Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014586.1 Kokia drynarioides strain JFW-HI SEQ_129625, 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: 138046
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Warning! 30 characters in sequence are not A, C, G, or T
Found at i:6519 original size:19 final size:20
Alignment explanation
Indices: 6497--6536 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
6487 TGGAGTTAGA
*
6497 TTTTT-CTTTTTTG-TAATT
1 TTTTTACTTTTTCGTTAATT
6515 TTTTTACTTTTTCGTTAATT
1 TTTTTACTTTTTCGTTAATT
6535 TT
1 TT
6537 ATTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTTACTTTTTCGTTAATT
Found at i:7432 original size:16 final size:16
Alignment explanation
Indices: 7407--7437 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
7397 CAAAATAAAG
7407 CGATAAAATATTAACA
1 CGATAAAATATTAACA
*
7423 CGATACAATATTAAC
1 CGATAAAATATTAAC
7438 TCGTTAATGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.06, T:0.26
Consensus pattern (16 bp):
CGATAAAATATTAACA
Found at i:9552 original size:6 final size:6
Alignment explanation
Indices: 9535--9592 Score: 80
Period size: 6 Copynumber: 9.7 Consensus size: 6
9525 ACAAAAGCAT
* * * *
9535 ATATAT ATATAC ATATAC ATGTAC ATGTAC ATATAC ATACAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
9583 ATATAC ATAT
1 ATATAC ATAT
9593 GTGCAGAGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:17272 original size:224 final size:222
Alignment explanation
Indices: 16897--17308 Score: 558
Period size: 224 Copynumber: 1.8 Consensus size: 222
16887 TGAAGCATCG
* * *
16897 TTTTACCATTATATTAATTTGTGATTTCTTAAAACCTAAAAGAGTTATATAAATAATTTTTCATT
1 TTTTACCATTATATTAATTTATGATTTCTCAAAACCTAAAAGAGTAATATAAATAATTTTTCATT
* ** * * * *
16962 TTTGGTGTCAAGGTCCACCAGCCCCCTCCCTTCGCCCTTAATAAAGATCATTTTTTTCTGGGTTC
66 TTCGGAATCAAGATCCACCAGCCCCCTCCCTTCGCCCCTAATAAAGATCAATCTTTTCTGGGTTC
* * * * *
17027 ATGGTTGTTTTTACTAACAACATTATTTCTCGGATTTGAACTTGAGTTCTTTCTCCAATAACAAA
131 ATGGTTGTTTCTACCAACAACATTATCTCTCGGATTTGAACTTGAGTTATTTCCCCAATAACAAA
17092 TCATCTCCAAGAAGATCTAAATTATCA
196 TCATCTCCAAGAAGATCTAAATTATCA
* ** * * *
17119 TTTTACCTTTATATTAATTTATGATTT-TCCAAAATTTAAAGGGGTAATATAAGTAATTTTTCAT
1 TTTTACCATTATATTAATTTATGATTTCT-CAAAACCTAAAAGAGTAATATAAATAATTTTTCAT
*
17183 TTTCGGAATCAAGAT-CACTGCATGCCCCCTCCCTTCGCCCCTAATAAAGATTAATCTTTTCTGG
65 TTTCGGAATCAAGATCCAC--CA-GCCCCCTCCCTTCGCCCCTAATAAAGATCAATCTTTTCTGG
* *
17247 GTTCATGGTTGTTTCTACCAACAACATTATCTCTTGGATTTGGACTTGAGTTATTTCCCCAA
127 GTTCATGGTTGTTTCTACCAACAACATTATCTCTCGGATTTGAACTTGAGTTATTTCCCCAA
17309 GAATACATTA
Statistics
Matches: 162, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
221 4 0.02
222 64 0.40
223 2 0.01
224 92 0.57
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (222 bp):
TTTTACCATTATATTAATTTATGATTTCTCAAAACCTAAAAGAGTAATATAAATAATTTTTCATT
TTCGGAATCAAGATCCACCAGCCCCCTCCCTTCGCCCCTAATAAAGATCAATCTTTTCTGGGTTC
ATGGTTGTTTCTACCAACAACATTATCTCTCGGATTTGAACTTGAGTTATTTCCCCAATAACAAA
TCATCTCCAAGAAGATCTAAATTATCA
Found at i:24664 original size:22 final size:23
Alignment explanation
Indices: 24624--24669 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
24614 TTATTTAAAA
