Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005054.1 Hibiscus syriacus cultivar Beakdansim tig00011347_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: 43436
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2298 original size:24 final size:24
Alignment explanation
Indices: 2206--2300 Score: 91
Period size: 24 Copynumber: 4.0 Consensus size: 24
2196 AAACAGAGAT
* * *
2206 ATCAGAAATAAAAACATAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2230 ATAAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
2254 ATCAAAAATTAGAACAGAATTTAG
1 ATCAGAAATCAGAACAGAATTCAG
* *
2278 ATCAGAAATCATAACATAATTCA
1 ATCAGAAATCAGAACAGAATTCA
2301 AAATCTGAAA
Statistics
Matches: 54, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:6983 original size:24 final size:24
Alignment explanation
Indices: 6954--7051 Score: 99
Period size: 24 Copynumber: 4.1 Consensus size: 24
6944 GAGATGTCAA
* *
6954 AAATCAAAACAGAATCCATATCAG
1 AAATCATAACAGAATCCAAATCAG
*
6978 ATATCATAACAGAATCCAAATCAG
1 AAATCATAACAGAATCCAAATCAG
** * * *
7002 AAATCATAACAGAATTTAGATAAA
1 AAATCATAACAGAATCCAAATCAG
* *
7026 AAATCATAACATAATTCAAATC-G
1 AAATCATAACAGAATCCAAATCAG
7049 AAA
1 AAA
7052 ATCAAATAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 3 0.05
24 57 0.95
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.21
Consensus pattern (24 bp):
AAATCATAACAGAATCCAAATCAG
Found at i:6985 original size:12 final size:11
Alignment explanation
Indices: 6955--7016 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
6945 AGATGTCAAA
*
6955 AATCAAAACAG
1 AATCATAACAG
*
6966 AATCCATATCAG
1 AAT-CATAACAG
6978 ATATCATAACAG
1 A-ATCATAACAG
6990 AATCCA-AATCAG
1 AAT-CATAA-CAG
7002 AAATCATAACAG
1 -AATCATAACAG
7014 AAT
1 AAT
7017 TTAGATAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 10 0.24
12 25 0.60
13 7 0.17
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.19
Consensus pattern (11 bp):
AATCATAACAG
Found at i:19611 original size:52 final size:52
Alignment explanation
Indices: 19549--19652 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
19539 ATTTGGCCCA
19549 CTTGGTTCTCCAATGCTCTCAAAGATGAGCTATAACTTTTTAATAAAGTTGT
1 CTTGGTTCTCCAATGCTCTCAAAGATGAGCTATAACTTTTTAATAAAGTTGT
19601 CTTGGTTCTCCAATGCTCTCAAAGATGAGCTATAACTTTTTAATAAAGTTGT
1 CTTGGTTCTCCAATGCTCTCAAAGATGAGCTATAACTTTTTAATAAAGTTGT
19653 TTGTAACAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (52 bp):
CTTGGTTCTCCAATGCTCTCAAAGATGAGCTATAACTTTTTAATAAAGTTGT
Found at i:23207 original size:30 final size:32
Alignment explanation
Indices: 23173--23234 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
23163 TGTTTTTCTG
23173 AAAAACGTCG-CAAAAGG-CAAGATCTATAGC
1 AAAAACGTCGTCAAAAGGTCAAGATCTATAGC
* * *
23203 AAAAATGTCGTTAAAAGGTCAAGCTCTATAGC
1 AAAAACGTCGTCAAAAGGTCAAGATCTATAGC
23235 GGCATTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 6 0.22
32 12 0.44
ACGTcount: A:0.44, C:0.18, G:0.19, T:0.19
Consensus pattern (32 bp):
AAAAACGTCGTCAAAAGGTCAAGATCTATAGC
Found at i:23856 original size:34 final size:36
Alignment explanation
Indices: 23812--23913 Score: 163
Period size: 34 Copynumber: 2.9 Consensus size: 36
23802 TTTCGTCCTA
*
23812 CTAGGATTCAAACTCCTAAAAATATGATAGAA-TTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
*
23847 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
23882 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
23914 GTTATACTAT
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
34 29 0.48
35 3 0.05
37 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (36 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTTT
Found at i:24344 original size:2 final size:2
Alignment explanation
Indices: 24337--24436 Score: 111
Period size: 2 Copynumber: 51.5 Consensus size: 2
24327 TTCATGTTAT
*
24337 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA T- TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
24376 TT TCA T- TA TT TT TA CTA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24418 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
24437 TTCTTTAATA
Statistics
Matches: 86, Mismatches: 5, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
1 5 0.06
2 78 0.91
3 3 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:24662 original size:24 final size:24
