Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005121.1 Hibiscus syriacus cultivar Beakdansim tig00011520_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: 56799
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6160 original size:74 final size:74
Alignment explanation
Indices: 6012--6217 Score: 259
Period size: 74 Copynumber: 2.8 Consensus size: 74
6002 CAAAGCCAAA
* * * * **
6012 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
6077 TTGGCTCCGAG
64 TTGGCTCCGAG
* *
6088 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCCTAAACATTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
* *
6153 TGTTCCGAG
66 GGCTCCGAG
* ** * *
6162 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCAGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCCT
6218 GTTCAACGGT
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 89 0.78
76 25 0.22
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.22
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:6995 original size:118 final size:118
Alignment explanation
Indices: 6777--7012 Score: 402
Period size: 118 Copynumber: 2.0 Consensus size: 118
6767 TTTGAGAAAT
* *
6777 TCGAACCACTGTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTTT
1 TCGAACCACTCTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTGT
* * *
6842 ATTGCCAATTCACCCCCCTCTTGGCCAATTTCGTCATTCGATTAACTCAACAG
66 ATTGCCAATTCACCCCCCTCTTGGCAAATTCCGTCAATCGATTAACTCAACAG
*
6895 TCGAACCACTCTAAATCGCTGTGCAATTTCTTTCAATTTTCTGCAAAAGCTTCCACCAAAATTTG
1 TCGAACCACTCTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCA-CAAAATTTG
6960 TATTGCCAATTCA-CCCCCTCTTGGCAAATTCCGTCAATCGATTAACTCAACAG
65 TATTGCCAATTCACCCCCCTCTTGGCAAATTCCGTCAATCGATTAACTCAACAG
7013 AGTTCTACTA
Statistics
Matches: 111, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 90 0.81
119 21 0.19
ACGTcount: A:0.28, C:0.28, G:0.11, T:0.32
Consensus pattern (118 bp):
TCGAACCACTCTAAATCGCTGTGCAATTACTTTCAATTTTCTGCAAAAGCTTCCACAAAATTTGT
ATTGCCAATTCACCCCCCTCTTGGCAAATTCCGTCAATCGATTAACTCAACAG
Found at i:7061 original size:37 final size:37
Alignment explanation
Indices: 7011--7117 Score: 187
Period size: 37 Copynumber: 2.9 Consensus size: 37
7001 TTAACTCAAC
*
7011 AGAGTTCTACTAGGATTCAAACTCCTAAAAATAAGAT
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGAT
*
7048 AGAGTTTTACTAGGATTCAAACTCCTAAAAATATGAT
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGAT
*
7085 AGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 AGAGTTTTACTAGGATTCAAACTCCTAAAAATA
7118 GGATCCACAA
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
AGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGAT
Found at i:7719 original size:40 final size:38
Alignment explanation
Indices: 7671--7787 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 38
