Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008089.1 Hibiscus syriacus cultivar Beakdansim tig00110599_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: 419803
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 2
Found at i:356092 original size:103 final size:104
Alignment explanation
Indices: 355973--356181 Score: 357
Period size: 103 Copynumber: 2.0 Consensus size: 104
355963 TTTCAAGGGA
*
355973 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGGGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGAGAAACTAT
*
356038 CTCAAGAGAGAAAAAAATCATTTCAA-GGAAATATTTTC
66 CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATATTTTC
*
356076 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGAGAAACTAT
1 AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGAGAAACTAT
* * *
356141 CTCAGGAGAGAAAAAATTAATTTCAAGGGAAATGTTTTC
66 CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATATTTTC
356180 AA
1 AA
356182 GAGAAACTGT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 86 0.87
104 13 0.13
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.30
Consensus pattern (104 bp):
AATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTATGTTTCGAGAGAAACTAT
CTCAAGAGAGAAAAAAATAATTTCAAGGGAAATATTTTC
Found at i:356128 original size:39 final size:39
Alignment explanation
Indices: 356084--356158 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
356074 TCAATGTTTA
* *
356084 TGTTTCAAGAGAAACTGTCTCAAGG-GAGACAAAATTTTC
1 TGTTTCAAGAGAAACTATCTC-AGGAGAGAAAAAATTTTC
*
356123 TGTTTCGAGAGAAACTATCTCAGGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATT
356159 AATTTCAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 29 0.91
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAGGAGAGAAAAAATTTTC
Found at i:356391 original size:72 final size:75
Alignment explanation
Indices: 356265--356412 Score: 205
Period size: 72 Copynumber: 2.0 Consensus size: 75
356255 AAAAAAATAG
* * * *
356265 TCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-TCTTGTTT
1 TCTTGAATGAAATGAAAT-CCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGT-ATGTTT
356329 TAAGAAAAACAA
64 TAAGAAAAACAA
*
356341 TCTTGAATGAAATG-AAT-CTTCTTTCGAG-AAAAACAGTCTCAAGTGAGACAAAGTATGTTTTA
1 TCTTGAATGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTA
356403 AGAAAAACAA
66 AGAAAAACAA
356413 ATTTGAGTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
72 38 0.58
73 12 0.18
75 3 0.05
76 13 0.20
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (75 bp):
TCTTGAATGAAATGAAATCCTTCTTTCGAGTAAAAACAGTCTCAAGCGAGACAAAGTATGTTTTA
AGAAAAACAA
Found at i:357969 original size:183 final size:183
Alignment explanation
Indices: 357563--358097 Score: 932
Period size: 183 Copynumber: 2.9 Consensus size: 183
357553 ATCAGGTTTA
* *
357563 ACTGAAAGGTTCATCTCATCACAAAGTCTTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* ** *
357628 GCC-AGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGATTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
357691 TTCCTCTATAACCAATTGCCTTAGTGG-ATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* *
357744 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCATGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* *
357809 GCCAAGTGTCCGAACTGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
357874 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
357927 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
357992 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
* *
358057 TCCTCTATAATCAATTGCCTTAGTGGAATAGCTCAACTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
358098 CGGATTTAAT
Statistics
Matches: 335, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
181 64 0.19
182 79 0.24
183 192 0.57
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:362419 original size:18 final size:18
Alignment explanation
Indices: 362384--362427 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
362374 TATAATAATG
*
362384 AATAAAAAAACGAAAAAT
1 AATAAAAAAAAGAAAAAT
* *
362402 AATAAAAAAAATATAAAT
1 AATAAAAAAAAGAAAAAT
362420 ATATAAAA
1 A-ATAAAA
362428 TTATAAGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.18
Consensus pattern (18 bp):
AATAAAAAAAAGAAAAAT
Found at i:362427 original size:15 final size:17
Alignment explanation
Indices: 362408--362440 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
362398 AAATAATAAA
*
362408 AAAAATATAA-ATATAT
1 AAAATTATAAGATATAT
362424 AAAATTATAAGATATAT
1 AAAATTATAAGATATAT
362441 TACATAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
AAAATTATAAGATATAT
Found at i:362703 original size:18 final size:17
Alignment explanation
