Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002707.1 Hibiscus syriacus cultivar Beakdansim tig00005587_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: 95446
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:80 original size:2 final size:2
Alignment explanation
Indices: 73--97 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63 ATTTATCCTT
73 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
98 TTGCATGTCT
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:7446 original size:18 final size:18
Alignment explanation
Indices: 7423--7465 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
7413 CCGGTCATGA
7423 CCCGACCCGACCCGTTGG
1 CCCGACCCGACCCGTTGG
7441 CCCGACCCGACCCGTTGG
1 CCCGACCCGACCCGTTGG
7459 CCCGACC
1 CCCGACC
7466 GTTGACCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.12, C:0.53, G:0.26, T:0.09
Consensus pattern (18 bp):
CCCGACCCGACCCGTTGG
Found at i:7534 original size:29 final size:29
Alignment explanation
Indices: 7502--7557 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
7492 ATTTGGTTTT
7502 GGTGCTATTCTGGAAATTAATTCGAAATG
1 GGTGCTATTCTGGAAATTAATTCGAAATG
* * **
7531 GGTGCTATTTTGGTAATTTTTTCGAAA
1 GGTGCTATTCTGGAAATTAATTCGAAA
7558 AGTGATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTGGAAATTAATTCGAAATG
Found at i:7576 original size:39 final size:38
Alignment explanation
Indices: 7531--7607 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
7521 ATTCGAAATG
** *
7531 GGTGCTATTTT-GGTAATTTTTTCGAAAAGTGATATTATT
1 GGTGCTATTTTAGG-AATTAATTCGAAAAG-GATACTATT
7570 GGTGCTATTTTAGGAATTAATTCGAAAAGGATACTATT
1 GGTGCTATTTTAGGAATTAATTCGAAAAGGATACTATT
7608 TGGGTAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 8 0.24
39 24 0.71
40 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.21, T:0.43
Consensus pattern (38 bp):
GGTGCTATTTTAGGAATTAATTCGAAAAGGATACTATT
Found at i:7627 original size:68 final size:68
Alignment explanation
Indices: 7500--7627 Score: 170
Period size: 68 Copynumber: 1.9 Consensus size: 68
7490 TAATTTGGTT
* * * * *
7500 TTGGTGCTATTCTGGAAATTAATTCGAAATGGGTGCTATTTTGGTAATTTTTTCGAAAAGTGATA
1 TTGGTGCTATTCTGGAAATTAATTCGAAAAGGATACTATTTGGGTAATTTTTTCAAAAAGTGATA
7565 TTA
66 TTA
*
7568 TTGGTGCTATTTTAGG-AATTAATTCGAAAAGGATACTATTTGGGTAATTATTTT-AAAAAG
1 TTGGTGCTATTCT-GGAAATTAATTCGAAAAGGATACTATTTGGGTAATT-TTTTCAAAAAG
7628 GGTGCTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
68 46 0.88
69 6 0.12
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.41
Consensus pattern (68 bp):
TTGGTGCTATTCTGGAAATTAATTCGAAAAGGATACTATTTGGGTAATTTTTTCAAAAAGTGATA
TTA
Found at i:13668 original size:15 final size:15
Alignment explanation
Indices: 13650--13683 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
13640 ATTATATAAA
13650 ATATAATGAATTATT
1 ATATAATGAATTATT
* *
13665 ATATTATGGATTATT
1 ATATAATGAATTATT
13680 ATAT
1 ATAT
13684 TTTGTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (15 bp):
ATATAATGAATTATT
Found at i:13832 original size:15 final size:15
Alignment explanation
Indices: 13812--13870 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
13802 AAAACCGGAT
13812 ATCGGGTACCCGATA
1 ATCGGGTACCCGATA
*
13827 ATCGGGTACCCGCAAA
1 ATCGGGTACCCG-ATA
*
13843 ATCCGGGTACCCGATT
1 AT-CGGGTACCCGATA
*
13859 ACCGGGTACCCG
1 ATCGGGTACCCG
13871 TAACATCCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
15 22 0.58
16 6 0.16
17 10 0.26
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (15 bp):
ATCGGGTACCCGATA
Found at i:13851 original size:17 final size:16
Alignment explanation
Indices: 13814--13882 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 16
13804 AACCGGATAT
*
