Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003700.1 Hibiscus syriacus cultivar Beakdansim tig00007914_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: 92510
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:14007 original size:46 final size:46
Alignment explanation
Indices: 13940--14033 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
13930 AAAAGCTTCC
*
13940 TCGGGTGATTTGTCTAGTAGGGTGCCATTTGCTGAGGCATCTAGCA
1 TCGGGTGATTTGTCTAGTAGGGTGCCATTTGCTGAGGCATATAGCA
13986 TCGGGTGATTTGTCTAGTAGGGTGCCATTTGCTGAGGCATATAGCA
1 TCGGGTGATTTGTCTAGTAGGGTGCCATTTGCTGAGGCATATAGCA
14032 TC
1 TC
14034 ATTCGAGTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.18, C:0.17, G:0.32, T:0.33
Consensus pattern (46 bp):
TCGGGTGATTTGTCTAGTAGGGTGCCATTTGCTGAGGCATATAGCA
Found at i:15040 original size:21 final size:19
Alignment explanation
Indices: 15002--15047 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
14992 AATTAATCCT
15002 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
15022 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
15043 A-TAAT
1 ACTAAT
15048 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:15957 original size:95 final size:95
Alignment explanation
Indices: 15786--16006 Score: 273
Period size: 95 Copynumber: 2.3 Consensus size: 95
15776 GAACGAAGTG
* * * *
15786 GTATTGATACCATGGTAAGGGTATTGATACCGGGCAACATCGAACCTAATTTTGGTATCGATACC
1 GTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACCTAATTTTGGTATCGATACC
* ** ** *
15851 ATATAGGGGTATCGGTACCATTGTATAGTA
66 AGATAGGGGTATCGCAACCAAAGTAGAGTA
* * * *
15881 GTATCGATACCATGGTAAGGGTATCGATACTGGACCACATCGAATCTAATTTTGGTATTGATACT
1 GTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACCTAATTTTGGTATCGATACC
* *
15946 GGA-AGGAGGTATCGCAACCAAAGTAGGGTA
66 AGATAGG-GGTATCGCAACCAAAGTAGAGTA
*
15976 GTATCGATACCATGGTAGGGGTATCGATACT
1 GTATCGATACCATGGTAAGGGTATCGATACT
16007 AAAGGGCCAG
Statistics
Matches: 108, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 3 0.03
95 105 0.97
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (95 bp):
GTATCGATACCATGGTAAGGGTATCGATACTGGACAACATCGAACCTAATTTTGGTATCGATACC
AGATAGGGGTATCGCAACCAAAGTAGAGTA
Found at i:15987 original size:22 final size:20
Alignment explanation
Indices: 15953--16010 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 20
15943 ACTGGAAGGA
15953 GGTATCGCA-ACCAAAGTAGG
1 GGTATCG-ATACCAAAGTAGG
**
15973 GTAGTATCGATACCATGGTAGG
1 G--GTATCGATACCAAAGTAGG
*
15995 GGTATCGATACTAAAG
1 GGTATCGATACCAAAG
16011 GGCCAGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
20 13 0.43
21 1 0.03
22 16 0.53
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (20 bp):
GGTATCGATACCAAAGTAGG
Found at i:16511 original size:45 final size:45
Alignment explanation
Indices: 16456--16581 Score: 171
Period size: 45 Copynumber: 2.8 Consensus size: 45
16446 TGCAATAGTT
*
16456 GAAATGTATATGGATACATTTTCAACATAAAAGTATACTAAAATG
1 GAAATGTATATGGGTACATTTTCAACATAAAAGTATACTAAAATG
* * * * *
16501 GAAATATATATGGGTACATTTTCAACAGAAAAGTATACTATAGTT
1 GAAATGTATATGGGTACATTTTCAACATAAAAGTATACTAAAATG
* * *
16546 GAAATGCATATGGGTGCATTATCAACATAAAAGTAT
1 GAAATGTATATGGGTACATTTTCAACATAAAAGTAT
16582 GGTATAGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.44, C:0.10, G:0.16, T:0.31
Consensus pattern (45 bp):
GAAATGTATATGGGTACATTTTCAACATAAAAGTATACTAAAATG
Found at i:16588 original size:45 final size:45
Alignment explanation
Indices: 16450--16601 Score: 169
Period size: 45 Copynumber: 3.4 Consensus size: 45
16440 GAAGGATGCA
* * *
16450 ATAGTTGAAATGTATATGGATACATTTTCAACATAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACATAAAAGTATACT
* * * ** * *
16495 AAAATGGAAATATATATGGGTACATTTTCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACATAAAAGTATACT
* **
16540 ATAGTTGAAATGCATATGGGTGCATTATCAACATAAAAGTATGGT
