Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001111.1 Hibiscus syriacus cultivar Beakdansim tig00002193_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: 3891333
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 17
Found at i:1390386 original size:30 final size:31
Alignment explanation
Indices: 1390265--1390409 Score: 96
Period size: 39 Copynumber: 4.1 Consensus size: 31
1390255 AACGATATTC
*
1390265 GAAAATATATATATTATATAGTTTTGAACATTTT
1 GAAAA-ATA-ATATAATATA-TTTTGAACATTTT
1390299 GAAAAAATATATATAATATATAGTTTTTGAAAACATTTT
1 G-AAAAATA-ATAT-A-ATATA--TTTTG--AACATTTT
1390338 GAAAACGATATAAATATAAT-TAGTTTTG-ACATTTT
1 G-AAA--A-AT-AATATAATATA-TTTTGAACATTTT
1390373 GAAAAATAATATAATAATATTTTGAAACATTTT
1 GAAAAATAATATAAT-ATATTTTG-AACATTTT
1390406 GAAA
1 GAAA
1390410 CGTATATAAT
Statistics
Matches: 94, Mismatches: 3, Indels: 29
0.75 0.02 0.23
Matches are distributed among these distances:
30 8 0.09
31 7 0.07
32 3 0.03
33 11 0.12
34 12 0.13
35 12 0.13
36 5 0.05
37 5 0.05
38 5 0.05
39 15 0.16
40 2 0.02
41 2 0.02
42 6 0.06
43 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (31 bp):
GAAAAATAATATAATATATTTTGAACATTTT
Found at i:1390441 original size:25 final size:26
Alignment explanation
Indices: 1390402--1390465 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
1390392 TTTTGAAACA
* * *
1390402 TTTTG-AAACGTATATAATTTATA-T
1 TTTTGAAAACATATATAATATACAGT
1390426 TTTTGAAAACATATATATAATATACAGT
1 TTTTGAAAAC--ATATATAATATACAGT
1390454 TTTTGAAAACAT
1 TTTTGAAAACAT
1390466 TTTGAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 5 0.15
25 4 0.12
26 2 0.06
27 11 0.33
28 11 0.33
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (26 bp):
TTTTGAAAACATATATAATATACAGT
Found at i:1390442 original size:27 final size:28
Alignment explanation
Indices: 1390412--1390465 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1390402 TTTTGAAACG
* *
1390412 TATATAATTTATA-TTTTTGAAAACATA
1 TATATAATATACAGTTTTTGAAAACATA
1390439 TATATAATATACAGTTTTTGAAAACAT
1 TATATAATATACAGTTTTTGAAAACAT
1390466 TTTGAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (28 bp):
TATATAATATACAGTTTTTGAAAACATA
Found at i:1390478 original size:62 final size:57
Alignment explanation
Indices: 1390369--1390488 Score: 136
Period size: 63 Copynumber: 2.0 Consensus size: 57
1390359 AGTTTTGACA
* *
1390369 TTTTGAAAAATAATATAATAATATTTTGAAACATTTTGAAACGTATATA-ATTTATAT
1 TTTTGAAAAATAATATAATAACATTTTGAAACATTTTGAAAC-TATATATATATATAT
1390426 TTTTGAAAACATATATATAATATACAGTTTTTGAAAACATTTTGAATA-TATATATATATATAT
1 TTTTGAAAA-ATA-ATATAATA-ACA--TTTTG-AAACATTTTGAA-ACTATATATATATATAT
1390489 ATATAGTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
57 9 0.17
58 3 0.06
59 8 0.15
60 2 0.04
62 11 0.21
63 19 0.36
64 1 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (57 bp):
TTTTGAAAAATAATATAATAACATTTTGAAACATTTTGAAACTATATATATATATAT
Found at i:1390562 original size:80 final size:79
Alignment explanation
Indices: 1390426--1390722 Score: 417
Period size: 78 Copynumber: 3.7 Consensus size: 79
1390416 TAATTTATAT
* *
1390426 TTTTGAAAACATATATATAATATACAGTTTTTGAAAACATTTTGAATATATATATATATATATAT
1 TTTTGAAAA-ATATATATAATATATAG-TTTTGAAAACATTTTGAAAATATATATATATATATAT
1390491 ATAGTTTTTGAAAACA
64 ATAGTTTTTGAAAACA
*
1390507 TTTTGAAAAAATATATATAATATATAGTTTTGAAAACATTTTGAATATATATATATATA-ATATA
1 TTTTG-AAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATATATATATA
1390571 TAGTTTTTGAAAACA
65 TAGTTTTTGAAAACA
*
1390586 TTTTGAAAAA-ATATATAATATATAATTTTTGAAAACATTTTGAAAATATATATATATATA-ATA
1 TTTTGAAAAATATATATAATATAT-AGTTTTGAAAACATTTTGAAAATATATATATATATATATA
*
1390649 TAG-TTTTGGAAACA
65 TAGTTTTTGAAAACA
* *
1390663 TTTTTGAAAACT-TATATAATATATAGTTTTGACAATCAATTTTTGAAAATATAT-TATATA
1 -TTTTGAAAAATATATATAATATATAGTTTTGA-AAAC-A-TTTTGAAAATATATATATATA
1390723 GTTTTGAAAA
Statistics
Matches: 201, Mismatches: 7, Indels: 18
0.89 0.03 0.08
Matches are distributed among these distances:
77 30 0.15
78 67 0.33
79 33 0.16
80 46 0.23
81 21 0.10
82 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (79 bp):
TTTTGAAAAATATATATAATATATAGTTTTGAAAACATTTTGAAAATATATATATATATATATAT
AGTTTTTGAAAACA
Found at i:1390753 original size:35 final size:35
Alignment explanation
Indices: 1390639--1390755 Score: 114
Period size: 35 Copynumber: 3.3 Consensus size: 35
1390629 AAATATATAT
* *
1390639 ATATATAATATAGTTTTGGAAA-C-ATTTTTGAAA
1 ATATATTATATAGTTTTGAAAATCAATTTTTGAAA
*
1390672 ACTTATATAATATATAGTTTTGACAATCAATTTTTGAAA
1 A--TATAT--TATATAGTTTTGAAAATCAATTTTTGAAA
** *
1390711 ATATATTATATAGTTTTGAAAAT-GTTTTTTGAAC
1 ATATATTATATAGTTTTGAAAATCAATTTTTGAAA
1390745 ATATTATTATA
1 ATA-TATTATA
1390756 CATTATATTA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
33 1 0.01
34 11 0.16
35 28 0.40
37 18 0.26
38 1 0.01
39 11 0.16
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.46
Consensus pattern (35 bp):
ATATATTATATAGTTTTGAAAATCAATTTTTGAAA
Found at i:1390767 original size:5 final size:5
Alignment explanation
Indices: 1390757--1390836 Score: 56
Period size: 5 Copynumber: 14.8 Consensus size: 5
1390747 ATTATTATAC
1390757 ATTAT ATTAT ATTACT ATTATT ATTTAT ATTAT ATCATAT ATTAT A--AT
1 ATTAT ATTAT ATTA-T ATTA-T A-TTAT ATTAT AT--TAT ATTAT ATTAT
* *
1390805 ATTAT ATTTTT ATTATGT ATTAT TTTAT ATTA
1 ATTAT A-TTAT ATTA--T ATTAT ATTAT ATTA
1390837 AATGTTTTTA
Statistics
Matches: 61, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
3 3 0.05
5 32 0.52
6 13 0.21
7 13 0.21
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:1390833 original size:31 final size:31
Alignment explanation
Indices: 1390748--1390820 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 31
1390738 TTTGAACATA
1390748 TTATTATA-CATTATATTATATTACTATTATTATTT
1 TTATTATATCA-TATATTATA--A-TATTA-TATTT
*
1390783 ATATTATATCATATATTATAATATTATATTT
1 TTATTATATCATATATTATAATATTATATTT
1390814 TTATTAT
1 TTATTAT
1390821 GTATTATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 11 0.31
32 5 0.14
33 1 0.03
35 16 0.46
36 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (31 bp):
TTATTATATCATATATTATAATATTATATTT
Found at i:1392291 original size:17 final size:17
Alignment explanation
Indices: 1392269--1392318 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
1392259 ATTTATTTAA
1392269 TATTTTACATATTTATT
1 TATTTTACATATTTATT
* *
1392286 TATTTTTCCA-ATTGATT
1 TA-TTTTACATATTTATT
1392303 TA-TTTA-ATATTTATT
1 TATTTTACATATTTATT
1392318 T
1 T
1392319 CTTATTTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 10 0.37
17 10 0.37
18 6 0.22
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (17 bp):
TATTTTACATATTTATT
Found at i:1397707 original size:85 final size:85
Alignment explanation
Indices: 1397564--1397803 Score: 340
Period size: 85 Copynumber: 2.8 Consensus size: 85
1397554 CCCCAGCGTA
* * *
1397564 TTACAGTATAGCTCAAGGCGAGAAGGGCTATCTATCAACCAAAACCTTT-GAGTTCGATTACATT
1 TTACAGTATAACTCAAGGCGAGAAGAGCTATCTATCAA-CAAAAACTTTCGAGTTCGATTACATT
1397628 CAGCTCAAGGACATATCAAAT
65 CAGCTCAAGGACATATCAAAT
* * *
1397649 TTACAGTATAACTCAAGGCGAGAAGAGTTATCTGTCAATAAAAACTTTCGAGTTCGATTACATTC
1 TTACAGTATAACTCAAGGCGAGAAGAGCTATCTATCAACAAAAACTTTCGAGTTCGATTACATTC
*
1397714 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGACATATCAAAT
** * * *
1397734 TTACAACATAACTCAAGGCGAGAA-AGGCTATATATCAACAAACACTTTCGAGTTCGATTTCATT
1 TTACAGTATAACTCAAGGCGAGAAGA-GCTATCTATCAACAAAAACTTTCGAGTTCGATTACATT
1397798 CAGCTC
65 CAGCTC
1397804 GAGGGCCTAT
Statistics
Matches: 138, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
84 9 0.07
85 129 0.93
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (85 bp):
TTACAGTATAACTCAAGGCGAGAAGAGCTATCTATCAACAAAAACTTTCGAGTTCGATTACATTC
AGCTCAAGGACATATCAAAT
Found at i:1398442 original size:39 final size:39
Alignment explanation
Indices: 1398418--1398532 Score: 129
Period size: 35 Copynumber: 3.1 Consensus size: 39
1398408 ATAATTTTTG
1398418 AAAAT-ATTTTTTGAAAA-ATATAATATATGATTTTTAA
1 AAAATGATTTTTTGAAAATATATAATATATGATTTTTAA
*
1398455 AAAATGATTTTTTGAAAATATAT-A-ATAT-ACTTTT-A
1 AAAATGATTTTTTGAAAATATATAATATATGATTTTTAA
*
1398490 AAAATCGA-TTTTTGAAAATATATATATTATAT-ATTTTTGA
1 AAAAT-GATTTTTTGAAAATATATA-A-TATATGATTTTTAA
1398530 AAA
1 AAA
1398533 CGGTATTCGA
Statistics
Matches: 68, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
35 21 0.31
36 7 0.10
37 10 0.15
38 13 0.19
39 13 0.19
40 4 0.06
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (39 bp):
AAAATGATTTTTTGAAAATATATAATATATGATTTTTAA
Found at i:1398473 original size:37 final size:34
Alignment explanation
Indices: 1398400--1398516 Score: 123
Period size: 35 Copynumber: 3.3 Consensus size: 34
1398390 TATTATTATT
* *
1398400 AATATAGTATA-ATTTTTGAAAAT-ATTTTTTGAAA
1 AATATA-TATATACTTTTAAAAATGATTTTTTG-AA
*
1398434 AATATAATATATGATTTTTAAAAAATGATTTTTTGAA
1 AATAT-ATATAT-ACTTTT-AAAAATGATTTTTTGAA
1398471 AATATATAATATACTTTTAAAAATCGA-TTTTTGAA
1 AATATAT-ATATACTTTTAAAAAT-GATTTTTTGAA
1398506 AATATATATAT
1 AATATATATAT
1398517 TATATATTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
34 13 0.18
35 22 0.30
36 15 0.20
37 16 0.22
38 8 0.11
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (34 bp):
AATATATATATACTTTTAAAAATGATTTTTTGAA
Found at i:1398617 original size:45 final size:40
Alignment explanation
Indices: 1398499--1398646 Score: 139
Period size: 37 Copynumber: 3.7 Consensus size: 40
1398489 AAAAATCGAT
*
1398499 TTTTGAAAATATATATATTATATA-TTTTTGAAAACGGTA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACGGTA
* *
1398538 -TTCGAAAATATATAT-ATCATATAG-TTTTGAAAAACGACATTACA
1 TTTTGAAAATATATATAAT-ATATAGTTTTTG-AAAACG---GT--A
1398582 TTTTGAAAATATATATAATATATAGTTTTTGAAAAC---A
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACGGTA
**
1398619 TTTTGAAAACGTATATAATATATAGTTT
1 TTTTGAAAATATATATAATATATAGTTT
1398647 CGAGAATCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 24
0.75 0.05 0.20
Matches are distributed among these distances:
37 28 0.30
38 24 0.26
39 6 0.07
42 1 0.01
44 1 0.01
45 25 0.27
46 7 0.08
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACGGTA
Found at i:1398671 original size:75 final size:75
Alignment explanation
Indices: 1398582--1398754 Score: 185
Period size: 75 Copynumber: 2.3 Consensus size: 75
1398572 CGACATTACA
* * *
1398582 TTTTGAAAATATATATAATATATAGTTTTTGAAAA-CATTT-TGAAAACGTATATAATATATAGT
