Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009378.1 Hibiscus syriacus cultivar Beakdansim tig00113253_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: 80867
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Found at i:250 original size:33 final size:34
Alignment explanation
Indices: 197--261 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
187 AACAATGCCA
*
197 AAGGTAAGAGAAGTACCTATACTCCCATGATGGT
1 AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
231 AAGGTAAGAG-AGTACCTATAATCCCATGATG
1 AAGGTAAGAGAAGTACCTATAATCCCATGATG
262 TATCGATACT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 20 0.67
34 10 0.33
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (34 bp):
AAGGTAAGAGAAGTACCTATAATCCCATGATGGT
Found at i:737 original size:14 final size:15
Alignment explanation
Indices: 707--743 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
697 CAATTATTTT
707 TCTTGTAAGCTTAAA
1 TCTTGTAAGCTTAAA
722 TCTTGTAAGC-TAAA
1 TCTTGTAAGCTTAAA
736 TCTTGTAA
1 TCTTGTAA
744 ACACATATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (15 bp):
TCTTGTAAGCTTAAA
Found at i:1188 original size:155 final size:155
Alignment explanation
Indices: 843--1225 Score: 434
Period size: 155 Copynumber: 2.5 Consensus size: 155
833 TGTAAATATT
* * * * * * * * * *
843 AATTAGTTAATTTGTT-AGAAATATTCAGTGTGGAACTAAGGTAGTGGATTCAAACTTCATTAAG
1 AATTAGTGAATTTGTTAAAAAAAATT-AATGTAGAGCTAAGGCAGTGGATACAAATTTCATTGAG
* * * * *
907 GAAGTTGAACT--AG-GGTATTGGTTCTATATTAGTCATTA-AAAAGATAGAGATTTGTAAGAGT
65 GAAGTTGAACTCAAGAGG---TGGTTCTATCTTCGCCTTTAGAAAAGATAGAGATTTGTAAAAGT
968 TACTCTTGAGCCTAGAAAAAGAAAGAACA
127 TACTCTTGAGCCTAGAAAAAGAAAGAACA
* * **** * * *
997 AATTAGTTAATTTGTTAGAATTCCTTATTGTGGAGCTAAGGCAGTGGATGCAAATTTCATTGAGG
1 AATTAGTGAATTTGTTAAAAAAAATTAATGTAGAGCTAAGGCAGTGGATACAAATTTCATTGAGG
*
1062 AATTTGAACTCAAGAGGTGGTTCTATCTTCGCCTTTAGAAAAGATAGAGATTTGTAAAAGTTACT
66 AAGTTGAACTCAAGAGGTGGTTCTATCTTCGCCTTTAGAAAAGATAGAGATTTGTAAAAGTTACT
*
1127 CTTGAGCCTAGAAAAAGAAATAACA
131 CTTGAGCCTAGAAAAAGAAAGAACA
* * *
1152 AATTAGTGGATTTGTTAAAAAAAATTAATGTAGAGCTAAGGTAGTGGATATAAATTTCATTGAGG
1 AATTAGTGAATTTGTTAAAAAAAATTAATGTAGAGCTAAGGCAGTGGATACAAATTTCATTGAGG
1217 AAGTTGAAC
66 AAGTTGAAC
1226 AACTATAAAT
Statistics
Matches: 192, Mismatches: 32, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
154 74 0.39
155 114 0.59
156 2 0.01
157 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (155 bp):
AATTAGTGAATTTGTTAAAAAAAATTAATGTAGAGCTAAGGCAGTGGATACAAATTTCATTGAGG
AAGTTGAACTCAAGAGGTGGTTCTATCTTCGCCTTTAGAAAAGATAGAGATTTGTAAAAGTTACT
CTTGAGCCTAGAAAAAGAAAGAACA
Found at i:15736 original size:21 final size:21
Alignment explanation
Indices: 15692--15736 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
15682 GATTTCTGGG
* * *
15692 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
15713 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
15734 CAA
1 CAA
15737 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:17372 original size:103 final size:103
Alignment explanation
Indices: 17188--17402 Score: 367
Period size: 103 Copynumber: 2.1 Consensus size: 103
17178 GTCGAGGGTC
**
17188 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTACTGAGACACATAC
* *
17253 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
17291 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTACTGAGACACATAC
1 TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTACTGAGACACATAC
*
17356 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
17394 TATGTGGTC
1 TATGTGGTC
17403 CTTATGGACA
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCATTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTACTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:17471 original size:23 final size:23
Alignment explanation
Indices: 17417--17489 Score: 96
Period size: 23 Copynumber: 3.3 Consensus size: 23
17407 TGGACATTAT
17417 TATATGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
***
17440 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
17463 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
17484 TATATG
1 TATATG
17490 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 6 0.14
22 3 0.07
23 34 0.79
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:22430 original size:103 final size:103
