Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 106 of 121
Found at i:18078203 original size:11 final size:12
Alignment explanation
Indices: 18078170--18078211 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
18078160 ATCACATATA
18078170 ATAATATAAATT
1 ATAATATAAATT
18078182 ATTAAAATATAAA-T
1 A-T--AATATAAATT
18078196 ATAATATAAATT
1 ATAATATAAATT
18078208 ATAA
1 ATAA
18078212 ATCATATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 8 0.31
12 6 0.23
13 2 0.08
14 2 0.08
15 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATATAAATT
Found at i:18078205 original size:18 final size:17
Alignment explanation
Indices: 18078165--18078257 Score: 64
Period size: 18 Copynumber: 5.2 Consensus size: 17
18078155 TATTTATCAC
18078165 ATATAATAATATAAAT-T
1 ATATAA-AATATAAATAT
18078182 AT-TAAAATATAAATAT
1 ATATAAAATATAAATAT
*
18078198 AATATAAATTATAAATCAT
1 -ATATAAAATATAAAT-AT
* * *
18078217 ATTTAAATTTTAAATAT
1 ATATAAAATATAAATAT
* *
18078234 GAATATAACATATTTAATAT
1 --ATATAAAATA-TAAATAT
18078254 ATAT
1 ATAT
18078258 GTTATATGTG
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
15 9 0.15
16 4 0.07
17 6 0.10
18 28 0.46
19 8 0.13
20 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (17 bp):
ATATAAAATATAAATAT
Found at i:18078528 original size:11 final size:11
Alignment explanation
Indices: 18078514--18078538 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
18078504 TTTAATACTC
18078514 ATTTAATATAT
1 ATTTAATATAT
18078525 ATTTAATATAT
1 ATTTAATATAT
18078536 ATT
1 ATT
18078539 AATTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTTAATATAT
Found at i:18078552 original size:27 final size:29
Alignment explanation
Indices: 18078515--18078573 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
18078505 TTAATACTCA
18078515 TTTAATATATATT-TA-ATA-TATATTAAT
1 TTTAATATATATTATATA-ACTATATTAAT
*
18078542 TTTAATTTATATTATATAACTATATTAAT
1 TTTAATATATATTATATAACTATATTAAT
18078571 TTT
1 TTT
18078574 TAGTATCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 12 0.43
28 3 0.11
29 13 0.46
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTTAATATATATTATATAACTATATTAAT
Found at i:18078918 original size:59 final size:59
Alignment explanation
Indices: 18078854--18078976 Score: 219
Period size: 59 Copynumber: 2.1 Consensus size: 59
18078844 TATTAAATAT
*
18078854 ATTTAACATATATTTGTATAACAAAATTAAATTAAATGTATTATTCGTGTCGTGTTGAA
1 ATTTAACATATATTTGTATAACAAAATTAAATTAAATGTATTATTCGTGTCGTGTTAAA
* *
18078913 ATTTAACATGTATTTGTATAACAAGATTAAATTAAATGTATTATTCGTGTCGTGTTAAA
1 ATTTAACATATATTTGTATAACAAAATTAAATTAAATGTATTATTCGTGTCGTGTTAAA
18078972 ATTTA
1 ATTTA
18078977 TGTCAATACT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (59 bp):
ATTTAACATATATTTGTATAACAAAATTAAATTAAATGTATTATTCGTGTCGTGTTAAA
Found at i:18078951 original size:28 final size:28
Alignment explanation
Indices: 18078864--18078954 Score: 71
Period size: 28 Copynumber: 3.1 Consensus size: 28
18078854 ATTTAACATA
*
18078864 TATTTGTATAACAAAATTAAATTAAATG
1 TATTTGTATAACAAGATTAAATTAAATG
* **
18078892 TATTATTCGTGT--CGTG-TTGAAATTTAACATG
1 TA-T-TT-GTATAACAAGATT-AAA-TTAA-ATG
18078923 TATTTGTATAACAAGATTAAATTAAATG
1 TATTTGTATAACAAGATTAAATTAAATG
18078951 TATT
1 TATT
18078955 ATTCGTGTCG
Statistics
Matches: 47, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
28 14 0.30
29 11 0.23
30 12 0.26
31 10 0.21
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (28 bp):
TATTTGTATAACAAGATTAAATTAAATG
Found at i:18078970 original size:28 final size:28
Alignment explanation
Indices: 18078880--18078971 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
18078870 TATAACAAAA
18078880 TTAAATTAAATGTATTATTCGTGTCGTG
1 TTAAATTAAATGTATTATTCGTGTCGTG
* **
18078908 TTGAAATTTAACATGTA-T-TT-GTATAACAAG
1 TT-AAA-TTAA-ATGTATTATTCGTGT--CGTG
18078938 ATTAAATTAAATGTATTATTCGTGTCGTG
1 -TTAAATTAAATGTATTATTCGTGTCGTG
18078967 TTAAA
1 TTAAA
18078972 ATTTATGTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
28 15 0.31
29 12 0.24
30 12 0.24
31 10 0.20
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (28 bp):
TTAAATTAAATGTATTATTCGTGTCGTG
Found at i:18080429 original size:36 final size:36
Alignment explanation
Indices: 18080384--18080472 Score: 90
Period size: 38 Copynumber: 2.4 Consensus size: 36
18080374 TTTAAATTTC
*
18080384 ATAATTTTTAATATTAAAAATAAAAATATCATAAAAAT
1 ATAA-TTTTAATATAAAAAATAAAAATATCA-AAAAAT
** * *
18080422 -TAATTTTAAAATATAAAAAATTTAAATGTTAAAAAAT
1 ATAATTTT--AATATAAAAAATAAAAATATCAAAAAAT
18080459 ATAATTTTAATATA
1 ATAATTTTAATATA
18080473 TTTAAAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
36 10 0.23
37 9 0.21
38 24 0.56
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (36 bp):
ATAATTTTAATATAAAAAATAAAAATATCAAAAAAT
Found at i:18080453 original size:23 final size:23
Alignment explanation
Indices: 18080406--18080455 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
18080396 ATTAAAAATA
*
18080406 AAAATATCATAAAAATTAATTTT
1 AAAATATCATAAAAATTAATGTT
18080429 AAAATAT-A-AAAAATTTAAATGTT
1 AAAATATCATAAAAA-TT-AATGTT
18080452 AAAA
1 AAAA
18080456 AATATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 5 0.21
22 3 0.12
23 16 0.67
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATATCATAAAAATTAATGTT
Found at i:18090566 original size:52 final size:52
Alignment explanation
Indices: 18090452--18090587 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
18090442 AAACTTGCTC
* * ** *
18090452 ATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGTCAAACTTGCCT
1 ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGTCAAACTTACCT
* * * *
18090504 ATTAAGAATCTCTTTCCTTTTAGAATTCTTTTCTTACAAGTCAGACTTACCT
1 ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGTCAAACTTACCT
18090556 ATTAAGAATCTTCTTT-CTCTT-GAAATTCTTCT
1 ATTAAGAATC-TCTTTCCTCTTAG-AATTCTTCT
18090588 TTTGCAAGTC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
51 1 0.01
52 65 0.92
53 5 0.07
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.43
Consensus pattern (52 bp):
ATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGTCAAACTTACCT
Found at i:18090653 original size:11 final size:11
Alignment explanation
Indices: 18090622--18090653 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18090612 GCAATATCTG
*
18090622 ACAAATCTCAA
1 ACAAATCTCTA
18090633 ACAAATCTCTA
1 ACAAATCTCTA
18090644 ACAAATCTCT
1 ACAAATCTCT
18090654 TATGTGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:18091600 original size:52 final size:52
Alignment explanation
Indices: 18091514--18091649 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
18091504 TATAACCATA
* * * **
18091514 CAAACTTG-CTCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCT-ATTAAGAATCTCTTTCATCTTAGAATTCTTCTCCTACAAGT
* *
18091566 CAAACTTGCCTATTAAGAATCTCTTTCATTTTAGAATTCTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCATCTTAGAATTCTTCTCCTACAAGT
* *
18091618 CAGACTTACCTATTAAGAATCCTCTTTC-TCTT
1 CAAACTTGCCTATTAAGAAT-CTCTTTCATCTT
18091650 GAAATTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
52 63 0.88
53 9 0.12
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCATCTTAGAATTCTTCTCCTACAAGT
Found at i:18091670 original size:52 final size:52
Alignment explanation
Indices: 18091546--18091670 Score: 137
Period size: 52 Copynumber: 2.4 Consensus size: 52
18091536 CTCTCCTCTT
* * *
18091546 AGAATTCTTCTCCTGTAAGTCAAACTTGCCTATTAAGAATCTCTTTCATTTT
1 AGAATTCTTCTCTTGTAAGTCAAACTTACCTATTAAGAATCTCTTTCATTTG
** *
18091598 AGAATTCTTCTCTTACAAGTCAGACTTACCTATTAAGAATCCTCTTTC-TCTTG
1 AGAATTCTTCTCTTGTAAGTCAAACTTACCTATTAAGAAT-CTCTTTCAT-TTG
* * *
18091651 A-AATTTTTTTTTTGTAAGTC
1 AGAATTCTTCTCTTGTAAGTC
18091671 TTCTTGTCCA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
52 50 0.83
53 10 0.17
ACGTcount: A:0.26, C:0.20, G:0.10, T:0.44
Consensus pattern (52 bp):
AGAATTCTTCTCTTGTAAGTCAAACTTACCTATTAAGAATCTCTTTCATTTG
Found at i:18091971 original size:23 final size:22
Alignment explanation
Indices: 18091941--18092008 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
18091931 TAAGCTTACT
*
18091941 TCTTCTCATGTCTCAAACCAAGC
1 TCTTCTCATGTCTCGAACCAA-C
*
18091964 TCTTCTCATATCTCGAACTGTCAAC
1 TCTTCTCATGTCTCGAAC---CAAC
*
18091989 TATTCTCATGTCTCGAACCA
1 TCTTCTCATGTCTCGAACCA
18092009 TCGGCTCTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.05
23 16 0.42
25 17 0.45
26 3 0.08
ACGTcount: A:0.25, C:0.32, G:0.09, T:0.34
Consensus pattern (22 bp):
TCTTCTCATGTCTCGAACCAAC
Found at i:18092761 original size:52 final size:53
Alignment explanation
Indices: 18092615--18092761 Score: 172
Period size: 53 Copynumber: 2.8 Consensus size: 53
18092605 AAACTTGCTC
* * * * *
18092615 ATTAAGAATCCCTC-TCCTCTTAGAATTCTTCTCCTGTAAGTCAAACTTGCCT
1 ATTAAGAATCTCTCTTTCTCTTAAAATTCTTCTCTTGTAAGTCAAACTTACCT
* * ** *
18092667 ATTAAGAATCTCTTTTTCTTTTAAAATTCTTCTCTTACAAGTCAGACTTACCT
1 ATTAAGAATCTCTCTTTCTCTTAAAATTCTTCTCTTGTAAGTCAAACTTACCT
* *
18092720 ATTAAGAATCT-TCTTTCTCTTGAAATTCTTCTTTTGTAAGTC
1 ATTAAGAATCTCTCTTTCTCTTAAAATTCTTCTCTTGTAAGTC
18092762 TTCTTATCCA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
52 37 0.47
53 41 0.53
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.44
Consensus pattern (53 bp):
ATTAAGAATCTCTCTTTCTCTTAAAATTCTTCTCTTGTAAGTCAAACTTACCT
Found at i:18092812 original size:22 final size:22
Alignment explanation
Indices: 18092786--18092828 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18092776 GCAATATTTG
*
18092786 ACAAATATTAAACAAATCTCTA
1 ACAAATACTAAACAAATCTCTA
* *
18092808 ACAAATCCTAAATAAATCTCT
1 ACAAATACTAAACAAATCTCT
18092829 TATGGGATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (22 bp):
ACAAATACTAAACAAATCTCTA
Found at i:18093132 original size:25 final size:24
Alignment explanation
Indices: 18093052--18093138 Score: 75
Period size: 25 Copynumber: 3.5 Consensus size: 24
