Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 51
Found at i:600388 original size:32 final size:32
Alignment explanation
Indices: 600347--600408 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
600337 GAAGAAATGA
*
600347 TTGTTATGCTCATCTTGTAGAGATACTTCTCG
1 TTGTTATGCTCATCTGGTAGAGATACTTCTCG
600379 TTGTTATGCTCATCTGGTAGAGATACTTCT
1 TTGTTATGCTCATCTGGTAGAGATACTTCT
600409 TGTGTCTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.18, G:0.19, T:0.44
Consensus pattern (32 bp):
TTGTTATGCTCATCTGGTAGAGATACTTCTCG
Found at i:600921 original size:8 final size:8
Alignment explanation
Indices: 600908--600955 Score: 51
Period size: 8 Copynumber: 5.4 Consensus size: 8
600898 CTTGGTTCAA
600908 TTTTTTCT
1 TTTTTTCT
600916 TTTTTTCCCT
1 TTTTTT--CT
600926 TTTTTTCT
1 TTTTTTCT
600934 TTTTTTCT
1 TTTTTTCT
600942 CCTTTTTTCCT
1 --TTTTTT-CT
600953 TTT
1 TTT
600956 GTTTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
8 16 0.46
9 3 0.09
10 14 0.40
11 2 0.06
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCT
Found at i:600931 original size:18 final size:19
Alignment explanation
Indices: 600908--600955 Score: 80
Period size: 18 Copynumber: 2.6 Consensus size: 19
600898 CTTGGTTCAA
600908 TTTTTTCTTTTTTTC-CCT
1 TTTTTTCTTTTTTTCTCCT
600926 TTTTTTCTTTTTTTCTCCT
1 TTTTTTCTTTTTTTCTCCT
*
600945 TTTTTCCTTTT
1 TTTTTTCTTTT
600956 GTTTTTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTCTTTTTTTCTCCT
Found at i:603729 original size:14 final size:14
Alignment explanation
Indices: 603710--603793 Score: 52
Period size: 14 Copynumber: 6.2 Consensus size: 14
603700 AAATGTAATT
603710 ATGTAAAAATGAAA
1 ATGTAAAAATGAAA
603724 ATGT--AAAT-ACAA
1 ATGTAAAAATGA-AA
*
603736 ACGTAAAAAATGAAA
1 ATGT-AAAAATGAAA
*
603751 ATGT--AAATGCAA
1 ATGTAAAAATGAAA
* **
603763 ATGTAAATATGTGA
1 ATGTAAAAATGAAA
* *
603777 ATGTAACAATAAAA
1 ATGTAAAAATGAAA
603791 ATG
1 ATG
603794 CAAATTGTAT
Statistics
Matches: 52, Mismatches: 11, Indels: 14
0.68 0.14 0.18
Matches are distributed among these distances:
11 1 0.02
12 20 0.38
14 21 0.40
15 9 0.17
16 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.14, T:0.24
Consensus pattern (14 bp):
ATGTAAAAATGAAA
Found at i:603744 original size:27 final size:27
Alignment explanation
Indices: 603714--603769 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
603704 GTAATTATGT
603714 AAAAATGAAAATGTAAATACAAACGTA
1 AAAAATGAAAATGTAAATACAAACGTA
* *
603741 AAAAATGAAAATGTAAATGCAAATGTA
1 AAAAATGAAAATGTAAATACAAACGTA
603768 AA
1 AA
603770 TATGTGAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.62, C:0.05, G:0.12, T:0.20
Consensus pattern (27 bp):
AAAAATGAAAATGTAAATACAAACGTA
Found at i:603863 original size:7 final size:7
Alignment explanation
Indices: 603829--603870 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
603819 ATAAAAGTAT
603829 AAATGCA
1 AAATGCA
* *
603836 CAATGAA
1 AAATGCA
603843 AAATGCA
1 AAATGCA
603850 AAGATGCA
1 AA-ATGCA
603858 AAATGC-
1 AAATGCA
603864 AAATGCA
1 AAATGCA
603871 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 6 0.21
7 16 0.55
8 7 0.24
ACGTcount: A:0.55, C:0.14, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:606223 original size:11 final size:12
Alignment explanation
Indices: 606209--606249 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
606199 GCTTAAAATA
606209 AAAATAATAA-T
1 AAAATAATAATT
606220 AAAATAATAATT
1 AAAATAATAATT
**
606232 AAAGCAATAATT
1 AAAATAATAATT
606244 AAAATA
1 AAAATA
606250 TAAAAGTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:606228 original size:20 final size:21
Alignment explanation
Indices: 606205--606261 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
606195 ATATGCTTAA
606205 AATAAAAATAATAA-TAAAAT
1 AATAAAAATAATAATTAAAAT
*
606225 AATAATTAAAGCAATAATTAAAAT
1 AATAA--AAA-TAATAATTAAAAT
*
606249 -ATAAAAGTAATAA
1 AATAAAAATAATAA
606262 AATAACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
20 10 0.33
21 2 0.07
22 3 0.10
23 9 0.30
24 6 0.20
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
AATAAAAATAATAATTAAAAT
Found at i:606282 original size:41 final size:41
Alignment explanation
Indices: 606201--606283 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
606191 TTAAATATGC
* *
606201 TTAAAATAAAAATAATAATAAAATAATAATTAAAGCAATAA
1 TTAAAATAAAAATAATAATAAAATAACAATTAAAGAAATAA
* * * *
606242 TTAAAATATAAA-AGTAATAAAATAACATTTCAAATAAATAA
1 TTAAAATAAAAATAATAATAAAATAACAATT-AAAGAAATAA
606283 T
1 T
606284 GATTAAAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
40 15 0.43
41 20 0.57
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (41 bp):
TTAAAATAAAAATAATAATAAAATAACAATTAAAGAAATAA
Found at i:607652 original size:3 final size:3
Alignment explanation
Indices: 607644--607694 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
607634 ATTTATTTAT
* * *
607644 ATA ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA ATA AAA ACA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
607690 ATA AT
1 ATA AT
607695 TTTAATTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:614788 original size:20 final size:20
Alignment explanation
Indices: 614763--614831 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
614753 CAACAACAAA
614763 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
614783 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
614803 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
614823 ATCGCAACG
1 ATCGCAACG
614832 AAAGAATCGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:614841 original size:34 final size:34
Alignment explanation
Indices: 614749--614850 Score: 89
Period size: 40 Copynumber: 2.8 Consensus size: 34
614739 CAACGAGAAA
* *
614749 ATCGCAAC-AACAAAATCGCAACGCGAAAATGACT
1 ATCGCAACGAA-AGAATCGCAATGCGAAAATGACT
**
614783 ATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACT
1 ATCGCAA--CG-AAA-GA--ATCGCAATGCGAAAATGACT
*
614823 ATCGCAACGAAAGAATCGCAATACGAAA
1 ATCGCAACGAAAGAATCGCAATGCGAAA
614851 TGAAAATCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
34 19 0.35
36 3 0.05
37 4 0.07
38 5 0.09
40 24 0.44
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.17
Consensus pattern (34 bp):
ATCGCAACGAAAGAATCGCAATGCGAAAATGACT
Found at i:617069 original size:33 final size:33
Alignment explanation
Indices: 617005--617232 Score: 189
Period size: 33 Copynumber: 6.8 Consensus size: 33
616995 TCGCAACTCG
617005 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* *
617039 CGTTGCGATTTTCATTTCGCATTACTATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** * *
617072 CGTTGCGATAGTCATTTCCGCGTTGCGATAGTCTGT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT--TCTCT
* ** * *
617108 -TTTGC-ATTCAACATAATGTAG-ATT-C-AGTT-TCG
1 CGTTGCGATT-TTCAT--T-TCGCATTGCGA-TTCTCT
617140 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
617174 CGTTGCAATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
**
617207 CGTTGCGATAGTCATTTCCGCATTGC
1 CGTTGCGATTTTCATTT-CGCATTGC
617233 TATAGTCAAA
Statistics
Matches: 153, Mismatches: 25, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
31 2 0.01
32 5 0.03
33 75 0.49
34 53 0.35
35 9 0.06
36 6 0.04
37 2 0.01
38 1 0.01
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:617158 original size:20 final size:20
Alignment explanation
Indices: 617130--617169 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
617120 ATAATGTAGA
*
617130 TTCAGTTTCGCGTTGCGATT
1 TTCAGTTTCGCATTGCGATT
*
617150 TTCATTTTCGCATTGCGATT
1 TTCAGTTTCGCATTGCGATT
617170 CTCTCGTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.20, G:0.20, T:0.47
Consensus pattern (20 bp):
TTCAGTTTCGCATTGCGATT
Found at i:619681 original size:24 final size:24
Alignment explanation
Indices: 619654--619707 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
619644 TTGAAAAATC
619654 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
619678 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
619702 ATCAAA
1 ATCAAA
619708 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:619721 original size:24 final size:24
Alignment explanation
Indices: 619654--619721 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
619644 TTGAAAAATC
* * *
619654 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
619678 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
619702 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
619722 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:620574 original size:20 final size:20
Alignment explanation
Indices: 620549--620647 Score: 128
Period size: 20 Copynumber: 5.0 Consensus size: 20
620539 AAATTCAGTA
*
620549 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGATTCGCG
* *
620569 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGATTCGCG
620589 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGATTCGCG
* * *
620609 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CAGATTCGCG
620629 TTGCGATAGTCAGATTCGC
1 TTGCGATAGTCAGATTCGC
620648 ATTACGATTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
19 1 0.01
20 67 0.97
21 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGATTCGCG
Found at i:620633 original size:40 final size:40
Alignment explanation
Indices: 620548--620674 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 40
620538 GAAATTCAGT
* * * * *
620548 ATTGCGATAGTCAGAATCGCGTTGCGATAGT-CAGAATCTC
1 ATTGCGATAGTCAGATTCGCGTTGCGAT-TTACATATTCGC
*
620588 GTTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGC
1 ATTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGC
* * *
620628 ATTGCGATAGTCAGATTCGCATTACGATTTACGTATTCGC
1 ATTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGC
620668 ATTGCGA
1 ATTGCGA
620675 ATTAGGAAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 75 0.99
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (40 bp):
ATTGCGATAGTCAGATTCGCGTTGCGATTTACATATTCGC
Found at i:620665 original size:20 final size:20
Alignment explanation
