Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 56 of 66
Found at i:20587249 original size:22 final size:22
Alignment explanation
Indices: 20587209--20587263 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
20587199 TTTTTACATC
*
20587209 CTTTTTTCCTCCTTGTTCCTTTT
1 CTTTTTT-CTTCTTGTTCCTTTT
*
20587232 CTTTTTTCTTCTTTTTCCTTTT
1 CTTTTTTCTTCTTGTTCCTTTT
20587254 CTTTTTTCTT
1 CTTTTTTCTT
20587264 TTTCAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 23 0.77
23 7 0.23
ACGTcount: A:0.00, C:0.25, G:0.02, T:0.73
Consensus pattern (22 bp):
CTTTTTTCTTCTTGTTCCTTTT
Found at i:20587919 original size:21 final size:21
Alignment explanation
Indices: 20587894--20587956 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
20587884 TTCACTTGTC
20587894 TTCTTTTTTTCCTCTTTCCTT
1 TTCTTTTTTTCCTCTTTCCTT
*
20587915 TTCTTATTTT-CTCTTTCTCTCT
1 TTCTTTTTTTCCTCTTTC-CT-T
* *
20587937 TT-TTTTTTTCATTTTTCCTT
1 TTCTTTTTTTCCTCTTTCCTT
20587957 ATACTTACCA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
20 8 0.23
21 19 0.54
22 8 0.23
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (21 bp):
TTCTTTTTTTCCTCTTTCCTT
Found at i:20592302 original size:18 final size:18
Alignment explanation
Indices: 20592279--20592324 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
20592269 ACACGTTTAC
*
20592279 TTAATCGTGTTATCGTGT
1 TTAATCGTGTTATCGTAT
20592297 TTAATCGTGTTATCGTAT
1 TTAATCGTGTTATCGTAT
*
20592315 TTAAACGTGT
1 TTAATCGTGT
20592325 ATATGTGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.22, C:0.11, G:0.20, T:0.48
Consensus pattern (18 bp):
TTAATCGTGTTATCGTAT
Found at i:20593006 original size:15 final size:15
Alignment explanation
Indices: 20592972--20593006 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20592962 AATTATTATT
*
20592972 ATATATATACTTTTA
1 ATATATATACTTTAA
*
20592987 GTATATATACTTTAA
1 ATATATATACTTTAA
20593002 ATATA
1 ATATA
20593007 AACATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (15 bp):
ATATATATACTTTAA
Found at i:20593256 original size:34 final size:35
Alignment explanation
Indices: 20593206--20593279 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
20593196 ACTTGTAATG
* * *
20593206 TTTAAGTTGTTGTTTGA-ATATTTGTTTTTAATTA
1 TTTAAGTTGATATTTGATATATTTATTTTTAATTA
*
20593240 TTTAAGTTGATATTTGATATATTTATTTTTTATTA
1 TTTAAGTTGATATTTGATATATTTATTTTTAATTA
20593275 TTTAA
1 TTTAA
20593280 ATTTAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
34 15 0.43
35 20 0.57
ACGTcount: A:0.27, C:0.00, G:0.11, T:0.62
Consensus pattern (35 bp):
TTTAAGTTGATATTTGATATATTTATTTTTAATTA
Found at i:20594864 original size:18 final size:18
Alignment explanation
Indices: 20594830--20594864 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20594820 TATAAAATAA
**
20594830 AAATATAAAAATTTAATC
1 AAATATAAAAAAATAATC
20594848 AAATATAAAAAAATAAT
1 AAATATAAAAAAATAAT
20594865 AATTTATTTT
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:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATATAAAAAAATAATC
Found at i:20595740 original size:21 final size:22
Alignment explanation
Indices: 20595697--20595745 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
20595687 AAAAAATTAG
*
20595697 TATTCTTAAAAATAAATATTA-T
1 TATT-TTAAAAATAAATAATATT
* *
20595719 TATTTTAAAAATTAGTAATATT
1 TATTTTAAAAATAAATAATATT
20595741 TATTT
1 TATTT
20595746 GTGAGGTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
TATTTTAAAAATAAATAATATT
Found at i:20596137 original size:16 final size:16
Alignment explanation
Indices: 20596113--20596146 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20596103 TATTAATAAG
*
20596113 AATTGATAATAAACTT
1 AATTAATAATAAACTT
*
20596129 AATTAATAATATACTT
1 AATTAATAATAAACTT
20596145 AA
1 AA
20596147 AATATATTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (16 bp):
AATTAATAATAAACTT
Found at i:20596623 original size:17 final size:17
Alignment explanation
Indices: 20596587--20596626 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
20596577 TCATTAATTT
20596587 CATAT-TTACATAAGTA
1 CATATATTACATAAGTA
*
20596603 -ATATATTACATATGTA
1 CATATATTACATAAGTA
20596619 CATATATT
1 CATATATT
20596627 TATACATAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 10 0.48
17 7 0.33
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (17 bp):
CATATATTACATAAGTA
Found at i:20596839 original size:17 final size:17
Alignment explanation
Indices: 20596801--20596857 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
20596791 TCATTAATTT
* *
20596801 CATATATATAATAAAGTA
1 CATATATTTAATATA-TA
20596819 -ATATA-TT-ATATATA
1 CATATATTTAATATATA
*
20596833 CATATATTTAATTTATA
1 CATATATTTAATATATA
20596850 CATA-ATTT
1 CATATATTT
20596858 GTATATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
14 2 0.06
15 9 0.27
16 7 0.21
17 15 0.45
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (17 bp):
CATATATTTAATATATA
Found at i:20609709 original size:2 final size:2
Alignment explanation
Indices: 20609702--20609737 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20609692 TAACTACTAC
20609702 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
20609738 GTGTGTGTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20613833 original size:20 final size:20
Alignment explanation
Indices: 20613785--20613833 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
20613775 TTAGCATAAA
*
20613785 GACCCAAATGGGTCAAATTT
1 GACCCAATTGGGTCAAATTT
* * * *
20613805 GATCTAATTGGGTTAGATTT
1 GACCCAATTGGGTCAAATTT
20613825 GACCCAATT
1 GACCCAATT
20613834 CGAAGTTGAA
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
GACCCAATTGGGTCAAATTT
Found at i:20617361 original size:18 final size:19
Alignment explanation
Indices: 20617333--20617380 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
20617323 GTTACGGACG
*
20617333 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
20617351 AAAATATTATTTTATAAAT
1 AAAATAATATTTTATAAAT
20617370 AAAATAATATT
1 AAAATAATATT
20617381 AAATATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:20618374 original size:34 final size:33
Alignment explanation
Indices: 20618313--20618503 Score: 211
Period size: 34 Copynumber: 5.6 Consensus size: 33
20618303 GAGAAAGAGC
* *
20618313 CGATTTTGAGGAGAAAGGAGCAACTTTGGTTGT
1 CGATTTTGAGGAGAAAAGAGCAGCTTTGGTTGT
*
20618346 CGATTTTGAGGAAAAAATGAGCAGCTTTGGTTGT
1 CGATTTTGAGGAGAAAA-GAGCAGCTTTGGTTGT
* **
20618380 CGATTTTGAGGGAGAAAAGAGGAGCTTTGTGTTAC
1 CGATTTTGA-GGAGAAAAGAGCAGCTTTG-GTTGT
* * *
20618415 CGATTTTGAGGGAGAAAAGAGCAGCTTTCGCTAT
1 CGATTTTGA-GGAGAAAAGAGCAGCTTTGGTTGT
* *
20618449 CAATTTTGAAGGAGAAAAGAGCAGCTTTGTGTTGC
1 CGATTTTG-AGGAGAAAAGAGCAGCTTTG-GTTGT
*
20618484 CAATTTTGAGAGAGAAAAGA
1 CGATTTTGAG-GAGAAAAGA
20618504 AAGAAACTTG
Statistics
Matches: 136, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
33 15 0.11
34 64 0.47
35 57 0.42
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.28
Consensus pattern (33 bp):
CGATTTTGAGGAGAAAAGAGCAGCTTTGGTTGT
Found at i:20618437 original size:69 final size:68
Alignment explanation
Indices: 20618313--20618503 Score: 233
Period size: 69 Copynumber: 2.8 Consensus size: 68
20618303 GAGAAAGAGC
* * * * *
20618313 CGATTTTGAGGAGAAAGGAGCAACTTTG-GTTGTCGATTTTGA-GGAAAAAATGAGCAGCTTTGG
1 CGATTTTGAGGAGAAAAGAGCAGCTTTGTGTTGCCGATTTTGAGGGAGAAAA-GAGCAGCTTTCG
* *
20618376 TTGT
65 CTAT
* *
20618380 CGATTTTGAGGGAGAAAAGAGGAGCTTTGTGTTACCGATTTTGAGGGAGAAAAGAGCAGCTTTCG
1 CGATTTTGA-GGAGAAAAGAGCAGCTTTGTGTTGCCGATTTTGAGGGAGAAAAGAGCAGCTTTCG
20618445 CTAT
65 CTAT
* * *
20618449 CAATTTTGAAGGAGAAAAGAGCAGCTTTGTGTTGCCAATTTTGAGAGAGAAAAGA
1 CGATTTTG-AGGAGAAAAGAGCAGCTTTGTGTTGCCGATTTTGAGGGAGAAAAGA
20618504 AAGAAACTTG
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
67 9 0.08
68 16 0.15
69 73 0.69
70 8 0.08
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.28
Consensus pattern (68 bp):
CGATTTTGAGGAGAAAAGAGCAGCTTTGTGTTGCCGATTTTGAGGGAGAAAAGAGCAGCTTTCGC
TAT
Found at i:20619347 original size:60 final size:59
Alignment explanation
Indices: 20619248--20619430 Score: 251
Period size: 60 Copynumber: 3.0 Consensus size: 59
20619238 ATATTTGATT
* *
20619248 GTAAAAGGGGAACCTAAAGCCTCGATTCATATTAGGTGGCGTGGGCAGTTCCCACGAGTAG
1 GTAAAAGGGG-ACCTGAAGCCCCGATTCATATT-GGTGGCGTGGGCAGTTCCCACGAGTAG
* **
20619309 GTAAAAGGGGACCGGAAGCCCCGATTCATATTGTGTGGCGTGAACAGTTCCCACGAGTAG
1 GTAAAAGGGGACCTGAAGCCCCGATTCATATTG-GTGGCGTGGGCAGTTCCCACGAGTAG
* *
20619369 GT-AAAGGGAGACCTGAAGCCCCGATTTATATATGGTGGTGTGGGCAGTTCCCACGAGTAG
1 GTAAAAGGG-GACCTGAAGCCCCGATTCATAT-TGGTGGCGTGGGCAGTTCCCACGAGTAG
20619429 GT
1 GT
20619431 GATGATGTCT
Statistics
Matches: 109, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
59 7 0.06
60 90 0.83
61 12 0.11
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (59 bp):
GTAAAAGGGGACCTGAAGCCCCGATTCATATTGGTGGCGTGGGCAGTTCCCACGAGTAG
Found at i:20626986 original size:2 final size:2
Alignment explanation
Indices: 20626946--20626978 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20626936 TGAAGCATAA
20626946 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20626979 TGCACACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:20637055 original size:19 final size:19
Alignment explanation
Indices: 20637014--20637056 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
20637004 TATTCAACAC
* * * *
20637014 ATTTAATATATTTAAACTC
1 ATTTAAAATATATAAAATA
20637033 ATTTAAAATATATAAAATA
1 ATTTAAAATATATAAAATA
20637052 ATTTA
1 ATTTA
20637057 TTATTTGTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAAATATATAAAATA
Found at i:20653644 original size:18 final size:18
Alignment explanation
Indices: 20653606--20653682 Score: 56
Period size: 18 Copynumber: 4.4 Consensus size: 18
20653596 ATTTAAAAAT
*
20653606 ATTAAATAATTTTTATTATA
1 ATTAATTAA-TTTT-TTATA
*
20653626 TTTAATTAATTTTTTAT-
1 ATTAATTAATTTTTTATA
*
20653643 ATT--TTTA-TTTTTA-A
1 ATTAATTAATTTTTTATA
* *
20653657 ATTAAATATTTTTTTATA
1 ATTAATTAATTTTTTATA
20653675 ATTAATTA
1 ATTAATTA
20653683 TTAATTATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
14 9 0.20
15 3 0.07
16 1 0.02
17 8 0.18
18 12 0.27
19 4 0.09
20 7 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
ATTAATTAATTTTTTATA
Found at i:20653684 original size:18 final size:18
Alignment explanation
Indices: 20653614--20653684 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 18
20653604 ATATTAAATA
*
20653614 ATTTTTATTATATTTAATT
1 ATTTTT-TTATAATTAATT
*
20653633 AATTTTTTAT-ATT--TT
1 ATTTTTTTATAATTAATT
* *
20653648 -TATTTTTA-AATTAAAT
1 ATTTTTTTATAATTAATT
20653664 ATTTTTTTATAATTAATT
1 ATTTTTTTATAATTAATT
20653682 ATT
1 ATT
20653685 AATTATTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
16 1 0.03
17 9 0.22
18 14 0.35
19 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTTATAATTAATT
Found at i:20653735 original size:11 final size:11
Alignment explanation
Indices: 20653719--20653752 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
20653709 ATATTATTTT
20653719 ATATTAATATA
1 ATATTAATATA
*
20653730 ATATTAATATT
1 ATATTAATATA
20653741 ATATTAATATA
1 ATATTAATATA
20653752 A
1 A
20653753 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAATATA
Found at i:20653737 original size:6 final size:6
Alignment explanation
Indices: 20653719--20653750 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20653709 ATATTATTTT
20653719 ATATTA ATA-TA ATATTA ATATT- ATATTA ATAT
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATAT
20653751 AAAAAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:20653744 original size:22 final size:21
Alignment explanation
Indices: 20653709--20653752 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
20653699 AAAATATCAC
*
20653709 ATATTATTTTATATTAATATA
1 ATATTATATTATATTAATATA
20653730 ATATTAATATTATATTAATATA
1 ATATT-ATATTATATTAATATA
20653752 A
1 A
20653753 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTATATTATATTAATATA
Found at i:20653914 original size:30 final size:30
Alignment explanation
Indices: 20653880--20653949 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
20653870 TCTAATTATT
*
20653880 AATTATAAAAATTTATTTAATTTAAAATAA
1 AATTATAAAAATTAATTTAATTTAAAATAA
* *
20653910 AATTATAAGAATTAATTTAGTTTAAAATAA
1 AATTATAAAAATTAATTTAATTTAAAATAA
*
20653940 AAATATAAAA
1 AATTATAAAA
20653950 TGTTGATTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
AATTATAAAAATTAATTTAATTTAAAATAA
Found at i:20673739 original size:32 final size:32
Alignment explanation
Indices: 20673698--20673759 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
20673688 CCCATTTGAA
*
20673698 ATGAGGCATTAAAGTAATGAATCAATTTAAAT
1 ATGAGGCATTAAAGTAATGAATCAACTTAAAT
*
20673730 ATGAGGCATTAAAGTAATGAGTCAACTTAA
1 ATGAGGCATTAAAGTAATGAATCAACTTAA
20673760 CACTGAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (32 bp):
ATGAGGCATTAAAGTAATGAATCAACTTAAAT
Found at i:20673749 original size:16 final size:16
Alignment explanation
Indices: 20673697--20673750 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
20673687 CCCCATTTGA
20673697 AATGAGGCATTAAAGT
1 AATGAGGCATTAAAGT
**
20673713 AATGAATCAATTTAAA-T
1 AATGAGGC-A-TTAAAGT
20673730 -ATGAGGCATTAAAGT
1 AATGAGGCATTAAAGT
20673745 AATGAG
1 AATGAG
20673751 TCAACTTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 5 0.17
15 2 0.07
16 16 0.53
17 2 0.07
18 5 0.17
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (16 bp):
AATGAGGCATTAAAGT
Found at i:20691084 original size:7 final size:7
Alignment explanation
Indices: 20691069--20691101 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
20691059 GTTCAAGTCT
*
20691069 TGACTCA
1 TGACCCA
20691076 TGACCCA
1 TGACCCA
20691083 TGACCCA
1 TGACCCA
20691090 TGA-CCA
1 TGACCCA
20691096 TGACCC
1 TGACCC
20691102 CCTCGCCCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.18
Consensus pattern (7 bp):
TGACCCA
Found at i:20691098 original size:13 final size:14
Alignment explanation
Indices: 20691069--20691101 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
20691059 GTTCAAGTCT
*
20691069 TGACTCATGACCCA
1 TGACCCATGACCCA
20691083 TGACCCATGA-CCA
1 TGACCCATGACCCA
20691096 TGACCC
1 TGACCC
20691102 CCTCGCCCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.27, C:0.39, G:0.15, T:0.18
Consensus pattern (14 bp):
TGACCCATGACCCA
Found at i:20706173 original size:23 final size:23
Alignment explanation
Indices: 20706128--20706174 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
20706118 TTATAGAACG
* *
20706128 TGATTCATATTTTCAATGCCAAT
1 TGATTCATACTTTCAATACCAAT
*
20706151 TGATTCATACTTTCAATATCAAT
1 TGATTCATACTTTCAATACCAAT
20706174 T
1 T
20706175 TTACCTTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (23 bp):
TGATTCATACTTTCAATACCAAT
Found at i:20730847 original size:1 final size:1
Alignment explanation
Indices: 20730837--20730890 Score: 54
Period size: 1 Copynumber: 54.0 Consensus size: 1
20730827 ACCACCCCAA
* * * * * *
20730837 CCCCCTCCCCCTCGCCCCCCCCCCCCCCCCCCCCCCCCCCTCCGCCCCCACCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
20730891 TCTCCCCGCG
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.89, G:0.04, T:0.06
Consensus pattern (1 bp):
C
Found at i:20730863 original size:29 final size:30
Alignment explanation
Indices: 20730826--20730890 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
20730816 CCTTACCCTA
* *
20730826 CACCACCCCAACCCCCTCCCCCT-CGCCCC
1 CACCCCCCCAACCCCCCCCCCCTCCGCCCC
* **
20730855 CCCCCCCCCCCCCCCCCCCCCCTCCGCCCC
1 CACCCCCCCAACCCCCCCCCCCTCCGCCCC
20730885 CACCCC
1 CACCCC
20730891 TCTCCCCGCG
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.08, C:0.85, G:0.03, T:0.05
Consensus pattern (30 bp):
CACCCCCCCAACCCCCCCCCCCTCCGCCCC
Found at i:20730891 original size:14 final size:14
Alignment explanation
Indices: 20730837--20730897 Score: 68
Period size: 15 Copynumber: 4.1 Consensus size: 14
20730827 ACCACCCCAA
*
20730837 CCCCCTCCCCCTCGC
1 CCCCCCCCCCCTC-C
*
20730852 CCCCCCCCCCCCCC
1 CCCCCCCCCCCTCC
20730866 CCCCCCCCCCCTCC
1 CCCCCCCCCCCTCC
*
20730880 GCCCCCACCCCTCTCC
1 -CCCCC-CCCCCCTCC
20730896 CC
1 CC
20730898 GCGAAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
14 14 0.35
15 18 0.45
16 8 0.20
ACGTcount: A:0.02, C:0.87, G:0.03, T:0.08
Consensus pattern (14 bp):
CCCCCCCCCCCTCC
Found at i:20736517 original size:3 final size:3
Alignment explanation
Indices: 20736509--20736538 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
20736499 TATTTTCAAT
20736509 ATA ATA ATA ATA ATA ATA ATA ATA AGTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA AT
20736539 TAATGAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:20739875 original size:27 final size:27
Alignment explanation
Indices: 20739835--20739891 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
20739825 ACATACGGCA
20739835 TGGCATTGTCGAGTCGAGCCATGCTGG
1 TGGCATTGTCGAGTCGAGCCATGCTGG
*
20739862 TGGCATTGTGGAGTCGAGCCATGCTGG
1 TGGCATTGTCGAGTCGAGCCATGCTGG
20739889 TGG
1 TGG
20739892 TGATGACGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.19, G:0.40, T:0.26
Consensus pattern (27 bp):
TGGCATTGTCGAGTCGAGCCATGCTGG
Found at i:20759261 original size:29 final size:28
Alignment explanation
Indices: 20759219--20759276 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
20759209 ATAAGAAATA
* *
20759219 ATGAGAAATGAACTGGAAGTTCTTCTCTC
1 ATGAGAAATAAACTAGAAGTT-TTCTCTC
*
20759248 ATGAGAAATAAACTAGAAGTTTTTTCTC
1 ATGAGAAATAAACTAGAAGTTTTCTCTC
20759276 A
1 A
20759277 ATTCTTCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (28 bp):
ATGAGAAATAAACTAGAAGTTTTCTCTC
Found at i:20773693 original size:15 final size:15
Alignment explanation
Indices: 20773673--20773702 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20773663 GAGCAATCTC
20773673 TGGAAGAGTTAGAGA
1 TGGAAGAGTTAGAGA
20773688 TGGAAGAGTTAGAGA
1 TGGAAGAGTTAGAGA
20773703 GAGGTTAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (15 bp):
TGGAAGAGTTAGAGA
Found at i:20791037 original size:14 final size:15
Alignment explanation
Indices: 20791017--20791076 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 15
20791007 TTGTAAAATT
20791017 TTAATTTTTATTATA
1 TTAATTTTTATTATA
*
20791032 TT-ATTTATT-TTTTA
1 TTAATTT-TTATTATA
20791046 TTAATTTTTATTTTATA
1 TTAATTTTTA--TTATA
20791063 TATATATTTTTATT
1 T-TA-ATTTTTATT
20791077 TGTGAATAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
14 12 0.33
15 8 0.22
17 7 0.19
18 2 0.06
19 7 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTAATTTTTATTATA
Found at i:20791042 original size:17 final size:16
Alignment explanation
Indices: 20791022--20791077 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
20791012 AAATTTTAAT
20791022 TTTTATTATATTATTTA
1 TTTTATTATATT-TTTA
20791039 TTTT-TTATTAATTTTTA
1 TTTTATTA-T-ATTTTTA
20791056 TTTTATATATATATTTTTA
1 -TTT-TAT-TATATTTTTA
20791075 TTT
1 TTT
20791078 GTGAATAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.09
17 9 0.27
18 9 0.27
19 8 0.24
20 2 0.06
21 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTATATTTTTA
Found at i:20791043 original size:35 final size:36
Alignment explanation
Indices: 20791000--20791077 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
20790990 TTTTTTGTTC
*
20791000 TTTTT-TTTTGTA-AAATTTTAATTTT-TAT-TATA
1 TTTTTATTTTTTATAAATTTTAATTTTATATATATA
* *
20791032 TTATTTATTTTTTATTAATTTTTATTTTATATATATA
1 TT-TTTATTTTTTATAAATTTTAATTTTATATATATA
20791069 TTTTTATTT
1 TTTTTATTT
20791078 GTGAATAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
32 2 0.05
33 3 0.08
34 6 0.16
35 11 0.29
36 10 0.26
37 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTTTATTTTTTATAAATTTTAATTTTATATATATA
Found at i:20791049 original size:29 final size:30
Alignment explanation
Indices: 20791017--20791073 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
20791007 TTGTAAAATT
*
20791017 TTAATTTTTATTATAT-TATTTATTTTTTA
1 TTAATTTTTATTATATATATATATTTTTTA
*
20791046 TTAATTTTTATTTTATATATATATTTTT
1 TTAATTTTTATTATATATATATATTTTT
20791074 ATTTGTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (30 bp):
TTAATTTTTATTATATATATATATTTTTTA
Found at i:20791059 original size:15 final size:15
Alignment explanation
Indices: 20791017--20791061 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
20791007 TTGTAAAATT
*
20791017 TTAATTTTTATTATA
1 TTAATTTTTATTTTA
20791032 TT-ATTTATT-TTTTA
1 TTAATTT-TTATTTTA
20791046 TTAATTTTTATTTTA
1 TTAATTTTTATTTTA
20791061 T
1 T
20791062 ATATATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTAATTTTTATTTTA
Found at i:20791075 original size:19 final size:17
Alignment explanation
Indices: 20791014--20791077 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 17
20791004 TTTTTGTAAA
*
20791014 ATTTTAATTTTTATTAT
1 ATTTTTATTTTTATTAT
20791031 ATTATTTATTTTTTATTA-
1 ATT-TTTA-TTTTTATTAT
20791049 ATTTTTATTTTATATATAT
1 ATTTTTATTTT-TAT-TAT
20791068 ATTTTTATTT
1 ATTTTTATTT
20791078 GTGAATAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 8 0.20
19 19 0.46
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTATTTTTATTAT
Found at i:20806395 original size:18 final size:18
Alignment explanation
Indices: 20806364--20806407 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
20806354 ATGAAAAAAT
*
20806364 AATATTTTAAAAAA-TTA
1 AATAATTTAAAAAATTTA
*
20806381 AATTATTTAATAAAATTTA
1 AATAATTTAA-AAAATTTA
20806400 AATAATTT
1 AATAATTT
20806408 TTTATTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAATTTAAAAAATTTA
Found at i:20824730 original size:3 final size:3
Alignment explanation
Indices: 20824722--20824746 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20824712 AGGTTTAAAA
20824722 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
20824747 GGGAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:20827168 original size:18 final size:18
Alignment explanation
Indices: 20827145--20827182 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
20827135 CATATTTCTA
*
20827145 TAATT-ATTATATTATAAT
1 TAATTAATTA-ATCATAAT
20827163 TAATTAATTAATCATAAT
1 TAATTAATTAATCATAAT
20827181 TA
1 TA
20827183 TAGTTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAATTAATCATAAT
Found at i:20827639 original size:21 final size:20
Alignment explanation
Indices: 20827610--20827649 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20827600 ATTTTCAATT
*
20827610 TGAATCTTAAAATAAATGAAG
1 TGAAACTTAAAA-AAATGAAG
*
20827631 TGAAACTTAATAAAATGAA
1 TGAAACTTAAAAAAATGAA
20827650 AAAGAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
TGAAACTTAAAAAAATGAAG
Found at i:20831359 original size:38 final size:39
Alignment explanation
Indices: 20831290--20831365 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 39
20831280 AATTGAATTT
20831290 TTGTACCTTAACTTTAATTTTTTAACCTTTTTCAGCTTG
1 TTGTACCTTAACTTTAATTTTTTAACCTTTTTCAGCTTG
**
20831329 TTGTACCTTGGCTTTAA-TTTTTAACCTTTTTCAGCTT
1 TTGTACCTTAACTTTAATTTTTTAACCTTTTTCAGCTT
20831366 TTCATTGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 20 0.57
39 15 0.43
ACGTcount: A:0.18, C:0.18, G:0.09, T:0.54
Consensus pattern (39 bp):
TTGTACCTTAACTTTAATTTTTTAACCTTTTTCAGCTTG
Found at i:20832200 original size:16 final size:17
Alignment explanation
Indices: 20832179--20832222 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
20832169 ATGTAGACAC
20832179 ATAAAT-TAAAAAAAAT
1 ATAAATATAAAAAAAAT
20832195 ATAAATAATAAAAAAAAT
1 ATAAAT-ATAAAAAAAAT
20832213 AT-AATATAAA
1 ATAAATATAAA
20832223 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.42
17 3 0.12
18 12 0.46
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (17 bp):
ATAAATATAAAAAAAAT
Found at i:20832208 original size:18 final size:18
Alignment explanation
Indices: 20832185--20832246 Score: 67
Period size: 18 Copynumber: 3.5 Consensus size: 18
20832175 ACACATAAAT
20832185 TAAAAAAAATATAAATAA
1 TAAAAAAAATATAAATAA
20832203 TAAAAAAAATAT-AAT-A
1 TAAAAAAAATATAAATAA
**
20832219 TAAATTAAAT-TAAATAA
1 TAAAAAAAATATAAATAA
20832236 GTAAATAAAAA
1 -TAAA-AAAAA
20832247 AAAATCGGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 12 0.33
17 4 0.11
18 16 0.44
19 3 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAAAAATATAAATAA
Found at i:20845763 original size:21 final size:21
Alignment explanation
Indices: 20845739--20845778 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20845729 TACAAAATAA
*
20845739 AAAGTAAATATATTTATATTT
1 AAAGTAAATATATATATATTT
*
20845760 AAAGTACATATATATATAT
1 AAAGTAAATATATATATAT
20845779 ACACACACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAGTAAATATATATATATTT
Found at i:20858664 original size:29 final size:29
Alignment explanation
Indices: 20858587--20859049 Score: 295
Period size: 29 Copynumber: 16.2 Consensus size: 29
20858577 GGCATATTCC
** * *
20858587 TTAATTTCCTCACATACACAGATTTGATA
1 TTAATTTCCAAACATACACAGGTATGATA
20858616 TTAATTT-CAAACATACACAGGTATGATA
1 TTAATTTCCAAACATACACAGGTATGATA
** *
20858644 TTAATTTATAAACATACACAGGTTTGATA
1 TTAATTTCCAAACATACACAGGTATGATA
* * * *
20858673 TTACTTTCCAGATATACACAGGT-T-ATG
1 TTAATTTCCAAACATACACAGGTATGATA
* * *
20858700 TTCATGTCCAAACGTACACAGGTATGATA
1 TTAATTTCCAAACATACACAGGTATGATA
* * *
20858729 TTAATTTCCAGACATGCACAGGTATAATA
1 TTAATTTCCAAACATACACAGGTATGATA
* * * * * * * *
20858758 TTGATTTACACATATACACAGATTTGGTT
1 TTAATTTCCAAACATACACAGGTATGATA
* * *
20858787 TTAATTT--ACACATACACAGATTTGATA
1 TTAATTTCCAAACATACACAGGTATGATA
** * *
20858814 TTAATTTCTC-AACATACACAAATTTGGTA
1 TTAATTTC-CAAACATACACAGGTATGATA
* *
20858843 TTAACTTT-TAAACGTACACAGGTATGATA
1 TTAA-TTTCCAAACATACACAGGTATGATA
* * * *
20858872 TTAATTTCCACATATACAAAGATATGATA
1 TTAATTTCCAAACATACACAGGTATGATA
* * *
20858901 TTAATTTAC-ACCCTACACAGGTATGATA
1 TTAATTTCCAAACATACACAGGTATGATA
* * * * *
20858929 TTAATTTCCAAACATGCTCAGATGTGGTA
1 TTAATTTCCAAACATACACAGGTATGATA
* * * *
20858958 TTAATTTCCAAA-AGTACACCGATTTGGTA
1 TTAATTTCCAAACA-TACACAGGTATGATA
* *
20858987 TTAA-TTCTCAGACATACACA-GAATTGATA
1 TTAATTTC-CAAACATACACAGGTA-TGATA
* **
20859016 TTAATTT--ACACATACACATATATGATA
1 TTAATTTCCAAACATACACAGGTATGATA
20859043 TTAATTT
1 TTAATTT
20859050 TTATACATAC
Statistics
Matches: 336, Mismatches: 82, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
27 65 0.19
28 55 0.16
29 210 0.62
30 6 0.02
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (29 bp):
TTAATTTCCAAACATACACAGGTATGATA
Found at i:20858803 original size:85 final size:84
Alignment explanation
Indices: 20858600--20858833 Score: 224
Period size: 85 Copynumber: 2.7 Consensus size: 84
20858590 ATTTCCTCAC
* **
20858600 ATACACAGATTTGATATTAATTTCAAACATACACAGGTATGATATTAATTTATAAACATACACAG
1 ATACACAGATTTGGT-TTAATTT-AAACATACACAGGTATGATATTAATTTCCAAACATACACAG
* * * *
20858665 GTTTGATATTACTTTCCAGAT
64 GTATAATATTACTTTACACAT
* * * * * *
20858686 ATACACAGGTTAT-G-TTCATGTCCAAACGTACACAGGTATGATATTAATTTCCAGACATGCACA
1 ATACACAGATT-TGGTTTAAT-T-TAAACATACACAGGTATGATATTAATTTCCAAACATACACA
20858749 GGTATAATATTGA-TTTACACAT
63 GGTATAATATT-ACTTTACACAT
* * *
20858771 ATACACAGATTTGGTTTTAATTTACACATACACAGATTTGATATTAATTTCTC-AACATACACA
1 ATACACAGATTTGG-TTTAATTTAAACATACACAGGTATGATATTAATTTC-CAAACATACACA
20858834 AATTTGGTAT
Statistics
Matches: 118, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
84 5 0.04
85 95 0.81
86 13 0.11
87 5 0.04
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (84 bp):
ATACACAGATTTGGTTTAATTTAAACATACACAGGTATGATATTAATTTCCAAACATACACAGGT
ATAATATTACTTTACACAT
Found at i:20858832 original size:114 final size:112
Alignment explanation
Indices: 20858587--20859049 Score: 396
Period size: 114 Copynumber: 4.1 Consensus size: 112
20858577 GGCATATTCC
**
20858587 TTAATTTCCTCACATACACAGATTTGATATTAATTTCAAACATACACAGGTATGATATTAATTTA
1 TTAATTTCCAAACATACACAGATTTGATATTAATTTCAAACATACACAGGTATGATATTAATTTA
* * * * * * * * *
20858652 TAAACATACACAGGTTTGATATTACTTTCCAGATATACACAGGTT-ATG
66 CACATATACACAGATTTGATATTAATTT--ACACATACACAGTTTGATA
* * * * * * * * *
20858700 TTCATGTCCAAACGTACACAGGTATGATATTAATTTCCAGACATGCACAGGTATAATATTGATTT
1 TTAATTTCCAAACATACACAGATTTGATATTAATTT-CAAACATACACAGGTATGATATTAATTT
* *
20858765 ACACATATACACAGATTTGGTTTTAATTTACACATACACAGATTTGATA
65 ACACATATACACAGATTTGATATTAATTTACACATACACAG-TTTGATA
* * * *
20858814 TTAATTTCTC-AACATACACAAATTTGGTATTAACTTTTAAACGTACACAGGTATGATATTAATT
1 TTAATTTC-CAAACATACACAGATTTGATATTAA-TTTCAAACATACACAGGTATGATATTAATT
* * * * *
20858878 TCCACATATACAAAGATATGATATTAATTTACACCCTACACAGGTATGATA
64 TACACATATACACAGATTTGATATTAATTTACA-CATACACA-GTTTGATA
* * * * * * * *
20858929 TTAATTTCCAAACATGCTCAGATGTGGTATTAATTTCCAAA-AGTACACCGATTTGGTATTAATT
