Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007351.1 Hibiscus syriacus cultivar Beakdansim tig00019699_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: 256012
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 2
Found at i:239949 original size:54 final size:54
Alignment explanation
Indices: 239890--240000 Score: 134
Period size: 53 Copynumber: 2.1 Consensus size: 54
239880 TTGACAACAC
* * *
239890 AAAGAGAAAAAAAGATATAGCATAAAAAAAAGAAAAAAAGG-AAAAACATAAAAG
1 AAAGAG-AAAAAAGAAAAAACATAAAAAAAAGAAAAAAAGGAAAAAACATAAAAG
* * * * *
239944 AAAGAGAGAAAGGAAAAAACATAAAAGAAAGAGAGAAAGGAAAAAACATAAAAG
1 AAAGAGAAAAAAGAAAAAACATAAAAAAAAGAAAAAAAGGAAAAAACATAAAAG
239998 AAA
1 AAA
240001 TTAGAGAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 26 0.54
54 22 0.46
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (54 bp):
AAAGAGAAAAAAGAAAAAACATAAAAAAAAGAAAAAAAGGAAAAAACATAAAAG
Found at i:239969 original size:27 final size:27
Alignment explanation
Indices: 239910--240009 Score: 148
Period size: 27 Copynumber: 3.7 Consensus size: 27
239900 AAAGATATAG
* * *
239910 CATAAAAAAAAGAAAAAAAGG-AAAAA
1 CATAAAAGAAAGAGAGAAAGGAAAAAA
239936 CATAAAAGAAAGAGAGAAAGGAAAAAA
1 CATAAAAGAAAGAGAGAAAGGAAAAAA
239963 CATAAAAGAAAGAGAGAAAGGAAAAAA
1 CATAAAAGAAAGAGAGAAAGGAAAAAA
*
239990 CATAAAAGAAATTAGAGAAA
1 CATAAAAGAAA-GAGAGAAA
240010 AAAATAAAGA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 18 0.26
27 43 0.63
28 7 0.10
ACGTcount: A:0.72, C:0.04, G:0.18, T:0.06
Consensus pattern (27 bp):
CATAAAAGAAAGAGAGAAAGGAAAAAA
Found at i:240029 original size:53 final size:52
Alignment explanation
Indices: 239913--240029 Score: 139
Period size: 53 Copynumber: 2.2 Consensus size: 52
239903 GATATAGCAT
* *
239913 AAAAAAAAGAAAAAAAGGAAAAACATAAAAGAAAGAGAGAAAGGAAAAAACAT
1 AAAAAAAAGAGAAAAAGGAAAAACATAAAAGAAAGAGAGAAA-GAAAAAACAG
* * *
239966 AAAAGAAAGAGAGAAAGGAAAAAACATAAAAGAAATTAGAGAAA-AAAATAA-AG
1 AAAAAAAAGAGAAAAAGG-AAAAACATAAAAGAAA-GAGAGAAAGAAAA-AACAG
240019 AAAAAAAAGAG
1 AAAAAAAAGAG
240030 TCAAAAAAGA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 30 0.55
54 18 0.33
55 7 0.13
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (52 bp):
AAAAAAAAGAGAAAAAGGAAAAACATAAAAGAAAGAGAGAAAGAAAAAACAG
Found at i:242236 original size:55 final size:54
Alignment explanation
Indices: 242099--242982 Score: 1074
Period size: 55 Copynumber: 16.1 Consensus size: 54
242089 TGTTACTCGG
* ** * *
242099 TTAACATGAGTTTTTAAAGAAACTAAAACTGGTTTTCAGAAGTTTCCTGATGATT
1 TTAA-ATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * * *
242154 TCAAATGAGTTTTTAAAGAAATTAAGTCTGATTTTCATAAGTTTCTTGATTATT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * *
242208 GTTAAATGAGCTTTCAAATAAACTAAGTCTTATTTTCAGAAGTTTCCTGATGATT
1 -TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * * *
242263 TTAAATGAGCTTTCAAAGAAACTAAGTATGATTTTCATAAGTTTCTTGACGTTTT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-ATT
* *
242318 TTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTCATAAGTTTCTTGATGATT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * *
242372 TTAAATGAGCTTTCAAAGAAATTAAGTCTGATTTTTAGAAGTTTCTTGACGATTT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TT
* *
242427 TTAAATGAGCTTTCAAAGAAACTAAGTATGATTTTCAGAAGTTTCTTGATGATT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * *
242481 TTCAAATGAGTTTTTAAAGAAACTAAGTCTGATTATT-ATAAGTTTCTTGACGTTT
1 TT-AAATGAGCTTTTAAAGAAACTAAGTCTGATT-TTCAGAAGTTTCTTGATGATT
* * *
242536 TTCAAATGAGTTTTTAAAGAAACTAAGTCCGATTTTC-GAAAGTTTCTTGATCATTT
1 TT-AAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAG-AAGTTTCTTGATGA-TT
*
242592 TTAAATGAGCTTTTAAAGAAA-TAAAGTCTAATTTTCAGAAGTTTCTTGATGATT
1 TTAAATGAGCTTTTAAAGAAACT-AAGTCTGATTTTCAGAAGTTTCTTGATGATT
* *
242646 TTCAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCGGAAGTTTCTTGATCATTT
1 TT-AAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TT
* * * *
242702 TTAAAAGAGCTTTTAAAGAAAGTAAGTCTGATGTTCAGAAGTTTCTTGACGATT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * * * *
242756 TTCAAATGAGTTTTTAAAGAAACCAAGTCCGATTTTCTGAAGTTTCTTGATCATTT
1 TT-AAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TT
* * *
242812 TTAAATAAGCTTTTAAAGAAACTAAGTTTGATTTTCAGAAGTTTCTTGACGATT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
* * *
242866 TTCAAATGAGTTTTTAAAGAAATTAAGTCTGATTTTCAGAAGTTTCTTGATCATTT
1 TT-AAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TT
* * * **
242922 TTAAATGAGCTTTCAAAGAAATTAAGTCTTATTTTCAGGGGTTTCTTGATG-TT
1 TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
242975 TTCAAATG
1 TT-AAATG
242983 TTTTTTCAAA
Statistics
Matches: 723, Mismatches: 88, Indels: 37
0.85 0.10 0.04
Matches are distributed among these distances:
53 4 0.01
54 162 0.22
55 537 0.74
56 20 0.03
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.41
Consensus pattern (54 bp):
TTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATT
Found at i:243190 original size:41 final size:41
Alignment explanation
Indices: 243090--243192 Score: 106
Period size: 42 Copynumber: 2.5 Consensus size: 41
243080 GATAAGTAAG
*
243090 TCCTTC-GTGCCATC-AGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAG-GCCATCTA-TAAGTCTTTCGAGCAAGAT-CTTAAA
* *
243132 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGAT-TATAAGA
1 TCCTTCAGGCCATCTATAAGTCTTTCGAGCAAGATCT-TAA-A
243174 -CCTTCAGGCCATCTATAAG
1 TCCTTCAGGCCATCTATAAG
243193 ACCTTCAGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.02
41 20 0.38
42 30 0.57
43 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (41 bp):
TCCTTCAGGCCATCTATAAGTCTTTCGAGCAAGATCTTAAA
Found at i:243571 original size:42 final size:40
Alignment explanation
Indices: 243509--243611 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 40
243499 ATTGAGTAAG
** *
243509 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCGTGATGTTTAAA
1 TCCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGATG-ATAAA
* *
243551 TCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAG
1 TCCTTCGGGCCATC-ATAAGTCTTTCGAGCAAGATGATAAA
243592 TCCTTCGGGCCATCCATAAG
1 TCCTTCGGGCCAT-CATAAG
243612 AACTTCGGGC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 20 0.38
42 32 0.60
43 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.31
Consensus pattern (40 bp):
TCCTTCGGGCCATCATAAGTCTTTCGAGCAAGATGATAAA
Found at i:244932 original size:139 final size:137
Alignment explanation
Indices: 244573--245078 Score: 517
Period size: 139 Copynumber: 3.7 Consensus size: 137
244563 AAGATGAACC
* * ** * *
