Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001706.1 Hibiscus syriacus cultivar Beakdansim tig00003424_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: 53729
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7232 original size:16 final size:16
Alignment explanation
Indices: 7231--7262 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
7221 ACGAACATAA
*
7231 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
7247 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
7263 TTAAACGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.22, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:7236 original size:10 final size:10
Alignment explanation
Indices: 7221--7269 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
7211 ATAAACGAAC
7221 ACGAACATAA
1 ACGAACATAA
7231 ACGAACATAA
1 ACGAACATAA
*
7241 ATGAAC----
1 ACGAACATAA
7247 ACGAACATAA
1 ACGAACATAA
*
7257 ACGAACTTAA
1 ACGAACATAA
7267 ACG
1 ACG
7270 TTGAAGACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
6 5 0.16
10 27 0.84
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.12
Consensus pattern (10 bp):
ACGAACATAA
Found at i:7247 original size:26 final size:26
Alignment explanation
Indices: 7211--7269 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
7201 CATTTAATAA
7211 ATAAACGAACACGAACATAAACGAAC
1 ATAAACGAACACGAACATAAACGAAC
*
7237 ATAAATGAACACGAACATAAACGAAC
1 ATAAACGAACACGAACATAAACGAAC
*
7263 TTAAACG
1 ATAAACG
7270 TTGAAGACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (26 bp):
ATAAACGAACACGAACATAAACGAAC
Found at i:8316 original size:14 final size:14
Alignment explanation
Indices: 8297--8337 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
8287 GATTTGGTTA
*
8297 AACATAAATGAATG
1 AACATAAATGAACG
*
8311 AACATAACTGAACG
1 AACATAAATGAACG
*
8325 AACATAAACGAAC
1 AACATAAATGAAC
8338 ATAACCGAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.56, C:0.17, G:0.12, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:8607 original size:26 final size:25
Alignment explanation
Indices: 8578--8656 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
8568 TTAATTTAAA
8578 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
8604 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
8629 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
8655 CT
1 CT
8657 TACTTTCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.43
26 19 0.47
27 2 0.05
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:8620 original size:25 final size:24
Alignment explanation
Indices: 8592--8672 Score: 58
Period size: 25 Copynumber: 3.2 Consensus size: 24
8582 ACTACTTAGT
8592 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
8617 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
*
8642 TAGTTATCTTTATCTTACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
8668 AGTTA
1 AGTTA
8673 GTGTTATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
24 2 0.05
25 21 0.50
26 17 0.40
27 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:8644 original size:51 final size:51
Alignment explanation
Indices: 8568--8709 Score: 194
Period size: 51 Copynumber: 2.8 Consensus size: 51
8558 GAACAAGTAT
8568 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* *
8619 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTTACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
8670 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
8710 TCGCATAACC
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 53 0.67
52 26 0.33
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:12839 original size:26 final size:25
Alignment explanation
