Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003912.1 Hibiscus syriacus cultivar Beakdansim tig00008461_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: 69281
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2543 original size:594 final size:604
Alignment explanation
Indices: 1347--2541 Score: 2028
Period size: 594 Copynumber: 2.0 Consensus size: 604
1337 TATTAAGTTC
*
1347 TTCAATTATTAAAAGTTATAAAATGATCATCTAACTATGAAGTGTTACTTTTTTGAGTCCATCGA
1 TTCAATTATTAAAAGTTATAAAATGATCATCTAACTATGAAGTGTTA-TTTTTTAAGTCCATCGA
1412 CTATTTAAAGTTACAAAATAGTCACTCGACTATTCATTATATTCTAGACTTAACCTTTTCCGTTA
65 CTATTTAAAGTTACAAAATAGTCACTCGACTATTCATTATATTCTAGACTTAACCTTTTCCGTTA
* *
1477 AAAATTAGTGGTTGGTTTTAAGCTGGATGTTAACATGATGACCGGGTACAATAGTTATTTGAGAT
130 AAAATTAGTGATTGGTTTTAAGCTGGATGTTAACATGATGACCGGGTACAATAGATATTTGAGAT
* *
1542 TTTAAGATCAATTTTATCATATCACAGTCAACAAGTTAACGTTCAACTCAGAATATCGTATATTT
195 TTTAAGATCAATTTTATCATATCACAGTCAACAAGTTAACATTCAACTCAGAATATCGTATATAT
* * *
1607 TTTAACAGAAATGATGAGTTTGGAACATAATGAATAGTTGGAGGACCATTTTGAATTTTTAATGG
260 TTTAACAGAAATGACGAGTTTGGAACATAATGAATAGTCGGAGGACCATTTTGAACTTTTAATGG
* *
1672 TCGAGAGACTCAACAAAGTAACACTCTATAGTCGAATGATCATTTTATAACTTTTGATAGTCAAA
325 GCGAGAGACTCAACAAAGCAACACTCTATAGTCGAATGATCATTTTATAACTTTTGATAGTCAAA
* * *
1737 TGATTTAATAAAATAATACCCTATAATCAGGGACCATTACGTTGTTTATCTTTAATAATTTCGTT
390 GGATTTAATAAAACAATACCCTATAATCAGGGACCATTACGTTGTTTATCTTTAATAAATTCGTT
1802 TATATTAAGATTTATTTTTAATTAATTCTCGAAATATACTTATTCTGTCGCATGGAATAAAGCTT
455 TATATTAAGATTTATTTTTAATTAATTCTCGAAATATACTTATTCTGTCGCATGGAATAAAGCTT
*
1867 GTCATATCAGCTTGGTCTAATAGTCTTTATGTAGATTTTGGAATATATAAAAAATTTACAATACG
520 GTAATATCAGCTTGGTCTAATAGTCTTTATGTAGATTTTGGAATATATAAAAAATTTACAATACG
*
1932 ATAAATAATATAAAAAATCA
585 ATAAATAATAAAAAAAATCA
1952 TTCAATTA-TAAAAGTTATAAAA-GATCATCTAACTATGAAGTG-T-TTTTTTAAGTCCATCGAC
1 TTCAATTATTAAAAGTTATAAAATGATCATCTAACTATGAAGTGTTATTTTTTAAGTCCATCGAC
*
2013 TATTTAAATTTACAAAATAGTCACTCGACTATTCATTATATTCTAGACTTAACCTTTT-CGTTAA
66 TATTTAAAGTTACAAAATAGTCACTCGACTATTCATTATATTCTAGACTTAACCTTTTCCGTT-A
2077 AAAATTAGTGATT-G-TTTAAGCTGGATGTTAACATGATGACCGGGTACAATA-ATA-TTGAGAT
130 AAAATTAGTGATTGGTTTTAAGCTGGATGTTAACATGATGACCGGGTACAATAGATATTTGAGAT
*
2138 TTTAGGATCAATTTTATCATATCACAGTCAACAAGTTAACATTCAACTCAGAATATC-TAT-TAT
195 TTTAAGATCAATTTTATCATATCACAGTCAACAAGTTAACATTCAACTCAGAATATCGTATATAT
2201 TTT-ACAGAAATGACGAGTTTGGAACATAATGAATAGTCGGAGGACCATTTTGTAACTTTTAATG
260 TTTAACAGAAATGACGAGTTTGGAACATAATGAATAGTCGGAGGACCATTTTG-AACTTTTAATG
*
2265 GGCGAGAGATTCAACAAAGCAACACTCTATAGTCGAATGATCATTTTATAACTTTTGATAGTCAA
324 GGCGAGAGACTCAACAAAGCAACACTCTATAGTCGAATGATCATTTTATAACTTTTGATAGTCAA
*
2330 AGGATTTAATAAAGCAATACCCTATAATCAGGGACCATTTACGTTGTTTACTCTTTAATAAATTC
389 AGGATTTAATAAAACAATACCCTATAATCAGGGACCA-TTACGTTGTTTA-TCTTTAATAAATTC
*
2395 G-TTATA-TAAGATTTA-TTTTAATTAATTCTTG-AA-ATACTTATTCTCGTCGCATGGAATAAA
452 GTTTATATTAAGATTTATTTTTAATTAATTCTCGAAATATACTTATTCT-GTCGCATGGAATAAA
2455 GCTTGTAATATCAGCTTGGTCTAATAGTCTTTATGTAAGATTTTGGAATATATAAAAAATTTACA
516 GCTTGTAATATCAGCTTGGTCTAATAGTCTTTATGT-AGATTTTGGAATATATAAAAAATTTACA
2520 ATACGATAAATAATAAAAAAAA
580 ATACGATAAATAATAAAAAAAA
2542 ATGAATTATT
Statistics
Matches: 564, Mismatches: 20, Indels: 24
0.93 0.03 0.04
Matches are distributed among these distances:
591 11 0.02
592 52 0.09
593 111 0.20
594 120 0.21
595 20 0.04
596 76 0.13
