Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005739.1 Hibiscus syriacus cultivar Beakdansim tig00013422_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: 51836
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:306 original size:127 final size:126
Alignment explanation
Indices: 29--311 Score: 408
Period size: 127 Copynumber: 2.2 Consensus size: 126
19 AGTTCTAGTC
* *
29 AGGGGATGACACTACTCATACGTGATGAAGAGTTCTTGGTCATCTAAAGGTGATAACACGGTTCC
1 AGGGGATGACAC-GCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCC
*
94 TACGTGATGAGGACGGCTGGTTATCTAAGGATGACACGGCTCCTACGTGATGAGGAGGTCTGT
65 TACGTGATGAGGACGGCTGGTTATCTAAGGATGA-ACGGCTCCTACGTAATGAGGAGGTCTGT
* *
157 CGAGGGATGACACGCTCATACGTGATGAA-AGTTCTTGGCCATCTAAGGGTGATAACACGGTTCC
1 AG-GGGATGACACGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCC
* * *
221 TATGTGATGAGGACGGCTGGTTATCTAAGGGTG-ACGGCTCCTATGTAATGAGGAGGTCTGGTT
65 TACGTGATGAGGACGGCTGGTTATCTAAGGATGAACGGCTCCTACGTAATGAGGAGGTCT-G-T
* *
284 AGGGGATGACACGGTTCCTACGTGATGA
1 AGGGGATGACAC-GCTCATACGTGATGA
312 GGATGGCTGG
Statistics
Matches: 140, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
125 24 0.17
126 11 0.08
127 79 0.56
128 16 0.11
129 10 0.07
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (126 bp):
AGGGGATGACACGCTCATACGTGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCT
ACGTGATGAGGACGGCTGGTTATCTAAGGATGAACGGCTCCTACGTAATGAGGAGGTCTGT
Found at i:381 original size:28 final size:28
Alignment explanation
Indices: 341--410 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
331 GGGATTATGG
* * * *
341 TTTCAAGAGAAACCGATTCAAAGATTTA
1 TTTCAAAAGAAACAGACTCAAAGATGTA
*
369 TTTCAAAAGAAACAGACTCAAAGATGTG
1 TTTCAAAAGAAACAGACTCAAAGATGTA
397 TTTCAAGAA-AAACA
1 TTTCAA-AAGAAACA
411 AGTTCAAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 34 0.94
29 2 0.06
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATGTA
Found at i:751 original size:30 final size:29
Alignment explanation
Indices: 717--794 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
707 AGAGATAAAA
* * *
717 TTTTATTTTAAAAGAAATAGACTCAAAGAT
1 TTTTA-TTCAAAAGAAACAAACTCAAAGAT
*
747 TTTTATTCAAAAGGAACAAACTCAAAGAT
1 TTTTATTCAAAAGAAACAAACTCAAAGAT
* * *
776 TTGT-TTCAAGAGAGACAAA
1 TTTTATTCAAAAGAAACAAA
795 AATCGTTTTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 12 0.30
29 23 0.57
30 5 0.12
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (29 bp):
TTTTATTCAAAAGAAACAAACTCAAAGAT
Found at i:5145 original size:32 final size:32
Alignment explanation
Indices: 5086--5147 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
5076 AATGAAAAAT
* *
5086 ACACAAACAAAAGAAAATAAATAAGTTAGTGC
1 ACACAAACAAAAAAAAAGAAATAAGTTAGTGC
* *
5118 ACACAAAGAAAAAAAAAGAAATTAGTTAGT
