Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011032.1 Kokia drynarioides strain JFW-HI SEQ_126003, 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: 24904
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Warning! 160 characters in sequence are not A, C, G, or T
Found at i:2626 original size:17 final size:17
Alignment explanation
Indices: 2544--2638 Score: 75
Period size: 17 Copynumber: 5.5 Consensus size: 17
2534 TCAATTTTAG
* * *
2544 ATTTTAAATTTTAAGTC
1 ATTTTAAATTTAAATTT
* * *
2561 ATTATAAGTTTAAATCT
1 ATTTTAAATTTAAATTT
* **
2578 ATTGTAAATTTAAGCTT
1 ATTTTAAATTTAAATTT
2595 A-TTTAAAGTTTAAATTT
1 ATTTTAAA-TTTAAATTT
*
2612 ATTTTAAATTTAAATCT
1 ATTTTAAATTTAAATTT
2629 ATTTTGAAAT
1 ATTTT-AAAT
2639 AAAATTTAAA
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
16 5 0.08
17 45 0.75
18 10 0.17
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:2632 original size:34 final size:35
Alignment explanation
Indices: 2544--2632 Score: 96
Period size: 34 Copynumber: 2.6 Consensus size: 35
2534 TCAATTTTAG
*
2544 ATTTTAAATTTTAAGTC-A-TTATAAGTTTAAATCT
1 ATTTTAAA-TTTAAATCTATTTATAAGTTTAAATCT
* * *
2578 ATTGTAAATTT-AAGCTTATTTA-AAGTTTAAATTT
1 ATTTTAAATTTAAATC-TATTTATAAGTTTAAATCT
2612 ATTTTAAATTTAAATCTATTT
1 ATTTTAAATTTAAATCTATTT
2633 TGAAATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
32 2 0.04
33 3 0.07
34 34 0.76
35 6 0.13
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (35 bp):
ATTTTAAATTTAAATCTATTTATAAGTTTAAATCT
Found at i:3300 original size:3 final size:3
Alignment explanation
Indices: 3292--3321 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3282 GCATTGAATG
3292 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3322 GATGACGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3326 original size:3 final size:3
Alignment explanation
Indices: 3320--3351 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3310 AATAATAATA
*
3320 ATG ATG ACG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3352 ATTAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (3 bp):
ATG
Found at i:4595 original size:30 final size:29
Alignment explanation
Indices: 4569--5006 Score: 201
Period size: 29 Copynumber: 14.9 Consensus size: 29
4559 ATATTTTAGC
* *
4569 CCCTGAAGTTTTCAAAAATTACATTTTGA
1 CCCTGAACTTTTCAAAAATTACATTTTAA
* ** * *
4598 CTCTCGAACTTCACAAAAATTATATTTCT-G
1 CCCT-GAACTTTTCAAAAATTACATTT-TAA
* *
4628 CCTTGAAC-TTCCAAAAATTACATTTTAAA
1 CCCTGAACTTTTCAAAAATTACATTTT-AA
* * * *
4657 CCCTAAAC-TTTCCAAAATTCCCTTTTTAA
1 CCCTGAACTTTTCAAAAATT-ACATTTTAA
* *
4686 CCCTAAACTTTTCCAAAATTACCATTTT-A
1 CCCTGAACTTTTCAAAAATTA-CATTTTAA
*
4715 CCCTCGAACTTTT-AAAAATTCCATTTTTAA
1 CCCT-GAACTTTTCAAAAATTACA-TTTTAA
* *
4745 CCCCGAACTTTTCCAAAATTATCATTTT-A
1 CCCTGAACTTTTCAAAAATTA-CATTTTAA
* * * * *
4774 CCCTTAAATCTCCAAAAATTCCATTTTTAA
1 CCCTGAACTTTTCAAAAATTACA-TTTTAA
* *
4804 CCCTGACATTTTTC-AAAATTACCATTTTAC
