Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008900.1 Hibiscus syriacus cultivar Beakdansim tig00112177_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: 45957
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Found at i:128 original size:14 final size:15
Alignment explanation
Indices: 87--131 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
77 TTTTAGTAAT
87 TTTACATATTTAATATA
1 TTTA-ATATTTAAT-TA
104 TTTAATATTTAATTA
1 TTTAATATTTAATTA
*
119 TTT-TTATTTAATT
1 TTTAATATTTAATT
132 CTTGATAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 9 0.33
17 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAATATTTAATTA
Found at i:7170 original size:13 final size:14
Alignment explanation
Indices: 7143--7178 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
7133 TTATAAATAT
7143 AATAATATTTAAAA
1 AATAATATTTAAAA
*
7157 AATAA-ATTTTAAA
1 AATAATATTTAAAA
7170 AATAATATT
1 AATAATATT
7179 GTGACACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
AATAATATTTAAAA
Found at i:9428 original size:2 final size:2
Alignment explanation
Indices: 9421--9465 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
9411 TAACTTTTTA
9421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9463 AT A
1 AT A
9466 AAATATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10116 original size:15 final size:16
Alignment explanation
Indices: 10098--10132 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
10088 TTGTTTCACT
10098 AAAAATGTTTT-C-TA
1 AAAAATGTTTTCCTTA
10112 AAAAATGTTTTCCTTA
1 AAAAATGTTTTCCTTA
10128 AAAAA
1 AAAAA
10133 ATTATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 11 0.58
15 1 0.05
16 7 0.37
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (16 bp):
AAAAATGTTTTCCTTA
Found at i:10686 original size:22 final size:25
Alignment explanation
Indices: 10636--10686 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
10626 AATAATTGAG
10636 TATTATTATAATATAAAAAATATAT
1 TATTATTATAATATAAAAAATATAT
*
10661 TATTATTATAA-ATAATTAAATATAT
1 TATTATTATAATATAA-AAAATATAT
10686 T
1 T
10687 TTAAATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTATTATAATATAAAAAATATAT
Found at i:11572 original size:41 final size:40
Alignment explanation
Indices: 11527--11654 Score: 109
Period size: 41 Copynumber: 3.1 Consensus size: 40
11517 TTTAGCGGTG
*
11527 TTTTTATACAAACACCGCAATAGGGTCATCTATAGTGGCAT
1 TTTTTATACAAACGCCGCAATAGGGT-ATCTATAGTGGCAT
* * * **
11568 TTTTTCA-ACAAACGCTGCAACA-GGTAGTACTTTAGCAGCA-
1 TTTTT-ATACAAACGCCGCAATAGGGTA-T-CTATAGTGGCAT
* *
11608 TTTTTATACAAACGTCGCAATAGGGTTAATCTATAGTGGCGT
1 TTTTTATACAAACGCCGCAATAGGG-T-ATCTATAGTGGCAT
11650 TTTTT
1 TTTTT
11655 CAACAATCAT
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
39 2 0.03
40 21 0.32
41 34 0.52
42 8 0.12
43 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (40 bp):
TTTTTATACAAACGCCGCAATAGGGTATCTATAGTGGCAT
Found at i:11653 original size:82 final size:83
Alignment explanation
Indices: 11484--11725 Score: 303
Period size: 82 Copynumber: 2.9 Consensus size: 83
11474 TTTTAACAGT
* * * * **
11484 GTTTTTTCAACAAACGCCGCAATAGAGAAGTACTTTAGCGGTGTTTTTATACAAACACCGCAATA
1 GTTTTTTCAACAAACGCTGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAATA
11549 GGG-TCATCTATAGTGGC
66 GGGTTCATCTATAGTGGC
* * *
