Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007009.1 Hibiscus syriacus cultivar Beakdansim tig00018091_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: 74794
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:499 original size:20 final size:20
Alignment explanation
Indices: 474--565 Score: 118
Period size: 20 Copynumber: 4.7 Consensus size: 20
464 TTTTCATAAT
474 TCGCAATGAGAATACGTAAA
1 TCGCAATGAGAATACGTAAA
494 TCGCAA-GCA-AATACGTAAA
1 TCGCAATG-AGAATACGTAAA
* *
513 TCGCAATGCGAATTA-GGAAA
1 TCGCAATGAGAA-TACGTAAA
*
533 TCGCAATGCGAATACGTAAA
1 TCGCAATGAGAATACGTAAA
553 TCGCAATGAGAAT
1 TCGCAATGAGAAT
566 CTGACTATCG
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
19 19 0.30
20 42 0.67
21 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGAGAATACGTAAA
Found at i:558 original size:40 final size:40
Alignment explanation
Indices: 474--565 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 40
464 TTTTCATAAT
*
474 TCGCAATGAGAA-TACGTAAATCGCAAGCAAATACGTAAA
1 TCGCAATGAGAATTACGGAAATCGCAAGCAAATACGTAAA
* *
513 TCGCAATGCGAATTA-GGAAATCGCAATGCGAATACGTAAA
1 TCGCAATGAGAATTACGGAAATCGCAA-GCAAATACGTAAA
553 TCGCAATGAGAAT
1 TCGCAATGAGAAT
566 CTGACTATCG
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
39 21 0.45
40 26 0.55
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (40 bp):
TCGCAATGAGAATTACGGAAATCGCAAGCAAATACGTAAA
Found at i:576 original size:40 final size:39
Alignment explanation
Indices: 474--583 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
464 TTTTCATAAT
*
474 TCGCAATGAGAA-TACGTAAATCGCAA-GCAAATACGTAAA
1 TCGCAATGAGAATTA-G-AAATCGCAATGCGAATACGTAAA
*
513 TCGCAATGCGAATTAGGAAATCGCAATGCGAATACGTAAA
1 TCGCAATGAGAATTA-GAAATCGCAATGCGAATACGTAAA
*
553 TCGCAATGAGAATCT-GACTATCGCAATGCGA
1 TCGCAATGAGAAT-TAGA-AATCGCAATGCGA
584 TTTACATAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
39 22 0.35
40 39 0.63
41 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (39 bp):
TCGCAATGAGAATTAGAAATCGCAATGCGAATACGTAAA
Found at i:1143 original size:20 final size:20
Alignment explanation
Indices: 1120--1191 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1110 TTCTAAACTT
**
1120 AAAATCGCAACATTAAAATG
1 AAAATCGCAACAAGAAAATG
*
1140 AAAATCGCAACACGAAAATG
1 AAAATCGCAACAAGAAAATG
**
1160 ACTATCGCAA-AGAGAGAAATG
1 AAAATCGCAACA-AGA-AAATG
1181 AAAATCGCAAC
1 AAAATCGCAAC
1192 GAGAGAATCG
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.02
20 28 0.67
21 13 0.31
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACAAGAAAATG
Found at i:1181 original size:21 final size:21
Alignment explanation
Indices: 1135--1198 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1125 CGCAACATTA
*
1135 AAATGAAAATCGCAACA-CGA-
1 AAATGAAAATCGCAA-AGAGAG
**
1155 AAATGACTATCGCAAAGAGAG
1 AAATGAAAATCGCAAAGAGAG
*
1176 AAATGAAAATCGCAACGAGAG
1 AAATGAAAATCGCAAAGAGAG
1197 AA
1 AA
1199 TCGCAACGCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 20 0.56
ACGTcount: A:0.53, C:0.16, G:0.20, T:0.11
Consensus pattern (21 bp):
AAATGAAAATCGCAAAGAGAG
Found at i:1218 original size:33 final size:33
Alignment explanation
Indices: 1175--1244 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1165 CGCAAAGAGA
* *
1175 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATAAAAATCGCAACAAGAGAATCGCAACGC
* *
1208 GAAATAAAAATCGCAACAAGAGAATTGCAATGC
1 GAAATAAAAATCGCAACAAGAGAATCGCAACGC
1241 GAAA
1 GAAA
1245 CCAAAATCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.50, C:0.17, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATAAAAATCGCAACAAGAGAATCGCAACGC
Found at i:1251 original size:33 final size:33
Alignment explanation
Indices: 1181--1252 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
1171 GAGAGAAATG
* *
1181 AAAATCGCAACGAGAGAATCGCAACGCGAAATA
1 AAAATCGCAACAAGAGAATCGCAACGCGAAACA
* * *
1214 AAAATCGCAACAAGAGAATTGCAATGCGAAACC
