Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007320.1 Hibiscus syriacus cultivar Beakdansim tig00019536_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: 245168
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:163115 original size:12 final size:12
Alignment explanation
Indices: 163094--163133 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
163084 GTTTGGATCA
*
163094 TCATCATCATCG
1 TCATCTTCATCG
163106 TCATCTTCATCG
1 TCATCTTCATCG
* *
163118 TCAGCTTCATCT
1 TCATCTTCATCG
163130 TCAT
1 TCAT
163134 TGATCGCTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:163951 original size:2 final size:2
Alignment explanation
Indices: 163944--163969 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
163934 TAGTTTCCAG
163944 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
163970 CCTTCCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:165135 original size:200 final size:200
Alignment explanation
Indices: 164594--166352 Score: 3153
Period size: 200 Copynumber: 8.8 Consensus size: 200
164584 AACATTAAGC
* * * * *
164594 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAATCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* * *
164658 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGATACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
164723 GGATCGACACTTTATGGTTGCATCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
164788 TACAAA
195 TACAAA
*
164794 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAA-CGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
164858 AAAATTACCTATTACATTATACTTATGGGTTTTGATATTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
164923 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTATGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
164988 ACAAA
196 ACAAA
*
164993 AGTGTCGATATATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
165058 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
165123 GATCAACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
165188 ACAAA
196 ACAAA
* *
165193 AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
165258 AAAATTACCTATTACATTATACTTATGGCTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
165323 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
165388 ACAAA
196 ACAAA
165393 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
165458 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
165523 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTAGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
165588 ACAAA
196 ACAAA
* *
165593 AGTGTCGATACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCTGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
165658 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGAGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
165723 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
165788 ACAAA
196 ACAAA
* *
165793 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAATCGGTATACTTGTACCGGTTAGATTAA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
165858 AAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
165923 GATCGACACTTTATTGTTGCACCCTATTTGCCATTCATTCTGGACCAAAAATATCGACACAGACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
165988 ACAAA
196 ACAAA
*
165993 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
166058 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
* *
166123 GATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
166188 ACAAA
196 ACAAA
*
166193 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
* *
166258 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGTGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
166323 GATCGACACTTTATGGTTGCACCCTGTTTG
131 GATCGACACTTTATTGTTGCACCCTGTTTG
166353 ACATATTGTA
Statistics
Matches: 1502, Mismatches: 55, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
199 188 0.13
200 1310 0.87
201 4 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:166599 original size:18 final size:18
Alignment explanation
Indices: 166576--166620 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
166566 TCTCATTCAT
*
166576 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
166594 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
166613 AATTATAA
