Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006747.1 Hibiscus syriacus cultivar Beakdansim tig00016971_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: 108124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8329 original size:21 final size:21
Alignment explanation
Indices: 8287--8329 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
8277 TTTCTGGGCT
*
8287 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
8308 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
8329 A
1 A
8330 CGTATATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:9023 original size:23 final size:23
Alignment explanation
Indices: 8979--9023 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
8969 ATTATTATAT
*
8979 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
9002 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
9024 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:15070 original size:20 final size:20
Alignment explanation
Indices: 15031--15070 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15021 TCTGGGCTAG
*
15031 GGGAATCGATACCCATTCAA
1 GGGAATCGATACCCACTCAA
*
15051 GGGAATCGATACCCCCTCAA
1 GGGAATCGATACCCACTCAA
15071 CGTATATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (20 bp):
GGGAATCGATACCCACTCAA
Found at i:15461 original size:14 final size:15
Alignment explanation
Indices: 15426--15465 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
15416 ATTATGAGAC
15426 ATGACATGAATTCAT
1 ATGACATGAATTCAT
*
15441 ATAACATGAATT-AT
1 ATGACATGAATTCAT
15455 ATGACATGAAT
1 ATGACATGAAT
15466 ATGCATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (15 bp):
ATGACATGAATTCAT
Found at i:15791 original size:23 final size:23
Alignment explanation
Indices: 15758--15802 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15748 ATTATTATAT
15758 GGCACTACGGTGCAATTT-TACGC
1 GGCACTACGGTGC-ATTTATACGC
*
15781 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCATTTATACG
15803 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCATTTATACGC
Found at i:20984 original size:3 final size:3
Alignment explanation
Indices: 20976--21004 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20966 AGGTATTTTA
20976 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
21005 GTGGAAATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:23362 original size:2 final size:2
Alignment explanation
Indices: 23355--23391 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
23345 AGTTTTTCTA
23355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23392 TTTAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24429 original size:158 final size:154
Alignment explanation
Indices: 24087--24479 Score: 520
Period size: 158 Copynumber: 2.5 Consensus size: 154
24077 ATTGATTTCA
* * * * * *
24087 TTATTTCTTCAATTTC-TCCTTCATTTTAAGTCCATTTTTTACCAAATTTGAACGCATGCTCATA
1 TTATTCCTTCAA-TTCGTCATTTATTTTAAGTCTA-TTTTTACCAAATTTGACCACATGCTCATA
*
