039 Score: 1195
Period size: 266 Copynumber: 3.6 Consensus size: 264
1306065 ACCAGTCTCA
* * *
1306075 ATTCAATCTTCCCTTAGTAATAGTGGAATGAATTAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCC-TAGGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * * * * * *
1306140 TAAGCGGAAAATATC-CCCCTCTTTAAGATTTGATATTCCCTAAATAACAGCGGAACGAGTCTAC
65 GAAG-AGAAAA-ATCATCTCT-TTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTAC
* * * * * *
1306204 CTCGATTCAATATTCCCTGGGGAACAATGGAATGAATCAACGTCCCCAGATCTAATTTTTCCTCA
127 CTCGATTCAATATTTCCTGAGGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTCA
* * * * *
1306269 AGAAGAAGCGGAACGTATCACTTTTTTTTTCAA-ATTTGATATTCCCTGAGTAACAGTGGAACAA
192 AGAAGAAGCAGAACATATCAC-TCTATTTT-AAGATTTGATATTCCCTGAGTAACAATGGAACAA
* *
1306333 GTCTTCCCCG
255 GTCTACCTCG
* *
1306343 ATTCAATCTTCCCCTTGGAACAGTGGAATGAATCAAATTCCCCCAGATCTGA-TTTCCCTCAAGA
1 ATTCAATCTT-CCCTAGGAACAGTGGAATGAATCAAAGT-CCCCAGATCTGATTTTCCCTCAAGA
* *
1306407 AGAAGCAGAACATATCATTCTCTTTTCAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTA
64 AGAAG-AGAA-AAATCA-TCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTA
* *
1306472 CCTCGATTCAATCTTTCCTAAGGAACAGTGGAATGAAA-CAACGTCCCCAGATCTGATTTTCCCT
126 CCTCGATTCAATATTTCCTGAGGAACAGTGGAAT-AAATCAACGTCCCCAGATCTGATTTTCCCT
* * * *
1306536 CAAGAAGACGCAGAACATATCTCTCTCTTTTAAGATTTGATATTCTCTGAGTAACAATGGAACAA
190 CAAGAAGAAGCAGAACATATCACTCTATTTTAAGATTTGATATTCCCTGAGTAACAATGGAACAA
1306601 GTCTACCTCG
255 GTCTACCTCG
* * * *
1306611 ATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCTTAAGAA
1 ATTCAATCTTCCCT-AGGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
* * *
1306676 GAAGTAGAATAAAT-ATTTCTTTTAAGATTTGATATTCCTTGAGTAACAGTGGAACAAGTCTGCC
65 GAAG-AGAA-AAATCATCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACC
*
1306740 TCGACTCAATATTTCCTGAGGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTCAA
128 TCGATTCAATATTTCCTGAGGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTCAA
* * * *
1306805 GAAGAAGCAGAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAATGGAATAAGCC
193 GAAGAAGCAGAACATATCACTCTATTTTAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTC
* *
1306870 TGCCTCA
258 TACCTCG
*
1306877 ATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
1 ATTCAATCTTCCCT-AGGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAA
* * * *
1306942 GAAGCGAAAAAGATCCATCTCTTTCAAGATTTGATATTCCCCGAGTGACAGTGGAACAAGTCTAC
65 GAAGAG-AAAA-AT-CATCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTAC
* * * *
1307007 CTTGATTCAAT-CTTCTCTGAAGAACAGAGGAAT
127 CTCGATTCAATATTTC-CTGAGGAACAGTGGAAT
1307040 GGGTCAACGT
Statistics
Matches: 606, Mismatches: 76, Indels: 30
0.85 0.11 0.04
Matches are distributed among these distances:
265 6 0.01
266 233 0.38
267 20 0.03
268 217 0.36
269 125 0.21
270 5 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (264 bp):
ATTCAATCTTCCCTAGGAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCAAGAAG
AAGAGAAAAATCATCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTACCTCG
ATTCAATATTTCCTGAGGAACAGTGGAATAAATCAACGTCCCCAGATCTGATTTTCCCTCAAGAA
GAAGCAGAACATATCACTCTATTTTAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTAC
CTCG
Found at i:1306817 original size:400 final size:399
Alignment explanation
Indices: 1306071--1307062 Score: 1273
Period size: 400 Copynumber: 2.5 Consensus size: 399
1306061 GCAAACCAGT
* * *
1306071 CTCAATTCAATCTTCCCTTAGTAATAGTGGAATGAATTAAAGTCCCCAGATCTGATTTTCCCTCA
1 CTCAATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * * * *
1306136 AGAATAAGCGGAAAATATCC-CCCTCTTTAAGATTTGATATTCCCTAAATAACAGCGGAACGAGT
66 AGAAGAAGC-GAAAATATCCTCTCT-TTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* * ** * * * *
1306200 CTACCTCGATTCAATATTCCCTGGGGAACAATGGAATGAATCAACGTCCCCAGATCTAATTTTTC
129 CTACCTCGATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCC
* * *
1306265 CTCAAGAAGAAGCGGAACGTATCACTTTTTTTTTCAAATTTGATATTCCCTGAGTAACAGTGGAA
194 CTCAAGAAGAAGCAGAAC-TA-CAATTTTCTTTTCAAATTTGATATTCCCTGAGTAACAGTGGAA
* * * * * *
1306330 CAAGTCTTCCCCGATTCAATCTTCCCCTTGGAACAGTGGAATGAATCAAATTCCCCCAGATCTGA
257 CAAGTCTGCCCCGACTCAATATTCCCCTAGGAACAGTGGAATAAATCAAAGTCCCCCAGATCTGA
*
1306395 TTTCCCTCAAGAAGAAGCAGAACATATCATTCTCT-TTTC-AGATTTGATATTCCCTGAGTAACA
322 TTTCCCTCAAGAAGAAGCAGAACATATC--CCTCTATTTCAAGATTTGATATTCCCTGAGTAACA
* *
1306458 GTGGAACAAGTCTAC
385 ATGGAACAAGCCTAC
* * * * *
1306473 CTCGATTCAATCTTTCCTAAGGAACAGTGGAATGAAACAACGTCCCCAGATCTGATTTTCCCTCA
1 CTCAATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * *
1306538 AGAAGACGCAGAACATATCTCTCTCTTTTAAGATTTGATATTCTCTGAGTAACAATGGAACAAGT
66 AGAAGAAGC-GAAAATATC-CTCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
1306603 CTACCTCGATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCC
129 CTACCTCGATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCC
* * *
1306668 CTTAAGAAGAAGTAGAA-TA-AATATTTCTTTT-AAGATTTGATATTCCTTGAGTAACAGTGGAA
194 CTCAAGAAGAAGCAGAACTACAAT-TTTCTTTTCAA-ATTTGATATTCCCTGAGTAACAGTGGAA
* * *
1306730 CAAGTCTGCCTCGACTCAATATT-TCCTGAGGAACAGTGGAATAAATCAACGT-CCCCAGATCTG
257 CAAGTCTGCCCCGACTCAATATTCCCCT-AGGAACAGTGGAATAAATCAAAGTCCCCCAGATCTG
1306793 ATTTTCCCTCAAGAAGAAGCAGAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACA
321 A-TTTCCCTCAAGAAGAAGCAGAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACA
* *
1306858 ATGGAATAAGCCTGC
385 ATGGAACAAGCCTAC
*
1306873 CTCAATTCAATCTTCCCTGAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
1 CTCAATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * *
1306938 AGAAGAAGCGAAAAAGATCCATCTCTTTCAAGATTTGATATTCCCCGAGTGACAGTGGAACAAGT
66 AGAAGAAGCG-AAAATATCC-TCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT
* * ** **
1307003 CTACCTTGATTCAATCTTCTCTGAA-GAACAGAGGAATGGGTCAACGTTTCTAGATCTGAT
129 CTACCTCGATTCAATCTTCTCT-AAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGAT
1307063 ATACCCTAGA
Statistics
Matches: 512, Mismatches: 67, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
398 4 0.01
399 25 0.05
400 299 0.58
401 4 0.01
402 72 0.14
403 105 0.21
404 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (399 bp):
CTCAATTCAATCTTCCCTAAGTAACAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGAAAATATCCTCTCTTTTAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
ACCTCGATTCAATCTTCTCTAAGGAACAGTGGAATGAATCAACGTCCCTAGATCTGATTTTCCCT
CAAGAAGAAGCAGAACTACAATTTTCTTTTCAAATTTGATATTCCCTGAGTAACAGTGGAACAAG
TCTGCCCCGACTCAATATTCCCCTAGGAACAGTGGAATAAATCAAAGTCCCCCAGATCTGATTTC
CCTCAAGAAGAAGCAGAACATATCCCTCTATTTCAAGATTTGATATTCCCTGAGTAACAATGGAA
CAAGCCTAC
Found at i:1310200 original size:16 final size:16
Alignment explanation
Indices: 1310181--1310220 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1310171 CTTAACGAGC
1310181 AACGAGCATAGTCCTT
1 AACGAGCATAGTCCTT
1310197 AACGAGCATAGTCCTT
1 AACGAGCATAGTCCTT
1310213 AACGAGCA
1 AACGAGCA
1310221 ACGAGGTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (16 bp):
AACGAGCATAGTCCTT
Found at i:1310252 original size:35 final size:35
Alignment explanation
Indices: 1310213--1310323 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
1310203 CATAGTCCTT
* *
1310213 AACGAGCAACGAGGTAAGCAACGAGCACCGAGCTA
1 AACGAGCAACGAGGCAAGCAACGAGCATCGAGCTA
** * * *
1310248 AACGAGCAACGAGGCAAATAACGAGAATTGAGCTT
1 AACGAGCAACGAGGCAAGCAACGAGCATCGAGCTA
*
1310283 AACGAGCAACGAGGCAAGCATCGAGCATCGAGC-A
1 AACGAGCAACGAGGCAAGCAACGAGCATCGAGCTA
1310317 TAACGAG
1 -AACGAG
1310324 AATCGAACTT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.41, C:0.23, G:0.28, T:0.09
Consensus pattern (35 bp):
AACGAGCAACGAGGCAAGCAACGAGCATCGAGCTA
Found at i:1310272 original size:19 final size:19
Alignment explanation
Indices: 1310212--1310272 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 19
1310202 GCATAGTCCT
* *
1310212 TAACGAGCAACGAGGTAAG
1 TAACGAGCAACGAGGCAAA
* * *
1310231 CAACGAGCACCGA-GC-TA
1 TAACGAGCAACGAGGCAAA
1310248 -AACGAGCAACGAGGCAAA
1 TAACGAGCAACGAGGCAAA
1310266 TAACGAG
1 TAACGAG
1310273 AATTGAGCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
16 11 0.34
17 2 0.06
18 2 0.06
19 17 0.53
ACGTcount: A:0.43, C:0.23, G:0.28, T:0.07
Consensus pattern (19 bp):
TAACGAGCAACGAGGCAAA
Found at i:1310360 original size:16 final size:15
Alignment explanation
Indices: 1310311--1310362 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
1310301 CATCGAGCAT
*
1310311 CGAGCATAACGAGAA
1 CGAGCTTAACGAGAA
* *
1310326 TCGAACTTAATGAGCAA
1 -CGAGCTTAACGAG-AA
1310343 CGAGCTTAACGAGTAA
1 CGAGCTTAACGAG-AA
1310359 CGAG
1 CGAG
1310363 TCGAGTCGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
16 27 0.93
17 2 0.07
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.15
Consensus pattern (15 bp):
CGAGCTTAACGAGAA
Found at i:1312694 original size:16 final size:16
Alignment explanation
Indices: 1312675--1312707 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1312665 TAAAAACAGT
1312675 AAATAAAAAGAAAATA
1 AAATAAAAAGAAAATA
*
1312691 AAATAAAAAGAAGATA
1 AAATAAAAAGAAAATA
1312707 A
1 A
1312708 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1318036 original size:2 final size:2
Alignment explanation
Indices: 1318031--1318058 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1318021 TTCTCTCGTG
1318031 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1318059 ATTCGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1331280 original size:117 final size:107
Alignment explanation
Indices: 1331012--1331289 Score: 378
Period size: 117 Copynumber: 2.5 Consensus size: 107
1331002 TAAGATTCAC
*
1331012 CGCAGAACGAGGTGAATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAG
1 CGCAGAAGGAGGTGAATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAG
* *
1331077 AGAAAGTTCATAATGAGAAGAACTTGTTCCTTTCTATTCCAT
66 AGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCGATTCCAT
* *
1331119 CGCAGAAGGAGGTGCATCAATATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAG
1 CGCAGAAGGAGGTGAATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGA--A-
1331184 GAAGA-AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTGTTTCGATTCCAT
63 -AAGAGA-AAGTTCATAATAAGAAGAACTTGTT---CC---TTTCGATTCCAT
* * *
1331236 CGTAGAAGGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACT
1 CGCAGAAGGAGGTGAATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACT
1331290 TGTTCCTTTC
Statistics
Matches: 151, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
107 58 0.38
109 1 0.01
110 1 0.01
111 28 0.19
114 2 0.01
117 61 0.40
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (107 bp):
CGCAGAAGGAGGTGAATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAAAAG
AGAAAGTTCATAATAAGAAGAACTTGTTCCTTTCGATTCCAT
Found at i:1331325 original size:72 final size:74
Alignment explanation
Indices: 1331192--1331361 Score: 254
Period size: 72 Copynumber: 2.3 Consensus size: 74
1331182 AGGAAGAAGA
* * *
1331192 AGTTCATAATAAGAAGAACTTGTTCAACCTTGTTTCGATTCCATCGTAGAAGGAGGTGGATCAAC
1 AGTTCATAATGAGAAGAACTTGTT--ACC-T-TTTCGATTCCATCGCAGAAGGAGGCGGATCAAC
1331257 ATTTTCAATGGAG
62 ATTTTCAATGGAG
*
1331270 AGTTCATAATGAGAAGAACTTGTT-CC-TTTCGATTCCATCGCAGAAGGAGGCGGATCAATATTT
1 AGTTCATAATGAGAAGAACTTGTTACCTTTTCGATTCCATCGCAGAAGGAGGCGGATCAACATTT
1331333 TCAATGGAG
66 TCAATGGAG
1331342 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1331362 CATCCAATGA
Statistics
Matches: 88, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
72 63 0.72
75 2 0.02
78 23 0.26
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.29
Consensus pattern (74 bp):
AGTTCATAATGAGAAGAACTTGTTACCTTTTCGATTCCATCGCAGAAGGAGGCGGATCAACATTT
TCAATGGAG
Found at i:1331401 original size:189 final size:189
Alignment explanation
Indices: 1331081--1331478 Score: 697
Period size: 189 Copynumber: 2.1 Consensus size: 189
1331071 GAAAAGAGAA
* *
1331081 AGTTCATAATGAGAAGAACTTGTTCCTTTCTATTCCATCGCAGAAGGAGGTGCATCAATATTTTC
1 AGTTCATAATGAGAAGAACTTGTTCCTTTCGATTCCATCGCAGAAGGAGGCGCATCAATATTTTC
* *
1331146 AGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGAAGAAGAAGTTCATAATAAGAAGAAC
66 AATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATAAGAAGAAC
**
1331211 TTGTTCAACCTTGTTTCGATTCCATCGTAGAAGGAGGTGGATCAACATTTTCAATGGAG
131 TTGTTCAACCTTGTTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAG
*
1331270 AGTTCATAATGAGAAGAACTTGTTCCTTTCGATTCCATCGCAGAAGGAGGCGGATCAATATTTTC
1 AGTTCATAATGAGAAGAACTTGTTCCTTTCGATTCCATCGCAGAAGGAGGCGCATCAATATTTTC
* *
1331335 AATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGATAAGAAC
66 AATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATAAGAAGAAC
* *
1331400 TTGTTCAACCTTGTTTCGATTCCATCACAGAAGGAGGTGGATCAATATTTTCAGTGGAG
131 TTGTTCAACCTTGTTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAG
1331459 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1331479 CGTCCTAAGG
Statistics
Matches: 198, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 198 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (189 bp):
AGTTCATAATGAGAAGAACTTGTTCCTTTCGATTCCATCGCAGAAGGAGGCGCATCAATATTTTC
AATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATAAGAAGAAC
TTGTTCAACCTTGTTTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAATGGAG
Found at i:1331470 original size:117 final size:111
Alignment explanation
Indices: 1331270--1331628 Score: 451
Period size: 117 Copynumber: 3.2 Consensus size: 111
1331260 TTCAATGGAG
* *
1331270 AGTTCATAATGAGAAGAACTTGTT-CCTTTCGATTCCATCGCAGAAGGAGGCGGATCAATATTTT
1 AGTTCATAATGAGAAGAACTTGTTACCTTTCGATTCCATCACAGAAGGAGGTGGATCAATATTTT
*
1331334 CAATGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGA
66 CAGTGGAGAGTTCATAATGAGAAGAACTCATCCAA-GAGGAAGAAGA
*
1331381 AGTTCATAATGATAAGAACTTGTTCAACCTTGTTTCGATTCCATCACAGAAGGAGGTGGATCAAT
1 AGTTCATAATGAGAAGAACTTGTT--ACC---TTTCGATTCCATCACAGAAGGAGGTGGATCAAT
*
1331446 ATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCGTCCTAAG-GG-AG-A-A
61 ATTTTCAGTGGAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAGAAGA
** * * ** * * * * *
1331494 AGTTCATAACAAGAAGAACTTGTTA-CTTTCAAGTCCATCACAGAATAAGATGTATCGACATTTC
1 AGTTCATAATGAGAAGAACTTGTTACCTTTCGATTCCATCACAGAAGGAGGTGGATCAATATTTT
*
1331558 CAGTGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGA
66 CAGTGGAGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAGAAGA
1331605 AGTTCATAATGAGAAGAACTTGTT
1 AGTTCATAATGAGAAGAACTTGTT
1331629 CAACCTTGCA
Statistics
Matches: 215, Mismatches: 22, Indels: 22
0.83 0.08 0.08
Matches are distributed among these distances:
107 63 0.29
108 2 0.01
109 2 0.01
110 2 0.01
111 47 0.22
113 22 0.10
114 3 0.01
115 2 0.01
116 2 0.01
117 68 0.32
118 2 0.01
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAACTTGTTACCTTTCGATTCCATCACAGAAGGAGGTGGATCAATATTTT
CAGTGGAGAGTTCATAATGAGAAGAACTCATCCAAGAGGAAGAAGA
Found at i:1331629 original size:20 final size:20
Alignment explanation
Indices: 1331566--1331630 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1331556 TCCAGTGAAG
1331566 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1331586 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
1331605 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1331625 TGTTCA
1 AGTTCA
1331631 ACCTTGCATT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1331652 original size:91 final size:91
Alignment explanation
Indices: 1331553--1331722 Score: 281
Period size: 91 Copynumber: 1.9 Consensus size: 91
1331543 ATGTATCGAC
*
1331553 ATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCATCC-A-AAGAGGAAGAAGAAGTTCATAATG
1 ATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCCAACAAGA-G-AGAAGAAGTTCATAATG
1331616 AGAAGAACTTGTTCAACCTTGCATTAAA
64 AGAAGAACTTGTTCAACCTTGCATTAAA
* *
1331644 ATTTCCAGTAAAGAGTTCATAATGAGAAGAATTCATCTAACAAGAGAGAAGAAGTTCATAATGAG
1 ATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCATAATGAG
1331709 AAGAACTTGTTCAA
66 AAGAACTTGTTCAA
1331723 TCCAACGCTT
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
91 68 0.92
92 2 0.03
93 4 0.05
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (91 bp):
ATTTCCAGTAAAGAGTTCATAATGAGAAGAACTCATCCAACAAGAGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGCATTAAA
Found at i:1331897 original size:3 final size:3
Alignment explanation
Indices: 1331891--1331927 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
1331881 TATATTTATT
1331891 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
1331928 TCATTTTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1333077 original size:16 final size:15
Alignment explanation
Indices: 1333053--1333088 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
1333043 GTATTATCAT
*
1333053 TTTTAATCCTTTTTA
1 TTTTAATCCGTTTTA
1333068 TTTTACATCCGTTTTA
1 TTTTA-ATCCGTTTTA
1333084 TTTTA
1 TTTTA
1333089 GTCATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.19, C:0.14, G:0.03, T:0.64
Consensus pattern (15 bp):
TTTTAATCCGTTTTA
Found at i:1342389 original size:17 final size:17
Alignment explanation
Indices: 1342351--1342390 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1342341 ATGGGCCTGA
1342351 GGGCACTTCCCTCATGT
1 GGGCACTTCCCTCATGT
*
1342368 AGGCACTTCCCTC-TGGT
1 GGGCACTTCCCTCAT-GT
1342385 GGGCAC
1 GGGCAC
1342391 CTACGCTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.12, C:0.35, G:0.28, T:0.25
Consensus pattern (17 bp):
GGGCACTTCCCTCATGT
Found at i:1343184 original size:27 final size:27
Alignment explanation
Indices: 1343146--1343223 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
1343136 ATATATATAT
1343146 ATAGATAGTCTTGCATTCAGTCAATAG
1 ATAGATAGTCTTGCATTCAGTCAATAG
*
1343173 ATAGGTAGTCTTGCATTCAGTCAATAG
1 ATAGATAGTCTTGCATTCAGTCAATAG
1343200 ATAGATAGTCTTGCATTCAGTCAA
1 ATAGATAGTCTTGCATTCAGTCAA
1343224 CAACTATTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
ATAGATAGTCTTGCATTCAGTCAATAG
Found at i:1344416 original size:14 final size:15
Alignment explanation
Indices: 1344381--1344413 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1344371 TCGAAATACA
1344381 GAAATCAGATATCAG
1 GAAATCAGATATCAG
1344396 GAAATCA-ATATTCAG
1 GAAATCAGATA-TCAG
1344411 GAA
1 GAA
1344414 TCACGTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.21
Consensus pattern (15 bp):
GAAATCAGATATCAG
Found at i:1345263 original size:28 final size:28
Alignment explanation
Indices: 1345149--1345296 Score: 161
Period size: 29 Copynumber: 5.1 Consensus size: 28
1345139 CATTTTACAG
** * *
1345149 AAATAGCACCATTTTTAAAATAATTACCA
1 AAATAGCACC-TTTTCGAATTAATTCCCA
* * *
1345178 AAATAGCTCCTTTTCAAATTAAATTCTCA
1 AAATAGCACCTTTTCGAATT-AATTCCCA
* *
1345207 AAATAGCACCTTTCCTGAATAAATTCCCA
1 AAATAGCACCTTTTC-GAATTAATTCCCA
*
1345236 AAATATCACCTTTTCGAATTAATTCCCA
1 AAATAGCACCTTTTCGAATTAATTCCCA
*
1345264 AAATAGCACCCATTTCGAATTAATTCCCA
1 AAATAGCA-CCTTTTCGAATTAATTCCCA
1345293 AAAT
1 AAAT
1345297 GTCACCCGGT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
28 27 0.27
29 71 0.70
30 3 0.03
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.32
Consensus pattern (28 bp):
AAATAGCACCTTTTCGAATTAATTCCCA
Found at i:1345269 original size:57 final size:58
Alignment explanation
Indices: 1345170--1345302 Score: 164
Period size: 57 Copynumber: 2.3 Consensus size: 58
1345160 TTTTTAAAAT
* * * *
1345170 AATTACCAAAATAGCTCCTTTTCAAATTAAATTCTCAAAATAGCA-CC-TTTCCTGAATA
1 AATTCCCAAAATATCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTT-C-GAATA