1 ACACAAACAAAAAAAAAGAAATAAGTTAGT
5148 ACAAGACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.61, C:0.10, G:0.13, T:0.16
Consensus pattern (32 bp):
ACACAAACAAAAAAAAAGAAATAAGTTAGTGC
Found at i:20553 original size:26 final size:27
Alignment explanation
Indices: 20496--20553 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 27
20486 ATATTTTATA
* * *
20496 TTAAAATATTTTGAAGTTAAAATAAAC
1 TTAAAATATATTGAAATCAAAATAAAC
* *
20523 ATAAAATATATT-AAATCAAAATAAAT
1 TTAAAATATATTGAAATCAAAATAAAC
20549 TTAAA
1 TTAAA
20554 TAAAGTTAGT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (27 bp):
TTAAAATATATTGAAATCAAAATAAAC
Found at i:21443 original size:19 final size:20
Alignment explanation
Indices: 21419--21456 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
21409 TTTTAACAAA
21419 TTTATTTTT-AAATAAATAC
1 TTTATTTTTAAAATAAATAC
21438 TTTATTTTTAAAATAAATA
1 TTTATTTTTAAAATAAATA
21457 AACAAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTATTTTTAAAATAAATAC
Found at i:22420 original size:727 final size:728
Alignment explanation
Indices: 20891--22994 Score: 2605
Period size: 727 Copynumber: 2.9 Consensus size: 728
20881 AACCAAGATA
* * *
20891 GCAATTGATAATTATGCAAAGAAAAAAAGAGGATGGCAGGTTGAACAAAGATGATGAACCATGAT
1 GCAATTGATGATTATGCAAAGAAAAAAAGAGGCT-GCAGGTTGAACAAAGATGATGAACAATGAT
* * **
20956 GAACT---A-AGAGAGATTATTCCTTA-------A-GTCAGTTTATATAAGAGTTTTTACTGTTC
65 GAACTAAGAGAGAGAGATTCTTCCTTAGCTTTGCATGTCAGTTTATAT-AGAGTTTTTAGTGACC
* * * * *
21009 GTGTCAGACTTAAAACAATGATTGTTATTTGTAGGTTGACAAAATGAATAAACTTGATTATTAAA
129 GTGTCAGACTTAAAATAATGATTGTTATTTATAGGTTGACAAAGTGAATAAATTTGATTATTATA
* * * * * *
21074 AAGCATACTTTATCAATGATGGGACTGAAAACAATCATGTCAAGAAAAAATTATTAGATCGACCT
194 TAGAAGAATTTATCAATGAAGGGATTG-AAACAATCATGTCAAGAAAAAATTATTAGATCGACCT
* * * *
21139 GGTTCATCACGTCATTCGTTCT-CTAAACCAATAAGATCCAAGTATGTCACTTTTTTTATTGTGA
258 GGTTCATCACGTCATTCG-TCTGCTAAATC-AT-A-ATCC-A-TCTGTCACTTTTTTCATGGTGA
* *
21203 ATCTTCATCTTTTTCCTACATGTAAATAAGGAGTTGATAATTATTTGAAGGTTTGATATAAAAAA
317 ATCTTCATCTTTTTCCTACATGTAAATAGGGAGTTGATAATTATTTGAAGGCTTGATAT--AAAA
* * * *
21268 AAAGTGTCAAAACTATATGCAAAATTAATTTTTGGTGTCTAAATAATTTTTCGATAAAAATAGAT
380 AAAGTATCCAAACTATACGCAAAATTAATTTTTGGTGTCTAAAGAATTTTTCGATAAAAATAGAT
* * *
21333 ACCTAACATTTT-GTCTATTACACTTTTAGGTATTTACCGTTAAAAAC-CGTTAAATGACACGTG
445 ACCTAACATTTTCTTC-ATTACACTTTTAGGTGTTTACCGTTAAAAACACGTTAAATGACAAGTG
* * * * *
21396 TCATGTTTAGA-TTTTTTAACAAATTTATTTTTAAATAAATACTTTATTTTTAAAATAAATAAAC
509 TCATGTTCAGATTTTTTTAAAAAATCTATTTTTAAATAAATATTTTATTTTTAAAATAAATAAAT
** * *
21460 AAATGTAAGGCTTAAATATAAAATAAGTGTCTAAACTATAGCGTTTTTCACGAATATGTTTCTAA
574 AAATGTAAGGCTTAAATATAAAATAAGTACCTAAACTATAGCGCTTTTCACGAATATGTGTCTAA
* *
21525 ACTATTTTTTTAATTAAATCAAAATTCTTCATCGAAAATTAGGTTGTGACATTTGTGAACAATTT