597 2 0.00
598 37 0.07
599 5 0.01
600 87 0.15
602 1 0.00
603 20 0.04
604 14 0.02
605 8 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (604 bp):
TTCAATTATTAAAAGTTATAAAATGATCATCTAACTATGAAGTGTTATTTTTTAAGTCCATCGAC
TATTTAAAGTTACAAAATAGTCACTCGACTATTCATTATATTCTAGACTTAACCTTTTCCGTTAA
AAATTAGTGATTGGTTTTAAGCTGGATGTTAACATGATGACCGGGTACAATAGATATTTGAGATT
TTAAGATCAATTTTATCATATCACAGTCAACAAGTTAACATTCAACTCAGAATATCGTATATATT
TTAACAGAAATGACGAGTTTGGAACATAATGAATAGTCGGAGGACCATTTTGAACTTTTAATGGG
CGAGAGACTCAACAAAGCAACACTCTATAGTCGAATGATCATTTTATAACTTTTGATAGTCAAAG
GATTTAATAAAACAATACCCTATAATCAGGGACCATTACGTTGTTTATCTTTAATAAATTCGTTT
ATATTAAGATTTATTTTTAATTAATTCTCGAAATATACTTATTCTGTCGCATGGAATAAAGCTTG
TAATATCAGCTTGGTCTAATAGTCTTTATGTAGATTTTGGAATATATAAAAAATTTACAATACGA
TAAATAATAAAAAAAATCA
Found at i:4361 original size:31 final size:31
Alignment explanation
Indices: 4271--4389 Score: 169
Period size: 31 Copynumber: 4.0 Consensus size: 31
4261 CCCGAAGGAC
* *
4271 CAGTCCATA-GAT-CCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
4301 CAGTCCATATGTCCCG-A-AA-ATA-GTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
4328 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
4359 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
4390 ACCCTCGACC
Statistics
Matches: 81, Mismatches: 2, Indels: 11
0.86 0.02 0.12
Matches are distributed among these distances:
27 20 0.25
28 3 0.04
29 4 0.05
30 14 0.17
31 40 0.49
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5994 original size:24 final size:24
Alignment explanation
Indices: 5966--6046 Score: 153
Period size: 24 Copynumber: 3.4 Consensus size: 24
5956 CATGGGATAG
5966 TGCATCGATGCACAAGTTAAGGGA
1 TGCATCGATGCACAAGTTAAGGGA
5990 TGCATCGATGCACAAGTTAAGGGA
1 TGCATCGATGCACAAGTTAAGGGA
*
6014 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCACAAGTTAAGGGA
6038 TGCATCGAT
1 TGCATCGAT
6047 ACACTATAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (24 bp):
TGCATCGATGCACAAGTTAAGGGA
Found at i:13322 original size:21 final size:21
Alignment explanation
Indices: 13293--13395 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
13283 GATTCTGACT
13293 ATCGTAACGAGTATCCGTAAA
1 ATCGTAACGAGTATCCGTAAA
* * *
13314 ATTGTAACGCGTATCTGT-AA
1 ATCGTAACGAGTATCCGTAAA
* * ** *
13334 ATCGCAATGACAATACGTAAA
1 ATCGTAACGAGTATCCGTAAA
* * *
13355 ATTGCAACGCGTATCCGT-AA
1 ATCGTAACGAGTATCCGTAAA
* *
13375 ATCGTAACGAGAATACGTAAA
1 ATCGTAACGAGTATCCGTAAA
13396 TCGCAATGCG
Statistics
Matches: 58, Mismatches: 22, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGTAACGAGTATCCGTAAA
Found at i:13353 original size:20 final size:20
Alignment explanation
Indices: 13330--13484 Score: 84
Period size: 20 Copynumber: 7.7 Consensus size: 20
13320 ACGCGTATCT
*
13330 GTAAATCGCAATGACAATAC
1 GTAAATCGCAACGACAATAC
* * *
13350 GTAAAATTGCAACG-CGTATCC
1 GT-AAATCGCAACGAC-AATAC
* *
13371 GTAAATCGTAACGAGAATAC
1 GTAAATCGCAACGACAATAC
* *
13391 GTAAATCGCAATG-C-GTATC
1 GTAAATCGCAACGACAATA-C
* * *
13410 TATAAATCGCAACGAGAATAT
1 -GTAAATCGCAACGACAATAC
* * * *
13431 ATAAATCGCAATG-CGTATCC
1 GTAAATCGCAACGAC-AATAC
13451 GTAAATCGCAACGACAATAC
1 GTAAATCGCAACGACAATAC
*
13471 ATAAAATCGCAACG
1 GT-AAATCGCAACG
13485 CGTATCCATA
Statistics
Matches: 97, Mismatches: 28, Indels: 19
0.67 0.19 0.13
Matches are distributed among these distances:
18 2 0.02
19 1 0.01
20 66 0.68
21 26 0.27
