Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2187
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: 29891
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Found at i:119 original size:7 final size:7
Alignment explanation
Indices: 84--115 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
74 TCAATAATAA
84 AAACCCT
1 AAACCCT
91 AAACCCT
1 AAACCCT
98 AAACCCT
1 AAACCCT
*
105 AAACTCT
1 AAACCCT
112 AAAC
1 AAAC
116 TCTACCCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:5678 original size:22 final size:22
Alignment explanation
Indices: 5631--5687 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
5621 CTGGACATGT
5631 TAAAAAAA--CATGAAACATAA
1 TAAAAAAATGCATGAAACATAA
5651 TAAAAAAAATGCATGAAACATAA
1 T-AAAAAAATGCATGAAACATAA
5674 TAAAAAAATGCATG
1 TAAAAAAATGCATG
5688 GTCAAAGGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 1 0.03
21 7 0.21
22 13 0.38
23 13 0.38
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.18
Consensus pattern (22 bp):
TAAAAAAATGCATGAAACATAA
Found at i:6660 original size:20 final size:20
Alignment explanation
Indices: 6596--6670 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
6586 AAAAAGACAT
* *
6596 AATGTATCGATACATTGTAG
1 AATGTATCGATACATTGAAA
* * * *
6616 AATATATCGATACAGTCATA
1 AATGTATCGATACATTGAAA
* *
6636 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
*
6656 AATGTATTGATACAT
1 AATGTATCGATACAT
6671 CAGGGTATGA
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:6668 original size:40 final size:39
Alignment explanation
Indices: 6593--6669 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 39
6583 GGTAAAAAGA
* *
6593 CATAATGTATCGATACATTGTAGAATATATCGATACAGT
1 CATAATGTATCGATACATTGAAAAATATATCGATACAGT
* * *
6632 CATACATGTATCGATATATTGAAAAATGTATTGATACA
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACA
6670 TCAGGGTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 28 0.88
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACAGT
Found at i:7381 original size:28 final size:28
Alignment explanation
Indices: 7280--8154 Score: 1004
Period size: 28 Copynumber: 30.6 Consensus size: 28
7270 CACTAACACA
* **
7280 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
7309 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
7339 TGCGTGGGCTTTGAAAGGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
* *
7369 CGTGGGATTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
7397 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7424 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
7452 TGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
7479 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
7507 CGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
7535 TGCGTGGGCTTTGAAAGGAGTGACATTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
*
7567 GTGTGGGCTTTGAAAGGGTGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
7596 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7624 CGTGGGCTTTGAAA-GAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
7652 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
7679 CGTGGGTTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
7707 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
7734 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
7762 CGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
7790 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
7822 GTGTGGGCTTTGAAAGGGA-GCCACTGACT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
7851 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
7879 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7907 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
7935 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
7964 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
7993 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
8022 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
8051 TGTGGGCTTTAAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
**
8080 TGTGGGCTTTGAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
8109 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
8139 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
8155 GATGAGCATT
Statistics
Matches: 753, Mismatches: 57, Indels: 71
0.85 0.06 0.08
Matches are distributed among these distances:
26 12 0.02
27 85 0.11
28 303 0.40
29 195 0.26
30 93 0.12
31 58 0.08
32 5 0.01
33 2 0.00
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:7395 original size:58 final size:57
Alignment explanation
Indices: 7280--8154 Score: 1109
Period size: 58 Copynumber: 15.3 Consensus size: 57
7270 CACTAACACA
* ** * *
7280 TGTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGACT
* *
7339 TGCGTGGGCTTTGAAAGGA-TGCCACTGACTCGTGGGATTTGAAAGAGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
7397 TGTGGGCTTTGAAA-G-GTGCCACTGACTCGTGGGCTTTGAAA-AGGTACCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
7452 TGTGGGC-TTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * *
7507 CGTGGGCTTTGAAAAG-GTGCCACTGACTTGCGTGGGCTTTGAAAGGAGTGACATTGACTT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTT--GTGGGCTTTGAAA-GAGTGCCACTGAC-T
7567 GTGTGGGCTTTGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAG-GATGCCACTGACT
1 -TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACT
* *
7624 CGTGGGCTTTGAAA-GAGTGCCACTAACTTGTGGGCTTTGAAAG-GTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* * * * * *
7679 CGTGGGTTTTGAAAAG-GTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
7734 TGTGGGCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTTGAAA-AGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGA-GTGCCACTGACT
* *
7790 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACT
1 T--GTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACT
* * *
7851 TGTGGGCTTTGAAA-GAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
* *
7907 TGTGGGCTTCGAAAGG-GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACT
* *
7964 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACT
* * *
8022 TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTT-GAAAGAGTGCCACTGACT
**
8080 TGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAA-GAGTGCCACTGAC-T
8139 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
8155 GATGAGCATT
Statistics
Matches: 735, Mismatches: 50, Indels: 62
0.87 0.06 0.07
Matches are distributed among these distances:
54 15 0.02
55 169 0.23
56 153 0.21
57 35 0.05
58 220 0.30
59 66 0.09
60 11 0.01
61 66 0.09
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:7720 original size:255 final size:256
Alignment explanation
Indices: 7281--8153 Score: 1346
Period size: 255 Copynumber: 3.4 Consensus size: 256
7271 ACTAACACAT
** * *
7281 GTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGG
*
7346 GCTTTGAAAGGA-TGCCACTGACTCGTGGGATTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAA
64 GCTTTGAAAGGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAA
7410 AGGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTTGAAAGGGTGCCACT
129 AGGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTTGAAAGGGTGCCACT
7475 GACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
194 GACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
* * *
7538 GTGGGCTTTGAAAGGAGTGACATTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
*
7603 TTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTAACTTGTGGGCTTTGAAAG
66 TTTGAAAGGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
* *
7667 GTGCCACTGACTCGTGGGTTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGA
131 GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTTGAAAGGGTGCCACTGA
*
7732 CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTTGC
196 CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
* *
7793 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTTGTGGGC
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
7858 TTTGAAA-GAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAAG
66 TTTGAAAGGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-
* * * *
7922 GGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCA
130 GGTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGACTTGTGGGC-TTG-AAAGGGTGCCA
* *
7987 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGACTT
192 CTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTGACTT
8052 --
255 GC
* **
8052 GTGGGCTTTAAAAAGAGTGCCACTGA-TT-TGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGG
1 GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGG
*
8115 CTTTGAAAGGAGTGCCACTGACTTTGTGGGCTTTGAAAG
65 CTTTGAAAGGAGTGCCACTGAC-TCGTGGGCTTTGAAAG
8154 GGATGAGCAT
Statistics
Matches: 570, Mismatches: 36, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
254 2 0.00
255 307 0.54
256 27 0.05
257 80 0.14
258 33 0.06
259 64 0.11
260 45 0.08
261 12 0.02
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (256 bp):
GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAGGAGTGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAG
GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTTGTGGGCTTGAAAGGGTGCCACTGA
CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTGACTTGC
Found at i:9388 original size:1 final size:1
Alignment explanation
Indices: 9384--9432 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
9374 TTTTTTGCTA
* * * * *
9384 TTTTTTCTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9433 GGGTGTAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:9418 original size:24 final size:24
Alignment explanation
Indices: 9386--9433 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
9376 TTTTGCTATT
9386 TTTTCTTTTTTTTTGTTTTTTTTG
1 TTTTCTTTTTTTTTGTTTTTTTTG
*
9410 TTTTGTTTTTTTTTGTTTTTTTTG
1 TTTTCTTTTTTTTTGTTTTTTTTG
9434 GGTGTAAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (24 bp):
TTTTCTTTTTTTTTGTTTTTTTTG
Found at i:9423 original size:10 final size:10
Alignment explanation
Indices: 9373--9432 Score: 59
Period size: 10 Copynumber: 5.6 Consensus size: 10
9363 GACCCTTCTA
9373 TTTTTTTGCTAT
1 TTTTTTTG-T-T
9385 TTTTTCTT-TT
1 TTTTT-TTGTT
*
9395 TTTTTGTTTTT
1 TTTTT-TTGTT
9406 TTTGTTTTGTT
1 TTT-TTTTGTT
9417 TTTTTTTGTT
1 TTTTTTTGTT
9427 TTTTTT
1 TTTTTT
9433 GGGTGTAAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
10 21 0.49
11 13 0.30
12 7 0.16
13 2 0.05
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.87
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:9433 original size:9 final size:9
Alignment explanation
Indices: 9373--9433 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
9363 GACCCTTCTA
9373 TTTTTTTGCT
