Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011927.1 Kokia drynarioides strain JFW-HI SEQ_126925, 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: 95113
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:144 original size:78 final size:77
Alignment explanation
Indices: 4--202 Score: 209
Period size: 78 Copynumber: 2.6 Consensus size: 77
1 CCT
* * * * *
4 CGAGCCTAGGGCAGATCACCGTTAGCCAATCTCTTACCCCACAATAGGGGCAGATTGTAGCCATC
1 CGAGCATAGGGCAGATCACCGTCAGCCAATCTCTTACCCC-GAGTAGGGGCAGATTGCAGCCATC
*
69 TAATCTTTTACCC
65 CAATCTTTTACCC
* * * * * * *
82 CGATCATGGGGCAGATCACCGTCAGCTAATCTCTTACCTCGAGTCTGGTGCAGGTTGCAGCCATC
1 CGAGCATAGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAGT-AGGGGCAGATTGCAGCCATC
* *
147 CGATCTTTTACCT
65 CAATCTTTTACCC
* * * *
160 TGAGCCTAGGGCAGATCATCGTCAACCAATCTCTTACCCCGAG
1 CGAGCATAGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAG
203 CCAACGGCAG
Statistics
Matches: 97, Mismatches: 23, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
77 2 0.02
78 95 0.98
ACGTcount: A:0.23, C:0.31, G:0.21, T:0.25
Consensus pattern (77 bp):
CGAGCATAGGGCAGATCACCGTCAGCCAATCTCTTACCCCGAGTAGGGGCAGATTGCAGCCATCC
AATCTTTTACCC
Found at i:725 original size:16 final size:16
Alignment explanation
Indices: 705--759 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
695 ACCCAAACAG
705 AATTTAAATTTAAATTT-
1 AATTTAAATTT--ATTTA
*
722 ATTTTAAA-TTATTTTA
1 AATTTAAATTTA-TTTA
*
738 AGTTTAAATTTATTTA
1 AATTTAAATTTATTTA
754 AATTTA
1 AATTTA
760 TTAATGTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 18 0.56
17 10 0.31
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
AATTTAAATTTATTTA
Found at i:761 original size:27 final size:27
Alignment explanation
Indices: 707--757 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
697 CCAAACAGAA
707 TTTAAATTTAAATTTATTTTAAATTAT
1 TTTAAATTTAAATTTATTTTAAATTAT
*
734 TTTAAGTTTAAATTTA-TTTAAATT
1 TTTAAATTTAAATTTATTTTAAATT
758 TATTAATGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTAAATTTAAATTTATTTTAAATTAT
Found at i:833 original size:19 final size:20
Alignment explanation
Indices: 793--834 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
783 TGAGTCCAAA
*
793 CAATTACAAGCCCAATGGCC
1 CAATTACAAGACCAATGGCC
*
813 CAATTACATGACCAA-GGCC
1 CAATTACAAGACCAATGGCC
832 CAA
1 CAA
835 AAGGCCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.38, C:0.33, G:0.14, T:0.14
Consensus pattern (20 bp):
CAATTACAAGACCAATGGCC
Found at i:2289 original size:29 final size:30
Alignment explanation
Indices: 2248--2463 Score: 222
Period size: 30 Copynumber: 7.2 Consensus size: 30
2238 CCTCATCGTA
2248 AAAATTACATTTTGA-CCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
2277 AAAACTATATTTTGA-CCCTAAACTTTCCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *
2306 AAAATCACATTTTTTTACCCCTAAACTTTTCT
1 AAAATTACA--TTTTGACCCCTAAACTTTTCC
*
2338 AAAATTACATTTTGACCCCTAAACTTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* * *** * * *
2368 GAAATCACATTTTGATTACAAAAATTTTTC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* *
