Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012912.1 Kokia drynarioides strain JFW-HI SEQ_127928, 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: 62588
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Warning! 69 characters in sequence are not A, C, G, or T
Found at i:18755 original size:18 final size:19
Alignment explanation
Indices: 18732--18775 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
18722 GACCTATTCA
*
18732 AAAAATTA-TAATAAAATT
1 AAAAATTATTAATAAAACT
* *
18750 AAAAATCATTAATTAAACT
1 AAAAATTATTAATAAAACT
18769 AAAAATT
1 AAAAATT
18776 GAAATATATC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTATTAATAAAACT
Found at i:30458 original size:12 final size:12
Alignment explanation
Indices: 30441--30480 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
30431 AAAGTAATGT
30441 ATTTATTTTTAA
1 ATTTATTTTTAA
30453 ATTTATTTTTAA
1 ATTTATTTTTAA
30465 A-TT-TTTTT-A
1 ATTTATTTTTAA
30474 ATTTATT
1 ATTTATT
30481 AGTTAATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.08
10 7 0.27
11 4 0.15
12 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTATTTTTAA
Found at i:30486 original size:22 final size:21
Alignment explanation
Indices: 30446--30486 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30436 AATGTATTTA
*
30446 TTTTTAAATTTATTTTTAAAT
1 TTTTTAAATTTATTGTTAAAT
*
30467 TTTTTTAATTTATTAGTTAA
1 TTTTTAAATTTATT-GTTAA
30487 TAGTAATAAT
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:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTTTAAATTTATTGTTAAAT
Found at i:30650 original size:12 final size:12
Alignment explanation
Indices: 30633--30679 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
30623 TATTTGTTTT
30633 TTTTTAATTTAA
1 TTTTTAATTTAA
*
30645 TTTTTAA-TTGA
1 TTTTTAATTTAA
30656 TTTATT-ATTTAA
1 TTT-TTAATTTAA
30668 TGTTTTAATTTA
1 T-TTTTAATTTA
30680 GTTGAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 7 0.24
12 15 0.52
13 7 0.24
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (12 bp):
TTTTTAATTTAA
Found at i:31125 original size:16 final size:16
Alignment explanation
Indices: 31081--31129 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
31071 AAATACTTTA
31081 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
*
31097 -A-TAATATA-AAAAAT
1 AATTAAT-TACCAAAAT
31111 AATTAATTACCAAAAT
1 AATTAATTACCAAAAT
31127 AAT
1 AAT
31130 ATATTCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.33
15 6 0.22
16 12 0.44
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (16 bp):
AATTAATTACCAAAAT
Found at i:31196 original size:30 final size:30
Alignment explanation
Indices: 31162--31248 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
31152 AAATGGTACA
31162 AAATAAATATTTATTTTATACCATTTTAGT
1 AAATAAATATTTATTTTATACCATTTTAGT
* * * ** *
31192 AAAT-AATGGTGT-GTGGATACCATTTTGGT
1 AAATAAAT-ATTTATTTTATACCATTTTAGT
* *
31221 ATATAAATATTTATTTTGTACCATTTTA
1 AAATAAATATTTATTTTATACCATTTTA
31249 ATATATAACT
Statistics
Matches: 40, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.47
Consensus pattern (30 bp):
AAATAAATATTTATTTTATACCATTTTAGT
Found at i:32536 original size:43 final size:43
Alignment explanation
Indices: 32453--32537 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
32443 ATTAACATGT
* * *
32453 TAAATTATATTACTTGACTCGTGTTAATATAGTTGTATGTTAC
1 TAAATTATATTACTTGACTCGTATTAATATACTTGCATGTTAC
* *
32496 TAAATTATATTACTTTACTCTTATTAATAT-CTTGACATGTTA
