Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2702
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: 121506
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2004 original size:21 final size:21
Alignment explanation
Indices: 1975--2019 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1965 AAGTTTTTAT
*
1975 TTTTCTTAG-CTAACTCATTA
1 TTTTCTTAGCCAAACTCATTA
*
1995 TTTTCATTAGCCAAATTCATTA
1 TTTTC-TTAGCCAAACTCATTA
2017 TTT
1 TTT
2020 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCTTAGCCAAACTCATTA
Found at i:4254 original size:20 final size:20
Alignment explanation
Indices: 4229--4280 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
4219 TACAAGCCAA
**
4229 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
4249 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
4268 TGTATCGATACAA
1 TGTATCGATACAA
4281 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:6287 original size:13 final size:13
Alignment explanation
Indices: 6269--6294 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6259 ACAATATTCC
6269 TTGTATCGATACA
1 TTGTATCGATACA
6282 TTGTATCGATACA
1 TTGTATCGATACA
6295 GTGGGTACTA
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):
TTGTATCGATACA
Found at i:6460 original size:20 final size:22
Alignment explanation
Indices: 6416--6462 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
6406 AATTTTCCAC
6416 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
6438 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
6458 AAATC
1 AAATC
6463 ATCAACAGAA
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:7478 original size:13 final size:13
Alignment explanation
Indices: 7460--7485 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7450 TACACCAAGT
7460 ATGTATCGATACA
1 ATGTATCGATACA
7473 ATGTATCGATACA
1 ATGTATCGATACA
7486 CAAAAAATTG
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:8006 original size:34 final size:35
Alignment explanation
Indices: 7943--8009 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
7933 CTAAGTGATT
7943 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
7979 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
8010 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:11230 original size:13 final size:13
Alignment explanation
Indices: 11212--11236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11202 TTTTCCAGAT
11212 TGTATCGATACAA
1 TGTATCGATACAA
11225 TGTATCGATACA
1 TGTATCGATACA
11237 TTGCTTCAGT
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:13036 original size:13 final size:13
Alignment explanation
Indices: 13018--13043 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
13008 TACACCAAGT
13018 ATGTATCGATACA
1 ATGTATCGATACA
13031 ATGTATCGATACA
1 ATGTATCGATACA
13044 CAAAAAATTG
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:13041 original size:32 final size:33
Alignment explanation
Indices: 13000--13063 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
12990 TAGCCAAACT
* **
13000 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
13032 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
13064 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:13564 original size:34 final size:35
Alignment explanation
Indices: 13501--13567 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
13491 CTAAGTGATT
13501 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
13537 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
13568 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:15538 original size:20 final size:20
Alignment explanation
Indices: 15497--15550 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
15487 ACATTCTGCT
*
15497 TTGTATCGATACAT-GTTAA
1 TTGTATCGATACATGGATAA
*
15516 TTGTATTGATACATGGATAA
1 TTGTATCGATACATGGATAA
15536 TTGTATCGATACATG
1 TTGTATCGATACATG
15551 AGATTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATGGATAA
Found at i:18750 original size:18 final size:18
Alignment explanation
Indices: 18727--18787 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 18
18717 TCTTTTTGGC
