Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014054.1 Kokia drynarioides strain JFW-HI SEQ_129085, 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: 125993
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:212 original size:27 final size:27
Alignment explanation
Indices: 181--237 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
171 ACACCCCTTA
181 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
208 GTGCCGCCACTTGATATTCCTCCATTG
1 GTGCCGCCACTTGATATTCCTCCATTG
235 GTG
1 GTG
238 TCAGGTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.32, G:0.21, T:0.33
Consensus pattern (27 bp):
GTGCCGCCACTTGATATTCCTCCATTG
Found at i:6621 original size:3 final size:3
Alignment explanation
Indices: 6613--6637 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6603 TATGCTTCAG
6613 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
6638 TGGTATACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:9796 original size:26 final size:26
Alignment explanation
Indices: 9759--9828 Score: 68
Period size: 29 Copynumber: 2.5 Consensus size: 26
9749 ATACATATTT
* * *
9759 AATTATTTATATTTAATCATATAATA
1 AATTATTAATATTTAATAAAATAATA
*
9785 AATTATTAATATAATTTATTAAAATAATA
1 AATTATT-A-AT-ATTTAATAAAATAATA
9814 AATTATTTAATATTT
1 AATTA-TTAATATTT
9829 CAATTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
26 7 0.19
27 4 0.11
28 4 0.11
29 19 0.53
30 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTATTAATATTTAATAAAATAATA
Found at i:9798 original size:16 final size:16
Alignment explanation
Indices: 9777--9826 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 16
9767 ATATTTAATC
9777 ATATAATAAATTATTA
1 ATATAATAAATTATTA
9793 ATATAAT---TTATTA
1 ATATAATAAATTATTA
*
9806 AAATAATAAATTATTTA
1 ATATAATAAATTA-TTA
9823 ATAT
1 ATAT
9827 TTCAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 12 0.43
16 10 0.36
17 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:9802 original size:29 final size:30
Alignment explanation
Indices: 9769--9826 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
9759 AATTATTTAT
* *
9769 ATTTAATCATATAATAAATTA-TTAATATA
1 ATTTAATAAAATAATAAATTATTTAATATA
*
9798 ATTTATTAAAATAATAAATTATTTAATAT
1 ATTTAATAAAATAATAAATTATTTAATAT
9827 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
ATTTAATAAAATAATAAATTATTTAATATA
Found at i:9899 original size:19 final size:19
Alignment explanation
Indices: 9872--9908 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9862 TCAATATTAA
*
9872 TATTCTAATAATAAATATT
1 TATTATAATAATAAATATT
*
9891 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
9909 ATTAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:11311 original size:18 final size:17
Alignment explanation
Indices: 11288--11339 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
11278 AAAAATAAAA
11288 TAAAAATCAACTTAAATT
1 TAAAAATCAA-TTAAATT
* *
11306 TAAAAAACAAATAATTATT
1 TAAAAATCAATTAA--ATT
11325 TAAAAATCAATTAAA
1 TAAAAATCAATTAAA
11340 ATATTATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 15 0.54
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAATCAATTAAATT
Found at i:18740 original size:5 final size:5