Indices: 620602--620674 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
620592 CGATAGTCAG
* *
620602 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
620622 ATTCGCATTGCGATAGT-CAG-
1 ATTCGCATTGCGAT-TTAC-GT
*
620642 ATTCGCATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
620662 ATTCGCATTGCGA
1 ATTCGCATTGCGA
620675 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.05
20 40 0.93
21 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:620695 original size:21 final size:21
Alignment explanation
Indices: 620671--620716 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
620661 TATTCGCATT
620671 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
620692 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
620713 GCGA
1 GCGA
620717 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:621044 original size:20 final size:20
Alignment explanation
Indices: 621024--621204 Score: 178
Period size: 20 Copynumber: 9.4 Consensus size: 20
621014 GAAACTTAAA
**
621024 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGACT
621044 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
621064 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
621084 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* ** **
621104 ATTGCAATGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
621124 ATCGC-A-ACG-CAA-GA--
1 ATCGCAACACGAAAATGACT
* **
621138 ATCGCAACGC-AAAATGAAA
1 ATCGCAACACGAAAATGACT
621157 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* ** *
621177 ATCGCAACGCGAATTTGATT
1 ATCGCAACACGAAAATGACT
621197 ATCGCAAC
1 ATCGCAAC
621205 GCAAGAATCG
Statistics
Matches: 133, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
14 5 0.04
15 1 0.01
16 5 0.04
17 2 0.02
18 2 0.02
19 10 0.08
20 108 0.81
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:621079 original size:40 final size:40
Alignment explanation
Indices: 621024--621237 Score: 186
Period size: 40 Copynumber: 5.7 Consensus size: 40
621014 GAAACTTAAA
*
621024 ATCGCAACACGAAAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
* **
621064 ATCGCAACACGAAAATGACTATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
* * ** ** *
621104 ATTGCAATGCGAATTTGACTATCGC-A-ACG-CAA-GA--
1 ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
621138 ATCGCAACGC-AAAATGAAAATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
** ** *
621177 ATCGCAACGCGAATTTGATTATCGC-A-ACG-CAA-GA--
1 ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
621211 ATCGCAACGC-AAAATGAAAATCGCAAC
1 ATCGCAACGCGAAAATGAAAATCGCAAC
621238 GACAGAATCG
Statistics
Matches: 141, Mismatches: 24, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
33 20 0.14
34 20 0.14
35 3 0.02
36 6 0.04
37 6 0.04
38 6 0.04
39 12 0.09
40 68 0.48
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (40 bp):
ATCGCAACGCGAAAATGAAAATCGCAACACGAAAATGACT
Found at i:621162 original size:73 final size:73
Alignment explanation
Indices: 621064--621237 Score: 285
Period size: 73 Copynumber: 2.4 Consensus size: 73
621054 GAAAATGACT
* ** * *
621064 ATCGCAACACGAAAATGACTATCGCAACACGAAAATGACTATTGCAATGCGAATTTGACTATCGC
1 ATCGCAACGC-AAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGC
621129 AACGCAAGA
65 AACGCAAGA
*
621138 ATCGCAACGCAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGATTATCGCA
1 ATCGCAACGCAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCA
621203 ACGCAAGA
66 ACGCAAGA
621211 ATCGCAACGCAAAATGAAAATCGCAAC
1 ATCGCAACGCAAAATGAAAATCGCAAC
621238 GACAGAATCG
Statistics
Matches: 94, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 85 0.90
74 9 0.10
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.17
Consensus pattern (73 bp):
ATCGCAACGCAAAATGAAAATCGCAACACGAAAATGACTATCGCAACGCGAATTTGACTATCGCA
ACGCAAGA
Found at i:621636 original size:22 final size:22
Alignment explanation
Indices: 621574--621639 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
621564 TGACCGTGAA
* *
621574 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
* *
621596 TGATATCGTCGGAGATGGGGAT
1 TGATTTCGTCGGAGATGGGGAC
621618 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
621640 GGATGTCGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.21, C:0.14, G:0.39, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:621870 original size:21 final size:21
Alignment explanation
Indices: 621846--621888 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
621836 TCGCATTGCA
621846 AATTAGGAAAATCGCAACGCG
1 AATTAGGAAAATCGCAACGCG
* *
621867 AATTTGGAAAATCGCAATGCG
1 AATTAGGAAAATCGCAACGCG
621888 A
1 A
621889 TAGTCAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (21 bp):
AATTAGGAAAATCGCAACGCG
Found at i:622893 original size:112 final size:113
Alignment explanation
Indices: 622682--623155 Score: 706
Period size: 112 Copynumber: 4.2 Consensus size: 113
622672 AAATTTCAAC
* * ** * *
622682 AAAGTATCGATACATTTTTATAAAAAGTATATATAATTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATACCTTTTTATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGT
* * *
622747 TTTTTCATAATGAAACTGGTTTTGGCATATTTTTACCTATTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
*
622795 AAAGTATTGAT-CCTTTTTATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGT
1 AAAGTATCGATACCTTTTTATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGT
* *
622859 TTTGTCATAACGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * * *
622907 AAAGTATCGAT-TCTTTTTATAAAAATGATCGATACTTTCAACATATTAGATAAATTTTACCGGT
1 AAAGTATCGATACCTTTTTATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGT
* *
622971 TTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGT
66 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
623019 AAAGTAAT-GATACATTTTTATAAAAAGGATCAATACTTTCAACATATCAA-GTAAATTTTACCG
1 AAAGT-ATCGATACCTTTTTATAAAAAGGATCGATACTTTCAACATAT-AAGGTAAATTTTACCG
623082 GTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
64 GTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
623132 AAAGTATCGATACAC-TTTTATAAA
1 AAAGTATCGATAC-CTTTTTATAAA
623156 GTATCGATAC
Statistics
Matches: 326, Mismatches: 30, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
112 203 0.62
113 122 0.37
114 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (113 bp):
AAAGTATCGATACCTTTTTATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGT
TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:623092 original size:225 final size:225
Alignment explanation
Indices: 622682--623155 Score: 756
Period size: 225 Copynumber: 2.1 Consensus size: 225
622672 AAATTTCAAC
* *
622682 AAAGTATCGATACATTTTTATAAAAAGTATATATAATTTCAACATATTAGGTAAATTTTACCGGT
1 AAAGTATCGATACATTTTTATAAAAAGTATAGATAATTTCAACATATTAGATAAATTTTACCGGT
* * * * *
622747 TTTTTCATAATGAAACTGGTTTTGGCATATTTTTACCTATTATATTGTAAAGTATTGATCCTTTT
66 TTTGTCATAATGAAACTGATTTTGGCATACTTTTACCTATTATATTGTAAAGTAATGATCATTTT
*
622812 TATAAAAAGGATCGATACTTTCAACATATAAGGTAAATTTTACCGGTTTTGTCATAACGAAACTG
131 TATAAAAAGGATCAATACTTTCAACATATAAGGTAAATTTTACCGGTTTTGTCATAACGAAACTG
622877 GTTTTGTCATATTTTTACATGTTATATTGT
196 GTTTTGTCATATTTTTACATGTTATATTGT
* * *
622907 AAAGTATCGATTC-TTTTTATAAAAA-TGATCGATACTTTCAACATATTAGATAAATTTTACCGG
1 AAAGTATCGATACATTTTTATAAAAAGT-ATAGATAATTTCAACATATTAGATAAATTTTACCGG
* *
622970 TTTTGTCATAATGAAACTGATTTTGTCATACTTTTACCTGTTATATTGTAAAGTAATGATACATT
65 TTTTGTCATAATGAAACTGATTTTGGCATACTTTTACCTATTATATTGTAAAGTAATGAT-CATT
*
623035 TTTATAAAAAGGATCAATACTTTCAACATATCAA-GTAAATTTTACCGGTTTTGTCATAATGAAA
129 TTTATAAAAAGGATCAATACTTTCAACATAT-AAGGTAAATTTTACCGGTTTTGTCATAACGAAA
*
623099 CTGGTTTTGTCATATTTTTACCTGTTATATTGT
193 CTGGTTTTGTCATATTTTTACATGTTATATTGT
*
623132 AAAGTATCGATACACTTTTATAAA
1 AAAGTATCGATACATTTTTATAAA
623156 GTATCGATAC
Statistics
Matches: 228, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
223 1 0.00
224 98 0.43
225 118 0.52
226 11 0.05
ACGTcount: A:0.34, C:0.11, G:0.12, T:0.42
Consensus pattern (225 bp):
AAAGTATCGATACATTTTTATAAAAAGTATAGATAATTTCAACATATTAGATAAATTTTACCGGT
TTTGTCATAATGAAACTGATTTTGGCATACTTTTACCTATTATATTGTAAAGTAATGATCATTTT
TATAAAAAGGATCAATACTTTCAACATATAAGGTAAATTTTACCGGTTTTGTCATAACGAAACTG
GTTTTGTCATATTTTTACATGTTATATTGT
Found at i:623439 original size:21 final size:23
Alignment explanation
Indices: 623412--623461 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
623402 ACCTATTTTA
*
623412 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
*
623435 TTATATAAGCGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
623458 TTAT
1 TTAT
623462 TGTGCTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:623542 original size:87 final size:87
Alignment explanation
Indices: 623394--623602 Score: 312
Period size: 87 Copynumber: 2.4 Consensus size: 87
623384 CAACAAATTA
* * * *
623394 AATAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGT
1 AATAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAGCGATACATAATATGT
*
623459 TATTGTGCTTGATAATGTTTCC
66 TATTGTGCTTAATAATGTTTCC
* *
623481 AGTAATTAACCTATTTTATTATATAAATGCTACCTATTACATTATATAA-CAGATACATAATATG
1 AATAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAGC-GATACATAATATG
*
623545 TTATTGTGTTTAATAATGTTTCC
65 TTATTGTGCTTAATAATGTTTCC
* *
623568 AATAATTAACCTATTTTATTATATAAGCACTACCT
1 AATAATTAACCTATTTTATTATATAAACGCTACCT
623603 CTGTGGAAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
86 1 0.01
87 108 0.99
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (87 bp):
AATAATTAACCTATTTTATTATATAAACGCTACCTATTACATTATATAAGCGATACATAATATGT
TATTGTGCTTAATAATGTTTCC
Found at i:624129 original size:112 final size:112
Alignment explanation
Indices: 623919--624516 Score: 925
Period size: 112 Copynumber: 5.3 Consensus size: 112
623909 AACTTTTAAC
* ** * * *
623919 AAAGTATCGATACATTTTTATTAAAAAGTATATATACTTTCAACATATCAAGTAATTTTTACCGA
1 AAAGTATCGAT-CATTTTTA-TAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGG
623984 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