11566 ATTTTTTCAACAAACGCTGCAACAG-GTAGTACTTTAGCAGCATTTTTATACAAACGTCGCAATA
1 GTTTTTTCAACAAACGCTGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAATA
*
11630 GGGTTAATCTATAGTGGC
66 GGGTTCATCTATAGTGGC
* * * * *
11648 GTTTTTTCAACAATC-ATCACAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGTCACAAT
1 GTTTTTTCAACAAACGCT-GCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAAT
11712 -GTGGTTCATCTATA
65 AG-GGTTCATCTATA
11726 ATAGTTTTTT
Statistics
Matches: 137, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
81 37 0.27
82 55 0.40
83 45 0.33
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (83 bp):
GTTTTTTCAACAAACGCTGCAACAGAGTAGTACTTTAGCGGCGTTTTTATACAAACGTCGCAATA
GGGTTCATCTATAGTGGC
Found at i:11709 original size:41 final size:40
Alignment explanation
Indices: 11585--11710 Score: 112
Period size: 42 Copynumber: 3.1 Consensus size: 40
11575 ACAAACGCTG
** * *
11585 CAACAGGTAGTACTTTAGCAGCATTTTTATACAAACGTCG
1 CAACAGGTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
* * * * *
11625 CAATAGGGTTAAT-CTATAGTGGCGTTTTT-TCAACAATCATCA
1 CAACA-GG-TAGTACTTTAGTGGCGTTTTTAT--ACAAACGTCA
11667 CAACAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
1 CAACAG-GTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
11708 CAA
1 CAA
11711 TGTGGTTCAT
Statistics
Matches: 65, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
40 5 0.08
41 29 0.45
42 30 0.46
43 1 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (40 bp):
CAACAGGTAGTACTTTAGTGGCGTTTTTATACAAACGTCA
Found at i:14128 original size:19 final size:19
Alignment explanation
Indices: 14104--14174 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
14094 AGTGTATTTG
14104 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
14123 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
14142 ATGCATCGATGCACAAACC
1 ATGCATCGATGCACAAACC
14161 ATGCATCGATGCAC
1 ATGCATCGATGCAC
14175 TCTGGCTATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.35, C:0.31, G:0.17, T:0.17
Consensus pattern (19 bp):
ATGCATCGATGCACAAACC
Found at i:15716 original size:55 final size:55
Alignment explanation
Indices: 15656--16026 Score: 367
Period size: 55 Copynumber: 6.7 Consensus size: 55
15646 TGGCGAGTCT
* * ** *
15656 GCTCCCTATTCTTTCAGGGAGTATAAGACTCTAATAATCTTCAACAAACGTTTCT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
* * * * * **
15711 TCTCCCTATTCGTTCAGGGAGTATAAGAAAT-GAACAATTTTCAGCAAACGTTTCC
1 GCTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCC
* * *
15766 ACTCCCTATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAGCAAACGGGTCC
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
* * * * *
15821 GCTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATATTCAGCAAATGAGTCC
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
* * * * * *
15876 GCTACCTATTCTTTTAGGGAGTAT-AGAACACGAACAATCTTCTGA-AAACGAGTTC
1 GCTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTTC-AACAAACGGGTCC
** * *
15931 TTTCCCTATTTTTTCAGGGAGTATACA-ACTCGAACAATCTTCTGA-AAACGGGTCC
1 GCTCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTC-AACAAACGGGTCC
*
15986 GCTCCCTATTCTTTCAGCGAGTAT-AGAACTCGAACAATCTT
1 GCTCCCTATTCTTTCAGGGAGTATAAG-ACTCGAACAATCTT
16027 GATTTGCTTC
Statistics
Matches: 266, Mismatches: 42, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
