Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014872.1 Kokia drynarioides strain JFW-HI SEQ_129915, 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: 46587
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:4964 original size:45 final size:45
Alignment explanation
Indices: 4913--5020 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
4903 TTATTCTTCT
*
4913 TCTGATAATTTATATACTTAATTA-TGATTCATTAGTTT-CTTTTTC
1 TCTGATAATTAATATA-TTAATTACT-ATTCATTAGTTTACTTTTTC
* * * *
4958 TCTGATAATTAATGTATTTATTACTATTCATTCGTTTATTTTTTC
1 TCTGATAATTAATATATTAATTACTATTCATTAGTTTACTTTTTC
*
5003 TCTTATAATTAATATATT
1 TCTGATAATTAATATATT
5021 CAAGATAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 17 0.31
45 37 0.69
ACGTcount: A:0.28, C:0.10, G:0.06, T:0.56
Consensus pattern (45 bp):
TCTGATAATTAATATATTAATTACTATTCATTAGTTTACTTTTTC
Found at i:7038 original size:17 final size:17
Alignment explanation
Indices: 7018--7051 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
7008 AATCAGTTGC
7018 TTGATTTGGTCAAATAT
1 TTGATTTGGTCAAATAT
* *
7035 TTGATTTTGTTAAATAT
1 TTGATTTGGTCAAATAT
7052 CAAAATTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.15, T:0.53
Consensus pattern (17 bp):
TTGATTTGGTCAAATAT
Found at i:18052 original size:97 final size:97
Alignment explanation
Indices: 17874--18060 Score: 236
Period size: 97 Copynumber: 1.9 Consensus size: 97
17864 GAAAAGGATG
* * * *
17874 TTCGATTATCTTGAATTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACGAATTTTCAGAATCAG
1 TTCGATTATCTTGAATTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAATCAG
* *
17939 AGACAAATAAACATTGCCTTAATTTAAGGGTA
66 AAACAAATAAACATTGCCTCAATTTAAGGGTA
* *
17971 TTCGATTAT-TCTGATTTGAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCAAAACTC
1 TTCGATTATCT-TGAATTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAA-TC
* *
18035 -GAAATAAA-AGAATATTGCCTCAATTT
64 AGAAACAAATA-AACATTGCCTCAATTT
18061 TAAAGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 2 0.03
97 73 0.95
98 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (97 bp):
TTCGATTATCTTGAATTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAATCAG
AAACAAATAAACATTGCCTCAATTTAAGGGTA
Found at i:18426 original size:58 final size:57
Alignment explanation
Indices: 18324--18663 Score: 317
Period size: 58 Copynumber: 5.8 Consensus size: 57
18314 CTTCGAGAAC
* ** * * * * *
18324 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTTAGGGGT
1 AAAATGGTAATTTTGGAAA-AATCAAGGTCAAAAATGGAATTTTTGGA-AGTTCGGGGT
* *
18383 AAAATGGTAATTTTGGAAAAATCAAGGCCAAAAATGGAATTTTTGGAAGTTCGAGTGT
1 AAAATGGTAATTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCG-GGGT
*
18441 AAAATGGTAATTTTTGGACAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGT
1 AAAATGGTAA-TTTTGGA-AAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTC-GGGGT
* * *** * * *
18501 AAAATGGTATTTTTTGAAAAATTTGGGTTAAAAATGGAATTTTTGAAAGTTCGGAGCT
1 AAAATGGTAATTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGG-GGT