13814 CGGGTACCCGATAAT-
1 CGGGTACCCGAAAATC
13829 CGGGTACCCGCAAAATC
1 CGGGTACCCG-AAAATC
**
13846 CGGGTACCCGATTA-C
1 CGGGTACCCGAAAATC
*
13861 CGGGTACCCGTAACATC
1 CGGGTACCCG-AAAATC
13878 CGGGT
1 CGGGT
13883 CGGGACACGG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
15 21 0.47
16 8 0.18
17 16 0.36
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (16 bp):
CGGGTACCCGAAAATC
Found at i:13855 original size:32 final size:32
Alignment explanation
Indices: 13814--13882 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
13804 AACCGGATAT
*
13814 CGGGTACCCGATAATCGGGTACCCGCAAAATC
1 CGGGTACCCGATAACCGGGTACCCGCAAAATC
* * *
13846 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATAACCGGGTACCCGCAAAATC
13878 CGGGT
1 CGGGT
13883 CGGGACACGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCCGATAACCGGGTACCCGCAAAATC
Found at i:15231 original size:13 final size:13
Alignment explanation
Indices: 15213--15250 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
15203 TGACTGGTCC
15213 TGACCCGACCCGT
1 TGACCCGACCCGT
*
15226 TGACCCTACCCGT
1 TGACCCGACCCGT
15239 TGACCCGACCCG
1 TGACCCGACCCG
15251 ACCGTTGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.16, C:0.47, G:0.21, T:0.16
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:15273 original size:31 final size:31
Alignment explanation
Indices: 15214--15274 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
15204 GACTGGTCCT
* *
15214 GACCCGACCCGTTGACCCTACCCGTTGACCC
1 GACCCGACCCGTTGACCCTAACCATTGACCC
*
15245 GACCCGA-CCGTTGACCGTTAACCATTGACC
1 GACCCGACCCGTTGACC-CTAACCATTGACC
15275 GATGATCGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.20, C:0.43, G:0.20, T:0.18
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCTAACCATTGACCC
Found at i:15437 original size:88 final size:88
Alignment explanation
Indices: 15287--15450 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
15277 TGATCGGTGC
** * * ** *
15287 TATTCTAGGAATTAATTCGATTTTGGTGTTATTATGATAATTAATTTGAAATTGATGCTATTTTA
1 TATTCTAGGAATTAATTCGAAATTGGTGCTATTATGAGAATTAATTTGAAAAAGATGATATTTTA
*
15352 GTAATTTTTTTGGAAAAAAGTGA
66 GTAATTATTTTGGAAAAAAGTGA
* * * *
15375 TATTCTGGGAATTAATTCGAAATTGGTGCTATTTTGGGAATTAATTTGAAAAAGATGATATTTTG
1 TATTCTAGGAATTAATTCGAAATTGGTGCTATTATGAGAATTAATTTGAAAAAGATGATATTTTA
15440 GTAATTATTTT
66 GTAATTATTTT
15451 AAAAAGGGTG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (88 bp):
TATTCTAGGAATTAATTCGAAATTGGTGCTATTATGAGAATTAATTTGAAAAAGATGATATTTTA
GTAATTATTTTGGAAAAAAGTGA
Found at i:15467 original size:28 final size:29
Alignment explanation
Indices: 15324--15466 Score: 108
Period size: 29 Copynumber: 4.9 Consensus size: 29
15314 GTTATTATGA
** * *
15324 TAATTAATTTGAAATTGATGCTATTTTAG
1 TAATTAATTTGAAAAAGGTGCTATTTTGG
** * * *
15353 TAATTTTTTTGGAAAAAAGTGATATTCTGG
1 TAATTAATTT-GAAAAAGGTGCTATTTTGG
* * **
15383 GAATTAATTCGAAATTGGTGCTATTTTGG
1 TAATTAATTTGAAAAAGGTGCTATTTTGG
* * *
15412 GAATTAATTTGAAAAAGATGATATTTTGG
1 TAATTAATTTGAAAAAGGTGCTATTTTGG
*
15441 TAATT-ATTTTAAAAAGGGTGCTATTT
1 TAATTAATTTGAAAAA-GGTGCTATTT
15467 GTGTAAAATG
Statistics
Matches: 85, Mismatches: 27, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
28 9 0.11
29 58 0.68
30 18 0.21
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (29 bp):
TAATTAATTTGAAAAAGGTGCTATTTTGG
Found at i:18648 original size:13 final size:13
Alignment explanation
Indices: 18630--18656 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18620 TTTGTTTCTC
18630 GAGAAACGAACAG
1 GAGAAACGAACAG
18643 GAGAAACGAACAG
1 GAGAAACGAACAG
18656 G
1 G
18657 TTGCGGTGGT
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:0.52, C:0.15, G:0.33, T:0.00
Consensus pattern (13 bp):
