Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002865.1 Hibiscus syriacus cultivar Beakdansim tig00005910_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: 47480
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:2112 original size:10 final size:10
Alignment explanation
Indices: 2088--2129 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2078 CTTGCAATTT
2088 TCATATTAAAC
1 TCATA-TAAAC
2099 -CATATAAAC
1 TCATATAAAC
*
2108 TCATATTAAC
1 TCATATAAAC
*
2118 TCATATTAAC
1 TCATATAAAC
2128 TC
1 TC
2130 GTACTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (10 bp):
TCATATAAAC
Found at i:2113 original size:20 final size:20
Alignment explanation
Indices: 2088--2129 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2078 CTTGCAATTT
2088 TCATATTAAAC-CATATAAAC
1 TCATATT-AACTCATATAAAC
*
2108 TCATATTAACTCATATTAAC
1 TCATATTAACTCATATAAAC
2128 TC
1 TC
2130 GTACTTTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (20 bp):
TCATATTAACTCATATAAAC
Found at i:4900 original size:86 final size:86
Alignment explanation
Indices: 4750--4917 Score: 246
Period size: 86 Copynumber: 2.0 Consensus size: 86
4740 GCGGTGGAGC
* ** *
4750 TTTTCGAAACGAGCATGGGGACTGGATCGAAGGATTTTCAAGAAATATCGGTTGCGCAACCATCT
1 TTTTCGAAACGAGCATGGGGACTGAATCGAAGGATTTTCAAGAAATATCGACTGCACAACCATCT
*
4815 TACAAGGTGAACTTTGGCCTA
66 TACAAGCTGAACTTTGGCCTA
* * *
4836 TTTTCGAAACGAGCATGGGGATTGAATCGAAGGATTTTCAAGAAATATCGACTGCACTATCATCT
1 TTTTCGAAACGAGCATGGGGACTGAATCGAAGGATTTTCAAGAAATATCGACTGCACAACCATCT
* *
4901 TACTAGCTGAATTTTGG
66 TACAAGCTGAACTTTGG
4918 TCGATCCTCG
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
86 72 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (86 bp):
TTTTCGAAACGAGCATGGGGACTGAATCGAAGGATTTTCAAGAAATATCGACTGCACAACCATCT
TACAAGCTGAACTTTGGCCTA
Found at i:14361 original size:29 final size:29
Alignment explanation
Indices: 14300--14360 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
14290 TTTAAATCTT
* * *
14300 AAACTAATCTTCTAATTTTTTTTTAAAAA
1 AAACTAATATTCTAAATTTGTTTTAAAAA
*
14329 AAACTAATATTCTAAAATTTGTTTTATAAA
1 AAACTAATATTCT-AAATTTGTTTTAAAAA
14359 AA
1 AA
14361 CACTTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (29 bp):
AAACTAATATTCTAAATTTGTTTTAAAAA
Found at i:15835 original size:32 final size:32
Alignment explanation
Indices: 15799--15860 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
15789 AAATACGACA
15799 CTAATACTCA-TATGCATTATCTGAATGCAAGC
1 CTAATACT-ATTATGCATTATCTGAATGCAAGC
**
15831 CTAATTGTATTATGCATTATCTGAATGCAA
1 CTAATACTATTATGCATTATCTGAATGCAA
15861 CATTGACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
CTAATACTATTATGCATTATCTGAATGCAAGC
Found at i:21571 original size:21 final size:20
Alignment explanation
Indices: 21541--21617 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 20
21531 TTTATCGATA
21541 ATTTTAATAATATAATATTTT
1 ATTTT-ATAATATAATATTTT
* *
21562 ATTGTTATAATTATATTATTAT
1 ATT-TTATAA-TATAATATTTT
* * * *
21584 AATATATAATATTATAATTT
1 ATTTTATAATATAATATTTT
21604 ATTTTAATAATATA
1 ATTTT-ATAATATA
21618 TAACAAATTA
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 10 0.24
21 19 0.45
22 13 0.31
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTTTATAATATAATATTTT
Found at i:21596 original size:15 final size:14
Alignment explanation
Indices: 21566--21602 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