1 CCCTGA-ACTTTTCAAAAATTA-CATTTTAA
* * *
4834 CCCCGAACTTCT-AAAAATTCCATTTTAA
1 CCCTGAACTTTTCAAAAATTACATTTTAA
4862 -CCTCGAACTTTTTC-AAAATTACGATTTT-A
1 CCCT-GAAC-TTTTCAAAAATTAC-ATTTTAA
* *
4891 CCCTCGAA--TGTCAAAAAATTCCATTTTTAA
1 CCCT-GAACTTTTC-AAAAATTACA-TTTTAA
* *
4921 -CCTCAAACTTTATC-TAAATTACCATTTT-A
1 CCCT-GAACTTT-TCAAAAATTA-CATTTTAA
* * *
4950 CCCTCGAA-TGTCCAAAAATT-CTAGTTTAA
1 CCCT-GAACTTTTCAAAAATTAC-ATTTTAA
* * *
4979 TCCTAAACTTTTCCAAAATTACCATTTT
1 CCCTGAACTTTTCAAAAATTA-CATTTT
5007 GCCCCCAAGT
Statistics
Matches: 308, Mismatches: 64, Indels: 73
0.69 0.14 0.16
Matches are distributed among these distances:
27 7 0.02
28 37 0.12
29 133 0.43
30 116 0.38
31 13 0.04
32 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (29 bp):
CCCTGAACTTTTCAAAAATTACATTTTAA
Found at i:4652 original size:28 final size:30
Alignment explanation
Indices: 4581--4653 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
4571 CTGAAGTTTT
4581 CAAAAATTACATTTTGACTCTCGAACTTCA
1 CAAAAATTACATTTTGACTCTCGAACTTCA
* *
4611 CAAAAATTATATTTCTG-C-CTTGAACTTC-
1 CAAAAATTACATTT-TGACTCTCGAACTTCA
4639 CAAAAATTACATTTT
1 CAAAAATTACATTTT
4654 AAACCCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.33
29 9 0.23
30 14 0.36
31 2 0.05
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (30 bp):
CAAAAATTACATTTTGACTCTCGAACTTCA
Found at i:4733 original size:59 final size:60
Alignment explanation
Indices: 4636--5034 Score: 387
Period size: 59 Copynumber: 6.8 Consensus size: 60
4626 TGCCTTGAAC
* * *
4636 TTCCAAAAATTA-CATTTTAAACCCT-AAACTTTCC-AAAATTCCCTTTTTAACCCTAAACTT
1 TTCC-AAAATTACCATTTT--ACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCTAAACTT
** **
4696 TTCCAAAATTACCATTTTACCCTCGAACT-TTTAAAAATTCCATTTTTAACCCCGAACTT
1 TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCTAAACTT
* * * * *
4755 TTCCAAAATTATCATTTTACCCT-TAAATCTCCAAAAATTCCATTTTTAACCCT-GACATT
1 TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCTAAAC-TT
* * * *
4814 TTTCAAAATTACCATTTTACCCCCGAACT-TCTAAAAATTCCA-TTTTAA-CCTCGAACTT
1 TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCT-AAACTT
* * *
4872 TTTCAAAATTACGATTTTACCCTCGAA-TGTCAAAAAATTCCATTTTTAA-CCTCAAACTT
1 TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCT-AAACTT
* * * *
4931 TAT-CTAAATTACCATTTTACCCTCGAA-TGTCCAAAAATTCTA-GTTTAATCCTAAACTT
1 T-TCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCTAAACTT
* * *
4989 TTCCAAAATTACCATTTTGCCC-CCAAGTGTCCAAAAATTACCATTT
1 TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATT-CCATTT
5035 GACCCCGAAG
Statistics
Matches: 289, Mismatches: 34, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
57 8 0.03
58 97 0.34
59 169 0.58
60 15 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.37
Consensus pattern (60 bp):
TTCCAAAATTACCATTTTACCCTCGAACTGTCCAAAAATTCCATTTTTAACCCTAAACTT
Found at i:4777 original size:117 final size:113
Alignment explanation