1 ATAGTTGAAATGCATATGGGTACATTATCAACATAAAAGTATACT
*
16585 ATAGTTTAAAGTGCATA
1 ATAGTTGAAA-TGCATA
16602 ATGGTGTATT
Statistics
Matches: 89, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
45 83 0.93
46 6 0.07
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGCATATGGGTACATTATCAACATAAAAGTATACT
Found at i:22751 original size:22 final size:20
Alignment explanation
Indices: 22720--22778 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
22710 ATACCGGAAG
22720 GGGGTATCGATACCAAAGTA
1 GGGGTATCGATACCAAAGTA
**
22740 GGGTAGTATCGATA-CATGGTA
1 GGG--GTATCGATACCAAAGTA
*
22761 GGGGTATCGATACTAAAG
1 GGGGTATCGATACCAAAG
22779 GGCTAGAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 9 0.29
20 5 0.16
21 8 0.26
22 9 0.29
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (20 bp):
GGGGTATCGATACCAAAGTA
Found at i:22758 original size:94 final size:94
Alignment explanation
Indices: 22556--22775 Score: 234
Period size: 94 Copynumber: 2.3 Consensus size: 94
22546 GAACGAAGTG
* *
22556 GTATCGATACCATGGTGAGGGTATCAATAAC-AGGTAACATTGAACCTAATTTTGGTATTAATAC
1 GTATCGATACCATGGTAAGGGTATCAAT-ACTAGGTAACATCGAACCTAATTTTGGTATTAATAC
* *
22620 CATATAGGGTATCAGTACCAGAATATAGTA
65 CATAGAGGGTATCAGTACCAGAATAGAGTA
** * * * *
22650 GTATTTATACCATGGTAAGGGTATCAATACTGGGTCACATCGAATCTAATTTTGGTATTGATACC
1 GTATCGATACCATGGTAAGGGTATCAATACTAGGTAACATCGAACCTAATTTTGGTATTAATACC
* *
22715 GGA-AGGGGGTATC-GATACCA-AAGTAGGGTA
66 --ATAGAGGGTATCAG-TACCAGAA-TAGAGTA
* *
22745 GTATCGATA-CATGGTAGGGGTATCGATACTA
1 GTATCGATACCATGGTAAGGGTATCAATACTA
22776 AAGGGCTAGA
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
93 2 0.02
94 76 0.73
95 25 0.24
96 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.30
Consensus pattern (94 bp):
GTATCGATACCATGGTAAGGGTATCAATACTAGGTAACATCGAACCTAATTTTGGTATTAATACC
ATAGAGGGTATCAGTACCAGAATAGAGTA
Found at i:23304 original size:41 final size:41
Alignment explanation
Indices: 23259--23448 Score: 202
Period size: 41 Copynumber: 4.5 Consensus size: 41
23249 ATTCACGTTG
*
23259 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
* * *
23300 CATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
*** *
23341 CATTTCGCGTTGCGATAGTTG-AAATCGCAACGCGATCTCCATCATC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCG-T-T---T-TTC
* * *
23387 GCAAATTCGCGTTGCGATAGTTGAAAATCGCGTTGTGGTTTTC
1 -C-ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
23430 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
23449 CTACAGTTGT
Statistics
Matches: 122, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
40 9 0.07
41 75 0.61
42 2 0.02
43 2 0.02
44 1 0.01
45 1 0.01
46 2 0.02
47 2 0.02
48 19 0.16
49 9 0.07
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGTTTTTC
Found at i:23355 original size:20 final size:20
Alignment explanation
Indices: 23284--23356 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
23274 TAGTTGAAAA
*
23284 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
23304 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGAT-TTTCCATT
23325 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
23345 TCGCGTTGCGAT
1 TCGCGTTGCGAT
23357 AGTTGAAATC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.11, C:0.22, G:0.27, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:23368 original size:20 final size:21
Alignment explanation
Indices: 23263--23368 Score: 67
Period size: 20 Copynumber: 5.2 Consensus size: 21
23253 ACGTTGCATT
*
23263 TCGCATTGCGATAGTT-GAAAA
1 TCGCGTTGCGATAGTTCG-AAA
** * **
23284 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
23304 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * **
23325 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
23345 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
23365 TCGC
1 TCGC
23369 AACGCGATCT
Statistics
Matches: 61, Mismatches: 21, Indels: 7
