Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold825
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: 20798
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Found at i:159 original size:24 final size:26
Alignment explanation
Indices: 132--185 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
122 TCAAAATTTT
132 ATTCAT-C-GGGGACACTCCAACCCC
1 ATTCATCCAGGGGACACTCCAACCCC
*
156 ATTCTTCCGAGGGGACACTCCAACCCC
1 ATTCATCC-AGGGGACACTCCAACCCC
183 ATT
1 ATT
186 TTCAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 1 0.04
27 20 0.77
ACGTcount: A:0.24, C:0.39, G:0.17, T:0.20
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCCC
Found at i:4933 original size:11 final size:11
Alignment explanation
Indices: 4917--4949 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4907 AGTCAAAAGT
4917 AAAAACAAAAA
1 AAAAACAAAAA
4928 AAAAAC-AAAA
1 AAAAACAAAAA
*
4938 CAAAACAAAAA
1 AAAAACAAAAA
4949 A
1 A
4950 CACATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAA
Found at i:4937 original size:16 final size:17
Alignment explanation
Indices: 4918--4951 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
4908 GTCAAAAGTA
4918 AAAACAAAA-AAAAAAC
1 AAAACAAAACAAAAAAC
4934 AAAACAAAACAAAAAAC
1 AAAACAAAACAAAAAAC
4951 A
1 A
4952 CATAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAACAAAACAAAAAAC
Found at i:6245 original size:31 final size:30
Alignment explanation
Indices: 6200--6389 Score: 211
Period size: 32 Copynumber: 6.1 Consensus size: 30
6190 TTCAAATACC
* *
6200 TTCTTAAAGTCCACGACTCAGTGGCAATCTC
1 TTCTCAAAGTCCACGACTCAGTGGC-ATCTT
* *
6231 TTCTCAAAGCCCACGACTTAGTGGCAT-TT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTT
6260 TGTCTCAAAGTCCACGACTCAGTGGCATCATT
1 T-TCTCAAAGTCCACGACTCAGTGGCATC-TT
6292 TTCTTCAAAGTCCACGACTCAGTGGCATCTTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATC-TT
*
6324 TGTCTCAAAGTCCACGACTTAGTGGCATCCTT
1 T-TCTCAAAGTCCACGACTCAGTGGCAT-CTT
* * * *
6356 TTCTGCAAAGCCCACAACTCCGTGACACTCTT
1 TTCT-CAAAGTCCACGACTCAGTGGCA-TCTT
6388 TT
1 TT
6390 TCCTTTTAAG
Statistics
Matches: 138, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
29 2 0.01
30 26 0.19
31 27 0.20
32 79 0.57
33 4 0.03
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (30 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTT
Found at i:6336 original size:64 final size:63
Alignment explanation
Indices: 6205--6389 Score: 241
Period size: 64 Copynumber: 2.9 Consensus size: 63
6195 ATACCTTCTT
* *
6205 AAAGTCCACGACTCAGTGGCAATCTCTTC-TCAAAGCCCACGACTTAGTGGCA--TTTTGTCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTTTTGTCTC
*
6266 AAAGTCCACGACTCAGTGGCATCATTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATC-TTTTCTTCAAAGCCCACGACTCAGTGGCATCTTTTGTCTC
* * * * *
6330 AAAGTCCACGACTTAGTGGCATCCTTTTCTGCAAAGCCCACAACTCCGTGACACTCTTTT
1 AAAGTCCACGACTCAGTGGCAT-CTTTTCTTCAAAGCCCACGACTCAGTGGCA-TCTTTT
6390 TCCTTTTAAG
Statistics
Matches: 109, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
60 3 0.03
61 24 0.22
62 21 0.19
64 54 0.50
65 7 0.06
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (63 bp):
AAAGTCCACGACTCAGTGGCATCTTTTCTTCAAAGCCCACGACTCAGTGGCATCTTTTGTCTC
Found at i:6407 original size:34 final size:33
Alignment explanation
Indices: 6363--6989 Score: 599
Period size: 34 Copynumber: 19.8 Consensus size: 33
6353 CTTTTCTGCA
*
6363 AAGCCCACAACTCCGTGACACTCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * *
6397 AAGTCTACAACTCTGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6424 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * *
6458 AAGTCCATAACTCCGTGGCACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6491 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
*
6526 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
