Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005206.1 Hibiscus syriacus cultivar Beakdansim tig00011774_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: 227869
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:137431 original size:35 final size:33
Alignment explanation
Indices: 137392--137476 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
137382 ATATTTCAGT
137392 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
137427 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
137462 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
137477 TAATTACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:140488 original size:15 final size:15
Alignment explanation
Indices: 140470--140501 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
140460 GGTTTCATCT
*
140470 TCTCGAATTTCACCA
1 TCTCGAATTTAACCA
140485 TCTCGAATTTAACCA
1 TCTCGAATTTAACCA
140500 TC
1 TC
140502 ATAATAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (15 bp):
TCTCGAATTTAACCA
Found at i:149693 original size:42 final size:42
Alignment explanation
Indices: 149605--149693 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
149595 GTTACAATGA
* * **
149605 AAAATATTATAAAAAATATAATATTTTAAGTTGTATTTAATT
1 AAAATATTATAAAAAATACAATATTTTAAGTTGTATCTAACC
* * *
149647 AAAATATTATGAAGAATACAATATTTTAAGTTGTGTCTAACC
1 AAAATATTATAAAAAATACAATATTTTAAGTTGTATCTAACC
149689 AAAAT
1 AAAAT
149694 GATATAATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.39
Consensus pattern (42 bp):
AAAATATTATAAAAAATACAATATTTTAAGTTGTATCTAACC
Found at i:159706 original size:31 final size:31
Alignment explanation
Indices: 159658--159724 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
159648 TTACGGACCT
* *
159658 AAGGTGATCTTTGGGTAGGCTCTCAGGCCCC
1 AAGGCGATCCTTGGGTAGGCTCTCAGGCCCC
159689 AAGGCGATCCTTGGGTAGGCTCTCAGGCCCC
1 AAGGCGATCCTTGGGTAGGCTCTCAGGCCCC
159720 AAGGC
1 AAGGC
159725 ACTTTCTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.33, T:0.21
Consensus pattern (31 bp):
AAGGCGATCCTTGGGTAGGCTCTCAGGCCCC
Found at i:160770 original size:47 final size:47
Alignment explanation
Indices: 160707--160797 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
160697 TACACTATCT
*
160707 CCAAAAGAGGGATTACAAATTTAGCAAATAAAAGAAAACTTCACTAA
1 CCAAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACTAA
* *
160754 CCAATAGAGGGATTACAAATCTAGCAAATAAAATAAAACTTCAC
1 CCAAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCAC
160798 AAAAGGCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.52, C:0.16, G:0.12, T:0.20
Consensus pattern (47 bp):
CCAAAAGAGGGATTACAAATCTAGCAAATAAAAGAAAACTTCACTAA
Found at i:161272 original size:20 final size:20
Alignment explanation
Indices: 161243--161282 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
161233 CACTGAAATA
161243 TTGGTATCGAGACCGACAAG
1 TTGGTATCGAGACCGACAAG
* *
161263 TTGGTCTCGAGACTGACAAG
1 TTGGTATCGAGACCGACAAG
161283 AGTTTTTGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (20 bp):
TTGGTATCGAGACCGACAAG
Found at i:164624 original size:21 final size:21
Alignment explanation
Indices: 164603--164643 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
164593 TCAAAAACAT
164603 TTAATTTTTCTTGCAA-TTCA
1 TTAATTTTTCTTGCAAGTTCA
* *
164623 TTGATTTTTCTTTCAAGTTCA
1 TTAATTTTTCTTGCAAGTTCA
164644 CTATTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (21 bp):
TTAATTTTTCTTGCAAGTTCA
Found at i:165114 original size:36 final size:36
Alignment explanation
Indices: 165067--165151 Score: 170
Period size: 36 Copynumber: 2.4 Consensus size: 36
165057 AGCTTGGACA
165067 TTTCTTTATCTTCTTCATCCACCTCTTCACTAGAAT
1 TTTCTTTATCTTCTTCATCCACCTCTTCACTAGAAT
165103 TTTCTTTATCTTCTTCATCCACCTCTTCACTAGAAT
1 TTTCTTTATCTTCTTCATCCACCTCTTCACTAGAAT
165139 TTTCTTTATCTTC
1 TTTCTTTATCTTC
165152 ATTGGTGGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.18, C:0.29, G:0.02, T:0.51
Consensus pattern (36 bp):
TTTCTTTATCTTCTTCATCCACCTCTTCACTAGAAT
Found at i:165960 original size:2 final size:2
Alignment explanation
Indices: 165953--165988 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
165943 TAATAAATAC
165953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
165989 ATACACATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:166437 original size:18 final size:18
Alignment explanation
Indices: 166414--166484 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
166404 GCGTAGAATT
*
166414 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
