Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001688.1 Hibiscus syriacus cultivar Beakdansim tig00003372_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: 75190
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:68 original size:20 final size:20
Alignment explanation
Indices: 43--117 Score: 105
Period size: 20 Copynumber: 3.7 Consensus size: 20
33 ATGCAATTAG
*
43 TGCATCGATGCATCTTGCTA
1 TGCATCGATGCATCTTGCCA
63 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCAT-CTTGCCA
* *
84 TGCATCGATGCATCCTGCGA
1 TGCATCGATGCATCTTGCCA
*
104 TGCATCCATGCATC
1 TGCATCGATGCATC
118 AAGGCTGTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 31 0.62
21 19 0.38
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCATCTTGCCA
Found at i:1469 original size:31 final size:28
Alignment explanation
Indices: 1430--1513 Score: 91
Period size: 27 Copynumber: 3.0 Consensus size: 28
1420 AATAAAAACT
1430 AAAAAAATTAAATAAAAAACAATTCAAAG
1 AAAAAAATTAAATAAAAAACAATT-AAAG
* *
1459 AAAATTAAATTAAAT-TAAAACAATTTAAG
1 AAAA--AAATTAAATAAAAAACAATTAAAG
* *
1488 AAAAAAA-TAAATAAAATACAAATAAA
1 AAAAAAATTAAATAAAAAACAATTAAA
1514 ATAATTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 5 0.11
27 12 0.26
29 11 0.24
30 9 0.20
31 9 0.20
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (28 bp):
AAAAAAATTAAATAAAAAACAATTAAAG
Found at i:3826 original size:151 final size:151
Alignment explanation
Indices: 3518--3899 Score: 482
Period size: 151 Copynumber: 2.5 Consensus size: 151
3508 ATCTGTTTGG
* * *
3518 TTTAAGTCTCTTTGTCGTTAATTCCCGTTAACCCTTAATGGAAGTGCTACATGACAGTTAATTTA
1 TTTAAGTCTCTTTGTCGTTAATTCCCATTAACCCTTAAAGGAAGTGCTACATGACAGTT-ACTT-
* * * * * *
3583 AAAAAATATCCACATTGACTTTTCTTCATCTTTATCGTCCACGTTTTTAATTAAGTATTCATGAT
64 AAAAAA-ATCCACGTTGACTTTTCTTCATCTTTATCATCCACATTTTTAACTAAATACTCATGAT
* * * *
3648 CCTTTGCGTTATCAATCTGTTCGA
128 ACTTTACGATATCAATCTATTCGA
* * *
3672 TTTAAGTCTCTCTGTTGTTAATTCCCATTAACCCTTAAAGGAATTGCTACATGACAGTTACTTAA
1 TTTAAGTCTCTTTGTCGTTAATTCCCATTAACCCTTAAAGGAAGTGCTACATGACAGTTACTTAA
*
3737 AAAAATCCACGTTGACTTTTCTTCATCTTTATCATCCACATTTTTAACTAAATACTCTTGATACT
66 AAAAATCCACGTTGACTTTTCTTCATCTTTATCATCCACATTTTTAACTAAATACTCATGATACT
* *
3802 TTACGATATCGATTTATTCGA
131 TTACGATATCAATCTATTCGA
* ** * *
3823 TTTAAGTATCTTTGTCGTTAATT-CCAGTTAACCCTTAACA-GAAGTATTGCATGAGAGTTACTT
1 TTTAAGTCTCTTTGTCGTTAATTCCCA-TTAACCCTTAA-AGGAAGTGCTACATGACAGTTACTT
3886 -AAAAAATCCACGTT
64 AAAAAAATCCACGTT
3900 TACAGTTACT
Statistics
Matches: 199, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
150 17 0.09
151 118 0.59
152 7 0.04
153 3 0.02
154 54 0.27
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (151 bp):
TTTAAGTCTCTTTGTCGTTAATTCCCATTAACCCTTAAAGGAAGTGCTACATGACAGTTACTTAA
AAAAATCCACGTTGACTTTTCTTCATCTTTATCATCCACATTTTTAACTAAATACTCATGATACT
TTACGATATCAATCTATTCGA
Found at i:4775 original size:36 final size:36
Alignment explanation
Indices: 4728--4801 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
4718 CCATTGTCGA
4728 AGTTAGTGCATAACTAAAAGGATCATAGTGGAAAGT
1 AGTTAGTGCATAACTAAAAGGATCATAGTGGAAAGT
4764 AGTTAGTGCATAACTAAAAGGATCATAGTGGAAAGT
1 AGTTAGTGCATAACTAAAAGGATCATAGTGGAAAGT
4800 AG
1 AG
4802 ACCTCTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (36 bp):
AGTTAGTGCATAACTAAAAGGATCATAGTGGAAAGT
Found at i:9506 original size:12 final size:12
Alignment explanation
Indices: 9477--9525 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
9467 AATTATTAAC
9477 ATATTTAA-AAT
1 ATATTTAATAAT
*
9488 ATATTTATTAAT
1 ATATTTAATAAT
*
9500 ATTTTTAATAAT
1 ATATTTAATAAT
*
9512 ATAATATAATAAT
1 AT-ATTTAATAAT
9525 A
1 A
9526 ATAATACAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 7 0.23
12 15 0.48
13 9 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:9506 original size:23 final size:23
Alignment explanation
Indices: 9459--9516 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
9449 CATTTTAATA
9459 AAAATATTAATTATTAACATATTT
1 AAAATA-TAATTATTAACATATTT
* * *
9483 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAACATATTT
9506 AATAATATAAT
1 AA-AATATAAT
9517 ATAATAATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 16 0.55
24 13 0.45
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATATAATTATTAACATATTT
Found at i:17199 original size:23 final size:23
Alignment explanation
Indices: 17173--17224 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
17163 ATCGATACCT
*
17173 CCCTTTGTA-GGGAAACCGATTCC
1 CCCTTTGAATGGG-AACCGATTCC
17196 CCCTTTGAATGGGAACCGATTCC
1 CCCTTTGAATGGGAACCGATTCC
17219 CCCTTT
1 CCCTTT
17225 AGGGAATCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 24 0.89
24 3 0.11
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.29
Consensus pattern (23 bp):
CCCTTTGAATGGGAACCGATTCC
Found at i:21358 original size:23 final size:24
Alignment explanation
Indices: 21320--21364 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
21310 CTATGGGCAC
*
21320 GTAGAAATTGTCCCGAATGACCGT
1 GTAGAAATTGTCCCGAAGGACCGT
21344 GTAGAAA-TGTCCCGAAGGACC
1 GTAGAAATTGTCCCGAAGGACC