6553 AAGCCTACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
*
6587 AAGTCCACAACTCCGTGGCACCTTTTT-CTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6619 AAGCCCACAACTCCATGGCACTCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* *
6653 AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6686 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 -AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* *
6721 AAGTCCACAACTCTGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
6748 AAGCCCACAACTCCTTGGCACTTTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* * *
6782 AAGTCTATAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6809 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
* *
6843 AAGTCCACAACTCCGTGGCA-C-----CCGTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
*
6870 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTT
*
6904 AAGTCCACAACTCCGTGGCA-C-----CCTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
6931 AAGCCCACAACTCCGTGACACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
6964 AAAGCCCACAACTCCGTGGCACCTTT
1 -AAGCCCACAACTCCGTGGCACCTTT
6990 CCCTTCTCCA
Statistics
Matches: 483, Mismatches: 62, Indels: 96
0.75 0.10 0.15
Matches are distributed among these distances:
27 136 0.28
28 1 0.00
29 4 0.01
32 28 0.06
33 38 0.08
34 256 0.53
35 20 0.04
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:6440 original size:61 final size:61
Alignment explanation
Indices: 6363--6986 Score: 899
Period size: 61 Copynumber: 9.9 Consensus size: 61
6353 CTTTTCTGCA
* * * *
6363 AAGCCCACAACTCCGTGACACTCTTTTTCCTTTTAAGTCTACAACTCTGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
*
6424 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCATAACTCCGTGGCACCTTTTTCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----C-TT
6489 TT
60 TT
6491 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
*
6553 AAGCCTACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----CTTT
6618 T
61 T
* *
6619 AAGCCCACAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----C-TT
6684 TT
60 TT
*
6686 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
1 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
6748 AAGCCCACAACTCCTTGGCACTTTTTTTCCTTCTAAGTCTATAACTCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
*
6809 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCGTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
6870 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
* * * *
6931 AAGCCCACAACTCCGTGACAC-CTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACC
1 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGTCCACAACTCCGTGGCACC
6987 TTTCCCTTCT
Statistics
Matches: 520, Mismatches: 28, Indels: 30
0.90 0.05 0.05
Matches are distributed among these distances:
60 10 0.02
61 319 0.61
62 8 0.02
63 2 0.00
66 65 0.12
67 8 0.02
68 108 0.21
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (61 bp):
AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:6510 original size:95 final size:87
Alignment explanation
Indices: 6452--6986 Score: 382
Period size: 95 Copynumber: 5.7 Consensus size: 87
6442 CACTCTTTTT
* * *
6452 CCTTCTAAGTCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCA--C--
*
6517 TTTCCTTCTAAGTCCACAACTCCGTGGCAC
61 ---CCTTCTAAGCCCACAACTCCGTGGCAC
* *
6547 CCTTTTAAG-CCTACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTT
1 CCTTTTAAGTCC-ACAACTCCGTGGCAC-CTTTTTCCTTTTAAGCCCACAACTCCGTGGCACC--
* *
6611 TTTCTTTTAAGCCCACAACTCCATGGCACTC
62 ---CTTCTAAGCCCACAACTCCGTGGCA--C
*
6642 TTTTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCA
1 -----CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCA
* *
6707 CTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCAC
60 --C-----CCTTCTAAGCCCACAACTCCGTGGCAC
* * * * * * *