1 AAAATCGCAACAAGAGAATCGCAACGCGAAACA
1247 AAAATC
1 AAAATC
1253 ACATGCGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (33 bp):
AAAATCGCAACAAGAGAATCGCAACGCGAAACA
Found at i:1280 original size:19 final size:20
Alignment explanation
Indices: 1256--1307 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1246 CAAAATCACA
**
1256 TGCGATTTTGGTT-TCGCGT
1 TGCGATTTTCATTCTCGCGT
*
1275 TGCGATTTTCATTCTCTCGT
1 TGCGATTTTCATTCTCGCGT
1295 TGCGATTTTCATT
1 TGCGATTTTCATT
1308 TCAACCAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.10, C:0.19, G:0.21, T:0.50
Consensus pattern (20 bp):
TGCGATTTTCATTCTCGCGT
Found at i:3184 original size:94 final size:93
Alignment explanation
Indices: 2968--3341 Score: 541
Period size: 94 Copynumber: 4.1 Consensus size: 93
2958 TAGATTACTT
* *
2968 AGTAAATTTATTCGTTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTGTG-AGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
3027 TATTTGTCTTTTGTTTTGTCTTTTGGTTG-
65 TATTTGTC-TTTGTTTTGTCTTTTGGTTGA
*
3056 AGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3121 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
*
3150 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3215 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * * *
3244 AGTAAATTTGTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTAAAGTTA
1 AGTAAA-TT-TATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTA
*
3309 GTA-TTGTCTTTG-TTTATCTTTTGGTTGA
64 GTATTTGTCTTTGTTTTGTCTTTTGGTTGA
3337 AGTAA
1 AGTAA
3342 TGCAATCCAT
Statistics
Matches: 266, Mismatches: 10, Indels: 15
0.91 0.03 0.05
Matches are distributed among these distances:
88 33 0.12
92 35 0.13
93 21 0.08
94 112 0.42
95 11 0.04
96 54 0.20
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:3294 original size:190 final size:179
Alignment explanation
Indices: 2968--3341 Score: 527
Period size: 190 Copynumber: 2.0 Consensus size: 179
2958 TAGATTACTT
*
2968 AGTAAATTTATTCGTTTGCTGCCAATACTGCTAAACTATTTATTAACACTGTGAGTTAGTATTTG
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTAACACTGTGAGTTAGTATTTG
3033 TCTTTTGTTTTGTCTTTTGGTTGAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTA
66 TCTTTTGTTTTGTCTTTTGGTTGAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTA
* * *
3098 TTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TTCTTTAACACTCTAAAGTTAGTA-TTGTCTTTG-TTTATCTTTTGGTTG-A
* *
3150 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAG
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACACTGTG-AGTTAG
* * *
3214 TATTTGTC-TTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTGTTCGTTTGCTGCCAATTCTGCT
60 TATTTGTCTTTTGTTTTGTCTTTTGGTTG--AGTAAA-TT-TATTCGGTTGCTGCCAATTATGCT
*
3278 AAACTGTGTATTCTTTAATACTCTAAAGTTAGTATTGTCTTTGTTTATCTTTTGGTTGA
121 AAACTGTGTATTCTTTAACACTCTAAAGTTAGTATTGTCTTTGTTTATCTTTTGGTTGA
3337 AGTAA
1 AGTAA
3342 TGCAATCCAT
Statistics
Matches: 172, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
182 33 0.19
186 35 0.20
187 21 0.12
188 20 0.12
189 11 0.06
190 52 0.30
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (179 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAACTATTTATTAACACTGTGAGTTAGTATTTG
TCTTTTGTTTTGTCTTTTGGTTGAGTAAATTTATTCGGTTGCTGCCAATTATGCTAAACTGTGTA
TTCTTTAACACTCTAAAGTTAGTATTGTCTTTGTTTATCTTTTGGTTGA
Found at i:3456 original size:20 final size:20
Alignment explanation
Indices: 3431--3492 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
3421 TTTTGGTTGA
3431 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
3451 AATGAAAATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
*
3470 AACGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
3490 AAT
1 AAT
3493 CGCAACTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 17 0.46
20 20 0.54
ACGTcount: A:0.50, C:0.18, G:0.23, T:0.10
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3659 original size:19 final size:19