7661 TTTAGATTAC
*
7671 ATATATATATGTTATTTTTTATTATATGTTTTATTAATTT
1 ATATATATAT-TTATTTTTT-TTATATGTTTTATTTATTT
*
7711 ATATATATATTTACTATTTTTT-TATGTTTTTATTTATTAT
1 ATATATATATTTA-TTTTTTTTATATG-TTTTATTTATT-T
* *
7751 ATATATATATTAATTTATTTTAT-TGTTTTATTTATTT
1 ATATATATATTTATTTTTTTTATATGTTTTATTTATTT
7788 GTTTTATTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 11
0.81 0.06 0.13
Matches are distributed among these distances:
37 1 0.01
38 15 0.22
39 23 0.34
40 29 0.43
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (38 bp):
ATATATATATTTATTTTTTTTATATGTTTTATTTATTT
Found at i:7737 original size:38 final size:38
Alignment explanation
Indices: 7671--7787 Score: 132
Period size: 38 Copynumber: 3.0 Consensus size: 38
7661 TTTAGATTAC
* * *
7671 ATATATATATGTTATTTTTTATTATATGTTTTATTAATTT
1 ATATATATATATTATATTTT-TT-TATGTTTTATTTATTT
7711 ATATATATAT-TTACTATTTTTTTATGTTTTTATTTA-TT
1 ATATATATATATTA-TATTTTTTTATG-TTTTATTTATTT
7749 ATATATATATATTA-ATTTATTTTATTGTTTTATTTATTT
1 ATATATATATATTATATTT-TTTTA-TGTTTTATTTATTT
7788 GTTTTATTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
37 4 0.06
38 30 0.43
39 20 0.29
40 15 0.22
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (38 bp):
ATATATATATATTATATTTTTTTATGTTTTATTTATTT
Found at i:7748 original size:4 final size:4
Alignment explanation
Indices: 7682--7859 Score: 80
Period size: 4 Copynumber: 43.5 Consensus size: 4
7672 TATATATATG
* * * * *
7682 TTAT TT-T TTAT TATAT GT-T TTAT TAAT TTAT ATAT ATAT TTA- CTAT
1 TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
7728 TTTT TTAT GTT-T TTAT TTAT TATAT ATAT ATAT TAAT TTATT TTAT TGT-T
1 TTAT TTAT -TTAT TTAT TTAT T-TAT TTAT TTAT TTAT TTA-T TTAT T-TAT
* * * * *
7778 TTAT TTAT TTGTT TTAT TTAT ATAT TT-T TTCT TCTTT TTAT TTAT TTTT
1 TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT T-TAT TTAT TTAT TTAT
* *
7827 TTAAT ATAT TTTT GTATAT TTAT TTAT TTAT TT
1 TT-AT TTAT TTAT -T-TAT TTAT TTAT TTAT TT
7860 TACTTGCTAT
Statistics
Matches: 132, Mismatches: 26, Indels: 32
0.69 0.14 0.17
Matches are distributed among these distances:
3 13 0.10
4 94 0.71
5 23 0.17
6 2 0.02
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:7785 original size:42 final size:40
Alignment explanation
Indices: 7671--7859 Score: 127
Period size: 42 Copynumber: 4.9 Consensus size: 40
7661 TTTAGATTAC
* *
7671 ATATATATATGTTATTTTTTATTATATGTTTTATTAATTTA-T
1 ATATATATATATTA-TTTTT-TTAT-TGTTTTATTTATTTATT
* *
7713 ATATATATTTACTATTTTTTTA-TG--TT-TTTATTTATT
1 ATATATATATATTATTTTTTTATTGTTTTATTTATTTATT
*
7749 ATATATATATATTAATTTATTTTATTGTTTTATTTATTTGTT
1 ATATATATATATT-ATTT-TTTTATTGTTTTATTTATTTATT
* * * *
7791 TTATTTATATATT-TTTTCTT-CT-TTTTATTTATTT-TT
1 ATATATATATATTATTTTTTTATTGTTTTATTTATTTATT
* *
7827 -T-TA-ATATATT-TTTGTATATT-TATTTATTTATTT
