Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003218.1 Kokia drynarioides strain JFW-HI SEQ_115845, 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: 92573
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:263 original size:23 final size:23
Alignment explanation
Indices: 68--261 Score: 203
Period size: 23 Copynumber: 8.3 Consensus size: 23
58 ACACTAGCGC
*
68 GCTCTCTGATTAGCATTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
91 GCTCTCTAATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
114 GCTCTCTAATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * * *
137 ACTCTCTGTTTAGCA-TGTCTCGT
1 GCTCTCTGATTAGCACTTTGT-GT
*
160 GCTCCCTGTTATTAGCA-TTGTGTGT
1 GCTCTCTG--ATTAGCACTT-TGTGT
185 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
208 GCTCTCTGATTAGTAATTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
231 GCTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
254 ACTCTCTG
1 GCTCTCTG
262 TTGCCCAGCA
Statistics
Matches: 144, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
22 3 0.02
23 121 0.84
24 2 0.01
25 16 0.11
26 2 0.01
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:263 original size:94 final size:94
Alignment explanation
Indices: 69--263 Score: 279
Period size: 94 Copynumber: 2.1 Consensus size: 94
59 CACTAGCGCG
* * *
69 CTCTCTG--ATTAGCATTTTGTGTGCTCTCTAATTAGTACTTTGTGTGCTCTCTAATTAGTACTT
1 CTCTCTGTTATTAGCATTGTGTGTGCTCTCTAATTAGCACTTTGTGTGCTCTCTAATTAGTAATT
*
132 TGTGTACTCTCTGTTTAGCATGTCTCGTG
66 TGTGTACTCTCTGTTTAGCATGTCTCGTA
* * *
161 CTCCCTGTTATTAGCATTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTAATT
1 CTCTCTGTTATTAGCATTGTGTGTGCTCTCTAATTAGCACTTTGTGTGCTCTCTAATTAGTAATT
* *
226 TGTGTGCTCTCTGTTTAGCACTGTGT-GTA
66 TGTGTACTCTCTGTTTAGCA-TGTCTCGTA
255 CTCTCTGTT
1 CTCTCTGTT
264 GCCCAGCACT
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
92 6 0.07
94 80 0.89
95 4 0.04
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (94 bp):
CTCTCTGTTATTAGCATTGTGTGTGCTCTCTAATTAGCACTTTGTGTGCTCTCTAATTAGTAATT
TGTGTACTCTCTGTTTAGCATGTCTCGTA
Found at i:280 original size:94 final size:94
Alignment explanation
Indices: 88--286 Score: 249
Period size: 94 Copynumber: 2.1 Consensus size: 94
78 TAGCATTTTG
* * *
88 TGTGCTCTCTAATTAGTACTTTGTGTGCTCTCTAATTAGTACTTTGTGTACTCTCTGTTTAGCAT
1 TGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTAATTAGTAATTTGTGTACTCTCTGTTTAGCAT
* ** * *
153 GTCTCGTGCTCCCTGTTATTAGCATTGTG
66 GTCTCGTACTCCCTGTTACCAGCACTGTA
* *
182 TGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTAATTTGTGTGCTCTCTGTTTAGCAC
1 TGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTAATTAGTAATTTGTGTACTCTCTGTTTAGCA-
* * *
247 TGTGT-GTACTCTCTGTTGCCCAGCACT-TA
65 TGTCTCGTACTCCCTGTT-ACCAGCACTGTA
276 TGTGCTCTCTG
1 TGTGCTCTCTG
287 TTTGTTCCGT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
94 81 0.90
95 9 0.10
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.44
Consensus pattern (94 bp):
TGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTAATTAGTAATTTGTGTACTCTCTGTTTAGCAT
GTCTCGTACTCCCTGTTACCAGCACTGTA
Found at i:3494 original size:21 final size:22
Alignment explanation
Indices: 3455--3514 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 22
3445 CAAGATTGAC
* **
3455 AAAAACAAAAAAATAAACA-GA
1 AAAAACAAATAAAGCAACATGA
*
3476 AAAAATAAATAAAGCAACATGA
1 AAAAACAAATAAAGCAACATGA
* *
3498 ATAAACAATTAAAGCAA
1 AAAAACAAATAAAGCAA
