Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002726.1 Hibiscus syriacus cultivar Beakdansim tig00005623_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: 72273
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:283 original size:2 final size:2
Alignment explanation
Indices: 276--324 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
266 AGAGTGTAAA
276 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
318 AT AT AT A
1 AT AT AT A
325 AAAACAATGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1561 original size:5 final size:5
Alignment explanation
Indices: 1551--1595 Score: 58
Period size: 5 Copynumber: 9.2 Consensus size: 5
1541 TATTAACAAC
*
1551 AATAT AATAT AATAT AATAA ATATAT AATA- AATAT AA-AT AATAT A
1 AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT AATAT AATAT A
1596 TAATAATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 8 0.23
5 23 0.66
6 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1578 original size:11 final size:11
Alignment explanation
Indices: 1552--1601 Score: 70
Period size: 10 Copynumber: 4.8 Consensus size: 11
1542 ATTAACAACA
*
1552 ATATAATATA-
1 ATATAATAAAT
1562 ATATAATAAAT
1 ATATAATAAAT
1573 ATATAATAAAT
1 ATATAATAAAT
1584 ATA-AAT-AAT
1 ATATAATAAAT
1593 ATATAATAA
1 ATATAATAA
1602 TGTACTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
9 6 0.17
10 15 0.42
11 15 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATATAATAAAT
Found at i:1711 original size:39 final size:35
Alignment explanation
Indices: 1643--1762 Score: 113
Period size: 39 Copynumber: 3.4 Consensus size: 35
1633 TTTAAAAAAC
*
1643 TATATATATG--TTTTCAAAAATA-TTT-AAACTA
1 TATATATATGTTTTTTAAAAAATATTTTAAAACTA
1674 TATAGTATATGTTTTTTAAAAAATATGTTTCAAAAACTA
1 TATA-TATATGTTTTTTAAAAAATAT-TTT--AAAACTA
*** * *
1713 TATTATATATACGTTTTCAAAAATATTTTAAAATTA
1 TA-TATATATGTTTTTTAAAAAATATTTTAAAACTA
1749 TATATATATGTTTT
1 TATATATATGTTTT
1763 CAAAAATGTT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
31 4 0.06
32 6 0.08
34 11 0.15
35 9 0.13
36 11 0.15
38 3 0.04
39 25 0.35
40 2 0.03
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATATATGTTTTTTAAAAAATATTTTAAAACTA
Found at i:1749 original size:31 final size:32
Alignment explanation
Indices: 1638--1949 Score: 179
Period size: 32 Copynumber: 9.1 Consensus size: 32
1628 ACCATTTTAA
* *
1638 AAAACTATATATATGTTTTCAAAAAT-ATTT-
1 AAAATTATATATATGTTTTCAAAAATGTTTTC
* * *
1668 AAACTATATAGTATATGTTTTTTAAAAAATATGTTTC
1 AAAAT-TATA-TATATG--TTTTCAAAAATGT-TTTC
*
1705 AAAAACTATATTATATATACGTTTTCAAAAATATTTT-
1 -AAAA-T-TA-TATATAT--GTTTTCAAAAATGTTTTC
1742 AAAATTATATATATATGTTTTCAAAAATGTTTTC
1 AAAA-T-TATATATATGTTTTCAAAAATGTTTTC
* * *
1776 AAAACTGTACA-ATAT-ATTTCAAAAGTGTTTTC
1 AAAA-T-TATATATATGTTTTCAAAAATGTTTTC
*
1808 AAAATTACTATTAATATGTTTTCAAAAGTGTTTTC
1 AAAATTA-TA-T-ATATGTTTTCAAAAATGTTTTC
* *
1843 AAAA-TAGATATATGTTTTCAAAAATGTTTTTTTA
1 AAAATTATATATATGTTTTCAAAAATG---TTTTC
*
1877 AAACTATATATTATATATGTTTTCAAAAAATGCTTT-
1 AAA--AT-TA-TATATATGTTTTC-AAAAATGTTTTC
* * * *
1913 AAAACTATATTTATATATTTCAAAAATGTTTTT
1 AAAATTATATATATGT-TTTCAAAAATGTTTTC
1946 AAAA
1 AAAA
1950 CCATATTATA
Statistics
Matches: 229, Mismatches: 24, Indels: 55
0.74 0.08 0.18
Matches are distributed among these distances:
30 5 0.02
31 22 0.10
32 43 0.19
33 31 0.14
34 32 0.14
35 27 0.12
36 15 0.07
37 3 0.01
38 8 0.03
39 33 0.14
40 9 0.04
41 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (32 bp):
AAAATTATATATATGTTTTCAAAAATGTTTTC
Found at i:1809 original size:12 final size:12
Alignment explanation
Indices: 1792--1846 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
1782 GTACAATATA
1792 TTTCAAAAGTGT
1 TTTCAAAAGTGT
* *
1804 TTTCAAAATTACT
1 TTTCAAAAGT-GT
* *
1817 ATT-AATA-TGT
1 TTTCAAAAGTGT
1827 TTTCAAAAGTGT
1 TTTCAAAAGTGT
1839 TTTCAAAA
1 TTTCAAAA
1847 TAGATATATG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
10 3 0.09
11 4 0.12
12 23 0.70
13 3 0.09
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (12 bp):
TTTCAAAAGTGT
Found at i:1959 original size:32 final size:32
