Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003490.1 Hibiscus syriacus cultivar Beakdansim tig00007384_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: 66191
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:3421 original size:62 final size:61
Alignment explanation
Indices: 3102--3581 Score: 532
Period size: 61 Copynumber: 8.0 Consensus size: 61
3092 TCTTGTGTCC
* * * * *
3102 TAGAATCAATCCTTGACTTCCTCATGAAGAGAAGTCAACTTTTGTTATTTCTGACTTCCAG
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCAG
* * * * *
3163 T--AGTCAATCCTTGACTTCCTCATAAAGAGAAGTCAACCTTTGTTATTTTTGACTCCCCAG
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACT-CCCAG
* * * *
3223 TAGAGTCAATCCTTGATTTCCTCGTG-AGAGAAGTCAACA-TT-TTATTTGTGAC-CCTAG
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCAG
* * * * * * * *
3280 TAGAGTTAAT-ATTTGACTTCCTCTTAAAGAGAAGTTAACCTTTATTATTT-TTACTCCTAGG
1 TAGAGTCAATCA-TTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCA-G
* *
3341 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTAAACATTTGTTATTTCTGACTCCTTAG
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCC-CAG
* * *
3403 TAGAGTCAATCATTGACTTCCTCGTG-A-AGAAGTCAACATTTGTTATTTCTGACAACTCAA
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGAC-TCCCAG
* * *
3463 TAGAGTCAATCTTTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTCCTGACTCCCAG
1 TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCAG
* * *
3524 TAGAGTCAAAT-TTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCC
1 TAGAGTC-AATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCC
3582 TCAGAGGAAC
Statistics
Matches: 362, Mismatches: 41, Indels: 32
0.83 0.09 0.07
Matches are distributed among these distances:
57 24 0.07
58 11 0.03
59 64 0.18
60 67 0.19
61 112 0.31
62 82 0.23
63 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (61 bp):
TAGAGTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACATTTGTTATTTCTGACTCCCAG
Found at i:3555 original size:183 final size:179
Alignment explanation
Indices: 3102--3585 Score: 589
Period size: 183 Copynumber: 2.7 Consensus size: 179
3092 TCTTGTGTCC
* * * *
3102 TAGAATCAATCCTTGACTTCCTCATGAAGAGAAGTCAACTTTTGTTATTTCTGACTTCCAGT--A
1 TAGAGTCAATCTTTGACTTCCTCATGAAGAGAAGTCAACATTTGTTA-TTCTGACTCCCAGTAGA
* * * * *
3165 GTCAATCCTTGACTTCCTCATAAAGAGAAGTCAACCTTTGTTATTTTTGACTCCCCAGTAGAGTC
65 GTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAGTAGAGTC
* * * * *
3230 AATCCTTGATTTCCTCGTGAGAGAAGTCAACATTTTATTTGTGACCCTAG
130 AATCATTGACTTCCTCGTGAGAGAAGTCAACATTTTATTTCTGACACTAA
* * * * * * * * * *
3280 TAGAGTTAATATTTGACTTCCTCTTAAAGAGAAGTTAACCTTTATTATTTTTACTCCTAGGTAGA
1 TAGAGTCAATCTTTGACTTCCTCATGAAGAGAAGTCAACATTTGTTATTCTGACTCCCA-GTAGA
* * *
3345 GTCAATCATTGACTTCCTCGTGAAGAGAAGTAAACATTTGTTATTTCTGACTCCTTAGTAGAGTC
65 GTCAATCATTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAGTAGAGTC
3410 AATCATTGACTTCCTCGTGA-AGAAGTCAACATTTGTTATTTCTGACAACTCAA
130 AATCATTGACTTCCTCGTGAGAGAAGTCAACA-TT-TTATTTCTGAC-ACT-AA
* *
3463 TAGAGTCAATCTTTGACTCCCTCGTGAAGAGAAGTCAACATTTGTTATTCCTGACTCCCAGTAGA
1 TAGAGTCAATCTTTGACTTCCTCATGAAGAGAAGTCAACATTTGTTATT-CTGACTCCCAGTAGA
* *
3528 GTCAAAT-TTTGACTTCCTCGTGAAGAGAAGTCAACCTTTATTATTTCTGACTCCTCAG
65 GTC-AATCATTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAG
3586 AGGAACTAAT
Statistics
Matches: 255, Mismatches: 42, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
177 8 0.03
178 40 0.16
179 11 0.04
180 78 0.31
181 10 0.04