Alignment explanation
Indices: 24617--24663 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
24607 ATTTTATATA
* * *
24617 TATTTTTTATTATTTTCGTTTTTT
1 TATTTATTATTATATTAGTTTTTT
24641 TATTTATTATTATATTA-TTTTTT
1 TATTTATTATTATATTAGTTTTTT
24664 AAAAAACCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (24 bp):
TATTTATTATTATATTAGTTTTTT
Found at i:24850 original size:2 final size:2
Alignment explanation
Indices: 24843--24876 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
24833 TAATACTTTG
*
24843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24877 TTTCCTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:27417 original size:8 final size:8
Alignment explanation
Indices: 27404--27442 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
27394 GAACATTTCA
*
27404 TGCATTCT
1 TGCATTTT
27412 TGCA-TTT
1 TGCATTTT
27419 TGCATTTT
1 TGCATTTT
*
27427 TGCCTTTT
1 TGCATTTT
27435 TGCATTTT
1 TGCATTTT
27443 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:28564 original size:7 final size:7
Alignment explanation
Indices: 28552--28625 Score: 62
Period size: 7 Copynumber: 10.0 Consensus size: 7
28542 TCCAATCAAG
28552 AAGAAAA
1 AAGAAAA
28559 AAGAAAA
1 AAGAAAA
28566 GAAGCAAAA
1 -AAG-AAAA
*
28575 AA-AACA
1 AAGAAAA
28581 AAGAAAA
1 AAGAAAA
28588 AAGAGAAA
1 AAGA-AAA
*
28596 CACGAACAA
1 -AAGAA-AA
28605 AAGGAAAA
1 AA-GAAAA
28613 AAGAAAA
1 AAGAAAA
28620 AA-AAAA
1 AAGAAAA
28626 GAATCAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
6 9 0.16
7 21 0.38
8 14 0.25
9 12 0.21
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:28583 original size:17 final size:15
Alignment explanation
Indices: 28549--28638 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 15
28539 AGATCCAATC
*
28549 AAGAAGAAAAAAGAA
1 AAGAAGAAAAAAAAA
*
28564 AAGAAGCAAAAAAAA
1 AAGAAGAAAAAAAAA
* *
28579 CA-AAGAAAAAAGAGA
1 AAGAAGAAAAAA-AAA
* * *
28594 AACACGAACAAAAGGAA
1 AAGAAGAA-AAAA-AAA
28611 AA-AAG-AAAAAAAA
1 AAGAAGAAAAAAAAA
*
28624 AAGAATCAAAAAAAA
1 AAGAA-GAAAAAAAA
28639 GAGGAACAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
13 4 0.07
14 14 0.25
15 18 0.32
16 13 0.23
17 8 0.14
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (15 bp):
AAGAAGAAAAAAAAA
Found at i:30212 original size:36 final size:36
Alignment explanation
Indices: 30165--30269 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
30155 GTGCTCACCA
30165 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
30201 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
30238 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
30270 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:30259 original size:37 final size:37
Alignment explanation
Indices: 30165--30274 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
30155 GTGCTCACCA
30165 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
30201 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
30238 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
30275 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:30332 original size:36 final size:37
Alignment explanation
Indices: 30285--30371 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
30275 ATTGAAAACA
** * *
30285 TTTCCCTTGAAA-TGAGTTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAG
* *
30321 TTTCCCTTGAAACAAATTTTTTTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAG
*
30358 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
30372 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.43
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAGACAG
Found at i:30359 original size:102 final size:102
Alignment explanation
Indices: 30183--30616 Score: 708
Period size: 102 Copynumber: 4.3 Consensus size: 102
30173 CTTGAGACAG
** * * *
30183 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
30248 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
30285 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAATTTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
30350 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
30387 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
30452 TGAGACAGTTTCTCTTGAATCATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
30489 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