24151 AACCATAATAGAATACATGTGTACTTTCAATTCCTCATTTTGATAATTTTTTTTATTTTTCAATT
64 AACCATAATAGAATACATGTGTACTTTCAATTCCTCATTTTGATAATATTTTTTATTTTTCAATT
* * *
24216 CAGTCATTCGATTTTTCGTAATTTCC
129 CAGTCATTCAATTTTTCATAATCTCC
* *
24242 TTATTTCTTCAATTCGTCATTTATTTTAAGTCTGATTTTTACCAAATTTGAGCCACATGCTCCTA
1 TTATTCCTTCAATTCGTCATTTATTTTAAGTCT-ATTTTTACCAAATTTGA-CCACATGCTCATA
* * *
24307 AACCATAGTAAAATACATGTGTACTTTCAATTCCT-ATTTTTGATAACTAATTTTTTATTTTTTA
64 AACCATAATAGAATACATGTGTACTTTCAATTCCTCA-TTTTGATAA-T-ATTTTTTATTTTTCA
*
24371 ATTTAGTCATTCAATTTTTCATAATCTCC
126 ATTCAGTCATTCAATTTTTCATAATCTCC
* * * *
24400 TTATTCCTTCAATTTGTTATTTATTTTAAGTCTCTTTTTACCAAATTTGAACCACATGCTCATAC
1 TTATTCCTTCAATTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTG-ACCACATGCTCATAA
24465 ACCATAATAGAATAC
65 ACCATAATAGAATAC
24480 GTATGTAACT
Statistics
Matches: 209, Mismatches: 22, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
154 3 0.01
155 43 0.21
156 53 0.25
157 41 0.20
158 69 0.33
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (154 bp):
TTATTCCTTCAATTCGTCATTTATTTTAAGTCTATTTTTACCAAATTTGACCACATGCTCATAAA
CCATAATAGAATACATGTGTACTTTCAATTCCTCATTTTGATAATATTTTTTATTTTTCAATTCA
GTCATTCAATTTTTCATAATCTCC
Found at i:30469 original size:16 final size:16
Alignment explanation
Indices: 30439--30468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30429 GTTAAAAGAG
30439 AAAATAAAAGTAAAAC
1 AAAATAAAAGTAAAAC
30455 AAAATAAAA-TAAAA
1 AAAATAAAAGTAAAA
30469 AAGTGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAATAAAAGTAAAAC
Found at i:30597 original size:18 final size:18
Alignment explanation
Indices: 30576--30618 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
30566 GTTGTTTTTA
*
30576 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
30594 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
30612 AAATAAA
1 AAATAAA
30619 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:37113 original size:29 final size:30
Alignment explanation
Indices: 37055--37114 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
37045 CCCTTTTAGC
*
37055 TTATTTTCTTTTTCAGTCCTTGAATGTAGT
1 TTATTTTCTTTTTCAGTCCTTGAACGTAGT
** *
37085 TTATTTTCTTTTTTGGT-CTTTAACGTAGT
1 TTATTTTCTTTTTCAGTCCTTGAACGTAGT
37114 T
1 T
37115 AAGTATAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.15, C:0.12, G:0.13, T:0.60
Consensus pattern (30 bp):
TTATTTTCTTTTTCAGTCCTTGAACGTAGT
Found at i:37540 original size:20 final size:19
Alignment explanation
Indices: 37515--37555 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
37505 CCTGCAAAAC
*
37515 TTTACCTAAAATATTATATT
1 TTTACCGAAAATATTAT-TT
*
37535 TTTACCGAAAATGTTATTT
1 TTTACCGAAAATATTATTT
37554 TT
1 TT
37556 GCTAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTACCGAAAATATTATTT
Found at i:39202 original size:154 final size:155
Alignment explanation
Indices: 38912--39217 Score: 508
Period size: 154 Copynumber: 2.0 Consensus size: 155
38902 CATTTTATTA
