Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011865.1 Kokia drynarioides strain JFW-HI SEQ_126862, 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: 96254
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3772 original size:12 final size:12
Alignment explanation
Indices: 3755--3786 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3745 TATCTAGCAG
3755 GAGGTGCAGGCT
1 GAGGTGCAGGCT
3767 GAGGTGCAGGCT
1 GAGGTGCAGGCT
3779 GAGGTGCA
1 GAGGTGCA
3787 ATACCAGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.50, T:0.16
Consensus pattern (12 bp):
GAGGTGCAGGCT
Found at i:7598 original size:148 final size:149
Alignment explanation
Indices: 7422--7718 Score: 515
Period size: 148 Copynumber: 2.0 Consensus size: 149
7412 ACATATATTG
* *
7422 TGATACATGATTGTGTTAATGTGTGTGAAAAGTGTATTGAAGTATGATCTGGTTAAAAAAATAAG
1 TGATACATGATTGAGTTAATGTGTGTGAAAAGTGTATTGAAGTATGATCTCGTTAAAAAAATAAG
* * *
7487 TATAGCCTACTTGAATGTGAA-CTTATGTTAGATTTATGGTGTGTGGGAAATTGGGTGAATTGGA
66 TATAGCCTACTTGAATGTGAATCTTATGTTAGATATATGGTGTGTGGGAAATGGGGTGAAATGGA
7551 GTGTTGAGAGATTATGTGA
131 GTGTTGAGAGATTATGTGA
* *
7570 TGATACATGATTGAGTTGATGTGTGTGAAAAGTGTATTGAAGTATGATCTCGTTAAAAAAATGAG
1 TGATACATGATTGAGTTAATGTGTGTGAAAAGTGTATTGAAGTATGATCTCGTTAAAAAAATAAG
*
7635 TATAGCCTACTTGAATGTGAATCTTATGTTATATATATGGTGTGTGGGAAATGGGGTGAAATGGA
66 TATAGCCTACTTGAATGTGAATCTTATGTTAGATATATGGTGTGTGGGAAATGGGGTGAAATGGA
7700 GTGTTGAGAGATTATGTGA
131 GTGTTGAGAGATTATGTGA
7719 AGTGATTTTT
Statistics
Matches: 140, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
148 82 0.59
149 58 0.41
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (149 bp):
TGATACATGATTGAGTTAATGTGTGTGAAAAGTGTATTGAAGTATGATCTCGTTAAAAAAATAAG
TATAGCCTACTTGAATGTGAATCTTATGTTAGATATATGGTGTGTGGGAAATGGGGTGAAATGGA
GTGTTGAGAGATTATGTGA
Found at i:9329 original size:27 final size:23
Alignment explanation
Indices: 9299--9373 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 23
9289 AATTTTTATG
9299 TTTAAAATATTTATAAAAATTTCAACA
1 TTTAAAAT-TTTA-AAAAATTT-AA-A
**
9326 TTTATATTTTTTAAAAAAATTTAAA
1 TTTA-AAATTTT-AAAAAATTTAAA
9351 -TTAAAATTTTAAAAAATTCTAAA
1 TTTAAAATTTTAAAAAATT-TAAA
9374 AAATATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 3 0.07
25 1 0.02
26 2 0.05
27 15 0.37
28 3 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
TTTAAAATTTTAAAAAATTTAAA
Found at i:9350 original size:10 final size:10
Alignment explanation
Indices: 9335--9394 Score: 59
Period size: 10 Copynumber: 5.7 Consensus size: 10
9325 ATTTATATTT
9335 TTTAAAAAAA
1 TTTAAAAAAA
9345 TTTAAATTAAAA
1 TTTAAA--AAAA
*
9357 TTTTAAAAAA
1 TTTAAAAAAA
9367 TTCTAAAAAATA
1 TT-TAAAAAA-A
*
9379 TATAAAAAAA
1 TTTAAAAAAA
9389 -TTAAAA
1 TTTAAAA
9395 TTTTAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 5 0.12
10 13 0.31
11 13 0.31
12 11 0.26
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:23548 original size:13 final size:13
Alignment explanation
Indices: 23525--23561 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
23515 TTTTTAAAGG
23525 AAAAT-AGAAAAA
1 AAAATGAGAAAAA
*
23537 AAAATGAGAAAAT
1 AAAATGAGAAAAA
23550 AAAA-GAGAAAAA
1 AAAATGAGAAAAA
23562 CAACTAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (13 bp):