6742 CCTTTTAAGCCCACAACTCCTTGGCACTTTTTTTCCTTCTAAGTCTATAACTCCGTGGCACCCTT
1 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCCTT
*
6807 TTAAGCCCACAACTCCGTGGCACTC
65 CTAAGCCCACAACTCCGTGGCA--C
* *
6832 TTTTTCCTTCTAAGTCCACAACTCCGTGGCA-C-----CCGTTTAAGCCCACAACTCCGTGGCAC
1 -----CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCA-
*
6891 TCTTTTTCCTTCTAAGTCCACAACTCCGTGGCAC
60 -C-----CCTTCTAAGCCCACAACTCCGTGGCAC
* * *
6925 CCTTTTAAGCCCACAACTCCGTGACACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACC
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCACC
6987 TTTCCCTTCT
Statistics
Matches: 353, Mismatches: 42, Indels: 97
0.72 0.09 0.20
Matches are distributed among these distances:
88 69 0.20
89 1 0.00
90 2 0.01
93 26 0.07
94 6 0.02
95 151 0.43
96 19 0.05
99 10 0.03
100 44 0.12
101 2 0.01
102 22 0.06
107 1 0.00
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (87 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCCTTC
TAAGCCCACAACTCCGTGGCAC
Found at i:7075 original size:33 final size:33
Alignment explanation
Indices: 6991--7134 Score: 181
Period size: 32 Copynumber: 4.5 Consensus size: 33
6981 GGCACCTTTC
*
6991 CCTTC-TCCAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAA
7023 CC--CTTCTCAAAGCCCACACAAGTCGGTGGCAA
1 CCTTCTTCT-AAAGCCCACACAAGTCGGTGGCAA
* *
7055 CCTTCTTCTAAAGCCTACACAAGTTGGTGGCAA
1 CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAA
* *
7088 TCC--CCTCTAAAGCCCACACAAGTCGGTGGAAA
1 -CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAA
*
7120 CCTTCTTCAAAAGCC
1 CCTTCTTCTAAAGCC
7135 TGCATAAGTT
Statistics
Matches: 96, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
30 1 0.01
31 4 0.04
32 53 0.55
33 31 0.32
34 7 0.07
ACGTcount: A:0.28, C:0.35, G:0.17, T:0.19
Consensus pattern (33 bp):
CCTTCTTCTAAAGCCCACACAAGTCGGTGGCAA
Found at i:7084 original size:65 final size:65
Alignment explanation
Indices: 6991--7151 Score: 227
Period size: 65 Copynumber: 2.5 Consensus size: 65
6981 GGCACCTTTC
* * * * *
6991 CCTTC-TCCAAAGCCCACACAAGTCGGTGGCAA-CCCTTCTCAAAGCCCACACAAGTCGGTGGCA
1 CCTTCTTCAAAAGCCTACACAAGTTGGTGGCAATCCCCTCT-AAAGCCCACACAAGTCGGTGGAA
7054 A
65 A
*
7055 CCTTCTTCTAAAGCCTACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGGAAA
1 CCTTCTTCAAAAGCCTACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGGAAA
* *
7120 CCTTCTTCAAAAGCCTGCATAAGTTGGTGGCA
1 CCTTCTTCAAAAGCCTACACAAGTTGGTGGCA
7152 TCTTCTTTTA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
64 5 0.06
65 76 0.87
66 6 0.07
ACGTcount: A:0.28, C:0.32, G:0.19, T:0.20
Consensus pattern (65 bp):
CCTTCTTCAAAAGCCTACACAAGTTGGTGGCAATCCCCTCTAAAGCCCACACAAGTCGGTGGAAA
Found at i:7226 original size:49 final size:48
Alignment explanation
Indices: 7158--7582 Score: 366
Period size: 49 Copynumber: 8.8 Consensus size: 48
7148 GGCATCTTCT
* * *
7158 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTATC
* *
7207 TTTAAGTCCAATGTAGCTGGCCTTGAATTAGCACATTGGCAC-----C
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTATC
* * *
7250 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTATCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACT-TTATC
* * *
7299 TTTAAGTCCAATGTAGTTGGCCTTGAATCAGCACATT-G-AC---ACC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTATC
** * * *
7342 TCCAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTATC
* *
7391 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATT
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTATC
* * * * *
7440 TTTAAGTCCAATATCACTAGCCTTGAATTAGCATATTGGCACCTTTATCATC
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C-TT-T-ATC
** * *
7492 TTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATC
1 TTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--CTT-T-ATC
* * * ** *
7545 TTCAAGTCTAATGTTGCTAACCGTGAATCAGCACATTG