244573 GATCAACATTTCAAATGAAGAGTTCATAATGAGAAGAACTCATCTAACAGAGGGAGAATAAGTTC
1 GATCAACATTTCTATTG-AGAGTTCATAAT-AGAAGAACTCATCCGA-TGAGGGAGAAAAAGTTC
* * ** * ** ** **
244638 ATAATGAGAAGAGCCTGTTTGACCTATCA-CTCGATTCATGGCAT-T----TCAAATCAGTGACA
63 ATAATGAGAAGAACTTGTTCAACCT-T-AGCTTGATTCATCACATATGAAGTTGAATCAGAAACA
244697 CCTCACTCGAGG
126 CCTCACTCGAGG
* * *
244709 GATCAACATTTCTAATGAAGAGTTCAT-AT-G-AGAAGTCATCCGATGAGGGAGAATAAGTTCAT
1 GATCAACATTTCTATTG-AGAGTTCATAATAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCAT
* *
244771 AATGAGAAGAAGTTGTTCAACCTTAGCTTGATTCATCACATATGAAGTTGAATCAGCAACACCTC
65 AATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGAAGTTGAATCAGAAACACCTC
244836 ACTCGAGG
130 ACTCGAGG
* * *
244844 GATCAACATTTCTAGTTGAGAGTTCATAATAAGAAGAACTCATCAGATGAGGGAGAAGAGGTTCA
1 GATCAACATTTCTA-TTGAGAGTTCATAAT-AGAAGAACTCATCCGATGAGGGAGAAAAAGTTCA
* * * *
244909 TAATGAGAAGAACTTGTTCAACCTTAACTCGATTCATCACATATGGAGTTTAATCAGAAACACCT
64 TAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGAAGTTGAATCAGAAACACCT
244974 CACTCGAGG
129 CACTCGAGG
* * * * * *
244983 GATCAACATGTCCATGGGAGAGTTCATAATGAGAAGAACTTAACCCGATAAGGGAGAAAAAGTTC
1 GATCAACATTTCTAT-TGAGAGTTCATAAT-AGAAGAAC-TCATCCGATGAGGGAGAAAAAGTTC
* *
245048 ATAATGAGAAGAACTTATTCAACCTTGGCTT
63 ATAATGAGAAGAACTTGTTCAACCTTAGCTT
245079 CTTTCCATCG
Statistics
Matches: 315, Mismatches: 42, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
129 1 0.00
130 13 0.04
131 37 0.12
132 10 0.03
133 1 0.00
135 47 0.15
136 30 0.10
138 2 0.01
139 128 0.41
140 46 0.15
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (137 bp):
GATCAACATTTCTATTGAGAGTTCATAATAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCATCACATATGAAGTTGAATCAGAAACACCTCA
CTCGAGG
Found at i:249152 original size:81 final size:80
Alignment explanation
Indices: 248829--249152 Score: 339
Period size: 81 Copynumber: 4.0 Consensus size: 80
248819 TTATAATTCC
* * * * *
248829 TTTAGTCTTTTACCCAAAGG-CATTTAACCTTTCATCTAACTTGCATGATTGACACTTGTCTGCC
1 TTTA-TCTTTTACTCAAAGGTC-TTTAACCGTTCATCTAACTGGCATAATTGACACTT-TCTGTC
* * *
248893 AAAGGCACCGCTAGGCTA
63 AAATGCACAGCTAGGCCA
* * **
248911 TTTATCTTTTACTTAATGGTCTTTAACCGTTCATCTAACTGAAATAATTGACACCTTTCTGTCAA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAA
*
248976 ATGCAC-GACTAGGACA
65 ATGCACAG-CTAGGCCA
* * * * * * * * *
248992 TTTATCTTTTACTCAACGGTCGTTAATCGTTCATCTAAATTGCATAACTAACATATTTCTTTCAA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAA
*
249057 ATGCACAACTAGGCCA
65 ATGCACAGCTAGGCCA
*
249073 TTTATCTTTTACTCAAAGGTCTTTAACCATTCATCTAACTGGCATAATAT-ACAGCTTTCTGTCA
1 TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAAT-TGACA-CTTTCTGTCA
249137 AATGCACAGCTAGGCC
64 AATGCACAGCTAGGCC
249153 TCAAAGGCAC
Statistics
Matches: 199, Mismatches: 38, Indels: 11
0.80 0.15 0.04
Matches are distributed among these distances:
80 1 0.01
81 189 0.95
82 9 0.05
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (80 bp):
TTTATCTTTTACTCAAAGGTCTTTAACCGTTCATCTAACTGGCATAATTGACACTTTCTGTCAAA
TGCACAGCTAGGCCA
Found at i:249174 original size:68 final size:68
Alignment explanation
Indices: 249102--249561 Score: 742
Period size: 68 Copynumber: 6.8 Consensus size: 68
249092 TCTTTAACCA
* *
249102 TTCATCTAACTGGCATAATAT-ACAGCTTTCTGTCAAATGCACAGCTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAT-TGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTA
249166 GCCT
65 GCCT
* * *
249170 TTCATCTAACTGGCATAATTGACACCTTTTTGTCAAATGAACAGTTAGGTCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
249235 CCT
66 CCT
* * *
249238 TTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATACATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
249303 CCT
66 CCT
* * * * *
249306 TTCATCTAACTGGCATAATTGACATCTTTCTTTCAAATACACAGTTAAGCTTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
249371 CCT
66 CCT
*
249374 TTCATCTAACTGGCATAATTGACACCTTTCTGTTAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
249439 CCT
66 CCT
*
249442 TTCATCTAACTGGCATAATTGACATCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
249507 CCT
66 CCT
** *
249510 TTCATCTAACTGGCATAATTGACACCTTTCCATCAAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
249562 ATTAATCTTT
Statistics
Matches: 362, Mismatches: 29, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
67 1 0.00
68 361 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (68 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:249883 original size:55 final size:55
Alignment explanation
Indices: 249770--249981 Score: 266
Period size: 55 Copynumber: 3.8 Consensus size: 55
249760 TCACTTACGA
* * * * *
249770 AAATTAATACACTTAGTATGGATTTCTTA-ATTTGCACACATAGTACCCATA-CG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCG
* *
249823 AAAATTCATACACATAGTATAAATTTCTTAGTTTTACACACATAGTGCCCATACCG
1 -AAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCG
* * * * *
249879 AAATTCATACACTTAGTATTAACTTCTTAGTTTTGCACACATAGTGTCCGTACCG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCG
*
249934 AAATTCATACACTTAGTATGAATTTCTTAAGGTTTTACACACTTAGTG
1 AAATTCATACACTTAGTATGAATTTCTT-A-GTTTTACACACATAGTG
249982 TCATTTGGTA
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
54 25 0.18
55 94 0.69
56 3 0.02
57 15 0.11
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.35
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTTAGTTTTACACACATAGTGCCCATACCG
Found at i:254545 original size:81 final size:81
Alignment explanation
Indices: 254451--254609 Score: 214
Period size: 81 Copynumber: 2.0 Consensus size: 81
254441 CCCAAAGGCA
* * * * **
254451 TTTAACCTTTCATCTAACT-AGCATGATTGACA-CTTGTTTGCCAAATACACTTCTAGGCCATTT
1 TTTAACCATTCATCTAACTGA-AATAATTGACACCTT-TCTGCCAAATACACAACTAGGCCATTT
254514 ATCTTTTACTCAACGGTC
64 ATCTTTTACTCAACGGTC
* *
254532 TTTAACCATTCATCTAACTGAAATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTTAT
1 TTTAACCATTCATCTAACTGAAATAATTGACACCTTTCTGCCAAATACACAACTAGGCCATTTAT
254597 CTTTTACTCAACG
66 CTTTTACTCAACG
254610 ATCATCTAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
81 64 0.94
82 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (81 bp):
TTTAACCATTCATCTAACTGAAATAATTGACACCTTTCTGCCAAATACACAACTAGGCCATTTAT
CTTTTACTCAACGGTC
Found at i:254658 original size:70 final size:70
Alignment explanation
Indices: 254541--254673 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 70
254531 CTTTAACCAT
* *
254541 TCATCTAACTGAAATAATTGACACCTTTCTGTCAAATGCACAACTAGGCCATTTATCTTTTACTC
1 TCATCTAACTGAAATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTACTC
254606 AACGA
66 AACGA
* * *
254611 TCATCTAACT-AGCATAATTGGCACATTTCTATCAAATGCACAGCTAGGCCATTTATCTTTTAC
