Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2650
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: 36847
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:115 original size:42 final size:43
Alignment explanation
Indices: 68--152 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 43
58 TAAAGATGCC
68 GGTGCCAATATGCTGATTCAAGGCCAGCGACATT-GACTTAGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGA
* *
110 GGTGCCAATATGCTTATTCAAGGCCAGCGATATTGGACTTAGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGA
153 AGAAGATGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 32 0.80
43 8 0.20
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (43 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGA
Found at i:237 original size:28 final size:29
Alignment explanation
Indices: 174--352 Score: 155
Period size: 28 Copynumber: 6.4 Consensus size: 29
164 CCAACTTGTA
**
174 TGGGCTTTTGAAAAGGTTG-CACCAACTTG
1 TGGGCTTTTG-AAAGGTTGCCACTGACTTG
* *
203 TGTGCTTTTG-AAGGTTGCCACTGATTTG
1 TGGGCTTTTGAAAGGTTGCCACTGACTTG
* * *
231 TGGGCTTTTGAAAAGAT-AC-CTGACTTG
1 TGGGCTTTTGAAAGGTTGCCACTGACTTG
*
258 TGGGC--TTGAAAGGGGTGCCACTGACTTG
1 TGGGCTTTTGAAA-GGTTGCCACTGACTTG
*
286 TGGGCTTTTG-AAGGTTGCCACTTAC-T-
1 TGGGCTTTTGAAAGGTTGCCACTGACTTG
* *
312 TGGGC-TTTGAAAAAGATGCCACTGACTTG
1 TGGGCTTTTG-AAAGGTTGCCACTGACTTG
341 TGGGC-TTTGAAA
1 TGGGCTTTTGAAA
353 AGGTGAGGAA
Statistics
Matches: 122, Mismatches: 17, Indels: 23
0.75 0.10 0.14
Matches are distributed among these distances:
25 10 0.08
26 7 0.06
27 33 0.27
28 45 0.37
29 24 0.20
30 3 0.02
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.33
Consensus pattern (29 bp):
TGGGCTTTTGAAAGGTTGCCACTGACTTG
Found at i:287 original size:83 final size:84
Alignment explanation
Indices: 198--352 Score: 219
Period size: 83 Copynumber: 1.9 Consensus size: 84
188 GGTTGCACCA
* *
198 ACTTGTGTGCTTTTGAAGGTTGCCACTGATTTGTGGGCTTTTG-AAAAGAT-AC-CTGACTTGTG
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGA-CT-TGGGC-TTTGAAAAAGATGACACTGACTTGTG
260 GGC-TTGAAAGGGGTGCCACTG
63 GGCTTTGAAAGGGGTGCCACTG
* *
281 ACTTGTGGGCTTTTGAAGGTTGCCACTTACTTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGC
1 ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGGGCTTTGAAAAAGATGACACTGACTTGTGGGC
346 TTTGAAA
66 TTTGAAA
353 AGGTGAGGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
80 4 0.06
81 12 0.19
82 2 0.03
83 40 0.62
84 6 0.09
ACGTcount: A:0.21, C:0.16, G:0.30, T:0.34
Consensus pattern (84 bp):
ACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGGGCTTTGAAAAAGATGACACTGACTTGTGGGC
TTTGAAAGGGGTGCCACTG
Found at i:7559 original size:20 final size:19
Alignment explanation
Indices: 7534--7640 Score: 91
Period size: 20 Copynumber: 5.7 Consensus size: 19
7524 TTTACCCAGA
7534 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
7554 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
7574 TGTATCGAT--A---T-AT
1 TGTATCGATACATTTTCAT
* *
7587 TGTATCGATACATTGCTAAT
1 TGTATCGATACATT-TTCAT
* *
7607 TGTATCGGTACATTTTACAA
1 TGTATCGATACATTTT-CAT
7627 TGTATCGATACATT
1 TGTATCGATACATT
7641 CAGGCATTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
13 11 0.15
14 1 0.01
15 1 0.01
18 1 0.01
19 2 0.03
20 55 0.76
21 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:7590 original size:13 final size:13
Alignment explanation
Indices: 7571--7601 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
7561 ATACATTGCT
7571 CATTGTATCGATA
1 CATTGTATCGATA
*
7584 TATTGTATCGATA
1 CATTGTATCGATA
7597 CATTG
1 CATTG
7602 CTAATTGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:7631 original size:53 final size:52
Alignment explanation
Indices: 7534--7636 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 52