0.69 0.24 0.08
Matches are distributed among these distances:
20 34 0.56
21 27 0.44
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:23564 original size:6 final size:6
Alignment explanation
Indices: 23553--23642 Score: 145
Period size: 6 Copynumber: 15.8 Consensus size: 6
23543 GACACGTATT
23553 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
23601 ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACCAC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCAC
23643 TATCACAACG
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
5 25 0.30
6 58 0.70
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:23672 original size:19 final size:19
Alignment explanation
Indices: 23648--23713 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
23638 ACCACTATCA
23648 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
23667 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
23689 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
23708 CAACGA
1 CAACGA
23714 CAACTGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 19 0.53
20 2 0.06
21 2 0.06
22 13 0.36
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:23690 original size:22 final size:22
Alignment explanation
Indices: 23663--23734 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
23653 AATTTGGAAA
23663 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
23685 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
23704 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
23726 ATCGCAACG
1 ATCGCAACG
23735 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 13 0.33
20 2 0.05
21 2 0.05
22 22 0.56
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:23698 original size:41 final size:41
Alignment explanation
Indices: 23641--23754 Score: 185
Period size: 41 Copynumber: 2.8 Consensus size: 41
23631 CGACCCGACC
*
23641 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
23682 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
*
23723 ACTATCGCAACGCGAA-ATGGAAAATCGCAACG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAACG
23755 CGAATTTCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
41 50 0.72
42 15 0.22
43 4 0.06
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
Found at i:23768 original size:41 final size:41
Alignment explanation
Indices: 23657--23864 Score: 248
Period size: 41 Copynumber: 5.0 Consensus size: 41
23647 ACAACGAATT
* *
23657 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAA-A
*
23698 TGGAAAATCGCAACGAC-AACTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGAA-TTTCA-ACTATCGCAACGCGAAA
*
23740 TGGAAAATCGCAACGCGAATTTCAACTATCACAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
*
23781 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
* *
23822 TGGAAAATCGCAATGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
23863 TG
1 TG
23865 CAACGCGAAT
Statistics
Matches: 157, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
41 135 0.86
42 18 0.11
43 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGAATTTCAACTATCGCAACGCGAAA
Found at i:23776 original size:21 final size:21
Alignment explanation
Indices: 23723--23861 Score: 113
Period size: 20 Copynumber: 6.8 Consensus size: 21
23713 ACAACTGTAG
* **
23723 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
*
23744 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAATTTCA
* * **
23764 ACTATCACAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* *
23785 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
* **
23805 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAATTTCA
* * *
23826 A-AATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAATTTCA
23846 ACTATCGCAACGCGAA
1 ACTATCGCAACGCGAA
23862 ATGCAACGCG
Statistics
Matches: 86, Mismatches: 29, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