AAAATGAGAAAAA
Found at i:24162 original size:16 final size:16
Alignment explanation
Indices: 24140--24177 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
24130 AATAAATATT
*
24140 TATATTATATTATTTTA
1 TATATTA-ATAATTTTA
24157 -ATATTAATAATTTTA
1 TATATTAATAATTTTA
24172 TATATT
1 TATATT
24178 TTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTAATAATTTTA
Found at i:24181 original size:26 final size:23
Alignment explanation
Indices: 24114--24182 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 23
24104 CCATTTATAT
*
24114 TATTTTAAAT-TTTTTTAATAAA
1 TATTTTATATATTTTTTAATAAA
24136 TATTTATATTATATTATTTTAATATTAA
1 TATTT-TA-TATATT-TTTTAATA--AA
24164 TAATTTTATATATTTTTTA
1 T-ATTTTATATATTTTTTA
24183 TTTATTGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
22 5 0.13
23 2 0.05
24 2 0.05
25 2 0.05
26 13 0.33
27 6 0.15
28 5 0.13
29 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTTTATATATTTTTTAATAAA
Found at i:24188 original size:27 final size:26
Alignment explanation
Indices: 24145--24202 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
24135 ATATTTATAT
24145 TATATTATTTTAATATTAATAATTTTA
1 TATATTATTTTAATATTAA-AATTTTA
* * *
24172 TATATT-TTTTATTTATTGAAATTTTT
1 TATATTATTTTA-ATATTAAAATTTTA
24198 TATAT
1 TATAT
24203 AATCATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (26 bp):
TATATTATTTTAATATTAAAATTTTA
Found at i:25962 original size:40 final size:40
Alignment explanation
Indices: 25917--26009 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
25907 ATAGGTTCAT
*
25917 AAGTCTTCCTTTTAATCAATCTTATGTTCTATCGAGTCAC
1 AAGTCTTCCTTTTAATCAATCTTATGCTCTATCGAGTCAC
* *
25957 AAGTCTTCCTTTTAATCACTCTTATGCTCTATCGAGTCAT
1 AAGTCTTCCTTTTAATCAATCTTATGCTCTATCGAGTCAC
25997 AAGTCTTCCTTTT
1 AAGTCTTCCTTTT
26010 TAAAAACAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.24, G:0.10, T:0.44
Consensus pattern (40 bp):
AAGTCTTCCTTTTAATCAATCTTATGCTCTATCGAGTCAC
Found at i:26081 original size:41 final size:40
Alignment explanation
Indices: 26036--26181 Score: 157
Period size: 41 Copynumber: 3.5 Consensus size: 40
26026 GCTCATTTTT
*
26036 AGACATGAGTCTTCATTTAATATAATCTCATTCTTATCTCG
1 AGACATGAGTCTTCATTTAATATAATCTCATTCTCATC-CG
* **
26077 AGACATGAGTCTTCCTTTAATATAATCTTTTTCTCATCCTG
1 AGACATGAGTCTTCATTTAATATAATCTCATTCTCATCC-G
* * * * *
26118 AGACATGAGTCTTCCTTTTATATAAATTCTCATGCTCAACCCA
1 AGACATGAGTCTTCATTTAATAT-AA-TCTCATTCTC-ATCCG
26161 AGACATGAGTCTTCCATTTAA
1 AGACATGAGTCTT-CATTTAA
26182 ATATTGAGTT
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 57 0.65
42 2 0.02
43 20 0.23
44 8 0.09
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (40 bp):
AGACATGAGTCTTCATTTAATATAATCTCATTCTCATCCG
Found at i:26194 original size:84 final size:82
Alignment explanation
Indices: 26036--26196 Score: 189
Period size: 84 Copynumber: 1.9 Consensus size: 82
26026 GCTCATTTTT
* * * * *
26036 AGACATGAGTCTTCATTTAATATAATCTCATTCTTATCTCGAGACATGAGTCTTCCTTTAATATA
1 AGACATGAGTCTTCATTTAATATAATCTCATGCTCAACCCAAGACATGAGTCTTCCTTTAATATA
**
26101 ATCTTTTTCTCATCCTG
66 ATCAGTTTCTCATCCTG
* *
26118 AGACATGAGTCTTCCTTTTATATAAATTCTCATGCTCAACCCAAGACATGAGTCTTCCATTTAA-
1 AGACATGAGTCTTCATTTAATAT-AA-TCTCATGCTCAACCCAAGACATGAGTCTTCC-TTTAAT
* *
26182 ATATTGAGTTTCTCA
