Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002584.1 Hibiscus syriacus cultivar Beakdansim tig00005230_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: 60918
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:337 original size:197 final size:198
Alignment explanation
Indices: 1--795 Score: 1182
Period size: 197 Copynumber: 4.1 Consensus size: 198
1 TTATAAATGTATCGACACTTTTTAGTGCACTTGG-TTTGAAATACATTCTGGACCAAAAGTATCG
1 TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
* * * *
65 ACACTTATTTGATTTGTGTCGATACTTTTTTTACACCTGTTTTCTCAAAAATTGGTATATTTAGA
66 ACACTT-GTTAATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGA
130 CCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGATGTTTTTGAGATCGACA
130 CCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGATGTTTTTGAGATCGACA
195 CTTG
195 CTTG
*
199 -TATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTTAAATACATTCTGGACCAAAAGTATCG
1 TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
* *
263 ACACTTGTTAGATTTGTGTCGATAC-TTTTGTACACC-GACTTTCTCAAAAACCGGTATATTTAG
66 ACACTTGTTA-ATTTGTGTCGATACTTTTTGTACACCTG-TTTTCTCAAAAATCGGTATATTTAG
*
326 ACCGGTTATATTGCTAATTTACCTATTACATTATAATTAT-AGTTTTCGATGTTTTTGGGATCGA
129 ACCGGTTATATTGCTAATTTACCTATTACATTATAATTATGA-TTTTCGATGTTTTTGAGATCGA
390 CACTTG
193 CACTTG
* * *
396 TTACAAATGTATCG--AC-TTTTAGTGCAC-TGTTTTTGAAATACATTATGGA-CAAAAGTATCG
1 TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
456 ACACTTGTTCAATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGA
66 ACACTTGTT-AATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGA
* * *
521 CCGGTTATATTTCTAATTTACCTATTAC---ATAATTATGGTTTTCGATGTTTTTGGGATCGACA
130 CCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGATGTTTTTGAGATCGACA
583 CTTG
195 CTTG
* * * *
587 TTATAAATGTATCTAC-CGTTTTAGTGCACTTGGTTTTGAAATACATTCTAGACCAAAAGTATCA
1 TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
*
651 ACACTTGTTTAATTCGTGTCGATACTTTTT-TACA--TGTTTTCTCAAAAATC-GTATATTTAGA
66 ACACTTG-TTAATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGA
* * * *
712 CTGGTAATATTACTAA-TTACCTATTA-ATTATAA-TAAGATTTTCGATGTTTTTGAGATCGACA
130 CCGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGATGTTTTTGAGATCGACA
774 CTTG
195 CTTG
778 TTATAAATGTATCGACAC
1 TTATAAATGTATCGACAC
796 ATAAGTTTAC
Statistics
Matches: 548, Mismatches: 30, Indels: 44
0.88 0.05 0.07
Matches are distributed among these distances:
190 10 0.02
191 117 0.21
192 22 0.04
193 45 0.08
194 105 0.19
195 48 0.09
196 6 0.01
197 134 0.24
198 61 0.11
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (198 bp):
TTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCG
ACACTTGTTAATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAATCGGTATATTTAGAC
CGGTTATATTGCTAATTTACCTATTACATTATAATTATGATTTTCGATGTTTTTGAGATCGACAC
TTG
Found at i:1219 original size:168 final size:174
Alignment explanation
Indices: 935--1395 Score: 485
Period size: 168 Copynumber: 2.7 Consensus size: 174
925 AAATTGTAAA
* * * *
935 TTTACCTATTATATT-GTTATGGATCGATACATTTTCAT-AAGTATCGAC-C--TTTAAGCGCAA
1 TTTACCTGTTATATTAG-TAAGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCTA
*
995 TAA-TTTTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATT-AATTATCGACACTTTTAACA
65 TAACTTCTTCTC-TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTTAACA
1058 TATACGGTAACTTTTTTCGG-TTTGTCATTTTT-G-AG-A-CATATT
129 TATACGGTAA-TTTTTTCGGTTTTGTCATTTTTAGAAGTATCATATT