2398 AAAATTGCATTTTGA-CCCTAAACTTCTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
* *
2427 AAAATTATATTTTTACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCCTAAACTTTTCC
2457 AAAATTA
1 AAAATTA
2464 TTATCCTTTG
Statistics
Matches: 150, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
29 52 0.35
30 73 0.49
31 5 0.03
32 20 0.13
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:4431 original size:7 final size:7
Alignment explanation
Indices: 4419--4448 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4409 CATGTCCGAT
4419 ATCCATC
1 ATCCATC
4426 ATCCATC
1 ATCCATC
4433 ATCCATC
1 ATCCATC
*
4440 ATCCCTC
1 ATCCATC
4447 AT
1 AT
4449 TTCCCCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.27, C:0.43, G:0.00, T:0.30
Consensus pattern (7 bp):
ATCCATC
Found at i:13783 original size:17 final size:17
Alignment explanation
Indices: 13761--13801 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13751 ATTTAATTAG
13761 TTAAATTAAATTTCCAA
1 TTAAATTAAATTTCCAA
* *
13778 TTAAATAAAATTTTCAA
1 TTAAATTAAATTTCCAA
*
13795 TTTAATT
1 TTAAATT
13802 CTAATTCTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATTAAATTTCCAA
Found at i:14037 original size:16 final size:16
Alignment explanation
Indices: 14016--14049 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
14006 TGTGACTCAT
14016 TTCTCTAACTTCATCA
1 TTCTCTAACTTCATCA
14032 TTCTCTAACTTCATCA
1 TTCTCTAACTTCATCA
14048 TT
1 TT
14050 TACATTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (16 bp):
TTCTCTAACTTCATCA
Found at i:14411 original size:13 final size:13
Alignment explanation
Indices: 14393--14418 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14383 CATTACATCT
14393 TTCTTCATGAAAA
1 TTCTTCATGAAAA
14406 TTCTTCATGAAAA
1 TTCTTCATGAAAA
14419 GTCAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TTCTTCATGAAAA
Found at i:17315 original size:27 final size:28
Alignment explanation
Indices: 17209--17319 Score: 170
Period size: 28 Copynumber: 4.0 Consensus size: 28
17199 TTGGTAACAG
17209 GCATGACCTTTGGGTCAATAGGGAGTAA
1 GCATGACCTTTGGGTCAATAGGGAGTAA
* * *
17237 ACATGACCTTTGGGTTAATAAGGAGTAA
1 GCATGACCTTTGGGTCAATAGGGAGTAA
*
17265 GCATGACCTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAATAGGGAGTAA
*
17293 GCATGACC-TTAGGTCAATAGGGAGTAA
1 GCATGACCTTTGGGTCAATAGGGAGTAA
17320 ATCGATCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 17 0.23
28 57 0.77
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.24
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAATAGGGAGTAA
Found at i:21388 original size:29 final size:30
Alignment explanation
Indices: 21228--21449 Score: 182
Period size: 30 Copynumber: 7.5 Consensus size: 30
21218 TGTTTTATCT
**
21228 AAAAATTACATTTTAA-CCCAAAACTTTCC
1 AAAAATTACATTTTAATCCTTAAACTTTCC
* * * * ** *
21257 AAAAATCATATTTTGACCCTCGAACTTTTC
1 AAAAATTACATTTTAATCCTTAAACTTTCC
* * *
21287 TAAAATTACATTTTAACCCTTTAACTTTCC
1 AAAAATTACATTTTAATCCTTAAACTTTCC
**
21317 AAAAATTGA-ATTTTAATCCCAAAACTTTCC
1 AAAAATT-ACATTTTAATCCTTAAACTTTCC
* *
21347 AAAAATTACATTTTGATCCTTAAACTTT-T
1 AAAAATTACATTTTAATCCTTAAACTTTCC
* * *
21376 AAAAATTGCATTTTTATCCTCAAACTTTCC