166432 TGTCCCAAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
166450 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
166468 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
166485 CCTTAAGAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 45 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:169220 original size:16 final size:17
Alignment explanation
Indices: 169189--169222 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
169179 TTAACTGCAA
169189 ACTTTTATCATATACAC
1 ACTTTTATCATATACAC
*
169206 ACTTTTA-CTTATACAC
1 ACTTTTATCATATACAC
169222 A
1 A
169223 ATACCATCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (17 bp):
ACTTTTATCATATACAC
Found at i:170626 original size:18 final size:18
Alignment explanation
Indices: 170605--170683 Score: 97
Period size: 18 Copynumber: 4.4 Consensus size: 18
170595 TGTCCTGTAG
170605 GACCACTATGTCCCGAAA
1 GACCACTATGTCCCGAAA
* * *
170623 GACCACTGTATCCTG-AA
1 GACCACTATGTCCCGAAA
*
170640 GAACCACTATGTCTCGAAA
1 G-ACCACTATGTCCCGAAA
*
170659 GACCACTATGTCCCGAAG
1 GACCACTATGTCCCGAAA
170677 GACCACT
1 GACCACT
170684 CCTTAAGAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
17 3 0.06
18 44 0.88
19 3 0.06
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.19
Consensus pattern (18 bp):
GACCACTATGTCCCGAAA
Found at i:170646 original size:36 final size:36
Alignment explanation
Indices: 170597--170683 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
170587 ATAGAATTTG
* *
170597 TCCTGTAGGACCACTATGTCCCGAAAGACCACTGTA
1 TCCTGAAGGACCACTATGTCCCGAAAGACCACTATA
* * *
170633 TCCTGAAGAACCACTATGTCTCGAAAGACCACTATG
1 TCCTGAAGGACCACTATGTCCCGAAAGACCACTATA
*
170669 TCCCGAAGGACCACT
1 TCCTGAAGGACCACT
170684 CCTTAAGAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.21
Consensus pattern (36 bp):
TCCTGAAGGACCACTATGTCCCGAAAGACCACTATA
Found at i:173511 original size:20 final size:20
Alignment explanation
Indices: 173488--173527 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
173478 CACTGAAATA
173488 TTGGTATCGAGACTGACAAG
1 TTGGTATCGAGACTGACAAG
* *
173508 TTGGTCTCTAGACTGACAAG
1 TTGGTATCGAGACTGACAAG
173528 GGTTTTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TTGGTATCGAGACTGACAAG
Found at i:173943 original size:20 final size:21
Alignment explanation
Indices: 173918--173969 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
173908 TTTTCCCAAT
*
173918 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
173938 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
173959 TCGCAATGCGA
1 TCGCAATGCGA
173970 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:173983 original size:20 final size:20
Alignment explanation
Indices: 173958--174071 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
173948 AATTGGGAAA
*
173958 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
173978 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
173998 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
174019 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
174039 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
174059 TTCGCAACGCGAT
1 ATCGCAACGCGAT
174072 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:174002 original size:61 final size:61
Alignment explanation
Indices: 173955--174071 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
173945 GCGAATTGGG
* * * * *
173955 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
174016 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
174072 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:174665 original size:18 final size:18
Alignment explanation
Indices: 174634--174668 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
174624 GAGAATCGCA
*
174634 ACGCGAAATAAAAATCGT
1 ACGCGAAACAAAAATCGT
*
174652 ACGCGAAACCAAAATCG
1 ACGCGAAACAAAAATCG
174669 CATTGCGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.23, G:0.17, T:0.11
Consensus pattern (18 bp):
ACGCGAAACAAAAATCGT
Found at i:174688 original size:19 final size:19
Alignment explanation
Indices: 174666--174797 Score: 123
Period size: 19 Copynumber: 7.1 Consensus size: 19
174656 GAAACCAAAA
*
174666 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
174685 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
174704 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
174718 TCTCGTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
174737 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
174756 TCCGCGTTGCGATTCTT-ATT
