Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002295.1 Hibiscus syriacus cultivar Beakdansim tig00004667_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: 69457
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:4114 original size:4 final size:4
Alignment explanation
Indices: 4107--4131 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4097 TAAAAAATAA
4107 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4132 GCAATCCTAC
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):
AAAT
Found at i:14107 original size:21 final size:21
Alignment explanation
Indices: 14082--14121 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14072 GTAAAAAAAT
* * *
14082 TAAAATATTATTATTTTTACC
1 TAAAACATTAATAATTTTACC
14103 TAAAACATTAATAATTTTA
1 TAAAACATTAATAATTTTA
14122 ATAATTCCGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAACATTAATAATTTTACC
Found at i:17751 original size:20 final size:21
Alignment explanation
Indices: 17721--17763 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
17711 TTGGGTTTTG
17721 TTGTCAATTGGGCCTCCAGAC
1 TTGTCAATTGGGCCTCCAGAC
*
17742 TTGT-AATTGGGCCTCTAGAC
1 TTGTCAATTGGGCCTCCAGAC
17762 TT
1 TT
17764 ATTATATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (21 bp):
TTGTCAATTGGGCCTCCAGAC
Found at i:17783 original size:3 final size:3
Alignment explanation
Indices: 17777--17810 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
17767 ATATTATTTG
17777 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17811 TTATTTATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:18387 original size:218 final size:219
Alignment explanation
Indices: 17993--18511 Score: 719
Period size: 218 Copynumber: 2.4 Consensus size: 219
17983 AAGTAAAAAA
* * * * * *
17993 ATCCTTCCCGAAGGTCTTACAGATGGC-CCAAATGACTTAACATCTTGCTCGAAAGACTAACAGA
1 ATCCTACCCGAAGGTCTTACGGATGACTCGAAA-GACTTAACATCTTGCTTGAAAGACTTACAGA
* * *
18057 TGA-CCTGAAGGATTTAGATATTATTGAGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCTCT
65 TGACCCT-AAGGATTTA-AAATCATTGAGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCT
**
18121 TTCTTACTTTTCAAAAAAATTCATTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTATC
128 TTCTTACTTTTCAAAAAAATTCATTTTCAAAACATTAAATGAGAAACTTTGGTAATCGCTTTATC
18186 ATTTTCATGTGAAAATCATGTGTAAAC
193 ATTTTCATGTGAAAATCATGTGTAAAC
* * * *
18213 ATCCTACCCGAAGGTCTTATGGAT-AGCAT-GAAAGACTTATCACCTTGCTTGAAAGACTTATAG
1 ATCCTACCCGAAGGTCTTACGGATGA-C-TCGAAAGACTTAACATCTTGCTTGAAAGACTTACAG
18276 ATGACCCTAAGGATTTAAAATCATT-AGGAAATAGTTTACTAGGTAAGAAACTTTG-AAATCGCT
64 ATGACCCTAAGGATTTAAAATCATTGA-GAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCT
* *
18339 TTCTTACTTTTC-AAAAATTTCATTTCTCAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCT
128 TTCTTACTTTTCAAAAAAATTCATTT-TCAAAACATTAAATGAGAAACTTTGGTAATCGCTTTAT
18403 CATTTTCATGTGAAAATCATGTGTAAAC
192 CATTTTCATGTGAAAATCATGTGTAAAC
* * * *
18431 ATCCTACCCGAAGGTCTTACGGATGACTCGAAGGATTTAACATCTTGCTTGAAAGACATACAAAT
1 ATCCTACCCGAAGGTCTTACGGATGACTCGAAAGACTTAACATCTTGCTTGAAAGACTTACAGAT
* *
18496 GACCCGAAAGATTTAA
66 GACCCTAAGGATTTAA
18512 GCATCATGCT
Statistics
Matches: 264, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
217 13 0.05
218 150 0.57
219 35 0.13
220 60 0.23
221 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (219 bp):
ATCCTACCCGAAGGTCTTACGGATGACTCGAAAGACTTAACATCTTGCTTGAAAGACTTACAGAT
GACCCTAAGGATTTAAAATCATTGAGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGCTTTC
TTACTTTTCAAAAAAATTCATTTTCAAAACATTAAATGAGAAACTTTGGTAATCGCTTTATCATT
TTCATGTGAAAATCATGTGTAAAC