GAGAAACGAACAG
Found at i:23189 original size:3 final size:3
Alignment explanation
Indices: 23181--23217 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
23171 GAGATGTCAT
23181 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23218 ATAATTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:26285 original size:5 final size:5
Alignment explanation
Indices: 26275--26299 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
26265 ATGCACTGTC
26275 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
26300 TTAGGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:32489 original size:7 final size:7
Alignment explanation
Indices: 32477--32553 Score: 133
Period size: 7 Copynumber: 11.4 Consensus size: 7
32467 TCGGTTGATT
32477 GAAGGGA
1 GAAGGGA
32484 GAAGGGA
1 GAAGGGA
32491 GAAGGGA
1 GAAGGGA
32498 GAA-GGA
1 GAAGGGA
32504 GAAGGGA
1 GAAGGGA
32511 G-A-GGA
1 GAAGGGA
32516 GAAGGGA
1 GAAGGGA
32523 GAAGGGA
1 GAAGGGA
32530 GAAGGGA
1 GAAGGGA
32537 GAAGGGA
1 GAAGGGA
32544 GAAGGGA
1 GAAGGGA
32551 GAA
1 GAA
32554 CTGTTTTTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
5 4 0.06
6 8 0.12
7 55 0.82
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAAGGGA
Found at i:37380 original size:31 final size:31
Alignment explanation
Indices: 37317--37388 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
37307 TTGTTAACAA
* * *
37317 TAGGTGTCTAATGTTTTCTCTATTACATTTT
1 TAGGTGTCTAAAGTTTTCTCCATTACACTTT
* * *
37348 TATGTGTCTAAAGTTTTCTCCGTTATACTTT
1 TAGGTGTCTAAAGTTTTCTCCATTACACTTT
37379 TAGGTGTCTA
1 TAGGTGTCTA
37389 TTGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.19, C:0.14, G:0.15, T:0.51
Consensus pattern (31 bp):
TAGGTGTCTAAAGTTTTCTCCATTACACTTT
Found at i:39641 original size:30 final size:30
Alignment explanation
Indices: 39607--39809 Score: 166
Period size: 30 Copynumber: 6.8 Consensus size: 30
39597 AAATGGGAGC
* *
39607 AATAGAAACTTAAGGGATTAAAATAGCAAA
1 AATAGAAACTTAAGGGACTAAAATAGAAAA
*
39637 AATAGAAAGC-TAAGGGACTAAAATAGCAAA
1 AATAGAAA-CTTAAGGGACTAAAATAGAAAA
* * * * *
39667 TATATAAACTTAAAGGACTAACACAGTAAAA
1 AATAGAAACTTAAGGGACTAAAATAG-AAAA
** * *
39698 ACCA-AAACTTAAGGG-TTGAAATAGAAAA
1 AATAGAAACTTAAGGGACTAAAATAGAAAA
* * *
39726 TATA-AACATTTAAAGGACTAAAATA-AAAA
1 AATAGAA-ACTTAAGGGACTAAAATAGAAAA
* *
39755 ATATAGACATTTAAAGGG-CTAAAATAGAAAA
1 A-ATAGAAACTT-AAGGGACTAAAATAGAAAA
39786 AATAGAAACTTAAGGGACTAAAAT
1 AATAGAAACTTAAGGGACTAAAAT
39810 GGTATTAACA
Statistics
Matches: 136, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
28 7 0.05
29 22 0.16
30 92 0.68
31 15 0.11
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (30 bp):
AATAGAAACTTAAGGGACTAAAATAGAAAA
Found at i:39769 original size:89 final size:90
Alignment explanation
Indices: 39612--39809 Score: 206
Period size: 89 Copynumber: 2.2 Consensus size: 90
39602 GGAGCAATAG
* ** *
39612 AAACTTAAGGGATTAAAATAGCAAAAATAGAAAGCTAAGGGACTAAAATAGCAAATATATAAACT
1 AAACTTAAGGGATTAAAATAGCAAAAATAGAAAGCTAAAGGACTAAAATAAAAAATATAGAAACT
39677 TAAAGGACTAACACAGTAAAAACCA
66 TAAAGGACTAACACAGTAAAAACCA
* ** *
39702 AAACTTAAGGG-TTGAAATAG-AAAATATA-AACATTTAAAGGACTAAAATAAAAAATATAGACA
1 AAACTTAAGGGATTAAAATAGCAAAA-ATAGAA-AGCTAAAGGACTAAAATAAAAAATATAGAAA
* * * * **
39764 TTTAAAGGGCTAAAATAG-AAAAAATA
64 CTTAAAGGACTAACACAGTAAAAACCA
*
39790 GAAACTTAAGGGACTAAAAT
1 -AAACTTAAGGGATTAAAAT
39810 GGTATTAACA
Statistics
Matches: 88, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
88 12 0.14
89 60 0.68
90 16 0.18
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (90 bp):
AAACTTAAGGGATTAAAATAGCAAAAATAGAAAGCTAAAGGACTAAAATAAAAAATATAGAAACT
TAAAGGACTAACACAGTAAAAACCA
Found at i:43434 original size:37 final size:36
