Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012758.1 Kokia drynarioides strain JFW-HI SEQ_127769, 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: 66220
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1983 original size:5 final size:5
Alignment explanation
Indices: 1975--2003 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1965 CTACATATCT
1975 CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTT
2004 ATTTTTATGT
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:0.38, G:0.00, T:0.62
Consensus pattern (5 bp):
CTTTC
Found at i:5710 original size:50 final size:48
Alignment explanation
Indices: 5656--5817 Score: 156
Period size: 50 Copynumber: 3.4 Consensus size: 48
5646 AGTTTATTTG
5656 CAAATCAGTGGTGGCTTGTCAAAAAAGTGTTATCAGTGGCAATTTATCTA
1 CAAATCAGTGGTGGCTTGTC--AAAAGTGTTATCAGTGGCAATTTATCTA
* * *
5706 CAAATTAGTGGTGGCTTGTCCACAAAGTGTT-TTAGTGGCAATATATCTA
1 CAAATCAGTGGTGGCTTGT-CA-AAAGTGTTATCAGTGGCAATTTATCTA
* * * * * *
5755 CATAT--GTGGTGTCTTGTC--CACT-TTATCAGTGGTAGTTTATCTA
1 CAAATCAGTGGTGGCTTGTCAAAAGTGTTATCAGTGGCAATTTATCTA
*
5798 CAAATCATTGGTGGCTTGTC
1 CAAATCAGTGGTGGCTTGTC
5818 CACAAATGGT
Statistics
Matches: 93, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
42 2 0.02
43 20 0.22
45 11 0.12
46 1 0.01
47 11 0.12
49 21 0.23
50 26 0.28
51 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.36
Consensus pattern (48 bp):
CAAATCAGTGGTGGCTTGTCAAAAGTGTTATCAGTGGCAATTTATCTA
Found at i:8723 original size:38 final size:36
Alignment explanation
Indices: 8642--8724 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 36
8632 TATATTCTTG
* * *
8642 GGTGCAATTTAAGAATACTTATGTAGTGATAGTTCT
1 GGTGCAATTGAAGAATACTTATGTAGCGACAGTTCT
* *
8678 GGATGCAAGTTGAAGAATATTTATGTAGCGACAGTTTTT
1 GG-TGCAA-TTGAAGAATACTTATGTAGCGACAG-TTCT
8717 GGTGCAAT
1 GGTGCAAT
8725 CTGGAAGTGC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 2 0.05
37 6 0.15
38 26 0.67
39 5 0.13
ACGTcount: A:0.30, C:0.08, G:0.25, T:0.36
Consensus pattern (36 bp):
GGTGCAATTGAAGAATACTTATGTAGCGACAGTTCT
Found at i:15224 original size:22 final size:22
Alignment explanation
Indices: 15196--15239 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15186 ACAGCTGTCA
15196 AAGTTAGTTACAGTACAGCTAT
1 AAGTTAGTTACAGTACAGCTAT
15218 AAGTTAGTTACAGTACAGCTAT
1 AAGTTAGTTACAGTACAGCTAT
15240 GCACTCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
AAGTTAGTTACAGTACAGCTAT
Found at i:19763 original size:11 final size:11
Alignment explanation
Indices: 19747--19780 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
19737 CAAAAATAAT
19747 TATTCAAAACA
1 TATTCAAAACA
19758 TATTC-AAACA
1 TATTCAAAACA
*
19768 CATTCAAAACA
1 TATTCAAAACA
19779 TA
1 TA
