Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002256.1 Hibiscus syriacus cultivar Beakdansim tig00004588_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: 73810
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:4452 original size:22 final size:22
Alignment explanation
Indices: 4424--4481 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
4414 GTCTACGCAT
*
4424 TCCTTCGGGACATACTCATAGG
1 TCCTTCGGGACATACTCACAGG
*
4446 TCCTTCGGGACATACTCGCAGG
1 TCCTTCGGGACATACTCACAGG
4468 TCCTTCGGGACATA
1 TCCTTCGGGACATA
4482 TTTCACATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.24, T:0.26
Consensus pattern (22 bp):
TCCTTCGGGACATACTCACAGG
Found at i:6988 original size:263 final size:263
Alignment explanation
Indices: 6485--7019 Score: 844
Period size: 262 Copynumber: 2.0 Consensus size: 263
6475 GTTTTTCTAC
* * *
6485 AATAAA-AAAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAATCTAATTAAGCCCAACGAC
1 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
6549 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
66 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
* ** *
6614 TTTGACATGTTACAAATGACAAAAACATTTATAGTAATATAAAATAGTTAACATCAGTTTAATAA
131 TTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAATAA
6679 TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
196 TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
6744 TAA
261 TAA
*
6747 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTTCAAACCCAATTAAGCCCAAC-AC
1 AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
* *
6811 TTAAATTAGAATTTTTGCGGGATACACTTACCCTCTCGGATAAAC-CTGAAACTATTAACC-CGA
66 TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTC-GAAACTACTAACCTC-A
** * ** *
6874 CTTTTGGCATGTTACAGCTGACATAAACATTGATAACAATATAAAATAGTTAACATCAATTTAAT
129 AATTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAAT
* * *
6939 AGTTTTGTTAATTTTTTTGTCAGTTGACTCAATTTAATAAAAATGTTTAAGAATGAGAACAGAAA
194 AATTTTGTTAA-TTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAA
7004 AAATAA
258 AAATAA
7010 AATAAAGATA
1 AATAAAGATA
7020 GATATAATAT
Statistics
Matches: 250, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
261 2 0.01
262 130 0.52
263 118 0.47
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (263 bp):
AATAAAGATAATCTCATTTTTATTGCTAATTGGGCCCGATTCCAAACCCAATTAAGCCCAACGAC
TTAAATTAGAATTTTCGCGGGATACACTTACCCTCTCGGATAAACTCGAAACTACTAACCTCAAA
TTTGACATGTTACAAATGACAAAAACATTGATAACAATATAAAATAGTTAACATCAATTTAATAA
TTTTGTTAATTTTTTGTCAATTGACTCAATTTAATAAAAATGTTTAAGAATGAAAACAGAAAAAA
TAA
Found at i:17572 original size:26 final size:26
Alignment explanation
Indices: 17542--17596 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
17532 TCTTTTCAAG
17542 GAGTTTGATGTGTTAGATATTGAGGA
1 GAGTTTGATGTGTTAGATATTGAGGA
17568 GAGTTTGATGTGTTAGATATTGAGGA
1 GAGTTTGATGTGTTAGATATTGAGGA
17594 GAG
1 GAG
17597 GTTGTGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (26 bp):
GAGTTTGATGTGTTAGATATTGAGGA
Found at i:21808 original size:22 final size:22
Alignment explanation
Indices: 21769--21810 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
21759 AGACACTTTA
*
21769 GTATCAGTGTAAATGCACTTCC
1 GTATCAGTGTAAAGGCACTTCC
**
21791 GTATCAGTGTTGAGGCACTT
1 GTATCAGTGTAAAGGCACTT
21811 TGACACCAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (22 bp):
GTATCAGTGTAAAGGCACTTCC
Found at i:33654 original size:28 final size:29
Alignment explanation
Indices: 33618--33677 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
