Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002129.1 Hibiscus syriacus cultivar Beakdansim tig00004358_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: 61977
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2090 original size:7 final size:8
Alignment explanation
Indices: 2065--2089 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2055 CGTTCGTCAG
2065 TTATTTTT
1 TTATTTTT
2073 TTATTTTT
1 TTATTTTT
2081 TTATTTTT
1 TTATTTTT
2089 T
1 T
2090 AATAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTATTTTT
Found at i:7146 original size:31 final size:31
Alignment explanation
Indices: 7111--7189 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
7101 ATAACGGTTG
*
7111 AGTGACCATTTTGTTACAAATTGATAAAGTT
1 AGTGACCATTTTGTTACAAATCGATAAAGTT
* *
7142 AGTGAACATTTTGTTACAAATCGATAATGTT
1 AGTGACCATTTTGTTACAAATCGATAAAGTT
* *
7173 AGCGACCAATTTGTTAC
1 AGTGACCATTTTGTTAC
7190 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (31 bp):
AGTGACCATTTTGTTACAAATCGATAAAGTT
Found at i:15095 original size:21 final size:21
Alignment explanation
Indices: 15071--15134 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
15061 GGTAAAAAAA
15071 TATTTAAAATATTATTATTTT
1 TATTTAAAATATTATTATTTT
*
15092 TATTTAAAATACTATTATTTT
1 TATTTAAAATATTATTATTTT
* *
15113 TACTTAAAATATTAATATTTT
1 TATTTAAAATATTATTATTTT
15134 T
1 T
15135 TAATATTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (21 bp):
TATTTAAAATATTATTATTTT
Found at i:19927 original size:62 final size:62
Alignment explanation
Indices: 19848--19966 Score: 211
Period size: 62 Copynumber: 1.9 Consensus size: 62
19838 GTCCCCGAAT
*
19848 AATAGATCTATGTTGACCATTATTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
1 AATAGATCCATGTTGACCATTATTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
* *
19910 AATAGGTCCATGTTGACCATTGTTTTATTGTCATTAATATGACTCGTCATCTCAACG
1 AATAGATCCATGTTGACCATTATTTTATTGTCATTAATATGACTCGTCATCTCAACG
19967 AGACAAATCT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (62 bp):
AATAGATCCATGTTGACCATTATTTTATTGTCATTAATATGACTCGTCATCTCAACGTGATA
Found at i:20170 original size:15 final size:15
Alignment explanation
Indices: 20150--20181 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
20140 TATTCGGTCG
20150 ATTAAAATTTAAAAA
1 ATTAAAATTTAAAAA
20165 ATTAAAATTTAAAAA
1 ATTAAAATTTAAAAA
20180 AT
1 AT
20182 AATTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATTAAAATTTAAAAA
Found at i:21390 original size:26 final size:25
Alignment explanation
Indices: 21343--21397 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
21333 TATAAACAAA
* **
21343 TAAAAAATAATTAAATTTATGAAAT
1 TAAAAAAAAATTAAATAAATGAAAT
*
21368 TAAAAAAAAAGTTAAATAAATGAAGT
1 TAAAAAAAAA-TTAAATAAATGAAAT
21394 TAAA
1 TAAA
21398 CAATTACCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (25 bp):
TAAAAAAAAATTAAATAAATGAAAT
Found at i:22055 original size:2 final size:2
Alignment explanation
Indices: 22048--22078 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
22038 CGAATTATTG
22048 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
22079 CAATATTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22218 original size:15 final size:15
Alignment explanation
Indices: 22198--22227 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22188 TGGACATTAT
*
22198 CCAAGTGGTCGTTGC
1 CCAAGTGATCGTTGC
22213 CCAAGTGATCGTTGC
1 CCAAGTGATCGTTGC
22228 ATTTGCTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (15 bp):
CCAAGTGATCGTTGC
Found at i:23561 original size:22 final size:22
Alignment explanation
Indices: 23536--23586 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
23526 ACGTGAGAAT
*
23536 CACGGGTTCTGCAAGGAGAGAG
