Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005140.1 Hibiscus syriacus cultivar Beakdansim tig00011576_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: 75446
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:959 original size:59 final size:60
Alignment explanation
Indices: 774--979 Score: 306
Period size: 60 Copynumber: 3.5 Consensus size: 60
764 AACATAAAAG
774 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * *
834 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGGACTTTGTGTGATAAAAGGATA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* * * * * *
894 AGGAAATCACACTAAGTGTAT-AATTTCTAGATAAGGGTACTTCGTGTTCTAAAATGACA
1 AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
* *
953 AAGAAATCATACTAAGTATATGAATTT
1 AGGAAATCATACTAAGTGTATGAATTT
980 TCGTATAGGA
Statistics
Matches: 131, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 49 0.37
60 82 0.63
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (60 bp):
AGGAAATCATACTAAGTGTATGAATTTCCAGATAAGGGCACTTTGTGTGCTAAAATGATA
Found at i:5471 original size:81 final size:81
Alignment explanation
Indices: 5352--5506 Score: 231
Period size: 81 Copynumber: 1.9 Consensus size: 81
5342 CCCAAAGGCC
* * *
5352 TTTATCCTTTCACCTAACTTGCATAATTGACACTTTTCTGCCGC-TTGCACAGCTAGGCCATTAA
1 TTTAACCTTTCACCTAACTGGCATAATTGACACCTTTCTGCC-CATTGCACAGCTAGGCCATTAA
5416 TCTTTTACTCAAATGTA
65 TCTTTTACTCAAATGTA
* * *
5433 TTTAACCTTTCATCTAACTGGTATAATTGACACCTTTCTGCCCAATTGCACATCTAGGCCATTAA
1 TTTAACCTTTCACCTAACTGGCATAATTGACACCTTTCTGCCC-ATTGCACAGCTAGGCCATTAA
5498 TCTTTTACT
65 TCTTTTACT
5507 TTAGAACTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 1 0.02
81 37 0.56
82 28 0.42
ACGTcount: A:0.25, C:0.26, G:0.10, T:0.39
Consensus pattern (81 bp):
TTTAACCTTTCACCTAACTGGCATAATTGACACCTTTCTGCCCATTGCACAGCTAGGCCATTAAT
CTTTTACTCAAATGTA
Found at i:5882 original size:20 final size:20
Alignment explanation
Indices: 5857--6003 Score: 123
Period size: 20 Copynumber: 6.7 Consensus size: 20
5847 TTCATTTATG
5857 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
5877 GCATCCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
5897 GCATCATTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
5922 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
5943 GCATTCGTTCATGCATTTTTAGTTAT
1 GCATCCTTTCATGC---CTTA---AT
5969 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
5990 GCATCCTTTCATGC
1 GCATCCTTTCATGC
6004 ATTTCATTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 26
0.73 0.09 0.19
Matches are distributed among these distances:
20 57 0.56
21 6 0.06
22 1 0.01
23 3 0.03
24 4 0.04
25 4 0.04
26 15 0.15
27 12 0.12
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.43
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:5987 original size:47 final size:46
Alignment explanation
Indices: 5877--6029 Score: 236
Period size: 46 Copynumber: 3.3 Consensus size: 46
5867 ATGCCTTAAT
*
5877 GCATCCTTTTATGCCTTAATGCA-TCATTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATTC-TTTCATGCATTTCATTTATG
* * *
5923 GCATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTTAGTTATG
1 GCATCCTTTCATGCCTTAATGCATTCTTTCATGCA-TTTCATTTATG
*
5970 GCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTCATTTATG
6016 GCATCCTTTCATGC
1 GCATCCTTTCATGC
6030 ATTTTAGTTA
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 53 0.55
47 44 0.45