7524 TTTACCCAGA
*
7534 TGTATCGATACATTTTGCATTGTATCGATACATTGCTCATTGTATCGATATAT
1 TGTATCGATACA-TTTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
* *
7587 TGTATCGATACA-TTGCTAATTGTATCGGTACATT-TTACAATGTATCGATA
1 TGTATCGATACATTTGC--ATTGTATCGATACATTGCT-CAATGTATCGATA
7637 CATTCAGGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
51 4 0.09
52 1 0.02
53 39 0.89
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.42
Consensus pattern (52 bp):
TGTATCGATACATTTGCATTGTATCGATACATTGCTCAATGTATCGATATAT
Found at i:10001 original size:51 final size:51
Alignment explanation
Indices: 9939--10133 Score: 171
Period size: 51 Copynumber: 3.8 Consensus size: 51
9929 TTTCATTTCG
* ** * *
9939 GGGATACTCCAATCCCGATTTCATTTCCAAAACATTAATTTTTCTTAATCA
1 GGGATACTCCAATCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCA
** * * *
9990 GGGATACTCCAATTTCGATTTTATTTCTAAAACACCCATTTTCCATAATCG
1 GGGATACTCCAATCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCA
* * * **
10041 GGGATACTCCAA-CTCTGATTTTATTTCCAAAACACCAACTTTT-TACAATTG
1 GGGATACTCCAATC-CCGATTTTATTTCCAAAACACCAA-TTTTCCATAATCA
* * * *
10092 GGGATACTCC-AGCCCCAGTTTTATTTTCAAAACATCAATTTT
1 GGGATACTCCAATCCCGA-TTTTATTTCCAAAACACCAATTTT
10134 TCATCGGGAA
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
50 7 0.06
51 107 0.91
52 4 0.03
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (51 bp):
GGGATACTCCAATCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCA
Found at i:10188 original size:76 final size:78
Alignment explanation
Indices: 10091--10261 Score: 251
Period size: 79 Copynumber: 2.2 Consensus size: 78
10081 TTTTACAATT
*
10091 GGGGATACTCCAGCCCCAGTTTTATTT-TCAAAACATCAATTTTT-C-ATCGGGAATACTCCAAC
1 GGGGATACTCCAACCCCAGTTTTATTTCT-AAAACATCAATTTTTACAATCGGGAATACTCCAAC
10153 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * *
10167 GGGGATAC-CCTAACCCCAGTTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCC-AACCCCAGTTTTATTTCTAAAACATCAATTTTT-ACAATCGGGAATACTCCAA
10231 CCCCGTTATTTTCGA
64 CCCCGTTATTTTCGA
10246 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
10262 TGTTGTTATC
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
75 2 0.02
76 36 0.42
77 1 0.01
78 1 0.01
79 43 0.51
80 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (78 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTACAATCGGGAATACTCCAACC
CCGTTATTTTCGA
Found at i:16599 original size:61 final size:61
Alignment explanation
Indices: 16444--17084 Score: 713
Period size: 61 Copynumber: 10.4 Consensus size: 61
16434 CCCTTTTAGC
* * * * *
16444 CCTTTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTCAAAGCCCACACGAGTTGATGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
16505 CCCTTTAGTCCTCAAAGAGTAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 -CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
16567 CCTTTAGTCCTCAAAGAGCATGACGCCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
16628 CCTTTAGTCCTCAAAGAGCATGACACTTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGC--CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* *
16691 CCTTTAGTCCTCAAAGAGCAGGACGCC-TTTTC-CTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
16750 CCTTTTAGTCTTTAAAAAGCAGGACACTTTTTTTCCCTTTT-GAAGCCCACACAAGTTGGTGGCA
1 CC-TTTAGTCCTCAAAGAGCAGGACGC-CTTTTT--CTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
16814 CTTTTCTAGTCCTCAGAA-AGTAGGACG-CGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 C-CTT-TAGTCCTCA-AAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
16876 TTTTCTAGTCCTCAAAGAGCATGACGCC-TTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTT-TAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
16937 -TTTTCCAGTCCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT--AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