1 AAAAATTACATTTTAATCCTTAAACTTTCC
* * * *
21406 AAAAGTTACGTTTTAACCCTTAAAATTTACC
1 AAAAATTACATTTTAATCCTTAAACTTT-CC
*
21437 AAAACTT-CATTTT
1 AAAAATTACATTTT
21450 GACCCCTTTT
Statistics
Matches: 152, Mismatches: 36, Indels: 9
0.77 0.18 0.05
Matches are distributed among these distances:
29 39 0.26
30 104 0.68
31 9 0.06
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAAATTACATTTTAATCCTTAAACTTTCC
Found at i:21407 original size:59 final size:60
Alignment explanation
Indices: 21228--21440 Score: 227
Period size: 59 Copynumber: 3.6 Consensus size: 60
21218 TGTTTTATCT
* * * * * *
21228 AAAAATTACATTTTAACCC-AAAACTTTCCAAAAA-TCATATTTTGACCCTCGAACTTTTC
1 AAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTGA-ATTTTAATCCTCAAACTTTCC
* *
21287 TAAAATTACATTTTAACCCTTTAACTTTCCAAAAATTGAATTTTAATCC-CAAAACTTTCC
1 AAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTGAATTTTAATCCTC-AAACTTTCC
* * * * *
21347 AAAAATTACATTTTGATCCTTAAACTTT-TAAAAATTGCATTTTTATCCTCAAACTTTCC
1 AAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTGAATTTTAATCCTCAAACTTTCC
* * *
21406 AAAAGTTACGTTTTAACCCTTAAAATTTACCAAAA
1 AAAAATTACATTTTAACCCTTAAACTTT-CCAAAA
21441 CTTCATTTTG
Statistics
Matches: 127, Mismatches: 21, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
59 68 0.54
60 53 0.42
61 6 0.05
ACGTcount: A:0.39, C:0.21, G:0.03, T:0.37
Consensus pattern (60 bp):
AAAAATTACATTTTAACCCTTAAACTTTCCAAAAATTGAATTTTAATCCTCAAACTTTCC
Found at i:52951 original size:88 final size:88
Alignment explanation
Indices: 52802--52977 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
52792 CAGATAACAG
52802 AACTTGGTTAGAGTTGTTATGCAACCTGCAATTTATTCGGGTTAGGATCTAAATTGAGCATGCAC
1 AACTTGGTTAGAGTTGTTATGCAACCTGCAATTTATTCGGGTTAGGATCTAAATTGAGCATGCAC
52867 ATTTCAATTATGTGTCCACTAGC
66 ATTTCAATTATGTGTCCACTAGC
52890 AACTTGGTTAGAGTTGTTATGCAACCTGCAATTTATTCGGGTTAGGATCTAAATTGAGCATGCAC
1 AACTTGGTTAGAGTTGTTATGCAACCTGCAATTTATTCGGGTTAGGATCTAAATTGAGCATGCAC
52955 ATTTCAATTATGTGTCCACTAGC
66 ATTTCAATTATGTGTCCACTAGC
52978 CGTCGTCTAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (88 bp):
AACTTGGTTAGAGTTGTTATGCAACCTGCAATTTATTCGGGTTAGGATCTAAATTGAGCATGCAC
ATTTCAATTATGTGTCCACTAGC
Found at i:55356 original size:23 final size:23
Alignment explanation
Indices: 55330--55377 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
55320 CTAAAGAACA
* *
55330 AATTTAACCCAATTTAATTAATT
1 AATTCAACCCAAATTAATTAATT
*
55353 AATTCAACCCAAATTATTTAATT
1 AATTCAACCCAAATTAATTAATT
55376 AA
1 AA
55378 ATATTTTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTCAACCCAAATTAATTAATT
Found at i:65313 original size:42 final size:42
Alignment explanation
Indices: 65266--65676 Score: 413
Period size: 42 Copynumber: 10.1 Consensus size: 42
65256 ACGGTGGAGA
65266 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
** *
65308 AAGACATCATCCAATCTCTTACCTTGATCATGGGGTAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* * *
65350 CAG-C--CATCCAATCTCTTACCCCGATCATTGGACAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* * * *
65389 AAGA-ATCA---AATCTCTTACCGCAATCATGAGGCAGATTA