1 CACGGGTTCTGCAAGGAGAAAG
*
23558 CACGGGTTCTGCAAGGAGAAAT
1 CACGGGTTCTGCAAGGAGAAAG
23580 CACGGGT
1 CACGGGT
23587 CCTGGGTCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.37, T:0.16
Consensus pattern (22 bp):
CACGGGTTCTGCAAGGAGAAAG
Found at i:23629 original size:23 final size:23
Alignment explanation
Indices: 23603--23646 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
23593 TCCTGCAAGG
23603 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
23626 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
23647 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:23653 original size:23 final size:23
Alignment explanation
Indices: 23604--23653 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
23594 CCTGCAAGGC
* *
23604 TGCACGTCTGCATGTGGGGGTCC
1 TGCACGTCTGCATGTGGGGGGCA
23627 TGCACGTCTGCATGTGGGGGGCA
1 TGCACGTCTGCATGTGGGGGGCA
23650 TGCA
1 TGCA
23654 ACTGATGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (23 bp):
TGCACGTCTGCATGTGGGGGGCA
Found at i:24127 original size:21 final size:22
Alignment explanation
Indices: 24089--24129 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
24079 TTTTGGAACA
* *
24089 TTGTAAAGTTTTAGGGACCATT
1 TTGTAAAGATTTAAGGACCATT
24111 TTGTAAA-ATTTAAGGACCA
1 TTGTAAAGATTTAAGGACCA
24130 ACAAAAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (22 bp):
TTGTAAAGATTTAAGGACCATT
Found at i:25509 original size:21 final size:21
Alignment explanation
Indices: 25485--25528 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
25475 GATAAAAATC
*
25485 ATTTATTAATATGTTGTCTTG
1 ATTTATTAATATATTGTCTTG
* *
25506 ATTTATTACTATATTGTGTTG
1 ATTTATTAATATATTGTCTTG
25527 AT
1 AT
25529 AATGTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (21 bp):
ATTTATTAATATATTGTCTTG
Found at i:27259 original size:183 final size:182
Alignment explanation
Indices: 26525--27376 Score: 1042
Period size: 182 Copynumber: 4.7 Consensus size: 182
26515 CGTTCCATAG
* * * * * * * *
26525 CAATATTACAGGTACAAATATGACAAAACCGGTC-CCAAAATGACAAAACCTGTAAAACGCTACC
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAAAGTTACC
* ** * * *
26589 GAATATGTTGTCGAGTGTCGATAATTTAATATAAATATCGAAACTTTCTGAATTTAAAAGAGAAT
65 GGATATGTTG-AAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAG
* * *
26654 AAGTTATAGCGCCTATAAAGTGTCGATACTTTAAAAAAATATATCGATCCACAA
129 AAGTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATATATCGATCCACAA
* * * *
26708 CAATATAATAGGTAAAAATATGATAAAACTGGTCTAAAAAATGACAAAACCGGAAAAAGTTACCA
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCG
* *
26773 GATATATTGAAAGTGTCGATAATTTAATATTAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
* * ** *
26838 GTTATAGCGCCTAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCTTAG
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATATATCGATCCACAA
* * * **
26890 CAATATAATAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAATATTTACTA
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCG
* * * *
26955 GATATGTTAAAAGTGTCGATAATTTAATATAAGTATCGACAATTTCTAAATTTAAAAGAGAAAAA
66 GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
** * * * * *
27020 GTTATTTCGCTTAAAAAATGTCGACACTTTATGAAAATGTATCGATCCATAA
131 GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATATATCGATCCACAA
* * * * *
27072 TAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAATTGACAAAACCAGTAAAACGCTACC
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAAAGTTACC
* * * * *
27137 GGATATATTGAAAGTGTCGATAATTTAATATAAGTATCAAAACCTTCTGAATTTAAAAGAAAAGA
65 GGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGA
* * *
27202 AGTTATAGCGCCTATAAAGTGTCGATACTTT-TAAAAAATATATCAATCCACAA
130 AGTTATAGCGCCTAAAAAGTGTCGACACTTTAT-AAAAATATATCGATCCACAA