1 T-CGCGTTGCGATT-TTCATT
*
174776 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
174796 TC
1 TC
174798 AACCAAAAGA
Statistics
Matches: 95, Mismatches: 9, Indels: 18
0.78 0.07 0.15
Matches are distributed among these distances:
14 9 0.09
16 2 0.02
17 3 0.03
19 51 0.54
20 28 0.29
21 2 0.02
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:176966 original size:42 final size:42
Alignment explanation
Indices: 176890--177091 Score: 185
Period size: 42 Copynumber: 4.8 Consensus size: 42
176880 GACTCGCCTG
* * * * * * *
176890 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
176932 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * * ** * * *
176974 TCATCCCTCAAGAGTCCACTCTTATCGTTAAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
177016 TCATTCCTCGAGAGTCCCCTCCCACAGTTCAAGAGGCCACT-
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
177057 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
177092 CCCGATTCAC
Statistics
Matches: 128, Mismatches: 30, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
40 4 0.03
41 23 0.18
42 101 0.79
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:177028 original size:84 final size:84
Alignment explanation
Indices: 176887--177061 Score: 316
Period size: 84 Copynumber: 2.1 Consensus size: 84
176877 CCTGACTCGC
*
176887 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
*
176952 CCCACCGTTCAAGAGGCCA
66 CCCACAGTTCAAGAGGCCA
*
176971 CTGTCATCCCTCAAGAGTCCACTCTTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
1 CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
177036 CCCACAGTTCAAGAGGCCA
66 CCCACAGTTCAAGAGGCCA
177055 CT-TCATC
1 CTGTCATC
177062 GTTGAAGAGG
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
83 5 0.06
84 83 0.94
ACGTcount: A:0.22, C:0.37, G:0.17, T:0.24
Consensus pattern (84 bp):
CTGTCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTATCATTCCTCGAGAGTCCCCT
CCCACAGTTCAAGAGGCCA
Found at i:178468 original size:14 final size:14
Alignment explanation
Indices: 178449--178484 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
178439 ATTGTTTAAT
178449 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
178463 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
178477 TGATTTGT
1 TGATTTGT
178485 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:178689 original size:33 final size:32
Alignment explanation
Indices: 178647--178773 Score: 139
Period size: 33 Copynumber: 3.9 Consensus size: 32
178637 ATTAAATTCG
*
178647 CGTTGCGATTTTCATTTCACATTGTGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGTGATT-CCT
* ** **
178680 CGTTGCGATTTTCATTTCGTATTGCAAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTG--TGATTCCT
*
178713 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGTGATTC-CT
*
178746 CGTTGAGATTTTCATTTCGCATTGTGAT
1 CGTTGCGATTTTCATTTCGCATTGTGAT
178774 AGTAATTTTC
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
31 3 0.04
33 71 0.92
35 3 0.04
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGTGATTCCT
Found at i:178739 original size:19 final size:19
Alignment explanation
Indices: 178715--178769 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
178705 AAAATTAGCG
178715 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
178734 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
178748 TTGAGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
178767 TTG
1 TTG
178770 TGATAGTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 10
0.68 0.07 0.24
Matches are distributed among these distances:
14 5 0.18
16 7 0.25
17 7 0.25
19 9 0.32
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:178748 original size:66 final size:66
Alignment explanation
Indices: 178640--178769 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
178630 ACGCGAAATT
* * * *
178640 AAATTCGCGTTGCGATTTTCATTTCACATTGTGATTCCCTCGTTGCGATTTTCATTTCGTATTGC
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGC
178705 A
66 A
* *
178706 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTG
178770 TGATAGTAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCACATTGCGATTCCCTCGTTGAGATTTTCATTTCGCATTGC
A
Found at i:181082 original size:12 final size:12
Alignment explanation
Indices: 181065--181089 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
181055 TCTTCGGGGA
181065 CTTTTTCTTCTT
1 CTTTTTCTTCTT
181077 CTTTTTCTTCTT
1 CTTTTTCTTCTT
181089 C
1 C
181090 AGGATAATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:182122 original size:21 final size:21