16998 CCTTCCAATCCTCAAAGAGTAGGGCGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTT-TAGTCCTCAAAGAGCAGGACGC-CTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
*
17061 CCTCCTAGTCCTCAAAGAGCAGGA
1 CCT-TTAGTCCTCAAAGAGCAGGA
17085 TGCACTTTAT
Statistics
Matches: 498, Mismatches: 59, Indels: 43
0.83 0.10 0.07
Matches are distributed among these distances:
59 27 0.05
60 31 0.06
61 204 0.41
62 85 0.17
63 108 0.22
64 25 0.05
65 16 0.03
66 2 0.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (61 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:16704 original size:124 final size:122
Alignment explanation
Indices: 16444--17084 Score: 754
Period size: 123 Copynumber: 5.2 Consensus size: 122
16434 CCCTTTTAGC
* * *
16444 CCTTTAGTCCTCAAAAAGCAGGACGTCTTTTCCTTTTCAAAGCCCACACGAGTTGATGGCACCCT
1 CCTTTAGTCCTCAAAGAGCAGGACG-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA-CCT
* * * *
16509 TTAGTCCTCAAAGAGTAGGACGC-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCA
64 TTAGTCCTCAAAGAGCAGGACGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
16567 CCTTTAGTCCTCAAAGAGCATGACGCCTTTTTCTTTTCAAAGCCCATACGAGTTGGTGGCACCTT
1 CCTTTAGTCCTCAAAGAGCAGGACG-CTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTT
* *
16632 TAGTCCTCAAAGAGCATGACACTTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
65 TAGTCCTCAAAGAGCAGGACGC-TTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* *
16691 CCTTTAGTCCTCAAAGAGCAGGACGCCTTTTC-CTTCAAAGCCCACACGAGTTGGTGGCACCTTT
1 CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC-TT
* * * * * *
16755 TAGTCTTTAAAAAGCAGGACACTTTTTTTCCCTTTTGAAGCCCACACAAGTTGGTGGCA
65 TAGTCCTCAAAGAGCAGGACGCTTTTTTT-CTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * **
16814 CTTTTCTAGTCCTCAGAA-AGTAGGACGCGTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCATT
1 C-CTT-TAGTCCTCA-AAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACC
* * * *
16878 TTCTAGTCCTCAAAGAGCATGACGC--CTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
63 TT-TAGTCCTCAAAGAGCAGGACGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
16937 -TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCT
1 CCTTT--AGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCT
* * * *
17001 TCCAATCCTCAAAGAGTAGGGCGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
64 T-TAGTCCTCAAAGAGCAGGACGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
*
17061 CCTCCTAGTCCTCAAAGAGCAGGA
1 CCT-TTAGTCCTCAAAGAGCAGGA
17085 TGCACTTTAT
Statistics
Matches: 447, Mismatches: 55, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
120 1 0.00
121 5 0.01
122 123 0.28
123 136 0.30
124 111 0.25
125 26 0.06
126 45 0.10
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.29
Consensus pattern (122 bp):
CCTTTAGTCCTCAAAGAGCAGGACGCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCTTT
AGTCCTCAAAGAGCAGGACGCTTTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:17302 original size:46 final size:44
Alignment explanation
Indices: 17068--17574 Score: 442
Period size: 43 Copynumber: 11.5 Consensus size: 44
17058 GCACCTCCTA
* * ** **
17068 GTCCTCAAAGAGCAGGATGCACTTTATT-TTCCGCTTC-CCCCTT
1 GTCCTCAAAGAGCAGGACGCACTTCATTCTT-CTTTTCTCCTTTT
* *
17111 GTCCTCAAAGAGCAGGATGCACTTCATTTCCTCATTTTC-CCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTCA-TTCTTC-TTTTCTCCTTTT
* * * *
17156 GTCCTCAAAGAGTAGGACACACTTTATT-TTCCTTTTCTCC-TCT
1 GTCCTCAAAGAGCAGGACGCACTTCATTCTT-CTTTTCTCCTTTT
* *
17199 GTCCTCAAAGAGCAGGACGCACTTTATT-TTCCTTCTCTCC-TTT
1 GTCCTCAAAGAGCAGGACGCACTTCATTCTT-CTTTTCTCCTTTT
*
17242 GTCCTCAAAGAGCAGGACACA-TTCCATTCCCTTCTTTTCTCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTT-CATT--CTTCTTTTCTCCTTTT
*