Indices: 4636--5006 Score: 413
Period size: 117 Copynumber: 3.2 Consensus size: 113
4626 TGCCTTGAAC
* *
4636 TTCCAAAAATTACATTTTAAACCCTAAACTTTCCAAAATTCCCTTTTTAACCCTAAACTTTTCCA
1 TTCC-AAAATTACATTTT--ACCCTAAA-TCTCCAAAATTCCATTTTTAACCCTAAACTTTT-CA
*
4701 AAATTACCATTTTACCCTCGAACTTTTAAAAATTCCATTTTTAACCCCGAACTT
61 AAATTACCATTTTACCCTCGAACTTCTAAAAATTCCA-TTTTAACCCCGAACTT
* *
4755 TTCCAAAATTATCATTTTACCCTTAAATCTCCAAAAATTCCATTTTTAACCCTGACATTTTTCAA
1 TTCCAAAATTA-CATTTTACCC-TAAATCTCC-AAAATTCCATTTTTAACCCT-AAACTTTTCAA
* *
4820 AATTACCATTTTACCCCCGAACTTCTAAAAATTCCATTTTAACCTCGAACTT
62 AATTACCATTTTACCCTCGAACTTCTAAAAATTCCATTTTAACCCCGAACTT
* * * * *
4872 TTTCAAAATTACGATTTTACCCTCGAATGTCAAAAAATTCCATTTTTAA-CCTCAAACTTTATCT
1 TTCCAAAATTAC-ATTTTACCCT-AAATCTC-CAAAATTCCATTTTTAACCCT-AAACTTT-TCA
* * * * **
4936 AAATTACCATTTTACCCTCGAA-TGTCCAAAAATTCTAGTTTAATCCTAAACTT
61 AAATTACCATTTTACCCTCGAACT-TCTAAAAATTCCATTTTAACCCCGAACTT
4989 TTCCAAAATTACCATTTT
1 TTCCAAAATTA-CATTTT
5007 GCCCCCAAGT
Statistics
Matches: 218, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
116 11 0.05
117 123 0.56
118 68 0.31
119 16 0.07
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (113 bp):
TTCCAAAATTACATTTTACCCTAAATCTCCAAAATTCCATTTTTAACCCTAAACTTTTCAAAATT
ACCATTTTACCCTCGAACTTCTAAAAATTCCATTTTAACCCCGAACTT
Found at i:5024 original size:28 final size:29
Alignment explanation
Indices: 4990--5062 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
4980 CCTAAACTTT
4990 TCCAAAATTACCATTTTG-CCCCCAAGTG
1 TCCAAAATTACCATTTTGACCCCCAAGTG
*
5018 TCCAAAAATTACCA-TTTGACCCCGAAGTG
1 TCC-AAAATTACCATTTTGACCCCCAAGTG
** *
5047 TTTAAAATTACTATTT
1 TCCAAAATTACCATTT
5063 ACCCCCGGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 16 0.42
29 22 0.58
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.33
Consensus pattern (29 bp):
TCCAAAATTACCATTTTGACCCCCAAGTG
Found at i:5487 original size:97 final size:97
Alignment explanation
Indices: 5305--5480 Score: 239
Period size: 97 Copynumber: 1.8 Consensus size: 97
5295 AACACCTTTA
* * * * *
5305 AAATCGAGACAATATTCCTTTATTTCGAGTTTTGAAAATTTGTTCCTTAACTTACTAGGCGCGAT
1 AAATCGAGACAATATTCCTTTATTTCGAGTTCTGAAAATTTGTGCCTTAACTCACTAGACGCGAC
*
5370 TTTTCTTCAAATCGGAATAATTGAATACCCTT
66 TTTTCTTCAAATCAGAATAATTGAATACCCTT
* * *
5402 AAATCGAGACAATTTTTCTTTATCTGT-G-GTTCTGAAAATTTGTGCCTTAACTCACTAGATGCG
1 AAATCGAGACAATATTCCTTTAT-T-TCGAGTTCTGAAAATTTGTGCCTTAACTCACTAGACGCG
5465 ACTTTTCTTCAAATCA
64 ACTTTTCTTCAAATCA
5481 AGATAATCAA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
97 65 0.96
98 2 0.03
99 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (97 bp):
AAATCGAGACAATATTCCTTTATTTCGAGTTCTGAAAATTTGTGCCTTAACTCACTAGACGCGAC
TTTTCTTCAAATCAGAATAATTGAATACCCTT
Found at i:13863 original size:113 final size:112
Alignment explanation
Indices: 13664--13889 Score: 425
Period size: 113 Copynumber: 2.0 Consensus size: 112
13654 ACCACCACCC