18093042 TCTTAAACCA
*
18093052 AACTCTTCTCATATCTCGAACTGTC
1 AACTCTTCTCATATCTTGAACT-TC
* * *
18093077 AACTATTTTCATATCTTGAACCATC
1 AACTCTTCTCATATCTTGAA-CTTC
** * *
18093102 GGCTCTTTTCATATCTTGAATCTTT
1 AACTCTTCTCATATCTTGAA-CTTC
18093127 AACTCTTCTCAT
1 AACTCTTCTCAT
18093139 GTTTCAAACC
Statistics
Matches: 48, Mismatches: 13, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.07, T:0.43
Consensus pattern (24 bp):
AACTCTTCTCATATCTTGAACTTC
Found at i:18093775 original size:52 final size:52
Alignment explanation
Indices: 18093689--18093814 Score: 155
Period size: 52 Copynumber: 2.4 Consensus size: 52
18093679 TATAACCATA
* **
18093689 CAAACTTG-CTCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCT-ATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTACAAGT
* * **
18093741 CAAACTTGCCTATTAAGAATCTCTGTCCTTTTAGAATTCTTCTTTTACAAGT
1 CAAACTTGCCTATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTACAAGT
* *
18093793 CAGACTTACCTATTAAGAATCT
1 CAAACTTGCCTATTAAGAATCT
18093815 TCTTTCTCTT
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 62 0.97
53 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTCTCCTCTTAGAATTCTTCTCCTACAAGT
Found at i:18093845 original size:52 final size:52
Alignment explanation
Indices: 18093700--18093845 Score: 145
Period size: 52 Copynumber: 2.8 Consensus size: 52
18093690 AAACTTGCTC
* * ** *
18093700 ATTAAGAATCCCTCTCCTCTT-AGAATTCTTCTCCTGTAAGTCAAACTTGCCT
1 ATTAAGAATCTCTGTCCT-TTGAGAATTCTTCTTTTGTAAGTCAAACTTACCT
* ** *
18093752 ATTAAGAATCTCTGTCCTTTTAGAATTCTTCTTTTACAAGTCAGACTTACCT
1 ATTAAGAATCTCTGTCCTTTGAGAATTCTTCTTTTGTAAGTCAAACTTACCT
* *
18093804 ATTAAGAATCTTCT-TTCTCTTGA-AATTCTTTTTTTGTAAGTC
1 ATTAAGAATC-TCTGTCCT-TTGAGAATTCTTCTTTTGTAAGTC
18093846 TTCTTGTCCA
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
51 2 0.03
52 70 0.90
53 6 0.08
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (52 bp):
ATTAAGAATCTCTGTCCTTTGAGAATTCTTCTTTTGTAAGTCAAACTTACCT
Found at i:18093901 original size:11 final size:11
Alignment explanation
Indices: 18093870--18093901 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
18093860 GCAATATCTG
*
18093870 ACAAATCTCAA
1 ACAAATCTCTA
18093881 ACAAATCTCTA
1 ACAAATCTCTA
18093892 ACAAATCTCT
1 ACAAATCTCT
18093902 TATGAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:18094398 original size:20 final size:17
Alignment explanation
Indices: 18094373--18094415 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 17
18094363 AAGAATAGAA
18094373 AATTAACTTAAACATCAACT
1 AATTAACTTAAA-A-CAA-T
18094393 AATTAACTTAAAACAAT
1 AATTAACTTAAAACAAT
18094410 AATTAA
1 AATTAA
18094416 AAGGTGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 1 0.04
20 12 0.52
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (17 bp):
AATTAACTTAAAACAAT
Found at i:18094862 original size:60 final size:61
Alignment explanation
Indices: 18094796--18094925 Score: 183
Period size: 60 Copynumber: 2.1 Consensus size: 61
18094786 CTTAAACTTA
* * * *
18094796 ATGAATTAAACTTCAAATTGCAAATTAAATTAAGAA-CAAAA-TTTAAAGAGTATAAATTGC
1 ATGAATTAAACTTCAAACTACAAATTAAATTAA-AAGCAAAACTTAAAAGAGCATAAATTGC
* *
18094856 ATGAATTAAACTTCAAACTACAAATTAATTTAAAAGCAAAACTTAAAAGAGCATGAATTGC
1 ATGAATTAAACTTCAAACTACAAATTAAATTAAAAGCAAAACTTAAAAGAGCATAAATTGC
18094917 ATGAATTAA
1 ATGAATTAA
18094926 TAGCATTTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
59 2 0.03
60 35 0.56
61 25 0.40
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (61 bp):
ATGAATTAAACTTCAAACTACAAATTAAATTAAAAGCAAAACTTAAAAGAGCATAAATTGC
Found at i:18095055 original size:29 final size:29
Alignment explanation
Indices: 18094991--18095066 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
18094981 TTTAAGAAAG
*
18094991 CTTGAATTGAATTGAAAA-TAAAATAGAA
1 CTTGAATTAAATTGAAAACTAAAATAGAA
* * *
18095019 CTTAAATTAAATTGAAAACTTAAATTGAA
1 CTTGAATTAAATTGAAAACTAAAATAGAA
18095048 CTTGAATTAAATTGAAAAC
1 CTTGAATTAAATTGAAAAC
18095067 AAATTAAAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 16 0.38
29 26 0.62
ACGTcount: A:0.51, C:0.07, G:0.11, T:0.32
Consensus pattern (29 bp):
CTTGAATTAAATTGAAAACTAAAATAGAA
Found at i:18095832 original size:19 final size:19
Alignment explanation
Indices: 18095788--18095838 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
18095778 ATCCTACCTT
18095788 AGGTAAGAATTCCAAGTCA
1 AGGTAAGAATTCCAAGTCA
** * *
18095807 AAATAAGATTTTCAAGTCA
1 AGGTAAGAATTCCAAGTCA
18095826 AGGTAAGAATTCC
1 AGGTAAGAATTCC
18095839 CAAATTGACT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (19 bp):
AGGTAAGAATTCCAAGTCA
Found at i:18096218 original size:7 final size:8
Alignment explanation
Indices: 18096186--18096232 Score: 60
Period size: 8 Copynumber: 5.9 Consensus size: 8
18096176 GATTTTATGG
18096186 AAAAATAA
1 AAAAATAA
*
18096194 AAAAAT-C
1 AAAAATAA
*
18096201 AAAAATCA
1 AAAAATAA
18096209 AAAAATAAA
1 AAAAAT-AA
18096218 AAAAATAA
1 AAAAATAA
18096226 AAAAATA
1 AAAAATA
18096233 GGTGTTGAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.18
8 21 0.62
9 7 0.21
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:18101474 original size:7 final size:7
Alignment explanation
Indices: 18101462--18101519 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
18101452 AGAATGAATG
18101462 AAAGAAA
1 AAAGAAA
18101469 AAAGAAA
1 AAAGAAA
18101476 AAAGGAAA
1 AAA-GAAA
*
18101484 AAA-ATA
1 AAAGAAA
*
18101490 AAA-AAT
1 AAAGAAA
18101496 AAA-AAA
1 AAAGAAA
*
18101502 AAATAAA
1 AAAGAAA
18101509 AAAGAGAA
1 AAAGA-AA
18101517 AAA
1 AAA
18101520 AACTCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
6 14 0.33
7 17 0.40
8 12 0.28
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:18101493 original size:17 final size:16
Alignment explanation
Indices: 18101466--18101521 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
18101456 TGAATGAAAG
*
18101466 AAAAAAGAAAAAAGGA
1 AAAAAATAAAAAAGGA
**
18101482 AAAAAATAAAAAATAAA
1 AAAAAATAAAAAA-GGA
18101499 AAAAAATAAAAAAGAGA
1 AAAAAATAAAAAAG-GA
18101516 AAAAAA
1 AAAAAA
18101522 CTCAAATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 12 0.36
17 21 0.64
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (16 bp):
AAAAAATAAAAAAGGA
Found at i:18102825 original size:21 final size:21
Alignment explanation
Indices: 18102799--18102974 Score: 113
Period size: 21 Copynumber: 7.8 Consensus size: 21
18102789 ATAAACCTTA
18102799 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
* * *
18102820 AAATGAGAATCTTTAAAAAATTTT
1 AAATGAGAATCTTT---GAGTCTT
*
18102844 CAAATGAAAATCTTTGAGTCTT
1 -AAATGAGAATCTTTGAGTCTT
* * * * *
18102866 AAATAAAAATCTTTAAAAAATTCTC
1 AAATGAGAATCTTT----GAGTCTT
18102891 AAATGAGAATCTTTGAGTCTT
1 AAATGAGAATCTTTGAGTCTT
*
18102912 AAATGAGAAT-TTTCAAGAAATCTT
1 AAATGAGAATCTTT---G-AGTCTT
*
18102936 CAAATGTGAATCTTTGAGT-TT
1 -AAATGAGAATCTTTGAGTCTT
18102957 CAAATGAGAATCTTTGAG
1 -AAATGAGAATCTTTGAG
18102975 ATGTGAAACT
Statistics
Matches: 121, Mismatches: 20, Indels: 28
0.72 0.12 0.17
Matches are distributed among these distances:
20 3 0.02
21 60 0.50
22 6 0.05
23 2 0.02
24 9 0.07
25 38 0.31
26 3 0.02
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTCTT
Found at i:18102855 original size:25 final size:25
Alignment explanation
Indices: 18102820--18102904 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
18102810 TTTGAGTCTT
*
18102820 AAATGAGAATCTTTAAAAAATTTTC
1 AAATGAAAATCTTTAAAAAATTTTC
* * *
18102845 AAATGAAAATCTTT---GAGTCTT-
1 AAATGAAAATCTTTAAAAAATTTTC
* *
18102866 AAATAAAAATCTTTAAAAAATTCTC
1 AAATGAAAATCTTTAAAAAATTTTC
*
18102891 AAATGAGAATCTTT
1 AAATGAAAATCTTT
18102905 GAGTCTTAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
21 13 0.29
22 4 0.09
24 3 0.07
25 25 0.56
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (25 bp):
AAATGAAAATCTTTAAAAAATTTTC
Found at i:18102856 original size:46 final size:46
Alignment explanation
Indices: 18102799--18102971 Score: 251
Period size: 46 Copynumber: 3.8 Consensus size: 46
18102789 ATAAACCTTA
18102799 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAAAAATTTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAAAAATTTTC
* * * *
18102845 AAATGAAAATCTTTGAGTCTTAAATAAAAATCTTTAAAAAATTCTC
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAAAAATTTTC
* *
18102891 AAATGAGAATCTTTGAGTCTTAAATGAGAAT-TTTCAAGAAATCTTC
1 AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTT-AAAAAATTTTC
*
18102937 AAATGTGAATCTTTGAGT-TTCAAATGAGAATCTTT
1 AAATGAGAATCTTTGAGTCTT-AAATGAGAATCTTT
18102972 GAGATGTGAA
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
45 5 0.04
46 105 0.93
47 3 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (46 bp):
AAATGAGAATCTTTGAGTCTTAAATGAGAATCTTTAAAAAATTTTC
Found at i:18103519 original size:40 final size:40
Alignment explanation
Indices: 18103440--18103620 Score: 195
Period size: 41 Copynumber: 4.5 Consensus size: 40
18103430 AAGCCTTTGC
* *
18103440 TTAGAGGAACATTTTACTTTTT-AAAGTTGTGGTGTCTCTAT
1 TTAGAGGAGCA-TTTA-TTTTTCAAAGTTGTGGTGCCTCTAT
18103481 TTAGAGGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTAT
1 TTAGAGGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTAT
* * * *
18103521 TTAGAAGAGCATTTTATTTTTCAAAAGTTATGGTGCATCTGT
1 TTAGAGGAGCA-TTTATTTTTC-AAAGTTGTGGTGCCTCTAT
* * *** *
18103563 TTAGAGGAGTAATTTATTTTTCAAAGTCGTTAAGCCTCTAC
1 TTAGAGGAG-CATTTATTTTTCAAAGTTGTGGTGCCTCTAT
18103604 TTAGAGGAGC-TTTATTT
1 TTAGAGGAGCATTTATTT
18103621 ACTTTTTCAA
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
39 12 0.10
40 32 0.27
41 40 0.34
42 34 0.29
43 1 0.01
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (40 bp):
TTAGAGGAGCATTTATTTTTCAAAGTTGTGGTGCCTCTAT
Found at i:18103566 original size:42 final size:40
Alignment explanation
Indices: 18103440--18103589 Score: 187
Period size: 42 Copynumber: 3.7 Consensus size: 40
18103430 AAGCCTTTGC
*