Alignment explanation
Indices: 182098--182171 Score: 148
Period size: 21 Copynumber: 3.5 Consensus size: 21
182088 TTTTCCTAAT
182098 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
182119 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
182140 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
182161 TCGCAATGCGA
1 TCGCAATGCGA
182172 TACTGACTAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:182193 original size:20 final size:20
Alignment explanation
Indices: 182160--182238 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
182150 AATTTGGAAA
* *
182160 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
182180 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
182201 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
182221 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
182239 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:182245 original size:20 final size:21
Alignment explanation
Indices: 182112--182247 Score: 79
Period size: 21 Copynumber: 6.6 Consensus size: 21
182102 AATGCGAATT
182112 TGGAAAATCGCAATGCGA-ATT-
1 TGGAAAATCGCAA--CGAGATTC
182133 TGGAAAATCGCAATGCGA-ATT-
1 TGGAAAATCGCAA--CGAGATTC
* * *
182154 TGGAAAATCGCAATGCGATAC
1 TGGAAAATCGCAACGAGATTC
** **
182175 T-GACTATCGCAACGAGATAA
1 TGGAAAATCGCAACGAGATTC
**
182195 TACAAAATCGCAACGAGATTC
1 TGGAAAATCGCAACGAGATTC
***
182216 T-GACTTTCGCAACGAGATTC
1 TGGAAAATCGCAACGAGATTC
182236 T-GAAAATCGCAA
1 TGGAAAATCGCAA
182248 TCATCTTCAA
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.01
20 41 0.45
21 50 0.54
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (21 bp):
TGGAAAATCGCAACGAGATTC
Found at i:182488 original size:34 final size:34
Alignment explanation
Indices: 182445--182523 Score: 158
Period size: 34 Copynumber: 2.3 Consensus size: 34
182435 ATTCATTTGA
182445 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
182479 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
182513 CTATCGCAACG
1 CTATCGCAACG
182524 CGAAAATGGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.34, C:0.25, G:0.28, T:0.13
Consensus pattern (34 bp):
CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
Found at i:182590 original size:20 final size:20
Alignment explanation
Indices: 182461--182582 Score: 123
Period size: 20 Copynumber: 6.4 Consensus size: 20
182451 CAACGGGGAA
*
182461 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGAT
*
182481 ATCGCAACG-G-----GGAA
1 ATCGCAACGCGAAAATGGAT
*
182495 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGAT
182515 ATCGCAACGCGAAAATGGAT
1 ATCGCAACGCGAAAATGGAT
** *
182535 ATCGCAATTCG-AAATGGAAA
1 ATCGCAACGCGAAAATGG-AT
*
182555 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGAT
182575 ATCGCAAC
1 ATCGCAAC
182583 TAGAAAATCG
Statistics
Matches: 82, Mismatches: 12, Indels: 16
0.75 0.11 0.15
Matches are distributed among these distances:
14 11 0.13
15 1 0.01
19 7 0.09
20 57 0.70
21 6 0.07
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGAT
Found at i:182594 original size:34 final size:36
Alignment explanation
Indices: 182515--182602 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 36
182505 GAAAATGGCT
*
182515 ATCGCAACGCGAAAATGGATATCGCAATTCGAAATGGAAA
1 ATCGCAACGCGAAAATGGATATCGCAA-TC---ATAGAAA
*
182555 ATCGCAACGCGAAAATGGCTATCGCAA-C-TAGAAA
1 ATCGCAACGCGAAAATGGATATCGCAATCATAGAAA
*
182589 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
182603 TTAAAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
34 18 0.40
38 1 0.02
40 26 0.58
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.16
Consensus pattern (36 bp):
ATCGCAACGCGAAAATGGATATCGCAATCATAGAAA
Found at i:182633 original size:14 final size:14
Alignment explanation
Indices: 182614--182667 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
182604 TAAAATCGCA
182614 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
182628 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
182645 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
182661 TTGCGAT
1 TTGCGAT
182668 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:182633 original size:33 final size:33
Alignment explanation
Indices: 182596--182666 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
182586 AAAATCGCAA
182596 TGCGAAATTAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATTAAAATCGCATTGCGATTTTCTCGT
** * **
182629 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATTAAAATCGCATTGCGATTTTCTCGT
182662 TGCGA
