Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010880.1 Kokia drynarioides strain JFW-HI SEQ_125848, 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: 95135
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 4 characters in sequence are not A, C, G, or T
Found at i:1281 original size:13 final size:13
Alignment explanation
Indices: 1263--1290 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1253 AGATATAGAC
1263 TATTAAAATAATA
1 TATTAAAATAATA
1276 TATTAAAATAATA
1 TATTAAAATAATA
1289 TA
1 TA
1291 ATTGTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TATTAAAATAATA
Found at i:4196 original size:2 final size:2
Alignment explanation
Indices: 4189--4214 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4179 TAGCTTTTTG
4189 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
4215 TTCACTGTAA
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:4395 original size:2 final size:2
Alignment explanation
Indices: 4388--4426 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4378 CTACAAACAG
4388 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4427 TAAGGGAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:16452 original size:3 final size:3
Alignment explanation
Indices: 16446--16484 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
16436 AGAAGAAGAA
* *
16446 GAT GAT GAT GAT GAT GAT GAT GAC GAC GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
16485 CTTTTTACAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.05, G:0.33, T:0.28
Consensus pattern (3 bp):
GAT
Found at i:16545 original size:186 final size:183
Alignment explanation
Indices: 16202--16578 Score: 619
Period size: 186 Copynumber: 2.0 Consensus size: 183
16192 TGCAAAAGGT
* * **
16202 TCGAAAACGAGCTTCCTGTCGTTTGTTCTCCTTAGATTTGTTGAACGGTGAAGAAGAAGATGATG
1 TCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGAAGATGATG
16267 ATGATGATGATGATGACAACGACGACGATGATCTTTTTAAAGCTATTGATGATGATGGTGATGAC
66 ATGATGATGATGATGACAACGACGACGATGATCTTTTTAAAGCTATTGATGATGATGGTGATGAC
*
16332 GACGATGAGGACAATGATGCGCCAGTTGCAGAGTTGTCAATTCTGCCCCGAAA
131 GACGATGAGGACAATGATGCACCAGTTGCAGAGTTGTCAATTCTGCCCCGAAA
16385 TCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGAAGAAGATG
1 TCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGT---GAAGAAGAAGATG
* * * *
16450 ATGATGATGATGATGATGACGACGATGATGATGATCTTTTTACAGCTATTGATGATGATGGTGAT
63 ATGATGATGATGATGATGACAACGACGACGATGATCTTTTTAAAGCTATTGATGATGATGGTGAT
* * *
16515 GATGCCGATGAGGACAATGATGCACCAGTTGCAGAGTTGTCAATTCTGCCTCGAAA
128 GACGACGATGAGGACAATGATGCACCAGTTGCAGAGTTGTCAATTCTGCCCCGAAA
16571 TCGAAAAC
1 TCGAAAAC
16579 TCAACTCGAA
Statistics
Matches: 179, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
183 45 0.25
186 134 0.75
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.28
Consensus pattern (183 bp):
TCGAAAACGAGCTTCCCGTCGTTTGTTCTCCTTAGATTGGTCAAACGGTGAAGAAGAAGATGATG
ATGATGATGATGATGACAACGACGACGATGATCTTTTTAAAGCTATTGATGATGATGGTGATGAC
GACGATGAGGACAATGATGCACCAGTTGCAGAGTTGTCAATTCTGCCCCGAAA
Found at i:16625 original size:18 final size:18
Alignment explanation
Indices: 16601--16651 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
16591 TGACCTGTTC
*
16601 CGATGATGATAATGAAGG
1 CGATGATGACAATGAAGG
* *
16619 TGATGATGACAATGATGG
1 CGATGATGACAATGAAGG
*
16637 CGATGATGGCAATGA
1 CGATGATGACAATGA
