Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014636.1 Kokia drynarioides strain JFW-HI SEQ_129675, 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: 117737
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:911 original size:15 final size:15
Alignment explanation
Indices: 891--922 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
881 GAGCCTCAAA
891 TTTCACATTTACTTT
1 TTTCACATTTACTTT
906 TTTCACATTTACTTT
1 TTTCACATTTACTTT
921 TT
1 TT
923 ACGAATGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTCACATTTACTTT
Found at i:4231 original size:17 final size:16
Alignment explanation
Indices: 4204--4237 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
4194 TATTTTTTAA
4204 TAAAAATTTATAATTT
1 TAAAAATTTATAATTT
4220 TAAAATATTTATAATTT
1 TAAAA-ATTTATAATTT
4237 T
1 T
4238 TCTTTATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAAAATTTATAATTT
Found at i:4245 original size:13 final size:13
Alignment explanation
Indices: 4227--4264 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
4217 TTTTAAAATA
4227 TTTATAATTTTTC
1 TTTATAATTTTTC
* *
4240 TTTATAAATTTTG
1 TTTATAATTTTTC
4253 TTTATAATTTTT
1 TTTATAATTTTT
4265 ATAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (13 bp):
TTTATAATTTTTC
Found at i:4265 original size:22 final size:21
Alignment explanation
Indices: 4240--4286 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4230 ATAATTTTTC
*
4240 TTTATAAATTTTGTTTAT-AATT
1 TTTAT-AATTTT-TTAATAAATT
4262 TTTATAATTTTTTAATAAATT
1 TTTATAATTTTTTAATAAATT
4283 TTTA
1 TTTA
4287 ATTTTAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 14 0.61
22 5 0.22
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATAATTTTTTAATAAATT
Found at i:4270 original size:21 final size:20
Alignment explanation
Indices: 4240--4291 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
4230 ATAATTTTTC
* *
4240 TTTATAAATTTTGTTTATAATT
1 TTTAT-AATTTT-TTAATAAAT
4262 TTTATAATTTTTTAATAAAT
1 TTTATAATTTTTTAATAAAT
4282 TTT-TAATTTT
1 TTTATAATTTT
4292 AAAAGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.25
20 10 0.36
21 6 0.21
22 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTATAATTTTTTAATAAAT
Found at i:6533 original size:24 final size:23
Alignment explanation
Indices: 6484--6533 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
6474 TAAAGTAGGT
* *
6484 TATATATTATTTTTATAATATTA
1 TATATATGATTTTTATAATATCA
6507 TATATTATGATTTTTATTAAT-TCA
1 TATA-TATGATTTTTA-TAATATCA
6531 TAT
1 TAT
6534 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 15 0.65
25 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TATATATGATTTTTATAATATCA
Found at i:6550 original size:39 final size:40
Alignment explanation
Indices: 6491--6578 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
6481 GGTTATATAT
* * * * *
6491 TATTTTTATAATATTATATATTATGATTTTTATT-AATTCA
1 TATTTTAATAATAATATATATTAAGAATGTTATTAAATT-A
6531 TATTTTAATAATAAT-TATATTAAGAATGTTATTAAATTA
1 TATTTTAATAATAATATATATTAAGAATGTTATTAAATTA
*
6570 TATATTAAT
1 TATTTTAAT
6579 TTACTAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 24 0.59
40 17 0.41
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (40 bp):
TATTTTAATAATAATATATATTAAGAATGTTATTAAATTA
Found at i:8127 original size:318 final size:318
Alignment explanation
Indices: 7550--8502 Score: 1822
Period size: 318 Copynumber: 3.0 Consensus size: 318
7540 GTATTTTAAT
7550 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACATGA-ATGAATGTGATG
1 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACAT-ACATGAATGTGATG
*
7614 GATAAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACT
65 GATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACT
7679 AAATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCA
130 AAATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCA
7744 AAAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAAC
195 AAAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAAC
7809 ACATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
260 ACATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
7868 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACATACATGAATGTGATGG
1 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACATACATGAATGTGATGG
7933 ATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACTA
66 ATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACTA
7998 AATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCAA
131 AATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCAA
8063 AAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAACA
196 AAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAACA
8128 CATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
261 CATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
*
8186 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCATACATACATGAATGTGATGG
1 ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACATACATGAATGTGATGG
*
8251 ATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTACCACTA
66 ATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACTA
*
8316 AATTATCACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCAA
131 AATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCAA
*
8381 AAGTATGGGTGTTTTGTATCCATTGATCAAAGATGGATTGTAATTAAATAGTAGTATATGAAACA
196 AAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAACA
*
8446 C--ATATATTATGGACGTTCTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
261 CATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
8502 A
1 A
8503 ACTATGAAAA
Statistics
Matches: 628, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
316 55 0.09
317 1 0.00
318 572 0.91
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (318 bp):
ATATATCAATATTTTTCAAGAGTATCAATACAGTCATATGAATCGTACATACATGAATGTGATGG
ATCAAAAAAATTTATGGTTCCTAATAAAATAGGTAACAAAGTAACTTTACTACCTACTGCCACTA
AATTATGACCTTCCCAAGTTGAACTGGTGCTTGTTGTTTCACAAGAGCCATTGCAATGGATGCAA
AAGTATGGGTGTTTTGTATCCATTGATCAAAGGTGGATTGTAATTAAATAGTAGTATATGAAACA
CATATATATTATGGACGTTTTAAAGTGCTCATAGTATTATTATGAATATATAAACTAA
Found at i:9187 original size:38 final size:41
Alignment explanation
Indices: 9121--9198 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 41
9111 CAAATTTAAA
*
9121 AAATATATAATATAACAAATAAACTTAAA-AACATTAAAAC
1 AAATATATAATATAACAAACAAACTTAAAGAACATTAAAAC
* * *
9161 AAATAT-TAATA-AATAAACAAATTTAAAGTACATTAAAA
1 AAATATATAATATAACAAACAAACTTAAAGAACATTAAAA
9199 ATTCTTTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
38 13 0.39
39 14 0.42
40 6 0.18
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.27
Consensus pattern (41 bp):
AAATATATAATATAACAAACAAACTTAAAGAACATTAAAAC
Found at i:9387 original size:12 final size:12
Alignment explanation
Indices: 9372--9424 Score: 79
Period size: 12 Copynumber: 4.4 Consensus size: 12
9362 CAATAATAAA
9372 AACAACAAAAAT
1 AACAACAAAAAT
* *
9384 AACAACAGAAAC
1 AACAACAAAAAT
9396 AACAACAAAAAT
1 AACAACAAAAAT
*
9408 AGCAACAAAAAT
1 AACAACAAAAAT
9420 AACAA
1 AACAA
9425 TATCAAAACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.72, C:0.19, G:0.04, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:9444 original size:21 final size:22
Alignment explanation
Indices: 9415--9455 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9405 AATAGCAACA
* *
9415 AAAATAACAATATCAAAACAGT