Indices: 12810--12890 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
12800 TTAATTTAAA
12810 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
** * *
12836 CT-AACTTTTTAAG-AGTAAAT-TTAAA
1 CTAAACTACTT-AGTAGT-TATCTT-AT
12861 CTAAACTACTTAGTAGTTATCGTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
12887 CTAA
1 CTAA
12891 CTTTCTAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 2 0.05
25 16 0.40
26 20 0.50
27 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:12878 original size:51 final size:51
Alignment explanation
Indices: 12802--12902 Score: 184
Period size: 51 Copynumber: 2.0 Consensus size: 51
12792 ACCAGTATTT
*
12802 AATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTTTAAGAGTA
1 AATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAGTA
*
12853 AATTTAAACTAAACTACTTAGTAGTTATCGTTATCTAACTTTCTAAGAGT
1 AATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAGT
12903 TAGTGTTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (51 bp):
AATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAGTA
Found at i:13135 original size:31 final size:31
Alignment explanation
Indices: 13100--13174 Score: 150
Period size: 31 Copynumber: 2.4 Consensus size: 31
13090 ATTCATATAT
13100 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
13131 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
1 TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
13162 TCGGGTCGGGTCG
1 TCGGGTCGGGTCG
13175 AGTTCGGGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.11, C:0.15, G:0.41, T:0.33
Consensus pattern (31 bp):
TCGGGTCGGGTCGGGTGAAACTTTATTTTGG
Found at i:13449 original size:38 final size:38
Alignment explanation
Indices: 13398--13475 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
13388 TCGGGTTAGG
13398 TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGGT
*
13436 TTTTTTAAGTGTGATATTCAGGTCGGGTCGGGTCGGGT
1 TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGGT
13474 TT
1 TT
13476 GAGTTTAGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.14, C:0.10, G:0.35, T:0.41
Consensus pattern (38 bp):
TTTTTTAAGTGTGATATTCAGGTCGAGTCGGGTCGGGT
Found at i:14380 original size:40 final size:38
Alignment explanation
Indices: 14324--14410 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 38
14314 ATTGGGTCGG
14324 ATATATATATATATTTAAATTAAATATATAAATATTAT
1 ATATATATATATATTTAAATTAAATATATAAATATTAT
* * *
14362 ATATATATATTTTAATTTAAATTAAATTTATTAATATTAT
1 ATATATATA-TAT-ATTTAAATTAAATATATAAATATTAT
14402 ATATATATA
1 ATATATATA
14411 ATAATTATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 9 0.20
39 2 0.05
40 33 0.75
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (38 bp):
ATATATATATATATTTAAATTAAATATATAAATATTAT
Found at i:23216 original size:10 final size:10
Alignment explanation
Indices: 23201--23226 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
23191 GTTAATATAG
23201 CCGTTTGTGA
1 CCGTTTGTGA
23211 CCGTTTGTGA
1 CCGTTTGTGA
23221 CCGTTT
1 CCGTTT
23227 TTTTCTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.23, G:0.27, T:0.42
Consensus pattern (10 bp):
CCGTTTGTGA
Found at i:25465 original size:21 final size:21
Alignment explanation
Indices: 25441--25480 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25431 TTTATTTTAT
25441 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
25462 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
25481 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:25528 original size:33 final size:33
Alignment explanation
Indices: 25475--25573 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
25465 TTTGTTTCAA
25475 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
