Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008902.1 Hibiscus syriacus cultivar Beakdansim tig00112180_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: 61541
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:11553 original size:25 final size:25
Alignment explanation
Indices: 11519--11569 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
11509 GATCGGAAAG
11519 AATGAGCTTTACATAGTCGTTGATC
1 AATGAGCTTTACATAGTCGTTGATC
11544 AATGAGCTTTACATAGTCGTTGATC
1 AATGAGCTTTACATAGTCGTTGATC
11569 A
1 A
11570 CTTTAGGCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (25 bp):
AATGAGCTTTACATAGTCGTTGATC
Found at i:19297 original size:2 final size:2
Alignment explanation
Indices: 19290--19325 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19280 AGATGCACAT
19290 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19326 GGGTATAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23657 original size:35 final size:36
Alignment explanation
Indices: 23618--23685 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
23608 TAATAACGTA
* * *
23618 TATGGTTTTTTAACGATATGCACCTATA-ATATGTG
1 TATGGTTTTTGAACAACATGCACCTATATATATGTG
*
23653 TATGGTTTTTGAACAACATGCAGCTATATATAT
1 TATGGTTTTTGAACAACATGCACCTATATATAT
23686 ATATATTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 24 0.86
36 4 0.14
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (36 bp):
TATGGTTTTTGAACAACATGCACCTATATATATGTG
Found at i:23791 original size:20 final size:20
Alignment explanation
Indices: 23766--23815 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
23756 TCAGATGCAG
23766 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
23786 ATGTCTGTATCCCCATAATC
1 ATGTCTGTATCCCCATAATC
*
23806 TTGTCTGTAT
1 ATGTCTGTAT
23816 ATGCTGCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.26, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTCTGTATCCCCATAATC
Found at i:25441 original size:23 final size:23
Alignment explanation
Indices: 25406--25464 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
25396 ATCAAGTACA
* *
25406 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
25429 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
25452 ATAATAAAATAGG
1 ATAATATAATAGG
25465 CATTTAACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:25540 original size:89 final size:87
Alignment explanation
Indices: 25378--25542 Score: 233
Period size: 89 Copynumber: 1.9 Consensus size: 87
25368 TATGTTATAT
* **
25378 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATATAATAGGT
1 CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATATAATACAT
*
25443 AGCGCTTATATAATAAAATAGG
66 AGCACTTATATAATAAAATAGG
* *
25465 CATTTAACC-GAAAATATTATCATATATATAATAACATATTAGGTAGCGCTTATATAATGTAATA
1 CATTTAACCAG-AAATATTATCA-A-ATACAATAACATATTAGGTAGCGCTTATATAATATAATA
*
25529 CATATCACTTATAT
63 CATAGCACTTATAT
25543 TTACCTATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 20 0.29
88 1 0.01
89 46 0.68
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATATAATACAT
AGCACTTATATAATAAAATAGG
Found at i:30746 original size:106 final size:106
Alignment explanation
Indices: 30561--31977 Score: 2431
Period size: 106 Copynumber: 13.4 Consensus size: 106
30551 TACAGCCTTT
*
30561 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
30626 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
30667 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
30732 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
30773 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
30838 CGAAGGGACCGTTGGTTGTCAATAAACAACTTCTCAGTTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
30879 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* * * *
30944 CAAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
30985 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
31050 CGAAGGAACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
31091 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* * *
31156 CGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCGATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
31197 AGAGCCAATTTCAACTTCTCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
31262 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
31303 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
31368 CGAAGGGACCGCTGGTTATCAATAACCAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
31409 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* * *
31474 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
31515 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAGCGTAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
*
31580 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
31621 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* *
31686 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* *
31727 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAAGTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG-TAAGTTCAACTTCACG
* *
31792 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