Indices: 362682--362724 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
362672 ATATATACAT
362682 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
362700 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
362717 ATAA-AATA
1 ATAATAATA
362725 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:363146 original size:37 final size:37
Alignment explanation
Indices: 363080--363184 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
363070 GTGCTTGTGG
* * * * *
363080 ATCCTATCTTTAAGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
* * * *
363117 ATCCTATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
363154 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAG
363185 GACGAAAATG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAGAACTCT
Found at i:364588 original size:21 final size:21
Alignment explanation
Indices: 364564--364605 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
364554 AGTTTATTTT
364564 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
364585 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
364606 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:364642 original size:33 final size:33
Alignment explanation
Indices: 364600--364703 Score: 165
Period size: 33 Copynumber: 3.2 Consensus size: 33
364590 TTTGTTTCAA
364600 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
364633 TTATCGAACTTAGAAGCTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
364666 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
364698 TTATCG
1 TTATCG
364704 TAAACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
32 6 0.09
33 59 0.91
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:364783 original size:15 final size:15
Alignment explanation
Indices: 364743--364776 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
364733 ATTTTAATAA
*
364743 TTTTATAATCGGTTT
1 TTTTATAACCGGTTT
364758 TTTTATAACCGGTTT
1 TTTTATAACCGGTTT
364773 TTTT
1 TTTT
364777 CAAACCGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTTATAACCGGTTT
Found at i:365400 original size:87 final size:87
Alignment explanation
Indices: 365254--365416 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
365244 TATGTTATAT
365254 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
1 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
365319 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* *
365341 TATTTAA-CGAGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATGGG
1 TATTTAACCG-GAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGA
365405 TAGCGCTTATAT
65 TAGCGCTTATAT
365417 TGACCTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
86 2 0.03
87 71 0.97
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (87 bp):
TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAAATAGG
Found at i:366268 original size:20 final size:19
Alignment explanation
Indices: 366239--366277 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
366229 TTTGGGTCGA
*
366239 TACTTGTTACATTATTAATT
1 TACTTATTACATTA-TAATT
366259 TACTTATTACATTATAATT
1 TACTTATTACATTATAATT
366278 ATTGGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (19 bp):
TACTTATTACATTATAATT
Found at i:375866 original size:21 final size:21
Alignment explanation
Indices: 375811--375874 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
375801 GATTCCCCTG
*
375811 TGGGGGGTATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTT-CCC-TCA
**
375834 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
375855 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
375875 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 19 0.56
22 3 0.09
23 12 0.35
ACGTcount: A:0.14, C:0.25, G:0.36, T:0.25
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:379723 original size:22 final size:21
Alignment explanation
Indices: 379681--379720 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
379671 GAGTTTGTTT
*
379681 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
379702 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
379721 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:382762 original size:16 final size:17
Alignment explanation
Indices: 382741--382772 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
382731 TTACTATTCA
382741 CGTGAATAGT-AAATTT
1 CGTGAATAGTGAAATTT
382757 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
382773 CAGTCGGCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:383544 original size:15 final size:16
Alignment explanation
Indices: 383526--383555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
383516 GGCAGATCAA
383526 AATCCA-AACGGGAAT
