Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2035
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: 20993
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Found at i:5088 original size:20 final size:20
Alignment explanation
Indices: 4992--5078 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
4982 ACTATGATAA
* **
4992 ATGTATCGATGCATTTTAAGC
1 ATGTATCGATACA-TTTACTC
*
5013 ATATATCGATACATTTACTC
1 ATGTATCGATACATTTACTC
*
5033 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTC
*
5053 ATATATCGATACATTTACTC
1 ATGTATCGATACATTTACTC
5073 ATGTAT
1 ATGTAT
5079 TTATATATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
20 46 0.81
21 11 0.19
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTACTC
Found at i:6400 original size:19 final size:18
Alignment explanation
Indices: 6374--6439 Score: 70
Period size: 19 Copynumber: 3.8 Consensus size: 18
6364 AATTTCAACG
6374 GTTTGTATCGATACATAA
1 GTTTGTATCGATACATAA
*
6392 GTGTTGTATTGATAC--AA
1 GT-TTGTATCGATACATAA
6409 ---TGTATCGATACATAA
1 GTTTGTATCGATACATAA
6424 GTTTTGTATCGATACA
1 G-TTTGTATCGATACA
6440 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
18 2 0.05
19 23 0.59
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (18 bp):
GTTTGTATCGATACATAA
Found at i:6418 original size:32 final size:32
Alignment explanation
Indices: 6377--6447 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
6367 TTCAACGGTT
*
6377 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
6409 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
6441 TGTATCG
1 TGTATCG
6448 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:6510 original size:13 final size:13
Alignment explanation
Indices: 6492--6516 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6482 ATTACTCAAA
6492 TGTATCGATACAT
1 TGTATCGATACAT
6505 TGTATCGATACA
1 TGTATCGATACA
6517 CTGATCTTTG
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:6568 original size:52 final size:52
Alignment explanation
Indices: 6525--6653 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
6515 CACTGATCTT
* * * *
6525 TGTATCGATACATGTAGGTAAATTTGCCCAGATGTATCGATACAATATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
*
6577 TGTATCGATACATACAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
6629 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
6654 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
Found at i:14982 original size:32 final size:32
Alignment explanation
Indices: 14889--15008 Score: 140
Period size: 32 Copynumber: 3.8 Consensus size: 32
14879 ATACCTTCTT
* * *
14889 AAAGTCCATGACTCAATGGCAATC-TCT-TCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTTGTCTC
* *
14920 AAAGCCCACGACTCAGTGGC--GTTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTTTGTCTC
14950 AAAGTCCACGACTCAGTGGCATCTTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTTTGTCTC
* *
14982 AAAGTCCACGACTTAGTGGCACCTTTT
1 AAAGTCCACGACTCAGTGGCATCTTTT
15009 TCTTTTTAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
29 2 0.03
30 23 0.30
31 17 0.22
32 34 0.45
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.29
Consensus pattern (32 bp):
AAAGTCCACGACTCAGTGGCATCTTTTGTCTC
Found at i:15061 original size:34 final size:34
Alignment explanation
Indices: 14951--15610 Score: 463
Period size: 34 Copynumber: 20.8 Consensus size: 34
14941 TTTTGTCTCA
* * *
14951 AAGTCCACGACTCAGTGGCA-TCTTTTGT-C-TCA
1 AAGTCCACAACTCCGTGGCACTCTTTT-TCCTTCT
* ** * *
14983 AAGTCCACGACTTAGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15016 AAAGCCCACAACTCCGTAGCACTCTTTTTCCTTCT
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
15051 AAGTCCACAACTCCGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
15078 AAG-CCTACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGTCC-ACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
15112 AAGTCTACAACTCTGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15139 AAGCCCACAACTCCATGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15173 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
15206 AAAGCCCACAACTCCGTGGCATTTTTTTTCCTTCT
1 -AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15241 AAGTCCACAACTCCATGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15268 AAGCCCACAACTCCGTGGCACTCTTTTTCTTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15302 AAGTCCACAACTCTGTGGCA--C-----CCTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15329 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