Alignment explanation
Indices: 1727--2030 Score: 163
Period size: 32 Copynumber: 9.0 Consensus size: 32
1717 ATATATACGT
* * *
1727 TTTCAAAAAT-ATTTTAAAATTATATATATATGT
1 TTTCAAAAATGTTTTTAAAACTATAT-TATAT-A
* * **
1760 TTTCAAAAATGTTTTCAAAACTGTACAATATA
1 TTTCAAAAATGTTTTTAAAACTATATTATATA
* * * *
1792 TTTCAAAAGTGTTTTCAAAATTACTATTAATATGT
1 TTTCAAAAATGTTTTTAAAACTA-TATT-ATAT-A
* * * *
1827 TTTCAAAAGTGTTTTCAAAA-TAGA-TATATGT
1 TTTCAAAAATGTTTTTAAAACTATATTATAT-A
1858 TTTCAAAAATGTTTTTTTAAAACTATATATTATATA
1 TTTCAAAAATG--TTTTTAAAAC--TATATTATATA
*
1894 TGTTTTCAAAAAATG-CTTTAAAACTATATTTATATA
1 ---TTTC-AAAAATGTTTTTAAAACTATA-TTATATA
*
1930 TTTCAAAAATGTTTTTAAAACCATATTATA-A
1 TTTCAAAAATGTTTTTAAAACTATATTATATA
* **
1961 TTTTTAAAAACATTTTTAAAAC--TATTATATTA
1 -TTTCAAAAATGTTTTTAAAACTATATTATA-TA
* *
1993 TATTCAAAAAATGTTCTCTCAAAATTTATATTATATA
1 T-TTC-AAAAATGTT-T-TTAAAA-CTATATTATATA
2030 T
1 T
2031 GTTATATGTA
Statistics
Matches: 216, Mismatches: 29, Indels: 48
0.74 0.10 0.16
Matches are distributed among these distances:
30 7 0.03
31 18 0.08
32 54 0.25
33 47 0.22
34 17 0.08
35 29 0.13
36 10 0.05
37 16 0.07
38 7 0.03
39 4 0.02
40 7 0.03
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (32 bp):
TTTCAAAAATGTTTTTAAAACTATATTATATA
Found at i:2954 original size:200 final size:202
Alignment explanation
Indices: 2468--2962 Score: 557
Period size: 201 Copynumber: 2.5 Consensus size: 202
2458 CAGAAGATAT
* *** * * * *
2468 TTCCTCGATGCTACCATGCAATTGATATGCCCTCGAGTTGAATAGAATCGAACTTGAAAGTTTTC
1 TTCCTCGCTGCTACCATGTGGTTGATATACCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTC
* * ** * * *
2533 ATTAACAGATATCCCTTCTCGCCTTGAGTTATGCTATAAATTCGGCTGAGAGGTAGTTCCTTGTT
66 ATTGACAGATAACCCTTCTCGCCTTGAGCCATGATATAAATTCAGCTGAGAGATAGTTCCTTGTT
* * * ** *
2598 GCTAGATAGCAGCCGACCTAGGTCTTCTTCTAGGCTTAAAGACCTTGGCTTAAAACTTCAACCGG
131 GCTAAATAGCAGCCAACCTAGGTCTTCTTCTAGACTTAAAGACCTTGAATTAAAACTTCAAACGG
*
2663 AAAGTAG
196 AAAATAG
* * ** * * *
2670 -TCCTCGCTACTACCATGTGGCTGATATACTATCGAGCTGAATGAAATTGAACTCAAAAGTTTTC
1 TTCCTCGCTGCTACCATGTGGTTGATATACCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTC
* * * * * *
2734 ATTGACAGATAACTCTTCTCGCCTTGAGCCATGATGTAAATTTAGTTGGGAGATAGTTCTTTGTT
66 ATTGACAGATAACCCTTCTCGCCTTGAGCCATGATATAAATTCAGCTGAGAGATAGTTCCTTGTT
* ** * *
2799 GCTAAATCGCTTCCAACCTAGGTCTTCTTCTTGACTTAAAGACCTT-AATTTAAACTTCAAAC-G
131 GCTAAATAGCAGCCAACCTAGGTCTTCTTCTAGACTTAAAGACCTTGAATTAAAACTTCAAACGG
2862 AAAATAG
196 AAAATAG
* *
2869 TTCCTCGCTGCTACCATGTGGTTGATACACCCTCGAGCTGAATGGAACCGAACTCGAAAGTTGTT
1 TTCCTCGCTGCTACCATGTGGTTGATATACCCTCGAGCTGAATGGAATCGAACTCGAAAGTT-TT
* *
2934 -GTTGATAGATAACCCTTCTCGCCTTGAGC
65 CATTGACAGATAACCCTTCTCGCCTTGAGC
2963 TATACTGCGA
Statistics
Matches: 239, Mismatches: 52, Indels: 6
0.80 0.18 0.02
Matches are distributed among these distances:
199 7 0.03
200 90 0.38
201 142 0.59
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (202 bp):
TTCCTCGCTGCTACCATGTGGTTGATATACCCTCGAGCTGAATGGAATCGAACTCGAAAGTTTTC
ATTGACAGATAACCCTTCTCGCCTTGAGCCATGATATAAATTCAGCTGAGAGATAGTTCCTTGTT
GCTAAATAGCAGCCAACCTAGGTCTTCTTCTAGACTTAAAGACCTTGAATTAAAACTTCAAACGG
AAAATAG
Found at i:11132 original size:16 final size:15
Alignment explanation
Indices: 11100--11186 Score: 71
Period size: 13 Copynumber: 6.1 Consensus size: 15
11090 TAAAAAAATG
11100 AAAA-ATAATATTAAT
1 AAAATATAATA-TAAT
11115 AACAATATAATATAAT
1 AA-AATATAATATAAT
11131 AAATATATAATA-AAT
1 AAA-ATATAATATAAT
*
11146 AATATAT-ATATAAT
1 AAAATATAATATAAT
*
11160 -ATATATAA-ATAAT
1 AAAATATAATATAAT
*
11173 -ATATATAA-ATAAT
1 AAAATATAATATAAT
11186 A
1 A
11187 TGTATATTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
13 27 0.42
14 8 0.12
15 8 0.12
16 16 0.25
17 6 0.09
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATATAATATAAT
Found at i:11138 original size:11 final size:11
Alignment explanation
Indices: 11124--11183 Score: 68
Period size: 11 Copynumber: 5.1 Consensus size: 11
11114 TAACAATATA
11124 ATATAATAAAT
1 ATATAATAAAT
11135 ATATAATAAAT
1 ATATAATAAAT
11146 AATATATATATAAT
