Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002507.1 Kokia drynarioides strain JFW-HI SEQ_114667, 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: 160088
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:14695 original size:16 final size:16
Alignment explanation
Indices: 14662--14708 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
14652 TCAGTCACTT
**
14662 GAAAAAGA-AAAATGA
1 GAAAAAGAGAAAAAAA
14677 GAAAAAG-GAAGAAAAA
1 GAAAAAGAGAA-AAAAA
14693 GAAAAAGAGAAAAAAA
1 GAAAAAGAGAAAAAAA
14709 TTTATGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 9 0.33
16 15 0.56
17 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (16 bp):
GAAAAAGAGAAAAAAA
Found at i:23063 original size:42 final size:42
Alignment explanation
Indices: 23017--23103 Score: 133
Period size: 42 Copynumber: 2.1 Consensus size: 42
23007 GTATTATTAT
23017 TTAAAAGAGTTTTAAATAAA-ATATAATT-AAATAGAATTTTAA
1 TTAAAAGAGTTTTAAATAAATA-ATAATTAAAATAGAA-TTTAA
*
23059 TTAAAAGAGTTTTAGATAAATAATAATTAAAATAGAATTTAA
1 TTAAAAGAGTTTTAAATAAATAATAATTAAAATAGAATTTAA
23101 TTA
1 TTA
23104 TTATTATTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
42 33 0.79
43 9 0.21
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (42 bp):
TTAAAAGAGTTTTAAATAAATAATAATTAAAATAGAATTTAA
Found at i:30263 original size:19 final size:20
Alignment explanation
Indices: 30218--30263 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
30208 AAAGCAAAAA
30218 AAGAAAGTTAAACAGATTAGT
1 AAGAAA-TTAAACAGATTAGT
30239 AA-AAATTAAA-AG-TTAAGT
1 AAGAAATTAAACAGATT-AGT
30257 AAGAAAT
1 AAGAAAT
30264 AATAATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 9 0.39
20 3 0.13
21 2 0.09
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (20 bp):
AAGAAATTAAACAGATTAGT
Found at i:35874 original size:15 final size:15
Alignment explanation
Indices: 35854--35890 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
35844 ATTGCAGCCA
*
35854 ATGAAGAAGTACGAG
1 ATGAAGAAGCACGAG
35869 ATGAAGAAGCACGAG
1 ATGAAGAAGCACGAG
*
35884 AAGAAGA
1 ATGAAGA
35891 GAAAGAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.51, C:0.08, G:0.32, T:0.08
Consensus pattern (15 bp):
ATGAAGAAGCACGAG
Found at i:35928 original size:21 final size:20
Alignment explanation
Indices: 35882--35928 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
35872 AAGAAGCACG
*
35882 AGAAGAAGAGAAAGAAGAAA
1 AGAAAAAGAGAAAGAAGAAA
*
35902 AGGAAAAAGAGAAGGAAGATAA
1 A-GAAAAAGAGAAAGAAGA-AA
35924 AGAAA
1 AGAAA
35929 GCATTGCCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (20 bp):
AGAAAAAGAGAAAGAAGAAA
Found at i:61435 original size:17 final size:17
Alignment explanation
Indices: 61411--61453 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
61401 TTTAGTTTTC
61411 GTTGCATTT-TACTTGTTA
1 GTTGCATTTGTA-TTG-TA
61429 GTT-CATTTGTATTGTA
1 GTTGCATTTGTATTGTA
61445 GTTGCATTT
1 GTTGCATTT
61454 CCATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.16, C:0.09, G:0.19, T:0.56
Consensus pattern (17 bp):
GTTGCATTTGTATTGTA
Found at i:62057 original size:23 final size:21
