Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004306.1 Hibiscus syriacus cultivar Beakdansim tig00009442_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: 61167
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3331 original size:62 final size:61
Alignment explanation
Indices: 3197--3340 Score: 141
Period size: 62 Copynumber: 2.4 Consensus size: 61
3187 CGAAGCGTAG
* * * * *
3197 GAGCCTACTTAAGGGGGTGCCTCAGGTCCATAAGGTCTCACACTAGGCTCATTGGTCGTAG
1 GAGCCTACCTAAAGGGGTGCCTCAGGTCCATAAGGTCTCACACTAGGCTCATTGGGCCTAA
* * * *
3258 GAGCC-ATCCTAAAGTGGTGCCTTAGGATCCATAAGGTCTTACCCTAGGC-CGATTGGGCCTAA
1 GAGCCTA-CCTAAAGGGGTGCCTCAGG-TCCATAAGGTCTCACACTAGGCTC-ATTGGGCCTAA
* *
3320 TAGCCTACCT-AAGGGTTGCCT
1 GAGCCTACCTAAAGGGGTGCCT
3341 TAATTCTATA
Statistics
Matches: 67, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
60 1 0.01
61 30 0.45
62 35 0.52
63 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.25
Consensus pattern (61 bp):
GAGCCTACCTAAAGGGGTGCCTCAGGTCCATAAGGTCTCACACTAGGCTCATTGGGCCTAA
Found at i:8367 original size:130 final size:130
Alignment explanation
Indices: 8180--8437 Score: 331
Period size: 130 Copynumber: 2.0 Consensus size: 130
8170 GTTATGTTAC
* * * * ** * *
8180 AATTAGGATTATATAACAAGTTGATTTCAATGAGTTGCTTTTGATGTTATTATTGGATGCTTGTT
1 AATTAGGACTACATAACAAGTTAATTTCAATGACTTGCTTTTGATGTTAAAAATGGATGCTTGCT
* * * * * *
8245 TTGTTGACATACATACCTCTCAG-AGTTCAAAAAGGGTGTAGCATCCAAATTTTGTAGTGTGTTG
66 TTGATGACATACATACCTATCAGAACTT-AAAAACGATGTAACATCCAAATTTTGTAGTGTGTTG
8309 A
130 A
*
8310 AATTAGGACTACATAACAAGTTAATTTCAGTGACTTAG-TTTTGATGTTAAAAATGGATGCTTGC
1 AATTAGGACTACATAACAAGTTAATTTCAATGACTT-GCTTTTGATGTTAAAAATGGATGCTTGC
* *
8374 TTTGATGACATACATACCTATTAGAACTTAAAAACGATGTAACATTCAAATTTTGTAGTGTGTT
65 TTTGATGACATACATACCTATCAGAACTTAAAAACGATGTAACATCCAAATTTTGTAGTGTGTT
8438 ACCATTATGA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
130 105 0.96
131 4 0.04
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (130 bp):
AATTAGGACTACATAACAAGTTAATTTCAATGACTTGCTTTTGATGTTAAAAATGGATGCTTGCT
TTGATGACATACATACCTATCAGAACTTAAAAACGATGTAACATCCAAATTTTGTAGTGTGTTGA
Found at i:8705 original size:2 final size:2
Alignment explanation
Indices: 8698--8747 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
8688 GTTTGATGAC
8698 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
8740 AT AT AT AT
1 AT AT AT AT
8748 GAGTTTAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9312 original size:18 final size:19
Alignment explanation
Indices: 9272--9309 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9262 TGGTTCACGA
*
9272 AATGTAAGATTTCCAGTGGG
1 AATGTAAGATTACCAG-GGG
9292 AATGTAAGATTACCAGGG
1 AATGTAAGATTACCAGGG
9310 AATAGGATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.34, C:0.11, G:0.29, T:0.26
Consensus pattern (19 bp):
AATGTAAGATTACCAGGGG
Found at i:9489 original size:30 final size:30
Alignment explanation
Indices: 9431--9490 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
9421 ATTGTCCTTA
* *
9431 TTATATATTTTTTTAACAAGTTGGAAATAT
1 TTATATATTTTTTTAACAAATTGAAAATAT
9461 TTATATATTTTTTT-ACAAAATTGAAAATAT
1 TTATATATTTTTTTAAC-AAATTGAAAATAT
9491 AAAAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (30 bp):
TTATATATTTTTTTAACAAATTGAAAATAT
Found at i:12710 original size:17 final size:17
Alignment explanation
Indices: 12688--12723 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12678 TCAAAGTATG
12688 ACTTTTAGAAAAAGTTA
1 ACTTTTAGAAAAAGTTA
**
12705 ACTTTTAGTCAAAGTTA