53 1 0.00
54 4 0.02
55 258 0.97
56 2 0.01
57 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (55 bp):
GCTCCCTATTCTTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCC
Found at i:15806 original size:110 final size:111
Alignment explanation
Indices: 15649--16026 Score: 419
Period size: 110 Copynumber: 3.4 Consensus size: 111
15639 ATTCGAATGG
* * * *
15649 CGAGTCTGCTCCCTATTCTTTCAGGGAGTATA-AGACTCTAATAATCTTCAACAAACGTTTCTTC
1 CGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGGTTCTTC
* * *
15713 TCCCTATTCGTTCAGGGAGTATAAGAAAT-GAACAATTTTCAGCAAA
65 TCCCTATTCTTTCAGGGAGTATAAGAACTCGAACAATATTCAGCAAA
** * * * * **
15759 CGTTTCCACTCCCTATTCTTTCAGAGAGTATA-AGACTCGAACAATCTTCAGCAAACGGGTCCGC
1 CGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGGTTCTTC
*
15823 TCCCTATTCTTTCAGGGAGTATAAG-ACTCAAACAATATTCAGCAAA
65 TCCCTATTCTTTCAGGGAGTATAAGAACTCGAACAATATTCAGCAAA
* * * * *
15869 TGAGTCCGCTACCTATTCTTTTAGGGAGTATAGAACACGAACAATCTTCTGA-AAACGAGTTCTT
1 CGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTC-AACAAACG-GTTCTT
* * * * *
15933 -TCCCTATTTTTTCAGGGAGTAT-ACAACTCGAACAATCTTCTGAAAA
64 CTCCCTATTCTTTCAGGGAGTATAAGAACTCGAACAATATTCAGCAAA
* *
15979 CGGGTCCGCTCCCTATTCTTTCAGCGAGTATAGAACTCGAACAATCTT
1 CGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTT
16027 GATTTGCTTC
Statistics
Matches: 222, Mismatches: 41, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
109 3 0.01
110 215 0.97
111 4 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (111 bp):
CGAGTCCGCTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGTTCTTCT
CCCTATTCTTTCAGGGAGTATAAGAACTCGAACAATATTCAGCAAA
Found at i:15939 original size:165 final size:165
Alignment explanation
Indices: 15656--16023 Score: 447
Period size: 165 Copynumber: 2.2 Consensus size: 165
15646 TGGCGAGTCT
* * * ** ** *
15656 GCTCCCTATTCTTTCAGGGAGTATAAGACTCTAATAATCTTCAACAAACGTTTCTTCTCCCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATATTCAACAAACGAGTCCGCTACCTATT
* * * *
15721 CGTTCAGGGAGTATAAGAAATGAACAATTTTCAGCAAACGTTTCCACTCCCTATTCTTTCAGAGA
66 CGTTCAGGGAGTATAAGAAACGAACAATCTTCAGAAAACGGTTCCACTCCCTATTCTTTCAGAGA
*
15786 GTATA-AGACTCGAACAATCTTCAGCAAACGGGTCC
131 GTATACA-ACTCGAACAATCTTCAGAAAACGGGTCC
* *
15821 GCTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATATTCAGCAAATGAGTCCGCTACCTATT
1 GCTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATATTCAACAAACGAGTCCGCTACCTATT
* * * ** * *
15886 CTTTTAGGGAGTAT-AGAACACGAACAATCTTCTGAAAACGAGTT-CTTTCCCTATTTTTTCAGG
66 CGTTCAGGGAGTATAAGAA-ACGAACAATCTTCAGAAAACG-GTTCCACTCCCTATTCTTTCAGA
*
15949 GAGTATACAACTCGAACAATCTTCTGAAAACGGGTCC
129 GAGTATACAACTCGAACAATCTTCAGAAAACGGGTCC
* *
15986 GCTCCCTATTCTTTCAGCGAGTAT-AGAACTCGAACAAT
1 GCTCCCTATTCTTTCAGGGAGTATAAG-ACTCAAACAAT
16024 CTTGATTTGC
Statistics
Matches: 174, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
164 6 0.03
165 165 0.95
166 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (165 bp):
GCTCCCTATTCTTTCAGGGAGTATAAGACTCAAACAATATTCAACAAACGAGTCCGCTACCTATT
CGTTCAGGGAGTATAAGAAACGAACAATCTTCAGAAAACGGTTCCACTCCCTATTCTTTCAGAGA
GTATACAACTCGAACAATCTTCAGAAAACGGGTCC
Found at i:17410 original size:9 final size:8
Alignment explanation
Indices: 17369--17488 Score: 122
Period size: 8 Copynumber: 14.5 Consensus size: 8
