Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014556.1 Kokia drynarioides strain JFW-HI SEQ_129595, 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: 28804
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Warning! 43 characters in sequence are not A, C, G, or T
Found at i:3430 original size:81 final size:81
Alignment explanation
Indices: 3338--4084 Score: 889
Period size: 81 Copynumber: 9.2 Consensus size: 81
3328 CTTGATTAGG
* * * * * * * *
3338 GGTAAAAGATTGGATGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3403 TTTGCCCCATGGTCGA
66 TCTGCCCCATGGTCGA
* * *
3419 GGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAAAAGATTGGATGACTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3484 TCTGCCCCATGGTCGG
66 TCTGCCCCATGGTCGA
* *
3500 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3565 TCTGCCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * *
3580 GGGTAAGAGATT-GAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 -GGTAAGAGATTGGA-TGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
3644 AATCTGCCCCATGGTC-A
64 AATCTGCCCCATGGTCGA
**
3661 GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATAACTTCA
1 -GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
* * * *
3726 ATTTGCCCCATGATTGG
65 ATCTGCCCCATGGTCGA
* * * *
3743 GGTAAGAGATTGAATGATGTCTTCAATCTACCCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
*
3808 TCTGCCTCATGGTC-A
66 TCTGCCCCATGGTCGA
* ** * *
3823 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTATTAGGGTAAAAGATTAGATGGTTTC
1 -GGTAAGAGA-TTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTC
* * *
3886 AATCTGCCCCTTGGTTGG
64 AATCTGCCCCATGGTCGA
* * *
3904 GGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGTAAAAGATTGGATGGCTTTAA
1 GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
** *
3969 TCTATCCTATGGTC-A
66 TCTGCCCCATGGTCGA
* * * * * *
3984 GAGTAAGAGATTAGATAGTGTCTTCAATATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCA
1 G-GTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCA
*
4049 ATCTGTCCCATGGTCTG-
65 ATCTGCCCCATGGTC-GA
*
4066 GGTAAGAGATTTGATGGTG
1 GGTAAGAGATTGGATGGTG
4085 ATGTAATTTC
Statistics
Matches: 570, Mismatches: 84, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
80 69 0.12
81 498 0.87
82 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (81 bp):
GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAA
TCTGCCCCATGGTCGA
Found at i:3790 original size:243 final size:243
Alignment explanation
Indices: 3337--4084 Score: 978
Period size: 243 Copynumber: 3.1 Consensus size: 243
3327 TCTTGATTAG
* * * *
3337 GGGTAAAAGATTGGA-TGGTGTTTTAAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
* * *
3401 AATTTGCCCCATGGTCGAGGTAAGAGATTGAATGGTGTCTTCAATCTGCCTTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTCG-GGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* *
3466 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGGATGGTGTCTTCAATCTGC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
* *
3531 CCTCTAGCTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
* * * *
3580 GGGTAAGAGA-TTGAGTGGTGTCTTCAATTTTCCCTCTGGTTATGATAAAAGATTGAATGGCTTC
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
3644 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
66 AATCTGCCCCATGGTC-GGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAA
* * * * *
3709 AAGATTGGATAACTTCAATTTGCCCCATGATTGGGGTAAGAGATTGAATGATGTCTTCAATCTAC
130 AAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGC
*
3774 CCTCTGGTTAGGGTAAAAGATTGGTTGGCTTCAATCTG-CCTCATGGTCA
195 CCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCT-ATGGTCA
* * *
3823 GGGTAAGA-ATTTGAAT-GTGTCTTCAATCTGCCCTCTTA-TTAGGGTAAAAGATT-AGATGGTT
1 GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTC-TAGTTAGGGTAAAAGATTGA-ATGGTT