1 TCATCTAACTGA-AATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTAC
254674 ACAAAGTTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 1 0.02
70 56 0.98
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (70 bp):
TCATCTAACTGAAATAATTGACACATTTCTATCAAATGCACAACTAGGCCATTTATCTTTTACTC
AACGA
Found at i:254799 original size:67 final size:67
Alignment explanation
Indices: 254691--255079 Score: 489
Period size: 67 Copynumber: 5.8 Consensus size: 67
254681 TCTTTAATCG
* ** *
254691 TTCATCTAATTGTTATAATTGACACCTTTTTGTCAAATGCACAGTTAGGCCTCAAAGGCCTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCCTTAGC
254756 CT
66 CT
* * *
254758 TTCATCTAACTGGAATAGTTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAGTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC-CTTAG
*
254823 TCT
65 CCT
* * *
254826 TTCATCTAACTGGCATAATTGACACCTTTTCTGTAAAATGCACAAG-TAGGCCTCAAAGGAACAT
1 TTCATCTAACTGGCATAATTGACACC-TTTCTGTCAAATGCAC-AGTTAGGCCTCAAAGG-CCTT
*
254890 AACCT
63 AGCCT
* * **
254895 TTCATCTAACTAGCATAATTAACACCTTTCTGTCAAAT-C-CAGTTAGGCCTCAAAAGTACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTC-AAAGGCCTTAG
254958 CCT
65 CCT
* *
254961 TTCATCTAACTGGCATAATTGACA-CATTCTGTCAAATGCACAGTTGGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGC-CTTAG
255025 CCT
65 CCT
* * ** *
255028 TTCATCTAACTGGCTTTATTGACACCTTTCCATCAAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
255080 ATTAATCTTT
Statistics
Matches: 278, Mismatches: 34, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
65 14 0.05
66 43 0.15
67 100 0.36
68 63 0.23
69 56 0.20
70 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCCTTAGC
CT
Found at i:254938 original size:135 final size:136
Alignment explanation
Indices: 254691--255079 Score: 511
Period size: 135 Copynumber: 2.9 Consensus size: 136
254681 TCTTTAATCG
* ** *
254691 TTCATCTAATTGTTATAATTGACACCTTTT-TGTCAAATGCACAGTTAGGCCTCAAAGGCCTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGACTTAG
* * * *
254755 CCTTTCATCTAACTGGAATAGTTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGCAGT
66 CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAAGCACT
*
254820 TAGTCT
131 TAGCCT
* *
254826 TTCATCTAACTGGCATAATTGACACCTTTTCTGTAAAATGCACAAG-TAGGCCTCAAAGGAACAT
1 TTCATCTAACTGGCATAATTGACACCTTTTCTGTCAAATGCAC-AGTTAGGCCTCAAAGG-ACTT
* * * *
254890 AACCTTTCATCTAACTAGCATAATTAACACCTTTCTGTCAAAT-C-CAGTTAGGCCTCAAAAGTA
64 AGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAAGCA
254953 CTTAGCCT
129 CTTAGCCT
* *
254961 TTCATCTAACTGGCATAATTGACA-C-ATTCTGTCAAATGCACAGTTGGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACACCTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGG-ACTTA
* * ** *
255024 GCCTTTCATCTAACTGGCTTTATTGACACCTTTCCATCAAATGCACAGTTAAGCCT
65 GCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCT
255080 ATTAATCTTT
Statistics
Matches: 220, Mismatches: 28, Indels: 12
0.85 0.11 0.05
Matches are distributed among these distances:
132 2 0.01
133 65 0.30
134 2 0.01
135 84 0.38
136 25 0.11
137 42 0.19
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (136 bp):
TTCATCTAACTGGCATAATTGACACCTTTTCTGTCAAATGCACAGTTAGGCCTCAAAGGACTTAG
CCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTAGGCCTCAAAAGCACT
TAGCCT
Done.