Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002415.1 Hibiscus syriacus cultivar Beakdansim tig00004937_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: 76267
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:6303 original size:32 final size:32
Alignment explanation
Indices: 6184--6308 Score: 132
Period size: 31 Copynumber: 4.0 Consensus size: 32
6174 AACCTCGACA
* * * *
6184 ACTGTCCATAGGTCCCGAAGAACTTAGGTAA-
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
*
6215 ACTGTCCATATGTTCCTTAGAACATAGGT-AT
1 ACTGTCCATATGTTCCGTAGAACATAGGTAAT
* *
6246 ACTGCCCATATG-TCTCG-AAAGACATAGGTAAT
1 ACTGTCCATATGTTC-CGTAGA-ACATAGGTAAT
*
6278 TCTGTCCATATGTTCCGTAGAACATAGGTAA
1 ACTGTCCATATGTTCCGTAGAACATAGGTAA
6309 ACCCTCGACT
Statistics
Matches: 77, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 5 0.06
31 44 0.57
32 24 0.31
33 4 0.05
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (32 bp):
ACTGTCCATATGTTCCGTAGAACATAGGTAAT
Found at i:6656 original size:22 final size:23
Alignment explanation
Indices: 6619--6662 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
6609 TATGTTTGTC
*
6619 TTATCTTATCTTATATCATATAA
1 TTATCTTAGCTTATATCATATAA
*
6642 TTAT-TTAGCTTATATCTTATA
1 TTATCTTAGCTTATATCATATA
6663 TCACATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATCTTAGCTTATATCATATAA
Found at i:8345 original size:18 final size:17
Alignment explanation
Indices: 8291--8339 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
8281 TTGGACCCTT
* *
8291 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
8309 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
8327 AGTGCATTCGATG
1 AGTGCA-TCGATG
8340 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:8444 original size:65 final size:65
Alignment explanation
Indices: 8291--8470 Score: 217
Period size: 65 Copynumber: 2.8 Consensus size: 65
8281 TTGGACCCTT
*
8291 AGTGCATCGGTGCACT-AAGA-GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCC
1 AGTGCATCGGTGCA-TGAA-ATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCC
*
8353 AG
64 AC
* ** *
8355 AGTGCATCGATGCATG-GCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCC
1 AGTGCATCGGTGCATGAAAT-GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCC
*
8418 TC
64 AC
*
8420 AGTGCATCGGTGCATGAAATGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCATGAAATGTGCATCGATGCATCAAATGCATTCGATGTT
8471 CAATTTAATT
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
63 1 0.01
64 41 0.41
65 53 0.54
66 4 0.04
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (65 bp):
AGTGCATCGGTGCATGAAATGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAC
Found at i:8445 original size:19 final size:19
Alignment explanation
Indices: 8421--8459 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
8411 AAAATCCTCA
*
8421 GTGCATCGGTGCATGAAAT
1 GTGCATCGATGCATGAAAT
8440 GTGCATCGATGCATGAAAT
1 GTGCATCGATGCATGAAAT
8459 G
1 G
8460 CATTCGATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (19 bp):
GTGCATCGATGCATGAAAT
Found at i:8509 original size:65 final size:65
Alignment explanation
Indices: 8311--8512 Score: 218
Period size: 65 Copynumber: 3.1 Consensus size: 65
8301 TGCACTAAGA
* * ** * *
8311 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGG-CT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGGTGCATGGAAT
8374 G
65 G
* *
8375 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGAA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGGTGCATGGA
8438 AT-
63 ATG
* * *
8440 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGGTGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGGTGCATGGAAT
8504 G
65 G
8505 GTGCATCG
1 GTGCATCG
8513 GTGCGTCACT
Statistics
Matches: 116, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 52 0.45
65 55 0.47
66 1 0.01
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGGTGCATGGAATG
Found at i:14979 original size:21 final size:22
Alignment explanation
Indices: 14944--14988 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
