Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2599
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: 50041
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:438 original size:13 final size:13
Alignment explanation
Indices: 420--458 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
410 ACATTTTTCC
420 TTGTATCGATACA
1 TTGTATCGATACA
433 TTGTATCGATACA
1 TTGTATCGATACA
*
446 CTGTATCGATACA
1 TTGTATCGATACA
459 GGGTGTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2323 original size:40 final size:40
Alignment explanation
Indices: 2248--2350 Score: 157
Period size: 40 Copynumber: 2.8 Consensus size: 40
2238 AATTTTGATA
2248 TGAATTACTTGATTAAGGGGGAGA------TTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTTTT
2282 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTTTT
2322 TGAATTACTTGATTAA-GGGGAGATTTTTT
1 TGAATTACTTGATTAAGGGGGAGATTTTTT
2351 AATAAACGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
34 24 0.38
39 13 0.21
40 26 0.41
ACGTcount: A:0.23, C:0.03, G:0.22, T:0.51
Consensus pattern (40 bp):
TGAATTACTTGATTAAGGGGGAGATTTTTTTTTTTTTTTT
Found at i:2994 original size:20 final size:20
Alignment explanation
Indices: 2971--3043 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2961 ACAATTCAAA
2971 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2991 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
3012 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
3032 GTATCGATACAT
1 GTATCGATACAT
3044 AAAAAAAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:3022 original size:41 final size:42
Alignment explanation
Indices: 2971--3065 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 42
2961 ACAATTCAAA
*
2971 GTATCGATACATGTTGCAATGTATCGATACAT-GAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3012 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
3054 GTATCGATACAT
1 GTATCGATACAT
3066 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 32 0.62
42 20 0.38
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (42 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAAGAT
Found at i:3122 original size:13 final size:13
Alignment explanation
Indices: 3104--3129 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3094 TACAGCAAGT
3104 ATGTATCGATACA
1 ATGTATCGATACA
3117 ATGTATCGATACA
1 ATGTATCGATACA
3130 CAAAAATTGT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3127 original size:32 final size:32
Alignment explanation
Indices: 3086--3148 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
3076 TAGCCAAACT
**
3086 TGTATCGATACAGCAAGTA-TGTATCGATACAA
1 TGTATCGATACA-CAAAAATTGTATCGATACAA
3118 TGTATCGATACACAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAATTGTATCGATACA
3149 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAAATTGTATCGATACAA
Found at i:5697 original size:33 final size:33
Alignment explanation
Indices: 5660--5726 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5650 TTCAACGATT
5660 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
5693 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
5726 T
1 T
5727 TTAAGCTACT
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:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:5698 original size:13 final size:13
Alignment explanation
Indices: 5680--5704 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5670 CATAAAATGT
5680 TGTATCGATACAA
1 TGTATCGATACAA
5693 TGTATCGATACA
1 TGTATCGATACA
5705 TATTTTTTTG
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:5841 original size:51 final size:49
Alignment explanation
Indices: 5782--5925 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 49
5772 ATCAATACAT
*
5782 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAATTTGCCCAGA
1 TGTATCGATACACT-AT-TATGTATCGATACATGCAGGCAATTTGCCCAGA
* *
5833 TGTATCGATACA-TTTTAAAATGTATCGATACATGCAGGCAAATTTTCCCAGA
1 TGTATCGATACACTATT---ATGTATCGATACATGCAGGC-AATTTGCCCAGA
*
5885 TGTATCGATACACTATTAAATGTATCGATACATGCAAGCAA
1 TGTATCGATACACTATT--ATGTATCGATACATGCAGGCAA
5926 CTTTTCATAT
Statistics