**
38912 AAATTTGTCAATAAAAAATATATTTTATTAGAACTCGTCTTGTCAACGTTAGTAAGTTCTAATCA
1 AAATTTGTCAATAAAAAATATATTTTATTAGAACTCGTCACGTCAACGTTAGTAAGTTCTAATCA
* *
38977 CTATAATAAATACAGTAGATTCCAAATTAATTTTAAAAATGACCTAATAAATTAAATTTTGGGTA
66 CTATAATAAATACAGTAAATTCCAAATTAATTTTAAAAATGACCTAATAAATTAAATTTTAGGTA
39042 AATTACGTGTTTAATACCTAAAGAC
131 AATTACGTGTTTAATACCTAAAGAC
* *
39067 AAATTT-T-AATAAAAAATATATTTTATTATAACTCGTCACGTCAATGTTAGTAAGTTCTAAATC
1 AAATTTGTCAATAAAAAATATATTTTATTAGAACTCGTCACGTCAACGTTAGTAAGTTCT-AATC
* *
39130 ACTATAATAAATACAGTAAATTCCAAATTAATTTTAAAAATGACCTAATGAATTAATTTTTAGGT
65 ACTATAATAAATACAGTAAATTCCAAATTAATTTTAAAAATGACCTAATAAATTAAATTTTAGGT
*
39195 AAGTTACGTGTTTAATACCTAAA
130 AAATTACGTGTTTAATACCTAAA
39218 ATTTCACTAT
Statistics
Matches: 141, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
153 47 0.33
154 88 0.62
155 6 0.04
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.37
Consensus pattern (155 bp):
AAATTTGTCAATAAAAAATATATTTTATTAGAACTCGTCACGTCAACGTTAGTAAGTTCTAATCA
CTATAATAAATACAGTAAATTCCAAATTAATTTTAAAAATGACCTAATAAATTAAATTTTAGGTA
AATTACGTGTTTAATACCTAAAGAC
Found at i:44841 original size:2 final size:2
Alignment explanation
Indices: 44836--44876 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
44826 TTTATATACA
44836 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT A
44877 CTCAACTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51981 original size:16 final size:16
Alignment explanation
Indices: 51955--51992 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
51945 TAAATTTTTG
*
51955 ATTTCATCTATCTATTT
1 ATTTCATCTAT-AATTT
51972 ATTT-ATCTATAATTT
1 ATTTCATCTATAATTT
51987 ATTTCA
1 ATTTCA
51993 CTTGAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 7 0.37
17 4 0.21
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (16 bp):
ATTTCATCTATAATTT
Found at i:69144 original size:189 final size:184
Alignment explanation
Indices: 68798--69169 Score: 575
Period size: 189 Copynumber: 2.0 Consensus size: 184
68788 TCAAAAATAA
68798 CTAAATATGTATAACTAGAATCAACTAGAAGTGTTTGTTTTAGACCAAAGAAGAATGAACTAGTT
1 CTAAATATGTATAACTAGAATCAACTAGAAGTGTTTGTTTTAGACCAAAGAAGAATGAACTAGTT
* * *
68863 CCAATTGTGGGAAGTCCAAAGCGAGACATCAATAAAGCACGTTGATATCGCTCAAAGTACTTCCC
66 CCAATAGTGGGAAGTCCAAAGCGAGAAATCAATAAAGCACATTGATATCGCTCAAAGTACTTCCC
68928 CTTATAGAAACAAATCAAAACCCGTAACGCTTGAGCATAATGAAGTAGATTATG
131 CTTATAGAAACAAATCAAAACCCGTAACGCTTGAGCATAATGAAGTAGATTATG
* * *
68982 CTAAATTTGTATAACTAGAATCAACTAGAAGTGTGTT-TTTTCCGACCAAAGTAGAATGAACTAG
1 CTAAATATGTATAACTAGAATCAACTAGAAGTGT-TTGTTTT-AGACCAAAGAAGAATGAACTAG
* *
69046 TTCCAATAGTGGGAAGTCCAAAGTGAGTGAGGAATCAATAAAGCACATTGATATCGCTCAACGTA
64 TTCCAATAGTGGGAAGTCCAAAGCGA--GA--AATCAATAAAGCACATTGATATCGCTCAAAGTA
* * * *
69111 CTTTCCCTTCTGGAAACAAATCAAAATCCGTAACGCTTGAGCATAATGAAGTAGATTAT
125 CTTCCCCTTATAGAAACAAATCAAAACCCGTAACGCTTGAGCATAATGAAGTAGATTAT
69170 ACGTTCAGAT
Statistics
Matches: 170, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
