Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006589.1 Hibiscus syriacus cultivar Beakdansim tig00016154_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: 92490
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:652 original size:198 final size:198
Alignment explanation
Indices: 204--876 Score: 968
Period size: 197 Copynumber: 3.4 Consensus size: 198
194 CTAACTATAT
*
204 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAA-TATAATGTAATA
1 GTGTCGATACATTTAT-AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
*
268 GGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTCATGAGAAAATAGTTCTACATAATGT
65 GGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTCATGAAAAAATAGTTCTACATAATGT
*
333 ATCGACACTTGTGGAATTGTGTCGATACTTGTTGTCCAGAATGAATGCCAAAA-ATGGTGCATGC
130 ATCGACACTTGTGGAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGA-GGTGCATGC
397 ATAAA
194 ATAAA
* *
402 GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAATCGATAATTATAATGTAATAT
1 GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
* * * * * *
467 GTAAATTTACAAT-AACCTG-TAGAAATTTACCGGTTTTACGAAAAAAATAGGTCTACATAA-GT
66 GTAAATTTACAATGTACCCGATAGAAATATACCGGTTTCATG-AAAAAATAGTTCTACATAATGT
* *
529 ATCGACACTTGTGGAACTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGGGTGCACGC
130 ATCGACACTTGTGGAA-TTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGAGGTGCATGC
594 ATAAA
194 ATAAA
* *
599 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTACAATGTAATA
1 GTGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* *
664 GGTAAATTTACAATGTACCCGATAGAAATATACCAGTTTCATG-AGAAATAGTTCTACATAATGT
65 GGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTCATGAAAAAATAGTTCTACATAATGT
** * * *
728 ATCGACACTT-TTTAAGTTTGTTTCGATACTTTTT-TCCAGAATGAATGCCCAACGAGGTGCATG
130 ATCGACACTTGTGGAA--TTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGAGGTGCATG
791 CATAAA
193 CATAAA
* * * * *
797 ATGCCGATATATTTA-AAATTGTATCGATCCCAAAAATATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
861 GGTAAATTTACAATGT
65 GGTAAATTTACAATGT
877 TACCGGTATT
Statistics
Matches: 425, Mismatches: 40, Indels: 21
0.87 0.08 0.04
Matches are distributed among these distances:
196 39 0.09
197 175 0.41
198 162 0.38
199 32 0.08
200 17 0.04
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTACCCGATAGAAATATACCGGTTTCATGAAAAAATAGTTCTACATAATGTA
TCGACACTTGTGGAATTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGAGGTGCATGCAT
AAA
Found at i:1016 original size:85 final size:85
Alignment explanation
Indices: 914--1073 Score: 261
Period size: 85 Copynumber: 1.9 Consensus size: 85
904 AAATAGGTCA
* * *
914 ATATAAGCGTACCTATTACATTATATAAGTGCTACCTAATATGTTATTGTATTTGAT-ATATTTC
1 ATATAAGCGTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTTC
978 C-AGTTAAATGCTTATTTATT
66 CGA-TTAAATGCTTATTTATT
998 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
1 ATATAAGCG-TACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTT
1063 CCGATTAAATG
65 CCGATTAAATG
1074 ATATAACATA
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
84 9 0.13
85 45 0.64
86 15 0.21
87 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (85 bp):
ATATAAGCGTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTGATAATATTTC
CGATTAAATGCTTATTTATT
Found at i:1045 original size:23 final size:23
Alignment explanation
Indices: 995--1039 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
985 ATGCTTATTT
*
995 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1018 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1040 TGTTATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:8622 original size:18 final size:17
Alignment explanation
Indices: 8573--8621 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
8563 CGAAAAACAT
8573 AAAAATATGACTTTTCAA
1 AAAAAT-TGACTTTTCAA
*
8591 AAAAATTAACTTTTCAA
1 AAAAATTGACTTTTCAA
8608 AAAAATTGACTTTT
1 AAAAATTGACTTTT
8622 TGGTCAAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.49, C:0.10, G:0.04, T:0.37
Consensus pattern (17 bp):