Matches: 83, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 1 0.01
51 33 0.40
52 44 0.53
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (49 bp):
TGTATCGATACACTATTATGTATCGATACATGCAGGCAATTTGCCCAGA
Found at i:5895 original size:52 final size:52
Alignment explanation
Indices: 5802--5931 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 52
5792 CACTGATCTT
* *
5802 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
5853 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
5905 TGTATCGATACATGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
5932 ATATTTTGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:16542 original size:11 final size:11
Alignment explanation
Indices: 16526--16592 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
16516 CGTCCTTTAC
16526 ACAAAAAAAAA
1 ACAAAAAAAAA
16537 AC-AAAAAAAA
1 ACAAAAAAAAA
16547 ACAAAACAAAAA
1 ACAAAA-AAAAA
16559 A-AAATGAAAAAA
1 ACAAA--AAAAAA
*
16571 CCAAGAAAAAATA
1 ACAA-AAAAAA-A
*
16584 GCAAAAAAA
1 ACAAAAAAA
16593 GAGAAAAGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 10 0.21
11 8 0.17
12 21 0.45
13 7 0.15
14 1 0.02
ACGTcount: A:0.82, C:0.10, G:0.04, T:0.03
Consensus pattern (11 bp):
ACAAAAAAAAA
Found at i:16552 original size:15 final size:14
Alignment explanation
Indices: 16528--16562 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
16518 TCCTTTACAC
16528 AAAAAAAAAACAAA
1 AAAAAAAAAACAAA
16542 AAAAAACAAAACAAA
1 AAAAAA-AAAACAAA
16557 AAAAAA
1 AAAAAA
16563 TGAAAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAACAAA
Found at i:17942 original size:28 final size:27
Alignment explanation
Indices: 17813--19002 Score: 1398
Period size: 28 Copynumber: 42.2 Consensus size: 27
17803 AATGTTCATC
**
17813 CCTTTCAAAGCCCATGAGTCAGTGGCA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
*
17840 CCATTTTCAAAGCCCACATGTCAGTGGCA
1 CC--TTTCAAAGCCCACAAGTCAGTGGCA
*
17869 CTCTTTTCAAAACCCACAAGTCAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
*
17898 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
17927 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
17955 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
17983 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
**
18011 CTCTTTCAAAGCCCATGAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* *
18039 CTATTTTCAAAGCCCACATGTCAGTGGCA
1 C--CTTTCAAAGCCCACAAGTCAGTGGCA
*
18068 CCCTTTTCAAAACCCACAAGTCAGTGGCA
1 -CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
18097 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
*
18126 TCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
18154 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
18182 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
18210 CTCTTTCAAAGCCCACAAGTCAGTGGTA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
18238 CCTTTTC-AAGCTCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
18265 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
18293 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
18320 CTCTTTTCAAAGCCCACAAGTTAGTGGCA
1 C-C-TTTCAAAGCCCACAAGTCAGTGGCA
18349 TCCTTTCAAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
18377 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
18405 TCCTTTCAAAGCCCACAAGTCAATGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
18433 CTCTTTCAAAGCCCACAAGTTAGTGGTA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
18461 CCTTTTC-AAGCCCACAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
18488 CTCTTTCAAAGCCCACAAGTTAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
18516 TCCTTTCAAAGCCCACAAGTAAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
18544 CTCTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
** *
18572 CCTTTTTAAGCCCACAAGTCAGTGGTA
1 CCTTTCAAAGCCCACAAGTCAGTGGCA
*
18599 CCTTTTC-AAGCCCATAAGTCAGTGGCA
1 CC-TTTCAAAGCCCACAAGTCAGTGGCA
*
18626 CTGTTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
* * *
18654 TCTTTTCAAAGCCCACGAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