1 TTTTTTTG-T
9383 ATTTTTTCT-T
1 -TTTTTT-TGT
9393 TTTTTTTGT
1 TTTTTTTGT
9402 TTTTTTTG-
1 TTTTTTTGT
*
9410 -TTTTGT-T
1 TTTTTTTGT
9417 TTTTTTTGT
1 TTTTTTTGT
9426 TTTTTTTG
1 TTTTTTTG
9434 GGTGTAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 5 0.12
8 6 0.14
9 24 0.56
10 1 0.02
11 6 0.14
12 1 0.02
ACGTcount: A:0.02, C:0.03, G:0.10, T:0.85
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:19961 original size:25 final size:25
Alignment explanation
Indices: 19933--19980 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
19923 ACCTTCTCTT
*
19933 CAAAAAAAAAAAAGAAAAAAAAAAA
1 CAAAAAAAAAAAACAAAAAAAAAAA
* *
19958 CAAAAAAACAAAACAAAGAAAAA
1 CAAAAAAAAAAAACAAAAAAAAA
19981 GAGAGAAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (25 bp):
CAAAAAAAAAAAACAAAAAAAAAAA
Found at i:21204 original size:55 final size:55
Alignment explanation
Indices: 20962--22025 Score: 1516
Period size: 55 Copynumber: 19.3 Consensus size: 55
20952 TCCGCTTTTT
20962 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
21017 AGTCCTCAAAGAGCAGGACACCTCTT-AAGCCCACACAAGTT-GTGGCA--TTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
**
21068 AGTCC-CAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
*
21123 AGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
21178 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
21233 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTT-T-C
21288 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
21343 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
21398 AGTCCTCAAAGAGCAGGACACCTCTTAAAG-CCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
21452 AGTCCTCAACGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
21507 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
21562 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCAC-CTAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACAC-AAGTTGGTGGCACCTTT-C
*
21617 AGTCCTCAAAGAGCAAGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
21672 AGTCCCCAAAGAGAAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
21727 AGTCCCCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * **
21781 TAGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACATAGGTTGGTGGCATTTTTC
1 -AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
**** * *
21837 AGTCCTCAAAGAGCAGGATGTTTTTTATTTTCAAAGCCTACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGA-----CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
21898 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * *
21953 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
22008 ACTCCTCAATGAGAAGGA
1 AGTCCTCAAAGAGCAGGA
22026 TACAATTTAT
Statistics
Matches: 926, Mismatches: 49, Indels: 68
0.89 0.05 0.07
Matches are distributed among these distances:
49 2 0.00
50 17 0.02
51 24 0.03
52 6 0.01
53 8 0.01
54 91 0.10
55 665 0.72
56 64 0.07
57 4 0.00
60 4 0.00
61 41 0.04
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:21255 original size:26 final size:26
Alignment explanation
Indices: 21009--21259 Score: 77
Period size: 27 Copynumber: 9.3 Consensus size: 26
20999 AAGTTGGTGG
*
21009 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * *
21035 CACCTCTTAAGCCCACACAAGTTG-TGG-
1 CACCT-TTCAGTCCACA-AAG-AGCAGGA
21062 CA--TTTCAGTCC-CAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
21085 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
** * *
21114 CATTTTTCCAGTCCTCAACGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* * * **
21141 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
21170 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * * **
21196 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCACA-AAG-AGCAGGA
*
21225 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
21251 CACCTTTCA
1 CACCTTTCA
21260 AAGCCCACAC
Statistics
Matches: 153, Mismatches: 49, Indels: 46
0.62 0.20 0.19
Matches are distributed among these distances:
21 1 0.01
22 5 0.03
23 4 0.03
24 6 0.04
25 11 0.07
26 28 0.18
27 33 0.22
28 31 0.20
29 24 0.16
30 10 0.07
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:21734 original size:29 final size:29
Alignment explanation
Indices: 21647--21734 Score: 71
Period size: 29 Copynumber: 3.1 Consensus size: 29
21637 CCTCTTAAAG
21647 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
** * *
21676 CCCA-A-AGAG-AAG-GACACCTCTTAAAG--
1 CCCACACA-AGTTGGTGGCACCT-TT-CAGTC
21702 CCCACACAAGTTGGTGGCACCTTTCAGTC
1 CCCACACAAGTTGGTGGCACCTTTCAGTC
21731 CCCA
1 CCCA
21735 AAGAGCAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 18
0.62 0.12 0.26
Matches are distributed among these distances:
26 10 0.24
27 9 0.21
28 9 0.21
29 14 0.33
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.19
Consensus pattern (29 bp):
CCCACACAAGTTGGTGGCACCTTTCAGTC
Found at i:21920 original size:26 final size:26
Alignment explanation
Indices: 21890--21979 Score: 67
Period size: 26 Copynumber: 3.3 Consensus size: 26
21880 AAGTTGGTGG
21890 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
21916 CACCTCTTAAAG-CCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCC-CA-AAG-AGCAGGA
*
21945 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
*
21971 CGCCTTTCA
1 CACCTTTCA
21980 AAGCCCACAC
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
25 3 0.06
26 16 0.34
27 9 0.19