1 ACTTTTAGAAAAAGTTA
12722 AC
1 AC
12724 GGTTAACGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (17 bp):
ACTTTTAGAAAAAGTTA
Found at i:22479 original size:12 final size:12
Alignment explanation
Indices: 22464--22529 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
22454 GTTATTTAAA
22464 CGGGTATTGGGC
1 CGGGTATTGGGC
*
22476 CGGGTATTGGGT
1 CGGGTATTGGGC
* *
22488 CGAGTATTGGGT
1 CGGGTATTGGGC
22500 C-GGTATTGGGC
1 CGGGTATTGGGC
* *
22511 CGGGAATCGGGC
1 CGGGTATTGGGC
22523 CGGGTAT
1 CGGGTAT
22530 ATATATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 9 0.20
12 37 0.80
ACGTcount: A:0.12, C:0.15, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:22494 original size:24 final size:24
Alignment explanation
Indices: 22467--22529 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
22457 ATTTAAACGG
*
22467 GTATTGGGCCGGGTATTGGGTCGA
1 GTATTGGGCCGGGTATTGGGCCGA
* *
22491 GTATTGGGTC-GGTATTGGGCCGG
1 GTATTGGGCCGGGTATTGGGCCGA
* *
22514 GAATCGGGCCGGGTAT
1 GTATTGGGCCGGGTAT
22530 ATATATATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.13, C:0.14, G:0.46, T:0.27
Consensus pattern (24 bp):
GTATTGGGCCGGGTATTGGGCCGA
Found at i:22534 original size:2 final size:2
Alignment explanation
Indices: 22527--22606 Score: 64
Period size: 2 Copynumber: 43.0 Consensus size: 2
22517 TCGGGCCGGG
* * * * *
22527 TA TA TA TA TA TT TA AA T- TA AA TA TA AA TA TA TA T- TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
22566 TA AA T- TA T- TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22605 TA
1 TA
22607 ATTATTTTTA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
1 6 0.10
2 54 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:35301 original size:131 final size:132
Alignment explanation
Indices: 34987--35334 Score: 545
Period size: 132 Copynumber: 2.6 Consensus size: 132
34977 ATTTTAAGAC
* * *
34987 AGAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATTCCTTAAAGCAGAC
1 AGAAAATCATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* * *
35052 ATTTATTACTCCAATCGAAATGAAGAGATATCAATATTTTGTCTTAAAGAATCAATGTTGATTCG
66 ATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTAGTCTTAAAGAATCAATATTGATTCG
35117 AG
131 AG
* * *
35119 AGAAAACCATAATATATAATTATTTCCAATTGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
1 AGAAAATCATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
* *
35184 ATTTATTACTCCAATCGAAACGAAGAGATATCACTATTTAGTCTTAAA-ATTCAATATTGATTCG
66 ATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTAGTCTTAAAGAATCAATATTGATTCG
35248 AG
131 AG
* * * *
35250 AGAAAATTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGTCTTTAAGCAATC
1 AGAAAATCATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
*
35315 ATTTATTACTCCAACCGAAA
66 ATTTATTACTCCAATCGAAA
35335 TGAAAAGGTA
Statistics
Matches: 197, Mismatches: 19, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
131 93 0.47
132 104 0.53
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (132 bp):
AGAAAATCATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTC
ATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTAGTCTTAAAGAATCAATATTGATTCG
AG
Found at i:38752 original size:118 final size:118
Alignment explanation
Indices: 38544--38761 Score: 312
Period size: 118 Copynumber: 1.8 Consensus size: 118
38534 TCTGTGCCTA
* * * * * *
38544 TGAACTATTGGTTTTATGTAGACATGACAGTCATGTATGTCATCAATCGGTTGCCAGCAAAGGTG
1 TGAACTATTGGTTTTATATAGACATGAAAATAATGTACGTCATCAATCGGTTGCCAACAAAGGTG
*