Alignment explanation
Indices: 3550--3651 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
3540 GAAACTATAA
*
3550 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
*
3569 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
3583 TCTCGTTGCAATTTTTATT
1 TCGCGTTGCGATTTTCATT
* *
3602 TCGCGTTACGATTTTCGTT
1 TCGCGTTGCGATTTTCATT
*
3621 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
3640 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3652 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
14 8 0.13
16 2 0.03
17 2 0.03
19 51 0.81
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:5547 original size:14 final size:14
Alignment explanation
Indices: 5528--5563 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
5518 ATTGTTTAAT
*
5528 TGATTTGTAAAAGG
1 TGATTTGTAAAAGA
5542 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
5556 TGATTTGT
1 TGATTTGT
5564 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5692 original size:19 final size:19
Alignment explanation
Indices: 5670--5754 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
5660 AAAAATGACT
*
5670 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
* *
5689 ATCGCAA--C--TA-GAGA
1 ATCGCAACGCGAAATGAAA
* *
5703 ATCGCAATGCGAAATTAAA
1 ATCGCAACGCGAAATGAAA
5722 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
5741 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
5755 CTAAATTCGC
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 39 0.72
20 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:5771 original size:19 final size:19
Alignment explanation
Indices: 5702--5764 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
5692 GCAACTAGAG
* *
5702 AATCGCAATGCGAAATTAA
1 AATCGCAACGCGAAACTAA
5721 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
5740 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
5759 ATTCGC
1 AATCGC
5765 GTTGCGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:5780 original size:19 final size:19
Alignment explanation
Indices: 5760--5882 Score: 86
Period size: 19 Copynumber: 6.9 Consensus size: 19
5750 CGAAACTAAA
*
5760 TTCGCGTTGCGATTTTCAA
1 TTCGCGTTGCGATTTTCAT
*
5779 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
5794 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
5812 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
5827 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
5845 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
5864 TTCCGCGTTGCGATTTTCA
1 TT-CGCGTTGCGATTTTCA
5883 CGTTGCGATT
Statistics
Matches: 77, Mismatches: 16, Indels: 21
0.68 0.14 0.18
Matches are distributed among these distances:
14 17 0.22
16 6 0.08
17 6 0.08
19 35 0.45
20 13 0.17
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:5806 original size:33 final size:33
Alignment explanation
Indices: 5764--5857 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
5754 ACTAAATTCG
*
5764 CGTTGCGATTTTCAATTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
5797 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
5830 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
5858 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:5888 original size:53 final size:52
Alignment explanation
Indices: 5799--5907 Score: 155
Period size: 53 Copynumber: 2.1 Consensus size: 52
5789 GATTCCCTCG
** *
5799 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
* * *
5851 TTGCGATAGTCATTTCCGCGTTGCGATTTTCACGTTGCGATTTTCATTTTGCA
1 TTGCGATAGTCATTT-CGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
5904 TTGC
1 TTGC
5908 AATTCTCTCG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
52 13 0.26
53 37 0.74
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (52 bp):
TTGCGATAGTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCGCA
Found at i:5902 original size:14 final size:14
Alignment explanation