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCCTTAATGCATTCTTTCATGCATTTCATTTATG
Found at i:6021 original size:26 final size:26
Alignment explanation
Indices: 5990--6053 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
5980 ATGCCTTAAT
*
5990 GCATCCTTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTCAGTTATG
*
6016 GCATCCTTTCATGCATTTTAGTTATG
1 GCATCCTTTCATGCATTTCAGTTATG
*
6042 GTATCCTTTCAT
1 GCATCCTTTCAT
6054 ACTAATAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.22, G:0.12, T:0.47
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTCAGTTATG
Found at i:6172 original size:44 final size:45
Alignment explanation
Indices: 6026--6217 Score: 234
Period size: 45 Copynumber: 4.4 Consensus size: 45
6016 GCATCCTTTC
* * * **
6026 ATGCATT-TTAGTTATGGTATCCTTTCAT-ACTAATAATGCAATCAT
1 ATGCATTATTA-TTTTGGCATCCTTTCATGCCT-ATAATGCACCCAT
* *
6071 ATGC---ATTATTTTGGCATCCTTTCATGCCAATAATGGACCCAT
1 ATGCATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCAT
* *
6113 ATGCATTATTATTTTGACATCCTTTCATGTCTATAATGCA-CCAT
1 ATGCATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCAT
6157 ATGCATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCAT
1 ATGCATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCAT
*
6202 ATACATTATTATTTTG
1 ATGCATTATTATTTTG
6218 TTCATTCATT
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
42 29 0.23
43 4 0.03
44 42 0.33
45 52 0.41
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.42
Consensus pattern (45 bp):
ATGCATTATTATTTTGGCATCCTTTCATGCCTATAATGCACCCAT
Found at i:6789 original size:95 final size:94
Alignment explanation
Indices: 6645--6821 Score: 234
Period size: 95 Copynumber: 1.9 Consensus size: 94
6635 CTACTCTGGA
* * * *
6645 ATCGATACTTCTATACTATGGTAGTGATACCCCCTTTCGATATCGATACCATTTCT-ATATTCTG
1 ATCGATACTACTATACTATGGTAATGATACCCCCTTTCGATATCAATACCATTT-TGACATTCTG
*
6709 CATTGCATGGTATCGATACCCTTCTTTCAGT
65 CA-TCCATGGTATCGATACCCTTCTTTCAGT
*
6740 ATCGATACTACTATACTATGG-AATCGATACTCCCTTTC-AGTATCAATACCATTTTGACATTCT
1 ATCGATACTACTATACTATGGTAAT-GATACCCCCTTTCGA-TATCAATACCATTTTGACATTCT
*
6803 GGATCCATGGTATCGATAC
64 GCATCCATGGTATCGATAC
6822 TTCCCTTTGT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
94 19 0.26
95 53 0.74
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.37
Consensus pattern (94 bp):
ATCGATACTACTATACTATGGTAATGATACCCCCTTTCGATATCAATACCATTTTGACATTCTGC
ATCCATGGTATCGATACCCTTCTTTCAGT
Found at i:9424 original size:137 final size:135
Alignment explanation
Indices: 9248--9619 Score: 439
Period size: 137 Copynumber: 2.7 Consensus size: 135
9238 GATTATTCAT
*
9248 TTTTAAAACTTATTCCTTAAATTAGGGGAATTTTTATTTGGTCCTCGTTTTTATTCGAGGTTCCA
1 TTTTCAAACTTA-TCCTTAAATTA-GGGAATTTTTATTTGGTCCTCGTTTTTATTCGAGGTTCCA
* * *
9313 TTTTAATTTTTTGAATCAAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCTATTTT
64 TTTTAATTATTCGAATCAAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTT
*
9378 AGATTTA
129 AGACTTA
* * * *
9385 TTTTCAAACTTAGTCCTTAAATTAGGGATTTTTTAATTTGGTCATCGTTTTT-TCTCGAAGTTCT
1 TTTTCAAACTTA-TCCTTAAATTAGGGAATTTTT-ATTTGGTCCTCGTTTTTAT-TCGAGGTTCC
*
9449 ATTTTAATTATTCGAATCAAGTAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTT
63 ATTTTAATTATTCGAATCAAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTT
*
9514 TAGGCTTA
128 TAGACTTA
* * * *
9522 ATTTCATAAC-TATACCTT-TATCTAGGAGAATTTTTGATTTGGTCCTCGCTTATGATT-GAGGT