64 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
*
624033 AAAGTATCGATCATTTTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTT
1 AAAGTATCGATCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* *
624098 TTGTCATAATGAAACTGGTTTAGTCATATTTTTACCTGTAATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * **
624145 AAAGTATCGATCCTTTTTATAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCTATT
1 AAAGTATCGATCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
* *
624210 CTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* * *
624257 AAAATATCGAT-ACTTTTTATTAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACC-GT
1 AAAGTATCGATCA-TTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGT
* *
624320 TTTGTCATAATGAAACTGATTTTGTCATATTTTTACATGTTATATTGT
65 TTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
*
624368 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
1 AAAGTATCGATCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
624433 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
* *
624480 AAAGTATCGAT-ATATTTT-TATAAAGTATCGATACTTT
1 AAAGTATCGATCAT-TTTTATAAAAAGGATCGATACTTT
624517 ATAGGCGCTA
Statistics
Matches: 445, Mismatches: 35, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
111 121 0.27
112 305 0.69
113 8 0.02
114 11 0.02
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (112 bp):
AAAGTATCGATCATTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGT
Found at i:624440 original size:223 final size:224
Alignment explanation
Indices: 623919--624516 Score: 970
Period size: 223 Copynumber: 2.7 Consensus size: 224
623909 AACTTTTAAC
* * * * *
623919 AAAGTATCGATACATTTTTATTAAAAAGTATATATACTTTCAACATATCAAGTAATTTTTACCGA
1 AAAGTATCGAT-CCTTTTTA-TAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCGA
623984 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGAT-CATT
64 TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATAC-TT
*
624048 TTTATAAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAAC
128 TTTATTAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAAC
* *
624113 TGGTTTAGTCATATTTTTACCTGTAATATTGT
193 TGATTTAGTCATATTTTTACATGTAATATTGT
*
624145 AAAGTATCGATCCTTTTTATAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCTATT
1 AAAGTATCGATCCTTTTTATAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCGATT
* * *
624210 CTGTCATAATGAAACTGGTTTTGTCATATTTTTACATGTTATATTGTAAAATATCGATACTTTTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACTTTTT
624275 ATTAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACC-GTTTTGTCATAATGAAACTGA
131 ATTAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGA
* *
624339 TTTTGTCATATTTTTACATGTTATATTGT
196 TTTAGTCATATTTTTACATGTAATATTGT
* *
624368 AAAGTATCGATCCTTTTTATAAAAAGGATCGATACTTTCAACATATCAGGTAAATTTTACCGGTT
1 AAAGTATCGATCCTTTTTATAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCGATT
*
624433 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATA-TATTT
66 TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACTTTTT
*
624497 -TTATAAAGTATCGATACTTT
131 ATTA-AAAGGATCGATACTTT
624517 ATAGGCGCTA
Statistics
Matches: 348, Mismatches: 22, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
221 3 0.01
222 19 0.05
223 164 0.47
224 143 0.41
225 8 0.02
226 11 0.03
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.43
Consensus pattern (224 bp):
AAAGTATCGATCCTTTTTATAAAAAGGATAGATACTTTCAACATATCAGGTAAATTTTACCGATT
TTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGTTATATTGTAAAGTATCGATACTTTTT
ATTAAAAGGATCGATACTTTCAACATATTAGGTAAATTTTACCGGTTTTGTCATAATGAAACTGA
TTTAGTCATATTTTTACATGTAATATTGT
Found at i:624832 original size:23 final size:23
Alignment explanation
Indices: 624760--624820 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
624750 ACATGTTTTA
624760 TTATATAAGCGCTACCTATTGCG
1 TTATATAAGCGCTACCTATTGCG
*
624783 TTATATAAACGCTACCTATTGCG
1 TTATATAAGCGCTACCTATTGCG
624806 TTATATAAGCGCTAC
1 TTATATAAGCGCTAC
624821 GTAATATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (23 bp):
TTATATAAGCGCTACCTATTGCG
Found at i:624895 original size:23 final size:23
Alignment explanation
Indices: 624860--624910 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
624850 CGAGTAATTA
**
624860 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
624883 ACCTATTACATTATATAAGTGGT
1 ACCTATTACATTATATAAGCGCT
624906 ACCTA
1 ACCTA
624911 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:624982 original size:23 final size:23
Alignment explanation
Indices: 624947--624997 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
624937 CCAGTAATTA
**
624947 ACCTATTTTATTATATAAACGCT
1 ACCTATTACATTATATAAACGCT
* *
624970 ACCTATTACATTATATAAGCGGT
1 ACCTATTACATTATATAAACGCT
624993 ACCTA
1 ACCTA
624998 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.08, T:0.37
Consensus pattern (23 bp):
ACCTATTACATTATATAAACGCT
Found at i:625025 original size:87 final size:87
Alignment explanation
Indices: 624783--625010 Score: 393
Period size: 87 Copynumber: 2.6 Consensus size: 87
624773 ACCTATTGCG
* * * *
624783 TTATATAAACGCTACCTATTGCGTTATATAAGCGCTACGTAATATGTTATTGTGTTTGATAATGT
1 TTATATAAACGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGTTTGATAATGT
*
624848 TTCGAGTAATTAACCTATTTTA
66 TTCCAGTAATTAACCTATTTTA
* *
624870 TTATATAAGCGCTACCTATTACATTATATAAGTGGTACCTAATATGTTATTGTGTTTGATAATGT
1 TTATATAAACGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGTTTGATAATGT
624935 TTCCAGTAATTAACCTATTTTA
66 TTCCAGTAATTAACCTATTTTA
624957 TTATATAAACGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTG
1 TTATATAAACGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTG
625011 CTCAATAATA
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 132 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (87 bp):
TTATATAAACGCTACCTATTACATTATATAAGCGGTACCTAATATGTTATTGTGTTTGATAATGT
TTCCAGTAATTAACCTATTTTA
Found at i:627830 original size:2 final size:2
Alignment explanation
Indices: 627823--627886 Score: 112
Period size: 2 Copynumber: 32.0 Consensus size: 2
627813 ATAATATAAT
627823 TA TA TA TA TA TA TA T- TA TGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
627865 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
627887 CACACTTATA
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:637125 original size:24 final size:24
Alignment explanation
Indices: 637098--637153 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
637088 CTATTTTTTC
637098 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
637122 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
637146 GCTTCAAT
1 GCTTCAAT
637154 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:638855 original size:38 final size:38
Alignment explanation
Indices: 638783--638858 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
638773 TAGATTTTTC
*
638783 ATTCTCAGTTCTTAAATTATTTTACACTAGTATTCTAA
1 ATTCTCAGTTCTTAAATTATTTAACACTAGTATTCTAA
*
638821 ATTCTTAGTTTCTTAAATTATTTAATCA-TA-TATTCTAA
1 ATTCTCAG-TTCTTAAATTATTTAA-CACTAGTATTCTAA
638859 GTTATTTCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 15 0.44
39 17 0.50
40 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (38 bp):
ATTCTCAGTTCTTAAATTATTTAACACTAGTATTCTAA
Found at i:639011 original size:18 final size:18
Alignment explanation
Indices: 638970--639012 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
638960 TGTAATTTAA
*
638970 ATTTTTAAATTTTAATAT
1 ATTTTTAAAATTTAATAT
* * *
638988 ACTTTTAAAATTTATTGT
1 ATTTTTAAAATTTAATAT
639006 ATTTTTA
1 ATTTTTA
639013 TGTGACTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (18 bp):
ATTTTTAAAATTTAATAT
Found at i:639244 original size:6 final size:6
Alignment explanation
Indices: 639233--639263 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
639223 ATCACCAATC
639233 ATAATT ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT ATAATT A
639264 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:639278 original size:22 final size:24
Alignment explanation
Indices: 639239--639305 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 24
639229 AATCATAATT
*
639239 ATAATTATAATTATAATTATAATT-A
1 ATAAATATAA-TA-AATTATAATTAA
639264 ATAAATA-AATAAATTAT--TTAA
1 ATAAATATAATAAATTATAATTAA
*
639285 ATAAATATAATAAGTT-TAATT
1 ATAAATATAATAAATTATAATT
639306 TCAAGAGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
20 2 0.06
21 9 0.25
22 13 0.36
23 4 0.11
24 2 0.06
25 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (24 bp):
ATAAATATAATAAATTATAATTAA
Found at i:639364 original size:30 final size:33
Alignment explanation
Indices: 639330--639399 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 33
639320 TTTAATTAGA
*
639330 AAAATTTTATAAAA-AAGAAT-TAAATTGA-TT
1 AAAATTTAATAAAATAAGAATGTAAATTGATTT
*
639360 AAAA--TAATAAAATGAGAATGTAAATTGATTT
1 AAAATTTAATAAAATAAGAATGTAAATTGATTT
639391 AAAATTTAA
1 AAAATTTAA
639400 GGTTAATCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 7 0.21
29 5 0.15
30 12 0.36
31 6 0.18
33 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (33 bp):
AAAATTTAATAAAATAAGAATGTAAATTGATTT
Found at i:640108 original size:183 final size:182
Alignment explanation
Indices: 639908--640325 Score: 586
Period size: 183 Copynumber: 2.3 Consensus size: 182
639898 GATACAAATA
* * * * *
639908 AAAAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATAACC
1 AAAAATGTATTGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCAAAATAACA
* * *
639973 AAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATATTTTAATATAAGCATCGACACTTT
66 AAACCAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGCATCGACACTTT
* *
640038 TGGAATTTAAAAGAGAATCAATAACAAACGCCTATAAAGTGTCGATACTTTAT
131 TGGAATTTAAAAGACAAGCAATAA-AAACGCCTATAAAGTGTCGATACTTTAT
* * *
640091 AAAAATGTATTGATCCATAACAATATAATAGGTAAAAATATGATAAAACTGGTCTCAAAATGACA
1 AAAAATGTATTGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCAAAATAACA
** * *
640156 AAATTAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
66 AAACCAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGCATCGACACTTT
* * ** *
640221 TGGAATTTAAAAGACAAGCAGTAATAGTGCCTATAAAGTGTTGATACTTTAT
131 TGGAATTTAAAAGACAAGCAATAAAAACGCCTATAAAGTGTCGATACTTTAT
* * *
640273 AAAAATGTA-TCAACACTTAACAATATAATAGGTAAAAATATGACAAAACCGGT
1 AAAAATGTATTGATC-CATAACAATATAATAGGTAAAAATATGACAAAACCGGT
640326 AAAGCGCTAC
Statistics
Matches: 207, Mismatches: 27, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
181 3 0.01
182 68 0.33
183 136 0.66
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAAATGTATTGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTCTCAAAATAACA
AAACCAGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTAATATAAGCATCGACACTTT
TGGAATTTAAAAGACAAGCAATAAAAACGCCTATAAAGTGTCGATACTTTAT
Found at i:640420 original size:162 final size:162
Alignment explanation
Indices: 640162--640487 Score: 562
Period size: 162 Copynumber: 2.0 Consensus size: 162
640152 GACAAAATTA
* *
640162 GTAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTTTGGAAT
1 GTAAAGAGCTACCGGATATGTTGAAAGTATAGATACTTTATTATAAGTATCGACACTTTTGGAAT
* *
640227 TTAAAAGACAAGCAGTAATAGTGCCTATAAAGTGTTGATACTTTATAAAAATGTATCAACACTTA
66 TTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCAACACTTA
640292 ACAATATAATAGGTAAAAATATGACAAAACCG
131 ACAATATAATAGGTAAAAATATGACAAAACCG
* * *
640324 GTAAAGCGCTACTGGATATGTTGAAAGTATAGATACTTTATTATATGTATCGACACTTTTGGAAT
1 GTAAAGAGCTACCGGATATGTTGAAAGTATAGATACTTTATTATAAGTATCGACACTTTTGGAAT
* *
640389 TTAAAAGACAAGCAGTAATAGCGCTTATAAAGTGTCGATACTTTATAAAAATGTATCGACACTTA
66 TTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCAACACTTA
*
640454 ACAATATAATAGGTAAAAATATGATAAAACCG
131 ACAATATAATAGGTAAAAATATGACAAAACCG
640486 GT
1 GT
640488 CTCGAAATGA
Statistics
Matches: 154, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 154 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (162 bp):
GTAAAGAGCTACCGGATATGTTGAAAGTATAGATACTTTATTATAAGTATCGACACTTTTGGAAT
TTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTATAAAAATGTATCAACACTTA
ACAATATAATAGGTAAAAATATGACAAAACCG
Found at i:641897 original size:16 final size:16
Alignment explanation
Indices: 641876--641907 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
641866 ATGTAGGAAG
*
641876 TTCACCGACTGTGAGA
1 TTCACCGACTATGAGA
641892 TTCACCGACTATGAGA
1 TTCACCGACTATGAGA
641908 AGGTAAGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (16 bp):
TTCACCGACTATGAGA
Found at i:643591 original size:2 final size:2
Alignment explanation
Indices: 643584--643613 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
643574 ATTTAAACAA
*
643584 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
643614 GACTAATATG
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:644942 original size:3 final size:3
Alignment explanation
Indices: 644936--644960 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
644926 GTTATTTTTT
644936 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
644961 GAAAAAATTA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:645328 original size:45 final size:45
Alignment explanation
Indices: 645276--645715 Score: 763
Period size: 45 Copynumber: 9.7 Consensus size: 45
645266 CACTATTGGT
*
645276 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGT
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
645321 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
645366 TTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
645411 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
645456 CTTACAGATGACCTGAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
* *
645501 ATTACAGATGACCCAAAGGTTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
*
645546 CTTACAGATGACCCGAAGGCTTTGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
645591 CTTACAGATGACCCGAAGGTTTTGGAAAACATCATGCACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTT-GAAAACATCATGCACTGAAGGG
* * *
645637 TTTACAGATGACCCAAAGGTTTTGGAAAACATCATACACTGAAGGG
1 CTTACAGATGACCCGAAGGTTTT-GAAAACATCATGCACTGAAGGG
* *
645683 CTTATAGATGACCTGAAGGTTTTGAAAACATCA
1 CTTACAGATGACCCGAAGGTTTTGAAAACATCA
645716 AAAAGCTCCC
Statistics
Matches: 376, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
45 292 0.78
46 84 0.22
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.23
Consensus pattern (45 bp):
CTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGG
Found at i:646574 original size:22 final size:22
Alignment explanation
Indices: 646474--646572 Score: 135
Period size: 22 Copynumber: 4.5 Consensus size: 22
646464 AATAAAGCTT
*
646474 TCATCTTTGAAAAGAGAAACTA
1 TCATCTTTGAAAAGAGAATCTA
* *
646496 TTATCTTTGAAAAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
* *
646518 TCCTCTTTTAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
646540 TCATTTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
646562 TCATCTTTGAA
1 TCATCTTTGAA
646573 GAATGTAGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:648020 original size:74 final size:73
Alignment explanation
Indices: 647927--648154 Score: 206
Period size: 74 Copynumber: 3.1 Consensus size: 73
647917 ATGCCCCAGT
* * * *
647927 ATTTGCTGATATAAACGTTCAAAATGTATCACCATTCTTGATTCTGATTGAAATGGGCTTTCAGC
1 ATTTGCTAATACATACGTTCAAAATGTATCAACATTC-TGATTCTGATTGAAATGGGCTTTCAGC
*
647992 ATGCCCATC
65 ATGCCCAAC
*** * ** *
648001 ATTTGCTAATACATACGTTCAAAATGCGCCAATATTCCAATTTCTGATTGAAATGGGCTTTCATC
1 ATTTGCTAATACATACGTTCAAAATGTATCAACATTCTGA-TTCTGATTGAAATGGGCTTTCAGC
648066 ATGCCCCAAC
65 ATG-CCCAAC
* * ** * * * * *
648076 ATTTGTTGATTTGAT-CTTTCAAAATATATCAACATTCATGTTTCTAATTGAAATAGGCTTTCAG
1 ATTTGCT-AATACATACGTTCAAAATGTATCAACATTC-TGATTCTGATTGAAATGGGCTTTCAG
648140 CATGCCCTAAC
64 CATGCCC-AAC
648151 ATTT
1 ATTT
648155 TCTTCTTGTT
Statistics
Matches: 121, Mismatches: 28, Indels: 9
0.77 0.18 0.06
Matches are distributed among these distances:
73 1 0.01
74 58 0.48
75 58 0.48
76 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (73 bp):
ATTTGCTAATACATACGTTCAAAATGTATCAACATTCTGATTCTGATTGAAATGGGCTTTCAGCA
TGCCCAAC
Found at i:650318 original size:72 final size:72
Alignment explanation
Indices: 650201--650344 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
650191 ATATAATAAT
*
650201 ATAACAAATTAGGTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAGGGGGATAA
1 ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAGGGGGATAA
650266 CTCAAGC
66 CTCAAGC
* * * *
650273 ATAACAGATTAGCTGAATATTATCCATAAAGCCGGGGCTATTAACCAATTTCTTTAGGGGGATAA
1 ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAGGGGGATAA
650338 CTCAAGC
66 CTCAAGC
650345 TTTATTGTAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (72 bp):
ATAACAAATTAGCTGAATATTATCCATAAAGCCGGGACGATTAACCAATTGCTTTAGGGGGATAA
CTCAAGC
Found at i:656891 original size:3 final size:3
Alignment explanation
Indices: 656885--656925 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
656875 TTATTATTTT
*
656885 TAA TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA T
656926 GAAAATATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:656907 original size:19 final size:19
Alignment explanation
Indices: 656883--656920 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
656873 TATTATTATT
656883 TTTAATAATAATAATAATA
1 TTTAATAATAATAATAATA
656902 TTTAATAATAATAATAATA
1 TTTAATAATAATAATAATA
656921 ATAATGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAATAATAATAATAATA
Found at i:657288 original size:18 final size:20
Alignment explanation
Indices: 657268--657304 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
657258 AAATCCATAA
*
657268 TTTT-AATGTAATAAGTAAT
1 TTTTCAATGTAACAAGTAAT
657287 TTTTCAATGTAACAAGTA
1 TTTTCAATGTAACAAGTA
657305 TAAATATACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (20 bp):
TTTTCAATGTAACAAGTAAT
Found at i:657686 original size:200 final size:200
Alignment explanation
Indices: 657216--658761 Score: 1922
Period size: 200 Copynumber: 7.7 Consensus size: 200
657206 GTTAGCAGAT
* * * *
657216 GTGTCGATACAGTTATAAAAAGTATCGATCCCAAAAATATTGAAATCC-ATAATTTTAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAATTATAATGTAAT
* ** * * *
657280 AAGTAATTTTTCAATGTAACAAGTATAAATATACCGATTTTATGAGAGAATGGGTCTACATAATG
65 AGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATG
* ** * * * *
657345 TATCGACACTTGTGGAATTTGTGTCGATACTTTTTTTCTAGAATGAATGCCAAAAAAGGGTGCAT
130 TATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCC-CAAAAGGGTGCAC
*
657410 GTATAAA
194 GCATAAA
* *
657417 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
657482 GGTAATTTTTCAATATAACCGGTATAAATATACCGATTTAATGAGATAATATGTCTATATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATGT
* * **
657547 ATAGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGC
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGC
657612 ATAAA
196 ATAAA
* * * *
657617 GTGTTGATACATTTATAAAAAGTATCGATCTCAAAAACATCGAAACCTATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* ** * *
657682 GGTAATTTTTCAATATAACTAGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATGT
* * * *
657747 ATCGACACTTGTGAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAAGGTACACGC
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGC
*
657812 ATAAC
196 ATAAA
* *
657817 GTGTCGATACATTTATAAAAAGTATTGATCCCAAAAACATCGAAACTGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * *
657882 GGTAAATTTTT-AATGTAACCGGTATAAATATACCGGTTTAATTAGA-AAAACGATCAACATAAT
66 GGT-AATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATA-GGTCTACATAAT
*
657945 GTATCGAAACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCAC
129 GTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCAC
* *
658010 GGATAAC
194 GCATAAA
658017 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * ** * * * *
658082 GGTAA-ATTTCTAATGTAACCGGAATAAATATACCTATTTAATTAGAAAAGAGGTCAACATAATG
66 GGTAATTTTTC-AATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATG
* * * *