1 TTTTGAAAATATATAT--TATACA-TTTTTGAAAATAATTTGTGAAAACATATATAATATATAGT
1398645 TTCGAGAATCAAT
63 TTCGAGAATCAAT
* *
1398658 TTTTGAAAA-ATATATTATACATTTTTGAAAATTAATTTGTGAAAACATATTTATTATATAGTTT
1 TTTTGAAAATATATATTATACATTTTTGAAAA-TAATTTGTGAAAACATATATAATATATAGTTT
* ***
1398722 CGAAAATGTTT
65 CGAGAATCAAT
*
1398733 TTTTG-ACATATA-ATTATACATT
1 TTTTGAAAATATATATTATACATT
1398755 ATATTAATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
72 10 0.12
73 5 0.06
74 16 0.19
75 43 0.52
76 9 0.11
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (75 bp):
TTTTGAAAATATATATTATACATTTTTGAAAATAATTTGTGAAAACATATATAATATATAGTTTC
GAGAATCAAT
Found at i:1400243 original size:44 final size:44
Alignment explanation
Indices: 1400195--1400279 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
1400185 AAAATTTAAA
* **
1400195 ATTTTTTATTTTTTATTTTCCCC-TTGATTTATTTAATATTTTAC
1 ATTTTTTATTTATT-TTCCCCCCTTTGATTTATTTAATATTTTAC
*
1400239 ATTTTTTATTTATTTTCCCCCCTTTGATTTATTTATTATTT
1 ATTTTTTATTTATTTTCCCCCCTTTGATTTATTTAATATTT
1400280 CTTATCTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 6 0.17
44 30 0.83
ACGTcount: A:0.19, C:0.13, G:0.02, T:0.66
Consensus pattern (44 bp):
ATTTTTTATTTATTTTCCCCCCTTTGATTTATTTAATATTTTAC
Found at i:1409910 original size:28 final size:28
Alignment explanation
Indices: 1409879--1409936 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1409869 AATTAAGCAT
1409879 GAATTGTTAACCACATGCAATTTCGGTG
1 GAATTGTTAACCACATGCAATTTCGGTG
**
1409907 GAATTGTTGGCCACATGCAATTTCGGTG
1 GAATTGTTAACCACATGCAATTTCGGTG
1409935 GA
1 GA
1409937 GAGTTGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (28 bp):
GAATTGTTAACCACATGCAATTTCGGTG
Found at i:1414422 original size:28 final size:28
Alignment explanation
Indices: 1414391--1414448 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
1414381 AATTAAGCAT
*
1414391 GAATTGTTGGCCACATGGAATTTCGGTG
1 GAATTGTTGGCCACATGCAATTTCGGTG
1414419 GAATTGTTGGCCACATGCAATTTCGGTG
1 GAATTGTTGGCCACATGCAATTTCGGTG
1414447 GA
1 GA
1414449 GAGTTTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.31
Consensus pattern (28 bp):
GAATTGTTGGCCACATGCAATTTCGGTG
Found at i:1414608 original size:30 final size:30
Alignment explanation
Indices: 1414572--1414633 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1414562 CTTAAGTTTT
1414572 AACTATAAATACCCTAGCTCATTTAGCTTC
1 AACTATAAATACCCTAGCTCATTTAGCTTC
1414602 AACTATAAATACCCTAGCTCATTTAGCTTC
1 AACTATAAATACCCTAGCTCATTTAGCTTC
1414632 AA
1 AA
1414634 AACCATCCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (30 bp):
AACTATAAATACCCTAGCTCATTTAGCTTC
Found at i:1414784 original size:59 final size:59
Alignment explanation
Indices: 1414715--1414833 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1414705 CTCCTTTTTA
*
1414715 TCAAGAGAGAATTATCATTGTTTTCTCCTTGGTAGATTGAGAGAAGTTGTAATTCCTAT
1 TCAAGAGAGAATTATCATTGCTTTCTCCTTGGTAGATTGAGAGAAGTTGTAATTCCTAT
1414774 TCAAGAGAGAATTATCATTGCTTTCTCCTTGGTAGATTGAGAGAAGTTGTAATTCCTAT
1 TCAAGAGAGAATTATCATTGCTTTCTCCTTGGTAGATTGAGAGAAGTTGTAATTCCTAT
1414833 T
1 T
1414834 TTCTCATAGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.39
Consensus pattern (59 bp):
TCAAGAGAGAATTATCATTGCTTTCTCCTTGGTAGATTGAGAGAAGTTGTAATTCCTAT
Found at i:1418173 original size:15 final size:15
Alignment explanation
Indices: 1418153--1418186 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1418143 CATAATTCAA
*
1418153 ATATATGTTATTTGG
1 ATATATGTTATTTAG
1418168 ATATATGTTATTTAG
1 ATATATGTTATTTAG
1418183 ATAT
1 ATAT
1418187 GTATTATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (15 bp):
ATATATGTTATTTAG
Found at i:1418483 original size:26 final size:26
Alignment explanation
Indices: 1418445--1418502 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
1418435 ATTTAACTTC
* * * *
1418445 ATGACTATCATTGTTTGATTCAGATT
1 ATGATTATCATTGGTTGATTCAAACT
*
1418471 ATGATTATTATTGGTTGATTCAAACT
1 ATGATTATCATTGGTTGATTCAAACT
1418497 ATGATT
1 ATGATT
1418503 TGAATATTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.47
Consensus pattern (26 bp):
ATGATTATCATTGGTTGATTCAAACT
Found at i:1422895 original size:18 final size:19
Alignment explanation
Indices: 1422868--1422903 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1422858 ATTGAAATTA
1422868 ATCGATTAATAAATTAAAT
1 ATCGATTAATAAATTAAAT
*
1422887 ATCGA-TAATTAATTAAA
1 ATCGATTAATAAATTAAA
1422904 AATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (19 bp):
ATCGATTAATAAATTAAAT
Found at i:1424410 original size:7 final size:7
Alignment explanation
Indices: 1424398--1424438 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
1424388 AATAAACTTT
1424398 TAAAAAA
1 TAAAAAA
1424405 T-AAAAA
1 TAAAAAA
1424411 TAAAATAA
1 TAAAA-AA
1424419 TAAAAAA
1 TAAAAAA
1424426 TAAAAAA
1 TAAAAAA
1424433 -AAAAAA
1 TAAAAAA
1424439 AAATATGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 12 0.38
7 13 0.41
8 7 0.22
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:1424427 original size:15 final size:15
Alignment explanation
Indices: 1424348--1424438 Score: 55
Period size: 16 Copynumber: 5.9 Consensus size: 15
1424338 TTAGAAAACT
*
1424348 AAATATATAAAAAATG
1 AAATA-ATAAAAAATA
* *
1424364 AAATTATGAAATAAATT
1 AAATAAT-AAA-AAATA
*
1424381 AAATAATAATAAACTTTTA
1 AAATAATAA-AAA---ATA
1424400 AAA-AAT-AAAAATA
1 AAATAATAAAAAATA
1424413 AAATAATAAAAAATA
1 AAATAATAAAAAATA
1424428 AAA-AA-AAAAAA
1 AAATAATAAAAAA
1424439 AAATATGCAA
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
13 11 0.18
14 5 0.08
15 12 0.20
16 14 0.23
17 12 0.20
18 3 0.05
19 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.02, T:0.24
Consensus pattern (15 bp):
AAATAATAAAAAATA
Found at i:1425651 original size:3 final size:3
Alignment explanation
Indices: 1425643--1425697 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
1425633 GGATTGGTTG
*
1425643 TAA TAA TAA T-A TATA TAA GAA TAA TAA T-A TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
1425687 TAT TAA TAA TA
1 TAA TAA TAA TA
1425698 TGGATGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 6 0.14
3 32 0.74
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1425667 original size:18 final size:17
Alignment explanation
Indices: 1425644--1425695 Score: 68
Period size: 18 Copynumber: 3.0 Consensus size: 17
1425634 GATTGGTTGT
*
1425644 AATAATAATATATATAA
1 AATAATAATATAAATAA
1425661 GAATAATAATATAAATAA
1 -AATAATAATATAAATAA
* *
1425679 TATAATAATATTAATAA
1 AATAATAATATAAATAA
1425696 TATGGATGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 15 0.48
18 16 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (17 bp):
AATAATAATATAAATAA
Found at i:1425681 original size:23 final size:24
Alignment explanation
Indices: 1425650--1425694 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
1425640 TTGTAATAAT
1425650 AATATATATAAGAATAATAATATA
1 AATATATATAAGAATAATAATATA
* *
1425674 AATA-ATATAATAATATTAATA
1 AATATATATAAGAATAATAATA
1425695 ATATGGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AATATATATAAGAATAATAATATA
Found at i:1425846 original size:17 final size:17
Alignment explanation
Indices: 1425821--1425859 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
1425811 CTGTGAACTC
*
1425821 TTCACTGGGAATGTCAA
1 TTCATTGGGAATGTCAA
1425838 TTCATTGGGAATGTCAA
1 TTCATTGGGAATGTCAA
1425855 TTCAT
1 TTCAT
1425860 CTATTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (17 bp):
TTCATTGGGAATGTCAA
Found at i:1426243 original size:42 final size:42
Alignment explanation
Indices: 1426175--1426263 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
1426165 AAGGTCATAT
* * *
1426175 CATCTTGCTCGAAAGTCTTATAAATGGTCCGAAGGACTTACG
1 CATCATGCTCGAAAGACTTATAAATGGCCCGAAGGACTTACG
*
1426217 CATCATGCTCGAAAGACTTACT-AATGGCCCGAAGGACTTACT
1 CATCATGCTCGAAAGACTTA-TAAATGGCCCGAAGGACTTACG
1426259 CATCA
1 CATCA
1426264 AGAAACCCTT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTATAAATGGCCCGAAGGACTTACG
Found at i:1426515 original size:42 final size:41
Alignment explanation
Indices: 1426413--1426519 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 41
1426403 GCTCGAAGGT
* * * *
1426413 CTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCAAAAGA
* * * *
1426454 CTTATATATGACCCAAAGGATTTAAGCATCATGCTCAAAAGA
1 CTTATAGATGGCCCGAAGGACTT-AGCATCATGCTCAAAAGA
1426496 CTTACT-GATGGCCCGAAGGACTTA
1 CTTA-TAGATGGCCCGAAGGACTTA
1426520 CTCAACAAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 19 0.37
42 32 0.62
43 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTAGCATCATGCTCAAAAGA
Found at i:1426531 original size:263 final size:263
Alignment explanation
Indices: 1426062--1426601 Score: 803
Period size: 263 Copynumber: 2.1 Consensus size: 263
1426052 TACTGGCGAT
* *
1426062 GTTGGTCCATCGAGTGAGGTGTTGCTGATTCAACTCTATATGTGATGAATCAAGTACAGGAAATG
1 GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCAAGTACAGGAAATG
* * *
1426127 TTGAAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAGGTCATATCATCTTGCTCGAAAGTC
66 TTAAAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAGGACATATCATCTTGCTCGAAAGAC
** * * *
1426192 TTATAAATGGTCCGAAGGACTTACGCATCATGCTCGAAAGACTTACTAATGGCCCGAAGGACTTA
131 TTATAAATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTA
* * * *
1426257 CTCATCAAGAAACCCTTGAAAACCAATATTATTTTCTTAGTTGTCATCAATGAACCCCTACATAT
196 CTCAACAAGAAACCCTTGAAAACCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATAT
*
1426322 TAC
261 CAC
* *
1426325 GTTGGTCCCTCGAGTGAGGTGTTGTTGATTCAACTCCATATGTGATGAATCGAGTATCA-GAAAT
1 GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCAAGTA-CAGGAAAT
* * * * * *
1426389 GTTAAAAATATCCTGCTCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGA
65 GTTAAAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAGGACATATCATCTTGCTCGAAAGA
* * *
1426454 CTTATATATGACCCAAAGGATTTAAGCATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTT
130 CTTATAAATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTT
* *
1426519 ACTCAACAAGAAACCCTTGAAAATCAAGCTTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATA
195 ACTCAACAAGAAACCCTTGAAAACCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATA
1426584 TCAC
260 TCAC
*
1426588 GTTGATCCCTCGAG
1 GTTGGTCCCTCGAG
1426602 CTTAGTTTCT
Statistics
Matches: 247, Mismatches: 29, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