1 TGCGA
182667 TAGTCAGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (33 bp):
TGCGAAATTAAAATCGCATTGCGATTTTCTCGT
Found at i:182813 original size:14 final size:14
Alignment explanation
Indices: 182794--182830 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
182784 CATCAATTAA
182794 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
182808 ACAAATCATCTTTT
1 ACAAATCAACATTT
182822 ACAAATCAA
1 ACAAATCAA
182831 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:184752 original size:19 final size:20
Alignment explanation
Indices: 184697--184764 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
184687 GAAACTTAAA
* *
184697 ATCGTAACGCGAAAATGACT
1 ATCGCAACGCGGAAATGACT
*
184717 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGGAAATGACT
* **
184737 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCGGAAATGACT
184756 ATCGCAACG
1 ATCGCAACG
184765 ACAAAATCGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:184772 original size:14 final size:14
Alignment explanation
Indices: 184753--184843 Score: 83
Period size: 14 Copynumber: 5.9 Consensus size: 14
184743 ATGCGAAATG
184753 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
184767 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
184786 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
184800 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
184816 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
184832 AAAATCGCAACG
1 AAAATCGCAACG
184844 CGAAACACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 31 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:184828 original size:32 final size:33
Alignment explanation
Indices: 184737--184848 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
184727 GGAAATGGCT
184737 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
184770 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
184803 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
184835 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
184849 CACAAATCGC
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 29 0.37
33 49 0.63
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:184856 original size:65 final size:66
Alignment explanation
Indices: 184737--184859 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
184727 GGAAATGGCT
* *
184737 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
184802 A
66 A
184803 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
184860 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.69
66 16 0.30
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:184877 original size:19 final size:19
Alignment explanation
Indices: 184855--184936 Score: 95
Period size: 18 Copynumber: 4.6 Consensus size: 19
184845 GAAACACAAA
184855 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
184874 TCGCGTTGTGA-TTTCATT
1 TCGCATTGCGATTTTCATT
*
184892 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
184908 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
184925 TCGCATTGCGAT
1 TCGCATTGCGAT
184937 AGCCATTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 4 0.08
17 4 0.08
18 19 0.37
19 16 0.31
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:185249 original size:21 final size:21
Alignment explanation
Indices: 185225--185271 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
185215 ATCGTCTTTG
* *
185225 CGTAAAGTATCGACCTCCTCA
1 CGTAAAGCATCGACCTCATCA
* *
185246 CGTAAGGCATTGACCTCATCA
1 CGTAAAGCATCGACCTCATCA
185267 CGTAA
1 CGTAA
185272 CTCCCCTAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (21 bp):
CGTAAAGCATCGACCTCATCA
Found at i:185457 original size:18 final size:18
Alignment explanation
Indices: 185431--185475 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
185421 GTCGATCAGA
*
185431 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
185449 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
185467 TGATGGCTC
1 TGATGGCTC
185476 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:186843 original size:20 final size:20
Alignment explanation
Indices: 186795--186853 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
186785 AATAGTTTCT
** *
186795 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
186815 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
186835 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
186854 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:187143 original size:22 final size:22
Alignment explanation