17288 GTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTC-CTTTTT
1 GTCCTCAAAGAGCAGGACGCACTTCA-TT-CTTCTTTTCTCCTTTT
* *
17333 AGTCCTCAAAGAGCAGGACGCACTTTATT-TTCCTTTTCTCC-TCT
1 -GTCCTCAAAGAGCAGGACGCACTTCATTCTT-CTTTTCTCCTTTT
* * * *
17377 GTCCTCAAAGAGCAAGACGCATTTTATT-TTC-CTTCTCTCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTCATTCTTCTTTTCTC-CTTTT
17420 GTCCTCAAAGAGCAGGA--CACGTTCCATTCCCTTCTTTTCTCCTTTT
1 GTCCTCAAAGAGCAGGACGCAC-TT-CATT--CTTCTTTTCTCCTTTT
*
17466 GTCCTCAAAGAGCAGGACGCACTTCATTTCTTTCTTTTC-CCTTCTA
1 GTCCTCAAAGAGCAGGACGCACTTCA-TTC-TTCTTTTCTCCTT-TT
*
17512 GTTCTCAAAGAGCAGGACGCACATT-ATT-TTCCTTTT-TCC-TTT
1 GTCCTCAAAGAGCAGGACGCAC-TTCATTCTT-CTTTTCTCCTTTT
* *
17554 ATCCTCAAAGAGCATGACGCA
1 GTCCTCAAAGAGCAGGACGCA
17575 TTTTGTTTTC
Statistics
Matches: 395, Mismatches: 38, Indels: 63
0.80 0.08 0.13
Matches are distributed among these distances:
41 7 0.02
42 25 0.06
43 149 0.38
44 23 0.06
45 53 0.13
46 120 0.30
47 15 0.04
48 3 0.01
ACGTcount: A:0.20, C:0.29, G:0.13, T:0.37
Consensus pattern (44 bp):
GTCCTCAAAGAGCAGGACGCACTTCATTCTTCTTTTCTCCTTTT
Found at i:17373 original size:178 final size:178
Alignment explanation
Indices: 17109--17603 Score: 789
Period size: 178 Copynumber: 2.8 Consensus size: 178
17099 CGCTTCCCCC
* *
17109 TTGTCCTCAAAGAGCAGGATGCACTTCATTTCC-TCATTTTCCCTTTT-GTCCTCAAAGAGTAGG
1 TTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTC-TTTTCCCTTTTAGTCCTCAAAGAGCAGG
* * *
17172 ACACACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTCTCT
65 ACGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAAGACGCATTTTATTTTCCTTCTCT
17237 CCTTTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCTT
130 CCTTTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCTT
*
17286 TTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCCTTTTTAGTCCTCAAAGAGCAGGA
1 TTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCCCTTTTAGTCCTCAAAGAGCAGGA
17351 CGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAAGACGCATTTTATTTTCCTTCTCTC
66 CGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAAGACGCATTTTATTTTCCTTCTCTC
* *
17416 TTTTGTCCTCAAAGAGCAGGACACGTTCCATTCCCTTCTTTTCTCCTT
131 CTTTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCTT
* * *
17464 TTGTCCTCAAAGAGCAGGACGCACTTCATTTCTTTCTTTTCCCTTCTAGTTCTCAAAGAGCAGGA
1 TTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCCCTTTTAGTCCTCAAAGAGCAGGA
* * * * * * *
17529 CGCACATTATTTTCCTTTT-TCCTTTATCCTCAAAGAGCATGACGCATTTTGTTTTCCTTTTTTT
66 CGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAAGACGCATTTTATTTTCC-TTCTCT
17593 CCTTTGTCCTC
130 CCTTTGTCCTC
17604 GAGAAGCAGG
Statistics
Matches: 295, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
177 76 0.26
178 219 0.74
ACGTcount: A:0.19, C:0.29, G:0.13, T:0.39
Consensus pattern (178 bp):
TTGTCCTCAAAGAGCAGGACGCACTTCATTTCCTTCTTTTCCCTTTTAGTCCTCAAAGAGCAGGA
CGCACTTTATTTTCCTTTTCTCCTCTGTCCTCAAAGAGCAAGACGCATTTTATTTTCCTTCTCTC
CTTTGTCCTCAAAGAGCAGGACACATTCCATTCCCTTCTTTTCTCCTT
Found at i:18580 original size:13 final size:13
Alignment explanation
Indices: 18562--18588 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18552 CATTGCTCAC
18562 TGTATCGATACAT
1 TGTATCGATACAT
18575 TGTATCGATACAT
1 TGTATCGATACAT
18588 T
1 T
18589 ACTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18585 original size:53 final size:53
Alignment explanation
Indices: 18439--18628 Score: 142
Period size: 53 Copynumber: 3.6 Consensus size: 53
18429 GCCAAGGAAA
* * * * *
18439 TGTATCGATCCATTATTCAATGTAT-GATACATTGTATCGATACATCGA-TCTT
1 TGTATCGATACATTCTACAATGTATCGATACATTGTATCGATACAT-TACTCAT
* ** * * * * *
18491 TGTATCAATACA-TCTAGGAGGTTTAC-CTAGA-TGTATCGATACATT-TTGCAT
1 TGTATCGATACATTCTACAATGTAT-CGATACATTGTATCGATACATTACT-CAT
* * *