1 TAAATTATATTACTTGACTCGTATTAATATACTTG-CATGTTA
32538 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 3 0.08
43 33 0.92
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGACTCGTATTAATATACTTGCATGTTAC
Found at i:33029 original size:18 final size:19
Alignment explanation
Indices: 33008--33049 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
32998 CCAGAGCCAG
*
33008 AGCAAAAGCAAGAGTAA-A
1 AGCAAAAGCAAGAGGAAGA
* *
33026 AGCAAGAGGAAGAGGAAGA
1 AGCAAAAGCAAGAGGAAGA
33045 AGCAA
1 AGCAA
33050 TGGATGACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.57, C:0.10, G:0.31, T:0.02
Consensus pattern (19 bp):
AGCAAAAGCAAGAGGAAGA
Found at i:33180 original size:45 final size:45
Alignment explanation
Indices: 33109--33200 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
33099 GCCTAGCTCA
* * * * *
33109 TCAAGCCAAAGATATTAGCATTAGTTTGACGAGCCATCGTAATAC
1 TCAAGCCAAAGATATCAGCATCAGTTTCACGAGCCACCGCAATAC
* *
33154 TCAAGCCAAGGATATCAGCCTCAGTTTCACGAGCCACCGCAATAC
1 TCAAGCCAAAGATATCAGCATCAGTTTCACGAGCCACCGCAATAC
33199 TC
1 TC
33201 TACTCCTCCC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (45 bp):
TCAAGCCAAAGATATCAGCATCAGTTTCACGAGCCACCGCAATAC
Found at i:33218 original size:21 final size:21
Alignment explanation
Indices: 33192--33251 Score: 120
Period size: 21 Copynumber: 2.9 Consensus size: 21
33182 ACGAGCCACC
33192 GCAATACTCTACTCCTCCCGA
1 GCAATACTCTACTCCTCCCGA
33213 GCAATACTCTACTCCTCCCGA
1 GCAATACTCTACTCCTCCCGA
33234 GCAATACTCTACTCCTCC
1 GCAATACTCTACTCCTCC
33252 AGGGAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.23, C:0.43, G:0.08, T:0.25
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGA
Found at i:34464 original size:24 final size:24
Alignment explanation
Indices: 34437--34483 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
34427 CACCATACAC
34437 GGAGTTGGATCTTCATTTTCTACT
1 GGAGTTGGATCTTCATTTTCTACT
34461 GGAGTTGGATCTTCATTTTCTAC
1 GGAGTTGGATCTTCATTTTCTAC
34484 AAGTTTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.45
Consensus pattern (24 bp):
GGAGTTGGATCTTCATTTTCTACT
Found at i:35514 original size:28 final size:30
Alignment explanation
Indices: 35459--35523 Score: 89
Period size: 28 Copynumber: 2.2 Consensus size: 30
35449 AAAATGAGAC
35459 TTTTCGGATTCTCGGAGGGGGTAAAATGGTAA
1 TTTT-GGATTCTCGGA-GGGGTAAAATGGTAA
*
35491 TTTTGGATTCTC-GA-GGGTGAAATGGTAA
1 TTTTGGATTCTCGGAGGGGTAAAATGGTAA
35519 TTTTG
1 TTTTG
35524 AGAAAATTCG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 18 0.56
30 2 0.06
31 8 0.25
32 4 0.12
ACGTcount: A:0.23, C:0.08, G:0.32, T:0.37
Consensus pattern (30 bp):
TTTTGGATTCTCGGAGGGGTAAAATGGTAA
Found at i:35598 original size:59 final size:59
Alignment explanation
Indices: 35535--35768 Score: 210
Period size: 59 Copynumber: 3.9 Consensus size: 59
35525 GAAAATTCGG
** * *
35535 GGTCAAAAATGAAATTTTTAGACA-TTCGAGGGTTAAAATGGAATTTTTGGAAGTTTCAA
1 GGTCAAAAATGGGATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAA
* ** ***
35594 GGTCAAAAATGGGATTTTGGGAAGTTTAAGGGTAAAAATGGAATTTTTTTGGAAGTTTTGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAA--TTTTTGGAAGTTTCAA
* ***
35655 GGTC-AAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAATGGGATTTTTGGAAGTTTGGG
1 GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTCAA
* *
35714 GGT-AAAAAT-AGAATTTTGAGAAGTTTCG-GGGTCAAAAATAGG-ATTTTTGGAAGTT
1 GGTCAAAAATGGGATTTTTG-GAAG-TTCGAGGGT-AAAAAT-GGAATTTTTGGAAGTT
35769 CGGGGGTAGA