19781 CCAAAACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (11 bp):
TATTCAAAACA
Found at i:20606 original size:13 final size:13
Alignment explanation
Indices: 20551--20611 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
20541 CAACAAGTAC
*
20551 TTCATATAAACAC
1 TTCATATAAACAT
*
20564 TTCATATAACCAT
1 TTCATATAAACAT
*
20577 TTCATAT-ATCTATT
1 TTCATATAAAC-A-T
20591 TTCATATAAACAT
1 TTCATATAAACAT
*
20604 TTCGTATA
1 TTCATATA
20612 GTCGTTTCAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 2 0.05
13 27 0.68
14 9 0.22
15 2 0.05
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.43
Consensus pattern (13 bp):
TTCATATAAACAT
Found at i:20810 original size:16 final size:16
Alignment explanation
Indices: 20789--20820 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20779 AAGATACACC
20789 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
20805 GGCACGAAGCCTGCTA
1 GGCACGAAGCCTGCTA
20821 AAATACACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.31, G:0.31, T:0.12
Consensus pattern (16 bp):
GGCACGAAGCCTGCTA
Found at i:20827 original size:41 final size:41
Alignment explanation
Indices: 20782--20991 Score: 156
Period size: 41 Copynumber: 5.2 Consensus size: 41
20772 GCCCATTAAG
* * * * *
20782 ATACACCGGCACGAAGCCTGCTAGGCACGAAGCCTGCTAAA
1 ATACACCGGCACTAAGCCTGCTAGGAACAAAGCCCGATAAA
** * * * *
20823 ATACACCAACACTAAGCTTGCCAGGAATAAAGCCCGATAAT
1 ATACACCGGCACTAAGCCTGCTAGGAACAAAGCCCGATAAA
* *
20864 ATACACCGGCACTAAGCCTGCTATGCAA-ATAGCCCGATAAA
1 ATACACCGGCACTAAGCCTGCTA-GGAACAAAGCCCGATAAA
** ** * * *
20905 ATACATTGGCACTAAGTTTTCTAGGCACAAAGTCCGAT-AA
1 ATACACCGGCACTAAGCCTGCTAGGAACAAAGCCCGATAAA
* ** * **
20945 TTACACTAGCACTAAGCGTGCTAGTCACAAAGCCCGAT-AA
1 ATACACCGGCACTAAGCCTGCTAGGAACAAAGCCCGATAAA
20985 ATACACC
1 ATACACC
20992 ACCATAACAA
Statistics
Matches: 130, Mismatches: 37, Indels: 5
0.76 0.22 0.03
Matches are distributed among these distances:
40 41 0.32
41 86 0.66
42 3 0.02
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (41 bp):
ATACACCGGCACTAAGCCTGCTAGGAACAAAGCCCGATAAA
Found at i:20905 original size:82 final size:81
Alignment explanation
Indices: 20782--20992 Score: 212
Period size: 82 Copynumber: 2.6 Consensus size: 81
20772 GCCCATTAAG
* * * *
20782 ATACACCGGCACGAAGCCTGCTAGGCACGAAGCCTGCTAAAATACACCAACACTAAGCTTGCCAG
1 ATACACCGGCACTAAGCCTGCTA-GCACAAAGCCCGATAAAATACACCAACACTAAGCTTGCCAG
*
20847 GAATAAAGCCCGATAAT
65 GAACAAAGCCCGATAAT
**** * * *
20864 ATACACCGGCACTAAGCCTGCTATGCA-AATAGCCCGATAAAATACATTGGCACTAAGTTTTCTA
1 ATACACCGGCACTAAGCCTGCTA-GCACAA-AGCCCGATAAAATACACCAACACTAAGCTTGCCA
* *
20928 GGCACAAAGTCCGATAAT
64 GGAACAAAGCCCGATAAT
** *
20946 -TACACTAGCACTAAGCGTGCTAGTCACAAAGCCCGAT-AAATACACCA
1 ATACACCGGCACTAAGCCTGCTAG-CACAAAGCCCGATAAAATACACCA