* *
1345228 AATTCCCAAAATATCACCTTTTCGAATT-AATTCCCAAAATAGCACCCATTTCGAATT
1 AATTCCCAAAATATCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTCGAATA
*
1345285 AATTCCCAAAATGTCACC
1 AATTCCCAAAATATCACC
1345303 CGGTCAACGG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 36 0.55
58 27 0.41
59 3 0.05
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (58 bp):
AATTCCCAAAATATCACCTTTTCAAATTAAATTCCCAAAATAGCACCCATTTCGAATA
Found at i:1352309 original size:29 final size:28
Alignment explanation
Indices: 1352203--1352331 Score: 150
Period size: 29 Copynumber: 4.5 Consensus size: 28
1352193 ATTTTTAAAA
* * *
1352203 TAATTACCATAATAGCACCTTTCCGAAT
1 TAATTCCCAAAATAGCACCTTTTCGAAT
*
1352231 TAAATTTCCAAAATAGCACCTTTTCCGAAT
1 T-AATTCCCAAAATAGCACCTTTT-CGAAT
* *
1352261 AAATTTCCAAAATAGCACCCTTTTCGAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAAT
* *
1352290 TAATTCCCAAAATAGCACCCATTTCAAAT
1 TAATTCCCAAAATAGCA-CCTTTTCGAAT
1352319 TAATTCCCAAAAT
1 TAATTCCCAAAAT
1352332 GTCACCCGGT
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.01
29 78 0.87
30 11 0.12
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (28 bp):
TAATTCCCAAAATAGCACCTTTTCGAAT
Found at i:1352329 original size:58 final size:58
Alignment explanation
Indices: 1352183--1352331 Score: 158
Period size: 58 Copynumber: 2.6 Consensus size: 58
1352173 CATTTTACAG
* ** * * *
1352183 AAATAACACCATTTTTAAAATAATTACCATAATAGCACCTTTCCGAATTAAATTTCCA
1 AAATAGCACCATTTCCAAATTAATTACCAAAATAGCACCTTTCCGAATTAAATTCCCA
* * * * *
1352241 AAATAGCACCTTTTCCGAATAAATTTCCAAAATAGCACCCTTTTCGAATT-AATTCCCA
1 AAATAGCACCATTTCCAAATTAATTACCAAAATAGCA-CCTTTCCGAATTAAATTCCCA
*
1352299 AAATAGCACCCATTT-CAAATTAATTCCCAAAAT
1 AAATAGCA-CCATTTCCAAATTAATTACCAAAAT
1352332 GTCACCCGGT
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
58 58 0.78
59 16 0.22
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (58 bp):
AAATAGCACCATTTCCAAATTAATTACCAAAATAGCACCTTTCCGAATTAAATTCCCA
Found at i:1353963 original size:37 final size:37
Alignment explanation
Indices: 1353920--1354007 Score: 108
Period size: 37 Copynumber: 2.4 Consensus size: 37
1353910 AAGTATAATT
*
1353920 TTAAAATATTATAA-TTAAAATAAAATAA-AAATAATAG
1 TTAAAATACTA-AACTTAAAATAAAA-AATAAATAATAG
** *
1353957 TTAAAATACTAAACTTGTAATAAAAAATATATAATAG
1 TTAAAATACTAAACTTAAAATAAAAAATAAATAATAG
1353994 TTAAAATACTAAAC
1 TTAAAATACTAAAC
1354008 GTGTAGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 4 0.09
37 41 0.91
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (37 bp):
TTAAAATACTAAACTTAAAATAAAAAATAAATAATAG
Found at i:1354150 original size:2 final size:2
Alignment explanation
Indices: 1354109--1354135 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1354099 TCTTTTTTAT
1354109 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 T
1354136 TTCTTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1354259 original size:3 final size:3
Alignment explanation
Indices: 1354246--1354297 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
1354236 TGGATAACTC
*
1354246 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1354292 TAT TAT
1 TAT TAT
1354298 ATACTTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1367269 original size:193 final size:193
Alignment explanation
Indices: 1366940--1367325 Score: 772
Period size: 193 Copynumber: 2.0 Consensus size: 193
1366930 GTTTCCGAGA
1366940 GCTGTGACGTTTATAGCTTCGGCATTTTACTTCTAGAGATCATTACTGCGAAGAAACCATTGGAG
1 GCTGTGACGTTTATAGCTTCGGCATTTTACTTCTAGAGATCATTACTGCGAAGAAACCATTGGAG
1367005 AAACTCCTGGGTGGAGTGAAATGTGACATAGTGCAATGGGTTACCCCATATGAGCAGAAGGGTGT
66 AAACTCCTGGGTGGAGTGAAATGTGACATAGTGCAATGGGTTACCCCATATGAGCAGAAGGGTGT
1367070 GTTTGATCGTACATCAGATCCTCGGTTGAAAGGGAAATTCGATCGAGCTCAGCTTTGTTGAGC
131 GTTTGATCGTACATCAGATCCTCGGTTGAAAGGGAAATTCGATCGAGCTCAGCTTTGTTGAGC
1367133 GCTGTGACGTTTATAGCTTCGGCATTTTACTTCTAGAGATCATTACTGCGAAGAAACCATTGGAG
1 GCTGTGACGTTTATAGCTTCGGCATTTTACTTCTAGAGATCATTACTGCGAAGAAACCATTGGAG
1367198 AAACTCCTGGGTGGAGTGAAATGTGACATAGTGCAATGGGTTACCCCATATGAGCAGAAGGGTGT
66 AAACTCCTGGGTGGAGTGAAATGTGACATAGTGCAATGGGTTACCCCATATGAGCAGAAGGGTGT
1367263 GTTTGATCGTACATCAGATCCTCGGTTGAAAGGGAAATTCGATCGAGCTCAGCTTTGTTGAGC
131 GTTTGATCGTACATCAGATCCTCGGTTGAAAGGGAAATTCGATCGAGCTCAGCTTTGTTGAGC
1367326 ATAGAAAAGT
Statistics
Matches: 193, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 193 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.28
Consensus pattern (193 bp):
GCTGTGACGTTTATAGCTTCGGCATTTTACTTCTAGAGATCATTACTGCGAAGAAACCATTGGAG
AAACTCCTGGGTGGAGTGAAATGTGACATAGTGCAATGGGTTACCCCATATGAGCAGAAGGGTGT
GTTTGATCGTACATCAGATCCTCGGTTGAAAGGGAAATTCGATCGAGCTCAGCTTTGTTGAGC
Found at i:1367902 original size:17 final size:16
Alignment explanation
Indices: 1367880--1367913 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1367870 TAAAGACAGT
1367880 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1367897 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1367913 A
1 A
1367914 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1372603 original size:47 final size:48
Alignment explanation
Indices: 1372503--1372594 Score: 134
Period size: 48 Copynumber: 2.0 Consensus size: 48
1372493 GAGAAATAAC
* *
1372503 AAAGAAAAAAGATGAATGAAAGAAAGAGAAAAGGTAAAAGTTAAAATG
1 AAAGAAAAAAAATGAATGAAAGAAAGAGAAAAGGAAAAAGTTAAAATG
* *
1372551 AAAGAAAAAAAATGAAT-AATGAAAGATAAAA-GAAAAAGTTAAAA
1 AAAGAAAAAAAATGAATGAAAGAAAGAGAAAAGGAAAAAGTTAAAA
1372595 ATTTAAGAAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 12 0.30
47 12 0.30
48 16 0.40
ACGTcount: A:0.68, C:0.00, G:0.18, T:0.13
Consensus pattern (48 bp):
AAAGAAAAAAAATGAATGAAAGAAAGAGAAAAGGAAAAAGTTAAAATG
Found at i:1386803 original size:13 final size:13
Alignment explanation
Indices: 1386785--1386809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1386775 AGAAAGAAAG
1386785 TAAAGTGAAAAAA
1 TAAAGTGAAAAAA
1386798 TAAAGTGAAAAA
1 TAAAGTGAAAAA
1386810 GTGGGGTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
TAAAGTGAAAAAA
Found at i:1388356 original size:18 final size:18
Alignment explanation
Indices: 1388335--1388379 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1388325 CGTCCCAAAA
1388335 ATAGAACTTGGCATTATG
1 ATAGAACTTGGCATTATG
1388353 ATAGAACTTGGCATTATG
1 ATAGAACTTGGCATTATG
1388371 ATAGAACTT
1 ATAGAACTT
1388380 CTTCTTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (18 bp):
ATAGAACTTGGCATTATG
Found at i:1390280 original size:43 final size:45
Alignment explanation
Indices: 1390157--1390281 Score: 159
Period size: 47 Copynumber: 2.8 Consensus size: 45
1390147 TATAAAATCT
*
1390157 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCATTTAAT-TCATAAGCTCGTAAGCTTATTTTACCAAACTA
*
1390202 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTATCAATA-TA
1 CTTACCATTT-AATTC-ATAAGCTCGTAAGCTTATTTTACCAA-ACTA
*
1390249 CTTGCCA-TT-ATTCATAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATTCATAAGCTCGTAAGCTTATTT
1390282 GCATACTTAC
Statistics
Matches: 73, Mismatches: 3, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
43 20 0.27
44 4 0.05
45 10 0.14
46 3 0.04
47 35 0.48
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTAATTCATAAGCTCGTAAGCTTATTTTACCAAACTA
Found at i:1390289 original size:38 final size:42
Alignment explanation
Indices: 1390157--1390295 Score: 133
Period size: 47 Copynumber: 3.2 Consensus size: 42
1390147 TATAAAATCT
* * *
1390157 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAACTA
1 CTTACCA-TTATTCTATAAGCTCGTAAGCTTATTTTAGC-AA-TA
*
1390202 CTTACCATTTAAATTCTATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATTCTATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
1390249 CTTGCCATTATTC-ATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCTATAAGCTCGTAAGCTTATTTTAGCAATA
1390287 CTTACCATT
1 CTTACCATT
1390296 TATTAACCAT
Statistics
Matches: 85, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 17 0.20
44 4 0.05
45 10 0.12
46 2 0.02
47 36 0.42
48 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (42 bp):
CTTACCATTATTCTATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:1397440 original size:20 final size:20
Alignment explanation
Indices: 1397411--1397453 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1397401 ATTACACCAC
1397411 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* *
1397431 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGCTCCTAA
1397451 ATG
1 ATG
1397454 GGCTCTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:1399767 original size:30 final size:31
Alignment explanation
Indices: 1399731--1399820 Score: 128
Period size: 32 Copynumber: 2.9 Consensus size: 31
1399721 GAAGGACCTA
* * *
1399731 TCCATATGTTCCGAAGAACATATGTAAC-TG
1 TCCATATGTCCCGAAGGACATAGGTAACTTG
*
1399761 TCCATATATCCCGAAGGACATAGGTAATCTTG
1 TCCATATGTCCCGAAGGACATAGGTAA-CTTG
1399793 TCCATATGTCCCGAAGGACATAGGTAAC
1 TCCATATGTCCCGAAGGACATAGGTAAC
1399821 CCTAACTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
30 23 0.43
31 2 0.04
32 28 0.53
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (31 bp):
TCCATATGTCCCGAAGGACATAGGTAACTTG
Found at i:1400302 original size:2 final size:2
Alignment explanation
Indices: 1400297--1400328 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1400287 ACACACACGC
*
1400297 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1400329 CAAATAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1400797 original size:11 final size:11
Alignment explanation
Indices: 1400781--1400811 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1400771 TTTAAGATGA
1400781 CTTAAGCTTTC
1 CTTAAGCTTTC
1400792 CTTAAGCTTTC