14934 TAAGTTTCAT
* *
14944 TTTTAAATTTTATATTTTATCA
1 TTTTAAATTTAATATTTAATCA
14966 TTTT-AATTTAATATTTAATCA
1 TTTTAAATTTAATATTTAATCA
14987 TT
1 TT
14989 AAACCAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTAAATTTAATATTTAATCA
Found at i:15927 original size:30 final size:30
Alignment explanation
Indices: 15860--15942 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 30
15850 AAGTATGCCT
*
15860 CTAATAATAAATATTAAAAAAATTAGGCTC
1 CTAATAATAAATATTAAAAAAATTAGACTC
* * * *
15890 CTGATAATAAATATTGAAGAAATTTGAC-C
1 CTAATAATAAATATTAAAAAAATTAGACTC
* * *
15919 CTTAATAATATATGTTAGAAAAAT
1 C-TAATAATAAATATTAAAAAAAT
15943 ATTGGCAAAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
29 2 0.05
30 39 0.95
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (30 bp):
CTAATAATAAATATTAAAAAAATTAGACTC
Found at i:21627 original size:20 final size:20
Alignment explanation
Indices: 21581--21620 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
21571 AAATATCAGA
21581 TATATAA-GTATCCGTATTT
1 TATATAATGTATCCGTATTT
21600 TATATAATGTATCCGTATTT
1 TATATAATGTATCCGTATTT
21620 T
1 T
21621 TTTTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TATATAATGTATCCGTATTT
Found at i:22007 original size:37 final size:37
Alignment explanation
Indices: 21961--22031 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
21951 AAAGACTTTG
*
21961 TTTAGGTAGGTACAAACATTAAATAAATATGCAATAT
1 TTTAGGTAGGTACAAACATCAAATAAATATGCAATAT
* *
21998 TTTATGTAGGTACAGACATCAAATAAATATGCAA
1 TTTAGGTAGGTACAAACATCAAATAAATATGCAA
22032 AATCAACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (37 bp):
TTTAGGTAGGTACAAACATCAAATAAATATGCAATAT
Found at i:22153 original size:13 final size:13
Alignment explanation
Indices: 22115--22157 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
22105 ACACATATTT
*
22115 ATATGTATCTTTA
1 ATATGTATCATTA
*
22128 ATGATTTAT-ATTA
1 AT-ATGTATCATTA
22141 ATATGTATCATTA
1 ATATGTATCATTA
22154 ATAT
1 ATAT
22158 AAAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 5 0.20
13 15 0.60
14 5 0.20
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (13 bp):
ATATGTATCATTA
Found at i:25267 original size:30 final size:30
Alignment explanation
Indices: 25208--25303 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
25198 CCCGAAGGAC
* *
25208 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25237 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
25267 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
25297 CTATCCA
1 CTATCCA
25304 TAAGTCCCGA
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 19 0.31
30 43 0.69
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:30554 original size:17 final size:18
Alignment explanation
Indices: 30516--30568 Score: 72
Period size: 17 Copynumber: 2.9 Consensus size: 18
30506 AAATATTAAT
*
30516 TATTAAAATATTTAATATA
1 TATTATAAT-TTTAATATA
30535 TATTATAATTTTAATA-A
1 TATTATAATTTTAATATA
*
30552 TATTATATTTTTAATAT
1 TATTATAATTTTAATAT
30569 TTTAAACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
17 16 0.52
18 7 0.23
19 8 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTATAATTTTAATATA
Found at i:33019 original size:23 final size:23
Alignment explanation
Indices: 32975--33023 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
32965 ATAAAGAACC
*
32975 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
32998 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
33021 AAA
1 AAA
33024 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:35382 original size:15 final size:14
Alignment explanation
Indices: 35348--35389 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
35338 TAACTAATAT
* *
35348 TAAAAATAAAGATA
1 TAAAAATAAACAAA
35362 -AAAAATAAAACAAA
1 TAAAAAT-AAACAAA
35376 TAAAAATAAACAAA
1 TAAAAATAAACAAA
35390 CAAACACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 6 0.25
14 12 0.50
15 6 0.25
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (14 bp):
TAAAAATAAACAAA