** *
18559 AAAATGGTAATTTTGGAAAAAT-TGGGTTC-AAAATAGAATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTGGAAAAATCAAGG-TCAAAAATGGAATTTTTGGAAGTTCG-GGGT
* * * ** *
18616 AAAATTGAAATTTTTGAAAAAATCGGGGTCAATAATGGAA-TTTTGGAA
1 AAAATGGTAA-TTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAA
18664 AGGTTCAAGG
Statistics
Matches: 238, Mismatches: 33, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
57 41 0.17
58 110 0.46
59 41 0.17
60 45 0.19
61 1 0.00
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGAAAAATCAAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGT
Found at i:18484 original size:31 final size:31
Alignment explanation
Indices: 18383--18664 Score: 135
Period size: 29 Copynumber: 9.6 Consensus size: 31
18373 ATTTAGGGGT
* *
18383 AAAATGGTAA-TTTTGGAAAAATCAAGGCCA
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCA
**
18413 AAAATGG-AATTTTTGG-AAGTTCGAGTGT--
1 AAAATGGTAATTTTTGGAAAAATCGAG-GTCA
18441 AAAATGGTAATTTTTGGACAAAATCGAGGTCA
1 AAAATGGTAATTTTTGGA-AAAATCGAGGTCA
** *
18473 AAAATGG-AATTTTTGG-AAGTTCGGGGGT--
1 AAAATGGTAATTTTTGGAAAAATC-GAGGTCA
* * *
18501 AAAATGGT-ATTTTTTGAAAAATTTG-GGTTA
1 AAAATGGTAATTTTTGGAAAAA-TCGAGGTCA
** *
18531 AAAATGG-AATTTTT-GAAAGTTCG-GAG-CT
1 AAAATGGTAATTTTTGGAAAAATCGAG-GTCA
*
18559 AAAATGGTAA-TTTTGGAAAAATTG-GGTTC-
1 AAAATGGTAATTTTTGGAAAAATCGAGG-TCA
* **
18588 AAAATAG-AATTTTTGG-AAGTTCGAGGGT--
1 AAAATGGTAATTTTTGGAAAAATCGA-GGTCA
* * * *
18616 AAAATTGAAATTTTTGAAAAAATCGGGGTCA
1 AAAATGGTAATTTTTGGAAAAATCGAGGTCA
*
18647 ATAATGG-AA-TTTTGGAAA
1 AAAATGGTAATTTTTGGAAA
18665 GGTTCAAGGG
Statistics
Matches: 193, Mismatches: 33, Indels: 53
0.69 0.12 0.19
Matches are distributed among these distances:
28 51 0.26
29 70 0.36
30 44 0.23
31 21 0.11
32 7 0.04
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTCA
Found at i:18500 original size:118 final size:116
Alignment explanation
Indices: 18324--18663 Score: 366
Period size: 118 Copynumber: 2.9 Consensus size: 116
18314 CTTCGAGAAC
* ** * * **
18324 AAAATGGTAATTTTCGAAAGGTTCGAGGTTAAAAATGGAATTTTTAGACA-TTTAGGGGTAAAAT
1 AAAATGGTAATTTTGGAAA-AATCGAGGTCAAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAT
* * *
18388 GGTAATTTTGGAAAAATCAAGGCCAAAAATGGAATTTTTGGAAGTTC-GAGTGT
64 GGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGAG-CT
18441 AAAATGGTAATTTTTGGACAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAT
1 AAAATGGTAA-TTTTGGA-AAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAT
* * ** * *
18506 GGTATTTTTTGAAAAATTTGGGTTAAAAATGGAATTTTTGAAAGTTCGGAGCT
64 GGTAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGAGCT
* * * *
18559 AAAATGGTAATTTTGGAAAAATTG-GGTTC-AAAATAGAATTTTTGGAAGTTCGAGGGTAAAATT
1 AAAATGGTAATTTTGGAAAAATCGAGG-TCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATG
* * * *
18622 GAAATTTTTGAAAAAATCGGGGTCAATAATGGAA-TTTTGGAA
65 GTAA-TTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAA
18664 AGGTTCAAGG
Statistics
Matches: 188, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
115 42 0.22
116 31 0.16
117 18 0.10
118 92 0.49
119 5 0.03