Alignment explanation
Indices: 18730--18758 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
18720 ATAGAGCTCT
18730 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
18759 TTTCCCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:24126 original size:20 final size:18
Alignment explanation
Indices: 24077--24111 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24067 AAATGTGTTC
24077 AAAATATTTTTTAAAAAT
1 AAAATATTTTTTAAAAAT
*
24095 AAAATATATTTTAAAAA
1 AAAATATTTTTTAAAAA
24112 ATTAAGCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATTTTTTAAAAAT
Found at i:33196 original size:14 final size:13
Alignment explanation
Indices: 33172--33203 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
33162 CTAACGAAAC
33172 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
33185 AGAAAGAAAAAAAA
1 AGAAA-AAAAAAAA
33199 AGAAA
1 AGAAA
33204 TATAACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:39413 original size:31 final size:31
Alignment explanation
Indices: 39378--39439 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
39368 CCCTAGCAAC
39378 AATAAAACATCACTCCAAAAATAAACTAATG
1 AATAAAACATCACTCCAAAAATAAACTAATG
39409 AATAAAACATCACTCCAAAAATAAACTAATG
1 AATAAAACATCACTCCAAAAATAAACTAATG
39440 CAAAAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.19, G:0.03, T:0.19
Consensus pattern (31 bp):
AATAAAACATCACTCCAAAAATAAACTAATG
Found at i:42436 original size:17 final size:18
Alignment explanation
Indices: 42398--42438 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42388 CTTTACTTTT
* *
42398 ATTTTATTTTACCATTGA
1 ATTTTATTTTAACATAGA
42416 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACATAGA
42433 ATTTTA
1 ATTTTA
42439 GTCATCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTTTATTTTAACATAGA
Found at i:48149 original size:574 final size:574
Alignment explanation
Indices: 47056--48203 Score: 2152
Period size: 574 Copynumber: 2.0 Consensus size: 574
47046 GACGAGTTGG
*
47056 TGGAGGAGATTAAAGATCTTCGAAGTGAGCTTTCCATTCACAAGAAAGTCGTAAAGAATGACATG
1 TGGAGGAGATCAAAGATCTTCGAAGTGAGCTTTCCATTCACAAGAAAGTCGTAAAGAATGACATG
* *
47121 ATGTCAGAAACAGTGGCACCCACACTTAGGATCGATGTCCCAAAGTCAAAGATGTATGCAGGGAC
66 ATGTCAGAAACAGTGGCACCCACACCTAGGATCGATGTCCCAAAGCCAAAGATGTATGCAGGGAC
47186 ACGATCAGCCCAAGATGTTGAGAATTTCATTTGGGCCATGGAGCAACACTTCCGAGCCATGGGGG
131 ACGATCAGCCCAAGATGTTGAGAATTTCATTTGGGCCATGGAGCAACACTTCCGAGCCATGGGGG
* *
47251 TCAAGGACGAAGCAATAAAGGTAAACACTGCTTCTGTCTATGTGACTGATATTGCTCTTTTATGG
196 TCAAGCACGAAGCAACAAAGGTAAACACTGCTTCTGTCTATGTGACTGATATTGCTCTTTTATGG
* * *
47316 TGGCGACATAGGTGTTCCGGGAAAGAGAATGGGGAAATTCTCATTATAACATGGAGTGAGTTCCA
261 TGGCGACATAGGTGTTCCGGGAAAGAGAATAGAGAAATTCCCATTATAACATGGAGTGAGTTCCA
47381 GTCCGAGCTCAAGGAACAGTTCTATCCCAAAAATACGCAACTAGAAGCCCGAGCAAAGTTGTGAC
326 GTCCGAGCTCAAGGAACAGTTCTATCCCAAAAATACGCAACTAGAAGCCCGAGCAAAGTTGTGAC
47446 AACTCAAGCATATTGACTCAATTCAAGACTATGTGAAGCAATTCACCGAGCTCAAGCTTCAAATC
391 AACTCAAGCATATTGACTCAATTCAAGACTATGTGAAGCAATTCACCGAGCTCAAGCTTCAAATC
47511 CCAAAGTTGGGTGAGGAAGAAGGATTCTTTGCCTTCATGGATGGACTCCAACGATGGAACAAAAT
456 CCAAAGTTGGGTGAGGAAGAAGGATTCTTTGCCTTCATGGATGGACTCCAACGATGGAACAAAAT