30554 TGAGACAGTTTCTCCTGAAACAT-AACATTGAAAATA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
30590 TTTCCCTTGAAATGAATTTCGTCTCTC
1 TTTCCCTTGAAATGAATTTTGTCTCTC
30617 CCTTGAAACA
Statistics
Matches: 310, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
101 37 0.12
102 273 0.88
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:30360 original size:37 final size:37
Alignment explanation
Indices: 30301--30371 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
30291 TTGAAATGAG
* *
30301 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAT
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
* *
30338 TTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
30372 TAAACATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACAAAT
Found at i:30556 original size:37 final size:37
Alignment explanation
Indices: 30489--30575 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
30479 ATTGGAAACA
** * *
30489 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
30525 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
30562 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
30576 TAACATTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:30630 original size:23 final size:23
Alignment explanation
Indices: 30592--30637 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
30582 TGAAAATATT
**
30592 TCCCTTGAAATGAATTTCGTCTC
1 TCCCTTGAAACAAATTTCGTCTC
*
30615 TCCCTTGAAACAAATTTTGTCTC
1 TCCCTTGAAACAAATTTCGTCTC
30638 CCTTGAGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (23 bp):
TCCCTTGAAACAAATTTCGTCTC
Found at i:30659 original size:36 final size:36
Alignment explanation
Indices: 30618--30729 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
30608 TCGTCTCTCC
30618 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
** * ** *
30654 CTTGAAACACAA------AACCTTTGAGATTGTTTCC
1 CTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCT
* *
30685 CTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCT
1 CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
30721 CTTGAAACA
1 CTTGAAACA
30730 CAAAATCTTT
Statistics
Matches: 54, Mismatches: 15, Indels: 14
0.65 0.18 0.17
Matches are distributed among these distances:
30 2 0.04
31 21 0.39
36 29 0.54
37 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.34
Consensus pattern (36 bp):
CTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:30753 original size:67 final size:68
Alignment explanation
Indices: 30613--30762 Score: 234
Period size: 67 Copynumber: 2.2 Consensus size: 68
30603 GAATTTCGTC
*
30613 TCTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGAT
1 TCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGAT
30678 TGT
66 TGT
* *
30681 T-TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-AT
1 TCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGAT
30744 T-T
66 TGT
*
30746 ATCTCCCTTAAAACAAA
1 -TCTCCCTTGAAACAAA
30763 ATTTCGTTTC
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 69 0.92
68 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (68 bp):
TCTCCCTTGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAACCTTTGAGAT
TGT
Found at i:30991 original size:37 final size:37
Alignment explanation
Indices: 30921--30992 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
30911 TGGAACTAAG
* * *
30921 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
* * *
30958 TTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAA
30993 CAGATATCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGTTTCTCATAAAACAAAA
Found at i:31826 original size:105 final size:105
Alignment explanation
Indices: 31596--32354 Score: 1006
Period size: 105 Copynumber: 7.3 Consensus size: 105
31586 GCCATCTGCG
* * * * * * *
31596 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAATGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
*
31661 GGGA-CGACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* *
31705 ATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGGCGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
31770 ACCGCTGCCTGTCAACAACAACTTCTCAATTTTAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
*
31810 ATTTTAACTTCACAAC----GA-A--GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
