Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008530.1 Hibiscus syriacus cultivar Beakdansim tig00111408_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: 724678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:655632 original size:21 final size:21
Alignment explanation
Indices: 655600--655650 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
655590 GTTTGTTTTA
*
655600 TTTTATCT-TTTTTTTAAA-AT
1 TTTTAT-TATTTTTTAAAACAT
655620 TTATTATTATTTTTTAAAACAT
1 TT-TTATTATTTTTTAAAACAT
655642 TTTTATTAT
1 TTTTATTAT
655651 ATGCATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 20 0.74
22 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATTATTTTTTAAAACAT
Found at i:655926 original size:21 final size:21
Alignment explanation
Indices: 655888--655927 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
655878 TTTTATTATT
*
655888 TCTATTTACCTTTTTTTTTCC
1 TCTATTTACATTTTTTTTTCC
655909 TCTATTT-CATTTTATTTTT
1 TCTATTTACATTTT-TTTTT
655928 ATTCCTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
TCTATTTACATTTTTTTTTCC
Found at i:656047 original size:22 final size:23
Alignment explanation
Indices: 656022--656068 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
656012 ATTATTATCA
* *
656022 TTATTATTCTT-TTTTCTTCATT
1 TTATTATTCTTATTGTATTCATT
*
656044 TTATTTTTCTTATTGTATTCATT
1 TTATTATTCTTATTGTATTCATT
656067 TT
1 TT
656069 TATCTCCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (23 bp):
TTATTATTCTTATTGTATTCATT
Found at i:656654 original size:31 final size:31
Alignment explanation
Indices: 656590--656656 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
656580 TTGTCTACAT
* * * * *
656590 AAATTGATCACTTAGTAATCTTTAATCATTA
1 AAATTGATCACTTAATAACCTTCAACCACTA
656621 AAATTGATCACTTAATAACCTTCAACCACTA
1 AAATTGATCACTTAATAACCTTCAACCACTA
656652 AAATT
1 AAATT
656657 ACACTAGAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (31 bp):
AAATTGATCACTTAATAACCTTCAACCACTA
Found at i:658695 original size:6 final size:6
Alignment explanation
Indices: 658684--658723 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
658674 ATTTGTTTCA
*
658684 TATATG TATATG TATATG TATATG TATGTG TATATG TATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATA
658724 CTTTGAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:659962 original size:2 final size:2
Alignment explanation
Indices: 659955--659994 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
659945 CTCAAGGATT
659955 TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
659995 TGCTTCTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:662758 original size:20 final size:21
Alignment explanation
Indices: 662712--662759 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
662702 CTATATATAT
* * *
662712 ATATATATATAATTTTATTAT
1 ATATATACATAATTTTAGTAG
*
662733 AAATATACA-AATTTTAGTAG
1 ATATATACATAATTTTAGTAG
662753 ATATATA
1 ATATATA
662760 TATATATGAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
ATATATACATAATTTTAGTAG
Found at i:676116 original size:195 final size:195
Alignment explanation
Indices: 675811--676206 Score: 539
Period size: 195 Copynumber: 2.0 Consensus size: 195
675801 TTTGCAACAA
* * * *
675811 CCAAGTTCAAGGGAGAAGGAATAACTTCTTTCATCTTAGTTTCTATCTCAACATCGTTTTGGTCT
1 CCAAGTCCAAGGGAGAAGGAATAACTTCTTCCATCTTAGTTTCTATCTCAACATCCTTTTGGTAT
*
675876 TCATCCTTGCACAACAACTTCTTCCGTTTCTTTCTTTGTCTTCCTTTCG-GATCAGATTCAGTGC
66 TCATCCTTGCACAACAACTCCTTCCGTTTCTTTCTTTGTCTTCC-TTCGAGATCAGATTCAGTGC
** * * *
675940 CTTTGCCGTTGCCC-GACGCTACCTCTGAAACCTTAGCTATTAGTGTAACATCATCTGTTGT-GA