47576 GGAGTTGAAGTGTATGGGGGTCCAAGAGTTTTCCAAAGCTTTTTCCCCAGCTGA
521 GGAGTTGAAGTGTATGGGGGTCCAAGAGTTTTCCAAAGCTTTTTCCCCAGCTGA
*
47630 TGGAGGAGATCAAGGATCTTCGAAGTGAGCTTTCCATTCACAAGAAAGTCGTAAAGAATGACATG
1 TGGAGGAGATCAAAGATCTTCGAAGTGAGCTTTCCATTCACAAGAAAGTCGTAAAGAATGACATG
47695 ATGTCAGAAACAGTGGCACCCACACCTAGGATCGATGTCCCAAAGCCAAAGATGTATGCAGGGAC
66 ATGTCAGAAACAGTGGCACCCACACCTAGGATCGATGTCCCAAAGCCAAAGATGTATGCAGGGAC
*
47760 ACGATCAGCCCAAGATGTTGAGAATTTCATTTGGGCCATGGAGCAACACTTCCGAGCTATGGGGG
131 ACGATCAGCCCAAGATGTTGAGAATTTCATTTGGGCCATGGAGCAACACTTCCGAGCCATGGGGG
47825 TCAAGCACGAAGCAACAAAGGTAAACACTGCTTCTGTCTATGTGACTGATATTGCTCTTTTATGG
196 TCAAGCACGAAGCAACAAAGGTAAACACTGCTTCTGTCTATGTGACTGATATTGCTCTTTTATGG
* *
47890 TGGTGACATAGGTGTTTCGGGAAAGAGAATAGAGAAATTCCCATTATAACATGGAGTGAGTTCCA
261 TGGCGACATAGGTGTTCCGGGAAAGAGAATAGAGAAATTCCCATTATAACATGGAGTGAGTTCCA
47955 GTCCGAGCTCAAGGAACAGTTCTATCCCAAAAATACGCAACTAGAAGCCCGAGCAAAGTTGTGAC
326 GTCCGAGCTCAAGGAACAGTTCTATCCCAAAAATACGCAACTAGAAGCCCGAGCAAAGTTGTGAC
* * *
48020 AACTCAAGCATATTGGCTCAATTCAAGATTATGTGAAGCAATTCATCGAGCTCAAGCTTCAAATC
391 AACTCAAGCATATTGACTCAATTCAAGACTATGTGAAGCAATTCACCGAGCTCAAGCTTCAAATC
*
48085 CCAAAGTTGGGTGAGGAAGAAGGATTCTTTGCCTTCATGGATGGACTCCAACGATGGGACAAAAT
456 CCAAAGTTGGGTGAGGAAGAAGGATTCTTTGCCTTCATGGATGGACTCCAACGATGGAACAAAAT
48150 GGAGTTGAAGTGTATGGGGGTCCAAGAGTTTTCCAAAGCTTTTTCCCCAGCTGA
521 GGAGTTGAAGTGTATGGGGGTCCAAGAGTTTTCCAAAGCTTTTTCCCCAGCTGA
48204 GTCCATTACC
Statistics
Matches: 558, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
574 558 1.00
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (574 bp):
TGGAGGAGATCAAAGATCTTCGAAGTGAGCTTTCCATTCACAAGAAAGTCGTAAAGAATGACATG
ATGTCAGAAACAGTGGCACCCACACCTAGGATCGATGTCCCAAAGCCAAAGATGTATGCAGGGAC
ACGATCAGCCCAAGATGTTGAGAATTTCATTTGGGCCATGGAGCAACACTTCCGAGCCATGGGGG
TCAAGCACGAAGCAACAAAGGTAAACACTGCTTCTGTCTATGTGACTGATATTGCTCTTTTATGG
TGGCGACATAGGTGTTCCGGGAAAGAGAATAGAGAAATTCCCATTATAACATGGAGTGAGTTCCA
GTCCGAGCTCAAGGAACAGTTCTATCCCAAAAATACGCAACTAGAAGCCCGAGCAAAGTTGTGAC
AACTCAAGCATATTGACTCAATTCAAGACTATGTGAAGCAATTCACCGAGCTCAAGCTTCAAATC
CCAAAGTTGGGTGAGGAAGAAGGATTCTTTGCCTTCATGGATGGACTCCAACGATGGAACAAAAT
GGAGTTGAAGTGTATGGGGGTCCAAGAGTTTTCCAAAGCTTTTTCCCCAGCTGA
Found at i:65251 original size:10 final size:10
Alignment explanation
Indices: 65236--65265 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
65226 AAACCGATAG
65236 TTCACATTCA
1 TTCACATTCA
*
65246 TTCACATACA
1 TTCACATTCA
65256 TTCACATTCA
1 TTCACATTCA
65266 CATATAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (10 bp):
TTCACATTCA
Found at i:66283 original size:22 final size:22
Alignment explanation
Indices: 66250--66316 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
66240 AATTTAAAAC
*
66250 AAACATAATGAGGAGAGTTACA
1 AAACATTATGAGGAGAGTTACA
* * *
66272 AAATATTATGAGAAGGGTTAC-
1 AAACATTATGAGGAGAGTTACA
*
66293 AAACATTATGAGGACAGTTACA
1 AAACATTATGAGGAGAGTTACA
66315 AA
1 AA
66317 CATAATGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.48, C:0.09, G:0.21, T:0.22
Consensus pattern (22 bp):
AAACATTATGAGGAGAGTTACA
Found at i:66302 original size:21 final size:21
Alignment explanation