38609 TTGTAAGGCATTGTCCCATTTGAAAAGTTATTTTATAAGAAGCCAGATTATAG
66 TTGTAAGGCATTGTCCCATGTGAAAAGTTATTTTATAAGAAGCCAGATTATAG
* * *
38662 TGAACTATTGGTTTTATATAGCCATGAAAATAATGTACGTCATCAATTGGTTTCCAACAAAGGTG
1 TGAACTATTGGTTTTATATAGACATGAAAATAATGTACGTCATCAATCGGTTGCCAACAAAGGTG
* *
38727 TTGTGAGGCGTT-TCCCCATGTGAAAAGTTATTTTA
66 TTGTAAGGCATTGT-CCCATGTGAAAAGTTATTTTA
38762 ATTGTTAATA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 1 0.01
118 86 0.99
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (118 bp):
TGAACTATTGGTTTTATATAGACATGAAAATAATGTACGTCATCAATCGGTTGCCAACAAAGGTG
TTGTAAGGCATTGTCCCATGTGAAAAGTTATTTTATAAGAAGCCAGATTATAG
Found at i:40963 original size:132 final size:131
Alignment explanation
Indices: 40797--41140 Score: 510
Period size: 131 Copynumber: 2.6 Consensus size: 131
40787 ACAGAAAATT
*
40797 ATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAGA-CATTTATT
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCA-ATCATTTATT
* * *
40861 ACTCCAATTGAAATGAAGAGATATCAATATTTTGTCTTAAAAAATCAATGTTGATTCGAGAGAAA
65 ACTCCAATCGAAATGAAGAGATATCAATATTTTATCTT-AAAAATCAATATTGATTCGAGAGAAA
40926 ACC
129 ACC
* * * *
40929 ATAATATCTAATTATTTCCAATTGAGAATAAATGATCTCTCATGCCTTAAAGCAATCATTTATTT
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATCATTTATTA
* * * *
40994 CTCCAATCGAAACGAAGAGATATCACTATTTTATCTTAAAATTCAATATTGATTCGAGAGAAAAT
66 CTCCAATCGAAATGAAGAGATATCAATATTTTATCTTAAAAATCAATATTGATTCGAGAGAAAAC
*
41059 T
131 C
* * *
41060 ATAATAACTAATTATTTCCAATCGAGAATAAATGACCTCCCATGGCTTTAAGCAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATCATTTATTA
*
41125 CTCCAACCGAAATGAA
66 CTCCAATCGAAATGAA
41141 AAGGTATTAA
Statistics
Matches: 189, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
131 98 0.52
132 91 0.48
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (131 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATCATTTATTA
CTCCAATCGAAATGAAGAGATATCAATATTTTATCTTAAAAATCAATATTGATTCGAGAGAAAAC
C
Found at i:41113 original size:131 final size:132
Alignment explanation
Indices: 40789--41136 Score: 520
Period size: 132 Copynumber: 2.6 Consensus size: 132
40779 ATTTTAAGAC
*
40789 AGAAAATTATAATATCTAATTATTTTCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAGA-
1 AGAAAATTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCA-AT
* * * *
40853 CATTTATTACTCCAATTGAAATGAAGAGATATCAATATTTTGTCTTAAAAAATCAATGTTGATTC
65 CATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTTATCTTAAAAAATCAATATTGATTC
40918 GAG
130 GAG
** * * *
40921 AGAAAACCATAATATCTAATTATTTCCAATTGAGAATAAATGATCTCTCATGCCTTAAAGCAATC
1 AGAAAATTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATC
* * *
40986 ATTTATTTCTCCAATCGAAACGAAGAGATATCACTATTTTATCTT-AAAATTCAATATTGATTCG
66 ATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTTATCTTAAAAAATCAATATTGATTCG
41050 AG
131 AG
* * *
41052 AGAAAATTATAATAACTAATTATTTCCAATCGAGAATAAATGACCTCCCATGGCTTTAAGCAATC
1 AGAAAATTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATC
*
41117 ATTTATTACTCCAACCGAAA
66 ATTTATTACTCCAATCGAAA
41137 TGAAAAGGTA
Statistics
Matches: 192, Mismatches: 23, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
131 95 0.49
132 97 0.51
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (132 bp):
AGAAAATTATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGGCTTAAAGCAATC
ATTTATTACTCCAATCGAAACGAAGAGATATCAATATTTTATCTTAAAAAATCAATATTGATTCG
AG
Found at i:44521 original size:118 final size:118
Alignment explanation
Indices: 44313--44528 Score: 360