1 TTAATTTCCAAACATACACAGATTTGATATTAATTT-CAAACA-TACACAGGTATGATATTAATT
* * *
20858993 CT-CAGACATACACAGAATTGATATTAATTTACACATACACA-TATATGATA
64 -TACACATATACACAGATTTGATATTAATTTACACATACACAGT-T-TGATA
20859043 TTAATTT
1 TTAATTT
20859050 TTATACATAC
Statistics
Matches: 278, Mismatches: 59, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
112 11 0.04
113 31 0.11
114 144 0.52
115 90 0.32
116 2 0.01
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (112 bp):
TTAATTTCCAAACATACACAGATTTGATATTAATTTCAAACATACACAGGTATGATATTAATTTA
CACATATACACAGATTTGATATTAATTTACACATACACAGTTTGATA
Found at i:20859173 original size:29 final size:29
Alignment explanation
Indices: 20859071--20859176 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 29
20859061 TACATACATA
* * *
20859071 CATAGGTATGATATTAATTTCTATATATG
1 CATAAGTATAATATTAATTTCTACATATG
* ** * * * * *
20859100 CACAAAAATAATATCACTTTCCACATTTT
1 CATAAGTATAATATTAATTTCTACATATG
* *
20859129 CAT-AGTATGATATTAATTTCTACATCTG
1 CATAAGTATAATATTAATTTCTACATATG
20859157 CATAAGTATAATATTAATTT
1 CATAAGTATAATATTAATTT
20859177 GGGAATACGT
Statistics
Matches: 55, Mismatches: 21, Indels: 2
0.71 0.27 0.03
Matches are distributed among these distances:
28 20 0.36
29 35 0.64
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (29 bp):
CATAAGTATAATATTAATTTCTACATATG
Found at i:20870763 original size:17 final size:17
Alignment explanation
Indices: 20870741--20870774 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20870731 GTGTGATGTA
20870741 TGTT-AAGCAATGCGATT
1 TGTTAAAGCAATG-GATT
20870758 TGTTAAAGCAATGGATT
1 TGTTAAAGCAATGGATT
20870775 CTCGAAGGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (17 bp):
TGTTAAAGCAATGGATT
Found at i:20875857 original size:337 final size:344
Alignment explanation
Indices: 20875477--20876194 Score: 906
Period size: 345 Copynumber: 2.1 Consensus size: 344
20875467 TAGTTTTGAG
* *
20875477 ATTA-AAAAATTATAACTTATAAAATTATTAATTATAATATATATATAATTGTTTATATAAACTT
1 ATTATAAAAATTATAACTTATAAAATTATTAATTATAATATATATACAATTATTTATATAAACTT
* * * * *
20875541 ATAATATATATACTTAAAAAG-TATT-TGAGATTAGAATAGTTTCGGAACCAAACTATTTTTT-T
66 ATAATATATAAACCTAAAAAGAAATTGTGAGATTAGAATAGTTTCGAAACCAAACTATTTTTTAA
* *
20875603 TAATTTCATGAAATTAAAGGTAA-AT-C-CATATAGTTAATTAAATTAATTCATGAAACTAT-GA
131 AAATTTCATGAAACT-AA-G-AATATACTCATATAGTTAATTAAATTAATTCATGAAACTATAG-
* * * *
20875664 TTATTAATTAACTTGCAATGTTTTTTAATATATATAGTTTATAAAT-TGT-GTTAATTTGT-AAG
192 TTATTAATTAACTTACAATGTTTTTTAATATATAAACTTTATAAATGT-TAGTTAATTTATAAAG
* *
20875726 AAATATAATT--ACTATTATATATATACTAAAATA-TTTTAATATATATATTTTAAATATAAACA
256 AAATATAATTAGATTA-TATATATATACTAAAATACTTTTAATATATATACTTTAAATATAAACA
* *
20875788 TATTTACTTTCTATTTTATGTTAAT
320 TATTTACTTTCTACTTTATGTTAAC
* * ** * * *
20875813 ATTATAAAAATCATAACGTATAAAATTATTAATTATAATATATATACCTTTATTTGTATTAGCTT
1 ATTATAAAAATTATAACTTATAAAATTATTAATTATAATATATATACAATTATTTATATAAACTT
* * * * * * **
20875878 ATAATGTATAAACCTAAAACGAAATTGTGATATTAGAATAGTTTTGAAATCTAGTTATTTTTTAA
66 ATAATATATAAACCTAAAAAGAAATTGTGAGATTAGAATAGTTTCGAAACCAAACTATTTTTTAA
* *
20875943 AAATTTCATGTAACTAAGAATATACTCATATAGTTAATTAAATTAATTCATGAAAGTATAGTTAT
131 AAATTTCATGAAACTAAGAATATACTCATATAGTTAATTAAATTAATTCATGAAACTATAGTTAT
* * * *
20876008 TAATTAACTTATAATGTTTTTTAATATATAAACTTTATATATGTTAAGTTCATTTATAAAGGAAT
196 TAATTAACTTACAATGTTTTTTAATATATAAACTTTATAAATGTT-AGTTAATTTATAAAGAAAT
* * *
20876073 ATAATTAGATTATATATATATATTAAAATACTTTTAGTGTATATACTTTAAATATAAACATATTT
260 ATAATTAGATTATATATATATACTAAAATACTTTTAATATATATACTTTAAATATAAACATATTT
20876138 ACTTTCTACTTTATGTTAAC
325 ACTTTCTACTTTATGTTAAC
20876158 ATTATAAAAATTATAACTTATAAAATTATTAATTATA
1 ATTATAAAAATTATAACTTATAAAATTATTAATTATA
20876195 CTTGAAATAT
Statistics
Matches: 324, Mismatches: 43, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
336 4 0.01
337 70 0.22
338 6 0.02
339 32 0.10
340 86 0.27
341 2 0.01
342 8 0.02
343 12 0.04
344 17 0.05
345 87 0.27
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (344 bp):
ATTATAAAAATTATAACTTATAAAATTATTAATTATAATATATATACAATTATTTATATAAACTT
ATAATATATAAACCTAAAAAGAAATTGTGAGATTAGAATAGTTTCGAAACCAAACTATTTTTTAA
AAATTTCATGAAACTAAGAATATACTCATATAGTTAATTAAATTAATTCATGAAACTATAGTTAT
TAATTAACTTACAATGTTTTTTAATATATAAACTTTATAAATGTTAGTTAATTTATAAAGAAATA
TAATTAGATTATATATATATACTAAAATACTTTTAATATATATACTTTAAATATAAACATATTTA
CTTTCTACTTTATGTTAAC
Found at i:20876184 original size:15 final size:17
Alignment explanation
Indices: 20876154--20876186 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
20876144 TACTTTATGT
20876154 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
20876171 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
20876186 T
1 T
20876187 TAATTATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:20879796 original size:6 final size:6
Alignment explanation
Indices: 20879785--20879815 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
20879775 TTACTCCATT
*
20879785 CTTTTA CTTTTA CTTTTA CTTTTA CCTTTA C
1 CTTTTA CTTTTA CTTTTA CTTTTA CTTTTA C
20879816 GTGGCTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (6 bp):
CTTTTA
Found at i:20882448 original size:30 final size:30
Alignment explanation
Indices: 20882397--20882469 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
20882387 GGTATAATGC
* * *
20882397 TGAGAATGTAACTACTAAAAATATAATTAT
1 TGAGAATATAATTATTAAAAATATAATTAT
* *
20882427 TGAGTATATAATTATTAAAAATATGATTAT
1 TGAGAATATAATTATTAAAAATATAATTAT
*
20882457 TGGGAATATAATT
1 TGAGAATATAATT
20882470 TTGTAACATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (30 bp):
TGAGAATATAATTATTAAAAATATAATTAT
Found at i:20882450 original size:15 final size:15
Alignment explanation
Indices: 20882412--20882457 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
20882402 ATGTAACTAC
20882412 TAAAAATATAATTAT
1 TAAAAATATAATTAT
* **
20882427 TGAGTATATAATTAT
1 TAAAAATATAATTAT
*
20882442 TAAAAATATGATTAT
1 TAAAAATATAATTAT
20882457 T
1 T
20882458 GGGAATATAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TAAAAATATAATTAT
Found at i:20883173 original size:4 final size:4
Alignment explanation
Indices: 20883164--20883236 Score: 78
Period size: 4 Copynumber: 18.2 Consensus size: 4
20883154 AGAAAAAGAT
* *
20883164 AGGA AGGA A-GA AGGA GAAGA AGGA TGGA AGGA AGGA AGGA AGGA AGGA
1 AGGA AGGA AGGA AGGA -AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA
* *
20883212 AGGA AGAA AGTGA A-GA AGGT AGGA A
1 AGGA AGGA AG-GA AGGA AGGA AGGA A
20883237 AGAGAAAAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 6 0.11
4 46 0.81
5 5 0.09
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.04
Consensus pattern (4 bp):
AGGA
Found at i:20883178 original size:24 final size:24
Alignment explanation
Indices: 20883148--20883203 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
20883138 GACAGTGAAT
20883148 AGAAGGAGAA-AAAGATAGGAAGGA
1 AGAAGGAGAAGAAAGAT-GGAAGGA
*
20883172 AGAAGGAGAAGAAGGATGGAAGGA
1 AGAAGGAGAAGAAAGATGGAAGGA
20883196 AGGAAGGA
1 A-GAAGGA
20883204 AGGAAGGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.54, C:0.00, G:0.43, T:0.04
Consensus pattern (24 bp):
AGAAGGAGAAGAAAGATGGAAGGA
Found at i:20895278 original size:17 final size:18
Alignment explanation
Indices: 20895248--20895281 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
20895238 GATTTAATCC
20895248 ATATATTGAAAAATAAAA
1 ATATATTGAAAAATAAAA
20895266 ATATATT-AAAAATAAA
1 ATATATTGAAAAATAAA
20895282 TAAATCACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATATTGAAAAATAAAA
Found at i:20898901 original size:11 final size:11
Alignment explanation
Indices: 20898885--20898911 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
20898875 ATAATGCTTT
20898885 AATTGAACACA
1 AATTGAACACA
20898896 AATTGAACACA
1 AATTGAACACA
20898907 AATTG
1 AATTG
20898912 TTGCTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (11 bp):
AATTGAACACA
Found at i:20916199 original size:354 final size:342
Alignment explanation
Indices: 20915524--20916647 Score: 1328
Period size: 354 Copynumber: 3.2 Consensus size: 342
20915514 ATCTCAAACA
* * * *
20915524 TAATTAATAGTTTTATAAGTTATAA-TTTTGTATTGTTAACACAAAATAGAAAGTAAATATGTTT
1 TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTTT
* * * *
20915588 ATATTCAAAGTGTATATATACCAAAATATTTTTAGTATATATATAATAGTAATTATAGTTCTTAT
66 ATATTTAAAGTATATATATACTAAAATA-TTTTA--ATATATATAATAGTAATTATATTTCTTAT
* * * * * * *
20915653 AAATGAACCCAATGTATAGAAAGTATATATATTAGAAGACATTACAAGTCAATTAATAATCATAA
128 AAAT-AAACTAATGTATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAG
* ** * *
20915718 TTTCATTAATTAATTTAATTAACTATATGGGTTTGTTCTTAATTACATGAAATTAAAAAAAAATA
192 TTTCATAAATTAATTTAATTAACTATATAAGTTTGTCCTTAATTATATGAAATTAAAAAAAAATA
* * *
20915783 ACTATGTTTCAAAATTATTTTAATCTCACAACTTCT-TTT-AGATTTCT-TAATTATAAGTTTAT
257 ACTAAGTTTCAAAACTATTTTAATCTCA-AACTTCTCTTTAAG-TTTATAT-ATTATAAGTTTAT
20915845 ATAAACAAATGTATATATATATATT
319 ATAAACAAATGTATATATAT-TATT
20915870 GTAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
1 -TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
* * *
20915935 TATATTTAAAGAACACACACACATATATACTAAAAGTATTTTAATATATACAATAGTAATTATAT
65 TATATTTAAAG--------TATATATATACTAAAA-TATTTTAATATATATAATAGTAATTATAT
* *
20916000 TTCTTATAAATAAAGCTAATGTATATAAATTATATATATTAAAAGGCATTACAAGTTAATTAATA
121 TTCTTATAAATAAA-CTAATGTATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATA
* * * *
20916065 ATTATAGTTTCATAAATTAATTTAATTAACTACATAAGTTTATCCTTAATTATATTG-AATT-TA
