Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007303.1 Hibiscus syriacus cultivar Beakdansim tig00019440_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: 62732
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4101 original size:33 final size:33
Alignment explanation
Indices: 4056--4118 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
4046 AAATAATGGG
*
4056 TATTTGAGTCCAACCCAACAGAACATTTTTGGA
1 TATTTGAATCCAACCCAACAGAACATTTTTGGA
4089 TATTTGAATCCAACCCAACAGAACATTTTT
1 TATTTGAATCCAACCCAACAGAACATTTTT
4119 ATTTTAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (33 bp):
TATTTGAATCCAACCCAACAGAACATTTTTGGA
Found at i:7872 original size:15 final size:16
Alignment explanation
Indices: 7834--7874 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
7824 ACAGAGTTTA
7834 TGAATCATTCAACATT
1 TGAATCATTCAACATT
7850 TGAATCATTCAAC-TCT
1 TGAATCATTCAACAT-T
7866 T-AATCATTC
1 TGAATCATTC
7875 TGAGATAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:8085 original size:17 final size:17
Alignment explanation
Indices: 8063--8106 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
8053 ATGTAAAAAT
8063 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
8080 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
8097 AAATATTTAA
1 AAATATTTAA
8107 TCAAAGAGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:14846 original size:20 final size:20
Alignment explanation
Indices: 14823--14864 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
14813 AGAAATTAGG
* *
14823 TTTTTTTAATAAATATAATT
1 TTTTTTTAAAAAATAAAATT
14843 TTTTTTTAAAAAATAAAATT
1 TTTTTTTAAAAAATAAAATT
14863 TT
1 TT
14865 CAAAAACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTTTTTAAAAAATAAAATT
Found at i:17790 original size:30 final size:30
Alignment explanation
Indices: 17732--17819 Score: 131
Period size: 30 Copynumber: 2.9 Consensus size: 30
17722 AATGTATGTC
* * * *
17732 TTGAACTTTAAAGTCAACTTCAATTACCTAA
1 TTGAAC-TTGAAGTGAAGTTCAAGTACCTAA
17763 TTGAACTTGAAGTGAAGTTCAAGTACCTAA
1 TTGAACTTGAAGTGAAGTTCAAGTACCTAA
17793 TTGAACTTGAAGTGAAGTTCAAGTACC
1 TTGAACTTGAAGTGAAGTTCAAGTACC
17820 AATACATATA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 47 0.89
31 6 0.11
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (30 bp):
TTGAACTTGAAGTGAAGTTCAAGTACCTAA
Found at i:18667 original size:13 final size:14
Alignment explanation
Indices: 18636--18670 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
18626 TATTTTATAC
18636 CCTAAACCCTAAAT
1 CCTAAACCCTAAAT
*
18650 TCTAAACCC-AAAT
1 CCTAAACCCTAAAT
18663 CCTAAACC
1 CCTAAACC
18671 ATAACCCTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:19032 original size:258 final size:259
Alignment explanation
Indices: 18575--19089 Score: 890
Period size: 258 Copynumber: 2.0 Consensus size: 259
18565 GTCATTTTTA
18575 CTTCTATCGTATTTTCACATCAATTTAACCTTAAAAATTATTTAATTATATTATTTTATACCCTA
1 CTTCTATCGTATTTTCACATCAATTTAACCTTAAAAATTATTTAATTATATTATTTTATACCCTA
18640 AACCCTAAATTCTAAACCCAAATCCTAAACCATAACCCTTGACCTCTAAACTACAAATCTTAAAC
66 AACCCTAAATTCTAAACCCAAATCCTAAACCATAACCCTTGACCTCTAAACTACAAATCTTAAAC
* * * **
18705 CCTAACTTATAACTCTGAACAACAATAAATATTTTAAACATTGGTGTAATTGAGTAACTTCGAAT
131 CCTAACTTACAACTCTAAACAACAATAAATATTTTAAACATTGGTGCAATTGAACAACTTCGAAT
*
18770 GTTAAATTAATATGATATACGATATTGACGAAAATGATAAATTCAGTCTATTACAG-GACAATG
196 GTTAAATTAATATGATATACGATATTGACGAAAATGATAAATTCAGTCTAATACAGAGACAATG
* *
18833 CTTCTATCGTATTTTCACATCAATTTAGTCC-TAAAAGTTATTTAATTATATTATTTTATACCCT
1 CTTCTATCGTATTTTCACATCAATTTA-ACCTTAAAAATTATTTAATTATATTATTTTATACCCT
* * * * *
18897 AAACTCTAAATTCTAAACCCAAATCCTAAACTATAACCCTTGATCTTTAAACTATAAATCTTAAA
65 AAACCCTAAATTCTAAACCCAAATCCTAAACCATAACCCTTGACCTCTAAACTACAAATCTTAAA
18962 CCCTAACTTACAACTCTAAACAACAATAAATATTTTAAACATTGGTGCAATTGAACAACTTCGAA
130 CCCTAACTTACAACTCTAAACAACAATAAATATTTTAAACATTGGTGCAATTGAACAACTTCGAA
19027 TGTTAAATTAATATGATATACGATATTGACGAAAATGATAAATTCAGTCTAATACAGAGACAA
195 TGTTAAATTAATATGATATACGATATTGACGAAAATGATAAATTCAGTCTAATACAGAGACAA
19090 GAAAATGACC
Statistics
Matches: 242, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
258 235 0.97
259 7 0.03
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.34
Consensus pattern (259 bp):
CTTCTATCGTATTTTCACATCAATTTAACCTTAAAAATTATTTAATTATATTATTTTATACCCTA
AACCCTAAATTCTAAACCCAAATCCTAAACCATAACCCTTGACCTCTAAACTACAAATCTTAAAC
CCTAACTTACAACTCTAAACAACAATAAATATTTTAAACATTGGTGCAATTGAACAACTTCGAAT
GTTAAATTAATATGATATACGATATTGACGAAAATGATAAATTCAGTCTAATACAGAGACAATG
Found at i:20241 original size:18 final size:19
Alignment explanation
Indices: 20206--20243 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
20196 CACAGAATGT
20206 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
20226 AAGATTATCA-GGGAATAA
1 AAGATTATCAGGGGAATAA