18103440 TTAGAGGAACATTTTACTTTTT-AAAGTTGTGGTGTCTCTAT
1 TTAGAGGAGCATTTTA-TTTTTCAAAGTTGTGGTG-CTCTAT
18103481 TTAGAGGAGCA-TTTATTTTTCAAAGTTGTGGTGCCTCTAT
1 TTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTG-CTCTAT
* * *
18103521 TTAGAAGAGCATTTTATTTTTCAAAAGTTATGGTGCATCTGT
1 TTAGAGGAGCATTTTATTTTTC-AAAGTTGTGGTGC-TCTAT
* *
18103563 TTAGAGGAGTAATTTATTTTTCAAAGT
1 TTAGAGGAGCATTTTATTTTTCAAAGT
18103590 CGTTAAGCCT
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
39 5 0.05
40 32 0.33
41 26 0.27
42 34 0.35
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (40 bp):
TTAGAGGAGCATTTTATTTTTCAAAGTTGTGGTGCTCTAT
Found at i:18103983 original size:22 final size:20
Alignment explanation
Indices: 18103943--18103985 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
18103933 AATACACGGG
18103943 CACACAAAACAAAAAAAAAA
1 CACACAAAACAAAAAAAAAA
18103963 CACACAGAAACAGAAATAAAAAA
1 CACACA-AAACA-AAA-AAAAAA
18103986 AATCACAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 3 0.15
23 6 0.30
ACGTcount: A:0.74, C:0.19, G:0.05, T:0.02
Consensus pattern (20 bp):
CACACAAAACAAAAAAAAAA
Found at i:18104783 original size:7 final size:7
Alignment explanation
Indices: 18104771--18104795 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
18104761 TTTTAATCCA
18104771 AAAAAAT
1 AAAAAAT
18104778 AAAAAAT
1 AAAAAAT
18104785 AAAAAAT
1 AAAAAAT
18104792 AAAA
1 AAAA
18104796 GTTTAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:18105180 original size:48 final size:47
Alignment explanation
Indices: 18105052--18105204 Score: 148
Period size: 48 Copynumber: 3.1 Consensus size: 47
18105042 AAAGAAGAAC
*
18105052 AAAGAATTTCTAAATAGG-CTCAAATGGTGAAAAATTTAAAATTTTCAAAA
1 AAAGAATTTCTAAATAGGCCT-AAATGGTGGAAAATTTAAAA---TCAAAA
* * * * *
18105102 AAAAAATTTCTAAATTGACCAAAATAGTGGAAAATTTAGAAAT-AATAA
1 AAAGAATTTCTAAATAGGCCTAAATGGTGGAAAATTTA-AAATCAA-AA
*
18105150 AAAGAATTTCTAAATAGGCCTAAATGGTGGAAATTTTAAAAATTCAAAA
1 AAAGAATTTCTAAATAGGCCTAAATGGTGGAAAATTT-AAAA-TCAAAA
*
18105199 AGAGAA
1 AAAGAA
18105205 AATATTTTTA
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
47 2 0.02
48 37 0.44
49 9 0.11
50 32 0.38
51 4 0.05
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.27
Consensus pattern (47 bp):
AAAGAATTTCTAAATAGGCCTAAATGGTGGAAAATTTAAAATCAAAA
Found at i:18117098 original size:7 final size:7
Alignment explanation
Indices: 18117086--18117111 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18117076 TTTTATCCCA
18117086 TCATGCT
1 TCATGCT
18117093 TCATGCT
1 TCATGCT
18117100 TCATGCT
1 TCATGCT
18117107 TCATG
1 TCATG
18117112 TAATTCACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.27, G:0.15, T:0.42
Consensus pattern (7 bp):
TCATGCT
Found at i:18117847 original size:24 final size:25
Alignment explanation
Indices: 18117815--18117863 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
18117805 ACAACCTCCT
18117815 TTATATCT-AAAAAAGAATAATGAA
1 TTATATCTAAAAAAAGAATAATGAA
18117839 TTATATCTAAAAAAAGAATAATGAA
1 TTATATCTAAAAAAAGAATAATGAA
18117864 ATTAAATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
TTATATCTAAAAAAAGAATAATGAA
Found at i:18118022 original size:25 final size:25
Alignment explanation
Indices: 18117969--18118018 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
18117959 TACAACCTTT
18117969 ATTATATCTGAAAAAAGAATAATGA
1 ATTATATCTGAAAAAAGAATAATGA
18117994 ATTATATCT-AAAAAAGAATAATGA
1 ATTATATCTGAAAAAAGAATAATGA
18118018 A
1 A
18118019 ATTAAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.58, C:0.04, G:0.10, T:0.28
Consensus pattern (25 bp):
ATTATATCTGAAAAAAGAATAATGA
Found at i:18118034 original size:155 final size:155
Alignment explanation
Indices: 18117747--18118034 Score: 492
Period size: 155 Copynumber: 1.9 Consensus size: 155
18117737 CGAATCCCAG
* * *
18117747 CAATATAAGGAGGAGATTTTTTAAACTTAAAACTTTAAGGTCTTGGGTTCCCCATGTTACAACCT
1 CAATATAAGGAAGAGATTTTTAAAACTTAAAACTTTAAGGTCTTGGATTCCCCATGTTACAACCT
18117812 CCTTTATATCTAAAAAAGAATAATGAATTATATCTAAAAAAAGAATAATGAAATTAAATCAATAA
66 CCTTTATATCTAAAAAAGAATAATGAATTATATCTAAAAAAAGAATAATGAAATTAAATCAATAA
18117877 GACTTTAGCTCCTAAAACTTTAGCT
131 GACTTTAGCTCCTAAAACTTTAGCT
18117902 CAATGATAAGGAAGAGA-TTTTAAAACTTAAAACTTTAAGGTCTTGGATTCCCCATGTTACAACC
1 CAAT-ATAAGGAAGAGATTTTTAAAACTTAAAACTTTAAGGTCTTGGATTCCCCATGTTACAACC
*
18117966 T-TTATTATATCTGAAAAAAGAATAATGAATTATATCT-AAAAAAGAATAATGAAATTAAATCAA
65 TCCT-TTATATCT-AAAAAAGAATAATGAATTATATCTAAAAAAAGAATAATGAAATTAAATCAA
18118029 TAAGAC
128 TAAGAC
18118035 CTCCTTTATA
Statistics
Matches: 126, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
154 1 0.01
155 90 0.71
156 35 0.28
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (155 bp):
CAATATAAGGAAGAGATTTTTAAAACTTAAAACTTTAAGGTCTTGGATTCCCCATGTTACAACCT
CCTTTATATCTAAAAAAGAATAATGAATTATATCTAAAAAAAGAATAATGAAATTAAATCAATAA
GACTTTAGCTCCTAAAACTTTAGCT
Found at i:18119423 original size:4 final size:4
Alignment explanation
Indices: 18119414--18119455 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
18119404 AAAAATCATC
* * *
18119414 AAAT AAAT AAAC AAAT AAAA AAAT AAAT AAA- AACT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
18119456 ATACCAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
3 2 0.06
4 29 0.94
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:18119437 original size:20 final size:20
Alignment explanation
Indices: 18119414--18119458 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
18119404 AAAAATCATC
18119414 AAATAAATAAACAAATAAA-A
1 AAATAAATAAA-AAATAAATA
*
18119434 AAATAAATAAAAACTAAATA
1 AAATAAATAAAAAATAAATA
18119454 AAATA
1 AAATA
18119459 CCAAAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.78, C:0.04, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAATAAAAAATAAATA
Found at i:18120874 original size:35 final size:34
Alignment explanation
Indices: 18120789--18120877 Score: 97
Period size: 35 Copynumber: 2.6 Consensus size: 34
18120779 TCACAAGACT
* * *
18120789 TTCATATTCATAATAATTTTTAGATTTGTAAAAA
1 TTCAAATTCATAAAAATTTTTAGATTTGCAAAAA
* *
18120823 TTCAAATTCTTAAAAAATTTTTAGATTTGCAAAGAT
1 TTCAAATTCAT-AAAAATTTTTAGATTTGCAAA-AA
* *
18120859 TTTAGATTCATAAAAATTT
1 TTCAAATTCATAAAAATTT
18120878 AATTCTTAAG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
34 9 0.20
35 27 0.60
36 9 0.20
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.45
Consensus pattern (34 bp):
TTCAAATTCATAAAAATTTTTAGATTTGCAAAAA
Found at i:18120908 original size:31 final size:31
Alignment explanation
Indices: 18120888--18120999 Score: 145
Period size: 31 Copynumber: 3.6 Consensus size: 31
18120878 AATTCTTAAG
18120888 ATTTCAGTTTTGCAAGAATTTGATTATCAAA
1 ATTTCAGTTTTGCAAGAATTTGATTATCAAA
* **
18120919 ATTTTAGTTGCGCAAGAATTTGATTTAT-AAA
1 ATTTCAGTTTTGCAAGAATTTGA-TTATCAAA
* * *
18120950 TTTTTTAGATTTGCAAGAATTTGATTATCAAA
1 -ATTTCAGTTTTGCAAGAATTTGATTATCAAA
18120982 ATTTCAGTTTTGCAAGAA
1 ATTTCAGTTTTGCAAGAA
18121000 CTCAGATTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
31 42 0.62
32 26 0.38
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (31 bp):
ATTTCAGTTTTGCAAGAATTTGATTATCAAA
Found at i:18121197 original size:26 final size:28
Alignment explanation
Indices: 18121157--18121216 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
18121147 AAAGATTCTT
*
18121157 AATTTCGCATTTAAG-ATTCACATCCAA
1 AATTTCGCATCTAAGAATTCACATCCAA
*
18121184 AATTT-GCATCTAAGATATTCATATCCAA
1 AATTTCGCATCTAAGA-ATTCACATCCAA
18121212 AATTT
1 AATTT
18121217 TAATTCAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 8 0.28
27 5 0.17
28 16 0.55
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (28 bp):
AATTTCGCATCTAAGAATTCACATCCAA
Found at i:18121917 original size:36 final size:36
Alignment explanation
Indices: 18121870--18121973 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 36
18121860 TCCTTTTTTC
* *
18121870 TCATTCTTTCACATTTTTCACTTTTTTTTTT-ACTTT
1 TCATTTTTTCACTTTTTTCA-TTTTTTTTTTCACTTT
*
18121906 TCATTTTTTCACTTTTTTCATTTTTCATTTTTCATTTT
1 TCATTTTTTCACTTTTTTCATTTTT--TTTTTCACTTT
*
18121944 TCA-TTTTTCA-TTTTTTCATTTTTCTTTTCA
1 TCATTTTTTCACTTTTTTCATTTTTTTTTTCA
18121974 TCCATTATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
34 6 0.10
35 5 0.08
36 31 0.51
37 12 0.20
38 7 0.11
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.69
Consensus pattern (36 bp):
TCATTTTTTCACTTTTTTCATTTTTTTTTTCACTTT
Found at i:18121929 original size:8 final size:7
Alignment explanation
Indices: 18121881--18121971 Score: 100
Period size: 7 Copynumber: 12.9 Consensus size: 7
18121871 CATTCTTTCA
18121881 CATTTTT
1 CATTTTT
18121888 CACTTTTT
1 CA-TTTTT
18121896 --TTTTT
1 CATTTTT
*
18121901 -ACTTTT
1 CATTTTT
18121907 CATTTTTT
1 CA-TTTTT
18121915 CACTTTTTT
1 CA--TTTTT
18121924 CATTTTT
1 CATTTTT
18121931 CATTTTT
1 CATTTTT
18121938 CATTTTT
1 CATTTTT
18121945 CATTTTT
1 CATTTTT
18121952 CATTTTTT
1 CA-TTTTT
18121960 CATTTTT
1 CATTTTT
18121967 C-TTTT
1 CATTTT
18121972 CATCCATTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.07
6 8 0.11
7 37 0.49
8 18 0.24
9 8 0.11
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
CATTTTT
Found at i:18127479 original size:3 final size:3
Alignment explanation
Indices: 18127471--18127497 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
18127461 TCAACAATTA
18127471 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
18127498 TGGGTCGGAC
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):
AAT
Found at i:18131644 original size:22 final size:22
Alignment explanation
Indices: 18131619--18131662 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
18131609 CAAAGTTTAG
18131619 AATTCGAACACCAAA-TTTATTA
1 AATTC-AACACCAAATTTTATTA
* *
18131641 AATTCAATACTAAATTTTATTA
1 AATTCAACACCAAATTTTATTA
18131663 TTATAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTCAACACCAAATTTTATTA
Found at i:18133083 original size:12 final size:12
Alignment explanation
Indices: 18133068--18133123 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
18133058 ACAACATGAA
*
18133068 CAGCTGCAACAG
1 CAGCAGCAACAG
*
18133080 CAGCAGCAACAA
1 CAGCAGCAACAG
* *
18133092 CAACAGCAGCAG
1 CAGCAGCAACAG
*
18133104 CAGCAGCAGCAG
1 CAGCAGCAACAG
18133116 CAGCAGCA
1 CAGCAGCA
18133124 GCAGTTACAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.39, C:0.34, G:0.25, T:0.02
Consensus pattern (12 bp):
CAGCAGCAACAG
Found at i:18133085 original size:3 final size:3
Alignment explanation
Indices: 18133077--18133127 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
18133067 ACAGCTGCAA
* * *
18133077 CAG CAG CAG CAA CAA CAA CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
18133125 CAG
1 CAG
18133128 TTACAATTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.39, C:0.33, G:0.27, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:18135097 original size:13 final size:13
Alignment explanation
Indices: 18135079--18135104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18135069 AATAAAATAA
18135079 ACTTTTCTTTTTT
1 ACTTTTCTTTTTT
18135092 ACTTTTCTTTTTT
1 ACTTTTCTTTTTT
18135105 TTTCTTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (13 bp):
ACTTTTCTTTTTT
Found at i:18135965 original size:25 final size:24
Alignment explanation
Indices: 18135936--18135993 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
18135926 AAATAATAAT
* **
18135936 AAAAATTATTGTAATTATGATTGAA
1 AAAAATTATTATAATTACAATT-AA
18135961 AAAAATTTATTATAATTACAATTAA
1 AAAAA-TTATTATAATTACAATTAA
18135986 AAAAATTA
1 AAAAATTA
18135994 ATAAAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.10
25 12 0.41
26 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (24 bp):
AAAAATTATTATAATTACAATTAA
Found at i:18135970 original size:26 final size:25
Alignment explanation
Indices: 18135936--18135992 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
18135926 AAATAATAAT
* **
18135936 AAAAA-TTATTGTAATTATGATTGAA
1 AAAAATTTATTATAATTACAATT-AA
18135961 AAAAATTTATTATAATTACAATTAA
1 AAAAATTTATTATAATTACAATTAA
18135986 AAAAATT
1 AAAAATT
18135993 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (25 bp):
AAAAATTTATTATAATTACAATTAA
Found at i:18136941 original size:24 final size:25
Alignment explanation
Indices: 18136896--18136943 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
18136886 TATAAGAGTT
* *
18136896 TATTTTTTATATATTAATATAAGAA
1 TATTTTTAATATAATAATATAAGAA
*
18136921 TATTTTTAATTTAATAA-ATAAGA
1 TATTTTTAATATAATAATATAAGA
18136944 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
TATTTTTAATATAATAATATAAGAA
Found at i:18143389 original size:12 final size:11
Alignment explanation
Indices: 18143341--18143395 Score: 53
Period size: 10 Copynumber: 5.1 Consensus size: 11
18143331 ATTAAATATG
18143341 TAAAA-TTTTA
1 TAAAATTTTTA
*
18143351 -AAAATTTTAA
1 TAAAATTTTTA
*
18143361 T-ATATTTTTA
1 TAAAATTTTTA
18143371 GTAAAATTATTTA
1 -TAAAATT-TTTA
18143384 TAAAATTTTTA
1 TAAAATTTTTA
18143395 T
1 T
18143396 TATTAAACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
9 4 0.11
10 11 0.31
11 6 0.17
12 11 0.31
13 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
TAAAATTTTTA
Found at i:18151377 original size:2 final size:2
Alignment explanation
Indices: 18151370--18151408 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
18151360 TGCAATTTTA
*
18151370 AT AT AT AT AT AT AT AT AT AT AT AC 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
18151409 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:18157779 original size:17 final size:18
Alignment explanation
Indices: 18157747--18157780 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18157737 CTAAAATAAA
*
18157747 AAAATAATTAATATATTC
1 AAAAGAATTAATATATTC
18157765 AAAAGAATT-ATATATT
1 AAAAGAATTAATATATT
18157781 TATAAAATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AAAAGAATTAATATATTC
Found at i:18159089 original size:29 final size:30
Alignment explanation
Indices: 18159035--18159098 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
18159025 TTTTGTTCAT
18159035 TTAAAAATTTAATTGAATTAAAATAAAAAA
1 TTAAAAATTTAATTGAATTAAAATAAAAAA
* ** *
18159065 TTAATAATTTAATT-AATTGTAATAAAATA
1 TTAAAAATTTAATTGAATTAAAATAAAAAA
18159094 TTAAA
1 TTAAA
18159099 CTTAAATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.55
30 13 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (30 bp):
TTAAAAATTTAATTGAATTAAAATAAAAAA
Found at i:18184115 original size:19 final size:20
Alignment explanation
Indices: 18184091--18184137 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
18184081 TTTTATTTTA
18184091 ATTTAAA-TTCAAAATATAT
1 ATTTAAATTTCAAAATATAT
*
18184110 ATTTAAAATTTTAAAATATAT
1 ATTT-AAATTTCAAAATATAT
18184131 ATTTAAA
1 ATTTAAA
18184138 GTTTTGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAATTTCAAAATATAT
Found at i:18184127 original size:21 final size:21
Alignment explanation
Indices: 18184101--18184142 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18184091 ATTTAAATTC
18184101 AAAATATATATTTAAAATTTT
1 AAAATATATATTTAAAATTTT
*
18184122 AAAATATATATTTAAAGTTTT
1 AAAATATATATTTAAAATTTT
18184143 GAATATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AAAATATATATTTAAAATTTT
Found at i:18184852 original size:18 final size:17
Alignment explanation
Indices: 18184829--18184865 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
18184819 CTAAATTATG
*
18184829 TATTTTTATTAATTTTTA
1 TATTTTTA-AAATTTTTA
18184847 TATTTTTAAAATTTTTA
1 TATTTTTAAAATTTTTA
18184864 TA
1 TA
18184866 AAATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTTTTAAAATTTTTA
Found at i:18184897 original size:57 final size:61
Alignment explanation
Indices: 18184836--18184958 Score: 146
Period size: 57 Copynumber: 2.1 Consensus size: 61
18184826 ATGTATTTTT
** * * * * * *
18184836 ATTAATTTTTATATTTTTAAAATTTTTA-TAAAATAA-AAATAA-TT-ATTTTATATTTAA
1 ATTAATTTAAATATATTAAAAATTCTTATTAAAATAATAAAAAATTTAAATTTAAATTTAA
18184893 ATTAATTTAAATATATTAAAAATTCTTATTAAAATAATAAAAAATTTAAATTTAAATTTAA
1 ATTAATTTAAATATATTAAAAATTCTTATTAAAATAATAAAAAATTTAAATTTAAATTTAA
18184954 ATTAA
1 ATTAA
18184959 AAACCAATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 23 0.43
58 8 0.15
59 5 0.09
60 2 0.04
61 16 0.30
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (61 bp):
ATTAATTTAAATATATTAAAAATTCTTATTAAAATAATAAAAAATTTAAATTTAAATTTAA
Found at i:18184949 original size:22 final size:23
Alignment explanation
Indices: 18184895--18184949 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
18184885 ATATTTAAAT
*
18184895 TAATTTAAATATATTAAAAATTC
1 TAATTTAAATATATAAAAAATTC
* *
18184918 TTATTAAAATA-ATAAAAAATT-
1 TAATTTAAATATATAAAAAATTC
18184939 TAAATTTAAAT
1 T-AATTTAAAT
18184950 TTAAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 1 0.04
22 16 0.62
23 9 0.35
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TAATTTAAATATATAAAAAATTC
Found at i:18186025 original size:37 final size:37
Alignment explanation
Indices: 18185984--18186058 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
18185974 GACTTAAAAC
*
18185984 AAATTATAAATGTAATAATATTAAATAAATATATTTT
1 AAATTATAAATGTAATAATATTAAATAAAAATATTTT
*
18186021 AAATTATATATGTAATAATATTAAATAAAAATATTTT
1 AAATTATAAATGTAATAATATTAAATAAAAATATTTT
18186058 A
1 A
18186059 CGTTTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.43
Consensus pattern (37 bp):
AAATTATAAATGTAATAATATTAAATAAAAATATTTT
Found at i:18186169 original size:70 final size:70
Alignment explanation
Indices: 18186095--18186472 Score: 305
Period size: 70 Copynumber: 5.3 Consensus size: 70
18186085 ACCAATAAAG
* * * *
18186095 ATTATATTTTTCTTTCAAAAGTGTGATTTTTATT-AAATTTTAAAATTTTAAAAATA-AAGTTTC
1 ATTATATTTTTATTT-AAAAATATGATTTTTGTTAAAATTTTAAAATTTTAAAAATATAA-TTTC
18186158 AATATCT
64 AATATCT
* * *
18186165 ATTATGTTTTTATTTTAAAAATATGATTTTTGTTAAAATTTTAAAA-TTTCAAAATATAATTTTA
1 ATTATATTTTTA-TTTAAAAATATGATTTTTGTTAAAATTTTAAAATTTTAAAAATATAATTTCA
18186229 ATATCT
65 ATATCT
* * *
18186235 ACTATATTTTTATCTTAAAAATATGATTTTTGTTAAAATTTTAAAA-TTTATAATATATAATTTT
1 ATTATATTTTTAT-TTAAAAATATGATTTTTGTTAAAATTTTAAAATTTTA-AAAATATAATTTC
* *
18186299 AACATCC
64 AATATCT
* * * * * * * *
18186306 ATTATATATTTTATATTAAAAACATAATTTTTGTTAAAAATTCACAATTTTGAAAATAAAATTTT
1 ATTATAT-TTTTAT-TTAAAAATATGATTTTTGTTAAAATTTTAAAATTTTAAAAATATAATTTC
* *
18186371 AACATCA
64 AATATCT
* * **** ** **
18186378 ATTATTTTTTTTTATCTTGAAAACGCAACATTAATTAAAATTTTAAAATTTTAAAAATATAATTT
1 ATTA--TATTTTTAT-TTAAAAATATGATTTTTGTTAAAATTTTAAAATTTTAAAAATATAATTT
* *
18186443 TAATAACT
63 CAATATCT
* *
18186451 ATTATGTCTTTTATTTTAAAAT
1 ATTATAT-TTTTATTTAAAAAT
18186473 GTAGAATTTA
Statistics
Matches: 254, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
69 1 0.00
70 89 0.35
71 47 0.19
72 60 0.24
73 55 0.22
74 2 0.01
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.49
Consensus pattern (70 bp):
ATTATATTTTTATTTAAAAATATGATTTTTGTTAAAATTTTAAAATTTTAAAAATATAATTTCAA
TATCT
Found at i:18186562 original size:18 final size:18
Alignment explanation
Indices: 18186530--18186564 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18186520 AATTTGAACA
18186530 GATTAAAAATGATAATTT
1 GATTAAAAATGATAATTT
18186548 GATTGAAAAAT-ATAATT
1 GATT-AAAAATGATAATT
18186565 AAATAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (18 bp):
GATTAAAAATGATAATTT
Found at i:18187505 original size:11 final size:12
Alignment explanation
Indices: 18187489--18187516 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18187479 ACTCGAAACC
18187489 AAAAAAGAAAAA
1 AAAAAAGAAAAA
18187501 AAAAAAGAAAAA
1 AAAAAAGAAAAA
18187513 AAAA
1 AAAA
18187517 GGTTTCTTTA
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Found at i:18202692 original size:10 final size:10
Alignment explanation