63 ATAATCAGTTTCTCA
26197 AGTACTTCCT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 21 0.32
83 2 0.03
84 37 0.57
85 5 0.08
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (82 bp):
AGACATGAGTCTTCATTTAATATAATCTCATGCTCAACCCAAGACATGAGTCTTCCTTTAATATA
ATCAGTTTCTCATCCTG
Found at i:27512 original size:37 final size:37
Alignment explanation
Indices: 27443--27513 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
27433 TTTTTATGAA
*
27443 ATAAAAGAATAAAGAGAATAAAGACAAAAGAAATTTC
1 ATAAAAGAATAAAGAGAATAAAAACAAAAGAAATTTC
* * * *
27480 ATAAAAGAATAGAGAGAGTAAAAATAAGAGAAAT
1 ATAAAAGAATAAAGAGAATAAAAACAAAAGAAAT
27514 AGGAAAGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.17, T:0.15
Consensus pattern (37 bp):
ATAAAAGAATAAAGAGAATAAAAACAAAAGAAATTTC
Found at i:31681 original size:20 final size:21
Alignment explanation
Indices: 31653--31704 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
31643 TTATTGATAT
*
31653 TATTCAAATAATGT-ATGTAA
1 TATTAAAATAATGTAATGTAA
31673 TATTAAAATAATGTAATGTAA
1 TATTAAAATAATGTAATGTAA
*
31694 TTTTAAAATAA
1 TATTAAAATAA
31705 ATAATACAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (21 bp):
TATTAAAATAATGTAATGTAA
Found at i:32778 original size:57 final size:59
Alignment explanation
Indices: 32621--32826 Score: 180
Period size: 53 Copynumber: 3.6 Consensus size: 59
32611 ACAATGGTCA
* * * * * *
32621 ACACTCCCTTTTTCAGATATCCAAAAAAAATATTTTTT-TGGTGTTTGTCAAGCTATG-GCTG
1 ACACTCCCTTTTTCAGATA--CAACAAAAATATTTTTTAAGG-ATCTGTCAAGCCATGATC-G
* * *
32682 ACACT-CTTTTTTCAGAT-----AAAAATATTTTTTAAGTATCTGTCAAGTCATGATCG
1 ACACTCCCTTTTTCAGATACAACAAAAATATTTTTTAAGGATCTGTCAAGCCATGATCG
* * * *
32735 ACAC-CCCTTTTTTAGATACAA-AAAAATATTTTTTAGGGGTCTGTCAAGCCATGATTG
1 ACACTCCCTTTTTCAGATACAACAAAAATATTTTTTAAGGATCTGTCAAGCCATGATCG
*
32792 ACACTCCCTTTTTCAGATACAACAAATATATTTTT
1 ACACTCCCTTTTTCAGATACAACAAAAATATTTTT
32827 GGGTGTTTGT
Statistics
Matches: 119, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
53 39 0.33
54 2 0.02
57 35 0.29
58 16 0.13
59 11 0.09
60 11 0.09
61 5 0.04
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (59 bp):
ACACTCCCTTTTTCAGATACAACAAAAATATTTTTTAAGGATCTGTCAAGCCATGATCG
Found at i:32838 original size:58 final size:58
Alignment explanation
Indices: 32621--32845 Score: 214
Period size: 57 Copynumber: 3.9 Consensus size: 58
32611 ACAATGGTCA
* * * **
32621 ACACTCCCTTTTTCAGATATCCAAAAAAAATATTTTTTTGGTGTTTGTCAAGCTATGGCTG
1 ACACTCCCTTTTTCAGATA--C-AAAAAAATATTTTTTGGGTGTCTGTCAAGCCATGATTG
* ** * * *
32682 ACACT-CTTTTTTCAGAT----AAAAATATTTTTTAAGTATCTGTCAAGTCATGATCG
1 ACACTCCCTTTTTCAGATACAAAAAAATATTTTTTGGGTGTCTGTCAAGCCATGATTG
*
32735 ACAC-CCCTTTTTTAGATACAAAAAAATATTTTTTAGGG-GTCTGTCAAGCCATGATTG
1 ACACTCCCTTTTTCAGATACAAAAAAATATTTTTT-GGGTGTCTGTCAAGCCATGATTG
* * *
32792 ACACTCCCTTTTTCAGATAC-AACAAATATATTTTTGGGTGTTTGTCAACCCATG
1 ACACTCCCTTTTTCAGATACAAAAAAATAT-TTTTTGGGTGTCTGTCAAGCCATG
32846 GGCGACACCC
Statistics
Matches: 134, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
53 41 0.31
57 44 0.33
58 33 0.25
60 11 0.08
61 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (58 bp):
ACACTCCCTTTTTCAGATACAAAAAAATATTTTTTGGGTGTCTGTCAAGCCATGATTG
Found at i:33617 original size:18 final size:18
