Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011291.1 Kokia drynarioides strain JFW-HI SEQ_126270, 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: 116653
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 11 characters in sequence are not A, C, G, or T
Found at i:264 original size:10 final size:11
Alignment explanation
Indices: 242--272 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
232 TTCTGACTTT
242 GAAAAATTATA
1 GAAAAATTATA
253 GAAAAATT-TA
1 GAAAAATTATA
263 GAAAAATTAT
1 GAAAAATTAT
273 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:906 original size:23 final size:23
Alignment explanation
Indices: 876--1024 Score: 141
Period size: 23 Copynumber: 6.5 Consensus size: 23
866 ACGCTAGCCC
876 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTTCGCACTGT-GTGT
*
899 GCTTACTGTTTCGTACT-TCGTGT
1 GCTTACTGTTTCGCACTGT-GTGT
922 GCTTACTGTTTCGCACT-TCGTGT
1 GCTTACTGTTTCGCACTGT-GTGT
* *
945 GCCTACTGATTTACG--CTATGTGT
1 GCTTACTG-TTT-CGCACTGTGTGT
*
968 GCTTACTGATT-GCACTGTGTGT
1 GCTTACTGTTTCGCACTGTGTGT
* *
990 GCTTACTGGATT-GCACTGTATGT
1 GCTTACT-GTTTCGCACTGTGTGT
1013 GCTTACTGTTTC
1 GCTTACTGTTTC
1025 CCTAGCACTT
Statistics
Matches: 111, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.01
22 19 0.17
23 85 0.77
24 4 0.04
25 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTGTGTGT
Found at i:943 original size:46 final size:46
Alignment explanation
Indices: 876--1024 Score: 157
Period size: 46 Copynumber: 3.3 Consensus size: 46
866 ACGCTAGCCC
876 GCTTACTGTTTCGCACTTCGTGTGCTTACTG-TTT-CG-TACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGTGCTTACTGATTTACGCTA--T-GTGT
*
922 GCTTACTGTTTCGCACTTCGTGTGCCTACTGATTTACGCTATGTGT
1 GCTTACTGTTTCGCACTTCGTGTGCTTACTGATTTACGCTATGTGT
* * * * *
968 GCTTACTGATT-GCACTGT-GTGTGCTTACTGGA-TTGCACTGTATGT
1 GCTTACTGTTTCGCACT-TCGTGTGCTTACT-GATTTACGCTATGTGT
1013 GCTTACTGTTTC
1 GCTTACTGTTTC
1025 CCTAGCACTT
Statistics
Matches: 89, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
45 34 0.38
46 47 0.53
47 4 0.04
48 2 0.02
49 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.43
Consensus pattern (46 bp):
GCTTACTGTTTCGCACTTCGTGTGCTTACTGATTTACGCTATGTGT
Found at i:8131 original size:33 final size:31
Alignment explanation
Indices: 8094--8174 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 31
8084 ATGATTATAT
8094 TTAAATATTTAAAATATAATTTATATATTCTAA
1 TTAAATATTTAAAATATAATTTAT-TATT-TAA
* *
8127 TTAAAT-TTTATAA-ATAA-TTATTATTTAC
1 TTAAATATTTAAAATATAATTTATTATTTAA
*
8155 TAGAAATATTTAAAAT-TAAT
1 T-TAAATATTTAAAATATAAT
8175 ATTTCATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
28 3 0.08
29 8 0.20
30 13 0.32
31 4 0.10
32 6 0.15
33 6 0.15
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (31 bp):
TTAAATATTTAAAATATAATTTATTATTTAA
Found at i:8279 original size:26 final size:25
Alignment explanation
Indices: 8250--8299 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
8240 TCATAATACT
8250 AATTAATTTAAACATTATTTCAAAAA
1 AATTAATTTAAACATT-TTTCAAAAA
* *
8276 AATTAATTTGAACATTTTTTAAAA
1 AATTAATTTAAACATTTTTCAAAA
8300 TACATATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTAATTTAAACATTTTTCAAAAA
Found at i:40202 original size:9 final size:9
Alignment explanation
Indices: 40188--40296 Score: 65
Period size: 10 Copynumber: 11.1 Consensus size: 9
40178 TTTTAGTAAG
40188 ATAATTTTT
1 ATAATTTTT
40197 ATAATTTTTT
1 ATAA-TTTTT
* *
40207 TTACGAATTTT
1 ATA--ATTTTT
40218 ATATATTTTT
1 ATA-ATTTTT
*
40228 ATATTTTTT