Alignment explanation
Indices: 22246--22471 Score: 409
Period size: 103 Copynumber: 2.2 Consensus size: 103
22236 GTCGAGGGTC
22246 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
22311 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
22349 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
22414 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
22452 TATGTGGTCCTT-GTGGACAT
1 TATGTGGTCCTTCG-GGACAT
22472 TATTATATGG
Statistics
Matches: 119, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
102 1 0.01
103 118 0.99
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:22537 original size:23 final size:23
Alignment explanation
Indices: 22479--22539 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
22469 CATTATTATA
*
22479 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
22502 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTACG
*
22525 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
22540 TTTATATGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:22547 original size:23 final size:23
Alignment explanation
Indices: 22470--22547 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
22460 CCTTGTGGAC
* *
22470 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
22494 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
22517 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
22540 TTTATATG
1 ATTATATG
22548 AGTTGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:23349 original size:15 final size:14
Alignment explanation
Indices: 23329--23388 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 14
23319 TCGAAGAAAG
23329 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAA-A
23344 AAAAAGAAAAAAAA
1 AAAAAGAAAAAAAA
23358 GAAAAAGAAAAAGGAAA
1 -AAAAAGAAAAA--AAA
23375 AAAAGAGAAAAAAA
1 AAAA-AGAAAAAAA
23389 CGTTTAGGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.02
15 26 0.63
16 4 0.10
17 10 0.24
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAA
Found at i:23359 original size:30 final size:31
Alignment explanation
Indices: 23325--23388 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
23315 TAAGTCGAAG
23325 AAAGAAAAAGAAAAAA-AGAAAAAAGA-AAAA
1 AAAGAAAAAGAAAAAAGA-AAAAAAGAGAAAA
*
23355 AAAGAAAAAGAAAAAGGAAAAAAAGAGAAAA
1 AAAGAAAAAGAAAAAAGAAAAAAAGAGAAAA
23386 AAA
1 AAA
23389 CGTTTAGGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 23 0.74
31 8 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (31 bp):
AAAGAAAAAGAAAAAAGAAAAAAAGAGAAAA
Found at i:26693 original size:13 final size:14
Alignment explanation
Indices: 26677--26725 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
26667 TATATATATA
26677 TATTTATATTTC-C
1 TATTTATATTTCTC
26690 TATTT-TATTTCTC
1 TATTTATATTTCTC
26703 TATTTTATATTT-T-
1 TA-TTTATATTTCTC
26716 TATTT-TATTT
1 TATTTATATTT
26726 TATTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 5 0.15
12 9 0.27
13 10 0.30
14 4 0.12
15 5 0.15
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTATATTTCTC
Found at i:26992 original size:15 final size:17
Alignment explanation
Indices: 26962--26993 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
26952 TATTCTATTC
26962 ATTTTTATATTTACTTT
1 ATTTTTATATTTACTTT
26979 ATTTTT-TA-TTACTTT
1 ATTTTTATATTTACTTT
26994 CTTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTTTTATATTTACTTT
Found at i:28477 original size:31 final size:31
Alignment explanation
Indices: 28415--28483 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
28405 TTATATAAAA
* *
28415 AATTTAAACTAATAATAAAATTAATTTATAT
1 AATTTAAACAAATAATAAAATTAATTAATAT
28446 AATTTAAA-AAATAAATAAAA-TAATTAAATAT
1 AATTTAAACAAAT-AATAAAATTAATT-AATAT
*
28477 AAATTAA
1 AATTTAA
28484 TAAGTGATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (31 bp):
AATTTAAACAAATAATAAAATTAATTAATAT
Found at i:28657 original size:35 final size:35
Alignment explanation
Indices: 28607--28676 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
28597 ACAAGTTATT
28607 GTTTCACGTGACAACCATATGATTTTTCCTATATC
1 GTTTCACGTGACAACCATATGATTTTTCCTATATC
*
28642 GTTTCACGTGGCAACCATATGATTTTTCCTATATC
1 GTTTCACGTGACAACCATATGATTTTTCCTATATC
28677 CATGTGTCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (35 bp):