1 -ATATA-ATA-AAT
11160 ATAT-ATAAAT
1 ATATAATAAAT
11170 AATATATATAAAT
1 -ATATA-ATAAAT
11183 A
1 A
11184 ATATGTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
10 3 0.07
11 18 0.42
12 6 0.14
13 13 0.30
14 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATAAAT
Found at i:11165 original size:13 final size:13
Alignment explanation
Indices: 11119--11197 Score: 81
Period size: 13 Copynumber: 6.0 Consensus size: 13
11109 ATTAATAACA
11119 ATATA-ATATAAT
1 ATATATATATAAT
*
11131 AAATATATAATAAAT
1 ATATATAT-AT-AAT
11146 AATATATATATAAT
1 -ATATATATATAAT
*
11160 ATATATAAATAAT
1 ATATATATATAAT
*
11173 ATATATAAATAAT
1 ATATATATATAAT
*
11186 ATGTATAT-TAAT
1 ATATATATATAAT
11198 TTATTGTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.14
13 33 0.57
14 5 0.09
15 5 0.09
16 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:11175 original size:9 final size:9
Alignment explanation
Indices: 11102--11187 Score: 52
Period size: 9 Copynumber: 9.0 Consensus size: 9
11092 AAAAAATGAA
11102 AAATAATAT
1 AAATAATAT
* *
11111 TAATAACAAT
1 AAATAA-TAT
11121 ATAAT-ATAAT
1 A-AATAAT-AT
11131 AAATATATAAT
1 AAATA-AT-AT
11142 AAATAATAT
1 AAATAATAT
11151 ATATATAATAT
1 A-A-ATAATAT
*
11162 ATATAA-AT
1 AAATAATAT
11170 -AATATATAT
1 AAATA-ATAT
11179 AAATAATAT
1 AAATAATAT
11188 GTATATTAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 21 0.34
10 13 0.21
11 21 0.34
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (9 bp):
AAATAATAT
Found at i:11313 original size:73 final size:72
Alignment explanation
Indices: 11206--11644 Score: 429
Period size: 72 Copynumber: 6.0 Consensus size: 72
11196 ATTTATTGTA
* **
11206 TTTTCAAAAACCA-TTTTAAAAAC-TATA-TACTATATGTTTTCAAAAATATTTAAAAAACTATA
1 TTTTCAAAAA-TATTTTTAAAAACATATATTA-TATATGTTTTCAAAAATATTTTCAAAACTATA
11268 TATTATATG
64 TATTATATG
* *
11277 TTTTTAAAAATACATTTTTAAAAAC-TATATTATATATGTTTTCAAAAATATTTT-AAAATTATA
1 TTTTCAAAAAT--ATTTTTAAAAACATATATTATATATGTTTTCAAAAATATTTTCAAAACTATA
11340 TATTATATG
64 TATTATATG
* * * * * * * * *
11349 TTTTCAAAAATGTTTTTCAAAACGGTATAATATTTATGTTTTCAAAAGTGTTTTCAAAATTACAT
1 TTTTCAAAAATATTTTTAAAAAC-ATATATTATATATGTTTTCAAAAATATTTTCAAAACTATAT
11414 ATTATATATG
65 A-T-TATATG
* * ** * * * * *
11424 TTTTCAAAAATGTTTTTTAAATTATATATTATATATGATTTCAAAAGTGTTTTCAAAATTACATA
1 TTTTCAAAAATATTTTTAAAAACATATATTATATATGTTTTCAAAAATATTTTCAAAACTATATA
11489 TTATATG
66 TTATATG
* *
11496 TTTTCAAAAATATTTTTTAAAACTATATATTATATATGTTTTCAAAAAAATGCTTTCAAAACTAT
1 TTTTCAAAAATATTTTTAAAAAC-ATATATTATATATGTTTTCAAAAATAT--TTTCAAAACTAT
*
11561 ATTATATATATA
63 A-TAT-TATATG
* * * * ** *
11573 TATTTCAAAAATGTTTTTAAAACCATATATTATATATATTTTTAAAAACGTTTTTAAAACTATAT
1 T-TTTCAAAAATATTTTTAAAAACATATATTATATATGTTTTCAAAAATATTTTCAAAACTATAT
11638 ATTATAT
65 ATTATAT
11645 ATATTTTCGA
Statistics
Matches: 316, Mismatches: 37, Indels: 28
0.83 0.10 0.07
Matches are distributed among these distances:
70 10 0.03
71 9 0.03
72 79 0.25
73 74 0.23
74 44 0.14
75 49 0.16
76 3 0.01
77 29 0.09
78 19 0.06
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (72 bp):
TTTTCAAAAATATTTTTAAAAACATATATTATATATGTTTTCAAAAATATTTTCAAAACTATATA
TTATATG
Found at i:11403 original size:37 final size:36
Alignment explanation
Indices: 11236--11684 Score: 376
Period size: 37 Copynumber: 12.1 Consensus size: 36
11226 AACTATATAC
* **
11236 TATATGTTTTCAAAAATATTTAAAAAACTATATA-T-
1 TATATGTTTTCAAAAATGTTTTCAAAA-TATATATTA
* * *
11271 TATATGTTTTTAAAAATACATTTTTAAAA-ACTATATTA
1 TATATGTTTTCAAAAAT--GTTTTCAAAATA-TATATTA
*
11309 TATATGTTTTCAAAAATATTTT-AAAAT-TATA-TA
1 TATATGTTTTCAAAAATGTTTTCAAAATATATATTA
** *
11342 TTATATGTTTTCAAAAATGTTTTTCAAAACGGTATAATA
1 -TATATGTTTTCAAAAATG-TTTTCAAAA-TATATATTA
* * *
11381 TTTATGTTTTCAAAAGTGTTTTCAAAATTACATATTA
1 TATATGTTTTCAAAAATGTTTTCAAAA-TATATATTA
* *
11418 TATATGTTTTCAAAAATGTTTTTTAAATTATATATTA
1 TATATGTTTTCAAAAATG-TTTTCAAAATATATATTA
* * *
11455 TATATGATTTCAAAAGTGTTTTCAAAAT-TACA-TA
1 TATATGTTTTCAAAAATGTTTTCAAAATATATATTA
* *
11489 TTATATGTTTTCAAAAATATTTTTTAAAACTATATATTA
1 -TATATGTTTTCAAAAAT-GTTTTCAAAA-TATATATTA