21365 ACATATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GTAGAAATTGTCCCGAAGGACCGT
Found at i:23086 original size:24 final size:24
Alignment explanation
Indices: 23059--23105 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
23049 TTTTTTCATA
*
23059 TAATAATATTATATATTTAATTAT
1 TAATAATATTATATATTAAATTAT
* *
23083 TAATAGTTTTATATATTAAATTA
1 TAATAATATTATATATTAAATTA
23106 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TAATAATATTATATATTAAATTAT
Found at i:23276 original size:17 final size:17
Alignment explanation
Indices: 23254--23292 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
23244 GAATTACGAA
*
23254 TACCCGTAAAATTTGAG
1 TACCCGTAAAATTCGAG
23271 TACCCGTAAAATTCGAG
1 TACCCGTAAAATTCGAG
23288 TACCC
1 TACCC
23293 AATTATCGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (17 bp):
TACCCGTAAAATTCGAG
Found at i:24720 original size:4 final size:4
Alignment explanation
Indices: 24713--24771 Score: 57
Period size: 4 Copynumber: 14.8 Consensus size: 4
24703 ACATATATAC
* * * *
24713 ATGT ATGT ATGT ATGT ATGT ATACT TTG- ATAT ATGT ATGT ATTT ATGT
1 ATGT ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT
*
24761 ATAT ATGT ATG
1 ATGT ATGT ATG
24772 CCTGATGAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
3 1 0.02
4 40 0.93
5 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.19, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:24749 original size:20 final size:20
Alignment explanation
Indices: 24716--24771 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
24706 TATATACATG
*
24716 TATGTATGTATGTATGTATACT
1 TATGTATATATGTATGTAT--T
24738 T-TG-ATATATGTATGTATT
1 TATGTATATATGTATGTATT
24756 TATGTATATATGTATG
1 TATGTATATATGTATG
24772 CCTGATGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.77
21 2 0.06
22 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.52
Consensus pattern (20 bp):
TATGTATATATGTATGTATT
Found at i:27544 original size:34 final size:34
Alignment explanation
Indices: 27501--27572 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
27491 ATTCAATCAT
* *
27501 ATATCTTTTAATATTTAAATTTAAACA-GATAATA
1 ATATATTTTAATATTCAAATTTAAACATG-TAATA
27535 ATATATTTTAATATTCAAATTTAAACATGTAATA
1 ATATATTTTAATATTCAAATTTAAACATGTAATA
27569 ATAT
1 ATAT
27573 CTTTAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (34 bp):
ATATATTTTAATATTCAAATTTAAACATGTAATA
Found at i:29373 original size:18 final size:15
Alignment explanation
Indices: 29350--29393 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
29340 CTCCTCGGCT
29350 GGCTTCTTCTCCGCC
1 GGCTTCTTCTCCGCC
29365 GGCTTCTTCTCCGCC
1 GGCTTCTTCTCCGCC
29380 GGCTTCTTCTCCGC
1 GGCTTCTTCTCCGC
29394 TTTAGGTGCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.00, C:0.45, G:0.20, T:0.34
Consensus pattern (15 bp):
GGCTTCTTCTCCGCC
Found at i:30215 original size:15 final size:15
Alignment explanation
Indices: 30197--30255 Score: 64
Period size: 15 Copynumber: 3.7 Consensus size: 15
30187 TAATAGTTTC
30197 TATAAAAATATAACA
1 TATAAAAATATAACA
* *
30212 TATAAAAATGTATCGA
1 TATAAAAATATAAC-A
*
30228 TCCATAACAATATAACA
1 T--ATAAAAATATAACA
30245 TATAAAAATAT
1 TATAAAAATAT
30256 GATATTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
15 21 0.60
16 2 0.06
17 2 0.06
18 10 0.29
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (15 bp):
TATAAAAATATAACA
Found at i:30590 original size:182 final size:182
Alignment explanation
Indices: 30256--30932 Score: 1004
Period size: 182 Copynumber: 3.7 Consensus size: 182
30246 ATAAAAATAT
*
30256 GATATTTTATTATAAGTATCGACACTTTT-AGAATTTAAAAGACAAGCAGTAATAGCGCCTATAA
1 GATACTTTATTATAAGTATCGACACTTTTGA-AATTTAAAAGACAAGCAGTAATAGCGCCTATAA
* ** * *
30320 AGTGTCGAT-TCAAATAAAAATGTATCGATCCATATCAATATAACAGATAAAAATATGACAAAAC
65 AGTGTCGATACCTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
* * *
30384 CGATCTCAAAATGACCAAACCGGTAAAGCACTTCCGGATATGTTGAAAGTGTC
130 CGGTCTCAAAATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTC
* *
30437 GATACTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGATAAGCAGTAATAGTGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
** * *
30502 GTGTCGATATTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATC
66 GTGTCGATACCTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
*
30567 GGTCTCAAAATGACAAAACCGGTAAAG-AGCTACCGGATATATTGAAAGTGTC
131 GGTCTCAAAATGACAAAACCGGTAAAGCA-CTACCGGATATGTTGAAAGTGTC
* *
30619 GATACTTTATTATAAGTATCAACACTTTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
* * *
30684 GTGTCGATACTTTATAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGATAAAACC
66 GTGTCGATACCTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
* * *
30749 AGTCTCAAAATGACAAAACCGGTAAAGCGCTACCAGATATGTTGAAAGTGTC
131 GGTCTCAAAATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTC
**
30801 GATACTTTATTATAAGTATCGACACTTTTTTAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
1 GATACTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
* * * * * *
30866 GTGTCGATGCCTTATAAAAACGTATTGA-CACTTAACGATATAATAGGTAAAAA-ATGACAAAAC