18727 AGCAAACAAAGTTTCAGT
1 AGCAAACAAAGTTTCAGT
* * *
18745 AGCAAAAAAACCCTTT-GGT
1 AGCAAACAAA--GTTTCAGT
* *
18764 AGAAAACAAAGTTTCAGC
1 AGCAAACAAAGTTTCAGT
18782 AGCAAA
1 AGCAAA
18788 AAAATCCTTC
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
17 3 0.10
18 15 0.48
19 10 0.32
20 3 0.10
ACGTcount: A:0.48, C:0.18, G:0.16, T:0.18
Consensus pattern (18 bp):
AGCAAACAAAGTTTCAGT
Found at i:18771 original size:37 final size:37
Alignment explanation
Indices: 18721--18796 Score: 116
Period size: 37 Copynumber: 2.1 Consensus size: 37
18711 AGAGGATCTT
* *
18721 TTTGGCAGCAAACAAAGTTTCAGTAGCAAAAAAACCC
1 TTTGGCAGAAAACAAAGTTTCAGCAGCAAAAAAACCC
* *
18758 TTTGGTAGAAAACAAAGTTTCAGCAGCAAAAAAATCC
1 TTTGGCAGAAAACAAAGTTTCAGCAGCAAAAAAACCC
18795 TT
1 TT
18797 CGAGAATCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.22
Consensus pattern (37 bp):
TTTGGCAGAAAACAAAGTTTCAGCAGCAAAAAAACCC
Found at i:20977 original size:79 final size:78
Alignment explanation
Indices: 20710--20977 Score: 288
Period size: 80 Copynumber: 3.4 Consensus size: 78
20700 TAAAATGTCG
* * * *
20710 ATTTTCCACAATCGGGGATACTCTAACCCTGTTATTTTCGAGGGGTTACTCCAACCCTGGTTTTT
1 ATTTTCCACAATCGAGGATACTCCAACCCTGTTATTTT-GAGGGGATACTCCAACCCCGG-TTTT
* *
20775 ATTTTCAGAACA-TCG
64 ATTTTCAAAACACT-A
* * *
20790 ATTTTTCACAATCGAGGATACTCCAACCCTGTTAGTTTTGAGGGGATACTCCAACCTCGATTTT-
1 ATTTTCCACAATCGAGGATACTCCAACCCTGTTA-TTTTGAGGGGATACTCCAACCCCGGTTTTA
*
20854 TATTTCTAAAACACAA
65 T-TTTC-AAAACACTA
** * * **
20870 ATTTTTAACAATCGAGGATACTCCAACCCTATTATTTCTGAGGGAATACTTTAACCCCGGTTTTA
1 ATTTTCCACAATCGAGGATACTCCAACCCTGTTATTT-TGAGGGGATACTCCAACCCCGGTTTTA
20935 TTTTCAAAACACTA
65 TTTTCAAAACACTA
* * *
20949 ATTTTCCACCATCGGGGATACCCCAACCC
1 ATTTTCCACAATCGAGGATACTCCAACCC
20978 CGATTTTATT
Statistics
Matches: 159, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 43 0.27
80 110 0.69
81 5 0.03
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
ATTTTCCACAATCGAGGATACTCCAACCCTGTTATTTTGAGGGGATACTCCAACCCCGGTTTTAT
TTTCAAAACACTA
Found at i:21011 original size:130 final size:132
Alignment explanation
Indices: 20831--21097 Score: 321
Period size: 130 Copynumber: 2.0 Consensus size: 132
20821 TTAGTTTTGA
* * *
20831 GGGGATACTCCAACCTCGATTTTTATTTCTAAAACACAAATTTTTAACAATCGAGGATACTCCAA
1 GGGGATACCCCAACCCCGATTTTTATTTCTAAAACACAAATTTTTAACAATCGAGGATACTCAAA
* * *
20896 CCCTATTA-TTTCTGAG-GGAATACTTTAACCCC-GGTTTTATTTTCAAAACA-CTAATTTTCCA
66 CCCTATTATTTTC-GAGAGG-ATACTCTAACCCCAAGTTTTATTTCCAAAACATC-AATTTTCCA
20957 CCATC
128 CCATC
** * * *
20962 GGGGATACCCCAACCCCGA-TTTTATTTCTAGTACATC-GATTTTTCACAATCGGGGATACTCAA
1 GGGGATACCCCAACCCCGATTTTTATTTCTAAAACA-CAAATTTTTAACAATCGAGGATACTCAA
* * * *
21025 ACTCTGTTATTTTCGAGAGGATACTCTAACCCCAATTTTTATTTCCAAAACATCAATTTTCCATC
65 ACCCTATTATTTTCGAGAGGATACTCTAACCCCAAGTTTTATTTCCAAAACATCAATTTTCCACC
21090 ATC
130 ATC
21093 GGGGA
1 GGGGA
21098 ATGTACTCCA
Statistics
Matches: 116, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
130 58 0.50
131 57 0.49
132 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.34
Consensus pattern (132 bp):
GGGGATACCCCAACCCCGATTTTTATTTCTAAAACACAAATTTTTAACAATCGAGGATACTCAAA
CCCTATTATTTTCGAGAGGATACTCTAACCCCAAGTTTTATTTCCAAAACATCAATTTTCCACCA
TC
Found at i:26591 original size:19 final size:19
Alignment explanation
Indices: 26567--26622 Score: 94
Period size: 19 Copynumber: 2.9 Consensus size: 19
26557 TGTATTGATA
26567 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGTT
*
26586 CATTGTATCGATACATATT
1 CATTGTATCGATACATGTT
26605 CAATTGTATCGATACATG
1 C-ATTGTATCGATACATG
26623 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
CATTGTATCGATACATGTT
Found at i:26695 original size:20 final size:20
Alignment explanation
Indices: 26648--26696 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
26638 ACCCTAAGTG
26648 AAAAGTATCGATACATGAGA
1 AAAAGTATCGATACATGAGA
* **
26668 CATTGTATCGATACATG-GTA
1 AAAAGTATCGATACATGAG-A
26688 AAAAGTATC
1 AAAAGTATC
26697 AACACATTGT
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
AAAAGTATCGATACATGAGA
Found at i:35463 original size:20 final size:20