1 ATAATTTTT
40237 ATAATTTTT
1 ATAATTTTT
* *
40246 TTAAGATTTT
1 ATAA-TTTTT
*
40256 ATAGTTTTT
1 ATAATTTTT
* *
40265 ATTAAAATTTA
1 A-T-AATTTTT
40276 ATAATTTTTT
1 ATAA-TTTTT
40286 AATAATTTTT
1 -ATAATTTTT
40296 A
1 A
40297 GTGTTTTTTT
Statistics
Matches: 75, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
9 28 0.37
10 31 0.41
11 15 0.20
12 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:40227 original size:10 final size:10
Alignment explanation
Indices: 40214--40245 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
40204 TTTTTACGAA
40214 TTTTATATAT
1 TTTTATATAT
40224 TTTTATAT-T
1 TTTTATATAT
40233 TTTTATA-AT
1 TTTTATATAT
40242 TTTT
1 TTTT
40246 TTAAGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATATAT
Found at i:40246 original size:10 final size:10
Alignment explanation
Indices: 40188--40323 Score: 58
Period size: 10 Copynumber: 14.0 Consensus size: 10
40178 TTTTAGTAAG
40188 ATAA-TTTTT
1 ATAATTTTTT
40197 ATAATTTTTT
1 ATAATTTTTT
* *
40207 TTACGA-ATTTT
1 ATA--ATTTTTT
40218 AT-ATATTTTT
1 ATAAT-TTTTT
40228 AT-ATTTTTT
1 ATAATTTTTT
40237 ATAATTTTTT
1 ATAATTTTTT
**
40247 -TAAGATTTT
1 ATAATTTTTT
*
40256 AT-AGTTTTT
1 ATAATTTTTT
** *
40265 ATTAAAATTTA
1 A-TAATTTTTT
40276 ATAATTTTTT
1 ATAATTTTTT
40286 AATAA-TTTTT
1 -ATAATTTTTT
*
40296 AGT-GTTTTTT
1 A-TAATTTTTT
40306 -T-ATTTTTT
1 ATAATTTTTT
*
40314 ATCATTTTTT
1 ATAATTTTTT
40324 GCCACATGTC
Statistics
Matches: 98, Mismatches: 15, Indels: 27
0.70 0.11 0.19
Matches are distributed among these distances:
8 8 0.08
9 27 0.28
10 48 0.49
11 14 0.14
12 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (10 bp):
ATAATTTTTT
Found at i:40255 original size:38 final size:38
Alignment explanation
Indices: 40192--40323 Score: 117
Period size: 39 Copynumber: 3.4 Consensus size: 38
40182 AGTAAGATAA
* *
40192 TTTTTATAATTTTTTTTACGAATTTTATATATTTTTATAT
1 TTTTTATAA-TTTTTTTAAG-ATTTTATATGTTTTTATAT
*
40232 TTTTTATAATTTTTTTAAGATTTTATA-GTTTTTATTAAA
1 TTTTTATAATTTTTTTAAGATTTTATATGTTTTTA-T-AT
* * * *
40271 ATTTAATAA-TTTTTTAATAATTTT-TAGTGTTTTTTTAT
1 TTTTTATAATTTTTTTAA-GATTTTATA-TGTTTTTATAT
*
40309 TTTTTATCATTTTTT
1 TTTTTATAATTTTTT
40324 GCCACATGTC
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
37 6 0.08
38 26 0.35
39 28 0.37
40 15 0.20
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (38 bp):
TTTTTATAATTTTTTTAAGATTTTATATGTTTTTATAT
Found at i:40553 original size:90 final size:88
Alignment explanation
Indices: 40410--40626 Score: 256
Period size: 90 Copynumber: 2.4 Consensus size: 88
40400 GAGTGTAAAA
* * * *
40410 AAAAATAATTTTGGGGTTTAATTGC-TTTTTTTGAAAAATTTTGAGGGTTTTTTTGATGCATTTT
1 AAAAATAATGTAGGGGTTTAATTGCATTTTTTT--AAAATTTTGAGGATCTTTTTGATGCATTTT
** * * *
40474 AAAAGTTTTAGTATCTAATTGAGTG
64 AAAAGTTCAAATACCCAATTGAGTG
*
40499 CAAAAATAATGTAGGGGTTTAATTACATTTTATTTAAAATTTTGAGGATCTTTTTGATGCATTTT
1 -AAAAATAATGTAGGGGTTTAATTGCATTTT-TTTAAAATTTTGAGGATCTTTTTGATGCATTTT
* *
40564 GAAAGTTCAAATACCCAATTGGGTG
64 AAAAGTTCAAATACCCAATTGAGTG
* *
40589 AAAAAAAATGTAGAGGTTTAATTGCTATTTTTTTAAAA
1 AAAAATAATGTAGGGGTTTAATTGC-ATTTTTTTAAAA
40627 AAAATTTAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
89 29 0.27
90 73 0.67
91 4 0.04
92 3 0.03
ACGTcount: A:0.34, C:0.06, G:0.18, T:0.43
Consensus pattern (88 bp):
AAAAATAATGTAGGGGTTTAATTGCATTTTTTTAAAATTTTGAGGATCTTTTTGATGCATTTTAA
AAGTTCAAATACCCAATTGAGTG
Found at i:47542 original size:2 final size:2
Alignment explanation
Indices: 47526--47562 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