33608 AATTTAATCC
33618 TTTTATTAT-TATTATATTTTATTA-TTTA
1 TTTTATTATATA-TATATTTTATTATTTTA
* *
33646 TTTTGTTATATATATATTTTTTTATTTTA
1 TTTTATTATATATATATTTTATTATTTTA
33675 TTT
1 TTT
33678 ATTTAACCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATATATATTTTATTATTTTA
Found at i:33726 original size:14 final size:13
Alignment explanation
Indices: 33704--33766 Score: 51
Period size: 14 Copynumber: 4.8 Consensus size: 13
33694 TATTATTATA
*
33704 TATAATTATATTTT
1 TATATTTAT-TTTT
*
33718 TATATTTATTTTC
1 TATATTTATTTTT
33731 TAT-TTT-TTGTTT
1 TATATTTATT-TTT
33743 T-TATTTATTTATT
1 TATATTTATTT-TT
33756 TATATTATATT
1 TATATT-TATT
33767 ATATTTTCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
11 3 0.08
12 10 0.25
13 11 0.28
14 12 0.30
15 4 0.10
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (13 bp):
TATATTTATTTTT
Found at i:33788 original size:37 final size:36
Alignment explanation
Indices: 33708--33788 Score: 83
Period size: 37 Copynumber: 2.2 Consensus size: 36
33698 ATTATATATA
* * * *
33708 ATTATATTTTTATATTTATTTTCTATTTTTTGTTTTT
1 ATTAT-TTTTTATATTTATATTATATTTTTTCTTCTT
33745 ATTTATTTATTTATA-TTATATTATATTTTCTTCTTCTT
1 A-TTATTT-TTTATATTTATATTATATTTT-TTCTTCTT
33783 ATTATT
1 ATTATT
33789 ATTATTATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
37 20 0.54
38 17 0.46
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.72
Consensus pattern (36 bp):
ATTATTTTTTATATTTATATTATATTTTTTCTTCTT
Found at i:33999 original size:16 final size:17
Alignment explanation
Indices: 33973--34007 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
33963 TTCACCAAAC
*
33973 TTATATTTTCTTTTGTT
1 TTATATTTTCTTTTCTT
33990 TTAT-TTTTCTTTTCTT
1 TTATATTTTCTTTTCTT
34006 TT
1 TT
34008 CGGTGGAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (17 bp):
TTATATTTTCTTTTCTT
Found at i:34118 original size:15 final size:15
Alignment explanation
Indices: 34076--34124 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
34066 ATAATAGTTA
34076 TATATTTTTGTTT-T
1 TATATTTTTGTTTAT
**
34090 TA-ATTTTTCATTAT
1 TATATTTTTGTTTAT
34104 TATATTTTTGTTTAT
1 TATATTTTTGTTTAT
34119 T-TATTT
1 TATATTT
34125 ATTTATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 8 0.28
14 10 0.34
15 11 0.38
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.73
Consensus pattern (15 bp):
TATATTTTTGTTTAT
Found at i:34123 original size:4 final size:4
Alignment explanation
Indices: 34114--34294 Score: 66
Period size: 4 Copynumber: 45.8 Consensus size: 4
34104 TATATTTTTG
* *
34114 TTTA TTTA TTTA TTTA -TT- TTTA TTTA TTTCA TTTTC TTTA TTTT TTGTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A -TTTA TTTA TTTA TT-TA
* * * **
34163 GTTT- TATA TTT- TTATA TTTA CTTA TTT- TCTA TTCCC TTTA --TA TTTA
1 -TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA
34209 TTT- TGTT- TCTTA TTTA TTTA TTTA -TT- TTTA TTTA TTTA -TTA TATTA
1 TTTA T-TTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
* * *
34255 -TTA -TTA TATTC TTTA TTTTA CTTA TTTTT TTTA TTTA TTT
1 TTTA TTTA T-TTA TTTA -TTTA TTTA -TTTA TTTA TTTA TTT
34295 TTACTTTTAC
Statistics
Matches: 133, Mismatches: 21, Indels: 46
0.67 0.10 0.23
Matches are distributed among these distances:
2 2 0.02
3 24 0.18
4 82 0.62
5 20 0.15
6 5 0.04
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:34135 original size:18 final size:18
Alignment explanation
Indices: 34100--34321 Score: 106
Period size: 18 Copynumber: 11.8 Consensus size: 18
