Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002525.1 Hibiscus syriacus cultivar Beakdansim tig00005138_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: 88918
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6328 original size:13 final size:13
Alignment explanation
Indices: 6310--6336 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6300 TATTAAAATC
6310 TTATATATATATA
1 TTATATATATATA
6323 TTATATATATATA
1 TTATATATATATA
6336 T
1 T
6337 AATTATAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATATATATATA
Found at i:14865 original size:12 final size:12
Alignment explanation
Indices: 14848--14924 Score: 50
Period size: 14 Copynumber: 6.0 Consensus size: 12
14838 TATATTATAG
14848 ATATTAATTTTA
1 ATATTAATTTTA
14860 ATATTAAATTTTTA
1 ATATT-AA-TTTTA
* *
14874 A-A-TAAATTAA
1 ATATTAATTTTA
14884 ATATTAATTTTTTA
1 ATATTAA--TTTTA
*
14898 ATATTATATTATA
1 ATATTA-ATTTTA
14911 TATATTTAATTTTA
1 -ATA-TTAATTTTA
14925 TATCATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
10 4 0.08
11 3 0.06
12 9 0.18
13 7 0.14
14 23 0.46
15 4 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTAATTTTA
Found at i:14918 original size:21 final size:21
Alignment explanation
Indices: 14894--14946 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
14884 ATATTAATTT
*
14894 TTTAATATTATATTATATATA
1 TTTAATTTTATATTATATATA
*
14915 TTTAATTTTATATCATATA-A
1 TTTAATTTTATATTATATATA
*
14935 ATT-ATTTTATAT
1 TTTAATTTTATAT
14947 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.31
20 3 0.10
21 17 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTAATTTTATATTATATATA
Found at i:14926 original size:14 final size:15
Alignment explanation
Indices: 14884--14950 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 15
14874 AATAAATTAA
*
14884 ATATTAATTTTTTA-
1 ATATTAATTTTATAT
*
14898 ATATT-ATATTATAT
1 ATATTAATTTTATAT
14912 ATATTTAATTTTATAT
1 ATA-TTAATTTTATAT
* *
14928 CATATAAATTATTTTAT
1 -ATATTAATT-TTATAT
14945 ATATTA
1 ATATTA
14951 TTAAAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.14
14 8 0.19
15 2 0.05
16 18 0.43
17 8 0.19
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATTAATTTTATAT
Found at i:18412 original size:61 final size:62
Alignment explanation
Indices: 18308--18439 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 62
18298 TATATATACG
** * *
18308 GTGACTAAATTATAAATAAAATAAAATTCGAATACTGAATTAAA-ATATATGAAAATTTATTGTA
1 GTGACT-AATTATAAATAAAATAAAATTAAAAGACTGAATTAAACATATA--AAAATTGATTGTA
*
18372 GTGACTAATTAT-AATAAAAT-AAATTAAAAGA-TAGAATTAAACATATAAAAATTGATTTTA
1 GTGACTAATTATAAATAAAATAAAATTAAAAGACT-GAATTAAACATATAAAAATTGATTGTA
*
18432 GTGGCTAA
1 GTGACTAA
18440 AATAGAAGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
60 19 0.32
61 16 0.27
62 13 0.22
63 6 0.10
64 6 0.10
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.33
Consensus pattern (62 bp):
GTGACTAATTATAAATAAAATAAAATTAAAAGACTGAATTAAACATATAAAAATTGATTGTA
Found at i:18656 original size:12 final size:14
Alignment explanation
Indices: 18623--18658 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
18613 TTTCCTCTCC
18623 TTTCTCTCTAAATG
1 TTTCTCTCTAAATG
18637 TTTCTCTCTAAATG
1 TTTCTCTCTAAATG
18651 TTTCTCTC
1 TTTCTCTC
18659 GTTGGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.25, G:0.06, T:0.53
Consensus pattern (14 bp):
TTTCTCTCTAAATG
Found at i:19188 original size:45 final size:45
Alignment explanation
Indices: 19120--19217 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
19110 TGGAACGGGG
* * *
19120 ACGTGGAGAGACTGTTGGTAGTGCTGGAAGCT-ACTGGAATTTACA
1 ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGA-TGGAATTTACA
* * **
19165 ACGTGGAGTGGCTGCTGGCAGTGCTGGAAACTGATGGAATTTGTA
1 ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGATGGAATTTACA
19210 ACGTGGAG
1 ACGTGGAG
19218 CTGCTGGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 44 0.98
46 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (45 bp):
ACGTGGAGAGACTGCTGGCAGTGCTGGAAACTGATGGAATTTACA
Found at i:19683 original size:39 final size:39
Alignment explanation
Indices: 19628--19927 Score: 413
Period size: 39 Copynumber: 7.7 Consensus size: 39
19618 AGGTTGAATA
* *
19628 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * * * *
19667 AGTTCTTCAGATTATGAACTCCTTCTTCTTCTTCATATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