1 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTG
7583 ACATCCTTTT
Statistics
Matches: 306, Mismatches: 53, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
43 73 0.24
44 1 0.00
45 1 0.00
46 1 0.00
47 2 0.01
48 2 0.01
49 152 0.50
50 2 0.01
52 33 0.11
53 38 0.12
54 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.34
Consensus pattern (48 bp):
TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACTTTATC
Found at i:7320 original size:92 final size:92
Alignment explanation
Indices: 7158--7533 Score: 484
Period size: 92 Copynumber: 4.0 Consensus size: 92
7148 GGCATCTTCT
* * *
7158 TTTAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
7223 CTGGCCTTGAATTAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
7250 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTATCATCTTTAAGTCCAATGTA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TCATCTTTAAGTCCAATGTA
* *
7314 GTTGGCCTTGAATCAGCACATTGACACC
65 GCTGGCCTTGAATCAGCACATTGGCACC
** * * *
7342 TCCAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
7407 CTGGCCTTGAATCAGCACATTGGCACCTTC
66 CTGGCCTTGAATCAGCACATTGGCA-C--C
* * * **
7437 ATTTTTAAGTCCAATATCACTAGCCTTGAATTAGCATATTGGCACCTTTATCATCTTTAAAACCC
1 ---TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTT-AAGTCC
* *
7502 AATGTTGTTGGCCTTGAATCAGCACATTGGCA
59 AATGTAGCTGGCCTTGAATCAGCACATTGGCA
7534 TTCTTCTCAT
Statistics
Matches: 249, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
91 2 0.01
92 164 0.66
93 3 0.01
95 1 0.00
98 37 0.15
100 1 0.00
101 7 0.03
102 34 0.14
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:7624 original size:55 final size:52
Alignment explanation
Indices: 7487--7629 Score: 142
Period size: 55 Copynumber: 2.7 Consensus size: 52
7477 GGCACCTTTA
* *
7487 TCATCTTTAAAACCCAATGTTGTTGGCCTTGAATCAGCACATTGGCATTCTTC
1 TCATCTTT-AAACCCAATGTTGTTGGCCGTGAATCAGCACATTGACATTCTTC
* ** * * ** *
7540 TCATCTTCAAGTCTAATGTTGCTAACCGTGAATCAGCACATTGACATCCTTTTTC
1 TCATCTTTAAACCCAATGTTGTTGGCCGTGAATCAGCACATTGACA---TTCTTC
* *
7595 TCATCTTTAAACCCAATATCGTTGGCCGTGAATCA
1 TCATCTTTAAACCCAATGTTGTTGGCCGTGAATCA
7630 ACGTATTGGT
Statistics
Matches: 68, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
52 30 0.44
53 7 0.10
55 31 0.46
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (52 bp):
TCATCTTTAAACCCAATGTTGTTGGCCGTGAATCAGCACATTGACATTCTTC
Found at i:8286 original size:13 final size:13
Alignment explanation
Indices: 8268--8388 Score: 71
Period size: 13 Copynumber: 7.9 Consensus size: 13
8258 TTCAACTATT
8268 TGTATCGATACAA
1 TGTATCGATACAA
8281 TGTATCGATACATAA
1 TGTATCGATAC--AA
8296 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
8313 TGTATCGATACATAA
1 TGTATCGATAC--AA
8328 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
8345 GGTATCGATACATAA
1 TGTATCGATAC--AA
8360 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
8377 TGTATCGATACA
1 TGTATCGATACA
8389 TAAGTTTTGT
Statistics
Matches: 88, Mismatches: 2, Indels: 36
0.70 0.02 0.29
Matches are distributed among these distances:
13 44 0.50
15 6 0.07
17 6 0.07
19 32 0.36
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:8305 original size:19 final size:19
Alignment explanation
Indices: 8281--8407 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
8271 ATCGATACAA
8281 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
8300 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
8313 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
8332 TGTATCGATAC--AA--G-
1 TGTATCGATACATAAGTGT
8346 -GTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
8364 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
8377 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
8396 TGTATCGATACA
1 TGTATCGATACA
8408 ATGTATCGCT
Statistics
Matches: 90, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 32 0.36