* * * * * * * *
27255 TAATATAACAGGTAAAAATATGATAAAACAGATCCCAAAATTGACAAAGCCAGTAAAACGATACC
1 CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACC-GGAAAAAGTTACC
* *
27320 GGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGACACTTTCTGAAATTAAA
65 GGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAA
27377 CTAAAAAGTG
Statistics
Matches: 583, Mismatches: 83, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
182 308 0.53
183 261 0.45
184 14 0.02
ACGTcount: A:0.45, C:0.13, G:0.14, T:0.28
Consensus pattern (182 bp):
CAATATAACAGGTAAAAATATGATAAAACAGGTCTCAAAAATGACAAAACCGGAAAAAGTTACCG
GATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAA
GTTATAGCGCCTAAAAAGTGTCGACACTTTATAAAAATATATCGATCCACAA
Found at i:27532 original size:163 final size:164
Alignment explanation
Indices: 27217--27539 Score: 434
Period size: 164 Copynumber: 2.0 Consensus size: 164
27207 TAGCGCCTAT
* *
27217 AAAGTGTCGATACTTTTAAAAAATATATCAATCCACAATAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGACACTTTTAAAAAATATATCAATCCACAACAATATAACAGGTAAAAATATGATAAA
* * * * *
27282 ACAGATCCCAAAATTGACAAAGCCAGTAAAACGATACCGGATATGTTGAAAGTGTCAATAATTTA
66 ACAGATCCCAAAAATGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTTA
*
27347 ATATAAGTATCGACACTTTCTGAAATTAAACTAA
131 ATATAAGTATCAACACTTTCTGAAATTAAACTAA
* * * *
27381 AAAGTGTCGACAC-TTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAA
1 AAAGTGTCGACACTTTTA-AAAAATATATCAATCCACAACAATATAACAGGTAAAAATATGATAA
** * * * * *
27445 AATTGCTCTCAAAAATGACAAAATC-GGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTT
65 AACAGATCCCAAAAATGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTT
* *
27509 AATATTAGTATCAACACTTTCTGAATTTAAA
130 AATATAAGTATCAACACTTTCTGAAATTAAA
27540 AGAGAATAAG
Statistics
Matches: 137, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
163 66 0.48
164 71 0.52
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (164 bp):
AAAGTGTCGACACTTTTAAAAAATATATCAATCCACAACAATATAACAGGTAAAAATATGATAAA
ACAGATCCCAAAAATGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTTA
ATATAAGTATCAACACTTTCTGAAATTAAACTAA
Found at i:27569 original size:163 final size:163
Alignment explanation
Indices: 27231--27569 Score: 396
Period size: 163 Copynumber: 2.1 Consensus size: 163
27221 TGTCGATACT
* * *
27231 TTTAAAAAATATATCAATCCACAATAATATAACAGGTAAAAATATGATAAAACAGATCCCAAAAT
1 TTTAAAAAATGTATCAATCCACAACAATATAACAGGTAAAAATATGATAAAACAGATCCCAAAAA
* * * * *
27296 TGACAAAGCCAGTAAAACGATACCGGATATGTTGAAAGTGTCAATAATTTAATATAAGTATCGAC
66 TGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATCAAC
** * *
27361 ACTTTCTGAAATTAAACTAAAAAGTGTCGACAC
131 ACTTTCTGAAATTAAAAGAAAAAGTATAGACAC
* * * ** * *
27394 TTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATTGCTCTCAAAA
1 TTTA-AAAAATGTATCAATCCACAACAATATAACAGGTAAAAATATGATAAAACAGATCCCAAAA
* * * *
27459 ATGACAAAATC-GGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATTTAATATTAGTATCAA
65 ATGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATCAA
* *
27523 CACTTTCTGAATTTAAAAGAGAATAAGTTATAG-CGC
130 CACTTTCTGAAATTAAAAGA-AA-AAG-TATAGACAC
27559 -TTAAAAAATGT
1 TTTAAAAAATGT
27570 CGGCACTTTA
Statistics
Matches: 146, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
163 74 0.51
164 64 0.44
165 5 0.03
166 3 0.02
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (163 bp):
TTTAAAAAATGTATCAATCCACAACAATATAACAGGTAAAAATATGATAAAACAGATCCCAAAAA
TGACAAAACCAGGAAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATCAAC
ACTTTCTGAAATTAAAAGAAAAAGTATAGACAC
Found at i:27710 original size:182 final size:182
Alignment explanation
Indices: 27378--27773 Score: 634
Period size: 182 Copynumber: 2.2 Consensus size: 182
27368 GAAATTAAAC