16652 CGATGCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.33, T:0.24
Consensus pattern (18 bp):
CGATGATGACAATGAAGG
Found at i:30463 original size:3 final size:3
Alignment explanation
Indices: 30455--30480 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30445 AAACACTCTT
30455 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
30481 TTGGTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:32840 original size:29 final size:30
Alignment explanation
Indices: 32806--32868 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
32796 CAAACTTGGA
*
32806 TACCAAATTGAGACA-AAATA-AAATTCAAG
1 TACCAAATTGA-ACATAAAAACAAATTCAAG
32835 TACCAAATTGAACATAAAAACTAAATTCAAG
1 TACCAAATTGAACATAAAAAC-AAATTCAAG
32866 TAC
1 TAC
32869 TAATTAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 3 0.10
29 15 0.50
31 12 0.40
ACGTcount: A:0.54, C:0.16, G:0.08, T:0.22
Consensus pattern (30 bp):
TACCAAATTGAACATAAAAACAAATTCAAG
Found at i:34440 original size:18 final size:18
Alignment explanation
Indices: 34409--34451 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
34399 TAAATTAACT
*
34409 AATAACATTATAAA-ATAA
1 AATAAAATTATAAAGAT-A
*
34427 AATAAAATTTTAAAGATA
1 AATAAAATTATAAAGATA
34445 AATAAAA
1 AATAAAA
34452 ATTAAAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (18 bp):
AATAAAATTATAAAGATA
Found at i:37087 original size:166 final size:166
Alignment explanation
Indices: 36813--37148 Score: 627
Period size: 166 Copynumber: 2.0 Consensus size: 166
36803 AACCTCTCAC
36813 TTTGCGACTGGGTTTTTGAAGACAACCCACAGCTGAGCTTCATTTATCTTCCTCTCCAATCAAAC
1 TTTGCGACTGGGTTTTTGAAGACAACCCACAGCTGAGCTTCATTTATCTTCCTCTCCAATCAAAC
*
36878 GGTACCATCTAATTCACTGTGTGCTTCACTTTCTGGGTTTCTTTTTCCTTTGTTGTTCTTTTCTT
66 GGTACCATCTAAATCACTGTGTGCTTCACTTTCTGGGTTTCTTTTTCCTTTGTTGTTCTTTTCTT
36943 TGCACCACAAAAAAGAAGTAGGGTGAAAGATTTACA
131 TGCACCACAAAAAAGAAGTAGGGTGAAAGATTTACA
* *
36979 TTTGCGACTGGGTTTTTGAAGACAACCCACAGCTGAGCTTCATTTATCTTCCTCTCCAATTAAAT
1 TTTGCGACTGGGTTTTTGAAGACAACCCACAGCTGAGCTTCATTTATCTTCCTCTCCAATCAAAC
37044 GGTACCATCTAAATCACTGTGTGCTTCACTTTCTGGGTTTCTTTTTCCTTTGTTGTTCTTTTCTT
66 GGTACCATCTAAATCACTGTGTGCTTCACTTTCTGGGTTTCTTTTTCCTTTGTTGTTCTTTTCTT
* *
37109 TGCACCACAAAAAAGATGTAGGGTGAAAGATTTAGA
131 TGCACCACAAAAAAGAAGTAGGGTGAAAGATTTACA
37145 TTTG
1 TTTG
37149 GGAGTTTAAG
Statistics
Matches: 165, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 165 1.00
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.38
Consensus pattern (166 bp):
TTTGCGACTGGGTTTTTGAAGACAACCCACAGCTGAGCTTCATTTATCTTCCTCTCCAATCAAAC
GGTACCATCTAAATCACTGTGTGCTTCACTTTCTGGGTTTCTTTTTCCTTTGTTGTTCTTTTCTT
TGCACCACAAAAAAGAAGTAGGGTGAAAGATTTACA
Found at i:44319 original size:84 final size:84
Alignment explanation
Indices: 44213--44381 Score: 338
Period size: 84 Copynumber: 2.0 Consensus size: 84
44203 AAACTTATGA
44213 TCTAAAAGGGGAATTAGAGATGCCACAATCTGCACACATAAACATATTTAACAACAATGATCAAT
1 TCTAAAAGGGGAATTAGAGATGCCACAATCTGCACACATAAACATATTTAACAACAATGATCAAT
44278 TTAGGAGCATAACATGATT
66 TTAGGAGCATAACATGATT
44297 TCTAAAAGGGGAATTAGAGATGCCACAATCTGCACACATAAACATATTTAACAACAATGATCAAT
1 TCTAAAAGGGGAATTAGAGATGCCACAATCTGCACACATAAACATATTTAACAACAATGATCAAT
44362 TTAGGAGCATAACATGATT
66 TTAGGAGCATAACATGATT
44381 T
1 T
44382 AACAAAAACA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (84 bp):
TCTAAAAGGGGAATTAGAGATGCCACAATCTGCACACATAAACATATTTAACAACAATGATCAAT
