Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010135.1 Kokia drynarioides strain JFW-HI SEQ_124930, 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: 84465
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:4341 original size:15 final size:15
Alignment explanation
Indices: 4318--4347 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4308 GAGTTGCGGG
4318 TATGAATTGTCTTAA
1 TATGAATTGTCTTAA
*
4333 TATGTATTGTCTTAA
1 TATGAATTGTCTTAA
4348 AACCATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (15 bp):
TATGAATTGTCTTAA
Found at i:7098 original size:59 final size:59
Alignment explanation
Indices: 6991--7280 Score: 197
Period size: 59 Copynumber: 4.9 Consensus size: 59
6981 TAAACATTTA
* *
6991 GGGGTAAAAGGGTAA-TTTTGAGAGTTTCAAGGTCGAAAATGGAGTTTTTGGACA-TCCG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCGAAAATGGAGTTTTTGGA-AGTCCG
* *
7049 GGGGTAAAATGGTAATTTTTGAAAGTTTC-AGTGT-TAAGAATGTGA-TTTTTGGAAGTTCG
1 GGGGTAAAATGGTAATTTTTGAAAGTTTCAAG-GTCGAA-AATG-GAGTTTTTGGAAGTCCG
* *** * **
7108 GGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATGG-GATTTTTGGAAGTTTG
1 GGGGT-AAAATGGTAATTTTTGAAAGTTTCAAGGTCGAAAATGGAG-TTTTTGGAAGTCCG
* * *** * ***
7167 AGGGTAAAAATGG-AATTTTTGGAAATTTTTGGGGTCAAAAATAGGA-TTTTTGGAAGTTTA
1 GGGGT-AAAATGGTAATTTTT-GAAAGTTTCAAGGTCGAAAAT-GGAGTTTTTGGAAGTCCG
* * *
7227 GGGGTAAAAATGG-AATTTTTGGAAGTTTCGAGGTCAAAAATAGGA-TTTTTGGAA
1 GGGGT-AAAATGGTAATTTTTGAAAGTTTCAAGGTCGAAAAT-GGAGTTTTTGGAA
7281 TTTTTGAACA
Statistics
Matches: 201, Mismatches: 18, Indels: 25
0.82 0.07 0.10
Matches are distributed among these distances:
58 20 0.10
59 116 0.58
60 63 0.31
61 2 0.01
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCGAAAATGGAGTTTTTGGAAGTCCG
Found at i:7125 original size:29 final size:29
Alignment explanation
Indices: 7026--7280 Score: 207
Period size: 30 Copynumber: 8.6 Consensus size: 29
7016 TTCAAGGTCG
* *
7026 AAAATGGAGTTTTTGGACA-TCCGGGGGT-
1 AAAATGGAATTTTTGGA-AGTTCGGGGGTA
* * * *
7054 AAAATGGTAATTTTTGAAAGTTTCAGTGTTA
1 AAAATGG-AATTTTTGGAAG-TTCGGGGGTA
*
7085 AGAATGTG-ATTTTTGGAAGTTCGGGGGTA
1 AAAATG-GAATTTTTGGAAGTTCGGGGGTA
**
7114 AAAATGGAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGGGGGT-A
* * *
7144 AAAATGGGATTTTTGGAAGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGGGGGTA
* **
7173 AAAATGGAATTTTTGGAAATTTTTGGGGTCA
1 AAAATGGAATTTTTGG-AAGTTCGGGGGT-A
**
7204 AAAATAGG-ATTTTTGGAAGTTTAGGGGTA
1 AAAAT-GGAATTTTTGGAAGTTCGGGGGTA
*
7233 AAAATGGAATTTTTGGAAGTTTC-GAGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGGGGGT-A
7263 AAAATAGG-ATTTTTGGAA
1 AAAAT-GGAATTTTTGGAA
7281 TTTTTGAACA
Statistics
Matches: 188, Mismatches: 25, Indels: 26
0.79 0.10 0.11
Matches are distributed among these distances:
28 11 0.06
29 75 0.40
30 78 0.41
31 21 0.11
32 3 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGGGGGTA
Found at i:7223 original size:60 final size:59
Alignment explanation
Indices: 7092--7280 Score: 299
Period size: 59 Copynumber: 3.2 Consensus size: 59
7082 TTAAGAATGT
* * *
7092 GATTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGG
1 GATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAG
*
7151 GATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAATTTTTGGGGTCAAAAATAG
1 GATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGG-AAGTTTTGGGGTCAAAAATAG
* *
7211 GATTTTTGGAAGTTT-AGGGGTAAAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATAG
1 GATTTTTGGAAGTTTGA-GGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAG
7270 GATTTTTGGAA
1 GATTTTTGGAA
7281 TTTTTGAACA
Statistics
Matches: 121, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
59 66 0.55
60 55 0.45
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (59 bp):
GATTTTTGGAAGTTTGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATAG
Found at i:8361 original size:16 final size:16
Alignment explanation
Indices: 8340--8393 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
8330 ACATTATTTA
8340 TTATTATTAAAAATAT
1 TTATTATTAAAAATAT
*
8356 TTATTATT---ATTA-
1 TTATTATTAAAAATAT
* *
8368 ATATTATTAAAAACAT
1 TTATTATTAAAAATAT
8384 TTATTATTAA
1 TTATTATTAA
8394 TAGTCATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 8
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
15 2 0.07
16 17 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATTATTAAAAATAT
Found at i:8362 original size:22 final size:21
Alignment explanation
Indices: 8319--8368 Score: 86
Period size: 19 Copynumber: 2.5 Consensus size: 21
8309 TTTCCTTTTT
8319 TTATTATTAAAACATTATTTA
1 TTATTATTAAAACATTATTTA
8340 TTATTATTAAAA-A-TATTTA
1 TTATTATTAAAACATTATTTA
8359 TTATTATTAA
1 TTATTATTAA
8369 TATTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 16 0.55
20 1 0.03
21 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATTATTAAAACATTATTTA
Found at i:8375 original size:19 final size:19
Alignment explanation
Indices: 8319--8375 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
8309 TTTCCTTTTT
8319 TTATTATTAAAACATTATTTA
1 TTATTATT-AAA-ATTATTTA
*
8340 TTATTATTAAAAATATTTA
1 TTATTATTAAAATTATTTA
*
8359 TTATTATTAATATTATT
1 TTATTATTAAAATTATT
8376 AAAAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 22 0.67
20 3 0.09
21 8 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATTATTAAAATTATTTA
Found at i:8379 original size:28 final size:29
Alignment explanation
Indices: 8332--8392 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
8322 TTATTAAAAC
* *
8332 ATTATTTATTATTATTAAAAATATTTATT
1 ATTATTTAATATTATTAAAAACATTTATT
8361 ATTA-TTAATATTATTAAAAACATTTATT
1 ATTATTTAATATTATTAAAAACATTTATT
8389 ATTA
1 ATTA
8393 ATAGTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 26 0.87
29 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTATTTAATATTATTAAAAACATTTATT
Found at i:9086 original size:17 final size:16
Alignment explanation
Indices: 9064--9148 Score: 91
Period size: 17 Copynumber: 5.1 Consensus size: 16
9054 TTGGACTTTC
*
9064 TAAATTTAATTTTATAA
1 TAAATTTAATTTCA-AA
9081 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
9098 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
*
9115 TAAACTTAAATTT-AAA