130 CTGCGCCGCTGCCCAG-CGCTACCTCCGAAACCTTAGCTATTAATGTAACATCATCT-TTGTCGA
676003 CAG
193 CAG
*
676006 CCAAGTCCAAGGGAGAAGGAATAACTTCTTCCATCTTGGTTTCTATCTCAACATCCTTTTGGTAT
1 CCAAGTCCAAGGGAGAAGGAATAACTTCTTCCATCTTAGTTTCTATCTCAACATCCTTTTGGTAT
* * * *
676071 TCATCCTTGCGCAA-AGTCTCCTTTCGTTTCTTTCTTTTTCTTCCTTCGAGATCAGATTCAGTGC
66 TCATCCTTGCACAACA-ACTCCTTCCGTTTCTTTCTTTGTCTTCCTTCGAGATCAGATTCAGTGC
* * * ** *
676135 CTGCGCTGCTGCCCAGTGCTACCTCCGAAACCTTAGCTGTTAATGTAAGGTCATCTTTTTCGACA
130 CTGCGCCGCTGCCCAGCGCTACCTCCGAAACCTTAGCTATTAATGTAACATCATCTTTGTCGACA
676200 G
195 G
676201 CCAAGT
1 CCAAGT
676207 TCGAAGGAGA
Statistics
Matches: 176, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
194 8 0.05
195 167 0.95
196 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (195 bp):
CCAAGTCCAAGGGAGAAGGAATAACTTCTTCCATCTTAGTTTCTATCTCAACATCCTTTTGGTAT
TCATCCTTGCACAACAACTCCTTCCGTTTCTTTCTTTGTCTTCCTTCGAGATCAGATTCAGTGCC
TGCGCCGCTGCCCAGCGCTACCTCCGAAACCTTAGCTATTAATGTAACATCATCTTTGTCGACAG
Found at i:679172 original size:42 final size:42
Alignment explanation
Indices: 679113--679203 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
679103 CAGGTAAGCA
*
679113 GTTAACGGCCAGGTAAGCTTTCCGTCACCCATTTTAACGGCG
1 GTTAACGGCCAGGTAAGCTTTCCGTCACCCATTTTAACGGAG
* *
679155 GTTAACGGCCAGGTAAGCTTTCCGTTACTCATTTTAACGGAG
1 GTTAACGGCCAGGTAAGCTTTCCGTCACCCATTTTAACGGAG
679197 GTTAACG
1 GTTAACG
679204 TTGAGTGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (42 bp):
GTTAACGGCCAGGTAAGCTTTCCGTCACCCATTTTAACGGAG
Found at i:683422 original size:30 final size:30
Alignment explanation
Indices: 683386--683626 Score: 341
Period size: 30 Copynumber: 8.2 Consensus size: 30
683376 GCTGAAAACA
* * *
683386 GGGAGATCTACTCTTGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
683416 GGGAGATCTGCTCCTGCTTCTCCAGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
* *
683446 GGGAGATCTGCTCCAGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
*
683476 AGGAGA------CCTGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
683500 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
*
683530 GGGAGACCTGCTCCCGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
683560 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
**
683590 GGGAGACCTGCTCCTGCTTCTCTTGTTTCT
1 GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
683620 GGGAGAC
1 GGGAGAC
683627 GAACTAAAAC
Statistics
Matches: 193, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
24 22 0.11
30 171 0.89
ACGTcount: A:0.09, C:0.31, G:0.26, T:0.34
Consensus pattern (30 bp):
GGGAGACCTGCTCCTGCTTCTCCGGTTTCT
Found at i:683534 original size:84 final size:85
Alignment explanation
Indices: 683400--683626 Score: 339
Period size: 84 Copynumber: 2.6 Consensus size: 85
683390 GATCTACTCT
* *
683400 TGCTTCTCCGGTTTCTGGGAGATCTGCTCCTGCTTCTCCAGTTTCTGGGAGATCTGCTCCAGCTT
1 TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCCAGTTTCTGGGAGACCTGCTCCAGCTT
683465 CTCCGGTTTCTAGGAGA-CC
66 CTCCGGTTTCTAGGAGACCC
* *
683484 TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCCGGTTTCTGGGAGACCTGCTCCCGCTT
1 TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCCAGTTTCTGGGAGACCTGCTCCAGCTT
*
683549 CTCCGGTTTCTGGGAGACCTGCTCC
66 CTCCGGTTTCTAGGAGA----C-CC
**
683574 TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCTTGTTTCTGGGAGAC
1 TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCCAGTTTCTGGGAGAC
683627 GAACTAAAAC
Statistics
Matches: 130, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
84 77 0.59
90 53 0.41