TTAGGAGCATAACATGATT
Found at i:45678 original size:6 final size:6
Alignment explanation
Indices: 45667--45691 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45657 AGTTGAAGGC
45667 ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT A
45692 AGAAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:48473 original size:57 final size:58
Alignment explanation
Indices: 48337--48491 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 58
48327 CTACCTGAAT
* * * ** * *
48337 TTGACACTTTTTACTAATTTGATATTTAAACTTTTTTTTGACCCAATTTGATACTTGAAC
1 TTGACAATTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGATACTT--AC
*
48397 TAGACAATTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGATACTT-C
1 TTGACAATTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGATACTTAC
*
48454 TTGACATTTTTTCCTAATTTGGTACCTAAGCTTTTTTT
1 TTGACAATTTTTCCTAATTTGGTACCTAAGCTTTTTTT
48492 TTTTTTTAAG
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
57 37 0.44
60 48 0.56
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (58 bp):
TTGACAATTTTTCCTAATTTGGTACCTAAGCTTTTTTTGGACCCAATTTGATACTTAC
Found at i:48491 original size:28 final size:28
Alignment explanation
Indices: 48404--48493 Score: 69
Period size: 28 Copynumber: 3.2 Consensus size: 28
48394 AACTAGACAA
48404 TTTTTCCTAATTTGGTACCTAAGCTTTT
1 TTTTTCCTAATTTGGTACCTAAGCTTTT
** * * * *
48432 TTTGGACCCAATTTGATA-CT--TCTTGACAT
1 TTT-TTCCTAATTTGGTACCTAAGCTT---TT
48461 TTTTTCCTAATTTGGTACCTAAGCTTTT
1 TTTTTCCTAATTTGGTACCTAAGCTTTT
48489 TTTTT
1 TTTTT
48494 TTTTTAAGAT
Statistics
Matches: 43, Mismatches: 12, Indels: 14
0.62 0.17 0.20
Matches are distributed among these distances:
26 3 0.07
28 21 0.49
29 16 0.37
31 3 0.07
ACGTcount: A:0.19, C:0.18, G:0.11, T:0.52
Consensus pattern (28 bp):
TTTTTCCTAATTTGGTACCTAAGCTTTT
Found at i:48701 original size:31 final size:32
Alignment explanation
Indices: 48663--48741 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 32
48653 AATATGAGGG
48663 ACCAAATTAGA-AAAAAGAGTCAAGTTTAAGT
1 ACCAAATTAGACAAAAAGAGTCAAGTTTAAGT
* ** *
48694 ACCAAATTA-AGAAAAATTGTCAAGTTTGAGT
1 ACCAAATTAGACAAAAAGAGTCAAGTTTAAGT
48725 ACCAAATTAGACAAAAA
1 ACCAAATTAGACAAAAA
48742 AGTTTAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
30 1 0.02
31 35 0.83
32 6 0.14
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (32 bp):
ACCAAATTAGACAAAAAGAGTCAAGTTTAAGT
Found at i:48776 original size:31 final size:30
Alignment explanation
Indices: 48663--48776 Score: 92
Period size: 31 Copynumber: 3.8 Consensus size: 30
48653 AATATGAGGG
* *
48663 ACCAAATTAGAAAAAAGAGTCAAGTTTAAGT
1 ACCAAATTA-AAAAAAAAGTCAAGTTTAAAT
** * *
48694 ACCAAATTAAGAAAAATTGTCAAGTTTGAGT
1 ACCAAATTAA-AAAAAAAGTCAAGTTTAAAT
* *
48725 ACCAAATT-AGACAAAA---AAGTTTAAAT
1 ACCAAATTAAAAAAAAAGTCAAGTTTAAAT
*
48751 ATCAAATTAAAAAAAAATGTCAAGTT
1 ACCAAATTAAAAAAAAA-GTCAAGTT
48777 CAGATATCAA
Statistics
Matches: 65, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
26 15 0.23
27 6 0.09
29 3 0.05
30 2 0.03
31 39 0.60
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (30 bp):
ACCAAATTAAAAAAAAAGTCAAGTTTAAAT
Found at i:55274 original size:30 final size:30
Alignment explanation
Indices: 55240--55318 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 30
55230 TAATTTTGAT
55240 TAATTAAGTGATCAATTTAAAAAATATCCA
1 TAATTAAGTGATCAATTTAAAAAATATCCA