20244 GATTACTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.47, C:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:20256 original size:15 final size:16
Alignment explanation
Indices: 20205--20248 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 16
20195 TCACAGAATG
20205 TAAGATTATCAGTGGGAA
1 TAAGATTATCA--GGGAA
20223 TAAAAGATTATCAGGGAA
1 T--AAGATTATCAGGGAA
20241 TAAGATTA
1 TAAGATTA
20249 CTGGGAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.29
18 7 0.29
20 10 0.42
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (16 bp):
TAAGATTATCAGGGAA
Found at i:27747 original size:22 final size:22
Alignment explanation
Indices: 27720--27761 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
27710 TAAACGAACG
* *
27720 AACATAAATGAATGGATTACTA
1 AACATAAACGAATAGATTACTA
27742 AACATAAACGAATAGATTAC
1 AACATAAACGAATAGATTAC
27762 CGAATGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (22 bp):
AACATAAACGAATAGATTACTA
Found at i:31288 original size:50 final size:50
Alignment explanation
Indices: 31224--31325 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
31214 AAAAATATTG
* *
31224 AATACAAAATAAGATATCCCAATAATCAATTTTAAAATAAATGCATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
31274 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
31324 AA
1 AA
31326 ATAGGATAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:31526 original size:30 final size:30
Alignment explanation
Indices: 31478--31534 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
31468 ATTTGCATGG
* *
31478 CGCCCAGACCATCTGGCGACCTTCATTGGT
1 CGCCCAGACCACCCGGCGACCTTCATTGGT
*
31508 CGCCTAGACCACCCGGCGACCTTCATT
1 CGCCCAGACCACCCGGCGACCTTCATT
31535 CGAACAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.21
Consensus pattern (30 bp):
CGCCCAGACCACCCGGCGACCTTCATTGGT
Found at i:34902 original size:31 final size:30
Alignment explanation
Indices: 34858--34917 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
34848 AAACTACGTA
34858 TTTAATATCTAAATTATTAATTTTATTTTAT
1 TTTAATATCTAAATTATTAATTTT-TTTTAT
* * *
34889 TTTAGTATTTAAATTTTTAATTTTTTTTA
1 TTTAATATCTAAATTATTAATTTTTTTTA
34918 AAATCATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (30 bp):
TTTAATATCTAAATTATTAATTTTTTTTAT
Found at i:35401 original size:21 final size:20
Alignment explanation
Indices: 35315--35472 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
35305 AAATGACCAA
**
35315 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
35334 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
35354 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
35374 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
35395 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
35416 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
*
35436 CCAAAATCGCAACGCGAATATT
1 -CAAAATCGCAACGCG-ATTTT
35458 -AAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
35473 ACACATAAAT
Statistics
Matches: 105, Mismatches: 27, Indels: 14
0.72 0.18 0.10
Matches are distributed among these distances:
19 17 0.16
20 40 0.38
21 44 0.42
22 4 0.04
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:35463 original size:20 final size:20
Alignment explanation
Indices: 35375--35491 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 20
35365 ATCAGTTTCC
* *
35375 AAAATCGCAACGCGATTCTT
1 AAAATCGCAACGCGAATATT
* *
35395 GAAAATCGCAATGCG-ATAGT
1 -AAAATCGCAACGCGAATATT
** *
35415 ACAAATTCGCATTGCG-ATTTT
1 A-AAA-TCGCAACGCGAATATT
35436 CCAAAATCGCAACGCGAATATT
1 --AAAATCGCAACGCGAATATT
* *
35458 AAAATCGCAACGCGAACA-C
1 AAAATCGCAACGCGAATATT
35477 ATAAATCGCAACGCG
1 A-AAATCGCAACGCG
35492 TATCCGTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 13
0.76 0.12 0.13
Matches are distributed among these distances:
19 2 0.03
20 35 0.45
21 33 0.42
22 7 0.09
23 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGAATATT
Found at i:35501 original size:20 final size:20
Alignment explanation
Indices: 35459--35688 Score: 234
Period size: 20 Copynumber: 11.5 Consensus size: 20
35449 GCGAATATTA
* *
35459 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
35479 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
35499 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
35519 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
35539 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
35559 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
35579 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
35599 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
35619 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
35639 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
35659 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
35679 AAATCACAAC
1 AAATCGCAAC
35689 ACTGAAATTT
Statistics