20993 CCATAACAAC
Statistics
Matches: 105, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
80 8 0.08
81 30 0.29
82 67 0.64
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (81 bp):
ATACACCGGCACTAAGCCTGCTAGCACAAAGCCCGATAAAATACACCAACACTAAGCTTGCCAGG
AACAAAGCCCGATAAT
Found at i:22424 original size:21 final size:22
Alignment explanation
Indices: 22385--22426 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
22375 GTTTAGAAAG
* *
22385 TGTGCAGATTTCTATCGATACC
1 TGTGCAGAGTTCTACCGATACC
22407 TGTGCA-AGTTCTACCGATAC
1 TGTGCAGAGTTCTACCGATAC
22427 AAGTATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (22 bp):
TGTGCAGAGTTCTACCGATACC
Found at i:31126 original size:27 final size:25
Alignment explanation
Indices: 31092--31144 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 25
31082 TTCTATTATT
31092 TTTACCTATTAT-CCCTTAATTACTAAA
1 TTTACCTATT-TGCCCTT-ATTA-TAAA
31119 TTTACCTATTTGCCCTTATTATAAA
1 TTTACCTATTTGCCCTTATTATAAA
31144 T
1 T
31145 CATCAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 5 0.20
26 5 0.20
27 15 0.60
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTACCTATTTGCCCTTATTATAAA
Found at i:34032 original size:3 final size:3
Alignment explanation
Indices: 34024--34087 Score: 64
Period size: 3 Copynumber: 22.3 Consensus size: 3
34014 TTGGGCAACG
* *
34024 TCT TCT TCT TCT TCT TCT TCT TCT TCCT TC- TCT TCT TTT TCA TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT
*
34069 T-T TTT TCT T-T TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT T
34088 TTGCTTCAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 8 0.16
3 40 0.78
4 3 0.06
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:34388 original size:359 final size:356
Alignment explanation
Indices: 33844--34576 Score: 793
Period size: 359 Copynumber: 2.0 Consensus size: 356
33834 ACAGTCACGT
* * * *
33844 TCGATGGCTAGATCTCAGCAGTGGTGCCAAATATGGCACAATTGCCAGAGGATTGGAATCCTTAT
1 TCGATGGATAGATCTCAGAAGTGGTGCCAAATATGGCACAATAGCCAGAGGATTGGAATCCTCAT
** * * * * * ** ** *
33909 TGTCGAATTTCATTACCTCGGCTAGCTCGCCTTAAATGGTGCCAATTGTTCAACAAATGCACCCA
66 TACCGAATGTCACTACCTCAGCCAGCTCACCCCAAATACTGCCAATTATTCAACAAATGCACCCA
* * * * ***
33974 CACTAGCAGGTACGTCGACAAATTTCTTCGATAAATTTGTTTGGGCAACG-TCTTCTTCTTCTTC
131 CACTAGCAGGTACATCGACAAATTTCTCCGACAAATTTATCAAGGCAACGTTCTTCTTCTTCTTC
* * * *
34038 TTCTTCTTCTTCCTTCTCTTCTTTTTCATCTTTTTTTCTTTTCTCTTCTTTTGCTTCAATACCCA
196 TTCTTCTTCTTCCTTCTCTTCTTTTTCATCTTCTTTTCTTTTCTCTTCTTCTACTTCAATACCAA
* * *
34103 CAGAAGCAATTGGTGTGTGCTCTTCCGCAACAGCAGCCTCTCTCTCCACCATAGTGGCCCCCAAA
261 CAGAAGCAATAGGTGTGTGCTCTT---CAACAACAGCCTCTCCCTCCACCATAGTGGCCCCCAAA
* * *
34168 TTGTTCAAGAGTTCGTCGTCAAAGAGGCTGGCTA
323 CTATTCAAGAGTTCATCGTCAAAGAGGCTGGCTA
* *