17359 TTTTCTTTTC
17369 TTTTTCAT
1 TTTTTCAT
17377 TTTTTCATT
1 TTTTTCA-T
17386 TCTTCTTCCAT
1 T-TT-TT-CAT
17397 TTTTTCATT
1 TTTTTCA-T
17406 TTTTTCAT
1 TTTTTCAT
17414 TTTTTCAT
1 TTTTTCAT
17422 TTTTTCAT
1 TTTTTCAT
17430 TTTTTCATT
1 TTTTTCA-T
17439 TTTTTC-T
1 TTTTTCAT
17446 TTTTTGC-T
1 TTTTT-CAT
*
17454 CTTTCTCAT
1 -TTTTTCAT
17463 TTTTTC--
1 TTTTTCAT
17469 TTTTTCAT
1 TTTTTCAT
*
17477 TTTTTAAT
1 TTTTTCAT
17485 TTTT
1 TTTT
17489 CTTCTTCAAG
Statistics
Matches: 98, Mismatches: 3, Indels: 22
0.80 0.02 0.18
Matches are distributed among these distances:
6 6 0.06
7 6 0.06
8 52 0.53
9 24 0.24
10 4 0.04
11 4 0.04
12 2 0.02
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTCAT
Found at i:17436 original size:33 final size:33
Alignment explanation
Indices: 17369--17488 Score: 133
Period size: 33 Copynumber: 3.6 Consensus size: 33
17359 TTTTCTTTTC
17369 TTTTTCATTTTTTCATTTCTTCTTCCATTTTTTCATT
1 TTTTTCATTTTTTCA-TT-TT-TT-CATTTTTTCATT
17406 TTTTTCATTTTTTCATTTTTTCATTTTTTCATT
1 TTTTTCATTTTTTCATTTTTTCATTTTTTCATT
*
17439 TTTTTC-TTTTTTGC-TCTTTCTCATTTTTTC---
1 TTTTTCATTTTTT-CAT-TTTTTCATTTTTTCATT
*
17469 TTTTTCATTTTTTAATTTTT
1 TTTTTCATTTTTTCATTTTT
17489 CTTCTTCAAG
Statistics
Matches: 76, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
30 9 0.12
31 7 0.09
32 7 0.09
33 32 0.42
34 2 0.03
35 2 0.03
36 2 0.03
37 15 0.20
ACGTcount: A:0.10, C:0.15, G:0.01, T:0.74
Consensus pattern (33 bp):
TTTTTCATTTTTTCATTTTTTCATTTTTTCATT
Found at i:20006 original size:17 final size:16
Alignment explanation
Indices: 19984--20017 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19974 TAAAAACAGT
19984 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
20001 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
20017 A
1 A
20018 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:20536 original size:24 final size:24
Alignment explanation
Indices: 20492--20541 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
20482 ATAAAGAACC
*
20492 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
20516 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
20540 AA
1 AA
20542 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:23581 original size:19 final size:20
Alignment explanation
Indices: 23559--23602 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
23549 GAGAAAAGGT
23559 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
23578 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
23598 AAAAG
1 AAAAG
23603 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:30512 original size:24 final size:24
Alignment explanation
Indices: 30468--30517 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
30458 ATAAAGAACC
*
30468 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
30492 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
30516 AA
1 AA
30518 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:36638 original size:21 final size:20
Alignment explanation
Indices: 36606--36644 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
36596 ATGTTTTGCC
*
36606 ATTTTAAATAAATGATAATA
1 ATTTTAAATAAAAGATAATA
*
36626 ATTTTAATTTAAAAGATAA
1 ATTTTAA-ATAAAAGATAA
36645 ATTTATGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTTTAAATAAAAGATAATA
Found at i:39336 original size:40 final size:41
Alignment explanation
Indices: 39202--39469 Score: 203
Period size: 41 Copynumber: 6.6 Consensus size: 41
39192 TGCTTTTTGA
* * * * *
39202 ACAAACGACACTATAGACTCTTACTTTAGCGGCATTTTTAT
1 ACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTAT
* ** * * *
39243 ATAAACGCCATTAAATACT-AGTACGTTAGTGGCGTTTTTAT
1 ACAAACGCCGCTATAGACTCA-TACTTTAGTGGCGTTTTTAT
*
39284 ACAAACGACGCTATAGACTCATACTTTAGTGGCG-TTTTAT
1 ACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTAT
* * * *
39324 GCAAACGTCGC--TAGATTTC-TAC-TTAGTGACGTTTTTAT
1 ACAAACGCCGCTATAGA-CTCATACTTTAGTGGCGTTTTTAT
* *
39362 GCAAATGCCGCTATAGACTCATACTTTA-TGGCG-TTTTAT
1 ACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTAT
* * * *
39401 ACAAACGCCGCTATACACT-AGTACTCTAGTGGCATTTCTGTTT
1 ACAAACGCCGCTATAGACTCA-TACTTTAGTGGCGTTT-T-TAT
* * *
39444 ACAAATGCCTCTATAAACTCATACTT
1 ACAAACGCCGCTATAGACTCATACTT
39470 AATGGTTTGT
Statistics
Matches: 179, Mismatches: 34, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
37 8 0.04
38 23 0.13
39 32 0.18
40 30 0.17
41 61 0.34
42 2 0.01
43 22 0.12
44 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (41 bp):
ACAAACGCCGCTATAGACTCATACTTTAGTGGCGTTTTTAT
Found at i:39360 original size:38 final size:40
Alignment explanation
Indices: 39268--39433 Score: 148
Period size: 39 Copynumber: 4.2 Consensus size: 40
39258 TACTAGTACG
*
39268 TTAGTGGCGTTTTTATACAAACGACGCTATAGACTCATACT
1 TTAGTGGCGTTTTTATGCAAACGACGC-ATAGACTCATACT
* *
39309 TTAGTGGCG-TTTTATGCAAACGTCGC-TAGATTTC-TAC-
1 TTAGTGGCGTTTTTATGCAAACGACGCATAGA-CTCATACT
* * *
39346 TTAGTGACGTTTTTATGCAAATGCCGCTATAGACTCATACT
1 TTAGTGGCGTTTTTATGCAAACGACGC-ATAGACTCATACT
* * *
39387 TTA-TGGCG-TTTTATACAAACGCCGCTATACACT-AGTACT
1 TTAGTGGCGTTTTTATGCAAACGACGC-ATAGACTCA-TACT
*
39426 CTAGTGGC
1 TTAGTGGC
39434 ATTTCTGTTT
Statistics
Matches: 105, Mismatches: 12, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
37 8 0.08
38 23 0.22
39 32 0.30
40 30 0.29
41 12 0.11
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (40 bp):
TTAGTGGCGTTTTTATGCAAACGACGCATAGACTCATACT
Found at i:39374 original size:78 final size:77
Alignment explanation
Indices: 39268--39413 Score: 229
Period size: 78 Copynumber: 1.9 Consensus size: 77
39258 TACTAGTACG
* * *
39268 TTAGTGGCGTTTTTATACAAACGACGCTATAGACTCATACTTTAGTGGCGTTTTATGCAAACGTC
1 TTAGTGACGTTTTTATACAAACGACGCTATAGACTCATACTTTA-TGGCGTTTTATACAAACGCC
39333 GCTAGATTTCTAC
65 GCTAGATTTCTAC
* * *
39346 TTAGTGACGTTTTTATGCAAATGCCGCTATAGACTCATACTTTATGGCGTTTTATACAAACGCCG
1 TTAGTGACGTTTTTATACAAACGACGCTATAGACTCATACTTTATGGCGTTTTATACAAACGCCG
39411 CTA
66 CTA
39414 TACACTAGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 22 0.35
78 40 0.65
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (77 bp):
TTAGTGACGTTTTTATACAAACGACGCTATAGACTCATACTTTATGGCGTTTTATACAAACGCCG
CTAGATTTCTAC
Found at i:41750 original size:21 final size:21
Alignment explanation
Indices: 41712--41752 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
41702 CCTATGGAGC
* *
41712 AGAGAAGCAGAGAGAGCAACG
1 AGAGAAGCAGAAAAAGCAACG
*
41733 AGAGAAGTAGAAAAAGCAAC
1 AGAGAAGCAGAAAAAGCAAC
41753 AACATTTCAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.12, G:0.32, T:0.02
Consensus pattern (21 bp):
AGAGAAGCAGAAAAAGCAACG
Done.