ACGTcount: A:0.08, C:0.31, G:0.26, T:0.34
Consensus pattern (85 bp):
TGCTTCTCCGGTTTCTGGGAGACCTGCTCCTGCTTCTCCAGTTTCTGGGAGACCTGCTCCAGCTT
CTCCGGTTTCTAGGAGACCC
Found at i:683586 original size:114 final size:114
Alignment explanation
Indices: 683386--683601 Score: 351
Period size: 114 Copynumber: 1.9 Consensus size: 114
683376 GCTGAAAACA
* * * *
683386 GGGAGATCTACTCTTGCTTCTCCGGTTTCTGGGAGATCTGCTCCTGCTTCTCCAGTTTCTGGGAG
1 GGGAGACCTACTCCTGCTTCTCCGGTTTCTGGGAGACCTGCTCCCGCTTCTCCAGTTTCTGGGAG
*
683451 ATCTGCTCCAGCTTCTCCGGTTTCTAGGAGACCTGCTTCTCCGGTTTCT
66 ACCTGCTCCAGCTTCTCCGGTTTCTAGGAGACCTGCTTCTCCGGTTTCT
* *
683500 GGGAGACCTGCTCCTGCTTCTCCGGTTTCTGGGAGACCTGCTCCCGCTTCTCCGGTTTCTGGGAG
1 GGGAGACCTACTCCTGCTTCTCCGGTTTCTGGGAGACCTGCTCCCGCTTCTCCAGTTTCTGGGAG
* *
683565 ACCTGCTCCTGCTTCTCCGGTTTCTGGGAGACCTGCT
66 ACCTGCTCCAGCTTCTCCGGTTTCTAGGAGACCTGCT
683602 CCTGCTTCTC
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.09, C:0.31, G:0.26, T:0.33
Consensus pattern (114 bp):
GGGAGACCTACTCCTGCTTCTCCGGTTTCTGGGAGACCTGCTCCCGCTTCTCCAGTTTCTGGGAG
ACCTGCTCCAGCTTCTCCGGTTTCTAGGAGACCTGCTTCTCCGGTTTCT
Found at i:685632 original size:24 final size:23
Alignment explanation
Indices: 685605--685661 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
685595 TGGTTGGATA
685605 GGCAGTGGAGAGGAGGGTGGAGGT
1 GGCAGTGGAGAGG-GGGTGGAGGT
* *
685629 GGCAGTGGCAGTGGGGGTGGGGGT
1 GGCAGTGG-AGAGGGGGTGGAGGT
*
685653 GGAAGTGGA
1 GGCAGTGGA
685662 TGTGGAGCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 24 0.83
25 4 0.14
ACGTcount: A:0.18, C:0.05, G:0.63, T:0.14
Consensus pattern (23 bp):
GGCAGTGGAGAGGGGGTGGAGGT
Found at i:685878 original size:27 final size:27
Alignment explanation
Indices: 685838--685937 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
685828 GAGATTGAGG
685838 AGGAGGTGGTGGAGGAGGTAATTCTCT
1 AGGAGGTGGTGGAGGAGGTAATTCTCT
* *
685865 ATGAGGTGGTGGAGGAGGTAATGCTCT
1 AGGAGGTGGTGGAGGAGGTAATTCTCT
* *
685892 AGGAGGTGGAGGAAGAGGTAATGT-TCT
1 AGGAGGTGGTGGAGGAGGTAAT-TCTCT
*
685919 AGGAGGTGATGGAGGAGGT
1 AGGAGGTGGTGGAGGAGGT
685938 GGCTGGGTCT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.25, C:0.05, G:0.47, T:0.23
Consensus pattern (27 bp):
AGGAGGTGGTGGAGGAGGTAATTCTCT
Found at i:694341 original size:21 final size:21
Alignment explanation
Indices: 694311--694423 Score: 110
Period size: 21 Copynumber: 5.4 Consensus size: 21
694301 GATTTACATA
*
694311 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
694332 TTCGCGTTGCGATTTATTCC-AG
1 TTCGCGTTGCGA--TAGTCCAAG
694354 ATT--CGTTGCGATAGTCCAAG
1 -TTCGCGTTGCGATAGTCCAAG
*
694374 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
694397 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
694416 TTCGCGTT
1 TTCGCGTT
694424 TTGCGATTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 20
0.75 0.06 0.20
Matches are distributed among these distances:
19 16 0.21
20 2 0.03
21 39 0.51
22 2 0.03
23 17 0.22
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:694368 original size:42 final size:42
Alignment explanation
Indices: 694317--694500 Score: 280
Period size: 42 Copynumber: 4.3 Consensus size: 42
694307 CATATTCGCA
*
694317 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAGATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
694359 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
694401 TTGCGATAGTCGAAGTTCGCGTTTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCG--TTGCGATTTATTCCAAATTCG
* * *
694445 TTGCGATAGT-CGACTATCGCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGT-TCGCGTTGCGATTTATTCCAAATTCG
