Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005374.1 Hibiscus syriacus cultivar Beakdansim tig00012251_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: 47379
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1419 original size:23 final size:23
Alignment explanation
Indices: 1357--1412 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
1347 GTAATGGATT
*
1357 TCACAAGGCTCCATTGCCGCACA
1 TCACAAGGCTTCATTGCCGCACA
* *
1380 TCACAATGCTTCATTGCCGCGCA
1 TCACAAGGCTTCATTGCCGCACA
1403 TCACAAGGCT
1 TCACAAGGCT
1413 ATGTTGCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (23 bp):
TCACAAGGCTTCATTGCCGCACA
Found at i:18309 original size:6 final size:6
Alignment explanation
Indices: 18298--18324 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
18288 ATCCTCCATG
18298 TTCTCC TTCTCC TTCTCC TTCTCC TTC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTC
18325 GTCGACCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCTCC
Found at i:24399 original size:3 final size:3
Alignment explanation
Indices: 24388--24444 Score: 64
Period size: 3 Copynumber: 19.7 Consensus size: 3
24378 ATTTTTTTCG
* * * *
24388 TTA TT- TTA TTA TTA TTA TTA CTA TTA TTG TCA TTT TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24434 TTA TTA TTA TT
1 TTA TTA TTA TT
24445 TAATATGTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27979 original size:31 final size:32
Alignment explanation
Indices: 27943--28004 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
27933 ATTTTACATG
27943 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
27974 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
28005 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:30973 original size:11 final size:11
Alignment explanation
Indices: 30945--30982 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
30935 AAGAGCAAAG
30945 AGAAAAATCAA
1 AGAAAAATCAA
30956 AGCAAAAATCAA
1 AG-AAAAATCAA
*
30968 AGAAAAAGCAA
1 AGAAAAATCAA
30979 AGAA
1 AGAA
30983 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:32174 original size:12 final size:11
Alignment explanation
Indices: 32157--32199 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
32147 CTCGAGAAAA
32157 ACATACATCAAC
1 ACATACAT-AAC
*
32169 ACATACATACAT
1 ACATACATA-AC
32181 ACATACAT-AC
1 ACATACATAAC
32191 ACATACATA
1 ACATACATA
32200 CATGATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 9 0.33
11 1 0.04
12 17 0.63
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (11 bp):
ACATACATAAC
Found at i:32176 original size:4 final size:4
Alignment explanation
Indices: 32169--32202 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
32159 ATACATCAAC
32169 ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
32203 GATACATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 26 0.93
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:32841 original size:105 final size:102
Alignment explanation
Indices: 32654--32892 Score: 281
Period size: 105 Copynumber: 2.3 Consensus size: 102
32644 TGAGAATTTT
* * *
32654 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCACT
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
*
32719 AAAAACAAAATTAATCTCACCTT-AGATTCTTGTTTCTTTC-
66 AAAAACAAAATTAATCTCA-CTTGAGA-TC--GTTT-TCTCA
* *
32759 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGAT-CAAAATTTCGAATTTGTTTCAC
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATAC-AAATTTCGAATTTGATTCAC
* * *
32823 -ATTAAACAAAGTTGATCTCACTTGAGATCGTTTTCTCA
65 TA-AAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
*
32861 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
32893 TCTAAAAACA
Statistics
Matches: 118, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
101 3 0.03
102 30 0.25
103 3 0.03
104 7 0.06
105 75 0.64
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (102 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACT
AAAAACAAAATTAATCTCACTTGAGATCGTTTTCTCA
Found at i:32883 original size:36 final size:36
Alignment explanation
Indices: 32838--32922 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
32828 ACAAAGTTGA
**
32838 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
32874 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
32910 TCTCATTTGAGAC
1 TCTCACTTGAGAC
32923 TGTATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:32954 original size:34 final size:34
Alignment explanation
Indices: 32860--32954 Score: 93
Period size: 36 Copynumber: 2.7 Consensus size: 34
32850 TCGTTTTCTC
* *
32860 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGAC-ATGTATCT
**
32896 AAAAACAAATTTTGTCTCATTTGAGAC-TGTATCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACATGTATCT
* *
32930 TAAAGCAAATTTCGTCTCGCTTGAG
1 AAAAACAAATTT-GTCTCGCTTGAG
32955 GCATCATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 3 0.06
34 22 0.45
36 24 0.49
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACATGTATCT
Found at i:33284 original size:29 final size:29
Alignment explanation
Indices: 33212--33339 Score: 181