13664 AGCACACAAAAAGAAGTTCGAAGGTTTCTAGGAAGACTAAATTACATTGCTAATTTCAATTCACA
1 AGCACACAAAAAGAAGTTCGAAGGTTTCTAGGAAGACTAAATTACATTGCTAATTTCAATTCACA
13729 GTTGATTGAGAAATATGATCTTATCTTCTGTTTGCTTAGAAAGCGCA
66 GTTGATTGAGAAATATGATCTTATCTTCTGTTTGCTTAGAAAGCGCA
**
13776 ANGCACACAAAAAGAAGTTCGAAGGTTTCTAGGAAGACTAAATTACATTGCTCGTTTCAATTCAC
1 A-GCACACAAAAAGAAGTTCGAAGGTTTCTAGGAAGACTAAATTACATTGCTAATTTCAATTCAC
13841 AGTTGATTGAGAAATATGATCTTATCTTCTGTTTGCTTAGAAAGCGCA
65 AGTTGATTGAGAAATATGATCTTATCTTCTGTTTGCTTAGAAAGCGCA
13889 A
1 A
13890 CCTAGGTGTG
Statistics
Matches: 111, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
112 1 0.01
113 110 0.99
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (112 bp):
AGCACACAAAAAGAAGTTCGAAGGTTTCTAGGAAGACTAAATTACATTGCTAATTTCAATTCACA
GTTGATTGAGAAATATGATCTTATCTTCTGTTTGCTTAGAAAGCGCA
Found at i:17276 original size:201 final size:201
Alignment explanation
Indices: 16924--17966 Score: 1523
Period size: 201 Copynumber: 5.2 Consensus size: 201
16914 TGATGTTGTT
* *
16924 ATCTTCTTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGTAAATCTTCGAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
* * ** *
16989 CTAGCTTCCTGATGAGATACTGAGAAGCAAGTTTAAGCAATAAAATGGTTAGCTTCCTGATAAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
17054 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGAG
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGAG
*
17119 GCAGTC
196 GCGGTC
* * *
17125 AACTTCCTGATGAGATATAGAGAAGTATACCAACTCAAGGATCAATACGAGCAAATCTTCGAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
* *
17190 CCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTTAGCTTCTTGATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * * *
17255 TACTGAGAAGTGCACCAAATTCGTCTCCCTGATAAGATA-AAGAGAAACGGATTCAAACAAGTGA
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAA-AGAAGCGGATTGAAACAAGTGA
17319 GGCGGTC
195 GGCGGTC
* ** *
17326 ATCTTCATGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATGTGAGCAAATCTTCGAACT
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
* *
17391 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCCTAATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* *
17456 TACTGAGAAGTGGACCAAATTCGTTTTCCTGAAAAGATACAAAGAAGCGGATTGAAACAAGTGAG
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGAG
*
17521 GCGGTT
196 GCGGTC
* * * *
17527 ATCTTCCTGATGAGATACAGAGAAGTATACCAACCCAAGGCTTAATGCGAGCAAATCTTCAAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
* *
17592 CCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * * *
17657 TACTGAGAAGTGGACCAAATTCATTTTCCTGATGAGATACAAAGAAGCGGATTGAAACATGTGAG
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGAG
17722 GCGGTC
196 GCGGTC
* *
17728 ATCTTCCTGATGAGATACAGAGAAGTATACCAACCCAAGGCTCAATATGAGCAAATCTTCGAACC
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
* * * * *
17793 CCAGCTTCCTAATGAGATACTGTGAAGCAGGTCGAAGCAGTAAAATGGTTAGCTTCCTAATGATA
