Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004331.1 Kokia drynarioides strain JFW-HI SEQ_117655, 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: 72717
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 76 characters in sequence are not A, C, G, or T
Found at i:631 original size:68 final size:68
Alignment explanation
Indices: 522--656 Score: 243
Period size: 68 Copynumber: 2.0 Consensus size: 68
512 TGATTAGCCA
* * *
522 TTTAAAGTTAAAGGCTTTTTATAACAGTAATCCATATTTTTTATTAGTTACGAAAATAATTCAAT
1 TTTAAAGTTAAAAGCTTTTTATAAAAGTAATCCATATTTTTTATTAATTACGAAAATAATTCAAT
587 TTT
66 TTT
590 TTTAAAGTTAAAAGCTTTTTATAAAAGTAATCCATATTTTTTATTAATTACGAAAATAATTCAAT
1 TTTAAAGTTAAAAGCTTTTTATAAAAGTAATCCATATTTTTTATTAATTACGAAAATAATTCAAT
655 TT
66 TT
657 AAAAATTATG
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.45
Consensus pattern (68 bp):
TTTAAAGTTAAAAGCTTTTTATAAAAGTAATCCATATTTTTTATTAATTACGAAAATAATTCAAT
TTT
Found at i:2073 original size:59 final size:57
Alignment explanation
Indices: 1993--2152 Score: 180
Period size: 59 Copynumber: 2.8 Consensus size: 57
1983 CTTCGGGAAC
* *
1993 AAAATGGTAATTTTTGAAAGGTTCGAGGTTAAAAATGAAATTTTTAGACATTTAGGGGT
1 AAAATGGTAA-TTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGACA-TCAGGGGT
** * *
2052 AAAATGGTAATATTTGGAAGGTTC-AGGGTTAAAAATGGTATTTTTAGATATCGGGGGT
1 AAAATGGTAAT-TTTGGAAGGTTCGA-GGTTAAAAATGAAATTTTTAGACATCAGGGGT
* * * *
2110 AAAATGGTAATTTTGGAAAGTTCGGGGGT-AAAATGTAATTTTT
1 AAAATGGTAATTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTT
2153 GGAAATTTTG
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
56 12 0.14
57 14 0.16
58 19 0.22
59 42 0.48
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (57 bp):
AAAATGGTAATTTTGGAAGGTTCGAGGTTAAAAATGAAATTTTTAGACATCAGGGGT
Found at i:2080 original size:29 final size:29
Alignment explanation
Indices: 2047--2156 Score: 111
Period size: 29 Copynumber: 3.8 Consensus size: 29
2037 TAGACATTTA
*
2047 GGGGTAAAATGGTAATATTTGGAAGGTTCA
1 GGGGTAAAATGGTAAT-TTTGGAAGGTTCG
* * *
2077 GGGTTAAAAATGGT-ATTTT--TAGATATCG
1 GGGGT-AAAATGGTAATTTTGGAAGGT-TCG
*
2105 GGGGTAAAATGGTAATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGAAGGTTCG
2134 GGGGTAAAAT-GTAATTTTTGGAA
1 GGGGTAAAATGGTAA-TTTTGGAA
2157 ATTTTGAGGA
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
27 11 0.17
28 15 0.23
29 24 0.36
30 8 0.12
31 8 0.12
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTGGAAGGTTCG
Found at i:2157 original size:29 final size:30
Alignment explanation
Indices: 1993--2201 Score: 139
Period size: 30 Copynumber: 7.1 Consensus size: 30
1983 CTTCGGGAAC
* *
1993 AAAATGGTAATTTTT-GAAAGGTTCGAGGTT
1 AAAATGGTAATTTTTGGAAA-GTTCGGGGGT
* * * **
2023 AAAAAT-GAAATTTTTAGACA-TTTAGGGGT
1 -AAAATGGTAATTTTTGGAAAGTTCGGGGGT
* * * *
2052 AAAATGGTAATATTTGGAAGGTTCAGGGTT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGGT
* *
2082 AAAAATGGT-ATTTTTAGATA--TCGGGGGT
1 -AAAATGGTAATTTTTGGAAAGTTCGGGGGT
2110 AAAATGGTAA-TTTTGGAAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGGT
* * * *
2139 AAAAT-GTAATTTTTGGAAATTTTGAGGAT
1 AAAATGGTAATTTTTGGAAAGTTCGGGGGT
* * *
2168 AAAAAT-GTAATTTTTGGAAAATTTGGGGTT
1 -AAAATGGTAATTTTTGGAAAGTTCGGGGGT
2198 AAAA
1 AAAA
2202 ATTGAATTTT
Statistics
Matches: 141, Mismatches: 28, Indels: 20
0.75 0.15 0.11
Matches are distributed among these distances:
27 15 0.11
28 16 0.11
29 46 0.33
30 48 0.34
31 16 0.11
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAAGTTCGGGGGT
Found at i:2212 original size:29 final size:30
Alignment explanation
Indices: 2110--2215 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
2100 TATCGGGGGT
* * *
2110 AAAATGGTAA-TTTTGGAAAGTTCGGGGGT-
1 AAAAT-GTAATTTTTGGAAAATTTGGGGATA
* *
2139 AAAATGTAATTTTTGGAAATTTTGAGGATA
1 AAAATGTAATTTTTGGAAAATTTGGGGATA
*
2169 AAAATGTAATTTTTGGAAAATTTGGGGTTA
1 AAAATGTAATTTTTGGAAAATTTGGGGATA
2199 AAAAT-TGAA-TTTTGGAA
1 AAAATGT-AATTTTTGGAA
2216 GTTTAAGGAC
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
28 4 0.06
29 29 0.43
30 34 0.51
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAATTTGGGGATA
Found at i:3298 original size:3 final size:3
Alignment explanation
Indices: 3290--3346 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
3280 CTCTTTTTAT
*
3290 TTA TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3338 TTA TTA TTA
1 TTA TTA TTA
3347 CCTTTCTTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4024 original size:46 final size:46
Alignment explanation
Indices: 3971--4065 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 46
3961 CTTTAAAATC
* * * *
3971 AAATTTAAAATTAAGTTAAAAACC-CTTTCAAATTTAA-AGTAAATTT
1 AAATTTAAAAATAAATTAAAAACCAATTT-AAACTTAATA-TAAATTT
*
4017 AAATTTAAAAATAAATTTAAAACCAATTTAAACTTAATATAAATTT
1 AAATTTAAAAATAAATTAAAAACCAATTTAAACTTAATATAAATTT
4063 AAA
1 AAA
4066 ATCAAAAGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 38 0.90
47 4 0.10
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (46 bp):
AAATTTAAAAATAAATTAAAAACCAATTTAAACTTAATATAAATTT
Found at i:4033 original size:18 final size:17
Alignment explanation
Indices: 4000--4037 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3990 AAACCCTTTC
*
4000 AAATTTAAAGTAAATTT
1 AAATTTAAAATAAATTT
4017 AAATTTAAAAATAAATTT
1 AAATTT-AAAATAAATTT
4035 AAA
1 AAA
4038 ACCAATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:4674 original size:49 final size:49
Alignment explanation
Indices: 4502--5123 Score: 402
Period size: 49 Copynumber: 12.7 Consensus size: 49
4492 TGATACTAAA
* * *
4502 TTCGCTGTTGCGGCTTAAAT-TTTCCTTTTCATG-CTTCTGAGGTA-TAAGG
1 TTCGCCGTTGCGACTTAAATCTTTCC-CTTCATGTC-TCTGAGGTACT-AGG
* * * * *
4551 TTCGTCATTGCGACTTAAACCTTTCCCTTTAGTGTCT-TCGCGGTACT-GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCA-TGTCTCT-GAGGTACTAGG
* * * *
4600 ATTTGCCGTTGTGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATTAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGG
* * * ** *
4650 TTCGCCATTGCTACTTAAACCTTTCCCTTTGTGTCT-TCGTGGTACT-GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCT-GAGGTACTAGG
* * *
4698 ATTCGCCGTTGCAACTTAAATATTTCCCTTCATGTCTCTGAGGTATTAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGG
* * * ** *
4748 TTCGCCATTGCGACTTAAACCTTTCCTTTTGTGTCT-TCGTGGTACT-GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCT-GAGGTACTAGG
* * *
4796 ATTCACCGTTGCGGCTTAAATCTTTCCCTTCATG-CTTCTGAGGTACAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGG
* ** *
4846 TTCGCCGTTGCGACTTAAACCTTTCCCTTTGTGTCT-TCGTGGTACT-GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCT-GAGGTACTAGG
* * * * *
4894 ATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATG-CTTCTAAGGTGCAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTC-TCTGAGGTACTAGG
