Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002424.1 Hibiscus syriacus cultivar Beakdansim tig00004961_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: 141735
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7999 original size:2 final size:2
Alignment explanation
Indices: 7992--8024 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7982 TCATAAAATT
7992 TA 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 TA T
8025 TTTACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21110 original size:6 final size:6
Alignment explanation
Indices: 21099--21128 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
21089 TGGGGGTGAT
*
21099 GATGGG GATGGG GATGGG GATGGA GATGGG
1 GATGGG GATGGG GATGGG GATGGG GATGGG
21129 CCCGAGTCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.63, T:0.17
Consensus pattern (6 bp):
GATGGG
Found at i:25383 original size:15 final size:15
Alignment explanation
Indices: 25363--25412 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
25353 ATATTTAGTT
*
25363 GGGCGGACGGATGCG
1 GGGCGGGCGGATGCG
*
25378 GGGCGGGTGGATGCG
1 GGGCGGGCGGATGCG
*
25393 GTGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
25408 GGGCG
1 GGGCG
25413 AGTAAGGTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.08, C:0.18, G:0.64, T:0.10
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:29237 original size:2 final size:2
Alignment explanation
Indices: 29230--29291 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
29220 AAAGATTATG
29230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29272 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
29292 CTTATATGGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32742 original size:23 final size:23
Alignment explanation
Indices: 32714--32768 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
32704 GTCGTTTAAC
*
32714 ATTCATTTAGTGTTCACGAACAT
1 ATTCATTTAGCGTTCACGAACAT
* *
32737 GTTCATTTAGCGTTCACGAACGT
1 ATTCATTTAGCGTTCACGAACAT
32760 ATTCATTTA
1 ATTCATTTA
32769 TATATTCAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (23 bp):
ATTCATTTAGCGTTCACGAACAT
Found at i:33254 original size:20 final size:20
Alignment explanation
Indices: 33229--33270 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
33219 TAAAAATTTT
33229 AAAAAGAGATGATTTTATAA
1 AAAAAGAGATGATTTTATAA
33249 AAAAAGAGATGATTTTATAA
1 AAAAAGAGATGATTTTATAA
33269 AA
1 AA
33271 TTCTAGAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAAAGAGATGATTTTATAA
Found at i:36679 original size:9 final size:9
Alignment explanation
Indices: 36667--36699 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
36657 CGATGACGAC
*
36667 GAAGAAGAA
1 GAAGAAAAA
36676 GAAGAAAAA
1 GAAGAAAAA
36685 GAAGAAAAA
1 GAAGAAAAA
36694 GAAGAA
1 GAAGAA
36700 TGAAAGGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:45980 original size:7 final size:7
Alignment explanation
Indices: 45968--45993 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45958 TCTATTATTA
45968 AAAATTC
1 AAAATTC
45975 AAAATTC
1 AAAATTC
45982 AAAATTC
1 AAAATTC
45989 AAAAT
1 AAAAT
45994 ATATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:46362 original size:4 final size:4
Alignment explanation
Indices: 46340--46386 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
46330 AATATTAGTG
* *
46340 AATA AA-A ATATA AAT- AATA AATA TATG AATA AATA AATA AATA AATA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
46387 CTATACTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 5 0.14
4 29 0.81
5 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:46372 original size:27 final size:29
Alignment explanation
Indices: 46327--46383 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
46317 TGCATTTCAT
46327 ATAAATATTAGTGAATAAA-AATATAAATA
1 ATAAATATTAGTGAATAAATAA-ATAAATA
46356 ATAAATA-TA-TGAATAAATAAATAAATA
1 ATAAATATTAGTGAATAAATAAATAAATA
46383 A
1 A
46384 ATACTATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 4 0.15
29 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
ATAAATATTAGTGAATAAATAAATAAATA
Found at i:47901 original size:112 final size:112
Alignment explanation
Indices: 47682--48551 Score: 1230
Period size: 112 Copynumber: 7.7 Consensus size: 112
47672 AGAGTCATGC
*
47682 AAAGGTTGAACAAGTTCTTCTCATTATGAAC-TCTTC-TCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
** *
47744 ATGAACTCGAACTGGCAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTC-TTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
* *
47792 AAATGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
*
47857 ATGAACTCTTCTGTAAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
47904 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
47969 ATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
48016 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
* * **
48081 ATGAACTCTTCTGGAAAAGCTGATCCATC-AGATGATGGATTTGAGCA
66 ATGAACTCTTCTGGAAATGCTGATCCATCGA-ATGATGAATTCAAGCA