**
18682 CCCTTTTGAAGCCCACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * *
18710 CCCTTGCGAAGCCCATAATTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
18738 CTATTTCAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
18766 CCCTTTCAAAGCCCACACAAGTCAGTGGCA
1 -CCTTTCAAAG-CC-CACAAGTCAGTGGCA
* *
18796 CTCCTTTTAGAGCCCACAAGTCAGTGGCA
1 --CCTTTCAAAGCCCACAAGTCAGTGGCA
* *
18825 CCCTTTCGAAGCCTACAAGTCAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
18853 CCCTTGCGAAGCCTACAATTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
*
18881 CTCTTTTAAAGCCCACAAGTCAGTGGCA
1 C-CTTTCAAAGCCCACAAGTCAGTGGCA
*
18909 CCCTTTCAAAGCCCACAAGTTAGTGGCA
1 -CCTTTCAAAGCCCACAAGTCAGTGGCA
* **
18937 CCCTTTTAAAGCCCACGCAAGTCAGTAACA
1 -CCTTTCAAAGCCCA--CAAGTCAGTGGCA
*
18967 CTCTTTTCAAAGCCCACACGTGTCAGTGGCA
1 C-C-TTTCAAAGCCCACA--AGTCAGTGGCA
*
18998 ACTTT
1 CCTTT
19003 TTTCGAAGCC
Statistics
Matches: 1025, Mismatches: 91, Indels: 92
0.85 0.08 0.08
Matches are distributed among these distances:
27 129 0.13
28 639 0.62
29 196 0.19
30 34 0.03
31 27 0.03
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (27 bp):
CCTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:19624 original size:20 final size:20
Alignment explanation
Indices: 19596--19670 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
19586 TTTTACCTAG
19596 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
19616 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* *
19636 ATGTATCGATATATTCTTCA
1 ATGTATCGATACATTTTTCA
19656 ATGTATCGATACATT
1 ATGTATCGATACATT
19671 ATGTCTTTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:19656 original size:40 final size:39
Alignment explanation
Indices: 19596--19673 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
19586 TTTTACCTAG
*
19596 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTTCAATATATCGATACAT-TATGA
* *
19636 ATGTATCGATATATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATACATTCTTCAATATATCGATACATTATG
19674 TCTTTTTACC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTTCAATATATCGATACATTATGA
Found at i:20606 original size:22 final size:22
Alignment explanation
Indices: 20580--20630 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
20570 AGCCTTTGAC
20580 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
20602 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
20624 CATGCAT
1 CATGCAT
20631 CTTTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:23230 original size:15 final size:15
Alignment explanation
Indices: 23209--23252 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
23199 AAATAAAAAA
23209 AATGAAAAGAGAGAAG
1 AATGAAAAGAGA-AAG
*
23225 AA-GAAAAAAGAAAG
1 AATGAAAAGAGAAAG
*
23239 AATGAAAAGGGAAA
1 AATGAAAAGAGAAA
23253 AGAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.21
15 17 0.71
16 2 0.08
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (15 bp):
AATGAAAAGAGAAAG
Found at i:23365 original size:17 final size:16
Alignment explanation
Indices: 23345--23406 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
23335 TTAAATTTCT
23345 TTTTTTAAAAAATTTAA
1 TTTTTTAAAAAA-TTAA
* *
23362 TTTTGTTAGAAAATAAA
1 TTTT-TTAAAAAATTAA
**
23379 TTATTTTTTAAAATTAA
1 TT-TTTTAAAAAATTAA
*
23396 TTTTTCAAAAA
1 TTTTTTAAAAA
23407 TATTTTATTG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
16 6 0.17
17 20 0.57
18 9 0.26
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTTTAAAAAATTAA
Found at i:23365 original size:18 final size:17
Alignment explanation
Indices: 23344--23400 Score: 53
Period size: 18 Copynumber: 3.3 Consensus size: 17
23334 ATTAAATTTC
23344 TTTTTTTAAAAAATTTAA
1 TTTTTTTAAAAAA-TTAA
* * *
23362 TTTTGTTAGAAAATAAA
1 TTTTTTTAAAAAATTAA
*
23379 TTATTTTT-TAAAATTAA
1 TT-TTTTTAAAAAATTAA
23396 TTTTT
1 TTTTT
23401 CAAAAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 3 0.09
17 14 0.44
18 15 0.47
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTTTTAAAAAATTAA
Found at i:24884 original size:20 final size:21
Alignment explanation
Indices: 24842--24889 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24832 ATTCAAACAA