22 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
GTAAATCGCAACGACAATAC
Found at i:13418 original size:40 final size:41
Alignment explanation
Indices: 13293--13504 Score: 241
Period size: 41 Copynumber: 5.2 Consensus size: 41
13283 GATTCTGACT
* * * * * *
13293 ATCGTAACGAGTATCCGTAAAATTGTAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
13334 ATCGCAATGACAATACGTAAAATTGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * **
13375 ATCGTAACGAGAATACGT-AAATCGCAATGCGTATCTATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
13415 ATCGCAACGAGAATA--TATAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTA-AAATCGCAACGCGTATCCGTAA
* * *
13455 ATCGCAACGACAATACATAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
13496 ATCGCAACG
1 ATCGCAACG
13505 CGATCGATAA
Statistics
Matches: 147, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
40 66 0.45
41 78 0.53
42 2 0.01
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:13499 original size:20 final size:20
Alignment explanation
Indices: 13353--13525 Score: 143
Period size: 20 Copynumber: 8.7 Consensus size: 20
13343 ACAATACGTA
* *
13353 AAATTGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCAT
* * * * *
13373 AAATCGTAACGAGAATACGT
1 AAATCGCAACGCGTATCCAT
* *
13393 AAATCGCAATGCGTATCTAT
1 AAATCGCAACGCGTATCCAT
* * **
13413 AAATCGCAACGAGAATATAT
1 AAATCGCAACGCGTATCCAT
* *
13433 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCAT
* *
13453 AAATCGCAACGAC-AATACAT
1 AAATCGCAACG-CGTATCCAT
13473 AAAATCGCAACGCGTATCCAT
1 -AAATCGCAACGCGTATCCAT
*
13494 AAATCGCAACGCG-ATCGAT
1 AAATCGCAACGCGTATCCAT
*
13513 AATTCGCAACGCG
1 AAATCGCAACGCG
13526 ATCTTCGGTA
Statistics
Matches: 120, Mismatches: 30, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
19 17 0.14
20 86 0.72
21 17 0.14
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCAT
Found at i:13520 original size:80 final size:80
Alignment explanation
Indices: 13319--13525 Score: 238
Period size: 81 Copynumber: 2.6 Consensus size: 80
13309 GTAAAATTGT
** * * * *
13319 AACGCGTATCTGTAAATCGCAATGACAATACGTAAAATT-GCAACGCGTATCCGTAAATCGTAAC
1 AACGCGTATCCATAAATCGCAACGAGAATA-G-ATAATTCGCAACGCGTATCCGTAAATCGCAAC
* *
13383 GAGAATACGTAAATCGC
64 GACAATACATAAATCGC
* * * * *
13400 AATGCGTATCTATAAATCGCAACGAGAATATATAAATCGCAATGCGTATCCGTAAATCGCAACGA
1 AACGCGTATCCATAAATCGCAACGAGAATAGATAATTCGCAACGCGTATCCGTAAATCGCAACGA
13465 CAATACATAAAATCGC
66 CAATACAT-AAATCGC
* *
13481 AACGCGTATCCATAAATCGCAACGCG-ATCGATAATTCGCAACGCG
1 AACGCGTATCCATAAATCGCAACGAGAATAGATAATTCGCAACGCG
13526 ATCTTCGGTA
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
79 4 0.04
80 46 0.43
81 56 0.53
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (80 bp):
AACGCGTATCCATAAATCGCAACGAGAATAGATAATTCGCAACGCGTATCCGTAAATCGCAACGA
CAATACATAAATCGC
Found at i:13643 original size:20 final size:20
Alignment explanation
Indices: 13618--13743 Score: 139
Period size: 20 Copynumber: 6.3 Consensus size: 20
13608 TTTTCCTAAT
13618 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
13638 TCGCAACGTGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
** * *
13658 TCATAATGCGATTATGTAAA
1 TCGCAATGCGAATACGTAAA
*
13678 TTGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
13698 TCGCAATGCGAAT-CTATAAA
1 TCGCAATGCGAATAC-GTAAA
13718 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
13738 TCGCAA