1 CTTAAGCTTTC
1400803 CTTAAGCTT
1 CTTAAGCTT
1400812 AATTATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.19, C:0.26, G:0.10, T:0.45
Consensus pattern (11 bp):
CTTAAGCTTTC
Found at i:1403623 original size:32 final size:31
Alignment explanation
Indices: 1403568--1403639 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 31
1403558 ATCCTGAAGA
*
1403568 ACATAGGT-AACTGTCCATTTGTCCCAAAGG
1 ACATAGGTAAACTGTCCATATGTCCCAAAGG
*
1403598 ACATAGGTAATACTGTCCATATGTCCCGAAGG
1 ACATAGGTAA-ACTGTCCATATGTCCCAAAGG
1403630 ACATAGGTAA
1 ACATAGGTAA
1403640 CCTTCAACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 8 0.21
31 1 0.03
32 29 0.76
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (31 bp):
ACATAGGTAAACTGTCCATATGTCCCAAAGG
Found at i:1414788 original size:60 final size:59
Alignment explanation
Indices: 1414713--1414825 Score: 145
Period size: 60 Copynumber: 1.9 Consensus size: 59
1414703 TTTTCGGATT
* * * *
1414713 ATAGAGTAATGTTTTGTTGAGTCTATTGGCTATTAAAAGTAACAAAATGATCATTCAATA
1 ATAGAGTAATGTTTTGTTGAATCCATCGACTATTAAAAGTAACAAAAT-ATCATTCAATA
** * *
1414773 ATAGAGTGTTGTTTTGTTGAATCCGTCGACTATTAAAAGTTACAAAATATCAT
1 ATAGAGTAATGTTTTGTTGAATCCATCGACTATTAAAAGTAACAAAATATCAT
1414826 CTGACTATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (59 bp):
ATAGAGTAATGTTTTGTTGAATCCATCGACTATTAAAAGTAACAAAATATCATTCAATA
Found at i:1424534 original size:16 final size:16
Alignment explanation
Indices: 1424513--1424545 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1424503 TGCATATACA
1424513 TGCTCACAACCCCAAC
1 TGCTCACAACCCCAAC
*
1424529 TGCTCACAACCCTAAC
1 TGCTCACAACCCCAAC
1424545 T
1 T
1424546 ACCTATGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.45, G:0.06, T:0.18
Consensus pattern (16 bp):
TGCTCACAACCCCAAC
Found at i:1426693 original size:31 final size:31
Alignment explanation
Indices: 1426655--1426839 Score: 336
Period size: 31 Copynumber: 6.0 Consensus size: 31
1426645 GGGTCGAGGG
1426655 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1426686 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1426717 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1426748 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1426779 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1426810 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1426840 GTCCTTCGGG
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
31 150 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1430875 original size:31 final size:31
Alignment explanation
Indices: 1430837--1431021 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
1430827 GGGTCGAGGG
1430837 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1430868 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1430899 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1430930 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
1430961 TTACCTATGTTCTTCGGGACATATGGACTAT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1430992 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1431022 GTCCTTCGGG
Statistics
Matches: 149, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 148 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1437657 original size:15 final size:15
Alignment explanation
Indices: 1437637--1437669 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1437627 AATAGTTAAG
1437637 ATAATATATTATATA
1 ATAATATATTATATA
*
1437652 ATAATATATTCTATA
1 ATAATATATTATATA
1437667 ATA
1 ATA
1437670 TTTTACTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATATATTATATA
Found at i:1438563 original size:26 final size:25
Alignment explanation
Indices: 1438527--1438575 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
1438517 TTTGGTAATC
*
1438527 CCCGCCCCGATTACCCGCCCCGATTA
1 CCCGCCCCGA-TACCCGACCCGATTA
1438553 CCCGCCCCGATACCCGACCCGAT
1 CCCGCCCCGATACCCGACCCGAT
1438576 AAATATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.16, C:0.55, G:0.16, T:0.12
Consensus pattern (25 bp):
CCCGCCCCGATACCCGACCCGATTA
Found at i:1438576 original size:12 final size:13
Alignment explanation
Indices: 1438527--1438575 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
1438517 TTTGGTAATC
1438527 CCCGCCCCGATTA
1 CCCGCCCCGATTA
1438540 CCCGCCCCGATTA
1 CCCGCCCCGATTA
1438553 CCCGCCCCGA-TA
1 CCCGCCCCGATTA
*
1438565 CCCGACCCGAT
1 CCCGCCCCGAT
1438576 AAATATTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.16, C:0.55, G:0.16, T:0.12
Consensus pattern (13 bp):
CCCGCCCCGATTA
Found at i:1438714 original size:12 final size:12
Alignment explanation
Indices: 1438699--1438733 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1438689 CGATTCTCGG
1438699 CCCAATACCCGA
1 CCCAATACCCGA
*
1438711 CCCAATACCCGG
1 CCCAATACCCGA
1438723 CCCAATACCCG
1 CCCAATACCCG
1438734 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:1440595 original size:16 final size:18
Alignment explanation
Indices: 1440574--1440606 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1440564 ATTCATACAA
1440574 ATTA-TTTAT-AATATTC
1 ATTATTTTATCAATATTC
1440590 ATTATTTTATCAATATT
1 ATTATTTTATCAATATT
1440607 TAATAACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTTTATCAATATTC
Found at i:1441795 original size:60 final size:60
Alignment explanation
Indices: 1441697--1441883 Score: 218
Period size: 60 Copynumber: 3.1 Consensus size: 60
1441687 CTTGAAATAA
* * ** *
1441697 TTTGGAGATGAAATTGGAA-GATTCAAAATTTTGGGGACTAATTTAGAATTAGAGTCATAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
* * *
1441757 TTTGGGGATGAAATTGTAGTGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAATCATAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
* * * *
1441817 TTTGAGGATGAAATTGGAATGTTTAAAAGTTTAA-GACCAATTTAAAATGAG-GATCATAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAG-TCATAG
*
1441876 TTTAGGGA
1 TTTGGGGA
1441884 CATATGATGT
Statistics
Matches: 108, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
59 27 0.25
60 80 0.74
61 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (60 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAG
Found at i:1442720 original size:132 final size:131
Alignment explanation
Indices: 1442535--1442795 Score: 427
Period size: 132 Copynumber: 2.0 Consensus size: 131
1442525 TTTAAGAGGA
* * *
1442535 AAAATGATAATATTTAATTATTTCCAATCAAGAATAAATGATCTCTCATGCCTTAAAGTAGTTAT
1 AAAATGATAATATTAAATTATTTCCAATCAAGAATAAATGATCTCTCATGCCTTAAAGCAGTCAT
1442600 TTATTACTCCAACCGAAATAAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATTCGAGA
66 TTATTACTCCAACCGAAATAAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATTCGAGA
1442665 G
131 G
1442666 AAAATGATAATATATAAATTATTTCCAATCGAA-AATAAATGA-CTTCTCATGCCTTAAAGCAGT
1 AAAATGATAATAT-TAAATTATTTCCAATC-AAGAATAAATGATC-TCTCATGCCTTAAAGCAGT
* * *
1442729 CATTTATTACTCCAACCGAAATAAAGAGATATTATTTTTTTATCCTAAAATTCAATATTGATTCG
63 CATTTATTACTCCAACCGAAATAAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATTCG
1442794 AG
128 AG
1442796 TATTACTTAT
Statistics
Matches: 121, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
131 14 0.12
132 105 0.87
133 2 0.02
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.35
Consensus pattern (131 bp):
AAAATGATAATATTAAATTATTTCCAATCAAGAATAAATGATCTCTCATGCCTTAAAGCAGTCAT
TTATTACTCCAACCGAAATAAAGAGATATTACTATTTCATCCTAAAATTCAATATTGATTCGAGA
G
Found at i:1444844 original size:2 final size:2
Alignment explanation
Indices: 1444837--1444873 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1444827 TTTTTAAAAC
1444837 AT AT 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 AT AT A
1444874 CCCCAATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1445075 original size:24 final size:24
Alignment explanation
Indices: 1445052--1445170 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
1445042 AAACATAAAT
*
1445052 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
1445076 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
1445100 CAAGTCAAGTATCAGATCCGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1445124 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
1445148 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
1445171 TCAAATAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 78 0.92
25 2 0.02
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1445186 original size:48 final size:48
Alignment explanation
Indices: 1445088--1445188 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
1445078 GGTCAAGTAA
* ** * * *
1445088 CAGATCAGAATCCAAGTCAAGTATCAGATCCGAATCCATGTCAGATAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAAAAAAT
* *
1445136 CAGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATAAAAAAT
1 CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAAAAAAT
1445184 CAGAT
1 CAGAT
1445189 AATATATTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.23
Consensus pattern (48 bp):
CAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCCAAATAAAAAAT
Found at i:1446389 original size:18 final size:18
Alignment explanation
Indices: 1446366--1446400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1446356 TGCCATCCGG
*
1446366 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1446384 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1446401 TTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1447741 original size:13 final size:13
Alignment explanation
Indices: 1447725--1447761 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1447715 GTCAACAGGT
1447725 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
1447738 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
1447751 CGGGTCGGGTC
1 CGGGTCGGGTC