Matches: 178, Mismatches: 25, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:35670 original size:40 final size:40
Alignment explanation
Indices: 35478--35688 Score: 282
Period size: 40 Copynumber: 5.3 Consensus size: 40
35468 CGCGAACACA
* * * *
35478 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
* ** * * * *
35518 TAAATCGCAACGCGT-ATGGGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
35558 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
35598 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
35638 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
*
35678 TAAATCACAAC
1 TAAATCGCAAC
35689 ACTGAAATTT
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
39 1 0.01
40 158 0.99
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
TAAATCGCAACGATAATCCGTAAATCGCAACGAGAATCTG
Found at i:36609 original size:12 final size:12
Alignment explanation
Indices: 36592--36616 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36582 ATATAATCCT
36592 GAAGAAGAAAAA
1 GAAGAAGAAAAA
36604 GAAGAAGAAAAA
1 GAAGAAGAAAAA
36616 G
1 G
36617 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:38975 original size:53 final size:52
Alignment explanation
Indices: 38912--39027 Score: 160
Period size: 53 Copynumber: 2.2 Consensus size: 52
38902 AACGAGAGAA
*
38912 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCA-TT
** ** **
38965 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
39017 TCGCATTGCGA
1 TCGCATTGCGA
39028 TTTTCATTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 13 0.23
53 43 0.77
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:38987 original size:19 final size:19
Alignment explanation
Indices: 38950--39047 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
38940 GATTCTCTCG
38950 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
38970 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38989 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
39003 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
39022 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
39041 TTGCGAT
1 TTGCGAT
39048 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 39 0.55
20 12 0.17
ACGTcount: A:0.14, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:39041 original size:52 final size:53
Alignment explanation
Indices: 38931--39047 Score: 227
Period size: 52 Copynumber: 2.2 Consensus size: 53
38921 GAAATGAAAA
38931 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
38984 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
39036 TCGCATTGCGAT
1 TCGCATTGCGAT
39048 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 33 0.52
53 31 0.48
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
Found at i:39158 original size:33 final size:33
Alignment explanation
Indices: 39106--39254 Score: 142
Period size: 33 Copynumber: 4.3 Consensus size: 33
39096 CCATTACATT
39106 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
39140 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
39172 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
39211 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
39244 TCGCAATGCGA
1 TCGCAATGCGA
39255 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 7 0.08
32 7 0.08
33 42 0.45
34 10 0.11
35 1 0.01
36 2 0.02
38 10 0.11
39 7 0.08
40 7 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:39162 original size:19 final size:19
Alignment explanation
Indices: 39106--39235 Score: 163
Period size: 19 Copynumber: 7.3 Consensus size: 19
39096 CCATTACATT
39106 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
39126 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
39140 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
39159 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
39178 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
39192 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
39211 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
39230 TCGCAA
1 TCGCAA
39236 CGAGAGAATC
Statistics
Matches: 96, Mismatches: 4, Indels: 21
0.79 0.03 0.17
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 58 0.60
20 6 0.06
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:39272 original size:19 final size:19
Alignment explanation
Indices: 39244--39379 Score: 166
Period size: 19 Copynumber: 7.6 Consensus size: 19
39234 AACGAGAGAA
*
39244 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
39263 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
39277 TCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
39296 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
39316 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
39332 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
39349 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