15 7 0.08
17 7 0.08
19 44 0.49
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:8308 original size:32 final size:32
Alignment explanation
Indices: 8267--8415 Score: 280
Period size: 32 Copynumber: 4.7 Consensus size: 32
8257 TTTCAACTAT
8267 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
8299 TTGTATCGATACAATGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
8331 TTGTATCGATACAAGGTATCGATACATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
8363 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
8395 TTGTATCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
8416 CTGCTGTCGT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 114 1.00
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:10985 original size:52 final size:52
Alignment explanation
Indices: 10837--10965 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
10827 CGAAATATGA
*
10837 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATATATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
* * *
10889 AAATTTGCCTGCATGTATCGATATATTTTATAATGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
10941 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
10966 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:11078 original size:13 final size:13
Alignment explanation
Indices: 11060--11084 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11050 ACAAAACTTA
11060 TGTATCGATACAT
1 TGTATCGATACAT
11073 TGTATCGATACA
1 TGTATCGATACA
11085 ACACTTTATA
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:11080 original size:32 final size:33
Alignment explanation
Indices: 11039--11104 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
11029 AGTAGCTTAA
*
11039 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATATATCGATAC
*
11071 ATTGTATCGATACAACACTTTATATATCGATAC
1 ATTGTATCGATACAAAACTTTATATATCGATAC
11104 A
1 A
11105 AATCGTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATATATCGATAC
Found at i:11919 original size:48 final size:48
Alignment explanation
Indices: 11841--12009 Score: 248
Period size: 48 Copynumber: 3.5 Consensus size: 48
11831 TTGAAAGTGA
* *
11841 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTGC
* * * * *
11889 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAGGTAC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTGC
* * *
11937 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTGC
11985 CAATATGCTGATTCAAGGCCAGCGA
1 CAATATGCTGATTCAAGGCCAGCGA
12010 TATCAGTCTT
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 105 1.00
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAGGTGC
Found at i:12099 original size:28 final size:28
Alignment explanation
Indices: 12042--12413 Score: 185
Period size: 28 Copynumber: 12.6 Consensus size: 28
12032 CACCAACTTG
*
12042 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* *
12071 TGTGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
12099 TGTGGGCTTTTAAAGATTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
12127 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
12155 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
* * * * * *
12185 CGTGGGC-TTAAAAGGAAAAAAAGTGCTACGGAGT
1 TGTGGGCTTTTAAAGG-------TTGCCACTGACT
* ** * * *
12219 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-TTAAAG-----G-TTGCCACTGACT
* * * *
12254 TGTGGACTTTGGAAAAGATGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
** * *
12283 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT--TTAAAGGTTGCCACTGACT
*
12313 TGTGGGCTTTGAAA-GTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * * *
12340 TGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
* * *
12369 TGTGGGCTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
*
12398 TGTGGGCTTTTGAAGG
1 TGTGGGCTTTTAAAGG
12414 GTGAGGAATG