Indices: 5869--5896 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5859 GTCATTTCCG
5869 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
5883 CGTTGCGATTTTCA
1 CGTTGCGATTTTCA
5897 TTTTGCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTTTCA
Found at i:7688 original size:20 final size:21
Alignment explanation
Indices: 7665--7712 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
7655 AGAATCTCGT
* *
7665 TGCGATTTA-CTAAATCGCAA
1 TGCGATTTAGCAAAATCGAAA
* *
7685 TGCGAATTAGGAAAATCGAAA
1 TGCGATTTAGCAAAATCGAAA
7706 TGCGATT
1 TGCGATT
7713 ACGTATTCGC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (21 bp):
TGCGATTTAGCAAAATCGAAA
Found at i:7701 original size:21 final size:21
Alignment explanation
Indices: 7676--7792 Score: 121
Period size: 21 Copynumber: 5.7 Consensus size: 21
7666 GCGATTTACT
7676 AAATCGCAATGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* *
7697 AAATCGAAATGCG-ATTACG-
1 AAATCGCAATGCGAATTAGGA
* * *
7716 TATTCGCATTGCGAATTAGGA
1 AAATCGCAATGCGAATTAGGA
* * *
7737 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
* * *
7758 AAATCGCAACGCGAATTTGGG
1 AAATCGCAATGCGAATTAGGA
7779 AAATCGCAATGCGA
1 AAATCGCAATGCGA
7793 TAGTCAGAAT
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 9 0.11
20 10 0.12
21 61 0.76
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTAGGA
Found at i:8353 original size:25 final size:25
Alignment explanation
Indices: 8325--8385 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
8315 TGAATTAATT
8325 ATTTAGTTTTAAACCGAGCCTTTAG
1 ATTTAGTTTTAAACCGAGCCTTTAG
8350 ATTTAGTTTTAAACCGAGCCTTTAG
1 ATTTAGTTTTAAACCGAGCCTTTAG
8375 ATTTAGATTTT
1 ATTTAG-TTTT
8386 TCACACTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 31 0.89
26 4 0.11
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (25 bp):
ATTTAGTTTTAAACCGAGCCTTTAG
Found at i:9149 original size:21 final size:21
Alignment explanation
Indices: 9125--9165 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9115 ATGTAAATCG
9125 CATTGCGATTTTCCAAATTCA
1 CATTGCGATTTTCCAAATTCA
9146 CATTGCGATTTTCCAAATTC
1 CATTGCGATTTTCCAAATTC
9166 GCAACACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (21 bp):
CATTGCGATTTTCCAAATTCA
Found at i:9184 original size:20 final size:20
Alignment explanation
Indices: 9159--9209 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
9149 TGCGATTTTC
9159 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
* *
9179 CAAATTCGCAATACATAAGT
1 CAAATTCGCAACACAGAAGT
*
9199 CAAGTTCGCAA
1 CAAATTCGCAA
9210 AGGGCGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:9389 original size:22 final size:22
Alignment explanation
Indices: 9357--9410 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
9347 TCACTCTTTA
*
9357 CGACGATATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
9379 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
9401 CGGCGAAATC
1 CGACGAAATC
9411 TATCTATCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:9828 original size:20 final size:20
Alignment explanation
Indices: 9751--9821 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
9741 TGAAACTTAA
**
9751 GTTGCGATTTTCATTTTCTT
1 GTTGCGATTTTCATTTTCGC
9771 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
9791 GTTGCGATTTTCATTTTCGC
1 GTTGCGATTTTCATTTTCGC
*
9811 GTTGCAATTTT
1 GTTGCGATTTT
9822 AAGTTTCAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.11, C:0.17, G:0.18, T:0.54
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGC
Found at i:11852 original size:21 final size:21
Alignment explanation
Indices: 11826--11906 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
11816 AGCACCTGTC
*
11826 ATCATTCAAGAGGCCTCTCCT
1 ATCATTCAAGAGGCCCCTCCT
*
11847 ATCATTCAAGAGGCCCCT-AT
1 ATCATTCAAGAGGCCCCTCCT
* *
11867 CATCCTTCAAGAGGCCCCTCCA
1 -ATCATTCAAGAGGCCCCTCCT
*
11889 ACCATTCAAGAGGCCCCT
1 ATCATTCAAGAGGCCCCT