66 GTGTCGATACCTTATAAAAATGTATCGATC-CATAACAATATAACAGGTAAAAATATGACAAAAC
30929 CGGT
130 CGGT
30933 AAAGCGCTAT
Statistics
Matches: 453, Mismatches: 38, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
181 82 0.18
182 371 0.82
ACGTcount: A:0.42, C:0.14, G:0.15, T:0.28
Consensus pattern (182 bp):
GATACTTTATTATAAGTATCGACACTTTTGAAATTTAAAAGACAAGCAGTAATAGCGCCTATAAA
GTGTCGATACCTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACC
GGTCTCAAAATGACAAAACCGGTAAAGCACTACCGGATATGTTGAAAGTGTC
Found at i:34134 original size:201 final size:201
Alignment explanation
Indices: 33787--34873 Score: 1594
Period size: 201 Copynumber: 5.4 Consensus size: 201
33777 AATAGATGTA
* *
33787 TCGATACAGTTATAGAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTTAA-AGG
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG-TAATAGG
*
33851 TAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATATGTCTACATAATGTAT
65 TAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGTAT
* * *
33916 CGACACTTGTGGAATTTGTGTCGAAACTTTTTGTCTAGAATGAATGCCCAAAAGGGGTGCACACA
130 CGACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACACA
33981 TAAAGTG
195 TAAAGTG
* * *
33988 TCGATACAATTATAAAAAATATCGATCCTAAAAACATCGAAACCCATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* *
34053 AATTTTTCAATGTAACCGGTACAAATATACTAGTTTTATGAGAGAATAGGTCTACATAATGTATC
66 AATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGTATC
* * *
34118 GACACTTGTAGAATTTGTGTCGAAACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGTACGCAT
131 GACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACACAT
34183 AAAGTG
196 AAAGTG
* *
34189 TCGATATATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATGTTAA-AGG
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATG-TAATAGG
* *
34253 TAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATATTGTAT
65 TAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGTAT
*
34318 CGACACTTGTGGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGGGTGCACA
130 CGACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAA--GGGGTGCACA
*
34383 CATAAAATG
193 CATAAAGTG
* *
34392 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGC
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* *
34457 AATTTTTCAATGTAACCGGTATAAATATAGC-GGTTTTATGAGAGAATAGGTATACGTAATGTAT
66 AATTTTTCAATGTAACCGGTATAAATATA-CTGGTTTTATGAGAGAATAGGTCTACATAATGTAT
* * * *
34521 CAACACTT-TTGAAATTTGTGTCGATACTTTTTGTCCGGAATGAATGCCTAAAA-GGGTGCACAC
130 CGACACTTGTAG-AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACAC
*
34584 ATAACGTG
194 ATAAAGTG
* * * * *
34592 TCGATACATTTATAAAAAGTGTCGATCCTAAAAACATCAAAATCGATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* * * * * * ** *
34657 AAATTTCCAATGTAACCGGTATAAATATATTGGTTTAATTAGAAAAGCGGTCAACATAATGTATC
66 AATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGTATC
* * * * * *
34722 AACACTTTTTA-AATTTGTGTCGATACTTTTTGTCCAGAATCAATGCCC-AACGAGGTGCACGCA
131 GACAC-TTGTAGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACACA
34785 TAAAGTG
195 TAAAGTG
*
34792 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGT
1 TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
* *
34857 AAATTTACAATGTAACC
66 AATTTTTCAATGTAACC
34874 AGGAGGAAAT
Statistics
Matches: 808, Mismatches: 67, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
199 2 0.00
200 263 0.33
201 355 0.44
202 9 0.01
203 178 0.22
204 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (201 bp):
TCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
AATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGAGAGAATAGGTCTACATAATGTATC
GACACTTGTAGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAGGGGTGCACACAT
AAAGTG
Found at i:36648 original size:199 final size:199
Alignment explanation
Indices: 36305--37017 Score: 1015
Period size: 199 Copynumber: 3.6 Consensus size: 199
36295 CAGGTAAACA
* *
36305 AAAGTGTCGATATATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
* *
36370 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCTGTTAATTAGAAAACAAGTCTACATAAT
66 ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAACAGGTCTACATAAT
* *
36435 GTATTGACATTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGTAC
131 GTATCGACATTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGCAC
*
36500 ACAT
196 GCAT
36504 AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACAGAA-AATTATAATGT
1 AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACA-AATAATTATAATGT
* *
36568 AATAGGTAAATTTCTAATGTAATCGGTAGAAATATACCGGTTAATTAGAAAACAGGTCTACATAA
65 AATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAACAGGTCTACATAA
* * * * * *
36633 TGTAACGATATTTTTTAAATTTGTATCGATATTTTTTGTCCAGAATGAATGACAAACGGGGTGCA
130 TGTATCGACATTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGCA
* *
36698 TGCGT
195 CGCAT
36703 AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
1 AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
* * * **
36768 ATAGGTAAATGTT-CAATGTAATCGGTAGATATATACCGGTTTAATTAGAAAATAGGTAAACATA