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* *
65427 AAGACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTA
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* *
65469 AAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATT-
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* * * ** * *
65510 -A-A-AGCATCCGATCTTTTACCCTAATTA-GAGGGTAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATG-GGGCAGATTG
* * ** *
65549 AAGAAATCATCCAATCTTTTACCCCGATCATGATGTAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
* * * *
65591 TAG---TCGTCCAATCTCTTACCCTGATCGTGGGGCAGATTG
1 AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
*
65630 CAA-CCATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
1 -AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
65672 AAGAC
1 AAGAC
65677 GACGAATCTT
Statistics
Matches: 305, Mismatches: 46, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
37 1 0.00
38 55 0.18
39 66 0.22
40 3 0.01
41 6 0.02
42 173 0.57
43 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (42 bp):
AAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTG
Found at i:65589 original size:122 final size:119
Alignment explanation
Indices: 65278--65611 Score: 350
Period size: 122 Copynumber: 2.8 Consensus size: 119
65268 GACATCATCC
* * * **
65278 AATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCTTGATCATGGGG
1 AATCTCTTACCGCAATCATGAGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
** * *
65343 TAGATTGCAGCCATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGAATCA
66 TAGATTAAAGCCATCCAATCTCTTACCCCAATCATTGGACAGATTAAAGAATCA
* *
65397 AATCTCTTACCGCAATCATGAGGCAGATTAAAGACATCATCCAATCTCTTACCCCAATCATGGGG
1 AATCTCTTACCGCAATCATGAGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
* * * *
65462 CAGATTAAAGACATCATCCAATCTCTTACCCCAATCA-TGAGGCAGATTAAAGCATCC
66 TAGATTAAAG-C--CATCCAATCTCTTACCCCAATCATTG-GACAGATTAAAGAATCA
* * * * * * *
65519 GATCTTTTACC-CTAATTA-GAGGGTAGATTGAAGAAATCATCCAATCTTTTACCCCGATCATGA
1 AATCTCTTACCGC-AATCATGA-GGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGG
* ** * *
65582 TGTAGATTGTAGTCGTCCAATCTCTTACCC
64 GGTAGATTAAAGCCATCCAATCTCTTACCC
65612 TGATCGTGGG
Statistics
Matches: 179, Mismatches: 30, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
119 81 0.45
120 1 0.01
121 5 0.03
122 92 0.51
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (119 bp):
AATCTCTTACCGCAATCATGAGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCATGGGG
TAGATTAAAGCCATCCAATCTCTTACCCCAATCATTGGACAGATTAAAGAATCA
Found at i:65603 original size:161 final size:159
Alignment explanation
Indices: 65271--65670 Score: 446
Period size: 161 Copynumber: 2.5 Consensus size: 159
65261 GGAGAAAGAC
* **
65271 ATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCTTGAT
1 ATCATCCAATCTCTTACCCCGATCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCCCGAT
* ** * **
65336 CATGGGGTAGATTGCAGCCATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGAATCAAATC
66 CATGGGGCAGATTAAAGCCATCCAATCTCTTACCCCAATCAGAGGACAGATTGAAGAATCAAATC
*
65401 TCTTACCGCAATCATGAGGCAGATTAAAG