184 37 0.22
185 46 0.27
187 2 0.01
189 85 0.50
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (184 bp):
CTAAATATGTATAACTAGAATCAACTAGAAGTGTTTGTTTTAGACCAAAGAAGAATGAACTAGTT
CCAATAGTGGGAAGTCCAAAGCGAGAAATCAATAAAGCACATTGATATCGCTCAAAGTACTTCCC
CTTATAGAAACAAATCAAAACCCGTAACGCTTGAGCATAATGAAGTAGATTATG
Found at i:75832 original size:46 final size:46
Alignment explanation
Indices: 75745--75872 Score: 141
Period size: 46 Copynumber: 2.8 Consensus size: 46
75735 ATTAAGTAAT
* *
75745 CGAAAATCTAAAGGTTGATCCGAACCTAAACTAATCCGAATTGACC
1 CGAAAATCTAAAGGTTGATCCGAACCGAAACCAATCCGAATTGACC
* * * *
75791 CGAAAATTTAAAGGTTGATCTGAGCCGATACCAA-CCTGAATTGACC
1 CGAAAATCTAAAGGTTGATCCGAACCGAAACCAATCC-GAATTGACC
* * * * *
75837 TGAAAATCTAAAGCTTGACCCGAACTGAAATCAATC
1 CGAAAATCTAAAGGTTGATCCGAACCGAAACCAATC
75873 GATCCGATAT
Statistics
Matches: 65, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
45 2 0.03
46 62 0.95
47 1 0.02
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (46 bp):
CGAAAATCTAAAGGTTGATCCGAACCGAAACCAATCCGAATTGACC
Found at i:92786 original size:20 final size:20
Alignment explanation
Indices: 92763--92826 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
92753 ATCGAAACTG
*
92763 ACCTTTCAGTATCGGTAC-TT
1 ACCTTT-AGTATCGATACTTT
92783 ACCTCTTAGTATCGATACTTT
1 ACCT-TTAGTATCGATACTTT
*
92804 ACC-TTAGATATCAATACTTT
1 ACCTTTAG-TATCGATACTTT
92824 ACC
1 ACC
92827 CTATTATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 4 0.10
20 28 0.72
21 7 0.18
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (20 bp):
ACCTTTAGTATCGATACTTT
Found at i:96455 original size:17 final size:16
Alignment explanation
Indices: 96425--96473 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
96415 GGTTGTCGTC
*
96425 TCTTTTCTCCTCCTAT
1 TCTTTTCTCTTCCTAT
*
96441 TCTTTCTCTCTTCCTCT
1 TCTTT-TCTCTTCCTAT
*
96458 TCATTT-TCTTCCTAT
1 TCTTTTCTCTTCCTAT
96473 T
1 T
96474 TTATCATTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 9 0.32
16 6 0.21
17 13 0.46
ACGTcount: A:0.06, C:0.35, G:0.00, T:0.59
Consensus pattern (16 bp):
TCTTTTCTCTTCCTAT
Found at i:99612 original size:2 final size:2
Alignment explanation
Indices: 99607--99633 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
99597 ACACACACAC
99607 AT 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 AT A
99634 GACTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102143 original size:346 final size:346
Alignment explanation
Indices: 101476--102163 Score: 848
Period size: 346 Copynumber: 2.0 Consensus size: 346
101466 GATTAAGTTT
* * * * * *
101476 GTATTATTTTGGGTAAACTATACATTTAGTATCTAAACTATCAGTTTTAATTTATTTTATTATCT
1 GTATTATTTTGGGTAAACTACACATTTAGTATCTAAACTATCAATTTTAAGTCATTTTAGTACCT
* * *
101541 AAACTTTCAATTTTTCAGAACCACACTTAATGTTTAGTTCTTATTTCATTTTAGTACTCTCTCCG
66 AAACTTTCAATTTTTCAAAACCACACTTAAAGTTTAGTTCTTATTTCATTTTAGTACTCCCTCCG
* * ** **
101606 TTAAAAACTTCAATTTTGTTTTATTTTAGTATCCAGTTCGAAATTTAATGTTAAGTTTTGAAAAA