21556 TATTTTATTG
*
21566 TTATAATTATATTA
1 TTATAATTATAATA
21580 TTATAATATATAATA
1 TTATAAT-TATAATA
21595 TTATAATT
1 TTATAATT
21603 TATTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATAATTATAATA
Found at i:21752 original size:25 final size:25
Alignment explanation
Indices: 21722--21773 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
21712 AATATATTCT
* *
21722 TATTTTAATATTATATATT-TTTTAA
1 TATTTTAACAATAT-TATTATTTTAA
21747 TATTTTAACAATATTATTATTTTAA
1 TATTTTAACAATATTATTATTTTAA
21772 TA
1 TA
21774 AATAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
TATTTTAACAATATTATTATTTTAA
Found at i:21786 original size:16 final size:16
Alignment explanation
Indices: 21762--21795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21752 TAACAATATT
*
21762 ATTATTTTAATAAATA
1 ATTAATTTAATAAATA
*
21778 ATTAATTTAATTAATA
1 ATTAATTTAATAAATA
21794 AT
1 AT
21796 ATATTATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATTTAATAAATA
Found at i:21804 original size:42 final size:41
Alignment explanation
Indices: 21758--21846 Score: 126
Period size: 42 Copynumber: 2.2 Consensus size: 41
21748 ATTTTAACAA
* *
21758 TATTATTATTTTAATAAATAATTAATTTAATTAATAATATAT
1 TATTATTATTTTAATAAATAATAAATATAATTAATAATA-AT
* *
21800 TATTATTGTTTTAATAAATAATAAATATAATTTATAATAAT
1 TATTATTATTTTAATAAATAATAAATATAATTAATAATAAT
21841 T-TTATT
1 TATTATT
21847 TTAATATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 5 0.12
41 3 0.07
42 35 0.81
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (41 bp):
TATTATTATTTTAATAAATAATAAATATAATTAATAATAAT
Found at i:21913 original size:14 final size:13
Alignment explanation
Indices: 21843--21917 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 13
21833 ATAATAATTT
21843 TATTTTAATATAAA
1 TATTTTAATAT-AA
* *
21857 TATATTAATCGTAA
1 TATTTTAAT-ATAA
*
21871 TATTTTTATTTATAA
1 TA-TTTTA-ATATAA
* *
21886 AATTATAGATATAA
1 TATTTTA-ATATAA
21900 TATTTTAATAATAA
1 TATTTTAAT-ATAA
21914 TATT
1 TATT
21918 GACATAAATA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 2 0.04
14 34 0.74
15 9 0.20
16 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (13 bp):
TATTTTAATATAA
Found at i:23428 original size:60 final size:60
Alignment explanation
Indices: 23347--23484 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
23337 AATCATTCAA
** *
23347 AATTCTGGGGATGAAATTGGAACATTCAAAAGTTTG-GGTATCAATATATCATGAGAGTCAT
1 AATT-TGGGGATGAAATTGGAACATTCAAAAGTTTGAGG-ATCAATATAGAATGAGAGTCAC
* * ** *
23408 AATTTGGGGATGCATTTGGAATGTTCAAAAGTTTGAGGATCAATTTAGAATGAGAGTCAC
1 AATTTGGGGATGAAATTGGAACATTCAAAAGTTTGAGGATCAATATAGAATGAGAGTCAC
* *
23468 AATTTAGAGATGAAATT
1 AATTTGGGGATGAAATT
23485 AGAATGTTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 58 0.91
61 6 0.09
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (60 bp):
AATTTGGGGATGAAATTGGAACATTCAAAAGTTTGAGGATCAATATAGAATGAGAGTCAC
Found at i:23520 original size:60 final size:60
Alignment explanation
Indices: 23356--23501 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 60
23346 AAATTCTGGG
* ** * * ** * * *
23356 GATGAAATTGGAACATTCAAAAGTTTG-GGTATCAATATATCATGAGAGTCATAATTTGGG
1 GATGAAATTAGAATGTTCAAAACTTTGAGG-ATCAATTTAGAATGAGAGTCACAATTTAGA
* * * *
23416 GATGCATTTGGAATGTTCAAAAGTTTGAGGATCAATTTAGAATGAGAGTCACAATTTAGA
1 GATGAAATTAGAATGTTCAAAACTTTGAGGATCAATTTAGAATGAGAGTCACAATTTAGA
*
23476 GATGAAATTAGAATGTTGAAAACTTT