34202 TCGATGGATGGATCTCAGTAAGTGGTGCCAAATATGGCACAATAGCTAGAGGATTGGAATCCTCA
1 TCGATGGATAGATCTCAG-AAGTGGTGCCAAATATGGCACAATAGCCAGAGGATTGGAATCCTCA
* * * * * *
34267 TTACCGGATGTGACTGCCTCAGCCAGCTCACCCCAAATACTTCCAATTATTTAACAGATGCACCC
65 TTACCGAATGTCACTACCTCAGCCAGCTCACCCCAAATACTGCCAATTATTCAACAAATGCACCC
* * * * *
34332 ACATTGGTAGGTGCATCGAGAAATTTCTCCGACAAATTTATCAAGGCAATGTCTTCTTCTTCTTC
130 ACACTAGCAGGTACATCGACAAATTTCTCCGACAAATTTATCAAGGCAA---------------C
*
34397 TTTTTCTTCTTCTTCTTCTTCTTCTTCTTCCTTCTCTTCTTTTTCATCTTCTTTTCTTTTCTCTT
180 --GTTCTTCTTCTTCTTCTTCTTCTTCTTCCTTCTCTTCTTTTTCATCTTCTTTTCTTTTCTCTT
* **
34462 CTTCTACTTTAATACCAACAGAAGCAATAGGTGTGTGCTCTTCAACAACAGCCTCTCCCTCCGTC
243 CTTCTACTTCAATACCAACAGAAGCAATAGGTGTGTGCTCTTCAACAACAGCCTCTCCCTCCACC
* * *
34527 ATAGTGGCCCCCAAACTATTCGAGAGTTCATCGTTAAAGAGGTTGGCTA
308 ATAGTGGCCCCCAAACTATTCAAGAGTTCATCGTCAAAGAGGCTGGCTA
34576 T
1 T
34577 GTTTCAAAAG
Statistics
Matches: 303, Mismatches: 53, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
358 16 0.05
359 126 0.42
374 64 0.21
377 97 0.32
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (356 bp):
TCGATGGATAGATCTCAGAAGTGGTGCCAAATATGGCACAATAGCCAGAGGATTGGAATCCTCAT
TACCGAATGTCACTACCTCAGCCAGCTCACCCCAAATACTGCCAATTATTCAACAAATGCACCCA
CACTAGCAGGTACATCGACAAATTTCTCCGACAAATTTATCAAGGCAACGTTCTTCTTCTTCTTC
TTCTTCTTCTTCCTTCTCTTCTTTTTCATCTTCTTTTCTTTTCTCTTCTTCTACTTCAATACCAA
CAGAAGCAATAGGTGTGTGCTCTTCAACAACAGCCTCTCCCTCCACCATAGTGGCCCCCAAACTA
TTCAAGAGTTCATCGTCAAAGAGGCTGGCTA
Found at i:34391 original size:3 final size:3
Alignment explanation
Indices: 34383--34466 Score: 104
Period size: 3 Copynumber: 29.0 Consensus size: 3
34373 CAAGGCAATG
*
34383 TCT TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TCCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT
* *
34429 TC- TCT TCT TTT TCA TCT TCT T-T TCT T-T TC- TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
34467 ACTTTAATAC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 8 0.11
3 59 0.84
4 3 0.04
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:38360 original size:41 final size:41
Alignment explanation
Indices: 38288--38451 Score: 186
Period size: 41 Copynumber: 4.0 Consensus size: 41
38278 AGGGTTAAGA
* * * *
38288 CCTGTTAAAATATACCGACACGAAGCCTGCTAGGCACAAAG
1 CCTGATAAAATACACCAACACTAAGCCTGCTAGGCACAAAG
* * *
38329 CCTGATCTAAA-ACACCAACACTAAGCTTGCTAGGCACAATG
1 CCTGAT-AAAATACACCAACACTAAGCCTGCTAGGCACAAAG
* * * *
38370 CTTGATAAAATACACCAACATTGAGCCTGTTAGGCACAAAG
1 CCTGATAAAATACACCAACACTAAGCCTGCTAGGCACAAAG
* * *
38411 CCCGATAAAATACACCAACACTAAGCCTACTAGGTACAAAG
1 CCTGATAAAATACACCAACACTAAGCCTGCTAGGCACAAAG
38452 TGATACGACC
Statistics
Matches: 100, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
40 3 0.03