263 245 0.99
264 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.28
Consensus pattern (263 bp):
GTTGGTCCCTCGAGTGAGGTGTTGCTGATTCAACTCCATATGTGATGAATCAAGTACAGGAAATG
TTAAAAACATCCTACCCAAAGGTCTTATGGATAGCCCGAAGGACATATCATCTTGCTCGAAAGAC
TTATAAATGACCCAAAGGACTTAAGCATCATGCTCAAAAGACTTACTAATGGCCCGAAGGACTTA
CTCAACAAGAAACCCTTGAAAACCAAGATTAGTTTCTTAGTTGTCATCAAGGAACCCCTACATAT
CAC
Found at i:1426679 original size:71 final size:71
Alignment explanation
Indices: 1426563--1426721 Score: 212
Period size: 71 Copynumber: 2.2 Consensus size: 71
1426553 TTCTTAGTTG
* *
1426563 TCATCAAGGAACCCCTACATATCACGTTGATCCCTCGAGCTTAGTTTCTTATA-AACATTCACTG
1 TCATCAAGGAACCCCTACATATCACGTTGATACCTCAAGCTTAGTTTCTTATACAA-ATTCACTG
1426627 AAAATCA
65 AAAATCA
* * * * *
1426634 TCATCAATGAACCCCTACATATTATGTTGGTACCTCAAGCTTAGTTTCTTATACAAATTCATTGA
1 TCATCAAGGAACCCCTACATATCACGTTGATACCTCAAGCTTAGTTTCTTATACAAATTCACTGA
*
1426699 AAATCG
66 AAATCA
*
1426705 TCATCAAGAAAACCCCT
1 TCATCAAG-GAACCCCT
1426722 GAAAGCCAGG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
71 67 0.88
72 9 0.12
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (71 bp):
TCATCAAGGAACCCCTACATATCACGTTGATACCTCAAGCTTAGTTTCTTATACAAATTCACTGA
AAATCA
Found at i:1434638 original size:149 final size:149
Alignment explanation
Indices: 1434362--1434657 Score: 389
Period size: 149 Copynumber: 2.0 Consensus size: 149
1434352 TCATCTTCAA
* * *
1434362 AGCTTCTACTTAATCTCCTACTTCCATAAATCTTTCGAGCTAGTTCGCGATCTTCAACTGTTGGC
1 AGCTCCTACTTAATCTCCTAATTCCAAAAATCTTTCGAGCTAGTTCGCGATCTTCAACTGTTGGC
* * * * * ** * *
1434427 TTTGACGTTGAATTGTCTTGAGTTCGACTTGTTACCTCAGCAGGCAAATGTTTAGATTGTCTCCT
66 TTTGACGTTAAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAACAAATGTCTAGATCGTCTCCT
1434492 TGGTAGATAGACTCCCTCT
131 TGGTAGATAGACTCCCTCT
* * *
1434511 AGCTCCTACTTTATCTCTTAATTCCAAAAATCTTTCGAGCTAGTTCGTGATCTTCAACTGTTGGC
1 AGCTCCTACTTAATCTCCTAATTCCAAAAATCTTTCGAGCTAGTTCGCGATCTTCAACTGTTGGC
* * *
1434576 TTT-A-GTGTCAAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAACAGATGTCTGGCTCGTCTC
66 TTTGACGT-T-AAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAACAAATGTCTAGATCGTCTC
*
1434639 CTTGGTAGGTAGACTCCCT
129 CTTGGTAGATAGACTCCCT
1434658 ATTGATGCTA
Statistics
Matches: 126, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
147 2 0.02
148 2 0.02
149 122 0.97
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (149 bp):
AGCTCCTACTTAATCTCCTAATTCCAAAAATCTTTCGAGCTAGTTCGCGATCTTCAACTGTTGGC
TTTGACGTTAAATCGTCTCGAGTCCAACTTGTTACCTCAGCAAACAAATGTCTAGATCGTCTCCT
TGGTAGATAGACTCCCTCT
Found at i:1436499 original size:12 final size:13
Alignment explanation
Indices: 1436482--1436510 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1436472 ATTAAAATCT
1436482 AATTATTAC-CTA
1 AATTATTACACTA
1436494 AATTATTACACTA
1 AATTATTACACTA
1436507 AATT
1 AATT
1436511 TTTTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
AATTATTACACTA
Found at i:1436759 original size:26 final size:25
Alignment explanation
Indices: 1436719--1436777 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 25
1436709 ATAGTAAACT
*
1436719 TAAATAAAAAAATCAAAATAACAAA
1 TAAAAAAAAAAATCAAAATAACAAA
1436744 TAATAAAAAAAAATCAAAATAACAAA
1 TAA-AAAAAAAAATCAAAATAACAAA
1436770 TAAAAAAA
1 TAAAAAAA
1436778 TAAAGAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (25 bp):
TAAAAAAAAAAATCAAAATAACAAA
Found at i:1438024 original size:3 final size:3
Alignment explanation
Indices: 1438016--1438070 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
1438006 GATTGGGTTG
*
1438016 TAA TAA TAA TATA TAT TAA -AA TAA TAA -AA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
*
1438060 TAT TAA TAA TA
1 TAA TAA TAA TA
1438071 TGGATGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
2 6 0.14
3 31 0.72
4 6 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1438056 original size:9 final size:8
Alignment explanation
Indices: 1438018--1438071 Score: 54
Period size: 8 Copynumber: 6.2 Consensus size: 8
1438008 TTGGGTTGTA
1438018 ATAATAAT
1 ATAATAAT
*
1438026 ATATATTAAA
1 ATA-A-TAAT
*
1438036 ATAATAAA
1 ATAATAAT
1438044 ATAAATAAT
1 AT-AATAAT
1438053 ATAATAAT
1 ATAATAAT
1438061 ATTAATAAT
1 A-TAATAAT
1438070 AT
1 AT
1438072 GGATGTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 17 0.43
9 17 0.43
10 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAATAAT
Found at i:1438058 original size:17 final size:17
Alignment explanation
Indices: 1438036--1438071 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1438026 ATATATTAAA
1438036 ATAATAAAATAAATAAT
1 ATAATAAAATAAATAAT
* *
1438053 ATAATAATATTAATAAT
1 ATAATAAAATAAATAAT
1438070 AT
1 AT
1438072 GGATGTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATAAAATAAATAAT
Found at i:1441042 original size:18 final size:18
Alignment explanation
Indices: 1441019--1441059 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1441009 TTTTTATGTA
1441019 ATAATTAATAACTTAAAT
1 ATAATTAATAACTTAAAT
1441037 ATAATT--TAACTTAAAT
1 ATAATTAATAACTTAAAT
1441053 AT-ATTAA
1 ATAATTAA
1441060 ACATGATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
18 6 0.29
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAATTAATAACTTAAAT
Found at i:1442735 original size:22 final size:22
Alignment explanation
Indices: 1442709--1442764 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1442699 ACTGTAATGG
* * *
1442709 AGTATCGGTACCATAGTATAAA
1 AGTATCGATACCATAGGAGAAA
1442731 AGTATCGATA-C-TAGGAGAAA
1 AGTATCGATACCATAGGAGAAA
1442751 AGTATCGATACCAT
1 AGTATCGATACCAT
1442765 GGATTCAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 17 0.59
21 2 0.07
22 10 0.34
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (22 bp):
AGTATCGATACCATAGGAGAAA
Found at i:1442829 original size:94 final size:95
Alignment explanation
Indices: 1442657--1442835 Score: 252
Period size: 94 Copynumber: 1.9 Consensus size: 95
1442647 TCCTGATGGG
* ** * *
1442657 GTATCGATACCATTGATTACAGAATGCAGAAATGGTATCGATACTGTAATGGAGTATCGGTACCA
1 GTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCA
*
1442722 TAGTATAAAAGTATCGATACTAGGAGAAAA
66 TAATATAAAAGTATCGATACTAGGAGAAAA
* * *
1442752 GTATCGATACCATGGATT-CAGAATGTAGAAATGGTATCGATGCTAAAAGGGGGTATCGATACCA
1 GTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCA
**
1442816 TAATATAGTAGTATCGATAC
66 TAATATAAAAGTATCGATAC
1442836 CATGGTAGGG
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
94 56 0.77
95 17 0.23
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (95 bp):
GTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGATACCA
TAATATAAAAGTATCGATACTAGGAGAAAA
Found at i:1442854 original size:94 final size:93
Alignment explanation
Indices: 1442654--1442855 Score: 226
Period size: 94 Copynumber: 2.1 Consensus size: 93
1442644 CGATCCTGAT
* ** * *
1442654 GGGGTATCGATACCATTGATTACAGAATGCAGAAATGGTATCGATACTGTAATGGAGTATCGGTA
1 GGGGTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGATA
* *
1442719 CCATAGTATAAAAGTATCGATACTAGGA
66 CCATAATATAAAAGTATCGATACCAGGA
** * * *
1442747 GAAAAGTATCGATACCATGGATT-CAGAATGTAGAAATGGTATCGATGCTAAAAGGGGGTATCGA
1 G--GGGTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGA
**
1442811 TACCATAATATAGTAGTATCGATACCATGGTA
64 TACCATAATATAAAAGTATCGATACCA-GG-A
*
1442843 GGGGTACCGATAC
1 GGGGTATCGATAC
1442856 TAGTGAGTCT
Statistics
Matches: 88, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
93 1 0.01
94 66 0.75
95 19 0.22
96 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (93 bp):
GGGGTATCGATACCATGGATTACAGAATGCAGAAATGGTATCGATACTAAAAGGGAGTATCGATA
CCATAATATAAAAGTATCGATACCAGGA
Found at i:1443268 original size:54 final size:54
Alignment explanation
Indices: 1443186--1443497 Score: 516
Period size: 54 Copynumber: 5.8 Consensus size: 54
1443176 GTACTATAGT
*
1443186 CACTATGTGTGCAACCCATGGAATTCATCATATGTTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
* * *
1443240 CACTATGTGTGCAACCCATGGAATTCATCATATGTTGATGAATAACCGTTTAGG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
* *
1443294 CACTATGTGTGTAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTAGG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
* *
1443348 CACTATGTGTGCAACCCACAGAATTCATCATATATTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
*
1443402 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
* * *
1443456 CACTATGTGTGCAACCCACGAAATTCATAATATGTTTATGAA
1 CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAA
1443498 TGACCGTATT
Statistics
Matches: 244, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 244 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACGGAATTCATCATATGTTGATGAACAACCATTTAGG
Found at i:1443273 original size:27 final size:27
Alignment explanation
Indices: 1443189--1443274 Score: 72
Period size: 27 Copynumber: 3.2 Consensus size: 27
1443179 CTATAGTCAC
1443189 TATGTGTGCAACCCATGGAATTCATCA
1 TATGTGTGCAACCCATGGAATTCATCA
** **
1443216 TATGTTGATG-AACAACCAT-TTAGGCA-C-
1 TATG-TG-TGCAAC--CCATGGAATTCATCA
1443243 TATGTGTGCAACCCATGGAATTCATCA
1 TATGTGTGCAACCCATGGAATTCATCA
1443270 TATGT
1 TATGT
1443275 TGATGAATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
24 4 0.09
25 5 0.12
26 6 0.14
27 13 0.30
28 6 0.14
29 5 0.12
30 4 0.09
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (27 bp):
TATGTGTGCAACCCATGGAATTCATCA
Found at i:1443462 original size:27 final size:27
Alignment explanation
Indices: 1443382--1443463 Score: 64
Period size: 27 Copynumber: 3.0 Consensus size: 27
1443372 TCATCATATA
1443382 TTGATGAACAACCATTTAGGCACTATG
1 TTGATGAACAACCATTTAGGCACTATG
* * * *
1443409 -TG-TGCAACCCACGAAATTCA-TCA-TATG
1 TTGATG-AA-CAAC--CATTTAGGCACTATG
1443436 TTGATGAACAACCATTTAGGCACTATG
1 TTGATGAACAACCATTTAGGCACTATG
1443463 T
1 T
1443464 GTGCAACCCA
Statistics
Matches: 39, Mismatches: 8, Indels: 16
0.62 0.13 0.25
Matches are distributed among these distances:
25 6 0.15
26 6 0.15
27 15 0.38
28 6 0.15
29 6 0.15
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (27 bp):
TTGATGAACAACCATTTAGGCACTATG
Found at i:1443512 original size:54 final size:54
Alignment explanation
Indices: 1443186--1443534 Score: 504
Period size: 54 Copynumber: 6.4 Consensus size: 54
1443176 GTACTATAGT
* *
1443186 CACTATGTGTGCAACCCATGGAATTCATCATATGTTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