1 TCGCAA
13744 CGAGATTCTG
Statistics
Matches: 89, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
19 1 0.01
20 88 0.99
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:14631 original size:24 final size:24
Alignment explanation
Indices: 14604--14657 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
14594 GTATTCGAAA
14604 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
14628 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
14652 TTTGAT
1 TTTGAT
14658 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:17120 original size:20 final size:20
Alignment explanation
Indices: 17095--17183 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
17085 TAACGCGGAA
17095 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
17115 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* ** *
17135 ATCGCAATGTAGAATTGACT
1 ATCGCAACGCGGAAATGACT
17155 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
17175 ATTGCAACG
1 ATCGCAACG
17184 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 54 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:17154 original size:40 final size:41
Alignment explanation
Indices: 17105--17181 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
17095 ATCGCAACGC
17105 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGTA
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAATGTA
* *
17146 GAAT-TGACTATCGCAACGCGGAAATGACTATTGCAA
1 GAATATGACTATCGCAACACGGAAATGACTATCGCAA
17182 CGAGAGAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (41 bp):
GAATATGACTATCGCAACACGGAAATGACTATCGCAATGTA
Found at i:17212 original size:19 final size:19
Alignment explanation
Indices: 17188--17273 Score: 101
Period size: 19 Copynumber: 4.7 Consensus size: 19
17178 GCAACGAGAG
17188 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17207 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
17226 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
17240 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
* *
17260 AATCCCAACGCGAA
1 AATCGCAATGCGAA
17274 CTCGTTGTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
14 8 0.14
16 5 0.09
17 2 0.04
18 3 0.05
19 29 0.51
20 10 0.18
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:17234 original size:52 final size:53
Alignment explanation
Indices: 17155--17273 Score: 168
Period size: 52 Copynumber: 2.2 Consensus size: 53
17145 AGAATTGACT
** *
17155 ATCGCAACGCGGAAATGACTATTGCAACGAGAGAATCGCAATGCG-AAATGAAA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
* *
17208 ATCGCAATGCGAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
*
17261 ATCCCAACGCGAA
1 ATCGCAACGCGAA
17274 CTCGTTGTGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 30 0.52
53 28 0.48
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (53 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAA
Found at i:17458 original size:14 final size:14
Alignment explanation
Indices: 17439--17475 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17429 CATCAATTAA
17439 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
17453 ACAAATCATCTTTT
1 ACAAATCAACATTT
17467 ACAAATCAA
1 ACAAATCAA
17476 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:19442 original size:20 final size:20
Alignment explanation
Indices: 19419--19505 Score: 120
Period size: 20 Copynumber: 4.3 Consensus size: 20