41 94 0.94
42 3 0.03
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (41 bp):
CCTGATAAAATACACCAACACTAAGCCTGCTAGGCACAAAG
Found at i:38866 original size:39 final size:39
Alignment explanation
Indices: 38801--38921 Score: 147
Period size: 39 Copynumber: 3.2 Consensus size: 39
38791 TGGACATTTT
* *
38801 TATTAAATAG--GGTTTTAATGTGTCTTAGTTTGATTCA
1 TATTAAATAGTTGTTTTTAATGTGTCTTAGTTTGATACA
* *
38838 TATTAAATAGTTGTTTTTAATGTTTCTTATTTTGATACA
1 TATTAAATAGTTGTTTTTAATGTGTCTTAGTTTGATACA
* * * *
38877 TATTTAATAGTTGTTTTTAAGGTGTCTAAGTTTGAGACA
1 TATTAAATAGTTGTTTTTAATGTGTCTTAGTTTGATACA
*
38916 AATTAA
1 TATTAA
38922 TTTCATTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
37 10 0.14
39 60 0.86
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (39 bp):
TATTAAATAGTTGTTTTTAATGTGTCTTAGTTTGATACA
Found at i:38993 original size:32 final size:32
Alignment explanation
Indices: 38957--39019 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
38947 AGCCCAAATT
* *
38957 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
38989 AATTAGCTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
39020 TATGGATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.38
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Found at i:41878 original size:16 final size:17
Alignment explanation
Indices: 41851--41882 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41841 GAAGTAATAG
41851 TTGGATGAAATAATTAC
1 TTGGATGAAATAATTAC
41868 TTGGATG-AATAATTA
1 TTGGATGAAATAATTA
41883 TTATCTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (17 bp):
TTGGATGAAATAATTAC
Found at i:44473 original size:27 final size:27
Alignment explanation
Indices: 44435--44504 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
44425 GAGAATTCTG
*
44435 ATGACAAGAAATCTGATTCGGATGAGA
1 ATGACAAGAAATCTGATTCCGATGAGA
*
44462 ATGACAAGAAATCTGGTTCCGATGAGA
1 ATGACAAGAAATCTGATTCCGATGAGA
44489 ATGACAAGAAATCTGA
1 ATGACAAGAAATCTGA
44505 AGAGAACAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.21
Consensus pattern (27 bp):
ATGACAAGAAATCTGATTCCGATGAGA
Found at i:47012 original size:66 final size:66
Alignment explanation
Indices: 46906--47037 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
46896 CTATTGCTTC
46906 ATCTTCTTTCCTTGATTCTGACTGTGGTATGCTTGCAGATTTGCTGCTGCACTCAAAGATTTGAG
1 ATCTTCTTTCCTTGATTCTGACTGTGGTATGCTTGCAGATTTGCTGCTGCACTCAAAGATTTGAG
46971 T
66 T
46972 ATCTTCTTTCCTTGATTCTGACTGTGGTATGCTTGCAGATTTGCTGCTGCACTCAAAGATTTGAG
1 ATCTTCTTTCCTTGATTCTGACTGTGGTATGCTTGCAGATTTGCTGCTGCACTCAAAGATTTGAG
47037 T
66 T
47038 TTATGGGTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (66 bp):
ATCTTCTTTCCTTGATTCTGACTGTGGTATGCTTGCAGATTTGCTGCTGCACTCAAAGATTTGAG
T
Found at i:54411 original size:21 final size:21