1 GATGAAATTAGAATGTTCAAAACTTT
23502 AGGGACAAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
60 68 0.97
61 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.32
Consensus pattern (60 bp):
GATGAAATTAGAATGTTCAAAACTTTGAGGATCAATTTAGAATGAGAGTCACAATTTAGA
Found at i:25459 original size:60 final size:59
Alignment explanation
Indices: 25352--25465 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 59
25342 ATTTGACACA
* * * * *
25352 ATGCCTTCAAGCTCTAGGGGAGGCATTCAACTGCAAGCTTCTTCGACCTCAATGCCTAT
1 ATGCCTTCAAGCTCAAGGGGAGACATGCAACTACAAGCTTCTTCGACCTAAATGCCTAT
* * *
25411 ATGCCTTCAAGTTCAAGGGGAAGACATGCAACTACCAGCTTGTTCGACCTAAATG
1 ATGCCTTCAAGCTCAAGGGG-AGACATGCAACTACAAGCTTCTTCGACCTAAATG
25466 TCGACAGCGT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
59 18 0.39
60 28 0.61
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.25
Consensus pattern (59 bp):
ATGCCTTCAAGCTCAAGGGGAGACATGCAACTACAAGCTTCTTCGACCTAAATGCCTAT
Found at i:26520 original size:59 final size:59
Alignment explanation
Indices: 26451--26683 Score: 360
Period size: 59 Copynumber: 3.9 Consensus size: 59
26441 TAAATTCAAT
* * * * ** *
26451 TGGAATTTCATACAATCAATAAGATTTTATTTCCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTAAGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
26510 TGGAAATTCATACACTTAGTATGATTTGCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTAAGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
26569 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACTTAGTAAGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
26628 TGGAAATTCATACACTTAGTATA-ATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACACTTAGTA-AGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
26684 TTGGTAACTT
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
59 163 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACTTAGTAAGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:27074 original size:53 final size:52
Alignment explanation
Indices: 27015--27185 Score: 245
Period size: 53 Copynumber: 3.2 Consensus size: 52
27005 CCTTCAGAAG
27015 GGTATCGATACACTACTGGGCTATCAGTACCCAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTGGG-TATCAGTACCCAAATTAACTTCGATGTTTACA
* * *
27068 TGTATCGATACACTACTGAGATAT-TGATACCCAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTG-GGTATCAG-TACCCAAATTAACTTCGATGTTTACA
* * *
27121 GGTATCAATACACTACTGAGGTATCGGTACCCAAATTAACTTTGATGTTTACA
1 GGTATCGATACACTACTG-GGTATCAGTACCCAAATTAACTTCGATGTTTACA
27174 GGTATCGATACA
1 GGTATCGATACA
27186 TGCCTGATGG
Statistics
Matches: 106, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
52 1 0.01
53 103 0.97
54 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (52 bp):
GGTATCGATACACTACTGGGTATCAGTACCCAAATTAACTTCGATGTTTACA
Found at i:33412 original size:59 final size:59
Alignment explanation
Indices: 33339--33548 Score: 341
Period size: 59 Copynumber: 3.6 Consensus size: 59
33329 TAATCAATAA
* * *
33339 GATTTTCTTTCCATTTTAGCACACAAATTGCCCTATCTAGAAATTCATACACTTAGTAT
1 GATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
*
33398 GATTTCCTTACCATTTTAGCACACAAAGTGCCTTATCTA-AAATTCATACACTTAGTAT
1 GATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
* *
33456 GATTTCCTTACCATTTTAGCACACAAAGTACCCTATCTGGAAATTCATACACTTAGTAT
1 GATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
* *
33515 AATTTCCTTATCATTTTAGCACACAAAGTGCCCT