* * * * * *
4944 TTCGTCATTTCGACTTAAATCTTTCCCTCCATATCT-TCGTGGTACT-GG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCT-GAGGTACTAGG
* * *
4992 ATTCACTGTTGCGACTTAAATATTTCCCTTCATGTCTCTGAGGTA-TAAGG
1 -TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACT-AGG
* * * * *
5042 TTCTCCATTGCGA-TCTAAA-CTTTTCCC-TCTATATC-CTCGTGGTACTAGA
1 TTCGCCGTTGCGACT-TAAATC-TTTCCCTTC-ATGTCTCT-GAGGTACTAGG
* * * *
5091 TTTGCCATTACGGCTTAAATCTTTCCCTTCATG
1 TTCGCCGTTGCGACTTAAATCTTTCCCTTCATG
5124 CTTCGTGATA
Statistics
Matches: 435, Mismatches: 101, Indels: 74
0.71 0.17 0.12
Matches are distributed among these distances:
48 20 0.05
49 354 0.81
50 59 0.14
51 2 0.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (49 bp):
TTCGCCGTTGCGACTTAAATCTTTCCCTTCATGTCTCTGAGGTACTAGG
Found at i:4732 original size:98 final size:98
Alignment explanation
Indices: 4501--5127 Score: 796
Period size: 98 Copynumber: 6.4 Consensus size: 98
4491 ATGATACTAA
* * *
4501 ATTCGCTGTTGCGGCTTAAAT-TTTCCTTTTCATGCTTCTGAGGTATAAGGTTCGTCATTGCGAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCC-CTTCATGCTTCTGAGGTATAAGGTTCGCCATTGCGAC
*
4565 TTAAACCTTTCCCTTTAGTGTCTTCGCGGTACTGG
65 TTAAACCTTTCCCTTT-GTGTCTTCGTGGTACTGG
* * * *
4600 ATTTGCCGTTGTGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATTAGGTTCGCCATTGCTAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGCCATTGCGAC
4664 TTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
65 TTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
** * *
4698 ATTCGCCGTTGCAACTTAAATATTTCCCTTCATG-TCTCTGAGGTATTAGGTTCGCCATTGCGAC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGCCATTGCGAC
*
4762 TTAAACCTTTCCTTTTGTGTCTTCGTGGTACTGG
65 TTAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
* * *
4796 ATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCCATTGCGACT
4861 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
66 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
* * ** * *
4894 ATTCGCCGTTGCGGCTTAAATCTTTCCTTTCATGCTTCTAAGGTGCAAGGTTCGTCATTTCGACT
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCCATTGCGACT
* *** *
4959 TAAATCTTTCCCTCCATATCTTCGTGGTACTGG
66 TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
* * * * *
4992 ATTCACTGTTGCGACTTAAATATTTCCCTTCATG-TCTCTGAGGTATAAGGTTCTCCATTGCGA-
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCT-TCTGAGGTATAAGGTTCGCCATTGCGAC
* * * * * *
5055 TCTAAACTTTTCCCTCTATATCCTCGTGGTACTAG
65 T-TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
* * *
5090 ATTTGCCATTACGGCTTAAATCTTTCCCTTCATGCTTC
1 ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTC
5128 GTGATACTGA
Statistics
Matches: 464, Mismatches: 58, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
97 2 0.00
98 390 0.84
99 67 0.14
100 5 0.01
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (98 bp):
ATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGAGGTATAAGGTTCGCCATTGCGACT
TAAACCTTTCCCTTTGTGTCTTCGTGGTACTGG
Found at i:14728 original size:86 final size:87
Alignment explanation
Indices: 14583--14757 Score: 316
Period size: 86 Copynumber: 2.0 Consensus size: 87
14573 CTAATATCAG
* *
14583 ATCCTTCAGACTCTTCCAAGTGATGCATTTATTATCCTCTTTTACTTTGATTCTATACGCCACTC
1 ATCCTTCAGACTCTTCCAAGTGATGCATTTATTATCCCCTTTTACTTTGATTCTATACGCCACCC
14648 ATTGTTCGCTCAT-CCAATTAT