*
11528 TATATGTTTTCAAAAAAATGCTTTCAAAACTATATTATATA
1 TATATGTTTTC--AAAAATGTTTTCAAAA-TATA-TAT-TA
* * *
11569 TATAT-ATTTCAAAAATGTTTTTAAAACCATATATTA
1 TATATGTTTTCAAAAATGTTTTCAAAA-TATATATTA
* * * *
11605 TATATATTTTTAAAAACGTTTTTAAAACTATATATTA
1 TATATGTTTTCAAAAATGTTTTCAAAA-TATATATTA
* *
11642 TATATATTTTCGAAAAATGTTCTCAAAATTATATATTA
1 TATATGTTTTC-AAAAATGTTTTCAAAA-TATATATTA
11680 TATAT
1 TATAT
11685 ATTATATGTA
Statistics
Matches: 346, Mismatches: 44, Indels: 45
0.80 0.10 0.10
Matches are distributed among these distances:
33 2 0.01
34 23 0.07
35 43 0.12
36 36 0.10
37 104 0.30
38 102 0.29
39 16 0.05
40 13 0.04
41 7 0.02
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (36 bp):
TATATGTTTTCAAAAATGTTTTCAAAATATATATTA
Found at i:11676 original size:75 final size:74
Alignment explanation
Indices: 11219--11687 Score: 424
Period size: 75 Copynumber: 6.4 Consensus size: 74
11209 TCAAAAACCA
* * * * ** *
11219 TTTTAAAAACTATATA--CTATATGTTTTCAAAAATATTTAAAAAACTATATA-T-TATATGTTT
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTTT
* *
11280 TTAAAAATACA
66 TCAAAAAT--G
* *
11291 TTTTTAAAA--ACTATATTATATATGTTTTCAAAAATATTTT-AAAATTATATA-T-TATATGTT
1 TTTTTAAAACTA-TATATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTT
11351 TTCAAAAATG
65 TTCAAAAATG
** * * * * *
11361 TTTTTCAAAACGGTATAATATTTATGTTTTCAAAAGTGTTTTCAAAATTACATATTATATATGTT
1 TTTTT-AAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTT
11426 TTCAAAAATG
65 TTCAAAAATG
* * * *
11436 TTTTTTAAATTATATATTATATATGA-TTTCAAAAGTGTTTTCAAAATTACATA-T-TATATGTT
1 TTTTTAAAACTATATATTATATAT-ATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTT
*
11498 TTCAAAAATAT
65 TTCAAAAAT-G
* * *
11509 TTTTTAAAACTATATATTATATATGTTTTCAAAAAAATGCTTTCAAAACTATATTATATATATAT
1 TTTTTAAAACTATATATTATATATATTTTC--AAAAATGTTTTCAAAATTATA-TAT-TATATAT
*
11574 -ATTTCAAAAATG
62 GTTTTCAAAAATG
* * * * * *
11586 TTTTTAAAACCATATATTATATATATTTTTAAAAACGTTTTTAAAACTATATATTATATATATTT
1 TTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTTT
11651 TCGAAAAATG
66 TC-AAAAATG
* * *
11661 TTCTCAAAATTATATATTATATATATT
1 TTTTTAAAACTATATATTATATATATT
11688 ATATGTATAT
Statistics
Matches: 337, Mismatches: 40, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
70 6 0.02
71 8 0.02
72 77 0.23
73 65 0.19
74 48 0.14
75 88 0.26
76 2 0.01
77 27 0.08
78 11 0.03
79 5 0.01
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (74 bp):
TTTTTAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATGTTT
TCAAAAATG
Found at i:14067 original size:30 final size:30
Alignment explanation
Indices: 14028--14270 Score: 234
Period size: 30 Copynumber: 8.3 Consensus size: 30
14018 CTATTTAAAA
* *
14028 GGACCAAAATAGCAAAAAAAGAAACTTAAG
1 GGACTAAAATAGCAAAAATAGAAACTTAAG
14058 GGACTAAAATAGCAAAAATAGAAA-TTGAAG
1 GGACTAAAATAGCAAAAATAGAAACTT-AAG
* *
14088 GGACTAAAATAGCAAAACTA-AAACATAAG
1 GGACTAAAATAGCAAAAATAGAAACTTAAG
* * * * *
14117 GGATTAAAATAGCATACATAGAAATTTAAA
1 GGACTAAAATAGCAAAAATAGAAACTTAAG
* * *
14147 GGACTAAAATAGAAAAAATAGACATTTAAG
1 GGACTAAAATAGCAAAAATAGAAACTTAAG
* *
14177 AGACTAAATTCA-CAAAAATAGAAACTTAAG
1 GGACTAAAAT-AGCAAAAATAGAAACTTAAG
* ** *
14207 GGACTAAAATAG-TAAAATAGTCA-TTCAAA
1 GGACTAAAATAGCAAAAATAGAAACTT-AAG
14236 GGACTAAAATAGC--AAA-A-AAACTTAAG
1 GGACTAAAATAGCAAAAATAGAAACTTAAG
14262 GGACTAAAA
1 GGACTAAAA
14271 CATAAATCAA
Statistics
Matches: 174, Mismatches: 31, Indels: 20
0.77 0.14 0.09
Matches are distributed among these distances:
26 12 0.07
27 3 0.02
28 5 0.03
29 47 0.27
30 106 0.61
31 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (30 bp):
GGACTAAAATAGCAAAAATAGAAACTTAAG
Found at i:14119 original size:59 final size:58
Alignment explanation
Indices: 14028--14270 Score: 212
Period size: 59 Copynumber: 4.2 Consensus size: 58
14018 CTATTTAAAA
* *
14028 GGACCAAAATAGCAAAAA-AAGAAACTTAAGGGACTAAAATAGCAAAAATAGAAATTGAAG
1 GGACTAAAATAGCAAAAATAA-ACA-TTAAGGGACTAAAATAGCAAAAATAGAAATT-AAG
* * * * *
14088 GGACTAAAATAGCAAAACTAAAACA-TAAGGGATTAAAATAGCATACATAGAAATTTAAA
1 GGACTAAAATAGCAAAAAT-AAACATTAAGGGACTAAAATAGCAAAAATAGAAA-TTAAG