24624 AATATTTATATAATATTAT-TTT
1 AATATTTATATAATATTATATTT
*
24646 AATATTT-TATACATTTTATATTT
1 AATATTTATATA-ATATTATATTT
24669 A
1 A
24670 TTTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
AATATTTATATAATATTATATTT
Found at i:24705 original size:31 final size:28
Alignment explanation
Indices: 24634--24711 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 28
24624 AATATTTATA
24634 TAATATTATTTTAATATTT-TATACATT
1 TAATATTATTTTAATATTTATATACATT
* *
24661 TTATATT-TATTTAATTTTTATATAGTCATCT
1 TAATATTAT-TTTAATATTTATATA--CAT-T
24692 TAATATTATTTTAATATTTA
1 TAATATTATTTTAATATTTA
24712 CATTAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 15 0.37
28 4 0.10
30 3 0.07
31 17 0.41
32 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (28 bp):
TAATATTATTTTAATATTTATATACATT
Found at i:29609 original size:378 final size:369
Alignment explanation
Indices: 28910--29666 Score: 851
Period size: 378 Copynumber: 2.0 Consensus size: 369
28900 ACTGTAGTCC
* ** *
28910 TCAAACTATTGTTGATGTTTTAATTTGGTCTCGAGCTTCAAGACTTCATCAGTGAATCATTTAAA
1 TCAAACTATTGTTGATGTTTTAATTTGGTCTCGAGCTTCAAGACTTCAGCAGAAAATCATTAAAA
*** *
28975 CAAGGATGAAGTTGGAAAATTGCTTTAATAAGGCCAATGATGAATCGTAAACTATTGGGCTAAAT
66 CAAGGATGAAGTCAAAAAATTAC-TT-AT-A---CAATGA-GAATCGTAAACTATTGGGCTAAAT
* * *
29040 GATAAATCTACCATGTTTTGAAGGGCCAAAGCTGTTGTTGCATGCCCTTTTAATCTTCGTTTTTG
124 GATAAATCTACCATGTTTTGAAAGGCCAAA-C-GATGTTGCATGCCCTTTTAATCTTCGTTGTTG
* * *
29105 CATTAAAATATCAGTGTTGTATCAATATAGTCTTCTCTAAATCTAACCATTAGCGTATTTAAAGC
187 CATTAAAATATCAGTGTTGCATCAATATAGTCTTCTCTAAATCTAACCATTAACATATTTAAAGC
* ** * *
29170 ACGTGAATCGAAATATAATCAGTGGGGGCTCCATTGATTAAACGGAATAATTTTAATTTTAACCC
252 ACGTGAATCGAAATATAACCAGCCGGAGCTCCATTGATTAAACAGAATAATTTTAATTTTAACCC
* * * *
29235 TTCTAAATAATTAATTATTCAATACAAGTCTTTTTAATCATTTGATTAATTAT
317 CTCTAAATAATTAATTATTCAATACAAGCCTTTTTAATCATTTAATCAATTAT
*
29288 TCAAACTATTGTTGATGTTTTAATTTGGTCTCGAGCTTCAAGACTTCAGGAGAAAATCATTAAAA
1 TCAAACTATTGTTGATGTTTTAATTTGGTCTCGAGCTTCAAGACTTCAGCAGAAAATCATTAAAA
* * *
29353 CAAGGATGAAGTCAAAAAATTAC-T-T-CAAT-A-AATTGTAAATTATTTGGCTAAATGATAAAT
66 CAAGGATGAAGTCAAAAAATTACTTATACAATGAGAATCGTAAACTATTGGGCTAAATGATAAAT
* * * * * *
29413 TTACCGTTTTTTGAAAGGCCAAA-GATGTTGCCTGCCCTTTTTATCTTCGTTGTTGCATTAAATT
131 CTACCATGTTTTGAAAGGCCAAACGATGTTGCATGCCCTTTTAATCTTCGTTGTTGCATTAAAAT
* * * * * *
29477 ATCAGTGTTGCATCGATCTAGTCTTCTTTAAGTCTAACCATTAATATATTTAAAGTACGTGAATC
196 ATCAGTGTTGCATCAATATAGTCTTCTCTAAATCTAACCATTAACATATTTAAAGCACGTGAATC
** * * *
29542 GAAATGCGACTAGAGAAAAACCAAAGACCTTAGCTCCTTTTGATTAAATAGAATAATTTTTATTT
261 GAAAT---A-T-------AACC--AG-CCGGAGCTCC-ATTGATTAAACAGAATAATTTTAATTT
*
29607 TAACCCCTCTAAATAATTAATTATTCAATACAAGCCTTTTTAGTCATTTAATCAATTAT
311 TAACCCCTCTAAATAATTAATTATTCAATACAAGCCTTTTTAATCATTTAATCAATTAT
29666 T
1 T
29667 TTTATCATCT
Statistics
Matches: 319, Mismatches: 45, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
363 97 0.30
366 47 0.15
367 1 0.00
368 1 0.00
369 4 0.01
374 4 0.01
376 3 0.01
377 5 0.02
378 157 0.49
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (369 bp):
TCAAACTATTGTTGATGTTTTAATTTGGTCTCGAGCTTCAAGACTTCAGCAGAAAATCATTAAAA