25507 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
25540 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
25573 T
1 T
25574 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:25602 original size:13 final size:13
Alignment explanation
Indices: 25559--25613 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
25549 TTGGAAGTAT
25559 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
25572 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
25586 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
25599 TTAAGTATTTGAA
1 TTAAGTATTTCAA
25612 TT
1 TT
25614 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:25836 original size:21 final size:21
Alignment explanation
Indices: 25810--25866 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
25800 TGGAGCATGG
*
25810 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
25831 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
25852 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
25867 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:26072 original size:17 final size:18
Alignment explanation
Indices: 26052--26085 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26042 GTTTTTTTAT
26052 AACCG-GTTTTTTAAAAA
1 AACCGAGTTTTTTAAAAA
*
26069 AACCGATTTTTTTAAAA
1 AACCGAGTTTTTTAAAA
26086 CCGAAACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (18 bp):
AACCGAGTTTTTTAAAAA
Found at i:26085 original size:15 final size:15
Alignment explanation
Indices: 26033--26089 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
26023 ATCTGGAATA
* *
26033 TTAAAATCGGTTTTT
1 TTAAAACCGATTTTT
* *
26048 TTATAACCGGTTTTT
1 TTAAAACCGATTTTT
*
26063 TAAAAAAACCGATTTTT
1 T--TAAAACCGATTTTT
26080 TTAAAACCGA
1 TTAAAACCGA
26090 AACCGGTTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 22 0.65
17 12 0.35
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (15 bp):
TTAAAACCGATTTTT
Found at i:26206 original size:15 final size:17
Alignment explanation
Indices: 26180--26211 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26170 TTCTATGGGA
26180 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
26196 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
26212 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:29131 original size:28 final size:26
Alignment explanation
Indices: 29092--29143 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
29082 AATTACGATG
29092 TAAGTACGA-TTTAGTTTTATATCAATT
1 TAAGTACGATTTTA--TTTATATCAATT
29119 TAAGTATCGATTTTATTTATATCAA
1 TAAGTA-CGATTTTATTTATATCAA
29144 ATTTTATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
27 16 0.70
28 3 0.13
29 4 0.17
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (26 bp):
TAAGTACGATTTTATTTATATCAATT
Found at i:32766 original size:30 final size:30
Alignment explanation
Indices: 32725--32796 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
32715 GAAAAGTTAT
**
32725 AAATCGGTCACTAATGTTATCGTTTGTAACA
1 AAAT-GGTCACTAACATTATCGTTTGTAACA
*
32756 AAATGGTCACTAACATTATCGTTTGTTACA
1 AAATGGTCACTAACATTATCGTTTGTAACA
32786 AAATGGTCACT
1 AAATGGTCACT
32797 CGACGTTAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 34 0.89
31 4 0.11
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (30 bp):
AAATGGTCACTAACATTATCGTTTGTAACA
Found at i:34000 original size:30 final size:30
Alignment explanation
Indices: 33966--34040 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
33956 TGTTAACGTC
**
33966 AAGTGACCATTTTGTAACAAACGATAATGT
1 AAGTGACCATTTTGTAACAAACGATAACAT
* *
33996 AAGTGATCATTTTGTAATAAACGATAACAT
1 AAGTGACCATTTTGTAACAAACGATAACAT
* *
34026 TAGTGACCAATTTGT
1 AAGTGACCATTTTGT