Found at i:39823 original size:23 final size:24
Alignment explanation
Indices: 39774--39823 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
39764 CATATTCGTT
* * *
39774 AACGTGTTCCTTTATATGTTCATG
1 AACGTGTTCATTTATACGTTCACG
39798 AACGTGTTCATTTA-ACGTTCACG
1 AACGTGTTCATTTATACGTTCACG
39821 AAC
1 AAC
39824 ATATTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (24 bp):
AACGTGTTCATTTATACGTTCACG
Found at i:42310 original size:32 final size:32
Alignment explanation
Indices: 42263--42326 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
42253 AGTCAGGTCA
* * *
42263 GATTAGGTCATTATCGAATTGGTTGGTTTTCG
1 GATTAGGTCAATATCGAATCGATTGGTTTTCG
* *
42295 GATTGGGTCAATATCGGATCGATTGGTTTTCG
1 GATTAGGTCAATATCGAATCGATTGGTTTTCG
42327 ATTTGGATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.30, T:0.41
Consensus pattern (32 bp):
GATTAGGTCAATATCGAATCGATTGGTTTTCG
Found at i:43137 original size:3 final size:3
Alignment explanation
Indices: 43129--43163 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
43119 TATTTATCAA
43129 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
43164 ATTATTCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44905 original size:2 final size:2
Alignment explanation
Indices: 44900--44925 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44890 TTAATGTTAG
44900 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
44926 CTAGTATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:63646 original size:20 final size:20
Alignment explanation
Indices: 63623--63710 Score: 86
Period size: 20 Copynumber: 4.3 Consensus size: 20
63613 GTTTTCAATT
* *
63623 TCGCAACGCGAATATATAAA
1 TCGCAACGCGAATTTGTAAA
** * **
63643 TCGCATTGCGATTTTCCAAA
1 TCGCAACGCGAATTTGTAAA
*
63663 TTCGCAACGCGAATCTGTAAA
1 -TCGCAACGCGAATTTGTAAA
*
63684 TCGCAACTCGAATTTGTAAA
1 TCGCAACGCGAATTTGTAAA
63704 TCGCAAC
1 TCGCAAC
63711 ACAGAAGTCA
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 39 0.74
21 14 0.26
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATTTGTAAA
Found at i:63727 original size:20 final size:20
Alignment explanation
Indices: 63704--63827 Score: 102
Period size: 20 Copynumber: 6.5 Consensus size: 20
63694 AATTTGTAAA
63704 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
63724 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
*
63744 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
63764 TCGCAACGC-GATAGTCAAAGT
1 TCGCAACACAGA-AGTCAAA-T
* ***
63785 T-GC--GA-ATTTGT-AAA-
1 TCGCAACACAGAAGTCAAAT
63799 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
63819 TCGCAACAC
1 TCGCAACAC
63828 GAAACACAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
14 1 0.01
15 2 0.03
16 3 0.04
17 3 0.04
18 3 0.04
19 6 0.08
20 58 0.73
21 3 0.04
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:63728 original size:40 final size:40
Alignment explanation
Indices: 63704--63782 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
63694 AATTTGTAAA
*
63704 TCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
63744 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
1 TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
63783 GTTGCGAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.16
Consensus pattern (40 bp):
TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:63961 original size:22 final size:22
Alignment explanation
Indices: 63936--63987 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
63926 ACTCTCTACA
*
63936 GCGACATCCGTCCCCATCTCCG
1 GCGAAATCCGTCCCCATCTCCG
63958 GCGAAATCCGTCCCCATCTCCG
1 GCGAAATCCGTCCCCATCTCCG
63980 GCGAAATC
1 GCGAAATC
63988 TGTCTATCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.44, G:0.19, T:0.17
Consensus pattern (22 bp):
GCGAAATCCGTCCCCATCTCCG
Found at i:64360 original size:20 final size:20
Alignment explanation
Indices: 64337--64399 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
64327 AAACTTAAAT
64337 TCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
64357 TCGCAACAC------CAAAA