1 GATTTCCTTACCATTTTAGCACACAAAGTGCCCT
33549 TTGGTAATTT
Statistics
Matches: 140, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
58 55 0.39
59 85 0.61
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.36
Consensus pattern (59 bp):
GATTTCCTTACCATTTTAGCACACAAAGTGCCCTATCTAGAAATTCATACACTTAGTAT
Found at i:33967 original size:53 final size:53
Alignment explanation
Indices: 33878--34068 Score: 249
Period size: 53 Copynumber: 3.6 Consensus size: 53
33868 CCTTTAGAAG
* * *
33878 GGTATCGATACACTACAGGGGTATCGATACCCAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTGAGGTATCGATACCTAAATTAACTTCGATGTTTACA
* * *
33931 TGTATCGATACACTACTGAGGTATCGGTACTTAAATTAACTTCGATGTTTACA
1 GGTATCGATACACTACTGAGGTATCGATACCTAAATTAACTTCGATGTTTACA
* * * *
33984 GGTATCAATACACTACTGAGGTATCGATACCTATATTAGCTTCAATGTTTACA
1 GGTATCGATACACTACTGAGGTATCGATACCTAAATTAACTTCGATGTTTACA
* *
34037 GGTATTGATACA-TGCCTGATGGTATCGATACC
1 GGTATCGATACACT-ACTGA-GGTATCGATACC
34069 CCTTGAAGAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
52 1 0.01
53 107 0.89
54 12 0.10
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (53 bp):
GGTATCGATACACTACTGAGGTATCGATACCTAAATTAACTTCGATGTTTACA
Found at i:36836 original size:17 final size:17
Alignment explanation
Indices: 36816--36850 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
36806 CAATTGTTGG
*
36816 TAAATAAAAGAATTAAA
1 TAAAAAAAAGAATTAAA
*
36833 TAAAAAAAATAATTAAA
1 TAAAAAAAAGAATTAAA
36850 T
1 T
36851 GTATGAATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
TAAAAAAAAGAATTAAA
Found at i:36961 original size:3 final size:3
Alignment explanation
Indices: 36953--37027 Score: 80
Period size: 3 Copynumber: 25.0 Consensus size: 3
36943 CTCCTCACTC
* * * * *
36953 TCA TCA TCA TCA TCA TCA TCA TCA TCA CCA CCA CCA CCA CCA TCA GT-A
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA -TCA
*
37001 TCA TCA TCA TCA TCA TTA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA
37028 GGAACAAATA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
2 1 0.02
3 64 0.97
4 1 0.02
ACGTcount: A:0.33, C:0.37, G:0.01, T:0.28
Consensus pattern (3 bp):
TCA
Found at i:38792 original size:17 final size:17
Alignment explanation
Indices: 38766--38809 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
38756 AAACTAATAC
*
38766 TAAAAAATTAAAAAAAA
1 TAAAATATTAAAAAAAA
*
38783 TAAAATATTAAAAATAA
1 TAAAATATTAAAAAAAA
*
38800 TTAAAT-TTAA
1 TAAAATATTAA
38810 TATAGAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAATATTAAAAAAAA
Found at i:40068 original size:4 final size:4
Alignment explanation
Indices: 40059--40097 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
40049 ATAAACAATA
*
40059 AAAT AAAT AAAT AAAT AAAT AAA- ATATT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAA
40098 AGAATTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 1 0.03
4 29 0.94
5 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:40068 original size:16 final size:14
Alignment explanation
Indices: 40049--40098 Score: 50
Period size: 16 Copynumber: 3.4 Consensus size: 14
40039 TAAATTAATG
40049 ATAAACAATAAAATAA
1 ATAAA-AAT-AAATAA
40065 AT--AAATAAATAA
1 ATAAAAATAAATAA
40077 ATAAAATATTAAATAA
1 ATAAAA-A-TAAATAA
40093 ATAAAA
1 ATAAAA
40099 GAATTAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
14 3 0.10
15 1 0.03
16 15 0.50
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