182 2 0.01
183 96 0.38
184 10 0.04
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (179 bp):
TAGAGTCAATCTTTGACTTCCTCATGAAGAGAAGTCAACATTTGTTATTCTGACTCCCAGTAGAG
TCAATCATTGACTTCCTCGTGAAGAGAAGTCAACCTTTGTTATTTCTGACTCCTCAGTAGAGTCA
ATCATTGACTTCCTCGTGAGAGAAGTCAACATTTTATTTCTGACACTAA
Found at i:3816 original size:36 final size:36
Alignment explanation
Indices: 3764--4292 Score: 735
Period size: 36 Copynumber: 14.7 Consensus size: 36
3754 TATTTCAAAT
*
3764 TTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
*
3800 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
3836 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
*
3872 TTAGCCTCCACGGAAGAGTAGTGAAGTAAAGTC-ATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
* * *
3908 TTAGCCTCCAAGGAAGAGTAGTGAAGAAAAACAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
3944 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
** * *
3980 TTAGCCTCCTTGGAAGAGTAGTAAAGCAAAGTC-ATT
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
*
4016 TTAGCCTCCACGGAAGAGTAGTGAAACAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* * * * *
4052 TTAGCATCCGCGGAATAGAAGTGAAGTAAAGTC-ATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAG-CAATC
*
4088 TTAGCCTCCACGGAAGAGTAGTGAACCAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* * * *
4124 TTAGCATCCACGAAAGACTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* *
4160 TTAGCCTCCATGGAAGAGTAGTGAAGTAAAGCAATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
* *
4196 TTAGCCTCCACGGAAGAGTAGTGAAGTAAATTC--TC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAA-GCAATC
* * *
4231 TTAGCCTTCACGGAAGATTAGTGAAGCAAAGCCATC
1 TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
4267 TTAGCCTCCACGGAAGAGTAGTGAAG
1 TTAGCCTCCACGGAAGAGTAGTGAAG
4293 TAAACATCAT
Statistics
Matches: 434, Mismatches: 50, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
34 1 0.00
35 32 0.07
36 397 0.91
37 4 0.01
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (36 bp):
TTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAATC
Found at i:4513 original size:3 final size:3
Alignment explanation
Indices: 4495--4538 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
4485 TTTCGTCCCG
*
4495 TAT TTT TAT ATAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4539 CAAAAAATAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4533 original size:23 final size:22
Alignment explanation
Indices: 4495--4538 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
4485 TTTCGTCCCG
*
4495 TATTTTTATATATTATTATTAT
1 TATTATTATATATTATTATTAT
4517 TATTATTATTATATTATTATTA
1 TATTATTA-TATATTATTATTA
4539 CAAAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTATTATATATTATTATTAT
Found at i:5710 original size:20 final size:22
Alignment explanation
Indices: 5665--5722 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
5655 TGCAGGGCTG
5665 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
5689 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
5709 TGTATCGATGCACT
1 TGCATCGATGCACT
5723 TCAAAGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:13510 original size:22 final size:21
Alignment explanation
Indices: 13468--13507 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13458 GAGTTTATTT
*
13468 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
13489 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
13508 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:15647 original size:65 final size:63