1 AAAATAACAACACCAAAACAGT
9437 AAAA-AACAACACCAAAACA
1 AAAATAACAACACCAAAACA
9456 ACAATCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.68, C:0.20, G:0.02, T:0.10
Consensus pattern (22 bp):
AAAATAACAACACCAAAACAGT
Found at i:9465 original size:24 final size:23
Alignment explanation
Indices: 9346--9465 Score: 68
Period size: 24 Copynumber: 5.2 Consensus size: 23
9336 AAACAGCAGT
* * *
9346 AAAAATAACAGCAAAACAATAAT-
1 AAAAACAACAACAAAA-AACAATC
*
9369 AAAAACAACAA-AAATAACAA-C
1 AAAAACAACAACAAAAAACAATC
*
9390 AGAAACAACAACAAAAATAGCAA-C
1 AAAAACAACAACAAAAA-A-CAATC
* * * * *
9414 AAAAATAACAATATCAAAACAGTA
1 AAAAACAACAACA-AAAAACAATC
*
9438 AAAAACAACACCAAAACAACAATC
1 AAAAACAACAACAAAA-AACAATC
9462 AAAA
1 AAAA
9466 CAGTAAAAAA
Statistics
Matches: 72, Mismatches: 18, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
21 14 0.19
22 7 0.10
23 14 0.19
24 34 0.47
25 3 0.04
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (23 bp):
AAAAACAACAACAAAAAACAATC
Found at i:9493 original size:17 final size:18
Alignment explanation
Indices: 9458--9494 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9448 CCAAAACAAC
9458 AATCAAAACAGTAAAAAA
1 AATCAAAACAGTAAAAAA
9476 AATCAAAACAGTAAAAAA
1 AATCAAAACAGTAAAAAA
9494 A
1 A
9495 CAACTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.73, C:0.11, G:0.05, T:0.11
Consensus pattern (18 bp):
AATCAAAACAGTAAAAAA
Found at i:9537 original size:24 final size:23
Alignment explanation
Indices: 9510--9554 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
9500 TCAAAATAAC
*
9510 AAAAAAAGAGCAACCAAAACAATA
1 AAAAAAAGAAC-ACCAAAACAATA
*
9534 AAAAAAATAACACCAAAACAA
1 AAAAAAAGAACACCAAAACAA
9555 CAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.73, C:0.18, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAAAAGAACACCAAAACAATA
Found at i:16268 original size:90 final size:90
Alignment explanation
Indices: 16115--16299 Score: 370
Period size: 90 Copynumber: 2.1 Consensus size: 90
16105 AAATTTTATT
16115 TTAATATTTTTATATATTTTAATTTTATTATGTACACTTTATTATTTCCATCAGTTGTATATATC
1 TTAATATTTTTATATATTTTAATTTTATTATGTACACTTTATTATTTCCATCAGTTGTATATATC
16180 TATGTCTATACTATTAATAAAACCC
66 TATGTCTATACTATTAATAAAACCC
16205 TTAATATTTTTATATATTTTAATTTTATTATGTACACTTTATTATTTCCATCAGTTGTATATATC
1 TTAATATTTTTATATATTTTAATTTTATTATGTACACTTTATTATTTCCATCAGTTGTATATATC
16270 TATGTCTATACTATTAATAAAACCC
66 TATGTCTATACTATTAATAAAACCC
16295 TTAAT
1 TTAAT
16300 TGAGTTGGTG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.51
Consensus pattern (90 bp):
TTAATATTTTTATATATTTTAATTTTATTATGTACACTTTATTATTTCCATCAGTTGTATATATC
TATGTCTATACTATTAATAAAACCC
Found at i:18424 original size:15 final size:15
Alignment explanation
Indices: 18406--18434 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18396 GAGCTCAATG
18406 TCATCTCTCCTGAAC
1 TCATCTCTCCTGAAC
18421 TCATCTCTCCTGAA
1 TCATCTCTCCTGAA
18435 TTAACATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.07, T:0.34
Consensus pattern (15 bp):
TCATCTCTCCTGAAC
Found at i:19609 original size:15 final size:16
Alignment explanation
Indices: 19578--19610 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19568 CTTCCTTTAG
*
19578 GAACTTGAAAGAGAAA
1 GAACTGGAAAGAGAAA
19594 GAACTGGAAA-AGAAA
1 GAACTGGAAAGAGAAA
19609 GA
1 GA
19611 CTAGAGACGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.58, C:0.06, G:0.27, T:0.09
Consensus pattern (16 bp):
GAACTGGAAAGAGAAA
Found at i:23430 original size:9 final size:8
Alignment explanation
Indices: 23398--23429 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
23388 TTGATTCAAC
23398 TCGAAAAA
1 TCGAAAAA
*
23406 CCGAAAAA
1 TCGAAAAA
23414 TCGAAAAA
1 TCGAAAAA
