Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001574.1 Hibiscus syriacus cultivar Beakdansim tig00003126_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: 1705968
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 5 of 7
Found at i:969056 original size:200 final size:201
Alignment explanation
Indices: 968697--969066 Score: 598
Period size: 200 Copynumber: 1.8 Consensus size: 201
968687 CTTTCATCTG
* *
968697 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGTCTCAAAGGCACTTAGCCTTTCATATAA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGACACTTAGCCTTTCATATAA
* *
968762 CTGGCATAATTGACACCTTTCTGTAAATGGACAGTTAGGCCTCAAAGTCACTTAACCTTTCATCT
66 CTGGCATAATTGACACCTTTCTGTAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCT
* * *
968827 AACTGGCATAATTGTCACCTTTGTGTCAATGCACAGTTAGTCCTCAAAGTCGCTTAGCCTTTCAT
131 AACTAGCATAATTGACACCTTTCTGTCAATGCACAGTTAGTCCTCAAAGTCGCTTAGCCTTTCAT
968892 CTAATT
196 CTAATT
** *
968898 GCATAATTGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGACACTTAGCCTTTCATCTAA
1 GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGACACTTAGCCTTTCATATAA
* * * *
968962 CTGGCATAATTGATACCTTTCTTTCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCT
66 CTGGCATAATTGACACCTTTCTGTAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCT
*
969027 AACTAGCATAATTGACATCTTTCTGTCAATGCACAGTTAG
131 AACTAGCATAATTGACACCTTTCTGTCAATGCACAGTTAG
969067 GCCTTTAATC
Statistics
Matches: 154, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
200 132 0.86
201 22 0.14
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (201 bp):
GCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCTCAAAGACACTTAGCCTTTCATATAA
CTGGCATAATTGACACCTTTCTGTAAATGCACAGTTAGGCCTCAAAGGCACTTAACCTTTCATCT
AACTAGCATAATTGACACCTTTCTGTCAATGCACAGTTAGTCCTCAAAGTCGCTTAGCCTTTCAT
CTAATT
Found at i:969436 original size:57 final size:57
Alignment explanation
Indices: 969245--969436 Score: 262
Period size: 57 Copynumber: 3.4 Consensus size: 57
969235 AAATTCATAT
* * * * *
969245 AATTTCTTA-GTTTTTGCACATAAATTTCTTATATGGAAATTCATAAACAAATTATG
1 AATTTCTTATCTTTTTGCACACAAAGTGCTCATATGGAAATTCATAAACAAATTATG
* * ** * *
969301 AATTCCTTAACTTTTTGCACACTCAGAGC-CTATAAGGAAATTCATAAACAAATTATG
1 AATTTCTTATCTTTTTGCACACAAAGTGCTC-ATATGGAAATTCATAAACAAATTATG
969358 AATTTCTTATCTTTTTGCACACAAAGTGCTCATATGGAAATTCATAAACAAATTATG
1 AATTTCTTATCTTTTTGCACACAAAGTGCTCATATGGAAATTCATAAACAAATTATG
969415 AATTTCTTATCTTTTTGCACAC
1 AATTTCTTATCTTTTTGCACAC
969437 TCAGTGTCAT
Statistics
Matches: 117, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
56 8 0.07
57 108 0.92
58 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (57 bp):
AATTTCTTATCTTTTTGCACACAAAGTGCTCATATGGAAATTCATAAACAAATTATG
Found at i:974995 original size:19 final size:18
Alignment explanation
Indices: 974969--975013 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
974959 AATTTAGTTT
*
974969 TTATATTAATTCCAATTC
1 TTATATTAATTACAATTC
* *
974987 TTAATATTATTTATAATTC
1 TT-ATATTAATTACAATTC
975006 TTATATTA
1 TTATATTA
975014 TAAATTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATATTAATTACAATTC
Found at i:975009 original size:13 final size:12
Alignment explanation
Indices: 974988--975030 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
974978 TTCCAATTCT
*
974988 TAATATTATTTA
1 TAATTTTATTTA
975000 TAATTCTTATATTA
1 TAATT-TTAT-TTA
975014 TAAATTTTATTTA
1 T-AATTTTATTTA
975027 TAAT
1 TAAT
975031 CACTAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 7 0.26
13 8 0.30
14 8 0.30
15 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TAATTTTATTTA
Found at i:975751 original size:20 final size:20
Alignment explanation
Indices: 975726--975763 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
975716 AACCCTTACA
**
975726 AATATCAAGTAGAAGCAAGT
1 AATATCAAACAGAAGCAAGT
975746 AATATCAAACAGAAGCAA
1 AATATCAAACAGAAGCAA
975764 ACAATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.13, G:0.16, T:0.16
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAGT
Found at i:975769 original size:20 final size:20
Alignment explanation
Indices: 975726--975776 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
975716 AACCCTTACA
** **
975726 AATATCAAGTAGAAGCAAGT
1 AATATCAAACAGAAGCAAAC
975746 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
*
975766 AATATAAAACA
1 AATATCAAACA
975777 AAATCAAGCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.16
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:977374 original size:2 final size:2
Alignment explanation
Indices: 977367--977403 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
977357 TTTATACCAG
977367 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
977404 CAAGAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:977928 original size:101 final size:104
Alignment explanation
Indices: 977808--978043 Score: 290
Period size: 101 Copynumber: 2.3 Consensus size: 104
977798 TGGGTGTTTG
*
977808 TAAGGGTTTAGGGAAGAACACGAATGAACAATG-GATGAACTT-TTGGGTGTTTGATCGAAAAA-
1 TAAGGGTTTAGGGAAGAACACGAATGAACAACGAGATGAA-TTATTGGGTGTTTGATCGAAAAAG
* * *
977870 A-A-GGAATGGGTTTAGGTTTTGGTGTTTGTGAAGATCAAA
65 ACACGAAAT-GGTATAGGTTTTGGTGTTTCTGAAGATCAAA
*
977909 TAATGGTTTAGGGAAGAACACGGAA-GAAC-ACGAGATGAATTATTGGGTGTTTGATCGAAAAAG
1 TAAGGGTTTAGGGAAGAACAC-GAATGAACAACGAGATGAATTATTGGGTGTTTGATCGAAAAAG
*
977972 ACACGAAATGGTATGGGTTTTGGTGTTTCTGAAGATCAAA
65 ACACGAAATGGTATAGGTTTTGGTGTTTCTGAAGATCAAA
* * *
978012 TGAGGGTTTTTGGGATGAACAC-AGATGAACAA
1 TAAGGG-TTTAGGGAAGAACACGA-ATGAACAA
978044 ATTATGAACA
Statistics
Matches: 115, Mismatches: 10, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
100 4 0.03
101 50 0.43
102 5 0.04
103 34 0.30
104 21 0.18
105 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.30, T:0.28
Consensus pattern (104 bp):
TAAGGGTTTAGGGAAGAACACGAATGAACAACGAGATGAATTATTGGGTGTTTGATCGAAAAAGA
CACGAAATGGTATAGGTTTTGGTGTTTCTGAAGATCAAA
Found at i:978145 original size:18 final size:18
Alignment explanation
Indices: 978082--978137 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
978072 GAAGGCAGAG
*
978082 GATTTTGAGAGAATCGAA
1 GATTTTGAGAGAATCGGA
978100 GATTTTGAGAGAATCGGA
1 GATTTTGAGAGAATCGGA
978118 GATTTTGAGAGAATCGGA
1 GATTTTGAGAGAATCGGA
978136 GA
1 GA
978138 GTTAGAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.36, C:0.05, G:0.32, T:0.27
Consensus pattern (18 bp):
GATTTTGAGAGAATCGGA
Found at i:978393 original size:61 final size:61
Alignment explanation
Indices: 978285--978422 Score: 204
Period size: 61 Copynumber: 2.3 Consensus size: 61
978275 TGTCTCCTAG
* *
978285 TTTTAAATTTGTTCAATTTAGTGCAAATTTAATGATGCAATACATTAATTTAAGCTTAATA
1 TTTTAAATTTGTTCAATTTAGTCCAAATTTAATGATACAATACATTAATTTAAGCTTAATA
* * ** *
978346 TTTTAAATTTCTTCAATTTAGTCCAAATTTAATGTTACAATTTATTAATTTAAGCTTCATA
1 TTTTAAATTTGTTCAATTTAGTCCAAATTTAATGATACAATACATTAATTTAAGCTTAATA
*
978407 TTTAAAATTTGTTCAA
1 TTTTAAATTTGTTCAA
978423 CTTGGTCCTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 68 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.47
Consensus pattern (61 bp):
TTTTAAATTTGTTCAATTTAGTCCAAATTTAATGATACAATACATTAATTTAAGCTTAATA
Found at i:978517 original size:17 final size:17
Alignment explanation
Indices: 978495--978552 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
978485 ATATATAGAT
978495 TATATATACTAATGAAC
1 TATATATACTAATGAAC
**
978512 TATATA-A-TATAT-AGTT
1 TATATATACTA-ATGA-AC
978528 TATATATACTAATGAAC
1 TATATATACTAATGAAC
978545 TATATATA
1 TATATATA
978553 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAC
Found at i:978520 original size:33 final size:33
Alignment explanation
Indices: 978483--978672 Score: 158
Period size: 33 Copynumber: 5.6 Consensus size: 33
978473 ATTAATAAAT
*
978483 TAATATATAGATTATATATACTAATGAACTATA
1 TAATATATAGTTTATATATACTAATGAACTATA
978516 TAATATATAGTTTATATATACTAATGAACTATATA
1 TAATATATAGTTTATATATACTAATGAAC--TATA
* * * *
978551 TAATGTATAGTTTATATATAC-CAT-ATAGTTTA
1 TAATATATAGTTTATATATACTAATGA-ACTATA
* * *
978583 T-ATATACTA-ATGA-ACTATA-TAATGTATAGTTTATA
1 TAATATA-TAGTTTATA-TATACTAATG-A-A--CTATA
*
978618 TATACCATATAGTTTATATATACTAATGAACTATA
1 TA-A-TATATAGTTTATATATACTAATGAACTATA
978653 TAATATATAGTTTATATATA
1 TAATATATAGTTTATATATA
978673 TTATATAGTT
Statistics
Matches: 125, Mismatches: 16, Indels: 32
0.72 0.09 0.18
Matches are distributed among these distances:
30 1 0.01
31 12 0.10
32 6 0.05
33 48 0.38
34 4 0.03
35 34 0.27
37 4 0.03
38 10 0.08
39 6 0.05
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (33 bp):
TAATATATAGTTTATATATACTAATGAACTATA
Found at i:978535 original size:18 final size:18
Alignment explanation
Indices: 978512--978740 Score: 155
Period size: 18 Copynumber: 13.3 Consensus size: 18
978502 ACTAATGAAC
978512 TATATAATATATAGTTTA
1 TATATAATATATAGTTTA
* **
978530 TATATACTA-AT-GAACTA
1 TATATAATATATAG-TTTA
*
978547 TATATAATGTATAGTTTA
1 TATATAATATATAGTTTA
**
978565 TATATACCATATAGTTTA
1 TATATAATATATAGTTTA
* *
978583 TATATACTA-AT-G--AA
1 TATATAATATATAGTTTA
*
978597 CTATATAATGTATAGTTTA
1 -TATATAATATATAGTTTA
**
978616 TATATACCATATAGTTTA
1 TATATAATATATAGTTTA
* *
978634 TATATACTA-AT-G--AA
1 TATATAATATATAGTTTA
978648 CTATATAATATATAGTTTA
1 -TATATAATATATAGTTTA
*
978667 TATATATTATATAGTTTA
1 TATATAATATATAGTTTA
*
978685 TATATACT-TATA----A
1 TATATAATATATAGTTTA
*
978698 CTATATAATATATAGTTTG
1 -TATATAATATATAGTTTA
* *
978717 TATATAACATATACTTTA
1 TATATAATATATAGTTTA
978735 TATATA
1 TATATA
978741 TAGTTTTTAT
Statistics
Matches: 163, Mismatches: 29, Indels: 38
0.71 0.13 0.17
Matches are distributed among these distances:
13 1 0.01
14 9 0.06
15 19 0.12
16 7 0.04
17 21 0.13
18 103 0.63
19 3 0.02
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (18 bp):
TATATAATATATAGTTTA
Found at i:978602 original size:51 final size:51
Alignment explanation
Indices: 978520--978740 Score: 345
Period size: 51 Copynumber: 4.3 Consensus size: 51
978510 ACTATATAAT
*
978520 ATATAGTTTATATATACTAATGAACTATATATAATGTATAGTTTATATATACC
1 ATATAGTTTATATATACTAATGAAC--TATATAATATATAGTTTATATATACC
*
978573 ATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTATATATACC
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
**
978624 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATATT
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
* * *
978675 ATATAGTTTATATATACTTAT-AACTATATAATATATAGTTTGTATATAAC
1 ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
*
978725 ATATACTTTATATATA
1 ATATAGTTTATATATA
978741 TAGTTTTTAT
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
50 41 0.26
51 94 0.59
53 25 0.16
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (51 bp):
ATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACC
Found at i:978668 original size:9 final size:9