Indices: 66248--66319 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
66238 GAAATTTAAA
*
66248 ACAAACATAATGAGGAGAGTT
1 ACAAACATTATGAGGAGAGTT
* * *
66269 ACAAAATATTATGAGAAGGGTT
1 AC-AAACATTATGAGGAGAGTT
*
66291 ACAAACATTATGAGGACAGTT
1 ACAAACATTATGAGGAGAGTT
66312 ACAAACAT
1 ACAAACAT
66320 AATGTTTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 25 0.60
22 17 0.40
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.22
Consensus pattern (21 bp):
ACAAACATTATGAGGAGAGTT
Found at i:66990 original size:3 final size:3
Alignment explanation
Indices: 66982--67018 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
66972 CTGTCTTTCT
66982 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
67019 ACTTATCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:71641 original size:27 final size:27
Alignment explanation
Indices: 71603--71658 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
71593 TATTATTTCT
71603 CATTAAACAAATCTTCACAAGGAATTC
1 CATTAAACAAATCTTCACAAGGAATTC
71630 CATTAAACAAATCTTCACAAGGAATTC
1 CATTAAACAAATCTTCACAAGGAATTC
71657 CA
1 CA
71659 GAAATATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.45, C:0.23, G:0.07, T:0.25
Consensus pattern (27 bp):
CATTAAACAAATCTTCACAAGGAATTC
Found at i:72520 original size:5 final size:5
Alignment explanation
Indices: 72510--72535 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
72500 ATTTATACAA
72510 AATAT AATAT AATAT AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
72536 TCTATATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:76789 original size:20 final size:20
Alignment explanation
Indices: 76732--76790 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
76722 TTATAAAAAA
* *
76732 AAATATTTTAGTTTTTCATTT
1 AAAT-TTTTACTTTTTTATTT
*
76753 AAATATTTACTTTTTTTATTT
1 AAATTTTTAC-TTTTTTATTT
76774 AAATTTTTACTTTTTTA
1 AAATTTTTACTTTTTTA
76791 ATCTTTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (20 bp):
AAATTTTTACTTTTTTATTT
Found at i:76789 original size:21 final size:21
Alignment explanation
Indices: 76743--76789 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
76733 AATATTTTAG
76743 TTTTTCATTTAAATATTTACT
1 TTTTTCATTTAAATATTTACT
* *
76764 TTTTTTATTTAAATTTTTACT
1 TTTTTCATTTAAATATTTACT
76785 TTTTT
1 TTTTT
76790 AATCTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTCATTTAAATATTTACT
Found at i:82487 original size:22 final size:21
Alignment explanation
Indices: 82440--82488 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
82430 ATACAATTAT
* * * *
82440 ATTTAATTCTTTTAAAATTTA
1 ATTTTATTCTCTTAAAAATAA
82461 ATTTTATTCTCTTAAAAATAA
1 ATTTTATTCTCTTAAAAATAA
82482 ACTTTTA
1 A-TTTTA
82489 GCTTCATCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTTATTCTCTTAAAAATAA
Found at i:84756 original size:18 final size:18
Alignment explanation
Indices: 84733--84768 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
84723 GTATACCAAA
84733 CTTTATCTTGATCTTGAT
1 CTTTATCTTGATCTTGAT
*
84751 CTTTATCTTGATGTTGAT
1 CTTTATCTTGATCTTGAT
84769 GGACATTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (18 bp):
CTTTATCTTGATCTTGAT