66 ATAGGTAAAT-TTCCAATGTAACCGGTAGAAATATACCGG-TTAATTAGAAAACAGGTCTACATA
** * * * *
36832 ATGTATCGACACATTTTAAA-TTATGTCGATAC-TTTTGTCCATAATGAATGCCCAACCTGGGTG
129 ATGTATCGACATTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAACGGGGTG
36895 CACGCAT
193 CACGCAT
* ** * *
36902 AAAGTGTCGATACATTAATT-AAATGTAGT-GATCTTAAAAACATCGAAACAGATAATTATAATA
1 AAAGTGTCGATACATTTATTAAAAT-TA-TCGATCCCAAAAACATCGAAACAAATAATTATAATG
**
36965 TAATAGGTAAATTTCCAATGTAACCGGTAGAAATATATTGGTTAATTAGAAAA
64 TAATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAA
37018 TGAGAAAATA
Statistics
Matches: 462, Mismatches: 44, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
198 37 0.08
199 383 0.83
200 42 0.09
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (199 bp):
AAAGTGTCGATACATTTATTAAAATTATCGATCCCAAAAACATCGAAACAAATAATTATAATGTA
ATAGGTAAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAACAGGTCTACATAAT
GTATCGACATTTTTTAAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAACGGGGTGCAC
GCAT
Found at i:37235 original size:21 final size:21
Alignment explanation
Indices: 37184--37236 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
37174 ATTATGACTA
37184 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
37205 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
37226 TCGCAATGCGA
1 TCGCAATGCGA
37237 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:37269 original size:21 final size:21
Alignment explanation
Indices: 37226--37319 Score: 127
Period size: 21 Copynumber: 4.5 Consensus size: 21
37216 TTTTCCCAAT
** *
37226 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
*
37246 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
37267 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
37288 TCGCAATGCAAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
37309 TCGCAACGCGA
1 TCGCAATGCGA
37320 TACTGACTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
20 11 0.17
21 54 0.83
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:37333 original size:20 final size:20
Alignment explanation
Indices: 37308--37422 Score: 149
Period size: 20 Copynumber: 5.7 Consensus size: 20
37298 AATTTGGAAA
37308 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* **
37328 ATCGCAACGCGATAATGCAAA
1 ATCGCAACGCGATACTG-ACT
37349 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
37369 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
37389 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
37409 TTCGCAACGAGATA
1 ATCGCAACGCGATA
37423 ATACATAATC
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
20 67 0.80
21 17 0.20
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:37350 original size:41 final size:40
Alignment explanation
Indices: 37305--37442 Score: 177
Period size: 41 Copynumber: 3.4 Consensus size: 40
37295 GCAAATTTGG
*
37305 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATGC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-C
* *
37346 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATACTT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATC
*** *
37386 ACTTTCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-C
* *
37427 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
37443 TTTCAAAGCG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 34 0.41
41 49 0.59
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATC
Found at i:37637 original size:22 final size:22
Alignment explanation
Indices: 37609--37652 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
37599 CACTCTCTCA
* *
37609 CCCATCTCCGTCTAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
37631 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
37653 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.14, T:0.23
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:37950 original size:20 final size:20
Alignment explanation
Indices: 37901--37959 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
37891 TTTATTCTCT
* **
37901 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
37921 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
37941 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
37960 AGAACTATTC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:39299 original size:18 final size:18
Alignment explanation
Indices: 39278--39325 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
39268 TCCACTTCGG
39278 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
39296 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
39314 GAGCCATCACCT
1 GAGCCATCACCT
39326 GATCGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:39891 original size:20 final size:20
Alignment explanation
Indices: 39866--39911 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
39856 TAGTTTACTT
39866 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
39886 TCGCAATGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
39906 TCGCAA
1 TCGCAA
39912 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:39920 original size:19 final size:20
Alignment explanation
