Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001526.1 Hibiscus syriacus cultivar Beakdansim tig00002992_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: 102155
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:10889 original size:45 final size:45
Alignment explanation
Indices: 10825--10928 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
10815 GAATGTAAAA
10825 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
10870 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
10915 GAGCAGAGCTAATT
1 GAGCAGAGCTAATT
10929 GATAGGTAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (45 bp):
GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
Found at i:12625 original size:106 final size:106
Alignment explanation
Indices: 12477--12686 Score: 341
Period size: 106 Copynumber: 2.0 Consensus size: 106
12467 ACAAATACAA
*
12477 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTGAATCTTAAAATATGA
1 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
* *
12542 TTTAATAAATTTAAACCTTGAAATAAAATCTATTAATTTAG
66 TCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTTAG
*
12583 TAGTTCT-TTAATAAAAAAATTATTCTTTCGCAATTTTTTCAATAAATTTAAATCTTAAAATATG
1 TAGTTCTCTT-ATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATG
* * *
12647 ATCTAATACATTTAAATCTTCAAATAAGATCTATTAATTT
65 ATCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTT
12687 GGCTAAATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 2 0.02
106 94 0.98
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (106 bp):
TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
TCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTTAG
Found at i:12659 original size:28 final size:28
Alignment explanation
Indices: 12623--12679 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
12613 CAATTTTTTC
*
12623 AATAAATTTAAATCTTAAAATATGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
* *
12651 AATACATTTAAATCTTCAAATAAGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
12679 A
1 A
12680 TTAATTTGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (28 bp):
AATAAATTTAAATCTTAAAATAAGATCT
Found at i:17246 original size:81 final size:81
Alignment explanation
Indices: 16992--17263 Score: 433
Period size: 80 Copynumber: 3.4 Consensus size: 81
16982 TGTAAGTCCT
*
16992 TACGGACCTAAGGATAT-CTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCC-TTTGCTGT
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGCTGT
*
17055 GTGCATAAGGTAACCC
66 GTGCTTAAGGTAACCC
* ** *
17071 TACAGATCTAAGGATGCCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTT-CCTTTTGTTGT
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGCTGT
17135 GTGCTTAAGGTAACCC
66 GTGCTTAAGGTAACCC
* * * *
17151 TACGAATCTAAGGATGTCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGCTGT
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGCTGT
17216 GTGCTTAAGGTAACCC
66 GTGCTTAAGGTAACCC
17232 TACGGATCTAAGGATATCCTTGGGTAGGCCCA
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCA
17264 TAGACCCCAA
Statistics
Matches: 175, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 15 0.09
80 105 0.60
81 55 0.31
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (81 bp):
TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTTGCTGT
GTGCTTAAGGTAACCC
Found at i:20416 original size:17 final size:17
Alignment explanation
Indices: 20394--20429 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
20384 CACTTCTCCC
20394 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