18542 TGTATTGTTACATTGCT-CACTGTATCGATACATTGTATCGATACATTACTCAT
1 TGTATCGATACATT-CTACAATGTATCGATACATTGTATCGATACATTACTCAT
*
18595 TGTATCGATACATTTTACAATGTATCGATACATT
1 TGTATCGATACATTCTACAATGTATCGATACATT
18629 CAGACATTTT
Statistics
Matches: 101, Mismatches: 27, Indels: 19
0.69 0.18 0.13
Matches are distributed among these distances:
50 1 0.01
51 31 0.31
52 21 0.21
53 47 0.47
54 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (53 bp):
TGTATCGATACATTCTACAATGTATCGATACATTGTATCGATACATTACTCAT
Found at i:18587 original size:33 final size:33
Alignment explanation
Indices: 18539--18608 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
18529 ATACATTTTG
* * *
18539 CATTGTATTGTTACATTGCTCACTGTATCGATA
1 CATTGTATCGATACATTACTCACTGTATCGATA
*
18572 CATTGTATCGATACATTACTCATTGTATCGATA
1 CATTGTATCGATACATTACTCACTGTATCGATA
18605 CATT
1 CATT
18609 TTACAATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (33 bp):
CATTGTATCGATACATTACTCACTGTATCGATA
Found at i:18595 original size:20 final size:20
Alignment explanation
Indices: 18570--18629 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
18560 ACTGTATCGA
18570 TACATTGTATCGATACATTAC
1 TACATTGTATCGATACATT-C
*
18591 T-CATTGTATCGATACATTT
1 TACATTGTATCGATACATTC
*
18610 TACAATGTATCGATACATTC
1 TACATTGTATCGATACATTC
18630 AGACATTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
TACATTGTATCGATACATTC
Found at i:20985 original size:51 final size:50
Alignment explanation
Indices: 20910--21138 Score: 252
Period size: 51 Copynumber: 4.6 Consensus size: 50
20900 AAATTTCTAG
* * *
20910 ATTTTTCAT-TTCGGGGATACTCCAATCCCGATTTCATTTCCAAAACATCA
1 ATTTTTCATAATCAGGGATACTCCAA-CCCGATTTTATTTCCAAAACATCA
* * * *
20960 ATTTTTCTTAATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACACCC
1 ATTTTTCATAATCAGGGATACTCCAAC-CCGATTTTATTTCCAAAACATCA
* *
21011 ATTTTCCATAATCAGGGATACTGCAACTCCGATTTTATTTCCAAAACA-CTA
1 ATTTTTCATAATCAGGGATACTCCAAC-CCGATTTTATTTCCAAAACATC-A
* * * *
21062 ACTTTTCACAATCGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCA
1 ATTTTTCATAATCAGGGATACTCCAACCCGA-TTTTATTTCCAAAACATCA
*
21113 ATTTTTC---ATCGGGGATACTCCAACCC
1 ATTTTTCATAATCAGGGATACTCCAACCC
21139 CGTTATTTTC
Statistics
Matches: 155, Mismatches: 19, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
48 19 0.12
50 13 0.08
51 122 0.79
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.34
Consensus pattern (50 bp):
ATTTTTCATAATCAGGGATACTCCAACCCGATTTTATTTCCAAAACATCA
Found at i:21167 original size:76 final size:76
Alignment explanation
Indices: 21075--21295 Score: 343
Period size: 76 Copynumber: 2.9 Consensus size: 76
21065 TTTCACAATC
* *
21075 GGGGATACTCCAACCCCAGTTTTATTTCCAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATTAATTTTTCATCGGGGATACTCCAACCCC
21140 GTTATTTTCGA
66 GTTATTTTCGA
* *
21151 GGGGATACCCCAACCCCAGTTTTATTTCTAAAACATTAATTTTTCATCGGGGATACTCCAACCCT
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATTAATTTTTCATCGGGGATACTCCAACCCC
21216 GTTATTTTCGA
66 GTTATTTTCGA
* * *
21227 GGGGATACTCCAACCCCGGTTTTATTTCTAAAATATTAATTTCTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATTAATTT-T--TCATCGGGGATACTCCAA-
21292 CCCC
62 CCCC
21296 ATTTTATTTC
Statistics
Matches: 132, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
76 111 0.84
77 1 0.01
79 17 0.13
80 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (76 bp):
GGGGATACTCCAACCCCAGTTTTATTTCTAAAACATTAATTTTTCATCGGGGATACTCCAACCCC
GTTATTTTCGA
Found at i:21303 original size:51 final size:51
Alignment explanation
Indices: 21227--21346 Score: 163
Period size: 51 Copynumber: 2.4 Consensus size: 51
21217 TTATTTTCGA
* * *
21227 GGGGATACTCCAACCCCGGTTTTATTTCTAAAAT-ATTAATTTCTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTCT-AAATCATCAATTTCTCACAATC