ATAAAAATAAATAA
Found at i:40080 original size:28 final size:27
Alignment explanation
Indices: 40029--40097 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
40019 AAAATTGTCC
* *
40029 TAAAATAAATTAAATTAATGATAAACA-A
1 TAAAATAAA-TAAATAAATAATAAA-ATA
40057 TAAAATAAATAAATAAATAAATAAAATA
1 TAAAATAAATAAATAAAT-AATAAAATA
*
40085 TTAAATAAATAAA
1 TAAAATAAATAAA
40098 AGAATTAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (27 bp):
TAAAATAAATAAATAAATAATAAAATA
Found at i:41369 original size:5 final size:5
Alignment explanation
Indices: 41347--41633 Score: 145
Period size: 5 Copynumber: 55.6 Consensus size: 5
41337 AAAACCAAAA
41347 ATAAT ATTAAT AT-A- ATAAT ATAAT ATAAT ATAAT A-AAT A-AAT ACTAAT
1 ATAAT A-TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT
* *
41395 ATATAT ATAAT ATTAT AATAA- ATAAA AT-AT ATAAT ATAGTAT ATAAT
1 ATA-AT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATA--AT ATAAT
* * *
41442 ATACCAT ATAA- ATATAT ATACT ATACT ATACT ATAATAT ATAAT ATAAT
1 ATA--AT ATAAT ATA-AT ATAAT ATAAT ATAAT AT-A-AT ATAAT ATAAT
*
41491 ATAAAT ATAACACT ATAAT AT-AT ATACT ATAGTAT ATAAT ATAAT ATAA-
1 AT-AAT AT-A-A-T ATAAT ATAAT ATAAT ATA--AT ATAAT ATAAT ATAAT
* * *
41540 ATATTT ATAAT ATATAGT ATTACT ATAAT AT-AT A-ATAT GTAAT ATACA-
1 ATA-AT ATAAT ATA-A-T A-TAAT ATAAT ATAAT ATA-AT ATAAT ATA-AT
* * *
41588 AT-AT ATAAT AT-AT AT-AT ATAAT ATAAA ATATAT ATTAT ATACT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATA
41634 TACTATCCCA
Statistics
Matches: 228, Mismatches: 18, Indels: 72
0.72 0.06 0.23
Matches are distributed among these distances:
3 3 0.01
4 40 0.18
5 118 0.52
6 41 0.18
7 21 0.09
8 5 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:41400 original size:2 final size:2
Alignment explanation
Indices: 41356--41635 Score: 132
Period size: 2 Copynumber: 148.5 Consensus size: 2
41346 AATAATATTA
* *
41356 AT AT A- AT A- AT AT A- AT AT A- AT AT A- AT AA AT AA AT ACT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
41393 AT AT AT AT AT A- AT AT -T AT A- AT AA AT A- AA AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
41430 AT AGT AT AT A- AT AT ACC AT AT AA AT AT AT AT ACT AT ACT AT ACT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A-T AT A-T
* *
41474 AT A- AT AT AT A- AT AT A- AT AT AA AT AT A- AC ACT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
41512 AT AT ACT AT AGT AT AT A- AT AT A- AT AT AA AT AT TT AT A- AT AT
1 AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
41553 AT AGT AT -T ACT AT A- AT AT AT A- AT AT GT A- AT AT AC A- AT AT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
41592 AT A- AT AT AT AT AT AT A- AT AT A- AA AT AT AT AT -T AT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
41631 AT AT A
1 AT AT A
41636 CTATCCCAGA
Statistics
Matches: 215, Mismatches: 22, Indels: 82
0.67 0.07 0.26
Matches are distributed among these distances:
1 29 0.13
2 164 0.76
3 22 0.10
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (2 bp):
AT
Found at i:41639 original size:7 final size:7
Alignment explanation
Indices: 41347--41635 Score: 175
Period size: 7 Copynumber: 39.4 Consensus size: 7
41337 AAAACCAAAA
41347 ATAATAT
1 ATAATAT
41354 -TAATAT
1 ATAATAT
41360 AATAATAT
1 -ATAATAT
41368 A-ATATAAT
1 ATA-AT-AT
*
41376 ATAATAA
1 ATAATAT
41383 ATAAATACT
1 AT-AATA-T
41392 AATATATAT
1 -ATA-ATAT