CAAGGATGAAGTCAAAAAATTACTTATACAATGAGAATCGTAAACTATTGGGCTAAATGATAAAT
CTACCATGTTTTGAAAGGCCAAACGATGTTGCATGCCCTTTTAATCTTCGTTGTTGCATTAAAAT
ATCAGTGTTGCATCAATATAGTCTTCTCTAAATCTAACCATTAACATATTTAAAGCACGTGAATC
GAAATATAACCAGCCGGAGCTCCATTGATTAAACAGAATAATTTTAATTTTAACCCCTCTAAATA
ATTAATTATTCAATACAAGCCTTTTTAATCATTTAATCAATTAT
Found at i:30258 original size:29 final size:30
Alignment explanation
Indices: 30224--30280 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
30214 TTTATATTTG
* *
30224 ATAAAAATAAT-ATATTTTAATTTTTAAAA
1 ATAAAAATAATAAAATTTTAATATTTAAAA
*
30253 ATAAAAATACTAAAATTTTAATATTTAA
1 ATAAAAATAATAAAATTTTAATATTTAA
30281 TTTAGATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (30 bp):
ATAAAAATAATAAAATTTTAATATTTAAAA
Found at i:30437 original size:15 final size:15
Alignment explanation
Indices: 30417--30445 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30407 AATCAATCTC
30417 AAATTCTTTATTTTA
1 AAATTCTTTATTTTA
30432 AAATTCTTTATTTT
1 AAATTCTTTATTTT
30446 GCTCAATTTT
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:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
AAATTCTTTATTTTA
Found at i:31616 original size:21 final size:22
Alignment explanation
Indices: 31579--31622 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
31569 GGGTCTTAGT
31579 TATGGTATGTATCCGACACGAG
1 TATGGTATGTATCCGACACGAG
* *
31601 TATGGTATG-GTCCGACATGAG
1 TATGGTATGTATCCGACACGAG
31622 T
1 T
31623 TACTGATTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (22 bp):
TATGGTATGTATCCGACACGAG
Found at i:31790 original size:197 final size:197
Alignment explanation
Indices: 31448--31803 Score: 586
Period size: 197 Copynumber: 1.8 Consensus size: 197
31438 ATATCATGTG
* * * *
31448 TTGTTGGTTACATGTTTGGTTTTATGTCTAACTTAGTAGTTTCTTATTTGATCTTTCAATGATAA
1 TTGTTGCTTACATGTTTGATTTTATGTCTAACTTAGTAGTTTATTATTTGATCCTTCAATGATAA
* *
31513 TGCAATTTTTGTGAGTTAAATATGGTTTTAAGGCTATGTTACTTGAACTTGGATGTGGGTCTTAG
66 TGCAATTTTTGTGAGTTAAATATGGTTTTAAGGCTATGTTACTTAAACTTGGATGTGGGTCTTAA
* * *
31578 TTATGGTATGTATCCGACACGAGTATGGTATGGTCCGACATGAGTTACTGATTAGAGTTTTGAAG
131 ATATGATATGTATCCGACACCAGTATGGTATGGTCCGACATGAGTTACTGATTAGAGTTTTGAAG
31643 TA
196 TA
*
31645 TTGTTGCTTACATGTTTGATTTTATGTCTAACTTGGTAGTTTATTATTTGATCCTTCAATGATAA
1 TTGTTGCTTACATGTTTGATTTTATGTCTAACTTAGTAGTTTATTATTTGATCCTTCAATGATAA
* * * *
31710 TGCAATTTTTGTGGGTTAGATGTGGTTTTAAGGCTATGTTACTTAAACTTGGATGTGGGTTTTAA
66 TGCAATTTTTGTGAGTTAAATATGGTTTTAAGGCTATGTTACTTAAACTTGGATGTGGGTCTTAA
31775 ATATGATATGTATCCGACACCAGTATGGT
131 ATATGATATGTATCCGACACCAGTATGGT
31804 CAGAGACAGG
Statistics
Matches: 145, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
197 145 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (197 bp):
TTGTTGCTTACATGTTTGATTTTATGTCTAACTTAGTAGTTTATTATTTGATCCTTCAATGATAA
TGCAATTTTTGTGAGTTAAATATGGTTTTAAGGCTATGTTACTTAAACTTGGATGTGGGTCTTAA
ATATGATATGTATCCGACACCAGTATGGTATGGTCCGACATGAGTTACTGATTAGAGTTTTGAAG
TA
Found at i:41811 original size:17 final size:18
Alignment explanation
Indices: 41777--41811 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
41767 AGAACCAGTA
*
41777 TGGACCAGATGAATTGGT
1 TGGACCAGATGAACTGGT
41795 TGGACCA-ATGAACTGGT
1 TGGACCAGATGAACTGGT