Alignment explanation
Indices: 33596--33646 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
33586 ATTACGAATT
33596 AAATTTAAAAAATAAATG
1 AAATTTAAAAAATAAATG
*
33614 AAA-TT-AGAAAT---T-
1 AAATTTAAAAAATAAATG
33626 AAATTTAAAAAATAAATG
1 AAATTTAAAAAATAAATG
33644 AAA
1 AAA
33647 AGAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 12
0.64 0.05 0.31
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 5 0.20
16 5 0.20
17 3 0.12
18 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AAATTTAAAAAATAAATG
Found at i:33660 original size:30 final size:29
Alignment explanation
Indices: 33592--33657 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 29
33582 AATAATTACG
33592 AATTAAATTTAAAAAATAAATGAAATTAGA
1 AATTAAATTTAAAAAATAAATGAAA-TAGA
33622 AATTAAATTTAAAAAATAAATGAAA-AGAA
1 AATTAAATTTAAAAAATAAATGAAATAG-A
33651 AATTAAA
1 AATTAAA
33658 ATTCTGTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 2 0.06
29 8 0.23
30 25 0.71
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (29 bp):
AATTAAATTTAAAAAATAAATGAAATAGA
Found at i:34086 original size:12 final size:12
Alignment explanation
Indices: 34071--34095 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34061 GGGCTCGAGA
34071 TCGTCCTCGGGG
1 TCGTCCTCGGGG
34083 TCGTCCTCGGGG
1 TCGTCCTCGGGG
34095 T
1 T
34096 TTGGCTCGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.32, G:0.40, T:0.28
Consensus pattern (12 bp):
TCGTCCTCGGGG
Found at i:34690 original size:21 final size:21
Alignment explanation
Indices: 34661--34774 Score: 97
Period size: 21 Copynumber: 5.3 Consensus size: 21
34651 ATTTCATTTA
34661 TAAAAAAATATTTCGAAAATG
1 TAAAAAAATATTTCGAAAATG
* *
34682 TAAACAAATATTTCGAAAATA
1 TAAAAAAATATTTCGAAAATG
* *
34703 TAAAAATATAATACTTT-TAAATTG
1 T-AAAA-A-AATA-TTTCGAAAATG
* *
34727 TAAATAAATATTTAG-AAATG
1 TAAAAAAATATTTCGAAAATG
* **
34747 TAAAAAAATATTTCAAAAAAA
1 TAAAAAAATATTTCGAAAATG
34768 TAAAAAA
1 TAAAAAA
34775 TAAATGTAAA
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
20 19 0.26
21 34 0.47
22 4 0.05
23 4 0.05
24 9 0.12
25 3 0.04
ACGTcount: A:0.60, C:0.04, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAAAAATATTTCGAAAATG
Found at i:38822 original size:16 final size:17
Alignment explanation
Indices: 38777--38820 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 17
38767 AATTTAATGT
*
38777 TTTTAGTAATTTTATTA
1 TTTTAATAATTTTATTA
38794 TTTTAATAA-TTTA-TA
1 TTTTAATAATTTTATTA
38809 TTTTAA-AATTTT
1 TTTTAATAATTTT
38821 TAAAGGATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 4 0.16
17 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTTTAATAATTTTATTA
Found at i:45431 original size:36 final size:37
Alignment explanation
Indices: 45390--45489 Score: 152
Period size: 36 Copynumber: 2.8 Consensus size: 37
45380 TAATTACCCT
*
45390 ACCCATGACCTTGAACTTGCTGCGA-TAAACCCTAAA
1 ACCCATGACCTTGAACTTACTGCGAGTAAACCCTAAA
*
45426 ACCCATGACCTTGAACTTACTAC-AGTAAACCCTAAA
1 ACCCATGACCTTGAACTTACTGCGAGTAAACCCTAAA
*
45462 ACCCATGACATTGAACTTACTGCG-GTAA
1 ACCCATGACCTTGAACTTACTGCGAGTAA
45490 TATTTACTCT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 1 0.02
36 57 0.98
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (37 bp):