Alignment explanation
Indices: 35422--35511 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
35412 TCCTAGAAAA
* *
35422 TATCGATACA-TATCCAAATG
1 TATCGATACATTATGC-ATTG
*
35442 TATCGATACATTATGCTTTG
1 TATCGATACATTATGCATTG
*
35462 TATCGATACATGT-T-CATTA
1 TATCGATACAT-TATGCATTG
*
35481 TATCGATACA-TACTGAATTG
1 TATCGATACATTA-TGCATTG
35501 TATCGATACAT
1 TATCGATACAT
35512 GAAACTGGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.02
19 14 0.25
20 37 0.65
21 5 0.09
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (20 bp):
TATCGATACATTATGCATTG
Found at i:38598 original size:88 final size:88
Alignment explanation
Indices: 38418--38715 Score: 277
Period size: 88 Copynumber: 3.4 Consensus size: 88
38408 ATCCCTTTTG
* * * * * * *
38418 AAAGCCCACAAGTTAGTGGCA-C-CCTCTT-AAAGCCAAAAAGTTAATGGCACCCTCTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCATCTCCT-TTCAAAGCCCACAAGTCAGTGCCACCCTTTCAAAGCC
* *** * * *
38480 CATAAGTTGGTGGCATC-TCTTATT
65 CACAAGTCAATGGCA-CACCCTATC
* * * *
38504 AAAGCCCACAAGTCTGTGCCATCGCCTTTCAAAGCCCACAAGTCTGTGGCGTC-CCCTTTCAAAG
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGT-GC--CACCCTTTCAAAG
*
38568 CCCACAAGTCAGT-GC-CACCCTATC
63 CCCACAAGTCAATGGCACACCCTATC
* *
38592 AAAGCCCATAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTCAAAGCCT
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTCAAAGCCC
* * *
38657 ACAAGTCAATGGCATATCCTTTC
66 ACAAGTCAATGGCACACCCTATC
*
38680 AAAGCCCACAAGTCAATGGCATCTCCTTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCC
38716 TATAAGTTAG
Statistics
Matches: 174, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
85 1 0.01
86 40 0.23
87 8 0.05
88 101 0.58
89 3 0.02
90 20 0.11
91 1 0.01
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.22
Consensus pattern (88 bp):
AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTCAAAGCCC
ACAAGTCAATGGCACACCCTATC
Found at i:38620 original size:58 final size:58
Alignment explanation
Indices: 38418--38745 Score: 324
Period size: 58 Copynumber: 5.6 Consensus size: 58
38408 ATCCCTTTTG
* * * * * * *
38418 AAAGCCCACAAGTTAGTGGCA-C-CCTCTT-AAAGCCAAAAAGTTAATGGCACCCTCTC
1 AAAGCCCACAAGTCAGTGGCATCTCCT-TTCAAAGCCCACAAGTCAGTGCCACCCTTTC
* ** * *
38474 AAAGCCCATAAGTTGGTGGCATCT-CTTATTAAAGCCCACAAGTCTGTGCCATCGCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTT-TCAAAGCCCACAAGTCAGTGCCA-C-CCTTTC
* * * *
38534 AAAGCCCACAAGTCTGTGGCGTCCCCTTTCAAAGCCCACAAGTCAGTGCCACCCTATC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTC
*
38592 AAAGCCCATAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTC
* * * * *
38650 AAAGCCTACAAGTCAATGGCATATCCTTTCAAAGCCCACAAGTCAATGGCATCTCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCA-C-CCTTTC
* * * *
38710 AAAGCCTATAAGTTAGTGGCA-CTCTTTTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCATCTC-CTTTCAAAGCC
38746 TACACCAATT
Statistics
Matches: 229, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
56 20 0.09
57 4 0.02
58 118 0.52
59 5 0.02
60 79 0.34
61 3 0.01
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (58 bp):
AAAGCCCACAAGTCAGTGGCATCTCCTTTCAAAGCCCACAAGTCAGTGCCACCCTTTC
Found at i:38747 original size:30 final size:30
Alignment explanation
Indices: 38418--38745 Score: 300
Period size: 30 Copynumber: 11.2 Consensus size: 30
38408 ATCCCTTTTG
*
38418 AAAGCCCACAAGTTAGTGGCA-C-CCTCTT-
1 AAAGCCCACAAGTCAGTGGCATCTCCT-TTC
* * * * *
38446 AAAGCCAAAAAGTTAATGGCA-C-CCTCTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
* ** *
38474 AAAGCCCATAAGTTGGTGGCATCT-CTTATT
1 AAAGCCCACAAGTCAGTGGCATCTCCTT-TC
* * *
38504 AAAGCCCACAAGTCTGTGCCATCGCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
* * *
38534 AAAGCCCACAAGTCTGTGGCGTCCCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
* *
38564 AAAGCCCACAAGTCAGTGCCA-C-CCTATC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
*
38592 AAAGCCCATAAGTCAGTGGCATCTCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
*
38622 AAAGCCCACAAGTCAGTGCCA-C-CCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
* * *
38650 AAAGCCTACAAGTCAATGGCATATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