1 TTTTCA-AACTTAT-CCTTAAAT-TAGG-GAATTTTT-ATTTGGTCCTCG-TTTTTATTCGAGGT
* * * *
9584 TCCATTTTGACTATTCGATTC-AATAATTTATTAAAA
60 TCCATTTTAATTATTCGAATCAAATAATTGATTAAAA
9620 ATGATTTTGA
Statistics
Matches: 201, Mismatches: 26, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
136 13 0.06
137 141 0.70
138 42 0.21
139 4 0.02
140 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (135 bp):
TTTTCAAACTTATCCTTAAATTAGGGAATTTTTATTTGGTCCTCGTTTTTATTCGAGGTTCCATT
TTAATTATTCGAATCAAATAATTGATTAAAATTGACTAGGTTAATAATTAGAGCCTCCATTTTAG
ACTTA
Found at i:12049 original size:16 final size:16
Alignment explanation
Indices: 12028--12058 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12018 ATAAAATAAT
12028 GATTCATGGTATTTAA
1 GATTCATGGTATTTAA
12044 GATTCATGGTATTTA
1 GATTCATGGTATTTA
12059 TTTCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (16 bp):
GATTCATGGTATTTAA
Found at i:13575 original size:377 final size:377
Alignment explanation
Indices: 12881--13634 Score: 1391
Period size: 377 Copynumber: 2.0 Consensus size: 377
12871 GGTATAAAAA
12881 TCAAATGTGTCCTACATGCCGCTAGTTACACTTGTACCGTACTCTTCAATCCAAGCCAAAGGAAC
1 TCAAATGTGTCCTACATGCCGCTAGTTACACTTGTACCGTACTCTTCAATCCAAGCCAAAGGAAC
12946 TCCCATTGCAAATGCCGATAGTTGAACGAGATCAATTCTTTTAACCTGATACGGTGAGTAAAATA
66 TCCCATTGCAAATGCCGATAGTTGAACGAGATCAATTCTTTTAACCTGATACGGTGAGTAAAATA
*
13011 GTGAGCTTTGGGAAGCTCAGTAATACAAAACTACCAAGTGATGCTGAAGGACATGTAGATAAATG
131 GTGAGCTTTGGGAAGCTCAGTAATACAAAACTACCAAGTGATGCTGAAGGACATATAGATAAATG
*
13076 GAAAAGTATACATTTTTCCTTATTGATTCAGACGTCCACAATTTTTTGGGATGGCCTAAGGTTTT
196 GAAAAGTATACATTTTTCCTTATTGATTCAGACGTCCACAATTTTTCGGGATGGCCTAAGGTTTT
*
13141 ATTGATTTTTCTTCAAGTAAAAGACATGAAATTTTCAGTTTAGAGGAATATTCAGAGGACCAAGT
261 ATTGATTTTTCTTCAAGTAAAAGACATGAAATTTTCAGTTCAGAGGAATATTCAGAGGACCAAGT
*
13206 TCAGGAGATCGGAATATGATGTTTAGTATGTTCCTATAAAATAGAGTAATAT
326 TCAGGAGATCGGAATATGATGTCTAGTATGTTCCTATAAAATAGAGTAATAT
*
13258 TCAAATGTGTCCTACATGCCGCTAGTTACACTTGTACCGTACTCTTCAATCCAAGTCAAAGGAAC
1 TCAAATGTGTCCTACATGCCGCTAGTTACACTTGTACCGTACTCTTCAATCCAAGCCAAAGGAAC
* *
13323 TCCCATTGCAAATGTCGATAGTTGAACGAGATCAATTCTTTTAACCTGATATGGTGAGTAAAATA
66 TCCCATTGCAAATGCCGATAGTTGAACGAGATCAATTCTTTTAACCTGATACGGTGAGTAAAATA
13388 GTGAGCTTTGGGAAGCTCAGTAATACAAAACTACCAAGTGATGCTGAAGGACATATAGATAAATG
131 GTGAGCTTTGGGAAGCTCAGTAATACAAAACTACCAAGTGATGCTGAAGGACATATAGATAAATG
* * *
13453 GAAAAGTATACATTTTTCCTTATTGATTTAGACGTCCATAGTTTTTCGGGATGGCCTAAGGTTTT
196 GAAAAGTATACATTTTTCCTTATTGATTCAGACGTCCACAATTTTTCGGGATGGCCTAAGGTTTT
*
13518 ATTGATTTTTCTTCAAGTAAAAGACATGAAATTTTTAGTTCAGAGGAATATTCAGAGGACCAAGT
261 ATTGATTTTTCTTCAAGTAAAAGACATGAAATTTTCAGTTCAGAGGAATATTCAGAGGACCAAGT
* *
13583 TTAGGAGATCGGAATATGATGTCTAGTGTGTTCCTATAAAATAGAGTAATAT
326 TCAGGAGATCGGAATATGATGTCTAGTATGTTCCTATAAAATAGAGTAATAT
13635 ATATATATCC
Statistics
Matches: 364, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
377 364 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (377 bp):
TCAAATGTGTCCTACATGCCGCTAGTTACACTTGTACCGTACTCTTCAATCCAAGCCAAAGGAAC
TCCCATTGCAAATGCCGATAGTTGAACGAGATCAATTCTTTTAACCTGATACGGTGAGTAAAATA
GTGAGCTTTGGGAAGCTCAGTAATACAAAACTACCAAGTGATGCTGAAGGACATATAGATAAATG
GAAAAGTATACATTTTTCCTTATTGATTCAGACGTCCACAATTTTTCGGGATGGCCTAAGGTTTT
ATTGATTTTTCTTCAAGTAAAAGACATGAAATTTTCAGTTCAGAGGAATATTCAGAGGACCAAGT
TCAGGAGATCGGAATATGATGTCTAGTATGTTCCTATAAAATAGAGTAATAT
Found at i:15539 original size:27 final size:26