15363 AAGTCCACAACTCTGT-GCA-AC---AT--TT-T
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15389 AAGCCCACAACTCCGTGGCACTCTTTTTTCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15423 AAGTCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
15456 AAAG-CCTACAACTCCGTGGCATTCTTTTTCCTTCT
1 -AAGTCC-ACAACTCCGTGGCACTCTTTTTCCTTCT
*
15491 AAGTCCACAACTCCGTGGCAC-C---AT--TT-T
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
15518 AAGCCCATAACTTCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
15552 AAGTCCACAACTCTGTGGCAC-CTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
15585 AAAGCCCACAACTCCATGGCAC-CTTT
1 -AAGTCCACAACTCCGTGGCACTCTTT
15611 CCCTTCTCCA
Statistics
Matches: 496, Mismatches: 75, Indels: 112
0.73 0.11 0.16
Matches are distributed among these distances:
26 17 0.03
27 112 0.23
28 4 0.01
29 5 0.01
30 1 0.00
31 3 0.01
32 28 0.06
33 40 0.08
34 254 0.51
35 32 0.06
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (34 bp):
AAGTCCACAACTCCGTGGCACTCTTTTTCCTTCT
Found at i:15112 original size:61 final size:61
Alignment explanation
Indices: 15012--15578 Score: 785
Period size: 61 Copynumber: 9.1 Consensus size: 61
15002 ACCTTTTTCT
*
15012 TTTTAAAGCCCACAACTCCGTAGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
* * * *
15074 TTTTAAGCCTACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCTACAACTCTGTGGCACCC
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
*
15135 TTTTAAGCCCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----
15200 C
61 C
* * *
15201 TTTTTAAAGCCCACAACTCCGTGGCATTTTTTTTCCTTCTAAGTCCACAACTCCATGGCACCC
1 -TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
* *
15264 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
* * * *
15325 TTTTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGT-GCAACA
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
*
15385 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTTCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC-----
15450 C
61 C
* * *
15451 TTTTTAAAGCCTACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
1 -TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
* * * *
15514 TTTTAAGCCCATAACTTCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
15575 TTTT
1 TTTT
15579 CTTTTTAAAG
Statistics
Matches: 452, Mismatches: 38, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
60 55 0.12
61 270 0.60
62 12 0.03
63 1 0.00
66 1 0.00
67 8 0.02
68 105 0.23
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (61 bp):
TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC
Found at i:15260 original size:129 final size:129
Alignment explanation
Indices: 15012--15610 Score: 870
Period size: 129 Copynumber: 4.8 Consensus size: 129
15002 ACCTTTTTCT
*
15012 TTTTAAAGCCCACAACTCCGTAGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACC----
1 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTT
* * * * *
15073 -C-TTTT-AAGCCTACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCTACAACTCTGTGGCACCC
65 TCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
*
15135 TTTTAAGCCCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
* * * *
15200 CTTTTTAAAGCCCACAACTCCGTGGCATTTTTTTTCCTTCTAAGTCCACAACTCCATGGCACCC
66 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
* *
15264 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCTGTGGCACC-----
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
15324 C-TTTT-AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGT-GCAACA
66 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
*
15385 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTTCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
* *
15450 CTTTTTAAAGCCTACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
66 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
* * *
15514 TTTTAAGCCCATAACTTCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
*
15579 CTTTTTAAAGCCCACAACTCCATGGCAC-CTTT
66 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTT
15611 CCCTTCTCCA
Statistics
Matches: 427, Mismatches: 34, Indels: 25
0.88 0.07 0.05
Matches are distributed among these distances:
121 61 0.14
122 99 0.23
123 8 0.02
124 1 0.00
126 1 0.00
127 5 0.01
128 54 0.13
129 198 0.46
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (129 bp):
TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTT
CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
Found at i:15495 original size:250 final size:251
Alignment explanation
Indices: 15012--15578 Score: 974
Period size: 250 Copynumber: 2.3 Consensus size: 251
15002 ACCTTTTTCT
* *
15012 TTTTAAAGCCCACAACTCCGTAGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCCTTT
1 TTTT-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTT
* * * *
15077 TAAGCCTACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCTACAACTCTGTGGCACCCTTTTAAG
65 TAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCAACATTTTAAG
15142 CCCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTA
130 CCCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTA
* *
15207 AAGCCCACAACTCCGTGGCATTTTTTTTCCTTCTAAGTCCACAACTCCATGGCACCC
195 AAGCCCACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCA
*
15264 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCTTTCTAAGTCCACAACTCTGTGGCACCCTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
15329 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGT-GCAACATTTTAAGC
66 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCAACATTTTAAGC
* *
15393 CCACAACTCCGTGGCACTCTTTTTTCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
131 CCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
* *
15458 AGCCTACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCA
196 AGCCCACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCA
* * *
15514 TTTTAAGCCCATAACTTCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
15579 CTTTTTAAAG
Statistics
Matches: 298, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
250 188 0.63
251 106 0.36
252 4 0.01
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (251 bp):
TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTT
AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCAACATTTTAAGC
CCACAACTCCATGGCACTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAA
AGCCCACAACTCCGTGGCATTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCA
Found at i:15570 original size:95 final size:95
Alignment explanation
Indices: 15422--15607 Score: 225
Period size: 95 Copynumber: 2.0 Consensus size: 95
15412 TTTTTTCTTC
* * * *
15422 TAAGTCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCTACAACTCCGTGGCATTCTTTTTCC
1 TAAGCCCACAACTCCGTGGCACCTTTTTCCTTCTAAAGCCTACAACTCCGTGGCA-CCTTTTTCC
* *
15487 TTCT-AAGTCCACAACTCCGTGGCACCATTT
65 TTCTAAAGCCCACAACTCCATGGCACCATTT
* * *
15517 TAAGCCCATAACTTCGTGGCACTCTTTTTCCTTCT-AAGTCC-ACAACTCTGTGGCACCTTTTTC
1 TAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTCTAAAG-CCTACAACTCCGTGGCACCTTTTTC
* *
15580 TTTTTAAAGCCCACAACTCCATGGCACC
64 CTTCTAAAGCCCACAACTCCATGGCACC
15608 TTTCCCTTCT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
94 10 0.13
95 55 0.71
96 12 0.16
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (95 bp):
TAAGCCCACAACTCCGTGGCACCTTTTTCCTTCTAAAGCCTACAACTCCGTGGCACCTTTTTCCT
TCTAAAGCCCACAACTCCATGGCACCATTT
Found at i:15697 original size:33 final size:32
Alignment explanation
Indices: 15612--15772 Score: 164
Period size: 32 Copynumber: 5.0 Consensus size: 32
15602 GGCACCTTTC
* * *
15612 CCTTCTCCAAAGCCCACACAATTCGGTGGCAA
1 CCTTCTTCAAAACCCACACAAGTCGGTGGCAA
* *
15644 CCCTTC-TCAAAGCCCACACAAGTCAGTGGCAA
1 -CCTTCTTCAAAACCCACACAAGTCGGTGGCAA
* *
15676 CCTTTTTCTAAAACCCACACAAGTTGGTGGCAA
1 CCTTCTTC-AAAACCCACACAAGTCGGTGGCAA
* * * *
15709 TCC-CCTTTAAAGCCCACACAAGTCGATGGCAA
1 -CCTTCTTCAAAACCCACACAAGTCGGTGGCAA
*
15741 CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTTCAAAA-CCCACACAAGTCGGTGGCA
15773 TCTTCTTTTA
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
31 6 0.06
32 52 0.50
33 45 0.43
34 2 0.02
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (32 bp):
CCTTCTTCAAAACCCACACAAGTCGGTGGCAA
Found at i:15705 original size:65 final size:64
Alignment explanation
Indices: 15612--15772 Score: 215
Period size: 65 Copynumber: 2.5 Consensus size: 64
15602 GGCACCTTTC
*
15612 CCTTC-TCCAAAGCCCACACAA-TTCGGTGGCAA-CCCTTCTCAAAGCCCACACAAGTC-AGTGG
1 CCTTCTTCAAAAGCCCACACAAGTT-GGTGGCAACCCCTT-T-AAAGCCCACACAAGTCGA-TGG