20 44 0.51
21 42 0.49
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAATTTCA
Found at i:23868 original size:21 final size:21
Alignment explanation
Indices: 23723--23868 Score: 127
Period size: 21 Copynumber: 7.1 Consensus size: 21
23713 ACAACTGTAG
*
23723 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * *
23744 A-AATCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGCA
* *
23764 ACTATCACAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
23785 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
23805 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
23826 A-AATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
23846 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
23867 AC
1 AC
23869 GCGAATTTGC
Statistics
Matches: 91, Mismatches: 31, Indels: 6
0.71 0.24 0.05
Matches are distributed among these distances:
20 44 0.48
21 47 0.52
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:24255 original size:45 final size:45
Alignment explanation
Indices: 24117--24268 Score: 214
Period size: 45 Copynumber: 3.4 Consensus size: 45
24107 AAAGGATGCC
* * *
24117 ATAGTTGAAATGTATATGGATACATTTTCAATAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTTTCAACAGAAAAGTATACT
* *
24162 ATAATTGAAATGTATATGGGTACATTTTCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTTTCAACAGAAAAGTATACT
* * *
24207 ATAGTTGAAATGCATATGGGTGCATTATCAACAGATAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTTTCAACAGAAAAGTATACT
*
24252 ATAGTTTAAAGTGCATA
1 ATAGTTGAAA-TGCATA
24269 ATGATGTATT
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 91 0.94
46 6 0.06
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (45 bp):
ATAGTTGAAATGCATATGGGTACATTTTCAACAGAAAAGTATACT
Found at i:25710 original size:20 final size:20
Alignment explanation
Indices: 25685--25736 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
25675 CTAAAGGGAG
* *
25685 TAGTATCAATATTCTACTTA
1 TAGTATCAATACTATACTTA
*
25705 TAGTATCAATACTATACTTG
1 TAGTATCAATACTATACTTA
25725 TAGTATCAATAC
1 TAGTATCAATAC
25737 CCTAAGATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (20 bp):
TAGTATCAATACTATACTTA
Found at i:27024 original size:28 final size:29
Alignment explanation
Indices: 26993--27067 Score: 134
Period size: 29 Copynumber: 2.6 Consensus size: 29
26983 ATTATCTCAA
26993 TTTAATCTGAAATTAAATAT-ATTTTTTC
1 TTTAATCTGAAATTAAATATAATTTTTTC
27021 TTTAATCTGAAATTAAATATAATTTTTTC
1 TTTAATCTGAAATTAAATATAATTTTTTC
*
27050 TTTAATCTGAATTTAAAT
1 TTTAATCTGAAATTAAAT
27068 TTTATTTGGA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 20 0.44
29 25 0.56
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (29 bp):
TTTAATCTGAAATTAAATATAATTTTTTC
Found at i:27436 original size:3 final size:3
Alignment explanation
Indices: 27428--27484 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
27418 TACTGAGTGC
27428 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
27476 ATT ATT ATT
1 ATT ATT ATT
27485 TATGTTAATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27868 original size:30 final size:31
Alignment explanation
Indices: 27824--27897 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
27814 ATTAAAAAAA
*
27824 TAAGTTTT-GATCACTTACGCTATCA-TTTAT
1 TAAGTTTTAG-TCACTCACGCTATCATTTTAT
* * *
27854 TAAGTTTTAGTCACTCATGTTATGATTTTAT
1 TAAGTTTTAGTCACTCACGCTATCATTTTAT
*
27885 TAAGATTTAGTCA
1 TAAGTTTTAGTCA
27898 TTGAGATGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 19 0.51
31 18 0.49
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
TAAGTTTTAGTCACTCACGCTATCATTTTAT
Found at i:32806 original size:45 final size:45
Alignment explanation
Indices: 32735--32832 Score: 144
Period size: 45 Copynumber: 2.2 Consensus size: 45
32725 ATGTTGCATT
* *
32735 TTTATGTATCGGCACTATGTGCGCAACCCA-ATGAATTCATAATAAG