19409 GAAACTTAAA
*
19419 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
19439 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
19459 ATCGCAATGCAAAAATGACT
1 ATCGCAATGCGAAAATGACT
* ** *
19479 ATCGCGATGCGAATTTGATT
1 ATCGCAATGCGAAAATGACT
19499 ATCGCAA
1 ATCGCAA
19506 CGAGAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:19572 original size:14 final size:14
Alignment explanation
Indices: 19550--19625 Score: 55
Period size: 14 Copynumber: 5.1 Consensus size: 14
19540 GCGATTATAG
*
19550 TTTCGCGTTGCGAT
1 TTTCTCGTTGCGAT
*
19564 TTTGTCGTTG-GAAT
1 TTTCTCGTTGCG-AT
*
19578 TCTCTCGTTGCGATTTT
1 TTTCTCGTTGCGA---T
19595 AATTTCTCGTTGCGAT
1 --TTTCTCGTTGCGAT
*
19611 TCTCTCGTTGCGAT
1 TTTCTCGTTGCGAT
19625 T
1 T
19626 CATTTCGCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
13 1 0.02
14 33 0.67
15 1 0.02
16 1 0.02
17 1 0.02
19 12 0.24
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (14 bp):
TTTCTCGTTGCGAT
Found at i:19613 original size:33 final size:31
Alignment explanation
Indices: 19568--19641 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 31
19558 TGCGATTTTG
19568 TCGTTG-GAATTCTCTCGTTGCGATTTTAATTTC
1 TCGTTGCG-ATTCTCTCGTTGCGA--TTAATTTC
*
19601 TCGTTGCGATTCTCTCGTTGCGATTCATTTC
1 TCGTTGCGATTCTCTCGTTGCGATTAATTTC
*
19632 GCGTTGCGAT
1 TCGTTGCGAT
19642 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
31 16 0.42
33 21 0.55
34 1 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.45
Consensus pattern (31 bp):
TCGTTGCGATTCTCTCGTTGCGATTAATTTC
Found at i:19637 original size:31 final size:32
Alignment explanation
Indices: 19576--19641 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 32
19566 TGTCGTTGGA
*
19576 ATTCTCTCGTTGCGATTTTAATTTCTCGTTGCG
1 ATTCTCTCGTTGCGA-TTTAATTTCGCGTTGCG
*
19609 ATTCTCTCGTTGCGA-TTCATTTCGCGTTGCG
1 ATTCTCTCGTTGCGATTTAATTTCGCGTTGCG
19640 AT
1 AT
19642 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 16 0.52
33 15 0.48
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (32 bp):
ATTCTCTCGTTGCGATTTAATTTCGCGTTGCG
Found at i:19638 original size:17 final size:17
Alignment explanation
Indices: 19580--19641 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 17
19570 GTTGGAATTC
*
19580 TCTCGTTGCGATTTTAATT
1 TCTCGTTGCGA--TTCATT
19599 TCTCGTTGCGATTC---
1 TCTCGTTGCGATTCATT
19613 TCTCGTTGCGATTCATT
1 TCTCGTTGCGATTCATT
*
19630 TCGCGTTGCGAT
1 TCTCGTTGCGAT
19642 AGTCATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 14 0.37
17 13 0.34
19 11 0.29
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.45
Consensus pattern (17 bp):
TCTCGTTGCGATTCATT
Found at i:19875 original size:94 final size:94
Alignment explanation
Indices: 19729--20108 Score: 620
Period size: 94 Copynumber: 4.1 Consensus size: 94
19719 ATGGATTACA
* * *
19729 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
19793 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
19822 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACGTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
19887 TTAGCAGAATTGGCAGCAACTGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
19916 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
19981 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
20010 TTAC-TTCAACCAAAATACAAAACAAAAGACAAATACTAACTTCACATTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
20074 TTTAGCAGTATTAGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
20104 TTACT
1 TTACT
20109 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
93 22 0.08
94 247 0.92
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:21829 original size:20 final size:20
Alignment explanation
Indices: 21806--21861 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
21796 TGAAATGAAA
21806 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
21826 ATCGCAATACG-GA-AATGGCT
1 ATCGC-A-ACGAGAGAATGACT
*
21846 ATCGCAACGAAAGAAT
1 ATCGCAACGAGAGAAT
21862 CGCAACGCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
18 3 0.10
19 2 0.07
20 19 0.63
21 3 0.10
22 3 0.10
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:21841 original size:40 final size:37
Alignment explanation
Indices: 21797--21947 Score: 130
Period size: 33 Copynumber: 4.3 Consensus size: 37
21787 TCTTTTGGTT
21797 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAATACG-
1 GAAATGAAAATCGCAACGAGAGAATGA--ATCGC-A-ACGC
***
21837 GAAATGGCTATCGCAAC--GA-AA-GAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
21870 GAAATGAAAATCGCAAC--GAG-A-GAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
* *
21903 GAAATTAAAATCGCAAC--GAG-A-GAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
21936 GAAATGAAAATC
1 GAAATGAAAATC
21948 ACAATGCGAT
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
32 3 0.03
33 72 0.72
34 5 0.05
36 2 0.02
37 2 0.02
38 2 0.02
40 14 0.14
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (37 bp):
GAAATGAAAATCGCAACGAGAGAATGAATCGCAACGC
Found at i:21865 original size:14 final size:14
Alignment explanation
Indices: 21846--21901 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
21836 GGAAATGGCT
21846 ATCGCAACGAAAGA
1 ATCGCAACGAAAGA
21860 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CGAAA-G--A
*
21879 ATCGCAACGAGAGA
1 ATCGCAACGAAAGA
21893 ATCGCAACG
1 ATCGCAACG
21902 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 17 0.47
16 6 0.17
17 5 0.14
19 8 0.22
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAAAGA
Found at i:21883 original size:33 final size:33
Alignment explanation
Indices: 21846--21947 Score: 177
Period size: 33 Copynumber: 3.1 Consensus size: 33
21836 GGAAATGGCT
*
21846 ATCGCAACGAAAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
*
21879 ATCGCAACGAGAGAATCGCAACGCGAAATTAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
*
21912 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
21945 ATC
1 ATC
21948 ACAATGCGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 65 1.00
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCGAAATGAAA
Found at i:22000 original size:33 final size:33
Alignment explanation
Indices: 21952--22044 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
21942 AAAATCACAA
** *
21952 TGCGATTTTGGTTTCGAGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGTGTTGCGATTATCTCGT
*
21985 TGCGATTTTCATTTCGTGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGTGTTGCGATTATCTCGT
**
22018 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGTGTTGCGATT
22045 TTAAGTTTAG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 38 0.72
34 15 0.28
ACGTcount: A:0.12, C:0.17, G:0.25, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGTGTTGCGATTATCTCGT
Found at i:22629 original size:20 final size:20
Alignment explanation