Alignment explanation
Indices: 43359--43434 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
43349 TTTTTATATT
*
43359 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
43395 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
43432 TTT
1 TTT
43435 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:44881 original size:2 final size:2
Alignment explanation
Indices: 44874--44916 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
44864 TTAGTACGTT
44874 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
44916 T
1 T
44917 TAATTTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45632 original size:12 final size:12
Alignment explanation
Indices: 45598--45624 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
45588 TAAATTTAGT
45598 AAAAAATATTAA
1 AAAAAATATTAA
45610 AAAAAATATTAA
1 AAAAAATATTAA
45622 AAA
1 AAA
45625 CATTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAATATTAA
Found at i:45782 original size:21 final size:21
Alignment explanation
Indices: 45752--45792 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45742 AAATTGTTAA
*
45752 AAATATTAATATTTTAGATAT
1 AAATAATAATATTTTAGATAT
45773 AAATAATAATATTTTAGATA
1 AAATAATAATATTTTAGATA
45793 ATTTTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (21 bp):
AAATAATAATATTTTAGATAT
Found at i:46532 original size:29 final size:29
Alignment explanation
Indices: 46473--46540 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 29
46463 ATCTAGTTTG
*
46473 ATAAGATTAGTTTGTGTATAAATCAAATAA
1 ATAA-ATTAATTTGTGTATAAATCAAATAA
46503 ATAACATTAATTTGTGTAT-AATCAAATAA
1 ATAA-ATTAATTTGTGTATAAATCAAATAA
46532 ATAAATTAA
1 ATAAATTAA
46541 GCCAACGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 5 0.14
29 14 0.39
30 17 0.47
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (29 bp):
ATAAATTAATTTGTGTATAAATCAAATAA
Found at i:46731 original size:4 final size:4
Alignment explanation
Indices: 46722--46746 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
46712 TTTTATATAC
46722 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
46747 GATTAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:46948 original size:13 final size:13
Alignment explanation
Indices: 46930--46956 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46920 TGCAGAATTT
46930 TGATTTGATCAAG
1 TGATTTGATCAAG
46943 TGATTTGATCAAG
1 TGATTTGATCAAG
46956 T
1 T
46957 AGATGGCGTC
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:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TGATTTGATCAAG
Found at i:49496 original size:10 final size:11
Alignment explanation
Indices: 49472--49510 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
49462 TTAAACTAAA
49472 TTTTTTAATAAT
1 TTTTTTAAT-AT
49484 TTTTTTAAT-T
1 TTTTTTAATAT
49494 TTTTTTAATAT
1 TTTTTTAATAT
49505 TGTTTT
1 T-TTTT
49511 GGATAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 10 0.40
11 2 0.08
12 13 0.52
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TTTTTTAATAT
Found at i:51187 original size:75 final size:74
Alignment explanation
Indices: 51061--51211 Score: 266
Period size: 75 Copynumber: 2.0 Consensus size: 74
51051 CAAACTTCGT
51061 ATCTGGCAGGTAATATATATATATAATATACACACACGCACATGTATGCTGCTTTGTACGTATTA
1 ATCTGGCAGGTAATATATATATATAATATACACACACGCACATGTATGCTGCTTTGTACGTATTA
51126 TGCTTAGGG
66 TGCTTAGGG
* * *
51135 ATCTGGGAGGTAATATATATATATATATATATATACACGCACATGTATGCTGCTTTGTACGTATT
1 ATCTGGCAGGTAATATATATATATA-ATATACACACACGCACATGTATGCTGCTTTGTACGTATT
51200 ATGCTTAGGG
65 ATGCTTAGGG
51210 AT
1 AT
51212 AGGCCTAGGT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 24 0.33
75 49 0.67