* * *
27378 TAAAAAGTGTCGACACTTTATGAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGAT
1 TAAAAAGTGTCGGCACTTTATGAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATAAT
*
27443 AAAATTGCTCTCAAAAATGACAAAATCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATT
66 AAAAATGCTCTCAAAAATGACAAAATCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATT
* * *
27508 TAATATTAGTATCAACACTTTCTGAATTTAAAAGAGAATAAGTTATAGCGCT
131 TAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
* * * *
27560 TAAAAAATGTCGGCACTTTATTAAAATGTATCGATCCTTACCAATATAACAAGTAAAAATATAAT
1 TAAAAAGTGTCGGCACTTTATGAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATAAT
*
27625 AAAACATG-TCTCAAAAATGACAAAA-CAGGAAAAAGTTACCGGATATGTTGAAAGTGTCGATAA
66 AAAA-ATGCTCTCAAAAATGACAAAATC-GGAAAAAGTTACCGGATATATTGAAAGTGTCGATAA
*
27688 TTTAATATAAGTATCGACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
129 TTTAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
*
27742 TAAAAAGTATCGGCACTTTATGAAAATGTATC
1 TAAAAAGTGTCGGCACTTTATGAAAATGTATC
27774 TGTAACATCC
Statistics
Matches: 196, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
181 1 0.01
182 193 0.98
183 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (182 bp):
TAAAAAGTGTCGGCACTTTATGAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATAAT
AAAAATGCTCTCAAAAATGACAAAATCGGAAAAAGTTACCGGATATATTGAAAGTGTCGATAATT
TAATATAAGTATCAACACTTTCTGAATTTAAAAGAGAAGAAGTTATAGCACT
Found at i:28572 original size:21 final size:21
Alignment explanation
Indices: 28547--28586 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
28537 AGTATGTCCA
28547 GGGGGTATCGATTCCCCCTGG
1 GGGGGTATCGATTCCCCCTGG
28568 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
28587 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.30, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTGG
Found at i:29245 original size:15 final size:15
Alignment explanation
Indices: 29227--29302 Score: 152
Period size: 15 Copynumber: 5.1 Consensus size: 15
29217 CGAGGGTATT
29227 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
29242 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
29257 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
29272 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
29287 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
29302 G
1 G
29303 CAGTGGTCCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 61 1.00
ACGTcount: A:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:30499 original size:18 final size:19
Alignment explanation
Indices: 30476--30520 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
30466 TAGTTAATAT
30476 TTATAGGTA-AAAATGATA
1 TTATAGGTAGAAAATGATA
30494 TTATAGGTAGAAAATGATA
1 TTATAGGTAGAAAATGATA
*
30513 TTTTAGGT
1 TTATAGGT
30521 TGTATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (19 bp):
TTATAGGTAGAAAATGATA
Found at i:30801 original size:18 final size:18
Alignment explanation
Indices: 30766--30804 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30756 TTGAAATGGT
30766 AATTGGATTAAAACTTTA
1 AATTGGATTAAAACTTTA
*
30784 AATT-GATTACAAATTTTA
1 AATTGGATTA-AAACTTTA
30802 AAT
1 AAT
30805 GTTGACAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (18 bp):
AATTGGATTAAAACTTTA
Found at i:31819 original size:22 final size:22
Alignment explanation
Indices: 31768--31823 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
31758 ATGTTTTTGT
*
31768 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAG-A
*
31791 TAGTTATTATATAAAATGATA-A
1 T-TTTATTATATAAAATGATAGA
31813 CTTTTATTATA
1 -TTTTATTATA
31824 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 2 0.07
24 17 0.61
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