1 AATCCAGAACGGGAAT
383541 AATCCAGAACGGGAA
1 AATCCAGAACGGGAA
383556 AGAAAGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (16 bp):
AATCCAGAACGGGAAT
Found at i:388623 original size:20 final size:21
Alignment explanation
Indices: 388578--388624 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
388568 AATGTTATTT
388578 AATA-TATCAAATACAATCTA
1 AATATTATCAAATACAATCTA
* *
388598 AA-ATTATCAAATATATTC-A
1 AATATTATCAAATACAATCTA
388617 AATATTAT
1 AATATTAT
388625 ATTTTAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
AATATTATCAAATACAATCTA
Found at i:389079 original size:160 final size:159
Alignment explanation
Indices: 388802--389185 Score: 515
Period size: 160 Copynumber: 2.4 Consensus size: 159
388792 TGTGATATAT
* * * * ** *
388802 GAGCATGTGGTTCAAATTTGGTAACAAAAAGTGACTTAAAATAAATCACAAATTGAAGGAATAAG
1 GAGCATGTGGTTCAAATTTGATTA-AAAAAGTGACTTAAAATAAATGACGAATTGAAAAAATAAT
* * *
388867 GAGATTATGAAAAATTGAATGACTAGATTGAAAAATAAAAAGATTATTATCAAAAAGAGGAATTG
65 AAGATTATGAAAAATTGAATGACTAAATTAAAAAATAAAAAGATTATTATCAAAAAGAGGAATTG
388932 AAAGTACACATGTATTCTATTAAGGTTTAG
130 AAAGTACACATGTATTCTATTAAGGTTTAG
*
388962 GAGCATGTGGCTCAAATTTGATTAAAAAA-TGACTTAAAATAAATGACGAATTGAAAAAAATAAT
1 GAGCATGTGGTTCAAATTTGATTAAAAAAGTGACTTAAAATAAATGACGAATTG-AAAAAATAAT
* *
389026 AAGATTATGAAAAATTGAA-GAATTAAATTAAAAAAATAAAACA-ATTGTTATCAAAAAGAGGAA
65 AAGATTATGAAAAATTGAATG-ACTAAATT-AAAAAATAAAA-AGATTATTATCAAAAAGAGGAA
* * *
389089 TTGAAAGTATACATGTATTCTATTATGTTTTAG
127 TTGAAAGTACACATGTATTCTATTAAGGTTTAG
* * *
389122 GAGCATGTGGTTCAAATTTGA-TAAAAAAGTAGACTTAAAATGAAGGACGAATTGAATAAATAAT
1 GAGCATGTGGTTCAAATTTGATTAAAAAAGT-GACTTAAAATAAATGACGAATTGAAAAAATAAT
389186 GAAATCAGGG
Statistics
Matches: 198, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
158 23 0.12
159 43 0.22
160 110 0.56
161 22 0.11
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.28
Consensus pattern (159 bp):
GAGCATGTGGTTCAAATTTGATTAAAAAAGTGACTTAAAATAAATGACGAATTGAAAAAATAATA
AGATTATGAAAAATTGAATGACTAAATTAAAAAATAAAAAGATTATTATCAAAAAGAGGAATTGA
AAGTACACATGTATTCTATTAAGGTTTAG
Found at i:389847 original size:19 final size:19
Alignment explanation
Indices: 389823--389865 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
389813 ACATCTATTT
389823 TTAAATGTTCATAATTAAA
1 TTAAATGTTCATAATTAAA
*
389842 TTAAATGTTCATTATTAAA
1 TTAAATGTTCATAATTAAA
389861 -TAAAT
1 TTAAAT
389866 CAAAATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
TTAAATGTTCATAATTAAA
Found at i:408130 original size:21 final size:21
Alignment explanation
Indices: 408106--408159 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
408096 TATCGCAAAT
408106 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
408127 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
408148 TCGCGTTGCGAT
1 TCGCGTTGCGAT
408160 GGTATACAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:408300 original size:20 final size:20
Alignment explanation
Indices: 408254--408304 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
408244 ATACAAAATT
* *
408254 GCAACGAGATACTGACTTTC
1 GCAACGCGATTCTGACTTTC
408274 GCAACGCGATTCTGACTTTC
1 GCAACGCGATTCTGACTTTC
408294 GCAACGCGATT
1 GCAACGCGATT
408305 TACATAGCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (20 bp):
GCAACGCGATTCTGACTTTC
Found at i:408906 original size:20 final size:19
Alignment explanation
Indices: 408863--409025 Score: 132
Period size: 20 Copynumber: 8.9 Consensus size: 19
408853 GAAATAAAAA
408863 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
408882 CGTTGCGATTTTTATTTCG
1 CGTTGCGATTTTCATTTCG
408901 CGGTTGCGATTTTCATTTCG
1 C-GTTGCGATTTTCATTTCG
*
408921 CGTTGCGATTGTC---T-G
1 CGTTGCGATTTTCATTTCG
* **
408936 -GTCGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
408954 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
*
408968 CGTTGCGATAGTT-ATTTCCG
1 CGTTGCGAT-TTTCATTT-CG
* *
408988 CGTTGCGATTCTCATTATCT
1 CGTTGCGATTTTCATT-TCG
409008 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
409026 AACCAAAAGA
Statistics
Matches: 116, Mismatches: 13, Indels: 30
0.73 0.08 0.19
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 1 0.01
17 5 0.04
18 1 0.01
19 40 0.34
20 47 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.21, G:0.23, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:408941 original size:39 final size:39
Alignment explanation
Indices: 408864--408941 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
408854 AAATAAAAAC
* **
408864 GTTGCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCG
1 GTTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
408903 GTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GGTCGCG