1 AATTATAA
166621 ATCTTATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.33
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:166612 original size:19 final size:19
Alignment explanation
Indices: 166588--166636 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
166578 TTATATTCAC
166588 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
166607 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
*
166626 ATATAAAATTA
1 ATACAAAATTA
166637 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:168375 original size:33 final size:33
Alignment explanation
Indices: 168338--168403 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
168328 CATCTTAATA
*
168338 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
168371 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
168404 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:168462 original size:21 final size:21
Alignment explanation
Indices: 168437--168501 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
168427 CCCCTTATGC
* *
168437 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
168458 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
168479 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
168500 CT
1 CT
168502 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:170785 original size:20 final size:19
Alignment explanation
Indices: 170730--170776 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
170720 TCCGGTATCG
170730 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
170749 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
170770 TTTTACC
1 TTTTACC
170777 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:171010 original size:181 final size:182
Alignment explanation
Indices: 170697--171169 Score: 714
Period size: 181 Copynumber: 2.6 Consensus size: 182
170687 CGTACTTACG
* *
170697 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
* * *
170762 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAAAGTACCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTACCGACACATTAT
* *
170827 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAACCTTATATT
* *
170878 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTTATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
* * *
170943 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTACCGACACATTAT
** *
171008 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGAACCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAACCTTATATT
* * * * * * *
171060 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCAATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
* * *
171125 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
171170 AATTTGGATC
Statistics
Matches: 264, Mismatches: 27, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
181 166 0.63
182 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTAATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTACCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGAACCTTATATT
Found at i:172039 original size:8 final size:9
Alignment explanation
Indices: 172026--172063 Score: 55
Period size: 8 Copynumber: 4.6 Consensus size: 9
172016 TAAAAATAAT
172026 TATTAT-TA
1 TATTATATA
172034 TATTATATA
1 TATTATATA
172043 TA-TATATA
1 TATTATATA
172051 TA-TATATA
1 TATTATATA
172059 TATTA
1 TATTA
172064 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATTATATA
Found at i:172044 original size:2 final size:2
Alignment explanation
Indices: 172032--172130 Score: 59
Period size: 2 Copynumber: 53.0 Consensus size: 2
172022 TAATTATTAT
* *
172032 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA AA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
172071 TA -A TT TA AA TT TA AA TA -A TA TA TA TA TA -A TA TT 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
* * *
172110 TT TA -A TT TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
172131 CCCGGCCCGA
Statistics
Matches: 70, Mismatches: 20, Indels: 14
0.67 0.19 0.13
Matches are distributed among these distances:
1 7 0.10
2 63 0.90
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:172092 original size:32 final size:37
Alignment explanation
Indices: 172052--172129 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 37