65 ACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
31834 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
* * * * *
31899 CGAAGGGA-CGACTGGTTGTCAACAAACAATTTCCCAGTTCC
66 CGAAGGGACCG-CTGGTTGTCAATAAACAACTTCTCAATTTC
* * *
31940 AAAGCCAATTTCAACTTCACGACGGAGGATATTGGACT
1 AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACT
31978 TGGAACAATA
Statistics
Matches: 1251, Mismatches: 58, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
105 2 0.00
106 1148 0.92
107 101 0.08
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
Found at i:36994 original size:19 final size:19
Alignment explanation
Indices: 36970--37017 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
36960 TTACATTCAC
36970 ATACAAAATTATAAACTAT
1 ATACAAAATTATAAACTAT
* * *
36989 ATACAAAATTATGAATTGT
1 ATACAAAATTATAAACTAT
37008 ATACAAAATT
1 ATACAAAATT
37018 TCCCCTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAACTAT
Found at i:39508 original size:20 final size:20
Alignment explanation
Indices: 39483--39523 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
39473 TTAAAATCAG
39483 TGTATATCTACCGATTACAT
1 TGTATATCTACCGATTACAT
* *
39503 TGTATATTTACCTATTACAT
1 TGTATATCTACCGATTACAT
39523 T
1 T
39524 ATAATTATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.46
Consensus pattern (20 bp):
TGTATATCTACCGATTACAT
Found at i:43861 original size:22 final size:22
Alignment explanation
Indices: 43833--43878 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
43823 GTTACATTAG
43833 AACACAAACACATTAAGGAAAA
1 AACACAAACACATTAAGGAAAA
43855 AACACAAACACATTAAGGAAAA
1 AACACAAACACATTAAGGAAAA
43877 AA
1 AA
43879 AAGAGTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.65, C:0.17, G:0.09, T:0.09
Consensus pattern (22 bp):
AACACAAACACATTAAGGAAAA
Found at i:44558 original size:201 final size:201
Alignment explanation
Indices: 44088--45246 Score: 1559
Period size: 200 Copynumber: 5.8 Consensus size: 201
44078 TGAAATTTAG
** * * * *
44088 AAAAA-TATCGACACAAATTTAAAAAGTTTTGATATATTATGTTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
*
44152 GGTATATTTATACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
44217 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTATGCGTACACCTCGTTTGGGCATTGATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCTTGCACCTCGTTTGGGCATTCATT
44281 CTGGAC
196 CTGGAC
* * ** * *
44287 AAAAATTATCGACGCAAATTTAAAAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAATC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
*
44352 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTTGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
*
44417 TTGGGATCGATACATTTTATAAATGTATCGAAACTTTATGCTTGCACCTCGTTTGGGCATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCTTGCACCTCGTTTGGGCATTCATT
44482 CTGGAC
196 CTGGAC
** * * ** * *
44488 AAAAAGTATCGACACAAATTCCACTTGTGTCGATATATTATGTAGACCTATTTTCTCATAAAACC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * * **
44553 GGTATATATCTACTGGTTACATTTTAAATTTACCTATTACATTATAATTATATGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * * *
44618 TTGGGATCGATATAATTT-TAAATGTATCGACAC-TTATTGCTTGCACCTCGTTTTGCCATTGAT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTA-TGCTTGCACCTCGTTTGGGCATTCAT
44681 TCTGGAC
195 TCTGGAC
** * * * * * *
44688 AAAAAGTATCGACACAAATTAAAAAAATGTCGATACATTATGTT-AACTCTTTTATAATTAAATC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* ** * *
44752 GATATATTTATACTTGTTATATTGTAGATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* *
44817 TTGGGA-CGATACTTTTTATAAATGTATCGACACTTTATGCTTGGACCTCGTTTGGGCATTCATT
131 TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCTTGCACCTCGTTTGGGCATTCATT
44881 CTGGAC
196 CTGGAC
* * *
44887 AAAAAGTATCGACATAAATTCCACATGTGTCGATACATTATATTGACCGCTTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
* * * *
44952 GGTATATTTATACAGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCAAAGTTT
66 GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
45017 TTTGGATCGATAC-TGTTTATAAATGTATCAACACTTTATGCGTGCACCTTGTTTGGGCATTCAT
131 TTGGGATCGATACAT-TTTATAAATGTATCGACACTTTATGCTTGCACCTCGTTTGGGCATTCAT
45081 TCTGGAC
195 TCTGGAC
45088 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCTG-TTTTCTAATT-AAC
1 AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACC-GCTTTTCTAATTAAAC
* * *
45151 CAGTATA--TATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGTT
65 CGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * *
45214 TTTGGGGTCTATAC-TTTTAGAAAATATATCGAC
130 TTTGGGATCGATACATTTTA-TAAATGTATCGAC
45247 GCATCTGTTT
Statistics
Matches: 843, Mismatches: 107, Indels: 21
0.87 0.11 0.02
Matches are distributed among these distances:
197 4 0.00
198 80 0.09
199 165 0.20
200 307 0.36
201 286 0.34
202 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (201 bp):
AAAAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACCGCTTTTCTAATTAAACC
GGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
TTGGGATCGATACATTTTATAAATGTATCGACACTTTATGCTTGCACCTCGTTTGGGCATTCATT
CTGGAC
Found at i:45704 original size:19 final size:19