* * * *
14147 GGACTAAAATAGAAAAAATAGACATTTAAGAGACTAAATTCA-CAAAAATAGAAACTTAAG
1 GGACTAAAATAGCAAAAATAAACA-TTAAGGGACTAAAAT-AGCAAAAATAGAAA-TTAAG
* ** * *
14207 GGACTAAAATAG-TAAAATAGTCATTCAAAGGACTAAAATAGC-AAAA-A-AACTTAAG
1 GGACTAAAATAGCAAAAATAAACATT-AAGGGACTAAAATAGCAAAAATAGAAATTAAG
14262 GGACTAAAA
1 GGACTAAAA
14271 CATAAATCAA
Statistics
Matches: 152, Mismatches: 23, Indels: 21
0.78 0.12 0.11
Matches are distributed among these distances:
55 14 0.09
56 2 0.01
57 1 0.01
58 11 0.07
59 64 0.42
60 55 0.36
61 3 0.02
62 2 0.01
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.18
Consensus pattern (58 bp):
GGACTAAAATAGCAAAAATAAACATTAAGGGACTAAAATAGCAAAAATAGAAATTAAG
Found at i:14156 original size:89 final size:89
Alignment explanation
Indices: 14028--14253 Score: 258
Period size: 89 Copynumber: 2.5 Consensus size: 89
14018 CTATTTAAAA
* * * * *
14028 GGACCAAAATAGCAAAAAAAGAAACTTAAGGGACTAAAATAGCAAAAATAGAAATTGAAGGGACT
1 GGACTAAAATAGC-AAAATAGAAATTTAAAGGACTAAAATAGCAAAAATAGAAATTGAAGAGACT
*
14093 AAAAT-AGCAAAACTA-AAACATAAG
65 AAAATCA-CAAAAATAGAAACATAAG
* * * * *
14117 GGATTAAAATAGCATACATAGAAATTTAAAGGACTAAAATAGAAAAAATAGACATTTAAGAGACT
1 GGACTAAAATAGCA-AAATAGAAATTTAAAGGACTAAAATAGCAAAAATAGAAATTGAAGAGACT
* *
14182 AAATTCACAAAAATAGAAACTTAAG
65 AAAATCACAAAAATAGAAACATAAG
* ** *
14207 GGACTAAAATAGTAAAATAGTCATTCAAAGGACTAAAATAGCAAAAA
1 GGACTAAAATAGCAAAATAGAAATTTAAAGGACTAAAATAGCAAAAA
14254 AACTTAAGGG
Statistics
Matches: 114, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
88 1 0.01
89 92 0.81
90 21 0.18
ACGTcount: A:0.57, C:0.10, G:0.15, T:0.18
Consensus pattern (89 bp):
GGACTAAAATAGCAAAATAGAAATTTAAAGGACTAAAATAGCAAAAATAGAAATTGAAGAGACTA
AAATCACAAAAATAGAAACATAAG
Found at i:14244 original size:119 final size:120
Alignment explanation
Indices: 14020--14249 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
14010 ATCATATTCT
*
14020 ATTTAAAAGGACCAAAATAGCAAAAAAAGAAACTTAAGGGACTAAAATAGCAAAAATAGAAATTG
1 ATTTAAAAGGACCAAAATAGCAAAAAAAGAAACTTAAGAGACTAAAATAGCAAAAATAGAAATTG
* *
14085 AAGGGACTAAAATAGCAAAACTAAAACATAAGGGATTAAAATAGCATACATAGAA
66 AAGGGACTAAAATAGCAAAACTAAAACATAAAGGACTAAAATAGCATACATAGAA
* * * *
14140 ATTT-AAAGGACTAAAATAG-AAAAAATAGACATTTAAGAGACTAAATTCA-CAAAAATAGAAAC
1 ATTTAAAAGGACCAAAATAGCAAAAAA-AGAAACTTAAGAGACTAAAAT-AGCAAAAATAGAAA-
* **
14202 TT-AAGGGACTAAAATAGTAAAA-T-AGTCATTCAAAGGACTAAAATAGCA
63 TTGAAGGGACTAAAATAGCAAAACTAAAACA-T-AAAGGACTAAAATAGCA
14250 AAAAAACTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
117 3 0.03
118 8 0.08
119 77 0.81
120 7 0.07
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (120 bp):
ATTTAAAAGGACCAAAATAGCAAAAAAAGAAACTTAAGAGACTAAAATAGCAAAAATAGAAATTG
AAGGGACTAAAATAGCAAAACTAAAACATAAAGGACTAAAATAGCATACATAGAA
Found at i:15888 original size:2 final size:2
Alignment explanation
Indices: 15881--15907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
15871 GAAAAATGTA
15881 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
15908 AAAGTAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25124 original size:59 final size:60
Alignment explanation
Indices: 25011--25126 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
25001 GTCATTTTAA
* *
25011 AACTTTTAATAATCAAGGGAATCAACAAAGCAATATCCTATATTCGGAGAACTATTTTGT
1 AACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATATTAGGAGAACTATTTTGT
* * * * *
25071 AACTTTTAATAGT-AAAGGACTCAATAAAGTAATATCCTATAGTTAGGTG-ACTATTT
1 AACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATA-TTAGGAGAACTATTT
25127 ATATACTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 31 0.65
60 17 0.35
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.34
Consensus pattern (60 bp):
AACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATATTAGGAGAACTATTTTGT
Found at i:25135 original size:59 final size:60
Alignment explanation
Indices: 25004--25135 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 60
24994 TTGAGGGGTC
* * *
25004 ATTTTAAAACTTTTAATAATCAAGGGAATCAACAAAGCAATATCCTATATTCGGAGAACT