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTTGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAATGG
TAATTTTGGAAAAATCAGGGTCAAAAATGGAATTTTTGGAAGTTCGGAGCT
Found at i:18619 original size:28 final size:28
Alignment explanation
Indices: 18324--18631 Score: 137
Period size: 29 Copynumber: 10.6 Consensus size: 28
18314 CTTCGAGAAC
* * *
18324 AAAATGGTAATTTTCGAAAGGTTCGAGGTT
1 AAAATGGTAATTTTTGGAA-GTTCG-GGGT
* * *
18354 AAAAATGG-AATTTTTAGACATTTAGGGGT
1 -AAAATGGTAATTTTTGGA-AGTTCGGGGT
** ***
18383 AAAATGGTAA-TTTTGGAAAAATCAAGGCCA
1 AAAATGGTAATTTTTGG-AAGTTC--GGGGT
*
18413 AAAATGG-AATTTTTGGAAGTTCGAGTGT
1 AAAATGGTAATTTTTGGAAGTTCG-GGGT
** *
18441 AAAATGGTAATTTTTGGACAAAATCGAGGT
1 AAAATGGTAATTTTTGG--AAGTTCGGGGT
18471 CAAAAATGG-AATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTC-GGGGT
* * * * *
18501 AAAATGGTATTTTTTGAAAAATTTGGGTT
1 AAAATGGTAATTTTTG-GAAGTTCGGGGT
* *
18530 AAAAATGG-AATTTTTGAAAGTTCGGAGCT
1 -AAAATGGTAATTTTTGGAAGTTCGG-GGT
* *
18559 AAAATGGTAA-TTTTGGAAAAATT-GGGTT
1 AAAATGGTAATTTTTGG--AAGTTCGGGGT
*
18587 CAAAATAG-AATTTTTGGAAGTTCGAGGGT
1 -AAAATGGTAATTTTTGGAAGTTCG-GGGT
* *
18616 AAAATTGAAATTTTTG
1 AAAATGGTAATTTTTG
18632 AAAAAATCGG
Statistics
Matches: 211, Mismatches: 41, Indels: 52
0.69 0.13 0.17
Matches are distributed among these distances:
27 5 0.02
28 59 0.28
29 72 0.34
30 46 0.22
31 22 0.10
32 7 0.03
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (28 bp):
AAAATGGTAATTTTTGGAAGTTCGGGGT
Found at i:20835 original size:46 final size:47
Alignment explanation
Indices: 20780--20870 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 47
20770 TCGGGTAAGA
*
20780 GATTGGTTGATGATGATCTGCCAC-AGGCTCGAGGTAAGAGATCGAAT
1 GATTGGTTGATGATGATCTGCC-CTAGGCTCGAGGTAAAAGATCGAAT
*
20827 GATT-GTTGATGATGATCTGCCCTAGGCTCGGGGTAAAAGATCGA
1 GATTGGTTGATGATGATCTGCCCTAGGCTCGAGGTAAAAGATCGA
20871 GGTTTTCAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 1 0.02
46 36 0.88
47 4 0.10
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.26
Consensus pattern (47 bp):
GATTGGTTGATGATGATCTGCCCTAGGCTCGAGGTAAAAGATCGAAT
Found at i:21196 original size:49 final size:49
Alignment explanation
Indices: 21143--21780 Score: 568
Period size: 49 Copynumber: 13.0 Consensus size: 49
21133 ATGCTTCTGA
* * * * *
21143 GGTACAAGGTTCACCGTTGCAACTTAAACCTTTCCCTCTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTCGT
* * ** ** *
21192 GGTACT-GGATTCACCGTTGCGGCTTAAAT-TTTTACTTCATGTC-TCTGA
1 GGTACTAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTC-GT
*
21240 GGTACTAGGTTCGTCGTTGCGACTTAAA-CTTTTCCCTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTTTGTGTCTTCGT
* * * ** *
21289 GGTACT-GGATTCGTCGTTGTGGCTTAAATCTTTCCCTTCATGTC-TCTGA
1 GGTACTAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTC-GT
*
21338 GGTACTAGGTTCGCTGTTGCGACTTAAA-CATTTCCCTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATC-TTTCCCTTTGTGTCTTCGT
** ** *
21387 GGTACT-GGATTTACCGTTGCGACTTAAATCTTTCCCTTCATGTC-TCTGA
1 GGTACTAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTC-GT
* *