Indices: 18202679--18202712 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
18202669 AGAAAAGTTC
18202679 AAAAAATTTT
1 AAAAAATTTT
*
18202689 AAAAATTTTT
1 AAAAAATTTT
*
18202699 AAAAAATTCT
1 AAAAAATTTT
18202709 AAAA
1 AAAA
18202713 TTCTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:18202964 original size:18 final size:19
Alignment explanation
Indices: 18202923--18202968 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
18202913 ACAAGTTTTC
18202923 AAAAAAATTTAAAAATTAT
1 AAAAAAATTTAAAAATTAT
* * *
18202942 GAAAAAATTTTAAATTTA-
1 AAAAAAATTTAAAAATTAT
18202960 AAAAAAATT
1 AAAAAAATT
18202969 AATTTTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (19 bp):
AAAAAAATTTAAAAATTAT
Found at i:18203015 original size:25 final size:26
Alignment explanation
Indices: 18202987--18203043 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
18202977 TAAATTATGA
18202987 AAAATGA-AAAAATATAAAAT-ATTTT
1 AAAATGAGAAAAAT-TAAAATAATTTT
* *
18203012 AAAATTAGAAAAATTAAGATAATTTT
1 AAAATGAGAAAAATTAAAATAATTTT
18203038 ATAAAT
1 A-AAAT
18203044 TCAAACAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 11 0.41
26 12 0.44
27 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
AAAATGAGAAAAATTAAAATAATTTT
Found at i:18203025 original size:26 final size:27
Alignment explanation
Indices: 18202994--18203044 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
18202984 TGAAAAATGA
18202994 AAAAATATAAAAT-ATTTTA-AAATTAG
1 AAAAAT-TAAAATAATTTTATAAATTAG
*
18203020 AAAAATTAAGATAATTTTATAAATT
1 AAAAATTAAAATAATTTTATAAATT
18203045 CAAACAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 12 0.55
27 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAAATTAAAATAATTTTATAAATTAG
Found at i:18203118 original size:17 final size:19
Alignment explanation
Indices: 18203083--18203127 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
18203073 ATCCAAAAAA
18203083 TTCA-AAAAACTTCAAATT
1 TTCATAAAAACTTCAAATT
18203101 TTCATAAAAA-TT-AAATT
1 TTCATAAAAACTTCAAATT
*
18203118 TCCATAAAAA
1 TTCATAAAAA
18203128 AATACAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 14 0.56
18 6 0.24
19 5 0.20
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
TTCATAAAAACTTCAAATT
Found at i:18203187 original size:9 final size:9
Alignment explanation
Indices: 18203175--18203286 Score: 50
Period size: 9 Copynumber: 12.1 Consensus size: 9
18203165 TCTAAAACTT
18203175 TTTTAAAAA
1 TTTTAAAAA
*
18203184 TTTTGAAAA
1 TTTTAAAAA
18203193 -TTTAAAAA
1 TTTTAAAAA
* *
18203201 ATATAAAAA
1 TTTTAAAAA
*
18203210 -ATTAAAAA
1 TTTTAAAAA
***
18203218 AAATAAAAA
1 TTTTAAAAA
18203227 CCTTTTAAAAAA
1 --TTTT-AAAAA
*
18203239 TTCTAAAAA
1 TTTTAAAAA
*
18203248 TTATTAAAATT
1 TT-TTAAAA-A
18203259 TTTTGAAAAA
1 TTTT-AAAAA
*
18203269 -TTTAATAA
1 TTTTAAAAA
*
18203277 TTTAAAAAA
1 TTTTAAAAA
18203286 T
1 T
18203287 CTAAAACCTT
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
8 17 0.22
9 39 0.50
10 10 0.13
11 7 0.09
12 5 0.06
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.37
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:18203549 original size:15 final size:18
Alignment explanation
Indices: 18203529--18203567 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 18
18203519 TTTTTTTTGA
18203529 ATTTTTAA-AAAAT-TT-
1 ATTTTTAATAAAATCTTC
18203544 ATTTTTAATAAAATCTTC
1 ATTTTTAATAAAATCTTC
18203562 ATTTTT
1 ATTTTT
18203568 TTGAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 5 0.24
17 2 0.10
18 6 0.29
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAATAAAATCTTC
Found at i:18203662 original size:11 final size:11
Alignment explanation
Indices: 18203605--18203677 Score: 53
Period size: 11 Copynumber: 6.9 Consensus size: 11
18203595 AAATTTTGGA
*
18203605 TATTTTAAGAT
1 TATTTTAAAAT
*
18203616 T-TTTTGAAAT
1 TATTTTAAAAT
*
18203626 TTTTTTAAAA-
1 TATTTTAAAAT
* * *
18203636 AATATTAGAA-
1 TATTTTAAAAT
18203646 TATTTTAAAAT
1 TATTTTAAAAT
*
18203657 TATTTTAAAGT
1 TATTTTAAAAT
*
18203668 TTTTTTAAAA
1 TATTTTAAAA
18203678 AGTTCTTAGA
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
10 21 0.45
11 26 0.55
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TATTTTAAAAT
Found at i:18203713 original size:42 final size:42
Alignment explanation
Indices: 18203608--18203713 Score: 105
Period size: 42 Copynumber: 2.6 Consensus size: 42
18203598 TTTTGGATAT
* *
18203608 TTTAAGATT-TTTTGAAA-TTTTTTTAAAAAATATTAGAATAT
1 TTTAAAATTATTTT-AAAGTTTTTTTAAAAAATATTAGAATAC
* *
18203649 TTTAAAATTATTTTAAAGTTTTTTTAAAAAGTTCTTAGAA-AC
1 TTTAAAATTATTTTAAAGTTTTTTTAAAAA-ATATTAGAATAC
*
18203691 TTTAGAATT-TTTATAAA-TTTTTT
1 TTTAAAATTATTT-TAAAGTTTTTT
18203714 ATAACTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 20 0.36
42 29 0.52
43 7 0.12
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.53
Consensus pattern (42 bp):
TTTAAAATTATTTTAAAGTTTTTTTAAAAAATATTAGAATAC
Found at i:18205982 original size:12 final size:12
Alignment explanation
Indices: 18205961--18206038 Score: 50
Period size: 12 Copynumber: 5.9 Consensus size: 12
18205951 TTTTAAATTA
*
18205961 TAATAAAATATT
1 TAATATAATATT
18205973 TAATATAATATT
1 TAATATAATATT
*
18205985 TAAATTTAAAAATATT
1 T-AA--T-ATAATATT
*
18206001 TAATGTAATATT
1 TAATATAATATT
18206013 TAAATTATAA-ATT
1 T-AA-TATAATATT
18206026 TATTATATAATAT
1 TA--ATATAATAT
18206039 GATATTTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
12 20 0.38
13 14 0.27
14 7 0.13
15 3 0.06
16 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (12 bp):
TAATATAATATT
Found at i:18205996 original size:28 final size:29
Alignment explanation
Indices: 18205952--18206023 Score: 110
Period size: 28 Copynumber: 2.4 Consensus size: 29
18205942 ATTAATGCGT
18205952 TTTAAATTATAATAAAATATTTAATATAATA
1 TTTAAATTAT-A-AAAATATTTAATATAATA
*
18205983 TTTAAATT-TAAAAATATTTAATGTAATA
1 TTTAAATTATAAAAATATTTAATATAATA
18206011 TTTAAATTATAAA
1 TTTAAATTATAAA
18206024 TTTATTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 25 0.64
29 5 0.13
30 1 0.03
31 8 0.21
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
TTTAAATTATAAAAATATTTAATATAATA
Found at i:18206122 original size:27 final size:28
Alignment explanation
Indices: 18206092--18206160 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
18206082 ATAATGTATA
18206092 AATAATTTTTTAAAT-ATTATATTA-ATT
1 AATAATTTTTTAAATCA-TATATTATATT
* * *
18206119 AATAAATCTATAAATCATATATTATATT
1 AATAATTTTTTAAATCATATATTATATT
*
18206147 AA-AATTTTTAAAAT
1 AATAATTTTTTAAAT
18206161 TTAAGTATCA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
AATAATTTTTTAAATCATATATTATATT
Found at i:18212334 original size:20 final size:20
Alignment explanation
Indices: 18212309--18212349 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
18212299 TTGACATTTG
*
18212309 TCAAATGTG-AACTTTTGAAC
1 TCAAATGAGAAAC-TTTGAAC
18212329 TCAAATGAGAAACTTTGAAC
1 TCAAATGAGAAACTTTGAAC
18212349 T
1 T
18212350 TTTGGATACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
TCAAATGAGAAACTTTGAAC
Found at i:18212712 original size:41 final size:42
Alignment explanation
Indices: 18212620--18212989 Score: 400
Period size: 42 Copynumber: 8.9 Consensus size: 42
18212610 ATTGTCAAAG
** * * *
18212620 AGCATTTATTTTTTTTAAATTTATGGTGCCTCTGTTTAGA-A
1 AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
* *
18212661 GAGCATTT-TATTTTTCAAAAGTTGTGATGCCTTTATTTAGAGA
1 -AGCATTTAT-TTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
* * *
18212704 AGCATTTATTTTTTC-AAAGTTGTGGTGCCCCTGTTTAGAGG
1 AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
* *
18212745 AGTATTT-TATTTTTCAAAAGTTGTGGTACCTCTATTTAGA-A
1 AGCATTTAT-TTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
*
18212786 GAGCATTTATTTTTTCAAAA-TTGTGGTGCCTCTATTTAGAGG
1 -AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
* * * *
18212828 AGCATTTATTTTTTC-GAAGTTGTGGTACCTCTGTTTAGAGG
1 AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
*
18212869 AGCATTT-TATTTTTCAAAAGTTGTGGTACCTCTATTTAGAGA
1 AGCATTTAT-TTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
* *
18212911 AGCATTTATTTTTTC-AAAGTTGTGGTGCTTCTATTTAGAGG
1 AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
** * *
18212952 AGTTTTTCA-TTTTTCAAAAGTTGTTGTGCTTCTATTTA
1 AGCATTT-ATTTTTTCAAAAGTTGTGGTGCCTCTATTTA
18212990 AAGGAGCCTT
Statistics
Matches: 282, Mismatches: 32, Indels: 28
0.82 0.09 0.08
Matches are distributed among these distances:
40 4 0.01
41 135 0.48
42 139 0.49
43 4 0.01
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (42 bp):
AGCATTTATTTTTTCAAAAGTTGTGGTGCCTCTATTTAGAGA
Found at i:18212760 original size:83 final size:82
Alignment explanation
Indices: 18212619--18213077 Score: 439
Period size: 83 Copynumber: 5.5 Consensus size: 82
18212609 GATTGTCAAA
* * * * *
18212619 GAGCATTTATTTTTTTTAAATTTATGGTGCCTCTGTTTAGAAGAGCATTTTATTTTTCAAAAGTT
1 GAGCATTTA-TTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTATTTTTC-AAAGTT
*
18212684 GTGATGCCTTTATTTAGAG
64 GTGGTGCCTTTATTTAGAG
* * * *
18212703 AAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTAGAGGAGTATTTTATTTTTCAAAAGTTG
1 GAGCATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTATTTTTC-AAAGTTG
* * *
18212768 TGGTACCTCTATTTAGAA
65 TGGTGCCTTTATTTAGAG
* *
18212786 GAGCATTTATTTTTTCAAAATTGTGGTGCCTCTATTTAGAGGAGCA-TTTATTTTTTCGAAGTTG
1 GAGCATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTA-TTTTTCAAAGTTG
* * *
18212850 TGGTACCTCTGTTTAGAG
65 TGGTGCCTTTATTTAGAG
* *
18212868 GAGCATTT-TATTTTTCAAAAGTTGTGGTACCTCTATTTAGAGAAGCA-TTTATTTTTTCAAAGT
1 GAGCATTTAT-TTTTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTA-TTTTTCAAAGT
18212931 TGTGGTG-CTTCTATTTAGAG
63 TGTGGTGCCTT-TATTTAGAG
** * * * *
18212951 GAGTTTTTCA-TTTTTCAAAAGTTGTTGTGCTTCTATTTAAAGGAGCCTTTTA--TTTCAAAGTT
1 GAGCATTT-ATTTTTTC-AAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTT
* * * *