23422 TCGAAAAA
1 TCGAAAAA
23430 AATTCAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.62, C:0.16, G:0.12, T:0.09
Consensus pattern (8 bp):
TCGAAAAA
Found at i:24116 original size:9 final size:9
Alignment explanation
Indices: 24102--24136 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
24092 ATTCAAGTTG
24102 ACTCGAATA
1 ACTCGAATA
*
24111 ACTCGATTA
1 ACTCGAATA
*
24120 ACTCAAATA
1 ACTCGAATA
24129 ACTCGAAT
1 ACTCGAAT
24137 TAATTACTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (9 bp):
ACTCGAATA
Found at i:24128 original size:18 final size:19
Alignment explanation
Indices: 24102--24139 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
24092 ATTCAAGTTG
*
24102 ACTCGAATAACTCG-ATTA
1 ACTCAAATAACTCGAATTA
24120 ACTCAAATAACTCGAATTA
1 ACTCAAATAACTCGAATTA
24139 A
1 A
24140 TTACTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
ACTCAAATAACTCGAATTA
Found at i:24304 original size:20 final size:20
Alignment explanation
Indices: 24278--24327 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
24268 AAAAAAACCT
*
24278 CAAAACTTTTTATTTTCCCT
1 CAAAACTTTTTATTTTCCCC
*
24298 TAAAACTTTTTATTTTCCCC
1 CAAAACTTTTTATTTTCCCC
24318 CAAAACTTTT
1 CAAAACTTTT
24328 ACTCTCTCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.24, G:0.00, T:0.48
Consensus pattern (20 bp):
CAAAACTTTTTATTTTCCCC
Found at i:33168 original size:20 final size:20
Alignment explanation
Indices: 33152--33187 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
33142 AATTTTATAA
33152 TATT-TTATTTT-ATTTTAT
1 TATTATTATTTTGATTTTAT
33170 TATTATTATTTTGATTTT
1 TATTATTATTTTGATTTT
33188 GGATTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 7 0.44
20 5 0.31
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (20 bp):
TATTATTATTTTGATTTTAT
Found at i:40470 original size:13 final size:13
Alignment explanation
Indices: 40452--40480 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40442 TCATAAGCTT
40452 TTTCCATCTCTAG
1 TTTCCATCTCTAG
40465 TTTCCATCTCTAG
1 TTTCCATCTCTAG
40478 TTT
1 TTT
40481 GATTCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.52
Consensus pattern (13 bp):
TTTCCATCTCTAG
Found at i:47230 original size:37 final size:36
Alignment explanation
Indices: 47181--47255 Score: 105
Period size: 37 Copynumber: 2.1 Consensus size: 36
47171 TCTTCCTTGC
*
47181 TTATCATTGAATCTGTGATACTGAAGAACCATAAAA
1 TTATCATTGAATCTGTGATACTGAAGAACAATAAAA
* * *
47217 TTATCAGTTGAATCTGTGATATTTAAGAACAATAGAA
1 TTATCA-TTGAATCTGTGATACTGAAGAACAATAAAA
47254 TT
1 TT
47256 GTGAAATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
36 6 0.18
37 28 0.82
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (36 bp):
TTATCATTGAATCTGTGATACTGAAGAACAATAAAA
Found at i:52231 original size:20 final size:21
Alignment explanation
Indices: 52208--52256 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
52198 AATCAAGGGA
**
52208 AAGATGTAG-ATATCACAAGG
1 AAGATGTAGCATAAAACAAGG
52228 AAGA-GTAGCATAAAACAAGG
1 AAGATGTAGCATAAAACAAGG
52248 AAGAATGTA
1 AAG-ATGTA
52257 CTAACTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 16 0.67
21 1 0.04
22 3 0.12
ACGTcount: A:0.51, C:0.08, G:0.24, T:0.16
Consensus pattern (21 bp):
AAGATGTAGCATAAAACAAGG
Found at i:59718 original size:19 final size:18
Alignment explanation
Indices: 59652--59718 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
59642 CGCGGAAGGA
*
59652 TTAA-CATATTGGCTCGT
1 TTAAGCATACTGGCTCGT
*
59669 TTAAGCATACTGGCCCGT
1 TTAAGCATACTGGCTCGT
*
59687 TTGAGCATACTGGCTCGT
1 TTAAGCATACTGGCTCGT
*
59705 TAAAGCATTACTGG
1 TTAAGCA-TACTGG
59719 ATCACAAGAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
17 4 0.10