Statistics
Matches: 149, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
58 8 0.05
59 84 0.56
60 31 0.21
61 26 0.17
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
GGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTCAA
Found at i:35605 original size:30 final size:30
Alignment explanation
Indices: 35534--35768 Score: 200
Period size: 30 Copynumber: 7.9 Consensus size: 30
35524 AGAAAATTCG
* *
35534 GGGTCAAAAATGAAATTTTTAGACA--TTCGA
1 GGGTCAAAAATGGAATTTTTGGA-AGTTTC-A
*
35564 GGGT-TAAAATGGAATTTTTGGAAGTTTCA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCA
* * * *
35593 AGGTCAAAAATGGGATTTTGGGAAGTTTAA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCA
**
35623 GGGT-AAAAATGGAATTTTTTTGGAAGTTTTG
1 GGGTCAAAAATGGAA--TTTTTGGAAGTTTCA
*
35654 GGGTC-AAAATGGGATTTTTGGAAG-TTCGA
1 GGGTCAAAAATGGAATTTTTGGAAGTTTC-A
* * **
35683 GGGTAAAAAATGGGATTTTTGGAAGTTTGG
1 GGGTCAAAAATGGAATTTTTGGAAGTTTCA
* *
35713 GGGT-AAAAATAGAA-TTTTGAGAAGTTTCG
1 GGGTCAAAAATGGAATTTTTG-GAAGTTTCA
35742 GGGTCAAAAATAGG-ATTTTTGGAAGTT
1 GGGTCAAAAAT-GGAATTTTTGGAAGTT
35769 CGGGGGTAGA
Statistics
Matches: 169, Mismatches: 23, Indels: 26
0.78 0.11 0.12
Matches are distributed among these distances:
28 8 0.05
29 62 0.37
30 67 0.40
31 32 0.19
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (30 bp):
GGGTCAAAAATGGAATTTTTGGAAGTTTCA
Found at i:35770 original size:29 final size:29
Alignment explanation
Indices: 35530--35773 Score: 198
Period size: 29 Copynumber: 8.2 Consensus size: 29
35520 TTTGAGAAAA
* *
35530 TTCGGGGTCAAAAATGAAATTTTTAGACA--
1 TTCGGGGTCAAAAATG-GATTTTTGGA-AGT
*
35559 TTCGAGGGT-TAAAATGGAATTTTTGGAAGT
1 TTCG-GGGTCAAAAATGG-ATTTTTGGAAGT
** *
35589 TTCAAGGTCAAAAATGGGATTTTGGGAAGT
1 TTCGGGGTCAAAAAT-GGATTTTTGGAAGT
**
35619 TTAAGGGT-AAAAATGGAATTTTTTTGGAAGT
1 TTCGGGGTCAAAAATGG-A--TTTTTGGAAGT
*
35650 TTTGGGGTC-AAAATGGGATTTTTGGAAG-
1 TTCGGGGTCAAAAAT-GGATTTTTGGAAGT
*
35678 TTCGAGGGTAAAAAATGGGATTTTTGGAAGT
1 TTCG-GGGTCAAAAAT-GGATTTTTGGAAGT
* * *
35709 TTGGGGGT-AAAAATAGAATTTTGAGAAGT
1 TTCGGGGTCAAAAATGGATTTTTG-GAAGT
35738 TTCGGGGTCAAAAATAGGATTTTTGGAAG-
1 TTCGGGGTCAAAAAT-GGATTTTTGGAAGT
35767 TTCGGGG
1 TTCGGGG
35774 GTAGAACGAA
Statistics
Matches: 178, Mismatches: 20, Indels: 34
0.77 0.09 0.15
Matches are distributed among these distances:
28 13 0.07
29 67 0.38
30 62 0.35
31 34 0.19
32 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.30, T:0.33
Consensus pattern (29 bp):
TTCGGGGTCAAAAATGGATTTTTGGAAGT
Found at i:35798 original size:59 final size:60
Alignment explanation
Indices: 35639--35798 Score: 166
Period size: 59 Copynumber: 2.7 Consensus size: 60
35629 AAATGGAATT
** * * * *
35639 TTTTTGGAAGTTTTGGGGTCAAAATGGGATTTTTG-GAAG-TTCGAGGGTAAAAAATGGGA
1 TTTTTGGAAGTTCGGGGGT-AAAAAGAGAATTTTGAGAAGTTTCGAGGGTAAAAAATAGGA
* * *
35698 TTTTTGGAAGTTTGGGGGTAAAAATAGAATTTTGAGAAGTTTCG-GGGTCAAAAATAGGA
1 TTTTTGGAAGTTCGGGGGTAAAAAGAGAATTTTGAGAAGTTTCGAGGGTAAAAAATAGGA
* * *
35757 TTTTTGGAAGTTCGGGGGTAGAACGA-AATTTTTAGATAGTTT
1 TTTTTGGAAGTTCGGGGGTAAAAAGAGAATTTTGAGA-AGTTT
35799 AGGGACCTCT
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
58 20 0.23
59 62 0.72
60 4 0.05
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (60 bp):
TTTTTGGAAGTTCGGGGGTAAAAAGAGAATTTTGAGAAGTTTCGAGGGTAAAAAATAGGA
Found at i:36923 original size:3 final size:3
Alignment explanation
Indices: 36917--37001 Score: 73
Period size: 3 Copynumber: 28.0 Consensus size: 3