* *
48128 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
* * * **
48193 ATGAACTTTTTATGGAAAAT-CTGATCCATC-AGATGATGGATTTGAGCA
66 ATGAAC-TCTTCTGG-AAATGCTGATCCATCGA-ATGATGAATTCAAGCA
* * * * *
48241 AAAGGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GTGTTCTTCTC
* * * * *
48306 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAACA
63 ATTATGAACTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
* *
48357 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTC
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GTGTTCTTCTC
* * * * * *
48422 ATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTTAAACA
63 ATTATGAACTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
*
48473 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGTTCTTCTCAT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG-TGTTCTTCTCAT
48538 TATGAACTTCTTCT
65 TATGAAC-TCTTCT
48552 TCCTTCTTCA
Statistics
Matches: 707, Mismatches: 39, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
110 29 0.04
111 6 0.01
112 322 0.46
113 114 0.16
114 23 0.03
115 8 0.01
116 204 0.29
117 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATT
ATGAACTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAAGCA
Found at i:48531 original size:41 final size:40
Alignment explanation
Indices: 48484--48586 Score: 188
Period size: 41 Copynumber: 2.5 Consensus size: 40
48474 AAAGTTGAAC
48484 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
*
48524 GATGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
1 -AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
48565 AAGTTCTTCTCATTATGAACTT
1 AAGTTCTTCTCATTATGAACTT
48587 TCTCTTGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
40 21 0.35
41 39 0.65
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (40 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT
Found at i:48564 original size:386 final size:384
Alignment explanation
Indices: 48142--48855 Score: 1137
Period size: 386 Copynumber: 1.9 Consensus size: 384
48132 GTTGAACAAA
* ** *
48142 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGTGTTCTTCTCATTATGAACTTTTTATG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTATG
* * ** * * *
48207 GAAAAT-CTGATCCATC-AGATGATGGATTTGAGCAAAAGGTTGAATAAATTCTTCTCATTATGA
66 G-AAATGATGATCCATCGA-ATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGA
* *
48270 ATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATC
129 ACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATC
*
48335 CATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
194 CATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTT
*
48400 CTTCAGATGACGAGTTCTTCTCATTATGAACTCT-ACCTGGCAATGTTGATCCATCAAATGATGA
259 CTTCAGATGA--AGTTCTTCTCATTATGAACT-TGACCTAGCAATGTTGATCCATCAAATGATGA
48464 ATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATG
321 ATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATG
* *
48528 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTATG
*
48593 GAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 GAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC
48658 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCA
131 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCA
* *
48723 TCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCT
196 TCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
* * ** *
48788 TCAGATGATGTTCTTCTCATTATGAACTTGACCTAGTAATGTTGATCCATTGAATGATGGATTTA
261 TCAGATGAAGTTCTTCTCATTATGAACTTGACCTAGCAATGTTGATCCATCAAATGATGAATTTA
48853 AAC
326 AAC
48856 TTTGCTAAAA
Statistics
Matches: 300, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
383 1 0.00
384 52 0.17
385 4 0.01
386 242 0.81
387 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (384 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTATG
GAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCA
TCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCT
TCAGATGAAGTTCTTCTCATTATGAACTTGACCTAGCAATGTTGATCCATCAAATGATGAATTTA
AACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATG
Found at i:48625 original size:270 final size:272
Alignment explanation
Indices: 48255--48816 Score: 1004
Period size: 270 Copynumber: 2.1 Consensus size: 272
48245 GTTGAATAAA
* *
48255 TTCTTCTCATTATGAATTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC-AGTTCTTCTCATTATGAACTCTAC
* * *
48320 CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATG
48385 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT
130 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT
48450 CCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
195 CCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
48515 TCTTCAGATGATG
260 TCTTCAGATGATG
*
48528 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-AGTTCTTCTCATTATGAACT-TTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATGAACTCTAC-
* * *