Alignment explanation
Indices: 15453--15658 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 63
15443 CTAAGAGTGT
* * * *
15453 ATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGC-CAAAGTGCATCGATGTATGGCTGGTG
1 ATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTTGGTG
15516 C
63 C
*
15517 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT-GTG
1 ATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-TGGTG
15581 C
63 C
* **
15582 ATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-TTGGT
15645 GC
62 GC
*
15647 ATCGGTGCATCA
1 ATCGATGCATCA
15659 CTCTGAAAAA
Statistics
Matches: 121, Mismatches: 11, Indels: 19
0.80 0.07 0.13
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 45 0.37
65 64 0.53
66 5 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTGGTGC
Found at i:17081 original size:23 final size:23
Alignment explanation
Indices: 17036--17081 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17026 ACATTTTATA
*
17036 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTATACG
*
17059 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCAATTATACG
17082 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTATACG
Found at i:18651 original size:20 final size:21
Alignment explanation
Indices: 18622--18660 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18612 TATTTAACCA
*
18622 TTTTACTTTTATC-ATCAATC
1 TTTTAATTTTATCAATCAATC
18642 TTTTAATTTTATCAATCAA
1 TTTTAATTTTATCAATCAA
18661 ATCACTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTAATTTTATCAATCAATC
Found at i:19104 original size:31 final size:30
Alignment explanation
Indices: 18997--19108 Score: 99
Period size: 31 Copynumber: 3.8 Consensus size: 30
18987 TATTTTATTT
* ** * *
18997 TTATCTTAACTTATTAAATATATTTATTT-
1 TTATTTTAACTTAAAAAATATATCTCTTTC
* *
19026 TTATTTTAACTT-AAAACTAT-T-T-TAATC
1 TTATTTTAACTTAAAAAATATATCTCT-TTC
19053 TTATTTTAACTTAAAAAATATATCTCTTTC
1 TTATTTTAACTTAAAAAATATATCTCTTTC
*
19083 TTATTTTAACATTTAAAAATATATCT
1 TTATTTTAAC-TTAAAAAATATATCT
19109 TAATTTTAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.01
26 2 0.03
27 13 0.19
28 12 0.18
29 12 0.18
30 13 0.19
31 15 0.22
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (30 bp):
TTATTTTAACTTAAAAAATATATCTCTTTC
Found at i:19118 original size:19 final size:18
Alignment explanation
Indices: 19093--19172 Score: 70
Period size: 19 Copynumber: 4.3 Consensus size: 18
19083 TTATTTTAAC
*
19093 ATTTAAAAATATATCTTA
1 ATTTTAAAATATATCTTA
* **
19111 ATTTTAAAATAAAAGTATA
1 ATTTTAAAATATATCT-TA
* *
19130 TATTTTAATATATATTTTA
1 -ATTTTAAAATATATCTTA
19149 ACTTTTAAAATATATCTTA
1 A-TTTTAAAATATATCTTA
*
19168 GTTTT
1 ATTTT
19173 CATATATTTG
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
18 17 0.35
19 19 0.40
20 12 0.25
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTTAAAATATATCTTA
Found at i:19313 original size:30 final size:30
Alignment explanation
Indices: 19277--19357 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
19267 AACGTATTAA
* *
19277 ATATATTTTATTCTTTTTTTGATTTAAAAT
1 ATATATTTTATTCTTTTTTAGATTAAAAAT
* *
19307 ATATATTTTAGTCTTATTTTAGCTTAAAAAT
1 ATATATTTTATTCTT-TTTTAGATTAAAAAT
*
19338 ATTTTATTTT-TATCTTTTTT
1 A-TATATTTTAT-TCTTTTTT
19358 GAGTCAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
30 14 0.33
31 17 0.40
32 11 0.26
ACGTcount: A:0.28, C:0.05, G:0.04, T:0.63
Consensus pattern (30 bp):
ATATATTTTATTCTTTTTTAGATTAAAAAT