Found at i:18551 original size:42 final size:41
Alignment explanation
Indices: 18459--18560 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
18449 ACGGATGACT
* * *
18459 CGAAGGATTTAACATCTTGCTTGAAAGACATACAAATGACC
1 CGAAGGATTTAACATCATGCTCGAAAGACATACAAATGAAC
* * **
18500 CGAAAGATTTAAGCATCATGCTCGAAAGACTTACTGATGAAC
1 CGAAGGATTTAA-CATCATGCTCGAAAGACATACAAATGAAC
*
18542 CTAAGGATTTAAACATCAT
1 CGAAGGATTT-AACATCAT
18561 TGGGAAATAG
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
41 11 0.22
42 37 0.74
43 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (41 bp):
CGAAGGATTTAACATCATGCTCGAAAGACATACAAATGAAC
Found at i:24125 original size:21 final size:19
Alignment explanation
Indices: 24087--24132 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
24077 AATTAATCCT
24087 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
24107 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
24128 A-TAAT
1 ACTAAT
24133 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:30682 original size:2 final size:2
Alignment explanation
Indices: 30675--30730 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
30665 TTTTCATGAT
30675 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
30717 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
30731 CTCTTGTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35248 original size:36 final size:36
Alignment explanation
Indices: 35100--35247 Score: 183
Period size: 36 Copynumber: 4.1 Consensus size: 36
35090 AGATTCTTTC
* *
35100 AAGCGATGCACATTAAGCCTTCACGGAAGAGTAATG
1 AAGCGATGCACATTCAGCCTTCACGAAAGAGTAATG
* *
35136 AAGCGATGCACATTCAGCCTTCACGGAAGAGTAGTG
1 AAGCGATGCACATTCAGCCTTCACGAAAGAGTAATG
* * *
35172 AAGTGATGCACATTCAACCTTCAC-AGAAGAGTAGTG
1 AAGCGATGCACATTCAGCCTTCACGA-AAGAGTAATG
* *
35208 AAGCAATGCACATCCAGCCTTCAC-AAAGAAGTAATG
1 AAGCGATGCACATTCAGCCTTCACGAAAG-AGTAATG
35244 AAGC
1 AAGC
35248 AGGAACATAT
Statistics
Matches: 100, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
35 3 0.03
36 97 0.97
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (36 bp):
AAGCGATGCACATTCAGCCTTCACGAAAGAGTAATG
Found at i:35443 original size:8 final size:8
Alignment explanation
Indices: 35430--35483 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
35420 TTTCAACATA
35430 ATTATATT
1 ATTATATT
35438 ATTATATT
1 ATTATATT
35446 A-TA-ATT
1 ATTATATT
35452 ACTT-TATT
1 A-TTATATT
*
35460 AGTATATTAT
1 ATTATA-T-T
35470 ATTATATT
1 ATTATATT
35478 ATTATA
1 ATTATA
35484 ACTAATTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
6 4 0.11
7 3 0.08
8 23 0.61
9 2 0.05
10 6 0.16
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (8 bp):
ATTATATT
Found at i:35448 original size:13 final size:13
Alignment explanation
Indices: 35430--35496 Score: 68
Period size: 13 Copynumber: 5.1 Consensus size: 13
35420 TTTCAACATA
35430 ATTATATTATTAT
1 ATTATATTATTAT
35443 ATTATAATTACTT-T
1 ATTAT-ATTA-TTAT
35457 ATTAGTA-TATTAT
1 ATTA-TATTATTAT
35470 ATTATATTATTAT
1 ATTATATTATTAT
*
35483 AACTA-ATTATTAT
1 -ATTATATTATTAT
35496 A
1 A
35497 ATTTTATTAC
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
12 5 0.11
13 26 0.55
14 13 0.28
15 3 0.06
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:35505 original size:32 final size:32
Alignment explanation
Indices: 35436--35505 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
35426 CATAATTATA
*
35436 TTATTATATTATAATTACTTTATTAGTATATT
1 TTATTATATTATAATAACTTTATTAGTATATT
* *
35468 ATATTATATTATTATAACTAATTATTA-TA-ATT
1 TTATTATATTATAATAACT--TTATTAGTATATT
35500 TTATTA
1 TTATTA