ACCCATGACCTTGAACTTACTGCGAGTAAACCCTAAA
Found at i:48431 original size:23 final size:23
Alignment explanation
Indices: 48401--48446 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
48391 TATTTAGTTA
48401 GTTTTGGGTTTAATTGACGGCTT
1 GTTTTGGGTTTAATTGACGGCTT
48424 GTTTTGGGTTTAATTGACGGCTT
1 GTTTTGGGTTTAATTGACGGCTT
48447 AGGAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.09, G:0.30, T:0.48
Consensus pattern (23 bp):
GTTTTGGGTTTAATTGACGGCTT
Found at i:51104 original size:2 final size:2
Alignment explanation
Indices: 51097--51124 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
51087 TTCTATCATA
51097 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
51125 CCACTGTGTT
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:55552 original size:20 final size:19
Alignment explanation
Indices: 55503--55558 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 19
55493 TTCTTACTAA
*
55503 ATATTTATAAATTTTAGTAT
1 ATATTTA-AAATTTAAGTAT
55523 ATATTATTAAAATATTAAGTAT
1 ATA-T-TTAAAAT-TTAAGTAT
55545 ATATTT-AAATTTAA
1 ATATTTAAAATTTAA
55559 AATTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 5 0.16
21 6 0.19
22 13 0.41
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (19 bp):
ATATTTAAAATTTAAGTAT
Found at i:55706 original size:18 final size:18
Alignment explanation
Indices: 55685--55724 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
55675 ATTTGAGATT
**
55685 AATATTTTATTATTTTAA
1 AATATTTTAAAATTTTAA
55703 AATATTTTAAAATTTTAA
1 AATATTTTAAAATTTTAA
55721 AATA
1 AATA
55725 AAAATTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATATTTTAAAATTTTAA
Found at i:56487 original size:21 final size:21
Alignment explanation
Indices: 56446--56488 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
56436 ATAAAAAGTA
* *
56446 AATAAACAATATCATACACTT
1 AATAAACAACATCATAAACTT
56467 AATAAA-AACATCATCAAACTT
1 AATAAACAACATCAT-AAACTT
56488 A
1 A
56489 CAACTTCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.26
Consensus pattern (21 bp):
AATAAACAACATCATAAACTT
Found at i:57906 original size:57 final size:57
Alignment explanation
Indices: 57765--57912 Score: 190
Period size: 57 Copynumber: 2.6 Consensus size: 57
57755 GGCATCGCAA
* * **
57765 CACATCCCTCCTAAACACACCAAAGATCACCTAAGTGCTAAACCCAAAGGCAAGAGAT
1 CACATCCCTTC-AAACACACCAAAGAGCACAGAAGTGCTAAACCCAAAGGCAAGAGAT
**** *
57823 CACATCCCTTCAAACACAATTGAGAGCACAGAAGTGCTAAACCCAAAGGCAATAGAAT
1 CACATCCCTTCAAACACACCAAAGAGCACAGAAGTGCTAAACCCAAAGGCAAGAG-AT
57881 -ACATCCCTTCAAACACACCAAAGAGCACAGAA
1 CACATCCCTTCAAACACACCAAAGAGCACAGAA
57913 ATGTTAAGTC
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
57 64 0.84
58 12 0.16
ACGTcount: A:0.43, C:0.30, G:0.13, T:0.14
Consensus pattern (57 bp):
CACATCCCTTCAAACACACCAAAGAGCACAGAAGTGCTAAACCCAAAGGCAAGAGAT
Found at i:59303 original size:18 final size:18
Alignment explanation
Indices: 59245--59305 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
59235 GATCATGATT
* *
59245 TTTTTAAATTTTTAATAA
1 TTTTTAAGTTTTTAATTA
59263 TTTTCTAAG-TTTTAA-TA
1 TTTT-TAAGTTTTTAATTA
*
59280 TTTTTTGAGTTTTTAATTA
1 -TTTTTAAGTTTTTAATTA
59299 TTTTTAA
1 TTTTTAA
59306 AAAAATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 4 0.11
18 26 0.74