1 TCGCAACACGAAAATGAAAA
*
64371 CCGCAACACGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
64391 TCGCAACAC
1 TCGCAACAC
64400 AATTTTAGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
14 12 0.36
20 21 0.64
ACGTcount: A:0.51, C:0.29, G:0.13, T:0.08
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:68006 original size:117 final size:118
Alignment explanation
Indices: 67795--68008 Score: 265
Period size: 117 Copynumber: 1.8 Consensus size: 118
67785 ATCTTATTTT
*
67795 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGGAGTTAGAGCTTTCAAAAA
1 GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
*
67860 TAAAATCGGAAAACTTTGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
66 TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
* * * * *
67913 GAAA-CTAAAATGGATTTTGAAAA-ACAAAATGAAAT-TTCGAAGAAGAATTTAGAGCTTTCAAA
1 GAAAGCTAAAAAGGACTTGGAAAATA-AAAATGAAATGTT-GAAAAAGAAGTTAGAGCTTTCAAA
* ** * *
67975 GATAAAATTTG-AAAGTATGGAAAAGGAAATTTTC
64 AATAAAATCGGAAAACT-TGGAAAAAGAAATTTTC
68009 GATTTAGAAG
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
116 7 0.09
117 70 0.86
118 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (118 bp):
GAAAGCTAAAAAGGACTTGGAAAATAAAAATGAAATGTTGAAAAAGAAGTTAGAGCTTTCAAAAA
TAAAATCGGAAAACTTGGAAAAAGAAATTTTCAAATTAAACAAACTTCTTCTA
Found at i:68575 original size:20 final size:21
Alignment explanation
Indices: 68542--68581 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
68532 TTTTAACGTA
**
68542 ATTGATATTCATTTT-AAACC
1 ATTGATATAAATTTTCAAACC
68562 ATTGATATAAATTTTCAAAC
1 ATTGATATAAATTTTCAAAC
68582 AATTTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTGATATAAATTTTCAAACC
Found at i:71957 original size:23 final size:21
Alignment explanation
Indices: 71901--71962 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
71891 TTTTGGTGCA
*
71901 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
* *
71921 GAGGGAACCAATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
71942 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
71963 ACAGGGGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.26
21 9 0.26
22 1 0.03
23 15 0.44
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:71983 original size:20 final size:21
Alignment explanation
Indices: 71944--71983 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
71934 CCCCCTTTGA
*
71944 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
71965 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
71984 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:73659 original size:34 final size:34
Alignment explanation
Indices: 73621--73730 Score: 162
Period size: 34 Copynumber: 3.4 Consensus size: 34
73611 AACAAAAAGG
73621 GGGAGAAGTGTTAAAATGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAATGTTTTTAAATGATAAAT
73655 -GG-G-A--G--AAAATGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAATGTTTTTAAATGATAAAT
*
73682 GGGAGAAGTGTTAAAGTGTTTTTAAATGATAAAT
1 GGGAGAAGTGTTAAAATGTTTTTAAATGATAAAT
73716 GGGAGAAGTGTTAAA
1 GGGAGAAGTGTTAAA
73731 GTAACGGGGA
Statistics
Matches: 68, Mismatches: 1, Indels: 14
0.82 0.01 0.17
Matches are distributed among these distances:
27 22 0.32
28 2 0.03
29 2 0.03
30 1 0.01
31 1 0.01
32 2 0.03
33 2 0.03
34 36 0.53
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (34 bp):
GGGAGAAGTGTTAAAATGTTTTTAAATGATAAAT
Found at i:73693 original size:26 final size:27
Alignment explanation
Indices: 73633--73722 Score: 117
Period size: 27 Copynumber: 3.1 Consensus size: 27
73623 GAGAAGTGTT
73633 AAAATGTTTTTAAATGATAAATGGGAG
1 AAAATGTTTTTAAATGATAAATGGGAG
73660 AAAATGTTTTTAAATGATAAATGGGAG
1 AAAATGTTTTTAAATGATAAATGGGAG
73687 AAGTGTTAAAGTGTTTTTAAATGATAAATGGGAG
1 -A-----AAA-TGTTTTTAAATGATAAATGGGAG
73721 AA
1 AA
73723 GTGTTAAAGT
Statistics
Matches: 56, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
27 27 0.48
28 2 0.04
33 4 0.07
34 23 0.41
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (27 bp):
AAAATGTTTTTAAATGATAAATGGGAG
Done.