639 ACTATTTTTTAAATTAAATCAAAATTCTTCATCGAAAATTAGGTTGTGACATGTGTGAACAATTT
* * *
21590 ATCTCTTTTGATTTGGATTAATAAC
704 ATCTCCTTTGATTTGGATCAAGAAC
* * * * * * *
21615 ACAACTGATGATTATGCAAAG-AAAAAAGAGAACCGCTGGTGGAACAAACATGATGAACAATGAT
1 GCAATTGATGATTATGCAAAGAAAAAAAGAG-GCTGCAGGTTGAACAAAGATGATGAACAATGAT
* *
21679 GAACTAAGAGAGAGAGATTCTCCCTTAGCTTTGCATGTTAGTTTATATACGAGTTTTTAGTGACC
65 GAACTAAGAGAGAGAGATTCTTCCTTAGCTTTGCATGTCAGTTTATATA-GAGTTTTTAGTGACC
* * * * * *
21744 ATATCAGACTTAAAATAATTATTGCTATTCATAAGTTGACAAAGTGAATAAATTTGATTATTATA
129 GTGTCAGACTTAAAATAATGATTGTTATTTATAGGTTGACAAAGTGAATAAATTTGATTATTATA
*
21809 TAGAAGAATTTATCAATGAAGGGATTGAAA-AGTCATGTCAAGAAAAAAATTATTAGATCGACCT
194 TAGAAGAATTTATCAATGAAGGGATTGAAACAATCATGTCAAG-AAAAAATTATTAGATCGACCT
* * * *
21873 GGTTCATCACGTCATTCGTCATGGTGAATC-T-TTACATCTGTCAC-TTTTTCATGGTGAATCTT
258 GGTTCATCACGTCATTCGTC-TGCTAAATCATAATCCATCTGTCACTTTTTTCATGGTGAATCTT
* *
21935 CATCTTTTTCTTACATATAAATAGGGAGTTGATAATTATTTGAAGGCTTGATAT-AAAAAAGTAT
322 CATCTTTTTCCTACATGTAAATAGGGAGTTGATAATTATTTGAAGGCTTGATATAAAAAAAGTAT
* * * *
21999 CCAAACTATACGCAAAATTGATTTTTGGTGTTTAAAGAATTTTTCGTTAAAAATAGGTACCTAAC
387 CCAAACTATACGCAAAATTAATTTTTGGTGTCTAAAGAATTTTTCGATAAAAATAGATACCTAAC
** * *
22064 ATTTTCTTCATTGTACTGTTAGGTGTTTACCGTTAAAAACACGTTAAATGTCAAGTGTCATGTTC
452 ATTTTCTTCATTACACTTTTAGGTGTTTACCGTTAAAAACACGTTAAATGACAAGTGTCATGTTC
*
22129 AGATTTTTTTAAAAAAATCTATTTTAAAATAAATATTTTATTTTTAAAATAAATAAATAAATGTA
517 AGATTTTTTT-AAAAAATCTATTTTTAAATAAATATTTTATTTTTAAAATAAATAAATAAATGTA
* * * * *
22194 AGGCTTAAATATAAAATAAGTACCTAAACTTTAACGCTTTTAATGAATATGTGTCTAATCTATAT
581 AGGCTTAAATATAAAATAAGTACCTAAACTATAGCGCTTTTCACGAATATGTGTCTAAACTAT-T
* * *
22259 TTTTAAATTAAATCAAAATTCTTCATCGAAAATTAGGTTGTGACGTGTGTGAACAGTTTTTCTCC
645 TTTTAAATTAAATCAAAATTCTTCATCGAAAATTAGGTTGTGACATGTGTGAACAATTTATCTCC
*
22324 TTTGATTTTGATCAAGAAC
710 TTTGATTTGGATCAAGAAC
*
22343 GCAATTGATGATTATGCAAAGAAAAAAAGAGGCTGACAGGTTGAACAAAGATGATGAAAAATGAT
1 GCAATTGATGATTATGCAAAGAAAAAAAGAGGCTG-CAGGTTGAACAAAGATGATGAACAATGAT
* * *
22408 GAAGTAAGAGAGAGAGATTCTTCCTTAGCTTTGCATGTCAATTTATAT-GAGTTTTTAGTGCCCG
65 GAACTAAGAGAGAGAGATTCTTCCTTAGCTTTGCATGTCAGTTTATATAGAGTTTTTAGTGACCG
* * *
22472 TGTTAGACCTAAAATAATGATTGTTATTTATAGGTTGATAAAGTGAATAAATTTGATTATTATAT
130 TGTCAGACTTAAAATAATGATTGTTATTTATAGGTTGACAAAGTGAATAAATTTGATTATTATAT
* * * *
22537 AGAAGATTTTATTAATGATA-GGACTTAAAACAATCATGTCAAGAAAAAATTATTAGGTCGACCT
195 AGAAGAATTTATCAATGA-AGGGA-TTGAAACAATCATGTCAAGAAAAAATTATTAGATCGACCT
** * * *
22601 GGTTCCCCACGTCA-TCTGT-TGTCTCAATCAATAAGATCCATCTATGTCACTTTTTTCATGATA
258 GGTTCATCACGTCATTC-GTCTG-CTAAATC-AT-A-ATCCATC--TGTCACTTTTTTCATGGTG
* * * *
22664 AATCTTTATATTTTTCCTACATGTAAATAGGAAGTTGGTAATTATTTGAAGGCTTGATATAAAAA