TTTTATTATATAAAATGATAGA
Found at i:34015 original size:19 final size:19
Alignment explanation
Indices: 33989--34037 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
33979 AAATGCATGG
33989 TTAA-TTTGTATAAGATTT
1 TTAATTTTGTATAAGATTT
*
34007 TTAATTTTGTATACGATTT
1 TTAATTTTGTATAAGATTT
*
34026 ATAATTTTGTAT
1 TTAATTTTGTAT
34038 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (19 bp):
TTAATTTTGTATAAGATTT
Found at i:35516 original size:198 final size:195
Alignment explanation
Indices: 34980--35686 Score: 692
Period size: 198 Copynumber: 3.5 Consensus size: 195
34970 ATACATATGT
* * * *
34980 AAGAAT-ATGTGTCGATACATTTTCAAAA-AGTATCGACCCCAAAAACATCGAAAC-AAATATTT
1 AAGAATAAAGTGTCGATACA-TTT-AAAATTGTATCGATCCCAAAAACATCAAAACGAAA-A-TT
* ** * * * * * *
35042 ATAATATAATATTTAAATTAACAATGTAACCAGTATACATATACCGA-TTAATTATAAAACAGGT
62 ATAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGT
* * * * *
35106 CAACATAAAGTATCGACACTTTTTAAGTTTGTGTCGATACTTTTTTCCA-AAAGAAAGCACAAAC
127 CAA-ATAAAGTATCGACACTTGTTAAGTTTGTGTCGATACATTTTTCCATAATGAATGC-CCAAC
* *
35170 AAGTTC
190 GAGTGC
* * * * * *
35176 ACGCATAAAGTGTCAATACATTTAAAATTGTATCGATCACAAAAACATCGAAACCGATAATTATA
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATC-AAAACGAAAATTATA
* * * * *
35241 ATGTAATAGGTCAATTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCAG
65 ATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCA-
35306 AATAAAGTATCGACACTTGTGTAA-TTTGTGTCGATACATTTTGTCCATAATGAATGCCCAACGA
129 AATAAAGTATCGACACTTGT-TAAGTTTGTGTCGATACATTTT-TCCATAATGAATGCCCAACGA
35370 GATGC
192 G-TGC
* *
35375 AAGAATAACGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACGAAAATTACAA
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACGAAAATTATAA
* * * * *
35440 TGTTATAGGTAAATTTACAATGTACCCAGTATAAATATATCGATTTTATGAGAAAATATGTTTAA
66 TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATA-GGTCAA
* * * *
35505 ATAATGTATCGACAC-CGTTATAGTTTGTGTCAATATATTTTTCCAGAATGAATTAGGAATGCCC
130 ATAAAGTATCGACACTTGTTA-AGTTTGTGTCGATACATTTTTCC---AT-AA-T--GAATGCCC
35569 AACGAGGTGC
187 AACGA-GTGC
* * * * *
35579 AAGCATAAAGTGTCGATACATTTAAAATTGTATCGATCCAAAAAACAACGAAACCAATAATTATA
1 AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACGAA-AATTATA
* ** *
35644 ATGCAATAGGTAAATTTGTAATGCT-ACCGGTATAAATATACCG
65 ATGTAATAGGTAAATTTACAATG-TAACCAGTATAAATATACCG
35687 GTTAAATGCC
Statistics
Matches: 421, Mismatches: 67, Indels: 37
0.80 0.13 0.07
Matches are distributed among these distances:
195 4 0.01
196 66 0.16
197 71 0.17
198 110 0.26
199 56 0.13
200 2 0.00
201 2 0.00
202 1 0.00
204 67 0.16
205 41 0.10
206 1 0.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (195 bp):
AAGAATAAAGTGTCGATACATTTAAAATTGTATCGATCCCAAAAACATCAAAACGAAAATTATAA
TGTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGAGAAAATAGGTCAAA
TAAAGTATCGACACTTGTTAAGTTTGTGTCGATACATTTTTCCATAATGAATGCCCAACGAGTGC
Found at i:50504 original size:29 final size:30
Alignment explanation
Indices: 50443--50506 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
50433 TATGATTTCA
* * *
50443 ATTTTTCTTAATATTTATTATTATGGGCTT
1 ATTTTTCTCAATATTAATTATTATGGGCCT
50473 ATTTTT-TCAATATTAATTATTA-GAGGCCT
1 ATTTTTCTCAATATTAATTATTATG-GGCCT
50502 ATTTT
1 ATTTT
50507 ATAATTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.77
30 6 0.20
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.56
Consensus pattern (30 bp):
ATTTTTCTCAATATTAATTATTATGGGCCT
Found at i:56343 original size:15 final size:14
Alignment explanation
Indices: 56318--56347 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
56308 CACCAAACAC
56318 TAAAAAAATAAAAA
1 TAAAAAAATAAAAA
56332 TAAAAAACATAAAAA
1 TAAAAAA-ATAAAAA