11907 GTCATCGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCCT
Found at i:11870 original size:42 final size:42
Alignment explanation
Indices: 11824--11929 Score: 140
Period size: 42 Copynumber: 2.5 Consensus size: 42
11814 GAAGCACCTG
* * *
11824 TCATCATTCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCCCTCCAACCATTCAAGAGGCCCCTA
* *
11866 TCATCCTTCAAGAGGCCCCTCCAACCATTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTCCAACCATTCAAGAGGCCCCTA
* * *
11908 TCATCGTTTAAGAGGTCCCTCC
1 TCATCATTCAAGAGGCCCCTCC
11930 CACCGTTCGA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.25
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCCCTCCAACCATTCAAGAGGCCCCTA
Found at i:11920 original size:21 final size:20
Alignment explanation
Indices: 11824--11927 Score: 100
Period size: 21 Copynumber: 5.0 Consensus size: 20
11814 GAAGCACCTG
*
11824 TCATCATTCAAGAGGCCTCT
1 TCATCATTCAAGAGGCCCCT
*
11844 CCTATCATTCAAGAGGCCCCT
1 TC-ATCATTCAAGAGGCCCCT
*
11865 ATCATCCTTCAAGAGGCCCCT
1 -TCATCATTCAAGAGGCCCCT
* *
11886 CCAACCATTCAAGAGGCCCCT
1 TC-ATCATTCAAGAGGCCCCT
* * *
11907 GTCATCGTTTAAGAGGTCCCT
1 -TCATCATTCAAGAGGCCCCT
11928 CCCACCGTTC
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (20 bp):
TCATCATTCAAGAGGCCCCT
Found at i:11936 original size:21 final size:21
Alignment explanation
Indices: 11830--11942 Score: 84
Period size: 21 Copynumber: 5.4 Consensus size: 21
11820 CCTGTCATCA
* * * *
11830 TTCAAGAGGCCTCTCCTATCA
1 TTCAAGAGGCCCCTCCCACCG
**
11851 TTCAAGAGGCCCCTATCATCC-
1 TTCAAGAGGCCCCTCCCA-CCG
* *
11872 TTCAAGAGGCCCCTCCAACCA
1 TTCAAGAGGCCCCTCCCACCG
** *
11893 TTCAAGAGGCCCCTGTCATCG
1 TTCAAGAGGCCCCTCCCACCG
* *
11914 TTTAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
11935 TTCGAGAG
1 TTCAAGAG
11943 CCCGATTCAC
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
20 2 0.03
21 67 0.96
22 1 0.01
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:13358 original size:63 final size:64
Alignment explanation
Indices: 13288--13435 Score: 228
Period size: 63 Copynumber: 2.3 Consensus size: 64
13278 AAATTGATGT
13288 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTT-TGCTT-GTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTCTGCTTCG-TTAATTG
* * ***
13351 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTCTGCTTCGTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTCTGCTTCGTTAATTG
13415 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
13436 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
63 44 0.56
64 33 0.42
65 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTCTGCTTCGTTAATTG
Found at i:13519 original size:20 final size:20
Alignment explanation
Indices: 13494--13569 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
13484 AAGGTACACT
13494 TTCGCAACGCGAAAGTTAAA
1 TTCGCAACGCGAAAGTTAAA
** *
13514 TTCGCATTGCGATAGTTAAA
1 TTCGCAACGCGAAAGTTAAA
** **
13534 TTCGCAACATGAAAGCCAAA
1 TTCGCAACGCGAAAGTTAAA
*
13554 TTTGCAACGCGAAAGT
1 TTCGCAACGCGAAAGT
13570 CAACTTCACA
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
TTCGCAACGCGAAAGTTAAA
Found at i:13813 original size:18 final size:18
Alignment explanation
Indices: 13790--13825 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
13780 GAAGCCGTTG
*
13790 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
13808 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
13826 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:16108 original size:12 final size:12
Alignment explanation
Indices: 16087--16120 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16077 GGTTACGGGT
*
16087 TTTGAGATTGTG
1 TTTGATATTGTG
16099 TTTGATATTGTG
1 TTTGATATTGTG
*
16111 TTTGGTATTG
1 TTTGATATTG
16121 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:17017 original size:20 final size:20
Alignment explanation
Indices: 16989--17035 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