3515 AACTTGTCTC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.72, C:0.10, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAAACAAATAAAGCAACATGA
Found at i:6914 original size:30 final size:30
Alignment explanation
Indices: 6862--6918 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
6852 ACAAAAAAGT
6862 TAAATACTAATATTTTAATATAAAATTTTA
1 TAAATACTAATATTTTAATATAAAATTTTA
* *
6892 TAAATATTAA-ATTTATATTATAAAATT
1 TAAATACTAATATTT-TAATATAAAATT
6919 GTTTGGTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAATACTAATATTTTAATATAAAATTTTA
Found at i:7355 original size:7 final size:7
Alignment explanation
Indices: 7343--7368 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
7333 TTCCCTGAAA
7343 AAAAAAG
1 AAAAAAG
7350 AAAAAAG
1 AAAAAAG
7357 AAAAAAG
1 AAAAAAG
7364 AAAAA
1 AAAAA
7369 CGATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:8730 original size:17 final size:17
Alignment explanation
Indices: 8703--8750 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
8693 CTGGACCCAT
*
8703 TAAACTTAAATTTATT-
1 TAAATTTAAATTTATTA
8719 TGAAATTTAAATTTATTA
1 T-AAATTTAAATTTATTA
8737 TAAATTTAAATTTA
1 TAAATTTAAATTTA
8751 AAATCTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 1 0.03
17 27 0.93
18 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:8763 original size:23 final size:24
Alignment explanation
Indices: 8716--8764 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8706 ACTTAAATTT
*
8716 ATTTGAAATTTAAATTTATTATAA
1 ATTTGAAATTTAAATCTATTATAA
8740 ATTT-AAATTTAAAATCTATT-TAA
1 ATTTGAAATTT-AAATCTATTATAA
8763 AT
1 AT
8765 AATGTCCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTGAAATTTAAATCTATTATAA
Found at i:10558 original size:29 final size:29
Alignment explanation
Indices: 10492--10811 Score: 285
Period size: 29 Copynumber: 10.9 Consensus size: 29
10482 CCTTGAAGGT
*
10492 CCCT-AAACTTCCAAAAATCTCATTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTT-A
**
10521 -CCTCGAAACTTCCAAAAATTTCATTTTTA
1 CCCTC-AAACTTCCAAAAATCCCATTTTTA
*
10550 CCCTCAAACTTCCAAAAATCCCAATTTTAA
1 CCCTCAAACTTCCAAAAATCCC-ATTTTTA
* *
10580 CCC-CAAAACTTCCAAAAAAT-TCGTTTTTA
1 CCCTC-AAACTTCC-AAAAATCCCATTTTTA
* * *
10609 CCCCCAAACTTCCAAAAATCCCACTTTTG
1 CCCTCAAACTTCCAAAAATCCCATTTTTA
* * *
10638 TCCTCAAAACTTCTAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATCCCATTTTTA
** * *
10668 CCCTTGAACTTCCAAAAATCACGTTTTGTA
1 CCCTCAAACTTCCAAAAATCCCATTTT-TA
*
10698 -CCTCGAAACTTCCAAAAATTCCATTTTTA
1 CCCTC-AAACTTCCAAAAATCCCATTTTTA
* * *
10727 CCCTCGAACTTCAAAAAATCCCGTTTTTGA
1 CCCTCAAACTTCCAAAAATCCCATTTTT-A
* * *
10757 TCC-CAAACTTCCAAAAATTCTATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTA
*
10785 CCCTCGAACTTCC-AAAATCTCCATTTT
1 CCCTCAAACTTCCAAAAATC-CCATTTT
10812 CGACCTCAAA
Statistics
Matches: 233, Mismatches: 43, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
28 17 0.07
29 115 0.49
30 95 0.41
31 6 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCTCAAACTTCCAAAAATCCCATTTTTA
Found at i:10589 original size:59 final size:59
Alignment explanation
Indices: 10492--10824 Score: 381
Period size: 59 Copynumber: 5.7 Consensus size: 59
10482 CCTTGAAGGT
* *
10492 CCCT-AAACTTCCAAAAATCTCATTTTTGACCTCGAAACTTCCAAAAATTTCATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCATTTTTA
* * * * *
10550 CCCTCAAACTTCCAAAAATCCCAATTTTAACCCCAAAACTTCCAAAAAATTCGTTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCATTTTTA
* * * * *