172042 ATATATATAT
172052 ATATATATATTA-ATAA-ATTTA-AT-TTAAATTTAA
1 ATATATATATTATATAATATTTATATATTAAATTTAA
*
172085 ATA-ATATA-TATATAATATTTATATATTTAATTTAA
1 ATATATATATTATATAATATTTATATATTAAATTTAA
172120 ATATATATAT
1 ATATATATAT
172130 ACCCGGCCCG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
31 2 0.05
32 9 0.24
33 8 0.21
34 2 0.05
35 12 0.32
36 5 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (37 bp):
ATATATATATTATATAATATTTATATATTAAATTTAA
Found at i:172107 original size:15 final size:15
Alignment explanation
Indices: 172031--172128 Score: 57
Period size: 13 Copynumber: 6.9 Consensus size: 15
172021 ATAATTATTA
172031 TTATAT-TATAT-AT
1 TTATATATATATAAT
*
172044 ATATATATATATATAT
1 TTATATATATATA-AT
* *
172060 ATTA-ATAAATTTAAT
1 -TTATATATATATAAT
* * *
172075 TTAAATTTAAATAAT
1 TTATATATATATAAT
*
172090 ATATATATA-AT-AT
1 TTATATATATATAAT
172103 TTATATAT-T-TAAT
1 TTATATATATATAAT
*
172116 TTAAATATATATA
1 TTATATATATATA
172129 TACCCGGCCC
Statistics
Matches: 63, Mismatches: 13, Indels: 16
0.68 0.14 0.17
Matches are distributed among these distances:
12 1 0.02
13 23 0.37
14 11 0.17
15 17 0.27
16 9 0.14
17 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATATATATAAT
Found at i:178479 original size:21 final size:21
Alignment explanation
Indices: 178454--178498 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
178444 AGATTTGTTA
* *
178454 AAAAATATTAATGTTTTATAT
1 AAAAATAATAATATTTTATAT
*
178475 AAAAATAATATTATTTTATAT
1 AAAAATAATAATATTTTATAT
178496 AAA
1 AAA
178499 TTTTTTTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAATAATAATATTTTATAT
Found at i:186702 original size:22 final size:24
Alignment explanation
Indices: 186677--186725 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
186667 TTTTGTATGA
186677 TAAATAT-AGTACTTTT-TTAGTT
1 TAAATATCAGTACTTTTATTAGTT
*
186699 TAAATATCATTACTTTTATTAGTT
1 TAAATATCAGTACTTTTATTAGTT
186723 TAA
1 TAA
186726 TGTATTTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
23 8 0.33
24 9 0.38
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (24 bp):
TAAATATCAGTACTTTTATTAGTT
Found at i:196814 original size:113 final size:113
Alignment explanation
Indices: 196616--196846 Score: 462
Period size: 113 Copynumber: 2.0 Consensus size: 113
196606 TTCTGCGGTT
196616 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
1 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
196681 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
66 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
196729 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
1 TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
196794 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
66 AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
196842 TAGCC
1 TAGCC
196847 TCGATAAATA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 118 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (113 bp):
TAGCCCTTCGGTTGGCATTAATCGAGCCTTGTTTATCATAACTATCTGCAAGACATGTGGCATTT
AATTCACTTACTGTTGCAATGTGGACTCCTTTAACTTACCCATCTTAC
Found at i:201117 original size:22 final size:22
Alignment explanation
Indices: 201074--201119 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
201064 TTATTATGAC
*
201074 AATGTATATACATCTTGCAGAT
1 AATGTATATACATATTGCAGAT
*
201096 AATGTATATATC-TATTGTAGAT
1 AATGTATATA-CATATTGCAGAT
201118 AA
1 AA
201120 AATTACTCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (22 bp):
AATGTATATACATATTGCAGAT
Found at i:203657 original size:18 final size:18
Alignment explanation
Indices: 203628--203671 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
203618 AAGTAAAGTT
*
203628 GAAGACGAGGAAGAGGAA
1 GAAGAAGAGGAAGAGGAA
*
203646 GAGGAAGAGGAAGAGGAA
1 GAAGAAGAGGAAGAGGAA
203664 GAAGAAGA
1 GAAGAAGA
203672 AGATTGTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.52, C:0.02, G:0.45, T:0.00
Consensus pattern (18 bp):
GAAGAAGAGGAAGAGGAA
Found at i:203674 original size:6 final size:6
Alignment explanation
Indices: 203634--203671 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
203624 AGTTGAAGAC
*
203634 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAAGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA
203672 AGATTGTGAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:214552 original size:21 final size:20
Alignment explanation
Indices: 214523--214607 Score: 100
Period size: 21 Copynumber: 4.2 Consensus size: 20
214513 TATATATATC
*
214523 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
214543 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
* **
214564 TAATAAGTACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
214585 TAATAGCACTA-AGAATAAAA
1 TAATAGCACTATA-AATAAAA
214605 TAA
1 TAA
214608 AATGAAATGG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.02
20 18 0.32
21 37 0.66
ACGTcount: A:0.58, C:0.08, G:0.07, T:0.27
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:215195 original size:30 final size:30
Alignment explanation
Indices: 215131--215324 Score: 128
Period size: 29 Copynumber: 6.6 Consensus size: 30
215121 TTTTGGTTAT
*
215131 GGTGTTATTTTCGTAATAATTTTT-AAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* *
215160 TGTGTTATTTTCGTATTTATTTTTAAAAAG
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* * *
215190 GGTGTTATTTTTGTAATTAATTTT-AAAAC
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* *** *
215219 GGTGATATTTTAACAATTATTGTTAAAACA-
1 GGTGTTATTTTCGTAATTATTTTTAAAA-AG
* * * * *
215249 -ATGATATTTTGGTAATTATTATT-AAAAC
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* * * * *
215277 GATGATATTTTGGTAATTATTGTTAAAAAC
1 GGTGTTATTTTCGTAATTATTTTTAAAAAG
* * *
215307 AGTGATATTTTGGTAATT
1 GGTGTTATTTTCGTAATT
215325 GTTTAAAAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 83 0.61
30 49 0.36
31 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.48
Consensus pattern (30 bp):
GGTGTTATTTTCGTAATTATTTTTAAAAAG
Found at i:215228 original size:59 final size:58
Alignment explanation
Indices: 215131--215324 Score: 180
Period size: 59 Copynumber: 3.3 Consensus size: 58
215121 TTTTGGTTAT
* * * * * *
215131 GGTGTTATTTTCGTAA-TAATTTTTAAAA-GTGTGTTATTTTCGTATTTATTTTTAAAAA
1 GGTGATATTTTGGTAATTAA-TTTTAAAACG-GTGATATTTTAGTAATTATTGTTAAAAA
* * **
215189 GGGTGTTATTTTTGTAATTAATTTTAAAACGGTGATATTTTAACAATTATTGTTAAAACA
1 -GGTGATATTTTGGTAATTAATTTTAAAACGGTGATATTTTAGTAATTATTGTTAAAA-A
* * *
215249 -ATGATATTTTGGTAATT-ATTATTAAAACGATGATATTTTGGTAATTATTGTTAAAAA
1 GGTGATATTTTGGTAATTAATT-TTAAAACGGTGATATTTTAGTAATTATTGTTAAAAA
*
215306 CAGTGATATTTTGGTAATT
1 -GGTGATATTTTGGTAATT
215325 GTTTAAAAAA
Statistics
Matches: 114, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
57 4 0.04
58 45 0.39
59 60 0.53
60 5 0.04
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.48
Consensus pattern (58 bp):
GGTGATATTTTGGTAATTAATTTTAAAACGGTGATATTTTAGTAATTATTGTTAAAAA
Found at i:215276 original size:58 final size:59
Alignment explanation
Indices: 215195--215324 Score: 183
Period size: 58 Copynumber: 2.2 Consensus size: 59
215185 AAAAGGGTGT
* *
215195 TATTTTTGTAATTAATTTTAAAACGGTGATATTTTAACAATTATTGTT-AAAACAATGA
1 TATTTTGGTAATTAATTTTAAAACGATGATATTTTAACAATTATTGTTAAAAACAATGA
*** *
215253 TATTTTGGTAATT-ATTATTAAAACGATGATATTTTGGTAATTATTGTTAAAAACAGTGA
1 TATTTTGGTAATTAATT-TTAAAACGATGATATTTTAACAATTATTGTTAAAAACAATGA
215312 TATTTTGGTAATT
1 TATTTTGGTAATT
215325 GTTTAAAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 3 0.05
58 39 0.61
59 22 0.34
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (59 bp):
TATTTTGGTAATTAATTTTAAAACGATGATATTTTAACAATTATTGTTAAAAACAATGA
Found at i:215288 original size:29 final size:29
Alignment explanation
Indices: 215195--215324 Score: 156
Period size: 29 Copynumber: 4.4 Consensus size: 29
215185 AAAAGGGTGT
* *
215195 TATTTTTGTAATTAATT-TTAAAACGGTGA
1 TATTTTGGTAATT-ATTGTTAAAACGATGA
*** *
215224 TATTTTAACAATTATTGTTAAAACAATGA
1 TATTTTGGTAATTATTGTTAAAACGATGA
*
215253 TATTTTGGTAATTATTATTAAAACGATGA
1 TATTTTGGTAATTATTGTTAAAACGATGA
215282 TATTTTGGTAATTATTGTTAAAAAC-AGTGA
1 TATTTTGGTAATTATTGTT-AAAACGA-TGA
215312 TATTTTGGTAATT
1 TATTTTGGTAATT
215325 GTTTAAAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
28 3 0.03
29 63 0.72
30 21 0.24
ACGTcount: A:0.37, C:0.04, G:0.13, T:0.46
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAACGATGA
Found at i:215335 original size:30 final size:29
Alignment explanation
Indices: 215243--215354 Score: 110
Period size: 29 Copynumber: 3.9 Consensus size: 29
215233 AATTATTGTT
* * *