66 CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
* * * * * ** * ** *
17858 TACTGAGAAGTGAACCAAATTCATCTTTCTGATGAGACACAGGGAAGTGGATCAAAACAA-TTAT
131 TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGA-
*
17922 TGCGGTC
195 GGCGGTC
** * *
17929 ATCTTCCTGATGAGATAGTGAGAAGTAGACCAAATCAA
1 ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAA
17967 TTACACCAAA
Statistics
Matches: 763, Mismatches: 76, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
200 4 0.01
201 757 0.99
202 2 0.00
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.24
Consensus pattern (201 bp):
ATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCAATACGAGCAAATCTTCGAACC
CCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGA
TACTGAGAAGTGGACCAAATTCGTCTTCCTGATAAGATACAAAGAAGCGGATTGAAACAAGTGAG
GCGGTC
Found at i:18362 original size:17 final size:17
Alignment explanation
Indices: 18273--18367 Score: 77
Period size: 17 Copynumber: 5.5 Consensus size: 17
18263 CTAATTTTAG
*
18273 ATTTTAAATTTTAAGTC-
1 ATTTTAAA-TTTAAATCT
* *
18290 ATTATAAGTTTAAATCT
1 ATTTTAAATTTAAATCT
*
18307 ATTGTAAATTTAAA-CTT
1 ATTTTAAATTTAAATC-T
** * *
18324 ATTTGGAGTTTAAATTT
1 ATTTTAAATTTAAATCT
18341 ATTTTAAATTTAAATCT
1 ATTTTAAATTTAAATCT
18358 ATTTTGAAAT
1 ATTTT-AAAT
18368 AAAATTTAAA
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
16 8 0.13
17 48 0.80
18 4 0.07
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTTTAAATTTAAATCT
Found at i:19038 original size:3 final size:3
Alignment explanation
Indices: 19030--19061 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
19020 TGAATGAATG
19030 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19062 AATGAGAAGT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20230 original size:30 final size:31
Alignment explanation
Indices: 20194--20504 Score: 213
Period size: 30 Copynumber: 10.5 Consensus size: 31
20184 CCCTCGAACA
20194 TCCAAAAATTCCATTTTTAACCCTAAAC-TT
1 TCCAAAAATTCCATTTTTAACCCTAAACTTT
*
20224 TCCAAAAATTCCATTTTTAACCCCAAACTTT
1 TCCAAAAATTCCATTTTTAACCCTAAACTTT
*
20255 TTC-AAAATTACCA-TTTT-ACCCTCAAAC--T
1 TCCAAAAATT-CCATTTTTAACCCT-AAACTTT
*
20283 TCCAAAAAATTCCATTTTTAA-CCTCGAACTTT
1 TCC-AAAAATTCCATTTTTAACCCT-AAACTTT
* *
20315 TCC-AAAATTAC-TATTTTACCCCTAAAC---
1 TCCAAAAATTCCAT-TTTTAACCCTAAACTTT
* *
20342 T--AAAAATTCCA-TTTTAACACTGAACTTT
1 TCCAAAAATTCCATTTTTAACCCTAAACTTT
*
20370 TTC-AAAATTACCA-TTTT-ACCCTCAAAC--T
1 TCCAAAAATT-CCATTTTTAACCCT-AAACTTT
* *
20398 TCCAAAAATTCTATTTTTAAACCTAAACTTT
1 TCCAAAAATTCCATTTTTAACCCTAAACTTT
* * * *
20429 TTC-TAAATTACCA-TTTT-ACCCTCGAA--TG
1 TCCAAAAATT-CCATTTTTAACCCT-AAACTTT
* *
20457 TCCAAAAATTCCATTTTTAACCTTGAACTTT
1 TCCAAAAATTCCATTTTTAACCCTAAACTTT
*
20488 TCCAAAAATACCATTTT
1 TCCAAAAATTCCATTTT
20505 GCCCCTAACT
Statistics
Matches: 221, Mismatches: 28, Indels: 63
0.71 0.09 0.20
Matches are distributed among these distances:
25 11 0.05
26 7 0.03
27 1 0.00
28 15 0.07
29 48 0.22