41812 AGCTTGATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.29, C:0.14, G:0.31, T:0.26
Consensus pattern (18 bp):
TGGACCAGATGAACTGGT
Found at i:46339 original size:15 final size:15
Alignment explanation
Indices: 46319--46352 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
46309 TTTTCTAAAG
46319 AAATAACCCGAATTT
1 AAATAACCCGAATTT
**
46334 AAATAATTCGAATTT
1 AAATAACCCGAATTT
46349 AAAT
1 AAAT
46353 TTAAATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (15 bp):
AAATAACCCGAATTT
Found at i:51339 original size:8 final size:8
Alignment explanation
Indices: 51328--51426 Score: 54
Period size: 8 Copynumber: 11.6 Consensus size: 8
51318 ATCATTCATT
*
51328 CATACATA
1 CATACACA
51336 CATACACA
1 CATACACA
*
51344 CATTGACATA
1 CA-T-ACACA
51354 CACTGACACA
1 CA-T-ACACA
*
51364 CACACACA
1 CATACACA
*
51372 CACACACA
1 CATACACA
*
51380 CACACACA
1 CATACACA
*
51388 CACACACA
1 CATACACA
* *
51396 TCCTTACATA
1 --CATACACA
*
51406 CATACATA
1 CATACACA
*
51414 CATACATA
1 CATACACA
51422 CATAC
1 CATAC
51427 CTGAGAGAGG
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
8 58 0.74
9 1 0.01
10 19 0.24
ACGTcount: A:0.45, C:0.36, G:0.02, T:0.16
Consensus pattern (8 bp):
CATACACA
Found at i:51364 original size:2 final size:2
Alignment explanation
Indices: 51359--51395 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51349 ACATACACTG
51359 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
51396 TCCTTACATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51407 original size:4 final size:4
Alignment explanation
Indices: 51400--51426 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
51390 CACACATCCT
51400 TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TAC
51427 CTGAGAGAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:63157 original size:22 final size:19
Alignment explanation
Indices: 63104--63157 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
63094 TATAACTTTT
*
63104 ATTTTAAATTAGTCTATAA
1 ATTTTAAATTATTCTATAA
63123 ATTTTAAGA-TATTCTAATAA
1 ATTTTAA-ATTATTCT-ATAA
63143 CATCTTTAAATTATT
1 -AT-TTTAAATTATT
63158 GATGTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 12 0.41
20 5 0.17
21 3 0.10
22 9 0.31
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (19 bp):
ATTTTAAATTATTCTATAA
Found at i:66691 original size:16 final size:16
Alignment explanation
Indices: 66659--66689 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
66649 GTATATAACT
66659 TTCACACAATAAAAAA
1 TTCACACAATAAAAAA
66675 TTCACA-AATAAAAAA
1 TTCACACAATAAAAAA
66690 ATAAATAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (16 bp):
TTCACACAATAAAAAA
Found at i:78579 original size:16 final size:16
Alignment explanation
Indices: 78555--78592 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
78545 CTCTATTTAC
**
78555 TAATT-TTATCATTTT
1 TAATTATTATCAAATT
78570 TAATTATTATCAAATT
1 TAATTATTATCAAATT
78586 TAATTAT
1 TAATTAT
78593 GAATCAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (16 bp):
TAATTATTATCAAATT
Found at i:78600 original size:17 final size:16
Alignment explanation
Indices: 78568--78601 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
78558 TTTTATCATT