1 ATATATATATATTATTTTTTTATTGT-TTTATTTATTT
7860 TACTTGCTAT
Statistics
Matches: 122, Mismatches: 16, Indels: 25
0.75 0.10 0.15
Matches are distributed among these distances:
33 11 0.09
34 3 0.02
35 19 0.16
36 16 0.13
37 16 0.13
38 8 0.07
39 5 0.04
40 6 0.05
41 7 0.06
42 31 0.25
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (40 bp):
ATATATATATATTATTTTTTTATTGTTTTATTTATTTATT
Found at i:7797 original size:13 final size:14
Alignment explanation
Indices: 7764--7800 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
7754 TATATATTAA
7764 TTTATTT-TATTGT
1 TTTATTTATATTGT
7777 TTTATTTAT-TTGT
1 TTTATTTATATTGT
7790 TTTATTTATAT
1 TTTATTTATAT
7801 ATTTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTATTTATATTGT
Found at i:25239 original size:32 final size:33
Alignment explanation
Indices: 25195--25273 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
25185 TTCTGGTTTT
* * * *
25195 GGTCGGGTTTTTTTAAGTTTGATATTCGGGTTG
1 GGTCGGGTTTTTTTAAATGTGATATTCGGATCG
25228 GGTCGGGTTTTTTTAAATGTGATATTCGGATCG
1 GGTCGGGTTTTTTTAAATGTGATATTCGGATCG
25261 GGTCGGGTTTTTT
1 GGTCGGGTTTTTT
25274 AAAAAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.13, C:0.08, G:0.33, T:0.47
Consensus pattern (33 bp):
GGTCGGGTTTTTTTAAATGTGATATTCGGATCG
Found at i:25291 original size:31 final size:32
Alignment explanation
Indices: 25255--25334 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 32
25245 TGTGATATTC
25255 GGATCGGGTCGGGTTT-TTTAAAAAAAAATC-
1 GGATCGGGTCGGGTTTGTTTAAAAAAAAATCA
* * *
25285 GAGATCGGTTCGGATTTGTTTTAAAAAAAATCA
1 G-GATCGGGTCGGGTTTGTTTAAAAAAAAATCA
*
25318 GGTTCGGGTCGGGTTTG
1 GGATCGGGTCGGGTTTG
25335 ATATTCGGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 1 0.02
31 13 0.32
32 26 0.63
33 1 0.02
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (32 bp):
GGATCGGGTCGGGTTTGTTTAAAAAAAAATCA
Found at i:25365 original size:28 final size:28
Alignment explanation
Indices: 25333--25434 Score: 152
Period size: 28 Copynumber: 3.7 Consensus size: 28
25323 GGGTCGGGTT
25333 TGATATTCGGGTCGGGTTTTTTTAAGTG
1 TGATATTCGGGTCGGGTTTTTTTAAGTG
* ** *
25361 TGATATTCAGGTCGGGGGTTTTTAAGTA
1 TGATATTCGGGTCGGGTTTTTTTAAGTG
25389 TGATATTCGGGTCGGG-TTTTTTAAGTG
1 TGATATTCGGGTCGGGTTTTTTTAAGTG
*
25416 TGATATTCGGGTCAGGTTT
1 TGATATTCGGGTCGGGTTT
25435 AGGGTGAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
27 24 0.37
28 41 0.63
ACGTcount: A:0.17, C:0.08, G:0.32, T:0.43
Consensus pattern (28 bp):
TGATATTCGGGTCGGGTTTTTTTAAGTG
Found at i:25839 original size:16 final size:16
Alignment explanation
Indices: 25815--25870 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
25805 AGGTTTCAGA
25815 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
* *
25831 TTCATATTCTAATTCC
1 TTCAGATTCCAATTCC