* * * *
1443240 CACTATGTGTGCAACCCATGGAATTCATCATATGTTGATGAATAACCGTTTAGG
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
* * *
1443294 CACTATGTGTGTAACCCACGGAATTCATCATATGTTGATGAACAACCGTTTAGG
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
*
1443348 CACTATGTGTGCAACCCAC-AGAATTCATCATATATTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAACCATTTAGG
1443402 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
* * ** *
1443456 CACTATGTGTGCAACCCACGAAATTCATAATATGTTTATGAATGACCGTATT-GG
1 CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCAT-TTAGG
* *
1443510 CACTACGTGTGCATACCAACGAAAT
1 CACTATGTGTGCA-ACCCACGAAAT
1443535 GATAATAACT
Statistics
Matches: 274, Mismatches: 17, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
54 261 0.95
55 13 0.05
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
CACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATTTAGG
Found at i:1449613 original size:22 final size:22
Alignment explanation
Indices: 1449585--1449642 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 22
1449575 TGTAATGGAA
1449585 TATCGATACCATAGTATAAAAG
1 TATCGATACCATAGTATAAAAG
* *
1449607 TATCGATA-C-TAGGAGAAAAG
1 TATCGATACCATAGTATAAAAG
1449627 TATCGATACCAT-GTAT
1 TATCGATACCATAGTAT
1449643 TCAGAATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
20 17 0.57
21 4 0.13
22 9 0.30
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (22 bp):
TATCGATACCATAGTATAAAAG
Found at i:1449631 original size:95 final size:92
Alignment explanation
Indices: 1449511--1449710 Score: 224
Period size: 94 Copynumber: 2.1 Consensus size: 92
1449501 TACTGATGGG
* * *
1449511 GTATCGATACTAAGAGGAAGTTATCGATACCAT-TGATTACAAAATGCAGAAATGGTATCGATAT
1 GTATCGATACTAGGAGAAAGTTATCGATACCATGT-ATT-CAAAATGCAGAAATGGTATCGATAC
* * *
1449575 TGTAATGGAATATCGATACCATAGTATAAAA
64 TGAAAGGGAACATCGATACCAT-G-ATAAAA
* * * *
1449606 GTATCGATACTAGGAGAAAAG-TATCGATACCATGTATTCAGAATGTAGAAATGGTATTGATGCT
1 GTATCGATACTAGGAG-AAAGTTATCGATACCATGTATTCAAAATGCAGAAATGGTATCGATACT
* *
1449670 GAAAGGGAGCATCGATACCATGGTAAAA
65 GAAAGGGAACATCGATACCATGATAAAA
*
1449698 GTACCGATACTAG
1 GTATCGATACTAG
1449711 TGAGCCTGGA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
92 17 0.19
93 1 0.01
94 38 0.42
95 30 0.33
96 4 0.04
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (92 bp):
GTATCGATACTAGGAGAAAGTTATCGATACCATGTATTCAAAATGCAGAAATGGTATCGATACTG
AAAGGGAACATCGATACCATGATAAAA
Found at i:1450099 original size:54 final size:54
Alignment explanation
Indices: 1450034--1450476 Score: 604
Period size: 54 Copynumber: 8.2 Consensus size: 54
1450024 ATATGTACTA
* ** *
1450034 TAGGCGCTATGTGTAAAACCCACGAAATTCATCATATGTTGATGAAAAACCGTT
1 TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
*
1450088 TAGGCACTATGTATGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
* *
1450142 TAGGCACTATGTGTGCAACCTC-CGGAATTCATCATATGTTGATGAACAACCATT
1 TAGGCACTATGTGTGCAACC-CACGAAATTCATCATATGTTGATGAACAACCGTT
* * *
1450196 TAGGCACTATGTGTGCAACCCACGGAATTCATCATATATTAATGAACAACCGTT
1 TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
* *
1450250 TAGGCACTATGTGTGCAATCCAC-AGAATTCATCATATGTTGATGAAAAACCGTT
1 TAGGCACTATGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACAACCGTT
* * * *
1450304 TAGGCACTATATGTGCAACCCACGAAATTTATCATATGTGGATGAACAACCATT
1 TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
* *
1450358 TATGCACTATGTGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCATT
1 TAGGCACTA--TGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
* * * * **
1450414 TAGGCTCTATGTGTGCAACCCACGGAATTCATAATATGTTTATGAATGACCGTAT
1 TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGT-T
1450469 T-GGCACTA
1 TAGGCACTA
1450477 CGTATTGATA
Statistics
Matches: 347, Mismatches: 35, Indels: 14
0.88 0.09 0.04
Matches are distributed among these distances:
53 1 0.00
54 293 0.84
55 4 0.01
56 49 0.14
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (54 bp):
TAGGCACTATGTGTGCAACCCACGAAATTCATCATATGTTGATGAACAACCGTT
Found at i:1450354 original size:31 final size:31
Alignment explanation
Indices: 1450319--1450410 Score: 76
Period size: 31 Copynumber: 3.2 Consensus size: 31
1450309 ACTATATGTG
1450319 CAACCCACGAAATTTATCATATGTGGATGAA
1 CAACCCACGAAATTTATCATATGTGGATGAA
1450350 CAA--C-C---ATTTATGCACTATGTGTG-TG--
1 CAACCCACGAAATTTAT-CA-TATGTG-GATGAA
* *
1450375 CAACCCACGAAATTCATCATATGTTGATGAA
1 CAACCCACGAAATTTATCATATGTGGATGAA
1450406 CAACC
1 CAACC
1450411 ATTTAGGCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 24
0.64 0.03 0.33
Matches are distributed among these distances:
25 9 0.19
26 2 0.04
27 9 0.19
28 4 0.09
29 8 0.17
30 2 0.04
31 13 0.28
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (31 bp):
CAACCCACGAAATTTATCATATGTGGATGAA
Found at i:1450358 original size:25 final size:25
Alignment explanation
Indices: 1450330--1450415 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 25
1450320 AACCCACGAA
1450330 ATTTATCATATGTGGATGAACAACC
1 ATTTATCATATGTGGATGAACAACC
* *
1450355 ATTTATGCACTATGTGTG-TGCAACCCACGAA
1 ATTTAT-CA-TATGTG-GATG-AA-CAAC--C
* *
1450386 ATTCATCATATGTTGATGAACAACC
1 ATTTATCATATGTGGATGAACAACC
1450411 ATTTA
1 ATTTA
1450416 GGCTCTATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
25 10 0.22
26 2 0.04
27 11 0.24
28 6 0.13
29 10 0.22
30 2 0.04
31 5 0.11
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (25 bp):
ATTTATCATATGTGGATGAACAACC
Found at i:1457063 original size:29 final size:29
Alignment explanation
Indices: 1457013--1457096 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
1457003 ACAAAAACAT
** *
1457013 ATAAAAAATAAAA-ACTTGTAAAATAAAAG
1 ATAAAAAATAAAACA-TAATAAAATAAAAC
1457042 ATAAAAAATAAAACATAATAAAATAAAAC
1 ATAAAAAATAAAACATAATAAAATAAAAC
*
1457071 A-AATAAAA-ACAACA-AATAAAATAAAA
1 ATAA-AAAATAAAACATAATAAAATAAAA
1457097 TAACATAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.24
28 7 0.14
29 29 0.59
30 1 0.02
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (29 bp):
ATAAAAAATAAAACATAATAAAATAAAAC
Found at i:1457086 original size:13 final size:14
Alignment explanation
Indices: 1457031--1457199 Score: 109
Period size: 14 Copynumber: 11.6 Consensus size: 14
1457021 TAAAAACTTG
*
1457031 TAAAATAAAAGATAA
1 TAAAATAAAACA-AA
1457046 -AAAATAAAACATAA
1 TAAAATAAAACA-AA
1457060 TAAAATAAAACAAA
1 TAAAATAAAACAAA
*
1457074 TAAAA-ACAACAAA
1 TAAAATAAAACAAA
*
1457087 TAAAATAAAATAACA
1 TAAAATAAAACAA-A
*
1457102 TAAAACAAAA-AAGA
1 TAAAATAAAACAA-A
*
1457116 TAATAACAGAAGACAAA
1 TAA-AATA-AA-ACAAA
1457133 TAAAAATAAAA-AAA
1 T-AAAATAAAACAAA
*
1457147 TAGAAAACAGAAAACAAA
1 T---AAA-ATAAAACAAA
*
1457165 T-AAATATAAC--A
1 TAAAATAAAACAAA
1457176 TAAATATAAAACAAA
1 TAAA-ATAAAACAAA
1457191 TAAAATAAA
1 TAAAATAAA
1457200 GTATAAATAA
Statistics
Matches: 127, Mismatches: 11, Indels: 33
0.74 0.06 0.19
Matches are distributed among these distances:
11 2 0.02
12 2 0.02
13 23 0.18
14 42 0.33
15 31 0.24
16 8 0.06
17 11 0.09
18 8 0.06
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.15
Consensus pattern (14 bp):
TAAAATAAAACAAA
Found at i:1457091 original size:37 final size:38
Alignment explanation
Indices: 1457033--1457195 Score: 104
Period size: 37 Copynumber: 4.2 Consensus size: 38
1457023 AAAACTTGTA
* *
1457033 AAATAAAAGATAAAAAATAAAACATAATAAAATAAAAC
1 AAATAAAAGACAAAAAATAAAACAAAATAAAATAAAAC
* * *
1457071 AAATAAAA-ACAACAAATAAAATAAAATAACATAAAAC
1 AAATAAAAGACAAAAAATAAAACAAAATAAAATAAAAC
* * * *
1457108 -AA-AAAAGATAATAACAGAAGAC-AAATAAAAATAAAA-
1 AAATAAAAGACAA-AAAATAAAACAAAAT-AAAATAAAAC
* *
1457144 AAATAGAAA-ACAGAAAACAAATAAATATAACATAAATATAAAAC
1 AAATA-AAAGAC---AAA-AAATAAA-ACAAAATAAA-ATAAAAC
1457188 AAATAAAA
1 AAATAAAA
1457196 TAAAGTATAA
Statistics
Matches: 93, Mismatches: 18, Indels: 23
0.69 0.13 0.17
Matches are distributed among these distances:
35 4 0.04
36 9 0.10
37 39 0.42
38 10 0.11
39 3 0.03
40 1 0.01
41 6 0.06
42 4 0.04
43 12 0.13
44 5 0.05
ACGTcount: A:0.75, C:0.07, G:0.04, T:0.14
Consensus pattern (38 bp):
AAATAAAAGACAAAAAATAAAACAAAATAAAATAAAAC
Found at i:1457109 original size:27 final size:28
Alignment explanation
Indices: 1457031--1457106 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 28
1457021 TAAAAACTTG
* *
1457031 TAAAATAAAAGATAA-AAAATAAAACATAA
1 TAAAATAAAACA-AATAAAA-ACAACATAA
1457060 TAAAATAAAACAAATAAAAACAACA-AA
1 TAAAATAAAACAAATAAAAACAACATAA
*
1457087 TAAAATAAAATAACATAAAA
1 TAAAATAAAACAA-ATAAAA
1457107 CAAAAAAGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 14 0.33
28 13 0.31
29 15 0.36
ACGTcount: A:0.76, C:0.07, G:0.01, T:0.16
Consensus pattern (28 bp):
TAAAATAAAACAAATAAAAACAACATAA
Found at i:1457144 original size:32 final size:32
Alignment explanation
Indices: 1457103--1457188 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 32
1457093 AAAATAACAT
* * *
1457103 AAAACAAAAAAGATA-ATAACAGAAGACAAATA
1 AAAATAAAAAA-ATAGAAAACAGAAAACAAATA
1457135 AAAATAAAAAAATAGAAAACAGAAAACAAATA
1 AAAATAAAAAAATAGAAAACAGAAAACAAATA
* * *
1457167 AATATAACATAAATATAAAACA
1 AAAATAA-AAAAATAGAAAACA
1457189 AATAAAATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 3 0.07
32 31 0.67
33 12 0.26
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (32 bp):
AAAATAAAAAAATAGAAAACAGAAAACAAATA
Found at i:1457180 original size:11 final size:10
Alignment explanation
Indices: 1457162--1457210 Score: 55
Period size: 11 Copynumber: 4.7 Consensus size: 10
1457152 AACAGAAAAC
1457162 AAATAAATAT
1 AAATAAATAT
1457172 AACATAAATAT
1 AA-ATAAATAT
*
1457183 AAAACAAATA-
1 -AAATAAATAT
1457193 AAATAAAGTAT
1 AAATAAA-TAT
1457204 AAATAAA
1 AAATAAA
1457211 AACAGAATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
9 6 0.18
10 4 0.12
11 21 0.64
12 2 0.06
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (10 bp):
AAATAAATAT
Found at i:1457186 original size:26 final size:26
Alignment explanation
Indices: 1457157--1457226 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
1457147 TAGAAAACAG
1457157 AAAACAAATAAATATAA-CATAAATA
1 AAAACAAATAAATATAAGCATAAATA
*
1457182 TAAAACAAATAAA-ATAAAGTATAAATA
1 -AAAACAAATAAATAT-AAGCATAAATA
*
1457209 AAAACAGAATACATATAA
1 AAAACA-AATAAATATAA
1457227 AGAGTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 20 0.53
27 14 0.37
28 2 0.05