GTTTCACGTGACAACCATATGATTTTTCCTATATC
Found at i:30802 original size:57 final size:57
Alignment explanation
Indices: 30718--30828 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 57
30708 GTCAAATCAT
* * *
30718 TCAAATGTCGAGTGTTATAACTGCGGCAAGCATGGGCACTATGCAAAAGAGTGCAAA
1 TCAAATGTCGAGTGCTATAACTACGGCAAGCATGGCCACTATGCAAAAGAGTGCAAA
* ** *
30775 TCAAATGTCGAGTGCTATAATTACGGCAATTATGGCCACTATGCAAAGGAGTGC
1 TCAAATGTCGAGTGCTATAACTACGGCAAGCATGGCCACTATGCAAAAGAGTGC
30829 TATTCCGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.23
Consensus pattern (57 bp):
TCAAATGTCGAGTGCTATAACTACGGCAAGCATGGCCACTATGCAAAAGAGTGCAAA
Found at i:36078 original size:21 final size:21
Alignment explanation
Indices: 36054--36138 Score: 104
Period size: 21 Copynumber: 4.2 Consensus size: 21
36044 TCGATAATTT
36054 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTCGACTATC
* * ** *
36075 GCAA--CGAATTTGGAAAACC
1 GCAACGCGAACTTCGACTATC
36094 GCAACGCGAACTTCGACTATC
1 GCAACGCGAACTTCGACTATC
36115 GCAACGCGAACTT-GACTATC
1 GCAACGCGAACTTCGACTATC
36135 GCAA
1 GCAA
36139 TACGAATATG
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
19 14 0.27
20 11 0.21
21 27 0.52
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (21 bp):
GCAACGCGAACTTCGACTATC
Found at i:46385 original size:77 final size:77
Alignment explanation
Indices: 46220--46517 Score: 314
Period size: 77 Copynumber: 3.9 Consensus size: 77
46210 GTAAATAAGA
* * * * * *
46220 AGAACGAAAAGAAGCATCACATTTTCGATTCAAGTAGAACGAAATGAGGCATAATACTTTCAATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
*
46285 CCCGTA--TAAAGT
66 --CTTACCTAAAGT
* * * * * *
46297 AGAACGAAAGGAAGCATCGCAGTTTCGATTCAAGTATAATGAAAGGAGGCATAACACTTTTGATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
** *
46362 CTTATTTAATGT
66 CTTACCTAAAGT
** * * * * *
46374 -GTATTGGAAGGAAGCATCACACTTTCAATTCAAGAAGAACGAAAGAAGACAAAACACTTTCGAT
1 AG-AACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGAT
46438 TCTTACCTAAAGT
65 TCTTACCTAAAGT
* * *
46451 AGAACGGAAGGAAGTATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGATT
1 AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
46516 CT
66 CT
46518 CGATGATAGA
Statistics
Matches: 180, Mismatches: 37, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
75 3 0.02
76 1 0.01
77 175 0.97
78 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (77 bp):
AGAACGGAAGGAAGCATCACACTTTCGATTCAAGTAGAACGAAAGGAGGCATAACACTTTCGATT
CTTACCTAAAGT
Found at i:46510 original size:154 final size:153
Alignment explanation
Indices: 46230--46517 Score: 373
Period size: 154 Copynumber: 1.9 Consensus size: 153
46220 AGAACGAAAA
* * * * * *
46230 GAAGCATCACATTTTCGATTCAAGTAGAACGAAATGAGGCATAATACTTTCAATTCCCGTATAAA
1 GAAGCATCACACTTTCAATTCAAGAAGAACGAAATGAGACAAAACACTTTCAATT-CCGTATAAA
* * * ** * *
46295 GTAGAACGAAAGGAAGCATCGCAGTTTCGATTCAAGTATAATGAAAGGAGGCATAACACTTTTGA
65 GTAGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGA
46360 TTCTTATTTAATGTGTATTGGAAG
130 TTCTTATTTAATGTGTATTGGAAG
* *
46384 GAAGCATCACACTTTCAATTCAAGAAGAACGAAA-GAAGACAAAACACTTTCGATT-CTTACCTA
1 GAAGCATCACACTTTCAATTCAAGAAGAACGAAATG-AGACAAAACACTTTCAATTCCGTA--TA
* *
46447 AAGTAGAACGGAAGGAAGTATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTC
63 AAGTAGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTC
46512 GATTCT
128 GATTCT
46518 CGATGATAGA
Statistics
Matches: 114, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
152 3 0.03
153 1 0.01
154 110 0.96
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (153 bp):
GAAGCATCACACTTTCAATTCAAGAAGAACGAAATGAGACAAAACACTTTCAATTCCGTATAAAG
TAGAACGAAAGGAAGCATCACACTTTCGATTCAAGTAGAACAAAAAGAGGCATAACACTTTCGAT
TCTTATTTAATGTGTATTGGAAG
Found at i:55342 original size:16 final size:15
Alignment explanation
Indices: 55309--55381 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 15
55299 AAATTCTAAA
55309 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
55324 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
* ** *
55339 T-TATCGAT-AATA-
1 TATTTAAATAAAAAT
55351 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
55366 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
55381 T
1 T
55382 CATCGATAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 1 0.02
13 7 0.16
14 7 0.16