10609 CCCCCAAACTTCCAAAAATCCCACTTTTGTCCTCAAAACTTCTAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCATTTTTA
** * * * *
10668 CCCTTGAACTTCCAAAAATCAC-GTTTTGTACCTCGAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTG-ACCTCAAAACTTCCAAAAATTTCATTTTTA
* * *
10727 CCCTCGAACTTCAAAAAATCCCGTTTTTGATCC-C-AAACTTCCAAAAA-TTCTATTTTTA
1 CCCTCAAACTTCCAAAAATCCCATTTTTGA-CCTCAAAACTTCCAAAAATTTC-ATTTTTA
* *
10785 CCCTCGAACTTCC-AAAATCTCCATTTTCGACCTCAAAACT
1 CCCTCAAACTTCCAAAAATC-CCATTTTTGACCTCAAAACT
10825 CTCAAAATTA
Statistics
Matches: 235, Mismatches: 32, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
57 10 0.04
58 50 0.21
59 168 0.71
60 7 0.03
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (59 bp):
CCCTCAAACTTCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAAATTTCATTTTTA
Found at i:13075 original size:30 final size:29
Alignment explanation
Indices: 13019--13075 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
13009 AATATTTATA
*
13019 ATTTTTAAAAATTCAAATCAAATTTTTTC
1 ATTTTTAAAAATTAAAATCAAATTTTTTC
13048 ATTTTTAAAATATTAAAAT-ATAATTTTT
1 ATTTTTAAAA-ATTAAAATCA-AATTTTT
13076 ATCAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAATCAAATTTTTTC
Found at i:16026 original size:21 final size:21
Alignment explanation
Indices: 16001--16069 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
15991 TTTGAACTAG
16001 TTATTAAAAAATCTTAAAATA
1 TTATTAAAAAATCTTAAAATA
* *
16022 TTATTTAAAAATC--ATAAT-
1 TTATTAAAAAATCTTAAAATA
16040 TT-TTAAAAAAAT-TATAAAA-A
1 TTATT-AAAAAATCT-TAAAATA
16060 TTATTAAAAA
1 TTATTAAAAA
16070 TTATAAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
17 2 0.05
18 8 0.21
19 4 0.11
20 10 0.26
21 14 0.37
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (21 bp):
TTATTAAAAAATCTTAAAATA
Found at i:16067 original size:10 final size:10
Alignment explanation
Indices: 16046--16107 Score: 55
Period size: 10 Copynumber: 6.7 Consensus size: 10
16036 TAATTTTTAA
16046 AAAAATTA-T
1 AAAAATTATT
16055 AAAAATTATT
1 AAAAATTATT
16065 AAAAATTA-T
1 AAAAATTATT
*
16074 --AAATAATT
1 AAAAATTATT
*
16082 -AAAA-TAAT
1 AAAAATTATT
16090 AATAAATTATT
1 AA-AAATTATT
16101 AAAAATT
1 AAAAATT
16108 TCAAAAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
7 5 0.12
8 3 0.07
9 13 0.30
10 17 0.40
11 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTATT
Found at i:16068 original size:19 final size:19
Alignment explanation
Indices: 16046--16107 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
16036 TAATTTTTAA
16046 AAAAATTATAAAAATTATT
1 AAAAATTATAAAAATTATT
*
16065 AAAAATTAT--AAATAATT
1 AAAAATTATAAAAATTATT
*
16082 -AAAATAATAATAAATTATT
1 AAAAATTATAA-AAATTATT
16101 AAAAATT
1 AAAAATT
16108 TCAAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
16 7 0.20
17 7 0.20
19 16 0.46
20 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTATAAAAATTATT
Found at i:16084 original size:38 final size:37
Alignment explanation
Indices: 16006--16107 Score: 102
Period size: 36 Copynumber: 2.7 Consensus size: 37
15996 ACTAGTTATT
* **
16006 AAAAAATCT-TAAAATATTATTTAAAAATCATAATTTTTA
1 AAAAAAT-TATAAAA-ATTA-TTAAAAATTATAATAATTA
16045 AAAAAATTATAAAAATTATTAAAAATTATAAATAATTA
1 AAAAAATTATAAAAATTATTAAAAATTAT-AATAATTA
* *
16083 AAATAA-TA-ATAAATTATTAAAAATT
1 AAAAAATTATAAAAATTATTAAAAATT
16108 TCAAAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
36 16 0.29
37 12 0.21
38 16 0.29
39 12 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (37 bp):
AAAAAATTATAAAAATTATTAAAAATTATAATAATTA