Alignment explanation
Indices: 62006--62058 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
61996 AGTCACGTAT
*
62006 AAAAAAAAT-AAGAAGAAAAG
1 AAAAAAAATAAAAAAGAAAAG
**
62026 AAAGCAAATAAAAAGAGAAAAG
1 AAAAAAAATAAAAA-AGAAAAG
62048 CAAAAAAAATA
1 -AAAAAAAATA
62059 TAAATATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.28
21 3 0.12
22 7 0.28
23 8 0.32
ACGTcount: A:0.77, C:0.04, G:0.13, T:0.06
Consensus pattern (21 bp):
AAAAAAAATAAAAAAGAAAAG
Found at i:71206 original size:17 final size:18
Alignment explanation
Indices: 71169--71208 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
71159 TAACAAAATG
71169 ATGCAGTGACAAAATAAA
1 ATGCAGTGACAAAATAAA
* *
71187 ATGCAGTGATAATA-AAA
1 ATGCAGTGACAAAATAAA
71204 ATGCA
1 ATGCA
71209 TTAAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
ATGCAGTGACAAAATAAA
Found at i:85907 original size:17 final size:16
Alignment explanation
Indices: 85885--85929 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
85875 GTAGTTATAA
85885 TTTAATTGTCATTACAT
1 TTTAATTGTCA-TACAT
*
85902 TTTAATTGTCCATGCAT
1 TTTAATTGT-CATACAT
*
85919 TTTATTTGTCA
1 TTTAATTGTCA
85930 ACGCATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.84
18 2 0.08
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.53
Consensus pattern (16 bp):
TTTAATTGTCATACAT
Found at i:85935 original size:17 final size:17
Alignment explanation
Indices: 85885--85937 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
85875 GTAGTTATAA
***
85885 TTTAATTGTCATTACAT
1 TTTAATTGTCAACGCAT
* *
85902 TTTAATTGTCCATGCAT
1 TTTAATTGTCAACGCAT
*
85919 TTTATTTGTCAACGCAT
1 TTTAATTGTCAACGCAT
85936 TT
1 TT
85938 GCATTGTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (17 bp):
TTTAATTGTCAACGCAT
Found at i:86553 original size:3 final size:3
Alignment explanation
Indices: 86545--86578 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
86535 TAAAAAGAAT
86545 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
86579 ATGTTGTATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:93768 original size:22 final size:20
Alignment explanation
Indices: 93740--93780 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
93730 CAAAAAATTT
93740 TAATTTTGAATTTATTATTATG
1 TAATTTT-AATTTATT-TTATG
*
93762 TAATTTTATTTTATTTTAT
1 TAATTTTAATTTATTTTAT
93781 TTTTGCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (20 bp):
TAATTTTAATTTATTTTATG
Found at i:103632 original size:15 final size:15
Alignment explanation
Indices: 103587--103633 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
103577 CCTGAAATAT
103587 ATTTATTTAAATAAAA
1 ATTT-TTTAAATAAAA
**
103603 ATTTTAAAAATAAAA
1 ATTTTTTAAATAAAA
103618 ATTTGTTTAAA-AAAA
1 ATTT-TTTAAATAAAA
103633 A
1 A
103634 CCCACAAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 18 0.69
16 8 0.31
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
ATTTTTTAAATAAAA
Found at i:106244 original size:23 final size:23
Alignment explanation
Indices: 106218--106261 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
106208 CTCATATTTC