* * * *
3884 TCAATCTGCCCCTTGGTTGGGGTAAGAGATTGGATGGTGTCTTCAATCTGCTCTCTGATTAGGGT
64 TCAATCTGCCCCATGG-TCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGT
* * ** * * *
3949 AAAAGATTGGATGGCTTTAATCTATCCTATGGTCAGAGTAAGAGATT-AGAT-AGTGTCTTCAAT
128 AAAAGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGA-ATGA-TGTCTTCAAT
* * * * *
4012 ATGCTCTCTGGTTAGGGTAAAAGATTTGATGGGTTCAATCTGTCCC-ATGGTCT
191 CTGCCCTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTG-CCCTATGGTCA
4065 GGGTAAGAGATTTGA-TGGTG
1 GGGTAAGAGATTTGAGTGGTG
4085 ATGTAATTTC
Statistics
Matches: 442, Mismatches: 50, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
241 3 0.01
242 200 0.45
243 236 0.53
244 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (243 bp):
GGGTAAGAGATTTGAGTGGTGTCTTCAATTTTCCCTCTAGTTAGGGTAAAAGATTGAATGGTTTC
AATCTGCCCCATGGTCGGGTAAGAGATTGGATGGTGTCTTCAATCTGCCCTCTGGTTAGGGTAAA
AGATTGGATGACTTCAATCTGCCCCATGGTCGGGGTAAGAGATTGAATGATGTCTTCAATCTGCC
CTCTGGTTAGGGTAAAAGATTGGATGGCTTCAATCTGCCCTATGGTCA
Found at i:4414 original size:93 final size:92
Alignment explanation
Indices: 4193--4800 Score: 357
Period size: 93 Copynumber: 6.4 Consensus size: 92
4183 GGTTTTGAAA
* * * * *** *
4193 CTTCACTCCATTCCACTTTAACCTTAGGGACATTAAGATCTGCTT-TTGGCTTTAATCTGA-CCT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCC-
* * * *
4256 ACAGCAACTTC-AGTGGTATAGGATCTAGTG
63 ACTGTAACTTCAAG-GATATAGGATCTGGTG
** *** * *
4286 CTTCACTCCATTCTGCTGTAACCTCAAACACATTGAGATTCATTACTCATTTTAATCCAATTCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
4351 TGTAACTTCAAGGATATAGGATCTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *** * **
4379 CTTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTT-CGTTGCTTTAATTCGGCCC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTAC-TCATTTTAATCCGATCC
* * * * *
4443 ATTATAACTT-ATGGGTATAGGATTTGGTATTG
63 ACTGTAACTTCAAGGATATAGGATCTGG---TG
* * * * *
4475 TAACTTCTCTCCATTCCACTGTAACCTTAGGGACATTGAGATCCGTACTCATTTTAATCCAATCC
1 ---CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCC
* * *
4540 ATTGCAACTTCAAAGATATAGGATCTGGTG
63 ACTGTAACTTCAAGGATATAGGATCTGGTG
* * * ** ** * *
4570 CTTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAATCTGACCCA
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT-T-CTTACTCATTTTAATCCGATCCA
** * * * *
4635 CTACAAC-TCTGAGG-TATGGGATTTGATATTGTAA
64 CTGTAACTTC-AAGGATATAGGATCTG-----GT-G
* * * * * * *
4669 CTTCTCTCCATTCCACTATAACCTTAGAGACATTAAGATTCGTTACTCATTTTGATTCGATCCAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTC-TTACTCATTTTAATCCGATCCAC
* * *
4734 TGTAACTTTAGGGATATAGGATTTGGTG
65 TGTAACTTCAAGGATATAGGATCTGGTG
* *
4762 CTTCACTCCATTCCATTGTAATCTCAGGGACATTGAGAT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGAT
4801 CTGCTTCATT
Statistics
Matches: 381, Mismatches: 107, Indels: 54
0.70 0.20 0.10
Matches are distributed among these distances:
91 1 0.00
92 37 0.10
93 154 0.40
94 47 0.12
95 3 0.01
96 2 0.01
97 21 0.06
98 38 0.10
99 78 0.20
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (92 bp):
CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATTCTTACTCATTTTAATCCGATCCACT
GTAACTTCAAGGATATAGGATCTGGTG
Found at i:4513 original size:192 final size:193
Alignment explanation
Indices: 4315--4849 Score: 695
Period size: 191 Copynumber: 2.8 Consensus size: 193
4305 AACCTCAAAC
*
4315 ACATTGAGATTCATTACTCATTTTAATCCAATTCACTGTAACTTCAAGGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * *
4380 TTCACTCCATTCCACTGTAACCTCAGGGATATTGAGATCTGCTTCGTTGCTTTAATTC-GGCCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* * * * *
4444 TTATAACTTATG-GGTATAGGATTTGGTATTGTAACTTCTCTCCATTCCACTGTAACCTTAGGG
131 CTACAAC-TATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
** * * *
4507 ACATTGAGA-TCCGTACTCATTTTAATCCAATCCATTGCAACTTCAAAGATATAGGATCTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