Alignment explanation
Indices: 978656--978688 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
978646 AACTATATAA
978656 TATATAGTT
1 TATATAGTT
978665 TATATA-TAT
1 TATATAGT-T
978674 TATATAGTT
1 TATATAGTT
978683 TATATA
1 TATATA
978689 TACTTATAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 1 0.05
9 20 0.91
10 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (9 bp):
TATATAGTT
Found at i:978673 original size:86 final size:83
Alignment explanation
Indices: 978483--978672 Score: 226
Period size: 86 Copynumber: 2.2 Consensus size: 83
978473 ATTAATAAAT
*
978483 TAATATATAGATTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAACTAT
1 TAATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAACTAT
*
978548 ATATAATGTATAGTTTATA
66 ATATAATGTATAG-CTATA
* * *
978567 TATACCATATAGTTTATATATACTAATGAACTATATAATGTATAGTTTATATATACCATATAGTT
1 TA-A-TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATA-C-TA-A-TG
*
978632 TA-TATATACTAATG-A-A-CTATA
60 AACTATATA-TAATGTATAGCTATA
978653 TAATATATAGTTTATATATA
1 TAATATATAGTTTATATATA
978673 TTATATAGTT
Statistics
Matches: 92, Mismatches: 7, Indels: 14
0.81 0.06 0.12
Matches are distributed among these distances:
84 18 0.20
85 2 0.02
86 53 0.58
87 1 0.01
88 3 0.03
89 8 0.09
90 7 0.08
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (83 bp):
TAATATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATACTAATGAACTAT
ATATAATGTATAGCTATA
Found at i:978710 original size:32 final size:32
Alignment explanation
Indices: 978573--978746 Score: 115
Period size: 33 Copynumber: 5.3 Consensus size: 32
978563 TATATATACC
978573 ATATAGTTTATATAT-AC-TAATGAACTATATAAT
1 ATATAGTTTATATATAACAT-AT--ACTATATAAT
* * * *
978606 GTATAGTTTATATATACCATATAGTTTAT-AT
1 ATATAGTTTATATATAACATATACTATATAAT
* ** * *
978637 ATACTAATGAACTATATAATATATAGTTTATATATATT
1 ATA-TAGTTTA-TATATAACATATA--CTATATA-A-T
*
978675 ATATAGTTTATATAT-ACTTATAACTATATAAT
1 ATATAGTTTATATATAACATAT-ACTATATAAT
* *
978707 ATATAGTTTGTATATAACATATACTTTAT-AT
1 ATATAGTTTATATATAACATATACTATATAAT
978738 ATATAGTTT
1 ATATAGTTT
978747 TTATTTATAG
Statistics
Matches: 109, Mismatches: 21, Indels: 24
0.71 0.14 0.16
Matches are distributed among these distances:
31 15 0.14
32 30 0.28
33 31 0.28
34 9 0.08
35 9 0.08
36 6 0.06
37 5 0.05
38 4 0.04
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (32 bp):
ATATAGTTTATATATAACATATACTATATAAT
Found at i:978807 original size:18 final size:17
Alignment explanation
Indices: 978512--978811 Score: 79
Period size: 18 Copynumber: 17.8 Consensus size: 17
978502 ACTAATGAAC
*
978512 TATATAA-TATATAGTT
1 TATATAACTATATAGTA
*
978528 TATATATACTA-ATGAACTA
1 TATATA-ACTATAT--AGTA
* *
978547 TATATAA-TGTATAGTT
1 TATATAACTATATAGTA
* *
978563 TATATATACCATATAGTT
1 TATATA-ACTATATAGTA
*
978581 TATATATACTA-AT-GAA
1 TATATA-ACTATATAGTA
* *
978597 CTATATAA-TGTATAGTT
1 -TATATAACTATATAGTA
* *
978614 TATATATACCATATAGTT
1 TATATA-ACTATATAGTA
*
978632 TATATATACTA-AT-GAA
1 TATATA-ACTATATAGTA
*
978648 CTATATAA-TATATAGTT
1 -TATATAACTATATAGTA
* *
978665 TATATATATTATATAGTT
1 TATATA-ACTATATAGTA
978683 TATATATACT-TATA--A
1 TATATA-ACTATATAGTA
*
978698 CTATATAA-TATATAGTTTG
1 -TATATAACTATATAG--TA
*
978717 TATATAAC-ATATACT-
1 TATATAACTATATAGTA
978732 T-TAT-A-TATATAGT-
1 TATATAACTATATAGTA
* *
978745 T-T-TTA-TTTATAGTTAA
1 TATATAACTATATAG-T-A
*
978761 TATGTAAACTATATAGTA
1 TATAT-AACTATATAGTA
978779 TATATAAACTATATATGTA
1 TATAT-AACTATATA-GTA
978798 GTATAT-ACTATATA
1 -TATATAACTATATA
978812 AATCGTTTAT
Statistics
Matches: 220, Mismatches: 29, Indels: 68
0.69 0.09 0.21
Matches are distributed among these distances:
12 1 0.00
13 16 0.07
14 5 0.02
15 9 0.04
16 42 0.19
17 30 0.14
18 93 0.42
19 13 0.06
20 11 0.05
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (17 bp):
TATATAACTATATAGTA
Found at i:978890 original size:15 final size:15
Alignment explanation
Indices: 978875--978909 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
978865 TACTTTGAAT
978875 TTATAT-AGTATAAA
1 TTATATAAGTATAAA
978889 TTATATAAGTATAAA
1 TTATATAAGTATAAA
978904 TTATAT
1 TTATAT
978910 TATATAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (15 bp):
TTATATAAGTATAAA
Found at i:978908 original size:27 final size:27
Alignment explanation
Indices: 978878--978949 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 27
978868 TTTGAATTTA
* * *
978878 TATAGTATAAATTATATAAGTATAAAT
1 TATAGTATAAAGTATATAAATATAAAC
* * *
978905 TATATTATATAGTATATAAATATCAAC
1 TATAGTATAAAGTATATAAATATAAAC
* *
978932 TATAGTATATAGTTTATA
1 TATAGTATAAAGTATATA
978950 TGGTTTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (27 bp):
TATAGTATAAAGTATATAAATATAAAC
Found at i:978996 original size:2 final size:2
Alignment explanation
Indices: 978979--979078 Score: 53
Period size: 2 Copynumber: 48.0 Consensus size: 2
978969 ATATGTAAAT
* **
978979 TA TA CTA TA TA T- TA TA TA TA GTT TA CG TA TA TA -A TA TA TA GTA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
* *
979022 TA TA AA TA TA AA CTA TA GTA TA TA TA TA TA GTA TA TA CTA TA TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA TA TA -TA TA TA
* *
979066 GA TA -A TT TA TA TA
1 TA TA TA TA TA TA TA
979079 GTTCACTAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 20
0.69 0.13 0.19
Matches are distributed among these distances:
1 3 0.04
2 59 0.80
3 12 0.16
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:979016 original size:7 final size:7
Alignment explanation
Indices: 979006--979065 Score: 54
Period size: 7 Copynumber: 8.9 Consensus size: 7
978996 ATAGTTTACG
979006 TATATAA
1 TATATAA
*
979013 TATATAG
1 TATATAA
979020 TATATAA
1 TATATAA
979027 -ATATAA
1 TATATAA
*
979033 -ACTATAG
1 TA-TATAA
979040 TATAT-A
1 TATATAA
*
979046 TATATAG
1 TATATAA
*
979053 TATATAC
1 TATATAA
979060 TATATA
1 TATATA
979066 GATAATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 12 0.27
7 31 0.70
8 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (7 bp):
TATATAA
Found at i:979030 original size:20 final size:20
Alignment explanation
Indices: 979007--979065 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
978997 TAGTTTACGT
979007 ATATAATATATAGTATATAA
1 ATATAATATATAGTATATAA
*
979027 ATATAA-ACTATAGTATATAT
1 ATATAATA-TATAGTATATAA
* *
979047 ATATAGTATATACTATATA
1 ATATAATATATAGTATATA
979066 GATAATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
ATATAATATATAGTATATAA
Found at i:979065 original size:27 final size:27
Alignment explanation
Indices: 978979--979080 Score: 85
Period size: 29 Copynumber: 4.0 Consensus size: 27
978969 ATATGTAAAT
* *
978979 TATACTATATATTATATATAGTTTACGTA
1 TATACTATATAGTATATATA-TATA-GTA
*
979008 TATAATATATAGTATATA-A-ATA-TA
1 TATACTATATAGTATATATATATAGTA
979032 -A-AC--TATAGTATATATATATAGTA
1 TATACTATATAGTATATATATATAGTA
*
979055 TATACTATATAG-ATAATTTATATAGT
1 TATACTATATAGTAT-ATATATATAGT
979081 TCACTAATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
20 11 0.18
21 1 0.02
22 4 0.07
23 3 0.05
24 3 0.05
25 2 0.03
26 4 0.07
27 15 0.25
28 1 0.02
29 16 0.27
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (27 bp):
TATACTATATAGTATATATATATAGTA
Found at i:979113 original size:22 final size:21
Alignment explanation
Indices: 979074--979174 Score: 81
Period size: 18 Copynumber: 4.9 Consensus size: 21
979064 TAGATAATTT
*
979074 ATATAGTTCACTA-ATAAACAA
1 ATATAGTTCA-TATGTAAACAA
979095 TATATAGTTCATATGTAAAC--
1 -ATATAGTTCATATGTAAACAA
979115 -TATAGTTCATATGT--A-AA
1 ATATAGTTCATATGTAAACAA
979132 ATATAGTTCATATGTAAATATCAA
1 ATATAGTTCATATGT-AA-A-CAA
* *
979156 CTATAGTTTATATGTAAAC
1 ATATAGTTCATATGTAAAC
979175 TATACTTCAT
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
16 1 0.02
18 28 0.42
21 3 0.05
22 17 0.26
23 2 0.03
24 15 0.23
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.38
Consensus pattern (21 bp):
ATATAGTTCATATGTAAACAA
Found at i:979120 original size:18 final size:18
Alignment explanation
Indices: 979097--979196 Score: 101
Period size: 18 Copynumber: 5.2 Consensus size: 18
979087 ATAAACAATA
979097 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
979115 TATAGTTCATATGTAAAA
1 TATAGTTCATATGTAAAC
979133 TATAGTTCATATGTAAATATCAAC
1 TATAGTTCATATG----TA--AAC
*
979157 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
* * *
979175 TATACTTCATATATCAAC
1 TATAGTTCATATGTAAAC
979193 TATA
1 TATA
979197 TAATTTATAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
18 51 0.74
20 2 0.03
22 2 0.03
24 14 0.20
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:979225 original size:20 final size:20
Alignment explanation
Indices: 978993--979207 Score: 56
Period size: 20 Copynumber: 10.8 Consensus size: 20
978983 CTATATATTA
978993 TATATAGTTTACGTATAT-AA-
1 TATATAGTTTA--TATATAAAC
*
979013 TATATAGTATATAAATATAAAC
1 TATATAGT-T-TATATATAAAC
* * *
979035 --TATAGTATATATATATAG
1 TATATAGTTTATATATAAAC
* * * **
979053 TATATACTATATAGATAATT
1 TATATAGTTTATATATAAAC
*
979073 TATATAGTTCACTA-ATAAAC
1 TATATAGTTTA-TATATAAAC
* *
979093 AATATATAGTTCATATGTAAAC
1 --TATATAGTTTATATATAAAC
* *
979115 --TATAGTTCATATGTAAA-
1 TATATAGTTTATATATAAAC
* *
979132 -ATATAGTTCATATGTAAATATC
1 TATATAGTTTATATAT-AA-A-C
* *
979154 AACTATAGTTTATATGTAAAC
1 TA-TATAGTTTATATATAAAC
* * *
979175 --TATACTTCATATATCAAC
1 TATATAGTTTATATATAAAC
*
979193 TATATAATTTATATA
1 TATATAGTTTATATA
979208 GTTTATATAT
Statistics
Matches: 153, Mismatches: 23, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
18 53 0.35
19 2 0.01
20 55 0.36
21 8 0.05
22 19 0.12
23 3 0.02
24 13 0.08
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (20 bp):
TATATAGTTTATATATAAAC
Found at i:979279 original size:34 final size:36
Alignment explanation
Indices: 979241--979315 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 36
979231 TATAGTTTTT
*
979241 TATATATAGTTCATATGTA-AAT-TATACTATATAA
1 TATATATAGTTCATATATATAATATATACTATATAA
* *
979275 TATATATAGTTTATATATATAATATATAGTATATAA
1 TATATATAGTTCATATATATAATATATACTATATAA
979311 -ATATA
1 TATATA
979316 AATTAAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
34 17 0.47
35 8 0.22
36 11 0.31
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATATAGTTCATATATATAATATATACTATATAA
Found at i:979293 original size:20 final size:20
Alignment explanation
Indices: 979193--979498 Score: 72
Period size: 20 Copynumber: 15.0 Consensus size: 20
979183 ATATATCAAC
*
979193 TATATAATTTATATAGTTTA
1 TATATAATATATATAGTTTA
*
979213 TATATAA-A-CTATAGTTTA
1 TATATAATATATATAGTTTA
** *
979231 TATAGTTTTTTATATATAGTTCA
1 TATA---TAATATATATAGTTTA
* *
979254 TATGTAA-AT-TATA----C
1 TATATAATATATATAGTTTA
979268 TATATAATATATATAGTTTA
1 TATATAATATATATAGTTTA
979288 TATAT-ATAATATATAGTATATA
1 TATATAAT-ATATATAGT-T-TA
* *
979310 AATATAA-AT-TAAAGTTTGTA