48590 CTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATG
48655 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT
130 AACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGAT
48720 CCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
195 CCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
48785 TCTTCAGATGATG
260 TCTTCAGATGATG
48798 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
48817 GACCTAGTAA
Statistics
Matches: 279, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
269 2 0.01
270 241 0.86
272 1 0.00
273 35 0.13
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (272 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATGAACTCTACC
TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAATTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATC
CATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT
CTTCAGATGATG
Found at i:48626 original size:154 final size:157
Alignment explanation
Indices: 48371--48701 Score: 544
Period size: 154 Copynumber: 2.1 Consensus size: 157
48361 GTTGAACAAA
48371 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC-AGTTCTTCTCATTATGAACTCTAC
* * *
48436 CTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
*
48501 AACTTCTTCTTCCTTCTTCAGATGA-TG
130 AACTTCTTCTTCCTTCTTCAGATGACAG
*
48528 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-AGTTCTTCTCATTATGAACT-TTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATGAACTCTAC-
* *
48590 CTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
65 CTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATG
48655 AACTTCTTCTTCCTTCTTCAGATGACGAG
130 AACTTCTTCTTCCTTCTTCAGATGAC-AG
48684 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
48702 CTACCTGGCA
Statistics
Matches: 164, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
153 2 0.01
154 105 0.64
156 20 0.12
157 37 0.23
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.40
Consensus pattern (157 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAGTTCTTCTCATTATGAACTCTACC
TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCTTCTCATTATGA
ACTTCTTCTTCCTTCTTCAGATGACAG
Found at i:48653 original size:113 final size:113
Alignment explanation
Indices: 48527--48855 Score: 480
Period size: 116 Copynumber: 2.9 Consensus size: 113
48517 TTCAGATGAT
*
48527 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-AAGTTCTTCTCATTATGAACTTTCTC
1 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGTTCTTCTCATTATGAACTTAC-C
* *
48591 TTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAA
65 TGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAA
48640 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTA
1 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA--AGTTCTTCTCATTATGAACT-TA
* * *
48705 CCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAA
63 CCTGGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAA
*
48756 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGATGTTCTTCTCATTATGAACTTGACC
1 GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGTTCTTCTCATTATGAACTT-ACC
* * * ** * *
48821 TAGTAATGTTGATCCATTGAATGATGGATTTAAAC
65 TGGAAATGATGATCCATCAAATGATGAATTCAAAC
48856 TTTGCTAAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
113 39 0.20
114 53 0.27
116 105 0.53
117 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (113 bp):
GTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAAGTTCTTCTCATTATGAACTTACCT
GGAAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAA
Found at i:49281 original size:22 final size:22
Alignment explanation
Indices: 49253--49307 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
49243 GATAAAGCTT
*
49253 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
49275 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
49297 TCATCTTTGAA
1 TCATCTTTGAA
49308 GAGTGTAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:49757 original size:54 final size:54
Alignment explanation
Indices: 49675--49830 Score: 242
Period size: 54 Copynumber: 2.9 Consensus size: 54
49665 AGAATAGCAG
** *
49675 GTTCGTAAAACATTTGA-AAGCGTATTCATCCTTTCATGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAA-CACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
49729 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTATGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
49783 GTTCGTAAAATATTTGACAACACATTCATCTTTTCCTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
49831 CAAGATTTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 92 0.98
55 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:52136 original size:114 final size:113
Alignment explanation
Indices: 51937--52160 Score: 385
Period size: 114 Copynumber: 2.0 Consensus size: 113
51927 ACGATCATGC
* * *
51937 AATTCATCCTTTAATTCCAATGATGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAG
1 AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
52002 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