* *
21278 GGGGATACTCCAATCCCC-ATTTTATTTCTAAATCATCGATTTTTCACAATC
1 GGGGATACTCCAA-CCCCGATTTTATTTCTAAATCATCAATTTCTCACAATC
21329 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
21347 TTATTTTCGA
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
50 8 0.13
51 49 0.80
52 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAATCATCAATTTCTCACAATC
Found at i:21355 original size:130 final size:127
Alignment explanation
Indices: 21151--21395 Score: 350
Period size: 130 Copynumber: 1.9 Consensus size: 127
21141 TTATTTTCGA
* *
21151 GGGGATACCCCAACCCCAGTTTTATTTCTAAAACATTAATTTTTCATCGGGGATACTCCAACCCT
1 GGGGATACCCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
* *
21216 GTTATTTTCGAGGGGATACTCCAACCCCGGTT-TTATTTCTAAAATATTAATTTCTCATAATC
66 GTTATTTTCGAGGGGATACTCCAA-CCCGGTTGTTATCTCCAAAATATTAATTTCTCATAATC
* * *
21278 GGGGATACTCCAATCCCCA-TTTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACCCCAA-CCCCAGTTTTATTTCTAAAACATCAATTTTT--C-ATCGGGGATACTCCAA
* *
21342 CCCCGTTATTTTCGAGGGGATACTCTAACCCTGTTGTTATCTCCAAAATATTAA
62 CCCCGTTATTTTCGAGGGGATACTCCAACCCGGTTGTTATCTCCAAAATATTAA
21396 ATTTTTCGTC
Statistics
Matches: 104, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
127 34 0.33
128 5 0.05
129 7 0.07
130 58 0.56
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (127 bp):
GGGGATACCCCAACCCCAGTTTTATTTCTAAAACATCAATTTTTCATCGGGGATACTCCAACCCC
GTTATTTTCGAGGGGATACTCCAACCCGGTTGTTATCTCCAAAATATTAATTTCTCATAATC
Found at i:26851 original size:52 final size:52
Alignment explanation
Indices: 26771--26890 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
26761 AAAAGTTACT
* * *
26771 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGCC
*
26823 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGACAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGCC
26875 TGCATGTATCGATACA
1 TGCATGTATCGATACA
26891 AAGATCGGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGACAAATTTGCC
Found at i:26903 original size:52 final size:52
Alignment explanation
Indices: 26771--26910 Score: 176
Period size: 52 Copynumber: 2.7 Consensus size: 52
26761 AAAAGTTACT
* * *
26771 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGACAAATTTGCC
*** *
26823 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGACAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGACAAATTTGCC
*
26875 TGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
26911 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGACAAATTTGCC
Found at i:27004 original size:13 final size:13
Alignment explanation
Indices: 26986--27010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
26976 CAAAAAAATA
26986 TGTATCGATACAT
1 TGTATCGATACAT
26999 TGTATCGATACA
1 TGTATCGATACA
27011 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:27021 original size:33 final size:33
Alignment explanation
Indices: 26964--27030 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
26954 AGTAGCTTAA
*
26964 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
* ***
26997 ATTGTATCGATACAACATTTTATGTATCAATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
27030 A
1 A
27031 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCAATAC
Found at i:27872 original size:67 final size:68
Alignment explanation
Indices: 27746--27872 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 68
27736 ATTGGGTTTT
* * * *
27746 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGTAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
27811 AGA
66 AGA
* * * *
27814 AAAG-TGATAAAGATGCTAATATGTTGATGCACGGCCAATGATATTAGG-CTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATT-GGACTTAAAGATGA
27873 GAAAAAGGAT
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
67 44 0.88
68 6 0.12