* *
1100 TTTACTTGTTATATTAGTAAGGATCGATACATTTTCATAAAGTGT-GACACTTTTTAGGCGCTAT
1 TTTACCTGTTATATTAGTAAGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCTAT
* * *
1164 AACTTCTTCTCTTTAAATTCAGAAAGTGTCGATAC-TATATTAAATTATTGACAC-TTTCATATA
66 AACTTCTTCTCTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTTAACATA
* *
1227 TCCGGTAATTTTTTCGGTTTTTTTTTCATTTTTGAGATCAGTTTTATCATATT
131 TACGGTAATTTTTTCGG---TTTTGTCATTTTT-AGA--AG---TATCATATT
* *** * ** *
1280 TTTACCTGTTATATTATTGTTGATTGAT--ATTTTTTTAAAGTATCG-CACTTTATAGGCGCTAT
1 TTTACCTGTTATATTAGTAAGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCTAT
*
1342 AACTTC-TCT-TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACACT
66 AACTTCTTCTCTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACT
1396 CGACACATCC
Statistics
Matches: 248, Mismatches: 24, Indels: 35
0.81 0.08 0.11
Matches are distributed among these distances:
165 36 0.15
166 16 0.06
167 20 0.08
168 47 0.19
169 7 0.03
170 11 0.04
172 1 0.00
175 2 0.01
176 23 0.09
177 21 0.08
178 34 0.14
179 2 0.01
180 28 0.11
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (174 bp):
TTTACCTGTTATATTAGTAAGGATCGATACATTTTCATAAAGTATCGACACTTTTTAGGCGCTAT
AACTTCTTCTCTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTTAACATA
TACGGTAATTTTTTCGGTTTTGTCATTTTTAGAAGTATCATATT
Found at i:1441 original size:19 final size:20
Alignment explanation
Indices: 1417--1454 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1407 GTAGCGTTTT
1417 ACCGGTTTTGTCAT-TTTGG
1 ACCGGTTTTGTCATATTTGG
1436 ACCGGTTTTGTCATATTTG
1 ACCGGTTTTGTCATATTTG
1455 TATATGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.13, C:0.16, G:0.24, T:0.47
Consensus pattern (20 bp):
ACCGGTTTTGTCATATTTGG
Found at i:1640 original size:2 final size:2
Alignment explanation
Indices: 1633--1664 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1623 CGATAACATC
1633 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
1665 TAACCGCCCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11296 original size:24 final size:24
Alignment explanation
Indices: 11264--11318 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 24
11254 ATGTTAAAAT
11264 AAATCAAA-TAATGATT-TATTATTTA
1 AAAT-AAATTAAT-ATTATATT-TTTA
11289 AAATAAATTAATATTATATTTTTA
1 AAATAAATTAATATTATATTTTTA
*
11313 TAATAA
1 AAATAA
11319 TGTAGTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
AAATAAATTAATATTATATTTTTA
Found at i:11309 original size:29 final size:28
Alignment explanation
Indices: 11257--11313 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
11247 AAATTATATG
11257 TTAAAATAAATCAAATAATGATTTATTAT
1 TTAAAATAAATCAAATAATGATTT-TTAT
* *
11286 TTAAAATAAATTAATATTAT-ATTTTTAT
1 TTAAAATAAATCAA-ATAATGATTTTTAT
11314 AATAATGTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.16
29 17 0.68
30 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TTAAAATAAATCAAATAATGATTTTTAT
Found at i:17093 original size:9 final size:10
Alignment explanation
Indices: 17079--17105 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17069 GGAATTTACC
17079 TTTTTTTAGT
1 TTTTTTTAGT
17089 TTTTTTTAGT
1 TTTTTTTAGT
17099 TTTTTTT
1 TTTTTTT
17106 CTGATTTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.85
Consensus pattern (10 bp):
TTTTTTTAGT
Found at i:17502 original size:3 final size:3
Alignment explanation
Indices: 17494--17523 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17484 GAAATTTGAA