Indices: 39877--39921 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39867 CGCAACACGA
39877 AAATGACTATCGCAATGCGG
1 AAATGACTATCGCAATGCGG
*
39897 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCGG
39916 AAATGA
1 AAATGA
39922 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCGG
Found at i:39927 original size:19 final size:19
Alignment explanation
Indices: 39885--39968 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
39875 GAAAATGACT
***
39885 ATCGCAATGCGGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
39905 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
39924 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
39938 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
39957 ATCGCAATGCGA
1 ATCGCAATGCGA
39969 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 27 0.51
20 10 0.19
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:40012 original size:33 final size:33
Alignment explanation
Indices: 39975--40054 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
39965 GCGATTTGTG
* *
39975 TTTCGCGTTACGATTTTTTCATTGCGATTTTCA
1 TTTCGCATTACGATTTTGTCATTGCGATTTTCA
** * *
40008 TTTCGCATTGTGATTTTGTCGTTGTGATTTTCA
1 TTTCGCATTACGATTTTGTCATTGCGATTTTCA
* *
40041 TTTTGCATTGCGAT
1 TTTCGCATTACGAT
40055 AGCCATTTCC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.14, C:0.15, G:0.19, T:0.53
Consensus pattern (33 bp):
TTTCGCATTACGATTTTGTCATTGCGATTTTCA
Found at i:40076 original size:20 final size:20
Alignment explanation
Indices: 40048--40113 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
40038 TCATTTTGCA
40048 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
*
40068 TTTCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* *
40088 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGCCATTTCCGCG
40108 TTGCGA
1 TTGCGA
40114 AAGTAAGTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:40124 original size:20 final size:20
Alignment explanation
Indices: 40084--40139 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
40074 TAGCCATTTC
* * *
40084 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
40104 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
40124 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
40140 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:40513 original size:21 final size:20
Alignment explanation
Indices: 40487--40555 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
40477 CTGTCATCCC
40487 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
40508 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
40529 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
40549 TCAAGAG
1 TCAAGAG
40556 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:40567 original size:41 final size:42
Alignment explanation
Indices: 40477--40567 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
40467 CTCGTCTCAC
* *
40477 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
40519 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
40560 CTGTCATC
1 CTGTCATC
40568 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:43175 original size:200 final size:200
Alignment explanation
Indices: 42830--43208 Score: 548
Period size: 200 Copynumber: 1.9 Consensus size: 200
42820 ACACTTGTGG
* ** *
42830 AATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGGGGTGCACGCATAAAGTGCCGAT
1 AATTTGTGTCGATACTTATTGTCCAGAATGAATACCCAAACAAGCTGCACGCATAAAGTGCCGAT
42895 ACATTTATTAAAAGTATCGATCCCAAAAATATCAAAACCGATAATTATAATGTAATAGGTAAATT
66 ACATTTA-TAAAAGTATCGATCCCAAAAATATCAAAACCGATAATTATAATGTAATAGGTAAATT
* * *
42960 TACAATGTAACCAGTATAAATATACCGGTTTTA-TGAGATAATAGGTCAACATAATGTATCGACA
130 TACAATGTAACCAGTATAAATAAACC-GATTTAGTGAGAAAATAGGTCAACATAATGTATCGACA
43024 CTTTTTA
194 CTTTTTA
* * * *
43031 AATTTGTGTCGATACTTTTTTTTCCAGAATGAATATCC-AACAAGCTGCACGCATAAAGTGTCGA
1 AATTTGTGTCGATAC-TTATTGTCCAGAATGAATACCCAAACAAGCTGCACGCATAAAGTGCCGA
* * *
43095 TACATTTA-AAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATACTGTAATAGGTAAAT
65 TACATTTATAAA-AGTATCGATCCCAAAAATATCAAAACCGATAATTATAATGTAATAGGTAAAT
* * *
43159 TTGCAATGTTACCAGTATAAATAAACCGATTTAGTTAGAAAATAGGTCAA
129 TTACAATGTAACCAGTATAAATAAACCGATTTAGTGAGAAAATAGGTCAA
43209 TATATGCGCT
Statistics
Matches: 158, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
199 8 0.05
200 87 0.55
201 45 0.28
202 18 0.11
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (200 bp):
AATTTGTGTCGATACTTATTGTCCAGAATGAATACCCAAACAAGCTGCACGCATAAAGTGCCGAT
ACATTTATAAAAGTATCGATCCCAAAAATATCAAAACCGATAATTATAATGTAATAGGTAAATTT
ACAATGTAACCAGTATAAATAAACCGATTTAGTGAGAAAATAGGTCAACATAATGTATCGACACT
TTTTA
Found at i:43321 original size:64 final size:64
Alignment explanation
Indices: 43228--43347 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 64
43218 TACCTATTAC
* * * *
43228 ATTATATAAGCGTTACCTACTATGTTATTGCACTTGATAATATTTTCGGTTAAATGCCTATTTT
1 ATTATATAAGCGCTACCTAATATGTTATTGCACTTCATAATATTTCCGGTTAAATGCCTATTTT
*
43292 ATTATATAAGCGCTACCTAATATGTTATTGTACTTCATAATATTTCCGGTTAAATG