56347 T
1 T
56348 GAAAGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:56950 original size:40 final size:41
Alignment explanation
Indices: 56891--57058 Score: 148
Period size: 40 Copynumber: 4.1 Consensus size: 41
56881 GAATTTACTC
* *
56891 ATTTTCTGAATCGCATTGCGATTCTTGGA-ATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
*
56931 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGG-AGATCGCGTTGCG
** **** *
56973 ATTCTTGGAAGATCGCGTTGCGA-TCTT-CTTTTCAACGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCGATTCTTGGAGATC-GCGTTGCG
* * *
57015 CTTTTCTAAATCGCGTTGCGGTT-TT-GATATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
57054 ATTTT
1 ATTTT
57059 GTTGGTCATT
Statistics
Matches: 103, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
39 11 0.11
40 42 0.41
41 8 0.08
42 23 0.22
43 7 0.07
44 12 0.12
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (41 bp):
ATTTTCTAAATCGCGTTGCGATTCTTGGAGATCGCGTTGCG
Found at i:56968 original size:22 final size:21
Alignment explanation
Indices: 56899--56996 Score: 128
Period size: 22 Copynumber: 4.7 Consensus size: 21
56889 TCATTTTCTG
*
56899 AATCGCATTGCGATTCTTGG-
1 AATCGCGTTGCGATTCTTGGA
***
56919 AATCGCGTTGCGATT-TTCTT
1 AATCGCGTTGCGATTCTTGGA
56939 AATCGCGTTGCGATTCTTGGA
1 AATCGCGTTGCGATTCTTGGA
56960 AGATCGCGTTGCGATTCTTGGA
1 A-ATCGCGTTGCGATTCTTGGA
56982 AGATCGCGTTGCGAT
1 A-ATCGCGTTGCGAT
56997 CTTCTTTTCA
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
19 2 0.03
20 29 0.42
21 3 0.04
22 35 0.51
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (21 bp):
AATCGCGTTGCGATTCTTGGA
Found at i:57031 original size:20 final size:20
Alignment explanation
Indices: 57008--57058 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
56998 TTCTTTTCAA
* *
57008 CGTTGCGCTTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
* *
57028 CGTTGCGGTTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
57047 CGTTGCGATTTT
1 CGTTGCGATTTT
57059 GTTGGTCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:58016 original size:22 final size:22
Alignment explanation
Indices: 57988--58088 Score: 91
Period size: 23 Copynumber: 4.4 Consensus size: 22
57978 ATATTTAATA
*
57988 TATATTAAATTTAAAATATTTT
1 TATATTTAATTTAAAATATTTT
*
58010 TATA-TTAATTTATTAAAGACTTTT
1 TATATTTAATTTA--AAATA-TTTT
58034 TA-ATTTAATTTAAAAATATTTT
1 TATATTTAATTT-AAAATATTTT
58056 GTAT-TTTAATTTAAAATATATTT
1 -TATATTTAATTTAAAATAT-TTT
*
58079 TTTATGTTAA
1 TATAT-TTAA
58089 AATATTTTGA
Statistics
Matches: 65, Mismatches: 4, Indels: 18
0.75 0.05 0.21
Matches are distributed among these distances:
21 7 0.11
22 17 0.26
23 23 0.35
24 17 0.26
25 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (22 bp):
TATATTTAATTTAAAATATTTT
Found at i:58025 original size:24 final size:23
Alignment explanation
Indices: 57988--58080 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 23
57978 ATATTTAATA
57988 TATATTAAATTT-AAA-ATATTTT
1 TATATT-AATTTAAAAGATATTTT
*
58010 TATATTAATTTATTAAAGA-CTTTT
1 TATATTAATTTA--AAAGATATTTT
58034 TA-ATTTAATTTAAAA-ATATTTT
1 TATA-TTAATTTAAAAGATATTTT
* *
58056 GTATTTTAATTTAAAATATATTTT
1 -TATATTAATTTAAAAGATATTTT
58080 T
1 T
58081 TATGTTAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 17
0.75 0.04 0.22
Matches are distributed among these distances:
21 6 0.10
22 13 0.22
23 15 0.25
24 24 0.41
25 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTAATTTAAAAGATATTTT
Found at i:58067 original size:23 final size:22
Alignment explanation
Indices: 57995--58080 Score: 93
Period size: 23 Copynumber: 3.8 Consensus size: 22
57985 ATATATATTA
*
57995 AATTT-AAAATATTTTTATATT
1 AATTTAAAAATATTTTTATTTT
* * *
58016 AATTTATTAAAGACTTTTTAATTT