*
38680 AAAGCCCACAAGTCAATGGCATCTCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCTCCTTTC
* * * *
38710 AAAGCCTATAAGTTAGTGGCA-CTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTC-CTTTC
38740 AAAGCC
1 AAAGCC
38746 TACACCAATT
Statistics
Matches: 251, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
27 1 0.00
28 87 0.35
29 9 0.04
30 151 0.60
31 3 0.01
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCATCTCCTTTC
Found at i:42119 original size:79 final size:79
Alignment explanation
Indices: 41994--42216 Score: 304
Period size: 79 Copynumber: 2.8 Consensus size: 79
41984 TATAATATCG
* * * * *
41994 AATTTTTCATCTCGAGGATACTCTAACCTCATTCTTTTCGAAGGGATACTCTAACCCCGTTTTTA
1 AATTTTTCATCTCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGTTTTTA
42059 TTTTCAAAATATTA
66 TTTTCAAAATATTA
* * *
42073 AATTTTTCATCGTGGA-GATACTCCAACCCCATTATTTCCGAGGGGATACTCTAATCTCGTTTTT
1 AATTTTTCATC-TCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGTTTTT
42137 ATTTTCAAAATATTA
65 ATTTTCAAAATATTA
* * * * * *
42152 AAATTTTCATCCCAAGGATACTCCAACCCCATTATTTTTGAGGGTATACTCTAACCTCGCTTTTA
1 AATTTTTCATCTCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGTTTTTA
42217 AACTTCTCAA
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
78 1 0.01
79 121 0.97
80 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (79 bp):
AATTTTTCATCTCGAGGATACTCCAACCCCATTATTTTCGAGGGGATACTCTAACCTCGTTTTTA
TTTTCAAAATATTA
Found at i:48820 original size:20 final size:22
Alignment explanation
Indices: 48795--48842 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
48785 AAAGTTTCGT
*
48795 TAAAAAAATTT-T-CCCTTTGA
1 TAAAAAAATTTCTCCCCCTTGA
48815 TAAAAAAATTTCTCCCCCTTGA
1 TAAAAAAATTTCTCCCCCTTGA
48837 TAAAAA
1 TAAAAA
48843 TTTATTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 11 0.44
21 1 0.04
22 13 0.52
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAAAAATTTCTCCCCCTTGA
Found at i:56464 original size:21 final size:21
Alignment explanation
Indices: 56438--56493 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
56428 ACATGTTGCA
56438 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
56459 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
56480 ATGTATCGATACAT
1 ATGTATCGATACAT
56494 TTCTTGGCAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:56550 original size:13 final size:13
Alignment explanation
Indices: 56532--56557 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56522 TACACCAAGT
56532 ATGTATCGATACA
1 ATGTATCGATACA
56545 ATGTATCGATACA
1 ATGTATCGATACA
56558 CAAAAAATTG
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:56555 original size:32 final size:33
Alignment explanation
Indices: 56514--56577 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
56504 TAGCCAAACT
* **
56514 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
56546 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
56578 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:58798 original size:21 final size:21
Alignment explanation
Indices: 58765--58814 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
58755 TTGCAAGTTG
*
58765 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
58787 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
58808 AAATAAA
1 AAATAAA
58815 AACTTGCATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:62730 original size:13 final size:13
Alignment explanation
Indices: 62712--62737 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
62702 ACATTTTTCT
62712 TTGTATCGATACA
1 TTGTATCGATACA
62725 TTGTATCGATACA
1 TTGTATCGATACA
62738 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:62901 original size:20 final size:20
Alignment explanation
Indices: 62863--62902 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
62853 TTTTGCGAAA
62863 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
62884 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
62903 ACCAGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:65292 original size:13 final size:13
Alignment explanation