Indices: 187116--187159 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
187106 GATGGAGATA
187116 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
*
187138 GACGGATTTCATCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
187160 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:187433 original size:20 final size:20
Alignment explanation
Indices: 187327--187481 Score: 152
Period size: 20 Copynumber: 7.7 Consensus size: 20
187317 CGCTTTGAAA
*
187327 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
187348 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
187368 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * * *
187388 ATCTCGTTGCTATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
187409 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
187429 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
187449 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
187469 ATCGCATTGCGAT
1 ATCGCATTGCGAT
187482 TTTCCCAATT
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
19 5 0.04
20 85 0.75
21 22 0.19
22 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:187439 original size:61 final size:61
Alignment explanation
Indices: 187333--187480 Score: 174
Period size: 61 Copynumber: 2.4 Consensus size: 61
187323 GAAAATCGCA
* * *
187333 TTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCG
1 TTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCTCG
* * * * * * *
187394 TTGCTATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCA
1 TTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCTCG
*
187455 TTGCGA-TA-GTCAGTATCGCATTGCGA
1 TTGCGATTATGT-ATTATCGCATTGCGA
187481 TTTTCCCAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 2 0.03
60 15 0.21
61 56 0.77
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
TTGCGATTATGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCTCG
Found at i:187484 original size:81 final size:82
Alignment explanation
Indices: 187327--187484 Score: 212
Period size: 81 Copynumber: 1.9 Consensus size: 82
187317 CGCTTTGAAA
* * * *
187327 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
* *
187392 CGTTGCTATTTTGTATT
66 CATTGCGATTTTGTATT
* * *
187409 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATC
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATC
187472 GCATTGCGATTTT
65 GCATTGCGATTTT
187485 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
80 2 0.03
81 52 0.79
82 12 0.18
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (82 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCG
CATTGCGATTTTGTATT
Found at i:187500 original size:81 final size:81
Alignment explanation
Indices: 187327--187502 Score: 194
Period size: 81 Copynumber: 2.2 Consensus size: 81
187317 CGCTTTGAAA
* * *
187327 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATC
1 ATCGCATTGCGA-TA-GTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATC
* * * ** *
187391 TCGTTGCTATTTTGTATT
64 GCATTGCGATTTTCCAAT
* * *
187409 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGC
1 ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGC
187474 ATTGCGATTTTCCCAAT
66 ATTGCGATTTT-CCAAT
*
187491 -TCGCGTTGCGAT
1 ATCGCATTGCGAT
187503 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
80 2 0.03
81 63 0.80
82 14 0.18
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (81 bp):
ATCGCATTGCGATAGTAAGTATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGC
ATTGCGATTTTCCAAT
Found at i:189426 original size:22 final size:19
Alignment explanation
Indices: 189401--189446 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 19
189391 CCGTTTCTTT
189401 AATATTAATAAATAGATAAATA
1 AATATTAAT-AATA-ATAAA-A
*
189423 AATATTAATGATAATAAAA
1 AATATTAATAATAATAAAA
189442 AATAT
1 AATAT
189447 AATTTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 3 0.13
22 9 0.39
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AATATTAATAATAATAAAA
Found at i:190355 original size:2 final size:2
Alignment explanation
Indices: 190342--190430 Score: 91
Period size: 2 Copynumber: 47.5 Consensus size: 2
190332 TTTAAATTAA
*
190342 AT AT AT AA AT 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 AT AT AT AT AT
* * * *
190384 AT AT -T A- AT TT AA AT -T AA AT TT AT -T A- AT AT -T 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
190420 AT AT AT AT AT A
1 AT AT AT AT AT A
190431 ATAATTATTT
Statistics
Matches: 71, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:191117 original size:26 final size:26