41401 ATAATATT
1 ATAATA-T
*
41409 ATAATAA
1 ATAATAT
*
41416 ATAAAAT
1 ATAATAT
41423 AT-ATAAT
1 ATAAT-AT
*
41430 ATAGTAT
1 ATAATAT
41437 ATAATAT
1 ATAATAT
**
41444 ACCATAT
1 ATAATAT
41451 A-AATAT
1 ATAATAT
41457 AT-ATACT
1 ATAATA-T
41464 ATACTATACT
1 ATA--ATA-T
41474 ATAATAT
1 ATAATAT
41481 ATAATAT
1 ATAATAT
*
41488 AATATAAAT
1 -ATA-ATAT
*
41497 ATAACACT
1 ATAATA-T
41505 ATAATAT
1 ATAATAT
41512 AT-ATACT
1 ATAATA-T
*
41519 ATAGTAT
1 ATAATAT
41526 AT-A-AT
1 ATAATAT
41531 ATAATAT
1 ATAATAT
41538 A-AATATTT
1 ATAATA--T
41546 ATAATAT
1 ATAATAT
41553 ATAGTATTACT
1 ATA--A-TA-T
41564 ATAATAT
1 ATAATAT
41571 ATAATAT
1 ATAATAT
*
41578 GTAATAT
1 ATAATAT
*
41585 ACAATAT
1 ATAATAT
41592 ATAATAT
1 ATAATAT
41599 AT-ATAT
1 ATAATAT
41605 ATAATAT
1 ATAATAT
*
41612 AAAATAT
1 ATAATAT
*
41619 ATATTAT
1 ATAATAT
*
41626 ATACTAT
1 ATAATAT
41633 ATA
1 ATA
41636 CTATCCCAGA
Statistics
Matches: 226, Mismatches: 24, Indels: 64
0.72 0.08 0.20
Matches are distributed among these distances:
5 4 0.02
6 30 0.13
7 114 0.50
8 47 0.21
9 12 0.05
10 15 0.07
11 4 0.02
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (7 bp):
ATAATAT
Found at i:42737 original size:201 final size:201
Alignment explanation
Indices: 42406--42870 Score: 584
Period size: 201 Copynumber: 2.3 Consensus size: 201
42396 AAATCGTAGT
* * * *
42406 CAACCTTGGTATTCTTCTTGGCTTAAAGACCTCAGTTTAAAATTCAA-TCGAAAAGTAGTTCCTC
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAACTTCAACT-GGAAAGTAGTTCCTC
* * * * * *
42470 GTTGTTACCATGCGGTTGATACGCCCTCGAGCTAAATGGAATCAAACTCGAAAGTTTTTATTGAT
65 GCTGCTACCATGCAGTTGATACACCCTCGAGCTAAATGAAATCAAACTCGAAAGTTTTCATTGAT
*
42535 AGA-AAACTTTTCTCAACTTAAGCTAT-ATTGTAAATTAAGT-TGGGAGATAGTTCATTGT-TGC
130 AGATAAA-TTTTCTCAACTTAAGCTATGA-TGTAAATTAA-TCTGGGAGATAGTTCATTATCT-C
42596 TAAATCACAAC
191 TAAATCACAAC
* * *
42607 CAACCTAGGTCTTTTTCTTGGTTTAAATACCTCAGTTTAAACTTCAACTGGAAAGTAGTTCCTCG
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAACTTCAACTGGAAAGTAGTTCCTCG
* ** *
42672 CTGCTACCATGCAGTTGAT-CTACCCTCGAGCTGAATGAAATTGAACTCGAAAGTTTTCGTTGAT
66 CTGCTACCATGCAGTTGATAC-ACCCTCGAGCTAAATGAAATCAAACTCGAAAGTTTTCATTGAT
* * * *
42736 AGATAGATTTTCTCGACTTAATCTATGATGTAAATTAATCTGGGAGATAGTTTATTATCTCTAAA
130 AGATAAATTTTCTCAACTTAAGCTATGATGTAAATTAATCTGGGAGATAGTTCATTATCTCTAAA
* *
42801 TCGCAGC
195 TCACAAC
* **
42808 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCGGTTTAAACTTCAACCAGAAAGT-GTTCCTC
1 CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAACTTCAACTGGAAAGTAGTTCCTC
42871 TAATTGAAGG
Statistics
Matches: 228, Mismatches: 30, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
200 9 0.04
201 214 0.94
202 5 0.02
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (201 bp):
CAACCTAGGTCTTCTTCTTGGCTTAAAGACCTCAGTTTAAACTTCAACTGGAAAGTAGTTCCTCG
CTGCTACCATGCAGTTGATACACCCTCGAGCTAAATGAAATCAAACTCGAAAGTTTTCATTGATA
GATAAATTTTCTCAACTTAAGCTATGATGTAAATTAATCTGGGAGATAGTTCATTATCTCTAAAT
CACAAC
Found at i:43290 original size:22 final size:22
Alignment explanation
Indices: 43262--43321 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
43252 ATTCATTCTA
43262 AATTGGCTCTCGAACCCGTCTG
1 AATTGGCTCTCGAACCCGTCTG
43284 AATTGGCTCTCGAACCCGTCTG
1 AATTGGCTCTCGAACCCGTCTG
* *
43306 AATTAGATCTCGAACC
1 AATTGGCTCTCGAACC
43322 AGATTTGATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (22 bp):
AATTGGCTCTCGAACCCGTCTG
Done.