1 ATTTTATAACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATATTAGGAGAACT
* * * * * *
25064 ATTTTGTAACTTTTAATAGT-AAAGGACTCAATAAAGTAATATCCTATAGTTAGGTG-ACT
1 ATTTTATAACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATA-TTAGGAGAACT
25123 A-TTTATATACTTT
1 ATTTTATA-ACTTT
25136 ACTCTATTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
58 5 0.08
59 33 0.55
60 22 0.37
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAATCAAAGGAATCAACAAAGCAATATCCTATATTAGGAGAACT
Found at i:26184 original size:32 final size:32
Alignment explanation
Indices: 26143--26206 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
26133 CTCGAGTGGG
26143 TTGAGATTACCCTGACTGTGTTTTCGATTACC
1 TTGAGATTACCCTGACTGTGTTTTCGATTACC
**
26175 TTGAGATTACCCTGGTTGTGTTTTCGATTACC
1 TTGAGATTACCCTGACTGTGTTTTCGATTACC
26207 GAAGGACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (32 bp):
TTGAGATTACCCTGACTGTGTTTTCGATTACC
Found at i:31479 original size:22 final size:22
Alignment explanation
Indices: 31454--31534 Score: 135
Period size: 22 Copynumber: 3.7 Consensus size: 22
31444 ATATGAAATT
*
31454 TGTCCCGAAAGACCATTGTATA
1 TGTCCCGAAGGACCATTGTATA
31476 TGTCCCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCATTGTATA
*
31498 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCATTGTATA
*
31520 TGTCCCGAATGACCA
1 TGTCCCGAAGGACCA
31535 CTATATATCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (22 bp):
TGTCCCGAAGGACCATTGTATA
Found at i:31545 original size:20 final size:21
Alignment explanation
Indices: 31454--31545 Score: 105
Period size: 22 Copynumber: 4.3 Consensus size: 21
31444 ATATGAAATT
* *
31454 TGTCCCGAAAGACCATTGTATA
1 TGTCCCGAAGGACCA-CGTATA
*
31476 TGTCCCGAAGGACCATTGTATA
1 TGTCCCGAAGGACCA-CGTATA
31498 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC-GTATA
*
31520 TGTCCCGAATGACCAC-TATA
1 TGTCCCGAAGGACCACGTATA
*
31540 TATCCC
1 TGTCCC
31546 TCGACTCTTG
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.14
22 56 0.86
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (21 bp):
TGTCCCGAAGGACCACGTATA
Found at i:32304 original size:20 final size:20
Alignment explanation
Indices: 32242--32292 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
32232 TTCCCTTTGA
32242 AGTGCATCGGTGCACTCTTT
1 AGTGCATCGGTGCACTCTTT
32262 AGTGCATCGGTGCACTCTTT
1 AGTGCATCGGTGCACTCTTT
32282 AGTGCATCGGT
1 AGTGCATCGGT
32293 ACATTCCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
AGTGCATCGGTGCACTCTTT
Found at i:41292 original size:58 final size:59
Alignment explanation
Indices: 41222--41369 Score: 237
Period size: 58 Copynumber: 2.5 Consensus size: 59
41212 TAATGCTTTA
*
41222 TTGAG-TCTCGACTATTAAAAATTATAAAATAATCCCTCAACTATATGAAGTTGTTTTG
1 TTGAGTTCTCGACTATTAAAAATTATAAAATAATCCCTCAACTATATGAAGTTATTTTG
*
41280 TTGAGTTC-CGACTATTAAAAATTATAAAATAATCTCTCAACTATATGAAGTTATTTTG
1 TTGAGTTCTCGACTATTAAAAATTATAAAATAATCCCTCAACTATATGAAGTTATTTTG
* *
41338 TTGAGTTTCTCGACTATTAAAAGTTAAAAAAT
1 TTGAG-TTCTCGACTATTAAAAATTATAAAAT
41370 GGTCATTCGG
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
58 58 0.70
59 5 0.06
60 20 0.24
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (59 bp):
TTGAGTTCTCGACTATTAAAAATTATAAAATAATCCCTCAACTATATGAAGTTATTTTG
Found at i:42108 original size:12 final size:12
Alignment explanation
Indices: 42091--42116 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42081 TGAAATGCCT
42091 TCTGGCCTATTC
1 TCTGGCCTATTC
42103 TCTGGCCTATTC
1 TCTGGCCTATTC
42115 TC
1 TC
42117 AAATGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.15, T:0.42
Consensus pattern (12 bp):
TCTGGCCTATTC
Found at i:47693 original size:696 final size:696
Alignment explanation
Indices: 46620--48088 Score: 2832
Period size: 696 Copynumber: 2.1 Consensus size: 696
46610 TTGACTGATG
* * *
46620 TAATACCATA-CCCAAGTCAAAAACCCTACCCTATCACTATCATCATCTCACCTAAACCACTACA
1 TAATATCATACCCCAAGTCAAAAACACTATCCTATCACTATCATCATCTCACCTAAACCACTACA
46684 CCATTAAAAAAACCACCTAATTAACTAATCCACATAAACATATCCCTTTACAATAAATCAACAAA
66 CCATTAAAAAAACCACCTAATTAACTAATCCACATAAACATATCCCTTTACAATAAATCAACAAA