Alignment explanation
Indices: 191087--191148 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
191077 GCGTGGCAGC
*
191087 AGCAGCGTCGTTGTGGGGTTTCTAGA
1 AGCAGCGACGTTGTGGGGTTTCTAGA
191113 AGCAGCGACGTTGTGGGGTTTCTAGA
1 AGCAGCGACGTTGTGGGGTTTCTAGA
191139 AGCAGCGACG
1 AGCAGCGACG
191149 ATGAGATGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.18, G:0.39, T:0.24
Consensus pattern (26 bp):
AGCAGCGACGTTGTGGGGTTTCTAGA
Found at i:191396 original size:2 final size:2
Alignment explanation
Indices: 191379--191459 Score: 139
Period size: 2 Copynumber: 41.5 Consensus size: 2
191369 GCTTGTAATA
*
191379 AT AT AT TT A- AT A- 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 AT AT AT AT AT
191419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
191460 ATAATAATAA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
1 2 0.03
2 73 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:191482 original size:18 final size:19
Alignment explanation
Indices: 191459--191497 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
191449 ATATATATAT
191459 AATAATAATAA-TAAAA-GA
1 AATAATAA-AAGTAAAATGA
191477 AATAATAAAAGTAAAATGA
1 AATAATAAAAGTAAAATGA
191496 AA
1 AA
191498 AATTAGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 13 0.68
19 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AATAATAAAAGTAAAATGA
Found at i:197213 original size:13 final size:13
Alignment explanation
Indices: 197192--197246 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
197182 AAGTTCGATA
*
197192 AATTCAAATACTT
1 AATTGAAATACTT
197205 AATTGAAATACTT
1 AATTGAAATACTT
* *
197218 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
197232 AATTGAAATACTT
1 AATTGAAATACTT
197245 AA
1 AA
197247 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:197328 original size:32 final size:33
Alignment explanation
Indices: 197232--197330 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
197222 AACTCAACAT
* * *
197232 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
197265 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
197298 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
197330 A
1 A
197331 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:197349 original size:21 final size:21
Alignment explanation
Indices: 197325--197364 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
197315 ACTTCAAGTT
197325 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
197346 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
197365 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:209108 original size:29 final size:29
Alignment explanation
Indices: 209071--209175 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
209061 TTTTTTCATT
*
209071 TAAGCACCTAAAGTATTTTTTGGTCAAAA
1 TAAGTACCTAAAGTATTTTTTGGTCAAAA
* *
209100 TAAGTACCTAGAGTTATCTTTTTTGATCAAAA
1 TAAGTACCTAAAG-TA--TTTTTTGGTCAAAA
*
209132 TAGGTACCTTAAA-TATTTTTTGGTC-AAA
1 TAAGTACC-TAAAGTATTTTTTGGTCAAAA
*
209160 TAGGTACCT-AAGTATT
1 TAAGTACCTAAAGTATT
209176 CCGTTTTTTC
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
26 2 0.03
27 5 0.08
28 11 0.17
29 20 0.31
30 2 0.03
31 2 0.03
32 20 0.31
33 3 0.05
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.39
Consensus pattern (29 bp):
TAAGTACCTAAAGTATTTTTTGGTCAAAA
Found at i:209325 original size:31 final size:28
Alignment explanation
Indices: 209284--209353 Score: 70
Period size: 31 Copynumber: 2.4 Consensus size: 28
209274 ACTTTCACAT
*
209284 AAAATACTTTACGTAC-CTATTTTGACCAA
1 AAAAAACTTTACGTACTC-ATTTTGA-CAA
* *
209313 AAATATAACTTTAGGTATTCATTTTGACAA
1 AAA-A-AACTTTACGTACTCATTTTGACAA
209343 AAAAAACTTTA
1 AAAAAACTTTA
209354 GGCACTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
28 7 0.20
29 4 0.11
30 7 0.20
31 16 0.46
32 1 0.03
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (28 bp):
AAAAAACTTTACGTACTCATTTTGACAA
Found at i:211625 original size:32 final size:31
Alignment explanation
Indices: 211583--211656 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
211573 AACTTTTAAA
* *
211583 ATTTGTAATATAATCCCCCCAATATTTAGTCC
1 ATTTGCAATATAAT-CCCCCAACATTTAGTCC
** * *
211615 ATTTGCAATATGGTCCCTCAACATTTAGTCT
1 ATTTGCAATATAATCCCCCAACATTTAGTCC
*
211646 ATTTACAATAT
1 ATTTGCAATAT
211657 GGTCCCGACG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (31 bp):
ATTTGCAATATAATCCCCCAACATTTAGTCC
Found at i:212302 original size:2 final size:2
Alignment explanation
Indices: 212295--212353 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