20411 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
20428 CT
1 CT
20430 GCTCCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.36
Consensus pattern (17 bp):
CTTTAAAACATTTAACA
Found at i:22711 original size:21 final size:20
Alignment explanation
Indices: 22679--22725 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
22669 GGGGTATCGA
22679 TTCCCCTAGGGGGGAATCAG
1 TTCCCCTAGGGGGGAATCAG
22699 TTCCCCTAGGGGGGAATCAG
1 TTCCCCTAGGGGGGAATCAG
22719 TTCCCCT
1 TTCCCCT
22726 TCAAAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
TTCCCCTAGGGGGGAATCAG
Found at i:26614 original size:22 final size:21
Alignment explanation
Indices: 26573--26612 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
26563 GAGTTTATTT
*
26573 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
26594 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
26613 ACTATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:29284 original size:35 final size:34
Alignment explanation
Indices: 29240--29347 Score: 94
Period size: 35 Copynumber: 3.2 Consensus size: 34
29230 AATGAATATC
29240 TATCTAAATGACTTTAGTGGTGAATAAAATGTAAA
1 TATCTAAATGACTTTAGTGGTGAAT-AAATGTAAA
** ** ** **
29275 TATCTAAATGACCGTAGTGGCAAATGCA--TATC
1 TATCTAAATGACTTTAGTGGTGAATAAATGTAAA
**
29307 TATCTAAACAACTTTAGTGGTGAATGAAATGTAAA
1 TATCTAAATGACTTTAGTGGTGAAT-AAATGTAAA
29342 TATCTA
1 TATCTA
29348 TGACCCTAGT
Statistics
Matches: 52, Mismatches: 18, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
32 21 0.40
33 1 0.02
34 1 0.02
35 29 0.56
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (34 bp):
TATCTAAATGACTTTAGTGGTGAATAAATGTAAA
Found at i:29389 original size:65 final size:65
Alignment explanation
Indices: 29205--29399 Score: 212
Period size: 67 Copynumber: 2.9 Consensus size: 65
29195 TAAATAAAAA
* * * * * *
29205 AAATATCTATATAATCCTAGCGACGAATGAATATCTATCTAAATGACTTTAGTGGTGAATAAAAT
1 AAATATCTA-ATGACCCTAGTGCCGAATG-ATATCTATCTAAATAACTTTAGTGGTGAATGAAAT
29270 GT
64 GT
* * * *
29272 AAATATCTAAATGACCGTAGTGGCAAATGCATATCTATCTAAACAACTTTAGTGGTGAATGAAAT
1 AAATATCT-AATGACCCTAGTGCCGAATG-ATATCTATCTAAATAACTTTAGTGGTGAATGAAAT
29337 GT
64 GT
* * *
29339 AAATATCT-ATGACCCTAGTGCCGAATGAGTATATATCTAAGTAACCTTAGTGGTGAGATGA
1 AAATATCTAATGACCCTAGTGCCGAATGA-TATCTATCTAAATAACTTTAGTGGTGA-ATGA
29400 TGAATACATA
Statistics
Matches: 108, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
64 1 0.01
65 39 0.36
66 4 0.04
67 63 0.58
68 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (65 bp):
AAATATCTAATGACCCTAGTGCCGAATGATATCTATCTAAATAACTTTAGTGGTGAATGAAATGT
Found at i:30750 original size:15 final size:16
Alignment explanation
Indices: 30730--30759 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30720 GTAAAGACAG
30730 TAAATAAAA-AATAAA
1 TAAATAAAATAATAAA
30745 TAAATAAAATAATAA
1 TAAATAAAATAATAA
30760 GAAAATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
TAAATAAAATAATAAA
Found at i:31285 original size:24 final size:24
Alignment explanation
Indices: 31241--31287 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31231 ATAAAGAACC
*
31241 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
31265 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
31288 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:34629 original size:14 final size:14
Alignment explanation
Indices: 34591--34638 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
34581 AGTAAAAGAG
*
34591 AGAAAAAAAGAAAA
1 AGAAAAAATGAAAA
** *
34605 AGTTAACATGAAAA
1 AGAAAAAATGAAAA
34619 AGAAAAAATGAATAA
1 AGAAAAAATGAA-AA
34634 AGAAA