31868 ACCGCTGCTTGTCAACAACAACTTCTTAATTTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
31908 ATTTCAACTTCACAACAAAAGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
31973 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
32013 ATTTCAACTTCACAACGAAGGATATTGGACTCCATACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
32078 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* *
32118 ATTTCAATTTCACAACGAAGGATATTGGATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
**
32183 ACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
* * *
32218 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** *
32283 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCA
* * *
32324 ATTTCAACTTCACGACGGAGGATATTAGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
32355 TGGAACAATG
Statistics
Matches: 585, Mismatches: 50, Indels: 33
0.88 0.07 0.05
Matches are distributed among these distances:
98 90 0.15
99 2 0.00
100 80 0.14
101 4 0.01
102 5 0.01
103 5 0.01
104 3 0.01
105 292 0.50
106 78 0.13
107 5 0.01
109 21 0.04
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
Found at i:32927 original size:33 final size:35
Alignment explanation
Indices: 32889--32988 Score: 168
Period size: 36 Copynumber: 2.9 Consensus size: 35
32879 TTTCGTCCTA
32889 CTAGGATTCAAACTCCT-AAAATAGGATAGAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
*
32923 -TAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
32957 GCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 -CTAGGATTCAAACTCCTAAAAATAGGATAGA
32989 GTTATACTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
33 16 0.26
34 16 0.26
36 29 0.48
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
Found at i:33475 original size:2 final size:2
Alignment explanation
Indices: 33468--33516 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
33458 ATTTTACTAT
33468 TA TA TA TA TA TA TA TA TA TA 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
33510 TA TA TA T
1 TA TA TA T
33517 TTCTTAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33712 original size:13 final size:12
Alignment explanation
Indices: 33685--33738 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 12
33675 ATCTTATAAC
33685 TTATATATTTTTT
1 TTAT-TATTTTTT
33698 TTATTATTTTGTT
1 TTATTATTTT-TT
* *
33711 TTTTTATTTATTA
1 TTATTATTT-TTT
33724 TTATTATTTTTT
1 TTATTATTTTTT
33736 TTA
1 TTA
33739 AAAAACCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.31
13 23 0.66
14 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTATTATTTTTT
Found at i:33715 original size:20 final size:21
Alignment explanation
Indices: 33692--33737 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
33682 AACTTATATA
*
33692 TTTTTTTTATTATT-TTGTTT
1 TTTTTTTTATTATTATTATTT
*
33712 TTTTATTTATTATTATTATTT
1 TTTTTTTTATTATTATTATTT
33733 TTTTT
1 TTTTT
33738 AAAAAACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (21 bp):
TTTTTTTTATTATTATTATTT
Found at i:33921 original size:2 final size:2
Alignment explanation
Indices: 33914--33945 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
33904 TAATACTTTG
33914 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
33946 TTTTCCTTTT
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:36960 original size:41 final size:41
Alignment explanation
Indices: 36907--37290 Score: 319
Period size: 41 Copynumber: 9.4 Consensus size: 41
36897 GCGTTTATTC
*
36907 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGACGTTTGTA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
* * * * *
36948 CAAAAATGCCACTAAAGTACGAGTATTTGGCGGCATTTGTA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
* * * *
36989 AAAAAATGCCACTAAAGTTAGGGTCTTTAGCGGCGTTTGTA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
* * * * *
37030 AAAAAA-GTCACTAAAGTACGGGTATTTGGCAGCGTTTGTA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
*
37070 TAAAAAATGCCACTAAAGTACAG-GTCTTTGGCGGCGTTTGTA
1 -AAAAAACGCCACTAAAGTA-AGAGTCTTTGGCGGCGTTTGTA
* *
37112 TAAAAACGCCACTAAAGTACAG-GTATTTGGCGGCGTTTGTA
1 AAAAAACGCCACTAAAGTA-AGAGTCTTTGGCGGCGTTTGTA
* * * * * *
37153 TAGAAACGCCACTAAAGTACGACTCTTTGGCGGCATTTGTGC
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGT-A
** * * * * ** *
37195 TTAAAACGCCACAAAAGT-ACATTATTTACCGGCGTTTATA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