*
24842 AAATGATTTAAATATTAAAAT
1 AAATAATTTAAATATTAAAAT
*
24863 AAATAATTTTAATATT-AAAT
1 AAATAATTTAAATATTAAAAT
*
24883 AAGTAAT
1 AAATAAT
24890 AAATATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATAATTTAAATATTAAAAT
Found at i:24899 original size:16 final size:16
Alignment explanation
Indices: 24880--24910 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24870 TTTAATATTA
*
24880 AATAAGTAATAAATAT
1 AATAAATAATAAATAT
24896 AATAAATAATAAATA
1 AATAAATAATAAATA
24911 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AATAAATAATAAATAT
Found at i:25990 original size:64 final size:64
Alignment explanation
Indices: 25884--26009 Score: 234
Period size: 64 Copynumber: 2.0 Consensus size: 64
25874 TGTTTGTATG
* *
25884 AAACTTATAGCTGTGGCTTGGATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
1 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
25948 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTT
1 AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTT
26010 TATAAAGTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.31
Consensus pattern (64 bp):
AAACATATAGCTGTGGCTTGAATATCAGCTAAGGAAATAAAATATTAACAGTGTTAATAGTTAC
Found at i:29518 original size:20 final size:19
Alignment explanation
Indices: 29489--29549 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 19
29479 GTTTTAAAAA
29489 AATTTAAATATAAATTAAAT
1 AATTTAAATATAAA-TAAAT
* *
29509 AATTTTAATATCAATAAAT
1 AATTTAAATATAAATAAAT
*
29528 -A-TTAAATAT-AGTAAAT
1 AATTTAAATATAAATAAAT
29544 -ATTTAA
1 AATTTAA
29550 CAAAATTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 7 0.19
17 11 0.31
18 1 0.03
19 5 0.14
20 12 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTTAAATATAAATAAAT
Found at i:29809 original size:2 final size:2
Alignment explanation
Indices: 29802--29828 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29792 AACTTTGGTG
29802 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
29829 TAAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30610 original size:12 final size:12
Alignment explanation
Indices: 30571--30613 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
30561 TTCCTGTGCT
*
30571 TATTTTTTTTCA
1 TATTTTTTTTTA
*
30583 TATTTAATTATTTA
1 TATTT--TTTTTTA
30597 TATTTTTTTTTA
1 TATTTTTTTTTA
30609 TATTT
1 TATTT
30614 CACCCACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.62
14 10 0.38
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (12 bp):
TATTTTTTTTTA
Found at i:32760 original size:80 final size:79
Alignment explanation
Indices: 32585--32873 Score: 307
Period size: 79 Copynumber: 3.6 Consensus size: 79
32575 TCTCTTGGAG
* * * * *
32585 ATAACGGGGTTGGAGTATCCCCGATGGTGGAAAATCAATGTTTTAGAAATAAAATCGAGGTTGGA
1 ATAACGGGGTTGGAGTATTCCCAATGGTAGAAAATCAATATTTTAGAAATAAAAACGAGGTTGGA
*
32650 GTATCCTCTCGAAA
66 GTATCCCCTCGAAA
* * * *
32664 ATAACGGGGTTGGAGTATTCCCAATGGT-GAAATATCAATATTTTAGAAAAAAAAAAGGAAGCTG
1 ATAACGGGGTTGGAGTATTCCCAATGGTAGAAA-ATCAATATTTTAG-AAATAAAAACGAGGTTG
*
32728 GAGTGTCCCCTCGAAA
64 GAGTATCCCCTCGAAA
* * *
32744 ATAATGGGGTTGGAGTA-TCCTCAATTGT-GAAAAATCAGTATTTTAGAAAT-AAAACTGAGGTT
1 ATAACGGGGTTGGAGTATTCC-CAATGGTAG-AAAATCAATATTTTAGAAATAAAAAC-GAGGTT
*
32806 GGAGTATCCCTTCGAAA
63 GGAGTATCCCCTCGAAA
* * * * * * *
32823 ATAATGGGATTAGAGTATTCTCGATGGTAGAAAATCGATGTTTTAGAAATA
1 ATAACGGGGTTGGAGTATTCCCAATGGTAGAAAATCAATATTTTAGAAATA
32874 TGTCGTAATG
Statistics
Matches: 175, Mismatches: 27, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
78 8 0.05
79 100 0.57
80 64 0.37
81 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
ATAACGGGGTTGGAGTATTCCCAATGGTAGAAAATCAATATTTTAGAAATAAAAACGAGGTTGGA
GTATCCCCTCGAAA
Found at i:36192 original size:14 final size:15
Alignment explanation
Indices: 36175--36207 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
36165 TTATTTTTTA
*
36175 TTTTGATTTTA-GAT
1 TTTTGATTTGATGAT
36189 TTTTGATTTGATGAT
1 TTTTGATTTGATGAT
36204 TTTT
1 TTTT
36208 TTATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (15 bp):
TTTTGATTTGATGAT