19706 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* *
19745 AGTTCTTCAGATTATGAAC-TCTTTTTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTC-TTCTTCCTCTTCAGACG
*
19784 AGTTCTTCAGACTATGAACTTCTTCTTTCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * * *
19823 AGTTCTTCAGATTATGAACTCCTTCTTCCTCTTCAAATG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* *
19862 AGTTCTTTAGACTATGAATTTCTTCTTCCTCTTCAGACG
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
* * *
19901 AGTTTTTCAGATTATGAACTCCTTCTT
1 AGTTCTTCAGACTATGAACTTCTTCTT
19928 GAAATGTTTT
Statistics
Matches: 228, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
38 2 0.01
39 224 0.98
40 2 0.01
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (39 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACG
Found at i:19748 original size:78 final size:78
Alignment explanation
Indices: 19628--19927 Score: 492
Period size: 78 Copynumber: 3.8 Consensus size: 78
19618 AGGTTGAATA
* *
19628 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTTAGATGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
* *
19693 TCTTCTTCATATG
66 TCCTCTTCAAATG
* *
19706 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCTTTTT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
* *
19771 TCCTCTTCAGACG
66 TCCTCTTCAAATG
*
19784 AGTTCTTCAGACTATGAACTTCTTCTTTCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
19849 TCCTCTTCAAATG
66 TCCTCTTCAAATG
* * *
19862 AGTTCTTTAGACTATGAATTTCTTCTTCCTCTTCAGACGAGTTTTTCAGATTATGAACTCCTTCT
1 AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
19927 T
66 T
19928 GAAATGTTTT
Statistics
Matches: 206, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 206 1.00
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (78 bp):
AGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCAGATTATGAACTCCTTCT
TCCTCTTCAAATG
Found at i:20053 original size:73 final size:73
Alignment explanation
Indices: 19932--20192 Score: 425
Period size: 73 Copynumber: 3.6 Consensus size: 73
19922 CTTCTTGAAA
* ** *
19932 TGTTTTAAGAAAAACAATCTTAAGTGAGATAAATTGCTATTTTGAGTGAAACTTTCTTCAACGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
*
19997 AAACAGTT
66 AAACAATT
* *
20005 TGTTTTAAGAAAAACAATGTCAAGTGAGATAAATTGTTATTTCAAGTGAAACTTTC-TCTAGCGA
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTC-AGCGA
20069 GAAACAATT
65 GAAACAATT
*
20078 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGAG
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
20143 AAACAATT
66 AAACAATT
*
20151 GGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
20193 GAAAACATCC
Statistics
Matches: 175, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
72 2 0.01
73 172 0.98
74 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (73 bp):
TGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTTCAGCGAG
AAACAATT
Found at i:20906 original size:22 final size:22
Alignment explanation
Indices: 20881--20935 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
20871 AATAAAGCTT
20881 TCATCTTTGAAAAAAGAATCTA
1 TCATCTTTGAAAAAAGAATCTA
* *
20903 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAAAGAATCTA
20925 TCATCTTTGAA
1 TCATCTTTGAA
20936 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAAAGAATCTA
Found at i:21398 original size:54 final size:54
Alignment explanation
Indices: 21304--21452 Score: 226
Period size: 54 Copynumber: 2.8 Consensus size: 54
21294 ATAATCAATG
* *
21304 GTTCATAAAATATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
* * *
21358 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
* * *
21412 GGTCGTAAAACATTTAACAACACATTCATCATTTCTTGTGG
1 GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGG
21453 CTTTTGCTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 86 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGTTTCTGCACAGAT
Found at i:23663 original size:15 final size:13
Alignment explanation
Indices: 23641--23679 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
23631 CAATTTTTTT
23641 TTTTTCTTCTTTCC
1 TTTTTCTTCTTT-C
23655 TTTTCTCTT-TTTC
1 TTTT-TCTTCTTTC
23668 TTTTTCTTCTTT
1 TTTTTCTTCTTT
23680 TTCATATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 7 0.30
15 4 0.17
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTCTTTC
Found at i:23672 original size:6 final size:6