1 AATTTA-AAAATA-TTTTTATTTT
58040 AATTTAAAAATATTTTGTATTTT
1 AATTTAAAAATATTTT-TATTTT
58063 AATTTAAAATATATTTTT
1 AATTTAAAA-ATATTTTT
58081 TATGTTAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 5 0.09
22 4 0.08
23 23 0.43
24 21 0.40
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (22 bp):
AATTTAAAAATATTTTTATTTT
Found at i:58195 original size:18 final size:19
Alignment explanation
Indices: 58174--58212 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
58164 GATAAAACAT
58174 ATAAT-TTAAAAAGTTAAA
1 ATAATATTAAAAAGTTAAA
* *
58192 ATAATATTAAATATTTAAA
1 ATAATATTAAAAAGTTAAA
58211 AT
1 AT
58213 TAAATTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
ATAATATTAAAAAGTTAAA
Found at i:58206 original size:54 final size:57
Alignment explanation
Indices: 58088--58232 Score: 149
Period size: 57 Copynumber: 2.6 Consensus size: 57
58078 TTTTATGTTA
* * * * *
58088 AAATATTTTGAAGTTAAGATAAAATAAAATATATTTAATAATTTAAAGTAATAATCT
1 AAATATTTAGAAATTAAGATAAAATAAAATATATTTAAAAAGTTAAAATAATAATCT
* *
58145 AATATATTTAGTAAATTAAGATAAAA-CATATA-ATTTAAAAAGTTAAAATAAT-AT-T
1 AA-ATATTTAG-AAATTAAGATAAAATAAAATATATTTAAAAAGTTAAAATAATAATCT
*
58200 AAATATTTA-AAATTAA-ATTAGAATAAAATATAT
1 AAATATTTAGAAATTAAGA-TAAAATAAAATATAT
58233 ATTTTTAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
51 1 0.01
52 11 0.15
53 4 0.05
54 9 0.12
55 3 0.04
56 2 0.03
57 19 0.26
58 11 0.15
59 13 0.18
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.37
Consensus pattern (57 bp):
AAATATTTAGAAATTAAGATAAAATAAAATATATTTAAAAAGTTAAAATAATAATCT
Found at i:58219 original size:19 final size:20
Alignment explanation
Indices: 58187--58224 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
58177 ATTTAAAAAG
58187 TTAAAATAATATTA-AATAT
1 TTAAAATAATATTAGAATAT
58206 TTAAAATTAA-ATTAGAATA
1 TTAAAA-TAATATTAGAATA
58225 AAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
TTAAAATAATATTAGAATAT
Found at i:58228 original size:25 final size:25
Alignment explanation
Indices: 58177--58286 Score: 69
Period size: 25 Copynumber: 4.2 Consensus size: 25
58167 AAAACATATA
* * *
58177 ATTTAAAAAGTTAAAATAATATTAAAT
1 ATTT-AAAA-TTAAATTAAAATAAAAT
*
58204 ATTTAAAATTAAATTAGAATAAAAT
1 ATTTAAAATTAAATTAAAATAAAAT
* ***
58229 ATATATTTTTAAATTAAAATAAATAT
1 ATTTAAAATTAAATTAAAATAAA-AT
* * *
58255 TTTTAAAA-TAAGTTAATAACAAATAT
1 ATTTAAAATTAAATTAA-AATAAA-AT
58281 ATTTAA
1 ATTTAA
58287 TAAGATAATA
Statistics
Matches: 64, Mismatches: 17, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
25 38 0.59
26 22 0.34
27 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (25 bp):
ATTTAAAATTAAATTAAAATAAAAT
Found at i:58248 original size:20 final size:20
Alignment explanation
Indices: 58223--58261 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
58213 TAAATTAGAA
*
58223 TAAAATATATATTTTTAAAT
1 TAAAATAAATATTTTTAAAT
58243 TAAAATAAATATTTTTAAA
1 TAAAATAAATATTTTTAAA
58262 ATAAGTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAAATAAATATTTTTAAAT
Found at i:59116 original size:15 final size:15
Alignment explanation
Indices: 59096--59127 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
59086 CACTTGGATT
59096 TTAGAAAGGGAAGTG
1 TTAGAAAGGGAAGTG
*
59111 TTAGAAAGGGGAGTG
1 TTAGAAAGGGAAGTG
59126 TT
1 TT
59128 TTTCCACACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.41, T:0.25
Consensus pattern (15 bp):
TTAGAAAGGGAAGTG
Found at i:59436 original size:14 final size:15
Alignment explanation
Indices: 59410--59438 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
59400 TATTTTATAT
59410 ATTTTATAATAATAA
1 ATTTTATAATAATAA
59425 ATTTTA-AATAATAA
1 ATTTTATAATAATAA
59439 CGACTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTATAATAATAA
Done.