1 TTTATG-ATCGGCACTAAGAGCGCAACCCACA-GAATTCATAATAAG
*
32781 TTTATGATCGGCACTAAGAGTGCAACCCACAGAATTCATAATAAG
1 TTTATGATCGGCACTAAGAGCGCAACCCACAGAATTCATAATAAG
32826 TTTATGA
1 TTTATGA
32833 ACGACCGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
45 41 0.85
46 7 0.15
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (45 bp):
TTTATGATCGGCACTAAGAGCGCAACCCACAGAATTCATAATAAG
Found at i:32995 original size:54 final size:54
Alignment explanation
Indices: 32787--33101 Score: 323
Period size: 54 Copynumber: 5.8 Consensus size: 54
32777 TAAGTTTATG
* * *
32787 ATCGGCACTAAGAGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGT
1 ATCGACACTAAGTGTGCAACACACAGAATTCATAATAAGTTTATGAACGACCGT
* * * * ** * **
32841 ATCGGCA-AAAGTGAGTAAC-CTATGGAATTCATAATAAGTTTATGAACGATCAC
1 ATCGACACTAAGTGTGCAACAC-ACAGAATTCATAATAAGTTTATGAACGACCGT
* * * * *
32894 ATCGGCACTATGTGTGCAACCCACCCACGAAATTCATAATAACTTTATGAATGACCGT
1 ATCGACACTAAGTGTGCAA--CACACA-G-AATTCATAATAAGTTTATGAACGACCGT
* * *
32952 ATCGACACAAAGTGTGCAACACAAAGAATTCATAATAAGTTTATGAACGACTGT
1 ATCGACACTAAGTGTGCAACACACAGAATTCATAATAAGTTTATGAACGACCGT
* * *
33006 ATCGACACTAAGTGTGCAACCCACATAATTCATAATAAATTTATTG-ACGACCGT
1 ATCGACACTAAGTGTGCAACACACAGAATTCATAATAAGTTTA-TGAACGACCGT
*
33060 -TACGACACTAAGTGTGCAACTCACAGAATTCATAATAAGTTT
1 AT-CGACACTAAGTGTGCAACACACAGAATTCATAATAAGTTT
33102 GAGAGATGTA
Statistics
Matches: 214, Mismatches: 38, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
52 1 0.00
53 43 0.20
54 121 0.57
55 3 0.01
56 5 0.02
57 2 0.01
58 39 0.18
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (54 bp):
ATCGACACTAAGTGTGCAACACACAGAATTCATAATAAGTTTATGAACGACCGT
Found at i:33077 original size:108 final size:107
Alignment explanation
Indices: 32787--33101 Score: 359
Period size: 108 Copynumber: 2.9 Consensus size: 107
32777 TAAGTTTATG
* * * *
32787 ATCGGCACTAAGAGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCA-AAA
1 ATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAATTTATGAACGACCGTATCGACACAAA
* * **
32851 GTGAGTAACCTATGGAATTCATAATAAGTTTATGAACGATCAC
66 GTGTGCAACC-AAAGAATTCATAATAAGTTTATGAACGATCAC
* * *
32894 ATCGGCACTATGTGTGCAACCCACCCACGAAATTCATAATAACTTTATGAATGACCGTATCGACA
1 ATCGGCACTAAGTGTGCAACCCA--CA--AAATTCATAATAAATTTATGAACGACCGTATCGACA
**
32959 CAAAGTGTGCAACACAAAGAATTCATAATAAGTTTATGAACGA-CTGT
62 CAAAGTGTGCAAC-CAAAGAATTCATAATAAGTTTATGAACGATC-AC
* * *
33006 ATCGACACTAAGTGTGCAACCCACATAATTCATAATAAATTTATTG-ACGACCGT-TACGACACT
1 ATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAATTTA-TGAACGACCGTAT-CGACACA
*
33069 AAGTGTGCAACTCACAGAATTCATAATAAGTTT
64 AAGTGTGCAAC-CAAAGAATTCATAATAAGTTT
33102 GAGAGATGTA
Statistics
Matches: 179, Mismatches: 20, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
107 22 0.12
108 60 0.34
109 4 0.02
110 2 0.01
111 33 0.18
112 57 0.32
113 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (107 bp):
ATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAATTTATGAACGACCGTATCGACACAAA
GTGTGCAACCAAAGAATTCATAATAAGTTTATGAACGATCAC
Found at i:42731 original size:19 final size:19
Alignment explanation
Indices: 42697--42736 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42687 TAAAATTTCT
42697 CTTATGGTTTCGAAAAACC
1 CTTATGGTTTCGAAAAACC
*
42716 CTTATTGGTTTC-AAAACCC
1 CTTA-TGGTTTCGAAAAACC
42735 CT
1 CT
42737 AGATGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (19 bp):
CTTATGGTTTCGAAAAACC
Found at i:47915 original size:3 final size:3
Alignment explanation
Indices: 47900--47969 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
47890 TAAACACACT
*
47900 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
47948 TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
47970 TTTTTTAACT
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:48338 original size:91 final size:91
Alignment explanation