1 AGAAA
34639 GAGAAAAGAA
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 19 0.73
15 7 0.27
ACGTcount: A:0.73, C:0.02, G:0.15, T:0.10
Consensus pattern (14 bp):
AGAAAAAATGAAAA
Found at i:34970 original size:11 final size:11
Alignment explanation
Indices: 34939--34963 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34929 AATTAATTAC
34939 AAAATAAAAAT
1 AAAATAAAAAT
34950 AAAATAAAAAT
1 AAAATAAAAAT
34961 AAA
1 AAA
34964 GAAAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:40126 original size:18 final size:18
Alignment explanation
Indices: 40105--40150 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 18
40095 TTTTCTTTTC
40105 TTTTGTTTTATTTAATCA
1 TTTTGTTTTATTTAATCA
40123 --TT-TTTTATTTAATCA
1 TTTTGTTTTATTTAATCA
40138 TTTTGTTTTATTT
1 TTTTGTTTTATTT
40151 CATCTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.52
16 2 0.08
17 2 0.08
18 8 0.32
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (18 bp):
TTTTGTTTTATTTAATCA
Found at i:41199 original size:2 final size:2
Alignment explanation
Indices: 41194--41240 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
41184 ATATACTTTA
*
41194 AT AT AT AT AT CT 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
41236 AT AT A
1 AT AT A
41241 GTGGAGTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42135 original size:70 final size:71
Alignment explanation
Indices: 42053--42192 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 71
42043 TTTATTATGG
42053 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTT-TCTAGACTATAGACTTAAT
1 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGACTATAGACTTAAT
*
42117 TAGGGA
66 CAGGGA
* *
42123 TACCAAATCCCATCATTGTAGGACCAATATAACTTGTATAGAGTTATCTAGACTATAGATTTAAT
1 TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGACTATAGACTTAAT
42188 CAGGG
66 CAGGG
42193 TAAGTGAATG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
70 44 0.67
71 22 0.33
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (71 bp):
TACCAAATCCCATCATAGTAGGACCAATATAACTTGTATAGAGTTATCTAGACTATAGACTTAAT
CAGGGA
Found at i:44205 original size:19 final size:21
Alignment explanation
Indices: 44181--44225 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
44171 TTTTATTGAA
44181 TTTTATT-CACTTTTAATT-T
1 TTTTATTGCACTTTTAATTAT
* *
44200 TTTTATTGCATTTTTATTTAT
1 TTTTATTGCACTTTTAATTAT
44221 TTTTA
1 TTTTA
44226 AAAAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 9 0.41
21 6 0.27
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTTATTGCACTTTTAATTAT
Found at i:47564 original size:11 final size:12
Alignment explanation
Indices: 47548--47606 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
47538 TTATTGTATC
47548 TCTTTCA-AATA
1 TCTTTCATAATA
47559 TCTTTCATAACTA
1 TCTTTCATAA-TA
* * *
47572 TATTTTTATTATCA
1 T-CTTTCATAAT-A
47586 TCTTTCA-AATA
1 TCTTTCATAATA
47597 TCTTTCATAA
1 TCTTTCATAA
47607 CTATATTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
11 15 0.41
12 6 0.16
13 8 0.22
14 8 0.22
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTTTCATAATA
Found at i:47574 original size:38 final size:38
Alignment explanation
Indices: 47534--47629 Score: 142
Period size: 38 Copynumber: 2.6 Consensus size: 38
47524 TGTGTATATA
*
47534 TATATTATT-GTATC-TCTTTCAAATATCTTTCATAAC
1 TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
*
47570 TATATTTTTATTATCATCTTTCAAATATCTTTCATAAC
1 TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
* *
47608 TATATTTTTATTATCATTTTTC
1 TATATTTTTAGTATCATCTTTC