131 TCTTACCCCAATCATGAGGCAGATTAAAG
* *
65430 ACATCATCCAATCTCTTACCCCAATCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCCCA
1 --ATCATCCAATCTCTTACCCCGATCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCCCG
* * * * * **
65495 ATCATGAGGCAGATTAAAG-CATCCGATCTTTTACCCTAATTAGAGGGTAGATTGAAGAAATCAT
64 ATCATGGGGCAGATTAAAGCCATCCAATCTCTTACCCCAATCAGAGGACAGATTGAAG-AATCA-
* * * * **
65559 CCAATCTTTTACCCCGATCATGATGTAGATTGTAG
127 --AATCTCTTACCCCAATCATGAGGCAGATTAAAG
* * * * *
65594 -TCGTCCAATCTCTTACCCTGATCGTGGGGCAGATTGCAA-CCATCATCCAATCTCTTACCCCGA
1 ATCATCCAATCTCTTACCCCGATCATGGGGCAGATT-AAAGACATCATCCAATCTCTTACCCCGA
65657 TCATGGGGCAGATT
65 TCATGGGGCAGATT
65671 GAAGACGACG
Statistics
Matches: 201, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
160 29 0.14
161 144 0.72
162 2 0.01
164 26 0.13
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (159 bp):
ATCATCCAATCTCTTACCCCGATCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCCCGAT
CATGGGGCAGATTAAAGCCATCCAATCTCTTACCCCAATCAGAGGACAGATTGAAGAATCAAATC
TCTTACCCCAATCATGAGGCAGATTAAAG
Found at i:65627 original size:203 final size:202
Alignment explanation
Indices: 65265--65676 Score: 471
Period size: 203 Copynumber: 2.0 Consensus size: 202
65255 TACGGTGGAG
* * *
65265 AAAGACATCATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTAC
1 AAAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATT-AAGACAGCATCCAATCTCTTAC
* * *
65330 CTTGATCATGGGGTAGATTGCAGCCATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGAAT
65 CCTAATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGAAT
65395 CAAATCTCTTACCGCAATCATGAGGCAGATT-AAAGACATCATCCAATCTCTTACCCCAATCATG
130 CAAATCTCTTACCGCAATCATGAGGCAGATTGAAA-ACATCATCCAATCTCTTACCCCAATCATG
65459 GGGCAGATT
194 GGGCAGATT
* *
65468 AAAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATT-A-A-AGCATCCGATCTTTTACC
1 AAAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATTAAGACAGCATCCAATCTCTTACC
* * * * *
65530 CTAATTA-GAGGGTAGATTGAAGAAATCATCCAATCTTTTACCCCGATCA-T-GATGTAGATTGT
66 CTAATCATG-GGGTAGATTGAAG---CCATCCAATCTCTTACCCCGATCATTGGA--CAGATTGA
** * * * * * * *
65592 AGTCGTCCAATCTCTTACC-CTGATCGTGGGGCAGATTGCAACCATCATCCAATCTCTTACCCCG
125 AG-AATCAAATCTCTTACCGC-AATCATGAGGCAGATTGAAAACATCATCCAATCTCTTACCCCA
65656 ATCATGGGGCAGATT
188 ATCATGGGGCAGATT
*
65671 GAAGAC
1 AAAGAC
65677 GACGAATCTT
Statistics
Matches: 177, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
198 1 0.01
199 31 0.18
200 3 0.02
201 2 0.01
202 31 0.18
203 107 0.60
204 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (202 bp):
AAAGACATCATCCAATCTCTTACCCCAATCATGAGGCAGATTAAGACAGCATCCAATCTCTTACC
CTAATCATGGGGTAGATTGAAGCCATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGAATC
AAATCTCTTACCGCAATCATGAGGCAGATTGAAAACATCATCCAATCTCTTACCCCAATCATGGG
GCAGATT
Found at i:65685 original size:81 final size:81
Alignment explanation
Indices: 65273--65674 Score: 431
Period size: 80 Copynumber: 5.0 Consensus size: 81
65263 AGAAAGACAT
**
65273 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCTTGATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
* * *