Alignment explanation
Indices: 15484--15541 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
15474 TAAAGGTATT
*
15484 TTTTTGTAATTTTACCCCATACGAATA
1 TTTTTGTAATTTTA-CCCAAACGAATA
*
15511 TTTTTGTACTTTTA-CCAAACAGAAGTA
1 TTTTTGTAATTTTACCCAAAC-GAA-TA
15538 TTTT
1 TTTT
15542 CATAACTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 5 0.19
26 3 0.11
27 19 0.70
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (26 bp):
TTTTTGTAATTTTACCCAAACGAATA
Found at i:19307 original size:22 final size:22
Alignment explanation
Indices: 19281--19326 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
19271 CTGAGTAAAC
*
19281 TTATATAAAAT-TTATAAAAATT
1 TTATAGAAAATATT-TAAAAATT
*
19303 TTATAGAAAGTATTTAAAAATT
1 TTATAGAAAATATTTAAAAATT
19325 TT
1 TT
19327 GTTAGATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
TTATAGAAAATATTTAAAAATT
Found at i:20102 original size:14 final size:14
Alignment explanation
Indices: 20077--20113 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
20067 ATTTCTAATC
20077 TTTATGTTATACATA
1 TTTAT-TTATACATA
20092 TTTATTTATACATA
1 TTTATTTATACATA
*
20106 TTTTTTTA
1 TTTATTTA
20114 AATAATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (14 bp):
TTTATTTATACATA
Found at i:22288 original size:14 final size:14
Alignment explanation
Indices: 22263--22298 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
22253 ATTTCTAATC
22263 TTTATGTTATACATA
1 TTTAT-TTATACATA
22278 TTTATTTATACATA
1 TTTATTTATACATA
22292 TTTATTT
1 TTTATTT
22299 TTTCAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTATTTATACATA
Found at i:23849 original size:5 final size:5
Alignment explanation
Indices: 23833--23866 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
23823 CAAATGCATG
*
23833 AATAA TAATAA AATAA AATAA AAAAA AATAA AAT
1 AATAA -AATAA AATAA AATAA AATAA AATAA AAT
23867 TTAAGGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:26511 original size:131 final size:131
Alignment explanation
Indices: 26153--26525 Score: 436
Period size: 130 Copynumber: 2.9 Consensus size: 131
26143 AGAGATTTTT
* *
26153 GAAGATCAAATCT--AAAAAGAGATATGCTCCGCTGCTCTTCAGGGTAGATC-AGATCTGGAAAT
1 GAAGATCAAATCTGAAAAAAGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAAG-TATGGAAAT
* * * * * * *
26215 GTTGATTTACTTCACTGCTCTTCAGGGAAGATTGAATTGAGGTAGATTTGTTTCACTGCTCCCCA
65 GTTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCGAGTTTGATTTGTTTCAATGCTCCCCA
26280 GG
130 GG
* * ** * *
26282 GAAGATCAAATATGAAAAAA-GGATTTGCTCAACTGCTCTTTAGGGTAGATCAAATATGGAAATG
1 GAAGATCAAATCTGAAAAAAGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAAGTATGGAAATG
* * *
26346 TTGATTC-CATCAACTACTCTTTAGGGAAGATTGAATCGAGTTTGATTTG-TTCTAATGCTCCTC
66 TTGATTCAC-TCCACTACTCTTCAGGGAAGATTGAATCGAGTTTGATTTGTTTC-AATGCTCCCC
26409 AGG
129 AGG
** * * **
26412 GAAGATCAAATCTGAAAAAAGGGATATGCTCCGCTTTTCTTCAAGGTAGATCAAGTATGAAAACA
1 GAAGATCAAATCTGAAAAAAGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAAGTATGGAAATG
*
26477 TTGATTCACTCCACTACTCTTCAAGGAAGATTGAATC-AGATTTGATTTG
66 TTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCGAG-TTTGATTTG
26526 ATTATATTAT
Statistics
Matches: 203, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
129 16 0.08
130 106 0.52
131 80 0.39
132 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (131 bp):
GAAGATCAAATCTGAAAAAAGGGATATGCTCCGCTGCTCTTCAGGGTAGATCAAGTATGGAAATG