*
106218 AGTCAAATAAGAGATTGCTTGCT
1 AGTCAAAGAAGAGATTGCTTGCT
106241 AGTCAAAGAAGAGATTGCTTG
1 AGTCAAAGAAGAGATTGCTTG
106262 TAAATCAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.27
Consensus pattern (23 bp):
AGTCAAAGAAGAGATTGCTTGCT
Found at i:106269 original size:23 final size:23
Alignment explanation
Indices: 106220--106269 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
106210 CATATTTCAG
* *
106220 TCAAATAAGAGATTGCTTGCTAG
1 TCAAAGAAGAGATTGCTTGCTAA
106243 TCAAAGAAGAGATTGCTTG-TAAA
1 TCAAAGAAGAGATTGCTTGCT-AA
106266 TCAA
1 TCAA
106270 GTTAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (23 bp):
TCAAAGAAGAGATTGCTTGCTAA
Found at i:107901 original size:20 final size:20
Alignment explanation
Indices: 107876--107917 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
107866 CTAGACGTCC
* *
107876 CTCGTTTGTTACGGAGTCAA
1 CTCGTTTGTAACGGAGACAA
107896 CTCGTTTGTAACGGAGACAA
1 CTCGTTTGTAACGGAGACAA
107916 CT
1 CT
107918 TTCATTGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (20 bp):
CTCGTTTGTAACGGAGACAA
Found at i:112096 original size:197 final size:197
Alignment explanation
Indices: 111752--112108 Score: 615
Period size: 197 Copynumber: 1.8 Consensus size: 197
111742 TGCAAGTATG
* **
111752 GAGCTTAATCTTCTATCCAAAGGGTAATTGAAGTAAATTTTTCCTTTTTGAAATGTGAATCTGTA
1 GAGCTTAATCTTCTATCCAAAGGGTAATTCAAGTAAATTGATCCTTTTTGAAATGTGAATCTGTA
* * *
111817 CGTACAATTTATTAGAAGTCCCCTTTTTCTTAAGTCATAAGATAATGAAGTACATTAAACTTCTG
66 CGTACAATTTATTAGAAGTCCCCCTTCTCTTAAGTCATAAAATAATGAAGTACATTAAACTTCTG
*
111882 AATATCAAGTTTTTGTCGTTTATTTGGTTTGCACTTTTGTTGTTCTACATTTTATTAATTCTCTC
131 AATATCAAGTGTTTGTCGTTTATTTGGTTTGCACTTTTGTTGTTCTACATTTTATTAATTCTCTC
111947 TA
196 TA
111949 GAGCTTAATCTTCTATCCAAAGGGTAATTCAAGTAAATTGATCCTTTTTGAAATGTGAATCTGTA
1 GAGCTTAATCTTCTATCCAAAGGGTAATTCAAGTAAATTGATCCTTTTTGAAATGTGAATCTGTA
* * *
112014 GGTACAATTTATTAGAAGTCCCCCTTCTCTTAAGTCGTAAAATAATGAAGTGCATTAAACTTCTG
66 CGTACAATTTATTAGAAGTCCCCCTTCTCTTAAGTCATAAAATAATGAAGTACATTAAACTTCTG
*
112079 AATATTAAGTGTTTGTCGTTTATTTGGTTT
131 AATATCAAGTGTTTGTCGTTTATTTGGTTT
112109 ATGCTTTTGT
Statistics
Matches: 149, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
197 149 1.00
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (197 bp):
GAGCTTAATCTTCTATCCAAAGGGTAATTCAAGTAAATTGATCCTTTTTGAAATGTGAATCTGTA
CGTACAATTTATTAGAAGTCCCCCTTCTCTTAAGTCATAAAATAATGAAGTACATTAAACTTCTG
AATATCAAGTGTTTGTCGTTTATTTGGTTTGCACTTTTGTTGTTCTACATTTTATTAATTCTCTC
TA
Found at i:121594 original size:17 final size:17
Alignment explanation
Indices: 121565--121626 Score: 65
Period size: 16 Copynumber: 3.7 Consensus size: 17
121555 AAAGATTCAG
*
121565 AAAAATTC-TAATTATA
1 AAAAATTCAAAATTATA
121581 AAAAATTCAAAATTACTA
1 AAAAATTCAAAATTA-TA
* * *
121599 AAACATTAAAAAATAT-
1 AAAAATTCAAAATTATA
121615 AAAAATTCAAAA
1 AAAAATTCAAAA
121627 AATTATAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
16 18 0.47
17 6 0.16
18 14 0.37
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAATTCAAAATTATA
Found at i:121610 original size:18 final size:16