34090 TAATTTTTCA
34100 TTATTATATTT-TTGTTTAT
1 TTATT-TATTTATT-TTTAT
34119 TTATTTATTTATTTTTAT
1 TTATTTATTTATTTTTAT
*
34137 TTATTTCATTT-TCTTTAT
1 TTATTT-ATTTATTTTTAT
*
34155 TTTTTGTAGTTTTATATTTT-T
1 TTATT-TA--TTTAT-TTTTAT
* *
34176 ATATTTACTTATTTTCTAT
1 TTATTTATTTATTTT-TAT
*
34195 TCCCT-TTATATTTATTTTGTTT
1 T---TATT-TATTTATTTT-TAT
34217 CTTATTTATTTATTTATT-T
1 -TTATTTATTTATTT-TTAT
*
34236 TTATTTATTTA-TTATA-
1 TTATTTATTTATTTTTAT
34252 TTA-TTATTATATTCTTTATT
1 TTATTTATT-TATT-TTTA-T
*
34272 TTACTTATTT-TTTTTAT
1 TTATTTATTTATTTTTAT
*
34289 TTA-TT-TTTACTTTTACTT
1 TTATTTATTTATTTTTA--T
*
34307 TTATTTTTTTATTTT
1 TTATTTATTTATTTT
34322 CTTATCTTTA
Statistics
Matches: 161, Mismatches: 14, Indels: 55
0.70 0.06 0.24
Matches are distributed among these distances:
15 8 0.05
16 13 0.08
17 10 0.06
18 54 0.34
19 18 0.11
20 27 0.17
21 15 0.09
22 15 0.09
23 1 0.01
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (18 bp):
TTATTTATTTATTTTTAT
Found at i:34224 original size:22 final size:20
Alignment explanation
Indices: 34199--34349 Score: 69
Period size: 22 Copynumber: 7.1 Consensus size: 20
34189 TTCTATTCCC
34199 TTTATATTTATTTTGTTTCTTA
1 TTTATATTTATTTT-TTT-TTA
*
34221 TTTATTTATTTATTTTTATTTA
1 TTTA--TATTTATTTTTTTTTA
34243 TTTATTATATTATTATTATATTCTTTA
1 TTTA-TAT-TTA-T-TT-T-TT-TTTA
*
34270 TTT-TACTTA-TTTTTTTTA
1 TTTATATTTATTTTTTTTTA
* *
34288 TTTATTTTTACTTTTACTTTTA
1 TTTATATTTA-TTTT-TTTTTA
* * *
34310 TTT-T-TTTATTTTCTTATC
1 TTTATATTTATTTTTTTTTA
*
34328 TTTAT-TTTATTATTTTATTA
1 TTTATATTTATT-TTTTTTTA
34348 TT
1 TT
34350 CTTTGTCTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 30
0.71 0.08 0.21
Matches are distributed among these distances:
18 14 0.14
19 17 0.17
20 11 0.11
21 10 0.10
22 22 0.21
23 3 0.03
24 15 0.15
25 3 0.03
26 1 0.01
27 7 0.07
ACGTcount: A:0.21, C:0.05, G:0.01, T:0.74
Consensus pattern (20 bp):
TTTATATTTATTTTTTTTTA
Found at i:34279 original size:29 final size:29
Alignment explanation
Indices: 34239--34367 Score: 87
Period size: 28 Copynumber: 4.6 Consensus size: 29
34229 TTTATTTTTA
34239 TTTA-TTTA-TTATATTATTATTATATTC
1 TTTATTTTACTTATATTATTATTATATTC
* *
34266 TTTATTTTACTTATTTTTTTTATT-TATT-
1 TTTATTTTACTTA-TATTATTATTATATTC
* * *
34294 TTTACTTTTACTTTTATT-TTTTTATTTTC
1 TTTA-TTTTACTTATATTATTATTATATTC
*
34323 -TTATCTTTA-TTTTATTATT-TTATTATTC
1 TTTAT-TTTACTTATATTATTATTA-TATTC
*
34351 TTTGTCTTTACTT-TATT
1 TTTAT-TTTACTTATATT
34368 TTCTTTTTTA
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
27 19 0.23
28 27 0.33
29 27 0.33
30 10 0.12
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (29 bp):
TTTATTTTACTTATATTATTATTATATTC
Found at i:34310 original size:85 final size:82
Alignment explanation
Indices: 34221--34415 Score: 209
Period size: 85 Copynumber: 2.3 Consensus size: 82
34211 TTGTTTCTTA
34221 TTTATTTATTTATTTTTATTTATTTATTATATTATTATTA-TATTCTTTAT-TTTAC-TTATTTT
1 TTTATTT-TTTATTTTT-TTTATTTATTATATTATT-TTATTATTCTTTATCTTTACTTTATTTT
* * *
34283 TTTTATTTATTTTTACTTTTACT
63 CTTT-TTTA-TCTCA-TTTTACT
* * * *
34306 TTTATTTTTTTATTTTCTTATCTTTATTTTATTATTTTATTATTCTTTGTCTTTACTTTATTTTC
1 TTTA-TTTTTTATTTT-TTTTATTTATTATATTATTTTATTATTCTTTATCTTTACTTTATTTTC
34371 TTTTTTATCTCATTTTACT
64 TTTTTTATCTCATTTTACT
34390 TTT-TTCTTTTATTATTTTTTATTTAT
1 TTTATT-TTTTATT-TTTTTTATTTAT
34416 GTACTTTCAT
Statistics
Matches: 94, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
82 2 0.02
83 15 0.16
84 15 0.16
85 39 0.41
86 13 0.14
87 10 0.11