215243 AAAACAATGATATTTTGGTAATTATTATT
1 AAAACAGTGATATTTTGGTAATTTTTATA
215272 AAAAC-GATGATATTTTGGTAATTATTGT-TA
1 AAAACAG-TGATATTTTGGTAATT-TT-TATA
215302 AAAACAGTGATATTTTGGTAATTGTTTA-A
1 AAAACAGTGATATTTTGGTAATT-TTTATA
215331 AAAA-A-TGATATTTCT-GTAATTTTT
1 AAAACAGTGATATTT-TGGTAATTTTT
215355 TTACTGTGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 15
0.79 0.04 0.16
Matches are distributed among these distances:
26 3 0.04
27 14 0.19
28 2 0.03
29 27 0.37
30 25 0.34
31 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.13, T:0.45
Consensus pattern (29 bp):
AAAACAGTGATATTTTGGTAATTTTTATA
Found at i:221979 original size:21 final size:20
Alignment explanation
Indices: 221950--222034 Score: 109
Period size: 21 Copynumber: 4.2 Consensus size: 20
221940 TATATATATC
*
221950 TAATAGCACTATAGATAAAA
1 TAATAGCACTATAAATAAAA
221970 TAATAAGCACTATAAATAAAA
1 TAAT-AGCACTATAAATAAAA
**
221991 TAATAAGCACTATAAATATTA
1 TAAT-AGCACTATAAATAAAA
222012 TAATAGCACTA-AGAATAAAA
1 TAATAGCACTATA-AATAAAA
222032 TAA
1 TAA
222035 AATGAAATGG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 1 0.02
20 19 0.33
21 38 0.66
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (20 bp):
TAATAGCACTATAAATAAAA
Found at i:222020 original size:41 final size:41
Alignment explanation
Indices: 221950--222034 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
221940 TATATATATC
*
221950 TAATAGCACTATAGATAAAATAATAAGCACTATA-AATAAAA
1 TAATAGCACTATAAATAAAATAATAAGCACTA-AGAATAAAA
**
221991 TAATAAGCACTATAAATATTATAAT-AGCACTAAGAATAAAA
1 TAAT-AGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
222032 TAA
1 TAA
222035 AATGAAATGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 1 0.03
41 21 0.54
42 17 0.44
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.26
Consensus pattern (41 bp):
TAATAGCACTATAAATAAAATAATAAGCACTAAGAATAAAA
Found at i:222592 original size:29 final size:29
Alignment explanation
Indices: 222564--222809 Score: 248
Period size: 29 Copynumber: 8.4 Consensus size: 29
222554 GTTATGGTGT
* * * *
222564 TATTTTCGTAATTATTTTTAAAAGTGTGT
1 TATTTTGGTAATTATTGTTAAAAGAGTGA
* * * * *
222593 TATTTTCGTATTTATTTTTAAAAAGGGTGT
1 TATTTTGGTAATTATTGTT-AAAAGAGTGA
*
222623 TATTTTCGTAATTAATT-TTAAAACG-GTGA
1 TATTTTGGTAATT-ATTGTTAAAA-GAGTGA
* * *
222652 TATTTTGGCAATTATTGTTAAAACAATGA
1 TATTTTGGTAATTATTGTTAAAAGAGTGA
*
222681 TATTTTGGTAATTATTGTTAAATG-GT-A
1 TATTTTGGTAATTATTGTTAAAAGAGTGA
* *
222708 CTATTTTGGTAATTATTGTTAAAACAGTGC
1 -TATTTTGGTAATTATTGTTAAAAGAGTGA
*
222738 TATTTTGGTAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAAGAGTGA
* *
222767 TATTTTGGTAATTATTGTTAAAAATAGTAA
1 TATTTTGGTAATTATTGTT-AAAAGAGTGA
222797 TATTTTGGTAATT
1 TATTTTGGTAATT
222810 GTTAAAAAAA
Statistics
Matches: 190, Mismatches: 18, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.01
28 26 0.14
29 115 0.61
30 45 0.24
31 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.48
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAAGAGTGA
Found at i:222727 original size:57 final size:58
Alignment explanation
Indices: 222564--222809 Score: 241
Period size: 59 Copynumber: 4.2 Consensus size: 58
222554 GTTATGGTGT
* * ** * * * * * *
222564 TATTTTCGTAATTATTTTTAAAAGTGTGTTATTTTCGTATTTATTTTTAAAA-AGGGTGT
1 TATTTTGGTAATTATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAACA--ATGA
* * *
222623 TATTTTCGTAATTAATT-TTAAAACGGTGATATTTTGGCAATTATTGTTAAAACAATGA
1 TATTTTGGTAATT-ATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAACAATGA
** * *
222681 TATTTTGGTAATTATTGTT-AAATGGT-ACTATTTTGGTAATTATTGTTAAAACAGTGC
1 TATTTTGGTAATTATTGTTAAAACAGTGA-TATTTTGGTAATTATTGTTAAAACAATGA
*
222738 TATTTTGGTAATTATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAA-ATAGTAA
1 TATTTTGGTAATTATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAACA-A-TGA
222797 TATTTTGGTAATT
1 TATTTTGGTAATT
222810 GTTAAAAAAA
Statistics
Matches: 160, Mismatches: 19, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 55 0.34
58 44 0.28
59 56 0.35
60 4 0.03
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.48
Consensus pattern (58 bp):
TATTTTGGTAATTATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAACAATGA
Found at i:222751 original size:86 final size:87
Alignment explanation
Indices: 222623--222809 Score: 279