*
46749 ATCTTTCACTTTTTTAATTAAAATTTTCAGTGCATATATGCATCACCGAAAAAACACCTAACATT
131 ATCTTTCACTTTTTTAATTAAAATTTTCAGTGCATAAATGCATCACCGAAAAAACACCTAACATT
46814 GTTGAATTTCCAACAATTGTTGACCACCAAAAATTAATTTTTAACCATCGCCCACTTGAAGATTT
196 GTTGAATTTCCAACAATTGTTGACCACCAAAAATTAATTTTTAACCATCGCCCACTTGAAGATTT
46879 GATTGGTGACTAACAATTGTTGAAAATTCAACAAGGTTAGGTGTTTTTTCGATAGTGCATTTATA
261 GATTGGTGACTAACAATTGTTGAAAATTCAACAAGGTTAGGTGTTTTTTCGATAGTGCATTTATA
46944 CACAGAAGATTTTAGTCAAAAAAGAGAAAGAATTTATTGATTTATTGTAAAGGGATAGATTTAGG
326 CACAGAAGATTTTAGTCAAAAAAGAGAAAGAATTTATTGATTTATTGTAAAGGGATAGATTTAGG
*
47009 TGGATTAGGTGGGTTTTTTTTAATGTTATAGTGGTTTAGGTGAGATGATGATAGTGGTAGAGTAG
391 TGGATTAGGTGGGTTTTTTTTAATATTATAGTGGTTTAGGTGAGATGATGATAGTGGTAGAGTAG
47074 AGTTTTTGACTTCGGTATAGTATTACAGTAGTTAAATCCCTCAGCCCACTGAAGATCTGACCTGG
456 AGTTTTTGACTTCGGTATAGTATTACAGTAGTTAAATCCCTCAGCCCACTGAAGATCTGACCTGG
47139 CTCGATATCCGACTCGGAGTTGACCCGAACCGATCGTTTCCCCAGTCGCACACCGTTGTCGTCGT
521 CTCGATATCCGACTCGGAGTTGACCCGAACCGATCGTTTCCCCAGTCGCACACCGTTGTCGTCGT
*
47204 CACCAAGACCTGCGAACAGTGCACTCAAGTTGTCATAAACAGTAAACAAACCTCCTAAATTCAAA
586 CACCAAAACCTGCGAACAGTGCACTCAAGTTGTCATAAACAGTAAACAAACCTCCTAAATTCAAA
47269 CAGTTATTTTAAAATATCTCAAAATCTCGAAAAATCGGGATTTACC
651 CAGTTATTTTAAAATATCTCAAAATCTCGAAAAATCGGGATTTACC
47315 TAATATCATACCCCAAGTCAAAAACACTATCCTATCACTATCATCATCTCACCTAAACCACTACA
1 TAATATCATACCCCAAGTCAAAAACACTATCCTATCACTATCATCATCTCACCTAAACCACTACA
47380 CCATTAAAAAAACCACCTAATTAACTAATCCACATAAACATATCCCTTTACAATAAATCAACAAA
66 CCATTAAAAAAACCACCTAATTAACTAATCCACATAAACATATCCCTTTACAATAAATCAACAAA
47445 ATCTTTCACTTTTTTAATTAAAATTTTCAGTGCATAAATGCATCACCGAAAAAACACCTAACATT
131 ATCTTTCACTTTTTTAATTAAAATTTTCAGTGCATAAATGCATCACCGAAAAAACACCTAACATT
47510 GTTGAATTTCCAACAATTGTTGACCACCAAAAATTAATTTTTAACCATCGCCCACTTGAAGATTT
196 GTTGAATTTCCAACAATTGTTGACCACCAAAAATTAATTTTTAACCATCGCCCACTTGAAGATTT
47575 GATTGGTGACTAACAATTGTTGAAAATTCAACAAGGTTAGGTGTTTTTTCGATAGTGCATTTATA
261 GATTGGTGACTAACAATTGTTGAAAATTCAACAAGGTTAGGTGTTTTTTCGATAGTGCATTTATA
47640 CACAGAAGATTTTAGTCAAAAAAGAGAAAGAATTTATTGATTTATTGTAAAGGGATAGATTTAGG
326 CACAGAAGATTTTAGTCAAAAAAGAGAAAGAATTTATTGATTTATTGTAAAGGGATAGATTTAGG
47705 TGGATTAGGTGGGTTTTTTTTAATATTATAGTGGTTTAGGTGAGATGATGATAGTGGTAGAGTAG
391 TGGATTAGGTGGGTTTTTTTTAATATTATAGTGGTTTAGGTGAGATGATGATAGTGGTAGAGTAG
47770 AGTTTTTGACTTCGGTATAGTATTACAGTAGTTAAATCCCTCAGCCCACTGAAGATCTGACCTGG
456 AGTTTTTGACTTCGGTATAGTATTACAGTAGTTAAATCCCTCAGCCCACTGAAGATCTGACCTGG
47835 CTCGATATCCGACTCGGAGTTGACCCGAACCGATCGTTTCCCCAGTCGCACACCGTTGTCGTCGT
521 CTCGATATCCGACTCGGAGTTGACCCGAACCGATCGTTTCCCCAGTCGCACACCGTTGTCGTCGT
47900 CACCAAAACCTGCGAACAGTGCACTCAAGTTGTCATAAACAGTAAACAAACCTCCTAAATTCAAA
586 CACCAAAACCTGCGAACAGTGCACTCAAGTTGTCATAAACAGTAAACAAACCTCCTAAATTCAAA
*
47965 CAGTTATTTTAAATTATCTCAAAATCTCGAAAAATCGGGATTTACC
651 CAGTTATTTTAAAATATCTCAAAATCTCGAAAAATCGGGATTTACC
* * * *
48011 TAATATCATACCCTAAGTCAAAAACACTATCATATCACTATGATCATCTCACATAAACCACTACA
1 TAATATCATACCCCAAGTCAAAAACACTATCCTATCACTATCATCATCTCACCTAAACCACTACA
48076 CCATTAAAAAAAC
66 CCATTAAAAAAAC
48089 AAACTTACCT
Statistics
Matches: 762, Mismatches: 11, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
695 9 0.01
696 753 0.99
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.30
Consensus pattern (696 bp):
TAATATCATACCCCAAGTCAAAAACACTATCCTATCACTATCATCATCTCACCTAAACCACTACA
CCATTAAAAAAACCACCTAATTAACTAATCCACATAAACATATCCCTTTACAATAAATCAACAAA
ATCTTTCACTTTTTTAATTAAAATTTTCAGTGCATAAATGCATCACCGAAAAAACACCTAACATT
GTTGAATTTCCAACAATTGTTGACCACCAAAAATTAATTTTTAACCATCGCCCACTTGAAGATTT
GATTGGTGACTAACAATTGTTGAAAATTCAACAAGGTTAGGTGTTTTTTCGATAGTGCATTTATA
CACAGAAGATTTTAGTCAAAAAAGAGAAAGAATTTATTGATTTATTGTAAAGGGATAGATTTAGG
TGGATTAGGTGGGTTTTTTTTAATATTATAGTGGTTTAGGTGAGATGATGATAGTGGTAGAGTAG
AGTTTTTGACTTCGGTATAGTATTACAGTAGTTAAATCCCTCAGCCCACTGAAGATCTGACCTGG
CTCGATATCCGACTCGGAGTTGACCCGAACCGATCGTTTCCCCAGTCGCACACCGTTGTCGTCGT
CACCAAAACCTGCGAACAGTGCACTCAAGTTGTCATAAACAGTAAACAAACCTCCTAAATTCAAA
CAGTTATTTTAAAATATCTCAAAATCTCGAAAAATCGGGATTTACC
Found at i:54547 original size:16 final size:16