Period size: 118 Copynumber: 1.8 Consensus size: 118
44303 TCTATGCCTA
* * *
44313 TGAACTATTAGTTTTATGTAGCCATGACAGTCGTGTATGTCATCAATCGGTTGCCAGCAAAGGTG
1 TGAACTATTAGTTTTATATAGCCATGACAATCGTGTATGTCATCAATCGGTTGCCAACAAAGGTG
*
44378 TTGTGAGGCGTTGCCCCATTTGAAAAGTTATTTGGTAAGAAGCCAGATTATAG
66 TTGTGAGGCGTTGCCCCATGTGAAAAGTTATTTGGTAAGAAGCCAGATTATAG
* * *
44431 TGAACTATTGGTTTTATATAGCCATGACAATTGTGTATGTCATCAATTGGTTGCCAACAAAGGTG
1 TGAACTATTAGTTTTATATAGCCATGACAATCGTGTATGTCATCAATCGGTTGCCAACAAAGGTG
*
44496 TTGTGAGGCGTTTCCCCATGTGAAAAGTTATTT
66 TTGTGAGGCGTTGCCCCATGTGAAAAGTTATTT
44529 AATTGTTAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
118 90 1.00
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (118 bp):
TGAACTATTAGTTTTATATAGCCATGACAATCGTGTATGTCATCAATCGGTTGCCAACAAAGGTG
TTGTGAGGCGTTGCCCCATGTGAAAAGTTATTTGGTAAGAAGCCAGATTATAG
Found at i:46396 original size:131 final size:131
Alignment explanation
Indices: 46170--46508 Score: 552
Period size: 131 Copynumber: 2.6 Consensus size: 131
46160 AAAGAAAATG
* *
46170 ATAATATCTGATTATTTCCAATCGAGAATAATTGACCTCTCATGCCTTAAAGCAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
* ** * *
46235 CTCCAATCGAAATGAAGAGATATCACTATTTTGTCTTAAAAATCAATGTTCATTCGAGAGAAAAC
66 CTCCAATCGAAACGAAGAGATATCACTATTTCATCTTAAAAATCAATATTCATTCGAGAGAAAAA
46300 C
131 C
* *
46301 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
* *
46366 CTCCAATCGAAACGAAGAGATATCACTATTTCATCTTAAAATTCAATATTGATTCGAGAGAAAAA
66 CTCCAATCGAAACGAAGAGATATCACTATTTCATCTTAAAAATCAATATTCATTCGAGAGAAAAA
*
46431 T
131 C
*
46432 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTTAAGCAATCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
*
46497 CTCCAACCGAAA
66 CTCCAATCGAAA
46509 TGAAAATGTA
Statistics
Matches: 192, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 192 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (131 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAATCATTTATTA
CTCCAATCGAAACGAAGAGATATCACTATTTCATCTTAAAAATCAATATTCATTCGAGAGAAAAA
C
Found at i:47026 original size:62 final size:61
Alignment explanation
Indices: 46960--47096 Score: 152
Period size: 62 Copynumber: 2.2 Consensus size: 61
46950 AACTAATCAG
* * * * *
46960 GGACTAAAATGAAATAACATA-AAAGCAACATG-CAAAAATTGAAATAAAACAACATGCAAATA
1 GGACTAAAAT-AAA-AACAAACAAAGCAACATGTCAAAAATTAAAACAAAACAAAACGCAAA-A
* * *
47022 GGACTAAAATAAAAACAAACAAATCATCATGTCAAAAATTAAAACAAAATAAAACGCAAAA
1 GGACTAAAATAAAAACAAACAAAGCAACATGTCAAAAATTAAAACAAAACAAAACGCAAAA
47083 GTGACTAAAATAAA
1 G-GACTAAAATAAA
47097 CATTTTTAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 5 0.08
61 14 0.22
62 45 0.70
ACGTcount: A:0.61, C:0.13, G:0.09, T:0.16
Consensus pattern (61 bp):
GGACTAAAATAAAAACAAACAAAGCAACATGTCAAAAATTAAAACAAAACAAAACGCAAAA
Found at i:47891 original size:21 final size:21
Alignment explanation
Indices: 47865--47904 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
47855 GAACCTAAGG
47865 CCTAAAC-CACCTAAAAAGCTC
1 CCTAAACAC-CCTAAAAAGCTC
*
47886 CCTAAAGACCCTAAAAAGC
1 CCTAAACACCCTAAAAAGC
47905 CCTTTCAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.45, C:0.35, G:0.07, T:0.12
Consensus pattern (21 bp):
CCTAAACACCCTAAAAAGCTC
Found at i:48675 original size:3 final size:3
Alignment explanation
Indices: 48658--48712 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
48648 ATGCACAAAT
* **
48658 TAA TAA -AA GTAA TAA TAA TAG TAA TAA TGG TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
48703 AAA TAA TAA T
