Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007947.1 Kokia drynarioides strain JFW-HI SEQ_122595, 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: 84438
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Warning! 136 characters in sequence are not A, C, G, or T
Found at i:4137 original size:1 final size:1
Alignment explanation
Indices: 4090--4117 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
4080 TAAATGGAAA
4090 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
4118 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4138 original size:1 final size:1
Alignment explanation
Indices: 4128--4154 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
4118 NNNNNNNNNN
4128 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
4155 GACAAACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:10053 original size:12 final size:12
Alignment explanation
Indices: 10038--10070 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
10028 ACGAACAAGT
*
10038 TCGTTTATTGGC
1 TCGTTTATTGAC
10050 TCGTTTATTGAC
1 TCGTTTATTGAC
10062 TCGTTTATT
1 TCGTTTATT
10071 TACTAATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (12 bp):
TCGTTTATTGAC
Found at i:10183 original size:24 final size:23
Alignment explanation
Indices: 10156--10215 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
10146 TCATTAACAT
*
10156 TGTTCGCGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * **
10180 TGTTCATGAAAATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
10203 TGTTCGTGAACAT
1 TGTTCGTGAACAT
10216 CAAACAATCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:15926 original size:2 final size:2
Alignment explanation
Indices: 15919--15950 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15909 TTGAATTCCA
15919 AT AT AT 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 AT AT AT
15951 TGATTTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17353 original size:12 final size:12
Alignment explanation
Indices: 17338--17379 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
17328 GTACAATTAT
*
17338 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
17350 ATGTTCGTTTA-
1 ATGTTCGTGAAC
17361 ATGTTCGTGAAC
1 ATGTTCGTGAAC
17373 ATGTTCG
1 ATGTTCG
17380 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:17371 original size:23 final size:23
Alignment explanation
Indices: 17315--17384 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
17305 TCATTAACAT
* * *
17315 TGTTTGTGAACATGTACAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
17339 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
17362 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
17385 GTTAAATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 22 0.56
24 17 0.44
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:21463 original size:28 final size:28
Alignment explanation
Indices: 21427--21506 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
21417 TGAACCTCTT
* *
21427 AAAGAAAGCCTTTGTGGCTATCTCAATG
1 AAAGGAAGCCTGTGTGGCTATCTCAATG
* *
21455 AAAGGAAGCCTGTGTGG-TGATCTCAGTT
1 AAAGGAAGCCTGTGTGGCT-ATCTCAATG
* *
21483 AAAGGAAGTCTGTGTGGCGATCTC
1 AAAGGAAGCCTGTGTGGCTATCTC
21507 TGCTAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.02
28 43 0.98
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (28 bp):
AAAGGAAGCCTGTGTGGCTATCTCAATG
Found at i:23984 original size:25 final size:26
Alignment explanation
Indices: 23941--23991 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
23931 AAAAATAGTG
**
23941 TTTAACTGAGAAACTAAAAAC-AAAA
1 TTTAACTGAGAAAAAAAAAACTAAAA
*
23966 TTTAATTGAGAAAAAAAAAACTAAAA
1 TTTAACTGAGAAAAAAAAAACTAAAA
23992 AAATGCGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.22
Consensus pattern (26 bp):
TTTAACTGAGAAAAAAAAAACTAAAA
Found at i:27746 original size:31 final size:30
Alignment explanation
Indices: 27672--27753 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 30
27662 GATATGCAAT
* *
27672 TGTATACATG-AACTTTAATTTGGTGTAAT
1 TGTATACTTGAAACTTTAATTTGGTGTAAA
* *
27701 TATATAATTGAAACTTTAATTGTGGT-TCAAA
1 TGTATACTTGAAACTTTAATT-TGGTGT-AAA
27732 TGTATACTTGAAACTTTAATTT
1 TGTATACTTGAAACTTTAATTT