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (26 bp):
AAAACAAATAAATATAAGCATAAATA
Found at i:1457205 original size:27 final size:26
Alignment explanation
Indices: 1457047--1457250 Score: 83
Period size: 27 Copynumber: 7.8 Consensus size: 26
1457037 AAAAGATAAA
*
1457047 AAAT-AAAACATAATAAAATAAAACAAAT
1 AAATAAAAACA-AATAAAATAAAGC--AT
*
1457075 AAA-AACAACAAATAAAATAAA--AT
1 AAATAAAAACAAATAAAATAAAGCAT
* *
1457098 AACAT-AAAACAAA-AAAGATAATAACAG
1 AA-ATAAAAACAAATAAA-ATAA-AGCAT
* *
1457125 AAGACAAATAA-AAATAAAAAAATAG-A-
1 AA-ATAAA-AACAAATAAAATAA-AGCAT
*
1457151 AAACAGAAAACAAAT-AAATATAA-CAT
1 AAATA-AAAACAAATAAAATA-AAGCAT
*
1457177 AAATATAAAACAAATAAAATAAAGTAT
1 AAATA-AAAACAAATAAAATAAAGCAT
*
1457204 AAATAAAAACAGAATACATATAAAG-AGT
1 AAATAAAAACA-AATA-AAATAAAGCA-T
* *
1457232 AAA-AAAAATAAAAAAAATA
1 AAATAAAAACAAATAAAATA
1457251 GTAGTTGTTA
Statistics
Matches: 141, Mismatches: 15, Indels: 43
0.71 0.08 0.22
Matches are distributed among these distances:
23 7 0.05
24 12 0.09
25 16 0.11
26 33 0.23
27 39 0.28
28 29 0.21
29 5 0.04
ACGTcount: A:0.74, C:0.07, G:0.04, T:0.15
Consensus pattern (26 bp):
AAATAAAAACAAATAAAATAAAGCAT
Found at i:1457239 original size:28 final size:26
Alignment explanation
Indices: 1457031--1457239 Score: 71
Period size: 28 Copynumber: 7.8 Consensus size: 26
1457021 TAAAAACTTG
1457031 TAAAATAAAAG-ATAAAAAATAAAACATAA
1 TAAAAT-AAAGTAT-AAAAA-AAAACA-AA
**
1457060 TAAAATAAAACA-AATAAAAACAACAAA
1 TAAAATAAAGTATAA-AAAAA-AACAAA
* *
1457087 TAAAATAAA--ATAACATAAAACAAA
1 TAAAATAAAGTATAAAAAAAAACAAA
** * *
1457111 -AAAGATAATAACAGAAGACAAATAA-AAA
1 TAAA-ATAA-AGTATAA-A-AAAAAACAAA
*
1457139 TAAAA-AAA-TAGAAAACAGAAAACAAA
1 TAAAATAAAGTATAAAA-A-AAAACAAA
* *
1457165 TAAATATAACA-TA-AATATAAAACAAA
1 TAAA-ATAA-AGTATAAAAAAAAACAAA
*
1457191 TAAAATAAAGTATAAATAAAAACAGAA
1 TAAAATAAAGTATAAAAAAAAACA-AA
*
1457218 TACATATAAAG-AGTAAAAAAAA
1 TA-AAATAAAGTA-TAAAAAAAA
1457240 TAAAAAAAAT
Statistics
Matches: 142, Mismatches: 16, Indels: 45
0.70 0.08 0.22
Matches are distributed among these distances:
23 4 0.03
24 13 0.09
25 18 0.13
26 30 0.21
27 26 0.18
28 34 0.24
29 17 0.12
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (26 bp):
TAAAATAAAGTATAAAAAAAAACAAA
Found at i:1457892 original size:198 final size:199
Alignment explanation
Indices: 1457665--1458091 Score: 485
Period size: 198 Copynumber: 2.2 Consensus size: 199
1457655 AATAAGAAAG
* * * *
1457665 ATTTGTGTTTTTTTAATCGAATAGGTTTTTTAGGGATGAACAAATGAA-GAACAAGAGTTTG-CT
1 ATTTATGTTTTTTTAATCGAATAGGTTTTTTAGAGATGAACAAAT-AAGGAAC-AGAGGTTGAAT
* * * *
1457728 ACCTGGGTTTGATCTAGAAAACAAGAAA-GAAAGAGTTTTTGTTGTTTATTTGGATCGAAGAGAG
64 ACCTGGGTTTGATCTAAAAAACAAAAAATG-AAGAGTTTTTG-T-TTTATCTGGATCAAAGAGAG
* * *
1457792 AAAATGATGAAGAAATAATGAATAAATTTTTAGG-GTTTT-TGTTTTGAT-AAAAAAATAGAA-A
126 AAAATCATGAAGAAATAATGAAT-AATTTTTAGGAATTTTGTGTTTTGATCAAAAAAATACAAGA
* *
1457853 TAAGATGAAT
190 AAAAATGAAT
* * * *
1457863 ATTTATGTTTTTTTAATCGAATAGGTTTTTTTGAGATGAACATATAAGGAACAGGGGTTGAATAT
1 ATTTATGTTTTTTTAATCGAATAGGTTTTTTAGAGATGAACAAATAAGGAACAGAGGTTGAATAC
* **
1457928 TTTTGTTTGATCTAAAAAACAAAAAATGAAGAGTTTTTGTTTTATCTGGATCAAAGAGAGAAAAT
66 CTGGGTTTGATCTAAAAAACAAAAAATGAAGAGTTTTTGTTTTATCTGGATCAAAGAGAGAAAAT
* ** * *
1457993 CATGAAGAACTAATGAATTTTTTTTAGGAATTTTGTGTTTTTATCCAAAAAATACAAGAAAAAAT
131 CATGAAGAAATAATGAATAATTTTTAGGAATTTTGTGTTTTGATCAAAAAAATACAAGAAAAAAT
1458058 GAAT
196 GAAT
* *
1458062 -TTTATATTTTTTT-ATCAAATAGGCTTTTTT
1 ATTTATGTTTTTTTAATCGAATAGG-TTTTTT
1458092 CGATGAATAG
Statistics
Matches: 194, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
195 8 0.04
196 43 0.22
197 26 0.13
198 107 0.55
199 10 0.05
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (199 bp):
ATTTATGTTTTTTTAATCGAATAGGTTTTTTAGAGATGAACAAATAAGGAACAGAGGTTGAATAC
CTGGGTTTGATCTAAAAAACAAAAAATGAAGAGTTTTTGTTTTATCTGGATCAAAGAGAGAAAAT
CATGAAGAAATAATGAATAATTTTTAGGAATTTTGTGTTTTGATCAAAAAAATACAAGAAAAAAT
GAAT
Found at i:1458142 original size:196 final size:198
Alignment explanation
Indices: 1457731--1458109 Score: 432
Period size: 196 Copynumber: 1.9 Consensus size: 198
1457721 GTTTGCTACC
* * * *
1457731 TGGGTTTGATCTAGAAAACAAGAAAGAAAGAGTTTTTGTTGTTTATTTGGATCGAAGAGAGAAAA
1 TGGGTTTGATCTAAAAAACAAAAAAGAAAGAGTTTTTGTTGTTTATCTGGATCAAAGAGAGAAAA
* * * * *
1457796 TGATGAAGAAATAATGAATAAATTTTTAGGGTTTTTGTTTTGATAAAAAAATAGAAATAAGATGA
66 TCATGAAGAAATAATGAATAAATTTTTAGGATTTTTGTTTTGATAAAAAAATACAAAAAAAATGA
* * * * * * *
1457861 ATATTTATGTTTTTTTAATCGAATAGGTTTTTTTGAGATGAACATATAAGGAACAGGGGTTGAAT
131 ATATTTATATTTTTTTAATCAAATAGGCTTTTTTGAGATGAACAGACAAAGAACA-GAGTTGAAT
1457926 ATTT
195 ATTT
*
1457930 T-TGTTTGATCTAAAAAACAAAAAATG-AAGAGTTTTTG-T-TTTATCTGGATCAAAGAGAGAAA
1 TGGGTTTGATCTAAAAAACAAAAAA-GAAAGAGTTTTTGTTGTTTATCTGGATCAAAGAGAGAAA
* ** * *
1457991 ATCATGAAGAACTAATGAAT-TTTTTTTAGGAATTTTGTGTTTTTATCCAAAAAATACAAGAAAA
65 ATCATGAAGAAATAATGAATAAATTTTTAGG-ATTTT-TGTTTTGAT-AAAAAAATACAA-AAAA
* *
1458055 AATGAAT-TTTATATTTTTTT-ATCAAATAGGCTTTTTT-CGATGAATAGACAAAGAA
126 AATGAATATTTATATTTTTTTAATCAAATAGGCTTTTTTGAGATGAACAGACAAAGAA
1458110 TAATTATGAG
Statistics
Matches: 152, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
195 8 0.05
196 56 0.37
197 24 0.16
198 53 0.35
199 11 0.07
ACGTcount: A:0.40, C:0.05, G:0.18, T:0.37
Consensus pattern (198 bp):
TGGGTTTGATCTAAAAAACAAAAAAGAAAGAGTTTTTGTTGTTTATCTGGATCAAAGAGAGAAAA
TCATGAAGAAATAATGAATAAATTTTTAGGATTTTTGTTTTGATAAAAAAATACAAAAAAAATGA
ATATTTATATTTTTTTAATCAAATAGGCTTTTTTGAGATGAACAGACAAAGAACAGAGTTGAATA
TTT
Found at i:1458557 original size:16 final size:16
Alignment explanation
Indices: 1458536--1458567 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1458526 ACTTATATGT
1458536 TATATAAATACTTATA
1 TATATAAATACTTATA
*
1458552 TATATATATACTTATA
1 TATATAAATACTTATA
1458568 AGCTATGAAG
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:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATAAATACTTATA
Found at i:1461931 original size:129 final size:126
Alignment explanation
Indices: 1461736--1461969 Score: 299
Period size: 129 Copynumber: 1.8 Consensus size: 126
1461726 ATGAGGACGA
* * * * *
1461736 CTGGTTATCTAGGTTGACATAGCTCCTACAAAAAGATAAAATCTAGTCGGGTGATGACACGGCTC
1 CTGGTTATCAAGGTTGACATAGCTCCTAC--AAAGATAAAATCAAGTCAGATGATGACACGACTC
* *
1461801 ATATGTGATGAAGAGTCCTGGCCATCCAAAGGTGATAACATGACTCATATGTGATGAAGAGTT
64 ATACGTGATGAAGAGTCCTGACCATCCAAAGGTGATAACATGACTCATATGTGATGAAGAGTT
* *
1461864 CTGGTTATCAAGGATTGACATAGCTCCTAC-ATGATAAGGAGATCAAGTCAGATGATGACATGAC
1 CTGGTTATCAAGG-TTGACATAGCTCCTACAAAGATAA--A-ATCAAGTCAGATGATGACACGAC
** *
1461928 TCATACGTGATGAAGAGTTTTGACCATCTAAAGGTGATAACA
62 TCATACGTGATGAAGAGTCCTGACCATCCAAAGGTGATAACA
1461970 CACACAACTC
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
126 6 0.07
128 13 0.14
129 71 0.79
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (126 bp):
CTGGTTATCAAGGTTGACATAGCTCCTACAAAGATAAAATCAAGTCAGATGATGACACGACTCAT
ACGTGATGAAGAGTCCTGACCATCCAAAGGTGATAACATGACTCATATGTGATGAAGAGTT
Found at i:1462006 original size:50 final size:50
Alignment explanation
Indices: 1461926--1462020 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
1461916 TGATGACATG
* *
1461926 ACTCATACGTGATGAAGAGTTTTGACCATCTAAAGGTGATAACACACACA
1 ACTCATACATGATGAAGAGTTCTGACCATCTAAAGGTGATAACACACACA
**
1461976 ACTCATACATGATGAAGAGTTCTGGTCATCTAAAGGTGATAACAC
1 ACTCATACATGATGAAGAGTTCTGACCATCTAAAGGTGATAACAC
1462021 GGCTCATAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (50 bp):
ACTCATACATGATGAAGAGTTCTGACCATCTAAAGGTGATAACACACACA
Found at i:1462044 original size:46 final size:48
Alignment explanation
Indices: 1461926--1462047 Score: 142
Period size: 50 Copynumber: 2.5 Consensus size: 48
1461916 TGATGACATG
* * **
1461926 ACTCATACGTGATGAAGAGTTTTGACCATCTAAAGGTGATAACACACACA
1 ACTCATAAGTGATGAAGAGTTCTGGTCATCTAAAGGTGAT-A-ACACACA
*
1461976 ACTCATACA-TGATGAAGAGTTCTGGTCATCTAAAGGTGAT-A-ACACG
1 ACTCATA-AGTGATGAAGAGTTCTGGTCATCTAAAGGTGATAACACACA
*
1462022 GCTCATAAGTGATGAAGAGTTCTGGT
1 ACTCATAAGTGATGAAGAGTTCTGGT
1462048 TATCAAGGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
45 1 0.02
46 27 0.42
47 1 0.02
50 35 0.55
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (48 bp):
ACTCATAAGTGATGAAGAGTTCTGGTCATCTAAAGGTGATAACACACA
Found at i:1463045 original size:85 final size:82
Alignment explanation
Indices: 1462759--1463065 Score: 287
Period size: 85 Copynumber: 3.6 Consensus size: 82
1462749 CATCGAGTTG
* * * *
1462759 AATGGAATCAAACTTGAAGGTGTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
1 AATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
* * *
1462824 CTTGACATAT-CCTGGAACT
66 TTTG--AT-TGCCTTGAGCT
** * * *
1462843 GAATGTAATCAAACTCGAAGGT-TTGTGTTGACAGATGGCCCTTCTCGCCTTAAGTTATGTTGTG
1 -AATGTAATCAAACTCGAAGGTCTTG-GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
*
1462907 AATTTGGTTGTCCTTGAGCT
64 AATTTGATTG-CCTTGAGCT
* ** * ** *
1462927 AAATGGAATTGAACTCAAAGGTATCTT-ACTGACAGATAACTCTTCTCGCCTTGAGTTATGCTGT
1 -AATGTAATCAAACTCGAAGG--TCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGT
1462991 AAATTTGATGTGCCTTTGAGCT
63 AAATTTGAT-TGCC-TTGAGCT
* *
1463013 AAGTGTAATCGAACTTGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGA
1 AA-TGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGA
1463066 TTTTTGCTAC
Statistics
Matches: 179, Mismatches: 33, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
82 1 0.01
83 1 0.01
84 29 0.16
85 122 0.68
86 24 0.13
87 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (82 bp):
AATGTAATCAAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAA
TTTGATTGCCTTGAGCT
Found at i:1463227 original size:86 final size:86
Alignment explanation
Indices: 1463132--1463397 Score: 331
Period size: 86 Copynumber: 3.1 Consensus size: 86
1463122 GCATGTCATA
* * * * *
1463132 ATTCTTCAGGTGGTTCTCCTTAACGAGTTTGAACCAAGTGAGATGATCTTTGGATAACTCCCCTT
1 ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTT
* *
1463197 CACGGGAAAACCATGTGGTAT
66 CACAGGAAAGCCATGTGGTAT
* * ** * *
1463218 ATTCCTCAGGTGATTCCCCTTAGCGGGTCTGAACTGAGTAAGATGAAT-TTTGGATGACTCCACT
1 ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATG-ATCTTTGGATGACTCCCCT
*
1463282 TCATAGGAAAGCCATGTGGTAT
65 TCACAGGAAAGCCATGTGGTAT
* *
1463304 ATTCCTCGGGTGGTTCCCCTTAGC-AGGTCTGAACCAAGTGAGATGATCTTTAGATGACTCCCCT