Alignment explanation
Indices: 23635--23721 Score: 51
Period size: 6 Copynumber: 14.7 Consensus size: 6
23625 TTAATTCAAT
*
23635 TTTTTT TTTTTC TTCTTTCC TTTTCTC TTTTTC TTTTTC ---TTC TTTTTC
1 TTTTTC TTTTTC TT-TTT-C TTTT-TC TTTTTC TTTTTC TTTTTC TTTTTC
* * *
23683 ATATGT- TTTTTC TTTTT- TTATTTC -TTCTC TTTTTC TTTT
1 -TTTTTC TTTTTC TTTTTC TT-TTTC TTTTTC TTTTTC TTTT
23722 CTGATGAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 22
0.68 0.08 0.24
Matches are distributed among these distances:
3 3 0.05
5 8 0.13
6 35 0.56
7 13 0.21
8 4 0.06
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:26683 original size:16 final size:16
Alignment explanation
Indices: 26662--26692 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26652 GAAATCCTTA
26662 TTTTAATGAATGATTG
1 TTTTAATGAATGATTG
*
26678 TTTTAATGCATGATT
1 TTTTAATGAATGATT
26693 TGGAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (16 bp):
TTTTAATGAATGATTG
Found at i:28627 original size:63 final size:63
Alignment explanation
Indices: 28524--28659 Score: 150
Period size: 63 Copynumber: 2.1 Consensus size: 63
28514 TATATATACG
* ** * ** *
28524 GTGACTAAGTTATAAATAAAATAAAATTCGAATACTGAATTAAAATATATGGAAATTTATTGTA
1 GTGACTAAATTATAAATAAAATAAAATTAAAATAC-GAATTAAAACATATAAAAATTGATTGTA
*
28588 GTGACTAAATTAT-AATAAAATAAAATTAAAAGGTA-GAATTAAAACATATAAAAATTGATTTTA
1 GTGACTAAATTATAAATAAAATAAAATTAAAA--TACGAATTAAAACATATAAAAATTGATTGTA
*
28651 GTGGCTAAA
1 GTGACTAAA
28660 ATAGAAGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
63 47 0.77
64 12 0.20
65 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.32
Consensus pattern (63 bp):
GTGACTAAATTATAAATAAAATAAAATTAAAATACGAATTAAAACATATAAAAATTGATTGTA
Found at i:30454 original size:18 final size:18
Alignment explanation
Indices: 30433--30477 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
30423 AGATCCACCT
30433 CCACCTCCACCACCCCCG
1 CCACCTCCACCACCCCCG
30451 CCACCTCCACCACCCCCG
1 CCACCTCCACCACCCCCG
*
30469 CCGCCTCCA
1 CCACCTCCA
30478 AGCCCTCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.71, G:0.07, T:0.07
Consensus pattern (18 bp):
CCACCTCCACCACCCCCG
Found at i:37869 original size:20 final size:20
Alignment explanation
Indices: 37834--37871 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37824 GGTAGCTTAC
*
37834 GATTTTTTATCATTGTTTAT
1 GATTTTTTACCATTGTTTAT
*
37854 GATTTTTTACCGTTGTTT
1 GATTTTTTACCATTGTTT
37872 TTGTTTATCT
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:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (20 bp):
GATTTTTTACCATTGTTTAT
Found at i:38746 original size:50 final size:50
Alignment explanation
Indices: 38665--38768 Score: 118
Period size: 50 Copynumber: 2.1 Consensus size: 50
38655 ACAGGCGCGT
* * ** * *
38665 CTTCTACTAATGTGGCAACCTGCTTGATAAGCGCGTTGTAAAGGGCGCAC
1 CTTCTACTAATGTGACAACCTACCCGATAAGCGCGTTGTAAAGGACACAC
* * * *
38715 CTTCTGCTAATGTGACAACCTACCCGGTAAGCGCTTTGTACAGGACACAC
1 CTTCTACTAATGTGACAACCTACCCGATAAGCGCGTTGTAAAGGACACAC
38765 CTTC
1 CTTC
38769 CCTCATTCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (50 bp):
CTTCTACTAATGTGACAACCTACCCGATAAGCGCGTTGTAAAGGACACAC
Found at i:39610 original size:19 final size:19
Alignment explanation
Indices: 39579--39635 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
39569 TTTCATACAT
*
39579 TAAAA-ATTGAAATATTCAA
1 TAAAATATT-AAATATTAAA
39598 TAAAATATTAAATATTTAAA
1 TAAAATATTAAATA-TTAAA
39618 TAAACATAATTAAATATT
1 TAAA-AT-ATTAAATATT
39636 TTTACCATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
19 10 0.30
20 11 0.33
21 4 0.12
22 8 0.24
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAAATATTAAATATTAAA
Found at i:39780 original size:14 final size:14
Alignment explanation
Indices: 39732--39780 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
39722 AAAATTAGTA
39732 ATTAAAATAAACTA-
1 ATTAAAATAAA-TAT
*
39746 A-TAAAATAAAAAAT
1 ATTAAAAT-AAATAT
39760 ATT-AAATAAATAT
1 ATTAAAATAAATAT
39773 ATTAAAAT
1 ATTAAAAT
39781 TAAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 15 0.52
14 13 0.45
15 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAATAT
Found at i:40085 original size:30 final size:30
Alignment explanation
Indices: 40029--40085 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
40019 CATATTGTCA
*
40029 TAAAGGATACTATTTTGATATATATTAGAC