1 TATATAATATATATAG-TT-TA
979330 GTATATAAATATAAATTATAGTTTA
1 -TATAT-AATAT--A-TATAGTTTA
* * *
979355 TATA-CATAGTATATACTATA
1 TATATAATA-TATATAGTTTA
* * * *
979375 TAAATAGTTTATATAGTTCA
1 TATATAATATATATAGTTTA
* *
979395 CTAATAAACTATATATATAGTTCA
1 -T-ATATA--ATATATATAGTTTA
* *
979419 TATGT-ATA-CTATAGTTTA
1 TATATAATATATATAGTTTA
*
979437 TATGTAAATATCAACTATAGTTTA
1 TATAT-AATAT--A-TATAGTTTA
*
979461 TATGTAA-AT-TATAG-TTA
1 TATATAATATATATAGTTTA
979478 GTATATAA-ACTATATAGTTTA
1 -TATATAATA-TATATAGTTTA
979499 ACTATAGTTT
Statistics
Matches: 210, Mismatches: 37, Indels: 77
0.65 0.11 0.24
Matches are distributed among these distances:
14 6 0.03
15 2 0.01
16 4 0.02
17 3 0.01
18 42 0.20
19 8 0.04
20 55 0.26
21 15 0.07
22 19 0.09
23 18 0.09
24 30 0.14
25 2 0.01
26 2 0.01
27 4 0.02
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (20 bp):
TATATAATATATATAGTTTA
Found at i:979314 original size:22 final size:22
Alignment explanation
Indices: 979268--979315 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
979258 TAAATTATAC
* *
979268 TATATAATATATATAGTTTATA
1 TATATAATATATATAGTATAAA
979290 TATATAATATATAGTA-TATAAA
1 TATATAATATATA-TAGTATAAA
979312 TATA
1 TATA
979316 AATTAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TATATAATATATATAGTATAAA
Found at i:979331 original size:27 final size:27
Alignment explanation
Indices: 979301--979353 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
979291 ATATAATATA
979301 TAGTATATAAATATAAATTAAAGTTTG
1 TAGTATATAAATATAAATTAAAGTTTG
*
979328 TAGTATATAAATATAAATTATAGTTT
1 TAGTATATAAATATAAATTAAAGTTT
979354 ATATACATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.43
Consensus pattern (27 bp):
TAGTATATAAATATAAATTAAAGTTTG
Found at i:979369 original size:27 final size:27
Alignment explanation
Indices: 979299--979362 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
979289 ATATATAATA
*
979299 TATAGTATATAAATATAAATTAAAGTT
1 TATAGTACATAAATATAAATTAAAGTT
* * *
979326 TGTAGTATATAAATATAAATTATAGTT
1 TATAGTACATAAATATAAATTAAAGTT
979353 TATA-TACATA
1 TATAGTACATA
979363 GTATATACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.48, C:0.02, G:0.08, T:0.42
Consensus pattern (27 bp):
TATAGTACATAAATATAAATTAAAGTT
Found at i:979374 original size:18 final size:18
Alignment explanation
Indices: 979353--979387 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
979343 AATTATAGTT
*
979353 TATATACATAGTATATAC
1 TATATAAATAGTATATAC
*
979371 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
979388 TAGTTCACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:979432 original size:42 final size:42
Alignment explanation
Indices: 979398--979493 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
979388 TAGTTCACTA
*
979398 ATAAACTATATA-TATAGTTCATATGTATACTATAGTTTATAT
1 ATAAACTATATACTATAGTTCATATGTAAACTATAG-TTATAT
* * *
979440 GTAAA-TATCA-ACTATAGTTTATATGTAAATTATAGTTAGTAT
1 ATAAACTAT-ATACTATAGTTCATATGTAAACTATAGTTA-TAT
979482 ATAAACTATATA
1 ATAAACTATATA
979494 GTTTAACTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
41 7 0.16
42 33 0.75
43 4 0.09
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (42 bp):
ATAAACTATATACTATAGTTCATATGTAAACTATAGTTATAT
Found at i:979475 original size:18 final size:19
Alignment explanation
Indices: 979407--979498 Score: 66
Period size: 18 Copynumber: 4.6 Consensus size: 19
979397 AATAAACTAT
*
979407 ATATATAGTTCATATGT--
1 ATATATAGTTTATATGTAA
979424 ATACTATAGTTTATATGTAAA
1 ATA-TATAGTTTATATGT-AA
979445 TATCAACTATAGTTTATATGTAA
1 -AT--A-TATAGTTTATATGTAA
*
979468 AT-TATAG-TTAGTATATAA
1 ATATATAGTTTA-TATGTAA
979486 ACTATATAGTTTA
1 A-TATATAGTTTA
979499 ACTATAGTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
17 6 0.10
18 25 0.40
19 1 0.02
20 5 0.08
21 3 0.05
22 4 0.06
23 2 0.03
24 16 0.26
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (19 bp):
ATATATAGTTTATATGTAA
Found at i:979491 original size:295 final size:285
Alignment explanation
Indices: 978939--979515 Score: 743
Period size: 284 Copynumber: 2.0 Consensus size: 285
978929 AACTATAGTA
*
978939 TATAGTTTATATGGTTTTTATATATAGTTCATATGTAAATTATACTATATATTATATATAGTTTA
1 TATAGTTTATATGGTTTTTATATATAGTTCATATGTAAATTATACTATATAATATATATAGTTTA
* * * *
979004 CGTATATAATATATAGTATATAAATATAAACTATAGTATATATATATAGTATATACTATATAGAT
66 CATATATAATATATAGTATATAAATATAAACTAAAGTATATATATATAATATATAATATATAGAT
* * *
979069 AATTTATATAGTTCACTAATAAACAATATATAGTTCATATGTAAACTATAGTTCATATGTAAAAT
131 AATATACATAGTTCACTAATAAACAATATATAGTTCATATCTAAACTATAGTTCATATGTAAAAT
*
979134 ATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAACTATACTTCATATATCAACTATATA
196 ATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAACTATACTTCATATATAAACTATATA
979199 ATTT-A-TATAGTTTATATATAAAC
261 ATTTAACTATAGTTTATATATAAAC
*
979222 TATAGTTTATATAGTTTTTTATATATAGTTCATATGTAAATTATACTATATAATATATATAGTTT
1 TATAGTTTATAT-GGTTTTTATATATAGTTCATATGTAAATTATACTATATAATATATATAGTTT
* * * *
979287 ATATATATAATATATAGTATATAAATATAAATTAAAGTTTGTAGTATATAA-ATATAA-ATTATA
65 ACATATATAATATATAGTATATAAATATAAACTAAAGTATATA-TATATAATATATAATA-TATA
* * * * *
979350 GTTTATATACATAGTATATACTATATAAATAGTTTATATAGTTCACTAATAAACTATATA-TATA
128 GATAATATACATAGT-T-CACTA-ATAAACA--ATATATAGTTCA-T-AT---CTA-A-ACTATA
* * * * *
979414 GTTCATATGTATACTATAGTTTATATGTAAATATCAACTATAGTTTATATGTAAATTATAGTT-A
181 GTTCATATGTAAAATATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAACTATACTTCA
*
979478 GTATATAAACTATATAGTTTAACTATAGTTTATATATA
246 -TATATAAACTATATAATTTAACTATAGTTTATATATA
979516 GTTCATATCA
Statistics
Matches: 251, Mismatches: 25, Indels: 22
0.84 0.08 0.07
Matches are distributed among these distances:
283 13 0.05
284 107 0.43
285 7 0.03
286 4 0.02
287 6 0.02
289 11 0.04
290 1 0.00
291 2 0.01
294 3 0.01
295 80 0.32
296 2 0.01
297 15 0.06
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (285 bp):
TATAGTTTATATGGTTTTTATATATAGTTCATATGTAAATTATACTATATAATATATATAGTTTA
CATATATAATATATAGTATATAAATATAAACTAAAGTATATATATATAATATATAATATATAGAT
AATATACATAGTTCACTAATAAACAATATATAGTTCATATCTAAACTATAGTTCATATGTAAAAT
ATAGTTCATATGTAAATATCAACTATAGTTTATATGTAAACTATACTTCATATATAAACTATATA
ATTTAACTATAGTTTATATATAAAC
Found at i:979539 original size:65 final size:59
Alignment explanation
Indices: 979460--979699 Score: 213
Period size: 58 Copynumber: 4.0 Consensus size: 59
979450 ACTATAGTTT
*
979460 ATATGTAAATTATAGTTAGTATATAAACTATATAGTTTAACTATAGTTTATATATAGTTCATATC
1 ATATGTAAACTATAGTTA-TATATAAACTATATAGTTT-A-TATAGTTTATATATA--T-ATATC
* * * *
979525 ATATGTAAACTATAGTTCATCTATCAACTATATAATTTATATAGTTTATATATAAATATC
1 ATATGTAAACTATAGTT-ATATATAAACTATATAGTTTATATAGTTTATATATATATATC
* * * * *
979585 A-ACTATAATCTATAGTTTATATATAAACTATA-A-TTTATATAGTTTTTATTTATATTTC
1 ATA-TGTAAACTATAG-TTATATATAAACTATATAGTTTATATAGTTTATATATATATATC
* * *
979643 ATATGTAAATTATA-TTGTATAT--ACTATATAGTTTATATATATATTATATAGTATATA
1 ATATGTAAACTATAGTTATATATAAACTATATAGTTTATATA-GT-TTATATA-TATATA
979700 AATATCAAAT
Statistics
Matches: 145, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
54 6 0.04
55 1 0.01
56 15 0.10
57 1 0.01
58 35 0.24
59 8 0.06
60 28 0.19
61 2 0.01
63 15 0.10
64 1 0.01
65 32 0.22
66 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (59 bp):
ATATGTAAACTATAGTTATATATAAACTATATAGTTTATATAGTTTATATATATATATC
Found at i:979615 original size:18 final size:18
Alignment explanation
Indices: 979588--979625 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
979578 AAATATCAAC
* *
979588 TATAATCTATAGTTTATA
1 TATAAACTATAATTTATA
979606 TATAAACTATAATTTATA
1 TATAAACTATAATTTATA
979624 TA
1 TA
979626 GTTTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (18 bp):
TATAAACTATAATTTATA
Found at i:979639 original size:31 final size:30
Alignment explanation
Indices: 979555--979639 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 30
979545 CTATCAACTA
* *
979555 TATAATTTATATAGTTTATATATAAATATCAAC
1 TATAATTTATATAGTTT-T-TAT-TATATAAAC
*
979588 TATAA--TCTATAG--TTTA-TATATAAAC
1 TATAATTTATATAGTTTTTATTATATAAAC
979613 TATAATTTATATAGTTTTTATTTATAT
1 TATAATTTATATAGTTTTTA-TTATAT
979640 TTCATATGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
25 12 0.29
27 8 0.19
28 1 0.02
29 5 0.12
31 11 0.26
33 5 0.12
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.51
Consensus pattern (30 bp):
TATAATTTATATAGTTTTTATTATATAAAC
Found at i:979683 original size:11 final size:11
Alignment explanation
Indices: 979675--979836 Score: 57
Period size: 11 Copynumber: 14.1 Consensus size: 11
979665 ACTATATAGT
979675 TTATATATATA
1 TTATATATATA
979686 TTATATAGTATA
1 TTATATA-TATA
*
979698 -TAAATATCA-A
1 TTATATAT-ATA
*
979708 ATATAGTATATA
1 TTATA-TATATA
*
979720 GTATATAGTATA
1 TTATATA-TATA
* *
979732 -TAAATATAAA
1 TTATATATATA
* *
979742 CTATAGTCTATA
1 TTATA-TATATA
979754 -TATAATATATA
1 TTAT-ATATATA
* *
979765 CTATATAAATA
1 TTATATATATA
979776 GTCTATATATATA
1 -T-TATATATATA
979789 GTT-TATATAGT-
1 -TTATATATA-TA
*
979800 TTATACATATA
1 TTATATATATA
* *
979811 GTTCATATGTAAA
1 -TT-ATATATATA
979824 TTATATAGTATA
1 TTATATA-TATA
979836 T
1 T
979837 ATAGTTTACA
Statistics
Matches: 115, Mismatches: 18, Indels: 35
0.68 0.11 0.21
Matches are distributed among these distances:
10 8 0.07
11 56 0.49
12 34 0.30
13 17 0.15
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (11 bp):
TTATATATATA
Found at i:979685 original size:20 final size:20
Alignment explanation
Indices: 979660--979855 Score: 99
Period size: 20 Copynumber: 9.9 Consensus size: 20
979650 AATTATATTG
*
979660 TATATACTATATAGTTTATA
1 TATATACTATATAGTATATA
*
979680 TATATATTATATAGTATATA
1 TATATACTATATAGTATATA
* *
979700 AATAT-CAAATATAGTATATA
1 TATATAC-TATATAGTATATA
* *
979720 GTATATAGTATATA-AATATA
1 -TATATACTATATAGTATATA
* * *
979740 AACTATAGTCTATA-TATA-A
1 TA-TATACTATATAGTATATA
979759 TATATACTATATA--A-ATA
1 TATATACTATATAGTATATA
*
979776 GTCTATA-TATATAGTTTATATA
1 -TATATACTATATAG--TATATA
*
979798 GTTTATAC-ATATAGT-TCATA
1 -TATATACTATATAGTAT-ATA
* * *
979818 TGTAAATTATATAGTATATA
1 TATATACTATATAGTATATA
*
979838 TAGTTTAC-ATATAGTATA
1 TA-TATACTATATAGTATA
979856 AGTTAGTATA
Statistics
Matches: 136, Mismatches: 24, Indels: 32
0.71 0.12 0.17
Matches are distributed among these distances:
16 1 0.01
17 8 0.06
18 14 0.10
19 8 0.06
20 77 0.57
21 13 0.10
22 15 0.11
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATACTATATAGTATATA
Found at i:979711 original size:27 final size:27
Alignment explanation
Indices: 979654--979739 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 27
979644 TATGTAAATT
* * ** *
979654 ATATTGTATATACTATATAGTTTATAT
1 ATATAGTATATAGTATATAGAATATAA
*
979681 ATATATTATATAGTATATA-AATATCAA
1 ATATAGTATATAGTATATAGAATAT-AA
*
979708 ATATAGTATATAGTATATAGTATATAA
1 ATATAGTATATAGTATATAGAATATAA
979735 ATATA
1 ATATA