21436 GGTACTAGGTTCGCCATTGCGACTTAAACCTTTCCCTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTCGT
* * * * ** *
21485 GGTACTTGATTCTCCGTTGCGGCTTAAATCTTTCCCTTCATGTC-TCTGA
1 GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTC-GT
* * *
21534 GGTACTAAGTTCGCCATTACGACTTAAA-CATTTCCCTTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATC-TTTCCC-TTTGTGTCTTCGT
* ** * *
21584 GGTACTAGATTCGCCGTTGC-AGCTTAAATCTTTCCCTTCATGTCTTTGA
1 GGTACTAGGTTCGCCGTTGCGA-CTTAAATCTTTCCCTTTGTGTCTTCGT
* *
21633 GGTACTAGGTT-GCCATTGCGACTTAAACCTTTCCCTTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCC-TTTGTGTCTTCGT
* * * ** *
21682 GGTACT-GGATTCGTCGTTGCGGCTTAAATTTTTCCCTTCATGTC-TCTGA
1 GGTACTAGG-TTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTC-GT
* *
21731 GGTACTAGGTTCGACGTTGAGACTTAAATCTTTCCCTTTGTGTCTTCGT
1 GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTCGT
21780 G
1 G
21781 TTTTTCTCAA
Statistics
Matches: 467, Mismatches: 92, Indels: 60
0.75 0.15 0.10
Matches are distributed among these distances:
47 2 0.00
48 70 0.15
49 322 0.69
50 70 0.15
51 3 0.01
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (49 bp):
GGTACTAGGTTCGCCGTTGCGACTTAAATCTTTCCCTTTGTGTCTTCGT
Found at i:21372 original size:98 final size:98
Alignment explanation
Indices: 21114--21780 Score: 982
Period size: 98 Copynumber: 6.8 Consensus size: 98
21104 TTCGTCTTTA
* * * *
21114 CGGCTTAAAT-TTTCCTTTCATG-CTTCTGAGGTACAAGGTTCACCGTTGCAACTTAAACCTTTC
1 CGGCTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTC
* *
21177 CCTCTGTGTCTTCGTGGTACTGGATTCACCGTTG
65 CCTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
** * *
21211 CGGCTTAAAT-TTTTACTTCATGTCTCTGAGGTACTAGGTTCGTCGTTGCGACTTAAACTTTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
*
21275 CTTTGTGTCTTCGTGGTACTGGATTCGTCGTTG
66 CTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
* * *
21308 TGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCTGTTGCGACTTAAACATTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
**
21373 CTTTGTGTCTTCGTGGTACTGGATTTACCGTTG
66 CTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
* *
21406 CGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCATTGCGACTTAAACCTTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
* *
21471 CTTTGTGTCTTCGTGGTACTTGATTCTCCGTTG
66 CTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
* * * *
21504 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAAGTTCGCCATTACGACTTAAACATTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
*
21569 CTTTTGTGTCTTCGTGGTACTAGATTCGCCGTTG
66 C-TTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
* * *
21603 CAGCTTAAATCTTTCCCTTCATGTCTTTGAGGTACTAGGTT-GCCATTGCGACTTAAACCTTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
*
21667 CTTTTGTGTCTTCGTGGTACTGGATTCGTCGTTG
66 C-TTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
* * * *
21701 CGGCTTAAATTTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGACGTTGAGACTTAAATCTTTCC
1 CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
21766 CTTTGTGTCTTCGTG