16979 GAAATTCAGT
*
16989 ATTGTGATTTACAGATTCGC
1 ATTGCGATTTACAGATTCGC
*
17009 GTTGCGATTTACAGATTCGC
1 ATTGCGATTTACAGATTCGC
17029 ATTGCGA
1 ATTGCGA
17036 ATTTGGAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTGCGATTTACAGATTCGC
Found at i:17087 original size:19 final size:19
Alignment explanation
Indices: 17050--17097 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
17040 GGAAACTGAG
* *
17050 TTGCGAAATTGGAGTTCGCA
1 TTGCG-AATTCGAGATCGCA
*
17070 TTGCGAATTCGAGATCGCG
1 TTGCGAATTCGAGATCGCA
17089 TTGCGAATT
1 TTGCGAATT
17098 TGTTGGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 20 0.80
20 5 0.20
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (19 bp):
TTGCGAATTCGAGATCGCA
Found at i:19280 original size:3 final size:3
Alignment explanation
Indices: 19272--19341 Score: 83
Period size: 3 Copynumber: 23.3 Consensus size: 3
19262 CTTGTTAATT
19272 TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
19319 TT- TTA -TA TTA GTT- TTA TTT TTA T
1 TTA TTA TTA TTA -TTA TTA TTA TTA T
19342 ATCTGCAGGC
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
2 6 0.10
3 45 0.76
4 8 0.14
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19293 original size:16 final size:16
Alignment explanation
Indices: 19266--19341 Score: 90
Period size: 16 Copynumber: 5.1 Consensus size: 16
19256 GGAGATCTTG
19266 TTAATT-TTATTATTA
1 TTAATTATTATTATTA
19281 TTAATTATTATTATTA
1 TTAATTATTATTATTA
*
19297 TTATTTATTATTATTA
1 TTAATTATTATTATTA
19313 TT-ATTATT-TTA-TA
1 TTAATTATTATTATTA
* *
19326 TTAGTT-TTATTTTTA
1 TTAATTATTATTATTA
19341 T
1 T
19342 ATCTGCAGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.11
14 7 0.13
15 14 0.26
16 26 0.49
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (16 bp):
TTAATTATTATTATTA
Found at i:19321 original size:19 final size:19
Alignment explanation
Indices: 19272--19341 Score: 92
Period size: 19 Copynumber: 3.7 Consensus size: 19
19262 CTTGTTAATT
*
19272 TTATTATTATTAATTATTA
1 TTATTATTATTTATTATTA
19291 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
19310 TTATTATTATTT-TATATTA
1 TTATTATTATTTAT-TATTA
19329 GTT-TTATT-TTTAT
1 -TTATTATTATTTAT
19342 ATCTGCAGGC
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
18 4 0.09
19 41 0.87
20 2 0.04
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (19 bp):
TTATTATTATTTATTATTA
Found at i:19333 original size:11 final size:10
Alignment explanation
Indices: 19273--19335 Score: 51
Period size: 10 Copynumber: 6.1 Consensus size: 10
19263 TTGTTAATTT
19273 TATTATTATTA
1 TATTATT-TTA
*
19284 -ATTATTAT-
1 TATTATTTTA
19292 TATTATTATT-
1 TATTATT-TTA
19302 TATTATTATTA
1 TATTATT-TTA
19313 TTATTATTTTA
1 -TATTATTTTA
19324 TATTAGTTTTA
1 TATTA-TTTTA
19335 T
1 T
19336 TTTTATATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
9 7 0.16
10 22 0.49
11 9 0.20
12 7 0.16
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TATTATTTTA
Found at i:20512 original size:106 final size:109
Alignment explanation
Indices: 20344--20564 Score: 310
Period size: 106 Copynumber: 2.1 Consensus size: 109
20334 ATCTGGCATA
* *
20344 TTTTTGTATGTTGGTCACCTGTGAGAACCAAGGTTGTTATTTACCCGTTTTCATGCATGTTATGT
1 TTTTTGTATGTTGGTCACCTATGAGAACCAAGGTTGTTATTTAACCGTTTTCATGCATGTTATGT
*
20409 ATTTT-TGG-ATATTTTCTATTTAG-TCCCCATAGTTTA-GCGTG
66 ATTTTCTGGAATATTTTATATTTAGTTCCCCATA-TTTAGGCGTG
* * *
20450 TTTTTGTATGTTGGTCACCGGTATG-GATCGAA-GTTGTTATTTAATCGTTTTCATGCATGTTAT
1 TTTTTGTATGTTGGTCACC--TATGAGAACCAAGGTTGTTATTTAACCGTTTTCATGCATGTTAT
*
20513 GTATTTTCTGGAATATTTTATATTTAGTTCCCCTTATTTAGGCGTG
64 GTATTTTCTGGAATATTTTATATTTAGTTCCCCATATTTAGGCGTG
20559 TTTTTG
1 TTTTTG
20565 CATTTTGATA
Statistics
Matches: 102, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
106 55 0.54
107 8 0.08
108 21 0.21
109 18 0.18
ACGTcount: A:0.19, C:0.13, G:0.20, T:0.48
Consensus pattern (109 bp):