25847 TTCACAGATTCCAATTCC
1 TT--CAGATTCCAATTCC
*
25865 CTCAGA
1 TTCAGA
25871 AACATTCATG
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 20 0.61
18 13 0.39
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:36131 original size:43 final size:43
Alignment explanation
Indices: 36083--36188 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 43
36073 TGCTCGAATA
* * *
36083 CTCTTCAGAGTAATCAGATCTGAAAAAAGGATTTGTTTCACTG
1 CTCTTCAGAGAAATCAGATCTGAAAAAAGAATATGTTTCACTG
* * * * *
36126 TTCTTCAGAAAAATCTG-TGTGGAAAAAGAATATGTTTCACTG
1 CTCTTCAGAGAAATCAGATCTGAAAAAAGAATATGTTTCACTG
*
36168 CTCTTCAGGGAAATCAGATCT
1 CTCTTCAGAGAAATCAGATCT
36189 TGAGATTTTG
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 34 0.69
43 15 0.31
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (43 bp):
CTCTTCAGAGAAATCAGATCTGAAAAAAGAATATGTTTCACTG
Found at i:36311 original size:128 final size:128
Alignment explanation
Indices: 36161--36633 Score: 383
Period size: 128 Copynumber: 3.7 Consensus size: 128
36151 AAGAATATGT
* * * * * *
36161 TTCACTGCTCTTCAGGGAAATCAGATCTTGAGATTTTGATTCACTTCACTACCCCTT-AGAGAAG
1 TTCACTACTCTTCAAGAAAATCAGATCTTGAAACTTTGATTCACTTCACT-CCTCTTCAGAGAAG
* * *
36225 ATTGAATCAGGATTGACTTGCTTCGCTGCTTTTTAGGAAGATCAAATCTGGAAAAAGGATTTGC
65 ATTGAATCAGGATTGATTTGCTTCACTGCTTTTTAGGAAGATCAAATCTGGAAAAAGGATTTAC
* * * *
36289 TTCACTACTCTTCAAGAAAATCAGATCTTGAAATTTTGATTCAC-TCTACTGCTCTTCACATAA-
1 TTCACTACTCTTCAAGAAAATCAGATCTTGAAACTTTGATTCACTTC-ACTCCTCTTCAGAGAAG
* ** *
36352 AGTTGAATCA-GAGTTAATTTGCTTCACTG-TTCTTTAGGAAGATCAAATCTGGGAATTA-GATG
65 A-TTGAATCAGGA-TTGATTTGCTTCACTGCTT-TTTAGGAAGATCAAATCT-GGAAAAAGGATT
36414 TAC
126 TAC
* * * * ** * *
36417 TTCACCACTCTTCGACAAAATTAGAT-TTGGAAACTTTGATTCACTTTGCTTCTCTTCAGGGAAT
1 TTCACTACTCTTCAAGAAAATCAGATCTT-GAAACTTTGATTCACTTCACTCCTCTTCAGAGAA-
* * * * * *
36481 G-TTGAATCAGTGA-TGATTTGCTTCACTGCTCTTCAAGAAGATCAAATTTGGGAAATGGATTTA
64 GATTGAATCAG-GATTGATTTGCTTCACTGCTTTTTAGGAAGATCAAATCTGGAAAAAGGATTTA
36544 C
128 C
** * * * * *** * *
36545 CACACTACTCTTCAAGAAAGTTAGATCTGGAAACTTTGATTTACTTTGTTGCTCTTTA-AGGAAG
1 TTCACTACTCTTCAAGAAAATCAGATCTTGAAACTTTGATTCACTTCACTCCTCTTCAGA-GAAG
*
36609 ATTGAATCTAGG-TTGATTTACTTCA
65 ATTGAATC-AGGATTGATTTGCTTCA
36634 TTGTTTACCA
Statistics
Matches: 277, Mismatches: 49, Indels: 38
0.76 0.13 0.10
Matches are distributed among these distances:
127 17 0.06
128 248 0.90
129 10 0.04
130 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (128 bp):
TTCACTACTCTTCAAGAAAATCAGATCTTGAAACTTTGATTCACTTCACTCCTCTTCAGAGAAGA
TTGAATCAGGATTGATTTGCTTCACTGCTTTTTAGGAAGATCAAATCTGGAAAAAGGATTTAC
Found at i:37714 original size:99 final size:98
Alignment explanation
Indices: 37535--37714 Score: 265
Period size: 99 Copynumber: 1.8 Consensus size: 98
37525 AAGCAAGAGA
*