34041 TACTTTTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (30 bp):
AAGTGACCATTTTGTAACAAACGATAACAT
Found at i:34159 original size:14 final size:16
Alignment explanation
Indices: 34129--34161 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
34119 ATTAGTTGGA
34129 ATAATTTTAATATTTT
1 ATAATTTTAATATTTT
34145 ATAA-TTTAA-ATTTT
1 ATAATTTTAATATTTT
34159 ATA
1 ATA
34162 GAATTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 5 0.29
16 4 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAATTTTAATATTTT
Found at i:36161 original size:20 final size:20
Alignment explanation
Indices: 36128--36182 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 20
36118 AACTTATGAA
36128 ATAATTATTAAAAAATATTT
1 ATAATTATTAAAAAATATTT
36148 ATAA-TATTATAAAAATATTT
1 ATAATTATTA-AAAAATATTT
36168 ATTTAATT-TTAAAAA
1 A--TAATTATTAAAAA
36183 TCAAATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 5 0.16
20 15 0.48
21 4 0.13
22 6 0.19
23 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAATTATTAAAAAATATTT
Found at i:36347 original size:21 final size:22
Alignment explanation
Indices: 36321--36362 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
36311 AGATAATTTA
36321 AAATAATATTATTT-AAATAAT
1 AAATAATATTATTTCAAATAAT
36342 AAATAATATTATTTCAAATAA
1 AAATAATATTATTTCAAATAA
36363 ATGATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATAATATTATTTCAAATAAT
Found at i:38552 original size:18 final size:16
Alignment explanation
Indices: 38492--38552 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 16
38482 AATAAATTGA
38492 TTATTATTTAATATTATT
1 TTATTATTTAAT-TTA-T
38510 TTATTATTTAA-TTAT
1 TTATTATTTAATTTAT
**
38525 AAACTTATTTAACTTTTAT
1 TTA-TTATTTAA--TTTAT
38544 TTATTATTT
1 TTATTATTT
38553 GTAGTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 2 0.06
16 11 0.31
18 17 0.49
19 5 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTATTTAATTTAT
Found at i:39360 original size:112 final size:105
Alignment explanation
Indices: 39153--39435 Score: 266
Period size: 112 Copynumber: 2.6 Consensus size: 105
39143 AAGAAAATTT
* * * * **
39153 AATGTAGAAAAATCAGATAAACTTAATGAAAGGCTCGTTGCAGGGGACACACTTT-CCTTTTTTT
1 AATGCAGAAAAATCAAACAAACTTAATGAAAAGCTCGTTGCA-GGGACACGTTTTCCCTTTTTTT
* * *
39217 CCCAGAGAATCTCTATCATGTCATGTAAAAAACAAACTTCAATTGAGA
65 TCCAGAGAATCTCTACCATGTCATG----AAA-AAA-TT-AACTGAGA
* *
39265 AATGCAGAAAACTCATACAAACTTAATGAAAAGCTCGTTGCAGGGAACACGTTTTCCCTTTTTTT
1 AATGCAGAAAAATCAAACAAACTTAATGAAAAGCTCGTTGCAGGG-ACACGTTTTCCCTTTTTTT
* * * * * *
39330 TGCAGAGAATCTTTGCCATTTCAT-AGAAAAATTGACTGATA
65 TCCAGAGAATCTCTACCATGTCATGA-AAAAATTAACTGAGA
* * *
39371 AATGCAGAAAAAT-AAACAAACATAATGAAAAGCTCGTTGCAAGGGACGCGTTTCCCCTTTTTTT
1 AATGCAGAAAAATCAAACAAACTTAATGAAAAGCTCGTTGC-AGGGACACGTTTTCCCTTTTTTT
39435 T
65 T
39436 TATAGAAAAT
Statistics
Matches: 146, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
105 43 0.29
106 21 0.14
107 2 0.01
108 4 0.03
109 2 0.01
111 3 0.02
112 44 0.30
113 27 0.18
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.29
Consensus pattern (105 bp):
AATGCAGAAAAATCAAACAAACTTAATGAAAAGCTCGTTGCAGGGACACGTTTTCCCTTTTTTTT
CCAGAGAATCTCTACCATGTCATGAAAAAATTAACTGAGA
Found at i:39462 original size:106 final size:106
Alignment explanation
Indices: 39264--39463 Score: 269
Period size: 106 Copynumber: 1.9 Consensus size: 106
39254 TTCAATTGAG
* * * *
39264 AAATGCAGAAAACTCATACAAACTTAATGAAAAGCTCGTTGCAGGGAACACGTTTTCCCTTTTTT
1 AAATGCAGAAAAATCAAACAAACATAATGAAAAGCTCGTTGCAGGGAACACGTTTCCCCTTTTTT
* * **
39329 TTGCAGAGAATCTTTGCCATTTCATAGAAAAATTGACTGAT
66 TTACAGAAAATCTCGGCCATTTCATAGAAAAATTGACTGAT
*
39370 AAATGCAGAAAAAT-AAACAAACATAATGAAAAGCTCGTTGCAAGGG-ACGCGTTTCCCCTTTTT