212285 GCTGTAACTT
212295 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
212337 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
212354 TTTAATTTGA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:213428 original size:36 final size:36
Alignment explanation
Indices: 213378--213451 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
213368 TTGAGGTAAT
*
213378 ATGTTGAAGAGTAAGGCTTTATAATATTCATGCAAC
1 ATGTTGAAGAGTAAGACTTTATAATATTCATGCAAC
*
213414 ATGTTGAAGTGTAAGACTTTATAATATTCATGCAAC
1 ATGTTGAAGAGTAAGACTTTATAATATTCATGCAAC
213450 AT
1 AT
213452 TTATGAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (36 bp):
ATGTTGAAGAGTAAGACTTTATAATATTCATGCAAC
Found at i:214268 original size:31 final size:31
Alignment explanation
Indices: 214208--214275 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
214198 TTGCAATACA
*
214208 GTCCCCCAACATTTAGTCTATTTACAATATG
1 GTCCCCCAACATTTAGTCCATTTACAATATG
*
214239 GTCCCCCAACATTTAGTCCGTTTGA-AATATG
1 GTCCCCCAACATTTAGTCCATTT-ACAATATG
*
214270 ATCCCC
1 GTCCCC
214276 AATATAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCATTTACAATATG
Found at i:215379 original size:122 final size:123
Alignment explanation
Indices: 215242--215487 Score: 449
Period size: 123 Copynumber: 2.0 Consensus size: 123
215232 CATAGCCGAG
*
215242 TTTGTGCTG-TTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGTCACGCGAC
1 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
215306 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
66 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
*
215364 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGTGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
1 TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
* *
215429 TCAAGACTATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGTGGACCCCTTTGGC
66 TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
215487 T
1 T
215488 ACTTAAATTC
Statistics
Matches: 119, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
122 9 0.08
123 110 0.92
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (123 bp):
TTTGTGCTGTTTTTTTTCAGTGTTTTAGTGCGGTTATTGCTTGGCTGTAGTTTGAGCCACGCGAC
TCAAGACGATATCAATTGTTTGAAGAGCATCAAAGATTCACTTGAGGACCCCTTTGGC
Found at i:218835 original size:23 final size:23
Alignment explanation
Indices: 218805--218890 Score: 127
Period size: 23 Copynumber: 3.6 Consensus size: 23
218795 GACAATCGTC
218805 CTCCATTAAAAAATATTTAATGT
1 CTCCATTAAAAAATATTTAATGT
218828 CTCCATTAAAAAATATTTAATGT
1 CTCCATTAAAAAATATTTAATGT
*
218851 CTCCATTAAAAAAGGCATTGTTAATGT
1 CTCCATTAAAAAA--TA-T-TTAATGT
218878 CTCCATTAAAAAA
1 CTCCATTAAAAAA
218891 GGCATTGTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 36 0.62
25 1 0.02
26 1 0.02
27 20 0.34
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (23 bp):
CTCCATTAAAAAATATTTAATGT
Found at i:218875 original size:27 final size:27
Alignment explanation
Indices: 218821--218906 Score: 135
Period size: 27 Copynumber: 3.3 Consensus size: 27
218811 TAAAAAATAT
*
218821 TTAATGTCTCCATTAAAAAA--TA-T-
1 TTAATGTCTCCATTAAAAAAGGCATTG
218844 TTAATGTCTCCATTAAAAAAGGCATTG
1 TTAATGTCTCCATTAAAAAAGGCATTG
218871 TTAATGTCTCCATTAAAAAAGGCATTG
1 TTAATGTCTCCATTAAAAAAGGCATTG
218898 TTAATGTCT
1 TTAATGTCT
218907 ACCTGTCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 20 0.34
25 1 0.02
26 1 0.02
27 36 0.62
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (27 bp):
TTAATGTCTCCATTAAAAAAGGCATTG
Found at i:222123 original size:20 final size:20
Alignment explanation
Indices: 222100--222147 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
222090 AAAATTATAG
222100 AAAATATAAAAAGTATAAATA
1 AAAATATAAAAAGTA-AAATA
* *
222121 AAAA-ATAATAATTAAAATA
1 AAAATATAAAAAGTAAAATA
222140 AAAATATA
1 AAAATATA
222148 TTTTATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.38
20 11 0.46
21 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAATATAAAAAGTAAAATA
Found at i:227281 original size:28 final size:28
Alignment explanation
Indices: 227230--227297 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
227220 ATACATTCCC
227230 GAACCATACCCCGAGTTGTAGTTTAAGCCA
1 GAACCATA--CCGAGTTGTAGTTTAAGCCA
*
227260 GAACCATACCGAGTTGTGGTTTAAGCCA
1 GAACCATACCGAGTTGTAGTTTAAGCCA
227288 GAACCATACC
1 GAACCATACC
227298 CTGCATCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 29 0.78
30 8 0.22
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (28 bp):
GAACCATACCGAGTTGTAGTTTAAGCCA
Done.