1 TAA TAA TAA T
48713 GTCGGGACGA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 38 0.90
4 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:50904 original size:23 final size:23
Alignment explanation
Indices: 50869--50916 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
50859 ATCAAGTACA
*
50869 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
50892 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
50915 AT
1 AT
50917 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:51728 original size:182 final size:181
Alignment explanation
Indices: 51349--51803 Score: 707
Period size: 182 Copynumber: 2.5 Consensus size: 181
51339 ACTTTTTTAC
* * *
51349 TACCGGTTTTGTCATTTCGAGAGCGATTTTGTCATATTTTTACATGTTATATTGTTATGGATCGA
1 TACC-GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
** *
51414 TACATTTTTATAAAGTATCGACA-TTTATTGGAGCTATAACTTCTTTTCTTTTAAATTCCAAAAA
65 TACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTCTTCTCTTTTAAATTCCAAAAA
** * *
51478 TGTTTATACTTATAATAAAATATCGACACTTTCAACATATCTGGTAGCTCTT
130 TGTCGATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCTCTT
51530 TACCGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 TACCG-TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* *
51595 TACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTCTTCTCTTTTAAATTTCAAAAG
65 TACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTCTTCTCTTTTAAATTCCAAAAA
*
51660 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAG-TGCTT
130 TGTCGATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCT-CTT
** * *
51712 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGTTCGA
1 TACC-GTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
51777 TACATTTTTATAAAGTATCGACACTTT
65 TACATTTTTATAAAGTATCGACACTTT
51804 CAATATATCC
Statistics
Matches: 253, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
180 1 0.00
181 84 0.33
182 167 0.66
183 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (181 bp):
TACCGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
ACATTTTTATAAAGTATCGACACTTTATTAAAGCTATAACTTCTTCTCTTTTAAATTCCAAAAAT
GTCGATACTTATAATAAAATATCGACACTATCAACATATCCGGTAGCTCTT
Found at i:51895 original size:93 final size:93
Alignment explanation
Indices: 51737--51933 Score: 378
Period size: 93 Copynumber: 2.1 Consensus size: 93
51727 TTATAGACCG
*
51737 GTTTTGTCA-TTTTTTTACCTGTTATATTGTTATGGTTCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
51801 TTTCAATATATCCGGTAGCGCTTTACCT
66 TTTCAATATATCCGGTAGCGCTTTACCT
51829 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
51894 TTTCAATATATCCGGTAGCGCTTTACCT
66 TTTCAATATATCCGGTAGCGCTTTACCT
51922 GTTTTGTCATTT
1 GTTTTGTCATTT
51934 ATAGACCGGT
Statistics
Matches: 103, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 9 0.09
93 94 0.91
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.48
Consensus pattern (93 bp):
GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
TTTCAATATATCCGGTAGCGCTTTACCT
Found at i:51966 original size:112 final size:113
Alignment explanation
Indices: 51829--52032 Score: 365
Period size: 112 Copynumber: 1.8 Consensus size: 113
51819 CGCTTTACCT
*
51829 GTTTTGTCATTTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACAC
*
51894 TTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
66 TTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
51942 GTTTTGTCA-TTTTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACAC
1 GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACAC
* *
52006 TTTCAATATATTCAGTAGCGTTTTACC
66 TTTCAATATATCCAGTAGCGCTTTACC
52033 GTTATATTTT
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
112 78 0.90
113 9 0.10
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (113 bp):
GTTTTGTCATTTTTTTTACCTGTTATATTATTATGGATCGATACATTTTTATAAAGTATCGACAC
TTTCAATATATCCAGTAGCGCTTTACCTGTTTTGTCATTTATAGACCG
Found at i:54825 original size:12 final size:12
Alignment explanation
Indices: 54808--54833 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54798 ATAAAAGTAA
54808 AAACATAAAAAT
1 AAACATAAAAAT
54820 AAACATAAAAAT
1 AAACATAAAAAT
54832 AA
1 AA
54834 TTTTATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACATAAAAAT
Found at i:54841 original size:20 final size:19
Alignment explanation
Indices: 54817--54863 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
54807 AAAACATAAA
54817 AATAAACATAAAAATAATTT
1 AATAAA-ATAAAAATAATTT
* *
54837 TATAATAATAAAATTAATTT
1 AATAA-AATAAAAATAATTT
54857 AATAAAA
1 AATAAAA
54864 AATAAAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 20 0.87
21 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AATAAAATAAAAATAATTT
Found at i:57098 original size:74 final size:74
Alignment explanation
Indices: 56977--57131 Score: 301
Period size: 74 Copynumber: 2.1 Consensus size: 74
56967 TCAACAAACG
56977 ATCAACATCTGAAATTAACTCGGTAGAAATAGATGGACACAGCTGCCTAGGTAGCACCTTCACTT
1 ATCAACATCTGAAATTAACTCGGTAGAAATAGATGGACACAGCTGCCTAGGTAGCACCTTCACTT
57042 CACTACTAC
66 CACTACTAC
57051 ATCAACATCTGAAATTAACTCGGTAGAAATAGATGGACACAGCTGCCTAGGTAGCACCTTCACTT
1 ATCAACATCTGAAATTAACTCGGTAGAAATAGATGGACACAGCTGCCTAGGTAGCACCTTCACTT
57116 CACTACTAC
66 CACTACTAC
*
57125 GTCAACA
1 ATCAACA
57132 ATTTCTTTTG
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (74 bp):
ATCAACATCTGAAATTAACTCGGTAGAAATAGATGGACACAGCTGCCTAGGTAGCACCTTCACTT
CACTACTAC
Found at i:60019 original size:3 final size:3
Alignment explanation
Indices: 60004--60068 Score: 93
Period size: 3 Copynumber: 23.0 Consensus size: 3
59994 TTTGGACCTG
*
60004 TAA TAA TAT TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60049 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
60069 ATGCAAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 8 0.14
3 48 0.86
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:60466 original size:121 final size:123
Alignment explanation
Indices: 60250--60919 Score: 788
Period size: 120 Copynumber: 5.6 Consensus size: 123
60240 AAAGTTAAAC
* * * *
60250 AAGTTATTCAGATTATGAACTTATTCTTCCTCTTCAGATGAG--CTTCTTATTACGAACTCTATA
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
* * * * * **
60313 T-AAAATGGCTTTGCTGCTCTACCTCCTTCTGCGATGGAGTCAATCAAAATATTGAAT
66 TGAAAATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
* * *
60370 AAGTTCTTCAGATTATGAAC-T-TTCTTTCTCTTCAGATGAGTTCTTTTTATTAC-AACTCTATC
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
* * * * *
60432 TTGGAAATGGCTTTATTGCTCTATCTCCTTCTGCGATAGAGTCAATC-AAAGATTGAAT
66 -TGAAAATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
* *
60490 AAGTTCTTCAGACTATGAACTTTTTCTT--TCTTCAGATGA-TTATTCTTATTACGAACTCTATC
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
* * * *
60552 TGAAAAT-G-TTGAGTGCTCTATCTCCTTCTGCGATAAAGTTAAGCAAAAGGTTGAAT
66 TGAAAATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
* * *
60608 AAG-TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGA-TTCTTCTTATTACAAACTTTGTC
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