1 ATTCCTCAGGTGGTTCCCCTTAGCGA-GTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCT
* *
1463368 TCACAGCAAAGCCATATGGT-T
65 TCACAGGAAAGCCATGTGGTAT
1463389 ATTCCTCAG
1 ATTCCTCAG
1463398 AGTGACATTG
Statistics
Matches: 151, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
85 11 0.07
86 138 0.91
87 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (86 bp):
ATTCCTCAGGTGGTTCCCCTTAGCGAGTCTGAACCAAGTGAGATGATCTTTGGATGACTCCCCTT
CACAGGAAAGCCATGTGGTAT
Found at i:1465042 original size:51 final size:52
Alignment explanation
Indices: 1464909--1465094 Score: 268
Period size: 52 Copynumber: 3.6 Consensus size: 52
1464899 TATTCTAACC
* * * * *
1464909 TTTTCATGTTGATGTGAGCCTTCAAGATGCCCCACATGGA-TAATATATGTCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACT-TCTGTCT
1464961 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
* *
1465013 TTTT-ATGCTAATGTAAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
1 TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
* *
1465064 TTTTCATGCTGATGTGAGCCTTCAATATGCC
1 TTTTCATGCTGATGTGAACCTTCAAGATGCC
1465095 CTACATAGAT
Statistics
Matches: 121, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
51 49 0.40
52 69 0.57
53 3 0.02
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (52 bp):
TTTTCATGCTGATGTGAACCTTCAAGATGCCTCACATGGATTACTTCTGTCT
Found at i:1466409 original size:5 final size:5
Alignment explanation
Indices: 1466399--1466466 Score: 68
Period size: 5 Copynumber: 13.4 Consensus size: 5
1466389 TATTTTTTTC
* * *
1466399 TTCTT TTCTT TTCTT TTCTC TT-TT CTCTT TTCTT TT-TT TTCATT TTTTCT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTC-TT TTCT-T
1466449 TTCTT TTCTTT TTCTT TT
1 TTCTT TTC-TT TTCTT TT
1466467 TTTATTTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 6 0.12
5 33 0.63
6 13 0.25
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (5 bp):
TTCTT
Found at i:1466422 original size:17 final size:17
Alignment explanation
Indices: 1466394--1466466 Score: 71
Period size: 16 Copynumber: 4.2 Consensus size: 17
1466384 CAAAATATTT
*
1466394 TTTTCTTCTTTTCTTTTC
1 TTTTCTT-TTCTCTTTTC
1466412 TTTTCTCTTTTCTCTTTTC
1 -TTT-TCTTTTCTCTTTTC
*
1466431 TTTT-TTTTCATTTTTTC
1 TTTTCTTTTC-TCTTTTC
1466448 -TTTCTTTTCT-TTTTC
1 TTTTCTTTTCTCTTTTC
1466463 TTTT
1 TTTT
1466467 TTTATTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
15 5 0.10
16 12 0.25
17 12 0.25
18 3 0.06
19 12 0.25
20 4 0.08
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTTTCTCTTTTC
Found at i:1466447 original size:41 final size:40
Alignment explanation
Indices: 1466391--1466510 Score: 132
Period size: 36 Copynumber: 3.1 Consensus size: 40
1466381 TTTCAAAATA
1466391 TTTTTTTC-TTCTTTTCTTTTCTTTTCTCTTTTCTCTTTTCT
1 TTTTTTTCATT-TTTTCTTTTCTTTT-TCTTTTCTCTTTTCT
1466432 TTTTTTTCATTTTTTC-TTTC-TTTTCTTTT-TCTTTT-T
1 TTTTTTTCATTTTTTCTTTTCTTTTTCTTTTCTCTTTTCT
* *
1466468 TTATTTT-ATTTTATT-TTTCCTTTTTC-TTTCT-TTTTCT
1 TTTTTTTCATTTT-TTCTTTTCTTTTTCTTTTCTCTTTTCT
1466505 TTTTTT
1 TTTTTT
1466511 CTAATAGATG
Statistics
Matches: 70, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
35 5 0.07
36 19 0.27
37 18 0.26
38 6 0.09
39 3 0.04
40 4 0.06
41 13 0.19
42 2 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (40 bp):
TTTTTTTCATTTTTTCTTTTCTTTTTCTTTTCTCTTTTCT
Found at i:1466452 original size:40 final size:39
Alignment explanation
Indices: 1466391--1466510 Score: 130
Period size: 37 Copynumber: 3.2 Consensus size: 39
1466381 TTTCAAAATA
1466391 TTTTTTTC-TTCTTTTCTTTTCTTTTCTCTTTTCTCTTTTCT
1 TTTTTTTCATT-TTTTC-TTTCTTTT-TCTTTTCTCTTTTCT
1466432 TTTTTTTCATTTTTTCTTTC-TTTTCTTTT-TCTTTT-T
1 TTTTTTTCATTTTTTCTTTCTTTTTCTTTTCTCTTTTCT
*
1466468 TTATTTT-ATTTTATT-TTTCCTTTTTC-TTTCT-TTTTCT
1 TTTTTTTCATTTT-TTCTTT-CTTTTTCTTTTCTCTTTTCT
1466505 TTTTTT
1 TTTTTT
1466511 CTAATAGATG
Statistics
Matches: 71, Mismatches: 2, Indels: 16
0.80 0.02 0.18
Matches are distributed among these distances:
35 8 0.11
36 17 0.24
37 18 0.25
38 6 0.08
39 3 0.04
40 4 0.06
41 13 0.18
42 2 0.03
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (39 bp):
TTTTTTTCATTTTTTCTTTCTTTTTCTTTTCTCTTTTCT
Found at i:1466492 original size:46 final size:40
Alignment explanation
Indices: 1466402--1466509 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
1466392 TTTTTTCTTC
* *
1466402 TTTTCTTTTCTTTTCTCTTTTCTCTTTTCT-TT-TTTTTCAT
1 TTTTCCTTTCTTTTCT-TTTTCTTTTTTCTATTCTTTTT-AT
* *
1466442 TTTTTCTTTCTTTTCTTTTTCTTTTTT-TATTTTATTTTAT
1 TTTTCCTTTCTTTTCTTTTTCTTTTTTCTATTCT-TTTTAT
*
1466482 TTTTCCTTTTTCTTTCTTTTTCTTTTTT
1 TTTTCCTTTCT-TTTCTTTTTCTTTTTT
1466510 TCTAATAGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
38 1 0.02
39 12 0.20
40 26 0.44
41 20 0.34
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.81
Consensus pattern (40 bp):
TTTTCCTTTCTTTTCTTTTTCTTTTTTCTATTCTTTTTAT
Found at i:1474331 original size:74 final size:74
Alignment explanation
Indices: 1474205--1474376 Score: 202
Period size: 74 Copynumber: 2.3 Consensus size: 74
1474195 TTGGGTTTAA
* *
1474205 TATTTTTCTAGACTTAATATTATGGTTTGAGTCTTAAGATTTGACACTTTAATATTATGATTTGA
1 TATTATTCTAGACTTAATATTATGGTTTGAATCTTAAGATTTGACACTTTAATATTATGATTTGA
1474270 TTATGAATT
66 TTATGAATT
* * * * *
1474279 TATTATTCTAGAGTTAATATTGTGGTTTGAATCTTGAA-ATTTGACATTTTAATATTGTGGTTTG
1 TATTATTCTAGACTTAATATTATGGTTTGAATCTT-AAGATTTGACACTTTAATATTATGATTTG
* *
1474343 TTTATGGATTT
65 ATTAT-GAATT
* * * *
1474354 TACTGTTTTAAACTTAATATTAT
1 TATTATTCTAGACTTAATATTAT
1474377 TGTGGTTTGA
Statistics
Matches: 81, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
74 58 0.72
75 23 0.28
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (74 bp):
TATTATTCTAGACTTAATATTATGGTTTGAATCTTAAGATTTGACACTTTAATATTATGATTTGA
TTATGAATT
Found at i:1479254 original size:18 final size:18
Alignment explanation
Indices: 1479231--1479269 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1479221 ACCAGTTACA
*
1479231 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACCCGTTG
1479249 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1479267 ACC
1 ACC
1479270 GTTGACTAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.49, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1484137 original size:24 final size:24
Alignment explanation
Indices: 1484035--1484125 Score: 148
Period size: 24 Copynumber: 3.8 Consensus size: 24
1484025 TCGATTTTAT
1484035 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
1484059 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
1484083 TTCTGATCTGATGCTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
1484107 TTCTGATCTGATACTTGAC
1 TTCTGATCTGATACTTGAC
1484126 CTGAACTATG
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
23 1 0.02
24 60 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:1484370 original size:57 final size:57
Alignment explanation
Indices: 1484203--1484371 Score: 257
Period size: 57 Copynumber: 3.0 Consensus size: 57
1484193 GGAGGAAGAA
**
1484203 TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGAAGAT
1 TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTGAT
* *
1484260 TACTTGCATGTTCCTCGGTTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTGAT
1 TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTGAT
* * * * *
1484317 TACTTACAGGTTCCTTGGCTTTGTGCTCAGGGCCTTACTGTTCGTGACAGGGTTG
1 TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTG
1484372 TATGGTTATG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
57 101 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.36
Consensus pattern (57 bp):
TACTTGCAGGTTCCTCGGCTTTGTGCTGAGAGCCTTACTGTTCGTGACGGGGTTGAT
Found at i:1491074 original size:11 final size:11
Alignment explanation
Indices: 1491058--1491086 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1491048 GATATGAGAA
1491058 AAATTTAAATT
1 AAATTTAAATT
1491069 AAATTTAAATT
1 AAATTTAAATT
1491080 -AATTTAA
1 AAATTTAA
1491087 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 7 0.39
11 11 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:1493112 original size:37 final size:34
Alignment explanation
Indices: 1493043--1493146 Score: 86
Period size: 37 Copynumber: 2.9 Consensus size: 34
1493033 ATTATTCTTA
* * *
1493043 ATATATATATATATATATATAATAAACTTTTATATAT
1 ATATATATATATATATATATTATATA--TTTATAT-G
1493080 ATATATATATACTTATATATATTATATATTTATATG
1 ATATATATATA--TATATATATTATATATTTATATG
* * *
1493116 TTATAAATATA-ATTTATATT-TATATTATATA
1 ATATATATATATATATATATTATATATT-TATA
1493147 CTTATATAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
32 6 0.10
33 12 0.21
36 9 0.16
37 18 0.31
39 13 0.22
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (34 bp):
ATATATATATATATATATATTATATATTTATATG
Found at i:1493120 original size:13 final size:12
Alignment explanation
Indices: 1493075--1493153 Score: 54
Period size: 13 Copynumber: 6.4 Consensus size: 12
1493065 TAAACTTTTA
* *
1493075 TATATATATATA
1 TATATTTATATT
*
1493087 TATACTTATA--
1 TATATTTATATT
1493097 TATATTATATATT
1 TATATT-TATATT
**
1493110 TATATGTTATAAA
1 TATAT-TTATATT
1493123 TATAATTTATATT
1 TAT-ATTTATATT
*
1493136 TATATTATATACT
1 TATATT-TATATT
1493149 TATAT
1 TATAT
1493154 AAGTATATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
10 5 0.09
11 4 0.08
12 11 0.21
13 30 0.57
14 3 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (12 bp):
TATATTTATATT
Found at i:1493162 original size:2 final size:2
Alignment explanation
Indices: 1493043--1493146 Score: 78
Period size: 2 Copynumber: 54.5 Consensus size: 2
1493033 ATTATTCTTA
* *
1493043 AT AT AT AT AT AT AT AT AT AT A- AT AA ACT -T TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
1493084 AT AT AT ACT -T AT AT AT AT -T AT AT AT TT AT AT GT -T AT AA AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1493124 AT A- AT TT AT AT TT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1493147 CTTATATAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
1 7 0.09
2 73 0.90
3 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1493991 original size:31 final size:32
Alignment explanation
Indices: 1493956--1494027 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
1493946 TTATTTTGAT
1493956 TTTATCCCCTTA-TTTTTAAGGTTA-ATTATAA
1 TTTATCCCCTTATTTTTTAAGGTTAGA-TATAA
* * *
1493987 TTTAT-CTCTCATTTTTTAAGGTTAGATATAC
1 TTTATCCCCTTATTTTTTAAGGTTAGATATAA
1494018 TTTA-CCCCTT
1 TTTATCCCCTT