*
78568 TTTAATTATTATCAAA
1 TTTAATTATAATCAAA
78584 TTTAATTATGAATCAAA
1 TTTAATTAT-AATCAAA
78601 T
1 T
78602 GATAGTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
TTTAATTATAATCAAA
Found at i:92648 original size:36 final size:36
Alignment explanation
Indices: 92601--92672 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
92591 TTTAAAATTT
92601 CCAATGCATATTAGGAGAAAAACCCATAGGTTTTAA
1 CCAATGCATATTAGGAGAAAAACCCATAGGTTTTAA
92637 CCAATGCATATTAGGAGAAAAACCCATAGGTTTTAA
1 CCAATGCATATTAGGAGAAAAACCCATAGGTTTTAA
92673 TGTTATGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (36 bp):
CCAATGCATATTAGGAGAAAAACCCATAGGTTTTAA
Found at i:98218 original size:4 final size:4
Alignment explanation
Indices: 98209--98263 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
98199 TATTTGCTTC
98209 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
98257 GCAT GTA
1 GTAT GTA
98264 CGAGGGTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:100937 original size:2 final size:2
Alignment explanation
Indices: 100930--100957 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
100920 TGTTACTTAG
100930 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
100958 TCATGATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103442 original size:2 final size:2
Alignment explanation
Indices: 103435--103459 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103425 AATAATTCAA
103435 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
103460 AGTGAATCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:107615 original size:30 final size:29
Alignment explanation
Indices: 107556--107620 Score: 69
Period size: 30 Copynumber: 2.2 Consensus size: 29
107546 AAAATATTTT
** *
107556 TTTTTGAAAAAGTTAAATATTATTGGATA
1 TTTTTGAAAAAAATAAATATTATTAGATA
107585 TTTTTGAAAAAAAATAAATATT-TTAAGATA
1 TTTTTG-AAAAAAATAAATATTATT-AGATA
107615 TATTTT
1 T-TTTT
107621 TTTTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 8 0.27
30 18 0.60
31 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (29 bp):
TTTTTGAAAAAAATAAATATTATTAGATA
Found at i:112271 original size:2 final size:2
Alignment explanation
Indices: 112264--112289 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
112254 CTTTGATCAC
112264 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
112290 CAAAAAGCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:112909 original size:2 final size:2
Alignment explanation
Indices: 112904--112932 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
112894 TTTATTTATT
112904 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
112933 NATAAAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:125350 original size:29 final size:31
Alignment explanation
Indices: 125318--125378 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
125308 TATATTTTTA
*
125318 TTTATATTTTTAAAAGG-TTAAAT-TAATTT
1 TTTATAGTTTTAAAAGGATTAAATGTAATTT
*
125347 TTTATCGTTTTAAAAGGATTAAATGTAATTT
1 TTTATAGTTTTAAAAGGATTAAATGTAATTT
125378 T
1 T
125379 ACCGTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
30 6 0.21
31 7 0.25
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (31 bp):
TTTATAGTTTTAAAAGGATTAAATGTAATTT