658146 TATTGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATCAATGCTC-AACGAGGTGCAC
130 TATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAG-GGTGCAC
*
658210 ACATAAA
194 GCATAAA
* * * *
658217 GTGTTGATATATTTATAAAAAGTATCGATCTCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * *
658282 GGTAAATTTTCAATGTAACCGGTATAAAAATACCGGTTTAATTAGAAAACAGATCTACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATGT
* * *
658347 ATCGACAATTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATG-TCAAACGGGGTGCACG
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAA-AGGGTGCACG
658411 CATAAA
195 CATAAA
* * **
658417 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAATATCGAAATAGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * *
658482 GGTAAATTTTCAATGTAACCAGTAGAAATATACCGGTTTTATGAGAGAATAAGTCAACATAATGT
66 GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATGT
* * * * *
658547 ATCGACACTTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATG-TCAAACGCAGTGCATG
131 ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAG-GGTGCACG
658611 CATAAA
195 CATAAA
* * * * * *
658617 GTGTCAATACATTTATTAACAGTATCAATCCCACAAACATCGAAACCGATAATTACAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * ** * * * * * * *
658682 GATACA-TTTACAATGT-ACTAAGTAGAAATATACTGATTTTATGAGAAAATATGTTTACATAAT
66 GGTA-ATTTTTCAATGTAAC-CGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAAT
* **
658745 ATATAAACACTTTTTAA
129 GTATCGACACTTTTTAA
658762 GATTGTGACT
Statistics
Matches: 1201, Mismatches: 131, Indels: 27
0.88 0.10 0.02
Matches are distributed among these distances:
198 3 0.00
199 13 0.01
200 1009 0.84
201 176 0.15
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (200 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
GGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTAATGAGAGAATAGGTCTACATAATGT
ATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGTGCACGC
ATAAA
Found at i:661148 original size:13 final size:13
Alignment explanation
Indices: 661105--661159 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
661095 CAATTGATAT
661105 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
661118 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
661132 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
661145 TTAAGTATTTGAA
1 TTAAGTATTTCAA
661158 TT
1 TT
661160 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:661398 original size:20 final size:21
Alignment explanation
Indices: 661351--661406 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
661341 TAGAGCGTGG
*
661351 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
661372 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
661393 -GGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
661407 AAGTGTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.29
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:661726 original size:15 final size:17
Alignment explanation
Indices: 661700--661731 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
661690 TTCTATGGGA
661700 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
661716 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
661732 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:661970 original size:23 final size:23
Alignment explanation
Indices: 661935--661982 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
661925 AAATAGGTCA
* *
661935 ATATAAACACTACTTATTATATT
1 ATATAAACACTACCTAATATATT
* *
661958 ATATAAGCGCTACCTAATATATT
1 ATATAAACACTACCTAATATATT
661981 AT
1 AT
661983 TGTACTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.40
Consensus pattern (23 bp):
ATATAAACACTACCTAATATATT
Found at i:662026 original size:87 final size:87
Alignment explanation
Indices: 661935--662096 Score: 270
Period size: 87 Copynumber: 1.9 Consensus size: 87
661925 AAATAGGTCA
* * *
661935 ATATAAACACTACTTATTATATTATATAAGCGCTACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAACACTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
662000 CCGGTTAAATACCTATTTTATT
66 CCGGTTAAATACCTATTTTATT
** *
662022 ATATAAACGTTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAACACTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
662087 CCGGTTAAAT
66 CCGGTTAAAT
662097 GATATAAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.42
Consensus pattern (87 bp):
ATATAAACACTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATACCTATTTTATT
Found at i:662035 original size:23 final size:23
Alignment explanation
Indices: 662008--662060 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
661998 TTCCGGTTAA
**
662008 ATACCTATTTTATTATATAAACG
1 ATACCTATTACATTATATAAACG
* *
662031 TTACCTATTACATTATATAAGCG
1 ATACCTATTACATTATATAAACG
662054 ATACCTA
1 ATACCTA
662061 ATATGTTATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.40
Consensus pattern (23 bp):
ATACCTATTACATTATATAAACG
Found at i:662344 original size:42 final size:42
Alignment explanation
Indices: 662285--662368 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
662275 TTTAAGGTGC
*
662285 AATGGCTACCAGTGGGAGAAGGCCATCAATGCATGGACATTT
1 AATGGCTACAAGTGGGAGAAGGCCATCAATGCATGGACATTT
662327 AATGGCTACAAGTGGGAGAAGGCCATCAATGCATGGACATTT
1 AATGGCTACAAGTGGGAGAAGGCCATCAATGCATGGACATTT
662369 GACCAAGTAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (42 bp):
AATGGCTACAAGTGGGAGAAGGCCATCAATGCATGGACATTT
Found at i:666053 original size:137 final size:137
Alignment explanation
Indices: 665804--666062 Score: 428
Period size: 137 Copynumber: 1.9 Consensus size: 137
665794 CATCCATTTA
*
665804 GGACCCATTTATTTCCTAAAATGTAGAACTACATGCAATTTTATAACCTGCTGCAAAGTAAGTTT
1 GGACCCATTAATTTCCTAAAATGTAGAACTACATGCAATTTTATAACCTGCTGCAAAGTAAGTTT
* *
665869 CTATACAAACAATTGCTCAAATTTATGTAACTGTGCAATCTACTACTCGGCTATCCATTTAGCAC
66 CTATACAAACAACTGCTCAAATTTATGTAACTGTGCAATCCACTACTCGGCTATCCATTTAGCAC
665934 TTTAAAT
131 TTTAAAT
* *
665941 GGACCCGTTAATTTCCTAACATGTAGAACTACATGCAATTTTATAACCTGCTGCAAAGTAAGTTT
1 GGACCCATTAATTTCCTAAAATGTAGAACTACATGCAATTTTATAACCTGCTGCAAAGTAAGTTT
* ** * *
666006 CTATATAAATTACTGCTCAAATTTGTGTAACTGTGCAATCCATTACTCGGCTATCCA
66 CTATACAAACAACTGCTCAAATTTATGTAACTGTGCAATCCACTACTCGGCTATCCA
666063 CCGTGGACCA
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 112 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (137 bp):
GGACCCATTAATTTCCTAAAATGTAGAACTACATGCAATTTTATAACCTGCTGCAAAGTAAGTTT
CTATACAAACAACTGCTCAAATTTATGTAACTGTGCAATCCACTACTCGGCTATCCATTTAGCAC
TTTAAAT
Found at i:669899 original size:21 final size:20
Alignment explanation
Indices: 669844--669910 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
669834 ATCTGAAATT
*
669844 ACAGTGGCTTTAGGAATTTCA
1 ACAGTGG-TTTAGGATTTTCA
* * *
669865 GCAATGGCTGTAGGATTTTCA
1 ACAGTGG-TTTAGGATTTTCA
669886 ACAGTGGTTATAGGATTTTCA
1 ACAGTGGTT-TAGGATTTTCA
669907 ACAG
1 ACAG
669911 GTTTTGTAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.03
21 37 0.97
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.33
Consensus pattern (20 bp):
ACAGTGGTTTAGGATTTTCA
Found at i:679816 original size:64 final size:64
Alignment explanation
Indices: 679710--679842 Score: 239
Period size: 64 Copynumber: 2.1 Consensus size: 64
679700 ACATGAAAAT
* *
679710 GACACAAAACAATGTGTTACTGATGTTATAACTATGAAGTAGAGTGTCTCAAACAAATAACAAA
1 GACAAAAAACAATGTGTTACTGATGTTATAACTATGAAGTAGAGTGTCTCAAACAAACAACAAA
*
679774 GACAAAAAACAATGTGTTACTGATGTTATGACTATGAAGTAGAGTGTCTCAAACAAACAACAAA
1 GACAAAAAACAATGTGTTACTGATGTTATAACTATGAAGTAGAGTGTCTCAAACAAACAACAAA
679838 GACAA
1 GACAA
679843 TAGACCATTC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (64 bp):
GACAAAAAACAATGTGTTACTGATGTTATAACTATGAAGTAGAGTGTCTCAAACAAACAACAAA
Found at i:689130 original size:15 final size:15
Alignment explanation
Indices: 689110--689140 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
689100 CAACAGATAG
689110 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
689125 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
689140 A
1 A
689141 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:690324 original size:15 final size:15
Alignment explanation
Indices: 690304--690342 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
690294 CTGGGTTTTT
690304 TTCTTCTCGACTAGC
1 TTCTTCTCGACTAGC
690319 TTCTTCTCGACTAGC
1 TTCTTCTCGACTAGC
690334 TTCTTCTCG
1 TTCTTCTCG
690343 GCTTTGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.33, G:0.13, T:0.44
Consensus pattern (15 bp):
TTCTTCTCGACTAGC
Found at i:691403 original size:20 final size:20
Alignment explanation
Indices: 691378--691422 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
691368 ATGCACCATT
691378 TGGCATCTAACTTGCATTAG
1 TGGCATCTAACTTGCATTAG
691398 TGGCATCTAACTTGCATTAG
1 TGGCATCTAACTTGCATTAG
691418 TGGCA
1 TGGCA
691423 CCTTTCTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (20 bp):
TGGCATCTAACTTGCATTAG
Found at i:691516 original size:47 final size:48
Alignment explanation
Indices: 691459--691614 Score: 136
Period size: 47 Copynumber: 3.2 Consensus size: 48
691449 TTAGGTATTG
* * * * *
691459 AACTTACATTAGTGGAACTTTTCTACCTAAAATGCACCATT-TCATCT
1 AACTTGCATTAATGGAACATTTCTACCAAAAATGCACCATTAGCATCT
* *
691506 AACTTGCATTAAT-GACACATTTCTTCCAAAAATGCACCATTAGGCATTT
1 AACTTGCATTAATGGA-ACATTTCTACCAAAAATGCACCATTA-GCATCT
* * * * * *
691555 AACTTGCATTATTGGCACCTTTCTGCCAGAAAATGCACCGTTAGGCATTT
1 AACTTGCATTAATGGAACATTTCTACCA-AAAATGCACCATTA-GCATCT
*
691605 AACTTTCATT
1 AACTTGCATT
691615 TTAGAGAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
46 2 0.02
47 33 0.36
49 26 0.29
50 30 0.33
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (48 bp):
AACTTGCATTAATGGAACATTTCTACCAAAAATGCACCATTAGCATCT
Found at i:691578 original size:49 final size:50
Alignment explanation
Indices: 691399--691614 Score: 197
Period size: 49 Copynumber: 4.3 Consensus size: 50
691389 TTGCATTAGT
* * *
691399 GGCATCTAACTTGCATTAGTGGCACCTTTCTGCAAAAACAAAATGCACCTTTA