694487 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
694501 AATCGCAACG
Statistics
Matches: 129, Mismatches: 9, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
42 91 0.71
43 4 0.03
44 34 0.26
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:694446 original size:86 final size:84
Alignment explanation
Indices: 694288--694500 Score: 290
Period size: 86 Copynumber: 2.5 Consensus size: 84
694278 GCGAACTTCG
*
694288 ACTATCGCATTGCGATTTA---CATATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGATTTATT
1 ACTATCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAGTTCGCGTTGCGATTTATT
*
694350 CCAGATTCGTTGCGATAGTCCA
64 CCAAATTCGTTGCGATAGT-CA
* * * *
694372 AGT-TCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTTTGCGATTTATT
1 ACTATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG--TTGCGATTTATT
*
694436 CCAAATTCGTTGCGATAGTCG
64 CCAAATTCGTTGCGATAGTCA
694457 ACTATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 ACTATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
694501 AATCGCAACG
Statistics
Matches: 112, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
83 14 0.12
84 22 0.20
85 3 0.03
86 73 0.65
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (84 bp):
ACTATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
AAATTCGTTGCGATAGTCA
Found at i:694450 original size:21 final size:21
Alignment explanation
Indices: 694336--694493 Score: 96
Period size: 21 Copynumber: 7.4 Consensus size: 21
694326 TCCAAGTTCG
*
694336 CGTTGCGATTTATTCCAGATT
1 CGTTGCGATTTATTCCAAATT
* *
694357 CGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATT
*
694376 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
* * *
694399 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
694418 CGCGTTTTGCGATTTATTCCAAATT
1 --CG--TTGCGATTTATTCCAAATT
* * *
694443 CGTTGCGA--TAGT-CGACTAT
1 CGTTGCGATTTATTCCAAAT-T
694462 CGCATTGCGATTTATTCCAAATT
1 CG--TTGCGATTTATTCCAAATT
694485 CGTTGCGAT
1 CGTTGCGAT
694494 AGTCCAAAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
18 3 0.03
19 23 0.22
21 45 0.42
23 24 0.23
24 3 0.03
25 8 0.08
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:694506 original size:42 final size:42
Alignment explanation
Indices: 694291--694507 Score: 251
Period size: 42 Copynumber: 5.1 Consensus size: 42
694281 AACTTCGACT
*
694291 ATCGCATTGCGATTTA---CATATTCGCATTGCGATAGTCCAAG
1 ATCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAG
* * *
694332 TTCGCGTTGCGATTTATTCCAGATTCGTTGCGATAGTCCAAG
1 ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
* * * *
694374 TTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAG
1 ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
* * * **
694416 TTCGCGTTTTGCGATTTATTCCAAATTCGTTGCGATAGTCGACT
1 ATCGC--ATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
*
694460 ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
1 ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
694502 ATCGCA
1 ATCGCA
694508 ACGACTGGTG
Statistics
Matches: 156, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
41 14 0.09
42 98 0.63
44 44 0.28
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
Found at i:694793 original size:21 final size:21
Alignment explanation
Indices: 694767--694806 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
694757 TTTTTAAAGG
694767 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
* *
694788 CATGCATCGGTGCATCAAT
1 CATGCACCGATGCATCAAT
694807 GAATAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:694856 original size:19 final size:19