18213013 ATTGAG-CTTCTATTCAGAG
64 GTGGTGCCTT-TATTTAGAG
* * * *
18213032 GAGCTTATTTATTTTTTTAAAGTAGTGGAGCCTCTGTTTAGAGGAG
1 GAGC--ATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAG
18213078 TTTTTCTGTT
Statistics
Matches: 318, Mismatches: 47, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
81 29 0.09
82 65 0.20
83 212 0.67
84 12 0.04
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (82 bp):
GAGCATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTTGT
GGTGCCTTTATTTAGAG
Found at i:18212850 original size:124 final size:124
Alignment explanation
Indices: 18212643--18212975 Score: 483
Period size: 124 Copynumber: 2.7 Consensus size: 124
18212633 TTTAAATTTA
* * * * *
18212643 TGGTGCCTCTGTTTAGAAGAGCATTT-TATTTTTCAAAAGTTGTGATGCCTTTATTTAGAGAAGC
1 TGGTACCTCTATTTAGAAGAGCATTTAT-TTTTTCAAAA-TTGTGGTGCCTCTATTTAGAGGAGC
* *
18212707 ATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTAGAGGAGTATTTTATTTTTCAAAAGTTG
64 ATTTATTTTTTCAAAGTTGTGGTACCCCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
18212768 TGGTACCTCTATTTAGAAGAGCATTTATTTTTTCAAAATTGTGGTGCCTCTATTTAGAGGAGCAT
1 TGGTACCTCTATTTAGAAGAGCATTTATTTTTTCAAAATTGTGGTGCCTCTATTTAGAGGAGCAT
* *
18212833 TTATTTTTTCGAAGTTGTGGTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
66 TTATTTTTTCAAAGTTGTGGTACCCCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
* * **
18212892 TGGTACCTCTATTTAG-AGAAGCATTTATTTTTTCAAAGTTGTGGTGCTTCTATTTAGAGGAGTT
1 TGGTACCTCTATTTAGAAG-AGCATTTATTTTTTCAAAATTGTGGTGCCTCTATTTAGAGGAGCA
18212956 TTTCA-TTTTTCAAAAGTTGT
65 TTT-ATTTTTTC-AAAGTTGT
18212976 TGTGCTTCTA
Statistics
Matches: 190, Mismatches: 14, Indels: 8
0.90 0.07 0.04
Matches are distributed among these distances:
123 2 0.01
124 145 0.76
125 42 0.22
126 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.44
Consensus pattern (124 bp):
TGGTACCTCTATTTAGAAGAGCATTTATTTTTTCAAAATTGTGGTGCCTCTATTTAGAGGAGCAT
TTATTTTTTCAAAGTTGTGGTACCCCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
Found at i:18213022 original size:39 final size:39
Alignment explanation
Indices: 18212645--18213045 Score: 225
Period size: 41 Copynumber: 9.7 Consensus size: 39
18212635 TAAATTTATG
* * * *
18212645 GTGCCTCTGTTTAGAAGAGCATTTTATTTTTCAAAAGTTG-T
1 GTGCTTCTATTTAGAGGAGC-TTTT-TATTTC-AAAGTTGTT
* * *
18212686 GATGCCTT-TATTTAGAGAAGCATTTATTTTTTCAAAGTTGTG
1 G-TG-CTTCTATTTAGAGGAGC-TTT-TTATTTCAAAGTTGTT
** * *
18212728 GTGCCCCTGTTTAGAGGAG-TATTTTATTTTTCAAAAGTTGTG
1 GTGCTTCTATTTAGAGGAGCT-TTTTA--TTTC-AAAGTTGTT
* * * * * *
18212770 GTACCTCTATTTAGAAGAGCATTTATTTTTTCAAAATTGTG
1 GTGCTTCTATTTAGAGGAGC-TTT-TTATTTCAAAGTTGTT
* * * *
18212811 GTGCCTCTATTTAGAGGAGCATTTATTTTTTCGAAGTTGTG
1 GTGCTTCTATTTAGAGGAGC-TTT-TTATTTCAAAGTTGTT
* * * * *
18212852 GTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTGTG
1 GTGCTTCTATTTAGAGGAGC-TTTT-TATTTC-AAAGTTGTT
* * * * *
18212894 GTACCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTG
1 GTGCTTCTATTTAGAGGAGC-TTT-TTATTTCAAAGTTGTT
18212935 GTGCTTCTATTTAGAGGAG-TTTTTCATTTTTCAAAAGTTGTT
1 GTGCTTCTATTTAGAGGAGCTTTTT-A--TTTC-AAAGTTGTT
* * *
18212977 GTGCTTCTATTTAAAGGAGCCTTTTATTTCAAAGTTATT
1 GTGCTTCTATTTAGAGGAGCTTTTTATTTCAAAGTTGTT
* *
18213016 GAGCTTCTATTCAGAGGAGCTTATTTATTT
1 GTGCTTCTATTTAGAGGAGCTT-TTTATTT
18213046 TTTTAAAGTA
Statistics
Matches: 302, Mismatches: 37, Indels: 43
0.79 0.10 0.11
Matches are distributed among these distances:
38 2 0.01
39 32 0.11
40 15 0.05
41 126 0.42
42 114 0.38
43 10 0.03
44 3 0.01
ACGTcount: A:0.24, C:0.12, G:0.19, T:0.45
Consensus pattern (39 bp):
GTGCTTCTATTTAGAGGAGCTTTTTATTTCAAAGTTGTT
Found at i:18213044 original size:207 final size:207
Alignment explanation
Indices: 18212619--18213077 Score: 597
Period size: 207 Copynumber: 2.2 Consensus size: 207
18212609 GATTGTCAAA
* * * *
18212619 GAGCATTTATTTTTTTTAAATTTA-TGGTGCCTCTGTTTAGAAGAGCATTTTATTTTTCAAAAGT
1 GAGCATTTA-TTTTTTCAAA-GTAGTGGTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGT
* * *
18212683 TGTGATGCCTTTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTAGAGGAGT
64 TGTGATACCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTATTTAGAGGAGT
* * * *
18212748 ATTTTATTTTTCAAAAGTTGTGGTACCTCTATTTAGAAGAGCATTTATTTTTTCAAAATTGTGGT
129 ATTTTATTTTTCAAAAGTTGTGGTACCTCTATTTAGAAGAGCACTTATTATTTCAAAATTATGGA
*
18212813 GCCTCTATTTAGAG
194 GCCTCTATTCAGAG
* *
18212827 GAGCATTTATTTTTTCGAAGTTGTGGTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
1 GAGCATTTATTTTTTCAAAGTAGTGGTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
* **
18212892 TGGTACCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTGGTGCTTCTATTTAGAGGAGT-T
66 TGATACCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTATTTAGAGGAGTAT
* * * * *
18212956 TTTCATTTTTCAAAAGTTGTTGTGCTTCTATTTA-AAGGAGC-CTT-TTATTTCAAAGTTATTGA
131 TTT-ATTTTTCAAAAGTTGTGGTACCTCTATTTAGAA-GAGCACTTATTATTTCAAAATTATGGA
*
18213018 GCTTCTATTCAGAG
194 GCCTCTATTCAGAG
*
18213032 GAGCTTATTTATTTTTTTAAAGTAGTGG-AGCCTCTGTTTAGAGGAG
1 GAGC--ATTTATTTTTTCAAAGTAGTGGTA-CCTCTGTTTAGAGGAG
18213078 TTTTTCTGTT
Statistics
Matches: 219, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
205 29 0.13
206 10 0.05
207 171 0.78
208 9 0.04
ACGTcount: A:0.24, C:0.11, G:0.20, T:0.45
Consensus pattern (207 bp):
GAGCATTTATTTTTTCAAAGTAGTGGTACCTCTGTTTAGAGGAGCATTTTATTTTTCAAAAGTTG
TGATACCTCTATTTAGAGAAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTATTTAGAGGAGTAT
TTTATTTTTCAAAAGTTGTGGTACCTCTATTTAGAAGAGCACTTATTATTTCAAAATTATGGAGC
CTCTATTCAGAG
Found at i:18213258 original size:6 final size:7
Alignment explanation
Indices: 18213241--18213266 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18213231 TTGTTAATAA
18213241 AAAAATT
1 AAAAATT
18213248 AAAAATT
1 AAAAATT
18213255 AAAAATT
1 AAAAATT
18213262 AAAAA
1 AAAAA
18213267 GCTAGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAAATT
Found at i:18213619 original size:31 final size:31
Alignment explanation
Indices: 18213573--18213639 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
18213563 GAATTTTCAG
* * * *
18213573 TTTTCGATGAATTTTTTGGTATCGGTTGAAT
1 TTTTTGATGAATTTTTTGGTACCCGTTAAAT
*
18213604 TTTTTGATGAGTTTTTTGGTACCCGTTAAAT
1 TTTTTGATGAATTTTTTGGTACCCGTTAAAT
18213635 TTTTT
1 TTTTT
18213640 AGTAGGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.18, C:0.07, G:0.19, T:0.55
Consensus pattern (31 bp):
TTTTTGATGAATTTTTTGGTACCCGTTAAAT
Found at i:18216539 original size:3 final size:3
Alignment explanation
Indices: 18216533--18216568 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
18216523 TGTAAATAGC
18216533 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
18216569 TTTCTTTCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:18216616 original size:23 final size:23
Alignment explanation
Indices: 18216567--18216618 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
18216557 ATTATTATTA
* * *
18216567 TTTTTCTTTCTTTTTTTTTTATT
1 TTTTTCTTTCTTTTTCTTCTATC
18216590 TTTTTCTTTCTTTTTCCTTCT-TC
1 TTTTTCTTTCTTTTT-CTTCTATC
18216613 TTTTTC
1 TTTTTC
18216619 AATTATCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 22 0.88
24 3 0.12
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTCTTTCTTTTTCTTCTATC
Found at i:18217176 original size:9 final size:9
Alignment explanation
Indices: 18217162--18217186 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
18217152 GACAGGCAAT
18217162 GGTGACGGC
1 GGTGACGGC
18217171 GGTGACGGC
1 GGTGACGGC
18217180 GGTGACG
1 GGTGACG
18217187 ACCGAAGGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.20, G:0.56, T:0.12
Consensus pattern (9 bp):
GGTGACGGC
Found at i:18217617 original size:20 final size:23
Alignment explanation
Indices: 18217594--18217638 Score: 69
Period size: 20 Copynumber: 2.1 Consensus size: 23
18217584 ATTTTTTTTA
18217594 AAACTTTA-AA-AATA-AAAAAT
1 AAACTTTATAATAATACAAAAAT
18217614 AAACTTTATAATAATACAAAAAT
1 AAACTTTATAATAATACAAAAAT
18217637 AA
1 AA
18217639 TAAAAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 2 0.09
22 4 0.18
23 8 0.36
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (23 bp):
AAACTTTATAATAATACAAAAAT
Found at i:18220096 original size:20 final size:20
Alignment explanation
Indices: 18220071--18220109 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
18220061 GGATTTTTTC
18220071 TAAATTTATCCCAAATAGTG
1 TAAATTTATCCCAAATAGTG
18220091 TAAATTTATCCCAAATAGT
1 TAAATTTATCCCAAATAGT
18220110 AGAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (20 bp):
TAAATTTATCCCAAATAGTG
Found at i:18220181 original size:15 final size:15
Alignment explanation
Indices: 18220158--18220190 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
18220148 ATTTATTTTC
18220158 AAACAAAAAAATAAA
1 AAACAAAAAAATAAA
*
18220173 AAACCAAAAAATAAA
1 AAACAAAAAAATAAA
18220188 AAA
1 AAA
18220191 TTTTGGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (15 bp):
AAACAAAAAAATAAA
Found at i:18224578 original size:12 final size:12
Alignment explanation
Indices: 18224563--18224604 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
18224553 AAAGATTAAA
18224563 AAAAAAAGGATG
1 AAAAAAAGGATG
18224575 -AAAAAAGG-TG
1 AAAAAAAGGATG
*
18224585 AAAAAAAAGAATG
1 -AAAAAAAGGATG
18224598 AAAAAAA
1 AAAAAAA
18224605 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
12 14 0.54
13 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (12 bp):
AAAAAAAGGATG
Found at i:18224578 original size:13 final size:13
Alignment explanation
Indices: 18224562--18224604 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
18224552 AAAAGATTAA
18224562 AAAAAAAAGGATG
1 AAAAAAAAGGATG
18224575 --AAAAAAGG-TG
1 AAAAAAAAGGATG
*
18224585 AAAAAAAAGAATG
1 AAAAAAAAGGATG
18224598 AAAAAAA
1 AAAAAAA
18224605 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
12 7 0.27
13 9 0.35
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (13 bp):