39368 TCGCATTGCGAT
1 TCGCATTGCGAT
39380 AGTCAATTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 10 0.10
19 47 0.47
20 18 0.18
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:39273 original size:52 final size:52
Alignment explanation
Indices: 39106--39254 Score: 289
Period size: 52 Copynumber: 2.8 Consensus size: 52
39096 CCATTACATT
39106 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
39159 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
39211 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
39255 TTTTCATTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 87 0.91
53 9 0.09
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:39287 original size:33 final size:33
Alignment explanation
Indices: 39244--39379 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 33
39234 AACGAGAGAA
*
39244 TCGCAATGCGATTTTCATTTCGCATTGCGATTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTC
*
39277 TCCCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTT-CGCATTGCGA--TTC
* * *
39313 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-
1 ---TCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTC
39349 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
39380 AGTCAATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
31 9 0.11
32 4 0.05
33 31 0.37
34 10 0.12
36 3 0.04
37 2 0.02
39 14 0.17
40 6 0.07
41 4 0.05
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTC
Found at i:39312 original size:53 final size:52
Alignment explanation
Indices: 39244--39379 Score: 236
Period size: 53 Copynumber: 2.6 Consensus size: 52
39234 AACGAGAGAA
*
39244 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
* *
39296 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
39349 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
39380 AGTCAATTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 31 0.39
53 49 0.61
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
Found at i:39505 original size:14 final size:14
Alignment explanation
Indices: 39486--39522 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
39476 CATCAATTAC
39486 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
39500 ACAAATCATCTTTT
1 ACAAATCAACTTTT
39514 ACAAATCAA
1 ACAAATCAA
39523 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:41517 original size:14 final size:14
Alignment explanation
Indices: 41498--41554 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
41488 GCGAAATGAA
*
41498 AATCGCAACGACAG
1 AATCGCAACGAAAG
41512 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
41529 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
41545 AATCGCAACG
1 AATCGCAACG
41555 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:41525 original size:33 final size:33
Alignment explanation
Indices: 41479--41571 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
41469 GCGAAACCAA
*
41479 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
41512 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
41545 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
41572 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:41536 original size:19 final size:19
Alignment explanation
Indices: 41442--41576 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
41432 TAGTTTACTT
* *
41442 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
41462 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
41481 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
41500 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
41514 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
41533 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
41547 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
41566 TCGCAATGCGA
1 TCGCAACGCGA
41577 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:41594 original size:19 final size:19
Alignment explanation
Indices: 41572--41700 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
41562 AAAATCGCAA
41572 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41591 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
41605 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41624 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
41638 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
41657 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
41676 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
41696 TGCGA
1 TGCGA
41701 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:41614 original size:33 final size:33
Alignment explanation
Indices: 41572--41663 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
41562 AAAATCGCAA
41572 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
41605 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