30 102 0.46
31 33 0.15
32 4 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (31 bp):
TCCAAAAATTCCATTTTTAACCCTAAACTTT
Found at i:20282 original size:60 final size:59
Alignment explanation
Indices: 20198--20504 Score: 371
Period size: 59 Copynumber: 5.2 Consensus size: 59
20188 CGAACATCCA
**
20198 AAAATT-CCATTTTTAACCCT-AAACTTTCCAAAAATTCCATTTTTAACCCCAAACTTTTTC
1 AAAATTACCA-TTTT-ACCCTCAAAC-TTCCAAAAATTCCATTTTTAACCCTGAACTTTTTC
*
20258 AAAATTACCATTTTACCCTCAAACTTCCAAAAAATTCCATTTTTAA-CCTCGAACTTTTCC
1 AAAATTACCATTTTACCCTCAAACTTCC-AAAAATTCCATTTTTAACCCT-GAACTTTTTC
* *
20318 AAAATTACTATTTTACCC-CTAAAC-T--AAAAATTCCA-TTTTAACACTGAACTTTTTC
1 AAAATTACCATTTTACCCTC-AAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTTTC
* * *
20373 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAAACCTAAACTTTTTC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTTTC
* * * *
20432 TAAATTACCATTTTACCCTCGAA-TGTCCAAAAATTCCATTTTTAACCTTGAACTTTTCC
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTAACCCTGAACTTTTTC
*
20491 AAAAATACCATTTT
1 AAAATTACCATTTT
20505 GCCCCTAACT
Statistics
Matches: 215, Mismatches: 20, Indels: 25
0.83 0.08 0.10
Matches are distributed among these distances:
55 36 0.17
56 14 0.07
58 10 0.05
59 92 0.43
60 60 0.28
61 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCCTGAACTTTTTC
Found at i:20316 original size:59 final size:58
Alignment explanation
Indices: 20198--20579 Score: 365
Period size: 59 Copynumber: 6.6 Consensus size: 58
20188 CGAACATCCA
* *
20198 AAAATT-CCATTTTTAACCCT-AAACTTTCCAAAAATTCCATTTTTAACCCCAAACTTTTTC
1 AAAATTACCA-TTTT-ACCCTCAAAC-TTCCAAAAATTCCATTTTTAACCTCGAAC-TTTTC
20258 AAAATTACCATTTTACCCTCAAACTTCCAAAAAATTCCATTTTTAACCTCGAACTTTTCC
1 AAAATTACCATTTTACCCTCAAACTTCC-AAAAATTCCATTTTTAACCTCGAACTTTT-C
*
20318 AAAATTACTATTTTACCC-CTAAAC-T--AAAAATTCCA-TTTTAACACT-GAACTTTTTC
1 AAAATTACCATTTTACCCTC-AAACTTCCAAAAATTCCATTTTTAAC-CTCGAAC-TTTTC
* *
20373 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCTATTTTTAAACCT-AAACTTTTTC
1 AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTT-AACCTCGAAC-TTTTC
* * *
20432 TAAATTACCATTTTACCCTCGAA-TGTCCAAAAATTCCATTTTTAACCTTGAACTTTTCC
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTAACCTCGAACTTTT-C
* * * * * * * * *
20491 AAAAATACCATTTTGCCC-CTAACTGTTCAAAAATTACAATTTT-GCCTCGAAGTGTTC
1 AAAATTACCATTTTACCCTCAAACT-TCCAAAAATTCCATTTTTAACCTCGAACTTTTC
* * * *
20548 AAAATTACTATTTTACCCCCAAGCATCCAAAA
1 AAAATTACCATTTTACCCTCAAACTTCCAAAA
20580 TCACATTTTC
Statistics
Matches: 276, Mismatches: 28, Indels: 39
0.80 0.08 0.11
Matches are distributed among these distances:
55 33 0.12
56 18 0.07
57 22 0.08
58 34 0.12
59 104 0.38
60 62 0.22
61 3 0.01
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTTAACCTCGAACTTTTC
Found at i:20471 original size:28 final size:30
Alignment explanation
Indices: 20138--20565 Score: 160
Period size: 30 Copynumber: 14.7 Consensus size: 30