979740 AACTATAGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 3 0.06
27 42 0.86
28 4 0.08
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (27 bp):
ATATAGTATATAGTATATAGAATATAA
Found at i:979718 original size:14 final size:13
Alignment explanation
Indices: 979701--979739 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
979691 TAGTATATAA
979701 ATATCAAATATAGT
1 ATAT-AAATATAGT
*
979715 ATATAGTATATAGT
1 ATATA-AATATAGT
979729 ATATAAATATA
1 ATATAAATATA
979740 AACTATAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:979724 original size:5 final size:4
Alignment explanation
Indices: 979660--979788 Score: 73
Period size: 4 Copynumber: 30.0 Consensus size: 4
979650 AATTATATTG
* *
979660 TATA TACTA TATA GTTTA TATA TATA T-TA TATA GTATA TAAA TATCA
1 TATA TA-TA TATA -TATA TATA TATA TATA TATA -TATA TATA TAT-A
* * * *
979707 AATA TAGTA TATA GTATA TAGTA TATA AATA TAAA CTATA GTCTA TATA
1 TATA TA-TA TATA -TATA TA-TA TATA TATA TATA -TATA -TATA TATA
* *
979756 TA-A TATA TACTA TATA AATA GTCTA TATA TATA
1 TATA TATA TA-TA TATA TATA -TATA TATA TATA
979789 GTTTATATAG
Statistics
Matches: 96, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
3 6 0.06
4 52 0.54
5 38 0.40
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:979746 original size:27 final size:26
Alignment explanation
Indices: 979662--979771 Score: 89
Period size: 27 Copynumber: 4.2 Consensus size: 26
979652 TTATATTGTA
* * * *
979662 TATACTATATAGTTTATATATATATTA
1 TATAGTATATA-TATATAAATATAGTA
*
979689 TATAGTATATAAATATCAAATATAGTA
1 TATAGTATATATATAT-AAATATAGTA
*
979716 TATAGTATATAGTATATAAATATA-AA
1 TATAGTATATA-TATATAAATATAGTA
* * *
979742 CTATAGTCTATATATA-ATATATACTA
1 -TATAGTATATATATATAAATATAGTA
979768 TATA
1 TATA
979772 AATAGTCTAT
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
25 10 0.14
26 9 0.13
27 46 0.67
28 4 0.06
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (26 bp):
TATAGTATATATATATAAATATAGTA
Found at i:979798 original size:22 final size:22
Alignment explanation
Indices: 979667--979885 Score: 79
Period size: 22 Copynumber: 10.1 Consensus size: 22
979657 TTGTATATAC
979667 TATATAGTTTATATATATA--T
1 TATATAGTTTATATATATAGTT
* *
979687 TATATAG--TATATAAATA-TCA
1 TATATAGTTTATATATATAGT-T
* *
979707 AATATAGTATATAGTATATAG--
1 TATATAGTTTATA-TATATAGTT
** * *
979728 TATATA-AATATAAACTATAGTC
1 TATATAGTTTATATA-TATAGTT
* *
979750 TATATA--TAATATATACTA-TA
1 TATATAGTTTATATATA-TAGTT
* *
979770 TAAATAGTCTATATATATAGTT
1 TATATAGTTTATATATATAGTT
*
979792 TATATAGTTTATACATATAGTT
1 TATATAGTTTATATATATAGTT
* ** *
979814 CATAT-GTAAAT-TATATAGTA
1 TATATAGTTTATATATATAGTT
979834 TATATAGTTTACATATAGTATAAGTT
1 TATATAGTTT--ATATA-TAT-AGTT
*
979860 AGTATATA-TTATTTATATATAGTT
1 --TATATAGTT-TATATATATAGTT
979884 TA
1 TA
979886 AATACTACTA
Statistics
Matches: 149, Mismatches: 28, Indels: 42
0.68 0.13 0.19
Matches are distributed among these distances:
18 9 0.06
19 1 0.01
20 42 0.28
21 19 0.13
22 43 0.29
23 7 0.05
24 6 0.04
25 6 0.04
26 7 0.05
27 2 0.01
28 7 0.05
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (22 bp):
TATATAGTTTATATATATAGTT
Found at i:979885 original size:11 final size:11
Alignment explanation
Indices: 979758--979885 Score: 51
Period size: 11 Copynumber: 12.1 Consensus size: 11
979748 TCTATATATA
* *
979758 ATATATACTAT
1 ATATATAGTTT
*
979769 ATAAATAGTCTAT
1 ATATATAGT-T-T
979782 ATATATAG-TT
1 ATATATAGTTT
979792 -TATATAGTTT
1 ATATATAGTTT
*
979802 ATACATATAGTTC
1 AT--ATATAGTTT
* **
979815 ATATGTA-AAT
1 ATATATAGTTT
979825 -TATATAG--T
1 ATATATAGTTT
979833 ATATATAGTTT
1 ATATATAGTTT
* *
979844 ACATATAGTAT
1 ATATATAGTTT
*
979855 A-AGT-TAGTAT
1 ATA-TATAGTTT
979865 ATAT-TA-TTT
1 ATATATAGTTT
979874 ATATATAGTTT
1 ATATATAGTTT
979885 A
1 A
979886 AATACTACTA
Statistics
Matches: 90, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
8 1 0.01
9 25 0.28
10 16 0.18
11 30 0.33
13 18 0.20
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.47
Consensus pattern (11 bp):
ATATATAGTTT
Found at i:979992 original size:22 final size:22
Alignment explanation
Indices: 979967--980018 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
979957 CCATATATAC
*
979967 TATATATATAAACTATATAGTT
1 TATATATATAAACTATATAATT
979989 TATAT-TAATAAACTATATAATT
1 TATATAT-ATAAACTATATAATT
*
980011 CATATATA
1 TATATATA
980019 ATTTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 24 0.92
23 1 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATATATAAACTATATAATT
Found at i:980015 original size:53 final size:53
Alignment explanation
Indices: 979958--980071 Score: 174
Period size: 53 Copynumber: 2.2 Consensus size: 53
979948 AACCTTAAAC
* *
979958 CATATATACTATATATATAAACTATATAGTTTATATTAATAAACTATATAATT
1 CATATATAATATATATATAAACTATATAATTTATATTAATAAACTATATAATT
* * *
980011 CATATATAATTTATATATAAACTATATAATTTATATTAATAAACTATGTAGTT
1 CATATATAATATATATATAAACTATATAATTTATATTAATAAACTATATAATT
*
980064 TATATATA
1 CATATATA
980072 GTTCAATAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (53 bp):
CATATATAATATATATATAAACTATATAATTTATATTAATAAACTATATAATT
Found at i:980016 original size:31 final size:30
Alignment explanation
Indices: 979981--980041 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 30
979971 TATATAAACT
*
979981 ATATAGTTTATATTAATAAACTATATAATTCA
1 ATATAATTTATA-T-ATAAACTATATAATTCA
980013 TATATAATTTATATATAAACTATATAATT
1 -ATATAATTTATATATAAACTATATAATT
980042 TATATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 15 0.56
32 1 0.04
33 11 0.41
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (30 bp):
ATATAATTTATATATAAACTATATAATTCA
Found at i:980025 original size:20 final size:20
Alignment explanation
Indices: 980013--980247 Score: 98
Period size: 20 Copynumber: 11.7 Consensus size: 20
980003 ATATAATTCA
980013 TATATAATTTATATATAAAC
1 TATATAATTTATATATAAAC
980033 TATATAATTTATATTAATAAAC
1 TATATAATTTATA-T-ATAAAC
* * **
980055 TATGTAGTTTATATAT-AGT
1 TATATAATTTATATATAAAC
* *
980074 TCA-ATAGTTCATATATAAAC
1 T-ATATAATTTATATATAAAC
* *
980094 TATAT-A-GTAT-TAT--AG
1 TATATAATTTATATATAAAC
* * *
980109 TTTATACATGGTATATAT--AG
1 TATATA-AT-TTATATATAAAC
* *
980129 TTTATACATAATATATATAATA-
1 TATATA-AT-TTATATATAA-AC
* *
980151 TATATAGTTTATATATAGTA-
1 TATATAATTTATATATA-AAC
* *
980171 TATAATAATATAAATATAAAC
1 TAT-ATAATTTATATATAAAC
*
980192 TATATAGTTTATATATATAA-
1 TATATAATTTATATATA-AAC
980212 TATATATACTTTATATATAAAC
1 TATATA-A-TTTATATATAAAC
*
980234 TATATAGTTTATAT
1 TATATAATTTATAT
980248 TATATATATA
Statistics
Matches: 167, Mismatches: 28, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
15 5 0.03
17 4 0.02
18 2 0.01
19 18 0.11
20 78 0.47
21 21 0.13
22 38 0.23
23 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (20 bp):
TATATAATTTATATATAAAC
Found at i:980127 original size:2 final size:2
Alignment explanation
Indices: 980120--980264 Score: 88
Period size: 2 Copynumber: 72.0 Consensus size: 2
980110 TTATACATGG
* * *
980120 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA -A TA TA TA TA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * *
980162 TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
980203 TA TA TA TA -A TA TA TA TA CTT TA TA TA TA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
980245 TA T- TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
980265 GTTGTTTCAA
Statistics
Matches: 110, Mismatches: 18, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
1 7 0.06
2 94 0.85
3 9 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:980134 original size:9 final size:9
Alignment explanation
Indices: 980094--980266 Score: 60
Period size: 9 Copynumber: 18.9 Consensus size: 9
980084 ATATATAAAC
980094 TATATAGTA
1 TATATAGTA
980103 T-TATAGTTTA
1 TATATAG--TA
* *
980113 TACATGGTA
1 TATATAGTA
980122 TATATAGTTTA
1 TATATAG--TA
* *
980133 TACATAATA
1 TATATAGTA
*
980142 TATATAATA
1 TATATAGTA
980151 TATATAGTTTA
1 TATATAG--TA
980162 TATATAGTA
1 TATATAGTA
*
980171 TATAATAATA
1 TAT-ATAGTA
*
980181 TAAATATA-AA
1 T--ATATAGTA
*
980191 CTATATAGTT
1 -TATATAGTA
980201 TATATA-TA
1 TATATAGTA
980209 TA-ATA-TA
1 TATATAGTA
*
980216 TATACT-TTA
1 TATA-TAGTA
*
980225 TATATA-AA
1 TATATAGTA
980233 CTATATAGT-
1 -TATATAGTA
*
980242 T-TATATTA
1 TATATAGTA
980250 TATATA-TA
1 TATATAGTA
980258 TATTATAGT
1 TA-TATAGT
980267 TGTTTCAATT
Statistics
Matches: 126, Mismatches: 16, Indels: 43
0.68 0.09 0.23
Matches are distributed among these distances:
7 12 0.10
8 17 0.13
9 61 0.48
10 11 0.09
11 23 0.18
12 2 0.02
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (9 bp):
TATATAGTA
Found at i:980134 original size:11 final size:10
Alignment explanation
Indices: 980120--980264 Score: 88
Period size: 11 Copynumber: 14.4 Consensus size: 10
980110 TTATACATGG
*
980120 TATATATAGTT
1 TATATATA-TA
*
980131 TATACATA-A
1 TATATATATA
980140 TATATATA-A
1 TATATATATA
*
980149 TATATATAGTT
1 TATATATA-TA
980160 TATATATAGTA
1 TATATATA-TA
980171 TATA-ATA-A
1 TATATATATA
*
980179 TATAAATATA
1 TATATATATA
* *
980189 AACTATATAGTT
1 TA-TATATA-TA
980201 TATATATATA
1 TATATATATA
980211 -ATATATATA
1 TATATATATA
*
980220 CTTTATATATA
1 -TATATATATA
* *
980231 AACTATATAGTT
1 TA-TATATA-TA
980243 TATAT-TATA
1 TATATATATA
980252 TATATATAT-
1 TATATATATA
980261 TATA
1 TATA
980265 GTTGTTTCAA
Statistics
Matches: 107, Mismatches: 16, Indels: 24
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.05
9 38 0.36
10 11 0.10
11 49 0.46
12 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (10 bp):
TATATATATA
Found at i:980817 original size:208 final size:210
Alignment explanation
Indices: 980369--980849 Score: 711
Period size: 208 Copynumber: 2.3 Consensus size: 210
980359 TTTGTCTTGT
*
980369 TTAATTTATTTAAATTTTTATTTGAAATTTCATATTTGTTCAATTTAGTCCTTAAAATTATATTT
1 TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTT-AAATTATATTT
980434 GCATATGAAATTGACCCATACTTATCACTTATTTATATTTTTTAATTGCCACATAACTTTTTAAA
65 GCATATGAAATTGACCCA-AC-TA-CACTTATTTATATTTTTTAATTGCCACATAACTTTTTAAA
* * * ** * *
980499 TGGGTATAATTTAATACTTTTTGTATTAATTTAAACTTTACAATTTAATTTTTTTTCAATTTGAT
127 TGGGTATAATTTAATACTTTTTATATTAATTTAAACCTCACAATTTAAAATTATTTCAATTTGAA
*
980564 CCCTCATCAATGTGTGTTG
192 CCCTCATCAACGTGTGTTG
980583 CTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAATTATATTT
1 -TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAATTATATTT
*
980648 GCATCTGAAATTGACCC-A-TA-A-TTATTTATATTTTTTAATTGGCC-CATAACTTTTTAAATG
65 GCATATGAAATTGACCCAACTACACTTATTTATATTTTTTAATT-GCCACATAACTTTTTAAATG
* * *
980708 GGTATAATTTAGTACTTTTTTATATTAATTTTAACCTCACAATTTAAAATTATTTCGATTTGAAC
129 GGTATAATTTAATAC-TTTTTATATTAATTTAAACCTCACAATTTAAAATTATTTCAATTTGAAC
980773 CCTCATCAACGTGTGTTG
193 CCTCATCAACGTGTGTTG
* * *
980791 TGTAATTTATTTAAATTTTAATTTGTAATTTCATATTTATTCAATTTAGTTCTTAAATT