Found at i:131804 original size:16 final size:17
Alignment explanation
Indices: 131783--131820 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
131773 ATTCCAATTC
131783 AAAATGATAT-AAATCT
1 AAAATGATATGAAATCT
* *
131799 AAAATGATTTGAAATTT
1 AAAATGATATGAAATCT
131816 AAAAT
1 AAAAT
131821 CGAAAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (17 bp):
AAAATGATATGAAATCT
Found at i:131818 original size:17 final size:16
Alignment explanation
Indices: 131778--131820 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
131768 ATACAATTCC
*
131778 AATTCAAAATGATATA
1 AATTTAAAATGATATA
* *
131794 AATCTAAAATGATTTGA
1 AATTTAAAATGATAT-A
131811 AATTTAAAAT
1 AATTTAAAAT
131821 CGAAAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (16 bp):
AATTTAAAATGATATA
Found at i:132587 original size:4 final size:4
Alignment explanation
Indices: 132570--132687 Score: 109
Period size: 4 Copynumber: 30.2 Consensus size: 4
132560 TTTCGGGTTC
* * * * *
132570 GTAT GTAT GCAT GTAT GTAT GTAT G--T GTAT GCAT GCAT GCAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
132616 GTAT GTA- -TAT GTCT GTAT GTAT GTGT GTAGT GTGT GTAT TTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTA-T GTAT GTAT GTAT GTAT
*
132663 TTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
132688 GTGTAGGTGT
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.04
4 88 0.93
5 3 0.03
ACGTcount: A:0.22, C:0.05, G:0.26, T:0.47
Consensus pattern (4 bp):
GTAT
Found at i:132650 original size:7 final size:8
Alignment explanation
Indices: 132633--132715 Score: 60
Period size: 8 Copynumber: 10.4 Consensus size: 8
132623 TATGTCTGTA
132633 TGTATGTG
1 TGTATGTG
132641 TGTAGTGTG
1 TGTA-TGTG
* *
132650 TGTATTTA
1 TGTATGTG
* *
132658 TGTATTTA
1 TGTATGTG
*
132666 TGTATGTA
1 TGTATGTG
*
132674 TGTATGTA
1 TGTATGTG
132682 TGTATG-G
1 TGTATGTG
*
132689 TGTAGGTG
1 TGTATGTG
* *
132697 TGCACGTG
1 TGTATGTG
*
132705 TGTGTGTG
1 TGTATGTG
132713 TGT
1 TGT
132716 GTACCTTCTT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
7 5 0.08
8 50 0.79
9 8 0.13
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (8 bp):
TGTATGTG
Found at i:135365 original size:81 final size:82
Alignment explanation
Indices: 135257--135472 Score: 229
Period size: 85 Copynumber: 2.6 Consensus size: 82
135247 CATAACCTTT
* * * * *
135257 GTAAATCCAATATTCGGATCTCAACATTT-ACAACCCTTTCTCCTATTTCAACCATAACCAATGT
1 GTAAGTCCAAGATTCGAATCTCGACATTTCACAACCCTTTCTCCTATTTCAACCAAAACCAATGT
** * *
135321 TTCATATTCATCTTTTA
66 TTCATACACAACTTTCA
*
135338 GTAAGTCCAAGATTCGAATCTCGACATTTACAGCAATCCCTTTCT-CTCGTTTCAACCAAAACCA
1 GTAAGTCCAAGATTCGAATCTCGACATTT-CA-CAA-CCCTTTCTCCT-ATTTCAACCAAAACCA
135402 ATGTTTCATACACAACTTTCA
62 ATGTTTCATACACAACTTTCA
* **
135423 GTGAGTTAAAGATTCGAATCTCTGACATTTCCAACAACCCTTTTCTCCTA
1 GTAAGTCCAAGATTCGAATCTC-GACATTT-C-ACAACCC-TTTCTCCTA
135473 ATGTAAAATC
Statistics
Matches: 111, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
81 25 0.23
83 1 0.01
84 5 0.05
85 61 0.55
86 16 0.14
87 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (82 bp):
GTAAGTCCAAGATTCGAATCTCGACATTTCACAACCCTTTCTCCTATTTCAACCAAAACCAATGT
TTCATACACAACTTTCA
Done.