66 CTTTGTGTCTTCGTG
21781 TTTTTCTCAA
Statistics
Matches: 518, Mismatches: 48, Indels: 7
0.90 0.08 0.01
Matches are distributed among these distances:
97 93 0.18
98 337 0.65
99 88 0.17
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (98 bp):
CGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGGTTCGCCGTTGCGACTTAAACCTTTCC
CTTTGTGTCTTCGTGGTACTGGATTCGCCGTTG
Found at i:22701 original size:19 final size:18
Alignment explanation
Indices: 22679--22755 Score: 79
Period size: 19 Copynumber: 4.3 Consensus size: 18
22669 CTATTTTTGT
*
22679 TTTTTCTTCTTGTTTTTC
1 TTTTTCTTCTTCTTTTTC
*
22697 CTTTT-TTC-TCTTTTTC
1 TTTTTCTTCTTCTTTTTC
22713 TTTTTCTT-TTGCTTTCTTC
1 TTTTTCTTCTT-CTTT-TTC
*
22732 TTCTTCTTCTTCTTTTTTC
1 TTTTTCTTCTTC-TTTTTC
22751 TTTTT
1 TTTTT
22756 TCTTTGTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
16 11 0.23
17 6 0.12
18 8 0.17
19 18 0.38
20 5 0.10
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTTCTTCTTCTTTTTC
Found at i:22708 original size:22 final size:22
Alignment explanation
Indices: 22678--22760 Score: 73
Period size: 22 Copynumber: 3.8 Consensus size: 22
22668 TCTATTTTTG
*
22678 TTTTT-TCTTCTTGTTTTTCCT
1 TTTTTCTCTTCTTCTTTTTCCT
* *
22699 TTTTTCTCTTTTTCTTTTTCTT
1 TTTTTCTCTTCTTCTTTTTCCT
*
22721 TTGCTTTCTTCTTCTTCTTCTT-CT
1 TT--TTTC-TCTTCTTCTTTTTCCT
*
22745 TTTTTCT-TTTTTCTTT
1 TTTTTCTCTTCTTCTTT
22761 GTTCATTGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 7 0.14
21 6 0.12
22 19 0.38
24 7 0.14
25 11 0.22
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (22 bp):
TTTTTCTCTTCTTCTTTTTCCT
Found at i:22714 original size:6 final size:6
Alignment explanation
Indices: 22679--22760 Score: 60
Period size: 6 Copynumber: 13.5 Consensus size: 6
22669 CTATTTTTGT
* * * * *
22679 TTTTTC TTCTTG TTTTTC -CTTT- TTTCTC TTTTTC TTTTTC TTTTGC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* *
22725 TTTCTTC TTCTTC TTCTTC TTTTTTC TTTTTTC TTT
1 TTT-TTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTT
22761 GTTCATTGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
5 5 0.08
6 39 0.65
7 16 0.27
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:27573 original size:97 final size:98
Alignment explanation
Indices: 27401--27579 Score: 229
Period size: 97 Copynumber: 1.8 Consensus size: 98
27391 TCAATTATCT
* * * * * * *
27401 CGATTTGAAGAAAAGTCGCACCTAGTAAGTTAATGCACAAATTTTTAGAATCAGAGACAAAGAAA
1 CGATTTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAATCAGAAAAAAAGAAA
*
27466 CATTGTCTCGA-TTTAAGGGTATTCGATTATTC
66 CATTGCCTCGACTTTAAGGGTATTCGATTATTC
*
27498 CGATTTGAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCAAAACTC-GAAATAAAAG-
1 CGATTTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAA-TCAGAAA-AAAAGA
*
27561 AATATTGCCTCGACTTTAA
64 AACATTGCCTCGACTTTAA
27580 AGGTTTCTTA
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
97 58 0.84
98 11 0.16
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (98 bp):
CGATTTGAAGAAAAATCGCACCTAGTAAATTAAGGCACAAATTTTCAAAATCAGAAAAAAAGAAA
CATTGCCTCGACTTTAAGGGTATTCGATTATTC