1 TAAA-TTTAATTTCAAA
* *
9131 TAAATTCAATTTCCAA
1 TAAATTTAATTTCAAA
9147 TA
1 TA
9149 GGTCCAGACA
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
15 7 0.11
16 11 0.18
17 35 0.57
18 8 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTCAAA
Found at i:9102 original size:34 final size:32
Alignment explanation
Indices: 9064--9148 Score: 107
Period size: 34 Copynumber: 2.6 Consensus size: 32
9054 TTGGACTTTC
* *
9064 TAAATTTAATTTTATAATAAATTTAAATTTCAAA
1 TAAATTTAATTTCA-AATAAACTTAAATTT-AAA
9098 TAAATTTAAATTTCAAATAAACTTAAATTTAAA
1 TAAATTT-AATTTCAAATAAACTTAAATTTAAA
* *
9131 TAAATTCAATTTCCAATA
1 TAAATTTAATTTCAAATA
9149 GGTCCAGACA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
32 10 0.22
33 9 0.20
34 21 0.46
35 6 0.13
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (32 bp):
TAAATTTAATTTCAAATAAACTTAAATTTAAA
Found at i:9148 original size:16 final size:17
Alignment explanation
Indices: 9064--9136 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
9054 TTGGACTTTC
*
9064 TAAATTT-AATTTTATAA
1 TAAATTTAAATTTCA-AA
9081 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
9098 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTCAAA
*
9115 TAAACTTAAATTT-AAA
1 TAAATTTAAATTTCAAA
9131 TAAATT
1 TAAATT
9137 CAATTTCCAA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.15
17 38 0.73
18 6 0.12
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTCAAA
Found at i:15294 original size:17 final size:17
Alignment explanation
Indices: 15272--15335 Score: 56
Period size: 17 Copynumber: 3.5 Consensus size: 17
15262 TATAAATTTT
15272 TTTTATATTTTTTGTAA
1 TTTTATATTTTTTGTAA
*
15289 TTTTATATTATTTTTAATAA
1 TTTTATA-T-TTTTT-GTAA
*
15309 TATTTAACATTTTTTGTAA
1 T-TTT-ATATTTTTTGTAA
*
15328 TTATATAT
1 TTTTATAT
15336 ATTTATAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
17 10 0.27
18 3 0.08
19 9 0.24
20 9 0.24
21 4 0.11
22 2 0.05
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTTTGTAA
Found at i:15382 original size:27 final size:30
Alignment explanation
Indices: 15332--15398 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 30
15322 TTGTAATTAT
* **
15332 ATATATTTATAATTTTTTGTTATTTT-TTT-
1 ATAT-TTTATAATTTTATAATATTTTCTTTA
15361 AT-TTTTATAATTTTATAATATTTTCTTTA
1 ATATTTTATAATTTTATAATATTTTCTTTA
15390 ATATTTTAT
1 ATATTTTAT
15399 GTTTTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
27 18 0.56
28 4 0.12
29 4 0.12
30 6 0.19
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.69
Consensus pattern (30 bp):
ATATTTTATAATTTTATAATATTTTCTTTA
Found at i:17791 original size:29 final size:29
Alignment explanation
Indices: 17710--17797 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
17700 TCTCAACACA
* * *
17710 AGATAAAATCACACAACAATCATATAACAC
1 AGATAAAAACACACAACAA-CATGTAGCAC
* *
17740 AGA-AAAAACACA-AGCAAATATGTAGCAC
1 AGATAAAAACACACAAC-AACATGTAGCAC
17768 AGATAAAAACACACAACAACATGTAGCAC
1 AGATAAAAACACACAACAACATGTAGCAC
17797 A
1 A
17798 AATAGAGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
28 12 0.25
29 31 0.65
30 5 0.10
ACGTcount: A:0.57, C:0.22, G:0.09, T:0.12