Period size: 86 Copynumber: 2.1 Consensus size: 87
222613 AAAAGGGTGT
* *
222623 TATTTTCGTAATTAATTTTAAAACGGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
1 TATTTTGGTAATTAATTTTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
* *
222688 GTAATTATTGTT-AAATGGTAC
66 GTAATTATTGTTAAAATAGTAA
* * *
222709 TATTTTGGTAATT-ATTGTTAAAACAGTGCTATTTTGGTAATTATTGTTAAAACAGTGATATTTT
1 TATTTTGGTAATTAATT-TTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTT
222773 GGTAATTATTGTTAAAAATAGTAA
65 GGTAATTATTGTT-AAAATAGTAA
222797 TATTTTGGTAATT
1 TATTTTGGTAATT
222810 GTTAAAAAAA
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
85 3 0.03
86 68 0.75
88 20 0.22
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.47
Consensus pattern (87 bp):
TATTTTGGTAATTAATTTTAAAACAGTGATATTTTGGCAATTATTGTTAAAACAATGATATTTTG
GTAATTATTGTTAAAATAGTAA
Found at i:222820 original size:30 final size:30
Alignment explanation
Indices: 222738--222821 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
222728 AAAACAGTGC
*** * *
222738 TATTTTGGTAATTATT-GTTAAAACAGTGA
1 TATTTTGGTAATTATTAAAAAAAATAGTAA
***
222767 TATTTTGGTAATTATTGTTAAAAATAGTAA
1 TATTTTGGTAATTATTAAAAAAAATAGTAA
*
222797 TATTTTGGTAATTGTTAAAAAAAAT
1 TATTTTGGTAATTATTAAAAAAAAT
222822 GATATTTCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
29 16 0.35
30 30 0.65
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.45
Consensus pattern (30 bp):
TATTTTGGTAATTATTAAAAAAAATAGTAA
Found at i:222826 original size:27 final size:29
Alignment explanation
Indices: 222648--222828 Score: 162
Period size: 29 Copynumber: 6.3 Consensus size: 29
222638 TTTTAAAACG
* *
222648 GTGATATTTTGGCAATTATTGTTAAAACAA
1 GTGATATTTTGGTAA-TATTGTTAAAAAAA
**
222678 -TGATATTTTGGTAATTATTGTT--AAATG
1 GTGATATTTTGGTAA-TATTGTTAAAAAAA
*
222705 GT-ACTATTTTGGTAATTATTGTT-AAAACA
1 GTGA-TATTTTGGTAA-TATTGTTAAAAAAA
* *
222734 GTGCTATTTTGGTAATTATTGTT-AAAACA
1 GTGATATTTTGGTAA-TATTGTTAAAAAAA
*
222763 GTGATATTTTGGTAATTATTGTTAAAAATA
1 GTGATATTTTGGTAA-TATTGTTAAAAAAA
*
222793 GTAATATTTTGGT-A-ATTGTTAAAAAAA
1 GTGATATTTTGGTAATATTGTTAAAAAAA
*
222820 ATGATATTT
1 GTGATATTT
222829 CTGTCTGTGG
Statistics
Matches: 133, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
27 22 0.17
28 20 0.15
29 74 0.56
30 17 0.13
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (29 bp):
GTGATATTTTGGTAATATTGTTAAAAAAA
Found at i:222828 original size:86 final size:85
Alignment explanation
Indices: 222649--222828 Score: 247
Period size: 86 Copynumber: 2.1 Consensus size: 85
222639 TTTAAAACGG
* *
222649 TGATATTTTGGCAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAATGGTACTATTT
1 TGATATTTTGGCAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAATAGTAATATTT
* *
222714 TGGTAATTATTGTTAAAACAG
66 TGGTAA-TATTGTTAAAAAAA
* * *
222735 TGCTATTTTGGTAATTATTGTTAAAACAGTGATATTTTGGTAATTATTGTTAAAAATAGTAATAT
1 TGATATTTTGGCAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTT--AAATAGTAATAT
222800 TTTGGT-A-ATTGTTAAAAAAAA
64 TTTGGTAATATTGTT-AAAAAAA
222821 TGATATTT
1 TGATATTT
222829 CTGTCTGTGG
Statistics
Matches: 83, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
85 6 0.07
86 60 0.72
87 1 0.01
88 16 0.19
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.46
Consensus pattern (85 bp):
TGATATTTTGGCAATTATTGTTAAAACAATGATATTTTGGTAATTATTGTTAAATAGTAATATTT
TGGTAATATTGTTAAAAAAA
Found at i:227479 original size:27 final size:28
Alignment explanation
Indices: 227448--227511 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 28
227438 GCTGGTAATT
*
227448 TTAAAAATTTTATTTA-AAATTAAAAAA
1 TTAAAAATTTTATATATAAATTAAAAAA
*
227475 TT-AAAATTTTATATATATATTAAAAAA
1 TTAAAAATTTTATATATAAATTAAAAAA
*
227502 -TAAACATTTT
1 TTAAAAATTTT
227512 GAAATAACCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 13 0.41
27 19 0.59
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAAAAATTTTATATATAAATTAAAAAA
Found at i:227483 original size:26 final size:26
Alignment explanation
Indices: 227451--227511 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
227441 GGTAATTTTA
*
227451 AAAATTTTATTTA-AAATTAAAAAATT
1 AAAATTTTATATATAAATTAAAAAA-T
*
227477 AAAATTTTATATATATATTAAAAAAT
1 AAAATTTTATATATAAATTAAAAAAT
227503 AAACATTTT
1 AAA-ATTTT
227512 GAAATAACCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 16 0.52