Alignment explanation
Indices: 121574--121638 Score: 58
Period size: 18 Copynumber: 3.7 Consensus size: 16
121564 GAAAAATTCT
*
121574 AATTATAAAAAATTCAA
1 AATTAT-AAAAATTAAA
121591 AATTACTAAAACATTAAA
1 AATTA-TAAAA-ATTAAA
*
121609 AAATATAAAAATTCAAAA
1 AATTATAAAAATT--AAA
121627 AATTATAGAAAA
1 AATTATA-AAAA
121639 AGAAATTAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 3 0.08
17 14 0.35
18 19 0.47
19 4 0.10
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (16 bp):
AATTATAAAAATTAAA
Found at i:121627 original size:17 final size:18
Alignment explanation
Indices: 121581--121629 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
121571 TCTAATTATA
*
121581 AAAAATTC-AAAATTACT
1 AAAAATTCAAAAAATACT
121598 AAAACATT-AAAAAATA-T
1 AAAA-ATTCAAAAAATACT
121615 AAAAATTCAAAAAAT
1 AAAAATTCAAAAAAT
121630 TATAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.11
17 16 0.57
18 9 0.32
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAATTCAAAAAATACT
Found at i:122549 original size:24 final size:24
Alignment explanation
Indices: 122521--122580 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
122511 AAAAATAATC
122521 TTTCAGTTAAACCCTGTTTATTTG
1 TTTCAGTTAAACCCTGTTTATTTG
* **
122545 TTTCAATTAAACTTTGTTTATTTG
1 TTTCAGTTAAACCCTGTTTATTTG
* *
122569 TTTGAGTCAAAC
1 TTTCAGTTAAAC
122581 TCTTATTAGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.12, T:0.50
Consensus pattern (24 bp):
TTTCAGTTAAACCCTGTTTATTTG
Found at i:124488 original size:24 final size:24
Alignment explanation
Indices: 124456--124501 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
124446 TAATCTTTCA
124456 ATTAAACTCTGTTTATTTGTTTTG
1 ATTAAACTCTGTTTATTTGTTTTG
124480 ATTAAACTCTGTTTATTTGTTT
1 ATTAAACTCTGTTTATTTGTTT
124502 GAGTCAAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.11, T:0.59
Consensus pattern (24 bp):
ATTAAACTCTGTTTATTTGTTTTG
Found at i:124510 original size:24 final size:24
Alignment explanation
Indices: 124459--124513 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
124449 TCTTTCAATT
*
124459 AAACTCTGTTTATTTGTTTTGATT
1 AAACTCTGTTTATTTGTTTTGATC
124483 AAACTCTGTTTATTTG-TTTGAGTC
1 AAACTCTGTTTATTTGTTTTGA-TC
124507 AAACTCT
1 AAACTCT
124514 TATTAGTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.51
Consensus pattern (24 bp):
AAACTCTGTTTATTTGTTTTGATC
Found at i:126302 original size:80 final size:80
Alignment explanation
Indices: 126174--126491 Score: 354
Period size: 80 Copynumber: 4.0 Consensus size: 80
126164 AACCAAATCC
* * *
126174 GTCAATTCATGGCACCCGA-TGCCTAGTGGATAAACCGCGACAAGTGAGCCCAGTTCTAGTTGGA
1 GTCAATTCATGGCA-CCGAGTGCCTAGTGGATAAACCGCGATAAATGAGCCCAGCTCTAGTTGGA
*
126238 TTAATCAACGAATTAT
65 TTAACCAACGAATTAT
*
126254 GTCAATTCATGGCACCGAGTGCCTAGTGGATAAATCGCGATAAATGAGCCCAGCTCTAGTTGGAT
1 GTCAATTCATGGCACCGAGTGCCTAGTGGATAAACCGCGATAAATGAGCCCAGCTCTAGTTGGAT
*
126319 TAACCAACGAATTCT
66 TAACCAACGAATTAT
* * * *
126334 GTCAATTCATGGCACCTAGTGCCTAATGGATAAACCACGATAAATGAGCCCAGCTCTAGTTGGTT
1 GTCAATTCATGGCACCGAGTGCCTAGTGGATAAACCGCGATAAATGAGCCCAGCTCTAGTTGGAT