1 GGCATTTAACTTGCATTAGTGGCACCTTTCTGC---CACAAAATGCACCATTA
* * * * * * *
691452 GGTATTGAACTTACATTAGTGGAACTTTTCTACC-TAAAATGCACCATT-
1 GGCATTTAACTTGCATTAGTGGCACCTTTCTGCCACAAAATGCACCATTA
* * * * * *
691500 -TCATCTAACTTGCATTAATGACACATTTCTTCCA-AAAATGCACCATTA
1 GGCATTTAACTTGCATTAGTGGCACCTTTCTGCCACAAAATGCACCATTA
* * *
691548 GGCATTTAACTTGCATTATTGGCACCTTTCTGCCAGAAAATGCACCGTTA
1 GGCATTTAACTTGCATTAGTGGCACCTTTCTGCCACAAAATGCACCATTA
*
691598 GGCATTTAACTTTCATT
1 GGCATTTAACTTGCATT
691615 TTAGAGAAAT
Statistics
Matches: 131, Mismatches: 28, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
47 36 0.27
49 40 0.31
50 29 0.22
53 26 0.20
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (50 bp):
GGCATTTAACTTGCATTAGTGGCACCTTTCTGCCACAAAATGCACCATTA
Found at i:692817 original size:25 final size:25
Alignment explanation
Indices: 692783--692838 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
692773 AATGAATTTT
*
692783 AAATTCATTTCACTCTAAAGGACCA
1 AAATGCATTTCACTCTAAAGGACCA
692808 AAATGCATTTCACTCTAAAGGACCA
1 AAATGCATTTCACTCTAAAGGACCA
692833 AAATGC
1 AAATGC
692839 CCTTTCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.41, C:0.23, G:0.11, T:0.25
Consensus pattern (25 bp):
AAATGCATTTCACTCTAAAGGACCA
Found at i:694697 original size:24 final size:23
Alignment explanation
Indices: 694650--694715 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
694640 ACTTTATGAT
* *
694650 CCATATAAATATGACACCGCTCA
1 CCATATAGATATGACGCCGCTCA
*
694673 CCATATAGATAGTGACGCCGTTCA
1 CCATATAGATA-TGACGCCGCTCA
*
694697 CCATACAGATAATGACGCC
1 CCATATAGAT-ATGACGCC
694716 AAATTTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 10 0.27
24 26 0.70
25 1 0.03
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (23 bp):
CCATATAGATATGACGCCGCTCA
Found at i:698435 original size:47 final size:47
Alignment explanation
Indices: 698384--698568 Score: 212
Period size: 47 Copynumber: 3.9 Consensus size: 47
698374 GTTAGGCATT
698384 TAACTTGCATTAGTGGCACATTTCTGCCAAAAATACACCATTTCATC
1 TAACTTGCATTAGTGGCACATTTCTGCCAAAAATACACCATTTCATC
* * * * * *
698431 TAACTTGCATTAGTGGTACCA-TTCTTCCAAAAATGCACCGTTAGGCATT
1 TAACTTGCATTAGTGGCA-CATTTCTGCCAAAAATACACCATT--TCATC
** *
698480 TAACTTGCATTAGTGGCACATTTAAGCCAAAAATGA-ACCATTTAATC
1 TAACTTGCATTAGTGGCACATTTCTGCCAAAAAT-ACACCATTTCATC
* * *
698527 TAACTTGCATTAGTGGCACCTTTTTGCCAAAAATGCACCATT
1 TAACTTGCATTAGTGGCACATTTCTGCCAAAAATACACCATT
698569 GGGCATTTAC
Statistics
Matches: 113, Mismatches: 19, Indels: 12
0.78 0.13 0.08
Matches are distributed among these distances:
47 74 0.65
48 4 0.04
49 35 0.31
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (47 bp):
TAACTTGCATTAGTGGCACATTTCTGCCAAAAATACACCATTTCATC
Found at i:698495 original size:96 final size:96
Alignment explanation
Indices: 698374--698585 Score: 313
Period size: 96 Copynumber: 2.2 Consensus size: 96
698364 AAAAAACATT
** *
698374 GTTAGGCATTTAACTTGCATTAGTGGCACATTTCTGCCAAAAAT-ACACCATTTCATCTAACTTG
1 GTTAGGCATTTAACTTGCATTAGTGGCACATTTAAGCCAAAAATGA-ACCATTTAATCTAACTTG
*
698438 CATTAGTGGTACCATTCTT-CCAAAAATGCACC
65 CATTAGTGGCACC-TTCTTGCCAAAAATGCACC
698470 GTTAGGCATTTAACTTGCATTAGTGGCACATTTAAGCCAAAAATGAACCATTTAATCTAACTTGC
1 GTTAGGCATTTAACTTGCATTAGTGGCACATTTAAGCCAAAAATGAACCATTTAATCTAACTTGC
*
698535 ATTAGTGGCACCTTTTTGCCAAAAATGCACC
66 ATTAGTGGCACCTTCTTGCCAAAAATGCACC
* * *
698566 ATTGGGCATTT-ACTTTCATT
1 GTTAGGCATTTAACTTGCATT
698586 TTAGAGCAGT
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
95 12 0.11
96 93 0.88
97 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (96 bp):
GTTAGGCATTTAACTTGCATTAGTGGCACATTTAAGCCAAAAATGAACCATTTAATCTAACTTGC
ATTAGTGGCACCTTCTTGCCAAAAATGCACC
Found at i:702592 original size:35 final size:35
Alignment explanation
Indices: 702546--702636 Score: 119
Period size: 35 Copynumber: 2.6 Consensus size: 35
702536 GTTTGCCTTT
* *
702546 GATCAAGCTGGTAATTTCTTATATAGGTTCAACGCC
1 GATCAA-CTGGTAATTCCTTATATAGGTTCAACACC
* * *
702582 GATCGACTGGTAATTCCTTCTATAGGTTCAGCACC
1 GATCAACTGGTAATTCCTTATATAGGTTCAACACC
*
702617 GATCAATTGGTAATTCCTTA
1 GATCAACTGGTAATTCCTTA
702637 CGGACCTAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
35 42 0.89
36 5 0.11
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (35 bp):
GATCAACTGGTAATTCCTTATATAGGTTCAACACC
Found at i:707636 original size:35 final size:35
Alignment explanation
Indices: 707590--707671 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
707580 GATTAAGCTG
* * * *
707590 GTAATTTCTTATATAGGTTCAGCGCCGATCAACTA
1 GTAATTCCTTATATAGGTTCAACACAGATCAACTA
* *
707625 GTAATTCCTTATATAGGTTCAACACAGATTAGCTA
1 GTAATTCCTTATATAGGTTCAACACAGATCAACTA
707660 GTAATTCCTTAT
1 GTAATTCCTTAT
707672 GGACCTAAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (35 bp):
GTAATTCCTTATATAGGTTCAACACAGATCAACTA
Found at i:708117 original size:16 final size:17
Alignment explanation
Indices: 708090--708121 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
708080 ACTATGGTTT
708090 TAAAATATGTTTTAAAC
1 TAAAATATGTTTTAAAC
708107 TAAAA-ATGTTTTAAA
1 TAAAATATGTTTTAAA
708122 GGATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (17 bp):
TAAAATATGTTTTAAAC
Found at i:709253 original size:42 final size:40
Alignment explanation
Indices: 709203--709284 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 40
709193 ATAATATTAT
* * *
709203 TTTTAATAAGTAATTAATATACTTAATAATATATTATTTTTA
1 TTTTAATAAATAATTAACATAATT-ATAATAT-TTATTTTTA
*
709245 TTTTAATAAATATTTAACATAATTATAATATTTATTTTTA
1 TTTTAATAAATAATTAACATAATTATAATATTTATTTTTA
709285 ATAAAATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
40 9 0.25
41 7 0.19
42 20 0.56
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (40 bp):
TTTTAATAAATAATTAACATAATTATAATATTTATTTTTA
Found at i:709257 original size:35 final size:36
Alignment explanation
Indices: 709187--709315 Score: 101
Period size: 35 Copynumber: 3.7 Consensus size: 36
709177 TTTTAATAGT
** *
709187 TTAATAATAATATTATTTTTAATAAGTAATTAATATAC
1 TTAATAATAATATTATTTTT-AT-TTTAATAAATATAC
709225 TTAATAAT-ATATTATTTTTATTTTAATAAATAT--
1 TTAATAATAATATTATTTTTATTTTAATAAATATAC
* * *
709258 TTAA-CATAATTATAATATTTATTTTTAATAAA-ATAC
1 TTAATAATAA-TATTATTTTTA-TTTTAATAAATATAC
* *
709294 --AATAATAACAATATTTTTATTT
1 TTAATAATAATATTATTTTTATTT
709316 AAAATTATAT
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
32 2 0.03
33 8 0.11
34 20 0.27
35 23 0.31
36 2 0.03
37 11 0.15
38 8 0.11
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (36 bp):
TTAATAATAATATTATTTTTATTTTAATAAATATAC
Found at i:709372 original size:14 final size:15
Alignment explanation
Indices: 709342--709373 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
709332 ATATTTTAAT
709342 AATAATATTGACATA
1 AATAATATTGACATA
709357 AATAATATT-ACATA
1 AATAATATTGACATA
709371 AAT
1 AAT
709374 TATTCTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
AATAATATTGACATA
Found at i:712229 original size:18 final size:17
Alignment explanation
Indices: 712193--712231 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
712183 CGTGAACTGG
**
712193 TTTTTTAATTTACCTTT
1 TTTTTTAATTTACAGTT
712210 TTTTTTAATTTAACAGTT
1 TTTTTTAATTT-ACAGTT
712228 TTTT
1 TTTT
712232 AGGCTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTTAATTTACAGTT
Found at i:712478 original size:20 final size:20
Alignment explanation
Indices: 712451--712502 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
712441 CTTGTGTTTA
712451 TTTTATTTTTTATT-CTATT
1 TTTTATTTTTTATTACTATT
712470 TTGTTATTTGTTT-TTACTATT
1 TT-TTATTT-TTTATTACTATT
712491 TTTTATTTTTTA
1 TTTTATTTTTTA
712503 ATTGTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 5 0.17
20 14 0.48
21 10 0.34
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (20 bp):
TTTTATTTTTTATTACTATT
Found at i:718835 original size:16 final size:16
Alignment explanation
Indices: 718811--718841 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
718801 CATTTCCAAA
718811 TCATACATTAAAATAC
1 TCATACATTAAAATAC
*
718827 TCATTCATTAAAATA
1 TCATACATTAAAATA
718842 ATGATGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (16 bp):
TCATACATTAAAATAC
Found at i:722381 original size:57 final size:55
Alignment explanation
Indices: 722179--722451 Score: 216
Period size: 57 Copynumber: 4.9 Consensus size: 55
722169 GTATTTTCAA
** * * * * *
722179 AAAGAATTTTTAAAGAAACTAAGCCTGGTTTTCAAGGGTTTCTTTAAGATGATTTTC
1 AAAGAATTTTT-AAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATTA-TTTC
* * *
722236 AATGATTTTTTTAAAAAAGCTAAGCCTAA-TTTTAGGGGTTTCTTGATG--TA-TTC
1 AAAGA-ATTTTTAAGAAA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTC
* * * *
722289 AAATGAGTTTTT-ATAAACTAAGCCTGATCTTTAGGGGTTTCTTGATGATTATTTCC
1 AAA-GAATTTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTT-C
* * **
722345 AAAGAATTTTTAGAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATAACTAG
1 AAAGAATTTTTA-AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTC
* * *
722401 AAACGAAAGATTTTAAGAAACCT-AGCTTAATTTTTAAGGGTTTCTTGATGA
1 AAA-G-AA-TTTTTAAGAAA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGA
722452 GTAAGTCCTC
Statistics
Matches: 176, Mismatches: 26, Indels: 27
0.77 0.11 0.12
Matches are distributed among these distances:
51 9 0.05
52 22 0.12
53 10 0.06
54 4 0.02
55 10 0.06
56 7 0.04
57 61 0.35
58 46 0.26
59 7 0.04
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (55 bp):
AAAGAATTTTTAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGATTATTTC
Found at i:722385 original size:109 final size:109
Alignment explanation
Indices: 722194--722392 Score: 269
Period size: 109 Copynumber: 1.8 Consensus size: 109
722184 ATTTTTAAAG
* * * * *
722194 AAACTAAGCCTGGTTTTCAAGGGTTTCTTTAAGATGATTTTCAATGATTTTTTTAAAAAAGCTAA
1 AAACTAAGCCTGATTTTCAAGGGTTTCTTGAAGATGATTTCCAAAGATATTTTTAAAAAAGCTAA
722259 GCCTAATTTTAGGGGTTTCTTGATGTATTCAAATGAGTTTTTAT
66 GCCTAATTTTAGGGGTTTCTTGATGTATTCAAATGAGTTTTTAT
* * * *
722303 AAACTAAGCCTGATCTTT-AGGGGTTTCTTGATGATTATTTCCAAAGA-ATTTTTAGAGAAA-CT