47516 ATGGAGGATT
* *
47526 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47563 TAAAAGATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:56668 original size:29 final size:29
Alignment explanation
Indices: 56634--56693 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
56624 AAACCCTAAA
* *
56634 TATTAACATTAATCCTAAATCCAAAACCT
1 TATTAACACTAATCATAAATCCAAAACCT
* *
56663 TATTAACACTACTCATAAATCCAAAATCT
1 TATTAACACTAATCATAAATCCAAAACCT
56692 TA
1 TA
56694 CTTCAGTACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (29 bp):
TATTAACACTAATCATAAATCCAAAACCT
Found at i:56843 original size:23 final size:23
Alignment explanation
Indices: 56812--56855 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
56802 ATTTTTTGAG
56812 ACGAAATT-AAATTGTATATTTTT
1 ACGAAATTAAAATTGTA-ATTTTT
*
56835 ACGATATTAAAATTGTAATTT
1 ACGAAATTAAAATTGTAATTT
56856 CATCATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (23 bp):
ACGAAATTAAAATTGTAATTTTT
Found at i:56958 original size:7 final size:7
Alignment explanation
Indices: 56948--56987 Score: 53
Period size: 7 Copynumber: 5.3 Consensus size: 7
56938 TACTATTTCT
56948 AATTTAA
1 AATTTAA
56955 AATTTAA
1 AATTTAA
56962 AATTTAA
1 AATTTAA
56969 AATTTTATA
1 AA-TTTA-A
56978 AATTATAA
1 AATT-TAA
56986 AA
1 AA
56988 AGCTTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 16 0.53
8 9 0.30
9 5 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:64880 original size:11 final size:11
Alignment explanation
Indices: 64864--64893 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
64854 TCCATTTACT
64864 CCATCCACCCG
1 CCATCCACCCG
64875 CCATCCACCCG
1 CCATCCACCCG
64886 CCATCCAC
1 CCATCCAC
64894 TTTCTATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.63, G:0.07, T:0.10
Consensus pattern (11 bp):
CCATCCACCCG
Found at i:66486 original size:3 final size:3
Alignment explanation
Indices: 66480--66507 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
66470 AGTACTACTC
66480 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
66508 ATAAAGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:67449 original size:27 final size:27
Alignment explanation
Indices: 67412--67465 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
67402 AAAATCGATT
*
67412 TTAAGTTGTTTAAAAGTTTAAAAAAAA
1 TTAAGTTGTTTAAAAGTTGAAAAAAAA
*
67439 TTAAGTTGTTTAAAAGTTGATAAAAAA
1 TTAAGTTGTTTAAAAGTTGAAAAAAAA
67466 GATTCGAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (27 bp):
TTAAGTTGTTTAAAAGTTGAAAAAAAA
Found at i:70449 original size:23 final size:23
Alignment explanation
Indices: 70423--70571 Score: 156
Period size: 23 Copynumber: 6.4 Consensus size: 23
70413 AGTGCTGAGC
70423 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
70446 AACAGAGAGTACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * **
70469 AACAGAGAGTACACAAAGTATTA
1 AACAGAGAGCACACACAGTGCTA
* * * *
70492 ATCAAAGAGCACATAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
70515 ATCAGAGAGCACACACAATGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
70539 TAACAGAGAGCAC-CAGACGTGCTA
1 -AACAGAGAGCACACACA-GTGCTA
70563 AACAGAGAG
1 AACAGAGAG
70572 TGCGCTAGTG
Statistics
Matches: 106, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
23 86 0.81
24 5 0.05
25 15 0.14
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:74120 original size:95 final size:95
Alignment explanation
Indices: 73939--74120 Score: 224
Period size: 95 Copynumber: 1.9 Consensus size: 95
73929 TTACTATAAT
* * ** *