Period size: 29 Copynumber: 4.5 Consensus size: 29
33202 TTTTGAAAAA
* *
33212 AAAAATCTTTGAGTTTGTTCCTCTTGAAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTG-AAT
33242 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
33271 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
* *
33300 AAAAATCTTTGAG-TTGTTTCGTTTG-A-
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
33326 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
33340 CTATTTATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
26 13 0.14
27 1 0.01
28 10 0.11
29 42 0.46
30 25 0.27
ACGTcount: A:0.30, C:0.10, G:0.16, T:0.44
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:33285 original size:59 final size:55
Alignment explanation
Indices: 33211--33339 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 55
33201 CTTTTGAAAA
*
33211 AAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAAATCTTTGAGTTTGTTCCTTTTG
1 AAAAAATCTTTGAGTTTGTTCCTCTTG-AAAAAAAATCTTTGAG-TTGTTCCGTTTG
* * * *
33268 AATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTGTTTCGTTTG
1 -A-AAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTGTTCCGTTTG
33325 AAAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
33340 CTATTTATTT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
55 13 0.20
56 1 0.02
57 10 0.16
58 16 0.25
59 24 0.38
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (55 bp):
AAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAAATCTTTGAGTTGTTCCGTTTG
Found at i:33470 original size:30 final size:30
Alignment explanation
Indices: 33436--33545 Score: 94
Period size: 30 Copynumber: 3.4 Consensus size: 30
33426 AGACAATTTT
33436 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
* * * **
33466 TTTTGAAACAAAATTTTGTCTCTCTTAAGATAATTTC
1 TTTTGAAACAAAA------ATCT-TTGAGTTTGTTTC
33503 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
1 TTTTGAAACAAAAATCTTTGAGTTTGTTTC
* *
33533 TTTGGAAGCAAAA
1 TTTTGAAACAAAA
33546 TTTTGTCTCT
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
30 33 0.54
31 3 0.05
36 3 0.05
37 22 0.36
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTTGAAACAAAAATCTTTGAGTTTGTTTC
Found at i:33510 original size:67 final size:67
Alignment explanation
Indices: 33402--33598 Score: 315
Period size: 67 Copynumber: 3.0 Consensus size: 67
33392 TCTCTGAGTC
* * * *
33402 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1 TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
33467 TT
66 TT
33469 TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1 TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
33534 TT
66 TT
* * * *
33536 GGAAGCAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAA-AAAAATCTTTGAATCTGTTTC
1 TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTC
33599 GCTTAAAATG
Statistics
Matches: 122, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 19 0.16
67 103 0.84
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (67 bp):
TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT
TT
Found at i:33512 original size:37 final size:37
Alignment explanation
Indices: 33462--33588 Score: 124
Period size: 37 Copynumber: 3.6 Consensus size: 37
33452 TTTGAGTTTG
33462 TTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
* * * **
33499 TTTCTTTTGAAACAAAA------ATCT-TTGAGTTTG
1 TTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
* *
33529 TTTCTTTGGAAGCAAAATTTTGTCTCTCTTAAGATAA
1 TTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
*
33566 TTTCTTTTGAAAAAAAATCTTTG
1 TTTCTTTTGAAACAAAAT-TTTG
33589 AATCTGTTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 15
0.69 0.15 0.15
Matches are distributed among these distances:
30 20 0.30
31 3 0.04
36 3 0.04
37 37 0.55
38 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (37 bp):
TTTCTTTTGAAACAAAATTTTGTCTCTCTTAAGATAA
Found at i:33839 original size:121 final size:119
Alignment explanation
Indices: 33700--33924 Score: 276
Period size: 121 Copynumber: 1.9 Consensus size: 119
33690 TTAACAAAAT
* * *
33700 CATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAAA
*
33763 ACTAACTTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATGGGATC
64 A--AA-TCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGGGATC
* ** **
33821 CATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
* * *
33886 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
33925 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
118 22 0.25
119 13 0.15
120 7 0.08
121 43 0.48
122 4 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (119 bp):
CATCTTTGAGTCTATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAAA
ATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATGGGATC
Found at i:33901 original size:64 final size:63
Alignment explanation
Indices: 33822--33946 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
33812 GATGGGATCC
* *
33822 ATCTTTGAGTCTGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
33886 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