1447762 GGGTTATGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1449873 original size:24 final size:24
Alignment explanation
Indices: 1449846--1449897 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1449836 AACGGATATA
*
1449846 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
1449870 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
1449894 TCAA
1 TCAA
1449898 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:1449898 original size:24 final size:24
Alignment explanation
Indices: 1449866--1449984 Score: 152
Period size: 24 Copynumber: 5.0 Consensus size: 24
1449856 AAACATAAAT
*
1449866 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
*
1449890 CAGGTCAAGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1449914 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
1449938 CATGTC-AGATATCAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
* *
1449962 CATGTCAAGTATCATATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
1449985 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.06
24 79 0.92
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:1450000 original size:48 final size:47
Alignment explanation
Indices: 1449869--1450002 Score: 153
Period size: 48 Copynumber: 2.8 Consensus size: 47
1449859 CATAAATCAG
* *
1449869 GTCAAGTATCATATCAGAAATCAGGTCAAGTAA-CAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAATTCAAGTCAA--AATCAGATCAGAATCCAA
* * * * *
1449917 GTCAAGTATCAGATCAGAATCCATGTCAGATATCAGATCAGAATCCAT
1 GTCAAGTATCATATCAGAATTCAAGTCA-AAATCAGATCAGAATCCAA
*
1449965 GTCAAGTATCATATCAGAATTCAAATCGAAAATCAGAT
1 GTCAAGTATCATATCAGAATTCAAGTC-AAAATCAGAT
1450003 AAAATATTCA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 1 0.01
48 69 0.96
49 2 0.03
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.24
Consensus pattern (47 bp):
GTCAAGTATCATATCAGAATTCAAGTCAAAATCAGATCAGAATCCAA
Found at i:1451194 original size:18 final size:18
Alignment explanation
Indices: 1451171--1451205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1451161 TGCCATCCAG
*
1451171 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1451189 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1451206 GTCCTTTCGA
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:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1452461 original size:18 final size:18
Alignment explanation
Indices: 1452438--1452478 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1452428 CAACGATCAA
1452438 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTCAACAGGT
*
1452456 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACAGGT
1452474 CGGGT
1 CGGGT
1452479 AAATGGGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACAGGT
Found at i:1452492 original size:31 final size:31
Alignment explanation
Indices: 1452434--1452497 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1452424 CGGTCAACGA
* *
1452434 TCAACGGGTCGGGTCAACAGGTCGGGTCGGG
1 TCAACGGGTCGGGTAAACAGGTCGGGTCAGG
** *
1452465 TCAACGGGTCGGGTAAATGGGTTGGGTCAGG
1 TCAACGGGTCGGGTAAACAGGTCGGGTCAGG
1452496 TC
1 TC
1452498 GGGTTATGAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.17, C:0.19, G:0.44, T:0.20
Consensus pattern (31 bp):
TCAACGGGTCGGGTAAACAGGTCGGGTCAGG
Found at i:1453972 original size:15 final size:15
Alignment explanation
Indices: 1453952--1453980 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1453942 AAACAACAAC
1453952 AACAATAATAATAAT
1 AACAATAATAATAAT
1453967 AACAATAATAATAA
1 AACAATAATAATAA
1453981 CCTGAACAAA
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:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AACAATAATAATAAT
Found at i:1461092 original size:6 final size:6
Alignment explanation
Indices: 1461081--1461125 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
1461071 AACGATTACT
1461081 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
1461126 GGAATGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1463302 original size:123 final size:124
Alignment explanation
Indices: 1463111--1463353 Score: 382
Period size: 123 Copynumber: 2.0 Consensus size: 124
1463101 AAATCATAGG
* *
1463111 TGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTGGATGTCCTTCGTTATGAAGTTGAAATCCAAT
1 TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCATTCGTTATGAAGTTGAAATCCAAT
* *
1463176 CTTGTAAATTGAATCGCTTT-GAGATT-AACATCTTTCGCTGTGAAGTTGAAATTGTGGA
66 CTTGTAAATTGAATCGCTTTCGAG-TTCAACATCTTTCACTGTGAAGCTGAAATTGTGGA
* *
1463234 TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCATTCGTTGTGAAGTTGAAATCCACT
1 TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCATTCGTTATGAAGTTGAAATCCAAT
* * *
1463299 CTTGTAAATTGCATTGCTTTCGAGTTCAATATCTTTCACTGTGAAGCTGAAATTG
66 CTTGTAAATTGAATCGCTTTCGAGTTCAACATCTTTCACTGTGAAGCTGAAATTG
1463354 ACTATAACAA
Statistics
Matches: 109, Mismatches: 9, Indels: 3
0.90 0.07 0.02
Matches are distributed among these distances:
123 81 0.74
124 28 0.26
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (124 bp):
TGGCTCATTCGCTGTGAAGTTGAGCTTTGAATTGGATGTCATTCGTTATGAAGTTGAAATCCAAT
CTTGTAAATTGAATCGCTTTCGAGTTCAACATCTTTCACTGTGAAGCTGAAATTGTGGA
Found at i:1467406 original size:550 final size:550
Alignment explanation
Indices: 1466359--1467450 Score: 1794
Period size: 550 Copynumber: 2.0 Consensus size: 550
1466349 ATTTCTTCCT
1466359 AGATTCTTCATGTTGGCCCATGACACATCCCATTGAATTCTCAAATATAGACAAATACAAGAATA
1 AGATTCTTCATGTTGGCCCATGACACATCCCATTGAATTCTCAAATATAGACAAATACAAGAATA
* *
1466424 GAGGTTTTCCCGGGATGGGGGCAATCAAGATAGGGGTGTGAGATAAATACTCCTTTATTTTCTCA
66 GAGGTTTTCCCGAGATGGGGACAATCAAGATAGGGGTGTGAGATAAATACTCCTTTATTTTCTCA
* * * * **
1466489 AATGTAGTCTAACAATCCTCATCCCATGCTTCGAAGTTGTTCTTTGGAAGAAGGTGAAAGATTGG
131 AATGCAGTCTAACAATCCTCATCCCATGCTCCGAAGTTATTCTTTCGAAGAAGGCAAAAGATTGG
* *
1466554 GTCTCACTTATCAGTTAGCTGAGATTTGAACCATGCTATGTAATTCAATCTACCCAAAAAACCTC
196 GTCTCACTTATCAGTTAGCTGAGATATGAACCATGATATGTAATTCAATCTACCCAAAAAACCTC
1466619 GTACTTCTTTTTCTATTTATGGGGAGGTAAATTCTGGATGGCCTTAACTTTATCGGGATCAACTT
261 GTACTTCTTTTTCTATTTATGGGGAGGTAAATTCTGGATGGCCTTAACTTTATCGGGATCAACTT
* *
1466684 CGATGCCTGTCCTGCTGACCACAAAGCCTAACAACTTTCTGGATGTTACTCCGAAGGTACACTTG
326 CGATGCCTGTCCTGCTGACCACAAAGCCTAACAACTTTCTGGATGTTACTCCAAAGGTACACTTA
*
1466749 CTGGGGTTCACACTCAGTTGGAACTTTCTTAATCTTTGAAAGAGCTTTATCAGATTTTCGACTTG
391 CTGGGGTTCACACTCAGTTGGAACTTTCTTAATCTTTGAAAGAGCTTTATCAGATTCTCGACTTG
* *
1466814 TTCATTTTCGATTTGTGCCTTGACAATCATGTAGTCGACATAAAACTCGATTTCTTTATGCATCA
456 TTCATTTTCGATTTGTGCATTGACAATCATGTAGTCGACATAAAACTCGATTTCTGTATGCATCA
*
1466879 TGTTATGAAACAGGGTCACCATCCCATCCC
521 TGTCATGAAACAGGGTCACCATCCCATCCC
1466909 AGATTCTTCATGTTGGCCCATGACACATCCCATTGAATTCTCAAATATAGACAAATACAAGAATA
1 AGATTCTTCATGTTGGCCCATGACACATCCCATTGAATTCTCAAATATAGACAAATACAAGAATA
*
1466974 GAGGTTTTCCTGAGATAGGGGAC-ATCAAGATAGGGGTGTGAGATAAATACTCCTTTATTTTCTC
66 GAGGTTTTCCCGAGAT-GGGGACAATCAAGATAGGGGTGTGAGATAAATACTCCTTTATTTTCTC
* * * *
1467038 AAATGCAGTCTGACAGTCCTTATCCCATGCTCCGGAGTTATTCTTTCGAAGAAGGCAAAAGATTG
130 AAATGCAGTCTAACAATCCTCATCCCATGCTCCGAAGTTATTCTTTCGAAGAAGGCAAAAGATTG
* * * * *
1467103 GGTCGT-ACTTATCAGTTAGTTGAGATATGAACCGTGATATGTAATTCAATCTGCCTAGAAAACC
195 GGTC-TCACTTATCAGTTAGCTGAGATATGAACCATGATATGTAATTCAATCTACCCAAAAAACC
* * *
1467167 TCGTACTTCTTTTTGTGTTTGTGGGGGAGGTAAATTCTGGATGGCCTTAACTTTATCGGGATCAA
259 TCGTACTTCTTTTTCTATTTAT-GGGGAGGTAAATTCTGGATGGCCTTAACTTTATCGGGATCAA
* *
1467232 CTTCGATGCCTTTCCTGCTGACCATAAAGCCTAACAACTTTCTGGATGTTACTCCAAAGGTACAC
323 CTTCGATGCCTGTCCTGCTGACCACAAAGCCTAACAACTTTCTGGATGTTACTCCAAAGGTACAC
** * * *
1467297 TTACTGGGGTTCAGTCTCAGTTGGAACTTTCTTATTCTTTGAAAGA-TTTTTTCAGATTCTCGAC
388 TTACTGGGGTTCACACTCAGTTGGAACTTTCTTAATCTTTGAAAGAGCTTTATCAGATTCTCGAC
* *
1467361 TTGTTCATTTTCGATTTGTGCATTGACAATCATGTCGTTGACATAAAACTCGATTTCTGTATGCA
453 TTGTTCATTTTCGATTTGTGCATTGACAATCATGTAGTCGACATAAAACTCGATTTCTGTATGCA
1467426 TCATGTCATGAAACAGGGTCACCAT
518 TCATGTCATGAAACAGGGTCACCAT
1467451 AGCTCTCTGA
Statistics
Matches: 501, Mismatches: 38, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
550 349 0.70
551 152 0.30
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.33
Consensus pattern (550 bp):
AGATTCTTCATGTTGGCCCATGACACATCCCATTGAATTCTCAAATATAGACAAATACAAGAATA
GAGGTTTTCCCGAGATGGGGACAATCAAGATAGGGGTGTGAGATAAATACTCCTTTATTTTCTCA
AATGCAGTCTAACAATCCTCATCCCATGCTCCGAAGTTATTCTTTCGAAGAAGGCAAAAGATTGG
GTCTCACTTATCAGTTAGCTGAGATATGAACCATGATATGTAATTCAATCTACCCAAAAAACCTC
GTACTTCTTTTTCTATTTATGGGGAGGTAAATTCTGGATGGCCTTAACTTTATCGGGATCAACTT
CGATGCCTGTCCTGCTGACCACAAAGCCTAACAACTTTCTGGATGTTACTCCAAAGGTACACTTA
CTGGGGTTCACACTCAGTTGGAACTTTCTTAATCTTTGAAAGAGCTTTATCAGATTCTCGACTTG
TTCATTTTCGATTTGTGCATTGACAATCATGTAGTCGACATAAAACTCGATTTCTGTATGCATCA
TGTCATGAAACAGGGTCACCATCCCATCCC
Found at i:1469002 original size:15 final size:15
Alignment explanation
Indices: 1468978--1469011 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1468968 CTATAGGACC
1468978 ACTACATCCCGAAGG
1 ACTACATCCCGAAGG
*
1468993 ACTACGTCCCGAAGG
1 ACTACATCCCGAAGG
1469008 ACTA
1 ACTA
1469012 TTATACCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.15
Consensus pattern (15 bp):
ACTACATCCCGAAGG
Found at i:1469138 original size:29 final size:29
Alignment explanation
Indices: 1469096--1469187 Score: 168
Period size: 29 Copynumber: 3.2 Consensus size: 29
1469086 TTTCATATGT
1469096 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
1469124 TCATGTAGCTCATGTCATTTCTCTTGTTA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1469153 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1469182 TCATGT
1 TCATGT
1469188 TCTCATATCA
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 7 0.11