27754 TGATTTAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
29 7 0.16
30 12 0.27
31 25 0.57
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (30 bp):
TGTATACTTGAAACTTTAATTTGGTGTAAA
Found at i:28082 original size:12 final size:12
Alignment explanation
Indices: 28065--28095 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
28055 TAAATGTGTA
28065 TGTTATTATTAT
1 TGTTATTATTAT
28077 TGTTATTATTAT
1 TGTTATTATTAT
*
28089 TATTATT
1 TGTTATT
28096 TGTGGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (12 bp):
TGTTATTATTAT
Found at i:30079 original size:24 final size:27
Alignment explanation
Indices: 30025--30076 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30015 AAAAATAATT
30025 TTTGAGCCTTTAAAAGTTGATAAAAAAA
1 TTTGAGCCTTTAAAAGTT-ATAAAAAAA
30053 TTTGA-CCTTTAAAAGTTA-AAAAAA
1 TTTGAGCCTTTAAAAGTTATAAAAAA
30077 TTTTTGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.25
26 1 0.04
27 12 0.50
28 5 0.21
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.33
Consensus pattern (27 bp):
TTTGAGCCTTTAAAAGTTATAAAAAAA
Found at i:31371 original size:121 final size:123
Alignment explanation
Indices: 31179--31404 Score: 384
Period size: 121 Copynumber: 1.9 Consensus size: 123
31169 TAATTTTGAT
* * *
31179 ATTTGATTTATAAAGTGTTGCAATCGGAGTTAAAATATCAAAGTTTGAATTTGATTTAGCTTCTT
1 ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAGTCTGAATTTAATTTAGCTTCTT
*
31244 TTGTGCTGAATTTTTAACTTTTAATTTCAGTTCCAAGTTAGTATCTTTTTTAAAATTA
66 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTATCTTTTTTAAAATTA
* *
31302 ATTTGATTTAGAGAGTGTTGCAATCGGAGTT-AAATATCAAA-TCTGAATTTAATTTAGTTTCTT
1 ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAGTCTGAATTTAATTTAGCTTCTT
31365 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTA
66 TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTA
31405 TTAACTTTGA
Statistics
Matches: 97, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
121 58 0.60
122 10 0.10
123 29 0.30
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (123 bp):
ATTTGATTTAGAAAGTGTTGCAATCGGAGTTAAAATATCAAAGTCTGAATTTAATTTAGCTTCTT
TTGTGCTGAATTTTGAACTTTTAATTTCAGTTCCAAGTTAGTATCTTTTTTAAAATTA
Found at i:36574 original size:6 final size:6
Alignment explanation
Indices: 36563--36595 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
36553 CATTATTAGT
36563 GGGATA GGGATA GGGATA GGGATA GGGATA GGG
1 GGGATA GGGATA GGGATA GGGATA GGGATA GGG
36596 CATGTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.55, T:0.15
Consensus pattern (6 bp):
GGGATA
Found at i:37546 original size:31 final size:31
Alignment explanation
Indices: 37504--37611 Score: 109
Period size: 31 Copynumber: 3.6 Consensus size: 31
37494 ATAAATATCA
37504 AATTTG-TACATAAACTTTAGTTCAACGTGC
1 AATTTGATACATAAACTTTAGTTCAACGTGC
* * ** *
37534 AATTTGATACATAAATTTTAATT--TGGTAC
1 AATTTGATACATAAACTTTAGTTCAACGTGC
* *
37563 -ATTT-ATGCGTAAACTTTAGTTCAACGTGC
1 AATTTGATACATAAACTTTAGTTCAACGTGC
*
37592 AATTTGATACATAAATTTTA
1 AATTTGATACATAAACTTTA
37612 ATTTGGTACA
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
27 13 0.22
28 4 0.07
29 6 0.10
30 10 0.17
31 25 0.43
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (31 bp):
AATTTGATACATAAACTTTAGTTCAACGTGC
Found at i:37604 original size:58 final size:58
Alignment explanation
Indices: 37514--37631 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
37504 AATTTGTACA
37514 TAAACTTTAGTTCAACGTGCAATTTGATACATAAATTTTAATTTGGTACATTTATGCG
1 TAAACTTTAGTTCAACGTGCAATTTGATACATAAATTTTAATTTGGTACATTTATGCG
37572 TAAACTTTAGTTCAACGTGCAATTTGATACATAAATTTTAATTTGGTACATTTATGCG
1 TAAACTTTAGTTCAACGTGCAATTTGATACATAAATTTTAATTTGGTACATTTATGCG
37630 TA
1 TA
37632 TGAAATTTTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.42
Consensus pattern (58 bp):
TAAACTTTAGTTCAACGTGCAATTTGATACATAAATTTTAATTTGGTACATTTATGCG
Found at i:41473 original size:19 final size:20
Alignment explanation
Indices: 41432--41484 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
41422 AAAAATTACA
41432 AAATAATTCAAAATCAATTT
1 AAATAATTCAAAATCAATTT
*
41452 AAA-AATTCAAAAT-ATTTAT
1 AAATAATTCAAAATCAATT-T
*
41471 AAATAAATCAAAAT
1 AAATAATTCAAAAT