65338 TGGGGTAGATTGCAGC
66 TGAGGCAGATTGAAGC
* * * *
65354 CATCCAATCTCTTACCCCGATCATTGGACAGATTGAAGA-ATCA---AATCTCTTACCGCAATCA
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
*
65415 TGAGGCAGATTAAAGAC
66 TGAGGCAGATTGAAG-C
* * *
65432 ATCATCCAATCTCTTACCCCAATCATGGGGCAGATTAAAGACATCATCCAATCTCTTACCCCAAT
1 --CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGAT
*
65497 CATGAGGCAGATTAAAG-
64 CATGAGGCAGATTGAAGC
* * ** * * * *
65514 CATCCGATCTTTTACCCTAATTA-GAGGGTAGATTGAAGAAATCATCCAATCTTTTACCCCGATC
1 CATCCAATCTCTTACCCCGATCATG-GGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATC
* * * *
65578 ATGATGTAGATTGTAGT
65 ATGAGGCAGATTGAAGC
* * * *
65595 CGTCCAATCTCTTACCCTGATCGTGGGGCAGATTGCAA-CCATCATCCAATCTCTTACCCCGATC
1 CATCCAATCTCTTACCCCGATCATGGGGCAGATTG-AAGACATCATCCAATCTCTTACCCCGATC
*
65659 ATGGGGCAGATTGAAG
65 ATGAGGCAGATTGAAG
65675 ACGACGAATC
Statistics
Matches: 269, Mismatches: 41, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
77 26 0.10
78 1 0.00
79 1 0.00
80 104 0.39
81 102 0.38
82 3 0.01
84 32 0.12
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (81 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
TGAGGCAGATTGAAGC
Found at i:67365 original size:17 final size:17
Alignment explanation
Indices: 67333--67366 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
67323 AAACTGCCCC
* *
67333 TTTAATTTATTTCTTTT
1 TTTAATTTAGTCCTTTT
67350 TTTAATTTAGTCCTTTT
1 TTTAATTTAGTCCTTTT
67367 ACTTTTGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTAATTTAGTCCTTTT
Found at i:67474 original size:30 final size:30
Alignment explanation
Indices: 67440--67666 Score: 227
Period size: 30 Copynumber: 7.6 Consensus size: 30
67430 TGTTTTATCT
67440 AAAAATTACATTTTGA-CCTTAAAACTTTCC
1 AAAAATTACATTTTGACCCTT-AAACTTTCC
*
67470 AAAAATTACATTTTGACTCC--AAACATTCC
1 AAAAATTACATTTTGAC-CCTTAAACTTTCC
*
67499 AAAAATTACATTTTGACCCCT-AAC-TTCTC
1 AAAAATTACATTTTGACCCTTAAACTTTC-C
* *
67528 AAAAATTATATTTTAACCCTTAAACTTTCC
1 AAAAATTACATTTTGACCCTTAAACTTTCC
* *
67558 AAAAATTACATTTTAACCCTTAAACTTTCA
1 AAAAATTACATTTTGACCCTTAAACTTTCC
* ** *
67588 AAAAATTACATTTTTACCCTCGATCTTTCC
1 AAAAATTACATTTTGACCCTTAAACTTTCC
* *
67618 AAAAGTTATGC-TTTT-ACCCTTAAAATTCTCC
1 AAAAATTA--CATTTTGACCCTTAAACTT-TCC
*
67649 AAAACTTA-ATTTTGACCC
1 AAAAATTACATTTTGACCC
67667 CTTTTTTTCC
Statistics
Matches: 168, Mismatches: 17, Indels: 24
0.80 0.08 0.11
Matches are distributed among these distances:
28 5 0.03
29 51 0.30
30 92 0.55
31 17 0.10
32 3 0.02
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATTACATTTTGACCCTTAAACTTTCC
Found at i:67512 original size:59 final size:59
Alignment explanation
Indices: 67440--67607 Score: 209
Period size: 59 Copynumber: 2.8 Consensus size: 59
67430 TGTTTTATCT
*
67440 AAAAATTACATTTTGA-CCTTAAAACTTTCCAAAAATTACATTTTGACTCC-AAACATTCC
1 AAAAATTACATTTTGACCCTT-AAACTTTCCAAAAATTACATTTTAAC-CCTAAACATTCC
* * *
67499 AAAAATTACATTTTGACCCCT-AAC-TTCTCAAAAATTATATTTTAACCCTTAAACTTTCC
1 AAAAATTACATTTTGACCCTTAAACTTTC-CAAAAATTACATTTTAACCC-TAAACATTCC
* * *
67558 AAAAATTACATTTTAACCCTTAAACTTTCAAAAAATTACATTTTTACCCT