Found at i:22427 original size:2 final size:2
Alignment explanation
Indices: 22422--22446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22412 AGTATATATA
22422 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
22447 TAATATCTAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:22530 original size:2 final size:2
Alignment explanation
Indices: 22525--22585 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
22515 AGGTTTAAAC
22525 AT AT AT AT AT 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 AT AT AT AT AT
22567 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
22586 CAATTAAACA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27209 original size:15 final size:14
Alignment explanation
Indices: 27180--27228 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
27170 TGGACCACTA
27180 AGTCAACTC-ATTG
1 AGTCAACTCTATTG
27193 AGTCAACTCGTATTG
1 AGTCAACTC-TATTG
* *
27208 AGTCAGCTCATATCG
1 AGTCAACTC-TATTG
27223 AGTCAA
1 AGTCAA
27229 GTCAGACCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 9 0.30
15 21 0.70
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (14 bp):
AGTCAACTCTATTG
Found at i:27289 original size:16 final size:16
Alignment explanation
Indices: 27253--27300 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
27243 TTTAACCCTA
*
27253 GGTTGACTTTGACTAG
1 GGTTGACTTTGACCAG
* *
27269 AGTTGACTTTGACCGG
1 GGTTGACTTTGACCAG
*
27285 GGTTGATTTTGACCAG
1 GGTTGACTTTGACCAG
27301 AAAGTCAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.31, T:0.35
Consensus pattern (16 bp):
GGTTGACTTTGACCAG
Found at i:38417 original size:7 final size:7
Alignment explanation
Indices: 38401--38472 Score: 72
Period size: 7 Copynumber: 9.3 Consensus size: 7
38391 AATCCCACAT
38401 AAAAAGA
1 AAAAAGA
*
38408 AAATAGA
1 AAAAAGA
38415 AAAAAGA
1 AAAAAGA
38422 AAAAAGA
1 AAAAAGA
38429 AGAATAAGA
1 A-AA-AAGA
38438 AGAATAAGA
1 A-AA-AAGA
38447 AAAAAGAAA
1 AAAAAG--A
38456 GAAAAAGA
1 -AAAAAGA
38464 AAAAAGA
1 AAAAAGA
38471 AA
1 AA
38473 GAAATAAAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
7 32 0.55
8 5 0.09
9 15 0.26
10 6 0.10
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (7 bp):
AAAAAGA
Found at i:38424 original size:6 final size:6
Alignment explanation
Indices: 38401--38476 Score: 57
Period size: 6 Copynumber: 12.5 Consensus size: 6
38391 AATCCCACAT
* * * *
38401 AAAAAG AAAATAG AAAAAAG AAAAAAG AAGAAT AAGAAG AATAAG AAAAA-
1 AAAAAG AAAA-AG -AAAAAG -AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* *
38451 AGAAAG AAAAAG AAAAA- AGAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
38477 TAAAAGTTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
5 8 0.14
6 34 0.60
7 11 0.19
8 4 0.07
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:38463 original size:17 final size:17
Alignment explanation
Indices: 38403--38476 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
38393 TCCCACATAA
38403 AAAGAAAATAGAAAAAAG
1 AAAGAAAA-AGAAAAAAG
*
38421 AAA-AAAGAAG-AATAAG
1 AAAGAAA-AAGAAAAAAG
*
38437 -AAGAATAAGAAAAAAG
1 AAAGAAAAAGAAAAAAG
38453 AAAGAAAAAGAAAAAAG
1 AAAGAAAAAGAAAAAAG
38470 AAAGAAA
1 AAAGAAA
38477 TAAAAGTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
15 5 0.10
16 12 0.25
17 27 0.56
18 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAAG
Found at i:45529 original size:27 final size:26
Alignment explanation
Indices: 45496--45591 Score: 93
Period size: 27 Copynumber: 3.6 Consensus size: 26