Found at i:27943 original size:30 final size:30
Alignment explanation
Indices: 27870--28065 Score: 117
Period size: 29 Copynumber: 6.7 Consensus size: 30
27860 GTTTGAGGTT
*
27870 AAAAATGGAATTTTT--AAACATTCGAGGGT-
1 AAAAATGGAATTTTTGGAAA-AATC-AGGGTA
27899 -AAAATGGTAA-TTTTGGAAAAATCAGGGTA
1 AAAAATGG-AATTTTTGGAAAAATCAGGGTA
* ** *
27928 AAAAATAGAATTTTTGG-AAGTTCGAGGCTA
1 AAAAATGGAATTTTTGGAAAAATC-AGGGTA
* * *
27958 AAATA-GTAATTTTTGGAAAAATC-GAGGTT
1 AAAAATGGAATTTTTGGAAAAATCAG-GGTA
* * ** *
27987 AAAGATGGAATTTTTGG--AAGTTTGGGGA
1 AAAAATGGAATTTTTGGAAAAATCAGGGTA
* * *
28015 TAAAATGGTAATTTTTGGAAAAATTAGGGTT
1 AAAAATGG-AATTTTTGGAAAAATCAGGGTA
28046 AAAAATGGAA-TTTTGGAAAA
1 AAAAATGGAATTTTTGGAAAA
28066 GTTTAGGGGT
Statistics
Matches: 128, Mismatches: 25, Indels: 28
0.71 0.14 0.15
Matches are distributed among these distances:
28 28 0.22
29 46 0.36
30 40 0.31
31 14 0.11
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAAAATCAGGGTA
Found at i:28001 original size:59 final size:60
Alignment explanation
Indices: 27866--28063 Score: 246
Period size: 59 Copynumber: 3.4 Consensus size: 60
27856 AAAGGTTTGA
* * *
27866 GGTTAAAAATGGAATTTTT-AAACATTCGAGGGTAAAATGGTAA-TTTTGGAAAAATC-AG
1 GGTTAAAAATGGAATTTTTGGAA-GTTCGAGGATAAAATGGTAATTTTTGGAAAAATCGAG
* * * *
27924 GGTAAAAAATAGAATTTTTGGAAGTTCGAGGCTAAAATAGTAATTTTTGGAAAAATCGA-
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTTGGAAAAATCGAG
* * * *
27983 GGTTAAAGATGGAATTTTTGGAAGTTTGGGGATAAAATGGTAATTTTTGGAAAAAT-TAG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTTGGAAAAATCGAG
28042 GGTTAAAAATGGAA-TTTTGGAA
1 GGTTAAAAATGGAATTTTTGGAA
28064 AAGTTTAGGG
Statistics
Matches: 121, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
58 43 0.36
59 77 0.64
60 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (60 bp):
GGTTAAAAATGGAATTTTTGGAAGTTCGAGGATAAAATGGTAATTTTTGGAAAAATCGAG
Found at i:28027 original size:29 final size:29
Alignment explanation
Indices: 27791--28034 Score: 119
Period size: 29 Copynumber: 8.3 Consensus size: 29
27781 AAAAAAAGTG
* * * *
27791 ATTTTTGGATGCTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGTTCGAGGATAAAATGGTA
*
27820 A-TTTT-GAATGCTTCG-GGAACAAAATGGTA
1 ATTTTTGGAA-G-TTCGAGG-ATAAAATGGTA
* * * *
27849 ATTTTCGAAAGGTTTGAGGTTAAAAATGG-A
1 ATTTTTGGAA-GTTCGAGGAT-AAAATGGTA
* * *
27879 ATTTTT-AAACATTCGAGGGTAAAATGGTA
1 ATTTTTGGAA-GTTCGAGGATAAAATGGTA
** * *
27908 A-TTTTGGAAAAATC-AGGGTAAAAAATAG-A
1 ATTTTTGG-AAGTTCGA-GG-ATAAAATGGTA
* *
27937 ATTTTTGGAAGTTCGAGGCTAAAATAGTA
1 ATTTTTGGAAGTTCGAGGATAAAATGGTA
** *
27966 ATTTTTGGAAAAATCGAGGTTAAAGATGG-A
1 ATTTTTGG-AAGTTCGAGGATAAA-ATGGTA
* *
27996 ATTTTTGGAAGTTTGGGGATAAAATGGTA
1 ATTTTTGGAAGTTCGAGGATAAAATGGTA
28025 ATTTTTGGAA
1 ATTTTTGGAA
28035 AAATTAGGGT
Statistics
Matches: 164, Mismatches: 33, Indels: 36
0.70 0.14 0.15
Matches are distributed among these distances:
27 2 0.01
28 30 0.18
29 69 0.42
30 48 0.29
31 15 0.09
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGATAAAATGGTA
Found at i:28059 original size:29 final size:30