Alignment explanation
Indices: 694832--694889 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
694822 TCGAATGCAT
694832 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
694851 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
694870 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
694889 T
1 T
694890 GATTTAATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.21, C:0.40, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:694909 original size:83 final size:85
Alignment explanation
Indices: 694767--694951 Score: 234
Period size: 83 Copynumber: 2.2 Consensus size: 85
694757 TTTTTAAAGG
*
694767 CATGCACCGATGCA-TCAATACCATGCATCGGTGCATCAATGAATAAATTAAAACATCGAATGCA
1 CATGCACCGATGCACTC-ATACCATGCATCGATGCATC-ATGAATAAATTAAAACATCGAATGCA
**
694831 TTCCATGCACCGATGCACTCTC
64 TTCCATGCACCGATGCACAATC
* *
694853 CATGCACCGATGCACTC-T-CCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCAT
1 CATGCACCGATGCACTCATACCATGCATCGATGCA-TCATGAATAAATTAAAACATCGAATGCAT
** *
694915 TTGATGCATCGATGCACAATC
65 TCCATGCACCGATGCACAATC
*
694936 CATGCATCGATGCACT
1 CATGCACCGATGCACT
694952 AGGCTATTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
83 55 0.62
84 14 0.16
85 3 0.03
86 14 0.16
87 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (85 bp):
CATGCACCGATGCACTCATACCATGCATCGATGCATCATGAATAAATTAAAACATCGAATGCATT
CCATGCACCGATGCACAATC
Found at i:694968 original size:64 final size:63
Alignment explanation
Indices: 694843--694995 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 63
694833 CCATGCACCG
* **
694843 ATGCACTCTCCATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCG
1 ATGCACT-T-CATGCATCGATGCACAATCCATGCATCGATGCACTCTGATTT-ATTAAAACATCG
694908 A
63 A
* * *
694909 ATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCACTAGGCT-ATTT-TTCAAACATCG
1 ATGCACTTCATGCATCGATGCACAATCCATGCATCGATGCACT---CTGATTTATTAAAACATCG
694972 A
63 A
*
694973 ATGCACTTCATGTATCGATGCAC
1 ATGCACTTCATGCATCGATGCAC
694996 TCTTAGTGCA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
64 62 0.83
65 1 0.01
66 10 0.13
67 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.29
Consensus pattern (63 bp):
ATGCACTTCATGCATCGATGCACAATCCATGCATCGATGCACTCTGATTTATTAAAACATCGA
Found at i:696342 original size:19 final size:19
Alignment explanation
Indices: 696318--696363 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
696308 AACGATTTTC
696318 TTTGAAAACAAAAAT-AGAT
1 TTTGAAAACAAAAATGA-AT
* *
696337 TTTGAAACCCAAAATGAAT
1 TTTGAAAACAAAAATGAAT
696356 TTTGAAAA
1 TTTGAAAA
696364 AGGATTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.28
Consensus pattern (19 bp):
TTTGAAAACAAAAATGAAT
Found at i:697095 original size:34 final size:33
Alignment explanation
Indices: 697056--697126 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 33
697046 TTTTGTAAAG
* * *
697056 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTATAGCTTAACCCGTG-AAAAACTA
*
697090 GGGAAAGGTTATAGTTTAACCCGTGAAAAACTA
1 GGGAAAGGTTATAGCTTAACCCGTGAAAAACTA
697123 GGGA
1 GGGA
697127 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 11 0.33
34 22 0.67
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTATAGCTTAACCCGTGAAAAACTA
Found at i:697421 original size:21 final size:21
Alignment explanation
Indices: 697365--697448 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 21
697355 CCCAACAGTC
697365 GACTATCGCAATGCGAACTTG
1 GACTATCGCAATGCGAACTTG
*
697386 GATATGTAAATCGCAATGCGAACTTG
1 G--A-CT--ATCGCAATGCGAACTTG
* * *
697412 GACTATCGCAACGCAAACTTC