Indices: 48230--48401 Score: 283
Period size: 91 Copynumber: 1.9 Consensus size: 91
48220 GATAGGTCGA
* *
48230 ACAAGCTCTTCTCATTATGAACTTCTTCT-TCCTCATTGGATGAGTTCTTCTCATTATGAGCTCT
1 ACAAGCTCTTCTCATTATGAACTTATTCTCT-CTCATTGGATGAGTTCTTCTCATTATGAACTCT
48294 CCATTGAAAATGTTGATGCGAAGTTAG
65 CCATTGAAAATGTTGATGCGAAGTTAG
* *
48321 ACAAGTTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTTATTATGAACTCTC
1 ACAAGCTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTCATTATGAACTCTC
*
48386 CATTGGAAATGTTGAT
66 CATTGAAAATGTTGAT
48402 CCATCTCTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
91 74 0.99
92 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (91 bp):
ACAAGCTCTTCTCATTATGAACTTATTCTCTCTCATTGGATGAGTTCTTCTCATTATGAACTCTC
CATTGAAAATGTTGATGCGAAGTTAG
Found at i:49577 original size:21 final size:21
Alignment explanation
Indices: 49517--49577 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
49507 CATTTTTCTC
*
49517 TTTTCATTTTTTATTTCTTTT
1 TTTTCATTTTTTTTTTCTTTT
**
49538 TTTTCATTTTTTTCATCTTTT
1 TTTTCATTTTTTTTTTCTTTT
*
49559 TATTT-GTTTTTTTTTTCTT
1 T-TTTCATTTTTTTTTTCTT
49578 CAAGCATAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 30 0.91
22 3 0.09
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (21 bp):
TTTTCATTTTTTTTTTCTTTT
Found at i:62833 original size:3 final size:3
Alignment explanation
Indices: 62818--62878 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
62808 TAAACACACT
*
62818 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
62866 TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TA
62879 TTTTTTAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:76709 original size:35 final size:35
Alignment explanation
Indices: 76663--76738 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
76653 AACACAATCC
*
76663 TCAATTTCATTTTAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTTTAAACCCCAAATTCCAAAATAAT
* * *
76698 TCAATTACATTTTAAACCTCAAATTCTAAAATACT
1 TCAATTACATTTTAAACCCCAAATTCCAAAATAAT
76733 TCAATT
1 TCAATT
76739 TAGGGTTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTACATTTTAAACCCCAAATTCCAAAATAAT
Found at i:76781 original size:35 final size:35
Alignment explanation
Indices: 76735--76809 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
76725 AAAATACTTC
76735 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
*
76770 AATTTGGGGTTTAGAATGTAATTGAAGTATTTTGG
1 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
76805 AATTT
1 AATTT
76810 TGAACATGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
Found at i:78735 original size:35 final size:36
Alignment explanation
Indices: 78694--78768 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
78684 TTCATGTTCA
78694 AAATTCCAAAACACTTCAA-TTACATTCTAAACCCT
1 AAATTCCAAAACACTTCAAGTTACATTCTAAACCCT
* * *
78729 AAATTCCAAAATACTTCAAGTTCCATTCTAAATCCT
1 AAATTCCAAAACACTTCAAGTTACATTCTAAACCCT
78765 AAAT
1 AAAT
78769 CGAAGTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 18 0.50
36 18 0.50
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.31
Consensus pattern (36 bp):
AAATTCCAAAACACTTCAAGTTACATTCTAAACCCT
Found at i:81544 original size:31 final size:31
Alignment explanation
Indices: 81509--81569 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
81499 AAAACAGATA
81509 GATGACCAAAAC-GTAATCAAAGTAATAGTTT
1 GATGACCAAAACAG-AATCAAAGTAATAGTTT
81540 GATGACCAAAACAGAATCAAAGTAATAGTT
1 GATGACCAAAACAGAATCAAAGTAATAGTT
81570 GGGTGACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.48, C:0.13, G:0.16, T:0.23
Consensus pattern (31 bp):
GATGACCAAAACAGAATCAAAGTAATAGTTT
Found at i:87121 original size:21 final size:20
Alignment explanation
Indices: 87072--87146 Score: 107
Period size: 21 Copynumber: 3.7 Consensus size: 20
87062 TTTTTGGTGG
* *
87072 AAAGTTTCGAAACTTTTATA
1 AAAGTTTCAAAACTCTTATA
87092 AAA-TTTCAAAACTCTTATTA