19 5 0.14
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTTAAGTTTTTAATTA
Found at i:63257 original size:25 final size:23
Alignment explanation
Indices: 63216--63261 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
63206 TCAATTAGGA
63216 AATTATTGTTTAGATTTAATTCT
1 AATTATTGTTTAGATTTAATTCT
*
63239 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TGTTTAG-ATTTAATT
63262 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTCT
Found at i:65262 original size:67 final size:66
Alignment explanation
Indices: 65160--65517 Score: 353
Period size: 67 Copynumber: 5.4 Consensus size: 66
65150 TGTCATAATC
* * * * * *
65160 GAGCTATGGTCTTATACATCATACCTCATGCTTAATGTTCTGACGAACTCTTTATTTTGCCATAG
1 GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCTGACGAACTCTCTATGTTGCCATAG
65225 CT
66 -T
* * * * * *
65227 GAGCTATGATCTTTCACATTATACCCCATGTTTAATGTCCTAGAAG-ACTCTCTATGTTGCCATA
1 GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCT-GACGAACTCTCTATGTTGCCATA
65291 GT
65 GT
* * * * * ** *
65293 CGAACTATGATCCTACACATTATTTCTCATGTTTAATGTCCTGGTGGACTCTCTATGTTGCCATA
1 -GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCTGACGAACTCTCTATGTTGCCATA
65358 GTT
65 G-T
* * * * * *
65361 GAGCTATGGTCTTATACATTATTCCTTATGTTTAATGTTTTGGCAAACTCTCTATGTTGCTATAA
1 GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCTGACGAACTCTCTATGTTGCCAT-A
**
65426 CC
65 GT
* * *
65428 GAGCTATGGCCTTACACATTATTCCCCATGTTTAATGTTCT-AGCGAACTCT-TATGTTGTCATA
1 GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCTGA-CGAACTCTCTATGTTGCCATA
65491 GT
65 GT
65493 CGAGCTATGGTCTTACACATTATTC
1 -GAGCTATGGTCTTACACATTATTC
65518 TCCATTATAA
Statistics
Matches: 240, Mismatches: 44, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
65 1 0.00
66 35 0.15
67 199 0.83
68 5 0.02
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.39
Consensus pattern (66 bp):
GAGCTATGGTCTTACACATTATTCCTCATGTTTAATGTTCTGACGAACTCTCTATGTTGCCATAG
T
Found at i:78106 original size:24 final size:23
Alignment explanation
Indices: 78066--78123 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
78056 TATACATTCT
78066 AATTAGAT-TTTATAAATAATTAA
1 AATTA-ATATTTATAAATAATTAA
* *
78089 TATTAATTATTTATAAATATTTAA
1 AATTAA-TATTTATAAATAATTAA
78113 AATTAATATTT
1 AATTAATATTT
78124 CATATATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 19 0.63
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATTAATATTTATAAATAATTAA
Found at i:78935 original size:59 final size:60
Alignment explanation
Indices: 78872--78984 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
78862 CCCTCTCAAA
* * * *
78872 AATCAATT-TTTATATGTTTAAATCAATTTTTATGGTAGAATATTGCTTTTTTTTTTTTG
1 AATCAATTGTTTACATGTTTAAATCAATTATTATGGTAGAATATTACTTCTTTTTTTTTG
** *
78931 AATCAATTGTTTACATGTTTAAATTGATTATTATGTTAGAATATTACTTCTTTT
1 AATCAATTGTTTACATGTTTAAATCAATTATTATGGTAGAATATTACTTCTTTT
78985 GAATAGACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 8 0.17
60 38 0.83
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.55
Consensus pattern (60 bp):
AATCAATTGTTTACATGTTTAAATCAATTATTATGGTAGAATATTACTTCTTTTTTTTTG
Found at i:79053 original size:56 final size:53
Alignment explanation
Indices: 78920--79078 Score: 185