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.25
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATGCAAGGCCAATAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:28094 original size:49 final size:49
Alignment explanation
Indices: 27885--28601 Score: 913
Period size: 49 Copynumber: 14.7 Consensus size: 49
27875 AAAAGGATGT
** *
27885 CAATGTGCTGATTCAAGGCCAGCTCCATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
27937 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
** *
27980 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
28028 CAATGTGCTGATTCAAGGCTAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
28077 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * * *
28126 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28175 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28224 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28273 CAATGTGCTAAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
* * *
28325 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28374 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
28426 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28469 CAATGTGCTGATTCAAGGCTAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
28517 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* * *
28566 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
28602 GAAGGGTTGC
Statistics
Matches: 576, Mismatches: 69, Indels: 43
0.84 0.10 0.06
Matches are distributed among these distances:
43 77 0.13
48 91 0.16
49 294 0.51
50 2 0.00
51 1 0.00
52 111 0.19
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:28645 original size:33 final size:32
Alignment explanation
Indices: 28594--28704 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 32
28584 CCAGCTATAT
*
28594 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
*
28624 TGGGCTTTAGAGAATGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAA-GGTTGCCACCGACTTGTG
28657 TGGGCTTTAGAGGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-GAAGGTTGCCACCGACTTGTG
28690 TGGGCTTTAGA-AAGG
1 TGGGCTTTAGAGAAGG
28705 GTGAAAGATG
Statistics
Matches: 74, Mismatches: 3, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
30 5 0.07
31 9 0.12
32 1 0.01
33 56 0.76
34 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.35, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAAGGTTGCCACCGACTTGTG
Found at i:28812 original size:34 final size:34
Alignment explanation
Indices: 28708--28936 Score: 319
Period size: 33 Copynumber: 6.9 Consensus size: 34
28698 AGAAAGGGTG
* * * *
28708 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* *
28741 CAAG-GTGCCACGGAGTTGTGGGCTT-TAA--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
28771 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
28805 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
28839 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
28872 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * * *
28905 AAAGAGTGCCACGTAGTCGTGGACTTAAAAGG
1 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
28937 GTGCCACGGA
Statistics
Matches: 181, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
30 5 0.03
31 21 0.12
32 4 0.02
33 83 0.46
34 68 0.38
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
Found at i:28942 original size:27 final size:27
Alignment explanation
Indices: 28904--28957 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
28894 GCTTAGAAGG
*
28904 AAAAGAGTGCCACGTAGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTCGTGGACTT
*
28931 AAAAGGGTGCCACGGAGTCGTGGACTT
1 AAAAGAGTGCCACGGAGTCGTGGACTT
28958 TGAAAAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.20
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTCGTGGACTT
Done.