66 ATTGTTCGCTCATCCCAATTAT
14669 ATCCTTCAGACTCTTCCAAGTGATGCATTTATTATCCCCTTTTACTTTGATTCTATACGCCACCC
1 ATCCTTCAGACTCTTCCAAGTGATGCATTTATTATCCCCTTTTACTTTGATTCTATACGCCACCC
*
14734 ATTGTTCGCTCATCCCAGTTAT
66 ATTGTTCGCTCATCCCAATTAT
14756 AT
1 AT
14758 TTATCAACCT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
86 76 0.89
87 9 0.11
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.41
Consensus pattern (87 bp):
ATCCTTCAGACTCTTCCAAGTGATGCATTTATTATCCCCTTTTACTTTGATTCTATACGCCACCC
ATTGTTCGCTCATCCCAATTAT
Found at i:16918 original size:29 final size:28
Alignment explanation
Indices: 16868--16928 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
16858 AAAATGTGAT
***
16868 TTTTGGATGCTCGAGGGTAAAACGATAA
1 TTTTGGATGCTCGAGAACAAAACGATAA
* *
16896 TTTTGGATGCTTCGAGAACAAAATGGTAA
1 TTTTGGATGC-TCGAGAACAAAACGATAA
16925 TTTT
1 TTTT
16929 CGAAAGGTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.31, C:0.10, G:0.25, T:0.34
Consensus pattern (28 bp):
TTTTGGATGCTCGAGAACAAAACGATAA
Found at i:17046 original size:29 final size:28
Alignment explanation
Indices: 16945--17105 Score: 93
Period size: 28 Copynumber: 5.5 Consensus size: 28
16935 GTTCGAGGTT
*
16945 TAAAATGG-AATTTTTAGACA-TCTGAGGG
1 TAAAATGGTAATTTTTAGA-ATTC-GGGGG
* *
16973 TAAAATGGTAATTTTTGGAAGGTTC-GGGA
1 TAAAATGGTAATTTTTAGAA--TTCGGGGG
*
17002 TCAAAAAAAGGT-ATTTTTAGACATTCGGGGG
1 T---AAAATGGTAATTTTTAGA-ATTCGGGGG
* *
17033 TAAAATGGTAA-TTTTGGAAGGTTC-GAGG
1 TAAAATGGTAATTTTTAGAA--TTCGGGGG
*
17061 TCAAAAATGG-AATTTTTAGATATTCGAGGG
1 T--AAAATGGTAATTTTTAGA-ATTCGGGGG
17091 TAAAATGGTAATTTT
1 TAAAATGGTAATTTT
17106 GGAAAGTTCG
Statistics
Matches: 103, Mismatches: 12, Indels: 35
0.69 0.08 0.23
Matches are distributed among these distances:
27 1 0.01
28 33 0.32
29 27 0.26
30 19 0.18
31 15 0.15
32 8 0.08
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.34
Consensus pattern (28 bp):
TAAAATGGTAATTTTTAGAATTCGGGGG
Found at i:17092 original size:58 final size:58
Alignment explanation
Indices: 16915--17127 Score: 279
Period size: 58 Copynumber: 3.6 Consensus size: 58
16905 CTTCGAGAAC
* **
16915 AAAATGGTAATTTTCGAAAGGTTCGAGGTTTAAAATGGAATTTTTAGACA-TCTGAGGGT
1 AAAATGGTAATTTT-GGAAGGTTCGAGGTCAAAAATGGAATTTTTAGACATTC-GAGGGT
* * *
16974 AAAATGGTAATTTTTGGAAGGTTCG-GGATCAAAAAAAGGTATTTTTAGACATTCGGGGGT
1 AAAATGGTAA-TTTTGGAAGGTTCGAGG-TC-AAAAATGGAATTTTTAGACATTCGAGGGT
*
17034 AAAATGGTAATTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTAGATATTCGAGGGT
1 AAAATGGTAATTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTAGACATTCGAGGGT
*
17092 AAAATGGTAATTTTGGAAAGTTCGAGGGT-AAAAATG
1 AAAATGGTAATTTTGGAAGGTTCGA-GGTCAAAAATG
17128 TATTTTTTGG
Statistics
Matches: 137, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
58 58 0.42
59 39 0.28
60 38 0.28
61 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAGGTTCGAGGTCAAAAATGGAATTTTTAGACATTCGAGGGT
Found at i:17115 original size:29 final size:30
Alignment explanation
Indices: 16915--17260 Score: 208
Period size: 30 Copynumber: 11.7 Consensus size: 30
16905 CTTCGAGAAC
* * *
16915 AAAATGGTAATTTTCGAAAGGTTCGAGGTTT
1 AAAATGGTAATTTTGGAAA-GTTCGAGGGTA
* *
16946 AAAATGG-AATTTTTAGACA--TCTGAGGGT-
1 AAAATGGTAA-TTTTGGAAAGTTC-GAGGGTA
* *
16974 AAAATGGTAATTTTTGGAAGGTTCG-GGATCAA
1 AAAATGGTAA-TTTTGGAAAGTTCGAGGGT--A
* * * * *
17006 AAAAAGGTATTTTTAGACA-TTCGGGGGT-