1494028 GAGTTAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
30 4 0.12
31 28 0.85
32 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (32 bp):
TTTATCCCCTTATTTTTTAAGGTTAGATATAA
Found at i:1495349 original size:47 final size:48
Alignment explanation
Indices: 1495226--1495355 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 48
1495216 ATATAAATTT
* *
1495226 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAATA
* *
1495271 CTTACCATTTAAAATTCCATAAGCTCGTAAGCTTATTTTTTTTCCAATATA
1 CTTACCATTT--AATTCCATAAGCTCATAAGCTTATTTTTTTACCAA-ATA
* *
1495322 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
1495356 GCATGGTTAC
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
45 6 0.08
46 3 0.04
47 23 0.32
48 20 0.28
50 11 0.15
51 9 0.12
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAATA
Found at i:1499823 original size:37 final size:37
Alignment explanation
Indices: 1499777--1499860 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 37
1499767 AATAAGTTAG
* *
1499777 AAAATATTTATAT-ATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATAATTTT-TTTAAAAAATTGAAAAT-AT
*
1499816 -AAAATTTATATAATTTTTTTACAAAATTGAAAATAT
1 AAAAATTTATATAATTTTTTTAAAAAATTGAAAATAT
1499852 AAAAATTTA
1 AAAAATTTA
1499861 ATGAAAGGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 2 0.05
37 30 0.75
38 8 0.20
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
AAAAATTTATATAATTTTTTTAAAAAATTGAAAATAT
Found at i:1504616 original size:13 final size:13
Alignment explanation
Indices: 1504598--1504622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1504588 GTAATAAACA
1504598 AAATTAACAAAAT
1 AAATTAACAAAAT
1504611 AAATTAACAAAA
1 AAATTAACAAAA
1504623 AGTCCAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (13 bp):
AAATTAACAAAAT
Found at i:1507396 original size:64 final size:64
Alignment explanation
Indices: 1507314--1507470 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
1507304 TTGAAGGTGT
* ** *
1507314 ATCGATGCACATGTAATGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAAGTAATGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-T
1507376 GC
63 GC
* * *
1507378 ATCGATGCATAAGGAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGC
1 ATCGATGCACAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
* *
1507442 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAAGTAATGCATCGATGCAT
1507471 ACCTTCATTA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
64 72 0.91
65 7 0.09
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAAGTAATGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGC
Found at i:1507889 original size:29 final size:29
Alignment explanation
Indices: 1507847--1507956 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
1507837 TATGTGATAT
*
1507847 GAGAACATGACATGAGCTAAATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
* *
1507877 GAGAAATAACATGAGCTGCATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
1507906 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1507935 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1507957 ACATATAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 7 0.10
29 61 0.84
30 5 0.07
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1509711 original size:13 final size:13
Alignment explanation
Indices: 1509692--1509778 Score: 111
Period size: 13 Copynumber: 6.3 Consensus size: 13
1509682 GTTATAACCC
1509692 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1509705 TACCCGACCCGTT
1 GACCCGACCCGTT
1509718 GACCCGACCCGTT
1 GACCCGACCCGTT
1509731 GACCCGACCCGACCTGTT
1 GACCCGA--C--CC-GTT
*
1509749 GACCCGACCCATT
1 GACCCGACCCGTT
1509762 GACCCGACCCGTT
1 GACCCGACCCGTT
1509775 GACC
1 GACC
1509779 GACGTTAACC
Statistics
Matches: 65, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
13 49 0.75
14 2 0.03
15 1 0.02
16 1 0.02
17 2 0.03
18 10 0.15
ACGTcount: A:0.17, C:0.46, G:0.21, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1509726 original size:31 final size:29
Alignment explanation
Indices: 1509688--1509772 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 29
1509678 ACCGGTTATA
1509688 ACCCGACCC-GACCCGTTTACCCGACCCGTTG
1 ACCCGACCCTGACCCG---ACCCGACCCGTTG
*
1509719 ACCCGACCCGTTGACCCGACCCGACCTGTTG
1 ACCCGACCC--TGACCCGACCCGACCCGTTG
1509750 ACCCGACCCATTGACCCGACCCG
1 ACCCGACCC--TGACCCGACCCG
1509773 TTGACCGACG
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
31 43 0.88
34 6 0.12
ACGTcount: A:0.18, C:0.48, G:0.20, T:0.14
Consensus pattern (29 bp):
ACCCGACCCTGACCCGACCCGACCCGTTG
Found at i:1509737 original size:44 final size:44
Alignment explanation
Indices: 1509688--1509778 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
1509678 ACCGGTTATA
* *
1509688 ACCCGACCCGACCCGTTTACCCGACCCGTTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCATTGACCCGACCCGTTG
*
1509732 ACCCGACCCGACCTGTTGACCCGACCCATTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTGACCCGACCCATTGACCCGACCCGTTG
1509776 ACC
1 ACC
1509779 GACGTTAACC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.15
Consensus pattern (44 bp):
ACCCGACCCGACCCGTTGACCCGACCCATTGACCCGACCCGTTG
Found at i:1509772 original size:18 final size:18
Alignment explanation
Indices: 1509718--1509758 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1509708 CCGACCCGTT
1509718 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGACCC
*
1509736 GACCCGACCTGTTGACCC
1 GACCCGACCCGTTGACCC
1509754 GACCC
1 GACCC
1509759 ATTGACCCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.49, G:0.22, T:0.12
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1512364 original size:12 final size:12
Alignment explanation
Indices: 1512327--1512389 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
1512317 ATATGATACT
1512327 TGACATGGATTC
1 TGACATGGATTC
1512339 TGATC-T-GATATC
1 TGA-CATGGAT-TC
1512351 TGACATGGATTC
1 TGACATGGATTC
* *
1512363 TGATAT-GATAC
1 TGACATGGATTC
*
1512374 TTGACTTGGATTC
1 -TGACATGGATTC
1512387 TGA
1 TGA
1512390 TATGATACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 8 0.20
12 24 0.60
13 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1512443 original size:24 final size:24
Alignment explanation
Indices: 1512311--1512429 Score: 186
Period size: 24 Copynumber: 5.0 Consensus size: 24
1512301 TTCGATTTGA
1512311 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1512335 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
1512359 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
1512383 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
1512407 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
1512430 AATTATGTTT
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 85 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1512606 original size:43 final size:43
Alignment explanation
Indices: 1512545--1512639 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
1512535 GGGCCTTACT
*
1512545 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1512588 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
*
1512631 TGGTATGTT
1 TGGTGTGTT
1512640 CGGTTGGAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.17, C:0.11, G:0.36, T:0.37
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCTGGGAAACCTACACATTA
Found at i:1514811 original size:17 final size:18
Alignment explanation
Indices: 1514770--1514829 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
1514760 GTCATAACCC
*
1514770 GACCCCACCCGACCCGTT
1 GACCCGACCCGACCCGTT
* *
1514788 AACCCGACCCG-CCTGTT
1 GACCCGACCCGACCCGTT
1514805 GACCCGACCCGTTGACCCGTT
1 GACCCGACCC---GACCCGTT
1514826 GACC
1 GACC
1514830 GTTGACCGGC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 14 0.42
18 9 0.27
20 1 0.03
21 9 0.27
ACGTcount: A:0.17, C:0.48, G:0.20, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:1514820 original size:13 final size:13
Alignment explanation
Indices: 1514776--1514823 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
1514766 ACCCGACCCC
*
1514776 ACCCGACCCGTTA
1 ACCCGACCCGTTG
1514789 ACCCGACCCGCCTGTTG
1 ACCCGA--C-CC-GTTG
1514806 ACCCGACCCGTTG
1 ACCCGACCCGTTG
1514819 ACCCG
1 ACCCG
1514824 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
13 15 0.50
14 2 0.07
15 2 0.07
16 2 0.07
17 9 0.30
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:1514823 original size:8 final size:8
Alignment explanation
Indices: 1514810--1514856 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1514800 CTGTTGACCC
1514810 GACCCGTT
1 GACCCGTT
1514818 GACCCGTT
1 GACCCGTT
1514826 GA-CCGTT
1 GACCCGTT
1514833 GACCGGCGTT
1 GACC--CGTT
1514843 GACCACTGTT
1 GACC-C-GTT
1514853 GACC
1 GACC
1514857 AAAACTTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
7 7 0.21
8 11 0.32
9 1 0.03
10 15 0.44
ACGTcount: A:0.15, C:0.34, G:0.28, T:0.23
Consensus pattern (8 bp):
GACCCGTT
Found at i:1514833 original size:15 final size:16
Alignment explanation
Indices: 1514813--1514846 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1514803 TTGACCCGAC
1514813 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
1514828 CCGTTGACCGGCGTTGA
1 CCGTTGACC-GCGTTGA
1514845 CC
1 CC
1514847 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:1517431 original size:12 final size:12
Alignment explanation
Indices: 1517394--1517456 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
1517384 TTATGATACT
1517394 TGACATGGATTC
1 TGACATGGATTC
1517406 TGATC-T-GATATC
1 TGA-CATGGAT-TC
1517418 TGACATGGATTC
1 TGACATGGATTC
* *
1517430 TGATAT-GATAC
1 TGACATGGATTC
*
1517441 TTGACTTGGATTC
1 -TGACATGGATTC
1517454 TGA
1 TGA
1517457 TATGATACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 8 0.20
12 24 0.60
13 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:1517510 original size:24 final size:24
Alignment explanation
Indices: 1517378--1517496 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
1517368 TTCGATTTGA
*
1517378 ATTCTGTTATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
1517402 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
1517426 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
1517450 ATTCTGATATGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
*
1517474 ATTTTGATATGATACTTGACATG
1 ATTCTGATATGATACTTGACATG
1517497 AATTATGTTT