17494 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17524 TAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18445 original size:29 final size:29
Alignment explanation
Indices: 18263--18452 Score: 161
Period size: 29 Copynumber: 6.6 Consensus size: 29
18253 CCGTTGATCG
* *
18263 GGTGACATTTTAGTAATTATTTTGGAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * * *
18292 GATGCTATTCTGGTAATTATTTTGAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * * *
18321 GGTGCTATTTT-GTAATTTTTTTTAAAAA
1 GGTGATATTTTAGTAATTATTTTGAAAAT
* * * * *
18349 GGTGACAATTTCGTAA-AATTTTTAAAA-
1 GGTGATATTTTAGTAATTATTTTGAAAAT
18376 GAGTGATATTTTAGTAATTATTTTGAAAAT
1 G-GTGATATTTTAGTAATTATTTTGAAAAT
* * * * *
18406 GATGCTATTTTGGTAATTAATTTCAAAAT
1 GGTGATATTTTAGTAATTATTTTGAAAAT
*
18435 GGTGATATTTTCGTAATT
1 GGTGATATTTTAGTAATT
18453 TAAAAAAATG
Statistics
Matches: 128, Mismatches: 29, Indels: 8
0.78 0.18 0.05
Matches are distributed among these distances:
27 1 0.01
28 43 0.34
29 83 0.65
30 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.46
Consensus pattern (29 bp):
GGTGATATTTTAGTAATTATTTTGAAAAT
Found at i:19587 original size:117 final size:117
Alignment explanation
Indices: 19381--19668 Score: 470
Period size: 117 Copynumber: 2.5 Consensus size: 117
19371 GCATTTCAAG
* * *
19381 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAAGTAGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
19446 CCTACACATTGTAGTGATTGGAGTGACTGGAT-GAGAAAGTTATTACCGCAGA
66 CCTACACATTGTAGTGATTGGAGTGACTGGATAGAG-AAGTTATTACCGCAGA
* *
19498 CTCCTTTACTGTGTGCTCAGGGTATGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
*
19563 CCTACACATTGTAGTGATTGGAGTGACTGGATAGAGAAGTTATTACTGCAGA
66 CCTACACATTGTAGTGATTGGAGTGACTGGATAGAGAAGTTATTACCGCAGA
** * *
19615 CTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
1 CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATG
19669 TTTCGGGAAA
Statistics
Matches: 158, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
117 155 0.98
118 3 0.02
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.33
Consensus pattern (117 bp):
CTCCTTTGCTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAA
CCTACACATTGTAGTGATTGGAGTGACTGGATAGAGAAGTTATTACCGCAGA
Found at i:19703 original size:117 final size:117
Alignment explanation
Indices: 19389--19705 Score: 352
Period size: 117 Copynumber: 2.7 Consensus size: 117
19379 AGCTCCTTTG
* * * * *
19389 CTGTGTGCTCAGGGTAAGTCCTTATTGGTGTGCAAGTAGGTGTATGGTTCTGGGGAACCTACACA
1 CTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACA
** ** * **
19454 TTGTAGTGATTGGAGTGACTGGATGAGAAAGTTATTACCGCAGACTCCTTTA
66 AAGTAGAAATCGGAGTGACTGGATGAGAAAGTTATTACCGCAGACTCCTCGA
* * *
19506 CTGTGTGCTCAGGGTATGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGGAACCTACACA
1 CTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACA
** ** * * *
19571 TTGTAGTGATTGGAGTGACTGGAT-AGAGAAGTTATTACTGCAGACTCCTCGG
66 AAGTAGAAATCGGAGTGACTGGATGAGA-AAGTTATTACCGCAGACTCCTCGA
* * * *
19623 CTTTGTGCTTAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGTTTC-GGGAAA-ATATACA
1 CTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACAC-
19686 AAAGATAGAAATCGGAGTGA
65 AAAG-TAGAAATCGGAGTGA
19706 TTGAATGGAA
Statistics
Matches: 177, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
115 4 0.02
116 10 0.06
117 163 0.92
ACGTcount: A:0.23, C:0.15, G:0.32, T:0.31
Consensus pattern (117 bp):
CTGTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGGGAAACATACACA
AAGTAGAAATCGGAGTGACTGGATGAGAAAGTTATTACCGCAGACTCCTCGA
Found at i:38294 original size:16 final size:16
Alignment explanation
Indices: 38270--38303 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
38260 TATCGCCGAC
*
38270 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
38286 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
38302 CG
1 CG
38304 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:45173 original size:17 final size:17
Alignment explanation
Indices: 45143--45175 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
45133 ACTCTCTAAC
45143 CTCTCTTGCTATCCCAT
1 CTCTCTTGCTATCCCAT
45160 CTCTCATTGC-ATCCCA
1 CTCTC-TTGCTATCCCA
45176 AAACTCTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.42, G:0.06, T:0.36
Consensus pattern (17 bp):
CTCTCTTGCTATCCCAT
Found at i:47481 original size:21 final size:21
Alignment explanation
Indices: 47429--47475 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
47419 GTTTCCAGAT
47429 TCGCAACGCGAACTTCGAATA
1 TCGCAACGCGAACTTCGAATA
*
47450 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGAATA
47471 TCGCA
1 TCGCA
47476 TTGCGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.32, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGAATA
Found at i:47560 original size:19 final size:19
Alignment explanation
Indices: 47515--47717 Score: 129
Period size: 19 Copynumber: 9.9 Consensus size: 19
47505 TCCAAGTTCG
* *
47515 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATAGTCCAAATT
*
47534 CGCGTTGCGAT-TTACCAAATT
1 --CGTTGCGATAGT-CCAAATT
*
47555 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATAGTCCAAATT
* *
47574 CGCGTTACGATTTATTCCAAATT
1 --CGTTGCGA--TAGTCCAAATT
* *
47597 TGTTGCGATAGTCCAAGTT
1 CGTTGCGATAGTCCAAATT
* *
47616 CGCGTTGCGATTTATTACAAATT
1 --CGTTGCGA--TAGTCCAAATT
*
47639 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATAGTCCAAATT
* *
47658 CGTTGCGATAGTCGAAGTT
1 CGTTGCGATAGTCCAAATT
* *
47677 CGCGTTGCGATTTATTTCAAATT
1 --CGTTGCGA--TAGTCCAAATT
47700 CGTTGCGATAGTCCAAAT
1 CGTTGCGATAGTCCAAAT
47718 CGCAACGATT
Statistics
Matches: 142, Mismatches: 26, Indels: 30
0.72 0.13 0.15
Matches are distributed among these distances:
19 58 0.41
20 2 0.01
21 58 0.41
23 24 0.17
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (19 bp):
CGTTGCGATAGTCCAAATT
Found at i:47607 original size:42 final size:42
Alignment explanation
Indices: 47515--47666 Score: 240
Period size: 42 Copynumber: 3.7 Consensus size: 42
47505 TCCAAGTTCG
*
47515 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA--CCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
*
47555 CGTTGCGATAGTCCAAGTTCGCGTTACGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
* *
47597 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
47639 CGTTGCGATAGTCCAAGTT--CGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGAT
47667 AGTCGAAGTT
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
40 40 0.38
42 64 0.62
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
Found at i:47654 original size:61 final size:61
Alignment explanation
Indices: 47589--47717 Score: 222
Period size: 61 Copynumber: 2.1 Consensus size: 61
47579 TACGATTTAT
*
47589 TCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
* * *
47650 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
47711 TCCAAAT
1 TCCAAAT
47718 CGCAACGATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (61 bp):
TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATTCGTTGCGATAG
Found at i:47703 original size:21 final size:20
Alignment explanation
Indices: 47618--47708 Score: 62
Period size: 21 Copynumber: 4.5 Consensus size: 20
47608 TCCAAGTTCG
*
47618 CGTTGCGATTTATTACAAATT
1 CGTTGCGA-TTATTTCAAATT
* * *
47639 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTATTTCAAATT
* *
47658 CGTTGCGA-TA-GTCGAAGTT
1 CGTTGCGATTATTTC-AAATT
47677 CGCGTTGCGATTTATTTCAAATT
1 --CGTTGCGA-TTATTTCAAATT
47700 CGTTGCGAT
1 CGTTGCGAT
47709 AGTCCAAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
18 1 0.02
19 23 0.40
20 1 0.02
21 24 0.42
23 6 0.11
24 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
CGTTGCGATTATTTCAAATT
Found at i:47827 original size:21 final size:21
Alignment explanation
Indices: 47778--47893 Score: 150
Period size: 21 Copynumber: 5.6 Consensus size: 21
47768 GATAGTATTC
*
47778 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTG
* *
47797 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTG
47820 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTG
47839 GACTATCGCAACGCGAACTTG
1 GACTATCGCAACGCGAACTTG
47860 GACTATCGCAACGCGAACTTG
1 GACTATCGCAACGCGAACTTG
*
47881 AACTATCGCAACG
1 GACTATCGCAACG
47894 AATTTGAAAA
Statistics
Matches: 85, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
19 21 0.25
21 55 0.65
23 9 0.11
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.20
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTG
Found at i:47848 original size:61 final size:60
Alignment explanation
Indices: 47778--47895 Score: 168
Period size: 61 Copynumber: 1.9 Consensus size: 60
47768 GATAGTATTC
*
47778 GACTATCGCAA-CGAATTTGGAATAAATCGCAACGCGAACTTCG-ACTATCGCAACGAACTTG
1 GACTATCGCAACCGAACTTGGAAT--ATCGCAACGCGAACTT-GAACTATCGCAACGAACTTG
*
47839 GACTATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTGAACTATCGCAACGAA
1 GACTATCGCAAC-CGAACTTGGAATATCGCAACGCGAACTTGAACTATCGCAACGAA
47896 TTTGAAAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
60 1 0.02
61 41 0.79
63 10 0.19
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
GACTATCGCAACCGAACTTGGAATATCGCAACGCGAACTTGAACTATCGCAACGAACTTG
Found at i:47934 original size:21 final size:21
Alignment explanation
Indices: 47905--47955 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
47895 ATTTGAAAAA
*
47905 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
47926 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
47947 TCGCGTTGC
1 TCGCGTTGC
47956 AAATCTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.31, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:51706 original size:17 final size:17
Alignment explanation
Indices: 51684--51716 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
51674 ACTTTAAATG
51684 TTAT-AAGTGAATTTAAT
1 TTATAAAGTG-ATTTAAT
51701 TTATAAAGTGATTTAA
1 TTATAAAGTGATTTAA
51717 GATATCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (17 bp):
TTATAAAGTGATTTAAT
Found at i:58208 original size:30 final size:30
Alignment explanation
Indices: 58172--58231 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
58162 GCAAATGGAC
58172 AACGCTGAATCTTCAAATGAGTTAGCTCTT
1 AACGCTGAATCTTCAAATGAGTTAGCTCTT
58202 AACGCTGAATCTTCAAATGAGTTAGCTCTT
1 AACGCTGAATCTTCAAATGAGTTAGCTCTT
58232 CTCAAGTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (30 bp):
AACGCTGAATCTTCAAATGAGTTAGCTCTT
Done.