Found at i:89019 original size:12 final size:12
Alignment explanation
Indices: 89002--89029 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
88992 TTACTAGTAG
89002 GTCCTCAACCAC
1 GTCCTCAACCAC
89014 GTCCTCAACCAC
1 GTCCTCAACCAC
89026 GTCC
1 GTCC
89030 ACGACCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.50, G:0.11, T:0.18
Consensus pattern (12 bp):
GTCCTCAACCAC
Found at i:103892 original size:14 final size:14
Alignment explanation
Indices: 103875--103914 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
103865 AAAAAAACAA
103875 AAAAGGAAAAAAAG
1 AAAAGGAAAAAAAG
103889 --AA--AAAAAAAG
1 AAAAGGAAAAAAAG
103899 AAAAGGAAAAAAAG
1 AAAAGGAAAAAAAG
103913 AA
1 AA
103915 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
10 8 0.36
12 4 0.18
14 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAAAAAG
Found at i:103892 original size:24 final size:23
Alignment explanation
Indices: 103865--103927 Score: 90
Period size: 24 Copynumber: 2.7 Consensus size: 23
103855 GAAATTTCAC
103865 AAAAAAACAAAAAAGGAAAAAAAG
1 AAAAAAA-AAAAAAGGAAAAAAAG
103889 AAAAAAAAAGAAAAGGAAAAAAAG
1 AAAAAAAAA-AAAAGGAAAAAAAG
* *
103913 AAGAAAAGAAAAAGG
1 AAAAAAAAAAAAAGG
103928 GGAGGTCGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 8 0.22
24 28 0.78
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAAAAAAAAAGGAAAAAAAG
Found at i:103902 original size:8 final size:8
Alignment explanation
Indices: 103865--103925 Score: 70
Period size: 8 Copynumber: 7.6 Consensus size: 8
103855 GAAATTTCAC
*
103865 AAAAAAAC
1 AAAAAAAG
*
103873 AAAAAAGG
1 AAAAAAAG
103881 AAAAAAAG
1 AAAAAAAG
103889 AAAAAAA-
1 AAAAAAAG
*
103896 AAGAAAAGG
1 AA-AAAAAG
103905 AAAAAAAG
1 AAAAAAAG
*
103913 AAGAAAAG
1 AAAAAAAG
103921 AAAAA
1 AAAAA
103926 GGGGAGGTCG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
7 2 0.05
8 40 0.91
9 2 0.05
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:103909 original size:17 final size:16
Alignment explanation
Indices: 103884--103925 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
103874 AAAAAGGAAA
103884 AAAAG-AAAAAAAAAG
1 AAAAGAAAAAAAAAAG
*
103899 AAAAGGAAAAAAAGAAG
1 AAAA-GAAAAAAAAAAG
103916 AAAAGAAAAA
1 AAAAGAAAAA
103926 GGGGAGGTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 7 0.29
17 13 0.54
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAG
Found at i:105279 original size:20 final size:20
Alignment explanation
Indices: 105254--105294 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
105244 AGAGGGTAAA
*
105254 TTGAAGATCA-CCAGATCTTT
1 TTGAAGACCATCCA-ATCTTT
105274 TTGAAGACCATCCAATCTTT
1 TTGAAGACCATCCAATCTTT
105294 T
1 T
105295 ACCCTAACCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (20 bp):
TTGAAGACCATCCAATCTTT
Found at i:106519 original size:14 final size:14
Alignment explanation
Indices: 106485--106512 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
106475 GATACGAATT
106485 AGCTTTACAATTTA
1 AGCTTTACAATTTA
106499 AGCTTTACAATTTA
1 AGCTTTACAATTTA
106513 GAGTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AGCTTTACAATTTA
Found at i:106525 original size:154 final size:154
Alignment explanation