45486 AAATTTTTAA
*
45496 AAGTTAAAATAAGAAAAAGACATTTTT
1 AAGTTAAAATAA-AAAAAAACATTTTT
* ** *
45523 TAGTTAAAATAATATTAAAATATTTTT
1 AAGTTAAAATAA-AAAAAAACATTTTT
* *
45550 AAGTTAAAATAAAAAAAAATATTTAAT
1 AAGTTAAAATAAAAAAAAACATTT-TT
*
45577 AAGTTAAGATAAAAA
1 AAGTTAAAATAAAAA
45592 TATAATATAT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 10 0.18
27 47 0.82
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (26 bp):
AAGTTAAAATAAAAAAAAACATTTTT
Found at i:45582 original size:54 final size:59
Alignment explanation
Indices: 45488--45615 Score: 142
Period size: 54 Copynumber: 2.2 Consensus size: 59
45478 ATTAAGATAA
* * * *
45488 ATTTTTAAAAGTTAAAATAAGAAAAAGACATTTTTTAGTTAAAAT-AATAT-TAA-A-AT
1 ATTTTT-AAAGTTAAAATAAGAAAAAAACATTTATAAGTTAAAATAAAAATATAATATAT
* *
45544 ATTTTT-AAGTTAAAATAA-AAAAAAATATTTAATAAGTTAAGATAAAAATATAATATAT
1 ATTTTTAAAGTTAAAATAAGAAAAAAACATTT-ATAAGTTAAAATAAAAATATAATATAT
45602 ATTTTTAAAGTTAA
1 ATTTTTAAAGTTAA
45616 GATATGAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
53 10 0.17
54 21 0.35
55 4 0.07
56 9 0.15
57 1 0.02
58 8 0.13
59 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (59 bp):
ATTTTTAAAGTTAAAATAAGAAAAAAACATTTATAAGTTAAAATAAAAATATAATATAT
Found at i:47615 original size:2 final size:2
Alignment explanation
Indices: 47608--47644 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
47598 TTTTCCTAAC
47608 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
47645 GGAGTCTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:51361 original size:17 final size:17
Alignment explanation
Indices: 51339--51396 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
51329 AAGATTAAAA
* *
51339 GAACTAGTTTGATTAAT
1 GAACTACTTTAATTAAT
* *
51356 GAACTAATTTTAATGAAT
1 GAACT-ACTTTAATTAAT
*
51374 GAACTACTTTAATTAGT
1 GAACTACTTTAATTAAT
51391 GAACTA
1 GAACTA
51397 TCAATCTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
17 20 0.59
18 14 0.41
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (17 bp):
GAACTACTTTAATTAAT
Found at i:56116 original size:18 final size:18
Alignment explanation
Indices: 56090--56144 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
56080 ACCGGTTCCA
56090 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
56108 ACCCAACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
56126 ACCTGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
56144 A
1 A
56145 TCGAGTGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:56192 original size:29 final size:29
Alignment explanation
Indices: 56149--56355 Score: 233
Period size: 29 Copynumber: 7.2 Consensus size: 29
56139 CGTTGATCGA
*
56149 GTGATATTTTAGTAATTATTTTTAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
*
56178 GTGATATTTTGGTAATTATTTTTAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
* *
56207 GTGATATTTTGGTAATTATTTTGAAAATG
1 GTGATATTTTCGTAATTATTTTTAAAATG
* * **
56236 GTGTTATTTTCATAA-T-TTTTTAAAAAA
1 GTGATATTTTCGTAATTATTTTTAAAATG
* * *
56263 GTGATAATTTCGTAATTTTTTTTTAAAT-
1 GTGATATTTTCGTAATTATTTTTAAAATG
*
56291 GTGATATTTTCATAATTAGTTTTTAAAA-G
1 GTGATATTTTCGTAATTA-TTTTTAAAATG
* * *
56320 GTGATATTTTAGTAAATATTTCTTAAAAGG
1 GTGATATTTTCGTAATTATTT-TTAAAATG
56350 GTGATA
1 GTGATA
56356 ATTGTGTAAA
Statistics
Matches: 152, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
27 20 0.13
28 20 0.13
29 105 0.69
30 7 0.05
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (29 bp):
GTGATATTTTCGTAATTATTTTTAAAATG