66 AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
* *
52050 AATTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCCTTTAAATCCAATGA-TGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
*
52115 GAACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
65 GAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
52161 TCACCTGGCA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
113 21 0.20
114 83 0.80
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (113 bp):
AATTCATCCTTTAAATCCAATGATGGTTCTGGGGTTCATACCAAATCAGATCAGATAACTCAAAG
AACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCA
Found at i:57745 original size:14 final size:15
Alignment explanation
Indices: 57711--57749 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
57701 CATAAAAATA
*
57711 CAAATGCAAAGATGC
1 CAAATGTAAAGATGC
*
57726 CAAATGTAAATATG-
1 CAAATGTAAAGATGC
57740 CAAATGTAAA
1 CAAATGTAAA
57750 CATGTAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (15 bp):
CAAATGTAAAGATGC
Found at i:57758 original size:14 final size:14
Alignment explanation
Indices: 57711--57758 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
57701 CATAAAAATA
* *
57711 CAAATGCAAAGATG
1 CAAATGTAAACATG
*
57725 CCAAATGTAAATATG
1 -CAAATGTAAACATG
57740 CAAATGTAAACATG
1 CAAATGTAAACATG
*
57754 TAAAT
1 CAAAT
57759 TATTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (14 bp):
CAAATGTAAACATG
Found at i:59824 original size:7 final size:7
Alignment explanation
Indices: 59812--59837 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59802 TCTATTATTA
59812 AAAATTC
1 AAAATTC
59819 AAAATTC
1 AAAATTC
59826 AAAATTC
1 AAAATTC
59833 AAAAT
1 AAAAT
59838 ATATTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTC
Found at i:60206 original size:4 final size:4
Alignment explanation
Indices: 60184--60230 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
60174 AATATTAGTG
* *
60184 AATA AA-A ATATA AAT- AATA AATA TATG AATA AATA AATA AATA AATA
1 AATA AATA A-ATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
60231 CTATACTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 5 0.14
4 29 0.81
5 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:60216 original size:27 final size:29
Alignment explanation
Indices: 60171--60227 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
60161 TGCATTTCAT
60171 ATAAATATTAGTGAATAAA-AATATAAATA
1 ATAAATATTAGTGAATAAATAA-ATAAATA
60200 ATAAATA-TA-TGAATAAATAAATAAATA
1 ATAAATATTAGTGAATAAATAAATAAATA
60227 A
1 A
60228 ATACTATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 4 0.15
29 7 0.26
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (29 bp):
ATAAATATTAGTGAATAAATAAATAAATA
Found at i:63792 original size:16 final size:17
Alignment explanation
Indices: 63761--63794 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
63751 TCATATTACA
63761 TTAATATTACTATATTTT
1 TTAATATTA-TATATTTT
63779 TTAATATT-TATATTTT
1 TTAATATTATATATTTT
63795 AATTTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
18 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTAATATTATATATTTT
Found at i:63835 original size:27 final size:26
Alignment explanation
Indices: 63776--63835 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
63766 ATTACTATAT
*
63776 TTTTTAATATTTATATTTTAATTTAA
1 TTTTTAATAATTATATTTTAATTTAA
* * *
63802 TTATTTAATAATTATTTGTTTATTTTTA
1 TT-TTTAATAATTATAT-TTTAATTTAA
63830 TTTTTA
1 TTTTTA
63836 GAAATTTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.07
27 16 0.57
28 10 0.36
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (26 bp):
TTTTTAATAATTATATTTTAATTTAA
Found at i:67716 original size:103 final size:103
Alignment explanation
Indices: 67523--67731 Score: 355
Period size: 104 Copynumber: 2.0 Consensus size: 103
67513 GTTTGAAAGC
67523 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
1 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
* *
67588 CCAATTCAGGTGATCATTAATTTTTTAACGGAAAAGAT
66 CCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
* * * *
67626 AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTTCTCGTATCCTGATCAATAAGTTAACG
1 AATGGCGGTGCCAATAGACATCATTAAAATATGA-TTTTATCGTATCCCGATCAACAAGTTAACA
67691 TCCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
65 TCCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
67730 AA
1 AA
67732 GTTTAGAACA
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
103 34 0.34
104 65 0.66
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (103 bp):
AATGGCGGTGCCAATAGACATCATTAAAATATGATTTTATCGTATCCCGATCAACAAGTTAACAT
CCAATTCAGGTGATCATTAATTTTTTAACGAAAAAAAT
Found at i:72206 original size:36 final size:36
Alignment explanation
Indices: 72153--72294 Score: 205
Period size: 36 Copynumber: 4.0 Consensus size: 36
72143 TGAATAAGAA
* * * *
72153 GAACGAAAGGTAGCATCGACACGTTCGATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
* *