Indices: 22604--22776 Score: 177
Period size: 20 Copynumber: 8.6 Consensus size: 20
22594 CTTTAAAAAT
*
22604 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22624 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
22644 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
** * *
22665 CGTATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
22685 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
22705 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
22725 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
22745 CGCGTTGAGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
**
22766 CTAGTTGCGAT
1 CGCGTTGCGAT
22777 AGTCAGAATC
Statistics
Matches: 122, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
20 88 0.72
21 34 0.28
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:22690 original size:40 final size:40
Alignment explanation
Indices: 22606--22776 Score: 243
Period size: 40 Copynumber: 4.2 Consensus size: 40
22596 TTAAAAATCG
* *
22606 CGTTACGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
**
22647 CGTTGCGATTTACGGATACGTATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
22687 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * *
22727 CGTTGCGATTTACGGATACGCGTTGAGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
22768 AGTTGCGAT
1 CGTTGCGAT
22777 AGTCAGAATC
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 74 0.63
41 43 0.37
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:22760 original size:101 final size:100
Alignment explanation
Indices: 22604--22837 Score: 235
Period size: 101 Copynumber: 2.3 Consensus size: 100
22594 CTTTAAAAAT
* * * * * * *
22604 CGCGTTACGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGTA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGA-TTTACGGATCGTCGTTGAGATTTACGGATAC-TA
* * * *
22669 -TTGCGAT--TTACGTATTCTCGTTGCGATTTACA-GATA
64 GTTGCGATAGTCA-G-AATCGCGTTACGATTTACATG-TA
22705 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG-CGTTGAGATTTTACGGATACTA
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGAT-CGTCGTTGAGA-TTTACGGATACTA
* *
22769 GTTGCGATAGTCAGAATCGCGTTACGATTTATATGTT
64 GTTGCGATAGTCAGAATCGCGTTACGATTTACATGTA
* *
22806 CGCGTTGCGATTTTCATATTCTCGTTGCGATT
1 CGCGTTGCGATTTACGTATTCTCGTTGCGATT
22838 CTGGAAAATC
Statistics
Matches: 112, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
100 17 0.15
101 91 0.81
102 2 0.02
103 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (100 bp):
CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATCGTCGTTGAGATTTACGGATACTAGT
TGCGATAGTCAGAATCGCGTTACGATTTACATGTA
Found at i:22790 original size:81 final size:80
Alignment explanation
Indices: 22611--22818 Score: 231
Period size: 81 Copynumber: 2.6 Consensus size: 80
22601 AATCGCGTTA
* * * * *
22611 CGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGTATTGCGAT
1 CGATGTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATACGCATTGAGAT
* * *
22676 TTACGTATTCTCGTTG
65 TTACGGATACTAGTTG
* *
22692 CGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGAGATT
1 CGATGTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGAGA-T
22757 TTACGGATACTAGTTG
65 TTACGGATACTAGTTG
* ** * *
22773 CGATAGT-CAGA-ATCGCGTTACGATTTATATGTTCGCGTTGCGATTT
1 CGAT-GTACAGATA-CGCGTTGCGATTTACGTATTCTCGTTGCGATTT
22819 TCATATTCTC
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