1 TAAAGGATACTATTTTGATACATATTAGAC
* *
40059 TAAAGG-TTCTATTTTGGTACATTATTA
1 TAAAGGATACTATTTTGATACA-TATTA
40086 TTTTTTGAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (30 bp):
TAAAGGATACTATTTTGATACATATTAGAC
Found at i:40469 original size:31 final size:31
Alignment explanation
Indices: 40434--40500 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
40424 AACAAATCAA
*
40434 TCACTAACAATATCGATTTATAACAAAATGG
1 TCACTAACAATATCAATTTATAACAAAATGG
** *
40465 TCACTAACGTTATCAATTTGTAACAAAATGG
1 TCACTAACAATATCAATTTATAACAAAATGG
40496 TCACT
1 TCACT
40501 CAACCGTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (31 bp):
TCACTAACAATATCAATTTATAACAAAATGG
Found at i:45894 original size:11 final size:11
Alignment explanation
Indices: 45878--45909 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
45868 CGACCGCACT
45878 TGCATCAAACA
1 TGCATCAAACA
45889 TGCATCAAACA
1 TGCATCAAACA
45900 TGCATCAAAC
1 TGCATCAAAC
45910 CAAGAAAGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.28, G:0.09, T:0.19
Consensus pattern (11 bp):
TGCATCAAACA
Found at i:48766 original size:28 final size:28
Alignment explanation
Indices: 48726--48791 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
48716 ATAATAATAG
48726 ATGCCAATATCTGGCCTCGGATAGGTTC
1 ATGCCAATATCTGGCCTCGGATAGGTTC
48754 ATGCCAATATCTGGCCTCGGATAGGTTC
1 ATGCCAATATCTGGCCTCGGATAGGTTC
48782 ATGCCAATAT
1 ATGCCAATAT
48792 TGACCAGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (28 bp):
ATGCCAATATCTGGCCTCGGATAGGTTC
Found at i:58764 original size:354 final size:348
Alignment explanation
Indices: 58132--58768 Score: 981
Period size: 348 Copynumber: 1.8 Consensus size: 348
58122 TTTTAGCAGT
* * * * * *
58132 GCGACGTTATTATATAAAAGGGTAAAGTACTCAGTTGACCACTTAACTATTTAATCTTTTTGCTC
1 GCGACATTATTATATAAAAGGGTAAACTACACAGTTGACCACTTAACTATTTAACCCTTTTACTC
* * *
58197 TTACTACTGATCTTTCAATTTTATCAACCACATCAATTAACTATTTTATTTGTTCAATCAGACAG
66 TTACTACTGATCTTTCAATTTTATCAACCACACCAATTAACTATTTAATTTGTTCAATCAGACAA
58262 CTAGCCATTAATAATTAACGAAAATGTAGCAGTTAAAAGAATTGATATATTTTTACATTTAGTCC
131 CTAGCCATTAATAATTAACGAAAATGTAGCAGTTAAAAGAATTGATATATTTTTACATTTAGTCC
* *
58327 TTAATATTTATATATTATCTCAATTTGGTCATAAATTAATTTTAATTTAATAAATTAACTATTCA
196 TTAATATTTATATATTATCTCAATTTGGTCATAAATTAAATTAAATTTAATAAATTAACTATTCA
58392 ATCAAGATTTGACATGTGTCAGCACAAGAGGTGACACGTGTAACCAACTAATTGGATAGAACTAC
261 ATCAAGATTTGACATGTGTCAGCACAAGAGGTGACACGTGTAACCAACTAATTGGATAGAACTAC
58457 TCAGTAGTTTTAGCAGTAGTTGA
326 TCAGTAGTTTTAGCAGTAGTTGA
58480 GCGACATTATTATATAAAAGGGTAAACTACACAGTTGACCACTTAACTATTTAACCCTTTTACT-
1 GCGACATTATTATATAAAAGGGTAAACTACACAGTTGACCACTTAACTATTTAACCCTTTTACTC
** * * * *
58544 TTTGTCACTTATCTTTTAATTTTGTCAACCACACCACTTAACTATTTAATTTGTTCAATCAGACA
66 TTACT-ACTGATCTTTCAATTTTATCAACCACACCAATTAACTATTTAATTTGTTCAATCAGACA
* * * *
58609 ACTAGCCATTAATATTTAACGAAAATATTGATGTGGTAGTTAAAAGAATTGATATATTTTTATAT
130 ACTAGCCATTAATAATTAACG--AA-A---ATGTAGCAGTTAAAAGAATTGATATATTTTTACAT
* *
58674 TTAGTTCTTAATATTTATATATTCTCTCAATTTGGTCATAAATTAAATTAAATTTAATAAATTAA
189 TTAGTCCTTAATATTTATATATTATCTCAATTTGGTCATAAATTAAATTAAATTTAATAAATTAA
58739 -TCATTCAATCAAGATTTGACATGTGTCAGC
254 CT-ATTCAATCAAGATTTGACATGTGTCAGC
58769 GTAGGAGCAT
Statistics
Matches: 258, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
347 3 0.01
348 130 0.50
350 2 0.01
351 1 0.00
353 1 0.00
354 121 0.47
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (348 bp):
GCGACATTATTATATAAAAGGGTAAACTACACAGTTGACCACTTAACTATTTAACCCTTTTACTC
TTACTACTGATCTTTCAATTTTATCAACCACACCAATTAACTATTTAATTTGTTCAATCAGACAA
CTAGCCATTAATAATTAACGAAAATGTAGCAGTTAAAAGAATTGATATATTTTTACATTTAGTCC
TTAATATTTATATATTATCTCAATTTGGTCATAAATTAAATTAAATTTAATAAATTAACTATTCA
ATCAAGATTTGACATGTGTCAGCACAAGAGGTGACACGTGTAACCAACTAATTGGATAGAACTAC
TCAGTAGTTTTAGCAGTAGTTGA
Found at i:60579 original size:20 final size:21
Alignment explanation
Indices: 60554--60646 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
60544 TTTTCCCAAT
*
60554 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
60574 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
60595 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
60615 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
60636 TCGCAATGCGA
1 TCGCAATGCGA
60647 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:60599 original size:41 final size:41