41638 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
41664 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:41903 original size:93 final size:93
Alignment explanation
Indices: 41744--42216 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
41734 TTGAATGGAT
41744 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41809 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
41837 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41902 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
41930 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41995 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
42023 AAATTTACTTTCAACCAAAAGACAAAACAAAGATAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
42088 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
42116 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
42180 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
42208 AAATTTACT
1 AAATTTACT
42217 AAGCAATCTA
Statistics
Matches: 375, Mismatches: 5, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
92 66 0.18
93 309 0.82
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:43936 original size:14 final size:14
Alignment explanation
Indices: 43917--44006 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
43907 TTGAAATGAA
43917 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43931 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
43948 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
43964 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
43983 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43997 AATCGCAACG
1 AATCGCAACG
44007 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:43954 original size:33 final size:33
Alignment explanation
Indices: 43909--44023 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
43899 TCTTTTGGTT
43909 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
43942 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
43975 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
44008 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
44024 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:43955 original size:19 final size:18
Alignment explanation
Indices: 43916--44028 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
43906 GTTGAAATGA
43916 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
43931 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
43948 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
43964 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
43981 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
43997 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
44014 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
44029 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:44059 original size:14 final size:14
Alignment explanation
Indices: 44040--44096 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
44030 TTTGGTTTCG
44040 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
44054 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
44073 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
44087 CGTTGCGATT
1 CGTTGCGATT
44097 GTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:44072 original size:33 final size:33
Alignment explanation
Indices: 44024--44104 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
44014 AAAATCGCAA
**
44024 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
44057 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
44090 TGCGATTGTCATTTC
1 TGCGATTTTCATTTC
44105 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:44107 original size:21 final size:21
Alignment explanation
Indices: 44081--44156 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
44071 CGCGTTGCGA
44081 TTCTCTCGTTGCGATTGTCAT
1 TTCTCTCGTTGCGATTGTCAT
**
44102 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTGTCAT
*
44122 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTGTCAT
*
44143 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
44157 CTCTTCTGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTGTCAT
Found at i:44137 original size:41 final size:41
Alignment explanation
Indices: 44080--44157 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
44070 TCGCGTTGCG
*
44080 ATTCTCTCGTTGCGATTGTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
*
44121 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGAC
44158 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTGTCATTTATCTCGTTGCGACAGTC
Found at i:44282 original size:33 final size:33
Alignment explanation
Indices: 44235--44305 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
44225 AATACTAACT
* *
44235 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