* * * * * * *
60671 TGTAAATATTGATGT--TG-TTTATCTCCTTCTGCGATAAAATCAAGCGAAAGGTTGAAC
66 TG-AAA-ATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
* * *
60728 ATGTTCTTC-GACTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTTATTACGAACTTTATC
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
* *
60792 TGGAAATGGATATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGG-TGAAT
66 TGAAAATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
* *
60849 AAG-TCTTCAGACTATGAACTTCTTCTACCTCTTCAGATGAG-TCTTCTTATTATGAACTCTATC
1 AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
60912 TGAAAATG
66 TGAAAATG
60920 TTGATCCATC
Statistics
Matches: 480, Mismatches: 50, Indels: 40
0.84 0.09 0.07
Matches are distributed among these distances:
117 54 0.11
118 32 0.07
119 64 0.13
120 183 0.38
121 110 0.23
122 36 0.08
123 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (123 bp):
AAGTTCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTACGAACTCTATC
TGAAAATGGATTTACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAAT
Found at i:60660 original size:238 final size:240
Alignment explanation
Indices: 60247--60912 Score: 784
Period size: 238 Copynumber: 2.8 Consensus size: 240
60237 GCTAAAGTTA
* * *
60247 AACAAGTTATTCAGATTATGAACTTATTCTTCCTCTTCAGATGA-GCTTCTTATTACGAACTCTA
1 AACAAGTTCTTCAGACTATGAACTTATTCTT-CTCTTCAGATGATTCTTCTTATTACGAACTCTA
* * * * * **
60311 TAT-AAAATGGCTTTG-CTGCTCTACCTCCTTCTGCGATGGAGTCAATCAAAATATTGAATAAGT
65 TCTGAAAATGG-ATTGACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAG-
* * *
60374 TCTTCAGATTATGAAC-T-TTCTTTCTCTTCAGATGAGTTCTTTTTATTACAACTCTATCTTGGA
128 TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGA-TTCTTCTTATTACAACTCTATCTTGGA
* * * *
60437 AATGGCTT-TATTGCTCTATCTCCTTCTGCGATAGAGTCAATC-AAAGATTG
192 AAT--ATTATATTG-TCTATCTCCTTCTGCGATAAAATCAAGCGAAAGATTG
* * *
60487 AATAAGTTCTTCAGACTATGAACTTTTTCTT-TCTTCAGATGATTATTCTTATTACGAACTCTAT
1 AACAAGTTCTTCAGACTATGAACTTATTCTTCTCTTCAGATGATTCTTCTTATTACGAACTCTAT
* * *
60551 CTGAAAAT-G-TTGAGTGCTCTATCTCCTTCTGCGATAAAGTTAAGCAAAAGGTTGAATAAGTCT
66 CTGAAAATGGATTGACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTCT
* * *
60614 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGATTCTTCTTATTACAAACTTTGTC-TGTAAAT
131 TCAGACTATGAACTTCTTCTTCCTCTTCAGATGATTCTTCTTATTAC-AACTCTATCTTGGAAAT
* * *
60678 ATTGATGTTGTTTATCTCCTTCTGCGATAAAATCAAGCGAAAGGTTG
195 ATT-ATATTGTCTATCTCCTTCTGCGATAAAATCAAGCGAAAGATTG
* * * *
60725 AACATGTTCTTC-GACTATGAACTTCTTCTTCCTCTTCATATGAGTTCTTCTTATTACGAACTTT
1 AACAAGTTCTTCAGACTATGAACTTATTCTT-CTCTTCAGATGA-TTCTTCTTATTACGAACTCT
*
60789 ATCTGGAAATGGATAT-ACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGG-TGAATAAG
64 ATCTGAAAATGGAT-TGACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAG
* * *
60852 TCTTCAGACTATGAACTTCTTCTACCTCTTCAGATGAGTCTTCTTATTATGAACTCTATCT
128 TCTTCAGACTATGAACTTCTTCTTCCTCTTCAGATGATTCTTCTTATTA-CAACTCTATCT
60913 GAAAATGTTG
Statistics
Matches: 366, Mismatches: 43, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
236 2 0.01
237 59 0.16
238 90 0.25
239 55 0.15
240 59 0.16
241 63 0.17
242 37 0.10
243 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (240 bp):
AACAAGTTCTTCAGACTATGAACTTATTCTTCTCTTCAGATGATTCTTCTTATTACGAACTCTAT
CTGAAAATGGATTGACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAAAAGGTTGAATAAGTCT
TCAGACTATGAACTTCTTCTTCCTCTTCAGATGATTCTTCTTATTACAACTCTATCTTGGAAATA
TTATATTGTCTATCTCCTTCTGCGATAAAATCAAGCGAAAGATTG
Done.