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (82 bp):
TTTATTTTTTATTTTTTTTATTTATTATATTATTTTATTATTCTTTATCTTTACTTTATTTTCTT
TTTTATCTCATTTTACT
Found at i:34318 original size:8 final size:8
Alignment explanation
Indices: 34086--34349 Score: 61
Period size: 8 Copynumber: 31.0 Consensus size: 8
34076 TATATTTTTG
*
34086 TTTTTAAT
1 TTTTTATT
*
34094 TTTTCATT
1 TTTTTATT
* *
34102 ATTATATTT
1 TTTTTA-TT
34111 TTGTTTATT
1 TT-TTTATT
*
34120 TATTTATTT
1 TTTTTA-TT
34129 ATTTTTATT
1 -TTTTTATT
*
34138 TATTTCATT
1 T-TTTTATT
34147 TTCTTTATT
1 TT-TTTATT
*
34156 TTTTGTAGT
1 TTTT-TATT
*
34165 TTTATATT
1 TTTTTATT
*
34173 TTTATATT
1 TTTTTATT
**
34181 TACTTA-T
1 TTTTTATT
*
34188 TTTCTATT
1 TTTTTATT
*
34196 CCCTTTATATT
1 ---TTTTTATT
*
34207 TATTTT-GT
1 T-TTTTATT
*
34215 TTCTTATT
1 TTTTTATT
*
34223 TATTTATTT
1 TTTTTA-TT
34232 ATTTTTATT
1 -TTTTTATT
*
34241 TATTTATT
1 TTTTTATT
* *
34249 ATATTATT
1 TTTTTATT
* *
34257 ATTATA-T
1 TTTTTATT
*
34264 TCTTTATT
1 TTTTTATT
*
34272 TTACTTATTT
1 TT-TTTA-TT
34282 TTTTTATTT
1 TTTTTA-TT
34291 ATTTTTACTTT
1 -TTTTTA--TT
34302 TACTTTTATT
1 T--TTTTATT
34312 TTTTTATT
1 TTTTTATT
*
34320 TTCTTA--
1 TTTTTATT
*
34326 TCTTTATT
1 TTTTTATT
*
34334 TTATTATT
1 TTTTTATT
*
34342 TTATTATT
1 TTTTTATT
34350 CTTTGTCTTT
Statistics
Matches: 187, Mismatches: 45, Indels: 48
0.67 0.16 0.17
Matches are distributed among these distances:
6 4 0.02
7 11 0.06
8 84 0.45
9 46 0.25
10 27 0.14
11 10 0.05
12 5 0.03
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (8 bp):
TTTTTATT
Found at i:34331 original size:14 final size:13
Alignment explanation
Indices: 34299--34352 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
34289 TTATTTTTAC
* *
34299 TTTTACTTTTATTT
1 TTTTA-TTTTCTTA
34313 TTTTATTTTCTTA
1 TTTTATTTTCTTA
*
34326 TCTTTATTTTATTA
1 T-TTTATTTTCTTA
34340 TTTTATTATTCTT
1 TTTTATT-TTCTT
34353 TGTCTTTACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 13 0.38
14 21 0.62
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTCTTA
Found at i:34400 original size:56 final size:54
Alignment explanation
Indices: 34269--34408 Score: 144
Period size: 56 Copynumber: 2.5 Consensus size: 54
34259 TATATTCTTT
*
34269 ATTTTACTTATTTTTTTTATTTATTTTTACTTTTACTTTTATTTTTTTATTTTCTT
1 ATTTTACTT-TTTTTTTTA-TTATTTTTACTTTTACTTTTATTTTTTTATTTTCTC
*
34325 ATCTTTA-TTTTATTATTTTATTATTCTTT-GTCTTTAC-TTTATTTTCTTT-TTTATCTC
1 AT-TTTACTTTT-TT-TTTTATTATT-TTTACT-TTTACTTTTATTTT-TTTATTT-TCTC
34382 ATTTTACTTTTTTCTTTTATTATTTTT
1 ATTTTACTTTTTT-TTTTATTATTTTT
34409 TATTTATGTA
Statistics
Matches: 73, Mismatches: 3, Indels: 17
0.78 0.03 0.18
Matches are distributed among these distances:
55 5 0.07
56 39 0.53
57 29 0.40
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (54 bp):
ATTTTACTTTTTTTTTTATTATTTTTACTTTTACTTTTATTTTTTTATTTTCTC
Found at i:34408 original size:22 final size:22
Alignment explanation
Indices: 34270--34408 Score: 60
Period size: 22 Copynumber: 6.2 Consensus size: 22
34260 ATATTCTTTA
34270 TTTTACTTATTTT-TTTTATTTAT
1 TTTTACTT-TTTTCTTTTA-TTAT
*
34293 TTTTAC-TTTTACTTTTATT-T
1 TTTTACTTTTTTCTTTTATTAT
*
34313 TTTTA-TTTTCTTATCTTTATT-T
1 TTTTACTTTT-TTCT-TTTATTAT
* * * *
34335 TATTA-TTTTATTATTCT-TTGT
1 TTTTACTTTT-TTCTTTTATTAT
*
34356 CTTTACTTTATTTTCTTTT-TTATCT
1 TTTTAC-TT-TTTTCTTTTATTA--T
34381 CATTTTACTTTTTTCTTTTATTAT
1 --TTTTACTTTTTTCTTTTATTAT
34405 TTTT
1 TTTT
34409 TATTTATGTA
Statistics
Matches: 91, Mismatches: 12, Indels: 27
0.70 0.09 0.21
Matches are distributed among these distances:
20 11 0.12
21 13 0.14
22 29 0.32
23 15 0.16
24 3 0.03
25 10 0.11
26 5 0.05
27 5 0.05
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (22 bp):
TTTTACTTTTTTCTTTTATTAT
Found at i:35189 original size:40 final size:40
Alignment explanation
Indices: 35144--35225 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 40
35134 CTAATCGAAT
* *
35144 TTATAAA-ATTTA-AATTATTTTGATTTTTATTTAAATTTAA
1 TTATAAATATTTATAA-TATTATGA-TATTATTTAAATTTAA
*
35184 TTATAAATATTTATAATATTATGATATTATTTAATTTTAA
1 TTATAAATATTTATAATATTATGATATTATTTAAATTTAA
35224 TT
1 TT
35226 TAGACCATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 23 0.62
41 12 0.32
42 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (40 bp):
TTATAAATATTTATAATATTATGATATTATTTAAATTTAA
Found at i:41555 original size:2 final size:2
Alignment explanation
Indices: 41548--41572 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41538 ACATGAAAAC
41548 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41573 CTTGTTACAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41725 original size:32 final size:30
Alignment explanation
Indices: 41658--41741 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 30
41648 AGGACCTATT
* * *
41658 CATATGTTCCAAAGAACATAGGTAACTGTC
1 CATATGTCCCGAAGGACATAGGTAACTGTC
41688 CATATGTCCCGAAGGACATAGGTAATCCTGTC
1 CATATGTCCCGAAGGACATAGGTAA--CTGTC
* *
41720 TATATGTCACGAAGGACATAGG
1 CATATGTCCCGAAGGACATAGG
41742 CAACCCTCGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 22 0.47
32 25 0.53
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.25
Consensus pattern (30 bp):
CATATGTCCCGAAGGACATAGGTAACTGTC
Found at i:47312 original size:33 final size:33
Alignment explanation
Indices: 47270--47334 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
47260 ATCAGTGAAA
* *
47270 ACAAACCCAATCCCTAGAAGTAGCTGGAGAGCG
1 ACAAACCCAATCCCAAGAAGTAGATGGAGAGCG
47303 ACAAACCCAATCCCAAGAAGTAGATGGAGAGC
1 ACAAACCCAATCCCAAGAAGTAGATGGAGAGC
47335 TCCAGCGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
ACAAACCCAATCCCAAGAAGTAGATGGAGAGCG
Found at i:49455 original size:19 final size:21
Alignment explanation
Indices: 49431--49471 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
49421 CCATCCCCGA
49431 ACCCG-ACCCG-AAATATTAT
1 ACCCGAACCCGAAAATATTAT
49450 ACCCGAACCCGAAAATATTAT
1 ACCCGAACCCGAAAATATTAT
49471 A
1 A
49472 TATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.41, C:0.29, G:0.10, T:0.20
Consensus pattern (21 bp):
ACCCGAACCCGAAAATATTAT
Found at i:49564 original size:11 final size:12
Alignment explanation
Indices: 49545--49575 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
49535 CCGAACCCGA
49545 CCCGAAAAAATC
1 CCCGAAAAAATC
49557 CCCGAAAAAATC
1 CCCGAAAAAATC
49569 CCCGAAA
1 CCCGAAA
49576 CCGAACCCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.35, G:0.10, T:0.06
Consensus pattern (12 bp):
CCCGAAAAAATC
Found at i:50443 original size:24 final size:24
Alignment explanation
Indices: 50416--50462 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
50406 GTTTTTGTTT
**
50416 CATTTTAGTATTTCGTTTAAAATC
1 CATTTTAGTAACTCGTTTAAAATC
50440 CATTTTAGTAACTCGTTTAAAAT
1 CATTTTAGTAACTCGTTTAAAAT
50463 TTAGGTTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.47
Consensus pattern (24 bp):
CATTTTAGTAACTCGTTTAAAATC
Found at i:51090 original size:17 final size:17
Alignment explanation
Indices: 51064--51098 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
51054 TTTTGGTTCG