36907 TTTTTTTTAC
* * * *
36917 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA ATG TCA TTA GTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
* * * *
36963 -TA TTTA TTA ATA TTA TTT TTA TTA TTT TTA TTT TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
37002 ATGTTATTAA
Statistics
Matches: 63, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.89
4 5 0.08
ACGTcount: A:0.32, C:0.01, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:37000 original size:24 final size:24
Alignment explanation
Indices: 36958--37010 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
36948 ATGTCATTAG
* *
36958 TATTATATTTATTAATATTATTTT
1 TATTATATTTATTAATATTAATGT
* **
36982 TATTATTTTTATTTTTATTAATGT
1 TATTATATTTATTAATATTAATGT
37006 TATTA
1 TATTA
37011 AAATCATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (24 bp):
TATTATATTTATTAATATTAATGT
Found at i:37740 original size:17 final size:17
Alignment explanation
Indices: 37720--37766 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
37710 AAATAAATTT
37720 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
37737 TAAACTTAACTTTAAAA
1 TAAATTTAAATTTAAAA
37754 TAAATTTAAATTT
1 TAAATTTAAATTT
37767 GTTAGGCCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:37745 original size:23 final size:23
Alignment explanation
Indices: 37706--37752 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37696 CTTGAACATT
*
37706 ATTTAAATAAATTTTAAATTTAA
1 ATTTAAATAAATCTTAAATTTAA
*
37729 ATTTAAAATAAA-CTTAACTTTAA
1 ATTT-AAATAAATCTTAAATTTAA
37752 A
1 A
37753 ATAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAAATAAATCTTAAATTTAA
Found at i:38482 original size:19 final size:20
Alignment explanation
Indices: 38453--38490 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
38443 TCGGTATCCT
38453 ATATCGTATTTAATTTTATG
1 ATATCGTATTTAATTTTATG
*
38473 ATAT-GTATTTCATTTTAT
1 ATATCGTATTTAATTTTAT
38491 TTTTATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.29, C:0.05, G:0.08, T:0.58
Consensus pattern (20 bp):
ATATCGTATTTAATTTTATG
Found at i:38568 original size:35 final size:36
Alignment explanation
Indices: 38498--38570 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
38488 TATTTTTATT
*
38498 AAATTAATAATTTTTTAATATTACTTTAGTCAAATA
1 AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
*
38534 AAATAAATAATTTTTGT-ATATTATTTTAGT-AAATA
1 AAATAAATAATTTTT-TAATATTACTTTAGTCAAATA
38569 AA
1 AA
38571 TATTTTTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 7 0.21
36 26 0.76
37 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATAAATAATTTTTTAATATTACTTTAGTCAAATA
Found at i:50610 original size:2 final size:2
Alignment explanation
Indices: 50605--50629 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50595 TTTATGTAGT
50605 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
50630 TAATTTTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51006 original size:20 final size:21
Alignment explanation
Indices: 50958--51009 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
50948 ATAAAATTTC
* * *
50958 AAAATTTTAAAATATTTTTTT
1 AAAATTTCAAAATATTTTATA
50979 AAAA-TTCAAAATA-TTTATA
1 AAAATTTCAAAATATTTTATA
50998 AAAATTTCAAAA
1 AAAATTTCAAAA
51010 AAAAATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 8 0.30
20 15 0.56
21 4 0.15
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTTCAAAATATTTTATA
Found at i:51019 original size:2 final size:2