1 AAATGCAGAAAAATCAAACAAACATAATGAAAAGCTCGTTGC-AGGGAACACGTTTCCCC-TTTT
* *
39433 TTTTATAGAAAATCTCGGTCATTTCATAGAA
64 TTTTACAGAAAATCTCGGCCATTTCATAGAA
39464 TTGGAAATTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
105 35 0.43
106 46 0.57
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.30
Consensus pattern (106 bp):
AAATGCAGAAAAATCAAACAAACATAATGAAAAGCTCGTTGCAGGGAACACGTTTCCCCTTTTTT
TTACAGAAAATCTCGGCCATTTCATAGAAAAATTGACTGAT
Found at i:39931 original size:121 final size:124
Alignment explanation
Indices: 39697--39988 Score: 367
Period size: 123 Copynumber: 2.4 Consensus size: 124
39687 AGAAATATAG
* ** * ** *
39697 AAAAATCAGACAAACTTAATGAAAGACTCGTTGCAGGGGACGTGTTTTCCCTTTTTTTTTTACAA
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAGGGGACGCATTTCCCCCCTTTTTTGTACAA
* * * *
39762 AGAATCTCTTCCATGTCATGCAAAAATCAAACTTCAATTAATTGACTAATAAATG-AAG
66 AGAATCTCTACCATGTAATGCAAAAATCAAACTTCAATTAATTGACTAAGAAATGCAAA
* * * *
39820 GAAATTCAGACAAGCTTAATGAAAGGCTCGTTGCAGGGGACGCATTTCCCCCCTTTTTTGTA-GA
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAGGGGACGCATTTCCCCCCTTTTTTGTACAA
*
39884 A-AATCTCTACCATTTAATAG-AAAAATCAAACTTCAATTAATTGACTAAGAAATGCAAA
66 AGAATCTCTACCATGTAAT-GCAAAAATCAAACTTCAATTAATTGACTAAGAAATGCAAA
* * * *
39942 AAAAATCAGAAAAACTTAATGAAAGGCTCGTTTCAAGGGACACATTT
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAGGGGACGCATTT
39989 TTCCCTTTTT
Statistics
Matches: 144, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
121 47 0.33
122 45 0.31
123 52 0.36
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (124 bp):
AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAGGGGACGCATTTCCCCCCTTTTTTGTACAA
AGAATCTCTACCATGTAATGCAAAAATCAAACTTCAATTAATTGACTAAGAAATGCAAA
Found at i:39995 original size:121 final size:122
Alignment explanation
Indices: 39697--39998 Score: 344
Period size: 121 Copynumber: 2.5 Consensus size: 122
39687 AGAAATATAG
* * * *
39697 AAAAATCAGACAAACTTAATGAAAGACTCGTTGC-AGGG-GACGTGTTTTCCCTTTTTTTTTTAC
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAAGGGACACAT-TTTTCCC--TTTTTTGTAC
* * * *
39760 AAAGAATCTCTTCCATGTCATGCAAAAATCAAACTTCAATTAATTGACTAATAAATGAAG
63 AAAGAATCTCTACCATGTAATGCAAAAATCAAACTTCAATTAATTGACTAAGAAATGAAA
* * * * * ** *
39820 GAAATTCAGACAAGCTTAATGAAAGGCTCGTTGCAGGGGACGCATTTCCCCCCTTTTTTGTA-GA
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAAGGGACACATTT-TTCCCTTTTTTGTACAA
*
39884 A-AATCTCTACCATTTAATAG-AAAAATCAAACTTCAATTAATTGACTAAGAAATGCAAA
65 AGAATCTCTACCATGTAAT-GCAAAAATCAAACTTCAATTAATTGACTAAGAAATG-AAA
* *
39942 AAAAATCAGAAAAACTTAATGAAAGGCTCGTTTCAAGGGACACATTTTTCCCTTTTT
1 AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAAGGGACACATTTTTCCCTTTTT
39999 ACAGAGAATC
Statistics
Matches: 148, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
121 55 0.37
122 45 0.30
123 38 0.26
124 5 0.03
125 5 0.03
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (122 bp):
AAAAATCAGACAAACTTAATGAAAGGCTCGTTGCAAGGGACACATTTTTCCCTTTTTTGTACAAA
GAATCTCTACCATGTAATGCAAAAATCAAACTTCAATTAATTGACTAAGAAATGAAA
Found at i:40220 original size:8 final size:8
Alignment explanation
Indices: 40140--40229 Score: 54
Period size: 8 Copynumber: 11.2 Consensus size: 8
40130 ATAGTTCCCC
*
40140 AACTCTCT
1 AACTCTCA
* *
40148 ATCTCTTA
1 AACTCTCA
*
40156 AACTCTTA
1 AACTCTCA
* *
40164 AATTATCA
1 AACTCTCA
*
40172 AACTCTCG
1 AACTCTCA
* * *
40180 AGCTTTGA
1 AACTCTCA
*
40188 AACTATCA
1 AACTCTCA
*
40196 AACTCTAA
1 AACTCTCA
*
40204 AACTTTCA
1 AACTCTCA
40212 AACTCTCA
1 AACTCTCA
*
40220 AATTCTCA
1 AACTCTCA
40228 AA
1 AA
40230 ATGGCTCATA
Statistics
Matches: 59, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
8 59 1.00