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (74 bp):
ATCTGGCAGGTAATATATATATATAATATACACACACGCACATGTATGCTGCTTTGTACGTATTA
TGCTTAGGG
Found at i:53691 original size:20 final size:20
Alignment explanation
Indices: 53654--53703 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
53644 AGTCGTTTCT
*
53654 AGCCGTTGGAGATATTTTGG
1 AGCCGTTGGGGATATTTTGG
* *
53674 AGCTGTTGGGGATGTTTTGG
1 AGCCGTTGGGGATATTTTGG
53694 AGCCGTTGGG
1 AGCCGTTGGG
53704 ACTTAATTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.14, C:0.10, G:0.42, T:0.34
Consensus pattern (20 bp):
AGCCGTTGGGGATATTTTGG
Found at i:59281 original size:72 final size:72
Alignment explanation
Indices: 59161--59309 Score: 199
Period size: 72 Copynumber: 2.1 Consensus size: 72
59151 CTTACTTTGG
* * * * *
59161 GGCTGTACACCTTTTCCGAGATGGTTCTCGTAAATTCCTTGGATGGAGTTGAGGTGGAGCTTGTT
1 GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
59226 AACTTCA
66 AACTTCA
* * * *
59233 GGCTGAACACTTTTTCTGAGATGGTTCTCCTAAATTCTTTGGAAGGAGTAGCGGTGGAGCTTGAT
1 GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
* *
59298 ACCTTCG
66 AACTTCA
59305 GGCTG
1 GGCTG
59310 CAAATGCGTC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.19, C:0.18, G:0.29, T:0.34
Consensus pattern (72 bp):
GGCTGAACACCTTTTCCGAGATGGTTCTCCTAAATTCCTTGGAAGGAGTAGAGGTGGAGCTTGAT
AACTTCA
Found at i:66051 original size:21 final size:21
Alignment explanation
Indices: 66025--66073 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
66015 TTACCGAAAA
66025 TATTATTATTTCTATCGATTT
1 TATTATTATTTCTATCGATTT
* *
66046 TGTTATTTTTTCTATCGATTT
1 TATTATTATTTCTATCGATTT
66067 TATTATT
1 TATTATT
66074 GTTGGACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.20, C:0.08, G:0.06, T:0.65
Consensus pattern (21 bp):
TATTATTATTTCTATCGATTT
Found at i:71116 original size:5 final size:5
Alignment explanation
Indices: 71106--71132 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
71096 TTCGACCCTC
71106 TTTAT TTTAT TTTAT TTTAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TT
71133 ATAGATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:74211 original size:23 final size:23
Alignment explanation
Indices: 74180--74241 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
74170 TGTTTGTGAT
* *
74180 TATTTATTTATTATTGACAAACA
1 TATTCATTTATTATTCACAAACA
* * *
74203 TATTCATTTAATATTCATAAATA
1 TATTCATTTATTATTCACAAACA
*
74226 TACTCATTTATATATT
1 TATTCATTTAT-TATT
74242 TATTAACGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 27 0.87
24 4 0.13
ACGTcount: A:0.39, C:0.10, G:0.02, T:0.50
Consensus pattern (23 bp):
TATTCATTTATTATTCACAAACA
Found at i:80903 original size:74 final size:74
Alignment explanation
Indices: 80782--80933 Score: 304
Period size: 74 Copynumber: 2.1 Consensus size: 74
80772 ACGGTGTGGC
80782 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
1 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
80847 CACACATAT
66 CACACATAT
80856 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
1 ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
80921 CACACATAT
66 CACACATAT
80930 ATAT
1 ATAT
80934 TTGACTAGCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.50, C:0.20, G:0.14, T:0.16
Consensus pattern (74 bp):
ATATCAAAACAGAAATCACATGCCGAAAAAGCTCGGAAAAAAATGAAGAAAGCATGTTGCACACA
CACACATAT
Found at i:81928 original size:2 final size:2
Alignment explanation
Indices: 81921--81946 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81911 TACAATGAAC
81921 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
81947 CGAGTGTGTA
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:82577 original size:22 final size:23
Alignment explanation