Indices: 65274--65299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
65264 TACACCAAGT
65274 ATGTATCGATACA
1 ATGTATCGATACA
65287 ATGTATCGATACA
1 ATGTATCGATACA
65300 CAAAAAATTG
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:65297 original size:32 final size:33
Alignment explanation
Indices: 65256--65319 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
65246 TAGCCAAACT
* **
65256 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
65288 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
65320 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:66826 original size:13 final size:13
Alignment explanation
Indices: 66808--66865 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 13
66798 CAATTCATCA
66808 TGTATCGATACAT
1 TGTATCGATACAT
*
66821 TGTATCGATACAA
1 TGTATCGATACAT
*
66834 TG--T-G--CCAT
1 TGTATCGATACAT
66842 T-TATCGATACAT
1 TGTATCGATACAT
66854 TGTATCGATACA
1 TGTATCGATACA
66866 ATGTGCCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
8 3 0.09
9 1 0.03
10 2 0.06
11 1 0.03
12 4 0.11
13 24 0.69
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:66830 original size:33 final size:33
Alignment explanation
Indices: 66788--66885 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
66778 TTTGAAGCAA
66788 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
*
66821 TGTATCGATACAATGTGCCATTTATCGATACAT
1 TGTATCGATACAATGTGCCATGTATCGATACAT
*
66854 TGTATCGATACAATGTGCCATTTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
66886 AATAGTGGTA
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
33 60 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:66848 original size:20 final size:20
Alignment explanation
Indices: 66818--66886 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
66808 TGTATCGATA
66818 CATTGTATCGATACAATGTGC
1 CATT-TATCGATACAATGTGC
66839 CATTTATCGATAC-AT-TG-
1 CATTTATCGATACAATGTGC
66856 ----TATCGATACAATGTGC
1 CATTTATCGATACAATGTGC
66872 CATTTATCGATACAA
1 CATTTATCGATACAA
66887 ATAGTGGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.22
14 2 0.05
15 2 0.05
18 2 0.05
19 2 0.05
20 20 0.49
21 4 0.10
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (20 bp):
CATTTATCGATACAATGTGC
Found at i:66940 original size:20 final size:19
Alignment explanation
Indices: 66915--66987 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
66905 CTGCTAGTTT
**
66915 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
66935 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
66954 CATATATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
66975 -ATGTATCGATACA
1 CATGTATCGATACA
66988 TCTGGGTGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:66963 original size:19 final size:20
Alignment explanation
Indices: 66919--66968 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
66909 TAGTTTCATG
** *
66919 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATA
66939 TATCGATACAA-TGAACATA
1 TATCGATACAATTGAACATA
66958 TATCGATACAA
1 TATCGATACAA
66969 AGCATAATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (20 bp):
TATCGATACAATTGAACATA
Found at i:71541 original size:24 final size:24
Alignment explanation
Indices: 71505--71552 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
71495 AGCTAATAAA
* *
71505 TTAATTTATTTGGGCCTATTTTAT
1 TTAATTTAGTTGGGCCAATTTTAT
*
71529 TTAATTTAGTTGGGTCAATTTTAT
1 TTAATTTAGTTGGGCCAATTTTAT
71553 AATTGAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (24 bp):
TTAATTTAGTTGGGCCAATTTTAT
Found at i:74511 original size:21 final size:21
Alignment explanation
Indices: 74478--74522 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
74468 TTGCAAGTTG
*
74478 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
74500 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
74520 AAA
1 AAA
74523 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:78520 original size:13 final size:13
Alignment explanation
Indices: 78502--78526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78492 CAAAGATCAG
78502 TGTATCGATACAA
1 TGTATCGATACAA
78515 TGTATCGATACA
1 TGTATCGATACA
78527 TTTAAGTGAT