AAAAAAAAGGATG
Found at i:18224588 original size:23 final size:22
Alignment explanation
Indices: 18224562--18224649 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 22
18224552 AAAAGATTAA
* *
18224562 AAAAAAAAGGATGAAAAAAGGTG
1 AAAAAAAAGAATGAAAAAA-ATG
18224585 AAAAAAAAGAATGAAAAAAATG
1 AAAAAAAAGAATGAAAAAAATG
*
18224607 ---AAAAATAATGAAAAATAA--
1 AAAAAAAAGAATGAAAAA-AATG
18224625 AAAATAAAA-AATGAAAAAAATG
1 AAAA-AAAAGAATGAAAAAAATG
18224647 AAA
1 AAA
18224650 GAATGGAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
19 14 0.25
20 4 0.07
21 10 0.18
22 9 0.16
23 18 0.33
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (22 bp):
AAAAAAAAGAATGAAAAAAATG
Found at i:18224601 original size:9 final size:8
Alignment explanation
Indices: 18224589--18224673 Score: 63
Period size: 7 Copynumber: 10.6 Consensus size: 8
18224579 AAGGTGAAAA
18224589 AAAAGAATG
1 AAAA-AATG
18224598 AAAAAAATG
1 -AAAAAATG
18224607 AAAAATAATG
1 -AAAA-AATG
18224617 -AAAAAT-
1 AAAAAATG
18224623 AAAAAAT-
1 AAAAAATG
18224630 AAAAAATG
1 AAAAAATG
18224638 AAAAAAATG
1 -AAAAAATG
*
18224647 AAAGAATG
1 AAAAAATG
*
18224655 -GAAAA-G
1 AAAAAATG
*
18224661 AAAATATG
1 AAAAAATG
18224669 AAAAA
1 AAAAA
18224674 GAGATAAAAG
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
6 1 0.02
7 22 0.35
8 15 0.24
9 17 0.27
10 8 0.13
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:18224601 original size:10 final size:10
Alignment explanation
Indices: 18224588--18224662 Score: 59
Period size: 10 Copynumber: 7.8 Consensus size: 10
18224578 AAAGGTGAAA
18224588 AAAAAGAATG
1 AAAAAGAATG
18224598 AAAAA-AATG
1 AAAAAGAATG
*
18224607 AAAAATAATG
1 AAAAAGAATG
* **
18224617 AAAAATAAAA
1 AAAAAGAATG
*
18224627 AATAAAAAATG
1 AA-AAAGAATG
18224638 AAAAA-AATG
1 AAAAAGAATG
18224647 --AAAGAATG
1 AAAAAGAATG
*
18224655 GAAAAGAA
1 AAAAAGAA
18224663 AATATGAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
7 3 0.05
8 4 0.07
9 13 0.24
10 28 0.51
11 7 0.13
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.12
Consensus pattern (10 bp):
AAAAAGAATG
Found at i:18224608 original size:32 final size:30
Alignment explanation
Indices: 18224535--18224673 Score: 104
Period size: 31 Copynumber: 4.4 Consensus size: 30
18224525 CAAATGGATG
*
18224535 AAAAAAT-AAAAAAGATTAAAAGATTAAAAAA-
1 AAAAAATGAAAAAA-ATGAAAA-A-TAAAAAAT
* * *
18224566 AAAAGGATGAAAAAAGGTGAAAAA-AAAGAAT
1 AAAA-AATGAAAAAA-ATGAAAAATAAAAAAT
18224597 GAAAAAAATGAAAAATAATGAAAAATAAAAAAT
1 --AAAAAATGAAAAA-AATGAAAAATAAAAAAT
** *
18224630 AAAAAATGAAAAAAATGAAAGAATGGAAAAG
1 AAAAAATGAAAAAAATGAAA-AATAAAAAAT
*
18224661 AAAATATGAAAAA
1 AAAAAATGAAAAA
18224674 GAGATAAAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
30 12 0.13
31 36 0.40
32 18 0.20
33 23 0.26
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.13
Consensus pattern (30 bp):
AAAAAATGAAAAAAATGAAAAATAAAAAAT
Found at i:18224622 original size:17 final size:16
Alignment explanation
Indices: 18224600--18224659 Score: 70
Period size: 16 Copynumber: 3.7 Consensus size: 16
18224590 AAAGAATGAA
18224600 AAAAATGAAAAATAATG
1 AAAAATGAAAAA-AATG
*
18224617 AAAAAT--AAAAAATA
1 AAAAATGAAAAAAATG
18224631 AAAAATGAAAAAAATG
1 AAAAATGAAAAAAATG
18224647 AAAGAATGGAAAA
1 AAA-AAT-GAAAA
18224660 GAAAATATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 9 0.24
15 4 0.11
16 10 0.27
17 9 0.24
18 5 0.14
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.13
Consensus pattern (16 bp):
AAAAATGAAAAAAATG
Found at i:18226095 original size:22 final size:22
Alignment explanation
Indices: 18226067--18226125 Score: 84
Period size: 21 Copynumber: 2.7 Consensus size: 22
18226057 AAAAATTCTC
18226067 AAATGAGAATCTTTGAAATTTT
1 AAATGAGAATCTTTGAAATTTT
* *
18226089 AGATGAGAATATTTG-AATTTT
1 AAATGAGAATCTTTGAAATTTT
*
18226110 AAATGAAAATCTTTGA
1 AAATGAGAATCTTTGA
18226126 GATGTGAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.39
Consensus pattern (22 bp):
AAATGAGAATCTTTGAAATTTT
Found at i:18226562 original size:41 final size:41
Alignment explanation
Indices: 18226454--18226998 Score: 539
Period size: 41 Copynumber: 13.1 Consensus size: 41
18226444 CGGGATTGTT
*
18226454 GAGGAGCATTTATTTTTTAAAAGTTTATGGTGCCTCTGTTTA
1 GAGGAGCATTTATTTTTTCAAAG-TTATGGTGCCTCTGTTTA
* *
18226496 GAAGAGCATTT-TATTTTTCAAAAGTTATGGTGCCTTTGTTTA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTA
* *
18226538 GAGGAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
* * *
18226579 GAAGAGTATTT-TATTTTTCAAAAGTTATGGTGCCTCTATTTA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTA
* * *
18226621 AAGGAGCATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
***
18226662 GAGGAGCATTTATTTTTTCAAAGTTACAATGCCTCTGTTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
* *
18226703 GAGGAGCATTT-TATTTTTCAAAAGTTATGGTGTCTCTATTTA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTA
* *
18226745 GAGAAGCATTTATTTTTTCAAAGTTACGGTGCCTCTGTTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
*
18226786 GA-GAGCATTT-TATTTTTCAAAAGTTATGGTACCTCTGTTTA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTA
* * * *
18226827 GAGAAGCATTTATTTTTTCAAAGTTGTGTTGCCTCTATTTA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
* ** * *
18226868 AAGGAGTTTTTCA-TTTTTCAAAAGTTATTGTGCCTCTATTTA
1 GAGGAGCATTT-ATTTTTTC-AAAGTTATGGTGCCTCTGTTTA
* * * * * * *
18226910 AAGGAGCCTTTCA--TTTTCAAAGTTGTTGAGCTTCTGTTCA
1 GAGGAGCATTT-ATTTTTTCAAAGTTATGGTGCCTCTGTTTA
* * * ** *
18226950 TAGGAGCTTATTTATTTTTTTAAAGTAATGAAGCCTTTGTTTA
1 GAGGAGC--ATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
18226993 GAGGAG
1 GAGGAG
18226999 TTTTTATGTT
Statistics
Matches: 420, Mismatches: 64, Indels: 37
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.00
40 38 0.09
41 188 0.45
42 161 0.38
43 32 0.08
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (41 bp):
GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTA
Found at i:18226594 original size:83 final size:82
Alignment explanation
Indices: 18226454--18226933 Score: 505
Period size: 83 Copynumber: 5.8 Consensus size: 82
18226444 CGGGATTGTT
*
18226454 GAGGAGCATTTATTTTTTAAAAGTTTATGGTGCCTCTGTTTAGAAGAGCATTT-TATTTTTCAAA
1 GAGGAGCATTTATTTTTTCAAAG-TTATGGTGCCTCTGTTTAGAAGAGCATTTAT-TTTTTC-AA
* *
18226518 AGTTATGGTGCCTTTGTTTA
63 AGTTACGGTGCCTCTGTTTA
* * *
18226538 GAGGAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTAGAAGAGTATTT-TATTTTTCAAAA
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAGCATTTAT-TTTTTC-AAA
* *
18226602 GTTATGGTGCCTCTATTTA
64 GTTACGGTGCCTCTGTTTA
* * * *
18226621 AAGGAGCATTTATTTTTTCAAAGTTGTGGTGCCTCTATTTAGAGGAGCATTTATTTTTTCAAAGT
1 GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAGCATTTATTTTTTCAAAGT
**
18226686 TACAATGCCTCTGTTTA
66 TACGGTGCCTCTGTTTA
* *
18226703 GAGGAGCATTT-TATTTTTCAAAAGTTATGGTGTCTCTATTTAG-AGAAGCATTTATTTTTTCAA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTAGAAG-AGCATTTATTTTTTCAA
18226766 AGTTACGGTGCCTCTGTTTA
63 AGTTACGGTGCCTCTGTTTA
*
18226786 GA-GAGCATTT-TATTTTTCAAAAGTTATGGTACCTCTGTTTAG-AGAAGCATTTATTTTTTCAA
1 GAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTAGAAG-AGCATTTATTTTTTCAA
** * *
18226848 AGTTGTGTTGCCTCTATTTA
63 AGTTACGGTGCCTCTGTTTA
* ** * * *
18226868 AAGGAGTTTTTCA-TTTTTCAAAAGTTATTGTGCCTCTATTTA-AAGGAGCCTTTCA--TTTTCA
1 GAGGAGCATTT-ATTTTTTC-AAAGTTATGGTGCCTCTGTTTAGAA-GAGCATTT-ATTTTTTCA
18226929 AAGTT
62 AAGTT
18226934 GTTGAGCTTC
Statistics
Matches: 351, Mismatches: 35, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
81 1 0.00
82 120 0.34
83 205 0.58
84 25 0.07
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (82 bp):
GAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAAGAGCATTTATTTTTTCAAAGT
TACGGTGCCTCTGTTTA
Found at i:18226700 original size:124 final size:125
Alignment explanation
Indices: 18226457--18226933 Score: 557
Period size: 124 Copynumber: 3.8 Consensus size: 125
18226447 GATTGTTGAG
* *
18226457 GAGCA-TTTATTTTTTAAAAGTTTATGGTGCCTCTGTTTAGAA-GAGCATTT-TATTTTTCAAAA
1 GAGCATTTTATTTTTCAAAAG-TTATGGTGCCTCTATTTA-AAGGAGCATTTAT-TTTTTCAAAA
* * * *
18226519 GTTATGGTGCCTTTGTTTAGAGGAGCATTTATTTTTTCAAAGTTGTGGTGCCCCTGTTTAGAA
63 GTTATGGTGCCTCTATTTAGAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAA
*
18226582 GAGTATTTTATTTTTCAAAAGTTATGGTGCCTCTATTTAAAGGAGCATTTATTTTTTC-AAAGTT
1 GAGCATTTTATTTTTCAAAAGTTATGGTGCCTCTATTTAAAGGAGCATTTATTTTTTCAAAAGTT
* *** *
18226646 GTGGTGCCTCTATTTAGAGGAGCATTTATTTTTTCAAAGTTACAATGCCTCTGTTTAGAG
66 ATGGTGCCTCTATTTAGAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAA
* * *
18226706 GAGCATTTTATTTTTCAAAAGTTATGGTGTCTCTATTTAGAGAAGCATTTATTTTTTC-AAAGTT
1 GAGCATTTTATTTTTCAAAAGTTATGGTGCCTCTATTTAAAGGAGCATTTATTTTTTCAAAAGTT
* * *
18226770 ACGGTGCCTCTGTTTAGA-GAGCATTT-TATTTTTCAAAAGTTATGGTACCTCTGTTTAG-A
66 ATGGTGCCTCTATTTAGAGGAGCATTTAT-TTTTTC-AAAGTTATGGTGCCTCTGTTTAGAA
* * **
18226829 GAAGCA-TTTATTTTTTC-AAAGTTGTGTTGCCTCTATTTAAAGGAGTTTTTCA-TTTTTCAAAA
1 G-AGCATTTTA-TTTTTCAAAAGTTATGGTGCCTCTATTTAAAGGAGCATTT-ATTTTTTCAAAA
* * *
18226891 GTTATTGTGCCTCTATTTAAAGGAGCCTTTCA--TTTTCAAAGTT
63 GTTATGGTGCCTCTATTTAGAGGAGCATTT-ATTTTTTCAAAGTT
18226934 GTTGAGCTTC
Statistics
Matches: 304, Mismatches: 36, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
122 1 0.00
123 57 0.19
124 189 0.62
125 42 0.14
126 15 0.05
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.44
Consensus pattern (125 bp):
GAGCATTTTATTTTTCAAAAGTTATGGTGCCTCTATTTAAAGGAGCATTTATTTTTTCAAAAGTT
ATGGTGCCTCTATTTAGAGGAGCATTTATTTTTTCAAAGTTATGGTGCCTCTGTTTAGAA
Found at i:18228074 original size:16 final size:16
Alignment explanation
Indices: 18228055--18228093 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
18228045 TTGTATAATT
*
18228055 AAATTTTAAAAAAATA
1 AAATTTGAAAAAAATA
*
18228071 AAATATGAAAAAAATA
1 AAATTTGAAAAAAATA
18228087 AAATTTG
1 AAATTTG