131 TTAAAAACTTCAATTTTGTTTTATTATAATATCCAGTTAAAAAACTAATGTTAAGTTTTG--AAA
* * * * *
101671 AAAATTGAAAGTTTAAGTACTAAAACATATCAAAACTGATAGTTTAGGTACAAATTGCGTTAAGT
194 AAAATTAAAAGTTTAAGTACTAAAACATACCAAAACTGATAGTTTAAGTACAAATTACGTTAAAT
**** * * * * * * * *
101736 TTTTAAAGATGGGGTGCTAAAATGAAATGAAAACTAAATGTTAAGTGTGGTTTTGAAAAAATTGA
259 TTTTAAAGATAAAATACTAAAATAAAATAAAAACTAAATATTAAATATGGTTTTAAAAAAATTAA
* **
101801 AAGTTTAGGTACTAAAACTGATA
324 AAATTTAAATACTAAAACTGATA
* ** *
101824 GTATTATTTTGGGTAAACTACATATTTAGTA-CATAAACTATCAATTTTGGGTCGTTTTAGTACC
1 GTATTATTTTGGGTAAACTACACATTTAGTATC-TAAACTATCAATTTTAAGTCATTTTAGTACC
* * *
101888 TAAACTTTCAATTTTTTTCAAAATCATACTTAAAGTTTAGTTTTTATTTCATTTTAGTAC-CCCT
65 TAAACTTTCAA--TTTTTCAAAACCACACTTAAAGTTTAGTTCTTATTTCATTTTAGTACTCCCT
* *
101952 CTGTTAAAAACTTCAAATTTTGTTTTATTATAATA-CCCGTTAAAAAACTAATGTTAAGTTTTG-
128 CCGTTAAAAACTTC-AATTTTGTTTTATTATAATATCCAGTTAAAAAACTAATGTTAAGTTTTGA
*
102015 AAAAAATTAAAAGTTTAAGTACTAAAACATACCAAAATTGATAGTTTAAGTACTAAA-TACGTTA
192 AAAAAATTAAAAGTTTAAGTACTAAAACATACCAAAACTGATAGTTTAAGTAC-AAATTACGTTA
*
102079 AATTTTTAAAGA-AAAATACTAAAATAAAATAAAAACTAAATATTAAATATGATTTTTAAAAAAA
256 AATTTTTAAAGATAAAATACTAAAATAAAATAAAAACTAAATATTAAATATG-GTTTTAAAAAAA
102143 TTAAAAATTTAAATACTAAAA
320 TTAAAAATTTAAATACTAAAA
102164 TAAATTAAAA
Statistics
Matches: 288, Mismatches: 46, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
345 29 0.10
346 93 0.32
347 4 0.01
348 63 0.22
349 39 0.14
350 60 0.21
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (346 bp):
GTATTATTTTGGGTAAACTACACATTTAGTATCTAAACTATCAATTTTAAGTCATTTTAGTACCT
AAACTTTCAATTTTTCAAAACCACACTTAAAGTTTAGTTCTTATTTCATTTTAGTACTCCCTCCG
TTAAAAACTTCAATTTTGTTTTATTATAATATCCAGTTAAAAAACTAATGTTAAGTTTTGAAAAA
AATTAAAAGTTTAAGTACTAAAACATACCAAAACTGATAGTTTAAGTACAAATTACGTTAAATTT
TTAAAGATAAAATACTAAAATAAAATAAAAACTAAATATTAAATATGGTTTTAAAAAAATTAAAA
ATTTAAATACTAAAACTGATA
Found at i:102226 original size:3 final size:3
Alignment explanation
Indices: 102218--102249 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
102208 CCTATTAGTT
102218 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
102250 TTACACCGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:102785 original size:16 final size:17
Alignment explanation
Indices: 102764--102803 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
102754 AATCTACTTA
102764 TATATTATTGTTAA-AT
1 TATATTATTGTTAATAT
102780 TATATTA-TGTTAATAT
1 TATATTATTGTTAATAT
102796 T-TATTATT
1 TATATTATT
102804 ATATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TATATTATTGTTAATAT
Found at i:106585 original size:18 final size:18
Alignment explanation
Indices: 106559--106594 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
106549 TTGACTCAGC
*
106559 TGAGTTGATCCAACCCGA
1 TGAGGTGATCCAACCCGA
*
106577 TGAGGTGATCCGACCCGA
1 TGAGGTGATCCAACCCGA
106595 CGGAGTCATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (18 bp):
TGAGGTGATCCAACCCGA
Done.