72189 GAACGGAAGGAATCATCGGCACTTTCGGTTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
*
72225 GAACGGAAGGAAGCATCGGCACTTTCAATTCAAGTC
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
*
72261 GAACGGAAGGAGGCATC-GCACTTTCGATTCAAGT
1 GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGT
72295 GTTCATCTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 16 0.17
36 79 0.83
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGGCACTTTCGATTCAAGTC
Found at i:76241 original size:36 final size:36
Alignment explanation
Indices: 76178--76246 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
76168 TTTAATAAAT
** * *
76178 TTTTAATTTTTAATAATCATATCAATTTGATCTTCA
1 TTTTAATTTGAAATAATCATATAAATTTAATCTTCA
76214 TTTTAATTTGAAATAATTCA-ATAAATTTAATCT
1 TTTTAATTTGAAATAA-TCATATAAATTTAATCT
76247 AACGATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 25 0.89
37 3 0.11
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.51
Consensus pattern (36 bp):
TTTTAATTTGAAATAATCATATAAATTTAATCTTCA
Found at i:77463 original size:15 final size:15
Alignment explanation
Indices: 77443--77472 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
77433 TTCTCAATAT
77443 TTTTTTGATTTTTAA
1 TTTTTTGATTTTTAA
*
77458 TTTTTTGGTTTTTAA
1 TTTTTTGATTTTTAA
77473 AAAGGGATAG
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:0.00, G:0.10, T:0.73
Consensus pattern (15 bp):
TTTTTTGATTTTTAA
Found at i:78145 original size:3 final size:3
Alignment explanation
Indices: 78130--78176 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
78120 GATGTGTAAG
* *
78130 AGA AGA AGG AGA AGA AGA AGG AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
78177 GGGGCTAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:85809 original size:14 final size:14
Alignment explanation
Indices: 85786--85823 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
85776 TCTATCTATA
*
85786 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
85799 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
85814 TGCAGGGATT
1 TGCAGGGATT
85824 ACTTCCCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:88598 original size:2 final size:2
Alignment explanation
Indices: 88586--88648 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
88576 TTTTTGTCAC
*
88586 CT CT CT TT CT CT CT -T CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
88627 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
88649 TATGCCACTC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:89667 original size:22 final size:22
Alignment explanation
Indices: 89642--89688 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
89632 CGGAGATGAA
89642 GACTGATATCGTCAGAGATGGG
1 GACTGATATCGTCAGAGATGGG
* *
89664 GACTGATTTCGTCGGAGATGGG
1 GACTGATATCGTCAGAGATGGG
89686 GAC
1 GAC
89689 GGATGTCGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.15, G:0.38, T:0.23
Consensus pattern (22 bp):
GACTGATATCGTCAGAGATGGG
Found at i:89909 original size:20 final size:20
Alignment explanation
Indices: 89886--90046 Score: 223
Period size: 20 Copynumber: 7.8 Consensus size: 20
89876 CGATAGTCAG
* *
89886 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
89906 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
89926 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
89946 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
89966 ATTCGCATTGCGATTTATTTACAT
1 ATTCGCATTGCG----ATTTACGT
*
89990 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
90010 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
90030 ATTCACATTGCGATTTA
1 ATTCGCATTGCGATTTA
90047 GGAAAATCGC
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
20 107 0.85
24 19 0.15
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:90071 original size:21 final size:22
Alignment explanation
Indices: 90042--90084 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
90032 TCACATTGCG
90042 ATTTAGGAAAATCGCAAGGCGA
1 ATTTAGGAAAATCGCAAGGCGA
*
90064 ATTT-GGAAAATCGCAATGCGA
1 ATTTAGGAAAATCGCAAGGCGA
90085 TAGTCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
ATTTAGGAAAATCGCAAGGCGA
Found at i:90565 original size:89 final size:89
Alignment explanation
Indices: 90413--90586 Score: 285
Period size: 89 Copynumber: 2.0 Consensus size: 89
90403 GAATCATCTA
* * *
90413 ACTATTAAAAGTTACAAAATAGCCCATCAACTATAGGTTCTGTTTTGTTGAGTTCTTCTACTATT
1 ACTATTAAAAGTTACAAAATAACCCATCAACTATAGGTTCTGCTTTGTTGAGTTCTTCGACTATT
90478 AAAAAATACAAAATGGTGACTATG
66 AAAAAATACAAAATGGTGACTATG
* * *
90502 ACTATTAAAAGTTACAAAATAATCCATCGACTGTAGGTTCTGCTTTGTTGAGTTCTTCGACTATT
1 ACTATTAAAAGTTACAAAATAACCCATCAACTATAGGTTCTGCTTTGTTGAGTTCTTCGACTATT
*
90567 AAAAATTACAAAATGGTGAC
66 AAAAAATACAAAATGGTGAC
90587 CCAACTATTC
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 78 1.00
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (89 bp):
ACTATTAAAAGTTACAAAATAACCCATCAACTATAGGTTCTGCTTTGTTGAGTTCTTCGACTATT
AAAAAATACAAAATGGTGACTATG
Found at i:90771 original size:29 final size:29