15673 CAA
62 CAA
*
15676 CCTTTTTCTAAAA-CCCACACAAGTTGGTGGCAATCCCCTTTAAAGCCCACACAAGTCGATGGCA
1 CCTTCTTC-AAAAGCCCACACAAGTTGGTGGCAA-CCCCTTTAAAGCCCACACAAGTCGATGGCA
15740 A
64 A
15741 CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
1 CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
15773 TCTTCTTTTA
Statistics
Matches: 87, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
64 8 0.09
65 67 0.77
66 7 0.08
67 5 0.06
ACGTcount: A:0.30, C:0.34, G:0.16, T:0.20
Consensus pattern (64 bp):
CCTTCTTCAAAAGCCCACACAAGTTGGTGGCAACCCCTTTAAAGCCCACACAAGTCGATGGCAA
Found at i:15839 original size:49 final size:48
Alignment explanation
Indices: 15779--16491 Score: 640
Period size: 49 Copynumber: 14.8 Consensus size: 48
15769 GGCATCTTCT
* * *
15779 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
* *
15828 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* * * * *
15871 TTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTCATC
*
15920 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* *
15963 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCATCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
* * *
16012 TTTAATTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTC--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* *
16058 ---AAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTCATC
* * *
16104 TTTTAAGCCCAATGTCACTGGCCTTGAATCAGCACATTGGCA---C--C
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCATC
* *
16148 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC----TCATC
*
16200 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
* ***
16249 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGTCGTCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTG--G-C-ACCTCATC
* *
16301 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACCTTCATC
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TCATC
* * * * * *
16351 TTTAAGTCCAGTA-CGCTAGCCTTGAATCAGTATATTGGCGCCTTCGTTATT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACC-TC---ATC
** * *
16402 TTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGCATTCTTCTCATC
1 TTT-AAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA--C--CTCATC
* * * * * *
16455 TTCAAGTCTAATGTCGCTGACCATGAATTAGCACATT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATT
16492 AACATCCTTT
Statistics
Matches: 545, Mismatches: 76, Indels: 83
0.77 0.11 0.12
Matches are distributed among these distances:
43 146 0.27
44 5 0.01
45 1 0.00
46 3 0.01
47 1 0.00
48 29 0.05
49 168 0.31
50 40 0.07
51 7 0.01
52 80 0.15
53 61 0.11
55 1 0.00
56 2 0.00
57 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (48 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTCATC
Found at i:15937 original size:92 final size:92
Alignment explanation
Indices: 15779--16443 Score: 803
Period size: 92 Copynumber: 7.0 Consensus size: 92
15769 GGCATCTTCT
* * *
15779 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATTTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
15844 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * * *
15871 TTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTTTATCTTTAAGTCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
15936 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
15963 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAATTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
16028 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
** * * *
16055 TCCAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGT-
16120 A-CTGGCCTTGAATCAGCACATTGGCACC
64 AGCTGGCCTTGAATCAGCACATTGGCACC
*
16148 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
*
16213 TCGCTGGCCTTGAATCAGCACATTGGCACCTTCATC
63 TAGCTGGCCTTGAATCAGCACATTGGCA----C--C
* * *
16249 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGTCGTCTTTGTCATCTTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC-CT-TCATC-TTTAAGTCCAAT
* *
16314 GTCGCTGGCCTTGAATCAACACATTGGCACCTTCATC
62 GTAGCTGGCCTTGAATCAGCACATTGGCA----C--C
* * * * * **
16351 TTTAAGTCCAGTA-CGCTAGCCTTGAATCAGTATATTGGCGCCTTCGTTATTTTTAAAACCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTC---ATCTTT-AAGTCCAAT
* *
16415 GTCGTTGGCCTTGAATCAGCACATTGGCA
62 GTAGCTGGCCTTGAATCAGCACATTGGCA
16444 TTCTTCTCAT
Statistics