29 54 0.89
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1469207 original size:12 final size:12
Alignment explanation
Indices: 1469190--1469214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1469180 GATCATGTTC
1469190 TCATATCACATA
1 TCATATCACATA
1469202 TCATATCACATA
1 TCATATCACATA
1469214 T
1 T
1469215 GTATTTGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1469217 original size:58 final size:57
Alignment explanation
Indices: 1469096--1469217 Score: 131
Period size: 58 Copynumber: 2.1 Consensus size: 57
1469086 TTTCATATGT
* ** * ***
1469096 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGCTCATGTCATTTCTCTTGTTA
1 TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGCTCATATCACATATCTTCACA
*
1469153 TCATGTAGCTCATGTCATTTCTCTTGTGATCATGT-TCTCATATCACATATCATATCACA
1 TCATGTA-CTCATGTCATTTCTCTTGTGATCATGTAGCTCATATCACATATC-T-TCACA
1469212 T-ATGTA
1 TCATGTA
1469218 TTTGAATCTA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
57 18 0.33
58 33 0.61
59 3 0.06
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.44
Consensus pattern (57 bp):
TCATGTACTCATGTCATTTCTCTTGTGATCATGTAGCTCATATCACATATCTTCACA
Found at i:1469637 original size:64 final size:64
Alignment explanation
Indices: 1469568--1469724 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 64
1469558 TAATGAAGGT
* * **
1469568 ATGCATCGATGCACTATTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTT-TATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTATATT-TTAAAAG
1469631 A
64 A
* * * * *
1469632 ATGCATCGATGCA-TGCCTTATACAGCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAAAAGA
* *
1469696 GTGCATCGATGCACTACCTGTGCATCGAT
1 ATGCATCGATGCACTACTTGTGCATCGAT
1469725 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
63 1 0.01
64 67 0.91
65 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTATATTTTAAAAGA
Found at i:1470187 original size:11 final size:11
Alignment explanation
Indices: 1470173--1470197 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1470163 ATCATCTAAT
1470173 AATCAAAACCC
1 AATCAAAACCC
1470184 AATCAAAACCC
1 AATCAAAACCC
1470195 AAT
1 AAT
1470198 AAGAAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (11 bp):
AATCAAAACCC
Found at i:1473435 original size:29 final size:29
Alignment explanation
Indices: 1473393--1473484 Score: 177
Period size: 29 Copynumber: 3.2 Consensus size: 29
1473383 TTTCATATGT
1473393 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1473421 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1473450 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1473479 TCATGT
1 TCATGT
1473485 TCTCATATCA
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.11
29 56 0.89
ACGTcount: A:0.17, C:0.21, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1473951 original size:45 final size:45
Alignment explanation
Indices: 1473884--1474034 Score: 216
Period size: 45 Copynumber: 3.4 Consensus size: 45
1473874 TGCACTACTT
* * **
1473884 GTGCATCGGTGCA-TAAAATGCATTCGATGTTT-TATTATTAATGGA
1 GTGCATCGATGCACT-AATTGCATTCGATGTTTATATT-TTAAAAGA
*
1473929 ATGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 GTGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
*
1473974 GTGCATTGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
1 GTGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
1474019 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
1474035 CCTGTGCATC
Statistics
Matches: 96, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 91 0.95
46 5 0.05
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAATTGCATTCGATGTTTATATTTTAAAAGA
Found at i:1475221 original size:157 final size:157
Alignment explanation
Indices: 1474935--1475249 Score: 630
Period size: 157 Copynumber: 2.0 Consensus size: 157
1474925 AGATCACCTA
1474935 TTGCTCCAGGTATAAGCGAATAGGGATAGTTTGGATATTACTCTGAAATAAATTTGAAAATCACA
1 TTGCTCCAGGTATAAGCGAATAGGGATAGTTTGGATATTACTCTGAAATAAATTTGAAAATCACA
1475000 CGTAGTTCTTCCGCTGACCAGTTGCTAAGCACAAACCTGAGTGGCAGTGGGCAGATTCCGGATCT
66 CGTAGTTCTTCCGCTGACCAGTTGCTAAGCACAAACCTGAGTGGCAGTGGGCAGATTCCGGATCT
1475065 ATCTGTATCTTTAGCATTCTCTGTGAT
131 ATCTGTATCTTTAGCATTCTCTGTGAT
1475092 TTGCTCCAGGTATAAGCGAATAGGGATAGTTTGGATATTACTCTGAAATAAATTTGAAAATCACA
1 TTGCTCCAGGTATAAGCGAATAGGGATAGTTTGGATATTACTCTGAAATAAATTTGAAAATCACA
1475157 CGTAGTTCTTCCGCTGACCAGTTGCTAAGCACAAACCTGAGTGGCAGTGGGCAGATTCCGGATCT
66 CGTAGTTCTTCCGCTGACCAGTTGCTAAGCACAAACCTGAGTGGCAGTGGGCAGATTCCGGATCT
1475222 ATCTGTATCTTTAGCATTCTCTGTGAT
131 ATCTGTATCTTTAGCATTCTCTGTGAT
1475249 T
1 T
1475250 ACGGCGTTGA
Statistics
Matches: 158, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (157 bp):
TTGCTCCAGGTATAAGCGAATAGGGATAGTTTGGATATTACTCTGAAATAAATTTGAAAATCACA
CGTAGTTCTTCCGCTGACCAGTTGCTAAGCACAAACCTGAGTGGCAGTGGGCAGATTCCGGATCT
ATCTGTATCTTTAGCATTCTCTGTGAT
Found at i:1481985 original size:6 final size:6
Alignment explanation
Indices: 1481976--1482002 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1481966 ACGATTTACT
1481976 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
1482003 GGAATGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:1483408 original size:12 final size:12
Alignment explanation
Indices: 1483391--1483429 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1483381 ATATAATATA
1483391 AATATACTATGT
1 AATATACTATGT
*
1483403 AATATACTATAT
1 AATATACTATGT
*
1483415 AAATATAATATGT
1 -AATATACTATGT
1483428 AA
1 AA
1483430 ATAAGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (12 bp):
AATATACTATGT
Found at i:1485623 original size:20 final size:20
Alignment explanation
Indices: 1485595--1485666 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
1485585 TAGTATACTA
*
1485595 GTATGGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
**
1485615 GTATCGATACCATAGTGTAGAA
1 GTATCGATACCAT-G-GTAGGG
1485637 GTATCGATACCATGGTAGGG
1 GTATCGATACCATGGTAGGG
*
1485657 GTTTCGATAC
1 GTATCGATAC
1485667 TATTGAGCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 25 0.57
21 2 0.05
22 17 0.39
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (20 bp):
GTATCGATACCATGGTAGGG
Found at i:1485625 original size:42 final size:42
Alignment explanation
Indices: 1485578--1485666 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
1485568 ATAGAGTCTA
* *
1485578 GATACCATAGTATACTAGTATGGATACCATGGTAGGGGTATC
1 GATACCATAGTATACAAGTATCGATACCATGGTAGGGGTATC
* * *
1485620 GATACCATAGTGTAGAAGTATCGATACCATGGTAGGGGTTTC
1 GATACCATAGTATACAAGTATCGATACCATGGTAGGGGTATC
1485662 GATAC
1 GATAC
1485667 TATTGAGCTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (42 bp):
GATACCATAGTATACAAGTATCGATACCATGGTAGGGGTATC
Found at i:1485640 original size:22 final size:22
Alignment explanation
Indices: 1485578--1485649 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 22
1485568 ATAGAGTCTA
* ** *
1485578 GATACCATAGTATACTAGTATG
1 GATACCATAGTGTAGAAGTATC
**
1485600 GATACCAT-G-GTAGGGGTATC
1 GATACCATAGTGTAGAAGTATC
1485620 GATACCATAGTGTAGAAGTATC
1 GATACCATAGTGTAGAAGTATC
1485642 GATACCAT
1 GATACCAT
1485650 GGTAGGGGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 14 0.34
21 2 0.05
22 25 0.61
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (22 bp):
GATACCATAGTGTAGAAGTATC
Found at i:1486060 original size:54 final size:54
Alignment explanation
Indices: 1485991--1487233 Score: 1501
Period size: 54 Copynumber: 23.2 Consensus size: 54
1485981 ACCAAAAGGT
* * *
1485991 ACTAAGTGTGTAATTCACGGAATTCATCATATGATGATGAATAACCGTTTTGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* *
1486045 ACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * * *
1486099 ACTAAGTGTGCAACTCACGAAATTCATCATATGTTGATGAATAACTGTTTCGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
**
1486153 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGAT
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* *
1486207 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * * **
1486261 ATTAAGTGTGCAATTCATGGAATTCATCATATGTTGATGAATAATCGTTTCGAA
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* *
1486315 ACTAAGTGTACAATTCACGAAATTCATCATATGTTGAT-ACATAACCGTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGA-ATAACCGTTTCGGC
* *
1486369 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCGTTTGGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
** * *
1486423 ACTAAGTGTGCAATTCAATGAATTCATCATAT-TTGGATGAATAACCATTTGGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTT-GATGAATAACCGTTTCGGC
* ** * *
1486477 ACCAAGTGTGCAATTCAATGAATTCATC-TATGTGGATGAATAACCGTTTGGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * ** *
1486530 ACCAAGTATGCAATTCAATGAATTCATCATAT-TTGGATGAATAACCTTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTT-GATGAATAACCGTTTCGGC
* *
1486584 ACTAAG-GTTGCAATTCACGGAATTCATCATATGTTAATGAATAACCGTTTGGGC
1 ACTAAGTG-TGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* ** ** * *
1486638 ACTAAGTATGCAATTCAATGAATTCATCATATGTTGATGAATAAATGTTTTGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * *
1486692 ACTAAGTGTGCAATTCACGAAATTCATCATAAGTTGATGAATAACCGTTTCGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* ** *
1486746 ACTAAGTGTGCAACTCACGGAATTCATCATATGTTGATGAATAATTGTTTCGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * **
1486800 ACTAAGTGTGCAATTCACGGAATTAATCATATGTTGATGAATAACCATTTCTAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * * * **
1486854 ACTAGGTGTGCAATTTACGAAATTCATCATATGTTGATGAATAACTGTTTCAAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* *
1486908 AC-AATGTGTGCATTTCACGG-----A--AT-T-TTGATGAATAACCGTTTAGGC
1 ACTAA-GTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* *