Alignment explanation
Indices: 60554--60646 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
60544 TTTTCCCAAT
60554 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
60595 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
60636 TCGCAATGCGA
1 TCGCAATGCGA
60647 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:60659 original size:41 final size:41
Alignment explanation
Indices: 60573--60707 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
60563 GAATAAGTAA
* *
60573 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
60614 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
60655 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
60696 TTCGCAACGCGA
1 ATCGCAACGCGA
60708 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:60660 original size:20 final size:20
Alignment explanation
Indices: 60635--60729 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
60625 AATTGGGAAA
*
60635 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
60655 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
60676 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
60696 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
60716 TTCGCAACGCGATA
1 ATCGCAACGCGATA
60730 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:60945 original size:22 final size:22
Alignment explanation
Indices: 60917--60960 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
60907 CACTCTCACA
60917 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
60939 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
60961 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:62599 original size:18 final size:18
Alignment explanation
Indices: 62578--62622 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
62568 TCCACTTCGG
*
62578 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
62596 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
62614 GAGCCATCA
1 GAGCCATCA
62623 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:63158 original size:19 final size:20
Alignment explanation
Indices: 63104--63169 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
63094 TAGTTTACTT
* *
63104 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
63124 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* *
63144 TCGCAATGC-GAAATGA-AA
1 TCGCAACGCGGAAATGACTA
63162 TCGCAACG
1 TCGCAACG
63170 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.21
19 6 0.15
20 25 0.64
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:63178 original size:14 final size:14
Alignment explanation
Indices: 63159--63215 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
63149 ATGCGAAATG
*
63159 AAATCGCAACGACA
1 AAATCGCAACGAAA
63173 AAATCGCAATGCGAAA
1 AAATCGCAA--CGAAA
63189 TGAAATCGCAACGAAA
1 --AAATCGCAACGAAA
63205 AAATCGCAACG
1 AAATCGCAACG
63216 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 20 0.53
16 9 0.24
18 9 0.24
ACGTcount: A:0.49, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGAAA
Found at i:63184 original size:32 final size:32
Alignment explanation
Indices: 63143--63232 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
63133 GGAAATGGCT
*
63143 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
63175 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAATCGCAACGAAAAA
*
63207 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
63233 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 46 0.84
33 9 0.16
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGAAAAA
Found at i:63268 original size:14 final size:14
Alignment explanation
Indices: 63249--63306 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
63239 TTGTGTTTCG
63249 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
63263 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
63279 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
63295 CGTTGAGATTTT
1 CGTTGCGATTTT
63307 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.16, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:63283 original size:32 final size:33
Alignment explanation
Indices: 63244--63322 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
63234 GCGATTTGTG
*
63244 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
63276 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