* ** *
126399 TGACCAATAAATAATCT
66 TAACCAACGAAT--TAT
* * * * ** * * ** * *
126416 GTCAAATCTTGGCAACTAGTGCCTAGCAGTTAAACCGCGA-AAGTGAG-CTTGCTTTGGTTGGAT
1 GTCAATTCATGGCACCGAGTGCCTAGTGGATAAACCGCGATAAATGAGCCCAGCTCTAGTTGGAT
126479 TAACCAACGAATT
66 TAACCAACGAATT
126492 TTTACAATTC
Statistics
Matches: 204, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
78 1 0.00
79 4 0.02
80 158 0.77
81 6 0.03
82 35 0.17
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (80 bp):
GTCAATTCATGGCACCGAGTGCCTAGTGGATAAACCGCGATAAATGAGCCCAGCTCTAGTTGGAT
TAACCAACGAATTAT
Found at i:130998 original size:13 final size:14
Alignment explanation
Indices: 130969--130998 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
130959 TTCTGTACAT
130969 TGACATTTAACCTC
1 TGACATTTAACCTC
130983 TGACATTTAA-CTC
1 TGACATTTAACCTC
130996 TGA
1 TGA
130999 TTGCGTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:139858 original size:16 final size:16
Alignment explanation
Indices: 139821--139869 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 16
139811 TTAGTCATTT
*
139821 GAAAAAGAAACAAAATAA
1 GAAAAAGAAA-GAAA-AA
*
139839 GAAAAAGGAAGAAAAA
1 GAAAAAGAAAGAAAAA
139855 GAAAAAGAAAGAAAA
1 GAAAAAGAAAGAAAA
139870 TTTTGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 16 0.57
17 3 0.11
18 9 0.32
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (16 bp):
GAAAAAGAAAGAAAAA
Found at i:144709 original size:3 final size:3
Alignment explanation
Indices: 144701--144753 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
144691 ACTATTTTCT
*
144701 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
144749 TTA TT
1 TTA TT
144754 TATAACTATA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:151221 original size:13 final size:14
Alignment explanation
Indices: 151203--151243 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
151193 ACAGAAATTT
151203 CTTTTTCTTTT-TG
1 CTTTTTCTTTTGTG
*
151216 CTTTTTCTTTGTGTT
1 CTTTTTCTTT-TGTG
151231 CTTTTTCTTTTGT
1 CTTTTTCTTTTGT
151244 CTCTGTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
14 4 0.16
15 11 0.44
ACGTcount: A:0.00, C:0.15, G:0.10, T:0.76
Consensus pattern (14 bp):
CTTTTTCTTTTGTG
Found at i:151855 original size:40 final size:40
Alignment explanation
Indices: 151783--152047 Score: 217
Period size: 40 Copynumber: 6.8 Consensus size: 40
151773 CCCTCTAGTT
* *
151783 AGGGTAAAATATTGG-ATGT-TTCAATCTGCCCCATGATC
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCCCCATGATC
* *
151821 AGGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATC
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCCCCATGATC
* * * * *
151861 AGGGTAAGAG-TTAGTGTATCTTCAATCTGCCATC-TGATT
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCC-CCATGATC
* ***
151900 AGGGTAAAAGATTGG-ATG-CTTCAATCTGCTATATGATC
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCCCCATGATC
* * * *
151938 GGGGAAAGAGATTGGTGTGTCTTCAATCTGCCCTC-TGATT
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCCC-CATGATC
* * * * **
151978 AAGGTAAAAGATT-GAAT-ACTTCAATCTGCTTCATGATC