37535 AGATTGAGTTTTCTAGAAGAAATGTCCTAAAAAATCAAGAATTAGGTTCCTTGGGGGAAAATCTT
1 AGATTGAGCTTTCTAGAAGAAATGTCCTAAAAAATCAAGAATTAGGTTCCTTGGGGGAAAATCTT
* * *
37600 TAGAAAGACCGAATTGTGATGTTAAGAAATACT
66 TAAAAAGAACAAATTGTGATGTTAAGAAATACT
* *
37633 AGATTGAGCTTTCTAGGATACAA-GTCCTAATAAAATCAAGAATTAGGTTCCTT-GGGGAACAAT
1 AGATTGAGCTTTCTAGAAGA-AATGTCCTAA-AAAATCAAGAATTAGGTTCCTTGGGGGAA-AAT
37696 CTTTAAAAAGAACAAATTG
63 CTTTAAAAAGAACAAATTG
37715 AGATTTCTAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
98 30 0.41
99 43 0.59
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (98 bp):
AGATTGAGCTTTCTAGAAGAAATGTCCTAAAAAATCAAGAATTAGGTTCCTTGGGGGAAAATCTT
TAAAAAGAACAAATTGTGATGTTAAGAAATACT
Found at i:37826 original size:114 final size:114
Alignment explanation
Indices: 37621--37909 Score: 359
Period size: 114 Copynumber: 2.5 Consensus size: 114
37611 AATTGTGATG
* * * * * * *
37621 TTAAGAAATACTAGATTGAGCTTTCTAGGATACAAGTCCTAATAAAATCAAGAATTAGGTTCCTT
1 TTAAGAAAGACTAGATTGAACTTTCTATGATACAAGTCTTAAGAAAATCAAGAATGAGGTTACTT
*
37686 GGGGAACAATCTTTAAAAAGAACAAATTGA-GATTTCTATAGAAACAATA
66 GGGGAACAATCTTTAAAAAGAACAAATTGATG-TTTCTAAAGAAACAATA
* * *
37735 TTAAGAAAGACTAGATTGAATTTTCTATGATACAAGTCTTAAGAAAATCAATAATGAGGTTATTT
1 TTAAGAAAGACTAGATTGAACTTTCTATGATACAAGTCTTAAGAAAATCAAGAATGAGGTTACTT
* * * **
37800 GGGGAATAATCTTTAAAAATACCAAATTGATGTTTCTAAAGAAATGATA
66 GGGGAACAATCTTTAAAAAGAACAAATTGATGTTTCTAAAGAAACAATA
* * *
37849 TTAAGAAAGACTAGATTGAACTTTCTAAT-ATATAAGTCTTAA-AAGAGTCAAGATTGAGGTT
1 TTAAGAAAGACTAGATTGAACTTTCT-ATGATACAAGTCTTAAGAA-AATCAAGAATGAGGTT
37910 TCTAGGGAAA
Statistics
Matches: 151, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
113 2 0.01
114 146 0.97
115 3 0.02
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (114 bp):
TTAAGAAAGACTAGATTGAACTTTCTATGATACAAGTCTTAAGAAAATCAAGAATGAGGTTACTT
GGGGAACAATCTTTAAAAAGAACAAATTGATGTTTCTAAAGAAACAATA
Found at i:37942 original size:114 final size:112
Alignment explanation
Indices: 37616--37942 Score: 297
Period size: 114 Copynumber: 2.9 Consensus size: 112
37606 GACCGAATTG
* * * ** * *
37616 TGATGTTAAGAAATACTAGATTGAGCTTTCTAGGATACAAGTCCTAATAAAATCAAGAATT-AGG
1 TGATATTAAGAAAGACTAGATTGAACTTTCTAATATACAAGTCTTAAGAAAATCAAG-ATTGAGG
* * * * *
37680 TTCCTTGGGGAACAATCTTTAAAAAGAACAAATTGAGATTTCTATAGAAA
65 TTTCTAGGGAAACAA-CTTTAAAATG-ACAAATTGAGATTTCTAAAGAAA
** * * *
37730 CAATATTAAGAAAGACTAGATTGAATTTTCT-ATGATACAAGTCTTAAGAAAATCAATAATGAGG
1 TGATATTAAGAAAGACTAGATTGAACTTTCTAAT-ATACAAGTCTTAAGAAAATCAAGATTGAGG
* * *
37794 TTATTTGGGGAATA-ATCTTTAAAAAT-ACCAAATTGATG-TTTCTAAAGAAA
65 TT-TCTAGGGAA-ACAACTTT-AAAATGA-CAAATTGA-GATTTCTAAAGAAA
* *
37844 TGATATTAAGAAAGACTAGATTGAACTTTCTAATATATAAGTCTTAA-AAGAGTCAAGATTGAGG
1 TGATATTAAGAAAGACTAGATTGAACTTTCTAATATACAAGTCTTAAGAA-AATCAAGATTGAGG
*
37908 TTTCTAGGGAAACAACCTTAAGAATGACAGAATTG