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.33
Consensus pattern (8 bp):
AACTCTCA
Found at i:40220 original size:24 final size:25
Alignment explanation
Indices: 40167--40230 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
40157 ACTCTTAAAT
* * *
40167 TATCAAACTCTC-GAGCTTTGAAAC
1 TATCAAACTCTCAAAACTTTCAAAC
40191 TATCAAACTCT-AAAACTTTCAAAC
1 TATCAAACTCTCAAAACTTTCAAAC
* *
40215 TCTCAAATTCTCAAAA
1 TATCAAACTCTCAAAA
40231 TGGCTCATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
24 29 0.88
25 4 0.12
ACGTcount: A:0.41, C:0.25, G:0.05, T:0.30
Consensus pattern (25 bp):
TATCAAACTCTCAAAACTTTCAAAC
Found at i:43141 original size:28 final size:29
Alignment explanation
Indices: 43086--43144 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
43076 CTCTAAAAAC
43086 CCTAAACCAATATAAAAATAAACCCTAAA
1 CCTAAACCAATATAAAAATAAACCCTAAA
*
43115 CCTAAACCAATCTAAAAGA-AAA-CCTAAA
1 CCTAAACCAATATAAAA-ATAAACCCTAAA
43143 CC
1 CC
43145 AAAAATTGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 8 0.29
29 19 0.68
30 1 0.04
ACGTcount: A:0.56, C:0.27, G:0.02, T:0.15
Consensus pattern (29 bp):
CCTAAACCAATATAAAAATAAACCCTAAA
Found at i:45866 original size:23 final size:23
Alignment explanation
Indices: 45790--45858 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
45780 TGTCACAGCT
* * *
45790 CATATAAATACACCGAAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
* *
45813 CATAGAATTGCACCGTAGTGCCG
1 CATATAATTGCACCGTAGTGCCA
*
45836 CGTATAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGTAGTGCCA
45859 TAAATAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CATATAATTGCACCGTAGTGCCA
Found at i:46044 original size:103 final size:98
Alignment explanation
Indices: 45873--46085 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 98
45863 TAATGTCCAT
45873 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
45938 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATATTCCAAAG---A-ATAT-TGTCCCG
45976 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
*
46041 GACTTCACACATGTTCCAAAGAATATTGTCCCG
66 GACTTCACACATATTCCAAAGAATATTGTCCCG
46074 AAGGACCACATA
1 AAGGACCACATA
46086 GACCCTCGAC
Statistics
Matches: 109, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
98 19 0.17
99 4 0.04
100 1 0.01
103 85 0.78
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (98 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATATTCCAAAGAATATTGTCCCG
Found at i:47155 original size:21 final size:20
Alignment explanation
Indices: 47125--47173 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
47115 TCAAAGATCT
* * *
47125 TATCACATAACTTATCTTTTA
1 TATCATATAACTTAT-TATCA
*
47146 TATCATATAATTTATTATCA
1 TATCATATAACTTATTATCA
47166 TATCATAT
1 TATCATAT
47174 GGTTTATCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (20 bp):
TATCATATAACTTATTATCA
Found at i:47170 original size:20 final size:20
Alignment explanation
Indices: 47145--47193 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
47135 CTTATCTTTT
*
47145 ATATCATATAATTTATTATC
1 ATATCATATAATTTATCATC
**
47165 ATATCATATGGTTTATCATC
1 ATATCATATAATTTATCATC
*
47185 ATAACATAT
1 ATATCATAT
47194 CACATATTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATCATATAATTTATCATC
Found at i:50941 original size:15 final size:15
Alignment explanation
Indices: 50921--50962 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
50911 CTTCATGGGG
*
50921 TAAGAAGACAACGTC
1 TAAGAAGAAAACGTC
50936 TAAGAAGAAAACGTC
1 TAAGAAGAAAACGTC
*
50951 AAAGAAGGAAAA
1 TAAGAA-GAAAA
50963 AGAAAGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.57, C:0.12, G:0.21, T:0.10
Consensus pattern (15 bp):
TAAGAAGAAAACGTC
Done.