Consensus pattern (29 bp):
AGATAAAAACACACAACAACATGTAGCAC
Found at i:22191 original size:15 final size:15
Alignment explanation
Indices: 22173--22223 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
22163 TTAATCCTTA
22173 TATTATTAAATTTAT
1 TATTATTAAATTTAT
*
22188 TATTTTTAAATTTATT
1 TATTATTAAATTTA-T
* *
22204 TGTTTTTAAATTTAT
1 TATTATTAAATTTAT
22219 TATTA
1 TATTA
22224 AATTTAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 17 0.55
16 14 0.45
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTATTAAATTTAT
Found at i:22211 original size:16 final size:16
Alignment explanation
Indices: 22173--22219 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
22163 TTAATCCTTA
*
22173 TATTATTAAATTTA-T
1 TATTTTTAAATTTATT
22188 TATTTTTAAATTTATT
1 TATTTTTAAATTTATT
*
22204 TGTTTTTAAATTTATT
1 TATTTTTAAATTTATT
22220 ATTAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 13 0.45
16 16 0.55
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (16 bp):
TATTTTTAAATTTATT
Found at i:22241 original size:31 final size:29
Alignment explanation
Indices: 22170--22242 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 29
22160 ATGTTAATCC
*
22170 TTATATTATTAAATTTATTATTTTTAAAT
1 TTATATTTTTAAATTTATTATTTTTAAAT
*
22199 TTATTTGTTTTTAAATTTATTATTAAATTTAAA-
1 TTA--TATTTTTAAATTTATTATT---TTTAAAT
22232 TTATATTTTTA
1 TTATATTTTTA
22243 TTTTTTATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 3 0.08
31 24 0.67
33 3 0.08
34 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (29 bp):
TTATATTTTTAAATTTATTATTTTTAAAT
Found at i:23443 original size:56 final size:56
Alignment explanation
Indices: 23357--23476 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
23347 ATATTTACTT
23357 AATTTTAATTATAAAATATAAATGTAGACACAATATTTTGTATGGACTTAATGAAA
1 AATTTTAATTATAAAATATAAATGTAGACACAATATTTTGTATGGACTTAATGAAA
*
23413 AATTTTAATTATAAAATATAAATGTAGACACAATATTTTGTATGGACTTCATGAAA
1 AATTTTAATTATAAAATATAAATGTAGACACAATATTTTGTATGGACTTAATGAAA
23469 AATTTTAA
1 AATTTTAA
23477 ATTCGTTTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (56 bp):
AATTTTAATTATAAAATATAAATGTAGACACAATATTTTGTATGGACTTAATGAAA
Found at i:25408 original size:19 final size:19
Alignment explanation
Indices: 25386--25463 Score: 65
Period size: 17 Copynumber: 4.1 Consensus size: 19
25376 TTTTGAAACT
25386 TTTTTATTTTTAATTAATA
1 TTTTTATTTTTAATTAATA
*
25405 TTTTGATGATTTTTTAA--ATTA
1 TTTT--T-A-TTTTTAATTAATA
*
25426 TTTTTATTTTTAATTAATG
1 TTTTTATTTTTAATTAATA
*
25445 TATTTA-TTTT-ATTAATA
1 TTTTTATTTTTAATTAATA
25462 TT
1 TT
25464 AGTTGGATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 14 0.30
18 5 0.11
19 12 0.26
21 8 0.17
22 1 0.02
23 7 0.15
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTATTTTTAATTAATA
Found at i:25448 original size:21 final size:20
Alignment explanation
Indices: 25386--25449 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
25376 TTTTGAAACT
25386 TTTTTATTTTTAATTAA-TA
1 TTTTTATTTTTAATTAATTA
*
25405 TTTTGATGATTTTT--TAAATTA
1 TTTT--T-ATTTTTAATTAATTA
25426 TTTTTATTTTTAATTAATGTA