Found at i:16123 original size:36 final size:35
Alignment explanation
Indices: 16047--16125 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 35
16037 AATTTTTAAA
* *
16047 AAAATTATAAAAATTATTAAAAATTATAAATAATT
1 AAAATAATAAAAATTATTAAAAATTATAAAAAATT
16082 AAAATAATAATAAATTATTAAAAATT-TCAAAAAA-T
1 AAAATAATAA-AAATTATTAAAAATTAT-AAAAAATT
16117 ATAAATAAT
1 A-AAATAAT
16126 TCTTTCTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 12 0.31
36 27 0.69
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (35 bp):
AAAATAATAAAAATTATTAAAAATTATAAAAAATT
Found at i:28974 original size:12 final size:12
Alignment explanation
Indices: 28957--28982 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28947 CTACCACTTC
28957 AATTTTCTTTCT
1 AATTTTCTTTCT
28969 AATTTTCTTTCT
1 AATTTTCTTTCT
28981 AA
1 AA
28983 CATTTCTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTCTTTCT
Found at i:35887 original size:29 final size:31
Alignment explanation
Indices: 35855--35917 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
35845 ATAGATAAGT
35855 TTAGAAATAAAG-TTTAAATAA-TTTTAATA
1 TTAGAAATAAAGTTTTAAATAATTTTTAATA
*
35884 TTAGAAATAAAGTTTTCAATAATTTTTAATA
1 TTAGAAATAAAGTTTTAAATAATTTTTAATA
35915 TTA
1 TTA
35918 ATTTTAGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.39
30 8 0.26
31 11 0.35
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (31 bp):
TTAGAAATAAAGTTTTAAATAATTTTTAATA
Found at i:41511 original size:52 final size:52
Alignment explanation
Indices: 41433--41537 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 52
41423 TGTTAATCTA
* * **
41433 AACAACATAATAATTAACTATTTAAAATTAAATAGTTTGATAATATTTTCTT
1 AACAACATAATAATTAACTATTTAAAAATAAATAATTAAATAATATTTTCTT
*
41485 AACATCATAATAATTAA-TGGA-TTAAAAATAAATAATTAAATAATATTTTCTT
1 AACAACATAATAATTAACT--ATTTAAAAATAAATAATTAAATAATATTTTCTT
41537 A
1 A
41538 CCATTTACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
51 1 0.02
52 44 0.96
53 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.40
Consensus pattern (52 bp):
AACAACATAATAATTAACTATTTAAAAATAAATAATTAAATAATATTTTCTT
Found at i:41756 original size:7 final size:7
Alignment explanation
Indices: 41744--41781 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
41734 TGTGAAAATA
41744 GAGAGTT
1 GAGAGTT
41751 GAGAGTT
1 GAGAGTT
41758 GAGAGTT
1 GAGAGTT
*
41765 AAGAGTT
1 GAGAGTT
*
41772 GAGAGAT
1 GAGAGTT
41779 GAG
1 GAG
41782 TTGAGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.42, T:0.24
Consensus pattern (7 bp):
GAGAGTT
Found at i:42219 original size:32 final size:33
Alignment explanation
Indices: 42179--42242 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
42169 TTAAAATGAT
*
42179 AAAAAAAAATAT-TAAATATTAAAATAATAATAA
1 AAAAAAAAATATAAAAATATTAAAATAATAAT-A
*
42212 AACAAAAAAATATAAAAATATTAGAATAATA
1 AA-AAAAAAATATAAAAATATTAAAATAATA
42243 GTTTTCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 10 0.37
35 15 0.56
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (33 bp):
AAAAAAAAATATAAAAATATTAAAATAATAATA
Found at i:47657 original size:18 final size:17
Alignment explanation
Indices: 47609--47657 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
47599 TAAATTTTTT
47609 GAAAAATAA-AAAAATA
1 GAAAAATAATAAAAATA
* *
47625 GAAAATTATTCAAAAATA
1 GAAAAATAAT-AAAAATA
47643 GAAAAATAAATAAAA
1 GAAAAAT-AATAAAA
47658 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
18 17 0.65
19 2 0.08