Indices: 82531--82575 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
82521 ATTTTGTATT
*
82531 TTAAATTTTAAATTTTAATAAAA
1 TTAAATTTTAAAATTTAATAAAA
* *
82554 TTAATTTTTAAAATTTATTAAA
1 TTAAATTTTAAAATTTAATAAA
82576 TTTTATAACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATTTTAAAATTTAATAAAA
Found at i:85041 original size:14 final size:14
Alignment explanation
Indices: 84975--85033 Score: 64
Period size: 14 Copynumber: 4.0 Consensus size: 14
84965 ACCCAGTCTG
*
84975 AATATATTTATATTTT
1 AATATATTTATA--AT
* *
84991 AATATAATTAAAAT
1 AATATATTTATAAT
85005 AATATATTTTATAAT
1 AATATA-TTTATAAT
85020 AATATATTTATAAT
1 AATATATTTATAAT
85034 TATTTATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
14 15 0.41
15 12 0.32
16 10 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATATATTTATAAT
Found at i:85592 original size:20 final size:21
Alignment explanation
Indices: 85547--85616 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
85537 AGAGCGCTGT
**
85547 CTAAAATGTT-ATTTTTCTAC
1 CTAAAATGTTAATTTAACTAC
*
85567 CGAAAATGTTAATTTAACTA-
1 CTAAAATGTTAATTTAACTAC
*
85587 CTAAAAATGTTAATTTAGCTAC
1 CT-AAAATGTTAATTTAACTAC
85609 CTAAAATG
1 CTAAAATG
85617 AATATTTCCG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.24
21 30 0.71
22 2 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (21 bp):
CTAAAATGTTAATTTAACTAC
Found at i:87648 original size:147 final size:147
Alignment explanation
Indices: 87403--87740 Score: 547
Period size: 147 Copynumber: 2.3 Consensus size: 147
87393 TTTTATATCA
* * *
87403 TTTTAGGATCGTTTGATTGAAATGAATCAAAAGTTGAGATTAACTCTTTGTTTTTTTCTCAGTGA
1 TTTTAGGATC-TTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGA
* *
87468 ATATCTTCTTATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
65 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
87533 GATGTAAGTTTTACATTC
130 GATGTAAGTTTTACATTC
87551 TTTTAGGATCTTTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTG-TTTTTTCTCAGTGA
1 TTTTAGGATC-TTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGA
87615 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
65 AGATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAA
87680 GATGTAAGTTTTACATTC
130 GATGTAAGTTTTACATTC
* *
87698 TTTTAGGATCGTTGAATTGAAGAA-AAT-AAAATGCTAAGATTAA
1 TTTTAGGATCTTTG-ATTGAA-AAGAATCAAAA-GCTGAGATTAA
87741 GATCCACATT
Statistics
Matches: 179, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
146 7 0.04
147 124 0.69
148 48 0.27
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (147 bp):
TTTTAGGATCTTTGATTGAAAAGAATCAAAAGCTGAGATTAACTCATTGTTTTTTTCTCAGTGAA
GATCTTCTCATTTTCCGCTGTTAATCTTAGCATTTGATTTCTCTTAATCCAACGATTCTAAAAAG
ATGTAAGTTTTACATTC
Found at i:88789 original size:14 final size:14
Alignment explanation
Indices: 88770--88802 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
88760 GTTATTTTAG
88770 ATTTAAATCTTAAT
1 ATTTAAATCTTAAT
88784 ATTTAAATCTTAAT
1 ATTTAAATCTTAAT
88798 ATTTA
1 ATTTA
88803 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATCTTAAT
Found at i:89567 original size:16 final size:16
Alignment explanation
Indices: 89546--89580 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
89536 CACTCGGAGA
89546 AACCATGGTTGGGGTT
1 AACCATGGTTGGGGTT
89562 AACCATGGTTGGGGTT
1 AACCATGGTTGGGGTT
89578 AAC
1 AAC
89581 GATGAAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (16 bp):
AACCATGGTTGGGGTT
Found at i:91523 original size:2 final size:2
Alignment explanation
Indices: 91516--91548 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
91506 TCCTATAAGG
91516 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
91549 TGATCCCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Done.