44268 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
44301 TGAAA
1 TGAAA
44306 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:44538 original size:22 final size:22
Alignment explanation
Indices: 44486--44540 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
44476 TGGTTGTGAG
**
44486 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
44508 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
44530 GGATTTCTTCG
1 GGATTTCTTCG
44541 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:44711 original size:20 final size:20
Alignment explanation
Indices: 44686--44879 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
44676 CTTTAAATAT
44686 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
44706 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
44728 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
44747 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
44767 CACATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
44787 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
44807 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
44827 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
44847 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
44867 CGCGTTGCGATTT
1 CGCGTTGCGATTT
44880 TGGAAAATCG
Statistics
Matches: 145, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:44873 original size:60 final size:60
Alignment explanation
Indices: 44686--44879 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
44676 CTTTAAATAT
**
44686 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
44747 CGCGTTGCGATATACGGATACACATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
44807 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
44867 CGCGTTGCGATTT
1 CGCGTTGCGATTT
44880 TGGAAAATCG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 83 0.75
61 27 0.25
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:44896 original size:21 final size:21
Alignment explanation
Indices: 44866--44948 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
44856 ATTTTCATAT
*
44866 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
44887 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
44908 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
44929 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
44949 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:44939 original size:42 final size:43
Alignment explanation
Indices: 44846--44944 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
44836 ATTTATGTGT
* *
44846 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
44887 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
44929 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
44945 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:45151 original size:23 final size:24
Alignment explanation
Indices: 45119--45163 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
45109 TTTTTTAACC
* *
45119 TTTTTTATTTAATA-TATTTTTTA
1 TTTTTAATTTAACATTATTTTTTA
45142 TTTTTAATTTAACATTATTTTT
1 TTTTTAATTTAACATTATTTTT
45164 GACTTTGTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTTTAATTTAACATTATTTTTTA
Found at i:53828 original size:124 final size:116
Alignment explanation
Indices: 53553--53835 Score: 273
Period size: 124 Copynumber: 2.4 Consensus size: 116
53543 TTAAATTTTT
* * *
53553 AAAAAATAAAAGTTTAGGTACT-AAACAAACTAAAACTTATAGTTTAGGTACTAAACACGTTAAG
1 AAAAAATTAAAGTTTAGGTACTAAAACAAACCAAAACTGATAGTTTAGGTACTAAACACGTTAAG
* * * * *
53617 TTTTTAATGATAGACACAAAAATGAAAACTAAACGATAGACATGATTTTGA
66 TTTTTAATGATAGAAAAAAAAATAAAAACTAAACGATAGACATAACTTTGA
* * * *** * *
53668 AAAAAATTGAAAGCTTAGATAATAAAATGGATCAAAACTGATAGTTTAGGTACTAAACATGTTAA
1 AAAAAATT-AAAGTTTAGGTACTAAAACAAACCAAAACTGATAGTTTAGGTACTAAACACGTTAA
* **
53733 GTTTTTTAATGGTGCATACTAAAAATAAAATAAAAACTAAAC-ATTAGGTATAACTTTGA
65 G-TTTTTAA---TG-ATA-GAAAAA-AAAATAAAAACTAAACGA-TAGACATAACTTTGA
* *
53792 AAAAAATTATAAGTTTAGGTACTAAAACATACCAAAATTGATAG
1 AAAAAATTA-AAGTTTAGGTACTAAAACAAACCAAAACTGATAG
53836 ACTAAGTATT
Statistics
Matches: 130, Mismatches: 27, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
115 7 0.05
116 11 0.08
117 35 0.27
118 7 0.05
121 2 0.02
122 3 0.02
123 5 0.04
124 60 0.46
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.29
Consensus pattern (116 bp):
AAAAAATTAAAGTTTAGGTACTAAAACAAACCAAAACTGATAGTTTAGGTACTAAACACGTTAAG
TTTTTAATGATAGAAAAAAAAATAAAAACTAAACGATAGACATAACTTTGA
Found at i:56744 original size:10 final size:10
Alignment explanation
Indices: 56729--56753 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
56719 TGAAGTTTTC
56729 ATTACCTTTA
1 ATTACCTTTA
56739 ATTACCTTTA
1 ATTACCTTTA
56749 ATTAC
1 ATTAC
56754 TTGGACGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTACCTTTA
Done.