1 GTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGGTCGCG
408942 ATAGTCATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.09, C:0.19, G:0.27, T:0.45
Consensus pattern (39 bp):
GTTGCGATTTTCATTTCGCGTTGCGATTTCTAGGTCGCG
Found at i:408995 original size:34 final size:33
Alignment explanation
Indices: 408913--409000 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
408903 GTTGCGATTT
* *
408913 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
408946 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
408979 TTATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
409001 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:411100 original size:21 final size:21
Alignment explanation
Indices: 411076--411142 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
411066 TCATTCCTCG
411076 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
411097 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
411118 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
411139 AGAG
1 AGAG
411143 CTCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:411100 original size:42 final size:42
Alignment explanation
Indices: 411020--411142 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
411010 GCCCGACTCA
* * * * * *
411020 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
411062 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
411104 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
411143 CTCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:412526 original size:13 final size:13
Alignment explanation
Indices: 412491--412528 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
412481 TTGATTGTTT
412491 AATTGATTTGTAA
1 AATTGATTTGTAA
412504 AATGTGATTTGTAA
1 AAT-TGATTTGTAA
*
412518 AGTTGATTTGT
1 AATTGATTTGT
412529 TTAATTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:412536 original size:13 final size:13
Alignment explanation
Indices: 412481--412537 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
412471 TGCTTATTTT
*
412481 TTGA-TTGTTTAA
1 TTGATTTGTTAAA
*
412493 TTGATTTGTAAAA
1 TTGATTTGTTAAA
412506 TGTGATTTG-TAAA
1 T-TGATTTGTTAAA
*
412519 GTTGATTTGTTTAA
1 -TTGATTTGTTAAA
412533 TTGAT
1 TTGAT
412538 GTTAACATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
12 4 0.11
13 22 0.59
14 11 0.30
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (13 bp):
TTGATTTGTTAAA
Found at i:412658 original size:18 final size:18
Alignment explanation
Indices: 412635--412692 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
412625 AAAAAGTACT
*
412635 ATCGCAATGCGAAATGAA
1 ATCGCAACGCGAAATGAA
412653 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCG-AAATG-AA
*
412673 ATCGCAACGCGAAATTAA
1 ATCGCAACGCGAAATGAA
412691 AT
1 AT
412693 TCGCGTTGCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
18 14 0.39
19 9 0.25
20 13 0.36
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.16
Consensus pattern (18 bp):
ATCGCAACGCGAAATGAA
Found at i:412676 original size:20 final size:19
Alignment explanation
Indices: 412635--412686 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
412625 AAAAAGTACT
*
412635 ATCGCAATGCG-AAATGAA
1 ATCGCAACGCGAAAATGAA
412653 ATCGCAACGCGAAAATGAAA
1 ATCGCAACGCGAAAATG-AA
412673 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
412687 TTAAATTCGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 10 0.32
19 5 0.16
20 16 0.52
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAAATGAA
Found at i:412703 original size:19 final size:19
Alignment explanation
Indices: 412636--412727 Score: 51
Period size: 19 Copynumber: 4.8 Consensus size: 19
412626 AAAAGTACTA
* *
412636 TCGCAATGCGAAATGAAA-
1 TCGCATTGCGAAATTAAAT
** * *
412654 TCGCAACGCGAAAATGAAAA
1 TCGCATTGCG-AAATTAAAT
**
412674 TCGCAACGCGAAATTAAAT
1 TCGCATTGCGAAATTAAAT
* ** * *
412693 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATTAAAT
412712 TCGCATTGCGAAATTA
1 TCGCATTGCGAAATTA
412728 GCGTTGCGAT
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
18 9 0.16
19 39 0.67
20 10 0.17
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.25
Consensus pattern (19 bp):
TCGCATTGCGAAATTAAAT
Found at i:412732 original size:33 final size:33
Alignment explanation
Indices: 412689--412787 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
412679 ACGCGAAATT
412689 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
*
412722 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
* *
412755 -ATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAAT-TCGCGTTGCGATTTTCATTTCGCATTGCG
412788 TTAGTAATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 2 0.03