65 TTTCTAGGGAAACAACTTTAA-AATGACA-AATTG
37943 GTTTCGCATA
Statistics
Matches: 170, Mismatches: 30, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
112 3 0.02
113 21 0.12
114 132 0.78
115 13 0.08
116 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (112 bp):
TGATATTAAGAAAGACTAGATTGAACTTTCTAATATACAAGTCTTAAGAAAATCAAGATTGAGGT
TTCTAGGGAAACAACTTTAAAATGACAAATTGAGATTTCTAAAGAAA
Found at i:40031 original size:20 final size:20
Alignment explanation
Indices: 40006--40049 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
39996 CCTGATGCCT
40006 CCATGTGGAAATCAAAAGTA
1 CCATGTGGAAATCAAAAGTA
40026 CCATGTGGAAATCAAAAGTA
1 CCATGTGGAAATCAAAAGTA
40046 CCAT
1 CCAT
40050 TTGGGTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (20 bp):
CCATGTGGAAATCAAAAGTA
Found at i:41840 original size:2 final size:2
Alignment explanation
Indices: 41772--41821 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
41762 TATTTAGCTC
41772 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
41814 AT AT AT AT
1 AT AT AT AT
41822 TAATCACTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41860 original size:23 final size:25
Alignment explanation
Indices: 41803--41868 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 25
41793 TATATATATA
*
41803 TATATATATATATATATATTAATCACT
1 TATAT-TATATA-ATATATTAATCACG
*
41830 TATATTATATAATATATTCAT-ACG
1 TATATTATATAATATATTAATCACG
41854 TAT-TTATATAATATA
1 TATATTATATAATATA
41869 AATATACATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
23 12 0.32
24 5 0.14
25 9 0.24
26 6 0.16
27 5 0.14
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATTATATAATATATTAATCACG
Found at i:48980 original size:17 final size:17
Alignment explanation
Indices: 48949--48981 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48939 AAAATATTAT
48949 TTATTATTTATTTTAAA
1 TTATTATTTATTTTAAA
48966 TTATT-TTTATATTTAA
1 TTATTATTTAT-TTTAA
48982 CAATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATTTTAAA
Found at i:52763 original size:26 final size:26
Alignment explanation
Indices: 52714--52764 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
52704 AATTAAAAGT
*
52714 TAAAAAATAATTATTAAACTAAAGAC
1 TAAAAAATAATTATTAAAATAAAGAC
*
52740 TAAAAAATAATTGTTAAAATAAAGA
1 TAAAAAATAATTATTAAAATAAAGA
52765 TTAAGTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (26 bp):
TAAAAAATAATTATTAAAATAAAGAC
Found at i:54933 original size:23 final size:23
Alignment explanation
Indices: 54903--54952 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
54893 GGGGACATTG
54903 TGGATACAAACTGAAGTTGAATT
1 TGGATACAAACTGAAGTTGAATT
54926 TGGATACAAACTGAAGTTGAATT
1 TGGATACAAACTGAAGTTGAATT
54949 TGGA
1 TGGA
54953 AGATGATAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGATACAAACTGAAGTTGAATT
Done.