TTTTTGTATGTTGGTCACCTATGAGAACCAAGGTTGTTATTTAACCGTTTTCATGCATGTTATGT
ATTTTCTGGAATATTTTATATTTAGTTCCCCATATTTAGGCGTG
Found at i:22094 original size:14 final size:14
Alignment explanation
Indices: 22075--22105 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
22065 ACACAAGATC
*
22075 TTTTAAAAATTAGA
1 TTTTAAAAATTAAA
22089 TTTTAAAAATTAAA
1 TTTTAAAAATTAAA
22103 TTT
1 TTT
22106 GTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTTTAAAAATTAAA
Found at i:22165 original size:12 final size:12
Alignment explanation
Indices: 22148--22196 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
22138 CTATAAATAT
22148 ATAAGTATATAC
1 ATAAGTATATAC
*
22160 ATAAGTATGTAC
1 ATAAGTATATAC
*
22172 ATATAGGTATATAT
1 ATA-A-GTATATAC
*
22186 ATAAATATATA
1 ATAAGTATATA
22197 TGTATGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 20 0.65
13 2 0.06
14 9 0.29
ACGTcount: A:0.49, C:0.04, G:0.10, T:0.37
Consensus pattern (12 bp):
ATAAGTATATAC
Found at i:22400 original size:14 final size:15
Alignment explanation
Indices: 22375--22413 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
22365 TACATAAGTA
22375 TATACTTATATATACT
1 TATAC-TATATATACT
*
22391 TATA-TATATATAGT
1 TATACTATATATACT
22405 TATACTATA
1 TATACTATA
22414 AATATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 4 0.19
16 4 0.19
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (15 bp):
TATACTATATATACT
Found at i:22408 original size:10 final size:10
Alignment explanation
Indices: 22373--22398 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
22363 TATACATAAG
22373 TATATACTTA
1 TATATACTTA
22383 TATATACTTA
1 TATATACTTA
22393 TATATA
1 TATATA
22399 TATAGTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (10 bp):
TATATACTTA
Found at i:28794 original size:23 final size:24
Alignment explanation
Indices: 28747--28795 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
28737 TCTACATTTT
*
28747 TGGCACATTTTAACTCTAATCTTG
1 TGGCACATTTTAACTCTAATATTG
* *
28771 TGGCACATTTT-ATTCTACTATTG
1 TGGCACATTTTAACTCTAATATTG
28794 TG
1 TG
28796 ACATGTTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.22, C:0.18, G:0.14, T:0.45
Consensus pattern (24 bp):
TGGCACATTTTAACTCTAATATTG
Found at i:30851 original size:2 final size:2
Alignment explanation
Indices: 30844--30932 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
30834 TCCCTCAAAT
30844 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
30886 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
30928 TA TA T
1 TA TA T
30933 GAACATGATT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44187 original size:23 final size:23
Alignment explanation
Indices: 44145--44273 Score: 165
Period size: 23 Copynumber: 5.7 Consensus size: 23
44135 TTAGTGCAGA
* *
44145 GGGAATCGATACCCCC-TTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
44167 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
44190 GAGAACCGACTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
44213 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
44236 GGGAACTGATTCCCCC--TGTAG
1 GGGAACCGATTCCCCCTTTGAAG
* *
44257 GGGAATCGATACCCCCT
1 GGGAACCGATTCCCCCT
44274 AGGGTTCTGG
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
21 17 0.18
22 14 0.15
23 63 0.67
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:49739 original size:24 final size:24
Alignment explanation
Indices: 49690--49736 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49680 GATTTACTAT
* *
49690 TATTATATATTTAATTATTAATAA
1 TATTATATATTAAATTATAAATAA
49714 TATTATATATTAAATTA-AAATAA
1 TATTATATATTAAATTATAAATAA
49737 ATAATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATTATATATTAAATTATAAATAA
Found at i:49864 original size:28 final size:28
Alignment explanation
Indices: 49829--49962 Score: 225
Period size: 28 Copynumber: 4.8 Consensus size: 28
49819 AAAGTCCCTA
*
49829 AAATTAAAATAAACAACTATTATATATT