Found at i:36209 original size:25 final size:25
Alignment explanation
Indices: 36181--36234 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
36171 TTTATTTTGA
*
36181 TTTTAGATTTTTGATTTGA-TGATTT
1 TTTTAGATTTTTGA-TTCATTGATTT
**
36206 TTTTATTTTTTTGATTCATTGATTT
1 TTTTAGATTTTTGATTCATTGATTT
36231 TTTT
1 TTTT
36235 TTGAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.17, C:0.02, G:0.11, T:0.70
Consensus pattern (25 bp):
TTTTAGATTTTTGATTCATTGATTT
Found at i:37408 original size:52 final size:52
Alignment explanation
Indices: 37325--37429 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
37315 GATGAGAAAA
* * **
37325 ATGATACAGGTACCAATATACTAATTCAAGGCCAGCGATATTGGACTTAAAG
1 ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
* * *
37377 ATGATAAAGGTGCCAATATACTGATTTAAGGCCAGCAATATCAGACTTAAAG
1 ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
37429 A
1 A
37430 AAAAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (52 bp):
ATGATAAAGGTACCAATATACTAATTCAAGGCCAGCAATATCAGACTTAAAG
Found at i:37513 original size:30 final size:31
Alignment explanation
Indices: 37477--37536 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
37467 CTAACGACAT
* * *
37477 TGGGC-TTAGAAGGATTGCCATTGACTTGTA
1 TGGGCTTTAAAAGGATTGCAATCGACTTGTA
*
37507 TGGGCTTTAAAAGGGTTGCAATCGACTTGT
1 TGGGCTTTAAAAGGATTGCAATCGACTTGT
37537 CTTTAAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (31 bp):
TGGGCTTTAAAAGGATTGCAATCGACTTGTA
Found at i:37710 original size:86 final size:86
Alignment explanation
Indices: 37598--38697 Score: 459
Period size: 86 Copynumber: 12.9 Consensus size: 86
37588 ACTTACATGA
* * * ** *
37598 GCTTTTGAAAGGGTTGCCACTG-ACTTGTGGGCTTTCCAAAGGGTGCCACCGACTTGTAAGCTAT
1 GCTTTTGAAA-GGATGCCACTGAACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTT
* *
37662 GAAAGGATGCCATTGA-TTCGTGG
64 GAAAGGGTGCCACTGACTT-GTGG
* * * *
37685 GC-TTTGAAAGGATGCAATTGAACTTGTGGGCTTTAAAAGGGTGCCACTGGCTCGTGGGCTTTGA
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-
37749 AAAGGGTGCCACTGACTTGTGG
65 AAAGGGTGCCACTGACTTGTGG
* * * *
37771 GCTTTTAAAAGGGTGCCACT-AACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTA
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGCTTT-AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
37835 AAAGGGTGCCACTAACTTGTAG
65 AAAGGGTGCCACTGACTTGTGG
* * * ** *
37857 GCTTTTGAAAGGATGCCACTG-ACTTGTGGGCTTTTAAAATGATGCCATTGA-GAG-GGATGCCA
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGC-TTTAAAAGGGTGCCACTGACTTGTGG--G-CT
* * ** ** **
37919 CTGACTCATGGGCTTTGAAAGGGA--TGCCACCG
62 TTGA---AAGGG---TGCCACTGACTTG---TGG
* ** ** ** * * * * * *
37951 ACTCGTG--AGCTTTGAAAAGTGCCAC-TGACTTATGGCTTTAAAAGGGTGACACTAACTTGGGG
1 GCTTTTGAAAG-GATG-CCACTG-AACTTG---T-GGGCTTTAAAAGGGTGCCACTGACTTGTGG
* * *
38013 GCTTT-AAAAGGTGCCACTAATTTGTGG
59 GCTTTGAAAGGGTGCCACTGACTTGTGG
** * * * * ** *
38040 GCTTTAAAAAGG-TGTCACTG-ACTTATGGGCTTTTGAAA--G-G--ATTGA-AAG-GATGC--T
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGC-TTTAAAAGGGTGCCACTGACTTGTG-GGCTTT
* * * *
38094 AAAAAGGTGTCATTGACTTGTGG
64 GAAAGGGTGCCACTGACTTGTGG
* * * **
38117 GCTTTTGAAAGGGTGCAACT-AACTTGTAGGCTTTAAAAGGGTATCACTGACTTGTGGGCTTTGA
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG-
* *
38181 AAAGGGTGCCACTGGCTTATGG
65 AAAGGGTGCCACTGACTTGTGG
* * * * *
38203 GC-TTTGAAAATGG-TTCCATTG-ACTTGTGGGCATTTGAAAGGATACCACTGACTTGTGGGCTT
1 GCTTTTG-AAA-GGATGCCACTGAACTTGTGGGC-TTTAAAAGGGTGCCACTGACTTGTGGGCTT
* ** *
38265 TAAAAGGGTATCACTCACTTGTGG
63 TGAAAGGGTGCCACTGACTTGTGG
* * * *
38289 GCTTTAT-AAATGG-TGCCACT-AACTTATGGGCTTTTGAAATGGTGCTACTGACTTGTGGGCTT
1 GCTTT-TGAAA-GGATGCCACTGAACTTGTGGGC-TTTAAAAGGGTGCCACTGACTTGTGGGCTT
* * * *
38351 TAAAAGGGTGTCACTCATTTGTGG
63 TGAAAGGGTGCCACTGACTTGTGG
* * *
38375 GC-TTTGAAAAGGGTGCCACTG-ACTTGT-GGCATTTGATAAGGATGCCACTGACTTGTGGGCTT
1 GCTTTTG-AAAGGATGCCACTGAACTTGTGGGC-TTT-AAAAGGGTGCCACTGACTTGTGGGCTT
* * *
38437 TGAAAGGATGCCACTGATTTATGG
63 TGAAAGGGTGCCACTGACTTGTGG
* * * * *
38461 GC-TTTGAAAGGATACCACTG-ACTCGTGGGCTTTTGAAAGGGTGCCACTGACTCGTGGACTTTT