1 GACTATCGCAATGCGAACTTG
*
697433 GACTATCGCATTGCGA
1 GACTATCGCAATGCGA
697449 TTTACATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
21 28 0.56
23 2 0.04
24 2 0.04
26 18 0.36
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
GACTATCGCAATGCGAACTTG
Found at i:697483 original size:21 final size:21
Alignment explanation
Indices: 697457--697634 Score: 229
Period size: 21 Copynumber: 8.6 Consensus size: 21
697447 GATTTACATA
697457 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
697478 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
*
697498 TTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
697519 TTCGCGTTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
697540 TTCGCATTGCGAT-TTACATA-
1 TTCGCATTGCGATAGTCCA-AG
697560 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
697581 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
697602 TTTGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
697623 TTCGCGTTGCGA
1 TTCGCATTGCGA
697635 ATCTGGAAAC
Statistics
Matches: 135, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
20 33 0.24
21 102 0.76
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:697483 original size:41 final size:42
Alignment explanation
Indices: 697438--697634 Score: 219
Period size: 41 Copynumber: 4.8 Consensus size: 42
697428 ACTTCGACTA
*
697438 TCGCATTGCGAT-TTACATA-TTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAGT
* *
697479 TCGCATTGCGAT-TTACATA-TTCGCATTGTGATAGTCCAAGT
1 TCGCATTGCGATAGTACA-AGTTCGCATTGCGATAGTCCAAGT
* * * *
697520 TCGCGTTGCGATAGTCCAAGTTCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCA-AGT
*
697561 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
* *
697603 TTGCATTGCGATAGT-CGAAGTTCGCGTTGCGA
1 TCGCATTGCGATAGTAC-AAGTTCGCATTGCGA
697635 ATCTGGAAAC
Statistics
Matches: 138, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
41 90 0.65
42 48 0.35
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
TCGCATTGCGATAGTACAAGTTCGCATTGCGATAGTCCAAGT
Found at i:697523 original size:62 final size:62
Alignment explanation
Indices: 697457--697614 Score: 289
Period size: 62 Copynumber: 2.5 Consensus size: 62
697447 GATTTACATA
*
697457 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGTGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
*
697519 TTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
*
697581 TTCGCATTGCGATAGTCCAAGTTTGCATTGCGAT
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGAT
697615 AGTCGAAGTT
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 92 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAG
Found at i:700122 original size:60 final size:60
Alignment explanation
Indices: 700041--700155 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
700031 ACGATCTCTC
* * * *
700041 GACTATAGGACATTACTTTGTTAAG-TCTCTTGATTATTAAAAGTTATAAAATGGTTCTTT
1 GACTATAAGACATTACTTTGTTAAGTTC-CTCGACTATTAAAAGTTAGAAAATGGTTCTTT
* * * *
700101 GACTATAAGACGTTGCTTTGTTGAGTTCCTCGACTATTAAAAGTTAGAAGATGGT
1 GACTATAAGACATTACTTTGTTAAGTTCCTCGACTATTAAAAGTTAGAAAATGGT
700156 CACCCAACAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
60 44 0.96
61 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.39
Consensus pattern (60 bp):
GACTATAAGACATTACTTTGTTAAGTTCCTCGACTATTAAAAGTTAGAAAATGGTTCTTT
Found at i:708273 original size:35 final size:36
Alignment explanation
Indices: 708225--708312 Score: 126
Period size: 37 Copynumber: 2.5 Consensus size: 36
708215 ATTTTGTAAA
708225 AAAAAATATATATAATTTTATGAA-ATTAATTTTTT
1 AAAAAATATATATAATTTTATGAATATTAATTTTTT