Period size: 56 Copynumber: 2.9 Consensus size: 53
78910 AATATTGCTT
* * * *
78920 TTTTTTTTTTGAATCA-ATTGTTTACATGTTTAAATTGATTATTATGTTAGAATA
1 TTTTTTTTTTGAAT-AGATTGTTTATATATTTAAATTGATTGTTAT-ATAGAATA
* * * *
78974 TTACTTCTTTTGAATAGACTGTTTATATATTTAAATCGATTGTTATATAGGAATA
1 TT-TTTTTTTTGAATAGATTGTTTATATATTTAAATTGATTGTTATATA-GAATA
79029 CTGTTTTTTTTTGAATAGATTGTTTATATATTTAAATTGATTGTTATATA
1 -T-TTTTTTTTTGAATAGATTGTTTATATATTTAAATTGATTGTTATATA
79079 ACATATCTAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
54 5 0.06
55 39 0.44
56 43 0.49
57 1 0.01
ACGTcount: A:0.30, C:0.04, G:0.12, T:0.53
Consensus pattern (53 bp):
TTTTTTTTTTGAATAGATTGTTTATATATTTAAATTGATTGTTATATAGAATA
Found at i:83850 original size:34 final size:34
Alignment explanation
Indices: 83775--83841 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
83765 GATTTCCCAT
*
83775 ACTTGATTGAAGCAAAAATAAAAAATAAGTAAAA
1 ACTTGATTGAAGCAAAAATAAAAAATAACTAAAA
* *
83809 ACTTGATTGAAGCAAAAA-AAAAATTGACTAAAA
1 ACTTGATTGAAGCAAAAATAAAAAATAACTAAAA
83842 GTTTTGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.21
Consensus pattern (34 bp):
ACTTGATTGAAGCAAAAATAAAAAATAACTAAAA
Found at i:84684 original size:2 final size:2
Alignment explanation
Indices: 84677--84701 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84667 CACTTTGTGG
84677 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
84702 GCAATTGAGG
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:90314 original size:19 final size:19
Alignment explanation
Indices: 90290--90331 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
90280 AATTGAACTT
90290 GAAAATTGAACCCAAGATC
1 GAAAATTGAACCCAAGATC
* *
90309 GAAAATTGAACCCGAGATT
1 GAAAATTGAACCCAAGATC
90328 GAAA
1 GAAA
90332 CCCAAAAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.17
Consensus pattern (19 bp):
GAAAATTGAACCCAAGATC
Found at i:90730 original size:16 final size:16
Alignment explanation
Indices: 90687--90733 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
90677 ATGAATTTAA
90687 TATTAAATTTAATA-TT
1 TATT-AATTTAATATTT
*
90703 TATCTAA-ATAATATTT
1 TAT-TAATTTAATATTT
90719 TATTAATTTAATATT
1 TATTAATTTAATATT
90734 AATGTGATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 8 0.31
16 17 0.65
17 1 0.04
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTAATTTAATATTT
Found at i:90733 original size:11 final size:11
Alignment explanation
Indices: 90663--90736 Score: 50
Period size: 11 Copynumber: 7.0 Consensus size: 11
90653 TTTTTCAAAG
90663 TTAATATT-AT
1 TTAATATTAAT
* *
90673 TTCA-ATGAAT
1 TTAATATTAAT
90683 TTAATATTAAAT
1 TTAATATT-AAT
*
90695 TTAATATTTAT
1 TTAATATTAAT
*
90706 CTAA-A-TAAT
1 TTAATATTAAT
*
90715 ATT-TTATTAAT
1 -TTAATATTAAT
90726 TTAATATTAAT
1 TTAATATTAAT
90737 GTGATTAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 13
0.67 0.14 0.19
Matches are distributed among these distances:
9 5 0.11
10 13 0.28
11 18 0.38
12 11 0.23
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (11 bp):
TTAATATTAAT
Found at i:96237 original size:6 final size:6
Alignment explanation
Indices: 96226--96254 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
96216 TGATCAAAAT
96226 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
TGAAAG
Done.