Alignment explanation
Indices: 90734--90790 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
90724 ACATTTATAA
*
90734 TATATCATC-AAATCAGTACTTGAAAACAT
1 TATACCATCGAAA-CAGTACTTGAAAACAT
* *
90763 TATACCATCGAGACAGTGCTTGAAAACA
1 TATACCATCGAAACAGTACTTGAAAACA
90791 ACGACGATGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.92
30 2 0.08
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.26
Consensus pattern (29 bp):
TATACCATCGAAACAGTACTTGAAAACAT
Found at i:92870 original size:60 final size:60
Alignment explanation
Indices: 92758--92871 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
92748 TCTTTAGATT
* * * * *
92758 TCTTTTTTTAATTTCAGTGGCAATGTAACAGTGTTGCTGTCACTTTCTATTTTCAATAAC
1 TCTTTTTTTAATTTAAATGGCAATGTAACAGTGTTGCCGTCACTATCCATTTTCAATAAC
*
92818 TCTTTTTTTAATTTAAATGGCAATGTAACAGTGTTGCCGTCTCTATCCATTTTC
1 TCTTTTTTTAATTTAAATGGCAATGTAACAGTGTTGCCGTCACTATCCATTTTC
92872 CTCATTAGTG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.13, T:0.46
Consensus pattern (60 bp):
TCTTTTTTTAATTTAAATGGCAATGTAACAGTGTTGCCGTCACTATCCATTTTCAATAAC
Found at i:95038 original size:23 final size:23
Alignment explanation
Indices: 94994--95038 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
94984 GAATTTTTTG
* *
94994 TTTAAAATTATATTAAATAAGAA
1 TTTAAAATAATATCAAATAAGAA
95017 TTTAAAATAATTATCAAA-AAGA
1 TTTAAAATAA-TATCAAATAAGA
95039 TTAAAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (23 bp):
TTTAAAATAATATCAAATAAGAA
Found at i:95225 original size:60 final size:60
Alignment explanation
Indices: 95143--95319 Score: 187
Period size: 60 Copynumber: 3.0 Consensus size: 60
95133 ATATGCCCCC
* * * * **
95143 AAACTATAACCTTCATTTTAAATTAATCCTTAAACTTTTGAATATTTCAATTTTGTCTCA
1 AAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATCTCA
* * * *
95203 AAACTATGACTCTCATTCTAAATTAGTCCTTAAACTTATGAACA-TTCTAATTTCATCTCT
1 AAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTC-AATTTCATCTCA
* * ** *
95263 AGACTATGACCCTC-TCTCTAAATTGGTCCCCAAACTTTTGAATATTCCAATTTCATC
1 AAACTATGACCCTCAT-TCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATC
95320 CCCAAATTCA
Statistics
Matches: 96, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
59 4 0.04
60 90 0.94
61 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
AAACTATGACCCTCATTCTAAATTAGTCCTTAAACTTTTGAATATTTCAATTTCATCTCA
Found at i:95621 original size:60 final size:59
Alignment explanation
Indices: 95493--95636 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 59
95483 AAAGACTGGG
* * *
95493 GACCAATTTAGAATGAAGATCATAGTTTAGGGATGAAATTGAAATGCTAAAGAGTTTGAA
1 GACCAATTTAAAATGAAG-TCATAGTTCAGGGATGAAATTGAAATGCTAAACAGTTTGAA
* *
95553 GACTAATTTAAAATGATAGTCATAGTTCAGGGATGAAATTGGAATAT-TTAAACA-TTT-AGA
1 GACCAATTTAAAATGA-AGTCATAGTTCAGGGATGAAATT-GAA-ATGCTAAACAGTTTGA-A
95613 GACCAATTTAAAATGAAAGTCATA
1 GACCAATTTAAAATG-AAGTCATA
95637 CTTTGAAGAC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
59 1 0.01
60 59 0.81
61 11 0.15
62 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.30
Consensus pattern (59 bp):
GACCAATTTAAAATGAAGTCATAGTTCAGGGATGAAATTGAAATGCTAAACAGTTTGAA
Found at i:99624 original size:2 final size:2
Alignment explanation
Indices: 99617--99650 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
99607 AATAGGTTTA
99617 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
99651 CTTATAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:105810 original size:23 final size:23
Alignment explanation
Indices: 105778--105840 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
105768 TTTTGATAAC
*
105778 TATTAATTACATTAACATTGTTAT
1 TATT-ATTACAATAACATTGTTAT
105802 TATTATTACAATAACATTGTTAT
1 TATTATTACAATAACATTGTTAT
105825 TATTATTACAATAACA
1 TATTATTACAATAACA
105841 AAGAAGTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 34 0.89
24 4 0.11
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (23 bp):
TATTATTACAATAACATTGTTAT
Found at i:106627 original size:20 final size:20
Alignment explanation
Indices: 106589--106627 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
106579 ATAATATTTT
* **
106589 ATTTAATTAAATTTTAAATA
1 ATTTAATAAAATTAAAAATA
106609 ATTTAATAAAATTAAAAAT
1 ATTTAATAAAATTAAAAAT
106628 TAAAATACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAATAAAATTAAAAATA
Found at i:106805 original size:24 final size:23
Alignment explanation
Indices: 106760--106834 Score: 69
Period size: 24 Copynumber: 3.0 Consensus size: 23
106750 TATTTTTGGT
*
106760 ATTTTATCATATTTAAGTTTTAGAATA
1 ATTTTAT-AT-TTTAA-ATTTA-AATA
106787 ATTTTATATTTTAAATTTAAAATA
1 ATTTTATATTTTAAATTT-AAATA
* *
106811 TTTTTATTTTTTAAAATTTAAATA
1 ATTTTATATTTT-AAATTTAAATA
106835 TGCTTCTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
24 22 0.51
25 12 0.28
26 2 0.05
27 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (23 bp):
ATTTTATATTTTAAATTTAAATA
Found at i:106835 original size:24 final size:23