Statistics
Matches: 276, Mismatches: 44, Indels: 47
0.75 0.12 0.13
Matches are distributed among these distances:
27 28 0.10
28 81 0.29
29 80 0.29
30 45 0.16
34 13 0.05
35 23 0.08
36 5 0.02
41 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:12228 original size:34 final size:35
Alignment explanation
Indices: 12190--12257 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
12180 TAACTCGTGG
* *
12190 GCTTA-AAAGGAAAAAAAGTGCTACGGAGTTGTGA
1 GCTTACAAAAGAAAAAAAGTGCCACGGAGTTGTGA
*
12224 GCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTG
1 GCTTACAAAAGAAAAAAAGTGCCACGGAGTTGTG
12258 GACTTTGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.19
Consensus pattern (35 bp):
GCTTACAAAAGAAAAAAAGTGCCACGGAGTTGTGA
Found at i:12285 original size:29 final size:29
Alignment explanation
Indices: 12236--12407 Score: 222
Period size: 29 Copynumber: 5.9 Consensus size: 29
12226 TTACAAAAGA
* * *
12236 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTTGG
*
12266 AAAAGATGCCACTGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
* *
12295 AAAAGGGTGCCACTGATTTGTGGGCTTT-G
1 AAAA-GATGCCACTGACTTGTGGGCTTTGG
* * *
12324 -AAAGTTGCCACTGACTTGTGGACTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
*
12352 AAAAGATGCCACTGACTTGTGGGCTTTGA
1 AAAAGATGCCACTGACTTGTGGGCTTTGG
12381 AAAAGATGCCACTGACTTGTGGGCTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
12408 TGAAGGGTGA
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
27 20 0.16
28 3 0.02
29 77 0.61
30 26 0.21
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (29 bp):
AAAAGATGCCACTGACTTGTGGGCTTTGG
Found at i:12411 original size:86 final size:86
Alignment explanation
Indices: 12243--12407 Score: 260
Period size: 86 Copynumber: 1.9 Consensus size: 86
12233 AGAAAAAGAG
* * * *
12243 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTCGGAAAAAGATGCCAC
*
12308 TGATTTGTGGGCTTTGAAAGT
66 TGACTTGTGGGCTTTGAAAGT
* *
12329 TGCCACTGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTT-TGAAAAAGATGCCAC
1 TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTCGGAAAAAGATGCCAC
12393 TGACTTGTGGGCTTT
66 TGACTTGTGGGCTTT
12408 TGAAGGGTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 26 0.36
86 46 0.64
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (86 bp):
TGCCACGGACTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTCGGAAAAAGATGCCAC
TGACTTGTGGGCTTTGAAAGT
Found at i:13857 original size:5 final size:5
Alignment explanation
Indices: 13844--13880 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
13834 CATCCGGACC
*
13844 TTTTT TTTTG TTTT- TTTTG TTTTG TTTTG TTTT- TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
13881 TTGTGGAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (5 bp):
TTTTG
Found at i:13859 original size:9 final size:9
Alignment explanation
Indices: 13845--13880 Score: 63
Period size: 9 Copynumber: 3.9 Consensus size: 9
13835 ATCCGGACCT
13845 TTTTTTTTG
1 TTTTTTTTG
13854 TTTTTTTTG
1 TTTTTTTTG
13863 TTTTGTTTTG
1 TTTT-TTTTG
13873 TTTTTTTT
1 TTTTTTTT
13881 TTGTGGAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:13859 original size:10 final size:10
Alignment explanation
Indices: 13844--13881 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
13834 CATCCGGACC
13844 TTTTTTTTTG
1 TTTTTTTTTG
13854 -TTTTTTTTG
1 TTTTTTTTTG
*
13863 TTTTGTTTTG
1 TTTTTTTTTG
13873 TTTTTTTTT
1 TTTTTTTTT
13882 TGTGGAGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:13866 original size:19 final size:19
Alignment explanation
Indices: 13844--13880 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13834 CATCCGGACC
*
13844 TTTTTTTTTGTTTTTTTTG
1 TTTTGTTTTGTTTTTTTTG
13863 TTTTGTTTTGTTTTTTTT
1 TTTTGTTTTGTTTTTTTT
13881 TTGTGGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
TTTTGTTTTGTTTTTTTTG
Done.