1 AAAGTTTCAAAACTCTTA-TA
87112 AAAGTTTCAAAACTCTTAATA
1 AAAGTTTCAAAACTCTT-ATA
87133 AAAGTTTCAAAACT
1 AAAGTTTCAAAACT
87147 ATTACAAAGT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
19 12 0.24
20 8 0.16
21 29 0.58
22 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAGTTTCAAAACTCTTATA
Found at i:87157 original size:19 final size:18
Alignment explanation
Indices: 87072--87167 Score: 68
Period size: 21 Copynumber: 4.9 Consensus size: 18
87062 TTTTTGGTGG
* *
87072 AAAGTTTCGAAACTTTTA
1 AAAGTTTCAAAACTATTA
*
87090 TAAAATTTCAAAACTCTTATTA
1 -AAAGTTTCAAAA--C-TATTA
*
87112 AAAGTTTCAAAACTCTTAATA
1 AAAGTTTCAAAA--C-TATTA
87133 AAAGTTTCAAAACTATTA
1 AAAGTTTCAAAACTATTA
87151 CAAAGTTT-ACAAACTAT
1 -AAAGTTTCA-AAACTAT
87168 GAACAATAAC
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
18 5 0.08
19 25 0.38
21 32 0.48
22 4 0.06
ACGTcount: A:0.46, C:0.14, G:0.05, T:0.35
Consensus pattern (18 bp):
AAAGTTTCAAAACTATTA
Found at i:87165 original size:40 final size:39
Alignment explanation
Indices: 87072--87163 Score: 107
Period size: 40 Copynumber: 2.3 Consensus size: 39
87062 TTTTTGGTGG
* *
87072 AAAGTTTCGAAACTTTTATAAAATTTCAAAACTCTTATTA
1 AAAGTTTCAAAACTTTAATAAAATTTCAAAAC-CTTATTA
87112 AAAGTTTCAAAACTCTTAATAAAAGTTTCAAAA-C-TATTA
1 AAAGTTTCAAAACT-TTAATAAAA-TTTCAAAACCTTATTA
87151 CAAAGTTTACAAA
1 -AAAGTTT-CAAA
87164 CTATGAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
39 5 0.11
40 21 0.46
41 12 0.26
42 8 0.17
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (39 bp):
AAAGTTTCAAAACTTTAATAAAATTTCAAAACCTTATTA
Found at i:87173 original size:20 final size:19
Alignment explanation
Indices: 87112--87173 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
87102 ACTCTTATTA
* *
87112 AAAGTTTCAAAACTCTTAATA
1 AAAGTTTCAAAACT-ATAA-C
*
87133 AAAGTTTCAAAACTATTAC
1 AAAGTTTCAAAACTATAAC
87152 AAAGTTT-ACAAACTATGAAC
1 AAAGTTTCA-AAACTAT-AAC
87172 AA
1 AA
87174 TAACCATGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.03
19 14 0.40
20 6 0.17
21 14 0.40
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (19 bp):
AAAGTTTCAAAACTATAAC
Found at i:87265 original size:20 final size:20
Alignment explanation
Indices: 87242--87279 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
87232 TATTTAAAAA
*
87242 ACTTTAAAGACATTTTAAAC
1 ACTTTAAACACATTTTAAAC
*
87262 ACTTTAAACATATTTTAA
1 ACTTTAAACACATTTTAA
87280 TTAACTCAAA
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:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
ACTTTAAACACATTTTAAAC
Found at i:89087 original size:6 final size:6
Alignment explanation
Indices: 89076--89103 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
89066 AGATTCCAAA
89076 ATTCTC ATTCTC ATTCTC ATTCTC ATTC
1 ATTCTC ATTCTC ATTCTC ATTCTC ATTC
89104 ATAAAGTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCTC
Found at i:90296 original size:2 final size:2
Alignment explanation
Indices: 90291--90367 Score: 120
Period size: 2 Copynumber: 38.5 Consensus size: 2
90281 AATACAAGCA
*
90291 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
90332 AT AT AT AT AT AT CAT AT AT AA AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
90368 AACAATGTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.01
2 66 0.96
3 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:91676 original size:31 final size:29
Alignment explanation
Indices: 91612--91672 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
91602 GGGCTTTGAG
*
91612 TTATAGATTAATCCTTTAAACTTTAAGAT
1 TTATAGATTAATCCTTTAAACTTTAAAAT
91641 TTATAGACTTAGATCC-TT-AACTTTTAAAAT
1 TTATAGA-TTA-ATCCTTTAAAC-TTTAAAAT
91671 TT
1 TT
91673 TATATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.36
30 14 0.50
31 4 0.14
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (29 bp):
TTATAGATTAATCCTTTAAACTTTAAAAT
Done.