*
63309 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
63323 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGAGATTTTCA
Found at i:63341 original size:20 final size:19
Alignment explanation
Indices: 63307--63361 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
63297 TTGAGATTTT
*
63307 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
63326 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
63346 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
63362 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:65388 original size:19 final size:19
Alignment explanation
Indices: 65366--65433 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
65356 ATCGCAACGA
65366 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
65385 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
65404 GAAAATCACAA--CG--A-
1 GAAAATCGCAATGCGAAAT
65418 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
65434 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:65509 original size:20 final size:20
Alignment explanation
Indices: 65452--65509 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
65442 TCGCATTGCG
* *
65452 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
65472 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
65492 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
65510 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:66596 original size:24 final size:24
Alignment explanation
Indices: 66569--66622 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
66559 GTATTCGAAA
* *
66569 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
66593 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
66617 TTTGAT
1 TTTGAT
66623 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:66814 original size:12 final size:12
Alignment explanation
Indices: 66797--66821 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66787 ATATAATCCT
66797 GAAGAAGAAAAA
1 GAAGAAGAAAAA
66809 GAAGAAGAAAAA
1 GAAGAAGAAAAA
66821 G
1 G
66822 TCCCCTAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:69129 original size:19 final size:19
Alignment explanation
Indices: 69107--69171 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
69097 GGAAATTACT
69107 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
69126 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
69140 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
69159 ATCGCAACGCGAA
1 ATCGCAATGCGAA
69172 TTTAATTTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:69130 original size:39 final size:36
Alignment explanation
Indices: 69087--69169 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 36
69077 CTTAATGTCT
*
69087 ATCGCAACGCGGAAATTACTATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAA-GA--ATCGCAATGCGAAATGAAA
*
69126 ATCGCAA--C-GAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
69159 ATCGCAACGCG
1 ATCGCAACGCG
69170 AATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
33 26 0.67
35 2 0.05
36 3 0.08
37 1 0.03
39 7 0.18
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (36 bp):
ATCGCAACGCGGAAAGAATCGCAATGCGAAATGAAA
Found at i:69189 original size:19 final size:20
Alignment explanation
Indices: 69167--69210 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
69157 AAATCGCAAC
69167 GCGA-ATTTAATTTCGCGTT
1 GCGATATTTAATTTCGCGTT
* *
69186 GCGATTTTTATTTTCGCGTT
1 GCGATATTTAATTTCGCGTT
69206 GCGAT
1 GCGAT
69211 TCTCTCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.45
Consensus pattern (20 bp):
GCGATATTTAATTTCGCGTT
Found at i:69200 original size:20 final size:20
Alignment explanation
Indices: 69172--69211 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
69162 GCAACGCGAA
69172 TTTAATTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
*
69192 TTTATTTTCGCGTTGCGATT
1 TTTAATTTCGCGTTGCGATT
69212 CTCTCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (20 bp):
TTTAATTTCGCGTTGCGATT
Found at i:69369 original size:14 final size:14
Alignment explanation
Indices: 69350--69386 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
69340 CATCAATTAA
69350 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
69364 ACAAATCACCTTTT
1 ACAAATCAACTTTT
69378 ACAAATCAA
1 ACAAATCAA
69387 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:70811 original size:21 final size:21