80 37 0.34
81 72 0.65
82 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.38
Consensus pattern (80 bp):
CGATGTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCATTGAGATT
TACGGATACTAGTTG
Found at i:22831 original size:20 final size:20
Alignment explanation
Indices: 22603--22837 Score: 140
Period size: 20 Copynumber: 11.7 Consensus size: 20
22593 GCTTTAAAAA
* *
22603 TCGCGTTACGATTTACGGAT
1 TCGCGTTGCGATTTACAGAT
*
22623 ACGCGTTGCGATTTTAC-GTAT
1 TCGCGTTGCGA-TTTACAG-AT
*
22644 T-GTCGTTGCGATTTACGGAT
1 TCG-CGTTGCGATTTACAGAT
* **
22664 ACGTATTGCGATTTAC-GTAT
1 TCGCGTTGCGATTTACAG-AT
*
22684 TCTCGTTGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
*
22704 ACGCGTTGCGATTTAC-GTAT
1 TCGCGTTGCGATTTACAG-AT
* *
22724 TCTCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTACAGAT
* * *
22744 ACGCGTTGAGATTTTACGGAT
1 TCGCGTTGCGA-TTTACAGAT
* ** * *
22765 ACTAGTTGCGATAGT-CAGAA
1 TCGCGTTGCGAT-TTACAGAT
* *
22785 TCGCGTTACGATTTATATG-T
1 TCGCGTTGCGATTTACA-GAT
* *
22805 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTACAGAT
*
22825 TCTCGTTGCGATT
1 TCGCGTTGCGATT
22838 CTGGAAAATC
Statistics
Matches: 166, Mismatches: 35, Indels: 28
0.72 0.15 0.12
Matches are distributed among these distances:
19 3 0.02
20 125 0.75
21 38 0.23
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAGAT
Found at i:54797 original size:60 final size:60
Alignment explanation
Indices: 54709--54821 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
54699 ACTGGTCCTT
* * * * * *
54709 AAACTTTTGAACATTCTAATTTCCTCCTCACATTGCGACTCTGATTCTAAATTTGTGTCC
1 AAACTTTTAAACATTCCAATTTCATCCTCAAATTACGACTCTCATTCTAAATTTGTGTCC
* *
54769 AAACTTTTAAACATTCCACA-TTCATCCTCAAATTATGATTCTCATTCTAAATT
1 AAACTTTTAAACATTCCA-ATTTCATCCTCAAATTACGACTCTCATTCTAAATT
54822 GATCCCTAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
60 43 0.98
61 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.40
Consensus pattern (60 bp):
AAACTTTTAAACATTCCAATTTCATCCTCAAATTACGACTCTCATTCTAAATTTGTGTCC
Found at i:60409 original size:3 final size:3
Alignment explanation
Indices: 60403--60432 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
60393 ACCGAAAAAA
60403 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
60433 GGTCTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:61031 original size:29 final size:31
Alignment explanation
Indices: 60961--61039 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 31
60951 GGAACACGCA
* *
60961 ATGATATATGTCACATTAATATTTATATACAT
1 ATGATA-ATATCACATTAAGATTTATATACAT
* * *
60993 TTGAAAATATCATATTAAGATTTA-A-ACAT
1 ATGATAATATCACATTAAGATTTATATACAT
61022 ATGATAATATCACATTAA
1 ATGATAATATCACATTAA
61040 CACTTATGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 19 0.49
30 1 0.03
31 15 0.38
32 4 0.10
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (31 bp):
ATGATAATATCACATTAAGATTTATATACAT
Found at i:61081 original size:23 final size:22
Alignment explanation
Indices: 61054--61105 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 22
61044 TATGATATAT
61054 AATGTGTCATATCAAAATTGTA
1 AATGTGTCATATCAAAATTGTA
61076 ATATGTGTCATATCAAAATTGTA
1 A-ATGTGTCATATCAAAATTGTA
61099 AATGTGT
1 AATGTGT
61106 GTGACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 7 0.24
23 22 0.76
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (22 bp):
AATGTGTCATATCAAAATTGTA
Done.