AAAAATTGACTTTTCAA
Found at i:13035 original size:21 final size:19
Alignment explanation
Indices: 13010--13053 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
13000 TATCTCTCTC
*
13010 TCTTTCTTTCTTCTTCTTTTT
1 TCTTTATTTCTT-TT-TTTTT
13031 TCTTTATTTCTTTTTTTTT
1 TCTTTATTTCTTTTTTTTT
13050 TCTT
1 TCTT
13054 CAGGTAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.41
20 2 0.09
21 11 0.50
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (19 bp):
TCTTTATTTCTTTTTTTTT
Found at i:24471 original size:32 final size:31
Alignment explanation
Indices: 24434--24510 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
24424 TGGGGCCACG
* * *
24434 GGGCCTACCTAAGAATATATCTTAGGGTCGCA
1 GGGCCTACCTAAGAAT-GATCTCAGGGCCGCA
**
24466 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAATGATCTCAGGGCCGCA
*
24497 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
24511 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (31 bp):
GGGCCTACCTAAGAATGATCTCAGGGCCGCA
Found at i:30317 original size:20 final size:19
Alignment explanation
Indices: 30284--30326 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30274 TTTCTATTTT
*
30284 TTTTCTTTTTTCTTCTTCA
1 TTTTCTTTTCTCTTCTTCA
*
30303 TTTTCTTTCTCTCTTCTTTA
1 TTTTCTTT-TCTCTTCTTCA
30323 TTTT
1 TTTT
30327 TCTTCATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTCTCTTCTTCA
Found at i:30328 original size:17 final size:16
Alignment explanation
Indices: 30289--30331 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
30279 ATTTTTTTTC
30289 TTTTTTCTTCTTCATT
1 TTTTTTCTTCTTCATT
*
30305 TTCTTTCTCTCTTC-TT
1 TTTTTTCT-TCTTCATT
30321 TATTTTTCTTC
1 T-TTTTTCTTC
30332 ATTCTCGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTCTTCTTCATT
Found at i:30336 original size:17 final size:15
Alignment explanation
Indices: 30289--30336 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
30279 ATTTTTTTTC
30289 TTTTTTCTTCTTCATT
1 TTTTTTCTTCTTC-TT
*
30305 TTCTTTCTCTCTTCTT
1 TTTTTTCT-TCTTCTT
30321 TATTTTTCTTCATTCT
1 T-TTTTTCTTC-TTCT
30337 CGATAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 12 0.44
17 15 0.56
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTTCTTCTTCTT
Found at i:31409 original size:29 final size:30
Alignment explanation
Indices: 31377--31461 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
31367 AATATTATGT
31377 ATGAAATTTG-ATTTGATAT-AATTATACAC
1 ATGAAATTTGAATTTGAT-TCAATTATACAC
* *
31406 ATGAAATTTTGAATTTGGTTCAATTGTACAC
1 ATGAAA-TTTGAATTTGATTCAATTATACAC
*
31437 ATGAAATTTTAATTT-AGTTCAATTA
1 ATGAAATTTGAATTTGA-TTCAATTA
31462 CATATTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.13
30 20 0.43
31 21 0.45
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.44
Consensus pattern (30 bp):
ATGAAATTTGAATTTGATTCAATTATACAC
Found at i:31457 original size:30 final size:31
Alignment explanation
Indices: 31396--31461 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
31386 GATTTGATAT
*
31396 AATTATACACATGAAATTTTGAATTTGGTTC
1 AATTATACACATGAAATTTTGAATTTAGTTC
*
31427 AATTGTACACATGAAATTTT-AATTTAGTTC
1 AATTATACACATGAAATTTTGAATTTAGTTC
31457 AATTA
1 AATTA
31462 CATATTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (31 bp):
AATTATACACATGAAATTTTGAATTTAGTTC
Found at i:35867 original size:32 final size:32
Alignment explanation
Indices: 35831--35901 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
35821 TGAATACCCT
35831 GTTTCCAAGTTAGAGCTTAGAGATATTTACAA
1 GTTTCCAAGTTAGAGCTTAGAGATATTTACAA
35863 GTTTCCAAGTTAGAGCTTAGAGATATTTACAA
1 GTTTCCAAGTTAGAGCTTAGAGATATTTACAA
35895 G-TTCCAA
1 GTTTCCAA
35902 CTCGAGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
31 6 0.15
32 33 0.85
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
GTTTCCAAGTTAGAGCTTAGAGATATTTACAA
Found at i:44577 original size:24 final size:24
Alignment explanation
Indices: 44492--44578 Score: 104
Period size: 24 Copynumber: 3.6 Consensus size: 24
44482 TAATGTTTTA
* *
44492 TATGATTTCTTATTTGAATTCTAT
1 TATGATTTCTGATATGAATTCTAT
* *