1 GCTTTTGAAAGGATGCCACTGAACTTGTGGGC-TTTAAAAGGGTGCCACTGACTTGTGGGC-TTT
* * * *
38524 GAAATGATGCCACTAACTCGTGG
64 GAAAGGGTGCCACTGACTTGTGG
** * *
38547 GC-TTTGAAAGGGATGCCACTG-ACTCATGGGCTTTGAAAGGGATGCCACCGACTTGTGGGCTTT
1 GCTTTTGAAA-GGATGCCACTGAACTTGTGGGCTTTAAAAGGG-TGCCACTGACTTGTGGGC-TT
*
38610 TG-AA---TG-----G-CTCGTGG
63 TGAAAGGGTGCCACTGACTTGTGG
* * * *
38624 GC-TTTGAAA-AAGTGCCACTG-ACTTGTGAGCTTTAAAA-GGTGCCATTGACTTGTGGACTTTG
1 GCTTTTGAAAGGA-TGCCACTGAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTG
*
38685 AAAGGATGCCACT
65 AAAGGGTGCCACT
38698 AACTCATGAG
Statistics
Matches: 768, Mismatches: 170, Indels: 155
0.70 0.16 0.14
Matches are distributed among these distances:
73 4 0.01
74 17 0.02
75 3 0.00
76 22 0.03
77 53 0.07
78 16 0.02
79 4 0.01
81 1 0.00
82 5 0.01
83 8 0.01
84 11 0.01
85 82 0.11
86 351 0.46
87 120 0.16
88 4 0.01
89 5 0.01
90 8 0.01
91 4 0.01
92 4 0.01
93 9 0.01
94 8 0.01
95 2 0.00
96 3 0.00
97 2 0.00
98 16 0.02
99 4 0.01
100 2 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (86 bp):
GCTTTTGAAAGGATGCCACTGAACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGA
AAGGGTGCCACTGACTTGTGG
Found at i:37767 original size:57 final size:56
Alignment explanation
Indices: 37605--38697 Score: 755
Period size: 57 Copynumber: 19.7 Consensus size: 56
37595 TGAGCTTTTG
* * ** * *
37605 AAAGGGTTGCCACTGACTTGTGGGCTTTCCAAAGGGTGCCACCGACTTGTAAGCTATG
1 AAAGGG-TGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGCTTTA
* * * * *
37663 AAAGGATGCCATTGA-TTCGTGGGCTTTGAAAGGATGCAATTGAACTTGTGGGCTTTA
1 AAAGGGTGCCACTGACTT-GTGGGCTTTGAAAGGGTGCCACTG-ACTTGTGGGCTTTA
* *
37720 AAAGGGTGCCACTGGCTCGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGC-TTTA
* *
37778 AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGGTGCCACTGACTTATGGGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTA
* * *
37835 AAAGGGTGCCACTAACTTGTAGGCTTTTGAAAGGATGCCACTGACTTGTGGGCTTTTA
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTGGGC-TTTA
* * * * * ** * * ** *
37893 AAATGATGCCATTGA---GAGGG--ATGCCA--CTG--ACT--CATG-GGCTTTGA
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
* * * * * * *
37937 AAGGGATGCCACCGACTCGTGAGCTTTGAAA-AGTGCCACTGACTTAT-GGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
* * * * * *
37991 AAAGGGTGACACTAACTTGGGGGCTTT-AAAAGGTGCCACTAATTTGTGGGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
* * * * ** *
38046 AAAAGGTGTCACTGACTTATGGGCTTTTGAAA--G-G--ATTGA-AAG-GATGC--TA
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTG-GGCTTTA
* * * * * *
38095 AAAAGGTGTCATTGACTTGTGGGCTTTTGAAAGGGTGCAACTAACTTGTAGGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
** * *
38152 AAAGGGTATCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGGCTTATGGGCTTTGA
1 AAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTT-A
* * * * *
38210 AAATGGTTCCATTGACTTGTGGGCATTTGAAAGGATACCACTGACTTGTGGGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
** * * * * * *
38267 AAAGGGTATCACTCACTTGTGGGCTTTATAAATGGTGCCACTAACTTATGGGCTTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGGTGCCACTGACTTGTGGGC-TTTA
* * * * * *
38325 AAATGGTGCTACTGACTTGTGGGCTTTAAAAGGGTGTCACTCATTTGTGGGCTTTGA
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTT-A
* *
38382 AAAGGGTGCCACTGACTTGT-GGCATTTGATAAGGATGCCACTGACTTGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGA-AAGGGTGCCACTGACTTGTGGGCTTTA
* * * * * * *
38439 AAAGGATGCCACTGATTTATGGGCTTTGAAAGGATACCACTGACTCGTGGGCTTTTG
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC-TTTA
* * * * * * *
38496 AAAGGGTGCCACTGACTCGTGGACTTTTGAAATGATGCCACTAACTCGTGGGCTTTG
1 AAAGGGTGCCACTGACTTGTGGGC-TTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
** *
38553 AAAGGGATGCCACTGACTCATGGGCTTTGAAAGGGATGCCACCGACTTGTGGGCTTT-
1 AAAGGG-TGCCACTGACTTGTGGGCTTTGAAAGGG-TGCCACTGACTTGTGGGCTTTA
* * * ** *
38610 ------TG--AATGGCTCGTGGGCTTTGAAAAAGTGCCACTGACTTGTGAGCTTTA
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
* * *
38658 AAA-GGTGCCATTGACTTGTGGACTTTGAAAGGATGCCACT
1 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACT
38698 AACTCATGAG
Statistics
Matches: 816, Mismatches: 166, Indels: 109
0.75 0.15 0.10
Matches are distributed among these distances:
44 14 0.02
45 2 0.00
46 3 0.00
47 22 0.03
48 22 0.03
49 35 0.04
50 7 0.01
51 4 0.00
52 10 0.01
53 5 0.01
54 41 0.05
55 57 0.07
56 49 0.06
57 299 0.37
58 242 0.30
59 4 0.00
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (56 bp):
AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTA
Found at i:37903 original size:29 final size:29
Alignment explanation
Indices: 37598--37895 Score: 318
Period size: 29 Copynumber: 10.3 Consensus size: 29
37588 ACTTACATGA
*
37598 GCTTTTGAAAGGGTTGCCACTGACTTGTGG
1 GCTTTTAAAAGGG-TGCCACTGACTTGTGG
** * **
37628 GCTTTCCAAAGGGTGCCACCGACTTGTAA
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* * * *
37657 GC-TATGAAAGGATGCCATTGA-TTCGTGG
1 GCTTTTAAAAGGGTGCCACTGACTT-GTGG
* * * *
37685 GC-TTTGAAAGGATGCAATTGAACTTGTGG
1 GCTTTTAAAAGGGTGCCACTG-ACTTGTGG
* *
37714 GC-TTTAAAAGGGTGCCACTGGCTCGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
*
37742 GCTTTGAAAAGGGTGCCACTGACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
*
37771 GCTTTTAAAAGGGTGCCACTAACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* *
37800 GCTTTGAAAAGGGTGCCACTGACTTATGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* *
37829 GC-TTTAAAAGGGTGCCACTAACTTGTAG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
* *
37857 GCTTTTGAAAGGATGCCACTGACTTGTGG
1 GCTTTTAAAAGGGTGCCACTGACTTGTGG
37886 GCTTTTAAAA
1 GCTTTTAAAA
37896 TGATGCCATT
Statistics
Matches: 225, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
27 2 0.01
28 65 0.29
29 145 0.64
30 13 0.06
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (29 bp):
GCTTTTAAAAGGGTGCCACTGACTTGTGG
Found at i:37946 original size:29 final size:28
Alignment explanation
Indices: 37904--38609 Score: 450
Period size: 29 Copynumber: 25.1 Consensus size: 28
37894 AATGATGCCA
* *
37904 TTGAGAGGGATGCCACTGACTCATGGGCT
1 TTGAAAGGG-TGCCACTGACTTATGGGCT
* ** *
37933 TTGAAAGGGATGCCACCGACTCGTGAGCT
1 TTGAAAGGG-TGCCACTGACTTATGGGCT
*
37962 TTGAAA-AGTGCCACTGACTTAT-GGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * * **
37988 TTAAAAGGGTGACACTAACTTGGGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * * *
38016 TT-AAAAGGTGCCACTAATTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * *
38043 TTAAAAAGGTGTCACTGACTTATGGGCTT
1 TTGAAAGGGTGCCACTGACTTATGGGC-T
* *
38072 TTGAAA--G-G--ATTGA---AAGGATGC-
1 TTGAAAGGGTGCCACTGACTTATGG--GCT
* * * * *
38093 -TAAAAAGGTGTCATTGACTTGTGGGCTT
1 TTGAAAGGGTGCCACTGACTTATGGGC-T
* * * *
38121 TTGAAAGGGTGCAACTAACTTGTAGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* ** *
38149 TTAAAAGGGTATCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
*
38177 TTGAAAAGGGTGCCACTGGCTTATGGGCT
1 TTG-AAAGGGTGCCACTGACTTATGGGCT
* * * *
38206 TTGAAAATGGTTCCATTGACTTGTGGGCAT
1 TTG-AAAGGGTGCCACTGACTTATGGGC-T
* * *
38236 TTGAAAGGATACCACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* ** * *
38264 TTAAAAGGGTATCACTCACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * *
38292 TTATAAATGGTGCCACTAACTTATGGGCTT
1 TT-GAAAGGGTGCCACTGACTTATGGGC-T
* * *
38322 TTGAAATGGTGCTACTGACTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * * * *
38350 TTAAAAGGGTGTCACTCATTTGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
*
38378 TTGAAAAGGGTGCCACTGACTTGT-GGCAT
1 TTG-AAAGGGTGCCACTGACTTATGGGC-T
* *
38407 TTGATAAGGATGCCACTGACTTGTGGGCT
1 TTGA-AAGGGTGCCACTGACTTATGGGCT
* *
38436 TTGAAAGGATGCCACTGATTTATGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
* * **
38464 TTGAAAGGATACCACTGACTCGTGGGCTT
1 TTGAAAGGGTGCCACTGACTTATGGGC-T
** *
38493 TTGAAAGGGTGCCACTGACTCGTGGACTT
1 TTGAAAGGGTGCCACTGACTTATGGGC-T
* * * **
38522 TTGAAATGATGCCACTAACTCGTGGGCT
1 TTGAAAGGGTGCCACTGACTTATGGGCT
*
38550 TTGAAAGGGATGCCACTGACTCATGGGCT
1 TTGAAAGGG-TGCCACTGACTTATGGGCT
* *
38579 TTGAAAGGGATGCCACCGACTTGTGGGCT
1 TTGAAAGGG-TGCCACTGACTTATGGGCT
38608 TT
1 TT
38610 TGAATGGCTC
Statistics
Matches: 549, Mismatches: 101, Indels: 54