1 ATTATATAAGCGCTACCTAATATGTTATTGCACTTCATAATATTTCCGGTTAAATG
43348 AAATAACATA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTAATATGTTATTGCACTTCATAATATTTCCGGTTAAATGCCTATTTT
Found at i:44711 original size:27 final size:27
Alignment explanation
Indices: 44660--44727 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 27
44650 AGGGATTTGG
44660 AAGTTTTTTAAA-ATTAAGAAAAA-TT
1 AAGTTTTTTAAATATTAAGAAAAATTT
44685 AGAGTTATTTTAAATA-TAA-AAATAATTTT
1 A-AGTT-TTTTAAATATTAAGAAA-AA-TTT
44714 AAGTTTTTTAAATA
1 AAGTTTTTTAAATA
44728 AAATTAGTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
25 1 0.03
26 7 0.19
27 21 0.57
28 5 0.14
29 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (27 bp):
AAGTTTTTTAAATATTAAGAAAAATTT
Found at i:45195 original size:19 final size:17
Alignment explanation
Indices: 45154--45192 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
45144 TCTTTTGAAA
45154 ATTTTAGATTTTCTTAT
1 ATTTTAGATTTTCTTAT
45171 ATTTTAGATTTT-TTAAT
1 ATTTTAGATTTTCTT-AT
45188 ATTTT
1 ATTTT
45193 TTATCAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (17 bp):
ATTTTAGATTTTCTTAT
Found at i:46065 original size:23 final size:23
Alignment explanation
Indices: 46025--46087 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
46015 TAGTATTTTA
**
46025 TTTATTTCATTTGCTTTTATGGAC-
1 TTTATTT-ATTTATTTTTAT-GACT
*
46049 TTTATTTATTTATTTTTATGTCT
1 TTTATTTATTTATTTTTATGACT
46072 TTTATTTTATTTATTT
1 TTTA-TTTATTTATTT
46088 ATTTCGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.06
23 14 0.41
24 18 0.53
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.70
Consensus pattern (23 bp):
TTTATTTATTTATTTTTATGACT
Found at i:46074 original size:32 final size:27
Alignment explanation
Indices: 46021--46116 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 27
46011 TTTCTAGTAT
46021 TTTATTTATTTCATTTGCTTTTATGGACTTTA
1 TTTATTTATTT-ATTTGCTTTTAT----TTTA
46053 TTTATTTATTT-TTATGTCTTTTATTTTA
1 TTTATTTATTTATT-TG-CTTTTATTTTA
*
46081 TTTATTTATTTCGTTT-C-TTTATTTTTA
1 TTTATTTATTT-ATTTGCTTTTA-TTTTA
46108 TTTAATTTA
1 TTT-ATTTA
46117 CTTGTTATCG
Statistics
Matches: 58, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
26 4 0.07
27 9 0.16
28 20 0.34
29 1 0.02
30 4 0.07
31 2 0.03
32 18 0.31
ACGTcount: A:0.19, C:0.06, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTATTTATTTATTTGCTTTTATTTTA
Found at i:46135 original size:33 final size:32
Alignment explanation
Indices: 46071--46142 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
46061 TTTTTATGTC
* * **
46071 TTTTATTTTATTTATTTATTTCGTTTCTTTAT
1 TTTTATTTAATTTACTTATTTCGTTAATTTAT
*
46103 TTTTATTTAATTTACTTGTTATCGTTAATTTAT
1 TTTTATTTAATTTACTTATT-TCGTTAATTTAT
*
46136 TATTATT
1 TTTTATT
46143 CTTTCCTTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.69
Consensus pattern (32 bp):
TTTTATTTAATTTACTTATTTCGTTAATTTAT
Found at i:49304 original size:14 final size:13
Alignment explanation
Indices: 49271--49312 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
49261 AACAAAAAGC
49271 AAAAAGAGAAAAA
1 AAAAAGAGAAAAA
*
49284 AGCAAAGAGAAAATA
1 A-AAAAGAGAAAA-A
49299 AAAAAG-GAAAAA
1 AAAAAGAGAAAAA
49311 AA
1 AA
49313 GGAAAATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 6 0.24
14 14 0.56
15 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:49509 original size:68 final size:68
Alignment explanation
Indices: 49391--49532 Score: 189
Period size: 68 Copynumber: 2.1 Consensus size: 68
49381 GATTTAAACT
* *
49391 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTAAACCATTTCACTCGAAGATCATAGAGCA
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTAAACCATCTCACTCGAAGATCACAGAGCA
49456 TCA
66 TCA
* * ** * *
49459 ATGAGATTGATCAAGCACAATCATTTCTGAATTACTGCATCA-CTCTACTCGAAGATCACGGAGC
1 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTAAACCATCTC-ACTCGAAGATCACAGAGC
49523 ATCA
65 ATCA
49527 A-GAGAT
1 ATGAGAT
49533 AGACATATAC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
67 7 0.11
68 58 0.89
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (68 bp):
ATGAGATTGATCAAGCACAATCATTTCCGAATCACTAAACCATCTCACTCGAAGATCACAGAGCA
TCA
Found at i:50503 original size:31 final size:31
Alignment explanation
Indices: 50463--50548 Score: 118
Period size: 31 Copynumber: 2.8 Consensus size: 31
50453 ATCTTTGAAT
*
50463 ATTCAACATCAAATGCTGGGGCATTTTTTAG
1 ATTCAACATCAAATGTTGGGGCATTTTTTAG
* * *
50494 ATTTAACATCAAATGTTGAGGCGTTTTTTAG
1 ATTCAACATCAAATGTTGGGGCATTTTTTAG
* *
50525 ATTCAACATCGAATATTGGGGCAT
1 ATTCAACATCAAATGTTGGGGCAT
50549 CCTTGGGAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (31 bp):
ATTCAACATCAAATGTTGGGGCATTTTTTAG
Found at i:51300 original size:106 final size:106
Alignment explanation
Indices: 51113--51374 Score: 409
Period size: 106 Copynumber: 2.5 Consensus size: 106
51103 ACGAAGGGGC
* *
51113 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGTGAAGAATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTT
*
51178 CAACTTCACAGTGAAGGGACGGCTGGTTGTAAACAAATAAT
66 CAACTTCACAGTGAAGGGACGGCTGGTTGTAAACAAACAAT
* * **
51219 TTCCCAGTTTCAAAACCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTT
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTT
*
51284 CAACTTCACA-TCGAAGGGACGGCTGGTTGTCAACAAACAAT
66 CAACTTCACAGT-GAAGGGACGGCTGGTTGTAAACAAACAAT
* * *
51325 TTCCCAGTTCCAGAGCCAATTTCAACTTCACGGTGGAGGATATTGGACTC
1 TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTC
51375 AGAACAATAC
Statistics
Matches: 140, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
105 1 0.01
106 139 0.99
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (106 bp):
TTCCCAGTTTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTT
CAACTTCACAGTGAAGGGACGGCTGGTTGTAAACAAACAAT
Found at i:51699 original size:102 final size:102
Alignment explanation
Indices: 51521--51707 Score: 234
Period size: 102 Copynumber: 1.8 Consensus size: 102
51511 GACAGTTTCC
* * * *
51521 AAGTTTTGTCTCTCTTGAGACAATTTCCCTTGAAACTAAATCTTTGAATATCTTTTCCTTGAAAC
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTAGAAACTAAATCATTGAATAACTTTCCCTTGAAAC
51586 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
66 AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
* * * *
51623 AAGTTTTGTCTCTCTTGAGATAGTTTCTCTAGAAAC-ATATACATTGAA-AACATTTCCCTTGAA
1 AAGTTTTGTCTCTCTTGAGACAATTTCCCTAGAAACTAAAT-CATTGAATAAC-TTTCCCTTGAA
** * *
51686 ATGAATTTTGTCTCTCTTGAGA
64 ACAAATTTCGTCTCCCTTGAGA
51708 TAGTTTCCCT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
101 5 0.07
102 66 0.93
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (102 bp):
AAGTTTTGTCTCTCTTGAGACAATTTCCCTAGAAACTAAATCATTGAATAACTTTCCCTTGAAAC
AAATTTCGTCTCCCTTGAGACATTTTCTTTTGGAACT
Found at i:51911 original size:38 final size:37
Alignment explanation
Indices: 51869--51949 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
51859 AACTTCAATA
51869 TTTGAATACAATTTCTCTTGAAAAACAAAAAAAAAACC
1 TTTGAA-ACAATTTCTCTTGAAAAACAAAAAAAAAACC
*** *
51907 TTTGAAATTGTTTCTCTTGAAACACAAAAAAAAAACC
1 TTTGAAACAATTTCTCTTGAAAAACAAAAAAAAAACC
*
51944 ATTGAA
1 TTTGAA
51950 GATGTTTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (37 bp):
TTTGAAACAATTTCTCTTGAAAAACAAAAAAAAAACC
Found at i:51966 original size:37 final size:37
Alignment explanation
Indices: 51880--51968 Score: 144
Period size: 37 Copynumber: 2.4 Consensus size: 37
51870 TTGAATACAA
* *
51880 TTTCTCTTGAAAAACAAAAAAAAAACCTTTGAAATTG
1 TTTCTCTTGAAACACAAAAAAAAAACCATTGAAATTG
51917 TTTCTCTTGAAACACAAAAAAAAAACCATTGAAGA-TG
1 TTTCTCTTGAAACACAAAAAAAAAACCATTGAA-ATTG
51954 TTTCTCTTGAAACAC
1 TTTCTCTTGAAACAC
51969 CAAACCCTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 48 0.98
38 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.29
Consensus pattern (37 bp):
TTTCTCTTGAAACACAAAAAAAAAACCATTGAAATTG
Found at i:53098 original size:2 final size:2
Alignment explanation
Indices: 53093--53142 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
53083 TTTACTTTAG
* *
53093 TA TA TA TA TA TA TT TA GA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53134 TA TA TA TA T
1 TA TA TA TA T
53143 TAATTTTCAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55973 original size:26 final size:24
Alignment explanation
Indices: 55911--55973 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
55901 CATTTTAATC
55911 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
55935 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
55958 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
55974 ATTTATAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:55975 original size:22 final size:23
Alignment explanation
Indices: 55928--55991 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
55918 TAATTATTAA
* *
55928 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
*
55949 AATATTTCTAATAATATAATATT
1 AATATTTATAATAATATAATATT
*
55972 -ATATTTATAATATTATAATA
1 AATATTTATAATAATATAATA
55992 AAATAATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.28
22 22 0.61
23 4 0.11
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:56132 original size:19 final size:19
Alignment explanation
Indices: 56108--56176 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
56098 ATATTATTAA
56108 ATTATTAATAATAAATAAT
1 ATTATTAATAATAAATAAT
* *
56127 ATTATTTAT-ATAATTAAT
1 ATTATTAATAATAAATAAT
*
56145 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAAT-AAATAAT
56167 ATT-TTAATAA
1 ATTATTAATAA
56177 AGATATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
18 11 0.27
19 16 0.39
20 4 0.10
21 2 0.05
22 8 0.20
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTATTAATAATAAATAAT
Found at i:56150 original size:24 final size:21
Alignment explanation
Indices: 56094--56169 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 21
56084 ATTTCATAGA
*
56094 AATAATATTATTAA-ATTATT
1 AATAATAATATTAATATTATT
56114 AATAATAA-A-TAATATTATTT
1 AATAATAATATTAATATTA-TT
*
56134 ATATAATTAATATTAATA-TAAT
1 A-ATAA-TAATATTAATATTATT
56156 AATCTAATAATATT
1 AA--TAATAATATT
56170 TTAATAAAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
18 3 0.07
19 5 0.11
20 10 0.22
21 5 0.11
22 12 0.26
23 6 0.13