41485 TTATATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 14 0.48
20 12 0.41
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATTCAAAATCAATTT
Found at i:50452 original size:28 final size:29
Alignment explanation
Indices: 50390--50452 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 29
50380 TATACTTATT
*
50390 TGTA-TTTTTAATATATATATTTATAGTA
1 TGTATTTTTTAATATAAATATTTATAGTA
* **
50418 -GTGTTTTTTAATATAAATATTT-TTTTA
1 TGTATTTTTTAATATAAATATTTATAGTA
50445 TGTATTTT
1 TGTATTTT
50453 AAATGTGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (29 bp):
TGTATTTTTTAATATAAATATTTATAGTA
Found at i:51141 original size:69 final size:69
Alignment explanation
Indices: 51028--51397 Score: 364
Period size: 69 Copynumber: 5.4 Consensus size: 69
51018 TCGCAGGGGA
* *
51028 TCCAACACAGTTAGCTAGAGCAAAGCTCACAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
1 TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
51093 AACC
66 AACC
* * * * ** * * *
51097 TTCAACACAGTTAGCGAGAGCAAATCTCCCAATTGCCATATTAAGGCTCATAAGTAAAGAGTCAC
1 TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
*
51162 AGCC
66 AACC
** * * ** ** **
51166 TCCAACACAGTTAGTAAGAGCAAATCTCCCAACTATCATATTAAAACTCGCAGGTAATTAATCGC
1 TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
51231 AACC
66 AACC
* * * * * * * *
51235 TCTAACACAGTTAGCAATAACAAAACTCCCAACTGTCATATTAAGGCTTGCAGGTGAAGAGCTGC
1 TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
51300 AACC
66 AACC
* * * ** * * *
51304 TCCAACACAATTAACGAGAGTAAAGCTCCCAGGTGTCATATTACGACTCTCAGGTCAAA-AGCCG
1 TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGT-AAAGAGCCG
51368 CAACC
65 CAACC
* *
51373 TCCAACACAGTTCGAGAGAGCAAAG
1 TCCAACACAGTTAGCGAGAGCAAAG
51398 GCCCAACAAC
Statistics
Matches: 236, Mismatches: 64, Indels: 2
0.78 0.21 0.01
Matches are distributed among these distances:
69 234 0.99
70 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (69 bp):
TCCAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATATTAAGGCTCGCAGGTAAAGAGCCGC
AACC
Found at i:51575 original size:39 final size:37
Alignment explanation
Indices: 51519--51594 Score: 98
Period size: 39 Copynumber: 2.0 Consensus size: 37
51509 GCTATCATAT
* * *
51519 TAATTATATTTGAAATAATTAATTTATATTTATTAAAAA
1 TAATTATATTCGAAATAATT-ATTT-GATTTAATAAAAA
*
51558 TAATTATATTCGTAATAATTATTTGATTTAATAAAAA
1 TAATTATATTCGAAATAATTATTTGATTTAATAAAAA
51595 AAGAGCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 11 0.33
38 4 0.12
39 18 0.55
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TAATTATATTCGAAATAATTATTTGATTTAATAAAAA
Found at i:56606 original size:20 final size:19
Alignment explanation
Indices: 56557--56607 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
56547 CATTATTTCA
56557 AAAAATAAATAA-ATAAATT
1 AAAAATAAA-AATATAAATT
** *
56576 ATTAATTAAAATGATAAATT
1 AAAAATAAAAAT-ATAAATT
56596 AAAAATAAAAAT
1 AAAAATAAAAAT
56608 TTGAAAATAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
18 2 0.08
19 6 0.25
20 16 0.67
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATAAAAATATAAATT
Found at i:57152 original size:22 final size:21
Alignment explanation
Indices: 57127--57174 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
57117 TATTTATATT
57127 TAATAATATAATAAATTATTAA
1 TAATAATATAATAAATT-TTAA
* **
57149 TAATTAATGTAATTTATTTTAA
1 TAA-TAATATAATAAATTTTAA
57171 TAAT
1 TAAT
57175 TTTTTTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 10 0.45
23 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAATAATATAATAAATTTTAA
Found at i:64487 original size:195 final size:195
Alignment explanation
Indices: 64069--64515 Score: 560
Period size: 195 Copynumber: 2.3 Consensus size: 195
64059 GAAATCGACG
* * *
64069 CGATGGTTGGGGTACCGCATATGTTGCAAGTCCTCAACAGCTCGTGTGAGCAGCATCGTGAGTCG
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
* *
64134 AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATTTATGCATAAGT
66 AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGC
* * * * * * *
64199 GCATTTTCTCGACAGTTTGTGTGAGCAGCATCGTTAGGGAACAGTTATATGCACAAATACCGTAT
131 GCATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAAGGAACAGTTATATACACAAACACCGTAC
* * **
64264 CGATGGCTGAGGCGCCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
* * * * * * * * *
64329 AGAAA-GAGATATGGATTCTA-AATGGATTATAGGCCCTACGATGGTTGGGA-CTATGCTTTA-C
66 AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGC
* *
64390 GCATATTCTCGACAGCTCGTGTGAGCAGCATTGTTAAGGAACAGTTTATAGTACAGACAAGCACC
131 GCATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAAGGAACAG-TTATA-TAC--ACAAACACC
64455 GTAC
192 GTAC
* * *
64459 CTATGGTTGGGGTACCACATACGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
1 CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATC
64516 AAGTACTGGT
Statistics
Matches: 214, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
191 39 0.18
192 12 0.06
193 30 0.14
194 10 0.05
195 123 0.57
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (195 bp):
CGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGACTCG
AGAAATGAGAAAAGAATCCAAGAATGGATTACAGGCCCTACGATGGTTGAGATCTATGCATAAGC
GCATATTCTCGACAGCTCGTGTGAGCAGCATCGTTAAGGAACAGTTATATACACAAACACCGTAC
Found at i:67295 original size:2 final size:2
Alignment explanation
Indices: 67288--67340 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
67278 TAATGCTATC
67288 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
67330 AT AT AT AT AT A
1 AT AT AT AT AT A
67341 CTAAATAAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:73946 original size:26 final size:25
Alignment explanation
Indices: 73883--73946 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
73873 AAACTTAATA
* *
73883 ACAAAATTTAACTTAAAATTTAAAC
1 ACAAAATTTAAATTAAAATTGAAAC
* *
73908 ACATACATCTAAATTAAAATTGAAAC
1 ACA-AAATTTAAATTAAAATTGAAAC
*
73934 TTCAAAATTTAAA
1 -ACAAAATTTAAA
73947 AATACATAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
25 3 0.10
26 25 0.83
27 2 0.07
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (25 bp):
ACAAAATTTAAATTAAAATTGAAAC
Found at i:75404 original size:3 final size:3
Alignment explanation
Indices: 75398--75437 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
75388 AAAGTGGTGG
*
75398 TGA TGA TGA TGA TGA TGA TGA TGG TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
75438 CAGGCCCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:81990 original size:17 final size:17
Alignment explanation
Indices: 81965--82018 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
81955 CCCAATCAAC
81965 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* * *
81982 TTAAGTTTATTCTAAAT
1 TTAAATTTATTTTAAAA
*
81999 TTAAATTTGGTTTTAAAA
1 TTAAATTT-ATTTTAAAA
82017 TT
1 TT
82019 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 21 0.72
18 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.54
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:83907 original size:29 final size:30
Alignment explanation
Indices: 83795--83906 Score: 126
Period size: 29 Copynumber: 3.8 Consensus size: 30
83785 TAGTGGTCCC
83795 CGAACCTTCCAAAAATTACCATTTTACCC-
1 CGAACCTTCCAAAAATTACCATTTTACCCT
* * * *
83824 CAAAACTTCCAAAAA-TCCCATTTTGGAACCT
1 CGAACCTTCCAAAAATTACCATTTT--ACCCT
83855 -GAACCTTCCAAAAATTACCATTTTACCCT
1 CGAACCTTCCAAAAATTACCATTTTACCCT
*
83884 CGAA-CTTCCAAAAA-TCCCATTTT
1 CGAACCTTCCAAAAATTACCATTTT
83907 TGACTCCGAA
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
28 16 0.23
29 27 0.39
30 18 0.26
31 8 0.12
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (30 bp):
CGAACCTTCCAAAAATTACCATTTTACCCT
Found at i:83916 original size:29 final size:28
Alignment explanation
Indices: 83793--83927 Score: 89
Period size: 29 Copynumber: 4.6 Consensus size: 28
83783 CCTAGTGGTC
*
83793 CCCGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCGAA-CTTCCAAAAA-TCCCATTTTTGA
* *
83821 CCCCAAAACTTCCAAAAATCCCATTTTGGAA
1 -CCC-GAACTTCCAAAAATCCCATTTTTG-A
* *
83852 CCTGAACCTTCCAAAAATTACCA-TTTT-A
1 CCCGAA-CTTCCAAAAA-TCCCATTTTTGA
83880 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 -CC-CGAACTTCCAAAAATCCCATTTTTGA
* *
83910 CTCCGAACATCTAAAAAT
1 C-CCGAACTTCCAAAAAT
83928 TACTACTTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
28 9 0.11
29 48 0.57
30 22 0.26
31 5 0.06
ACGTcount: A:0.36, C:0.31, G:0.05, T:0.27
Consensus pattern (28 bp):
CCCGAACTTCCAAAAATCCCATTTTTGA
Done.