1 TTTTTATTTTTAATTAAT-TA
25447 TTT
1 TTT
25450 ATTTTATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
18 6 0.17
19 5 0.14
20 7 0.19
21 12 0.33
22 6 0.17
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTATTTTTAATTAATTA
Found at i:33294 original size:111 final size:111
Alignment explanation
Indices: 33100--33322 Score: 428
Period size: 111 Copynumber: 2.0 Consensus size: 111
33090 AAATGAAATC
33100 TAGGTGGATTCTTTCCTGGGTATTGTTTGGCTTCTTGATTGTTTAATCGTATGTTTTGCTGATTC
1 TAGGTGGATTCTTTCCTGGGTATTGTTTGGCTTCTTGATTGTTTAATCGTATGTTTTGCTGATTC
*
33165 GTTCTTTGTTGTGTTCTTTCGTTAATTAATTTAGTTATTTTTGGTT
66 GTTCTTTGTTATGTTCTTTCGTTAATTAATTTAGTTATTTTTGGTT
*
33211 TAGGTGGATTCTTTCCTGGGTATTGTTTGGCTTCTTGATTGTTTAATCGTTTGTTTTGCTGATTC
1 TAGGTGGATTCTTTCCTGGGTATTGTTTGGCTTCTTGATTGTTTAATCGTATGTTTTGCTGATTC
33276 GTTCTTTGTTATGTTCTTTCGTTAATTAATTTAGTTATTTTTGGTT
66 GTTCTTTGTTATGTTCTTTCGTTAATTAATTTAGTTATTTTTGGTT
33322 T
1 T
33323 TAATTAATCA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.57
Consensus pattern (111 bp):
TAGGTGGATTCTTTCCTGGGTATTGTTTGGCTTCTTGATTGTTTAATCGTATGTTTTGCTGATTC
GTTCTTTGTTATGTTCTTTCGTTAATTAATTTAGTTATTTTTGGTT
Found at i:47295 original size:18 final size:18
Alignment explanation
Indices: 47265--47306 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
47255 AAATTTCTAT
*
47265 CTTTTT-TCTTTTTCTTC
1 CTTTTTCTCATTTTCTTC
* *
47282 CTTTTTCTCATTTTTTTT
1 CTTTTTCTCATTTTCTTC
47300 CTTTTTC
1 CTTTTTC
47307 AAATGACTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTTCTCATTTTCTTC
Found at i:65214 original size:17 final size:17
Alignment explanation
Indices: 65192--65225 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
65182 ACATTTATAG
65192 CAAACATAATTTTTTCT
1 CAAACATAATTTTTTCT
65209 CAAACATAATTTTTTCT
1 CAAACATAATTTTTTCT
65226 TCTTTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (17 bp):
CAAACATAATTTTTTCT
Found at i:65268 original size:24 final size:21
Alignment explanation
Indices: 65220--65269 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 21
65210 AAACATAATT
*
65220 TTTTCTTCTTTTTCTTCTCTC
1 TTTTCTTCTTTTTCTTATCTC
65241 TTTTCTTCTTCTTTCTTTATCTC
1 TTTTCTTCTT-TTTC-TTATCTC
65264 ATTTTC
1 -TTTTC
65270 CTTTTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 10 0.40
22 4 0.16
23 6 0.24
24 5 0.20
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTTCTTTTTCTTATCTC
Found at i:69579 original size:60 final size:59
Alignment explanation
Indices: 69445--69567 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 59
69435 AAGAAATAAT
* *
69445 ATTT-TTGAAATTTTTAGAATTAAAACTAAATTGACAAATTTGTAAATGTTGAGGGCTAG
1 ATTTATTG-AATTTTTAGAATTAAAACTAAATTGACAAATTTGTAAATATTGAGGGCTAA
* ** * *
69504 CTTTATTGAATTTTTAGAATTCGAACTAAATTGATAAATTTTGTAAATATTGAGGTCTAA
1 ATTTATTGAATTTTTAGAATTAAAACTAAATTGACAAA-TTTGTAAATATTGAGGGCTAA
69564 ATTT
1 ATTT
69568 GTTAGTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 30 0.56
60 24 0.44
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (59 bp):
ATTTATTGAATTTTTAGAATTAAAACTAAATTGACAAATTTGTAAATATTGAGGGCTAA