1486953 ACTAAGTGTACAATTCACGGAATTCATCATATGTTGATGAATAACTGTTTCGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * ** * *
1487007 ACTAAGTATGCAACTGGCGAAATTCATCATATGTTGATGAATAACCGTTTCAGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * *
1487061 ACTAATTGTGCAATTCAAGGAATTCATCATATGTTGATGAATAACCGTTTCGAC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* ** * * **
1487115 ACTAAGTGTGTAATTCACATAATTTATCATATGTTGATGAATAACCGTTTTGAT
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
* * * * * * * * *
1487169 ACTATGTGTGTAATCCATGGAATTCATAATATGTT-TTGAATGACCGTATGGGC
1 ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
*
1487222 ACTACGTGTGCA
1 ACTAAGTGTGCA
1487234 TTGCAACAAT
Statistics
Matches: 1032, Mismatches: 137, Indels: 41
0.85 0.11 0.03
Matches are distributed among these distances:
45 32 0.03
46 3 0.00
47 2 0.00
49 1 0.00
50 1 0.00
52 2 0.00
53 76 0.07
54 912 0.88
55 3 0.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (54 bp):
ACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGGC
Found at i:1486970 original size:45 final size:45
Alignment explanation
Indices: 1486887--1486976 Score: 112
Period size: 45 Copynumber: 2.0 Consensus size: 45
1486877 TCATCATATG
* * *
1486887 TTGATGAATAACTGTTTCAACACAATGTGTGCATTTCACGGAATT
1 TTGATGAATAACCGTTTCAACACAATGTGTACAATTCACGGAATT
*
1486932 TTGATGAATAACCGTTT-AGGCACTAA-GTGTACAATTCACGGAATT
1 TTGATGAATAACCGTTTCA-ACAC-AATGTGTACAATTCACGGAATT
1486977 CATCATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 1 0.03
45 36 0.92
46 2 0.05
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (45 bp):
TTGATGAATAACCGTTTCAACACAATGTGTACAATTCACGGAATT
Found at i:1487058 original size:26 final size:26
Alignment explanation
Indices: 1487029--1487111 Score: 64
Period size: 26 Copynumber: 3.1 Consensus size: 26
1487019 ACTGGCGAAA
1487029 TTCATCATATGTTGATGAATAACCGT
1 TTCATCATATGTTGATGAATAACCGT
* * * *
1487055 TTCAGCACTA-ATTG-TGCAATTCAA-GGAA
1 TTCATCA-TATGTTGATG-AA-T-AACCG-T
1487083 TTCATCATATGTTGATGAATAACCGT
1 TTCATCATATGTTGATGAATAACCGT
1487109 TTC
1 TTC
1487112 GACACTAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 16
0.63 0.12 0.25
Matches are distributed among these distances:
25 2 0.05
26 16 0.39
27 8 0.20
28 13 0.32
29 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (26 bp):
TTCATCATATGTTGATGAATAACCGT
Found at i:1493381 original size:22 final size:22
Alignment explanation
Indices: 1493355--1493413 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
1493345 TACCGTAATA
*
1493355 AAGTATCAATACTATAGTATAG
1 AAGTATCAATACCATAGTATAG
* *
1493377 TAGTAT-AGATACCATAGTGTAG
1 AAGTATCA-ATACCATAGTATAG
*
1493399 AAGTATCGATACCAT
1 AAGTATCAATACCAT
1493414 GGTAGGGGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.31
Consensus pattern (22 bp):
AAGTATCAATACCATAGTATAG
Found at i:1493814 original size:54 final size:54
Alignment explanation
Indices: 1493751--1494035 Score: 338
Period size: 54 Copynumber: 5.3 Consensus size: 54
1493741 ATTACCAAAA
* *
1493751 GGCACTAAGTATGCAATTCACATAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
**
1493805 GGCACTAAGTGCACAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * *
1493859 GTCACTAAGTGTACAATTCACGGAATTCATCATATATTGATGAATAACCTTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * *
1493913 GGCACTAAGTGAGCAATTCACGGAATTCATCATATATTGATGAATAACCATTTT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
* * * * * * * * *
1493967 GACACTATGTGTGCAATCCACATAATTCATAATATGTTTATTAATGACCGTAT-
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
*
1494020 GAGCACTACGTGTGCA
1 G-GCACTAAGTGTGCA
1494036 TTGCAACATT
Statistics
Matches: 201, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
53 1 0.00
54 200 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:1504443 original size:236 final size:230
Alignment explanation
Indices: 1503991--1504639 Score: 795
Period size: 236 Copynumber: 2.8 Consensus size: 230
1503981 TTTATAAGTT
* * *
1503991 AAAAAATGAGAAAAGATTCTCATTTAAATATGAAAATGGAAATTGTTGAAAAGTAAGGAAAGTTT
1 AAAAAATGAGAAAAGTTTCTCA-TTAAATATGAAAATTGAAATT-TTGAAAAGTAAGAAAAGTTT
** ** * * *
1504056 CTTACCTAGTAAACTATTTCCAAAATCAGTAAGTTTTTTGGGACATCAGTAAGTTTTTCGAGCAT
64 CTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * * *
1504121 GATGCTTAAACCCTTC-AGGTCATCTGTAAGTCTTCTGAGCAAGGTGATAAGTGCCTCAGGACAT
129 GATGCTTAAA-TCTTCGA-GTCATCTATAAGTTTTC-GAGCAAGATGATAAGTGCCTCAGGACAT
* **
1504185 CTATAAGACCTTCGGGCAGGATGTTTTCATGTGTCTCTTG
191 CCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTTG
* *
1504225 AAAAAAATAAGAAATGTTTCTCACTTAAATATGAAAATTGAAATTTTAGAAAAGTAAGAAAAGTT
1 -AAAAAATGAGAAAAGTTTCTCA-TTAAATATGAAAATTGAAATTTT-GAAAAGTAAGAAAAGTT
* *
1504290 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGT
63 TCTTACCTAGTAAACTATTTCCAAAATTGGT-AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
* ** *
1504355 ATGATGCTTAAATTCTTCGAGTCATCTATAAGTGTTTCAAGCAAGATGATAAGT-CCTTTGAGCC
127 ATGATGCTTAAA-TCTTCGAGTCATCTATAAGT-TTTCGAGCAAGATGATAAGTGCCTCAG-GAC
* * *
1504419 ATCCATAAGACCTTCGGTCAGGATGTTTTCACATGTTTTTTG
189 ATCCATAAGACCTTCGGGCAGGATGTTTTCACATGTCTCTTG
* *
1504461 -AAAAATGAGAAAAGTTTCTTATCTAAATCT-AAAATTTGAAATTTTTGAAAAGTAAGAAAAGTT
1 AAAAAATGAGAAAAGTTTCTCAT-TAAATATGAAAA-TTGAAA-TTTTGAAAAGTAAGAAAAGTT
*
1504524 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
63 TCTTACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
** *
1504589 TGATGAGTAAATCTTTCGGGTCATCTATAAGCCTTTT-GAGCAAGATGATAA
128 TGATGCTTAAATC-TTCGAGTCATCTATAAG--TTTTCGAGCAAGATGATAA
1504640 TTTCTTCGGG
Statistics
Matches: 362, Mismatches: 41, Indels: 24
0.85 0.10 0.06
Matches are distributed among these distances:
232 2 0.01
233 74 0.20
234 83 0.23
235 93 0.26
236 106 0.29
237 4 0.01
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (230 bp):
AAAAAATGAGAAAAGTTTCTCATTAAATATGAAAATTGAAATTTTGAAAAGTAAGAAAAGTTTCT
TACCTAGTAAACTATTTCCAAAATTGGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGA
TGCTTAAATCTTCGAGTCATCTATAAGTTTTCGAGCAAGATGATAAGTGCCTCAGGACATCCATA
AGACCTTCGGGCAGGATGTTTTCACATGTCTCTTG
Found at i:1505349 original size:134 final size:134
Alignment explanation
Indices: 1505132--1505688 Score: 694
Period size: 134 Copynumber: 4.2 Consensus size: 134
1505122 GCGAATCGAA
* * * * *
1505132 CTCGATTTAATCTTCCCTAAGTAATAGTGGAATGAATAAAAGAT-CCTAGATTTGATTTTCCCTC
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAAAG-TCCCCAGATCTGATTTTCCCTC
* * * * * *
1505196 AAGAAGAAGTGGAATATATCAATCTTTTTCAAGATTTGATGTTCCTTGAGTAACAGTAGAATAAG
65 AAGAAGAAGCGGAACATATCTATCTTTTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACAAG
*
1505261 TCTGC
130 TTTGC
* *
1505266 CTCGATTCAATTTTCCTTGAGTAATAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
1505331 AGAAGAAGCGGAACATATCTAT-TTCTTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACAAG
66 AGAAGAAGCGGAACATATCTATCTT-TTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACAAG
*
1505395 TTTTC
130 TTTGC
* * * *
1505400 CTTGATTCAATTTTCCCTGAGTATTAGTGGAATGAATCAAAGTCCCCAGATTTGATTTTCCCTCA
1 CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
* * * * * *
1505465 AGATGAAGCAGAACATATCCATCTCTTTT-GAGATTTGATATTCCCTGAGTAATAGTGGAACAAG
66 AGAAGAAGCGGAACATATCTATCT-TTTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACAAG
1505529 TTTGC
130 TTTGC
* * *
1505534 CTCGATTCAATCTTCCTTGAAG-AACAGTGGAATGAATCAACA-TCCCCAAATCTGATTTTCCCT
1 CTCGATTCAATCTTCCCTG-AGTAATAGTGGAATGAATCAA-AGTCCCCAGATCTGATTTTCCCT
* * * * * * *
1505597 CAAGAAGAAGTGAAAC-TAATCTATCTCTTTCAAGATTTGATATTTCCTGAGTAACTGTGGAATA
64 CAAGAAGAAGCGGAACAT-ATCTATCTTTTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACA
1505661 AGTTTGC
128 AGTTTGC
*
1505668 CTCGATTCAATCTTCTCTGAG
1 CTCGATTCAATCTTCCCTGAG
1505689 GAACAATGGA
Statistics
Matches: 369, Mismatches: 46, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
133 9 0.02
134 352 0.95
135 7 0.02
136 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.34
Consensus pattern (134 bp):
CTCGATTCAATCTTCCCTGAGTAATAGTGGAATGAATCAAAGTCCCCAGATCTGATTTTCCCTCA
AGAAGAAGCGGAACATATCTATCTTTTTCAAGATTTGATGTTCCCTGAGTAACAGTGGAACAAGT
TTGC
Found at i:1505705 original size:41 final size:41
Alignment explanation
Indices: 1505654--1505731 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
1505644 TGAGTAACTG
* *
1505654 TGGAATAAGTTTGCCTCGATTCAATCTTCTCTGAGGAACAA
1 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTGAGGAACAA
*
1505695 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTTAGGA
1 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTGAGGA
1505732 TTAGCGGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
TGGAACAAGTTTGCCTCAATTCAATCTTCTCTGAGGAACAA
Found at i:1505719 original size:175 final size:174
Alignment explanation
Indices: 1505520--1505853 Score: 440
Period size: 175 Copynumber: 1.9 Consensus size: 174
1505510 TGAGTAATAG
* *
1505520 TGGAACAAGTTTGCCTCGATTCAATCTTC-CTTGAAGAACAGTGGAATGAATCAACATCCCCAAA
1 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTT-AAGAACAGCGGAATGAATCAACATCCCCAAA
* * * * *
1505584 TCTGATTTTCCCTCAAGAAGAAG-TGAA-ACTAATCTATCTCTTTCAAGATTTGATATTTCCTGA
65 TCTGATTTTCCCTCAAGAAAAAGCAGAACA-T-ATCCATCTATTTCAAGATTTGATATTCCCTGA
* * *
1505647 GTAACTGTGGAATAAGTTTGCCTCGATTCAATCTTCTCTGAGGAACAA
128 GT-ACAGTGGAATAAATCTGCCTCGATTCAATCTTCTCTGAGGAACAA
* ** * * *
1505695 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTTAGGATTAGCGGAATGAATCAACGTCCTCATAT
1 TGGAACAAGTTTGCCTCAATTCAATCTTCTCTTAAGAACAGCGGAATGAATCAACATCCCCAAAT
* * *
1505760 CTTATTTTCCCTCAAGAAAAAGCAGAACATGTCCATCTATTTCAAGATTTGATATTCCCTGGGTA
66 CTGATTTTCCCTCAAGAAAAAGCAGAACATATCCATCTATTTCAAGATTTGATATTCCCTGAGTA
1505825 CAGTGGAATAAATCTGCCTCGATTCAATC