1 AAACTAAGCCTGAT-TTTCAAGGGTTTCTTGAAGATGATTTCCAAAGATATTTTTA-AAAAAGCT
722365 AAGCCTAATTTTTAGGGGTTTCTTGATG
64 AAGCCTAA-TTTTAGGGGTTTCTTGATG
722393 ATAACTAGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
108 16 0.21
109 59 0.76
110 3 0.04
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (109 bp):
AAACTAAGCCTGATTTTCAAGGGTTTCTTGAAGATGATTTCCAAAGATATTTTTAAAAAAGCTAA
GCCTAATTTTAGGGGTTTCTTGATGTATTCAAATGAGTTTTTAT
Found at i:722751 original size:38 final size:38
Alignment explanation
Indices: 722700--722811 Score: 179
Period size: 38 Copynumber: 2.9 Consensus size: 38
722690 GAGGGATCAA
*
722700 TATCTCGCTTGAGATATTTTCACTCGAAACAGAAGAAT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAAT
* * *
722738 TATCTCACTTGAGATAGTTTCACTCGAAACAGAATATT
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAAT
*
722776 TATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
1 TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA
722812 TTTTAAGACA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 67 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (38 bp):
TATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGAAT
Found at i:722924 original size:42 final size:41
Alignment explanation
Indices: 722878--722960 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
722868 CATCAGTAAA
* * * *
722878 TCTTTAGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAG
1 TCTTTAGAGCAAGATG-ATAAATCATTCGGGTCATCCATAAG
* *
722920 TCTTTCGAGCAAGATGATAAGTCATTCGGGTCATCCATAAG
1 TCTTTAGAGCAAGATGATAAATCATTCGGGTCATCCATAAG
722961 AACTTCGGGC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
41 21 0.60
42 14 0.40
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (41 bp):
TCTTTAGAGCAAGATGATAAATCATTCGGGTCATCCATAAG
Found at i:723383 original size:38 final size:38
Alignment explanation
Indices: 723336--723411 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
723326 AGGGATCAAC
723336 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
*
723374 ATCTTGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
723412 TAAGAAACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (38 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGATTT
Found at i:723516 original size:42 final size:41
Alignment explanation
Indices: 723470--723564 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
723460 CGGACAATCA
* * * *
723470 ATAAGTCCTTTGAGCATGATGCTTAAATCCTTCAGGTCATCT
1 ATAAGTCCTTTGAGCAAGATG-ATAAATCCTTCAGGCCATCC
* *
723512 ATAAGT-CTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCC
1 ATAAGTCCTTT-GAGCAAGATGATAAATCCTTCAGGCCATCC
*
723553 ATAAGACCTTTG
1 ATAAGTCCTTTG
723565 GGAAGGATGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 25 0.57
42 19 0.43
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (41 bp):
ATAAGTCCTTTGAGCAAGATGATAAATCCTTCAGGCCATCC
Found at i:723557 original size:41 final size:41
Alignment explanation
Indices: 723445--723564 Score: 107
Period size: 42 Copynumber: 2.9 Consensus size: 41
723435 AGGGTTTCTT
* * * *
723445 GATGAGTAACTCCTTCGGACAATCAATAAGTCCTTTGAGCAT
1 GATGA-TAAATCCTTCGGGCCATCAATAAGTCCTTTGAGCAA
* * * *
723487 GATGCTTAAATCCTTCAGGTCATCTATAAGT-CTTTCGAGCAA
1 GATG-ATAAATCCTTCGGGCCATCAATAAGTCCTTT-GAGCAA
* * *
723529 GATGATAAGTCCTTCGGGCCATCCATAAGACCTTTG
1 GATGATAAATCCTTCGGGCCATCAATAAGTCCTTTG
723565 GGAAGGATGT
Statistics
Matches: 61, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
41 25 0.41
42 36 0.59
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (41 bp):
GATGATAAATCCTTCGGGCCATCAATAAGTCCTTTGAGCAA
Found at i:723683 original size:58 final size:59
Alignment explanation
Indices: 723621--723734 Score: 158
Period size: 59 Copynumber: 1.9 Consensus size: 59
723611 AATCAATGAC
* * *
723621 GCCCCACCAGAGTGGTTAACATTTCAT-TGCTTAATTCACGACACTTCGAATCAGCAAT
1 GCCCCACCAGAGAGGATAACATTTCATGTGCTTAATTCACAACACTTCGAATCAGCAAT
* * * *
723679 GCCCCACTAGAGAGGATGACATTTCATGTGCTTGATTCACAACACTTTGAATCAGC
1 GCCCCACCAGAGAGGATAACATTTCATGTGCTTAATTCACAACACTTCGAATCAGC
723735 CACGCCTCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 23 0.48
59 25 0.52
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (59 bp):
GCCCCACCAGAGAGGATAACATTTCATGTGCTTAATTCACAACACTTCGAATCAGCAAT
Found at i:723927 original size:91 final size:91
Alignment explanation
Indices: 723713--723949 Score: 259
Period size: 91 Copynumber: 2.6 Consensus size: 91
723703 CATGTGCTTG
* * *
723713 ATTCACAACACTTT-GAATCAGCCACGCCTCA-TATGAGGGACAAACA-TTCTCAGTAGAGAATT
1 ATTCACGACA-TTTCGAATCAACGACGCCTCACT-TGAGGGACAAACATTTC-CAGTAGAGAATT
*
723775 CATGAGAAGAACTTATTCAACCTTGGCTCA
63 CATAAGAAGAACTTATT-AACCTTGGCTCA
** *
723805 ATTCACGACATTTCGAATCAGTGACGCCTCACTTGAGGGACCAACATTTCCAGTAGAGAATTCAT
1 ATTCACGACATTTCGAATCAACGACGCCTCACTTGAGGGACAAACATTTCCAGTAGAGAATTCAT
* * *
723870 AAAGAA-AAGCTTGTT-TCCTTTGCTCA
66 -AAGAAGAA-CTTATTAACCTTGGCTCA
* * * *
723896 ATTCAGGACATTTCGAATCAACGATGCCTCACTTGAAGGACGAACATTTCCAGT
1 ATTCACGACATTTCGAATCAACGACGCCTCACTTGAGGGACAAACATTTCCAGT
723950 GGACATATCA
Statistics
Matches: 126, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
91 60 0.48
92 53 0.42
93 13 0.10
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (91 bp):
ATTCACGACATTTCGAATCAACGACGCCTCACTTGAGGGACAAACATTTCCAGTAGAGAATTCAT
AAGAAGAACTTATTAACCTTGGCTCA
Found at i:725553 original size:12 final size:12
Alignment explanation
Indices: 725538--725574 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
725528 TCTATTTTTG
725538 TTTTTT-CTATT
1 TTTTTTACTATT
725549 TTTTTTACTA--
1 TTTTTTACTATT
725559 TTTTTTACTATT
1 TTTTTTACTATT
725571 TTTT
1 TTTT
725575 ATATTTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
11 6 0.26
12 7 0.30
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTACTATT
Found at i:725575 original size:10 final size:10
Alignment explanation
Indices: 725549--725580 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
725539 TTTTTCTATT
725549 TTTTTTACTA
1 TTTTTTACTA
725559 TTTTTTACTA
1 TTTTTTACTA
725569 TTTTTTA-TA
1 TTTTTTACTA
725578 TTT
1 TTT
725581 ATATTTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.23
10 17 0.77
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTACTA
Found at i:729602 original size:35 final size:35
Alignment explanation
Indices: 729563--729630 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
729553 TAATTGTTGC
*
729563 GCATTCTCTAAATGCAACACATGACACACTATTGT
1 GCATTATCTAAATGCAACACATGACACACTATTGT
* * ** *
729598 GCATTATCTGATTGTGACACATGACACATTATT
1 GCATTATCTAAATGCAACACATGACACACTATT
729631 AGTATATGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (35 bp):
GCATTATCTAAATGCAACACATGACACACTATTGT
Found at i:734639 original size:16 final size:17
Alignment explanation
Indices: 734599--734640 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
734589 GTGTTTGTTG
*
734599 CTCGAACGAGAGTTTTT
1 CTCGAAAGAGAGTTTTT
*
734616 CTCGAAAGAGATTTTTT
1 CTCGAAAGAGAGTTTTT
734633 CTC-AAAGA
1 CTCGAAAGA
734641 AAGGGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (17 bp):
CTCGAAAGAGAGTTTTT
Found at i:738202 original size:21 final size:20
Alignment explanation
Indices: 738159--738203 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
738149 ATCCAAAATG
*
738159 AGTAGTATCGATACCCTACA
1 AGTAGTATCGATACCCCACA
738179 AGTAGTATCGATACCCCCACA
1 AGTAGTATCGATA-CCCCACA
738200 AGTA
1 AGTA
738204 TCGATACTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.22
Consensus pattern (20 bp):
AGTAGTATCGATACCCCACA
Found at i:747305 original size:45 final size:45
Alignment explanation
Indices: 747249--747418 Score: 290
Period size: 45 Copynumber: 3.8 Consensus size: 45
747239 GCATAAATTT
* * *
747249 CTTATCATTTA-TCCTATAAGCTCGTAAGCTTAATCTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
747294 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
747339 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
747384 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
747419 CATGTTTACC
Statistics
Matches: 121, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
44 28 0.23
45 90 0.74
46 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:747579 original size:40 final size:40
Alignment explanation
Indices: 747522--747680 Score: 246
Period size: 40 Copynumber: 4.0 Consensus size: 40
747512 ACCATAGTGC
*
747522 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
747562 TACACATAAGGTTGTGCCCAACATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* * *
747602 TACACAGAAGGTCGTGCCCACCATATACACCGAAGTATTT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
747642 TACACATAAGGTCGTGCCCACCATATACACTGAAGTGTA
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTA
747681 CTATAAACCT
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 105 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:752729 original size:22 final size:22
Alignment explanation
Indices: 752699--752742 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
752689 CATATAATCA
* *
752699 TCACCATGAGTAATGTTGTAAC
1 TCACAATGAGAAATGTTGTAAC
752721 TCACAATGAGAAATGTTGTAAC
1 TCACAATGAGAAATGTTGTAAC
752743 CATCACATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (22 bp):
TCACAATGAGAAATGTTGTAAC
Found at i:758858 original size:22 final size:22
Alignment explanation
Indices: 758833--758874 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
758823 TTATAGAATG
*
758833 GAAAAGTGT-GAGATAAGAAAAA
1 GAAAAGT-TAGAGAAAAGAAAAA
758855 GAAAAGTTAGAGAAAAGAAA
1 GAAAAGTTAGAGAAAAGAAA
758875 TCTTCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (22 bp):
GAAAAGTTAGAGAAAAGAAAAA
Found at i:762103 original size:83 final size:83
Alignment explanation
Indices: 761964--762130 Score: 325
Period size: 83 Copynumber: 2.0 Consensus size: 83
761954 TCTTATTTCT
*
761964 TCATGCACAATATCCTCTAAAGGTTTGTTTAAGAAGATTATCTTGTTTAAAGGCCTTTATTTGAG
1 TCATGCACAATATCCTCTAAAGGTTTGTTTAAGAAGATTATCTTCTTTAAAGGCCTTTATTTGAG
762029 TTCAATGTTACCAACATG