Alignment explanation
Indices: 27866--28065 Score: 127
Period size: 30 Copynumber: 6.8 Consensus size: 30
27856 AAAGGTTTGA
*
27866 GGTTAAAAATGGAATTTTT--AAACATTCGAG
1 GGTTAAAAATGGAATTTTTGGAAAAATT--AG
*
27896 GG-T-AAAATGGTAA-TTTTGGAAAAATCAG
1 GGTTAAAAATGG-AATTTTTGGAAAAATTAG
* * * *
27924 GGTAAAAAATAGAATTTTTGG--AAGTTCG
1 GGTTAAAAATGGAATTTTTGGAAAAATTAG
* * *
27952 AGGCT-AAAATAGTAATTTTTGGAAAAA-TCG
1 -GGTTAAAAAT-GGAATTTTTGGAAAAATTAG
* ** *
27982 AGGTTAAAGATGGAATTTTTGG-AAGTTTGG
1 -GGTTAAAAATGGAATTTTTGGAAAAATTAG
*
28012 GGAT-AAAATGGTAATTTTTGGAAAAATTAG
1 GGTTAAAAATGG-AATTTTTGGAAAAATTAG
28042 GGTTAAAAATGGAA-TTTTGGAAAA
1 GGTTAAAAATGGAATTTTTGGAAAA
28066 GTTTAGGGGT
Statistics
Matches: 131, Mismatches: 24, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
28 30 0.23
29 40 0.31
30 48 0.37
31 13 0.10
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (30 bp):
GGTTAAAAATGGAATTTTTGGAAAAATTAG
Found at i:28072 original size:30 final size:31
Alignment explanation
Indices: 27840--28073 Score: 110
Period size: 30 Copynumber: 7.9 Consensus size: 31
27830 CTTCGGGAAC
* *
27840 AAAATGGTAA-TTTTCGAAAGGTTT-GAGGTTA
1 AAAATGG-AATTTTTGGAAAAGTTTAG-GGTTA
*
27871 AAAATGGAATTTTT--AAACA-TTCGAGGG-T-
1 AAAATGGAATTTTTGGAAA-AGTT-TAGGGTTA
* * *
27899 AAAATGGTAA-TTTTGGAAAA-ATCAGGGTAA
1 AAAATGG-AATTTTTGGAAAAGTTTAGGGTTA
* * *
27929 AAAATAGAATTTTTGG--AAG-TTCGAGGCT-
1 AAAATGGAATTTTTGGAAAAGTTTAG-GGTTA
* * **
27957 AAAATAGTAATTTTTGGAAAAATCGA-GGTTA
1 AAAAT-GGAATTTTTGGAAAAGTTTAGGGTTA
* * *
27988 AAGATGGAATTTTTGG--AAGTTTGGGGAT-
1 AAAATGGAATTTTTGGAAAAGTTTAGGGTTA
*
28016 AAAATGGTAATTTTTGGAAAA-ATTAGGGTTA
1 AAAATGG-AATTTTTGGAAAAGTTTAGGGTTA
28047 AAAATGGAA-TTTTGGAAAAGTTTAGGG
1 AAAATGGAATTTTTGGAAAAGTTTAGGG
28074 GTCAAAATAT
Statistics
Matches: 151, Mismatches: 29, Indels: 47
0.67 0.13 0.21
Matches are distributed among these distances:
28 33 0.22
29 45 0.30
30 46 0.30
31 27 0.18
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (31 bp):
AAAATGGAATTTTTGGAAAAGTTTAGGGTTA
Found at i:28081 original size:30 final size:30
Alignment explanation
Indices: 27986--28081 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 30
27976 AAATCGAGGT
27986 TAAAGATGGAATTTTTGG--AAGTTT-GGGG
1 TAAA-ATGGAATTTTTGGAAAAGTTTAGGGG
* *
28014 ATAAAATGGTAATTTTTGGAAAA-ATTAGGGT
1 -TAAAATGG-AATTTTTGGAAAAGTTTAGGGG
28045 TAAAAATGGAA-TTTTGGAAAAGTTTAGGGG
1 T-AAAATGGAATTTTTGGAAAAGTTTAGGGG
28075 TCAAAAT
1 T-AAAAT
28082 ATGATTTTTG
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
28 4 0.07
29 23 0.41
30 17 0.30
31 12 0.21
ACGTcount: A:0.39, C:0.01, G:0.27, T:0.33
Consensus pattern (30 bp):
TAAAATGGAATTTTTGGAAAAGTTTAGGGG
Found at i:44022 original size:18 final size:18
Alignment explanation
Indices: 43999--44041 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
43989 ACGGTAGGTG
43999 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
44017 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
44035 TAATTAA
1 TAATTAA
44042 AAATCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Done.