27 15 0.48
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATTTTATATATAAATTAAAAAAT
Found at i:231643 original size:181 final size:182
Alignment explanation
Indices: 231338--231724 Score: 616
Period size: 181 Copynumber: 2.1 Consensus size: 182
231328 AATTTTCTAA
* * * * * *
231338 TTTATATAAAAATTAAATGTTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TTTATATATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
231403 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
66 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
* *
231468 TGGATCTTAAATTATTAATTGAGTTTTAAATTGTTTGGGCTTAGCCCAAATG
131 TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATG
231520 -TTATATATATATTTAATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TTTATATATATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* * *
231584 ATTATAAAATAAAAATTT-ATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
* *
231648 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATG
130 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATG
231701 TTATATATAATATATTTAATATTT
1 TT-TATAT-ATATATTTAATATTT
231725 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
181 122 0.65
182 46 0.24
183 5 0.03
184 15 0.08
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.46
Consensus pattern (182 bp):
TTTATATATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTAT
TGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGCTGAGCCCAAATG
Found at i:231749 original size:9 final size:9
Alignment explanation
Indices: 231730--231763 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
231720 TATTTAAAAT
231730 TTAATTTCGG
1 TTAA-TTCGG
231740 TTAATTCGG
1 TTAATTCGG
231749 TTAATTCGG
1 TTAATTCGG
231758 TTAATT
1 TTAATT
231764 AACCGAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 20 0.83
10 4 0.17
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.50
Consensus pattern (9 bp):
TTAATTCGG
Found at i:235753 original size:217 final size:217
Alignment explanation
Indices: 235378--236046 Score: 1221
Period size: 217 Copynumber: 3.0 Consensus size: 217
235368 CCTTTTCATT
235378 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
235443 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
66 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
235508 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
131 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
235573 AGGGCAAGTTTCATCGCAGGCC
196 AGGGCAAGTTTCATCGCAGGCC
235595 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
235660 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
66 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
235725 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
131 CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
235790 AGGGCAAGTTTCATCGCAGGCC
196 AGGGCAAGTTTCATCGCAGGCC
235812 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
1 CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
235877 ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAA
66 ATTAGCAGATCCT-----------A-CAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAA
235942 CTACAGCAGCAGCAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACA
119 CTACAGCAGCAGCAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACA
236007 ATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCC
184 ATTAGTTTCTCAAGGGCAAGTTTCATCGCAGGCC
*
236041 TTATCT
1 CTATCT
236047 ATCATGCCTG
Statistics
Matches: 439, Mismatches: 1, Indels: 12
0.97 0.00 0.03
Matches are distributed among these distances:
217 295 0.67
228 1 0.00
229 143 0.33
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (217 bp):
CTATCTGAACTAAGATCTGTGTGGAATCCAGGATAATGTATTCCTTACATCAAACCAGCATCAGC
ATTAGCAGATCCTACAGCAGCAGCAGCAGCAGCAGCTCCCTCAGCTGCAACAACTACAGCAGCAG
CAAGCAACAATAATGTTTGGATCAGGTTATGTACAAGGTCCAGGCTGATCACAATTAGTTTCTCA
AGGGCAAGTTTCATCGCAGGCC
Found at i:235899 original size:3 final size:3
Alignment explanation
Indices: 235891--235924 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
235881 GCAGATCCTA
235891 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
235925 TCCCTCAGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.32, T:0.00
Consensus pattern (3 bp):
CAG
Done.