Found at i:63542 original size:29 final size:28
Alignment explanation
Indices: 63500--63679 Score: 131
Period size: 29 Copynumber: 6.4 Consensus size: 28
63490 CGTGACCGAG
63500 GATATTTTAGTAATTATTTTTAAAATGGT
1 GATATTTT-GTAATTATTTTTAAAATGGT
* *
63529 GATATTTTGGTAATGA-TTTCAAAATGGT
1 GATATTTT-GTAATTATTTTTAAAATGGT
* **
63557 GCTATTTT-T--TTAATTTTTAAAAAAGT
1 GATATTTTGTAATT-ATTTTTAAAATGGT
* *
63583 GATAATTT-T-ATTTTTTTTAAAAT-GT
1 GATATTTTGTAATTATTTTTAAAATGGT
** *
63608 GATATTTTCGTAATTAGCTTTAAAAAGGT
1 GATATTTT-GTAATTATTTTTAAAATGGT
* *
63637 GATATTTTAGTAAATATTTCTTAAAAGGGT
1 GATATTTT-GTAATTATTT-TTAAAATGGT
*
63667 GATAATTGTGTAA
1 GAT-ATTTTGTAA
63680 AATGGTTGAT
Statistics
Matches: 119, Mismatches: 23, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
24 1 0.01
25 10 0.08
26 26 0.22
27 3 0.03
28 28 0.24
29 31 0.26
30 16 0.13
31 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (28 bp):
GATATTTTGTAATTATTTTTAAAATGGT
Found at i:63562 original size:28 final size:29
Alignment explanation
Indices: 63500--63564 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 29
63490 CGTGACCGAG
* *
63500 GATATTTTAGTAATTATTTTTAAAATGGT
1 GATATTTTAGTAATGATTTTCAAAATGGT
*
63529 GATATTTTGGTAATGA-TTTCAAAATGGT
1 GATATTTTAGTAATGATTTTCAAAATGGT
*
63557 GCTATTTT
1 GATATTTT
63565 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (29 bp):
GATATTTTAGTAATGATTTTCAAAATGGT
Found at i:63597 original size:24 final size:24
Alignment explanation
Indices: 63564--63615 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
63554 GGTGCTATTT
63564 TTTTA-ATTTTTAAAAAAGTGATAA
1 TTTTATATTTTTAAAAAAGTGAT-A
* * *
63588 TTTTATTTTTTTTAAAATGTGATA
1 TTTTATATTTTTAAAAAAGTGATA
63612 TTTT
1 TTTT
63616 CGTAATTAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.58
Consensus pattern (24 bp):
TTTTATATTTTTAAAAAAGTGATA
Found at i:65677 original size:16 final size:16
Alignment explanation
Indices: 65656--65686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65646 AAAAAAATAA
*
65656 AAAAATATGATAAAGG
1 AAAAATAAGATAAAGG
65672 AAAAATAAGATAAAG
1 AAAAATAAGATAAAG
65687 TTAAGATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (16 bp):
AAAAATAAGATAAAGG
Found at i:65711 original size:4 final size:4
Alignment explanation
Indices: 65702--65813 Score: 54
Period size: 4 Copynumber: 27.2 Consensus size: 4
65692 ATAGGGAATA
* *
65702 AAAT AAAT AAAT AAAG ATAA- AAAT GAAAT AGAAAT AAAA AAAT -AAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT -AAAT --AAAT AAAT AAAT AAAT
* * * *
65748 AAAT ATAAT -AAT ATAT ATAT ATAT AAAT AATAT ATAT AAA- AAAT -AAT
1 AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT
*
65795 AATAT ACCAT AAAT AAAT A
1 AA-AT A-AAT AAAT AAAT A
65814 GAACAAGAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 24
0.73 0.08 0.20
Matches are distributed among these distances:
3 14 0.16
4 50 0.57
5 18 0.21
6 5 0.06
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:65778 original size:19 final size:18
Alignment explanation
Indices: 65749--65810 Score: 69
Period size: 19 Copynumber: 3.6 Consensus size: 18
65739 AAAAATAATA
65749 AATAT-AATAATATATAT
1 AATATAAATAATATATAT
65766 ATATATAAATAATATATAT
1 A-ATATAAATAATATATAT
65785 AA-A-AAATAATA-ATAT
1 AATATAAATAATATATAT
**
65800 ACCATAAATAA
1 AATATAAATAA
65811 ATAGAACAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 5 0.12
16 9 0.22
17 8 0.20
18 5 0.12
19 13 0.32
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
AATATAAATAATATATAT
Done.