1 T-TAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAATT
980850 GGTATTTTTC
Statistics
Matches: 247, Mismatches: 16, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
207 50 0.20
208 115 0.47
210 2 0.01
212 1 0.00
214 27 0.11
215 52 0.21
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.51
Consensus pattern (210 bp):
TTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAATTATATTTG
CATATGAAATTGACCCAACTACACTTATTTATATTTTTTAATTGCCACATAACTTTTTAAATGGG
TATAATTTAATACTTTTTATATTAATTTAAACCTCACAATTTAAAATTATTTCAATTTGAACCCT
CATCAACGTGTGTTG
Found at i:983628 original size:23 final size:25
Alignment explanation
Indices: 983588--983634 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
983578 TAATAGTTAC
*
983588 AAAACCCGAAGGCCCA-TTTACAAT
1 AAAACCCGAAAGCCCATTTTACAAT
983612 AAAACCC-AAAGCCCATTTTACAA
1 AAAACCCGAAAGCCCATTTTACAA
983635 GTTCAACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.17
Consensus pattern (25 bp):
AAAACCCGAAAGCCCATTTTACAAT
Found at i:995958 original size:35 final size:35
Alignment explanation
Indices: 995912--996330 Score: 240
Period size: 35 Copynumber: 12.6 Consensus size: 35
995902 TAATTAATCA
*
995912 TTCACAAAAGAGTAGTGAAGTAATGCAATCCAACC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* *
995947 TTCACAAAAGAGTAATGAAGCAATGCAATCCAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * **
995982 TTCACAAAAGAGTAATGAAGCAATGCAGTTTAACC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* *** * * *
996017 TTTACAGTGGAGTAGT--A--AAT-TAATGCATCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * *
996047 TTTACATAAGAGTAGT--A--AA-GTAATCCAACC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * *
996077 TTCACAAAAGAGTAGTGAAACAATGCAGTTCAAATCC
1 TTCACAAAAGAGTAGTGAAGCAATGCA-ATCCAA-CC
* * * ** *
996114 TTTACAGAAGAGTAGT--A--AA-GAAATTTAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* **
996144 TTCACAAAAGAGTAGTGAAGCAATGCAGTTTAACC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * * *
996179 TTTACAGAAGAGTAGT--A--AA-GTAATCCAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * *
996209 TTCACATAAGAGTAGTGAAGCAATGCAATACATCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * * * * *
996244 TTTAGAGAAGAGTAGT--A--AA-GAAATTCAGCC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
* * *
996274 TTTACCAAAGAGTAGTGAAGCAATACAATCCAACC
1 TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
996309 TTCACAAAAGAGTAGTGAAGCA
1 TTCACAAAAGAGTAGTGAAGCA
996331 GGAACAGATC
Statistics
Matches: 295, Mismatches: 66, Indels: 46
0.72 0.16 0.11
Matches are distributed among these distances:
30 100 0.34
31 9 0.03
32 6 0.02
33 5 0.02
34 8 0.03
35 147 0.50
36 4 0.01
37 16 0.05
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (35 bp):
TTCACAAAAGAGTAGTGAAGCAATGCAATCCAACC
Found at i:996088 original size:30 final size:30
Alignment explanation
Indices: 996026--996324 Score: 114
Period size: 30 Copynumber: 9.2 Consensus size: 30
996016 CTTTACAGTG
* * * *
996026 GAGTAGTAAATTAATGCATCCTTTACATAA
1 GAGTAGTAAAGTAATCCAACCTTTACAAAA
*
996056 GAGTAGTAAAGTAATCCAACCTTCACAAAA
1 GAGTAGTAAAGTAATCCAACCTTTACAAAA
* *
996086 GAGTAGTGAAA-CAATGCAGTTCAAATCCTTTACAGAA
1 GAGTAGT-AAAGTAAT-C----C-AA-CCTTTACAAAA
* ** * *
996123 GAGTAGTAAAGAAATTTAGCCTTCACAAAA
1 GAGTAGTAAAGTAATCCAACCTTTACAAAA
* * * *
996153 GAGTAGTGAAGCAATGCAGTTTAACCTTTACAGAA
1 GAGTAGTAAAGTAAT-C----CAACCTTTACAAAA
* * *
996188 GAGTAGTAAAGTAATCCAGCCTTCACATAA
1 GAGTAGTAAAGTAATCCAACCTTTACAAAA
* * * * *
996218 GAGTAGTGAAGCAATGCAATACATCCTTTAGAGAA
1 GAGTAGT--A--AA-GTAATCCAACCTTTACAAAA
* * * *
996253 GAGTAGTAAAGAAATTCAGCCTTTACCAAA
1 GAGTAGTAAAGTAATCCAACCTTTACAAAA
* *
996283 GAGTAGTGAAGCAATACAATCCAACCTTCACAAAA
1 GAGTAGT-AA--AGT--AATCCAACCTTTACAAAA
996318 GAGTAGT
1 GAGTAGT
996325 GAAGCAGGAA
Statistics
Matches: 201, Mismatches: 44, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
30 95 0.47
31 9 0.04
32 1 0.00
33 2 0.01
34 3 0.01
35 67 0.33
36 5 0.02
37 19 0.09
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (30 bp):
GAGTAGTAAAGTAATCCAACCTTTACAAAA
Found at i:996213 original size:65 final size:65
Alignment explanation
Indices: 996045--996324 Score: 353
Period size: 65 Copynumber: 4.3 Consensus size: 65
996035 ATTAATGCAT
* * * * *
996045 CCTTTACATAAGAGTAGTAAAGTAATCCAACCTTCACAAAAGAGTAGTGAAACAATGCAGTTCAA
1 CCTTTACAGAAGAGTAGTAAAGAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCAATTC-A
996110 A
65 A
** * *
996111 TCCTTTACAGAAGAGTAGTAAAGAAATTTAGCCTTCACAAAAGAGTAGTGAAGCAATGCAGTTTA
1 -CCTTTACAGAAGAGTAGTAAAGAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCAATTCA
996176 A
65 A
* * * *
996177 CCTTTACAGAAGAGTAGTAAAGTAATCCAGCCTTCACATAAGAGTAGTGAAGCAATGCAATACAT
1 CCTTTACAGAAGAGTAGTAAAGAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAA
* * * * * *
996242 CCTTTAGAGAAGAGTAGTAAAGAAATTCAGCCTTTACCAAAGAGTAGTGAAGCAATACAATCCAA
1 CCTTTACAGAAGAGTAGTAAAGAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAA
* *
996307 CCTTCACAAAAGAGTAGT
1 CCTTTACAGAAGAGTAGT
996325 GAAGCAGGAA
Statistics
Matches: 186, Mismatches: 27, Indels: 2
0.87 0.13 0.01
Matches are distributed among these distances:
65 128 0.69
66 2 0.01
67 56 0.30
ACGTcount: A:0.42, C:0.17, G:0.18, T:0.23
Consensus pattern (65 bp):
CCTTTACAGAAGAGTAGTAAAGAAATCCAGCCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAA
Found at i:997773 original size:24 final size:24
Alignment explanation
Indices: 997733--997802 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
997723 AAACGGAGAT
*
997733 ATCAGAAATCA-AACAGAATTCAG
1 ATCAGAAATAAGAACAGAATTCAG
* *
997756 ATCAGATATAAGAACAGAATCCAG
1 ATCAGAAATAAGAACAGAATTCAG
*
997780 ATCAGAAATCAGAACAGAATTCA
1 ATCAGAAATAAGAACAGAATTCA
997803 AGTAATGTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 9 0.22
24 31 0.77
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (24 bp):
ATCAGAAATAAGAACAGAATTCAG
Found at i:997785 original size:12 final size:11
Alignment explanation
Indices: 997739--997799 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
997729 AGATATCAGA
997739 AATCA-AACAG
1 AATCAGAACAG
*
997749 AATTCAGATCAG
1 AA-TCAGAACAG
*
997761 ATATAAGAACAG
1 A-ATCAGAACAG
*
997773 AATCCAGATCAG
1 AAT-CAGAACAG
997785 AAATCAGAACAG
1 -AATCAGAACAG
997797 AAT
1 AAT
997800 TCAAGTAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
10 2 0.05
11 8 0.20
12 26 0.65
13 4 0.10
ACGTcount: A:0.52, C:0.16, G:0.15, T:0.16
Consensus pattern (11 bp):
AATCAGAACAG
Found at i:997838 original size:24 final size:25
Alignment explanation
Indices: 997733--997840 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 25
997723 AAACGGAGAT
*
997733 ATCAGAAATCA-AACAGAATTC-AG
1 ATCAAAAATCAGAACAGAATTCAAG
* * * *
997756 ATCAGATATAAGAACAGAA-TCCAG
1 ATCAAAAATCAGAACAGAATTCAAG
*
997780 ATCAGAAATCAGAACAGAATTCAAG
1 ATCAAAAATCAGAACAGAATTCAAG
** *
997805 -T-AATGTATCATAACAGAATTCAAG
1 ATCAA-AAATCAGAACAGAATTCAAG
997829 -TCAAAAATCAGA
1 ATCAAAAATCAGA
997841 TAAAATATTT
Statistics
Matches: 68, Mismatches: 12, Indels: 9
0.76 0.13 0.10
Matches are distributed among these distances:
23 12 0.18
24 50 0.74
25 6 0.09
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (25 bp):
ATCAAAAATCAGAACAGAATTCAAG
Found at i:1003290 original size:37 final size:37
Alignment explanation
Indices: 1003214--1003290 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1003204 TTTTTATATT
* *
1003214 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTCTAAAAAAAATTATATAAATATTATCAA
* *
1003251 TTTAATTTTCTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTCTAAAAAAAATTATATAAATATTAT-CAA
1003288 TTT
1 TTT
1003291 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAATTTTCTAAAAAAAATTATATAAATATTATCAA
Found at i:1003641 original size:30 final size:30
Alignment explanation
Indices: 1003517--1003632 Score: 214
Period size: 30 Copynumber: 3.9 Consensus size: 30
1003507 AAAATGGCCT
1003517 GGAAGCTAAAAAGTTAAAGCATATAAGCCG
1 GGAAGCTAAAAAGTTAAAGCATATAAGCCG
*
1003547 GGAAGCTAAAAAGTTAATGCATATAAGCCG
1 GGAAGCTAAAAAGTTAAAGCATATAAGCCG
*
1003577 GGAAGCTAAAAAGTTAATGCATATAAGCCG
1 GGAAGCTAAAAAGTTAAAGCATATAAGCCG
1003607 GGAAGCTAAAAAGTTAAAGCATATAA
1 GGAAGCTAAAAAGTTAAAGCATATAA
1003633 ACTTGGAAGT
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 84 1.00
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (30 bp):
GGAAGCTAAAAAGTTAAAGCATATAAGCCG
Found at i:1003691 original size:30 final size:30
Alignment explanation
Indices: 1003655--1003714 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
1003645 GGATGGCAAC
1003655 TCAACCCGAATCCGACGGGTTCCGACCCGA
1 TCAACCCGAATCCGACGGGTTCCGACCCGA
1003685 TCAACCCGAATCCGACGGGTTCCGACCCGA
1 TCAACCCGAATCCGACGGGTTCCGACCCGA
1003715 CCCGATCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.13
Consensus pattern (30 bp):
TCAACCCGAATCCGACGGGTTCCGACCCGA
Found at i:1003796 original size:5 final size:5
Alignment explanation
Indices: 1003786--1003811 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1003776 AATGTACTGT
1003786 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
1003812 TTAGGGTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:1004267 original size:13 final size:13
Alignment explanation
Indices: 1004249--1004274 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1004239 TAATAATTAA
1004249 AAGTTATTACTAT
1 AAGTTATTACTAT
1004262 AAGTTATTACTAT
1 AAGTTATTACTAT
1004275 TTATTGAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (13 bp):
AAGTTATTACTAT
Found at i:1005449 original size:24 final size:23
Alignment explanation
Indices: 1005422--1005482 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
1005412 AATTTTTATA
*
1005422 CTTGTGACACATTTTTTCTTTGCT
1 CTTGTG-CACATTTTTTCTTTACT
**
1005446 CTTGTGGTCATCTTTTTCTTTACT
1 CTTGTGCACAT-TTTTTCTTTACT
1005470 CTTGTGGCACATT
1 CTTGT-GCACATT
1005483 ACTTATGGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 3 0.10
24 23 0.77
25 4 0.13
ACGTcount: A:0.11, C:0.21, G:0.15, T:0.52
Consensus pattern (23 bp):
CTTGTGCACATTTTTTCTTTACT
Found at i:1007121 original size:14 final size:15
Alignment explanation
Indices: 1007010--1007127 Score: 139
Period size: 15 Copynumber: 7.5 Consensus size: 15
1007000 TAATAAGGTT
1007010 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1007025 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
1007040 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
1007055 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1007070 AATTATTATAAATTATGGA
1 ATTTATTTTAAA--AT--A
1007089 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
1007107 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
1007121 ATTTATT
1 ATTTATT
1007128 AGTATAGATT
Statistics
Matches: 90, Mismatches: 6, Indels: 15