47630 CATCTATCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 8 0.15
37 4 0.07
38 43 0.78
ACGTcount: A:0.29, C:0.15, G:0.01, T:0.55
Consensus pattern (38 bp):
TATATTTTTAGTATCATCTTTCAAATATCTTTCATAAC
Found at i:48042 original size:2 final size:2
Alignment explanation
Indices: 48037--48062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48027 CCATTTTTTC
48037 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
48063 TATCTCTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49916 original size:148 final size:149
Alignment explanation
Indices: 49648--49940 Score: 579
Period size: 148 Copynumber: 2.0 Consensus size: 149
49638 TACAATTAAT
49648 AAAACAAATAAATAACGGAAGAAAATTTGAATTTTAATGTTCACCTAAAACAAACGATAGATCCG
1 AAAACAAATAAATAACGGAAGAAAATTTGAATTTTAATGTTCACCTAAAACAAACGATAGATCCG
49713 TCCCTTATTGGAGACTTGTATTCTAAACCAATCACAAAATAAAAATTTTGAAAAAAAT-AAAAAC
66 TCCCTTATTGGAGACTTGTATTCTAAACCAATCACAAAATAAAAATTTTGAAAAAAATAAAAAAC
49777 TAATAGAAGAACTCTATTA
131 TAATAGAAGAACTCTATTA
49796 AAAACAAATAAATAACGGAAGAAAATTTGAATTTTAATGTTCACCTAAAACAAACGATAGATCCG
1 AAAACAAATAAATAACGGAAGAAAATTTGAATTTTAATGTTCACCTAAAACAAACGATAGATCCG
49861 TCCCTTATTGGAGACTTGTATTCTAAACCAATCACAAAATAAAAATTTTGAAAAAAATAAAAAAC
66 TCCCTTATTGGAGACTTGTATTCTAAACCAATCACAAAATAAAAATTTTGAAAAAAATAAAAAAC
49926 TAATAGAAGAACTCT
131 TAATAGAAGAACTCT
49941 GAAAAGAAGA
Statistics
Matches: 144, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 123 0.85
149 21 0.15
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.26
Consensus pattern (149 bp):
AAAACAAATAAATAACGGAAGAAAATTTGAATTTTAATGTTCACCTAAAACAAACGATAGATCCG
TCCCTTATTGGAGACTTGTATTCTAAACCAATCACAAAATAAAAATTTTGAAAAAAATAAAAAAC
TAATAGAAGAACTCTATTA
Found at i:50429 original size:60 final size:60
Alignment explanation
Indices: 50326--50472 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
50316 GAACATATGA
* *
50326 ATAGTC-AAGTGACCATTTTGTAACTTTTAATAGTCGAGAAACTCAACAAAACAACACCCT
1 ATAGTCGAAG-GATCATTTTGTAACTTTTAATAGTAGAGAAACTCAACAAAACAACACCCT
* * * * * *
50386 ATAGTCGAAGGATCATTTTGTAACTTTTAATATTA-AGGGAACTCACCAAAATAATATCCT
1 ATAGTCGAAGGATCATTTTGTAACTTTTAATAGTAGA-GAAACTCAACAAAACAACACCCT
**
50446 ATAGTCGGGGGATCATTTGTGT-ACTTT
1 ATAGTCGAAGGATCATTT-TGTAACTTT
50473 ACCCAAAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.01
60 67 0.91
61 6 0.08
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
ATAGTCGAAGGATCATTTTGTAACTTTTAATAGTAGAGAAACTCAACAAAACAACACCCT
Found at i:52478 original size:18 final size:19
Alignment explanation
Indices: 52457--52498 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
52447 TAATATTGAG
*
52457 TTATTATAA-AATATATTT
1 TTATTATAATAATATAATT
*
52475 TTATTATAATTATATAATT
1 TTATTATAATAATATAATT
52494 TTATT
1 TTATT
52499 TTTATTCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATAATAATATAATT
Found at i:53580 original size:123 final size:132
Alignment explanation
Indices: 53444--53739 Score: 348
Period size: 141 Copynumber: 2.2 Consensus size: 132
53434 TCATACTTAT
*
53444 TTTTAACCAATTATTGAA-TCG-AA-TAACCAATATGGTCTCTTGAGCA-T-T-A-ACAACTCAG
1 TTTTAATCAATTATTGAATTCGAAATTAA--AATATGGTCTCTTGAGCATTGTGAGACAACTCAG
*
53502 ATTATT-C-AAATT-A-TTAGATTGAAATCTAACCTTAAAGTGGAGACTTTAATTAATAACCTAT
64 ATTATTCCTAAATTAAGCTAGATTGAAATCTAACCTTAAAGTGGAGACTTTAATTAATAACCTAT
53563 TTAA
129 TTAA
53567 TTTTAATCAATTA-TGAATTCGAAATTAAAATATGGTCTCTTGAGCATTTAGGTGAGGGACAACT
1 TTTTAATCAATTATTGAATTCGAAATTAAAATATGGTCTCTTGAGCA-TT--GTGA--GACAACT
53631 CAGATTATTCCTTAAATTAGAGGGCCTAGATTGAAATCTAACCTTAAAGTGGAGACTTTAATTAA
61 CAGATTATTCC-TAAATTA-A--G-CTAGATTGAAATCTAACCTTAAAGTGGAGACTTTAATTAA