4571 TTCACTCTATTCCACTGTAGCCTCAAGGACATTGAGATCTGCTTTGTTGTTTTAA-TCTGACCCA
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
* *
4635 CTACAACTCTGAGGTATGGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
131 CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
* * * * * * * *
4698 ACATTAAGATTCGTTACTCATTTTGATTCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGC
1 ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
* * * *
4763 TTCACTCCATTCCATTGTAATCTCAGGGACATTGAGATCTGCTTCATTGTTTTAA-TCTG-CTTC
66 TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGAC-CC
* * *
4826 ACTTCAACTTTGAGGTATAAGATT
130 ACTACAACTATGAGGTATAGGATT
4850 CACCATTACA
Statistics
Matches: 295, Mismatches: 44, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
190 5 0.02
191 164 0.56
192 126 0.43
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (193 bp):
ACATTGAGATTCATTACTCATTTTAATCCAATCCACTGTAACTTCAAGGATATAGGATCTGGTGC
TTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCGTTGTTTTAATTCTGACCCA
CTACAACTATGAGGTATAGGATTTGATATTGTAACTTCTCTCCATTCCACTATAACCTTAGAG
Found at i:5078 original size:49 final size:49
Alignment explanation
Indices: 5023--5328 Score: 307
Period size: 49 Copynumber: 6.2 Consensus size: 49
5013 TCACCTTCAA
* *
5023 GGTATAAGATTCTCTATTGC-AGCTTCAATCTTTGCCTTCACATCTCTAG
1 GGTATAAGATTCTCCATTGCGA-CTTCAATCTTTCCCTTCACATCTCTAG
* * * *
5072 GCTATAAGATT-TGTCATTGCGGCTTCAAT-TGTTCACCCT-ACATCTCTAG
1 GGTATAAGATTCT-CCATTGCGACTTCAATCT-TTC-CCTTCACATCTCTAG
* * * *
5121 GGTACAAGATTCACCGTTGCGACTTCAATCTTTCCCTTCACGTCTCTAG
1 GGTATAAGATTCTCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * * * *
5170 GGTAGAAGATTCACCATTACGACTTCAATCTTTCCCTTCATATCTTTAG
1 GGTATAAGATTCTCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * * ** *
5219 GGTACAAGATTCGT-TATTGCGACTTTAATCTTTCCCTTCTTATCTCTAA
1 GGTATAAGATTC-TCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
* * * *
5268 GGTAAAAGATTCGCCATTGGGACTTCAATCTTTCCCTTCACATCTTTAG
1 GGTATAAGATTCTCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
5317 GGTATAAGATTC
1 GGTATAAGATTC
5329 AACGTTTCCT
Statistics
Matches: 210, Mismatches: 38, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
48 5 0.02
49 201 0.96
50 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.15, T:0.37
Consensus pattern (49 bp):
GGTATAAGATTCTCCATTGCGACTTCAATCTTTCCCTTCACATCTCTAG
Found at i:5130 original size:98 final size:97
Alignment explanation
Indices: 4979--5328 Score: 329
Period size: 98 Copynumber: 3.6 Consensus size: 97
4969 CTATAGTCTT
* * * * *
4979 AAGATTCGCCTTTGCGGCTTCAATCTGATTTTCC-TCAC--CTTCAAGGTATAAGATTCTCTATT
1 AAGATTCGCCATTGCGGCTTCAATC---TTTCCCTTCACATCTTTAGGGTACAAGATTCTCTATT
* *
5041 GC-AGCTTCAATCTTTGCCTTCACATCTCTAGGCTAT
63 GCGA-CTTCAATCTTTCCCTTCACATCTCTAGG-TAA
* * * * * **
5077 AAGATTTGTCATTGCGGCTTCAAT-TGTTCACCCT-ACATCTCTAGGGTACAAGATTCACCGTTG
1 AAGATTCGCCATTGCGGCTTCAATCT-TTC-CCTTCACATCTTTAGGGTACAAGATTCTCTATTG
* *
5140 CGACTTCAATCTTTCCCTTCACGTCTCTAGGGTAG
64 CGACTTCAATCTTTCCCTTCACATCTCTA-GGTAA
* * * *
5175 AAGATTCACCATTACGACTTCAATCTTTCCCTTCATATCTTTAGGGTACAAGATTCGT-TATTGC
1 AAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTTTAGGGTACAAGATTC-TCTATTGC
* **
5239 GACTTTAATCTTTCCCTTCTTATCTCTAAGGTAA
65 GACTTCAATCTTTCCCTTCACATCTCT-AGGTAA
*
5273 AAGATTCGCCATTG-GGACTTCAATCTTTCCCTTCACATCTTTAGGGTATAAGATTC
1 AAGATTCGCCATTGCGG-CTTCAATCTTTCCCTTCACATCTTTAGGGTACAAGATTC
5329 AACGTTTCCT
Statistics
Matches: 205, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
94 1 0.00
95 2 0.01
96 4 0.02
97 5 0.02
98 188 0.92
99 5 0.02
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (97 bp):
AAGATTCGCCATTGCGGCTTCAATCTTTCCCTTCACATCTTTAGGGTACAAGATTCTCTATTGCG
ACTTCAATCTTTCCCTTCACATCTCTAGGTAA
Found at i:6292 original size:22 final size:23