0.81 0.05 0.14
Matches are distributed among these distances:
14 12 0.13
15 62 0.69
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
22 10 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1007146 original size:22 final size:22
Alignment explanation
Indices: 1007130--1007172 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1007120 AATTTATTAG
1007130 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
1007152 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
1007173 TAATTATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:1007169 original size:106 final size:101
Alignment explanation
Indices: 1007055--1007396 Score: 327
Period size: 106 Copynumber: 3.2 Consensus size: 101
1007045 TTATAAAATA
1007055 ATTTATTTTAAAATAAATTATTATAAATTATGGATTGATTTATTTTAAAATAATTTATTTTAAAT
1 ATTTATTTT-AAAT-AATTATTAT--ATTAT-GATTGATTTATTTTAAAATAATTTATTTTAAAT
* *
1007120 AATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
61 AATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1007161 ATTTATTTTAAATAATTATTAGTA-TA-GATTGATTTATTTTAAAATATGGATTGATTTACTTTA
1 ATTTATTTTAAATAATTATTA-TATTATGATTGATTTATTTT-AAA-AT--A---ATTTATTTTA
1007224 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
58 AATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * ** * *
1007268 ATTTATTATT--GTAGTT-GTATGGATTGATTTATT-ATTGTAGTTGTATGGATTGATTTATTTT
1 ATTTATT-TTAAATAATTATTAT--ATT-A-TGATTGATT-TA-TT-T-TAAAATAATTTATTTT
*
1007329 AAATAATTTATTAGTATGGATTGATTTGTTTTAAAATATGGATTG
57 AAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1007374 ATTTATTTTAAATAAATTATTAT
1 ATTTATTTTAAAT-AATTATTAT
1007397 TGTAGTTGTA
Statistics
Matches: 197, Mismatches: 16, Indels: 43
0.77 0.06 0.17
Matches are distributed among these distances:
100 14 0.07
101 3 0.02
102 4 0.02
103 1 0.01
104 10 0.05
105 9 0.05
106 73 0.37
107 60 0.30
108 6 0.03
109 6 0.03
110 5 0.03
111 3 0.02
112 2 0.01
113 1 0.01
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (101 bp):
ATTTATTTTAAATAATTATTATATTATGATTGATTTATTTTAAAATAATTTATTTTAAATAATTT
ATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1007172 original size:54 final size:54
Alignment explanation
Indices: 1007107--1007395 Score: 387
Period size: 54 Copynumber: 5.4 Consensus size: 54
1007097 TTTTAAAATA
* *
1007107 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1007161 ATTTATTTTAAATAA-TTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1007214 ATTTACTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* ***
1007268 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
1007320 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTGTTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
1007374 ATTTATTTTAAATAAATTATTA
1 ATTTATTTTAAATAATTTATTA
1007396 TTGTAGTTGT
Statistics
Matches: 209, Mismatches: 13, Indels: 26
0.84 0.05 0.10
Matches are distributed among these distances:
48 18 0.09
49 3 0.01
50 4 0.02
51 2 0.01
52 16 0.08
53 51 0.24
54 89 0.43
55 2 0.01
56 4 0.02
57 3 0.01
58 17 0.08
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:1007172 original size:69 final size:67
Alignment explanation
Indices: 1007025--1007206 Score: 199
Period size: 69 Copynumber: 2.7 Consensus size: 67
1007015 TTTTAAAATA
* *
1007025 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAATTATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATAGAT
1007090 TG
66 TG
* * * * * *
1007092 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT--T-TAAAATAAATTATTATAAAATATA
1007156 GATTG
63 GATTG
* *
1007161 ATTTATTTT-AAATAA-TTATTAGTATAGATTGATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTA-TA-A-AATAATTTATTTTAAAATA
1007207 TGGATTGATT
Statistics
Matches: 94, Mismatches: 14, Indels: 13
0.78 0.12 0.11
Matches are distributed among these distances:
66 13 0.14
67 27 0.29
68 11 0.12
69 33 0.35
70 1 0.01
71 9 0.10
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTTTAAAATAAATTATTATAAAATATAGAT
TG
Found at i:1007187 original size:31 final size:31
Alignment explanation
Indices: 1007152--1007257 Score: 122
Period size: 31 Copynumber: 3.7 Consensus size: 31
1007142 TATTTTAAAA
1007152 TATAGATTGATTTATTTTAAATAATTATTAG
1 TATAGATTGATTTATTTTAAATAATTATTAG
1007183 TATAGATTGATTTATTTT-AA-AA-TA-T-G
1 TATAGATTGATTTATTTTAAATAATTATTAG
*
1007209 ----GATTGATTTACTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAA-TTATTAG
*
1007237 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
1007258 ATATGGATTG
Statistics
Matches: 63, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
22 13 0.21
23 2 0.03
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
29 2 0.03
30 2 0.03
31 18 0.29
32 16 0.25
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (31 bp):
TATAGATTGATTTATTTTAAATAATTATTAG
Found at i:1007251 original size:18 final size:18
Alignment explanation
Indices: 1007228--1007275 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
1007218 ACTTTAAATA
*
1007228 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
1007246 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
1007268 ATTTATTA
1 ATTTATTA
1007276 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:1007288 original size:26 final size:26
Alignment explanation
Indices: 1007259--1007326 Score: 136
Period size: 26 Copynumber: 2.6 Consensus size: 26
1007249 TATTTTAAAA
1007259 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTAGTTG
1007285 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTATTATTGTAGTTG
1007311 TATGGATTGATTTATT
1 TATGGATTGATTTATT
1007327 TTAAATAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (26 bp):
TATGGATTGATTTATTATTGTAGTTG
Found at i:1007368 original size:22 final size:22
Alignment explanation
Indices: 1007343--1007385 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1007333 AATTTATTAG
*
1007343 TATGGATTGATTTGTTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1007365 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1007386 TAAATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1007457 original size:31 final size:31
Alignment explanation
Indices: 1007410--1007468 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1007400 AGTTGTATGG
* * *
1007410 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTAAAATCTCAGTATTGCAAAACTAAA
1007441 ATTATTAAAATCTCAGTATTGCAAAACT
1 ATTATTAAAATCTCAGTATTGCAAAACT
1007469 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTATTAAAATCTCAGTATTGCAAAACTAAA
Found at i:1008780 original size:20 final size:20
Alignment explanation
Indices: 1008755--1008824 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
1008745 CGATTTTCCA
1008755 AATTCGCAACGCGTATCTGT
1 AATTCGCAACGCGTATCTGT
1008775 AATTCGCAACGCGTATCTGT
1 AATTCGCAACGCGTATCTGT
1008795 AATTCGCAACGCGTATCTGT
1 AATTCGCAACGCGTATCTGT
1008815 AATTCGCAAC
1 AATTCGCAAC
1008825 ACAGAAGTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.29
Consensus pattern (20 bp):
AATTCGCAACGCGTATCTGT
Found at i:1008838 original size:20 final size:20
Alignment explanation
Indices: 1008815--1008863 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1008805 GCGTATCTGT
1008815 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
1008835 AATTCGTAACATAGAAGTCA
1 AATTCGCAACACAGAAGTCA
1008855 AATTCGCAA
1 AATTCGCAA
1008864 AGCGCGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:1008839 original size:40 final size:38
Alignment explanation
Indices: 1008753--1008840 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 38
1008743 CGCGATTTTC
* *
1008753 CAAATTCGCAACGCGTATCTGTAATTCGCAACGCGTAT
1 CAAATTCGCAACGCGTATCTGTAATTCGCAACACGAAT
*
1008791 CTGTAATTCGCAACGCGTATCTGTAATTCGCAACACAGAAGT
1 C--AAATTCGCAACGCGTATCTGTAATTCGCAACAC-GAA-T
1008833 CAAATTCG
1 CAAATTCG
1008841 TAACATAGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
38 1 0.02
40 37 0.88
41 2 0.05
42 2 0.05
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (38 bp):
CAAATTCGCAACGCGTATCTGTAATTCGCAACACGAAT
Found at i:1009369 original size:20 final size:19
Alignment explanation
Indices: 1009345--1009450 Score: 97
Period size: 20 Copynumber: 5.9 Consensus size: 19
1009335 TTGAAACTTA
1009345 AATTCGCAACACGAAAATG
1 AATTCGCAACACGAAAATG
1009364 ATATTCGCAACAC--AAA--
1 A-ATTCGCAACACGAAAATG
1009380 AATT-GCAACACGAAAATG
1 AATTCGCAACACGAAAATG
1009398 AAATTCGCAACAC--AAA--
1 -AATTCGCAACACGAAAATG
*
1009414 AA-TCGCAACGCGAAAATG
1 AATTCGCAACACGAAAATG
*
1009432 AAATTCGCAACACAAAAAT
1 -AATTCGCAACACGAAAAT
1009451 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 25
0.72 0.03 0.25
Matches are distributed among these distances:
14 15 0.21
15 5 0.07
16 7 0.10
18 6 0.08
19 7 0.10
20 31 0.44
ACGTcount: A:0.51, C:0.22, G:0.12, T:0.15
Consensus pattern (19 bp):
AATTCGCAACACGAAAATG
Found at i:1009388 original size:34 final size:34
Alignment explanation
Indices: 1009348--1009469 Score: 208
Period size: 34 Copynumber: 3.6 Consensus size: 34
1009338 AAACTTAAAT
*
1009348 TCGCAACACGAAAATGATATTCGCAACACAAAAA
1 TCGCAACACGAAAATGAAATTCGCAACACAAAAA
*
1009382 TTGCAACACGAAAATGAAATTCGCAACACAAAAA
1 TCGCAACACGAAAATGAAATTCGCAACACAAAAA
*
1009416 TCGCAACGCGAAAATGAAATTCGCAACACAAAAA
1 TCGCAACACGAAAATGAAATTCGCAACACAAAAA
*
1009450 TCGCAACGCGAAAATGAAAT
1 TCGCAACACGAAAATGAAAT
1009470 CGCGTTGCGA
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 84 1.00
ACGTcount: A:0.50, C:0.22, G:0.14, T:0.14
Consensus pattern (34 bp):
TCGCAACACGAAAATGAAATTCGCAACACAAAAA
Found at i:1009421 original size:14 final size:14
Alignment explanation
Indices: 1009368--1009456 Score: 52
Period size: 14 Copynumber: 5.5 Consensus size: 14
1009358 AAAATGATAT
1009368 TCGCAACACAAAAA
1 TCGCAACACAAAAA
*
1009382 TTGCAACACGAAAATGAAA
1 TCGCAACAC---AA--AAA
1009401 TTCGCAACACAAAAA
1 -TCGCAACACAAAAA
*
1009416 TCGCAACGCGAAAATGAAA
1 TCGCAA--C-ACAA--AAA
1009435 TTCGCAACACAAAAA
1 -TCGCAACACAAAAA
1009450 TCGCAAC
1 TCGCAAC
1009457 GCGAAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 24
0.68 0.05 0.28
Matches are distributed among these distances:
14 21 0.36
15 6 0.10
16 1 0.02
17 10 0.17
18 1 0.02
19 6 0.10
20 14 0.24
ACGTcount: A:0.51, C:0.25, G:0.12, T:0.12
Consensus pattern (14 bp):
TCGCAACACAAAAA
Found at i:1009530 original size:20 final size:20
Alignment explanation
Indices: 1009469--1009523 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1009459 GAAAATGAAA
1009469 TCGCGTTGCGAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
* *
1009489 TTGCGTTGCAAATTTCATTT
1 TCGCGTTGCGAATTTCATTT
*
1009509 TCGTGTTGCGAATTT
1 TCGCGTTGCGAATTT
1009524 AAGTTTCAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGAATTTCATTT
Found at i:1011114 original size:11 final size:11
Alignment explanation
Indices: 1011098--1011160 Score: 81