44516 TCTGATTTCTGACT-TGGATTCTAT
1 TATGATTTCTGA-TATGAATTCTAT
*
44540 TATGATATCTGATATGAATTCTAT
1 TATGATTTCTGATATGAATTCTAT
*
44564 TTTGATTTCTGATAT
1 TATGATTTCTGATAT
44579 CTCCATTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 1 0.02
24 51 0.96
25 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (24 bp):
TATGATTTCTGATATGAATTCTAT
Found at i:61416 original size:299 final size:299
Alignment explanation
Indices: 60878--61476 Score: 1135
Period size: 299 Copynumber: 2.0 Consensus size: 299
60868 TGTATCTCCA
*
60878 TCCTCAAAGTGTTCAATCATATGTTTTCGCTGCGCTTCTTGCTTTACTCTTTGGCTTTTGTACCA
1 TCCTCAAAGTGTTCAATCATATGTTTTCGCTGCGCTTCTTGCTTTACTCCTTGGCTTTTGTACCA
* *
60943 TGTGATGTTGGAAACATCTGGAATCATGTATTGCTCTCATAAGCATGGATTCTGTTTGGAGCTTT
66 TGTGATGTTGGAAACATCTAGAATCATGTATTGCTCTCATAAGCATGGATTCTGTTTAGAGCTTT
*
61008 ATACTGATACAATATGAGTTGAGATTGTAGAATTACTAAGGAATGAGAAAGAGATATGTCATGCG
131 AGACTGATACAATATGAGTTGAGATTGTAGAATTACTAAGGAATGAGAAAGAGATATGTCATGCG
61073 AAGAAAGAGCAGAGAATCTGTTTGAATTGCTTATTGAAAAGAAGAAAGCAACTTATTTTTAGTAG
196 AAGAAAGAGCAGAGAATCTGTTTGAATTGCTTATTGAAAAGAAGAAAGCAACTTATTTTTAGTAG
61138 GCTGAAAATTACAATGGTAGAATACAACTTGGTATTTTT
261 GCTGAAAATTACAATGGTAGAATACAACTTGGTATTTTT
61177 TCCTCAAAGTGTTCAATCATATGTTTTCGCTGCGCTTCTTGCTTTACTCCTTGGCTTTTGTACCA
1 TCCTCAAAGTGTTCAATCATATGTTTTCGCTGCGCTTCTTGCTTTACTCCTTGGCTTTTGTACCA
*
61242 TGTGATGTTGGAAACATCTAGAATCATGTATTGCTCTTATAAGCATGGATTCTGTTTAGAGCTTT
66 TGTGATGTTGGAAACATCTAGAATCATGTATTGCTCTCATAAGCATGGATTCTGTTTAGAGCTTT
*
61307 AGACTGATATAATATGAGTTGAGATTGTAGAATTACTAAGGAATGAGAAAGAGATATGTCATGCG
131 AGACTGATACAATATGAGTTGAGATTGTAGAATTACTAAGGAATGAGAAAGAGATATGTCATGCG
*
61372 AAGAAAGAGCAGAGAATCTGTTTGAATTTCTTATTGAAAAGAAGAAAGCAACTTATTTTTAGTAG
196 AAGAAAGAGCAGAGAATCTGTTTGAATTGCTTATTGAAAAGAAGAAAGCAACTTATTTTTAGTAG
61437 GCTGAAAATTACAATGGTAGAATACAACTTGGTATTTTT
261 GCTGAAAATTACAATGGTAGAATACAACTTGGTATTTTT
61476 T
1 T
61477 TCCTGATCTT
Statistics
Matches: 293, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
299 293 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (299 bp):
TCCTCAAAGTGTTCAATCATATGTTTTCGCTGCGCTTCTTGCTTTACTCCTTGGCTTTTGTACCA
TGTGATGTTGGAAACATCTAGAATCATGTATTGCTCTCATAAGCATGGATTCTGTTTAGAGCTTT
AGACTGATACAATATGAGTTGAGATTGTAGAATTACTAAGGAATGAGAAAGAGATATGTCATGCG
AAGAAAGAGCAGAGAATCTGTTTGAATTGCTTATTGAAAAGAAGAAAGCAACTTATTTTTAGTAG
GCTGAAAATTACAATGGTAGAATACAACTTGGTATTTTT
Found at i:61900 original size:20 final size:20
Alignment explanation
Indices: 61875--61923 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
61865 TAAATGTCAC
*
61875 TTTGAATCTTGAAGTGATCA
1 TTTGAATCATGAAGTGATCA
61895 TTTGAATCATGAAGTGATCA
1 TTTGAATCATGAAGTGATCA
61915 TTTGAATCA
1 TTTGAATCA
61924 ACCTTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (20 bp):
TTTGAATCATGAAGTGATCA
Found at i:63554 original size:2 final size:2
Alignment explanation
Indices: 63547--63584 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
63537 AGCAAAATTG
63547 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
63585 GTTTAACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64360 original size:4 final size:4
Alignment explanation
Indices: 64351--64380 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
64341 CTATTTCTTC
64351 TCCT TCCT TCCT TCCT TCCT TCCT TCCT TC
1 TCCT TCCT TCCT TCCT TCCT TCCT TCCT TC
64381 TTCTTCCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (4 bp):
TCCT
Found at i:66265 original size:19 final size:20
Alignment explanation
Indices: 66238--66282 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
66228 ATTAGCAACA
*
66238 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
66257 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
66277 TAATAA
1 TAATAA
66283 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:66266 original size:20 final size:20
Alignment explanation
Indices: 66241--66280 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
66231 AGCAACATAA
*
66241 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