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.20
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:22712 original size:19 final size:19
Alignment explanation
Indices: 22688--22755 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
22678 AATTCAACGA
22688 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
22707 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
22722 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
22739 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
22756 TTAGCTACTA
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:22726 original size:32 final size:32
Alignment explanation
Indices: 22690--22752 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
22680 TTCAACGATT
*
22690 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
22722 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
22753 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:22727 original size:13 final size:13
Alignment explanation
Indices: 22709--22733 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22699 ACATAAGTTT
22709 TGTATCGATACAA
1 TGTATCGATACAA
22722 TGTATCGATACA
1 TGTATCGATACA
22734 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:22816 original size:13 final size:13
Alignment explanation
Indices: 22798--22823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22788 CATTTTTCTG
22798 TGTATCGATACAT
1 TGTATCGATACAT
22811 TGTATCGATACAT
1 TGTATCGATACAT
22824 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:22820 original size:33 final size:33
Alignment explanation
Indices: 22778--22844 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
22768 GCCAAGGAAA
***
22778 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
22811 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
22844 T
1 T
22845 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:25371 original size:52 final size:51
Alignment explanation
Indices: 25298--25467 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 51
25288 TTATTTTCGA
*
25298 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT--TTCAAAACACCAATTTTTCCACAATC
* **
25350 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTA-TTTCAAAACACCAATTTTTCC-ACAATC
* *
25402 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATTT-C-AAAACACCAATTTTTCCACAATC
*
25454 GAGGATACTCCAAC
1 GGGGATACTCCAAC
25468 CTCGTTATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
51 14 0.14
52 69 0.69
53 13 0.13
54 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACTCCGGTTTTATTTCAAAACACCAATTTTTCCACAATC
Found at i:25487 original size:28 final size:28
Alignment explanation
Indices: 25451--25527 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
25441 ATTTTTCACA
* * *
25451 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
25479 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
25507 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
25528 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:25657 original size:76 final size:78
Alignment explanation
Indices: 25481--25682 Score: 214
Period size: 76 Copynumber: 2.6 Consensus size: 78
25471 GTTATTTCAT
* * * *
25481 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCC-GATTTATTCCCAAAATAT
* * *
25546 TGATTTCTCATAAT
65 CGATTTCTCACAAC
** * * * *
25560 TAGGGATACTCCAACCTCGTTATTTTCGAAGGGATACTCCAATCCCGATTT-TT-TC-TAATCAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAAT-AT
25622 CGATTTCTCACAAC
65 CGATTTCTCACAAC
* *
25636 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCCCG
25683 TTATTATCTC
Statistics
Matches: 102, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
75 8 0.08
76 49 0.48
77 2 0.02
78 4 0.04
79 39 0.38
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.28
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGATTTATTCCCAAAATATC
GATTTCTCACAAC
Found at i:26812 original size:13 final size:13
Alignment explanation
Indices: 26794--26829 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
26784 ATATTCCTTT
26794 TATCGATACATTG
1 TATCGATACATTG
26807 TATCGATACATTG
1 TATCGATACATTG
26820 TATCGATACA
1 TATCGATACA
26830 GTGGGTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:26996 original size:20 final size:22
Alignment explanation
Indices: 26952--26998 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
26942 AATTTTCCAC
26952 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
26974 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
26994 AAATC
1 AAATC
26999 ATCAATAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:29394 original size:13 final size:13
Alignment explanation
Indices: 29373--29403 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29363 CAATACATGG
*
29373 TACAATGTATCGA
1 TACATTGTATCGA
29386 TACATTGTATCGA
1 TACATTGTATCGA
29399 TACAT
1 TACAT
29404 GATGAATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:29402 original size:33 final size:33
Alignment explanation
Indices: 29357--29423 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
29347 CTTCCACTGT
*
29357 TTGTATCAATACATGGT-ACAATGTATCGATACA
1 TTGTATCAATACATGATGA-AATGTATCGATACA
* *
29390 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCAATACATGATGAAATGTATCGATACA
29423 T
1 T
29424 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCAATACATGATGAAATGTATCGATACA
Done.