1 AAATTAAAGTAAACAACTATTATATATT
49857 AAATTAAAGTAAACAACTATTATATATT
1 AAATTAAAGTAAACAACTATTATATATT
*
49885 AAATTAAAATAAA-AACTATTATATATT
1 AAATTAAAGTAAACAACTATTATATATT
*
49912 AAATTAAAGTAAATAACTATTATATATT
1 AAATTAAAGTAAACAACTATTATATATT
*
49940 AAATTAAAGTAAACAATTATTAT
1 AAATTAAAGTAAACAACTATTAT
49963 TTTAAAATAT
Statistics
Matches: 100, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
27 26 0.26
28 74 0.74
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (28 bp):
AAATTAAAGTAAACAACTATTATATATT
Found at i:49910 original size:55 final size:56
Alignment explanation
Indices: 49829--49962 Score: 234
Period size: 55 Copynumber: 2.4 Consensus size: 56
49819 AAAGTCCCTA
49829 AAATTAAAATAAACAACTATTATATATTAAATTAAAGTAAACAACTATTATATATT
1 AAATTAAAATAAACAACTATTATATATTAAATTAAAGTAAACAACTATTATATATT
*
49885 AAATTAAAATAAA-AACTATTATATATTAAATTAAAGTAAATAACTATTATATATT
1 AAATTAAAATAAACAACTATTATATATTAAATTAAAGTAAACAACTATTATATATT
* *
49940 AAATTAAAGTAAACAATTATTAT
1 AAATTAAAATAAACAACTATTAT
49963 TTTAAAATAT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
55 53 0.72
56 21 0.28
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (56 bp):
AAATTAAAATAAACAACTATTATATATTAAATTAAAGTAAACAACTATTATATATT
Found at i:51083 original size:16 final size:16
Alignment explanation
Indices: 51062--51092 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51052 TCTAGTTTTT
51062 CCGAGTACCCGGTTAC
1 CCGAGTACCCGGTTAC
51078 CCGAGTACCCGGTTA
1 CCGAGTACCCGGTTA
51093 GTTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (16 bp):
CCGAGTACCCGGTTAC
Found at i:51376 original size:14 final size:15
Alignment explanation
Indices: 51357--51386 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
51347 CCGAAAGTTC
51357 CGGGTACC-GAAAAT
1 CGGGTACCTGAAAAT
51371 CGGGTACCTGAAAAT
1 CGGGTACCTGAAAAT
51386 C
1 C
51387 CAGGTACCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.33, C:0.23, G:0.27, T:0.17
Consensus pattern (15 bp):
CGGGTACCTGAAAAT
Found at i:56150 original size:2 final size:2
Alignment explanation
Indices: 56143--56191 Score: 66
Period size: 2 Copynumber: 25.0 Consensus size: 2
56133 ACTTTGTATG
*
56143 AT AT AT AT AT AT AT AT -T AC AT AT GA- 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 AT AT AT AT AT
56184 AT AT AT AT
1 AT AT AT AT
56192 GTATTATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 2 0.05
2 39 0.93
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58807 original size:24 final size:24
Alignment explanation
Indices: 58778--58823 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
58768 ACATGATATG
58778 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
58802 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
58824 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:64744 original size:30 final size:29
Alignment explanation
Indices: 64687--64744 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
64677 GATTTATTTA
* *
64687 GTGACCAAATTATAATTTGGTAAAGTTTG
1 GTGACCAAAGTATAATTTGGAAAAGTTTG
64716 GTGACCAAAGTATAAACTTT-GAAAAGTTT
1 GTGACCAAAGTAT-AA-TTTGGAAAAGTTT
64745 AGGAACAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 12 0.48
30 10 0.40
31 3 0.12
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (29 bp):
GTGACCAAAGTATAATTTGGAAAAGTTTG
Found at i:70372 original size:29 final size:28
Alignment explanation
Indices: 70330--70412 Score: 148
Period size: 29 Copynumber: 2.9 Consensus size: 28
70320 TCACCTAACT
70330 AAATTGATGTAAGCAATGACATCAAAAC
1 AAATTGATGTAAGCAATGACATCAAAAC
70358 AAAATTGATGTAAGCAATGACATCAAAAC
1 -AAATTGATGTAAGCAATGACATCAAAAC
*
70387 TAATTGATGTAAGCAATGACATCAAA
1 AAATTGATGTAAGCAATGACATCAAA
70413 TTAATATAGG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 25 0.47
29 28 0.53
ACGTcount: A:0.49, C:0.13, G:0.14, T:0.23
Consensus pattern (28 bp):
AAATTGATGTAAGCAATGACATCAAAAC
Done.