66261 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
66281 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:66323 original size:20 final size:21
Alignment explanation
Indices: 66294--66333 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
66284 TAATAGAATA
*
66294 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
66315 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
66334 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:66377 original size:52 final size:52
Alignment explanation
Indices: 66239--66386 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
66229 TTAGCAACAT
66239 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
66290 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
**
66343 AATAAAAACTGATTCTATCTAATTAAAACGGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
66387 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.47
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:66380 original size:20 final size:20
Alignment explanation
Indices: 66347--66385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66337 TAATAGAATA
* *
66347 AAAACTGATTCTATCTAATT
1 AAAACGGATCCTATCTAATT
66367 AAAACGGATCCTATCTAAT
1 AAAACGGATCCTATCTAAT
66386 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAACGGATCCTATCTAATT
Found at i:70980 original size:19 final size:20
Alignment explanation
Indices: 70953--70997 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
70943 ATTAGCAACA
*
70953 TAAT-AAAAATGATTCTATC
1 TAATAAAAAATGATCCTATC
*
70972 TAATTAAAAATGATCCTATC
1 TAATAAAAAATGATCCTATC
70992 TAATAA
1 TAATAA
70998 CTAATAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (20 bp):
TAATAAAAAATGATCCTATC
Found at i:70981 original size:20 final size:20
Alignment explanation
Indices: 70956--70995 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
70946 AGCAACATAA
*
70956 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
70976 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
70996 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:71038 original size:20 final size:21
Alignment explanation
Indices: 71009--71048 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
70999 TAATAGAATA
*
71009 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
71030 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
71049 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:71092 original size:52 final size:52
Alignment explanation
Indices: 70954--71101 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
70944 TTAGCAACAT
70954 AATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
71005 AATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
**
71058 AATAAAAACTGATTCTATCTAATTAAAACGGATCCTATCTAATA
1 AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATA
71102 TTTAATTTAG
Statistics
Matches: 93, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 3 0.03
52 44 0.47
53 46 0.49
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (52 bp):
AATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
Found at i:71095 original size:20 final size:20
Alignment explanation
Indices: 71062--71100 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
71052 TAATAGAATA
* *
71062 AAAACTGATTCTATCTAATT
1 AAAACGGATCCTATCTAATT
71082 AAAACGGATCCTATCTAAT
1 AAAACGGATCCTATCTAAT
71101 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (20 bp):
AAAACGGATCCTATCTAATT
Found at i:80192 original size:17 final size:18
Alignment explanation
Indices: 80149--80198 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
80139 GTTAACCGAC
80149 CGAACCGAATTAGTTCGA
1 CGAACCGAATTAGTTCGA
80167 CGAACCGAATTAGTTCGA
1 CGAACCGAATTAGTTCGA
*
80185 C-CACCGAATTAGTT
1 CGAACCGAATTAGTT
80199 TGGTCGGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (18 bp):
CGAACCGAATTAGTTCGA
Found at i:80645 original size:185 final size:185
Alignment explanation
Indices: 80286--80675 Score: 633
Period size: 185 Copynumber: 2.1 Consensus size: 185
80276 ATTAAATTTT
* * * *