35506 CAGGCTCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
32 24 0.75
33 2 0.06
34 6 0.19
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (32 bp):
TTATTATATTATAATAACTTTATTAGTATATT
Found at i:35596 original size:17 final size:16
Alignment explanation
Indices: 35575--35633 Score: 73
Period size: 17 Copynumber: 3.5 Consensus size: 16
35565 CCATATTACA
*
35575 ACCAGACCCGGTGCAC
1 ACCAGACCCGGTGCAG
*
35591 ATCCAGACTCGGTGCAG
1 A-CCAGACCCGGTGCAG
35608 ACCTAGACCCGGTGCAG
1 ACC-AGACCCGGTGCAG
35625 ACCCAGACC
1 A-CCAGACC
35634 AAATCCAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.08
17 32 0.86
18 2 0.05
ACGTcount: A:0.25, C:0.39, G:0.25, T:0.10
Consensus pattern (16 bp):
ACCAGACCCGGTGCAG
Found at i:36542 original size:19 final size:19
Alignment explanation
Indices: 36496--36533 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
36486 CCCTCCCCGA
36496 ACGGTGTCGTTTTAGGGAG
1 ACGGTGTCGTTTTAGGGAG
36515 ACGGTGTCGTTTTAGGGAG
1 ACGGTGTCGTTTTAGGGAG
36534 GGAGTGTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.11, G:0.42, T:0.32
Consensus pattern (19 bp):
ACGGTGTCGTTTTAGGGAG
Found at i:36842 original size:28 final size:28
Alignment explanation
Indices: 36811--36870 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
36801 AACTAGGTTA
* *
36811 ATTAATT-TTAATATTTTATGTTTTAATT
1 ATTAATTATTAATATTATATG-ATTAATT
*
36839 ATTAATTATTATTATTATATGATTAATT
1 ATTAATTATTAATATTATATGATTAATT
36867 ATTA
1 ATTA
36871 TTAGTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (28 bp):
ATTAATTATTAATATTATATGATTAATT
Found at i:37825 original size:22 final size:23
Alignment explanation
Indices: 37800--37842 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
37790 TATACTTTAA
37800 AAATTAT-TCTTTTTTAAAAAAG
1 AAATTATATCTTTTTTAAAAAAG
* *
37822 AAATTATATTTTTTTTCAAAA
1 AAATTATATCTTTTTTAAAAA
37843 TGAGGGCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATTATATCTTTTTTAAAAAAG
Found at i:38168 original size:48 final size:47
Alignment explanation
Indices: 38094--38202 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 47
38084 AGAATTAGGC
* * **
38094 GTATACTA-TGTTTTGGAGAAGTTATTAGATTTAATGGAAATTTAGT
1 GTATACTATTTTTTTGGAAAAGTTATTAGATTTAATGGAAAGCTAGT
*
38140 GTATACTATTTTTTTGGAAAAAGTTATTAGATTTAATGGAGAGCTAGT
1 GTATACTATTTTTTTGG-AAAAGTTATTAGATTTAATGGAAAGCTAGT
38188 GTATACTATTTTTTT
1 GTATACTATTTTTTT
38203 TTTGTAGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
46 8 0.14
47 7 0.12
48 41 0.73
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (47 bp):
GTATACTATTTTTTTGGAAAAGTTATTAGATTTAATGGAAAGCTAGT
Found at i:38223 original size:50 final size:47
Alignment explanation
Indices: 38094--38226 Score: 151
Period size: 48 Copynumber: 2.8 Consensus size: 47
38084 AGAATTAGGC
* * **
38094 GTATACTA-TGTTTTGGAGAAGTTATTAGATTTAATGGAAATTTAGT
1 GTATACTATTTTTTTGGAGAAATTATTAGATTTAATGGAAAGCTAGT
* *
38140 GTATACTATTTTTTTGGAAAAAGTTATTAGATTTAATGGAGAGCTAGT
1 GTATACTATTTTTTTGGAGAAA-TTATTAGATTTAATGGAAAGCTAGT
* *
38188 GTATACTATTTTTTTTTTGTAGAAATTGTTAGATTTAAT
1 GTATACTA---TTTTTTTGGAGAAATTATTAGATTTAAT
38227 TTAATATGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 8 0.11
47 10 0.14
48 30 0.41
50 13 0.18
51 12 0.16
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.47
Consensus pattern (47 bp):
GTATACTATTTTTTTGGAGAAATTATTAGATTTAATGGAAAGCTAGT
Found at i:42597 original size:28 final size:28
Alignment explanation
Indices: 42555--42621 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
42545 TTTGTTCGGG
*
42555 TCGGGTCGGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAATGTGATAT
42582 TCGGGTCGGGTTTTTTTAAATGTGATAT
1 TCGGGTCGGGTTTTTTTAAATGTGATAT
42610 TCGGGTCGGGTT
1 TCGGGTCGGGTT
42622 CGGTTTTAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.13, C:0.09, G:0.34, T:0.43
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAATGTGATAT
Found at i:43234 original size:18 final size:17
Alignment explanation
Indices: 43196--43247 Score: 70
Period size: 18 Copynumber: 3.0 Consensus size: 17
43186 TATGGAATTG
*
43196 GATTCCAATTCCT-ACA
1 GATTCCAATTCCTCATA
43212 GATTCCAATTCCTTCATA
1 GATTCCAATTCC-TCATA
43230 GATTCCAATTCCCTCATA
1 GATTCCAATT-CCTCATA
43248 AACATTCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 12 0.38
17 1 0.03
18 17 0.53
19 2 0.06
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (17 bp):
GATTCCAATTCCTCATA
Found at i:45166 original size:12 final size:12
Alignment explanation
Indices: 45143--45173 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
45133 AACTTTTGAC
45143 TTATTCTTTTTAT
1 TTATT-TTTTTAT
45156 TTATTTTTTTAT
1 TTATTTTTTTAT
45168 TTATTT
1 TTATTT
45174 ACTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTTTTAT
Found at i:45295 original size:27 final size:28
Alignment explanation
Indices: 45247--45300 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
45237 ATATATATAT
*
45247 ATATATATATTATTTTTCATTAATATTA
1 ATATATATAATATTTTTCATTAATATTA
* *
45275 ATATAT-TAATATTTTTTATTATTATT
1 ATATATATAATATTTTTCATTAATATT
45301 TTCTCATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (28 bp):
ATATATATAATATTTTTCATTAATATTA
Found at i:48974 original size:95 final size:95
Alignment explanation
Indices: 48800--49061 Score: 348
Period size: 95 Copynumber: 2.7 Consensus size: 95
48790 ACATTATAAT
* * * * *
48800 ATTATATATACACAATAAAGCTTGAGCTATCCCTCTAAAGCAATTGGTTAAACGCCCTGGCTTTA
1 ATTATA-ATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
* *
48865 TGGATAAGATTCAGCTAGCCTGATAAAGGTG
65 TGGATAAAATTCAGCTAGCCTGATAAAGGCG
*
48896 ATTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
1 ATTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
48961 GGATAAAATTCAGCTAGCCTGATAAAGGCG
66 GGATAAAATTCAGCTAGCCTGATAAAGGCG
* * * * *
48991 ATTATAATAT-CTATACAATGATATTAAGATGTCCCTATAGAGCAATTGGTTAAA-GGCCCGGCT
1 ATTATAATATACAATA-AA-G--CTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCT
49054 TTATGGAT
62 TTATGGAT
49062 TCAACTAGCC
Statistics
Matches: 149, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
94 4 0.03
95 94 0.63
96 7 0.05
97 16 0.11
98 28 0.19
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (95 bp):
ATTATAATATACAATAAAGCTTGAGATGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTAT
GGATAAAATTCAGCTAGCCTGATAAAGGCG
Found at i:50396 original size:36 final size:36
Alignment explanation
Indices: 50347--50463 Score: 135
Period size: 36 Copynumber: 3.2 Consensus size: 36
50337 TAATTTACTC
* * *
50347 AAAAAAAAGTTTTGTCTCTCTTGATACAGTTTCTTTT
1 AAAACAAA-TTTTGTCTCTCTTGAGACAGTTTCTCTT
* *
50384 AAAACAAATTTTGTCTATCTTGAGACATTTTCTCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
** * *
50420 AAAACAAATTTTGTCTCTCTAAAGAAAGTTTCCCTT
1 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
*
50456 GAAACAAA
1 AAAACAAA
50464 ATCTTTGAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 61 0.90
37 7 0.10
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
Found at i:50543 original size:36 final size:36
Alignment explanation
Indices: 50478--50598 Score: 140
Period size: 36 Copynumber: 3.4 Consensus size: 36
50468 TTGAATCTGT
* * * *
50478 TTTC-CTTGAAACAAATTTCGTTTCCCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