51064 GTCTGACCTGTTTAAAA
1 GTCTGACCTGTTTAAAA
*
51081 GTCTGGCCTGTTTAAAA
1 GTCTGACCTGTTTAAAA
51098 G
1 G
51099 CTTGTTTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (17 bp):
GTCTGACCTGTTTAAAA
Found at i:58687 original size:17 final size:17
Alignment explanation
Indices: 58667--58708 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
58657 TTCATATTTT
58667 AAATAAATTTTAACAT-A
1 AAATAAATTTTAA-ATGA
*
58684 AAATATATTTTTAAATGA
1 AAATA-AATTTTAAATGA
58702 AAATAAA
1 AAATAAA
58709 ATAAAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AAATAAATTTTAAATGA
Found at i:58806 original size:25 final size:25
Alignment explanation
Indices: 58752--58815 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
58742 CATATTTAAT
* * *
58752 AATTTAATAGA-A-AAAATATTTTT
1 AATTTAATATATATAAAATATTATG
*
58775 AAGTTAATATATATAAAATATTATG
1 AATTTAATATATATAAAATATTATG
*
58800 AATTTAAGTATTTATA
1 AATTTAA-TATATATA
58816 CACTAAGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 9 0.28
24 1 0.03
25 15 0.47
26 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (25 bp):
AATTTAATATATATAAAATATTATG
Found at i:62890 original size:22 final size:19
Alignment explanation
Indices: 62844--62892 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
62834 AGTCATCATG
62844 TATCATCATTTTCGTCCAC
1 TATCATCATTTTCGTCCAC
62863 TATCATCATTTTCGTCCAC
1 TATCATCATTTTCGTCCAC
*
62882 TATCGTCATTT
1 TATCATCATTT
62893 ATCTTATTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.45
Consensus pattern (19 bp):
TATCATCATTTTCGTCCAC
Found at i:68170 original size:2 final size:2
Alignment explanation
Indices: 68163--68194 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
68153 TTACCAACTA
68163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68195 GCAATGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69424 original size:3 final size:3
Alignment explanation
Indices: 69413--69470 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
69403 TTTTTTTCCG
*
69413 TTA TT- TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
69458 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
69471 CAATTTTTGC
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 6 0.12
3 40 0.82
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:69599 original size:26 final size:25
Alignment explanation
Indices: 69546--69744 Score: 371
Period size: 25 Copynumber: 7.9 Consensus size: 25
69536 CAACCCCAGA
69546 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
69571 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
*
69597 TTAGGGGTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
69623 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
69648 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
69673 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
69698 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
69723 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
69745 CCCAACTGCA
Statistics
Matches: 171, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
25 122 0.71
26 49 0.29
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Found at i:71673 original size:15 final size:16
Alignment explanation
Indices: 71645--71681 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
71635 CTTATAGAAA
*
71645 TTATTTTATTGTTATT
1 TTATTTTATTGTTAAT
71661 TTATTTT-TTGTTAAT
1 TTATTTTATTGTTAAT
71676 TTATTT
1 TTATTT
71682 GATGTTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
TTATTTTATTGTTAAT
Done.