53696 TAACCTATTTAA
121 TAACCTATTTAA
53708 TTTTAATCAATTA-TGCAATTCGAGGAATTAAA
1 TTTTAATCAATTATTG-AATTCGA--AATTAAA
53740 TTGGAACCTC
Statistics
Matches: 147, Mismatches: 2, Indels: 27
0.84 0.01 0.15
Matches are distributed among these distances:
122 4 0.03
123 33 0.22
124 2 0.01
125 4 0.03
128 1 0.01
129 1 0.01
132 15 0.10
133 1 0.01
135 5 0.03
137 1 0.01
141 66 0.45
142 7 0.05
144 7 0.05
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (132 bp):
TTTTAATCAATTATTGAATTCGAAATTAAAATATGGTCTCTTGAGCATTGTGAGACAACTCAGAT
TATTCCTAAATTAAGCTAGATTGAAATCTAACCTTAAAGTGGAGACTTTAATTAATAACCTATTT
AA
Found at i:55262 original size:29 final size:29
Alignment explanation
Indices: 55220--55309 Score: 153
Period size: 29 Copynumber: 3.1 Consensus size: 29
55210 CCCGACCCGA
55220 GTGCTATTTTCGTAAATATTTTTAAAAGG
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
**
55249 GTGCTATTTTCGTAAATATTTTTAAAAAT
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
*
55278 GTGTTATTTTCGTAAATATTTTTAAAAGG
1 GTGCTATTTTCGTAAATATTTTTAAAAGG
55307 GTG
1 GTG
55310 TTAGTTTCAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (29 bp):
GTGCTATTTTCGTAAATATTTTTAAAAGG
Found at i:55943 original size:2 final size:2
Alignment explanation
Indices: 55936--55987 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
55926 GATTTGATAA
* * *
55936 AT AT AT AT GT TT AC 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
*
55978 AT AT AC AT AT
1 AT AT AT AT AT
55988 TTCACTGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56931 original size:22 final size:20
Alignment explanation
Indices: 56906--56948 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
56896 TCATGATGAG
56906 ATATGGAAGATAAAGATGGTTT
1 ATATGG-AGAT-AAGATGGTTT
*
56928 ATATGGATATAAGATGGTTT
1 ATATGGAGATAAGATGGTTT
56948 A
1 A
56949 AGTAATGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 3 0.15
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.35
Consensus pattern (20 bp):
ATATGGAGATAAGATGGTTT
Found at i:57248 original size:64 final size:63
Alignment explanation
Indices: 57114--57272 Score: 212
Period size: 64 Copynumber: 2.5 Consensus size: 63
57104 TTGTTCAGTG
* * * *
57114 TGTATCGATGCACAGGAAGTGCATCGATGCACCCCTTAAAATGGAAACATCGAATGCAATTGG
1 TGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGA
* * *
57177 TGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTA
1 TGTATCGATGCAT-AGGAAGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAATTGA
* *
57241 TGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGTATCGATGCATAGGAAGTGCATCGATGCAC
57273 ATGTTAAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 28 0.33
64 56 0.67
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (63 bp):
TGTATCGATGCATAGGAAGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGA
Found at i:57305 original size:20 final size:20
Alignment explanation
Indices: 57260--57317 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
57250 GCATGGGTAG
57260 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
57284 TGCGTCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
57304 TGCATCGATGCACT
1 TGCATCGATGCACT
57318 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:58635 original size:2 final size:2
Alignment explanation
Indices: 58617--58691 Score: 132
Period size: 2 Copynumber: 36.5 Consensus size: 2
58607 GAATACAATG
58617 TA TA TGA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58661 TA TA TA TA TA TA TA 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 T