33947 TACCCACATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:33991 original size:40 final size:40
Alignment explanation
Indices: 33928--34007 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
33918 TTGTCTCTCG
33928 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
33968 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
34008 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:34126 original size:15 final size:15
Alignment explanation
Indices: 34103--34146 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
34093 TTTTGAGTCG
*
34103 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
34118 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
34133 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
34147 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:34987 original size:46 final size:43
Alignment explanation
Indices: 34868--35069 Score: 112
Period size: 40 Copynumber: 4.7 Consensus size: 43
34858 TCATCCTCTG
*
34868 ACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
* * * ** * * *
34911 ACCAG-CCGTCCTCATCACGTAGGAATCGTGTTATCACCTTTAGATG
1 ACCAGAAC-TCTTCATCACGTATGAGCCGTGTCA--ACC-ATAGATA
* * **
34957 GCCAGAACTCTTCATCACGTATGAGCCGTGTCATTCC-CCG---
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCA-ACCATAGATA
* * * *
34997 ACCAGATCTCTTCATCGCGTATGAGCCGTGTC-ACCCTAGGTA
1 ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
* * * *
35039 ACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 ACCAGAAC-TCTTCATCACGTATGAGCCGTGT
35070 TATCACCACT
Statistics
Matches: 119, Mismatches: 30, Indels: 21
0.70 0.18 0.12
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 29 0.24
41 1 0.01
42 25 0.21
43 26 0.22
45 5 0.04
46 29 0.24
47 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (43 bp):
ACCAGAACTCTTCATCACGTATGAGCCGTGTCAACCATAGATA
Found at i:35156 original size:133 final size:130
Alignment explanation
Indices: 34836--35236 Score: 494
Period size: 133 Copynumber: 3.1 Consensus size: 130
34826 ATGGCCAGTA
*
34836 GTCCTCAT-ACATAGGAACCGTGTCAT-CCTCTGACCAGATCTCTTCATCACGTATGAGCCGTGT
1 GTCCTCATCACGTAGGAACCGTGTCATCCCTC-GACCAGATCTCTTCATCACGTATGAGCCGTGT
* * * *
34899 CAACCATAGATAACCAGCCGTCCTCATCACGTAGGAATCGTGTTATCA-CCTTTAGATGGCCAGA
65 C-ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAAGATGACCAGA
34963 AC
129 AC
* * * *
34965 -TCTTCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCTTCATCGCGTATGAGCCGTGT
1 GTCCTCATCACGTAGGAACCGTGTCA-TCCCTCGACCAGATCTCTTCATCACGTATGAGCCGTGT
*
35028 CACCCTAGGTAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCACTCCTAAAGATGACC
65 CACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACC-CT--T-AAGATGACC
*
35093 AG-CC
126 AGAAC
* * * *
35097 GTCCTCATCACGTAGGAATCGTGTCATCCCTCGACCAGACCTCCTCATCACGTAAGAGCCGTGTC
1 GTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCATCACGTATGAGCCGTGTC
* * *
35162 ACCCTTAGATAACCAGCCGTCCTCATCATGTAGGAACCGTGTTATCA-CCTTTAGATGGCCAAGA
66 ACCC-TAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAAGATGACC-AGA
35226 AC
129 AC
*
35228 -TCTTCATCA
1 GTCCTCATCA
35237 TGTATGAGCA
Statistics
Matches: 234, Mismatches: 25, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
128 49 0.21
129 54 0.23
130 15 0.06
131 3 0.01
132 8 0.03
133 65 0.28
134 40 0.17
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (130 bp):
GTCCTCATCACGTAGGAACCGTGTCATCCCTCGACCAGATCTCTTCATCACGTATGAGCCGTGTC
ACCCTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCCTTAAGATGACCAGAAC
Found at i:35160 original size:40 final size:39
Alignment explanation
Indices: 35089--35203 Score: 115
Period size: 40 Copynumber: 2.8 Consensus size: 39
35079 TCCTAAAGAT
* *
35089 GACCAGCCGTCCTCATCACGTAGGAATCGTGTCATCCCTC
1 GACCAGCCGTCCTCATCACGTAAGAACCGTGTCA-CCCTC
* *
35129 GACCAGACC-TCCTCATCACGTAAGAGCCGTGTCACCCTTA
1 GACCAG-CCGTCCTCATCACGTAAGAACCGTGTCACCC-TC
* *
35169 GATAACCAGCCGTCCTCATCATGTAGGAACCGTGT
1 G---ACCAGCCGTCCTCATCACGTAAGAACCGTGT
35204 TATCACCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 3 0.05
40 30 0.48
41 2 0.03
42 2 0.03
43 25 0.40
ACGTcount: A:0.23, C:0.35, G:0.20, T:0.22
Consensus pattern (39 bp):
GACCAGCCGTCCTCATCACGTAAGAACCGTGTCACCCTC
Found at i:35418 original size:3 final size:3
Alignment explanation
Indices: 35407--35464 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
35397 GTTTTTTTCG
* * * *
35407 TTA TT- TTA TTA TTA TTA TTA TTA CTA TTA TTG TCA TTT TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35453 TTA TTA TTA TTA
1 TTA TTA TTA TTA
35465 ATTAATATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:42366 original size:19 final size:19
Alignment explanation
Indices: 42319--42370 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
42309 ACGACGATAC
*
42319 AAACATATATATTTGTAAA
1 AAACATATTTATTTGTAAA
*
42338 AATC-TAATTTATTTGTAAA
1 AAACAT-ATTTATTTGTAAA
42357 AAACATATTTATTT
1 AAACATATTTATTT
42371 ATTCTAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 1 0.04
19 26 0.93
20 1 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (19 bp):
AAACATATTTATTTGTAAA
Done.