66 TTCAATGTTACCAACATG
762047 TCATGCACAATATCCTCTAAAGGTTTGTTTAAGAAGATTATCTTCTTTAAAGGCCTTTATTTGAG
1 TCATGCACAATATCCTCTAAAGGTTTGTTTAAGAAGATTATCTTCTTTAAAGGCCTTTATTTGAG
762112 TTCAATGTTACCAACATG
66 TTCAATGTTACCAACATG
762130 T
1 T
762131 ACCTTATTTG
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 83 1.00
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (83 bp):
TCATGCACAATATCCTCTAAAGGTTTGTTTAAGAAGATTATCTTCTTTAAAGGCCTTTATTTGAG
TTCAATGTTACCAACATG
Found at i:773447 original size:21 final size:20
Alignment explanation
Indices: 773429--773468 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
773419 TGAAATATCA
*
773429 TTCATGATAAATATCATATATG
1 TTCATGAT-AACATCATATA-G
773451 TTCATGATAACATCATAT
1 TTCATGATAACATCATAT
773469 GTAACGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (20 bp):
TTCATGATAACATCATATAG
Found at i:775523 original size:31 final size:31
Alignment explanation
Indices: 775488--775549 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
775478 ATAATTACCA
775488 TCAAACCAAGACACCTCAACCTTATCATCTT
1 TCAAACCAAGACACCTCAACCTTATCATCTT
*
775519 TCAAACCAAGACACCTCAACTTTATCATCTT
1 TCAAACCAAGACACCTCAACCTTATCATCTT
775550 CCTTAAGTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.27
Consensus pattern (31 bp):
TCAAACCAAGACACCTCAACCTTATCATCTT
Found at i:781066 original size:21 final size:20
Alignment explanation
Indices: 781042--781081 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
781032 AGACGACAGT
*
781042 GAGGAACAGATTTTTCTTGCC
1 GAGGAA-AGATTTATCTTGCC
*
781063 GAGGCAAGATTTATCTTGC
1 GAGGAAAGATTTATCTTGC
781082 AGATCTGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (20 bp):
GAGGAAAGATTTATCTTGCC
Found at i:794279 original size:13 final size:13
Alignment explanation
Indices: 794261--794295 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
794251 GCATCATGGC
794261 ATGACATTGTGGT
1 ATGACATTGTGGT
794274 ATGACATTGTGGT
1 ATGACATTGTGGT
794287 ATGATCATT
1 ATGA-CATT
794296 AAGGTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.40
Consensus pattern (13 bp):
ATGACATTGTGGT
Found at i:794945 original size:13 final size:13
Alignment explanation
Indices: 794903--794938 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
794893 CTATGACGTG
794903 CATTTATGACACA
1 CATTTATGACACA
794916 CATTTATGACACA
1 CATTTATGACACA
794929 CATTTATGAC
1 CATTTATGAC
794939 GTTCATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.33
Consensus pattern (13 bp):
CATTTATGACACA
Found at i:795023 original size:85 final size:85
Alignment explanation
Indices: 794917--795116 Score: 285
Period size: 85 Copynumber: 2.4 Consensus size: 85
794907 TATGACACAC
* * * *
794917 ATTTATGACACACATTTATGACGTT-CATTGAGCATCATTGAACCCCCCGTCATAAATAAAGATG
1 ATTTATGACACGCATGTATGAC-TTACATTGAACATCATTGAACCCCCCGTCATAAATAAACATG
794981 ACACACATTTGTGTGTCATAA
65 ACACACATTTGTGTGTCATAA
* * * ** *
795002 ATTTATGACTCGCATGTATGACTTACATTGAACGTCATTGAAGCCCCCGTCATAAATCTACTTGA
1 ATTTATGACACGCATGTATGACTTACATTGAACATCATTGAACCCCCCGTCATAAATAAACATGA
*
795067 CATACATTTGTGTGTCATAA
66 CACACATTTGTGTGTCATAA
795087 ATTTATGACACGCATGTATGACTTACATTG
1 ATTTATGACACGCATGTATGACTTACATTG
795117 CGTGAAATTG
Statistics
Matches: 102, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
84 2 0.02
85 100 0.98
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (85 bp):
ATTTATGACACGCATGTATGACTTACATTGAACATCATTGAACCCCCCGTCATAAATAAACATGA
CACACATTTGTGTGTCATAA
Found at i:795127 original size:85 final size:84
Alignment explanation
Indices: 794917--795167 Score: 267
Period size: 85 Copynumber: 3.0 Consensus size: 84
794907 TATGACACAC
* * * * * *
794917 ATTTATGACACACATTTATGACGTT-CATTGAGCATCATTGAACCCCCCGTCATAAATAAAGATG
1 ATTTATGACACGCATGTATGAC-TTACATTGA-CGTAATTGAAGCCCCCGTCATAAATAAACATG
794981 ACACACATTTGTGTGTCATAA
64 ACACACATTTGTGTGTCATAA
* * ** *
795002 ATTTATGACTCGCATGTATGACTTACATTGAACGTCATTGAAGCCCCCGTCATAAATCTACTTGA
1 ATTTATGACACGCATGTATGACTTACATTG-ACGTAATTGAAGCCCCCGTCATAAATAAACATGA
*
795067 CATACATTTGTGTGTCATAA
65 CACACATTTGTGTGTCATAA
* * *
795087 ATTTATGACACGCATGTATGACTTACATTG-CGTGAAATTGAAGCACGCGTCATTAAAAAAGACA
1 ATTTATGACACGCATGTATGACTTACATTGACGT--AATTGAAGCCCCCGTCA-TAAATAA-ACA
*
795151 --ACACACATTCGTGTGTC
62 TGACACACATTTGTGTGTC
795168 GTGATTGTAT
Statistics
Matches: 140, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
83 3 0.02
84 2 0.01
85 128 0.91
86 5 0.04
87 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.31
Consensus pattern (84 bp):
ATTTATGACACGCATGTATGACTTACATTGACGTAATTGAAGCCCCCGTCATAAATAAACATGAC
ACACATTTGTGTGTCATAA
Found at i:798051 original size:14 final size:15
Alignment explanation
Indices: 798027--798055 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
798017 GGTAAAGACA
798027 TTAACTTAGAATCTC
1 TTAACTTAGAATCTC
798042 TTAA-TTAGAATCTC
1 TTAACTTAGAATCTC
798056 AGTAACAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (15 bp):
TTAACTTAGAATCTC
Found at i:800929 original size:20 final size:20
Alignment explanation
Indices: 800904--800955 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
800894 TTCTAAAAAA
*
800904 AAAGATTGATCCCTTGTCCT
1 AAAGATCGATCCCTTGTCCT
800924 AAAGATCGATCCCTTGTCCT
1 AAAGATCGATCCCTTGTCCT
800944 AAAGATCGATCC
1 AAAGATCGATCC
800956 AATTCTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (20 bp):
AAAGATCGATCCCTTGTCCT
Found at i:806876 original size:12 final size:12
Alignment explanation
Indices: 806859--806886 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
806849 TGTGTCTAAC
806859 ATAAATTGAAAG
1 ATAAATTGAAAG
806871 ATAAATTGAAAG
1 ATAAATTGAAAG
806883 ATAA
1 ATAA
806887 TAAAGTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (12 bp):
ATAAATTGAAAG
Found at i:812953 original size:60 final size:61
Alignment explanation
Indices: 812850--812985 Score: 193
Period size: 60 Copynumber: 2.2 Consensus size: 61
812840 ATAGTGATGA
* *
812850 AACTCAATAAAATAATGTTTTATAGTCAAAAAAATTATTTTATAACTTTTAATAATCGAAT
1 AACTCAATAAAATAATATTTTATAATCAAAAAAATTATTTTATAACTTTTAATAATCGAAT
* * * * **
812911 GACTTAATAAAATAATATTTTATAAT-TATAAAATTATTTTATAACTTTTAATAATTTAAT
1 AACTCAATAAAATAATATTTTATAATCAAAAAAATTATTTTATAACTTTTAATAATCGAAT
812971 AACTCAATAAAATAA
1 AACTCAATAAAATAA
812986 CACTATATAA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 43 0.66
61 22 0.34
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (61 bp):
AACTCAATAAAATAATATTTTATAATCAAAAAAATTATTTTATAACTTTTAATAATCGAAT
Found at i:813007 original size:60 final size:60
Alignment explanation
Indices: 812880--813018 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
812870 TATAGTCAAA
* * * * * **
812880 AAAATTATTTTATAACTTTTAATAATCGAATGACTTAATAAAATAATATTTTATAATTAT
1 AAAATTATTTTATAACTTTTAATAATCGAATAACTCAATAAAATAACACTATATAAACAT
**
812940 AAAATTATTTTATAACTTTTAATAATTTAATAACTCAATAAAATAACACTATATAAACAT
1 AAAATTATTTTATAACTTTTAATAATCGAATAACTCAATAAAATAACACTATATAAACAT
**
813000 ATGATTATTTGTAT-ACTTT
1 AAAATTATTT-TATAACTTT
813019 ACCCTAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
60 64 0.96
61 3 0.04
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (60 bp):
AAAATTATTTTATAACTTTTAATAATCGAATAACTCAATAAAATAACACTATATAAACAT
Found at i:814178 original size:21 final size:21
Alignment explanation
Indices: 814152--814195 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
814142 TTTGCTAGCT
814152 TTTCTGCTGCTCTTGTATATG
1 TTTCTGCTGCTCTTGTATATG
814173 TTTCTGCTGCTCTTGTATATG
1 TTTCTGCTGCTCTTGTATATG
814194 TT
1 TT
814196 ACTTGTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.18, T:0.55
Consensus pattern (21 bp):
TTTCTGCTGCTCTTGTATATG
Found at i:816341 original size:24 final size:24
Alignment explanation
Indices: 816305--816353 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
816295 ATAAAAAGAA
*
816305 GTTTGTGCTTCACTTCCTGTTGTG
1 GTTTGTGCGTCACTTCCTGTTGTG
816329 GTTTGTGCGTCACTTCCTGTTGTG
1 GTTTGTGCGTCACTTCCTGTTGTG
816353 G
1 G
816354 CTATCTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.20, G:0.29, T:0.47
Consensus pattern (24 bp):
GTTTGTGCGTCACTTCCTGTTGTG
Found at i:820249 original size:19 final size:19
Alignment explanation
Indices: 820217--820256 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
820207 AGGGTTCTCA
*
820217 ATATCATAATCACCTATTT
1 ATATCATAACCACCTATTT
* *
820236 ATATCTTAACCACCTGTTT
1 ATATCATAACCACCTATTT
820255 AT
1 AT
820257 GGTTCAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.42
Consensus pattern (19 bp):
ATATCATAACCACCTATTT
Found at i:820688 original size:27 final size:27
Alignment explanation
Indices: 820658--820709 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
820648 AACCGAATCA
820658 AAAAAATGAAGCC-TTTAAA-CCGAACTG
1 AAAAAA-GAA-CCGTTTAAAGCCGAACTG
*
820685 AAAATAGAACCGTTTAAAGCCGAAC
1 AAAAAAGAACCGTTTAAAGCCGAAC
820710 CGAACCGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.09
26 9 0.41
27 11 0.50
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.17
Consensus pattern (27 bp):
AAAAAAGAACCGTTTAAAGCCGAACTG
Found at i:820714 original size:5 final size:5
Alignment explanation
Indices: 820704--820746 Score: 86
Period size: 5 Copynumber: 8.6 Consensus size: 5
820694 CCGTTTAAAG
820704 CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCG
1 CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCGAA CCG
820747 TTTTACTCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.37, C:0.42, G:0.21, T:0.00
Consensus pattern (5 bp):
CCGAA
Found at i:821214 original size:41 final size:42
Alignment explanation
Indices: 821127--821214 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 42
821117 GACATATTTG
* *
821127 CTTGTGTTCACATTTCATAGATAAATGAATTGACATGCTTGT
1 CTTGTGTTCACATTGCAAAGATAAATGAATTGACATGCTTGT
*
821169 -TTGTGTTCACATTGCAAAGATGAATGAATTGACATGCTT-T
1 CTTGTGTTCACATTGCAAAGATAAATGAATTGACATGCTTGT
821209 CTTGTG
1 CTTGTG
821215 ACATGCTTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (42 bp):
CTTGTGTTCACATTGCAAAGATAAATGAATTGACATGCTTGT
Done.