50513 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAAACAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
50549 TTTCTCTTAAAACAAA--TTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
50583 TTTCCCTTGAAACAAA
1 TTTCTCTTAAAACAAA
50599 ATCTTTGAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
34 30 0.41
35 4 0.05
36 39 0.53
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:50556 original size:15 final size:15
Alignment explanation
Indices: 50536--50596 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
50526 AAATTTTGTC
50536 TCTCTTGAAACATTT
1 TCTCTTGAAACATTT
*
50551 TCTCTTAAAACAAATTGT
1 TCTCTTGAAAC--ATT-T
* *
50569 CTCTCTTGAGACAGTT
1 -TCTCTTGAAACATTT
*
50585 TCCCTTGAAACA
1 TCTCTTGAAACA
50597 AAATCTTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
15 20 0.56
16 1 0.03
17 5 0.14
18 1 0.03
19 9 0.25
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.38
Consensus pattern (15 bp):
TCTCTTGAAACATTT
Found at i:50575 original size:19 final size:19
Alignment explanation
Indices: 50519--50575 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 19
50509 ACAGTTTCTT
50519 TTAAAACAAATTTTGTCTCTC
1 TTAAAACAAA--TTGTCTCTC
*
50540 TTGAAAC--ATT-T-TCTC
1 TTAAAACAAATTGTCTCTC
50555 TTAAAACAAATTGTCTCTC
1 TTAAAACAAATTGTCTCTC
50574 TT
1 TT
50576 GAGACAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 10 0.33
16 1 0.03
17 5 0.17
18 1 0.03
19 7 0.23
21 6 0.20
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAAAACAAATTGTCTCTC
Found at i:50715 original size:36 final size:36
Alignment explanation
Indices: 50613--50737 Score: 144
Period size: 36 Copynumber: 3.4 Consensus size: 36
50603 TTGAATCTGT
* *
50613 TTTC-CTTGAAACATATTTTGTCTCCCTTGAAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTG-AGACAG
* * * *
50649 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAG
1 TTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
50686 TTTCTCTTAAAACAAATTTTGTCTATCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
50722 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
50738 AACTTTGAAT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
36 38 0.52
37 21 0.29
38 14 0.19
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:50758 original size:139 final size:137
Alignment explanation
Indices: 50356--50903 Score: 760
Period size: 137 Copynumber: 4.0 Consensus size: 137
50346 CAAAAAAAAG
* * * *
50356 TTTTGTCTCTCTTGATACAGTTTCTTTTAAAACAAATTTTGTCTATCTTGAGACATTTTCTCTTA
1 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
** *
50421 AAACAAATTTTGTCTCTCTAAAGAAAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
50486 AAACAAA
131 AAACAAA
* * * *
50493 TTTCGTTTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAAACATTTTCTCTTA
1 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
50558 AAACAAA--TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
66 AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
*
50621 AAACATA
131 AAACAAA
** * *
50628 TTTTGTCTCCCTTGAAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGATAGTTTCTCT
1 TTTTGTCTCCCTTG-AGACAGTTTCTTTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCT
* *
50693 TAAAACAAATTTTGTCTATCTTGAGACAGTTTCCCTTGAAACAAAAACTTTGAATCTGTTTTCCT
64 TAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCT
50758 TGAAACAAA
129 TGAAACAAA
* ** * * *
50767 TTTTGTCTCCCTTGAGATAGTTTCTTTTGGAACTAAGTTTTGTCTCTTTTGAGACAGTTTCCCTT
1 TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTT
* * * * * *
50832 GAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAACCTTTGAATATG-TTTCTC