131 CAGTGGAATAAATCTGCCTCGATTCAATC
1505854 ATCCCCGAAG
Statistics
Matches: 137, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
174 27 0.20
175 102 0.74
176 7 0.05
177 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (174 bp):
TGGAACAAGTTTGCCTCAATTCAATCTTCTCTTAAGAACAGCGGAATGAATCAACATCCCCAAAT
CTGATTTTCCCTCAAGAAAAAGCAGAACATATCCATCTATTTCAAGATTTGATATTCCCTGAGTA
CAGTGGAATAAATCTGCCTCGATTCAATCTTCTCTGAGGAACAA
Found at i:1506078 original size:22 final size:22
Alignment explanation
Indices: 1506053--1506094 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1506043 GTCCGGGTTT
* *
1506053 TAATTATTATTATTATTATTTA
1 TAATTATTATGACTATTATTTA
*
1506075 TAATTGTTATGACTATTATT
1 TAATTATTATGACTATTATT
1506095 ATTATAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
TAATTATTATGACTATTATTTA
Found at i:1508734 original size:27 final size:27
Alignment explanation
Indices: 1508680--1508731 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1508670 TCTAAATATT
*
1508680 TTAATTTTGAATTCTAAAATCTTAAAC
1 TTAATTTTGAATTATAAAATCTTAAAC
* *
1508707 TTAATTTTTAATTATTAAAT-TTAAA
1 TTAATTTTGAATTATAAAATCTTAAA
1508732 ACTCTTAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (27 bp):
TTAATTTTGAATTATAAAATCTTAAAC
Found at i:1510678 original size:60 final size:60
Alignment explanation
Indices: 1510545--1510680 Score: 150
Period size: 60 Copynumber: 2.3 Consensus size: 60
1510535 ATTATAAGAT
* * * * *
1510545 ATTGCTTTATTGAGTCTTCTGATTATTAAAAGTTACAAAATGATCCCCTAACTATAGGAT
1 ATTGCTTTATTGAGTCTCCTAACTATAAAAAGTTACAAAATGATCCCCTAACTATAGGAC
** * * *
1510605 ATTATTTTGTTGAGTC-CCTAACTATAAAAAAGTTACAAAATGATCCCTTGACTATAAGG-C
1 ATTGCTTTATTGAGTCTCCTAACTAT-AAAAAGTTACAAAATGATCCCCTAACTAT-AGGAC
1510665 ATTGCTTTATTGAGTC
1 ATTGCTTTATTGAGTC
1510681 ATCCGACTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
59 6 0.10
60 52 0.85
61 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (60 bp):
ATTGCTTTATTGAGTCTCCTAACTATAAAAAGTTACAAAATGATCCCCTAACTATAGGAC
Found at i:1512343 original size:2 final size:2
Alignment explanation
Indices: 1512336--1512363 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1512326 TAATAATTGA
1512336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1512364 TCTGGCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1513298 original size:21 final size:21
Alignment explanation
Indices: 1513273--1513314 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1513263 GAAATAACTT
* *
1513273 TAACTAGTTAAAGAAATTTAA
1 TAACTAGTGAAAAAAATTTAA
*
1513294 TAACTCGTGAAAAAAATTTAA
1 TAACTAGTGAAAAAAATTTAA
1513315 GAAAAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.10, T:0.31
Consensus pattern (21 bp):
TAACTAGTGAAAAAAATTTAA
Found at i:1513776 original size:19 final size:17
Alignment explanation
Indices: 1513732--1513775 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
1513722 TAGATCTTTG
1513732 AAGACTCTCTTTGAAAA
1 AAGACTCTCTTTGAAAA
1513749 AAGACTCTCTTTGAAAA
1 AAGACTCTCTTTGAAAA
*
1513766 AAGGCTCTCT
1 AAGACTCTCT
1513776 CCAATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (17 bp):
AAGACTCTCTTTGAAAA
Found at i:1514513 original size:2 final size:2
Alignment explanation
Indices: 1514506--1514550 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1514496 AATGCTACCA
1514506 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1514548 AT A
1 AT A
1514551 ATTATTCCAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1525369 original size:29 final size:29
Alignment explanation
Indices: 1525333--1525431 Score: 121
Period size: 29 Copynumber: 3.4 Consensus size: 29
1525323 AAAAAAATAT
*
1525333 AAATTTACAATAAAAGGCAAAACTTTTTG
1 AAATTTACAATAAAAAGCAAAACTTTTTG
* *
1525362 AAATTTACAAAAAAAAG-ACAACTTTTTG
1 AAATTTACAATAAAAAGCAAAACTTTTTG
* **
1525390 AAATTTACAATAAAAAACAAAACTAATT-
1 AAATTTACAATAAAAAGCAAAACTTTTTG
1525418 ATAATTTACAATAA
1 A-AATTTACAATAA
1525432 CGGCAACAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 26 0.43
29 34 0.57
ACGTcount: A:0.56, C:0.10, G:0.05, T:0.29
Consensus pattern (29 bp):
AAATTTACAATAAAAAGCAAAACTTTTTG
Found at i:1525841 original size:31 final size:32
Alignment explanation
Indices: 1525803--1525866 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1525793 AATGTTTTAA
* *
1525803 AACTTTGTGTCA-TTTTTTCTAAAACATCGTT
1 AACTTTGTGGCATTTTTTTCTAAAACACCGTT
1525834 AACTTTGTGGCATTTTTTTCTAAAACACCGTT
1 AACTTTGTGGCATTTTTTTCTAAAACACCGTT
1525866 A
1 A
1525867 TTGATTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.45
Consensus pattern (32 bp):
AACTTTGTGGCATTTTTTTCTAAAACACCGTT
Found at i:1526023 original size:21 final size:22
Alignment explanation
Indices: 1525999--1526051 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
1525989 AAACATGACA
*
1525999 TCCATAACAACT-AAATTTATT
1 TCCATAACAACTAAAATTTAGT
1526020 TCCATAACAA-TAAAATTTAGT
1 TCCATAACAACTAAAATTTAGT
1526041 TCCATAACAAC
1 TCCATAACAAC
1526052 CAACTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (22 bp):
TCCATAACAACTAAAATTTAGT
Found at i:1526065 original size:21 final size:21
Alignment explanation
Indices: 1525998--1526066 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
1525988 TAAACATGAC
* *
1525998 ATCCATAACAACTAAATTTAT
1 ATCCATAACAACAAAATTTAA
* * *
1526019 TTCCATAACAATAAAATTTAG
1 ATCCATAACAACAAAATTTAA
* * *
1526040 TTCCATAACAACCAACTTTAA
1 ATCCATAACAACAAAATTTAA
1526061 ATCCAT
1 ATCCAT
1526067 TATAATAAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.32
Consensus pattern (21 bp):
ATCCATAACAACAAAATTTAA
Found at i:1530547 original size:10 final size:10
Alignment explanation
Indices: 1530532--1530563 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
1530522 TAGGATTTAG
1530532 TTCATAAAAC
1 TTCATAAAAC
1530542 TTCATAAAAC
1 TTCATAAAAC
1530552 TTCATAAAAC
1 TTCATAAAAC
1530562 TT
1 TT
1530564 ATGTACGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (10 bp):
TTCATAAAAC
Found at i:1535918 original size:42 final size:40
Alignment explanation
Indices: 1535805--1535938 Score: 121
Period size: 41 Copynumber: 3.3 Consensus size: 40
1535795 TATCATTTTA
*
1535805 TAGCGGCGTTTTCTAAA-AAATGCC-TCTAAAGTACATGTTT
1 TAGCGGCGTTTTC-AAATAAATGCCAT-TAAAGTACATATTT
* ** * * *
1535845 TTGCGGCGTTTTCTTATAAAACGCCACTAAAGTACTTATCTT
1 TAGCGGCGTTTTCAAAT-AAATGCCATTAAAGTACATAT-TT
1535887 TAGCGGCGTTTGTCAAATAAATGCCATTAAAGTACA-AGTTT
1 TAGCGGCGTTT-TCAAATAAATGCCATTAAAGTACATA-TTT
*
1535928 TAGCGGTGTTT
1 TAGCGGCGTTT
1535939 GTTGAAAAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 12 0.16
41 29 0.39
42 28 0.38
43 4 0.05
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (40 bp):
TAGCGGCGTTTTCAAATAAATGCCATTAAAGTACATATTT
Found at i:1536897 original size:83 final size:83
Alignment explanation
Indices: 1536664--1536934 Score: 257
Period size: 82 Copynumber: 3.3 Consensus size: 83
1536654 GTTCGTAAGA
* * * *
1536664 AAAAAACACCACTATAGGTGAATCC--TATTGCGACGTTTGTATAAAAATGCCACTAAAGTACTA
1 AAAAAATACCACTATAGGTGAACCCTATATTG-G-TGTTTGTATAAAAATGTCACTAAAGTACTA
* *
1536727 ATCTGTTG-TGACATTTATTG
64 ATCTGTTGCAG-CTTTTATTG
* * * ** * *
1536747 ACAAAATGCCACTATA-GTAAACCCTAT-TTCAATATTTGTATAAAAATGTCACTAAAGTATTAA
1 AAAAAATACCACTATAGGTGAACCCTATATT-GGTGTTTGTATAAAAATGTCACTAAAGTACTAA
1536810 TCTGTTGCAGCTTTTATTG
65 TCTGTTGCAGCTTTTATTG
* * * *
1536829 AAAAAATATCACTATAGGTGAACCCTATATTGGTGTTTGTATAAAAAAGTCGCTAAAGTACTACT
1 AAAAAATACCACTATAGGTGAACCCTATATTGGTGTTTGTATAAAAATGTCACTAAAGTACTAAT
* * *
1536894 CTGTTGCAACTTTTGTCG
66 CTGTTGCAGCTTTTATTG
* * *
1536912 -AACAATTCCACTATAGATGAACC
1 AAAAAATACCACTATAGGTGAACC
1536935 TTATTGTTGC
Statistics
Matches: 151, Mismatches: 31, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
82 80 0.53
83 68 0.45
84 3 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (83 bp):
AAAAAATACCACTATAGGTGAACCCTATATTGGTGTTTGTATAAAAATGTCACTAAAGTACTAAT
CTGTTGCAGCTTTTATTG
Found at i:1536966 original size:82 final size:83
Alignment explanation
Indices: 1536700--1536969 Score: 214
Period size: 82 Copynumber: 3.3 Consensus size: 83
1536690 ATTGCGACGT
* * * ** * * * **
1536700 TTGTATAAAAATGCCACTAAAGTACTAATCTGTTGTGACATTTATTGACAAAATGCCACTATAG-
1 TTGTATAAAAAAGTCGCTAAAGTACTAATCTGTTGCAACTTTTATCGAAAAAATATCACTATAGA
* **
1536764 TAAACCCTAT-TTCAAT-A
66 TGAACCCTATATT-GGTGA
* * * * *
1536781 TTTGTATAAAAATGTCACTAAAGTATTAATCTGTTGCAGCTTTTATTGAAAAAATATCACTATAG
1 -TTGTATAAAAAAGTCGCTAAAGTACTAATCTGTTGCAACTTTTATCGAAAAAATATCACTATAG
* *
1536846 GTGAACCCTATATTGGTGT
65 ATGAACCCTATATTGGTGA
* * *
1536865 TTGTATAAAAAAGTCGCTAAAGTACTACTCTGTTGCAACTTTTGTCG-AACAAT-TCCACTATAG
1 TTGTATAAAAAAGTCGCTAAAGTACTAATCTGTTGCAACTTTTATCGAAAAAATAT-CACTATAG
*
1536928 ATGAA-CCT-TATTGTTGCA
65 ATGAACCCTATATTGGTG-A
1536946 TT-TATAAAGAAACGTCGCTAAAGT
1 TTGTATAAA-AAA-GTCGCTAAAGT
1536970 TACCATTTTG
Statistics
Matches: 157, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
80 13 0.08
81 9 0.06
82 83 0.53
83 50 0.32
84 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (83 bp):
TTGTATAAAAAAGTCGCTAAAGTACTAATCTGTTGCAACTTTTATCGAAAAAATATCACTATAGA
TGAACCCTATATTGGTGA
Found at i:1537452 original size:30 final size:30
Alignment explanation
Indices: 1537377--1537453 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
1537367 AAATAATAAT
1537377 AAAAAATAAATATTAAATAAATCAAAGGAAATA
1 AAAAAATAAA-A--AAATAAATCAAAGGAAATA
* *
1537410 AAAACATTAAAAAATAAATCAAAGGAAA-A
1 AAAAAATAAAAAAATAAATCAAAGGAAATA
1537439 AATAAAATAAAAAAA
1 AA-AAAATAAAAAAA
1537454 ATTAAAGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 3 0.08
30 27 0.69
32 1 0.03
33 8 0.21
ACGTcount: A:0.74, C:0.04, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAAAATAAAAAAATAAATCAAAGGAAATA
Done.