Alignment explanation
Indices: 54385--54436 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
54375 CTGACTTCTT
54385 TGTCGTGACATACATGGGCTA
1 TGTCGTGACATACATGGGCTA
54406 TGTCGTGACATACATGGGCTA
1 TGTCGTGACATACATGGGCTA
54427 TGTCGTGACA
1 TGTCGTGACA
54437 ATGCCCGTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TGTCGTGACATACATGGGCTA
Found at i:57129 original size:2 final size:2
Alignment explanation
Indices: 57122--57158 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
57112 GTATAATAAT
*
57122 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AA AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
57159 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57851 original size:16 final size:17
Alignment explanation
Indices: 57817--57857 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
57807 ACTACAATGC
57817 AAATGCTAGAACAAAT-A
1 AAATGC-AGAACAAATAA
57834 AAATGCAGAGAC-AATAA
1 AAATGCAGA-ACAAATAA
57851 AAATGCA
1 AAATGCA
57858 ATGAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (17 bp):
AAATGCAGAACAAATAA
Found at i:63716 original size:227 final size:227
Alignment explanation
Indices: 63321--63774 Score: 829
Period size: 227 Copynumber: 2.0 Consensus size: 227
63311 CAAACTTATC
*
63321 AACATGGACTAGGACATCTTTAATCTATCCTTTAGGTTGTGCCAAAGATCTGTCTGCAAGTTGTA
1 AACATGGACTAGGACATCTTTAATCTATCCTTCAGGTTGTGCCAAAGATCTGTCTGCAAGTTGTA
*
63386 ATGTCACCGCAGTGGGCTTCAAATGACCAATCCATAATTTCCTGAAAGTTGACAATGGTATAAGG
66 ATGTCACCGCAGTGGGCTTCAAATAACCAATCCATAATTTCCTGAAAGTTGACAATGGTATAAGG
*
63451 TTAATGATAGCTCCTAGGTCACATAGAGCTTTACCTAAGTAATGGTTTCCAATAGAGCATGGAAT
131 TTAATGATAGCTCCTAGGTCACATAGAGCTTTACCTAAGTAATGGTTTCCAATAAAGCATGGAAT
63516 TGTGAAACTGCCAGGATCTTTCATTTTTGGTG
196 TGTGAAACTGCCAGGATCTTTCATTTTTGGTG
*
63548 AACATGGA-TGAGGACATCTTTAATCTATCCTTCAGGTTGTGCCAAAGATCTGTCTGTAAGTTGT
1 AACATGGACT-AGGACATCTTTAATCTATCCTTCAGGTTGTGCCAAAGATCTGTCTGCAAGTTGT
*
63612 AATGTCACCGTAGTGGGCTTCAAATAACCAATCCATAATTTCCTGAAAGTTGACAATGGTATAAG
65 AATGTCACCGCAGTGGGCTTCAAATAACCAATCCATAATTTCCTGAAAGTTGACAATGGTATAAG
*
63677 GTTAATGCTAGCTCCTAGGTCACATAGAGCTTTACCTAAGTAATGGTTTCCAATAAAGCATGGAA
130 GTTAATGATAGCTCCTAGGTCACATAGAGCTTTACCTAAGTAATGGTTTCCAATAAAGCATGGAA
*
63742 TTGTGAAACTGCTAGGATCTTTCATTTTTGGTG
195 TTGTGAAACTGCCAGGATCTTTCATTTTTGGTG
63775 GTAATTTATT
Statistics
Matches: 219, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
226 1 0.00
227 218 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (227 bp):
AACATGGACTAGGACATCTTTAATCTATCCTTCAGGTTGTGCCAAAGATCTGTCTGCAAGTTGTA
ATGTCACCGCAGTGGGCTTCAAATAACCAATCCATAATTTCCTGAAAGTTGACAATGGTATAAGG
TTAATGATAGCTCCTAGGTCACATAGAGCTTTACCTAAGTAATGGTTTCCAATAAAGCATGGAAT
TGTGAAACTGCCAGGATCTTTCATTTTTGGTG
Done.