73939 ATTTGGTACCTAAACTTGACACGTTTTTCTAATTTGGTACCTAAACTTTTTTTGGTTCAATTTGG
1 ATTTGATACCTAAACTTGACACGTTTTTCTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTGG
* *
74004 TACTCAAACTTGACATTTTTTTTTTCCCTA
66 TACCCAAACTTGACATCTTTTTTTTCCCTA
* * * *
74034 ATTTGATACCTAAATTTGACA-TTTTTTATTAAGTTGGTACTTAAACTTTTTGGGGTCCAATTTT
1 ATTTGATACCTAAACTTGACACGTTTTT-CTAAGTTGGTACCTAAACTTTTTGGGGTCCAA-TTT
*
74098 GGTACCCAAATTTGAC-TCTTTTT
64 GGTACCCAAACTTGACATCTTTTT
74121 CCTAATTTGG
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
94 5 0.07
95 51 0.70
96 17 0.23
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (95 bp):
ATTTGATACCTAAACTTGACACGTTTTTCTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTGG
TACCCAAACTTGACATCTTTTTTTTCCCTA
Found at i:74422 original size:42 final size:44
Alignment explanation
Indices: 74351--74450 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
74341 TGCCAAGTTT
* * * *
74351 AAGTGTCAAATTGGGTCCAAAAAAGTTTAGGTACCAAATTA-GAA
1 AAGTGTCAAATTAGAT-CAAAAAAGTTTAGATACAAAATTAGGAA
74395 AAGTGTCAAATTAGAT-AAAAAAGTTTAGATACAAAATTAGGAA
1 AAGTGTCAAATTAGATCAAAAAAGTTTAGATACAAAATTAGGAA
*
74438 AGAATGTCAAATT
1 A-AGTGTCAAATT
74451 CAAGTACAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 21 0.43
43 4 0.08
44 24 0.49
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.26
Consensus pattern (44 bp):
AAGTGTCAAATTAGATCAAAAAAGTTTAGATACAAAATTAGGAA
Found at i:77201 original size:2 final size:2
Alignment explanation
Indices: 77196--77236 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
77186 TTCTCTCTTT
77196 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77237 AAAGTAAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:88058 original size:57 final size:57
Alignment explanation
Indices: 87994--88115 Score: 244
Period size: 57 Copynumber: 2.1 Consensus size: 57
87984 AAGGAGAAGG
87994 AAGATGAAGAACGGAAGAAGACGAAGAAGGAAAGAATTTAGAGTAAAGTTTCTTGGA
1 AAGATGAAGAACGGAAGAAGACGAAGAAGGAAAGAATTTAGAGTAAAGTTTCTTGGA
88051 AAGATGAAGAACGGAAGAAGACGAAGAAGGAAAGAATTTAGAGTAAAGTTTCTTGGA
1 AAGATGAAGAACGGAAGAAGACGAAGAAGGAAAGAATTTAGAGTAAAGTTTCTTGGA
88108 AAGATGAA
1 AAGATGAA
88116 AAAAGAGAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.48, C:0.05, G:0.30, T:0.17
Consensus pattern (57 bp):
AAGATGAAGAACGGAAGAAGACGAAGAAGGAAAGAATTTAGAGTAAAGTTTCTTGGA
Found at i:88521 original size:18 final size:17
Alignment explanation
Indices: 88484--88518 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
88474 ATTTTTTAAG
88484 TGAAAAAAGTAAAATAT
1 TGAAAAAAGTAAAATAT
88501 TGAAGAAAAG-AAAATAT
1 TGAA-AAAAGTAAAATAT
88518 T
1 T
88519 TGATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.63, C:0.00, G:0.14, T:0.23
Consensus pattern (17 bp):
TGAAAAAAGTAAAATAT
Found at i:90509 original size:112 final size:112
Alignment explanation
Indices: 90312--90535 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
90302 TTACGTTTGT
90312 CTCAATTCAAGTTTAAATAGGTAGAGAAATCTACTACTATCATCATGTAATCAAATTCAAAGTGA
1 CTCAATTCAAGTTTAAATAGGTAGAGAAATCTACTACTATCATCATGTAATCAAATTCAAAGTGA
90377 TAACATATAGCCTATATATATATCAGTAACAACGTACACAATTCCTA
66 TAACATATAGCCTATATATATATCAGTAACAACGTACACAATTCCTA
90424 CTCAATTCAAGTTTAAATAGGTAGAGAAATCTACTACTATCATCATGTAATCAAATTCAAAGTGA
1 CTCAATTCAAGTTTAAATAGGTAGAGAAATCTACTACTATCATCATGTAATCAAATTCAAAGTGA
90489 TAACATATAGCCTATATATATATCAGTAACAACGTACACAATTCCTA
66 TAACATATAGCCTATATATATATCAGTAACAACGTACACAATTCCTA
90536 ATAATAATAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (112 bp):