Indices: 106341--106618 Score: 459
Period size: 154 Copynumber: 1.8 Consensus size: 154
106331 TAATTTATCT
* * *
106341 TTTAGGCTTTATAATTTAGAGTTTAATTTGGATCCAATTAGGGAATTATTGTTCAGATTTAATTC
1 TTTAAGCTTTACAATTTAGAGTTTAATTTGGATCCAATTAGAGAATTATTGTTCAGATTTAATTC
* *
106406 TAATTATCTTTTTAGAATTTAATTTAGATTCAACTAGAGATTTT-ATGTATTATAAATAGGGGAT
66 TAATTATC-TTTTAGAATTTAATTTAGATCCAACTAAAGATTTTCATGTATTATAAATAGGGGAT
106470 GGAGTGATACGAATTAGCTTTACAA
130 GGAGTGATACGAATTAGCTTTACAA
*
106495 TTTAAGCTTTACAATTTAGAGTTTAATTTGGATCCAATTAGAGAATTATTGTTTAGATTTAATTC
1 TTTAAGCTTTACAATTTAGAGTTTAATTTGGATCCAATTAGAGAATTATTGTTCAGATTTAATTC
* * *
106560 TAATTATCTTTTAGAATTTAATTTGGATCCAATTAAATATTTTCATGTATTATAAATAG
66 TAATTATCTTTTAGAATTTAATTTAGATCCAACTAAAGATTTTCATGTATTATAAATAG
106619 AGCATTTAAT
Statistics
Matches: 114, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
153 30 0.26
154 84 0.74
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (154 bp):
TTTAAGCTTTACAATTTAGAGTTTAATTTGGATCCAATTAGAGAATTATTGTTCAGATTTAATTC
TAATTATCTTTTAGAATTTAATTTAGATCCAACTAAAGATTTTCATGTATTATAAATAGGGGATG
GAGTGATACGAATTAGCTTTACAA
Found at i:106564 original size:23 final size:24
Alignment explanation
Indices: 106538--106582 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
106528 CCAATTAGAG
106538 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCT-TTTAGAATTTAATTCT
106561 AATTATCTTTTAGAATTTAATT
1 AATTATCTTTTAGAATTTAATT
106583 TGGATCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (24 bp):
AATTATCTTTTAGAATTTAATTCT
Found at i:122560 original size:29 final size:29
Alignment explanation
Indices: 122448--122563 Score: 79
Period size: 29 Copynumber: 4.2 Consensus size: 29
122438 GACATAATTT
122448 TTTTAATTCATAAATAAAAAAATAATATA
1 TTTTAATTCATAAATAAAAAAATAATATA
** *
122477 TTTTAA-T-AT--AT--TTAAAT-TTATA
1 TTTTAATTCATAAATAAAAAAATAATATA
* *** *
122499 TTTT-ATTCTATTAATATAATTCATAAT-TT
1 TTTTAATTC-ATAAATA-AAAAAATAATATA
122528 TTTTAATTCATAAATAAAAAAATAATATA
1 TTTTAATTCATAAATAAAAAAATAATATA
122557 TTTTAAT
1 TTTTAAT
122564 ATATTTAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 22
0.64 0.13 0.22
Matches are distributed among these distances:
21 1 0.02
22 9 0.14
23 4 0.06
24 2 0.03
25 2 0.03
26 2 0.03
27 2 0.03
28 8 0.13
29 28 0.44
30 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTAATTCATAAATAAAAAAATAATATA
Found at i:122573 original size:80 final size:81
Alignment explanation
Indices: 122440--122600 Score: 315
Period size: 80 Copynumber: 2.0 Consensus size: 81
122430 TAAAATTAGA
122440 CATAATTTTTTTAATTCATAAATAAAAAAATAATATATTTTAATATATTTAAATTTATATTTTAT
1 CATAATTTTTTTAATTCATAAATAAAAAAATAATATATTTTAATATATTTAAATTTATATTTTAT
122505 TCTATTAAT-ATAATT
66 TCTATTAATAATAATT
122520 CATAATTTTTTTAATTCATAAATAAAAAAATAATATATTTTAATATATTTAAATTTATATTTTAT
1 CATAATTTTTTTAATTCATAAATAAAAAAATAATATATTTTAATATATTTAAATTTATATTTTAT
122585 TCTATTAATAATAATT
66 TCTATTAATAATAATT
122601 TTATATCAAT
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 74 0.93
81 6 0.08
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (81 bp):
CATAATTTTTTTAATTCATAAATAAAAAAATAATATATTTTAATATATTTAAATTTATATTTTAT
TCTATTAATAATAATT
Done.