185 ATCATAGTTTCATAAATTAATTTAATTAACTATATAAGTTTGTCCTTAATTATA-TGAAATTAAA
* * * *
20916128 AAACAATAACTAAGTTTTAAAACTATTCTAATCTCATAACTTCTCTTTAAGTTTATATATTATAT
249 AAAAAATAACTAAGTTTCAAAACTATTTTAATCTCA-AACTTCTCTTTAAGTTTATATATTATAA
*
20916193 GTTTATATAAACAAA-ATA-ATAT-TTATT
313 GTTTATATAAACAAATGTATATATATTATT
* *
20916220 ATAATTAATAATTTTATAAGTTATAATTTTTTTAATGTTAATACAAAATAGAAAGTAAATATGTT
1 -TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
** *
20916285 TATATTTAAAGTATATATATACTAAAAATATTTTTGTATATATAATAGTAATTATATTTATTATA
65 TATATTTAAAGTATATATATACT-AAAATATTTTAATATATATAATAGTAATTATATTTCTTATA
* * *
20916350 AATTAACTCAA--TATGTAAACTATATATATTAAAAGACATTACAAATTAATTAATAATCATAGT
129 AATAAACT-AATGTATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAGT
* *
20916413 TTCATGAATTAATTTAATTAATTATATGAA-TTTGTCCTTAATT-TCATGAAATTAAAAAAAAAT
193 TTCATAAATTAATTTAATTAACTATAT-AAGTTTGTCCTTAATTAT-ATGAAATTAAAAAAAAAT
** * * **
20916476 AGTTAGGTTCCAAAACTATTTTAATCTCCAAAGC-TCTCTTTAAGTACATATATTATAAGTTTAT
256 AACTAAGTTTCAAAACTATTTTAATCT-CAAA-CTTCTCTTTAAGTTTATATATTATAAGTTTAT
*
20916540 ATAAAC-AATGGTGTATATATTA--
319 ATAAACAAAT-GTATATATATTATT
* * * *
20916562 TAATTAATAATTTTTTAAGTTATAATTTTTGTAATGGTAAGACAAAATAGAAAGTGAATATATTT
1 TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTTT
*
20916627 ATATTAAAAGTATTATATATA
66 ATATTTAAAGTA-TATATATA
20916648 ATAGTAATTA
Statistics
Matches: 673, Mismatches: 76, Indels: 61
0.83 0.09 0.08
Matches are distributed among these distances:
339 3 0.00
340 90 0.13
341 137 0.20
342 62 0.09
343 8 0.01
344 3 0.00
347 24 0.04
348 45 0.07
350 77 0.11
351 1 0.00
352 4 0.01
353 43 0.06
354 152 0.23
355 5 0.01
356 17 0.03
357 2 0.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (342 bp):
TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTTT
ATATTTAAAGTATATATATACTAAAATATTTTAATATATATAATAGTAATTATATTTCTTATAAA
TAAACTAATGTATATAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAGTTTC
ATAAATTAATTTAATTAACTATATAAGTTTGTCCTTAATTATATGAAATTAAAAAAAAATAACTA
AGTTTCAAAACTATTTTAATCTCAAACTTCTCTTTAAGTTTATATATTATAAGTTTATATAAACA
AATGTATATATATTATT
Found at i:20916672 original size:341 final size:340
Alignment explanation
Indices: 20915523--20916662 Score: 1262
Period size: 341 Copynumber: 3.3 Consensus size: 340
20915513 TATCTCAAAC
* * * *
20915523 ATAATTAATAGTTTTATAAGTTATAA-TTTTGTATTGTTAACACAAAATAGAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
* * * * * * * *
20915587 TATATTCAAAGTGTATATATACCAAAATATTTTTAGTATATATATAATAGTAATTATAGTTCTTA
66 TATATTAAAAGTATATATATA-C-ATATAATTATATTTTATATATAATAGTAATTATATTTCTTA
* * * * *
20915652 TAAATGAACCCAATGTATAG-AAAGTATATATATTAGAAGACATTACAAGTCAATTAATAATCAT
129 TAAATAAACTCAA-GTAT-GTAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCAT
* * ** * *
20915716 AATTTCATTAATTAATTTAATTAACTATATGGGTTTGTTCTTAATTACATGAAATTAAAAAAAAA
192 AGTTTCATAAATTAATTTAATTAACTATATGAATTTGTCCTTAATTTCATGAAATTAAAAAAAAA
* * * *
20915781 TAACTATGTTTCAAAATTATTTTAATCTCACAACT-TCTTTTAGATTTCTTA-ATTATAAGTTTA
257 TAACTAAGTTTCAAAACTATTTTAATCTCACAACTCTC-TTTA-AGTTCATATATTATAAGTTTA
20915844 TATAAACAAATGTATATATATAT
320 TATAAAC-AATGTATATATAT-T
20915867 ATTGTAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATAT
1 A---TAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATAT
* * * * * * *
20915932 GTTTATATTTAAAGAACACACACACATATATACTAAAAGTATTTTAATATATACAATAGTAATTA
63 GTTTATATTAAAAGTATATATATACATATA-A-T--TA-TATTTT-ATATAT--AATAGTAATTA
* * *
20915997 TATTTCTTATAAATAAAGCT-AATGTATATAAATTATATATATTAAAAGGCATTACAAGTTAATT
120 TATTTCTTATAAATAAA-CTCAA-GTATGTAAACTATATATATTAAAAGACATTACAAGTTAATT
* * *
20916061 AATAATTATAGTTTCATAAATTAATTTAATTAACTACAT-AAGTTTATCCTTAATTAT-ATTG-A
183 AATAATCATAGTTTCATAAATTAATTTAATTAACTATATGAA-TTTGTCCTTAATT-TCA-TGAA
* * * * * *
20916123 ATT-TAAAACAATAACTAAGTTTTAAAACTATTCTAATCTCATAACTTCTCTTTAAGTTTATATA
245 ATTAAAAAAAAATAACTAAGTTTCAAAACTATTTTAATCTCACAAC-TCTCTTTAAGTTCATATA
* ** *
20916187 TTATATGTTTATATAAACAAAATAATATTTATT
309 TTATAAGTTTATATAAACAATGT-ATATATATT
* *
20916220 ATAATTAATAATTTTATAAGTTATAATTTTTTTAATGTTAATACAAAATAGAAAGTAAATATGTT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
* * * * *
20916285 TATATTTAAAGTATATATATAC-TAAAAATATTTTTGTATATATAATAGTAATTATATTTATTAT
66 TATATTAAAAGTATATATATACATATAATTATATTT-TATATATAATAGTAATTATATTTCTTAT
* *
20916349 AAATTAACTCAA-TATGTAAACTATATATATTAAAAGACATTACAAATTAATTAATAATCATAGT
130 AAATAAACTCAAGTATGTAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAGT
* * *
20916413 TTCATGAATTAATTTAATTAATTATATGAATTTGTCCTTAATTTCATGAAATTAAAAAAAAATAG
195 TTCATAAATTAATTTAATTAACTATATGAATTTGTCCTTAATTTCATGAAATTAAAAAAAAATAA
* * * *
20916478 TTAGGTTCCAAAACTATTTTAATCTC-CAAAGCTCTCTTTAAGTACATATATTATAAGTTTATAT
260 CTAAGTTTCAAAACTATTTTAATCTCAC-AA-CTCTCTTTAAGTTCATATATTATAAGTTTATAT
*
20916542 AAACAATGGTGTATATATT
323 AAACAAT-GTATATATATT
* * * *
20916561 ATAATTAATAATTTTTTAAGTTATAATTTTTGTAATGGTAAGACAAAATAGAAAGTGAATATATT
1 ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
20916626 TATATTAAAAGTATTATATATA-ATAGTAATTATATTT
66 TATATTAAAAGTA-TATATATACATA-TAATTATATTT
20916663 CTTTATAATA
Statistics
Matches: 667, Mismatches: 96, Indels: 67
0.80 0.12 0.08
Matches are distributed among these distances:
339 3 0.00
340 88 0.13
341 148 0.22
342 40 0.06
343 8 0.01
344 11 0.02
345 2 0.00
346 4 0.01
347 25 0.04
348 51 0.08
349 3 0.00
350 79 0.12
351 4 0.01
352 6 0.01
353 45 0.07
354 145 0.22
355 5 0.01
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (340 bp):
ATAATTAATAATTTTATAAGTTATAATTTTTGTAATGGTAATACAAAATAGAAAGTAAATATGTT
TATATTAAAAGTATATATATACATATAATTATATTTTATATATAATAGTAATTATATTTCTTATA
AATAAACTCAAGTATGTAAACTATATATATTAAAAGACATTACAAGTTAATTAATAATCATAGTT
TCATAAATTAATTTAATTAACTATATGAATTTGTCCTTAATTTCATGAAATTAAAAAAAAATAAC
TAAGTTTCAAAACTATTTTAATCTCACAACTCTCTTTAAGTTCATATATTATAAGTTTATATAAA
CAATGTATATATATT
Found at i:20924156 original size:2 final size:2
Alignment explanation
Indices: 20924149--20924205 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
20924139 TAATGTGGAG
20924149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20924190 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
20924206 GGTTTGAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:20927905 original size:150 final size:150
Alignment explanation
Indices: 20927722--20928052 Score: 653
Period size: 150 Copynumber: 2.2 Consensus size: 150
20927712 GTATAATTAT
20927722 CTTTGGTTTCATAAAATATCCGAATGAGTTAATTGTATAATTAACTATCTAAGTTAATTATTTAA
1 CTTTGGTTTCATAAAATATCCGAATGAGTTAATTGTATAATTAACTATCTAAGTTAATTATTTAA
20927787 TTTAAAATTTTTGATGTCTACATCATTACAAATTAATTTGTTAAATTAACATGTTAATTAATAAT
66 TTTAAAATTTTTGATGTCTACATCATTACAAATTAATTTGTTAAATTAACATGTTAATTAATAAT
20927852 TCTTGATGAACCAACATGTG
131 TCTTGATGAACCAACATGTG
20927872 CTTTGGTTTCATAAAATATCCGAATGAGTTAATTGTATAATTAACTATCTAAGTTAATTATTTAA
1 CTTTGGTTTCATAAAATATCCGAATGAGTTAATTGTATAATTAACTATCTAAGTTAATTATTTAA
20927937 TTTAAAATTTTTGATGTCTACATCATTACAAATTAATTTGTTAAATTAACATGTTAATTAATAAT
66 TTTAAAATTTTTGATGTCTACATCATTACAAATTAATTTGTTAAATTAACATGTTAATTAATAAT
20928002 TCTTGATGAACCAACATGTG
131 TCTTGATGAACCAACATGTG
*
20928022 CTTTGGTTTCATAAAATATCCTAATGAGTTA
1 CTTTGGTTTCATAAAATATCCGAATGAGTTA
20928053 CAATACCCAA
Statistics
Matches: 180, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 180 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (150 bp):
CTTTGGTTTCATAAAATATCCGAATGAGTTAATTGTATAATTAACTATCTAAGTTAATTATTTAA
TTTAAAATTTTTGATGTCTACATCATTACAAATTAATTTGTTAAATTAACATGTTAATTAATAAT
TCTTGATGAACCAACATGTG
Found at i:20928745 original size:35 final size:34
Alignment explanation
Indices: 20928706--20928784 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 34
20928696 TTTGACTTCC
* * *
20928706 ATCAAATGAAGGGTAGTTATCTCCTTGGTTTCTAT
1 ATCAAAT-AAGGCTAGGTATCTCCGTGGTTTCTAT
* *
20928741 ATCAAACATTAGGCTAGGTATCTCCGTGGTTTCTTT
1 ATC-AA-ATAAGGCTAGGTATCTCCGTGGTTTCTAT
20928777 ATCAAATA
1 ATCAAATA
20928785 TTTTATTATT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
34 2 0.06
35 5 0.14
36 27 0.75
37 2 0.06
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (34 bp):
ATCAAATAAGGCTAGGTATCTCCGTGGTTTCTAT
Found at i:20929421 original size:14 final size:14
Alignment explanation
Indices: 20929402--20929429 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20929392 CAGACCCTTA
20929402 TCGTACCCAGTGTC
1 TCGTACCCAGTGTC
20929416 TCGTACCCAGTGTC
1 TCGTACCCAGTGTC
20929430 AATCAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (14 bp):
TCGTACCCAGTGTC
Found at i:20944544 original size:29 final size:29
Alignment explanation
Indices: 20944503--20944558 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
20944493 GAAACTACAT
*
20944503 TCTCTGCAGATATACACAATGAGTTGTAC
1 TCTCCGCAGATATACACAATGAGTTGTAC
*
20944532 TCTCCGCAGATATATACAATGAGTTGT
1 TCTCCGCAGATATACACAATGAGTTGT
20944559 CTTATGATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (29 bp):
TCTCCGCAGATATACACAATGAGTTGTAC
Found at i:20947037 original size:28 final size:28
Alignment explanation
Indices: 20946979--20947037 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20946969 ACATTGTTAG
**
20946979 CAATATAATAGTTTTTTATGATAAATAT
1 CAATATAATAGTTTACTATGATAAATAT
20947007 CAATATAATAGTTTAACTA-GACTAAAT-T
1 CAATATAATAGTTT-ACTATGA-TAAATAT
20947035 CAA
1 CAA
20947038 ATCTAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 20 0.74
29 7 0.26
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (28 bp):
CAATATAATAGTTTACTATGATAAATAT