CTCAATTCAAGTTTAAATAGGTAGAGAAATCTACTACTATCATCATGTAATCAAATTCAAAGTGA
TAACATATAGCCTATATATATATCAGTAACAACGTACACAATTCCTA
Found at i:96807 original size:6 final size:6
Alignment explanation
Indices: 96796--96826 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
96786 ATATATTTTG
*
96796 CAAAAC CAAAAC CAAAAC CAAAAC GAAAAC C
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC C
96827 GTCTTTGCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.32, G:0.03, T:0.00
Consensus pattern (6 bp):
CAAAAC
Found at i:100683 original size:3 final size:3
Alignment explanation
Indices: 100675--100711 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
100665 TTAGAGAAAT
100675 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G
100712 GAATAGTAGA
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:103731 original size:27 final size:26
Alignment explanation
Indices: 103687--103756 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
103677 TATTGTACTC
*
103687 CGAACTCGAAAC-CTGAATCACAAACTT
1 CGAACTCCAAACTC-GAATCACAAA-TT
* *
103714 TGAACTCCAAACTCGAATCTCAAATT
1 CGAACTCCAAACTCGAATCACAAATT
103740 CGAACT-CAAACCTCGAA
1 CGAACTCCAAA-CTCGAA
103757 CCTCGACCCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 13 0.35
27 19 0.51
28 1 0.03
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (26 bp):
CGAACTCCAAACTCGAATCACAAATT
Found at i:103742 original size:13 final size:12
Alignment explanation
Indices: 103715--103757 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
103705 CACAAACTTT
103715 GAACTCCAAACTC
1 GAACT-CAAACTC
*
103728 GAATCTCAAATTC
1 GAA-CTCAAACTC
103741 GAACTCAAACCTC
1 GAACTCAAA-CTC
103754 GAAC
1 GAAC
103758 CTCGACCCTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 6 0.23
13 18 0.69
14 2 0.08
ACGTcount: A:0.40, C:0.33, G:0.09, T:0.19
Consensus pattern (12 bp):
GAACTCAAACTC
Found at i:108368 original size:45 final size:45
Alignment explanation
Indices: 108304--108393 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
108294 CCCCACTCAA
* *
108304 CTAATTGTGTGGTTGTGGTTGAGACTTGAGATTATTAAATTAAAT
1 CTAATTATGTGATTGTGGTTGAGACTTGAGATTATTAAATTAAAT
* *
108349 CTAATTATGTGATTGTGGTTGAGACTTGAGGTTGTTAAATTAAAT
1 CTAATTATGTGATTGTGGTTGAGACTTGAGATTATTAAATTAAAT
108394 ATAGTCAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (45 bp):
CTAATTATGTGATTGTGGTTGAGACTTGAGATTATTAAATTAAAT
Found at i:108595 original size:25 final size:26
Alignment explanation
Indices: 108566--108630 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 26
108556 TGATATATAT
108566 AATAAATATTTTTATTAAAA-ATAAA
1 AATAAATATTTTTATTAAAAGATAAA
108591 AATAAATAAATTTTTATTAAAATGATAAA
1 AATAAAT--ATTTTTATTAAAA-GATAAA
*
108620 ATTAAATATTT
1 AATAAATATTT
108631 AAAATTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 7 0.20
27 17 0.49
29 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
AATAAATATTTTTATTAAAAGATAAA
Found at i:109826 original size:2 final size:2
Alignment explanation
Indices: 109819--109849 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
109809 AGATTCTTTG
109819 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
109850 TGACTAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:110298 original size:2 final size:2
Alignment explanation
Indices: 110291--110316 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
110281 AGTTATAGCA
110291 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
110317 TATTATAGCA
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
Done.