Alignment explanation
Indices: 54522--54559 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
54512 CCGCGAACAT
*
54522 TAAATGAATATATTTA
1 TAAATAAATATATTTA
54538 TAAATAAATATATTTA
1 TAAATAAATATATTTA
54554 TAAATA
1 TAAATA
54560 TATCTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAATAAATATATTTA
Found at i:54938 original size:21 final size:21
Alignment explanation
Indices: 54905--54949 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
54895 GTTTTGAAAA
* *
54905 AAAATTAAAAGTTTTGGTACT
1 AAAACTAAAAGTTTAGGTACT
*
54926 AAAACTAATAGTTTAGGTACT
1 AAAACTAAAAGTTTAGGTACT
54947 AAA
1 AAA
54950 TATGTAGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (21 bp):
AAAACTAAAAGTTTAGGTACT
Found at i:56674 original size:25 final size:25
Alignment explanation
Indices: 56623--56674 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56613 AAAATAAACT
*
56623 TAAAAATAATTAAAATAACAAATAA
1 TAAAAATAATTAAAACAACAAATAA
*
56648 TAAAAATAGTTAAAACAACCAAA-AA
1 TAAAAATAATTAAAACAA-CAAATAA
56673 TA
1 TA
56675 TATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (25 bp):
TAAAAATAATTAAAACAACAAATAA
Found at i:56830 original size:22 final size:21
Alignment explanation
Indices: 56793--56843 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 21
56783 AACAATGATC
56793 AAATT-AAAATAACAGTAACT
1 AAATTAAAAATAACAGTAACT
*
56813 AAATTAAAAACTAACAGTGACT
1 AAATTAAAAA-TAACAGTAACT
56835 AAATTAAAA
1 AAATTAAAA
56844 CAAAACCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 19 0.68
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.24
Consensus pattern (21 bp):
AAATTAAAAATAACAGTAACT
Found at i:61163 original size:43 final size:43
Alignment explanation
Indices: 61102--61199 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
61092 ATACGCGTAA
61102 ATAATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
1 ATAATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
61145 ATAATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
1 ATAATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
*
61188 ATAATTTTTGGG
1 ATAATTTCTGGG
61200 CGATTGATTA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.41
Consensus pattern (43 bp):
ATAATTTCTGGGTCTTACTCCTTCCTCTTAAGGATGCTAAGTC
Found at i:62523 original size:75 final size:75
Alignment explanation
Indices: 62400--62550 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
62390 ATAGCTGATT
*
62400 CTCGAATGCATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
1 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
62465 CATACGCGAA
66 CATACGCGAA
62475 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
1 CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
62540 CATACGCGAA
66 CATACGCGAA
62550 C
1 C
62551 CCCAACTCGT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (75 bp):
CTCGAATACATTCAACTTTAATCTAATGTCTTTATTAATGATGTCATCACGACATAGGATCTCTT
CATACGCGAA
Found at i:63479 original size:64 final size:64
Alignment explanation
Indices: 63411--63567 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
63401 TTGAAGGTGT
** * *
63411 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGT
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATACATATTA-T
63473 GC
63 GC
* * *
63475 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATACATTTTATGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACATATTATGC
* *
63539 ACCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAGGTAGTGCATCGATGCAT
63568 ACCTTCATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.82
65 11 0.14
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATACATATTATGC
Found at i:63985 original size:29 final size:29
Alignment explanation
Indices: 63946--64026 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
63936 TATGTGATAT
63946 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
63976 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
64005 GAGAAATGGCATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
64027 ACATATAAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Done.