Found at i:20965867 original size:20 final size:20
Alignment explanation
Indices: 20965830--20965867 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20965820 TTTCAGAAGC
*
20965830 TTTTCTTCTTGAAGAATTAT
1 TTTTCTTCTTCAAGAATTAT
*
20965850 TTTTCTTCTTCAATAATT
1 TTTTCTTCTTCAAGAATT
20965868 GACATTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (20 bp):
TTTTCTTCTTCAAGAATTAT
Found at i:20968665 original size:12 final size:12
Alignment explanation
Indices: 20968648--20968674 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20968638 TTAGCCCCAC
20968648 TTCGTTGATGAA
1 TTCGTTGATGAA
20968660 TTCGTTGATGAA
1 TTCGTTGATGAA
20968672 TTC
1 TTC
20968675 ATCAAACCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (12 bp):
TTCGTTGATGAA
Found at i:20974924 original size:27 final size:28
Alignment explanation
Indices: 20974889--20974952 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
20974879 TATCTATATA
* * *
20974889 ATTATTAATTTTTATTAATT-TTTAAAT
1 ATTAATAATTTTTATAAATTATTAAAAT
20974916 ATTAATAA--TTTATAAATTAATTAAAAT
1 ATTAATAATTTTTATAAATT-ATTAAAAT
20974943 ATTAATAATT
1 ATTAATAATT
20974953 AATAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 9 0.30
27 21 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTAATAATTTTTATAAATTATTAAAAT
Found at i:20974934 original size:15 final size:14
Alignment explanation
Indices: 20974909--20974976 Score: 55
Period size: 15 Copynumber: 4.3 Consensus size: 14
20974899 TTTATTAATT
20974909 TTTAAATATTAATAA
1 TTTAAA-ATTAATAA
20974924 TTTATAAATTAATTAAAA
1 TTTA-AAATTAA-T--AA
20974942 TATTAATAATTAATAA
1 T-TTAA-AATTAATAA
*
20974958 TTTAAATATTAATAT
1 TTTAAA-ATTAATAA
20974973 TTTA
1 TTTA
20974977 TTTATAATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
14 1 0.02
15 24 0.53
16 6 0.13
18 5 0.11
19 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TTTAAAATTAATAA
Found at i:20974964 original size:22 final size:22
Alignment explanation
Indices: 20974909--20975258 Score: 102
Period size: 22 Copynumber: 15.5 Consensus size: 22
20974899 TTTATTAATT
20974909 TTTAAATATTAATAATTTATAAATTAA
1 TTTAAATATTAATAA--T-T-AA-TAA
*
20974936 TTAAAATATTAATAATTAATAA
1 TTTAAATATTAATAATTAATAA
*
20974958 TTTAAATATTAAT-ATT--TTA
1 TTTAAATATTAATAATTAATAA
* *
20974977 TTTATAAT-TTAATTATTGAA-AT
1 TTTA-AATATTAATAATT-AATAA
* * *
20974999 TTTAAAATATTAACATTTTATTTAA
1 TTT-AAATATTAATA-ATTA-ATAA
* *
20975024 TTTAAATATT-ATTA-TGATCAA
1 TTTAAATATTAATAATTAAT-AA
* * * * *
20975045 TTT--TTATT-TTATTTTAT-T
1 TTTAAATATTAATAATTAATAA
* *
20975063 TTTAAATATTAATAATTGATCA
1 TTTAAATATTAATAATTAATAA
*
20975085 TTTAAATATTAAT-ATT--TTA
1 TTTAAATATTAATAATTAATAA
* * *
20975104 TTT-ATTATTTAATCACTAAT-A
1 TTTAAATA-TTAATAATTAATAA
*
20975125 TTTAAAATATTAATAATTTATTTAA
1 TTT-AAATATTAATAA-TTA-ATAA
*
20975150 TTTAAATATTATTATGATTAATTATTTTA
1 TTTAAATATTA--ATAATTAA-TA----A
* *
20975179 TTTTAAATATTAATAATTGATTA
1 -TTTAAATATTAATAATTAATAA
* *
20975202 TTTAAATATTAATATTTTATAA
1 TTTAAATATTAATAATTAATAA
* * *
20975224 TTTAATTATTAATATTTTATTTAA
1 TTTAAATATTAATA-ATTA-ATAA
20975248 TTTAAATATTA
1 TTTAAATATTA
20975259 TTATGATCCG
Statistics
Matches: 243, Mismatches: 45, Indels: 73
0.67 0.12 0.20
Matches are distributed among these distances:
18 6 0.02
19 26 0.11
20 16 0.07
21 22 0.09
22 73 0.30
23 18 0.07
24 32 0.13
25 14 0.06
26 3 0.01
27 15 0.06
28 6 0.02
29 1 0.00
30 11 0.05
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (22 bp):
TTTAAATATTAATAATTAATAA
Found at i:20975024 original size:117 final size:117
Alignment explanation
Indices: 20974898--20975221 Score: 361
Period size: 127 Copynumber: 2.7 Consensus size: 117
20974888 AATTATTAAT
** * * *
20974898 TTTTA-TTAATTTTTAAATATTA-ATAATTTA-TAAATTAATTAAAATATTAATAATTAATAATT
1 TTTTATTTAA-TTTTAAATATTATATAATTTATTATTTTATTTTAAATATTAATAATTGATAATT
* *
20974960 TAAATATTAATATTTTATTTATAATTTAATTATTGAA-ATTTTAAAATATTAACA
65 TAAATATTAATATTTTATTTATAATTTAATCACT-AATA-TTTAAAATATTAACA
*
20975014 TTTTATTTAATTTAAATATTATTATGATCAATTTTTATTTTATTTTATTTTTAAATATTAATAAT
1 TTTTATTTAATTTTAA-A-TATTAT-AT-AA--TTTA--TTATTTTA-TTTTAAATATTAATAAT
* * *
20975079 TGATCATTTAAATATTAATATTTTATTTATTATTTAATCACTAATATTTAAAATATTAATA
57 TGATAATTTAAATATTAATATTTTATTTATAATTTAATCACTAATATTTAAAATATTAACA
* * * *
20975140 ATTTATTTAA-TTTAAATATTATTATGATTAATTATTTTATTTTAAATATTAATAATTGATTATT
1 TTTTATTTAATTTTAAATATTA-TATAATTTATTATTTTATTTTAAATATTAATAATTGATAATT
20975204 TAAATATTAATATTTTAT
65 TAAATATTAATATTTTAT
20975222 AATTTAATTA
Statistics
Matches: 178, Mismatches: 16, Indels: 27
0.81 0.07 0.12
Matches are distributed among these distances:
116 10 0.06
117 47 0.26
118 13 0.07
120 5 0.03
121 2 0.01
122 1 0.01
123 11 0.06
124 2 0.01
125 4 0.02
126 30 0.17
127 53 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (117 bp):
TTTTATTTAATTTTAAATATTATATAATTTATTATTTTATTTTAAATATTAATAATTGATAATTT
AAATATTAATATTTTATTTATAATTTAATCACTAATATTTAAAATATTAACA
Found at i:20975070 original size:127 final size:117
Alignment explanation
Indices: 20974939--20975221 Score: 379
Period size: 127 Copynumber: 2.3 Consensus size: 117
20974929 AAATTAATTA
* * *
20974939 AAATATTAATAATTAATAATTTAAATATTAATATTTTATTTATAATTTAATTATTGAA-ATTTTA
1 AAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCACT-AATA-TTTA
* *
20975003 AAATATTAACATTTTATTTAATTTAAATATTATTATGATCAATTTTTATTTTATTTTATTTTT
64 AAATATTAACAATTTATTTAATTTAAATATTATTATG----A---TTA-ATTATTTTA-TTTT
* *
20975066 AAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATTATTTAATCACTAATATTTAAA
1 AAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCACTAATATTTAAA
*
20975131 ATATTAATAATTTATTTAATTTAAATATTATTATGATTAATTATTTTATTTT
66 ATATTAACAATTTATTTAATTTAAATATTATTATGATTAATTATTTTATTTT
*
20975183 AAATATTAATAATTGATTATTTAAATATTAATATTTTAT
1 AAATATTAATAATTGATAATTTAAATATTAATATTTTAT
20975222 AATTTAATTA
Statistics
Matches: 146, Mismatches: 9, Indels: 12
0.87 0.05 0.07
Matches are distributed among these distances:
117 42 0.29
118 8 0.05
119 3 0.02
122 1 0.01
126 41 0.28
127 51 0.35
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (117 bp):
AAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCACTAATATTTAAA
ATATTAACAATTTATTTAATTTAAATATTATTATGATTAATTATTTTATTTT
Found at i:20975172 original size:30 final size:30
Alignment explanation
Indices: 20975138--20975265 Score: 82
Period size: 30 Copynumber: 4.0 Consensus size: 30
20975128 AAAATATTAA
*
20975138 TAATTTATTTAATTTAAATATTATTATGAT
1 TAATTTATTTAATTTAAATATTATAATGAT
*
20975168 TAA-TTATTTTATTTTAAATATTAATAATTGAT
1 TAATTTA-TTTAATTTAAATATT-ATAA-TGAT
** *
20975200 T-ATTTAAATATTAATATTTTATAATT-TAATTAT
1 TAATTT--AT-TTAAT-TTAAAT-ATTATAATGAT
*
20975233 TAATATTTTATTTAATTTAAATATTATTATGAT
1 T-A-A-TTTATTTAATTTAAATATTATAATGAT
20975266 CCGTTATTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 25
0.68 0.09 0.23
Matches are distributed among these distances:
29 3 0.04
30 17 0.23
31 4 0.05
32 10 0.14
33 14 0.19
34 13 0.18
35 6 0.08
36 4 0.05
37 3 0.04
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (30 bp):
TAATTTATTTAATTTAAATATTATAATGAT
Found at i:20976592 original size:105 final size:105
Alignment explanation
Indices: 20976410--20976619 Score: 393
Period size: 105 Copynumber: 2.0 Consensus size: 105
20976400 ACTAAGATTC
* *
20976410 TTGTTTGTGTACAACATTGAGTAGTTCTATGGTTTTAAACTTCTTATTTCACATCGAATTCTAAT
1 TTGTTTGTGTACAACATTGAGTAGTTCTATAGTTTTAAACTTCTTATTTCACATCGAATCCTAAT
20976475 CACATTCTATTTTGATCGATCTTTAGGTTTTAGAATAGTA
66 CACATTCTATTTTGATCGATCTTTAGGTTTTAGAATAGTA
*
20976515 TTGTTTGTGTACAACATTGAGTAGTTGTATAGTTTTAAACTTCTTATTTCACATCGAATCCTAAT
1 TTGTTTGTGTACAACATTGAGTAGTTCTATAGTTTTAAACTTCTTATTTCACATCGAATCCTAAT
20976580 CACATTCTATTTTGATCGATCTTTAGGTTTTAGAATAGTA
66 CACATTCTATTTTGATCGATCTTTAGGTTTTAGAATAGTA
20976620 AGTAGTGCTT
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.45
Consensus pattern (105 bp):
TTGTTTGTGTACAACATTGAGTAGTTCTATAGTTTTAAACTTCTTATTTCACATCGAATCCTAAT
CACATTCTATTTTGATCGATCTTTAGGTTTTAGAATAGTA
Found at i:20988200 original size:127 final size:127
Alignment explanation
Indices: 20988034--20988287 Score: 481
Period size: 127 Copynumber: 2.0 Consensus size: 127
20988024 CCTTTCTTCC
20988034 TTAGCCTTCGGAATCTCTTTGTGTCCCTTGTCTTTACTCCCTTGATGAATAAATCCGCGATTCAT
1 TTAGCCTTCGGAATCTCTTTGTGTCCCTTGTCTTTACTCCCTTGATGAATAAATCCGCGATTCAT
* *
20988099 GTGTCAATAGGAACATCCATGTCACTCTCCGTGGTTTCTTGGTGTTGAGGGCTTTGTAGTGG
66 GTGTCAATAGGAACATCCATGTCACCCTCCGTGGTTTCTTGGTGTTGAAGGCTTTGTAGTGG
20988161 TTAGCCTTCGGAATCTCTTTGTGTCCCTTGTCTTTACTCCCTTGATGAATAAATCCGCGATTCAT
1 TTAGCCTTCGGAATCTCTTTGTGTCCCTTGTCTTTACTCCCTTGATGAATAAATCCGCGATTCAT
*
20988226 GTGTCAATAGGAACATCCATGTCACCCTCCGTGGTTTCTTGGTGTTGAAGGCTTTGTGGTGG
66 GTGTCAATAGGAACATCCATGTCACCCTCCGTGGTTTCTTGGTGTTGAAGGCTTTGTAGTGG
20988288 CTGAGCTGAA
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
127 124 1.00
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (127 bp):
TTAGCCTTCGGAATCTCTTTGTGTCCCTTGTCTTTACTCCCTTGATGAATAAATCCGCGATTCAT
GTGTCAATAGGAACATCCATGTCACCCTCCGTGGTTTCTTGGTGTTGAAGGCTTTGTAGTGG
Found at i:20988844 original size:2 final size:2
Alignment explanation
Indices: 20988837--20988866 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20988827 AGAACCAATG
*
20988837 CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20988867 TTAGTAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:20990390 original size:23 final size:23
Alignment explanation
Indices: 20990360--20990405 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
20990350 CATCTTCAAC