Alignment explanation
Indices: 51014--51039 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
51004 TCAAAAAAAA
51014 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
51040 TAAAAAATCT
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:57893 original size:15 final size:15
Alignment explanation
Indices: 57859--57899 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
57849 AATTGAATTT
*
57859 CAAT-TTAAATATAA
1 CAATATTAAAAATAA
57873 -AATATTAAAAATAA
1 CAATATTAAAAATAA
*
57887 CAATATTATAAAT
1 CAATATTAAAAAT
57900 GTATTTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 11 0.48
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (15 bp):
CAATATTAAAAATAA
Found at i:58507 original size:30 final size:30
Alignment explanation
Indices: 58471--58528 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
58461 TTAATAAAGG
58471 TAAAATTGTACTTTAATCTTTTAAAAATGA
1 TAAAATTGTACTTTAATCTTTTAAAAATGA
* *
58501 TAAAATTTTATTTTAATCTTTTAAAAAT
1 TAAAATTGTACTTTAATCTTTTAAAAAT
58529 TACACTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (30 bp):
TAAAATTGTACTTTAATCTTTTAAAAATGA
Found at i:58970 original size:39 final size:40
Alignment explanation
Indices: 58927--59014 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 40
58917 TTTATAAATA
58927 TTTTATTTTAATA-A-TAATTATAATCTAAAACTTTT-ATAT
1 TTTTATTTTAATATATTAATT-TAATCTAAAA-TTTTGATAT
* *
58966 TTTTATTGTTAATATATTGATTTAATTTAAAATTTTGATAT
1 TTTTATT-TTAATATATTAATTTAATCTAAAATTTTGATAT
59007 TTTT-TTTT
1 TTTTATTTT
59015 GTTAATAACA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
39 9 0.21
40 12 0.28
41 18 0.42
42 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (40 bp):
TTTTATTTTAATATATTAATTTAATCTAAAATTTTGATAT
Found at i:59007 original size:41 final size:41
Alignment explanation
Indices: 58927--59022 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 41
58917 TTTATAAATA
* *
58927 TTTTATT-TTAATAA-TAATTATAATCTAAAACTTTTATA-T
1 TTTTATTGTTAATAATTGATT-TAATTTAAAACTTTTATATT
58966 TTTTATTGTTAATATATTGATTTAATTTAAAA-TTTTGATATT
1 TTTTATTGTTAATA-ATTGATTTAATTTAAAACTTTT-ATATT
*
59008 TTTTTTTGTTAATAA
1 TTTTATTGTTAATAA
59023 CATTGTCTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
39 7 0.14
40 10 0.20
41 14 0.29
42 18 0.37
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (41 bp):
TTTTATTGTTAATAATTGATTTAATTTAAAACTTTTATATT
Found at i:59020 original size:42 final size:41
Alignment explanation
Indices: 58947--59042 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 41
58937 ATAATAATTA
* * *
58947 TAATCTAAAACTTTTATATTTTTATTGTTAAT-ATATTGATT
1 TAATTTAAAACTTTTATATTTTTATTGTTAATAACATTG-TC
*
58988 TAATTTAAAA-TTTTGATATTTTTTTTTGTTAATAACATTGTC
1 TAATTTAAAACTTTT-ATA-TTTTTATTGTTAATAACATTGTC
59030 TAATTT-AAACTTT
1 TAATTTAAAACTTT
59043 ATGGGAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 4 0.09
41 15 0.32
42 23 0.49
43 5 0.11
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (41 bp):
TAATTTAAAACTTTTATATTTTTATTGTTAATAACATTGTC
Found at i:60375 original size:17 final size:15
Alignment explanation
Indices: 60352--60390 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
60342 TAATTATTTA
60352 AAAATTATAAATATAT
1 AAAATTATAAATA-AT
60368 AAATATTA-AAATAAT
1 AAA-ATTATAAATAAT
60383 AAAATTAT
1 AAAATTAT
60391 TTTTTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.19
15 5 0.24
16 8 0.38
17 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATTATAAATAAT
Done.