316 AATCTTCATCTTTTTCCTACATGTAAATAGGGAGTTGATAATTATTTGAAGGCTTGATAT-AAAA
* * * * *
22729 AAAGTATCCAAACTATAC-CTAAAATTAATTTTTTGTGTCTAAAGATTTTTTAGAGAAAAATATA
380 AAAGTATCCAAACTATACGC-AAAATTAATTTTTGGTGTCTAAAGAATTTTTCGATAAAAATAGA
* * ** ** *
22793 TACCTAACATTTTCTCCATTACACTTTTAGGTGATTATAGTTAAAAA-ATTATTAAATGACATGT
444 TACCTAACATTTTCTTCATTACACTTTTAGGTGTTTACCGTTAAAAACA-CGTTAAATGACAAGT
* *
22857 GTCATGTTCATATTTTTTT--TAAATCTATTTTTAAATAAATATTTTATTTTTAAAATAAATAAA
508 GTCATGTTCAGATTTTTTTAAAAAATCTATTTTTAAATAAATATTTTATTTTTAAAATAAATAAA
* * *
22920 TAAATGTAAGGCTTAAATATAAAATAAGTAACC-AAACTATAGTGCTTTTCACGAATATGTGACG
573 TAAATGTAAGGCTTAAATATAAAATAAGT-ACCTAAACTATAGCGCTTTTCACGAATATGTGTCT
22984 AAACTATTTTT
637 AAACTATTTTT
22995 AATGATCCCG
Statistics
Matches: 1181, Mismatches: 157, Indels: 75
0.84 0.11 0.05
Matches are distributed among these distances:
723 40 0.03
724 117 0.10
725 26 0.02
726 9 0.01
727 281 0.24
728 144 0.12
729 91 0.08
730 2 0.00
732 5 0.00
733 18 0.02
734 152 0.13
735 169 0.14
736 2 0.00
737 125 0.11
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (728 bp):
GCAATTGATGATTATGCAAAGAAAAAAAGAGGCTGCAGGTTGAACAAAGATGATGAACAATGATG
AACTAAGAGAGAGAGATTCTTCCTTAGCTTTGCATGTCAGTTTATATAGAGTTTTTAGTGACCGT
GTCAGACTTAAAATAATGATTGTTATTTATAGGTTGACAAAGTGAATAAATTTGATTATTATATA
GAAGAATTTATCAATGAAGGGATTGAAACAATCATGTCAAGAAAAAATTATTAGATCGACCTGGT
TCATCACGTCATTCGTCTGCTAAATCATAATCCATCTGTCACTTTTTTCATGGTGAATCTTCATC
TTTTTCCTACATGTAAATAGGGAGTTGATAATTATTTGAAGGCTTGATATAAAAAAAGTATCCAA
ACTATACGCAAAATTAATTTTTGGTGTCTAAAGAATTTTTCGATAAAAATAGATACCTAACATTT
TCTTCATTACACTTTTAGGTGTTTACCGTTAAAAACACGTTAAATGACAAGTGTCATGTTCAGAT
TTTTTTAAAAAATCTATTTTTAAATAAATATTTTATTTTTAAAATAAATAAATAAATGTAAGGCT
TAAATATAAAATAAGTACCTAAACTATAGCGCTTTTCACGAATATGTGTCTAAACTATTTTTTAA
ATTAAATCAAAATTCTTCATCGAAAATTAGGTTGTGACATGTGTGAACAATTTATCTCCTTTGAT
TTGGATCAAGAAC
Found at i:24725 original size:43 final size:43
Alignment explanation
Indices: 24658--24879 Score: 175
Period size: 43 Copynumber: 5.2 Consensus size: 43
24648 TGAGAATAAA
* * **
24658 AAACGCCGCAATAGGTAAAGATCTATAACGGCGTTTTTGAAAC
1 AAACGCCACAAAAGGTCGAGATCTATAACGGCGTTTTTGAAAC
* *
24701 AAACACCACAAAAGGTCGAGATCTACAACGGCGTTTTT-AGAAC
1 AAACGCCACAAAAGGTCGAGATCTATAACGGCGTTTTTGA-AAC
* * * * **
24744 AAATGCCGCAAAAGGTC-ATATCTATAGCAACGTTTTTGAAA-
1 AAACGCCACAAAAGGTCGAGATCTATAACGGCGTTTTTGAAAC
* * * * * *
24785 AAAAGCCAC--AAGATTGAAATCTATAACGGCATTTTTTGGAAC
1 AAACGCCACAAAAGGTCGAGATCTATAACGGC-GTTTTTGAAAC
* * * * *
24827 AAATGCCGCGAAATGTCGAGATCTATAGCGGCGTTTTTGAATAC
1 AAACGCCACAAAAGGTCGAGATCTATAACGGCGTTTTTGAA-AC
24871 AAACGCCAC
1 AAACGCCAC
24880 TAATTACCTT
Statistics
Matches: 136, Mismatches: 35, Indels: 15
0.73 0.19 0.08
Matches are distributed among these distances:
39 4 0.03
40 10 0.07
41 15 0.11
42 25 0.18
43 57 0.42
44 25 0.18
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCACAAAAGGTCGAGATCTATAACGGCGTTTTTGAAAC
Found at i:24862 original size:84 final size:84
Alignment explanation
Indices: 24662--24879 Score: 226
Period size: 84 Copynumber: 2.6 Consensus size: 84
24652 AATAAAAAAC
* * * * *
24662 GCCGCAATAGGTAAAGATCTATAACGGCGTTTTTGAAACAAACACCACAAAAGGTCGAGATCTAC
1 GCCGCAAAAGGT-CAGATCTATAGCGGCGTTTTTGAAACAAACACCAC-AAAGATCGAAATCTAC
24727 AACGGCGTTTTTAGAACAAAT
64 AACGGCGTTTTTAGAACAAAT
* ** * *
24748 GCCGCAAAAGGTCATATCTATAGCAACGTTTTTGAAA-AAA-AGCCAC-AAGATTGAAATCTATA
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACA-CCACAAAGATCGAAATCTACA
* *
24810 ACGGCATTTTTTGGAACAAAT
65 ACGGC-GTTTTTAGAACAAAT
* * *
24831 GCCGCGAAATGTCGAGATCTATAGCGGCGTTTTTGAATACAAACGCCAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGAA-ACAAACACCAC
24880 TAATTACCTT
Statistics
Matches: 108, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
82 17 0.16
83 25 0.23
84 27 0.25
85 21 0.19
86 18 0.17
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (84 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACACCACAAAGATCGAAATCTACAA
CGGCGTTTTTAGAACAAAT
Found at i:29441 original size:41 final size:41
Alignment explanation
Indices: 29396--29523 Score: 179
Period size: 40 Copynumber: 3.1 Consensus size: 41
29386 TAAAATTGCA
29396 GCGTTTGTATAGAAATGCCACTAAAGTACGAGTCTATAGCG
1 GCGTTTGTATAGAAATGCCACTAAAGTACGAGTCTATAGCG
* * *
29437 GCGTTTGTAT-GAAAAGCCATTAAAGTACAAGTCTATAGCG
1 GCGTTTGTATAGAAATGCCACTAAAGTACGAGTCTATAGCG
* *
29477 GCGTTTGTATAAAAAAT-CCACTAAAGTACGAGTCTTTAGCG
1 GCGTTTGTAT-AGAAATGCCACTAAAGTACGAGTCTATAGCG
*
29518 GGGTTT
1 GCGTTT
29524 ATTGGAAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 37 0.49
41 36 0.47
42 3 0.04
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (41 bp):
GCGTTTGTATAGAAATGCCACTAAAGTACGAGTCTATAGCG
Found at i:29470 original size:40 final size:41
Alignment explanation
Indices: 29396--29523 Score: 186
Period size: 41 Copynumber: 3.1 Consensus size: 41
29386 TAAAATTGCA
*
29396 GCGTTTGTATAGAAATGCCACTAAAGTACGAGTCTATAGCG
1 GCGTTTGTATAGAAAAGCCACTAAAGTACGAGTCTATAGCG
* *
29437 GCGTTTGTAT-GAAAAGCCATTAAAGTACAAGTCTATAGCG
1 GCGTTTGTATAGAAAAGCCACTAAAGTACGAGTCTATAGCG
* * *
29477 GCGTTTGTATAAAAAATCCACTAAAGTACGAGTCTTTAGCG
1 GCGTTTGTATAGAAAAGCCACTAAAGTACGAGTCTATAGCG
*
29518 GGGTTT
1 GCGTTT
29524 ATTGGAAAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
40 37 0.48
41 40 0.52
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (41 bp):
GCGTTTGTATAGAAAAGCCACTAAAGTACGAGTCTATAGCG
Found at i:31003 original size:45 final size:45
Alignment explanation
Indices: 30948--31039 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