* *
55270 TAATTGAA-TG----A-TT-GAAAATTTCCA
1 TAATT-AAGTGATCAATTTAAAAAATATCCA
55294 TAATTAAGTGATCAATTTAAAAAAT
1 TAATTAAGTGATCAATTTAAAAAAT
55319 TTATAATTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
23 2 0.05
24 16 0.42
25 2 0.05
26 1 0.03
28 1 0.03
29 2 0.05
30 12 0.32
31 2 0.05
ACGTcount: A:0.48, C:0.08, G:0.09, T:0.35
Consensus pattern (30 bp):
TAATTAAGTGATCAATTTAAAAAATATCCA
Found at i:55350 original size:54 final size:54
Alignment explanation
Indices: 55240--55352 Score: 149
Period size: 54 Copynumber: 2.1 Consensus size: 54
55230 TAATTTTGAT
***
55240 TAATTAAGTGATCAATTTAAAAAATATCCATAATTGAATGATTGAAAATTTCCA
1 TAATTAAGTGATCAATTTAAAAAATATCCATAATTGAATGATTGAAAAAACCCA
* *
55294 TAATTAAGTGATCAATTTAAAAAAT-T-TATAATTGAGTGATTGAAAAAAACCACA
1 TAATTAAGTGATCAATTTAAAAAATATCCATAATTGAATGATTG-AAAAAACC-CA
55348 TAATT
1 TAATT
55353 TAAAAGATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 14 0.27
53 6 0.12
54 32 0.62
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (54 bp):
TAATTAAGTGATCAATTTAAAAAATATCCATAATTGAATGATTGAAAAAACCCA
Found at i:55789 original size:14 final size:15
Alignment explanation
Indices: 55758--55791 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55748 TAAAAAGGTC
*
55758 TTTATTTATTTAATT
1 TTTATTTACTTAATT
55773 TTTATTTACTT-ATT
1 TTTATTTACTTAATT
55787 TTTAT
1 TTTAT
55792 CACGATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTTACTTAATT
Found at i:62320 original size:25 final size:25
Alignment explanation
Indices: 62291--62356 Score: 105
Period size: 25 Copynumber: 2.6 Consensus size: 25
62281 AAAATCAAGT
* *
62291 AAATATTTAAATATAATTCTTCAAA
1 AAATATTTAAACATAATTATTCAAA
62316 AAATATTTAAACATAATTATTCAAA
1 AAATATTTAAACATAATTATTCAAA
*
62341 AAATATTTAGACATAA
1 AAATATTTAAACATAA
62357 AATATATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (25 bp):
AAATATTTAAACATAATTATTCAAA
Found at i:66506 original size:75 final size:75
Alignment explanation
Indices: 66152--66493 Score: 540
Period size: 75 Copynumber: 4.6 Consensus size: 75
66142 TGAACAAGCT
* * * * *
66152 AATATGGGCCAGAGTACAAGAGAGTCAGTCGGGTCAGAACCCTGGTTCCAGAATCCACCATGGCA
1 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGGCA
66217 ACCACCTCAA
66 ACCACCTCAA
* * * *
66227 AATATGGGCCATAATAAAAGAGAGCCAGTCGGGTCAGAACCCCGGTTCCAAAATCCACCACGGCA
1 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGGCA
66292 ACCACCTCAA
66 ACCACCTCAA
*
66302 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGTCA
1 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGGCA
66367 ACCACCTCAA
66 ACCACCTCAA
* * * *
66377 AATATGGGCCAGAATATAAGAGAGCCAGTCCGATCAGAACCCTGGTTCCAATATCCACCACGGCA
1 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGGCA
66442 ACCACCTCAA
66 ACCACCTCAA
* *
66452 AATATGGTCCAGAATACAAGAGAGCCAGTTAGGTCAGAACCC
1 AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCC
66494 CAATTCCCAT
Statistics
Matches: 245, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 245 1.00
ACGTcount: A:0.35, C:0.29, G:0.21, T:0.15
Consensus pattern (75 bp):
AATATGGGCCAGAATACAAGAGAGCCAGTCAGGTCAGAACCCTGGTTCCAAAATCCACCACGGCA
ACCACCTCAA
Found at i:83611 original size:175 final size:175
Alignment explanation
Indices: 83320--83669 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
83310 CTAAATTTTG
83320 CACCACTCCATTGCCAGTATGAAAGCATGAATAAGACCTATATACAACTATTTTAATTGGTTGTG