Alignment explanation
Indices: 6266--6318 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
6256 TCGACTACTC
*
6266 CTTTTTTTCTTTTTTTTC-TTCT
1 CTTTTTTTCTCTTTTTTCTTTCT
*
6288 TTTTTTTTCTCTTTTTTCTTTCT
1 CTTTTTTTCTCTTTTTTCTTTCT
6311 CTTTTTTT
1 CTTTTTTT
6319 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
CTTTTTTTCTCTTTTTTCTTTCT
Found at i:6293 original size:13 final size:12
Alignment explanation
Indices: 6267--6318 Score: 72
Period size: 13 Copynumber: 4.3 Consensus size: 12
6257 CGACTACTCC
6267 TTTTTT-TC-TT
1 TTTTTTCTCTTT
6277 TTTTTTCTTCTTT
1 TTTTTTC-TCTTT
6290 TTTTTTCTCTTT
1 TTTTTTCTCTTT
6302 TTTCTTTCTCTTT
1 TTT-TTTCTCTTT
6315 TTTT
1 TTTT
6319 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 6 0.16
12 11 0.29
13 21 0.55
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:10227 original size:82 final size:82
Alignment explanation
Indices: 10090--10241 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 82
10080 CTAGTATACT
* * * * *
10090 ATGCTGCTCACAAAAGTTGATGAGAAACTGCAACATATGCAGAAACTCAGCCATCG-ATATGGTC
1 ATGCTGCTCACAAAAGCTAATGAGAAACCGCAACATATGAAGAAACTCAGCCATCGTA-AAGGTC
10154 CATAATTTCCCACTCCTG
65 CATAATTTCCCACTCCTG
* * * * *
10172 ATGCTGCTCACACAAGCTAATGAGAATCCGTAACGTATGAAGAAACTCATCCATCGTAAAGGTCC
1 ATGCTGCTCACAAAAGCTAATGAGAAACCGCAACATATGAAGAAACTCAGCCATCGTAAAGGTCC
10237 ATAAT
66 ATAAT
10242 ATTAGTTTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
82 58 0.98
83 1 0.02
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (82 bp):
ATGCTGCTCACAAAAGCTAATGAGAAACCGCAACATATGAAGAAACTCAGCCATCGTAAAGGTCC
ATAATTTCCCACTCCTG
Found at i:19018 original size:13 final size:14
Alignment explanation
Indices: 19001--19040 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
18991 CAACAAACAT
19001 TTTTTCTTCTTTTC
1 TTTTTCTTCTTTTC
19015 -TTTTC-TCTTTTC
1 TTTTTCTTCTTTTC
19027 TTTTTCTTTCTTTT
1 TTTTTC-TTCTTTT
19041 TTTCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 7 0.30
13 10 0.43
15 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTCTTTTC
Found at i:19025 original size:12 final size:12
Alignment explanation
Indices: 19002--19040 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
18992 AACAAACATT
19002 TTTTCTTCTTTTC
1 TTTTC-TCTTTTC
19015 TTTTCTCTTTTC
1 TTTTCTCTTTTC
19027 TTTT-TC-TTTC
1 TTTTCTCTTTTC
19037 TTTT
1 TTTT
19041 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 8 0.31
11 2 0.08
12 11 0.42
13 5 0.19
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:19042 original size:17 final size:20
Alignment explanation
Indices: 19000--19042 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
18990 ACAACAAACA
19000 TTTTTTCTTCTTTTCTTTTC
1 TTTTTTCTTCTTTTCTTTTC
*
19020 TCTTTTC-T-TTTTC-TTTC
1 TTTTTTCTTCTTTTCTTTTC
19037 TTTTTT
1 TTTTTT
19043 TCATTTTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 9 0.43
18 5 0.24
19 1 0.05
20 6 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTCTTCTTTTCTTTTC
Found at i:21804 original size:15 final size:14
Alignment explanation
Indices: 21778--21816 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
21768 GCAAAGAATT
* *
21778 TAAAACAAAACAAG
1 TAAAAGAAAACAAA
21792 TAAAAGTAAAACAAA
1 TAAAAG-AAAACAAA
21807 TAAAAGAAAA
1 TAAAAGAAAA
21817 GGTGAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.74, C:0.08, G:0.08, T:0.10
Consensus pattern (14 bp):
TAAAAGAAAACAAA
Found at i:21816 original size:20 final size:20
Alignment explanation
Indices: 21778--21817 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
21768 GCAAAGAATT
*
21778 TAAAACAAAACAAGTAAAAG
1 TAAAACAAAAAAAGTAAAAG
21798 TAAAACAAATAAAAG-AAAAG
1 TAAAACAAA-AAAAGTAAAAG
21818 GTGAAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.72, C:0.07, G:0.10, T:0.10
Consensus pattern (20 bp):
TAAAACAAAAAAAGTAAAAG
Done.