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTA
*
17034 AAAATGGTAATTTTGGAAGGTTCGA-GGTCA
1 AAAATGGTAATTTTGGAAAGTTCGAGGGT-A
* *
17064 AAAATGG-AATTTTTAGATA-TTCGAGGGT-
1 AAAATGGTAA-TTTTGGAAAGTTCGAGGGTA
17092 AAAATGGTAATTTTGGAAAGTTCGAGGGTA
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTA
* * *
17122 AAAAT-GTATTTTTTGGAAATTTTG-GGGTCA
1 AAAATGGTA-ATTTTGGAAAGTTCGAGGGT-A
* *
17152 AAAAT-GAAATTTTGGAAAGTT-TAGGGGTA
1 AAAATGGTAATTTTGGAAAGTTCGA-GGGTA
* **
17181 AAAAT-GTAATTTTAGGAAATTTTAAGGGTA
1 AAAATGGTAATTTT-GGAAAGTTCGAGGGTA
* * *
17211 AAAAT-GTATTTTTTGGAAAATTCGA-GGTC
1 AAAATGGTA-ATTTTGGAAAGTTCGAGGGTA
17240 AAAATGG-AATTTTGGAAAGTT
1 AAAATGGTAATTTTGGAAAGTT
17261 TAGGGATCTT
Statistics
Matches: 249, Mismatches: 41, Indels: 53
0.73 0.12 0.15
Matches are distributed among these distances:
28 51 0.20
29 79 0.32
30 81 0.33
31 30 0.12
32 8 0.03
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (30 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGTA
Found at i:17135 original size:58 final size:58
Alignment explanation
Indices: 16915--17193 Score: 257
Period size: 59 Copynumber: 4.7 Consensus size: 58
16905 CTTCGAGAAC
* * * *
16915 AAAATGGTAATTTTCGAAAGGTTCGAGGTTTAAAATGGAATTTTTAGACA-TCTGAGGGT
1 AAAATGGTAATTTTGGAAA-GTTCGAGGGTAAAAATGTAATTTTTAGACATTC-GAGGGT
* * * *
16974 AAAATGGTAATTTTTGGAAGGTTCG-GGATCAAAAAAAGGT-ATTTTTAGACATTCGGGGGT
1 AAAATGGTAA-TTTTGGAAAGTTCGAGGGT---AAAAATGTAATTTTTAGACATTCGAGGGT
* * *
17034 AAAATGGTAATTTTGGAAGGTTCGA-GGTCAAAAATGGAATTTTTAGATATTCGAGGGT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGT-AAAAATGTAATTTTTAGACATTCGAGGGT
* * * *
17092 AAAATGGTAATTTTGGAAAGTTCGAGGGTAAAAATGTATTTTTTGGAAATTTTG-GGGT
1 AAAATGGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTAGACA-TTCGAGGGT
* *
17150 CAAAAAT-GAAATTTTGGAAAGTT-TAGGGGTAAAAATGTAATTTT
1 --AAAATGGTAATTTTGGAAAGTTCGA-GGGTAAAAATGTAATTTT
17194 AGGAAATTTT
Statistics
Matches: 186, Mismatches: 22, Indels: 24
0.80 0.09 0.10
Matches are distributed among these distances:
57 6 0.03
58 66 0.35
59 69 0.37
60 38 0.20
61 7 0.04
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTAGACATTCGAGGGT
Found at i:17180 original size:59 final size:59
Alignment explanation
Indices: 17087--17262 Score: 173
Period size: 59 Copynumber: 3.0 Consensus size: 59
17077 TAGATATTCG
* * * *
17087 AGGGT-AAAATGGTAATTTTGGAAAGTTCGAGGGTAAAAATGTATTTTTTGGAAATTTT-
1 AGGGTAAAAAT-GAAATTTTGGAAAGTTAGAGGGTAAAAATGTAATTTTAGGAAATTTTA
*
17145 GGGGTCAAAAATGAAATTTTGGAAAGTTTAG-GGGTAAAAATGTAATTTTAGGAAATTTTA
1 AGGGT-AAAAATGAAATTTTGGAAAG-TTAGAGGGTAAAAATGTAATTTTAGGAAATTTTA
** * * * * *
17205 AGGGTAAAAATGTATTTTTTGGAAAATTCGA-GGTCAAAATGGAATTTT-GGAAAGTTTA
1 AGGGTAAAAATG-AAATTTTGGAAAGTTAGAGGGTAAAAATGTAATTTTAGGAAATTTTA
17263 GGGATCTTCA
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 13 0.13
59 64 0.65
60 22 0.22
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.35
Consensus pattern (59 bp):
AGGGTAAAAATGAAATTTTGGAAAGTTAGAGGGTAAAAATGTAATTTTAGGAAATTTTA
Found at i:18026 original size:18 final size:18
Alignment explanation
Indices: 18005--18046 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17995 TTTGTCTTTT
*
18005 AAAAACTTTTTG-TTTCGA
1 AAAAACTTTTAGATTT-GA
*
18023 AAAAAATTTTAGATTTGA
1 AAAAACTTTTAGATTTGA
18041 AAAAAC
1 AAAAAC
18047 AAAACAAGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.48, C:0.07, G:0.10, T:0.36