Period size: 11 Copynumber: 5.6 Consensus size: 11
1011088 ATTTTTTTCA
*
1011098 AAAAAAAAAAC
1 AAAAAAAAAGC
* *
1011109 AAAAAAAAGGT
1 AAAAAAAAAGC
1011120 AAAAAAAAAGGC
1 AAAAAAAAA-GC
*
1011132 ACAAAAAAAGC
1 AAAAAAAAAGC
1011143 AAAAAAAAAGC
1 AAAAAAAAAGC
1011154 AAAAAAA
1 AAAAAAA
1011161 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 35 0.80
12 9 0.20
ACGTcount: A:0.81, C:0.08, G:0.10, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAGC
Found at i:1018872 original size:21 final size:21
Alignment explanation
Indices: 1018829--1018878 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1018819 GTTAGGGGAG
*
1018829 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* **
1018850 TTGCGTGATGAGGTTGGTACT
1 TTACGTGATGAGGTCAGTACT
1018871 TTACGTGA
1 TTACGTGA
1018879 CGAAAATGGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.34, T:0.36
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1018919 original size:21 final size:22
Alignment explanation
Indices: 1018895--1019011 Score: 68
Period size: 21 Copynumber: 5.5 Consensus size: 22
1018885 TGGTGCATGG
1018895 CGTGATGAGGTACGGT-CTTTA
1 CGTGATGAGGTACGGTACTTTA
* * **
1018916 CGTGGTGAGGTA-GTTGTTTTA
1 CGTGATGAGGTACGGTACTTTA
* ** * *
1018937 CGCGATGA-AAATGGTGCTTTA
1 CGTGATGAGGTACGGTACTTTA
*
1018958 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
*
1018979 CGTGGTGAGGTATC--TACTTTA
1 CGTGATGAGGTA-CGGTACTTTA
1019000 CGTGATGAGGTA
1 CGTGATGAGGTA
1019012 GCCACTCTAC
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.04
21 72 0.95
22 1 0.01
ACGTcount: A:0.21, C:0.12, G:0.32, T:0.35
Consensus pattern (22 bp):
CGTGATGAGGTACGGTACTTTA
Found at i:1019000 original size:63 final size:62
Alignment explanation
Indices: 1018831--1019007 Score: 171
Period size: 63 Copynumber: 2.8 Consensus size: 62
1018821 TAGGGGAGTT
* * * * *
1018831 ACGTGATGAGGT-CAGTGCTTTGCGTGATGAGGTTGGTACTTTACGTGACGAAAATGGTGCATG
1 ACGTGATGAGGTAC-GT-CTTTACGTGGTGAGGTAGTTACTTTACGTGATGAAAATGGTGCATG
* ** * * *
1018894 GCGTGATGAGGTACGGTCTTTACGTGGTGAGGTAGTTGTTTTACGCGATGAAAATGGTGCTTT
1 ACGTGATGAGGTAC-GTCTTTACGTGGTGAGGTAGTTACTTTACGTGATGAAAATGGTGCATG
*
1018957 ACGTGGTGAGGTATC-TACTTTACGTGGTGAGGTA-TCTACTTTACGTGATGA
1 ACGTGATGAGGTA-CGT-CTTTACGTGGTGAGGTAGT-TACTTTACGTGATGA
1019008 GGTAGCCACT
Statistics
Matches: 93, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
62 2 0.02
63 87 0.94
64 4 0.04
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.33
Consensus pattern (62 bp):
ACGTGATGAGGTACGTCTTTACGTGGTGAGGTAGTTACTTTACGTGATGAAAATGGTGCATG
Found at i:1019022 original size:21 final size:21
Alignment explanation
Indices: 1018953--1019025 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
1018943 GAAAATGGTG
*
1018953 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTATCTA
*
1018974 CTTTACGTGGTGAGGTATCTA
1 CTTTACGTGATGAGGTATCTA
* *
1018995 CTTTACGTGATGAGGTAGCCA
1 CTTTACGTGATGAGGTATCTA
*
1019016 CTCTACGTGA
1 CTTTACGTGA
1019026 GTTTCATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (21 bp):
CTTTACGTGATGAGGTATCTA
Found at i:1019338 original size:21 final size:20
Alignment explanation
Indices: 1019285--1019378 Score: 93
Period size: 21 Copynumber: 4.7 Consensus size: 20
1019275 ATTCACCTGT
1019285 CATCGTTCAAGAGGCCTCTCC
1 CATCGTTCAAGAGGCC-CTCC
**
1019306 CATTATTCAAGAGGCCACTCC
1 CATCGTTCAAGAGGCC-CTCC
* *
1019327 CATCGTT-AA-AGACCCTCT
1 CATCGTTCAAGAGGCCCTCC
1019345 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGG-CCCTCC
* *
1019366 CACCATTCAAGAG
1 CATCGTTCAAGAG
1019379 CCCGATTCAC
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
18 10 0.17
19 6 0.10
20 4 0.07
21 39 0.66
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (20 bp):
CATCGTTCAAGAGGCCCTCC
Found at i:1023509 original size:24 final size:24
Alignment explanation
Indices: 1023482--1023528 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1023472 TAAAATCCGA
*
1023482 GTATTGACAAAGCTCAAAGTTCGG
1 GTATTGACAAAGATCAAAGTTCGG
* *
1023506 GTATTGACCAAGATCAAATTTCG
1 GTATTGACAAAGATCAAAGTTCG
1023529 AATACTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACAAAGATCAAAGTTCGG
Found at i:1024284 original size:14 final size:15
Alignment explanation
Indices: 1024248--1024285 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1024238 GAAATCATTG
1024248 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1024263 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1024278 AAAAATTA
1 AAAAATTA
1024286 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1024467 original size:20 final size:20
Alignment explanation
Indices: 1024442--1024591 Score: 69
Period size: 20 Copynumber: 7.5 Consensus size: 20
1024432 AAATAAAAGC
1024442 TGTTGCGAAATTAAAATTCG
1 TGTTGCGAAATTAAAATTCG
1024462 TGTTGCG-AATTCGAAAATT-G
1 TGTTGCGAAATT--AAAATTCG
* * * *
1024482 AGTTGCG-ATTTAGAAAATCT
1 TGTTGCGAAATTA-AAATTCG
* ** *
1024502 TGTTACGAAAAGGAAACTT-G
1 TGTTGCG-AAATTAAAATTCG
*
1024522 TGTTGCGAAA-AAGAAATTCG
1 TGTTGCGAAATTA-AAATTCG
*
1024542 CGTTGCG-AATTCAAAATTCG
1 TGTTGCGAAATT-AAAATTCG
* * *
1024562 AGTTGCGAATTTGAAATTCTG
1 TGTTGCGAAATTAAAATTC-G
*
1024583 CGTTGCGAA
1 TGTTGCGAA
1024592 TTTTAAAATC
Statistics
Matches: 97, Mismatches: 21, Indels: 23
0.69 0.15 0.16
Matches are distributed among these distances:
18 2 0.02
19 17 0.18
20 54 0.56
21 22 0.23
22 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTTGCGAAATTAAAATTCG
Found at i:1024489 original size:40 final size:40
Alignment explanation
Indices: 1024443--1024673 Score: 130
Period size: 40 Copynumber: 5.8 Consensus size: 40
1024433 AATAAAAGCT
*
1024443 GTTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATTGA
1 GTTGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATTGA
* * ** * *** * *
1024483 GTTGCG-ATTTAGAAAATCTTGTTACGAAAAGGAAACTTGT
1 GTTGCGAAATTA-AAATTCGCGTTGCGAATTCGAAAATTGA
*
1024523 GTTGCGAAA-AAGAAATTCGCGTTGCGAATTC-AAAATTCGA
1 GTTGCGAAATTA-AAATTCGCGTTGCGAATTCGAAAATT-GA
* * ** * *
1024563 GTTGCGAATTTGAAATTCTGCGTTGCGAATTTTAAAATCGC
1 GTTGCGAAATTAAAATTC-GCGTTGCGAATTCGAAAATTGA
* * * * *
1024604 GTCGTGAGAAA--GAAATTCGCGTTGCGAATTTGGAAATTGT
1 GT--TGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATTGA
** * *
1024644 GTTGCGAAATTGGAGTTCACGTTGCGAATT
1 GTTGCGAAATTAAAATTCGCGTTGCGAATT
1024674 TGTTGGTTAT
Statistics
Matches: 145, Mismatches: 36, Indels: 20
0.72 0.18 0.10
Matches are distributed among these distances:
38 6 0.04
39 9 0.06
40 97 0.67
41 23 0.16
42 5 0.03
43 5 0.03
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (40 bp):
GTTGCGAAATTAAAATTCGCGTTGCGAATTCGAAAATTGA
Found at i:1025125 original size:13 final size:13
Alignment explanation
Indices: 1025107--1025137 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1025097 GAGACTTGAC
1025107 TCAAACTTGAAAA
1 TCAAACTTGAAAA
1025120 TCAAACTTGAAAA
1 TCAAACTTGAAAA
1025133 TCAAA
1 TCAAA
1025138 TTTCTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.23
Consensus pattern (13 bp):
TCAAACTTGAAAA
Found at i:1025501 original size:2 final size:2
Alignment explanation
Indices: 1025494--1025518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1025484 ATTACTCCCT
1025494 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1025519 TTCTTGTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1028730 original size:60 final size:60
Alignment explanation
Indices: 1028646--1028825 Score: 218
Period size: 60 Copynumber: 3.0 Consensus size: 60
1028636 CATATGTCTC
* * *
1028646 TAAACTATGTCTCTCATTTTAAATTGGTCCTTAAAATTTTGAATATTCCAATTTCATCCA
1 TAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCA
* * * * *
1028706 TAAATTATGACTCTCATTCTAAATTAGTCTTTAAACTTTTGAACATTCTC-ATTTCATCCC
1 TAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAATATTC-CAATTTCATCCA
* * * * * *
1028766 CAAACTATAACCCTCATTTTAAATTAATCCTCAAACTTTTGAATATTCCAATTCCATCCA
1 TAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCA
1028826 CATATGTAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
59 1 0.01
60 97 0.98
61 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.41
Consensus pattern (60 bp):
TAAACTATGACTCTCATTTTAAATTAGTCCTTAAACTTTTGAATATTCCAATTTCATCCA
Found at i:1030594 original size:59 final size:58
Alignment explanation
Indices: 1030450--1030579 Score: 210
Period size: 59 Copynumber: 2.2 Consensus size: 58
1030440 TTGTTTTTGT
*
1030450 CTTGTTATTTTTTAATCAATATTATATCTCGACATTTCCCTTAGAATATTTCTTCCTAA
1 CTTGTTATTTTTTAATCAATATTATGTCTCGACATTTCCCTTAGAATA-TTCTTCCTAA
1030509 CTTGTTATTTTTTAATCAATATTATGTCTCGACATTTCCCTTAGAATA-T-TTCCTAA
1 CTTGTTATTTTTTAATCAATATTATGTCTCGACATTTCCCTTAGAATATTCTTCCTAA
*
1030565 CTTGTTTTTATTTTA
1 CTTGTTATT-TTTTA
1030580 CTTTGTGTCA
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
56 15 0.22
57 6 0.09
59 47 0.69
ACGTcount: A:0.25, C:0.17, G:0.06, T:0.52
Consensus pattern (58 bp):
CTTGTTATTTTTTAATCAATATTATGTCTCGACATTTCCCTTAGAATATTCTTCCTAA
Found at i:1036794 original size:2 final size:2
Alignment explanation
Indices: 1036789--1036814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1036779 ATGTGTGGTG
1036789 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1036815 AATTAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1039388 original size:15 final size:14
Alignment explanation
Indices: 1039368--1039420 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
1039358 GGTCTAATAC
1039368 CGAGTCAACTCGGTT
1 CGAGTCAACTCGG-T
* *
1039383 CGAGTCGACCCGGT
1 CGAGTCAACTCGGT
1039397 CGAGTCAACTCGGT
1 CGAGTCAACTCGGT
1039411 CTGAGTCAAC
1 C-GAGTCAAC
1039421 CCATCCGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 14 0.42
15 19 0.58
ACGTcount: A:0.21, C:0.30, G:0.28, T:0.21
Consensus pattern (14 bp):
CGAGTCAACTCGGT
Found at i:1039429 original size:29 final size:30
Alignment explanation
Indices: 1039367--1039432 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
1039357 TGGTCTAATA
* *
1039367 CCGAGTCAACTCGGTTCGAGTCGACCCGGT
1 CCGAGTCAACTCGGTTCGAGTCAACCCGAT
1039397 -CGAGTCAACTCGG-TCTGAGTCAACCC-AT
1 CCGAGTCAACTCGGTTC-GAGTCAACCCGAT
1039425 CCGAGTCA
1 CCGAGTCA
1039433 TACTGTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 3 0.09
29 29 0.91
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.20
Consensus pattern (30 bp):
CCGAGTCAACTCGGTTCGAGTCAACCCGAT
Found at i:1040436 original size:27 final size:28
Alignment explanation
Indices: 1040406--1040464 Score: 102
Period size: 27 Copynumber: 2.1 Consensus size: 28
1040396 GAATTACCCT
*
1040406 TAAAGTGTAAAATGACCAAAA-TGCCTC
1 TAAAGTGTAAAATGACCAAAAGTACCTC
1040433 TAAAGTGTAAAATGACCAAAAGTACCTC
1 TAAAGTGTAAAATGACCAAAAGTACCTC
1040461 TAAA
1 TAAA
1040465 CCCTAGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 21 0.70
28 9 0.30
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (28 bp):