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:78604 original size:33 final size:33
Alignment explanation
Indices: 78567--78633 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
78557 AGTAGCTTAA
78567 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
78600 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
78633 A
1 A
78634 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:78607 original size:13 final size:13
Alignment explanation
Indices: 78589--78613 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78579 CAAAAAAATA
78589 TGTATCGATACAT
1 TGTATCGATACAT
78602 TGTATCGATACA
1 TGTATCGATACA
78614 ACACTTTATG
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:79716 original size:49 final size:49
Alignment explanation
Indices: 79507--79976 Score: 624
Period size: 49 Copynumber: 9.8 Consensus size: 49
79497 AAAAGGATGT
* * *
79507 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAAGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
79559 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
79602 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
79650 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * * * * *
79699 CAATGTGCGGAGTCAAGGCCAACTACATTGGGCGTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
79748 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
79797 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
79846 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
79889 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
79938 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
79977 GTGCCACCGA
Statistics
Matches: 374, Mismatches: 31, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
43 77 0.21
45 1 0.00
47 1 0.00
48 47 0.13
49 216 0.58
52 32 0.09
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:79778 original size:98 final size:98
Alignment explanation
Indices: 79441--79976 Score: 666
Period size: 98 Copynumber: 5.5 Consensus size: 98
79431 TGAGAAAAGT
* * * * * *
79441 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAATGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G---AAGG-TG
* *
79506 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* *
79545 GATGGAAAAAGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCA
*
79604 ATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAA
63 ATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* * * * *
79640 GGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
* * * * *
79704 TGCGGAGTCAAGGCCAACTACATTGGGCGTAAA
66 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
* *
79737 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
*
79802 TGCTGATTCAAGGCCAGCTATATTGGACTTAAA
66 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
*
79835 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
79894 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
*
79927 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
79977 GTGCCACCGA
Statistics
Matches: 382, Mismatches: 36, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
91 38 0.10
92 89 0.23
94 1 0.00
95 41 0.11
96 4 0.01
97 41 0.11
98 128 0.34
103 1 0.00
104 3 0.01
107 36 0.09
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGATTCAAGGCCAGCTACATTGGACTTAAA
Found at i:80010 original size:30 final size:29
Alignment explanation
Indices: 79976--80326 Score: 205
Period size: 30 Copynumber: 11.8 Consensus size: 29
79966 TGGACTTAAA
* *
79976 GGTGCCACCGACTTGTGGGCTTCGGAAAAG
1 GGTGCCACTGACTTGTGGGCTT-TGAAAAG
*
80006 GGTGCCACTGATTTGTGGGCTTTG--AAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG
* * *
80033 GTTGCCACTGACTTGTCGGCTTT-TAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG
* *
80061 GTTGCCACTGACTTGTGGGCTTTTGAAAAA
1 GGTGCCACTGACTTGTGGGC-TTTGAAAAG
**
80091 TATGCCACTGACTTGTGGGCTTTTGAAAAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAAG
* **
80121 GGTGCCACTAACTTGTGGGCTGAAAAAGAAAAAG
1 GGTGCCACTGACTTGTGGGCT----TTG-AAAAG
* * * * *
80155 AGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAAAG
1 GGTGCCACT-GACTTGTGGGCTT-----TG-AAAAG