1 CACCACTCCATTGCCAGTATGAAAGCATGAATAAGACCTATATACAACTATTTTAATTGGTTGTG
83385 CTAGACTTTTGCATATATTTTTTCATATTCGTTGTAAAGGTTAACTTCCAGGTTGGTCGTTTTTA
66 CTAGACTTTTGCATATATTTTTTCATATTCGTTGTAAAGGTTAACTTCCAGGTTGGTCGTTTTTA
83450 CTTCATTAACTAGACTTCAGTTATATTGATACTACATGAGGAGAA
131 CTTCATTAACTAGACTTCAGTTATATTGATACTACATGAGGAGAA
83495 CACCACTCCATTGCCAGTATGAAAGCATGAATAAGACCTATATACAACTATTTTAATTGGTTGTG
1 CACCACTCCATTGCCAGTATGAAAGCATGAATAAGACCTATATACAACTATTTTAATTGGTTGTG
83560 CTAGACTTTTGCATATATTTTTTCATATTCGTTGTAAAGGTTAACTTCCAGGTTGGTCGTTTTTA
66 CTAGACTTTTGCATATATTTTTTCATATTCGTTGTAAAGGTTAACTTCCAGGTTGGTCGTTTTTA
83625 CTTCATTAACTAGACTTCAGTTATATTGATACTACATGAGGAGAA
131 CTTCATTAACTAGACTTCAGTTATATTGATACTACATGAGGAGAA
83670 TGAGTTTAAG
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (175 bp):
CACCACTCCATTGCCAGTATGAAAGCATGAATAAGACCTATATACAACTATTTTAATTGGTTGTG
CTAGACTTTTGCATATATTTTTTCATATTCGTTGTAAAGGTTAACTTCCAGGTTGGTCGTTTTTA
CTTCATTAACTAGACTTCAGTTATATTGATACTACATGAGGAGAA
Found at i:84540 original size:21 final size:22
Alignment explanation
Indices: 84514--84563 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
84504 ATAAAGTAAG
84514 TTATATATTAT-TTTT-CTAAT
1 TTATATATTATATTTTACTAAT
84534 ATTATATATTATAATTTTACTAAT
1 -TTATATATTAT-ATTTTACTAAT
84558 TTATAT
1 TTATAT
84564 TTTAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 11 0.42
23 10 0.38
24 5 0.19
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATATTATATTTTACTAAT
Found at i:84551 original size:23 final size:23
Alignment explanation
Indices: 84514--84572 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
84504 ATAAAGTAAG
84514 TTATATATTAT--TTTT-CTAAT
1 TTATATATTATAATTTTACTAAT
84534 ATTATATATTATAATTTTACTAAT
1 -TTATATATTATAATTTTACTAAT
*
84558 TTATATTTTAATAAT
1 TTATATATT-ATAAT
84573 AATTATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 11 0.33
23 12 0.36
24 10 0.30
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (23 bp):
TTATATATTATAATTTTACTAAT
Found at i:84661 original size:48 final size:47
Alignment explanation
Indices: 84564--84657 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
84554 TAATTTATAT
* *
84564 TTTAATAATAATTATATTAAAAACGTTATTAAATTATATATTATTTTA
1 TTTAATAATAAATATATTAAAAAC-TAATTAAATTATATATTATTTTA
* *
84612 TTTAATAATAAATATGTTAAAATA-TAATTAAATTATTTATTATTTT
1 TTTAATAATAAATATATTAAAA-ACTAATTAAATTATATATTATTTT
84658 TATTAAATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 20 0.49
48 20 0.49
49 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (47 bp):
TTTAATAATAAATATATTAAAAACTAATTAAATTATATATTATTTTA
Found at i:86160 original size:16 final size:16
Alignment explanation
Indices: 86139--86170 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
86129 ATTACAATTA
*
86139 TATTACAGTTCTATTC
1 TATTACAATTCTATTC
86155 TATTACAATTCTATTC
1 TATTACAATTCTATTC
86171 AATTGCAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.03, T:0.50
Consensus pattern (16 bp):
TATTACAATTCTATTC
Found at i:90429 original size:19 final size:19
Alignment explanation
Indices: 90405--90447 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
90395 AAATAATCTC
90405 ATCATTGTTCGGTTATTCT
1 ATCATTGTTCGGTTATTCT
90424 ATCATTGTTCGGTTATTCT
1 ATCATTGTTCGGTTATTCT
90443 ATCAT
1 ATCAT
90448 AAACATCAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (19 bp):
ATCATTGTTCGGTTATTCT
Done.