Found at i:69640 original size:50 final size:49
Alignment explanation
Indices: 69565--69664 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 49
69555 GAGGTCTAAA
* *
69565 TTTGTTAGTTTTTTATATTGTTGATCAAATTGATAAAATGTGTAAGCAT
1 TTTGTTAGTTTTTTATATTGATGATCAAATTGATAAAATATGTAAGCAT
* *
69614 TTTGTTGGTTTTTTTATATTGATGATCAAATTGATAGAATATGTAAGCAT
1 TTTGTTAG-TTTTTTATATTGATGATCAAATTGATAAAATATGTAAGCAT
69664 T
1 T
69665 AGAGAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 7 0.15
50 39 0.85
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (49 bp):
TTTGTTAGTTTTTTATATTGATGATCAAATTGATAAAATATGTAAGCAT
Found at i:70207 original size:48 final size:47
Alignment explanation
Indices: 70117--70209 Score: 111
Period size: 48 Copynumber: 1.9 Consensus size: 47
70107 ATGATATAAA
*
70117 ATAAAAGAAAAGTAATCTTAATAATTACAAAAATGTTTTTAAATATAT
1 ATAAAAGAAAAGTAATCTTAATAATTACAAAAA-GTTCTTAAATATAT
70165 ATAAAAGAAATA-TAATCTTAA-AATTATACGAAAAA-TTCTTAAATA
1 ATAAAAGAAA-AGTAATCTTAATAA-T-TAC-AAAAAGTTCTTAAATA
70210 AAAAAATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
47 2 0.05
48 29 0.73
49 4 0.10
50 5 0.12
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (47 bp):
ATAAAAGAAAAGTAATCTTAATAATTACAAAAAGTTCTTAAATATAT
Found at i:71027 original size:21 final size:20
Alignment explanation
Indices: 70994--71038 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
70984 TATTACTTAG
*
70994 ATAATTCAATAAAATAAATAA
1 ATAATACAATAAAATAAA-AA
* *
71015 ATAATACATTAAATTAAAAA
1 ATAATACAATAAAATAAAAA
71035 ATAA
1 ATAA
71039 CTCTTAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
ATAATACAATAAAATAAAAA
Found at i:71719 original size:16 final size:16
Alignment explanation
Indices: 71697--71754 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
71687 TTTTAAATTC
71697 TATTTATCTAATTAAA
1 TATTTATCTAATTAAA
* *
71713 CATTTATTTAATTTTTAAA
1 TATTTATCTAA---TTAAA
*
71732 TTTTTATCTAATTAAA
1 TATTTATCTAATTAAA
71748 TATTTAT
1 TATTTAT
71755 TATAAACATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 20 0.61
19 13 0.39
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTTATCTAATTAAA
Found at i:71767 original size:35 final size:35
Alignment explanation
Indices: 71699--71768 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
71689 TTAAATTCTA
***
71699 TTTATCTAATTAAACATTTATTTAATTTTTAAATT
1 TTTATCTAATTAAACATTTATTTAATACATAAATT
*
71734 TTTATCTAATTAAATATTTATTATAA-ACATAAATT
1 TTTATCTAATTAAACATTTATT-TAATACATAAATT
71769 AAGTACAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (35 bp):
TTTATCTAATTAAACATTTATTTAATACATAAATT
Found at i:84141 original size:34 final size:34
Alignment explanation
Indices: 84101--84174 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
84091 GCTCAGTGTG
84101 ACAAATTATACTTTTCAAAACCCAACACCCCAAA
1 ACAAATTATACTTTTCAAAACCCAACACCCCAAA
*
84135 ACAAATTATACTTTTCACAACCCAACACCCCAAA
1 ACAAATTATACTTTTCAAAACCCAACACCCCAAA
84169 ACAAAT
1 ACAAAT
84175 AAAAACCCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.20
Consensus pattern (34 bp):
ACAAATTATACTTTTCAAAACCCAACACCCCAAA
Done.