* * * *
80190 AGTGCCACGGAGTTGTGGACTTTGGAAAA-
1 GGTGCCACTGACTTGTGGGCTTT-GAAAAG
* * *
80219 GATGCCACCGACTTGTGGGCTTCGGAAAAG
1 GGTGCCACTGACTTGTGGGCTT-TGAAAAG
* * *
80249 GATGCCACTGATTTATGGGCTTTG--AAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG
* *
80276 GTTGCCACTGACTTGTGGGCTTT-TAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAAG
* *
80304 GTTGCCACTGACTTGTGGACTTT
1 GGTGCCACTGACTTGTGGGCTTT
80327 TGAAGGGTGA
Statistics
Matches: 258, Mismatches: 42, Indels: 44
0.75 0.12 0.13
Matches are distributed among these distances:
27 46 0.18
28 47 0.18
29 28 0.11
30 90 0.35
31 1 0.00
33 2 0.01
34 19 0.07
35 25 0.10
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (29 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAAG
Found at i:80234 original size:29 final size:28
Alignment explanation
Indices: 80185--80326 Score: 124
Period size: 28 Copynumber: 5.0 Consensus size: 28
80175 TTACAAAAGA
* * *
80185 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACTGACTTGTGGGCTTT-G
* *
80215 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACTGACTTGTGGGCTT-TG
* *
80244 AAAAGGATGCCACTGATTTATGGGCTTTG
1 AAAA-GATGCCACTGACTTGTGGGCTTTG
* * *
80273 -AAGGTTGCCACTGACTTGTGGGCTTTT
1 AAAAGATGCCACTGACTTGTGGGCTTTG
* * *
80300 AAAGGTTGCCACTGACTTGTGGACTTT
1 AAAAGATGCCACTGACTTGTGGGCTTT
80327 TGAAGGGTGA
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
27 20 0.21
28 27 0.28
29 23 0.24
30 25 0.26
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
AAAAGATGCCACTGACTTGTGGGCTTTG
Found at i:80284 original size:27 final size:28
Alignment explanation
Indices: 80221--80332 Score: 127
Period size: 28 Copynumber: 4.0 Consensus size: 28
80211 TTGGAAAAGA
* ** *
80221 TGCCACCGACTTGTGGGCTTCGGAAAAGGA
1 TGCCACTGACTTGTGGGCTTTTG--AAGGT
* *
80251 TGCCACTGATTTATGGGC-TTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
*
80278 TGCCACTGACTTGTGGGCTTTTAAAGGT
1 TGCCACTGACTTGTGGGCTTTTGAAGGT
*
80306 TGCCACTGACTTGTGGACTTTTGAAGG
1 TGCCACTGACTTGTGGGCTTTTGAAGG
80333 GTGATGAATG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
27 20 0.29
28 33 0.47
29 2 0.03
30 15 0.21
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (28 bp):
TGCCACTGACTTGTGGGCTTTTGAAGGT
Found at i:81734 original size:1 final size:1
Alignment explanation
Indices: 81730--81815 Score: 73
Period size: 1 Copynumber: 86.0 Consensus size: 1
81720 CCGGACCCCC
* * * * * ** ** *
81730 TTTTTTTTGTTTTTGTTTGTTTTTTTTTTGTTTTTTTGTTTTTTCGTTTTTTTCGTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
81795 TTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTT
81816 GGAGGACGCC
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 65 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.87
Consensus pattern (1 bp):
T
Found at i:81752 original size:9 final size:8
Alignment explanation
Indices: 81730--81813 Score: 95
Period size: 8 Copynumber: 10.9 Consensus size: 8
81720 CCGGACCCCC
81730 TTTTTTT-
1 TTTTTTTG
*
81737 TGTTTTTG
1 TTTTTTTG
*
81745 TTTGTTT-
1 TTTTTTTG
81752 TTTTTTTG
1 TTTTTTTG
81760 TTTTTTTG
1 TTTTTTTG
*
81768 TTTTTTCG
1 TTTTTTTG
81776 TTTTTTTCG
1 TTTTTTT-G
81785 TTTTTTT-
1 TTTTTTTG
*
81792 TTGTTTT-
1 TTTTTTTG
81799 TTTTTTTG
1 TTTTTTTG
81807 TTTTTTT
1 TTTTTTT
81814 TTGGAGGACG
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
7 24 0.37
8 33 0.51
9 8 0.12
ACGTcount: A:0.00, C:0.02, G:0.11, T:0.87
Consensus pattern (8 bp):
TTTTTTTG
Found at i:91521 original size:10 final size:10
Alignment explanation
Indices: 91506--91532 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
91496 ATGTATCAAG
91506 CAAAAACAAA
1 CAAAAACAAA
91516 CAAAAACAAA
1 CAAAAACAAA
91526 CAAAAAC
1 CAAAAAC
91533 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Found at i:95753 original size:52 final size:51
Alignment explanation
Indices: 95675--95823 Score: 226
Period size: 52 Copynumber: 2.9 Consensus size: 51
95665 CGAAATATGA
95675 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
95727 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
* **
95779 AAATTTTCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