15 30 0.67
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:55354 original size:42 final size:42
Alignment explanation
Indices: 55308--55391 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
55298 GAAATTCTAA
*
55308 ATATTTAAATAAAAATTATTTATATAAAAATTTATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
55350 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
1 ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
55392 TTAATTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (42 bp):
ATATTTAAATAAAAATTATTTATATAAAAATTCATCGATAAT
Found at i:56011 original size:22 final size:23
Alignment explanation
Indices: 55947--56012 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 23
55937 AACTGTTGAA
55947 AATTAAAATCCACCGAAAGGTGG
1 AATTAAAATCCACCGAAAGGTGG
* * *
55970 CATTAAACAAATCTATCGAAAGGTGG
1 AATT--A-AAATCCACCGAAAGGTGG
55996 AATT-AAATCCACCGAAA
1 AATTAAAATCCACCGAAA
56013 ATAATAAGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 11 0.32
23 3 0.09
25 1 0.03
26 19 0.56
ACGTcount: A:0.45, C:0.18, G:0.17, T:0.20
Consensus pattern (23 bp):
AATTAAAATCCACCGAAAGGTGG
Found at i:59794 original size:29 final size:30
Alignment explanation
Indices: 59752--59833 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 30
59742 CCCAAAGGAC
*
59752 CTATCCAGATGTCACAAAG-ACCCCGACAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* * *
59781 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCCCGACAA
* * * *
59811 CTGTCCATAGGTCCCGAAGAACC
1 CTATCCAGAGGTCACAAAGAACC
59834 TAGGTAAACT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 17 0.40
30 26 0.60
ACGTcount: A:0.34, C:0.32, G:0.18, T:0.16
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCCCGACAA
Found at i:59823 original size:30 final size:31
Alignment explanation
Indices: 59778--59850 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
59768 AAGACCCCGA
* * * *
59778 CAACTATCCAGAGGTCATAAAGAACCTCGG-
1 CAACTGTCCATAGGTCACAAAGAACCTAGGT
* *
59808 CAACTGTCCATAGGTCCCGAAGAACCTAGGT
1 CAACTGTCCATAGGTCACAAAGAACCTAGGT
*
59839 AAACTGTCCATA
1 CAACTGTCCATA
59851 TGTCTCGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 24 0.69
31 11 0.31
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (31 bp):
CAACTGTCCATAGGTCACAAAGAACCTAGGT
Found at i:59847 original size:31 final size:31
Alignment explanation
Indices: 59809--59873 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
59799 GAACCTCGGC
*
59809 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
59840 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
59871 AAC
1 AAC
59874 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:72126 original size:21 final size:23
Alignment explanation
Indices: 72078--72132 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
72068 AGAGTTCTAA
72078 TTGTACATTCATATTGATCAGTT
1 TTGTACATTCATATTGATCAGTT
72101 TTGTACATTCATA-TGATCAG-T
1 TTGTACATTCATATTGATCAGTT
*
72122 TTGTATATTCA
1 TTGTACATTCA
72133 GATCGAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 11 0.35
22 7 0.23
23 13 0.42
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (23 bp):
TTGTACATTCATATTGATCAGTT
Found at i:75031 original size:11 final size:11
Alignment explanation
Indices: 75015--75039 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
75005 TAAAAATTGA
75015 TATATATACTT
1 TATATATACTT
75026 TATATATACTT
1 TATATATACTT
75037 TAT
1 TAT
75040 TTTGGGATCT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (11 bp):
TATATATACTT
Found at i:75907 original size:3 final size:3
Alignment explanation
Indices: 75889--75931 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
75879 CTACAAAAAC
*
75889 ATT A-T ATT ACT ATT ATT ATT ATT A-T ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
75932 CTATTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
2 4 0.11
3 32 0.89
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:75914 original size:20 final size:20
Alignment explanation
Indices: 75889--75937 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
75879 CTACAAAAAC
75889 ATTATATTACTATTATTATT
1 ATTATATTACTATTATTATT
*
75909 ATTATATTATTATTATTATT
1 ATTATATTACTATTATTATT
*
75929 ATTCTATTA
1 ATTATATTA
75938 ATTTATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATATTACTATTATTATT
Found at i:75916 original size:14 final size:14
Alignment explanation
Indices: 75889--75927 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
75879 CTACAAAAAC
75889 ATTA-TATTACTATT
1 ATTATTATTA-TATT
75903 ATTATTATTATATT
1 ATTATTATTATATT
75917 ATTATTATTAT
1 ATTATTATTAT
75928 TATTCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:75936 original size:17 final size:17
Alignment explanation
Indices: 75889--75937 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
75879 CTACAAAAAC
75889 ATTA-TATTACTATTATT
1 ATTATTATT-CTATTATT
75906 ATTATTATAT-TATTATT
1 ATTATTAT-TCTATTATT
75923 ATTATTATTCTATTA
1 ATTATTATTCTATTA
75938 ATTTATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 24 0.83
18 3 0.10
19 1 0.03
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATTATTCTATTATT
Found at i:75948 original size:20 final size:20
Alignment explanation
Indices: 75889--75949 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
75879 CTACAAAAAC
*
75889 ATTATATTACTATTATTATT
1 ATTATATTAATATTATTATT
*
75909 ATTATATTATTATTATTATT
1 ATTATATTAATATTATTATT
*
75929 ATTCTATTAAT-TTATATATT
1 ATTATATTAATATTAT-TATT
75949 A
1 A
75950 CAATTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 4 0.11
20 33 0.89
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTATATTAATATTATTATT
Found at i:75958 original size:17 final size:17
Alignment explanation
Indices: 75891--75958 Score: 61
Period size: 20 Copynumber: 3.9 Consensus size: 17
75881 ACAAAAACAT
75891 TATATTACTATTATTATTA
1 TATATTACTATTA-T-TTA
*
75910 TTATATTATTATTA-TTA
1 -TATATTACTATTATTTA
75927 T-TATT-CTATTAATTTA
1 TATATTACTATT-ATTTA
*
75943 TATATTACAATTATTT
1 TATATTACTATTATTT
75959 TGCAGGCAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 5 0.12
17 11 0.27
18 4 0.10
20 12 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTACTATTATTTA
Found at i:76883 original size:29 final size:29
Alignment explanation
Indices: 76841--76899 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
76831 TTACATACCG
76841 CTTCCCTTCCCCTATATATTCAACAAACA
1 CTTCCCTTCCCCTATATATTCAACAAACA
76870 CTTCCCTTCCCCTATATATTCAACAAACA
1 CTTCCCTTCCCCTATATATTCAACAAACA
76899 C
1 C
76900 GCTGCTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.31
Consensus pattern (29 bp):
CTTCCCTTCCCCTATATATTCAACAAACA
Found at i:77834 original size:15 final size:14
Alignment explanation
Indices: 77812--77848 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
77802 TTTAATTGTA
77812 TTTTATTATTTCTT
1 TTTTATTATTTCTT
77826 TTATTATTATTTCTT
1 TT-TTATTATTTCTT
77841 TTTTATTA
1 TTTTATTA
77849 ACTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTATTTCTT
Found at i:79201 original size:27 final size:27
Alignment explanation
Indices: 79170--79234 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
79160 TTTGTTCGGG
79170 TCGGGTCGGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
*
79197 TCGGGTCAGGTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTAAGTGTGATAT
*
79224 TCAGGTCGGGT
1 TCGGGTCGGGT
79235 CGGGTTCGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.15, C:0.09, G:0.34, T:0.42
Consensus pattern (27 bp):
TCGGGTCGGGTTTTTTAAGTGTGATAT
Found at i:79203 original size:32 final size:31
Alignment explanation
Indices: 79168--79240 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 31
79158 ATTTTGTTCG
79168 GGTCGGGTCGGGTTTTTTAAGTGTGATA-T-
1 GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
*
79197 --TCGGGTCAGGTTTTTTAAGTGTGATATTC
1 GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
79226 AGGTCGGGTCGGGTT
1 -GGTCGGGTCGGGTT
79241 CGGGTTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 25 0.68
28 1 0.03
32 11 0.30
ACGTcount: A:0.14, C:0.10, G:0.37, T:0.40
Consensus pattern (31 bp):
GGTCGGGTCGGGTTTTTTAAGTGTGATATTC
Found at i:79834 original size:17 final size:18
Alignment explanation
Indices: 79790--79841 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 18
79780 AATGGAATTG
* *
79790 GATTCCAATT-CCTGAAA
1 GATTCCAATTCCCTCATA
*
79807 GATTCCAATTCCTTCATA
1 GATTCCAATTCCCTCATA
79825 GATTCC-ATTCCCTCATA
1 GATTCCAATTCCCTCATA
79842 AAACATTCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 20 0.67
18 10 0.33
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCCTCATA
Done.