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.18
Consensus pattern (17 bp):
GAAAAATAATAAAAATA
Found at i:50833 original size:3 final size:3
Alignment explanation
Indices: 50825--50849 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
50815 TGTGCTTCTA
50825 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
50850 TTATTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:50854 original size:3 final size:3
Alignment explanation
Indices: 50848--50884 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
50838 ATAATAATAA
50848 TAT TAT TAT TAT TAT TAT TAT T-T TAT T-T TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
50885 TTTACTCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.19
3 25 0.81
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TAT
Found at i:50857 original size:6 final size:5
Alignment explanation
Indices: 50848--50886 Score: 51
Period size: 5 Copynumber: 7.2 Consensus size: 5
50838 ATAATAATAA
50848 TATTAT TATTAT TATTAT TATTT TATTT TATTT TATTT T
1 TATT-T TATT-T TATT-T TATTT TATTT TATTT TATTT T
50887 TACTCTCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 17 0.52
6 16 0.48
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (5 bp):
TATTT
Found at i:52533 original size:16 final size:17
Alignment explanation
Indices: 52498--52535 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
52488 TATTTCATAA
52498 AAATAATGAAAATAAAT
1 AAATAATGAAAATAAAT
52515 AAATAA-GAAAA-AAATT
1 AAATAATGAAAATAAA-T
52531 AAATA
1 AAATA
52536 TAAATTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 11 0.55
17 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
AAATAATGAAAATAAAT
Found at i:53546 original size:18 final size:18
Alignment explanation
Indices: 53506--53548 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
53496 GAGTAGATTT
53506 TTAATTAAATAAATTTAA
1 TTAATTAAATAAATTTAA
* *
53524 CTAATTAAA-AATTTTAAA
1 TTAATTAAATAAATTT-AA
53542 TTAATTA
1 TTAATTA
53549 CATATTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAATTAAATAAATTTAA
Found at i:59355 original size:23 final size:23
Alignment explanation
Indices: 59299--59386 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
59289 TCATTAACAT
*
59299 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
59323 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
*
59346 TGTTCGTGAATATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
59369 -GTT-GAATGAACATGTTCG
1 TGTTCG--TGAACATGTTCG
59387 TCAACATTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
21 1 0.02
22 3 0.05
23 32 0.58
24 19 0.35
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:59676 original size:68 final size:69
Alignment explanation
Indices: 59594--59729 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 69
59584 ATTTATTTAA
* * * * *
59594 AAAGTCAGAAAGATTGTTTTCATTTGATTTC-ATTATTACTTATTTTAATGTTTTATTTTTTACT
1 AAAGTCAAAAAGATTATTTTCATTTGACTTCTATTATTACTTATTTTAATATGTTATTTTTTACT
59658 ATTC
66 ATTC
* * * *
59662 AAAGTCAAAAAGATTATTTTCATTTTACTTCTTTTTTTACTTATTTTAATATGTTATTTTTTATT
1 AAAGTCAAAAAGATTATTTTCATTTGACTTCTATTATTACTTATTTTAATATGTTATTTTTTACT
59727 ATT
66 ATT
59730 TTGGGAATAG
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
68 27 0.47
69 31 0.53
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.57
Consensus pattern (69 bp):
AAAGTCAAAAAGATTATTTTCATTTGACTTCTATTATTACTTATTTTAATATGTTATTTTTTACT
ATTC
Found at i:64523 original size:17 final size:17
Alignment explanation