Consensus pattern (18 bp):
AAAAACTTTTAGATTTGA
Found at i:18302 original size:3 final size:3
Alignment explanation
Indices: 18289--18361 Score: 71
Period size: 3 Copynumber: 24.0 Consensus size: 3
18279 TTTCCCCTTT
* *
18289 TTA TT- TTA TTA TTA ATA TTA ATA TTA TTA TTA -TA TT- TATA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA -TTA
18333 TTA TTA TTA TTA TTA TTA TATA TTTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA -TTA TTA
18362 CCTTTCTTGA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
2 5 0.08
3 46 0.78
4 6 0.10
5 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:18327 original size:30 final size:30
Alignment explanation
Indices: 18289--18361 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
18279 TTTCCCCTTT
18289 TTAT-TTTATTATTAATATTAATATTATTA
1 TTATATTTATTATTAATATTAATATTATTA
* *
18318 TTATATTTA-TATTTATTATTATTATTATTA
1 TTATATTTATTA-TTAATATTAATATTATTA
*
18348 TTATATAT-TTATTA
1 TTATATTTATTATTA
18362 CCTTTCTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 9 0.24
30 29 0.76
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TTATATTTATTATTAATATTAATATTATTA
Found at i:19052 original size:17 final size:17
Alignment explanation
Indices: 19032--19086 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
19022 AAACCCTTTC
19032 AAATTTAAAATAAATTT
1 AAATTTAAAATAAATTT
*
19049 AAATTTAAAAATCAATTT
1 AAATTT-AAAATAAATTT
* *
19067 AAACTTAATATAAATTT
1 AAATTTAAAATAAATTT
19084 AAA
1 AAA
19087 ATCAATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 18 0.55
18 15 0.45
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
AAATTTAAAATAAATTT
Found at i:19065 original size:29 final size:28
Alignment explanation
Indices: 19033--19092 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
19023 AACCCTTTCA
*
19033 AATTTAAAATAAATTTAAATTTAAAAATC
1 AATTTAAAATAAATATAAATTT-AAAATC
* *
19062 AATTTAAACTTAATATAAATTTAAAATC
1 AATTTAAAATAAATATAAATTTAAAATC
19090 AAT
1 AAT
19093 AATTTGATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (28 bp):
AATTTAAAATAAATATAAATTTAAAATC
Found at i:30306 original size:19 final size:17
Alignment explanation
Indices: 30271--30303 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
30261 ACTTGAACAA
30271 AATTTTATTTTTTTATT
1 AATTTTATTTTTTTATT
30288 AATTTT-TTTTATTTAT
1 AATTTTATTTT-TTTAT
30304 ATTCGTCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
AATTTTATTTTTTTATT
Found at i:32347 original size:3 final size:3
Alignment explanation
Indices: 32339--32366 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
32329 GCAAATTTGA
32339 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
32367 TATTATCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:35747 original size:2 final size:2
Alignment explanation
Indices: 35737--35769 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
35727 ACACACGTGA
35737 AT AT GAT 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 AT AT
35770 GATTATTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41973 original size:2 final size:2
Alignment explanation
Indices: 41966--41996 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41956 TTGTTTCTTT
*
41966 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41997 TTGTGATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56488 original size:17 final size:18