Alignment explanation
Indices: 45680--45725 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
45670 TCATCACATG
45680 CAAAATTATAAATCGTATA
1 CAAAATTATAAATCGTATA
*
45699 CAAAATTATAAATCTTATA
1 CAAAATTATAAATCGTATA
45718 CAAAATTA
1 CAAAATTA
45726 ACCCTACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.54, C:0.11, G:0.02, T:0.33
Consensus pattern (19 bp):
CAAAATTATAAATCGTATA
Found at i:47298 original size:18 final size:18
Alignment explanation
Indices: 47275--47313 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
47265 TCCTCCTCAT
*
47275 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTATTC
47293 TTCCTCCATCTTTTATTC
1 TTCCTCCATCTTTTATTC
47311 TTC
1 TTC
47314 ATATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCCTCCATCTTTTATTC
Found at i:48042 original size:22 final size:23
Alignment explanation
Indices: 48014--48068 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
48004 AACCTGCATT
*
48014 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATATTATCAGTTTA
*
48036 TATAATAACTATATTATCAGTTTA
1 TATAATAA-AATATTATCAGTTTA
48060 TATAA-AAAA
1 TATAATAAAA
48069 CAAAAATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.32
23 4 0.14
24 15 0.54
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (23 bp):
TATAATAAAATATTATCAGTTTA
Found at i:50379 original size:181 final size:182
Alignment explanation
Indices: 49987--50824 Score: 1348
Period size: 181 Copynumber: 4.6 Consensus size: 182
49977 TACGCGTACT
*
49987 TATTAAAGTATCGACACTTTCAACATATCCAGTAGCGCTTTACC-GTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
*
50051 GTTTTGTCATATTTTTACCTG-T-TATTGTTATGGATCGATACATTTTTATAAAGTATCAACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
50114 TTACA-GCGCTATTACTGCTTCCCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
50165 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
*
50230 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGACACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
50295 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* *
50347 TATTAAAGTATCGACACTTTCAACA-ATCCGGTAGCGCTTTATCAGTTTTGTCATTTCGAAACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
* * * *
50411 ATTTTGTCTTATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
50476 TTATAGGCTCTA-TACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
* * *
50527 TATTAAAGTATCGACACTTTAAACATATCCGGTAGTGTTTTACCAGTTTTGTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
**
50592 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATTAATACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
* *
50657 TTATAGGCGCTATTACTTCTTCTCTTTTAAATTCCAAAAGTATCGATACTTA
131 TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
** * * * *
50709 T-TTCAATCTAATTGATACTTTCAACATATCCGGTAGCGCTTTACCGGTTTTTTTCATTTCGAGA
1 TATT-AAAGT-ATCGACACTTTCAACATATCCGGTAGCGCTTTACCAG-TTTTGTCATTTCGAGA
* *
50773 CCGGTTTTGTCATATTTTTACATGTTATATTATTATGGATCGATACATTTTT
63 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
50825 TATTTGTATC
Statistics
Matches: 611, Mismatches: 40, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
178 43 0.07
179 41 0.07
180 63 0.10
181 258 0.42
182 112 0.18
183 31 0.05
184 63 0.10
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGCTTTACCAGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATTACTGCTTCTCTTTTAAATTCCAAAAGTGTCGATACTTA
Found at i:52779 original size:19 final size:18
Alignment explanation
Indices: 52743--52781 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
52733 GAAAAGGCTC
*
52743 GAACTCAAAAAAATTCAA
1 GAACTCAAAAAAACTCAA
*
52761 GAACTCAATTAAAACTCAA
1 GAACTCAA-AAAAACTCAA
52780 GA
1 GA
52782 CTCGAACTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.56, C:0.18, G:0.08, T:0.18
Consensus pattern (18 bp):
GAACTCAAAAAAACTCAA
Found at i:52822 original size:11 final size:11
Alignment explanation
Indices: 52808--52859 Score: 77
Period size: 11 Copynumber: 4.7 Consensus size: 11
52798 ACTCGATTTT
52808 AAGCTCGAATC
1 AAGCTCGAATC
*
52819 AAGCTCAAATC
1 AAGCTCGAATC
*
52830 AAGCTCAAATC
1 AAGCTCGAATC
*
52841 AAACTCGAATC
1 AAGCTCGAATC
52852 AAGCTCGA
1 AAGCTCGA
52860 CTCTTAGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 37 1.00
ACGTcount: A:0.42, C:0.27, G:0.13, T:0.17
Consensus pattern (11 bp):
AAGCTCGAATC
Found at i:55070 original size:11 final size:11
Alignment explanation
Indices: 55054--55116 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
55044 GTATTATAGA
55054 ATTTTTAATAT
1 ATTTTTAATAT
55065 ATTTTTAA-A-
1 ATTTTTAATAT
55074 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
55085 ATCAATAGTGT
1 ATTTTTAATAT
55096 ATTTTTAATAT
1 ATTTTTAATAT
55107 ATTTTTAATA
1 ATTTTTAATA
55117 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:57804 original size:2 final size:2
Alignment explanation
Indices: 57797--57834 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
57787 CATTCACAAC
57797 AT AT 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
57835 CTAGAATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.