30938 GTTTTGCAAT
30948 GGAGGCAATCTCACCAAGCTCATTGTGTACAACAATTCTTTCTCA
1 GGAGGCAATCTCACCAAGCTCATTGTGTACAACAATTCTTTCTCA
* * *
30993 GGAGGGAATCTCACCAAGCTCATTGTGTTCAACAATTCTTTTTCA
1 GGAGGCAATCTCACCAAGCTCATTGTGTACAACAATTCTTTCTCA
31038 GG
1 GG
31040 TCCAGTGCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (45 bp):
GGAGGCAATCTCACCAAGCTCATTGTGTACAACAATTCTTTCTCA
Found at i:46284 original size:131 final size:130
Alignment explanation
Indices: 46114--46510 Score: 483
Period size: 132 Copynumber: 3.0 Consensus size: 130
46104 TGGATCTTAA
* *
46114 GAGAGAAAACAATAATATCTTATTATTTCCAATCGAGAATAAATGACATCTCATG-TCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGAC-TCTCATGCT-TTAAAGC
** *
46178 AATCATTTATTACTCCAATTAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGAT
64 AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGAT
46243 TC
129 TC
* * * * ** * *
46245 GAGAGAAAATGATAACATCTGATTATTTCCAATCCAGAATAAACAACCTCTTATGCCTTATAAAA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATG-CTT-TAAAG
*
46310 CAATCATTT-TTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATATTGA
63 CAATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGA
46374 TTC
128 TTC
* * *
46377 GAGAGAAAACGATAATATATAATTATATCCAATCGAGAATAAATGATCTCTCATGCTTTAAAGTA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGA-CTCTCATGCTTTAAAGCA
* * * * * * * * * *
46442 GTCATTTATTAATCCAACCGGAATGAAAAGATATTATTATCTCATCCTAAAATTCAATATTAATT
65 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATT
46507 C
130 C
46508 GAG
1 GAG
46511 TGTTACTATT
Statistics
Matches: 225, Mismatches: 36, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
130 11 0.05
131 99 0.44
132 101 0.45
133 14 0.06
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (130 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACTCTCATGCTTTAAAGCAA
TCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTC
Found at i:46350 original size:132 final size:131
Alignment explanation
Indices: 46114--46510 Score: 492
Period size: 131 Copynumber: 3.0 Consensus size: 131
46104 TGGATCTTAA
* * *
46114 GAGAGAAAACAATAATATCTTATTATTTCCAATCGAGAATAAATGACATCTCATG-TCTTAAAGC
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCT-TTAAAGC
** *
46178 AATCATTTATTACTCCAATTAAAATGAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGAT
65 AATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGAT
46243 TC
130 TC
* * * * ** * *
46245 GAGAGAAAATGATAACATCTGATTATTTCCAATCCAGAATAAACAACCTCTTATGCCTTATAAAA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATG-CTT-TAAAG
*
46310 CAATCATTT-TTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAAATCAATATTGA
64 CAATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGA
46374 TTC