Alignment explanation
Indices: 106778--106835 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
106768 ATATTTAAGT
*
106778 TTTAGAATAATTTTATATTTTAAA
1 TTTA-AATATTTTTATATTTTAAA
*
106802 TTTAAAATATTTTTATTTTTTAAAA
1 TTT-AAATATTTTTATATTTT-AAA
106827 TTTAAATAT
1 TTTAAATAT
106836 GCTTCTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTTAAATATTTTTATATTTTAAA
Found at i:112426 original size:6 final size:6
Alignment explanation
Indices: 112415--112444 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
112405 ATAACAAGTT
*
112415 CGAATC CGAATC CGAATC CGAATC CAAATC
1 CGAATC CGAATC CGAATC CGAATC CGAATC
112445 GATTACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.13, T:0.17
Consensus pattern (6 bp):
CGAATC
Found at i:114280 original size:16 final size:17
Alignment explanation
Indices: 114230--114281 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
114220 AAAAATATTA
114230 AATTTGAAAGTTAGAGT
1 AATTTGAAAGTTAGAGT
*
114247 GA-TT-AAA-TTAGGAGT
1 AATTTGAAAGTTA-GAGT
114262 AATTTGAAAGTTA-AGT
1 AATTTGAAAGTTAGAGT
114278 AATT
1 AATT
114282 AAATATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 3 0.10
15 8 0.28
16 11 0.38
17 4 0.14
18 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.37
Consensus pattern (17 bp):
AATTTGAAAGTTAGAGT
Found at i:114638 original size:65 final size:66
Alignment explanation
Indices: 114564--114693 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 66
114554 CTACAGAAAA
*
114564 AAAGAAGCTTTATTTAATAATTACATTTTATTTACAGTTTCATCA-TTTTTTAATCCTAATTTCA
1 AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
114628 G
66 G
*
114629 AAAGAAGCTTTATTTAATAGTTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
1 AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
114694 AATTTAACAC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
65 43 0.69
66 19 0.31
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (66 bp):
AAAGAAGCTTTATTTAATAATTACATTTTATTTAAAGTTTCATCATTTTTTTAATCCTAATTTCA
G
Found at i:116738 original size:15 final size:15
Alignment explanation
Indices: 116692--116757 Score: 53
Period size: 15 Copynumber: 4.2 Consensus size: 15
116682 CAACTCCATT
116692 TTCC-TTTCTCTCTTC
1 TTCCTTTTCT-TCTTC
* * * *
116707 TTCATTCTGTTCCTC
1 TTCCTTTTCTTCTTC
116722 TTCCTTTTCTTCTTC
1 TTCCTTTTCTTCTTC
116737 TTCCTCTCTTTCTTCTTC
1 TT-C-CT-TTTCTTCTTC
116755 TTC
1 TTC
116758 ATCTTCCTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
15 20 0.51
16 4 0.10
17 3 0.08
18 12 0.31
ACGTcount: A:0.02, C:0.36, G:0.02, T:0.61
Consensus pattern (15 bp):
TTCCTTTTCTTCTTC
Found at i:119404 original size:36 final size:36
Alignment explanation
Indices: 119364--119480 Score: 173
Period size: 36 Copynumber: 3.2 Consensus size: 36
119354 CTCCTTGTTC
* *
119364 CTCTTCATCTTCTCCTTTCAA-TGCATCTTCAGCCTT
1 CTCTTCATCTTCTTCTTTCAACT-CTTCTTCAGCCTT
119400 CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCT
1 CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCC-T-T
119438 CTTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
1 C-TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
119475 CTCTTC
1 CTCTTC
119481 TTGTTCCTCT
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
36 35 0.47
37 4 0.05
38 3 0.04
39 33 0.44
ACGTcount: A:0.11, C:0.37, G:0.03, T:0.49
Consensus pattern (36 bp):
CTCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTT
Found at i:119406 original size:12 final size:12
Alignment explanation
Indices: 119389--119480 Score: 57
Period size: 12 Copynumber: 7.4 Consensus size: 12
119379 TTTCAATGCA
119389 TCTTCAGCCTTC-
1 TCTTCA-CCTTCT
*
119401 TCTTCATCTTCT
1 TCTTCACCTTCT
*
119413 TCTTTCAAC-TCT
1 TC-TTCACCTTCT
119425 TCTTCAGCCTTCTCT
1 TCTTCA-CC-T-TCT
*
119440 TCTTCATCTTCT
1 TCTTCACCTTCT
*
119452 TCTTTCAAC-TCT
1 TC-TTCACCTTCT
119464 TCTTCAGCCTTC-
1 TCTTCA-CCTTCT
119476 TCTTC
1 TCTTC
119481 TTGTTCCTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
11 12 0.18
12 30 0.46
13 13 0.20
14 1 0.02
15 9 0.14
ACGTcount: A:0.10, C:0.37, G:0.03, T:0.50
Consensus pattern (12 bp):
TCTTCACCTTCT
Found at i:119444 original size:39 final size:39
Alignment explanation
Indices: 119365--119482 Score: 181
Period size: 39 Copynumber: 3.1 Consensus size: 39
119355 TCCTTGTTCC
* *
119365 TCTTCATCTTCTCCTTTCAA-TGCATCTTCAGCC-T-TC-
1 TCTTCATCTTCTTCTTTCAACT-CTTCTTCAGCCTTCTCT
119401 TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCTCT
1 TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCTCT
119440 TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCTCT
1 TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCTCT
119479 TCTT
1 TCTT
119483 GTTCCTCTGC
Statistics
Matches: 76, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
36 29 0.38
37 2 0.03
38 2 0.03
39 43 0.57
ACGTcount: A:0.11, C:0.36, G:0.03, T:0.50
Consensus pattern (39 bp):
TCTTCATCTTCTTCTTTCAACTCTTCTTCAGCCTTCTCT
Found at i:119482 original size:18 final size:18