Alignment explanation
Indices: 70745--70811 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
70735 GTGAATCGGG
*
70745 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
70765 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
70787 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
70808 CTCT
1 CTCT
70812 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:72950 original size:33 final size:33
Alignment explanation
Indices: 72893--72991 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
72883 ACGAGATAAT
*
72893 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
72927 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
72960 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
72992 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:72985 original size:19 final size:19
Alignment explanation
Indices: 72868--73052 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
72858 TCTTTTGGTT
* *
72868 GAAATGAAATTCGCAACGA
1 GAAATGAAAATCGCAACGC
*
72887 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
72907 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
72925 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
72941 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
72959 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
72974 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
72994 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
73013 GAAATGAAAATTGCAACGC
1 GAAATGAAAATCGCAACGC
*
73032 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
73051 GA
1 GA
73053 TTTTGGTTTC
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 60 0.44
20 44 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:73006 original size:39 final size:38
Alignment explanation
Indices: 72963--73052 Score: 144
Period size: 39 Copynumber: 2.3 Consensus size: 38
72953 GCGACCAGAC
72963 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
* *
73002 AATCGCAACGCGAAATGAAAATTGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
73040 AATCGCAATGCGA
1 AATCGCAACGCGA
73053 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:73081 original size:19 final size:19
Alignment explanation
Indices: 73048--73148 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 19
73038 AAAATCGCAA
**
73048 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
73067 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
73086 TGCGA---TTA--TCTCGT
1 TGCGATTTTTATTTCGCGT
** *
73100 TGCGATAGTTATTTCCTCGT
1 TGCGATTTTTATTT-CGCGT
**
73120 TGCGATAGTTATTTACGCGT
1 TGCGATTTTTATTT-CGCGT
73140 TGCGATTTT
1 TGCGATTTT
73149 CATTCTCGAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 23 0.33
20 30 0.43
ACGTcount: A:0.13, C:0.17, G:0.24, T:0.47
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:73120 original size:20 final size:20
Alignment explanation
Indices: 73095--73145 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
73085 TTGCGATTAT
*
73095 CTCGTTGCGATAGTTATTTC
1 CTCGTTGCGATAGTTATTTA
73115 CTCGTTGCGATAGTTATTTA
1 CTCGTTGCGATAGTTATTTA
*
73135 CGCGTTGCGAT
1 CTCGTTGCGAT
73146 TTTCATTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.41
Consensus pattern (20 bp):
CTCGTTGCGATAGTTATTTA
Found at i:73693 original size:20 final size:20
Alignment explanation
Indices: 73668--73720 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
73658 GCGCTATGTA
*
73668 AATCGCGTTGCGAAATTCAG
1 AATCGCGTTGCGAAAGTCAG
*
73688 AATCGCGTTGCGCAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
73708 TATCTCGTTGCGA
1 AATCGCGTTGCGA
73721 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:73781 original size:41 final size:41
Alignment explanation
Indices: 73731--73843 Score: 138
Period size: 41 Copynumber: 2.8 Consensus size: 41
73721 TTTTGTATTA
*
73731 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAAT
* ** *
73772 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCGCAAT
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
* **
73813 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCGTTGCGATGTAAGTATTCGCATTGCGA
73844 ATTGGAAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 4 0.06
41 62 0.94
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATGTAAGTATTCGCATTGCGATTTTCCCAAT
Found at i:73795 original size:20 final size:20
Alignment explanation