95824 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:95830 original size:13 final size:13
Alignment explanation
Indices: 95812--95836 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95802 CAAAGATCAG
95812 TGTATCGATACAA
1 TGTATCGATACAA
95825 TGTATCGATACA
1 TGTATCGATACA
95837 TTTAAGTGAT
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:95914 original size:33 final size:33
Alignment explanation
Indices: 95877--95943 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
95867 AGTAGCTTAA
95877 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
95910 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
95943 A
1 A
95944 AATCGTTGAA
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:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:95917 original size:13 final size:13
Alignment explanation
Indices: 95899--95923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95889 CAAAAAAATA
95899 TGTATCGATACAT
1 TGTATCGATACAT
95912 TGTATCGATACA
1 TGTATCGATACA
95924 ACACTTTATG
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:99354 original size:13 final size:13
Alignment explanation
Indices: 99336--99361 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
99326 ACATTTTTCT
99336 TTGTATCGATACA
1 TTGTATCGATACA
99349 TTGTATCGATACA
1 TTGTATCGATACA
99362 GGGTGATTAT
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):
TTGTATCGATACA
Found at i:99525 original size:20 final size:20
Alignment explanation
Indices: 99482--99527 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
99472 AAATCTTTTG
99482 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
99503 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
99523 CAAAA
1 CAAAA
99528 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:101923 original size:13 final size:13
Alignment explanation
Indices: 101905--101930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
101895 TACAGCAAGC
101905 ATGTATCGATACA
1 ATGTATCGATACA
101918 ATGTATCGATACA
1 ATGTATCGATACA
101931 CAAAAATATT
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:104746 original size:21 final size:19
Alignment explanation
Indices: 104720--104774 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
104710 TTTTACAATT
104720 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
104741 TGTATCGATACATAAGTTT
1 TGTATCGATACAAAAGTAA
104760 TGTATCGATACAAAA
1 TGTATCGATACAAAA
104775 CTGCCCTGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:104765 original size:19 final size:21
Alignment explanation
Indices: 104717--104773 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
104707 AATTTTTACA
104717 ATTTGTATCGATACAAACAGT
1 ATTTGTATCGATACAAACAGT
** *
104738 AAATGTATCGATACATA-AGT
1 ATTTGTATCGATACAAACAGT
104758 -TTTGTATCGATACAAA
1 ATTTGTATCGATACAAA
104774 ACTGCCCTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 13 0.43
20 3 0.10
21 14 0.47
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
ATTTGTATCGATACAAACAGT
Found at i:104923 original size:51 final size:49
Alignment explanation
Indices: 104829--104941 Score: 129
Period size: 51 Copynumber: 2.3 Consensus size: 49
104819 TGTATTGATA
* *
104829 CATTGTATCGATACATTTGCATTTTTATCAAATGTATCAATACATT-TGT
1 CATTGTATCGATACATCTGCATTTTTACCAAATGTATCAATACATTAT-T
** * *
104878 CATTGTATCGATACATCTGGGTATTTTACCTAGATGTATCGATACATTATT
1 CATTGTATCGATACATCTGCAT-TTTTACC-AAATGTATCAATACATTATT
*
104929 CAATGTATCGATA
1 CATTGTATCGATA
104942 ATGTATCGAT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
49 19 0.35
50 6 0.11
51 28 0.52
52 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (49 bp):
CATTGTATCGATACATCTGCATTTTTACCAAATGTATCAATACATTATT
Found at i:112894 original size:15 final size:16
Alignment explanation
Indices: 112854--112886 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
112844 AGGGGATCAT
112854 ATCGAAAT-AATGATA
1 ATCGAAATCAATGATA
112869 ATCGAAATCAATG-TA
1 ATCGAAATCAATGATA
112884 ATC
1 ATC
112887 AACATCAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.27
Consensus pattern (16 bp):
ATCGAAATCAATGATA
Done.