TTGATTCACTCCACTACTCTTCAGGGAAGATTGAATCGAGTTTGATTTGTTTCAATGCTCCCCAG
G
Found at i:27870 original size:23 final size:25
Alignment explanation
Indices: 27834--27890 Score: 73
Period size: 23 Copynumber: 2.3 Consensus size: 25
27824 ACCCATATTT
27834 TATTTATTTTCTCTCTTTT-TTCTTA
1 TATTT-TTTTCTCTCTTTTATTCTTA
* *
27859 -ATTTTTTTCTCTTTTTTATTTTTA
1 TATTTTTTTCTCTCTTTTATTCTTA
27883 TATTTTTT
1 TATTTTTT
27891 ATATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 12 0.43
24 9 0.32
25 7 0.25
ACGTcount: A:0.12, C:0.11, G:0.00, T:0.77
Consensus pattern (25 bp):
TATTTTTTTCTCTCTTTTATTCTTA
Found at i:27906 original size:24 final size:23
Alignment explanation
Indices: 27849--27906 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
27839 ATTTTCTCTC
* * *
27849 TTTTTTCTTAATTTTTTTCTCTT
1 TTTTTTCTTTATTTTTTTATATT
27872 TTTTATT-TTTATATTTTTTATATT
1 TTTT-TTCTTTAT-TTTTTTATATT
27896 TTTTTTCTTTA
1 TTTTTTCTTTA
27907 GGAAAAATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTTTCTTTATTTTTTTATATT
Found at i:33793 original size:61 final size:64
Alignment explanation
Indices: 33681--33825 Score: 188
Period size: 61 Copynumber: 2.3 Consensus size: 64
33671 GTATGTTTAT
* *
33681 ATTAGCACTAGTGTGTAAGGACACTAAGTGCAGGTGGTGGGCACAATCTTATGTGTCATATCCGG
1 ATTAGCACTAGAGTGTAA-GACACTAAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCGG
* ** *
33746 ATTAGCACTAGAGTGTAA-AC-CT-AGTGTAGGTGGTGGGCATGACCTTATGTGTCATATCTGG
1 ATTAGCACTAGAGTGTAAGACACTAAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCGG
* *
33807 ATTAGCACTATAGCGTAAG
1 ATTAGCACTAGAGTGTAAG
33826 CTTAGTACAT
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
61 50 0.70
62 2 0.03
63 2 0.03
65 17 0.24
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (64 bp):
ATTAGCACTAGAGTGTAAGACACTAAGTGCAGGTGGTGGGCACAACCTTATGTGTCATATCCGG
Found at i:37814 original size:102 final size:102
Alignment explanation
Indices: 37638--37823 Score: 309
Period size: 102 Copynumber: 1.8 Consensus size: 102
37628 TTTATACTTC
* * *
37638 AAGGGGAGTTATCTCATCACACTACCATCCCATACTCTAAGTGAAAGGGAGCATACCTTCCACCC
1 AAGGGGAGTCAACTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAGCATACCTTCCACCC
*
37703 CAAGCTAGTCACGTAGAGTTTTTCTTAAGCATAGTTT
66 CAAGCTAGTCAAGTAGAGTTTTTCTTAAGCATAGTTT
*
37740 AAGGGGAGTCAACTCATCATACTACCATCCCACACTCTAAGTGAAAGGGAGCATACCTTCCACCC
1 AAGGGGAGTCAACTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAGCATACCTTCCACCC
**
37805 TGAGCTAGTCAAGTAGAGT
66 CAAGCTAGTCAAGTAGAGT
37824 CATCCTGTGA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (102 bp):
AAGGGGAGTCAACTCATCACACTACCATCCCACACTCTAAGTGAAAGGGAGCATACCTTCCACCC
CAAGCTAGTCAAGTAGAGTTTTTCTTAAGCATAGTTT
Found at i:45028 original size:19 final size:20
Alignment explanation
Indices: 45004--45048 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
44994 CGGGGTAGCA
45004 GCATGGTGGAT-AGGAG-AGG
1 GCATGGT-GATAAGGAGCAGG
45023 GCATGGTGATAAGGAGCAGG
1 GCATGGTGATAAGGAGCAGG
45043 GCATGG
1 GCATGG
45049 GCAGCAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 12 0.50
20 9 0.38
ACGTcount: A:0.27, C:0.09, G:0.49, T:0.16
Consensus pattern (20 bp):
GCATGGTGATAAGGAGCAGG
Found at i:47236 original size:19 final size:20
Alignment explanation
Indices: 47212--47254 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
47202 AGCATTTATC
*
47212 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