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.01
21 3 0.01
22 1 0.00
23 3 0.01
24 4 0.01
25 5 0.01
26 11 0.02
27 46 0.08
28 163 0.30
29 299 0.54
30 10 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (28 bp):
TTGAAAGGGTGCCACTGACTTATGGGCT
Found at i:38656 original size:76 final size:75
Alignment explanation
Indices: 38540--38683 Score: 182
Period size: 74 Copynumber: 1.9 Consensus size: 75
38530 ATGCCACTAA
** * *
38540 CTCGTGGGCTTTGAAAGGGATGCCACTGACTCATGGGCTTTGAAAGGGATGCCACCGACTTGTGG
1 CTCGTGGGCTTTGAAAAAGATGCCACTGACTCATGAGCTTT-AAAAGG-TGCCACCGACTTGTGG
*
38605 GCTTTTGAATGG
64 ACTTTTGAATGG
** **
38617 CTCGTGGGCTTTGAAAAAG-TGCCACTGACTTGTGAGCTTTAAAAGGTGCCATTGACTTGTGGAC
1 CTCGTGGGCTTTGAAAAAGATGCCACTGACTCATGAGCTTTAAAAGGTGCCACCGACTTGTGGAC
38681 TTT
66 TTT
38684 GAAAGGATGC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
74 18 0.31
75 5 0.09
76 18 0.31
77 17 0.29
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.30
Consensus pattern (75 bp):
CTCGTGGGCTTTGAAAAAGATGCCACTGACTCATGAGCTTTAAAAGGTGCCACCGACTTGTGGAC
TTTTGAATGG
Found at i:38665 original size:27 final size:28
Alignment explanation
Indices: 38624--38718 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 28
38614 TGGCTCGTGG
*
38624 GCTTTGAAAAAGTGCCACTGACTTGTGA
1 GCTTTGAAAAGGTGCCACTGACTTGTGA
*
38652 GCTTT-AAAAGGTGCCATTGACTTGTG-
1 GCTTTGAAAAGGTGCCACTGACTTGTGA
* **
38678 GACTTTG-AAAGGATGCCACTAACTCATGA
1 G-CTTTGAAAAGG-TGCCACTGACTTGTGA
38707 GCTTTGAAAAGG
1 GCTTTGAAAAGG
38719 AAAAAGATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
26 1 0.02
27 28 0.50
28 21 0.38
29 6 0.11
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Consensus pattern (28 bp):
GCTTTGAAAAGGTGCCACTGACTTGTGA
Found at i:39912 original size:22 final size:23
Alignment explanation
Indices: 39866--39955 Score: 88
Period size: 22 Copynumber: 4.2 Consensus size: 23
39856 CATGTCCTTG
*
39866 TTTTTTGATTTTG-TTGTT-C-CC
1 TTTTTTGATTTTGCTT-TTGCACT
39887 TTTTTT-ATTTTGCTTTTGCACT
1 TTTTTTGATTTTGCTTTTGCACT
39909 TTTTTTGATTTT-CTTTT-CA-T
1 TTTTTTGATTTTGCTTTTGCACT
*
39929 TTTTTATGCTTTTGCTTTTG-ACT
1 TTTTT-TGATTTTGCTTTTGCACT
39952 TTTT
1 TTTT
39956 CGTAATTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 14
0.79 0.03 0.19
Matches are distributed among these distances:
20 14 0.24
21 17 0.29
22 18 0.31
23 10 0.17
ACGTcount: A:0.08, C:0.12, G:0.10, T:0.70
Consensus pattern (23 bp):
TTTTTTGATTTTGCTTTTGCACT
Found at i:39914 original size:43 final size:41
Alignment explanation
Indices: 39866--39955 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 41
39856 CATGTCCTTG
* *
39866 TTTTTTGATTTTGTTGTTCCCTTTTTTA-TTTTGCTTTTGCACT
1 TTTTTTGATTTTCTT-TT-CATTTTTTACTTTTGCTTTTG-ACT
39909 TTTTTTGATTTTCTTTTCATTTTTTATGCTTTTGCTTTTGACT
1 TTTTTTGATTTTCTTTTCATTTTTTA--CTTTTGCTTTTGACT
39952 TTTT
1 TTTT
39956 CGTAATTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
41 8 0.19
42 2 0.05
43 21 0.50
44 11 0.26
ACGTcount: A:0.08, C:0.12, G:0.10, T:0.70
Consensus pattern (41 bp):
TTTTTTGATTTTCTTTTCATTTTTTACTTTTGCTTTTGACT
Found at i:45213 original size:14 final size:15
Alignment explanation
Indices: 45194--45226 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
45184 TTATTTTTTA
*
45194 TTTTGATTTTA-GAT
1 TTTTGATTTGATGAT
45208 TTTTGATTTGATGAT
1 TTTTGATTTGATGAT
45223 TTTT
1 TTTT
45227 TTTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.67
Consensus pattern (15 bp):
TTTTGATTTGATGAT
Found at i:48783 original size:11 final size:11
Alignment explanation
Indices: 48745--48785 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
48735 AAATTTAGGT
48745 AAAAAAGAAAG
1 AAAAAAGAAAG
*
48756 AAAGAAGATGAAG
1 AAAAAAGA--AAG
48769 AAAAAAGAAAG
1 AAAAAAGAAAG
48780 AAAAAA
1 AAAAAA
48786 AATATGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:49181 original size:2 final size:2
Alignment explanation
Indices: 49168--49200 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49158 TTATTTTATT
*
49168 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49201 TTTGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Done.