Indices: 64463--64523 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
64453 GATACTCGAC
64463 TGAAAACTGTTGTTGTA
1 TGAAAACTGTTGTTGTA
* ***
64480 TGCAAACTCGGTTAACGATA
1 TGAAAACT--GTTGTTG-TA
64500 TGAAAACTGTTGTTGTA
1 TGAAAACTGTTGTTGTA
*
64517 TGTAAAC
1 TGAAAAC
64524 GTTAAAGTGT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 4 0.12
20 9 0.28
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.34
Consensus pattern (17 bp):
TGAAAACTGTTGTTGTA
Found at i:66405 original size:25 final size:23
Alignment explanation
Indices: 66365--66418 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
66355 GATGTTAGAT
66365 ATATTTAAATTGTTGTGAATTTG
1 ATATTTAAATTGTTGTGAATTTG
* *
66388 ATATTTAACTATTTTTGTTAATTTG
1 ATATTTAA--ATTGTTGTGAATTTG
66413 -TATTTA
1 ATATTTA
66419 TTTATCGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 8 0.30
24 6 0.22
25 13 0.48
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (23 bp):
ATATTTAAATTGTTGTGAATTTG
Found at i:71416 original size:13 final size:14
Alignment explanation
Indices: 71398--71439 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
71388 TTTCAAAATT
71398 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
71411 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
71426 ATTTTAAATAATAT
1 ATTTT-AATAATAT
71440 TCTTCATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:71422 original size:16 final size:16
Alignment explanation
Indices: 71402--71438 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
71392 AAAATTATTT
71402 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
71419 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
71434 TAATA
1 TAATA
71439 TTCTTCATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:80593 original size:35 final size:35
Alignment explanation
Indices: 80547--80616 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
80537 ACAAGTCCCC
*
80547 AAAATTGTGGTGCAGCAGTCAAAAGCATTGGAAGT
1 AAAATTATGGTGCAGCAGTCAAAAGCATTGGAAGT
*
80582 AAAATTATGGTGTAGCAGTCAAAAGCATTGGAAGT
1 AAAATTATGGTGCAGCAGTCAAAAGCATTGGAAGT
80617 TTTTACTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.27, T:0.24
Consensus pattern (35 bp):
AAAATTATGGTGCAGCAGTCAAAAGCATTGGAAGT
Found at i:85674 original size:16 final size:17
Alignment explanation
Indices: 85640--85676 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
85630 AAAAACTTAT
85640 TAAATATTAAAATAAAA
1 TAAATATTAAAATAAAA
*
85657 TAAATATTTAAA-AAAA
1 TAAATATTAAAATAAAA
85673 TAAA
1 TAAA
85677 AAATAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATATTAAAATAAAA
Found at i:86679 original size:27 final size:26
Alignment explanation
Indices: 86632--86686 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
86622 TTATATCATA
*
86632 AAAATAAAATTAATTATATTTTAAAT
1 AAAATAAAATTAATTATATTTCAAAT
*
86658 AAAATAAAATTCGATT-TGATTTCAAAT
1 AAAATAAAATT-AATTAT-ATTTCAAAT
86685 AA
1 AA
86687 CTATAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 12 0.48
27 13 0.52
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AAAATAAAATTAATTATATTTCAAAT
Found at i:90651 original size:23 final size:23
Alignment explanation
Indices: 90615--90660 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
90605 TTTCCTACAA
*
90615 AATTTTTATTTTAAATTATTTTT
1 AATTTTTATCTTAAATTATTTTT
* * *
90638 AATTTTTGTCTTAACTTTTTTTT
1 AATTTTTATCTTAAATTATTTTT
90661 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (23 bp):
AATTTTTATCTTAAATTATTTTT
Done.