1 AAAAATTACATTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCT
67608 CGATCTTTCC
Statistics
Matches: 94, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
57 5 0.05
58 19 0.20
59 44 0.47
60 23 0.24
61 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAAATTACATTTTGACCCTTAAACTTTCCAAAAATTACATTTTAACCCTAAACATTCC
Found at i:74483 original size:6 final size:6
Alignment explanation
Indices: 74472--74503 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
74462 GCTGCCTTTG
74472 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TT
74504 GGGTGCTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:74551 original size:24 final size:24
Alignment explanation
Indices: 74522--74569 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
74512 ACCCTCTTCC
*
74522 TTGTGCTTCTT-CTTCTTTTTATCT
1 TTGTGCCTCTTCCTT-TTTTTATCT
74546 TTGTGCCTCTTCCTTTTTTTATCT
1 TTGTGCCTCTTCCTTTTTTTATCT
74570 ATTGAACCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.04, C:0.23, G:0.08, T:0.65
Consensus pattern (24 bp):
TTGTGCCTCTTCCTTTTTTTATCT
Found at i:74880 original size:18 final size:18
Alignment explanation
Indices: 74859--74894 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
74849 GGTTCTTTCA
74859 TTTCATTCTTT-TCTTCTT
1 TTTC-TTCTTTGTCTTCTT
74877 TTTCTTCTTTGTCTTCTT
1 TTTCTTCTTTGTCTTCTT
74895 CTTCCTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTCTTCTTTGTCTTCTT
Found at i:90983 original size:28 final size:28
Alignment explanation
Indices: 90943--91054 Score: 134
Period size: 28 Copynumber: 4.0 Consensus size: 28
90933 TGGTAATAGG
* * *
90943 CATGTCCTTTGGGTTAACAAAGAGTAAA
1 CATGACCTTTGGGTCAACAAGGAGTAAA
* *
90971 CATGACCTTTGGGTCAATAAGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAA
* * *
90999 GATGACCTTTGGGTCAACAGGGAGTAAG
1 CATGACCTTTGGGTCAACAAGGAGTAAA
* *
91027 CATGACCTTTAGGTCAACAGGGAGTAAA
1 CATGACCTTTGGGTCAACAAGGAGTAAA
91055 TCGGATATTA
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 73 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (28 bp):
CATGACCTTTGGGTCAACAAGGAGTAAA
Found at i:91034 original size:56 final size:56
Alignment explanation
Indices: 90948--91053 Score: 149
Period size: 56 Copynumber: 1.9 Consensus size: 56
90938 ATAGGCATGT
* * *
90948 CCTTTGGGTTAACAAAGAGTAAACATGACCTTTGGGTCAATAAGGAGTAAGGATGA
1 CCTTTGGGTCAACAAAGAGTAAACATGACCTTTAGGTCAACAAGGAGTAAGGATGA
** * *
91004 CCTTTGGGTCAACAGGGAGTAAGCATGACCTTTAGGTCAACAGGGAGTAA
1 CCTTTGGGTCAACAAAGAGTAAACATGACCTTTAGGTCAACAAGGAGTAA
91054 ATCGGATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
56 43 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (56 bp):
CCTTTGGGTCAACAAAGAGTAAACATGACCTTTAGGTCAACAAGGAGTAAGGATGA
Found at i:91808 original size:20 final size:21
Alignment explanation
Indices: 91771--91818 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
91761 TTTTGGTACT
* *
91771 GGTAGAAGCATGATTTGT-TC
1 GGTAGAAGCATCACTTGTATC
*
91791 GGTAGAAGCTTCACTTGTATC
1 GGTAGAAGCATCACTTGTATC
*
91812 AGTAGAA
1 GGTAGAA
91819 CTGTCATAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.31
Consensus pattern (21 bp):
GGTAGAAGCATCACTTGTATC
Done.