58692 GTTTTGTTAT
Statistics
Matches: 71, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
2 67 0.94
3 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:58723 original size:31 final size:29
Alignment explanation
Indices: 58679--58738 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
58669 TATATATATA
*
58679 TATATATATATATGT-TTTGTTATATGAAT
1 TATATATATATATGTGTGTGTTA-ATGAAT
58708 TATATGATATGATATGTGTGTGTTAATGAAT
1 TATAT-ATAT-ATATGTGTGTGTTAATGAAT
58739 ATTGTATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 5 0.19
30 4 0.15
31 12 0.44
32 6 0.22
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (29 bp):
TATATATATATATGTGTGTGTTAATGAAT
Found at i:65049 original size:20 final size:20
Alignment explanation
Indices: 65024--65071 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
65014 CCTCAATCGC
*
65024 GTTGCGATTTTCTATTTCGA
1 GTTGCGATTTTCCATTTCGA
*
65044 GTTGCGATTTTCCATTTCGC
1 GTTGCGATTTTCCATTTCGA
65064 GTTGCGAT
1 GTTGCGAT
65072 AGTTGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (20 bp):
GTTGCGATTTTCCATTTCGA
Found at i:65365 original size:6 final size:6
Alignment explanation
Indices: 65349--65392 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
65339 TCTCGTCTCG
65349 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
65393 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:66669 original size:29 final size:29
Alignment explanation
Indices: 66632--66730 Score: 99
Period size: 29 Copynumber: 3.3 Consensus size: 29
66622 AATCATTCAA
* * * *
66632 GTATATAAAGTATTTTTTGATCAAAGTTG
1 GTATCTAAAGTATTTTTTGGTCAAAATAG
* *
66661 GTATCTAAACTTATCTTTTTGGTCAAAATAC
1 GTATCTAAA-GTAT-TTTTTGGTCAAAATAG
* *
66692 GTACCTAAAGTATTTTATGGTCAAAATAG
1 GTATCTAAAGTATTTTTTGGTCAAAATAG
*
66721 GTAGCTAAAG
1 GTATCTAAAG
66731 CAGGTTTCAA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 31 0.54
30 6 0.11
31 20 0.35
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (29 bp):
GTATCTAAAGTATTTTTTGGTCAAAATAG
Found at i:88858 original size:45 final size:45
Alignment explanation
Indices: 88794--88897 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
88784 GAATGTAAAA
88794 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
88839 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
1 GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
88884 GAGCAGAGCTAATT
1 GAGCAGAGCTAATT
88898 GATAGGTAGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.34
Consensus pattern (45 bp):
GAGCAGAGCTAATTTAAAATATATTATGAGTTTTACTTGGCTCAG
Found at i:89902 original size:21 final size:21
Alignment explanation
Indices: 89877--89924 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
89867 AGTGAACCGG
*
89877 CGGTTCAAACCGGTTTTCAGC
1 CGGTTCAAACCGATTTTCAGC
**
89898 CGGTTCACCCCGATTTTCAGC
1 CGGTTCAAACCGATTTTCAGC
89919 CGGTTC
1 CGGTTC
89925 TTTGCTCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.33, G:0.23, T:0.29
Consensus pattern (21 bp):
CGGTTCAAACCGATTTTCAGC
Found at i:90616 original size:106 final size:106
Alignment explanation
Indices: 90468--90677 Score: 341
Period size: 106 Copynumber: 2.0 Consensus size: 106
90458 ACAAATACAA
*
90468 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTGAATCTTAAAATATGA
1 TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
* *
90533 TTTAATAAATTTAAACCTTGAAATAAAATCTATTAATTTAG
66 TCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTTAG
*
90574 TAGTTCT-TTAATAAAAAAATTATTCTTTCGCAATTTTTTCAATAAATTTAAATCTTAAAATATG
1 TAGTTCTCTT-ATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATG
* * *
90638 ATCTAATACATTTAAATCTTCAAATAAGATCTATTAATTT
65 ATCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTT
90678 GACTAAAATT
Statistics
Matches: 96, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
105 2 0.02
106 94 0.98
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (106 bp):
TAGTTCTCTTATAAAAAAATTATTCTTTCACAATTTTTTCAATAAATTTAAATCTTAAAATATGA
TCTAATAAATTTAAACCTTCAAATAAAATCTATTAATTTAG
Found at i:90650 original size:28 final size:28
Alignment explanation
Indices: 90614--90670 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
90604 CAATTTTTTC
*
90614 AATAAATTTAAATCTTAAAATATGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
* *
90642 AATACATTTAAATCTTCAAATAAGATCT
1 AATAAATTTAAATCTTAAAATAAGATCT
90670 A
1 A
90671 TTAATTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.37
Consensus pattern (28 bp):
AATAAATTTAAATCTTAAAATAAGATCT
Found at i:95162 original size:81 final size:80
Alignment explanation
Indices: 94988--95253 Score: 401
Period size: 81 Copynumber: 3.3 Consensus size: 80
94978 CCTTACGGAC
* * *
94988 CTAAGGATAT-CTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCATAA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTGTGCTTAA
*
95052 GGTAACCCTA-AAGAT
66 GGTAACCCTACGA-AT
** *
95067 CTAAGGATGCCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTTGTTGTGTGCTTA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCC-TTTTGCTGTGTGCTTA
95132 AGGTAACCCTACGAAT
65 AGGTAACCCTACGAAT
* *
95148 CTAAGGATGTCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTCCCTTTTGCTGTGTGCTTA
1 CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTT-CCTTTTGCTGTGTGCTTA
*
95213 AGGTAACCCTACGGAT
65 AGGTAACCCTACGAAT
95229 CTAAGGATATCCTTGGGTAGGCCCA
1 CTAAGGATATCCTTGGGTAGGCCCA
95254 TAGACCCTAA
Statistics
Matches: 170, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
79 8 0.05
80 36 0.21
81 123 0.72
82 3 0.02
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (80 bp):
CTAAGGATATCCTTGGGTAGGCCCAAGGTATATCCTTAGGTTGGTTCCTTTTGCTGTGTGCTTAA
GGTAACCCTACGAAT
Found at i:98382 original size:17 final size:17
Alignment explanation
Indices: 98360--98396 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
98350 CACTTCTCCC
98360 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
98377 CTTTAAAACATTTAACA
1 CTTTAAAACATTTAACA
98394 CTT
1 CTT
98397 CTCCCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (17 bp):
CTTTAAAACATTTAACA
Found at i:100655 original size:21 final size:20
Alignment explanation
Indices: 100623--100669 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
100613 GGGGTATCGA
100623 TTCCCCTAGGGGGGAATCAG
1 TTCCCCTAGGGGGGAATCAG
100643 TTCCCCTAGGGGGGAATCAG
1 TTCCCCTAGGGGGGAATCAG
100663 TTCCCCT
1 TTCCCCT
100670 TCAAAGGGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
TTCCCCTAGGGGGGAATCAG
Found at i:100710 original size:43 final size:40
Alignment explanation
Indices: 100607--100710 Score: 90
Period size: 43 Copynumber: 2.6 Consensus size: 40
100597 AAAACCAGAA
*
100607 CCCC-AGG-GGGTATCGATTCCCCTAGGGGGGAATCAGTT
1 CCCCTAGGAGGGTATCGATTCCCCTAAGGGGGAATCAGTT
* * *
100645 CCCCTAGGGGGGAATC-AGTTCCCCTTCAAAGGGGGAATCGGTT
1 CCCCTAGGAGGGTATCGA-TTCCCC-T--AAGGGGGAATCAGTT
*
100688 -CCCTCATGAGGGTATCGATTCCC
1 CCCCT-AGGAGGGTATCGATTCCC
100711 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
38 4 0.08
39 4 0.08
40 12 0.23
41 1 0.02
42 4 0.08
43 26 0.50
44 1 0.02
ACGTcount: A:0.19, C:0.28, G:0.31, T:0.22
Consensus pattern (40 bp):
CCCCTAGGAGGGTATCGATTCCCCTAAGGGGGAATCAGTT
Done.