*
20990360 TTCATGCATGTAAGTCGAAAAAA
1 TTCATGCACGTAAGTCGAAAAAA
20990383 TTCATGCACGTAAGTCGAAAAAA
1 TTCATGCACGTAAGTCGAAAAAA
20990406 AGAAATGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.24
Consensus pattern (23 bp):
TTCATGCACGTAAGTCGAAAAAA
Found at i:20990801 original size:20 final size:20
Alignment explanation
Indices: 20990778--20990815 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
20990768 ATTATAAATG
20990778 TGTTAATCGTATATTAATCA
1 TGTTAATCGTATATTAATCA
*
20990798 TGTTAATCGTATTTTAAT
1 TGTTAATCGTATATTAAT
20990816 TATATTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (20 bp):
TGTTAATCGTATATTAATCA
Found at i:20990827 original size:20 final size:20
Alignment explanation
Indices: 20990780--20990827 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
20990770 TATAAATGTG
*
20990780 TTAATCGTATATTAATCATG
1 TTAATCGTATATTAATCATA
* *
20990800 TTAATCGTATTTTAATTATA
1 TTAATCGTATATTAATCATA
*
20990820 TTATTCGT
1 TTAATCGT
20990828 GTTAATCGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.52
Consensus pattern (20 bp):
TTAATCGTATATTAATCATA
Found at i:21007130 original size:18 final size:17
Alignment explanation
Indices: 21007074--21007141 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
21007064 GAAGAAAATC
* *
21007074 TTTTGAATAATTATGCA
1 TTTTAAATAATTATGTA
* * *
21007091 TGTTAAAT-ATTATATT
1 TTTTAAATAATTATGTA
21007107 TGTTTAAATAATTATGTA
1 T-TTTAAATAATTATGTA
21007125 TATTTAAA-AAGTTATGT
1 T-TTTAAATAA-TTATGT
21007142 CAATAAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 6 0.15
17 14 0.36
18 19 0.49
ACGTcount: A:0.38, C:0.01, G:0.10, T:0.50
Consensus pattern (17 bp):
TTTTAAATAATTATGTA
Found at i:21027155 original size:20 final size:22
Alignment explanation
Indices: 21027109--21027156 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
21027099 ATAATTATGG
*
21027109 TAATTTTTTTTTTCTATATATA
1 TAATATTTTTTTTCTATATATA
* *
21027131 AAATATTTTTTTTC-A-ATTTA
1 TAATATTTTTTTTCTATATATA
21027151 TAATAT
1 TAATAT
21027157 CCACTTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.41
21 1 0.05
22 12 0.55
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATATTTTTTTTCTATATATA
Found at i:21031162 original size:15 final size:15
Alignment explanation
Indices: 21031142--21031180 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
21031132 AAAATTAAAA
21031142 AAATATTAATATTTT-
1 AAATATTAAT-TTTTG
21031157 AAATATTAATTTTTG
1 AAATATTAATTTTTG
*
21031172 AATTATTAA
1 AAATATTAA
21031181 GTGAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
AAATATTAATTTTTG
Found at i:21031972 original size:42 final size:41
Alignment explanation
Indices: 21031917--21031996 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
21031907 TCGTACCAAA
* *
21031917 TTACGTAATAATTATTTTATTTTATTTTTATCTTATTTTCTC
1 TTACATAATAATTATTTTATTTCATTTTTATC-TATTTTCTC
21031959 TTACATAATAATTATTTTATTTCATTTTTATCTATTTT
1 TTACATAATAATTATTTTATTTCATTTTTATCTATTTT
21031997 GTGAAGCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 6 0.17
42 30 0.83
ACGTcount: A:0.26, C:0.09, G:0.01, T:0.64
Consensus pattern (41 bp):
TTACATAATAATTATTTTATTTCATTTTTATCTATTTTCTC
Found at i:21052247 original size:2 final size:2
Alignment explanation
Indices: 21052242--21052267 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21052232 TTTTTTTCAG
21052242 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
21052268 TGCCAGGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21058219 original size:16 final size:17
Alignment explanation
Indices: 21058191--21058225 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
21058181 AATTAATTAG
21058191 ATTAAAAATATATAAAA
1 ATTAAAAATATATAAAA
21058208 ATTAAAAA-ATATAAAA
1 ATTAAAAATATATAAAA
21058224 AT
1 AT
21058226 AATTAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTAAAAATATATAAAA
Found at i:21058517 original size:21 final size:21
Alignment explanation
Indices: 21058468--21058517 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
21058458 TTTCTATATA
*
21058468 TAAAATA-AATTATTATTTTT
1 TAAAATATAATTATTACTTTT
*
21058488 TCAATATATAA-TATCTACTTTT
1 T-AAAATATAATTAT-TACTTTT
21058510 TAAAATAT
1 TAAAATAT
21058518 TCCTTTCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAAATATAATTATTACTTTT
Found at i:21059269 original size:5 final size:5
Alignment explanation
Indices: 21059258--21059299 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
21059248 GAAAAAAGAG
*
21059258 GAAAA -AAAA -AAAA GAAAA GAAAA GAAAA GAAAG GAGAAA GAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA GAA
21059300 GCGAGCAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 8 0.24
5 21 0.64
6 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:21060549 original size:69 final size:69
Alignment explanation
Indices: 21060438--21060577 Score: 253
Period size: 69 Copynumber: 2.0 Consensus size: 69
21060428 CCTTGACCAT
*
21060438 CTCTAGAACCTTTATGGCAGATTTAGTTTTTGGTACAAGACAGAGCACCATGGCATGAGGATCTG
1 CTCTAGAACCTTTATGGCAGATTTAGTTTTTGGTACAAGACAGAGCACCATGACATGAGGATCTG
21060503 TACC
66 TACC
* *
21060507 CTCTAGAACCTTTATGGGAGATTTAGTTTTTGGTGCAAGACAGAGCACCATGACATGAGGATCTG
1 CTCTAGAACCTTTATGGCAGATTTAGTTTTTGGTACAAGACAGAGCACCATGACATGAGGATCTG
21060572 TACC
66 TACC
21060576 CT
1 CT
21060578 AACACGCCCC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (69 bp):
CTCTAGAACCTTTATGGCAGATTTAGTTTTTGGTACAAGACAGAGCACCATGACATGAGGATCTG
TACC
Found at i:21066416 original size:3 final size:3
Alignment explanation
Indices: 21066408--21066441 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
21066398 TTGAAATTGG
21066408 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21066442 TGTAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21073747 original size:3 final size:3
Alignment explanation
Indices: 21073726--21073773 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
21073716 GAAAGCTGGT
* *
21073726 GAA GAA GAGA GAA G-G GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA
1 GAA GAA GA-A GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
21073771 GAA
1 GAA
21073774 AAGTAGCCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.03
3 35 0.90
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:21082045 original size:2 final size:2
Alignment explanation
Indices: 21082038--21082081 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
21082028 AACGATTACG
21082038 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
21082080 AT
1 AT
21082082 CTCTAAGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21084864 original size:2 final size:2
Alignment explanation
Indices: 21084852--21084889 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
21084842 TTCACAGCAA
21084852 CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
21084890 ATCATCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:21086075 original size:18 final size:17
Alignment explanation
Indices: 21086043--21086077 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
21086033 TTGGATTTAG
*
21086043 ATTTTTATTTTTAAAAT
1 ATTTTGATTTTTAAAAT
21086060 ATTTTGATTATTTAAAAT
1 ATTTTGATT-TTTAAAAT
21086078 TCTTAAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
ATTTTGATTTTTAAAAT
Found at i:21112159 original size:21 final size:21
Alignment explanation
Indices: 21112135--21112175 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
21112125 TGCTTAATTA
*
21112135 TTGAAGACTTACTTTATAATG
1 TTGAAAACTTACTTTATAATG
* *
21112156 TTGAAAACTTATTTTTTAAT
1 TTGAAAACTTACTTTATAAT
21112176 ATAGATTTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.49
Consensus pattern (21 bp):
TTGAAAACTTACTTTATAATG
Found at i:21118224 original size:29 final size:29
Alignment explanation
Indices: 21118191--21118247 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
21118181 CATGCACCAT
21118191 TACCATCAATAACTACCACT-AGCAAACAA
1 TACCATCAATAACTACCA-TGAGCAAACAA
*
21118220 TACCATCAATAACTGCCATGAGCAAACA
1 TACCATCAATAACTACCATGAGCAAACA
21118248 TCATTAGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.46, C:0.30, G:0.07, T:0.18
Consensus pattern (29 bp):
TACCATCAATAACTACCATGAGCAAACAA
Found at i:21129201 original size:27 final size:27
Alignment explanation
Indices: 21129171--21129386 Score: 283
Period size: 27 Copynumber: 8.0 Consensus size: 27
21129161 TTATGAAAGT
* * *
21129171 AATGTACTGTTTTGATTAAAGTAAAAC
1 AATGTATTATTTTGATGAAAGTAAAAC
21129198 AATGTATTATTTTGATGAAAGTAAAAC
1 AATGTATTATTTTGATGAAAGTAAAAC
* * * * *
21129225 CATATATTATTTTAATGAAAATAAAAT
1 AATGTATTATTTTGATGAAAGTAAAAC
21129252 AATGTATTATTTTGATGAAAGTAAAATC
1 AATGTATTATTTTGATGAAAGTAAAA-C
* *
21129280 -ATGTATTATTTTGATGAAAATAAAAT
1 AATGTATTATTTTGATGAAAGTAAAAC
*
21129306 AATGTATTATTTTAATGAAAGTAAAATC
1 AATGTATTATTTTGATGAAAGTAAAA-C
*
21129334 -ATATATTATTTTGATGAAAGTAAAAC
1 AATGTATTATTTTGATGAAAGTAAAAC
*
21129360 AATGTATTATTTTGATGAAAATAAAAC
1 AATGTATTATTTTGATGAAAGTAAAAC
21129387 TTACAAAAAT
Statistics
Matches: 163, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
26 1 0.01
27 162 0.99
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.39
Consensus pattern (27 bp):
AATGTATTATTTTGATGAAAGTAAAAC
Found at i:21129256 original size:54 final size:54
Alignment explanation
Indices: 21129180--21129386 Score: 315
Period size: 54 Copynumber: 3.8 Consensus size: 54
21129170 TAATGTACTG
* *
21129180 TTTTGATTAAAGTAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTA
1 TTTTGATGAAAATAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTA
* * * *
21129234 TTTTAATGAAAATAAAATAATGTATTATTTTGATGAAAGTAAAATCATGTATTA
1 TTTTGATGAAAATAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTA
* * *
21129288 TTTTGATGAAAATAAAATAATGTATTATTTTAATGAAAGTAAAATCATATATTA
1 TTTTGATGAAAATAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTA
* *
21129342 TTTTGATGAAAGTAAAACAATGTATTATTTTGATGAAAATAAAAC
1 TTTTGATGAAAATAAAACAATGTATTATTTTGATGAAAGTAAAAC
21129387 TTACAAAAAT
Statistics
Matches: 139, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 139 1.00
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.39
Consensus pattern (54 bp):
TTTTGATGAAAATAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTA
Found at i:21129314 original size:81 final size:81
Alignment explanation
Indices: 21129170--21129386 Score: 328
Period size: 81 Copynumber: 2.7 Consensus size: 81
21129160 TTTATGAAAG
* * * * *
21129170 TAATGTACTGTTTTGATTAAAGTAAAACAATGTATTATTTTGATGAAAGTAAAACCATATATTAT
1 TAATGTATTATTTTGATGAAAGTAAAACAATGTATTATTTTGATGAAAATAAAACAATATATTAT
21129235 TTTAATGAAAATAAAA
66 TTTAATGAAAATAAAA
* *
21129251 TAATGTATTATTTTGATGAAAGTAAAATC-ATGTATTATTTTGATGAAAATAAAATAATGTATTA
1 TAATGTATTATTTTGATGAAAGTAAAA-CAATGTATTATTTTGATGAAAATAAAACAATATATTA
*
21129315 TTTTAATGAAAGTAAAA
65 TTTTAATGAAAATAAAA
* *
21129332 TCATATATTATTTTGATGAAAGTAAAACAATGTATTATTTTGATGAAAATAAAAC
1 TAATGTATTATTTTGATGAAAGTAAAACAATGTATTATTTTGATGAAAATAAAAC
21129387 TTACAAAAAT
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
80 1 0.01
81 121 0.98
82 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.39
Consensus pattern (81 bp):
TAATGTATTATTTTGATGAAAGTAAAACAATGTATTATTTTGATGAAAATAAAACAATATATTAT
TTTAATGAAAATAAAA
Found at i:21131178 original size:20 final size:21
Alignment explanation
Indices: 21131148--21131196 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
21131138 TGCATAGTTT
* *
21131148 TATGTTTTCAAAC-AAAATTG
1 TATGGTTTCAAACTAAAATAG
*
21131168 TGTGGTTTCAAACTAAAATAG
1 TATGGTTTCAAACTAAAATAG
21131189 TATGGTTT
1 TATGGTTT
21131197 ATTAAATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (21 bp):
TATGGTTTCAAACTAAAATAG
Found at i:21132639 original size:2 final size:2
Alignment explanation
Indices: 21132634--21132666 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
21132624 TATATATATA
21132634 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
21132667 TAACAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:21133602 original size:38 final size:40
Alignment explanation
Indices: 21133514--21133618 Score: 144
Period size: 38 Copynumber: 2.7 Consensus size: 40
21133504 CACACCCGGC
*
21133514 TCATGTACATCCCCCCACATCGTGCACATAGCTGGCGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCTAGCGCCA
* * *
21133554 TCATG-GCATCCCCCCACATCGTGCACA-ATC-AGTGCCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCTAGCGCCA
*
21133591 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
21133619 CGGACACTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
37 9 0.16
38 23 0.40
39 21 0.36
40 5 0.09
ACGTcount: A:0.23, C:0.41, G:0.16, T:0.20
Consensus pattern (40 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCTAGCGCCA
Found at i:21133743 original size:2 final size:2
Alignment explanation
Indices: 21133736--21133774 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
21133726 CATGCACAAC
21133736 AT 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 AT A
21133775 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21135347 original size:3 final size:3
Alignment explanation
Indices: 21135339--21135365 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
21135329 ATAAAACTGG
21135339 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
21135366 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:21135370 original size:3 final size:3
Alignment explanation
Indices: 21135364--21135402 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
21135354 ATAATAATAA
21135364 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CTAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
21135403 CATGTACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:21136982 original size:71 final size:71
Alignment explanation
Indices: 21136903--21137054 Score: 297
Period size: 71 Copynumber: 2.2 Consensus size: 71
21136893 ATCTGATTTT
21136903 TTATGTTAAAAAACAAAATCATGGATTTTGCTTGTTTATTGAGATTTCTCCGGGCTTTTTTGGGG
1 TTATGTTAAAAAACAAAATCATGGATTTTGCTTGTTTATTGAGATTTCTCCGGGCTTTTTTGGGG
21136968 ATTCTA
66 ATTCTA
21136974 TTATGTTAAAAAACAAAATCATGGATTTTGCTTGTTTATTGAGATTTCTCCGGGCTTTTTTGGGG
1 TTATGTTAAAAAACAAAATCATGGATTTTGCTTGTTTATTGAGATTTCTCCGGGCTTTTTTGGGG
21137039 ATTCTA
66 ATTCTA
21137045 TT-TGTTAAAA
1 TTATGTTAAAA
21137055 TTTTTTCCTT
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
70 8 0.10
71 73 0.90
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (71 bp):
TTATGTTAAAAAACAAAATCATGGATTTTGCTTGTTTATTGAGATTTCTCCGGGCTTTTTTGGGG
ATTCTA
Found at i:21140768 original size:56 final size:56
Alignment explanation
Indices: 21140677--21140793 Score: 198
Period size: 56 Copynumber: 2.1 Consensus size: 56
21140667 ATTTAAGGTG
* *
21140677 TTTCTCTCTCAATTTTTGGCATCAAAAACATAAATTTTTCTCAAAACACTTTCAAA
1 TTTCTCTCTCAATTTTTGACATCAAAAACACAAATTTTTCTCAAAACACTTTCAAA
* *
21140733 TTTCTCTCTCAATTTTTGACATCAAAAACACAAATTTTTCTCAAAATATTTTCAAA
1 TTTCTCTCTCAATTTTTGACATCAAAAACACAAATTTTTCTCAAAACACTTTCAAA
21140789 TTTCT
1 TTTCT
21140794 TGAAAATTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.35, C:0.21, G:0.03, T:0.42
Consensus pattern (56 bp):
TTTCTCTCTCAATTTTTGACATCAAAAACACAAATTTTTCTCAAAACACTTTCAAA
Found at i:21141883 original size:22 final size:21
Alignment explanation
Indices: 21141855--21141898 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
21141845 AAAAGAATTG
*
21141855 AAAAAGAGATAAAAATGAAAAA
1 AAAAAGAAATAAAAAT-AAAAA
*
21141877 AAAAAGAAATGAAAATAAAAA
1 AAAAAGAAATAAAAATAAAAA
21141898 A
1 A
21141899 TTATATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (21 bp):
AAAAAGAAATAAAAATAAAAA
Found at i:21143720 original size:16 final size:18
Alignment explanation
Indices: 21143698--21143739 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
21143688 GATAGCTCTT
21143698 TCTCTCTC-CCACCC-TTC
1 TCTCTCTCACC-CCCATTC
21143715 -CTCTCTCACCCCCATTC
1 TCTCTCTCACCCCCATTC
21143732 TCTCTCTC
1 TCTCTCTC
21143740 TCTCTGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.07, C:0.57, G:0.00, T:0.36
Consensus pattern (18 bp):
TCTCTCTCACCCCCATTC
Found at i:21157002 original size:2 final size:2
Alignment explanation
Indices: 21156995--21157042 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
21156985 TGCTTGATCA
21156995 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
21157037 AT AT AT
1 AT AT AT
21157043 CTGATCAGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21179900 original size:17 final size:17
Alignment explanation
Indices: 21179880--21179916 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
21179870 TGTTCTTTAC
21179880 TTCTTTTCTTTCC-TTTT
1 TTCTTTT-TTTCCATTTT
21179897 TTC-TTTTTTCCATTTT
1 TTCTTTTTTTCCATTTT
21179913 TTCT
1 TTCT
21179917 CCCTTTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
15 5 0.28
16 10 0.56
17 3 0.17
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTTTTTCCATTTT
Found at i:21209443 original size:12 final size:13
Alignment explanation
Indices: 21209426--21209454 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
21209416 GGTTTCTACC
21209426 CATTAAAACA-TA
1 CATTAAAACATTA
21209438 CATTAAAACATTA
1 CATTAAAACATTA
21209451 CATT
1 CATT
21209455 TCATCATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.52, C:0.17, G:0.00, T:0.31
Consensus pattern (13 bp):
CATTAAAACATTA
Found at i:21210544 original size:88 final size:88
Alignment explanation
Indices: 21210399--21210572 Score: 330
Period size: 88 Copynumber: 2.0 Consensus size: 88
21210389 TACAGGCGTA
*
21210399 TATTATTATTATTATTTAAGAACTATAGGTATAATAAAATTCTTCATTTACTTGTATTAGTACTT
1 TATTATTATTATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTT
21210464 TAAGCTAGTCATGTTCTATTTAT
66 TAAGCTAGTCATGTTCTATTTAT
*
21210487 TATTATTATTATTATTTAAGAACTATAGGTACAATAAAATTCTTCCTTTACTTGTATTAGTACTT
1 TATTATTATTATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTT
21210552 TAAGCTAGTCATGTTCTATTT
66 TAAGCTAGTCATGTTCTATTT
21210573 TGGAATATAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 84 1.00
ACGTcount: A:0.32, C:0.10, G:0.09, T:0.48
Consensus pattern (88 bp):
TATTATTATTATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTT
TAAGCTAGTCATGTTCTATTTAT
Found at i:21210591 original size:88 final size:88
Alignment explanation
Indices: 21210409--21210591 Score: 280
Period size: 88 Copynumber: 2.1 Consensus size: 88
21210399 TATTATTATT
*
21210409 ATTATTTAAGAACTATAGGTATAATAAAATTCTTCATTTACTTGTATTAGTACTTTAAGCTAGTC
1 ATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTTTAAGCTAGTC
* * **
21210474 ATGTTCTATTTATTATTATTATT
66 ATGTTCTATTTATGAATATTAAC
*
21210497 ATTATTTAAGAACTATAGGTACAATAAAATTCTTCCTTTACTTGTATTAGTACTTTAAGCTAGTC
1 ATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTTTAAGCTAGTC
21210562 ATGTTCTATTT-TGGAATA-TAAC
66 ATGTTCTATTTAT-GAATATTAAC
21210584 ATCTATTT
1 AT-TATTT
21210592 TATTTAAATC
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 5 0.06
88 82 0.94
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (88 bp):
ATTATTTAAGAACTATAGGTACAATAAAATTCTTCATTTACTTGTATTAGTACTTTAAGCTAGTC
ATGTTCTATTTATGAATATTAAC
Done.