20128 TTCAAGTTTT
* *
20138 CAAAAATTA-GATTTTGACCCCCGAACT-TC
1 CAAAAATTACCATTTT-ACCCTCGAACTGTC
* * *
20167 ATAAAAATTA-CATTTTTCCCTCGAAC-ATC
1 -CAAAAATTACCATTTTACCCTCGAACTGTC
* *
20196 CAAAAATT-CCATTTTTAACCCT-AAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGAACTGTC
* * *
20226 CAAAAATT-CCATTTTTAACCC-CAAACTTTTT
1 CAAAAATTACCA-TTTT-ACCCTCGAAC-TGTC
*
20257 C-AAAATTACCATTTTACCCTCAAACT-TC
1 CAAAAATTACCATTTTACCCTCGAACTGTC
* *
20285 CAAAAAATT-CCATTTTTAACCTCGAACTTTTC
1 C-AAAAATTACCA-TTTTACCCTCGAAC-TGTC
* *
20317 C-AAAATTACTATTTTACCC-CTAAAC--T-
1 CAAAAATTACCATTTTACCCTC-GAACTGTC
* * *
20343 -AAAAATT-CCATTTTAACACT-GAACTTTTT
1 CAAAAATTACCATTTT-ACCCTCGAAC-TGTC
*
20372 C-AAAATTACCATTTTACCCTCAAACT-TC
1 CAAAAATTACCATTTTACCCTCGAACTGTC
* * * * *
20400 CAAAAATT-CTATTTTTAAACCT-AAACTTTTT
1 CAAAAATTACCA-TTTT-ACCCTCGAAC-TGTC
*
20431 C-TAAATTACCATTTTACCCTCGAA-TGTC
1 CAAAAATTACCATTTTACCCTCGAACTGTC
* * *
20459 CAAAAATT-CCATTTTTAACCTTGAACTTTTC
1 CAAAAATTACCA-TTTTACCCTCGAAC-TGTC
* * *
20490 CAAAAA-TACCATTTTGCCC-CTAACTGTT
1 CAAAAATTACCATTTTACCCTCGAACTGTC
* * * *
20518 CAAAAATTACAATTTT-GCCTCGAAGTGTT
1 CAAAAATTACCATTTTACCCTCGAACTGTC
*
20547 C-AAAATTACTATTTTACCC
1 CAAAAATTACCATTTTACCC
20566 CCAAGCATCC
Statistics
Matches: 311, Mismatches: 46, Indels: 83
0.71 0.10 0.19
Matches are distributed among these distances:
25 9 0.03
26 9 0.03
27 1 0.00
28 45 0.14
29 92 0.30
30 126 0.41
31 26 0.08
32 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (30 bp):
CAAAAATTACCATTTTACCCTCGAACTGTC
Found at i:20532 original size:29 final size:29
Alignment explanation
Indices: 20481--20566 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
20471 TTTTAACCTT
* *
20481 GAACTTTTCCAAAAA-TACCATTTTGCCCC
1 GAACTGTT-CAAAAATTACAATTTTGCCCC
* *
20510 TAACTGTTCAAAAATTACAATTTTGCCTC
1 GAACTGTTCAAAAATTACAATTTTGCCCC
* * *
20539 GAAGTGTTC-AAAATTACTATTTTACCCC
1 GAACTGTTCAAAAATTACAATTTTGCCCC
20567 CAAGCATCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
28 22 0.47
29 25 0.53
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.35
Consensus pattern (29 bp):
GAACTGTTCAAAAATTACAATTTTGCCCC
Found at i:23857 original size:21 final size:21
Alignment explanation
Indices: 23826--23873 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
23816 TTAAAAGAAA
*
23826 TAAAAATAAAAGGATTAAATT
1 TAAAAACAAAAGGATTAAATT
* * *
23847 TTAAAACAAAAGGGTTTAATT
1 TAAAAACAAAAGGATTAAATT
23868 TAAAAA
1 TAAAAA
23874 AACGAATAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.29
Consensus pattern (21 bp):
TAAAAACAAAAGGATTAAATT
Found at i:24887 original size:4 final size:4
Alignment explanation
Indices: 24878--24904 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
24868 GTGTTTTTTT
24878 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
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:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Done.