Alignment explanation
Indices: 56450--56489 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
56440 TTATTTTTTG
*
56450 CTATTTTGGTTTTTTTTA
1 CTATTTTGGTTTTTTCTA
56468 CTATTTTGGTTTTTTCT-
1 CTATTTTGGTTTTTTCTA
56485 CTATT
1 CTATT
56490 GTTTTGGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.70
Consensus pattern (18 bp):
CTATTTTGGTTTTTTCTA
Found at i:56498 original size:20 final size:18
Alignment explanation
Indices: 56420--56482 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
56410 TTTGATGCTG
*
56420 TTTTTTTACTGTTTTGATTGT
1 TTTTTTTACTATTTTG---GT
*
56441 TATTTTTTGCTATTTTGGT
1 T-TTTTTTACTATTTTGGT
56460 TTTTTTTACTATTTTGGT
1 TTTTTTTACTATTTTGGT
56478 TTTTT
1 TTTTT
56483 CTCTATTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
18 21 0.55
19 3 0.08
21 1 0.03
22 13 0.34
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.73
Consensus pattern (18 bp):
TTTTTTTACTATTTTGGT
Found at i:56570 original size:12 final size:12
Alignment explanation
Indices: 56552--56596 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
56542 GTTGCTATTT
56552 TTGTTGTTTTTG
1 TTGTTGTTTTTG
*
56564 TTATTG-TTTTG
1 TTGTTGTTTTTG
*
56575 TTGTTATTTTTG
1 TTGTTGTTTTTG
*
56587 CTGTTGTTTT
1 TTGTTGTTTT
56597 GATTGTTTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.33
12 18 0.67
ACGTcount: A:0.04, C:0.02, G:0.20, T:0.73
Consensus pattern (12 bp):
TTGTTGTTTTTG
Found at i:56583 original size:32 final size:32
Alignment explanation
Indices: 56538--56617 Score: 99
Period size: 32 Copynumber: 2.5 Consensus size: 32
56528 ATGCTGATAT
* * *
56538 TTTTGTTGCTATTTTTGTTGTT-TTTGTTATTG
1 TTTTGTTGTTATTTTTGCTGTTGTTT-TGATTG
56570 TTTTGTTGTTATTTTTGCTGTTGTTTTGATTG
1 TTTTGTTGTTATTTTTGCTGTTGTTTTGATTG
* *
56602 TTTGGATGTTATTTTT
1 TTTTGTTGTTATTTTT
56618 ATGCGTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 39 0.93
33 3 0.07
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (32 bp):
TTTTGTTGTTATTTTTGCTGTTGTTTTGATTG
Found at i:56584 original size:23 final size:24
Alignment explanation
Indices: 56552--56603 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
56542 GTTGCTATTT
* *
56552 TTGTTGTTTTTGTTATTGTTTTG-
1 TTGTTATTTTTGCTATTGTTTTGA
*
56575 TTGTTATTTTTGCTGTTGTTTTGA
1 TTGTTATTTTTGCTATTGTTTTGA
56599 TTGTT
1 TTGTT
56604 TGGATGTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.06, C:0.02, G:0.21, T:0.71
Consensus pattern (24 bp):
TTGTTATTTTTGCTATTGTTTTGA
Found at i:56591 original size:20 final size:20
Alignment explanation
Indices: 56488--56579 Score: 60
Period size: 20 Copynumber: 4.2 Consensus size: 20
56478 TTTTTCTCTA
*
56488 TTGTTTTGGTTACTGTTTTG
1 TTGTTTTTGTTACTGTTTTG
*
56508 GTGATTTTT-TTACTGTTTTG
1 TTG-TTTTTGTTACTGTTTTG
* *
56528 ATGCTGATATTTTTGTTGCTATTTTTG
1 -T--TG---TTTTTGTTACT-GTTTTG
*
56555 TTGTTTTTGTTATTGTTTTG
1 TTGTTTTTGTTACTGTTTTG
56575 TTGTT
1 TTGTT
56580 ATTTTTGCTG
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
20 23 0.41
21 13 0.23
23 2 0.04
24 2 0.04
25 6 0.11
26 5 0.09
27 5 0.09
ACGTcount: A:0.09, C:0.04, G:0.21, T:0.66
Consensus pattern (20 bp):
TTGTTTTTGTTACTGTTTTG
Found at i:56603 original size:12 final size:11
Alignment explanation
Indices: 56552--56603 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
56542 GTTGCTATTT
56552 TTGTTGTTTTTG
1 TTGTTG-TTTTG
*
56564 TTATTGTTTTG
1 TTGTTGTTTTG