Indices: 73751--73843 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
73741 ATAGTAAGTA
* **
73751 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
73772 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
73792 TCGCATTGCGATTTTCGCAAT
1 TCGCATTGCGATTTAC-TTAT
*
73813 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
73833 TCGCATTGCGA
1 TCGCATTGCGA
73844 ATTGGAAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:78932 original size:13 final size:13
Alignment explanation
Indices: 78914--78939 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
78904 TTGCTGGTGA
78914 CCAAAATGTAAGT
1 CCAAAATGTAAGT
78927 CCAAAATGTAAGT
1 CCAAAATGTAAGT
78940 TTTGAAAGTT
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:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
CCAAAATGTAAGT
Found at i:81884 original size:21 final size:21
Alignment explanation
Indices: 81858--81913 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
81848 TTCTGGGCAG
81858 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
81879 AGTGCATCGATGCACATTCAT
1 AGTGCATCGATGCACATTCAT
81900 AGTGCATCGATGCA
1 AGTGCATCGATGCA
81914 TCAAGGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (21 bp):
AGTGCATCGATGCACATTCAT
Found at i:82017 original size:64 final size:64
Alignment explanation
Indices: 81948--82106 Score: 187
Period size: 64 Copynumber: 2.5 Consensus size: 64
81938 TTGAAGGTGT
** ***
81948 ATCGATGCATTGGTAGTGCATCGATGCACT-CTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAAGTAGTGCATCGATGCA-TACCAGTAATAAT-AAAACATCGAATGCAATTCATG
82011 C
64 C
* * *
82012 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATACAACATCGAATGCATTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
* * *
82076 ACCGATGCATCAGTAGTGCATCGATGTATAC
1 ATCGATGCATAAGTAGTGCATCGATGCATAC
82107 TTTCATTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 78 0.95
65 3 0.04
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATACCAGTAATAATAAAACATCGAATGCAATTCATGC
Found at i:82799 original size:31 final size:31
Alignment explanation
Indices: 82761--82851 Score: 132
Period size: 31 Copynumber: 2.9 Consensus size: 31
82751 GGGGTCGAGG
*
82761 GTTTACCTATGTTCTTCGTGACATAT-GAACT
1 GTTTACCTATGTTCTTCGGGACATATGGAA-T
82792 GTTTACCTATGTTCTTCGGGACATATGGAAT
1 GTTTACCTATGTTCTTCGGGACATATGGAAT
*
82823 GTTTACCTAGGTTCTTCGGGATC-TATGGA
1 GTTTACCTATGTTCTTCGGGA-CATATGGA
82852 CTGGTCCTTC
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
31 52 0.93
32 4 0.07
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGAAT
Found at i:84624 original size:18 final size:19
Alignment explanation
Indices: 84587--84653 Score: 70
Period size: 18 Copynumber: 3.7 Consensus size: 19
84577 AAAATAGAAA
84587 CATCGAATGCA-ATTAGTG
1 CATCGAATGCATATTAGTG
*
84605 CATCGAATGCATTTTA-TG
1 CATCGAATGCATATTAGTG
* *
84623 CACCG-ATGCATCAGTAGTG
1 CATCGAATGCAT-ATTAGTG
84642 CATCG-ATGCATA
1 CATCGAATGCATA
84654 CTTTCATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
17 6 0.15
18 20 0.49
19 15 0.37
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (19 bp):
CATCGAATGCATATTAGTG
Found at i:85802 original size:31 final size:31
Alignment explanation
Indices: 85725--85859 Score: 150
Period size: 31 Copynumber: 4.4 Consensus size: 31
85715 GCCAAGAGTC
85725 GACAGTATACCTATGTTCTACGGAACATATG
1 GACAGTATACCTATGTTCTACGGAACATATG
* *
85756 GACAGAATTACCTATG-TCTTTC-GAGACATATG
1 GACAGTA-TACCTATGTTC-TACGGA-ACATATG
* *
85788 GATAGTATACCTATGTTCTAAGGAACATATG
1 GACAGTATACCTATGTTCTACGGAACATATG
* * * *
85819 GACAGTTTACCTAGGTTCTTCGGAACCTATG
1 GACAGTATACCTATGTTCTACGGAACATATG
85850 GACAGT-TACC
1 GACAGTATACC
85860 GAGGATCTTT
Statistics
Matches: 87, Mismatches: 12, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
30 4 0.05
31 57 0.66
32 26 0.30
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (31 bp):
GACAGTATACCTATGTTCTACGGAACATATG
Found at i:85876 original size:30 final size:31
Alignment explanation
Indices: 85810--85868 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
85800 ATGTTCTAAG
* * * *
85810 GAACATATGGACAGTTTACCTAGGTTCTTCG
1 GAACCTATGGACAGTTTACCGAGGATCTTCA
85841 GAACCTATGGACAG-TTACCGAGGATCTT
1 GAACCTATGGACAGTTTACCGAGGATCTT
85869 TATAACCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (31 bp):
GAACCTATGGACAGTTTACCGAGGATCTTCA
Done.