24 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
AATAATAATATTAATATTATT
Found at i:56151 original size:27 final size:27
Alignment explanation
Indices: 56058--56156 Score: 87
Period size: 27 Copynumber: 3.6 Consensus size: 27
56048 ATAATAAGTT
*
56058 ATTAATA-AAATTTATATTATTTAT-TA
1 ATTAATATAAA-TAATATTATTTATATA
* * * *
56084 ATTTCATAGAAATAATATTA-TTAAATT
1 A-TTAATATAAATAATATTATTTATATA
56111 ATTAATAATAAATAATATTATTTATATA
1 ATTAAT-ATAAATAATATTATTTATATA
56139 ATTAATATTAATATAATA
1 ATTAATA-TAA-ATAATA
56157 ATCTAATAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
26 8 0.14
27 27 0.47
28 17 0.29
29 6 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
ATTAATATAAATAATATTATTTATATA
Found at i:56492 original size:14 final size:14
Alignment explanation
Indices: 56473--56507 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
56463 CAAATATCAT
56473 AAAATATTTTTCAG
1 AAAATATTTTTCAG
56487 AAAATATTTTTCAG
1 AAAATATTTTTCAG
56501 AAAATAT
1 AAAATAT
56508 AATTCATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (14 bp):
AAAATATTTTTCAG
Found at i:57889 original size:31 final size:32
Alignment explanation
Indices: 57854--57916 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 32
57844 AATAAAAAGC
57854 TTTTAAAAT-TAGATTTTGT-TTTT-TATTTTAA
1 TTTTAAAATGTA-ATTTT-TATTTTATATTTTAA
57885 TTTTAAAATGTAATTTTTATTTTATATTTTAA
1 TTTTAAAATGTAATTTTTATTTTATATTTTAA
57917 AATACGTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 1 0.03
31 18 0.62
32 10 0.34
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (32 bp):
TTTTAAAATGTAATTTTTATTTTATATTTTAA
Found at i:59550 original size:32 final size:33
Alignment explanation
Indices: 59513--59586 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
59503 AAAATTTCCA
* * *
59513 GGGTCGGGTCGGGTTTTTAAAAGTTTGATATTC
1 GGGTCGGGTCCGCTTTTTAAAAGTGTGATATTC
**
59546 -GGTCGGGTCCGCTTTTTGTAAGTGTGATATTC
1 GGGTCGGGTCCGCTTTTTAAAAGTGTGATATTC
59578 GGGTCGGGT
1 GGGTCGGGT
59587 TTTTTTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 27 0.77
33 8 0.23
ACGTcount: A:0.14, C:0.12, G:0.36, T:0.38
Consensus pattern (33 bp):
GGGTCGGGTCCGCTTTTTAAAAGTGTGATATTC
Found at i:59685 original size:27 final size:27
Alignment explanation
Indices: 59652--59704 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
59642 GGTCGGGTTG
*
59652 GGTTTTTTTAAGTGTGATATTTGGGTC
1 GGTTTTTTTAAGTGTGATATTCGGGTC
59679 GGTTTTTTTAAGTGTGATATTCGGGT
1 GGTTTTTTTAAGTGTGATATTCGGGT
59705 TGGGTCGGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.30, T:0.51
Consensus pattern (27 bp):
GGTTTTTTTAAGTGTGATATTCGGGTC
Found at i:59724 original size:37 final size:38
Alignment explanation
Indices: 59674--59752 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
59664 TGTGATATTT
*
59674 GGGTC-GGTTTTTTTAAGTGTGATATTCGGGTTGGGTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTC
*
59711 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGTTC
1 GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTC
59749 GGGT
1 GGGT
59753 TTAGGGTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.10, C:0.09, G:0.39, T:0.42
Consensus pattern (38 bp):
GGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTC
Found at i:62403 original size:20 final size:20
Alignment explanation
Indices: 62355--62395 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
62345 TTTACTATGC
*
62355 TTGAATTTAATGTTATAATG
1 TTGAATTTGATGTTATAATG
62375 TTGAATTTGATGTTATAATG
1 TTGAATTTGATGTTATAATG
62395 T
1 T
62396 GAAATTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (20 bp):
TTGAATTTGATGTTATAATG
Found at i:64108 original size:19 final size:19
Alignment explanation
Indices: 64048--64130 Score: 103
Period size: 19 Copynumber: 4.4 Consensus size: 19
64038 TGCATTGGGA
*
64048 TATGAATGTGAAATTAAGT
1 TATGAATATGAAATTAAGT
* *
64067 TATAAATATGAAATTAAGC
1 TATGAATATGAAATTAAGT
64086 TATGAATATGAAATTAAGT
1 TATGAATATGAAATTAAGT
* * *
64105 TATGAATCTAAAAGTAAGT
1 TATGAATATGAAATTAAGT
*
64124 TTTGAAT
1 TATGAAT
64131 CTGGAAATCG
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 55 1.00
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (19 bp):
TATGAATATGAAATTAAGT
Found at i:67989 original size:34 final size:34
Alignment explanation
Indices: 67945--68018 Score: 130
Period size: 34 Copynumber: 2.1 Consensus size: 34
67935 TTGCCTACTC
67945 ACAACTATCAGTATTAATAAATAAATACTCAGATG
1 ACAA-TATCAGTATTAATAAATAAATACTCAGATG
*
67980 ACAATATCAGTATTAATAAATAAATACTCGGATG
1 ACAATATCAGTATTAATAAATAAATACTCAGATG
68014 ACAAT
1 ACAAT
68019 TTAATTGTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (34 bp):
ACAATATCAGTATTAATAAATAAATACTCAGATG
Found at i:69608 original size:26 final size:26
Alignment explanation
Indices: 69572--69621 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
69562 AATGACTCGG
69572 ACATAATACTTTACTCAAGCGATAGA
1 ACATAATACTTTACTCAAGCGATAGA
69598 ACATAATACTTTACTCAAGCGATA
1 ACATAATACTTTACTCAAGCGATA
69622 TCAAACTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (26 bp):
ACATAATACTTTACTCAAGCGATAGA
Done.