* * * * ** *
37235 CAAAAACGCCAATAAAGT-ACAGTATTTATCGGCGTTTATA
1 AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
* *
37275 CAAAAACACCACTAAA
1 AAAAAACGCCACTAAA
37291 TCACAATTAT
Statistics
Matches: 286, Mismatches: 52, Indels: 11
0.82 0.15 0.03
Matches are distributed among these distances:
40 77 0.27
41 165 0.58
42 43 0.15
43 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (41 bp):
AAAAAACGCCACTAAAGTAAGAGTCTTTGGCGGCGTTTGTA
Found at i:37252 original size:40 final size:40
Alignment explanation
Indices: 36908--37337 Score: 288
Period size: 41 Copynumber: 10.5 Consensus size: 40
36898 CGTTTATTCA
* * ** *
36908 AAAAACGCCACTAAAGTAAGAGTCTTTGGCGACGTTTGTAC
1 AAAAACGCCACTAAAGT-ACAGTATTTACCGGCGTTTGTAC
* ** * *
36949 AAAAATGCCACTAAAGTACGAGTATTTGGCGGCATTTGTAA
1 AAAAACGCCACTAAAGTAC-AGTATTTACCGGCGTTTGTAC
* ** * *
36990 AAAAATGCCACTAAAGTTAGGGTCTTTAGCGGCGTTTGTA-
1 AAAAACGCCACTAAAG-TACAGTATTTACCGGCGTTTGTAC
* * * ** * *
37030 AAAAAAGTCACTAAAGTACGGGTATTTGGCAGCGTTTGTATA
1 AAAAACGCCACTAAAGTAC-AGTATTTACCGGCGTTTGTA-C
* * ** *
37072 AAAAATGCCACTAAAGTACAGGTCTTTGGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACA-GTATTTACCGGCGTTTGTAC
** *
37113 AAAAACGCCACTAAAGTACAGGTATTTGGCGGCGTTTGTAT
1 AAAAACGCCACTAAAGTACA-GTATTTACCGGCGTTTGTAC
* * * ** * *
37154 AGAAACGCCACTAAAGTACGACTCTTTGGCGGCATTTGTGC
1 AAAAACGCCACTAAAGTAC-AGTATTTACCGGCGTTTGTAC
* * * *
37195 TTAAAACGCCACAAAAGTACATTATTTACCGGCGTTTATAC
1 -AAAAACGCCACTAAAGTACAGTATTTACCGGCGTTTGTAC
* * *
37236 AAAAACGCCAATAAAGTACAGTATTTATCGGCGTTTATAC
1 AAAAACGCCACTAAAGTACAGTATTTACCGGCGTTTGTAC
* * * *
37276 AAAAACACCACTAAA-TCACAATTATTTACCGGTGTTTGTTC
1 AAAAACGCCACTAAAGT-AC-AGTATTTACCGGCGTTTGTAC
*
37317 AAAAAACGCCGCTAAAAGTAC
1 -AAAAACGCCACT-AAAGTAC
37338 CGCTAAAAAC
Statistics
Matches: 321, Mismatches: 55, Indels: 24
0.80 0.14 0.06
Matches are distributed among these distances:
39 3 0.01
40 82 0.26
41 167 0.52
42 63 0.20
43 5 0.02
44 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (40 bp):
AAAAACGCCACTAAAGTACAGTATTTACCGGCGTTTGTAC
Found at i:37253 original size:164 final size:163
Alignment explanation
Indices: 36895--37290 Score: 417
Period size: 164 Copynumber: 2.4 Consensus size: 163
36885 TGATAAATTG
* * *
36895 CGGCGTTTATTCAAAAAACGCCACTAAAGTA-AGAGTCTTTGGCGACGTTTGTACAAAAATGCCA
1 CGGCGTTTATAC-AAAAACGCCACTAAAGTACAG-GTCTTTGGCGGCGTTTGTACAAAAACGCCA
* ** *
36959 CTAAAGTACGAGTATTTGGCGGCATTTGTAAAAAAATGCCACTAAAGTTAGGGTCTTTAGCGGCG
64 CTAAAGTACGAGTATTTGGCGGCATTTGTAAAAAAACGCCACTAAAGTTAGACTCTTTAGCGGCA
* * * **
37024 TTTGTAAAAAAAGTCACTAAAGTACGGGTATTTGG
129 TTTGTAAAAAAAGCCACAAAAGTACGAGTATTTAC
* * *
37059 CAGCGTTTGTATA-AAAAATGCCACTAAAGTACAGGTCTTTGGCGGCGTTTGTATAAAAACGCCA
1 CGGCG-TT-TATACAAAAACGCCACTAAAGTACAGGTCTTTGGCGGCGTTTGTACAAAAACGCCA
* * * *
37123 CTAAAGTAC-AGGTATTTGGCGGCGTTTGTATAGAAACGCCACTAAAG-TACGACTCTTTGGCGG
64 CTAAAGTACGA-GTATTTGGCGGCATTTGTAAAAAAACGCCACTAAAGTTA-GACTCTTTAGCGG
** * *
37186 CATTTGTGCTTAAAACGCCACAAAAGTAC-ATTATTTAC
127 CATTTGT--AAAAAAAGCCACAAAAGTACGAGTATTTAC
* * ** * *
37224 CGGCGTTTATACAAAAACGCCAATAAAGTACA-GTATTTATCGGCGTTTATACAAAAACACCACT
1 CGGCGTTTATACAAAAACGCCACTAAAGTACAGGTCTTTGGCGGCGTTTGTACAAAAACGCCACT
37288 AAA
66 AAA
37291 TCACAATTAT
Statistics
Matches: 192, Mismatches: 32, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
163 36 0.19
164 125 0.65
165 13 0.07
166 18 0.09
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (163 bp):
CGGCGTTTATACAAAAACGCCACTAAAGTACAGGTCTTTGGCGGCGTTTGTACAAAAACGCCACT
AAAGTACGAGTATTTGGCGGCATTTGTAAAAAAACGCCACTAAAGTTAGACTCTTTAGCGGCATT
TGTAAAAAAAGCCACAAAAGTACGAGTATTTAC
Found at i:37320 original size:41 final size:40
Alignment explanation
Indices: 37208--37321 Score: 140
Period size: 40 Copynumber: 2.8 Consensus size: 40
37198 AAACGCCACA
*
37208 AAAGTACATTATTTACCGGCGTTTATACAAAAACGCCAAT
1 AAAGTACATTATTTACCGGCGTTTATACAAAAACACCAAT
* * *
37248 AAAGTACAGTATTTATCGGCGTTTATACAAAAACACCACT
1 AAAGTACATTATTTACCGGCGTTTATACAAAAACACCAAT
* * *
37288 AAA-TCACAATTATTTACCGGTGTTTGTTCAAAAA
1 AAAGT-AC-ATTATTTACCGGCGTTTATACAAAAA
37322 ACGCCGCTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 41 0.65
41 21 0.33
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (40 bp):
AAAGTACATTATTTACCGGCGTTTATACAAAAACACCAAT
Done.