80286 AAATATCAAATATATTATATATAACATATGGGTTCAGCTCAAACCATTTAAAATCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
80351 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
80416 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATGTTTTTGTGAATTAAA
131 TTATTTTATAATTATATATTATTTAAATTAATTGTAAATGTTTTTGTGAATTAAA
*
80471 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
* * *
80536 TTTAAGATTCAATAACTTTTAAATCTAAATCAATATTAATTAATT-AAAATTTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
* *
80600 TTATTTTATAATTATATATTATTTAAATTAATTAG-AAATTGTTTTTTTGAATTAGA
131 TTATTTTATAATTATATATTATTTAAATTAATT-GTAAA-TGTTTTTGTGAATTAAA
* *
80656 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
80676 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
184 62 0.32
185 129 0.68
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (185 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAGCCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTGTAAATGTTTTTGTGAATTAAA
Found at i:82606 original size:2 final size:2
Alignment explanation
Indices: 82599--82625 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
82589 TTATTTATGG
82599 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 T
82626 TATGCAGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87853 original size:31 final size:31
Alignment explanation
Indices: 87815--87879 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
87805 AAAGTCGAGG
*
87815 GTTTACCTATGTCTTTCGAGACATATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
* * *
87846 GTTTACCTAGGTTTTTCGGGACCTATGGACA
1 GTTTACCTAGGTCTTTCGAGACATATGGACA
87877 GTT
1 GTT
87880 GCTGAGGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTAGGTCTTTCGAGACATATGGACA
Found at i:87928 original size:29 final size:30
Alignment explanation
Indices: 87865--87936 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
87855 GGTTTTTCGG
* * * *
87865 GACCTATGGACAGTTGCTGAGGTTCTTTAT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
*
87895 GACCTCTGGATAGTTGCCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGCCGAGGGTCTTTAT
87924 GACCTCTGGATAG
1 GACCTCTGGATAG
87937 GTCTTTCTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 21 0.57
30 16 0.43
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTGCCGAGGGTCTTTAT
Found at i:88208 original size:4 final size:4
Alignment explanation
Indices: 88199--88309 Score: 222
Period size: 4 Copynumber: 27.8 Consensus size: 4
88189 TAATGACATA
88199 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
88247 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
88295 TATG TATG TATG TAT
1 TATG TATG TATG TAT
88310 TTGTTACATA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 107 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:90870 original size:64 final size:61
Alignment explanation
Indices: 90755--90893 Score: 147
Period size: 63 Copynumber: 2.2 Consensus size: 61
90745 CATATTCAAT
* *
90755 GTGCATCGATGCACTCTTTAAGAAGAAACATCGAATGCAAATGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAGAAGAAACATCGAAGGCAAATGGTGCATCGAT-CAT-AGGTA
* * * * *
90817 GTGCATCGATGCATCCCTTTAA-AATGAAAACATCGAAGGTAATTTGTGTATCGATCATGGGTA
1 GTGCATCGATGCA-CCCTTTAAGAA-G-AAACATCGAAGGCAAATGGTGCATCGATCATAGGTA
*
90880 GTTCATCGATGCAC
1 GTGCATCGATGCAC
90894 TTCAAGAGGA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
62 18 0.28
63 24 0.37
64 23 0.35
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (61 bp):
GTGCATCGATGCACCCTTTAAGAAGAAACATCGAAGGCAAATGGTGCATCGATCATAGGTA
Found at i:91870 original size:29 final size:30
Alignment explanation
Indices: 91806--91877 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
91796 GATTTTTCGA
* * *
91806 GACCTATGAATAGTTGTCGAGGTTCTTTAT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
*
91836 GACCTCTGGATAGTTGTCG-GGGTCTTTGT
1 GACCTCTGGATAGTTGTCGAGGGTCTTTAT
91865 GACCTCTGGATAG
1 GACCTCTGGATAG
91878 GTCATTCAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.18, C:0.17, G:0.29, T:0.36
Consensus pattern (30 bp):
GACCTCTGGATAGTTGTCGAGGGTCTTTAT
Done.