Alignment explanation
Indices: 119389--119444 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
119379 TTTCAATGCA
*
119389 TCTTCAGCCTTCTCTTCA
1 TCTTCAGCCTTCTCTTCT
** * *
119407 TCTTCTTCTTTCAAC-TCT
1 TCTTCAGCCTTC-TCTTCT
119425 TCTTCAGCCTTCTCTTCT
1 TCTTCAGCCTTCTCTTCT
119443 TC
1 TC
119445 ATCTTCTTCT
Statistics
Matches: 27, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 1 0.04
18 25 0.93
19 1 0.04
ACGTcount: A:0.09, C:0.38, G:0.04, T:0.50
Consensus pattern (18 bp):
TCTTCAGCCTTCTCTTCT
Found at i:122320 original size:21 final size:21
Alignment explanation
Indices: 122274--122321 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
122264 AAAAATTAAA
*
122274 ATAAAACAAAGAAAAACTTTG
1 ATAAAACAAAAAAAAACTTTG
* *
122295 A-AAAAGAAAAAAAAACTTTT
1 ATAAAACAAAAAAAAACTTTG
122315 ATAAAAC
1 ATAAAAC
122322 CATAGGAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.19
Consensus pattern (21 bp):
ATAAAACAAAAAAAAACTTTG
Found at i:122998 original size:9 final size:9
Alignment explanation
Indices: 122984--123013 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
122974 TGAAAGCTAC
122984 GAAGCAGAA
1 GAAGCAGAA
122993 GAAGCAGAA
1 GAAGCAGAA
*
123002 GAAGTAGAA
1 GAAGCAGAA
123011 GAA
1 GAA
123014 TTAATGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.33, T:0.03
Consensus pattern (9 bp):
GAAGCAGAA
Found at i:123522 original size:60 final size:59
Alignment explanation
Indices: 123385--123522 Score: 143
Period size: 60 Copynumber: 2.3 Consensus size: 59
123375 GAACAAATGA
* * * * * *
123385 ATAGTCGAACGACTATTTTATAACTTTTAATAATAGAAAGATTCAATAAAATAATGTCTC
1 ATAGTCGAA-GACCATTTTATAACTTTCAATAATAGAAAAACTCAATAAAACAATATCTC
* * *
123445 ATAGTCAGAAGATCATTTTATAACTTTCAATTATTA-AAAAACTCAATAAAACAATATCTT
1 ATAGTC-GAAGACCATTTTATAACTTTCAA-TAATAGAAAAACTCAATAAAACAATATCTC
*
123505 ATAGTCGATGGACCATTT
1 ATAGTCGA-AGACCATTT
123523 GTGTACTTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
59 2 0.03
60 55 0.86
61 7 0.11
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (59 bp):
ATAGTCGAAGACCATTTTATAACTTTCAATAATAGAAAAACTCAATAAAACAATATCTC
Found at i:129010 original size:11 final size:11
Alignment explanation
Indices: 128980--129013 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
128970 AATTTGAAAA
*
128980 TTTTAATTAAT
1 TTTTAATTGAT
128991 TTTTAATTGAT
1 TTTTAATTGAT
129002 TTTTAATTGAT
1 TTTTAATTGAT
129013 T
1 T
129014 AATTAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (11 bp):
TTTTAATTGAT
Found at i:131109 original size:16 final size:15
Alignment explanation
Indices: 131076--131109 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
131066 GAGGATTTTT
*
131076 TTTAAAAAAATAATA
1 TTTAAAAAAATAAAA
131091 TTTAAAAAAAGTAAAA
1 TTTAAAAAAA-TAAAA
131107 TTT
1 TTT
131110 GTTAAGTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (15 bp):
TTTAAAAAAATAAAA
Found at i:131275 original size:29 final size:29
Alignment explanation
Indices: 131199--131275 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
131189 TTTTTAACAG
131199 TAGACACCTAAAAGTATAACGAAAAAAATAT
1 TAGACACC-AAAAGT-TAACGAAAAAAATAT
*** * *
131230 TAGACA-CAACTTTTTAACGAAAAAATTTT
1 TAGACACCAA-AAGTTAACGAAAAAAATAT
131259 TAGACACCAAAAGTTAA
1 TAGACACCAAAAGTTAA
131276 TTTTAACTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
29 25 0.69
30 5 0.14
31 6 0.17
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (29 bp):
TAGACACCAAAAGTTAACGAAAAAAATAT
Found at i:131418 original size:29 final size:32
Alignment explanation
Indices: 131353--131429 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 32
131343 TGTTAAAATC
* *
131353 AATTAT-AC-TAATTATTTTATGAAAAATAAT
1 AATTATAACATAATAATATTATGAAAAATAAT
*
131383 AATTATAATATAA-AATATTAT-AAAAAT-AT
1 AATTATAACATAATAATATTATGAAAAATAAT
*
131412 ATTTATAACATAATAATA
1 AATTATAACATAATAATA
131430 AAGAAATTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
29 13 0.33
30 16 0.41
31 7 0.18
32 3 0.08
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (32 bp):
AATTATAACATAATAATATTATGAAAAATAAT
Found at i:131965 original size:21 final size:20
Alignment explanation
Indices: 131924--131966 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
131914 ATTTTGAAAT
* *
131924 TTATTTTTAAAAAAATATTA
1 TTATATTTAAAAAAACATTA
*
131944 TTATATTTATAAAAAACCTTA
1 TTATATTTA-AAAAAACATTA
131965 TT
1 TT
131967 TCTTTTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATATTTAAAAAAACATTA
Found at i:132520 original size:29 final size:30
Alignment explanation
Indices: 132465--132525 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
132455 CATTTTGAGT
* *
132465 AACGGAATGAAATGTTAGGCATCAAACTGG
1 AACGAAATGAAATGTTAGACATCAAACTGG
132495 AACGAAAT-AAATGTTAGACA-CTAAACTGG
1 AACGAAATGAAATGTTAGACATC-AAACTGG
132524 AA
1 AA
132526 AAACGAGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 20 0.71
30 7 0.25
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (30 bp):
AACGAAATGAAATGTTAGACATCAAACTGG
Done.