65 AAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAATCTTTGAATCTGTTTTC-C
50896 TTGAAACA
128 TTGAAACA
50904 CAAAAGACCT
Statistics
Matches: 373, Mismatches: 32, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
135 71 0.19
136 17 0.05
137 101 0.27
138 89 0.24
139 95 0.25
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (137 bp):
TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTA
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTCCTTG
AAACAAA
Found at i:50819 original size:37 final size:36
Alignment explanation
Indices: 50752--50873 Score: 165
Period size: 36 Copynumber: 3.4 Consensus size: 36
50742 TTGAATCTGT
* * *
50752 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGATAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
* * *
50787 TTTCTTTTGGAACTAAGTTTTGTCTCTTTTGAGACAG
1 TTTCTCTTGAAAC-AAGTTTTGTCTCTCTTGAGACAG
*
50824 TTTCCCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
50860 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
50874 CCAACCTTTG
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
35 4 0.05
36 41 0.55
37 29 0.39
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAAACAAGTTTTGTCTCTCTTGAGACAG
Found at i:54480 original size:28 final size:28
Alignment explanation
Indices: 54440--54505 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
54430 TCTTTATAAG
54440 GGTTTAGAG-TAATGTGATAGGATTTAA
1 GGTTTAGAGTTAATGTGATAGGATTTAA
54467 GGTTTAGAGTTAATGTGATAGGATTTAA
1 GGTTTAGAGTTAATGTGATAGGATTTAA
54495 GGTTTAGAGTT
1 GGTTTAGAGTT
54506 TAGGATTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.39
Consensus pattern (28 bp):
GGTTTAGAGTTAATGTGATAGGATTTAA
Found at i:54523 original size:28 final size:28
Alignment explanation
Indices: 54492--54545 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
54482 TGATAGGATT
54492 TAAGGTTTAGAGTTTAGGATTTATGTAG
1 TAAGGTTTAGAGTTTAGGATTTATGTAG
* *
54520 TAAGGTTTAGGGTTTAGGGTTTATGT
1 TAAGGTTTAGAGTTTAGGATTTATGT
54546 TTAAGGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.44
Consensus pattern (28 bp):
TAAGGTTTAGAGTTTAGGATTTATGTAG
Found at i:62058 original size:21 final size:21
Alignment explanation
Indices: 62016--62058 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
62006 TTTCTGGGCT
* *
62016 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
62037 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
62058 A
1 A
62059 ACGAACCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:63643 original size:103 final size:103
Alignment explanation
Indices: 63423--63635 Score: 363
Period size: 103 Copynumber: 2.1 Consensus size: 103
63413 GGGTCTACGC
*
63423 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATATTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
63488 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* * *
63526 GGTTCTTCGGGACATATATGTATTTTTTGGAACATGTGTGAAGTCTGGTGAGACATATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
63591 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
63629 GGTCCTT
1 GGTCCTT
63636 ATGGACATTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:63703 original size:23 final size:23
Alignment explanation
Indices: 63650--63714 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
63640 ACATTATTAT
63650 ATGGCACTACT-GTGCAATTCTAC
1 ATGGCACT-CTGGTGCAATTCTAC
** *
63673 GCGACACTCTGGTGCAATTCTAC
1 ATGGCACTCTGGTGCAATTCTAC
63696 ATGGCACT-TCGGTGCAATT
1 ATGGCACTCT-GGTGCAATT
63715 ATACGAGCTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (23 bp):
ATGGCACTCTGGTGCAATTCTAC
Done.