18 32 0.76
19 6 0.14
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (18 bp):
TTAAGCATACTGGCTCGT
Found at i:66760 original size:36 final size:36
Alignment explanation
Indices: 66709--66779 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
66699 TGGTAACAGG
* * * *
66709 CATGACCTTTGGGTCAACAGGGGGTAAAATGAGTAA
1 CATGACATTTAGGTCAACAGAGAGTAAAATGAGTAA
*
66745 CATGACATTTAGGTCAACAGAGAGTAAACTGAGTA
1 CATGACATTTAGGTCAACAGAGAGTAAAATGAGTA
66780 TCGATAATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (36 bp):
CATGACATTTAGGTCAACAGAGAGTAAAATGAGTAA
Found at i:69275 original size:20 final size:21
Alignment explanation
Indices: 69252--69290 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
69242 AAATAGGGGA
*
69252 AAAAAC-AAGAAAATAGCAAT
1 AAAAACAAAAAAAATAGCAAT
69272 AAAAACAAAAAAAATAGCA
1 AAAAACAAAAAAAATAGCA
69291 GATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.74, C:0.10, G:0.08, T:0.08
Consensus pattern (21 bp):
AAAAACAAAAAAAATAGCAAT
Found at i:76808 original size:9 final size:9
Alignment explanation
Indices: 76794--76827 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
76784 AAAATCAATT
76794 TTTTTTCAA
1 TTTTTTCAA
76803 TTTTTTCAGA
1 TTTTTTCA-A
*
76813 TTTTTTGAA
1 TTTTTTCAA
76822 TTTTTT
1 TTTTTT
76828 AAAATAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (9 bp):
TTTTTTCAA
Found at i:86864 original size:20 final size:20
Alignment explanation
Indices: 86817--86884 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
86807 TTAGTGGGCG
86817 GATTAAAA-TGATTTATATTAA
1 GATTAAAAGTG-TTTA-ATTAA
86838 -ATGTAAATAG-GTTTAATTAA
1 GAT-TAAA-AGTGTTTAATTAA
*
86858 GATTAAAAGTGATTAATTAA
1 GATTAAAAGTGTTTAATTAA
86878 GACTTAA
1 GA-TTAA
86885 TGATGAAAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
19 2 0.05
20 22 0.55
21 14 0.35
22 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.38
Consensus pattern (20 bp):
GATTAAAAGTGTTTAATTAA
Found at i:98629 original size:11 final size:11
Alignment explanation
Indices: 98603--98641 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
98593 AATTTATCAA
98603 TTTAATTATATT
1 TTTAATTAT-TT
*
98615 TTTATTTATTT
1 TTTAATTATTT
98626 TTTACATTATTT
1 TTTA-ATTATTT
98638 TTTA
1 TTTA
98642 TAAACATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTAATTATTT
Found at i:99262 original size:25 final size:27
Alignment explanation
Indices: 99208--99266 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
99198 TTATTATTAT
* *
99208 ATATTTATTATTAAAATATTCATATAA
1 ATATTTATTATTAAAATATTAAAATAA
99235 ATATTT-TTA-TAAAATATTAAAA-ATA
1 ATATTTATTATTAAAATATTAAAATA-A
99260 ATATTTA
1 ATATTTA
99267 AAATGTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 1 0.04
25 18 0.64
26 3 0.11
27 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATATTTATTATTAAAATATTAAAATAA
Found at i:99649 original size:3 final size:3
Alignment explanation
Indices: 99641--99672 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
99631 TAAAACTCCT
99641 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA
99673 AGATTCTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.34, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:106316 original size:22 final size:23
Alignment explanation
Indices: 106286--106337 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
106276 TTTATATTAT
*
106286 TTTTA-ATTTAGTATTTA-ATAA
1 TTTTATATTTAGTATTTATAAAA
**
106307 TTTTATATTTTTTATTTATAAAA
1 TTTTATATTTAGTATTTATAAAA
106330 TTTTATAT
1 TTTTATAT
106338 AGACATCTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 10 0.38
23 11 0.42
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTTATATTTAGTATTTATAAAA
Done.