TAAAGTGTAAAATGACCAAAAGTACCTC
Found at i:1041595 original size:23 final size:23
Alignment explanation
Indices: 1041569--1041639 Score: 142
Period size: 23 Copynumber: 3.1 Consensus size: 23
1041559 AAATCCTTAC
1041569 GGACCTAAGGATACCCTTGGGTA
1 GGACCTAAGGATACCCTTGGGTA
1041592 GGACCTAAGGATACCCTTGGGTA
1 GGACCTAAGGATACCCTTGGGTA
1041615 GGACCTAAGGATACCCTTGGGTA
1 GGACCTAAGGATACCCTTGGGTA
1041638 GG
1 GG
1041640 CCCATAGGCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.25, C:0.21, G:0.32, T:0.21
Consensus pattern (23 bp):
GGACCTAAGGATACCCTTGGGTA
Found at i:1042135 original size:15 final size:15
Alignment explanation
Indices: 1042115--1042150 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1042105 GGAGTACGGT
1042115 GCATGTGATTAGGGG
1 GCATGTGATTAGGGG
1042130 GCATGTGATTAGGGG
1 GCATGTGATTAGGGG
1042145 GCATGT
1 GCATGT
1042151 AGGTTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.08, G:0.44, T:0.28
Consensus pattern (15 bp):
GCATGTGATTAGGGG
Found at i:1050676 original size:41 final size:40
Alignment explanation
Indices: 1050601--1050679 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
1050591 TATATACCCG
* * *
1050601 TGTTTTAGTGGTGTTTTGAACAAACGTTGCTAAAGACTCA
1 TGTTTTAGTGGCGTTTTGAACAAACATCGCTAAAGACTCA
* *
1050641 TGTTTTAGTGGCGTTTTTGAACAAATATCGGTAAAGACT
1 TGTTTTAGTGGCG-TTTTGAACAAACATCGCTAAAGACT
1050680 TGTACATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 12 0.36
41 21 0.64
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (40 bp):
TGTTTTAGTGGCGTTTTGAACAAACATCGCTAAAGACTCA
Found at i:1052315 original size:25 final size:25
Alignment explanation
Indices: 1052286--1052338 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1052276 AGCTCAATTT
* *
1052286 CATAACTCAGTTTCATAGAGTTAAA
1 CATAACTCAATTTAATAGAGTTAAA
1052311 CATAACTCAATTTAATAGAGTTAAA
1 CATAACTCAATTTAATAGAGTTAAA
1052336 CAT
1 CAT
1052339 TACCATCCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (25 bp):
CATAACTCAATTTAATAGAGTTAAA
Found at i:1053560 original size:19 final size:19
Alignment explanation
Indices: 1053538--1053597 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
1053528 CTTTAGTGGT
1053538 GTTTGTTAACTTTTGCGAC
1 GTTTGTTAACTTTTGCGAC
* *
1053557 GTTTG-T---TTTAGCGGC
1 GTTTGTTAACTTTTGCGAC
1053572 GTTTGTTAACTTTTGCGAC
1 GTTTGTTAACTTTTGCGAC
1053591 GTTTGTT
1 GTTTGTT
1053598 TTAGCGGCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 12 0.36
16 1 0.03
18 1 0.03
19 19 0.58
ACGTcount: A:0.12, C:0.13, G:0.25, T:0.50
Consensus pattern (19 bp):
GTTTGTTAACTTTTGCGAC
Found at i:1053576 original size:34 final size:34
Alignment explanation
Indices: 1053529--1053605 Score: 136
Period size: 34 Copynumber: 2.3 Consensus size: 34
1053519 AAGTGCAACC
* *
1053529 TTTAGTGGTGTTTGTTAACTTTTGCGACGTTTGT
1 TTTAGCGGCGTTTGTTAACTTTTGCGACGTTTGT
1053563 TTTAGCGGCGTTTGTTAACTTTTGCGACGTTTGT
1 TTTAGCGGCGTTTGTTAACTTTTGCGACGTTTGT
1053597 TTTAGCGGC
1 TTTAGCGGC
1053606 ACTTTTTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.12, C:0.13, G:0.27, T:0.48
Consensus pattern (34 bp):
TTTAGCGGCGTTTGTTAACTTTTGCGACGTTTGT
Found at i:1053975 original size:18 final size:19
Alignment explanation
Indices: 1053954--1053997 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
1053944 AGAACAAAAG
1053954 AAGAAAGAT-GAATAC-AAT
1 AAGAAAGATGGAA-ACGAAT
1053972 AAGAAA-ATGGAAACGAAT
1 AAGAAAGATGGAAACGAAT
1053990 AA-AAAGAT
1 AAGAAAGAT
1053998 TGGTGTTGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.64, C:0.05, G:0.18, T:0.14
Consensus pattern (19 bp):
AAGAAAGATGGAAACGAAT
Found at i:1061586 original size:20 final size:20
Alignment explanation
Indices: 1061546--1061592 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1061536 ATTTTTTTTA
* *
1061546 AATAGTGAACAATACCCGTG
1 AATAGTGAACAATAACAGTG
1061566 AATAGTGAACAATAACAGTG
1 AATAGTGAACAATAACAGTG
*
1061586 AACAGTG
1 AATAGTG
1061593 CGATGAACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (20 bp):
AATAGTGAACAATAACAGTG
Found at i:1061722 original size:66 final size:66
Alignment explanation
Indices: 1061616--1061744 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 66
1061606 GGGAATCGGT
* *
1061616 TTCTCTATGGGGGAAATCGGTTCCCCTTTTACATTATGGAAAATTTTTGCTAATTCGTGGTTATT
1 TTCTCTATGGGGGAAATCGATTCCCCTTTTACATTATGGAAAATTTTTGCTAATTCGTAGTTATT
1061681 G
66 G
1061682 TTCTCTATGGGGGAAATCGATTCCCCTTTTACATTATGGAAAATTTTTGCTAATTCGTAGTTA
1 TTCTCTATGGGGGAAATCGATTCCCCTTTTACATTATGGAAAATTTTTGCTAATTCGTAGTTA
1061745 CTAATCCGAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (66 bp):
TTCTCTATGGGGGAAATCGATTCCCCTTTTACATTATGGAAAATTTTTGCTAATTCGTAGTTATT
G
Found at i:1063387 original size:407 final size:407
Alignment explanation
Indices: 1062632--1063449 Score: 1555
Period size: 407 Copynumber: 2.0 Consensus size: 407
1062622 CAAACACGTC
1062632 CCCAATATACTTTTCCTTGAATTCCCTCAAAAAGAATTCCATGTGATTTGCTCAGTAGAAACTCG
1 CCCAATATACTTTTCCTTGAATTCCCTCAAAAAGAATTCCATGTGATTTGCTCAGTAGAAACTCG
1062697 TGCGGCGACTGTATTCCACCACACACTGGCTTGCTCCATCAGTAGAGACACAACCCAATACATCT
66 TGCGGCGACTGTATTCCACCACACACTGGCTTGCTCCATCAGTAGAGACACAACCCAATACATCT
1062762 TTCCTTAATCATCACAATGAATCCTGTTGAGCATATTCTTGACATCATTCAACCAGAAGTCAGCA
131 TTCCTTAATCATCACAATGAATCCTGTTGAGCATATTCTTGACATCATTCAACCAGAAGTCAGCA
*
1062827 GCCATCGGATTAGCATCCGAATCACCTCGAAATTCAGGTGCTCTCATCTTCCTCAATTCTTTCGG
196 GCCATCGGATTAGCATCCGAATCACCTCGAAATTCAGGTGCTCTCATCTTCCTCAATTCTTTCGA
1062892 AACTGACACTGGGGTTCGATGATTAATAATGGTATCTAGGGCTTGTAAAAACAACCCCCGATCTT
261 AACTGACACTGGGGTTCGATGATTAATAATGGTATCTAGGGCTTGTAAAAACAACCCCCGATCTT
* *
1062957 GAACAGTCATATCCTGTTGATTCATATTAGACAGCTCTACATTCGACTGAGCATTGGGTGGATTC
326 GAACAGGCATATCCTGTTGATTCAGATTAGACAGCTCTACATTCGACTGAGCATTGGGTGGATTC
1063022 TGATTCACCTCGTTACT
391 TGATTCACCTCGTTACT
1063039 CCCAATATACTTTTCCTTGAATTCCCTCAAAAAGAATTCCATGTGATTTGCTCAGTAGAAACTCG
1 CCCAATATACTTTTCCTTGAATTCCCTCAAAAAGAATTCCATGTGATTTGCTCAGTAGAAACTCG
* *
1063104 TGCGGTGACTGTATTCCACCACACACTGGCTTGCTCCATCAGTAGAGACACAACCCAATCCATCT
66 TGCGGCGACTGTATTCCACCACACACTGGCTTGCTCCATCAGTAGAGACACAACCCAATACATCT
*
1063169 TTCCTTGATCATCACAATGAATCCTGTTGAGCATATTCTTGACATCATTCAACCAGAAGTCAGCA
131 TTCCTTAATCATCACAATGAATCCTGTTGAGCATATTCTTGACATCATTCAACCAGAAGTCAGCA
1063234 GCCATCGGATTAGCATCCGAATCACCTCGAAATTCAGGTGCTCTCATCTTCCTCAATTCTTTCGA
196 GCCATCGGATTAGCATCCGAATCACCTCGAAATTCAGGTGCTCTCATCTTCCTCAATTCTTTCGA
*
1063299 AACTGACACTGGGGTTCGATGATTAATAATGGTGTCTAGGGCTTGTAAAAACAACCCCCGATCTT
261 AACTGACACTGGGGTTCGATGATTAATAATGGTATCTAGGGCTTGTAAAAACAACCCCCGATCTT
* *
1063364 GAATAGGCATATCCTGTTGATTCAGATTAGACAGCTCTACATTCGGCTGAGCATTGGGTGGATTC
326 GAACAGGCATATCCTGTTGATTCAGATTAGACAGCTCTACATTCGACTGAGCATTGGGTGGATTC
1063429 TGATTCACCTCGTTACT
391 TGATTCACCTCGTTACT
1063446 CCCA
1 CCCA
1063450 CTCTGTACAG
Statistics
Matches: 402, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
407 402 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (407 bp):
CCCAATATACTTTTCCTTGAATTCCCTCAAAAAGAATTCCATGTGATTTGCTCAGTAGAAACTCG
TGCGGCGACTGTATTCCACCACACACTGGCTTGCTCCATCAGTAGAGACACAACCCAATACATCT
TTCCTTAATCATCACAATGAATCCTGTTGAGCATATTCTTGACATCATTCAACCAGAAGTCAGCA
GCCATCGGATTAGCATCCGAATCACCTCGAAATTCAGGTGCTCTCATCTTCCTCAATTCTTTCGA
AACTGACACTGGGGTTCGATGATTAATAATGGTATCTAGGGCTTGTAAAAACAACCCCCGATCTT
GAACAGGCATATCCTGTTGATTCAGATTAGACAGCTCTACATTCGACTGAGCATTGGGTGGATTC
TGATTCACCTCGTTACT
Found at i:1073017 original size:22 final size:22
Alignment explanation
Indices: 1072989--1073030 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1072979 AAGAATAGAA
1072989 AGCAATATTGGAACCAAATGAT
1 AGCAATATTGGAACCAAATGAT
*
1073011 AGCAATATTGGTACCAAATG
1 AGCAATATTGGAACCAAATG
1073031 GTGTCTAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (22 bp):
AGCAATATTGGAACCAAATGAT
Found at i:1078129 original size:25 final size:25
Alignment explanation
Indices: 1078083--1078136 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 25
1078073 ACATTTTCAT
1078083 TTTCAATTTTATTTTTAATTTT-TTA
1 TTTCAATTTTA-TTTTAATTTTATTA
1078108 TTTCAATTTTCA-TTTAATTTTTATTA
1 TTTCAATTTT-ATTTTAA-TTTTATTA
1078134 TTT
1 TTT
1078137 TGCAGGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.19
25 14 0.54
26 7 0.27
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTCAATTTTATTTTAATTTTATTA
Found at i:1080842 original size:21 final size:21
Alignment explanation
Indices: 1080816--1080860 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
1080806 AAATCTTTTC
1080816 TTTATT-TTACTTTAAATCA-CT
1 TTTATTATTA-TTTAAA-CATCT
1080837 TTTATTATTATTTAAACATCT
1 TTTATTATTATTTAAACATCT
1080858 TTT
1 TTT
1080861 TACCAAATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 17 0.77
22 3 0.14
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTATTATTATTTAAACATCT
Found at i:1089411 original size:20 final size:20
Alignment explanation
Indices: 1089386--1089427 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1089376 ATGTAAGTTC
1089386 AAATATCCAATTATCCAACA
1 AAATATCCAATTATCCAACA
1089406 AAATATCCAATTATCCAACA
1 AAATATCCAATTATCCAACA
1089426 AA
1 AA
1089428 TTCAAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (20 bp):
AAATATCCAATTATCCAACA
Found at i:1090940 original size:21 final size:21
Alignment explanation
Indices: 1090861--1090940 Score: 74
Period size: 22 Copynumber: 3.8 Consensus size: 21
1090851 CAGAACCCAT
*
1090861 GGGGGTATCGATTCCC-TCAA
1 GGGGGAATCGATTCCCTTCAA
* *
1090881 -GGAGAATCGATTCTCATTCAA
1 GGGGGAATCGATTC-CCTTCAA
* *
1090902 AGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTCAA
*
1090924 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
1090941 CTGCACTAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
19 11 0.23
20 1 0.02
21 8 0.17
22 26 0.55
23 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.28, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:1100422 original size:29 final size:31
Alignment explanation
Indices: 1100358--1100433 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
1100348 CTTTCCTTGG
* *
1100358 CTTTACTTTCTTTTTGAAATTATTTTTTGTT
1 CTTTTCTTTCTTTTTGAAATTATTTGTTGTT
1100389 CTTTT-TCTTCTTTTCTG-AATT-TTTGTTG-T
1 CTTTTCT-TTCTTTT-TGAAATTATTTGTTGTT
1100418 CTTTTCTTTCTTTTTG
1 CTTTTCTTTCTTTTTG
1100434 TACTCCAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 2 0.05
29 13 0.32
30 8 0.20
31 15 0.38
32 2 0.05
ACGTcount: A:0.09, C:0.13, G:0.08, T:0.70
Consensus pattern (31 bp):
CTTTTCTTTCTTTTTGAAATTATTTGTTGTT
Found at i:1104458 original size:10 final size:10
Alignment explanation
Indices: 1104445--1104469 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1104435 TTTTCCTGAT
1104445 TTTTTTTGTC
1 TTTTTTTGTC
1104455 TTTTTTTGTC
1 TTTTTTTGTC
1104465 TTTTT
1 TTTTT
1104470 GTACTCCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTC
Done.