1 AGGGTAAGAGATTGGTATGTCTTCAATCTGCCCCATGATC
*
152016 -GGAGTAAGAGATTGGTATGTCTTTAATCTGCC
1 AGG-GTAAGAGATTGGTATGTCTTCAATCTGCC
152048 ATTTGATTAG
Statistics
Matches: 174, Mismatches: 41, Indels: 22
0.73 0.17 0.09
Matches are distributed among these distances:
37 2 0.01
38 64 0.37
39 42 0.24
40 66 0.38
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (40 bp):
AGGGTAAGAGATTGGTATGTCTTCAATCTGCCCCATGATC
Found at i:151977 original size:78 final size:77
Alignment explanation
Indices: 151802--152073 Score: 287
Period size: 78 Copynumber: 3.5 Consensus size: 77
151792 TATTGGATGT
* * * * * ** *
151802 TTCAATCTGCC-CCATGATCAGGGTAAGAGATTGGTGTGTCTTCAATCTACCCCATGATCAGGGT
1 TTCAATCTGCCATC-TGATTAGGGTAAAAGATTGG-ATG-CTTCAATCT-GCTTATGATCGGGGT
* *
151866 AAGAG-TTAGTGTATC
62 AAGAGATTGGTGTGTC
*
151881 TTCAATCTGCCATCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCTATATGATCGGGGAAAG
1 TTCAATCTGCCATCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCT-TATGATCGGGGTAAG
151946 AGATTGGTGTGTC
65 AGATTGGTGTGTC
* * * * *
151959 TTCAATCTGCCCTCTGATTAAGGTAAAAGATTGAATACTTCAATCTGCTTCATGATCGGAGTAAG
1 TTCAATCTGCCATCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCTT-ATGATCGGGGTAAG
*
152024 AGATTGGTATGTC
65 AGATTGGTGTGTC
* * * *
152037 TTTAATCTGCCATTTGATTAGTGTAAATGATTGGATG
1 TTCAATCTGCCATCTGATTAGGGTAAAAGATTGGATG
152074 GTAGCTTCAC
Statistics
Matches: 163, Mismatches: 26, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
76 1 0.01
77 24 0.15
78 108 0.66
79 29 0.18
80 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (77 bp):
TTCAATCTGCCATCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCTTATGATCGGGGTAAGA
GATTGGTGTGTC
Found at i:151984 original size:117 final size:117
Alignment explanation
Indices: 151762--151984 Score: 306
Period size: 117 Copynumber: 1.9 Consensus size: 117
151752 TTGGATGGTG
* * * * *
151762 TCTTCAAGCTGCCCTCTAGTTAGGGTAAAATATTGGATGTTTCAATCTGCCCCATGATCAGGGTA
1 TCTTCAAGCTGCCATCTAGTTAGGGTAAAAGATTGGATGCTTCAATCTGCCACATGATCAGGGAA
*
151827 AGAGATTGGTGTGTCTTCAATCTACCCCATGATCAGGGTAAGAGTTAGTGTA
66 AGAGATTGGTGTGTCTTCAATCTACCCCATGATCAAGGTAAGAGTTAGTGTA
* * * *
151879 TCTTCAATCTGCCATCT-GATTAGGGTAAAAGATTGGATGCTTCAATCTGCTATATGATCGGGGA
1 TCTTCAAGCTGCCATCTAG-TTAGGGTAAAAGATTGGATGCTTCAATCTGCCACATGATCAGGGA
* *
151943 AAGAGATTGGTGTGTCTTCAATCTGCCCTC-TGATTAAGGTAA
65 AAGAGATTGGTGTGTCTTCAATCTACCC-CATGATCAAGGTAA
151985 AAGATTGAAT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 90 0.98
118 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (117 bp):
TCTTCAAGCTGCCATCTAGTTAGGGTAAAAGATTGGATGCTTCAATCTGCCACATGATCAGGGAA
AGAGATTGGTGTGTCTTCAATCTACCCCATGATCAAGGTAAGAGTTAGTGTA
Found at i:159567 original size:16 final size:18
Alignment explanation
Indices: 159540--159577 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
159530 TTTTTTTAAT
*
159540 TAAAAAATAAAATAAG-A
1 TAAAAAATAAAAAAAGAA
159557 TAAAAAA-AAAAAAAGAA
1 TAAAAAATAAAAAAAGAA
159574 TAAA
1 TAAA
159578 GGTCTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (18 bp):
TAAAAAATAAAAAAAGAA
Done.