Matches: 511, Mismatches: 43, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
92 214 0.42
93 78 0.15
94 1 0.00
95 38 0.07
96 5 0.01
98 2 0.00
99 2 0.00
100 4 0.01
101 106 0.21
102 61 0.12
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:16225 original size:52 final size:52
Alignment explanation
Indices: 16147--16491 Score: 357
Period size: 52 Copynumber: 6.7 Consensus size: 52
16137 ACATTGGCAC
* *
16147 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
*
16199 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
* * * *
16248 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGTCGTCTTTGTCAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
* *
16300 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACC--T-TCAT
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
* * * * *
16350 CTTTAAGTCC-A-GTACGCTAGCCTTGAATCAGTATATTGGCGCCTTCGTTAT
1 CTTTAAGTCCAATGT-CGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
* ** * ** *
16401 TTTTAAAACCCAATGTCGTTGGCCTTGAATCAGCACATTGGC-ATTCTTCTCAT
1 CTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCT-TTGTCAT
* * * * *
16454 CTTCAAGTCTAATGTCGCTGACCATGAATTAGCACATT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
16492 AACATCCTTT
Statistics
Matches: 239, Mismatches: 42, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
47 2 0.01
48 25 0.10
49 52 0.22
50 6 0.03
51 8 0.03
52 78 0.33
53 66 0.28
54 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (52 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCGCCTTTGTCAT
Found at i:16454 original size:154 final size:152
Alignment explanation
Indices: 15870--16491 Score: 502
Period size: 154 Copynumber: 4.2 Consensus size: 152
15860 ACATTGGCAC
* * * * * *
15870 CTTTAAGTCCAATATTGTTGGCCTTGAATCAGCATATTGGCATCTT-T-ATCTTTAAGTCCAATA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATG
* * ** *
15933 TAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATTGCTGGCCTTGAATC
66 TCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAACCCAATATCGCTGGCCTTGAATC
* *
15992 AGCATATTGGC-AC---CATCAT
131 AGCACATTGGCGTCTTTC-TCAT
* * *
16011 CTTTAATTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC---TC--C---AAGTCCAATA
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATG
* * * * * * *
16068 TCGCTGGCCTTGAATTAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTCACTGGCCTTGAAT
66 TCGCTAGCCTTGAATCAGCACATTGGCACCTTCATC-TTTAAACCCAATATCGCTGGCCTTGAAT
*
16133 CAGCACATT-G-G-------CAC
130 CAGCACATTGGCGTCTTTCTCAT
* * *
16147 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TTGTCATCTTTAAGTCCAAT
* **
16212 GTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
65 GTCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAACCCAATATCGCTGGCCTTGAAT
* * *
16277 CAGCATATTGTCGTCTTTGTCAT
130 CAGCACATTGGCGTCTTTCTCAT
*
16300 CTTTTAAGTCCAATGTCGCTGGCCTTGAATCAACACATTGGCACC-T-TCATCTTTAAGTCC-A-
1 C-TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAAT
* * * * * *
16361 GTACGCTAGCCTTGAATCAGTATATTGGCGCCTTCGTTATTTTTAAAACCCAATGTCGTTGGCCT
65 GT-CGCTAGCCTTGAATCAGCACATTGGCACCTTC---ATCTTT-AAACCCAATATCGCTGGCCT
*
16426 TGAATCAGCACATTGGCAT-TCTTCTCAT
125 TGAATCAGCACATTGGCGTCT-TTCTCAT
* * * * *
16454 CTTCAAGTCTAATGTCGCTGACCATGAATTAGCACATT
1 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT
16492 AACATCCTTT
Statistics
Matches: 394, Mismatches: 53, Indels: 56
0.78 0.11 0.11
Matches are distributed among these distances:
135 35 0.09
136 41 0.10
138 1 0.00
139 2 0.01
140 2 0.01
141 40 0.10
142 33 0.08
144 33 0.08
145 42 0.11
146 1 0.00
149 2 0.01
150 29 0.07
151 14 0.04
152 1 0.00
153 40 0.10
154 78 0.20
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.33
Consensus pattern (152 bp):
CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTGTCATCTTTAAGTCCAATG
TCGCTAGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAACCCAATATCGCTGGCCTTGAATC
AGCACATTGGCGTCTTTCTCAT
Found at i:17346 original size:52 final size:52
Alignment explanation
Indices: 17302--17430 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
17292 CACTGATTTT
*
17302 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
*
17354 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
17406 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
17431 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Done.