18228094 GGAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (16 bp):
AAATTTGAAAAAAATA
Found at i:18231107 original size:24 final size:26
Alignment explanation
Indices: 18231079--18231137 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
18231069 TTTTTATCTT
18231079 GTATATTTAGATA-ATTTTTT-ATAAA
1 GTATATTTA-ATATATTTTTTAATAAA
18231104 -TATATATTAATATATTTTTTCAATAAA
1 GTATAT-TTAATATATTTTTT-AATAAA
18231131 GTATATT
1 GTATATT
18231138 AATTCTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
24 8 0.28
25 10 0.34
27 6 0.21
28 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.53
Consensus pattern (26 bp):
GTATATTTAATATATTTTTTAATAAA
Found at i:18232147 original size:195 final size:185
Alignment explanation
Indices: 18231855--18232277 Score: 439
Period size: 195 Copynumber: 2.2 Consensus size: 185
18231845 AGAATATTGA
* * * * * *
18231855 AATTTAAAATGAACAAATTTCAAAATTTTC-TTTTCA-AATTTTTTATTTTTTAAATATTACATA
1 AATTTAATATAAATAAATTTCAAAATTTTCTTTTTAATAATTTTTTATTTTTTAAATATAAAATA
* *
18231918 GTTTTAATATATTTCATCAAAATTTATCGTTTAAAATAATTAAAATTTAAAAT-TTACTA-ATTT
66 GTTTTAATATATTTCATCAAAATTTATAGTTTAAAATAAATAAAATTTAAAATCTT-CTAGATTT
* * *
18231981 TAGAAGTTTTCATTTTATTTAAAAT-TTTAGGAATAATATATTTTTACATTTTATATAGTTCTAT
130 AAGAA----T--TGTT-TTT-AAATGTTTAGAAATAATATA-TTTTACATTTTATATAGTTCTAT
*
18232045 AATTTAATATAAATAAATTTCAAAAATTTTCTTTTTTTATAAGTTTTGTTA-TTTTTAAATATAA
1 AATTTAATATAAATAAATTTC-AAAATTTTC-TTTTTAATAA-TTTT-TTATTTTTTAAATATAA
* * ** * *
18232109 AATA-TTTTAATATGTTTTTATCAACTTTTATAGTTTAAAATAAATAAATTTTAAAATCTTTTAG
62 AATAGTTTTAATAT-ATTTCATCAAAATTTATAGTTTAAAATAAATAAAATTTAAAATCTTCTAG
* * * * *
18232173 CTTTAAGAATTGTTTTTAAATGTTTATAAATAATATATTTTATATTTTATCTAGTTTTAT
126 ATTTAAGAATTGTTTTTAAATGTTTAGAAATAATATATTTTACATTTTATATAGTTCTAT
18232233 AATTTAATATAAATAAATTTC-AAATTTTCATTTTTAATAATTTTT
1 AATTTAATATAAATAAATTTCAAAATTTTC-TTTTTAATAATTTTT
18232278 AAATATAGTA
Statistics
Matches: 199, Mismatches: 24, Indels: 26
0.80 0.10 0.10
Matches are distributed among these distances:
184 1 0.01
185 4 0.02
186 17 0.09
188 45 0.23
189 16 0.08
190 21 0.11
191 9 0.05
192 1 0.01
193 5 0.03
194 11 0.06
195 57 0.29
196 12 0.06
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (185 bp):
AATTTAATATAAATAAATTTCAAAATTTTCTTTTTAATAATTTTTTATTTTTTAAATATAAAATA
GTTTTAATATATTTCATCAAAATTTATAGTTTAAAATAAATAAAATTTAAAATCTTCTAGATTTA
AGAATTGTTTTTAAATGTTTAGAAATAATATATTTTACATTTTATATAGTTCTAT
Found at i:18233092 original size:16 final size:16
Alignment explanation
Indices: 18233063--18233119 Score: 59
Period size: 16 Copynumber: 3.7 Consensus size: 16
18233053 AAAATAATTT
18233063 TTAATATAAA-ATAAAA
1 TTAA-ATAAATATAAAA
18233079 TTAAATAAATATAAAA
1 TTAAATAAATATAAAA
*
18233095 AT-AA-AAATA-AATAA
1 TTAAATAAATATAA-AA
18233109 TTAAATAAATA
1 TTAAATAAATA
18233120 ATTAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.06
14 8 0.23
15 9 0.26
16 16 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAATAAATATAAAA
Found at i:18233095 original size:22 final size:21
Alignment explanation
Indices: 18233065--18233108 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
18233055 AATAATTTTT
*
18233065 AATATAAAATAAAATTAAATA
1 AATATAAAATAAAAATAAATA
18233086 AATATAAAAATAAAAATAAATA
1 AATAT-AAAATAAAAATAAATA
18233108 A
1 A
18233109 TTAAATAAAT
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:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
AATATAAAATAAAAATAAATA
Found at i:18233118 original size:22 final size:22
Alignment explanation
Indices: 18233070--18233133 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
18233060 TTTTTAATAT
* *
18233070 AAAATAAAATTAAATAAATATA
1 AAAATAAAAATAAATAATTATA
18233092 AAAATAAAAATAAATAATTA-A
1 AAAATAAAAATAAATAATTATA
18233113 ATAAATAATTAAA-AAATAATT
1 A-AAATAA--AAATAAATAATT
18233134 TATATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.05
22 24 0.65
23 8 0.22
24 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAAAAATAAATAATTATA
Found at i:18234917 original size:2 final size:2
Alignment explanation
Indices: 18234910--18234938 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18234900 GGTTTTTGTT
18234910 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18234939 CTCAGCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18237197 original size:63 final size:63
Alignment explanation
Indices: 18237127--18237264 Score: 176
Period size: 63 Copynumber: 2.2 Consensus size: 63
18237117 TTAACTCAAT
* * *
18237127 AAATTTTTATT-AAA-GATTATTGAAGGTGTTTTTGAG-TAAAAACA-CATTTAATAATTTTTTT
1 AAATTTTT-TTCAAAGGATTATTAAAGGTGTTTTTG-GTTAAAAACATC-TTCAATAATTCTTTT
18237188 C
63 C
*
18237189 AAATTTTTTTCAAAGGATTATTAAAGGTGTTTTTGGTTAAAAATATCTTCAATAATTCTTTTC
1 AAATTTTTTTCAAAGGATTATTAAAGGTGTTTTTGGTTAAAAACATCTTCAATAATTCTTTTC
*
18237252 AAATTTTGTTCAA
1 AAATTTTTTTCAA
18237265 GAGATTGTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
61 2 0.03
62 12 0.18
63 52 0.78
64 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (63 bp):
AAATTTTTTTCAAAGGATTATTAAAGGTGTTTTTGGTTAAAAACATCTTCAATAATTCTTTTC
Found at i:18237285 original size:63 final size:63
Alignment explanation
Indices: 18237164--18237307 Score: 150
Period size: 63 Copynumber: 2.3 Consensus size: 63
18237154 GTTTTTGAGT
* * * * ** * **
18237164 AAAAACACATTTAATAATTTTTTTCAAATTTTTTTCAAAGGATTATTAAAGGTGTTTTTGGTT
1 AAAAATACATTCAATAATTCTTTTCAAATTTTGTTCAAAGGATTATTAAAGGCATTTTTAGCC
*
18237227 AAAAATATC-TTCAATAATTCTTTTCAAATTTTGTTC-AAGAGATTGTTGAAA-GCATTTTTAGC
1 AAAAATA-CATTCAATAATTCTTTTCAAATTTTGTTCAAAG-GATTATT-AAAGGCATTTTTAGC
18237289 C
63 C
18237290 AAAAATACATTCAATAAT
1 AAAAATACATTCAATAAT
18237308 CTATTCCATA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
62 4 0.06
63 59 0.88
64 4 0.06
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (63 bp):
AAAAATACATTCAATAATTCTTTTCAAATTTTGTTCAAAGGATTATTAAAGGCATTTTTAGCC
Found at i:18237597 original size:39 final size:39
Alignment explanation
Indices: 18237552--18237630 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 39
18237542 ATTTTTCCTA
*
18237552 TATATCTATCATATG-TATTAATAATTAAAATATTATTTG
1 TATATCTATCATA-GATATTAATAATAAAAATATTATTTG
18237591 TATATCTATCATAGATATTAATAATAAAAATATTATTTG
1 TATATCTATCATAGATATTAATAATAAAAATATTATTTG
18237630 T
1 T
18237631 TTTTGTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (39 bp):
TATATCTATCATAGATATTAATAATAAAAATATTATTTG
Found at i:18242708 original size:28 final size:28
Alignment explanation
Indices: 18242656--18242731 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
18242646 AAGTGAAAAT
* *
18242656 TATATTA-ATTAACAAA-TTCATAATTCA
1 TATATTATATTAA-AAATTTTAAAATTCA
*
18242683 TATATTATATTAAAAATTTTAAAATTTA
1 TATATTATATTAAAAATTTTAAAATTCA
* * *
18242711 GATATCATATTAAACATTTTA
1 TATATTATATTAAAAATTTTA
18242732 TTATAATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.24
28 31 0.76
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (28 bp):
TATATTATATTAAAAATTTTAAAATTCA
Found at i:18244595 original size:176 final size:176
Alignment explanation
Indices: 18244294--18244611 Score: 378
Period size: 176 Copynumber: 1.8 Consensus size: 176
18244284 AGTTTTGTTA
* *
18244294 TTTTTAAATATAAAATAGTTTTAATATATTTTATCAACTTTTATAGTTTAAAATAAAAAAATTCT
1 TTTTTAAATATAAAATAGTTTTAATAGATTTTATCAACTGTTATAGTTTAAAATAAAAAAATTCT
* * * * * * *
18244359 AAAATCTTTTAGCTTTAAGAATTTTTTAAAATTTTATATGTAATATATTTTTATATTTTATCTAG
66 AAAATCTTTTAGCTTTAAGAATTTTTTAAAATTTTAAATATAATATAATATAACATTTTATATAG
* *
18244424 TTTTATTATTTAATATAAATAAATTCAAATTTTCATTTTTTAATAC
131 TTGTATGATTTAATATAAATAAATTCAAATTTTCATTTTTTAATAC
* * *
18244470 TTTTTAAATATAATATAGTTTT-A-AGATTTTATCATA-TGTTATTGTTTAAAATAAATGAAATT
1 TTTTTAAATATAAAATAGTTTTAATAGATTTTATCA-ACTGTTATAGTTTAAAATAAA-AAAATT
* * * *
18244532 -TAAAAAT-TTTCTA-CTTTTAGGATTTTTTTTGAATTTTTAAATATAATATAATATAACATTTT
64 CT-AAAATCTTT-TAGC-TTTAAGA-ATTTTTTAAAATTTTAAATATAATATAATATAACATTTT
18244594 ATATAGTTGTATGATTTA
125 ATATAGTTGTATGATTTA
18244612 GTAAGTTTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
174 32 0.27
175 20 0.17
176 66 0.56
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (176 bp):
TTTTTAAATATAAAATAGTTTTAATAGATTTTATCAACTGTTATAGTTTAAAATAAAAAAATTCT
AAAATCTTTTAGCTTTAAGAATTTTTTAAAATTTTAAATATAATATAATATAACATTTTATATAG
TTGTATGATTTAATATAAATAAATTCAAATTTTCATTTTTTAATAC
Found at i:18245244 original size:16 final size:18
Alignment explanation
Indices: 18245225--18245263 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18245215 TAATTCGTTT
18245225 TAAAATT-AATA-AAATA
1 TAAAATTAAATATAAATA
*
18245241 TAAAATTAAATATATATA
1 TAAAATTAAATATAAATA
18245259 TAAAA
1 TAAAA
18245264 ATATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATTAAATATAAATA
Found at i:18245265 original size:14 final size:14
Alignment explanation
Indices: 18245235--18245275 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
18245225 TAAAATTAAT
18245235 AAAATATA-AAAT-
1 AAAATATATAAATA
* *
18245247 TAAATATATATATA
1 AAAATATATAAATA
18245261 AAAATATATAAATA
1 AAAATATATAAATA
18245275 A
1 A
18245276 TAATTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 7 0.30
13 3 0.13
14 13 0.57
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
AAAATATATAAATA
Found at i:18253006 original size:2 final size:2
Alignment explanation
Indices: 18252999--18253036 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18252989 TTTTATTGCC
*
18252999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18253037 CATACATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18259381 original size:14 final size:15
Alignment explanation
Indices: 18259362--18259390 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18259352 TCATATAATC
18259362 ATTTTTAA-AAATTT
1 ATTTTTAATAAATTT
18259376 ATTTTTAATAAATTT
1 ATTTTTAATAAATTT
18259391 TAATTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAATAAATTT
Done.