*
56575 TTGTTATTTTTG
1 TTGTT-GTTTTG
*
56587 CTGTTGTTTTG
1 TTGTTGTTTTG
56598 ATTGTT
1 -TTGTT
56604 TGGATGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
11 14 0.44
12 18 0.56
ACGTcount: A:0.06, C:0.02, G:0.21, T:0.71
Consensus pattern (11 bp):
TTGTTGTTTTG
Found at i:56788 original size:8 final size:9
Alignment explanation
Indices: 56730--56788 Score: 50
Period size: 9 Copynumber: 6.3 Consensus size: 9
56720 ATATAAATAA
56730 TTTTTAATG
1 TTTTTAATG
*
56739 TATTTTAATT
1 T-TTTTAATG
*
56749 TTTTTTAT-
1 TTTTTAATG
56757 TTTTTAATG
1 TTTTTAATG
56766 TTTGTTTTAATG
1 --T-TTTTAATG
56778 TTTTTAA-G
1 TTTTTAATG
56786 TTT
1 TTT
56789 ATTTGATATA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
8 11 0.26
9 13 0.31
10 9 0.21
11 1 0.02
12 8 0.19
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.71
Consensus pattern (9 bp):
TTTTTAATG
Found at i:62473 original size:129 final size:130
Alignment explanation
Indices: 62320--62578 Score: 511
Period size: 129 Copynumber: 2.0 Consensus size: 130
62310 ATGTTGAAGC
62320 AGTATACAATTGTTTAAGAAAAAATGTCTAAAGCCATGCGATTTGTCAAAACCTAAGTTCTGACA
1 AGTATACAATTGTTTAAGAAAAAATGTCTAAAGCCATGCGATTTGTCAAAACCTAAGTTCTGACA
62385 CAAGAAAATATTTCCTTAGATGTTGAAGCAGTATACAATTG-TTAGGAAAGATGCTTTTAGAAAG
66 CAAGAAAATATTTCCTTAGATGTTGAAGCAGTATACAATTGTTTAGGAAAGATGCTTTTAGAAAG
62449 AGTATACAATTGTTTAAGAAAAAATGTCTAAAGCCATGCGATTTGTCAAAACCTAAGTTCTGACA
1 AGTATACAATTGTTTAAGAAAAAATGTCTAAAGCCATGCGATTTGTCAAAACCTAAGTTCTGACA
62514 CAAGAAAATATTTCCTTAGATGTTGAAGCAGTATACAATTGTTTAGGAAAGATGCTTTTAGAAAG
66 CAAGAAAATATTTCCTTAGATGTTGAAGCAGTATACAATTGTTTAGGAAAGATGCTTTTAGAAAG
62579 TTAAAACATG
Statistics
Matches: 129, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
129 106 0.82
130 23 0.18
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (130 bp):
AGTATACAATTGTTTAAGAAAAAATGTCTAAAGCCATGCGATTTGTCAAAACCTAAGTTCTGACA
CAAGAAAATATTTCCTTAGATGTTGAAGCAGTATACAATTGTTTAGGAAAGATGCTTTTAGAAAG
Found at i:67652 original size:19 final size:20
Alignment explanation
Indices: 67620--67661 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
67610 TGGTTTTAAT
67620 ATTTTTATAATTTT-TTGTATA
1 ATTTTTAT-ATTTTGTTG-ATA
67641 ATTTTTAT-TTTTGTTGATA
1 ATTTTTATATTTTGTTGATA
67660 AT
1 AT
67662 GCATGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
21 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (20 bp):
ATTTTTATATTTTGTTGATA
Found at i:68632 original size:67 final size:67
Alignment explanation
Indices: 68561--68690 Score: 224
Period size: 67 Copynumber: 1.9 Consensus size: 67
68551 TCGAATCGAA
* *
68561 TGAAAAAATTTTGAGTTAATCGAATTCATAAATCTTATTTTATCATCCTAATTCAATTTGAAACG
1 TGAAAAAATTTTGAGTTAATCGAATTCACAAATCCTATTTTATCATCCTAATTCAATTTGAAACG
68626 AG
66 AG
* *
68628 TGAAAAAATTTTGAGTTAGTCGAATTCACGAATCCTATTTTATCATCCTAATTCAATTTGAAA
1 TGAAAAAATTTTGAGTTAATCGAATTCACAAATCCTATTTTATCATCCTAATTCAATTTGAAA
68691 TTTTTTCGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (67 bp):
TGAAAAAATTTTGAGTTAATCGAATTCACAAATCCTATTTTATCATCCTAATTCAATTTGAAACG
AG
Found at i:68929 original size:2 final size:2
Alignment explanation
Indices: 68924--68954 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
68914 ATTAATTAAT
68924 TA TA TA 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 TA TA TA T
68955 TAGAATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.