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 84 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:1517675 original size:43 final size:43
Alignment explanation
Indices: 1517612--1517706 Score: 163
Period size: 43 Copynumber: 2.2 Consensus size: 43
1517602 GGGCCTTACT
* * *
1517612 TGGTGTGATGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGTGGGCGTATGGTTCTGGGAAACCTACACATTA
1517655 TGGTGTGTTGGTGGGCGTATGGTTCTGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGCGTATGGTTCTGGGAAACCTACACATTA
1517698 TGGTGTGTT
1 TGGTGTGTT
1517707 CGGTTGGAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.17, C:0.12, G:0.37, T:0.35
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGCGTATGGTTCTGGGAAACCTACACATTA
Found at i:1518716 original size:12 final size:12
Alignment explanation
Indices: 1518699--1518755 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 12
1518689 AAAAGAATTA
1518699 ATTAAATAAAAT
1 ATTAAATAAAAT
*
1518711 ATT-AA-AATA-
1 ATTAAATAAAAT
1518720 ATTAAATAAAAT
1 ATTAAATAAAAT
* *
1518732 ACT-AACAAAAT
1 ATTAAATAAAAT
*
1518743 ATTAAATATAAT
1 ATTAAATAAAAT
1518755 A
1 A
1518756 AAATATACAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
9 3 0.09
10 5 0.15
11 14 0.41
12 12 0.35
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAAATAAAAT
Found at i:1518722 original size:21 final size:22
Alignment explanation
Indices: 1518697--1518755 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
1518687 AAAAAAGAAT
*
1518697 TAATTAAATAAAATATTAA-AA
1 TAATTAAATAAAATACTAACAA
1518718 TAATTAAATAAAATACTAACAA
1 TAATTAAATAAAATACTAACAA
* *
1518740 AATATTAAATATAATA
1 TA-ATTAAATAAAATA
1518756 AAATATACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 18 0.55
22 3 0.09
23 12 0.36
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (22 bp):
TAATTAAATAAAATACTAACAA
Found at i:1521081 original size:20 final size:19
Alignment explanation
Indices: 1521056--1521105 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1521046 TGAAAAGATT
1521056 TAATAAAATAAAACA-GATAA
1 TAATAAAATAAAA-AGGA-AA
1521076 TAAT-AAATAAAAAGGGAAA
1 TAATAAAATAAAAA-GGAAA
1521095 TAATAAAATAA
1 TAATAAAATAA
1521106 TAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (19 bp):
TAATAAAATAAAAAGGAAA
Found at i:1521860 original size:24 final size:25
Alignment explanation
Indices: 1521833--1521889 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1521823 TATCCTAAAA
* **
1521833 AAAATACTTAAAAC-TATTTAAACT
1 AAAATACTTAAAACAAAGATAAACT
*
1521857 AAAATACCTAAAACAAAGATAAACT
1 AAAATACTTAAAACAAAGATAAACT
1521882 AAAATACT
1 AAAATACT
1521890 ATTAAAATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 13 0.48
25 14 0.52
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAATACTTAAAACAAAGATAAACT
Found at i:1523513 original size:15 final size:14
Alignment explanation
Indices: 1523489--1523527 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 14
1523479 CAACGATCCC
1523489 AACATATCAATATCA
1 AACA-ATCAATATCA
1523504 AACAACTCAATATCA
1 AACAA-TCAATATCA
1523519 AACAATCAA
1 AACAATCAA
1523528 ACAAGTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.56, C:0.23, G:0.00, T:0.21
Consensus pattern (14 bp):
AACAATCAATATCA
Found at i:1524181 original size:16 final size:15
Alignment explanation
Indices: 1524147--1524187 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
1524137 AAAAAAAAAT
1524147 AAAATAAAATTAATG
1 AAAATAAAATTAATG
* *
1524162 AAAATAAAGTTTACTG
1 AAAATAAA-ATTAATG
1524178 AAAATAAAAT
1 AAAATAAAAT
1524188 AAAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.27
Consensus pattern (15 bp):
AAAATAAAATTAATG
Found at i:1529801 original size:20 final size:19
Alignment explanation
Indices: 1529776--1529825 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
1529766 TGAAAAGATT
1529776 TAATAAAATAAAATA-GATAA
1 TAATAAAATAAAA-AGGA-AA
1529796 TAAT-AAATAAAAAGGGAAA
1 TAATAAAATAAAAA-GGAAA
1529815 TAATAAAATAA
1 TAATAAAATAA
1529826 TAAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 12 0.44
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (19 bp):
TAATAAAATAAAAAGGAAA
Found at i:1529897 original size:11 final size:11
Alignment explanation
Indices: 1529881--1529915 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1529871 AAAGAAGTAC
1529881 AATTAAATAAA
1 AATTAAATAAA
1529892 AATTAAATAAA
1 AATTAAATAAA
*
1529903 CAAATAAATAAA
1 -AATTAAATAAA
1529915 A
1 A
1529916 GAACTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AATTAAATAAA
Found at i:1536348 original size:3 final size:3
Alignment explanation
Indices: 1536340--1536394 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
1536330 GTAATGAAGT
1536340 ATA ATA ATA ATA ATA ATA AT- ATA ATA AT- ATA ATTA ATA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA
*
1536383 ATA CTA ATA ATA
1 ATA ATA ATA ATA
1536395 TTTTTGTGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:1536376 original size:23 final size:22
Alignment explanation
Indices: 1536340--1536391 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
1536330 GTAATGAAGT
1536340 ATAATAATAATAATAATAATATA
1 ATAAT-ATAATAATAATAATATA
1536363 ATAATATAATTAATAATAATATA
1 ATAATATAA-TAATAATAATATA
*
1536386 CTAATA
1 ATAATA
1536392 ATATTTTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATATAATAATAATAATATA
Found at i:1536383 original size:26 final size:25
Alignment explanation
Indices: 1536343--1536395 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
1536333 ATGAAGTATA
1536343 ATAATAATAATAATAATA-TAATAAT
1 ATAATAATAATAAT-ATACTAATAAT
1536368 ATAATTAATAATAATATACTAATAAT
1 ATAA-TAATAATAATATACTAATAAT
1536394 AT
1 AT
1536396 TTTTGTGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
ATAATAATAATAATATACTAATAAT
Found at i:1540028 original size:32 final size:32
Alignment explanation
Indices: 1539957--1540019 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1539947 ATATCTTCCG
* *
1539957 AACATGCTTTAATTAAATAACATTCCTGCCCA
1 AACATGCTTTAATTAAATAACACTCCTACCCA
1539989 AACATGCTTTAATTAAATAACACTCCTACCC
1 AACATGCTTTAATTAAATAACACTCCTACCC
1540020 GGATATGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (32 bp):
AACATGCTTTAATTAAATAACACTCCTACCCA
Found at i:1543277 original size:3 final size:3
Alignment explanation
Indices: 1543269--1543340 Score: 103
Period size: 3 Copynumber: 24.3 Consensus size: 3
1543259 AAGTATGTAA
*
1543269 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGA- ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
*
1543314 AAT AAT AAT AAT AAT -AT ACT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1543341 TTTTTGTAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1545490 original size:185 final size:187
Alignment explanation
Indices: 1545173--1545548 Score: 738
Period size: 185 Copynumber: 2.0 Consensus size: 187
1545163 ACATCCGAAG
1545173 GCTTGAGGCGAACTTTCTTGGTGGCGTCAGGGTTTGTCGGAGTATCACGGAGGGACTTATCGCTA
1 GCTTGAGGCGAACTTTCTTGGTGGCGTCAGGGTTTGTCGGAGTATCACGGAGGGACTTATCGCTA
1545238 TTCAATTATACTTATGCTGATTTGAAGTAACCTTCTAATCTATCTTCAAGACTGCAATTGTCAAA
66 TTCAATTATACTTATGCTGATTTGAAGTAACCTTCTAATCTATCTTCAAGACTGCAATTGTCAAA
1545303 GGAT-AACCATATCCTATTATTTGAACGTGAAAAAATATCTTACAAAAGAGTGAGAT
131 GGATAAACCATATCCTATTATTTGAACGTGAAAAAATATCTTACAAAAGAGTGAGAT
1545359 GCTT-AGGCGAACTTTCTTGGTGGCGTCAGGGTTTGTCGGAGTATCACGGAGGGACTTATCGCTA
1 GCTTGAGGCGAACTTTCTTGGTGGCGTCAGGGTTTGTCGGAGTATCACGGAGGGACTTATCGCTA
1545423 TTCAATTATACTTATGCTGATTTGAAGTAACCTTCTAATCTATCTTCAAGACTGCAATTGTCAAA
66 TTCAATTATACTTATGCTGATTTGAAGTAACCTTCTAATCTATCTTCAAGACTGCAATTGTCAAA
1545488 GGATAAACCATATCCTATTATTTGAACGTGAAAAAATATCTTACAAAAGAGTGAGAT
131 GGATAAACCATATCCTATTATTTGAACGTGAAAAAATATCTTACAAAAGAGTGAGAT
1545545 GCTT
1 GCTT
1545549 TGGACTCAAG
Statistics
Matches: 189, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 129 0.68
186 60 0.32
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (187 bp):
GCTTGAGGCGAACTTTCTTGGTGGCGTCAGGGTTTGTCGGAGTATCACGGAGGGACTTATCGCTA
TTCAATTATACTTATGCTGATTTGAAGTAACCTTCTAATCTATCTTCAAGACTGCAATTGTCAAA
GGATAAACCATATCCTATTATTTGAACGTGAAAAAATATCTTACAAAAGAGTGAGAT
Found at i:1546084 original size:3 final size:3
Alignment explanation
Indices: 1546076--1546111 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1546066 AATTAACTAA
* *
1546076 TAT TAT TAT TAT TAT TAT TAT TAA TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1546112 AAAGGTTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1549668 original size:23 final size:23
Alignment explanation
Indices: 1549619--1549720 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
1549609 GAGTTGAGGG
* * *
1549619 TTCTACGTGGTCCTTCAGGATAA
1 TTCTACGTGGTCCTTCGGGACAT
*
1549642 TTCTACGTGGTCCTACGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*** *
1549665 TTCTACACAGTCCTTCGGGATAAT
1 TTCTACGTGGTCCTTCGGGA-CAT
* *
1549689 AT-TATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
1549711 TTCTATGTGG
1 TTCTACGTGG
1549721 CAATTCGGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
22 3 0.05
23 55 0.90
24 3 0.05
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:1549678 original size:46 final size:46
Alignment explanation
Indices: 1549628--1549715 Score: 133
Period size: 46 Copynumber: 1.9 Consensus size: 46
1549618 GTTCTACGTG
1549628 GTCCTTCAGGATAAT-TCTACGTGGTCCTACGGGACATTTCTACACA
1 GTCCTTCAGGATAATAT-TACGTGGTCCTACGGGACATTTCTACACA
* * *
1549674 GTCCTTCGGGATAATATTATGTGGTCCTTCGGGACATTTCTA
1 GTCCTTCAGGATAATATTACGTGGTCCTACGGGACATTTCTA
1549716 TGTGGCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
46 37 0.97
47 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (46 bp):
GTCCTTCAGGATAATATTACGTGGTCCTACGGGACATTTCTACACA
Found at i:1549854 original size:6 final size:6
Alignment explanation
Indices: 1549843--1549933 Score: 92
Period size: 6 Copynumber: 14.7 Consensus size: 6
1549833 TAATGAATTG
* * **
1549843 TGATAA TGATAA TGATAG TGACAA TGATAA TGATAA TGATGT TGATAA
1 TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA TGATAA
* * *
1549891 TGATAT TGATGA TGATTATGA TGATAA TGATAA TGATGA TGAT
1 TGATAA TGATAA TGA-TA--A TGATAA TGATAA TGATAA TGAT
1549934 GTTGATAAGG
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
6 62 0.90
7 1 0.01
8 2 0.03
9 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.22, T:0.36
Consensus pattern (6 bp):
TGATAA
Done.