33 59 0.97
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.41
Consensus pattern (33 bp):
AAATTCGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:412755 original size:19 final size:19
Alignment explanation
Indices: 412692--412787 Score: 77
Period size: 19 Copynumber: 5.6 Consensus size: 19
412682 CGAAATTAAA
*
412692 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
412711 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
412725 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
412744 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
412760 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
412777 TTCGCATTGCG
1 TTCGCATTGCG
412788 TTAGTAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 17 0.29
16 7 0.12
17 7 0.12
19 27 0.47
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:416381 original size:20 final size:20
Alignment explanation
Indices: 416356--416453 Score: 187
Period size: 20 Copynumber: 4.9 Consensus size: 20
416346 ATTCATTTGA
416356 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
416376 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
416396 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
416416 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
416436 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
416454 CACAATGCGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.37, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:416622 original size:14 final size:14
Alignment explanation
Indices: 416603--416639 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
416593 CATCAATTAA
416603 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
416617 ACAAATCATCTTTT
1 ACAAATCAACATTT
416631 ACAAATCAA
1 ACAAATCAA
416640 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:418515 original size:19 final size:19
Alignment explanation
Indices: 418493--418558 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 19
418483 CGAAACTTAA
418493 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
* *
418512 ATCGCAACGTGGAAATGGCT
1 ATCGCAACG-CGAAATGACT
* *
418532 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
418550 ATCGCAACG
1 ATCGCAACG
418559 ACAAAATCGA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 8 0.21
19 15 0.38
20 16 0.41
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:418528 original size:20 final size:20
Alignment explanation
Indices: 418493--418558 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 20
418483 CGAAACTTAA
*
418493 ATCGCAACG-CGAAATGACT
1 ATCGCAACGTGGAAATGACT
*
418512 ATCGCAACGTGGAAATGGCT
1 ATCGCAACGTGGAAATGACT
*
418532 ATCGCAA--TGCGAAATGA-A
1 ATCGCAACGTG-GAAATGACT
418550 ATCGCAACG
1 ATCGCAACG
418559 ACAAAATCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.23
19 15 0.38
20 15 0.38
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (20 bp):
ATCGCAACGTGGAAATGACT
Found at i:418606 original size:14 final size:14
Alignment explanation
Indices: 418587--418644 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
418577 TTTCATTTCG
418587 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
418601 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
418617 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
418633 CGTTGCGATTTT
1 CGTTGCGATTTT
418645 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:418651 original size:33 final size:33
Alignment explanation
Indices: 418570--418660 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
418560 CAAAATCGAA
*
418570 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
418603 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
418635 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
418661 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:418679 original size:20 final size:19
Alignment explanation
Indices: 418645--418699 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
418635 TTGCGATTTT
*
418645 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
418664 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
418684 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
418700 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:419210 original size:17 final size:18
Alignment explanation
Indices: 419174--419217 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
419164 GTCGATCAGA
*
419174 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
419192 TGATAGCTCT-GGCGAGG
1 TGATGGCTCTGGGCGAGG
419209 TGATGGCTC
1 TGATGGCTC
419218 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.14, C:0.16, G:0.43, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Done.