** *
708260 TTAAAATATATATAAATTTTATGAATTTTAATTTTTT
1 AAAAAATATATAT-AATTTTATGAATATTAATTTTTT
708297 AAAAAATATATA-AATT
1 AAAAAATATATATAATT
708313 AATTATAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
35 15 0.33
36 11 0.24
37 20 0.43
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (36 bp):
AAAAAATATATATAATTTTATGAATATTAATTTTTT
Found at i:708291 original size:37 final size:34
Alignment explanation
Indices: 708227--708312 Score: 120
Period size: 35 Copynumber: 2.5 Consensus size: 34
708217 TTTGTAAAAA
708227 AAAATATATAT-AATTTTATGAAATTAATTTTTTTT
1 AAAATATATATAAATTTTATGAAATTAA--TTTTTT
*
708262 AAAATATATATAAATTTTATGAATTTTAATTTTTT
1 AAAATATATATAAATTTTATGAA-ATTAATTTTTT
*
708297 AAAAAATATATAAATT
1 AAAATATATATAAATT
708313 AATTATAGTA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
35 32 0.68
36 11 0.23
37 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (34 bp):
AAAATATATATAAATTTTATGAAATTAATTTTTT
Found at i:709116 original size:19 final size:19
Alignment explanation
Indices: 709094--709152 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
709084 TAAAGCAAGT
709094 CATAATATATATTAAAAAC
1 CATAATATATATTAAAAAC
* **
709113 CATAA-A-ATA--AGCAAGT
1 CATAATATATATTA-AAAAC
709129 CATAATATATATTAAAAAC
1 CATAATATATATTAAAAAC
709148 CATAA
1 CATAA
709153 AATCAAGTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
15 1 0.03
16 7 0.24
17 4 0.14
18 4 0.14
19 12 0.41
20 1 0.03
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (19 bp):
CATAATATATATTAAAAAC
Found at i:709125 original size:35 final size:35
Alignment explanation
Indices: 709086--709155 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
709076 GTCATATTTA
709086 AAGCAAGTCATAATATATATTAAAAACCATAAAAT
1 AAGCAAGTCATAATATATATTAAAAACCATAAAAT
709121 AAGCAAGTCATAATATATATTAAAAACCATAAAAT
1 AAGCAAGTCATAATATATATTAAAAACCATAAAAT
709156 CAAGTGAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (35 bp):
AAGCAAGTCATAATATATATTAAAAACCATAAAAT
Found at i:709227 original size:14 final size:14
Alignment explanation
Indices: 709210--709252 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
709200 AGGTAAACAT
709210 ATTAAATAAATATA
1 ATTAAATAAATATA
* *
709224 ATTATATAACTATA
1 ATTAAATAAATATA
709238 ATTAAA-AAATA-A
1 ATTAAATAAATATA
709250 ATT
1 ATT
709253 TGAGGCTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 4 0.16
13 4 0.16
14 17 0.68
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (14 bp):
ATTAAATAAATATA
Found at i:710088 original size:14 final size:13
Alignment explanation
Indices: 710060--710106 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
710050 AAGGTGAAAC
*
710060 ATATAAATAATAA
1 ATATAATTAATAA
710073 ATATAATTATATAA
1 ATATAATTA-ATAA
* *
710087 ATATAATCAAAAA
1 ATATAATTAATAA
710100 ATA-AATT
1 ATATAATT
710107 GGGGTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 3 0.10
13 14 0.48
14 12 0.41
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATAATTAATAA
Found at i:712518 original size:44 final size:44
Alignment explanation
Indices: 712470--712558 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
712460 ATTATGACCC
712470 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
1 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
712514 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
1 TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
712558 T
1 T
712559 CCCCAAACTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.44
Consensus pattern (44 bp):
TAATTCTATATTTAATCCCTAAACTTTAGAATATTATAAATTCA
Done.