47231 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
47251 TTCA
1 TTCA
47255 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:53738 original size:45 final size:46
Alignment explanation
Indices: 53639--53746 Score: 121
Period size: 45 Copynumber: 2.3 Consensus size: 46
53629 ATATGCTATG
* * * *
53639 TGATCATAATCTATGTGTTTTATGATCTATGTGATTACATGATAATA
1 TGAT-ATAAGCTATGTGTTATATGACCTAAGTGATTACATGATAATA
* *
53686 TGATATAAGCTATGTGTTAT-TGACCTAAGTGATTATATGA-ACATG
1 TGATATAAGCTATGTGTTATATGACCTAAGTGATTACATGATA-ATA
*
53731 TGCTATAAGCTATGTG
1 TGATATAAGCTATGTG
53747 ATAAGTATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 1 0.02
45 34 0.64
46 14 0.26
47 4 0.08
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (46 bp):
TGATATAAGCTATGTGTTATATGACCTAAGTGATTACATGATAATA
Found at i:53970 original size:23 final size:23
Alignment explanation
Indices: 53944--54045 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
53934 GGTTCTACAC
*
53944 GGTCCTTTGGGACAATTCTACGT
1 GGTCCTTCGGGACAATTCTACGT
* * **
53967 GGTCCTACGGGACATTTCTACAC
1 GGTCCTTCGGGACAATTCTACGT
* * *
53990 GGTCCTTCGGGATAATACTATGT
1 GGTCCTTCGGGACAATTCTACGT
* * *
54013 GGTCATTCGGGACATTTCTATGT
1 GGTCCTTCGGGACAATTCTACGT
54036 GG-CACTTCGG
1 GGTC-CTTCGG
54046 TGCAAATTTC
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
22 1 0.02
23 60 0.98
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAATTCTACGT
Found at i:54015 original size:46 final size:46
Alignment explanation
Indices: 53936--54032 Score: 140
Period size: 46 Copynumber: 2.1 Consensus size: 46
53926 GAGTCGAGGG
* * *
53936 TTCTACACGGTCCTTTGGGACAATTCTACGTGGTCCTACGGGACAT
1 TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
* * *
53982 TTCTACACGGTCCTTCGGGATAATACTATGTGGTCATTCGGGACAT
1 TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
54028 TTCTA
1 TTCTA
54033 TGTGGCACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.33
Consensus pattern (46 bp):
TTCTACACGGTCCTTCGGGACAATACTACGTGGTCATACGGGACAT
Found at i:54060 original size:25 final size:24
Alignment explanation
Indices: 54026--54083 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
54016 CATTCGGGAC
*
54026 ATTTCTATGTGGCACTTCGGTGCAA
1 ATTTCTATGTAGCACTTCGGTGC-A
*
54051 ATTTCTATGTAGTACTTCGGTGCA
1 ATTTCTATGTAGCACTTCGGTGCA
*
54075 ATTTATATG
1 ATTTCTATG
54084 AGTTGTGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 9 0.30
25 21 0.70
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (24 bp):
ATTTCTATGTAGCACTTCGGTGCA
Found at i:54246 original size:6 final size:6
Alignment explanation
Indices: 54179--54242 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
54169 AAATATATAT
* *
54179 ATGA-A ATGATA ATGATG ATGATA ATGATA ATGATA ATGGTA ATGATA
1 ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA ATGATA
* * *
54226 GTGATA GTGATG ATGAT
1 ATGATA ATGATA ATGAT
54243 GATGTGTGTA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
5 4 0.08
6 47 0.92
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (6 bp):
ATGATA
Found at i:73420 original size:20 final size:20
Alignment explanation
Indices: 73395--73434 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
73385 CCATGACATG
73395 TAAATGATAT-TAAAACATAA
1 TAAATGA-ATCTAAAACATAA
*
73415 TAAATGAATCTAAATCATAA
1 TAAATGAATCTAAAACATAA
73435 AAACTAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAATGAATCTAAAACATAA
Done.