129 TTC
* * * *
46377 GAGAGAAAACGATAATATATAATTATATCCAATCGAGAATAAATGATCTCTCATGCTTTAAAGTA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCTTTAAAGCA
* * * * * * * * * *
46442 GTCATTTATTAATCCAACCGGAATGAAAAGATATTATTATCTCATCCTAAAATTCAATATTAATT
66 ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATT
46507 C
131 C
46508 GAG
1 GAG
46511 TGTTACTATT
Statistics
Matches: 225, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
130 11 0.05
131 100 0.44
132 100 0.44
133 14 0.06
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCTTTAAAGCA
ATCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATT
C
Found at i:46981 original size:26 final size:25
Alignment explanation
Indices: 46950--47025 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 25
46940 TGACTAAAAT
*
46950 AAAATAAAATAAAAGCAATATGCAA
1 AAAATAAAATAAAAGCAAAATGCAA
*
46975 AACAATAAAATAAAAGCAACATGCAA
1 AA-AATAAAATAAAAGCAAAATGCAA
*
47001 AAATTAAAATAAAA-CAAAATGCAA
1 AAAATAAAATAAAAGCAAAATGCAA
47025 A
1 A
47026 TAGGACTAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 10 0.21
25 13 0.28
26 24 0.51
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAATAAAATAAAAGCAAAATGCAA
Found at i:47075 original size:63 final size:62
Alignment explanation
Indices: 46984--47101 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 62
46974 AAACAATAAA
*
46984 ATAAAAGCAACATGCAAAAATTAAAATAAAACAAAATGCAAATAG-GACTAGAATGTAAACGG
1 ATAAAAGCAACATGCAAAAATTAAAATAAAACAAAATGCAAA-AGTGACTAAAATGTAAACGG
* * * *
47046 ATAAAATCATCATGTCAAAAATTAAAATAAAATAAAGTGCAAAAGTGACTAAAATG
1 ATAAAAGCAACATG-CAAAAATTAAAATAAAACAAAATGCAAAAGTGACTAAAATG
47102 AACATTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 14 0.29
63 35 0.71
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (62 bp):
ATAAAAGCAACATGCAAAAATTAAAATAAAACAAAATGCAAAAGTGACTAAAATGTAAACGG
Found at i:47552 original size:3 final size:3
Alignment explanation
Indices: 47544--47593 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
47534 GATTCATTTG
* *
47544 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATG ATAT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
47590 ATT A
1 ATT A
47594 AATAATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.98
4 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:48990 original size:28 final size:28
Alignment explanation
Indices: 48922--48992 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
48912 ATTTTAATTT
* *
48922 TATTATAATTTA-GTCACTAATTTTAAA
1 TATTATAATTTATTTTACTAATTTTAAA
* * *
48949 TATTTTCATTTATTTTACTACTTTTAAA
1 TATTATAATTTATTTTACTAATTTTAAA
48977 TA-TATAATTGTATTTT
1 TATTATAATT-TATTTT
48993 TATTGTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (28 bp):
TATTATAATTTATTTTACTAATTTTAAA
Done.